Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006578.1 Kokia drynarioides strain JFW-HI SEQ_121165, 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: 38728
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:419 original size:21 final size:21
Alignment explanation
Indices: 394--716 Score: 198
Period size: 21 Copynumber: 16.6 Consensus size: 21
384 TGTGCTTAGA
*
394 AGGCTTTGTGCCGGTGTTATA
1 AGGCTTTGTGCCGGTGTTATC
*
415 AGGCTTTATGCC-----TAGT-
1 AGGCTTTGTGCCGGTGTTA-TC
*
431 AGGCTTTGTGCCGATGTTATC
1 AGGCTTTGTGCCGGTGTTATC
*
452 AGGCTTTGTGCCGGTGTTATT
1 AGGCTTTGTGCCGGTGTTATC
*
473 AGGCTTTGTGCTGGTGTTATC
1 AGGCTTTGTGCCGGTGTTATC
* *
494 AGGCATTGTGCCGGTGTTATA
1 AGGCTTTGTGCCGGTGTTATC
*
515 AGGCTTTATGCC-----TAGT-
1 AGGCTTTGTGCCGGTGTTA-TC
*
531 AGGCTTTGTGCCAGTGTTATC
1 AGGCTTTGTGCCGGTGTTATC
*
552 AGGCTTTGTGCC----TTGT-
1 AGGCTTTGTGCCGGTGTTATC
568 AGGCTTTGTGCCGGTGTTATC
1 AGGCTTTGTGCCGGTGTTATC
** * *
589 ACACTTTGTGCTGATGTTATC
1 AGGCTTTGTGCCGGTGTTATC
*
610 AGGCTTTATGCC-----TAGT-
1 AGGCTTTGTGCCGGTGTTA-TC
* *
626 AGGCTTTATGCAGGTGTTATC
1 AGGCTTTGTGCCGGTGTTATC
* * *
647 AAGCTTCGTGCC----TAAT-
1 AGGCTTTGTGCCGGTGTTATC
* * *
663 ATGCTTTATGCCGGTGTTAAC
1 AGGCTTTGTGCCGGTGTTATC
* *
684 AGGCTTTGCGCCTGTGTTATC
1 AGGCTTTGTGCCGGTGTTATC
705 AGGCTTTGTGCC
1 AGGCTTTGTGCC
717 TAATAGGCAT
Statistics
Matches: 232, Mismatches: 39, Indels: 62
0.70 0.12 0.19
Matches are distributed among these distances:
16 60 0.26
17 9 0.04
20 8 0.03
21 155 0.67
ACGTcount: A:0.15, C:0.18, G:0.28, T:0.38
Consensus pattern (21 bp):
AGGCTTTGTGCCGGTGTTATC
Found at i:435 original size:37 final size:37
Alignment explanation
Indices: 378--463 Score: 127
Period size: 37 Copynumber: 2.3 Consensus size: 37
368 ATACAAATCC
* *
378 AGGCTTTGTGCTTAGAAGGCTTTGTGCCGGTGTTATA
1 AGGCTTTGTGCCTAGAAGGCTTTGTGCCGATGTTATA
* * *
415 AGGCTTTATGCCTAGTAGGCTTTGTGCCGATGTTATC
1 AGGCTTTGTGCCTAGAAGGCTTTGTGCCGATGTTATA
452 AGGCTTTGTGCC
1 AGGCTTTGTGCC
464 GGTGTTATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.15, C:0.17, G:0.30, T:0.37
Consensus pattern (37 bp):
AGGCTTTGTGCCTAGAAGGCTTTGTGCCGATGTTATA
Found at i:573 original size:16 final size:16
Alignment explanation
Indices: 515--579 Score: 58
Period size: 16 Copynumber: 3.8 Consensus size: 16
505 CGGTGTTATA
* *
515 AGGCTTTATGCCTAGT
1 AGGCTTTGTGCCTTGT
*
531 AGGCTTTGTGCCAGTGTTAT
1 AGGCTTTGTGCC----TTGT
551 CAGGCTTTGTGCCTTGT
1 -AGGCTTTGTGCCTTGT
568 AGGCTTTGTGCC
1 AGGCTTTGTGCC
580 GGTGTTATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
16 23 0.57
17 3 0.08
20 2 0.05
21 12 0.30
ACGTcount: A:0.12, C:0.20, G:0.29, T:0.38
Consensus pattern (16 bp):
AGGCTTTGTGCCTTGT
Found at i:588 original size:37 final size:37
Alignment explanation
Indices: 452--599 Score: 163
Period size: 37 Copynumber: 3.9 Consensus size: 37
