Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 38 of 344
Found at i:12728303 original size:30 final size:31
Alignment explanation
Indices: 12728262--12728321 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
12728252 GGTACCCATA
*
12728262 TAAAAATTTTAAA-ACAAAT-AATGTATATAT
1 TAAAAAGTTTAAATACAAATGAAT-TATATAT
*
12728292 TAAAAAGTTTAAATATAAATGAATTATATA
1 TAAAAAGTTTAAATACAAATGAATTATATA
12728322 AATAAAACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 11 0.42
32 3 0.12
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.37
Consensus pattern (31 bp):
TAAAAAGTTTAAATACAAATGAATTATATAT
Found at i:12739966 original size:17 final size:17
Alignment explanation
Indices: 12739921--12739966 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
12739911 CGACTTTATC
*
12739921 CGAATCGAGCAAGCTTT
1 CGAATCGAGCATGCTTT
12739938 CGAATCGAGCATGC-TT
1 CGAATCGAGCATGCTTT
12739954 CTGAATCGAGCAT
1 C-GAATCGAGCAT
12739967 TATAAACGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 3 0.11
17 24 0.89
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (17 bp):
CGAATCGAGCATGCTTT
Found at i:12740731 original size:27 final size:27
Alignment explanation
Indices: 12740693--12740748 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
12740683 ATTTAAATTT
12740693 AGATTCTAATTATACGAACTTACCTCG
1 AGATTCTAATTATACGAACTTACCTCG
12740720 AGATTCTAATTATACGAACTTACCTCG
1 AGATTCTAATTATACGAACTTACCTCG
12740747 AG
1 AG
12740749 TTGCTCGGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.32
Consensus pattern (27 bp):
AGATTCTAATTATACGAACTTACCTCG
Found at i:12743580 original size:34 final size:34
Alignment explanation
Indices: 12743520--12743614 Score: 131
Period size: 33 Copynumber: 2.8 Consensus size: 34
12743510 GTTCAGAGTT
12743520 TTTTAAA-AAATTAATTAAATTAGGTTTTAAGGG
1 TTTTAAATAAATTAATTAAATTAGGTTTTAAGGG
* *
12743553 TTTTAAATAAATAAATT-AATTAGGGTTTAAGGG
1 TTTTAAATAAATTAATTAAATTAGGTTTTAAGGG
* *
12743586 TTCTAAATAAATTAATTGAATTAAGGTTT
1 TTTTAAATAAATTAATTAAATT-AGGTTT
12743615 AGTTTTTTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
33 37 0.69
34 12 0.22
35 5 0.09
ACGTcount: A:0.42, C:0.01, G:0.15, T:0.42
Consensus pattern (34 bp):
TTTTAAATAAATTAATTAAATTAGGTTTTAAGGG
Found at i:12743937 original size:125 final size:124
Alignment explanation
Indices: 12743715--12744230 Score: 653
Period size: 125 Copynumber: 4.1 Consensus size: 124
12743705 AGGATTTTGT
* * * ** * *
12743715 TTTTTCTACAGTAGTT-TCAGAAAAATTAATTTTGAGAAGACGGTTCTGAAAAAATAATATAAAA
1 TTTTTCTACAGTAGTTCT-TGAAAAAATAATTTTGAGAAAACAATTCT-AAAAAATAGTATCAAA
* * *
12743779 AACGCTTCAAGCAAGATGCATTGTCAGCAAAATTACTGAAAAAGCT-TCCACGTGGACGCTC
64 AACGCTTTAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAGCTCT-CACGTGGACGCTC
* * *
12743840 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGATAATTCTAAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAAACAATTCT-AAAAAATAGTATCAAAA
* * * *
12743905 ACGCTTTAAGCAGGATTCACTGTCAGCAAAATTACTGAAAAAGCTCTAATGTAGACGCTC
65 ACGCTTTAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAGCTCTCACGTGGACGCTC
* * **
12743965 TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAAATGATTCTCAAAAAATAGTATCAAAA
1 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAAACAATTCT-AAAAAATAGTATCAAAA
* *
12744030 ATGC-TTAAGGCAGTATGCACTGTCAGCAAAATTACTGAAAAAGGCTCTCACGT-GACGCTC
65 ACGCTTTAA-GCAGGATGCACTGTCAGCAAAATTACTGAAAAA-GCTCTCACGTGGACGCTC
* *
12744090 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAAACAATTCTGAAAAATAGTGTCAAAAA
1 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAAACAATTCTAAAAAATAGTATCAAAAA
* * * * * *
12744155 CGCTTTAAGCATGATGCACTATCAGTAAAATTACTGAAAAAAGCTCCCACGTGAACGCTA
66 CGCTTTAAGCAGGATGCACTGTCAGCAAAATTACTG-AAAAAGCTCTCACGTGGACGCTC
12744215 TTTTTCTACAGTAGTT
1 TTTTTCTACAGTAGTT
12744231 TCTGCTTGGC
Statistics
Matches: 343, Mismatches: 41, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
124 55 0.16
125 278 0.81
126 10 0.03
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (124 bp):
TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAAACAATTCTAAAAAATAGTATCAAAAA
CGCTTTAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAGCTCTCACGTGGACGCTC
Found at i:12744198 original size:250 final size:250
Alignment explanation
Indices: 12743715--12744230 Score: 729
Period size: 250 Copynumber: 2.1 Consensus size: 250
12743705 AGGATTTTGT
* * * * *
12743715 TTTTTCTACAGTAGTTTCAGAAAAATTAATTTTGAGAAGACGGTTCTGAAAAAATAATATAAAAA
1 TTTTTCTACAGTAGTTCCAGAAAAAATAATTTTGAGAAAACGATTCTCAAAAAATAATATAAAAA
*
12743780 ACGCTTCAAGCAAGATGCATTGTCAGCAAAATTACTGAAAAAGCTTCCACGTGGACGCTCTTTTT
66 ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAGCTTCCACGTGGACGCTCTTTTT
* *
12743845 CTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGATAATTCTAAAAAAATAGTGTCAAAAACGCT
131 CTACAGTAGTTCTTGAAAAAATAATTTTGAGAAAACAATTCTAAAAAAATAGTGTCAAAAACGCT
* *
12743910 TTAAGCAGGATTCACTGTCAGCAAAATTACTGAAAAAGCTCTAATGTAGACGCTC
196 TTAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAGCTCTAATGTAGACGCTC
* * * * *
12743965 TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAAATGATTCTCAAAAAATAGTATCAAAA
1 TTTTTCTACAGTAGTTCCAGAAAAAATAATTTTGAGAAAACGATTCTCAAAAAATAATATAAAAA
*
12744030 ATGCTT-AAGGC-AGTATGCACTGTCAGCAAAATTACTGAAAAAGGC-TCTCACGT-GACGCTCT
66 ACGCTTCAA-GCAAG-ATGCACTGTCAGCAAAATTACTGAAAAA-GCTTC-CACGTGGACGCTCT
*
12744091 TTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAAACAATTCT-GAAAAATAGTGTCAAAAA
127 TTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAAACAATTCTAAAAAAATAGTGTCAAAAA
* * ** * *
12744155 CGCTTTAAGCATGATGCACTATCAGTAAAATTACTGAAAAAAGCTCCCACGT-GAACGCTA
192 CGCTTTAAGCAGGATGCACTATCAGCAAAATTACTG-AAAAAGCTCTAATGTAG-ACGCTC
12744215 TTTTTCTACAGTAGTT
1 TTTTTCTACAGTAGTT
12744231 TCTGCTTGGC
Statistics
Matches: 236, Mismatches: 24, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
249 54 0.23
250 175 0.74
251 7 0.03
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (250 bp):
TTTTTCTACAGTAGTTCCAGAAAAAATAATTTTGAGAAAACGATTCTCAAAAAATAATATAAAAA
ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAGCTTCCACGTGGACGCTCTTTTT
CTACAGTAGTTCTTGAAAAAATAATTTTGAGAAAACAATTCTAAAAAAATAGTGTCAAAAACGCT
TTAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAGCTCTAATGTAGACGCTC
Found at i:12746319 original size:21 final size:20
Alignment explanation
Indices: 12746290--12746336 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
12746280 ATATAATAAT
12746290 ATAATAACATAAAATAAAAGAA
1 ATAA-AACATAAAAT-AAAGAA
* *
12746312 ATAAAACATGAAATAAATAA
1 ATAAAACATAAAATAAAGAA
12746332 ATAAA
1 ATAAA
12746337 GAATGAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 9 0.39
22 4 0.17
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.19
Consensus pattern (20 bp):
ATAAAACATAAAATAAAGAA
Found at i:12746371 original size:17 final size:15
Alignment explanation
Indices: 12746334--12746372 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
12746324 ATAAATAAAT
*
12746334 AAAGAATGAAAACAA
1 AAAGAATGAAAAAAA
12746349 AAAGAATGAAAAAAGA
1 AAAGAATGAAAAAA-A
12746365 AACAGAAT
1 AA-AGAAT
12746373 AGCAAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 3 0.14
17 5 0.24
ACGTcount: A:0.72, C:0.05, G:0.15, T:0.08
Consensus pattern (15 bp):
AAAGAATGAAAAAAA
Found at i:12747571 original size:22 final size:23
Alignment explanation
Indices: 12747528--12747572 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
12747518 ATATAGTGAA
12747528 TTGAAAATAGAATGTGAAATATG
1 TTGAAAATAGAATGTGAAATATG
12747551 TTGAAAATA-AATG-GAATATATG
1 TTGAAAATAGAATGTGAA-ATATG
12747573 AGTTATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 3 0.14
22 9 0.43
23 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (23 bp):
TTGAAAATAGAATGTGAAATATG
Found at i:12749963 original size:18 final size:18
Alignment explanation
Indices: 12749940--12749980 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
12749930 CTGAGAAAAT
*
12749940 GATACATATAAGGGTTAG
1 GATACATATAAGGGCTAG
12749958 GATACATATAAGGGCTAG
1 GATACATATAAGGGCTAG
12749976 GATAC
1 GATAC
12749981 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.39, C:0.10, G:0.27, T:0.24
Consensus pattern (18 bp):
GATACATATAAGGGCTAG
Found at i:12763448 original size:23 final size:23
Alignment explanation
Indices: 12763421--12763465 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
12763411 GTAATAAATT
12763421 TGAAAAGGCAACAACTGTTTATC
1 TGAAAAGGCAACAACTGTTTATC
12763444 TGAAAAGGCAACAACTGTTTAT
1 TGAAAAGGCAACAACTGTTTAT
12763466 GAATATATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (23 bp):
TGAAAAGGCAACAACTGTTTATC
Found at i:12770212 original size:27 final size:28
Alignment explanation
Indices: 12770182--12770292 Score: 104
Period size: 27 Copynumber: 4.1 Consensus size: 28
12770172 AGACTATCCC
* *
12770182 TTCATGATT-AGCCATAAAGGCGTTCCT
1 TTCATGATTGCGCCACAAAGGCGTTCCT
* *
12770209 TTCAT-ATTGCGCCACAAAGGCTTTCTT
1 TTCATGATTGCGCCACAAAGGCGTTCCT
* * ** *
12770236 TTTATG-TTGTGCCACAAAGATGTTCAT
1 TTCATGATTGCGCCACAAAGGCGTTCCT
*
12770263 TTCATAATT-CGCCACAAAGGCGTTCCT
1 TTCATGATTGCGCCACAAAGGCGTTCCT
12770290 TTC
1 TTC
12770293 CTAATGTGTT
Statistics
Matches: 65, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
26 3 0.05
27 60 0.92
28 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.36
Consensus pattern (28 bp):
TTCATGATTGCGCCACAAAGGCGTTCCT
Found at i:12772105 original size:40 final size:40
Alignment explanation
Indices: 12772060--12772194 Score: 146
Period size: 40 Copynumber: 3.4 Consensus size: 40
12772050 TGGTTATTTG
* *
12772060 TGGCACTTTGTGTGCGATACGACATAGCTTCGGCTATATA
1 TGGCACTTAGTGTGCGATTCGACATAGCTTCGGCTATATA
** *** *
12772100 TGGCACTTAGTGTGCGATTCGACATAATTTCAAATATTTA
1 TGGCACTTAGTGTGCGATTCGACATAGCTTCGGCTATATA
* * *
12772140 TGGCACTTAGTGT-CTGATTTGAGATAGCTTCGGCTATGTA
1 TGGCACTTAGTGTGC-GATTCGACATAGCTTCGGCTATATA
*
12772180 TGACACTTAGTGTGC
