Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 93 of 316
Found at i:28279124 original size:70 final size:68
Alignment explanation
Indices: 28279050--28279406 Score: 222
Period size: 70 Copynumber: 5.1 Consensus size: 68
28279040 AGGCTCCCAA
* * *
28279050 GTTCAATTCCACAGCCTCCAAAAAAATTAACAAATGCTCAAGCTGCCATCTATGATCTTAAGGCT
1 GTTCAATACCACAGCCTCCAAAAAAATTAACAAA-GCCCAAGCT-CCAACTATGATCTTAAGGCT
28279115 CATAG
64 CATAG
* * * * * * * * *
28279120 GTTCAATATCGCAGCATCTAAAACAATTAGCGAGAGCCCAAGCTCCCAACTGT-AGCTTTAAGGC
1 GTTCAATACCACAGCCTCCAAAAAAATTAAC-AAAGCCCAAGCT-CCAACTATGATC-TTAAGGC
28279184 TTGCAT--
63 -T-CATAG
* ** * * * * *
28279190 GTTTAATACTGCAGCCTCCAAAATAGTTAACAAGAGCCCAAGCTCTTAGCTACGATCTTAAGGCT
1 GTTCAATACCACAGCCTCCAAAAAAATTAACAA-AGCCCAAGCTC-CAACTATGATCTTAAGGCT
28279255 CATAG
64 CATAG
* * * * * *
28279260 GTTCAATACCACAGCCTCCAAAATAGTTAGTAC-GATCCCAAGCTCCCAACTAT-AGCTTGAAAG
1 GTTCAATACCACAGCCTCCAAAAAAATTA--ACAAAGCCCAAGCT-CCAACTATGATCTT-AAGG
*
28279323 CTCACAG
62 CTCATAG
* * * * * * *
28279330 GTTCAATACTACA-ACTCCAAAACAATTAGCGAGAGCCTAAGCTCCCAACTATAATCTTAAGGCT
1 GTTCAATACCACAGCCTCCAAAAAAATTAAC-AAAGCCCAAGCT-CCAACTATGATCTTAAGGCT
*
28279394 CACAG
64 CATAG
28279399 GTTCAATA
1 GTTCAATA
28279407 TCATAGCTTC
Statistics
Matches: 224, Mismatches: 47, Indels: 33
0.74 0.15 0.11
Matches are distributed among these distances:
67 1 0.00
68 3 0.01
69 57 0.25
70 152 0.68
71 6 0.03
72 5 0.02
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.24
Consensus pattern (68 bp):
GTTCAATACCACAGCCTCCAAAAAAATTAACAAAGCCCAAGCTCCAACTATGATCTTAAGGCTCA
TAG
Found at i:28279469 original size:139 final size:140
Alignment explanation
Indices: 28279018--28279474 Score: 427
Period size: 140 Copynumber: 3.3 Consensus size: 140
28279008 AGCGATAGCT
** * ** * * * * *
28279018 CAAGCTCCCAACTGTAGTTTTGAGGCTCCCAAGTTCAATTCCACAGCCTCCAAAAAAATTAACAA
1 CAAGCTCCCAACTGTAGCCTTAAGGCTTACAGGTTCAATACTACAGACTCCAAAACAATTAACAA
* * * * * *
28279083 -ATGCTCAAGCTGCCATCTATGATCTTAAGGCTCATAGGTTCAATATCGCAGCATCTAAAACAAT
66 GA-GCCCAAGCTCCCAACTATGATCTTAAGGCTCATAGGTTCAATATCACAGCATCTAAAATAGT
*
28279147 TAGCGAGAGCC
130 TAGTGAGAGCC
* * * * * * * *
28279158 CAAGCTCCCAACTGTAGCTTTAAGGCTTGCATGTTTAATACTGCAGCCTCCAAAATAGTTAACAA
1 CAAGCTCCCAACTGTAGCCTTAAGGCTTACAGGTTCAATACTACAGACTCCAAAACAATTAACAA
** * * * * *
28279223 GAGCCCAAGCTCTTAGCTACGATCTTAAGGCTCATAGGTTCAATACCACAGCCTCCAAAATAGTT
66 GAGCCCAAGCTCCCAACTATGATCTTAAGGCTCATAGGTTCAATATCACAGCATCTAAAATAGTT
*
28279288 AGT-ACGATCC
131 AGTGA-GAGCC
* * * * *
28279298 CAAGCTCCCAACTATAG-CTTGAAAGCTCACAGGTTCAATACTACA-ACTCCAAAACAATTAGCG
1 CAAGCTCCCAACTGTAGCCTT-AAGGCTTACAGGTTCAATACTACAGACTCCAAAACAATTAACA
* * * * *
28279361 AGAGCCTAAGCTCCCAACTATAATCTTAAGGCTCACAGGTTCAATATCATAGCTTCTAAAATAGT
65 AGAGCCCAAGCTCCCAACTATGATCTTAAGGCTCATAGGTTCAATATCACAGCATCTAAAATAGT
* *
28279426 TAGTGTGAGCT
130 TAGTGAGAGCC
* * *
28279437 GAAGCTCCCAACTGTTGCCTTAGGGCTTACAGGTTCAA
1 CAAGCTCCCAACTGTAGCCTTAAGGCTTACAGGTTCAA
28279475 CACCGCAACC
Statistics
Matches: 254, Mismatches: 58, Indels: 11
0.79 0.18 0.03
Matches are distributed among these distances:
139 105 0.41
140 148 0.58
141 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (140 bp):
CAAGCTCCCAACTGTAGCCTTAAGGCTTACAGGTTCAATACTACAGACTCCAAAACAATTAACAA
GAGCCCAAGCTCCCAACTATGATCTTAAGGCTCATAGGTTCAATATCACAGCATCTAAAATAGTT
AGTGAGAGCC
Found at i:28282572 original size:23 final size:23
Alignment explanation
Indices: 28282545--28282658 Score: 115
Period size: 23 Copynumber: 4.9 Consensus size: 23
28282535 TCAAATCCTA
28282545 AGAGCTTACTGTTTCAGCTCATT
1 AGAGCTTACTGTTTCAGCTCATT
* *
28282568 GGAGCTTACTGTTTCAGCTCGTT
1 AGAGCTTACTGTTTCAGCTCATT
*
28282591 TGAGCTTACTGTTT-AGCTCGA-T
1 AGAGCTTACTGTTTCAGCTC-ATT
** * *
28282613 AGAGCTTACCATTTCAGCTTAAT
1 AGAGCTTACTGTTTCAGCTCATT
*
28282636 AGAGCTTATTGTTCATCAGCTCA
1 AGAGCTTACTGTT--TCAGCTCA
28282659 GGAGGAGCTT
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
22 18 0.24
23 49 0.66
25 7 0.09
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (23 bp):
AGAGCTTACTGTTTCAGCTCATT
Found at i:28282641 original size:45 final size:46
Alignment explanation
Indices: 28282545--28282658 Score: 115
Period size: 45 Copynumber: 2.5 Consensus size: 46
28282535 TCAAATCCTA
* ** **
28282545 AGAGCTTACTGTTTCAGCTCATTGGAGCTTACTGTTTCAGCTCGTT
1 AGAGCTTACTGTTTCAGCTCATTAGAGCTTACCATTTCAGCTCAAT
* *
28282591 TGAGCTTACTGTTT-AGCTCGA-TAGAGCTTACCATTTCAGCTTAAT
1 AGAGCTTACTGTTTCAGCTC-ATTAGAGCTTACCATTTCAGCTCAAT
*
28282636 AGAGCTTATTGTTCATCAGCTCA
1 AGAGCTTACTGTT--TCAGCTCA
28282659 GGAGGAGCTT
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
45 34 0.62
46 14 0.25
47 2 0.04
48 5 0.09
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (46 bp):
AGAGCTTACTGTTTCAGCTCATTAGAGCTTACCATTTCAGCTCAAT
Found at i:28294859 original size:13 final size:13
Alignment explanation
Indices: 28294841--28294868 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28294831 ATAATCCTTA
28294841 ATTAATTCTAACC
1 ATTAATTCTAACC
28294854 ATTAATTCTAACC
1 ATTAATTCTAACC
28294867 AT
1 AT
28294869 CTCCTTTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (13 bp):
ATTAATTCTAACC
Found at i:28304552 original size:62 final size:62
Alignment explanation
Indices: 28304476--28304600 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
28304466 AAATGTTGAT
*
28304476 TAGATGACTATGTTTCCTGGTGTTTCTATTCGACATCTACCATATTCTTTTTTAGATAATTG
1 TAGATGACTATGTTTCCTGGTGTTTCTATTCGACATCTACCATATTCATTTTTAGATAATTG
28304538 TAGATGACTATGTTTCCTGGTGTTTCTATTCGACATCTACCATATTCATTTTTAGATAATTG
1 TAGATGACTATGTTTCCTGGTGTTTCTATTCGACATCTACCATATTCATTTTTAGATAATTG
28304600 T
1 T
28304601 CTTTTCCTTA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.46
Consensus pattern (62 bp):
TAGATGACTATGTTTCCTGGTGTTTCTATTCGACATCTACCATATTCATTTTTAGATAATTG
Found at i:28309208 original size:7 final size:7
Alignment explanation
Indices: 28309196--28309220 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28309186 GACCAATCCT
28309196 TTTTAAA
1 TTTTAAA
28309203 TTTTAAA
1 TTTTAAA
28309210 TTTTAAA
1 TTTTAAA
28309217 TTTT
1 TTTT
28309221 TTATATTATG
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:28316043 original size:48 final size:48
Alignment explanation
Indices: 28315971--28316245 Score: 415
Period size: 48 Copynumber: 5.7 Consensus size: 48
28315961 TAAAGTACCA
* *
28315971 ATGCCATGTCCCAGACATGGTCTTACACGGGCACACATATCATCATCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCGTCG
* *
28316019 ATGCCATGTCCCAGACATGATCTTACACTGGCACACATATCATTGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCGTCG
* *
28316067 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCGTCG
* * * *
28316115 ATGTCATGTCTCAGACATGGTTTTACACTGGCACATATATCATCGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCGTCG
* *
28316163 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCATCGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCGTCG
* * *
28316211 ATTCCATGTCCCAAACATGGTCTTACACAGGCACA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACA
28316246 TTTAGCACGG
Statistics
Matches: 203, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 203 1.00
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.25
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCGTCG
Found at i:28317369 original size:33 final size:33
Alignment explanation
Indices: 28317327--28317396 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
28317317 GTAAAATTTC
28317327 TCATCGATATTTTCACACAGGCATGCATATATA
1 TCATCGATATTTTCACACAGGCATGCATATATA
28317360 TCATCGATATTTTCACACAGGCATGCATATATA
1 TCATCGATATTTTCACACAGGCATGCATATATA
28317393 TCAT
1 TCAT
28317397 GGTCTCAACC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.34
Consensus pattern (33 bp):
TCATCGATATTTTCACACAGGCATGCATATATA
Found at i:28322798 original size:48 final size:48
Alignment explanation
Indices: 28322707--28323077 Score: 406
Period size: 48 Copynumber: 7.7 Consensus size: 48
28322697 TAAAGTACCA
* * * *
28322707 ATGCCATGTCCCCGACATGGTCTTACA-T-GAATCTACATCTCATCGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCA-C-ACATATCATCACCG
* * * *
28322755 ATGCCATCTTCTAGACATGGTCTTACACTGGCACACATATCATCATCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCG
* * *
28322803 ATGCCATGTCCCAAACATGGTCTTACACCGGCATACATATCATCACCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCG
* ** * * * * *
28322851 ATACCATGTCCCAGACATATTCTTACACCGGCTCACAGATCATCCCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCG
* * * ** * *
28322899 ATGCCATGTCCCAGAAATGATCTTACATTGGCACTTATATCATCGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCG
* **
28322947 ATGCCATGTCCCAGACATGGTCTTACACTGGCACATATATCATTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCG
* * *
28322995 ATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCATCACTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCG
28323043 ATGCCATGTCCCAGACATGGTCTTACA-TAGGCACA
1 ATGCCATGTCCCAGACATGGTCTTACACT-GGCACA
28323078 TTTAGCATGG
Statistics
Matches: 271, Mismatches: 49, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
47 1 0.00
48 266 0.98
49 2 0.01
50 2 0.01
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCG
Found at i:28324515 original size:29 final size:29
Alignment explanation
Indices: 28324469--28324551 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
28324459 TATGATATGC
* *
28324469 GAACCCTAGGAACATGCGAGCCTATGTGCA
1 GAACCCTAGAAACGTGCGAGCCTATGTG-A
* *
28324499 -AACCTTAGTAACGTGCGAGCCTATGTGA
1 GAACCCTAGAAACGTGCGAGCCTATGTGA
* *
28324527 GAACCCTAGAAACTTGCAAGCCTAT
1 GAACCCTAGAAACGTGCGAGCCTAT
28324552 ATACAATCCC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
28 1 0.02
29 44 0.98
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.20
Consensus pattern (29 bp):
GAACCCTAGAAACGTGCGAGCCTATGTGA
Found at i:28329278 original size:27 final size:27
Alignment explanation
Indices: 28329237--28329288 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
28329227 ATTGGTACCA
* *
28329237 TTAAAATTAAGATGCATAATGGGACCG
1 TTAAAATTAAAATGCACAATGGGACCG
28329264 TTAAAATTAAAATGCACAATGGGAC
1 TTAAAATTAAAATGCACAATGGGAC
28329289 GATTATGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (27 bp):
TTAAAATTAAAATGCACAATGGGACCG
Found at i:28333855 original size:25 final size:24
Alignment explanation
Indices: 28333826--28333874 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
28333816 AGCTAAAGTC
*
28333826 GGTTTTGGCTGAAGCACTTATATTG
1 GGTTTTGGCTGAAGAACTTA-ATTG
28333851 GGTTTTGGCTGAAGAACTTAATTG
1 GGTTTTGGCTGAAGAACTTAATTG
28333875 ACACAGCCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.22, C:0.10, G:0.29, T:0.39
Consensus pattern (24 bp):
GGTTTTGGCTGAAGAACTTAATTG
Found at i:28336376 original size:40 final size:40
Alignment explanation
Indices: 28336332--28336519 Score: 254
Period size: 40 Copynumber: 4.7 Consensus size: 40
28336322 GCTACTTGCT
* * *
28336332 CAAATGCCTTCGGGGCTCAACCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
28336372 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
28336412 CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCTCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * ** *
