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 200 of 230
Found at i:60009478 original size:41 final size:41
Alignment explanation
Indices: 60009409--60009553 Score: 200
Period size: 41 Copynumber: 3.5 Consensus size: 41
60009399 TTTAACATAT
* *
60009409 TCACCGGCACTTAACCTGCTAAGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* * * *
60009450 TCACTGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAAA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* * * *
60009491 TCACCAGCACTTAGCCTGGTAGACTTATAGCCTGTTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
60009532 TCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
60009554 ACGTAAAGTC
Statistics
Matches: 88, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 88 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
Found at i:60010139 original size:114 final size:113
Alignment explanation
Indices: 60010021--60010375 Score: 613
Period size: 114 Copynumber: 3.1 Consensus size: 113
60010011 CTCAAGATCT
*
60010021 TATACATATTCATATATAC-ATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAAC
1 TATACATA-T-ATATTTACAATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAAC
* * * *
60010085 TAATTTCAATTTATATACTTTCAATTATAGCTCATCAAGTATACAATAGA
64 TAATTTCAATTCATATATTTTTAATTATAGCTCATCAAATATACAATAGA
60010135 TATACATATATATTTACATATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACT
1 TATACATATATATTTACA-ATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACT
60010200 AATTTCAATTCATATATTTTTAATTATAGCTCATCAAATATACAATAGA
65 AATTTCAATTCATATATTTTTAATTATAGCTCATCAAATATACAATAGA
*
60010249 TATACATATATATTTACATATATTCGAACTTCATTTATGCATATATATAGCATTCATACTTAACT
1 TATACATATATATTTACA-ATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACT
60010314 AATTTCAATTCATATATTTTTAATTATAGCTCATCAAATATACAATAGA
65 AATTTCAATTCATATATTTTTAATTATAGCTCATCAAATATACAATAGA
60010363 TATACATATATAT
1 TATACATATATAT
60010376 ATGCTGATTT
Statistics
Matches: 233, Mismatches: 6, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
112 7 0.03
113 1 0.00
114 225 0.97
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.42
Consensus pattern (113 bp):
TATACATATATATTTACAATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACTA
ATTTCAATTCATATATTTTTAATTATAGCTCATCAAATATACAATAGA
Found at i:60011370 original size:13 final size:13
Alignment explanation
Indices: 60011352--60011376 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60011342 CAATCAAATG
60011352 CACACAAAATAAA
1 CACACAAAATAAA
60011365 CACACAAAATAA
1 CACACAAAATAA
60011377 TATTAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:60012720 original size:21 final size:20
Alignment explanation
Indices: 60012694--60012745 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
60012684 TATACGAATG
*
60012694 AATTTAACATCAATTTAATAC
1 AATTT-ACATCAATTCAATAC
*
60012715 AATTTACATTCAATTCAATCC
1 AATTTACA-TCAATTCAATAC
60012736 AATTTACATC
1 AATTTACATC
60012746 TTAGGTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTTACATCAATTCAATAC
Found at i:60015599 original size:24 final size:23
Alignment explanation
Indices: 60015547--60015600 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
60015537 CCTTACTGGT
*
60015547 AGTCACCACCGTCCGACGTCCACC
1 AGTCA-CACCGTCCGACGTACACC
* *
60015571 AGTCACACCGTTCGATGTACACC
1 AGTCACACCGTCCGACGTACACC
60015594 AGGTCAC
1 A-GTCAC
60015601 CATCATTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.24, C:0.41, G:0.19, T:0.17
Consensus pattern (23 bp):
AGTCACACCGTCCGACGTACACC
Found at i:60017647 original size:25 final size:25
Alignment explanation
Indices: 60017580--60017655 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
60017570 ATTCATATTG
**
60017580 GGGAATGCTCATACAAGCACATA-AAC
1 GGGAA-GCTCATATGAGC-CATATAAC
* *
60017606 GGAAAGCTC-TTTCGAGCCATATAAC
1 GGGAAGCTCATAT-GAGCCATATAAC
*
60017631 GGGAAGCTCATATGAGCCATGTAAC
1 GGGAAGCTCATATGAGCCATATAAC
60017656 AGAAATTTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
24 5 0.12
25 29 0.73
26 6 0.15
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (25 bp):
GGGAAGCTCATATGAGCCATATAAC
Found at i:60017720 original size:25 final size:25
Alignment explanation
Indices: 60017692--60017788 Score: 80
Period size: 25 Copynumber: 3.9 Consensus size: 25
60017682 GAAGCTCTGG
*
60017692 AGAGCCATTAATTAGGAAGCTCATA
1 AGAGCCATTAATCAGGAAGCTCATA
*
60017717 AGAGCCAGTT-ATCGGGAAG-TACATA
1 AGAGCCA-TTAATCAGGAAGCT-CATA
*
60017742 AGAGCCA-TAAACAGGAAGCTC--A
1 AGAGCCATTAATCAGGAAGCTCATA
60017764 AGAGCGTCATTAATC-GAGAAGCTCA
1 AGAGC--CATTAATCAG-GAAGCTCA
60017789 CGAGAACCAT
Statistics
Matches: 58, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
22 6 0.10
23 1 0.02
24 12 0.21
25 37 0.64
26 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.19
Consensus pattern (25 bp):
AGAGCCATTAATCAGGAAGCTCATA
Found at i:60018148 original size:40 final size:40
Alignment explanation
Indices: 60018093--60018174 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
60018083 TTCATGTGCA
60018093 AAAAAGCTACTAATCCGCTACTTTCTCTTTTCCTCGATTT
1 AAAAAGCTACTAATCCGCTACTTTCTCTTTTCCTCGATTT
60018133 AAAAAGCTACTAATCCGCTACTTTCTCTTTTCCTCGATTT
1 AAAAAGCTACTAATCCGCTACTTTCTCTTTTCCTCGATTT
60018173 AA
1 AA
60018175 CTTTGTATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.39
Consensus pattern (40 bp):
AAAAAGCTACTAATCCGCTACTTTCTCTTTTCCTCGATTT
Found at i:60023025 original size:21 final size:21
Alignment explanation
Indices: 60022993--60023169 Score: 122
Period size: 21 Copynumber: 8.4 Consensus size: 21
60022983 GAAGCCCGAA
* *
60022993 AGCTTAACAGAAGCTCATGAG
1 AGCTAAACAGAAGCTCATAAG
*
60023014 AGCTAAATAGAAGCTCATAAG
1 AGCTAAACAGAAGCTCATAAG
* *
60023035 AGCTAAACAGAAACCCATAAG
1 AGCTAAACAGAAGCTCATAAG
* * * * ** *
60023056 GGTTGATCAGAAGCTCGCAAA
1 AGCTAAACAGAAGCTCATAAG
* *
60023077 AGCTTAACAGAAACTCATAAG
1 AGCTAAACAGAAGCTCATAAG
* * *
60023098 AGTTTAACAAAAGCT-AGTAAG
1 AGCTAAACAGAAGCTCA-TAAG
* * * *
60023119 AGCTGAACAGAAACTCGTATG
1 AGCTAAACAGAAGCTCATAAG
* *
60023140 AGTTAAACAGAAGCTCGTAAG
1 AGCTAAACAGAAGCTCATAAG
*
60023161 AGCTGAACA
1 AGCTAAACA
60023170 AAAAGTAAAA
Statistics
Matches: 116, Mismatches: 38, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
20 1 0.01
21 115 0.99
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.18
Consensus pattern (21 bp):
AGCTAAACAGAAGCTCATAAG
Found at i:60023068 original size:42 final size:42
Alignment explanation
Indices: 60022993--60023169 Score: 167
Period size: 42 Copynumber: 4.2 Consensus size: 42
60022983 GAAGCCCGAA
* * * * *
60022993 AGCTTAACAGAAGCTCATGAGAGCTAAATAGAAGCTCATAAG
1 AGCTGAACAGAAACTCATAAGAGTTAAACAGAAGCTCATAAG
* * * * * ** *
60023035 AGCTAAACAGAAACCCATAAGGGTTGATCAGAAGCTCGCAAA
1 AGCTGAACAGAAACTCATAAGAGTTAAACAGAAGCTCATAAG
* * *
60023077 AGCTTAACAGAAACTCATAAGAGTTTAACAAAAGCT-AGTAAG
1 AGCTGAACAGAAACTCATAAGAGTTAAACAGAAGCTCA-TAAG
* * *
60023119 AGCTGAACAGAAACTCGTATGAGTTAAACAGAAGCTCGTAAG
1 AGCTGAACAGAAACTCATAAGAGTTAAACAGAAGCTCATAAG
60023161 AGCTGAACA
1 AGCTGAACA
60023170 AAAAGTAAAA
Statistics
Matches: 106, Mismatches: 27, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
42 106 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.18
Consensus pattern (42 bp):
AGCTGAACAGAAACTCATAAGAGTTAAACAGAAGCTCATAAG
Found at i:60023151 original size:84 final size:84
Alignment explanation
Indices: 60022991--60023156 Score: 199
Period size: 84 Copynumber: 2.0 Consensus size: 84
60022981 CAGAAGCCCG
* * * *
60022991 AAAGCTTAACAGAAGCTCATGAGAGCTAAATAGAAGCTCATAAGAGCTAAACAGAAACCCATAAG
1 AAAGCTTAACAGAAACTCATAAGAGCTAAACAAAAGCTCATAAGAGCTAAACAGAAACCCATAAG
* * *
60023056 GGTTGATCAGAAGCTCGCA
66 AGTTAAACAGAAGCTCGCA
* * * * * *
60023075 AAAGCTTAACAGAAACTCATAAGAGTTTAACAAAAGCT-AGTAAGAGCTGAACAGAAACTCGTAT
1 AAAGCTTAACAGAAACTCATAAGAGCTAAACAAAAGCTCA-TAAGAGCTAAACAGAAACCCATAA
60023139 GAGTTAAACAGAAGCTCG
65 GAGTTAAACAGAAGCTCG
60023157 TAAGAGCTGA
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
83 1 0.01
84 67 0.99
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.18
Consensus pattern (84 bp):
AAAGCTTAACAGAAACTCATAAGAGCTAAACAAAAGCTCATAAGAGCTAAACAGAAACCCATAAG
AGTTAAACAGAAGCTCGCA
Found at i:60023647 original size:21 final size:20
Alignment explanation
Indices: 60023621--60023674 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
60023611 ATTTAATCTT
60023621 TTAACTAATTTATCTATCAAA
1 TTAACTAATTTATCTATC-AA
*
60023642 TTAACTAATTT-TC-CTCAA
1 TTAACTAATTTATCTATCAA
60023660 TTAA-TAATTTATCTA
1 TTAACTAATTTATCTA
60023675 AATACTCTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 6 0.21
18 8 0.28
19 2 0.07
20 2 0.07
21 11 0.38
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAACTAATTTATCTATCAA
Found at i:60027952 original size:27 final size:28
Alignment explanation
Indices: 60027916--60027974 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
60027906 ATTTTATATT
*
60027916 TTTAATTTTTAAAAAATATAT-TTTTAA
1 TTTAAATTTTAAAAAATATATATTTTAA
* *
60027943 TTTAAATTTTAATAATTATATATTTTAA
1 TTTAAATTTTAAAAAATATATATTTTAA
60027971 TTTA
1 TTTA
60027975 TTAAATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 18 0.64
28 10 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTAAATTTTAAAAAATATATATTTTAA
Found at i:60027958 original size:15 final size:15
Alignment explanation
Indices: 60027940--60027987 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
60027930 AATATATTTT
60027940 TAATTTAAATTTTAA
1 TAATTTAAATTTTAA
*
60027955 TAATTATATATTTTAA
1 TAATT-TAAATTTTAA
*
60027971 T-TTATTAAATTTTAA
1 TAAT-TTAAATTTTAA
60027986 TA
1 TA
60027988 TATAATTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TAATTTAAATTTTAA
Found at i:60028002 original size:31 final size:31
Alignment explanation
Indices: 60027944--60028002 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
60027934 TATTTTTAAT
* **
60027944 TTAAATTTTAATAATTATATATTTTAATTTA
1 TTAAATTTTAATAATAATATAACTTAATTTA
60027975 TTAAATTTTAATATATAAT-TAACTTAAT
1 TTAAATTTTAATA-ATAATATAACTTAAT
60028003 ATTTTTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 20 0.83
32 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (31 bp):
TTAAATTTTAATAATAATATAACTTAATTTA
Found at i:60031324 original size:73 final size:71
Alignment explanation
Indices: 60031171--60031341 Score: 270
Period size: 73 Copynumber: 2.4 Consensus size: 71
60031161 AAAATAGGCA
60031171 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCGTTTCCCGAGCTTTC
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCGTTTCCCGAGCTTTC
*
