Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 40 of 141
Found at i:12051871 original size:20 final size:20
Alignment explanation
Indices: 12051846--12051885 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
12051836 GATGAAAGAA
12051846 AGAAACGGGAATAGCTTTTG
1 AGAAACGGGAATAGCTTTTG
12051866 AGAAACGGGAATAGCTTTTG
1 AGAAACGGGAATAGCTTTTG
12051886 GGTAACAGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25
Consensus pattern (20 bp):
AGAAACGGGAATAGCTTTTG
Found at i:12055007 original size:32 final size:30
Alignment explanation
Indices: 12054908--12055007 Score: 73
Period size: 32 Copynumber: 3.2 Consensus size: 30
12054898 CACATCTATT
* *
12054908 AAAAATAAATAAAATAT-ATA-ATACATAATTC
1 AAAAATAAA-AAATTATAATATATACAT-A-TA
12054939 AAAAATAAAAAATTATAATATATACATTATA
1 AAAAATAAAAAATTATAATATATACA-TATA
*
12054970 TAAAATATAAAAATTCA-AATATATATCA-ATCA
1 AAAAATA-AAAAATT-ATAATATATA-CATAT-A
12055002 AAAAAT
1 AAAAAT
12055008 TATTAAATTA
Statistics
Matches: 58, Mismatches: 4, Indels: 13
0.77 0.05 0.17
Matches are distributed among these distances:
30 6 0.10
31 21 0.36
32 27 0.47
33 4 0.07
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (30 bp):
AAAAATAAAAAATTATAATATATACATATA
Found at i:12055024 original size:41 final size:40
Alignment explanation
Indices: 12054964--12055050 Score: 106
Period size: 41 Copynumber: 2.1 Consensus size: 40
12054954 TAATATATAC
*
12054964 ATTATATAAAATATAAAAATTCA-AATATATATCAATCAAAAA
1 ATTATATAAAATAAAAAAATT-ATAATATATA-CAA-CAAAAA
* *
12055006 ATTAT-TAAATTAAAAAAATTATAATATATAGAACAAAAA
1 ATTATATAAAATAAAAAAATTATAATATATACAACAAAAA
12055045 ATTATA
1 ATTATA
12055051 AACACATGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
39 11 0.28
40 3 0.08
41 21 0.52
42 5 0.12
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.32
Consensus pattern (40 bp):
ATTATATAAAATAAAAAAATTATAATATATACAACAAAAA
Found at i:12055176 original size:17 final size:16
Alignment explanation
Indices: 12055144--12055189 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
12055134 ACATCAATTA
12055144 TATAAAATAAAA-AAT
1 TATAAAATAAAATAAT
12055159 TATAAAATAAAAATAAT
1 TATAAAAT-AAAATAAT
12055176 TCA-AAAATGAAAAT
1 T-ATAAAAT-AAAAT
12055190 TTTATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 8 0.30
16 4 0.15
17 14 0.52
18 1 0.04
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (16 bp):
TATAAAATAAAATAAT
Found at i:12061688 original size:7 final size:7
Alignment explanation
Indices: 12061647--12061688 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
12061637 ATAAATATTT
12061647 ATTTTT-
1 ATTTTTA
12061653 ATTTTTA
1 ATTTTTA
*
12061660 TTTTTTA
1 ATTTTTA
*
12061667 TTTTTTA
1 ATTTTTA
12061674 ATTTTTA
1 ATTTTTA
12061681 ATTTTTA
1 ATTTTTA
12061688 A
1 A
12061689 ATACTTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
6 6 0.18
7 27 0.82
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
ATTTTTA
Found at i:12061731 original size:6 final size:7
Alignment explanation
Indices: 12061705--12061730 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12061695 TAAAAATATT
12061705 TTTTTTA
1 TTTTTTA
12061712 TTTTTTA
1 TTTTTTA
12061719 TTTTTTA
1 TTTTTTA
12061726 TTTTT
1 TTTTT
12061731 AAAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:12062160 original size:18 final size:18
Alignment explanation
Indices: 12062118--12062183 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
12062108 TTGTAAAATT
*
12062118 AATTATTAAAAATAGTAAA
1 AATTA-TAAAAATATTAAA
*
12062137 TGATTATAAAAATATTAAA
1 -AATTATAAAAATATTAAA
* *
12062156 AATTAT-AACATACTAAAA
1 AATTATAAAAATA-TTAAA
12062174 AATTATAAAA
1 AATTATAAAA
12062184 TTTATTGTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
17 5 0.13
18 15 0.39
19 14 0.37
20 4 0.11
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (18 bp):
AATTATAAAAATATTAAA
Found at i:12070259 original size:29 final size:29
Alignment explanation
Indices: 12070210--12070266 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
12070200 CCAACGTGCC
* *
12070210 TTCAAACCAATAACTCGGATATCACTTGG
1 TTCAAACCAACAACTCGGATACCACTTGG
* *
12070239 TTCAAACCAACAGCTCTGATACCACTTG
1 TTCAAACCAACAACTCGGATACCACTTG
12070267 TCACAGGGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.26
Consensus pattern (29 bp):
TTCAAACCAACAACTCGGATACCACTTGG
Found at i:12071459 original size:22 final size:22
Alignment explanation
Indices: 12071411--12071459 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
12071401 AAAAGATTCA
12071411 ATATTTATCGTTTAAAAAATGT
1 ATATTTATCGTTTAAAAAATGT
* *
12071433 -CATTTATTGTTTAATAAAAT-T
1 ATATTTATCGTTTAA-AAAATGT
12071454 ATATTT
1 ATATTT
12071460 TAAATGTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (22 bp):
ATATTTATCGTTTAAAAAATGT
Found at i:12074532 original size:8 final size:8
Alignment explanation
Indices: 12074515--12074544 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
12074505 TACTTTTATG
*
12074515 TTTTATTT
1 TTTTAATT
12074523 TTTTAATT
1 TTTTAATT
12074531 TTTTAATT
1 TTTTAATT
12074539 TTTTAA
1 TTTTAA
12074545 CTGAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTAATT
Found at i:12078917 original size:60 final size:60
Alignment explanation
Indices: 12078824--12078960 Score: 202
Period size: 60 Copynumber: 2.3 Consensus size: 60
12078814 CCACTATTCG
*
12078824 GCCCATTATTCTGCCCACTAACAAACCTAAGAGACTGACCTACATTCGGCCCAAAATGCT
1 GCCCATTATTCTGCCCACTAACAAACCCAAGAGACTGACCTACATTCGGCCCAAAATGCT
* * * ** *
12078884 GCCCATTATTCTGTCCACTAACAAGCCCAAGAGACTGGCCTGTATTCGGCCCAAAATGTT
1 GCCCATTATTCTGCCCACTAACAAACCCAAGAGACTGACCTACATTCGGCCCAAAATGCT
*
12078944 GCCTATTATTCTGCCCA
1 GCCCATTATTCTGCCCA
12078961 AGAAACTGGC
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 68 1.00
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (60 bp):
GCCCATTATTCTGCCCACTAACAAACCCAAGAGACTGACCTACATTCGGCCCAAAATGCT
Found at i:12083464 original size:120 final size:121
Alignment explanation
Indices: 12083317--12083542 Score: 391
Period size: 120 Copynumber: 1.9 Consensus size: 121
12083307 ATTTAATCAT
*
12083317 ATTTAAACATAAATATTATTAAATATATTATAATTAAAATATGTAATTTAATAAAATTCTTAATA
1 ATTTAAACATAAATATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
12083382 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
66 ATCAAAATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
* *
12083438 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAAATATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
12083502 ATCAAAATTTTTATATGAATTTACTAAAATCATAATATATG
66 ATCAAAATTCTTATATGAATTTACTAAAATCATAATATATG
12083543 CTTGAGAATT
Statistics
Matches: 99, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
120 95 0.96
121 4 0.04
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (121 bp):
ATTTAAACATAAATATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATCAAAATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
Found at i:12083480 original size:18 final size:17
Alignment explanation
Indices: 12083459--12083493 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12083449 TTATTATTAA
*
12083459 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
12083477 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
12083494 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:12085988 original size:33 final size:33
Alignment explanation
Indices: 12085946--12086011 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
12085936 ATCATAAAGC
12085946 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
*
12085979 ATGTGTAATTGACCTAAAATTAATTGTTGGTAT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
12086012 TTTTTAGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTAT
Found at i:12086311 original size:37 final size:37
Alignment explanation
Indices: 12086226--12086312 Score: 147
Period size: 37 Copynumber: 2.4 Consensus size: 37
12086216 GTATAAATAT
* * *
12086226 ATTGATTAGTTCATTAAAGCATGTTCAAAGTTTTAAC
1 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
12086263 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
1 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
12086300 ATTGATTAGTTTA
1 ATTGATTAGTTTA
12086313 TTTATTTATG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (37 bp):
ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
Found at i:12087526 original size:23 final size:23
Alignment explanation
Indices: 12087487--12087549 Score: 94
Period size: 23 Copynumber: 2.7 Consensus size: 23
12087477 TCTACTGACT
12087487 AACAAATCAAGAACAATTTCCAG
1 AACAAATCAAGAACAATTTCCAG
12087510 TAGAC-AATCAA-AACAATTTCCAG
1 -A-ACAAATCAAGAACAATTTCCAG
12087533 AACAAATCAAGAACAAT
1 AACAAATCAAGAACAAT
12087550 ATCAAAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
21 2 0.06
22 7 0.19
23 18 0.50
24 7 0.19
25 2 0.06
ACGTcount: A:0.54, C:0.21, G:0.08, T:0.17
Consensus pattern (23 bp):
AACAAATCAAGAACAATTTCCAG
Found at i:12087593 original size:107 final size:107
Alignment explanation
Indices: 12087463--12087752 Score: 472
Period size: 107 Copynumber: 2.7 Consensus size: 107
12087453 ACAAATCAAG
* * *
12087463 TTCCAGTTTCATATTCTACTGACTAACAAATCAAGAACAATTTCCAGTAGACAATCAAAACAATT
1 TTCCAGTTTCATCTTCTACTGACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACAATT
12087528 TCCAGAACAAATCAAGAACAATATCAAAACAAATGCAACAAT
66 TCCAGAACAAATCAAGAACAATATCAAAACAAATGCAACAAT
* * *
12087570 TTTCAGTTTTATCTTCTACTGACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACAACT
1 TTCCAGTTTCATCTTCTACTGACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACAATT
* *
12087635 GCCAGAACAATTCAAGAACAATATCAAAACAAATGCAACAAT
66 TCCAGAACAAATCAAGAACAATATCAAAACAAATGCAACAAT
* * * *
12087677 TTCCAGTTTCATCTTCTACTCACTAACAAATCAATAACATTTTTCAGCAGACTATCAAAACAATT
1 TTCCAGTTTCATCTTCTACTGACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACAATT
12087742 TCCAGAACAAA