28336452 CAATTGCCTTCGGG-CTTAGCCCGG-AATTAGTCGCTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
28336491 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
28336520 CATCCGAATA
Statistics
Matches: 130, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
38 1 0.01
39 30 0.23
40 98 0.75
41 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:28336493 original size:39 final size:40
Alignment explanation
Indices: 28336299--28336515 Score: 253
Period size: 40 Copynumber: 5.5 Consensus size: 40
28336289 AAACCAAGTA
* * * *
28336299 CCTTCGGAATTTAG-CCGGATATAGCT-ACTTGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * * *
28336338 CCTTCGGGGCTCAACCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
28336378 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
28336418 CCTTCGGGACTTAGCCCGGATATAATAACTCTCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
** *
28336458 CCTTCGGG-CTTAGCCCGGA-ATTAGTCGCTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
28336497 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
28336516 TTATCATCCG
Statistics
Matches: 153, Mismatches: 21, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
38 1 0.01
39 41 0.27
40 111 0.73
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:28340267 original size:35 final size:35
Alignment explanation
Indices: 28340221--28340310 Score: 162
Period size: 35 Copynumber: 2.6 Consensus size: 35
28340211 TCAGATTTGA
*
28340221 ATTACCAGTCCAGGCTAAATTTAGACCCTAATCAG
1 ATTACCTGTCCAGGCTAAATTTAGACCCTAATCAG
*
28340256 ATTACCTGTCCAGGCTAAATTTAGACCCTAATCGG
1 ATTACCTGTCCAGGCTAAATTTAGACCCTAATCAG
28340291 ATTACCTGTCCAGGCTAAAT
1 ATTACCTGTCCAGGCTAAAT
28340311 CCTCAATGCA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (35 bp):
ATTACCTGTCCAGGCTAAATTTAGACCCTAATCAG
Found at i:28344356 original size:42 final size:42
Alignment explanation
Indices: 28344294--28344386 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
28344284 GGATTAGGAT
* *
28344294 CACACGGGCAGGTGATATCGGCATGTGTCAAGCTGTATGGGA
1 CACACGGGCAGGTGACATCGGCATGTGTCAAGCTGTATGGAA
28344336 CACACGGGCAGGTGACATCGGCATGTGTCAAGCTGTATGGAA
1 CACACGGGCAGGTGACATCGGCATGTGTCAAGCTGTATGGAA
28344378 CACACGGGC
1 CACACGGGC
28344387 GTGTGCTAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.25, C:0.23, G:0.34, T:0.18
Consensus pattern (42 bp):
CACACGGGCAGGTGACATCGGCATGTGTCAAGCTGTATGGAA
Found at i:28353384 original size:57 final size:57
Alignment explanation
Indices: 28353296--28353410 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
28353286 CTTATGGCTC
*
28353296 TTTCATTCTACAAGTTTGATGTAATTTTGGGCATAGATTGGTTATCCAAATATGAGT
1 TTTCATTCCACAAGTTTGATGTAATTTTGGGCATAGATTGGTTATCCAAATATGAGT
28353353 TTTCATTCCACAAGTTTGATGTAATTTTGGGCATAGATTGGTTATCCAAATATGAGT
1 TTTCATTCCACAAGTTTGATGTAATTTTGGGCATAGATTGGTTATCCAAATATGAGT
28353410 T
1 T
28353411 ATAGTGGATT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (57 bp):
TTTCATTCCACAAGTTTGATGTAATTTTGGGCATAGATTGGTTATCCAAATATGAGT
Found at i:28357209 original size:40 final size:40
Alignment explanation
Indices: 28357150--28357377 Score: 375
Period size: 40 Copynumber: 5.7 Consensus size: 40
28357140 GAGCATTGGA
*
28357150 ATATATCCGGGCTAAGACCCGAAGGCAATTACGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
28357190 ATATATCCGGGCTATGACCCGAAGGCAATTACGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
28357230 ATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
28357270 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
28357310 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
28357350 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
28357378 ATGTGTTTGC
Statistics
Matches: 180, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 180 1.00
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:28359618 original size:15 final size:15
Alignment explanation
Indices: 28359598--28359627 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28359588 TATGGGGGAA
28359598 ATGTAGAACTTTGGT
1 ATGTAGAACTTTGGT
28359613 ATGTAGAACTTTGGT
1 ATGTAGAACTTTGGT
28359628 GTGTTGGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.27, T:0.40
Consensus pattern (15 bp):
ATGTAGAACTTTGGT
Found at i:28361734 original size:28 final size:27
Alignment explanation
Indices: 28361667--28361727 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
28361657 AAATTAGCTC
* *
28361667 GCTTATCGTATTATGTTGCACTTTGTT
1 GCTTATCGTATTATGTTACACTTTGGT
* *
28361694 GCTTATCAATATTATTTTACACTTTGGT
1 GCTTATC-GTATTATGTTACACTTTGGT
28361722 GCTTAT
1 GCTTAT
28361728 TGTTATTTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.51
Consensus pattern (27 bp):
GCTTATCGTATTATGTTACACTTTGGT
Found at i:28370501 original size:24 final size:24
Alignment explanation
Indices: 28370467--28370559 Score: 114
Period size: 24 Copynumber: 3.9 Consensus size: 24
28370457 GGACCATAGT
* *
28370467 CGAATGTGGCTCAAAATTATCTGC
1 CGAATGTGGCCCAGAATTATCTGC
* * * **
28370491 CAAATGTGGCTCAGAATTATATAT
1 CGAATGTGGCCCAGAATTATCTGC
*
28370515 CGAATGTGGCCCAGAATTATCAGC
1 CGAATGTGGCCCAGAATTATCTGC
28370539 CGAATGTGGCCCAGAATTATC
1 CGAATGTGGCCCAGAATTATC
28370560 AAAATTCACT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (24 bp):
CGAATGTGGCCCAGAATTATCTGC
Found at i:28370545 original size:48 final size:48
Alignment explanation
Indices: 28370466--28370558 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
28370456 AGGACCATAG
* * *
28370466 TCGAATGTGGCTCAAAATTATCTGCCAAATGTGGCTCAGAATTATATA
1 TCGAATGTGGCCCAAAATTATCAGCCAAATGTGGCCCAGAATTATATA
* *
28370514 TCGAATGTGGCCCAGAATTATCAGCCGAATGTGGCCCAGAATTAT
1 TCGAATGTGGCCCAAAATTATCAGCCAAATGTGGCCCAGAATTAT
28370559 CAAAATTCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (48 bp):
TCGAATGTGGCCCAAAATTATCAGCCAAATGTGGCCCAGAATTATATA
Found at i:28374189 original size:21 final size:20
Alignment explanation
Indices: 28374165--28374203 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28374155 TGAATTGATT
28374165 AAATGTGTGATTAAATTAGTG
1 AAATGTGT-ATTAAATTAGTG
* *
28374186 AAATTTGTATTAATTTAG
1 AAATGTGTATTAAATTAG
28374204 ATCAAGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (20 bp):
AAATGTGTATTAAATTAGTG
Found at i:28377572 original size:49 final size:48
Alignment explanation
Indices: 28377463--28377635 Score: 197
Period size: 49 Copynumber: 3.6 Consensus size: 48
28377453 AGGATAAGAT
* * * *
28377463 TCGATGCCATGTCCTAGACATGGTCTTACATTGGCTATC--ACATCAAAG
1 TCGATGCCATGTCCCAGACA-GGTCTTACACTGGCTATCATATATC-AGG
* *
28377511 TCGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGG
1 TCGATGCCATGTCCCAGACAGGTCTTACACTGGCTATCATATATC-AGG
* * * *
28377560 TTGATGCCATGTCCTAGACAGGTCTTACACTGGCTCTCATCTATCAGTG
1 TCGATGCCATGTCCCAGACAGGTCTTACACTGGCTATCATATATCAG-G
*
28377609 TCGATGTCATGTCCCAGACAGGTCTTA
1 TCGATGCCATGTCCCAGACAGGTCTTA
28377636 TACTAACACA
Statistics
Matches: 107, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
47 15 0.14
48 21 0.20
49 71 0.66
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (48 bp):
TCGATGCCATGTCCCAGACAGGTCTTACACTGGCTATCATATATCAGG
Found at i:28386550 original size:18 final size:18
Alignment explanation
Indices: 28386516--28386550 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28386506 TTTTCAGAAA
*
28386516 TATGGGCCAACATGCCCG
1 TATGGGCCAACACGCCCG
*
28386534 TATGGGCCCACACGCCC
1 TATGGGCCAACACGCCC
28386551 AGATTGGCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.40, G:0.26, T:0.14
Consensus pattern (18 bp):
TATGGGCCAACACGCCCG
Found at i:28387938 original size:17 final size:17
Alignment explanation
Indices: 28387916--28387950 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
28387906 TAGGTGGTGT
28387916 TAGAAGCATAGAATGCA
1 TAGAAGCATAGAATGCA
28387933 TAGAAGCATAGAATGCA
1 TAGAAGCATAGAATGCA
28387950 T
1 T
28387951 GAAAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.20
Consensus pattern (17 bp):
TAGAAGCATAGAATGCA
Found at i:28387941 original size:8 final size:9
Alignment explanation
Indices: 28387916--28387950 Score: 56
Period size: 8 Copynumber: 4.1 Consensus size: 9
28387906 TAGGTGGTGT
28387916 TAGAA-GCA
1 TAGAATGCA
28387924 TAGAATGCA
1 TAGAATGCA
28387933 TAGAA-GCA
1 TAGAATGCA
28387941 TAGAATGCA
1 TAGAATGCA
28387950 T
1 T
28387951 GAAAATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 13 0.52
9 12 0.48
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.20
Consensus pattern (9 bp):
TAGAATGCA
Found at i:28388844 original size:13 final size:13
Alignment explanation
Indices: 28388826--28388859 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
28388816 ATATAATTAT
28388826 TAATAATATTTAA
1 TAATAATATTTAA
28388839 TAATAAT-TTTAA
1 TAATAATATTTAA
28388851 T-ATAATATT
1 TAATAATATT
28388860 ATTATTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.25
12 8 0.40
13 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATAATATTTAA
Found at i:28391903 original size:4 final size:4
Alignment explanation
Indices: 28391894--28391918 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
28391884 ATATAATTTA
28391894 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
28391919 TATATATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:28393528 original size:27 final size:27
Alignment explanation
Indices: 28393490--28393548 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
28393480 GTTTAGTAAT
28393490 TATGTAACATATGTTTACACTTCACAG
1 TATGTAACATATGTTTACACTTCACAG
28393517 TATGTAACATATGTTTACACTTCACAG
1 TATGTAACATATGTTTACACTTCACAG
28393544 TATGT
1 TATGT
28393549 TTCTTTGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (27 bp):
TATGTAACATATGTTTACACTTCACAG
Found at i:28395174 original size:3 final size:3
Alignment explanation
Indices: 28395168--28395195 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
28395158 AAAAAAAAAA
28395168 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
28395196 GCAAAATAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:28400942 original size:23 final size:23
Alignment explanation
Indices: 28400904--28401015 Score: 93
Period size: 23 Copynumber: 4.8 Consensus size: 23
28400894 AGGTCTTCCC
28400904 GAGCTGATGAACAGTAAGCTCTATT
1 GAGCTGA--AACAGTAAGCTCTATT
*
28400929 GAGCTGAAACAGTAAGCTCTATA
1 GAGCTGAAACAGTAAGCTCTATT
* *
28400952 GAGTTG-AACAGTAAGCTC-ATAC
1 GAGCTGAAACAGTAAGCTCTAT-T
** * *
28400974 GAGCTGAAATGGTAAGCTCCAAT
1 GAGCTGAAACAGTAAGCTCTATT
* *
28400997 GAGCTAAAAATAGTAAGCT
1 GAGCT-GAAACAGTAAGCT
28401016 TTTACGAGCT
Statistics
Matches: 73, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
21 2 0.03
22 17 0.23
23 35 0.48
24 12 0.16
25 7 0.10
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (23 bp):
GAGCTGAAACAGTAAGCTCTATT
Found at i:28400964 original size:22 final size:22
Alignment explanation
Indices: 28400911--28400981 Score: 99
Period size: 22 Copynumber: 3.2 Consensus size: 22
28400901 CCCGAGCTGA
*
28400911 TGAACAGTAAGCTCTATTGAGC
1 TGAACAGTAAGCTCTATAGAGC
*
28400933 TGAAACAGTAAGCTCTATAGAGT
1 TG-AACAGTAAGCTCTATAGAGC
28400956 TGAACAGTAAGCTC-ATACGAGC
1 TGAACAGTAAGCTCTATA-GAGC
28400978 TGAA
1 TGAA
28400982 ATGGTAAGCT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
