Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 65 of 141
Found at i:21125758 original size:141 final size:139
Alignment explanation
Indices: 21125516--21125796 Score: 336
Period size: 141 Copynumber: 2.0 Consensus size: 139
21125506 CAATATATTT
* **
21125516 ATTAATTAAAAATAAAAAAAGTTTGAAACAACATAAAATAAAAAATACAAAAGGTGCTTAAAAGA
1 ATTAATTAAAAATAAAAAAAGTTTGAAACAACATAAAAAAAAAAATACAAAA-GTGAGTAAAAGA
* * *
21125581 GGAATTGAACCTAAGACTTAAGAATGAAATCACTATTATTTAAT-TATAACCAGATG-AGCTAAT
65 GAAATTGAACCTAAGACTTAAGAATAAAACCACTATTATTTAATATATAACCAGA-GAAGCTAAT
*
21125644 GTGTTAAAAAC
129 GTGTCAAAAAC
**
21125655 ATTAATTAAAAATAAAAAAAAGTTTGAAACAACATGAAATAAAAAAAATACAAATA-TGAGTAGG
1 ATTAATTAAAAAT-AAAAAAAGTTTGAAACAACAT-AAA-AAAAAAAATACAAA-AGTGAGTAAA
* * * * *
21125719 AGAGAAATTGAATCTGAGGCTTAA-AGATAAAACCACTATTATTTAATCATCTGACCAGAGAAGC
62 AGAGAAATTGAACCTAAGACTTAAGA-ATAAAACCACTATTATTTAAT-ATATAACCAGAGAAGC
21125783 TAATGTGTCAAAAA
125 TAATGTGTCAAAAA
21125797 AGTCAGAAAA
Statistics
Matches: 120, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
139 13 0.11
140 22 0.18
141 46 0.38
142 14 0.12
143 25 0.21
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (139 bp):
ATTAATTAAAAATAAAAAAAGTTTGAAACAACATAAAAAAAAAAATACAAAAGTGAGTAAAAGAG
AAATTGAACCTAAGACTTAAGAATAAAACCACTATTATTTAATATATAACCAGAGAAGCTAATGT
GTCAAAAAC
Found at i:21126798 original size:4 final size:4
Alignment explanation
Indices: 21126789--21126814 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
21126779 CCTTCGCCTC
21126789 TCTT TCTT TCTT TCTT TCTT TCTT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TC
21126815 GTTGTTGCTG
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:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TCTT
Found at i:21129635 original size:34 final size:38
Alignment explanation
Indices: 21129565--21129635 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 38
21129555 TACAGATGTC
* *
21129565 TAGGATTATAAGTTATCTTCAAGGTTTCAATTTAGGGA
1 TAGGATTATAAGTTATCTTCAAGGTTTAAATCTAGGGA
21129603 TAGGATTATAAG-T-T-TT-AAGGTTTAAATCTAGGG
1 TAGGATTATAAGTTATCTTCAAGGTTTAAATCTAGGG
21129636 GTAGTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 15 0.48
35 2 0.06
36 1 0.03
37 1 0.03
38 12 0.39
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.39
Consensus pattern (38 bp):
TAGGATTATAAGTTATCTTCAAGGTTTAAATCTAGGGA
Found at i:21141811 original size:135 final size:137
Alignment explanation
Indices: 21141551--21141831 Score: 449
Period size: 135 Copynumber: 2.1 Consensus size: 137
21141541 GAGAACATAG
* *
21141551 ATATAATTAATATATGAATTTGATTAATACAAAATATGAATTGTATATATTTTATCGAATTTATT
1 ATATAATTAATATATGAATTTGATTAATACAAAATA-GAATTGTATATATTTTACCAAATTTATT
* *
21141616 AATATAAACAATTATATTAATTAATTTAGGTCAAAATATAAAAGACATGAAAATCAATATTCTTT
65 AATATAAACAAGTATATTAATTAATTTAGATCAAAATATAAAAGACATGAAAATCAATATTCTTT
*
21141681 TGGAAAGA
130 TGGAAAAA
*
21141689 ATATAATTAATATATGAATTTGATTCATACAAAATA-AATTGTATATATTTTACCAAATTTATTA
1 ATATAATTAATATATGAATTTGATTAATACAAAATAGAATTGTATATATTTTACCAAATTTATTA
* * * *
21141753 ATATAAA-TAGTATATTAATTAATTTCGATCAAAATATAAAAGACATGGAAATTAATATTCTTTT
66 ATATAAACAAGTATATTAATTAATTTAGATCAAAATATAAAAGACATGAAAATCAATATTCTTTT
21141817 GGAAAAA
131 GGAAAAA
21141824 ATATAATT
1 ATATAATT
21141832 TATTTTCTAA
Statistics
Matches: 133, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
135 65 0.49
136 33 0.25
138 35 0.26
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (137 bp):
ATATAATTAATATATGAATTTGATTAATACAAAATAGAATTGTATATATTTTACCAAATTTATTA
ATATAAACAAGTATATTAATTAATTTAGATCAAAATATAAAAGACATGAAAATCAATATTCTTTT
GGAAAAA
Found at i:21142148 original size:288 final size:287
Alignment explanation
Indices: 21141781--21142351 Score: 1009
Period size: 288 Copynumber: 2.0 Consensus size: 287
21141771 TTAATTTCGA
21141781 TCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAAAATATAATTTATTTTCTAACTTT
1 TCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAAAATATAATTTATTTTCTAACTTT
*
21141846 CCATTTGCCTTCTCCATTAATAAAGGAATAATCCCGGTTTTCCTTTTTAATATGTGATATCAAAG
66 CCATTTGCCTTCTCCATTAATAAAGGAATAATCCCGATTTTCCTTTTTAATATGTGATATCAAAG
*
21141911 AGGATAAAAGGATGATAGTCCCTTAGTGTGTTAATGTTACCAACTTAATAATTTAAAAGGTCT-A
131 AGGATAAAAGGATGATAGTCCCTTAGTGTGTTAATGTTACCAACTCAATAATTTAAAAGGTCTAA
* *
21141975 GCAACTGTTTTTAATTCTCTTTGAAAAGTTCAAAAGAAAGTGGTTGTTCGTTTTTAACTGGGTGG
196 G-AACTGTTTTTAATTCTCTTTAAAAAGTTCAAAAGAAAGTGGTTGTTCGTTTTTAACGGGGTGG
*
21142040 ACTATGTAAAGGCCGAGACATTTTATTT
260 ACTACGTAAAGGCCGAGACATTTTATTT
* * *
21142068 TCAAAATTATAAAAGGCATGGAAATTAATATTCTTTTGGAAAGAATATAATTTCTTTTCTAACTT
1 TCAAAA-TATAAAAGACATGGAAATTAATATTCTTTTGGAAAAAATATAATTTATTTTCTAACTT
*
21142133 TCCATTTGCCTTCTCCATTAATAAAGGAATAGTCCCGATTTTCCTTTTTAATATGTGATATCAAA
65 TCCATTTGCCTTCTCCATTAATAAAGGAATAATCCCGATTTTCCTTTTTAATATGTGATATCAAA
21142198 GAGGATAAAAGGATGATAGTCCCTTAGTGTGTTAATGTTACCAACTCAATAATTTAAAAGGTCTA
130 GAGGATAAAAGGATGATAGTCCCTTAGTGTGTTAATGTTACCAACTCAATAATTTAAAAGGTCTA
*
21142263 AGAACTGTTTTTAATTCTCTTTAAAAAGTTCAAAAGAAAGTGGTTGTTTGTTTTTAACGGGGTGG
195 AGAACTGTTTTTAATTCTCTTTAAAAAGTTCAAAAGAAAGTGGTTGTTCGTTTTTAACGGGGTGG
* *
21142328 ACTACGTAGAGGCTGAGACATTTT
260 ACTACGTAAAGGCCGAGACATTTT
21142352 CGTTGTGGCT
Statistics
Matches: 270, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
287 6 0.02
288 262 0.97
289 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (287 bp):
TCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAAAATATAATTTATTTTCTAACTTT
CCATTTGCCTTCTCCATTAATAAAGGAATAATCCCGATTTTCCTTTTTAATATGTGATATCAAAG
AGGATAAAAGGATGATAGTCCCTTAGTGTGTTAATGTTACCAACTCAATAATTTAAAAGGTCTAA
GAACTGTTTTTAATTCTCTTTAAAAAGTTCAAAAGAAAGTGGTTGTTCGTTTTTAACGGGGTGGA
CTACGTAAAGGCCGAGACATTTTATTT
Found at i:21145149 original size:75 final size:75
Alignment explanation
Indices: 21145016--21145160 Score: 200
Period size: 75 Copynumber: 1.9 Consensus size: 75
21145006 ATGGAAATCA
* * ** * * *
21145016 ATATTCTTTTGGAAAGAATATAATTTATTTTTCTAACTTTCCCTTTGCATTCTTTATTAATAAGG
1 ATATTCTTTTGGAAAGAATATAATTGATTTTTCTAACTTTCCATCAGCATTATCTATTAATAAGA
21145081 GAATAATCCT
66 GAATAATCCT
* * *
21145091 ATATTCTTTTGGAAAGAATATAGTTGCTTTTTCTAACTTTCCATCAGCCTTATCTATTAATAAGA
1 ATATTCTTTTGGAAAGAATATAATTGATTTTTCTAACTTTCCATCAGCATTATCTATTAATAAGA
21145156 GAATA
66 GAATA
21145161 TTTTTAGTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 60 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (75 bp):
ATATTCTTTTGGAAAGAATATAATTGATTTTTCTAACTTTCCATCAGCATTATCTATTAATAAGA
GAATAATCCT
Found at i:21146348 original size:51 final size:53
Alignment explanation
Indices: 21146285--21146427 Score: 188
Period size: 51 Copynumber: 2.8 Consensus size: 53
21146275 TGAAAGTGAA
* *
21146285 AGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTAC-T-GGAT
1 AGTGATGATCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACATCAGAT
* *
21146336 AGCT-TTGATCACGTGTGTAGTACTATGTGCAGGCTACTA--CGTGCATCAGAT
1 AG-TGATGATCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACATCAGAT
* *
21146387 AGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTATG
1 AGTGATGATCACGTGTGTAGTACTATGTGCAGGCTACTATG
21146428 TGAACCGGTA
Statistics
Matches: 79, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
49 4 0.05
50 2 0.03
51 72 0.91
52 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (53 bp):
AGTGATGATCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACATCAGAT
Found at i:21146674 original size:16 final size:16
Alignment explanation
Indices: 21146653--21146684 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21146643 TGATTGAAAG
*
21146653 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
21146669 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
21146685 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:21153422 original size:51 final size:50
Alignment explanation
Indices: 21153351--21153467 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 50
21153341 AGATATACCA
* * **
21153351 TCCATAAACACACCTAGGCATTGAGTGCCAAGCCTGTAGGCTACACATCCC
1 TCCA-AAACACACCTAGGCATTGAATGCAAAGCCCATAGGCTACACATCCC
* *
21153402 TCCAGAAACACACCTGGGCATTGAATGCAAAGCCCATAGGCTACACATCTC
1 TCCA-AAACACACCTAGGCATTGAATGCAAAGCCCATAGGCTACACATCCC
21153453 TCCAAAACACACCTA
1 TCCAAAACACACCTA
21153468 AATCTCCATA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 10 0.17
51 48 0.83
ACGTcount: A:0.33, C:0.33, G:0.15, T:0.18
Consensus pattern (50 bp):
TCCAAAACACACCTAGGCATTGAATGCAAAGCCCATAGGCTACACATCCC
Found at i:21160620 original size:22 final size:22
Alignment explanation
Indices: 21160592--21160636 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
21160582 GTAGCCTAAG
21160592 AATGTGCGCGAAGTGGAATAAA
1 AATGTGCGCGAAGTGGAATAAA
21160614 AATGTGCGCGAAGTGGAATAAA
1 AATGTGCGCGAAGTGGAATAAA
21160636 A
1 A
21160637 CTTGAGCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.31, T:0.18
Consensus pattern (22 bp):
AATGTGCGCGAAGTGGAATAAA
Found at i:21166304 original size:17 final size:17
Alignment explanation
Indices: 21166279--21166319 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
21166269 TGGCATCTGT
*
21166279 GAAGTATGCCAACTTAG
1 GAAGCATGCCAACTTAG
21166296 GAAGCATGCCAACTTAG
1 GAAGCATGCCAACTTAG
21166313 GAAGCAT
1 GAAGCAT
21166320 ATGAGGTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (17 bp):
GAAGCATGCCAACTTAG
Found at i:21168560 original size:13 final size:14
Alignment explanation
Indices: 21168542--21168570 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
21168532 TGTGTGCAAG
21168542 TTATGTTTT-TAGA
1 TTATGTTTTCTAGA
21168555 TTATGTTTTCTAGA
1 TTATGTTTTCTAGA
21168569 TT
1 TT
21168571 TTTAGAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.21, C:0.03, G:0.14, T:0.62
Consensus pattern (14 bp):
TTATGTTTTCTAGA
Found at i:21171412 original size:536 final size:541
Alignment explanation
Indices: 21170397--21171428 Score: 1304
Period size: 536 Copynumber: 1.9 Consensus size: 541
21170387 ATCCAATAGA
* *
21170397 GATTTTGTTATTCCATATAAGCTTGTGAAAGCTATAACAAAATACCATCATCTCTCTAATGTACC
