Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 1 of 230
Found at i:381 original size:3 final size:3
Alignment explanation
Indices: 373--407 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
363 GATTTAGTCC
373 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
408 CCTATTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1051 original size:24 final size:25
Alignment explanation
Indices: 1009--1061 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
999 AAATATACTT
*
1009 TATACATTTTGTTAATTTATATATA
1 TATACATATTGTTAATTTATATATA
* * *
1034 TATACATATT-TTAGTTTATGTCTA
1 TATACATATTGTTAATTTATATATA
1058 TATA
1 TATA
1062 TATCTTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.55
Consensus pattern (25 bp):
TATACATATTGTTAATTTATATATA
Found at i:10997 original size:6 final size:7
Alignment explanation
Indices: 10980--11004 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
10970 CAACAAAGTT
10980 TTTTTCC
1 TTTTTCC
10987 TTTTTCC
1 TTTTTCC
10994 TTTTTCC
1 TTTTTCC
11001 TTTT
1 TTTT
11005 ATATATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCC
Found at i:19584 original size:12 final size:14
Alignment explanation
Indices: 19559--19591 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
19549 TACAGAACAG
19559 GAAAAAAGGAAAAA
1 GAAAAAAGGAAAAA
19573 GAAAAAA-G-AAAA
1 GAAAAAAGGAAAAA
19585 GAAAAAA
1 GAAAAAA
19592 AGGGATTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 1 0.05
14 7 0.37
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
GAAAAAAGGAAAAA
Found at i:22004 original size:20 final size:22
Alignment explanation
Indices: 21979--22021 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
21969 TAAAAATTTT
*
21979 ATTTATTTTTAT-CGTTA-CAA
1 ATTTATCTTTATACGTTAGCAA
21999 ATTTATCTTTATACGTTAGCAA
1 ATTTATCTTTATACGTTAGCAA
22021 A
1 A
22022 ATGTACAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 5 0.25
22 4 0.20
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.49
Consensus pattern (22 bp):
ATTTATCTTTATACGTTAGCAA
Found at i:27776 original size:27 final size:27
Alignment explanation
Indices: 27746--27831 Score: 127
Period size: 27 Copynumber: 3.2 Consensus size: 27
27736 GTGGCTGAAG
** *
27746 AGGTGGGACCTTTGAAGGTGCCTTCAC
1 AGGTGGGACCTTCAAAGGTGCCTTCGC
*
27773 AGGTGGGACCTTCAAAGGTGCCTCCGC
1 AGGTGGGACCTTCAAAGGTGCCTTCGC
*
27800 AGGTGGGACCTTCAAAGGCGCCTTCGC
1 AGGTGGGACCTTCAAAGGTGCCTTCGC
27827 AGGTG
1 AGGTG
27832 TCTAAACCAG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.19, C:0.26, G:0.35, T:0.21
Consensus pattern (27 bp):
AGGTGGGACCTTCAAAGGTGCCTTCGC
Found at i:28383 original size:13 final size:14
Alignment explanation
Indices: 28356--28384 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28346 TATTTGGTTA
28356 TTGGTTTAGTTAGG
1 TTGGTTTAGTTAGG
28370 TTGGTTTA-TTAGG
1 TTGGTTTAGTTAGG
28383 TT
1 TT
28385 ATGTTGGTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.14, C:0.00, G:0.31, T:0.55
Consensus pattern (14 bp):
TTGGTTTAGTTAGG
Found at i:34251 original size:17 final size:18
Alignment explanation
Indices: 34229--34262 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
34219 ATCCCATGTT
34229 ATTTTTTTTA-ATTTTTA
1 ATTTTTTTTATATTTTTA
34246 ATTTTTTTTATATTTTT
1 ATTTTTTTTATATTTTT
34263 TAAATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (18 bp):
ATTTTTTTTATATTTTTA
Found at i:40844 original size:6 final size:6
Alignment explanation
Indices: 40833--40876 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
40823 CTTTCAGTAC
*
40833 ATACAT ATACAT ATGCAT GCAATACAT ATACAT ATACAT ATACA
1 ATACAT ATACAT ATACAT ---ATACAT ATACAT ATACAT ATACA
40877 AAGATTAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 28 0.85
9 5 0.15
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.30
Consensus pattern (6 bp):
ATACAT
Found at i:50937 original size:23 final size:23
Alignment explanation
Indices: 50907--50953 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
50897 CTGAACCTAC
50907 TATAACCCATCAATAAAATAAAT
1 TATAACCCATCAATAAAATAAAT
50930 TATAACCCATCAATAAAATAAAT
1 TATAACCCATCAATAAAATAAAT
50953 T
1 T
50954 CATTCAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TATAACCCATCAATAAAATAAAT
Found at i:51179 original size:42 final size:42
Alignment explanation
Indices: 51118--51273 Score: 150
Period size: 42 Copynumber: 3.7 Consensus size: 42
51108 AAAGTCTGAA
* * *
51118 GGTTGAACAGAGGCACATAAGTGCTAAACAGAAACTCATAAG
1 GGTTGAACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAG
* * * *
51160 GGTTGAACGGAAGCTCATAAGAGCTAAACGGAAACCCATACG
1 GGTTGAACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAG
* * * * * * * *
51202 GGTTAAACAGAGGCTCAAAAGAGTTGAACGGTAACTCATATG
1 GGTTGAACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAG
* * *
51244 AGTTGAACAGAAGCTCGTGAGAGCTAAACA
1 GGTTGAACAGAAGCTCATAAGAGCTAAACA
51274 AAAAGTAAAC
Statistics
Matches: 89, Mismatches: 25, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 89 1.00
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (42 bp):
GGTTGAACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAG
Found at i:51208 original size:21 final size:21
Alignment explanation
Indices: 51133--51241 Score: 74
Period size: 21 Copynumber: 5.2 Consensus size: 21
51123 AACAGAGGCA
* * *
51133 CATAAGTGCTAAACAGAAACT
1 CATAAGGGTTAAACGGAAACT
* *
51154 CATAAGGGTTGAACGGAAGCT
1 CATAAGGGTTAAACGGAAACT
* * *
51175 CATAAGAGCTAAACGGAAACC
1 CATAAGGGTTAAACGGAAACT
* * **
51196 CATACGGGTTAAACAGAGGCT
1 CATAAGGGTTAAACGGAAACT
* * * *
51217 CAAAAGAGTTGAACGGTAACT
1 CATAAGGGTTAAACGGAAACT
51238 CATA
1 CATA
51242 TGAGTTGAAC
Statistics
Matches: 62, Mismatches: 26, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.17
Consensus pattern (21 bp):
CATAAGGGTTAAACGGAAACT
Found at i:54135 original size:24 final size:24
Alignment explanation
Indices: 54108--54159 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
54098 TTAGTAAGTC
*
54108 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
54132 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
54156 AAAT
1 AAAT
54160 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:76117 original size:16 final size:17
Alignment explanation
Indices: 76085--76127 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
76075 TTTTATCTCG
76085 AATTATTTTAAATTTAA-
1 AATT-TTTTAAATTTAAT
76102 AATATTTTTAAA-TTAAT
1 AAT-TTTTTAAATTTAAT
76119 AATTTTTTA
1 AATTTTTTA
76128 TAATCAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.42
17 13 0.54
18 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTTTTAAATTTAAT
Found at i:84704 original size:16 final size:16
Alignment explanation
Indices: 84685--84718 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
84675 TATATATATA
*
84685 TATATAGACACACACT
1 TATATACACACACACT
*
84701 TATATACATACACACT
1 TATATACACACACACT
84717 TA
1 TA
84719 ACAGAAGCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.24, G:0.03, T:0.29
Consensus pattern (16 bp):
TATATACACACACACT
Found at i:87233 original size:24 final size:23
Alignment explanation
Indices: 87195--87239 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
87185 GAAAACTTAA
87195 AATAATTATGATAAATTTAAAAT
1 AATAATTATGATAAATTTAAAAT
*
87218 AATAATATGTGATAAATTTAAA
1 AATAAT-TATGATAAATTTAAA
87240 CAACATTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (23 bp):
AATAATTATGATAAATTTAAAAT
Found at i:99743 original size:21 final size:21
Alignment explanation
Indices: 99718--99759 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
99708 TGTTTTTACA
* *
99718 AAATTATCCCTTTTAACTTTT
1 AAATTATACCTTTTAAATTTT
*
99739 AAATTTTACCTTTTAAATTTT
1 AAATTATACCTTTTAAATTTT
99760 TTTTTAAGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (21 bp):
AAATTATACCTTTTAAATTTT
Found at i:99751 original size:14 final size:14
Alignment explanation
Indices: 99728--99759 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
99718 AAATTATCCC
99728 TTTTAACTTTTAAA
1 TTTTAACTTTTAAA
*
99742 TTTTACCTTTTAAA
1 TTTTAACTTTTAAA
99756 TTTT
1 TTTT
99760 TTTTTAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTAACTTTTAAA
Found at i:101978 original size:3 final size:3
Alignment explanation
Indices: 101970--102003 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
101960 AACCAAACAA
*
101970 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
102004 GTCCAAAGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:111196 original size:19 final size:19
Alignment explanation
Indices: 111172--111208 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
111162 TATCTAAACT
111172 CACCCTAAGTCACTAGGAA
1 CACCCTAAGTCACTAGGAA
111191 CACCCTAAGTCACTAGGA
1 CACCCTAAGTCACTAGGA