21 3 0.07
22 21 0.48
23 20 0.45
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.24
Consensus pattern (22 bp):
TGAACAGTAAGCTCTATAGAGC
Found at i:28402244 original size:59 final size:59
Alignment explanation
Indices: 28402158--28402278 Score: 224
Period size: 59 Copynumber: 2.1 Consensus size: 59
28402148 TCAAATAGTA
* *
28402158 AAATTTCTTTACAAAACTTTCATATAATAATTCTATCATGCTGTAAACCTTCTTAAAAT
1 AAATTTCTTTACAAAAATTTCACATAATAATTCTATCATGCTGTAAACCTTCTTAAAAT
28402217 AAATTTCTTTACAAAAATTTCACATAATAATTCTATCATGCTGTAAACCTTCTTAAAAT
1 AAATTTCTTTACAAAAATTTCACATAATAATTCTATCATGCTGTAAACCTTCTTAAAAT
28402276 AAA
1 AAA
28402279 ATGATAGTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (59 bp):
AAATTTCTTTACAAAAATTTCACATAATAATTCTATCATGCTGTAAACCTTCTTAAAAT
Found at i:28407513 original size:43 final size:43
Alignment explanation
Indices: 28407206--28407501 Score: 484
Period size: 43 Copynumber: 6.9 Consensus size: 43
28407196 GCATGAAACT
*
28407206 CGGTGATGTGTATTGGGGCCTTCGTGCCTAGCAGGCTTCGTGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
28407249 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
** * *
28407292 CAATGATGTGTATTCGGGCCTTCATGCCTAGCAGGCTTTGTGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
* * *
28407335 CGATGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGT
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
*
28407378 CGGTGATATGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
* *
28407421 CGGTGATATGTATTCGGGCCTTCGTACCTAGCAGGCTTCGTGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
*
28407464 CGGTGATGTGTATTCGGGTCTTCGTGCCTAGCAGGCTT
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTT
28407502 AATGACGGTG
Statistics
Matches: 235, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 235 1.00
ACGTcount: A:0.12, C:0.24, G:0.33, T:0.32
Consensus pattern (43 bp):
CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
Found at i:28407732 original size:29 final size:27
Alignment explanation
Indices: 28407692--28407833 Score: 124
Period size: 29 Copynumber: 5.0 Consensus size: 27
28407682 CAAATTCCTT
28407692 TAACCGAGCACTATGTGTGCGAGATCAG
1 TAACCGAGCACTATGTGTGCGAGATC-G
** * *
28407720 TAATTGAGGCACTGTGTGTGCGA-ATTCCTT
1 TAACCGA-GCACTATGTGTGCGAGA-T-C-G
28407750 TAACCGAGCACTATGTGTGCGAGATCGG
1 TAACCGAGCACTATGTGTGCGAGATC-G
** * * *
28407778 TAATTGAGGCACTGTGTGTGCGAGTTCT
1 TAACCGA-GCACTATGTGTGCGAGATCG
28407806 TCAACCGAGCACTATGTGTGCGAGATCG
1 T-AACCGAGCACTATGTGTGCGAGATCG
28407834 GTCAGTGGGC
Statistics
Matches: 88, Mismatches: 20, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
28 30 0.34
29 51 0.58
30 7 0.08
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (27 bp):
TAACCGAGCACTATGTGTGCGAGATCG
Found at i:28407736 original size:58 final size:58
Alignment explanation
Indices: 28407667--28407832 Score: 271
Period size: 58 Copynumber: 2.9 Consensus size: 58
28407657 CGAATGATTA
* * *
28407667 GAGGCATTGTGTTTGCAAATTCCTTTAACCGAGCACTATGTGTGCGAGATCAGTAATT
1 GAGGCACTGTGTGTGCGAATTCCTTTAACCGAGCACTATGTGTGCGAGATCAGTAATT
*
28407725 GAGGCACTGTGTGTGCGAATTCCTTTAACCGAGCACTATGTGTGCGAGATCGGTAATT
1 GAGGCACTGTGTGTGCGAATTCCTTTAACCGAGCACTATGTGTGCGAGATCAGTAATT
* *
28407783 GAGGCACTGTGTGTGCGAGTT-CTTCAACCGAGCACTATGTGTGCGAGATC
1 GAGGCACTGTGTGTGCGAATTCCTTTAACCGAGCACTATGTGTGCGAGATC
28407833 GGTCAGTGGG
Statistics
Matches: 102, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
57 28 0.27
58 74 0.73
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (58 bp):
GAGGCACTGTGTGTGCGAATTCCTTTAACCGAGCACTATGTGTGCGAGATCAGTAATT
Found at i:28407845 original size:28 final size:28
Alignment explanation
Indices: 28407699--28407853 Score: 89
Period size: 29 Copynumber: 5.4 Consensus size: 28
28407689 CTTTAACCGA
* * *
28407699 GCACTATGTGTGCGAGATCAGTAATTGAG
1 GCACTATGTGTGCGAGATCGGTCACTG-G
* ** * * *
28407728 GCACTGTGTGTGCGA-ATTCCTTTAACCGA
1 GCACTATGTGTGCGAGA-T-CGGTCACTGG
* *
28407757 GCACTATGTGTGCGAGATCGGTAATTGAG
1 GCACTATGTGTGCGAGATCGGTCACTG-G
* * * * *
28407786 GCACTGTGTGTGCGAGTTC-TTCAACCGA
1 GCACTATGTGTGCGAGATCGGTC-ACTGG
*
28407814 GCACTATGTGTGCGAGATCGGTCAGTGG
1 GCACTATGTGTGCGAGATCGGTCACTGG
*
28407842 GCACTAAGTGTG
1 GCACTATGTGTG
28407854 TGAAATGAGA
Statistics
Matches: 94, Mismatches: 26, Indels: 13
0.71 0.20 0.10
Matches are distributed among these distances:
28 37 0.39
29 51 0.54
30 6 0.06
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.28
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGGTCACTGG
Found at i:28416596 original size:37 final size:37
Alignment explanation
Indices: 28416537--28416719 Score: 305
Period size: 37 Copynumber: 4.9 Consensus size: 37
28416527 AGCTCAGACG
* * *
28416537 AAATCTCCACATGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
28416574 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
28416611 TAAA-CTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 -AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
28416648 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
28416685 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
28416720 ATATATTTCC
Statistics
Matches: 140, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
36 2 0.01
37 135 0.96
38 3 0.02
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:28416921 original size:46 final size:46
Alignment explanation
Indices: 28416864--28416954 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
28416854 TATATATACA
* * *
28416864 CATCTCGTACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACATATCTCACATTAGCCATTCGGCCTTACCACATATC
* * *
28416910 CATCTCATACATGTTTCGCATTAGCCATTCGGCCTTACCACATAT
1 CATCTCATACATATCTCACATTAGCCATTCGGCCTTACCACATAT
28416955 ATTCATGTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.25, C:0.31, G:0.10, T:0.34
Consensus pattern (46 bp):
CATCTCATACATATCTCACATTAGCCATTCGGCCTTACCACATATC
Found at i:28416990 original size:47 final size:47
Alignment explanation
Indices: 28416928--28417604 Score: 967
Period size: 47 Copynumber: 14.1 Consensus size: 47
28416918 ACATGTTTCG
* * * **
28416928 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* * *
28416975 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
28417022 CATTGGCCATTTGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
***
28417069 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCAT----GTTCACATTCATCA
28417120 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
28417167 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
***
28417214 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCAT----GTTCACATTCATCA
*
28417265 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
28417312 CAGTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
***
28417359 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCAT----GTTCACATTCATCA
*
28417410 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
28417457 CAGTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
***
28417504 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCAT----GTTCACATTCATCA
*
28417555 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
28417602 CAT
1 CAT
28417605 AAAATCCTAA
Statistics
Matches: 570, Mismatches: 44, Indels: 32
0.88 0.07 0.05
Matches are distributed among these distances:
47 395 0.69
51 175 0.31
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.30
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
Found at i:28417116 original size:145 final size:145
Alignment explanation
Indices: 28416928--28417604 Score: 1218
Period size: 145 Copynumber: 4.7 Consensus size: 145
28416918 ACATGTTTCG
* **
28416928 CATTAGCCATTCGGCCTTA-C-CACATATAT-T-CATGTTCACATTCATCACATTGGCCATTCGG
1 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCGG
* * * * *
28416989 CCTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTTGGCCTTATCACACATACGCA
66 CCTTATCACACATACGCATGTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATACGCA
28417054 TGTTCACATTCATCA
131 TGTTCACATTCATCA
28417069 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCGG
1 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCGG
*
28417134 CCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCA
66 CCTTATCACACATACGCATGTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATACGCA
*
28417199 TGTTCACATCCATCA
131 TGTTCACATTCATCA
28417214 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCGG
1 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCGG
*
28417279 CCTTATCACACATACGCATGTTCACATCCATCACAGTGGCCATTCGGCCTTATCACACATACGCA
66 CCTTATCACACATACGCATGTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATACGCA
28417344 TGTTCACATTCATCA
131 TGTTCACATTCATCA
28417359 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCGG
1 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCGG
*
28417424 CCTTATCACACATACGCATGTTCACATCCATCACAGTGGCCATTCGGCCTTATCACACATACGCA
66 CCTTATCACACATACGCATGTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATACGCA
28417489 TGTTCACATTCATCA
131 TGTTCACATTCATCA
28417504 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCGG
1 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCGG
28417569 CCTTATCACACATACGCATGTTCACATCCATCACAT
66 CCTTATCACACATACGCATGTTCACATCCATCACAT
28417605 AAAATCCTAA
Statistics
Matches: 520, Mismatches: 12, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
141 18 0.03
142 1 0.00
143 9 0.02
144 1 0.00
145 491 0.94
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.30
Consensus pattern (145 bp):
CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCGG
CCTTATCACACATACGCATGTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATACGCA
TGTTCACATTCATCA
Found at i:28425800 original size:16 final size:16
Alignment explanation
Indices: 28425772--28425804 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28425762 TTCCTTCCAC
28425772 TATATGTTTTTTTTAT
1 TATATGTTTTTTTTAT
28425788 TATAT-TTTATTTTTAT
1 TATATGTTT-TTTTTAT
28425804 T
1 T
28425805 TTCTTTATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (16 bp):
TATATGTTTTTTTTAT
Found at i:28442391 original size:30 final size:30
Alignment explanation
Indices: 28442355--28442413 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
28442345 AAGAATGTCT
28442355 TGAAAATAATATTTAAAAATCTTTTTATCA
1 TGAAAATAATATTTAAAAATCTTTTTATCA
28442385 TGAAAATAATATTTAAAAATCTTTTTATC
1 TGAAAATAATATTTAAAAATCTTTTTATC
28442414 TCTATGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (30 bp):
TGAAAATAATATTTAAAAATCTTTTTATCA
Found at i:28448510 original size:13 final size:13
Alignment explanation
Indices: 28448492--28448516 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28448482 CCGAACACAC
28448492 GCTCGTGTCCCTG
1 GCTCGTGTCCCTG
28448505 GCTCGTGTCCCT
1 GCTCGTGTCCCT
28448517 CACATGGCCT
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:0.00, C:0.40, G:0.28, T:0.32
Consensus pattern (13 bp):
GCTCGTGTCCCTG
Found at i:28451706 original size:20 final size:20
Alignment explanation
Indices: 28451683--28451726 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
28451673 GGACATGGGC
28451683 GTGTCCCGAGCCACATGAGA
