Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013287.1 Kokia drynarioides strain JFW-HI SEQ_128308, 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: 67398
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Found at i:164 original size:20 final size:22
Alignment explanation
Indices: 139--178 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
129 GATCCCCAAC
*
139 AATAATTAAA-AAAT-ATAACT
1 AATAATCAAATAAATCATAACT
159 AATAATCAAATAAATCATAA
1 AATAATCAAATAAATCATAA
179 AAATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 4 0.24
22 4 0.24
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (22 bp):
AATAATCAAATAAATCATAACT
Found at i:3792 original size:19 final size:20
Alignment explanation
Indices: 3767--3816 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
3757 TATGTAAAAC
3767 GAAATGATAAAATCAATATA
1 GAAATGATAAAATCAATATA
*
3787 -AAATGATAAAATCAATGTA
1 GAAATGATAAAATCAATATA
*
3806 GAAATGCTAAA
1 GAAATGATAAA
3817 GTTCTATTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.24
Consensus pattern (20 bp):
GAAATGATAAAATCAATATA
Found at i:6083 original size:26 final size:26
Alignment explanation
Indices: 6047--6104 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
6037 TTGTGTTACT
6047 TAATTTCTTTTGCGGCTTAGCAGCTC
1 TAATTTCTTTTGCGGCTTAGCAGCTC
6073 TAATTTCTTTTGCGGCTTAGCAGCTC
1 TAATTTCTTTTGCGGCTTAGCAGCTC
6099 TCAATT
1 T-AATT
6105 GTTGTTGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 27 0.87
27 4 0.13
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.43
Consensus pattern (26 bp):
TAATTTCTTTTGCGGCTTAGCAGCTC
Found at i:6112 original size:27 final size:26
Alignment explanation
Indices: 6047--6112 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
6037 TTGTGTTACT
*
6047 TAATTTCTTTTGCGGCTTAGCAGCTC
1 TAATTTCTGTTGCGGCTTAGCAGCTC
*
6073 TAATTTCTTTTGCGGCTTAGCAGCTC
1 TAATTTCTGTTGCGGCTTAGCAGCTC
6099 TCAATTGT-TGTTGC
1 T-AATT-TCTGTTGC
6113 CTTCTTGATG
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
26 27 0.73
27 9 0.24
28 1 0.03
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (26 bp):
TAATTTCTGTTGCGGCTTAGCAGCTC
Found at i:8727 original size:37 final size:37
Alignment explanation
Indices: 8686--8765 Score: 133
Period size: 37 Copynumber: 2.2 Consensus size: 37
8676 ATACGTACTA
*
8686 AAGTGCTCTAACCTACACTCCAAAATGAAATGCATCG
1 AAGTGCTCCAACCTACACTCCAAAATGAAATGCATCG
* *
8723 AAGTGATCCAACCTACACTCCAAAATGAAATGCATTG
1 AAGTGCTCCAACCTACACTCCAAAATGAAATGCATCG
8760 AAGTGC
1 AAGTGC
8766 CATAATATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.39, C:0.25, G:0.15, T:0.21
Consensus pattern (37 bp):
AAGTGCTCCAACCTACACTCCAAAATGAAATGCATCG
Found at i:11925 original size:2 final size:2
Alignment explanation
Indices: 11918--11947 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11908 CATTTCAAAT
