Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007925.1 Corchorus capsularis cultivar CVL-1 contig07946, whole genome shotgun sequence
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: 140277
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4738 original size:21 final size:21
Alignment explanation
Indices: 4690--4730 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4680 GCCTTGTTCT
*
4690 TGCCTTATTTCTTCTTGTGAA
1 TGCCTCATTTCTTCTTGTGAA
4711 TGCCTCATTTCTTCTTGTGA
1 TGCCTCATTTCTTCTTGTGA
4731 TTGTCTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.22, G:0.15, T:0.51
Consensus pattern (21 bp):
TGCCTCATTTCTTCTTGTGAA
Found at i:6587 original size:88 final size:87
Alignment explanation
Indices: 6309--6634 Score: 483
Period size: 87 Copynumber: 3.7 Consensus size: 87
6299 ATTATCATTA
* * * * *
6309 TTAAATATATATCCTAAATCTCCCACAATCTGGCAAGATTTAAAGAAATATTCTCATTACTATTC
1 TTAAA-ATATCTCCTAAACCTCCCACAATTTGGCAAGATTTAGA-AAATATTCTCATTATTATTC
* * *
6374 AATCTTTATTATTTATTTA-TTTC
64 TATTTTTATAATTTATTTATTTTC
* *
6397 TTAAAATATCTCCTAAATCTCCCACAGTTTGGCAAGATTTAGAAAATATTCTCATTATTATTCTA
1 TTAAAATATCTCCTAAACCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTATTCTA
* *
6462 TTTTTATATTTTATTTGTTTTC
66 TTTTTATAATTTATTTATTTTC
*
6484 TTAAAATATCTCCTAAACCTTCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTAATTCT
1 TTAAAATATCTCCTAAACCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATT-ATTCT
6549 ATTTTTATAATTTATTTATTTTC
65 ATTTTTATAATTTATTTATTTTC
*
6572 TTAAAATATCTCCTAAACCTTCCACAATTTGGCAAGATTTAGAAAATATTCTCATTAATTATT
1 TTAAAATATCTCCTAAACCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATT-ATTATT
6635 TTGTTAATTT
Statistics
Matches: 220, Mismatches: 15, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
86 33 0.15
87 94 0.43
88 90 0.41
89 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (87 bp):
TTAAAATATCTCCTAAACCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTATTCTA
TTTTTATAATTTATTTATTTTC
Found at i:6615 original size:175 final size:176
Alignment explanation
Indices: 6309--6634 Score: 505
Period size: 175 Copynumber: 1.9 Consensus size: 176
6299 ATTATCATTA
*
6309 TTAAATATATATCCTAAATCTCCCACAATCTGGCAAGATTTAAAGAAATATTCTCATTACTATTC
1 TTAAATATATATCCTAAACCTCCCACAATCTGGCAAGATTTAAAGAAATATTCTCATTACTATTC
* * *
6374 AATCTTTATTATTTATTTATTTCTTAAAATATCTCCTAAATCTCCCACAGTTTGGCAAGATTTAG
66 AATCTTTATAATTTATTTATTTCTTAAAATATCTCCTAAACCTCCCACAATTTGGCAAGATTTAG
6439 AAAATATTCTCATT-ATTATTCTATTTTTATATTTTATTTGTTTTC
131 AAAATATTCTCATTAATTATTCTATTTTTATATTTTATTTGTTTTC
* * * * *
6484 TTAAA-ATATCTCCTAAACCTTCCACAATTTGGCAAGATTTAGA-AAATATTCTCATTATTAATT
1 TTAAATATATATCCTAAACCTCCCACAATCTGGCAAGATTTAAAGAAATATTCTCATTACT-ATT
* * *
6547 CTATTTTTATAATTTATTTATTTTCTTAAAATATCTCCTAAACCTTCCACAATTTGGCAAGATTT
65 CAATCTTTATAATTTATTTA-TTTCTTAAAATATCTCCTAAACCTCCCACAATTTGGCAAGATTT
6612 AGAAAATATTCTCATTAATTATT
129 AGAAAATATTCTCATTAATTATT
6635 TTGTTAATTT
Statistics
Matches: 136, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
173 15 0.11
174 53 0.39
175 62 0.46
176 6 0.04
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (176 bp):
TTAAATATATATCCTAAACCTCCCACAATCTGGCAAGATTTAAAGAAATATTCTCATTACTATTC
AATCTTTATAATTTATTTATTTCTTAAAATATCTCCTAAACCTCCCACAATTTGGCAAGATTTAG
AAAATATTCTCATTAATTATTCTATTTTTATATTTTATTTGTTTTC
Found at i:7086 original size:2 final size:2
Alignment explanation
Indices: 7074--7107 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
7064 CACTATATCA
