Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010714.1 Kokia drynarioides strain JFW-HI SEQ_125664, 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: 61012
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 234 characters in sequence are not A, C, G, or T
Found at i:1319 original size:27 final size:28
Alignment explanation
Indices: 1272--1331 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 28
1262 AATTTTCAAC
* * *
1272 TAATGATTGTTTTCTTTGATCCTCTTTT
1 TAATGATTGTTTCCTTCGATCCTCTTCT
1300 TAAT-ATTGTTTCCTTCGATCCTCTTCT
1 TAATGATTGTTTCCTTCGATCCTCTTCT
1327 TAATG
1 TAATG
1332 GAATTTTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.17, C:0.18, G:0.10, T:0.55
Consensus pattern (28 bp):
TAATGATTGTTTCCTTCGATCCTCTTCT
Found at i:2694 original size:17 final size:17
Alignment explanation
Indices: 2649--2736 Score: 72
Period size: 17 Copynumber: 5.1 Consensus size: 17
2639 ATTTTAACTC
*
2649 ATTTTGAGTTTAAATTT
1 ATTTTAAGTTTAAATTT
*
2666 AATTTAAAGTTTAAACTTT
1 -ATTTTAAGTTTAAA-TTT
2685 -TTTTAAGTTTAAATTT
1 ATTTTAAGTTTAAATTT
** *
2701 AAATTAAGTTTAAAATTA
1 ATTTTAAGTTT-AAATTT
*
2719 ATTTGAA-TTTAAAATTT
1 ATTTTAAGTTT-AAATTT
2736 A
1 A
2737 ATTAATTTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
16 3 0.05
17 30 0.53
18 21 0.37
19 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (17 bp):
ATTTTAAGTTTAAATTT
Found at i:2701 original size:6 final size:6
Alignment explanation
Indices: 2657--2737 Score: 55
Period size: 6 Copynumber: 13.8 Consensus size: 6
2647 TCATTTTGAG
* *
2657 TTTAAA TTT-AA TTTAAA GTTTAAA CTTT--T TTTAAG TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA -TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA
* * *
2704 -TTAAG TTTAAA ATT-AA TTTGAA TTTAAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAA
2738 TTAATTTAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
4 3 0.05
5 13 0.22
6 29 0.49
7 14 0.24
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:2734 original size:35 final size:33
Alignment explanation
Indices: 2651--2748 Score: 101
Period size: 34 Copynumber: 2.9 Consensus size: 33
2641 TTTAACTCAT
* * * *
2651 TTTGAGTTTAAATTTAATTTAAAGTTTAAACTTT
1 TTTGAATTTAAATTTAAATT-AAGTTTAAAATTA
*
2685 TTTTAAGTTTAAATTTAAATTAAGTTTAAAATTAA
1 TTTGAA-TTTAAATTTAAATTAAGTTTAAAATT-A
2720 TTTGAATTTAAAATTT-AATTAA-TTTAAAA
1 TTTGAATTT-AAATTTAAATTAAGTTTAAAA
2749 AAAAGGTCCA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
33 7 0.13
34 24 0.44
35 24 0.44
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (33 bp):
TTTGAATTTAAATTTAAATTAAGTTTAAAATTA
Found at i:2749 original size:17 final size:16
Alignment explanation
Indices: 2695--2748 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
2685 TTTTAAGTTT
2695 AAATTTAAATTAAGTTTA
1 AAATTT-AATTAA-TTTA
2713 AAA-TTAATTTGAATTTA
1 AAATTTAA-TT-AATTTA
2730 AAATTTAATTAATTTA
1 AAATTTAATTAATTTA
2746 AAA
1 AAA
2749 AAAAGGTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 11 0.33
17 13 0.39
18 9 0.27
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (16 bp):
AAATTTAATTAATTTA