442 CGATGTTATC
*
452 AGGCTTTGTGCCGGTGTTATTAGGCTTTGTG-CTGGTGTTAT
1 AGGCTTTGTGCCGGTGTTATCAGGCTTTGTGCCT--TG---T
* * * *
493 CAGGCATTGTGCCGGTGTTATAAGGCTTTATGCCTAGT
1 -AGGCTTTGTGCCGGTGTTATCAGGCTTTGTGCCTTGT
*
531 AGGCTTTGTGCCAGTGTTATCAGGCTTTGTGCCTTGT
1 AGGCTTTGTGCCGGTGTTATCAGGCTTTGTGCCTTGT
**
568 AGGCTTTGTGCCGGTGTTATCACACTTTGTGC
1 AGGCTTTGTGCCGGTGTTATCAGGCTTTGTGC
600 TGATGTTATC
Statistics
Matches: 93, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
37 61 0.66
38 1 0.01
41 1 0.01
42 28 0.30
43 2 0.02
ACGTcount: A:0.13, C:0.18, G:0.30, T:0.39
Consensus pattern (37 bp):
AGGCTTTGTGCCGGTGTTATCAGGCTTTGTGCCTTGT
Found at i:596 original size:58 final size:58
Alignment explanation
Indices: 534--647 Score: 167
Period size: 58 Copynumber: 2.0 Consensus size: 58
524 GCCTAGTAGG
* * * *
534 CTTTGTGCCAG-TGTTATCAGGCTTTGTGCCTTGTAGGCTTTGTGCCGGTGTTATCACA
1 CTTTGTG-CAGATGTTATCAGGCTTTATGCCTAGTAGGCTTTATGCAGGTGTTATCACA
*
592 CTTTGTGCTGATGTTATCAGGCTTTATGCCTAGTAGGCTTTATGCAGGTGTTATCA
1 CTTTGTGCAGATGTTATCAGGCTTTATGCCTAGTAGGCTTTATGCAGGTGTTATCA
648 AGCTTCGTGC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
57 2 0.04
58 48 0.96
ACGTcount: A:0.15, C:0.18, G:0.26, T:0.40
Consensus pattern (58 bp):
CTTTGTGCAGATGTTATCAGGCTTTATGCCTAGTAGGCTTTATGCAGGTGTTATCACA
Found at i:659 original size:37 final size:37
Alignment explanation
Indices: 603--681 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
593 TTTGTGCTGA
* * *
603 TGTTATCAGGCTTTATGCCTAGTAGGCTTTATGCAGG
1 TGTTATCAAGCTTCATGCCTAATAGGCTTTATGCAGG
* * *
640 TGTTATCAAGCTTCGTGCCTAATATGCTTTATGCCGG
1 TGTTATCAAGCTTCATGCCTAATAGGCTTTATGCAGG
677 TGTTA
1 TGTTA
682 ACAGGCTTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (37 bp):
TGTTATCAAGCTTCATGCCTAATAGGCTTTATGCAGG
Found at i:5478 original size:36 final size:36
Alignment explanation
Indices: 5402--5478 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
5392 ACATAATTAG
**
5402 TCACATGGCATGAAGAACATACCCACATATTTTCTA
1 TCACATGGCATGAAGAACATACCCACATATTCACTA
* *
5438 TCACATGGCATGAATAACATACCCACATATTCACTT
1 TCACATGGCATGAAGAACATACCCACATATTCACTA
5474 TCACA
1 TCACA
5479 ACAGTCATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.27
Consensus pattern (36 bp):
TCACATGGCATGAAGAACATACCCACATATTCACTA
Found at i:7293 original size:44 final size:44
Alignment explanation
Indices: 7227--7313 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
7217 GGTCAAATAA
* * * **
7227 TATTAAAATAATCTGCATTAATCAATGTTTAAGTAGGAAACTAG
1 TATTAAAATAACCTACACTAATCAAAATTTAAGTAGGAAACTAG
* *
7271 TATTTAAATAACCTACACTAATCAAAATTTAAGTGGGAAACTA
1 TATTAAAATAACCTACACTAATCAAAATTTAAGTAGGAAACTA
7314 AAAACAAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (44 bp):
TATTAAAATAACCTACACTAATCAAAATTTAAGTAGGAAACTAG
Found at i:8413 original size:11 final size:11
Alignment explanation