7074 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7108 CATAAATCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11005 original size:29 final size:29
Alignment explanation
Indices: 10952--11008 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
10942 AAGAGAAAGC
** *
10952 GGATTTCGAATGTGAAAGGAGAAAGCTAG
1 GGATTTCGAATGACAAAAGAGAAAGCTAG
*
10981 GGATTTCGAATGACAAAAGATAAAGCTA
1 GGATTTCGAATGACAAAAGAGAAAGCTA
11009 CAGAAAAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (29 bp):
GGATTTCGAATGACAAAAGAGAAAGCTAG
Found at i:15682 original size:20 final size:19
Alignment explanation
Indices: 15659--15706 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
15649 ATTAAAACGG
* *
15659 AAAGCAAATAATTATTATGA
1 AAAG-AAATAAATATAATGA
*
15679 AAAGAAAAAAAATATAATGA
1 AAAG-AAATAAATATAATGA
15699 AAAGAAAT
1 AAAGAAAT
15707 TATAATAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.67, C:0.02, G:0.10, T:0.21
Consensus pattern (19 bp):
AAAGAAATAAATATAATGA
Found at i:22734 original size:16 final size:16
Alignment explanation
Indices: 22713--22768 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
22703 ATTATGCTTA
22713 TCGGGTTTAACGGGTT
1 TCGGGTTTAACGGGTT
* * *
22729 TCGGGTTATTA-TGCTT
1 TCGGGTT-TAACGGGTT
22745 ATCGGGTTTAACGGGTT
1 -TCGGGTTTAACGGGTT
22762 TCGGGTT
1 TCGGGTT
22769 ATTTTAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
16 19 0.61
17 12 0.39
ACGTcount: A:0.12, C:0.12, G:0.34, T:0.41
Consensus pattern (16 bp):
TCGGGTTTAACGGGTT
Found at i:22751 original size:17 final size:17
Alignment explanation
Indices: 22696--22752 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
22686 ATAATCGGGT
*
22696 TCGGGTCATTATGCTTA
1 TCGGGTTATTATGCTTA
* * *
22713 TCGGGTT-TAACGGGTT-
1 TCGGGTTATTA-TGCTTA
22729 TCGGGTTATTATGCTTA
1 TCGGGTTATTATGCTTA
22746 TCGGGTT
1 TCGGGTT
22753 TAACGGGTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
16 12 0.40
17 18 0.60
ACGTcount: A:0.14, C:0.14, G:0.30, T:0.42
Consensus pattern (17 bp):
TCGGGTTATTATGCTTA
Found at i:22768 original size:33 final size:33
Alignment explanation
Indices: 22691--22771 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
22681 CGGATATAAT
*
22691 CGGG-TTCGGGTCATTATGCTTATCGGGTTTAA
1 CGGGTTTCGGGTTATTATGCTTATCGGGTTTAA
22723 CGGGTTTCGGGTTATTATGCTTATCGGGTTTAA
1 CGGGTTTCGGGTTATTATGCTTATCGGGTTTAA
22756 CGGGTTTCGGGTTATT
1 CGGGTTTCGGGTTATT
22772 TTAAATTGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 4 0.09
33 43 0.91
ACGTcount: A:0.14, C:0.14, G:0.32, T:0.41
Consensus pattern (33 bp):
CGGGTTTCGGGTTATTATGCTTATCGGGTTTAA
Found at i:23439 original size:15 final size:15
Alignment explanation
Indices: 23419--23453 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
23409 TAAAACCATA
*
23419 AATTCAGTTCAGGTT
1 AATTCAATTCAGGTT
*
23434 AATTCAATTCGGGTT
1 AATTCAATTCAGGTT
23449 AATTC
1 AATTC
23454 GGGTTCGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (15 bp):
AATTCAATTCAGGTT
Found at i:23882 original size:19 final size:18
Alignment explanation
Indices: 23858--23897 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
23848 TTGAAGATTT
*
23858 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
23877 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
23895 ATT
1 ATT
23898 ATTTCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:25865 original size:20 final size:21
Alignment explanation
Indices: 25814--25865 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
25804 ATTTTAATGA
*
25814 AAAATAATTTTATACGTATCT
1 AAAATAAATTTATACGTATCT
* *