1 GATTTTGTTATTCCACATAAGCTTGTGAAAGCTATAACAAAATACCATAATCTCTCTAATGTACC
* * * * * *
21170462 AAATGCCCTATACCAAATAGCAAAATTCCTCGTGTATAATTAAATCTCTAATCAGATATCAAATG
66 AAATGCCCTATACCAAATAGCAAAATTCCTCGCGTATAATCAAATCTCTAACCAAATACCAAATA
* * * *
21170527 ATTTCTAATGATACAAAAATTACATATCAAATTCCAAATTTCCCGATCATTTCATCATCATCATC
131 ATTTCTAATGATACAAAAATTACATAACAAATTCCAAATTTCCCAATCAATTCACCATCATCATC
* *
21170592 ATCTTCCCTCAGGTGCCTGAATTTTCCAAAAAAATTTAAACAAAAATGCAAACATAACTTTTACT
196 ATCTTCCCTCAGATGCCTGAATTGTCC--AAAAA--TAAACAAAAATGCAAACA-AACTTTTACT
* * * *
21170657 TTATTTGGGGCAAGTACTCTCCTCCTCCTCCTCTTCTTTTTTTTTTCTTCTAATTCTAGACTACA
256 TTATTTGGGGCAAATACTCTCCT-CTCCTCCTCTTATTTTTTTTTTCTTCTAATTCTAAAATACA
* * * *
21170722 CAAAAATTTCCTCATCCATTTTCAAATGGGAGTTGCTTGCAATTCTTGCATGTTTTGTTATTCAT
320 CAAAAATAT-CTCATCCATTTTCAAATGGGAGTTGCTTGAAATTCATGCATGTTTTGTTATCCAT
* **
21170787 TAAAACACCGTGTATACCATAGATATTTGTGTACTACATTAGGGGTTTTGTATCCTTTAATTTAT
384 TAAAACACCATGTATACCATAGATATTTGTGTACTACATTAGGGGTTTTGTATCCTTT-ATCAAT
** *
21170852 TTTGTTATTCCATATAAATTTGTGAAATGTATAACAAAATACCATAATCTCTACATATTTTGGTA
448 TTTGTTATTCCATATAAATTTGTGAAAACTATAAAAAAATACCATAATCTCTACATATTTTGGTA
21170917 TAGCATTAGGTATTTTAGCATTTGATTGG
513 TAGCATTAGGTATTTTAGCATTTGATTGG
* *
21170946 GATTTTGTTATTCCACATAAGCTTGTGAAAGCTATAACAAAATACTATAATCTCTCTCATGTACC
1 GATTTTGTTATTCCACATAAGCTTGTGAAAGCTATAACAAAATACCATAATCTCTCTAATGTACC
* * * *
21171011 AAATGTCTTATACCAAAATAGCAAAATTCCTCGCGTATAATCAAATCTTTGACCAAATACCAAAT
66 AAATGCCCTATACC-AAATAGCAAAATTCCTCGCGTATAATCAAATCTCTAACCAAATACCAAAT
* ** *
21171076 AATTTCTAATGATACAAAAATTAC-TAACCAATTACTGAATTTCCCAATCAATTCACCATCTTTT
130 AATTTCTAATGATACAAAAATTACATAACAAATT-CCAAATTTCCCAATCAATTCACCATC---A
** * * **
21171140 TTTTCTTCTTCCCTCATATGCCTGAATCTGT-C-AAAA-AAA-AAAAA-G-AGTC-AACTTTTAC
191 TCATCATCTTCCCTCAGATGCCTGAAT-TGTCCAAAAATAAACAAAAATGCAAACAAACTTTTAC
21171198 TTTATTTGGGGCAAATACTCTCCT-T-CTCCTCTTATTCTTTTTTTT-TTCTAATTCTAAAATAC
255 TTTATTTGGGGCAAATACTCTCCTCTCCTCCTCTTATT-TTTTTTTTCTTCTAATTCTAAAATAC
*
21171260 AGAAAAA-AT-TCATCCATTTTCAAATGGGAGTTGCTTGAAATTCATGCA-GATTTTGTTATCCA
319 ACAAAAATATCTCATCCATTTTCAAATGGGAGTTGCTTGAAATTCATGCATG-TTTTGTTATCCA
* ** * * * *
21171322 TTACAACATTATGTATA-CATTAGATATTTGTGTATTGCATTAAGGGTTTTTGTGTCCTTT-TGC
383 TTAAAACACCATGTATACCA-TAGATATTTGTGTACTACATT-AGGGGTTTTGTATCCTTTAT-C
*
21171385 AATTTTGTTATTCCATATAAGTTTGTGAAAACTATAAAAAAATA
445 AATTTTGTTATTCCATATAAATTTGTGAAAACTATAAAAAAATA
21171429 TGATGGTCAC
Statistics
Matches: 419, Mismatches: 53, Indels: 35
0.83 0.10 0.07
Matches are distributed among these distances:
535 4 0.01
536 119 0.28
537 16 0.04
538 1 0.00
539 31 0.07
540 9 0.02
542 32 0.08
544 2 0.00
545 1 0.00
546 5 0.01
547 3 0.01
549 80 0.19
550 91 0.22
553 23 0.05
554 2 0.00
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (541 bp):
GATTTTGTTATTCCACATAAGCTTGTGAAAGCTATAACAAAATACCATAATCTCTCTAATGTACC
AAATGCCCTATACCAAATAGCAAAATTCCTCGCGTATAATCAAATCTCTAACCAAATACCAAATA
ATTTCTAATGATACAAAAATTACATAACAAATTCCAAATTTCCCAATCAATTCACCATCATCATC
ATCTTCCCTCAGATGCCTGAATTGTCCAAAAATAAACAAAAATGCAAACAAACTTTTACTTTATT
TGGGGCAAATACTCTCCTCTCCTCCTCTTATTTTTTTTTTCTTCTAATTCTAAAATACACAAAAA
TATCTCATCCATTTTCAAATGGGAGTTGCTTGAAATTCATGCATGTTTTGTTATCCATTAAAACA
CCATGTATACCATAGATATTTGTGTACTACATTAGGGGTTTTGTATCCTTTATCAATTTTGTTAT
TCCATATAAATTTGTGAAAACTATAAAAAAATACCATAATCTCTACATATTTTGGTATAGCATTA
GGTATTTTAGCATTTGATTGG
Found at i:21187063 original size:40 final size:40
Alignment explanation
Indices: 21186999--21187117 Score: 152
Period size: 40 Copynumber: 3.0 Consensus size: 40
21186989 ATCCAGTGTT
*
21186999 CCATTTTATATATCTTTTTCCATATAACCGGTTCGTATAA
1 CCATTTTATATATCTTTTTCCATATAACCGATTCGTATAA
* * *
21187039 CTATTTCATATATCATTTTT-CATATAACCGATTTGTATAA
1 CCATTTTATATATC-TTTTTCCATATAACCGATTCGTATAA
* *
21187079 CCATTTTATATAT-TTATTTCCATATAACCAATTCATATA
1 CCATTTTATATATCTT-TTTCCATATAACCGATTCGTATA
21187118 TCATTTTTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.03
39 3 0.04
40 57 0.85
41 5 0.07
ACGTcount: A:0.32, C:0.18, G:0.04, T:0.46
Consensus pattern (40 bp):
CCATTTTATATATCTTTTTCCATATAACCGATTCGTATAA
Found at i:21187146 original size:68 final size:67
Alignment explanation
Indices: 21187034--21187165 Score: 210
Period size: 68 Copynumber: 2.0 Consensus size: 67
21187024 AACCGGTTCG
* * * *
21187034 TATAACTATTTCATATATCATTTTTCATATAACCGATTTGTATAACCATTTTATATATTTATTTC
1 TATAACCAATTCATATATCATTTTTCAGATAACCGATTTGTATAACCATTTCATATATTTATTTC
21187099 CA
66 CA
*
21187101 TATAACCAATTCATATATCATTTTTTTAGATAACCGATTTGTATAACCATTTCATATATTTATTT
1 TATAACCAATTCATATATCA-TTTTTCAGATAACCGATTTGTATAACCATTTCATATATTTATTT
21187166 TCATTTACAC
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
67 18 0.31
68 41 0.69
ACGTcount: A:0.33, C:0.14, G:0.04, T:0.48
Consensus pattern (67 bp):
TATAACCAATTCATATATCATTTTTCAGATAACCGATTTGTATAACCATTTCATATATTTATTTC
CA
Found at i:21188406 original size:20 final size:20
Alignment explanation
Indices: 21188359--21188406 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
21188349 TAATCCATTT
*
21188359 AATTAATAAAATTCAATAGC
1 AATTAATTAAATTCAATAGC
21188379 AATTAATTAAATTCAATAGC
1 AATTAATTAAATTCAATAGC
21188399 AATTAATT
1 AATTAATT
21188407 TTTGCAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.35
Consensus pattern (20 bp):
AATTAATTAAATTCAATAGC
Found at i:21190252 original size:14 final size:15
Alignment explanation
Indices: 21190233--21190264 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
21190223 GTGGTTATAG
21190233 TTAAAATA-ATAAAA
1 TTAAAATAGATAAAA
21190247 TTAAAATAGATAAAA
1 TTAAAATAGATAAAA
21190262 TTA
1 TTA
21190265 TGATGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
TTAAAATAGATAAAA
Found at i:21195010 original size:30 final size:30
Alignment explanation
Indices: 21194974--21195056 Score: 112
Period size: 30 Copynumber: 2.8 Consensus size: 30
21194964 TCAGAATATG
*
21194974 GAAGCCTTTGTGGCTGTTCTCTGATAAGTA
1 GAAGCCTTTGTGGCTATTCTCTGATAAGTA
* ** *
21195004 GAAGCCTTTGTTGCTATTCTCAAATAAGTG
1 GAAGCCTTTGTGGCTATTCTCTGATAAGTA
*
21195034 GAAGCCTATGTGGCTATTCTCTG
1 GAAGCCTTTGTGGCTATTCTCTG
21195057 TTATACGTGA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (30 bp):
GAAGCCTTTGTGGCTATTCTCTGATAAGTA
Found at i:21195150 original size:55 final size:56
Alignment explanation
Indices: 21195055--21195176 Score: 192
Period size: 55 Copynumber: 2.2 Consensus size: 56
21195045 GGCTATTCTC
* * *
21195055 TGTTATACGTGAGCCGTTGTGGCTGATTCTGTTAAATGCGCCTTCGTGACAAAGTA
1 TGTTATATGTGAGCCATTGTGGCTGATTCTGTTAAATGCGCCTTCATGACAAAGTA
* *
21195111 TGTTATATGTGAGCCATTGT-GCTGATTTTGTTAAATGCGCCTTCATGACAAAGTC
1 TGTTATATGTGAGCCATTGTGGCTGATTCTGTTAAATGCGCCTTCATGACAAAGTA
21195166 TGTTATATGTG
1 TGTTATATGTG
21195177 GACTCTTTTG
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
55 43 0.70
56 18 0.30
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.38
Consensus pattern (56 bp):
TGTTATATGTGAGCCATTGTGGCTGATTCTGTTAAATGCGCCTTCATGACAAAGTA
Found at i:21199194 original size:176 final size:177
Alignment explanation
Indices: 21198879--21199223 Score: 620
Period size: 176 Copynumber: 2.0 Consensus size: 177
21198869 TCGAATCTCG
*
21198879 ATTTTGGCTTACACAGGTTTTTTTTACTCAAGGAAATTTTTTAAAGTGTATAATGTCTCAACAAC
1 ATTTTGGCTTACACAGGTTTTTTTTACTCAAAGAAATTTTTTAAAGTGTATAATGTCTCAACAAC
21198944 AAACAATAAAGTAAAGACCCTCAAACAAGAAAATAAATAAAAGCCACAATTTCCACTTAGTAATA
66 AAACAATAAAGTAAAGACCCTCAAACAAGAAAATAAATAAAAGCCACAATTTCCACTTAGTAATA
21199009 AAAAATAAACAAGAGATAAATCATGTATCACATAAGACCCATATATT
131 AAAAATAAACAAGAGATAAATCATGTATCACATAAGACCCATATATT
* *
21199056 ATTTTGGCTTACACAGGTTTTTTTTACTCAAAGTAATTTTTTAGAGTGTATAATGTCTCAACAAC
1 ATTTTGGCTTACACAGGTTTTTTTTACTCAAAGAAATTTTTTAAAGTGTATAATGTCTCAACAAC
* * *
21199121 GAACAATAAAGTAAAGA-CCTCAAACAAGAAAATAAATAAAAGCCACAATTTCCATTTAGTAATC
66 AAACAATAAAGTAAAGACCCTCAAACAAGAAAATAAATAAAAGCCACAATTTCCACTTAGTAATA
*
21199185 AACAATAAACAAGAGATAAATCATGTATCACATAAGACC
131 AAAAATAAACAAGAGATAAATCATGTATCACATAAGACC
21199224 GATACATCAA
Statistics
Matches: 161, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
176 83 0.52
177 78 0.48
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (177 bp):
ATTTTGGCTTACACAGGTTTTTTTTACTCAAAGAAATTTTTTAAAGTGTATAATGTCTCAACAAC
AAACAATAAAGTAAAGACCCTCAAACAAGAAAATAAATAAAAGCCACAATTTCCACTTAGTAATA
AAAAATAAACAAGAGATAAATCATGTATCACATAAGACCCATATATT
Found at i:21202334 original size:6 final size:6
Alignment explanation
Indices: 21202315--21202363 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
21202305 TAGGTTTCCA
* * * *
21202315 AAAATG GAAATG AAATTG AAAATG AAAATG AAAACG AAAATG GAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
21202363 A
1 A
21202364 TCCATTTATA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.61, C:0.02, G:0.20, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:21202338 original size:18 final size:18
Alignment explanation
Indices: 21202315--21202363 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
21202305 TAGGTTTCCA
**
21202315 AAAATGGAAATGAAATTG
1 AAAATGGAAATGAAAACG
*
21202333 AAAATGAAAATGAAAACG
1 AAAATGGAAATGAAAACG
21202351 AAAATGGAAATGA
1 AAAATGGAAATGA
21202364 TCCATTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.61, C:0.02, G:0.20, T:0.16
Consensus pattern (18 bp):
AAAATGGAAATGAAAACG
Found at i:21210717 original size:12 final size:12
Alignment explanation
Indices: 21210664--21210709 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
21210654 TGTTCCAAAA
*
21210664 TTAATA-TTATT
1 TTAATATTTAAT
21210675 TTAATAGTTTAAT
1 TTAATA-TTTAAT
21210688 ATTAA-ATTTAAT
1 -TTAATATTTAAT
21210700 TTAATATTTA
1 TTAATATTTA
21210710 TCTTAATAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 10 0.33
12 11 0.37
13 5 0.17
14 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (12 bp):
TTAATATTTAAT
Found at i:21210719 original size:37 final size:38
Alignment explanation
Indices: 21210663--21210772 Score: 101
Period size: 37 Copynumber: 3.0 Consensus size: 38
21210653 TTGTTCCAAA
*
21210663 ATTAATA-TTATTTTAATAGTTTAATATTAAATTTAAT
1 ATTAATATTTATCTTAATAGTTTAATATTAAATTTAAT
