Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009447.1 Kokia drynarioides strain JFW-HI SEQ_124154, 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: 150078
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 169 characters in sequence are not A, C, G, or T
Found at i:322 original size:59 final size:59
Alignment explanation
Indices: 259--689 Score: 241
Period size: 59 Copynumber: 7.4 Consensus size: 59
249 TACTTTTGGG
* *
259 AAAG-TTCGAGGTTAAAAGATGGAATTTTT-AGA-TATTCG-GGGATAAAAATGGAATTTTTC
1 AAAGTTTCGAGGTCAAAA-ATGAAATTTTTGAGAGT-TT-GAGGG-TAAAAATGGAATTTTTC
* * *
318 AAAGTTTCGGGGTCAAAAATGAAATTTTTGGGAGTTTGAGGGTAAAAATGGAATTTTTG
1 AAAGTTTCGAGGTCAAAAATGAAATTTTTGAGAGTTTGAGGGTAAAAATGGAATTTTTC
** * * * * *
377 GGAGTTTCG-GAGTCAAAAATAAAATTTTTG-GAAGTTCGGGGGTAAAAATAGAATTTTTGG
1 AAAGTTTCGAG-GTCAAAAATGAAATTTTTGAG-AGTTTGAGGGTAAAAATGGAATTTTT-C
* * * **
437 AAA-TTTC-AGGGTCGAAAATGGAATTTTTG-GAAGTTTAAGGGTAAAAATGGAAATTTTGG
1 AAAGTTTCGA-GGTCAAAAATGAAATTTTTGAG-AGTTTGAGGGTAAAAATGG-AATTTTTC
* ** * * * * *
496 AAA-TTTTGAGGTCAAAAATGGGATTTTTG-GAAGTTCGGGGGCAAAAAGGGAATTTTTG
1 AAAGTTTCGAGGTCAAAAATGAAATTTTTGAG-AGTTTGAGGGTAAAAATGGAATTTTTC
* * * * * *
554 GAAGTTTTGGGGTCAAAAA-GAGAATTTTGGA-AGTTT-AGGGGCAAAAATGGAATTTTTG
1 AAAGTTTCGAGGTCAAAAATGA-AATTTTTGAGAGTTTGA-GGGTAAAAATGGAATTTTTC
* * * ** * *
612 GAAGTTTGGGGGT-AAAAATGGGATTCTTG-GAAGTTTG-GGGTAAAAATTGG-ATTTTTG
1 AAAGTTTCGAGGTCAAAAATGAAATTTTTGAG-AGTTTGAGGGTAAAAA-TGGAATTTTTC
* *
669 AAAGTTTCGGGGTCGAAAATG
1 AAAGTTTCGAGGTCAAAAATG
690 GTTTTTGAAT
Statistics
Matches: 304, Mismatches: 47, Indels: 43
0.77 0.12 0.11
Matches are distributed among these distances:
57 36 0.12
58 62 0.20
59 177 0.58
60 28 0.09
61 1 0.00
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.32
Consensus pattern (59 bp):
AAAGTTTCGAGGTCAAAAATGAAATTTTTGAGAGTTTGAGGGTAAAAATGGAATTTTTC
Found at i:327 original size:30 final size:29
Alignment explanation
Indices: 271--690 Score: 381
Period size: 29 Copynumber: 14.3 Consensus size: 29
261 AGTTCGAGGT
*
271 TAAAAGATGGAATTTTTAG-A-TATTCGGGG
1 TAAAA-ATGGAATTTTTGGAAGT-TTCGGGG
**
300 ATAAAAATGGAATTTTTCAAAGTTTCGGGG
1 -TAAAAATGGAATTTTTGGAAGTTTCGGGG
* *
330 TCAAAAATGAAATTTTTGGGAGTTT-GAGGG
1 T-AAAAATGGAATTTTTGGAAGTTTCG-GGG
* *
360 TAAAAATGGAATTTTTGGGAGTTTCGGAG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
**
389 TCAAAAATAAAATTTTTGGAAG-TTCGGGGG
1 T-AAAAATGGAATTTTTGGAAGTTTC-GGGG
* * *
419 TAAAAATAGAATTTTTGGAAATTTCAGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
* **
448 TCGAAAATGGAATTTTTGGAAGTTTAAGGG
1 T-AAAAATGGAATTTTTGGAAGTTTCGGGG
* * * *
478 TAAAAATGGAAATTTTGGAAATTTTGAGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
*
507 TCAAAAATGGGATTTTTGGAAG-TTCGGGGG
1 T-AAAAATGGAATTTTTGGAAGTTTC-GGGG
* * *
537 CAAAAAGGGAATTTTTGGAAGTTTTGGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
*
566 TCAAAAA-GAGAA-TTTTGGAAGTTTAGGGG
1 T-AAAAATG-GAATTTTTGGAAGTTTCGGGG
* *
595 CAAAAATGGAATTTTTGGAAGTTTGGGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
* *
624 TAAAAATGGGATTCTTGGAAGTTT-GGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
*
652 TAAAAATTGG-ATTTTTGAAAGTTTCGGGG
1 TAAAAA-TGGAATTTTTGGAAGTTTCGGGG
*
681 TCGAAAATGG
1 T-AAAAATGG
691 TTTTTGAATG
