Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold419
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: 1725835
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 213561 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:4679 original size:16 final size:15
Alignment explanation
Indices: 4642--4679 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
4632 TAAGTTTTAA
4642 TATTAAATTTAGATT
1 TATTAAATTTAGATT
4657 TATTAAATTTTAG-TT
1 TATTAAA-TTTAGATT
4672 TATATAAA
1 TAT-TAAA
4680 GTGACCGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (15 bp):
TATTAAATTTAGATT
Found at i:35457 original size:21 final size:21
Alignment explanation
Indices: 35431--35488 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
35421 TAAGCACCTT
35431 TATATATAAAGGAATTGCCAA
1 TATATATAAAGGAATTGCCAA
*
35452 TATATATAAAGGAATTACCAA
1 TATATATAAAGGAATTGCCAA
35473 TATATATAAA-GAATTG
1 TATATATAAAGGAATTG
35489 TGTACACATG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 5 0.14
21 30 0.86
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (21 bp):
TATATATAAAGGAATTGCCAA
Found at i:37052 original size:23 final size:21
Alignment explanation
Indices: 36994--37051 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
36984 ATGTGTACAC
36994 AATT-CTTTATATATATTGGT
1 AATTCCTTTATATATATTGGT
37014 AATTCCTTTATATATATTGGT
1 AATTCCTTTATATATATTGGT
37035 AATTCCTTTATATATAT
1 AATTCCTTTATATATAT
37052 AAAGGTGCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.11
21 33 0.89
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.53
Consensus pattern (21 bp):
AATTCCTTTATATATATTGGT
Found at i:37885 original size:2 final size:2
Alignment explanation
Indices: 37878--37911 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
37868 TAGAAGGTAT
*
37878 AC AC AC AC AC AC AC AC AC AC AC AA AC AC -C AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
37912 GATGGGGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:45560 original size:2 final size:2
Alignment explanation
Indices: 45553--45609 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
45543 GGACCAACAC
45553 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
45595 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
45610 TTCTTGCAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:46782 original size:2 final size:2
Alignment explanation
Indices: 46775--46820 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
46765 TGTGGCAGTC
46775 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
46817 AG AG
1 AG AG
46821 CGGCAGGAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:51584 original size:177 final size:176
Alignment explanation
Indices: 51288--51640 Score: 697
Period size: 177 Copynumber: 2.0 Consensus size: 176
51278 TCACGCACAT
51288 TAATGAAATCAGTATTTTGGGGAGTAAAGCACATTCTATATCACAAATGGTGCTGAATTGGCTTG
1 TAATGAAATCAGTATTTTGGGGAGTAAAGCACATTCTATATCACAAATGGTGCTGAATTGGCTTG
51353 CCGAATCATTTATACTTCTAGACTGAGTACTTACAAGGTCTATATTTGCGTTGGCATTCTGTAAT
66 CCGAATCATTTATACTTCTAGACTGAGTACTTACAAGGTCTATATTTGCGTTGGCATTCTGTAAT
51418 TCGATGTAAGCTTTCTCAGGTAGAGCGACATGACCAGTCGTGACCA
131 TCGATGTAAGCTTTCTCAGGTAGAGCGACATGACCAGTCGTGACCA
51464 NTAATGAAATCAGTATTTTGGGGAGTAAAGCACATTCTATATCACAAATGGTGCTGAATTGGCTT
1 -TAATGAAATCAGTATTTTGGGGAGTAAAGCACATTCTATATCACAAATGGTGCTGAATTGGCTT
51529 GCCGAATCATTTATACTTCTAGACTGAGTACTTACAAGGTCTATATTTGCGTTGGCATTCTGTAA
65 GCCGAATCATTTATACTTCTAGACTGAGTACTTACAAGGTCTATATTTGCGTTGGCATTCTGTAA
51594 TTCGATGTAAGCTTTCTCAGGTAGAGCGACATGACCAGTCGTGACCA
130 TTCGATGTAAGCTTTCTCAGGTAGAGCGACATGACCAGTCGTGACCA
51641 GCGCCATTTT
Statistics
Matches: 176, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
177 176 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (176 bp):
TAATGAAATCAGTATTTTGGGGAGTAAAGCACATTCTATATCACAAATGGTGCTGAATTGGCTTG
CCGAATCATTTATACTTCTAGACTGAGTACTTACAAGGTCTATATTTGCGTTGGCATTCTGTAAT
TCGATGTAAGCTTTCTCAGGTAGAGCGACATGACCAGTCGTGACCA
Found at i:65192 original size:104 final size:104
Alignment explanation
Indices: 65012--65220 Score: 418
Period size: 104 Copynumber: 2.0 Consensus size: 104
65002 NNNNNNNNNN
65012 ACGGTACAACAGATGAATGTACTTCCTGAGAAATCAACGCCCTGTGGTTGTTTCTTATACCCCTG
1 ACGGTACAACAGATGAATGTACTTCCTGAGAAATCAACGCCCTGTGGTTGTTTCTTATACCCCTG
65077 GGGAGAGAATGTCTTTTACCCTTGCGTCACAAACTTAAA
66 GGGAGAGAATGTCTTTTACCCTTGCGTCACAAACTTAAA
65116 ACGGTACAACAGATGAATGTACTTCCTGAGAAATCAACGCCCTGTGGTTGTTTCTTATACCCCTG
1 ACGGTACAACAGATGAATGTACTTCCTGAGAAATCAACGCCCTGTGGTTGTTTCTTATACCCCTG
65181 GGGAGAGAATGTCTTTTACCCTTGCGTCACAAACTTAAA
66 GGGAGAGAATGTCTTTTACCCTTGCGTCACAAACTTAAA
65220 A
1 A
65221 ACAGTTGTAC
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 105 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (104 bp):
ACGGTACAACAGATGAATGTACTTCCTGAGAAATCAACGCCCTGTGGTTGTTTCTTATACCCCTG
GGGAGAGAATGTCTTTTACCCTTGCGTCACAAACTTAAA
Found at i:72145 original size:18 final size:18
Alignment explanation
Indices: 72090--72156 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 18
72080 ATTTGATCAC
*
72090 ATAATACAATATCATAAAAT
1 ATAATACAATATCAT--ATT
72110 ATAATACAATAT-AGTATT
1 ATAATACAATATCA-TATT
*
72128 ATATTACAATATCATATT
1 ATAATACAATATCATATT
72146 ACATAATACAA
1 --ATAATACAA
72157 CATAACATTG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 17 0.43
19 2 0.05
20 21 0.52
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (18 bp):
ATAATACAATATCATATT
Found at i:74544 original size:43 final size:43
Alignment explanation
Indices: 74495--74581 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
74485 AAACAAGTTT
*
74495 ATAAATCCATCTTCTGTATAAAATTATGGAATGAAAAACAATC
1 ATAAATCCATCTTCTGTACAAAATTATGGAATGAAAAACAATC
* * *
74538 ATAAATCCATTTTCTGTACAATATTATGGAATTAAAAACAATC
1 ATAAATCCATCTTCTGTACAAAATTATGGAATGAAAAACAATC
74581 A
1 A
74582 ATTAAAATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (43 bp):
ATAAATCCATCTTCTGTACAAAATTATGGAATGAAAAACAATC
Found at i:74604 original size:54 final size:55
Alignment explanation
Indices: 74539--74711 Score: 172
Period size: 60 Copynumber: 2.9 Consensus size: 55
74529 AAAACAATCA
* *
74539 TAAATCCATTTTCTGTA-C-AATA-TTATGGAATTAAAAACAATCAATTAAAATTCC
1 TAAATTCATTTTCTGTACCAAATACTTA-GG-ATTAAAAACAATCAATTAAAATACC
74593 TAAATTCATTTTCTGTTTACCAGGAAATACTTAGGATTAAAAACAATCAATTAAAATACC
1 TAAATTCATTTTCTG--TACC---AAATACTTAGGATTAAAAACAATCAATTAAAATACC
*
74653 TAAATTCATTTTCTGTTTACCAGGTAATACTTAGGATTAAAAAAAAAATCAATTAAAAT
1 TAAATTCATTTTCTG--TACCA---AATACTTAGGATT--AAAAACAATCAATTAAAAT
74712 TCATAAATCC
Statistics
Matches: 103, Mismatches: 3, Indels: 18
0.83 0.02 0.15
Matches are distributed among these distances:
54 14 0.14
56 2 0.02
57 2 0.02
60 58 0.56
61 6 0.06
62 21 0.20
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.35
Consensus pattern (55 bp):
TAAATTCATTTTCTGTACCAAATACTTAGGATTAAAAACAATCAATTAAAATACC
Found at i:74641 original size:60 final size:60
Alignment explanation
Indices: 74568--74728 Score: 250
Period size: 60 Copynumber: 2.6 Consensus size: 60
74558 ATATTATGGA
74568 ATTAAAAACAATCAATTAAAATTCCTAAATTCATTTTCTGTTTACCAGGAAATACTTAGG
1 ATTAAAAACAATCAATTAAAATTCCTAAATTCATTTTCTGTTTACCAGGAAATACTTAGG
* *
74628 ATTAAAAACAATCAATTAAAATACCTAAATTCATTTTCTGTTTACCAGGTAATACTTAGG
1 ATTAAAAACAATCAATTAAAATTCCTAAATTCATTTTCTGTTTACCAGGAAATACTTAGG
* * * *
74688 ATTAAAAAAAAAATCAATTAAAATTCATAAATCCATCTTCT
1 ATT--AAAAACAATCAATTAAAATTCCTAAATTCATTTTCT
74729 ATACCGGTAT
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
60 61 0.66
62 31 0.34
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (60 bp):
ATTAAAAACAATCAATTAAAATTCCTAAATTCATTTTCTGTTTACCAGGAAATACTTAGG
Found at i:76545 original size:16 final size:16
Alignment explanation
Indices: 76526--76557 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
76516 ATTTCACACA
*
76526 GTTTTTCTGTCAGACT
1 GTTTTCCTGTCAGACT
76542 GTTTTCCTGTCAGACT
1 GTTTTCCTGTCAGACT
76558 CCAGGTTGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.47
Consensus pattern (16 bp):
GTTTTCCTGTCAGACT
Found at i:83431 original size:53 final size:50
Alignment explanation
Indices: 83331--83463 Score: 124
Period size: 53 Copynumber: 2.6 Consensus size: 50
83321 ATATCTGCAG
* * * * * *
83331 GTGCATCTCAATGTGTATTGACATAAAAATGTCTCATAATTAAAATACATGTC
1 GTGCATCTCAATGCGAAATAACATAAAAATGTCTCACAACTAAAATACA---C
* **
83384 GTGCATCTCAATGCGAAATAACATAAAAATGTCTCGCAACTGCAATACAC
1 GTGCATCTCAATGCGAAATAACATAAAAATGTCTCACAACTAAAATACAC
* *
83434 GTGCATTTCAATGCTAAA-ACACATAAAAAT
1 GTGCATCTCAATGCGAAATA-ACATAAAAAT
83464 CTGTCATAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
49 1 0.01
50 27 0.40
53 40 0.59
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.28
Consensus pattern (50 bp):
GTGCATCTCAATGCGAAATAACATAAAAATGTCTCACAACTAAAATACAC
Found at i:91748 original size:2 final size:2
Alignment explanation
Indices: 91741--91773 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
91731 ATTATGCAAT
91741 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
91774 TCTTGCATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:98949 original size:24 final size:24
Alignment explanation
Indices: 98922--98992 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 24
98912 ATTATGAAAA
98922 GTTAGTAAAATTCACTAAATTACT
1 GTTAGTAAAATTCACTAAATTACT
* * *
98946 G-T--T--AATGCACAAAAGTAC-
1 GTTAGTAAAATTCACTAAATTACT
98964 GTTAGCTAAAATTCACTAAATTACT
1 GTTAG-TAAAATTCACTAAATTACT
98989 GTTA
1 GTTA
98993 ATGCACAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 13
0.64 0.11 0.25
Matches are distributed among these distances:
18 1 0.03
19 13 0.38
21 1 0.03
22 1 0.03
23 1 0.03
24 13 0.38
25 4 0.12
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (24 bp):
GTTAGTAAAATTCACTAAATTACT
Found at i:98977 original size:43 final size:43
Alignment explanation
Indices: 98922--99017 Score: 185
Period size: 43 Copynumber: 2.3 Consensus size: 43
98912 ATTATGAAAA
98922 GTTAG-TAAAATTCACTAAATTACTGTTAATGCACAAAAGTAC
1 GTTAGCTAAAATTCACTAAATTACTGTTAATGCACAAAAGTAC
98964 GTTAGCTAAAATTCACTAAATTACTGTTAATGCACAAAAGTAC
1 GTTAGCTAAAATTCACTAAATTACTGTTAATGCACAAAAGTAC
99007 GTTAGCTAAAA
1 GTTAGCTAAAA
99018 GAAACAGCCA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 5 0.09
43 48 0.91
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (43 bp):
GTTAGCTAAAATTCACTAAATTACTGTTAATGCACAAAAGTAC
Found at i:100621 original size:2 final size:2
Alignment explanation
Indices: 100616--100659 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
100606 AAAAATTGGT
100616 TC 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 TC
100658 TC
1 TC
100660 CGATTTACAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:111159 original size:180 final size:180
Alignment explanation
Indices: 110855--111215 Score: 643
Period size: 180 Copynumber: 2.0 Consensus size: 180
110845 GGCTGCCAAA
* *
110855 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACAGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
* *
110920 GATCAATTGTGCATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCAATAATTTAT-AG
66 GATCAATTGTACATATATAAGAGGTGTGCATATTGCTAGGATTTTGATTTCCAATAATTTATGA-
110984 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
130 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
111035 AGGGTACCCTCATTGTACAGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACAGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
* *
111100 GATTAATTGTACATATATAAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATGAA
66 GATCAATTGTACATATATAAGAGGTGTGCATATTGCTAGGATTTTGATTTCCAATAATTTATGAA
*
111165 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATGTTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
111215 A
1 A
111216 CATGTAGGGT
Statistics
Matches: 173, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
180 172 0.99
181 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (180 bp):
AGGGTACCCTCATTGTACAGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
GATCAATTGTACATATATAAGAGGTGTGCATATTGCTAGGATTTTGATTTCCAATAATTTATGAA
AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
Found at i:112235 original size:32 final size:34
Alignment explanation
Indices: 112168--112237 Score: 92
Period size: 37 Copynumber: 2.1 Consensus size: 34
112158 CATGTACTAC
112168 ATATTTTTTTTAATCAACCACAATCTATAATATAAG
1 ATATTTTTTTTAATCAACCACAA--TATAATATAAG
112204 ATATTTTCTTTTAATCAACCA-AA-AT-ATATAAG
1 ATATTTT-TTTTAATCAACCACAATATAATATAAG
112236 AT
1 AT
112238 TTGATGAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
32 9 0.27
33 2 0.06
36 9 0.27
37 13 0.39
ACGTcount: A:0.43, C:0.13, G:0.03, T:0.41
Consensus pattern (34 bp):
ATATTTTTTTTAATCAACCACAATATAATATAAG
Found at i:116602 original size:27 final size:27
Alignment explanation
Indices: 116564--116616 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
116554 CCAAAGAAAC
*
116564 CATATTGTTTAACCAGAAAAATTATTA
1 CATAATGTTTAACCAGAAAAATTATTA
* *
116591 CATAATGTTTAACCTGAGAAATTATT
1 CATAATGTTTAACCAGAAAAATTATT
116617 GAATTATACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (27 bp):
CATAATGTTTAACCAGAAAAATTATTA
Found at i:116665 original size:42 final size:42
Alignment explanation
Indices: 116619--116761 Score: 99
Period size: 42 Copynumber: 3.1 Consensus size: 42
116609 AAATTATTGA
116619 ATTATACTTAAACAGAGATTGCTTAACCAAAGAAATCATTAC
1 ATTATACTTAAACAGAGATTGCTTAACCAAAGAAATCATTAC
** * ** *
116661 ATTATGTTTAACCAGAGAAATTATTGCATAATGTTTAACCCTAGAAATTATTGA-
1 ATTATACTTAAACAGAG-----ATTGC-------TTAACCAAAGAAATCATT-AC
*
116715 ATTATAGTTAAACAGAGATTGCTTAACCAAAGAAATCATTAC
1 ATTATACTTAAACAGAGATTGCTTAACCAAAGAAATCATTAC
116757 ATTAT
1 ATTAT
116762 GTTTAACCAA
Statistics
Matches: 75, Mismatches: 12, Indels: 28
0.65 0.10 0.24
Matches are distributed among these distances:
41 1 0.01
42 34 0.45
47 5 0.07
49 5 0.07
54 29 0.39
55 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (42 bp):
ATTATACTTAAACAGAGATTGCTTAACCAAAGAAATCATTAC
Found at i:116706 original size:27 final size:27
Alignment explanation
Indices: 116641--116713 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
116631 CAGAGATTGC
* * * *
116641 TTAACCAAAGAAATCATTACATTATGT
1 TTAACCAGAGAAATTATTGCATAATGT
116668 TTAACCAGAGAAATTATTGCATAATGT
1 TTAACCAGAGAAATTATTGCATAATGT
**
116695 TTAACCCTAGAAATTATTG
1 TTAACCAGAGAAATTATTG
116714 AATTATAGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (27 bp):
TTAACCAGAGAAATTATTGCATAATGT
Found at i:116707 original size:96 final size:97
Alignment explanation
Indices: 116569--116795 Score: 386
Period size: 96 Copynumber: 2.4 Consensus size: 97
116559 GAAACCATAT
*
116569 TGTTTAACCAGAAAAATTATTACATAATGTTTAA-CCTGAGAAATTATTGAATTATACTTAAACA
1 TGTTTAACCAGAGAAATTATTACATAATGTTTAACCCTGAGAAATTATTGAATTATACTTAAACA
116633 GAGATTGCTTAACCAAAGAAATCATTACATTA
66 GAGATTGCTTAACCAAAGAAATCATTACATTA
* *
116665 TGTTTAACCAGAGAAATTATTGCATAATGTTTAACCCT-AGAAATTATTGAATTATAGTTAAACA
1 TGTTTAACCAGAGAAATTATTACATAATGTTTAACCCTGAGAAATTATTGAATTATACTTAAACA
116729 GAGATTGCTTAACCAAAGAAATCATTACATTA
66 GAGATTGCTTAACCAAAGAAATCATTACATTA
* * *
116761 TGTTTAACCAAAGAAATCATTACATTATGTTTAAC
1 TGTTTAACCAGAGAAATTATTACATAATGTTTAAC
116796 TAGAAGGCGC
Statistics
Matches: 123, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
96 120 0.98
97 3 0.02
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (97 bp):
TGTTTAACCAGAGAAATTATTACATAATGTTTAACCCTGAGAAATTATTGAATTATACTTAAACA
GAGATTGCTTAACCAAAGAAATCATTACATTA
Found at i:116775 original size:27 final size:27
Alignment explanation
Indices: 116737--116795 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
116727 CAGAGATTGC
116737 TTAACCAAAGAAATCATTACATTATGT
1 TTAACCAAAGAAATCATTACATTATGT
116764 TTAACCAAAGAAATCATTACATTATGT
1 TTAACCAAAGAAATCATTACATTATGT
116791 TTAAC
1 TTAAC
116796 TAGAAGGCGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (27 bp):
TTAACCAAAGAAATCATTACATTATGT
Found at i:120326 original size:15 final size:16
Alignment explanation
Indices: 120308--120345 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
120298 CACTCGATGG
120308 CTCGAACTTC-GATCT
1 CTCGAACTTCTGATCT
*
120323 CTCGAAGTTCTTGATCT
1 CTCGAACTTC-TGATCT
120340 CTCGAA
1 CTCGAA
120346 GTGAACTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
17 11 0.55
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (16 bp):
CTCGAACTTCTGATCT
Found at i:120434 original size:17 final size:17
Alignment explanation
Indices: 120395--120443 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
120385 GCAAATTTAC
*
120395 TCTTGATCTCTCGAA-C
1 TCTTGATCTCTCGAAGT
*
120411 TC-CGATCTCTCGAAGT
1 TCTTGATCTCTCGAAGT
120427 TCTTGATCTCTCGAAGT
1 TCTTGATCTCTCGAAGT
120444 AAAACCTGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.39
16 4 0.14
17 13 0.46
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.37
Consensus pattern (17 bp):
TCTTGATCTCTCGAAGT
Found at i:125049 original size:436 final size:437
Alignment explanation
Indices: 123239--125089 Score: 2695
Period size: 437 Copynumber: 4.2 Consensus size: 437
123229 ATCTTTCAGC
* * *
123239 TGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTA-GGGACCTAGAGGGCTCTTAAA-TCTTTTA
1 TGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGA-CAAAAAGGCTC-TAAAGTCTTTTA
* * * * * * *
123302 CCCGTAACTCTTTACCGAGGGATATTTTGT--AATAGATTATAGAAGCAAATATGTTTTATCTCA
64 TCTGTAGCCCTTTACTGAGAGATATTTTGTGAAAT-G-TTATAGAAGCAAATGTG-TTTATCTCA
* * * * * *
123365 ATGTTATTTAGTCAAGCAATGTAATGATTTTATTATGTGCTATGTAATTAAGGGTTTTTAGGGGT
126 ATGTTATGTATTCAAGCAATGTAATGATTTTATCATGTGTTACGTAATTAAGGGTTTTTAGGGGC
* *
123430 CAAAAGTCCAAAACTTCGATCACCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAGTACAAA
191 CAAAAGTCCAAAATTTTGATCACCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAGTACAAA
* * * *
123495 AGAAAAGTTGTTCAAAATGATGTTCTTACCAAAATGCAACCGTCAAAATTTCGTTAAACGACCCC
256 AGAAAAGTTGTTCAAAATGATGTTCTCAACAAAATGCAACCTTCAAAATTTCGTTAAACGGCCCC
* *
123560 TAAAAGGAGATAAGGGACCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAGAACGGTAACGAA
321 TATAAGGAGATAAGGGATCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAGAACGGTAACGAA
* * *
123625 TTTCTAAACACTTGTTTAACAAATTTTGTGTAGAATTAAATGACCTTTTATT
386 TTTCTAAACACTTGTTTAACAAAATGTGTGTAGAATTAAATGACCTTTCATT
* *
123677 TGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACAAAAAGGCTCTAAAGTCTCTAATC
1 TGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACAAAAAGGCTCTAAAGTCTTTTATC
*
123742 TGTAGCCCTTTACTGAGAGATATTATGTGAAATGTTATAGAAGCAAATGTGTTTATCTCAATGTT
66 TGTAGCCCTTTACTGAGAGATATTTTGTGAAATGTTATAGAAGCAAATGTGTTTATCTCAATGTT
123807 ATGTATTCAAGCAATGTAATGATTTTATCATGTGTTACGTAATTAAGGGTTTTTAGGGGCCAAAA
131 ATGTATTCAAGCAATGTAATGATTTTATCATGTGTTACGTAATTAAGGGTTTTTAGGGGCCAAAA
* *
123872 GTCCAAAATTTTGATCACCCATATCTCAGAAAGGAAATATATTTTGTAATGCAGTACAGAAGAAA
196 GTCCAAAATTTTGATCACCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAGTACAAAAGAAA
* * * * *
123937 AGTTGTTTAAAATGATGTTCTTACCAAAATGCAACCTTCAAAATTTCGTTAAATGGCCCTTATAA
261 AGTTGTTCAAAATGATGTTCTCAACAAAATGCAACCTTCAAAATTTCGTTAAACGGCCCCTATAA
*
124002 GGAGATAAGGGATCGGCCCCTAAAACTTTCTTTCTCATATATCTCCAGAACGGTAACGAATTTCT
326 GGAGATAAGGGATCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAGAACGGTAACGAATTTCT
* * *
124067 AAACACTTGTTTAACAAATTTTGTGTAGAATTAAATGACCTTTTATT
391 AAACACTTGTTTAACAAAATGTGTGTAGAATTAAATGACCTTTCATT
* * *
124114 TGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGAGGACAAAAAGGCTCTAAAGTCTCTAATC
1 TGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACAAAAAGGCTCTAAAGTCTTTTATC
*
124179 TGTAGCCCTTTACTGAGAGATATTATGTGAAATGTTATAGAAGCAAATGTGTTTATCTCAATGTT
66 TGTAGCCCTTTACTGAGAGATATTTTGTGAAATGTTATAGAAGCAAATGTGTTTATCTCAATGTT
*
124244 ATGTATTCAAGCAATGTAATGATTTTATCATGTGTTATGTAATTAAGGGTTTTTAGGGGCCAAAA
131 ATGTATTCAAGCAATGTAATGATTTTATCATGTGTTACGTAATTAAGGGTTTTTAGGGGCCAAAA
* *
124309 ATCCAAAATTTTGATCACCCATATCTCAGAAAGAAAAAAATATTTTGTAATGCAGTACAAAAGAA
196 GTCCAAAATTTTGATCACCCATATCTCAGAAAG-GAAAAATATTTTGTAATGCAGTACAAAAGAA
*
124374 AAGTTGTTCAAAATGATGTTCTCAACAAAATGCAACCTTCAAAAATTCGTTAAACGGCCCCTATA
260 AAGTTGTTCAAAATGATGTTCTCAACAAAATGCAACCTTCAAAATTTCGTTAAACGGCCCCTATA
* *
124439 AGGAGTTATGGGATCGGCCCCTAAAACCTTCTTT-TCATATATCTCCAGAACGGTAACGAATTTC
325 AGGAGATAAGGGATCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAGAACGGTAACGAATTTC
*
124503 TAAACACTTGTTGAACAAAATGTGT-TCAGAATTAAAT-ATCCTTTCATT
390 TAAACACTTGTTTAACAAAATGTGTGT-AGAATTAAATGA-CCTTTCATT
* * * * * * *
124551 TAATATCAAGAAAAAAGGACTGGCCCCTAAAATTAGGGGACCAAAGGGCTCTAAGGTCTTTTATC
1 TGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACAAAAAGGCTCTAAAGTCTTTTATC
* * * * * *
124616 TATAACCCTTTATTGAGGGATATTTTGTGAAATGTTATAGAAACAAATGTGTTTATCT-TATAGT
66 TGTAGCCCTTTACTGAGAGATATTTTGTGAAATGTTATAGAAGCAAATGTGTTTATCTCAAT-GT
* * * *
124680 TATGTA-TCAAAGCAATGTAATGATTTTATCATGTGTAACGTAATTAAGGGTTTTTACGGACCAG
130 TATGTATTC-AAGCAATGTAATGATTTTATCATGTGTTACGTAATTAAGGGTTTTTAGGGGCCAA
* *
124744 AAGTCCAAAATTTTGATCACCCATATCTCAGAAAGGAAATATATTTTGTAATGCAGTACAGAAGA
194 AAGTCCAAAATTTTGATCACCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAGTACAAAAGA
* * *
124809 AAAGTTGTTTAAAATGATGTTCTCAACAAAATGCAACCTTCAAAATTTCGTTAAATGGCCCTTAT
259 AAAGTTGTTCAAAATGATGTTCTCAACAAAATGCAACCTTCAAAATTTCGTTAAACGGCCCCTAT
124874 AAGGAGATAAGGGATCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAGAACGGTAACGAATTT
324 AAGGAGATAAGGGATCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAGAACGGTAACGAATTT
* *
124939 CTAAACACTTG-TTGACAAAATGTGT-TAAGAATTAAATGTCCTTTCATT
389 CTAAACACTTGTTTAACAAAATGTGTGT-AGAATTAAATGACCTTTCATT
** ** * *
124987 TGA-ATCCAAG-AAAAGGGGACTTCCCCCTTGAATTAGGGGATCAAAGA-GCTCTAAAATCTTTT
1 TGATAT-CAAGAAAAAGGGG-CTGGCCCCTCAAATTAGGGGA-CAAAAAGGCTCTAAAGTCTTTT
* * ** *
125049 ATCTATAGCCCTTTAATGAGAGCCATTTTGTGAAAGGTTAT
63 ATCTGTAGCCCTTTACTGAGAGATATTTTGTGAAATGTTAT
125090 TAAAGCTAGA
Statistics
Matches: 1295, Mismatches: 104, Indels: 30
0.91 0.07 0.02
Matches are distributed among these distances:
435 8 0.01
436 230 0.18
437 844 0.65
438 205 0.16
439 5 0.00
440 3 0.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (437 bp):
TGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACAAAAAGGCTCTAAAGTCTTTTATC
TGTAGCCCTTTACTGAGAGATATTTTGTGAAATGTTATAGAAGCAAATGTGTTTATCTCAATGTT
ATGTATTCAAGCAATGTAATGATTTTATCATGTGTTACGTAATTAAGGGTTTTTAGGGGCCAAAA
GTCCAAAATTTTGATCACCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAGTACAAAAGAAA
AGTTGTTCAAAATGATGTTCTCAACAAAATGCAACCTTCAAAATTTCGTTAAACGGCCCCTATAA
GGAGATAAGGGATCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAGAACGGTAACGAATTTCT
AAACACTTGTTTAACAAAATGTGTGTAGAATTAAATGACCTTTCATT
Found at i:139607 original size:2 final size:2
Alignment explanation
Indices: 139600--139665 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
139590 CCGTCAATAT
139600 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
*
139642 GA GA GA GA GA GA GA GA GA AA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA
139666 AAGAAAGATG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:144376 original size:2 final size:2
Alignment explanation
Indices: 144369--144413 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
144359 GGACGACGTA
144369 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
144411 CT C
1 CT C
144414 ATGTAAAAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:148595 original size:24 final size:24
Alignment explanation
Indices: 148567--149380 Score: 828
Period size: 24 Copynumber: 33.8 Consensus size: 24
148557 GTAGTCAGAC
*
148567 CTGTTACATTCAACTGGCAGGTAA
1 CTGTTACATTCAACTGACAGGTAA
148591 CTGTTACATTCAACTGACAGGTAA
1 CTGTTACATTCAACTGACAGGTAA
* * *
148615 CTGTTACATTCAACTGGCAGGGAC
1 CTGTTACATTCAACTGACAGGTAA
148639 CTGTTACATTCAACTGACAGGTAA
1 CTGTTACATTCAACTGACAGGTAA
* *
148663 CTTTTACATTCAACTGACAGGTAC
1 CTGTTACATTCAACTGACAGGTAA
*
148687 CTGTTACATTCAACTGGCAGGTAA
1 CTGTTACATTCAACTGACAGGTAA
* * *
148711 CTGTTACATTCAATTGGCAGGTAC
1 CTGTTACATTCAACTGACAGGTAA
* * *
148735 CTGTTACATTCAACGGACAGATAC
1 CTGTTACATTCAACTGACAGGTAA
148759 CTGTTACATTCAACTGACAGACGGTAA
1 CTGTTACATTCAACTGAC--A-GGTAA
* * *
148786 CTGTTACATTCAAGTGGCAGGTAC
1 CTGTTACATTCAACTGACAGGTAA
148810 CTGTTACATTCAACTGACAGGTAA
1 CTGTTACATTCAACTGACAGGTAA
* *
148834 CTTTTACATTCAACTGACAGGTAC
1 CTGTTACATTCAACTGACAGGTAA
148858 CTGTTACATTCAACTGACAGGTAA
1 CTGTTACATTCAACTGACAGGTAA
* *
148882 CTGTTACATTCAACTGGCAGGTAC
1 CTGTTACATTCAACTGACAGGTAA
148906 CTGTTACATTCAACTGACAGGTAA
1 CTGTTACATTCAACTGACAGGTAA
* * *
148930 CTGTTACATTCAATTGGCAGGTAC
1 CTGTTACATTCAACTGACAGGTAA
* *
148954 CTGTTACATTCAACTGACAGATAC
1 CTGTTACATTCAACTGACAGGTAA
*
148978 CTGTTACATTCAACTGTCAGGTAA
1 CTGTTACATTCAACTGACAGGTAA
*
149002 CTGTTACATTCAA-AGTACAGGTAA
1 CTGTTACATTCAACTG-ACAGGTAA
* * *
149026 GTTTTACATTCAACTGACATGTAA
1 CTGTTACATTCAACTGACAGGTAA
* * * *
149050 CTGTTACATTAAACTGACATGCAG
1 CTGTTACATTCAACTGACAGGTAA
* * *
149074 CTGTAACATTCAACTGACATGTGA
1 CTGTTACATTCAACTGACAGGTAA
* **
149098 CTGTAACACCCAACTGACAGGTAA
1 CTGTTACATTCAACTGACAGGTAA
*
149122 TTGTTACATTCAACT-----G--A
1 CTGTTACATTCAACTGACAGGTAA
149139 CTGTTACATTCAACTGACAGGTAA
1 CTGTTACATTCAACTGACAGGTAA
* * ** * * *
149163 CTGTAAAATTTTATTGACATGTTA
1 CTGTTACATTCAACTGACAGGTAA
* *
149187 CTGTTACTTTC-ACTCAACAGGTAA
1 CTGTTACATTCAACT-GACAGGTAA
* * * *
149211 -TAGTCACATTC-ACTCAACAGATTA
1 CT-GTTACATTCAACT-GACAGGTAA
149235 -TGATTACATTCAACTGACAGGCAACATGTAA
1 CTG-TTACATTCAACTGACA-G------GTAA
149266 CTGTTACATTCAAC-GACAGGTAA
1 CTGTTACATTCAACTGACAGGTAA
* **
149289 CTGTTACAGTCAACTGACATTTAA
1 CTGTTACATTCAACTGACAGGTAA
*
149313 CTGTTACATTCAACTGATAGGTAA
1 CTGTTACATTCAACTGACAGGTAA
* * *
149337 CTTTTACATTCAACTGACAGATGA
1 CTGTTACATTCAACTGACAGGTAA
*
149361 CTGTTCCATTTC-ACTGACAG
1 CTGTTACA-TTCAACTGACAG
149381 ATGAATTATT
Statistics
Matches: 659, Mismatches: 105, Indels: 52
0.81 0.13 0.06
Matches are distributed among these distances:
17 15 0.02
19 1 0.00
22 1 0.00
23 22 0.03
24 571 0.87
25 9 0.01
26 1 0.00
27 19 0.03
29 1 0.00
30 4 0.01
31 13 0.02
32 2 0.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (24 bp):
CTGTTACATTCAACTGACAGGTAA
Found at i:149145 original size:17 final size:17
Alignment explanation
Indices: 149123--149156 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
149113 GACAGGTAAT
149123 TGTTACATTCAACTGAC
1 TGTTACATTCAACTGAC
149140 TGTTACATTCAACTGAC
1 TGTTACATTCAACTGAC
149157 AGGTAACTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (17 bp):
TGTTACATTCAACTGAC
Found at i:149303 original size:13 final size:13
Alignment explanation
Indices: 149287--149328 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
149277 AACGACAGGT
*
149287 AACTGTTACAGTC
1 AACTGTTACATTC
*
149300 AACTG--ACATTT
1 AACTGTTACATTC
149311 AACTGTTACATTC
1 AACTGTTACATTC
149324 AACTG
1 AACTG
149329 ATAGGTAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
11 9 0.38
13 15 0.62
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (13 bp):
AACTGTTACATTC
Found at i:155690 original size:11 final size:11
Alignment explanation
Indices: 155674--155699 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
155664 CTATTGTTCC
155674 TTTTATATATA
1 TTTTATATATA
155685 TTTTATATATA
1 TTTTATATATA
155696 TTTT
1 TTTT
155700 GATTTCCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTATATATA
Found at i:158164 original size:438 final size:436
Alignment explanation
Indices: 157336--158135 Score: 1022
Period size: 438 Copynumber: 1.8 Consensus size: 436
157326 TTAAATCAAG
* *
157336 AGCTTTCATTTGAGATCATGAAAAAGGGGCTGGCCCTTCAAATTAGGGGCTGAGGGGGCTCTAAA
1 AGCTTTCATTTGAAATCATGAAAAAGGGGCTGGCCCTTCAAATAAGGGGCTGAGGGGGCTCTAAA
* * * * *
157401 GTATTTTTATAATAACTTTTTACCGTGAAATATTTTGTGATGCGTTATAGAAGCAATTATGTTTA
66 GTATATTAATAATAACTTTTTACCGTGAAATATTTGGTGATACGTTATAGAAGCAATTATGTTCA
* * * *
157466 TTCTTAGGTTATTTACCTATACATGGCAATCATATACTTCTATGTTACGTAATTAGTAATTTTTA
131 TTCTAAGGTTATGTACCTATACATGGCAATCATATACCTCTATGTTACGTAATTAGGAATTTTTA
* * *
157531 AGGGGCCAGAAGTCCAAAACTTTAATGCATAATATCTCAAAATGAAGAAACATTTGGATAAGCAA
196 AGAGACAAGAAGTCCAAAACTTTAATGCATAATATCTCAAAATGAAGAAACATTTGGATAAGCAA
*
157596 TATTAAACAAAAGATGCTCAAAATATAGAGCTTAACAATAATCAACTATAATTTCTTTGTTATGC
261 TATTAAACAAAAGATGCTCAAAATATAGAGCTTAACAATAATCAACCATAATTTCTTTGTTATGC
* *** * * * *
157661 GGTCCCTAAAAGGAGATACAGGGTTGGCCCCTAACACAACCCTCTCAAGATATCTCGAGAACGGT
326 GGACCCTAAAAGGAGATACAGGACCGG--CATAACAAAACCCTCTCAAGATATCTCAAAAACGGT
157726 ACAAAATTTGTAATTACTTGTTGAACAAAAAGTGTTAGAATTGACAAT
389 ACAAAATTTGTAATTACTTGTTGAACAAAAAGTGTTAGAATTGACAAT
* * *
157774 AGCTTTCATTTGAAATCATGAAAAAGGTGCTGGCCCTTCTAATAAGGGGCTGAGGGGGCTCTTAA
1 AGCTTTCATTTGAAATCATGAAAAAGGGGCTGGCCCTTCAAATAAGGGGCTGAGGGGGCTCTAAA
* * * *
157839 GTCTATTAATGATAACTTTTTACTGTTAAATATTTGGTGATACGTTATAGAAGCAATTATGTTCA
66 GTATATTAATAATAACTTTTTACCGTGAAATATTTGGTGATACGTTATAGAAGCAATTATGTTCA
* * * *
157904 TTCTAATGTTATGTACCTGTACATGGCAATCATTTACACT-TATGTTACGTAATTAGGGA-TTTT
131 TTCTAAGGTTATGTACCTATACATGGCAATCATATAC-CTCTATGTTACGTAATTAGGAATTTTT
* * * * ** *
157967 AAGAGACAAGAGGTCTAAAGCTTTGATGTTTAATATCTCAAAATAGAGGAAA-ACTTTGGA-AAG
195 AAGAGACAAGAAGTCCAAAACTTTAATGCATAATATCTCAAAAT-GAAGAAACA-TTTGGATAAG
* * * *
158030 CAATATTTAACAAAAGATGCTCAAAATATTGAGCTTAACAAT-GTACAACCATATATATTGTTT-
258 CAATATTAAACAAAAGATGCTCAAAATATAGAGCTTAACAATAAT-CAACCATA-AT-TTCTTTG
* ** *
158093 TTAT-CTGGACCCTAAAAGGAGTTTTAGGACCGG-ATATCAAAAC
320 TTATGC-GGACCCTAAAAGGAGATACAGGACCGGCATAACAAAAC
158136 GATTTTTCCC
Statistics
Matches: 308, Mismatches: 47, Indels: 17
0.83 0.13 0.05
Matches are distributed among these distances:
435 7 0.02
436 1 0.00
437 91 0.30
438 203 0.66
439 6 0.02
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (436 bp):
AGCTTTCATTTGAAATCATGAAAAAGGGGCTGGCCCTTCAAATAAGGGGCTGAGGGGGCTCTAAA
GTATATTAATAATAACTTTTTACCGTGAAATATTTGGTGATACGTTATAGAAGCAATTATGTTCA
TTCTAAGGTTATGTACCTATACATGGCAATCATATACCTCTATGTTACGTAATTAGGAATTTTTA
AGAGACAAGAAGTCCAAAACTTTAATGCATAATATCTCAAAATGAAGAAACATTTGGATAAGCAA
TATTAAACAAAAGATGCTCAAAATATAGAGCTTAACAATAATCAACCATAATTTCTTTGTTATGC
GGACCCTAAAAGGAGATACAGGACCGGCATAACAAAACCCTCTCAAGATATCTCAAAAACGGTAC
AAAATTTGTAATTACTTGTTGAACAAAAAGTGTTAGAATTGACAAT
Found at i:172989 original size:26 final size:26
Alignment explanation
Indices: 172955--173028 Score: 130
Period size: 26 Copynumber: 2.8 Consensus size: 26
172945 AATTGTGCTG
* *
172955 ATGGCCAGTAAACTAGTCAACAACCA
1 ATGGTCAGTGAACTAGTCAACAACCA
172981 ATGGTCAGTGAACTAGTCAACAACCA
1 ATGGTCAGTGAACTAGTCAACAACCA
173007 ATGGTCAGTGAACTAGTCAACA
1 ATGGTCAGTGAACTAGTCAACA
173029 GCTGTCAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (26 bp):
ATGGTCAGTGAACTAGTCAACAACCA
Found at i:173708 original size:2 final size:2
Alignment explanation
Indices: 173703--173747 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
173693 NNNNNTATAT
173703 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
173745 AC A
1 AC A
173748 TTTATGAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:204606 original size:15 final size:15
Alignment explanation
Indices: 204588--204617 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
204578 AGGAGGAGGG
*
204588 GGAGGTGGAGAAAGA
1 GGAGGAGGAGAAAGA
204603 GGAGGAGGAGAAAGA
1 GGAGGAGGAGAAAGA
204618 TGATAAGGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.53, T:0.03
Consensus pattern (15 bp):
GGAGGAGGAGAAAGA
Found at i:209464 original size:4 final size:4
Alignment explanation
Indices: 209450--209480 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
209440 TAAAAAAATG
*
209450 TAAA AAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
209481 TGCGATATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:209802 original size:31 final size:31
Alignment explanation
Indices: 209764--209824 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
209754 TATTTTTATA
209764 GGGTACGTTTTCTCCAAGAGAAAACGTACCT
1 GGGTACGTTTTCTCCAAGAGAAAACGTACCT
**
209795 GGGTACGTTTTCTCCTGGAGAAAACGTACC
1 GGGTACGTTTTCTCCAAGAGAAAACGTACC
209825 CTATAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (31 bp):
GGGTACGTTTTCTCCAAGAGAAAACGTACCT
Found at i:209852 original size:16 final size:16
Alignment explanation
Indices: 209833--209864 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
209823 CCCTATAAAT
209833 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
209849 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
209865 AGCATTCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.25, T:0.44
Consensus pattern (16 bp):
TGGGTACGTTTTCTCC
Found at i:216660 original size:176 final size:173
Alignment explanation
Indices: 216348--216664 Score: 408
Period size: 176 Copynumber: 1.8 Consensus size: 173
216338 AAGGGTTCTT
* * * **
216348 GTGTTAAGGTGAGGCTTTAATGATTATATAGTGAAAATGCCTTAATTCTTTGAAAATCTTCTCCT
1 GTGTTAAGGTGAGGCTTAAATGATTATATAGAGAAAATGCATTAATTCTTCAAAAATCTTCTCCT
* *
216413 CTGCTCCTGGGAATTAAGCTAATGAACTAAGCACATATACATAGTTATGATGAGGAAGAATGCCT
66 CTGCTCCTGGGAATTAAGCCAATGAACTAAGCACACATACA-AGTTATGATGAGGAAGAA-GCCT
216478 CTTCCAAAATTGATAAGTTCATGGCCCTTGGGTCAGGGAATTTTG
129 CTTCCAAAATTGATAAGTTCATGGCCCTTGGGTCAGGGAATTTTG
* * *
216523 GTGTTAGGGTGGGGCTCTAAATGATTATATAGAGAAAATGCATTGATTCTTCAAAAATCTTCTCC
1 GTGTTAAGGTGAGGCT-TAAATGATTATATAGAGAAAATGCATTAATTCTTCAAAAATCTTCTCC
* * *
216588 TCTGCTCCT-GGATATTAAGCCCAA-GTACTAAGTACACACATGC-AGTTTTGATGAGGTAGAGA
65 TCTGCTCCTGGGA-ATTAAG-CCAATGAACTAAG--CACACATACAAGTTATGATGAGG-A-AGA
216650 A-CCTCTTCCAAAATT
124 AGCCTCTTCCAAAATT
216665 ATTAATTTTT
Statistics
Matches: 122, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
175 17 0.14
176 90 0.74
177 4 0.03
178 11 0.09
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Consensus pattern (173 bp):
GTGTTAAGGTGAGGCTTAAATGATTATATAGAGAAAATGCATTAATTCTTCAAAAATCTTCTCCT
CTGCTCCTGGGAATTAAGCCAATGAACTAAGCACACATACAAGTTATGATGAGGAAGAAGCCTCT
TCCAAAATTGATAAGTTCATGGCCCTTGGGTCAGGGAATTTTG
