Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011607.1 Kokia drynarioides strain JFW-HI SEQ_126597, 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: 146773
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 217 characters in sequence are not A, C, G, or T
Found at i:332 original size:96 final size:96
Alignment explanation
Indices: 201--392 Score: 244
Period size: 96 Copynumber: 2.0 Consensus size: 96
191 AAAACTTTAA
* * ** **
201 AATCAAGGCAATATTCTTTCATTTCGAGTTTCGAAAATTTGTGCCTTAACTCACTAGGTGCAATT
1 AATCAAGGCAATATTCCTTCATTTCGAGTTCCGAAAATTTGCACCTTAACTCACTAGGTGCAACC
*
266 TTTCTTCAAATCGAAATAATCGAATACCCTT
66 TTTCTTCAAATCGAAATAATCAAATACCCTT
* * *
297 AATCAAGGCAATGTTTCCTT-ATCTTCGA-TTCCGAAATTTTGCACCTTAACTTACTAGGTGCAA
1 AATCAAGGCAAT-ATTCCTTCAT-TTCGAGTTCCGAAAATTTGCACCTTAACTCACTAGGTGCAA
* *
360 CCTTTCTTCAAATCGAGATAATCAAATATCCTT
64 CCTTTCTTCAAATCGAAATAATCAAATACCCTT
393 TTCGCAAAGA
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
96 72 0.88
97 10 0.12
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (96 bp):
AATCAAGGCAATATTCCTTCATTTCGAGTTCCGAAAATTTGCACCTTAACTCACTAGGTGCAACC
TTTCTTCAAATCGAAATAATCAAATACCCTT
Found at i:10794 original size:18 final size:17
Alignment explanation
Indices: 10770--10811 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
10760 AATTAAGATT
*
10770 TTATTTTGATATTT-TTA
1 TTATTTTAAT-TTTATTA
10787 TATATTTTAATTTTATTA
1 T-TATTTTAATTTTATTA
10805 TTATTTT
1 TTATTTT
10812 TTGGTGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTATTTTAATTTTATTA
Found at i:32613 original size:31 final size:31
Alignment explanation
Indices: 32577--32644 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
32567 CTTAATAGCC
* *
32577 CAGTGACTTAAATAAAAACTTTTGACTAGTT
1 CAGTGACTTAAATAAAAACTTTTAAATAGTT
* *
32608 TAGTGACTTAAATGAAAACTTTTAAATAGTT
1 CAGTGACTTAAATAAAAACTTTTAAATAGTT
32639 CAGTGA
1 CAGTGA
32645 TCAAATTGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (31 bp):
CAGTGACTTAAATAAAAACTTTTAAATAGTT
Found at i:37050 original size:18 final size:18
Alignment explanation
Indices: 37029--37068 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
37019 TATATATATT
37029 TAAAAAATTCAAAATAAA
1 TAAAAAATTCAAAATAAA
* **
37047 TAAATAATTTTAAATAAA
1 TAAAAAATTCAAAATAAA
37065 TAAA
1 TAAA
37069 TTATCAAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAAATTCAAAATAAA
Found at i:42158 original size:20 final size:19
Alignment explanation
Indices: 42135--42180 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
42125 TTACTTTTAC
* *
42135 AAAATATTTTTTTTATCTCA
1 AAAATAATTTTTTTA-CCCA
42155 AAAATAAATTTTTTTACCCA
1 AAAAT-AATTTTTTTACCCA
42175 AAAATA
1 AAAATA
42181 CTTTGGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 13 0.57
21 9 0.39
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAATAATTTTTTTACCCA
Found at i:42168 original size:21 final size:20
Alignment explanation
Indices: 42142--42180 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42132 TACAAAATAT
*
42142 TTTTTTTATCTCAAAAATAAA
1 TTTTTTTA-CCCAAAAATAAA
42163 TTTTTTTACCCAAAAATA
1 TTTTTTTACCCAAAAATA
42181 CTTTGGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTTTTTACCCAAAAATAAA
Found at i:43007 original size:22 final size:23
Alignment explanation
Indices: 42977--43025 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
