Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold501
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: 1397941
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 110142 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:4746 original size:2 final size:2
Alignment explanation
Indices: 4739--4800 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
4729 ACGCAATGAA
4739 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
4781 AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG
4801 GGGGGTTAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12251 original size:21 final size:20
Alignment explanation
Indices: 12213--12251 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12203 TCTTGTGGTT
* *
12213 TTTTTTTTTTTTGGTTTGTA
1 TTTTTTTTTTCTGATTTGTA
12233 TTTTTTTTTTCTGTATTTG
1 TTTTTTTTTTCTG-ATTTG
12252 AAAAAGTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.05, C:0.03, G:0.13, T:0.79
Consensus pattern (20 bp):
TTTTTTTTTTCTGATTTGTA
Found at i:13302 original size:21 final size:22
Alignment explanation
Indices: 13254--13302 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
13244 ATTTAACAAG
* *
13254 ATATTTAAAATATTTTTTAAAA
1 ATATTGAAAATATTCTTTAAAA
13276 ATATTGAAAATATTCTTTAAAA
1 ATATTGAAAATATTCTTTAAAA
13298 A-ATTG
1 ATATTG
13303 CATTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (22 bp):
ATATTGAAAATATTCTTTAAAA
Found at i:18998 original size:42 final size:42
Alignment explanation
Indices: 18945--19407 Score: 398
Period size: 42 Copynumber: 10.8 Consensus size: 42
18935 TCTTCATAAT
* * *
18945 ATGATGATACTTTAACATTACGT-ACTGATACTTCAACATTAC
1 ATGATGATACTTCAACATTACATGA-TGGTACTTCAACATTAC
*
18987 ATGATGGTACTTCAACATTACATGATGGTACTTCAACATTAC
1 ATGATGATACTTCAACATTACATGATGGTACTTCAACATTAC
*
19029 ATGATGGA-ACTTCAACATTACATGATGGTTCTTCAACATTAC
1 ATGAT-GATACTTCAACATTACATGATGGTACTTCAACATTAC
* * * *
19071 ATGCTGATACTTCAACATAACATCATGGTTCTTCAACATTAC
1 ATGATGATACTTCAACATTACATGATGGTACTTCAACATTAC
* *
19113 ATGCTGATACTTTAACATTACATGATGGTACTTCAACATTAC
1 ATGATGATACTTCAACATTACATGATGGTACTTCAACATTAC
* * *
19155 AAGCTGATACTTTAACATTACATGATGGTACCTT-AACATTAC
1 ATGATGATACTTCAACATTACATGATGGTA-CTTCAACATTAC
* * *
19197 GA-GGTGATACTTCAACATTACATGATGGCCATGGTACTTTAACATTGC
1 -ATGATGATACTTCAACATTAC---AT-G--ATGGTACTTCAACATTAC
* * * *
19245 GTGCTGATATTTCAACATTACATGATGGTACTTTAACATTAC
1 ATGATGATACTTCAACATTACATGATGGTACTTCAACATTAC
* * * * ** * ** *
19287 GTGCTGATACTTTAACATTACATGTTCATGCTGAAACTTCTTTA-
1 ATGATGATACTTCAACATTACATGATGGTACTTCAA---CATTAC
* * * *
19331 ATTTATGATACTTTAACATTACATGCTGATACTT-AACATTAC
1 A-TGATGATACTTCAACATTACATGATGGTACTTCAACATTAC
* * * * *
19373 ATGCTGAAACTTCAACATTATATGCTGGTATTTCA
1 ATGATGATACTTCAACATTACATGATGGTACTTCA
19408 TAAAATGATT
Statistics
Matches: 357, Mismatches: 45, Indels: 38
0.81 0.10 0.09
Matches are distributed among these distances:
41 31 0.09
42 249 0.70
43 6 0.02
44 3 0.01
45 34 0.10
46 1 0.00
47 3 0.01
48 30 0.08
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.36
Consensus pattern (42 bp):
ATGATGATACTTCAACATTACATGATGGTACTTCAACATTAC
Found at i:19368 original size:20 final size:20
Alignment explanation
Indices: 19336--19399 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
19326 CTTTAATTTA
19336 TGATACTTTAACATTACATGC
1 TGATAC-TTAACATTACATGC
19357 TGATACTTAACATTACATGC
1 TGATACTTAACATTACATGC
* *
19377 TGAAACTTCAACATTATATGC
1 TGATACTT-AACATTACATGC
19398 TG
1 TG
19400 GTATTTCATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
20 21 0.52
21 19 0.47
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (20 bp):
TGATACTTAACATTACATGC
Found at i:19407 original size:21 final size:21
Alignment explanation
Indices: 18949--19399 Score: 347
Period size: 21 Copynumber: 21.1 Consensus size: 21
18939 CATAATATGA
* * *
18949 TGATACTTTAACATTACGTAC
1 TGATACTTCAACATTACATGC
*
18970 TGATACTTCAACATTACATGA
1 TGATACTTCAACATTACATGC
* *
18991 TGGTACTTCAACATTACATGA
1 TGATACTTCAACATTACATGC
* *
19012 TGGTACTTCAACATTACATGA
1 TGATACTTCAACATTACATGC
*
19033 TGGA-ACTTCAACATTACATGA
1 T-GATACTTCAACATTACATGC
* *
19054 TGGTTCTTCAACATTACATGC
1 TGATACTTCAACATTACATGC
*
19075 TGATACTTCAACATAACAT-C
1 TGATACTTCAACATTACATGC
* *
19095 ATGGTTCTTCAACATTACATGC
1 -TGATACTTCAACATTACATGC
* *
19117 TGATACTTTAACATTACATGA
1 TGATACTTCAACATTACATGC
* *
19138 TGGTACTTCAACATTACAAGC
1 TGATACTTCAACATTACATGC
* *
19159 TGATACTTTAACATTACATGA
1 TGATACTTCAACATTACATGC
* *
19180 TGGTACCTT-AACATTACGA-GG
1 TGATA-CTTCAACATTAC-ATGC
19201 TGATACTTCAACATTACATGATGGCC
1 TGATACTTCAACATTAC---AT-G-C
* * * *
19227 ATGGTACTTTAACATTGCGTGC
1 -TGATACTTCAACATTACATGC
* *
19249 TGATATTTCAACATTACATGA
1 TGATACTTCAACATTACATGC
* * *
19270 TGGTACTTTAACATTACGTGC
1 TGATACTTCAACATTACATGC
* *
19291 TGATACTTTAACATTACATGT
1 TGATACTTCAACATTACATGC
* * ** * **
19312 TCATGCTGAAACTTCTTTA-ATTTA
1 TGATACTTCAA---CATTACA-TGC
*
19336 TGATACTTTAACATTACATGC
1 TGATACTTCAACATTACATGC
19357 TGATACTT-AACATTACATGC
1 TGATACTTCAACATTACATGC
* *
19377 TGAAACTTCAACATTATATGC
1 TGATACTTCAACATTACATGC
19398 TG
1 TG
19400 GTATTTCATA
Statistics
Matches: 346, Mismatches: 65, Indels: 38
0.77 0.14 0.08
Matches are distributed among these distances:
20 24 0.07
21 282 0.82
22 8 0.02
23 4 0.01
24 13 0.04
25 1 0.00
27 14 0.04
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (21 bp):
TGATACTTCAACATTACATGC
Found at i:25544 original size:13 final size:13
Alignment explanation
Indices: 25526--25550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25516 TATCATGTAC
25526 TGTATGTAAAACA
1 TGTATGTAAAACA
25539 TGTATGTAAAAC
1 TGTATGTAAAAC
25551 CTTCAATAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATGTAAAACA
Found at i:26466 original size:180 final size:180
Alignment explanation
Indices: 26164--26523 Score: 639
Period size: 180 Copynumber: 2.0 Consensus size: 180
26154 GCTGCCAAAT
* *
26164 GGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCAG
1 GGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAG
*
26229 ATCAATTGTACATATATCAGAGGTGTGCATATCGCTAGGATTTTGATTTCCGATAATTTATCGAA
66 ATCAATTGTACATATATCAGAGGTGTGCATATCGCTAGGATTTTGATTTCCGATAATTTATCAAA
*
26294 AAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATA
131 AAAATACCAGCTTTTGAACTTAGTAATTTTTTGGCAAAATATTGCATATA
26344 GGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAG
1 GGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAG
*
26409 ATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCAAA
66 ATCAATTGTACATATATCAGAGGTGTGCATATCGCTAGGATTTTGATTTCCGATAATTTATCAAA
** * *
26474 AAAATATTAGCTTTTGAACTTAGTAATTTTTTTGCAAAATGTTGCATATA
131 AAAATACCAGCTTTTGAACTTAGTAATTTTTTGGCAAAATATTGCATATA
26524 CATGTAGGGT
Statistics
Matches: 171, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
180 171 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (180 bp):
GGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAG
ATCAATTGTACATATATCAGAGGTGTGCATATCGCTAGGATTTTGATTTCCGATAATTTATCAAA
AAAATACCAGCTTTTGAACTTAGTAATTTTTTGGCAAAATATTGCATATA
Found at i:36008 original size:16 final size:16
Alignment explanation
Indices: 35987--36021 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
35977 TAAAGGTGGT
35987 CTCATAAAGCTGATGC
1 CTCATAAAGCTGATGC
*
36003 CTCATAAAGGTGATGC
1 CTCATAAAGCTGATGC
36019 CTC
1 CTC
36022 GTCTCTGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (16 bp):
CTCATAAAGCTGATGC
Found at i:36568 original size:14 final size:13
Alignment explanation
Indices: 36535--36569 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
36525 ACTTTTGCTC
36535 CTTCGCCTTTGCA
1 CTTCGCCTTTGCA
36548 CTATCGCCTTTGCAA
1 CT-TCGCCTTTGC-A
36563 CTTCGCC
1 CTTCGCC
36570 CTAAGGTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 15 0.75
15 3 0.15
ACGTcount: A:0.11, C:0.40, G:0.14, T:0.34
Consensus pattern (13 bp):
CTTCGCCTTTGCA
Found at i:37648 original size:32 final size:32
Alignment explanation
Indices: 37602--37663 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
37592 TCCAGGCAAA
* *
37602 GGGGTCATTTTTCTACGTAGAATAATGACCGG
1 GGGGTCATTATTCTACGTAGAAAAATGACCGG
* *
37634 GGGGTTATTATTCTACGTCGAAAAATGACC
1 GGGGTCATTATTCTACGTAGAAAAATGACC
37664 CCCGGTCATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (32 bp):
GGGGTCATTATTCTACGTAGAAAAATGACCGG
Found at i:37789 original size:11 final size:11
Alignment explanation
Indices: 37773--37797 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
37763 CTACCAAATG
37773 AAGTCCTGAAT
1 AAGTCCTGAAT
37784 AAGTCCTGAAT
1 AAGTCCTGAAT
37795 AAG
1 AAG
37798 GCATGGCCAA
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:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (11 bp):
AAGTCCTGAAT
Found at i:39120 original size:12 final size:12
Alignment explanation
Indices: 39103--39136 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
39093 TGCTAAAACG
39103 CGGAACGGAAAA
1 CGGAACGGAAAA
*
39115 CGGAACGGAAAG
1 CGGAACGGAAAA
39127 CGGAACGGAA
1 CGGAACGGAA
39137 CGCAAGACGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.44, C:0.18, G:0.38, T:0.00
Consensus pattern (12 bp):
CGGAACGGAAAA
Found at i:43219 original size:16 final size:17
Alignment explanation