1 TGGCACTTAGTGTGC
12772195 TAGATATTGA
Statistics
Matches: 76, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
39 1 0.01
40 74 0.97
41 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (40 bp):
TGGCACTTAGTGTGCGATTCGACATAGCTTCGGCTATATA
Found at i:12772231 original size:28 final size:28
Alignment explanation
Indices: 12772177--12772236 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
12772167 CTTCGGCTAT
*
12772177 GTATGACACTTAGTGTGCTAGATATTGA
1 GTATGACACTTAGTGTGCTAGACATTGA
*
12772205 GTATGACACTTAGTGTG-TAAGGCATTGA
1 GTATGACACTTAGTGTGCT-AGACATTGA
12772233 GTAT
1 GTAT
12772237 TCAACGACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 1 0.03
28 28 0.97
ACGTcount: A:0.28, C:0.10, G:0.27, T:0.35
Consensus pattern (28 bp):
GTATGACACTTAGTGTGCTAGACATTGA
Found at i:12779694 original size:40 final size:40
Alignment explanation
Indices: 12779623--12779710 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
12779613 TGGCACTTAG
* *
12779623 TGTGCGATACGACATAGCTTCGGCTAGATATGACACTTGA
1 TGTGCGATACGACATAGCTTCAGATAGATATGACACTTGA
* * * * *
12779663 TGTGTGATTCGACATAGTTTCAGATATATATGGCACTT-A
1 TGTGCGATACGACATAGCTTCAGATAGATATGACACTTGA
12779702 GTGTGCGAT
1 -TGTGCGAT
12779711 TTGAGATGGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
39 1 0.03
40 38 0.97
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (40 bp):
TGTGCGATACGACATAGCTTCAGATAGATATGACACTTGA
Found at i:12781395 original size:35 final size:35
Alignment explanation
Indices: 12781333--12781440 Score: 85
Period size: 40 Copynumber: 2.9 Consensus size: 35
12781323 TTTCCTCATT
*
12781333 GAAATACCATACCTACATTTTGCAACTCGGTATCG
1 GAAATACCATACCTACATTTTGCAACTCAGTATCG
* * * *
12781368 GAAATGCCATACCTACGTTTCT-TAACTCAGTATGG
1 GAAATACCATACCTACATTT-TGCAACTCAGTATCG
*
12781403 ATTTGATAATACCATACCTACGTTTCT-CAACTCAGTAT
1 ----GA-AATACCATACCTACATTT-TGCAACTCAGTAT
12781441 AGATGATATC
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
35 28 0.47
36 1 0.02
39 2 0.03
40 29 0.48
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (35 bp):
GAAATACCATACCTACATTTTGCAACTCAGTATCG
Found at i:12781455 original size:35 final size:38
Alignment explanation
Indices: 12781375--12781463 Score: 121
Period size: 40 Copynumber: 2.4 Consensus size: 38
12781365 TCGGAAATGC
* *
12781375 CATACCTACGTTTCTTAACTCAGTATGGATTTGATAATA
1 CATACCTACGTTTCTCAACTCAGTATAGA-TTGATAATA
12781414 CCATACCTACGTTTCTCAACTCAGTATAGA-TGAT-AT-
1 -CATACCTACGTTTCTCAACTCAGTATAGATTGATAATA
12781450 CATACCTACGTTTC
1 CATACCTACGTTTC
12781464 ACACTTTTCC
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
35 14 0.30
37 2 0.04
38 4 0.09
40 27 0.57
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (38 bp):
CATACCTACGTTTCTCAACTCAGTATAGATTGATAATA
Found at i:12784884 original size:21 final size:21
Alignment explanation
Indices: 12784843--12784889 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
12784833 TAACAAATTT
*
12784843 AGTTAATTACATATTATATAA
1 AGTTAATTAAATATTATATAA
*
12784864 AGTTAATTATAATTTTA-ATAA
1 AGTTAATTA-AATATTATATAA
12784885 A-TTAA
1 AGTTAA
12784890 CCCTAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 14 0.61
22 5 0.22
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (21 bp):
AGTTAATTAAATATTATATAA
Found at i:12787099 original size:3 final size:3
Alignment explanation
Indices: 12787091--12787118 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12787081 CTTTCTTTCT
12787091 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12787119 GTTTTATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12787180 original size:17 final size:18
Alignment explanation
Indices: 12787159--12787201 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
12787149 AAATTATATA
12787159 ATATAATA-TATTTTACTT
1 ATATAATACTA-TTTACTT
*
12787177 -TATATTACTATTTACTT
1 ATATAATACTATTTACTT
12787194 ATATAATA
1 ATATAATA
12787202 AGTAAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATAATACTATTTACTT
Found at i:12788887 original size:17 final size:17
Alignment explanation
Indices: 12788865--12788897 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12788855 AAACTTCACA
12788865 AATTTTTAAGATTTTTC
1 AATTTTTAAGATTTTTC
12788882 AATTTTTAAGATTTTT
1 AATTTTTAAGATTTTT
12788898 TTTAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (17 bp):
AATTTTTAAGATTTTTC
Found at i:12788927 original size:14 final size:15
Alignment explanation
Indices: 12788894--12788927 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
12788884 TTTTTAAGAT
12788894 TTTTTTTAAAATTAA
1 TTTTTTTAAAATTAA
*
12788909 ATTTTTTAAAA-TAA
1 TTTTTTTAAAATTAA
12788923 TTTTT
1 TTTTT
12788928 ACTAATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTTTAAAATTAA
Found at i:12794365 original size:6 final size:6
Alignment explanation
Indices: 12794292--12794362 Score: 133
Period size: 6 Copynumber: 11.8 Consensus size: 6
12794282 AGGCATGGAC
12794292 GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA
1 GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA
*
12794340 GATGAA GATGAA GATGAT GATGA
1 GATGAA GATGAA GATGAA GATGA
12794363 TGAGGAGGAG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.48, C:0.00, G:0.34, T:0.18
Consensus pattern (6 bp):
GATGAA
Found at i:12803368 original size:12 final size:12
Alignment explanation
Indices: 12803351--12803375 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12803341 TATTAAAATA
12803351 TATTAATTATTT
1 TATTAATTATTT
12803363 TATTAATTATTT
1 TATTAATTATTT
12803375 T
1 T
12803376 GATAACGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTAATTATTT
Found at i:12804041 original size:44 final size:43
Alignment explanation
Indices: 12803916--12804046 Score: 97
Period size: 44 Copynumber: 3.0 Consensus size: 43
12803906 CTTTTATTTC
* * * * *
12803916 AATTATAATTATTTTAATTA-AAAAATATAATAAATGTAAATTA
1 AATTATAATTATTTTAAATATATAATTATTATAAAT-TATATTA
* * *
12803959 AATTAATAATTATTTTTAAATAT-TCAATTATCT-CAAATTCTATTG
1 AATT-ATAATTA-TTTTAAATATAT-AATTAT-TATAAATTATATTA
* *
12804004 AATTATAATTATTGTTAAGTATATAATTATTATAAATTTTATT
1 AATTATAATTATT-TTAAATATATAATTATTATAAATTATATT
12804047 TTATGTCAAT
Statistics
Matches: 69, Mismatches: 11, Indels: 15
0.73 0.12 0.16
Matches are distributed among these distances:
43 7 0.10
44 36 0.52
45 17 0.25
46 9 0.13
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (43 bp):
AATTATAATTATTTTAAATATATAATTATTATAAATTATATTA
Found at i:12806506 original size:20 final size:21
Alignment explanation
Indices: 12806472--12806525 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
12806462 TGATGATATT
*
12806472 TTATGATTA-TTTAATTAGATA
1 TTAT-ATTATTTTAATGAGATA
12806493 -TATATTATTTTAATGAGATA
1 TTATATTATTTTAATGAGATA
*
12806513 TTTTATTATTTTA
1 TTATATTATTTTA
12806526 TTATTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTATATTATTTTAATGAGATA
Found at i:12806531 original size:11 final size:11
Alignment explanation
Indices: 12806515--12806542 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
12806505 ATGAGATATT
12806515 TTATTATTTTA
1 TTATTATTTTA
12806526 TTATTATTTTA
1 TTATTATTTTA
12806537 TTATTA
1 TTATTA
12806543 ATTATTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:12808825 original size:24 final size:23
Alignment explanation
Indices: 12808696--12808825 Score: 111
Period size: 23 Copynumber: 5.5 Consensus size: 23
12808686 CCCGATATAT
*
12808696 GGCTCTTCGTGAGCTTCCCGATA
1 GGCTCTTTGTGAGCTTCCCGATA
*
12808719 GGCTCTTTGTGAGCTTTCCGATA
1 GGCTCTTTGTGAGCTTCCCGATA
** * *
12808742 GTGCTCGCT-TGAACTTCCTGATATA
1 G-GCTCTTTGTGAGCTTCCCG--ATA
* **
12808767 TGGCTATCCG-GAGCTTCCCGATA
1 -GGCTCTTTGTGAGCTTCCCGATA
12808790 GGCTCTTTGTGAGCTTCCCGATA
1 GGCTCTTTGTGAGCTTCCCGATA
*
12808813 TGGTTCTTTGTGA
1 -GGCTCTTTGTGA
12808826 ACTACCTAAT
Statistics
Matches: 84, Mismatches: 16, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
22 6 0.07
23 46 0.55
24 16 0.19
25 15 0.18
26 1 0.01
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (23 bp):
GGCTCTTTGTGAGCTTCCCGATA
Found at i:12808852 original size:71 final size:71
Alignment explanation
Indices: 12808690--12808856 Score: 176
Period size: 71 Copynumber: 2.3 Consensus size: 71
12808680 GAGTGTCCCG
* * *
12808690 ATATATGGCTCTTCGTGAGCTTCCCGATAGGCTCTTTGTGAGCTTTCCGATAGTGCTCGCTTGAA
1 ATATATGGCTATAC-TGAGCTTCCCGATAGGCTCTTTGTGAGCTTCCCGATAGTGCTCGCTTGAA
* *
12808755 CTTCCTG
65 CTACCTA
* * * **
12808762 ATATATGGCTATCCGGAGCTTCCCGATAGGCTCTTTGTGAGCTTCCCGATA-TGGTTCTTTGTGA
1 ATATATGGCTATACTGAGCTTCCCGATAGGCTCTTTGTGAGCTTCCCGATAGT-GCTCGCT-TGA
12808826 ACTACCTA
64 ACTACCTA
* * *
12808834 AT-TTTGGCTCTATTGAGCTTCCC
1 ATATATGGCTATACTGAGCTTCCC
12808857 ATTATAGCCC
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
70 1 0.01
71 55 0.70
72 23 0.29
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.37
Consensus pattern (71 bp):
ATATATGGCTATACTGAGCTTCCCGATAGGCTCTTTGTGAGCTTCCCGATAGTGCTCGCTTGAAC
TACCTA
Found at i:12813608 original size:3 final size:3
Alignment explanation
Indices: 12813602--12813640 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
12813592 ACACTACTAT
12813602 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12813641 TAGAAATGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12813810 original size:38 final size:37
Alignment explanation
Indices: 12813739--12813816 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 37
12813729 GATATACACT
* *
12813739 AATATATAATAATAGTAATAATAATAAAGTAGTAAAA
1 AATATATAATAATAGTAAAAATAACAAAGTAGTAAAA
*
12813776 AATATAATTATAATAGTAAAATATAACAAATAGTAGTAAAA
1 AATAT-ATAATAATAGTAAAA-ATAAC-AA-AGTAGTAAAA
12813817 GAAAATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 5 0.15
38 13 0.38
39 4 0.12
40 2 0.06
41 10 0.29
ACGTcount: A:0.62, C:0.01, G:0.08, T:0.29
Consensus pattern (37 bp):
AATATATAATAATAGTAAAAATAACAAAGTAGTAAAA
Found at i:12815556 original size:45 final size:43
Alignment explanation
Indices: 12815450--12815659 Score: 134