111209 GTCAATTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.32, G:0.16, T:0.16
Consensus pattern (19 bp):
CACCCTAAGTCACTAGGAA
Found at i:115452 original size:37 final size:37
Alignment explanation
Indices: 115402--115479 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
115392 TTCTACAGGC
* *
115402 TAAATTTGTTAAAT-TATGACTAATTTGACAGAATGTG
1 TAAATTTGTTAAATCAATAAC-AATTTGACAGAATGTG
* *
115439 TAAATTTTTTAAATCAATAACAATTTGATAGAATGTG
1 TAAATTTGTTAAATCAATAACAATTTGACAGAATGTG
115476 TAAA
1 TAAA
115480 CTTTAAAGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 32 0.89
38 4 0.11
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.40
Consensus pattern (37 bp):
TAAATTTGTTAAATCAATAACAATTTGACAGAATGTG
Found at i:129356 original size:7 final size:7
Alignment explanation
Indices: 129344--129376 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
129334 TTGTAAGCAA
129344 AAAAAAG
1 AAAAAAG
129351 AAAAAAG
1 AAAAAAG
129358 -AAAAAG
1 AAAAAAG
129364 AAAAAAAG
1 -AAAAAAG
129372 AAAAA
1 AAAAA
129377 CCAAATGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
7 12 0.50
8 6 0.25
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:140644 original size:16 final size:17
Alignment explanation
Indices: 140623--140655 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
140613 TCCACACAAC
*
140623 AAAATTGATTTG-TTTT
1 AAAATTAATTTGCTTTT
140639 AAAATTAATTTGCTTTT
1 AAAATTAATTTGCTTTT
140656 GGTCCCTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (17 bp):
AAAATTAATTTGCTTTT
Found at i:151343 original size:97 final size:97
Alignment explanation
Indices: 151227--151417 Score: 364
Period size: 97 Copynumber: 2.0 Consensus size: 97
151217 AATCCTCACA
*
151227 CCTTCTAGCTTCTATTCAAGCATACAAAAGCAAAGAGAAATCACCTTAGAACCAGAAATCGCGTC
1 CCTTCTAGCTTCTATTCAAGCATACAAAAGCAAAGAGAAATCACCTTAGAACCAGAAATCGCATC
151292 GTTTCCTCTGCTTCGAAGCCTTCTTTTTCGGG
66 GTTTCCTCTGCTTCGAAGCCTTCTTTTTCGGG
*
151324 CCTTCTAGCTTCTATTCAAGCATACAAAAGCAAAGAGAAATCATCTTAGAACCAGAAATCGCATC
1 CCTTCTAGCTTCTATTCAAGCATACAAAAGCAAAGAGAAATCACCTTAGAACCAGAAATCGCATC
151389 GTTTCCTCTGCTTCGAAGCCTTCTTTTTC
66 GTTTCCTCTGCTTCGAAGCCTTCTTTTTC
151418 TCCGGGCTGC
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 92 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.30
Consensus pattern (97 bp):
CCTTCTAGCTTCTATTCAAGCATACAAAAGCAAAGAGAAATCACCTTAGAACCAGAAATCGCATC
GTTTCCTCTGCTTCGAAGCCTTCTTTTTCGGG
Found at i:155796 original size:59 final size:58
Alignment explanation
Indices: 155678--155800 Score: 133
Period size: 59 Copynumber: 2.1 Consensus size: 58
155668 CTCTAGGTCT
* * * *
155678 TTCAAGGACTAACTTGGACAAAAAAATTTCAAGCCCCAATATAGGAATAATTGTCAAG
1 TTCAAGGACTAACTTGAAAAAAAAAATTTCAAGCCCCAATATAGGAACAATTATCAAG
* * * * *
155736 TTCAAGGCCTAACTTGAATAAAAAAAAGTTT-AATCCCCAGTGTGGGAACAATTATCAAG
1 TTCAAGGACTAACTTGAA-AAAAAAAA-TTTCAAGCCCCAATATAGGAACAATTATCAAG
155795 TT-AAGG
1 TTCAAGG
155801 GCCTTTAAAC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
58 20 0.37
59 31 0.57
60 3 0.06
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.25
Consensus pattern (58 bp):
TTCAAGGACTAACTTGAAAAAAAAAATTTCAAGCCCCAATATAGGAACAATTATCAAG
Found at i:157291 original size:31 final size:31
Alignment explanation
Indices: 157256--157331 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
157246 ATAAAGGAAT
* *
157256 AATTGCCAAGTTCA-GACCTCAATGTGAGAAC
1 AATTGCCAAGTTCAGGACC-CAATATAAGAAC
* *
157287 AATTGCTAAGTTCAGGTCCCAATATAAGAAC
1 AATTGCCAAGTTCAGGACCCAATATAAGAAC
*
157318 AATTACCAAGTTCA
1 AATTGCCAAGTTCA
157332 AATATTAACT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 35 0.92
32 3 0.08
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (31 bp):
AATTGCCAAGTTCAGGACCCAATATAAGAAC
Found at i:161731 original size:21 final size:21
Alignment explanation
Indices: 161705--161745 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
161695 AGACGAGCAA
*
161705 TACTCCACAACAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
161726 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
161746 TTGAGCAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:167806 original size:44 final size:46
Alignment explanation
Indices: 167748--167842 Score: 104
Period size: 44 Copynumber: 2.1 Consensus size: 46
167738 GATTTTGATG
* * *
167748 TTTTTTGGAGATTTCAAAGG-GGGATCGATAGTATTTTA-GGGGGA
1 TTTTTTGGAGATTTCAAAGGAAGAAGCGATAGTATTTTAGGGGGGA
* * * * *
167792 TTTTTTTGATATTTCGATGGAAGAAGGGATAGTATTTTAGGGGGGA
1 TTTTTTGGAGATTTCAAAGGAAGAAGCGATAGTATTTTAGGGGGGA
167838 TTTTT
1 TTTTT
167843 AGAGAGGAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
44 16 0.39
45 14 0.34
46 11 0.27
ACGTcount: A:0.24, C:0.03, G:0.32, T:0.41
Consensus pattern (46 bp):
TTTTTTGGAGATTTCAAAGGAAGAAGCGATAGTATTTTAGGGGGGA
Found at i:168025 original size:17 final size:17
Alignment explanation
Indices: 168003--168036 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
167993 GTTTCCTTTT
168003 CATTTTTTTTTAAAAAA
1 CATTTTTTTTTAAAAAA
168020 CATTTTTTTTTAAAAAA
1 CATTTTTTTTTAAAAAA
168037 AAAAAGAGAG
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:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
CATTTTTTTTTAAAAAA
Found at i:168657 original size:15 final size:15
Alignment explanation
Indices: 168639--168688 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
168629 AATTATTTTC
168639 CTATTATTTATTATA
1 CTATTATTTATTATA
*
168654 CTA-T-TTT-TTACA
1 CTATTATTTATTATA
168666 CTATTATTTATTATA
1 CTATTATTTATTATA
168681 CTTATTAT
1 C-TATTAT
168689 ATCATTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
12 7 0.24
13 4 0.14
14 4 0.14
15 8 0.28
16 6 0.21
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (15 bp):
CTATTATTTATTATA
Found at i:180291 original size:30 final size:29
Alignment explanation
Indices: 180246--180337 Score: 105
Period size: 30 Copynumber: 3.0 Consensus size: 29
180236 AATTCAAATG
**
180246 TATATGTTTTATATATTGCCGAATTGATT
1 TATATGTAATATATATTGCCGAATTGATT
180275 TATATGTAGATATATATATTGCCGAATTGATTT
1 TATATGT--A-ATATATATTGCCGAATTGA-TT
*
180308 GTATATGT-ATATATATTGCCAAATTGATT
1 -TATATGTAATATATATTGCCGAATTGATT
180337 T
1 T
180338 GAGATCCCGT
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
28 1 0.02
29 9 0.16
30 18 0.33
32 18 0.33
33 2 0.04
34 7 0.13
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.48
Consensus pattern (29 bp):
TATATGTAATATATATTGCCGAATTGATT
Found at i:180338 original size:30 final size:31
Alignment explanation
Indices: 180244--180338 Score: 129
Period size: 32 Copynumber: 3.1 Consensus size: 31
180234 TGAATTCAAA
* *
180244 TGTATATGTTTTATATATTGCCGAATTGATT
1 TGTATATGATATATATATTGCCGAATTGATT
* *
180275 TATATGTAGATATATATATTGCCGAATTGATT
1 TGTATAT-GATATATATATTGCCGAATTGATT
*
180307 TGTATATG-TATATATATTGCCAAATTGATT
1 TGTATATGATATATATATTGCCGAATTGATT
180337 TG
1 TG
180339 AGATCCCGTA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
30 23 0.41
31 6 0.11
32 27 0.48
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (31 bp):
TGTATATGATATATATATTGCCGAATTGATT
Found at i:180568 original size:48 final size:48
Alignment explanation
Indices: 180333--180567 Score: 328
Period size: 48 Copynumber: 4.9 Consensus size: 48
180323 TTGCCAAATT
* * *
180333 GATTTGAGATCCCGTATAAGACTATATTTGGGATATGACATCGGCATC
1 GATTTGAGATCTCGTATAAGACCATATCTGGGATATGACATCGGCATC
* *
180381 GATTTGAGATC-CTGTATAAGACCATGTCTGGGATATGGCATCGGCATC
1 GATTTGAGATCTC-GTATAAGACCATATCTGGGATATGACATCGGCATC
* * * *
180429 GATTTGAGATCTCGTATAATACCATGTCTAGGATATGACATCGGTATC
1 GATTTGAGATCTCGTATAAGACCATATCTGGGATATGACATCGGCATC
* * *
180477 GATTTGAGATCTCGTATAAGACCATATCTTGGATATGACATCGACATT
1 GATTTGAGATCTCGTATAAGACCATATCTGGGATATGACATCGGCATC
* *
180525 GATTTGAGATTTCGTATAAGACCATATCTGGGATATGAGATCG
1 GATTTGAGATCTCGTATAAGACCATATCTGGGATATGACATCG
180568 ATGTGAGACT
Statistics
Matches: 168, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
47 1 0.01
48 166 0.99
49 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (48 bp):
GATTTGAGATCTCGTATAAGACCATATCTGGGATATGACATCGGCATC
Found at i:180588 original size:42 final size:42
Alignment explanation
Indices: 180474--180622 Score: 131
Period size: 48 Copynumber: 3.4 Consensus size: 42
180464 TGACATCGGT
* * * *
180474 ATCGATTTGAGATCTCGTATAAGACCATATCTTGGATATGAC
1 ATCGATGTGAGATTTCGTATAAGACCATATCTGGGATATGAG
180516 ATCGACATTGATTTGAGATTTCGTATAAGACCATATCTGGGATATGAG
1 ATCG--A-TG---TGAGATTTCGTATAAGACCATATCTGGGATATGAG
* * *
180564 ATCGATGTGAGACTTCGTGTAAGACCATAGT-TGGGCTATTG-G
1 ATCGATGTGAGATTTCGTATAAGACCATA-TCTGGGATA-TGAG
*
180606 CATCGATATGAGATTTC
1 -ATCGATGTGAGATTTC
180623 CATGTAAGAC
Statistics
Matches: 89, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
