Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014293.1 Kokia drynarioides strain JFW-HI SEQ_129328, 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: 43242
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:3527 original size:29 final size:29
Alignment explanation
Indices: 3485--3542 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
3475 CTCTTCACAA
3485 CACTGAATAATATATTAAAAGAAGATCAT
1 CACTGAATAATATATTAAAAGAAGATCAT
3514 CACTGAATAATATATTAAAAGAAGATCAT
1 CACTGAATAATATATTAAAAGAAGATCAT
3543 AGATATATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (29 bp):
CACTGAATAATATATTAAAAGAAGATCAT
Found at i:4743 original size:17 final size:17
Alignment explanation
Indices: 4707--4745 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
4697 TAATCTTATC
* **
4707 AATTTAATATTTTATGT
1 AATTTAAAATTTTAAAT
4724 AATTTAAAATTTTAAAT
1 AATTTAAAATTTTAAAT
4741 AATTT
1 AATTT
4746 TATATAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
AATTTAAAATTTTAAAT
Found at i:5220 original size:75 final size:72
Alignment explanation
Indices: 5073--5223 Score: 203
Period size: 75 Copynumber: 2.0 Consensus size: 72
5063 TTTTATTAAA
* * *
5073 AAAAGTTCATATATCTAATATTCTTAATTTAACTTTAAATTAAATAATACACATTTTATAATTTT
1 AAAAGTTCATATATCTAATAATCTTAATTTAAATTTAAATTAAATAATACACATTTTATAAATTT
5138 TAAAAATT
66 T-AAAATT
* *
5146 AAAAGTTCATATATCTAGTAATCTTAAATTTGAAATTTAAATTAAATAATACACGTTTTATGATA
1 AAAAGTTCATATATCTAATAATCTT-AATTT-AAATTTAAATTAAATAATACACATTTTAT-A-A
*
5211 ATTTTAAATTT
62 ATTTTAAAATT
5222 AA
1 AA
5224 TAAAATAAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
73 23 0.34
74 5 0.07
75 27 0.40
76 8 0.12
77 5 0.07
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (72 bp):
AAAAGTTCATATATCTAATAATCTTAATTTAAATTTAAATTAAATAATACACATTTTATAAATTT
TAAAATT
Found at i:5290 original size:24 final size:25
Alignment explanation
Indices: 5245--5300 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
5235 TTAAGCAAAA
* *
5245 TTTAAATAAAATTAGATAATAATGT
1 TTTAAATAAAATCAAATAATAATGT
* **
5270 TTTAAA-AAAATCAAATGATAATAA
1 TTTAAATAAAATCAAATAATAATGT
5294 TTTAAAT
1 TTTAAAT
5301 CTTAAGATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (25 bp):
TTTAAATAAAATCAAATAATAATGT
Found at i:5422 original size:20 final size:20
Alignment explanation
Indices: 5397--5442 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
5387 TTCTTACATA
*
5397 CAAAATCTATATAAAGTTTT
1 CAAAATCTATATAAACTTTT
* * *
5417 CAAAATTTATCTAATCTTTT
1 CAAAATCTATATAAACTTTT
5437 CAAAAT
1 CAAAAT
5443 TTAGATAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.41
Consensus pattern (20 bp):
CAAAATCTATATAAACTTTT
Found at i:5456 original size:20 final size:20
Alignment explanation
Indices: 5413--5456 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
5403 CTATATAAAG
** **
5413 TTTTCAAAATTTATCTAATC
1 TTTTCAAAATTTAGATAAGA
5433 TTTTCAAAATTTAGATAAGA
1 TTTTCAAAATTTAGATAAGA
5453 TTTT
1 TTTT
5457 AAATTTTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATTTAGATAAGA
Found at i:7293 original size:39 final size:39
Alignment explanation
Indices: 7250--7327 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
7240 ACTTAAAATT
7250 TCTTTACACGTGTCATACTATAATCAATTAATATTGGTC
1 TCTTTACACGTGTCATACTATAATCAATTAATATTGGTC
*
7289 TCTTTACACGTGTCATATTATAATCAATTAATATTGGTC
1 TCTTTACACGTGTCATACTATAATCAATTAATATTGGTC