Indices: 8383--8413 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
8373 ATAAAATTAC
*
8383 TAAAATTAGTT
1 TAAAATTATTT
8394 TAAAATTATTT
1 TAAAATTATTT
8405 TAAAATTAT
1 TAAAATTAT
8414 AATCATCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:9001 original size:87 final size:87
Alignment explanation
Indices: 8853--9026 Score: 312
Period size: 87 Copynumber: 2.0 Consensus size: 87
8843 GAGCAAAATT
* *
8853 CTCATATGATCCTTTCCGAAATATGAGCAAAGACGTAAGTGACAAAGCCAGCCCCATTTTTATCG
1 CTCATATGATCCTTTCCAAAATATGAGCAAAGACGTAAGTGACAAAGCCAGCCCCAGTTTTATCG
8918 CAAATATAACTTTCCTGGGATC
66 CAAATATAACTTTCCTGGGATC
*
8940 CTCATATGATCCTTTCCAAAATATGAGCAAAGATGTAAGTGACAAAGCCAGCCCCAGTTTTATCG
1 CTCATATGATCCTTTCCAAAATATGAGCAAAGACGTAAGTGACAAAGCCAGCCCCAGTTTTATCG
*
9005 CAAATATAACTTTCTTGGGATC
66 CAAATATAACTTTCCTGGGATC
9027 AGAACGTCCC
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (87 bp):
CTCATATGATCCTTTCCAAAATATGAGCAAAGACGTAAGTGACAAAGCCAGCCCCAGTTTTATCG
CAAATATAACTTTCCTGGGATC
Found at i:9410 original size:10 final size:10
Alignment explanation
Indices: 9395--9482 Score: 51
Period size: 10 Copynumber: 9.0 Consensus size: 10
9385 ATATTTTAAA
9395 AAATTAATTT
1 AAATTAATTT
9405 AAATTAATTT
1 AAATTAATTT
*
9415 AAAAT-ATTT
1 AAATTAATTT
*
9424 TAA-TAATTTT
1 AAATTAA-TTT
* *
9434 ATATT--TTAA
1 AAATTAATT-T
*
9443 AAATAAATTT
1 AAATTAATTT
9453 AAATTAATTTT
1 AAATTAA-TTT
*
9464 AAAATAATTT
1 AAATTAATTT
*
9474 TAA-TAATTT
1 AAATTAATTT
9483 TATATTTTAA
Statistics
Matches: 60, Mismatches: 11, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
8 3 0.05
9 16 0.27
10 29 0.48
11 12 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
AAATTAATTT
Found at i:9443 original size:49 final size:50
Alignment explanation
Indices: 9368--9563 Score: 238
Period size: 50 Copynumber: 4.1 Consensus size: 50
9358 GATGATGATT
9368 ATAATTTTAATAATTTTATATTTTAAAAAATTAATTTAAATTAA-TTTAAA
1 ATAATTTTAATAATTTTATATTTT-AAAAATTAATTTAAATTAATTTTAAA
*
9418 AT-ATTTTAATAATTTTATATTTTAAAAATAAATTTAAATTAATTTTAAA
1 ATAATTTTAATAATTTTATATTTTAAAAATTAATTTAAATTAATTTTAAA
*
9467 ATAATTTTAATAATTTTATATTTT--AAA--AA-CT--A-T--TTTTAAA
1 ATAATTTTAATAATTTTATATTTTAAAAATTAATTTAAATTAATTTTAAA
* *
9507 ATAATTTTAATAATTTTATATTTTAAAAAAATAATTTTAA-TAATTTTAAA
1 ATAATTTTAATAATTTTATATTTT-AAAAATTAATTTAAATTAATTTTAAA
*
9557 ATCATTT
1 ATAATTT
9564 GTTGACGTGG
Statistics
Matches: 130, Mismatches: 4, Indels: 24
0.82 0.03 0.15
Matches are distributed among these distances:
40 31 0.24
42 1 0.01
43 4 0.03
45 3 0.02
46 3 0.02
48 23 0.18
49 29 0.22
50 36 0.28
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (50 bp):
ATAATTTTAATAATTTTATATTTTAAAAATTAATTTAAATTAATTTTAAA
Found at i:9466 original size:11 final size:10
Alignment explanation
Indices: 9368--9524 Score: 72
Period size: 9 Copynumber: 15.9 Consensus size: 10