25835 AAAATATATTTATATGTAT-T
1 AAAATAAATTTATACGTATCT
*
25855 GAAATAAATTT
1 AAAATAAATTT
25866 TTTACCCTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (21 bp):
AAAATAAATTTATACGTATCT
Found at i:28389 original size:168 final size:170
Alignment explanation
Indices: 28122--28432 Score: 430
Period size: 168 Copynumber: 1.8 Consensus size: 170
28112 GGTCGCTAAG
* * * * *
28122 CATTTCAATTATTTTTTAAAAAAATATTGCATATAATTTATGCAACGAAGTCACCATCATTGGTG
1 CATTTCAATAACTTTTTAAAAAAATATTGCATAGAATTTATACAACGAAGTCACCATCACTGGTG
* *
28187 AACGTCGAAAAGTCTTAGATATTCAAGAAGAGATAACGG-TTTTTAA-GTGTCGTTGAAATTCCA
66 AACGTCGAAAAGTCGTAGATATTCAAGAAGAGATAACGGTTTTTTAAGGTATCGTTGAAATTCCA
28250 AATGATGAGATTCTTCTTATGTCCATGATAGGTTACTGAT
131 AATGATGAGATTCTTCTTATGTCCATGATAGGTTACTGAT
** * * * * *
28290 CATTTCAATAACTTTTTGGAAAAATGTTGCATAGAATTTATACGACTAAGTTATCATCACTGGTG
1 CATTTCAATAACTTTTTAAAAAAATATTGCATAGAATTTATACAACGAAGTCACCATCACTGGTG
* * *
28355 AACGTCTAAAAGTCGTAGATATTCAA-ATAGAGATAATGGTTTTTTAAGGTATCGTTGCAATTCC
66 AACGTCGAAAAGTCGTAGATATTCAAGA-AGAGATAACGGTTTTTTAAGGTATCGTTGAAATTCC
*
28419 AAATGTTGAGATTC
130 AAATGATGAGATTC
28433 ATATTGCCAC
Statistics
Matches: 122, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
167 1 0.01
168 87 0.71
169 7 0.06
170 27 0.22
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (170 bp):
CATTTCAATAACTTTTTAAAAAAATATTGCATAGAATTTATACAACGAAGTCACCATCACTGGTG
AACGTCGAAAAGTCGTAGATATTCAAGAAGAGATAACGGTTTTTTAAGGTATCGTTGAAATTCCA
AATGATGAGATTCTTCTTATGTCCATGATAGGTTACTGAT
Found at i:29370 original size:15 final size:15
Alignment explanation
Indices: 29350--29382 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
29340 GAAAACTCTA
29350 AAGAATCAAGATCTG
1 AAGAATCAAGATCTG
*
29365 AAGAATCAATATCTG
1 AAGAATCAAGATCTG
29380 AAG
1 AAG
29383 TATTTCAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (15 bp):
AAGAATCAAGATCTG
Found at i:36598 original size:58 final size:58
Alignment explanation
Indices: 36527--36820 Score: 534
Period size: 58 Copynumber: 5.1 Consensus size: 58
36517 AACTACTTGC
* * *
36527 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAAGAAAAAGTTAGAGCACAA
1 AAAGCTCGCTCAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAA
* *
36585 AAAGCTCTCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAA
1 AAAGCTCGCTCAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAA
36643 AAAGCTCGCTCAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAA
1 AAAGCTCGCTCAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAA
36701 AAAGCTCGCTCAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAA
1 AAAGCTCGCTCAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAA
36759 AAAGCTCGCTCAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCAACAA
1 AAAGCTCGCTCAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGC-ACAA
36818 AAA
1 AAA
36821 AAAAAAAAAA
Statistics
Matches: 230, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
58 223 0.97
59 7 0.03
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (58 bp):
AAAGCTCGCTCAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAA
Found at i:42073 original size:38 final size:38
Alignment explanation
Indices: 42022--42122 Score: 166
Period size: 38 Copynumber: 2.7 Consensus size: 38
42012 ACTCCAGGAC
* * *
42022 AAGCGAATAATAAATTTGGTCGCTTGGGTCTTGATCGA
1 AAGCGAATAATAAATTTGATCGCTTAGGTCTTGATCAA
*
42060 AAGCGAATAATAAATTTGATTGCTTAGGTCTTGATCAA
1 AAGCGAATAATAAATTTGATCGCTTAGGTCTTGATCAA
42098 AAGCGAATAATAAATTTGATCGCTT
1 AAGCGAATAATAAATTTGATCGCTT