7328 AATGATCGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (39 bp):
TCTTTACACGTGTCATACTATAATCAATTAATATTGGTC
Found at i:7510 original size:28 final size:29
Alignment explanation
Indices: 7450--7510 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
7440 ATCTATAACT
* * *
7450 AAAAGATTGTTTAAATATTAAATTAAGAC
1 AAAAGAATGTTTAAATATAAAATTAAGAA
7479 AAAAGAAT-TTTAAATATCAAAATTAA-AA
1 AAAAGAATGTTTAAATAT-AAAATTAAGAA
7507 AAAA
1 AAAA
7511 TGGTAGTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.30
Consensus pattern (29 bp):
AAAAGAATGTTTAAATATAAAATTAAGAA
Found at i:9360 original size:36 final size:36
Alignment explanation
Indices: 9320--9392 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
9310 GAATTGAATG
*
9320 TTAAAAAGAGATTATAAATGAAGTGTGGTGAAATAA
1 TTAAAAAGAGATTACAAATGAAGTGTGGTGAAATAA
9356 TTAAAAAGAGATTACAAATGAAGTGTGGTGAAATAA
1 TTAAAAAGAGATTACAAATGAAGTGTGGTGAAATAA
9392 T
1 T
9393 GTTTACATCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.49, C:0.01, G:0.22, T:0.27
Consensus pattern (36 bp):
TTAAAAAGAGATTACAAATGAAGTGTGGTGAAATAA
Found at i:11343 original size:21 final size:21
Alignment explanation
Indices: 11304--11343 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11294 CCAGGACAGG
* *
11304 GGTATCAATACTTGAAGTAAA
1 GGTACCAATACCTGAAGTAAA
*
11325 GGTACCAATACCTGTAGTA
1 GGTACCAATACCTGAAGTA
11344 CCGATACTTA
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:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (21 bp):
GGTACCAATACCTGAAGTAAA
Found at i:13353 original size:19 final size:20
Alignment explanation
Indices: 13326--13381 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 20
13316 TTTTTTATCA
* *
13326 AAAAAATTTAATATT-TAGT
1 AAAATATTTAATATTATAAT
*
13345 AAAATATTT-TTATTATAAT
1 AAAATATTTAATATTATAAT
13364 AACAATAATTTAATATTA
1 AA-AAT-ATTTAATATTA
13382 AATGCCATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 4 0.14
19 13 0.45
20 3 0.10
21 4 0.14
22 5 0.17
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
AAAATATTTAATATTATAAT
Found at i:14187 original size:26 final size:27
Alignment explanation
Indices: 14126--14194 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
14116 TTTATTTAAA
*
14126 AATAATTATATTATATTATTTTAATATTT
1 AATAATT-T-TTATATTATTTTAATATTG
* *
14155 AATAA-TTTTATATTTTTTTACTTATTG
1 AATAATTTTTATATTATTTTA-ATATTG
14182 AA-AATTTTTATAT
1 AATAATTTTTATAT
14195 AGTGATCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
26 14 0.40
27 15 0.43
28 1 0.03
29 5 0.14
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (27 bp):
AATAATTTTTATATTATTTTAATATTG
Found at i:16166 original size:18 final size:18
Alignment explanation
Indices: 16143--16191 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
16133 TTTGATCAAA
*
16143 TAACTAACATTCTTGACT
1 TAACTAACATTCTTGAAT
16161 TAACTAACATTCTTGAAT
1 TAACTAACATTCTTGAAT
16179 TAACTAACATTCT
1 TAACTAACATTCT
16192 AATAAAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.39
Consensus pattern (18 bp):
TAACTAACATTCTTGAAT
Found at i:16622 original size:11 final size:12
Alignment explanation
Indices: 16598--16627 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
16588 CAATACAAAT
16598 TTTATTATTTTA
1 TTTATTATTTTA
16610 TTTATTA-TTTA
1 TTTATTATTTTA
16621 TTTATTA
1 TTTATTA
16628 AATAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:17168 original size:11 final size:9
Alignment explanation