11918 TA TA 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 TA TA
11948 AACAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23546 original size:15 final size:14
Alignment explanation
Indices: 23526--23565 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
23516 AAATTAATAA
23526 TTTAATTTAAATATT
1 TTTAATTTAAAT-TT
*
23541 TTTAATATAAATTT
1 TTTAATTTAAATTT
23555 TTTAACTTTAA
1 TTTAA-TTTAA
23566 CCCTTCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATTTAAATTT
Found at i:24131 original size:15 final size:15
Alignment explanation
Indices: 24111--24164 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
24101 ATACTGCAAA
24111 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
24126 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
24143 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
24160 ATATT
1 ATATT
24165 ACTATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:27311 original size:29 final size:29
Alignment explanation
Indices: 27178--27372 Score: 173
Period size: 30 Copynumber: 6.6 Consensus size: 29
27168 AGAAGGTCCT
*
27178 TAAA-TTTTCCAAAATTCATATTTTAACCCC
1 TAAACTTTTCCAAAATT-ACATTTTAA-CCC
* *
27208 TAAACTTCTCCAAAATTATATTTTAACCCC
1 TAAACTTTTCCAAAATTACATTTTAA-CCC
* * * *
27238 CAAAATATTCTAAAATTACATTTTAACCC
1 TAAACTTTTCCAAAATTACATTTTAACCC
* *
27267 TCAAACTTTTCTAAAATTACATTTTGACCC
1 T-AAACTTTTCCAAAATTACATTTTAACCC
* *
27297 TAAACTTTTACAAAATCACATTTTAA-CC
1 TAAACTTTTCCAAAATTACATTTTAACCC
*
27325 TAAAACTTCTT-AAAAATCT-CATTTTAACCC
1 T-AAACTT-TTCCAAAAT-TACATTTTAACCC
* *
27355 CAAACTTCTCCAAAATTA
1 TAAACTTTTCCAAAATTA
27373 TGATTTTACC
Statistics
Matches: 137, Mismatches: 20, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
28 5 0.04
29 54 0.39
30 67 0.49
31 11 0.08
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (29 bp):
TAAACTTTTCCAAAATTACATTTTAACCC
Found at i:27348 original size:58 final size:59
Alignment explanation
Indices: 27187--27370 Score: 155
Period size: 58 Copynumber: 3.1 Consensus size: 59
27177 TTAAATTTTC
* * * * *
27187 CAAAATTCATATTTTAACCCCT-AAACTTCTCCAAAATTATATTTTAACCCCCAAAATAT-T-
1 CAAAA-TCACATTTTAA-CCCTAAAACTTTTCAAAAATTACATTTTAA-CCCCAAACT-TCTA
* * * * * *
27247 CTAAAATTACATTTTAACCCTCAAACTTTTCTAAAATTACATTTTGACCCTAAACTTTTA
1 C-AAAATCACATTTTAACCCTAAAACTTTTCAAAAATTACATTTTAACCCCAAACTTCTA
*
27307 CAAAATCACATTTTAA-CCTAAAACTTCTT-AAAAATCT-CATTTTAACCCCAAACTTCTC
1 CAAAATCACATTTTAACCCTAAAACTT-TTCAAAAAT-TACATTTTAACCCCAAACTTCTA
27365 CAAAAT
1 CAAAAT
27371 TATGATTTTA
Statistics
Matches: 103, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
58 38 0.37
59 29 0.28
60 32 0.31
61 4 0.04
ACGTcount: A:0.40, C:0.24, G:0.01, T:0.35
Consensus pattern (59 bp):
CAAAATCACATTTTAACCCTAAAACTTTTCAAAAATTACATTTTAACCCCAAACTTCTA
Found at i:27409 original size:30 final size:29
Alignment explanation
Indices: 27344--27486 Score: 112