66 TCCAGAACAAA
12087753 CCAATAAAAT
Statistics
Matches: 166, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
107 166 1.00
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (107 bp):
TTCCAGTTTCATCTTCTACTGACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACAATT
TCCAGAACAAATCAAGAACAATATCAAAACAAATGCAACAAT
Found at i:12088408 original size:5 final size:5
Alignment explanation
Indices: 12088398--12088424 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
12088388 TGAGATAAAC
12088398 ATCTA ATCTA ATCTA ATCTA ATCTA AT
1 ATCTA ATCTA ATCTA ATCTA ATCTA AT
12088425 GATTGTAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (5 bp):
ATCTA
Found at i:12090310 original size:12 final size:13
Alignment explanation
Indices: 12090288--12090317 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
12090278 GTAATTTAAT
12090288 TAATATTTTTTTA
1 TAATATTTTTTTA
12090301 TAAT-TTTTTTTA
1 TAATATTTTTTTA
12090313 TAATA
1 TAATA
12090318 GTCAGTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TAATATTTTTTTA
Found at i:12092307 original size:59 final size:59
Alignment explanation
Indices: 12092233--12092458 Score: 337
Period size: 59 Copynumber: 3.8 Consensus size: 59
12092223 ATTGATTTAT
* *
12092233 TTTTGAATATATTTGTACAAATTATTTTTATATTGTTTTATTTAATAAAATAGAAGTTC
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
* * * *
12092292 TTTTGAATATTTTTGTACAAATTATTTTTATATTATTTCTTTTAATAAAACAAAAGTTC
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
* *
12092351 TTTTGAATATTTTTGTACAAAATATTTTTATATTGTTTCATTCAATAAAATAGAAGTTC
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
* * *
12092410 TTTAGAATATGTTTGTGCAAATTATTTTT-TCATTGTTTCATTTAATAAA
1 TTTTGAATATTTTTGTACAAATTATTTTTAT-ATTGTTTCATTTAATAAA
12092459 TTAGGAATTA
Statistics
Matches: 149, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
58 1 0.01
59 148 0.99
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.52
Consensus pattern (59 bp):
TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
Found at i:12095738 original size:156 final size:155
Alignment explanation
Indices: 12095476--12095793 Score: 422
Period size: 156 Copynumber: 2.0 Consensus size: 155
12095466 CAACTGGGAA
* * * ** *
12095476 CTTTTTCAGTACTTTTGCTGACAGTGTATCCTGCTTGAAGCGTTTTTCATCCCCAACTATCAGAT
1 CTTTTTCAGTACTTTTGCTAACAGTGCATCCTACTTGAAGCACTTTTCAACCCCAACTATCAGAT
* ** * *
12095541 TTCCCATGAATCCCAGGATATTTTTTGAAAACCATCTTCTCAAAATTATTTTTTCAGAACCAATA
66 TTCCCAAGAATCCCAGGATAAATTTTCAAAACCAGCTTCTCAAAATTA-TTTTTCAGAACCAATA
12095606 GTACAAAAAAAGTATCTAGCTAGGAG
130 GTACAAAAAAAGTATCTAGCTAGGAG
* * *
12095632 CTTTTTTAGTATTTTTGCTAACAGTGCATCCTACTTGAAGCACTTTTCAACCCCAACTATTAGAT
1 CTTTTTCAGTACTTTTGCTAACAGTGCATCCTACTTGAAGCACTTTTCAACCCCAACTATCAGAT
* * * *
12095697 TTCCCAAGAATCTCGGGATAAATTTTCAAAACCCGCTTCTCAAAATTATTTTTCAGAATCAATAG
66 TTCCCAAGAATCCCAGGATAAATTTTCAAAACCAGCTTCTCAAAATTATTTTTCAGAACCAATAG
** *
12095762 TACAAAAAAACCATCCAGCT-GGAAG
131 TACAAAAAAAGTATCTAGCTAGG-AG
12095787 CTTTTTC
1 CTTTTTC
12095794 TATACAATTA
Statistics
Matches: 139, Mismatches: 22, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
154 2 0.01
155 41 0.29
156 96 0.69
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (155 bp):
CTTTTTCAGTACTTTTGCTAACAGTGCATCCTACTTGAAGCACTTTTCAACCCCAACTATCAGAT
TTCCCAAGAATCCCAGGATAAATTTTCAAAACCAGCTTCTCAAAATTATTTTTCAGAACCAATAG
TACAAAAAAAGTATCTAGCTAGGAG
Found at i:12095883 original size:30 final size:30
Alignment explanation
Indices: 12095847--12095919 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
12095837 ATCAAAATAA
12095847 TTTTTTCAGAACACATCACGTCAAATTTAT
1 TTTTTTCAGAACACATCACGTCAAATTTAT
* * * **
12095877 TTTTTTCATATCTCATCTTGTCAAATTTAT
1 TTTTTTCAGAACACATCACGTCAAATTTAT
* *
12095907 TTCTTCCAGAACA
1 TTTTTTCAGAACA
12095920 ATACTTACCA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.45
Consensus pattern (30 bp):
TTTTTTCAGAACACATCACGTCAAATTTAT
Found at i:12103867 original size:16 final size:17
Alignment explanation
Indices: 12103847--12103905 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
12103837 CGTAGGTTCT
12103847 TCTTTCTTTCTCTTTT-
1 TCTTTCTTTCTCTTTTG
12103863 TCTTTTTCTTTCT-TTTTG
1 TC--TTTCTTTCTCTTTTG
*
12103881 T-TTTGTTT-TGCTTTTG
1 TCTTTCTTTCT-CTTTTG
12103897 TCTTTCTTT
1 TCTTTCTTT
12103906 ATTTCTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
14 1 0.03
15 6 0.17
16 8 0.23
17 10 0.29
18 10 0.29
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (17 bp):
TCTTTCTTTCTCTTTTG
Found at i:12116032 original size:40 final size:40
Alignment explanation
Indices: 12115977--12116053 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
12115967 CACCATTCTA
* *
12115977 CTACAGGGTACTAACAACTGTGCGATATCTTTTATTTTTG
1 CTACAGGGTACTAACAACTGTGCGACATCTTTCATTTTTG
12116017 CTACAGGGTACTAACAACTGTGCGACATCTTTCATTT
1 CTACAGGGTACTAACAACTGTGCGACATCTTTCATTT
12116054 CATTCCTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (40 bp):
CTACAGGGTACTAACAACTGTGCGACATCTTTCATTTTTG
Found at i:12126533 original size:7 final size:7
Alignment explanation
Indices: 12126523--12126578 Score: 62
Period size: 7 Copynumber: 8.0 Consensus size: 7
12126513 AGGAATGAGG
12126523 ATTGAAA
1 ATTGAAA
12126530 ATTGAAA
1 ATTGAAA
*
12126537 ACTGAAA
1 ATTGAAA
12126544 ATT-AAA
1 ATTGAAA
*
12126550 ATTTGAAT
1 A-TTGAAA
12126558 ATTGAAA
1 ATTGAAA
12126565 ATAT-AAA
1 AT-TGAAA
12126572 ATTGAAA
1 ATTGAAA
12126579 TTGGGAAAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
6 5 0.12
7 32 0.78
8 4 0.10
ACGTcount: A:0.57, C:0.02, G:0.11, T:0.30
Consensus pattern (7 bp):
ATTGAAA
Found at i:12128426 original size:13 final size:13
Alignment explanation
Indices: 12128408--12128434 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12128398 TCTTACAACT
12128408 ATGCATTAACCAA
1 ATGCATTAACCAA
12128421 ATGCATTAACCAA
1 ATGCATTAACCAA
12128434 A
1 A
12128435 AACTCATCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.07, T:0.22
Consensus pattern (13 bp):
ATGCATTAACCAA
Found at i:12129347 original size:16 final size:16
Alignment explanation
Indices: 12129326--12129360 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12129316 TACTATTTGT
12129326 TTTCATT-TTATTTTTA
1 TTTCATTGTTA-TTTTA
12129342 TTTCATTGTTATTTTA
1 TTTCATTGTTATTTTA
12129358 TTT
1 TTT
12129361 ACTCATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTCATTGTTATTTTA
Found at i:12132304 original size:20 final size:20
Alignment explanation
Indices: 12132275--12132350 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
12132265 TATTTTCTAA
*
12132275 CCATTCCATTTACTTACTTT
1 CCATTTCATTTACTTACTTT
* *
12132295 CTATTTCATTTACTCACTTT
1 CCATTTCATTTACTTACTTT
12132315 CCATTTCATTTACTTACTTT
1 CCATTTCATTTACTTACTTT
*
12132335 CCATTCCATTTACTTA
1 CCATTTCATTTACTTA
12132351 GCATAAACTT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.21, C:0.28, G:0.00, T:0.51
Consensus pattern (20 bp):
CCATTTCATTTACTTACTTT
Found at i:12133383 original size:138 final size:139
Alignment explanation
Indices: 12133134--12133407 Score: 356
Period size: 138 Copynumber: 2.0 Consensus size: 139
12133124 CCATAAAATA
* * *
12133134 GGTTTGTTCACACAAGCTGACGGTCGGAATATAAACTATACGATACCGCTCACACAAACTGAACG
1 GGTTTGCTCACACAAGCTGACGGTCGGAATATAAACTACACAATACCGCTCACACAAACTGAACG
*
12133199 ACTATCCGCAACAAATGTCGAAACTCAACCATTGGTAGGACATTCAGGA-CTAGCACTCGAAACA
66 ACTATCCGCAACAAATGTCGAAACTCAACCATTGGTAGGACATTCAGGATC-AGCACTCGAAAAA
*
12133263 TGGTAACTTG
130 TGATAACTTG
* * * * * * * *
12133273 GGTTTGCTCACACAAGTTGATGGTCGGAATGTAAGCTACACAATGCTGCTCACACAAGCTG-ATG
1 GGTTTGCTCACACAAGCTGACGGTCGGAATATAAACTACACAATACCGCTCACACAAACTGAACG
* * * *
12133337 AGTATCC-CAAACAAATGTCGAACCTCAGCCATTGGTAGGATATTCAGGATCAGCACTCGAAAAA
66 ACTATCCGC-AACAAATGTCGAAACTCAACCATTGGTAGGACATTCAGGATCAGCACTCGAAAAA
12133401 TGATAAC
130 TGATAAC
12133408 CATAATGACA
Statistics
Matches: 116, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
137 1 0.01
138 63 0.54
139 52 0.45
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.22
Consensus pattern (139 bp):
GGTTTGCTCACACAAGCTGACGGTCGGAATATAAACTACACAATACCGCTCACACAAACTGAACG
ACTATCCGCAACAAATGTCGAAACTCAACCATTGGTAGGACATTCAGGATCAGCACTCGAAAAAT
GATAACTTG
Found at i:12142248 original size:41 final size:41
Alignment explanation
Indices: 12142191--12142299 Score: 175
Period size: 41 Copynumber: 2.7 Consensus size: 41
12142181 TTTAACATAT
*
12142191 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCCA-A
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT-CAGA
*
12142232 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
12142273 TCACCGGCACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
12142300 AAGTCCGAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 2 0.03
41 61 0.97
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:12142318 original size:41 final size:40
Alignment explanation
Indices: 12142191--12142336 Score: 165
Period size: 41 Copynumber: 3.6 Consensus size: 40
12142181 TTTAACATAT
*
12142191 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCCAA
1 TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT-CAA
*
12142232 TCACCGGCACTTAGCCTGCTAGGTTTATAA-CCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTA-AAGCCTGATTCA-A
* *
12142273 TCACCGGCACTTAGCCTGCTAGACTTAAAGTCC-GAATT-ATT
1 TCACCGGCACTTAGCCTGCTAGGCTTAAAG-CCTG-ATTCA-A
12142314 TCACCGGC-CTTAAGCCTGCTAGG
1 TCACCGGCACTT-AGCCTGCTAGG
12142337 TTTTAAATCT
Statistics
Matches: 92, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
40 7 0.08
41 79 0.86
42 6 0.07
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.27
Consensus pattern (40 bp):
TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAA
Found at i:12165080 original size:15 final size:16
Alignment explanation
Indices: 12165060--12165089 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12165050 CTTGTTTCCC