1 GTGTCCCGAGCCACATGAGA
* *
28451703 GTGTCCTGAGCCACATGAGC
1 GTGTCCCGAGCCACATGAGA
28451723 GTGT
1 GTGT
28451727 TTGACCACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.27, G:0.32, T:0.20
Consensus pattern (20 bp):
GTGTCCCGAGCCACATGAGA
Found at i:28452731 original size:37 final size:36
Alignment explanation
Indices: 28452690--28452773 Score: 96
Period size: 37 Copynumber: 2.3 Consensus size: 36
28452680 TGTGAGTACG
* *
28452690 TGTAAAACCATAACTAGGCTATGACATTGTAATAGCC
1 TGTAAGACCATAACTAGGCTATGACATTGTAATA-CA
** * * *
28452727 TGTAAGACCATATTTGGGCTATGGCATTGTGATACA
1 TGTAAGACCATAACTAGGCTATGACATTGTAATACA
28452763 TGTAAGACCAT
1 TGTAAGACCAT
28452774 GTCTGGGACA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 12 0.30
37 28 0.70
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (36 bp):
TGTAAGACCATAACTAGGCTATGACATTGTAATACA
Found at i:28452810 original size:42 final size:41
Alignment explanation
Indices: 28452763--28452957 Score: 142
Period size: 42 Copynumber: 4.7 Consensus size: 41
28452753 TTGTGATACA
28452763 TGTAAGACCATGTCTGGGACATGGCATCGATATGAAATTATG
1 TGTAAGACCATGTCTGGGACATGGCATCGATATGAAATT-TG
* * * * * * *
28452805 TGTAAGACTATATCTGAGATATGGCTTCGGTATGAGATTTCG
1 TGTAAGACCATGTCTGGGACATGGCATCGATATGAAATTT-G
* * ** * *
28452847 TGTAAGACCGTGTCTAGGATGTGGCATCGATATGTGATTTTG
1 TGTAAGACCATGTCTGGGACATGGCATCGATATG-AAATTTG
* * * * * * *
28452889 TATAAGACCATGTTTGGGACATAGCATTGATGTGAGACTTCG
1 TGTAAGACCATGTCTGGGACATGGCATCGATATGA-AATTTG
28452931 TGTAAGACCATAGT-T-GGACTATGGCAT
1 TGTAAGACCAT-GTCTGGGAC-ATGGCAT
28452958 TAAGTAAACG
Statistics
Matches: 116, Mismatches: 32, Indels: 10
0.73 0.20 0.06
Matches are distributed among these distances:
41 5 0.04
42 106 0.91
43 5 0.04
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.32
Consensus pattern (41 bp):
TGTAAGACCATGTCTGGGACATGGCATCGATATGAAATTTG
Found at i:28456947 original size:40 final size:40
Alignment explanation
Indices: 28456903--28456978 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
28456893 TGGCTAAGAA
** *
28456903 TGGCACTTAGTGTGCGGTTTGAGATAGCTTTGGCTAAATG
1 TGGCACTTAGTGTGCAATTTGAGATAGCTTCGGCTAAATG
* * *
28456943 TGGCATTTGGTGTGCAATTTGTGATAGCTTCGGCTA
1 TGGCACTTAGTGTGCAATTTGAGATAGCTTCGGCTA
28456979 TATATATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.18, C:0.13, G:0.32, T:0.37
Consensus pattern (40 bp):
TGGCACTTAGTGTGCAATTTGAGATAGCTTCGGCTAAATG
Found at i:28457069 original size:28 final size:28
Alignment explanation
Indices: 28456995--28457069 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
28456985 TATATGTGTG
* *
28456995 TGGCACTTAGTGTGCGAAATATTGAGAA
1 TGGCACTTAGTGTGCGAGATATTAAGAA
* * *
28457023 TGGCACTTGGTATGTGAGATATTAAGTAA
1 TGGCACTTAGTGTGCGAGATATTAAG-AA
28457052 -GGCACTTAGTGTGCGAGA
1 TGGCACTTAGTGTGCGAGA
28457070 CATCGAAGAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
28 36 0.95
29 2 0.05
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (28 bp):
TGGCACTTAGTGTGCGAGATATTAAGAA
Found at i:28464603 original size:28 final size:28
Alignment explanation
Indices: 28464563--28464626 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
28464553 GTGTCCTTAT
28464563 CCCGTGTCCCTCACATGGCCTAGACACA
1 CCCGTGTCCCTCACATGGCCTAGACACA
28464591 CCCGTGTCCCTCACATGGCCTAGACACA
1 CCCGTGTCCCTCACATGGCCTAGACACA
*
28464619 CCCTTGTC
1 CCCGTGTC
28464627 ATAGTCTATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.19, C:0.44, G:0.17, T:0.20
Consensus pattern (28 bp):
CCCGTGTCCCTCACATGGCCTAGACACA
Found at i:28470624 original size:46 final size:46
Alignment explanation
Indices: 28470557--28470649 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
28470547 TTTAATCAAG
*
28470557 ATTATTTACAAGTGTATAATTGTGTTTTACTTTGAATTTGGTAACC
1 ATTATTTACAAGTCTATAATTGTGTTTTACTTTGAATTTGGTAACC
28470603 ATTATTTACAAGTCTATAATTGTGTTTTACTTTGAATTTGGTAACC
1 ATTATTTACAAGTCTATAATTGTGTTTTACTTTGAATTTGGTAACC
28470649 A
1 A
28470650 CTAAGCACAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (46 bp):
ATTATTTACAAGTCTATAATTGTGTTTTACTTTGAATTTGGTAACC
Found at i:28470660 original size:46 final size:46
Alignment explanation
Indices: 28470564--28470661 Score: 151
Period size: 46 Copynumber: 2.1 Consensus size: 46
28470554 AAGATTATTT
* * ***
28470564 ACAAGTGTATAATTGTGTTTTACTTTGAATTTGGTAACCATTATTT
1 ACAAGTCTATAATTGTGTTTTACTTTGAATTTGGTAACCACTAAGC
28470610 ACAAGTCTATAATTGTGTTTTACTTTGAATTTGGTAACCACTAAGC
1 ACAAGTCTATAATTGTGTTTTACTTTGAATTTGGTAACCACTAAGC
28470656 ACAAGT
1 ACAAGT
28470662 AGTAGAAAGG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (46 bp):
ACAAGTCTATAATTGTGTTTTACTTTGAATTTGGTAACCACTAAGC
Found at i:28480477 original size:7 final size:6
Alignment explanation
Indices: 28480449--28480487 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
28480439 TTTAAACTCA
* *
28480449 TTTTAT TTTTATT TTTTAT TTTTAC TTTTAT TTCTAT TT
1 TTTTAT TTTTA-T TTTTAT TTTTAT TTTTAT TTTTAT TT
28480488 ATTTTTGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:28485297 original size:9 final size:9
Alignment explanation
Indices: 28485285--28485340 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
28485275 AAAATTTAAA
28485285 AAAAATATT
1 AAAAATATT
28485294 AAAAATA-T
1 AAAAATATT
*
28485302 AAAAATTTT
1 AAAAATATT
* *
28485311 AAATAAAATA
1 AAA-AATATT
28485321 AAAAATAGTT
1 AAAAATA-TT
28485331 AAAAAT-TT
1 AAAAATATT
28485339 AA
1 AA
28485341 GTCAAGAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
8 11 0.29
9 14 0.37
10 13 0.34
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAATATT
Found at i:28485299 original size:27 final size:26
Alignment explanation
Indices: 28485269--28485328 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
28485259 TTTCAATTTC
28485269 AAATAGAAAA-TTTAAAAAAAATATTAA
1 AAATAGAAAATTTTAAAAAAAATA--AA
* *
28485296 AAATATAAAAATTTTAAATAAAATAAA
1 AAATA-GAAAATTTTAAAAAAAATAAA
28485323 AAATAG
1 AAATAG
28485329 TTAAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 12 0.43
28 4 0.14
29 12 0.43
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (26 bp):
AAATAGAAAATTTTAAAAAAAATAAA
Found at i:28485318 original size:29 final size:28
Alignment explanation
Indices: 28485275--28485338 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
28485265 TTTCAAATAG
28485275 AAAA-TTTAAAAAAAATATTAAAAATA-TA
1 AAAATTTTAAAAAAAATA--AAAAATAGTA
*
28485303 AAAATTTTAAATAAAATAAAAAATAGTTA
1 AAAATTTTAAAAAAAATAAAAAATAG-TA
28485332 AAAATTT
1 AAAATTT
28485339 AAGTCAAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 7 0.22
28 4 0.12
29 21 0.66
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (28 bp):
AAAATTTTAAAAAAAATAAAAAATAGTA
Found at i:28485332 original size:20 final size:18
Alignment explanation
Indices: 28485284--28485335 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 18
28485274 GAAAATTTAA
*
28485284 AAAAAATATTAAAAATAT
1 AAAAAATATTAAAAAAAT
*
28485302 -AAAAATTTTAAATAAAAT
1 AAAAAATATTAAA-AAAAT
28485320 AAAAAATAGTTAAAAA
1 AAAAAATA-TTAAAAA
28485336 TTTAAGTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 11 0.39
18 4 0.14
19 8 0.29
20 5 0.18
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAAAATATTAAAAAAAT
Found at i:28485339 original size:28 final size:28
Alignment explanation
Indices: 28485275--28485340 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
28485265 TTTCAAATAG
*
28485275 AAAATTTAAAAAAAATATTAAAAATATA
1 AAAATTTAAAAAAAATATAAAAAATATA
* *
28485303 AAAATTTTAAATAAA-ATAAAAAATAGTTA
1 AAAATTTAAAAAAAATATAAAAAATA--TA
28485332 AAAATTTAA
1 AAAATTTAA
28485341 GTCAAGAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 9 0.28
28 13 0.41
29 10 0.31
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAATTTAAAAAAAATATAAAAAATATA
Found at i:28489207 original size:16 final size:17
Alignment explanation
Indices: 28489176--28489208 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28489166 TTCATAAGTA
28489176 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
28489193 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
28489209 GCTCCATCAT
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:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:28489859 original size:46 final size:46
Alignment explanation
Indices: 28489504--28489857 Score: 507
Period size: 46 Copynumber: 7.7 Consensus size: 46
28489494 TGGCATACTG
* * * *
28489504 TCTTTCAACTATGGTCTTACTCATTTTC-TATCATGTTGCCATGGAA
1 TCTTTCAACCATGGTCTTACACA-TTTCATATCACGTTGCCATGGTA
**
28489550 TCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTA
** ** *
28489596 TCTTTCAACCATGGTCTTATTCATTTCCCATCATGTT-CCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTA
** * *
28489641 TCTTTCAACCATGGTCTTATTCATTTCATATCACGTTACCTTGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTA
*
28489687 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTA
*
28489733 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTA
*
28489779 TCTTTCAAACATGGTCTTACACATTTCATATCA-GATTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCACG-TTGCCATGGTA
28489825 TCTTTCAACCATGGTCTTACACATTTCATATCA
1 TCTTTCAACCATGGTCTTACACATTTCATATCA
28489858 GAGAGTACAC
Statistics
Matches: 287, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
45 47 0.16
46 240 0.84
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.40
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTA
Found at i:28492009 original size:30 final size:30
Alignment explanation
Indices: 28491942--28492009 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
28491932 CACCATTAAA
* * *
28491942 ATATTTGCACTATTAGTCCTTCAACTTTTC
1 ATATTTACACTATTAATCCTTCAAATTTTC
*
28491972 ATATTTACACT-TTAATCCTTCAAATTTTG
1 ATATTTACACTATTAATCCTTCAAATTTTC
28492001 AGTATTTAC
1 A-TATTTAC
28492010 TCTTGGGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTCAAATTTTC
Found at i:28494473 original size:16 final size:17
Alignment explanation
Indices: 28494442--28494474 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28494432 TTCATAAGTA
28494442 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
28494459 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
28494475 GCTCCATCAT
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:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:28495080 original size:46 final size:46
Alignment explanation
Indices: 28494770--28495078 Score: 469
Period size: 46 Copynumber: 6.7 Consensus size: 46
28494760 TGGCATACTG
* *
28494770 TCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCA-TTTCATATCATGTTGCCATGGTA
*
28494816 TCTTTCAACCATGGTCTTATTCATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTA
* * *
28494862 TCTTTCAACCATGGTCTTATTCATTTCCTGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTA
* * *
28494908 TTTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTA
* *
28494954 TCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTA
*
28495000 TCTTTCAACCATGGTCTTACACATTTCATATCA-GATTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTCATATCATG-TTGCCATGGTA
*
28495046 TCTTTCAACCATGGTCTTACACATTTCATATCA
1 TCTTTCAACCATGGTCTTACTCATTTCATATCA
28495079 GAGAGCACAC
Statistics
Matches: 249, Mismatches: 12, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