Period size: 44 Copynumber: 4.8 Consensus size: 43
12815440 ATTTGTAATT
* * *
12815450 TTCAGCCTGTTACCCTACTGCATAGGGGTTTAAGGCCCATCAA
1 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGACCCATCAA
* * * * **
12815493 TTCTGCTATGTTTCCCTACTACTTAGGGGGTTAAGATTCATCAA
1 TTCAGC-CTGTTACCCTACTGCTTAGGGGGTTAAGACCCATCAA
* * * * *** *
12815537 TGTTCAGCCTGTTACCCTACTGTTTAGGGGTTTAGGGCTTGTCACC
1 --TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGACCCATCA-A
* * * * * *
12815583 TT-TGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTATGAA
1 TTCAG-CCTGTTACCCTACTGCTTAGGGGGTTAAGACCCATCAA
* * *
12815626 TTCAACCTGTTACCCTACTGTTTAGGGGGGTAAG
1 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
12815660 GTTTGTCAAT
Statistics
Matches: 122, Mismatches: 39, Indels: 12
0.71 0.23 0.07
Matches are distributed among these distances:
43 33 0.27
44 58 0.48
45 26 0.21
46 5 0.04
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (43 bp):
TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGACCCATCAA
Found at i:12815601 original size:89 final size:87
Alignment explanation
Indices: 12815450--12815911 Score: 251
Period size: 86 Copynumber: 5.3 Consensus size: 87
12815440 ATTTGTAATT
** *
12815450 TTCAGCCTGTTACCCTACTGCATAGGGGTTTAAGGCCCATCAATTCTGCTATGTTTCCCTACTAC
1 TTCAGCCTGTTACCCTACTGTTTAGGGGTTTAAGGCCCATCAATTCTGATATGTTTCCCTACTAC
12815515 TTAGGGGGTTAAGAT-TCATCAA
66 TTAGGGGGTTAAGATCT-ATCAA
* *** * *
12815537 TGTTCAGCCTGTTACCCTACTGTTTAGGGGTTTAGGGCTTGTCACCTT-TGATCTGTTTCCCTAC
1 --TTCAGCCTGTTACCCTACTGTTTAGGGGTTTAAGGCCCATCA-ATTCTGATATGTTTCCCTAC
* *
12815601 TGCTTAGGGGGTTAAGATCTATGAA
63 TACTTAGGGGGTTAAGATCTATCAA
* ** **** ** *
12815626 TTCAACCTGTTACCCTACTGTTTAGGGGGGTAAGGTTTGTCAA-TCTTCGACCTG-CTCCACTAC
1 TTCAGCCTGTTACCCTACTGTTTAGGGGTTTAAGGCCCATCAATTC-T-GATATGTTTCC-CTAC
* * * *
12815689 TGCTTAGGGAGATAAGATCT-CCAA
63 TACTTAGGGGGTTAAGATCTATCAA
** * * * * ** * **
12815713 TTTGGTCTGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTC-GATCT-ACTCCACTACT
1 TTCAGCCTGTTACCCTACTGTTTAGGGGTTTAAGGCCCATC-AATTCTGATATGTTTCC-CTACT
* * * * *
12815776 GCTTAGGGAGATCAGATCT-GCAA
64 ACTTAGGGGGTTAAGATCTATCAA
** * * * * ** * *
12815799 TTTGGTCTGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTC-GATCTGTTTCCCTACTG
1 TTCAGCCTGTTACCCTACTGTTTAGGGGTTTAAGGCCCATC-AATTCTGATATGTTTCCCTACTA
* *
12815863 CCTAGGGGGTTAAGATCTGT-AA
65 CTTAGGGGGTTAAGATCTATCAA
** * *
12815885 TTTGGTCTGTTACCCTACTGCTTAGGG
1 TTCAGCCTGTTACCCTACTGTTTAGGG
12815912 AGATAAGGCT
Statistics
Matches: 315, Mismatches: 47, Indels: 25
0.81 0.12 0.06
Matches are distributed among these distances:
85 1 0.00
86 136 0.43
87 75 0.24
88 27 0.09
89 73 0.23
90 3 0.01
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.35
Consensus pattern (87 bp):
TTCAGCCTGTTACCCTACTGTTTAGGGGTTTAAGGCCCATCAATTCTGATATGTTTCCCTACTAC
TTAGGGGGTTAAGATCTATCAA
Found at i:12815735 original size:42 final size:42
Alignment explanation
Indices: 12815685--12815918 Score: 181
Period size: 42 Copynumber: 5.5 Consensus size: 42
12815675 ACCTGCTCCA
*
12815685 CTACTGCTTAGGGAGATAAGATCTCCAATTTGGTCTGTTACC
1 CTACTGCTTAGGGAGATAAGATCTGCAATTTGGTCTGTTACC
* * * * * **
12815727 CTACTGCTTAGGG-GTTTAAGACCCTTC-GTCTTCGATCTACT-CC
1 CTACTGCTTAGGGAG-ATAAGA-TCTGCAAT-TT-GGTCTGTTACC
*
12815770 ACTACTGCTTAGGGAGATCAGATCTGCAATTTGGTCTGTTACC
1 -CTACTGCTTAGGGAGATAAGATCTGCAATTTGGTCTGTTACC
* * * * * *
12815813 CTACTGCTTAGGG-GTTTAAGACCCTTC-GTCTTCGATCTGTTTCC
1 CTACTGCTTAGGGAG-ATAAGA-TCTGCAAT-TT-GGTCTGTTACC
* * * *
12815857 CTACTGCCTAGGGGGTTAAGATCTGTAATTTGGTCTGTTACC
1 CTACTGCTTAGGGAGATAAGATCTGCAATTTGGTCTGTTACC
12815899 CTACTGCTTAGGGAGATAAG
1 CTACTGCTTAGGGAGATAAG
12815919 GCTCGTGGAT
Statistics
Matches: 146, Mismatches: 32, Indels: 28
0.71 0.16 0.14
Matches are distributed among these distances:
41 2 0.01
42 68 0.47
43 23 0.16
44 51 0.35
45 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (42 bp):
CTACTGCTTAGGGAGATAAGATCTGCAATTTGGTCTGTTACC
Found at i:12815779 original size:86 final size:86
Alignment explanation
Indices: 12815669--12815911 Score: 380
Period size: 86 Copynumber: 2.8 Consensus size: 86
12815659 GGTTTGTCAA
* * *
12815669 TCTTCGACCTGCTCCACTACTGCTTAGGGAGATAAGATCTCCAATTTGGTCTGTTACCCTACTGC
1 TCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTGGTCTGTTACCCTACTGC
12815734 TTAGGGGTTTAAGACCCTTCG
66 TTAGGGGTTTAAGACCCTTCG
*
12815755 TCTTCGATCTACTCCACTACTGCTTAGGGAGATCAGATCTGCAATTTGGTCTGTTACCCTACTGC
1 TCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTGGTCTGTTACCCTACTGC
12815820 TTAGGGGTTTAAGACCCTTCG
66 TTAGGGGTTTAAGACCCTTCG
** * * * *
12815841 TCTTCGATCTGTTTCC-CTACTGCCTAGGGGGTTAAGATCTGTAATTTGGTCTGTTACCCTACTG
1 TCTTCGATCT-ACTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTGGTCTGTTACCCTACTG
12815905 CTTAGGG
65 CTTAGGG
12815912 AGATAAGGCT
Statistics
Matches: 145, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
86 142 0.98
87 3 0.02
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.35
Consensus pattern (86 bp):
TCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTGGTCTGTTACCCTACTGC
TTAGGGGTTTAAGACCCTTCG
Found at i:12815781 original size:44 final size:43
Alignment explanation
Indices: 12815725--12815877 Score: 134
Period size: 44 Copynumber: 3.5 Consensus size: 43
12815715 TGGTCTGTTA
*
12815725 CCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCGATCTACT
1 CCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCGATCTATT
* * * * * * *
12815768 CCACTACTGCTTAGGGAG-ATCAGA-TCTGCAAT-TT-GGTCTGTT
1 CC-CTACTGCTTAGGG-GTTTAAGACCCTTC-GTCTTCGATCTATT
*
12815810 ACCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTT
1 -CCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCGATCT-ATT
* *
12815855 CCCTACTGCCTAGGGGGTTAAGA
1 CCCTACTGCTTAGGGGTTTAAGA
12815878 TCTGTAATTT
Statistics
Matches: 84, Mismatches: 17, Indels: 17
0.71 0.14 0.14
Matches are distributed among these distances:
41 1 0.01
42 23 0.27
43 14 0.17
44 43 0.51
45 3 0.04
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.33
Consensus pattern (43 bp):
CCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCGATCTATT
Found at i:12825156 original size:3 final size:3
Alignment explanation
Indices: 12825150--12825188 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
12825140 ACACTACTAT
12825150 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12825189 TAGAAATGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12825358 original size:38 final size:37
Alignment explanation
Indices: 12825287--12825364 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 37
12825277 GATATACACT
* *
12825287 AATATATAATAATAGTAATAATAATAAAGTAGTAAAA
1 AATATATAATAATAGTAAAAATAACAAAGTAGTAAAA
*
12825324 AATATAATTATAATAGTAAAATATAACAAATAGTAGTAAAA
1 AATAT-ATAATAATAGTAAAA-ATAAC-AA-AGTAGTAAAA
12825365 GAAAATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 5 0.15
38 13 0.38
39 4 0.12
40 2 0.06
41 10 0.29
ACGTcount: A:0.62, C:0.01, G:0.08, T:0.29
Consensus pattern (37 bp):
AATATATAATAATAGTAAAAATAACAAAGTAGTAAAA
Found at i:12826796 original size:45 final size:45
Alignment explanation
Indices: 12826745--12826870 Score: 121
Period size: 49 Copynumber: 2.7 Consensus size: 45
12826735 ACTCAATTGC
12826745 AACTTCAGAGAAATAATATTTGCTATCTTCAGTCTGTTCCACTGA
1 AACTTCAGAGAAATAATATTTGCTATCTTCAGTCTGTTCCACTGA
* * * *
12826790 AACTTCAGAGAGATAGGATCTATAATT--TAGCTTCAATCTGTTCCACTGC
1 AACTTCAGAGAAATA--A--TAT--TTGCTATCTTCAGTCTGTTCCACTGA
* * *
12826839 AACTTCAGGGAAATAAGATTTGCTATTTTCAG
1 AACTTCAGAGAAATAATATTTGCTATCTTCAG
12826871 CCTACTCCAC
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
43 2 0.03
45 22 0.35
47 2 0.03
49 35 0.56
51 2 0.03
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (45 bp):
AACTTCAGAGAAATAATATTTGCTATCTTCAGTCTGTTCCACTGA
Found at i:12827075 original size:44 final size:44
Alignment explanation
Indices: 12827002--12827164 Score: 159
Period size: 44 Copynumber: 3.7 Consensus size: 44
12826992 GTAATTTTCA
* * * *
12827002 GCTTGTTACCCTACTGCATAGGGGTTTAAGGCCCATCA-CTTCT
1 GCTTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTCACCTTCT
* ** * *
12827045 GCTATGTTTCCCTACTGCTTAGGGGGTTAAGATTCGTCAATCTTCA
1 GCT-TGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTC-ACCTTCT
* * *
12827091 GCTTGTTACCCTACTGTTTAGGGGTTTAAGGCTTGTCACCTT-T
1 GCTTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTCACCTTCT
* *
12827134 GATCTGTTTCCCTACTGCTTAGGGGGTTAAG
1 GCT-TGTTACCCTACTGCTTAGGGGGTTAAG
12827165 ATCTGTGAAT
Statistics
Matches: 96, Mismatches: 20, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
43 5 0.05
44 55 0.57
45 29 0.30
46 7 0.07
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (44 bp):
GCTTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTCACCTTCT
Found at i:12827271 original size:87 final size:86
Alignment explanation
Indices: 12827005--12827459 Score: 395
Period size: 86 Copynumber: 5.2 Consensus size: 86
12826995 ATTTTCAGCT
* * * * * *
12827005 TGTTACCCTACTGCATAGGGGTTTAAGGCCCATCA-CTTCTGCTATGTTTCCCTACTGCTTAGGG
1 TGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCATCTTC-GATCTGTCTCCCTACTGCTTAGGG
*
12827069 GGTTAAGAT-TCGTCAATCTTCAG-C
65 GGATAAGATCT-G-CAAT-TT-AGTC
* * * * * *
12827093 TTGTTACCCTACTGTTTAGGGGTTTAAG-GCTTGTCACCTTTGATCTGTTTCCCTACTGCTTAGG
1 -TGTTACCCTACTGCTTAGGGGTTTAAGACCCT-TCATCTTCGATCTGTCTCCCTACTGCTTAGG
* * * **
12827157 GGGTTAAGATCTGTGAATTCAACC
64 GGGATAAGATCTG-CAATTTAGTC
* ** ***
12827181 TGTTACCCTACTGTTTAGGGGGGTAAG-GTTTGTCAATCTTCGATCTG-CTCCACTACTGCTTAG
1 TGTTACCCTACTGCTTAGGGGTTTAAGACCCT-TC-ATCTTCGATCTGTCTCC-CTACTGCTTAG
* *
12827244 GGTGATAAGATCTGCAATTTGGTC
63 GGGGATAAGATCTGCAATTTAGTC
*
12827268 TGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCGATCTG-CTCCACTACTGCTTAGGG
1 TGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCATCTTCGATCTGTCTCC-CTACTGCTTAGGG
*
12827332 AGATAAGATCTGCAATTTAG-C