Found at i:3362 original size:3 final size:3
Alignment explanation
Indices: 3354--3409 Score: 87
Period size: 3 Copynumber: 18.7 Consensus size: 3
3344 TAATAGTCAT
*
3354 TAA TAA TAA TAGC T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3399 TAA TAA TAA TA
1 TAA TAA TAA TA
3410 GCATTAATGA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 1 0.02
3 47 0.96
4 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4531 original size:30 final size:29
Alignment explanation
Indices: 4482--4744 Score: 251
Period size: 29 Copynumber: 8.9 Consensus size: 29
4472 CCCTAAATTA
*
4482 TCCAAAAATTCCATTTTTACCCCCGAACT
1 TCCAAAAATCCCATTTTTACCCCCGAACT
* **
4511 TCCAATAATCCCATTTTTTACCCCAAAACT
1 TCCAAAAATCCCA-TTTTTACCCCCGAACT
* * **
4541 TCCAAAAATTCTATTTTTACCCCTAAACT
1 TCCAAAAATCCCATTTTTACCCCCGAACT
* ***
4570 TCTAAAAATCCCATTTTTAACCCAAAAACT
1 TCCAAAAATCCCATTTTT-ACCCCCGAACT
* * *
4600 TCCAAAAATTCCATTTCTACCCTCGAACT
1 TCCAAAAATCCCATTTTTACCCCCGAACT
**
4629 TCCAAAAAATCCCATTTTTAACCCCAAAACT
1 TCC-AAAAATCCCATTTTT-ACCCCCGAACT
* * **
4660 TCCAAAAAATTCTATTTTTACCCTTGAACT
1 TCC-AAAAATCCCATTTTTACCCCCGAACT
*
4690 TCCAAAAATCCCATTTTTA-ACCCGAACT
1 TCCAAAAATCCCATTTTTACCCCCGAACT
*
4718 TCCAAAAATTACC-TTTTTACCCCCGAA
1 TCCAAAAA-TCCCATTTTTACCCCCGAA
4745 TGTCTGAAGA
Statistics
Matches: 192, Mismatches: 36, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
28 20 0.10
29 75 0.39
30 72 0.38
31 25 0.13
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.32
Consensus pattern (29 bp):
TCCAAAAATCCCATTTTTACCCCCGAACT
Found at i:4580 original size:59 final size:59
Alignment explanation
Indices: 4482--4740 Score: 355
Period size: 59 Copynumber: 4.4 Consensus size: 59
4472 CCCTAAATTA
* * *
4482 TCCAAAAATTCCATTTTTACCCCCGAACTTCCAATAATCCCATTTTTTACCCCAAAACT
1 TCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
* * * *
4541 TCCAAAAATTCTATTTTTACCCCTAAACTTCTAAAAATCCCATTTTTAACCCAAAAACT
1 TCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
*
4600 TCCAAAAATTCCATTTCTA-CCCTCGAACTTCCAAAAAATCCCATTTTTAACCCCAAAACT
1 TCCAAAAATTCCATTTTTACCCCT-GAACTTCC-AAAAATCCCATTTTTAACCCCAAAACT
* * *
4660 TCCAAAAAATTCTATTTTTACCCTTGAACTTCCAAAAATCCCATTTTTAA-CCC-GAACT
1 TCC-AAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
4718 TCCAAAAATTACC-TTTTTACCCC
1 TCCAAAAATT-CCATTTTTACCCC
4741 CGAATGTCTG
Statistics
Matches: 177, Mismatches: 18, Indels: 12
0.86 0.09 0.06
Matches are distributed among these distances:
57 16 0.09
58 12 0.07
59 78 0.44
60 46 0.26
61 22 0.12
62 3 0.02
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.32
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
Found at i:7656 original size:27 final size:27
Alignment explanation
Indices: 7603--7665 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
7593 AACATGCCAA
* *
7603 AAAATGAAAGCCTTTGTGACGACCTAT
1 AAAATGAAAACCTTTGTGACAACCTAT
* *
7630 AAAATGAAAACCTTTGTGGCAATCTAT
1 AAAATGAAAACCTTTGTGACAACCTAT
**
7657 GGAATGAAA
1 AAAATGAAA
7666 GCTTGGGTGG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.25
Consensus pattern (27 bp):
AAAATGAAAACCTTTGTGACAACCTAT