42967 AGAGGTTGGG
42977 TTTAGGGTTTAAAA-TTTA-AAAA
1 TTTAGGG-TTAAAAGTTTATAAAA
* *
42999 TTTATGGTTAAAAGTTTATAAGA
1 TTTAGGGTTAAAAGTTTATAAAA
43022 TTTA
1 TTTA
43026 AAATTTAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 6 0.26
22 10 0.43
23 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (23 bp):
TTTAGGGTTAAAAGTTTATAAAA
Found at i:46918 original size:29 final size:32
Alignment explanation
Indices: 46853--46931 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 32
46843 TTAGAATTTG
*
46853 AATTAAAATGATA-AATTTTATAAATATTAGA
1 AATTAAATTGATAGAATTTTATAAATATTAGA
* *
46884 GATTAAATTGATAGAATTTT-TATAT-TTA-A
1 AATTAAATTGATAGAATTTTATAAATATTAGA
*
46913 AATTAAATCGATAGAATTT
1 AATTAAATTGATAGAATTT
46932 GTAAAGAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 18 0.43
30 3 0.07
31 15 0.36
32 6 0.14
ACGTcount: A:0.48, C:0.01, G:0.09, T:0.42
Consensus pattern (32 bp):
AATTAAATTGATAGAATTTTATAAATATTAGA
Found at i:55477 original size:25 final size:25
Alignment explanation
Indices: 55423--55469 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
55413 AGTTGGATCC
55423 AAATTAAATTCTAAAAAGATAATTT
1 AAATTAAATTCTAAAAAGATAATTT
*
55448 AAATTAAA-TCTAAACA-ATAATT
1 AAATTAAATTCTAAAAAGATAATT
55470 CTCTAATTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 7 0.33
25 8 0.38
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.34
Consensus pattern (25 bp):
AAATTAAATTCTAAAAAGATAATTT
Found at i:55556 original size:13 final size:13
Alignment explanation
Indices: 55535--55568 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
55525 ACAATATAAT
55535 AATAATAATCCTA
1 AATAATAATCCTA
*
55548 AATATTAATCCTA
1 AATAATAATCCTA
*
55561 AAAAATAA
1 AATAATAA
55569 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:56518 original size:21 final size:22
Alignment explanation
Indices: 56493--56540 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
56483 CTCAGACATA
*
56493 TTTTTGTC-TTTTTCTTCTCTT
1 TTTTTGTCAATTTTCTTCTCTT
* *
56514 TTTTT-TCAATTTTCTTTTTTT
1 TTTTTGTCAATTTTCTTCTCTT
56535 TTTTTG
1 TTTTTG
56541 GATTTTTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.79
Consensus pattern (22 bp):
TTTTTGTCAATTTTCTTCTCTT
Found at i:56547 original size:21 final size:21
Alignment explanation
Indices: 56493--56539 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
56483 CTCAGACATA
*
56493 TTTTTGTC-TTTTTCTTCTCT
1 TTTTTTTCATTTTTCTTCTCT
* *
56513 TTTTTTTCAATTTTCTT-TTT
1 TTTTTTTCATTTTTCTTCTCT
56533 TTTTTTT
1 TTTTTTT
56540 GGATTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.81
Consensus pattern (21 bp):
TTTTTTTCATTTTTCTTCTCT
Found at i:56593 original size:23 final size:24
Alignment explanation
Indices: 56544--56596 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
56534 TTTTTTGGAT
* *
56544 TTTTTTCGACTTTTTTTATTTTTA
1 TTTTTTCGACTTTTTTTATATTCA
56568 TTTTTT-GACTTTTTTCT-TATTCA
1 TTTTTTCGACTTTTTT-TATATTCA
56591 TTTTTT
1 TTTTTT
56597 AAATAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.75
Consensus pattern (24 bp):
TTTTTTCGACTTTTTTTATATTCA
Found at i:56596 original size:25 final size:22
Alignment explanation
Indices: 56542--56596 Score: 56
Period size: 25 Copynumber: 2.3 Consensus size: 22
56532 TTTTTTTTGG
56542 ATTTTTTTCGACTTTTTTTATT