*
21210700 -TTAATATTTATCTTAATAGTATT-TTATT-AATTTAAT
1 ATTAATATTTATCTTAATAGT-TTAATATTAAATTTAAT
*
21210736 ATTAA-AGTGATTATCTTTATA--TTAA-ATTAAATTTAAT
1 ATTAATA-T--TTATCTTAATAGTTTAATATTAAATTTAAT
21210773 GTTTGTCCTA
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
36 20 0.33
37 29 0.48
38 2 0.03
39 10 0.16
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (38 bp):
ATTAATATTTATCTTAATAGTTTAATATTAAATTTAAT
Found at i:21210740 original size:11 final size:11
Alignment explanation
Indices: 21210664--21210740 Score: 54
Period size: 11 Copynumber: 6.9 Consensus size: 11
21210654 TGTTCCAAAA
*
21210664 TTAATATTATT
1 TTAATATTAAT
21210675 TTAATAGTTTAAT
1 TTAATA--TTAAT
21210688 ATTAA-ATTTAAT
1 -TTAATA-TTAAT
*
21210700 TTAATATTTAT
1 TTAATATTAAT
*
21210711 CTTAATAGT-AT
1 -TTAATATTAAT
21210722 TT--TATTAAT
1 TTAATATTAAT
21210731 TTAATATTAA
1 TTAATATTAA
21210741 AGTGATTATC
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
8 3 0.06
9 4 0.07
10 2 0.04
11 22 0.41
12 14 0.26
13 5 0.09
14 4 0.07
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (11 bp):
TTAATATTAAT
Found at i:21211810 original size:22 final size:22
Alignment explanation
Indices: 21211779--21211823 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
21211769 ATTACTTATC
*
21211779 TTATTATATATCTATTT-TATTA
1 TTATTATATA-ATATTTATATTA
*
21211801 TTATTTTATAATATTTATATTA
1 TTATTATATAATATTTATATTA
21211823 T
1 T
21211824 GTAATGCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
TTATTATATAATATTTATATTA
Found at i:21212174 original size:14 final size:14
Alignment explanation
Indices: 21212155--21212182 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21212145 TCTTGCGAAT
21212155 GAATGTGAATATTA
1 GAATGTGAATATTA
21212169 GAATGTGAATATTA
1 GAATGTGAATATTA
21212183 TAAAATTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (14 bp):
GAATGTGAATATTA
Found at i:21214328 original size:16 final size:16
Alignment explanation
Indices: 21214309--21214343 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
21214299 TAGTAATTTT
21214309 AATGTTAAAG-GACTAA
1 AATGTTAAAGTGA-TAA
21214325 AATGTTAAAGTGATAA
1 AATGTTAAAGTGATAA
21214341 AAT
1 AAT
21214344 TATGAGGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.51, C:0.03, G:0.17, T:0.29
Consensus pattern (16 bp):
AATGTTAAAGTGATAA
Found at i:21224836 original size:49 final size:46
Alignment explanation
Indices: 21224732--21224852 Score: 134
Period size: 49 Copynumber: 2.6 Consensus size: 46
21224722 ATTTCCATAC
* * * * *
21224732 AAGACCATATCTGGGATATGGCATCAGTCTGATATGCGATCCGTGT
1 AAGACCATAGCTGGGCTATGGCATCGGTATGATATGCGATACGTGT
* *
21224778 AAGACCATAGCTGGGCTATGGCATCGGTATGTATTATGTGATTATGTGT
1 AAGACCATAGCTGGGCTATGGCATCGGTATG-A-TATGCGA-TACGTGT
* *
21224827 AAGACCATAGTTGGACTATGGCATCG
1 AAGACCATAGCTGGGCTATGGCATCG
21224853 AGAAAACGAA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
46 27 0.43
47 1 0.02
48 6 0.10
49 29 0.46
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (46 bp):
AAGACCATAGCTGGGCTATGGCATCGGTATGATATGCGATACGTGT
Found at i:21225093 original size:2 final size:2
Alignment explanation
Indices: 21225086--21225111 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21225076 ATGTTAATTC
21225086 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
21225112 GTATTTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21232540 original size:11 final size:11
Alignment explanation
Indices: 21232508--21232541 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
21232498 GTCGTAAAAT
*
21232508 TTATTTTAATT
1 TTATTTTAATA
21232519 TTATTTTAATA
1 TTATTTTAATA
21232530 TTATTTTAATA
1 TTATTTTAATA
21232541 T
1 T
21232542 CTACAGCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:21237012 original size:22 final size:22
Alignment explanation
Indices: 21236978--21237027 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
21236968 TCTTTTAACA
* *
21236978 CATAAACATTCAATTATATTAG
1 CATAATCAATCAATTATATTAG
*
21237000 CATAATCAATCAATTATATTGG
1 CATAATCAATCAATTATATTAG
21237022 CATAAT
1 CATAAT
21237028 ACATCCATGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (22 bp):
CATAATCAATCAATTATATTAG
Found at i:21237661 original size:21 final size:21
Alignment explanation
Indices: 21237637--21237678 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
21237627 ATCCAATATG
**
21237637 CAATTAAGTCATTAATAACAC
1 CAATTAAACCATTAATAACAC
*
21237658 CAATTAAACCTTTAATAACAC
1 CAATTAAACCATTAATAACAC
21237679 ATAATCATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.21, G:0.02, T:0.29
Consensus pattern (21 bp):
CAATTAAACCATTAATAACAC
Found at i:21241548 original size:16 final size:18
Alignment explanation
Indices: 21241529--21241561 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21241519 TTAGAATTTG
21241529 TACTTA-TT-ATTTTTAT
1 TACTTAGTTAATTTTTAT
21241545 TACTTAGTTAATTTTTA
1 TACTTAGTTAATTTTTA
21241562 GTTTTCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (18 bp):
TACTTAGTTAATTTTTAT
Found at i:21242476 original size:18 final size:18
Alignment explanation
Indices: 21242455--21242491 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
21242445 GTAGGTTTCC
* *
21242455 AAAAATGGAAATGGAAAT
1 AAAAATGAAAATGAAAAT
21242473 AAAAATGAAAATGAAAAT
1 AAAAATGAAAATGAAAAT
21242491 A
1 A
21242492 GGGATGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (18 bp):
AAAAATGAAAATGAAAAT
Found at i:21245229 original size:16 final size:15
Alignment explanation
Indices: 21245201--21245251 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
21245191 TGATTGTTAA
*
21245201 AAAAATTTTAATATT
1 AAAAATTCTAATATT
*
21245216 AAAAA-TCTAAAATAT
1 AAAAATTCTAATAT-T
21245231 AAATAATTCTAATATT
1 AAA-AATTCTAATATT
21245247 AAAAA
1 AAAAA
21245252 ATTTTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 6 0.20
15 11 0.37
16 6 0.20
17 7 0.23
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAAATTCTAATATT
Found at i:21245254 original size:16 final size:16
Alignment explanation
Indices: 21245200--21245254 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
21245190 ATGATTGTTA
*
21245200 AAAAAATTTTAATATT
1 AAAAAATTCTAATATT
*
21245216 -AAAAA-TCTAAAATAT
1 AAAAAATTCTAATAT-T
*
21245231 AAATAATTCTAATATT
1 AAAAAATTCTAATATT
21245247 AAAAAATT
1 AAAAAATT
21245255 TTAAAATACC
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 6 0.19
15 6 0.19
16 12 0.39
17 7 0.23
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAAAATTCTAATATT
Found at i:21256034 original size:23 final size:23
Alignment explanation
Indices: 21255991--21256034 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
21255981 TTTATAGTGA
* *
21255991 TATTATATTAGATGATGAATTCT
1 TATTATAGTAGATGATAAATTCT
21256014 TATTATAGTA-ATGATTAAATT
1 TATTATAGTAGATGA-TAAATT
21256035 GTAAAAGTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (23 bp):
TATTATAGTAGATGATAAATTCT
Found at i:21266081 original size:25 final size:25
Alignment explanation
Indices: 21266047--21266119 Score: 94
Period size: 25 Copynumber: 3.0 Consensus size: 25
21266037 TAGGGTTGTC
*
21266047 GATTTATAGCTCGTGAGAGTATACT
1 GATTTATAGCTCGTGAGAGCATACT
*
21266072 GATTTATAGCTCGTAAGAGCATA-T
1 GATTTATAGCTCGTGAGAGCATACT
* * *
21266096 CATTCATAGCTCATGAGAGCATAC
1 GATTTATAGCTCGTGAGAGCATAC
21266120 CGATCTTCAG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 20 0.49
25 21 0.51
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (25 bp):
GATTTATAGCTCGTGAGAGCATACT
Found at i:21266114 original size:24 final size:25
Alignment explanation
Indices: 21266052--21266119 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 25
21266042 TTGTCGATTT
* * *
21266052 ATAGCTCGTGAGAGTATACTGATTT
1 ATAGCTCGTGAGAGCATACTCATTC
*
21266077 ATAGCTCGTAAGAGCATA-TCATTC
1 ATAGCTCGTGAGAGCATACTCATTC
*
21266101 ATAGCTCATGAGAGCATAC
1 ATAGCTCGTGAGAGCATAC
21266120 CGATCTTCAG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
24 20 0.56
25 16 0.44
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (25 bp):
ATAGCTCGTGAGAGCATACTCATTC
Found at i:21266163 original size:25 final size:25
Alignment explanation
Indices: 21266079--21266169 Score: 71
Period size: 25 Copynumber: 3.7 Consensus size: 25
21266069 ACTGATTTAT
* * * *
21266079 AGCTCGTAAGAGCATATC-ATTCAT
1 AGCTCATATGAGCATACCGATTCAC
*
21266103 AGCTCATGA-GAGCATACCGA-TCTTC
1 AGCTCAT-ATGAGCATACCGATTC-AC
* *
21266128 AGCACAAATGAGCATACCGATTCAC
1 AGCTCATATGAGCATACCGATTCAC
*
21266153 AGCTCGTATGAGCATAC
1 AGCTCATATGAGCATAC
21266170 ATGTAGATAA
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
24 17 0.33
25 33 0.63
26 2 0.04
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (25 bp):
AGCTCATATGAGCATACCGATTCAC
Found at i:21273650 original size:25 final size:25
Alignment explanation
Indices: 21273612--21273668 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
21273602 TCATTAGGGT
**
21273612 TATCGATTTGTAGCTCGTGAGAGCA
1 TATCGATTCATAGCTCGTGAGAGCA
21273637 TATCGATTCATAGCTCGTGAGAGCA
1 TATCGATTCATAGCTCGTGAGAGCA
*
21273662 TACCGAT
1 TATCGAT
21273669 CTTCAGCTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (25 bp):
TATCGATTCATAGCTCGTGAGAGCA
Found at i:21273676 original size:25 final size:26
Alignment explanation
Indices: 21273623--21273714 Score: 88
Period size: 25 Copynumber: 3.7 Consensus size: 26
21273613 ATCGATTTGT
* *
21273623 AGCTCGTGA-GAGCATATCGATTCAT-
1 AGCTCGTGATGAGCATACCGA-TCTTC
21273648 AGCTCGTGA-GAGCATACCGATCTTC
1 AGCTCGTGATGAGCATACCGATCTTC
**
21273673 AGCTC-AAATGAGCATACCGAT-TTAC
1 AGCTCGTGATGAGCATACCGATCTT-C
21273698 AGCTCGT-ATGAGCATAC
1 AGCTCGTGATGAGCATAC
21273715 ATGTACATGA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
24 6 0.10
25 52 0.90
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (26 bp):
AGCTCGTGATGAGCATACCGATCTTC
Found at i:21274947 original size:12 final size:12
Alignment explanation
Indices: 21274930--21274959 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
21274920 TCAGGCTGTT
21274930 ACACGGCCTAGC
1 ACACGGCCTAGC
*
21274942 ACACGGCCTGGC
1 ACACGGCCTAGC
21274954 ACACGG