Indices: 17136--17162 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
17126 TGTACTATTA
17136 ATTACATTT
1 ATTACATTT
17145 ATTACATTT
1 ATTACATTT
17154 ATTACATTT
1 ATTACATTT
17163 TTATTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTACATTT
Found at i:18516 original size:21 final size:20
Alignment explanation
Indices: 18469--18520 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
18459 GATGTTGGTG
*
18469 GATTAATT-AAATTAATAAA
1 GATTAATTAAAAGTAATAAA
* *
18488 GGTTAATTAAAAGTAAGTCAA
1 GATTAATTAAAAGTAA-TAAA
18509 GATTAATTAAAA
1 GATTAATTAAAA
18521 AGTACTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 7 0.26
20 6 0.22
21 14 0.52
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.33
Consensus pattern (20 bp):
GATTAATTAAAAGTAATAAA
Found at i:18676 original size:25 final size:24
Alignment explanation
Indices: 18648--18705 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
18638 TTTAAGTTGT
*
18648 TAAGCTTTTGGTATTC-AATTTCAAG
1 TAAG-TTTTGGT-TTCGAATTTCAAA
*
18673 TAAGTATTTGGTTTCGATTTTCAAA
1 TAAGT-TTTGGTTTCGAATTTCAAA
18698 TAAGTTTT
1 TAAGTTTT
18706 TCATAGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 7 0.24
25 22 0.76
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.48
Consensus pattern (24 bp):
TAAGTTTTGGTTTCGAATTTCAAA
Found at i:26466 original size:7 final size:7
Alignment explanation
Indices: 26454--26493 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
26444 TTGATTTGGT
26454 ATTGGAA
1 ATTGGAA
26461 ATTGGAA
1 ATTGGAA
26468 ATTGGAA
1 ATTGGAA
26475 ATTGGAA
1 ATTGGAA
26482 ATTGGAA
1 ATTGGAA
26489 ATTGG
1 ATTGG
26494 TTCACATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (7 bp):
ATTGGAA
Found at i:28302 original size:18 final size:18
Alignment explanation
Indices: 28281--28328 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
28271 ATTTAAAAAA
28281 TAAATTTTATTTTTTATT
1 TAAATTTTATTTTTTATT
*
28299 TAAA-TTTA-ATTTTATT
1 TAAATTTTATTTTTTATT
*
28315 CAAATTTTTATTTT
1 TAAA-TTTTATTTT
28329 CCGATCAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
16 10 0.42
17 4 0.17
18 8 0.33
19 2 0.08
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TAAATTTTATTTTTTATT
Found at i:28327 original size:17 final size:17
Alignment explanation
Indices: 28282--28328 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
28272 TTTAAAAAAT
* *
28282 AAATTTTATTTTTTATTT
1 AAATTTT-TATTTTATTC
*
28300 AAA-TTTAATTTTATTC
1 AAATTTTTATTTTATTC
28316 AAATTTTTATTTT
1 AAATTTTTATTTT
28329 CCGATCAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 10 0.42
17 11 0.46
18 3 0.12
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (17 bp):
AAATTTTTATTTTATTC
Found at i:29115 original size:22 final size:21
Alignment explanation
Indices: 29087--29191 Score: 72
Period size: 20 Copynumber: 4.8 Consensus size: 21
29077 TATATTGTTA
29087 TTTTGGTGCTTTTTTTTAATTG
1 TTTTGGTGCTTTTTTTT-ATTG
* *
29109 TTTTGGTTG-TTGTTTTTTGCTGTT
1 TTTTGG-TGCTT-TTTTTT-AT-TG
*
29133 TTTATGTTG-TTTTTTTTATTG
1 TTT-TGGTGCTTTTTTTTATTG
* *
29154 TTTTGATAC-TTTTTTTATTG
1 TTTTGGTGCTTTTTTTTATTG
*
29174 TTTTGGTAGCTGTTTTTT
1 TTTTGGT-GCTTTTTTTT
29192 GTTTTTTTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
20 20 0.31
21 5 0.08
22 15 0.23
23 15 0.23
24 8 0.12
25 2 0.03
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.70
Consensus pattern (21 bp):
TTTTGGTGCTTTTTTTTATTG