42123 TGTTGCAAGT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 58 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (38 bp):
AAGCGAATAATAAATTTGATCGCTTAGGTCTTGATCAA
Found at i:56276 original size:15 final size:15
Alignment explanation
Indices: 56256--56287 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
56246 TAGCAATTAA
56256 AACCTTGACGTAATC
1 AACCTTGACGTAATC
*
56271 AACCTTGCCGTAATC
1 AACCTTGACGTAATC
56286 AA
1 AA
56288 TTGAGTTAAT
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:0.34, C:0.28, G:0.12, T:0.25
Consensus pattern (15 bp):
AACCTTGACGTAATC
Found at i:71104 original size:12 final size:11
Alignment explanation
Indices: 71076--71102 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
71066 CCTACGTGGC
71076 TTTTTAAAATA
1 TTTTTAAAATA
71087 TTTTTAAAATA
1 TTTTTAAAATA
71098 TTTTT
1 TTTTT
71103 TATTTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTTTAAAATA
Found at i:73094 original size:22 final size:24
Alignment explanation
Indices: 73062--73109 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
73052 GGTTTTGAAG
*
73062 AAGGAGAAGGAAGA-AGAAAATAA
1 AAGGAGAAGGAAGAGAGAAAAAAA
73085 AAGGA-AAGGAAGAGAGAAAAAAA
1 AAGGAGAAGGAAGAGAGAAAAAAA
73108 AA
1 AA
73110 TTATATTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (24 bp):
AAGGAGAAGGAAGAGAGAAAAAAA
Found at i:73148 original size:11 final size:10
Alignment explanation
Indices: 73114--73149 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
73104 AAAAAATTAT
*
73114 ATTTCTTTAA
1 ATTTTTTTAA
73124 ATTTTTTTAA
1 ATTTTTTTAA
73134 ATTTTTTTAA
1 ATTTTTTTAA
73144 TATTTT
1 -ATTTT
73150 ATATTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 19 0.79
11 5 0.21
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (10 bp):
ATTTTTTTAA
Found at i:73162 original size:17 final size:17
Alignment explanation
Indices: 73136--73168 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
73126 TTTTTTAAAT
*
73136 TTTTTTAATATTTTATA
1 TTTTTAAATATTTTATA
73153 TTTTTAAATATTTTAT
1 TTTTTAAATATTTTAT
73169 GGGGTGAAAG
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTAAATATTTTATA
Found at i:73163 original size:10 final size:10
Alignment explanation
Indices: 73119--73166 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
73109 ATTATATTTC
*
73119 TTTAAATTTT
1 TTTAAATATT
73129 TTTAAAT-TT
1 TTTAAATATT
*
73138 TTTTAATA-T
1 TTTAAATATT
73147 TTT--ATATT
1 TTTAAATATT
73155 TTTAAATATT
1 TTTAAATATT
73165 TT
1 TT
73167 ATGGGGTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
7 3 0.09
8 4 0.12
9 12 0.36
10 14 0.42
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTAAATATT
Found at i:79685 original size:28 final size:28
Alignment explanation
Indices: 79653--79708 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
79643 TCCTCAACAA
79653 TTCTATCCCATTTGTTGTCTCCATCTCT
1 TTCTATCCCATTTGTTGTCTCCATCTCT
*
79681 TTCTATCTCATTTGTTGTCTCCATCTCT
1 TTCTATCCCATTTGTTGTCTCCATCTCT
79709 AACTTGTCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.11, C:0.30, G:0.07, T:0.52
Consensus pattern (28 bp):
TTCTATCCCATTTGTTGTCTCCATCTCT
Found at i:86607 original size:134 final size:134
Alignment explanation
Indices: 86357--87248 Score: 1064
Period size: 134 Copynumber: 6.7 Consensus size: 134
86347 ACCAAGCTAA
* * * * * * * *
86357 CCCTTTGACTGAAAGGGTAG-TTTGGG-AAA-TAGGATCTAAATGCAAGAAATGTGACGAGACTG
1 CCCTTTGTCTGAAAGGG-CGTTTTGGGAAAACTAGAACCTAAATGCAAG-AATATGACAAAACTA
** * * * * *
86419 ACCCTTTGTGTGAAAGTGTACTTTGGGAACCGAAAATACTGAACTTAGATGAAGGAATGTGACAA