1 ACACGG
21274960 GCGTTTGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:21277962 original size:26 final size:27
Alignment explanation
Indices: 21277929--21277996 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 27
21277919 TAATTTAATA
*
21277929 TAAA-AATATTATTATTAAATTAT-AT
1 TAAATAATATTATTATTAAAATATGAT
*
21277954 TTAATAATAATTA-TATTAAAATATGAT
1 TAAATAAT-ATTATTATTAAAATATGAT
*
21277981 TAAATTAT-TTATTATT
1 TAAATAATATTATTATT
21277997 TATTTATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
25 6 0.17
26 17 0.49
27 12 0.34
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (27 bp):
TAAATAATATTATTATTAAAATATGAT
Found at i:21283243 original size:45 final size:44
Alignment explanation
Indices: 21283153--21283245 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 44
21283143 ATTACAACAT
21283153 CATTCCATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
* * *
21283197 CATTCTATTCAACCAAACA-ATTGAATTAGTATTACGCCTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACGCCTCTATTC
21283242 CATT
1 CATT
21283246 ACAGCGAACC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.48
45 22 0.50
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.32
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
Found at i:21289688 original size:24 final size:25
Alignment explanation
Indices: 21289644--21289695 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
21289634 TTATTTGTAC
* *
21289644 TAATTATATACATTATCTATATATA
1 TAATTATATACATTATATATATACA
21289669 TAATT-TATA-ATATATATATATACA
1 TAATTATATACAT-TATATATATACA
21289693 TAA
1 TAA
21289696 AAGCAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 2 0.08
24 17 0.71
25 5 0.21
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (25 bp):
TAATTATATACATTATATATATACA
Found at i:21293570 original size:49 final size:49
Alignment explanation
Indices: 21293498--21294035 Score: 1058
Period size: 49 Copynumber: 11.0 Consensus size: 49
21293488 CCGTTCTCTC
21293498 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
1 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
21293547 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
1 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
21293596 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
1 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
21293645 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
1 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
21293694 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
1 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
21293743 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
1 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
21293792 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
1 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
21293841 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
1 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
21293890 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
1 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
21293939 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
1 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
**
21293988 AATCTCATAACATATACCGATGCCATATTCCAGCTATGGTCTTACACG
1 AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACG
21294036 GAATTACATA
Statistics
Matches: 487, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 487 1.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (49 bp):
AATCTCATAACATATACCGATGCCATAGCCCAGCTATGGTCTTACACGT
Found at i:21295253 original size:23 final size:23
Alignment explanation
Indices: 21295227--21295348 Score: 154
Period size: 23 Copynumber: 5.3 Consensus size: 23
21295217 ATAAGTGCCA
*
21295227 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCTGAAGCTAC
* *
21295250 CACTGATACGTAGCTGTAGCTAC
1 CACTGATATGTAGCTGAAGCTAC
* * * *
21295273 CACTAAAATGTAGCCGAAACTAC
1 CACTGATATGTAGCTGAAGCTAC
*
21295296 CACTGATATGTAGCTGTAGCTAC
1 CACTGATATGTAGCTGAAGCTAC
* *
21295319 CATTGAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGCTGAAGCTAC
21295342 CACTGAT
1 CACTGAT
21295349 CAATAACACT
Statistics
Matches: 80, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 80 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (23 bp):
CACTGATATGTAGCTGAAGCTAC
Found at i:21295301 original size:46 final size:46
Alignment explanation
Indices: 21295234--21295348 Score: 185
Period size: 46 Copynumber: 2.5 Consensus size: 46
21295224 CCACACTGAT
21295234 ATGTAGCCGAAGCTACCACTGATACGTAGCTGTAGCTACCACTAAA
1 ATGTAGCCGAAGCTACCACTGATACGTAGCTGTAGCTACCACTAAA
* * * *
21295280 ATGTAGCCGAAACTACCACTGATATGTAGCTGTAGCTACCATTGAA
1 ATGTAGCCGAAGCTACCACTGATACGTAGCTGTAGCTACCACTAAA
*
21295326 ATGTAGCTGAAGCTACCACTGAT
1 ATGTAGCCGAAGCTACCACTGAT
21295349 CAATAACACT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.24
Consensus pattern (46 bp):
ATGTAGCCGAAGCTACCACTGATACGTAGCTGTAGCTACCACTAAA
Found at i:21302342 original size:13 final size:13
Alignment explanation
Indices: 21302324--21302353 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
21302314 GTTTGAAATA
21302324 ATTATGGTATTTG
1 ATTATGGTATTTG
21302337 ATTATGGTATTTG
1 ATTATGGTATTTG
21302350 ATTA
1 ATTA
21302354 GAAATTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (13 bp):
ATTATGGTATTTG
Found at i:21324449 original size:18 final size:17
Alignment explanation
Indices: 21324421--21324455 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21324411 ATTTTTAAGA
*
21324421 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
21324438 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
21324456 TTAATAATAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:21324684 original size:43 final size:45
Alignment explanation
Indices: 21324620--21324709 Score: 112
Period size: 43 Copynumber: 2.0 Consensus size: 45
21324610 ACCTCTATTC
* * *
21324620 CATTCAACCAAACACAAGATTA-C-ATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
21324663 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
21324708 CA
1 CA
21324710 CCTCTAATCC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 19 0.49
44 1 0.03
45 19 0.49
ACGTcount: A:0.38, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:21324711 original size:16 final size:16
Alignment explanation
Indices: 21324690--21324758 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
21324680 GATTAGCTAT
21324690 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
21324706 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
21324723 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
21324739 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
21324755 TACA
1 TACA
21324759 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:21324732 original size:33 final size:32
Alignment explanation
Indices: 21324690--21324758 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
21324680 GATTAGCTAT
21324690 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
21324723 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
21324755 TACA
1 TACA
21324759 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:21334067 original size:12 final size:12
Alignment explanation
Indices: 21334052--21334082 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
21334042 TACACGGGTG
21334052 AGGACACAGCCT
1 AGGACACAGCCT
21334064 AGGACACAGCCT
1 AGGACACAGCCT
21334076 AGGACAC
1 AGGACAC
21334083 GACCGTGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.32, G:0.26, T:0.06
Consensus pattern (12 bp):
AGGACACAGCCT
Found at i:21339345 original size:11 final size:10
Alignment explanation
Indices: 21339304--21339342 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
21339294 TTTGTGTTCT
21339304 AAAAAAATATG
1 AAAAAAA-ATG
**
21339315 AAATGAAATG
1 AAAAAAAATG
21339325 AAAAAAAATG
1 AAAAAAAATG
21339335 AAAAAAAA
1 AAAAAAAA
21339343 ATGTGATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 19 0.79
11 5 0.21
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:21343984 original size:31 final size:31
Alignment explanation
Indices: 21343936--21343994 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
21343926 TTGCAATGCG
* * *
21343936 TTGACTTGATTATGTTACTATAAGCATGCCA
1 TTGAATTGATTACGTTACCATAAGCATGCCA
21343967 TTGAATTGATTACGTTACCATAAGCATG
1 TTGAATTGATTACGTTACCATAAGCATG
21343995 TTGACCATGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (31 bp):
TTGAATTGATTACGTTACCATAAGCATGCCA
Found at i:21344015 original size:40 final size:40
Alignment explanation
Indices: 21343956--21344048 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 40
21343946 TATGTTACTA
*
21343956 TAAG-CATGCCATTGAATTGATTACGTTACCATAAGCATG
1 TAAGACATGCCATTAAATTGATTACGTTACCATAAGCATG
* * *
21343995 T-TGACCATGCCATTAAATTGATTATGTTTCCATAAGCATG
1 TAAGA-CATGCCATTAAATTGATTACGTTACCATAAGCATG
21344035 TAAGACATGCCATT
1 TAAGACATGCCATT
21344049 GTACTTAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
38 1 0.02
39 1 0.02
40 42 0.91
41 2 0.04
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (40 bp):
TAAGACATGCCATTAAATTGATTACGTTACCATAAGCATG
Found at i:21350346 original size:29 final size:30
Alignment explanation
Indices: 21350304--21350360 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
21350294 TACATGTATG
*
21350304 CTCATACGAGCTGTA-AATGGGAAGCTCCA
1 CTCATACGAGCTGTAGAACGGGAAGCTCCA
*
21350333 CTCATATGAGCTGTAGAACGGGAAGCTC
1 CTCATACGAGCTGTAGAACGGGAAGCTC
21350361 ATAAGAGCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (30 bp):
CTCATACGAGCTGTAGAACGGGAAGCTCCA
Found at i:21356659 original size:35 final size:35
Alignment explanation
Indices: 21356613--21356686 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
21356603 GTTAATATTA
21356613 TAAACTGAGAGAGACAAGGATTTCCAAACTGAGAC
1 TAAACTGAGAGAGACAAGGATTTCCAAACTGAGAC
21356648 TAAACTGAGAGAGACAAGGATTTCCAAACTGAGAC
1 TAAACTGAGAGAGACAAGGATTTCCAAACTGAGAC
21356683 TAAA
1 TAAA
21356687 TTCAAGTCTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.18