60031236 GGGGAT
66 GAGGAT
* * *
60031242 TTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAACCATAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACC-TAAGCCCAACGACG-CGTTTCCCGAGCTT
60031307 TCGAGGAT
64 TCGAGGAT
* *
60031315 TTAGCGGCGTTTTTAAGGAAGCGCCGC
1 TTAGCGGCGTTTTTGAGAAAGCGCCGC
60031342 TAATGCTCAG
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
71 34 0.37
72 14 0.15
73 43 0.47
ACGTcount: A:0.25, C:0.26, G:0.27, T:0.22
Consensus pattern (71 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCGTTTCCCGAGCTTTC
GAGGAT
Found at i:60031396 original size:114 final size:114
Alignment explanation
Indices: 60031241--60031609 Score: 605
Period size: 114 Copynumber: 3.2 Consensus size: 114
60031231 CTTTCGGGGA
60031241 TTTAGCGGCGTTTCTGAGAAAGCGCCGC-AAAAAACCATAAGCCCAACGACGCCGTTTTCTGAGC
1 TTTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAAACC-TAAGCCCAACGACGCCGTTTTCTGAGC
* *
60031305 TTTCGAGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGC
65 TTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* * *
60031355 TTTAGCGGTGTTTCTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCGGTTTTCTAAGCT
1 TTTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
*
60031420 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGTCGCTAATGCTCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* * * * * *
60031469 TTTAGTGGCGTTTTTGGGAAAGTGCCGCAAAAAAACCTAAGCCCAACGATGCCGTTTTCTGAACT
1 TTTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
60031534 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
*
60031583 TTTAGCGGCGTTTTTGAGAAAGCGCCG
1 TTTAGCGGCGTTTCTGAGAAAGCGCCG
60031610 TTAACAATAT
Statistics
Matches: 235, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
114 227 0.97
115 8 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (114 bp):
TTTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:60031880 original size:22 final size:22
Alignment explanation
Indices: 60031855--60031900 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
60031845 GAGTTCATAT
*
60031855 TTTAATGTTTAGGGAGTATGGA
1 TTTAATGATTAGGGAGTATGGA
* * *
60031877 TTTAGTGATTATGGATTATGGA
1 TTTAATGATTAGGGAGTATGGA
60031899 TT
1 TT
60031901 AGGGGTTGGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (22 bp):
TTTAATGATTAGGGAGTATGGA
Found at i:60031940 original size:15 final size:15
Alignment explanation
Indices: 60031903--60031953 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
60031893 TATGGATTAG
*
60031903 GGGTT-GGGATTTAA
1 GGGTTAGGGGTTTAA
*
60031917 GGTTTAGGGG-TTAGA
1 GGGTTAGGGGTTTA-A
60031932 GGGTTAGGGGTTTAA
1 GGGTTAGGGGTTTAA
60031947 GGGTTAG
1 GGGTTAG
60031954 ACGTGCTAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 7 0.23
15 21 0.68
16 3 0.10
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (15 bp):
GGGTTAGGGGTTTAA
Found at i:60032222 original size:14 final size:14
Alignment explanation
Indices: 60032203--60032237 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
60032193 AAGTTGAGGG
60032203 GTTAGGGGTT-AGA
1 GTTAGGGGTTAAGA
60032216 TGTTAGGGGTTAAGA
1 -GTTAGGGGTTAAGA
60032231 GTTAGGG
1 GTTAGGG
60032238 ATTTAAGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.23, C:0.00, G:0.46, T:0.31
Consensus pattern (14 bp):
GTTAGGGGTTAAGA
Found at i:60033593 original size:106 final size:107
Alignment explanation
Indices: 60033471--60033668 Score: 364
Period size: 107 Copynumber: 1.9 Consensus size: 107
60033461 AGCGGCGTTT
60033471 AAAACGTCGCAAAAAATAAATCAATTTAT-AAAAAATAAAATAAAAAATTTTTAGCATAGCAAAA
1 AAAACGTCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAA
60033535 CGGCGTCATTTTGTTCAAAATGAAATAGCGGCGTTTTTATCA
66 CGGCGTCATTTTGTTCAAAATGAAATAGCGGCGTTTTTATCA
*
60033577 AAAACG-CAGCAAAAAATAAATCAATTTATAAAAAAATATAATAAAAAATTTTTAGCATAGCAAA
1 AAAACGTC-GCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAA
60033641 ACGGCGTCATTTTGTTCAAAATGAAATA
65 ACGGCGTCATTTTGTTCAAAATGAAATA
60033669 ATATTTTGCG
Statistics
Matches: 89, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
105 1 0.01
106 27 0.30
107 61 0.69
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.27
Consensus pattern (107 bp):
AAAACGTCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAA
CGGCGTCATTTTGTTCAAAATGAAATAGCGGCGTTTTTATCA
Found at i:60033805 original size:96 final size:97
Alignment explanation
Indices: 60033633--60033820 Score: 265
Period size: 96 Copynumber: 1.9 Consensus size: 97
60033623 AATTTTTAGC
* *
60033633 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTTCATAAAAACGC
1 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAAAAATTTTGCGGCGTTTTTCATAAAAACGC
*
60033698 CGCAAATAATAAAT-ATATTAATAAAAACCAAA
66 CGCAAAAAATAAATCA-ATTAATAAAAACCAAA
* * *
60033730 ATAGCAAAACGGCGTCATTTTGTTTAAAAT-AAAAAAAATTTTGTGGCGTTTTT-ATAAAAAATG
1 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAAAAATTTTGCGGCGTTTTTCAT-AAAAACG
* *
60033793 CGGCAAAAAATAAATCAATTTATAAAAA
65 CCGCAAAAAATAAATCAATTAATAAAAA
60033821 ATAAAATAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
95 2 0.02
96 49 0.60
97 30 0.37
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.30
Consensus pattern (97 bp):
ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAAAAATTTTGCGGCGTTTTTCATAAAAACGC
CGCAAAAAATAAATCAATTAATAAAAACCAAA
Found at i:60036475 original size:95 final size:94
Alignment explanation
Indices: 60036291--60036475 Score: 271
Period size: 95 Copynumber: 2.0 Consensus size: 94
60036281 TTAGCCTGAG
60036291 TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAATA
1 TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAATA
** *
60036356 CCATTCTTGCAGTAGGTACCTTTTTCTCA
66 CCATTCTTGCAACACGTACCTTTTTCTCA
* ** * **
60036385 TGCTTCCTCTTTCATTGCCTTTGTGCGCTTCCCTTTTTTGTTTTTGAAGTTCTAGAGTTGGTGAT
1 TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCC-TTTTTGTTTTTGAAGTTCTAGAGCTGGCAAT
*
60036450 ACCATTCTTGCAACACGTACTTTTTT
65 ACCATTCTTGCAACACGTACCTTTTT
60036476 TTTCTCAATT
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
94 30 0.38
95 50 0.62
ACGTcount: A:0.14, C:0.24, G:0.16, T:0.45
Consensus pattern (94 bp):
TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAATA
CCATTCTTGCAACACGTACCTTTTTCTCA
Found at i:60037936 original size:43 final size:43
Alignment explanation
Indices: 60037860--60038066 Score: 254
Period size: 43 Copynumber: 4.8 Consensus size: 43
60037850 TTTTTTCGAG
* * * *
60037860 AAGCGTCGCTAAAGG-CTTGTTCTATAGTGGCGTTTGTAGAAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
* *
60037902 AAGTGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAAAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
* * * *
60037945 AATCGCCGCTAAAGGTCTTGAGCTATAGCAGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
* * * *
60037988 AGGCGCTGCTAAAGGCCTTGATCTATAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
* * *
60038031 AAGCGCCGCTAAATGTCATGATCAATAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTT
60038067 ATTTTTAAAA
Statistics
Matches: 140, Mismatches: 24, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
42 13 0.09
43 127 0.91
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
Found at i:60040011 original size:42 final size:42
Alignment explanation
Indices: 60039901--60040013 Score: 147
Period size: 42 Copynumber: 2.7 Consensus size: 42
60039891 CAACAAAAAA
* * *
60039901 CGCCGCTAAAGATCATGTTCTTTAGCAGCGTTTTTCCATAAG
1 CGCCGCTAGAGATCATGTTCTTTAGCGGCATTTTTCCATAAG
* *
60039943 CGCCGCT-GAAGAACATGTTCTTTAGCGGCATTTTTCTATAAG
1 CGCCGCTAG-AGATCATGTTCTTTAGCGGCATTTTTCCATAAG
**
60039985 CGCCGCTAGAGATCATAATCTTTAGCGGC
1 CGCCGCTAGAGATCATGTTCTTTAGCGGC
60040014 GCTTTTTTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 60 0.98
43 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (42 bp):
CGCCGCTAGAGATCATGTTCTTTAGCGGCATTTTTCCATAAG
Found at i:60040467 original size:21 final size:21
Alignment explanation
Indices: 60040443--60040493 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
60040433 TTCTTTTGAA
60040443 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCTCTCGCTGCAG
* *
60040464 CCTCTGCTTCTTTCGCTGCCG
1 CCTCTGCTTCTCTCGCTGCAG
*
60040485 CGTCTGCTT
1 CCTCTGCTT
60040494 TAAGTTGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.02, C:0.41, G:0.20, T:0.37
Consensus pattern (21 bp):
CCTCTGCTTCTCTCGCTGCAG
Found at i:60044889 original size:9 final size:9
Alignment explanation
Indices: 60044854--60044894 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
60044844 ATTATGTATT
60044854 ATGTAAGT-
1 ATGTAAGTC
*
60044862 ACTGTAAGTA
1 A-TGTAAGTC
60044872 ATGTAAGTC
1 ATGTAAGTC
60044881 ATGTAAGTC
1 ATGTAAGTC
60044890 ATGTA
1 ATGTA
60044895 TTATGTAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 1 0.03
9 28 0.93
10 1 0.03
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (9 bp):
ATGTAAGTC
Found at i:60048871 original size:21 final size:20
Alignment explanation
Indices: 60048831--60048885 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
60048821 CGCTGAAATG
* * *
60048831 TAAACTCTAAACCTTAAACC
1 TAAACTCCAAGCCCTAAACC
*
60048851 TCAATCTCCAAGCCCTAAACC
1 T-AAACTCCAAGCCCTAAACC
*
60048872 TAAACTCTAAGCCC
1 TAAACTCCAAGCCC
60048886 AGATCACAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.36, G:0.04, T:0.22
Consensus pattern (20 bp):
TAAACTCCAAGCCCTAAACC
Found at i:60049697 original size:133 final size:135
Alignment explanation
Indices: 60049237--60049664 Score: 487
Period size: 133 Copynumber: 3.2 Consensus size: 135
60049227 CCATTTCCGA
* * * *
60049237 CGTTTTTTAACATTTCGCCACTAAAG-CATAAAAAGGAAACAACAAAACGGTACCGTTTTGCTCA
1 CGTTTTTTAA-AATGCGCCACTAAAGAAAT-AAAATGAAACAACAAAACGGTACCGTTTTGCTCA
* * * *
60049301 AAATTTTTTCTCAAATTAGATATCTTTACCGGCGTTTCTCCA-ATAACGCCACTATATCCCAA-T
64 AATTTTTTTCTCAAATTAGATATCTTTACCGGCGTTTCT-CAGAAAACGCCGCTATATTCCAATT
*
60049364 ATTTGCGG
128 TTTTGCGG
* * * * *
60049372 CGTTTTTTACAATGCGCCACTAAAGAAATAAAATGAAGCAATAAAATGGTAGCGTTTTG-TCCAA
1 CGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTACCGTTTTGCT-CAA
* * * * * *
60049436 ATTTTTTCCTCAAATTAAATATCTTTACCGGCGTTTCCCTGAAAATGCCGCTA-A-TGC-ATTCT
65 ATTTTTTTCTCAAATTAGATATCTTTACCGGCGTTTCTCAGAAAACGCCGCTATATTCCAATT-T
60049498 TTT-CTGG
129 TTTGC-GG
* *
60049505 CGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTACTGTTTTGCTCAGA
1 CGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTACCGTTTTGCTCAAA
* * *
60049570 TTTTTTTCTCAAATTCGTTATCGTTACCGGCGTTTCTCAGAAAACGCCGCTATATTCCAATTTTT
66 TTTTTTTCTCAAATTAGATATCTTTACCGGCGTTTCTCAGAAAACGCCGCTATATTCCAATTTTT
