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 95 of 316
Found at i:29114713 original size:19 final size:18
Alignment explanation
Indices: 29114691--29114726 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29114681 TTAATAATTA
*
29114691 TTTAATATTAAAATTTTAT
1 TTTAATAAT-AAATTTTAT
29114710 TTTAATAATAAATTTTA
1 TTTAATAATAAATTTTA
29114727 GAAATTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAATAATAAATTTTAT
Found at i:29117490 original size:24 final size:24
Alignment explanation
Indices: 29117392--29117494 Score: 68
Period size: 24 Copynumber: 4.2 Consensus size: 24
29117382 TGGCTATCCG
* * *
29117392 GAGCTTCCTGA-TATGGTTCTTTGT
1 GAGCTTCCCGATTATGGCTC-TTAT
* *
29117416 GAGCTTCCTGATTAATGGCT-TTTT
1 GAGCTTCCCGATT-ATGGCTCTTAT
* ***
29117440 GGAGCTACCCG-TTATTGGCTAGCAT
1 -GAGCTTCCCGATTA-TGGCTCTTAT
29117465 GAGCTTCCCGATTATGGCTCTTAT
1 GAGCTTCCCGATTATGGCTCTTAT
29117489 GAGCTT
1 GAGCTT
29117495 TGTAACAGTC
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
23 1 0.02
24 43 0.69
25 13 0.21
26 5 0.08
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (24 bp):
GAGCTTCCCGATTATGGCTCTTAT
Found at i:29117784 original size:38 final size:38
Alignment explanation
Indices: 29117733--29117810 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
29117723 ATAATTGAAA
*
29117733 GGTCCTTATGTTGTTATTTGACCATTGAACTTATGAGT
1 GGTCCTTATGTTGTTATTTGACCATTGAACCTATGAGT
29117771 GGTCCTTATGTTGTTATTTGACCATTGAACCTATGAGT
1 GGTCCTTATGTTGTTATTTGACCATTGAACCTATGAGT
29117809 GG
1 GG
29117811 ACATTAATGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.42
Consensus pattern (38 bp):
GGTCCTTATGTTGTTATTTGACCATTGAACCTATGAGT
Found at i:29118863 original size:43 final size:42
Alignment explanation
Indices: 29118778--29118893 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 42
29118768 CATCGACTTA
29118778 TGATTTACGTGTAAGACCATGTCTAGGACATCGACATCATATT
1 TGATTT-CGTGTAAGACCATGTCTAGGACATCGACATCATATT
* * *
29118821 TGATTTCGTGTAAGACCCTGTCTGGGACAAT-GGCATCAATATT
1 TGATTTCGTGTAAGACCATGTCTAGGAC-ATCGACATC-ATATT
* * * *
29118864 TGATTACATGTAAGACCACGTCAAGGACAT
1 TGATTTCGTGTAAGACCATGTCTAGGACAT
29118894 TGGCATTGTA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
42 27 0.44
43 35 0.56
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCATGTCTAGGACATCGACATCATATT
Found at i:29118898 original size:43 final size:43
Alignment explanation
Indices: 29118741--29118899 Score: 128
Period size: 43 Copynumber: 3.7 Consensus size: 43
29118731 TATGTGTTCT
** * *
29118741 CATGTAAGACCACGTCTAA-GATGTTGGCATCGACT-TATGATTTA
1 CATGTAAGACCACGTC-AAGGACATTGGCATC-AATATTTGA-TTA
* * * * * *
29118785 CGTGTAAGACCATGTCTAGGACATCGACATC-ATATTTGATTT
1 CATGTAAGACCACGTCAAGGACATTGGCATCAATATTTGATTA
* ** *
29118827 CGTGTAAGACC-CTGTCTGGGACAATGGCATCAATATTTGATTA
1 CATGTAAGACCAC-GTCAAGGACATTGGCATCAATATTTGATTA
29118870 CATGTAAGACCACGTCAAGGACATTGGCAT
1 CATGTAAGACCACGTCAAGGACATTGGCAT
29118900 TGTACGAGCT
Statistics
Matches: 90, Mismatches: 20, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
42 28 0.31
43 39 0.43
44 23 0.26
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (43 bp):
CATGTAAGACCACGTCAAGGACATTGGCATCAATATTTGATTA
Found at i:29121805 original size:22 final size:22
Alignment explanation
Indices: 29121775--29121827 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
29121765 TGTATATAAG
*
29121775 AAAATTTTTGAAATTTTGTTAG
1 AAAATTTTTGAAATTTTGTTAA
*
29121797 ACAATTTTTGAAATTTTGTTAA
1 AAAATTTTTGAAATTTTGTTAA
29121819 AAAATTTTT
1 AAAATTTTT
29121828 AAGTTCCCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (22 bp):
AAAATTTTTGAAATTTTGTTAA
Found at i:29122454 original size:5 final size:5
Alignment explanation
Indices: 29122444--29122481 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
29122434 CAAAAATAAA
29122444 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TAT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TAT
29122482 GGTTGGTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:29122744 original size:23 final size:24
Alignment explanation
Indices: 29122704--29122760 Score: 82
Period size: 23 Copynumber: 2.4 Consensus size: 24
29122694 TCCATGGAAA
29122704 AATTAGAAAAAATAATATGATAATT
1 AATTA-AAAAAATAATATGATAATT
29122729 AA-TAAAAATAAT-ATATGATAATT
1 AATTAAAAA-AATAATATGATAATT
29122752 AATTAAAAA
1 AATTAAAAA
29122761 GAAAAAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 17 0.57
24 11 0.37
25 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (24 bp):
AATTAAAAAAATAATATGATAATT
Found at i:29128196 original size:14 final size:14
Alignment explanation
Indices: 29128177--29128209 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
29128167 AAAGTGGGAA
29128177 AAATAATGGATGAT
1 AAATAATGGATGAT
29128191 AAATAATGGATGAT
1 AAATAATGGATGAT
29128205 AAATA
1 AAATA
29128210 TTTAAATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (14 bp):
AAATAATGGATGAT
Found at i:29129403 original size:24 final size:24
Alignment explanation
Indices: 29129302--29129404 Score: 77
Period size: 24 Copynumber: 4.2 Consensus size: 24
29129292 GGCTATCCGA
* * *
29129302 AGCTTCCTGA-TATGGTTCTTCGTG
1 AGCTTCCCGATTATGGCTCTT-ATG
* *
29129326 AGATTCCTGATTAATGGCTCTT-TCG
1 AGCTTCCCGATT-ATGGCTCTTAT-G
* **
29129351 AGCTACCCG-TTATTGGCTCGCATG
1 AGCTTCCCGATTA-TGGCTCTTATG
29129375 AGCTTCCCGATTATGGCTCTTATG
1 AGCTTCCCGATTATGGCTCTTATG
29129399 AGCTTC
1 AGCTTC
29129405 TCATTATATA
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
23 1 0.02
24 42 0.67
25 12 0.19
26 8 0.13
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (24 bp):
AGCTTCCCGATTATGGCTCTTATG
Found at i:29133672 original size:26 final size:26
Alignment explanation
Indices: 29133642--29133749 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
29133632 TGAAATTCCC
29133642 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
29133668 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
29133694 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
29133720 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
29133746 ATCA
1 ATCA
29133750 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:29153623 original size:26 final size:26
Alignment explanation
Indices: 29153593--29153700 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
29153583 TGAAATTCCC
29153593 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
29153619 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
29153645 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
29153671 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
29153697 ATCA
1 ATCA
29153701 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:29159353 original size:34 final size:33
Alignment explanation
Indices: 29159310--29159374 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 33
29159300 ACTTATTATA
29159310 TATATATATA-TTATAATATATAATAAGAAATGTG
1 TATATATATAGTTATAATAT-TAATAA-AAATGTG
29159344 TATATATATATGTTATAATATTAATAAAAAT
1 TATATATATA-GTTATAATATTAATAAAAAT
29159375 AAAAGTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 14 0.48
35 6 0.21
36 9 0.31
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (33 bp):
TATATATATAGTTATAATATTAATAAAAATGTG
Found at i:29159360 original size:36 final size:34
Alignment explanation
Indices: 29159308--29159374 Score: 107
Period size: 36 Copynumber: 1.9 Consensus size: 34
29159298 TGACTTATTA
29159308 TATATATATATATTATAATATATAATAAGAAATGTG
1 TATATATATATATTATAATAT-TAATAA-AAATGTG
*
29159344 TATATATATATGTTATAATATTAATAAAAAT
1 TATATATATATATTATAATATTAATAAAAAT
29159375 AAAAGTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 4 0.13
35 6 0.20
36 20 0.67
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (34 bp):
TATATATATATATTATAATATTAATAAAAATGTG
Found at i:29165333 original size:40 final size:40
Alignment explanation
Indices: 29165266--29165433 Score: 205
Period size: 40 Copynumber: 4.2 Consensus size: 40
29165256 TAAGATCCGG
*
29165266 AGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCCCCGA
1 AGGCATTTGTGCGAGATACTAAA-TCCGGGTTAAGTCCCGA
* *
29165306 AGGCCTTTGTGTGAGATACTAAATCCGGGTTAAGTCCCGA
1 AGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGA
* * * *
29165346 AGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGA
1 AGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGA
* * * * *
29165386 AGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTCCCGA
1 AGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGA
29165425 AGGCATTTG
1 AGGCATTTG
29165434 AACGAGGAGC
Statistics
Matches: 112, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
39 34 0.30
40 75 0.67
41 3 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
AGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGA
Found at i:29165350 original size:80 final size:79
Alignment explanation
Indices: 29165266--29165433 Score: 221
Period size: 79 Copynumber: 2.1 Consensus size: 79
29165256 TAAGATCCGG
* *
29165266 AGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGTGAGATACTAAAT
1 AGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGTGAGATACTAAAA
*
29165330 CCGGGTTAAGTCCCGA
64 CCGGGCTAAGTCCCGA
* * * * * *
29165346 AGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACC
1 AGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGTGAGATACTAAAACC
*
29165411 GGGCTATGTCCCGA
66 GGGCTAAGTCCCGA
29165425 AGGCATTTG
1 AGGCATTTG
29165434 AACGAGGAGC
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
79 39 0.51
80 34 0.45
81 3 0.04
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (79 bp):
AGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGTGAGATACTAAAACC
GGGCTAAGTCCCGA
Found at i:29165451 original size:79 final size:80
Alignment explanation