Period size: 30 Copynumber: 4.9 Consensus size: 29
27334 TTAAAAATCT
* * *
27344 CATTTTAACCCCAAACT-TCTCCAAAATTAT
1 CATTTTACCCCCAAA-TATC-CAAAAATTAC
* *
27374 GATTTTACCCTCAAATATCCAAAAAAATT-C
1 CATTTTACCCCCAAATATCC--AAAAATTAC
* * *
27404 CATTTT-TCCTCGAATATCCAAAAATTAC
1 CATTTTACCCCCAAATATCCAAAAATTAC
* *
27432 CATTTTTACCCCCGAACATCCAAAAATTAC
1 CA-TTTTACCCCCAAATATCCAAAAATTAC
* *
27462 CATTTTGCCCCCAAATTTCCAAAAA
1 CATTTTACCCCCAAATATCCAAAAA
27487 CCCCATTTTC
Statistics
Matches: 92, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
27 7 0.08
28 3 0.03
29 36 0.39
30 40 0.43
31 6 0.07
ACGTcount: A:0.38, C:0.29, G:0.03, T:0.31
Consensus pattern (29 bp):
CATTTTACCCCCAAATATCCAAAAATTAC
Found at i:27569 original size:29 final size:30
Alignment explanation
Indices: 27420--27567 Score: 108
Period size: 30 Copynumber: 5.0 Consensus size: 30
27410 TCCTCGAATA
* * **
27420 TCCAAAAATTACCATTTTTACCCCCGAACA
1 TCCAAAAATTACCATTTTGACCCCCAAATT
27450 TCCAAAAATTACCATTTTG-CCCCCAAATT
1 TCCAAAAATTACCATTTTGACCCCCAAATT
** * * *
27479 TCCAAAAA-CCCCATTTTCAACCTCAAATTT
1 TCCAAAAATTACCATTTTGACCCCCAAA-TT
* **
27509 TCCAAAAGTTTA--ATTTT-AATCCCAAATTT
1 TCCAAAA-ATTACCATTTTGACCCCCAAA-TT
* *
27538 TCCAAAAATTTCAATTTTGACCCCCAAATT
1 TCCAAAAATTACCATTTTGACCCCCAAATT
27568 CCTCGAAAAT
Statistics
Matches: 93, Mismatches: 18, Indels: 14
0.74 0.14 0.11
Matches are distributed among these distances:
28 9 0.10
29 38 0.41
30 39 0.42
31 7 0.08
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.32
Consensus pattern (30 bp):
TCCAAAAATTACCATTTTGACCCCCAAATT
Found at i:32435 original size:14 final size:16
Alignment explanation
Indices: 32416--32447 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
32406 TACACCTGTT
32416 TTGTTT-ATA-TTTAA
1 TTGTTTAATAGTTTAA
32430 TTGTTTAATAGTTTAA
1 TTGTTTAATAGTTTAA
32446 TT
1 TT
32448 TGAGTGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 3 0.19
16 7 0.44
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.62
Consensus pattern (16 bp):
TTGTTTAATAGTTTAA
Found at i:42449 original size:65 final size:65
Alignment explanation
Indices: 42375--42505 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
42365 TTAGATCTGG
42375 ATCTCAAGTAATACCACTCCATGATAGACTTACACTTACTCAAAATATGAAAACTTTCTTCCAAT
1 ATCTCAAGTAATACCACTCCATGATAGACTTACACTTACTCAAAATATGAAAACTTTCTTCCAAT
42440 ATCTCAAGTAATACCACTCCATGATAGACTTACACTTACTCAAAATATGAAAACTTTCTTCCAAT
1 ATCTCAAGTAATACCACTCCATGATAGACTTACACTTACTCAAAATATGAAAACTTTCTTCCAAT
42505 A
1 A
42506 CATCTACATC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (65 bp):
ATCTCAAGTAATACCACTCCATGATAGACTTACACTTACTCAAAATATGAAAACTTTCTTCCAAT
Found at i:50164 original size:30 final size:31
Alignment explanation
Indices: 50095--50188 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 31
50085 AGATTTTTAA
* *
50095 AAAGGGTTTAATTAAAATTTTCAAAATTTTT
1 AAAGGGCTTAATTAAAATTTTCAAAATATTT