60049635 TGCGG
131 TGCGG
**
60049640 CGTTTTTGTGGAA-GCGCCACTAAAG
1 CGTTTTT-TAAAATGCGCCACTAAAG
60049665 TCATAAAGTA
Statistics
Matches: 243, Mismatches: 38, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
131 1 0.00
132 3 0.01
133 108 0.44
134 86 0.35
135 38 0.16
136 7 0.03
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (135 bp):
CGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTACCGTTTTGCTCAAA
TTTTTTTCTCAAATTAGATATCTTTACCGGCGTTTCTCAGAAAACGCCGCTATATTCCAATTTTT
TGCGG
Found at i:60051868 original size:58 final size:58
Alignment explanation
Indices: 60051789--60051898 Score: 166
Period size: 58 Copynumber: 1.9 Consensus size: 58
60051779 TAGTAGTTAC
* *
60051789 TCAACTATTAGTAAGTATTTTTTGATCACTCAACTATGAAAAATTACAAAATGACCAT
1 TCAACTATTAGTAAATATTTTTTGATCACCCAACTATGAAAAATTACAAAATGACCAT
* * * *
60051847 TCAATTATTAGTAAATTTTTTTTGATTACCCAACTATGAAAAGTTACAAAAT
1 TCAACTATTAGTAAATATTTTTTGATCACCCAACTATGAAAAATTACAAAAT
60051899 AGCCACCTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 46 1.00
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (58 bp):
TCAACTATTAGTAAATATTTTTTGATCACCCAACTATGAAAAATTACAAAATGACCAT
Found at i:60055173 original size:23 final size:23
Alignment explanation
Indices: 60055143--60055188 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
60055133 TAAAATTACG
60055143 AGAATACTTTTGATAGGATCTAC
1 AGAATACTTTTGATAGGATCTAC
60055166 AGAATACTTTTGATAGGATCTAC
1 AGAATACTTTTGATAGGATCTAC
60055189 CTATGTGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (23 bp):
AGAATACTTTTGATAGGATCTAC
Found at i:60055213 original size:74 final size:74
Alignment explanation
Indices: 60055092--60055239 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
60055082 TAAAATTACG
60055092 AGAATACTTTTGATAGGATCTACCTATGTGAGTGGAAGTGTTAAAATTACGAGAATACTTTTGAT
1 AGAATACTTTTGATAGGATCTACCTATGTGAGTGGAAGTGTTAAAATTACGAGAATACTTTTGAT
60055157 AGGATCTAC
66 AGGATCTAC
60055166 AGAATACTTTTGATAGGATCTACCTATGTGAGTGGAAGTGTTAAAATTACGAGAATACTTTTGAT
1 AGAATACTTTTGATAGGATCTACCTATGTGAGTGGAAGTGTTAAAATTACGAGAATACTTTTGAT
60055231 AGGATCTAC
66 AGGATCTAC
60055240 CTATGTGAGT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.34
Consensus pattern (74 bp):
AGAATACTTTTGATAGGATCTACCTATGTGAGTGGAAGTGTTAAAATTACGAGAATACTTTTGAT
AGGATCTAC
Found at i:60056314 original size:11 final size:12
Alignment explanation
Indices: 60056284--60056326 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
60056274 GACGTGGGTA
*
60056284 AAAATAATTATGT
1 AAAA-AATTATAT
60056297 AATAAAATTAT-T
1 AA-AAAATTATAT
60056309 AAAAAATTATAT
1 AAAAAATTATAT
60056321 AAAAAA
1 AAAAAA
60056327 AACAAATGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 8 0.29
12 10 0.36
13 8 0.29
14 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (12 bp):
AAAAAATTATAT
Found at i:60066205 original size:4 final size:5
Alignment explanation
Indices: 60066178--60066206 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
60066168 GTGAAACAAT
60066178 ATAAA ATAAA ATAAA ATAAA AT-AA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
60066207 GCACTTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:60066683 original size:20 final size:20
Alignment explanation
Indices: 60066646--60066683 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
60066636 ATGCATGTAA
*
60066646 ATATATAGAAAAATATATTT
1 ATATATAGAAAAAAATATTT
60066666 ATATATA-AAAGAAAATAT
1 ATATATAGAAA-AAAATAT
60066684 ACGTGTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
ATATATAGAAAAAAATATTT
Found at i:60080980 original size:21 final size:20
Alignment explanation
Indices: 60080954--60080992 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
60080944 AATTTTTTCC
60080954 CCAAATTTTGGATAACTTTTT
1 CCAAATTTTGGAT-ACTTTTT
60080975 CCAAATTTTGGATACTTT
1 CCAAATTTTGGATACTTT
60080993 ACATATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.46
Consensus pattern (20 bp):
CCAAATTTTGGATACTTTTT
Found at i:60088262 original size:20 final size:20
Alignment explanation
Indices: 60088239--60088278 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
60088229 TATTCAAACT
* *
60088239 ATATTACTTGAATAGTTATA
1 ATATTACATGAATAATTATA
*
60088259 ATATTAGATGAATAATTATA
1 ATATTACATGAATAATTATA
60088279 TGTCTTTGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (20 bp):
ATATTACATGAATAATTATA
Found at i:60089847 original size:27 final size:27
Alignment explanation
Indices: 60089809--60089863 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
60089799 CTTCCGGAAA
*
60089809 AGGTTTTAACCTTGAATGACGTATATT
1 AGGTTTTAACCTTGAATGACGCATATT
*
60089836 AGGTTTTAACCTTGAATGATGCATATT
1 AGGTTTTAACCTTGAATGACGCATATT
60089863 A
1 A
60089864 TGTATCAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (27 bp):
AGGTTTTAACCTTGAATGACGCATATT
Found at i:60091446 original size:24 final size:25
Alignment explanation
Indices: 60091384--60091447 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
60091374 TCTTGGTACT
* * *
60091384 TAATTAGAAATA-TGTTAAAATCAT
1 TAATTAAAAATATTTTTAAAATCAC
60091408 TAATTAAAAAATATTTTTAAAAT-AC
1 TAATT-AAAAATATTTTTAAAATCAC
*
60091433 TAATTACAAATATTT
1 TAATTAAAAATATTT
60091448 AATGGTTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
24 14 0.41
25 12 0.35
26 8 0.24
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (25 bp):
TAATTAAAAATATTTTTAAAATCAC
Found at i:60094715 original size:9 final size:9
Alignment explanation
Indices: 60094703--60094761 Score: 75
Period size: 9 Copynumber: 6.4 Consensus size: 9
60094693 AAAATAAAAA
60094703 AATTCGGGT
1 AATTCGGGT
60094712 AATTCGGGT
1 AATTCGGGT
*
60094721 ATTTTTC-GGT
1 A--ATTCGGGT
*
60094731 AATTCGGTT
1 AATTCGGGT
60094740 AATTCGGGT
1 AATTCGGGT
60094749 AATTCGGGT
1 AATTCGGGT
60094758 AATT
1 AATT
60094762 TTTAACCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
8 3 0.07
9 33 0.77
10 4 0.09
11 3 0.07
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.41
Consensus pattern (9 bp):
AATTCGGGT
Found at i:60095610 original size:28 final size:28
Alignment explanation
Indices: 60095570--60095639 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
60095560 TACATGGACG
*
60095570 GATTATTTAACTAGTAGATAAAGTGCAA
1 GATTATTTAACTACTAGATAAAGTGCAA
* *
60095598 GATTATTTAACTACTAGATGAAGTGTAA
1 GATTATTTAACTACTAGATAAAGTGCAA
60095626 GATTATTTAACTAC
1 GATTATTTAACTAC
60095640 ATAAACAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (28 bp):
GATTATTTAACTACTAGATAAAGTGCAA
Found at i:60100089 original size:29 final size:29
Alignment explanation
Indices: 60100045--60100114 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
60100035 AAATAAAAAA
*
60100045 TTACCAAAAT-TCTATAAAATTTTTTTAT
1 TTACCAAAATATATATAAAATTTTTTTAT
*
60100073 TTACCAAAATATATATAAATTTTTTTTAT
1 TTACCAAAATATATATAAAATTTTTTTAT
*
60100102 TTATCAAAATATA
1 TTACCAAAATATA
60100115 CCAAAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
28 10 0.26
29 28 0.74
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (29 bp):
TTACCAAAATATATATAAAATTTTTTTAT
Found at i:60100149 original size:17 final size:17
Alignment explanation
Indices: 60100116--60100148 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
60100106 CAAAATATAC
60100116 CAAAAAAAACTAAAAAA
1 CAAAAAAAACTAAAAAA
60100133 CAAAAAAAA-TAAAAAA
1 CAAAAAAAACTAAAAAA
60100149 AAATGGACCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.06
Consensus pattern (17 bp):
CAAAAAAAACTAAAAAA
Found at i:60100320 original size:14 final size:14
Alignment explanation
Indices: 60100289--60100458 Score: 59
Period size: 14 Copynumber: 12.9 Consensus size: 14
60100279 GTTGGTGGGG
* **
60100289 GGAAGAAGGAGAGG
1 GGAAGAAGAAGAAA
60100303 GGAAGAAGAAGAAA
1 GGAAGAAGAAGAAA
60100317 GGAAG--GAAGAAA
1 GGAAGAAGAAGAAA
*
60100329 -GAAAAAGAAGGAAAA
1 GGAAGAAGAA-G-AAA
*
60100344 GGAAAGAAGAGGAAA
1 GG-AAGAAGAAGAAA
* *
60100359 GAAAGAAAAAG-AA
1 GGAAGAAGAAGAAA
60100372 GGAAAGAA-AAGGAAA
1 GG-AAGAAGAA-GAAA
*
60100387 GG--G--GAGGAAA
1 GGAAGAAGAAGAAA
*
60100397 GAAAGAA-AA-ATAA
1 GGAAGAAGAAGA-AA
*
60100410 GGAAAGAAAAAGAAA
1 GG-AAGAAGAAGAAA
60100425 GG-AGAAG-AGAAA
1 GGAAGAAGAAGAAA
*
60100437 --AA-AAAAAGAAA
1 GGAAGAAGAAGAAA
60100448 -GAAGAAGAAGA
1 GGAAGAAGAAGA
60100459 GGGAAGGAAG
Statistics
Matches: 117, Mismatches: 17, Indels: 45
0.65 0.09 0.25
Matches are distributed among these distances:
10 7 0.06
11 10 0.09
12 17 0.15
13 22 0.19
14 35 0.30
15 17 0.15
16 3 0.03
17 6 0.05
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (14 bp):
GGAAGAAGAAGAAA
Found at i:60100381 original size:38 final size:38
Alignment explanation
Indices: 60100305--60100483 Score: 162
Period size: 38 Copynumber: 4.8 Consensus size: 38
60100295 AGGAGAGGGG
60100305 AAGAAGAA-GAAAGGA-AGG-AAGAAAGAAAAAGAA-G-
1 AAGAA-AAGGAAAGGAGAGGAAAGAAAGAAAAAGAAGGA
*
60100339 --GAAAAGGAAAGAAGAGGAAAGAAAGAAAAAGAAGGA
1 AAGAAAAGGAAAGGAGAGGAAAGAAAGAAAAAGAAGGA
* *
60100375 AAGAAAAGGAAAGGGGAGGAAAGAAAGAAAAATAAGGA
1 AAGAAAAGGAAAGGAGAGGAAAGAAAGAAAAAGAAGGA
* * *
60100413 AAGAAAAAGAAAGGAGAAGAGAA-AAA-AAAAAGAAAGAA
1 AAGAAAAGGAAAGGAGAGGA-AAGAAAGAAAAAG-AAGGA
* * *
60100451 GAAGAAGAGGGAAGGA-AGGAAAAAAAAGAAAAA
1 -AAGAAAAGGAAAGGAGAGG-AAAGAAAGAAAAA
60100484 AAAGTAATTT
Statistics
Matches: 119, Mismatches: 13, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
31 2 0.02
32 9 0.08
33 3 0.03
34 15 0.13
35 1 0.01
37 5 0.04
38 61 0.51
39 18 0.15
40 5 0.04
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (38 bp):
AAGAAAAGGAAAGGAGAGGAAAGAAAGAAAAAGAAGGA
Found at i:60100387 original size:10 final size:10
Alignment explanation
Indices: 60100325--60100425 Score: 79
Period size: 10 Copynumber: 10.5 Consensus size: 10
60100315 AAGGAAGGAA
*
60100325 GAAAGAAAAA
1 GAAAGAAAAG
*
60100335 GAAGGAAAAG
1 GAAAGAAAAG
*
60100345 GAAAGAAGAG
1 GAAAGAAAAG
60100355 GAAAG-AAA-
1 GAAAGAAAAG
60100363 GAAA-AAGAAG
1 GAAAGAA-AAG
60100373 GAAAGAAAAG
1 GAAAGAAAAG
***
60100383 GAAAGGGGAG
1 GAAAGAAAAG
60100393 GAAAG-AAA-
1 GAAAGAAAAG
60100401 GAAA-AATAAG
1 GAAAGAA-AAG
*
60100411 GAAAGAAAAA
1 GAAAGAAAAG
60100421 GAAAG
1 GAAAG
60100426 GAGAAGAGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
8 10 0.14
9 7 0.10
10 51 0.71
11 4 0.06
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:60101202 original size:19 final size:18
Alignment explanation
Indices: 60101162--60101212 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
60101152 AAAATATATA
**
60101162 TAATATTTTGGTATTTTT
1 TAATATTTTATTATTTTT
60101180 TAATATTTTATTATTTTT
1 TAATATTTTATTATTTTT
*