Indices: 43193--43228 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
43183 AAACTGAAGT
43193 GGAACAGACAGACGGAC
1 GGAACAGACAGACGGAC
*
43210 GGAA-AGACAGACTGAC
1 GGAACAGACAGACGGAC
43226 GGA
1 GGA
43229 CGCAGAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.42, C:0.19, G:0.36, T:0.03
Consensus pattern (17 bp):
GGAACAGACAGACGGAC
Found at i:51196 original size:2 final size:2
Alignment explanation
Indices: 51191--51236 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
51181 AAAAAGTCTT
* *
51191 TA TA TA CA TA CA 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
51233 TA TA
1 TA TA
51237 AGTCACGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:54760 original size:2 final size:2
Alignment explanation
Indices: 54753--54802 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
54743 AAAAGCATAT
54753 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
54795 GA GA GA GA
1 GA GA GA GA
54803 TTTCCAGTCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:62567 original size:20 final size:20
Alignment explanation
Indices: 62522--62568 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
62512 GGTATTATAT
*
62522 TGTATCATATTAAACAATAG
1 TGTATCATATTAAACAATAC
* *
62542 TGTATCATATTATACGATAC
1 TGTATCATATTAAACAATAC
*
62562 TTTATCA
1 TGTATCA
62569 AAGGGATCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (20 bp):
TGTATCATATTAAACAATAC
Found at i:64481 original size:3 final size:3
Alignment explanation
Indices: 64475--64512 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
64465 TGTTAATGTA
64475 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
64513 ATAATACTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:65977 original size:23 final size:23
Alignment explanation
Indices: 65931--65990 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
65921 TTTTTTGAAT
65931 AATCAAATTAATAA---TTCTTA
1 AATCAAATTAATAATTTTTCTTA
* *
65951 AATCAAATTAATAATTTTTTTTG
1 AATCAAATTAATAATTTTTCTTA
65974 AATCAAATTAAT-ATTTT
1 AATCAAATTAATAATTTT
65991 GTAAATCTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.40
22 5 0.14
23 16 0.46
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.47
Consensus pattern (23 bp):
AATCAAATTAATAATTTTTCTTA
Found at i:65985 original size:20 final size:20
Alignment explanation
Indices: 65960--66012 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
65950 AAATCAAATT
* *
65960 AATAATTTTTTTTGAATC-A
1 AATAATTTTTTGTAAATCTA
*
65979 AATTAATATTTTGTAAATCTA
1 AA-TAATTTTTTGTAAATCTA
66000 AATAATTTTTTGT
1 AATAATTTTTTGT
66013 TTTTTGTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.07
20 23 0.82
21 3 0.11
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.53
Consensus pattern (20 bp):
AATAATTTTTTGTAAATCTA
Found at i:66869 original size:4 final size:4
Alignment explanation
Indices: 66853--66893 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
66843 CTTTCCTCTG
* *
66853 CGTC CGTC AGTC CGTC CGTC CGTC CGTC CGTC CGTC TGTC C
1 CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC C
66894 CACTTCAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.02, C:0.46, G:0.24, T:0.27
Consensus pattern (4 bp):
CGTC
Found at i:76979 original size:12 final size:13
Alignment explanation
Indices: 76934--76967 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
76924 TGCTAAAACG
76934 CGGAACGGAAA-A
1 CGGAACGGAAAGA
76946 CGGAACGGAAAGA
1 CGGAACGGAAAGA
76959 -GGAACGGAA
1 CGGAACGGAA
76968 CGGAAAACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 20 0.95
13 1 0.05
ACGTcount: A:0.47, C:0.15, G:0.38, T:0.00
Consensus pattern (13 bp):
CGGAACGGAAAGA
Found at i:92806 original size:35 final size:35
Alignment explanation
Indices: 92760--92879 Score: 154
Period size: 35 Copynumber: 3.4 Consensus size: 35
92750 GGGTCCCTGC
*
92760 ATGGTGTCAACCCAGGTTCCATTCCTTAAATCCCG
1 ATGGTGTCAACCCGGGTTCCATTCCTTAAATCCCG
**
92795 ATGGTGTCAACCCGGGAACCATTCCTTAAATCCCG
1 ATGGTGTCAACCCGGGTTCCATTCCTTAAATCCCG
* *
92830 ATGGTGTCAACCCGGGAATT--ACTCTTTAAATCCCG
1 ATGGTGTCAACCCGGG--TTCCATTCCTTAAATCCCG
*
92865 ATGATGTCAACCCGG
1 ATGGTGTCAACCCGG
92880 AAACCATTAT
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
35 75 1.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (35 bp):
ATGGTGTCAACCCGGGTTCCATTCCTTAAATCCCG
Found at i:95212 original size:2 final size:2
Alignment explanation
Indices: 95197--95232 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
95187 ATGTGTGGCA
95197 AT AT A- AT AT A- 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
95233 CCAGAGCCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:95330 original size:22 final size:22
Alignment explanation
Indices: 95305--95346 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
95295 AATCATTTGT
*
95305 ATTTTCTGATATCAGAAAATCG
1 ATTTTCTGATATAAGAAAATCG
*
95327 ATTTTTTGATATAAGAAAAT
1 ATTTTCTGATATAAGAAAAT
95347 AAGACCTAAT
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:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (22 bp):
ATTTTCTGATATAAGAAAATCG
Found at i:114024 original size:13 final size:13
Alignment explanation
Indices: 114006--114031 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
113996 GTGTAATGAT
114006 AATATCATAACAA
1 AATATCATAACAA
114019 AATATCATAACAA
1 AATATCATAACAA
114032 CAACAACAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (13 bp):
AATATCATAACAA
Found at i:114068 original size:3 final size:3
Alignment explanation
Indices: 114027--114060 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
114017 AAAATATCAT
114027 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A
114061 GAACAACAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:114478 original size:36 final size:36
Alignment explanation
Indices: 114431--114501 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
114421 TTTCAAAAAT
*
114431 AAAAGTTCCAAGAACGCACTAGTTCTTTTGTCTTTC
1 AAAAGTTCCAAGAACGCACTAGTTCTTTTCTCTTTC
114467 AAAAGTTCCAAGAACGCACTAGTTCTTTTCTCTTT
1 AAAAGTTCCAAGAACGCACTAGTTCTTTTCTCTTT
114502 ATTATACGAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.37
Consensus pattern (36 bp):
AAAAGTTCCAAGAACGCACTAGTTCTTTTCTCTTTC
Found at i:116906 original size:1 final size:1
Alignment explanation
Indices: 116900--116924 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
116890 GAAAAGGTGT
116900 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
116925 AGATGTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:118453 original size:20 final size:19
Alignment explanation
Indices: 118424--118466 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
118414 TTGTTGTTGA
* *
118424 ATAAATTTAAAATACAATC
1 ATAAATTTAAAAAACAAAC
118443 ATAAGATTTAAAAAACAAAC
1 ATAA-ATTTAAAAAACAAAC
118463 ATAA
1 ATAA
118467 CAAATCTACG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (19 bp):
ATAAATTTAAAAAACAAAC
Found at i:143241 original size:41 final size:41
Alignment explanation
Indices: 143123--143250 Score: 107
Period size: 41 Copynumber: 3.1 Consensus size: 41
143113 ACAAACATTT
*
143123 AAAAATGACAAAGTCCAAATTAGTTACAAAAAAGTTATACTG
1 AAAAATGACAAAGTCCAAA-TAGGTACAAAAAAGTTATACTG
* * * ** * ****
143165 AACAAT-TCTAAGTCTGAATAAGGCACAGTTTAGTTATACT-
1 AAAAATGACAAAGTCCAAAT-AGGTACAAAAAAGTTATACTG
*
143205 AAGAAATGACAAAGTCCAAATAGGTACAAAAAAGTTATAGTG
1 AA-AAATGACAAAGTCCAAATAGGTACAAAAAAGTTATACTG
143247 AAAA
1 AAAA
143251 TTTTCTAAGT
Statistics
Matches: 60, Mismatches: 22, Indels: 9
0.66 0.24 0.10
Matches are distributed among these distances:
40 3 0.05
41 41 0.68
42 16 0.27
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (41 bp):
AAAAATGACAAAGTCCAAATAGGTACAAAAAAGTTATACTG
Found at i:143342 original size:84 final size:84
Alignment explanation
Indices: 143121--143402 Score: 337
Period size: 84 Copynumber: 3.4 Consensus size: 84
143111 AAACAAACAT
* * *
143121 TTAA-AAATGACAAAGTCCAAATTAGTTACAAAAAAGTTATACTGAACAA-TTCTAAGTCTGA-A
1 TTAAGAAATGACAAAGTCCAAATTAGGTACAAAAAAGTTATAGTGAA-AATTTCTAAGTGTGATA
* *
143183 TAAGGCACAGTTTAGTTATAC
65 T-AGGTACATTTTAGTTATAC
143204 -TAAGAAATGACAAAGTCCAAA-TAGGTACAAAAAAGTTATAGTGAAAATTTTCTAAGTGTGATA
1 TTAAGAAATGACAAAGTCCAAATTAGGTACAAAAAAGTTATAGTGAAAA-TTTCTAAGTGTGATA
143267 TAGGTACATTTTAGTTATAC
65 TAGGTACATTTTAGTTATAC
* * * * *
143287 TTTA-ATATGACTAAGTTCAAATTAGGTACAGAAAAGTTATAGTGAAAATTGTCTAAGTGTGATA
1 TTAAGAAATGACAAAGTCCAAATTAGGTACAAAAAAGTTATAGTGAAAATT-TCTAAGTGTGATA
143351 TAGGTACATTTTAGTTATAC
65 TAGGTACATTTTAGTTATAC
* * * *
143371 TTCA-AAACGACAAAG-ACAAATATAGTTACAAA
1 TTAAGAAATGACAAAGTCCAAAT-TAGGTACAAA
143403 TCAGTCATAA
Statistics
Matches: 174, Mismatches: 17, Indels: 15
0.84 0.08 0.07
Matches are distributed among these distances:
81 2 0.01
82 25 0.14
83 66 0.38
84 81 0.47
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (84 bp):
TTAAGAAATGACAAAGTCCAAATTAGGTACAAAAAAGTTATAGTGAAAATTTCTAAGTGTGATAT
AGGTACATTTTAGTTATAC
Found at i:143367 original size:42 final size:42
Alignment explanation
Indices: 143237--143369 Score: 135
Period size: 42 Copynumber: 3.2 Consensus size: 42
143227 GGTACAAAAA
*
143237 AGTTATAGTGAAAATTTTCTAAGTGTGATATAGGTACATTTT
1 AGTTATAGTGAAAATTGTCTAAGTGTGATATAGGTACATTTT
* ** * * * ****
