Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011437.1 Kokia drynarioides strain JFW-HI SEQ_126421, 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: 91597
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
Found at i:5419 original size:26 final size:22
Alignment explanation
Indices: 5374--5419 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 22
5364 AGAGAAACGT
5374 AAATGTGATATGAAATTATGAG
1 AAATGTGATATGAAATTATGAG
5396 AAATGATGAATATGAGAGATTATG
1 AAATG-TG-ATATGA-A-ATTATG
5420 CCCATGTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.25
23 2 0.10
24 6 0.30
25 1 0.05
26 6 0.30
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (22 bp):
AAATGTGATATGAAATTATGAG
Found at i:5517 original size:23 final size:23
Alignment explanation
Indices: 5483--5670 Score: 126
Period size: 23 Copynumber: 8.4 Consensus size: 23
5473 CACTAGTGCA
*
5483 CTCTCTGATTAGCACTGTGTGTG
1 CTCTCTGTTTAGCACTGTGTGTG
* *
5506 CTCTTTGTTTAGTACT-TCGTGTG
1 CTCTCTGTTTAGCACTGT-GTGTG
** *
5529 CTCTCTGACTAGCACTGCGTGTG
1 CTCTCTGTTTAGCACTGTGTGTG
* *
5552 CCCTCTGTTTAGCAC-GTCTCGTG
1 CTCTCTGTTTAGCACTGTGT-GTG
*
5575 CTCTCAGTTATTAGCACT-TCGTGTG
1 CTCTCTG-T-TTAGCACTGT-GTGTG
* *
5600 CTCTCTGATTAGCACTTTGTGTG
1 CTCTCTGTTTAGCACTGTGTGTG
* * *
5623 --CTC-----AGTACTTTGTGTA
1 CTCTCTGTTTAGCACTGTGTGTG
*
5639 CTCTCTGTTTAGCACTTTGTGTG
1 CTCTCTGTTTAGCACTGTGTGTG
5662 CTCTCTGTT
1 CTCTCTGTT
5671 GCCCAGCACT
Statistics
Matches: 128, Mismatches: 22, Indels: 30
0.71 0.12 0.17
Matches are distributed among these distances:
16 11 0.09
18 3 0.02
21 3 0.02
22 3 0.02
23 88 0.69
24 2 0.02
25 17 0.13
26 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (23 bp):
CTCTCTGTTTAGCACTGTGTGTG
Found at i:5551 original size:46 final size:46
Alignment explanation
Indices: 5483--5625 Score: 162
Period size: 46 Copynumber: 3.1 Consensus size: 46
5473 CACTAGTGCA
* * *
5483 CTCTCTGATTAGCACTGTGTGTGCTCTTTGTTTAGTACTTCGTGTG
1 CTCTCTGATTAGCACTGCGTGTGCTCTCTGTTTAGCACTTCGTGTG
* * *
5529 CTCTCTGACTAGCACTGCGTGTGCCCTCTGTTTAGCACGTC-TCGTG
1 CTCTCTGATTAGCACTGCGTGTGCTCTCTGTTTAGCACTTCGT-GTG
* * * *
5575 CTCTCAGTTATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGTG
1 CTCTC--TGATTAGCACTGCGTGTGCTCTCTGTTTAGCACTTCGTGTG
5623 CTC
1 CTC
5626 AGTACTTTGT
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
45 1 0.01
46 43 0.54
48 35 0.44
49 1 0.01
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (46 bp):
CTCTCTGATTAGCACTGCGTGTGCTCTCTGTTTAGCACTTCGTGTG
Found at i:5557 original size:25 final size:23
Alignment explanation
Indices: 5483--5625 Score: 128
Period size: 23 Copynumber: 6.1 Consensus size: 23
5473 CACTAGTGCA
*
5483 CTCTCTGATTAGCACTGTGTGTG
1 CTCTCTGATTAGCACTGCGTGTG
* * * *
5506 CTCTTTGTTTAGTACTTCGTGTG
1 CTCTCTGATTAGCACTGCGTGTG
*
5529 CTCTCTGACTAGCACTGCGTGTG
1 CTCTCTGATTAGCACTGCGTGTG
* *
5552 CCCTCTGTTTAGCAC-GTC-TCGTG
1 CTCTCTGATTAGCACTG-CGT-GTG
* *
5575 CTCTCAGTTATTAGCACTTCGTGTG
1 CTCTC--TGATTAGCACTGCGTGTG
**
5600 CTCTCTGATTAGCACTTTGTGTG
1 CTCTCTGATTAGCACTGCGTGTG
5623 CTC
1 CTC
5626 AGTACTTTGT
Statistics
Matches: 95, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
22 2 0.02
23 75 0.79
25 17 0.18
26 1 0.01
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (23 bp):
CTCTCTGATTAGCACTGCGTGTG
Found at i:5654 original size:39 final size:39
Alignment explanation
Indices: 5590--5664 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
5580 AGTTATTAGC
*
5590 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
5629 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
5665 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:25988 original size:31 final size:32