60101198 GTAATGTTTTATTAT
1 -TAATATTTTATTAT
60101213 GGGTTTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 16 0.55
19 13 0.45
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (18 bp):
TAATATTTTATTATTTTT
Found at i:60101279 original size:28 final size:26
Alignment explanation
Indices: 60101248--60101472 Score: 264
Period size: 28 Copynumber: 8.5 Consensus size: 26
60101238 AAATAAAAAA
60101248 TTACCAAAATATTATAAATTTTTTTTAT
1 TTACCAAAATA-TAT-AATTTTTTTTAT
*
60101276 TTACCGAAATATAT-A--TTTTTTAT
1 TTACCAAAATATATAATTTTTTTTAT
*
60101299 TTACCAAAATATTATAAAATTTTTTTAT
1 TTACCAAAATA-TAT-AATTTTTTTTAT
* *
60101327 TTACCGAAATATAT-ATATTTTTTAT
1 TTACCAAAATATATAATTTTTTTTAT
60101352 TTACCAAAATATTATAATTTTTTTTAT
1 TTACCAAAATA-TATAATTTTTTTTAT
*
60101379 TTACCGAAATATAT-A-TTTTTTTAT
1 TTACCAAAATATATAATTTTTTTTAT
*
60101403 TTACCAAAATATATATAATTTTGTTTAT
1 TTACC-AAA-ATATATAATTTTTTTTAT
*
60101431 TTACCAAAATATATATAGTTTTGTTTAT
1 TTACCAAAATATATA-A-TTTTTTTTAT
60101459 TTACCAAAATATAT
1 TTACCAAAATATAT
60101473 CAAAAAAAAC
Statistics
Matches: 174, Mismatches: 10, Indels: 26
0.83 0.05 0.12
Matches are distributed among these distances:
23 18 0.10
24 17 0.10
25 23 0.13
26 20 0.11
27 31 0.18
28 65 0.37
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (26 bp):
TTACCAAAATATATAATTTTTTTTAT
Found at i:60101304 original size:51 final size:53
Alignment explanation
Indices: 60101248--60101470 Score: 332
Period size: 51 Copynumber: 4.2 Consensus size: 53
60101238 AAATAAAAAA
60101248 TTACCAAAATATTATAAATTTTTTTTATTTACCGAA-ATATATA-TTTTTTAT
1 TTACCAAAATATTATAAATTTTTTTTATTTACCGAATATATATATTTTTTTAT
*
60101299 TTACCAAAATATTATAAAATTTTTTTATTTACCGAA-ATATATATATTTTTTAT
1 TTACCAAAATATTATAAATTTTTTTTATTTACCGAATATATATAT-TTTTTTAT
60101352 TTACCAAAATATTAT-AATTTTTTTTATTTACCGAA-ATATATATTTTTTTAT
1 TTACCAAAATATTATAAATTTTTTTTATTTACCGAATATATATATTTTTTTAT
* *
60101403 TTACCAAAATA-TATATAATTTTGTTTATTTACCAAAATATATATAGTTTTGTTTAT
1 TTACCAAAATATTATA-AATTTTTTTTATTTACC-GAATATATATA-TTTT-TTTAT
60101459 TTACCAAAATAT
1 TTACCAAAATAT
60101471 ATCAAAAAAA
Statistics
Matches: 159, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
50 3 0.02
51 61 0.38
52 43 0.27
53 25 0.16
54 7 0.04
55 4 0.03
56 16 0.10
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (53 bp):
TTACCAAAATATTATAAATTTTTTTTATTTACCGAATATATATATTTTTTTAT
Found at i:60101374 original size:52 final size:53
Alignment explanation
Indices: 60101248--60101470 Score: 348
Period size: 52 Copynumber: 4.2 Consensus size: 53
60101238 AAATAAAAAA
60101248 TTACCAAAATATTATAAATTTTTTTTATTTACCG-AA-ATATATATTTTTTAT
1 TTACCAAAATATTATAAATTTTTTTTATTTACCGAAATATATATATTTTTTAT
*
60101299 TTACCAAAATATTATAAAATTTTTTTATTTACCGAAATATATATATTTTTTAT
1 TTACCAAAATATTATAAATTTTTTTTATTTACCGAAATATATATATTTTTTAT
60101352 TTACCAAAATATTAT-AATTTTTTTTATTTACCGAAATATATAT-TTTTTTAT
1 TTACCAAAATATTATAAATTTTTTTTATTTACCGAAATATATATATTTTTTAT
* *
60101403 TTACCAAAATA-TATATAATTTTGTTTATTTACCAAAATATATATAGTTTTGTTTAT
1 TTACCAAAATATTATA-AATTTTTTTTATTTACCGAAATATATATA--TTT-TTTAT
60101459 TTACCAAAATAT
1 TTACCAAAATAT
60101471 ATCAAAAAAA
Statistics
Matches: 159, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
50 3 0.02
51 52 0.33
52 55 0.35
53 30 0.19
55 3 0.02
56 16 0.10
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (53 bp):
TTACCAAAATATTATAAATTTTTTTTATTTACCGAAATATATATATTTTTTAT
Found at i:60103545 original size:18 final size:18
Alignment explanation
Indices: 60103504--60103545 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
60103494 CCAATGATTG
* *
60103504 CCACCACCTTCTTCTTCG
1 CCACCACATTCTTCTTCA
*
60103522 CAACCACATTCTTCTTCA
1 CCACCACATTCTTCTTCA
60103540 CCACCA
1 CCACCA
60103546 ACCATATCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.48, G:0.02, T:0.29
Consensus pattern (18 bp):
CCACCACATTCTTCTTCA
Found at i:60104647 original size:27 final size:27
Alignment explanation
Indices: 60104601--60104665 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
60104591 AACACGAGTA
** * *
60104601 GTGCCGCCAACCTGGTTTCCTCCACTG
1 GTGCCGCCAACAGGGATTCCTCAACTG
60104628 GTGCCGCCAACAGGGATTCCTCAACTG
1 GTGCCGCCAACAGGGATTCCTCAACTG
60104655 GTGCCGCCAAC
1 GTGCCGCCAAC
60104666 CTGGTCCCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.17, C:0.38, G:0.25, T:0.20
Consensus pattern (27 bp):
GTGCCGCCAACAGGGATTCCTCAACTG
Found at i:60104759 original size:15 final size:16
Alignment explanation
Indices: 60104735--60104765 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
60104725 GGTCCAGTTT
60104735 TTTTTCTATTTTTTTG
1 TTTTTCTATTTTTTTG
60104751 TTTTT-TATTTTTTTG
1 TTTTTCTATTTTTTTG
60104766 GTATATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (16 bp):
TTTTTCTATTTTTTTG
Found at i:60104798 original size:28 final size:29
Alignment explanation
Indices: 60104767--60104823 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
60104757 ATTTTTTTGG
*
60104767 TATATTTTGGTAAAT-AAAAAAATTTATA
1 TATATTTTGGCAAATAAAAAAAATTTATA
60104795 TATATTTTGGCAAATAAAAAAAATTTATA
1 TATATTTTGGCAAATAAAAAAAATTTATA
60104824 GCATTTTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (29 bp):
TATATTTTGGCAAATAAAAAAAATTTATA
Found at i:60104829 original size:28 final size:28
Alignment explanation
Indices: 60104770--60104832 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
60104760 TTTTTGGTAT
* *
60104770 ATTTTGGTAAATAAAAAAATTTATATAT
1 ATTTTGGCAAATAAAAAAATTTATATAC
*
60104798 ATTTTGGCAAATAAAAAAAATTTATA-GC
1 ATTTTGGCAAAT-AAAAAAATTTATATAC
60104826 ATTTTGG
1 ATTTTGG
60104833 TAATTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 18 0.58
29 13 0.42
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.40
Consensus pattern (28 bp):
ATTTTGGCAAATAAAAAAATTTATATAC
Found at i:60114496 original size:22 final size:23
Alignment explanation
Indices: 60114468--60114515 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
60114458 AAGTGTGTGT
*
60114468 AGGTTACTTGACTGTT-GGAGGC
1 AGGTTACTTGACTGTTAAGAGGC
60114490 AGGTTACTTGACTGTTAAGAGGC
1 AGGTTACTTGACTGTTAAGAGGC
60114513 AGG
1 AGG
60114516 AGATGTGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.23, C:0.12, G:0.35, T:0.29
Consensus pattern (23 bp):
AGGTTACTTGACTGTTAAGAGGC
Found at i:60128462 original size:14 final size:14
Alignment explanation
Indices: 60128418--60128463 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
60128408 TCTATGTCAA
*
60128418 TTTAGGATTAAGGG
1 TTTAGGGTTAAGGG
* * *
60128432 TTAAGGGTTTAGTG
1 TTTAGGGTTAAGGG
60128446 TTTAGGGTTAAGGG
1 TTTAGGGTTAAGGG
60128460 TTTA
1 TTTA
60128464 AAGTACTCTA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (14 bp):
TTTAGGGTTAAGGG
Found at i:60131215 original size:18 final size:18
Alignment explanation
Indices: 60131192--60131236 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
60131182 AAACAATTTT
60131192 TAAATTATATAACTTACA
1 TAAATTATATAACTTACA
60131210 TAAATTATATAACTTACA
1 TAAATTATATAACTTACA
*
60131228 TAACTTATA
1 TAAATTATA
60131237 AATATTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATTATATAACTTACA
Found at i:60131221 original size:9 final size:9
Alignment explanation
Indices: 60131196--60131236 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
60131186 AATTTTTAAA
60131196 TTATATAAC
1 TTATATAAC
* *
60131205 TTACATAAA
1 TTATATAAC
60131214 TTATATAAC
1 TTATATAAC
*
60131223 TTACATAAC
1 TTATATAAC
60131232 TTATA
1 TTATA
60131237 AATATTTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (9 bp):
TTATATAAC
Found at i:60131278 original size:17 final size:18
Alignment explanation
Indices: 60131258--60131291 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
60131248 ACATTTTTAA
60131258 TATATATTTTT-AAAATC
1 TATATATTTTTCAAAATC
*
60131275 TATATTTTTTTCAAAAT
1 TATATATTTTTCAAAAT
60131292 TTATCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATTTTTCAAAATC
Found at i:60131393 original size:23 final size:27
Alignment explanation
Indices: 60131339--60131408 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 27
60131329 TCAATCATAT
60131339 CATAACTTATATATAAACATACATAATA
1 CATAACTTATATATAAACATACA-AATA
60131367 CATAACTTA-A-AT-AACATAC-AATA
1 CATAACTTATATATAAACATACAAATA
*
60131390 CATAAACTTACATATAAAC
1 CAT-AACTTATATATAAAC
60131409 TTGCATAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
23 7 0.18
24 6 0.16
25 8 0.21
26 4 0.11
27 4 0.11
28 9 0.24
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (27 bp):
CATAACTTATATATAAACATACAAATA
Found at i:60131425 original size:9 final size:9
Alignment explanation
Indices: 60131406--60131465 Score: 75
Period size: 9 Copynumber: 6.7 Consensus size: 9
60131396 CTTACATATA
*
60131406 AACTTGCAT
1 AACTTACAT
*
60131415 AACTTATAT
1 AACTTACAT
*
60131424 AAATTACAT
1 AACTTACAT
60131433 AACTTACAT
1 AACTTACAT
* *
60131442 AAATTATAT
1 AACTTACAT
60131451 AACTTACAT
1 AACTTACAT
60131460 AACTTA
1 AACTTA
60131466 TAAATATTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.37
Consensus pattern (9 bp):
AACTTACAT
Found at i:60131435 original size:18 final size:18
Alignment explanation
Indices: 60131388--60131461 Score: 85
Period size: 18 Copynumber: 3.9 Consensus size: 18
60131378 TAACATACAA
60131388 TACATAAACTTACATATAAACT
1 TACAT-AACTTAC--ATAAA-T
* *
60131410 TGCATAACTTATATAAAT
1 TACATAACTTACATAAAT
60131428 TACATAACTTACATAAAT
1 TACATAACTTACATAAAT
*
60131446 TATATAACTTACATAA
1 TACATAACTTACATAA
60131462 CTTATAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 32 0.68
19 5 0.11
21 6 0.13
22 4 0.09
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.35
Consensus pattern (18 bp):
TACATAACTTACATAAAT
Found at i:60131442 original size:27 final size:27
Alignment explanation
Indices: 60131406--60131465 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
60131396 CTTACATATA
* *
60131406 AACTTGCATAACTTATATAAATTACAT
1 AACTTACATAAATTATATAAATTACAT
*
60131433 AACTTACATAAATTATATAACTTACAT
1 AACTTACATAAATTATATAAATTACAT
60131460 AACTTA
1 AACTTA
60131466 TAAATATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.37
Consensus pattern (27 bp):
AACTTACATAAATTATATAAATTACAT
Found at i:60131455 original size:231 final size:233
Alignment explanation
Indices: 60131192--60131619 Score: 806
Period size: 231 Copynumber: 1.8 Consensus size: 233
60131182 AAACAATTTT
*
60131192 TAAATTATATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
1 TAAATTACATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
60131257 ATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTC
66 ATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTC
*
60131322 AAATTTATCAATCATATCATAACTTATATATAAACATACAT-AA-TACATAACTTAAATAACATA
131 AAATTTATCAATCATATCATAACTTATATATAAACATACATAAATTAAATAACTTAAATAACATA
60131385 CAATACATAAACTTACATATAAACTTGCATAACTTATA
196 CAATACATAAACTTACATATAAACTTGCATAACTTATA
60131423 TAAATTACATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
1 TAAATTACATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
60131488 ATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTC
66 ATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTC
* *
60131553 AAATTTATCAATCATATCATAACTTATATATAAACTTACATAAATTAAATAACTTAAATAACTTA
131 AAATTTATCAATCATATCATAACTTATATATAAACATACATAAATTAAATAACTTAAATAACATA
60131618 CA
196 CA
60131620 TAACTTAAAT
Statistics
Matches: 191, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
231 169 0.88
232 2 0.01
233 20 0.10
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.40
Consensus pattern (233 bp):
TAAATTACATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
ATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTC
AAATTTATCAATCATATCATAACTTATATATAAACATACATAAATTAAATAACTTAAATAACATA
CAATACATAAACTTACATATAAACTTGCATAACTTATA
Found at i:60131466 original size:18 final size:18
Alignment explanation
Indices: 60131413--60131467 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
60131403 ATAAACTTGC
* *
60131413 ATAACTTATATAAATTAC
1 ATAACTTACATAAATTAT
60131431 ATAACTTACATAAATTAT
1 ATAACTTACATAAATTAT
*
60131449 ATAACTTACATAACTTAT
1 ATAACTTACATAAATTAT
60131467 A
1 A
60131468 AATATTTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAACTTACATAAATTAT
Found at i:60131509 original size:17 final size:18
Alignment explanation
Indices: 60131489--60131522 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
60131479 ACATTTTTAA
60131489 TATATATTTTT-AAAATC
1 TATATATTTTTCAAAATC
*
60131506 TATATTTTTTTCAAAAT
1 TATATATTTTTCAAAAT
60131523 TTATCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATTTTTCAAAATC
Found at i:60131609 original size:9 final size:9
Alignment explanation
Indices: 60131585--60131832 Score: 206
Period size: 9 Copynumber: 27.3 Consensus size: 9
60131575 CTTATATATA
60131585 AACTTACAT
1 AACTTACAT
* *
60131594 AAATTAAAT
1 AACTTACAT
*
60131603 AACTTAAAT
1 AACTTACAT
60131612 AACTTACAT
1 AACTTACAT
*
60131621 AACTTAAAT
1 AACTTACAT
60131630 AACTTACAT
1 AACTTACAT
60131639 AA--TACAT
1 AACTTACAT
*
60131646 AACCTT-CCT
1 AA-CTTACAT
*
60131655 AACTTAAAT
1 AACTTACAT
* *
60131664 TATTTACAT
1 AACTTACAT
60131673 AA--TACAT
1 AACTTACAT
60131680 AACTTAGTACAT
1 AAC-T--TACAT
60131692 AACTTACAT
1 AACTTACAT
* *
60131701 AATTTTTTC-T
1 AA--CTTACAT
60131711 AAATTGCTTACAT
1 -AA---CTTACAT
* *
60131724 AAATTATAT
1 AACTTACAT
60131733 AACTTACAT
1 AACTTACAT
60131742 AACTTACAT
1 AACTTACAT
* *
60131751 AAATTAAAT
1 AACTTACAT
60131760 AACTTACAT
1 AACTTACAT
60131769 AACTTACAT
1 AACTTACAT
*
60131778 AACTTAAAT
1 AACTTACAT
*
60131787 AGCTTACAT
1 AACTTACAT
60131796 AACTTACAT
1 AACTTACAT
60131805 AACTTACAT
1 AACTTACAT
60131814 AACTTACAT
1 AACTTACAT
60131823 AA--TACAT
1 AACTTACAT
60131830 AAC
1 AAC
60131833 CTTCCTTACT
Statistics
Matches: 194, Mismatches: 30, Indels: 31
0.76 0.12 0.12
Matches are distributed among these distances:
7 21 0.11
8 3 0.02
9 147 0.76
10 2 0.01
11 6 0.03
12 14 0.07
13 1 0.01
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.35
Consensus pattern (9 bp):
AACTTACAT
Found at i:60131673 original size:231 final size:230
Alignment explanation
Indices: 60131192--60131674 Score: 749
Period size: 231 Copynumber: 2.1 Consensus size: 230
60131182 AAACAATTTT
*
60131192 TAAATTATATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
1 TAAATTAAATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
60131257 ATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTC
66 ATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTC
*
60131322 AAATTTATCAATCATATCATAACTTATATATAAACATACATAATACATAACTTAAATAACATACA
131 AAATTTATCAATCATATCATAACTTATATATAAACATACATAATAAATAACTTAAATAACATACA
* * * *
60131387 ATACATAAACTTACATATAAACTTGCATAACTTATA
196 ATACATAAACTAACATACAAAC-TACATAACTTACA
*
60131423 TAAATTACATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
1 TAAATTAAATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
60131488 ATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTC
66 ATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTC
* *
60131553 AAATTTATCAATCATATCATAACTTATATATAAACTTACATAAATTAAATAACTTAAATAACTTA
131 AAATTTATCAATCATATCATAACTTATATATAAACATACAT-AA-TAAATAACTTAAATAACATA
* * *
60131618 C-ATAACTTAAA-TAACTTACATAA-TACATAACCTT-CC
194 CAAT-ACATAAACTAACATACA-AACTACATAA-CTTACA
* * *
60131654 TAACTTAAATTATTTACATAA
1 TAAATTAAATAACTTACATAA
60131675 TACATAACTT
Statistics
Matches: 232, Mismatches: 15, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
231 192 0.83
232 13 0.06
233 27 0.12
ACGTcount: A:0.46, C:0.14, G:0.01, T:0.40
Consensus pattern (230 bp):
TAAATTAAATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
ATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTC
AAATTTATCAATCATATCATAACTTATATATAAACATACATAATAAATAACTTAAATAACATACA
ATACATAAACTAACATACAAACTACATAACTTACA
Found at i:60132806 original size:21 final size:21
Alignment explanation
Indices: 60132781--60132846 Score: 89
Period size: 21 Copynumber: 3.1 Consensus size: 21
60132771 CAACTTAAAA
*
60132781 CAGAGGCAGCAGCGAGGGAAG
1 CAGAGGCAGCAGCGAGAGAAG
*
60132802 CAGAGGCTGCAGCGAGAGAAG
1 CAGAGGCAGCAGCGAGAGAAG
*
60132823 CAGAGACCA-CAGCGAGAGAAG
1 CAGAG-GCAGCAGCGAGAGAAG
60132844 CAG
1 CAG
60132847 CGAGAGAAGC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 39 0.98
22 1 0.03
ACGTcount: A:0.36, C:0.21, G:0.41, T:0.02
Consensus pattern (21 bp):
CAGAGGCAGCAGCGAGAGAAG
Found at i:60132849 original size:12 final size:12
Alignment explanation
Indices: 60132810--60132858 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
60132800 AGCAGAGGCT
60132810 GCAGCGAGAGAA
1 GCAGCGAGAGAA
**
60132822 GCA--GAGACCA
1 GCAGCGAGAGAA
60132832 -CAGCGAGAGAA
1 GCAGCGAGAGAA
60132843 GCAGCGAGAGAA
1 GCAGCGAGAGAA
60132855 GCAG
1 GCAG
60132859 AGGTTCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
9 2 0.07
10 5 0.17
11 5 0.17
12 18 0.60
ACGTcount: A:0.41, C:0.20, G:0.39, T:0.00
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:60133407 original size:85 final size:85
Alignment explanation
Indices: 60133318--60133543 Score: 222
Period size: 85 Copynumber: 2.7 Consensus size: 85
60133308 AACACTACTT
* * * *
60133318 TTAGCGGT-ATTTGTAGATGAAGCGCCGCTAAAGAACATTA-CTTTTAGCGGCGTTTTCTCCCAA
1 TTAGCGGTGATTTGTACAT-AAGCGCCGCTAAAGAACATGATC-ATTAGCGGCATTTTCTCCCAA
60133381 GCGCCGCTAAAGAACATGATCA
64 GCGCCGCTAAAGAACATGATCA
* * * * * * *
60133403 TTAGCGGTGTTTTTTTCCTAAGCGCCGCTAAAGAACATGATCATTAGCGGCATTTTTTTCTAAGC
1 TTAGCGGTGATTTGTACATAAGCGCCGCTAAAGAACATGATCATTAGCGGCATTTTCTCCCAAGC
*
60133468 GCCGCTAAAGAACATGATTA
66 GCCGCTAAAGAACATGATCA
* * * * * * * * * *
60133488 TTAGCGGCGTTTTTTTCTTAAGCACCACTAAAGAACATGACCTTTAGCGGCGTTTT
1 TTAGCGGTGATTTGTACATAAGCGCCGCTAAAGAACATGATCATTAGCGGCATTTT
60133544 TTTATGTAAG
Statistics
Matches: 120, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
85 114 0.95
86 6 0.05
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (85 bp):
TTAGCGGTGATTTGTACATAAGCGCCGCTAAAGAACATGATCATTAGCGGCATTTTCTCCCAAGC
GCCGCTAAAGAACATGATCA
Found at i:60133439 original size:43 final size:43
Alignment explanation
Indices: 60133337--60133564 Score: 282
Period size: 43 Copynumber: 5.3 Consensus size: 43
60133327 TTTGTAGATG
* * * *
60133337 AAGCGCCGCTAAAGAACATTA-CTTTTAGCGGCG-TTTTCTCCC
1 AAGCGCCGCTAAAGAACATGATC-ATTAGCGGCGTTTTTTTCCT
*
60133379 AAGCGCCGCTAAAGAACATGATCATTAGCGGTGTTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCT
*
60133422 AAGCGCCGCTAAAGAACATGATCATTAGCGGCATTTTTTT-CT
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCT
* *
60133464 AAGCGCCGCTAAAGAACATGATTATTAGCGGCGTTTTTTTCTT
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCT
* * * * **
60133507 AAGCACCACTAAAGAACATGACCTTTAGCGGCGTTTTTTTATGT
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTT-CCT
*
60133551 AAGCGCCGCAAAAG
1 AAGCGCCGCTAAAG
60133565 TTAGCGACGT
Statistics
Matches: 162, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
42 68 0.42
43 82 0.51
44 12 0.07
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (43 bp):
AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCT
Found at i:60133544 original size:85 final size:85
Alignment explanation
Indices: 60133345--60133564 Score: 287
Period size: 85 Copynumber: 2.6 Consensus size: 85
60133335 TGAAGCGCCG
* * * * *
60133345 CTAAAGAACATTACTTTTAGCGGCGTTTTCTCCCAAGCGCCGCTAAAGAACATGATCATTAGCGG
1 CTAAAGAACATGACCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCATTAGCGG
* * *
60133410 TGTTTTTTTCCTAAGCGCCG
66 CGTTTTTTTCCTAAGCACCA
* * * *
60133430 CTAAAGAACATGATCATTAGCGGCATTTTTTTCTAAGCGCCGCTAAAGAACATGATTATTAGCGG
1 CTAAAGAACATGACCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCATTAGCGG
*
60133495 CGTTTTTTTCTTAAGCACCA
66 CGTTTTTTTCCTAAGCACCA
* *
60133515 CTAAAGAACATGACCTTTAGCGGCGTTTTTTTATGTAAGCGCCGCAAAAG
1 CTAAAGAACATGACCTTTAGCGGCG-TTTTTT-TCTAAGCGCCGCTAAAG
60133565 TTAGCGACGT
Statistics
Matches: 115, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
85 94 0.82
86 6 0.05
87 15 0.13
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (85 bp):
CTAAAGAACATGACCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCATTAGCGG
CGTTTTTTTCCTAAGCACCA
Found at i:60133602 original size:12 final size:12
Alignment explanation
Indices: 60133585--60133614 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
60133575 TATCCTTAGC
60133585 GGCGTTTTTTGT
1 GGCGTTTTTTGT
60133597 GGCGTTTTTTGT
1 GGCGTTTTTTGT
60133609 GGCGTT
1 GGCGTT
60133615 GCAAATGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.10, G:0.37, T:0.53
Consensus pattern (12 bp):
GGCGTTTTTTGT
Found at i:60135217 original size:23 final size:24
Alignment explanation
Indices: 60135177--60135224 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
60135167 ATAATAATAA
60135177 ATTTTTTTAATAAAATATAATTTTAT
1 ATTTTTTTAAT--AATATAATTTTAT
*
60135203 ATTTTTTTAAT-ATATATTTTTA
1 ATTTTTTTAATAATATAATTTTA
60135225 AAAAATACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
26 11 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTTTTTAATAATATAATTTTAT
Found at i:60135462 original size:20 final size:18
Alignment explanation
