Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold241
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1040028
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 103832 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:1035 original size:65 final size:65
Alignment explanation
Indices: 966--1096 Score: 253
Period size: 65 Copynumber: 2.0 Consensus size: 65
956 GCACTCGCCT
*
966 CCGGCTCGTGCACTATGTATCAAACCCTGACTACTATTTAGGCATAGTACATGCACAACACAACA
1 CCGGCTCGTGCACGATGTATCAAACCCTGACTACTATTTAGGCATAGTACATGCACAACACAACA
1031 CCGGCTCGTGCACGATGTATCAAACCCTGACTACTATTTAGGCATAGTACATGCACAACACAACA
1 CCGGCTCGTGCACGATGTATCAAACCCTGACTACTATTTAGGCATAGTACATGCACAACACAACA
1096 C
1 C
1097 TATTATATAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (65 bp):
CCGGCTCGTGCACGATGTATCAAACCCTGACTACTATTTAGGCATAGTACATGCACAACACAACA
Found at i:1135 original size:25 final size:25
Alignment explanation
Indices: 1107--1154 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1097 TATTATATAA
1107 ATATCATACAATACAATATCATACT
1 ATATCATACAATACAATATCATACT
* *
1132 ATATTATACAATATAATATCATA
1 ATATCATACAATACAATATCATA
1155 TGTTTCAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (25 bp):
ATATCATACAATACAATATCATACT
Found at i:3060 original size:61 final size:60
Alignment explanation
Indices: 2965--3086 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 60
2955 TTGGCTCATC
2965 AATCTCACAAACAACATCGTCAATACTATACCAGCTCATATCAATCATACATTTTGGATA
1 AATCTCACAAACAACATCGTCAATACTATACCAGCTCATATCAATCATACATTTTGGATA
3025 NAATCTCACAAACAACATCGTCAATACTATACCAGCTCATATCAATCATACATTTTGGATA
1 -AATCTCACAAACAACATCGTCAATACTATACCAGCTCATATCAATCATACATTTTGGATA
3086 A
1 A
3087 TAATATTGAA
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 1 0.02
61 60 0.98
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.28
Consensus pattern (60 bp):
AATCTCACAAACAACATCGTCAATACTATACCAGCTCATATCAATCATACATTTTGGATA
Found at i:11110 original size:21 final size:20
Alignment explanation
Indices: 11084--11150 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
11074 CGCTTTGCCT
11084 GAAACGCTAAATGGTTTACAC
1 GAAACGCTAAA-GGTTTACAC
** *** *
11105 GAAACGCTTCACAATCACAC
1 GAAACGCTAAAGGTTTACAC
11125 GAAACGCTAAACGGTTTACAC
1 GAAACGCTAAA-GGTTTACAC
11146 GAAAC
1 GAAAC
11151 ATTTCTCGCA
Statistics
Matches: 33, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.18
Consensus pattern (20 bp):
GAAACGCTAAAGGTTTACAC
Found at i:13361 original size:2 final size:2
Alignment explanation
Indices: 13354--13401 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
13344 GCCCGTTTAC
* *
13354 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG TG TG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
13396 AG AG AG
1 AG AG AG
13402 GGAAACTTAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.00, G:0.50, T:0.04
Consensus pattern (2 bp):
AG
Found at i:16048 original size:180 final size:179
Alignment explanation
Indices: 15740--16071 Score: 488
Period size: 180 Copynumber: 1.8 Consensus size: 179
15730 GCCAAAAGGT
* * *
15740 TACCCTTATTGTACAGAAAATTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCAGATT
1 TACCCCTATTGTACAGAAAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCAGATC
*
15805 ATTTGGACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTATGATAATTTATGAAAAAA
66 AATTGGACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTATGATAATTTATG-AAAAA
*
15870 ATACAAGCTGTTAAACTTGGTCATTTTTCGGCAAAACATTGCATGTAGGG
130 ATACAAGCTGTTAAACTTAGTCATTTTTCGGCAAAACATTGCATGTAGGG
** * *
15920 TACCCCTATTGTACAGTTAACTCCTCCTATAGTTTTCAAGATAGGAATTTGTTCTTTTGCAGATC
1 TACCCCTATTGTACAGAAAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCAGATC
* * * *
15985 AATTGGACATATATTAGAGGTGTGCATATT-TTGAGTG-TTTTGATTTTTGATTATTTATGAAAA
66 AATTGGACATATATCAGAGGTGTGCATATTGCT-AG-GATTTTGATTTATGATAATTTATGAAAA
* *
16048 AATACCAGCTGTTGAACTTAGTCA
129 AATACAAGCTGTTAAACTTAGTCA
16072 GATCAATTGG
Statistics
Matches: 135, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
179 26 0.19
180 108 0.80
181 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (179 bp):
TACCCCTATTGTACAGAAAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCAGATC
AATTGGACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTATGATAATTTATGAAAAAA
TACAAGCTGTTAAACTTAGTCATTTTTCGGCAAAACATTGCATGTAGGG
Found at i:19054 original size:55 final size:55
Alignment explanation
Indices: 18976--19115 Score: 243
Period size: 55 Copynumber: 2.6 Consensus size: 55
18966 TCGACGAAGG
18976 AGACGGCTGGTTTCGCTAGCTACTTTTCTCCTGAAGCAGAGAGGGGGAGGGAGAC
1 AGACGGCTGGTTTCGCTAGCTACTTTTCTCCTGAAGCAGAGAGGGGGAGGGAGAC
*
19031 AGACGGCTGGTTTCGTTAGCTACTTTTCTCCTGAAGCAGAGAGGGGGAGGGAGAC
1 AGACGGCTGGTTTCGCTAGCTACTTTTCTCCTGAAGCAGAGAGGGGGAGGGAGAC
19086 --A--GCTGGTTTCGCTAGCTACTTTTCTCCTGA
1 AGACGGCTGGTTTCGCTAGCTACTTTTCTCCTGA
19116 GTCCAGACCC
Statistics
Matches: 83, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
51 28 0.34
53 1 0.01
55 54 0.65
ACGTcount: A:0.20, C:0.21, G:0.33, T:0.26
Consensus pattern (55 bp):
AGACGGCTGGTTTCGCTAGCTACTTTTCTCCTGAAGCAGAGAGGGGGAGGGAGAC
Found at i:20360 original size:21 final size:21
Alignment explanation
Indices: 20313--20411 Score: 81
Period size: 21 Copynumber: 4.7 Consensus size: 21
20303 TACAAGATAA
**
20313 ACGATAGGATAGGATTCATGC
1 ACGATAGGATAGGATTCACAC
*
20334 ATGATAGGATAGGATTCACAC
1 ACGATAGGATAGGATTCACAC
* * * * *
20355 ACGATAGAACAGTATACGCAC
1 ACGATAGGATAGGATTCACAC
* * * *
20376 ACGATATGATAAGATTGATAC
1 ACGATAGGATAGGATTCACAC
*
20397 ACGATAGGAAAGGAT
1 ACGATAGGATAGGAT
20412 AAACGATTTT
Statistics
Matches: 57, Mismatches: 21, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.21
Consensus pattern (21 bp):
ACGATAGGATAGGATTCACAC
Found at i:21424 original size:21 final size:21
Alignment explanation
Indices: 21400--21441 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
21390 CGATAATCCT
*
21400 GATAGGATTAACGCATGATAG
1 GATAGGATTAACACATGATAG
21421 GATAGGATTAACACATGATAG
1 GATAGGATTAACACATGATAG
21442 AACAGTATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (21 bp):
GATAGGATTAACACATGATAG
Found at i:26835 original size:19 final size:19
Alignment explanation
Indices: 26788--26827 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
26778 TTTCGGATGC
* *
26788 TGGAGGAGGTTAAGGTTTT
1 TGGAGCAGGTTAAAGTTTT
26807 TGGAGCAGGTTAAAGTTTT
1 TGGAGCAGGTTAAAGTTTT
26826 TG
1 TG
26828 TTGCAGGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.38, T:0.38
Consensus pattern (19 bp):
TGGAGCAGGTTAAAGTTTT
Found at i:35888 original size:337 final size:334
Alignment explanation
Indices: 35275--35902 Score: 1035
Period size: 337 Copynumber: 1.9 Consensus size: 334
35265 CACTGATATA
* * * * * * *
35275 AATCAATCGATTTTGCAGTTAGATGAATGTAAACTGAAAAGTCTGGAGACATGCGCAGTTTCAAT
1 AATCAATCAATTTTGCAGTGAGATCAATGTAAACTCAAAAGTATGAAGACATGCACAGTTTCAAT
35340 GTAGCGCAAACTGTTGTTACATTTGTGTCGCTAAAATTCCTTTTACTGGTCGAGATTAGACGTGA
66 GTAGCGCAAACTGTTGTTACATTTGTGTCGCTAAAATTCCTTTTACTGGTCGAGATTAGACGTGA
35405 AAAGTATGCATTGTACCAAACATTGTGAACACAATGGGAACAAAATGTTAGCTGAGAGTCGGGCA
131 AAAGTATGCATTGTACCAAACATTGTGAACACAATGGGAACAAAATGTTAGCTGAGAGTCGGGCA
* * * *
35470 ACGTTGATTCGATACGATTTTAACACTTTTGAATAGTATGTTATCAAGTGTGATTTTTCACTGTC
196 ACGTTGAATCGATACGATTTCAACACTTTTGAATAGCATGTTATCAAGTGTGATTTTACACTGTC
35535 TTGCAGGCATCTGAAGTAGAAACATTCACGNGCAAGTGCGTTGTCCAATACGCAACTTGGACACT
261 TTGCAGGCATCTGAAGTAGAAACATTCACG-GCAAGTGCGTTGTCCAATACGCAACTTGGACACT
35600 GATATAAATC
325 GATATAAATC
* * *
35610 AATCAATCAATTTTGCAGTGAGATCTAT-TAAAACTCAATAGTATGAAGCCATGCACAGTTTCAA
1 AATCAATCAATTTTGCAGTGAGATCAATGT-AAACTCAAAAGTATGAAGACATGCACAGTTTCAA
*
35674 TGTAGCGCAAACTGTTGTTACATTTGTGTCGCTTAAAATTTCTTTTACTGGTCGAGATTAGACGT
65 TGTAGCGCAAACTGTTGTTACATTTGTGTCGC-TAAAATTCCTTTTACTGGTCGAGATTAGACGT
*
35739 GAAAAGTATGTACTTGTACCAATA-ATTGTGAACACAATGGGAACAAAATGTTAGCTGAGAGTCG
129 GAAAAGTATGCA-TTGTACCAA-ACATTGTGAACACAATGGGAACAAAATGTTAGCTGAGAGTCG
*
35803 GGCAGCGTTGAATCGATACGATTTCAACACTTTTGAATAGCATGTTATCAAGTGTGATTTTACAC
192 GGCAACGTTGAATCGATACGATTTCAACACTTTTGAATAGCATGTTATCAAGTGTGATTTTACAC
*
35868 TGTCTTGCAGGCATCTGAAGTAGCAACATTCACGG
257 TGTCTTGCAGGCATCTGAAGTAGAAACATTCACGG
35903 ACTTGCAGGC
Statistics
Matches: 271, Mismatches: 18, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
334 1 0.00
335 84 0.31
336 43 0.16
337 142 0.52
338 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (334 bp):
AATCAATCAATTTTGCAGTGAGATCAATGTAAACTCAAAAGTATGAAGACATGCACAGTTTCAAT
GTAGCGCAAACTGTTGTTACATTTGTGTCGCTAAAATTCCTTTTACTGGTCGAGATTAGACGTGA
AAAGTATGCATTGTACCAAACATTGTGAACACAATGGGAACAAAATGTTAGCTGAGAGTCGGGCA
ACGTTGAATCGATACGATTTCAACACTTTTGAATAGCATGTTATCAAGTGTGATTTTACACTGTC
TTGCAGGCATCTGAAGTAGAAACATTCACGGCAAGTGCGTTGTCCAATACGCAACTTGGACACTG
ATATAAATC
Found at i:51041 original size:2 final size:2
Alignment explanation
Indices: 51022--51065 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
51012 TGATATGATG
*
51022 AT AT A- AT AT -T AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51062 AT AT
1 AT AT
51066 TTAAACGTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59243 original size:1 final size:1
Alignment explanation
Indices: 59206--59231 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
59196 CCCCCCCCCC
59206 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
59232 CACCAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:76027 original size:4 final size:4
Alignment explanation
Indices: 76018--76099 Score: 148
Period size: 4 Copynumber: 20.5 Consensus size: 4
76008 AATTAAAAGT
76018 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA -ACGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TA-GA TAGA
76066 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TA
76100 CATGGCAACA
Statistics
Matches: 76, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
3 1 0.01
4 74 0.97
5 1 0.01
ACGTcount: A:0.50, C:0.01, G:0.24, T:0.24
Consensus pattern (4 bp):
TAGA
Found at i:80581 original size:18 final size:18
Alignment explanation
Indices: 80532--80581 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
80522 TAATTTCTTC
*
80532 ATCGTCAACAGTCTCCAG
1 ATCGTCACCAGTCTCCAG
* *
80550 ATTGTCACTAGTCTCCAG
1 ATCGTCACCAGTCTCCAG
*
80568 ATCGTCACCGGTCT
1 ATCGTCACCAGTCT
80582 TTAGATTGTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.22, C:0.32, G:0.18, T:0.28
Consensus pattern (18 bp):
ATCGTCACCAGTCTCCAG
Found at i:93664 original size:24 final size:23
Alignment explanation
Indices: 93602--93671 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 23
93592 AAGGCCTCAA
93602 GCAAACAGTTGCCGCAAATTT--
1 GCAAACAGTTGCCGCAAATTTGC
* * *
93623 GCAGAGAGTTTGCTGCAAATTTGC
1 GCAAACAG-TTGCCGCAAATTTGC
93647 GACAAACAGTTGCCGCAAATTTGC
1 G-CAAACAGTTGCCGCAAATTTGC
93671 G
1 G
93672 GCAAGTTCAG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 6 0.15
22 12 0.31
24 16 0.41
25 5 0.13
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24
Consensus pattern (23 bp):
GCAAACAGTTGCCGCAAATTTGC
Found at i:93730 original size:59 final size:59
Alignment explanation
Indices: 93656--93794 Score: 215
Period size: 59 Copynumber: 2.4 Consensus size: 59
93646 CGACAAACAG
* * * *
93656 TTGCCGCAAATTTGCGGCAAGTTCAGAATTCGTATGCAAATTATCTTCTGGCAAACTGT
1 TTGCGGCAAATTTGCGGCAAGTACAGAATTCGTATGCAAATCAGCTTCTGGCAAACTGT
* *
93715 TTGCGGCAAAGTTGCGGCAAGTACAGAATTCGTATGCAAATCAGCTTCTGGGAAACTGT
1 TTGCGGCAAATTTGCGGCAAGTACAGAATTCGTATGCAAATCAGCTTCTGGCAAACTGT
*
93774 TTGCGGCAAATTTGCCGCAAG
1 TTGCGGCAAATTTGCGGCAAG
93795 CTTACAGATA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 72 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.28
Consensus pattern (59 bp):
TTGCGGCAAATTTGCGGCAAGTACAGAATTCGTATGCAAATCAGCTTCTGGCAAACTGT
Found at i:97070 original size:11 final size:11
Alignment explanation
Indices: 97053--97088 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
97043 AGTTTGCCGA
*
97053 AAATTTGCGGC
1 AAATTTGCTGC
*
97064 AAGTTTGCTGC
1 AAATTTGCTGC
97075 AAATTTGCTGC
1 AAATTTGCTGC
97086 AAA
1 AAA
97089 CAATTCATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (11 bp):
AAATTTGCTGC
Found at i:97071 original size:22 final size:22
Alignment explanation
Indices: 97043--97087 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
97033 TAAACTAATC
97043 AGTTTGCCGAAAATTTGCGGCA
1 AGTTTGCCGAAAATTTGCGGCA
* * *
97065 AGTTTGCTGCAAATTTGCTGCA
1 AGTTTGCCGAAAATTTGCGGCA
97087 A
1 A
97088 ACAATTCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (22 bp):
AGTTTGCCGAAAATTTGCGGCA
Found at i:99120 original size:2 final size:2
Alignment explanation
Indices: 99113--99156 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
99103 NNCTGTGCTT
99113 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
99155 TA
1 TA
99157 CTATTTTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:99474 original size:11 final size:11
Alignment explanation
Indices: 99458--99482 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
99448 CGTCGACTGA
99458 AGCCTGTTTGT
1 AGCCTGTTTGT
99469 AGCCTGTTTGT
1 AGCCTGTTTGT
99480 AGC
1 AGC
99483 TAGTCTATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.12, C:0.20, G:0.28, T:0.40
Consensus pattern (11 bp):
AGCCTGTTTGT
Found at i:102571 original size:23 final size:23
Alignment explanation
Indices: 102539--102601 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
102529 ATCCTTATAT
102539 CCTTATCCTTATAACCTGATAAA
1 CCTTATCCTTATAACCTGATAAA
* * *
102562 CGTTATCCTTATAGCCTTATAAA
1 CCTTATCCTTATAACCTGATAAA
102585 CCTTATCCTTATAACCT
1 CCTTATCCTTATAACCT
102602 TATCCTTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.30, C:0.27, G:0.05, T:0.38
Consensus pattern (23 bp):
CCTTATCCTTATAACCTGATAAA
Found at i:102605 original size:37 final size:35
Alignment explanation
Indices: 102516--102612 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 35
102506 ACATATTGAC
*
102516 CCTTATAATCCTTATCCTTATATCCTTATCCTTATAA
1 CCTTATAA-CCTTATCCTTATAGCCTTATCCTTAT-A
* *
102553 CCTGATAAACGTTATCCTTATAGCCTTATAAACCTTAT-
1 CCTTAT-AACCTTATCCTTATAGCCTTAT---CCTTATA
102591 CCTTATAACCTTATCCTTATAG
1 CCTTATAACCTTATCCTTATAG