42 31 0.35
43 17 0.19
44 1 0.01
45 3 0.03
46 1 0.01
48 36 0.40
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (42 bp):
ATCGATGTGAGATTTCGTATAAGACCATATCTGGGATATGAG
Found at i:194468 original size:14 final size:15
Alignment explanation
Indices: 194439--194471 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
194429 TCAAAAGTTT
*
194439 AATTTATTTCATCTA
1 AATTTATTTAATCTA
194454 AATTTA-TTAATCTA
1 AATTTATTTAATCTA
194468 AATT
1 AATT
194472 CAATTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTTATTTAATCTA
Found at i:194809 original size:17 final size:17
Alignment explanation
Indices: 194787--194819 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
194777 CATTTACTTT
*
194787 ATAATATTTTATAAAAA
1 ATAATATTTCATAAAAA
194804 ATAATATTTCATAAAA
1 ATAATATTTCATAAAA
194820 TAATTGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAATATTTCATAAAAA
Found at i:195788 original size:17 final size:17
Alignment explanation
Indices: 195738--195788 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
195728 GTAAATAAAA
* *
195738 GAATAAAATTTTTATTT
1 GAATAAAAATCTTATTT
195755 GAA-AATAAATACTTATTT
1 GAATAA-AAAT-CTTATTT
195773 GAATAAAAATCTTATT
1 GAATAAAAATCTTATT
195789 CGAGTATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 2 0.07
17 12 0.41
18 13 0.45
19 2 0.07
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (17 bp):
GAATAAAAATCTTATTT
Found at i:201390 original size:2 final size:2
Alignment explanation
Indices: 201383--201407 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
201373 GAATTTACAA
201383 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 A
201408 ACAATGCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:201598 original size:30 final size:31
Alignment explanation
Indices: 201552--201615 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
201542 ATTTCTTATG
201552 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATATCTCGATACCCATATCTTTGACTTT
*
201583 CCAATAT-TTGATACCCATATCTTTGACTTT
1 CCAATATCTCGATACCCATATCTTTGACTTT
201613 CCA
1 CCA
201616 TAAATATGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 25 0.78
31 7 0.22
ACGTcount: A:0.27, C:0.28, G:0.06, T:0.39
Consensus pattern (31 bp):
CCAATATCTCGATACCCATATCTTTGACTTT
Found at i:201607 original size:15 final size:15
Alignment explanation
Indices: 201562--201608 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
201552 CCAATATCTC
201562 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
201577 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
201592 GATACCCATATCTTT
1 GATACCCATATCTTT
201607 GA
1 GA
201609 CTTTCCATAA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:205093 original size:18 final size:19
Alignment explanation
Indices: 205060--205095 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
205050 TTCTTTTATT
*
205060 TGAAAATGATATAAATGTA
1 TGAAAATGATAAAAATGTA
205079 TGAAAA-GATAAAAATGT
1 TGAAAATGATAAAAATGT
205096 CATCATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.17, T:0.28
Consensus pattern (19 bp):
TGAAAATGATAAAAATGTA
Found at i:208737 original size:44 final size:43
Alignment explanation
Indices: 208589--208738 Score: 113
Period size: 44 Copynumber: 3.3 Consensus size: 43
208579 GTTAAATATG
* *
208589 AATTAATTGAATTAATCACATATGAAGTTCATTAGCAATAGTT
1 AATTATTTTAATTAATCACATATGAAGTTCATTAGCAATAGTT
** **** * * *
208632 AATTAATTTTAATTAAAT-AGTTAATTTTTTTCTTATTAGTATTGAGTC
1 AATT-ATTTTAATT-AATCACAT-ATGAAGTTC--ATTAGCAAT-AGTT
* *
208680 AATTAATTGAATTAATCACATATGAAGTTCATTAGCAATAGTT
1 AATTATTTTAATTAATCACATATGAAGTTCATTAGCAATAGTT
208723 AATTGATTTTAATTAA
1 AATT-ATTTTAATTAA
208739 ATAGTTAATT
Statistics
Matches: 75, Mismatches: 24, Indels: 15
0.66 0.21 0.13
Matches are distributed among these distances:
43 11 0.15
44 25 0.33
45 8 0.11
46 8 0.11
47 16 0.21
48 7 0.09
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (43 bp):
AATTATTTTAATTAATCACATATGAAGTTCATTAGCAATAGTT
Found at i:208744 original size:91 final size:91
Alignment explanation
Indices: 208589--208770 Score: 346
Period size: 91 Copynumber: 2.0 Consensus size: 91
208579 GTTAAATATG
208589 AATTAATTGAATTAATCACATATGAAGTTCATTAGCAATAGTTAATTAATTTTAATTAAATAGTT
1 AATTAATTGAATTAATCACATATGAAGTTCATTAGCAATAGTTAATTAATTTTAATTAAATAGTT
*
208654 AATTTTTTTCTTATTAGTATTGAGTC
66 AATTTTTTTCGTATTAGTATTGAGTC
*
208680 AATTAATTGAATTAATCACATATGAAGTTCATTAGCAATAGTTAATTGATTTTAATTAAATAGTT
1 AATTAATTGAATTAATCACATATGAAGTTCATTAGCAATAGTTAATTAATTTTAATTAAATAGTT
208745 AATTTTTTTCGTATTAGTATTGAGTC
66 AATTTTTTTCGTATTAGTATTGAGTC
208771 GATTGTTAAT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.46
Consensus pattern (91 bp):
AATTAATTGAATTAATCACATATGAAGTTCATTAGCAATAGTTAATTAATTTTAATTAAATAGTT
AATTTTTTTCGTATTAGTATTGAGTC
Found at i:210201 original size:20 final size:18
Alignment explanation
Indices: 210167--210217 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
210157 TTTTGCATCA
210167 TAAAAATTAAAATTAATT
1 TAAAAATTAAAATTAATT
210185 TAAATAATTATAAATTAA--
1 TAAA-AATTA-AAATTAATT
210203 TAAAAA-TAAAATTAA
1 TAAAAATTAAAATTAA
210218 CTTCCATTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 7 0.23
16 2 0.06
17 2 0.06
18 8 0.26
19 5 0.16
20 7 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAAATTAAAATTAATT
Found at i:212560 original size:2 final size:2
Alignment explanation
Indices: 212553--212587 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
212543 TTAGCTGCGC
*
212553 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
212588 GGCATATAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:214950 original size:29 final size:29
Alignment explanation
Indices: 214913--214982 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
214903 AAACGGAATC
214913 AAATCAAAATTTCATATATAAAATTGCACA
1 AAAT-AAAATTTCATATATAAAATTGCACA
* * * * *
214943 AAATAAAAGTTCATGTATGACATTGTACA
1 AAATAAAATTTCATATATAAAATTGCACA
*
214972 AAATCAAATTT
1 AAATAAAATTT
214983 ATCCCATTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 29 0.88
30 4 0.12
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.31
Consensus pattern (29 bp):
AAATAAAATTTCATATATAAAATTGCACA
Found at i:221238 original size:12 final size:13
Alignment explanation
Indices: 221209--221254 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
221199 AAAAACAATC
*
221209 TAAAGATTAAATAT
1 TAAATATTAAA-AT
221223 TAAATATT-AAAT
1 TAAATATTAAAAT
221235 TAAA-ATTAAAAT
1 TAAATATTAAAAT
221247 TAATATAT
1 TAA-ATAT
221255 ATTTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 3 0.11
12 13 0.46
13 3 0.11
14 9 0.32
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (13 bp):
TAAATATTAAAAT
Found at i:228067 original size:6 final size:6
Alignment explanation
Indices: 228056--228080 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
228046 AAAAATATAT
228056 AATTAA AATTAA AATTAA AATTAA A
1 AATTAA AATTAA AATTAA AATTAA A
228081 GTTTTATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATTAA
Found at i:228127 original size:32 final size:31
Alignment explanation
Indices: 228062--228139 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 31
228052 ATATAATTAA
*
228062 AATTAAAATTAAAATTAAAGTTTTATGTGTAT
1 AATT-AAATTAAAATTAAAGTTTTATGTATAT
* *
228094 AATTAAATTAAAATTAAAGTTTTGTTTTATAT
1 AATTAAATTAAAATTAAAGTTTT-ATGTATAT
* *
228126 AATTACACTAAAAT
1 AATTAAATTAAAAT
228140 AATATATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 19 0.47
32 21 0.52
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (31 bp):
AATTAAATTAAAATTAAAGTTTTATGTATAT
Found at i:229437 original size:30 final size:30
Alignment explanation
Indices: 229401--229463 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
229391 GGCTTTGACA
229401 TTAAGTTTATGGACCATTTATGAAATTACC
1 TTAAGTTTATGGACCATTTATGAAATTACC
229431 TTAAGTTTATGGACCATTTATGAAATTACC
1 TTAAGTTTATGGACCATTTATGAAATTACC
229461 TTA
1 TTA
229464 GCAATCAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (30 bp):
TTAAGTTTATGGACCATTTATGAAATTACC
Found at i:247356 original size:17 final size:18
Alignment explanation
Indices: 247315--247358 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
247305 ATAGATAAGT
*
247315 ATGTACATATATATAAAA
1 ATGTAAATATATATAAAA
*
247333 TTGGTAAATAT-TATAAAA
1 AT-GTAAATATATATAAAA
247351 ATGTAAAT
1 ATGTAAAT
247359 GTGTATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 6 0.27
18 9 0.41
19 7 0.32
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.36
Consensus pattern (18 bp):
ATGTAAATATATATAAAA
Found at i:247608 original size:3 final size:3
Alignment explanation
Indices: 247600--247631 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
247590 AAGCATAAAC