Indices: 60135437--60135488 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
60135427 TAGAGAAAAA
60135437 AAAAGAGAGAAAGGAGAAGG
1 AAAAGA-AGAAAGGAGAA-G
*
60135457 AAAAGAAGAAGAAGAGAAG
1 AAAAGAAGAA-AGGAGAAG
60135476 AAGAAGAAGAAAG
1 AA-AAGAAGAAAG
60135489 AAAAAAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (18 bp):
AAAAGAAGAAAGGAGAAG
Found at i:60135478 original size:14 final size:13
Alignment explanation
Indices: 60135439--60135490 Score: 61
Period size: 14 Copynumber: 3.9 Consensus size: 13
60135429 GAGAAAAAAA
*
60135439 AAGAGAGAAAGGAG
1 AAGA-AGAAAGAAG
*
60135453 AAGGA-AAAGAAG
1 AAGAAGAAAGAAG
60135465 AAGAAGAGAAGAAG
1 AAGAAGA-AAGAAG
60135479 AAGAAGAAAGAA
1 AAGAAGAAAGAA
60135491 AAAAAAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 10 0.30
13 7 0.21
14 16 0.48
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAGAAG
Found at i:60135697 original size:19 final size:19
Alignment explanation
Indices: 60135641--60135832 Score: 95
Period size: 19 Copynumber: 9.4 Consensus size: 19
60135631 TATAGCTTAG
* *
60135641 ATTAGAATTTTGTATGAAT
1 ATTATAATTTTTTATGAAT
*
60135660 ATTTTAACTTTTTTGTATGAAT
1 ATTATAA--TTTTT-TATGAAT
60135682 ATTATAATTTTTTATGAAT
1 ATTATAATTTTTTATGAAT
* * *
60135701 ATTGTAATGTTGTATGAAT
1 ATTATAATTTTTTATGAAT
* *
60135720 ACTGTAATTATTTTAT--A-
1 ATTATAATT-TTTTATGAAT
**
60135737 ATTA-AATTTGTATTTATAGTTTT
1 ATTATAA-TT-T-TTTAT-G-AAT
60135760 GGATTAGTAATTTTTTGTATGAAT
1 --ATTA-TAA-TTTTT-TATGAAT
*
60135784 ATTATAATTTTGTATGAAT
1 ATTATAATTTTTTATGAAT
60135803 ATTATAAATTTTTTGTATGAAT
1 ATTAT-AA-TTTTT-TATGAAT
*
60135825 ATTGTAAT
1 ATTATAAT
60135833 ATTATAGTTT
Statistics
Matches: 135, Mismatches: 19, Indels: 37
0.71 0.10 0.19
Matches are distributed among these distances:
16 2 0.01
17 5 0.04
18 6 0.04
19 47 0.35
20 17 0.13
21 13 0.10
22 28 0.21
24 1 0.01
25 7 0.05
26 4 0.03
27 5 0.04
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (19 bp):
ATTATAATTTTTTATGAAT
Found at i:60135825 original size:41 final size:41
Alignment explanation
Indices: 60135768--60135887 Score: 132
Period size: 49 Copynumber: 2.7 Consensus size: 41
60135758 TTGGATTAGT
*
60135768 AATTTTTTGTATGAATATTATAATTTTGTATGAATATTATA
1 AATTTTTTGTATGAATATTATAATTTTGTATGAATATTACA
*
60135809 AATTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTGCA
1 AATTTTTTGTATGAATA---T--TA-TA-A-TTTTGTATGAATATTACA
* *
60135858 ATTTTTTTGTATGAATATTGTAATTTTGTA
1 AATTTTTTGTATGAATATTATAATTTTGTA
60135888 ATTTTGTATG
Statistics
Matches: 67, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
41 24 0.36
42 1 0.01
43 2 0.03
44 2 0.03
46 3 0.04
47 2 0.03
48 1 0.01
49 32 0.48
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (41 bp):
AATTTTTTGTATGAATATTATAATTTTGTATGAATATTACA
Found at i:60135834 original size:49 final size:49
Alignment explanation
Indices: 60135781--60136002 Score: 329
Period size: 49 Copynumber: 4.5 Consensus size: 49
60135771 TTTTTGTATG
* *
60135781 AATATTATAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
1 AATATTATAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTGT
* *
60135830 AATATTATAGTTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AATATTATAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTGT
* * *
60135879 AATTTTGTAATTTTGTATGAATATTA-TATTTTTTTGTATGAATATTGT
1 AATATTATAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTGT
* *
60135927 AATATTATAATTTTGCATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AATATTATAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTGT
*
60135976 AATATTGTAATTTTTTGTATGAATATT
1 AATATTATAA--TTTTGTATGAATATT
60136003 GTAATTATTT
Statistics
Matches: 154, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
48 43 0.28
49 97 0.63
51 14 0.09
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.54
Consensus pattern (49 bp):
AATATTATAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTGT
Found at i:60135848 original size:27 final size:25
Alignment explanation
Indices: 60135781--60136012 Score: 211
Period size: 22 Copynumber: 9.3 Consensus size: 25
60135771 TTTTTGTATG
*
60135781 AATATTATAATTTTGTATGAATATTAT
1 AATATT-T-ATTTTGTATGAATATTGT
60135808 AA-A-TT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
60135830 AATATTATAGTTTTGTATGAATATTG-
1 AATATT-TA-TTTTGTATGAATATTGT
*
60135856 CA-ATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
*
60135879 AATTTTGTAATTTTGTATGAATA-T-T
1 AATATT-T-ATTTTGTATGAATATTGT
60135904 -ATATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
*
60135927 AATATTATAATTTTGCATGAATATTG-
1 AATATT-T-ATTTTGTATGAATATTGT
*
60135953 CA-ATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
60135976 AATATTGTAATTTTTTGTATGAATATTGT
1 AATATT-T-A--TTTTGTATGAATATTGT
60136005 AATTATTT
1 AA-TATTT
60136013 TATAATTAAT
Statistics
Matches: 172, Mismatches: 9, Indels: 46
0.76 0.04 0.20
Matches are distributed among these distances:
21 13 0.08
22 50 0.29
23 5 0.03
24 18 0.10
25 12 0.07
26 4 0.02
27 46 0.27
29 20 0.12
30 4 0.02
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.54
Consensus pattern (25 bp):
AATATTTATTTTGTATGAATATTGT
Found at i:60135930 original size:29 final size:29
Alignment explanation
Indices: 60135898--60136007 Score: 112
Period size: 29 Copynumber: 4.1 Consensus size: 29
60135888 ATTTTGTATG
60135898 AATATTATATTTTTTTGTATGAATATTGT
1 AATATTATATTTTTTTGTATGAATATTGT
* *
60135927 AATATTATA--ATTTTGCATGAATATTG-
1 AATATTATATTTTTTTGTATGAATATTGT
*
60135953 -----CA-ATTTTTTTGTATGAATATTGT
1 AATATTATATTTTTTTGTATGAATATTGT
* *
60135976 AATATTGTAATTTTTTGTATGAATATTGT
1 AATATTATATTTTTTTGTATGAATATTGT
60136005 AAT
1 AAT
60136008 TATTTTATAA
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 15 0.23
27 15 0.23
29 32 0.50
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.54
Consensus pattern (29 bp):
AATATTATATTTTTTTGTATGAATATTGT
Found at i:60135939 original size:78 final size:77
Alignment explanation
Indices: 60135781--60136007 Score: 235
Period size: 78 Copynumber: 3.0 Consensus size: 77
60135771 TTTTTGTATG
* ** * *
60135781 AATATTATAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTAT-A-GTTTT
1 AATATTATAATTTTGCATGAATATTGCAATTTTTTTGTATG-ATATTGTAATATTATAATTTTTT
60135844 GTATGAATATTG-
65 GTATGAATATTGT
* * * *
60135856 CA-ATT-T--TTTTGTATGAATATTGTAATTTTGTAATT-T-TG-TA-TG-AATATTATATTTTT
1 AATATTATAATTTTGCATGAATATTGCAATTTT-T--TTGTATGATATTGTAATATTATAATTTT
60135912 TTGTATGAATATTGT
63 TTGTATGAATATTGT
*
60135927 AATATTATAATTTTGCATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTGTAATTTTTT
1 AATATTATAATTTTGCATGAATATTGCAATTTTTTTGTATG-ATATTGTAATATTATAATTTTTT
60135992 GTATGAATATTGT
65 GTATGAATATTGT
60136005 AAT
1 AAT
60136008 TATTTTATAA
Statistics
Matches: 126, Mismatches: 10, Indels: 29
0.76 0.06 0.18
Matches are distributed among these distances:
68 8 0.06
69 2 0.02
70 18 0.14
71 22 0.17
72 8 0.06
73 4 0.03
74 8 0.06
75 22 0.17
76 2 0.02
77 2 0.02
78 30 0.24
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (77 bp):
AATATTATAATTTTGCATGAATATTGCAATTTTTTTGTATGATATTGTAATATTATAATTTTTTG
TATGAATATTGT
Found at i:60135941 original size:97 final size:98
Alignment explanation
Indices: 60135781--60136002 Score: 374
Period size: 97 Copynumber: 2.3 Consensus size: 98
60135771 TTTTTGTATG
* * *
60135781 AATATTATAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAGTTTTGT
1 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGC
60135846 ATGAATATTGCAATTTTTTTGTATGAATATTGT
66 ATGAATATTGCAATTTTTTTGTATGAATATTGT
* *
60135879 AATTTTGTAATTTTGTATGAATATTAT-ATTTTTTTGTATGAATATTGTAATATTATAATTTTGC
1 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGC
60135943 ATGAATATTGCAATTTTTTTGTATGAATATTGT
66 ATGAATATTGCAATTTTTTTGTATGAATATTGT
60135976 AATATTGTAATTTTTTGTATGAATATT
1 AATATTGTAA--TTTTGTATGAATATT
60136003 GTAATTATTT
Statistics
Matches: 116, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
97 76 0.66
98 25 0.22
99 15 0.13
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.54
Consensus pattern (98 bp):
AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGC
ATGAATATTGCAATTTTTTTGTATGAATATTGT
Found at i:60136067 original size:60 final size:60
Alignment explanation
Indices: 60136001--60136122 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 60
60135991 TGTATGAATA
* * * * * *
60136001 TTGTAATTATTTTATAA-TTAATTTGTTAGCAATTTGGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTA-TTTAAAATTTAATTTATTAGCAATTTAGGATTAAGCTATAAATTGTTGTGT
* *
60136061 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTAAAATTTAATTTATTAGCAATTTAGGATTAAGCTATAAATTGTTGTGT
60136121 TT
1 TT
60136123 AGTTTAGTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 6 0.11
60 47 0.89
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.53
Consensus pattern (60 bp):
TTGTAATTATTTAAAATTTAATTTATTAGCAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:60136201 original size:38 final size:38
Alignment explanation
Indices: 60136156--60136237 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
60136146 CATATAAAGT
60136156 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
*
60136194 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
60136232 TTATAA
1 TTATAA
60136238 CTGACTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
Found at i:60136315 original size:15 final size:15
Alignment explanation
Indices: 60136274--60136315 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
60136264 GTTAAATCAT
*
60136274 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
60136289 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
60136305 TTAAATTTTAT
1 TTAAATTTTAT
60136316 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:60141233 original size:22 final size:21
Alignment explanation
Indices: 60141198--60141242 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
60141188 TACCTAATTT
*
60141198 TTTTCTTCTTTTCCTTCCTTC
1 TTTTCTTCTCTTCCTTCCTTC
60141219 TTTTCTTCTGCTTCCTTCCTTC
1 TTTTCTTCT-CTTCCTTCCTTC
60141241 TT
1 TT
60141243 ATTTCTTTCG
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:0.00, C:0.33, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTCTTCTCTTCCTTCCTTC
Found at i:60141346 original size:27 final size:27
Alignment explanation
Indices: 60141308--60141383 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 27
60141298 AAAATAACAG
60141308 CATTGGCGCCT-CTCAGA-ATGGCACCAC
1 CATTGGCGCCTCCT-AGATA-GGCACCAC
*
60141335 CATTGGCGCCTCCTAGGTAGGCACCAC
1 CATTGGCGCCTCCTAGATAGGCACCAC
* *
60141362 CATTGGCGCTTCCCAGATAGGC
1 CATTGGCGCCTCCTAGATAGGC
