Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold590
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: 107263
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:2008 original size:163 final size:164
Alignment explanation
Indices: 1792--2225 Score: 438
Period size: 163 Copynumber: 2.6 Consensus size: 164
1782 GGAAATGACT
* * * * * * *
1792 GAATTATTGAAAAATGAATTAATATAAAATAAATAATAATATTTATGAATTTTAAAAATCAAAAA
1 GAATTTTTGAAAACTGATTTAATGTGAGATAAATAATAATATTGATGAATTTTAAAAAT-AAAAA
1857 CCAAGAAAAATCCCCCCAAAAAAATTTACGGAGTAGAAAAAATCTGTATTC-AGAA-AAAGGGAA
65 CCAAGAAAAATCCCCCCAAAAAAATTTACGGAGTAGAAAAAATC-GTATTCGA-AAGAAAGGG-A
* *
1920 ATTTCAAGAAAAAAA-T-CAAAATTTATG-AAGATGAATA
127 ATTTCAA-AAAAAAATTAAAAAAATTATGAAAG-TGAATA
* * * *
1957 -AATTTTTGAAAA-TGATTTGATGTGAGTTAAATAATAATATTGATAAATTTTAAAAATTAAAA-
1 GAATTTTTGAAAACTGATTTAATGTGAGATAAATAATAATATTGATGAATTTTAAAAATAAAAAC
* * * * * ** *
2019 CAGAGAAAAAT-CTCTCTAAAACATTTACCGAGTAGAAAATTTCGTATTCGAAAGAAAGGGAGTT
66 CA-AGAAAAATCCCCCCAAAAAAATTTACGGAGTAGAAAAAATCGTATTCGAAAGAAAGGGAATT
* *
2083 TTAAAAAAAAATTAAAAAAATTCTGAAAGTGAATA
130 TCAAAAAAAAATTAAAAAAATTATGAAAGTGAATA
* *
2118 TGAATTTTTGAAAACTGATTTAATGTGAGATAAATAATCATATTTGATGAATTTGAAAAATTAAA
1 -GAATTTTTGAAAACTGATTTAATGTGAGATAAATAATAATA-TTGATGAATTTTAAAAA-TAAA
* * *
2183 AACCAA-AAAAATCCTCCCGAAAGAAAATTTACGAAGAAGAAAA
63 AACCAAGAAAAATCC-CCCCAAA-AAAATTTACGGAGTAGAAAA
2226 TCTCGTAATT
Statistics
Matches: 218, Mismatches: 36, Indels: 27
0.78 0.13 0.10
Matches are distributed among these distances:
159 7 0.03
160 15 0.07
161 48 0.22
162 15 0.07
163 49 0.22
164 35 0.16
165 21 0.10
166 7 0.03
167 5 0.02
168 16 0.07
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (164 bp):
GAATTTTTGAAAACTGATTTAATGTGAGATAAATAATAATATTGATGAATTTTAAAAATAAAAAC
CAAGAAAAATCCCCCCAAAAAAATTTACGGAGTAGAAAAAATCGTATTCGAAAGAAAGGGAATTT
CAAAAAAAAATTAAAAAAATTATGAAAGTGAATA
Found at i:3602 original size:33 final size:33
Alignment explanation
Indices: 3547--3609 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
3537 TTAGAAGCAA
* *
3547 TGTATCGATACAATTCATCATGTATTGATACAT
1 TGTATCGATACAATTCACCATGTATCGATACAT
3580 TGTATCGATACAATGT-ACCATGTATCGATA
1 TGTATCGATACAAT-TCACCATGTATCGATA
3610 TAAACAGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (33 bp):
TGTATCGATACAATTCACCATGTATCGATACAT
Found at i:5530 original size:13 final size:13
Alignment explanation
Indices: 5512--5538 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5502 ATAGTAACCC
5512 ATGTATCGATACA
1 ATGTATCGATACA
5525 ATGTATCGATACA
1 ATGTATCGATACA
5538 A
1 A
5539 GGAATATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:11987 original size:13 final size:13
Alignment explanation
Indices: 11969--11993 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11959 ATTACTCACA
11969 TGTATCGATACAT
1 TGTATCGATACAT
11982 TGTATCGATACA
1 TGTATCGATACA
11994 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:12130 original size:52 final size:52
Alignment explanation
Indices: 12002--12121 Score: 222
Period size: 52 Copynumber: 2.3 Consensus size: 52
11992 CACTGATCTT
*
12002 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
12054 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
12106 TGTATCGATACATGCA
1 TGTATCGATACATGCA
12122 AATAAATTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:17603 original size:13 final size:13
Alignment explanation
Indices: 17585--17609 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17575 ACATTATGCT
17585 TTGTATCGATACA
1 TTGTATCGATACA
17598 TTGTATCGATAC
1 TTGTATCGATAC
17610 CGGTTCATTC
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:17649 original size:19 final size:19
Alignment explanation
Indices: 17596--17650 Score: 83
Period size: 19 Copynumber: 2.9 Consensus size: 19
17586 TGTATCGATA
* **
17596 CATTGTATCGATACCGGTT
1 CATTCTATCGATACATGTT
17615 CATTCTATCGATACATGTT
1 CATTCTATCGATACATGTT
17634 CATTCTATCGATACATG
1 CATTCTATCGATACATG
17651 AACAAATGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (19 bp):
CATTCTATCGATACATGTT
Found at i:23909 original size:13 final size:13
Alignment explanation
Indices: 23891--23927 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
23881 ATGTTCTTTA
23891 TATCGATACATTG
1 TATCGATACATTG
*
23904 TATCGATACAATG
1 TATCGATACATTG
*
23917 TATGGATACAT
1 TATCGATACAT
23928 GGGTTACTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:26071 original size:33 final size:33
Alignment explanation
Indices: 26034--26112 Score: 104
Period size: 34 Copynumber: 2.4 Consensus size: 33
26024 GATAGGGAGA
*
26034 TTGTTCTATCAACCAAATTTATTTTTAAAAGTT
1 TTGTTATATCAACCAAATTTATTTTTAAAAGTT
* * * *
26067 TTGTTAAGATCAACCAATTTTTTTTTTTAAAGTT
1 TTGTT-ATATCAACCAAATTTATTTTTAAAAGTT
26101 TTGTTATATCAA
1 TTGTTATATCAA