143279 AGTTATACT-TTAATATGACTAAGT-TCAAATTAGGTACAGAAA
1 AGTTATAGTGAAAAT-TGTCTAAGTGTGATA-TAGGTACATTTT
143321 AGTTATAGTGAAAATTGTCTAAGTGTGATATAGGTACATTTT
1 AGTTATAGTGAAAATTGTCTAAGTGTGATATAGGTACATTTT
143363 AGTTATA
1 AGTTATA
143370 CTTCAAAACG
Statistics
Matches: 66, Mismatches: 21, Indels: 8
0.69 0.22 0.08
Matches are distributed among these distances:
41 6 0.09
42 54 0.82
43 6 0.09
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.39
Consensus pattern (42 bp):
AGTTATAGTGAAAATTGTCTAAGTGTGATATAGGTACATTTT
Found at i:147807 original size:2 final size:2
Alignment explanation
Indices: 147800--147852 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
147790 CGAGATTTTG
147800 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
147842 GA GA GA GA GA G
1 GA GA GA GA GA G
147853 GCGCATGGCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:151293 original size:2 final size:2
Alignment explanation
Indices: 151286--151338 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
151276 GTCTGATCTC
151286 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
151328 AG AG AG AG AG A
1 AG AG AG AG AG A
151339 TATGCTGCAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:163720 original size:13 final size:13
Alignment explanation
Indices: 163702--163726 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
163692 TAGATACACA
163702 TGCAAAAGCTGGG
1 TGCAAAAGCTGGG
163715 TGCAAAAGCTGG
1 TGCAAAAGCTGG
163727 ATCCACCCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (13 bp):
TGCAAAAGCTGGG
Found at i:169291 original size:23 final size:23
Alignment explanation
Indices: 169235--169291 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 23
169225 ACCTAATTAA
* *
169235 TGCAAATAAAAACTGTATTTTTG
1 TGCAAATAACAACTGCATTTTTG
* *
169258 TG-AAGTTACAA-TGCATATTTTG
1 TGCAAATAACAACTGCAT-TTTTG
169280 TGCAAATAACAA
1 TGCAAATAACAA
169292 AATAAATAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
21 4 0.15
22 13 0.50
23 9 0.35
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (23 bp):
TGCAAATAACAACTGCATTTTTG
Found at i:174532 original size:69 final size:69
Alignment explanation
Indices: 174421--174647 Score: 341
Period size: 69 Copynumber: 3.3 Consensus size: 69
174411 AGTTGTACAT
** * * * *
174421 CTACCCATCTTCTCCATGTCTAGTACATAGCCCCCTCTGACATGCCTACCATTGATTATCTTTCT
1 CTACCCATCTTCTCGGTGTCTAGTATATAACCCCCTTTGACATGCCTACCATTGATTACCTTTCT
174486 GCAC
66 GCAC
174490 CTACCCATCTTCTCGGTGTCTAGTATATAACCCCCTTTGACATGCCTA-CAGTTG-TTAACCTTT
1 CTACCCATCTTCTCGGTGTCTAGTATATAACCCCCTTTGACATGCCTACCA-TTGATT-ACCTTT
174553 CTGCAC
64 CTGCAC
* * *
174559 CTACCCATATTCTCAGTGTCTAGTATATAACCCCCTTTGACATGCCTACCATTGATAACCTTTCT
1 CTACCCATCTTCTCGGTGTCTAGTATATAACCCCCTTTGACATGCCTACCATTGATTACCTTTCT
174624 GCAC
66 GCAC
174628 CTACCCATCTTCTCGGTGTC
1 CTACCCATCTTCTCGGTGTC
174648 GAGGTCCATC
Statistics
Matches: 143, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
68 4 0.03
69 136 0.95
70 3 0.02
ACGTcount: A:0.21, C:0.34, G:0.11, T:0.34
Consensus pattern (69 bp):
CTACCCATCTTCTCGGTGTCTAGTATATAACCCCCTTTGACATGCCTACCATTGATTACCTTTCT
GCAC
Found at i:208143 original size:16 final size:16
Alignment explanation
Indices: 208105--208135 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
208095 CAAACAAGGT
*
208105 TTAGGGCAAACGATAA
1 TTAGAGCAAACGATAA
208121 TTAGAGCAAACGATA
1 TTAGAGCAAACGATA
208136 TTAAGAGCGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19
Consensus pattern (16 bp):
TTAGAGCAAACGATAA
Found at i:226111 original size:2 final size:2
Alignment explanation
Indices: 226104--226159 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
226094 TCTTTCAATT
226104 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
226146 GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA
226160 AAANNNNNNN
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:231024 original size:2 final size:2
Alignment explanation
Indices: 231019--231057 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
231009 TATATATATT
*
231019 TG TG TG TG TG TG CG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
231058 CCTATTTAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.03, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:234042 original size:2 final size:2
Alignment explanation
Indices: 234035--234083 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
234025 TCTTTCAATT
234035 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
234077 GA GA GA G
1 GA GA GA G
234084 CATGCTGAAT
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:250047 original size:196 final size:188
Alignment explanation
Indices: 249688--250058 Score: 580
Period size: 196 Copynumber: 1.9 Consensus size: 188
249678 CTACTCATTC
*
249688 GGAGGACACTCGAGGAAGACTCGAAAAACAATCGCAGGAACTCGTTAGTTTTCTATGAATGTTAA
1 GGAGGACACTCGAGGAAGACTCGAAAAACAATCGCAGGAACTCGTAAGTTTTCTATGAATGTTAA
* *
249753 AGATTTACTGCGCATGTGTGCAGTGCGAGTGTCATACGAAAGTCTAAAAATAACTAAAAATCCTA
66 AGATTTACTGCGCATGAGTGCAGTGCGAGTGTCACACGAAAGTCTAAAAATAACTAAAAATCCTA
* *
249818 TTGTGGGCACAATTGTTTTTAATATGCTCTCAACAATTGTCGTATTTAGCTATTATTT
131 CTGTGGGCACAATTGTTTTTAATATGCTCTCAACAATTGCCGTATTTAGCTATTATTT
* *
249876 GGAGGACACTCGAGGAGGACTCGAAAAACAATCGCAGGAACTCGTAAGTTTTCTATGAATGTTTA
1 GGAGGACACTCGAGGAAGACTCGAAAAACAATCGCAGGAACTCGTAAGTTTTCTATGAATGTTAA
* **
249941 AGATTTACTGCGATTATGTGCATGAGTGCAGTGCGAGTGTCACACGAAAGTCTAAGAATGCCTAA
66 AGATTTACTGC--------GCATGAGTGCAGTGCGAGTGTCACACGAAAGTCTAAAAATAACTAA
250006 AAATCCTACTGTGGGCACAATTGTTTTTAATATGCTCTCAACAATTGCCGTAT
123 AAATCCTACTGTGGGCACAATTGTTTTTAATATGCTCTCAACAATTGCCGTAT
250059 ATTTCAATGA
Statistics
Matches: 165, Mismatches: 10, Indels: 8
0.90 0.05 0.04
Matches are distributed among these distances:
188 73 0.44
196 92 0.56
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.30
Consensus pattern (188 bp):
GGAGGACACTCGAGGAAGACTCGAAAAACAATCGCAGGAACTCGTAAGTTTTCTATGAATGTTAA
AGATTTACTGCGCATGAGTGCAGTGCGAGTGTCACACGAAAGTCTAAAAATAACTAAAAATCCTA
CTGTGGGCACAATTGTTTTTAATATGCTCTCAACAATTGCCGTATTTAGCTATTATTT
Found at i:256641 original size:39 final size:39
Alignment explanation
Indices: 256582--256662 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
256572 TGCTATCCAG
* * *
256582 CACCAAATGCCCAGTTTATTGAACGTGGATACGGATTTC
1 CACCAAATGCCCAGTATATTGAACGCGGAGACGGATTTC
* *
256621 CACCAAATGCCCAGTATATTGATCGCGGCGACGGATTTC
1 CACCAAATGCCCAGTATATTGAACGCGGAGACGGATTTC
256660 CAC
1 CAC
256663 AATCAAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
CACCAAATGCCCAGTATATTGAACGCGGAGACGGATTTC
Found at i:258216 original size:11 final size:11
Alignment explanation
Indices: 258200--258250 Score: 57
Period size: 12 Copynumber: 4.3 Consensus size: 11
258190 CCCCCCCAAA
258200 AAAAAAAAAAC
1 AAAAAAAAAAC
258211 AAAAAAAAAAAC
1 -AAAAAAAAAAC
258223 AACAACAACAAAAC
1 AA-AA-AA-AAAAC
*
258237 AAACAAAAAAC
1 AAAAAAAAAAC
258248 AAA
1 AAA
258251 CGTTTTAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
11 10 0.29
12 15 0.43
13 3 0.09
14 7 0.20
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:258217 original size:15 final size:15
Alignment explanation
Indices: 258197--258246 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
258187 CCCCCCCCCC
258197 AAAAAAAAAAAAACA
1 AAAAAAAAAAAAACA
*
258212 AAAAAAAAAACAACA
1 AAAAAAAAAAAAACA
* * *
258227 ACAACAAAACAAACA
1 AAAAAAAAAAAAACA
258242 AAAAA
1 AAAAA
258247 CAAACGTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAACA
Found at i:258251 original size:15 final size:14
Alignment explanation
Indices: 258196--258251 Score: 58
Period size: 14 Copynumber: 3.8 Consensus size: 14
258186 CCCCCCCCCC
*
258196 CAAAAAAAAAAAAA
1 CAAAAAAAAACAAA
*
258210 CAAAAAAAAAAACAA
1 CAAAAAAAAACA-AA
*
258225 CAACAACAAAACAAA
1 CAA-AAAAAAACAAA
258240 CAAAAAACAAAC
1 CAAAAAA-AAAC
258252 GTTTTAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
14 15 0.42
15 14 0.39
16 7 0.19
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (14 bp):
CAAAAAAAAACAAA
Found at i:263786 original size:17 final size:18
Alignment explanation
Indices: 263764--263797 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
263754 AGACATTGCG
263764 TTTCTTAAAA-ACATTTA
1 TTTCTTAAAAGACATTTA
263781 TTTCTTAAAAGACATTT
1 TTTCTTAAAAGACATTT
263798 TTATGCATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (18 bp):
TTTCTTAAAAGACATTTA
Found at i:264119 original size:44 final size:44
Alignment explanation
Indices: 264069--264156 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
264059 TGTACTTGTT
264069 AAATCTATAAATCCATTTGTTTAATCTCATTGCTTACTATATAA
1 AAATCTATAAATCCATTTGTTTAATCTCATTGCTTACTATATAA
*
264113 AAATCTATAAATCCATTTGTTTAATCTCATTGCTTATTATATAA
1 AAATCTATAAATCCATTTGTTTAATCTCATTGCTTACTATATAA
264157 TTATAACATC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (44 bp):
AAATCTATAAATCCATTTGTTTAATCTCATTGCTTACTATATAA
Found at i:265024 original size:2 final size:2
Alignment explanation
Indices: 265017--265041 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
265007 ATATGTGAAT
265017 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
265042 NNNNNNNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:268663 original size:20 final size:20
