Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012582.1 Kokia drynarioides strain JFW-HI SEQ_127591, 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: 70427
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 61 characters in sequence are not A, C, G, or T
Found at i:408 original size:28 final size:29
Alignment explanation
Indices: 345--408 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
335 AAAATGAGAC
*
345 TTTTCGGATTCTCGAGGGCAAAAATGATAA
1 TTTT-GGATTCTCGAGGGCAAAAACGATAA
* * *
375 TTTTGGATTCTCG-GGGGAGAAACGGTAA
1 TTTTGGATTCTCGAGGGCAAAAACGATAA
403 TTTTGG
1 TTTTGG
409 GAAAATTCGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 17 0.57
29 9 0.30
30 4 0.13
ACGTcount: A:0.27, C:0.11, G:0.30, T:0.33
Consensus pattern (29 bp):
TTTTGGATTCTCGAGGGCAAAAACGATAA
Found at i:464 original size:59 final size:59
Alignment explanation
Indices: 401--514 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
391 GAGAAACGGT
*
401 AATTTTGGGAAAATTCGGGGTCAAAAATGAGATTTTTAGAAGTTCGAGGGTAAAAATGG
1 AATTTTGGGAAAATTCGGGGTCAAAAATGAGATTTTTAAAAGTTCGAGGGTAAAAATGG
* *** * * * *
460 AATTTTTGGATGTTTTGGGGTCAAAAATGGGATTTTTAAAAGTTTGGGGGTAAAA
1 AATTTTGGGAAAATTCGGGGTCAAAAATGAGATTTTTAAAAGTTCGAGGGTAAAA
515 GGGGATTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 46 1.00
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (59 bp):
AATTTTGGGAAAATTCGGGGTCAAAAATGAGATTTTTAAAAGTTCGAGGGTAAAAATGG
Found at i:558 original size:28 final size:29
Alignment explanation
Indices: 417--559 Score: 137
Period size: 28 Copynumber: 4.9 Consensus size: 29
407 GGGAAAATTC
* * *
417 GGGGTCAAAAATGAGATTTTTAGAAGTTCG
1 GGGGT-AAAAAGGGGATTTTTAGAAGTTTG
* * * * * *
447 AGGGTAAAAATGGAATTTTTGGATGTTTT
1 GGGGTAAAAAGGGGATTTTTAGAAGTTTG
* *
476 GGGGTCAAAAATGGGATTTTTAAAAGTTTG
1 GGGGT-AAAAAGGGGATTTTTAGAAGTTTG
*
506 GGGGT-AAAAGGGGATTTTTAAAAGTTTG
1 GGGGTAAAAAGGGGATTTTTAGAAGTTTG
*
534 GGGGT-AAAAGGGGATTTTTGGAAGTT
1 GGGGTAAAAAGGGGATTTTTAGAAGTT
560 CGAGGTAAAA
Statistics
Matches: 96, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
28 46 0.48
29 22 0.23
30 28 0.29
ACGTcount: A:0.31, C:0.02, G:0.33, T:0.34
Consensus pattern (29 bp):
GGGGTAAAAAGGGGATTTTTAGAAGTTTG
Found at i:2414 original size:17 final size:18
Alignment explanation
Indices: 2394--2505 Score: 83
Period size: 17 Copynumber: 6.4 Consensus size: 18
2384 GGCTTTATTT
**
2394 ATTTTAAATTT-ATGATA
1 ATTTTAAATTTGAAAATA
2411 ATTTTAAATTTGAAAATA
1 ATTTTAAATTTGAAAATA
* *
2429 ATTTTAAACTT-AAATTA
1 ATTTTAAATTTGAAAATA
*
2446 AATTTAAATTT-AAAATAA
1 ATTTTAAATTTGAAAAT-A
* *
2464 ATTTAAAATTTTAAACA-A
1 ATTTTAAATTTGAAA-ATA
*
2482 A-TTT-AATTTTAAAATA
1 ATTTTAAATTTGAAAATA
*
2498 AATTTAAA
1 ATTTTAAA
2506 GGGAGTTTGG
Statistics
Matches: 78, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
15 1 0.01
16 11 0.14
17 34 0.44
18 28 0.36
19 3 0.04
20 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTTTAAATTTGAAAATA
Found at i:2452 original size:35 final size:34
Alignment explanation
Indices: 2413--2505 Score: 107
Period size: 35 Copynumber: 2.7 Consensus size: 34
2403 TTATGATAAT
*
2413 TTTAAATTTGAAAATAATTTTAAA-CTTAAATTAAA
1 TTTAAATTT-AAAATAATTTTAAATCTTAAA-CAAA
* *
2448 TTTAAATTTAAAATAAATTTAAAATTTTAAACAAA
1 TTTAAATTTAAAAT-AATTTTAAATCTTAAACAAA
* *
2483 TTTAATTTTAAAATAAATTTAAA
1 TTTAAATTTAAAATAATTTTAAA
2506 GGGAGTTTGG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
34 12 0.24
35 33 0.66
36 5 0.10
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (34 bp):
TTTAAATTTAAAATAATTTTAAATCTTAAACAAA