Indices: 29165289--29165466 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
29165279 AGATACAAAT
* * * *
29165289 TCCGGGTTAAGCCCCGAAGGCCTTTGTGTGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGTGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
29165354 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
29165369 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGTGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
29165433 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
29165448 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
29165467 TACGTGATTT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
78 15 0.18
79 49 0.60
80 18 0.22
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGTGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:29179313 original size:68 final size:64
Alignment explanation
Indices: 29179241--29179448 Score: 213
Period size: 67 Copynumber: 3.2 Consensus size: 64
29179231 CATCATGTGT
29179241 ACAAGAGAGCTACGAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
1 ACAAGAGAGCTACGAG--A-TAT-ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
29179306 TAG
62 TAG
* * * * * * *
29179309 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGT
29179374 AG
63 AG
* * * * * *
29179376 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-G
1 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG
29179438 TACAAGAGAGC
1 -ACAAGAGAGC
29179449 CAAAATTATG
Statistics
Matches: 117, Mismatches: 19, Indels: 13
0.79 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.16
64 21 0.18
65 11 0.09
66 18 0.15
67 32 0.27
68 15 0.13
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (64 bp):
ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG
Found at i:29181798 original size:20 final size:21
Alignment explanation
Indices: 29181760--29181798 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
29181750 GCTCTTAAAA
* *
29181760 TATGAAAATTTTTCTAAGTGT
1 TATGAAAATTTTCCAAAGTGT
29181781 TATG-AAATTTTCCAAAGT
1 TATGAAAATTTTCCAAAGT
29181799 TCTCGGTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.44
Consensus pattern (21 bp):
TATGAAAATTTTCCAAAGTGT
Found at i:29185645 original size:41 final size:41
Alignment explanation
Indices: 29185600--29185776 Score: 210
Period size: 41 Copynumber: 4.3 Consensus size: 41
29185590 CTTTGTGATG
* * * *
29185600 GTGTATTATATCTGGCTTTGTGCCTAGAAGGCTTTGTGCCT
1 GTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCGTGCCA
* *
29185641 GTGTATTATATCAGGCTCTATGCCTAGCAGGCTTCGTGCCA
1 GTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCGTGCCA
* * * * *
29185682 GTGTATTATATCAGGCATTGTGCCTAGTAGGCTTCATGTCG
1 GTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCGTGCCA
* * * * *
29185723 GTGTGTTATATCAAGCTTTGAGCCTAGCATGCTTCGTGACA
1 GTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCGTGCCA
29185764 GTGTATTATATCA
1 GTGTATTATATCA
29185777 AGTAGGTTGT
Statistics
Matches: 113, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 113 1.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
GTGTATTATATCAGGCTTTGTGCCTAGCAGGCTTCGTGCCA
Found at i:29187427 original size:40 final size:40
Alignment explanation
Indices: 29187383--29187489 Score: 105
Period size: 37 Copynumber: 2.7 Consensus size: 40
29187373 AGATAATTCA
**
29187383 AAGTATTAAATTGACACCCAGTGTCTCATCGGTTAAA-CCG
1 AAGTA-TAAATTGACACCCAGTGTCTCATCGAATAAATCCG
* * **
29187423 AAG--TAAATTGGCACCCAGTGCCTCATCGAATAAATTTG
1 AAGTATAAATTGACACCCAGTGTCTCATCGAATAAATCCG
*
29187461 AAGTAATAAATTAACACCCA-TGTCTCATC
1 AAGT-ATAAATTGACACCCAGTGTCTCATC
29187490 AACTCGAAGT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
37 27 0.50
38 4 0.07
40 11 0.20
41 12 0.22
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (40 bp):
AAGTATAAATTGACACCCAGTGTCTCATCGAATAAATCCG
Found at i:29192671 original size:43 final size:44
Alignment explanation
Indices: 29192559--29192672 Score: 101
Period size: 43 Copynumber: 2.7 Consensus size: 44
29192549 CAATGCCAAC
* * *
29192559 GTCCCAGGCGTGGTCTTACATGT-AACCAAATATCGATGCCACT
1 GTCCCAGGCATGGTCTTACATGTAAATCAAATATCGAAGCCACT
* * * ** **
29192602 ATCCCAGACAGGGTCTTACA-CAAAATCAAATA-CGACAGTGA-T
1 GTCCCAGGCATGGTCTTACATGTAAATCAAATATCGA-AGCCACT
29192644 GTCCCAGGCATGGTCTTACATGTAAATCA
1 GTCCCAGGCATGGTCTTACATGTAAATCA
29192673 TAAGTCGATG
Statistics
Matches: 53, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
42 21 0.40
43 32 0.60
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (44 bp):
GTCCCAGGCATGGTCTTACATGTAAATCAAATATCGAAGCCACT
Found at i:29192708 original size:86 final size:85
Alignment explanation
Indices: 29192559--29192715 Score: 203
Period size: 86 Copynumber: 1.8 Consensus size: 85
29192549 CAATGCCAAC
* *
29192559 GTCCCAGGCGTGGTCTTACATGTAACCAAATATCGATGCCACTATCCCAGACAGGGTCTTACACA
1 GTCCCAGGCATGGTCTTACATGTAACCAAATATCGATGCCACTATCCCAAACAGGGTCTTACACA
29192624 AAATCAAATACGACAGTGAT
66 AAATCAAATACGACAGTGAT
* * *
29192644 GTCCCAGGCATGGTCTTACATGTAAATCATAA-GTCGATGCCAAC-GTCCCAAAC-GTGGTCTTA
1 GTCCCAGGCATGGTCTTACATGT-AACCA-AATATCGATGCC-ACTATCCCAAACAG-GGTCTTA
*
29192706 CACGAAATCA
62 CACAAAATCA
29192716 CATATCGGAT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
85 23 0.37
86 35 0.56
87 4 0.06
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (85 bp):
GTCCCAGGCATGGTCTTACATGTAACCAAATATCGATGCCACTATCCCAAACAGGGTCTTACACA
AAATCAAATACGACAGTGAT
Found at i:29195163 original size:27 final size:27
Alignment explanation
Indices: 29195132--29195309 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29195122 TAAATTGTAC
29195132 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
29195159 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29195185 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
29195213 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
29195241 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29195268 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
29195295 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
29195310 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:29195246 original size:82 final size:81
Alignment explanation
Indices: 29195133--29195288 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29195123 AAATTGTACA
* *
29195133 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
29195197 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
29195214 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
29195279 TGCGAGTTGA
65 TGCGAATTGA
29195289 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:29195300 original size:82 final size:81
Alignment explanation
Indices: 29195129--29195309 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
29195119 GATTAAATTG
* *
29195129 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
29195194 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
29195210 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
29195274 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
29195292 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
29195310 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:29197735 original size:16 final size:16
Alignment explanation
Indices: 29197698--29197758 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
29197688 CCTAAAGCCC
*
29197698 TTCTTCTTC-TTCTTT
1 TTCTTTTTCTTTCTTT
*
29197713 CTCCTTTTTCTTTCTTT
1 -TTCTTTTTCTTTCTTT
*
29197730 TTCTTTTTCTTTCTGT
1 TTCTTTTTCTTTCTTT
*
29197746 TTCATTTTGCTTT
1 TTC-TTTTTCTTT
29197759 GTTTCTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
16 24 0.63
17 14 0.37
ACGTcount: A:0.02, C:0.23, G:0.03, T:0.72
Consensus pattern (16 bp):
TTCTTTTTCTTTCTTT
Found at i:29200487 original size:23 final size:23
Alignment explanation
Indices: 29200460--29200505 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
29200450 ACTAACAAAA
29200460 ACAATAGAAAAACAGTTAAATTC
1 ACAATAGAAAAACAGTTAAATTC
29200483 ACAATAGAAAAACAGTTAAATTC
1 ACAATAGAAAAACAGTTAAATTC
29200506 GTATGTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.13, G:0.09, T:0.22
Consensus pattern (23 bp):
ACAATAGAAAAACAGTTAAATTC
Found at i:29200571 original size:24 final size:24
Alignment explanation
Indices: 29200539--29200585 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
29200529 GCAACTTTTT
29200539 TTTTAAAGATTTTTCAAAACCTTA
1 TTTTAAAGATTTTTCAAAACCTTA
29200563 TTTTAAAGATTTTTCAAAACCTT
1 TTTTAAAGATTTTTCAAAACCTT
29200586 GCATTGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (24 bp):
TTTTAAAGATTTTTCAAAACCTTA
Found at i:29201550 original size:18 final size:18
Alignment explanation
Indices: 29201507--29201542 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29201497 CCCTGGCCTG
*
29201507 TTGATTATATAATTTAAA
1 TTGATTATATAATTAAAA
29201525 TTGATTATATAATTAAAA
1 TTGATTATATAATTAAAA
29201543 ATTATTATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
TTGATTATATAATTAAAA
Found at i:29209286 original size:26 final size:26
Alignment explanation
Indices: 29209257--29209340 Score: 91
Period size: 26 Copynumber: 3.1 Consensus size: 26
29209247 AGTTTGTTCC
29209257 AATTAGATTAATGTTGTAATGTATTT
1 AATTAGATTAATGTTGTAATGTATTT
*
29209283 AATTA-ATGTTCCAAT-TAGATTAATGTATTT
1 AATTAGA--TT--AATGTTG--TAATGTATTT
29209313 AATTAGATTAATGTTGTAATGTATTT
1 AATTAGATTAATGTTGTAATGTATTT
29209339 AA
1 AA
29209341 ATTTTGTTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
25 1 0.02
26 17 0.35
27 5 0.10
28 4 0.08
29 5 0.10
30 15 0.31
31 1 0.02
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.48
Consensus pattern (26 bp):
AATTAGATTAATGTTGTAATGTATTT
Found at i:29209304 original size:17 final size:17
Alignment explanation
Indices: 29209251--29209327 Score: 64