45 5 0.02
46 244 0.98
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTA
Found at i:28497257 original size:30 final size:30
Alignment explanation
Indices: 28497190--28497257 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
28497180 CACCATTAAA
* *
28497190 ATATTTGCACTATTAGTCCTTCAAATTTTC
1 ATATTTACACTATTAATCCTTCAAATTTTC
*
28497220 ATATTTACACT-TTAATCCTTCAAATTTTG
1 ATATTTACACTATTAATCCTTCAAATTTTC
28497249 AGTATTTAC
1 A-TATTTAC
28497258 TCTTGGGCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 17 0.50
30 17 0.50
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTCAAATTTTC
Found at i:28501963 original size:12 final size:12
Alignment explanation
Indices: 28501946--28501976 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
28501936 CTCAAGTTTT
28501946 CACACGGCCTAG
1 CACACGGCCTAG
28501958 CACACGGCCTAG
1 CACACGGCCTAG
28501970 CACACGG
1 CACACGG
28501977 GTATATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.42, G:0.26, T:0.06
Consensus pattern (12 bp):
CACACGGCCTAG
Found at i:28509083 original size:7 final size:7
Alignment explanation
Indices: 28509073--28509099 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
28509063 GAGTTCTGGA
28509073 TTCAAGG
1 TTCAAGG
28509080 TTCAAGG
1 TTCAAGG
28509087 TTCAAGG
1 TTCAAGG
28509094 TTCAAG
1 TTCAAG
28509100 ATTCGAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (7 bp):
TTCAAGG
Found at i:28509114 original size:7 final size:7
Alignment explanation
Indices: 28509104--28509142 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
28509094 TTCAAGATTC
28509104 GAGTTTG
1 GAGTTTG
28509111 GAGTTTG
1 GAGTTTG
28509118 GAGTTTAG
1 GAGTTT-G
28509126 G-GTTTG
1 GAGTTTG
*
28509132 GAGTTTA
1 GAGTTTG
28509139 GAGT
1 GAGT
28509143 AAAACAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
6 2 0.07
7 25 0.86
8 2 0.07
ACGTcount: A:0.18, C:0.00, G:0.41, T:0.41
Consensus pattern (7 bp):
GAGTTTG
Found at i:28511456 original size:27 final size:27
Alignment explanation
Indices: 28511426--28511599 Score: 160
Period size: 27 Copynumber: 6.4 Consensus size: 27
28511416 GTACGTTGCC
* **
28511426 AAGGCATTCCTTTCAGAGT-TTTCCATG
1 AAGGCATTCCTTTCAGA-TATTGCCACA
* *
28511453 AAGGCATTCCCTTT-AGAGTCTT-CCACG
1 AAGGCATT-CCTTTCAGA-TATTGCCACA
*
28511480 AAGGCATTCCCTTT-AGAGT-CTGCCACA
1 AAGGCATT-CCTTTCAGA-TATTGCCACA
*
28511507 AAGGCATTCCTTTCATATATTGCCACA
1 AAGGCATTCCTTTCAGATATTGCCACA
*
28511534 AAGGCATTCCTTTCATATATTGCCACA
1 AAGGCATTCCTTTCAGATATTGCCACA
* * * *
28511561 AAGGAATTCCTTTCATATATTTCCACT
1 AAGGCATTCCTTTCAGATATTGCCACA
28511588 AAGGCATTCCTT
1 AAGGCATTCCTT
28511600 CTCTAGCATG
Statistics
Matches: 133, Mismatches: 9, Indels: 10
0.88 0.06 0.07
Matches are distributed among these distances:
26 7 0.05
27 119 0.89
28 7 0.05
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.33
Consensus pattern (27 bp):
AAGGCATTCCTTTCAGATATTGCCACA
Found at i:28513598 original size:26 final size:26
Alignment explanation
Indices: 28513569--28513675 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
28513559 TGGTACAAAT
28513569 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
28513595 TGATAAT-GGTTAGATAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28513620 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
28513646 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28513672 TGAT
1 TGAT
28513676 GGGCATTCCA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
25 23 0.31
26 52 0.69
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:28513629 original size:51 final size:52
Alignment explanation
Indices: 28513569--28513675 Score: 189
Period size: 51 Copynumber: 2.1 Consensus size: 52
28513559 TGGTACAAAT
28513569 TGATAATGGGTTAGGTAAATGTTCCATGATAATGG-TTAGATAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTTAGATAAATATTCCA
* *
28513620 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTTAGATAAATATTCCA
28513672 TGAT
1 TGAT
28513676 GGGCATTCCA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
51 35 0.66
52 18 0.34
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (52 bp):
TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTTAGATAAATATTCCA
Found at i:28520300 original size:26 final size:26
Alignment explanation
Indices: 28520271--28520378 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
28520261 TGGTACAAAT
28520271 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
28520297 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28520323 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
28520349 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28520375 TGAT
1 TGAT
28520379 GGGCATTCCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:28523445 original size:21 final size:21
Alignment explanation
Indices: 28523401--28523450 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
28523391 TAATTATTAT
28523401 TATATAAATTAAAAAATCATAA
1 TATATAAATTAAAAAA-CATAA
*
28523423 TATATAATATTATAAAA-ATAA
1 TATATAA-ATTAAAAAACATAA
28523444 TATATAA
1 TATATAA
28523451 CCTACTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 11 0.42
22 7 0.27
23 8 0.31
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TATATAAATTAAAAAACATAA
Found at i:28528660 original size:24 final size:24
Alignment explanation
Indices: 28528635--28528678 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
28528625 GCATGTTATT
28528635 TTTTTGTTC-TGT-TTCTTCTTGG
1 TTTTTGTTCTTGTGTTCTTCTTGG
28528657 TTTTTGTTCTTGTGTTCTTCTT
1 TTTTTGTTCTTGTGTTCTTCTT
28528679 TTTGCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.45
23 3 0.15
24 8 0.40
ACGTcount: A:0.00, C:0.14, G:0.16, T:0.70
Consensus pattern (24 bp):
TTTTTGTTCTTGTGTTCTTCTTGG
Found at i:28553404 original size:25 final size:25
Alignment explanation
Indices: 28553372--28553427 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
28553362 AGGTTATTCT
* * *
28553372 AGATAATTTTCCCTAAATACTTTAC
1 AGATAATTTTCCATAAAGACCTTAC
28553397 AGATAATTTTCCATAAAGACCTTAC
1 AGATAATTTTCCATAAAGACCTTAC
28553422 AGATAA
1 AGATAA
28553428 CACGCCACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (25 bp):
AGATAATTTTCCATAAAGACCTTAC
Found at i:28554717 original size:16 final size:16
Alignment explanation
Indices: 28554693--28554741 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
28554683 CAAAACTCTA
28554693 AGGCGTACTCTTTCTT
1 AGGCGTACTCTTTCTT
*
28554709 AGTCGTACTCTTTCTT
1 AGGCGTACTCTTTCTT
*
28554725 AGGCGTAATCTTTCTT
1 AGGCGTACTCTTTCTT
28554741 A
1 A
28554742 ACTTGAAGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.45
Consensus pattern (16 bp):
AGGCGTACTCTTTCTT
Found at i:28556909 original size:44 final size:42
Alignment explanation
Indices: 28556833--28556986 Score: 116
Period size: 43 Copynumber: 3.6 Consensus size: 42
28556823 TGATATGTGT
* ** *
28556833 TTTCATGTAAGACCACGTCTGGGATGTTGGCATCG-ACTTATGA
1 TTTCGTGTAAGACCACGTCTGGGACATCGGCATCGTA-TT-TGA
* *
28556876 TTTACGTGTAAGACCATGTTTGGGACATCGGCATCGTATTTGA
1 TTT-CGTGTAAGACCACGTCTGGGACATCGGCATCGTATTTGA
* * *
28556919 TTTCGTGTAAGACC-CTGTCTAGGACAGT-GGCATTGATATTTGG
1 TTTCGTGTAAGACCAC-GTCTGGGACA-TCGGCATCG-TATTTGA
* * * *
28556962 TTACATGTATGACCACGTTTGGGAC
1 TTTCGTGTAAGACCACGTCTGGGAC
28556987 GTTGGCATTG
Statistics
Matches: 89, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
42 25 0.28
43 34 0.38
44 29 0.33
45 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (42 bp):
TTTCGTGTAAGACCACGTCTGGGACATCGGCATCGTATTTGA
Found at i:28556951 original size:42 final size:42
Alignment explanation
Indices: 28556860--28556960 Score: 107
Period size: 42 Copynumber: 2.3 Consensus size: 42
28556850 TCTGGGATGT
* *
28556860 TGGCATCG-ACTTATGATTTACGTGTAAGACCATGTTTGGGACA
1 TGGCATCGTA-TT-TGATTTACGTGTAAGACCATGTCTAGGACA
*
28556903 TCGGCATCGTATTTGATTT-CGTGTAAGACCCTGTCTAGGACA
1 T-GGCATCGTATTTGATTTACGTGTAAGACCATGTCTAGGACA
*
28556945 GTGGCATTGATATTTG
1 -TGGCATCG-TATTTG
28556961 GTTACATGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
42 26 0.52
43 14 0.28
44 9 0.18
45 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.35
Consensus pattern (42 bp):
TGGCATCGTATTTGATTTACGTGTAAGACCATGTCTAGGACA
Found at i:28556960 original size:43 final size:43
Alignment explanation
Indices: 28556838--28556944 Score: 110
Period size: 44 Copynumber: 2.5 Consensus size: 43
28556828 TGTGTTTTCA
* * ** *
28556838 TGTAAGACCACGTCTGGGATGTTGGCATCG-ACTTATGATTTACG
1 TGTAAGACCATGTCTAGGACATCGGCATCGTA-TT-TGATTTACG
* *
28556882 TGTAAGACCATGTTTGGGACATCGGCATCGTATTTGATTT-CG
1 TGTAAGACCATGTCTAGGACATCGGCATCGTATTTGATTTACG
*
28556924 TGTAAGACCCTGTCTAGGACA
1 TGTAAGACCATGTCTAGGACA
28556945 GTGGCATTGA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
42 20 0.37
43 6 0.11
44 27 0.50
45 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (43 bp):
TGTAAGACCATGTCTAGGACATCGGCATCGTATTTGATTTACG
Found at i:28568294 original size:21 final size:22
Alignment explanation
Indices: 28568258--28568308 Score: 86
Period size: 21 Copynumber: 2.3 Consensus size: 22
28568248 TTGAAAGCAA
28568258 AAATGAATAGTGTGTTTGAATAG
1 AAATGAATA-TGTGTTTGAATAG
28568281 AAATGAAT-TGTGTTTGAATAG
1 AAATGAATATGTGTTTGAATAG
28568302 AAATGAA
1 AAATGAA
28568309 AGGAATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 20 0.71
23 8 0.29
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.33
Consensus pattern (22 bp):
AAATGAATATGTGTTTGAATAG
Found at i:28576360 original size:46 final size:48
Alignment explanation
Indices: 28576174--28576446 Score: 226
Period size: 46 Copynumber: 5.8 Consensus size: 48
28576164 AACGTGTAAT
* ** **
28576174 GCCGATGCCACGTCCCAGACATGGTCTTACACT-GACTAACGAAATCG-A
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCTC-ATCTCGTA
* * *
28576222 GGCCGACGTCATGTCCTAGACATGGTCTTACACTAGCTCTCACATCTCTGT-
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT--CATCTC-GTA
* * *
28576273 GCCGATGCCATGCCCCAGACATGGTCTTACACT-G-GCACATCTCGTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCGTA
* * * *
28576319 GCCGGTG-CATGTCCTAGACAT-GTCTTACTCTAGCTCTCATCTC-AA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCGTA
* * * *
28576364 TGCCGATGCCATGTCCCAGACATGGTCTTGCACTGGCTCTCATAAT-GTG
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-CTCGTA
28576413 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGC
28576447 GCACAAATGA
Statistics
Matches: 180, Mismatches: 31, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
44 9 0.05
45 16 0.09
46 36 0.20
47 27 0.15
48 24 0.13
49 33 0.18
50 33 0.18
51 2 0.01
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.26
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCGTA
Found at i:28576437 original size:94 final size:95
Alignment explanation
Indices: 28576171--28576446 Score: 319
Period size: 94 Copynumber: 2.9 Consensus size: 95
28576161 CATAACGTGT
* * ** * *
28576171 AATGCCGATGCCACGTCCCAGACATGGTCTTACACTGACTAACGA-AATCGAGGCCGACGTCATG
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC-ATAAT-GTGGCCGATG-CATG
28576235 TCCTAGACATGGTCTTACACTAGCTCTCACATCTC
63 TCCTAGACAT-GTCTTACACTAGCTCT-ACATCTC