1 ATTTTTTTCGACTTTTTTTATT
* *
56564 TTTATTTTTTGACTTTTTTCTTATT
1 ATT-TTTTTCGAC-TTTTT-TTATT
56589 CATTTTTT
1 -ATTTTTT
56597 AAATAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 2 0.08
23 8 0.31
24 5 0.19
25 9 0.35
26 2 0.08
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.75
Consensus pattern (22 bp):
ATTTTTTTCGACTTTTTTTATT
Found at i:57591 original size:21 final size:21
Alignment explanation
Indices: 57565--57620 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
57555 TAAATATACT
* *
57565 ATTTTTTTTTGAACTTTTCAA
1 ATTTTTTTTTAAAATTTTCAA
** *
57586 ATTTTTTTCAAAAATTTTTAA
1 ATTTTTTTTTAAAATTTTCAA
57607 ATTTTTTTTTAAAA
1 ATTTTTTTTTAAAA
57621 CATGAAAGCA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTTTTTTTTAAAATTTTCAA
Found at i:64309 original size:13 final size:13
Alignment explanation
Indices: 64288--64321 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
64278 ATATAATAAT
64288 AATAATAATCCTA
1 AATAATAATCCTA
*
64301 AATATTAATCCTA
1 AATAATAATCCTA
*
64314 AAAAATAA
1 AATAATAA
64322 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:71010 original size:16 final size:16
Alignment explanation
Indices: 70985--71016 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
70975 ATGTTAGAGC
70985 ATATAAATTTGAAATT
1 ATATAAATTTGAAATT
*
71001 ATATATATTTGAAATT
1 ATATAAATTTGAAATT
71017 TTTTCAAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
ATATAAATTTGAAATT
Found at i:71423 original size:2 final size:2
Alignment explanation
Indices: 71418--71446 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
71408 TATAGTTTTT
71418 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
71447 TTGCATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:72219 original size:14 final size:14
Alignment explanation
Indices: 72182--72226 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
72172 GAAAGGATTT
72182 AGAAT-AAAAATCG
1 AGAATAAAAAATCG
** *
72195 AGAATTGAAAATTG
1 AGAATAAAAAATCG
72209 AGAATAAAAAATCG
1 AGAATAAAAAATCG
72223 AGAA
1 AGAA
72227 AAATAATTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 5 0.19
14 21 0.81
ACGTcount: A:0.60, C:0.04, G:0.18, T:0.18
Consensus pattern (14 bp):
AGAATAAAAAATCG
Found at i:72237 original size:28 final size:27
Alignment explanation
Indices: 72178--72239 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
72168 CTATGAAAGG
*
72178 ATTT-AGAATAAAAATCGAGAATTGAAA
1 ATTTGAGAATAAAAATCGAGAA-TAAAA
72205 A-TTGAGAATAAAAAATCGAGAA-AAATA
1 ATTTGAGAAT-AAAAATCGAGAATAAA-A
72232 ATTTGAGA
1 ATTTGAGA
72240 GTTAAGAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 4 0.13
27 8 0.27
28 18 0.60
ACGTcount: A:0.56, C:0.03, G:0.16, T:0.24
Consensus pattern (27 bp):
ATTTGAGAATAAAAATCGAGAATAAAA
Found at i:77963 original size:155 final size:155
Alignment explanation
Indices: 77778--78152 Score: 732
Period size: 155 Copynumber: 2.4 Consensus size: 155
77768 AAATGTATGT
77778 TTGAAACATCATGTTAGGGTAATAATATTTAGTTTTTAAAGTTACCATTTATGATCATATTAATA
1 TTGAAACATCATGTTAGGGTAATAATATTTAGTTTTTAAAGTTACCATTTATGATCATATTAATA
*
77843 GCTATCATCAAAATCAATTATTACAAGTATAAAATTGAATAATTAATTTAATAAATTAATTTTAT
66 GCTATCATCAAAATCAATTATTACAAGTATAAAATTGAATAATTAATTCAATAAATTAATTTTAT
77908 CAAATCAATTATTACAAGTATAAAA
131 CAAATCAATTATTACAAGTATAAAA