Statistics
Matches: 327, Mismatches: 44, Indels: 39
0.80 0.11 0.10
Matches are distributed among these distances:
28 30 0.09
29 176 0.54
30 120 0.37
31 1 0.00
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTTCGGGG
Found at i:710 original size:87 final size:85
Alignment explanation
Indices: 296--696 Score: 319
Period size: 89 Copynumber: 4.6 Consensus size: 85
286 TTAGATATTC
* * * * * *
296 GGGGATAAAAATGGAATTTTTCAAAGTTTCGGGGTCAAAAATGAAATTTTTGGGAGTTTGAGGGT
1 GGGG-TAAAAATGG-ATTTTTGAAAGTTTAGGGGTCAAAAATG-GATTTTTGGAAGTTTGGGGGC
* *
361 AAAAATGGAATTTTTGGGAGTTT
63 AAAAATGGGATTTTTGGAAGTTT
* ** * ** * * *
384 CGGAGTCAAAAATAAAATTTTTGGAAGTTCGGGGGT-AAAAATAGAATTTTTGGAAATTTCAGGG
1 -GGGGT-AAAAAT-GGATTTTTGAAAGTTTAGGGGTCAAAAAT-GGATTTTTGGAAGTTT-GGGG
* * *
448 TCGAAAATGGAATTTTTGGAAGTTT
61 GCAAAAATGGGATTTTTGGAAGTTT
* * * * *
473 AAGGGTAAAAATGGAAATTTTGGAAA-TTTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
1 -GGGGTAAAAATGG--ATTTTTGAAAGTTTAGGGGTCAAAAAT-GGATTTTTGGAAGTTTGGGGG
537 CAAAAA-GGGAATTTTTGGAAGTTTT
62 CAAAAATGGG-ATTTTTGGAAG-TTT
* * *
562 GGGGTCAAAAA-GAGAATTTTGGAAGTTTAGGGG-CAAAAATGGAATTTTTGGAAGTTTGGGGGT
1 GGGGT-AAAAATG-GATTTTTGAAAGTTTAGGGGTCAAAAATGG-ATTTTTGGAAGTTTGGGGGC
*
625 AAAAATGGGATTCTTGGAAGTTT
63 AAAAATGGGATTTTTGGAAGTTT
* *
648 GGGGTAAAAATTGGATTTTTGAAAGTTTCGGGGTCGAAAATGG-TTTTTG
1 GGGGTAAAAA-TGGATTTTTGAAAGTTTAGGGGTCAAAAATGGATTTTTG
697 AATGGTTTAG
Statistics
Matches: 249, Mismatches: 46, Indels: 38
0.75 0.14 0.11
Matches are distributed among these distances:
85 11 0.04
86 27 0.11
87 58 0.23
88 65 0.26
89 88 0.35
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (85 bp):
GGGGTAAAAATGGATTTTTGAAAGTTTAGGGGTCAAAAATGGATTTTTGGAAGTTTGGGGGCAAA
AATGGGATTTTTGGAAGTTT
Found at i:1934 original size:19 final size:19
Alignment explanation
Indices: 1910--1951 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1900 AAAATTTATT
1910 TTTATTTA-ATATTATAATA
1 TTTATTTATATATTAT-ATA
*
1929 TTTA-TTATTTATTATATA
1 TTTATTTATATATTATATA
1947 TTTAT
1 TTTAT
1952 GGTTAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATTTATATATTATATA
Found at i:2695 original size:28 final size:28
Alignment explanation
Indices: 2663--2721 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
2653 GTTTTTTGAC
* * **
2663 TTTTAATTAAGTTTTAAATCCATTTAAA
1 TTTTAATTAAATTTAAAATAAATTTAAA
2691 TTTTAATTAAATTTAAAATAAATTTAAA
1 TTTTAATTAAATTTAAAATAAATTTAAA
2719 TTT
1 TTT
2722 AAAAATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (28 bp):
TTTTAATTAAATTTAAAATAAATTTAAA
Found at i:2698 original size:6 final size:6
Alignment explanation
Indices: 2684--2724 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
2674 TTTTAAATCC
* *
2684 ATTTAA ATTTTA A-TTAA ATTTAA A-ATAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
2725 AATAAATTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
5 8 0.28
6 21 0.72
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
ATTTAA
Found at i:2702 original size:11 final size:11
Alignment explanation
Indices: 2686--2720 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2676 TTAAATCCAT
*
2686 TTAAATTTTAA
1 TTAAATTTAAA
2697 TTAAATTTAAA
1 TTAAATTTAAA
*
2708 ATAAATTTAAA
1 TTAAATTTAAA
2719 TT
1 TT