9358 GATGATGATT
9368 ATAATTTT-A
1 ATAATTTTAA
9377 ATAATTTT--
1 ATAATTTTAA
9385 AT-ATTTTAA
1 ATAATTTTAA
*
9394 AAAATTAATTTAA
1 ATAA-T--TTTAA
*
9407 ATTAATTTAAA
1 A-TAATTTTAA
9418 AT-ATTTT-A
1 ATAATTTTAA
9426 ATAATTTT--
1 ATAATTTTAA
9434 AT-ATTTTAAAA
1 ATAATTTT--AA
*
9445 ATAAATTTAA
1 ATAATTTTAA
9455 ATTAATTTTAAA
1 A-TAATTTT-AA
9467 ATAATTTT-A
1 ATAATTTTAA
9476 ATAATTTT--
1 ATAATTTTAA
9484 AT-ATTTTAAAA
1 ATAATTTT--AA
*
9495 ACTATTTTTAAA
1 A-TAATTTT-AA
9507 ATAATTTT-A
1 ATAATTTTAA
9516 ATAATTTTA
1 ATAATTTTA
9525 TATTTTAAAA
Statistics
Matches: 118, Mismatches: 8, Indels: 43
0.70 0.05 0.25
Matches are distributed among these distances:
7 15 0.13
8 9 0.08
9 36 0.31
10 5 0.04
11 28 0.24
12 12 0.10
13 11 0.09
14 2 0.02
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.52
Consensus pattern (10 bp):
ATAATTTTAA
Found at i:9539 original size:21 final size:23
Alignment explanation
Indices: 9515--9557 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
9505 AAATAATTTT
9515 AATAATTTT-AT-ATTTTAAAAA
1 AATAATTTTAATAATTTTAAAAA
9536 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
9558 TCATTTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
23 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATAATTTTAATAATTTTAAAAA
Found at i:9555 original size:39 final size:39
Alignment explanation
Indices: 9457--9555 Score: 146
Period size: 40 Copynumber: 2.5 Consensus size: 39
9447 AAATTTAAAT
*
9457 TAATTTTAAAATAATTTTAATAATTTTATATTTTAAAAAC
1 TAATTTT-AAATAATTTTAATAATTTTATATTTTAAAAAA
*
9497 TATTTTTAAAATAATTTTAATAATTTTATATTTTAAAAAAA
1 TAATTTT-AAATAATTTTAATAATTTTATATTTT-AAAAAA
9538 TAATTTT-AATAATTTTAA
1 TAATTTTAAATAATTTTAA
9556 AATCATTTGT
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
39 11 0.20
40 33 0.60
41 11 0.20
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (39 bp):
TAATTTTAAATAATTTTAATAATTTTATATTTTAAAAAA
Found at i:11506 original size:12 final size:12
Alignment explanation
Indices: 11489--11524 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
11479 ATATGTATAC
11489 GTATGCATGTAT
1 GTATGCATGTAT
11501 GTATGCATGTAT
1 GTATGCATGTAT
*
11513 GT-TGTATGTAT
1 GTATGCATGTAT
11524 G
1 G
11525 ATCATTTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.22, C:0.06, G:0.28, T:0.44
Consensus pattern (12 bp):
GTATGCATGTAT
Found at i:14632 original size:21 final size:20
Alignment explanation
Indices: 14608--14646 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
14598 CCCTTTAAAT
14608 TTTCACTCAATTTATCTCATA
1 TTTCACTCAATTT-TCTCATA
*
14629 TTTCTCTCAATTTTCTCA
1 TTTCACTCAATTTTCTCA
14647 CAAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTCACTCAATTTTCTCATA
Found at i:14679 original size:9 final size:9
Alignment explanation
Indices: 14665--14689 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