Period size: 18 Copynumber: 4.2 Consensus size: 17
29209241 TTACAAAGTT
29209251 TGTTCCAATTAGATTAA
1 TGTTCCAATTAGATTAA
** *
29209268 TGTTGTAATGTATTTAATTAA
1 TGTTCCAAT-TA---GATTAA
29209289 TGTTCCAATTAGATTAA
1 TGTTCCAATTAGATTAA
**
29209306 TGTATTTAATTAGATTAA
1 TGT-TCCAATTAGATTAA
29209324 TGTT
1 TGTT
29209328 GTAATGTATT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
17 16 0.34
18 17 0.36
20 2 0.04
21 12 0.26
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (17 bp):
TGTTCCAATTAGATTAA
Found at i:29212444 original size:293 final size:284
Alignment explanation
Indices: 29212042--29212994 Score: 1204
Period size: 293 Copynumber: 3.3 Consensus size: 284
29212032 TTGTTCGGTG
* * * *
29212042 ATTTTGGCCCTTTGTTTGTATTTTTTTATTCTCGGATTTTATTTTTAAAATATACTATTTTTATA
1 ATTTTGGCCCTTTATTTGTATATTTTTATTCTCAGATTTTATTTTTAAAATATACTATTTTCATA
29212107 TTTTATTTTTTATATTATTTTAGT-CAATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATAT
66 TTTTATTTTTTATATTATTTTA-TAC-ATAATGTTTCAAATGTATTATTTTAGT-TTTTTTATAT
*
29212171 TAATTTAGTAAAAAATCCTGATTTTGGCTCTTTGTTTGTATTTTTTTCAGATTTTATTTTCTAAA
128 TAATTTAGTAAAAAATCCTGATTTTGGC-CTTTGTTTGTATTTTTTTCGGATTTTATTTTCT-AA
*
29212236 ATATACTATTTTCGTATTTTATTTTTTTTATATTATTTTAGTTTCAAATGTATTGTATTAGTTTT
191 ATATACTATTTTCTTATTTTA--TTTTTTATATTATTTTAGTTTCAAATGTATTGTATTAGTTTT
29212301 TTTATATATATTAATTTAGTAAAAAAACCCTGA
254 TTT-T-TATATTAATTTAGTAAAAAAACCCTGA
*
29212334 ATTTTGGCCATTTATTTGTA-ATTTTTATTCTCAGATTTTATTTTTTAAAATATACTATTTTCAT
1 ATTTTGGCCCTTTATTTGTATATTTTTATTCTCAGATTTTA-TTTTTAAAATATACTATTTTCAT
29212398 ATTTTATTTTTTTATATTATTTTAATACATAATGTTTCAAATGTATTATTTTAGTATTTTTTATA
65 ATTTTA-TTTTTTATATTATTTT-ATACATAATGTTTCAAATGTATTATTTTAGT-TTTTTTATA
*
29212463 TTAATTTAGTAAAAAATCCTGATTTTGGCCCTTTATTTGTATTTTTTTCGGATTTTATTTTCTCA
127 TTAATTTAGTAAAAAATCCTGATTTTGG-CCTTTGTTTGTATTTTTTTCGGATTTTATTTTCT-A
* * * * *
29212528 ATTATACTATTTTTTTATTTTA-TTTTTATATTATTTTAGTTTTAAATGTATTATTTTAGTGTTC
190 AATATACTATTTTCTTATTTTATTTTTTATATTATTTTAGTTTCAAATGTATTGTATTAGT-TT-
* *
29212592 TTTTTTATATTAATTTGGTAAAAAAATCCTGA
253 TTTTTTATATTAATTTAGTAAAAAAACCCTGA
* **
29212624 ATTTTGGCCCTTT-TTTGTATTTTTTTATTCTC-GTATTTTATTTTTTAAAATATACTATTTTTG
1 ATTTTGGCCCTTTATTTGTATATTTTTATTCTCAG-ATTTTA-TTTTTAAAATATACTATTTTCA
* *
29212687 TATTTTATTTTTTATATTA-TTT-TA-GT-A--TTTCAAAAGTATTATTTTAGTTTTTTTATATT
64 TATTTTATTTTTTATATTATTTTATACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATT
* * *
29212746 AATTTAGTAAAAAATCTTGATTTTGACCATTTGTTTGTATTTTTTATTCTCGGATTTTATTTTGT
129 AATTTAGTAAAAAATCCTGATTTTGGCC-TTTGTTTGTA--TTTT-TT-TCGGATTTTATTTTCT
*
29212811 AAATATACTATTTTCTTATTTTATTTTTTATATTATTTTAG-TACATAATGT-TTCAAAAGTATT
189 AAATATACTATTTTCTTATTTTATTTTTTATATTATTTTAGTTTCA-AATGTATT-----GTATT
* *
29212874 ATTTTAGTTTTTTATATTAATTTAGT-AAAAAACACTG-
248 AGTTT--TTTTTTATATTAATTTAGTAAAAAAACCCTGA
* * * * *
29212911 ATTTTGGCCCTTTATTTG--TATTTGTATT-TTATATTTTATTTTTAAAATATACTACTTTCGTA
1 ATTTTGGCCCTTTATTTGTATATTTTTATTCTCAGATTTTATTTTTAAAATATACTATTTTCATA
*
29212973 TTTTCTTTTTTATATTATTTTA
66 TTTTATTTTTTATATTATTTTA
29212995 GTAAAAAACC
Statistics
Matches: 590, Mismatches: 45, Indels: 58
0.85 0.06 0.08
Matches are distributed among these distances:
280 2 0.00
281 44 0.07
282 20 0.03
283 4 0.01
284 66 0.11
285 48 0.08
286 10 0.02
287 13 0.02
288 18 0.03
289 42 0.07
290 117 0.20
291 21 0.04
292 50 0.08
293 132 0.22
294 3 0.01
ACGTcount: A:0.27, C:0.07, G:0.08, T:0.59
Consensus pattern (284 bp):
ATTTTGGCCCTTTATTTGTATATTTTTATTCTCAGATTTTATTTTTAAAATATACTATTTTCATA
TTTTATTTTTTATATTATTTTATACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAA
TTTAGTAAAAAATCCTGATTTTGGCCTTTGTTTGTATTTTTTTCGGATTTTATTTTCTAAATATA
CTATTTTCTTATTTTATTTTTTATATTATTTTAGTTTCAAATGTATTGTATTAGTTTTTTTTTAT
ATTAATTTAGTAAAAAAACCCTGA
Found at i:29212678 original size:144 final size:139
Alignment explanation
Indices: 29212040--29212997 Score: 1028
Period size: 144 Copynumber: 6.6 Consensus size: 139
29212030 TTTTGTTCGG
* *
29212040 TGATTTTGGCCCTTTGTTTGTATTTTTTTATTCTCGGATTTTA-TTTTTAAAATATACTATTTTT
1 TGATTTTGGCCCTTTATTTGTA--TTTTTATT-TCGGATTTTATTTTTTAAAATATACTATTTTC
* *
29212104 ATATTTTATTTTTTATATTATTTTAGTCAATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAT
63 GTATTTTATTTTTTATATTATTTTAG----T-A--TTTCAAAAGTATTATTTTAGT-TTTTTTAT
29212169 ATTAATTTAGTAAAAAATCC
120 ATTAATTTAGTAAAAAATCC
* * * *
29212189 TGATTTTGGCTCTTTGTTTGTA-TTTT-TTTCAGATTTTATTTTCTAAAATATACTATTTTCGTA
1 TGATTTTGGCCCTTTATTTGTATTTTTATTTCGGATTTTATTTTTTAAAATATACTATTTTCGTA
* * *
29212252 TTTTATTTTTTTTATATTATTTTAG--TTTCAAATGTATTGTATTAGTTTTTTTATATATATTAA
66 TTTTA--TTTTTTATATTATTTTAGTATTTCAAAAGTATTATTTTAG--TTTTT-T-TATATTAA
*
29212315 TTTAGTAAAAAAACCC
125 TTTAGT-AAAAAATCC
* *
29212331 TGAATTTTGGCCATTTATTTGTAATTTTTATTCTCAGATTTTATTTTTTAAAATATACTATTTTC
1 TG-ATTTTGGCCCTTTATTTGT-ATTTTTATT-TCGGATTTTATTTTTTAAAATATACTATTTTC
* * *
29212396 ATATTTTATTTTTTTATATTATTTTAATACATAATGTTTCAAATGTATTATTTTAGTATTTTTTA
63 GTATTTTA-TTTTTTATATTA-TTT--TA-GT-A--TTTCAAAAGTATTATTTTAGT-TTTTTTA
29212461 TATTAATTTAGTAAAAAATCC
119 TATTAATTTAGTAAAAAATCC
* * * **
29212482 TGATTTTGGCCCTTTATTTGTA-TTTT-TTTCGGATTTTATTTTCTCAATTATACTATTTTTTTA
1 TGATTTTGGCCCTTTATTTGTATTTTTATTTCGGATTTTATTTTTTAAAATATACTATTTTCGTA
*
29212545 TTTTA-TTTTTATATTATTTTAGT-TTT-AAATGTATTATTTTAGTGTTCTTTTTTATATTAATT
66 TTTTATTTTTTATATTATTTTAGTATTTCAAAAGTATTATTTTA--G-T-TTTTTTATATTAATT
*
29212607 TGGTAAAAAAATCC
127 TAGT-AAAAAATCC
*
29212621 TGAATTTTGGCCCTTT-TTTGTATTTTTTTATTCTCGTATTTTATTTTTTAAAATATACTATTTT
1 TG-ATTTTGGCCCTTTATTTGTA--TTTTTATT-TCGGATTTTATTTTTTAAAATATACTATTTT
*
29212685 TGTATTTTATTTTTTATATTATTTTAGTATTTCAAAAGTATTATTTTAGTTTTTTTATATTAATT
62 CGTATTTTATTTTTTATATTATTTTAGTATTTCAAAAGTATTATTTTAGTTTTTTTATATTAATT
*
29212750 TAGTAAAAAATCT
127 TAGTAAAAAATCC
* * * * *
29212763 TGATTTTGACCATTTGTTTGTATTTTTTATTCTCGGATTTTATTTTGT-AAATATACTATTTTCT
1 TGATTTTGGCCCTTTATTTGTA-TTTTTATT-TCGGATTTTATTTTTTAAAATATACTATTTTCG
29212827 TATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAAAAGTATTATTTTAG-TTTTTTATAT
64 TATTTTATTTTTTATATTATTTTAG----T-A--TTTCAAAAGTATTATTTTAGTTTTTTTATAT
29212891 TAATTTAGTAAAAAA-CAC
122 TAATTTAGTAAAAAATC-C
* *** *
29212909 TGATTTTGGCCCTTTATTTGTATTTGTATTTTATATTTTA-TTTTTAAAATATACTACTTTCGTA
1 TGATTTTGGCCCTTTATTTGTATTTTTATTTCGGATTTTATTTTTTAAAATATACTATTTTCGTA
*
29212973 TTTTCTTTTTTATATTATTTTAGTA
66 TTTTATTTTTTATATTATTTTAGTA
29212998 AAAAACCCAT
Statistics
Matches: 710, Mismatches: 53, Indels: 102
0.82 0.06 0.12
Matches are distributed among these distances:
135 15 0.02
136 3 0.00
137 1 0.00
138 37 0.05
139 22 0.03
140 56 0.08
141 51 0.07
142 30 0.04
143 43 0.06
144 103 0.15
145 60 0.08
146 100 0.14
147 95 0.13
148 4 0.01
149 24 0.03
150 18 0.03
151 10 0.01
152 14 0.02
153 2 0.00
154 4 0.01
155 18 0.03
ACGTcount: A:0.27, C:0.07, G:0.08, T:0.58
Consensus pattern (139 bp):
TGATTTTGGCCCTTTATTTGTATTTTTATTTCGGATTTTATTTTTTAAAATATACTATTTTCGTA
TTTTATTTTTTATATTATTTTAGTATTTCAAAAGTATTATTTTAGTTTTTTTATATTAATTTAGT
AAAAAATCC
Found at i:29212745 original size:19 final size:20
Alignment explanation
Indices: 29212692--29212754 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 20
29212682 TTTTGTATTT
29212692 TATTTTTTATATTATTTTAG
1 TATTTTTTATATTATTTTAG
***
29212712 TATTTCAAAAGTATTATTTTAG
1 TATTT-TTTA-TATTATTTTAG
*
29212734 T-TTTTTTATATTAATTTAG
1 TATTTTTTATATTATTTTAG
29212753 TA
1 TA
29212755 AAAAATCTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
19 11 0.33
20 6 0.18
21 4 0.12
22 12 0.36
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (20 bp):
TATTTTTTATATTATTTTAG
Found at i:29213457 original size:25 final size:25
Alignment explanation
Indices: 29213429--29213480 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
29213419 TGCCGCCTCC
*
29213429 TTCTCCTTCTCCTTTTTC-TCTTCTT
1 TTCTCCTTCTCCTTCTTCTTC-TCTT
*
29213454 TTCTTCTTCTCCTTCTTCTTCTCTT
1 TTCTCCTTCTCCTTCTTCTTCTCTT
29213479 TT
1 TT
29213481 TTTTTCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (25 bp):
TTCTCCTTCTCCTTCTTCTTCTCTT
Found at i:29213500 original size:28 final size:29
Alignment explanation
Indices: 29213428--29213502 Score: 91
Period size: 27 Copynumber: 2.6 Consensus size: 29
29213418 GTGCCGCCTC
*
29213428 CTTCTCCTTCTCCTTTTTCTCTTCTTTTCTT
1 CTTCTCCTTCT--TTCTTCTCTTCTTTTCTT
*
29213459 CTTCTCCTTC-TTCTTCTCTT-TTTTTTT
1 CTTCTCCTTCTTTCTTCTCTTCTTTTCTT
*
29213486 CTTTTCCTTCTTTCTTC
1 CTTCTCCTTCTTTCTTC
29213503 CTAGCCGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 15 0.38
28 15 0.38
31 10 0.25
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (29 bp):
CTTCTCCTTCTTTCTTCTCTTCTTTTCTT
Found at i:29213713 original size:17 final size:16
Alignment explanation
Indices: 29213690--29213728 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
29213680 TCATTTCTTG
*
29213690 TTTTTTGTTACAGCTT
1 TTTTTTGTTACAGATT
*
29213706 TCTTTTTGTTTCAGATT
1 T-TTTTTGTTACAGATT
29213723 TTTTTT
1 TTTTTT
29213729 CATATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.69
Consensus pattern (16 bp):
TTTTTTGTTACAGATT
Found at i:29214329 original size:21 final size:21
Alignment explanation
Indices: 29214288--29214329 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29214278 AAAACTATTT
*
29214288 AAAAATTTAAAAAAATCATTA
1 AAAAATTTAAAAAAATAATTA
29214309 AAAAATTGTAAAAAAA-AATTA
1 AAAAATT-TAAAAAAATAATTA
29214330 TAAGATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (21 bp):
AAAAATTTAAAAAAATAATTA
Found at i:29214613 original size:9 final size:9
Alignment explanation
Indices: 29214601--29214701 Score: 60
Period size: 9 Copynumber: 10.3 Consensus size: 9
29214591 TTTGTAATTT
*
29214601 TTTTTATGA
1 TTTTTATAA
29214610 TTTTTATAA
1 TTTTTATAA
29214619 TATTTTATAA