Found at i:2464 original size:11 final size:11
Alignment explanation
Indices: 2415--2472 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
2405 ATGATAATTT
2415 TAAATTTGAAAA
1 TAAATTT-AAAA
* *
2427 TAATTTTAAACT
1 TAAATTTAAA-A
*
2439 TAAA-TTAAATT
1 TAAATTTAAA-A
2450 TAAATTTAAAA
1 TAAATTTAAAA
2461 TAAATTTAAAA
1 TAAATTTAAAA
2472 T
1 T
2473 TTTAAACAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 25 0.64
12 14 0.36
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:2469 original size:52 final size:52
Alignment explanation
Indices: 2396--2505 Score: 125
Period size: 52 Copynumber: 2.1 Consensus size: 52
2386 CTTTATTTAT
** * *
2396 TTTAAATTTATGAT-AATTTTAAATTTGAAA-ATAATTTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAATTTAAAATTTGAAACA-AA-TTTAAACTTAAAATAAA
* **
2448 TTTAAATTTAAAATAAATTTAAAATTTTAAACAAATTTAATTTTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAAATTTGAAACAAATTTAAACTTAAAATAAA
2500 TTTAAA
1 TTTAAA
2506 GGGAGTTTGG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
52 32 0.65
53 16 0.33
54 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (52 bp):
TTTAAATTTAAAATAAATTTAAAATTTGAAACAAATTTAAACTTAAAATAAA
Found at i:7158 original size:6 final size:6
Alignment explanation
Indices: 7147--7185 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
7137 GGACAACGGC
7147 CTAATG CTAATG CTAATG CTAATG CTAATG CTAATG CTA
1 CTAATG CTAATG CTAATG CTAATG CTAATG CTAATG CTA
7186 TTCCACTCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (6 bp):
CTAATG
Found at i:16959 original size:2 final size:2
Alignment explanation
Indices: 16952--16978 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16942 ATTTAAAATT
16952 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 T
16979 GTATGCATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23262 original size:13 final size:13
Alignment explanation
Indices: 23241--23287 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
23231 TTTTTTATAT
23241 AAATAATACAAAA
1 AAATAATACAAAA
*
23254 AAATTATACACCAAA
1 AAATAATACA--AAA
*
23269 ATATAATACAAAA
1 AAATAATACAAAA
23282 AAATAA
1 AAATAA
23288 AATTAATAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 17 0.61
15 11 0.39
ACGTcount: A:0.70, C:0.11, G:0.00, T:0.19
Consensus pattern (13 bp):
AAATAATACAAAA
Found at i:23284 original size:15 final size:15
Alignment explanation
Indices: 23243--23286 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
23233 TTTTATATAA
23243 ATAATACAAAAAAAT
1 ATAATACAAAAAAAT
**
23258 -T-ATACACCAAAAT
1 ATAATACAAAAAAAT
23271 ATAATACAAAAAAAT
1 ATAATACAAAAAAAT
23286 A
1 A
23287 AAATTAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
13 10 0.43
14 2 0.09
15 11 0.48
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.20
Consensus pattern (15 bp):
ATAATACAAAAAAAT
Found at i:26602 original size:28 final size:28
Alignment explanation
Indices: 26549--26606 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
26539 CATTTTTCTG
*
26549 TTGGAATTAATTAAGTTTATGATTGAAT
1 TTGGAATTAATTAAGTTTATAATTGAAT
**
26577 TTGGAATTAATTCTGTTTA-AATTTGAAT
1 TTGGAATTAATTAAGTTTATAA-TTGAAT
26605 TT
1 TT
26607 ATTTAATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.50
Consensus pattern (28 bp):
TTGGAATTAATTAAGTTTATAATTGAAT
Found at i:26647 original size:26 final size:26
Alignment explanation
Indices: 26598--26647 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
26588 TCTGTTTAAA
**
26598 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTTATTTAATAAGGTTTATG
* *
26624 TTTGTATTTATTTAATGAGGTTTA
1 TTTGAATTTATTTAATAAGGTTTA
26648 GCAAATGACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (26 bp):
TTTGAATTTATTTAATAAGGTTTATG
Found at i:26724 original size:6 final size:6
Alignment explanation
Indices: 26713--26753 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
26703 ATATTTGCAG
*
26713 ACATAA ACATAA ATA-AGA ACATAA ACATAA ACATAA ACATA
1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATA
26754 TTTAATTCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 29 0.94
7 1 0.03
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:29694 original size:17 final size:17
Alignment explanation
Indices: 29674--29707 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
29664 TTTTACATGA
29674 TTAAATAATATTTAAAT
1 TTAAATAATATTTAAAT
29691 TTAAATAATATTTAAAT
1 TTAAATAATATTTAAAT
29708 GAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAATAATATTTAAAT
Found at i:30656 original size:16 final size:17
Alignment explanation
Indices: 30635--30674 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
30625 GAAAATTTTA
*
30635 ACTTTTT-CTCAAAAAT
1 ACTTTTTACTCAAAAAC
30651 ACTTTTTGACTCAAAAAC
1 ACTTTTT-ACTCAAAAAC
30669 ACTTTT
1 ACTTTT
30675 AAAAACATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
18 14 0.67
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (17 bp):
ACTTTTTACTCAAAAAC
Found at i:31521 original size:21 final size:21
Alignment explanation
Indices: 31471--31525 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
31461 AATGAAAAAT
*
31471 AGTAAAAATGCATAAAAATAAC
1 AGTAAAAAT-AATAAAAATAAC
** *
31493 A-TTTAAATAATCAAAATAAC
1 AGTAAAAATAATAAAAATAAC
31513 AGTAAAAATAATA
1 AGTAAAAATAATA
31526 GCAAAACAAC
Statistics
Matches: 25, Mismatches: 7, Indels: 3
0.71 0.20 0.09
Matches are distributed among these distances:
20 11 0.44
21 13 0.52
22 1 0.04
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.24
Consensus pattern (21 bp):
AGTAAAAATAATAAAAATAAC
Found at i:31531 original size:12 final size:12
Alignment explanation
Indices: 31505--31587 Score: 60
Period size: 12 Copynumber: 7.0 Consensus size: 12
31495 TTAAATAATC
*
31505 AAAATAACAGTA
1 AAAATAACAGCA
*
31517 AAAATAATAGC-
1 AAAATAACAGCA
* *
31528 AAAACAACAACA
1 AAAATAACAGCA
* *
31540 AAAACAACAACA
1 AAAATAACAGCA
* *
31552 AAAATAGCAACA
1 AAAATAACAGCA
* * *
31564 AAAACAATAACA
1 AAAATAACAGCA
31576 AAAATAACAGCA
1 AAAATAACAGCA
31588 TCAAAATAGT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
11 8 0.14
12 49 0.86
ACGTcount: A:0.70, C:0.17, G:0.05, T:0.08
Consensus pattern (12 bp):
AAAATAACAGCA
Found at i:31545 original size:6 final size:6
Alignment explanation
Indices: 31528--31579 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
31518 AAATAATAGC
* * * ** *
31528 AAAACA ACAACA AAAACA ACAACA AAAATA GCAACA AAAACA ATAACA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA
31576 AAAA
1 AAAA
31580 TAACAGCATC
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.75, C:0.19, G:0.02, T:0.04
Consensus pattern (6 bp):
AAAACA
Found at i:31550 original size:15 final size:15
Alignment explanation
Indices: 31530--31576 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
31520 ATAATAGCAA
31530 AACAACAACAAAAAC
1 AACAACAACAAAAAC
*
31545 AACAACAA-AAATAGC
1 AACAACAACAAA-AAC
* *
31560 AACAAAAACAATAAC
1 AACAACAACAAAAAC
31575 AA
1 AA
31577 AAATAACAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 3 0.12
15 21 0.81
16 2 0.08
ACGTcount: A:0.72, C:0.21, G:0.02, T:0.04
Consensus pattern (15 bp):