77933 TTGAAACATCATGTTAGGGTAATAATATTTAGTTTTTAAAGTTACCATTTATGATCATATTAATA
1 TTGAAACATCATGTTAGGGTAATAATATTTAGTTTTTAAAGTTACCATTTATGATCATATTAATA
77998 GCTATCATCAAAATCAATTATTACAAGTATAAAATTGAATAATTAATTCAATAAATTAATTTTAT
66 GCTATCATCAAAATCAATTATTACAAGTATAAAATTGAATAATTAATTCAATAAATTAATTTTAT
78063 CAAATCAATTATTACAAGTATAAAA
131 CAAATCAATTATTACAAGTATAAAA
*
78088 TTGAAACATCATGTTAGGGTAATAATATTTAGTTTTTACAGTTACCATTTATGATCATATTAATA
1 TTGAAACATCATGTTAGGGTAATAATATTTAGTTTTTAAAGTTACCATTTATGATCATATTAATA
78153 TTTAGTTTCG
Statistics
Matches: 218, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
155 218 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (155 bp):
TTGAAACATCATGTTAGGGTAATAATATTTAGTTTTTAAAGTTACCATTTATGATCATATTAATA
GCTATCATCAAAATCAATTATTACAAGTATAAAATTGAATAATTAATTCAATAAATTAATTTTAT
CAAATCAATTATTACAAGTATAAAA
Found at i:79228 original size:18 final size:18
Alignment explanation
Indices: 79198--79233 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
79188 AAATTAAATA
79198 ATTATTTCAAATATCATT
1 ATTATTTCAAATATCATT
79216 ATTATTTCAAATATCATT
1 ATTATTTCAAATATCATT
79234 GTTTTTCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTATTTCAAATATCATT
Found at i:80333 original size:32 final size:32
Alignment explanation
Indices: 80287--80351 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
80277 TAAACTCAAA
*
80287 TTTTTACATTCTTTTTCCAAAAATAACCTACC
1 TTTTTACATACTTTTTCCAAAAATAACCTACC
80319 TTTTTACATACTTTTTCCAAAAATAACCTACC
1 TTTTTACATACTTTTTCCAAAAATAACCTACC
80351 T
1 T
80352 CCCTAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.43
Consensus pattern (32 bp):
TTTTTACATACTTTTTCCAAAAATAACCTACC
Found at i:89712 original size:2 final size:2
Alignment explanation
Indices: 89707--89746 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
89697 AAGAAAACAT
*
89707 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AC AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
89747 GGGGGAAGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:93825 original size:27 final size:27
Alignment explanation
Indices: 93795--93850 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
93785 TTCAGTGGTG
93795 TTAGAAAAAGTTGTTTCGAAACCCCAT
1 TTAGAAAAAGTTGTTTCGAAACCCCAT
93822 TTAGAAAAAGTTGTTTCGAAACCCCAT
1 TTAGAAAAAGTTGTTTCGAAACCCCAT
93849 TT
1 TT
93851 TTGTAAACCG
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:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (27 bp):
TTAGAAAAAGTTGTTTCGAAACCCCAT
Found at i:102292 original size:21 final size:21
Alignment explanation
Indices: 102267--102321 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
102257 ATGGTGCAGA
* *
102267 CTTCTACTGATACAAGTGACT
1 CTTCTACCGATACAAGCGACT
*
102288 GTTCTACCGATACAAGCGACT
1 CTTCTACCGATACAAGCGACT
102309 CTTCTACCGATAC
1 CTTCTACCGATAC
102322 TAAAAACTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (21 bp):
CTTCTACCGATACAAGCGACT
Found at i:102330 original size:21 final size:21
Alignment explanation
Indices: 102267--102331 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
102257 ATGGTGCAGA
* **
102267 CTTCTACTGATACAAGTGACT
1 CTTCTACCGATACAAGAAACT
* **
102288 GTTCTACCGATACAAGCGACT
1 CTTCTACCGATACAAGAAACT
102309 CTTCTACCGATACTAA-AAACT
1 CTTCTACCGATAC-AAGAAACT
102330 CT
1 CT
102332 AGAGAGCTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 35 0.95