64 ACCCTTTGTCCGAAAGGGTATTTTGGGAATCAAAAATGCTGAACTTAGATGAAGGAATGTGACAA
86484 AACTAG
129 AACTAG
* * * * * *
86490 CCCTTTGTCTGAATGGGCATTTTAGGAAAA-TCAGTTA-CTAAATACAAAAATATGACAAAACTA
1 CCCTTTGTCTGAAAGGGCGTTTTGGGAAAACT-AG-AACCTAAATGCAAGAATATGACAAAACTA
* * ** * *
86553 ACTCTTTATCCGAAAGGGTATTTTGGGAATCGGAAATGCTAAACTTAGATGAAGGAATGTGTCAA
64 ACCCTTTGTCCGAAAGGGTATTTTGGGAATCAAAAATGCTGAACTTAGATGAAGGAATGTGACAA
86618 AACTAG
129 AACTAG
* * * * **
86624 CCCCTTCTCCGAAAGGGCGTTTTGGGAAAACTAGAACCTAAATGCACGAATGCGACAAAACTAAC
1 CCCTTTGTCTGAAAGGGCGTTTTGGGAAAACTAGAACCTAAATGCAAGAATATGACAAAACTAAC
* * ** * *
86689 CTTTTGTCCGAAAGGGTATTTTAGGAATCAAAAATGCTGAGTTTAGATGAAGGATTGTGACAGAA
66 CCTTTGTCCGAAAGGGTATTTTGGGAATCAAAAATGCTGAACTTAGATGAAGGAATGTGACAAAA
86754 CTAG
131 CTAG
* * *
86758 CCCTTTGTCTAAAAAGGCGTTTTGGGAAAACTAGAACCTAAATGCAAGAATATAACAAAACTAAC
1 CCCTTTGTCTGAAAGGGCGTTTTGGGAAAACTAGAACCTAAATGCAAGAATATGACAAAACTAAC
* * * * **
86823 CCTTTGTCCGAAAGCGTGTTTTGGGAATCGAAAATGCTGCACTT-GAATGTTGGAATGTGACAAA
66 CCTTTGTCCGAAAGGGTATTTTGGGAATCAAAAATGCTGAACTTAG-ATGAAGGAATGTGACAAA
86887 ACTAG
130 ACTAG
* * * *
86892 CCCTTTGTCTGAAAGGGCATTTTGGGAAAACTAGAACCTAAATGAAAGAATGTGACCAAACTAAC
1 CCCTTTGTCTGAAAGGGCGTTTTGGGAAAACTAGAACCTAAATGCAAGAATATGACAAAACTAAC
* * * * **
86957 CCTTTGACCGGAAGGGTACTTTGGGAATCAAAAATGCTGAACTTAGGTGTTGGAATGTGACAAAA
66 CCTTTGTCCGAAAGGGTATTTTGGGAATCAAAAATGCTGAACTTAGATGAAGGAATGTGACAAAA
87022 CTAG
131 CTAG
* * *
87026 CCCTTTGTCTAAAAGGGCGTTTCGGGAAAACTAGAACCTAAATGCAAGAATGTGACAAAACTAAC
1 CCCTTTGTCTGAAAGGGCGTTTTGGGAAAACTAGAACCTAAATGCAAGAATATGACAAAACTAAC
** *
87091 CCTTTGTCCGAAAGGGTATTTTGGGAATCAAAAATGCTGAACTTAGATGTTGGAATCTGACAAAA
66 CCTTTGTCCGAAAGGGTATTTTGGGAATCAAAAATGCTGAACTTAGATGAAGGAATGTGACAAAA
87156 C---
131 CTAG
* * * *
87157 CCCTTTGTCTGAAAAGGCGTTCTGGGAAAACTAGAACCTAAATGCATGAATACGACAAAACTAAC
1 CCCTTTGTCTGAAAGGGCGTTTTGGGAAAACTAGAACCTAAATGCAAGAATATGACAAAACTAAC
87222 CCTTTGTCCGAAAGGGTATTTTGGGAA
66 CCTTTGTCCGAAAGGGTATTTTGGGAA
87249 ATGGAACTTG
Statistics
Matches: 651, Mismatches: 100, Indels: 18
0.85 0.13 0.02
Matches are distributed among these distances:
131 85 0.13
133 22 0.03
134 530 0.81
135 13 0.02
136 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (134 bp):
CCCTTTGTCTGAAAGGGCGTTTTGGGAAAACTAGAACCTAAATGCAAGAATATGACAAAACTAAC
CCTTTGTCCGAAAGGGTATTTTGGGAATCAAAAATGCTGAACTTAGATGAAGGAATGTGACAAAA
CTAG
Found at i:86699 original size:64 final size:64
Alignment explanation
Indices: 86353--87327 Score: 470
Period size: 64 Copynumber: 14.8 Consensus size: 64
86343 CATAACCAAG
* * * * * * * *
86353 CTAACCCTTTGACTGAAAGGGTAGTTTGGG-AAA-TAGGATCTAAATGCAAGAAATGTGACGAGA
1 CTAACCCTTTGTCCGAAAGGGTATTTTGGGAAAACTAGAACCTAAATGC-AGGAATGTGACAAAA
* ** * * * * * *
86416 CTGACCCTTTGTGTGAAAGTGTACTTTGGGAACCGAAAATACTGAACTTAGATGAAGGAATGTGA
1 CTAACCCTTTGTCCGAAAGGGTATTTTGGG-A---AAACTA--GAACCTAAATGCAGGAATGTGA
86481 CAAAA
60 CAAAA
* * * * * * * ** *
86486 CTAGCCCTTTGTCTGAATGGGCATTTTAGGAAAA-TCAGTTA-CTAAATACAAAAATATGACAAA
1 CTAACCCTTTGTCCGAAAGGGTATTTTGGGAAAACT-AG-AACCTAAATGCAGGAATGTGACAAA
86549 A
64 A
* * * * *
86550 CTAACTCTTTATCCGAAAGGGTATTTTGGGAATCGGAAATGCTA-AACTTAGATGAAGGAATGTG
1 CTAACCCTTTGTCCGAAAGGGTATTTTGGG-A----AAA--CTAGAACCTAAATGCAGGAATGTG
*
86614 TCAAAA
59 ACAAAA
* * * ** * *
86620 CTAGCCCCTTCTCCGAAAGGGCGTTTTGGGAAAACTAGAACCTAAATGCACGAATGCGACAAAA
1 CTAACCCTTTGTCCGAAAGGGTATTTTGGGAAAACTAGAACCTAAATGCAGGAATGTGACAAAA
* * *** * * *
86684 CTAACCTTTTGTCCGAAAGGGTATTTTAGGAATCAAAAATGCT-GAGTTTAGATGAAGGATTGTG
1 CTAACCCTTTGTCCGAAAGGGTATTTT-GG----GAAAA--CTAGAACCTAAATGCAGGAATGTG