Alignment explanation
Indices: 268640--268682 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
268630 TCATCATGTG
*
268640 CTACTAGTGAGTTTATAATT
1 CTACTAGTGAGTTGATAATT
268660 CTACTAGTGAGTTGATAATT
1 CTACTAGTGAGTTGATAATT
268680 CTA
1 CTA
268683 TTATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (20 bp):
CTACTAGTGAGTTGATAATT
Found at i:276564 original size:1 final size:1
Alignment explanation
Indices: 276560--276589 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
276550 TTTAATATTG
276560 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
276590 GAAATAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:278050 original size:119 final size:119
Alignment explanation
Indices: 277839--278059 Score: 442
Period size: 119 Copynumber: 1.9 Consensus size: 119
277829 ATATTAGGCC
277839 ACCTTTGAATTTGCTTGTTTGCTCTTGTCCTAGTGAATTCTCATGGTAAATATAATAAAGATTCT
1 ACCTTTGAATTTGCTTGTTTGCTCTTGTCCTAGTGAATTCTCATGGTAAATATAATAAAGATTCT
277904 AAGAATTTGTTTTTTCTCAACGCACTTGTTCGTAAATAAAGTCGTATTTTCTAT
66 AAGAATTTGTTTTTTCTCAACGCACTTGTTCGTAAATAAAGTCGTATTTTCTAT
277958 ACCTTTGAATTTGCTTGTTTGCTCTTGTCCTAGTGAATTCTCATGGTAAATATAATAAAGATTCT
1 ACCTTTGAATTTGCTTGTTTGCTCTTGTCCTAGTGAATTCTCATGGTAAATATAATAAAGATTCT
278023 AAGAATTTGTTTTTTCTCAACGCACTTGTTCGTAAAT
66 AAGAATTTGTTTTTTCTCAACGCACTTGTTCGTAAAT
278060 GCTATAATAT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 102 1.00
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.43
Consensus pattern (119 bp):
ACCTTTGAATTTGCTTGTTTGCTCTTGTCCTAGTGAATTCTCATGGTAAATATAATAAAGATTCT
AAGAATTTGTTTTTTCTCAACGCACTTGTTCGTAAATAAAGTCGTATTTTCTAT
Found at i:288011 original size:35 final size:35
Alignment explanation
Indices: 287972--288040 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
287962 ACTGTATTAT
287972 ATTGTGCTTTTATGTATACAAACGTTATGTATAAC
1 ATTGTGCTTTTATGTATACAAACGTTATGTATAAC
**
288007 ATTGTGCTTTTATGTATACCGACGTTATGTATAA
1 ATTGTGCTTTTATGTATACAAACGTTATGTATAA
288041 TATTTCAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (35 bp):
ATTGTGCTTTTATGTATACAAACGTTATGTATAAC
Found at i:290856 original size:18 final size:18
Alignment explanation
Indices: 290823--290857 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
290813 TTTGCCGTTA
* *
290823 CAGTCATTTAACCATTTG
1 CAGTCATTAAAACATTTG
290841 CAGTCATTAAAACATTT
1 CAGTCATTAAAACATTT
290858 AAAATTTGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (18 bp):
CAGTCATTAAAACATTTG
Found at i:304020 original size:15 final size:15
Alignment explanation
Indices: 304000--304031 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
303990 ATAATGAGGC
304000 TTGTGATTAAATAAA
1 TTGTGATTAAATAAA
304015 TTGTGATTAAATAAA
1 TTGTGATTAAATAAA
304030 TT
1 TT
304032 AAGAGGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (15 bp):
TTGTGATTAAATAAA
Found at i:308915 original size:15 final size:15
Alignment explanation
Indices: 308897--308939 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
308887 CTAGAATGAA
*
308897 GTTCTCTATCTCTGG
1 GTTCCCTATCTCTGG
* *
308912 GTTCCCTATCCCTTG
1 GTTCCCTATCTCTGG
308927 GTTCCCTATCTCT
1 GTTCCCTATCTCT
308940 AGACATGTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.07, C:0.35, G:0.14, T:0.44
Consensus pattern (15 bp):
GTTCCCTATCTCTGG
Found at i:320881 original size:33 final size:33
Alignment explanation
Indices: 320838--320918 Score: 153
Period size: 33 Copynumber: 2.5 Consensus size: 33
320828 AGACAATGTC
*
320838 GTCTAACTGTGTCCCAAAGTATATACAGGTAAA
1 GTCTACCTGTGTCCCAAAGTATATACAGGTAAA
320871 GTCTACCTGTGTCCCAAAGTATATACAGGTAAA
1 GTCTACCTGTGTCCCAAAGTATATACAGGTAAA
320904 GTCTACCTGTGTCCC
1 GTCTACCTGTGTCCC
320919 CTTAGAGGGC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (33 bp):
GTCTACCTGTGTCCCAAAGTATATACAGGTAAA
Found at i:334206 original size:33 final size:33
Alignment explanation
Indices: 334168--334269 Score: 114
Period size: 33 Copynumber: 3.0 Consensus size: 33
334158 GGGCTTGGGA
*
334168 GGACCTCCAAATGGAGGTGGTGGAGGGGGAGGG
1 GGACCTCCAAATGGAGGTGGTGGAGGAGGAGGG
* * * * * *
334201 GGACCTCCAAAAGGTGGAGGAGGCGGTGGAGGG
1 GGACCTCCAAATGGAGGTGGTGGAGGAGGAGGG
334234 GGACCTCCAAAGGGTGGAGGTGGTGGAGGAGGAGGG
1 GGACCTCCAAA---TGGAGGTGGTGGAGGAGGAGGG
334270 ATCATTCCTG
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
33 38 0.70
36 16 0.30
ACGTcount: A:0.23, C:0.13, G:0.54, T:0.11
Consensus pattern (33 bp):
GGACCTCCAAATGGAGGTGGTGGAGGAGGAGGG
Found at i:353994 original size:95 final size:95
Alignment explanation
Indices: 353831--354020 Score: 380
Period size: 95 Copynumber: 2.0 Consensus size: 95
353821 NAGCCTATGC
353831 TAGGATAAAAGTTTTGTTTTTACCGGTAGATTATCACCCTTTTACTACTCAGAAAAACAGTGTGG
1 TAGGATAAAAGTTTTGTTTTTACCGGTAGATTATCACCCTTTTACTACTCAGAAAAACAGTGTGG
353896 AAATAGAACCACTGTAAAATTTGCATATAT
66 AAATAGAACCACTGTAAAATTTGCATATAT
353926 TAGGATAAAAGTTTTGTTTTTACCGGTAGATTATCACCCTTTTACTACTCAGAAAAACAGTGTGG
1 TAGGATAAAAGTTTTGTTTTTACCGGTAGATTATCACCCTTTTACTACTCAGAAAAACAGTGTGG
353991 AAATAGAACCACTGTAAAATTTGCATATAT
66 AAATAGAACCACTGTAAAATTTGCATATAT
354021 ATATATANTA
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Consensus pattern (95 bp):
TAGGATAAAAGTTTTGTTTTTACCGGTAGATTATCACCCTTTTACTACTCAGAAAAACAGTGTGG
AAATAGAACCACTGTAAAATTTGCATATAT
Found at i:364896 original size:2 final size:2
Alignment explanation
Indices: 364889--364938 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
364879 CATTCTACTA
364889 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
364931 AG AG AG AG
1 AG AG AG AG
364939 GGGATGTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:366442 original size:2 final size:2
Alignment explanation
Indices: 366435--366474 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
366425 CAGGAACCGG
366435 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
366475 CCCCTCCCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:366611 original size:2 final size:2
Alignment explanation
Indices: 366604--366629 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
366594 NNNNNNNNNN
366604 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
366630 GGGGTAGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:372807 original size:2 final size:2
Alignment explanation
Indices: 372800--372834 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
372790 CAACAACAAC
372800 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 G
372835 TCCCTTACGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:381635 original size:2 final size:2
Alignment explanation
Indices: 381630--381668 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
381620 TCCGATTGAT
381630 GA 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 GA G
381669 TTTGCTCACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:382596 original size:26 final size:26
Alignment explanation
Indices: 382563--382614 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
382553 AATAAATATG
382563 AAACATATCACAAAATGAAAGTAATA
1 AAACATATCACAAAATGAAAGTAATA
*
382589 AAACATATCACAAAATGGAAGTAATA
1 AAACATATCACAAAATGAAAGTAATA
382615 TTATATTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.19
Consensus pattern (26 bp):
AAACATATCACAAAATGAAAGTAATA
Found at i:385747 original size:129 final size:128
Alignment explanation
Indices: 385517--385763 Score: 485
Period size: 129 Copynumber: 1.9 Consensus size: 128
385507 ATAATTTAAC
385517 GCTGTGAATTTCACTAAAATAATGTTAAAGTGTTGTTTCTGTTCACACCAATCATCATTATAAAA
1 GCTGTGAATTTCACTAAAATAATGTTAAAGTGTTGTTTCTGTTCACACCAATCATCATTATAAAA
385582 TTGTTGAAATTGGAAAAAAATAATTTCATCAGTTGCCTTTATTGGGGGGGGGGGGGGGGGGGG
66 TTGTTGAAATTGGAAAAAAATAATTTCATCAGTTGCCTTTATTGGGGGGGGGGGGGGGGGGGG
385645 NGCTGTGAATTTCACTAAAATAATGTTAAAGTGTTGTTTCTGTTCACACCAATCATCATTATAAA
1 -GCTGTGAATTTCACTAAAATAATGTTAAAGTGTTGTTTCTGTTCACACCAATCATCATTATAAA
385710 ATTGTTGAAATTGGAAAAAAATAATTTCATCAGTTGCCTTTATTGGGGGGGGGG
65 ATTGTTGAAATTGGAAAAAAATAATTTCATCAGTTGCCTTTATTGGGGGGGGGG
385764 TGTAAGTGTT
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 118 1.00
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34
Consensus pattern (128 bp):
GCTGTGAATTTCACTAAAATAATGTTAAAGTGTTGTTTCTGTTCACACCAATCATCATTATAAAA
TTGTTGAAATTGGAAAAAAATAATTTCATCAGTTGCCTTTATTGGGGGGGGGGGGGGGGGGGG
Found at i:397408 original size:16 final size:17
Alignment explanation
Indices: 397377--397408 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
397367 CTTGAATATA
397377 ATAAATATCTTTAACAG
1 ATAAATATCTTTAACAG
397394 ATAAATATC-TTAACA
1 ATAAATATCTTTAACA
397409 AGAAATCCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.34
Consensus pattern (17 bp):
ATAAATATCTTTAACAG
Found at i:406149 original size:22 final size:22
Alignment explanation
Indices: 406121--406166 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
406111 GAAATCACAA
406121 AACTTCATTACTCTTACATGAT
1 AACTTCATTACTCTTACATGAT
406143 AACTTCATTACTCTTACATGAT
1 AACTTCATTACTCTTACATGAT
406165 AA
1 AA
406167 AACAGTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (22 bp):
AACTTCATTACTCTTACATGAT
Found at i:411730 original size:2 final size:2
Alignment explanation