50126 AAAGGGCTTAATTAAAATTTTCAACAA-ATTT
1 AAAGGGCTTAATTAAAATTTTCAA-AATATTT
* * *
50157 -GAGGGCTTAAGT-AAATTTTCAATAATTTTT
1 AAAGGGCTTAATTAAAATTTTCAA-AATATTT
50187 AA
1 AA
50189 GGGTTTATTG
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
29 12 0.23
30 13 0.25
31 26 0.49
32 2 0.04
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.40
Consensus pattern (31 bp):
AAAGGGCTTAATTAAAATTTTCAAAATATTT
Found at i:50591 original size:11 final size:12
Alignment explanation
Indices: 50565--50604 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
50555 ATTTTATGCT
50565 TTTTAATATTTTA
1 TTTTAATA-TTTA
50578 TTTTAATA-TTA
1 TTTTAATATTTA
50589 TTTTAATAATTTA
1 TTTTAAT-ATTTA
50602 TTT
1 TTT
50605 AATCAACCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.40
12 1 0.04
13 14 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTAATATTTA
Found at i:54320 original size:36 final size:36
Alignment explanation
Indices: 54264--54339 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
54254 GACACAAAAA
* * *
54264 ATTTATAGTGATTTAGCCCCAAATGTCTACTCCACT
1 ATTTAGAGTGATTTAACCCCAAATGCCTACTCCACT
* *
54300 ATTTAGAGTGGTTTAACCCCAAATGCCTACTCCATT
1 ATTTAGAGTGATTTAACCCCAAATGCCTACTCCACT
54336 ATTT
1 ATTT
54340 TAGCTTTCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.37
Consensus pattern (36 bp):
ATTTAGAGTGATTTAACCCCAAATGCCTACTCCACT
Found at i:56973 original size:16 final size:16
Alignment explanation
Indices: 56952--56983 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
56942 GATTTTTTTT
56952 GCCCAAGCTCGGCTCG
1 GCCCAAGCTCGGCTCG
56968 GCCCAAGCTCGGCTCG
1 GCCCAAGCTCGGCTCG
56984 ACCCGATTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.44, G:0.31, T:0.12
Consensus pattern (16 bp):
GCCCAAGCTCGGCTCG
Found at i:57069 original size:33 final size:34
Alignment explanation
Indices: 57026--57165 Score: 133
Period size: 33 Copynumber: 4.0 Consensus size: 34
57016 AAAAATTATA
57026 TTGTTGTTTTGGTGCT-TTTTTTTACTGTTTTGG
1 TTGTTGTTTTGGTGCTATTTTTTTACTGTTTTGG
* *
57059 TTGTTTTTTTGCTGTTTTGGTGTTATTTTTTTACTGTTTTAG
1 TTG------T--TGTTTTGGTGCTATTTTTTTACTGTTTTGG
** *
57101 -TGTTGTTTTTTTGCTA-TTTTTTACTGTTTTGA
1 TTGTTGTTTTGGTGCTATTTTTTTACTGTTTTGG
*
57133 TTGTTGTTTTGATGCTATTTTTTTACTGTTTTG
1 TTGTTGTTTTGGTGCTATTTTTTTACTGTTTTG
57166 ATGCTATTAT
Statistics
Matches: 87, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
32 14 0.16
33 27 0.31
34 15 0.17
35 1 0.01
39 1 0.01
41 13 0.15
42 16 0.18
ACGTcount: A:0.07, C:0.06, G:0.19, T:0.68
Consensus pattern (34 bp):
TTGTTGTTTTGGTGCTATTTTTTTACTGTTTTGG
Found at i:57087 original size:22 final size:22
Alignment explanation
Indices: 57030--57112 Score: 109
Period size: 22 Copynumber: 3.9 Consensus size: 22
57020 ATTATATTGT
*
57030 TGTTTTGGTGCT-TTTTTTTAC
1 TGTTTTGGTGTTGTTTTTTTAC
*
57051 TGTTTT-G-GTTGTTTTTTTGC
1 TGTTTTGGTGTTGTTTTTTTAC