2721 TAAAAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:2717 original size:17 final size:18
Alignment explanation
Indices: 2697--2733 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2687 TAAATTTTAA
2697 TTAAATTT-AAAATAAAT
1 TTAAATTTAAAAATAAAT
2714 TTAAATTTAAAAATAAAT
1 TTAAATTTAAAAATAAAT
2732 TT
1 TT
2734 GAATCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAATTTAAAAATAAAT
Found at i:2742 original size:28 final size:28
Alignment explanation
Indices: 2678--2746 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
2668 ATTAAGTTTT
* * *
2678 AAATCCATTTAAATTTTAATTAAATTTA
1 AAATCAATTTAAATTTAAAATAAATTTA
*
2706 AAATAAATTTAAATTTAAAAATAAATTT-
1 AAATCAATTTAAATTT-AAAATAAATTTA
*
2734 GAATCAATTTAAA
1 AAATCAATTTAAA
2747 CTCAATAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 25 0.74
29 9 0.26
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (28 bp):
AAATCAATTTAAATTTAAAATAAATTTA
Found at i:3597 original size:5 final size:5
Alignment explanation
Indices: 3587--3614 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3577 GATGGTGTTT
3587 GCATG GCATG GCATG GCATG GCATG GCA
1 GCATG GCATG GCATG GCATG GCATG GCA
3615 ATGCATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.39, T:0.18
Consensus pattern (5 bp):
GCATG
Found at i:3620 original size:15 final size:14
Alignment explanation
Indices: 3586--3621 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
3576 AGATGGTGTT
3586 TGCATGGCATGGCA
1 TGCATGGCATGGCA
3600 TGGCATGGCATGGCAA
1 T-GCATGGCATGGC-A
3616 TGCATG
1 TGCATG
3622 AAAGGAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 1 0.05
15 17 0.85
16 2 0.10
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.22
Consensus pattern (14 bp):
TGCATGGCATGGCA
Found at i:11728 original size:2 final size:2
Alignment explanation
Indices: 11721--11755 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
11711 AAGAAATTAG
11721 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 A
11756 GCATGATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15752 original size:24 final size:26
Alignment explanation
Indices: 15714--15761 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
15704 TCTACATGGA
15714 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
15740 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
15762 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:20669 original size:34 final size:35
Alignment explanation
Indices: 20620--20688 Score: 122
Period size: 34 Copynumber: 2.0 Consensus size: 35
20610 TGGATGACTC
*
20620 AAACATTAAGAAATGTAATGCTTTACCTTGCTTCA
1 AAACATTAAGAAATGTAATGATTTACCTTGCTTCA
20655 AAACATTAAG-AATGTAATGATTTACCTTGCTTCA
1 AAACATTAAGAAATGTAATGATTTACCTTGCTTCA
20689 TGAACCGTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 23 0.70
35 10 0.30
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.35
Consensus pattern (35 bp):
AAACATTAAGAAATGTAATGATTTACCTTGCTTCA
Found at i:24451 original size:29 final size:27
Alignment explanation
Indices: 24419--24482 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
24409 CGAGAATGCA
24419 AGAAAAAAATAAATAAAAGAATGTATTTT
1 AGAAAAAAATAAATAAAAGAAT-TA-TTT
* * *
24448 AGAAAAAAATTAATGAAATAATTATTT
1 AGAAAAAAATAAATAAAAGAATTATTT