22 2 0.05
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (21 bp):
CTTCTACCGATACAAGAAACT
Found at i:102513 original size:21 final size:21
Alignment explanation
Indices: 102475--102514 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
102465 TACCCTATAC
* * *
102475 TTCTACTGATACATGTATGGG
1 TTCTACCGAAACAAGTATGGG
102496 TTCTACCGAAACAAGTATG
1 TTCTACCGAAACAAGTATG
102515 CAGATTCACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (21 bp):
TTCTACCGAAACAAGTATGGG
Found at i:103049 original size:25 final size:25
Alignment explanation
Indices: 103021--103081 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
103011 TTTAGCTGAT
*
103021 ACGAGCCCAGACCAA-ATTAGCTCTC
1 ACGAGCCCAGA-AAAGATTAGCTCTC
* *
103046 ACGAGCCTA-AAAAGATTAGCTCTT
1 ACGAGCCCAGAAAAGATTAGCTCTC
103070 ACGAGCCCAGAA
1 ACGAGCCCAGAA
103082 TGGTTAACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 2 0.07
24 18 0.60
25 10 0.33
ACGTcount: A:0.36, C:0.30, G:0.18, T:0.16
Consensus pattern (25 bp):
ACGAGCCCAGAAAAGATTAGCTCTC
Found at i:106817 original size:15 final size:15
Alignment explanation
Indices: 106797--106828 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
106787 GGCCCTACAA
106797 GTTGGATGCATGTAG
1 GTTGGATGCATGTAG
106812 GTTGGATGCATGTAG
1 GTTGGATGCATGTAG
106827 GT
1 GT
106829 CTCACGGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.41, T:0.34
Consensus pattern (15 bp):
GTTGGATGCATGTAG
Found at i:107774 original size:16 final size:17
Alignment explanation
Indices: 107753--107785 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
107743 GAAAAGCTCG
107753 AATTTAAATC-AGAATA
1 AATTTAAATCGAGAATA
107769 AATTTAAATCGAGAATA
1 AATTTAAATCGAGAATA
107786 TACATGCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (17 bp):
AATTTAAATCGAGAATA
Found at i:108267 original size:2 final size:2
Alignment explanation
Indices: 108260--108285 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
108250 TCTATCTATC
108260 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
108286 ATTAAAGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:112220 original size:25 final size:25
Alignment explanation
Indices: 112183--112232 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
112173 TCGTTAAATA
112183 GACTTAGACCTAAGATATGTTTATC
1 GACTTAGACCTAAGATATGTTTATC
* * *
112208 GACTTGGATCTAAGGTATGTTTATC
1 GACTTAGACCTAAGATATGTTTATC
112233 TACTCGTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (25 bp):
GACTTAGACCTAAGATATGTTTATC
Found at i:112458 original size:2 final size:2
Alignment explanation
Indices: 112453--112489 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
112443 AAAACAGTTG
112453 AT AT AT AT 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 AT A
112490 ATAAAAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:117390 original size:19 final size:19
Alignment explanation
Indices: 117355--117409 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 19
117345 TTTTTAAAAA
*
117355 TATAAAT-TTTAGAATTTT
1 TATAAATATTTTGAATTTT
117373 TATAAATATTTTGAA-TTT
1 TATAAATATTTTGAATTTT
*
117391 TATAATTATTTTG-ATTTT
1 TATAAATATTTTGAATTTT
117409 T
1 T
117410 TTTTTGTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 1 0.03
18 26 0.79
19 6 0.18