Alignment explanation
Indices: 25945--26012 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 32
25935 GATGTAATTT
* *
25945 AATTAAATTGAAGGTGAATGATG-AATATGAA
1 AATTAAATTGAAGGTCAATGATGTAAAATGAA
* *
25976 AATTAAGA-TGAAGTTCAATGATGTAAAATGTA
1 AATTAA-ATTGAAGGTCAATGATGTAAAATGAA
26008 AATTA
1 AATTA
26013 CCCGATAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 19 0.61
32 12 0.39
ACGTcount: A:0.49, C:0.01, G:0.19, T:0.31
Consensus pattern (32 bp):
AATTAAATTGAAGGTCAATGATGTAAAATGAA
Found at i:27564 original size:11 final size:11
Alignment explanation
Indices: 27523--27563 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
27513 ATAATTTTAT
*
27523 ATTTAAAAATA
1 ATTTTAAAATA
*
27534 ATTTTAAATTA
1 ATTTTAAAATA
27545 ATTTTAAAAT-
1 ATTTTAAAATA
27555 ATTTTAAAA
1 ATTTTAAAA
27564 AATAATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTTTAAAATA
Found at i:30979 original size:58 final size:61
Alignment explanation
Indices: 30919--31035 Score: 166
Period size: 61 Copynumber: 2.0 Consensus size: 61
30909 TCTATAGGTC
* *
30919 AAACCCAAAAAAA-TATTTTTTTATCT-TTATGAGACTTGGCGTCGACCATTAGATGATCA
1 AAACCCAAAAAAATTATTTTTTTATCTATGATGAGACTTGGCATCGACCATTAGATGATCA
* * * *
30978 AAATCTAAAAAAATTATTTTTTTATCTATGATGAGACTTTGTATCGACCATTAGATGA
1 AAACCCAAAAAAATTATTTTTTTATCTATGATGAGACTTGGCATCGACCATTAGATGA
31036 CTAAAACTCA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
59 11 0.22
60 13 0.26
61 26 0.52
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (61 bp):
AAACCCAAAAAAATTATTTTTTTATCTATGATGAGACTTGGCATCGACCATTAGATGATCA
Found at i:41002 original size:94 final size:94
Alignment explanation
Indices: 40841--41029 Score: 369
Period size: 94 Copynumber: 2.0 Consensus size: 94
40831 ATCTCTAAAG
*
40841 AACCTTGAAACTTCCTTCAAAATTTGCTTGAAGTCCATTGACATTGTTGTTGCAATTCATGAGAA
1 AACCTTGAAACTTCCTTCAAAATTTGCCTGAAGTCCATTGACATTGTTGTTGCAATTCATGAGAA
40906 AATTGCCTCATGGGCTGCTTGTTGAATGA
66 AATTGCCTCATGGGCTGCTTGTTGAATGA
40935 AACCTTGAAACTTCCTTCAAAATTTGCCTGAAGTCCATTGACATTGTTGTTGCAATTCATGAGAA
1 AACCTTGAAACTTCCTTCAAAATTTGCCTGAAGTCCATTGACATTGTTGTTGCAATTCATGAGAA
41000 AATTGCCTCATGGGCTGCTTGTTGAATGA
66 AATTGCCTCATGGGCTGCTTGTTGAATGA
41029 A
1 A
41030 GAACAATGAT
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (94 bp):
AACCTTGAAACTTCCTTCAAAATTTGCCTGAAGTCCATTGACATTGTTGTTGCAATTCATGAGAA
AATTGCCTCATGGGCTGCTTGTTGAATGA
Found at i:48152 original size:28 final size:28
Alignment explanation
Indices: 48094--48154 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
48084 TGAAAAAAAA
** *
48094 AAAAAATGGTTTTAAAATTCTATGCATT
1 AAAAAATGGTTTTAAAATTCTACACAAT
*
48122 AAAAAATGGTTTTAAAGTT-TAACACAAT
1 AAAAAATGGTTTTAAAATTCT-ACACAAT
48150 AAAAA
1 AAAAA
48155 TAATGTGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.33
Consensus pattern (28 bp):
AAAAAATGGTTTTAAAATTCTACACAAT
Found at i:51895 original size:3 final size:3
Alignment explanation
Indices: 51889--51918 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
51879 TTGTTGTTGT
*
51889 TGA TGA TGA TGA TGA TGA TGA TGG TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
51919 AATTGATGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:58079 original size:2 final size:2
Alignment explanation
Indices: 58072--58106 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
58062 TACAGTAGGC
58072 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
58107 GAATGCCCCA
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:61436 original size:5 final size:5
Alignment explanation
Indices: 61421--61449 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
61411 GCTCGTGTTT