*
24475 AGTAAAAA
1 AGAAAAAA
24483 TAGGCGAGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 10 0.32
28 2 0.06
29 19 0.61
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.28
Consensus pattern (27 bp):
AGAAAAAAATAAATAAAAGAATTATTT
Found at i:31450 original size:8 final size:8
Alignment explanation
Indices: 31439--31470 Score: 50
Period size: 7 Copynumber: 4.2 Consensus size: 8
31429 ATTCACTTCA
31439 TTTCTTTT
1 TTTCTTTT
31447 TTTC-TTT
1 TTTCTTTT
31454 TTTCTTTT
1 TTTCTTTT
31462 TTT-TTTT
1 TTTCTTTT
31469 TT
1 TT
31471 AATTTTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 13 0.57
8 10 0.43
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (8 bp):
TTTCTTTT
Found at i:31459 original size:15 final size:14
Alignment explanation
Indices: 31439--31470 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
31429 ATTCACTTCA
31439 TTTCTTTTTTTCTTT
1 TTTCTTTTTTT-TTT
31454 TTTCTTTTTTTTTT
1 TTTCTTTTTTTTTT
31468 TTT
1 TTT
31471 AATTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (14 bp):
TTTCTTTTTTTTTT
Found at i:33655 original size:2 final size:2
Alignment explanation
Indices: 33648--33673 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33638 TAGTATTAAA
33648 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
33674 GCCAATAAGA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41089 original size:6 final size:6
Alignment explanation
Indices: 41078--41117 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
41068 CTGTGTCTGA
41078 AGAAGC AGAAGC AGAAGC AGAAGC AGAAGC AGAAGC AGAA
1 AGAAGC AGAAGC AGAAGC AGAAGC AGAAGC AGAAGC AGAA
41118 AACTGAGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.53, C:0.15, G:0.33, T:0.00
Consensus pattern (6 bp):
AGAAGC
Found at i:44320 original size:24 final size:24
Alignment explanation
Indices: 44283--44357 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
44273 AGAAATAATC
* * *
44283 TTTCAGTTACACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
44307 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
* * *
44331 TTTTAATTAAACTATGCTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
44355 TTT
1 TTT
44358 GAGTCAAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:44366 original size:24 final size:24
Alignment explanation
Indices: 44304--44369 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 24
44294 CTCTGTTTAA
* * * *
44304 TTGTTTCAATTAAACTCTGTTTAT
1 TTGTTTGAATCAAACTATGCTTAT
* *
44328 TTGTTTTAATTAAACTATGCTTAT
1 TTGTTTGAATCAAACTATGCTTAT
*
44352 TTGTTTGAGTCAAACTAT
1 TTGTTTGAATCAAACTAT
44370 TATTAGTCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.52
Consensus pattern (24 bp):
TTGTTTGAATCAAACTATGCTTAT
Found at i:45148 original size:18 final size:19
Alignment explanation
Indices: 45125--45160 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
45115 GTTTATATTG
45125 AATTTCCTC-AAGATTTTC
1 AATTTCCTCAAAGATTTTC
*
45143 AATTTCTTCAAAGATTTT
1 AATTTCCTCAAAGATTTT
45161 TTTTTTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.47
Consensus pattern (19 bp):
AATTTCCTCAAAGATTTTC
Found at i:61236 original size:14 final size:14
Alignment explanation
Indices: 61217--61246 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