247600 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
247632 GTAACATTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:247773 original size:3 final size:3
Alignment explanation
Indices: 247759--247809 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
247749 ACACTAGTAC
* * * * *
247759 ATA ATT ATA ATA ATA GTA ATA CTA ATA ATA CTA ATA ATA TTA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
247806 ATA A
1 ATA A
247810 GGATATTTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:249272 original size:42 final size:42
Alignment explanation
Indices: 249225--249374 Score: 182
Period size: 42 Copynumber: 3.6 Consensus size: 42
249215 GTGTTTTTAG
* **
249225 TCTGCTCCACTGCTATTTAGGGAGATAAGATCTGTGGTTTCT
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTCT
* * * * *
249267 TCTGCTCCGCTACTGCTTAAGGAGATAAGA-CT-T-GATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTC-T
249307 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTT-T
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTCT
249348 GTCTGCTCCACTACTGCTTAGGGAGAT
1 -TCTGCTCCACTACTGCTTAGGGAGAT
249375 GAGTTATCGG
Statistics
Matches: 90, Mismatches: 13, Indels: 10
0.80 0.12 0.09
Matches are distributed among these distances:
39 3 0.03
40 29 0.32
41 4 0.04
42 52 0.58
43 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (42 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTCT
Found at i:249698 original size:44 final size:45
Alignment explanation
Indices: 249584--250211 Score: 550
Period size: 44 Copynumber: 14.3 Consensus size: 45
249574 TCGCTTGCCA
* * * * * *
249584 AATACAGGAAGGCAAGATCTGCAACCTTCAATCTACTTCACCACC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * * * *
249629 AGTATGGGAAGACAAGATCTG-TATCTTGGATCCACTTC-CTATC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * * * *
249672 AATATAGGAAGATAGGACCTGCTATCTTCGATCTTCTTCAC-GCC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * * * *
249716 AATACATGAAGACAAGATCTGCTTTCTGT-GATCTACTTCGCCACC
1 AATATAGGAAGACAAGATCTGCTATCT-TCGATCTACTTCACTACC
* * *
249761 AATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACT
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * * *
249804 AATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCAC-GCC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * * * * *
249848 AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * *
249893 AATATGGGAAGACAAGATCTG-TATCGTCGATCCACTTC-CTACC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * * *
249936 AATATAGGAAGACAAGACCTACTATCTTTGATCTACTTCAC-GCC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * * * * *
249980 AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * *
250025 AATATGGGAAGACAAGATCTGC-ATCGTCGATCCACTTC-CTACC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * * * *
250068 AATATAGTAAGACAAGACCTACTATCTTTGATCTACTTCAC-GCC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * * * *
250112 AATACATGAAGACAAGATCTGCTTTCTGT-GATCTACTTCGCCACC
1 AATATAGGAAGACAAGATCTGCTATCT-TCGATCTACTTCACTACC
* * * *
250157 AATATGGGAAGACCAGATCTGC-ATCTTTGATCCACTTC-CTACC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
250200 AATATAGGAAGA
1 AATATAGGAAGA
250212 TAGGATATGT
Statistics
Matches: 458, Mismatches: 109, Indels: 34
0.76 0.18 0.06
Matches are distributed among these distances:
43 101 0.22
44 252 0.55
45 105 0.23
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (45 bp):
AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
Found at i:249821 original size:132 final size:132
Alignment explanation
Indices: 249614--250216 Score: 999
Period size: 132 Copynumber: 4.6 Consensus size: 132
249604 GCAACCTTCA
* * * * *
249614 ATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTATCTTGGATCCACTTCCTATCAATATAG
1 ATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAG
* *
249679 GAAGATAGGACCTGCTATCTTCGATCTTCTTCACGCCAATACATGAAGACAAGATCTGCTTTCTG
66 GAAGATAGGACCTACTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTG
*
249744 TG
131 CG
*
249746 ATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACTAATATAG
1 ATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAG
*
249811 GAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTG
66 GAAGATAGGACCTACTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTG
249876 CG
131 CG
* *
249878 ATCTACTTCGCCACCAATATGGGAAGACAAGATCTGTATCGTCGATCCACTTCCTACCAATATAG
1 ATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAG
* * *
249943 GAAGACAAGACCTACTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTG
66 GAAGATAGGACCTACTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTG
250008 CG
131 CG
*
250010 ATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAG
1 ATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAG
* * * *
250075 TAAGACAAGACCTACTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTG
66 GAAGATAGGACCTACTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTG
*
250140 TG
131 CG
* *
250142 ATCTACTTCGCCACCAATATGGGAAGACCAGATCTGCATCTTTGATCCACTTCCTACCAATATAG
1 ATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAG
250207 GAAGATAGGA
66 GAAGATAGGA
250217 TATGTTCCTT
Statistics
Matches: 447, Mismatches: 24, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 447 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (132 bp):
ATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAG
GAAGATAGGACCTACTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTG
CG
Found at i:270614 original size:38 final size:37
Alignment explanation
Indices: 270530--270624 Score: 97
Period size: 38 Copynumber: 2.5 Consensus size: 37
270520 TATACGTACT
*
270530 TATACATACTTAAATATATTTTTCATATTTCATAATTC
1 TATACATACTTAAATATATTTTACATATTT-ATAATTC
* *
270568 T-TATATACTTACATATATTTATACATATTT-TACA-TC
1 TATACATACTTAAATATATTT-TACATATTTATA-ATTC
*
270604 ATATACATACTTATATATATT
1 -TATACATACTTAAATATATT
270625 CTTTATATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
36 4 0.08
37 19 0.40
38 25 0.52
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (37 bp):
TATACATACTTAAATATATTTTACATATTTATAATTC
Found at i:275724 original size:16 final size:16
Alignment explanation
Indices: 275705--275736 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
275695 AAATGATACA
275705 AACCCAAAATGACATG
1 AACCCAAAATGACATG
*
275721 AACCCGAAATGACATG
1 AACCCAAAATGACATG
275737 TGCAAGTAAC
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:0.47, C:0.25, G:0.16, T:0.12
Consensus pattern (16 bp):
AACCCAAAATGACATG
Found at i:280784 original size:14 final size:15
Alignment explanation
Indices: 280754--280787 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
280744 TCAACATGTT
280754 TTTTA-ATATTTACA
1 TTTTATATATTTACA
280768 TTTTATATATTTA-A
1 TTTTATATATTTACA
280782 TTTTAT
1 TTTTAT
280788 GTGATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTATATATTTACA
Found at i:284879 original size:15 final size:15
Alignment explanation
Indices: 284861--284894 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
284851 TAAAGTCCTC
*
284861 TCAATAATGTCGATT
1 TCAACAATGTCGATT
284876 TCAACAATGTCGATT
1 TCAACAATGTCGATT
284891 TCAA
1 TCAA
284895 GATTCGAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (15 bp):
TCAACAATGTCGATT
Found at i:290918 original size:3 final size:3
Alignment explanation
Indices: 290910--290935 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
290900 TTCACTCTCC
290910 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
290936 TAAAAAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:297076 original size:20 final size:20
Alignment explanation
Indices: 297024--297076 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 20
297014 TAAATCATTG
297024 TAATATATGTAAAAATAATT
1 TAATATATGTAAAAATAATT
* *
297044 TAA-A-ATATAAAAAT-TTAT
1 TAATATATGTAAAAATAAT-T
297062 TAATATATGTAAAAA
1 TAATATATGTAAAAA
297077 CAACTTTTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 1 0.04
18 13 0.48
19 2 0.07
20 11 0.41
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (20 bp):
TAATATATGTAAAAATAATT
Found at i:297220 original size:34 final size:35
Alignment explanation
Indices: 297154--297220 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 35
297144 CAAACACCAA
* *
297154 AAAATATTTTCCAGTAAATAATTTTATAGAAAAGT
1 AAAACATTTTCCAGTAAATAATTTTACAGAAAAGT
* * *
297189 AAAACATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATAATTTTACAGAAAA
297221 TATTTTACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 15 0.56
35 12 0.44
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATAATTTTACAGAAAAGT
Found at i:298662 original size:21 final size:21
Alignment explanation