65 GGATAAGATCTGCAATTTAGTC
* * * * * * *
12827353 TTGTTACCTTACTGCTTAGGTGTTTAAGACCCTTCGTTTTTGATCTGTTTCCCTACTGCATAGGG
1 -TGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCATCTTCGATCTGTCTCCCTACTGCTTAGGG
* * *
12827418 GGTTAAGATCTGTAATTTGGTC
65 GGATAAGATCTGCAATTTAGTC
12827440 TGTTACCCTACTGCTTAGGG
1 TGTTACCCTACTGCTTAGGG
12827460 AGATAAGGCT
Statistics
Matches: 311, Mismatches: 45, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
85 1 0.00
86 135 0.43
87 70 0.23
88 37 0.12
89 64 0.21
90 4 0.01
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.37
Consensus pattern (86 bp):
TGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCATCTTCGATCTGTCTCCCTACTGCTTAGGGG
GATAAGATCTGCAATTTAGTC
Found at i:12827283 original size:42 final size:42
Alignment explanation
Indices: 12827049--12827459 Score: 258
Period size: 44 Copynumber: 9.5 Consensus size: 42
12827039 ACTTCTGCTA
* * *
12827049 TGTTTCCCTACTGCTTAGGGGGTTAAGAT-TCGTCAATCTTCAGC
1 TGTTACCCTACTGCTTAGGGGGTTAAGATCT-G-CAAT-TTGATC
* * * *
12827093 TTGTTACCCTACTGTTTAGGGGTTTAAG-GCTTGTCACCTTTGATC
1 -TGTTACCCTACTGCTTAGGGGGTTAAGATC-TG-CA-ATTTGATC
* * ** *
12827138 TGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTGAATTCAACC
1 TGTTACCCTACTGCTTAGGGGGTTAAGATCTG-CAATTTGATC
* * * *
12827181 TGTTACCCTACTGTTTAGGGGGGTAAGGTTTGTCAATCTTCGATC
1 TGTTACCCTACTGCTTAGGGGGTTAAGATCTG-CAAT-TT-GATC
* * * *
12827226 TGCT-CCACTACTGCTTAGGGTGATAAGATCTGCAATTTGGTC
1 TGTTACC-CTACTGCTTAGGGGGTTAAGATCTGCAATTTGATC
* * * *
12827268 TGTTACCCTACTGCTTAGGGGTTTAAGACCCTTC-GTCTTCGATC
1 TGTTACCCTACTGCTTAGGGGGTTAAGA-TCTGCAAT-TT-GATC
* * * *
12827312 TGCT-CCACTACTGCTTAGGGAGATAAGATCTGCAATTT-AGC
1 TGTTACC-CTACTGCTTAGGGGGTTAAGATCTGCAATTTGATC
* * * * * **
12827353 TTGTTACCTTACTGCTTAGGTGTTTAAGACCCTTCGTTTTTGATC
1 -TGTTACCCTACTGCTTAGGGGGTTAAGA-TCTGC-AATTTGATC
* * * *
12827398 TGTTTCCCTACTGCATAGGGGGTTAAGATCTGTAATTTGGTC
1 TGTTACCCTACTGCTTAGGGGGTTAAGATCTGCAATTTGATC
12827440 TGTTACCCTACTGCTTAGGG
1 TGTTACCCTACTGCTTAGGG
12827460 AGATAAGGCT
Statistics
Matches: 276, Mismatches: 72, Indels: 39
0.71 0.19 0.10
Matches are distributed among these distances:
41 2 0.01
42 68 0.25
43 58 0.21
44 86 0.31
45 60 0.22
46 2 0.01
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (42 bp):
TGTTACCCTACTGCTTAGGGGGTTAAGATCTGCAATTTGATC
Found at i:12835430 original size:43 final size:43
Alignment explanation
Indices: 12835337--12835433 Score: 106
Period size: 43 Copynumber: 2.3 Consensus size: 43
12835327 AGATGTGATT
* * * * * *
12835337 ACATGTAAGACCATGTTTGGGATATTGGCATTGTATTGTGATT
1 ACATGTAAGACCATGTCTGAGACATTGGCATCGTATTGTAATA
* *
12835380 GCGTGTAAGACCATGTCTGAGACATTGGCATCG-ATATGTAATA
1 ACATGTAAGACCATGTCTGAGACATTGGCATCGTAT-TGTAATA
12835423 ACATGTAAGAC
1 ACATGTAAGAC
12835434 TATATCTGGG
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
42 2 0.05
43 41 0.95
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (43 bp):
ACATGTAAGACCATGTCTGAGACATTGGCATCGTATTGTAATA
Found at i:12839184 original size:18 final size:19
Alignment explanation
Indices: 12839157--12839192 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
12839147 GAATGTACTA
12839157 TTCATATACA-CATATATT
1 TTCATATACATCATATATT
*
12839175 TTCATTTACATCATATAT
1 TTCATATACATCATATAT
12839193 AAATTGCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.47
Consensus pattern (19 bp):
TTCATATACATCATATATT
Found at i:12839483 original size:56 final size:56
Alignment explanation
Indices: 12839422--12839557 Score: 218
Period size: 56 Copynumber: 2.4 Consensus size: 56
12839412 TCCCAGACAG
* * *
12839422 GGTCTTACTCGCACACATAAATTGGAATCACATATCGATGCCAACGTATTAAACTT
1 GGTCTTACTCGCACACATAAATCGGAATCACATATCGATGCCAACATATTAAACAT
*
12839478 GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACATATTAAACAT
1 GGTCTTACTCGCACACATAAATCGGAATCACATATCGATGCCAACATATTAAACAT
* *
12839534 AGTCTTACTCGCACACATATATCG
1 GGTCTTACTCGCACACATAAATCG
12839558 ATGCCATGGT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 75 1.00
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (56 bp):
GGTCTTACTCGCACACATAAATCGGAATCACATATCGATGCCAACATATTAAACAT
Found at i:12840486 original size:16 final size:18
Alignment explanation
Indices: 12840455--12840487 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
12840445 GAATTTTAGT
12840455 ATAACATATATTATTATA
1 ATAACATATATTATTATA
12840473 ATAACAT-T-TTATTAT
1 ATAACATATATTATTAT
12840488 TCATTTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (18 bp):
ATAACATATATTATTATA
Found at i:12853884 original size:22 final size:21
Alignment explanation
Indices: 12853857--12853897 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
12853847 CATGTTTGAC
*
12853857 TGTTGTTATTTACTGCATGCTA
1 TGTTGTTATTAACTG-ATGCTA
12853879 TGTTGTTATTAACTGATGC
1 TGTTGTTATTAACTGATGC
12853898 ATGGGACTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.49
Consensus pattern (21 bp):
TGTTGTTATTAACTGATGCTA
Found at i:12856348 original size:23 final size:23
Alignment explanation
Indices: 12856279--12856348 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 23
12856269 ATTATGGGAA
*
12856279 TTGAAAAAGCTAAAATAGAAA-T
1 TTGAAAAAGCTAAAGTAGAAATT
* **
12856301 TTGAAAAAGC-ATAAGGAGGTGATT
1 TTGAAAAAGCTA-AAGTA-GAAATT
*
12856325 TTGAAAAGGCTAAAGTAGAAATT
1 TTGAAAAAGCTAAAGTAGAAATT
12856348 T
1 T
12856349 GGTGTACATT
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
21 1 0.03
22 13 0.36
23 7 0.19
24 14 0.39
25 1 0.03
ACGTcount: A:0.49, C:0.04, G:0.21, T:0.26
Consensus pattern (23 bp):
TTGAAAAAGCTAAAGTAGAAATT
Found at i:12859773 original size:13 final size:13
Alignment explanation
Indices: 12859757--12859781 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12859747 TGATTAGTTT
12859757 TATTAATTAATTC
1 TATTAATTAATTC
12859770 TATTAATTAATT
1 TATTAATTAATT
12859782 ATTTAAAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTAATTAATTC
Found at i:12861432 original size:16 final size:16
Alignment explanation
Indices: 12861411--12861441 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12861401 TTTGGCCCCT
12861411 GAACTTGGATTATGTC
1 GAACTTGGATTATGTC
*
12861427 GAACTTTGATTATGT
1 GAACTTGGATTATGT
12861442 GACTAATTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (16 bp):
GAACTTGGATTATGTC
Found at i:12862624 original size:18 final size:18
Alignment explanation
Indices: 12862584--12862630 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
12862574 ATATCTAATA
*
12862584 AGTAATCAGTAACGGTAGC
1 AGTAA-CAGTAACAGTAGC
*
12862603 AGTAGCAGTAACAGTAAG-
1 AGTAACAGTAACAGT-AGC
12862621 AGTAACAGTA
1 AGTAACAGTA
12862631 TTCAACACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.43, C:0.13, G:0.26, T:0.19
Consensus pattern (18 bp):
AGTAACAGTAACAGTAGC
Found at i:12864098 original size:20 final size:20
Alignment explanation
Indices: 12864075--12864129 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 20
12864065 TTATTTTTAA
12864075 TAATAATAATAATCATAATT
1 TAATAATAATAATCATAATT
*
12864095 TAATAAT-ATAAATTATAATT
1 TAATAATAAT-AATCATAATT
12864115 TAATAGAATAATAAT
1 TAAT--AATAATAAT
12864130 AAATAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.07
20 20 0.67
22 6 0.20
23 2 0.07
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
TAATAATAATAATCATAATT
Found at i:12866922 original size:119 final size:120
Alignment explanation
Indices: 12866746--12866968 Score: 301
Period size: 119 Copynumber: 1.9 Consensus size: 120
12866736 TACTCGTTCA
* * *
12866746 AATGCCTTCGTGACATAGCCCGGTTATAGTAACTCGTACAAATGCCTTCGGGACTTAGCCCGGTT
1 AATGCCTTCGTGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
*
12866811 ATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * *
12866866 AATGCCTTCG-GGCTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGTGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGG
* * *
12866928 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
12866969 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 4 0.04
119 68 0.76
120 18 0.20
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGTGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:12866968 original size:40 final size:40
Alignment explanation
Indices: 12866725--12866968 Score: 291
Period size: 40 Copynumber: 6.1 Consensus size: 40
12866715 CGGAATTTAA
** * *
12866725 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGTGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
12866765 CCGGTTATAGTAACTCGTACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
12866805 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
12866845 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
12866884 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
12866924 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
12866964 CCGGA
1 CCGGA
12866969 CATCATTCAA
Statistics
Matches: 180, Mismatches: 17, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
38 2 0.01
39 33 0.18
40 133 0.74
41 12 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:12883785 original size:23 final size:22
Alignment explanation
Indices: 12883759--12883814 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
12883749 AAAAATATAT
**
12883759 ATATACATATAATATTTATAAAA
1 ATATACATATAATATACAT-AAA
* *
12883782 ATATATACATAATATACATAAA
1 ATATACATATAATATACATAAA
*
12883804 GTATACATATA
1 ATATACATATA
12883815 TACATATATA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (22 bp):
ATATACATATAATATACATAAA
Found at i:12886029 original size:205 final size:204
Alignment explanation
Indices: 12885660--12886142 Score: 682
Period size: 205 Copynumber: 2.4 Consensus size: 204
12885650 GGGAACATCC
* * * ** *
12885660 GAAAGTCAAATCTGCTATGTCTTTGATTTGTTCCTTGTAAGCACAAGGATGCCGGATCC-TCTTG
1 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATG-CAAAACCATCTTG
* * ** *
12885724 GATCTTGCTTCAGTATAAACATCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGG
65 GATC-TGCTTCAGCATAAACATCCGAAGGTCAGATCTGCTATGTATCTGCTCTCCATCAAAGTGA
* *
12885789 AGATGCCAGACTTCGATTTGTTCTCTGAAAATACAGAGACGACAAATCATCTTAGATTTGTTTCA
129 AGATGCCAGACTTCGATTCGTTCTCTGAAAATACAGAGACGACAAATCATCTTAGA-TTGCTTCA
12885854 AAGTAAACACGT
193 AAGTAAACACGT
*
12885866 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCAAAACCATCTTGG
1 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCAAAACCATCTTGG
* *
12885931 ATCCGCTTCAGCATAAACATCCGAAGG-CAAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGAA
66 ATCTGCTTCAGCATAAACATCCGAAGGTC-AGATCTGCTATGTATCTGCTCTCCATCAAAGTGAA
* * * **
12885995 GATGCCATACTTTGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTGCTTCATC
130 GATGCCAGACTTCGATTCGTTCTCTGAAAATACAGAGACGACAAATCATCTTAGATTGCTTCAAA
*
12886060 GTAAGCACGT
195 GTAAACACGT
* * * *
12886070 GAAAGCCAAATCGGCTATGTCTTCAATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGG
1 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCAAAACCATCTTGG
12886135 ATCTGCTT
66 ATCTGCTT
12886143 TAGCCAGATC
Statistics
Matches: 247, Mismatches: 28, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
204 84 0.34
205 107 0.43
206 56 0.23
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (204 bp):
GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCAAAACCATCTTGG
ATCTGCTTCAGCATAAACATCCGAAGGTCAGATCTGCTATGTATCTGCTCTCCATCAAAGTGAAG
ATGCCAGACTTCGATTCGTTCTCTGAAAATACAGAGACGACAAATCATCTTAGATTGCTTCAAAG
TAAACACGT
Found at i:12898675 original size:18 final size:18
Alignment explanation
Indices: 12898654--12898695 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
12898644 AAAGATAAAA
12898654 ATAATAACA-ATAATAATG
1 ATAATAA-ATATAATAATG
*
12898672 ATAATAAATATAGTAATG
1 ATAATAAATATAATAATG
12898690 ATAATA
1 ATAATA
12898696 GTAAGAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (18 bp):
ATAATAAATATAATAATG
Found at i:12899167 original size:28 final size:30
Alignment explanation
Indices: 12899096--12899168 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 30
12899086 TTAAAATGAG
12899096 TACATGATAATATTAAAAGTATGTACACAATA
1 TACAT-ATAATATTAAAAG-ATGTACACAATA
* * *
12899128 TGCATA-ATATATTAAAA-ATGTATA-TATA
1 TACATATA-ATATTAAAAGATGTACACAATA
12899156 TACATATAATATT
1 TACATATAATATT
12899169 TATAAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
28 13 0.37
29 7 0.20
30 1 0.03
31 10 0.29
32 4 0.11
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (30 bp):
TACATATAATATTAAAAGATGTACACAATA
Found at i:12899179 original size:23 final size:22
Alignment explanation
Indices: 12899153--12899208 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
12899143 AAATGTATAT
**
12899153 ATATACATATAATATTTATAAAA
1 ATATACATATAATATACAT-AAA
* *
12899176 ATATATACATAATATACATAAA
1 ATATACATATAATATACATAAA
*
12899198 GTATACATATA
1 ATATACATATA
12899209 TACATATATA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (22 bp):
ATATACATATAATATACATAAA
Found at i:12899191 original size:11 final size:9
Alignment explanation
Indices: 12899178--12899220 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
12899168 TTATAAAAAT
12899178 ATATACATA
1 ATATACATA
12899187 ATATACATAA
1 ATATACAT-A
12899197 AGTATACAT-
1 A-TATACATA
12899206 ATATACATA
1 ATATACATA
12899215 TATATA
1 -ATATA
12899221 ATACTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 7 0.23
9 9 0.30
10 7 0.23
11 7 0.23
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.35
Consensus pattern (9 bp):
ATATACATA
Found at i:12903031 original size:30 final size:29
Alignment explanation
Indices: 12902963--12903035 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
12902953 ACAAAATAAT
*
12902963 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATTGCA
12902992 AACATAAGTGACTAAAATGTAAC-TTGGGCA
1 AACATAAGTGACTAAAATGTAACATT--GCA
*
12903022 AACAAAAGTGACTA
1 AACATAAGTGACTA
12903036 TTTTTGTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
28 2 0.05
29 23 0.57
30 15 0.38
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.23
Consensus pattern (29 bp):
AACATAAGTGACTAAAATGTAACATTGCA
Found at i:12903202 original size:35 final size:35
Alignment explanation
Indices: 12903136--12903201 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
12903126 AAAATAATAT
*
12903136 ACTTATTCATAAAAAAATATTATAACTTTTTTCTC
1 ACTTATTCATAAAAAAATAATATAACTTTTTTCTC
*
12903171 ACTTATTTATAAAAAAATAATAT-ACTTTTTT
1 ACTTATTCATAAAAAAATAATATAACTTTTTT
12903202 TTATGGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 8 0.28
35 21 0.72
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (35 bp):
ACTTATTCATAAAAAAATAATATAACTTTTTTCTC
Found at i:12904911 original size:17 final size:17
Alignment explanation
Indices: 12904889--12904921 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12904879 AGGTTTATGT
12904889 TTTCT-ATACTATGTTAA
1 TTTCTAATA-TATGTTAA
12904906 TTTCTAATATATGTTA
1 TTTCTAATATATGTTA
12904922 TATATTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (17 bp):
TTTCTAATATATGTTAA
Found at i:12906789 original size:134 final size:135
Alignment explanation
Indices: 12906619--12906888 Score: 479
Period size: 134 Copynumber: 2.0 Consensus size: 135
12906609 CATATGGGGT
12906619 GGGTTTGGATATGATGGAGGAAGTGTTTTTGGCAGTACCACTATAATTTTGGCGGTTTAACTGCA
1 GGGTTTGGATATGATGGAGGAAGTGTTTTTGGCAGTACCACTATAATTTTGGCGGTTTAACTGCA
*
12906684 AATTATCTGTCTGGAAGCATAGCTACAT-TTTAATAGTGACATACCACCACTTTCTGGTGTGATT
66 AATTATCTGTCTGGAAGCATAGCTACATATTTAATAGTGACATACCACCACTTTCCGGTGTGATT
12906748 GGATG
131 GGATG
* **
12906753 GGGTTTGGATATGATGGAGGAAGTGTTTTTGGCAGTATCACTATGTTTTTGGCGGTTTAACTGCA
1 GGGTTTGGATATGATGGAGGAAGTGTTTTTGGCAGTACCACTATAATTTTGGCGGTTTAACTGCA
* *
12906818 AATTATCTGTCTGGCAGCATAGCTACATATTTAATAGTGACATACCACTACTTTCCGGTGTGATT
66 AATTATCTGTCTGGAAGCATAGCTACATATTTAATAGTGACATACCACCACTTTCCGGTGTGATT
12906883 GGATG
131 GGATG
12906888 G
1 G
12906889 ATGGACTCAT
Statistics
Matches: 129, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
134 89 0.69
135 40 0.31
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (135 bp):
GGGTTTGGATATGATGGAGGAAGTGTTTTTGGCAGTACCACTATAATTTTGGCGGTTTAACTGCA
AATTATCTGTCTGGAAGCATAGCTACATATTTAATAGTGACATACCACCACTTTCCGGTGTGATT
GGATG
Found at i:12915868 original size:19 final size:22
Alignment explanation
Indices: 12915829--12915868 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
12915819 AGAAACCCAA
12915829 CCATATCCAACCGTATACACCC
1 CCATATCCAACCGTATACACCC
12915851 CCATA-CCAACC-T-TACACC
1 CCATATCCAACCGTATACACC
12915869 GTGTGGGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.33, C:0.47, G:0.03, T:0.17
Consensus pattern (22 bp):
CCATATCCAACCGTATACACCC
Found at i:12916010 original size:27 final size:27
Alignment explanation
Indices: 12915972--12916044 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
12915962 ACAGATAATC
12915972 GTGGCAGAGCCACCAGAACAAATATAT
1 GTGGCAGAGCCACCAGAACAAATATAT
* * *
12915999 GTGGCAGAGCCACCAGATCAGATATTT
1 GTGGCAGAGCCACCAGAACAAATATAT
*
12916026 GTGGCATAGCCACCAGAAC
1 GTGGCAGAGCCACCAGAAC
12916045 GCTTCCTCCA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.16
Consensus pattern (27 bp):
GTGGCAGAGCCACCAGAACAAATATAT
Found at i:12916021 original size:54 final size:54
Alignment explanation
Indices: 12915930--12916044 Score: 142
Period size: 54 Copynumber: 2.1 Consensus size: 54
12915920 AGCATGGCTG
* * * *
12915930 CCAGAACAGATAATGTGACAGGGTCACTAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAAATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * * *
12915984 CCAGAACAAATATATGTGGCAGAGCCACCAGAT-CAGATATTTGTGGCATAGCCA
1 CCAGAACAAATA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
12916038 CCAGAAC
1 CCAGAAC
12916045 GCTTCCTCCA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 36 0.69
55 16 0.31
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAAATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:12917698 original size:26 final size:26
Alignment explanation
Indices: 12917662--12917771 Score: 168
Period size: 26 Copynumber: 4.2 Consensus size: 26
12917652 CATGAAATTC
12917662 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
12917688 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
12917714 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
12917740 TTATCATTG-AATATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
12917766 TTATCA
1 TTATCA
12917772 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 78 0.98
27 2 0.03
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:12921500 original size:16 final size:16
Alignment explanation
Indices: 12921479--12921516 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
12921469 TATTAGAATA
12921479 ACTTAAGTTATTAATC
1 ACTTAAGTTATTAATC
*
12921495 ACTTAAGTTATTAGTC
1 ACTTAAGTTATTAATC
12921511 ACTTAA
1 ACTTAA
12921517 TTTTTAGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (16 bp):
ACTTAAGTTATTAATC
Found at i:12932812 original size:11 final size:11
Alignment explanation
Indices: 12932784--12932837 Score: 65
Period size: 11 Copynumber: 5.0 Consensus size: 11
12932774 TTGACCTTTC
12932784 CAAGGTATGGG
1 CAAGGTATGGG
*
12932795 -TAGGTATGGG
1 CAAGGTATGGG
*
12932805 AAAGGTATGGG
1 CAAGGTATGGG
*
12932816 CAAGGGATGGG
1 CAAGGTATGGG
*
12932827 CAAGGGATGGG
1 CAAGGTATGGG
12932838 TATATTCTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
10 9 0.24
11 29 0.76
ACGTcount: A:0.28, C:0.06, G:0.50, T:0.17
Consensus pattern (11 bp):
CAAGGTATGGG
Found at i:12936907 original size:18 final size:18
Alignment explanation
Indices: 12936880--12936976 Score: 122
Period size: 18 Copynumber: 5.4 Consensus size: 18
12936870 CAATCCCAAC
*
12936880 TACTGTATACATGAACAG
1 TACTGTATACATGAATAG
* *
12936898 TACCGTATACGTGAATAG
1 TACTGTATACATGAATAG
* *
12936916 TGCTGTATATATGAATAG
1 TACTGTATACATGAATAG
12936934 TACTGTATACATGAATAG
1 TACTGTATACATGAATAG
* * *
12936952 TACTATATACGTAAATAG
1 TACTGTATACATGAATAG
12936970 TACTGTA
1 TACTGTA