Indices: 411725--411790 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
411715 CCCTTCTTCA
411725 TC TC TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
411766 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
411791 GTACAACATT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:415266 original size:2 final size:2
Alignment explanation
Indices: 415259--415317 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
415249 GTCATGAATT
415259 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
415301 GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA G
415318 TACCTGTTCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:421566 original size:13 final size:13
Alignment explanation
Indices: 421548--421578 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
421538 CTTCCAACAC
421548 AAAAAAAAATGGA
1 AAAAAAAAATGGA
421561 AAAAAAAAATGGA
1 AAAAAAAAATGGA
421574 AAAAA
1 AAAAA
421579 CCTTGCCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (13 bp):
AAAAAAAAATGGA
Found at i:421770 original size:18 final size:18
Alignment explanation
Indices: 421747--421782 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
421737 AGCATGAACA
421747 AGTGGT-TTTCACAGCATT
1 AGTGGTATTTCACA-CATT
421765 AGTGGTATTTCACACATT
1 AGTGGTATTTCACACATT
421783 TTTGCTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (18 bp):
AGTGGTATTTCACACATT
Found at i:425858 original size:12 final size:12
Alignment explanation
Indices: 425841--425866 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
425831 TTTTTCTGTT
425841 TGTCGAATTGTC
1 TGTCGAATTGTC
425853 TGTCGAATTGTC
1 TGTCGAATTGTC
425865 TG
1 TG
425867 CAACTTGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.42
Consensus pattern (12 bp):
TGTCGAATTGTC
Found at i:427839 original size:4 final size:4
Alignment explanation
Indices: 427830--427858 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
427820 CTTCCCAGTT
427830 TTGA TTGA TTGA TTGA TTGA TTG- TTGA TT
1 TTGA TTGA TTGA TTGA TTGA TTGA TTGA TT
427859 TACATCCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.21, C:0.00, G:0.24, T:0.55
Consensus pattern (4 bp):
TTGA
Found at i:431232 original size:26 final size:26
Alignment explanation
Indices: 431211--431283 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 26
431201 GTAAAATCAA
431211 CAGGTATGATTAGTGCACAAAA-AAC
1 CAGGTATGATTAGTGCACAAAACAAC
*
431236 CAGGTATGCATGATTAGTGCAC-GAACAAGC
1 CAGG--T--ATGATTAGTGCACAAAACAA-C
431266 CAGGTATGATTAGTGCAC
1 CAGGTATGATTAGTGCAC
431284 GAACAAGTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
25 4 0.10
26 13 0.32
27 1 0.02
28 3 0.07
29 15 0.37
30 5 0.12
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.22
Consensus pattern (26 bp):
CAGGTATGATTAGTGCACAAAACAAC
Found at i:431248 original size:29 final size:30
Alignment explanation
Indices: 431216--431273 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
431206 ATCAACAGGT
431216 ATGATTAGTGCAC-AAAAAACCAGGTATGC
1 ATGATTAGTGCACGAAAAAACCAGGTATGC
* *
431245 ATGATTAGTGCACGAACAAGCCAGGTATG
1 ATGATTAGTGCACGAAAAAACCAGGTATG
431274 ATTAGTGCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (30 bp):
ATGATTAGTGCACGAAAAAACCAGGTATGC
Found at i:431284 original size:26 final size:26
Alignment explanation
Indices: 431211--431290 Score: 99
Period size: 26 Copynumber: 3.0 Consensus size: 26
431201 GTAAAATCAA
* *
431211 CAGGTATGATTAGTGCAC-AAAAAAC
1 CAGGTATGATTAGTGCACGAACAAGC
431236 CAGGTATGCATGATTAGTGCACGAACAAGC
1 CAGG--T--ATGATTAGTGCACGAACAAGC
431266 CAGGTATGATTAGTGCACGAACAAG
1 CAGGTATGATTAGTGCACGAACAAG
431291 TATCATCCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
25 4 0.08
26 20 0.42
27 1 0.02
28 1 0.02
29 13 0.27
30 9 0.19
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (26 bp):
CAGGTATGATTAGTGCACGAACAAGC
Found at i:446938 original size:29 final size:29
Alignment explanation
Indices: 446896--446956 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
446886 AATCCTACGC
*
446896 AATCTTTAATCATATACATGT-TCATAGAG
1 AATCTTCAATCATATACATGTAT-ATAGAG
446925 AATCTTCAATCATATACATGTATATAGAG
1 AATCTTCAATCATATACATGTATATAGAG
446954 AAT
1 AAT
446957 ACAAATAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (29 bp):
AATCTTCAATCATATACATGTATATAGAG
Found at i:458155 original size:5 final size:5
Alignment explanation
Indices: 458145--458203 Score: 79
Period size: 5 Copynumber: 12.4 Consensus size: 5
458135 AAGCAATCAA
*
458145 AAAAT AAAAT AAAAT AAAAT -AAAT -AAAT AGAAT AAAAT AAAAT -AAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
*
458192 AAAAA AAAAT AA
1 AAAAT AAAAT AA
458204 GAAAAAAACT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
4 12 0.25
5 36 0.75
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:458178 original size:23 final size:23
Alignment explanation
Indices: 458146--458199 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
458136 AGCAATCAAA
458146 AAATAAAATAAAATAAAATAAAT
1 AAATAAAATAAAATAAAATAAAT
*
458169 AAATAGAATAAAATAAAATAAAT
1 AAATAAAATAAAATAAAATAAAT
*
458192 AAAAAAAA
1 AAATAAAA
458200 ATAAGAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.19
Consensus pattern (23 bp):
AAATAAAATAAAATAAAATAAAT
Found at i:458208 original size:10 final size:9
Alignment explanation
Indices: 458143--458211 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
458133 TGAAGCAATC
458143 AAAAAATAA
1 AAAAAATAA
458152 AATAAAATAA
1 AA-AAAATAA
*
458162 AATAAATAA
1 AAAAAATAA
* *
458171 ATAGAATAA
1 AAAAAATAA
458180 AATAAAATAA
1 AA-AAAATAA
*
458190 ATAAAA-AA
1 AAAAAATAA
* *
458198 AAATAAGAA
1 AAAAAATAA
458207 AAAAA
1 AAAAA
458212 CTTTGCAGCC
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
8 6 0.13
9 25 0.53
10 16 0.34
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (9 bp):
AAAAAATAA
Found at i:458209 original size:9 final size:8
Alignment explanation
Indices: 458143--458198 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
458133 TGAAGCAATC
458143 AAAAAATA
1 AAAAAATA
*
458151 AAATAA-A
1 AAAAAATA
*
458158 ATAAAATA
1 AAAAAATA
*
458166 AATAAATA
1 AAAAAATA
458174 GAATAAAATA
1 -AA-AAAATA
458184 AAATAAATA
1 AAA-AAATA
458193 AAAAAA
1 AAAAAA
458199 AATAAGAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
7 5 0.13
8 16 0.42
9 12 0.32
10 5 0.13
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (8 bp):
AAAAAATA
Found at i:458209 original size:14 final size:13
Alignment explanation
Indices: 458143--458211 Score: 57
Period size: 13 Copynumber: 5.1 Consensus size: 13
458133 TGAAGCAATC
458143 AAAAAATAAAATAA
1 AAAAAATAAAA-AA
*
458157 AATAAAATAAATAA
1 AA-AAAATAAAAAA
* *
458171 ATAGAATAAAATAA
1 AAAAAATAAAA-AA
*
458185 AATAAATAAAAAA
1 AAAAAATAAAAAA
* *
458198 AAATAAGAAAAAA
1 AAAAAATAAAAAA
458211 A
1 A
458212 CTTTGCAGCC
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
13 20 0.47
14 15 0.35
15 8 0.19
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (13 bp):
AAAAAATAAAAAA
Found at i:466741 original size:12 final size:12
Alignment explanation
Indices: 466724--466758 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
466714 GATGTATCTA
466724 TTTCAGACTTGT
1 TTTCAGACTTGT
* *
466736 TTTCAGTCATGT
1 TTTCAGACTTGT
466748 TTTCAGACTTG
1 TTTCAGACTTG
466759 GCACAACTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (12 bp):
TTTCAGACTTGT
Found at i:469702 original size:2 final size:2
Alignment explanation
Indices: 469697--469725 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
469687 TGGATTTAAC
469697 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
469726 TGAAACACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:472058 original size:99 final size:99
Alignment explanation
Indices: 471909--472091 Score: 242
Period size: 99 Copynumber: 1.8 Consensus size: 99
471899 TGTACTTTTA
* * *
471909 TTACTGAGTAATGGAGCAGACATTAATTTGTGCAAAGAAAACAGAACCAGTCCTCTCCT-TATAG
1 TTACTGAGTAATGAAGCAGACATTAATTTATGCAAAGAAAACAGAACCAGTCCTCT-CTATAAAG
471973 CTTGCGAAAACGGACATGATAGCACTGTACAGGTT
65 CTTGCGAAAACGGACATGATAGCACTGTACAGGTT
* *** * *
472008 TTACTGAGTAATGAAGCAGACATTAATTTATGCACAGTGGACGGAGCCAGTCCTCTCTATAAAGC
1 TTACTGAGTAATGAAGCAGACATTAATTTATGCAAAGAAAACAGAACCAGTCCTCTCTATAAAGC
***
472073 TTGTTTAAACGGACATGAT
66 TTGCGAAAACGGACATGAT
472092 GCAATTGCGA
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
98 2 0.03
99 69 0.97
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (99 bp):
TTACTGAGTAATGAAGCAGACATTAATTTATGCAAAGAAAACAGAACCAGTCCTCTCTATAAAGC
TTGCGAAAACGGACATGATAGCACTGTACAGGTT
Found at i:472646 original size:99 final size:99
Alignment explanation
Indices: 472543--472734 Score: 217
Period size: 99 Copynumber: 1.9 Consensus size: 99
472533 TGCTCAAACC
* **
472543 ACGGAACCAGTCCGCTCTATACAGCCTGTTACGAAGGACATTG-TAACATTGTAC-AACTTTTAC
1 ACGGAACCAGTCCGCTCTATACAGCCTGTCAAAAAGGACA-TGATAACATTGT-CGAACTTTTAC
* *
472606 TTAGTAATGGAGCAGACACCAGTTTATGTTGTATTG
64 TTAGCAATGGAGCAGACACCAATTTATGTTGTATTG
** * * * * * * *
472642 ACGGATTCAGTCCTCTCTTTGCCGCTTGTCAAAAAGGATATGATAGCATTGTCGAACTTTTACTT
1 ACGGAACCAGTCCGCTCTATACAGCCTGTCAAAAAGGACATGATAACATTGTCGAACTTTTACTT
*
472707 AGCAATGGAGCAGACATCAATTTATGTT
66 AGCAATGGAGCAGACACCAATTTATGTT
472735 CAAAAGATAA