1 T-TTTTATAA
29214629 TTTTTTTAATAA
1 --TTTTT-ATAA
29214641 TTTTTA-AA
1 TTTTTATAA
*
29214649 TATCTTTTTATA
1 T-T-TTTATA-A
29214661 TTTTTATTAAA
1 TTTTTA-T-AA
* *
29214672 ATTTAATAA
1 TTTTTATAA
*
29214681 TTTGTATAA
1 TTTTTATAA
*
29214690 CTTTTATAA
1 TTTTTATAA
29214699 TTT
1 TTT
29214702 CTTTTGCAAC
Statistics
Matches: 71, Mismatches: 11, Indels: 20
0.70 0.11 0.20
Matches are distributed among these distances:
8 3 0.04
9 28 0.39
10 20 0.28
11 12 0.17
12 8 0.11
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:29214624 original size:31 final size:30
Alignment explanation
Indices: 29214589--29214675 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
29214579 TTTTTGATGC
* * *
29214589 ATTTTGTAATTTTTTTTATGATTTTTATAAT
1 ATTTTATAATTTTTTTAATAATTTTTA-AAT
29214620 ATTTTATAATTTTTTTAATAATTTTTAAAT
1 ATTTTATAATTTTTTTAATAATTTTTAAAT
*
29214650 ATCTTTTTATATTTTTATTAA-AATTT
1 AT-TTTATA-ATTTTT-TTAATAATTT
29214676 AATAATTTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 5 0.10
31 29 0.59
32 11 0.22
33 4 0.08
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.66
Consensus pattern (30 bp):
ATTTTATAATTTTTTTAATAATTTTTAAAT
Found at i:29214626 original size:19 final size:20
Alignment explanation
Indices: 29214602--29214644 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
29214592 TTGTAATTTT
*
29214602 TTTTATGATTTTTATAAT-A
1 TTTTATAATTTTTATAATAA
*
29214621 TTTTATAATTTTTTTAATAA
1 TTTTATAATTTTTATAATAA
29214641 TTTT
1 TTTT
29214645 TAAATATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTATAATTTTTATAATAA
Found at i:29214635 original size:22 final size:22
Alignment explanation
Indices: 29214610--29214667 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 22
29214600 TTTTTTATGA
29214610 TTTTTATAATATTTTATAAT-T-
1 TTTTTATAAT-TTTTATAATATC
29214631 TTTTTAATAATTTTTA-AATATC
1 TTTTT-ATAATTTTTATAATATC
29214653 TTTTTAT-ATTTTTAT
1 TTTTTATAATTTTTAT
29214668 TAAAATTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 10 0.30
21 13 0.39
22 10 0.30
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTTATAATTTTTATAATATC
Found at i:29215038 original size:91 final size:90
Alignment explanation
Indices: 29214818--29215067 Score: 218
Period size: 91 Copynumber: 2.7 Consensus size: 90
29214808 TTTTTATATA
* * * * *
29214818 TTTGACAGTTCAAGTACCCAATTGAGTGTAAAAAAAATTAGGGGCTTAATTCTTTTTTTTTTTTT
1 TTTGAAAGTTCAAGTACCCAATTAAGTGAAAAAAAAAGTAAGGGCTTAATTC--TTTTTTTTTTT
** *
29214883 GAAAAAAGTTTGAGGGTCTTTTTGATGTAT
64 ---AAAAGTTTGAGGACCTTTTTGATGCAT
* * * **
29214913 TTTAAAAGTTTAAATATTCAATTGAA-TGAAAAAAAAAAGTAAGGGCTTAATTACTTTTTTTTTT
1 TTTGAAAGTTCAAGTACCCAATT-AAGTG-AAAAAAAAAGTAAGGGCTTAATT-CTTTTTTTTTT
* *
29214977 T-AAATTTTGCGGACCTTTTTGATGCAT
63 TAAAAGTTTGAGGACCTTTTTGATGCAT
* **
29215004 TTTGAAAGTTCCAAGTACCCAATTAAGTGCAAAAAAAAAG-CAGTGGCTTAATTGGTTTTTTTTT
1 TTTGAAAGTT-CAAGTACCCAATTAAGTG-AAAAAAAAAGTAAG-GGCTTAATTCTTTTTTTTTT
29215068 ATAGTTTGAG
Statistics
Matches: 125, Mismatches: 24, Indels: 16
0.76 0.15 0.10
Matches are distributed among these distances:
91 43 0.34
92 30 0.24
95 30 0.24
96 21 0.17
97 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.41
Consensus pattern (90 bp):
TTTGAAAGTTCAAGTACCCAATTAAGTGAAAAAAAAAGTAAGGGCTTAATTCTTTTTTTTTTTAA
AAGTTTGAGGACCTTTTTGATGCAT
Found at i:29219080 original size:56 final size:58
Alignment explanation
Indices: 29218988--29219147 Score: 234
Period size: 59 Copynumber: 2.8 Consensus size: 58
29218978 CCATATTGTT
*
29218988 TGGATATTATTATGGGGATATTATATTTTAGCAATTTGATTCCTAATGAGATGTTA-TA
1 TGGATATTATTAT-GGGATATTATCTTTTAGCAATTTGATTCCTAATGAGATGTTATTA
* * * * *
29219046 -GGATATTATTATGAGATATTATCTCTTAGAAATTTGATTCCTTATGTGATGTTATTA
1 TGGATATTATTATGGGATATTATCTTTTAGCAATTTGATTCCTAATGAGATGTTATTA
29219103 TGAGATATTATTATGGGATATTATCTTTTAGCAATTTGATTCCTA
1 TG-GATATTATTATGGGATATTATCTTTTAGCAATTTGATTCCTA
29219148 CGTAACTACT
Statistics
Matches: 89, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
56 36 0.40
57 14 0.16
58 1 0.01
59 38 0.43
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (58 bp):
TGGATATTATTATGGGATATTATCTTTTAGCAATTTGATTCCTAATGAGATGTTATTA
Found at i:29219113 original size:13 final size:13
Alignment explanation
Indices: 29219087--29219126 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
29219077 ATTTGATTCC
* *
29219087 TTATGTGATGTTA
1 TTATGAGATATTA
29219100 TTATGAGATATTA
1 TTATGAGATATTA
*
29219113 TTATGGGATATTA
1 TTATGAGATATTA
29219126 T
1 T
29219127 CTTTTAGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (13 bp):
TTATGAGATATTA
Found at i:29225157 original size:36 final size:36
Alignment explanation
Indices: 29225097--29225167 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
29225087 TCTTTTAGCA
* *
29225097 ATTTGATTCCTAATAGGATGTTATAGGATATTATTG
1 ATTTAATTCCTAATAGGATATTATAGGATATTATTG
*
29225133 ATTTAATTCCTAATGGGATATTATAGGATATTATT
1 ATTTAATTCCTAATAGGATATTATAGGATATTATT
29225168 ATGGGATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.45
Consensus pattern (36 bp):
ATTTAATTCCTAATAGGATATTATAGGATATTATTG
Found at i:29231846 original size:29 final size:30
Alignment explanation
Indices: 29231787--29231844 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
29231777 TCCGAGCCTT
*
29231787 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
29231817 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
29231845 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:29232074 original size:13 final size:13
Alignment explanation
Indices: 29232056--29232087 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
29232046 TTTCCAGCAA
29232056 TTATGAATTTATT
1 TTATGAATTTATT
29232069 TTATGAATTTATT
1 TTATGAATTTATT
*
29232082 TGATGA
1 TTATGA
29232088 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:29232295 original size:50 final size:50
Alignment explanation
Indices: 29232182--29232423 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
29232172 ATTTGGGTAA
* * *
29232182 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
29232238 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
29232288 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
29232338 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
29232388 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
29232424 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:29232371 original size:100 final size:103
Alignment explanation
Indices: 29232182--29232431 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
29232172 ATTTGGGTAA
29232182 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
29232247 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
29232288 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
29232350 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
29232388 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
29232432 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:29234422 original size:15 final size:17
Alignment explanation
Indices: 29234402--29234434 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29234392 ACCTGAAGAA
29234402 TTTTCAT-G-AGTACAT
1 TTTTCATCGTAGTACAT
29234417 TTTTCATCGTAGTACAT
1 TTTTCATCGTAGTACAT
29234434 T
1 T
29234435 CATCAACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.48
Consensus pattern (17 bp):
TTTTCATCGTAGTACAT
Found at i:29253381 original size:27 final size:27
Alignment explanation
Indices: 29253333--29253491 Score: 184
Period size: 27 Copynumber: 5.9 Consensus size: 27
29253323 GCGAGGCTGC
* *
29253333 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
29253360 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
29253386 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* * *
29253413 CAAATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
29253440 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
29253467 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
29253492 GACGCTTCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 16
0.82 0.06 0.11
Matches are distributed among these distances:
26 10 0.09
27 100 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:29253426 original size:54 final size:54
Alignment explanation
Indices: 29253351--29253491 Score: 239
Period size: 54 Copynumber: 2.6 Consensus size: 54
29253341 GTGACGAAGT
*
29253351 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
* *
29253405 CACCAGATCAAATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
29253459 CACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAG
29253492 GACGCTTCCT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 4 0.05
54 77 0.95
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.17
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:29255123 original size:26 final size:26
Alignment explanation
Indices: 29255093--29255200 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
29255083 TGAAATTCCC
29255093 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
29255119 ATCATGGAACATTTACCTAACCTATT
1 ATCATGGAACATTTACCTAACCCATT
*
29255145 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
29255171 ATCATGGAACATTTACCTAACCTATT
1 ATCATGGAACATTTACCTAACCCATT
29255197 ATCA
1 ATCA
29255201 ATTTGTATCA
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:0.36, C:0.25, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:29256593 original size:40 final size:39
Alignment explanation
Indices: 29256549--29256649 Score: 113
Period size: 34 Copynumber: 2.7 Consensus size: 39
29256539 GTAACGATTT
29256549 GGGCCTTAGCCCATCTCAGTACAGTATCAAATATGCAGTA
1 GGGCCTTAGCCCATCTCAGTACAGTATC-AATATGCAGTA
* *
29256589 GGGCCTTAGCCCA--TCA-T--AGTATCAGTATGCATTA
1 GGGCCTTAGCCCATCTCAGTACAGTATCAATATGCAGTA
* *