Consensus pattern (35 bp):
TAAACTGAGAGAGACAAGGATTTCCAAACTGAGAC
Found at i:21357476 original size:6 final size:6
Alignment explanation
Indices: 21357467--21357501 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
21357457 ACTGATACTA
21357467 CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAA
1 CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAA
21357502 CTTATTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (6 bp):
CAAAAT
Found at i:21366020 original size:9 final size:9
Alignment explanation
Indices: 21366006--21366039 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
21365996 CACATTGCCA
21366006 CCTCTTTCC
1 CCTCTTTCC
21366015 CCTCTTTCC
1 CCTCTTTCC
*
21366024 TCTCTTTCC
1 CCTCTTTCC
21366033 CCTCTTT
1 CCTCTTT
21366040 TTTCTCTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (9 bp):
CCTCTTTCC
Found at i:21367214 original size:38 final size:38
Alignment explanation
Indices: 21367171--21367260 Score: 144
Period size: 38 Copynumber: 2.4 Consensus size: 38
21367161 ATGTGATTTT
* * **
21367171 AAGTGAAAACTGATATAATGAGCATGTCTCACATGTTA
1 AAGTGAAAAGTGATATAATGAGCATGTCTCACAGGCCA
21367209 AAGTGAAAAGTGATATAATGAGCATGTCTCACAGGCCA
1 AAGTGAAAAGTGATATAATGAGCATGTCTCACAGGCCA
21367247 AAGTGAAAAGTGAT
1 AAGTGAAAAGTGAT
21367261 TTTTAAGTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.24
Consensus pattern (38 bp):
AAGTGAAAAGTGATATAATGAGCATGTCTCACAGGCCA
Found at i:21367270 original size:18 final size:19
Alignment explanation
Indices: 21367247--21367282 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
21367237 TCACAGGCCA
21367247 AAGTG-AAAAGTGATTTTT
1 AAGTGAAAAAGTGATTTTT
21367265 AAGTGAAAAAGTGATTTT
1 AAGTGAAAAAGTGATTTT
21367283 GTGGCCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (19 bp):
AAGTGAAAAAGTGATTTTT
Found at i:21367480 original size:47 final size:47
Alignment explanation
Indices: 21367371--21367480 Score: 139
Period size: 47 Copynumber: 2.3 Consensus size: 47
21367361 TATCCACAAC
* * * *
21367371 ATGTGGCAGTTTATCTGCGAAAGTAGTGGCTTGTCCACAATTTTATT
1 ATGTGGCAGTTTATCTACAAAAGTAGTGACTTGTCCACAATTTGATT
* * * *
21367418 ATGTGGCAATATATCTACAAAAGTGGTGACTTGTCCATAATTTGATT
1 ATGTGGCAGTTTATCTACAAAAGTAGTGACTTGTCCACAATTTGATT
*
21367465 ATGTGGTAGTTTATCT
1 ATGTGGCAGTTTATCT
21367481 GCATTACCAT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (47 bp):
ATGTGGCAGTTTATCTACAAAAGTAGTGACTTGTCCACAATTTGATT
Found at i:21374488 original size:8 final size:8
Alignment explanation
Indices: 21374475--21374500 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
21374465 TTATGAGTGA
21374475 TGACATTT
1 TGACATTT
21374483 TGACATTT
1 TGACATTT
21374491 TGACATTT
1 TGACATTT
21374499 TG
1 TG
21374501 GTGCTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (8 bp):
TGACATTT
Found at i:21379886 original size:20 final size:19
Alignment explanation
Indices: 21379802--21379886 Score: 53
Period size: 20 Copynumber: 4.2 Consensus size: 19
21379792 TAAGTCTTTG
21379802 AATTTTATTTTTATTTATTA
1 AATTTTATTTTTATTT-TTA
** **
21379822 AATTATTTATTTAGACCTTTA
1 AA-T-TTTATTTTTATTTTTA
* * * *
21379843 GACTTTAGTTTTAGTTTTA
1 AATTTTATTTTTATTTTTA
21379862 GAATTTTATTTTTATTTATTA
1 -AATTTTATTTTTATTT-TTA
21379883 AATT
1 AATT
21379887 ATTTGTAATT
Statistics
Matches: 46, Mismatches: 15, Indels: 8
0.67 0.22 0.12
Matches are distributed among these distances:
19 11 0.24
20 18 0.39
21 8 0.17
22 9 0.20
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.61
Consensus pattern (19 bp):
AATTTTATTTTTATTTTTA
Found at i:21379946 original size:18 final size:18
Alignment explanation
Indices: 21379903--21379946 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
21379893 AATTTTTATG
*
21379903 ATTGGGTTAGGTTGGGTA
1 ATTGGGTTAGGTTGGATA
* *
21379921 ATTAGGTTGGGTTGGATA
1 ATTGGGTTAGGTTGGATA
*
21379939 CTTGGGTT
1 ATTGGGTT
21379947 CGGATTGGGT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.16, C:0.02, G:0.41, T:0.41
Consensus pattern (18 bp):
ATTGGGTTAGGTTGGATA
Found at i:21381402 original size:27 final size:27
Alignment explanation
Indices: 21381371--21381422 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
21381361 ATTGTAAACA
21381371 CATTAGGAAAGAAATGACTTCGTGGCG
1 CATTAGGAAAGAAATGACTTCGTGGCG
* * *
21381398 CATTATGAAAGAAATGCCTTTGTGG
1 CATTAGGAAAGAAATGACTTCGTGG
21381423 TGAAAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (27 bp):
CATTAGGAAAGAAATGACTTCGTGGCG
Found at i:21383136 original size:27 final size:28
Alignment explanation
Indices: 21383102--21383202 Score: 100
Period size: 27 Copynumber: 3.7 Consensus size: 28
21383092 CTTGTTCTTA
*
21383102 GCCACAAAGACAATTCTTTCATAATGCT
1 GCCACAAAGACATTTCTTTCATAATGCT
* * ** *
21383130 -CCGCAAAGGCATTTCTTTTGTGATG-T
1 GCCACAAAGACATTTCTTTCATAATGCT
*
21383156 GCCACAAATACATTTCTTTCATAATGC-
1 GCCACAAAGACATTTCTTTCATAATGCT
* *
21383183 GCCAAAAAGGCATTTCTTTC
1 GCCACAAAGACATTTCTTTC
21383203 TTGACATGTT
Statistics
Matches: 56, Mismatches: 15, Indels: 5
0.74 0.20 0.07
Matches are distributed among these distances:
26 1 0.02
27 55 0.98
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.33
Consensus pattern (28 bp):
GCCACAAAGACATTTCTTTCATAATGCT
Found at i:21388096 original size:85 final size:85
Alignment explanation
Indices: 21387997--21388176 Score: 297
Period size: 85 Copynumber: 2.1 Consensus size: 85
21387987 ATAGAAATGG
* *
21387997 AAATGAAAATTTGCAATCCTATATGGATTACTTAAAAACTGATCGGAAGAATAAGTTTATGTTTT
1 AAATGAAAATTTGCAATCCTATATAGATTACTTAAAAACTAATCGGAAGAATAAGTTTATGTTTT
* *
21388062 TGGACTATTTTGAAGCTTGA
66 TGGACTAATTTGAAGCCTGA
* *
21388082 AAATGAAAATTTGCAATCTTATATAGATTACTTAAAAACTAATTGGAAGAATAAGTTTATGTTTT
1 AAATGAAAATTTGCAATCCTATATAGATTACTTAAAAACTAATCGGAAGAATAAGTTTATGTTTT
*
21388147 TGGACTAATTTGAAGCCTGG
66 TGGACTAATTTGAAGCCTGA
21388167 AAATGAAAAT
1 AAATGAAAAT
21388177 AAACTATTCG
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 88 1.00
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (85 bp):
AAATGAAAATTTGCAATCCTATATAGATTACTTAAAAACTAATCGGAAGAATAAGTTTATGTTTT
TGGACTAATTTGAAGCCTGA
Found at i:21390662 original size:49 final size:50
Alignment explanation
Indices: 21390604--21391428 Score: 779
Period size: 50 Copynumber: 15.7 Consensus size: 50
21390594 TTTTTTGTAC
* * **
21390604 TGCCAATGCCATATCCCAGA-ATGATCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
21390653 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * * * *
21390703 TGCCAACGCCATGTCCTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
21390759 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * * * *
21390809 TGCCAACGCCATGTCCTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
21390865 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * * * *
21390915 TGCCAACGCCATGTCCTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
21390971 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * * * *
21391021 TGCCAACGCCATGTCCTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
21391077 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * * * *
21391127 TGCCAACGCCATGTCCTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
21391183 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * * * *
21391233 TGCCAACGCCATGTCCTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
21391289 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * * * *
21391339 TGCCAACGCCATGTCCTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
21391395 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
21391429 AGATCTCTTT
Statistics
Matches: 632, Mismatches: 101, Indels: 79
0.78 0.12 0.10
Matches are distributed among these distances:
49 18 0.03
50 303 0.48
51 7 0.01
53 26 0.04
55 6 0.01
56 272 0.43
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:21390782 original size:106 final size:106
Alignment explanation
Indices: 21390653--21391426 Score: 1539
Period size: 106 Copynumber: 7.3 Consensus size: 106
21390643 CTCATATCGG
*
21390653 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTC
21390718 CTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
66 CTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
21390759 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTC
21390824 CTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
66 CTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
21390865 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTC
21390930 CTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
66 CTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
21390971 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTC
21391036 CTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
66 CTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
21391077 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTC
21391142 CTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
66 CTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
21391183 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTC
21391248 CTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
66 CTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
21391289 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTC
21391354 CTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
66 CTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
21391395 TGCCAATGCCATGTCCCAGACATGGTCTTACA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA
21391427 TGAGATCTCT
Statistics
Matches: 667, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 667 1.00
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (106 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTC
CTACACATGGTCTTACATGGGAACTCTAATAACCTCAATGA
Found at i:21397124 original size:21 final size:22
Alignment explanation
Indices: 21397095--21397135 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
21397085 AATTTTGAAA
21397095 AAAGAAAAAAAGAAAAGAATTG
1 AAAGAAAAAAAGAAAAGAATTG
*
21397117 AAAG-AAAAAGGAAAAGAAT
1 AAAGAAAAAAAGAAAAGAAT
21397136 GAATAAGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (22 bp):