60141384 GCCAATACTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 40 0.93
28 3 0.07
ACGTcount: A:0.20, C:0.36, G:0.25, T:0.20
Consensus pattern (27 bp):
CATTGGCGCCTCCTAGATAGGCACCAC
Found at i:60142355 original size:90 final size:90
Alignment explanation
Indices: 60142200--60142376 Score: 248
Period size: 90 Copynumber: 2.0 Consensus size: 90
60142190 TCTTAGTTGT
* * * * *
60142200 TTATAATTGAGGAGACTTGTATAGTTGATGCATTGATTCATGAGCACTTATTTTGTTCATTGAGG
1 TTATAATTGAGGACACTTGTATAGTTGATGCACTGATTCATGAACACTTATTTTATTCATCGAGG
*
60142265 AGCATTTCTTTGGAGTGCATTGTGC
66 AACATTTCTTTGGAGTGCATTGTGC
*
60142290 TTATAATTGAGGACACTTGTATAGTTGATGCACTGA-TCTTCGAACACTTATTTTATTCATCGAG
1 TTATAATTGAGGACACTTGTATAGTTGATGCACTGATTCAT-GAACACTTATTTTATTCATCGAG
* * *
60142354 GAACATTTTTTTGTATTGCATTG
65 GAACATTTCTTTGGAGTGCATTG
60142377 AATGTAAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
89 3 0.04
90 73 0.96
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (90 bp):
TTATAATTGAGGACACTTGTATAGTTGATGCACTGATTCATGAACACTTATTTTATTCATCGAGG
AACATTTCTTTGGAGTGCATTGTGC
Found at i:60151016 original size:25 final size:25
Alignment explanation
Indices: 60150988--60151035 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
60150978 TCAATAAGTA
60150988 GGGGAATCAACACTTAGCAACCCTC
1 GGGGAATCAACACTTAGCAACCCTC
*
60151013 GGGGAATCAGCACTTAGCAACCC
1 GGGGAATCAACACTTAGCAACCC
60151036 CTTCACATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.31, G:0.23, T:0.15
Consensus pattern (25 bp):
GGGGAATCAACACTTAGCAACCCTC
Found at i:60151036 original size:99 final size:99
Alignment explanation
Indices: 60150855--60151209 Score: 436
Period size: 98 Copynumber: 3.6 Consensus size: 99
60150845 TAACCGTTAT
* * ** *
60150855 CGGTGGATTCCGCA-TTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
1 CGGTGGA-TCAGCACTTAGCAACCACCAAT-AATAGGGGAATCAGCACTTAGCAACCCCTCGGGG
*
60150919 AATCAACACTTAGC-ACCCCCTT-ACATTTAGAAATA
64 AATCAGCACTTAGCAACCCCCTTCACATTTA-AAATA
* * *
60150954 CGGTGGATCAGCAGTTAGCAACCATCAATAAGTAGGGGAATCAACACTTAGCAA-CCCTCGGGGA
1 CGGTGGATCAGCACTTAGCAACCACCAATAA-TAGGGGAATCAGCACTTAGCAACCCCTCGGGGA
60151018 ATCAGCACTTAGCAA-CCCCTTCACATTTAAAATA
65 ATCAGCACTTAGCAACCCCCTTCACATTTAAAATA
*
60151052 -GGTGGAATCAGCACTTAGCAACCACCATTAATA-GGGAATCAGCACTTAGCAACCCCTCGGGGA
1 CGGTGG-ATCAGCACTTAGCAACCACCAATAATAGGGGAATCAGCACTTAGCAACCCCTCGGGGA
60151115 ATCAGCACTTAGCAACCCCCTTTCACATTTAAAAATA
65 ATCAGCACTTAGCAACCCCC-TTCACATTT-AAAATA
* * ** **
60151152 CGATGGGATCAGCACTTAGCAACCACCGATGAACCGGGGAATCAGCACACAGCAACCC
1 CGGT-GGATCAGCACTTAGCAACCACCAAT-AATAGGGGAATCAGCACTTAGCAACCC
60151210 TTTATATGCA
Statistics
Matches: 224, Mismatches: 19, Indels: 22
0.85 0.07 0.08
Matches are distributed among these distances:
96 18 0.08
97 32 0.14
98 65 0.29
99 56 0.25
100 6 0.03
101 23 0.10
102 4 0.02
103 20 0.09
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (99 bp):
CGGTGGATCAGCACTTAGCAACCACCAATAATAGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
TCAGCACTTAGCAACCCCCTTCACATTTAAAATA
Found at i:60169429 original size:45 final size:45
Alignment explanation
Indices: 60169356--60169449 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
60169346 AAGAGTCCTA
* *
60169356 GTAAACGAGGATTGCATTGGTGTGATTGGGAATCTCTATGTGGAT
1 GTAAACGAGGATTGCATTGATGTAATTGGGAATCTCTATGTGGAT
60169401 GTAAACGAGGATTGCATTGATGTAATTGGGAATCTCTATGTGGAT
1 GTAAACGAGGATTGCATTGATGTAATTGGGAATCTCTATGTGGAT
60169446 -TAAA
1 GTAAA
60169450 GGAAAATGGT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 4 0.09
45 43 0.91
ACGTcount: A:0.29, C:0.09, G:0.30, T:0.33
Consensus pattern (45 bp):
GTAAACGAGGATTGCATTGATGTAATTGGGAATCTCTATGTGGAT
Found at i:60172879 original size:42 final size:42
Alignment explanation
Indices: 60172794--60172885 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
60172784 GTTTTTTAAA
* * ** * * **
60172794 AGTTACACGGCCTATCACATGGGCGTGTGAGGCCATTTCGAG
1 AGTTACACGGCCTAGCACACGGGCGTGTGACACAAGTGAGAG
60172836 AGTTACACGGCCTAGCACACGGGCGTGTGACACAAGTGAGAG
1 AGTTACACGGCCTAGCACACGGGCGTGTGACACAAGTGAGAG
60172878 AGTTACAC
1 AGTTACAC
60172886 AGGCATGGAC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (42 bp):
AGTTACACGGCCTAGCACACGGGCGTGTGACACAAGTGAGAG
Found at i:60176246 original size:41 final size:41
Alignment explanation
Indices: 60176196--60176287 Score: 132
Period size: 41 Copynumber: 2.2 Consensus size: 41
60176186 GGCTTAGCAC
*
60176196 CTAGCAGGCTTATTGCC-AGTGAAACAATTCAGACTATATGT
1 CTAGCAGGCTTAATGCCGA-TGAAACAATTCAGACTATATGT
* * *
60176237 CTAGTAGGCTTAATGTCGATGAAACATTTCAGACTATATGT
1 CTAGCAGGCTTAATGCCGATGAAACAATTCAGACTATATGT
60176278 CTAGCAGGCT
1 CTAGCAGGCT
60176288 AAGTGCCTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
41 44 0.98
42 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGATGAAACAATTCAGACTATATGT
Found at i:60180721 original size:131 final size:131
Alignment explanation
Indices: 60180465--60180899 Score: 658
Period size: 131 Copynumber: 3.3 Consensus size: 131
60180455 ATTGACTATA
* ** * * *
60180465 TTCGATCCGCTCTGCTACTGCTTAGGGAGATAGGATCTGCAATTTCCAACCTATTCCACTGCT-G
1 TTCGATCTGCTCCACTATTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
* * * * **
60180529 TTAGAGATATAGGACTTGTGGCCTAAATCTATTTCCCTACTC-CCGAGGAAGATAAGATTCGCCG
66 TCAGGGACATAGGACTTGTGGCTTAAATCTATTTCCCTACTCTTAG-GGAAGATAAGATTCGCCG
60180593 TC
130 TC
* * *
60180595 TTCGATCTGCTCCATTATTGCTTAGGGAGACAAGATCTACAATTTCTAACCTATTCCACTGCTGG
1 TTCGATCTGCTCCACTATTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
*
60180660 TCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCTTAGGGAAGATAAGATTCGCCGT
66 TCAGGGACATAGGACTTGTGGCTTAAATCTATTTCCCTACTCTTAGGGAAGATAAGATTCGCCGT
60180725 C
131 C
*
60180726 TTCGATCTGCTCCACTATTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGA
1 TTCGATCTGCTCCACTATTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
* *
60180791 TCAGGGACATAGGACTTGTGGCTTAAATCTTTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGT
66 TCAGGGACATAGGACTTGTGGCTTAAATCTATTTCCCTACTCTTAGGGAAGATAAGATTCGCCGT
60180856 C
131 C
* *
60180857 TTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAAT
1 TTCGATCTGCTCCACTATTGCTTAGGGAGACAAGATCTGCAAT
60180900 CTTTACTGAT
Statistics
Matches: 279, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
130 54 0.19
131 224 0.80
132 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (131 bp):
TTCGATCTGCTCCACTATTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
TCAGGGACATAGGACTTGTGGCTTAAATCTATTTCCCTACTCTTAGGGAAGATAAGATTCGCCGT
C
Found at i:60194167 original size:14 final size:14
Alignment explanation
Indices: 60194148--60194180 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
60194138 TGGTGCTTTT
60194148 TGATTTTTGTATTC
1 TGATTTTTGTATTC
60194162 TGATTTTTGTATTC
1 TGATTTTTGTATTC
60194176 TGATT
1 TGATT
60194181 GCGTATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.64
Consensus pattern (14 bp):
TGATTTTTGTATTC
Found at i:60196396 original size:17 final size:17
Alignment explanation
Indices: 60196364--60196398 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
60196354 AAGATATGAT
60196364 TCAACAACTTAATTAAC
1 TCAACAACTTAATTAAC
60196381 TCAA-AACTTAACTTAAC
1 TCAACAACTTAA-TTAAC
60196398 T
1 T
60196399 AACTCAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (17 bp):
TCAACAACTTAATTAAC
Found at i:60197229 original size:3 final size:3
Alignment explanation
Indices: 60197215--60197267 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
60197205 AAAGCTTCTT
*
60197215 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
60197263 TTA TT
1 TTA TT
60197268 TTGCATTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:60197659 original size:4 final size:4
Alignment explanation
Indices: 60197650--60197691 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
60197640 ACAAAACGGC
* * *
60197650 TACA TACA TACA TACA TGCA TGCA TACA TACA TACA AACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
60197692 TATATATGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.48, C:0.24, G:0.05, T:0.24
Consensus pattern (4 bp):
TACA
Found at i:60201022 original size:4 final size:4
Alignment explanation
Indices: 60201015--60201062 Score: 87
Period size: 4 Copynumber: 12.0 Consensus size: 4
60201005 ATATGCATGC
*
60201015 CTAT CTAT TTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
60201063 ATAGTAATCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.52
Consensus pattern (4 bp):
CTAT
Found at i:60203466 original size:13 final size:13
Alignment explanation
Indices: 60203448--60203472 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60203438 TGATTATGAA
60203448 ACTAACAATAAAT
1 ACTAACAATAAAT
60203461 ACTAACAATAAA
1 ACTAACAATAAA
60203473 CATTTGGTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (13 bp):
ACTAACAATAAAT
Found at i:60206580 original size:22 final size:21
Alignment explanation
Indices: 60206532--60206584 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
60206522 TTTTTTGTCA
* * *
60206532 AAAAAATATTTTTTTAAATGT
1 AAAAAATATTATTTCAAATCT
60206553 ATAAAAATATATATTTCAAATCT
1 A-AAAAATAT-TATTTCAAATCT
60206576 -AAAAATATT
1 AAAAAATATT
60206585 TTAAAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 1 0.04
21 9 0.33
22 8 0.30
23 9 0.33
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (21 bp):
AAAAAATATTATTTCAAATCT
Found at i:60211448 original size:9 final size:9
Alignment explanation
Indices: 60211436--60211460 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
60211426 ACTTAATGGA
60211436 TTTATTTTT
1 TTTATTTTT
60211445 TTTATTTTT
1 TTTATTTTT
60211454 TTTATTT
1 TTTATTT
60211461 GGTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTATTTTT
Found at i:60213008 original size:28 final size:28
Alignment explanation
Indices: 60212968--60213093 Score: 173
Period size: 28 Copynumber: 4.5 Consensus size: 28
60212958 TGACTTTCGA
*
60212968 CACTAAGTGTGCGAATTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
60212996 CACTAAGTGTGCGAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* *
60213024 CACTAAGTGTGCGAGTTTAATGGCAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * * *
60213052 CACTAGGTGTGCGAGTTTGATTATTGAA-
1 CACTAAGTGTGCGAGTTTAATT-GTAAAG
60213080 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
60213094 ACTTATTAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
28 85 0.98
29 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:60213859 original size:23 final size:23
Alignment explanation
Indices: 60213794--60214092 Score: 209