14655 TCTCTAAAGC
14665 TCTCAAAAT
1 TCTCAAAAT
14674 TCTCAAAAT
1 TCTCAAAAT
14683 TCTCAAA
1 TCTCAAA
14690 TATTTCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (9 bp):
TCTCAAAAT
Found at i:16148 original size:26 final size:23
Alignment explanation
Indices: 16102--16174 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 23
16092 TTTAAGTTGG
* *
16102 TTTAAATTTATTTTTAAATTTAAA
1 TTTAAATTT-TCTTTCAATTTAAA
*
16126 TTT-ATTTTTC-TT-AATTTAAA
1 TTTAAATTTTCTTTCAATTTAAA
16146 TTTAAATTTTCTTTCAATTTAAAA
1 TTTAAATTTTCTTTCAATTT-AAA
16170 TTTAA
1 TTTAA
16175 TCAAAATTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 11 0.26
21 8 0.19
22 3 0.07
23 9 0.21
24 11 0.26
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTAAATTTTCTTTCAATTTAAA
Found at i:18134 original size:30 final size:30
Alignment explanation
Indices: 18099--18195 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
18089 CGAAAAATTC
*
18099 CATTTTTAACCCCAAAATTTCTAAAAAATA
1 CATTTTTAACCCCAAAACTTCTAAAAAATA
* ** * * *
18129 TATTTTT-ACCCCCGAACTCCTAAAAATTC
1 CATTTTTAACCCCAAAACTTCTAAAAAATA
* * *
18158 CATTTTTGACCTCAAAACTTCCAAAAAATA
1 CATTTTTAACCCCAAAACTTCTAAAAAATA
18188 CATTTTTA
1 CATTTTTA
18196 CTCTCGAACT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 22 0.44
30 28 0.56
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (30 bp):
CATTTTTAACCCCAAAACTTCTAAAAAATA
Found at i:18162 original size:29 final size:28
Alignment explanation
Indices: 18130--18398 Score: 148
Period size: 29 Copynumber: 9.2 Consensus size: 28
18120 TAAAAAATAT
18130 ATTTTTACCCCCGAACTCCTAAAAATTCC
1 ATTTTTACCCCCGAACTCC-AAAAATTCC
* ** * *
18159 ATTTTTGACCTCAAAACTTCCAAAAAATAC
1 ATTTTT-ACCCCCGAAC-TCCAAAAATTCC
* *
18189 ATTTTTACTCTCGAACTTCCAAAAATTCC
1 ATTTTTACCCCCGAAC-TCCAAAAATTCC
* * * * *
18218 ATTCTTAACCTCGAAACTTCCAAAATTTTC
1 ATTTTTACCCCCG-AAC-TCCAAAAATTCC
*
18248 ATTTTTACCCCCAAACTTCCAAAAATTCC
1 ATTTTTACCCCCGAAC-TCCAAAAATTCC
* **
18277 ATTTTGA-CCTTGAAACTTCCAAAAATTACC
1 ATTTTTACCCCCG-AAC-TCCAAAAATT-CC
* * *
18307 A-TTTTGCCCCCGAATGTCCAAAAATTTC
1 ATTTTTACCCCCGAA-CTCCAAAAATTCC
** *
18335 ATTTTTAACCCCAAAACTTTCAAAAATTACC
1 ATTTTT-ACCCCCGAAC-TCCAAAAATT-CC
* * * *
18366 -CTTCTATCCCCGAATGTCCAAAAATTCC
1 ATTTTTACCCCCGAA-CTCCAAAAATTCC
18394 ATTTT
1 ATTTT
18399 GATCTCGATT
Statistics
Matches: 179, Mismatches: 48, Indels: 26
0.71 0.19 0.10
Matches are distributed among these distances:
28 6 0.03
29 102 0.57
30 67 0.37
31 4 0.02
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.33
Consensus pattern (28 bp):
ATTTTTACCCCCGAACTCCAAAAATTCC
Found at i:18184 original size:59 final size:59
Alignment explanation
Indices: 18091--18398 Score: 311
Period size: 59 Copynumber: 5.2 Consensus size: 59
18081 TAAACTGTCG
* * * *
18091 AAAAATTCCATTTTTAACCCCAAAATTTCTAAAAAATATATTTTTACCCCCGAAC-TCC