AAAGAAAAAAAGAAAAGAATTG
Found at i:21405820 original size:89 final size:89
Alignment explanation
Indices: 21405692--21405885 Score: 354
Period size: 89 Copynumber: 2.2 Consensus size: 89
21405682 ATAATTGTTA
21405692 AAATTTCTAAATAAATTTATAAAACGTTTTCCATATATATCAAATAAATAATAAAATCAATTGCT
1 AAATTTCTAAA-AAATTTATAAAACGTTTTCCATATATATCAAATAAATAATAAAATCAATTGCT
21405757 AAATATAATATAAACAACATACAAC
65 AAATATAATATAAACAACATACAAC
21405782 AAATTTCTAAAAAATTTATAAAACGTTTTCCATATATATCAAATAAATAATAAAATCAATTGCTA
1 AAATTTCTAAAAAATTTATAAAACGTTTTCCATATATATCAAATAAATAATAAAATCAATTGCTA
21405847 AATATAATATAAACAACATACAAC
66 AATATAATATAAACAACATACAAC
21405871 ATAATATT-TAAAAAA
1 A-AAT-TTCTAAAAAA
21405886 ATCATATTAT
Statistics
Matches: 102, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
89 79 0.77
90 21 0.21
91 2 0.02
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (89 bp):
AAATTTCTAAAAAATTTATAAAACGTTTTCCATATATATCAAATAAATAATAAAATCAATTGCTA
AATATAATATAAACAACATACAAC
Found at i:21406341 original size:16 final size:16
Alignment explanation
Indices: 21406320--21406358 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
21406310 ATTTGGTTCA
*
21406320 TTGTAATGGAATAAAG
1 TTGTAATAGAATAAAG
*
21406336 TTGTAATAGAATAGAG
1 TTGTAATAGAATAAAG
21406352 TTGTAAT
1 TTGTAAT
21406359 CCGTAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.23, T:0.36
Consensus pattern (16 bp):
TTGTAATAGAATAAAG
Found at i:21406899 original size:44 final size:44
Alignment explanation
Indices: 21406849--21406933 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
21406839 TAATTGTAAA
* *
21406849 TTAAATTATAGTTACTTTTAAATGTGTAATTATCACAACTTTTG
1 TTAAATTATAATTACTTTTAAATGTATAATTATCACAACTTTTG
* *
21406893 TTAAATTATAATTATTTTTAAATGTATAATTTTCACAACTT
1 TTAAATTATAATTACTTTTAAATGTATAATTATCACAACTT
21406934 ATATATATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.49
Consensus pattern (44 bp):
TTAAATTATAATTACTTTTAAATGTATAATTATCACAACTTTTG
Found at i:21415160 original size:14 final size:13
Alignment explanation
Indices: 21415145--21415197 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
21415135 TCTATCTTTC
21415145 TTTTCTTTAATTT
1 TTTTCTTTAATTT
*
21415158 CTTTACTTTAATTT
1 -TTTTCTTTAATTT
* *
21415172 TGTTCTTATTATTT
1 TTTTCTT-TAATTT
*
21415186 TTATCTTTAATT
1 TTTTCTTTAATT
21415198 ACTTAATGTT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
13 9 0.29
14 22 0.71
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.70
Consensus pattern (13 bp):
TTTTCTTTAATTT
Found at i:21421808 original size:17 final size:15
Alignment explanation
Indices: 21421776--21421813 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
21421766 TGTTATTGGT
21421776 TGATTGTTGGTTGTG
1 TGATTGTTGGTTGTG
21421791 TGATTGTGTGGTT-TG
1 TGATTGT-TGGTTGTG
21421806 TG-TTGTTG
1 TGATTGTTG
21421814 AAGCGTCGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.09
14 4 0.18
15 11 0.50
16 5 0.23
ACGTcount: A:0.05, C:0.00, G:0.39, T:0.55
Consensus pattern (15 bp):
TGATTGTTGGTTGTG
Found at i:21427514 original size:19 final size:20
Alignment explanation
Indices: 21427458--21427514 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
21427448 ATTAAACTGC
*
21427458 ATTATTATT-GTATTATGGT
1 ATTATTATTAGTATTATGAT
*
21427477 ATTATCTATTATTTATTAT-AT
1 ATTAT-TATTA-GTATTATGAT
21427498 ATTATTATTAGTATTAT
1 ATTATTATTAGTATTAT
21427515 TACTTCCATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 11 0.34
20 9 0.28
21 6 0.19
22 6 0.19
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.60
Consensus pattern (20 bp):
ATTATTATTAGTATTATGAT
Found at i:21427972 original size:13 final size:13
Alignment explanation
Indices: 21427954--21427979 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21427944 TGCTTGTAAA
21427954 TTTACTTGTATAT
1 TTTACTTGTATAT
21427967 TTTACTTGTATAT
1 TTTACTTGTATAT
21427980 ATATTTGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (13 bp):
TTTACTTGTATAT
Found at i:21433349 original size:7 final size:7
Alignment explanation
Indices: 21433324--21433356 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
21433314 AGTGATGTGA
21433324 AAAAATG
1 AAAAATG
21433331 AAAAGATG
1 AAAA-ATG
21433339 -AAAATG
1 AAAAATG
21433345 AAAAATG
1 AAAAATG
21433352 AAAAA
1 AAAAA
21433357 ATAAAACCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 3 0.12
7 18 0.75
8 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:21434936 original size:132 final size:132
Alignment explanation
Indices: 21434699--21436511 Score: 2813
Period size: 132 Copynumber: 13.7 Consensus size: 132
21434689 CAACGGCGGA
* * * *
21434699 TATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGTAGATTTTACCTCCCTAAGGTTGCAATA
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTAAGGTTACAATG
*
21434764 GAGTACATTGATGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGAT
66 GAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGAT
21434829 CT
131 CT
* * * *
21434831 TATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGTAGATTTTACCTCCCTAAGGTTGCAATA
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTAAGGTTACAATG
*
21434896 GAGTACATTGATGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGAT
66 GAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGAT
21434961 CT
131 CT
* * * *
21434963 TATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGTAGATTTTACCTCCCTAAGGTTGCAATA
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTAAGGTTACAATG
*
21435028 GAGTACATTGATGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGAT
66 GAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGAT
21435093 CT
131 CT
* * * *
21435095 TATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGTAGATTTTACCTCCCTAAGGTTGCAATA
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTAAGGTTACAATG
*
21435160 GAGTACATTGATGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGAT
66 GAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGAT
21435225 CT
131 CT
* * * *
21435227 TATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGTAGATTTTACCTCCCTAAGGTTGCAATA
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTAAGGTTACAATG
*
21435292 GAGTACATTGATGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGAT
66 GAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGAT
21435357 CT
131 CT
* * * *
21435359 TATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGTAGATTTTACCTCCCTAAGGTTGCAATA
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTAAGGTTACAATG
* *
21435424 GAGTACATTGATGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGAT
66 GAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGAT
21435489 CT
131 CT
* * ** *
21435491 TATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTAAGGTTACAATG
* * * *
21435556 GAGTACATTGAAGCCAGTAATTTTA-CTTCCCTCGGCAGCAGTAGAATAGATTGAAGATTATAGA
66 GAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGA
21435620 TCT
130 TCT
* * * * *
21435623 TATTTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAAATTTTACCTCCCTGAGGTTACAGTG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTAAGGTTACAATG
* *
21435688 GAGTATATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGAT
66 GAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGAT
21435753 CT
131 CT
* * ** *
21435755 TATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTAAGGTTACAATG
* * * *
21435820 GAGTACATTGAAGCCAGTAATTTTA-CTTCCCTCGGCAGCAGTAGAATAGATTGAAGATTATAGA
66 GAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGA
21435884 TCT
130 TCT
* * * * *
21435887 TATTTCCCTAAGCAGTAGTGGAGCAGATCAAGGATGGCGGATTTTACCTCCCTGAGGTTACAGTG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTAAGGTTACAATG
* * *
21435952 GAGTACATTGAAGCCGGAAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGAT
66 GAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGAT
21436017 CT
131 CT
* *
21436019 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTAAGGTTACAATG
* *
21436084 GAGTACATTGAAGCCAGTAATTCTATCTCCCTAGGCAACAGTGGAATAGATTGAAGATTACAGAT
66 GAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGAT
21436149 CT
131 CT
* * *
21436151 TATCTCCCTAAGCAGTAGTGGGGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTAAGGTTACAATG
* *
21436216 GAGTACATTGAAGCCAGTAATTCTATCTCCCTAGGCAACAGTGGAATAGATTGAAGATTACAGAT
66 GAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGAT
21436281 CT
131 CT
* * * * *
21436283 TATCTCCGTAAGCAGTAGTAGAGCACATCAAAGATGGCAGATTTTACCTCTCTGAGGTTACAATG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTAAGGTTACAATG
* * *
21436348 GAGTACATTGAAGCCAGTAATTCTATCTCACTGGGCAACAATGGAATAGATTGAAGATTACAGAT
66 GAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGAT
21436413 CT
131 CT
* * *
21436415 TATCTCCCTAAGCAGTAGTGGGGCAGATCAAAGATGGCAGATTTTACCTCCCTGAA-GTTATAGT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCT-AAGGTTACAAT
*
21436479 GGAGTATATTGAAGCCAGTAATTCTATCTCCCT
65 GGAGTACATTGAAGCCAGTAATTCTATCTCCCT
21436512 AGTCGGGGTG
Statistics
Matches: 1599, Mismatches: 77, Indels: 10
0.95 0.05 0.01
Matches are distributed among these distances:
131 2 0.00
132 1594 1.00
133 3 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (132 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTAAGGTTACAATG
GAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGAT
CT
Found at i:21438104 original size:3 final size:3
Alignment explanation
Indices: 21438096--21438157 Score: 54
Period size: 3 Copynumber: 19.3 Consensus size: 3
21438086 ATTAAACTGC
*
21438096 ATT ATT ATT ATT -GT ATT ATGGT ATT ATCT ATT ATCT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT AT--T ATT AT-T ATT AT-T ATT AT-T ATT
*
21438142 ATT ATT AGT ATT ATT A
1 ATT ATT ATT ATT ATT A
21438158 CTTCCATACG
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
2 1 0.02
3 36 0.73
4 9 0.18
5 3 0.06
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:21438122 original size:19 final size:18
Alignment explanation
Indices: 21438098--21438155 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 18
21438088 TAAACTGCAT