26113 AAAGGGGGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 11 0.28
34 28 0.72
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.51
Consensus pattern (33 bp):
TTGTTATATCAACCAAATTTATTTTTAAAAGTT
Found at i:26079 original size:34 final size:34
Alignment explanation
Indices: 26041--26106 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
26031 AGATTGTTCT
26041 ATCAACCAAATTTATTTTTAAAAGTTTTGTTAAG
1 ATCAACCAAATTTATTTTTAAAAGTTTTGTTAAG
* * *
26075 ATCAACCAATTTTTTTTTTTAAAGTTTTGTTA
1 ATCAACCAAATTTATTTTTAAAAGTTTTGTTA
26107 TATCAAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.33, C:0.09, G:0.08, T:0.50
Consensus pattern (34 bp):
ATCAACCAAATTTATTTTTAAAAGTTTTGTTAAG
Found at i:26456 original size:33 final size:32
Alignment explanation
Indices: 26414--26475 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
26404 CACTTTCAAA
*
26414 TGTATCGATACACTATGCTTTGTATCGATATAT
1 TGTATCGATACA-TATGCATTGTATCGATATAT
* *
26447 TGTATCGATACATGTTCATTGTATCGATA
1 TGTATCGATACATATGCATTGTATCGATA
26476 CATGACCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.54
33 12 0.46
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATATGCATTGTATCGATATAT
Found at i:26469 original size:19 final size:20
Alignment explanation
Indices: 26445--26500 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
26435 GTATCGATAT
**
26445 ATTGTATCGATACATGTTC-
1 ATTGTATCGATACATGACCA
26464 ATTGTATCGATACATGACCA
1 ATTGTATCGATACATGACCA
*
26484 AATGTATCGATACATGA
1 ATTGTATCGATACATGA
26501 AACTGGTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
ATTGTATCGATACATGACCA
Found at i:26491 original size:20 final size:19
Alignment explanation
Indices: 26447--26500 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
26437 ATCGATATAT
** *
26447 TGTATCGATACATGTTCAT
1 TGTATCGATACATGACCAA
26466 TGTATCGATACATGACCAAA
1 TGTATCGATACATGACC-AA
26486 TGTATCGATACATGA
1 TGTATCGATACATGA
26501 AACTGGTAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (19 bp):
TGTATCGATACATGACCAA
Found at i:26573 original size:33 final size:34
Alignment explanation
Indices: 26531--26626 Score: 119
Period size: 33 Copynumber: 2.9 Consensus size: 34
26521 CCACTATTTC
*
26531 TATCGATACATTGCACAATGTAT-T-GATACAATG
1 TATCGATACATTGAACAAT-TATATCGATACAATG
*
26564 TATCGATACA-TGAAGAATTATATCGATACAATG
1 TATCGATACATTGAACAATTATATCGATACAATG
* *
26597 TATCGATACA-TGAAGAATTGTATCGATACA
1 TATCGATACATTGAACAATTATATCGATACA
26627 TTGCCTCAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
31 3 0.05
32 7 0.12
33 48 0.83
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31
Consensus pattern (34 bp):
TATCGATACATTGAACAATTATATCGATACAATG
Found at i:26589 original size:20 final size:20
Alignment explanation
Indices: 26562--26627 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
26552 ATTGATACAA
26562 TGTATCGATACATGAAGAAT
1 TGTATCGATACATGAAGAAT
*
26582 TATATCGATAC------AA-
1 TGTATCGATACATGAAGAAT
26595 TGTATCGATACATGAAGAAT
1 TGTATCGATACATGAAGAAT
26615 TGTATCGATACAT
1 TGTATCGATACAT
26628 TGCCTCAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 10 0.27
14 2 0.05
19 2 0.05
20 23 0.62
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATGAAGAAT
Found at i:32153 original size:18 final size:19
Alignment explanation
Indices: 32119--32155 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
32109 TTTAAAATCC
*
32119 ATATTTATCTCAATAAATA
1 ATATTCATCTCAATAAATA
32138 ATATTCATCT-AATAAATA
1 ATATTCATCTCAATAAATA
32156 TAATTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATTCATCTCAATAAATA
Found at i:32174 original size:17 final size:16
Alignment explanation
Indices: 32148--32188 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
32138 ATATTCATCT
*
32148 AATAAATATAATTATTA
1 AATAAATATAA-AATTA
*
32165 AATAATTATAAAATTA
1 AATAAATATAAAATTA
32181 AATAAATA
1 AATAAATA
32189 AATTAGAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATAAATATAAAATTA
Found at i:36280 original size:20 final size:19
Alignment explanation
Indices: 36218--36289 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
36208 TACATCCAGA
*
36218 TGTATCGATACATTA-TGCTT
1 TGTATCGATACA-TACT-CAT
**
36238 TGTATCGATACATGTTCAT
1 TGTATCGATACATACTCAT
*
36257 TGTATCAATACATACTCAAT
1 TGTATCGATACATACTC-AT
36277 TGTATCGATACAT
1 TGTATCGATACAT
36290 TAAACTGGCA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
19 17 0.39
20 27 0.61
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATACTCAT
Found at i:36338 original size:13 final size:13
Alignment explanation
Indices: 36320--36344 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36310 TATCATTGTT
36320 TGTATCGATACAG
1 TGTATCGATACAG
36333 TGTATCGATACA
1 TGTATCGATACA
36345 TGAAGAATTG
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:37978 original size:15 final size:15
Alignment explanation