AACAACAACAAAAAC
Found at i:31555 original size:24 final size:24
Alignment explanation
Indices: 31528--31584 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
31518 AAATAATAGC
*
31528 AAAACAACAACAAAAACAACAACA
1 AAAATAACAACAAAAACAACAACA
* *
31552 AAAATAGCAACAAAAACAATAACA
1 AAAATAACAACAAAAACAACAACA
31576 AAAATAACA
1 AAAATAACA
31585 GCATCAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.74, C:0.19, G:0.02, T:0.05
Consensus pattern (24 bp):
AAAATAACAACAAAAACAACAACA
Found at i:31701 original size:21 final size:21
Alignment explanation
Indices: 31612--31709 Score: 75
Period size: 22 Copynumber: 4.9 Consensus size: 21
31602 AACCAGCACC
*
31612 AAAACAGCAATCAAAACAGT-
1 AAAAAAGCAATCAAAACAGTA
31632 -AAAAA--AATC-AAACAGTA
1 AAAAAAGCAATCAAAACAGTA
* * *
31649 AACAAA-CAACACCAAAACAGCA
1 AAAAAAGC-A-ATCAAAACAGTA
31671 AAAAATAGCAATCAAAACAGTA
1 AAAAA-AGCAATCAAAACAGTA
*
31693 AAAAAAGC-ACCAAAACA
1 AAAAAAGCAATCAAAACA
31710 ACAATAAATT
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
16 7 0.11
17 4 0.06
18 4 0.06
19 4 0.06
20 9 0.15
21 5 0.08
22 26 0.42
23 2 0.03
24 1 0.02
ACGTcount: A:0.65, C:0.20, G:0.07, T:0.07
Consensus pattern (21 bp):
AAAAAAGCAATCAAAACAGTA
Found at i:31709 original size:42 final size:43
Alignment explanation
Indices: 31637--31718 Score: 114
Period size: 42 Copynumber: 1.9 Consensus size: 43
31627 ACAGTAAAAA
*
31637 AATCAAACAGTAAACAAACAACACCAAAACAGCAAAAAATAGC
1 AATCAAACAGTAAACAAACAACACCAAAACAACAAAAAATAGC
* *
31680 AATCAAAACAGTAAA-AAA-AGCACCAAAACAACAATAAAT
1 AATC-AAACAGTAAACAAACAACACCAAAACAACAAAAAAT
31719 TTTTATATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 18 0.51
43 7 0.20
44 10 0.29
ACGTcount: A:0.65, C:0.21, G:0.06, T:0.09
Consensus pattern (43 bp):
AATCAAACAGTAAACAAACAACACCAAAACAACAAAAAATAGC
Found at i:33136 original size:2 final size:2
Alignment explanation
Indices: 33129--33175 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
33119 TAATCATCAA
33129 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
33171 AT AT A
1 AT AT A
33176 CACGGAGTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42922 original size:24 final size:25
Alignment explanation
Indices: 42875--42922 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
42865 GGTTAATATA
* *
42875 ATTTTTTCCTCTATTTTCGTATTTGT
1 ATTTTTT-CTCTATTTTAGAATTTGT
42901 ATTTTTT-TCTATTTTAGAATTT
1 ATTTTTTCTCTATTTTAGAATTT
42923 AAACTTGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
26 7 0.35
ACGTcount: A:0.17, C:0.10, G:0.06, T:0.67
Consensus pattern (25 bp):
ATTTTTTCTCTATTTTAGAATTTGT
Found at i:55627 original size:36 final size:36
Alignment explanation
Indices: 55576--55649 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
55566 CCCGTTCCAG
*
55576 TCCCTACAGAGTGAAAAGTCCTCACTTCTGGTTCTT
1 TCCCTACAGAATGAAAAGTCCTCACTTCTGGTTCTT
* *
55612 TCCCTATAGAATGAAAAGTCCTGACTTCTGGTTCTT
1 TCCCTACAGAATGAAAAGTCCTCACTTCTGGTTCTT
55648 TC
1 TC
55650 TTCTTCTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (36 bp):
TCCCTACAGAATGAAAAGTCCTCACTTCTGGTTCTT
Found at i:55655 original size:3 final size:3
Alignment explanation
Indices: 55647--55676 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
55637 TTCTGGTTCT
55647 TTC TTC TTC TTC TTC TTC TTC TT- TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
55677 ACCTTGATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:57188 original size:21 final size:21
Alignment explanation
Indices: 57159--57199 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