Found at i:17570 original size:20 final size:22
Alignment explanation
Indices: 17539--17582 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
17529 TGCTTTTATT
17539 TTTCATATATTATA-TAAAATA
1 TTTCATATATTATACTAAAATA
*
17560 TTTCA-ATATTATACTAATATA
1 TTTCATATATTATACTAAAATA
17581 TT
1 TT
17583 ATATTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTCATATATTATACTAAAATA
Found at i:18836 original size:24 final size:24
Alignment explanation
Indices: 18804--18851 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
18794 AATCCTATTA
*
18804 AAATCTAAAAATTCAAAAATAAAT
1 AAATATAAAAATTCAAAAATAAAT
18828 AAATATAAAAATTCAAAAATAAAT
1 AAATATAAAAATTCAAAAATAAAT
18852 TAAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (24 bp):
AAATATAAAAATTCAAAAATAAAT
Found at i:19646 original size:24 final size:24
Alignment explanation
Indices: 19614--19661 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
19604 ATAATTTTTA
*
19614 TGAACTTTTTATATTTTTTAAATT
1 TGAACTTTTTATAATTTTTAAATT
*
19638 TGAATTTTTTATAATTTTTAAATT
1 TGAACTTTTTATAATTTTTAAATT
19662 ATTTGTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (24 bp):
TGAACTTTTTATAATTTTTAAATT
Found at i:20314 original size:21 final size:20
Alignment explanation
Indices: 20290--20359 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
20280 AAAAATTCCG
20290 AATATTTTTATAAAAAATTAA
1 AATATTTTTA-AAAAAATTAA
* *
20311 AATATGTTTTAGATAAATTAA
1 AATAT-TTTTAAAAAAATTAA
* *
20332 AA-AATTTTAAAATAATTTAA
1 AATATTTTTAAAA-AAATTAA
20352 AATTATTT
1 AA-TATTT
20360 AGAATTGATT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
19 6 0.16
20 9 0.24
21 15 0.39
22 8 0.21
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
AATATTTTTAAAAAAATTAA
Found at i:27491 original size:17 final size:17
Alignment explanation
Indices: 27469--27548 Score: 81
Period size: 17 Copynumber: 4.7 Consensus size: 17
27459 TCTTTTAGCA
27469 GGTGAGCTCGCACACTT
1 GGTGAGCTCGCACACTT
* ***
27486 GGTGAGTTCGCGTTCTT
1 GGTGAGCTCGCACACTT
*
27503 GGTAAGCTCGCA-ATCTT
1 GGTGAGCTCGCACA-CTT
* *
27520 TGTGAGCTTGCACACTT
1 GGTGAGCTCGCACACTT
27537 GGTGAGCTCGCA
1 GGTGAGCTCGCA
27549 ATTCACAATT
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
17 47 0.98
18 1 0.02
ACGTcount: A:0.16, C:0.24, G:0.30, T:0.30
Consensus pattern (17 bp):
GGTGAGCTCGCACACTT
Found at i:32471 original size:34 final size:34
Alignment explanation
Indices: 32420--32497 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
32410 TCTTTTAGTA
* *
32420 GGTGAGCTTGCACACTTGATGAGCCCGCAATCTC
1 GGTGAGCTCGCATACTTGATGAGCCCGCAATCTC
* * ** *
32454 GGTGATCTCGCATACTTGGTGAGCTTGCAATCTT
1 GGTGAGCTCGCATACTTGATGAGCCCGCAATCTC
32488 GGTGAGCTCG
1 GGTGAGCTCG
32498 TATTTACAGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.28
Consensus pattern (34 bp):
GGTGAGCTCGCATACTTGATGAGCCCGCAATCTC
Found at i:32474 original size:17 final size:17
Alignment explanation
Indices: 32420--32497 Score: 70
Period size: 17 Copynumber: 4.6 Consensus size: 17
32410 TCTTTTAGTA
*
32420 GGTGAGCTTGCACA-CTT
1 GGTGAGCTCGCA-ATCTT
* * *
32437 GATGAGCCCGCAATCTC