Indices: 37958--37989 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
37948 AACCGTCAAA
37958 GATGATGAAAATGAT
1 GATGATGAAAATGAT
*
37973 GATGATGATAATGAT
1 GATGATGAAAATGAT
37988 GA
1 GA
37990 GGTTGACTCG
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:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (15 bp):
GATGATGAAAATGAT
Found at i:41125 original size:27 final size:27
Alignment explanation
Indices: 41093--41154 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
41083 GAATGATGTT
*
41093 TCGATACATCTGGGTTTTCCAGATGCA
1 TCGATACATCTGGGTTTTCCAGATACA
* *
41120 TCGATACATTTGGGTTTTCCAGATATA
1 TCGATACATCTGGGTTTTCCAGATACA
41147 TCGATACA
1 TCGATACA
41155 ATGTTCTCTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (27 bp):
TCGATACATCTGGGTTTTCCAGATACA
Found at i:41309 original size:22 final size:20
Alignment explanation
Indices: 41284--41332 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
41274 CAAATCTTTT
* *
41284 TCAAAATTCTTTTTTTTTCAAA
1 TCAAAATTATTTGTTTTTC--A
*
41306 TCAAAACTATTTGTTTTTCA
1 TCAAAATTATTTGTTTTTCA
41326 TCAAAAT
1 TCAAAAT
41333 CATCAACAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 7 0.30
22 16 0.70
ACGTcount: A:0.35, C:0.14, G:0.02, T:0.49
Consensus pattern (20 bp):
TCAAAATTATTTGTTTTTCA
Found at i:43670 original size:13 final size:13
Alignment explanation
Indices: 43652--43678 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
43642 ACATTATGCT
43652 TTGTATCGATACA
1 TTGTATCGATACA
43665 TTGTATCGATACA
1 TTGTATCGATACA
43678 T
1 T
43679 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:43687 original size:19 final size:19
Alignment explanation
Indices: 43663--43718 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
43653 TGTATCGATA
*
43663 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGCT
** *
43682 CATTGTATCGATGTATACT
1 CATTGTATCGATACATGCT
43701 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
43719 AAACTGGCAG
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:43772 original size:20 final size:20
Alignment explanation
Indices: 43747--43798 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
43737 TTATCACTGT
43747 TTGTATCGATACATG-GCACA
1 TTGTATCGATACATGAGCA-A
*
43767 TTGTATCGATACATGAGGAA
1 TTGTATCGATACATGAGCAA
43787 TTGTATCGATAC
1 TTGTATCGATAC
43799 GTTATGCCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATGAGCAA
Found at i:45078 original size:19 final size:19
Alignment explanation
Indices: 45051--45105 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
45041 TGTATCGATA
*
45051 CATTATATCGATACATACT
1 CATTGTATCGATACATACT
*
45070 CATTGTATCAATACATACT
1 CATTGTATCGATACATACT
*
45089 CAATTGTATCGAAACAT
1 C-ATTGTATCGATACAT
45106 GAAACTGGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (19 bp):
CATTGTATCGATACATACT
Found at i:47341 original size:13 final size:13
Alignment explanation
Indices: 47323--47348 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47313 CAATTTTTTG
47323 TGTATCGATACAT
1 TGTATCGATACAT
47336 TGTATCGATACAT
1 TGTATCGATACAT
47349 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:48088 original size:21 final size:21
Alignment explanation
Indices: 48047--48090 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
48037 CTCTCTTTTA
* *
48047 TCTCCCCCATTTATTAATAAT
1 TCTCCCCCATTAATCAATAAT
48068 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCATTAATCAA-TAAT
48089 TC
1 TC
48091 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (21 bp):
TCTCCCCCATTAATCAATAAT
Found at i:49755 original size:21 final size:20
Alignment explanation
Indices: 49709--49755 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
49699 TTTGATGCTG
49709 ATTTTGATGAAAAACGAAGT
1 ATTTTGATGAAAAACGAAGT
49729 -TATTTGAAGTGAAAAAC-AAGT
1 AT-TTTG-A-TGAAAAACGAAGT
49750 ATTTTG
1 ATTTTG
49756 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (20 bp):
ATTTTGATGAAAAACGAAGT
Found at i:49894 original size:13 final size:13
Alignment explanation
Indices: 49876--49914 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
49866 ATAATCACCC
*
49876 TGTATCGATACAG
1 TGTATCGATACAA
*
49889 TGTATCGATATAA
1 TGTATCGATACAA
49902 TGTATCGATACAA
1 TGTATCGATACAA
49915 AGAAAAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:49925 original size:20 final size:20
Alignment explanation
Indices: 49900--49976 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
49890 GTATCGATAT
49900 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
49920 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
49945 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
49965 CATGTATCGATA
1 AATGTATCGATA
49977 TATTTTGGAC
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
20 30 0.62
25 18 0.38
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:52018 original size:15 final size:15