102613 AAGTTTTATA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
37 38 0.75
38 7 0.14
40 6 0.12
ACGTcount: A:0.29, C:0.26, G:0.04, T:0.41
Consensus pattern (35 bp):
CCTTATAACCTTATCCTTATAGCCTTATCCTTATA
Found at i:103444 original size:230 final size:227
Alignment explanation
Indices: 103016--103479 Score: 750
Period size: 230 Copynumber: 2.0 Consensus size: 227
103006 TATCAACGTC
*
103016 ATTTTTGGGAGTTGATTTTAATCAACTCTCCTATGCAGTCACTCTGACAAACCGAAAGTGAAAGA
1 ATTTTTGGGAGTTGATTTTAATCAACTCTCCTATGCAGTCACTCGGACAAACCGAAAGTGAAAGA
** * *
103081 GTGTTTGGACCAAAGCACAAATCATCGCCGCTGACACTAATTAGTTGTTGAGAATAATTGATATA
66 GTGTTTGGACCAAAGCACAAATCATCGCCGCTGACAAGAATTAGTTGTTCAGAATAATTGATAAA
*
103146 TTCGAAATAATGTATGCTAAAGCATTGTTTTTCAAGGAAACATATTTATAAATACTTTGAAAATA
131 TTCGAAATAATGTATGCTAAAGCATTGTTTTTCAAGGAAACATATTTATAAATACCTTGAAAATA
103211 GTCAGATTTTAAATGGTACGAACAATTTAGAT
196 GTCAGATTTTAAATGGTACGAACAATTTAGAT
*
103243 ATTTTTGGGAGTTGATTTTAATCAACTCTCCTATGCAGTTACTCGGACAAACCGAAAGTGAAAGA
1 ATTTTTGGGAGTTGATTTTAATCAACTCTCCTATGCAGTCACTCGGACAAACCGAAAGTGAAAGA
** * *
103308 GTGTTTGGACCTCAG-ACAAATCATCGCTGCTGACAAGACTTAGTTAGTTCATGAACATAATTGA
66 GTGTTTGGACCAAAGCACAAATCATCGCCGCTGACAAGAATTAGTT-GTTCA-G-A-ATAATTGA
** *
103372 TAAATTCGATGTAATGTATGCTAAAGCATTGTTTTTCAAGGAAACTTATTTATAAATACCTTGAA
127 TAAATTCGAAATAATGTATGCTAAAGCATTGTTTTTCAAGGAAACATATTTATAAATACCTTGAA
*
103437 AATAGTCAGATTTTAAATGGTACGAGCAATTTAGAT
192 AATAGTCAGATTTTAAATGGTACGAACAATTTAGAT
103473 ATTTTTG
1 ATTTTTG
103480 TAGTCGTATG
Statistics
Matches: 218, Mismatches: 15, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
226 26 0.12
227 80 0.37
228 1 0.00
229 1 0.00
230 110 0.50
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (227 bp):
ATTTTTGGGAGTTGATTTTAATCAACTCTCCTATGCAGTCACTCGGACAAACCGAAAGTGAAAGA
GTGTTTGGACCAAAGCACAAATCATCGCCGCTGACAAGAATTAGTTGTTCAGAATAATTGATAAA
TTCGAAATAATGTATGCTAAAGCATTGTTTTTCAAGGAAACATATTTATAAATACCTTGAAAATA
GTCAGATTTTAAATGGTACGAACAATTTAGAT
Found at i:104896 original size:10 final size:11
Alignment explanation
Indices: 104865--104897 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
104855 CTATTAAATT
104865 CTTATTAGATAA
1 CTTATTA-ATAA
104877 CTTATTAATAA
1 CTTATTAATAA
104888 CTT-TTAATAA
1 CTTATTAATAA
104898 TAATGCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 7 0.33
12 7 0.33
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (11 bp):
CTTATTAATAA
Found at i:111322 original size:3 final size:3
Alignment explanation
Indices: 111314--111343 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
111304 AAGCAAAATT
111314 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
111344 CATATAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:114505 original size:114 final size:113
Alignment explanation
Indices: 114122--114580 Score: 681
Period size: 115 Copynumber: 4.0 Consensus size: 113
114112 TTTGTCTGGG
* * *
114122 GATATCGAAGACTGTTGTTCTTTTAAGGTAAATTTAATTTGGTGTATCTATAAAAACACACACAG
1 GATATCGAAGACTGTTGTTCTTTTAAGATAAATTTAATTTGGAGTATTTATAAAAACACACACAG
114187 ACATACAAGCCATGATCCAATT--AAAAAAAACTATTCAAGTTGATAC
66 ACATACAAGCCATGATCCAATTAAAAAAAAAACTATTCAAGTTGATAC
* *
114233 GATATCGAAGACTGTTGTTCTTTTAAGATAAATTTAATTTGAAGTATTTATAAAAACACACACAA
1 GATATCGAAGACTGTTGTTCTTTTAAGATAAATTTAATTTGGAGTATTTATAAAAACACACACAG
114298 ACATACAAGCCATGATCCAATTAAAACAAAAAAACTATTCAAGTTGATAC
66 ACATACAAGCCATGATCCAATT-AAA-AAAAAAACTATTCAAGTTGATAC
* *
114348 GATATCGAAGACTGTTGTT-TTTTAAAGATTAATTTAATTTGGAGTATTTACAAAAACACACACA
1 GATATCGAAGACTGTTGTTCTTTT-AAGATAAATTTAATTTGGAGTATTTATAAAAACACACACA
* *
114412 GACATACAAGCCATGATCCAATTAAAATAAAAAACGATTCAAGTTGAAAC
65 GACATACAAGCCATGATCCAATTAAAA-AAAAAACTATTCAAGTTGATAC
* * *
114462 GATATCGAAGACTGTTGTTCTTTGAAGGTAAATTTAATTTGGAGAATTTATAAAAACACACACAC
1 GATATCGAAGACTGTTGTTCTTTTAAGATAAATTTAATTTGGAGTATTTAT--AAA-A-ACACAC
* *
114527 ACAGACGTACAAGCCATGATCCAATTAAAACAAGCAAACTATTCAAGTTGATAC
62 ACAGACATACAAGCCATGATCCAATTAAAA-AA-AAAACTATTCAAGTTGATAC
114581 AATTCTATAG
Statistics
Matches: 315, Mismatches: 21, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
111 82 0.26
113 1 0.00
114 70 0.22
115 104 0.33
116 3 0.01
117 1 0.00
118 37 0.12
119 17 0.05
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (113 bp):
GATATCGAAGACTGTTGTTCTTTTAAGATAAATTTAATTTGGAGTATTTATAAAAACACACACAG
ACATACAAGCCATGATCCAATTAAAAAAAAAACTATTCAAGTTGATAC
Found at i:133106 original size:14 final size:14
Alignment explanation
Indices: 133081--133114 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
133071 ATGAAATTAT
133081 ATAAAA-ATATAAG
1 ATAAAACATATAAG
133094 ATAAAACATATAAG
1 ATAAAACATATAAG
133108 ATAAAAC
1 ATAAAAC
133115 TTTGGCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.21
Consensus pattern (14 bp):
ATAAAACATATAAG
Found at i:135399 original size:195 final size:194
Alignment explanation
Indices: 135067--135452 Score: 664
Period size: 195 Copynumber: 2.0 Consensus size: 194
135057 ACAAAATTGG
*
135067 AAGTTAGATGTGAAAATAAACAACAAAACATTTTATTTCTGACAGAGCTCGCTACTTTTATACCT
1 AAGTTAGATGTGAAAATAAACAACAAAACATTCTATTTCTGACAGAGCTCGCTACTTTTATACCT
* *
135132 TTAAAAAATAAATTGTTAAAACGCACATTACTTTTACATCAAACGTGTTCGTTTTTCCTAAAATC
66 TTAAAAAATAAATTGTTAAAACGCACATTACTTTTACATCAAACGTGTTCATTGTTCCTAAAATC
*
135197 GAGATTGAGTTAAAGTCATGACTTTTTTTATAATGTGTAATTTAACATAAACTTATATATATATT
131 GAGATTGAGTTAAAGTCATGAC-TTTTTTATAATATGTAATTTAACATAAACTTATATATATATT
* * *
135262 AAGTTAGATGTGAAAATAAACAACATAACATTCTATTTCTGCCATAGCTCGCTACTTTTATACCT
1 AAGTTAGATGTGAAAATAAACAACAAAACATTCTATTTCTGACAGAGCTCGCTACTTTTATACCT
*
135327 TTAAAAAATAAATTGTTAAAACGCATATTACTTTTACATCAAACGTGTTCATTGTTCCTAAAATC
66 TTAAAAAATAAATTGTTAAAACGCACATTACTTTTACATCAAACGTGTTCATTGTTCCTAAAATC
* * *
135392 GAGATTGAGTTAAAGTCATGACTTTTTTATAATATGTAATTTAATATATATTTATATATAT
131 GAGATTGAGTTAAAGTCATGACTTTTTTATAATATGTAATTTAACATAAACTTATATATAT
135453 NATATATATA
Statistics
Matches: 180, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
194 35 0.19
195 145 0.81
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (194 bp):
AAGTTAGATGTGAAAATAAACAACAAAACATTCTATTTCTGACAGAGCTCGCTACTTTTATACCT
TTAAAAAATAAATTGTTAAAACGCACATTACTTTTACATCAAACGTGTTCATTGTTCCTAAAATC
GAGATTGAGTTAAAGTCATGACTTTTTTATAATATGTAATTTAACATAAACTTATATATATATT
Found at i:135442 original size:2 final size:2
Alignment explanation
Indices: 135435--135482 Score: 78
Period size: 2 Copynumber: 23.5 Consensus size: 2
135425 ATGTAATTTA
*
135435 AT AT AT AT TT AT AT AT AT NAT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
135478 AT AT A
1 AT AT A
135483 GTAAATATGC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:142074 original size:56 final size:57
Alignment explanation
Indices: 142004--142113 Score: 204
Period size: 58 Copynumber: 1.9 Consensus size: 57
141994 GCAGTTCGCA
142004 ATTGAATAGTGAACTGCGTTCTA-TAGAACGCAGTTCGCAATTCAAAATTTAGTGCG
1 ATTGAATAGTGAACTGCGTTCTACTAGAACGCAGTTCGCAATTCAAAATTTAGTGCG
142060 ATTGAATAGTGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAATTTAG
1 ATTGAATAGTGAACTGCGTTCTA-CTAGAACGCAGTTCGCAATTCAAAATTTAG
142114 AATTCATATT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
56 23 0.44
58 29 0.56
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (57 bp):
ATTGAATAGTGAACTGCGTTCTACTAGAACGCAGTTCGCAATTCAAAATTTAGTGCG
Found at i:143130 original size:16 final size:16
Alignment explanation
Indices: 143109--143157 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
143099 AACTGAAGTG
143109 GGACAGACAGACGGAC
1 GGACAGACAGACGGAC
* *
143125 GGACAGACAAACGGAT
1 GGACAGACAGACGGAC
* *
143141 GGACGGACTGACGGAC
1 GGACAGACAGACGGAC
143157 G
1 G
143158 CAGAGGAAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.35, C:0.22, G:0.39, T:0.04
Consensus pattern (16 bp):
GGACAGACAGACGGAC
Found at i:144480 original size:5 final size:5
Alignment explanation
Indices: 144472--144500 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
144462 TCGTTTTTCT
144472 TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
144501 TTTGTATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
TTTTG
Found at i:155952 original size:12 final size:12
Alignment explanation
Indices: 155927--155959 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
155917 TGAAAAATGC
155927 ATAA-ATTC-AA
1 ATAACATTCAAA
155937 ATAACATTCAAA
1 ATAACATTCAAA
155949 ATAACATTCAA
1 ATAACATTCAA
155960 TACCAAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 4 0.19
11 4 0.19
12 13 0.62
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (12 bp):
ATAACATTCAAA
Found at i:160536 original size:2 final size:2
Alignment explanation
Indices: 160529--160566 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
160519 ACGATCTTTA
160529 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
160567 AGAGAGAGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:160571 original size:2 final size:2
Alignment explanation
Indices: 160566--160596 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
160556 GTGTGTGTGT
160566 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
160597 GGTAATGCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:160958 original size:2 final size:2
Alignment explanation
Indices: 160951--160981 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
160941 AAACTAATTT
*
160951 TC TC TC TC TC TC TC TC TC TC CC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
160982 TCGGGGGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:178370 original size:26 final size:26
Alignment explanation
Indices: 178341--178625 Score: 276
Period size: 26 Copynumber: 10.9 Consensus size: 26
178331 AAGGAAATTG
178341 TGTACATAATGCTGTATACAGGGTGA
1 TGTACATAATGCTGTATACAGGGTGA
178367 TGTACATAATGCTGTATACAGGGTGA
1 TGTACATAATGCTGTATACAGGGTGA
178393 TGTACATAATGCTGTATACAGGGTGA
1 TGTACATAATGCTGTATACAGGGTGA
* *
178419 TGTACATAATGCTGCATACAGGATGA
1 TGTACATAATGCTGTATACAGGGTGA
* ** **
178445 TACTTTATACA-GGGGTATAC----T-A
1 T-GTACATA-ATGCTGTATACAGGGTGA
* * * *
178467 TGTACATTATACTGTATACAGAGTTATTTTA
1 TGTACATAATGCTGTATACAG-G----GTGA
* *
178498 TGTACATGATACTGTATACAGGGTGA
1 TGTACATAATGCTGTATACAGGGTGA
178524 TGTACATAATGCTGTATACAGGGTGA
1 TGTACATAATGCTGTATACAGGGTGA
* * *
178550 TGTACATGATACTGTATACAGGGCGA
1 TGTACATAATGCTGTATACAGGGTGA
*
178576 TGTACATAATACTGTATACAGGGTGA
1 TGTACATAATGCTGTATACAGGGTGA
** * *
178602 TGTACACGATACTGTATTCAGGGT
1 TGTACATAATGCTGTATACAGGGT
178626 TATTTTATGT
Statistics
Matches: 218, Mismatches: 28, Indels: 26
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.00
21 9 0.04
22 2 0.01
23 1 0.00
26 171 0.78
27 10 0.05
28 1 0.00
30 2 0.01
31 21 0.10
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (26 bp):
TGTACATAATGCTGTATACAGGGTGA
Found at i:178479 original size:31 final size:31
Alignment explanation
Indices: 178441--178655 Score: 128
Period size: 26 Copynumber: 7.6 Consensus size: 31
178431 TGCATACAGG
*
178441 ATGATACTTTATACAGGGGTATACTATGTAC
1 ATGATACTGTATACAGGGGTATACTATGTAC
* * * **
178472 ATTATACTGTATACAGAGTTATTTTATGTAC
1 ATGATACTGTATACAGGGGTATACTATGTAC
*
178503 ATGATACTGTATACA-GGG--T--GATGTAC
1 ATGATACTGTATACAGGGGTATACTATGTAC
* * *
178529 ATAATGCTGTATACA-GGG--T--GATGTAC
1 ATGATACTGTATACAGGGGTATACTATGTAC
*
178555 ATGATACTGTATACA-GGG----CGATGTAC
1 ATGATACTGTATACAGGGGTATACTATGTAC
* *
178581 ATAATACTGTATACA-GGG--T--GATGTAC
1 ATGATACTGTATACAGGGGTATACTATGTAC
* * * **
178607 ACGATACTGTATTCAGGGTTATTTTATGTAC
1 ATGATACTGTATACAGGGGTATACTATGTAC
178638 ATGATACTGTATACAGGG
1 ATGATACTGTATACAGGG
178656 TTATTTTCGC
Statistics
Matches: 155, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
26 89 0.57
27 2 0.01
28 1 0.01
29 1 0.01
30 1 0.01
31 61 0.39
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.34
Consensus pattern (31 bp):
ATGATACTGTATACAGGGGTATACTATGTAC
Found at i:178662 original size:31 final size:26
Alignment explanation
Indices: 178497--178656 Score: 212
Period size: 26 Copynumber: 6.0 Consensus size: 26
178487 GAGTTATTTT
178497 ATGTACATGATACTGTATACAGGGTG
1 ATGTACATGATACTGTATACAGGGTG
* *
178523 ATGTACATAATGCTGTATACAGGGTG
1 ATGTACATGATACTGTATACAGGGTG
*
178549 ATGTACATGATACTGTATACAGGGCG
1 ATGTACATGATACTGTATACAGGGTG
*
178575 ATGTACATAATACTGTATACAGGGTG
1 ATGTACATGATACTGTATACAGGGTG
* * *
178601 ATGTACACGATACTGTATTCAGGGTTATTTT
1 ATGTACATGATACTGTATACAGGG-----TG
178632 ATGTACATGATACTGTATACAGGGT
1 ATGTACATGATACTGTATACAGGGT
178657 TATTTTCGCC
Statistics
Matches: 116, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
26 93 0.80
31 23 0.20
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (26 bp):
ATGTACATGATACTGTATACAGGGTG
Found at i:179583 original size:20 final size:20
Alignment explanation
Indices: 179558--179595 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
179548 GTTTACCCCA
*
179558 GGGTTACTATGATGTCCTTG
1 GGGTTACTATGACGTCCTTG
179578 GGGTTACTATGACGTCCT
1 GGGTTACTATGACGTCCT
179596 CTTGGACCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.18, G:0.29, T:0.37
Consensus pattern (20 bp):
GGGTTACTATGACGTCCTTG
Found at i:181203 original size:21 final size:21
Alignment explanation
Indices: 181170--181248 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
181160 AAGATATAAA
*
181170 TTGTTGACAGATGAAGATTGCT
1 TTGTTGAGAGATGAAGATTG-T
* *
181192 TT-TTGAGCGATGAAGGTTGT
1 TTGTTGAGAGATGAAGATTGT
* * *
181212 TTGTTGAGAGATGATGAATCGC
1 TTGTTGAGAGATGAAG-ATTGT
*
181234 TTGGTGAGAGATGAA
1 TTGTTGAGAGATGAA
181249 TTGCTTGTTA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 3 0.07
21 25 0.56
22 17 0.38
ACGTcount: A:0.27, C:0.06, G:0.33, T:0.34
Consensus pattern (21 bp):
TTGTTGAGAGATGAAGATTGT
Found at i:181248 original size:19 final size:20
Alignment explanation
Indices: 181219--181287 Score: 81
Period size: 19 Copynumber: 3.6 Consensus size: 20
181209 TGTTTGTTGA
181219 GAGATGATGAATCGCTTGGT
1 GAGATGATGAATCGCTTGGT
*
181239 GAGA-GATGAATTGCTT-GT
1 GAGATGATGAATCGCTTGGT
* * *
181257 TAGGTGATGAATCGCTTGTT
1 GAGATGATGAATCGCTTGGT
181277 GA-ATGATGAAT
1 GAGATGATGAAT
181288 ATGACTTGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
18 4 0.10
19 30 0.75
20 6 0.15
ACGTcount: A:0.28, C:0.07, G:0.32, T:0.33