Period size: 23 Copynumber: 12.9 Consensus size: 23
60213784 TAAAATTGGA
* *
60213794 ATATATATGCTGCCCAATTTTGGT
1 ATATACATGCTGTCCAATTTT-GT
*
60213818 GA-ATAAATGCTGTCCAATTTTGT
1 -ATATACATGCTGTCCAATTTTGT
* *
60213841 ATATACATGCCGTCAAATTTTGT
1 ATATACATGCTGTCCAATTTTGT
* *
60213864 GTATA-AGTGCTGTCCAA-ATTGCT
1 ATATACA-TGCTGTCCAATTTTG-T
* * **
60213887 ACATATATGCTACCCAATTTTGGT
1 ATATACATGCTGTCCAATTTT-GT
* *
60213911 GA-ATAAATTCTGTCCAATTTTGT
1 -ATATACATGCTGTCCAATTTTGT
60213934 ATATACATGCTGTCCAATTTTGT
1 ATATACATGCTGTCCAATTTTGT
* * *
60213957 GTATA-AGTGCTGTCCAAATTGGT
1 ATATACA-TGCTGTCCAATTTTGT
* *
60213980 ATATATATGCTGCCCAATTTTGGT
1 ATATACATGCTGTCCAATTTT-GT
* *
60214004 GA-ATAAATGTTGTCCAATTTTGT
1 -ATATACATGCTGTCCAATTTTGT
*
60214027 ATATACATGCTGTCAAATTTTGT
1 ATATACATGCTGTCCAATTTTGT
* * * *
60214050 GTATGA-GTGCTGTCCAAATTGGT
1 ATAT-ACATGCTGTCCAATTTTGT
*
60214073 ATATACGTGCTG-CTCAATTT
1 ATATACATGCTGTC-CAATTT
60214093 CTGATGTATA
Statistics
Matches: 218, Mismatches: 40, Indels: 34
0.75 0.14 0.12
Matches are distributed among these distances:
22 10 0.05
23 148 0.68
24 56 0.26
25 4 0.02
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.40
Consensus pattern (23 bp):
ATATACATGCTGTCCAATTTTGT
Found at i:60213903 original size:93 final size:93
Alignment explanation
Indices: 60213796--60214114 Score: 478
Period size: 93 Copynumber: 3.4 Consensus size: 93
60213786 AAATTGGAAT
*
60213796 ATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCCGTCAAATTT
1 ATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTT
60213861 TGTGTATAAGTGCTGTCCAAATTGCTAC
66 TGTGTATAAGTGCTGTCCAAATTGCTAC
* * *
60213889 ATATATGCTACCCAATTTTGGTGAATAAATTCTGTCCAATTTTGTATATACATGCTGTCCAATTT
1 ATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTT
* *
60213954 TGTGTATAAGTGCTGTCCAAATTGGTAT
66 TGTGTATAAGTGCTGTCCAAATTGCTAC
*
60213982 ATATATGCTGCCCAATTTTGGTGAATAAATGTTGTCCAATTTTGTATATACATGCTGTCAAATTT
1 ATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTT
* * *
60214047 TGTGTATGAGTGCTGTCCAAATTGGTAT
66 TGTGTATAAGTGCTGTCCAAATTGCTAC
** * * *
60214075 ATACGTGCTGCTCAATTTCTGATGTATAAGA-GCTGTCCAA
1 ATATATGCTGCCCAATTT-TGGTGAATAA-ATGCTGTCCAA
60214115 ACAGGGTAGA
Statistics
Matches: 207, Mismatches: 17, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
93 190 0.92
94 16 0.08
95 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.39
Consensus pattern (93 bp):
ATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTT
TGTGTATAAGTGCTGTCCAAATTGCTAC
Found at i:60221491 original size:9 final size:9
Alignment explanation
Indices: 60221477--60221552 Score: 68
Period size: 9 Copynumber: 8.7 Consensus size: 9
60221467 AATTAAACCA
60221477 TTATGTAAG
1 TTATGTAAG
*
60221486 TTATGTAAT
1 TTATGTAAG
*
60221495 TTATGTAAT
1 TTATGTAAG
*
60221504 TTATGATATG
1 TTATG-TAAG
* * *
60221514 ATATAT-AT
1 TTATGTAAG
60221522 TTATGT-A-
1 TTATGTAAG
60221529 TTATGTAAG
1 TTATGTAAG
60221538 TTATGTAAG
1 TTATGTAAG
60221547 TTATGT
1 TTATGT
60221553 TCTAAAGTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
7 6 0.11
8 6 0.11
9 38 0.69
10 5 0.09
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (9 bp):
TTATGTAAG
Found at i:60223921 original size:22 final size:22
Alignment explanation
Indices: 60223878--60223921 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
60223868 ATATTTTGAT
*
60223878 TAAATTAATCAAAATTTACAAA
1 TAAATTAATCAAAAATTACAAA
*
60223900 TAAA-TAATCCAAAAATTGCAAA
1 TAAATTAAT-CAAAAATTACAAA
60223922 CAACAGCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.27
Consensus pattern (22 bp):
TAAATTAATCAAAAATTACAAA
Found at i:60225559 original size:41 final size:41
Alignment explanation
Indices: 60225492--60225765 Score: 406
Period size: 41 Copynumber: 6.7 Consensus size: 41
60225482 CCATTCGGGG
* * *
60225492 CTTTAGTGGCGTTTTTTAGAAAAGCGCCGCTAATGCTCAGGGT
1 CTTTAGCGGCG-TTTTTGGAAAAGCGCCGCTAATGCTC-TGGT
*
60225535 -TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTTTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
* ** *
60225575 CTTTAGTGGCGTTTTTGGGGAAGCGCCGTTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
60225616 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
* *
60225657 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCTAGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
*
60225698 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
* *
60225739 CTTTAGCGGCGTTTTCGGGAAAGCGCC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCC
60225766 ACAAAAACAT
Statistics
Matches: 209, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
40 3 0.01
41 197 0.94
42 9 0.04
ACGTcount: A:0.16, C:0.20, G:0.31, T:0.32
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
Found at i:60226161 original size:22 final size:23
Alignment explanation
Indices: 60226115--60226171 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 23
60226105 GATTTAGAGC
*
60226115 TTAAGGTTTA-GGAGTTACTATT
1 TTAAGGTTTATGGAGTTACTAGT
60226137 TTAAGGTTTATGGA-TTA-TGAGT
1 TTAAGGTTTATGGAGTTACT-AGT
* *
60226159 TTAGGGGTTATGG
1 TTAAGGTTTATGG
60226172 TTTACACTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 1 0.03
22 26 0.87
23 3 0.10
ACGTcount: A:0.25, C:0.02, G:0.30, T:0.44
Consensus pattern (23 bp):
TTAAGGTTTATGGAGTTACTAGT
Found at i:60226203 original size:21 final size:21
Alignment explanation
Indices: 60226187--60226272 Score: 81
Period size: 21 Copynumber: 4.1 Consensus size: 21
60226177 ACTTTATGGT
60226187 TTAAGATTTAGGGTTTAAGGG
1 TTAAGATTTAGGGTTTAAGGG
* *
60226208 TTACGATTTATGGTTTAAGGG
1 TTAAGATTTAGGGTTTAAGGG
*
60226229 -TATAGATTAAGGGTTT--GGG
1 TTA-AGATTTAGGGTTTAAGGG
*
60226248 TTTAA-AGTTTAGGGGTTAAGGG
1 -TTAAGA-TTTAGGGTTTAAGGG
60226270 TTA
1 TTA
60226273 GGGGTTGAGG
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
19 4 0.08
20 11 0.21
21 34 0.65
22 3 0.06
ACGTcount: A:0.27, C:0.01, G:0.33, T:0.40
Consensus pattern (21 bp):
TTAAGATTTAGGGTTTAAGGG
Found at i:60226283 original size:14 final size:14
Alignment explanation
Indices: 60226235--60226286 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
60226225 AGGGTATAGA
* *
60226235 TTAAGGGTTTGGGT
1 TTAAGGGTTAGGGG
* *
60226249 TTAAAGTTTAGGGG
1 TTAAGGGTTAGGGG
60226263 TTAAGGGTTAGGGG
1 TTAAGGGTTAGGGG
*
60226277 TTGAGGGTTA
1 TTAAGGGTTA
60226287 AGAGTTAGGG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:60226284 original size:21 final size:21
Alignment explanation
Indices: 60226260--60226299 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
60226250 TAAAGTTTAG
*
60226260 GGGTTAAGGGTTAGGGGTTGA
1 GGGTTAAGAGTTAGGGGTTGA
60226281 GGGTTAAGAGTTAGGGGTT
1 GGGTTAAGAGTTAGGGGTT
60226300 TAAAATTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.50, T:0.30
Consensus pattern (21 bp):
GGGTTAAGAGTTAGGGGTTGA
Found at i:60226650 original size:21 final size:22
Alignment explanation
Indices: 60226626--60226666 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
60226616 ACGGTTTATT
60226626 GTTTAAGGGTT-GGGATTTAAA
1 GTTTAAGGGTTAGGGATTTAAA
* *
60226647 GTTTAGGGGTTAGGGGTTTA
1 GTTTAAGGGTTAGGGATTTA
60226667 GGATTTCAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.22, C:0.00, G:0.39, T:0.39
Consensus pattern (22 bp):
GTTTAAGGGTTAGGGATTTAAA
Found at i:60231765 original size:43 final size:42
Alignment explanation
Indices: 60231672--60231934 Score: 140
Period size: 43 Copynumber: 6.2 Consensus size: 42
60231662 ATGTTTTTAG
*
60231672 GGCGTTT-TTGTAAGAAGCG-TCGCTAAAGGTTTGTTCTATAGC
1 GGCGTTTGTGGTAA-AAGCGCT-GCTAAAGGTTTGTTCTATAGC
60231714 GGCGTTTGTGGTAAAAGCGCTGCTAAAGGTTT-TTAGCTATAGC
1 GGCGTTTGTGGTAAAAGCGCTGCTAAAGGTTTGTT--CTATAGC
* * * ** * * *
60231757 GGCGTTTGTGGGAAAAGTGCCGCTAAAGGCCATGGTCTTTAAC
1 GGCGTTTGTGGTAAAAGCGCTGCTAAAGG-TTTGTTCTATAGC
* * * * * * *
60231800 GGTGTTTGTTGG-AGAAGTGCTGCTAAAGATTAGGATCTTTAGC
1 GGCGTTTG-TGGTAAAAGCGCTGCTAAAGGTT-TGTTCTATAGC
* * * * * ** *
60231843 GGCGTTTTTAG-AAAAGCGCCGCTGAAGGTCATGGCCTTTAGC
1 GGCGTTTGTGGTAAAAGCGCTGCTAAAGGT-TTGTTCTATAGC
* * * * * *
60231885 GGCGTTTTTGGGAAAAGCGTTGCTAAAGGTCATGGTCTTTAGC
1 GGCGTTTGTGGTAAAAGCGCTGCTAAAGGT-TTGTTCTATAGC
60231928 GGCGTTT
1 GGCGTTT
60231935 ATTTCTAAAA
Statistics
Matches: 176, Mismatches: 35, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
41 2 0.01
42 56 0.32
43 113 0.64
44 4 0.02
45 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.32, T:0.32
Consensus pattern (42 bp):
GGCGTTTGTGGTAAAAGCGCTGCTAAAGGTTTGTTCTATAGC
Found at i:60231909 original size:85 final size:86
Alignment explanation
Indices: 60231710--60231934 Score: 231
Period size: 85 Copynumber: 2.6 Consensus size: 86
60231700 GTTTGTTCTA
* * *** * * * *
60231710 TAGCGGCGTTTGTGGTAAAAGCGCTGCTAAAGGTTTTTAGCTATAGCGGCGTTTGTGGGAAAAGT
1 TAGCGGCGTTTTTGGGAAAAGCGCTGCTAAAGGTTAGGATCTTTAGCGGCGTTTGTGAGAAAAGC
*
60231775 GCCGCTAAAGGCCATGGTCTT
66 GCCGCTAAAGGCCATGGCCTT
* * * * * *
60231796 TAACGGTGTTTGTT-GGAGAAGTGCTGCTAAAGATTAGGATCTTTAGCGGCGTTT-TTAGAAAAG
1 TAGCGGCGTTT-TTGGGAAAAGCGCTGCTAAAGGTTAGGATCTTTAGCGGCGTTTGTGAGAAAAG
* *
60231859 CGCCGCTGAAGGTCATGGCCTT
65 CGCCGCTAAAGGCCATGGCCTT
* *
60231881 TAGCGGCGTTTTTGGGAAAAGCGTTGCTAAAGGTCATGG-TCTTTAGCGGCGTTT
1 TAGCGGCGTTTTTGGGAAAAGCGCTGCTAAAGGTTA-GGATCTTTAGCGGCGTTT
60231935 ATTTCTAAAA
Statistics
Matches: 111, Mismatches: 25, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
84 2 0.02
85 66 0.59
86 42 0.38
87 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.31
Consensus pattern (86 bp):
TAGCGGCGTTTTTGGGAAAAGCGCTGCTAAAGGTTAGGATCTTTAGCGGCGTTTGTGAGAAAAGC
GCCGCTAAAGGCCATGGCCTT
Found at i:60232916 original size:25 final size:25
Alignment explanation
Indices: 60232882--60232929 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
60232872 AGAGAGGATT
60232882 TTGTTAAATGAAATAATAAAAATAA
1 TTGTTAAATGAAATAATAAAAATAA
60232907 TTGTTAAATGAAATAATAAAAAT
1 TTGTTAAATGAAATAATAAAAAT
60232930 TGAGCTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (25 bp):
TTGTTAAATGAAATAATAAAAATAA
Found at i:60233155 original size:27 final size:27
Alignment explanation
Indices: 60233124--60233197 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
60233114 GCAGAGGAGT
* *
60233124 GTCGACGGCGATGCAATAGAGGGGATA
1 GTCGACGGCGATGCAACAGAGGGGACA
*
60233151 GTCGACGGTGATGCAACAGAGGGGACA
1 GTCGACGGCGATGCAACAGAGGGGACA
* *
60233178 GTTGACGGCGATGCAGCAGA
1 GTCGACGGCGATGCAACAGA
60233198 TGGTCGGGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.28, C:0.18, G:0.41, T:0.14
Consensus pattern (27 bp):
GTCGACGGCGATGCAACAGAGGGGACA
Done.