Found at i:218611 original size:18 final size:17
Alignment explanation
Indices: 218588--218626 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
218578 TCGGAATGCC
*
218588 TAAAGAGTATCTTTTTTT
1 TAAAGAATAT-TTTTTTT
*
218606 TAAAGAATGTTTTTTTT
1 TAAAGAATATTTTTTTT
218623 TAAA
1 TAAA
218627 TTGATACATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (17 bp):
TAAAGAATATTTTTTTT
Found at i:220407 original size:14 final size:14
Alignment explanation
Indices: 220385--220414 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
220375 TAAAGCAACA
220385 CTATAGTGGCATAT
1 CTATAGTGGCATAT
*
220399 CTATGGTGGCATAT
1 CTATAGTGGCATAT
220413 CT
1 CT
220415 CTGTCCTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (14 bp):
CTATAGTGGCATAT
Found at i:220471 original size:21 final size:21
Alignment explanation
Indices: 220446--220501 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
220436 TTTTTCTATC
*
220446 AAATATGTCGACATGAAAGAT
1 AAATATGTCAACATGAAAGAT
* *
220467 AAATATGTTAA-ATGCAAGAT
1 AAATATGTCAACATGAAAGAT
*
220487 ATATATGTCAACATG
1 AAATATGTCAACATG
220502 CAACATAAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.46, C:0.09, G:0.16, T:0.29
Consensus pattern (21 bp):
AAATATGTCAACATGAAAGAT
Found at i:220504 original size:21 final size:21
Alignment explanation
Indices: 220446--220509 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
220436 TTTTTCTATC
* *
220446 AAATATGTCGACATGAAAGAT
1 AAATATGTCAACATGCAAGAT
*
220467 AAATATGTTAA-ATGCAAGAT
1 AAATATGTCAACATGCAAGAT
* *
220487 ATATATGTCAACATGCAACAT
1 AAATATGTCAACATGCAAGAT
220508 AA
1 AA
220510 GTATAAAGAC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
20 17 0.49
21 18 0.51
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (21 bp):
AAATATGTCAACATGCAAGAT
Found at i:220646 original size:21 final size:21
Alignment explanation
Indices: 220600--220807 Score: 156
Period size: 21 Copynumber: 10.0 Consensus size: 21
220590 TGCTTCCTAT
*
220600 TTATGTCGACATGCAA-TTAT
1 TTATGTCGACATGCAACTTAG
*
220620 TTATGTCAACATGCAACTTAG
1 TTATGTCGACATGCAACTTAG
* * *
220641 TTATGTTC-AAATGCTACTTAT
1 TTATG-TCGACATGCAACTTAG
*
220662 TTATGTCGACATGCAACTTAT
1 TTATGTCGACATGCAACTTAG
* *
220683 TTTTGTTC-ACATGCTACTTA-
1 TTATG-TCGACATGCAACTTAG
*
220703 TATATGTCAACATGCAACTTAG
1 T-TATGTCGACATGCAACTTAG
* ** *
220725 TTATGTTGACATGCAAGATAA
1 TTATGTCGACATGCAACTTAG
* *
220746 CTATGTTGACATGCAACTTAG
1 TTATGTCGACATGCAACTTAG
* ** *
220767 TTATGTTC-ACATGCGAGATAA
1 TTATG-TCGACATGCAACTTAG
* *
220788 ATATGTTGACATGCAACTTA
1 TTATGTCGACATGCAACTTA
220808 TAAGTTGCAT
Statistics
Matches: 148, Mismatches: 31, Indels: 17
0.76 0.16 0.09
Matches are distributed among these distances:
20 21 0.14
21 121 0.82
22 6 0.04
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (21 bp):
TTATGTCGACATGCAACTTAG
Found at i:220663 original size:42 final size:42
Alignment explanation
Indices: 220616--220780 Score: 213
Period size: 42 Copynumber: 3.9 Consensus size: 42
220606 CGACATGCAA
*
220616 TTATTTATGTCAACATGCAACTTAGTTATGTTCAAATGCTAC
1 TTATTTATGTCAACATGCAACTTAGTTATGTTCACATGCTAC
* * *
220658 TTATTTATGTCGACATGCAACTTATTTTTGTTCACATGCTAC
1 TTATTTATGTCAACATGCAACTTAGTTATGTTCACATGCTAC
* * * *
220700 TTATATATGTCAACATGCAACTTAGTTATGTTGACATGCAAG
1 TTATTTATGTCAACATGCAACTTAGTTATGTTCACATGCTAC
* ** **
220742 ATAACTATGTTGACATGCAACTTAGTTATGTTCACATGC
1 TTATTTATGTCAACATGCAACTTAGTTATGTTCACATGC
220781 GAGATAAATA
Statistics
Matches: 106, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 106 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (42 bp):
TTATTTATGTCAACATGCAACTTAGTTATGTTCACATGCTAC
Found at i:220723 original size:63 final size:62
Alignment explanation
Indices: 220597--220780 Score: 203
Period size: 63 Copynumber: 2.9 Consensus size: 62
220587 AGATGCTTCC
*
220597 TATTTATGTCGACATGCAATTATTTATGTCAACATGCAACTTAGTTATGTTCAAATGCTACT
1 TATTTATGTCGACATGCAATTATTTATGTCAACATGCAACTTAGTTATGTTCAAATGCAACT
* *
220659 TATTTATGTCGACATGCAACTTATTTTTGTTC-ACATGCTACTTA-TATATG-TCAACATGCAAC
1 TATTTATGTCGACATGCAA-TTATTTATG-TCAACATGCAACTTAGT-TATGTTCAA-ATGCAAC
220721 T
62 T
* * * ** ** *
220722 TAGTTATGTTGACATGCAAGATAACTATGTTGACATGCAACTTAGTTATGTTCACATGC
1 TATTTATGTCGACATGCAA-TTATTTATGTCAACATGCAACTTAGTTATGTTCAAATGC
220781 GAGATAAATA
Statistics
Matches: 102, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
62 25 0.25
63 71 0.70
64 6 0.06
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (62 bp):
TATTTATGTCGACATGCAATTATTTATGTCAACATGCAACTTAGTTATGTTCAAATGCAACT
Found at i:220751 original size:84 final size:84
Alignment explanation
Indices: 220616--220807 Score: 231
Period size: 84 Copynumber: 2.3 Consensus size: 84
220606 CGACATGCAA
* * * **
220616 TTATTTATGTCAACATGCAACTTAGTTATGTTCAAATGCTACTTATTTATGTCGACATGCAACTT
1 TTATATATGTCAACATGCAACTTAGTTATGTTCAAATGCAACATAACTATGTCGACATGCAACTT
* * *
220681 ATTTTTGTTCACATGCTAC
66 AGTTATGTTCACATGCGAC
* * * *
220700 TTATATATGTCAACATGCAACTTAGTTATGTTGACATGCAAGATAACTATGTTGACATGCAACTT
1 TTATATATGTCAACATGCAACTTAGTTATGTTCAAATGCAACATAACTATGTCGACATGCAACTT
*
220765 AGTTATGTTCACATGCGAG
66 AGTTATGTTCACATGCGAC
* * **
220784 ATAAATATGTTGACATGCAACTTA
1 TTATATATGTCAACATGCAACTTA
220808 TAAGTTGCAT
Statistics
Matches: 91, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
84 91 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (84 bp):
TTATATATGTCAACATGCAACTTAGTTATGTTCAAATGCAACATAACTATGTCGACATGCAACTT
AGTTATGTTCACATGCGAC
Found at i:220786 original size:42 final size:41
Alignment explanation
Indices: 220621--220807 Score: 203
Period size: 42 Copynumber: 4.5 Consensus size: 41
220611 TGCAATTATT
* * * *
220621 TATGTCAACATGCAACTTAGTTATGTTCAAATGCTACTTATT
1 TATGTCGACATGCAACTTAGTTATGTTCACATGCTACATA-A
* * *
220663 TATGTCGACATGCAACTTATTTTTGTTCACATGCTACTTATA
1 TATGTCGACATGCAACTTAGTTATGTTCACATGCTACATA-A
* * * *
220705 TATGTCAACATGCAACTTAGTTATGTTGACATGCAAGATAA
1 TATGTCGACATGCAACTTAGTTATGTTCACATGCTACATAA
* * *
220746 CTATGTTGACATGCAACTTAGTTATGTTCACATGCGAGATAAA
1 -TATGTCGACATGCAACTTAGTTATGTTCACATGCTACAT-AA
*
220789 TATGTTGACATGCAACTTA
1 TATGTCGACATGCAACTTA
220808 TAAGTTGCAT
Statistics
Matches: 127, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
41 1 0.01
42 124 0.98
43 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (41 bp):
TATGTCGACATGCAACTTAGTTATGTTCACATGCTACATAA
Found at i:220834 original size:21 final size:21
Alignment explanation
Indices: 220807--221048 Score: 216
Period size: 21 Copynumber: 11.5 Consensus size: 21
220797 CATGCAACTT
220807 ATAAGTTGCATGTCAACATAA
1 ATAAGTTGCATGTCAACATAA
* * *
220828 CTGAGTTGCATGTCGACATAA
1 ATAAGTTGCATGTCAACATAA
** *
220849 ATACCTTGCATGTCAACATAT
1 ATAAGTTGCATGTCAACATAA
* ** *
220870 TTATCTTGCATGTAAACATAA
1 ATAAGTTGCATGTCAACATAA
* *
220891 CTAAGTTGCATGTCGACATAA
1 ATAAGTTGCATGTCAACATAA
220912 ATAAGTTGCATGTCGAA-ATAA
1 ATAAGTTGCATGTC-AACATAA
* ** * *
220933 AGAAAATGCATGTTAGCATAA
1 ATAAGTTGCATGTCAACATAA
*
220954 ATAAGTTGCATGTCGACATAA
1 ATAAGTTGCATGTCAACATAA
* *
220975 ATGAGTTGCATGTCAACATAT
1 ATAAGTTGCATGTCAACATAA
* ** * * *
220996 TTATCTCGCATGTAAACATGA
1 ATAAGTTGCATGTCAACATAA
*
221017 ATAAGTTGCATGTCGACATAA
1 ATAAGTTGCATGTCAACATAA
*
221038 ATAAGTAGCAT
1 ATAAGTTGCAT
221049 CTAGCATCTT
Statistics
Matches: 169, Mismatches: 50, Indels: 4
0.76 0.22 0.02
Matches are distributed among these distances:
20 1 0.01
21 167 0.99
22 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
ATAAGTTGCATGTCAACATAA
Found at i:220889 original size:63 final size:62
Alignment explanation
Indices: 220812--221040 Score: 282
Period size: 63 Copynumber: 3.6 Consensus size: 62
220802 AACTTATAAG
* * *
220812 TTGCATGTCAACATAACTGAGTTGCATGTCGACATAAATACCTTGCATGTCAACATATTTATC
1 TTGCATGTAAACATAACTAAGTTGCATGTCGACATAAATA-GTTGCATGTCAACATATTTATC
*** **
220875 TTGCATGTAAACATAACTAAGTTGCATGTCGACATAAATAAGTTGCATGTCGAA-ATAAAGAAA
1 TTGCATGTAAACATAACTAAGTTGCATGTCGACATAAAT-AGTTGCATGTC-AACATATTTATC
* * * *
220938 ATGCATGTTAGCATAAATAAGTTGCATGTCGACATAAATGAGTTGCATGTCAACATATTTATC
1 TTGCATGTAAACATAACTAAGTTGCATGTCGACATAAAT-AGTTGCATGTCAACATATTTATC
*
221001 TCGCATGTAAACATGAA-TAAGTTGCATGTCGACATAAATA
1 TTGCATGTAAACAT-AACTAAGTTGCATGTCGACATAAATA
221041 AGTAGCATCT
Statistics
Matches: 140, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
62 3 0.02
63 132 0.94
64 5 0.04
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (62 bp):
TTGCATGTAAACATAACTAAGTTGCATGTCGACATAAATAGTTGCATGTCAACATATTTATC
Found at i:221152 original size:21 final size:21
Alignment explanation
Indices: 221122--221208 Score: 122
Period size: 21 Copynumber: 4.2 Consensus size: 21
221112 TTTGATTGCA
*
221122 ATTT-TCTTGCATGTCAATAT
1 ATTTATCTTGCATGTCAACAT
* *
221142 AATTATGTTGCATGTCAACAT
1 ATTTATCTTGCATGTCAACAT
*
221163 ATTTATCTTTCATGTCAACAT
1 ATTTATCTTGCATGTCAACAT
*
221184 ATTTATCTTGCATGTCGACAT
1 ATTTATCTTGCATGTCAACAT
221205 ATTT
1 ATTT
221209 GATGGAAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
20 3 0.05
21 55 0.95
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (21 bp):
ATTTATCTTGCATGTCAACAT
Found at i:222526 original size:2 final size:2
Alignment explanation
Indices: 222521--222552 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
222511 ATATATATAT
*
222521 AC AC AC AC AC AC AC AC AC TC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
222553 CAAGAGAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.50, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:223990 original size:2 final size:2
Alignment explanation
Indices: 223983--224036 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
223973 TGCATGCCAC
223983 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
224025 AG AG AG AG AG AG
1 AG AG AG AG AG AG
224037 GGGGGGGGGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:230797 original size:31 final size:31
Alignment explanation
Indices: 230759--230822 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
230749 TTGACTGCAC
230759 GAGTCGTAAGTTTTTTAGTCTAAGATATATT
1 GAGTCGTAAGTTTTTTAGTCTAAGATATATT
230790 GAGTCGTAAGTTTTTTAGTCTAAGATATATT
1 GAGTCGTAAGTTTTTTAGTCTAAGATATATT
230821 GA
1 GA
230823 CTGCACGAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (31 bp):
GAGTCGTAAGTTTTTTAGTCTAAGATATATT
Found at i:230880 original size:38 final size:38
Alignment explanation
Indices: 230790--231000 Score: 248
Period size: 38 Copynumber: 5.6 Consensus size: 38
230780 AAGATATATT
* * * *
230790 GAGTCGTAAGTTTTTTAGTCTAAGATATATTGAC-TGCAC
1 GAGTCGTAAGTTTTCTAGTCTTAGACA-A-CGACTTGCAC
*
230829 GAGTCGTAAGTTTTCTAGTCTTAGAC-ACAGACTTGCAT
1 GAGTCGTAAGTTTTCTAGTCTTAGACAAC-GACTTGCAC
* * *
230867 GAGTCGTAAGTTTTCTAGTCCTATACAACGACTCGCAC
1 GAGTCGTAAGTTTTCTAGTCTTAGACAACGACTTGCAC
* * *
230905 AAGTCGTAAGTTTTCTAGTCTAAGACACCGAC-TGCAC
1 GAGTCGTAAGTTTTCTAGTCTTAGACAACGACTTGCAC
* *
230942 GAGTCGTAAGTTTTCTAGTCCTATACAACGACTTGCAC
1 GAGTCGTAAGTTTTCTAGTCTTAGACAACGACTTGCAC
*
230980 AAGTCGTAAGTTTTCTAGTCT
1 GAGTCGTAAGTTTTCTAGTCT
231001 AAGATACCGA
Statistics
Matches: 146, Mismatches: 22, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
37 35 0.24
38 86 0.59
39 25 0.17
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (38 bp):
GAGTCGTAAGTTTTCTAGTCTTAGACAACGACTTGCAC
Found at i:230956 original size:113 final size:114