*
86748 ACAGAA
59 ACAAAA
* ** * ** * * *
86754 CTAGCCCTTTGTCTAAAAAGGCGTTTTGGGAAAACTAGAACCTAAATGCAAGAATATAACAAAA
1 CTAACCCTTTGTCCGAAAGGGTATTTTGGGAAAACTAGAACCTAAATGCAGGAATGTGACAAAA
* * * * * **
86818 CTAACCCTTTGTCCGAAAGCGTGTTTTGGGAATCGAAAATGCT-GCACTTGAATGTTGGAATGTG
1 CTAACCCTTTGTCCGAAAGGGTATTTT-GG----GAAAA--CTAGAACCTAAATGCAGGAATGTG
86882 ACAAAA
59 ACAAAA
* * * * * *
86888 CTAGCCCTTTGTCTGAAAGGGCATTTTGGGAAAACTAGAACCTAAATGAAAGAATGTGACCAAA
1 CTAACCCTTTGTCCGAAAGGGTATTTTGGGAAAACTAGAACCTAAATGCAGGAATGTGACAAAA
* * * * ** **
86952 CTAACCCTTTGACCGGAAGGGTACTTTGGGAATCAAAAATGCT-GAACTTAGGTGTTGGAATGTG
1 CTAACCCTTTGTCCGAAAGGGTATTTTGGG-----AAAA--CTAGAACCTAAATGCAGGAATGTG
87016 ACAAAA
59 ACAAAA
* ** ** * *
87022 CTAGCCCTTTGTCTAAAAGGGCGTTTCGGGAAAACTAGAACCTAAATGCAAGAATGTGACAAAA
1 CTAACCCTTTGTCCGAAAGGGTATTTTGGGAAAACTAGAACCTAAATGCAGGAATGTGACAAAA
* * ** *
87086 CTAACCCTTTGTCCGAAAGGGTATTTTGGGAATCAAAAATGCT-GAACTTAGATGTTGGAATCTG
1 CTAACCCTTTGTCCGAAAGGGTATTTTGGG-----AAAA--CTAGAACCTAAATGCAGGAATGTG
87150 ACAAAA
59 ACAAAA
* * ** * * **
87156 C---CCCTTTGTCTGAAAAGGCGTTCTGGGAAAACTAGAACCTAAATGCATGAATACGACAAAA
1 CTAACCCTTTGTCCGAAAGGGTATTTTGGGAAAACTAGAACCTAAATGCAGGAATGTGACAAAA
* * * * *
87217 CTAACCCTTTGTCCGAAAGGGTATTTTGGG-AAA-TGGAACTTGAATGC-GAGAATGTGACAGAG
1 CTAACCCTTTGTCCGAAAGGGTATTTTGGGAAAACTAGAACCTAAATGCAG-GAATGTGACAAAA
**
87279 CTGGCCCTTTGTCCGAAAGGGTATTTT-GGAAAAGCTAGAACCTAAATGC
1 CTAACCCTTTGTCCGAAAGGGTATTTTGGGAAAA-CTAGAACCTAAATGC
87328 GGCAGATTTG
Statistics
Matches: 666, Mismatches: 187, Indels: 117
0.69 0.19 0.12
Matches are distributed among these distances:
60 2 0.00
61 23 0.03
62 52 0.08
63 37 0.06
64 240 0.36
65 23 0.03
66 4 0.01
67 21 0.03
68 3 0.00
69 29 0.04
70 215 0.32
71 16 0.02
72 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (64 bp):
CTAACCCTTTGTCCGAAAGGGTATTTTGGGAAAACTAGAACCTAAATGCAGGAATGTGACAAAA
Found at i:86896 original size:70 final size:69
Alignment explanation
Indices: 86542--87156 Score: 323
Period size: 70 Copynumber: 9.1 Consensus size: 69
86532 TACAAAAATA
* * * * **
86542 TGACAAAACTAACTCTTTATCCGAAAGGGTATTTTGGGAATCGGAAATGCTAAACTTAGATGAAG
1 TGACAAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAATCGAAAATGCTGAACTTA-ATGTTG
86607 GAATG
65 GAATG
* * * * ** * **
86612 TGTCAAAACTAGCCCCTTCTCCGAAAGGGCGTTTT-GG----GAAAA--CTAGAACCTAAATGCA
1 TGACAAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAATCGAAAATGCT-GAA-CTTAATGTT
*
86670 CGAATG
64 GGAATG
* * * * ** **
86676 CGACAAAACTAACCTTTTGTCCGAAAGGGTATTTTAGGAATCAAAAATGCTGAGTTTAGATGAAG
1 TGACAAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAATCGAAAATGCTGAACTTA-ATGTTG
*
86741 GATTG
65 GAATG
* * ** * ** * **
86746 TGACAGAACTAGCCCTTTGTCTAAAAAGGCGTTTT-GG----GAAAA--CTAGAACCTAAATGCA
1 TGACAAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAATCGAAAATGCT-GAA-CTTAATGTT
* *
86804 AGAATA
64 GGAATG
* * * *
86810 TAACAAAACTAACCCTTTGTCCGAAAGCGTGTTTTGGGAATCGAAAATGCTGCACTTGAATGTTG
1 TGACAAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAATCGAAAATGCTGAACTT-AATGTTG
86875 GAATG
65 GAATG
* * * * **
86880 TGACAAAACTAGCCCTTTGTCTGAAAGGGCATTTT-GG----GAAAA--CTAGAACCTAAATGAA
1 TGACAAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAATCGAAAATGCT-GAA-CTTAATGTT
*
86938 AGAATG
64 GGAATG
* * * * * *
86944 TGACCAAACTAACCCTTTGACCGGAAGGGTACTTTGGGAATCAAAAATGCTGAACTTAGGTGTTG
1 TGACAAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAATCGAAAATGCTGAACTTA-ATGTTG
87009 GAATG
65 GAATG
* ** ** * * **