*
21438098 TATTATTATTGTATTATGG
1 TATTATTATTGTATTAT-A
*
21438117 TATTATCTATTATCTATTATA
1 TATTAT-TA-T-TGTATTATA
21438138 TATTATTATTAGTATTAT
1 TATTATTATT-GTATTAT
21438156 TACTTCCATA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 1 0.03
19 13 0.41
20 4 0.12
21 7 0.22
22 7 0.22
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (18 bp):
TATTATTATTGTATTATA
Found at i:21438136 original size:14 final size:13
Alignment explanation
Indices: 21438096--21438157 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 13
21438086 ATTAAACTGC
*
21438096 ATTATTATTATTGT
1 ATTATTATTA-TAT
*
21438110 ATTATGGTATTATCT
1 ATTAT--TATTATAT
21438125 ATTATCTATTATAT
1 ATTAT-TATTATAT
*
21438139 ATTATTATTA-GT
1 ATTATTATTATAT
21438151 ATTATTA
1 ATTATTA
21438158 CTTCCATACG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
12 8 0.19
13 5 0.12
14 17 0.40
15 7 0.17
16 5 0.12
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (13 bp):
ATTATTATTATAT
Found at i:21438613 original size:13 final size:13
Alignment explanation
Indices: 21438595--21438620 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21438585 TGCTTGTAAA
21438595 TTTACTTGTATAT
1 TTTACTTGTATAT
21438608 TTTACTTGTATAT
1 TTTACTTGTATAT
21438621 ATATTTGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (13 bp):
TTTACTTGTATAT
Found at i:21443494 original size:71 final size:71
Alignment explanation
Indices: 21443405--21443542 Score: 231
Period size: 71 Copynumber: 1.9 Consensus size: 71
21443395 TCAAAGTGTT
* **
21443405 TTTCAACTTATTTTAACATGATTAGAAGGTTTCTAATGTTACATTGAATTTTTTGTTAAGAATTT
1 TTTCAACTTATTTTAACATGATTAGAAGGTTTCTAATGTTACATTGAATTGTTCATTAAGAATTT
21443470 TTTGAG
66 TTTGAG
* *
21443476 TTTCAACTTGTTTTAACATGATTAGAAGGTTTCTAATGTTACTTTGAATTGTTCATTAAGAATTT
1 TTTCAACTTATTTTAACATGATTAGAAGGTTTCTAATGTTACATTGAATTGTTCATTAAGAATTT
21443541 TT
66 TT
21443543 CAGTTTTAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 62 1.00
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (71 bp):
TTTCAACTTATTTTAACATGATTAGAAGGTTTCTAATGTTACATTGAATTGTTCATTAAGAATTT
TTTGAG
Found at i:21448111 original size:22 final size:21
Alignment explanation
Indices: 21448086--21448127 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
21448076 TTAAATAAAT
*
21448086 TTTAGTTAATTTAGTTTAAGTA
1 TTTAATTAATTTAG-TTAAGTA
21448108 TTTAATTAATTTAGTTAAGT
1 TTTAATTAATTTAGTTAAGT
21448128 GTTAAATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTAATTAATTTAGTTAAGTA
Found at i:21448135 original size:21 final size:22
Alignment explanation
Indices: 21448091--21448135 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
21448081 TAAATTTTAG
*
21448091 TTAATTTAGTTTAAGTATTTAA
1 TTAATTTAGTTTAAGTATTAAA
*
21448113 TTAATTTAG-TTAAGTGTTAAA
1 TTAATTTAGTTTAAGTATTAAA
21448134 TT
1 TT
21448136 GTGTTTTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (22 bp):
TTAATTTAGTTTAAGTATTAAA
Found at i:21460806 original size:2 final size:2
Alignment explanation
Indices: 21460799--21460823 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21460789 TTCAATTTTA
21460799 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
21460824 AATTTAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21464575 original size:29 final size:29
Alignment explanation
Indices: 21464543--21464611 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
21464533 CATACACAGT
* *
21464543 CAGATTCAGATTCGGTCTTAAGTCCTTTA
1 CAGATTCAGATTCAGACTTAAGTCCTTTA
*
21464572 CAGATTCAGATTCAGACTTAAGTCTTTTA
1 CAGATTCAGATTCAGACTTAAGTCCTTTA
* *
21464601 CAAATTTAGAT
1 CAGATTCAGAT
21464612 AACAGAATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (29 bp):
CAGATTCAGATTCAGACTTAAGTCCTTTA
Found at i:21465127 original size:16 final size:18
Alignment explanation
Indices: 21465096--21465129 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
21465086 CCTTATGGCT
21465096 TGCCTGTGTGGGCCCACA
1 TGCCTGTGTGGGCCCACA
21465114 TGCC-GTGT-GGCCCACA
1 TGCCTGTGTGGGCCCACA
21465130 CAGCCTGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 4 0.25
18 4 0.25
ACGTcount: A:0.12, C:0.35, G:0.32, T:0.21
Consensus pattern (18 bp):
TGCCTGTGTGGGCCCACA
Found at i:21465131 original size:18 final size:18
Alignment explanation
Indices: 21465096--21465136 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
21465086 CCTTATGGCT
*
21465096 TGCCTGTGTGGGCCCACA
1 TGCCTGTGTGGCCCCACA
21465114 TGCC-GTGTGGCCCACACA
1 TGCCTGTGTGGCCC-CACA
21465132 -GCCTG
1 TGCCTG
21465137 ACCCAAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.12, C:0.37, G:0.32, T:0.20
Consensus pattern (18 bp):
TGCCTGTGTGGCCCCACA
Found at i:21472585 original size:43 final size:43
Alignment explanation
Indices: 21472524--21472609 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
21472514 ATGCACAAAG
21472524 TAAGCTTTGGAAGCTTAGTAAGCCATAAGAAAATAAATCATCT
1 TAAGCTTTGGAAGCTTAGTAAGCCATAAGAAAATAAATCATCT
21472567 TAAGCTTTGGAAGCTTAGTAAGCCATAAGAAAATAAATCATCT
1 TAAGCTTTGGAAGCTTAGTAAGCCATAAGAAAATAAATCATCT
21472610 CAATGATATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (43 bp):
TAAGCTTTGGAAGCTTAGTAAGCCATAAGAAAATAAATCATCT
Found at i:21473157 original size:30 final size:29
Alignment explanation
Indices: 21473098--21473422 Score: 357
Period size: 30 Copynumber: 10.8 Consensus size: 29
21473088 ATCCAATGCT
* *
21473098 CAAATCAATTCGGCAATATATATGTATACATTTA
1 CAAATCAATTCGG---TA-ATATATAT-CATATA
21473132 CAAATCAATTCGGTAATATATATACATATA
1 CAAATCAATTCGGTAATATATAT-CATATA
*
21473162 CAAATCAATTCGGTAATTTATATCAATATA
1 CAAATCAATTCGGTAATATATATC-ATATA
* *
21473192 CAAAT-AATTCGGCAATGTATATCCATATA
1 CAAATCAATTCGGTAATATATAT-CATATA
* * *
21473221 CAAATCAATTCGATTATATTTATCTATATA
1 CAAATCAATTCGGTAATATATATC-ATATA
*
21473251 TAAATCAATTCGGTAATATATATCCATATA
1 CAAATCAATTCGGTAATATATAT-CATATA
* *
21473281 CAAATCAACTCGGTAATTTATATCAATATA
1 CAAATCAATTCGGTAATATATATC-ATATA
*
21473311 CAAATCAATTCGGCAATATATATCCATATA
1 CAAATCAATTCGGTAATATATAT-CATATA
* *
21473341 CAAATCAATTCTGCT-ATATTTATCTATATA
1 CAAATCAATTC-GGTAATATATATC-ATATA
*
21473371 TAAATCAATTCGGTAATATATATCCATATA
1 CAAATCAATTCGGTAATATATAT-CATATA
*
21473401 CAAATCAATTCGGCAATATATA
1 CAAATCAATTCGGTAATATATA
21473423 AAACATATAC
Statistics
Matches: 252, Mismatches: 28, Indels: 26
0.82 0.09 0.08
Matches are distributed among these distances:
29 31 0.12
30 202 0.80
31 6 0.02
34 13 0.05
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.35
Consensus pattern (29 bp):
CAAATCAATTCGGTAATATATATCATATA
Found at i:21473284 original size:60 final size:60
Alignment explanation
Indices: 21473130--21473422 Score: 405
Period size: 60 Copynumber: 4.9 Consensus size: 60
21473120 TGTATACATT
*
21473130 TACAAATCAATTCGGTAATATATATACATATACAAATCAATTCGGTAATTTATATCAATA
1 TACAAATCAATTCGGTAATATATATCCATATACAAATCAATTCGGTAATTTATATCAATA
* * * * *
21473190 TACAAAT-AATTCGGCAATGTATATCCATATACAAATCAATTCGATTATATT-TATCTATA
1 TACAAATCAATTCGGTAATATATATCCATATACAAATCAATTCGGTAAT-TTATATCAATA
* *
21473249 TATAAATCAATTCGGTAATATATATCCATATACAAATCAACTCGGTAATTTATATCAATA
1 TACAAATCAATTCGGTAATATATATCCATATACAAATCAATTCGGTAATTTATATCAATA
* * *
21473309 TACAAATCAATTCGGCAATATATATCCATATACAAATCAATTCTGCT-ATATT-TATCTATA
1 TACAAATCAATTCGGTAATATATATCCATATACAAATCAATTC-GGTAAT-TTATATCAATA
* * *
21473369 TATAAATCAATTCGGTAATATATATCCATATACAAATCAATTCGGCAATATATA
1 TACAAATCAATTCGGTAATATATATCCATATACAAATCAATTCGGTAATTTATA
21473423 AAACATATAC
Statistics
Matches: 203, Mismatches: 23, Indels: 14
0.85 0.10 0.06
Matches are distributed among these distances:
59 53 0.26
60 146 0.72
61 4 0.02
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.35
Consensus pattern (60 bp):
TACAAATCAATTCGGTAATATATATCCATATACAAATCAATTCGGTAATTTATATCAATA
Found at i:21473346 original size:90 final size:90
Alignment explanation
Indices: 21473098--21473422 Score: 393
Period size: 90 Copynumber: 3.6 Consensus size: 90
21473088 ATCCAATGCT
* * * * *
21473098 CAAATCAATTCGGCAATATATATGTATACATTTACAAATCAATTCGGTAATATATATACATATAC
1 CAAATCAATTCGG---TA-ATATATATCCATATACAAATCAATTCGGCAATATATATCCATATAC
*
21473163 AAATCAATTCGGTAATTTATATCAATATA
62 AAATCAATTCGGTAATATATATCAATATA
* * *** * * *
21473192 CAAAT-AATTCGGCAATGTATATCCATATACAAATCAATTCGATTATATTTATCTATATATAAAT
1 CAAATCAATTCGGTAATATATATCCATATACAAATCAATTCGGCAATATATATCCATATACAAAT
*
21473256 CAATTCGGTAATATATATCCATATA
66 CAATTCGGTAATATATATCAATATA
* * *
21473281 CAAATCAACTCGGTAATTTATATCAATATACAAATCAATTCGGCAATATATATCCATATACAAAT
1 CAAATCAATTCGGTAATATATATCCATATACAAATCAATTCGGCAATATATATCCATATACAAAT
* * *
21473346 CAATTCTGCT-ATATTTATCTATATA
66 CAATTC-GGTAATATATATCAATATA
*
21473371 TAAATCAATTCGGTAATATATATCCATATACAAATCAATTCGGCAATATATA
1 CAAATCAATTCGGTAATATATATCCATATACAAATCAATTCGGCAATATATA
21473423 AAACATATAC
Statistics
Matches: 199, Mismatches: 30, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
89 68 0.34
90 117 0.59
91 2 0.01
93 7 0.04
94 5 0.03
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.35
Consensus pattern (90 bp):
CAAATCAATTCGGTAATATATATCCATATACAAATCAATTCGGCAATATATATCCATATACAAAT
CAATTCGGTAATATATATCAATATA
Found at i:21477144 original size:33 final size:33
Alignment explanation
Indices: 21477067--21477192 Score: 130
Period size: 33 Copynumber: 3.8 Consensus size: 33
21477057 CCCACCCATT
* *
21477067 TTTACTGT-CCAAGTGGACTATCTCTTTTTTGTG
1 TTTACTATCCCAA-TGGACTATCTCTGTTTTGTG
* * * *
21477100 TTTATTGTCCCAATGTACTATCTATGTTTTGTG
1 TTTACTATCCCAATGGACTATCTCTGTTTTGTG
** * *
21477133 TTTACTATCCCAGCGGACTATATCTGTTATGTG
1 TTTACTATCCCAATGGACTATCTCTGTTTTGTG
21477166 TTTACTATCCCAATTGG-CTATCTCTGT
1 TTTACTATCCCAA-TGGACTATCTCTGT
21477193 GGATGCCATG
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
33 70 0.92
34 6 0.08
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.46
Consensus pattern (33 bp):
TTTACTATCCCAATGGACTATCTCTGTTTTGTG
Found at i:21479698 original size:55 final size:55
Alignment explanation
Indices: 21479635--21479741 Score: 153
Period size: 55 Copynumber: 1.9 Consensus size: 55
21479625 TGAGATTCAT
*
21479635 AAGTTAGTCATAGCACTGAAATTAC-GAGAATTTATGGTTCTATTTGAATGAGTGC