Alignment explanation
Indices: 51998--52028 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
51988 ATTTCGTTTG
*
51998 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
52013 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
52028 G
1 G
52029 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:53860 original size:21 final size:21
Alignment explanation
Indices: 53831--53875 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
53821 AAGTTTTCAT
*
53831 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
53851 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
53873 TTT
1 TTT
53876 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:56864 original size:131 final size:132
Alignment explanation
Indices: 56615--56865 Score: 306
Period size: 131 Copynumber: 1.9 Consensus size: 132
56605 CAGATGCATG
* * * * *
56615 TGAAATAATATAAATGCAAATGTCATATAATGGTGCAGATGCACGTGAAACAATGTAAATACAAA
1 TGAAACAATACAAATACAAATGTCATATAATGGTGCAGATGCACGCGAAACAATGAAAATACAAA
* * * * * *
56680 TGTCATCTAATGGTGTCGACACATGTGAAATGATATAAATGAAAGTATTAGTAAAAGGCAATACA
66 TGTCATCTAATAGAGTAGACACACGTGAAATGATACAAATGAAAGTATAAGTAAAAGGCAATACA
56745 CA
131 CA
* * ** *
56747 TGAAACAATACAAATACTAATGTCATCTAATGGTTTAGATGCACGCGAAAC-ATGAAAATGCAAA
1 TGAAACAATACAAATACAAATGTCATATAATGGTGCAGATGCACGCGAAACAATGAAAATACAAA
** * * *
56811 TGTCATCTAATAGAGTAGATGCACGTTAAATGATGCAAATGCAAGTATAAGTAAA
66 TGTCATCTAATAGAGTAGACACACGTGAAATGATACAAATGAAAGTATAAGTAAA
56866 GAGGTAAATG
Statistics
Matches: 98, Mismatches: 21, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
131 55 0.56
132 43 0.44
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.25
Consensus pattern (132 bp):
TGAAACAATACAAATACAAATGTCATATAATGGTGCAGATGCACGCGAAACAATGAAAATACAAA
TGTCATCTAATAGAGTAGACACACGTGAAATGATACAAATGAAAGTATAAGTAAAAGGCAATACA
CA
Found at i:56933 original size:88 final size:88
Alignment explanation
Indices: 56802--57032 Score: 252
Period size: 88 Copynumber: 2.6 Consensus size: 88
56792 CGAAACATGA
* * * * *
56802 AAATGCAAATGTCATCTAATAGAGTAGATGCACGTTAAATGATGCAAATGCAAGTATAAGTAAAG
1 AAATGCTAATGTCATATAATAGAGTAGATGCATG-TAAATGATGCAAATGCAAATATAAGTAAAA
* * *
56867 AGGTAAATGCATGTTAAACT-AAGC
65 AGGAAAATGCATATGAAA-TGAAGC
*
56891 AAATGCTAATGTCATATAAT-GAGTAGCA-GCATGTGAAATGATGCAAATGCAAATATTAGTAAA
1 AAATGCTAATGTCATATAATAGAGTAG-ATGCATGT-AAATGATGCAAATGCAAATATAAGTAAA
* *
56954 AAGGAAAATTCATATGAAATGATGC
64 AAGGAAAATGCATATGAAATGAAGC
* * * * * *
56979 AACTGCTAATGTCATTTAATGGTGTAGATGCATGTTAATGATGCAAATACAAAT
1 AAATGCTAATGTCATATAATAGAGTAGATGCATGTAAATGATGCAAATGCAAAT
57033 GTTATCTAAT
Statistics
Matches: 121, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
87 2 0.02
88 89 0.74
89 30 0.25
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.27
Consensus pattern (88 bp):
AAATGCTAATGTCATATAATAGAGTAGATGCATGTAAATGATGCAAATGCAAATATAAGTAAAAA
GGAAAATGCATATGAAATGAAGC
Found at i:57078 original size:45 final size:45
Alignment explanation
Indices: 56518--57388 Score: 307
Period size: 45 Copynumber: 19.6 Consensus size: 45
56508 AAAGAGGTAA
*
56518 ATGCATGTGAAACT-ATACCAATGCAAATGTCATCTAATGGTGTAG
1 ATGCATGTGAAA-TGATACAAATGCAAATGTCATCTAATGGTGTAG
* * * * *
56563 ATGCATATGAAATTATGA-AAATGCGAATGTCATATAATGGTGCAG
1 ATGCATGTGAAATGAT-ACAAATGCAAATGTCATCTAATGGTGTAG
* * * *
56608 ATGCATGTGAAATAATATAAATGCAAATGTCATATAATGGTGCAG
1 ATGCATGTGAAATGATACAAATGCAAATGTCATCTAATGGTGTAG
* ** ** * *
56653 ATGCACGTGAAACAATGTAAATACAAATGTCATCTAATGGTGTCG
1 ATGCATGTGAAATGATACAAATGCAAATGTCATCTAATGGTGTAG
** * * ** *
56698 ACACATGTGAAATGATATAAATG-AAA-GT-ATTAGTAAAAG-GCA-
1 ATGCATGTGAAATGATACAAATGCAAATGTCA-T-CTAATGGTGTAG
* ** ** * * *
56740 ATACACATGAAACAATACAAATACTAATGTCATCTAATGGTTTAG
1 ATGCATGTGAAATGATACAAATGCAAATGTCATCTAATGGTGTAG
* * * * *
56785 ATGCACGCGAAA-CATGA-AAATGCAAATGTCATCTAATAGAGTAG
1 ATGCATGTGAAATGAT-ACAAATGCAAATGTCATCTAATGGTGTAG
* * * * * ** * *
56829 ATGCACGTTAAATGATGCAAATGCAAGTAT-AAGTAAAGAG-GTAA
1 ATGCATGTGAAATGATACAAATGCAAATGTCATCTAATG-GTGTAG
* * * *
56873 ATGCATGTTAAACT-A-AGCAAATGCTAATGTCATATAAT-GAGTAG
1 ATGCATGTGAAA-TGATA-CAAATGCAAATGTCATCTAATGGTGTAG
* * * * ** * *
56917 CA-GCATGTGAAATGATGCAAATGCAAATATTAGT-AAAAAG-GAAA
1 -ATGCATGTGAAATGATACAAATGCAAATGTCA-TCTAATGGTGTAG
* * * * * *
56961 ATTCATATGAAATGATGCAACTGCTAATGTCATTTAATGGTGTAG
1 ATGCATGTGAAATGATACAAATGCAAATGTCATCTAATGGTGTAG
* * * * *
57006 ATGCATGT-TAATGATGCAAATACAAATGTTATCTAATGGTGTAA
1 ATGCATGTGAAATGATACAAATGCAAATGTCATCTAATGGTGTAG
* * *
57050 ATGCACGTGAAATGATACAAATGCAAATGTCATTTAATGGTTTAG
1 ATGCATGTGAAATGATACAAATGCAAATGTCATCTAATGGTGTAG
* ** * ** * * * * * * * *
57095 ATGTACATGAAATAATGTAAATGGAAGTATTA-ATAAAGAG-GCAA
1 ATGCATGTGAAATGATACAAATGCAAATGTCATCTAATG-GTGTAG
** * * * * *
57139 ATGCACATGAAACT-ATAAAAATGCCAATGCCATCTAATGGTCTAT
1 ATGCATGTGAAA-TGATACAAATGCAAATGTCATCTAATGGTGTAG