1 AAAAATTCCATTTTTAACCTCAAAACTTCCAAAAAATACATTTTTACCCCCGAACTTCC
* * *
18149 TAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAAATACATTTTTACTCTCGAACTTCC
1 -AAAAATTCCATTTTTAACCTCAAAACTTCCAAAAAATACATTTTTACCCCCGAACTTCC
* * ** * *
18209 AAAAATTCCATTCTTAACCTCGAAACTTCCAAAATTTTCATTTTTACCCCCAAACTTCC
1 AAAAATTCCATTTTTAACCTCAAAACTTCCAAAAAATACATTTTTACCCCCGAACTTCC
* ** * *
18268 AAAAATTCCA-TTTTGACCTTGAAACTTCCAAAAATTACCA-TTTTGCCCCCGAA-TGTCC
1 AAAAATTCCATTTTTAACCTCAAAACTTCCAAAAAATA-CATTTTTACCCCCGAACT-TCC
* * * * ** * *
18326 AAAAATTTCATTTTTAACCCCAAAACTTTCAAAAATTACCCTTCTATCCCCGAA-TGTCC
1 AAAAATTCCATTTTTAACCTCAAAACTTCCAAAAAATACATTTTTACCCCCGAACT-TCC
18385 AAAAATTCCATTTT
1 AAAAATTCCATTTT
18399 GATCTCGATT
Statistics
Matches: 210, Mismatches: 34, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
57 1 0.00
58 46 0.22
59 160 0.76
60 3 0.01
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (59 bp):
AAAAATTCCATTTTTAACCTCAAAACTTCCAAAAAATACATTTTTACCCCCGAACTTCC
Found at i:18344 original size:117 final size:117
Alignment explanation
Indices: 18086--18458 Score: 398
Period size: 117 Copynumber: 3.2 Consensus size: 117
18076 GTCCCTAAAC
* * * *
18086 TGTCGAAAAATTCCATTTTTAACCCCAAAATTTCTAAAAAATAT-ATTTTTACCCCCGAAC-TCC
1 TGTCCAAAAATTCCATTTTTAACCCCAAAACTTC-CAAAAATTTCATTTTTACCCCCGAACTTCC
* * * *
18149 TAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAAATA-CATTTTTACTCTCGAA
65 -AAAAATTCCA-TTTTGACCTCGAAACTTCCAAAAATTACCA-TTTTACCCCCGAA
* * * * *
18204 CT-TCCAAAAATTCCATTCTTAACCTCGAAACTTCCAAAATTTTCATTTTTACCCCCAAACTTCC
1 -TGTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTTCATTTTTACCCCCGAACTTCC
* *
18268 AAAAATTCCATTTTGACCTTGAAACTTCCAAAAATTACCATTTTGCCCCCGAA
65 AAAAATTCCATTTTGACCTCGAAACTTCCAAAAATTACCATTTTACCCCCGAA
* * * ** * *
18321 TGTCCAAAAATTTCATTTTTAACCCCAAAACTTTCAAAAATTACCCTTCTATCCCCGAA-TGTCC
1 TGTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTTCATTTTTACCCCCGAACT-TCC
* **
18385 AAAAATTCCATTTTGATCTCG-ATTTTCCTAAAAATTACCATTTTACCCCCGAA
65 AAAAATTCCATTTTGACCTCGAAACTTCC-AAAAATTACCATTTTACCCCCGAA
*
18438 TGTCCAAAAAATTCTATTTTT
1 TGTCC-AAAAATTCCATTTTT
18459 GATCCTGATT
Statistics
Matches: 213, Mismatches: 34, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
116 7 0.03
117 135 0.63
118 67 0.31
119 4 0.02
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (117 bp):
TGTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTTCATTTTTACCCCCGAACTTCCA
AAAATTCCATTTTGACCTCGAAACTTCCAAAAATTACCATTTTACCCCCGAA
Found at i:18361 original size:88 final size:85
Alignment explanation
Indices: 18132--18364 Score: 261
Period size: 88 Copynumber: 2.6 Consensus size: 85
18122 AAAAATATAT
* * * * *
18132 TTTTACCCCCGAACTCCTAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAAATACATTTTTAC
1 TTTTACCCCCGAATTCC-AAAAATTTCATTTTT-ACCCCAAAACTTCCAAAAATTACATTTTGAC
18197 TCTCGAACTTCCAAAAATTCCA
64 TCTCGAACTTCCAAAAATTCCA
* * * * *
18219 TTCTTAACCTCGAAACTTCCAAAATTTTCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTGA
1 TT-TTACCCCCG-AA-TTCCAAAAATTTCATTTTTACCCCAAAACTTCCAAAAATTACATTTTGA
*
18284 C-CTTGAAACTTCCAAAAATTACCA
63 CTCTCG-AACTTCCAAAAATT-CCA
* *
18308 TTTTGCCCCCGAATGTCCAAAAATTTCATTTTTAACCCCAAAACTTTCAAAAATTAC
1 TTTTACCCCCGAAT-TCCAAAAATTTCATTTTT-ACCCCAAAACTTCCAAAAATTAC
18365 CCTTCTATCC
Statistics
Matches: 121, Mismatches: 18, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
86 1 0.01
87 24 0.20
88 73 0.60
89 20 0.17
90 3 0.02
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (85 bp):
TTTTACCCCCGAATTCCAAAAATTTCATTTTTACCCCAAAACTTCCAAAAATTACATTTTGACTC
TCGAACTTCCAAAAATTCCA
Found at i:18448 original size:59 final size:59
Alignment explanation
Indices: 18086--18554 Score: 257
Period size: 59 Copynumber: 8.0 Consensus size: 59
18076 GTCCCTAAAC
* * * * * * * *
18086 TGTCGAAAAATTCCATTTTTAACCCCAAAATTTCTAAAAAATA-TATTTTTACCCCCGAA
1 TGTCCAAAAATTCCATTTTTGACCTCAGATTTTCCAAAAATTACCA-TTTTACCCCCGAA
* * ** * * *
18145 -CTCCTAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAAATA-CATTTTTACTCTCGAA
1 TGTCC-AAAAATTCCATTTTTGACCTCAGATTTTCCAAAAATTACCA-TTTTACCCCCGAA
* * ** ** *
18204 CT-TCCAAAAATTCCATTCTTAACCTC-GAAACTTCC-AAAATTTTCATTTTTACCCCCAAA
1 -TGTCCAAAAATTCCATTTTTGACCTCAG-ATTTTCCAAAAATTACCA-TTTTACCCCCGAA
* ** *
18263 CT-TCCAAAAATTCCA-TTTTGACCT-TGAAACTTCCAAAAATTACCATTTTGCCCCCGAA
1 -TGTCCAAAAATTCCATTTTTGACCTCAG-ATTTTCCAAAAATTACCATTTTACCCCCGAA
* * * * * * * *
18321 TGTCCAAAAATTTCATTTTTAACCCCAAAACTTT-CAAAAATTACCCTTCTATCCCCGAA
1 TGTCCAAAAATTCCATTTTTGACCTC-AGATTTTCCAAAAATTACCATTTTACCCCCGAA
*
18380 TGTCCAAAAATTCCA-TTTTGATCTC-GATTTTCCTAAAAATTACCATTTTACCCCCGAA
1 TGTCCAAAAATTCCATTTTTGACCTCAGATTTTCC-AAAAATTACCATTTTACCCCCGAA
* *** * * * **
18438 TGTCCAAAAAATTCTATTTTTGATCCT--GATTTTTTTAAAGTTACCGTTTTACCCTCGGG
1 TGTCC-AAAAATTCCATTTTTGA-CCTCAGATTTTCCAAAAATTACCATTTTACCCCCGAA
* * * * * * *
18497 TGTCTAAATATTCCATTTTTAACC-CCGAACTTTCCCAAAATTACCATTTTGCCCCCGA
1 TGTCCAAAAATTCCATTTTTGACCTCAG-ATTTTCCAAAAATTACCATTTTACCCCCGA
18555 GAATCCAAAA
Statistics
Matches: 325, Mismatches: 66, Indels: 38
0.76 0.15 0.09
Matches are distributed among these distances:
56 4 0.01
57 4 0.01
58 94 0.29
59 203 0.62
60 18 0.06
61 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (59 bp):
TGTCCAAAAATTCCATTTTTGACCTCAGATTTTCCAAAAATTACCATTTTACCCCCGAA
Found at i:18450 original size:30 final size:29
Alignment explanation
Indices: 18294--18447 Score: 127
Period size: 29 Copynumber: 5.3 Consensus size: 29
18284 CCTTGAAACT
*
18294 TCCAAAAATTACCATTTTGCCCCCGAATG
1 TCCAAAAATTACCATTTTACCCCCGAATG
* **
18323 TCCAAAAATT-TCATTTTTAACCCCAAAACT-