Alignment explanation
Indices: 230791--230999 Score: 314
Period size: 113 Copynumber: 1.8 Consensus size: 114
230781 AGATATATTG
* * ** *
230791 AGTCGTAAGTTTTTTAGTCTAAGATATATTGACTGCACGAGTCGTAAGTTTTCTAGTCTTAGAC-
1 AGTCGTAAGTTTTCTAGTCTAAGA-ACACCGACTGCACGAGTCGTAAGTTTTCTAGTCCTAGACA
**
230855 ACAGACTTGCATGAGTCGTAAGTTTTCTAGTCCTATACAACGACTCGCACA
65 AC-GACTTGCACAAGTCGTAAGTTTTCTAGTCCTATACAACGACTCGCACA
*
230906 AGTCGTAAGTTTTCTAGTCTAAG-ACACCGACTGCACGAGTCGTAAGTTTTCTAGTCCTATACAA
1 AGTCGTAAGTTTTCTAGTCTAAGAACACCGACTGCACGAGTCGTAAGTTTTCTAGTCCTAGACAA
230970 CGACTTGCACAAGTCGTAAGTTTTCTAGTC
66 CGACTTGCACAAGTCGTAAGTTTTCTAGTC
231000 TAAGATACCG
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
113 61 0.72
114 2 0.02
115 22 0.26
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (114 bp):
AGTCGTAAGTTTTCTAGTCTAAGAACACCGACTGCACGAGTCGTAAGTTTTCTAGTCCTAGACAA
CGACTTGCACAAGTCGTAAGTTTTCTAGTCCTATACAACGACTCGCACA
Found at i:230967 original size:75 final size:75
Alignment explanation
Indices: 230821--231011 Score: 312
Period size: 75 Copynumber: 2.5 Consensus size: 75
230811 AAGATATATT
* * * *
230821 GACTGCACGAGTCGTAAGTTTTCTAGTCTTAGACACAGACTTGCATGAGTCGTAAGTTTTCTAGT
1 GACTGCACAAGTCGTAAGTTTTCTAGTCTAAGACACCGACTTGCACGAGTCGTAAGTTTTCTAGT
230886 CCTATACAAC
66 CCTATACAAC
230896 GACTCGCACAAGTCGTAAGTTTTCTAGTCTAAGACACCGAC-TGCACGAGTCGTAAGTTTTCTAG
1 GACT-GCACAAGTCGTAAGTTTTCTAGTCTAAGACACCGACTTGCACGAGTCGTAAGTTTTCTAG
230960 TCCTATACAAC
65 TCCTATACAAC
*
230971 GACTTGCACAAGTCGTAAGTTTTCTAGTCTAAGATACCGAC
1 GAC-TGCACAAGTCGTAAGTTTTCTAGTCTAAGACACCGAC
231012 GTATGAATAA
Statistics
Matches: 109, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
75 75 0.69
76 34 0.31
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (75 bp):
GACTGCACAAGTCGTAAGTTTTCTAGTCTAAGACACCGACTTGCACGAGTCGTAAGTTTTCTAGT
CCTATACAAC
Found at i:236331 original size:111 final size:111
Alignment explanation
Indices: 236137--236361 Score: 432
Period size: 111 Copynumber: 2.0 Consensus size: 111
236127 AAAATTAACA
*
236137 TATGTTTCAAAAGAAAAAATTAGCGCTAAAATGAAAAATCTTTACAACAAAATTGAACGCGAGAG
1 TATGTTTCAAAAGAAAAAATAAGCGCTAAAATGAAAAATCTTTACAACAAAATTGAACGCGAGAG
236202 TTTCAAATAAAAATGCATTCTGTATTTTAGCTTTCCAGTCAATCTT
66 TTTCAAATAAAAATGCATTCTGTATTTTAGCTTTCCAGTCAATCTT
*
236248 TATGTTTCAAAAGAAAAAATAAGCGCTAAAATGAAAAATCTTTACAACGAAATTGAACGCGAGAG
1 TATGTTTCAAAAGAAAAAATAAGCGCTAAAATGAAAAATCTTTACAACAAAATTGAACGCGAGAG
236313 TTTCAAATAAAAATGCATTCTGTATTTTAGCTTTCCAGTCAATCTT
66 TTTCAAATAAAAATGCATTCTGTATTTTAGCTTTCCAGTCAATCTT
236359 TAT
1 TAT
236362 TATCATCCAG
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 112 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (111 bp):
TATGTTTCAAAAGAAAAAATAAGCGCTAAAATGAAAAATCTTTACAACAAAATTGAACGCGAGAG
TTTCAAATAAAAATGCATTCTGTATTTTAGCTTTCCAGTCAATCTT
Found at i:240673 original size:24 final size:24
Alignment explanation
Indices: 240646--240820 Score: 305
Period size: 24 Copynumber: 7.3 Consensus size: 24
240636 CCAGGAAGTT
240646 TAAAATAGGATCCCTACCCTCGTG
1 TAAAATAGGATCCCTACCCTCGTG
240670 TAAAATAGGATCCCTACCCTCGTG
1 TAAAATAGGATCCCTACCCTCGTG
**
240694 TAAAATAGGATCCCTTTCCTCGTG
1 TAAAATAGGATCCCTACCCTCGTG
*
240718 TAAAATAGGACCCCTACCCTCGTG
1 TAAAATAGGATCCCTACCCTCGTG
240742 TAAAATAGGATCCCTACCCTCGTG
1 TAAAATAGGATCCCTACCCTCGTG
*
240766 TAAAATAGGACCCCTACCCTCGTG
1 TAAAATAGGATCCCTACCCTCGTG
*
240790 TAAAATAGGATCCCTACCCTCATG
1 TAAAATAGGATCCCTACCCTCGTG
240814 TAAAATA
1 TAAAATA
240821 AACACTTTTG
Statistics
Matches: 142, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 142 1.00
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (24 bp):
TAAAATAGGATCCCTACCCTCGTG
Found at i:243850 original size:15 final size:16
Alignment explanation
Indices: 243820--243855 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
243810 TCACCGAGAC
243820 GAGACATCACCCTTAT
1 GAGACATCACCCTTAT
*
243836 GAGACTTCA-CCTTAT
1 GAGACATCACCCTTAT
243851 GAGAC
1 GAGAC
243856 CACCTTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.25
Consensus pattern (16 bp):
GAGACATCACCCTTAT
Found at i:243861 original size:13 final size:14
Alignment explanation
Indices: 243820--243861 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
243810 TCACCGAGAC
243820 GAGACATCACCCTTAT
1 GAGAC-TCA-CCTTAT
243836 GAGACTTCACCTTAT
1 GAGAC-TCACCTTAT
243851 GAGAC-CACCTT
1 GAGACTCACCTT
243862 TATCATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 6 0.24
15 11 0.44
16 8 0.32
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (14 bp):
GAGACTCACCTTAT
Found at i:245399 original size:13 final size:13
Alignment explanation
Indices: 245381--245418 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
245371 GATACAATAT
245381 AATTTGATACAAC
1 AATTTGATACAAC
245394 AATTTGATACAAC
1 AATTTGATACAAC
245407 AATTTGATACAA
1 AATTTGATACAA
245419 TATTGTATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (13 bp):
AATTTGATACAAC
Found at i:246532 original size:177 final size:177
Alignment explanation
Indices: 246236--246804 Score: 788
Period size: 177 Copynumber: 3.2 Consensus size: 177
246226 TAACCATATT
* * * *
246236 CAGCATCTGAAACCTATAGCTCAGACTCAGCATTCAAGCCTGTCAGGTGCATCATTATCATAAGA
1 CAGCATCCGAAACCTATAGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAAGA
* *
246301 CGCACCATCCATGGAAGTCTGGTGAGGTTAGGACAAGTAATAACTAAGATATAATCATCAGAGGG
66 CGCACCATCCATGGAAGTCTGGTGAAGTTAGGACAAGTAGTAACTAAGATATAATCATCAGAGGG
*** * * *
246366 CACCTGTTTCAAAAGCTTTAACCAGCTCTAAAAACATTAACCTCCTC
131 CACCTGCAACAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTC
* *
246413 CAGCATCCGAAACCTATTGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAAAA
1 CAGCATCCGAAACCTATAGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAAGA
246478 CGCACCATCCATGGAAGTCTGGTGAAGTTAGGACAAGTAGTAACTAAGATATAATCATCAGAGGG
66 CGCACCATCCATGGAAGTCTGGTGAAGTTAGGACAAGTAGTAACTAAGATATAATCATCAGAGGG
*
246543 CACCTGCAACAAAAACTTTAACCAGCTCCAAAAACCTAAACCTCCTC
131 CACCTGCAACAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTC
* *
246590 CAGCATCCGTAACCTATAGCTCAGATTCAGCACTCAAGCCTGTCTGGTGCATCAGTATCATAAGA
1 CAGCATCCGAAACCTATAGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAAGA
* * * ** * * *
246655 CACACCATCCATGCAAGTTTGGTGAAG-TACGGACCTGCAGTAACTTAGATAT--TGCTATCAAA
66 CGCACCATCCATGGAAGTCTGGTGAAGTTA-GGACAAGTAGTAACTAAGATATAAT-C-ATCAGA
* *
246717 GGGCACCTGCAACAAAAACTTTAACCTGGTCCAAAAACCTTAACCTCCTC
128 GGGCACCTGCAACAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTC
* * *
246767 CAGCATCTGAAA--TTTAGGACTCAGATTCAGCATCCAAG
1 CAGCATCCGAAACCTATA-G-CTCAGATTCAGCATTCAAG
246805 TCTTTCAATT
Statistics
Matches: 352, Mismatches: 35, Indels: 10
0.89 0.09 0.03
Matches are distributed among these distances:
175 4 0.01
176 4 0.01
177 344 0.98
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (177 bp):
CAGCATCCGAAACCTATAGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAAGA
CGCACCATCCATGGAAGTCTGGTGAAGTTAGGACAAGTAGTAACTAAGATATAATCATCAGAGGG
CACCTGCAACAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTC
Found at i:246768 original size:19 final size:19
Alignment explanation
Indices: 246729--246768 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
246719 GCACCTGCAA
* **
246729 CAAAAACTTTAACCTGGTC
1 CAAAAACCTTAACCTCCTC
246748 CAAAAACCTTAACCTCCTC
1 CAAAAACCTTAACCTCCTC
246767 CA
1 CA
246769 GCATCTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.35, G:0.05, T:0.23
Consensus pattern (19 bp):
CAAAAACCTTAACCTCCTC
Found at i:246881 original size:177 final size:174
Alignment explanation
Indices: 246236--246882 Score: 584
Period size: 177 Copynumber: 3.7 Consensus size: 174
246226 TAACCATATT
* * * * * * * * *
246236 CAGCATCTGAAACCTATAGCTCAGACTCAGCATTCAAGCCTGTCAGGTGCATCATTATCATAAGA
1 CAGCATCCGTAACATATAGCTCAGATTCAGCACTCAAGCCTGTCAAGTCCATAAGTATCA-AAGA
* * * * * * *
246301 CGCACCATCCATGGAAGTCTGGTGAGGTTAGGACAAGTAATAACTAAGATATAATCATCAGAGGG
65 CACACCATCCATGCAAGTTTGGTGAAG-TAGGACAAGTAGTAACTTAGATAT-ATCATCAAAGGG
*** * * * *
246366 CACCTGTTTCAAAAGCTTTAACCAGCTCTAAAAACATTAACCTCCTC
128 CACCTGCAACAAAAACTTTAACCAGCTCCAAAAACCTAAACCTCCTC
* * * * ** * * *
246413 CAGCATCCGAAACCTATTGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAAAA
1 CAGCATCCGTAACATATAGCTCAGATTCAGCACTCAAGCCTGTCAAGTCCATAAGTATCA-AAGA
* * * * *
246478 CGCACCATCCATGGAAGTCTGGTGAAGTTAGGACAAGTAGTAACTAAGATATAATCATCAGAGGG
65 CACACCATCCATGCAAGTTTGGTGAAG-TAGGACAAGTAGTAACTTAGATAT-ATCATCAAAGGG
246543 CACCTGCAACAAAAACTTTAACCAGCTCCAAAAACCTAAACCTCCTC
128 CACCTGCAACAAAAACTTTAACCAGCTCCAAAAACCTAAACCTCCTC
* ** * *
246590 CAGCATCCGTAACCTATAGCTCAGATTCAGCACTCAAGCCTGTCTGGTGCATCAGTATCATAAGA
1 CAGCATCCGTAACATATAGCTCAGATTCAGCACTCAAGCCTGTCAAGTCCATAAGTATCA-AAGA
** *
246655 CACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAACTTAGATAT-TGCTATCAAAGG
65 CACACCATCCATGCAAGTTTGGTGAAGTA-GGACAAGTAGTAACTTAGATATAT-C-ATCAAAGG
* * *
246719 GCACCTGCAACAAAAACTTTAACCTGGTCCAAAAACCTTAACCTCCTC
127 GCACCTGCAACAAAAACTTTAACCAGCTCCAAAAACCTAAACCTCCTC
* * * * *
246767 CAGCATCTG-AA-ATTTAGGACTCAGATTCAGCA-TCCAAGTCTTTCAATTCCATAAGTAGGTC-
1 CAGCATCCGTAACATATA-G-CTCAGATTCAGCACT-CAAGCCTGTCAAGTCCATAAGTA--TCA
* ** * * *
246828 CAGATGCATCATCCATGCAAGTTTGGTGAAGATAGGACAAGTAATAGCTTAGATA
61 AAGACACACCATCCATGCAAGTTTGGTGAAG-TAGGACAAGTAGTAACTTAGATA
246883 CAGGACCTGC
Statistics
Matches: 412, Mismatches: 49, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
175 4 0.01
176 7 0.02
177 397 0.96
178 2 0.00
179 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (174 bp):
CAGCATCCGTAACATATAGCTCAGATTCAGCACTCAAGCCTGTCAAGTCCATAAGTATCAAAGAC
ACACCATCCATGCAAGTTTGGTGAAGTAGGACAAGTAGTAACTTAGATATATCATCAAAGGGCAC
CTGCAACAAAAACTTTAACCAGCTCCAAAAACCTAAACCTCCTC
Found at i:249002 original size:166 final size:166
Alignment explanation
Indices: 248728--249063 Score: 575
Period size: 166 Copynumber: 2.0 Consensus size: 166
248718 AAAGAATCAT
* *
248728 CTGGCTGATTAGTTTCTGAGAAGCAGATTTTTAAAGATTTACTCTATATATTCCTATGAAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCATATGAAAAACT
248793 TCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCATAACTTTGAATCTACA
66 TCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCATAACTTTGAATCTACA
** *
248858 CTACCTGAGGATGC-TTCAACACAAGTTTCACCTTTC
131 CTACCTGACAATACTTTC-ACACAAGTTTCACCTTTC
* **
248894 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAATATTTACTCTATATATTCATATGTTAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCATATGAAAAACT
248959 TCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCATAACTTTGAATCTACA
66 TCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCATAACTTTGAATCTACA
*
249024 CTACCTGACAATACTTTCACACAAGTTTCAGCTTTC
131 CTACCTGACAATACTTTCACACAAGTTTCACCTTTC
249060 CTGG
1 CTGG
249064 TCTTACGGTT
Statistics
Matches: 160, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
166 157 0.98
167 3 0.02
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (166 bp):
CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCATATGAAAAACT
TCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCATAACTTTGAATCTACA
CTACCTGACAATACTTTCACACAAGTTTCACCTTTC
Found at i:249281 original size:12 final size:12
Alignment explanation
Indices: 249264--249306 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