Indices: 298638--298682 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
298628 TTTCCTCCTC
*
298638 CCTCT-CTCACACGTGCCTTCT
1 CCTCTCCTCACACGTGAC-TCT
*
298659 CCTCTCCTCGCACGTGACTCT
1 CCTCTCCTCACACGTGACTCT
298680 CCT
1 CCT
298683 ACCCCCCTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.09, C:0.49, G:0.11, T:0.31
Consensus pattern (21 bp):
CCTCTCCTCACACGTGACTCT
Found at i:301667 original size:29 final size:29
Alignment explanation
Indices: 301625--301683 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
301615 GTACAAAGGT
*
301625 TTTTATGATACTTTTATCGTTGAGTTTTA
1 TTTTATGATACTTTTATCATTGAGTTTTA
301654 TTTTATGATACTTTTATCATTGAGTTTTA
1 TTTTATGATACTTTTATCATTGAGTTTTA
301683 T
1 T
301684 CTTGAGTGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.22, C:0.07, G:0.12, T:0.59
Consensus pattern (29 bp):
TTTTATGATACTTTTATCATTGAGTTTTA
Found at i:309384 original size:17 final size:17
Alignment explanation
Indices: 309362--309394 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
309352 TAATTAAATT
*
309362 ATTCGTTAGATATTTGA
1 ATTCGTTAAATATTTGA
309379 ATTCGTTAAATATTTG
1 ATTCGTTAAATATTTG
309395 GATTTAGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.48
Consensus pattern (17 bp):
ATTCGTTAAATATTTGA
Found at i:312768 original size:4 final size:4
Alignment explanation
Indices: 312759--312795 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
312749 AAATGAGAAA
*
312759 TATG TATG TATG TATG TATA TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
312796 TATTGGCTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:314849 original size:16 final size:17
Alignment explanation
Indices: 314828--314863 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
314818 TAGGGCGTGG
*
314828 AATAGAGGTGTAAT-GT
1 AATAGAGCTGTAATAGT
314844 AATAGAGCTGTAATAGT
1 AATAGAGCTGTAATAGT
314861 AAT
1 AAT
314864 TCAATTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.31
Consensus pattern (17 bp):
AATAGAGCTGTAATAGT
Found at i:315054 original size:26 final size:26
Alignment explanation
Indices: 315024--315120 Score: 77
Period size: 26 Copynumber: 3.5 Consensus size: 26
315014 TTGTTATTAA
315024 ATTTTAATAAAATTATTATTAAAAAT
1 ATTTTAATAAAATTATTATTAAAAAT
* **
315050 ATTTTAATAAAAATAATAAATAATTTAACCAT
1 ATTTTAAT-AAAAT--T--ATTA-TTAAAAAT
* * *
315082 ATTTTAACATAATTATTATTAAATAT
1 ATTTTAATAAAATTATTATTAAAAAT
*
315108 AATTTAATAAAAT
1 ATTTTAATAAAAT
315121 AATATATAAT
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
26 24 0.44
27 8 0.15
29 2 0.04
31 7 0.13
32 13 0.24
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (26 bp):
ATTTTAATAAAATTATTATTAAAAAT
Found at i:315062 original size:14 final size:14
Alignment explanation
Indices: 315024--315064 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
315014 TTGTTATTAA
315024 ATTTTAAT-AAAAT
1 ATTTTAATAAAAAT
* *
315037 -TATTATTAAAAAT
1 ATTTTAATAAAAAT
315050 ATTTTAATAAAAAT
1 ATTTTAATAAAAAT
315064 A
1 A
315065 ATAAATAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
12 5 0.23
13 5 0.23
14 12 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTTTAATAAAAAT
Found at i:315088 original size:58 final size:57
Alignment explanation
Indices: 315022--315158 Score: 184
Period size: 58 Copynumber: 2.4 Consensus size: 57
315012 TATTGTTATT
* * *
315022 AAATTTTAATAAAATTATTATTAAAAATATTTTAATAAAAATAATAAATAATTTAACC
1 AAATTTTAATATAATTATTATTAAAAATAATTTAAT-AAAATAATAAATAATTTAACA
* * * * *
315080 ATATTTTAACATAATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATA
1 AAATTTTAATATAATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACA
315137 AAATTCTTAATATAATTATTAT
1 AAATT-TTAATATAATTATTAT
315159 ATGAATTTAC
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
57 22 0.32
58 46 0.68
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (57 bp):
AAATTTTAATATAATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACA
Found at i:323863 original size:19 final size:19
Alignment explanation
Indices: 323839--323880 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
323829 CTTCAGATAT
323839 TTTTATTTCTTTTA-TTTTA
1 TTTTATTT-TTTTACTTTTA
*
323858 TTTTATTTTTTTACTTTTC
1 TTTTATTTTTTTACTTTTA
323877 TTTT
1 TTTT
323881 GGTGCTGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTATTTTTTTACTTTTA
Found at i:343873 original size:21 final size:21
Alignment explanation
Indices: 343833--343874 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
343823 CCTTTTATAA
*
343833 TAAATTCAATTAAGTTAAATT
1 TAAATTCAATTAAGTCAAATT
343854 TAAATTCAATTTAA-TCAAATT
1 TAAATTCAA-TTAAGTCAAATT
343875 AATTTCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (21 bp):
TAAATTCAATTAAGTCAAATT
Found at i:353813 original size:21 final size:21
Alignment explanation
Indices: 353787--353827 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
353777 ATCTGCTCAA
* *
353787 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
353808 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
353828 TTGCTCATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:361060 original size:30 final size:29
Alignment explanation
Indices: 360998--361174 Score: 247
Period size: 29 Copynumber: 6.2 Consensus size: 29
360988 AAACATTTAA
*
360998 TAAAATACACTACATATA---TATA-TTT
1 TAAAATACACTACATATATTTTTTATTTT
*
361023 TAAAATACACTACATATATTTTTTTATTTC
1 TAAAATACACTACATATA-TTTTTTATTTT
*
361053 TAGAATACACTACATATATTTTTTATTTT
1 TAAAATACACTACATATATTTTTTATTTT
361082 TAAAATACACTACATATATTTTTTATTTT
1 TAAAATACACTACATATATTTTTTATTTT
*
361111 TAAAATACACTACATGTATTTTTTATTTT
1 TAAAATACACTACATATATTTTTTATTTT
* *
361140 TAAAATCCATTACATATATTTTTT-TATTT
1 TAAAATACACTACATATATTTTTTAT-TTT
361169 TAAAAT
1 TAAAAT
361175 TTTAAATACA
Statistics
Matches: 137, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
25 18 0.13
28 1 0.01
29 99 0.72
30 19 0.14
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (29 bp):
TAAAATACACTACATATATTTTTTATTTT
Found at i:361307 original size:28 final size:28
Alignment explanation
Indices: 361267--361369 Score: 93
Period size: 28 Copynumber: 3.6 Consensus size: 28
361257 CAATACCCAT
*
361267 TCCCATTTCCCATTCCACCGTGCCCTCC
1 TCCCATTTCCCATTCCACCGTCCCCTCC
* *
361295 TCCCATTTCCCATTCCCATC-TCCCCTCT
1 TCCCATTTCCCATT-CCACCGTCCCCTCC
* * *
361323 TCCATCGATTCCCCTCTTCCACCGTTCCCTCC
1 TCC--C-ATTTCCC-ATTCCACCGTCCCCTCC
361355 TCCCA-TTCCCATTCC
1 TCCCATTTCCCATTCC
361370 CATTCCCATT
Statistics
Matches: 59, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
27 4 0.07
28 27 0.46
29 5 0.08
30 2 0.03
31 10 0.17
32 11 0.19
ACGTcount: A:0.11, C:0.53, G:0.04, T:0.32
Consensus pattern (28 bp):
TCCCATTTCCCATTCCACCGTCCCCTCC
Found at i:361363 original size:21 final size:21
Alignment explanation
Indices: 361274--361363 Score: 50
Period size: 21 Copynumber: 4.4 Consensus size: 21
361264 CATTCCCATT
*
361274 TCCCATTCCACCGTGCCCTCC
1 TCCCATTCCACCGTTCCCTCC
* *
361295 TCCCATTTC-CCATTCCCAT-C
1 TCCCATTCCACCGTTCCC-TCC
* *
361315 TCCCCTCTTCCATCGATT-CC-CC
1 T-CCC-ATTCCACCG-TTCCCTCC
361337 T--C-TTCCACCGTTCCCTCC
1 TCCCATTCCACCGTTCCCTCC
361355 TCCCATTCC
1 TCCCATTCC
361364 CATTCCCATT
Statistics
Matches: 50, Mismatches: 8, Indels: 22
0.62 0.10 0.28
Matches are distributed among these distances:
16 2 0.04
17 9 0.18
18 3 0.06
19 1 0.02
20 9 0.18
21 16 0.32
22 5 0.10
23 3 0.06
24 2 0.04
ACGTcount: A:0.10, C:0.54, G:0.04, T:0.31
Consensus pattern (21 bp):
TCCCATTCCACCGTTCCCTCC
Found at i:361366 original size:6 final size:6
Alignment explanation
Indices: 361355--361392 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
361345 CGTTCCCTCC
361355 TCCCAT TCCCAT TCCCAT TCCCAT TCCCATT TCCCAT T
1 TCCCAT TCCCAT TCCCAT TCCCAT TCCCA-T TCCCAT T
361393 ATCAACAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.16, C:0.47, G:0.00, T:0.37
Consensus pattern (6 bp):
TCCCAT
Found at i:361921 original size:21 final size:21
Alignment explanation
Indices: 361897--361940 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
361887 TTAAATAGAT
361897 TAAATTAA-TGTTTGTTAATAA
1 TAAATTAAGT-TTTGTTAATAA
361918 TAAATTAAGTTTTGTTAATAA
1 TAAATTAAGTTTTGTTAATAA
361939 TA
1 TA
361941 TATATCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (21 bp):
TAAATTAAGTTTTGTTAATAA
Found at i:365947 original size:22 final size:21
Alignment explanation
Indices: 365919--365991 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 21
365909 TTTAACAATA
365919 AAAATAAATAAAAATTTTAACT
1 AAAAT-AATAAAAATTTTAACT
365941 AAAATAAT--AAA-TTTAA-T
1 AAAATAATAAAAATTTTAACT
365958 AAAAATAAATAAAAATTTTAACT
1 -AAAAT-AATAAAAATTTTAACT
365981 AAAATAATAAA
1 AAAATAATAAA
365992 TTTACTCTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