Consensus pattern (20 bp):
GAGATGATGAATCGCTTGGT
Found at i:181307 original size:40 final size:38
Alignment explanation
Indices: 181223--181307 Score: 102
Period size: 38 Copynumber: 2.2 Consensus size: 38
181213 TGTTGAGAGA
*
181223 TGATGAATCGCTTGGTGAGAGATGAATTGCTTGTTAGG
1 TGATGAATCGCTTGGTGAGAGATGAATTGCTTGTGAGG
*
181261 TGATGAATCGCTTGTTGA-ATGATGAATATGACTTGTG-GAG
1 TGATGAATCGCTTGGTGAGA-GATGAAT-TG-CTTGTGAG-G
181301 TGATGAA
1 TGATGAA
181308 AGGGCATTGC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
37 1 0.02
38 24 0.59
39 3 0.07
40 13 0.32
ACGTcount: A:0.27, C:0.07, G:0.32, T:0.34
Consensus pattern (38 bp):
TGATGAATCGCTTGGTGAGAGATGAATTGCTTGTGAGG
Found at i:182296 original size:2 final size:2
Alignment explanation
Indices: 182291--182321 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
182281 TTTTTGGGTT
*
182291 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
182322 TATCCAGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:188302 original size:250 final size:249
Alignment explanation
Indices: 187861--188359 Score: 980
Period size: 250 Copynumber: 2.0 Consensus size: 249
187851 GAAGGCCAAA
187861 TGACATTCTCTCAGTTGCTCTATCTCAACATGTGTATATTCGGGTTGTATAACAGGTGCAGGTAT
1 TGACATTCTCTCAGTTGCTCTATCTCAACATGTGTATATTCGGGTTGTATAACAGGTGCAGGTAT
187926 ACTCTGAATATCAGTGGATAGGTGACCCATTATTGTACAGCCTGACTGGTATGAAGTCCCTTCTC
66 ACTCTGAATATCAGTGGATAGGTGACCCATTATTGTACAGCCTGACTGGTATGAAGTCCCTTCTC
187991 TCACCTCTAAGCTTGCATTTCTTTGGTACCTGTTATCAACAGAATTATCTATTTAATATATAATG
131 TCACCTCTAAGCTTGCATTTCTTTGGTACCTGTTATCAACAGAATTATCTATTTAATATATAATG
*
188056 CATCTTTTAGCTTATCTCATAGGCGTCGGAACCAGGGGGCTAGGGAGGCTTAGC
196 CATCTTTTAGCTTATCTCATAGCCGTCGGAACCAGGGGGCTAGGGAGGCTTAGC
188110 NTGACATTCTCTCAGTTGCTCTATCTCAACATGTGTATATTCGGGTTGTATAACAGGTGCAGGTA
1 -TGACATTCTCTCAGTTGCTCTATCTCAACATGTGTATATTCGGGTTGTATAACAGGTGCAGGTA
188175 TACTCTGAATATCAGTGGATAGGTGACCCATTATTGTACAGCCTGACTGGTATGAAGTCCCTTCT
65 TACTCTGAATATCAGTGGATAGGTGACCCATTATTGTACAGCCTGACTGGTATGAAGTCCCTTCT
188240 CTCACCTCTAAGCTTGCATTTCTTTGGTACCTGTTATCAACAGAATTATCTATTTAATATATAAT
130 CTCACCTCTAAGCTTGCATTTCTTTGGTACCTGTTATCAACAGAATTATCTATTTAATATATAAT
188305 GCATCTTTTAGCTTATCTCATAGCCGTCGGAACCAGGGGGCTAGGGAGGCTTAGC
195 GCATCTTTTAGCTTATCTCATAGCCGTCGGAACCAGGGGGCTAGGGAGGCTTAGC
188360 CCCCCCCCCC
Statistics
Matches: 248, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
250 248 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (249 bp):
TGACATTCTCTCAGTTGCTCTATCTCAACATGTGTATATTCGGGTTGTATAACAGGTGCAGGTAT
ACTCTGAATATCAGTGGATAGGTGACCCATTATTGTACAGCCTGACTGGTATGAAGTCCCTTCTC
TCACCTCTAAGCTTGCATTTCTTTGGTACCTGTTATCAACAGAATTATCTATTTAATATATAATG
CATCTTTTAGCTTATCTCATAGCCGTCGGAACCAGGGGGCTAGGGAGGCTTAGC
Found at i:190970 original size:35 final size:35
Alignment explanation
Indices: 190931--191002 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
190921 TACAAATTTT
* *
190931 CATAATGTACTAACGTGCGTTACTCAATTTGTATG
1 CATAATGCACTAACGCGCGTTACTCAATTTGTATG
* *
190966 CATAATGCGCTAATGCGCGTTACTCAATTTGTATG
1 CATAATGCACTAACGCGCGTTACTCAATTTGTATG
191001 CA
1 CA
191003 CACACGGCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (35 bp):
CATAATGCACTAACGCGCGTTACTCAATTTGTATG
Found at i:193368 original size:12 final size:12
Alignment explanation
Indices: 193351--193389 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
193341 ATTCGTCATT
193351 CAAGGCACAACA
1 CAAGGCACAACA
193363 CAAGGCACAACA
1 CAAGGCACAACA
*
193375 CAAGGTACAACA
1 CAAGGCACAACA
193387 CAA
1 CAA
193390 TTTAAAACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.51, C:0.31, G:0.15, T:0.03
Consensus pattern (12 bp):
CAAGGCACAACA
Found at i:195568 original size:28 final size:28
Alignment explanation
Indices: 195547--197082 Score: 2079
Period size: 28 Copynumber: 54.4 Consensus size: 28
195537 CATGTTATAA
*
195547 TTCTATCCTACAGGTGC-ACATGTACTAG
1 TTCTATTCTACAGGT-CAACATGTACTAG
*
195575 TTCTATTCTACATGTCAACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
*
195603 TTCTATTCTACAGGTCTACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
*
195631 TTCTATTCTACATGTCAACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
*
195659 TTCTATTCTACAGGTCTACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
195687 TTCTATTCTACAGGTCAACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
*
195715 TTCTATTCTGCAGGTCAACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
195743 TTCTATTCTACAGGTCAACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* * *
195771 TTCTACTCTACATGTCAACATATACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
*
195799 ATCGATCTATTCTACAGGTCTACATGTACTAG
1 -T---TCTATTCTACAGGTCAACATGTACTAG
*
195831 TTCTATTCTACAGGTCTACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
*
195859 TTCTATTCTACAGGTCTACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
195887 TTCTATTCTACAGGTCAACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
195915 TTCTATTCTACAGGTCAACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
*
195943 TTCTATTCTACAGGTCTACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* *
195971 TTCTATTCTACAGGTCTATATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* * *
195999 TTCTACTCTACATGTCAACATATACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
*
196027 ATCGATCTATTCTACAGGTCTACATGTACTAG
1 -T---TCTATTCTACAGGTCAACATGTACTAG
* *
196059 TTCTATTCTACAGGTCTATATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
*
196087 TTCTATTCTACAGGTCTACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* *
196115 TTCTATTCTGCAGGTCTACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* * *
196143 TTCTACTCTACATGTCAACATATACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
196171 ATCGATCTATTCTACAGGT-ATACATGTACTAG
1 -T---TCTATTCTACAGGTCA-ACATGTACTAG
* * *
196203 TTCTATTCTAAAGGTCTACATGAACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
196231 TTCTATTCTACAGGTCAACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
*
196259 TTCTATTCTACAGGTCTACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
196287 TTCTATTCTACAGGTCAACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
**
196315 TTCTATTCTACAGGTCTTCATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* * *
196343 TTCTGTTCTACAGGTCTACATGTACTTG
1 TTCTATTCTACAGGTCAACATGTACTAG
* * *
196371 TTCTTTTCTACAGGTCTACATGTACTAA
1 TTCTATTCTACAGGTCAACATGTACTAG
*
196399 TTCTATTCTACATGTCAACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* *
196427 TTCTATTCTACAGGTCTACATGTACTAA
1 TTCTATTCTACAGGTCAACATGTACTAG
*
196455 TTCTATTCTACATGTCAACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
*
196483 TTCTATTCTACAGGTCTACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* * *
196511 TCCTGTTCTACAGGTCTACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* * *
196539 TTCTGTGCTACTGGTCAACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* * * *
196567 TTTTATTTTACAGGTCTACATGTATTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
*
196595 TTTTATTCTACAGGTCAACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* * * *
196623 TTTTATTTTACAGGTCTACATGTATTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
*
196651 TTTTATTCTACAGGTCAACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* * *
196679 TTCTGTTCTACAGGTCTACATGTACGAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* *
196707 TTCTGTTCTACAGGTCTACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* *
196735 TTCTATTTTACAGGTCTACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* **
196763 TTCTATTTTACAGGTCTTCATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
*
196791 TTCTGTTCTACAGGTCAACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* *
196819 TTCTGTTCTACATGTCAACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* *
196847 TTTTATTCTACAGGTCTACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* *
196875 TTCTATTCTACAGGTCTACATATACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
*
196903 TTCTATTCTAAAGGTCAACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
*
196931 TTCTATTCTACAGGTCTACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* *
196959 TTCTATTCTACAGGTCTACATGTACTTG
1 TTCTATTCTACAGGTCAACATGTACTAG
* *
196987 ATCTTTTCTACAGGTCAACATGTACTAG
1 TTCTATTCTACAGGTCAACATGTACTAG
* * * *
197015 TTTTATTTTACAGGTCTACAGGTGTACCAG
1 TTCTATTCTACAGGTCAACA--TGTACTAG
* * * *
197045 TTTTATTCAAGAGGT-ATACATGTATTAG
1 TTCTATTCTACAGGTCA-ACATGTACTAG
197073 TTCTATTCTA
1 TTCTATTCTA
197083 TAACACCTCA
Statistics
Matches: 1356, Mismatches: 134, Indels: 36
0.89 0.09 0.02
Matches are distributed among these distances:
27 1 0.00
28 1258 0.93
29 3 0.00
30 22 0.02
31 4 0.00
32 68 0.05
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.39
Consensus pattern (28 bp):
TTCTATTCTACAGGTCAACATGTACTAG
Found at i:197835 original size:23 final size:23
Alignment explanation
Indices: 197803--197856 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
197793 TGCACATACC
197803 TGCACGGGCTATTGTGAATCTAA
1 TGCACGGGCTATTGTGAATCTAA
* *
197826 TGCACTGGCTATTGTGAATTTAA
1 TGCACGGGCTATTGTGAATCTAA
*
197849 TGTACGGG
1 TGCACGGG
197857 GCTTACAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (23 bp):
TGCACGGGCTATTGTGAATCTAA
Found at i:202667 original size:105 final size:105
Alignment explanation
Indices: 202493--202769 Score: 455
Period size: 105 Copynumber: 2.6 Consensus size: 105
202483 ATCTAGCGCA
* * * * * * *
202493 CATTTTAACTCTTTATTATTTGAAAAACTCACCCACCCTCTCTACTCGTACAAGGTTCCCTGTTA
1 CATTATAACTCTTTATTATGTGAGAAACCCACTCACCCTGTCTACTCGTACAAAGTTCCCTGTTA
202558 CAATCATATCATTGTATAGTTTTACACCATAACTAGCACC
66 CAATCATATCATTGTATAGTTTTACACCATAACTAGCACC
*
202598 CATTATAACTCTTTATTATGTGAGAAACCCACTCACCCTGTCTACTCGTACAATGTTCCCTGTTA
1 CATTATAACTCTTTATTATGTGAGAAACCCACTCACCCTGTCTACTCGTACAAAGTTCCCTGTTA
*
202663 CAATCATATCATTGTATAGTTTTACCCCATAACTAGCACC
66 CAATCATATCATTGTATAGTTTTACACCATAACTAGCACC
* *
202703 CATTATAACTCTTTATTATGTGAGAAACCCACTCACCTTGTCTACTCGTACAAAGGTCCCTGTTA
1 CATTATAACTCTTTATTATGTGAGAAACCCACTCACCCTGTCTACTCGTACAAAGTTCCCTGTTA
202768 CA
66 CA
202770 GTTAGTCCCT
Statistics
Matches: 161, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 161 1.00
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.34
Consensus pattern (105 bp):
CATTATAACTCTTTATTATGTGAGAAACCCACTCACCCTGTCTACTCGTACAAAGTTCCCTGTTA
CAATCATATCATTGTATAGTTTTACACCATAACTAGCACC
Found at i:206623 original size:65 final size:65
Alignment explanation
Indices: 206511--207370 Score: 839
Period size: 65 Copynumber: 13.1 Consensus size: 65
206501 TAATTTGGAC
* * * * * *
206511 TGGGATTGTCACACAGTTGTACGTAACAACAATCCCTATCATGAGATTTATTAGTTACTTACGTA
1 TGGGAATGTCACACAGTTGTACATTACAATAATCCCTGTCATGAGATTTATCAGTTACTTACGTA
* * * * *
206576 TGGGAATGTCACACGGTTGTACATTAAAACAATCCCTGTCATTAGATTGATCAGTTACTTACGTA
1 TGGGAATGTCACACAGTTGTACATTACAATAATCCCTGTCATGAGATTTATCAGTTACTTACGTA
* * * * * *
206641 TGGGATTGTTACACAGTTGTACGTTACAATAATCCATGTCTTGTGATTTATCAGTTACTTACGTA
1 TGGGAATGTCACACAGTTGTACATTACAATAATCCCTGTCATGAGATTTATCAGTTACTTACGTA
** * * * * * *
206706 AAGGAATGTCACACAGCTGTACTTTACAATAGTCCATGTCGTGGGATTTATCAGTTACTTACGTA
1 TGGGAATGTCACACAGTTGTACATTACAATAATCCCTGTCATGAGATTTATCAGTTACTTACGTA
* * * * * * *
206771 TGGGAATGTTACACAGTTGTACGTTAAAATACTCCATGTCTTGTGATTTATCAGTTACTTACGTA
1 TGGGAATGTCACACAGTTGTACATTACAATAATCCCTGTCATGAGATTTATCAGTTACTTACGTA
* *
206836 TGGGAATGTCACACAGTTGTACGTTACAATAATCCCTGTCATGCA-ATTTATCCGTTACTTACGT
1 TGGGAATGTCACACAGTTGTACATTACAATAATCCCTGTCATG-AGATTTATCAGTTACTTACGT
206900 AA
65 -A
* * * * * * *
206902 AGGATCGAATGTCACACAGCTGTAGATTACAATAGTCCCTGTCATGGGATTGACCAGTTACTTAC
1 TGG---GAATGTCACACAGTTGTACATTACAATAATCCCTGTCATGAGATTTATCAGTTACTTAC
206967 GTA
63 GTA
* * * * * * *
206970 TAGGAATGTCACACAGCTGTACTTTACAATAGTCCCTGTCGTGGGATTGATCAGTTACTTACGTA
1 TGGGAATGTCACACAGTTGTACATTACAATAATCCCTGTCATGAGATTTATCAGTTACTTACGTA
* ** * * * * *
207035 TAGGAATGTCACACAGTTGTACATTACAGGAATCCCTCTTAAG-GAATTTATAAGTTACTTATGT
1 TGGGAATGTCACACAGTTGTACATTACAATAATCCCTGTCATGAG-ATTTATCAGTTACTTACGT
207099 A
65 A
* * *
207100 TGGGAATGCCACACAGTTGTACGTTACAATAATCCCTGCCATGCA-ATTTATCAGTTACTTACGT
1 TGGGAATGTCACACAGTTGTACATTACAATAATCCCTGTCATG-AGATTTATCAGTTACTTACGT
207164 AAA
65 --A
* * * * *
207167 TGATCGAATGTCACACAGCTGTACATTACAATAGTCCCTGTCGTGGGATTTATCAGTTACTTACG
1 TG--GGAATGTCACACAGTTGTACATTACAATAATCCCTGTCATGAGATTTATCAGTTACTTACG
207232 TA
64 TA
** * * * * * * *
207234 AAGGAATGTCACACAGCTGCACTTTACAATAAT-CGTGGTCGTGGGATTGATCAGTTACTTACGT
1 TGGGAATGTCACACAGTTGTACATTACAATAATCCCT-GTCATGAGATTTATCAGTTACTTACGT
207298 A
65 A
** * * * * * *
207299 TAAGAATGTCACACAGTTGTACATTACAGTAATCCCTCTTAAG-GAATTTATAAGTTACTTATGT
1 TGGGAATGTCACACAGTTGTACATTACAATAATCCCTGTCATGAG-ATTTATCAGTTACTTACGT
207363 A
65 A
207364 TGGGAAT
1 TGGGAAT
207371 TTATCAGTTA
Statistics
Matches: 663, Mismatches: 115, Indels: 34
0.82 0.14 0.04
Matches are distributed among these distances:
64 4 0.01
65 543 0.82
66 5 0.01
67 4 0.01
68 2 0.00
69 105 0.16
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (65 bp):
TGGGAATGTCACACAGTTGTACATTACAATAATCCCTGTCATGAGATTTATCAGTTACTTACGTA
Found at i:207029 original size:264 final size:262
Alignment explanation
Indices: 206517--207370 Score: 1098
Period size: 264 Copynumber: 3.2 Consensus size: 262
206507 GGACTGGGAT
* * * * *
206517 TGTCACACAGTTGTAC-GTAACAACAATCCCTATCATGAGATTTATTAGTTACTTACGTATGGGA
1 TGTCACACAGTTGTACATTAA-AAGAATCCCTCTTA-G-GATTTATAAGTTACTTACGTATGGGA
* * * * * * *
206581 ATGTCACACGGTTGTACATTAAAACAATCCCTGTCAT-TAGATTGATCAGTTACTTACGT-ATGG
63 ATGTCACACAGTTGTACGTTACAATAATCCCTGTCATGCA-ATTTATCAGTTACTTACGTAAAGG
* * * * * * *
206644 ---GATTGTTACACAGTTGTACG-TTACAATAATCCATGTCTTGTGATTTATCAGTTACTTACGT
127 ATCGAATGTCACACAGCTGTA-GATTACAATAGTCCCTGTCATGGGATTTATCAGTTACTTACGT
*
206705 AAAGGAATGTCACACAGCTGTACTTTACAATAGTCCATGTCGTGGGATTTATCAGTTACTTACGT
191 AAAGGAATGTCACACAGCTGTACTTTACAATAGTCCATGTCGTGGGATTGATCAGTTACTTACGT
*
206770 ATGGGAA
256 ATAGGAA
* * * * * *
206777 TGTTACACAGTTGTACGTTAAAATACTCCATGTCTT-GTGATTTATCAGTTACTTACGTATGGGA
1 TGTCACACAGTTGTACATTAAAAGAATCC--CTCTTAG-GATTTATAAGTTACTTACGTATGGGA
*
206841 ATGTCACACAGTTGTACGTTACAATAATCCCTGTCATGCAATTTATCCGTTACTTACGTAAAGGA