12165060 AAAGTGGA-GGAAAGA
1 AAAGTGGATGGAAAGA
12165075 AAAGTGGATGGAAAG
1 AAAGTGGATGGAAAG
12165090 GGGATCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.00, G:0.40, T:0.10
Consensus pattern (16 bp):
AAAGTGGATGGAAAGA
Found at i:12175796 original size:70 final size:70
Alignment explanation
Indices: 12175683--12175818 Score: 254
Period size: 70 Copynumber: 1.9 Consensus size: 70
12175673 GTTGCCCAAC
* *
12175683 GTTGTCTTTCTTCTTGTTTTTACTTATTTCATTTTGAGTTCAAATTATTTATTTCATTTCTTGCA
1 GTTGTCTTTCTTCTTGTTTTTACTTATGTCATTTTGAGTTCAAAATATTTATTTCATTTCTTGCA
12175748 TCAAT
66 TCAAT
12175753 GTTGTCTTTCTTCTTGTTTTTACTTATGTCATTTTGAGTTCAAAATATTTATTTCATTTCTTGCA
1 GTTGTCTTTCTTCTTGTTTTTACTTATGTCATTTTGAGTTCAAAATATTTATTTCATTTCTTGCA
12175818 T
66 T
12175819 TGGCTTGTTG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.18, C:0.14, G:0.10, T:0.58
Consensus pattern (70 bp):
GTTGTCTTTCTTCTTGTTTTTACTTATGTCATTTTGAGTTCAAAATATTTATTTCATTTCTTGCA
TCAAT
Found at i:12186800 original size:29 final size:29
Alignment explanation
Indices: 12186755--12186837 Score: 130
Period size: 29 Copynumber: 2.9 Consensus size: 29
12186745 AAAGAGGTGG
* *
12186755 AGAACTTGTTCGTTGAGAGTTCGTGGTAA
1 AGAACTTATTCATTGAGAGTTCGTGGTAA
* *
12186784 AGAGCTTATTCATTGAGAATTCGTGGTAA
1 AGAACTTATTCATTGAGAGTTCGTGGTAA
12186813 AGAACTTATTCATTGAGAGTTCGTG
1 AGAACTTATTCATTGAGAGTTCGTG
12186838 TCATGGTGGA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.28, C:0.11, G:0.27, T:0.35
Consensus pattern (29 bp):
AGAACTTATTCATTGAGAGTTCGTGGTAA
Found at i:12193658 original size:28 final size:26
Alignment explanation
Indices: 12193611--12193662 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
12193601 ATATTATTAA
*
12193611 TATAATATATATATGTTATAATAAGG
1 TATAATATATATATATTATAATAAGG
12193637 TATAATATATTATTATATTATAATAA
1 TATAATATA-TA-TATATTATAATAA
12193663 ACATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 9 0.39
27 2 0.09
28 12 0.52
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (26 bp):
TATAATATATATATATTATAATAAGG
Found at i:12194561 original size:41 final size:41
Alignment explanation
Indices: 12194504--12194655 Score: 182
Period size: 41 Copynumber: 3.7 Consensus size: 41
12194494 CTGTAAGTTT
*
12194504 AGGCTTTATGCCTAGCAGGTTTTATGCCAGTAAATTATATC
1 AGGCTTTATGCCTAGCAGGCTTTATGCCAGTAAATTATATC
* * *
12194545 AGGCTTTATGCCTAGCAGGCTTTGTGCCGGTGAATTATATC
1 AGGCTTTATGCCTAGCAGGCTTTATGCCAGTAAATTATATC
* * * * *
12194586 AGACTTTAT-TCTAGCAGGCTTTGTGCCGGTGAAA-TGTATC
1 AGGCTTTATGCCTAGCAGGCTTTATGCCAGT-AAATTATATC
* *
12194626 GGGCTTTGTGCCTAGCAGGCTTTATGCCAG
1 AGGCTTTATGCCTAGCAGGCTTTATGCCAG
12194656 CGTTTTATAC
Statistics
Matches: 95, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
40 31 0.33
41 64 0.67
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (41 bp):
AGGCTTTATGCCTAGCAGGCTTTATGCCAGTAAATTATATC
Found at i:12195384 original size:112 final size:112
Alignment explanation
Indices: 12195248--12195470 Score: 437
Period size: 112 Copynumber: 2.0 Consensus size: 112
12195238 GGATATGTGA
*
12195248 ATATGAGCCATGCGAAAATGGCTTATTCATTTTGGTTAAGCTTGGTTTTATGTTTTTGATCTATT
1 ATATGAGCCAAGCGAAAATGGCTTATTCATTTTGGTTAAGCTTGGTTTTATGTTTTTGATCTATT
12195313 GATATATATATGATGTTTAAGTTTATGCAAATTTCGGTTATATATAG
66 GATATATATATGATGTTTAAGTTTATGCAAATTTCGGTTATATATAG
12195360 ATATGAGCCAAGCGAAAATGGCTTATTCATTTTGGTTAAGCTTGGTTTTATGTTTTTGATCTATT
1 ATATGAGCCAAGCGAAAATGGCTTATTCATTTTGGTTAAGCTTGGTTTTATGTTTTTGATCTATT
12195425 GATATATATATGATGTTTAAGTTTATGCAAATTTCGGTTATATATA
66 GATATATATATGATGTTTAAGTTTATGCAAATTTCGGTTATATATA
12195471 TATAGAAGTG
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 110 1.00
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.45
Consensus pattern (112 bp):
ATATGAGCCAAGCGAAAATGGCTTATTCATTTTGGTTAAGCTTGGTTTTATGTTTTTGATCTATT
GATATATATATGATGTTTAAGTTTATGCAAATTTCGGTTATATATAG
Found at i:12195705 original size:24 final size:24
Alignment explanation
Indices: 12195678--12195780 Score: 63
Period size: 23 Copynumber: 4.5 Consensus size: 24
12195668 TATGCTATTA
12195678 AATTTTGGTATAAAAATGCTGCTC
1 AATTTTGGTATAAAAATGCTGCTC
** * *
12195702 AA-TTTGGTATGTATATGTTGC-C
1 AATTTTGGTATAAAAATGCTGCTC
* * * * * *
12195724 TATTTGTTGTAT--ATATGTTGTTA
1 AATTT-TGGTATAAAAATGCTGCTC
*
12195747 AATTTTGGTGTAAAAATGCTGCTC
1 AATTTTGGTATAAAAATGCTGCTC
12195771 AA-TTTGGTAT
1 AATTTTGGTAT
12195781 GTATATGCTG
Statistics
Matches: 58, Mismatches: 16, Indels: 11
0.68 0.19 0.13
Matches are distributed among these distances:
22 14 0.24
23 28 0.48
24 16 0.28
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (24 bp):
AATTTTGGTATAAAAATGCTGCTC
Found at i:12195783 original size:69 final size:69
Alignment explanation
Indices: 12195572--12195975 Score: 593
Period size: 69 Copynumber: 5.9 Consensus size: 69
12195562 GTATATGATG
*
12195572 TGGTATGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTATAAAAATGCTGCTC
1 TGGTATGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTC
12195637 AATT
66 AATT
* *
12195641 TGGTATGTATATGCTGCCTATTTGTTG----TATGCTATTAAATTTTGGTATAAAAATGCTGCTC
1 TGGTATGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTC
12195702 AATT
66 AATT
* *
12195706 TGGTATGTATATGTTGCCTATTTGTTGTATATATGTTGTTAAATTTTGGTGTAAAAATGCTGCTC
1 TGGTATGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTC
12195771 AATT
66 AATT
* * ** * *
12195775 TGGTATGTATATGCTGCCCATTTGTTGTATATATGCTGTTAAATTTTTGTGTAAATGTGCTGTTA
1 TGGTATGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTC
12195840 AATT
66 AATT
* * *
12195844 TGGTATGTATATGCTGCCTATTTGCTGTATATATGCTGTTAAATTTTGGTGTAAAAGTGCTG-TT
1 TGGTATGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTC
12195908 AATTT
66 AA-TT
* * * *
12195913 TGGTATGTATATGCTGCCCATTTGTTGTATATAAGCTGTCCAAATTTTGGTGTATAAATGCTG
1 TGGTATGTATATGCTGCCTATTTGTTGTATATATGCTGT-TAAATTTTGGTGTAAAAATGCTG
12195976 TCCAAATTGA
Statistics
Matches: 305, Mismatches: 24, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
65 63 0.21
68 3 0.01
69 219 0.72
70 20 0.07
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.46
Consensus pattern (69 bp):
TGGTATGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTC
AATT
Found at i:12195827 original size:24 final size:24
Alignment explanation
Indices: 12195726--12195976 Score: 137
Period size: 24 Copynumber: 10.8 Consensus size: 24
12195716 ATGTTGCCTA
* *
12195726 TTTGTTGTATATATGTTGTTAAAT
1 TTTGGTGTATATATGCTGTTAAAT
* * * *
12195750 TTTGGTGTAAAAATGCTGCTCAA-
1 TTTGGTGTATATATGCTGTTAAAT
* * ***
12195773 TTTGGTATGTATATGCTG-CCCA-
1 TTTGGTGTATATATGCTGTTAAAT
*
12195795 TTTGTTGTATATATGCTGTTAAAT
1 TTTGGTGTATATATGCTGTTAAAT
* * *
12195819 TTTTGTGTAAATGTGCTGTTAAA-
1 TTTGGTGTATATATGCTGTTAAAT
* * *
12195842 TTTGGTATGTATATGCTGCCT--A-
1 TTTGGTGTATATATGCTG-TTAAAT
*
12195864 TTTGCTGTATATATGCTGTTAAAT
1 TTTGGTGTATATATGCTGTTAAAT
*
12195888 TTTGGTGTA-AAAGTGCTGTT-AAT
1 TTTGGTGTATATA-TGCTGTTAAAT
* * ***
12195911 TTTGGTATGTATATGCTG-CCCA-
1 TTTGGTGTATATATGCTGTTAAAT
* * *
12195933 TTTGTTGTATATAAGCTGTCCAAAT
1 TTTGGTGTATATATGCTGT-TAAAT
*
12195958 TTTGGTGTATAAATGCTGT
1 TTTGGTGTATATATGCTGT
12195977 CCAAATTGAT
Statistics
Matches: 167, Mismatches: 48, Indels: 23
0.70 0.20 0.10
Matches are distributed among these distances:
21 1 0.01
22 47 0.28
23 47 0.28
24 56 0.34
25 16 0.10
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.46
Consensus pattern (24 bp):
TTTGGTGTATATATGCTGTTAAAT
Found at i:12195989 original size:23 final size:23
Alignment explanation
Indices: 12195932--12196004 Score: 85
Period size: 23 Copynumber: 3.0 Consensus size: 23
12195922 TATGCTGCCC
*
12195932 ATTTGTTGTATATAAGCTGTCCAA
1 ATTTGATGTATA-AAGCTGTCCAA
*
12195956 ATTTTGGTGTATAAATGCTGTCCAA
1 A-TTTGATGTATAAA-GCTGTCCAA
12195981 A-TTGATGTATAAGAGCTGTCCAA
1 ATTTGATGTATAA-AGCTGTCCAA
12196004 A
1 A
12196005 CAAGGTAGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
23 20 0.45
24 4 0.09
25 20 0.45
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (23 bp):
ATTTGATGTATAAAGCTGTCCAA
Found at i:12200277 original size:25 final size:25
Alignment explanation
Indices: 12200248--12200299 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
12200238 GTTATCAAAG
*
12200248 TCCCATTGATAGTAAGTGGAATCAT
1 TCCCACTGATAGTAAGTGGAATCAT
12200273 TCCCACTGATAGTAAGTGGAATCAT
1 TCCCACTGATAGTAAGTGGAATCAT
12200298 TC
1 TC
12200300 ACATCGGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (25 bp):
TCCCACTGATAGTAAGTGGAATCAT
Found at i:12210593 original size:13 final size:14
Alignment explanation
Indices: 12210565--12210599 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
12210555 AAAAATATTA
12210565 TTATTTAATAATTT
1 TTATTTAATAATTT
12210579 TTATTTAATAA-TT
1 TTATTTAATAATTT
12210592 TTATTTAA
1 TTATTTAA
12210600 GTGGATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTATTTAATAATTT
Found at i:12217891 original size:37 final size:37
Alignment explanation
Indices: 12217830--12217975 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
12217820 TACGTATGAT
* *
12217830 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
12217865 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
12217902 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
12217939 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
12217976 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:12217992 original size:46 final size:46
Alignment explanation
Indices: 12217939--12218207 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
12217929 TAAGTGTAGC
* **
12217939 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
12217985 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
12218031 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
12218083 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