17 1 0.02
18 10 0.22
19 6 0.13
21 12 0.27
22 15 0.33
23 1 0.02
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAATAATAAAAATTTTAACT
Found at i:365960 original size:40 final size:40
Alignment explanation
Indices: 365915--365995 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
365905 AATTTTTAAC
365915 AATAAAAATAAATAAAAATTTTAACTAAAATAATAAATTT
1 AATAAAAATAAATAAAAATTTTAACTAAAATAATAAATTT
365955 AATAAAAATAAATAAAAATTTTAACTAAAATAATAAATTT
1 AATAAAAATAAATAAAAATTTTAACTAAAATAATAAATTT
365995 A
1 A
365996 CTCTTTAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.32
Consensus pattern (40 bp):
AATAAAAATAAATAAAAATTTTAACTAAAATAATAAATTT
Found at i:365995 original size:18 final size:19
Alignment explanation
Indices: 365924--365994 Score: 85
Period size: 18 Copynumber: 3.7 Consensus size: 19
365914 CAATAAAAAT
365924 AAATAA-AAATTTTAACTA
1 AAATAATAAATTTTAACTA
365942 AAATAATAAA-TTTAA-TAA
1 AAATAATAAATTTTAACT-A
365960 AAATAAATAAAAATTTTAACTA
1 AAAT-AAT--AAATTTTAACTA
365982 AAATAATAAATTT
1 AAATAATAAATTT
365995 ACTCTTTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
17 1 0.02
18 16 0.35
19 12 0.26
21 6 0.13
22 10 0.22
23 1 0.02
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATAATAAATTTTAACTA
Found at i:371571 original size:31 final size:31
Alignment explanation
Indices: 371536--371614 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
371526 AATTAAACTG
371536 TTAATATATT-ATTTAGTACTT-GAGTTTAGTT
1 TTAATAT-TTAATTTAGTA-TTCGAGTTTAGTT
* * *
371567 TTAATGTTTAATTTTGTATTCGAGTTTATTT
1 TTAATATTTAATTTAGTATTCGAGTTTAGTT
* *
371598 TTAATATTCATTTTAGT
1 TTAATATTTAATTTAGT
371615 GCCTAAATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
30 4 0.10
31 35 0.90
ACGTcount: A:0.27, C:0.04, G:0.11, T:0.58
Consensus pattern (31 bp):
TTAATATTTAATTTAGTATTCGAGTTTAGTT
Found at i:379194 original size:21 final size:21
Alignment explanation
Indices: 379170--379212 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
379160 ATTGTATTAT
379170 ATATACAATT-TATAAAAATAA
1 ATATA-AATTATATAAAAATAA
*
379191 ATATAATTTAGTATAAAAATAA
1 ATATAAATTA-TATAAAAATAA
379213 TTTAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.16
21 5 0.26
22 11 0.58
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
ATATAAATTATATAAAAATAA
Found at i:379212 original size:16 final size:16
Alignment explanation
Indices: 379187--379221 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
379177 ATTTATAAAA
* *
379187 ATAAATATAATTTAGT
1 ATAAAAATAATTTAAT
379203 ATAAAAATAATTTAAT
1 ATAAAAATAATTTAAT
379219 ATA
1 ATA
379222 TTTTAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
ATAAAAATAATTTAAT
Found at i:381502 original size:11 final size:11
Alignment explanation
Indices: 381488--381517 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
381478 ATAATAAAAA
381488 AATAATAATTT
1 AATAATAATTT
*
381499 AATAATAGTTT
1 AATAATAATTT
381510 AATAATAA
1 AATAATAA
381518 AAATACTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (11 bp):
AATAATAATTT
Found at i:381941 original size:16 final size:16
Alignment explanation
Indices: 381908--381941 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
381898 TGAAAATGTT
* *
381908 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
381924 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
381940 AA
1 AA
381942 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:386721 original size:16 final size:16
Alignment explanation
Indices: 386688--386721 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
386678 GGAGATTGTT
* *
386688 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
386704 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
386720 AA
1 AA
386722 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:393825 original size:21 final size:21
Alignment explanation
Indices: 393801--393840 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
393791 CTTTTTATGT
393801 TTTTATTTC-ACCTTTAAATGA
1 TTTTATTTCTA-CTTTAAATGA
*
393822 TTTTTTTTCTACTTTAAAT
1 TTTTATTTCTACTTTAAAT
393841 TGGAATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.25, C:0.12, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTTATTTCTACTTTAAATGA
Found at i:396042 original size:26 final size:26
Alignment explanation
Indices: 396009--396080 Score: 119
Period size: 26 Copynumber: 2.8 Consensus size: 26
395999 TGCTGCTGTG
396009 CGAA-CTGGGCCTGCTGGGCTGCTAC
1 CGAATCTGGGCCTGCTGGGCTGCTAC
*
396034 CGAATCTGGGCCCGCTGGGCTGCTAC
1 CGAATCTGGGCCTGCTGGGCTGCTAC
*
396060 CGAATTTGGGCCTGCTGGGCT
1 CGAATCTGGGCCTGCTGGGCT
396081 TGCGCTGGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
25 4 0.09
26 39 0.91
ACGTcount: A:0.11, C:0.31, G:0.36, T:0.22
Consensus pattern (26 bp):
CGAATCTGGGCCTGCTGGGCTGCTAC
Found at i:396290 original size:19 final size:20
Alignment explanation
Indices: 396257--396297 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
396247 GACTGTGATA
*
396257 TTTTTTTTCTTTTTTCCTTC
1 TTTTTTTTCTCTTTTCCTTC
*
396277 TTTTTTTTC-CTTTTCTTTC
1 TTTTTTTTCTCTTTTCCTTC
396296 TT
1 TT
396298 CTTCTTCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTTTTCTCTTTTCCTTC
Found at i:396298 original size:22 final size:20
Alignment explanation
Indices: 396257--396300 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
396247 GACTGTGATA
396257 TTTTTTTTCTTTTTTCCTTC
1 TTTTTTTTCTTTTTTCCTTC
*
396277 TTTTTTTTCCTTTTCTTTCTTC
1 TTTTTTTT-CTTTT-TTCCTTC
396299 TT
1 TT
396301 CTTCGTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 5 0.24
22 8 0.38
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTTTTCTTTTTTCCTTC
Found at i:396704 original size:30 final size:30
Alignment explanation
Indices: 396671--396768 Score: 110
Period size: 30 Copynumber: 3.3 Consensus size: 30
396661 AGGGCTGAAG
* *
396671 TGTAATTTTGAGAAATTTTAGGGGTCAAAG
1 TGTAATTTTGAGAAAGTTTAGGGGTCAAAA
* * *
396701 TGTAGTATT-AGGAAAGTTTAAGGGTCAAAA
1 TGTAATTTTGA-GAAAGTTTAGGGGTCAAAA
* *
396731 TATAATTTTG-GGAAGTTTAGGGGTCAAAA
1 TGTAATTTTGAGAAAGTTTAGGGGTCAAAA
396760 TGTAATTTT
1 TGTAATTTT
396769 TTTTAAAAAC
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
29 26 0.47
30 29 0.53
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.37
Consensus pattern (30 bp):
TGTAATTTTGAGAAAGTTTAGGGGTCAAAA
Found at i:396754 original size:29 final size:29
Alignment explanation
Indices: 396671--396768 Score: 115
Period size: 29 Copynumber: 3.3 Consensus size: 29
396661 AGGGCTGAAG
* *
396671 TGTAATTTTGAGAAATTTTAGGGGTCAAAG
1 TGTAATTTTG-GAAAGTTTAGGGGTCAAAA
* * *
396701 TGTAGTATTAGGAAAGTTTAAGGGTCAAAA
1 TGTAAT-TTTGGAAAGTTTAGGGGTCAAAA
* *
396731 TATAATTTTGGGAAGTTTAGGGGTCAAAA
1 TGTAATTTTGGAAAGTTTAGGGGTCAAAA
396760 TGTAATTTT
1 TGTAATTTT
396769 TTTTAAAAAC
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
29 28 0.50
30 25 0.45
31 3 0.05
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.37
Consensus pattern (29 bp):
TGTAATTTTGGAAAGTTTAGGGGTCAAAA
Found at i:397128 original size:81 final size:80
Alignment explanation
Indices: 396972--398009 Score: 1181
Period size: 81 Copynumber: 13.1 Consensus size: 80
396962 ATAGAAATTG
* *
396972 AAAATACCTC-G-ACGTGACCTGAGGCTCAACTCACCTCTCGCAAT-TGGAGTTGATTTTTTTTG
1 AAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATAT-GAGTTGA-TTTTTTTG
397034 AAAAAAAACAGAAA-TTAAA
64 ---AAAAACAGAAATTTAAA
* * *
397053 AAAATACCTCGGCGTGTGACCCGAGGTTCAACT-ATCTCTCGCAATATGAGTTGATTTTTTTTTT
1 AAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTT
397117 GAAAAACAGAAA-TTAAA
63 GAAAAACAGAAATTTAAA
* * *
397134 AAAATACCTCGGCGTGTGACCCAAGGCTCAACTCACCTCTCGCAATTTGAGTTGA--TTTTTGAA
1 AAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
* * *
397197 AAATAGGAA-TT-GA
66 AAACAGAAATTTAAA
* * * *
397210 GAAATACCTCAGCGTATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
1 AAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
397275 AAACAGAAATTTAAA
66 AAACAGAAATTTAAA
* * *
397290 AGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTTGTATTATGAGTTGATTTTTTTTG
1 A-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTG
397355 AAAAACAGAAATTTAAA
64 AAAAACAGAAATTTAAA
* * * ***
397372 AGAAATACCTCGGCATGTGACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAA
1 A-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-TTG
*
397437 AAAAATAGAAATTTAAA
64 AAAAACAGAAATTTAAA
** * * *
397454 AAAATACCTCGGCATACG-CCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-ATTTTTGAA
1 AAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
397517 AAACAGAAATTTAAA
66 AAACAGAAATTTAAA
* * * *
397532 AGAAATACCTTGGCATGTG-TCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGA-ATTTTTGA