63 ATGTCACACAGTTGTACGTTACAATAATCCCTGTCATGCAATTTATCAGTTACTTACGTAAAGGA
* * *
206906 TCGAATGTCACACAGCTGTAGATTACAATAGTCCCTGTCATGGGATTGACCAGTTACTTACGTAT
128 TCGAATGTCACACAGCTGTAGATTACAATAGTCCCTGTCATGGGATTTATCAGTTACTTACGTAA
*
206971 AGGAATGTCACACAGCTGTACTTTACAATAGTCCCTGTCGTGGGATTGATCAGTTACTTACGTAT
193 AGGAATGTCACACAGCTGTACTTTACAATAGTCCATGTCGTGGGATTGATCAGTTACTTACGTAT
207036 AGGAA
258 AGGAA
* * *
207041 TGTCACACAGTTGTACATTACAGGAATCCCTCTTAAGGAATTTATAAGTTACTTATGTATGGGAA
1 TGTCACACAGTTGTACATTAAAAGAATCCCTCTT-AGG-ATTTATAAGTTACTTACGTATGGGAA
* * *
207106 TGCCACACAGTTGTACGTTACAATAATCCCTGCCATGCAATTTATCAGTTACTTACGTAAATGAT
64 TGTCACACAGTTGTACGTTACAATAATCCCTGTCATGCAATTTATCAGTTACTTACGTAAAGGAT
* *
207171 CGAATGTCACACAGCTGTACATTACAATAGTCCCTGTCGTGGGATTTATCAGTTACTTACGTAAA
129 CGAATGTCACACAGCTGTAGATTACAATAGTCCCTGTCATGGGATTTATCAGTTACTTACGTAAA
* * *
207236 GGAATGTCACACAGCTGCACTTTACAATAAT-CGTGGTCGTGGGATTGATCAGTTACTTACGTAT
194 GGAATGTCACACAGCTGTACTTTACAATAGTCCAT-GTCGTGGGATTGATCAGTTACTTACGTAT
*
207300 AAGAA
258 AGGAA
* *
207305 TGTCACACAGTTGTACATT-ACAGTAATCCCTCTTAAGGAATTTATAAGTTACTTATGTATGGGA
1 TGTCACACAGTTGTACATTAAAAG-AATCCCTCTT-AGG-ATTTATAAGTTACTTACGTATGGGA
207369 AT
63 AT
207371 TTATCAGTTA
Statistics
Matches: 525, Mismatches: 55, Indels: 24
0.87 0.09 0.04
Matches are distributed among these distances:
260 97 0.18
261 7 0.01
262 6 0.01
263 5 0.01
264 410 0.78
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (262 bp):
TGTCACACAGTTGTACATTAAAAGAATCCCTCTTAGGATTTATAAGTTACTTACGTATGGGAATG
TCACACAGTTGTACGTTACAATAATCCCTGTCATGCAATTTATCAGTTACTTACGTAAAGGATCG
AATGTCACACAGCTGTAGATTACAATAGTCCCTGTCATGGGATTTATCAGTTACTTACGTAAAGG
AATGTCACACAGCTGTACTTTACAATAGTCCATGTCGTGGGATTGATCAGTTACTTACGTATAGG
AA
Found at i:207349 original size:199 final size:196
Alignment explanation
Indices: 206517--207370 Score: 848
Period size: 199 Copynumber: 4.3 Consensus size: 196
206507 GGACTGGGAT
* * * * * *
206517 TGTCACACAGTTGTACGTAACAACAATCCCTATCAT-GAGATTTATTAGTTACTTACGTATG-GG
1 TGTCACACAGCTGTACATTACAATAATCCCTCTCATGGA-ATTTATCAGTTACTTACGTATGAGG
* * * * * ** *
206580 AATGTCACACGGTTGTACATTAAAACAATCCCTGTCATTAGATTGATCAGTTACTTACGTATGGG
65 AATGTCACACAGCTGTACATTAAAATAGTCCCTGTCGTGGGATTGATCAGTTACTTACGTATAGG
* *
206645 ATTGTTACACAGTTGTACGTTACAATAATCCATGTCTTGTG-ATTTATCAGTTACTTACGTA-AA
130 AATGTCACACAGTTGTACGTTACAATAATCC-TGTCTTG-GAATTTATCAGTTACTTACGTATAA
*
206708 GGAA
193 CGAA
* * * * * *
206712 TGTCACACAGCTGTACTTTACAATAGTCCATGTCGTGGGATTTATCAGTTACTTACGTATG-GGA
1 TGTCACACAGCTGTACATTACAATAATCCCTCTCATGGAATTTATCAGTTACTTACGTATGAGGA
* * * * * * * * *
206776 ATGTTACACAGTTGTACGTTAAAATACTCCATGTCTTGTGATTTATCAGTTACTTACGTATGGGA
66 ATGTCACACAGCTGTACATTAAAATAGTCCCTGTCGTGGGATTGATCAGTTACTTACGTATAGGA
* * * *
206841 ATGTCACACAGTTGTACGTTACAATAATCCCTGTCATGCAATTTATCCGTTACTTACGTAAAGGA
131 ATGTCACACAGTTGTACGTTACAATAAT-CCTGTCTTGGAATTTATCAGTTACTTACGTATA--A
206906 TCGAA
193 -CGAA
* * * * * *
206911 TGTCACACAGCTGTAGATTACAATAGTCCCTGTCATGGGATTGACCAGTTACTTACGTAT-AGGA
1 TGTCACACAGCTGTACATTACAATAATCCCTCTCATGGAATTTATCAGTTACTTACGTATGAGGA
* *
206975 ATGTCACACAGCTGTACTTTACAATAGTCCCTGTCGTGGGATTGATCAGTTACTTACGTATAGGA
66 ATGTCACACAGCTGTACATTAAAATAGTCCCTGTCGTGGGATTGATCAGTTACTTACGTATAGGA
* ** * * * **
207040 ATGTCACACAGTTGTACATTACAGGAATCC-CTCTTAAGGAATTTATAAGTTACTTATGTAT-GG
131 ATGTCACACAGTTGTACGTTACAATAATCCTGTCTT--GGAATTTATCAGTTACTTACGTATAAC
207103 GAA
194 GAA
* * * *
207106 TGCCACACAGTTGTACGTTACAATAATCCCTGC-CATGCAATTTATCAGTTACTTACGTAAATGA
1 TGTCACACAGCTGTACATTACAATAATCCCT-CTCATGGAATTTATCAGTTACTTACGT--ATGA
* * * *
207170 TCGAATGTCACACAGCTGTACATTACAATAGTCCCTGTCGTGGGATTTATCAGTTACTTACGTAA
63 -GGAATGTCACACAGCTGTACATTAAAATAGTCCCTGTCGTGGGATTGATCAGTTACTTACGTAT
* * * * * * *
207235 AGGAATGTCACACAGCTGCACTTTACAATAATCGTGGTCGTGGGATTGATCAGTTACTTACGTAT
127 AGGAATGTCACACAGTTGTACGTTACAATAATCCT-GTCTTGGAATTTATCAGTTACTTACGTAT
207300 AA-GAA
191 AACGAA
* * * * * *
207305 TGTCACACAGTTGTACATTACAGTAATCCCTCTTAAGGAATTTATAAGTTACTTATGTATG-GGA
1 TGTCACACAGCTGTACATTACAATAATCCCTCTCATGGAATTTATCAGTTACTTACGTATGAGGA
207369 AT
66 AT
207371 TTATCAGTTA
Statistics
Matches: 550, Mismatches: 90, Indels: 38
0.81 0.13 0.06
Matches are distributed among these distances:
195 212 0.39
196 4 0.01
197 8 0.01
198 5 0.01
199 318 0.58
201 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (196 bp):
TGTCACACAGCTGTACATTACAATAATCCCTCTCATGGAATTTATCAGTTACTTACGTATGAGGA
ATGTCACACAGCTGTACATTAAAATAGTCCCTGTCGTGGGATTGATCAGTTACTTACGTATAGGA
ATGTCACACAGTTGTACGTTACAATAATCCTGTCTTGGAATTTATCAGTTACTTACGTATAACGA
A
Found at i:207480 original size:69 final size:66
Alignment explanation
Indices: 207363--207619 Score: 293
Period size: 65 Copynumber: 3.8 Consensus size: 66
207353 TTACTTATGT
*
207363 ATGGGAATTTATCAGTTACTTACGTAAAGGATCGAATGTCACACAGCTGTACATTACAATAGTCC
1 ATGGG-ATTTATCAGTTACTTACGT--ATGA-CGAATGTCACACAGCTGTACATTACAATAGTCC
207428 CTGTC
62 CTGTC
* * * * **
207433 GTGGGATTTATCAGTTACCTACGTAAATGATCGAATGTCACACAGCTGTACATTAGAATAATCAT
1 ATGGGATTTATCAGTTACTTACGT--ATGA-CGAATGTCACACAGCTGTACATTACAATAGTCCC
207498 TGTC
63 TGTC
*** * * *
207502 ATTTAATTTATCAGTTACTTACGTATG-GGAATGTCACACAGTTGTACGTTACAATAGTCCCTGT
1 ATGGGATTTATCAGTTACTTACGTATGACGAATGTCACACAGCTGTACATTACAATAGTCCCTGT
207566 C
66 C
* * *
207567 ATGGGATTTATCAGTTACTTACGTAT-AGGAATGTCACACAGTTGTACGTTACA
1 ATGGGATTTATCAGTTACTTACGTATGACGAATGTCACACAGCTGTACATTACA
207620 GTAATCTTTG
Statistics
Matches: 164, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
65 80 0.49
67 3 0.02
69 77 0.47
70 4 0.02
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (66 bp):
ATGGGATTTATCAGTTACTTACGTATGACGAATGTCACACAGCTGTACATTACAATAGTCCCTGT
C
Found at i:207895 original size:36 final size:36
Alignment explanation
Indices: 207854--208107 Score: 311
Period size: 36 Copynumber: 7.1 Consensus size: 36
207844 ATTCCTCACG
207854 CGAGACAGTCCTTGTCGTATGGTTGTTATAATAACA
1 CGAGACAGTCCTTGTCGTATGGTTGTTATAATAACA
*
207890 CGAGACAGTCCTTGTCGTATGGTTGTTATAATGACAA
1 CGAGACAGTCCTTGTCGTATGGTTGTTATAATAAC-A
* * * * ** * ** *
207927 C-CGTC-TTCTATTCACAAGTA-GCATT-TT-TCGTAACG
1 CGAGACAGTC-CTTGTC--GTATG-GTTGTTATAATAACA
*
207962 CGAGACAGTCCTTGTCGTATGGTTGTTATAATAACG
1 CGAGACAGTCCTTGTCGTATGGTTGTTATAATAACA
*
207998 CGAGACAGTCCTTGTCGTATGGTTGTTATAATAACG
1 CGAGACAGTCCTTGTCGTATGGTTGTTATAATAACA
208034 CGAGACAGTCCTTGTCGTATGGTTGTTATAATAACA
1 CGAGACAGTCCTTGTCGTATGGTTGTTATAATAACA
208070 CGAGACAGTCCTTGTCGTATGGTTGTTATAATAACA
1 CGAGACAGTCCTTGTCGTATGGTTGTTATAATAACA
208106 CG
1 CG
208108 GGCCTCAATG
Statistics
Matches: 186, Mismatches: 22, Indels: 20
0.82 0.10 0.09
Matches are distributed among these distances:
34 5 0.03
35 6 0.03
36 163 0.88
37 7 0.04
38 5 0.03
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (36 bp):
CGAGACAGTCCTTGTCGTATGGTTGTTATAATAACA
Found at i:209406 original size:23 final size:23
Alignment explanation
Indices: 209375--209418 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
209365 AGAGTAACAT
*
209375 AAAAGTCCGGACACTGGAAATAA
1 AAAAATCCGGACACTGGAAATAA
209398 AAAAATCCGGACACTGGAAAT
1 AAAAATCCGGACACTGGAAAT
209419 TAATTTTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (23 bp):
AAAAATCCGGACACTGGAAATAA
Found at i:210392 original size:51 final size:54
Alignment explanation
Indices: 210284--210428 Score: 183
Period size: 51 Copynumber: 2.7 Consensus size: 54
210274 GTAATTTTGT
* *
210284 GTCTTTTAAGGAATATATAAGTGGTTTGATATTGA-AAGATGTTATAATCATAC
1 GTCTTTTAAGGAATATATAAGTGGTTTAATATTGATAAGATGTTATAATCATAA
* * * *
210337 GTCTTTCAAGGAATATAT-A-T-GTTTAAATATTGATAA-ATTTTGTAATTATAA
1 GTCTTTTAAGGAATATATAAGTGGTTT-AATATTGATAAGATGTTATAATCATAA
210388 GTCTTTTAAGGAATATATAAGTGGTTTAATATTGATGAAGA
1 GTCTTTTAAGGAATATATAAGTGGTTTAATATTGAT-AAGA
210429 CTATAATTAT
Statistics
Matches: 78, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
50 4 0.05
51 36 0.46
52 4 0.05
53 27 0.35
54 6 0.08
55 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.41
Consensus pattern (54 bp):
GTCTTTTAAGGAATATATAAGTGGTTTAATATTGATAAGATGTTATAATCATAA
Found at i:210434 original size:104 final size:105
Alignment explanation
Indices: 210284--210477 Score: 268
Period size: 104 Copynumber: 1.8 Consensus size: 105
210274 GTAATTTTGT
* * *
210284 GTCTTTTAAGGAATATATAAGTGGTTTGATATTGAAAGATGTTATAATCATACGTCTTTCAAGG-
1 GTCTTTTAAGGAATATATAAGTGGTTTAATATTGAAAGA-GCTATAATCATACGTATTTCAAGGT
* *
210348 A-ATATATATGTTTAAATATTGATAAATTTTGTAATTATAA
65 ACATAAAGATGTTTAAATATTGATAAATTTTGTAATTATAA
* *
210388 GTCTTTTAAGGAATATATAAGTGGTTTAATATTGATGAAGA-CTATAATTATTCGTATTTCAAGG
1 GTCTTTTAAGGAATATATAAGTGGTTTAATATTGA--AAGAGCTATAATCATACGTATTTCAAGG
*
210452 TACATAAAGGTGTTTAAATATTGATA
64 TACATAAAGATGTTTAAATATTGATA
210478 GAGACTATTT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
104 53 0.68
105 1 0.01
106 24 0.31
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.41
Consensus pattern (105 bp):
GTCTTTTAAGGAATATATAAGTGGTTTAATATTGAAAGAGCTATAATCATACGTATTTCAAGGTA
CATAAAGATGTTTAAATATTGATAAATTTTGTAATTATAA
Found at i:210436 original size:53 final size:52
Alignment explanation
Indices: 210244--210438 Score: 168
Period size: 53 Copynumber: 3.7 Consensus size: 52
210234 TTCCAGAAAT
* * * * * **
210244 ATATATTAGTGTTTTAATAATGAT-AGATATGTAATTTTGTGTCTTTTAAGGA
1 ATATATAAGTGGTTTAATATTGATAAGAT-TATAATTATAAGTCTTTTAAGGA
* * * *
210296 ATATATAAGTGGTTTGATATTGA-AAGATGTTATAATCATACGTCTTTCAAGGA
1 ATATATAAGTGGTTTAATATTGATAAGA--TTATAATTATAAGTCTTTTAAGGA
*
210349 ATATAT-A-T-GTTTAAATATTGATAA-ATTTTGTAATTATAAGTCTTTTAAGGA
1 ATATATAAGTGGTTT-AATATTGATAAGA--TTATAATTATAAGTCTTTTAAGGA
*
210400 ATATATAAGTGGTTTAATATTGATGAAGACTATAATTAT
1 ATATATAAGTGGTTTAATATTGAT-AAGATTATAATTAT
210439 TCGTATTTCA
Statistics
Matches: 115, Mismatches: 18, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
50 4 0.03
51 36 0.31
52 26 0.23
53 41 0.36
54 7 0.06
55 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.16, T:0.44
Consensus pattern (52 bp):
ATATATAAGTGGTTTAATATTGATAAGATTATAATTATAAGTCTTTTAAGGA
Found at i:210472 original size:53 final size:53
Alignment explanation
Indices: 210411--210561 Score: 143
Period size: 51 Copynumber: 2.9 Consensus size: 53
210401 TATATAAGTG
*
210411 GTTT-AATATTGATGAAGACTATAATTATTCGTATTTCAAGGTAC-ATAAAGGT
1 GTTTAAATATTGATGAAGACTATAATTATACGTATTTCAAGG-ACAATAAAGGT
** * * **
210463 GTTTAAATATTGAT-AGAGACTATTTTTATACGTCTTTCAA--ACAATATATTT
1 GTTTAAATATTGATGA-AGACTATAATTATACGTATTTCAAGGACAATAAAGGT
* * *
210514 GTTTAAATATTAATAGAA-ACTATAATTATACGTACTTCAAGGAAAATA
1 GTTTAAATATTGAT-GAAGACTATAATTATACGTATTTCAAGGACAATA
210562 TCAGTGTTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 13
0.75 0.12 0.12
Matches are distributed among these distances:
50 2 0.03
51 36 0.46
52 6 0.08
53 35 0.44
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.39
Consensus pattern (53 bp):
GTTTAAATATTGATGAAGACTATAATTATACGTATTTCAAGGACAATAAAGGT
Found at i:210830 original size:2 final size:2
Alignment explanation
Indices: 210825--210861 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
210815 AAAGAATTAG
210825 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
210862 TTTTAACATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:213824 original size:3 final size:3
Alignment explanation
Indices: 213778--213812 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
213768 GATTTTGTTA
213778 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
213813 AAGTATGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:213934 original size:3 final size:3
Alignment explanation
Indices: 213919--213955 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
213909 GTTATTAATT
*
213919 TGA TGA CGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
213956 AAGGATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.32
Consensus pattern (3 bp):
TGA
Found at i:216864 original size:17 final size:17
Alignment explanation
Indices: 216844--216876 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
216834 AACTCTCAGT
216844 TTAGCCGATAACTGGTC
1 TTAGCCGATAACTGGTC
216861 TTAGCCGATAACTGGT
1 TTAGCCGATAACTGGT
216877 ACAGTAGCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (17 bp):
TTAGCCGATAACTGGTC
Found at i:222440 original size:170 final size:164
Alignment explanation
Indices: 222229--222537 Score: 401
Period size: 166 Copynumber: 1.8 Consensus size: 164
222219 TTCAATTTTA
* *
222229 GTCCGGGGTCATGACTTTTTCAATTTAGGATCTTTACTATATATATATACAAAATTTTGCT-TAA
1 GTCCGGGGTCATGACTTTTTCAATTTAGAATC-TT-C-A-CTATATATACAAAATTTTG-TGTAA
* ** *
222293 ATATTGGCATTTCTGGTGCAGTGGTTCTTGAGAAGAAGATTTTAAAACATTATTCCTATTTATTT
61 ATATTGGCATTTCTGGTGCAATGGTTCTAAAGAAGAAGATTTTAAAACATTA-CCCTATTT-TTT
*
222358 T-TATGTTAAACTGTGAACCACGCCTGGGGCCCCTATGTTG
124 TCTATGTTAAAATGTGAACCACGCCTGGGGCCCCTATGTTG
*
222398 GTCCGGAGGTCATGA-TTATTAT-AATTTAGAATCTTCACTATATATACAAACTTTTGTGTAAAT
1 GTCCGG-GGTCATGACTT-TT-TCAATTTAGAATCTTCACTATATATACAAAATTTTGTGTAAAT
* * *
222461 ATTGGCATTTCTGTTGCAATGGTTCTAAAGAGGAAGATTTTTAAACATTACCCTATTTTTTTCTA
63 ATTGGCATTTCTGGTGCAATGGTTCTAAAGAAGAAGATTTTAAAACATTACCCTATTTTTTTCTA
222526 TGTTAAAATGTG
128 TGTTAAAATGTG
222538 CACCCCACCT
Statistics
Matches: 124, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
164 4 0.03
165 21 0.17
166 66 0.53
167 1 0.01
168 1 0.01
169 10 0.08
170 20 0.16
171 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.40
Consensus pattern (164 bp):
GTCCGGGGTCATGACTTTTTCAATTTAGAATCTTCACTATATATACAAAATTTTGTGTAAATATT
GGCATTTCTGGTGCAATGGTTCTAAAGAAGAAGATTTTAAAACATTACCCTATTTTTTTCTATGT
TAAAATGTGAACCACGCCTGGGGCCCCTATGTTG
Found at i:224629 original size:23 final size:23
Alignment explanation
Indices: 224603--224674 Score: 108
Period size: 23 Copynumber: 3.1 Consensus size: 23
224593 GGAGTGAATT
* *
224603 AATTACCGAAAATATGTTATATG
1 AATTACTGAAAATATGTTATATA
*
224626 AATTACTAAAAATATGTTATATA
1 AATTACTGAAAATATGTTATATA
*
224649 AATTACTGAAAATATGTTACATA
1 AATTACTGAAAATATGTTATATA
224672 AAT
1 AAT
224675 GACGTTCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.49, C:0.07, G:0.08, T:0.36
Consensus pattern (23 bp):
AATTACTGAAAATATGTTATATA