*
57071 TGTTTTGGTGTTATTTTTTTAC
1 TGTTTTGGTGTTGTTTTTTTAC
*
57093 TGTTTTAGTGTTGTTTTTTT
1 TGTTTTGGTGTTGTTTTTTT
57113 GCTATTTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
19 2 0.04
20 15 0.28
21 7 0.13
22 29 0.55
ACGTcount: A:0.05, C:0.05, G:0.20, T:0.70
Consensus pattern (22 bp):
TGTTTTGGTGTTGTTTTTTTAC
Found at i:57154 original size:24 final size:23
Alignment explanation
Indices: 57127--57398 Score: 137
Period size: 24 Copynumber: 11.7 Consensus size: 23
57117 TTTTTTACTG
*
57127 TTTTGATTGTTGTTTTGATGCTAT
1 TTTTG-TTGTTGTTTTGTTGCTAT
** *
57151 TTTT-TTACTGTTTTGATGCTATTAT
1 TTTTGTTGTTGTTTTGTTGC---TAT
* *
57176 TTTTGTTGTTATTTTTGTTACTAT
1 TTTTGTTGTT-GTTTTGTTGCTAT
** *
57200 TTTT-TTACTGTTTTGATGCTGTTAT
1 TTTTGTTGTTGTTTTG-T--TGCTAT
*
57225 TTTTGTTGTTATTTTTGTTGCTAT
1 TTTTGTTGTT-GTTTTGTTGCTAT
* *
57249 TTTTGCTGTTATTTTTGTTGCTAT
1 TTTTGTTGTT-GTTTTGTTGCTAT
* * * *
57273 TCTTGTTGCT-ATTT-TTGTTAT
1 TTTTGTTGTTGTTTTGTTGCTAT
* **
57294 TTTTGTTGTTG-TTTGCTATTAT
1 TTTTGTTGTTGTTTTGTTGCTAT
* *
57316 TTTTGCTGTTATTTTTGTTGCTAT
1 TTTTGTTGTT-GTTTTGTTGCTAT
* * *
57340 TCTTGTTGTT-ATTT-TTGTTAT
1 TTTTGTTGTTGTTTTGTTGCTAT
* *
57361 TTTTGTTGTTG-TTTGCTGTTAT
1 TTTTGTTGTTGTTTTGTTGCTAT
* *
57383 TTTTGCTGTTATTTTG
1 TTTTGTTGTTGTTTTG
57399 GTTGTTTGGA
Statistics
Matches: 192, Mismatches: 39, Indels: 35
0.72 0.15 0.13
Matches are distributed among these distances:
21 35 0.18
22 53 0.28
23 8 0.04
24 62 0.32
25 15 0.08
26 7 0.04
27 12 0.06
ACGTcount: A:0.10, C:0.06, G:0.17, T:0.67
Consensus pattern (23 bp):
TTTTGTTGTTGTTTTGTTGCTAT
Found at i:57162 original size:22 final size:22
Alignment explanation
Indices: 57030--57228 Score: 102
Period size: 22 Copynumber: 8.9 Consensus size: 22
57020 ATTATATTGT
*
57030 TGTTTTGGTGCT-TTTTTTTAC
1 TGTTTTGATGCTATTTTTTTAC
* * *
57051 TGTTTTG--GTTGTTTTTTTGC
1 TGTTTTGATGCTATTTTTTTAC
* *
57071 TGTTTTGGTGTTATTTTTTTAC
1 TGTTTTGATGCTATTTTTTTAC
* * *
57093 TGTTTT-AGTGTTGTTTTTTTGC
1 TGTTTTGA-TGCTATTTTTTTAC
* * * * * **
57115 TATTTT-TTACTGTTTTGATTGT
1 TGTTTTGATGCTATTTT-TTTAC
57137 TGTTTTGATGCTATTTTTTTAC
1 TGTTTTGATGCTATTTTTTTAC
**
57159 TGTTTTGATGCTATTATTTTTGT
1 TGTTTTGATGCTATT-TTTTTAC
* *
57182 TGTTATTTTTGTTACTATTTTTTTAC
1 TG----TTTTGATGCTATTTTTTTAC
*
57208 TGTTTTGATGCTGTTATTTTT
1 TGTTTTGATGCTATT-TTTTT
57229 GTTGTTATTT
Statistics
Matches: 137, Mismatches: 29, Indels: 22
0.73 0.15 0.12
Matches are distributed among these distances:
19 2 0.01
20 15 0.11
21 14 0.10
22 69 0.50
23 19 0.14
26 7 0.05
27 11 0.08
ACGTcount: A:0.10, C:0.06, G:0.17, T:0.67
Consensus pattern (22 bp):
TGTTTTGATGCTATTTTTTTAC
Found at i:57189 original size:12 final size:12
Alignment explanation
Indices: 57172--57404 Score: 182
Period size: 12 Copynumber: 20.2 Consensus size: 12
57162 TTTGATGCTA
57172 TTATTTTTGTTG
1 TTATTTTTGTTG
*
57184 TTATTTTTGTTA
1 TTATTTTTGTTG
* *