1 A-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA
397595 AAAACAGAAATTTAAA
65 AAAACAGAAATTTAAA
* * *
397611 AGAAATACCTTGGCATGTG-TCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGA-TTTTTTGA
1 A-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-
*
397674 AAAAAACAGAAATTAAAA
64 -AAAAACAGAAATTTAAA
* *
397692 AAAATACCTCAGCATGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
1 AAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
*
397757 AAACATAAA-TTAAA
66 AAACAGAAATTTAAA
** * *
397771 AAATATACCTCAACGTGTGACCCGAGGCTCAACTCAACTCTCGCAATATGAGTTGA-TTTTTTGA
1 AAA-ATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA
*
397835 AAAACAGAAA-TT-GA
65 AAAACAGAAATTTAAA
** *
397849 AAAATACCTC-G-ATGTGTGTCCGAGGCTCAACTCATCTCTCGCAATATGAGTTGA--TTTTTGA
1 AAAATACCTCGGCATGTG-ACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA
397910 AAAACAGAAATTTAAA
65 AAAACAGAAATTTAAA
* * * * ** * ***
397926 AGAAATACCTCGGCATGAG-TCCGATGCTCAACTCACCTATCATATTATGAGTTGATTTTTGAAA
1 A-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA
* *
397990 AAAATAGAAATATAAA
65 AAAACAGAAATTTAAA
398006 AAAA
1 AAAA
398010 ATTCCAGGCT
Statistics
Matches: 848, Mismatches: 82, Indels: 56
0.86 0.08 0.06
Matches are distributed among these distances:
75 21 0.02
76 87 0.10
77 26 0.03
78 75 0.09
79 166 0.20
80 130 0.15
81 176 0.21
82 141 0.17
83 17 0.02
84 9 0.01
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (80 bp):
AAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
AAACAGAAATTTAAA
Found at i:397393 original size:239 final size:234
Alignment explanation
Indices: 396957--398009 Score: 1188
Period size: 239 Copynumber: 4.4 Consensus size: 234
396947 CTTTTTTTAA
* *
396957 AAAAAATAGAAATT--GAAAATACCTCGACG--TGACCTGAGGCTCAACTCACCTCTCGCAAT-T
1 AAAAAATAGAAATTAAAAAAATACCTCG-CGTATGACCCGAGGCTCAACTCACCTCTCGCAATAT
* *
397017 GGAGTTGATTTTTTTTGAAAAAAAACAGAAATTAAAAAAATACCTCGGCGTGTGACCCGAGGTTC
65 -GAGTTGA-TTTTTTTG---AAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCCGAGGCTC
*
397082 AACT-ATCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAACAGAAATTAAAAAAATACCTCGG
125 AACTCACCTCTCGCAATATGAGTTGA----TTTTTTGAAAAACAGAAATTAAAAAAATACCTCGG
* * *
397146 CGTGTGACCCAAGGCTCAACTCACCTCTCGCAATTTGAGTTGATTTTTG
186 CATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
* * *
397195 -AAAAATAGGAATT-GAGAAATACCTCAGCGTATGACCCGAGGCTCAACTCACCTCTCGCAATAT
1 AAAAAATAGAAATTAAAAAAATACCTC-GCGTATGACCCGAGGCTCAACTCACCTCTCGCAATAT
397258 GAGTTGATTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGACCCGAGGCTCAAC
65 GAGTTGATTTTTTTGAAAAACAGAAA-TTAAAA-AAATACCTCGGCATGTGACCCGAGGCTCAAC
* * *
397323 TCACCTCTTGTATTATGAGTTGATTTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCAT
128 TCACCTCTCGCAATATGAGTTGA--TTTTTTGAAAAACAGAAA-TTAAAA-AAATACCTCGGCAT
* * *
397388 GTGACCTGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTG
189 GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
* *
397434 AAAAAAAATAGAAATTTAAAAAAATACCTCG-GCAT-ACGCCTGAGGCTCAACTCACTTCTCGCA
1 --AAAAAATAGAAA-TTAAAAAAATACCTCGCGTATGAC-CC-GAGGCTCAACTCACCTCTCGCA
* * *
397497 ATATGAGTTGA-ATTTTTGAAAAACAGAAATTTAAAAGAAATACCTTGGCATGTG-TCCGAGGCT
61 ATATGAGTTGATTTTTTTGAAAAACAGAAA-TTAAAA-AAATACCTCGGCATGTGACCCGAGGCT
* * *
397560 CAACTCACCTCTTGCAATATGAGTTGAATTTTTGAAAAACAGAAATTTAAAAGAAATACCTTGGC
124 CAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAA-TTAAAA-AAATACCTCGGC
* *
397625 ATGTG-TCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTG
187 ATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG
* * * *
397673 AAAAAAACAGAAATTAAAAAAAATACCTCAGCATGTGTCCCGAGGCTCAACTCACCTCTCGCAAT
1 -AAAAAATAGAAATT-AAAAAAATACCTC-GCGTATGACCCGAGGCTCAACTCACCTCTCGCAAT
* ** *
397738 ATGAGTTGATTTTTTTGAAAAACATAAATTAAAAAATATACCTCAACGTGTGACCCGAGGCTCAA
63 ATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAAA-ATACCTCGGCATGTGACCCGAGGCTCAA
* *
397803 CTCAACTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATT-GAAAAATACCTC-G-ATGTG
127 CTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAAAAAATACCTCGGCATGTG
** *
397865 TGTCCGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTG
192 -ACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
* * * * * ** *
397909 -AAAAACAGAAATTTAAAAGAAATACCTCG-GCATGAGTCCGATGCTCAACTCACCTATCATATT
1 AAAAAATAGAAA-TTAAAA-AAATACCTCGCGTATGA-CCCGAGGCTCAACTCACCTCTCGCAAT
*** *
397972 ATGAGTTGATTTTTGAAAAAAATAGAAATATAAAAAAA
63 ATGAGTTGATTTTTTTGAAAAACAGAAAT-TAAAAAAA
398010 ATTCCAGGCT
Statistics
Matches: 716, Mismatches: 68, Indels: 66
0.84 0.08 0.08
Matches are distributed among these distances:
233 2 0.00
234 62 0.09
235 23 0.03
236 18 0.03
237 82 0.11
238 107 0.15
239 179 0.25
240 105 0.15
241 37 0.05
242 56 0.08
243 35 0.05
244 10 0.01
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (234 bp):
AAAAAATAGAAATTAAAAAAATACCTCGCGTATGACCCGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTTTGAAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCA
CCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCC
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
Found at i:409394 original size:17 final size:17
Alignment explanation
Indices: 409372--409409 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
409362 CTCAATCAAC
409372 AAATCTACCTTAATTTT
1 AAATCTACCTTAATTTT
*
409389 AAATCTACTTTAATTTT
1 AAATCTACCTTAATTTT
409406 AAAT
1 AAAT
409410 GGAAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATCTACCTTAATTTT
Found at i:411635 original size:13 final size:13
Alignment explanation
Indices: 411596--411635 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
411586 AGTTCTTCAT
411596 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
411609 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
411622 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
411635 T
1 T
411636 TTGGTTTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.28, C:0.07, G:0.30, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:414779 original size:39 final size:39
Alignment explanation
Indices: 414733--414807 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
414723 ATATTATTAT
* *
414733 GAGAGTATTTTTGTCATTTTATATTTTATGTAAAATTTA
1 GAGAGTATTTTTATCATTTTATATTTTATATAAAATTTA
** *
414772 GAGAGTATTTTTATTGTTTTATATTTTTTATAAAAT
1 GAGAGTATTTTTATCATTTTATATTTTATATAAAAT
414808 CTAAAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.56
Consensus pattern (39 bp):
GAGAGTATTTTTATCATTTTATATTTTATATAAAATTTA
Found at i:415872 original size:15 final size:15
Alignment explanation
Indices: 415852--415880 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
415842 TGGTCGACTA
415852 ATTGTTTATTTAATT
1 ATTGTTTATTTAATT
415867 ATTGTTTATTTAAT
1 ATTGTTTATTTAAT
415881 CTGATCGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (15 bp):
ATTGTTTATTTAATT
Found at i:420547 original size:16 final size:16
Alignment explanation
Indices: 420526--420556 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
420516 ACATACTAGC
420526 AGATCAATTAAATGTA
1 AGATCAATTAAATGTA
420542 AGATCAATTAAATGT
1 AGATCAATTAAATGT
420557 TTTAAATTTA
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:0.48, C:0.06, G:0.13, T:0.32
Consensus pattern (16 bp):
AGATCAATTAAATGTA
Found at i:431642 original size:11 final size:11
Alignment explanation
Indices: 431628--431653 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
431618 TAGCAAGATA
431628 GTAGTGAAATG
1 GTAGTGAAATG
431639 GTAGTGAAATG
1 GTAGTGAAATG
431650 GTAG
1 GTAG
431654 CAAAATAGTG
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:0.35, C:0.00, G:0.38, T:0.27
Consensus pattern (11 bp):
GTAGTGAAATG
Found at i:433644 original size:25 final size:27
Alignment explanation
Indices: 433592--433650 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 27
433582 TAGGCGCCAA
* *
433592 TGAATAAAATAATAATTTTTTTATTTTT
1 TGAATAAAATAATAA-TTTTATACTTTT
433620 TGAATAAAAT-ATAA-TTTATACTTTT
1 TGAATAAAATAATAATTTTATACTTTT
*
433645 TTAATA
1 TGAATA
433651 TATATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 14 0.50
27 4 0.14
28 10 0.36
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (27 bp):
TGAATAAAATAATAATTTTATACTTTT
Found at i:433645 original size:27 final size:28
Alignment explanation
Indices: 433592--433646 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
433582 TAGGCGCCAA
**
433592 TGAATAAAATAATAATTTTTTTATTTTT
1 TGAATAAAATAATAATTTTACTATTTTT
433620 TGAATAAAAT-ATAATTTATACT-TTTTT
1 TGAATAAAATAATAATTT-TACTATTTTT
433647 AATATATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (28 bp):
TGAATAAAATAATAATTTTACTATTTTT
Found at i:433743 original size:27 final size:27