61207 TTATTTATTC
*
61217 AAATAATAAAATAA
1 AAATAAAAAAATAA
61231 AAATAAAAAAATAA
1 AAATAAAAAAATAA
61245 AA
1 AA
61247 CCCCAATCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAATAAAAAAATAA
Found at i:62717 original size:19 final size:19
Alignment explanation
Indices: 62666--62731 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 19
62656 TTTATATATA
* *
62666 TGTGCAAGCCTA-ATATTT
1 TGTGCGAGCCTATATATCT
* *
62684 TATGCGAG-CTAATATATGT
1 TGTGCGAGCCT-ATATATCT
*
62703 TGTGCGAGCCTATATA-CA
1 TGTGCGAGCCTATATATCT
62721 TGTGCGAGCCT
1 TGTGCGAGCCT
62732 CATGTTATCT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 2 0.05
18 18 0.46
19 17 0.44
20 2 0.05
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (19 bp):
TGTGCGAGCCTATATATCT
Found at i:62796 original size:36 final size:36
Alignment explanation
Indices: 62756--62855 Score: 155
Period size: 36 Copynumber: 2.8 Consensus size: 36
62746 TCCCATGTTG
*
62756 TGTGCGAACCTATATGTTGTATGCGAGCCATGAACA
1 TGTGCGAACCCATATGTTGTATGCGAGCCATGAACA
* * *
62792 TGTGCGAACCCATATCTTGTATGCGAACCATGAATA
1 TGTGCGAACCCATATGTTGTATGCGAGCCATGAACA
*
62828 TGTGCGAACCCATATGTTATATGCGAGC
1 TGTGCGAACCCATATGTTGTATGCGAGC
62856 ATTATGTTGT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (36 bp):
TGTGCGAACCCATATGTTGTATGCGAGCCATGAACA
Found at i:63172 original size:18 final size:18
Alignment explanation
Indices: 63149--63184 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
63139 TGTTGAGAGA
63149 TAAGGGAATGTCGAGCAT
1 TAAGGGAATGTCGAGCAT
63167 TAAGGGAATGTCGAGCAT
1 TAAGGGAATGTCGAGCAT
63185 AGCTCCATTC
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:0.33, C:0.11, G:0.33, T:0.22
Consensus pattern (18 bp):
TAAGGGAATGTCGAGCAT
Found at i:76120 original size:3 final size:3
Alignment explanation
Indices: 76112--76137 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
76102 CTTTGCCTTT
76112 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
76138 TACTTTTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:79790 original size:18 final size:18
Alignment explanation
Indices: 79767--79803 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
79757 TTTTAATTTT
79767 ATTTAATAAT-TTTATAAA
1 ATTTAATAATGTTT-TAAA
79785 ATTTAATAATGTTTTAAA
1 ATTTAATAATGTTTTAAA
79803 A
1 A
79804 ATTATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
ATTTAATAATGTTTTAAA
Found at i:101448 original size:19 final size:18
Alignment explanation
Indices: 101402--101455 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
101392 TTTTAATTCA
*
101402 TTTTAAGTTTAAATTTAG
1 TTTTAAGTTTAAATTTAC
* *
101420 TTTAAAGTTTAAACTTTTC
1 TTTTAAGTTTAAA-TTTAC
101439 TTTTAAGTTTAAATTTA
1 TTTTAAGTTTAAATTTA
101456 AAAAGTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (18 bp):
TTTTAAGTTTAAATTTAC
Found at i:101480 original size:17 final size:17
Alignment explanation
Indices: 101441--101506 Score: 75
Period size: 17 Copynumber: 4.0 Consensus size: 17
101431 AACTTTTCTT
*
101441 TTAAGTTTAAATTTAAA
1 TTAAGTTTAAAATTAAA
*
101458 --AAGTTTAAACTTAAA
1 TTAAGTTTAAAATTAAA
*
101473 TTAAGTTTAAAATTAAT
1 TTAAGTTTAAAATTAAA
101490 TTGAA-TTTAAAATTAAA
1 TT-AAGTTTAAAATTAAA
101507 AAAAAAAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