87014 TGACAAAACTAGCCCTTTGTCTAAAAGGG-CGTTTCGG----GAAAA--CTAGAACCTAAATGCA
1 TGACAAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAATCGAAAATGCT-GAA-CTTAATGTT
*
87072 AGAATG
64 GGAATG
*
87078 TGACAAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAATCAAAAATGCTGAACTTAGATGTTG
1 TGACAAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAATCGAAAATGCTGAACTTA-ATGTTG
*
87143 GAATC
65 GAATG
87148 TGACAAAAC
1 TGACAAAAC
87157 CCCTTTGTCT
Statistics
Matches: 396, Mismatches: 109, Indels: 80
0.68 0.19 0.14
Matches are distributed among these distances:
63 8 0.02
64 149 0.38
65 38 0.10
69 38 0.10
70 155 0.39
71 8 0.02
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (69 bp):
TGACAAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAATCGAAAATGCTGAACTTAATGTTGG
AATG
Found at i:88765 original size:45 final size:45
Alignment explanation
Indices: 88710--88795 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
88700 TTTGTAATCA
* * * * * *
88710 ACTCATCAAAATTTAAACTTTTTGAGTCTCAATATTGTATTACCG
1 ACTCACCAAAATTGAAACTTTTTAAGACTAAAGATTGTATTACCG
88755 ACTCACCAAAATTGAAACTTTTTAAGACTAAAGATTGTATT
1 ACTCACCAAAATTGAAACTTTTTAAGACTAAAGATTGTATT
88796 TTTATTTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (45 bp):
ACTCACCAAAATTGAAACTTTTTAAGACTAAAGATTGTATTACCG
Found at i:101462 original size:12 final size:12
Alignment explanation
Indices: 101442--101478 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
101432 GGAGAAAGTG
*
101442 ATATATATATAT
1 ATATGTATATAT
*
101454 ATATGTATATGT
1 ATATGTATATAT
101466 ATATGTATATAT
1 ATATGTATATAT
101478 A
1 A
101479 GTGGGAGCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (12 bp):
ATATGTATATAT
Found at i:107956 original size:21 final size:20
Alignment explanation
Indices: 107909--107962 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
107899 ATTTGTCAAA
* *
107909 TATATTTCTATACTGTCATT
1 TATATTTATATATTGTCATT
* *
107929 TAGATTTATATATTGTTTATT
1 TATATTTATATATTG-TCATT
107950 TATATTTAT-TATT
1 TATATTTATATATT
107963 CATATTTACC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (20 bp):
TATATTTATATATTGTCATT
Found at i:108300 original size:17 final size:17
Alignment explanation
Indices: 108274--108308 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
108264 ATTACTATAC
* *
108274 AATATGGATGGAATTTT
1 AATATAGATGAAATTTT
108291 AATATAGATGAAATTTT
1 AATATAGATGAAATTTT
108308 A
1 A
108309 TATTCACTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (17 bp):
AATATAGATGAAATTTT
Found at i:110883 original size:3 final size:3
Alignment explanation
Indices: 110870--110907 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
110860 TCCTCTCTGC
*
110870 TCT TCCT TCT TCT TCT TCT TAT TCT TCT TCT TCT TCT T
1 TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
110908 TTTTCCTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:120615 original size:61 final size:58
Alignment explanation
Indices: 120470--120630 Score: 198
Period size: 61 Copynumber: 2.7 Consensus size: 58
120460 TATATATATA
* * *
120470 TATAAAGACGAACGTCTCCTTCGAGACCGTTTTATTTCAAATCTAAACGATTCAATCGT
1 TATAAAGACGAACGTCTCCTTCGAGACCG-TTTATTTTAAAACTAAACGATCCAATCGT
* * * *
120529 TCTAAAAACGAATGTCTCCTTCGAGACCGTTTATTTTAAAACTTAAATGATCCAATATCGT
1 TATAAAGACGAACGTCTCCTTCGAGACCGTTTATTTTAAAAC-TAAACGATCC-A-ATCGT
*
120590 TATAAAGATGAACGTCTCCTTCGAGACCGTTT-TGTTTAAAA
1 TATAAAGACGAACGTCTCCTTCGAGACCGTTTAT-TTTAAAA
120631 GTTTTTGAAC
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
58 11 0.13
59 34 0.39
60 2 0.02