1 AAGTTAGTCAGAGCACTGAAATTACAG-GAATTTATGGTTCTATTTGAATGAGTGC
* * * *
21479690 AAGTTAGTCGGGGCACTGGAATTACAGGAATTTGTGGTTCTATTTGAATGAG
1 AAGTTAGTCAGAGCACTGAAATTACAGGAATTTATGGTTCTATTTGAATGAG
21479742 CGCGGAAATG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
55 45 0.98
56 1 0.02
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.34
Consensus pattern (55 bp):
AAGTTAGTCAGAGCACTGAAATTACAGGAATTTATGGTTCTATTTGAATGAGTGC
Found at i:21489955 original size:25 final size:24
Alignment explanation
Indices: 21489921--21489973 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
21489911 AAGTTCAAGT
21489921 GAGCCATATCAGGAAGCTCACAAA
1 GAGCCATATCAGGAAGCTCACAAA
* *
21489945 GAGCCTATATCAGGACGCTCATAAA
1 GAGCC-ATATCAGGAAGCTCACAAA
21489970 GAGC
1 GAGC
21489974 TACGGTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.15
Consensus pattern (24 bp):
GAGCCATATCAGGAAGCTCACAAA
Found at i:21495963 original size:20 final size:21
Alignment explanation
Indices: 21495940--21495987 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
21495930 CACTCTCTAG
*
21495940 GCTTTTATCACACTC-GCAAT
1 GCTTTTATCACACTCACCAAT
*
21495960 GCTTTTA--ACCCTCACCAAT
1 GCTTTTATCACACTCACCAAT
21495979 GCTTTTATC
1 GCTTTTATC
21495988 CGCTCATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 5 0.22
19 11 0.48
20 7 0.30
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (21 bp):
GCTTTTATCACACTCACCAAT
Found at i:21498948 original size:16 final size:16
Alignment explanation
Indices: 21498904--21498948 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
21498894 CATTAGGAAT
21498904 CAAATAACTAAAATAAA
1 CAAATAACT-AAATAAA
* *
21498921 TAAATAATTAAATAAA
1 CAAATAACTAAATAAA
*
21498937 CAAATGACTAAA
1 CAAATAACTAAA
21498949 CCAATAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.67, C:0.09, G:0.02, T:0.22
Consensus pattern (16 bp):
CAAATAACTAAATAAA
Found at i:21507309 original size:20 final size:19
Alignment explanation
Indices: 21507254--21507320 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
21507244 GATGCAAAAT
*
21507254 AGGGGCACCAAAGTGCAATC
1 AGGGGCA-CGAAGTGCAATC
* * *
21507274 AGGAGCACGAGTGTGCAACC
1 AGGGGCACGA-AGTGCAATC
*
21507294 AGGGGCATCGAAGTGCATTC
1 AGGGGCA-CGAAGTGCAATC
21507314 AGGGGCA
1 AGGGGCA
21507321 ATGAGGTGCA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 2 0.05
20 32 0.86
21 3 0.08
ACGTcount: A:0.30, C:0.22, G:0.36, T:0.12
Consensus pattern (19 bp):
AGGGGCACGAAGTGCAATC
Found at i:21519590 original size:3 final size:3
Alignment explanation
Indices: 21519584--21519640 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
21519574 CTAAAAAAAG
* * * * * *
21519584 ATA ATA ATA ATA TTA ATTA ATA CTA ATA GTA GTA GTA ATG ATA ATA
1 ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
21519630 ATA ATA ATA AT
1 ATA ATA ATA AT
21519641 TTGGGCCTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:21521484 original size:12 final size:12
Alignment explanation
Indices: 21521467--21521496 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
21521457 AGACATACGA
21521467 CCGTGTCCTAGC
1 CCGTGTCCTAGC
*
21521479 CCGTGTCCTTGC
1 CCGTGTCCTAGC
21521491 CCGTGT
1 CCGTGT
21521497 AACTCTCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.03, C:0.40, G:0.27, T:0.30
Consensus pattern (12 bp):
CCGTGTCCTAGC
Found at i:21526251 original size:2 final size:2
Alignment explanation
Indices: 21526244--21526272 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21526234 ACCTAACAAA
21526244 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
21526273 TATATATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:21526644 original size:15 final size:15
Alignment explanation
Indices: 21526624--21526655 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21526614 TTGGATAGGA
21526624 TTTTATTTTATGTTG
1 TTTTATTTTATGTTG
*
21526639 TTTTATTTTATTTTG
1 TTTTATTTTATGTTG
21526654 TT
1 TT
21526656 ATTTTCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (15 bp):
TTTTATTTTATGTTG
Found at i:21526659 original size:13 final size:13
Alignment explanation
Indices: 21526626--21526668 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
21526616 GGATAGGATT
*
21526626 TTATTTTATGTTGTT
1 TTATTTTAT-TT-TG
21526641 TTATTTTATTTTG
1 TTATTTTATTTTG
*
21526654 TTATTTTCTTTTG
1 TTATTTTATTTTG
21526667 TT
1 TT
21526669 TGAAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 15 0.58
14 2 0.08
15 9 0.35
ACGTcount: A:0.12, C:0.02, G:0.09, T:0.77
Consensus pattern (13 bp):
TTATTTTATTTTG
Found at i:21532389 original size:15 final size:15
Alignment explanation
Indices: 21532369--21532400 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
21532359 TTTTGTACTG
21532369 AATTGTAAACAATTA
1 AATTGTAAACAATTA
21532384 AATTGTAAACAATTA
1 AATTGTAAACAATTA
21532399 AA
1 AA
21532401 ATTTTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.31
Consensus pattern (15 bp):
AATTGTAAACAATTA
Found at i:21535591 original size:24 final size:24
Alignment explanation
Indices: 21535564--21535625 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
21535554 TGGCTCTTCG
*
21535564 GAGCTACCCGTTATTGGCTCGTAT
1 GAGCTTCCCGTTATTGGCTCGTAT
** *
21535588 GAGCTTCCTAATTA-TGGCTCTTAT
1 GAGCTTCC-CGTTATTGGCTCGTAT
21535612 GAGCTTCCCGTTAT
1 GAGCTTCCCGTTAT
21535626 ACAGCCTGGA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
23 3 0.10
24 24 0.80
25 3 0.10
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (24 bp):
GAGCTTCCCGTTATTGGCTCGTAT
Found at i:21539862 original size:19 final size:20
Alignment explanation
Indices: 21539821--21539868 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
21539811 GAGGCACCGG
* * *
21539821 AGTGCAAGCAGAAGCATCGA
1 AGTGCAAACAGAAGCACCAA
21539841 AGTGCAAACAG-AGCACCAA
1 AGTGCAAACAGAAGCACCAA
21539860 AGTGCAAAC
1 AGTGCAAAC
21539869 CCATACAAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.08
Consensus pattern (20 bp):
AGTGCAAACAGAAGCACCAA
Found at i:21540783 original size:11 final size:10
Alignment explanation
Indices: 21540763--21540808 Score: 56
Period size: 11 Copynumber: 4.4 Consensus size: 10
21540753 TGTTTTTATG
21540763 TTTTAACATA
1 TTTTAACATA
21540773 TTTTAAACATA
1 TTTT-AACATA
*
21540784 ATTTAACATTA
1 TTTTAACA-TA
*
21540795 TTTTAACTTA
1 TTTTAACATA
21540805 TTTT
1 TTTT
21540809 TCTCTAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 14 0.45
11 17 0.55
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTTAACATA
Found at i:21541198 original size:2 final size:2
Alignment explanation
Indices: 21541185--21541215 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
21541175 ACTTCTTCAA
*
21541185 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21541216 ACTTAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:21545232 original size:14 final size:14
Alignment explanation
Indices: 21545200--21545260 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
21545190 TCACAATTTG
* *
21545200 ATTCTCAATTTCTT
1 ATTCTCGATTTGTT
*
21545214 GTTCTCGATTTGTT
1 ATTCTCGATTTGTT
* *
21545228 ATTCTC-AATTGTCA
1 ATTCTCGATTTGT-T
*
21545242 ATTCTCGATTTTTT
1 ATTCTCGATTTGTT
21545256 ATTCT
1 ATTCT
21545261 AAATTATTCG
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
13 5 0.14
14 27 0.75
15 4 0.11
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.56
Consensus pattern (14 bp):
ATTCTCGATTTGTT
Found at i:21545343 original size:15 final size:16
Alignment explanation
Indices: 21545321--21545357 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
21545311 GTAATAAAAT
*
21545321 ATTATTAAATTATTTA
1 ATTATTAAATTAGTTA
21545337 A-TATT-AATTAGTTA
1 ATTATTAAATTAGTTA
21545351 ATTATTA
1 ATTATTA
21545358 TGATGTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 4
0.78 0.04 0.17
Matches are distributed among these distances:
14 9 0.50
15 8 0.44
16 1 0.06
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
ATTATTAAATTAGTTA
Found at i:21545376 original size:51 final size:51
Alignment explanation
Indices: 21545316--21545517 Score: 350
Period size: 51 Copynumber: 3.9 Consensus size: 51
21545306 AAATGGTAAT
* * * *
21545316 AAAATATTATTAAATTATTTAATATTAATTAGTTAATTATTATGATGTTAAG
1 AAAA-ATTATTTAATGATTTAATTTTAAATAGTTAATTATTATGATGTTAAG
21545368 AAAAATTATTTAATGATTTAATTTTAAATAGTTAATTATTATGATGTTAAG
1 AAAAATTATTTAATGATTTAATTTTAAATAGTTAATTATTATGATGTTAAG
21545419 AAAAATTATTTAATGATTTAATTTTAAATAGTTAATTATTATGATGTTAAG
1 AAAAATTATTTAATGATTTAATTTTAAATAGTTAATTATTATGATGTTAAG
*
21545470 AAAAATTATTTAATGATTTAATTTTAAATAGTTAATTATTATGTTGTT
1 AAAAATTATTTAATGATTTAATTTTAAATAGTTAATTATTATGATGTT
21545518 TAGATTAGTA
Statistics
Matches: 145, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
51 141 0.97
52 4 0.03
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (51 bp):
AAAAATTATTTAATGATTTAATTTTAAATAGTTAATTATTATGATGTTAAG
Found at i:21551009 original size:15 final size:15
Alignment explanation
Indices: 21550989--21551084 Score: 119
Period size: 15 Copynumber: 6.5 Consensus size: 15
21550979 TTGTTAATTC
21550989 TATTTATGTAATTAA
1 TATTTATGTAATTAA
21551004 TATTTATGTAATT-A
1 TATTTATGTAATTAA
*
21551018 TAAGTT-TGTAATTAA
1 T-ATTTATGTAATTAA
21551033 TATTTATGTAATT-A
1 TATTTATGTAATTAA
*
21551047 TAAGTT-TGTAATTAA
1 T-ATTTATGTAATTAA
21551062 TATTTATGTAATTAA
1 TATTTATGTAATTAA
*
21551077 AATTTATG
1 TATTTATG
21551085 ATTTTAGTCC
Statistics
Matches: 70, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
14 24 0.34
15 46 0.66
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (15 bp):
TATTTATGTAATTAA
Found at i:21551027 original size:29 final size:29
Alignment explanation
Indices: 21550995--21551075 Score: 162
Period size: 29 Copynumber: 2.8 Consensus size: 29
21550985 ATTCTATTTA
21550995 TGTAATTAATATTTATGTAATTATAAGTT
1 TGTAATTAATATTTATGTAATTATAAGTT
21551024 TGTAATTAATATTTATGTAATTATAAGTT
1 TGTAATTAATATTTATGTAATTATAAGTT
21551053 TGTAATTAATATTTATGTAATTA
1 TGTAATTAATATTTATGTAATTA
21551076 AAATTTATGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (29 bp):
TGTAATTAATATTTATGTAATTATAAGTT
Done.