Found at i:226484 original size:4 final size:4
Alignment explanation
Indices: 226477--226597 Score: 199
Period size: 4 Copynumber: 30.2 Consensus size: 4
226467 CGTCCGTCCG
* *
226477 TCTA TCTA TTTA TCTA TCTA TC-A TTTTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA -TCTA TCTA TCTA TCTA TCTA TCTA
226525 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
*
226573 TCTA TCTA TCTA TATA TCTA TCTA T
1 TCTA TCTA TCTA TCTA TCTA TCTA T
226598 GAAGAATTAA
Statistics
Matches: 109, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
3 1 0.01
4 107 0.98
5 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (4 bp):
TCTA
Found at i:228475 original size:166 final size:166
Alignment explanation
Indices: 227972--228792 Score: 1036
Period size: 166 Copynumber: 5.0 Consensus size: 166
227962 ATTCTTTAAA
* *
227972 AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTA-AGTAAAAATTCATCCCCC-ATTGTGGCC
1 AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATA-TAAAACTTGATCCCCCAATTGTGGCC
* * * * * * * *
228035 TCACCCTA-CCCC-TGGACTATTATTTAAACAAACTTGAATCTATA-TGATCTGGGGATGCTTCC
65 CCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACT-ACCTGAGGATGCTTCC
*
228097 ACTCAAATTTGGGCTTTCCTGGCCTAATAG-TTTTGAG
129 ACTCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAG
* * *
228134 AAGAAGACTTTTAAAGATTTTCTC----TA-T-CTATA-AAAA-TTCATCCCCC-ATTGTGACCC
1 AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATATAAAACTTGATCCCCCAATTGTGGCCC
* * * * * *
228190 CGCCCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTTCCTAAGGATGGTTACA-
66 CACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCAC
* * * *
228254 TGCCAATTTGAGATTTCTTGGCCAAATA-TTTTTGAG
131 T-CAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAG
* * *
228290 AAGAAGATTTTTAAAAGATTTCCTTTATACATTCCTATATAAAACTTGATCCCCCAATTGTGGCC
1 AAGAAGATTTTT-AAAGATTTTCTCTATATATTCCTATATAAAACTTGATCCCCCAATTGTGGCC
* *
228355 CCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTATACTATCTGAGGATGCTTCCA
65 CCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCA
*
228420 CTCAAATTTGAGCTTTCCTGGCCTAATGGTTTTTGAG
130 CTCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAG
* *
228457 AAGAAGATTTTTAAAGATTTTCTCAATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCC
1 AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATATAAAACTTGATCCCCCAATTGTGGCCC
** * *
228522 CACCCTACCCATGGGAACTATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCAT
66 CACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCA-
* * *
228587 TTC-AATTCGAGCTTTTCTGGCCTAATAGTTTTT---
130 CTCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAG
* * ** * * *
228620 CAGAAGATTTTTAAAGATTTTATCTATATATTATTATGTAAAACATGATCCCCCTATTGTGGCCC
1 AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATATAAAACTTGATCCCCCAATTGTGGCCC
228685 CACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCAC
66 CACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCAC
228750 TCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAG
131 TCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAG
228786 AAGAAGA
1 AAGAAGA
228793 CTTTGGCTCA
Statistics
Matches: 567, Mismatches: 69, Indels: 42
0.84 0.10 0.06
Matches are distributed among these distances:
154 24 0.04
155 9 0.02
156 80 0.14
157 13 0.02
158 2 0.00
161 1 0.00
162 26 0.05
163 151 0.27
164 4 0.01
165 9 0.02
166 225 0.40
167 23 0.04
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (166 bp):
AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATATAAAACTTGATCCCCCAATTGTGGCCC
CACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCAC
TCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAG
Found at i:228712 original size:329 final size:318
Alignment explanation
Indices: 227972--228796 Score: 1081
Period size: 329 Copynumber: 2.6 Consensus size: 318
227962 ATTCTTTAAA
* * *
227972 AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTAAGTAAAA-ATTCATCCCCCATTGTGGCCT
1 AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACA-TGATCCCCCATTGTGGCCC
* * * * *
228036 CACCCTA-CCCC-TGGACTATTATTTAAACAAACTTGAATCTATA-TGATCTGGGGATGCTTCCA
65 CACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTATACT-ATCTGAGGATGCTTCCA
*
228098 CTCAAATTTGGGCTTTCCTGGCCTAATAG-TTTTGAGAAGAAGACTTTTAAAGATTTTCTCTATC
129 CTCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAGAAGAAGACTTTTAAAGATTTTCTCTATC
*
228162 TATAAAAATTCATCCCCCATTGTGACCCCGCCCTACCCCCAGGGACCATGATTTGAACAAACTTG
194 TATAAAAATTCATCCCCCATTGTGACCCCACCCTA-CCCCAGGGACCATGATTTGAACAAACTTG
* * *
228227 AATCTACACTTCCTAAGGATGGTTACATGCCAATTTGAGATTTCTTGGCCAAATATTTTTGAG
258 AATCTACACTACCTAAGGATGCTTACATGCCAATTCGAGATTTCTTGGCCAAATATTTTT--G
* * * * *
228290 AAGAAGATTTTTAAAAGATTTCCTTTATACATTCCTATATAAAACTTGATCCCCCAATTGTGGCC
1 AAGAAGATTTTT-AAAGATTTTCTCTATATATTCCTATGTAAAACATGATCCCCC-ATTGTGGCC
228355 CCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTATACTATCTGAGGATGCTTCCA
64 CCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTATACTATCTGAGGATGCTTCCA
* *
228420 CTCAAATTTGAGCTTTCCTGGCCTAATGGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCAATA
129 CTCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAGAAGAAGACTTTTAAAGATTTTCTC----
* * * *
228485 TATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCACCCTA-CCCATGGGAACTATGATTTG
190 TA-T-CTA--TAAAAATTCATCCCCC-ATTGTGACCCCACCCTACCCCA-GGG-ACCATGATTTG
* * ** * *
228549 AACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTCAATTCGAGCTTT-TCTGGCCTAAT
248 AACAAACTTGAATCTACACTACCTAAGGATGCTTACATGCCAATTCGAGATTTCT-TGGCCAAAT
228613 AGTTTTT-
312 A-TTTTTG
* * **
228620 CAGAAGATTTTTAAAGATTTTATCTATATATTATTATGTAAAACATGATCCCCCTATTGTGGCCC
1 AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACATGATCCCCC-ATTGTGGCCC
* *
228685 CACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCAC
65 CACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTATACTATCTGAGGATGCTTCCAC
228750 TCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAGAAGAAGACTTT
130 TCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAGAAGAAGACTTT
228797 GGCTCAGGTG
Statistics
Matches: 443, Mismatches: 44, Indels: 29
0.86 0.09 0.06
Matches are distributed among these distances:
318 12 0.03
319 34 0.08
320 16 0.04
321 4 0.01
322 71 0.16
323 31 0.07
327 2 0.00
328 1 0.00
329 155 0.35
330 15 0.03
331 18 0.04
332 79 0.18
333 5 0.01
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (318 bp):
AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACATGATCCCCCATTGTGGCCCC
ACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTATACTATCTGAGGATGCTTCCACT
CAAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAGAAGAAGACTTTTAAAGATTTTCTCTATCTA
TAAAAATTCATCCCCCATTGTGACCCCACCCTACCCCAGGGACCATGATTTGAACAAACTTGAAT
CTACACTACCTAAGGATGCTTACATGCCAATTCGAGATTTCTTGGCCAAATATTTTTG
Found at i:230281 original size:4 final size:4
Alignment explanation
Indices: 230238--230299 Score: 81
Period size: 4 Copynumber: 15.8 Consensus size: 4
230228 AAAGTTTACA
* * * *
230238 GACG GACA GACA GACG GACA GACG GACG GACG GACA GACG GACG GACG
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
230286 GACG GAC- GACG GAC
1 GACG GACG GACG GAC
230300 AAAAAGTGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
3 3 0.06
4 48 0.94
ACGTcount: A:0.32, C:0.26, G:0.42, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:231928 original size:10 final size:11
Alignment explanation
Indices: 231910--231966 Score: 57
Period size: 10 Copynumber: 5.3 Consensus size: 11
231900 GATATCATTT
*
231910 TATATGATACAA
1 TATA-GATATAA
231922 TA-AGATATAA
1 TATAGATATAA
231932 TATA-ATATAA
1 TATAGATATAA
*
231942 TATATGATACAA
1 TATA-GATATAA
231954 TAT-GATATAA
1 TATAGATATAA
231964 TAT
1 TAT
231967 CATATGATAC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 27 0.69
11 2 0.05
12 10 0.26
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.37
Consensus pattern (11 bp):
TATAGATATAA
Found at i:231948 original size:32 final size:32
Alignment explanation
Indices: 231910--231971 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
231900 GATATCATTT
231910 TATATGATACAATAAGATATAATATAATATAA
1 TATATGATACAATAAGATATAATATAATATAA
* *
231942 TATATGATACAATATGATATAATATCATAT
1 TATATGATACAATAAGATATAATATAATAT
231972 GATACAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.37
Consensus pattern (32 bp):
TATATGATACAATAAGATATAATATAATATAA
Found at i:231950 original size:22 final size:22
Alignment explanation
Indices: 231925--231966 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
231915 GATACAATAA
*
231925 GATATAATATAATATAATATAT
1 GATACAATATAATATAATATAT
*
231947 GATACAATATGATATAATAT
1 GATACAATATAATATAATAT
231967 CATATGATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.38
Consensus pattern (22 bp):
GATACAATATAATATAATATAT
Found at i:231971 original size:15 final size:15
Alignment explanation
Indices: 231896--231975 Score: 51
Period size: 15 Copynumber: 5.5 Consensus size: 15
231886 AAATAACATA
* * *
231896 ATATGATATCATTTT
1 ATATGATATAATATC
* **
231911 ATATGATACAATAAG
1 ATATGATATAATATC
*
231926 ATATAATATAATAT-
1 ATATGATATAATATC
*
231940 A-AT-ATATGATA-C
1 ATATGATATAATATC
231952 AATATGATATAATATC
1 -ATATGATATAATATC
231968 ATATGATA
1 ATATGATA
231976 CAAAAGTATA
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
12 7 0.14
13 3 0.06
14 3 0.06
15 36 0.72
16 1 0.02
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (15 bp):
ATATGATATAATATC
Found at i:232001 original size:15 final size:15
Alignment explanation
Indices: 231962--232010 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
231952 AATATGATAT
*
231962 AATATCATATGATAC
1 AATATCATATCATAC
*
231977 AAAAGT-ATATCATAC
1 AATA-TCATATCATAC
231992 AATATCATATCATAC
1 AATATCATATCATAC
232007 AATA
1 AATA
232011 CGATTCGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 1 0.03
15 27 0.93
16 1 0.03
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (15 bp):
AATATCATATCATAC
Found at i:232312 original size:15 final size:15
Alignment explanation
Indices: 232274--232312 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
232264 TAACAATGTC
* *
232274 ATATTACATGATACA
1 ATATTATATGAAACA
*
232289 ATATCATATGAAACA
1 ATATTATATGAAACA
232304 ATATTATAT
1 ATATTATAT
232313 CATATAATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (15 bp):
ATATTATATGAAACA
Found at i:233188 original size:180 final size:180
Alignment explanation
Indices: 232883--233260 Score: 720
Period size: 180 Copynumber: 2.1 Consensus size: 180
232873 TTCGAAAATC
*
232883 CCAGATTCAGCATCTAAGCCTGAGAAATGTATCATTATCACAAGACGCATCATGTATTTATTTAT
1 CCAGATTCAGCATCCAAGCCTGAGAAATGTATCATTATCACAAGACGCATCATGTATTTATTTAT
* *
232948 TTTTTTAAAAATTGAACCAATAATAACTAAAATTTGTATATCAAAGGGCACCTATTAGAAAAAAT
66 TCTTTTAAAAATTGAACCAATAATAACTAAAATTTGTATATCAAAGGGCACATATTAGAAAAAAT
233013 TTAACCTTTTCCAAAAACCTTACCCTCATCCAGCATCCGAAACCTATGGT
131 TTAACCTTTTCCAAAAACCTTACCCTCATCCAGCATCCGAAACCTATGGT
233063 CCAGATTCAGCATCCAAGCCTGAGAAATGTATCATTATCACAAGACGCATCATGTATTTATTTAT
1 CCAGATTCAGCATCCAAGCCTGAGAAATGTATCATTATCACAAGACGCATCATGTATTTATTTAT
*
233128 TCTTTTAAAAATTGAACCAATAATAACTAAAATTTGTATATCAAAGGGCACATGTTAGAAAAAAT
66 TCTTTTAAAAATTGAACCAATAATAACTAAAATTTGTATATCAAAGGGCACATATTAGAAAAAAT
233193 TTAACCTTTTCCAAAAACCTTACCCTCATCCAGCATCCGAAACCTATGGT
131 TTAACCTTTTCCAAAAACCTTACCCTCATCCAGCATCCGAAACCTATGGT
233243 CCAGATTCAGCATCCAAG
1 CCAGATTCAGCATCCAAG
233261 GTTGTGAAGT
Statistics
Matches: 194, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
180 194 1.00
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (180 bp):
CCAGATTCAGCATCCAAGCCTGAGAAATGTATCATTATCACAAGACGCATCATGTATTTATTTAT
TCTTTTAAAAATTGAACCAATAATAACTAAAATTTGTATATCAAAGGGCACATATTAGAAAAAAT
TTAACCTTTTCCAAAAACCTTACCCTCATCCAGCATCCGAAACCTATGGT
Found at i:244899 original size:19 final size:19
Alignment explanation
Indices: 244871--244921 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
244861 CGACCATATG
* * *
244871 TGTACACAAGTCTCGTATA
1 TGTACACAAGCCTCCTACA
*
244890 TGTCCACAAGCCTCCTACA
1 TGTACACAAGCCTCCTACA
244909 TGTACACAAGCCT
1 TGTACACAAGCCT
244922 ATGATGCATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.25
Consensus pattern (19 bp):
TGTACACAAGCCTCCTACA
Found at i:247248 original size:146 final size:145
Alignment explanation
Indices: 247089--247634 Score: 763
Period size: 146 Copynumber: 3.7 Consensus size: 145
247079 CTTCCTCAAT
* * * *
247089 TGACCTTGTGTCAAGGTCATGACACATCCTTACGTCATAAGCAATATTTGTGTGAAGTAAGAACA
1 TGACCTTGAGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAAC-
* * *
247154 TT-CAATGCTTCTCCATAATAATGATATGGACCAGACACGAATTTTGCATTTTTTCTGCCAGTGA
65 TTCCAATGTTTCTCCATAAGAAAGATATGGACCAGACACGAATTTTGCATTTTTTCTGCCAGTGA
*
247218 CCTTGACCTTGCACAAA
130 CCTTGACCTTGC-CGAA
** *
247235 CAACCTTGAGTCAAGGTCATGACACACCCTTAGGCCATAAGCAATCTTTGTGTGAAGTAAGAACT
1 TGACCTTGAGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
** * *
247300 TCCAATGTCAATGTTTCTCTTTAAGGAAGATATGAACCAGACACGAATTTTGCATTTTTTCTGCC
66 T-C-----CAATGTTTCTCCATAAGAAAGATATGGACCAGACACGAATTTTGCATTTTTTCTGCC
247365 AGTGACCTTGACCTTGCCTGAA
125 AGTGACCTTGACCTTGCC-GAA
* *
247387 TGACCTT-AGGTCATGGTCATGACACACCCTCAGGTCATAAGCAATCTTTGTGTGAAGTAAGAAC
1 TGACCTTGA-GTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAAC
* * * *
247451 TTCCAATATTTCTCCATAAGAAAGATATTGACCAGACATGAATTTTGCAATTTTTCTGCCAGTGA
65 TTCCAATGTTTCTCCATAAGAAAGATATGGACCAGACACGAATTTTGCATTTTTTCTGCCAGTGA
247516 CCTTGACCTTGCGCGAA
130 CCTTGACCTTGC-CGAA
* *
247533 TGACCTTGGGTCAAGGTCATGACACACCCTTAAGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
1 TGACCTTGAGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
*
247598 TCCAATGTTTCTCTATAAGAAAGATATGGACCAGACA
66 TCCAATGTTTCTCCATAAGAAAGATATGGACCAGACA
247635 GACGGACAGA
Statistics
Matches: 354, Mismatches: 35, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
145 2 0.01
146 220 0.62
147 1 0.00
151 3 0.01
152 128 0.36
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (145 bp):
TGACCTTGAGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
TCCAATGTTTCTCCATAAGAAAGATATGGACCAGACACGAATTTTGCATTTTTTCTGCCAGTGAC