29256623 GGGCCTTAGCCTATCACAGTATCAGTA
1 GGGCCTTAGCCCATCTCAGTA-CAGTA
29256650 GTAGTCATGC
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
34 21 0.41
35 6 0.12
36 2 0.04
37 2 0.04
38 3 0.06
40 17 0.33
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.27
Consensus pattern (39 bp):
GGGCCTTAGCCCATCTCAGTACAGTATCAATATGCAGTA
Found at i:29256625 original size:34 final size:34
Alignment explanation
Indices: 29256569--29256649 Score: 117
Period size: 34 Copynumber: 2.4 Consensus size: 34
29256559 CCATCTCAGT
*
29256569 ACAGTATCAAATATGCAGTAGGGCCTTAGCCCATC
1 ACAGTATC-AGTATGCAGTAGGGCCTTAGCCCATC
* * *
29256604 ATAGTATCAGTATGCATTAGGGCCTTAGCCTATC
1 ACAGTATCAGTATGCAGTAGGGCCTTAGCCCATC
29256638 ACAGTATCAGTA
1 ACAGTATCAGTA
29256650 GTAGTCATGC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
34 34 0.83
35 7 0.17
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (34 bp):
ACAGTATCAGTATGCAGTAGGGCCTTAGCCCATC
Found at i:29265686 original size:15 final size:15
Alignment explanation
Indices: 29265666--29265695 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29265656 AGAACAAAGA
29265666 AAATCAGACTTAGAT
1 AAATCAGACTTAGAT
29265681 AAATCAGACTTAGAT
1 AAATCAGACTTAGAT
29265696 CGGGGAAAGT
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:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (15 bp):
AAATCAGACTTAGAT
Found at i:29266043 original size:42 final size:43
Alignment explanation
Indices: 29265931--29266067 Score: 122
Period size: 43 Copynumber: 3.2 Consensus size: 43
29265921 TGAGATATCA
* *
29265931 TGTAAGACCGTGTCTGGGACATAGG-ACTCG--ATTGAGATTTACG
1 TGTAAGACCATGTCTGGGACAGAGGCA-TCGATATTG-GATTT-CG
* **
29265974 TATAAGACCATGTCTGGGACATCGGCATCG-TACTT-GATTTCG
1 TGTAAGACCATGTCTGGGACAGAGGCATCGATA-TTGGATTTCG
* * * *
29266016 TGTAAGACCCTGTCTGGGATAGAGGCATCGATATTGGATTACA
1 TGTAAGACCATGTCTGGGACAGAGGCATCGATATTGGATTTCG
29266059 TGTAAGACC
1 TGTAAGACC
29266068 TCGTCCGGGA
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
42 29 0.37
43 46 0.58
44 2 0.03
45 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.28
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACAGAGGCATCGATATTGGATTTCG
Found at i:29269857 original size:22 final size:23
Alignment explanation
Indices: 29269814--29269867 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
29269804 TTTATGCATA
29269814 ATAATTTATTTGATCTTATATTTT
1 ATAATTT-TTTGATCTTATATTTT
*
29269838 ATAATTTTTTTAT-TTATATTTT
1 ATAATTTTTTGATCTTATATTTT
*
29269860 -TTATTTTT
1 ATAATTTTT
29269868 AACTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 7 0.25
22 9 0.32
23 5 0.18
24 7 0.25
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (23 bp):
ATAATTTTTTGATCTTATATTTT
Found at i:29269861 original size:13 final size:13
Alignment explanation
Indices: 29269843--29269903 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
29269833 ATTTTATAAT
29269843 TTTTTTATTTATA
1 TTTTTTATTTATA
*
29269856 TTTTTTATTTTTAA
1 TTTTTTATTTAT-A
**
29269870 CTTTTAAATTTATA
1 -TTTTTTATTTATA
* * *
29269884 TTATTTATTAATT
1 TTTTTTATTTATA
29269897 TTTTTTA
1 TTTTTTA
29269904 AAATAAATAA
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
13 25 0.69
14 2 0.06
15 9 0.25
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTATTTATA
Found at i:29269874 original size:28 final size:29
Alignment explanation
Indices: 29269832--29269892 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
29269822 TTTGATCTTA
* ** *
29269832 TATTTTATAATTTTTTTATTTATATTTTT
1 TATTTTATAACTTTTAAATTTATATTATT
29269861 TATTTT-TAACTTTTAAATTTATATTATT
1 TATTTTATAACTTTTAAATTTATATTATT
29269889 TATT
1 TATT
29269893 AATTTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 22 0.79
29 6 0.21
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (29 bp):
TATTTTATAACTTTTAAATTTATATTATT
Found at i:29270552 original size:26 final size:26
Alignment explanation
Indices: 29270522--29270597 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
29270512 TCAAAAATAT
29270522 TATTAAATTATATTTAATAATAATTA
1 TATTAAATTATATTTAATAATAATTA
* * * * *
29270548 TATTAAAATATGATTAAATTAT-TTTT
1 TATTAAATTAT-ATTTAATAATAATTA
*
29270574 TATTAAATTATTTTTAATAATAAT
1 TATTAAATTATATTTAATAATAAT
29270598 CCGTTTAAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
25 7 0.18
26 23 0.61
27 8 0.21
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (26 bp):
TATTAAATTATATTTAATAATAATTA
Found at i:29270580 original size:15 final size:15
Alignment explanation
Indices: 29270560--29270588 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29270550 TTAAAATATG
29270560 ATTAAATTATTTTTT
1 ATTAAATTATTTTTT
29270575 ATTAAATTATTTTT
1 ATTAAATTATTTTT
29270589 AATAATAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTAAATTATTTTTT
Found at i:29272332 original size:19 final size:19
Alignment explanation
Indices: 29272284--29272335 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
29272274 AAATTGATAA
29272284 AATCATGTTAAAATGGTTTC
1 AATCATGTTAAAAT-GTTTC
*
29272304 AATTGA-GTTAAACAT-TTTC
1 AA-TCATGTTAAA-ATGTTTC
29272323 AATCATGTTAAAA
1 AATCATGTTAAAA
29272336 ATGTATTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
18 3 0.11
19 12 0.44
20 8 0.30
21 4 0.15
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (19 bp):
AATCATGTTAAAATGTTTC
Found at i:29273845 original size:39 final size:39
Alignment explanation
Indices: 29273791--29273868 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
29273781 ACCAAACATA
29273791 GCCTCAACCACAACCATATATACAAATAACCATTATTTC
1 GCCTCAACCACAACCATATATACAAATAACCATTATTTC
29273830 GCCTCAACCACAACCATATATACAAATAACCATTATTTC
1 GCCTCAACCACAACCATATATACAAATAACCATTATTTC
29273869 ACTTGAAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.41, C:0.31, G:0.03, T:0.26
Consensus pattern (39 bp):
GCCTCAACCACAACCATATATACAAATAACCATTATTTC
Found at i:29291167 original size:19 final size:20
Alignment explanation
Indices: 29291143--29291181 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
29291133 TAAGGGGGTG
29291143 AAGTTAAAA-AAAATTTTAA
1 AAGTTAAAATAAAATTTTAA
29291162 AAGTTAAAATAAAATTTTAA
1 AAGTTAAAATAAAATTTTAA
29291182 TTTTTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
AAGTTAAAATAAAATTTTAA
Found at i:29298417 original size:65 final size:65
Alignment explanation
Indices: 29298313--29298435 Score: 219
Period size: 65 Copynumber: 1.9 Consensus size: 65
29298303 ACCCCCAATA
29298313 GTTAACGGTTGCAAATTGGAGGAGGATTATTATTGAACAGAACAGGTAAATTTCTGATTATGTTT
1 GTTAACGGTTGCAAATTGGAGGAGGATTATTATTGAACAGAACAGGTAAATTTCTGATTATGTTT
* * *
29298378 GTTAACGGTTGCAAATTGGAGGAGGATTATTATTGAACAGAATAGGTAATTTTTTGAT
1 GTTAACGGTTGCAAATTGGAGGAGGATTATTATTGAACAGAACAGGTAAATTTCTGAT
29298436 CATTTTTTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 55 1.00
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.36
Consensus pattern (65 bp):
GTTAACGGTTGCAAATTGGAGGAGGATTATTATTGAACAGAACAGGTAAATTTCTGATTATGTTT
Found at i:29301555 original size:78 final size:75
Alignment explanation
Indices: 29301452--29301633 Score: 220
Period size: 78 Copynumber: 2.3 Consensus size: 75
29301442 GTATTCGGGC
* * *
29301452 TTAAAGACCCGCAGGCTATATGCTGGTAAAATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGT
1 TTAAA-ACCCGCAGGCT-TGTGCTGGTAAAATATCCAGGATAAATCCCGCAGGCTTCGTGCTGGT
**
29301517 AATATATATCTGGG
64 -AT-TATATCCAGG
**
29301531 TTAAAACCCGCAGGCTTCGTGCTGGTATTATATCCAGGATAAATCCCGCAGGCTTCGTGCTGGTA
1 TTAAAACCCGCAGGCTT-GTGCTGGTAAAATATCCAGGATAAATCCCGCAGGCTTCGTGCTGGTA
29301596 TTATATCCAGG
65 TTATATCCAGG
* * *
29301607 ATAAATCCCGCAGGCCTAGTGCTGGTA
1 TTAAAACCCGCAGG-CTTGTGCTGGTA
29301634 TTATATTCGG
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
76 29 0.32
77 5 0.05
78 52 0.57
79 5 0.05
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (75 bp):
TTAAAACCCGCAGGCTTGTGCTGGTAAAATATCCAGGATAAATCCCGCAGGCTTCGTGCTGGTAT
TATATCCAGG
Found at i:29301634 original size:38 final size:38
Alignment explanation
Indices: 29301459--29301639 Score: 229
Period size: 38 Copynumber: 4.7 Consensus size: 38
29301449 GGCTTAAAGA
* ** * *
29301459 CCCGCAGGCTAT-ATGCTGGTAAAATATCCGGGTTAAAT
1 CCCGCAGGCT-TCGTGCTGGTATTATATCCAGGATAAAT
** * *
29301497 CCCGCAGGCTTCGTGCTGGTAATATATATCTGGGTTAAAA
1 CCCGCAGGCTTCGTGCTGGT-AT-TATATCCAGGATAAAT
29301537 CCCGCAGGCTTCGTGCTGGTATTATATCCAGGATAAAT
1 CCCGCAGGCTTCGTGCTGGTATTATATCCAGGATAAAT
29301575 CCCGCAGGCTTCGTGCTGGTATTATATCCAGGATAAAT
1 CCCGCAGGCTTCGTGCTGGTATTATATCCAGGATAAAT
* *
29301613 CCCGCAGGCCTAGTGCTGGTATTATAT
1 CCCGCAGGCTTCGTGCTGGTATTATAT
29301640 TCGGGCTTTC
Statistics
Matches: 129, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
37 1 0.01
38 92 0.71
39 3 0.02
40 33 0.26
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (38 bp):
CCCGCAGGCTTCGTGCTGGTATTATATCCAGGATAAAT
Found at i:29301700 original size:43 final size:43
Alignment explanation
Indices: 29301625--29301790 Score: 194
Period size: 43 Copynumber: 3.9 Consensus size: 43
29301615 CGCAGGCCTA
* *
29301625 GTGCTGGT-AT-TATATTCGGGCTTTCGTGCCTAGCAAGCTTC
1 GTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAAGCTTC
* * * * *
29301666 GTGCTGGTGACGTGTATTTGGGCCTTTGTGCCTAGTAGGCTTC
1 GTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAAGCTTC
* * * *
29301709 -TGCTGGTGATGTGTATTCGGGCCTCCGTGCCTAGTAGGCTTT
1 GTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAAGCTTC
* *
29301751 GTGCCGGTGATGTGTATTCGGGCCTTCGTTCCTAGCAAGC
1 GTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAAGC
29301791 GTAATGCCAG
Statistics
Matches: 105, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
41 8 0.08
42 38 0.36
43 59 0.56
ACGTcount: A:0.11, C:0.22, G:0.32, T:0.35
Consensus pattern (43 bp):
GTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAAGCTTC
Found at i:29302186 original size:45 final size:45
Alignment explanation
Indices: 29302119--29302245 Score: 154
Period size: 45 Copynumber: 2.9 Consensus size: 45
29302109 TTGATTTGAT
* * * *
29302119 TATTCGGGCCTTTGAGCTTAGCAGACTATAATGCCGGTGAGAT-A
1 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAATGA
*
29302163 CTATTCGGGCCTTCGAGCCTAGCAGGCTATAATACCGGTGAAATGA
1 -TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAATGA
* *
29302209 TA-TCAGGCC-TCGAGCCTAGCAGGCGA-AATGCCGGTGA
1 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
29302246 TTTGAGAAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
42 10 0.14
43 16 0.22
44 6 0.08
45 40 0.55
46 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (45 bp):
TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAATGA
Found at i:29307686 original size:14 final size:14
Alignment explanation
Indices: 29307669--29307698 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29307659 ATTTAATTTG
29307669 GATTAATAAATTAT
1 GATTAATAAATTAT
*
29307683 GATTAATTAATTAT
1 GATTAATAAATTAT
29307697 GA
1 GA
29307699 AAAAGTGGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (14 bp):
GATTAATAAATTAT
Found at i:29313493 original size:179 final size:181
Alignment explanation
Indices: 29313189--29313542 Score: 606
Period size: 179 Copynumber: 2.0 Consensus size: 181
29313179 AGTGAATGGC
* *
29313189 TTCTTCACTTTTGCACTGATTCCCTTTGAGCCTTTCTTCTTCTTTTTTTGGTTATTGTTGATTCC
1 TTCTTCACTTTTGCACTAATTCCCTTTGAGCCTTTCTTCTTCTTTTTTTCGTTATTGTTGATTCC
*
29313254 AAAATTCTATCTCAATCCTTTTTTTCTTACTCCTTAAATGCACCATAACACTAGATGCACTTACG
66 AAAATTCTATCTCAATCCTTTTTTTCTTACCCCTTAAATGCACCATAACACTAGATGCACTTACG
29313319 TTATCGTTCTCATTTAAGGCTTAGTGTAGCATTACTTCTCAAAAGGTGACT
131 TTATCGTTCTCATTTAAGGCTTAGTGTAGCATTACTTCTCAAAAGGTGACT
29313370 TTCTTCACTTTTGCACTAATTCCCTTTGAGCCTTTCTTC-T-TTTTTTTCGTTATTGTTGATTCC
1 TTCTTCACTTTTGCACTAATTCCCTTTGAGCCTTTCTTCTTCTTTTTTTCGTTATTGTTGATTCC
* * * *
29313433 AAAATTTTGTCTCAATCCTTTTTTTCTTCCCCCTTAAATGCACCATAACACTCA-ATGCACTTAT
66 AAAATTCTATCTCAATCCTTTTTTTCTTACCCCTTAAATGCACCATAACACT-AGATGCACTTAC
*
29313497 GTTATCGTTCTCATTTAAGGCTTAGTTTAGCATTACTTCTCAAAAG
130 GTTATCGTTCTCATTTAAGGCTTAGTGTAGCATTACTTCTCAAAAG
29313543 TGCTTTTGGT
Statistics
Matches: 164, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
179 124 0.76
180 2 0.01
181 38 0.23
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.45
Consensus pattern (181 bp):
TTCTTCACTTTTGCACTAATTCCCTTTGAGCCTTTCTTCTTCTTTTTTTCGTTATTGTTGATTCC
AAAATTCTATCTCAATCCTTTTTTTCTTACCCCTTAAATGCACCATAACACTAGATGCACTTACG
TTATCGTTCTCATTTAAGGCTTAGTGTAGCATTACTTCTCAAAAGGTGACT
Found at i:29313710 original size:18 final size:18
Alignment explanation
Indices: 29313687--29313728 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
29313677 TTTAATAATG
* *
29313687 TTTTTATCTCAAAAGTAT
1 TTTTTACCTCAAAAATAT
29313705 TTTTTACCTCAAAAATAT
1 TTTTTACCTCAAAAATAT
29313723 TTTTTA
1 TTTTTA
29313729 GAAACAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.52
Consensus pattern (18 bp):
TTTTTACCTCAAAAATAT
Found at i:29330815 original size:12 final size:11
Alignment explanation
Indices: 29330782--29330808 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
29330772 TCTTCATAAA
29330782 TTTTACCCAAT
1 TTTTACCCAAT
29330793 TTTTACCCAAT
1 TTTTACCCAAT
29330804 TTTTA
1 TTTTA
29330809 TGCCAATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTTACCCAAT
Found at i:29333592 original size:8 final size:8
Alignment explanation
Indices: 29333579--29333610 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
29333569 TCACAAATGC
29333579 CGGCTTTT
1 CGGCTTTT
29333587 CGGCTTTT
1 CGGCTTTT
29333595 CGGCTTTT
1 CGGCTTTT
*
29333603 CCGCTTTT
1 CGGCTTTT
29333611 GCCGATCTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.00, C:0.28, G:0.22, T:0.50
Consensus pattern (8 bp):
CGGCTTTT
Found at i:29335397 original size:19 final size:18
Alignment explanation
Indices: 29335360--29335403 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
29335350 ATACATGCAG
29335360 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
29335377 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
29335396 TACTAATT
1 TAATAATT
29335404 AAAATTTCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:29338649 original size:27 final size:27
Alignment explanation
Indices: 29338619--29338694 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 27
29338609 AAATTATCTT
29338619 AGTATATATCTATGTTTTCATACTTGA
1 AGTATATATCTATGTTTTCATACTTGA
**
29338646 AGTA-A-AT-TA--AATT-AT-CTT--
1 AGTATATATCTATGTTTTCATACTTGA
29338664 AGTATATATCTATGTTTTCATACTTGA
1 AGTATATATCTATGTTTTCATACTTGA
29338691 AGTA
1 AGTA
29338695 ATGATTTATG
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
18 4 0.11
19 1 0.03
20 5 0.14
21 4 0.11
22 2 0.06
23 2 0.06
24 4 0.11
25 5 0.14
26 1 0.03
27 8 0.22
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (27 bp):
AGTATATATCTATGTTTTCATACTTGA
Found at i:29338665 original size:45 final size:45
Alignment explanation
Indices: 29338601--29338695 Score: 190
Period size: 45 Copynumber: 2.1 Consensus size: 45
29338591 CTTGTTTTAT
29338601 AGTAAATTAAATTATCTTAGTATATATCTATGTTTTCATACTTGA
1 AGTAAATTAAATTATCTTAGTATATATCTATGTTTTCATACTTGA
29338646 AGTAAATTAAATTATCTTAGTATATATCTATGTTTTCATACTTGA
1 AGTAAATTAAATTATCTTAGTATATATCTATGTTTTCATACTTGA
29338691 AGTAA
1 AGTAA
29338696 TGATTTATGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.45
Consensus pattern (45 bp):
AGTAAATTAAATTATCTTAGTATATATCTATGTTTTCATACTTGA
Found at i:29352931 original size:24 final size:24
Alignment explanation
Indices: 29352904--29352962 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
29352894 AGCTCATCAA
*
29352904 AGCTTACTGTTTCCAGCTCGTTAG
1 AGCTTACTGTTTCCAGCTCGATAG
* *
29352928 AGCTTACTATTTCTAGCTCGATAG
1 AGCTTACTGTTTCCAGCTCGATAG
29352952 AGCTTACTGTT
1 AGCTTACTGTT
29352963 CATCAGCTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (24 bp):
AGCTTACTGTTTCCAGCTCGATAG
Found at i:29359143 original size:18 final size:19
Alignment explanation
Indices: 29359100--29359145 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
29359090 TTGTAATGAT
*
29359100 TTGAAATGAATGTATGTAA
1 TTGAAATAAATGTATGTAA
*
29359119 TTG-AATAAATG-ATGTAC
1 TTGAAATAAATGTATGTAA
29359136 TTGAAATAAA
1 TTGAAATAAA
29359146 AATGCCTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.33
18 13 0.54
19 3 0.12
ACGTcount: A:0.46, C:0.02, G:0.17, T:0.35
Consensus pattern (19 bp):
TTGAAATAAATGTATGTAA
Found at i:29359344 original size:24 final size:24
Alignment explanation
Indices: 29359308--29359353 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
29359298 TTAGCTCATA
* *
29359308 AGAGCTTATTGTTCCCAACTCGTC
1 AGAGCATACTGTTCCCAACTCGTC
* *
29359332 AGAGCATACTGTTTCCAGCTCG
1 AGAGCATACTGTTCCCAACTCG
29359354 ATGGAGCTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (24 bp):
AGAGCATACTGTTCCCAACTCGTC
Found at i:29361085 original size:20 final size:22
Alignment explanation
Indices: 29361045--29361085 Score: 59
Period size: 20 Copynumber: 1.9 Consensus size: 22
29361035 AAATCATTGT
29361045 GAGTGAGAAAAGAGGAAAAAGTC
1 GAGTGAGAAAAGA-GAAAAAGTC
29361068 GAGTGA-AAAAGA-AAAAAG
1 GAGTGAGAAAAGAGAAAAAG
29361086 AAAATGTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
22 6 0.33
23 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.32, T:0.07
Consensus pattern (22 bp):
GAGTGAGAAAAGAGAAAAAGTC
Found at i:29363021 original size:27 final size:27
Alignment explanation
Indices: 29362959--29363070 Score: 129
Period size: 27 Copynumber: 4.1 Consensus size: 27
29362949 AGCATGGCTG
* * *
29362959 CCAGAATAGATAA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
* *
29362985 CTAGACACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAATTGTGGCAGAGCCA
29363013 CCAGAACAGA-AATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* *
29363040 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
29363067 CCAG
1 CCAG
29363071 GACGTTTCCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 7 0.10
27 49 0.67
28 17 0.23
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:29368802 original size:27 final size:27
Alignment explanation
Indices: 29368740--29368851 Score: 120
Period size: 27 Copynumber: 4.1 Consensus size: 27
29368730 AGCATGGCTG
** *
29368740 CCAGAACAGATAA-TGTGATAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
* *
29368766 CTAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAATTGTGGCAGAGCCA
29368794 CCAGAACAGA-AATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* * *
29368821 CCAGATCAAATAATTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
29368848 CCAG
1 CCAG
29368852 GACGCTTCCT
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
26 7 0.10
27 49 0.68
28 16 0.22
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.17
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:29368834 original size:54 final size:54
Alignment explanation
Indices: 29368740--29368851 Score: 136
Period size: 54 Copynumber: 2.1 Consensus size: 54
29368730 AGCATGGCTG
* * * * *
29368740 CCAGAACAGATAATGTGATAGAGTCACTAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAAATAATCGTGGCAGAGCCA
* * *
29368794 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAAATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAAATAATCGTGGCAGAGCCA
29368848 CCAG
1 CCAG
29368852 GACGCTTCCT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
54 33 0.67
55 16 0.33
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACCAGATACAAATAATCGTGGCAGAGCCA
Found at i:29371749 original size:28 final size:28
Alignment explanation
Indices: 29371709--29371765 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