12218129 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
12218181 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
12218208 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:12218058 original size:52 final size:52
Alignment explanation
Indices: 12217982--12218201 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
12217972 TAGCTAAAGC
* *
12217982 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
12218035 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
12218087 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
12218133 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
12218185 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
12218202 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:12218104 original size:98 final size:98
Alignment explanation
Indices: 12217939--12218207 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
12217929 TAAGTGTAGC
* * *
12217939 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
12218004 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
12218038 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
12218103 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
12218136 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
12218201 GATCAGA
66 GATCAGA
12218208 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:12221566 original size:26 final size:24
Alignment explanation
Indices: 12221525--12221574 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
12221515 TTTTCATTCT
* *
12221525 TTTTAAATAATTTTAATAATTTTTAA
1 TTTTAAAAAATATTAAT--TTTTTAA
12221551 TTTTAAAAAATATTAATTTTTTAA
1 TTTTAAAAAATATTAATTTTTTAA
12221575 AATTTTCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
26 15 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTTAAAAAATATTAATTTTTTAA
Found at i:12221577 original size:16 final size:16
Alignment explanation
Indices: 12221532--12221570 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
12221522 TCTTTTTAAA
* * *
12221532 TAATTTTAATAATTTT
1 TAATTTTAAAAAATAT
12221548 TAATTTTAAAAAATAT
1 TAATTTTAAAAAATAT
12221564 TAATTTT
1 TAATTTT
12221571 TTAAAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATTTTAAAAAATAT
Found at i:12223859 original size:29 final size:29
Alignment explanation
Indices: 12223764--12223879 Score: 112
Period size: 29 Copynumber: 4.0 Consensus size: 29
12223754 ACATTCAGCG
*
12223764 CACTCTTGTTCTGTTA-TGCACTTCGGTGC
1 CACT-TTGTTCTGATATTGCACTTCGGTGC
* * **
12223793 CACTCTATTCTGATAGAGCACTTCGGTGC
1 CACTTTGTTCTGATATTGCACTTCGGTGC
*
12223822 TA-TTCTGTT-TGGATATTGCACTTCGGTGC
1 CACTT-TGTTCT-GATATTGCACTTCGGTGC
* *
12223851 CACTTTGTTCTGTTATTGCACTTTGGTGC
1 CACTTTGTTCTGATATTGCACTTCGGTGC
12223880 AACTCTGCAT
Statistics
Matches: 70, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
28 10 0.14
29 57 0.81
30 3 0.04
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.41
Consensus pattern (29 bp):
CACTTTGTTCTGATATTGCACTTCGGTGC
Found at i:12225666 original size:43 final size:43
Alignment explanation
Indices: 12225601--12225686 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
12225591 TATGTGATTT
12225601 ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAAA
1 ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAAA
* *
12225644 ATATTGAAATGGCAAAGTTGAGAAATGATTATGAGATGAGAAA
1 ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAAA
12225687 TGAAATATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.49, C:0.02, G:0.26, T:0.23
Consensus pattern (43 bp):
ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAAA
Found at i:12229618 original size:18 final size:17
Alignment explanation
Indices: 12229595--12229629 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12229585 ATATACTCAT
*
12229595 AAAATAACAAAGTAAATA
1 AAAATAAAAAAG-AAATA
12229613 AAAATAAAAAAGAAATA
1 AAAATAAAAAAGAAATA
12229630 TGAGAACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAATAAAAAAGAAATA
Found at i:12233911 original size:19 final size:20
Alignment explanation
Indices: 12233873--12233911 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
12233863 TGGAATGCTA
* *
12233873 AAATAAATTTTTATACTTTT
1 AAATAAATTTTAATAATTTT
12233893 AAAT-AATTTTAATAATTTT
1 AAATAAATTTTAATAATTTT
12233912 TATGAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
AAATAAATTTTAATAATTTT
Found at i:12233922 original size:10 final size:9
Alignment explanation
Indices: 12233878--12233929 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
12233868 TGCTAAAATA
12233878 AATTTTTAT
1 AATTTTTAT
* *
12233887 ACTTTTAAAT
1 AATTTT-TAT
*
12233897 AATTTTAAT
1 AATTTTTAT
12233906 AATTTTTAT
1 AATTTTTAT
*
12233915 GAATTTTTAA
1 -AATTTTTAT
12233925 AATTT
1 AATTT
12233930 AAAAATTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 21 0.58
10 15 0.42
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (9 bp):
AATTTTTAT
Found at i:12234577 original size:26 final size:26
Alignment explanation
Indices: 12234548--12234635 Score: 106
Period size: 26 Copynumber: 3.4 Consensus size: 26
12234538 TTGCTATTAA
* *
12234548 AATTTAATAAGATTATTATTAAATAT
1 AATTTAATAATATCATTATTAAATAT
* *
12234574 AATTTAATAATA-CATAATTTAATCAT
1 AATTTAATAATATCATTATTAAAT-AT
* *
12234600 ATTTTAATATTATCATTATTAAATAT
1 AATTTAATAATATCATTATTAAATAT
12234626 AATTTAATAA
1 AATTTAATAA
12234636 AAATAAAATA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
25 8 0.16
26 33 0.66
27 9 0.18
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (26 bp):
AATTTAATAATATCATTATTAAATAT
Found at i:12234655 original size:49 final size:52
Alignment explanation
Indices: 12234548--12234658 Score: 138
Period size: 52 Copynumber: 2.2 Consensus size: 52
12234538 TTGCTATTAA
* * **
12234548 AATTTAATAAGATTATTATTAAATATAATTTAATAATACATAATTTAATCAT
1 AATTTAATAAGATCATTATTAAATATAATTTAATAATAAATAAAATAATCAT
* **
12234600 ATTTTAATATTATCATTATTAAATATAATTTAATAA-AAATAAAAT-AT-AT
1 AATTTAATAAGATCATTATTAAATATAATTTAATAATAAATAAAATAATCAT
12234649 AATTTAATAA
1 AATTTAATAA
12234659 CATTCTTAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
49 10 0.20
50 2 0.04
51 6 0.12
52 32 0.64
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (52 bp):
AATTTAATAAGATCATTATTAAATATAATTTAATAATAAATAAAATAATCAT
Found at i:12234910 original size:10 final size:10
Alignment explanation
Indices: 12234895--12234919 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12234885 TTTATTTTCA
12234895 TTCTTCCCTT
1 TTCTTCCCTT
12234905 TTCTTCCCTT
1 TTCTTCCCTT
12234915 TTCTT
1 TTCTT
12234920 TTTTTGGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (10 bp):
TTCTTCCCTT
Found at i:12237445 original size:13 final size:13
Alignment explanation
Indices: 12237427--12237456 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12237417 AAACTAGATT
*
12237427 TTAACTAAGTAAA
1 TTAACTAAGAAAA
12237440 TTAACTAAGAAAA
1 TTAACTAAGAAAA
12237453 TTAA
1 TTAA
12237457 AAAGGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (13 bp):
TTAACTAAGAAAA
Found at i:12251850 original size:100 final size:96
Alignment explanation
Indices: 12251727--12252018 Score: 387
Period size: 100 Copynumber: 3.0 Consensus size: 96
12251717 ATTACAGTGG
*
12251727 AAAAGATTGAAGCCACGACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
*
12251792 CAACGGCAGATCTGGTTTCTCCGACATTGCAATT
66 CGACGGC-GATCTGGTTTC-CCGACATTGCAA-T
* * *
12251826 AAAAAAATTGAAGCCACAATGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCT
1 -AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCT
* *
12251891 ATGACGGCGGATTTGGTTTCCCTGACATTGC---
65 ACGACGGC-GATCTGGTTTCCC-GACATTGCAAT
*
12251922 -AAAGATTGAAG-CACAACGACGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
* *
12251985 CGACGACGAATCTTGTTTCCTCGACATTGCAAT
66 CGACGGCG-ATCTGGTTTCC-CGACATTGCAAT
12252018 A
1 A
12252019 GGTCGGATTA
Statistics
Matches: 169, Mismatches: 16, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
92 1 0.01
93 71 0.42
94 11 0.07
99 2 0.01
100 84 0.50
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.25
Consensus pattern (96 bp):
AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
CGACGGCGATCTGGTTTCCCGACATTGCAAT
Found at i:12251998 original size:50 final size:50
Alignment explanation
Indices: 12251721--12251985 Score: 206
Period size: 50 Copynumber: 5.4 Consensus size: 50
12251711 TTTAGCATTA
* * *
12251721 CAGTGGAAAAGATTGAAGCCACGACGGCGGATCTTACTTCCCTGGCGGTG
1 CAGTGGAACAGATTGAAGCTACAACGGCGGATCTTACTTCCCTGGCGGTG
* * *** * **
12251771 TAGTGGAACAGATTGAAGCTACAACGGCAGATCTGGTTTCTCC-GACATTG
1 CAGTGGAACAGATTGAAGCTACAACGGCGGATCTTACTTC-CCTGGCGGTG
* ** * * * *
12251821 CAATTAAAAAAATTGAAGCCACAATGGCGGATCTTACTTCCCTGGCGGTG
1 CAGTGGAACAGATTGAAGCTACAACGGCGGATCTTACTTCCCTGGCGGTG
** ** *
12251871 CAGTGGAACAGATTGAAGCTATGACGGCGGAT-TTGGTTTCCCT----G-A
1 CAGTGGAACAGATTGAAGCTACAACGGCGGATCTT-ACTTCCCTGGCGGTG
* * *
12251916 CATTGCAA-AGATTGAAGC-ACAACGACGGATCTTACTTCCCTGGCGGTG
1 CAGTGGAACAGATTGAAGCTACAACGGCGGATCTTACTTCCCTGGCGGTG
*
12251964 TAGTGGAACAGATTGAAGCTAC
1 CAGTGGAACAGATTGAAGCTAC
12251986 GACGACGAAT
Statistics
Matches: 155, Mismatches: 49, Indels: 22
0.69 0.22 0.10
Matches are distributed among these distances:
43 15 0.10
44 12 0.08
45 6 0.04
46 1 0.01
47 1 0.01
48 5 0.03
49 14 0.09
50 99 0.64
51 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
CAGTGGAACAGATTGAAGCTACAACGGCGGATCTTACTTCCCTGGCGGTG
Found at i:12252734 original size:22 final size:22
Alignment explanation
Indices: 12252709--12252751 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12252699 AACTCCATTT
12252709 TTCTTTTCTTTTCAC-TGTTTTG
1 TTCTTTT-TTTTCACTTGTTTTG
*
12252731 TTCTTTTTTTTCCCTTGTTTT
1 TTCTTTTTTTTCACTTGTTTT
12252752 TAAAACGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.02, C:0.19, G:0.07, T:0.72
Consensus pattern (22 bp):
TTCTTTTTTTTCACTTGTTTTG
Found at i:12254753 original size:22 final size:22