12936977 AACTGTCATA
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (18 bp):
TACTGTATACATGAATAG
Found at i:12937524 original size:11 final size:11
Alignment explanation
Indices: 12937508--12937540 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
12937498 TTGACCTTTC
12937508 CAAGGTATGGG
1 CAAGGTATGGG
12937519 CAAGGTATGGG
1 CAAGGTATGGG
*
12937530 CAAGGGATGGG
1 CAAGGTATGGG
12937541 TATATTCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.27, C:0.09, G:0.48, T:0.15
Consensus pattern (11 bp):
CAAGGTATGGG
Found at i:12939372 original size:33 final size:33
Alignment explanation
Indices: 12939335--12939433 Score: 77
Period size: 33 Copynumber: 3.2 Consensus size: 33
12939325 CGATATTTTA
12939335 TATTTATGGTAAATATTATAACATTTAATAATT
1 TATTTATGGTAAATATTATAACATTTAATAATT
* ** * *
12939368 TATTTTTCTTGAAA-A--ATAGC--TT-AT-TTT
1 TATTTATGGT-AAATATTATAACATTTAATAATT
*
12939395 ATATTTATGGTTAATATTATAACATTTAATAATT
1 -TATTTATGGTAAATATTATAACATTTAATAATT
12939429 TATTT
1 TATTT
12939434 TTCTTGAAAA
Statistics
Matches: 46, Mismatches: 11, Indels: 18
0.61 0.15 0.24
Matches are distributed among these distances:
27 4 0.09
28 10 0.22
29 2 0.04
30 4 0.09
31 4 0.09
32 2 0.04
33 15 0.33
34 5 0.11
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (33 bp):
TATTTATGGTAAATATTATAACATTTAATAATT
Found at i:12939401 original size:61 final size:62
Alignment explanation
Indices: 12939328--12939457 Score: 235
Period size: 61 Copynumber: 2.1 Consensus size: 62
12939318 TATATAACGA
12939328 TATTTTATATTTATGGTAAATATTATAACATTTAATAATTTATTTTTCTTG-AAAAATAGCT
1 TATTTTATATTTATGGTAAATATTATAACATTTAATAATTTATTTTTCTTGAAAAAATAGCT
*
12939389 TATTTTATATTTATGGTTAATATTATAACATTTAATAATTTATTTTTCTTGAAAAAAATAGCT
1 TATTTTATATTTATGGTAAATATTATAACATTTAATAATTTATTTTTCTTG-AAAAAATAGCT
12939452 TATTTT
1 TATTTT
12939458 GTCGTTATGT
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
61 50 0.76
63 16 0.24
ACGTcount: A:0.37, C:0.05, G:0.06, T:0.52
Consensus pattern (62 bp):
TATTTTATATTTATGGTAAATATTATAACATTTAATAATTTATTTTTCTTGAAAAAATAGCT
Found at i:12943292 original size:12 final size:11
Alignment explanation
Indices: 12943266--12943291 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12943256 GGGATATAGC
12943266 AAAATATTTAA
1 AAAATATTTAA
12943277 AAAATATTTAA
1 AAAATATTTAA
12943288 AAAA
1 AAAA
12943292 AGAGACACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAATATTTAA
Found at i:12947503 original size:15 final size:14
Alignment explanation
Indices: 12947435--12947563 Score: 70
Period size: 15 Copynumber: 8.9 Consensus size: 14
12947425 TTATTCCTAT
12947435 TATTTTTATGTT-TC
1 TATTTTTAT-TTATC
*
12947449 TATTTATATTTAT-
1 TATTTTTATTTATC
*
12947462 T-TTGTTATTCTAATAC
1 TATTTTTATT-T-AT-C
*
12947478 TATTATTATTTATC
1 TATTTTTATTTATC
12947492 TAATTTTTATTTATC
1 T-ATTTTTATTTATC
* *
12947507 TATTTATATTTCTAC
1 TATTTTTATTTAT-C
*
12947522 TATTATTATGTT-TC
1 TATTTTTAT-TTATC
*
12947536 TATTTATTATATT-TT
1 TATTT-TTAT-TTATC
*
12947551 TATTTCTATTTAT
1 TATTTTTATTTAT
12947564 ATACTAATAT
Statistics
Matches: 91, Mismatches: 13, Indels: 22
0.72 0.10 0.17
Matches are distributed among these distances:
12 6 0.07
13 6 0.07
14 32 0.35
15 36 0.40
16 4 0.04
17 7 0.08
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.66
Consensus pattern (14 bp):
TATTTTTATTTATC
Found at i:12947516 original size:29 final size:28
Alignment explanation
Indices: 12947435--12947542 Score: 82
Period size: 29 Copynumber: 3.8 Consensus size: 28
12947425 TTATTCCTAT
12947435 TATTTTTATGTTTCTATTTATATTTAT-
1 TATTTTTATGTTTCTATTTATATTTATC
*
12947462 T-TTGTTAT-TCTAATACTA-TTATTATTTATC
1 TATTTTTATGT-T--T-CTATTTA-TATTTATC
*
12947492 TAATTTTTAT-TTATCTATTTATATTTCTAC
1 T-ATTTTTATGTT-TCTATTTATATTTAT-C
*
12947522 TATTATTATGTTTCTATTTAT
1 TATTTTTATGTTTCTATTTAT
12947543 TATATTTTTA
Statistics
Matches: 66, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
25 1 0.02
26 7 0.11
27 1 0.02
28 4 0.06
29 35 0.53
30 10 0.15
31 1 0.02
32 7 0.11
ACGTcount: A:0.25, C:0.07, G:0.03, T:0.65
Consensus pattern (28 bp):
TATTTTTATGTTTCTATTTATATTTATC
Found at i:12947548 original size:23 final size:23
Alignment explanation
Indices: 12947435--12947589 Score: 86
Period size: 23 Copynumber: 7.0 Consensus size: 23
12947425 TTATTCCTAT
*
12947435 TATTTTTATGTTTCTATTTA-TA-
1 TATTATTAT-TTTCTATTTATTAC
* *
12947457 T-TTATT-TTGT-TATTCTAATAC
1 TATTATTATTTTCTATT-TATTAC
12947478 TATTATTATTTATCTAATTT-TTA-
1 TATTATTATTT-TCT-ATTTATTAC
* *
12947501 T-TTATCTA-TTTATATTT-CTAC
1 TATTAT-TATTTTCTATTTATTAC
12947522 TATTATTATGTTTCTATTTATTA-
1 TATTATTAT-TTTCTATTTATTAC
*
12947545 TATTTTTA-TTTCTATTTATATAC
1 TATTATTATTTTCTATTTAT-TAC
*
12947568 TAATATTATTTTC-A-TTATTAC
1 TATTATTATTTTCTATTTATTAC
12947589 T
1 T
12947590 TTTTTCTTAT
Statistics
Matches: 105, Mismatches: 11, Indels: 35
0.70 0.07 0.23
Matches are distributed among these distances:
18 4 0.04
19 4 0.04
20 9 0.09
21 25 0.24
22 22 0.21
23 27 0.26
24 9 0.09
25 2 0.02
26 3 0.03
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (23 bp):
TATTATTATTTTCTATTTATTAC
Found at i:12947574 original size:20 final size:21
Alignment explanation
Indices: 12947532--12947574 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
12947522 TATTATTATG
* **
12947532 TTTCTATTTATTATATTTTTA
1 TTTCTATTTATTATACTAATA
12947553 TTTCTATTTA-TATACTAATA
1 TTTCTATTTATTATACTAATA
12947573 TT
1 TT
12947575 ATTTTCATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTCTATTTATTATACTAATA
Found at i:12947747 original size:25 final size:23
Alignment explanation
Indices: 12947688--12947747 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 23
12947678 TATACCGCTC
*
12947688 ATTTC-AATTTTATATATTATTT
1 ATTTCAAATTTTATATATTATGT
12947710 ACTTT-AATATTTTCATATATTATGT
1 A-TTTCAA-ATTTT-ATATATTATGT
12947735 ATTTCAAACTTTT
1 ATTTCAAA-TTTT
12947748 TTACACATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
22 1 0.03
23 4 0.13
24 9 0.29
25 17 0.55
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (23 bp):
ATTTCAAATTTTATATATTATGT
Found at i:12967793 original size:10 final size:11
Alignment explanation
Indices: 12967768--12967793 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12967758 ATGTGTCTCT
12967768 TTTTTTAAATA
1 TTTTTTAAATA
12967779 TTTTTTAAATA
1 TTTTTTAAATA
12967790 TTTT
1 TTTT
12967794 GCTATATCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTTAAATA
Found at i:12971695 original size:61 final size:62
Alignment explanation
Indices: 12971601--12971730 Score: 235
Period size: 61 Copynumber: 2.1 Consensus size: 62
12971591 ACATAACGAC
12971601 AAAATAAGCTATTTTTTTCAAGAAAAATAAATTATTAAATGTTATAATATTAACCATAAATAT
1 AAAATAAGCTA-TTTTTTCAAGAAAAATAAATTATTAAATGTTATAATATTAACCATAAATAT
*
12971664 AAAATAAGCTA-TTTTTCAAGAAAAATAAATTATTAAATGTTATAATATTTACCATAAATAT
1 AAAATAAGCTATTTTTTCAAGAAAAATAAATTATTAAATGTTATAATATTAACCATAAATAT
12971725 AAAATA
1 AAAATA
12971731 TCGTTATATA
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
61 55 0.83
63 11 0.17
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.37
Consensus pattern (62 bp):
AAAATAAGCTATTTTTTCAAGAAAAATAAATTATTAAATGTTATAATATTAACCATAAATAT
Found at i:12976217 original size:22 final size:21
Alignment explanation
Indices: 12976187--12976233 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
12976177 TACAAATTAA
12976187 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
12976209 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
12976230 ATCT
1 ATCT
12976234 AAGATTGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:12976239 original size:19 final size:21
Alignment explanation
Indices: 12976204--12976243 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
12976194 AGATTACAAG
12976204 ATCATATCTTCAAGATTGCAT
1 ATCATATCTTCAAGATTGCAT
12976225 ATCATATC-T-AAGATTGCAT
1 ATCATATCTTCAAGATTGCAT
12976244 GTCCTAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 1 0.05
21 8 0.42
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (21 bp):
ATCATATCTTCAAGATTGCAT
Found at i:12982151 original size:20 final size:20
Alignment explanation
Indices: 12982126--12982167 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
12982116 AGTCATTGAC
12982126 TGATATATGTAATGGCAATA
1 TGATATATGTAATGGCAATA
12982146 TGATATATGTAATGGCAATA
1 TGATATATGTAATGGCAATA
12982166 TG
1 TG
12982168 CCAATGTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (20 bp):
TGATATATGTAATGGCAATA
Found at i:12984259 original size:36 final size:36
Alignment explanation
Indices: 12984219--12984291 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
12984209 AGTATATACG
*
12984219 TATTGTATTTTATATTGCGAACAGATAGTTTGCGTT
1 TATTGTATTTTATATTGCCAACAGATAGTTTGCGTT
*
12984255 TATTGTATTTTATATTGCCAACGGATAGTTTGCGTT
1 TATTGTATTTTATATTGCCAACAGATAGTTTGCGTT
12984291 T
1 T
12984292 CTTGCATTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.23, C:0.10, G:0.19, T:0.48
Consensus pattern (36 bp):
TATTGTATTTTATATTGCCAACAGATAGTTTGCGTT
Found at i:12984306 original size:36 final size:36
Alignment explanation
Indices: 12984230--12984306 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
12984220 ATTGTATTTT
* * **
12984230 ATATTGCGAACAGATAGTTTGCGTTTATTGTATTTT
1 ATATTGCCAACAGATAGTTTGCGTTTATTGCATTCC
* *
12984266 ATATTGCCAACGGATAGTTTGCGTTTCTTGCATTCC
1 ATATTGCCAACAGATAGTTTGCGTTTATTGCATTCC
12984302 ATATT
1 ATATT
12984307 ACCACCAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.44
Consensus pattern (36 bp):
ATATTGCCAACAGATAGTTTGCGTTTATTGCATTCC
Found at i:12991240 original size:12 final size:13
Alignment explanation
Indices: 12991198--12991243 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
12991188 TATTTTTAAA
12991198 AAATATATAATACAT
1 AAATAT-TAATA-AT
*
12991213 AAATAATAATAA-
1 AAATATTAATAAT
12991225 AAATATTAA-AAT
1 AAATATTAATAAT
12991237 AAATATT
1 AAATATT
12991244 TTCTATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 2 0.07