29371699 GGTTACCATG
29371709 AGATAAAATAGAATCATATCGAGAGAAC
1 AGATAAAATAGAATCATATCGAGAGAAC
29371737 AGATAAAATAGAATCATATCGAGAGAAC
1 AGATAAAATAGAATCATATCGAGAGAAC
29371765 A
1 A
29371766 AGTATTACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.54, C:0.11, G:0.18, T:0.18
Consensus pattern (28 bp):
AGATAAAATAGAATCATATCGAGAGAAC
Found at i:29372313 original size:57 final size:57
Alignment explanation
Indices: 29372222--29372338 Score: 162
Period size: 57 Copynumber: 2.1 Consensus size: 57
29372212 TTTCAGGTAT
* * *
29372222 TTTTCATTTTCATTTTGGAGAAAACCGCATTCATTTCCAAATGATTCCATTTCTCCA
1 TTTTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCCAATTCTCCA
* * * * *
29372279 TTTTCATTTTCATTTTGGAGAAAACTATAATCATTTCCCAATGTTTCCAATTCTCTA
1 TTTTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCCAATTCTCCA
29372336 TTT
1 TTT
29372339 ACACCATTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (57 bp):
TTTTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCCAATTCTCCA
Found at i:29379835 original size:11 final size:11
Alignment explanation
Indices: 29379819--29379855 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
29379809 TTTAAGTAAA
29379819 TATTATTTTAT
1 TATTATTTTAT
29379830 TATTATTTTAT
1 TATTATTTTAT
29379841 TATTATTTTA-
1 TATTATTTTAT
29379851 TATTA
1 TATTA
29379856 ATTAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 5 0.19
11 21 0.81
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:29379865 original size:4 final size:4
Alignment explanation
Indices: 29379858--29379901 Score: 61
Period size: 4 Copynumber: 10.2 Consensus size: 4
29379848 TTATATTAAT
29379858 TAAA TAAA TTAAA TAAA TAAA TAAAA TAAA TAAA TAAAA TAAA T
1 TAAA TAAA -TAAA TAAA TAAA T-AAA TAAA TAAA T-AAA TAAA T
29379902 TGTGACAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 25 0.68
5 12 0.32
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:29379868 original size:13 final size:13
Alignment explanation
Indices: 29379852--29379901 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
29379842 ATTATTTTAT
*
29379852 ATTAATTAAATAA
1 ATTAAATAAATAA
29379865 ATTAAATAAATAA
1 ATTAAATAAATAA
*
29379878 ATAAAATAAATAA
1 ATTAAATAAATAA
*
29379891 ATAAAATAAAT
1 ATTAAATAAAT
29379902 TGTGACAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
ATTAAATAAATAA
Found at i:29379869 original size:9 final size:9
Alignment explanation
Indices: 29379855--29379902 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
29379845 ATTTTATATT
29379855 AATTAAATA
1 AATTAAATA
29379864 AATTAAATA
1 AATTAAATA
29379873 AA-TAAATA
1 AATTAAATA
*
29379881 AAATAAATA
1 AATTAAATA
*
29379890 AATAAAATA
1 AATTAAATA
29379899 AATT
1 AATT
29379903 GTGACAAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
8 8 0.23
9 27 0.77
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AATTAAATA
Found at i:29380060 original size:22 final size:22
Alignment explanation
Indices: 29380023--29380079 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
29380013 AATAAATAAT
29380023 AAATG-AAAA-AGAAACAAAAG-
1 AAATGAAAAAGAGAAAC-AAAGC
29380043 AAATGAAAAAGAGAAACAAAGC
1 AAATGAAAAAGAGAAACAAAGC
*
29380065 AAATGAAACAGAGAA
1 AAATGAAAAAGAGAA
29380080 GAATAGGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 5 0.15
21 8 0.24
22 20 0.61
ACGTcount: A:0.70, C:0.07, G:0.18, T:0.05
Consensus pattern (22 bp):
AAATGAAAAAGAGAAACAAAGC
Found at i:29381401 original size:18 final size:18
Alignment explanation
Indices: 29381378--29381419 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
29381368 TAAATAAAGG
29381378 TACTGAATAATTGACTGC
1 TACTGAATAATTGACTGC
* *
29381396 TACTGAATATTTGACTGT
1 TACTGAATAATTGACTGC
29381414 TACTGA
1 TACTGA
29381420 GTTACTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (18 bp):
TACTGAATAATTGACTGC
Found at i:29383396 original size:6 final size:6
Alignment explanation
Indices: 29383387--29383421 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
29383377 AACGAAATAG
29383387 AAAGAA AAAGAA AAAGGAGA AAAGAA AAAGAA AAA
1 AAAGAA AAAGAA AAA-GA-A AAAGAA AAAGAA AAA
29383422 AGAGAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.70
7 4 0.15
8 4 0.15
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:29383412 original size:20 final size:20
Alignment explanation
Indices: 29383387--29383428 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
29383377 AACGAAATAG
*
29383387 AAAGAAAAAGAAAAAGGAGA
1 AAAGAAAAAGAAAAAAGAGA
29383407 AAAGAAAAAGAAAAAAGAGA
1 AAAGAAAAAGAAAAAAGAGA
29383427 AA
1 AA
29383429 TTAGGATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAAAAGAGA
Found at i:29391658 original size:55 final size:55
Alignment explanation
Indices: 29391538--29391663 Score: 139
Period size: 55 Copynumber: 2.3 Consensus size: 55
29391528 AAGCCTACCA
* * * * *
29391538 AAAC-AACATGGGCGTGCGACATGCCCGTGTGGAAGACCCGTGGTTGAAACTGAG
1 AAACTAACACGGGCGTGCGACACGCCCGTGTCGAACACCCGTGGTCGAAACTGAG
* * * *
29391592 AAACTAGCACGGGCGTGCGACACGCCCGTGTCTAACACCCGTGGTCGAACCT-AT
1 AAACTAACACGGGCGTGCGACACGCCCGTGTCGAACACCCGTGGTCGAAACTGAG
*
29391646 TAACTTAACACGGGCGTG
1 AAAC-TAACACGGGCGTG
29391664 GAGCTTGAGC
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
54 8 0.14
55 51 0.86
ACGTcount: A:0.26, C:0.27, G:0.29, T:0.17
Consensus pattern (55 bp):
AAACTAACACGGGCGTGCGACACGCCCGTGTCGAACACCCGTGGTCGAAACTGAG
Found at i:29398169 original size:6 final size:5
Alignment explanation
Indices: 29398135--29398223 Score: 67
Period size: 6 Copynumber: 16.8 Consensus size: 5
29398125 TATGTCTTTC
* *
29398135 AAAAT AAAAT AAAAT --AAT AAAATT GAAAT GAAAAT AAGAAT CAAAAGA
1 AAAAT AAAAT AAAAT AAAAT AAAA-T AAAAT -AAAAT AA-AAT -AAAA-T
29398183 AAAATT AAAAT AAAAT AAAAT AAAAAT AAGAAT AAAA- AAAA
1 AAAA-T AAAAT AAAAT AAAAT -AAAAT AA-AAT AAAAT AAAA
29398224 AAATAGGAGT
Statistics
Matches: 70, Mismatches: 5, Indels: 19
0.74 0.05 0.20
Matches are distributed among these distances:
3 3 0.04
4 4 0.06
5 30 0.43
6 31 0.44
7 2 0.03
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:29398180 original size:12 final size:10
Alignment explanation
Indices: 29398135--29398223 Score: 67
Period size: 11 Copynumber: 8.4 Consensus size: 10
29398125 TATGTCTTTC
29398135 AAAATAAAAT
1 AAAATAAAAT
29398145 AAAAT--AAT
1 AAAATAAAAT
*
29398153 AAAATTGAAAT
1 AAAA-TAAAAT
29398164 GAAAATAAGAAT
1 -AAAATAA-AAT
*
29398176 CAAAAGAAAAATT
1 -AAAA-TAAAA-T
29398189 AAAATAAAAT
1 AAAATAAAAT
29398199 AAAATAAAAAT
1 AAAAT-AAAAT
29398210 AAGAATAAAA-
1 AA-AATAAAAT
29398220 AAAA
1 AAAA
29398224 AAATAGGAGT
Statistics
Matches: 66, Mismatches: 4, Indels: 19
0.74 0.04 0.21
Matches are distributed among these distances:
8 7 0.11
9 3 0.05
10 13 0.20
11 20 0.30
12 20 0.30
13 3 0.05
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:29398212 original size:40 final size:41
Alignment explanation
Indices: 29398150--29398227 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 41
29398140 AAAATAAAAT
* * * *
29398150 AATAAAATTGAAATGAAAATAAGAATCAAAAGAAAAATTAA
1 AATAAAATTAAAATAAAAATAAGAATAAAAAAAAAAATTAA
29398191 AATAAAA-TAAAATAAAAATAAGAATAAAAAAAAAAAT
1 AATAAAATTAAAATAAAAATAAGAATAAAAAAAAAAAT
29398228 AGGAGTCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
40 26 0.79
41 7 0.21
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.18
Consensus pattern (41 bp):
AATAAAATTAAAATAAAAATAAGAATAAAAAAAAAAATTAA
Found at i:29398225 original size:17 final size:16
Alignment explanation
Indices: 29398135--29398225 Score: 65
Period size: 17 Copynumber: 5.2 Consensus size: 16
29398125 TATGTCTTTC
29398135 AAAATAAAATAAAATAA
1 AAAATAAAATAAAA-AA
* *
29398152 TAAAATTGAAATGAAAATA
1 -AAAA-TAAAAT-AAAAAA
* * *
29398171 AGAATCAAAAGAAAAATT
1 AAAAT-AAAATAAAAA-A
*
29398189 AAAATAAAATAAAATA
1 AAAATAAAATAAAAAA
29398205 AAAATAAGAATAAAAAA
1 AAAATAA-AATAAAAAA
29398222 AAAA
1 AAAA
29398226 ATAGGAGTCA
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
16 7 0.12
17 25 0.45
18 14 0.25
19 6 0.11
20 4 0.07
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (16 bp):
AAAATAAAATAAAAAA
Found at i:29401737 original size:34 final size:34
Alignment explanation
Indices: 29401694--29401764 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
29401684 CGTCATCGCT
*
29401694 TTAGGATATGGCACATGAGGTTCATGATTCGTAC
1 TTAGGATATGGCACACGAGGTTCATGATTCGTAC
29401728 TTAGGATATGGCACACGAGGTTCATGATTCGTAC
1 TTAGGATATGGCACACGAGGTTCATGATTCGTAC
29401762 TTA
1 TTA
29401765 CCTGTTTGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.32
Consensus pattern (34 bp):
TTAGGATATGGCACACGAGGTTCATGATTCGTAC
Found at i:29408687 original size:35 final size:35
Alignment explanation
Indices: 29408640--29408712 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
29408630 GGTCCAAAAA
* *
29408640 TACAAAAATCATCAAGAATAACCTTCTAAATGACT
1 TACAAAAATCATCAAGAATAACCTTATAAATGAAT
*
29408675 TACAAAACTCATCAAGAATAACCTTATAAATGAAT
1 TACAAAAATCATCAAGAATAACCTTATAAATGAAT
29408710 TAC
1 TAC
29408713 TTGCAAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.49, C:0.19, G:0.05, T:0.26
Consensus pattern (35 bp):
TACAAAAATCATCAAGAATAACCTTATAAATGAAT
Found at i:29419613 original size:45 final size:45
Alignment explanation
Indices: 29419507--29419681 Score: 223
Period size: 45 Copynumber: 4.0 Consensus size: 45
29419497 TGAATTCATC
* * * * *
29419507 CACCGGCATT-TTGCCTGCTAGGTTCGAA-GACCG-ATA-TCATTT
1 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGT-ATCT
* *
29419549 CACTGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGTATCT
1 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
29419594 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
1 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
* * *