61421 TTATA -TATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA
61450 GATAGAGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:79586 original size:72 final size:71
Alignment explanation
Indices: 79457--79590 Score: 171
Period size: 73 Copynumber: 1.9 Consensus size: 71
79447 AATTTCAGTA
** *** * *
79457 ATTATAATATTTTTATTTTTATTTTTATAGAATATGTAATCATTTATTGTTTGTATAAATAATGA
1 ATTATAATATTTTTATTTTTATTTTTATAGAATATGTAAAAAAAAATTGATTATAT-AATAATGA
79522 TGTAATT
65 TGTAATT
*
79529 ATTATAATATTTTTATTTTTTATTTTTATTGAATATGTAAAAAAAAATT-ATTATATAATAAT
1 ATTATAATATTTTTA-TTTTTATTTTTATAGAATATGTAAAAAAAAATTGATTATATAATAAT
79591 TTATCAAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
71 6 0.11
72 20 0.38
73 27 0.51
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (71 bp):
ATTATAATATTTTTATTTTTATTTTTATAGAATATGTAAAAAAAAATTGATTATATAATAATGAT
GTAATT
Found at i:79902 original size:4 final size:4
Alignment explanation
Indices: 79893--79917 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
79883 ATTAAGAATC
79893 GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT G
79918 AAATAATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:81342 original size:23 final size:23
Alignment explanation
Indices: 81299--81344 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
81289 AATCCTCCTC
**
81299 CCTTTCTTGGTCTTAGTTTTATG
1 CCTTTCTTGGTCTTAACTTTATG
81322 CCTTTCTTGG-CTCTAACTTTATG
1 CCTTTCTTGGTCT-TAACTTTATG
81345 TCATGATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.11, C:0.22, G:0.15, T:0.52
Consensus pattern (23 bp):
CCTTTCTTGGTCTTAACTTTATG
Found at i:84049 original size:33 final size:33
Alignment explanation
Indices: 84007--84071 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
83997 ATGCTCATGA
84007 GAGAGATGATATGTGGGATTTATTACGTCGTTG
1 GAGAGATGATATGTGGGATTTATTACGTCGTTG
84040 GAGAGATGATATGTGGGATTTATTACGTCGTT
1 GAGAGATGATATGTGGGATTTATTACGTCGTT
84072 TAGGTCAGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.25, C:0.06, G:0.32, T:0.37
Consensus pattern (33 bp):
GAGAGATGATATGTGGGATTTATTACGTCGTTG
Found at i:88468 original size:20 final size:19
Alignment explanation
Indices: 88430--88495 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
88420 GTTATAAAAG
*
88430 ATTA-TAAAATT-TAGAAA
1 ATTATTAAAATTATTGAAA
88447 ATTATTTAAAATTATTGAAA
1 ATTA-TTAAAATTATTGAAA
*
88467 ATTATAATAAATTATT-AAA
1 ATTATTA-AAATTATTGAAA
*
88486 ATTAATAAAA
1 ATTATTAAAA
88496 AATATTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
17 4 0.10
18 3 0.07
19 17 0.41
20 17 0.41
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
ATTATTAAAATTATTGAAA
Found at i:88488 original size:19 final size:19
Alignment explanation
Indices: 88444--88510 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
88434 TAAAATTTAG
* *
88444 AAAATTATTTAAAATTATT
1 AAAATTAATAAAAATTATT
88463 GAAAATT-ATAATAAATTATT
1 -AAAATTAATAA-AAATTATT
*
88483 AAAATTAATAAAAAATATT
1 AAAATTAATAAAAATTATT
*
88502 AAAAATAAT
1 AAAATTAAT
88511 GTCCTCAATG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 23 0.56
20 18 0.44
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (19 bp):
AAAATTAATAAAAATTATT
Found at i:88506 original size:10 final size:10
Alignment explanation
Indices: 88444--88507 Score: 69
Period size: 10 Copynumber: 6.5 Consensus size: 10
88434 TAAAATTTAG
*
88444 AAAATTATTT
1 AAAATTATTA
*
88454 AAAATTATTG
1 AAAATTATTA
88464 AAAATTA-TA
1 AAAATTATTA
88473 ATAAATTATT-
1 A-AAATTATTA
*
88483 AAAATTAATA
1 AAAATTATTA
*
88493 AAAAATATTA
1 AAAATTATTA
88503 AAAAT
1 AAAAT
88508 AATGTCCTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
9 9 0.20
10 35 0.78
11 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (10 bp):