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
98 3 0.04
99 73 0.96
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (99 bp):
ACGGAACCAGTCCGCTCTATACAGCCTGTCAAAAAGGACATGATAACATTGTCGAACTTTTACTT
AGCAATGGAGCAGACACCAATTTATGTTGTATTG
Found at i:475389 original size:11 final size:11
Alignment explanation
Indices: 475373--475397 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
475363 TAGCCATTAA
475373 ATTTTCTTGCT
1 ATTTTCTTGCT
475384 ATTTTCTTGCT
1 ATTTTCTTGCT
475395 ATT
1 ATT
475398 GGAATTAATT
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:0.16, G:0.08, T:0.64
Consensus pattern (11 bp):
ATTTTCTTGCT
Found at i:479920 original size:14 final size:14
Alignment explanation
Indices: 479870--479919 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
479860 CATTCATACA
479870 CCTCTCTCACTACTC
1 CCTCTCTCACT-CTC
*
479885 TCT-TCTCACTCTC
1 CCTCTCTCACTCTC
* *
479898 CCTTTCTCTCTCTC
1 CCTCTCTCACTCTC
479912 CCTCTCTC
1 CCTCTCTC
479920 TATTTTCTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 5 0.17
14 23 0.77
15 2 0.07
ACGTcount: A:0.06, C:0.52, G:0.00, T:0.42
Consensus pattern (14 bp):
CCTCTCTCACTCTC
Found at i:480442 original size:13 final size:13
Alignment explanation
Indices: 480428--480518 Score: 69
Period size: 13 Copynumber: 7.0 Consensus size: 13
480418 ACACCACCCT
480428 CTCACTCCTCACT-
1 CTCACT-CTCACTC
*
480441 CTCAATCTCACTC
1 CTCACTCTCACTC
* * *
480454 CCCAGTCTCTCTC
1 CTCACTCTCACTC
*
480467 CTC-CTTCACACTC
1 CTCAC-TCTCACTC
480480 CTCACTCTCACTC
1 CTCACTCTCACTC
* *
480493 CTCCCTCTCATTC
1 CTCACTCTCACTC
* *
480506 CCCACTCTTACTC
1 CTCACTCTCACTC
480519 TTCCCGCTCA
Statistics
Matches: 60, Mismatches: 15, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
12 6 0.10
13 53 0.88
14 1 0.02
ACGTcount: A:0.14, C:0.53, G:0.01, T:0.32
Consensus pattern (13 bp):
CTCACTCTCACTC
Found at i:480449 original size:19 final size:18
Alignment explanation
Indices: 480427--480503 Score: 59
Period size: 19 Copynumber: 4.1 Consensus size: 18
480417 CACACCACCC
480427 TCTCACTCCTCACTCTCAA
1 TCTCACTCCTCACTCTC-A
* *
480446 TCTCACTCCCCAGTCTC-
1 TCTCACTCCTCACTCTCA
480463 TCTC-CTCCTTCACACTCCTCA
1 TCTCACTCC-T--CACT-CTCA
*
480484 CTCTCACTCCTCCCTCTCA
1 -TCTCACTCCTCACTCTCA
480503 T
1 T
480504 TCCCCACTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 15
0.70 0.08 0.23
Matches are distributed among these distances:
16 4 0.09
17 4 0.09
18 1 0.02
19 22 0.48
20 6 0.13
22 5 0.11
23 4 0.09
ACGTcount: A:0.14, C:0.52, G:0.01, T:0.32
Consensus pattern (18 bp):
TCTCACTCCTCACTCTCA
Found at i:480469 original size:32 final size:31
Alignment explanation
Indices: 480350--480456 Score: 101
Period size: 32 Copynumber: 3.4 Consensus size: 31
480340 TATTCCTTAC
* *
480350 TCTCACTCCCCCTCTCTCT-CTCCACTCTCAC
1 TCTCACTCCCCCTCTCACTCCT-CACTCTCAA
* * *
480381 TCCTCCCTCCCCACTCTCAC-CTCTCTCTCTCTA
1 T-CTCACTCCCC-CTCTCACTC-CTCACTCTCAA
*
480414 TCTCACACCACCCTCTCACTCCTCACTCTCAA
1 TCTCACTCC-CCCTCTCACTCCTCACTCTCAA
480446 TCTCACTCCCC
1 TCTCACTCCCC
480457 AGTCTCTCTC
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
31 3 0.05
32 39 0.65
33 16 0.27
34 2 0.03
ACGTcount: A:0.13, C:0.57, G:0.00, T:0.30
Consensus pattern (31 bp):
TCTCACTCCCCCTCTCACTCCTCACTCTCAA
Found at i:480511 original size:26 final size:26
Alignment explanation
Indices: 480348--480700 Score: 143
Period size: 26 Copynumber: 13.8 Consensus size: 26
480338 ATTATTCCTT
* *
480348 ACTCTCACTCC-CCCTCTCTCTCTCC
1 ACTCTCACTCCTCCCTCTCACTCCCC
* *
480373 ACTCTCACTCCTCCCTCCCCACT-CTC
1 ACTCTCACTCCTCCCT-CTCACTCCCC
* ** *
480399 AC-CTCTCTCTCTCTATCTCACACCACC
1 ACTCTCACTC-CTCCCTCTCACTCC-CC
480426 -CTCTCACTCCTCACTCTCAATCTCACTCCCC
1 ACTCTCACTCCT--C-C-C--TCTCACTCCCC
* * * * *
480457 AGTCTCTCTCCTCCTTCACACTCCTC
1 ACTCTCACTCCTCCCTCTCACTCCCC
*
480483 ACTCTCACTCCTCCCTCTCATTCCCC
1 ACTCTCACTCCTCCCTCTCACTCCCC
* * * *
480509 ACTCTTACTCTTCCCGCTCACTCACC
1 ACTCTCACTCCTCCCTCTCACTCCCC
* * * * *
480535 AATCTTACTCCCTTCCCTCT--TTGCCA
1 ACTCTCACT-CC-TCCCTCTCACTCCCC
* * * *
480561 ACTCTCACTACATCCCTCGCTCTTCCC
1 ACTCTCACT-CCTCCCTCTCACTCCCC
*
480588 ACTCTCACTCCTCACTCTCA-----C
1 ACTCTCACTCCTCCCTCTCACTCCCC
* * *
480609 -CTCTCTCTCC-CCACTTTTACTCCCC
1 ACTCTCACTCCTCC-CTCTCACTCCCC
* *
480634 ACTCTCAGTCCTCCCTCTCTCTCCTCC
1 ACTCTCACTCCTCCCTCTCACTCC-CC
480661 -CTCTCA--CCT--CTCT--CTCCCC
1 ACTCTCACTCCTCCCTCTCACTCCCC
480680 ACTCTCACTCCTCCCTCTCAC
1 ACTCTCACTCCTCCCTCTCAC
480701 CTCTCTCTCC
Statistics
Matches: 237, Mismatches: 58, Indels: 65
0.66 0.16 0.18
Matches are distributed among these distances:
19 3 0.01
20 23 0.10
21 1 0.00
22 7 0.03
24 7 0.03
25 28 0.12
26 112 0.47
27 28 0.12
28 7 0.03
29 1 0.00
30 1 0.00
31 2 0.01
32 17 0.07
ACGTcount: A:0.13, C:0.54, G:0.01, T:0.31
Consensus pattern (26 bp):
ACTCTCACTCCTCCCTCTCACTCCCC
Found at i:480605 original size:13 final size:13
Alignment explanation
Indices: 480587--480700 Score: 55
Period size: 13 Copynumber: 9.2 Consensus size: 13
480577 TCGCTCTTCC
480587 CACT-CTCACTCCT
1 CACTCCTCACT-CT
480600 CACT-CTCACCTCT
1 CACTCCTCA-CTCT
* * *
480613 CTCTCCCCACTTT
1 CACTCCTCACTCT
* *
480626 TACTCCCCACTCT
1 CACTCCTCACTCT
* *
480639 CAGTCCTCCCTCT
1 CACTCCTCACTCT
* *
480652 CTCTCCTCCCTCT
1 CACTCCTCACTCT
480665 CA--CCT--CTCT
1 CACTCCTCACTCT
*
480674 --CTCCCCACTCT
1 CACTCCTCACTCT
*
480685 CACTCCTCCCTCT
1 CACTCCTCACTCT
480698 CAC
1 CAC
480701 CTCTCTCTCC
Statistics
Matches: 77, Mismatches: 16, Indels: 16
0.71 0.15 0.15
Matches are distributed among these distances:
9 6 0.08
11 7 0.09
13 59 0.77
14 5 0.06
ACGTcount: A:0.11, C:0.57, G:0.01, T:0.32
Consensus pattern (13 bp):
CACTCCTCACTCT
Found at i:480623 original size:33 final size:33
Alignment explanation
Indices: 480575--480710 Score: 117
Period size: 33 Copynumber: 4.3 Consensus size: 33
480565 TCACTACATC
* *
480575 CCTCGCTCTTCCCACTCTCACTCCTCACTCTCA
1 CCTCGCTCTCCCCACTCTCACTCCCCACTCTCA
* * *
480608 CCTCTCTCTCCCCACTTTTACTCCCCACTCTCA
1 CCTCGCTCTCCCCACTCTCACTCCCCACTCTCA
* * *
480641 -GTC-CTC-CCTCTCTCTC-CT--CC-CTCTCA
1 CCTCGCTCTCCCCACTCTCACTCCCCACTCTCA
*
480667 CCTCTCTCTCCCCACTCTCACTCCTCC-CTCTCA
1 CCTCGCTCTCCCCACTCTCACTCC-CCACTCTCA
*
480700 CCTCTCTCTCC
1 CCTCGCTCTCC
480711 AATTTTACTC
Statistics
Matches: 83, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
26 6 0.07
27 4 0.05
28 3 0.04
29 10 0.12
30 8 0.10
31 3 0.04
32 2 0.02
33 47 0.57
ACGTcount: A:0.09, C:0.57, G:0.01, T:0.32
Consensus pattern (33 bp):
CCTCGCTCTCCCCACTCTCACTCCCCACTCTCA
Found at i:480670 original size:11 final size:11
Alignment explanation
Indices: 480650--480709 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
480640 AGTCCTCCCT
*
480650 CTCTCTCCTCC
1 CTCTCACCTCC
*
480661 CTCTCACCTCT
1 CTCTCACCTCC
*
480672 CTCTC-CC-CA
1 CTCTCACCTCC
480681 CTCTCACTCCTCC
1 CTCTCA--CCTCC
*
480694 CTCTCACCTCT
1 CTCTCACCTCC
480705 CTCTC
1 CTCTC
480710 CAATTTTACT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
9 6 0.15
10 2 0.05
11 23 0.57
12 2 0.05
13 7 0.17
ACGTcount: A:0.07, C:0.60, G:0.00, T:0.33
Consensus pattern (11 bp):
CTCTCACCTCC
Found at i:480704 original size:20 final size:20
Alignment explanation
Indices: 480647--480710 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
480637 CTCAGTCCTC
480647 CCTCTCTCTCCTCCCTCTCA
1 CCTCTCTCTCCTCCCTCTCA
480667 -C-CTCTCT-CT-CC-C-CA
1 CCTCTCTCTCCTCCCTCTCA
*
480681 -CTCTCACTCCTCCCTCTCA
1 CCTCTCTCTCCTCCCTCTCA
480700 CCTCTCTCTCC
1 CCTCTCTCTCC
480711 AATTTTACTC
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
14 3 0.08
15 6 0.17
16 4 0.11
17 4 0.11
18 7 0.19
19 3 0.08
20 9 0.25
ACGTcount: A:0.06, C:0.61, G:0.00, T:0.33
Consensus pattern (20 bp):
CCTCTCTCTCCTCCCTCTCA
Found at i:480731 original size:46 final size:45
Alignment explanation
Indices: 480585--480789 Score: 165
Period size: 46 Copynumber: 4.5 Consensus size: 45
480575 CCTCGCTCTT
*
480585 CCCACTCTCACTCCTCACTCTCACCTCTCTCTCCCCACTTTTACT-C
1 CCCACTCTCACTCCTCCCTCTCACCTCTCTCT--CCACTTTTACTCC
* * * * *
480631 CCCACTCTCAGTCCTCCCTCTC-TCTCCTCCCTCTCACCTCT-CTCTC
1 CCCACTCTCACTCCTCCCTCTCACCT-CTCTCTC-CACTTTTACTC-C
*
480677 CCCACTCTCACTCCTCCCTCTCACCTCTCTCTCCAATTTTACTCC
1 CCCACTCTCACTCCTCCCTCTCACCTCTCTCTCCACTTTTACTCC
* * *
480722 CCC-CTCTCTCT-CTCCCTCTTA-CTCCTCCCTCACACATTTCT-CTCTC
1 CCCACTCTCACTCCTCCCTCTCACCT-CTCTCTC-CAC-TTT-TACTC-C
480768 CCCACTCTCACTTCC-CCCTCTC
1 CCCACTCTCAC-TCCTCCCTCTC
480790 CCTACTCACC
Statistics
Matches: 127, Mismatches: 18, Indels: 26
0.74 0.11 0.15
Matches are distributed among these distances:
42 2 0.02
43 15 0.12
44 12 0.09
45 21 0.17
46 61 0.48
47 8 0.06
48 7 0.06
49 1 0.01
ACGTcount: A:0.10, C:0.56, G:0.00, T:0.33
Consensus pattern (45 bp):
CCCACTCTCACTCCTCCCTCTCACCTCTCTCTCCACTTTTACTCC
Found at i:484007 original size:12 final size:12
Alignment explanation
Indices: 483990--484017 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
483980 TTTTGTTTAG
483990 CATTGTATAAAA
1 CATTGTATAAAA
484002 CATTGTATAAAA
1 CATTGTATAAAA
484014 CATT
1 CATT
484018 AAATTCGCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (12 bp):
CATTGTATAAAA
Found at i:489562 original size:3 final size:3
Alignment explanation