** * * * * *
28576270 TGTGCCGATGCCATGCCCCAGACATGGTCTTACACTGGCACATC-T--CGTAGCCGGTGCATGTC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCATAATGTGGCCGATGCATGTC
*
28576332 CTAGACATGTCTTACTCTAGCTCT-CATCTC
65 CTAGACATGTCTTACACTAGCTCTACATCTC
*
28576362 AATGCCGATGCCATGTCCCAGACATGGTCTTGCACTGGCTCTCATAATGTGGCCGATGCATGTCC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCC
*
28576427 CAGACATGTCTTACACTAGC
66 TAGACATGTCTTACACTAGC
28576447 GCACAAATGA
Statistics
Matches: 148, Mismatches: 24, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
91 2 0.01
92 43 0.29
94 48 0.32
95 14 0.09
96 6 0.04
99 34 0.23
100 1 0.01
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (95 bp):
AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCC
TAGACATGTCTTACACTAGCTCTACATCTC
Found at i:28578118 original size:27 final size:27
Alignment explanation
Indices: 28578096--28578301 Score: 254
Period size: 27 Copynumber: 7.6 Consensus size: 27
28578086 TTAGTTTACC
28578096 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* * * *
28578123 AAATTACCAAAATGCCCTTGGTTTATA
1 AAATTACCAAAATACCCCTAGTTTGTA
28578150 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* ** *
28578177 AAATTACTAAAATACCTTTTA-TTTATA
1 AAATTACCAAAATACC-CCTAGTTTGTA
*
28578204 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
28578231 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* *
28578258 AAATTATCAAAATACCCCT-GATTTGTG
1 AAATTACCAAAATACCCCTAG-TTTGTA
**
28578285 AAATTACTGAAATACCC
1 AAATTACCAAAATACCC
28578302 TCGACCTGTA
Statistics
Matches: 154, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
26 2 0.01
27 150 0.97
28 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTAGTTTGTA
Found at i:28578155 original size:54 final size:54
Alignment explanation
Indices: 28578096--28578302 Score: 290
Period size: 54 Copynumber: 3.8 Consensus size: 54
28578086 TTAGTTTACC
*
28578096 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATGCCCTTGGTTTATA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
* * **
28578150 AAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAAATACCTTTTATTTATA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
* * *
28578204 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
* * **
28578258 AAATTATCAAAATACCCCT-GATTTGTGAAATTACTGAAATACCCT
1 AAATTACCAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCT
28578303 CGACCTGTAA
Statistics
Matches: 135, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
53 1 0.01
54 134 0.99
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (54 bp):
AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
Found at i:28578289 original size:81 final size:81
Alignment explanation
Indices: 28578096--28578371 Score: 288
Period size: 81 Copynumber: 3.4 Consensus size: 81
28578086 TTAGTTTACC
* * *
28578096 AAATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATGCCCTTGGTTTATAAAATTACCAA
1 AAATTACCAAAATACCCCTGA-TTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAA
*
28578160 AATACCCCTAGTTTGTA
65 AATACCCCTGGTTTGTA
* ** * *
28578177 AAATTACTAAAATACCTTTTATTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAA
1 AAATTACCAAAATACCCCTGATTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAA
28578242 ATACCCCTGGTTTGTA
66 ATACCCCTGGTTTGTA
* * ** *** ***
28578258 AAATTATCAAAATACCCCTGATTTGTGAAATTACTGAAATA-CCCTCGACCTGTAAAATTATTGA
1 AAATTACCAAAATACCCCTGATTTGTAAAATTACCAAAATACCCCT-GGTTTGTAAAATTACCAA
**
28578322 AATA-CCCTCGACTTGTA
65 AATACCCCT-GGTTTGTA
* * *
28578339 AAATTACCAAAGTACCCCTGATTTATAGAATTA
1 AAATTACCAAAATACCCCTGATTTGTAAAATTA
28578372 TCATTTTACC
Statistics
Matches: 162, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
80 8 0.05
81 153 0.94
82 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (81 bp):
AAATTACCAAAATACCCCTGATTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAA
ATACCCCTGGTTTGTA
Found at i:28578354 original size:27 final size:26
Alignment explanation
Indices: 28578096--28578371 Score: 228
Period size: 27 Copynumber: 10.2 Consensus size: 26
28578086 TTAGTTTACC
*
28578096 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCGA-TTTGTA
* * * *
28578123 AAATTACCAAAATGCCCTTGGTTTATA
1 AAATTACCAAAATACCC-CGATTTGTA
*
28578150 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCGA-TTTGTA
* *** *
28578177 AAATTACTAAAATACCTTTTATTTATA
1 AAATTACCAAAATACC-CCGATTTGTA
*
28578204 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCC-GATTTGTA
*
28578231 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCC-GATTTGTA
* *
28578258 AAATTATCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCC-GATTTGTA
** **
28578285 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCC-CGATTTGTA
*** *
28578312 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCC-CGATTTGTA
* *
28578339 AAATTACCAAAGTACCCCTGATTTATA
1 AAATTACCAAAATACCCC-GATTTGTA
*
28578366 GAATTA
1 AAATTA
28578372 TCATTTTACC
Statistics
Matches: 205, Mismatches: 38, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
26 1 0.00
27 201 0.98
28 3 0.01
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (26 bp):
AAATTACCAAAATACCCCGATTTGTA
Found at i:28578382 original size:81 final size:81
Alignment explanation
Indices: 28578230--28578410 Score: 188
Period size: 81 Copynumber: 2.2 Consensus size: 81
28578220 CCTGGTTTGT
* ** * * *
28578230 AAAATTACCAAAATACCC-CTGGTTTGTAAAATTATCAAAATACCCCTGATTTGTGAAATTACTG
1 AAAATTACCGAAATACCCTC-GACTTGTAAAATTACCAAAATACCCCTGATTTATGAAATTACTC
**
28578294 AAATACCCTCGACCTGT
65 AAATACCCTCGACCTAC
** *
28578311 AAAATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCCTGATTTAT-AGAATTA-TC
1 AAAATTACCGAAATACCCTCGACTTGTAAAATTACCAAAATACCCCTGATTTATGA-AATTACTC
** *
28578374 ATTTTACCCTCGATCTAC
65 A-AATACCCTCGACCTAC
28578392 AAAATTACCGAAATACCCT
1 AAAATTACCGAAATACCCT
28578411 TGTAGGGTAG
Statistics
Matches: 81, Mismatches: 16, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
80 3 0.04
81 77 0.95
82 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (81 bp):
AAAATTACCGAAATACCCTCGACTTGTAAAATTACCAAAATACCCCTGATTTATGAAATTACTCA
AATACCCTCGACCTAC
Found at i:28578427 original size:27 final size:27
Alignment explanation
Indices: 28578394--28578570 Score: 203
Period size: 27 Copynumber: 6.6 Consensus size: 27
28578384 CGATCTACAA
*
28578394 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28578421 AAATACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*** *
28578448 AATTATAAAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
28578475 AATTACTGAAATACCCCTATAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28578502 -ATTACCGAAATACCCTTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28578528 AAATACCGAAATACCCCTGTAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28578555 AATTACTGAGATACCC
1 AATTACCGAAATACCC
28578571 TTATGGGGTA
Statistics
Matches: 124, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
26 21 0.17
27 103 0.83
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.24
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:28578452 original size:54 final size:54
Alignment explanation
Indices: 28578394--28578572 Score: 225
Period size: 54 Copynumber: 3.3 Consensus size: 54
28578384 CGATCTACAA
*
28578394 AATTACCGAAATACCCTTGTAGGGTAGAAATACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAG
*** * * * * * *
28578448 AATTATAAAAATACCCCTATAGGGTAGAATTACTGAAATACCCCTATAAGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAG
* *
28578502 -ATTACCGAAATACCCTTGTAGGGTAAAAATACCGAAATACCCCTGTAGGATAG
1 AATTACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAG
* *
28578555 AATTACTGAGATACCCTT
1 AATTACCGAAATACCCTT
28578573 ATGGGGTAAA
Statistics
Matches: 101, Mismatches: 23, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
53 42 0.42
54 59 0.58
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (54 bp):
AATTACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAG
Found at i:28579042 original size:6 final size:6
Alignment explanation
Indices: 28579033--28579130 Score: 85
Period size: 6 Copynumber: 15.8 Consensus size: 6
28579023 TTGCATTCAC
* * *
28579033 ATTCTG ATTCTG ACTCTG -TTACCTG ATACTG ATTCTG ATTCTG -TTACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATT--CTG
*
28579083 ATTCTG ATTCTG ATTCT- ATTACCTG ATTCTG ATTTTG ATTCTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCT
28579131 AGTTCCGATA
Statistics
Matches: 75, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
5 6 0.08
6 56 0.75
7 7 0.09
8 6 0.08
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:28579064 original size:25 final size:25
Alignment explanation
Indices: 28579033--28579125 Score: 141
Period size: 25 Copynumber: 3.7 Consensus size: 25
28579023 TTGCATTCAC
*
28579033 ATTCTGATTCTGACTCTGTTACCTG
1 ATTCTGATTCTGATTCTGTTACCTG
* *
28579058 ATACTGATTCTGATTCTGTTACCTA
1 ATTCTGATTCTGATTCTGTTACCTG
*
28579083 ATTCTGATTCTGATTCTATTACCTG
1 ATTCTGATTCTGATTCTGTTACCTG
*
28579108 ATTCTGATTTTGATTCTG
1 ATTCTGATTCTGATTCTG
28579126 ATTCTAGTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 60 1.00
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.47
Consensus pattern (25 bp):
ATTCTGATTCTGATTCTGTTACCTG
Found at i:28620267 original size:5 final size:5
Alignment explanation
Indices: 28620253--28620285 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
28620243 ATTTGTGAAA
28620253 AAAAT AAAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAA
28620286 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 17 0.65
6 5 0.19
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:28620989 original size:13 final size:13
Alignment explanation
Indices: 28620973--28621028 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
28620963 ATTTTTAAAT
28620973 TATTTAGTGATAA
1 TATTTAGTGATAA
28620986 TATTTAGTGGA-AA
1 TATTTAGT-GATAA
28620999 TATTTAG-GAT--
1 TATTTAGTGATAA
* *
28621009 TATTTTGAGATAA
1 TATTTAGTGATAA
28621022 TATTTAG
1 TATTTAG
28621029 GAAAAACCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
10 6 0.17
11 5 0.14
13 23 0.64
14 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:28631566 original size:16 final size:15
Alignment explanation
Indices: 28631525--28631558 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28631515 CTAAGTTTGA
* *
28631525 AAAAAATAAAAAAAT
1 AAAAAATATATAAAT
28631540 AAAAAATATATAAAT
1 AAAAAATATATAAAT
28631555 AAAA
1 AAAA
28631559 GTATATATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAAAATATATAAAT
Found at i:28632143 original size:13 final size:13
Alignment explanation
Indices: 28632127--28632158 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
28632117 ATTTTTAAGT
28632127 TATTTAGTGATAA
1 TATTTAGTGATAA
28632140 TATTTAGTGATAA
1 TATTTAGTGATAA
28632153 TATTTA
1 TATTTA
28632159 AGAAAAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:28633039 original size:19 final size:19
Alignment explanation
Indices: 28633015--28633063 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
28633005 TTTATTTACC
28633015 AATTTATTTTATT-TTCTTA
1 AATTTATTTT-TTCTTCTTA
*
28633034 AATTTATTTTTTCTTTTTA
1 AATTTATTTTTTCTTCTTA
*
28633053 AATCTATTTTT
1 AATTTATTTTT