249254 AAAGTTTACA
249264 GACAGACGGATG
1 GACAGACGGATG
*
249276 GACAGATGGATG
1 GACAGACGGATG
* *
249288 GACGGATGGATG
1 GACAGACGGATG
249300 GACAGAC
1 GACAGAC
249307 AGTTGGACGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.33, C:0.14, G:0.42, T:0.12
Consensus pattern (12 bp):
GACAGACGGATG
Found at i:252168 original size:11 final size:11
Alignment explanation
Indices: 252152--252176 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
252142 CTCAGAAAAG
252152 TGAGAATCATA
1 TGAGAATCATA
252163 TGAGAATCATA
1 TGAGAATCATA
252174 TGA
1 TGA
252177 AAGGGGCATC
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:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (11 bp):
TGAGAATCATA
Found at i:252512 original size:16 final size:16
Alignment explanation
Indices: 252491--252521 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
252481 CACCAAGGAC
252491 TAGGTAGGTAAGTAGG
1 TAGGTAGGTAAGTAGG
252507 TAGGTAGGTAAGTAG
1 TAGGTAGGTAAGTAG
252522 TTGATCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.42, T:0.26
Consensus pattern (16 bp):
TAGGTAGGTAAGTAGG
Found at i:267742 original size:2 final size:2
Alignment explanation
Indices: 267735--267771 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
267725 CTTCTAAGTT
267735 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
267772 NNNNNNNNNN
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:269214 original size:2 final size:2
Alignment explanation
Indices: 269160--269204 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
269150 TAAGTTATAC
269160 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
269202 AG A
1 AG A
269205 AAATGAGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:275913 original size:187 final size:186
Alignment explanation
Indices: 275598--275936 Score: 669
Period size: 187 Copynumber: 1.8 Consensus size: 186
275588 TGATTCAGAG
275598 GTGACATTTAAATCAACTTGAACTCTGTACTAAAGTCAATGTCTTTTTCAGGTCAGGGCCACTCG
1 GTGACATTTAAATCAACTTGAACTCTGTACTAAAGTCAATGTCTTTTTCAGGTCAGGGCCACTCG
275663 GAAAAAAAGCCTTGGCAACTTTGGCGAGCGATTGCTTTAGCTGTCATTACTGCGGTAACACCCCC
66 GAAAAAAAGCCTTGGCAACTTTGGCGAGCGATTGCTTTAGCTGTCATTACTGCGGTAACACCCCC
275728 CCCCTTAAACACAAAACAAAACNTGTCTACACACGTCTTTGTCTTTCTATAAAGTAT
131 CCCCTTAAACACAAAACAAAAC-TGTCTACACACGTCTTTGTCTTTCTATAAAGTAT
275785 GTGACATTTAAATCAACTTGAACTCTGTACTAAAGTCAATGTCTTTTTCAGGTCAGGGCCACTCG
1 GTGACATTTAAATCAACTTGAACTCTGTACTAAAGTCAATGTCTTTTTCAGGTCAGGGCCACTCG
275850 GAAAAAAAGCCTTGGCAACTTTGGCGAGCGATTGCTTTAGCTGTCATTACTGCGGTAACACCCCC
66 GAAAAAAAGCCTTGGCAACTTTGGCGAGCGATTGCTTTAGCTGTCATTACTGCGGTAACACCCCC
275915 CCCCTTAAACACAAAACAAAAC
131 CCCCTTAAACACAAAACAAAAC
275937 ATTATTCACA
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
187 152 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (186 bp):
GTGACATTTAAATCAACTTGAACTCTGTACTAAAGTCAATGTCTTTTTCAGGTCAGGGCCACTCG
GAAAAAAAGCCTTGGCAACTTTGGCGAGCGATTGCTTTAGCTGTCATTACTGCGGTAACACCCCC
CCCCTTAAACACAAAACAAAACTGTCTACACACGTCTTTGTCTTTCTATAAAGTAT
Found at i:285265 original size:12 final size:12
Alignment explanation
Indices: 285248--285273 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
285238 TGGTTCAGCA
285248 TTTTTTATTCGT
1 TTTTTTATTCGT
285260 TTTTTTATTCGT
1 TTTTTTATTCGT
285272 TT
1 TT
285274 ACACAAACAT
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:0.08, C:0.08, G:0.08, T:0.77
Consensus pattern (12 bp):
TTTTTTATTCGT
Found at i:287750 original size:146 final size:145
Alignment explanation
Indices: 287444--287984 Score: 752
Period size: 146 Copynumber: 3.7 Consensus size: 145
287434 CTTCCTAAAT
* *
287444 TGACCTTGGGTCAAGGTCATGACACA--CTCAGGTTATAAGCAATC-TTGATGTGAATCAAGAAC
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTG-TGTGAAT-AAGAAC
* * * * * *
287506 TTCCAATATTTGTCCATTAG--AGATATGGACTGGACATGAATTTTGC-TCTTTTCTGCCAGTGA
64 TTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCATTTTTTCTGCCAGTGA
* *
287568 CATTGGCCTTGCCCAAA
129 CATTGACCTTGCCCGAA
* * *
287585 TGACCTTGGGTCAAAGTCATGACATACCCTTAGGTCATAAGCAATCTTTGTGTGAACTGAGAACT
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAA-TAAGAACT
287650 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCATTTTTTCTGCCAGTGAC
65 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCATTTTTTCTGCCAGTGAC
* *
287715 GTTAACCTTGCCCGAA
130 ATTGACCTTGCCCGAA
* * *
287731 TGACCTTGGTTCAAGGTCATGACACACCCTTAGCTCATAAGCAATCTTTGTGTGAAGGAAGAACT
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAA-TAAGAACT
* * *
287796 TCCAATGTTTCTCCAAAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGTCAGTGAC
65 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCATTTTTTCTGCCAGTGAC
*
287861 ATTGACCTTGCCTGAA
130 ATTGACCTTGCCCGAA
* * * *
287877 TGACCTTGGTTCAAGGTCATAACACACCGTTAGGTGATAAGCAATCTTTGTGTGAAGTAAGAACT
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAA-TAAGAACT
*
287942 TCCAATGTTTCTCCATAAGAAAGATATGGACCAGACACGAATT
65 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATT
287985 GAACAGACAG
Statistics
Matches: 358, Mismatches: 35, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
141 24 0.07
143 44 0.12
144 4 0.01
145 24 0.07
146 262 0.73
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (145 bp):
TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAATAAGAACTT
CCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCATTTTTTCTGCCAGTGACA
TTGACCTTGCCCGAA
Found at i:288011 original size:12 final size:12
Alignment explanation
Indices: 287987--288021 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
287977 CACGAATTGA
*
287987 ACAGACAGACAG
1 ACAGACGGACAG
*
287999 ACGGACGGACAG
1 ACAGACGGACAG
288011 ACAGACGGACA
1 ACAGACGGACA
288022 AGGTGATTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.43, C:0.26, G:0.31, T:0.00
Consensus pattern (12 bp):
ACAGACGGACAG
Found at i:288011 original size:16 final size:16
Alignment explanation
Indices: 287990--288020 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
287980 GAATTGAACA
287990 GACAGACAGACGGACG
1 GACAGACAGACGGACG
288006 GACAGACAGACGGAC
1 GACAGACAGACGGAC
288021 AAGGTGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.26, G:0.35, T:0.00
Consensus pattern (16 bp):
GACAGACAGACGGACG
Found at i:299300 original size:22 final size:22
Alignment explanation
Indices: 299272--299322 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
299262 ACTAAAAAAG
* *
299272 GCGAAGGCGAGAGTGCGAAGTT
1 GCGAAGGCGAAAGTGCAAAGTT
299294 GCGAAGGCGAAAGTGCAAAGTT
1 GCGAAGGCGAAAGTGCAAAGTT
*
299316 GCAAAGG
1 GCGAAGG
299323 GGAAGGAGCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.14, G:0.41, T:0.12
Consensus pattern (22 bp):
GCGAAGGCGAAAGTGCAAAGTT
Found at i:299376 original size:22 final size:22
Alignment explanation
Indices: 299351--299420 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
299341 GTATCACTCC
* *
299351 TTCGCCTTCGCACCTTCGCACT
1 TTCGCCGTCGCATCTTCGCACT
*
299373 TTCGCCGTCGCATCTTCGCGC-
1 TTCGCCGTCGCATCTTCGCACT
*
299394 TTCGCCGTCGCATCTTCGCCCT
1 TTCGCCGTCGCATCTTCGCACT
299416 TTCGC
1 TTCGC
299421 TCCTTCGCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 20 0.47
22 23 0.53
ACGTcount: A:0.06, C:0.44, G:0.19, T:0.31
Consensus pattern (22 bp):
TTCGCCGTCGCATCTTCGCACT
Found at i:299399 original size:21 final size:21
Alignment explanation
Indices: 299350--299412 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
299340 AGTATCACTC
* *
299350 CTTCGCCTTCGCACCTTCGCA
1 CTTCGCCGTCGCATCTTCGCA
*
299371 CTTTCGCCGTCGCATCTTCGCG
1 C-TTCGCCGTCGCATCTTCGCA
299393 CTTCGCCGTCGCATCTTCGC
1 CTTCGCCGTCGCATCTTCGC
299413 CCTTTCGCTC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 20 0.53
22 18 0.47
ACGTcount: A:0.06, C:0.44, G:0.19, T:0.30
Consensus pattern (21 bp):
CTTCGCCGTCGCATCTTCGCA
Found at i:301625 original size:12 final size:12
Alignment explanation
Indices: 301608--301645 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
301598 AAATCCAGGA
301608 TTTGTTAAGAAT
1 TTTGTTAAGAAT
*
301620 TTTGTTAAGAAA
1 TTTGTTAAGAAT
*
301632 ATTGTTAAGAAT
1 TTTGTTAAGAAT
301644 TT
1 TT
301646 GTTTTAACAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (12 bp):
TTTGTTAAGAAT
Found at i:301687 original size:62 final size:62
Alignment explanation
Indices: 301531--301692 Score: 297
Period size: 62 Copynumber: 2.6 Consensus size: 62
301521 ATTTTGTTTG
*
301531 GCCGCAAATCCAGGATTTGTTAAGAATTTTGTGAAGAAAATTGTTAAGAATTTGTTTTAACA
1 GCCGCAAATCCAGGATTTGTTAAGAATTTTGTTAAGAAAATTGTTAAGAATTTGTTTTAACA
301593 GCCGCAAATCCAGGATTTGTTAAGAATTTTGTTAAGAAAATTGTTAAGAATTTGTTTTAACA
1 GCCGCAAATCCAGGATTTGTTAAGAATTTTGTTAAGAAAATTGTTAAGAATTTGTTTTAACA
**
301655 GCCGCAAATCCAGGATTTGTTAAGAAAATTGTTAAGAA
1 GCCGCAAATCCAGGATTTGTTAAGAATTTTGTTAAGAA
301693 TTTGTCACTA
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 97 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.34
Consensus pattern (62 bp):
GCCGCAAATCCAGGATTTGTTAAGAATTTTGTTAAGAAAATTGTTAAGAATTTGTTTTAACA
Found at i:303933 original size:21 final size:21
Alignment explanation
Indices: 303909--303957 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
303899 GACAGAGGAG
303909 GGAGAAGA-AAAGCAGGAAGAT
1 GGAGAAGAGAAAG-AGGAAGAT
*
303930 GGAGAAGAGAAAGGGGAAGAT
1 GGAGAAGAGAAAGAGGAAGAT
*
303951 GAAGAAG
1 GGAGAAG
303958 GGGAAGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.51, C:0.02, G:0.43, T:0.04
Consensus pattern (21 bp):
GGAGAAGAGAAAGAGGAAGAT
Found at i:305121 original size:20 final size:20
Alignment explanation
Indices: 305096--305133 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
305086 AGGAGGGAGA
*
305096 AAAAGAAGGAGAAAAAGATG
1 AAAAGAAGAAGAAAAAGATG
305116 AAAAGAAGAAGAAAAAGA
1 AAAAGAAGAAGAAAAAGA
305134 AAGGAGAAAA
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:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (20 bp):
AAAAGAAGAAGAAAAAGATG
Found at i:305138 original size:33 final size:33
Alignment explanation
Indices: 305093--305169 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
305083 GAGAGGAGGG
*
305093 AGAAAAAG-AAGGAGAAAAAGATGA-AAAGAAGA
1 AGAAAAAGAAAGGAGAAAAAGAGGAGAAA-AAGA
*
305125 AGAAAAAGAAAGGAGAAAAAGAGGAGAAACAGA
1 AGAAAAAGAAAGGAGAAAAAGAGGAGAAAAAGA
*
305158 AGAAGAAGAAAG
1 AGAAAAAGAAAG
305170 CTCCAGTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
32 8 0.20
33 29 0.73
34 3 0.08
ACGTcount: A:0.68, C:0.01, G:0.30, T:0.01
Consensus pattern (33 bp):
AGAAAAAGAAAGGAGAAAAAGAGGAGAAAAAGA
Found at i:308555 original size:21 final size:21
Alignment explanation
Indices: 308531--308618 Score: 95
Period size: 21 Copynumber: 4.2 Consensus size: 21
308521 AGTAAAAAGC
* *
308531 AAGAAAAAGAAGAGGAGGAAG
1 AAGAAGAAGATGAGGAGGAAG
* *
308552 AAGAAGATGATGATGAGGAAG
1 AAGAAGAAGATGAGGAGGAAG
* *
308573 ATGATGAAGATGAGGAGGAAG
1 AAGAAGAAGATGAGGAGGAAG
* * *
308594 ATGAAGAAGAGGATGAGGAAG
1 AAGAAGAAGATGAGGAGGAAG
308615 AAGA
1 AAGA
308619 GTCTGAAAGT
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.40, T:0.09
Consensus pattern (21 bp):
AAGAAGAAGATGAGGAGGAAG
Found at i:308558 original size:18 final size:18
Alignment explanation
Indices: 308531--308618 Score: 68
Period size: 18 Copynumber: 4.6 Consensus size: 18
308521 AGTAAAAAGC
*
308531 AAGAAAAAGAAGAGGAGG
1 AAGAAGAAGAAGAGGAGG
*