Indices: 489554--489583 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
489544 GCTGATGTCT
489554 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
489584 CGGCGATGGT
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):
TGA
Found at i:490777 original size:21 final size:21
Alignment explanation
Indices: 490733--490778 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
490723 AAAAAATCTG
* *
490733 ATTTGTTCGGACGAATTAGAT
1 ATTTGTTCGGACAAATAAGAT
*
490754 ATTTGTTCGGACAAATAAGTT
1 ATTTGTTCGGACAAATAAGAT
490775 ATTT
1 ATTT
490779 ATATCAACAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (21 bp):
ATTTGTTCGGACAAATAAGAT
Found at i:491034 original size:2 final size:2
Alignment explanation
Indices: 491029--491054 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
491019 AAAGCACAAT
491029 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
491055 CAATTGCAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:498016 original size:398 final size:397
Alignment explanation
Indices: 497280--498074 Score: 1536
Period size: 398 Copynumber: 2.0 Consensus size: 397
497270 GTGGGCAGTA
497280 ATGGCCAACAGCAGGAAGACCGAACGGATGGGCCGTGGAAGGAATTTGGTCCTTTGTGGAAAACT
1 ATGGCCAACAGCAGGAAGACCGAACGGATGGGCCGTGGAAGGAATTTGGTCCTTTGTGGAAAACT
497345 GATAAAAATCGAGAATTGGGTGTAGATATCGATGGAGCTTCATCTGTATGGGCCGTCGATGCCAA
66 GATAAAAATCGAGAATTGGGTGTAGATATCGATGGAGCTTCATCTGTATGGGCCGTCGATGCCAA
497410 GAAGAAAACCATTCTTGAAATATCTCCATCTTCTGGAAACATATTGAAAAGTTTGAATGTTTCTC
131 GAAGAAAACCATTCTTGAAATATCTCCATCTTCTGGAAACATATTGAAAAGTTTGAATGTTTCTC
*
497475 AGCTGTTACAAGCTAAAGCGGTTGTAACATCAGATCTAATGGTCACCAGAGCAGACAAGAAAGAC
196 AGCTGTTACAAGCTAAAGCGGTTGTAACATCAGATCTAATGATCACCAGAGCAGACAAGAAAGAC
497540 GAGGACCATCTTGTGTTTGCTGTTACTCTTGTCAACGGGCCATCTACTGCGTTTCACTCTCTTTT
261 GAGGACCATCTTGTGTTTGCTGTTACTCTTGTCAACGGGCCATCTACTGCGTTTCACTCTCTTTT
497605 GAAATCGTTTGGTGGCGATCGATCAGACAACAAGAACTACGTGATTCAGATGAAAGGTGACACAG
326 GAAATCGTTTGGTGGCGATCGATCAGACAACAAGAACTACGTGATTCAGATGAAAGGTGACACAG
497670 TAGAATG
391 TAGAATG
497677 NATGGCCAACAGCAGGAAGACCGAACGGATGGGCCGTGGAAGGAATTTGGTCCTTTGTGGAAAAC
1 -ATGGCCAACAGCAGGAAGACCGAACGGATGGGCCGTGGAAGGAATTTGGTCCTTTGTGGAAAAC
497742 TGATAAAAATCGAGAATTGGGTGTAGATATCGATGGAGCTTCATCTGTATGGGCCGTCGATGCCA
65 TGATAAAAATCGAGAATTGGGTGTAGATATCGATGGAGCTTCATCTGTATGGGCCGTCGATGCCA
497807 AGAAGAAAACCATTCTTGAAATATCTCCATCTTCTGGAAACATATTGAAAAGTTTGAATGTTTCT
130 AGAAGAAAACCATTCTTGAAATATCTCCATCTTCTGGAAACATATTGAAAAGTTTGAATGTTTCT
* * *
497872 CAGCTGTTACAAGCTAAAGCGGTTGTAACTTCAGATCTAATGATCACCAGATCAGACAAGAATGA
195 CAGCTGTTACAAGCTAAAGCGGTTGTAACATCAGATCTAATGATCACCAGAGCAGACAAGAAAGA
*
497937 TGAGGACCATCTTGTGTTTGCTGTTACTCTTGTCAACGGGCCATCTACTGCGTTTCACTCTCTTT
260 CGAGGACCATCTTGTGTTTGCTGTTACTCTTGTCAACGGGCCATCTACTGCGTTTCACTCTCTTT
498002 TGAAATCGTTTGGTGGCGATCGATCAGACAACAAGAACTACGTGATTCAGATGAAAGGTGACACA
325 TGAAATCGTTTGGTGGCGATCGATCAGACAACAAGAACTACGTGATTCAGATGAAAGGTGACACA
498067 GTAGAATG
390 GTAGAATG
498075 GGCCGTGCCA
Statistics
Matches: 392, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
398 392 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (397 bp):
ATGGCCAACAGCAGGAAGACCGAACGGATGGGCCGTGGAAGGAATTTGGTCCTTTGTGGAAAACT
GATAAAAATCGAGAATTGGGTGTAGATATCGATGGAGCTTCATCTGTATGGGCCGTCGATGCCAA
GAAGAAAACCATTCTTGAAATATCTCCATCTTCTGGAAACATATTGAAAAGTTTGAATGTTTCTC
AGCTGTTACAAGCTAAAGCGGTTGTAACATCAGATCTAATGATCACCAGAGCAGACAAGAAAGAC
GAGGACCATCTTGTGTTTGCTGTTACTCTTGTCAACGGGCCATCTACTGCGTTTCACTCTCTTTT
GAAATCGTTTGGTGGCGATCGATCAGACAACAAGAACTACGTGATTCAGATGAAAGGTGACACAG
TAGAATG
Found at i:498895 original size:492 final size:490
Alignment explanation
Indices: 497971--498952 Score: 1865
Period size: 492 Copynumber: 2.0 Consensus size: 490
497961 TACTCTTGTC
*
497971 AACGGGCCATCTACTGCGTTTCACTCTCTTTTGAAATCGTTTGGTGGCGATCGATCAGACAACAA
1 AACGGGCCATCTACTGCGTTTCACTCTCTTCTGAAATCGTTTGGTGGCGATCGATCAGACAACAA
498036 GAACTACGTGATTCAGATGAAAGGTGACACAGTAGAATGGGCCGTGCCAACCGTTGAAGATCTAC
66 GAACTACGTGATTCAGATGAAAGGTGACACAGTAGAATGGGCCGTGCCAACCGTTGAAGATCTAC
* *
498101 CAGGGGTAGGGCAAATTGCCGGCATCAAAACACATGACAGCACGGACGATGACTTGAAAGATTTG
131 CAGGGGTAGGCCAAATTGCCGGCATCAAAACACATGACAGCACGGAAGATGACTTGAAAGATTTG
498166 TATGTTGTGTTCGCTGGCGATGACAAATCGTCGGTGGTCTTTGGTATTCATTAGATACTAGTGGA
196 TATGTTGTGTTCGCTGGCGATGACAAATCGTCGGTGGTCTTTGGTATTCATTAGATACTAGTGGA
*
498231 TAAAACAACAGCATCAACGAAACACTAACTAATGTCGATTATATGTAGATATCCTTAATTCATGT
261 TAAAACAACAGCATCAACGAAACACTAACTAATGTCGATTATATGTAGATATCCATAATTCATGT
* *
498296 ACATGTATATTGTAAAATATGACAGTGGAGCCAAAAGAAAAAGAAAAGAAAATTGATATAAAACG
326 ACATGAATATTGTAAAATATGACAATGGAGCCAAAAGAAAAAGAAAAGAAAATTGATATAAAACG
498361 TATTCATGTTACAATGTATAATAAAGTAAGACGGGTGTGGAATTGTTCATGGAATGGTTTATTTG
391 TATTCATGTTACAATGTATAATAAAGTAAGACGGGTGTGGAATTGTTCATGGAATGGTTTATTTG
498426 AGAAAAAAAACTACACGTATGCAATCAATATTATAT
456 AG-AAAAAAACTACACGTATGCAATCAATATTATAT
498462 NAACGGGCCATCTACTGCGTTTCACTCTCTTCTGAAATCGTTTGGTGGCGATCGATCAGACAACA
1 -AACGGGCCATCTACTGCGTTTCACTCTCTTCTGAAATCGTTTGGTGGCGATCGATCAGACAACA
*
498527 AGAACTACGTGATTCAGATGAAAGGTGACACAGTAGAATGGGTCGTGCCAACCGTTGAAGATCTA
65 AGAACTACGTGATTCAGATGAAAGGTGACACAGTAGAATGGGCCGTGCCAACCGTTGAAGATCTA
498592 CCAGGGGTAGGCCAAATTGCCGGCATCAAAACACATGACAGCACGGAAGATGACTTGAAAGATTT
130 CCAGGGGTAGGCCAAATTGCCGGCATCAAAACACATGACAGCACGGAAGATGACTTGAAAGATTT
498657 GTATGTTGTGTTCGCTGGCGATGACAAATCGTCGGTGGTCTTTGGTATTCATTAGATACTAGTGG
195 GTATGTTGTGTTCGCTGGCGATGACAAATCGTCGGTGGTCTTTGGTATTCATTAGATACTAGTGG
*
498722 ATAAAACAACAGCATCAACGAAACACTAACTGATGTCGATTATATGTAGATATCCATAATTCATG
260 ATAAAACAACAGCATCAACGAAACACTAACTAATGTCGATTATATGTAGATATCCATAATTCATG
*
498787 TACATGAATATTGTAAAATATGACAATGGAGCCAAAATAAAAAGAAAAGAAAATTGATATAAAAC
325 TACATGAATATTGTAAAATATGACAATGGAGCCAAAAGAAAAAGAAAAGAAAATTGATATAAAAC
498852 GTATTCATGTTACAATGTATAATAAAGTAAGACGGGTGTGGAATTGTTCATGGAATGGTTTATTT
390 GTATTCATGTTACAATGTATAATAAAGTAAGACGGGTGTGGAATTGTTCATGGAATGGTTTATTT
498917 GAGAAAAAAACTACACGTATGCAATCAATATTATAT
455 GAGAAAAAAACTACACGTATGCAATCAATATTATAT
498953 GGCAATAACA
Statistics
Matches: 481, Mismatches: 9, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
491 33 0.07
492 448 0.93
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (490 bp):
AACGGGCCATCTACTGCGTTTCACTCTCTTCTGAAATCGTTTGGTGGCGATCGATCAGACAACAA
GAACTACGTGATTCAGATGAAAGGTGACACAGTAGAATGGGCCGTGCCAACCGTTGAAGATCTAC
CAGGGGTAGGCCAAATTGCCGGCATCAAAACACATGACAGCACGGAAGATGACTTGAAAGATTTG
TATGTTGTGTTCGCTGGCGATGACAAATCGTCGGTGGTCTTTGGTATTCATTAGATACTAGTGGA
TAAAACAACAGCATCAACGAAACACTAACTAATGTCGATTATATGTAGATATCCATAATTCATGT
ACATGAATATTGTAAAATATGACAATGGAGCCAAAAGAAAAAGAAAAGAAAATTGATATAAAACG
TATTCATGTTACAATGTATAATAAAGTAAGACGGGTGTGGAATTGTTCATGGAATGGTTTATTTG
AGAAAAAAACTACACGTATGCAATCAATATTATAT
Found at i:502103 original size:126 final size:125
Alignment explanation
Indices: 501878--502128 Score: 493
Period size: 126 Copynumber: 2.0 Consensus size: 125
501868 ATTTATATCT
501878 TATAAACATCACATTAGAATTATATCTTAGTTTTTTTTAACCTATTCAAAACCATTAACTGAAAA
1 TATAAACATCACATTAGAATTATATCTTAGTTTTTTTTAACCTATTCAAAACCATTAACTGAAAA
501943 TTAGAAAGATAACTATAAGATCGTAGTCCAAGACATTTTCAAAAGATCTGACAGTGTGTG
66 TTAGAAAGATAACTATAAGATCGTAGTCCAAGACATTTTCAAAAGATCTGACAGTGTGTG
502003 NTATAAACATCACATTAGAATTATATCTTAGTTTTTTTTAACCTATTCAAAACCATTAACTGAAA
1 -TATAAACATCACATTAGAATTATATCTTAGTTTTTTTTAACCTATTCAAAACCATTAACTGAAA
502068 ATTAGAAAGATAACTATAAGATCGTAGTCCAAGACATTTTCAAAAGATCTGACAGTGTGTG
65 ATTAGAAAGATAACTATAAGATCGTAGTCCAAGACATTTTCAAAAGATCTGACAGTGTGTG
502129 CATGAATATC
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 125 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (125 bp):
TATAAACATCACATTAGAATTATATCTTAGTTTTTTTTAACCTATTCAAAACCATTAACTGAAAA
TTAGAAAGATAACTATAAGATCGTAGTCCAAGACATTTTCAAAAGATCTGACAGTGTGTG
Found at i:502556 original size:17 final size:18
Alignment explanation
Indices: 502534--502568 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
502524 TGATGATTTC
502534 TTTTTT-ACCTTATATGT
1 TTTTTTAACCTTATATGT
502551 TTTTTTAAACCTTATATG
1 TTTTTT-AACCTTATATG
502569 CTATGACCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60
Consensus pattern (18 bp):
TTTTTTAACCTTATATGT
Found at i:506632 original size:54 final size:54
Alignment explanation
Indices: 506550--506656 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
506540 GGTAGTTTTA
*
506550 ATGAAAAAATTAACTGGTACGTTAAAAAACAATCAATCAATCAATCAATCAATT
1 ATGAAAAAATTAACTGGGACGTTAAAAAACAATCAATCAATCAATCAATCAATT
506604 ATGAAAAAATTAACTGGGACGTTAAAAAACAATCAATCAATCAATCAATCAAT
1 ATGAAAAAATTAACTGGGACGTTAAAAAACAATCAATCAATCAATCAATCAAT
506657 CAATTAAATG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.24
Consensus pattern (54 bp):
ATGAAAAAATTAACTGGGACGTTAAAAAACAATCAATCAATCAATCAATCAATT
Found at i:506642 original size:4 final size:4
Alignment explanation
Indices: 506633--506660 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
506623 CGTTAAAAAA
506633 CAAT CAAT CAAT CAAT CAAT CAAT CAAT
1 CAAT CAAT CAAT CAAT CAAT CAAT CAAT
506661 TAAATGTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CAAT
Found at i:506912 original size:17 final size:17
Alignment explanation
Indices: 506892--506925 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