1 GGTGAGCTCGCAATCTT
*
32454 GGTGATCTCGC-ATACTT
1 GGTGAGCTCGCAAT-CTT
*
32471 GGTGAGCTTGCAATCTT
1 GGTGAGCTCGCAATCTT
32488 GGTGAGCTCG
1 GGTGAGCTCG
32498 TATTTACAGT
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
16 3 0.06
17 42 0.89
18 2 0.04
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.28
Consensus pattern (17 bp):
GGTGAGCTCGCAATCTT
Found at i:41691 original size:17 final size:17
Alignment explanation
Indices: 41669--41707 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
41659 CTCCACCTTG
* * *
41669 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACAA
41686 ACAAGAACTCTCAACAA
1 ACAAGAACTCTCAACAA
41703 ACAAG
1 ACAAG
41708 TTCTCCACCT
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:0.49, C:0.26, G:0.10, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACAA
Found at i:46802 original size:59 final size:59
Alignment explanation
Indices: 46706--46886 Score: 197
Period size: 59 Copynumber: 3.0 Consensus size: 59
46696 TTGATACTTG
* * *
46706 AACTTGACACTTTTTTTTAATTTGGCATCTAAA-TTTTTTTTGACTTAATTTGGTACCTA
1 AACTTGACAC-TTTTTTTAATTTGGTACCTAAACTTTTTTTAGACTTAATTTGGTACCTA
* * **
46765 AACTTGACACTTTTTTTAATTTGGTACCTAAACTTTTTTTGGACTCAATTTGGTGTCTA
1 AACTTGACACTTTTTTTAATTTGGTACCTAAACTTTTTTTAGACTTAATTTGGTACCTA
* * * *
46824 AACTTGGTC-TTTTTTCTTAATTTGGTACTTAAGCTTTGTTTTAGA-TTCAATTTGGTACCTA
1 AACTT-GACACTTTTT-TTAATTTGGTACCTAAACTTT-TTTTAGACTT-AATTTGGTACCTA
46885 AA
1 AA
46887 TTTATTAAAT
Statistics
Matches: 103, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
58 20 0.19
59 42 0.41
60 22 0.21
61 19 0.18
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.49
Consensus pattern (59 bp):
AACTTGACACTTTTTTTAATTTGGTACCTAAACTTTTTTTAGACTTAATTTGGTACCTA
Found at i:47082 original size:31 final size:31
Alignment explanation
Indices: 47045--47114 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
47035 GAACCTCAAA
*
47045 AAGTTTAAGTACCAACTTAAAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
* *
47076 AAGTTTAGGTACCAAATTAGAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
47107 AAGTTTAA
1 AAGTTTAA
47115 AAATCAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.47, C:0.10, G:0.16, T:0.27
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
Found at i:47123 original size:31 final size:31
Alignment explanation
Indices: 47045--47133 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
47035 GAACCTCAAA
** * *
47045 AAGTTTAAGTACCAACTTAAAAAAAAGTGTC
1 AAGTTTAAAAACCAAATTAGAAAAAAGTGTC
***
47076 AAGTTTAGGTACCAAATTAGAAAAAAGTGTC
1 AAGTTTAAAAACCAAATTAGAAAAAAGTGTC
* *
47107 AAGTTTAAAAATCAAATTGGACAAAAA
1 AAGTTTAAAAACCAAATTAGA-AAAAA
47134 AAAAAATTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 44 0.90
32 5 0.10
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.25
Consensus pattern (31 bp):
AAGTTTAAAAACCAAATTAGAAAAAAGTGTC
Found at i:51084 original size:43 final size:43
Alignment explanation
Indices: 51032--51118 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
51022 AACATGATCC
*
51032 TACTCAAAGTGATAGTTACTTTTATTAACGATCAAATTTATCT