Alignment explanation
Indices: 433713--433778 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
433703 CCTACCTAGT
433713 AGGCGCCAATGGAGGAGCCTCATGCAG
1 AGGCGCCAATGGAGGAGCCTCATGCAG
* * *
433740 AGGCGCTAATGAAGGAGCCTCATGGAG
1 AGGCGCCAATGGAGGAGCCTCATGCAG
433767 AGGCGCCAATGG
1 AGGCGCCAATGG
433779 TGTCCTCTGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.27, C:0.23, G:0.38, T:0.12
Consensus pattern (27 bp):
AGGCGCCAATGGAGGAGCCTCATGCAG
Found at i:434022 original size:22 final size:21
Alignment explanation
Indices: 433987--434061 Score: 95
Period size: 20 Copynumber: 3.7 Consensus size: 21
433977 TAGATTAGAA
*
433987 TTTTGTA-GAATATTTTAACTT
1 TTTTGTATGAATATTATAA-TT
434008 TTTTGTATGAATATTATAATT
1 TTTTGTATGAATATTATAATT
*
434029 TTTT-TATGAATATTGTAA--
1 TTTTGTATGAATATTATAATT
434047 TTTTGTATGAATATT
1 TTTTGTATGAATATT
434062 GAAATCTTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
18 4 0.08
19 10 0.20
20 13 0.26
21 13 0.26
22 10 0.20
ACGTcount: A:0.31, C:0.01, G:0.11, T:0.57
Consensus pattern (21 bp):
TTTTGTATGAATATTATAATT
Found at i:434036 original size:20 final size:20
Alignment explanation
Indices: 433994--434061 Score: 84
Period size: 19 Copynumber: 3.4 Consensus size: 20
433984 GAATTTTGTA
*
433994 GAATATTTTAACTTTTTTGTAT
1 GAATATTATAA-TTTTTT-TAT
434016 GAATATTATAATTTTTTTAT
1 GAATATTATAATTTTTTTAT
* *
434036 GAATATTGTAA-TTTTGTAT
1 GAATATTATAATTTTTTTAT
434055 GAATATT
1 GAATATT
434062 GAAATCTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 14 0.33
20 13 0.30
21 6 0.14
22 10 0.23
ACGTcount: A:0.32, C:0.01, G:0.10, T:0.56
Consensus pattern (20 bp):
GAATATTATAATTTTTTTAT
Found at i:437091 original size:22 final size:21
Alignment explanation
Indices: 437056--437100 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
437046 TACCTAATTT
*
437056 TTTTCTTCTTTTCCTTCCTTC
1 TTTTCTTCTCTTCCTTCCTTC
437077 TTTTCTTCTACTTCCTTCCTTC
1 TTTTCTTCT-CTTCCTTCCTTC
437099 TT
1 TT
437101 CTTTCTTCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTCTTCTCTTCCTTCCTTC
Found at i:437108 original size:18 final size:18
Alignment explanation
Indices: 437058--437109 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 18
437048 CCTAATTTTT
437058 TTCTTC-TT-TTCCTTCC
1 TTCTTCTTTCTTCCTTCC
437074 TTCTTTTCTTCTACTTCCTTCC
1 TTC--TTCTT-T-CTTCCTTCC
437096 TTCTTCTTTCTTCC
1 TTCTTCTTTCTTCC
437110 GTTTCTGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
16 3 0.10
18 8 0.27
19 2 0.07
20 6 0.20
22 11 0.37
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCTTCTTTCTTCCTTCC
Found at i:437215 original size:27 final size:27
Alignment explanation
Indices: 437166--437268 Score: 156
Period size: 27 Copynumber: 3.8 Consensus size: 27
437156 AAAATCACAG
437166 CATTGGCGCCTTCCA-ATATGGCACCAC
1 CATTGGCGCCTTCCAGATA-GGCACCAC
437193 CATTGGCGCC-TCCTAGATAGGCACCAC
1 CATTGGCGCCTTCC-AGATAGGCACCAC
* *
437220 CATTGGCGCCTCCCAAATAGGCACCAC
1 CATTGGCGCCTTCCAGATAGGCACCAC
437247 CATTGGCGCCTTCCAGATAGGC
1 CATTGGCGCCTTCCAGATAGGC
437269 GCCAATATTA
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
26 3 0.04
27 61 0.88
28 5 0.07
ACGTcount: A:0.22, C:0.37, G:0.21, T:0.19
Consensus pattern (27 bp):
CATTGGCGCCTTCCAGATAGGCACCAC
Found at i:437701 original size:77 final size:77
Alignment explanation
Indices: 437611--437767 Score: 260
Period size: 77 Copynumber: 2.0 Consensus size: 77
437601 TTTAAAAGTA
* *
437611 CTGCACATTAAATTGCTTTGGAAAGTGAACAATGCAGAGAAATTTTAATTACATGTGAGAGGACC
1 CTGCACATTAAATTGCTTCGAAAAGTGAACAATGCAGAGAAATTTTAATTACATGTGAGAGGACC
437676 AGTCCCTTCTGC
66 AGTCCCTTCTGC
*
437688 CTGCACATTAAATTGCTTCGAAAAGTGAACTATGCAGAGAAATTTTAATTACATGTGAGAGGACC
1 CTGCACATTAAATTGCTTCGAAAAGTGAACAATGCAGAGAAATTTTAATTACATGTGAGAGGACC
** *
437753 TTTCCGTTCTGC
66 AGTCCCTTCTGC
437765 CTG
1 CTG
437768 TAATTCTTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (77 bp):
CTGCACATTAAATTGCTTCGAAAAGTGAACAATGCAGAGAAATTTTAATTACATGTGAGAGGACC
AGTCCCTTCTGC
Found at i:438401 original size:20 final size:21
Alignment explanation
Indices: 438368--438408 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
438358 ATGTAGTACT
*
438368 ATTTCAATTTGAAAATTTTAA
1 ATTTCAATTTGAAAATCTTAA
438389 ATTTCAA-TTGAAAATCTTAA
1 ATTTCAATTTGAAAATCTTAA
438409 TTAATGAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (21 bp):
ATTTCAATTTGAAAATCTTAA
Found at i:442163 original size:31 final size:30
Alignment explanation
Indices: 442128--442190 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
442118 TAGTAAAGAT
442128 AAAATTACATTTTAACCCTTTAAAAATGATA
1 AAAATTACA-TTTAACCCTTTAAAAATGATA
** * * *
442159 AAAATTTGATTTAATCTTTTAAAAATTATA
1 AAAATTACATTTAACCCTTTAAAAATGATA
442189 AA
1 AA
442191 GATATAAGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.40
Consensus pattern (30 bp):
AAAATTACATTTAACCCTTTAAAAATGATA
Found at i:443478 original size:18 final size:18
Alignment explanation
Indices: 443457--443502 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
443447 GTTAGAATTT
443457 TTTTTATATTTTATATGA
1 TTTTTATATTTTATATGA
* * *
443475 TTTTTTTATCTTATATTA
1 TTTTTATATTTTATATGA
*
443493 TTTATATATT
1 TTTTTATATT
443503 AATTTTTTTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTTATATTTTATATGA
Found at i:443687 original size:40 final size:40
Alignment explanation
Indices: 443643--443720 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
443633 ATGACTAATT
443643 AATATAATATATAACTAAT-TAAT-TTATTGAACCTTTTCCA
1 AATAT-ATATATAACTAATAT-ATCTTATTGAACCTTTTCCA
* * *
443683 AATATCTATATGACTAATATATCTTATTGAACTTTTTC
1 AATATATATATAACTAATATATCTTATTGAACCTTTTC
443721 TAGGGTCGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 13 0.39
40 20 0.61
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.45
Consensus pattern (40 bp):
AATATATATATAACTAATATATCTTATTGAACCTTTTCCA
Found at i:445215 original size:33 final size:30
Alignment explanation
Indices: 445123--445219 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 30
445113 AATTTTTTTG
* *
445123 AAAATTCTCATTAATCTCATAAATTTTTAA
1 AAAATTCTCATTAAACTCCTAAATTTTTAA
* * *
445153 AAAATTTTAATTTAAAC-CCTAATTCTTTTAA
1 AAAATTCTCA-TTAAACTCCTAAAT-TTTTAA
445184 AAAATAATCTCATTAAACTCCTAAAATTTTTAA
1 AAAAT--TCTCATTAAACTCCT-AAATTTTTAA
445217 AAA
1 AAA
445220 TTTTAATTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
30 13 0.25
31 16 0.30
32 6 0.11
33 15 0.28
34 3 0.06
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.40
Consensus pattern (30 bp):
AAAATTCTCATTAAACTCCTAAATTTTTAA
Found at i:445241 original size:31 final size:31
Alignment explanation
Indices: 445143--445242 Score: 98
Period size: 31 Copynumber: 3.2 Consensus size: 31
445133 TTAATCTCAT
445143 AAATTTTTAAAAAATTTTAATTTAAA-CCCT-
1 AAATTTTTAAAAAATTTTAA-TTAAACCCCTA
* * * *
445173 AATTCTTTTAAAAAATAATCTCATTAAACTCCTA
1 AAAT-TTTTAAAAAAT--TTTAATTAAACCCCTA
445207 AAATTTTT-AAAAATTTTAATTAAACCCCCTA
1 AAATTTTTAAAAAATTTTAATTAAA-CCCCTA
445238 AAATT
1 AAATT
445243 ATTCCCAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
30 11 0.20
31 21 0.38
32 11 0.20
33 10 0.18
34 3 0.05
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (31 bp):
AAATTTTTAAAAAATTTTAATTAAACCCCTA
Found at i:453405 original size:21 final size:19
Alignment explanation
Indices: 453379--453437 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 19
453369 TATAGAAAAA
453379 TAATTTTTTTATAAAATTT
1 TAATTTTTTTATAAAATTT
*
453398 TATGATTTTAATTAT-AAATTT
1 TA--ATTTT-TTTATAAAATTT
*
453419 TAATTTTTTAAT-AAATTT
1 TAATTTTTTTATAAAATTT
453437 T
1 T
453438 TTATAATTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
18 10 0.29
19 7 0.21
21 13 0.38
22 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TAATTTTTTTATAAAATTT
Found at i:457098 original size:9 final size:9
Alignment explanation
Indices: 457084--457157 Score: 60
Period size: 9 Copynumber: 8.0 Consensus size: 9
457074 TTAAAATTTT
457084 TTTTATAAA
1 TTTTATAAA
457093 TTTTATAACA
1 TTTTATAA-A
* *
457103 TGTTATGAA
1 TTTTATAAA
* *
457112 TTTAATTAA
1 TTTTATAAA
457121 TTTCTAATAAA
1 TTT-T-ATAAA
*
457132 TTTTATAAG
1 TTTTATAAA
457141 TTTTA-AAA
1 TTTTATAAA
*
457149 TTTTTTAAA
1 TTTTATAAA
457158 ATTCCAGAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
8 6 0.12
9 30 0.59
10 8 0.16
11 7 0.14
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (9 bp):
TTTTATAAA
Found at i:459323 original size:17 final size:17
Alignment explanation
Indices: 459289--459321 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
459279 ATTTATGTCC
*
459289 TTTTAAAATTTATAAAA
1 TTTTAAAATTAATAAAA
459306 TTTT-AAATTAATAAAA
1 TTTTAAAATTAATAAAA
459322 ATAATACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTTAAAATTAATAAAA
Done.