28633064 CTTTTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 2 0.07
19 25 0.93
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.69
Consensus pattern (19 bp):
AATTTATTTTTTCTTCTTA
Found at i:28633064 original size:18 final size:19
Alignment explanation
Indices: 28633031--28633068 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
28633021 TTTTATTTTC
*
28633031 TTAAATTTATTTTTTCTTT
1 TTAAATCTATTTTTTCTTT
28633050 TTAAATCTA-TTTTTCTTT
1 TTAAATCTATTTTTTCTTT
28633068 T
1 T
28633069 CTTTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (19 bp):
TTAAATCTATTTTTTCTTT
Found at i:28633489 original size:22 final size:22
Alignment explanation
Indices: 28633461--28633538 Score: 113
Period size: 22 Copynumber: 3.6 Consensus size: 22
28633451 TAATTAGTTT
28633461 AGTACAAGTGGTTCAATCCTAA
1 AGTACAAGTGGTTCAATCCTAA
28633483 AGTACAAGTGGTTCAATCCTAA
1 AGTACAAGTGGTTCAATCCTAA
* ** *
28633505 AGTACAAGTGGCTCGTTCGTAA
1 AGTACAAGTGGTTCAATCCTAA
28633527 AGT-CAAGTGGTT
1 AGTACAAGTGGTT
28633539 TTGGAAAATG
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 8 0.16
22 43 0.84
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (22 bp):
AGTACAAGTGGTTCAATCCTAA
Found at i:28635380 original size:46 final size:46
Alignment explanation
Indices: 28635325--28635476 Score: 143
Period size: 46 Copynumber: 3.3 Consensus size: 46
28635315 ACTCATTAAT
*
28635325 TTGAGTCCGAGTTCACTTGTGGATGCGAATGTCCGAACTCGTTGAG
1 TTGAGTCCGAGTTCACTTGTGGATGCGAATGTCCGAGCTCGTTGAG
*
28635371 TTGAGTCCGAGTT--C--GTGAGATG-TAACTAGGCATCCGAGCTCGTTGAG
1 TTGAGTCCGAGTTCACTTGTG-GATGCGAA-T--G--TCCGAGCTCGTTGAG
* * * *
28635418 TTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGTTTGTTGAG
1 TTGAGTCCGAGTTCACTTGTGGATGCGAATGTCCGAGCTCGTTGAG
* *
28635464 TTGCGTCTGAGTT
1 TTGAGTCCGAGTT
28635477 TGCTTATGGG
Statistics
Matches: 86, Mismatches: 9, Indels: 22
0.74 0.08 0.19
Matches are distributed among these distances:
42 5 0.06
43 5 0.06
44 1 0.01
45 1 0.01
46 36 0.42
47 27 0.31
48 1 0.01
49 1 0.01
50 5 0.06
51 4 0.05
ACGTcount: A:0.19, C:0.18, G:0.31, T:0.32
Consensus pattern (46 bp):
TTGAGTCCGAGTTCACTTGTGGATGCGAATGTCCGAGCTCGTTGAG
Found at i:28637647 original size:46 final size:46
Alignment explanation
Indices: 28637505--28637673 Score: 155
Period size: 46 Copynumber: 3.7 Consensus size: 46
28637495 CCATGTTTCG
* * * *
28637505 AGCTCCTGCATATGTTGTGGAATCGAGGATACATGAATAGG-TTTA
1 AGCTCCTACATATGTTGCGGAATCGAGAATACAAGAATAGGTTTTA
* * * ** * *
28637550 GAGCTCCTACACATGTTGCGGATTCAAGAATACAAGAATAAATTCTG
1 -AGCTCCTACATATGTTGCGGAATCGAGAATACAAGAATAGGTTTTA
**
28637597 AGCTCCTACATATGTTGCGGACA-CGAGAATACAAGTTTAGGTTTTA
1 AGCTCCTACATATGTTGCGGA-ATCGAGAATACAAGAATAGGTTTTA
* *
28637643 AGCTCTTGA-ATATGTTGTGGAATCGAGAATA
1 AGCTCCT-ACATATGTTGCGGAATCGAGAATA
28637674 TGTGAATATT
Statistics
Matches: 97, Mismatches: 22, Indels: 8
0.76 0.17 0.06
Matches are distributed among these distances:
45 1 0.01
46 93 0.96
47 3 0.03
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (46 bp):
AGCTCCTACATATGTTGCGGAATCGAGAATACAAGAATAGGTTTTA
Found at i:28640272 original size:24 final size:26
Alignment explanation
Indices: 28640222--28640276 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
28640212 CAATGCGTAT
*
28640222 AATTCATGATAGCAATTAAGCATTTA
1 AATTCATGATAACAATTAAGCATTTA
*
28640248 AATTCAT-ATAAC-ATTAAAGCATTAA
1 AATTCATGATAACAATT-AAGCATTTA
28640273 AATT
1 AATT
28640277 TGTAACACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 3 0.12
25 16 0.62
26 7 0.27
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.35
Consensus pattern (26 bp):
AATTCATGATAACAATTAAGCATTTA
Found at i:28656046 original size:40 final size:41
Alignment explanation
Indices: 28655976--28656187 Score: 226
Period size: 40 Copynumber: 5.3 Consensus size: 41
28655966 AAATCACGTA
* * **
28655976 CCTTCGGAATTTAA-CCGGA-TATAGCT-ACTCGTTCAAATG
1 CCTTCGGGACTTAACCCGGATTATAG-TAACTCGCACAAATG
* *
28656015 CCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCCGGATTATAGTAACTCGCACAAATG
*
28656055 CCTTCGGGAGTTAACCCGGATTA-AGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCCGGATTATAGTAACTCGCACAAATG
28656095 CCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCCGGATTATAGTAACTCGCACAAATG
** * * *
28656135 CCTTC-GGATCTTAGTCCGGA-TATGGTCACTTAGCACAAA-G
1 CCTTCGGGA-CTTAACCCGGATTATAGTAAC-TCGCACAAATG
28656175 CCTTCGGGACTTA
1 CCTTCGGGACTTA
28656188 GCCCAGACAT
Statistics
Matches: 149, Mismatches: 15, Indels: 17
0.82 0.08 0.09
Matches are distributed among these distances:
39 15 0.10
40 120 0.81
41 14 0.09
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (41 bp):
CCTTCGGGACTTAACCCGGATTATAGTAACTCGCACAAATG
Found at i:28664102 original size:40 final size:40
Alignment explanation
Indices: 28664052--28664237 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
28664042 AGCTACTCTT
*
28664052 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
28664092 CAAATACCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
28664132 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
28664172 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
28664213 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28664238 CATCATCAAA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
39 3 0.02
40 115 0.88
41 13 0.10
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:28672146 original size:38 final size:39
Alignment explanation
Indices: 28672040--28672222 Score: 239
Period size: 40 Copynumber: 4.7 Consensus size: 39
28672030 GCTACTCGTT
*
28672040 CAAATGCCTTCGGGACATAGCCCGG-TTACAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT--AGTAACTCGCA
*
28672080 CAAATGCCTTCGGGACTTAACCCGGATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
*
28672119 CAAATGCCTTCGGG-CTTAACCCGGATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
* * *
28672157 CAAATGCCTTC-GGATCTTAGCCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TAGTAAC-TCGCA
28672198 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28672223 CATCATTCAA
Statistics
Matches: 131, Mismatches: 6, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
37 2 0.02
38 35 0.27
39 36 0.27
40 45 0.34
41 13 0.10
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.22
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
Found at i:28691859 original size:40 final size:40
Alignment explanation
Indices: 28691815--28691941 Score: 254
Period size: 40 Copynumber: 3.2 Consensus size: 40
28691805 GCTACTAGCT
28691815 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
28691855 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
28691895 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
28691935 CAAATGC
1 CAAATGC
28691942 TGTAACACCC
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:28693575 original size:47 final size:47
Alignment explanation
Indices: 28693497--28694186 Score: 1105
Period size: 47 Copynumber: 14.6 Consensus size: 47
28693487 CCCTTCGGAA
* * * * * *
28693497 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28693544 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28693591 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28693638 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28693685 CTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28693732 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
28693781 CTTATCACATATATATACACTTTCACACTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28693830 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28693877 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28693924 CTTATCACATATATACACTTTCACATTCATCATATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28693971 CTTATCACATATATATACACTTTCACATTCATCACATAGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
28694020 CTTATCACATATATATACACTTTCACACTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28694069 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28694116 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28694163 CTCATCACATATATACA--TTCACAT
1 CTTATCACATATATACACTTTCACAT
28694187 CACAATTATC
Statistics
Matches: 607, Mismatches: 32, Indels: 10
0.94 0.05 0.02
Matches are distributed among these distances:
45 7 0.01
47 417 0.69
49 183 0.30
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28693853 original size:192 final size:190
Alignment explanation
Indices: 28693497--28694177 Score: 1123
Period size: 192 Copynumber: 3.6 Consensus size: 190
28693487 CCCTTCGGAA
* * * * * * * *
28693497 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
28693562 TTTCACATTCATCACATCGGCCATTAGGCCTCATCAC--ATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATATACACTTTCACATTCATCACA
* * *
28693625 TCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
131 TAGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28693685 CTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
* *
28693750 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACACTCATCA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATATACACTTTCACATTCATCA
* *
28693815 CATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
129 CATAGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28693877 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* *
28693942 TTTCACATTCATCATATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATATACACTTTCACATTCATCACA
* * *
28694007 TAGGCCATTAGGCCTTATCACATATATATACACTTTCACACTCATCACATTGGCCATTCGGC
131 TAGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28694069 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
28694134 TTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATA
66 TTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATA
28694178 CATTCACATC
Statistics
Matches: 462, Mismatches: 25, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
188 46 0.10
190 138 0.30
192 278 0.60
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (190 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATATACACTTTCACATTCATCACA
TAGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28693925 original size:239 final size:239
Alignment explanation
Indices: 28693497--28694186 Score: 1185
Period size: 239 Copynumber: 2.9 Consensus size: 239
28693487 CCCTTCGGAA
* * * * * * *
28693497 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATAGGCCATTAGGCCTTATCACATATATAT
* * * *
28693558 ACACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCA
66 ACACTTTCACACTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
* *
28693623 CATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTT
131 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
*
28693688 ATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
196 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28693732 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATAGGCCATTAGGCCTTATCACATATATAT
28693797 ACACTTTCACACTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
66 ACACTTTCACACTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
28693862 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
131 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
*