57196 CTATTTTTTTACTG
1 TTATTTTTGT--TG
** *
57210 TT-TTGATGCTG
1 TTATTTTTGTTG
57221 TTATTTTTGTTG
1 TTATTTTTGTTG
57233 TTATTTTTGTTG
1 TTATTTTTGTTG
* *
57245 CTATTTTTGCTG
1 TTATTTTTGTTG
57257 TTATTTTTGTTG
1 TTATTTTTGTTG
* *
57269 CTATTCTTGTTG
1 TTATTTTTGTTG
*
57281 CTA--TTT-TTG
1 TTATTTTTGTTG
57290 TTATTTTTGTTG
1 TTATTTTTGTTG
* * *
57302 -T-TGTTTGCTA
1 TTATTTTTGTTG
*
57312 TTATTTTTGCTG
1 TTATTTTTGTTG
57324 TTATTTTTGTTG
1 TTATTTTTGTTG
* *
57336 CTATTCTTGTTG
1 TTATTTTTGTTG
57348 TTA--TTT-TTG
1 TTATTTTTGTTG
57357 TTATTTTTGTTG
1 TTATTTTTGTTG
* *
57369 -T-TGTTTGCTG
1 TTATTTTTGTTG
*
57379 TTATTTTTGCTG
1 TTATTTTTGTTG
*
57391 TTATTTTGGTTG
1 TTATTTTTGTTG
57403 TT
1 TT
57405 TGGATATTAT
Statistics
Matches: 173, Mismatches: 35, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
9 11 0.06
10 17 0.10
11 14 0.08
12 126 0.73
13 3 0.02
14 2 0.01
ACGTcount: A:0.09, C:0.06, G:0.17, T:0.68
Consensus pattern (12 bp):
TTATTTTTGTTG
Found at i:57200 original size:49 final size:49
Alignment explanation
Indices: 57147--57252 Score: 194
Period size: 49 Copynumber: 2.2 Consensus size: 49
57137 TGTTTTGATG
57147 CTATTTTTTTACTGTTTTGATGCTATTATTTTTGTTGTTATTTTTGTTA
1 CTATTTTTTTACTGTTTTGATGCTATTATTTTTGTTGTTATTTTTGTTA
* *
57196 CTATTTTTTTACTGTTTTGATGCTGTTATTTTTGTTGTTATTTTTGTTG
1 CTATTTTTTTACTGTTTTGATGCTATTATTTTTGTTGTTATTTTTGTTA
57245 CTATTTTT
1 CTATTTTT
57253 GCTGTTATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 55 1.00
ACGTcount: A:0.12, C:0.07, G:0.13, T:0.68
Consensus pattern (49 bp):
CTATTTTTTTACTGTTTTGATGCTATTATTTTTGTTGTTATTTTTGTTA
Found at i:57329 original size:67 final size:67
Alignment explanation
Indices: 57167--57402 Score: 294
Period size: 67 Copynumber: 3.4 Consensus size: 67
57157 ACTGTTTTGA
* * * * *
57167 TGCTATTATTTTTGTTGTTATTTTTGTTACTATT-TTTTTACTGTTTTGATGCTGTTATTTTTGT
1 TGCTATTATTTTTGCTGTTATTTTTGTTGCTATTCTTGTTGCT-ATTT--T--TGTTATTTTTGT
*
57231 TGTTATTTT
61 TG-T-TGTT
* **
57240 TGTTGCTATTTTTGCTGTTATTTTTGTTGCTATTCTTGTTGCTATTTTTGTTATTTTTGTTGTTG
1 TGCTATTATTTTTGCTGTTATTTTTGTTGCTATTCTTGTTGCTATTTTTGTTATTTTTGTTGTTG
57305 TT
66 TT
*
57307 TGCTATTATTTTTGCTGTTATTTTTGTTGCTATTCTTGTTGTTATTTTTGTTATTTTTGTTGTTG
1 TGCTATTATTTTTGCTGTTATTTTTGTTGCTATTCTTGTTGCTATTTTTGTTATTTTTGTTGTTG
57372 TT
66 TT
* *
57374 TGCTGTTATTTTTGCTGTTATTTTGGTTG
1 TGCTATTATTTTTGCTGTTATTTTTGTTG
57403 TTTGGATATT
Statistics
Matches: 147, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
67 93 0.63
68 1 0.01
69 14 0.10
71 1 0.01
73 32 0.22
74 6 0.04
ACGTcount: A:0.09, C:0.06, G:0.17, T:0.67
Consensus pattern (67 bp):
TGCTATTATTTTTGCTGTTATTTTTGTTGCTATTCTTGTTGCTATTTTTGTTATTTTTGTTGTTG
TT
Found at i:57615 original size:38 final size:38
Alignment explanation
Indices: 57533--57616 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 38
57523 TATAAAAAAA
* * * *
57533 TTTTTAATGTATTTTAAATTTGTTTATTTTTTAATGTT