* * * * * * * * * *
57184 ATGCACGTGAAAAGATAGAAATGTAAGTATCA-ATAAAGAG-GCAA
1 ATGCATGTGAAATGATACAAATGCAAATGTCATCTAATG-GTGTAG
* * ** * * * * *
57228 ATGCATATAAAACAATGCAAATTTC-AATGTCATATAATAGTGCAG
1 ATGCATGTGAAATGATACAAA-TGCAAATGTCATCTAATGGTGTAG
* * * * * * *
57273 ATGCATATAAAATGATGA-AAATGCAATTGCCATTTAATGGTATAA
1 ATGCATGTGAAATGAT-ACAAATGCAAATGTCATCTAATGGTGTAG
* * * *
57318 ATGCACGTGAAATAATGCAAATGTAAATGTCATCTAATGGTGTAG
1 ATGCATGTGAAATGATACAAATGCAAATGTCATCTAATGGTGTAG
* *
57363 ATGCATATGAAATGATAAAAATGCAA
1 ATGCATGTGAAATGATACAAATGCAA
57389 GTATCAATAA
Statistics
Matches: 598, Mismatches: 189, Indels: 78
0.69 0.22 0.09
Matches are distributed among these distances:
42 17 0.03
43 14 0.02
44 222 0.37
45 344 0.58
46 1 0.00
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (45 bp):
ATGCATGTGAAATGATACAAATGCAAATGTCATCTAATGGTGTAG
Found at i:57141 original size:89 final size:89
Alignment explanation
Indices: 57048--57232 Score: 223
Period size: 89 Copynumber: 2.1 Consensus size: 89
57038 CTAATGGTGT
* * * * * *
57048 AAATGCACGTGAAA-TGATACAAATGCAAATGTCATTTAATGGTTTAGATGTACATGAAATA-AT
1 AAATGCACATGAAACT-ATAAAAATGCAAATGCCATCTAATGGTCTAGATGCACATGAAA-AGAT
*
57111 -GTAAATGGAAGTATTAATAAAGAGGC
64 AG-AAATGGAAGTATCAATAAAGAGGC
* * *
57137 AAATGCACATGAAACTATAAAAATGCCAATGCCATCTAATGGTCTATATGCACGTGAAAAGATAG
1 AAATGCACATGAAACTATAAAAATGCAAATGCCATCTAATGGTCTAGATGCACATGAAAAGATAG
*
57202 AAATGTAAGTATCAATAAAGAGGC
66 AAATGGAAGTATCAATAAAGAGGC
57226 AAATGCA
1 AAATGCA
57233 TATAAAACAA
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
88 1 0.01
89 79 0.96
90 2 0.02
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.25
Consensus pattern (89 bp):
AAATGCACATGAAACTATAAAAATGCAAATGCCATCTAATGGTCTAGATGCACATGAAAAGATAG
AAATGGAAGTATCAATAAAGAGGC
Found at i:57277 original size:89 final size:89
Alignment explanation
Indices: 57113--57277 Score: 197
Period size: 89 Copynumber: 1.9 Consensus size: 89
57103 GAAATAATGT
* * * * *
57113 AAATGGAAGTATTAATAAAGAGGCAAATGCACATGAAACTATAAAAATGCCAATGCCATCTAATG
1 AAATGGAAGTATCAATAAAGAGGCAAATGCACATAAAACAATAAAAATGCCAATGCCATATAATA
*
57178 GTCTATATGCACGTGAAAAGATAG
66 GTCTAGATGCACGTGAAAAGATAG
* * ** ** *
57202 AAATGTAAGTATCAATAAAGAGGCAAATGCATATAAAACAATGCAAATTTCAATGTCATATAATA
1 AAATGGAAGTATCAATAAAGAGGCAAATGCACATAAAACAATAAAAATGCCAATGCCATATAATA
57267 GTGC-AGATGCA
66 GT-CTAGATGCA
57278 TATAAAATGA
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
89 61 0.98
90 1 0.02
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.24
Consensus pattern (89 bp):
AAATGGAAGTATCAATAAAGAGGCAAATGCACATAAAACAATAAAAATGCCAATGCCATATAATA
GTCTAGATGCACGTGAAAAGATAG
Found at i:57429 original size:134 final size:135
Alignment explanation
Indices: 57036--57434 Score: 330
Period size: 134 Copynumber: 3.0 Consensus size: 135
57026 TACAAATGTT
* * * * * * * *
57036 ATCTAATGGTGTAAATGCACGTGAAATGATACAAATGCAAATGTCATTTAATGGTTTAGATGTAC
1 ATCTAATGGTATAAATGCACGTGAAATAATGCAAATGTAAATGTCATATAATGGTGTAGATGCAT
** * * * * * *
57101 ATGAAATAATGTAAATGGAAGTATTAATAAAGAGGCAAATGCACATGAAACTATAAAAATGCCAA
66 ATGAAATAATAAAAATGCAAGTATCAATAAAAAGGCAAATGCATATGAAACTATGAAAATGACAA
57166 -TGCC
131 TTGCC
* * * * * * *
57170 ATCTAATGGTCTATATGCACGTGAAA-AGATAG-AAATGTAAGTATCA-ATAAAGAG-GCAAATG
1 ATCTAATGGTATAAATGCACGTGAAATA-AT-GCAAATGTAAATGTCATATAATG-GTGTAGATG
* * * * * * * * *
57231 CATATAAAACAATGCAAATTTCAA-TGTC-ATATAATAGTGCAGATGCATAT-AAAATGATGAAA
63 CATATGAAATAAT-AAAAATGCAAGTATCAATA-AAAAG-GCAAATGCATATGAAACT-ATGAAA
57293 ATG-CAATTGCC
124 ATGACAATTGCC
* *
57304 ATTTAATGGTATAAATGCACGTGAAATAATGCAAATGTAAATGTCATCTAATGGTGTAGATGCAT
1 ATCTAATGGTATAAATGCACGTGAAATAATGCAAATGTAAATGTCATATAATGGTGTAGATGCAT
* * * *
57369 ATGAAATGATAAAAATGCAAGTATCAATAAAAAGGCAAATGTATGTGAAACTATGTAAATGACAA
66 ATGAAATAATAAAAATGCAAGTATCAATAAAAAGGCAAATGCATATGAAACTATGAAAATGACAA
57434 T
131 T
57435 GTCATATAAG
Statistics
Matches: 199, Mismatches: 50, Indels: 31
0.71 0.18 0.11
Matches are distributed among these distances:
132 3 0.02
133 31 0.16
134 127 0.64
135 35 0.18
136 3 0.02
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (135 bp):
ATCTAATGGTATAAATGCACGTGAAATAATGCAAATGTAAATGTCATATAATGGTGTAGATGCAT
ATGAAATAATAAAAATGCAAGTATCAATAAAAAGGCAAATGCATATGAAACTATGAAAATGACAA
TTGCC
Found at i:58278 original size:108 final size:108
Alignment explanation
Indices: 58089--58308 Score: 413
Period size: 108 Copynumber: 2.0 Consensus size: 108
58079 AGCTATTAGC
*
58089 ACTTCGATAGGTACCAAGATTGGTAGTAAAAGGTTAAAAAACTTTGAAAAAGTAAAGGATTTAAT
1 ACTTCGATAGGTACCAAGATTGGCAGTAAAAGGTTAAAAAACTTTGAAAAAGTAAAGGATTTAAT
58154 TTTCAGAGTTGTTCTGACCAACTTAGAGTTTACAACCTAGGGT
66 TTTCAGAGTTGTTCTGACCAACTTAGAGTTTACAACCTAGGGT
* *
58197 ACTTCGATAGGTACCAAGATTGGCAGTAAAAGGTTAAAGAACTTTGAAAAGGTAAAGGATTTAAT