CTTGACCTTGCCGAA
Found at i:247605 original size:298 final size:298
Alignment explanation
Indices: 247069--247605 Score: 837
Period size: 298 Copynumber: 1.8 Consensus size: 298
247059 TTCGAAACAA
* *
247069 TGACCTTGAACTTCCTCAATTGACCTTGTGTCAAGGTCATGACACATCCTTACGTCATAAGCAAT
1 TGACCTTGAACTTCCTCAATTGACCTTGTGTCAAGGTCATGACACACCCTCACGTCATAAGCAAT
* * *
247134 ATTTGTGTGAAGTAAGAACATTCAATGCTTCTCCATAATAATGATATGGACCAGACACGAATTTT
66 ATTTGTGTGAAGTAAGAACATTCAATACTTCTCCATAAGAAAGATATGGACCAGACACGAATTTT
*
247199 GCATTTTTTCTGCCAGTGACCTTGACCTTGCACAAACAACCTTGAGTCAAGGTCATGACACACCC
131 GCAATTTTTCTGCCAGTGACCTTGACCTTGCACAAACAACCTTGAGTCAAGGTCATGACACACCC
*
247264 TTAGGCCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTCAATGTTTCTCTTTAAGGAAG
196 TTAAGCCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTCAATGTTTCTCTTTAAGGAAG
247329 ATATGAACCAGACACGAATTTTGCATTTTTTCTGCCAG
261 ATATGAACCAGACACGAATTTTGCATTTTTTCTGCCAG
* * * *
247367 TGACCTTGACCTTGCCTGAA-TGACCTTAG-GTCATGGTCATGACACACCCTCAGGTCATAAGCA
1 TGACCTTGAACTT-CCTCAATTGACCTT-GTGTCAAGGTCATGACACACCCTCACGTCATAAGCA
* * * *
247430 ATCTTTGTGTGAAGTAAGAAC-TTCCAATATTTCTCCATAAGAAAGATATTGACCAGACATGAAT
64 ATATTTGTGTGAAGTAAGAACATT-CAATACTTCTCCATAAGAAAGATATGGACCAGACACGAAT
* * ** *
247494 TTTGCAATTTTTCTGCCAGTGACCTTGACCTTGCGCGAATGACCTTGGGTCAAGGTCATGACACA
128 TTTGCAATTTTTCTGCCAGTGACCTTGACCTTGCACAAACAACCTTGAGTCAAGGTCATGACACA
*
247559 CCCTTAAGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGT
193 CCCTTAAGCCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGT
247606 TTCTCTATAA
Statistics
Matches: 215, Mismatches: 21, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
297 2 0.01
298 207 0.96
299 6 0.03
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (298 bp):
TGACCTTGAACTTCCTCAATTGACCTTGTGTCAAGGTCATGACACACCCTCACGTCATAAGCAAT
ATTTGTGTGAAGTAAGAACATTCAATACTTCTCCATAAGAAAGATATGGACCAGACACGAATTTT
GCAATTTTTCTGCCAGTGACCTTGACCTTGCACAAACAACCTTGAGTCAAGGTCATGACACACCC
TTAAGCCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTCAATGTTTCTCTTTAAGGAAG
ATATGAACCAGACACGAATTTTGCATTTTTTCTGCCAG
Found at i:248308 original size:43 final size:42
Alignment explanation
Indices: 248152--248306 Score: 193
Period size: 43 Copynumber: 3.6 Consensus size: 42
248142 TGATGAACAC
*
248152 ATGAAATAACATCACACAGATTTTACCTAATGCCAGAAAGTTG
1 ATGAAATAACATCACACAGATTTTACCTAATGACAG-AAGTTG
* *
248195 ATGAAATAACATCACACAGATTTTACCGAATGACAGGAACTTG
1 ATGAAATAACATCACACAGATTTTACCTAATGACA-GAAGTTG
* * *
248238 ATGAAATAACATCACATAGATTTTACTTAATGTCAGAAGTTTG
1 ATGAAATAACATCACACAGATTTTACCTAATGACAGAAG-TTG
** * *
248281 ACAAAATAACATCACACTGAATTTAC
1 ATGAAATAACATCACACAGATTTTAC
248307 TTGATAAAAA
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
42 3 0.03
43 93 0.96
44 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (42 bp):
ATGAAATAACATCACACAGATTTTACCTAATGACAGAAGTTG
Found at i:248581 original size:46 final size:45
Alignment explanation
Indices: 248438--248589 Score: 236
Period size: 44 Copynumber: 3.4 Consensus size: 45
248428 TAAGAATTTC
*
248438 ATGAAATAACATCACACAGAATC-TACCTAATTCTATAAAACTTG
1 ATGAAATAACATCACACAGAATCTTACCTAATCCTATAAAACTTG
* * *
248482 ATGAAATAACATCACACAGAAT-TTACCTCATGCTATAAAGCTTG
1 ATGAAATAACATCACACAGAATCTTACCTAATCCTATAAAACTTG
*
248526 ATGAAATAACATTACACAGAATCTTAACCTAATCCTATAAAACTTG
1 ATGAAATAACATCACACAGAATCTT-ACCTAATCCTATAAAACTTG
248572 ATGAAATAACATCACACA
1 ATGAAATAACATCACACA
248590 ATATTTACCT
Statistics
Matches: 97, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
44 61 0.63
45 2 0.02
46 34 0.35
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.26
Consensus pattern (45 bp):
ATGAAATAACATCACACAGAATCTTACCTAATCCTATAAAACTTG
Found at i:249202 original size:22 final size:22
Alignment explanation
Indices: 249177--249246 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
249167 TGACTGTTTG
* *
249177 CTCAGAGTGTGCTCAATGTTCA
1 CTCAAAGTGCGCTCAATGTTCA
* ***
249199 CTCAAAGTGCCCTCACCATTCA
1 CTCAAAGTGCGCTCAATGTTCA
249221 CTCAAAGTGCGCTCAATGTTCA
1 CTCAAAGTGCGCTCAATGTTCA
249243 CTCA
1 CTCA
249247 CTGTTCAAGT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (22 bp):
CTCAAAGTGCGCTCAATGTTCA
Found at i:253944 original size:15 final size:15
Alignment explanation
Indices: 253924--253954 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
253914 CAAATCTACT
253924 TTATGTTTTAAGCTA
1 TTATGTTTTAAGCTA
253939 TTATGTTTTAAGCTA
1 TTATGTTTTAAGCTA
253954 T
1 T
253955 AAACTTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (15 bp):
TTATGTTTTAAGCTA
Found at i:259971 original size:2 final size:2
Alignment explanation
Indices: 259958--260007 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
259948 TGCATAAACT
*
259958 GA GA GC GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
260000 GA GA GA GA
1 GA GA GA GA
260008 TGATAATGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.02, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:261931 original size:15 final size:15
Alignment explanation
Indices: 261911--262182 Score: 167
Period size: 15 Copynumber: 19.7 Consensus size: 15
261901 AATAATGTAC
261911 ATGGCTACATTTTGT
1 ATGGCTACATTTTGT
*
261926 ATGGCTACA---TGC
1 ATGGCTACATTTTGT
*
261938 ATGGCTACA-ATTGT
1 ATGGCTACATTTTGT
** *
261952 ATGGCTACATAATCT
1 ATGGCTACATTTTGT
* *
261967 ATGGCTATATTTTGC
1 ATGGCTACATTTTGT
* *
261982 ATGGCTACATGTTGC
1 ATGGCTACATTTTGT
* *
261997 ATTGATACA---TGT
1 ATGGCTACATTTTGT
*
262009 ATGGCTACATTTTGC
1 ATGGCTACATTTTGT
* *
262024 ATGCCTACA---T-C
1 ATGGCTACATTTTGT
262035 ATGGCTACATTTTGT
1 ATGGCTACATTTTGT
*
262050 ATGCCTACA---TGT
1 ATGGCTACATTTTGT
262062 ATGGCTACA---TGT
1 ATGGCTACATTTTGT
* *
262074 ATGGCTATATTTTGC
1 ATGGCTACATTTTGT
**
262089 ATGGCTACATGATGT
1 ATGGCTACATTTTGT
* *
262104 ATGGATACATTTTGC
1 ATGGCTACATTTTGT
*
262119 ATGGCTATATTTTGT
1 ATGGCTACATTTTGT
* *
262134 ATGACT--A-TATGT
1 ATGGCTACATTTTGT
262146 ATGGCTACATTTTGT
1 ATGGCTACATTTTGT
262161 ATGGCTACA---TGT
1 ATGGCTACATTTTGT
262173 ATGGCTACAT
1 ATGGCTACAT
262183 GTATCTAAAC
Statistics
Matches: 201, Mismatches: 39, Indels: 36
0.73 0.14 0.13
Matches are distributed among these distances:
11 9 0.04
12 64 0.32
13 1 0.00
14 13 0.06
15 114 0.57
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (15 bp):
ATGGCTACATTTTGT
Found at i:261957 original size:26 final size:27
Alignment explanation
Indices: 261910--261961 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
261900 TAATAATGTA
*
261910 CATGGCTACATTTTGTATGGCTACATG
1 CATGGCTACATATTGTATGGCTACATG
261937 CATGGCTACA-ATTGTATGGCTACAT
1 CATGGCTACATATTGTATGGCTACAT
261962 AATCTATGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (27 bp):
CATGGCTACATATTGTATGGCTACATG
Found at i:262045 original size:26 final size:27
Alignment explanation
Indices: 261979--262182 Score: 121
Period size: 27 Copynumber: 7.5 Consensus size: 27
261969 GGCTATATTT
* *
261979 TGCATGGCTACATGTTGCATTG-ATACA
1 TGCATGGCTACATTTTGCA-TGCCTACA
*
262006 TGTATGGCTACATTTTGCATGCCTACA
1 TGCATGGCTACATTTTGCATGCCTACA
*
262033 T-CATGGCTACATTTTGTATGCCTACA
1 TGCATGGCTACATTTTGCATGCCTACA
* * * *
262059 TGTATGGCTACA---TGTATGGCTATA
1 TGCATGGCTACATTTTGCATGCCTACA
** * **
262083 TTTTGCATGGCTACATGATGTATGGATACA
1 ---TGCATGGCTACATTTTGCATGCCTACA
* * * *
262113 TTTTGCATGGCTATATTTTGTATGACTATA
1 ---TGCATGGCTACATTTTGCATGCCTACA
* * *
262143 TGTATGGCTACATTTTGTATGGCTACA
1 TGCATGGCTACATTTTGCATGCCTACA
*
262170 TGTATGGCTACAT
1 TGCATGGCTACAT
262183 GTATCTAAAC
Statistics
Matches: 148, Mismatches: 21, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
24 10 0.07
26 26 0.18
27 78 0.53
30 34 0.23
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (27 bp):
TGCATGGCTACATTTTGCATGCCTACA
Found at i:262169 original size:137 final size:137
Alignment explanation
Indices: 261923--262182 Score: 353
Period size: 137 Copynumber: 1.9 Consensus size: 137
261913 GGCTACATTT
* * *
261923 TGTATGGCTACATGCATGGCTACAATTGTATGGCTACATAATCTATGGCTATATTTTGCATGGCT
1 TGTATGGCTACATGCATGGCTACAATTGCATGGCTACATAATCTATGGATACATTTTGCATGGCT
261988 ACATGTTGCATTGATACATGTATGGCTACATTTTGCATGCCTACAT-CATGGCTACATTTTGTAT
66 ACATGTTGCATTGATACATGTATGGCTACATTTTGCATGCCTACATGCATGGCTACATTTTGTAT
262052 GCCTACA
131 GCCTACA
* * * * *
262059 TGTATGGCTACATGTATGGCTATATTTTGCATGGCTACATGATGTATGGATACATTTTGCATGGC
1 TGTATGGCTACATGCATGGCTACA-ATTGCATGGCTACATAATCTATGGATACATTTTGCATGGC
* * * * * * *
262124 TATATTTTGTA-TGACTATATGTATGGCTACATTTTGTATGGCTACATGTATGGCTACAT
65 TACATGTTGCATTGA-TACATGTATGGCTACATTTTGCATGCCTACATGCATGGCTACAT
262183 GTATCTAAAC
Statistics
Matches: 106, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
136 25 0.24
137 71 0.67
138 10 0.09
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (137 bp):
TGTATGGCTACATGCATGGCTACAATTGCATGGCTACATAATCTATGGATACATTTTGCATGGCT
ACATGTTGCATTGATACATGTATGGCTACATTTTGCATGCCTACATGCATGGCTACATTTTGTAT
GCCTACA
Found at i:262175 original size:12 final size:12
Alignment explanation
Indices: 262131--262186 Score: 67
Period size: 12 Copynumber: 4.4 Consensus size: 12
262121 GGCTATATTT
* *
262131 TGTATGACTATA
1 TGTATGGCTACA
262143 TGTATGGCTACA
1 TGTATGGCTACA
262155 TTTTGTATGGCTACA
1 ---TGTATGGCTACA
262170 TGTATGGCTACA
1 TGTATGGCTACA
262182 TGTAT
1 TGTAT
262187 CTAAACAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
12 27 0.69
15 12 0.31
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.41
Consensus pattern (12 bp):
TGTATGGCTACA
Found at i:263566 original size:14 final size:15
Alignment explanation
Indices: 263547--263579 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
263537 ACCCCCGCGT
263547 AAATTT-TCAGATCA
1 AAATTTATCAGATCA
263561 AAATTTATCAGATCA
1 AAATTTATCAGATCA
263576 AAAT
1 AAAT
263580 AAATATGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (15 bp):
AAATTTATCAGATCA
Found at i:279684 original size:5 final size:5
Alignment explanation
Indices: 279659--279769 Score: 66
Period size: 5 Copynumber: 22.4 Consensus size: 5
279649 CTGTAAATTG
* * * * * *
279659 CGAAA CAAAA TCGAAA GGAAA CGAAA TGAAA CGAAA CGAAA CAAAA CCAAT
1 CGAAA CGAAA -CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA
* * * * * * *
279710 CAAAA CCAAT CAAAA CAAAA CCAAA CCAAA CGAAA CGAAA C--AA C-AAA
1 CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA
279757 TCGAAA CGAAA CG
1 -CGAAA CGAAA CG
279770 GAATTAAACA
Statistics
Matches: 85, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
3 3 0.04
4 2 0.02
5 73 0.86
6 7 0.08
ACGTcount: A:0.61, C:0.23, G:0.12, T:0.05
Consensus pattern (5 bp):
CGAAA
Found at i:281354 original size:5 final size:5
Alignment explanation
Indices: 281344--281397 Score: 63
Period size: 5 Copynumber: 10.8 Consensus size: 5
281334 TTGATTTTTG
* * * * *
281344 GTTTC GTTTC GTTTC GATTG GTTTC GTTTC GTTTC GATTG GTTTC ATTTC
1 GTTTC GTTTC GTTTC GTTTC GTTTC GTTTC GTTTC GTTTC GTTTC GTTTC
281394 GTTT
1 GTTT
281398 TGCACTTTAC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.06, C:0.15, G:0.22, T:0.57
Consensus pattern (5 bp):
GTTTC
Found at i:281366 original size:20 final size:20
Alignment explanation
Indices: 281341--281397 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
281331 TAATTGATTT
281341 TTGGTTTCGTTTCGTTTCGA
1 TTGGTTTCGTTTCGTTTCGA
281361 TTGGTTTCGTTTCGTTTCGA
1 TTGGTTTCGTTTCGTTTCGA
*
281381 TTGGTTTCATTTCGTTT
1 TTGGTTTCGTTTCGTTT
281398 TGCACTTTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.05, C:0.14, G:0.23, T:0.58
Consensus pattern (20 bp):
TTGGTTTCGTTTCGTTTCGA
Found at i:292006 original size:21 final size:21
Alignment explanation
Indices: 291980--292207 Score: 276
Period size: 21 Copynumber: 10.8 Consensus size: 21
291970 TCCGTGCAAG
* * *
291980 AAACGAACCTTACCTTTCACA
1 AAACGAAACGTACCGTTCACA
292001 AAACGAAACGTACCGTTCACA
1 AAACGAAACGTACCGTTCACA
292022 AAACGAAACGTACCGTTCACA
1 AAACGAAACGTACCGTTCACA
* * *
292043 AAGCGTACCGTACCGTTCACA
1 AAACGAAACGTACCGTTCACA
292064 AAACGAAACGTACCGTTCACA
1 AAACGAAACGTACCGTTCACA
* * *
292085 AAGCGTACCGTACCGTTCACA
1 AAACGAAACGTACCGTTCACA
292106 AAACGAAACGTACCGTTCACA
1 AAACGAAACGTACCGTTCACA
* * *
292127 AAGCGTACCGTACCGTTCACA
1 AAACGAAACGTACCGTTCACA
292148 AAACGAAACGTACCGTTCACA
1 AAACGAAACGTACCGTTCACA
* * * *
292169 AATCTAACCGTACCTTTCACA
1 AAACGAAACGTACCGTTCACA
* *
292190 TTTAACGAACCGTACCGT
1 --AAACGAAACGTACCGT
292208 GGAAAAAGCG
Statistics
Matches: 176, Mismatches: 29, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
21 164 0.93
23 12 0.07
ACGTcount: A:0.36, C:0.31, G:0.14, T:0.19
Consensus pattern (21 bp):
AAACGAAACGTACCGTTCACA
Found at i:292041 original size:42 final size:42
Alignment explanation
Indices: 291980--292207 Score: 332
Period size: 42 Copynumber: 5.4 Consensus size: 42
291970 TCCGTGCAAG
* * * * * *
291980 AAACGAACCTTACCTTTCACAAAACGAAACGTACCGTTCACA
1 AAACGAAACGTACCGTTCACAAAGCGTACCGTACCGTTCACA
292022 AAACGAAACGTACCGTTCACAAAGCGTACCGTACCGTTCACA
1 AAACGAAACGTACCGTTCACAAAGCGTACCGTACCGTTCACA
292064 AAACGAAACGTACCGTTCACAAAGCGTACCGTACCGTTCACA
1 AAACGAAACGTACCGTTCACAAAGCGTACCGTACCGTTCACA
292106 AAACGAAACGTACCGTTCACAAAGCGTACCGTACCGTTCACA
1 AAACGAAACGTACCGTTCACAAAGCGTACCGTACCGTTCACA
* *
292148 AAACGAAACGTACCGTTCACAAATC-TAACCGTACCTTTCACA
1 AAACGAAACGTACCGTTCACAAAGCGT-ACCGTACCGTTCACA
* *
292190 TTTAACGAACCGTACCGT
1 --AAACGAAACGTACCGT
292208 GGAAAAAGCG
Statistics
Matches: 173, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
41 1 0.01
42 158 0.91
44 14 0.08
ACGTcount: A:0.36, C:0.31, G:0.14, T:0.19
Consensus pattern (42 bp):
AAACGAAACGTACCGTTCACAAAGCGTACCGTACCGTTCACA
Found at i:292455 original size:18 final size:18
Alignment explanation
Indices: 292434--292468 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
292424 GTTATATTTA
*
292434 TTAAAACATGTTTGAATG
1 TTAAAAAATGTTTGAATG
292452 TTAAAAAATGTTTGAAT
1 TTAAAAAATGTTTGAAT
292469 TTAGTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (18 bp):
TTAAAAAATGTTTGAATG
Found at i:292654 original size:2 final size:2
Alignment explanation
Indices: 292647--292702 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
292637 TTAAGTGATT
292647 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
292689 AG AG AG A- AG AG AG A