1 TTTTTAATGTATTTTAAATTTATTTATGTATTAATGAT
57571 TGTTTTAATGT-TTTTAAATTTATTTGATGTATTATAT-AT
1 T-TTTTAATGTATTTTAAATTTATTT-ATGTATTA-ATGAT
57610 TTTTTAA
1 TTTTTAA
57617 ATTTGTTGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
38 20 0.51
39 17 0.44
40 2 0.05
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.65
Consensus pattern (38 bp):
TTTTTAATGTATTTTAAATTTATTTATGTATTAATGAT
Found at i:59605 original size:45 final size:45
Alignment explanation
Indices: 59541--59741 Score: 190
Period size: 45 Copynumber: 4.5 Consensus size: 45
59531 AAACTACATG
*
59541 TACAGGAAACAAGAAGTTTCCCTGAAGCCGGAAACAGGCTATGGA
1 TACAGGAAACAAGAAGTTTCCCTGAAGCCGGAAACAGGATATGGA
* * * * *
59586 TACAGGAAACAAGAAGTTTCCATGGAGCTGGAAACATGCTATGGA
1 TACAGGAAACAAGAAGTTTCCCTGAAGCCGGAAACAGGATATGGA
* * * ** * *
59631 TACAGGAAACAAGGAGCTTCCTTGGTGTC--AAACAGGATATAGA
1 TACAGGAAACAAGAAGTTTCCCTGAAGCCGGAAACAGGATATGGA
* * * ** *
59674 TATAGGAAACAAGAAGTTTCCTTGATGCTAGCAACAGGATATGGA
1 TACAGGAAACAAGAAGTTTCCCTGAAGCCGGAAACAGGATATGGA
* * *
59719 CAGAGGAAACAAGATGTTTCCCT
1 TACAGGAAACAAGAAGTTTCCCT
59742 AATACAGGGT
Statistics
Matches: 129, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
43 34 0.26
45 95 0.74
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.20
Consensus pattern (45 bp):
TACAGGAAACAAGAAGTTTCCCTGAAGCCGGAAACAGGATATGGA
Found at i:62584 original size:15 final size:15
Alignment explanation
Indices: 62566--62595 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
62556 ATAAAAAAAC
62566 CTGAAATAAATACTT
1 CTGAAATAAATACTT
62581 CTGAAATAAATACTT
1 CTGAAATAAATACTT
62596 GACAAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (15 bp):
CTGAAATAAATACTT
Found at i:63244 original size:21 final size:21
Alignment explanation
Indices: 63222--63279 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
63212 AAATATCAAT
63222 TTTGAATTTTTTTATAAA-TA
1 TTTGAATTTTTTTATAAATTA
* * *
63242 TTTAAAATTTTTGA-AAATTAA
1 TTTGAATTTTTTTATAAATT-A
*
63263 TTTGAATTATTTTATAA
1 TTTGAATTTTTTTATAA
63280 TTTTTGTTGA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
19 3 0.11
20 12 0.43
21 11 0.39
22 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTGAATTTTTTTATAAATTA
Found at i:67202 original size:25 final size:25
Alignment explanation
Indices: 67163--67248 Score: 68
Period size: 25 Copynumber: 3.4 Consensus size: 25
67153 AGACAATGAA
* *
67163 GATATTCTGTCTGGCTCGTAAGAGC
1 GATATTTTGTTTGGCTCGTAAGAGC
* *
67188 GATATTTTGTTTGGCTAGT--GGGC
1 GATATTTTGTTTGGCTCGTAAGAGC
*
67211 GATATTTTGAATTCTGGCTCATAAGAGC
1 GATATTTTG--TT-TGGCTCGTAAGAGC
* *
67239 GTTAATTTGT
1 GATATTTTGT
67249 CTGGGCTCAT
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
23 12 0.26
25 18 0.38
26 7 0.15
28 10 0.21
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.40
Consensus pattern (25 bp):
GATATTTTGTTTGGCTCGTAAGAGC
Done.