12 15 0.54
13 1 0.04
14 5 0.18
15 5 0.18
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATATTAATAAT
Found at i:12991393 original size:14 final size:14
Alignment explanation
Indices: 12991374--12991401 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12991364 TACAATATTC
12991374 AAATAATAACAATA
1 AAATAATAACAATA
12991388 AAATAATAACAATA
1 AAATAATAACAATA
12991402 TAATGGTGAA
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:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:12993795 original size:16 final size:16
Alignment explanation
Indices: 12993769--12993838 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
12993759 TTTGGTTCAT
* *
12993769 TGTAATGGAATAGGGC
1 TGTAATTGAATAGAGC
* *
12993785 TATAATTGAATAAAGC
1 TGTAATTGAATAGAGC
12993801 TGTAATTGAATAGAGC
1 TGTAATTGAATAGAGC
*
12993817 TGTAATTGAATAGAGT
1 TGTAATTGAATAGAGC
12993833 TGTAAT
1 TGTAAT
12993839 CAGTAATTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (16 bp):
TGTAATTGAATAGAGC
Found at i:12994101 original size:17 final size:17
Alignment explanation
Indices: 12994076--12994108 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12994066 AATTATCATT
12994076 AAATATAATTTAATAAA
1 AAATATAATTTAATAAA
*
12994093 AAATTTAATTTAATAA
1 AAATATAATTTAATAA
12994109 CATTCTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATATAATTTAATAAA
Found at i:12994577 original size:43 final size:43
Alignment explanation
Indices: 12994516--12994600 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
12994506 TACAAATACA
12994516 TAAGGCAACCAATTTGATGCCTTTTCCAACTTGATACCCAACC
1 TAAGGCAACCAATTTGATGCCTTTTCCAACTTGATACCCAACC
* *
12994559 TAAGGCAACCAATTTGATGTCTTTTCTAACTTGATACCCAAC
1 TAAGGCAACCAATTTGATGCCTTTTCCAACTTGATACCCAAC
12994601 TAATTCCTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.31
Consensus pattern (43 bp):
TAAGGCAACCAATTTGATGCCTTTTCCAACTTGATACCCAACC
Found at i:12999019 original size:66 final size:69
Alignment explanation
Indices: 12998891--12999043 Score: 197
Period size: 66 Copynumber: 2.2 Consensus size: 69
12998881 ATAGAAGCAT
* *
12998891 GAAAAAGAGAGAGATGGTTGGAAGGAAATAGGAAGAAGAATGAAAAAAAGAAGATGATTCAGACG
1 GAAAAAGAG-GAGAAGGTTCGAAGGAAATAGG-AGAAGAATGAAAAAAAGAAGATGATTCAGACG
*
12998956 TGACAAT
64 TGA-AAC
* * *
12998963 G-AAAAGAGGAGAAGTTTCGAAGGAAAT-GG-GAAGAATG-AAAAAAGAAGTTGCTTCAGACGTG
1 GAAAAAGAGGAGAAGGTTCGAAGGAAATAGGAGAAGAATGAAAAAAAGAAGATGATTCAGACGTG
12999024 AAAC
66 AAAC
12999028 GAAAAAGAGGAGAAGG
1 GAAAAAGAGGAGAAGG
12999044 GTAAAGTTGA
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
65 3 0.04
66 36 0.49
67 8 0.11
69 2 0.03
70 16 0.22
71 7 0.10
72 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.32, T:0.13
Consensus pattern (69 bp):
GAAAAAGAGGAGAAGGTTCGAAGGAAATAGGAGAAGAATGAAAAAAAGAAGATGATTCAGACGTG
AAAC
Found at i:13001117 original size:17 final size:18
Alignment explanation
Indices: 13001097--13001130 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13001087 AAGTGAATTG
13001097 AAATTGC-GAAATTAAAT
1 AAATTGCAGAAATTAAAT
13001114 AAATTGCAGAAATTAAA
1 AAATTGCAGAAATTAAA
13001131 AAAAGAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (18 bp):
AAATTGCAGAAATTAAAT
Found at i:13001724 original size:37 final size:37
Alignment explanation
Indices: 13001622--13001803 Score: 298
Period size: 37 Copynumber: 5.0 Consensus size: 37
13001612 TACGTATGAT
* *
13001622 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
13001657 CACCTATCACTTTGTTT-TTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
13001693 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
13001730 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
13001767 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
13001804 TAAAGCTATC
Statistics
Matches: 139, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
35 9 0.06
36 37 0.27
37 93 0.67
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:13001779 original size:74 final size:74
Alignment explanation
Indices: 13001622--13001850 Score: 302
Period size: 74 Copynumber: 3.0 Consensus size: 74
13001612 TACGTATGAT
* * * *
13001622 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGCCACCTATCACTTTGT-TTTTGATCAGAT
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACTTATCACTTTGTCTCTTGATCAGAT
13001684 AAGTGTAGC
66 AAGTGTAGC
13001693 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACTTATCACTTTGTCTCTTGATCAGAT
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACTTATCACTTTGTCTCTTGATCAGAT
13001758 AAGTGTAGC
66 AAGTGTAGC
*
13001767 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T--AGC---CACTTATCACTTTGTCTCT
*
13001832 TGATCAGATAAGTATAGC
57 TGATCAGATAAGTGTAGC
13001850 C
1 C
13001851 GAAGCTATCA
Statistics
Matches: 140, Mismatches: 6, Indels: 12
0.89 0.04 0.08
Matches are distributed among these distances:
71 10 0.07
72 3 0.02
73 34 0.24
74 49 0.35
76 2 0.01
77 1 0.01
78 1 0.01
80 3 0.02
83 37 0.26
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (74 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACTTATCACTTTGTCTCTTGATCAGAT
AAGTGTAGC
Found at i:13001820 original size:46 final size:46
Alignment explanation
Indices: 13001767--13002033 Score: 322
Period size: 46 Copynumber: 5.6 Consensus size: 46
13001757 TAAGTGTAGC
* **
13001767 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
13001813 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
13001859 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAA-CTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
13001910 CACTTATCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
13001955 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
13002007 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
13002034 AGTACTCAAA
Statistics
Matches: 195, Mismatches: 12, Indels: 28
0.83 0.05 0.12
Matches are distributed among these distances:
44 29 0.15
45 13 0.07
46 69 0.35
49 1 0.01
50 1 0.01
51 14 0.07
52 68 0.35
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:13001886 original size:52 final size:52
Alignment explanation
Indices: 13001810--13002027 Score: 281
Period size: 52 Copynumber: 4.3 Consensus size: 52
13001800 TAGCTAAAGC
* *
13001810 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
13001863 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAA-CTATCAC-
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
13001913 T-T-A----TCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
13001959 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
13002011 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
13002028 ATCAGAAGTA
Statistics
Matches: 144, Mismatches: 12, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
44 33 0.23
45 6 0.04
46 1 0.01
47 1 0.01
48 2 0.01
49 1 0.01
50 1 0.01
51 7 0.05
52 74 0.51
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:13001926 original size:44 final size:45
Alignment explanation
Indices: 13001863--13002033 Score: 209
Period size: 44 Copynumber: 3.6 Consensus size: 45
13001853 AGCTATCACT
*
13001863 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAA-C
1 TATCACTTATCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
*
13001907 TATCACTTATCACTTGTCACTTGATCAGATAAGTATAGCCGAAGC
1 TATCACTTATCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
* **
13001952 TATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGC
1 TATCAC-T-T-A---T-CACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
*
13002004 TACCACTTATCACTTTGTCACTTGATCAGA
1 TATCACTTATCAC-TTGTCACTTGATCAGA
13002034 AGTACTCAAA
Statistics
Matches: 110, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
44 41 0.37
45 9 0.08
46 18 0.16
47 1 0.01
48 1 0.01
49 1 0.01
50 1 0.01
51 2 0.02
52 36 0.33
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (45 bp):
TATCACTTATCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
Found at i:13001945 original size:96 final size:98
Alignment explanation
Indices: 13001767--13002033 Score: 439
Period size: 96 Copynumber: 2.7 Consensus size: 98
13001757 TAAGTGTAGC
* * *
13001767 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
13001832 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
13001866 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAA-CTATCACTTATCAC-TTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
13001929 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
13001962 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
13002027 GATCAGA
66 GATCAGA
13002034 AGTACTCAAA
Statistics
Matches: 156, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
96 77 0.49
97 27 0.17
98 43 0.28
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:13005180 original size:49 final size:50
Alignment explanation
Indices: 13005125--13005326 Score: 228
Period size: 49 Copynumber: 3.9 Consensus size: 50
13005115 CGTTTTCTCA
*
13005125 ATGCCATAGTCCAACTATGGTCTTACACGTAATCACA-AATCACATACCG
1 ATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACATACCG
* * * *
13005174 ATGCCATAGCCCAACTACGGTCTTACACGAAATCACA-TATCACTTACCG
1 ATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACATACCG
* *
13005223 ATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACACATATCACTTACCG
1 ATGCCATAGCCCAACTATGGTCTTACAC-G--T---A-ATCACACA-ATCACATACCG
* * *
13005281 ATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCACAT
1 ATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACAT
13005327 GTTCACATGT
Statistics
Matches: 132, Mismatches: 12, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
49 70 0.53
50 7 0.05
51 7 0.05
52 1 0.01
55 1 0.01
56 6 0.05
57 1 0.01
58 39 0.30
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.24
Consensus pattern (50 bp):
ATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACATACCG
Found at i:13005293 original size:58 final size:59
Alignment explanation
Indices: 13005207--13005325 Score: 231