1 ACTTCGATAGGTACCAAGATTGGCAGTAAAAGGTTAAAAAACTTTGAAAAAGTAAAGGATTTAAT
58262 TTTCAGAGTTGTTCTGACCAACTTAGAGTTTACAACCTAGGGT
66 TTTCAGAGTTGTTCTGACCAACTTAGAGTTTACAACCTAGGGT
58305 ACTT
1 ACTT
58309 AGGGATTTTT
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 109 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (108 bp):
ACTTCGATAGGTACCAAGATTGGCAGTAAAAGGTTAAAAAACTTTGAAAAAGTAAAGGATTTAAT
TTTCAGAGTTGTTCTGACCAACTTAGAGTTTACAACCTAGGGT
Found at i:64517 original size:13 final size:13
Alignment explanation
Indices: 64499--64524 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
64489 TACAGCAAGT
64499 ATGTATCGATACA
1 ATGTATCGATACA
64512 ATGTATCGATACA
1 ATGTATCGATACA
64525 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:66775 original size:21 final size:21
Alignment explanation
Indices: 66742--66786 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
66732 TTGCAAGTTG
*
66742 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
66764 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
66784 AAA
1 AAA
66787 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:68609 original size:15 final size:15
Alignment explanation
Indices: 68589--68619 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
68579 TAAAAATGTC
*
68589 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
68604 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
68619 C
1 C
68620 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:70836 original size:21 final size:20
Alignment explanation
Indices: 70812--70858 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
70802 AAATCTTTTG
70812 CAAAATACTT-ATTCTTCACTT
1 CAAAATACTTCATTCTTCA--T
* *
70833 CAAATTACTTCATTTTTCAT
1 CAAAATACTTCATTCTTCAT
70853 CAAAAT
1 CAAAAT
70859 CAGCATCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.27
21 9 0.41
22 7 0.32
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (20 bp):
CAAAATACTTCATTCTTCAT
Found at i:73308 original size:20 final size:20
Alignment explanation
Indices: 73262--73311 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
73252 ATCGATACAA
*
73262 TGTATCAATACACAAAAAAT
1 TGTATCGATACACAAAAAAT
73282 TGTATCGATACACAAAAAAT
1 TGTATCGATACACAAAAAAT
73302 TGTATCGATA
1 TGTATCGATA
73312 AATTAGCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (20 bp):
TGTATCGATACACAAAAAAT
Found at i:85555 original size:20 final size:20
Alignment explanation
Indices: 85530--85567 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
85520 ATTTTCCAGA
85530 ATGTATCAATACAT-TGAATG
1 ATGTATC-ATACATCTGAATG
85550 ATGTATCATACATCTGAA
1 ATGTATCATACATCTGAA
85568 AAAAGCCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (20 bp):
ATGTATCATACATCTGAATG
Found at i:86627 original size:28 final size:28
Alignment explanation
Indices: 86546--86627 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
86536 TTTTGGAGAT
*
86546 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
86574 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
86602 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
86628 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:86674 original size:52 final size:52
Alignment explanation
Indices: 86611--86739 Score: 158
Period size: 51 Copynumber: 2.5 Consensus size: 52
86601 AAATAACGAG
*
86611 GTTGGAGTATCCTCGATTGTGA-AAAATTGGTAT-TTTTGGAAA-TAAAATCGGA
1 GTTGGAGTATCCTCGATTGTGAGAAAATT--AATGTTTT-GAAAGTAAAATCGGA
* *
86663 GTTGGAGTATCCCCGATTAT-AGAAAATTAATGTTTTGAAAGTAAAATCGGA
1 GTTGGAGTATCCTCGATTGTGAGAAAATTAATGTTTTGAAAGTAAAATCGGA
*
86714 GTTGGAATATCCTCGATTGTGGAGAA
1 GTTGGAGTATCCTCGATTGT-GAGAA
86740 TTGAGCAACT
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
50 6 0.09
51 32 0.48
52 24 0.36
53 4 0.06
ACGTcount: A:0.33, C:0.09, G:0.25, T:0.33
Consensus pattern (52 bp):
GTTGGAGTATCCTCGATTGTGAGAAAATTAATGTTTTGAAAGTAAAATCGGA
Found at i:89118 original size:13 final size:13
Alignment explanation
Indices: 89100--89125 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
89090 ACAAAGATCC
89100 ATGTATCGATACA
1 ATGTATCGATACA
89113 ATGTATCGATACA
1 ATGTATCGATACA
89126 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:89121 original size:33 final size:33
Alignment explanation
Indices: 89079--89145 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
89069 AAAATTTCCA
***
89079 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
89112 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
89145 A
1 A
89146 TTTCTTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:89189 original size:19 final size:18
Alignment explanation
Indices: 89165--89231 Score: 81
Period size: 19 Copynumber: 3.9 Consensus size: 18
89155 CAGTAGCTAA
89165 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
89184 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