28693927 ATCACATATATACACTTTCACATTCATCATATCGGCCATTAGGC
196 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28693971 CTTATCACATATATATACACTTTCACATTCATCACATAGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATAGGCCATTAGGCCTTATCACATATATAT
28694036 ACACTTTCACACTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
66 ACACTTTCACACTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
*
28694101 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTC
131 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
28694166 ATCACATATATACA--TTCACAT
196 ATCACATATATACACTTTCACAT
28694187 CACAATTATC
Statistics
Matches: 434, Mismatches: 17, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
235 10 0.02
236 1 0.00
237 44 0.10
239 379 0.87
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (239 bp):
CTTATCACATATATATACACTTTCACATTCATCACATAGGCCATTAGGCCTTATCACATATATAT
ACACTTTCACACTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28694222 original size:286 final size:282
Alignment explanation
Indices: 28693497--28694198 Score: 1104
Period size: 286 Copynumber: 2.5 Consensus size: 282
28693487 CCCTTCGGAA
* * * * * *
28693497 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
28693562 TTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACAC-TTCACATTCATCA-ATC
** * *
28693627 GGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCA
129 ATCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
* *
28693692 CATATATACACTTTCATATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCA
194 CATATATACACTTTCACATTCATCACATAGGCCATTAGGCCTTATCACATATATATACACTTTCA
*
28693757 CATTCATCACATCGGCCATTAGGC
259 CACTCATCACATCGGCCATTAGGC
*
28693781 CTTATCACATATATATACACTTTCACACTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
*
28693846 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACAC-TTCACATTCATCA-A
** *
28693911 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCATATCGGCCATTAGGCCTTAT
127 TCATCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
28693976 CACATATATATACACTTTCACATTCATCACATAGGCCATTAGGCCTTATCACATATATATACACT
192 CAC--ATATATACACTTTCACATTCATCACATAGGCCATTAGGCCTTATCACATATATATACACT
* *
28694041 TTCACACTCATCACATTGGCCATTCGGC
255 TTCACACTCATCACATCGGCCATTAGGC
* *
28694069 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
*
28694134 TTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACA-TTCACA-TCA-CAATTAT
66 TTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTCACATTCATCAATCAT
28694196 CCA
131 CCA
28694199 AATATACTTC
Statistics
Matches: 391, Mismatches: 23, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
281 5 0.01
282 2 0.01
283 3 0.01
284 14 0.04
286 276 0.71
288 91 0.23
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (282 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTCACATTCATCAATCAT
CCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
TATATACACTTTCACATTCATCACATAGGCCATTAGGCCTTATCACATATATATACACTTTCACA
CTCATCACATCGGCCATTAGGC
Found at i:28696740 original size:39 final size:40
Alignment explanation
Indices: 28696618--28696842 Score: 343
Period size: 40 Copynumber: 5.7 Consensus size: 40
28696608 TTAGGGCTGT
*
28696618 CACAAATGCCTTCGGGACTTAGCCCAGATATAGTAACTCA-
1 CACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACT-AG
*
28696658 CACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCG
1 CACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAG
*
28696698 CACAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTCACTAG
1 CACAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTAG
*
28696737 CACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCG
1 CACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAG
*
28696777 CACAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTCACTAG
1 CACAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTAG
28696816 CACAAATGCCTTCGGGACTTAGCCCGG
1 CACAAATGCCTTCGGGACTTAGCCCGG
28696843 TTATCAATCC
Statistics
Matches: 171, Mismatches: 8, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
38 2 0.01
39 70 0.41
40 98 0.57
41 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.22
Consensus pattern (40 bp):
CACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAG
Found at i:28696750 original size:79 final size:79
Alignment explanation
Indices: 28696618--28696842 Score: 391
Period size: 79 Copynumber: 2.8 Consensus size: 79
28696608 TTAGGGCTGT
* *
28696618 CACAAATGCCTTCGGGACTTAGCCCAG-ATATAGTAACTCA-CACAAATGCCTTCGGGACTTAGC
1 CACAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTCACT-AGCACAAATGCCTTCGGGACTTAGC
28696681 CCGGATATAGTAACTCG
63 CCGGATATAGTAACTCG
28696698 CACAAATGCCTTCGGGCTTAGCCCGGAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCG
1 CACAAATGCCTTCGGGCTTAGCCCGGAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCG
28696763 GATATAGTAACTCG
66 GATATAGTAACTCG
28696777 CACAAATGCCTTCGGGCTTAGCCCGGAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCG
1 CACAAATGCCTTCGGGCTTAGCCCGGAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCG
28696842 G
66 G
28696843 TTATCAATCC
Statistics
Matches: 141, Mismatches: 2, Indels: 5
0.95 0.01 0.03
Matches are distributed among these distances:
78 1 0.01
79 122 0.87
80 18 0.13
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.22
Consensus pattern (79 bp):
CACAAATGCCTTCGGGCTTAGCCCGGAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCG
GATATAGTAACTCG
Found at i:28700830 original size:184 final size:184
Alignment explanation
Indices: 28700521--28700882 Score: 607
Period size: 184 Copynumber: 2.0 Consensus size: 184
28700511 GGATTTTCAA
* * *
28700521 AGGCACATGGCCGTATAGTCCACCTGTATGGGAGACCGTGTGGCCCTAAACCTACATAAAGTTTG
1 AGGCACATGGCCGTATAGTCCACCTGTATGGGAGACCGTATGGCCCTAAACCTACACAAAATTTG
* *
28700586 CCAAAATTTACTTGTAAAAGAACACACACCTTTCACCGAAGGTCTTATCGACGTTCCTCACGATC
66 CCAAAATTCACTTGCAAAAGAACACACACCTTTCACCGAAGGTCTTATCGACGTTCCTCACGATC
28700651 AAATCTAATCCAATTCACCTAAATCAAGTCCTTCAAACGACATTTTCACATCAG
131 AAATCTAATCCAATTCACCTAAATCAAGTCCTTCAAACGACATTTTCACATCAG
* * *
28700705 AGGCACATGGCCGTATGGTCCACCTGTGTGGGAGATCGTATGGCCCTAAACCTACACAAAATTTG
1 AGGCACATGGCCGTATAGTCCACCTGTATGGGAGACCGTATGGCCCTAAACCTACACAAAATTTG
* *
28700770 CCACAATTCACTTGCAAAAGAACACACACCTTTCACCGAAGGTCTTATCGACTTTCCTCACGATC
66 CCAAAATTCACTTGCAAAAGAACACACACCTTTCACCGAAGGTCTTATCGACGTTCCTCACGATC
** *
28700835 AAATCTAATCTGATTCACCTAAATCAGGTCCTTCAAACGACATTTTCA
131 AAATCTAATCCAATTCACCTAAATCAAGTCCTTCAAACGACATTTTCA
28700883 AATGAATTAA
Statistics
Matches: 165, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
184 165 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (184 bp):
AGGCACATGGCCGTATAGTCCACCTGTATGGGAGACCGTATGGCCCTAAACCTACACAAAATTTG
CCAAAATTCACTTGCAAAAGAACACACACCTTTCACCGAAGGTCTTATCGACGTTCCTCACGATC
AAATCTAATCCAATTCACCTAAATCAAGTCCTTCAAACGACATTTTCACATCAG
Found at i:28726028 original size:66 final size:66
Alignment explanation
Indices: 28725917--28726049 Score: 203
Period size: 66 Copynumber: 2.0 Consensus size: 66
28725907 GATAAGGTTA
* *
28725917 GATTGATTCTAGATCGTCTAAAAATGACTTCTGATAGACAAAAATCTTATGCAAACCTGAAAAGG
1 GATTGATTCTAGATCATCTAAAAATAACTTCTGATAGACAAAAATCTTATGCAAACCTGAAAAGG
28725982 C
66 C
* * * **
28725983 GATTGATTCTAGATCATTTAAAAATAACTTCTGATAGACAGAAATCTTATGCAGATTTGAAAAGG
1 GATTGATTCTAGATCATCTAAAAATAACTTCTGATAGACAAAAATCTTATGCAAACCTGAAAAGG
28726048 C
66 C
28726049 G
1 G
28726050 TGATATTGAG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (66 bp):
GATTGATTCTAGATCATCTAAAAATAACTTCTGATAGACAAAAATCTTATGCAAACCTGAAAAGG
C
Found at i:28729232 original size:23 final size:24
Alignment explanation
Indices: 28729200--28729246 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
28729190 CGTACCGCAC
*
28729200 ATGTTTCTTTT-TTAATAAA-ATTT
1 ATGTTCCTTTTATTAA-AAATATTT
28729223 ATGTTCCTTTTATTAAAAATATTT
1 ATGTTCCTTTTATTAAAAATATTT
28729247 TCTGGCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (24 bp):
ATGTTCCTTTTATTAAAAATATTT
Found at i:28739506 original size:6 final size:6
Alignment explanation
Indices: 28739495--28739527 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
28739485 TCCCACCACC
28739495 CCCATA CCCATA CCCATA CCCATA CCCATA CCC
1 CCCATA CCCATA CCCATA CCCATA CCCATA CCC
28739528 TCTCCCACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.30, C:0.55, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCATA
Found at i:28739865 original size:3 final size:3
Alignment explanation
Indices: 28739857--28739970 Score: 60
Period size: 3 Copynumber: 38.0 Consensus size: 3
28739847 TGTACCCTCT
* * *
28739857 TTA TTA TTA TTA GTA TTA TTA TTA TTTA TT- TTA TTTC TTG TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA
* * *
28739902 TTA TT- TTA TTA TT- TTA TT- TTCT TTA CTGA TTA TT- TTT TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA -TTA TTA TTA TTA TTA -TTA
* *
28739946 TTA TCTT TTA CTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA
28739971 GTCATTTTAG
Statistics
Matches: 87, Mismatches: 12, Indels: 24
0.71 0.10 0.20
Matches are distributed among these distances:
2 12 0.14
3 61 0.70
4 14 0.16
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28739890 original size:15 final size:14
Alignment explanation
Indices: 28739856--28739966 Score: 52
Period size: 16 Copynumber: 7.6 Consensus size: 14
28739846 TTGTACCCTC
*
28739856 TTTATTATTATTAGT
1 TTTATTATTTTTA-T
*
28739871 ATTATTATTATTTAT
1 TTTATTATT-TTTAT
* *
28739886 TTTA-T-TTCTTGT
1 TTTATTATTTTTAT
28739898 TTTATTATTTTATTAT
1 TTTATTA-TTT-TTAT
28739914 TTTATT-TTCTTTACT
1 TTTATTATT-TTTA-T
*
28739929 GATTATT-TTTTTA-
1 -TTTATTATTTTTAT
28739942 TTTATTATCTTTTACT
1 TTTATTAT-TTTTA-T
*
28739958 ATTATTATT
1 TTTATTATT
28739967 ATTAGTCATT
Statistics
Matches: 74, Mismatches: 10, Indels: 24
0.69 0.09 0.22
Matches are distributed among these distances:
12 12 0.16
13 4 0.05
14 11 0.15
15 21 0.28
16 26 0.35
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTATTATTTTTAT
Found at i:28739945 original size:28 final size:29
Alignment explanation
Indices: 28739856--28739970 Score: 105
Period size: 29 Copynumber: 4.0 Consensus size: 29
28739846 TTGTACCCTC
* *
28739856 TTTATTAT-TATTAGTATTATTATTATTTAT
1 TTTATTATCTTTTACTATTATT-TTA-TTAT
*
28739886 TTTATT-TCTTGTT-TTATTATTTTATTAT
1 TTTATTATCTT-TTACTATTATTTTATTAT
* *
28739914 TTTATTTTC-TTTACTGATTATTTTTTTA-
1 TTTATTATCTTTTACT-ATTATTTTATTAT
28739942 TTTATTATCTTTTACTATTATTATTATTA
1 TTTATTATCTTTTACTATTATT-TTATTA
28739971 GTCATTTTAG
Statistics
Matches: 72, Mismatches: 6, Indels: 15
0.77 0.06 0.16
Matches are distributed among these distances:
27 2 0.03
28 26 0.36
29 28 0.39
30 14 0.19
31 2 0.03
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.70
Consensus pattern (29 bp):
TTTATTATCTTTTACTATTATTTTATTAT
Found at i:28741003 original size:13 final size:13
Alignment explanation
Indices: 28740985--28741017 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
28740975 GGTTGTTTAT
28740985 TAAACTAATTAAC
1 TAAACTAATTAAC
28740998 TAAACTAATTAAC
1 TAAACTAATTAAC
28741011 T-AACTAA
1 TAAACTAA
28741018 ACTAAAGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAACTAATTAAC
Done.