1 TACTCAAAGTGATAGTTACTTTTATCAACGATCAAATTTATCT
* * * *
51075 TACTTAAAGTGATAGTTCCTTTTATCGATGATCAAATTTATCT
1 TACTCAAAGTGATAGTTACTTTTATCAACGATCAAATTTATCT
51118 T
1 T
51119 TCATAATTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (43 bp):
TACTCAAAGTGATAGTTACTTTTATCAACGATCAAATTTATCT
Found at i:51966 original size:22 final size:21
Alignment explanation
Indices: 51927--51967 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
51917 AAAAAATATT
*
51927 AAAAAGTCCATTTTAAAATAA
1 AAAAAGTCCATTTCAAAATAA
51948 AAAAAGTCCATTTACAAAAT
1 AAAAAGTCCATTT-CAAAAT
51968 TAACCCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.27
Consensus pattern (21 bp):
AAAAAGTCCATTTCAAAATAA
Found at i:51994 original size:15 final size:16
Alignment explanation
Indices: 51974--52006 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
51964 AAATTAACCC
*
51974 AATTTAC-CCAAACTA
1 AATTTACTCAAAACTA
51989 AATTTACTCAAAACTA
1 AATTTACTCAAAACTA
52005 AA
1 AA
52007 CCCACTAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (16 bp):
AATTTACTCAAAACTA
Found at i:54451 original size:2 final size:2
Alignment explanation
Indices: 54444--54468 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54434 CTTTTGCATG
54444 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 T
54469 CTTTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60047 original size:22 final size:22
Alignment explanation
Indices: 60024--60065 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
60014 CCCTCTTAAT
60024 TTTCTATTA-TTTATTTATTTA
1 TTTCTATTATTTTATTTATTTA
*
60045 TTTGTATTATTTTATTTATTT
1 TTTCTATTATTTTATTTATTT
60066 TGGGTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTCTATTATTTTATTTATTTA
Found at i:60056 original size:9 final size:9
Alignment explanation
Indices: 60030--60127 Score: 58
Period size: 9 Copynumber: 10.7 Consensus size: 9
60020 TAATTTTCTA
60030 TTATTTA-T
1 TTATTTATT
60038 TTATTTATT
1 TTATTTATT
60047 TGTA-TTATT
1 T-TATTTATT
60056 TTATTTATT
1 TTATTTATT
***
60065 TTGGGTATT
1 TTATTTATT
* *
60074 TAATTTGTAT
1 TTATTTAT-T
*
60084 TTATTTATGGG
1 TTATTTAT--T
60095 TT-TTTATT
1 TTATTTATT
*
60103 TCATTTCATT
1 TTATTT-ATT
*
60113 TCATTTATT
1 TTATTTATT
60122 TTATTT
1 TTATTT
60128 TCTTTTAGTT
Statistics
Matches: 68, Mismatches: 15, Indels: 13
0.71 0.16 0.14
Matches are distributed among these distances:
8 10 0.15
9 33 0.49
10 23 0.34
11 2 0.03
ACGTcount: A:0.20, C:0.03, G:0.08, T:0.68
Consensus pattern (9 bp):
TTATTTATT
Found at i:60089 original size:24 final size:24
Alignment explanation
Indices: 60033--60113 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
60023 TTTTCTATTA
**
60033 TTTATTTATTTATTTGTA-TT-AT
1 TTTATTTATTTATGGGTATTTAAT
60055 TTTATTTATTT-TGGGTATTTAAT
1 TTTATTTATTTATGGGTATTTAAT
*
60078 TTGTATTTATTTATGGGT-TTTTAT
1 TT-TATTTATTTATGGGTATTTAAT
*
60102 TTCATTTCATTT
1 TTTATTT-ATTT
60114 CATTTATTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
21 4 0.08
22 13 0.26
23 8 0.16
24 20 0.40
25 5 0.10
ACGTcount: A:0.20, C:0.02, G:0.10, T:0.68
Consensus pattern (24 bp):
TTTATTTATTTATGGGTATTTAAT
Done.