15 14 0.33
17 26 0.62
18 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (17 bp):
TTAAGTTTAAAATTAAA
Found at i:101601 original size:41 final size:39
Alignment explanation
Indices: 101534--101615 Score: 92
Period size: 40 Copynumber: 2.1 Consensus size: 39
101524 GCAAATGTCC
* * * * *
101534 AATTACAAAGCCCCAATTAGGCCCAAATTCAGATGACCCA
1 AATTACAAAGCCCCAAATAAGACCAAA-CCAAATGACCCA
*
101574 AATTACAAAAGGCCCAAATAAGACCAAACCAAATGACCCA
1 AATTAC-AAAGCCCCAAATAAGACCAAACCAAATGACCCA
101614 AA
1 AA
101616 CTAGCCTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
40 18 0.51
41 17 0.49
ACGTcount: A:0.48, C:0.28, G:0.11, T:0.13
Consensus pattern (39 bp):
AATTACAAAGCCCCAAATAAGACCAAACCAAATGACCCA
Found at i:102183 original size:3 final size:3
Alignment explanation
Indices: 102177--102211 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
102167 ATAGCTGTTT
102177 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
102212 GCATTAATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:103311 original size:30 final size:29
Alignment explanation
Indices: 103270--103505 Score: 183
Period size: 30 Copynumber: 7.9 Consensus size: 29
103260 TTACACCTCG
*
103270 AACTTCCAAAAATCCCATTTTTGACCTCGA
1 AACTTCCAAAAATCCCATTTTT-ACCCCGA
* *** *
103300 AACTTCTAAAAATTTTAGTTTTACTCCCG-
1 AACTTCCAAAAATCCCATTTTTAC-CCCGA
* *
103329 AACTTTCAAAAATCCCATTTTTTAACCCGA
1 AACTTCCAAAAATCCCA-TTTTTACCCCGA
* *
103359 AACTTCTAAAAAAT-TCATTTTTATCCCCG-
1 AACTTC-CAAAAATCCCATTTTTA-CCCCGA
* **
103388 ATCTTCCAAAAATCCCATTTTTGACAGCGA
1 AACTTCCAAAAATCCCATTTTT-ACCCCGA
**** *
103418 AACTTCCAAAAATTTTGTTTTTACCCCCCA
1 AACTTCCAAAAATCCCATTTTTA-CCCCGA
103448 AACTTCCAAAAATCCCATTTTTTGACCCCGA
1 AACTTCCAAAAATCCCA-TTTTT-ACCCCGA
*
103479 AACTTCCAAAAATTACCA-TTTTACCCC
1 AACTTCCAAAAA-TCCCATTTTTACCCC
103506 CGGATGTCCA
Statistics
Matches: 158, Mismatches: 36, Indels: 25
0.72 0.16 0.11
Matches are distributed among these distances:
28 6 0.04
29 45 0.28
30 74 0.47
31 28 0.18
32 5 0.03
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTTACCCCGA
Found at i:103360 original size:59 final size:58
Alignment explanation
Indices: 103258--103492 Score: 249
Period size: 59 Copynumber: 3.9 Consensus size: 58
103248 AGTATTCTGC
* * *
103258 TTTTACACCTCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCTAAAAATTTTAG
1 TTTTACTCC-CGAACTTCCAAAAATCCCATTTTTAACC-CGAAACTTCCAAAAATTTTAG
* * * * *
103318 TTTTACTCCCGAACTTTCAAAAATCCCATTTTTTAACCCGAAACTTCTAAAAAATTCAT
1 TTTTACTCCCGAACTTCCAAAAATCCCA-TTTTTAACCCGAAACTTCCAAAAATTTTAG
* * *
103377 TTTTA-TCCCCGATCTTCCAAAAATCCCATTTTTGACAGCGAAACTTCCAAAAATTTT-G
1 TTTTACT-CCCGAACTTCCAAAAATCCCATTTTTAAC-CCGAAACTTCCAAAAATTTTAG
* * *
103435 TTTTTACCCCCCAAACTTCCAAAAATCCCATTTTTTGACCCCGAAACTTCCAAAAATT
1 -TTTTA-CTCCCGAACTTCCAAAAATCCCA-TTTTT-AACCCGAAACTTCCAAAAATT
103493 ACCATTTTAC
Statistics
Matches: 147, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
58 8 0.05
59 81 0.55
60 35 0.24
61 22 0.15
62 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (58 bp):
TTTTACTCCCGAACTTCCAAAAATCCCATTTTTAACCCGAAACTTCCAAAAATTTTAG
Found at i:103663 original size:29 final size:29
Alignment explanation
Indices: 103598--103663 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