308549 AAGAAGAAGATGATGATGAGG
1 AAGAAGAAGA--A-GAGGAGG
*
308570 AAGATGATGAAGATGAGGAGG
1 AAGA--A-GAAGAAGAGGAGG
* *
308591 AAGATGAAGAAGAGGATG
1 AAGAAGAAGAAGAGGAGG
*
308609 AGGAAGAAGA
1 AAGAAGAAGA
308619 GTCTGAAAGT
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
18 28 0.51
20 1 0.02
21 20 0.36
23 1 0.02
24 5 0.09
ACGTcount: A:0.51, C:0.00, G:0.40, T:0.09
Consensus pattern (18 bp):
AAGAAGAAGAAGAGGAGG
Found at i:308635 original size:18 final size:18
Alignment explanation
Indices: 308611--308654 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
308601 AGAGGATGAG
308611 GAAGAAGAGTCTGAAAGT
1 GAAGAAGAGTCTGAAAGT
*
308629 GAGGAAGAGTCTGAAAGT
1 GAAGAAGAGTCTGAAAGT
308647 GAAGAAGA
1 GAAGAAGA
308655 AGATTTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.45, C:0.05, G:0.36, T:0.14
Consensus pattern (18 bp):
GAAGAAGAGTCTGAAAGT
Found at i:310764 original size:146 final size:146
Alignment explanation
Indices: 310401--311230 Score: 1307
Period size: 146 Copynumber: 5.7 Consensus size: 146
310391 GTCTTTGCAA
*
310401 TCGTGTCCAGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
310466 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
*
310531 TGAAAAAAATGCAAAAT
131 AG-AAAAAATGCAAAAT
* * * *
310548 TTGTGTCCGTTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACATAAAGGTTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* *
310613 TTATGACCTAAGGGTGTGTCATGACCTTGACTCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
310678 AGAAAAAATGCAAAAT
131 AGAAAAAATGCAAAAT
*
310694 TCGTGTCCGGTCAATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
*
310759 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATT------AGGTCAAGGTCACTGAC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
*
310818 AGAAAAAGTGCAAAAT
131 AGAAAAAATGCAAAAT
* * *
310834 TTGTGTCAGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACATAAA-AGTTG
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGA-TTG
* *
310898 CTTATGACCTAAGGGTGTATCATGACCTTGACTCAAGGTCATTCGGGCAAGGTCAAGGTCACTGG
65 CTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGG
310963 CAGAAAAAATGCAAAAT
130 CAGAAAAAATGCAAAAT
* * *
310980 TCGTGCCCGGTCCATATCTTTCTTGTGGAGAAACATTGGATGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* * * *
311045 CTATGACCTAAGGGTGTGTCATGATCTTGACCCAAGGTCATTCAGGCAAGGTCAAGGTCACTGAC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
*
311110 AGAAAAAGTGCAAAAT
131 AGAAAAAATGCAAAAT
* * * * * *
311126 TTGTGTCC-ATATCATATCTTCCTTATGGAGAAACATTGGAAGTTCTTACTTCACATAAAGGTTG
1 TCGTGTCCGGT-CCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTG
311190 CTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCA
65 CTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCA
311231 GTTGCAGAAG
Statistics
Matches: 626, Mismatches: 48, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
139 1 0.00
140 130 0.21
145 1 0.00
146 369 0.59
147 125 0.20
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (146 bp):
TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
AGAAAAAATGCAAAAT
Found at i:310940 original size:286 final size:287
Alignment explanation
Indices: 310401--311230 Score: 1367
Period size: 286 Copynumber: 2.9 Consensus size: 287
310391 GTCTTTGCAA
*
310401 TCGTGTCCAGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
*
310466 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATT---G--AGGTCAAGGTCACTGAC
* * * *
310531 TGAAAAAAATGCAAAATTTGTGTCCGTTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTA
126 AG-AAAAAGTGCAAAATTTGTGTCAGATCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTA
*
310596 CTTCACATAAAGGTTGCTTATGACCTAAGGGTGTGTCATGACCTTGACTCAAGGTCATTTGGGCA
190 CTTCACATAAAGGTTGCTTATGACCTAAGGGTGTGTCATGACCTTGACTCAAGGTCATTCGGGCA
310661 AGGTCAAGGTCACTGGCAGAAAAAATGCAAAAT
255 AGGTCAAGGTCACTGGCAGAAAAAATGCAAAAT
*
310694 TCGTGTCCGGTCAATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
310759 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATT-AGGTCAAGGTCACTGACAGAAA
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTGAGGTCAAGGTCACTGACAGAAA
*
310823 AAGTGCAAAATTTGTGTCAGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCAC
131 AAGTGCAAAATTTGTGTCAGATCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCAC
* *
310888 ATAAAAGTTGCTTATGACCTAAGGGTGTATCATGACCTTGACTCAAGGTCATTCGGGCAAGGTCA
196 ATAAAGGTTGCTTATGACCTAAGGGTGTGTCATGACCTTGACTCAAGGTCATTCGGGCAAGGTCA
310953 AGGTCACTGGCAGAAAAAATGCAAAAT
261 AGGTCACTGGCAGAAAAAATGCAAAAT
* * *
310980 TCGTGCCCGGTCCATATCTTTCTTGTGGAGAAACATTGGATGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* *
311045 CTATGACCTAAGGGTGTGTCATGATCTTGACCCAAGGTCATTCAGGCAAGGTCAAGGTCACTGAC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATT---G--AGGTCAAGGTCACTGAC
* *
311110 AGAAAAAGTGCAAAATTTGTGTCCATAT-CATATCTTCCTTATGGAGAAACATTGGAAGTTCTTA
126 AGAAAAAGTGCAAAATTTGTGT-CAGATCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTA
*
311174 CTTCACATAAAGGTTGCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCA
190 CTTCACATAAAGGTTGCTTATGACCTAAGGGTGTGTCATGACCTTGACTCAAGGTCA
311231 GTTGCAGAAG
Statistics
Matches: 508, Mismatches: 22, Indels: 15
0.93 0.04 0.03
Matches are distributed among these distances:
286 255 0.50
287 17 0.03
292 128 0.25
293 108 0.21
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (287 bp):
TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTGAGGTCAAGGTCACTGACAGAAA
AAGTGCAAAATTTGTGTCAGATCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCAC
ATAAAGGTTGCTTATGACCTAAGGGTGTGTCATGACCTTGACTCAAGGTCATTCGGGCAAGGTCA
AGGTCACTGGCAGAAAAAATGCAAAAT
Found at i:311214 original size:432 final size:433
Alignment explanation
Indices: 310410--311230 Score: 1387
Period size: 432 Copynumber: 1.9 Consensus size: 433
310400 ATCGTGTCCA
*
310410 GTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGCTTATGACCT
1 GTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACAAAAAGATTGCTTATGACCT
* *
310475 AAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGCTGAAAAAAA
66 AAGGGTGTATCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGCAGAAAAAAA
* * * *
310540 TGCAAAATTTGTGTCCGTTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACATA
131 TGCAAAATTCGTGCCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACA
* * * **
310605 AAGGTTGCTTATGACCTAAGGGTGTGTCATGACCTTGACTCAAGGTCATTTGGGCAAGGTCAAGG
196 AAGATTGCCTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCAGGCAAGGTCAAGG
* * *
310670 TCACTGGCAGAAAAAATGCAAAATTCGTGTCCGGTCAATATCTTTCTTATGGAGAAACATTGGAA
261 TCACTGACAGAAAAAATGCAAAATTCGTGTCCGATCAATATCTTCCTTATGGAGAAACATTGGAA
310735 GTTCTTACTTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCAT
326 GTTCTTACTTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCAT
310800 TAGGTCAAGGTCACTGACAGAAAAAGTGCAAAATTTGTGTCAG
391 TAGGTCAAGGTCACTGACAGAAAAAGTGCAAAATTTGTGTCAG
310843 GTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACATAAAAG-TTGCTTATGACC
1 GTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACA-AAAAGATTGCTTATGACC
*
310907 TAAGGGTGTATCATGACCTTGACTCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGCAG-AAAAA
65 TAAGGGTGTATCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGCAGAAAAAA
* *
310971 ATGCAAAATTCGTGCCCGGTCCATATCTTTCTTGTGGAGAAACATTGGATGTTCTTACTTCACAC
130 ATGCAAAATTCGTGCCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACAC
*
311036 AAAGATTGCCTATGACCTAAGGGTGTGTCATGATCTTGACCCAAGGTCATTCAGGCAAGGTCAAG
195 AAAGATTGCCTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCAGGCAAGGTCAAG
* * *
311101 GTCACTGACAGAAAAAGTGCAAAATTTGTGTCCATATC-ATATCTTCCTTATGGAGAAACATTGG
260 GTCACTGACAGAAAAAATGCAAAATTCGTGTCC-GATCAATATCTTCCTTATGGAGAAACATTGG
* *
311165 AAGTTCTTACTTCACATAAAGGTTGCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTC
324 AAGTTCTTACTTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTC
311230 A
389 A
311231 GTTGCAGAAG
Statistics
Matches: 362, Mismatches: 24, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
432 242 0.67
433 116 0.32
434 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (433 bp):
GTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACAAAAAGATTGCTTATGACCT
AAGGGTGTATCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGCAGAAAAAAA
TGCAAAATTCGTGCCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACA
AAGATTGCCTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCAGGCAAGGTCAAGG
TCACTGACAGAAAAAATGCAAAATTCGTGTCCGATCAATATCTTCCTTATGGAGAAACATTGGAA
GTTCTTACTTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCAT
TAGGTCAAGGTCACTGACAGAAAAAGTGCAAAATTTGTGTCAG
Found at i:319046 original size:17 final size:17
Alignment explanation
Indices: 319021--319069 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 17
319011 TCAAAATCAG
*
319021 TTCGCTATATCCATAAA
1 TTCGTTATATCCATAAA
*
319038 TTCGTTATATCC--GAA
1 TTCGTTATATCCATAAA
*
319053 TTCGTTATAACCATAAA
1 TTCGTTATATCCATAAA
319070 AATTTGCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 13 0.50
17 13 0.50
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (17 bp):
TTCGTTATATCCATAAA
Found at i:343108 original size:2 final size:2
Alignment explanation
Indices: 343101--343150 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
343091 TTCGAGAAAA
* *
343101 TC TC TC TC TC AC TC TC TC TC TC TC TC TC TC TC AC 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
*
343143 TT TC TC TC
1 TC TC TC TC
343151 ATGATTTTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.04, C:0.48, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:346843 original size:22 final size:22
Alignment explanation
Indices: 346817--346860 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
346807 TGTTGAGGAT
346817 GGAAGTTTGTGGGTGAGGGGGC
1 GGAAGTTTGTGGGTGAGGGGGC
346839 GGAAGTTTGTGGGTGAGGGGGC
1 GGAAGTTTGTGGGTGAGGGGGC
346861 CCCTGAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.05, G:0.59, T:0.23
Consensus pattern (22 bp):
GGAAGTTTGTGGGTGAGGGGGC
Found at i:359089 original size:16 final size:16
Alignment explanation
Indices: 359056--359091 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
359046 CAACGGTGGC
* *
359056 CTATATAGGTACAGAG
1 CTATATAGGTAAAAAG
359072 CTATATAGGTAAAAAG
1 CTATATAGGTAAAAAG
359088 CTAT
1 CTAT
359092 TAAAGTGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (16 bp):
CTATATAGGTAAAAAG
Found at i:364009 original size:2 final size:2
Alignment explanation
Indices: 364002--364032 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
363992 CTACAAAGCA
364002 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
364033 ATAAGTCAAG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:369024 original size:36 final size:36
Alignment explanation
Indices: 368984--369077 Score: 152
Period size: 36 Copynumber: 2.6 Consensus size: 36
368974 TGGAGTGTTC
* * *
368984 GATGAGTTCTGATTGTTGCATTATGTGGAGACTTTT
1 GATGAGTTCTGATTGTTGCATTATGCGGAAACATTT
369020 GATGAGTTCTGATTGTTGCATTATGCGGAAACATTT
1 GATGAGTTCTGATTGTTGCATTATGCGGAAACATTT
*
369056 GATGAGTCCTGATTGTTGCATT
1 GATGAGTTCTGATTGTTGCATT
369078 TGTTCTACAT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.21, C:0.11, G:0.27, T:0.41
Consensus pattern (36 bp):
GATGAGTTCTGATTGTTGCATTATGCGGAAACATTT
Found at i:373688 original size:39 final size:39