1 AG AG AG AG AG AG AG A
292703 TCGTTACATG
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:302768 original size:21 final size:21
Alignment explanation
Indices: 302744--302835 Score: 141
Period size: 21 Copynumber: 4.4 Consensus size: 21
302734 TCTGCGTCGT
*
302744 TGTTGTTTTTGTTGTCTCTGA
1 TGTTGTTTTTGTTGTCTCTAA
*
302765 TGTTGTTATTGTTGTCTCTAA
1 TGTTGTTTTTGTTGTCTCTAA
*
302786 TGTTGTTTTTGTTGTCTCTGA
1 TGTTGTTTTTGTTGTCTCTAA
*
302807 TGTTGTTATTGTTGTCT-TAA
1 TGTTGTTTTTGTTGTCTCTAA
302827 TGTTGTTTT
1 TGTTGTTTT
302836 CGTAGTAGAA
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
20 10 0.16
21 54 0.84
ACGTcount: A:0.09, C:0.08, G:0.22, T:0.62
Consensus pattern (21 bp):
TGTTGTTTTTGTTGTCTCTAA
Found at i:302770 original size:42 final size:41
Alignment explanation
Indices: 302744--302835 Score: 159
Period size: 42 Copynumber: 2.2 Consensus size: 41
302734 TCTGCGTCGT
302744 TGTTGTTTTTGTTGTCTCTGATGTTGTTATTGTTGTCTCTAA
1 TGTTGTTTTTGTTGTCTCTGATGTTGTTATTGTTGTCTCT-A
302786 TGTTGTTTTTGTTGTCTCTGATGTTGTTATTGTTGTCT-TAA
1 TGTTGTTTTTGTTGTCTCTGATGTTGTTATTGTTGTCTCT-A
302827 TGTTGTTTT
1 TGTTGTTTT
302836 CGTAGTAGAA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 12 0.24
42 38 0.76
ACGTcount: A:0.09, C:0.08, G:0.22, T:0.62
Consensus pattern (41 bp):
TGTTGTTTTTGTTGTCTCTGATGTTGTTATTGTTGTCTCTA
Found at i:312777 original size:17 final size:16
Alignment explanation
Indices: 312750--312784 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
312740 ACGTCACAAT
312750 GTACTGGCGAGAAATG
1 GTACTGGCGAGAAATG
*
312766 GTACTCGGCGAGAACTG
1 GTACT-GGCGAGAAATG
312783 GT
1 GT
312785 CGCACGCCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.26, C:0.17, G:0.37, T:0.20
Consensus pattern (16 bp):
GTACTGGCGAGAAATG
Found at i:340372 original size:20 final size:20
Alignment explanation
Indices: 340312--340373 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
340302 TCGCCAGAAG
340312 AAAG-TAATTCGTCCAAACA
1 AAAGCTAATTCGTCCAAACA
*
340331 GAAAGCTTATTCGTCCAAACA
1 -AAAGCTAATTCGTCCAAACA
340352 AAA-CTAATTTCGTCCAAACA
1 AAAGCTAA-TTCGTCCAAACA
340372 AA
1 AA
340374 TAACTGAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.08
20 21 0.55
21 14 0.37
ACGTcount: A:0.45, C:0.23, G:0.10, T:0.23
Consensus pattern (20 bp):
AAAGCTAATTCGTCCAAACA
Found at i:341745 original size:24 final size:24
Alignment explanation
Indices: 341716--341776 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
341706 GAGGAAAAGA
*
341716 AACCTGCTCCAGGACAAAACGAAC
1 AACCTGATCCAGGACAAAACGAAC
*
341740 ACCCTGATCCAGGACAAAACGAAC
1 AACCTGATCCAGGACAAAACGAAC
341764 AACCTGATCCAGG
1 AACCTGATCCAGG
341777 TAACCTCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.39, C:0.33, G:0.18, T:0.10
Consensus pattern (24 bp):
AACCTGATCCAGGACAAAACGAAC
Found at i:343505 original size:21 final size:22
Alignment explanation
Indices: 343480--343540 Score: 90
Period size: 21 Copynumber: 2.9 Consensus size: 22
343470 TATTTACGTG
343480 TAATAAAGCACCATCTTCAA-A
1 TAATAAAGCACCATCTTCAATA
* *
343501 TAATAGAGCACCATCTT-AATG
1 TAATAAAGCACCATCTTCAATA
343522 TAATAAAGCACCATCTTCA
1 TAATAAAGCACCATCTTCA
343541 CATGAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.06
21 32 0.91
22 1 0.03
ACGTcount: A:0.43, C:0.23, G:0.08, T:0.26
Consensus pattern (22 bp):
TAATAAAGCACCATCTTCAATA
Found at i:350677 original size:19 final size:19
Alignment explanation
Indices: 350653--350690 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
350643 TTTAACACGT
*
350653 CATACACAATACATACATA
1 CATACACAATACACACATA
350672 CATACACAATACACACATA
1 CATACACAATACACACATA
350691 GTTATAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18
Consensus pattern (19 bp):
CATACACAATACACACATA
Found at i:353120 original size:14 final size:14
Alignment explanation
Indices: 353101--353127 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
353091 GATGTGTAAT
353101 ATATTTATCATTTA
1 ATATTTATCATTTA
353115 ATATTTATCATTT
1 ATATTTATCATTT
353128 GATAAGATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (14 bp):
ATATTTATCATTTA
Found at i:355332 original size:2 final size:2
Alignment explanation
Indices: 355327--355375 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
355317 GTGTGTGTGT
355327 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
355369 GA GA GA G
1 GA GA GA G
355376 GATGAATAGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:366322 original size:66 final size:66
Alignment explanation
Indices: 366252--366453 Score: 298
Period size: 66 Copynumber: 3.1 Consensus size: 66
366242 AAAAAAAAGT
** * * * * * * * *
366252 ATAATAATAAAGAAAAAGAAACCGTAGAATAACAGA-AGGGTTTTCCGTTGAAAACGGAAAACCC
1 ATAATAATAGGGAAGAAGAAACCGAAGAAAAACA-ATAAGGTCTTCCGTTGGAAACGGAAGACCT
366316 TA
65 TA
366318 ATAATAATAGGGAAGAAGAAACCGAAGAAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTT
1 ATAATAATAGGGAAGAAGAAACCGAAGAAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTT
366383 A
66 A
366384 ATAATAATAGGGAAGAAGAAACCGAAGAAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTT
1 ATAATAATAGGGAAGAAGAAACCGAAGAAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTT
366449 A
66 A
366450 ATAA
1 ATAA
366454 GAAGAATATG
Statistics
Matches: 125, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
65 1 0.01
66 124 0.99
ACGTcount: A:0.49, C:0.13, G:0.21, T:0.17
Consensus pattern (66 bp):
ATAATAATAGGGAAGAAGAAACCGAAGAAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTT
A
Found at i:366472 original size:18 final size:17
Alignment explanation
Indices: 366449--366507 Score: 86
Period size: 18 Copynumber: 3.5 Consensus size: 17
366439 GGAAGACCTT
366449 AATAAGAAGAATATGAAG
1 AATAAGAAGAATA-GAAG
366467 AATAAGAAGAATAAGAAG
1 AATAAGAAGAAT-AGAAG
366485 AATAAGAAG-A-AGAAG
1 AATAAGAAGAATAGAAG
366500 AATAAGAA
1 AATAAGAA
366508 AGTCGACAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.32
17 1 0.03
18 25 0.62
19 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.22, T:0.12
Consensus pattern (17 bp):
AATAAGAAGAATAGAAG
Found at i:366482 original size:6 final size:6
Alignment explanation
Indices: 366452--366507 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
366442 AGACCTTAAT
* * * * *
366452 AAGAAG AATATG AAGAAT AAGAAG AATAAG AAGAAT AAGAAG AAGAAG
1 AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG
*
366500 AATAAG AA
1 AAGAAG AA
366508 AGTCGACAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (6 bp):
AAGAAG
Found at i:366482 original size:15 final size:15
Alignment explanation
Indices: 366452--366507 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
366442 AGACCTTAAT
*
366452 AAGAAGAATATGAAG
1 AAGAAGAATAAGAAG
* *
366467 AATAAG---AAGAAT
1 AAGAAGAATAAGAAG
366479 AAGAAGAATAAGAAG
1 AAGAAGAATAAGAAG
366494 AAGAAGAATAAGAA
1 AAGAAGAATAAGAA
366508 AGTCGACAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
12 9 0.27
15 24 0.73
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (15 bp):
AAGAAGAATAAGAAG
Found at i:366507 original size:9 final size:9
Alignment explanation
Indices: 366449--366501 Score: 88
Period size: 9 Copynumber: 5.9 Consensus size: 9
366439 GGAAGACCTT
366449 AATAAGAAG
1 AATAAGAAG
*
366458 AATATGAAG
1 AATAAGAAG
366467 AATAAGAAG
1 AATAAGAAG
366476 AATAAGAAG
1 AATAAGAAG
366485 AATAAGAAG
1 AATAAGAAG
*
366494 AAGAAGAA
1 AATAAGAA
366502 TAAGAAAGTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (9 bp):
AATAAGAAG
Found at i:395994 original size:21 final size:21
Alignment explanation
Indices: 395950--395997 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
395940 TATGTTTCTG
* **
395950 AGTGACCGGGTTATATTTTTC
1 AGTGACCGGGTTATACTTCCC
*
395971 AGTGACCGGGTTATGCTTCCC
1 AGTGACCGGGTTATACTTCCC
395992 AGTGAC
1 AGTGAC
395998 TAGATTATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (21 bp):
AGTGACCGGGTTATACTTCCC
Found at i:396024 original size:42 final size:41
Alignment explanation
Indices: 395978--397461 Score: 947
Period size: 42 Copynumber: 35.2 Consensus size: 41
395968 TTCAGTGACC
* * * *
395978 GGGTTATGCTTCCCAGTGACTAGATTATGTTGTACAGGGACT
1 GGGTTATGTTTCTCAGTGACTAG-TTATGTTATACAAGGACT
** *
396020 GGGTTATGTTTCTCAGAAACCAGTATATGTTATACAAGGACT
1 GGGTTATGTTTCTCAGTGACTAGT-TATGTTATACAAGGACT
* * *
396062 GGGTTATGTTTCTCAATGACTGGGTTATGTT-T-CTCAGTGACCT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATAC-AAG-GA-CT
* * * * *
396105 -GATTATGTTTCTCAGAGACTGGGCTATGTTATA-TAGTGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAG-GACT
* * * *
396146 GGGTTATGTTTCTCTGTGACTGGGTAATGTTATA-TAGTGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAG-GACT
* * **
396188 GGGTTATGTTTCTCTGTGACTGGGTTATGTT-T-CTCCGTGACTGCAT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATAC-AAG-GA---C-T
* * * * **
396234 GGGTTGTGTTAT-ACAGGGACTGGGTTATGTT-T-CTCCGTGACT
1 GGGTTATGTT-TCTCAGTGACT-AGTTATGTTATAC-AAG-GACT
* * *
396276 GGGTTATGTTAT-ACAGGGACTGGGTTATGTTATAC-AGGATCT
1 GGGTTATGTT-TCTCAGTGACT-AGTTATGTTATACAAGGA-CT
* * ** **
396318 GGGTTATGTTATAT-AGGGAACGGGTTATGTT-T-CTCTGTGACT
1 GGGTTATGTT-TCTCAGTG-ACTAGTTATGTTATAC-AAG-GACT
* * ** **
396360 GGGTTATGTTAT-ACAGGGACCGGGTTATGTT-T-CTCTGTGACT
1 GGGTTATGTT-TCTCAGTGA-CTAGTTATGTTATAC-AAG-GACT
* *
396402 GGGTTATGTTAT-ACAG-GATCTGGGTTATGTTATA-AAGTGACT
1 GGGTTATGTT-TCTCAGTGA-CT-AGTTATGTTATACAAG-GACT
* *
396444 GGGTTATGTTTCTCTGTGACTGGGTTATGTTATA-AAGTGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAG-GACT
* *
396486 GGGTTATGTTTCTCTGTGACTGGGTTATGTTATA-AAGTGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAG-GACT
* **
396528 GGGTTATGTTTCTCCA-TGACTGGGTTATGTT-T-CTCTGTGACT
1 GGGTTATGTTTCT-CAGTGACT-AGTTATGTTATAC-AAG-GACT
* * * *
396570 GGGTTATGTTTCTCCGTGACTGGGTTGTGTTATACAGGGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAGGACT
* *
396612 GGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAAGGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAGGACT
* * * *
396654 AGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAGGGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAGGACT
* *
396696 GGGTTATGTTTCTCTGTGACTGGGTTATGTTATA-AAGTGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAG-GACT
* * *
396738 GGGTTATGTTTCTCTGTGACTGGGTTGTGTTATACAAGGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAGGACT
* **
396780 GGGTTATGTTTCTCCA-TGACTGGGTTATGTT-T-CTCTGTGACT
1 GGGTTATGTTTCT-CAGTGACT-AGTTATGTTATAC-AAG-GACT
* * * *
396822 GGGTTATGTTTCTCCGTGACTGGGTTGTGTTATACAGGGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAGGACT
* *
396864 GGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAAGGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAGGACT
* * *
396906 GGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAGGGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAGGACT
* * *
396948 AGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAAGGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAGGACT
* * * *
396990 AGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAGGGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAGGACT
* * * *
397032 AGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAATGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAGGACT
* * *
397074 GGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAGGGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAGGACT
* *
397116 GGGTTATGTTTCTCTGTGACTGGGTTATGTTATA-AAGTGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAG-GACT
* *
397158 GGGTTATGTTTCTCTGTGACTGGGTTATGTTATA-AAGTGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAG-GACT
* **
397200 GGGTTATGTTTCTCCA-TGACTGGGTTATGTT-T-CTCTGTGACT
1 GGGTTATGTTTCT-CAGTGACT-AGTTATGTTATAC-AAG-GACT
* * * *
397242 GGGTTATGTTTCTCCGTGACTGGGTTGTGTTATACAGGGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAGGACT
* *
397284 GGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAAGGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAGGACT
* * * *
397326 AGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAGGGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAGGACT
* * * * *
397368 TGGTTATGTTTCTCAGAGACTGGGTTATGTTTTAC-TGTGACT
1 GGGTTATGTTTCTCAGTGACT-AGTTATGTTATACAAG-GACT
* *
397410 GGGTTTTGTTTCTCCA-TGACTGTGTTATGTTATAC-AGTGACT
1 GGGTTATGTTTCT-CAGTGACT-AGTTATGTTATACAAG-GACT
397452 GGGTTATGTT
1 GGGTTATGTT
397462 ATATAGTGAC
Statistics
Matches: 1288, Mismatches: 101, Indels: 106
0.86 0.07 0.07
Matches are distributed among these distances:
40 3 0.00
41 27 0.02
42 1189 0.92
43 28 0.02
44 4 0.00
45 1 0.00
46 35 0.03
47 1 0.00
ACGTcount: A:0.18, C:0.13, G:0.29, T:0.40
Consensus pattern (41 bp):
GGGTTATGTTTCTCAGTGACTAGTTATGTTATACAAGGACT
Found at i:396069 original size:21 final size:21
Alignment explanation
Indices: 396053--397461 Score: 626
Period size: 21 Copynumber: 66.9 Consensus size: 21
396043 TATATGTTAT
396053 ACAAGGACTGGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
396074 TCAATGACTGGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
396095 TC-AGTGACCT-GATTATGTTTC
1 ACAAG-GA-CTGGGTTATGTTTC
* *
396116 TC-AGAGACTGGGCTATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
*
396137 A-TAGTGACTGGGTTATGTTTC
1 ACAAG-GACTGGGTTATGTTTC
* * *
396158 TC-TGTGACTGGGTAATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
*
396179 A-TAGTGACTGGGTTATGTTTC
1 ACAAG-GACTGGGTTATGTTTC
* *
396200 TC-TGTGACTGGGTTATGTTTC
1 ACAAG-GACTGGGTTATGTTTC
* * *
396221 TC-CGTGACTGCATGGGTTGTGTTAT-
1 ACAAG-GA---C-TGGGTTATGTT-TC
*
396246 ACAGGGACTGGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
396267 TC-CGTGACTGGGTTATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
*
396288 ACAGGGACTGGGTTATGTTAT-
1 ACAAGGACTGGGTTATGTT-TC
396309 AC-AGGATCTGGGTTATGTTAT-
1 ACAAGGA-CTGGGTTATGTT-TC
* *
396330 ATAGGGAAC-GGGTTATGTTTC
1 ACAAGG-ACTGGGTTATGTTTC
* *
396351 TC-TGTGACTGGGTTATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
* *
396372 ACAGGGACCGGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
396393 TC-TGTGACTGGGTTATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
396414 AC-AGGATCTGGGTTATGTTAT-
1 ACAAGGA-CTGGGTTATGTT-TC
396435 A-AAGTGACTGGGTTATGTTTC