29419639 CACCGGCATTATAACCTGCTAGGCTCAAAGGTCTGAATAGTAT
1 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTAT
29419682 TGTACGATAT
Statistics
Matches: 119, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
42 9 0.08
43 16 0.13
44 4 0.03
45 89 0.75
46 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (45 bp):
CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
Found at i:29426810 original size:6 final size:5
Alignment explanation
Indices: 29426775--29426809 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
29426765 TTTAACATAT
29426775 AAATA AAGATAA AAATA AAATA AAATA AAATA AAA
1 AAATA AA-AT-A AAATA AAATA AAATA AAATA AAA
29426810 AATGTAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 21 0.75
6 4 0.14
7 3 0.11
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (5 bp):
AAATA
Found at i:29436122 original size:43 final size:43
Alignment explanation
Indices: 29436041--29436125 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
29436031 AAATCATACA
**
29436041 ATGCCAACGTCCCAGACGTGGTCTTACATGTAGTCACATATCC
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAAACACATATCC
29436084 ATGCC-ACTGTCCCAGACAG-GGTCTTAC-TCGTAAACACATATC
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACAT-GTAAACACATATC
29436126 AGAATCACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
42 3 0.08
43 33 0.89
44 1 0.03
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAAACACATATCC
Found at i:29440070 original size:36 final size:36
Alignment explanation
Indices: 29440022--29440102 Score: 137
Period size: 36 Copynumber: 2.2 Consensus size: 36
29440012 ATACCTGAAC
*
29440022 CTCTTC-TAGGGTTTTATAAAAAATTATGCCTTGGGT
1 CTCTTCAT-GGGTTATATAAAAAATTATGCCTTGGGT
29440058 CTCTTCATGGGTTATATAAAAAATTATGCCTTGGGT
1 CTCTTCATGGGTTATATAAAAAATTATGCCTTGGGT
29440094 CTCTTCATG
1 CTCTTCATG
29440103 AGTAACCACC
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
36 42 0.98
37 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (36 bp):
CTCTTCATGGGTTATATAAAAAATTATGCCTTGGGT
Found at i:29451306 original size:12 final size:13
Alignment explanation
Indices: 29451283--29451311 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
29451273 GATTATTGTC
29451283 ATTTTGGATTGGT
1 ATTTTGGATTGGT
29451296 ATTTT-GATTGGT
1 ATTTTGGATTGGT
29451308 ATTT
1 ATTT
29451312 AAGTTTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.17, C:0.00, G:0.24, T:0.59
Consensus pattern (13 bp):
ATTTTGGATTGGT
Found at i:29452779 original size:49 final size:49
Alignment explanation
Indices: 29452707--29452946 Score: 293
Period size: 49 Copynumber: 4.9 Consensus size: 49
29452697 CGAAGCTATT
* * *
29452707 TGGTACGCATAGTA-CCTGCACTTAGTACTACACATGCGACCAATTATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATC
* * **
29452755 CGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACC-AATTATC
* * *
29452805 TGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATC
* * * * *
29452856 AGGTACGCATAGTAGCCTGCACTTAGTACTACCCATGCGACCAATTATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATC
* *
29452905 TGGTACACGTAGTAGCCTACACTTAGTACTACACACGTGACC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACC
29452947 TCACAATAGC
Statistics
Matches: 161, Mismatches: 27, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
48 11 0.07
49 65 0.40
50 48 0.30
51 37 0.23
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (49 bp):
TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATC
Found at i:29452936 original size:100 final size:99
Alignment explanation
Indices: 29452707--29452946 Score: 313
Period size: 100 Copynumber: 2.4 Consensus size: 99
29452697 CGAAGCTATT
* * * * * *
29452707 TGGTACGCATAGTA-CCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCAGGTACACATAGTAGC
*
29452771 CTGCACTTAGTACTACACACGTGACCTAACCATC
66 CTGCACTTAGTACTACACACGCGACCTAACCATC
* * *
29452805 TGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACGCATAGTA
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCAGGTACACATAGTA
* * **
29452870 GCCTGCACTTAGTACTACCCATGCGACC-AATTATC
64 GCCTGCACTTAGTACTACACACGCGACCTAACCATC
*
29452905 TGGTACACGTAGTAGCCTACACTTAGTACTACACACGTGACC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
29452947 TCACAATAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
98 11 0.09
99 24 0.20
100 46 0.38
101 41 0.34
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (99 bp):
TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCAGGTACACATAGTAGC
CTGCACTTAGTACTACACACGCGACCTAACCATC
Found at i:29461455 original size:34 final size:34
Alignment explanation
Indices: 29461417--29461492 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
29461407 TTAGCCCCTC
* * *
29461417 TTTCAGTAGCAGAAGCATTCCGGGCCTGAGCCCG
1 TTTCAGTAACAGAAGCAGTCCGGGCCTGAGCCCA
** * *
29461451 TTTCAGTAACAGTGGCAGTCTGGGCCTTAGCCCA
1 TTTCAGTAACAGAAGCAGTCCGGGCCTGAGCCCA
29461485 TTTCAGTA
1 TTTCAGTA
29461493 CAGTATCCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (34 bp):
TTTCAGTAACAGAAGCAGTCCGGGCCTGAGCCCA
Found at i:29464733 original size:49 final size:49
Alignment explanation
Indices: 29464659--29464789 Score: 133
Period size: 49 Copynumber: 2.7 Consensus size: 49
29464649 TAAGAGTTGT
** * *
29464659 GCTAGTGTAAGA-CATGTCCGGGACAT-ACATCAGTACGTATAT-ATGAGA
1 GCTAGTGTAAGACCATGTTTGGGACATGACATC-G-ACCTAGATGATGAGA
* * * *
29464707 GCTAGTATAAGACCATGTTTGGGACATGGCATCGACCTCGATGATGATA
1 GCTAGTGTAAGACCATGTTTGGGACATGACATCGACCTAGATGATGAGA
* *
29464756 GCTAGTGTAAGACCATGTTTGGTACATGGCATCG
1 GCTAGTGTAAGACCATGTTTGGGACATGACATCG
29464790 GCAACTTATC
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
48 16 0.23
49 50 0.71
50 4 0.06
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (49 bp):
GCTAGTGTAAGACCATGTTTGGGACATGACATCGACCTAGATGATGAGA
Found at i:29468612 original size:35 final size:35
Alignment explanation
Indices: 29468566--29468636 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
29468556 AATTCCAAAA
29468566 TTCCAATTAACAGCTTGATATCTTCATTTAGCCCT
1 TTCCAATTAACAGCTTGATATCTTCATTTAGCCCT
29468601 TTCCAATTAACAGCTTGATATCTTCATTTAGCCCT
1 TTCCAATTAACAGCTTGATATCTTCATTTAGCCCT
29468636 T
1 T
29468637 CTTCAATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.41
Consensus pattern (35 bp):
TTCCAATTAACAGCTTGATATCTTCATTTAGCCCT
Found at i:29473882 original size:16 final size:15
Alignment explanation
Indices: 29473853--29473902 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 15
29473843 TAATATAAAG
29473853 TGAATTGAAATATAT
1 TGAATTGAAATATAT
29473868 TGAATTGAGAATATAT
1 TGAATTGA-AATATAT
29473884 CTGATTAATTGAAATATAT
1 -TG---AATTGAAATATAT
29473903 ATTGATTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.27
16 7 0.23
17 2 0.07
19 7 0.23
20 6 0.20
ACGTcount: A:0.44, C:0.02, G:0.14, T:0.40
Consensus pattern (15 bp):
TGAATTGAAATATAT
Found at i:29473912 original size:16 final size:16
Alignment explanation
Indices: 29473862--29473913 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 16
29473852 GTGAATTGAA
29473862 ATATATTGAATTGAGAAT
1 ATATATTG-ATTGA-AAT
*
29473880 ATATCTGATTAATTGAAAT
1 ATA--T-ATTGATTGAAAT
29473899 ATATATTGATTGAAA
1 ATATATTGATTGAAA
29473914 ACTGAAAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 10 0.34
17 1 0.03
18 3 0.10
19 6 0.21
20 6 0.21
21 3 0.10
ACGTcount: A:0.44, C:0.02, G:0.13, T:0.40
Consensus pattern (16 bp):
ATATATTGATTGAAAT
Found at i:29474150 original size:45 final size:45
Alignment explanation
Indices: 29474055--29474156 Score: 116
Period size: 45 Copynumber: 2.3 Consensus size: 45
29474045 TTACCATTAC
* * * *
29474055 TGTTACTGTTACCGACTCGACACTTTGTGTGTCAAATACTGTTAC
1 TGTTACTGTTACCGACTCAACACTTTGTGTGTCAAATACTATCAA
* * **
29474100 CGTTACTGTT-CCAGATTCAACACTTTGTGTGTTGAATACTATCAA
1 TGTTACTGTTACC-GACTCAACACTTTGTGTGTCAAATACTATCAA
29474145 TGTTACTGTTAC
1 TGTTACTGTTAC
29474157 TGCTACCATT
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
44 2 0.04
45 43 0.93
46 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.39
Consensus pattern (45 bp):
TGTTACTGTTACCGACTCAACACTTTGTGTGTCAAATACTATCAA
Found at i:29474306 original size:18 final size:18
Alignment explanation
Indices: 29474283--29474371 Score: 117
Period size: 18 Copynumber: 4.9 Consensus size: 18
29474273 TAAATAAAGG
29474283 TACTGAATAACTGATTAT
1 TACTGAATAACTGATTAT
* *
29474301 TACTGAATAATTGACTAT
1 TACTGAATAACTGATTAT
* *
29474319 TACTGAATAAAC-GACTGT
1 TACTGAAT-AACTGATTAT
*
29474337 TACTGAATAAATGATTAT
1 TACTGAATAACTGATTAT
29474355 TACTGAATAACTGATTA
1 TACTGAATAACTGATTA
29474372 ATATTGATGA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
17 2 0.03
18 57 0.93
19 2 0.03
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.36
Consensus pattern (18 bp):
TACTGAATAACTGATTAT
Found at i:29479378 original size:9 final size:9
Alignment explanation
Indices: 29479364--29479398 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
29479354 TTATATTAAT
29479364 TAAATAAAA
1 TAAATAAAA
29479373 TAAAT-AAA
1 TAAATAAAA
29479381 TAAATAAAA
1 TAAATAAAA
29479390 TAAAATAAA
1 T-AAATAAA
29479399 GACAAATGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 9 0.38
10 7 0.29
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
TAAATAAAA
Found at i:29479544 original size:16 final size:16
Alignment explanation
Indices: 29479496--29479549 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
29479486 ATTTACTATT
29479496 TATAA-AAGATATTTA
1 TATAATAAGATATTTA
*
29479511 T-TAACTAAG-TAATTA
1 TATAA-TAAGATATTTA
*
29479526 TATTATAAGATATTTA
1 TATAATAAGATATTTA
29479542 TATAATAA
1 TATAATAA
29479550 ATAAATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
14 3 0.10
15 11 0.35
16 17 0.55
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (16 bp):
TATAATAAGATATTTA
Done.