Alignment explanation
Indices: 373634--373712 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
373624 TGCAAAAAAT
373634 TAAGACTTTTTTCAATTTCATTATTCTTATTTGGATATG
1 TAAGACTTTTTTCAATTTCATTATTCTTATTTGGATATG
373673 TAAGACTTTTTTCAATTTCATTATTCTTATTTGGATATG
1 TAAGACTTTTTTCAATTTCATTATTCTTATTTGGATATG
373712 T
1 T
373713 TAATGGGTGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.54
Consensus pattern (39 bp):
TAAGACTTTTTTCAATTTCATTATTCTTATTTGGATATG
Found at i:375796 original size:2 final size:2
Alignment explanation
Indices: 375789--375846 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
375779 TGAAAACAAA
375789 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
375831 CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT
375847 GCACTAACTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:377669 original size:2 final size:2
Alignment explanation
Indices: 377662--377706 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
377652 CTGATGTCCT
377662 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
377704 AG A
1 AG A
377707 TCAATTTTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:384683 original size:2 final size:2
Alignment explanation
Indices: 384676--384710 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
384666 AAAATCTCAA
384676 TC TC TC TC TC 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 TC TC TC TC TC T
384711 TTTAGAAAAG
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:394111 original size:123 final size:123
Alignment explanation
Indices: 393728--394096 Score: 657
Period size: 123 Copynumber: 3.0 Consensus size: 123
393718 ATAACTTTCA
* * *
393728 AAATTATCACTGTAAATAATTACAGGTTTATTTACAGTTAGTATTTTTGCATCTTATTCTCTGAA
1 AAATTATCAATGTAAATAATTACAGGTTTATTTACAGTTAGTATTTTTACATCGTATTCTCTGAA
393793 ACCAATAAAAATATTAATGTGAGAAGAAAAAACAAATCCCGCCAAATACTGAAAAACC
66 ACCAATAAAAATATTAATGTGAGAAGAAAAAACAAATCCCGCCAAATACTGAAAAACC
*
393851 AAATTATCAATGTAAATAATTACAAGTTTATTTACAGTTAGTATTTTTACATCGTATTCTCTGAA
1 AAATTATCAATGTAAATAATTACAGGTTTATTTACAGTTAGTATTTTTACATCGTATTCTCTGAA
* * *
393916 CCCAATAAAAATATCAATGTGAGAAGAAAAAACAAATCCCGCCAAACACTGAAAAACC
66 ACCAATAAAAATATTAATGTGAGAAGAAAAAACAAATCCCGCCAAATACTGAAAAACC
393974 AAATTATCAATGTAAATAATTACAGGTTTATTTACAGTTAGTATTTTTACATCGTATTCTCTGAA
1 AAATTATCAATGTAAATAATTACAGGTTTATTTACAGTTAGTATTTTTACATCGTATTCTCTGAA
* *
394039 ACCAATAAAAATATTATTGTGAGAAGAAAAAACAAATCCCGCCGAATACTGAAAAACC
66 ACCAATAAAAATATTAATGTGAGAAGAAAAAACAAATCCCGCCAAATACTGAAAAACC
394097 GATTTCAGTT
Statistics
Matches: 233, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
123 233 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.30
Consensus pattern (123 bp):
AAATTATCAATGTAAATAATTACAGGTTTATTTACAGTTAGTATTTTTACATCGTATTCTCTGAA
ACCAATAAAAATATTAATGTGAGAAGAAAAAACAAATCCCGCCAAATACTGAAAAACC
Found at i:396653 original size:21 final size:21
Alignment explanation
Indices: 396629--396735 Score: 124
Period size: 21 Copynumber: 5.1 Consensus size: 21
396619 GTGCTAGAAT
396629 CGTTTCGTGTAAACCGTTCAG
1 CGTTTCGTGTAAACCGTTCAG
* * *
396650 CGTTTCGTGTTAATCGTTTAG
1 CGTTTCGTGTAAACCGTTCAG
* * * *
396671 CGTTTCGGGCAAAGCGTGCAG
1 CGTTTCGTGTAAACCGTTCAG
*
396692 CGTATCGTGTAAACCGTTCAG
1 CGTTTCGTGTAAACCGTTCAG
* *
396713 CGTTTCGTGTGAACCGTTTAG
1 CGTTTCGTGTAAACCGTTCAG
396734 CG
1 CG
396736 AGCGTGTAGC
Statistics
Matches: 69, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 69 1.00
ACGTcount: A:0.18, C:0.21, G:0.28, T:0.33
Consensus pattern (21 bp):
CGTTTCGTGTAAACCGTTCAG
Found at i:396747 original size:11 final size:11
Alignment explanation
Indices: 396731--396764 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
396721 GTGAACCGTT
396731 TAGCGAGCGTG
1 TAGCGAGCGTG
396742 TAGCGAGCGTG
1 TAGCGAGCGTG
*
396753 CAGCGAGCGTG
1 TAGCGAGCGTG
396764 T
1 T
396765 GGTGTAGTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.18, C:0.21, G:0.44, T:0.18
Consensus pattern (11 bp):
TAGCGAGCGTG
Found at i:396764 original size:63 final size:63
Alignment explanation
Indices: 396634--396764 Score: 160
Period size: 63 Copynumber: 2.1 Consensus size: 63
396624 AGAATCGTTT
* * ** *
396634 CGTGTAAACCGTTCAGCGTTTCGTGTTAATCGTTTAGCGTTTCGGGCAAAGCGTGCAGCGTAT
1 CGTGTAAACCGTTCAGCGTTTCGTGTGAACCGTTTAGCGTAGCGGGCAAAGCGTGCAGCGTAG
*
396697 CGTGTAAACCGTTCAGCGTTTCGTGTGAACCGTTTAGCG-AGCGTGTAGC-GAGCGTGCAGCG-A
1 CGTGTAAACCGTTCAGCGTTTCGTGTGAACCGTTTAGCGTAGCG-G--GCAAAGCGTGCAGCGTA
396759 G
63 G
396760 CGTGT
1 CGTGT
396765 GGTGTAGTAG
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
62 2 0.03
63 44 0.75
64 11 0.19
65 2 0.03
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.28
Consensus pattern (63 bp):
CGTGTAAACCGTTCAGCGTTTCGTGTGAACCGTTTAGCGTAGCGGGCAAAGCGTGCAGCGTAG
Found at i:399849 original size:7 final size:7
Alignment explanation
Indices: 399837--399903 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
399827 GAGAAGGATC
399837 ATTCGAG
1 ATTCGAG
399844 ATTCGAG
1 ATTCGAG
*
399851 ATTCGAA
1 ATTCGAG
*
399858 ATACGAG
1 ATTCGAG
*
399865 ATTCGAA
1 ATTCGAG
*
399872 ATACGAG
1 ATTCGAG
399879 ATTCGAG
1 ATTCGAG
*
399886 ATTCGAA
1 ATTCGAG
399893 ATTCGAG
1 ATTCGAG
399900 ATTC
1 ATTC
399904 AATATCTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (7 bp):
ATTCGAG
Found at i:402614 original size:7 final size:7
Alignment explanation
Indices: 402599--402651 Score: 79
Period size: 7 Copynumber: 7.6 Consensus size: 7
402589 TTTAGATATT
402599 GAATCTC
1 GAATCTC
*
402606 GAATTTC
1 GAATCTC
402613 GAATCTC
1 GAATCTC
402620 GAATCTC
1 GAATCTC
* *
402627 GTATTTC
1 GAATCTC
402634 GAATCTC
1 GAATCTC
402641 GAATCTC
1 GAATCTC
402648 GAAT
1 GAAT
402652 GATCCTTCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (7 bp):
GAATCTC
Found at i:402624 original size:21 final size:21
Alignment explanation
Indices: 402599--402651 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
402589 TTTAGATATT
402599 GAATCTCGAATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
*
402620 GAATCTCGTATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
402641 GAATCTCGAAT
1 GAATCTCGAAT
402652 GATCCTTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (21 bp):
GAATCTCGAATTTCGAATCTC
Found at i:407560 original size:11 final size:11
Alignment explanation
Indices: 407546--407587 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
407536 ACTAGAGTGG
407546 ACCCAGAGTAA
1 ACCCAGAGTAA
*
407557 ACCCAGATTAA
1 ACCCAGAGTAA
407568 ACCACA-AGTAA
1 ACC-CAGAGTAA
407579 ACCCAGAGT
1 ACCCAGAGT
407588 GGACACAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 2 0.07
11 23 0.85
12 2 0.07
ACGTcount: A:0.45, C:0.29, G:0.14, T:0.12
Consensus pattern (11 bp):
ACCCAGAGTAA
Found at i:407778 original size:11 final size:11
Alignment explanation
Indices: 407764--407798 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
407754 GTAAATCCAA
407764 AGTAAACCCCG
1 AGTAAACCCCG
*
407775 AGTAAA-CCCA
1 AGTAAACCCCG
407785 AGTAAACCCCG
1 AGTAAACCCCG
407796 AGT
1 AGT
407799 GGATCCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.40, C:0.31, G:0.17, T:0.11
Consensus pattern (11 bp):
AGTAAACCCCG
Found at i:407789 original size:21 final size:22
Alignment explanation
Indices: 407751--407807 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
407741 AAGCAATTCT
407751 CGAGTAAATCCAAAGTAAACCC
1 CGAGTAAATCCAAAGTAAACCC
*
407773 CGAGTAAA-CCCAAGTAAACCC
1 CGAGTAAATCCAAAGTAAACCC
**
407794 CGAGTGGATCCAAA
1 CGAGTAAATCCAAA
407808 TTTTCAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.42, C:0.28, G:0.18, T:0.12
Consensus pattern (22 bp):
CGAGTAAATCCAAAGTAAACCC
Found at i:407790 original size:10 final size:11
Alignment explanation
Indices: 407753--407794 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
407743 GCAATTCTCG
* *
407753 AGTAAATCCAA
1 AGTAAACCCCA
*
407764 AGTAAACCCCG
1 AGTAAACCCCA
407775 AGTAAA-CCCA
1 AGTAAACCCCA
407785 AGTAAACCCC
1 AGTAAACCCC
407795 GAGTGGATCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.45, C:0.31, G:0.12, T:0.12
Consensus pattern (11 bp):
AGTAAACCCCA
Found at i:407831 original size:11 final size:12
Alignment explanation
Indices: 407814--407849 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
407804 CAAATTTTCA
407814 AAAAGTAAACCC
1 AAAAGTAAACCC
407826 -AAAGTAAACCC
1 AAAAGTAAACCC
407837 AGAAAGTAAACCC
1 A-AAAGTAAACCC
407850 GGAGTTTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.50
13 11 0.50
ACGTcount: A:0.56, C:0.25, G:0.11, T:0.08
Consensus pattern (12 bp):
AAAAGTAAACCC
Found at i:410849 original size:2 final size:2
Alignment explanation
Indices: 410844--410890 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
410834 ACACCCCCCC
410844 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
410886 CT CT C
1 CT CT C
410891 GTGTGTGATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:412176 original size:2 final size:2
Alignment explanation
Indices: 412169--412208 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
412159 CATGTACATG
412169 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
412209 NNNNNNNNNN
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:417647 original size:21 final size:20
Alignment explanation
Indices: 417621--417697 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 20
417611 CTCTCTATTT
417621 ATGTCGACTTGTCAGATCTTG
1 ATGTCGACTTGTCAGATC-TG
* *
417642 ATGTCGACTTGTCAGATAATA
1 ATGTCGACTTGTCAGAT-CTG
* *
417663 ATGTGGACTTGTCAGTTCTG
1 ATGTCGACTTGTCAGATCTG
*
417683 TAAGTCGACTTGTCA
1 -ATGTCGACTTGTCA
417698 CTTATCCCCG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 1 0.02
21 45 0.98
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATGTCGACTTGTCAGATCTG
Found at i:417804 original size:21 final size:21
Alignment explanation
Indices: 417774--417907 Score: 117
Period size: 21 Copynumber: 6.4 Consensus size: 21
417764 AATAATATTT
* *
417774 TCTGACAAGTCAACATAAGGA
1 TCTGACAAGTCGACATAAGTA
* * *
417795 TCTGATAAGTCGACATTAGCA
1 TCTGACAAGTCGACATAAGTA
** *
417816 TCTGTTAAGTCGACATAATTA
1 TCTGACAAGTCGACATAAGTA
* * *
417837 TTTGAAAAGTCGACATAATTA
1 TCTGACAAGTCGACATAAGTA
* *
417858 TCTGACAAGTCGACATAACTT
1 TCTGACAAGTCGACATAAGTA
* * *
417879 TTTGACAAGACGACATAA-CA
1 TCTGACAAGTCGACATAAGTA
417899 TCTGACAAG
1 TCTGACAAG
417908 ACAACATCAT
Statistics
Matches: 93, Mismatches: 20, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
20 8 0.09
21 85 0.91
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (21 bp):
TCTGACAAGTCGACATAAGTA
Found at i:418125 original size:21 final size:21
Alignment explanation
Indices: 418099--418215 Score: 92
Period size: 21 Copynumber: 5.6 Consensus size: 21
418089 ATTATGTTAA
*
418099 TTATGTTAACTTGTCAGATCG
1 TTATGTCAACTTGTCAGATCG
* * * * **
418120 TTATGTCGACTGGACAAATAA
1 TTATGTCAACTTGTCAGATCG
* *
418141 TTATGTTAACTTGTCAGATCT
1 TTATGTCAACTTGTCAGATCG
*
418162 TTATGTCGACTTGTCAGAT-G
1 TTATGTCAACTTGTCAGATCG
* **
418182 ATTATGTAAACTTGTCAGATAT
1 -TTATGTCAACTTGTCAGATCG
*
418204 TTATGTCGACTT
1 TTATGTCAACTT
418216 ATATGATATT
Statistics
Matches: 72, Mismatches: 22, Indels: 4
0.73 0.22 0.04
Matches are distributed among these distances:
21 72 1.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (21 bp):
TTATGTCAACTTGTCAGATCG
Done.