1 ACAAG-GACTGGGTTATGTTTC
* *
396456 TC-TGTGACTGGGTTATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
396477 A-AAGTGACTGGGTTATGTTTC
1 ACAAG-GACTGGGTTATGTTTC
* *
396498 TC-TGTGACTGGGTTATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
396519 A-AAGTGACTGGGTTATGTTTC
1 ACAAG-GACTGGGTTATGTTTC
* * *
396540 TCCATGACTGGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
396561 TC-TGTGACTGGGTTATGTTTC
1 ACAAG-GACTGGGTTATGTTTC
* * *
396582 TC-CGTGACTGGGTTGTGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
*
396603 ACAGGGACTGGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
396624 TC-CGTGACTGGGTTATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
*
396645 ACAAGGACTAGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
396666 TC-CGTGACTGGGTTATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
*
396687 ACAGGGACTGGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
396708 TC-TGTGACTGGGTTATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
396729 A-AAGTGACTGGGTTATGTTTC
1 ACAAG-GACTGGGTTATGTTTC
* * *
396750 TC-TGTGACTGGGTTGTGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
396771 ACAAGGACTGGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* * *
396792 TCCATGACTGGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
396813 TC-TGTGACTGGGTTATGTTTC
1 ACAAG-GACTGGGTTATGTTTC
* * *
396834 TC-CGTGACTGGGTTGTGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
*
396855 ACAGGGACTGGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
396876 TC-CGTGACTGGGTTATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
396897 ACAAGGACTGGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
396918 TC-CGTGACTGGGTTATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
* *
396939 ACAGGGACTAGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
396960 TC-CGTGACTGGGTTATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
*
396981 ACAAGGACTAGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
397002 TC-CGTGACTGGGTTATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
* *
397023 ACAGGGACTAGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
397044 TC-CGTGACTGGGTTATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
*
397065 ACAATGACTGGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
397086 TC-CGTGACTGGGTTATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
*
397107 ACAGGGACTGGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
397128 TC-TGTGACTGGGTTATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
397149 A-AAGTGACTGGGTTATGTTTC
1 ACAAG-GACTGGGTTATGTTTC
* *
397170 TC-TGTGACTGGGTTATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
397191 A-AAGTGACTGGGTTATGTTTC
1 ACAAG-GACTGGGTTATGTTTC
* * *
397212 TCCATGACTGGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
397233 TC-TGTGACTGGGTTATGTTTC
1 ACAAG-GACTGGGTTATGTTTC
* * *
397254 TC-CGTGACTGGGTTGTGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
*
397275 ACAGGGACTGGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
397296 TC-CGTGACTGGGTTATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
*
397317 ACAAGGACTAGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
397338 TC-CGTGACTGGGTTATGTTAT-
1 ACAAG-GACTGGGTTATGTT-TC
* *
397359 ACAGGGACTTGGTTATGTTTC
1 ACAAGGACTGGGTTATGTTTC
* *
397380 TC-AGAGACTGGGTTATGTTTT
1 ACAAG-GACTGGGTTATGTTTC
* *
397401 AC-TGTGACTGGGTTTTGTTTC
1 ACAAG-GACTGGGTTATGTTTC
* * * *
397422 TCCATGACTGTGTTATGTTAT-
1 ACAAGGACTGGGTTATGTT-TC
397443 AC-AGTGACTGGGTTATGTT
1 ACAAG-GACTGGGTTATGTT
397462 ATATAGTGAC
Statistics
Matches: 1103, Mismatches: 167, Indels: 236
0.73 0.11 0.16
Matches are distributed among these distances:
20 51 0.05
21 985 0.89
22 50 0.05
23 1 0.00
24 1 0.00
25 13 0.01
26 2 0.00
ACGTcount: A:0.18, C:0.13, G:0.29, T:0.40
Consensus pattern (21 bp):
ACAAGGACTGGGTTATGTTTC
Found at i:396090 original size:84 final size:85
Alignment explanation
Indices: 395940--397546 Score: 1718
Period size: 84 Copynumber: 19.1 Consensus size: 85
395930 ATATATATGG
* * * * * * * * *
395940 TATGTTTCTGAGTGACCGGGTTATATTTTTC-AGTGACCGGGTTATGCTTC-CCAGTGACTAGAT
1 TATGTTTCTCAGTGACTGGGTTATGTTATACAAGTGACTGGGTTATGTTTCTCC-GTGACTGGGT
*
396003 TATGTTGTACAGGGACTGGGT
65 TATGTTATACAGGGACTGGGT
** ** **
396024 TATGTTTCTCAGAAAC-CAGTATATGTTATACAAG-GACTGGGTTATGTTTCTCAATGACTGGGT
1 TATGTTTCTCAGTGACTGGGT-TATGTTATACAAGTGACTGGGTTATGTTTCTCCGTGACTGGGT
* * *
396087 TATGTT-TCTCAGTGACCT-GAT
65 TATGTTAT-ACAGGGA-CTGGGT
* * * * *
396108 TATGTTTCTCAGAGACTGGGCTATGTTATA-TAGTGACTGGGTTATGTTTCTCTGTGACTGGGTA
1 TATGTTTCTCAGTGACTGGGTTATGTTATACAAGTGACTGGGTTATGTTTCTCCGTGACTGGGTT
* *
396172 ATGTTATATAGTGACTGGGT
66 ATGTTATACAGGGACTGGGT
* ** * * * *
396192 TATGTTTCTCTGTGACTGGGTTATGTT-T-CTCCGTGACTGCATGGGTTGTGTTAT-ACAGGGAC
1 TATGTTTCTCAGTGACTGGGTTATGTTATAC-AAGTGA---C-TGGGTTATGTT-TCTCCGTGAC
* * *
396254 TGGGTTATGTT-TCTCCGTGACTGGGT
60 TGGGTTATGTTAT-ACAGGGACTGGGT
* * * * *
396280 TATGTTAT-ACAGGGACTGGGTTATGTTATAC-AG-GATCTGGGTTATGTTATAT-AGGGAAC-G
1 TATGTT-TCTCAGTGACTGGGTTATGTTATACAAGTGA-CTGGGTTATGTT-TCTCCGTG-ACTG
* * *
396340 GGTTATGTT-TCTCTGTGACTGGGT
62 GGTTATGTTAT-ACAGGGACTGGGT
* * * ** * *
396364 TATGTTAT-ACAGGGACCGGGTTATGTT-T-CTCTGTGACTGGGTTATGTTAT-ACAG-GATCTG
1 TATGTT-TCTCAGTGACTGGGTTATGTTATAC-AAGTGACTGGGTTATGTT-TCTCCGTGA-CTG
* *
396424 GGTTATGTTATAAAGTGACTGGGT
62 GGTTATGTTATACAGGGACTGGGT
* *
396448 TATGTTTCTCTGTGACTGGGTTATGTTATA-AAGTGACTGGGTTATGTTTCTCTGTGACTGGGTT
1 TATGTTTCTCAGTGACTGGGTTATGTTATACAAGTGACTGGGTTATGTTTCTCCGTGACTGGGTT
* *
396512 ATGTTATAAAGTGACTGGGT
66 ATGTTATACAGGGACTGGGT
**
396532 TATGTTTCTCCA-TGACTGGGTTATGTT-T-CTCTGTGACTGGGTTATGTTTCTCCGTGACTGGG
1 TATGTTTCT-CAGTGACTGGGTTATGTTATAC-AAGTGACTGGGTTATGTTTCTCCGTGACTGGG
*
396594 TTGTGTTATACAGGGACTGGGT
64 TTATGTTATACAGGGACTGGGT
* *
396616 TATGTTTCTCCGTGACTGGGTTATGTTATACAAG-GACTAGGTTATGTTTCTCCGTGACTGGGTT
1 TATGTTTCTCAGTGACTGGGTTATGTTATACAAGTGACTGGGTTATGTTTCTCCGTGACTGGGTT
396680 ATGTTATACAGGGACTGGGT
66 ATGTTATACAGGGACTGGGT
* *
396700 TATGTTTCTCTGTGACTGGGTTATGTTATA-AAGTGACTGGGTTATGTTTCTCTGTGACTGGGTT
1 TATGTTTCTCAGTGACTGGGTTATGTTATACAAGTGACTGGGTTATGTTTCTCCGTGACTGGGTT
* *
396764 GTGTTATACAAGGACTGGGT
66 ATGTTATACAGGGACTGGGT
**
396784 TATGTTTCTCCA-TGACTGGGTTATGTT-T-CTCTGTGACTGGGTTATGTTTCTCCGTGACTGGG
1 TATGTTTCT-CAGTGACTGGGTTATGTTATAC-AAGTGACTGGGTTATGTTTCTCCGTGACTGGG
*
396846 TTGTGTTATACAGGGACTGGGT
64 TTATGTTATACAGGGACTGGGT
*
396868 TATGTTTCTCCGTGACTGGGTTATGTTATACAAG-GACTGGGTTATGTTTCTCCGTGACTGGGTT
1 TATGTTTCTCAGTGACTGGGTTATGTTATACAAGTGACTGGGTTATGTTTCTCCGTGACTGGGTT
*
396932 ATGTTATACAGGGACTAGGT
66 ATGTTATACAGGGACTGGGT
* *
396952 TATGTTTCTCCGTGACTGGGTTATGTTATACAAG-GACTAGGTTATGTTTCTCCGTGACTGGGTT
1 TATGTTTCTCAGTGACTGGGTTATGTTATACAAGTGACTGGGTTATGTTTCTCCGTGACTGGGTT
*
397016 ATGTTATACAGGGACTAGGT
66 ATGTTATACAGGGACTGGGT
*
397036 TATGTTTCTCCGTGACTGGGTTATGTTATACAA-TGACTGGGTTATGTTTCTCCGTGACTGGGTT
1 TATGTTTCTCAGTGACTGGGTTATGTTATACAAGTGACTGGGTTATGTTTCTCCGTGACTGGGTT
397100 ATGTTATACAGGGACTGGGT
66 ATGTTATACAGGGACTGGGT
* *
397120 TATGTTTCTCTGTGACTGGGTTATGTTATA-AAGTGACTGGGTTATGTTTCTCTGTGACTGGGTT
1 TATGTTTCTCAGTGACTGGGTTATGTTATACAAGTGACTGGGTTATGTTTCTCCGTGACTGGGTT
* *
397184 ATGTTATAAAGTGACTGGGT
66 ATGTTATACAGGGACTGGGT
**
397204 TATGTTTCTCCA-TGACTGGGTTATGTT-T-CTCTGTGACTGGGTTATGTTTCTCCGTGACTGGG
1 TATGTTTCT-CAGTGACTGGGTTATGTTATAC-AAGTGACTGGGTTATGTTTCTCCGTGACTGGG
*
397266 TTGTGTTATACAGGGACTGGGT
64 TTATGTTATACAGGGACTGGGT
* *
397288 TATGTTTCTCCGTGACTGGGTTATGTTATACAAG-GACTAGGTTATGTTTCTCCGTGACTGGGTT
1 TATGTTTCTCAGTGACTGGGTTATGTTATACAAGTGACTGGGTTATGTTTCTCCGTGACTGGGTT
*
397352 ATGTTATACAGGGACTTGGT
66 ATGTTATACAGGGACTGGGT
* * * * * *
397372 TATGTTTCTCAGAGACTGGGTTATGTTTTAC-TGTGACTGGGTTTTGTTTCTCCATGACTGTGTT
1 TATGTTTCTCAGTGACTGGGTTATGTTATACAAGTGACTGGGTTATGTTTCTCCGTGACTGGGTT
*
397436 ATGTTATACAGTGACTGGGT
66 ATGTTATACAGGGACTGGGT
* * * * ** * * * *
397456 TATGTTATAT-AGTGACCGGGTTTTGTT-T-CATAATGACCAGGTTTTGTTTATCCATGACTAGG
1 TATGTT-TCTCAGTGACTGGGTTATGTTATACA-AGTGACTGGGTTATGTTTCTCCGTGACTGGG
*
397518 TGATGTTATACAGGGACT-GGT
64 TTATGTTATACAGGGACTGGGT
397539 ATATGTTT
1 -TATGTTT
397547 AGTGAGTGTG
Statistics
Matches: 1330, Mismatches: 133, Indels: 121
0.84 0.08 0.08
Matches are distributed among these distances:
82 3 0.00
83 30 0.02
84 1201 0.90
85 27 0.02
86 3 0.00
87 4 0.00
88 58 0.04
89 3 0.00
90 1 0.00
ACGTcount: A:0.18, C:0.13, G:0.28, T:0.40
Consensus pattern (85 bp):
TATGTTTCTCAGTGACTGGGTTATGTTATACAAGTGACTGGGTTATGTTTCTCCGTGACTGGGTT
ATGTTATACAGGGACTGGGT
Found at i:397477 original size:126 final size:126
Alignment explanation
Indices: 395940--397461 Score: 1715
Period size: 126 Copynumber: 12.0 Consensus size: 126
395930 ATATATATGG
** * * * * * * * * *
395940 TATGTTTCTGAGTGACCGGGTTATATTTTTCAGTGACCGGGTTATGCTTCCCAGTGACTAGATTA
1 TATGTTTCTCCGTGACTGGGTTATGTTATACAGTGACTGGGTTATGTTTCTCAGTGACTGGGTTA
* * * ** **
396005 TGTTGTACAGGGACTGGGTTATGTTTCTCAGAAAC-CAGTATATGTTATACAAG-GACTGGGT
66 TGTTATACAGTGACTGGGTTATGTTTCTCCGTGACTGGGT-TATGTTATAC-AGTGACTGGGT
** * * * *
396066 TATGTTTCTCAATGACTGGGTTATGTT-TCTCAGTGACCT-GATTATGTTTCTCAGAGACTGGGC
1 TATGTTTCTCCGTGACTGGGTTATGTTAT-ACAGTGA-CTGGGTTATGTTTCTCAGTGACTGGGT
* * * *
396129 TATGTTATATAGTGACTGGGTTATGTTTCTCTGTGACTGGGTAATGTTATATAGTGACTGGGT
64 TATGTTATACAGTGACTGGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAGTGACTGGGT
* * * * * *
396192 TATGTTTCTCTGTGACTGGGTTATGTT-TCTCCGTGACTGCATGGGTTGTGTTAT-ACAGGGACT
1 TATGTTTCTCCGTGACTGGGTTATGTTAT-ACAGTGA---C-TGGGTTATGTT-TCTCAGTGACT
* * * * *
396255 GGGTTATGTT-TCTCCGTGACTGGGTTATGTTAT-ACAGGGACTGGGTTATGTTATACAG-GATC
60 GGGTTATGTTAT-ACAGTGACTGGGTTATGTT-TCTCCGTGACTGGGTTATGTTATACAGTGA-C
396317 TGGGT
122 TGGGT
* * * * * * * *
396322 TATGTTATAT-AGGGAAC-GGGTTATGTT-TCTCTGTGACTGGGTTATGTTAT-ACAGGGACCGG
1 TATGTT-TCTCCGTG-ACTGGGTTATGTTAT-ACAGTGACTGGGTTATGTT-TCTCAGTGACTGG
* * * * *
396383 GTTATGTT-TCTCTGTGACTGGGTTATGTTAT-ACAG-GATCTGGGTTATGTTATAAAGTGACTG
62 GTTATGTTAT-ACAGTGACTGGGTTATGTT-TCTCCGTGA-CTGGGTTATGTTATACAGTGACTG
396445 GGT
124 GGT
* * *
396448 TATGTTTCTCTGTGACTGGGTTATGTTATAAAGTGACTGGGTTATGTTTCTCTGTGACTGGGTTA
1 TATGTTTCTCCGTGACTGGGTTATGTTATACAGTGACTGGGTTATGTTTCTCAGTGACTGGGTTA
* * * *
396513 TGTTATAAAGTGACTGGGTTATGTTTCTCCATGACTGGGTTATGTT-TCTCTGTGACTGGGT
66 TGTTATACAGTGACTGGGTTATGTTTCTCCGTGACTGGGTTATGTTAT-ACAGTGACTGGGT
* * *
396574 TATGTTTCTCCGTGACTGGGTTGTGTTATACAGGGACTGGGTTATGTTTCTCCGTGACTGGGTTA
1 TATGTTTCTCCGTGACTGGGTTATGTTATACAGTGACTGGGTTATGTTTCTCAGTGACTGGGTTA
* *
396639 TGTTATACAAG-GACTAGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAGGGACTGGGT
66 TGTTATAC-AGTGACTGGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAGTGACTGGGT
* * * *
396700 TATGTTTCTCTGTGACTGGGTTATGTTATAAAGTGACTGGGTTATGTTTCTCTGTGACTGGGTTG
1 TATGTTTCTCCGTGACTGGGTTATGTTATACAGTGACTGGGTTATGTTTCTCAGTGACTGGGTTA
* * *
396765 TGTTATACAAG-GACTGGGTTATGTTTCTCCATGACTGGGTTATGTT-TCTCTGTGACTGGGT
66 TGTTATAC-AGTGACTGGGTTATGTTTCTCCGTGACTGGGTTATGTTAT-ACAGTGACTGGGT
* * *
396826 TATGTTTCTCCGTGACTGGGTTGTGTTATACAGGGACTGGGTTATGTTTCTCCGTGACTGGGTTA
1 TATGTTTCTCCGTGACTGGGTTATGTTATACAGTGACTGGGTTATGTTTCTCAGTGACTGGGTTA
* *
396891 TGTTATACAAG-GACTGGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAGGGACTAGGT
66 TGTTATAC-AGTGACTGGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAGTGACTGGGT
* *
396952 TATGTTTCTCCGTGACTGGGTTATGTTATACAAG-GACTAGGTTATGTTTCTCCGTGACTGGGTT
1 TATGTTTCTCCGTGACTGGGTTATGTTATAC-AGTGACTGGGTTATGTTTCTCAGTGACTGGGTT
* * *
397016 ATGTTATACAGGGACTAGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAATGACTGGGT
65 ATGTTATACAGTGACTGGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAGTGACTGGGT
* *
397078 TATGTTTCTCCGTGACTGGGTTATGTTATACAGGGACTGGGTTATGTTTCTCTGTGACTGGGTTA
1 TATGTTTCTCCGTGACTGGGTTATGTTATACAGTGACTGGGTTATGTTTCTCAGTGACTGGGTTA
* * *
397143 TGTTATAAAGTGACTGGGTTATGTTTCTCTGTGACTGGGTTATGTTATAAAGTGACTGGGT
66 TGTTATACAGTGACTGGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAGTGACTGGGT
* * * *
397204 TATGTTTCTCCATGACTGGGTTATGTT-TCTCTGTGACTGGGTTATGTTTCTCCGTGACTGGGTT
1 TATGTTTCTCCGTGACTGGGTTATGTTAT-ACAGTGACTGGGTTATGTTTCTCAGTGACTGGGTT
* * *
397268 GTGTTATACAGGGACTGGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAAG-GACTAGGT
65 ATGTTATACAGTGACTGGGTTATGTTTCTCCGTGACTGGGTTATGTTATAC-AGTGACTGGGT
* * *
397330 TATGTTTCTCCGTGACTGGGTTATGTTATACAGGGACTTGGTTATGTTTCTCAGAGACTGGGTTA
1 TATGTTTCTCCGTGACTGGGTTATGTTATACAGTGACTGGGTTATGTTTCTCAGTGACTGGGTTA
* * * * *
397395 TGTTTTACTGTGACTGGGTTTTGTTTCTCCATGACTGTGTTATGTTATACAGTGACTGGGT
66 TGTTATACAGTGACTGGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAGTGACTGGGT
397456 TATGTT
1 TATGTT
397462 ATATAGTGAC
Statistics
Matches: 1222, Mismatches: 139, Indels: 70
0.85 0.10 0.05
Matches are distributed among these distances:
125 20 0.02
126 1081 0.88
127 19 0.02
128 1 0.00
129 4 0.00
130 91 0.07
131 6 0.00
ACGTcount: A:0.18, C:0.13, G:0.28, T:0.40
Consensus pattern (126 bp):
TATGTTTCTCCGTGACTGGGTTATGTTATACAGTGACTGGGTTATGTTTCTCAGTGACTGGGTTA
TGTTATACAGTGACTGGGTTATGTTTCTCCGTGACTGGGTTATGTTATACAGTGACTGGGT
Found at i:400229 original size:22 final size:22
Alignment explanation
Indices: 400187--400248 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
400177 TACAGTACAG
*
400187 TTGGCTAATACAGAACGGTTTA
1 TTGGCTAATACAGAACAGTTTA
* *
400209 TTGGCTAATACCGCACAGTTTA
1 TTGGCTAATACAGAACAGTTTA
* *
400231 TCAGG-TAATACAGTACAG
1 T-TGGCTAATACAGAACAG
400249 CAAATAGCTC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 31 0.94
23 2 0.06
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (22 bp):
TTGGCTAATACAGAACAGTTTA
Found at i:422495 original size:19 final size:17
Alignment explanation
Indices: 422464--422506 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
422454 TTTATTTAAA
* *
422464 TTTTTTTTGGTGTTTTG
1 TTTTTTTTGGTGTGTGG
422481 TTTTTTTTGGTGTGTGTGG
1 TTTTTTTT-G-GTGTGTGG
422500 TTTTTTT
1 TTTTTTT
422507 CTTTGTTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 8 0.36
18 1 0.05
19 13 0.59
ACGTcount: A:0.00, C:0.00, G:0.26, T:0.74
Consensus pattern (17 bp):
TTTTTTTTGGTGTGTGG
Done.