AAAATTATTA
Found at i:88682 original size:20 final size:20
Alignment explanation
Indices: 88634--88684 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
88624 TTGTAGTTAT
* *
88634 AATTATTGAGAATTATAACA
1 AATTATTTAAAATTATAACA
88654 AATTA-TTAAAATTAATAA-A
1 AATTATTTAAAATT-ATAACA
88673 AATTATTTAAAA
1 AATTATTTAAAA
88685 ACGATTGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (20 bp):
AATTATTTAAAATTATAACA
Found at i:89173 original size:2 final size:2
Alignment explanation
Indices: 89168--89192 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
89158 TTGCTATATA
89168 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
89193 TTTTCTTTAG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:90543 original size:20 final size:20
Alignment explanation
Indices: 90502--90543 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
90492 TATTTATTTA
*
90502 TTACTATTTTGGTGCTTTTT
1 TTACTATTTTGGTGCTTATT
90522 TTACTATTTTGGT-CGTTATT
1 TTACTATTTTGGTGC-TTATT
90542 TT
1 TT
90544 CGTGTTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (20 bp):
TTACTATTTTGGTGCTTATT
Found at i:90561 original size:12 final size:12
Alignment explanation
Indices: 90546--90585 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
90536 GTTATTTTCG
*
90546 TGTTGTTTTTGC
1 TGTTGTTTTTGT
*
90558 TGTTATTTTTGT
1 TGTTGTTTTTGT
*
90570 TGCTGTTTTTGT
1 TGTTGTTTTTGT
90582 TGTT
1 TGTT
90586 TTTAATGGTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.03, C:0.05, G:0.23, T:0.70
Consensus pattern (12 bp):
TGTTGTTTTTGT
Found at i:90567 original size:24 final size:23
Alignment explanation
Indices: 90536--90585 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
90526 TATTTTGGTC
*
90536 GTTATTTTCG-TGTTGTTTTTGCT
1 GTTATTTT-GTTGCTGTTTTTGCT
*
90559 GTTATTTTTGTTGCTGTTTTTGTT
1 GTTA-TTTTGTTGCTGTTTTTGCT
90583 GTT
1 GTT
90586 TTTAATGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.04, C:0.06, G:0.22, T:0.68
Consensus pattern (23 bp):
GTTATTTTGTTGCTGTTTTTGCT
Found at i:90574 original size:15 final size:15
Alignment explanation
Indices: 90548--90585 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
90538 TATTTTCGTG
*
90548 TTGTTTTTGCTGTTAT
1 TTGTTGTTGCTGTT-T
90564 TT-TTGTTGCTGTTT
1 TTGTTGTTGCTGTTT
90578 TTGTTGTT
1 TTGTTGTT
90586 TTTAATGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 3 0.15
15 15 0.75
16 2 0.10
ACGTcount: A:0.03, C:0.05, G:0.21, T:0.71
Consensus pattern (15 bp):
TTGTTGTTGCTGTTT
Found at i:90582 original size:21 final size:21
Alignment explanation
Indices: 90558--90638 Score: 63
Period size: 22 Copynumber: 3.7 Consensus size: 21
90548 TTGTTTTTGC
90558 TGTTATTTTTGTTGCTGTTTT
1 TGTTATTTTTGTTGCTGTTTT
* ** *
90579 TGTTGTTTTTAATGGTGTTTTT
1 TGTTATTTTTGTTGCTG-TTTT
** *
90601 TGTTATTTTTCCTGCTATTTTGAT
1 TGTTATTTTTGTTGCT-GTTT--T
90625 TGTTATTTTTGTTG
1 TGTTATTTTTGTTG
90639 TTTGGATGTT
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
21 13 0.29
22 19 0.42
24 13 0.29
ACGTcount: A:0.09, C:0.05, G:0.19, T:0.68
Consensus pattern (21 bp):
TGTTATTTTTGTTGCTGTTTT
Found at i:90640 original size:12 final size:12
Alignment explanation
Indices: 90526--90585 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 12
90516 CTTTTTTTAC
* *
90526 TATTTTGGTCGT
1 TATTTTTGTTGT
*
90538 TATTTTCG-TGT
1 TATTTTTGTTGT
* *
90549 TGTTTTTGCTGT
1 TATTTTTGTTGT
*
90561 TATTTTTGTTGC
1 TATTTTTGTTGT
*
90573 TGTTTTTGTTGT
1 TATTTTTGTTGT
90585 T
1 T
90586 TTTAATGGTG
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
11 8 0.21
12 30 0.79
ACGTcount: A:0.05, C:0.07, G:0.22, T:0.67
Consensus pattern (12 bp):
TATTTTTGTTGT
Done.