Found at i:29143 original size:11 final size:10
Alignment explanation
Indices: 29115--29304 Score: 54
Period size: 10 Copynumber: 18.0 Consensus size: 10
29105 ATTGTTTTGG
29115 TTGTTGTTTT
1 TTGTTGTTTT
*
29125 TTGCTGTTTT
1 TTGTTGTTTT
29135 TATGTTGTTTT
1 T-TGTTGTTTT
*
29146 TT-TTATTGTT
1 TTGTTGTT-TT
29156 TTGATACT-TTTT
1 TTG-T--TGTTTT
*
29168 TTATTGTTTT
1 TTGTTGTTTT
* *
29178 GGTAGCTGTTTT
1 --TTGTTGTTTT
29190 TTGTT-TTTT
1 TTGTTGTTTT
29199 TT-TTGTTTT
1 TTGTTGTTTT
*
29208 GGTGTT-TTTT
1 -TTGTTGTTTT
* **
29218 TTACTGTGTTGG
1 TT-GT-TGTTTT
29230 TTGTTGTTTT
1 TTGTTGTTTT
*
29240 CGTGTT-TTTT
1 -TTGTTGTTTT
*
29250 ATTGTT-ATTT
1 -TTGTTGTTTT
*
29260 TTGTCGCTATTT
1 TTGTTG-T-TTT
29272 TT-TTGCTATTT
1 TTGTTG-T-TTT
29283 TTGTTGTTTTT
1 TTGTTG-TTTT
29294 TATGTTGTTTT
1 T-TGTTGTTTT
29305 GCTATTATTT
Statistics
Matches: 134, Mismatches: 25, Indels: 41
0.67 0.12 0.20
Matches are distributed among these distances:
8 2 0.01
9 20 0.15
10 43 0.32
11 36 0.27
12 30 0.22
13 2 0.01
14 1 0.01
ACGTcount: A:0.06, C:0.04, G:0.18, T:0.72
Consensus pattern (10 bp):
TTGTTGTTTT
Found at i:29168 original size:19 final size:21
Alignment explanation
Indices: 29143--29191 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
29133 TTTATGTTGT
29143 TTTTTTTATTGTTTTGATA-C
1 TTTTTTTATTGTTTTGATAGC
*
29163 TTTTTTTATTGTTTTGGTAGC
1 TTTTTTTATTGTTTTGATAGC
29184 TGTTTTTT
1 T-TTTTTT
29192 GTTTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 18 0.69
21 2 0.08
22 6 0.23
ACGTcount: A:0.10, C:0.04, G:0.14, T:0.71
Consensus pattern (21 bp):
TTTTTTTATTGTTTTGATAGC
Found at i:29217 original size:50 final size:52
Alignment explanation
Indices: 29139--29249 Score: 136
Period size: 50 Copynumber: 2.2 Consensus size: 52
29129 TGTTTTTATG
* *
29139 TTGTTTTTTTTATTGTTTTGATACTTTTTTTATTGTTTTGGTAGCTGTTTT-
1 TTGTTTTTTTTATTGTTTTGATACTTTTTTTACTGTGTTGGTAGCTGTTTTC
* ** * *
29190 TTGTTTTTTTT-TTGTTTTGGTGTTTTTTTTACTGTGTTGGTTGTTGTTTTC
1 TTGTTTTTTTTATTGTTTTGATACTTTTTTTACTGTGTTGGTAGCTGTTTTC
*
29241 GTGTTTTTT
1 TTGTTTTTT
29250 ATTGTTATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
50 32 0.63
51 19 0.37
ACGTcount: A:0.05, C:0.04, G:0.19, T:0.72
Consensus pattern (52 bp):
TTGTTTTTTTTATTGTTTTGATACTTTTTTTACTGTGTTGGTAGCTGTTTTC
Found at i:29229 original size:20 final size:19
Alignment explanation
Indices: 29191--29230 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
29181 AGCTGTTTTT
* *
29191 TGTTTTTTTTTTGTTTTGG
1 TGTTTTTTTTCTGTGTTGG
29210 TGTTTTTTTTACTGTGTTGG
1 TGTTTTTTTT-CTGTGTTGG
29230 T
1 T
29231 TGTTGTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.03, C:0.03, G:0.23, T:0.72
Consensus pattern (19 bp):
TGTTTTTTTTCTGTGTTGG
Found at i:29623 original size:5 final size:6
Alignment explanation
Indices: 29597--29622 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
29587 GAGCCAAGTC
29597 GGGTCG GGGTCG GGGTCG GGGTCG GG
1 GGGTCG GGGTCG GGGTCG GGGTCG GG
29623 TTTAACTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.69, T:0.15
Consensus pattern (6 bp):
GGGTCG
Found at i:34170 original size:2 final size:2
Alignment explanation
Indices: 34163--34190 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
34153 CCTTTGGCTC
34163 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34191 CCTTTCGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35423 original size:11 final size:11
Alignment explanation