Alignment explanation
Indices: 12254709--12254753 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
12254699 AAAATAAATC
* * * *
12254709 AAAATTTATGAAAATTTATTAT
1 AAAATTAATCAAAATTAAATAT
12254731 AAAATTAATCAAAATTAAATAT
1 AAAATTAATCAAAATTAAATAT
12254753 A
1 A
12254754 TATGAATAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAATTAATCAAAATTAAATAT
Found at i:12255125 original size:16 final size:16
Alignment explanation
Indices: 12255104--12255134 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12255094 AATAAACTAA
12255104 TTTTTTTCTTAATAAT
1 TTTTTTTCTTAATAAT
12255120 TTTTTTTCTTAATAA
1 TTTTTTTCTTAATAA
12255135 AGACATGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTTTCTTAATAAT
Found at i:12257856 original size:12 final size:13
Alignment explanation
Indices: 12257839--12257871 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
12257829 CACTAGTTTA
12257839 GACACGGGCT-AG
1 GACACGGGCTAAG
12257851 GACACGGG-TAAG
1 GACACGGGCTAAG
12257863 GACACGGGC
1 GACACGGGC
12257872 GTGTGGCCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.05
12 18 0.95
ACGTcount: A:0.27, C:0.24, G:0.42, T:0.06
Consensus pattern (13 bp):
GACACGGGCTAAG
Found at i:12270782 original size:14 final size:14
Alignment explanation
Indices: 12270763--12270792 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12270753 TTTTAGAGCT
12270763 TTTATACTATTTTC
1 TTTATACTATTTTC
12270777 TTTATACTATTTTC
1 TTTATACTATTTTC
12270791 TT
1 TT
12270793 AGTTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATACTATTTTC
Found at i:12274890 original size:9 final size:9
Alignment explanation
Indices: 12274830--12275102 Score: 269
Period size: 9 Copynumber: 29.8 Consensus size: 9
12274820 AATATTTAAT
12274830 TTATGTAAG
1 TTATGTAAG
* *
12274839 TTATTTAAT
1 TTATGTAAG
*
12274848 TTATGTAGG
1 TTATGTAAG
*
12274857 TTATGTCAG
1 TTATGTAAG
* * *
12274866 TCCATGGAAT
1 T-TATGTAAG
12274876 TTATGTAAG
1 TTATGTAAG
12274885 TTATGTAAG
1 TTATGTAAG
* *
12274894 TTATTTAAT
1 TTATGTAAG
12274903 TTATGTAAG
1 TTATGTAAG
12274912 TTATGTAAG
1 TTATGTAAG
* *
12274921 TTATTTAAT
1 TTATGTAAG
*
12274930 TTATGTAGG
1 TTATGTAAG
12274939 TTATGTAAG
1 TTATGTAAG
*
12274948 TAATGTAAG
1 TTATGTAAG
* *
12274957 TTATTTAAT
1 TTATGTAAG
*
12274966 TTATGCAAG
1 TTATGTAAG
12274975 TTTATGTAAG
1 -TTATGTAAG
12274985 TTATGTAAG
1 TTATGTAAG
* *
12274994 TTATTTAAT
1 TTATGTAAG
12275003 TTATGTAAG
1 TTATGTAAG
12275012 TTATGTAAG
1 TTATGTAAG
* *
12275021 TTATTTAAT
1 TTATGTAAG
12275030 TTATGT-AG
1 TTATGTAAG
12275038 CTTATGTAAG
1 -TTATGTAAG
12275048 TTATGTAAG
1 TTATGTAAG
* *
12275057 TTATTTAAT
1 TTATGTAAG
12275066 TTATGTAAG
1 TTATGTAAG
*
12275075 TTATGCAAG
1 TTATGTAAG
*
12275084 CTTATATACAAG
1 -TTATGT--AAG
12275096 TTATGTA
1 TTATGTA
12275103 TTATAACATA
Statistics
Matches: 209, Mismatches: 48, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
8 1 0.00
9 181 0.87
10 19 0.09
11 5 0.02
12 3 0.01
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:12275062 original size:100 final size:99
Alignment explanation
Indices: 12274822--12275076 Score: 377
Period size: 100 Copynumber: 2.5 Consensus size: 99
12274812 TGTTAATAAA
* * * * * ** *
12274822 TATTTAATTTATGTAAGTTATTTAATTTATGTAGGTTATGTCAGTCCATGGAA-TTTATGTAAGT
1 TATTTAATTTATGT-AGTTATGTAAGTTATGTAAGTTAT-TTAATTTATGCAAGTTTATGTAAGT
12274886 TATGTAAGTTATTTAATTTATGTAAGTTATGTAAGT
64 TATGTAAGTTATTTAATTTATGTAAGTTATGTAAGT
*
12274922 TATTTAATTTATGTAGGTTATGTAAGTAATGTAAGTTATTTAATTTATGCAAGTTTATGTAAGTT
1 TATTTAATTTATGTA-GTTATGTAAGTTATGTAAGTTATTTAATTTATGCAAGTTTATGTAAGTT
12274987 ATGTAAGTTATTTAATTTATGTAAGTTATGTAAGT
65 ATGTAAGTTATTTAATTTATGTAAGTTATGTAAGT
*
12275022 TATTTAATTTATGTAGCTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTT
1 TATTTAATTTATGTAG-TTATGTAAGTTATGTAAGTTATTTAATTTATGCAAGTT
12275077 ATGCAAGCTT
Statistics
Matches: 141, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
99 10 0.07
100 131 0.93
ACGTcount: A:0.32, C:0.02, G:0.16, T:0.50
Consensus pattern (99 bp):
TATTTAATTTATGTAGTTATGTAAGTTATGTAAGTTATTTAATTTATGCAAGTTTATGTAAGTTA
TGTAAGTTATTTAATTTATGTAAGTTATGTAAGT
Found at i:12275190 original size:21 final size:21
Alignment explanation
Indices: 12275166--12275216 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
12275156 AATTATTATG
12275166 TAAGTTATGCAAGCTTAAATA
1 TAAGTTATGCAAGCTTAAATA
*
12275187 TAAGTTATGCAAGCTTATATA
1 TAAGTTATGCAAGCTTAAATA
*
12275208 CAAGTTATG
1 TAAGTTATG
12275217 TATTATAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (21 bp):
TAAGTTATGCAAGCTTAAATA
Found at i:12275200 original size:116 final size:116
Alignment explanation
Indices: 12275071--12275311 Score: 448
Period size: 116 Copynumber: 2.1 Consensus size: 116
12275061 TTAATTTATG
12275071 TAAGTTATGCAAGCTTATATACAAGTTATGTATTATAACATAAAGTATTATGTAATTTAT-TATG
1 TAAGTTATGCAAGCTTATATACAAGTTATGTATTATAACATAAAGTATTATGTAATTTATGT-TG
12275135 CTATTATATATAAGTTATGTAAATTATTATGTAAGTTATGCAAGCTTAAATA
65 CTATTATATATAAGTTATGTAAATTATTATGTAAGTTATGCAAGCTTAAATA
*
12275187 TAAGTTATGCAAGCTTATATACAAGTTATGTATTATAACATAAAGTATTATGTAATTTATGTTGT
1 TAAGTTATGCAAGCTTATATACAAGTTATGTATTATAACATAAAGTATTATGTAATTTATGTTGC
*
12275252 TATTATATATAAGTTCTGTAAATTATTATGTAAGTTATGCAAGCTTAAATA
66 TATTATATATAAGTTATGTAAATTATTATGTAAGTTATGCAAGCTTAAATA
12275303 TAAGTTATG
1 TAAGTTATG
12275312 TATTATATAA
Statistics
Matches: 122, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
116 121 0.99
117 1 0.01
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.43
Consensus pattern (116 bp):
TAAGTTATGCAAGCTTATATACAAGTTATGTATTATAACATAAAGTATTATGTAATTTATGTTGC
TATTATATATAAGTTATGTAAATTATTATGTAAGTTATGCAAGCTTAAATA
Found at i:12275455 original size:15 final size:15
Alignment explanation
Indices: 12275435--12275473 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
12275425 GAAAACGAAG
*
12275435 TAAATTTAATACTAA
1 TAAATTTAATACAAA
12275450 TAAATTTTAATACAAA
1 TAAA-TTTAATACAAA
*
12275466 TAATTTTA
1 TAAATTTA
12275474 GAAAACTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAATTTAATACAAA
Found at i:12275460 original size:16 final size:16
Alignment explanation
Indices: 12275435--12275473 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
12275425 GAAAACGAAG
*
12275435 TAAA-TTTAATACTAA
1 TAAATTTTAATACAAA
12275450 TAAATTTTAATACAAA
1 TAAATTTTAATACAAA
12275466 T-AATTTTA
1 TAAATTTTA
12275474 GAAAACTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATTTTAATACAAA
Found at i:12275508 original size:17 final size:17
Alignment explanation
Indices: 12275482--12275514 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12275472 TAGAAAACTT
*
12275482 ATTTATAAAACTTATAA
1 ATTTAGAAAACTTATAA
12275499 ATTTAGAAAACTTATA
1 ATTTAGAAAACTTATA
12275515 TAGATATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (17 bp):
ATTTAGAAAACTTATAA
Found at i:12278041 original size:17 final size:18
Alignment explanation
Indices: 12278019--12278059 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
12278009 TAAGTATTTT
*
12278019 ATTATTTTGAATT-ATAC
1 ATTATTTTAAATTGATAC
*
12278036 ATTATTTTAAATTGATGC
1 ATTATTTTAAATTGATAC
12278054 ATTATT
1 ATTATT
12278060 ACGAAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (18 bp):
ATTATTTTAAATTGATAC
Found at i:12279936 original size:21 final size:20
Alignment explanation
Indices: 12279896--12279950 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
12279886 CGCTGAAATG
* * *
12279896 TAAACTCTAAACCTTAAACC
1 TAAACTCCAAGCCCTAAACC
*
12279916 TCAATCTCCAAGCCCTAAACC
1 T-AAACTCCAAGCCCTAAACC
*
12279937 TAAACTCTAAGCCC
1 TAAACTCCAAGCCC
12279951 AGATCACAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.36, G:0.04, T:0.22
Consensus pattern (20 bp):
TAAACTCCAAGCCCTAAACC
Found at i:12280625 original size:133 final size:132
Alignment explanation
Indices: 12280298--12280710 Score: 467
Period size: 133 Copynumber: 3.1 Consensus size: 132
12280288 GAACCGTTTC
* * * *
12280298 CGGCGTTTTTTAACATTTCGCCACTAAAG-CATAAAAGGAAACAACAAAACGGTACCGTTTTGCT
1 CGGCGTTTTTTAA-AATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTA-CGTTTTGCT
* * *
12280362 CAAAATTTTTCCTCAAATTAGATTTCTTTACCGGCGTTTCTCC-AATAACGCCACTATATCCCAA
64 CAAATTTTTTCCTCAAATTAGATATCTTTACCGGCGTTTC-CCGAA-AACGCCGCTATATCCCAA
*
12280426 TATTTG
127 TATTTT
* * * *
12280432 CGGCGTTTTTTACAATGCGCCACTAAGGAAATAAAATGAAGCAATAAAACGGTAGCGTTTTG-TC
1 CGGCGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTA-CGTTTTGCT-
* * *
12280496 CAAATTTTTTCCTCAAATTAGATATCTTTATCGGCGTTTCCCTGAAAACGCCGCTA-AT-GCATT
64 CAAATTTTTTCCTCAAATTAGATATCTTTACCGGCGTTTCCC-GAAAACGCCGCTATATCCCAAT
*
12280559 CTTTT
128 ATTTT
*
12280564 CTGGCGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACAGTACTGTTTTGCT
1 C-GGCGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTAC-GTTTTGCT
* * * * * *
12280629 CAGATTTTTTCCTCAAATTCGTTATCGTTACCGGCGTTTCTCAGAAAACGCCGCTATATTCCAAT
64 CAAATTTTTTCCTCAAATTAGATATCTTTACCGGCGTTTC-CCGAAAACGCCGCTATATCCCAA-
*
12280694 TTTTTT
127 TATTTT
12280700 GCGGCGTTTTT
1 -CGGCGTTTTT
12280711 GGGGAAGCGC
Statistics
Matches: 236, Mismatches: 31, Indels: 22
0.82 0.11 0.08
Matches are distributed among these distances:
132 8 0.03
133 119 0.50
134 90 0.38
135 4 0.02
136 14 0.06
137 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.34
Consensus pattern (132 bp):
CGGCGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTACGTTTTGCTCA
AATTTTTTCCTCAAATTAGATATCTTTACCGGCGTTTCCCGAAAACGCCGCTATATCCCAATATT
TT
Found at i:12280758 original size:133 final size:134
Alignment explanation
Indices: 12280298--12280760 Score: 407
Period size: 133 Copynumber: 3.5 Consensus size: 134
12280288 GAACCGTTTC
* * * *
12280298 CGGCGTTTTTTAACATTTCGCCACTAAAGCATAA-AAGGAAACAAC-AAAACGGTACCGTTTTGC
1 CGGCGTTTTTTAA-AATGCGCCACTAAAG-A-AATAAAGTAAC-ACTAAAACGGTACCGTTTTGC
* * * *