103588 TACCCAAAAT
*
103598 TTTCCCAAAAATACCATTTTGCCCCCGAG
1 TTTCCTAAAAATACCATTTTGCCCCCGAG
** * *
103627 AAT-CTAAAATTACTATTTTGCCCCCGAG
1 TTTCCTAAAAATACCATTTTGCCCCCGAG
103655 TTTCCTAAA
1 TTTCCTAAA
103664 GTCTCATTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (29 bp):
TTTCCTAAAAATACCATTTTGCCCCCGAG
Found at i:106584 original size:17 final size:18
Alignment explanation
Indices: 106550--106585 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
106540 TGAATTTCTA
106550 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
106568 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
106585 T
1 T
106586 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:107008 original size:32 final size:32
Alignment explanation
Indices: 106972--107032 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
106962 TTCTTTTTTC
106972 CTTCTCTTCTCTCCATTCCTT-TTTCGTTTAAG
1 CTTCTCTTCT-TCCATTCCTTCTTTCGTTTAAG
* * *
107004 CTTCTGTTCTTCTATTCCTTCTTTTGTTT
1 CTTCTCTTCTTCCATTCCTTCTTTCGTTT
107033 CTTTTTCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 9 0.36
32 16 0.64
ACGTcount: A:0.07, C:0.28, G:0.07, T:0.59
Consensus pattern (32 bp):
CTTCTCTTCTTCCATTCCTTCTTTCGTTTAAG
Found at i:114130 original size:15 final size:15
Alignment explanation
Indices: 114094--114142 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
114084 TCGTTTAAGC
*
114094 TTCTGTTCTTATATTCT
1 TTCTTTTCTT-TATT-T
* *
114111 TTCTTTTGTTTCTTT
1 TTCTTTTCTTTATTT
114126 TTCTTTTCTTTATTT
1 TTCTTTTCTTTATTT
114141 TT
1 TT
114143 TTATGTCTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 16 0.59
16 3 0.11
17 8 0.30
ACGTcount: A:0.06, C:0.14, G:0.04, T:0.76
Consensus pattern (15 bp):
TTCTTTTCTTTATTT
Found at i:115154 original size:2 final size:2
Alignment explanation
Indices: 115149--115175 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
115139 TTAAACATTC
115149 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
115176 GAATTCAATC
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:116413 original size:2 final size:2
Alignment explanation
Indices: 116406--116432 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
116396 CCTGTTTCTT
116406 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
116433 TGTTTCACTG
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:117440 original size:2 final size:2
Alignment explanation
Indices: 117433--117464 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
117423 TTTTTCTCAA
117433 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
117465 GATTAAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:117616 original size:2 final size:2
Alignment explanation
Indices: 117609--117640 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
117599 TGAAGTTAAT
*
117609 TA TA TA TA GA 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 TA
117641 CAGTACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:119310 original size:2 final size:2
Alignment explanation
Indices: 119303--119328 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
119293 GGTGGGGATT
119303 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
119329 GGCAAGTATG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:123257 original size:47 final size:47