57149 TGAATATTCT
*
57159 ATAAAATTTGGATTTAAAACA
1 ATAAAATTTGGATCTAAAACA
*
57180 ATAATATTTGGATCTAAAAC
1 ATAAAATTTGGATCTAAAAC
57200 GGATTCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (21 bp):
ATAAAATTTGGATCTAAAACA
Found at i:60992 original size:29 final size:28
Alignment explanation
Indices: 60955--61013 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
60945 AGTACTAACT
* * *
60955 ATTTGAACTAGTTAATTACATTATAAAAA
1 ATTTAAACTAATTAATAACATTA-AAAAA
60984 ATTTAAACTAATTAATAACATTAAAAAA
1 ATTTAAACTAATTAATAACATTAAAAAA
61012 AT
1 AT
61014 ATAGAGACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (28 bp):
ATTTAAACTAATTAATAACATTAAAAAA
Found at i:62227 original size:3 final size:3
Alignment explanation
Indices: 62221--62253 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
62211 TTTAAGCAGC
62221 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
62254 CCCGGTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:62753 original size:18 final size:18
Alignment explanation
Indices: 62730--62764 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
62720 GTAAAGCTTT
62730 ATTTTAATATTT-TTATAC
1 ATTTTAAT-TTTATTATAC
62748 ATTTTAATTTTATTATA
1 ATTTTAATTTTATTATA
62765 TGCACATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTAATTTTATTATAC
Found at i:66475 original size:20 final size:20
Alignment explanation
Indices: 66454--66490 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
66444 TAGCAGTCTA
66454 AAATTATT-TTTACTAATCT
1 AAATTATTATTTACTAATCT
*
66473 AAATTATTATTTTCTAAT
1 AAATTATTATTTACTAAT
66491 TGAGTCGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (20 bp):
AAATTATTATTTACTAATCT
Found at i:70032 original size:31 final size:30
Alignment explanation
Indices: 69997--70081 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 30
69987 ATTATTAAAG
69997 GGTTTAATTAATTTTTTAATTATTATATTAA
1 GGTTTAATTAATTTTTTAATTATTATA-TAA
* * * * *
70028 GGTTTAAATAGTTATTTATTTATTTTATAA
1 GGTTTAATTAATTTTTTAATTATTATATAA
* *
70058 GGATTAAATTAATTTTTAAATTAT
1 GG-TTTAATTAATTTTTTAATTAT
70082 CTAAGTTTAA
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
30 5 0.12
31 37 0.88
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.55
Consensus pattern (30 bp):
GGTTTAATTAATTTTTTAATTATTATATAA
Found at i:70145 original size:10 final size:10
Alignment explanation
Indices: 70126--70229 Score: 56
Period size: 9 Copynumber: 10.3 Consensus size: 10
70116 AAAAAGTAAT
70126 TAAAAT-TTA
1 TAAAATATTA
70135 TAAAATATTA
1 TAAAATATTA
*
70145 TTAATATATTA
1 -TAAAATATTA
70156 TGAAAAAATATTA
1 T---AAAATATTA
* *
70169 T-ATATATTTT
1 TAAAATA-TTA
*
70179 TAGAAATTTTA
1 TA-AAATATTA
*
70190 GAAAATATT-
1 TAAAATATTA
*
70199 GAAAA-ATTA
1 TAAAATATTA
70208 TAAAAT-TTA
1 TAAAATATTA
*
70217 TTAAATATTA
1 TAAAATATTA
70227 TAA
1 TAA
70230 TATCTATGAA
Statistics
Matches: 72, Mismatches: 12, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
8 3 0.04
9 27 0.38
10 18 0.25
11 12 0.17
12 3 0.04
13 9 0.12
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (10 bp):
TAAAATATTA
Found at i:70308 original size:18 final size:19
Alignment explanation
Indices: 70285--70328 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
70275 AAAAATTATA
70285 TATAAAACTATA-AAATTT
1 TATAAAACTATATAAATTT
*
70303 TAT-AAATTATATAAATTT
1 TATAAAACTATATAAATTT
70321 TATTAAAA
1 TA-TAAAA
70329 TGGTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 11 0.50
19 1 0.05
20 3 0.14
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TATAAAACTATATAAATTT
Done.