12280361 TCAAAATTTTTCCTCAAATTAGATT-TCTTTACCGGCGTTTCTCCA-ATAACGCCACTATATCCC
62 TCAAATTTTTTCCTCAAATTAG-TTATCTTTACCGGCGTTTCT-CAGAAAACGCCGCTATATTCC
*
12280424 AA--TATTTG
125 AATTTTTTTG
* * * * *
12280432 CGGCGTTTTTTACAATGCGCCACTAAGGAAATAAAATGAAGCAATAAAACGGTAGCGTTTTG-TC
1 CGGCGTTTTTTAAAATGCGCCACTAAAGAAATAAAGT-AA-CACTAAAACGGTACCGTTTTGCT-
* * * * *
12280496 CAAATTTTTTCCTCAAATTAGATATCTTTATCGGCGTTTCCCTGAAAACGCCGCTA-A-TGC-AT
63 CAAATTTTTTCCTCAAATTAGTTATCTTTACCGGCGTTTCTCAGAAAACGCCGCTATATTCCAAT
*
12280558 TCTTTT-
128 TTTTTTG
* * *
12280564 CTGGCGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAAC-AAAACAGTACTGTTTTGC
1 C-GGCGTTTTTTAAAATGCGCCACTAAAGAAAT-AAA-GTAAC-ACTAAAACGGTACCGTTTTGC
* * *
12280628 TCAGATTTTTTCCTCAAATTCGTTATCGTTACCGGCGTTTCTCAGAAAACGCCGCTATATTCCAA
62 TCAAATTTTTTCCTCAAATTAGTTATCTTTACCGGCGTTTCTCAGAAAACGCCGCTATATTCCAA
12280693 TTTTTTTG
127 TTTTTTTG
*** **
12280701 CGGCGTTTTTGGGGAA-GCGCCACTAAAGTCATAAAGTAAC-CTAAAACGG-AGCCGTTTTGC
1 CGGCGTTTTT-TAAAATGCGCCACTAAAGAAATAAAGTAACACTAAAACGGTA-CCGTTTTGC
12280761 AAAGAAGTAT
Statistics
Matches: 263, Mismatches: 45, Indels: 43
0.75 0.13 0.12
Matches are distributed among these distances:
131 3 0.01
132 7 0.03
133 129 0.49
134 86 0.33
135 5 0.02
136 30 0.11
137 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (134 bp):
CGGCGTTTTTTAAAATGCGCCACTAAAGAAATAAAGTAACACTAAAACGGTACCGTTTTGCTCAA
ATTTTTTCCTCAAATTAGTTATCTTTACCGGCGTTTCTCAGAAAACGCCGCTATATTCCAATTTT
TTTG
Found at i:12286942 original size:38 final size:38
Alignment explanation
Indices: 12286900--12286977 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
12286890 TATCTCAAGT
*
12286900 CAGACTCGCACAAAGCGCGATATAACCTATTGACATGC
1 CAGACTCACACAAAGCGCGATATAACCTATTGACATGC
*
12286938 CAGACTCATACAAAGCGCGATATAACCTATTGACATGC
1 CAGACTCACACAAAGCGCGATATAACCTATTGACATGC
12286976 CA
1 CA
12286978 ATTGTATCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (38 bp):
CAGACTCACACAAAGCGCGATATAACCTATTGACATGC
Found at i:12289060 original size:60 final size:60
Alignment explanation
Indices: 12288967--12289089 Score: 228
Period size: 60 Copynumber: 2.0 Consensus size: 60
12288957 AGAGTGGAAA
* *
12288967 GAATGCCTTGCTACCAAAGGCAATGGTATGGAACTCTTGATAATAGATTCTTGTTTAATG
1 GAATGCCTAGCTACCAAAGGCAATGGTATGGAACTCTTGATAATAGATTCTTGTATAATG
12289027 GAATGCCTAGCTACCAAAGGCAATGGTATGGAACTCTTGATAATAGATTCTTGTATAATG
1 GAATGCCTAGCTACCAAAGGCAATGGTATGGAACTCTTGATAATAGATTCTTGTATAATG
12289087 GAA
1 GAA
12289090 GACTCAATAG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.31
Consensus pattern (60 bp):
GAATGCCTAGCTACCAAAGGCAATGGTATGGAACTCTTGATAATAGATTCTTGTATAATG
Found at i:12303859 original size:6 final size:6
Alignment explanation
Indices: 12303848--12303909 Score: 124
Period size: 6 Copynumber: 10.3 Consensus size: 6
12303838 AAATACGATG
12303848 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
12303896 TTCTTT TTCTTT TT
1 TTCTTT TTCTTT TT
12303910 GTGATGGGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTCTTT
Found at i:12304683 original size:13 final size:13
Alignment explanation
Indices: 12304665--12304695 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
12304655 TCAAAGAGAT
12304665 TAAGGATATCACA
1 TAAGGATATCACA
12304678 TAAGGATATCACA
1 TAAGGATATCACA
12304691 TAAGG
1 TAAGG
12304696 GTAATACACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (13 bp):
TAAGGATATCACA
Found at i:12305056 original size:4 final size:4
Alignment explanation
Indices: 12305049--12305074 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
12305039 ATGGTTTTTC
12305049 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
12305075 AGTTCAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:12305692 original size:19 final size:20
Alignment explanation
Indices: 12305645--12305694 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
12305635 TTACAAAAAG
12305645 AAAA-TCAAAATAATTTTCA
1 AAAATTCAAAATAATTTTCA
*
12305664 AAAATT-AAAATAATTTT-T
1 AAAATTCAAAATAATTTTCA
*
12305682 AAATTTCAAAATA
1 AAAATTCAAAATA
12305695 TTGATAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 5 0.19
19 21 0.78
20 1 0.04
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATTCAAAATAATTTTCA
Found at i:12310309 original size:20 final size:21
Alignment explanation
Indices: 12310272--12310312 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
12310262 ATATTTTCAA
12310272 TAAAATATTAAGAATATTATT
1 TAAAATATTAAGAATATTATT
12310293 TAAAAT-TTAA-AATTATTATT
1 TAAAATATTAAGAA-TATTATT
12310313 AATGTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 11 0.58
21 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TAAAATATTAAGAATATTATT
Found at i:12311281 original size:13 final size:14
Alignment explanation
Indices: 12311263--12311302 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
12311253 ATATGAGGAA
12311263 TATTATTTAAAAT-
1 TATTATTTAAAATC
12311276 TATTATTTTAAAATC
1 TATTA-TTTAAAATC
12311291 TATTA-TTAAAAT
1 TATTATTTAAAAT
12311303 AAATTTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.48
14 8 0.32
15 5 0.20
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTATTTAAAATC
Found at i:12311296 original size:15 final size:14
Alignment explanation
Indices: 12311263--12311297 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
12311253 ATATGAGGAA
12311263 TATTA-TTTAAAAT
1 TATTATTTTAAAAT
12311276 TATTATTTTAAAAT
1 TATTATTTTAAAAT
12311290 CTATTATT
1 -TATTATT
12311298 AAAATAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.25
14 8 0.40
15 7 0.35
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTATTTTAAAAT
Found at i:12311510 original size:27 final size:25
Alignment explanation
Indices: 12311455--12311510 Score: 58
Period size: 27 Copynumber: 2.2 Consensus size: 25
12311445 AATTTTAAAT
*
12311455 ATTTTTAAAAATAAAAATAAAATTT
1 ATTTTTAAAAATAAAAATAAAATTG
* * *
12311480 ATTTTTAATATAATAATATTAAACTTG
1 ATTTTTAA-A-AATAAAAATAAAATTG
12311507 ATTT
1 ATTT
12311511 AAGTTAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 8 0.32
26 1 0.04
27 16 0.64
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (25 bp):
ATTTTTAAAAATAAAAATAAAATTG
Found at i:12315887 original size:30 final size:30
Alignment explanation
Indices: 12315851--12315910 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
12315841 ACTTAACAAG
12315851 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
12315881 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
12315911 TAATAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.57, C:0.15, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:12319395 original size:16 final size:17
Alignment explanation
Indices: 12319371--12319404 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
12319361 ATAAGAAATA
*
12319371 ATTCTATTTTTAT-AAT
1 ATTCAATTTTTATCAAT
12319387 ATTCAATTTTTATCAAT
1 ATTCAATTTTTATCAAT
12319404 A
1 A
12319405 AATAAAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTCAATTTTTATCAAT
Found at i:12321750 original size:51 final size:51
Alignment explanation
Indices: 12321622--12321815 Score: 198
Period size: 51 Copynumber: 3.8 Consensus size: 51
12321612 TGAAAGTGAC
* * *
12321622 GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GA-AATGAT
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTAAT
* * * * * *
12321671 AGGTCGCATGTGTAGTGCTATGTACAGGCTACTATGCGTACCGGATAGT-TT
1 -GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTAAT
* * * *
12321722 CGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAAT
1 -GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTAAT
* *
12321774 GGTCACAT-TGATAGTACTATGTGCAGGCTACTATGTGAACCG
1 GGTCACATGTG-TAGTACTATGTGCAGGCTACTACGTGTACCG
12321816 AACATCATTA
Statistics
Matches: 116, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
50 37 0.32
51 76 0.66
52 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (51 bp):
GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTAAT
Found at i:12321868 original size:45 final size:45
Alignment explanation
Indices: 12321817--12321903 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
12321807 TGTGAACCGA
* *
12321817 ACATCATTAATTAGTAAGGTGGTTGCTATGTGCTGATTCCACTGG
1 ACATCATTAATTAATAAGGTGGTTGCTATGTGCTGAATCCACTGG
*
12321862 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCAC
1 ACATCATTAATTAATAAGGTGGTTGCTATGTGCTGAATCCAC
12321904 CGAGTATCTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.34
Consensus pattern (45 bp):
ACATCATTAATTAATAAGGTGGTTGCTATGTGCTGAATCCACTGG
Found at i:12328037 original size:19 final size:19
Alignment explanation
Indices: 12328015--12328053 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
12328005 GTTATAATTT
12328015 TAATAT-ATATTATTTAATA
1 TAATATAATATT-TTTAATA
12328034 TAATATAAATATTTTTAATA
1 TAATAT-AATATTTTTAATA
12328054 ATTTCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 7 0.39
21 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATATAATATTTTTAATA
Found at i:12334292 original size:18 final size:17
Alignment explanation
Indices: 12334271--12334311 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
12334261 GTTTTTATAA
* *
12334271 TTTTATTTTTGTTTATTT
1 TTTTATTTTT-TTAAATT
12334289 TTTTATTTTTTTAAATT
1 TTTTATTTTTTTAAATT
12334306 TTTTAT
1 TTTTAT
12334312 GATTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTTATTTTTTTAAATT
Found at i:12334317 original size:17 final size:17
Alignment explanation
Indices: 12334287--12334320 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12334277 TTTTGTTTAT
**
12334287 TTTTTTATTTTTTTAAA
1 TTTTTTATGATTTTAAA
12334304 TTTTTTATGATTTTAAA
1 TTTTTTATGATTTTAAA
12334321 AAAAGATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTTATGATTTTAAA
Found at i:12336416 original size:21 final size:21
Alignment explanation
Indices: 12336391--12336442 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