89199 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
89216 TTATGTATCGATACAA
1 TTATGTATCGATACAA
89232 GTCGTTGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 3 0.07
19 25 0.60
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:89205 original size:13 final size:13
Alignment explanation
Indices: 89187--89211 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
89177 ACAATACTTA
89187 TGTATCGATACAT
1 TGTATCGATACAT
89200 TGTATCGATACA
1 TGTATCGATACA
89212 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:89209 original size:32 final size:32
Alignment explanation
Indices: 89168--89230 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
89158 TAGCTAATTA
*
89168 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
89200 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
89231 AGTCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:89765 original size:21 final size:21
Alignment explanation
Indices: 89723--89765 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
89713 ATCCTTCCAA
**
89723 TCTTACAGTTTAGGTTGTTTT
1 TCTTACAGTTTAGGTTCCTTT
* *
89744 TCTTAGAGTTTTGGTTCCTTT
1 TCTTACAGTTTAGGTTCCTTT
89765 T
1 T
89766 TATTCACCTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.58
Consensus pattern (21 bp):
TCTTACAGTTTAGGTTCCTTT
Found at i:91941 original size:20 final size:20
Alignment explanation
Indices: 91918--91968 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
91908 ATATCCAGAC
91918 GTATCGATACACTATGCTTT
1 GTATCGATACACTATGCTTT
*
91938 GTATCGATATACTATGCTTT
1 GTATCGATACACTATGCTTT
91958 GTATCGATACA
1 GTATCGATACA
91969 TGCTCATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (20 bp):
GTATCGATACACTATGCTTT
Found at i:91980 original size:19 final size:20
Alignment explanation
Indices: 91956--92009 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
91946 ATACTATGCT
91956 TTGTATCGATACATGCTC-A
1 TTGTATCGATACATGCTCAA
* *
91975 TTGTATCAATACATACTCAA
1 TTGTATCGATACATGCTCAA
91995 TTGTATCGATACATG
1 TTGTATCGATACATG
92010 AAACTGGCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGCTCAA
Found at i:92678 original size:289 final size:289
Alignment explanation
Indices: 92159--92739 Score: 1126
Period size: 289 Copynumber: 2.0 Consensus size: 289
92149 ATGGCCAAAA
92159 ACATAATCATTCAATCTCCAACGAGTATGTCAACATTCTAGCCTACAAATTTGAGTTTTCAACAG
1 ACATAATCATTCAATCTCCAACGAGTATGTCAACATTCTAGCCTACAAATTTGAGTTTTCAACAG
* * *
92224 CTGAAGGATAAGAGAACCATCAAGAAACACTAAGAGATCAAAGCATTCAACAGTTTAATTTATTT
66 CTAAAGGATAAGAGAACCATCAAGAAACACCAAGAGATCAAAGCATTCAAAAGTTTAATTTATTT
92289 TCTCATTTTTAAGAGCTTTTACATTCATTGGTGTTAACTTCTTTGAAAGCTCTTTGTATTTGATT
131 TCTCATTTTTAAGAGCTTTTACATTCATTGGTGTTAACTTCTTTGAAAGCTCTTTGTATTTGATT
92354 TGTGTTTATTCTTTCAGAAACATTAGCCTAGTTAGAGGTAATTTTCGTTTCTATAATTTCCTTGA
196 TGTGTTTATTCTTTCAGAAACATTAGCCTAGTTAGAGGTAATTTTCGTTTCTATAATTTCCTTGA
92419 TTGTGTAAGGTTGCATAAAACCTTGGGTT
261 TTGTGTAAGGTTGCATAAAACCTTGGGTT
92448 ACATAATCATTCAATCTCCAACGAGTATGTCAACATTCTAGCCTACAAATTTGAGTTTTCAACAG
1 ACATAATCATTCAATCTCCAACGAGTATGTCAACATTCTAGCCTACAAATTTGAGTTTTCAACAG
92513 CTAAAGGATAAGAGAACCATCAAGAAACACCAAGAGATCAAAGCATTCAAAAGTTTAATTTATTT
66 CTAAAGGATAAGAGAACCATCAAGAAACACCAAGAGATCAAAGCATTCAAAAGTTTAATTTATTT
*
92578 TGTCATTTTTAAGAGCTTTTACATTCATTGGTGTTAACTTCTTTGAAAGCTCTTTGTATTTGATT
131 TCTCATTTTTAAGAGCTTTTACATTCATTGGTGTTAACTTCTTTGAAAGCTCTTTGTATTTGATT
92643 TGTGTTTATTCTTTCAGAAACATTAGCCTAGTTAGAGGTAATTTTCGTTTCTATAATTTCCTTGA
196 TGTGTTTATTCTTTCAGAAACATTAGCCTAGTTAGAGGTAATTTTCGTTTCTATAATTTCCTTGA
92708 TTGTGTAAGGTTGCATAAAACCTTGGGTT
261 TTGTGTAAGGTTGCATAAAACCTTGGGTT
92737 ACA
1 ACA
92740 ATTTCTCAAG
Statistics
Matches: 288, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
289 288 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (289 bp):
ACATAATCATTCAATCTCCAACGAGTATGTCAACATTCTAGCCTACAAATTTGAGTTTTCAACAG
CTAAAGGATAAGAGAACCATCAAGAAACACCAAGAGATCAAAGCATTCAAAAGTTTAATTTATTT
TCTCATTTTTAAGAGCTTTTACATTCATTGGTGTTAACTTCTTTGAAAGCTCTTTGTATTTGATT
TGTGTTTATTCTTTCAGAAACATTAGCCTAGTTAGAGGTAATTTTCGTTTCTATAATTTCCTTGA
TTGTGTAAGGTTGCATAAAACCTTGGGTT
Found at i:95737 original size:320 final size:323
Alignment explanation
Indices: 95210--95794 Score: 804
Period size: 320 Copynumber: 1.8 Consensus size: 323
95200 TTTTTATCGC
* * * * * * *
95210 TTCAAAATTTTTAATATTCATCAAGTATTATTATTTAACTCATATTAAATTAGTTTTCAAAAATT
1 TTCAAAATTTTTAATATTAATCAAATATCATCATTTAAATCATAGTAAATTAGTTTTAAAAAATT
* * * * *
95275 CATTTATTTTCTTGAGTTTTTCATTCCTTTCCTTGAAGCTCCCTTGTTTTCGAAATACAGAGTTT
66 CATTTATTTTCATGAGTTTTTAATTCCTTTCCTTAAAACTCCCTTGTTTTCGAAAAACAGAGTTT
** *
95340 TCTACTCCATAAACATTTTCAAGGGGTTTTTTCTTCTTTTCAAAATTTTTAATATTCATCAAATA
131 TCTACTCCATAAACATTTTCAAGGGGTTTTTTCTTCGGTTCAAAATTTTTAATACTCATCAAATA
* * *
95405 TCATCATTTAAATCATAGTAAATTAGTTTTAAAAAATTCATTTA-TTTTCATTTTTTCCTTGAAA