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:117517 original size:18 final size:18
Alignment explanation
Indices: 117494--117528 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
117484 CGATATTTTA
117494 TTTGAGTTATTCGAATTT
1 TTTGAGTTATTCGAATTT
117512 TTTGAGTTATTCGAATT
1 TTTGAGTTATTCGAATT
117529 GTAAAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.54
Consensus pattern (18 bp):
TTTGAGTTATTCGAATTT
Found at i:121490 original size:40 final size:40
Alignment explanation
Indices: 121435--121515 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
121425 CCCCTATCTT
* *
121435 AACAAGTTCAAGATTCGTTTACTTGTTGAACAGAAGAATC
1 AACAAGTTCAAGATTCGTTCACTTGTTAAACAGAAGAATC
*
121475 AACAAGTTCAAGATTCGTTCACTTGTTAAAGAGAAGAATC
1 AACAAGTTCAAGATTCGTTCACTTGTTAAACAGAAGAATC
121515 A
1 A
121516 CTCATTTCAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (40 bp):
AACAAGTTCAAGATTCGTTCACTTGTTAAACAGAAGAATC
Found at i:123289 original size:20 final size:19
Alignment explanation
Indices: 123262--123306 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
123252 ATTATTATGT
*
123262 TTTA-ATATTTAAATTATAA
1 TTTATATATTAAAATTA-AA
123281 TTTATATATTAAAATTAAA
1 TTTATATATTAAAATTAAA
123300 TTT-TATA
1 TTTATATA
123307 AATAATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 9 0.38
20 11 0.46
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTATATATTAAAATTAAA
Found at i:128448 original size:17 final size:18
Alignment explanation
Indices: 128426--128464 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
128416 AGACATACTT
*
128426 TTTAAACA-TTAAATAAA
1 TTTAAACATTTAAAAAAA
*
128443 TTTAAATATTTAAAAAAA
1 TTTAAACATTTAAAAAAA
128461 TTTA
1 TTTA
128465 TTTAAAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTAAACATTTAAAAAAA
Found at i:129318 original size:370 final size:370
Alignment explanation
Indices: 128637--129383 Score: 1185
Period size: 370 Copynumber: 2.0 Consensus size: 370
128627 ACATTTAAAA
*
128637 TTGTATTAAAAGGTAATTTTTATTTTGAATTGAAAGGTAACTTTTGTTGAATAAAATTAATATAT
1 TTGTATTAAAAGGTAATTTTTATTTTGAATTAAAAGGTAACTTTTGTTGAATAAAATTAATATAT
* * * ** *
128702 ATCTTTATATATAATATTTTATTTTTTAATTGTTTAATAAGTCATTATTTTTGGATTTTTTTGTC
66 ATCTTTATATATAATATTTTATTTTTTAATTGTTTAATAAGTCATCACTTTTAGACGTTCTTGTC
* * *
128767 TACTTTTGTAGTACGCTTTTTAGTCTTACTTATACATGTAATCTTGCTTTTGCGAGTAATTTTAG
131 TACTCTTGTAGTACGCTATTTAGTCTTACTTATACATGTAATCTTGCTTTTGCAAGTAATTTTAG
*
128832 GGTTGGTTTTGTTGTCGTCTTCTCTAATTTGGTGGATGCTCGATTCTTTTACCGATTTATGTCTG
196 GGTTGGTTTTGTTGTCGTCTTCTCTAATTTGGTGGATGCTCGATTCTTTTACCGATTTATGTCTA
* *
128897 CCGTTTTAGACCATCCGAGGTTGATTTCTCTATTGTATTAAGTACTTGCAATCACTTCTAATATG
261 CCGTTTTAGACCATCCGAGGTTGATTTCCCTATTGTATTAAGTACTTGCAATAACTTCTAATATG
*
128962 TTGTGCTTGAGTTGTGACAGAGCCGATTGTCAACGTG-CTATAATG
326 TTGTGCTTGAGCTGTGACAGAGCCGATTGTCAACGTGTC-ATAATG
129007 TTGTATTAAAAGGTAATTTTTATTTTGAATTAAAAGGTAACTTTTGTTGAATAAAATTAATATAT
1 TTGTATTAAAAGGTAATTTTTATTTTGAATTAAAAGGTAACTTTTGTTGAATAAAATTAATATAT
* *
129072 ATCTTTATATATAATATTTTGTTTTTTCATTGTTTAATAAGTCATCACTTTTAGACGTTCTTGTC
66 ATCTTTATATATAATATTTTATTTTTTAATTGTTTAATAAGTCATCACTTTTAGACGTTCTTGTC
* * *
129137 TACTCTTGTAGTACGCTATTTAGTTTTACTTATGCATGTAGTCTTGCTTTTGCAAGTAATTTTAG
131 TACTCTTGTAGTACGCTATTTAGTCTTACTTATACATGTAATCTTGCTTTTGCAAGTAATTTTAG
*
129202 GGTTGGTTTTGTTG-CTGTCTTCTCTAGTTTGGTGGATGCTCGATTCTTTTACCGATTTATGTCT