12336381 TAATGGTGGC
*
12336391 GGTGAAATTAGTTAATGTAGT
1 GGTGAAATTAGATAATGTAGT
* * *
12336412 GGTGATATTGGATACTGTAGT
1 GGTGAAATTAGATAATGTAGT
*
12336433 GGTGAGATTA
1 GGTGAAATTA
12336443 AAATAACGGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.02, G:0.33, T:0.37
Consensus pattern (21 bp):
GGTGAAATTAGATAATGTAGT
Found at i:12341810 original size:19 final size:19
Alignment explanation
Indices: 12341786--12341843 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 19
12341776 AATCTTTAAG
12341786 GATATGTAATCTTAGATAT
1 GATATGTAATCTTAGATAT
*
12341805 GATATGCAATCTTAGAATATAT
1 GATATGTAATCTTAG---ATAT
*
12341827 GATTTTGTAATCTTAGA
1 GA-TATGTAATCTTAGA
12341844 AATTTAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 14 0.44
20 1 0.03
22 6 0.19
23 11 0.34
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (19 bp):
GATATGTAATCTTAGATAT
Found at i:12354985 original size:20 final size:20
Alignment explanation
Indices: 12354962--12354999 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12354952 ATGTGTAATT
12354962 AGAGGCA-TAAAAGTGCAAAC
1 AGAGGCACT-AAAGTGCAAAC
12354982 AGAGGCACTAAAGTGCAA
1 AGAGGCACTAAAGTGCAA
12355000 TCCCGTACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.47, C:0.16, G:0.26, T:0.11
Consensus pattern (20 bp):
AGAGGCACTAAAGTGCAAAC
Found at i:12363400 original size:411 final size:411
Alignment explanation
Indices: 12362638--12363434 Score: 1522
Period size: 411 Copynumber: 1.9 Consensus size: 411
12362628 CATAATAGAT
* * *
12362638 ACAATTATCAGAATCAGAAAAACAGAACAGAGATAGCGAGTCCTACCTCCGTCCTCTACACACCA
1 ACAATTATCAGAATCAGAAAAACAGAACAGAGATAGCGAGTCATACCCCCATCCTCTACACACCA
*
12362703 TCTCCGACCATCCCATCACACCATGTAAGGTTAAAAACACTCACCCATCCCTACACACCATATAG
66 TCTCCGACCATCCCATCACACCATGTAAGGTTAAAAACACCCACCCATCCCTACACACCATATAG
* *
12362768 TGTCGATGTGACACATTACAGGTAATATGCAGTCAAGCTACCAGAAAATAGGCGAAATGTCGTTG
131 TGTCGATGTGACACATTACAGGTAATATGCAGTCAAGCTACCAGAAAATAGGCGAAATATCGCTG
12362833 TAATACCCAAATTTTTCCCGACCCGAGCCCAACTATTAAAACCCAAATATGAAAAAATATCAAAT
196 TAATACCCAAATTTTTCCCGACCCGAGCCCAACTATTAAAACCCAAATATGAAAAAATATCAAAT
12362898 AAATAAAGGTCCAATAATAGTCCAACTACAATCGAATATAAGAGGCCCAATTTCAATACACTCTA
261 AAATAAAGGTCCAATAATAGTCCAACTACAATCGAATATAAGAGGCCCAATTTCAATACACTCTA
12362963 GCCCAATAACCCGAATTACATCAAACCCGAGCCCAAAATACTCTAACCCAGTTTACATAGCAGGT
326 GCCCAATAACCCGAATTACATCAAACCCGAGCCCAAAATACTCTAACCCAGTTTACATAGCAGGT
12363028 AATATGCACCCATCTCCGAGA
391 AATATGCACCCATCTCCGAGA
12363049 ACAATTATCAGAATCAGAAAAACAGAACAGAGATAGCGAGTCATACCCCCATCCTCTACACACCA
1 ACAATTATCAGAATCAGAAAAACAGAACAGAGATAGCGAGTCATACCCCCATCCTCTACACACCA
12363114 TCTCCGACCATCCCATCACACCATGTAAGGTTAAAAACACCCACCCATCCCTACACACCATATAG
66 TCTCCGACCATCCCATCACACCATGTAAGGTTAAAAACACCCACCCATCCCTACACACCATATAG
12363179 TGTCGATGTGACACATTACAGGTAATATGCAGTCAAGCTACCAGAAAATAGGCGAAATATCGCTG
131 TGTCGATGTGACACATTACAGGTAATATGCAGTCAAGCTACCAGAAAATAGGCGAAATATCGCTG
12363244 TAATACCCAAATTTTTCCCGACCCGAGCCCAACTATTAAAACCCAAATATGAAAAAATATCAAAT
196 TAATACCCAAATTTTTCCCGACCCGAGCCCAACTATTAAAACCCAAATATGAAAAAATATCAAAT
* *
12363309 AAATAAAGGTCCAATAATAGTCCAACTACAATCGAATATAATAGGCCCAATTTCAGTACACTCTA
261 AAATAAAGGTCCAATAATAGTCCAACTACAATCGAATATAAGAGGCCCAATTTCAATACACTCTA
12363374 GCCCAATAACCCGAATTACATCAAACCCGAGCCCAAAATACTCTAACCCAGTTTACATAGC
326 GCCCAATAACCCGAATTACATCAAACCCGAGCCCAAAATACTCTAACCCAGTTTACATAGC
12363435 CCGATTCCAA
Statistics
Matches: 378, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
411 378 1.00
ACGTcount: A:0.39, C:0.28, G:0.12, T:0.21
Consensus pattern (411 bp):
ACAATTATCAGAATCAGAAAAACAGAACAGAGATAGCGAGTCATACCCCCATCCTCTACACACCA
TCTCCGACCATCCCATCACACCATGTAAGGTTAAAAACACCCACCCATCCCTACACACCATATAG
TGTCGATGTGACACATTACAGGTAATATGCAGTCAAGCTACCAGAAAATAGGCGAAATATCGCTG
TAATACCCAAATTTTTCCCGACCCGAGCCCAACTATTAAAACCCAAATATGAAAAAATATCAAAT
AAATAAAGGTCCAATAATAGTCCAACTACAATCGAATATAAGAGGCCCAATTTCAATACACTCTA
GCCCAATAACCCGAATTACATCAAACCCGAGCCCAAAATACTCTAACCCAGTTTACATAGCAGGT
AATATGCACCCATCTCCGAGA
Found at i:12371145 original size:29 final size:29
Alignment explanation
Indices: 12371113--12371168 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
12371103 AAAGGCTGTT
12371113 TTTTTTCAA-AATTTACCGAAATGGGCCGG
1 TTTTTT-AATAATTTACCGAAATGGGCCGG
* *
12371142 TTTTTTAATTATTTACCGGAATGGGCC
1 TTTTTTAATAATTTACCGAAATGGGCC
12371169 ATTTTTCCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (29 bp):
TTTTTTAATAATTTACCGAAATGGGCCGG
Found at i:12372464 original size:30 final size:30
Alignment explanation
Indices: 12372422--12372507 Score: 106
Period size: 29 Copynumber: 2.9 Consensus size: 30
12372412 ATTTTTTACA
*
12372422 AAATTGTATTTTGACCCCTAAATTTTCTT-
1 AAATTATATTTTGACCCCTAAATTTTCTTG
*
12372451 AAATTTATATTTTGA-CTCTAAACTTTT-TTG
1 AAA-TTATATTTTGACCCCTAAA-TTTTCTTG
*
12372481 AAATTATATTTTGACCCCTAAAATTTC
1 AAATTATATTTTGACCCCTAAATTTTC
12372508 CAAAATTACA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
29 25 0.52
30 23 0.48
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.48
Consensus pattern (30 bp):
AAATTATATTTTGACCCCTAAATTTTCTTG
Found at i:12372471 original size:29 final size:29
Alignment explanation
Indices: 12372422--12372502 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 29
12372412 ATTTTTTACA
*
12372422 AAATTGTATTTTGACCCCTAAA-TTTTCTT-
1 AAATTATATTTTGA-CCCTAAACTTTT-TTG
*
12372451 AAATTTATATTTTGACTCTAAACTTTTTTG
1 AAA-TTATATTTTGACCCTAAACTTTTTTG
12372481 AAATTATATTTTGACCCCTAAA
1 AAATTATATTTTGA-CCCTAAA
12372503 ATTTCCAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
29 22 0.49
30 23 0.51
ACGTcount: A:0.32, C:0.15, G:0.06, T:0.47
Consensus pattern (29 bp):
AAATTATATTTTGACCCTAAACTTTTTTG
Found at i:12372513 original size:29 final size:29
Alignment explanation
Indices: 12372415--12372526 Score: 100
Period size: 29 Copynumber: 3.8 Consensus size: 29
12372405 ATCTCGTATT
* *
12372415 TTTTACAAAATTGTATTTTGACCCCTAAA
1 TTTTCCAAAATTATATTTTGACCCCTAAA
* * *
12372444 TTTTCTTAAATTTATATTTTGA-CTCTAAA
1 TTTTC-CAAAATTATATTTTGACCCCTAAA
***
12372473 CTTTTTTGAAATTATATTTTGACCCCTAAA
1 -TTTTCCAAAATTATATTTTGACCCCTAAA
* * *
12372503 ATTTCCAAAATTACACTTTGACCC
1 TTTTCCAAAATTATATTTTGACCC
12372527 TAGAAGTTTT
Statistics
Matches: 65, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
29 42 0.65
30 23 0.35
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (29 bp):
TTTTCCAAAATTATATTTTGACCCCTAAA
Found at i:12372785 original size:14 final size:14
Alignment explanation
Indices: 12372766--12372803 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
12372756 GAGGCAGGTT
*
12372766 AAAAAAAAGAGAGG
1 AAAAAAAAGAGAGA
*
12372780 AGAAAAAAGAGAGA
1 AAAAAAAAGAGAGA
12372794 AAAAAAAAGA
1 AAAAAAAAGA
12372804 AAAAGGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAGAGA
Found at i:12372812 original size:7 final size:7
Alignment explanation
Indices: 12372780--12372830 Score: 59
Period size: 7 Copynumber: 7.1 Consensus size: 7
12372770 AAAAGAGAGG
12372780 AGAAAAA
1 AGAAAAA
*
12372787 AGAGAGAA
1 AGA-AAAA
12372795 A-AAAAA
1 AGAAAAA
12372801 AGAAAAA
1 AGAAAAA
*
12372808 GGAAAAA
1 AGAAAAA
12372815 AGAAAAA
1 AGAAAAA
12372822 AGAGAAAA
1 AGA-AAAA
12372830 A
1 A
12372831 AAAGGTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 4 0.11
7 24 0.65
8 9 0.24
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:12372987 original size:14 final size:13
Alignment explanation
Indices: 12372968--12373014 Score: 55
Period size: 14 Copynumber: 3.8 Consensus size: 13
12372958 TTTATGCATT
12372968 TTTATATTTTTATA
1 TTTATATTTTTA-A
12372982 TTTATATTTTTAA
1 TTTATATTTTTAA
12372995 TTTA-A--TTTAA
1 TTTATATTTTTAA
*
12373005 TTTTTATTTT
1 TTTATATTTT
12373015 ATTTTATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 8 0.28
11 1 0.03
12 1 0.03
13 7 0.24
14 12 0.41
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATATTTTTAA
Found at i:12373009 original size:17 final size:16
Alignment explanation
Indices: 12372976--12373024 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
12372966 TTTTTATATT
12372976 TTTATATTTATATTTTTAA
1 TTTA-ATTTA-ATTTTT-A
12372995 TTTAATTTAATTTTTA
1 TTTAATTTAATTTTTA
* *
12373011 TTTTATTTTATTTT
1 TTTAATTTAATTTT
12373025 AAATAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 13 0.46
17 6 0.21
18 5 0.18
19 4 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTAATTTAATTTTTA
Found at i:12373463 original size:19 final size:19
Alignment explanation
Indices: 12373441--12373502 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 19
12373431 TTCGTCTTTC
12373441 AAAATTCTCATGTTTTCAAAAA
1 AAAATTCTCATGTTTTC---AA
*
12373463 AAAATTCT-GTGTTTTC-A
1 AAAATTCTCATGTTTTCAA
* *
12373480 AAAATTTTCATATTTTCAA
1 AAAATTCTCATGTTTTCAA
12373499 AAAA
1 AAAA
12373503 AAAAATTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
17 8 0.24
18 6 0.18
19 5 0.15
21 7 0.21
22 8 0.24
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (19 bp):
AAAATTCTCATGTTTTCAA
Found at i:12373475 original size:21 final size:22
Alignment explanation
Indices: 12373441--12373483 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
12373431 TTCGTCTTTC
12373441 AAAATTCTCATGTTTTCAAAAA
1 AAAATTCTCATGTTTTCAAAAA
*
12373463 AAAATTCT-GTGTTTTCAAAAA
1 AAAATTCTCATGTTTTCAAAAA
12373484 TTTTCATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (22 bp):
AAAATTCTCATGTTTTCAAAAA
Found at i:12373484 original size:39 final size:38
Alignment explanation
Indices: 12373437--12373541 Score: 140
Period size: 40 Copynumber: 2.7 Consensus size: 38
12373427 AGATTTCGTC
12373437 TTTC-AAAATTCTCATGTTTTCAAAAAAAAATTCTGTG
1 TTTCAAAAATTCTCATGTTTTCAAAAAAAAATTCTGTG
* * *
12373474 TTTTCAAAAATTTTCATATTTTCAAAAAAAAAAATTTTGTG
1 -TTTCAAAAATTCTCATGTTTTC--AAAAAAAAATTCTGTG
*
12373515 TTTCAAAAATCCTCATGTTTTCAAAAA
1 TTTCAAAAATTCTCATGTTTTCAAAAA