Period size: 58 Copynumber: 2.0 Consensus size: 59
13005197 TACACGAAAT
13005207 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAT-ATCA
1 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCA
13005265 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCA
1 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCA
13005324 CA
1 CA
13005326 TGTTCACATG
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 54 0.90
59 6 0.10
ACGTcount: A:0.32, C:0.31, G:0.13, T:0.24
Consensus pattern (59 bp):
CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCA
Found at i:13005306 original size:28 final size:28
Alignment explanation
Indices: 13005216--13005306 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
13005206 TCACATATCA
13005216 CTTACCGATGCCATAGCCCAGCTATGGT
1 CTTACCGATGCCATAGCCCAGCTATGGT
* * **
13005244 CTTACACGGAAT-CACATATCACA-CATAT-CA
1 CTTAC-C-G-ATGC-CATAGCCCAGC-TATGGT
13005274 CTTACCGATGCCATAGCCCAGCTATGGT
1 CTTACCGATGCCATAGCCCAGCTATGGT
13005302 CTTAC
1 CTTAC
13005307 ACGGAATCAC
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
27 12 0.26
28 13 0.28
29 2 0.04
30 8 0.17
31 12 0.26
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.25
Consensus pattern (28 bp):
CTTACCGATGCCATAGCCCAGCTATGGT
Found at i:13007906 original size:96 final size:97
Alignment explanation
Indices: 13007741--13007927 Score: 286
Period size: 96 Copynumber: 1.9 Consensus size: 97
13007731 ATTTTATTTA
* * ** * * *
13007741 TTTATTTTTACTTAGGAATATATTGAACCTTTTGATGCGAAGAGAGATGACAGCCAAGCACCCCA
1 TTTATTTTTACTTAAGAACATATCAAACCTTTTGACGCAAAGAGAAATGACAGCCAAGCACCCCA
13007806 CCCTGGTTACTCAGCCCAACACATTCCTAATT
66 CCCTGGTTACTCAGCCCAACACATTCCTAATT
* *
13007838 TTTATTTTT-CTTAAGAACATATCAAACCTTTTGACGTAAAGAGAAATGACAGCCAAGCACCTCA
1 TTTATTTTTACTTAAGAACATATCAAACCTTTTGACGCAAAGAGAAATGACAGCCAAGCACCCCA
13007902 CCCTGGTTACTCAGCCCAACACATTC
66 CCCTGGTTACTCAGCCCAACACATTC
13007928 TTAAAAATTA
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
96 72 0.89
97 9 0.11
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.29
Consensus pattern (97 bp):
TTTATTTTTACTTAAGAACATATCAAACCTTTTGACGCAAAGAGAAATGACAGCCAAGCACCCCA
CCCTGGTTACTCAGCCCAACACATTCCTAATT
Found at i:13008649 original size:10 final size:10
Alignment explanation
Indices: 13008632--13008695 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
13008622 TATTAATATC
13008632 TAAA-AATAA
1 TAAATAATAA
13008641 TAAATAATAA
1 TAAATAATAA
*
13008651 AATAATAATAA
1 TA-AATAATAA
*
13008662 AAAATAA-AA
1 TAAATAATAA
13008671 TAAACTAA-AA
1 TAAA-TAATAA
*
13008681 TAAAATAAAAA
1 T-AAATAATAA
13008692 TAAA
1 TAAA
13008696 AATTGGGTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
9 9 0.19
10 23 0.48
11 16 0.33
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.22
Consensus pattern (10 bp):
TAAATAATAA
Found at i:13008670 original size:5 final size:5
Alignment explanation
Indices: 13008646--13008696 Score: 57
Period size: 5 Copynumber: 9.4 Consensus size: 5
13008636 AATAATAAAT
*
13008646 AATAA AATAA TAATAAAA AATAA AATAA ACTAA AATAA AATAAA AATAA
1 AATAA AATAA -AAT--AA AATAA AATAA AATAA AATAA AAT-AA AATAA
13008695 AA
1 AA
13008697 ATTGGGTTGC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 27 0.68
6 8 0.20
7 3 0.08
8 2 0.05
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:13008672 original size:15 final size:15
Alignment explanation
Indices: 13008634--13008696 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
13008624 TTAATATCTA
*
13008634 AAAATAATAAATAAT
1 AAAATAATAAAAAAT
*
13008649 AAAATAAT-AATAA-
1 AAAATAATAAAAAAT
*
13008662 AAAATAA-AATAAACT
1 AAAATAATAA-AAAAT
*
13008677 AAAATAAAATAAAAAT
1 AAAATAATA-AAAAAT
13008693 AAAA
1 AAAA
13008697 ATTGGGTTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
13 8 0.20
14 7 0.17
15 15 0.38
16 9 0.22
17 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATAATAAAAAAT
Found at i:13011468 original size:12 final size:12
Alignment explanation
Indices: 13011451--13011483 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
13011441 TTCCCTGTAA
13011451 AATAGTAAAAAT
1 AATAGTAAAAAT
13011463 AATAGTAAAAAT
1 AATAGTAAAAAT
*
13011475 AATAATAAA
1 AATAGTAAA
13011484 GGGGAAGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (12 bp):
AATAGTAAAAAT
Found at i:13011659 original size:17 final size:18
Alignment explanation
Indices: 13011639--13011672 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
13011629 AAGTGAATTG
13011639 AAATTGCA-AAATTAAAT
1 AAATTGCAGAAATTAAAT
13011656 AAATTGCAGAAATTAAA
1 AAATTGCAGAAATTAAA
13011673 AAAAAGAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.26
Consensus pattern (18 bp):
AAATTGCAGAAATTAAAT
Found at i:13012949 original size:19 final size:18
Alignment explanation
Indices: 13012910--13012962 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
13012900 AAAGTTATTG
*
13012910 AATAAAAAAAGATAAAAT
1 AATAAATAAAGATAAAAT
13012928 AATAAATAAA-ATAATAAGT
1 AATAAATAAAGATAA-AA-T
*
13012947 AATTAATAAAGGATAA
1 AATAAATAAA-GATAA
13012963 TTATTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 4 0.14
18 11 0.38
19 10 0.34
21 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.23
Consensus pattern (18 bp):
AATAAATAAAGATAAAAT
Found at i:13014697 original size:13 final size:13
Alignment explanation
Indices: 13014681--13014706 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13014671 TTTAATAAGA
13014681 TATTTTTTTATTT
1 TATTTTTTTATTT
13014694 TATTTTTTTATTT
1 TATTTTTTTATTT
13014707 AGTCTATATA
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TATTTTTTTATTT
Found at i:13017989 original size:16 final size:18
Alignment explanation
Indices: 13017962--13017994 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
13017952 CAAAGTTGAG
13017962 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
13017979 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
13017995 TTTAATTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:13022334 original size:18 final size:18
Alignment explanation
Indices: 13022283--13022335 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
13022273 CCGGCACTCT
* *
13022283 ATAACAGTCAGTTATGCA
1 ATAACAGTCAATTATTCA
* * *
13022301 GTAACAATCATTTATTCA
1 ATAACAGTCAATTATTCA
13022319 ATAACAGTCAATTATTC
1 ATAACAGTCAATTATTC
13022336 CGTAGCAGTC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (18 bp):
ATAACAGTCAATTATTCA
Found at i:13022547 original size:48 final size:48
Alignment explanation
Indices: 13022472--13022580 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 48
13022462 CCGTAACTGT
* ** * *
13022472 AACAGTCTCAGTCATGGTACACAAAGTACCTCATCAGAACGAATCCGG
1 AACAGTCACAGTCACAGTACACAAAGTACCTCATCAGAACAAATCCGA
* * * *
13022520 AACAGTCACAGTCACAGTACACTAAGTACCTTATCGGAATAAATCCGA
1 AACAGTCACAGTCACAGTACACAAAGTACCTCATCAGAACAAATCCGA
13022568 AACAGTCACAGTC
1 AACAGTCACAGTC
13022581 TGGCGACACT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.19
Consensus pattern (48 bp):
AACAGTCACAGTCACAGTACACAAAGTACCTCATCAGAACAAATCCGA
Found at i:13025792 original size:25 final size:24
Alignment explanation
Indices: 13025755--13025802 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
13025745 CATTTCACTT
*
13025755 TTTTTAGATTAGATTTTCTCTTTTC
1 TTTTTAGAATAGATTTTCT-TTTTC
13025780 TTTTTAGAATAGATTTTCTTTTT
1 TTTTTAGAATAGATTTTCTTTTT
13025803 GTTGTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.65
Consensus pattern (24 bp):
TTTTTAGAATAGATTTTCTTTTTC
Found at i:13026171 original size:26 final size:26
Alignment explanation
Indices: 13026140--13026191 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
13026130 ATTAGATAGT
13026140 GCGATATAATTGTGCCGAATAGTGAG
1 GCGATATAATTGTGCCGAATAGTGAG
13026166 GCGATATAATTGTGCCGAATAGTGAG
1 GCGATATAATTGTGCCGAATAGTGAG
13026192 ACTGAAAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.27
Consensus pattern (26 bp):
GCGATATAATTGTGCCGAATAGTGAG
Found at i:13030375 original size:22 final size:22
Alignment explanation
Indices: 13030332--13030376 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
13030322 ATGTATTTAC
* *
13030332 TTATTATTTAAGTAAATAATAA
1 TTATTATTAAAATAAATAATAA
13030354 TTATTATTAAAATATAAT-ATAA
1 TTATTATTAAAATA-AATAATAA
13030376 T
1 T
13030377 AATAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TTATTATTAAAATAAATAATAA
Found at i:13032401 original size:6 final size:6
Alignment explanation
Indices: 13032390--13032416 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
13032380 CACCGTAGAG
13032390 GTAACA GTAACA GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTA
13032417 GTGTACACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
GTAACA
Found at i:13032504 original size:51 final size:53
Alignment explanation
Indices: 13032398--13032509 Score: 140
Period size: 51 Copynumber: 2.2 Consensus size: 53
13032388 AGGTAACAGT
* *
13032398 AACAGTAACAGTAACAGTAGTGTACACAGAGTACCTCATCGGAACAAATCTGG
1 AACAGTAACAGTAACAGTAGTGTACACAGAGTACCTCATCAGAACAAATCCGG
* * * *
13032451 AACAGTAACAGTAATAGTCAG-GTACA-A-AGTACTTCTTCAGAATAAATCCGG
1 AACAGTAACAGTAACAGT-AGTGTACACAGAGTACCTCATCAGAACAAATCCGG
13032502 AACAGTAA
1 AACAGTAA
13032510 TAGTGGTTGA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
51 27 0.52
52 1 0.02
53 22 0.42
54 2 0.04
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (53 bp):
AACAGTAACAGTAACAGTAGTGTACACAGAGTACCTCATCAGAACAAATCCGG
Found at i:13033606 original size:24 final size:25
Alignment explanation
Indices: 13033574--13033630 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
13033564 ATAACTAGAC
13033574 TTTTACTCTTTATACAATCTAGTCA
1 TTTTACTCTTTATACAATCTAGTCA
* *
13033599 TTTT-CTCTTTATGCAATCTAGTCC
1 TTTTACTCTTTATACAATCTAGTCA
13033623 TTTCTACT
1 TTT-TACT
13033631 AATTAATCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 21 0.75
25 5 0.18
26 2 0.07
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (25 bp):
TTTTACTCTTTATACAATCTAGTCA
Done.