196 TAATCATTTAAATCATAGTAAATTAGTTTTAAAAAATGCATTCATTTTTCATTTTTTCCTTGAAA
95469 CTCTCACATTTCCAAAATATGAAGTTTTCTACTCCATAAATATTTTTGGGGCGATTTTCTTGA
261 CTCTCACATTTCCAAAATATGAAGTTTTCTACTCCATAAATATTTTTGGGGCGATTTTCTTGA
* *
95532 TTCAAATTTTTTAATATTAATTAAATATCATCATTTAAATCATAGTAAATTAGTTTTAAAAAA-T
1 TTCAAAATTTTTAATATTAATCAAATATCATCATTTAAATCATAGTAAATTAGTTTTAAAAAATT
* * * *
95596 CTATTTATTTTCATGAGTTTTTAATT-TTTTCCTTAAAAAC-CCTTTGTTTT-TAAAAACTGAGT
66 C-ATTTATTTTCATGAGTTTTTAATTCCTTTCCTT-AAAACTCCCTTGTTTTCGAAAAACAGAGT
* *** * * *
95658 TTTCTATTCCATAATTGTTTTCGAGGAGGTTTTTT-TTGGGTTCAAAATTTTTGATACTCATCAA
129 TTTCTACTCCATAAACATTTTCAAGG-GGTTTTTTCTTCGGTTCAAAATTTTTAATACTCATCAA
*
95722 ATATAATCATTTAAATCATAGTAAATTAGTTTTGAAAAATGCATTCATTTTTCATTTTTTCCTTG
193 ATATAATCATTTAAATCATAGTAAATTAGTTTTAAAAAATGCATTCATTTTTCATTTTTTCCTTG
*
95787 AAATTCTC
258 AAACTCTC
95795 TTATTTTTGA
Statistics
Matches: 226, Mismatches: 33, Indels: 9
0.84 0.12 0.03
Matches are distributed among these distances:
320 97 0.43
321 50 0.22
322 79 0.35
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.47
Consensus pattern (323 bp):
TTCAAAATTTTTAATATTAATCAAATATCATCATTTAAATCATAGTAAATTAGTTTTAAAAAATT
CATTTATTTTCATGAGTTTTTAATTCCTTTCCTTAAAACTCCCTTGTTTTCGAAAAACAGAGTTT
TCTACTCCATAAACATTTTCAAGGGGTTTTTTCTTCGGTTCAAAATTTTTAATACTCATCAAATA
TAATCATTTAAATCATAGTAAATTAGTTTTAAAAAATGCATTCATTTTTCATTTTTTCCTTGAAA
CTCTCACATTTCCAAAATATGAAGTTTTCTACTCCATAAATATTTTTGGGGCGATTTTCTTGA
Found at i:95907 original size:321 final size:322
Alignment explanation
Indices: 95210--95909 Score: 763
Period size: 321 Copynumber: 2.2 Consensus size: 322
95200 TTTTTATCGC
* * * * * * * * * *
95210 TTCAAAATTTTTAATATTCATCAAGTATTATTATTTAACTCATATTAAATTAGTTTTCAAAAATT
1 TTCAAAATATTTAATATTAATTAAATATCATCATTGAAATCACATTAAATTAGTTTTAAAAAATT
* * * * *
95275 CATTTATTTTCTTGAGTTTTTCATTCCTTTCCTTGAAGCTCCCTTGTTTTCGAAATACAGAGTTT
66 CATTTATTTTCATGAGTTTTTAATTCCTTTCCTTAAAACTCCCTTGTTTTCGAAAAACAGAGTTT
** *
95340 TCTACTCCATAAACATTTTCAAGGGGTTTTTTCTTCTTTTCAAAATTTTTAATATTCATCAAATA
131 TCTACTCCATAAACATTTTCAAGGGGTTTTTTCTTCGGTTCAAAATTTTTAATACTCATCAAATA
* * *
95405 TCATCATTTAAATCATAGTAAATTAGTTTTAAAAAATTCATTTATTTTCATTTTTTCCTTGAAAC
196 TAATCATTTAAATCATAGTAAATTAGTTTTAAAAAATGCATTCATTTTCATTTTTTCCTTGAAAC
* *
95470 TCTCACATTTCCAAAATATGAAGTTTTCTACTCCATAAATATTTTTGGGGCGATTTTCTTGA
261 TCTCACATTTCCAAAATATGAAGTTTTCTACTCCATAAACATTTTCGGGGCGATTTTCTTGA
* * * * *
95532 TTCAAATTTTTTAATATTAATTAAATATCATCATTTAAATCATAGTAAATTAGTTTTAAAAAA-T
1 TTCAAAATATTTAATATTAATTAAATATCATCATTGAAATCACATTAAATTAGTTTTAAAAAATT
* * * *
95596 CTATTTATTTTCATGAGTTTTTAATT-TTTTCCTTAAAAAC-CCTTTGTTTT-TAAAAACTGAGT
66 C-ATTTATTTTCATGAGTTTTTAATTCCTTTCCTT-AAAACTCCCTTGTTTTCGAAAAACAGAGT
* *** * * *
95658 TTTCTATTCCATAATTGTTTTCGAGGAGGTTTTTT-TTGGGTTCAAAATTTTTGATACTCATCAA
129 TTTCTACTCCATAAACATTTTCAAGG-GGTTTTTTCTTCGGTTCAAAATTTTTAATACTCATCAA
*
95722 ATATAATCATTTAAATCATAGTAAATTAGTTTTGAAAAATGCATTCATTTTTCATTTTTTCCTTG
193 ATATAATCATTTAAATCATAGTAAATTAGTTTTAAAAAATGCATTCA-TTTTCATTTTTTCCTTG
* ** ** * *
95787 AAATTCTCTTATTTTTGAAAA-ACTG-AGTTTTCTATTCCATAAGCATTTTCGAGGG-GATTTTT
257 AAACTCTCACA-TTTCCAAAATA-TGAAGTTTTCTACTCCATAAACATTTTCG-GGGCGA-TTTT
95849 CTCTG-
318 CT-TGA
* * * ** * *
95854 TTTAAAATATTTAA-ATTCATTTAATATTTTCATTGAATTCGCATTAAATTAGTTTT
1 TTCAAAATATTTAATATTAATTAAATATCATCATTGAAATCACATTAAATTAGTTTT
95910 GGATAATTCA
Statistics
Matches: 316, Mismatches: 53, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
320 97 0.31
321 109 0.34
322 108 0.34
323 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (322 bp):
TTCAAAATATTTAATATTAATTAAATATCATCATTGAAATCACATTAAATTAGTTTTAAAAAATT
CATTTATTTTCATGAGTTTTTAATTCCTTTCCTTAAAACTCCCTTGTTTTCGAAAAACAGAGTTT
TCTACTCCATAAACATTTTCAAGGGGTTTTTTCTTCGGTTCAAAATTTTTAATACTCATCAAATA
TAATCATTTAAATCATAGTAAATTAGTTTTAAAAAATGCATTCATTTTCATTTTTTCCTTGAAAC
TCTCACATTTCCAAAATATGAAGTTTTCTACTCCATAAACATTTTCGGGGCGATTTTCTTGA
Found at i:96464 original size:11 final size:11
Alignment explanation
Indices: 96431--96482 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
96421 TTTAGCAGGT
96431 GAAA-AAAAAA
1 GAAAGAAAAAA
96441 GGAAAGAATAAAA
1 -GAAAGAA-AAAA
*
96454 GAAGGAAAAAA
1 GAAAGAAAAAA
96465 GAAAGAAAAAA
1 GAAAGAAAAAA
*
96476 GAGAGAA
1 GAAAGAA
96483 TAGAAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
11 24 0.67
12 8 0.22
13 4 0.11
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (11 bp):
GAAAGAAAAAA
Found at i:97348 original size:16 final size:15
Alignment explanation
Indices: 97326--97369 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
97316 ATGAAATTTT
* *
97326 TAAAAATTAAAAAAT
1 TAAAAAATAAAAAAG
97341 TAAAAAATAAATAAAG
1 TAAAAAATAAA-AAAG
*
97357 TAATAAATAAAAA
1 TAAAAAATAAAAA
97370 TTATTTTATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (15 bp):
TAAAAAATAAAAAAG
Done.