506882 TGATAAATGA
*
506892 AACGAGTTATCAAATTT
1 AACGAGTTAACAAATTT
506909 AACGAGTTAACAAATTT
1 AACGAGTTAACAAATTT
506926 TAAAAATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (17 bp):
AACGAGTTAACAAATTT
Found at i:508338 original size:15 final size:15
Alignment explanation
Indices: 508318--508348 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
508308 AATAACCCTT
508318 ATTATAAAAAAAAAA
1 ATTATAAAAAAAAAA
508333 ATTATAAAAAAAAAA
1 ATTATAAAAAAAAAA
508348 A
1 A
508349 GAAATTACAG
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
ATTATAAAAAAAAAA
Found at i:518464 original size:7 final size:7
Alignment explanation
Indices: 518452--518476 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
518442 GTTTTTAGAA
518452 CGCAGTT
1 CGCAGTT
518459 CGCAGTT
1 CGCAGTT
518466 CGCAGTT
1 CGCAGTT
518473 CGCA
1 CGCA
518477 ATTGAATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.32, G:0.28, T:0.24
Consensus pattern (7 bp):
CGCAGTT
Found at i:518548 original size:56 final size:57
Alignment explanation
Indices: 518477--518586 Score: 204
Period size: 58 Copynumber: 1.9 Consensus size: 57
518467 GCAGTTCGCA
518477 ATTGAATAGTGAACTGCGTTCTA-TAGAACGCAGTTCGCAATTCAAAATTTAGTTCG
1 ATTGAATAGTGAACTGCGTTCTACTAGAACGCAGTTCGCAATTCAAAATTTAGTTCG
518533 ATTGAATAGTGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAATTTAG
1 ATTGAATAGTGAACTGCGTTCTA-CTAGAACGCAGTTCGCAATTCAAAATTTAG
518587 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:0.19, T:0.32
Consensus pattern (57 bp):
ATTGAATAGTGAACTGCGTTCTACTAGAACGCAGTTCGCAATTCAAAATTTAGTTCG
Found at i:518680 original size:86 final size:86
Alignment explanation
Indices: 518533--518881 Score: 653
Period size: 86 Copynumber: 4.0 Consensus size: 86
518523 ATTTAGTTCG
*
518533 ATTGAATAGTGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATATTT
1 ATTGAATAGTGAACTGCGTTCTA--TAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATACTT
*
518598 GGGGCCCGATTGCCTTATATGCA
64 GGGGCCCGCTTGCCTTATATGCA
*
518621 ATTGAATAGTGAACTGCGTTCTATAGAATGCAGTTCGCAATTCAAAATTTAGAATTCATACTTGG
1 ATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATACTTGG
518686 GGCCCGCTTGCCTTATATGCA
66 GGCCCGCTTGCCTTATATGCA
518707 ATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATACTTGG
1 ATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATACTTGG
518772 GGCCCGCTTGCCTTATATGCA
66 GGCCCGCTTGCCTTATATGCA
518793 ATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATACTTGG
1 ATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATACTTGG
518858 GGCCCGCTTGCCTTATATGCA
66 GGCCCGCTTGCCTTATATGCA
518879 ATT
1 ATT
518882 NNNNNNNNNN
Statistics
Matches: 257, Mismatches: 4, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
86 234 0.91
88 23 0.09
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (86 bp):
ATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATACTTGG
GGCCCGCTTGCCTTATATGCA
Found at i:528804 original size:14 final size:13
Alignment explanation
Indices: 528784--528819 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
528774 TTTTTGCATT
528784 TTTAATTTTTAGG
1 TTTAATTTTTAGG
*
528797 TTTAAATTTTTTGG
1 TTT-AATTTTTAGG
528811 TTTAATTTT
1 TTTAATTTT
528820 GCGTTTCACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (13 bp):
TTTAATTTTTAGG
Found at i:545590 original size:20 final size:22
Alignment explanation
Indices: 545561--545610 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
545551 AATACAAATA
545561 TCTT-ATATCAGAAA-ATGAAT
1 TCTTGATATCAGAAATATGAAT
*
545581 T-TTGATATCAGAAATTTGAAT
1 TCTTGATATCAGAAATATGAAT
545602 TCTTGATAT
1 TCTTGATAT
545611 TATAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 2 0.08
20 11 0.42
21 6 0.23
22 7 0.27
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (22 bp):
TCTTGATATCAGAAATATGAAT
Found at i:548960 original size:12 final size:12
Alignment explanation
Indices: 548943--548967 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
548933 ATAAATATCT
548943 AATTATTATATA
1 AATTATTATATA
548955 AATTATTATATA
1 AATTATTATATA
548967 A
1 A
548968 TTGGAAAGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTATTATATA
Found at i:555142 original size:12 final size:12
Alignment explanation
Indices: 555106--555144 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
555096 TTCACTTATG
*
555106 TTTTTAATGCAA
1 TTTTTAATTCAA
*
555118 TTTCTTAAGTCAA
1 TTT-TTAATTCAA
555131 TTTTTAATTCAA
1 TTTTTAATTCAA
555143 TT
1 TT
555145 GCATTAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.54
Consensus pattern (12 bp):
TTTTTAATTCAA
Found at i:565430 original size:165 final size:165
Alignment explanation
Indices: 565125--565518 Score: 436
Period size: 165 Copynumber: 2.4 Consensus size: 165
565115 ATGCATAATA
* * *
565125 ATCTCACAAACTGTAGCATTATAGTTCTCGAGAAAAA-ACTTTTTAATAACATTTTCAATATATC
1 ATCTCACAAACTGAAGCATTATAGTTCTCGAGAAAAAGA-TTTTT-A-AACATTTTCCATATATA
* * * * *
565189 TTTCTATGTTAAACTTTGAACCCCTCTTGGGGCCACAGTATTAGTCCAGGGCTAAAGTTTTAATT
63 TTTCTATGCTAAACTTTGAACACCTCTTGGGGCCACAGTATTAGTCCAAGACTAAAGTTTTAATA
* * *
565254 ATTTGGAATCTACATTATTCAAGGATGCTTGCATAGTT
128 ATTTCGAATCTACACTATTCAAGGATGCTTACATAGTT
* * * * * *
565292 ATCTCACAAGCTGAAGCATTATAGTTCCCTAGAAAAAGATTTTTCAACATTTTCCCTCTATATTT
1 ATCTCACAAACTGAAGCATTATAGTTCTCGAGAAAAAGATTTTTAAACATTTTCCATATATATTT
* ** **
565357 CTATGCTAAACTTTGAACACCTCTTGGGGCCCCAGTATTAGATTGAAGAC-ACGGCTTTT-ATAA
66 CTATGCTAAACTTTGAACACCTCTTGGGGCCACAGTATTAG-TCCAAGACTAAAG-TTTTAATAA
** * *
565420 TTTCGAATCTACACTATTTGAGGGTGCTTACGTAGTT
129 TTTCGAATCTACACTATTCAAGGATGCTTACATAGTT
* * * *
565457 ATCTGACAAATTGATGCATTGTAGTTCTCGA-AAAGAAGATTTTTAAACATTTTCCATATATA
1 ATCTCACAAACTGAAGCATTATAGTTCTCGAGAAA-AAGATTTTTAAACATTTTCCATATATA
565519 CTGGTACTTC
Statistics
Matches: 187, Mismatches: 36, Indels: 10
0.80 0.15 0.04
Matches are distributed among these distances:
164 3 0.02
165 137 0.73
166 8 0.04
167 38 0.20
168 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (165 bp):
ATCTCACAAACTGAAGCATTATAGTTCTCGAGAAAAAGATTTTTAAACATTTTCCATATATATTT
CTATGCTAAACTTTGAACACCTCTTGGGGCCACAGTATTAGTCCAAGACTAAAGTTTTAATAATT
TCGAATCTACACTATTCAAGGATGCTTACATAGTT
Found at i:566614 original size:332 final size:332
Alignment explanation
Indices: 566070--566985 Score: 1489
Period size: 332 Copynumber: 2.8 Consensus size: 332
566060 GGTCACGATT
* * * ** * *
566070 TTTACAATCTTCACTATGTATACAACCTTTTGTGTATGTATTGGCATTTTTGGTGAAGTGGTTCT
1 TTTAAAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT
* * *
566135 TGAGAAGAAAATTTTTAAACATTTTTCATATGTAGTTCTATGTTAAACTTTGAACCCCGCCTGGG
66 TGAGAAGAAGATTTTTAAACA-TTTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCCTGGG
* * * *
566200 GCCCCAGTCTTGGTCCGAGGGTCACGATTTCTACAATTTAGAATCTTCATTATACATACAAGCTT
130 GCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAAGCTT
* * * * *
566265 TTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTGAGAACAACATTTTTTAAACATTTT-CC
195 TTGTGTAAATATTGGCATTTCTGGTGCTGTGGTTCTTGAGAAGAAGATTTTTAAAAAATTTTCCC
*
566329 TAAGGTAT-TTCTATGTTAAACTTTGAACCCCGCCTGGGGCCCCAGTCTTGGTCCGAGGGGCACG
260 T-AGGT-TGTTCTATGTTAAACTTTGAACCCCGCCTGGGGCCCCAGTCTTGGTCCGAGGGGCACC
566393 ATTTTTACAA
323 ATTTTTACAA
566403 TTTAAAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT
1 TTTAAAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT
* *
566468 TGAGAAGAAGATTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTAAACCCCGCTTGGGG
66 TGAGAAGAAGATTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCCTGGGG
*
566533 CCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAAAATCTTCACTATATATACAAGCTTT
131 CCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAAGCTTT
566598 TGTGTAAATATTGGCATTTCTGGTGCTGTGGTTCTTGAGAAGAAGATTTTTAAAAAATTTTCCCT
196 TGTGTAAATATTGGCATTTCTGGTGCTGTGGTTCTTGAGAAGAAGATTTTTAAAAAATTTTCCCT
* * *
566663 ATGTTGTTCTATGTTAAACTTTGAACCCCGCCTGGGGCCCCAGTTTTGGTCCGAGGGTCACCATT
261 AGGTTGTTCTATGTTAAACTTTGAACCCCGCCTGGGGCCCCAGTCTTGGTCCGAGGGGCACCATT
566728 TTTACAA
326 TTTACAA
*
566735 TTTAGAATCTTCACTATATATGA-AAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTC
1 TTTAAAATCTTCACTATATAT-ACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTC
*
566799 TTGAGAAGAAGATTTTTAAAAAATTTTCCATATGT-TGTTCTATGTTAAACTTTGAACCCCGCCT
65 TTGAGAAGAAGATTTTT-AAACATTTTCC-TATGTAT-TTCTATGTTAAACTTTGAACCCCGCCT
566863 GGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAAG
127 GGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAAG
566928 CTTTTGTGTAAATATTGGCATTTCTGGTGCTGTGGTTCTTGAGAAGAAGATTTTTAAA
192 CTTTTGTGTAAATATTGGCATTTCTGGTGCTGTGGTTCTTGAGAAGAAGATTTTTAAA
566986 GACATGCACC
Statistics
Matches: 546, Mismatches: 31, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
331 1 0.00
332 300 0.55
333 93 0.17
334 152 0.28
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (332 bp):
TTTAAAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT
TGAGAAGAAGATTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCCTGGGG
CCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAAGCTTT
TGTGTAAATATTGGCATTTCTGGTGCTGTGGTTCTTGAGAAGAAGATTTTTAAAAAATTTTCCCT
AGGTTGTTCTATGTTAAACTTTGAACCCCGCCTGGGGCCCCAGTCTTGGTCCGAGGGGCACCATT
TTTACAA
Done.