Indices: 35407--35489 Score: 55
Period size: 11 Copynumber: 7.5 Consensus size: 11
35397 TACTATGATA
35407 TTTATTATTAT
1 TTTATTATTAT
35418 TTTATT-TTA-
1 TTTATTATTAT
* *
35427 TTAATTAATTAG
1 TTTATT-ATTAT
* *
35439 TTAAATATTAT
1 TTTATTATTAT
*
35450 TTTATTAATAT
1 TTTATTATTAT
*
35461 TTTACTTA-GAT
1 TTTA-TTATTAT
*
35472 ATTTATTATCAT
1 -TTTATTATTAT
35484 TTTATT
1 TTTATT
35490 TAGAAAATAG
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
9 5 0.09
10 3 0.05
11 36 0.62
12 14 0.24
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (11 bp):
TTTATTATTAT
Found at i:35476 original size:23 final size:23
Alignment explanation
Indices: 35450--35493 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
35440 TAAATATTAT
35450 TTTATTAAT-ATTTTACTTAGATA
1 TTTATT-ATCATTTTACTTAGATA
*
35473 TTTATTATCATTTTATTTAGA
1 TTTATTATCATTTTACTTAGA
35494 AAATAGTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (23 bp):
TTTATTATCATTTTACTTAGATA
Found at i:42608 original size:30 final size:30
Alignment explanation
Indices: 42572--42843 Score: 207
Period size: 29 Copynumber: 9.3 Consensus size: 30
42562 GTAAAAGGGT
* **
42572 AATTTTTGAAAGTTTCTTGGTCAAAAATTG
1 AATTTTTGGAAGTTTCGGGGTCAAAAATTG
* *
42602 AATTTTTGAAAG-TTCAGGTGT-AAAAA-TG
1 AATTTTTGGAAGTTTC-GGGGTCAAAAATTG
42630 TAATTTTTGGAAGTTTCGGGGTCAAAAA-TG
1 -AATTTTTGGAAGTTTCGGGGTCAAAAATTG
42660 AAATTTTTGGAAG--TCGGGGGT--AAAA-TG
1 -AATTTTTGGAAGTTTC-GGGGTCAAAAATTG
* ** *
42687 TAATTTTTGAAAGTTTTAGGGTCAAAAATGG
1 -AATTTTTGGAAGTTTCGGGGTCAAAAATTG
42718 AATTTTTGGAAG-TT-GAGGGT--AAAATTG
1 AATTTTTGGAAGTTTCG-GGGTCAAAAATTG
* *
42745 TAATTTTTGAAAGTTTCGAGGTCAAAAA-TG
1 -AATTTTTGGAAGTTTCGGGGTCAAAAATTG
* *
42775 AAATTTTGGAAGTTTGGGGGT-AAAAATAT-
1 AATTTTTGGAAGTTTCGGGGTCAAAAAT-TG
* * * *
42804 AATTTTTGGAAGTTTTGAGGTTAAAAATGG
1 AATTTTTGGAAGTTTCGGGGTCAAAAATTG
42834 AATTTTTGGA
1 AATTTTTGGA
42844 GAGCTTAGGG
Statistics
Matches: 198, Mismatches: 24, Indels: 40
0.76 0.09 0.15
Matches are distributed among these distances:
27 23 0.12
28 24 0.12
29 75 0.38
30 71 0.36
31 5 0.03
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.38
Consensus pattern (30 bp):
AATTTTTGGAAGTTTCGGGGTCAAAAATTG
Found at i:42773 original size:58 final size:58
Alignment explanation
Indices: 42533--42843 Score: 351
Period size: 59 Copynumber: 5.3 Consensus size: 58
42523 AAAATCGGGA
* * ** **
42533 TCAAGAATAGAATTTTTGGACA-TTCGAGGGTAAAAGGGTAATTTTTGAAAGTTTCTTGG
1 TCAAAAATGGAATTTTTGGA-AGTT-GAGGGTAAAAATGTAATTTTTGAAAGTTTCGAGG
* * * * *
42592 TCAAAAATTGAATTTTTGAAAGTTCAGGTGTAAAAATGTAATTTTTGGAAGTTTCGGGG
1 TCAAAAATGGAATTTTTGGAAGTTGAGG-GTAAAAATGTAATTTTTGAAAGTTTCGAGG
* * * *
42651 TCAAAAATGAAATTTTTGGAAGTCGGGGGT-AAAATGTAATTTTTGAAAGTTT-TAGGG
1 TCAAAAATGGAATTTTTGGAAGTTGAGGGTAAAAATGTAATTTTTGAAAGTTTCGA-GG
*
42708 TCAAAAATGGAATTTTTGGAAGTTGAGGGTAAAATTGTAATTTTTGAAAGTTTCGAGG
1 TCAAAAATGGAATTTTTGGAAGTTGAGGGTAAAAATGTAATTTTTGAAAGTTTCGAGG
* * * * *
42766 TCAAAAAT-GAAATTTTGGAAGTTTGGGGGTAAAAATATAATTTTTGGAAGTTTTGAGG
1 TCAAAAATGGAATTTTTGGAAG-TTGAGGGTAAAAATGTAATTTTTGAAAGTTTCGAGG
*
42824 TTAAAAATGGAATTTTTGGA
1 TCAAAAATGGAATTTTTGGA
42844 GAGCTTAGGG
Statistics
Matches: 214, Mismatches: 31, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
57 62 0.29
58 75 0.35
59 77 0.36
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (58 bp):
TCAAAAATGGAATTTTTGGAAGTTGAGGGTAAAAATGTAATTTTTGAAAGTTTCGAGG
Done.