Alignment explanation
Indices: 123194--123322 Score: 131
Period size: 47 Copynumber: 2.8 Consensus size: 47
123184 AGTCACGTGT
**
123194 TCTACTCATCAAAAGCATGTTTACAATGACTCTTCACAAACACATGC
1 TCTACTCATCGGAAGCATGTTTACAATGACTCTTCACAAACACATGC
* * *
123241 TTTACTCATCGGAAGCATGTTTTC-ATAACTCCTT-ACAAACACATGC
1 TCTACTCATCGGAAGCATGTTTACAATGACT-CTTCACAAACACATGC
* * *
123287 TCCACTCCTCGGAAAAG-ATGTTTA-AATGACTTTTCA
1 TCTACTCATCGG--AAGCATGTTTACAATGACTCTTCA
123323 TTGACATGTA
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
46 28 0.42
47 35 0.53
48 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.31
Consensus pattern (47 bp):
TCTACTCATCGGAAGCATGTTTACAATGACTCTTCACAAACACATGC
Found at i:123299 original size:46 final size:47
Alignment explanation
Indices: 123197--123300 Score: 122
Period size: 46 Copynumber: 2.2 Consensus size: 47
123187 CACGTGTTCT
** * **
123197 ACTCATCAAAAGCATGTTTACAATGACTCTTCACAAACACATGCTTT
1 ACTCATCGGAAGCATGTTTACAATAACTCTTCACAAACACATGCTCC
*
123244 ACTCATCGGAAGCATGTTTTC-ATAACTCCTT-ACAAACACATGCTCC
1 ACTCATCGGAAGCATGTTTACAATAACT-CTTCACAAACACATGCTCC
*
123290 ACTCCTCGGAA
1 ACTCATCGGAA
123301 AAGATGTTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
46 28 0.57
47 21 0.43
ACGTcount: A:0.33, C:0.29, G:0.11, T:0.28
Consensus pattern (47 bp):
ACTCATCGGAAGCATGTTTACAATAACTCTTCACAAACACATGCTCC
Found at i:133555 original size:88 final size:89
Alignment explanation
Indices: 133449--133627 Score: 306
Period size: 91 Copynumber: 2.0 Consensus size: 89
133439 TTATTTCTCA
* *
133449 GCATGGTTTGTAACAAATT-AATTTTAATAAATTACCAATAAGTGTCGAGTGTAACGGTAACGTG
1 GCATGGTTTGTAACAAATTAAATTTTAATAAATTACCAATAAGTGTCGAGTGTAACGATAACATG
133513 CATTATACTTTCAAAGAGAGATGT
66 CATTATACTTTCAAAGAGAGATGT
133537 GCATGGTTTGTAACAAATTAAAAATTTTAATAAATTACCAATAAGTGTCGAGTGTAACGATAACA
1 GCATGGTTTGTAACAAATT--AAATTTTAATAAATTACCAATAAGTGTCGAGTGTAACGATAACA
*
133602 TGCATTATACTTTTAAAGAGAGATGT
64 TGCATTATACTTTCAAAGAGAGATGT
133628 AAATTCGAAC
Statistics
Matches: 85, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
88 19 0.22
91 66 0.78
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.33
Consensus pattern (89 bp):
GCATGGTTTGTAACAAATTAAATTTTAATAAATTACCAATAAGTGTCGAGTGTAACGATAACATG
CATTATACTTTCAAAGAGAGATGT
Found at i:135116 original size:20 final size:20
Alignment explanation
Indices: 135082--135119 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
135072 TTAGTAATAA
*
135082 TTATTTGAACTAATTATTAT
1 TTATTTGAACAAATTATTAT
*
135102 TTATTTGAAGAAATTATT
1 TTATTTGAACAAATTATT
135120 TCTATTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.53
Consensus pattern (20 bp):
TTATTTGAACAAATTATTAT
Found at i:143836 original size:23 final size:22
Alignment explanation
Indices: 143777--143836 Score: 52
Period size: 23 Copynumber: 2.7 Consensus size: 22
143767 TTTAACTCCT
*
143777 TTTAAATAT-TAAATAACCTTA
1 TTTAAATATATAAATAACCTAA
* * *
143798 TATT-AATAAATTAATAGATCTAA
1 T-TTAAATATATAAATA-ACCTAA
143821 TTTAAATATATAAATA
1 TTTAAATATATAAATA
143837 CACTATTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
21 5 0.17
22 9 0.31
23 15 0.52
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (22 bp):
TTTAAATATATAAATAACCTAA
Done.