12373542 TTCTGGTGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
38 9 0.16
39 15 0.26
40 19 0.33
41 15 0.26
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (38 bp):
TTTCAAAAATTCTCATGTTTTCAAAAAAAAATTCTGTG
Found at i:12373502 original size:40 final size:39
Alignment explanation
Indices: 12373437--12373541 Score: 142
Period size: 39 Copynumber: 2.7 Consensus size: 39
12373427 AGATTTCGTC
12373437 TTTC-AAAATTCTCATGTTTTC-AAAAAAAAATTCTGTG
1 TTTCAAAAATTCTCATGTTTTCAAAAAAAAAATTCTGTG
* * *
12373474 TTTTCAAAAATTTTCATATTTTCAAAAAAAAAAATTTTGTG
1 -TTTCAAAAATTCTCATGTTTTC-AAAAAAAAAATTCTGTG
*
12373515 TTTCAAAAATCCTCATGTTTTCAAAAA
1 TTTCAAAAATTCTCATGTTTTCAAAAA
12373542 TTCTGGTGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
38 4 0.07
39 20 0.34
40 19 0.33
41 15 0.26
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (39 bp):
TTTCAAAAATTCTCATGTTTTCAAAAAAAAAATTCTGTG
Found at i:12373551 original size:35 final size:35
Alignment explanation
Indices: 12373503--12373594 Score: 98
Period size: 35 Copynumber: 2.7 Consensus size: 35
12373493 TTTCAAAAAA
*
12373503 AAAAATT-TTGTGTTTCAAAAATCCTCATGTTTTC
1 AAAAATTCTGGTGTTTCAAAAATCCTCATGTTTTC
** *
12373537 AAAAATTCTGGTGTTT-AGAAAATTTTCGTGTTTTC
1 AAAAATTCTGGTGTTTCA-AAAATCCTCATGTTTTC
* * *
12373572 AAAAATTCCGGTGATCCAAAAAT
1 AAAAATTCTGGTGTTTCAAAAAT
12373595 TTTTGTGTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
34 8 0.17
35 39 0.81
36 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (35 bp):
AAAAATTCTGGTGTTTCAAAAATCCTCATGTTTTC
Found at i:12373575 original size:17 final size:18
Alignment explanation
Indices: 12373503--12373579 Score: 72
Period size: 18 Copynumber: 4.4 Consensus size: 18
12373493 TTTCAAAAAA
*
12373503 AAAAATT-TTGTG-TTTC
1 AAAAATTCTCGTGTTTTC
* *
12373519 AAAAATCCTCATGTTTTC
1 AAAAATTCTCGTGTTTTC
*
12373537 AAAAATTCTGGTG-TTT-
1 AAAAATTCTCGTGTTTTC
*
12373553 AGAAAATTTTCGTGTTTTC
1 A-AAAATTCTCGTGTTTTC
12373572 AAAAATTC
1 AAAAATTC
12373580 CGGTGATCCA
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
16 7 0.15
17 16 0.34
18 23 0.49
19 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.43
Consensus pattern (18 bp):
AAAAATTCTCGTGTTTTC
Found at i:12373595 original size:35 final size:35
Alignment explanation
Indices: 12373530--12373611 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
12373520 AAAATCCTCA
* **
12373530 TGTTTTCAAAAATTCTGGTGTTTAGAAAATTTTCG
1 TGTTTTCAAAAATTCCGGTGTCCAGAAAATTTTCG
*
12373565 TGTTTTCAAAAATTCCGGTGATCCA-AAAATTTTTG
1 TGTTTTCAAAAATTCCGGTG-TCCAGAAAATTTTCG
*
12373600 TGTTTTGAAAAA
1 TGTTTTCAAAAA
12373612 ATTTAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
35 39 0.95
36 2 0.05
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.43
Consensus pattern (35 bp):
TGTTTTCAAAAATTCCGGTGTCCAGAAAATTTTCG
Found at i:12373662 original size:18 final size:17
Alignment explanation
Indices: 12373639--12373750 Score: 89
Period size: 17 Copynumber: 6.4 Consensus size: 17
12373629 AGTGTTTCAG
*
12373639 AAATTTTTGTGTTTTAAA
1 AAATTTTCGTG-TTTAAA
*
12373657 AAATTTTTGTGTTTTGAAA
1 AAATTTTCGTG-TTT-AAA
* *
12373676 AAATTCTCGTGTTTCAA
1 AAATTTTCGTGTTTAAA
*
12373693 AAATTGTCGTGTTTAAA
1 AAATTTTCGTGTTTAAA
** **
12373710 AAACAATTCGTGTTTCTA
1 AAA-TTTTCGTGTTTAAA
* *
12373728 AAATTTCCGTGTTTGAA
1 AAATTTTCGTGTTTAAA
12373745 AAATTT
1 AAATTT
12373751 CATTTAAAAA
Statistics
Matches: 77, Mismatches: 15, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
17 35 0.45
18 30 0.39
19 12 0.16
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (17 bp):
AAATTTTCGTGTTTAAA
Found at i:12373740 original size:17 final size:17
Alignment explanation
Indices: 12373630--12373751 Score: 68
Period size: 18 Copynumber: 6.9 Consensus size: 17
12373620 AAAAGCTCTA
* **
12373630 GTGTTTCAGAAATTTTT
1 GTGTTTCAAAAATTTCC
* **
12373647 GTGTTTTAAAAAATTTTT
1 GTG-TTTCAAAAATTTCC
* *
12373665 GTGTTTTGAAAAAATTCTC
1 GTG-TTTCAAAAATTTC-C
12373684 GTGTTTCAAAAATTGT-C
1 GTGTTTCAAAAATT-TCC
* *
12373701 GTGTTTAAAAAACAATT-C
1 GTGTTT-CAAAA-ATTTCC
*
12373719 GTGTTTCTAAAATTTCC
1 GTGTTTCAAAAATTTCC
*
12373736 GTGTTTGAAAAATTTC
1 GTGTTTCAAAAATTTC
12373752 ATTTAAAAAA
Statistics
Matches: 84, Mismatches: 15, Indels: 12
0.76 0.14 0.11
Matches are distributed among these distances:
16 3 0.04
17 28 0.33
18 47 0.56
19 6 0.07
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (17 bp):
GTGTTTCAAAAATTTCC
Found at i:12381131 original size:15 final size:15
Alignment explanation
Indices: 12381111--12381146 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
12381101 TATTATGCCT
12381111 AAAAAAAC-AAAACA
1 AAAAAAACAAAAACA
12381125 AAAAAAACAAAAACA
1 AAAAAAACAAAAACA
12381140 AAAAAAA
1 AAAAAAA
12381147 AAGAAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAACAAAAACA
Found at i:12381133 original size:9 final size:9
Alignment explanation
Indices: 12381114--12381155 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
12381104 TATGCCTAAA
12381114 AAAACAAAAC
1 AAAA-AAAAC
12381124 AAAAAAAAC
1 AAAAAAAAC
*
12381133 AAAAACAA-
1 AAAAAAAAC
*
12381141 AAAAAAAAG
1 AAAAAAAAC
12381150 AAAAAA
1 AAAAAA
12381156 GAAGGAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 7 0.24
9 18 0.62
10 4 0.14
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:12382142 original size:75 final size:76
Alignment explanation
Indices: 12382007--12382312 Score: 400
Period size: 75 Copynumber: 4.0 Consensus size: 76
12381997 CAAAAATTAT
* * *
12382007 TTTTTCAATTTTTGTTTTTGCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCG
1 TTTTTAAATTTCTGTTTTT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
12382072 CACGCTGAGGTA
65 CACGCTGAGGTA
* * * * *
12382084 -TTTTAAATTTCTATTTTTCAAAAATCAGCTCATATTGCGTGAGGTGAGTTGAGTCTCGGGTCGC
1 TTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
12382148 ACGCTGATGTA
66 ACGCTGAGGTA
* * *
12382159 TTTTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGACA
1 -TTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
12382223 CATGCTGAGGTA
65 CACGCTGAGGTA
*
12382235 TTTCTTTTAAATTTTTGTTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
1 --T-TTTTAAATTTCTGTTTTTC-A-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
*
12382300 GTCACACGGTGAG
61 GTCACACGCTGAG
12382313 TTGAGCCTCG
Statistics
Matches: 199, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
75 53 0.27
76 28 0.14
77 53 0.27
78 17 0.09
79 1 0.01
80 36 0.18
81 11 0.06
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (76 bp):
TTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
ACGCTGAGGTA
Found at i:12382197 original size:152 final size:155
Alignment explanation
Indices: 12382004--12382307 Score: 436
Period size: 157 Copynumber: 2.0 Consensus size: 155
12381994 TTTCAAAAAT
* *
12382004 TATTTTTTCAATTTTTGTTTTTGCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTTCAATTTCTGTTTTTGCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GG
* * * *
12382069 TCGCACGCTGAGGTA-TTTTAAATTTCTATTTTTC-A-AAAATCAGCTCATATTGCGTGAGGTGA
65 ACACACGCTGAGGTATTTTTAAATTTCTATTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGA
* *
12382131 GTTGAGTCTCGGGTCGCACGCTGATG
130 GTTGAGCCTCGGGTCACACGCTGATG
*
12382157 TATTTTTTTAATTTCTGTTTTT-CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGA
1 TATTTTTTCAATTTCTGTTTTTGCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGA
* * *
12382221 CACATGCTGAGGTATTTCTTTTAAATTTTTGTTTTTCAAGAAAATCAACTCATATTGCGAGAGGT
66 CACACGCTGAGGTA--T-TTTTAAATTTCTATTTTTCAAGAAAATCAACTCATATTGCGAGAGGT
12382286 GAGTTGAGCCTCGGGTCACACG
128 GAGTTGAGCCTCGGGTCACACG
12382308 GTGAGTTGAG
Statistics
Matches: 133, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
151 14 0.11
152 38 0.29
153 20 0.15
155 17 0.13
156 1 0.01
157 43 0.32
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (155 bp):
TATTTTTTCAATTTCTGTTTTTGCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGA
CACACGCTGAGGTATTTTTAAATTTCTATTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAG
TTGAGCCTCGGGTCACACGCTGATG
Found at i:12382208 original size:77 final size:77
Alignment explanation
Indices: 12382004--12382312 Score: 417
Period size: 77 Copynumber: 4.0 Consensus size: 77
12381994 TTTCAAAAAT
* *
12382004 TATTTTTTCAATTTTTGTTTTTGCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTTTAATTTCTGTTTTT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
*
12382069 TCGCACGCTGAGG
65 TCACACGCTGAGG
* * * * *
12382082 TA--TTTTAAATTTCTATTTTTCAAAAATCAGCTCATATTGCGTGAGGTGAGTTGAGTCTCGGGT
1 TATTTTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
* *
12382145 CGCACGCTGATG
66 CACACGCTGAGG
* *
12382157 TATTTTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGA
1 TATTTTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
*
12382221 CACATGCTGAGG
66 CACACGCTGAGG
*
12382233 TATTTCTTTTAAATTTTTGTTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 TATTT-TTTT-AATTTCTGTTTTTC-A-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
*
12382298 GGGTCACACGGTGAG
62 GGGTCACACGCTGAG
12382313 TTGAGCCTCG
Statistics
Matches: 202, Mismatches: 22, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
75 53 0.26
76 31 0.15
77 55 0.27
78 15 0.07
79 1 0.00
80 36 0.18
81 11 0.05
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (77 bp):
TATTTTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
CACACGCTGAGG
Found at i:12382315 original size:24 final size:24
Alignment explanation
Indices: 12382283--12382336 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
12382273 TATTGCGAGA
*
12382283 GGTGAGTTGAGCCTCGGGTCACAC
1 GGTGAGTTGAGCCTCGGATCACAC
12382307 GGTGAGTTGAGCCTCGGATCACAC
1 GGTGAGTTGAGCCTCGGATCACAC
*
12382331 GCTGAG
1 GGTGAG
12382337 GTATTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.19, C:0.24, G:0.37, T:0.20
Consensus pattern (24 bp):
GGTGAGTTGAGCCTCGGATCACAC
Done.