196 GGTTGGTTTTGTTGTC-GTCTTCTCTAATTTGGTGGATGCTCGATTCTTTTACCGATTTATGTCT
* * * * * *
129266 ATCGTTTTAGATCATCCG-GGATTGATTTCCCTATTGTATTAAGTGCTTGCAATAATTTTTGATA
260 ACCGTTTTAGACCATCCGAGG-TTGATTTCCCTATTGTATTAAGTACTTGCAATAACTTCTAATA
* *
129330 TGTTGTGTTTGAGCTGTGACAGAGTCGATTGTCAACGTGTCATAATG
324 TGTTGTGCTTGAGCTGTGACAGAGCCGATTGTCAACGTGTCATAATG
*
129377 TTCTATT
1 TTGTATT
129384 GATGCTGAAG
Statistics
Matches: 345, Mismatches: 29, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
369 3 0.01
370 341 0.99
371 1 0.00
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (370 bp):
TTGTATTAAAAGGTAATTTTTATTTTGAATTAAAAGGTAACTTTTGTTGAATAAAATTAATATAT
ATCTTTATATATAATATTTTATTTTTTAATTGTTTAATAAGTCATCACTTTTAGACGTTCTTGTC
TACTCTTGTAGTACGCTATTTAGTCTTACTTATACATGTAATCTTGCTTTTGCAAGTAATTTTAG
GGTTGGTTTTGTTGTCGTCTTCTCTAATTTGGTGGATGCTCGATTCTTTTACCGATTTATGTCTA
CCGTTTTAGACCATCCGAGGTTGATTTCCCTATTGTATTAAGTACTTGCAATAACTTCTAATATG
TTGTGCTTGAGCTGTGACAGAGCCGATTGTCAACGTGTCATAATG
Found at i:129957 original size:11 final size:11
Alignment explanation
Indices: 129941--129980 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
129931 AAATATTAAC
*
129941 TTAAAATCTAT
1 TTAAAATATAT
129952 TTAAAATATAAT
1 TTAAAATAT-AT
129964 TTAAAAATATAT
1 TT-AAAATATAT
129976 TTAAA
1 TTAAA
129981 TTAGTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 11 0.42
12 8 0.31
13 7 0.27
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (11 bp):
TTAAAATATAT
Found at i:129967 original size:12 final size:12
Alignment explanation
Indices: 129930--129980 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
129920 GCCCAAATAA
*
129930 AAAATATTAACTT
1 AAAATA-TAATTT
*
129943 AAAATCT-ATTT
1 AAAATATAATTT
129954 AAAATATAATTT
1 AAAATATAATTT
129966 AAAA-ATATATTT
1 AAAATATA-ATTT
129978 AAA
1 AAA
129981 TTAGTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
11 12 0.36
12 16 0.48
13 5 0.15
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (12 bp):
AAAATATAATTT
Found at i:129970 original size:24 final size:24
Alignment explanation
Indices: 129930--129980 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
129920 GCCCAAATAA
*
129930 AAAATATTAACTTAAAATCTATTT
1 AAAATATTAACTTAAAATATATTT
*
129954 AAAATA-TAATTTAAAAATATATTT
1 AAAATATTAACTT-AAAATATATTT
129978 AAA
1 AAA
129981 TTAGTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAATATTAACTTAAAATATATTT
Found at i:130451 original size:19 final size:19
Alignment explanation
Indices: 130429--130473 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
130419 TTGTTTATAT
130429 TTTTAAAT-ATTTATTTTAA
1 TTTTAAATAATTTA-TTTAA
130448 TTTT-AATAATTTATTTAA
1 TTTTAAATAATTTATTTAA
130466 TTTATAAA
1 TTT-TAAA
130474 AATAATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 11 0.48
19 10 0.43
20 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTAAATAATTTATTTAA
Found at i:146095 original size:17 final size:17
Alignment explanation
Indices: 146070--146117 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
146060 CTGAGCCCAA
* *
146070 TAAACTTAAATTTATTT
1 TAAAATTAAATTTATTC
*
146087 TAAAATTAAGTTTATTC
1 TAAAATTAAATTTATTC
*
146104 TAAATTTAAATTTA
1 TAAAATTAAATTTA
146118 GCTGAAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (17 bp):
TAAAATTAAATTTATTC
Done.