61 40 0.46
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.34
Consensus pattern (58 bp):
TATAAAGACGAACGTCTCCTTCGAGACCGTTTATTTTAAAACTAAACGATCCAATCGT
Found at i:120683 original size:43 final size:43
Alignment explanation
Indices: 120630--120712 Score: 157
Period size: 43 Copynumber: 1.9 Consensus size: 43
120620 TTTGTTTAAA
*
120630 AGTTTTTGAACGATTCAGTAAAGCAACAAAAAGGCTTTAACTG
1 AGTTTTTGAACGATTCAATAAAGCAACAAAAAGGCTTTAACTG
120673 AGTTTTTGAACGATTCAATAAAGCAACAAAAAGGCTTTAA
1 AGTTTTTGAACGATTCAATAAAGCAACAAAAAGGCTTTAA
120713 TTGCAAACAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (43 bp):
AGTTTTTGAACGATTCAATAAAGCAACAAAAAGGCTTTAACTG
Found at i:125537 original size:2 final size:2
Alignment explanation
Indices: 125530--125572 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
125520 ATAATTTAAA
* *
125530 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT CT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
125572 A
1 A
125573 ATTCATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:128603 original size:19 final size:20
Alignment explanation
Indices: 128565--128605 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
128555 TATTTTATTG
* *
128565 TACTATATTTTGTTAATTAA
1 TACTATATTTAGTAAATTAA
128585 TACTATATTTAG-AAATTAA
1 TACTATATTTAGTAAATTAA
128604 TA
1 TA
128606 ATTAACTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (20 bp):
TACTATATTTAGTAAATTAA
Found at i:137258 original size:31 final size:30
Alignment explanation
Indices: 137223--137308 Score: 122
Period size: 28 Copynumber: 2.9 Consensus size: 30
137213 AATTATACTC
*
137223 TTAAAAATATCCATGTGAAATTTTTTATATT
1 TTAAAAATAACCATGTGAAATTTTTT-TATT
*
137254 TTAAAAATAGCCATGTG--ATTTTTTTATT
1 TTAAAAATAACCATGTGAAATTTTTTTATT
*
137282 TTAAAAAAAACCATGTGAAATTTTTTT
1 TTAAAAATAACCATGTGAAATTTTTTT
137309 TATTGTCAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
28 19 0.38
29 7 0.14
30 8 0.16
31 16 0.32
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (30 bp):
TTAAAAATAACCATGTGAAATTTTTTTATT
Found at i:137309 original size:31 final size:31
Alignment explanation
Indices: 137223--137323 Score: 118
Period size: 31 Copynumber: 3.4 Consensus size: 31
137213 AATTATACTC
* * *
137223 TTAAAAATATCCATGTGAAATTTTTTATATT
1 TTAAAAAAAACCATGTGAAATTTTTTTTATT
* *
137254 TTAAAAATAGCCATGTG--A-TTTTTTTATT
1 TTAAAAAAAACCATGTGAAATTTTTTTTATT
137282 TTAAAAAAAACCATGTGAAATTTTTTTTATT
1 TTAAAAAAAACCATGTGAAATTTTTTTTATT
* *
137313 GTCAAAAAAAC
1 TTAAAAAAAAC
137324 TTTTTAGGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
28 24 0.39
29 1 0.02
30 1 0.02
31 35 0.57
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (31 bp):
TTAAAAAAAACCATGTGAAATTTTTTTTATT
Found at i:137568 original size:7 final size:7
Alignment explanation
Indices: 137556--137581 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
137546 ACTAGTATAA
137556 TTTTTAT
1 TTTTTAT
137563 TTTTTAT
1 TTTTTAT
137570 TTTTTAT
1 TTTTTAT
137577 TTTTT
1 TTTTT
137582 TGGTACCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:137999 original size:15 final size:14
Alignment explanation
Indices: 137963--138005 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
137953 TTATTAGAAG
137963 TATTATTAT-TAT-
1 TATTATTATATATA
137975 TATTATTATATATA
1 TATTATTATATATA
137989 TATATATTATATATA
1 TAT-TATTATATATA
138004 TA
1 TA
138006 GGAATAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.32
13 3 0.11
14 3 0.11
15 13 0.46
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATTATTATATATA
Done.