1 TCCAAAAATTACCA-TTTT-ACCCCCGAA-TG
* * * *
18353 TTCAAAAATTACCCTTCTATCCCCGAATG
1 TCCAAAAATTACCATTTTACCCCCGAATG
* * * *
18382 TCCAAAAATT-CCATTTTGA-TCTCGATTT
1 TCCAAAAATTACCATTTT-ACCCCCGAATG
18410 TCCTAAAAATTACCATTTTACCCCCGAATG
1 TCC-AAAAATTACCATTTTACCCCCGAATG
18440 TCCAAAAA
1 TCCAAAAA
18448 ATTCTATTTT
Statistics
Matches: 94, Mismatches: 22, Indels: 18
0.70 0.16 0.13
Matches are distributed among these distances:
28 16 0.17
29 43 0.46
30 33 0.35
31 2 0.02
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCCCGAATG
Found at i:21860 original size:22 final size:21
Alignment explanation
Indices: 21804--21883 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 21
21794 AATTTTTCAT
21804 AACCCTTAATTTAAAATATCCTA
1 AACCC-TAATTTAAAATA-CCTA
* * *
21827 AACTCTTATTTAAAATACCAA
1 AACCCTAATTTAAAATACCTA
*
21848 AACCCTAATTTTAAAA-ACTTA
1 AACCCTAA-TTTAAAATACCTA
*
21869 AACCATAATTTAAAA
1 AACCCTAATTTAAAA
21884 ATGCTAAATC
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
20 7 0.15
21 19 0.40
22 18 0.38
23 4 0.08
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.33
Consensus pattern (21 bp):
AACCCTAATTTAAAATACCTA
Found at i:27275 original size:20 final size:21
Alignment explanation
Indices: 27247--27285 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
27237 AATTCTCTCC
*
27247 TCAATCTCTCAAAATTCTCAT
1 TCAATCTCTCAAAAATCTCAT
27268 TCAA-CTCTCAAAAATCTC
1 TCAATCTCTCAAAAATCTC
27286 TCAAATGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (21 bp):
TCAATCTCTCAAAAATCTCAT
Found at i:29070 original size:5 final size:5
Alignment explanation
Indices: 29060--29090 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
29050 ATATTTAGTT
29060 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA A
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA A
29091 CTTCGTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATTAA
Found at i:32498 original size:13 final size:14
Alignment explanation
Indices: 32482--32518 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
32472 GAGAGAAAGT
*
32482 TAAATAAATAA-AA
1 TAAATAAACAAGAA
32495 TAAATAAACAAGAA
1 TAAATAAACAAGAA
32509 -AAATAAACAA
1 TAAATAAACAA
32519 ACGAACTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 20 0.91
14 2 0.09
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (14 bp):
TAAATAAACAAGAA
Found at i:32674 original size:21 final size:18
Alignment explanation
Indices: 32650--32694 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
32640 TGCCAAGTCA
32650 TTTTAGGGTTTTAGTTTGTAG
1 TTTTAGGGTTTTA--TT-TAG
*
32671 TTTTAGGTTTTTATTTAG
1 TTTTAGGGTTTTATTTAG
32689 TTTTAG
1 TTTTAG
32695 TTTATTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 9 0.39
19 2 0.09
21 12 0.52
ACGTcount: A:0.16, C:0.00, G:0.22, T:0.62
Consensus pattern (18 bp):
TTTTAGGGTTTTATTTAG
Done.