Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009000.1 Kokia drynarioides strain JFW-HI SEQ_123698, 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: 54151
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3620 original size:57 final size:57
Alignment explanation
Indices: 3552--3732 Score: 231
Period size: 57 Copynumber: 3.1 Consensus size: 57
3542 AAATTCAAGT
* * *
3552 CATTTTCATTTTCATTTTTGAGAAAATCACATTCATTTCCAAATGATTTCATTTCTC
1 CATTTTCATTTTCATTTTTGAGAAAACCATAATCATTTCCAAATGATTTCATTTCTC
*
3609 CATTTTTATTTTC-TTTTTGGAGAAAACCATAATCATTTCCAAATG-TTTCCATTTCTC
1 CATTTTCATTTTCATTTTT-GAGAAAACCATAATCATTTCCAAATGATTT-CATTTCTC
* * * * *
3666 CATTTTCATTTTTATTTTGGAGAAGACCATAATAATTTCCAAATGATTTCTTGTTTCTC
1 CATTTTCATTTTCATTTTTGAGAAAACCATAATCATTTCCAAATGATTTC--ATTTCTC
3725 CATTTTCA
1 CATTTTCA
3733 CCATTTCTCT
Statistics
Matches: 108, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
56 8 0.07
57 79 0.73
58 7 0.06
59 14 0.13
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (57 bp):
CATTTTCATTTTCATTTTTGAGAAAACCATAATCATTTCCAAATGATTTCATTTCTC
Found at i:5525 original size:3 final size:3
Alignment explanation
Indices: 5519--5565 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
5509 CCTACTCTTA
5519 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT CAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
5564 AA
1 AA
5566 AAGGTAATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5678 original size:17 final size:17
Alignment explanation
Indices: 5655--5696 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
5645 ACTTTTCCTT
5655 TTAAAAATTATT-TTTATC
1 TTAAAAA-TATTATTT-TC
5673 TTAAAAATATTATTTTC
1 TTAAAAATATTATTTTC
5690 TTAAAAA
1 TTAAAAA
5697 GTTTTATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAAAATATTATTTTC
Found at i:12582 original size:17 final size:17
Alignment explanation
Indices: 12556--12598 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
12546 AGAAAAAAGT
*
12556 AGTTACAAGAATAT-GAA
1 AGTTA-AAGAAGATGGAA
12573 AGGTTAAAGAAGATGGAA
1 A-GTTAAAGAAGATGGAA
12591 AGTTAAAG
1 AGTTAAAG
12599 GTCAAAGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.51, C:0.02, G:0.26, T:0.21
Consensus pattern (17 bp):
AGTTAAAGAAGATGGAA
Found at i:12598 original size:24 final size:23
Alignment explanation
Indices: 12571--12615 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
12561 CAAGAATATG
*
12571 AAAGGTTAAAGAAGATGGAAAGTT
1 AAAGGTCAAAGAAGAT-GAAAGTT
*
12595 AAAGGTCAAAGGAGATGAAAG
1 AAAGGTCAAAGAAGATGAAAG
12616 GTTGAACATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.51, C:0.02, G:0.31, T:0.16
Consensus pattern (23 bp):
AAAGGTCAAAGAAGATGAAAGTT
Found at i:18640 original size:21 final size:21
Alignment explanation
Indices: 18614--18662 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
18604 TATTTATTTA
18614 ATAAT-ATAGTAAATTATTAAT
1 ATAATAATA-TAAATTATTAAT
* *
18635 ATAATAATATAATTTATTATT
1 ATAATAATATAAATTATTAAT
*
18656 GTAATAA
1 ATAATAA
18663 ATTATTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (21 bp):
ATAATAATATAAATTATTAAT
Found at i:18687 original size:18 final size:18
Alignment explanation
Indices: 18664--18702 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
18654 TTGTAATAAA
*
18664 TTATTT-AATATTACAATT
1 TTATTTCAATAGTA-AATT
18682 TTATTTCAATAGTAAATT
1 TTATTTCAATAGTAAATT
18700 TTA
1 TTA
18703 ACAATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (18 bp):
TTATTTCAATAGTAAATT
Found at i:22467 original size:52 final size:52
Alignment explanation
Indices: 22345--22522 Score: 227
Period size: 52 Copynumber: 3.4 Consensus size: 52
22335 ATTTCACTTC
* * *
22345 ATTCATATACTCACGATGACACATAGCCA-CTGGACCT-TATAATTCGCAAGGG
1 ATTCATATACTCACGATGACACTTAGCCATC-GGACCTCT-TAATTCGTAAAGG
* * * *
22397 A-TCATATACTCACTATGACACTTAGGCATCGGACCTCTTAATCCATAAAGG
1 ATTCATATACTCACGATGACACTTAGCCATCGGACCTCTTAATTCGTAAAGG
*
22448 ATTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATTCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGCCATCGGACCTCTTAATTCGTAAAGG
* *
22500 ATTCATATGCTCACGACGACACT
1 ATTCATATACTCACGATGACACT
22523 GTCATTGGAC
Statistics
Matches: 110, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
51 40 0.36
52 70 0.64
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACTTAGCCATCGGACCTCTTAATTCGTAAAGG
Found at i:32225 original size:2 final size:2
Alignment explanation
Indices: 32218--32248 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
32208 TGAATTTAAT
32218 TA TA 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 TA TA T
32249 GAAATGCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37981 original size:41 final size:43
Alignment explanation
Indices: 37912--38036 Score: 164
Period size: 44 Copynumber: 2.9 Consensus size: 43
37902 AGCGTTTTTG
* * * *
37912 GAAAAAAAGGCCGCGAAAGGTAATAGCATTAGCGGCGTTTAT-
1 GAAAAAAACGCCGCAAAAGGTAAGAGCATTAGCGGCATTTATA
* * *
37954 G-ACAAAATGCCGCAAAAGATAAGAGCATTAGCGGCATTTATGA
1 GAAAAAAACGCCGCAAAAGGTAAGAGCATTAGCGGCATTTAT-A
37997 GAAAAAAACGCCGCAAAAGGTAAGAGCATTAGCGGCATTT
1 GAAAAAAACGCCGCAAAAGGTAAGAGCATTAGCGGCATTT
38037 TCCCATAAAC
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
41 34 0.48
42 1 0.01
43 1 0.01
44 35 0.49
ACGTcount: A:0.41, C:0.16, G:0.26, T:0.18
Consensus pattern (43 bp):
GAAAAAAACGCCGCAAAAGGTAAGAGCATTAGCGGCATTTATA
Found at i:39578 original size:42 final size:41
Alignment explanation
Indices: 39490--39579 Score: 110
Period size: 42 Copynumber: 2.2 Consensus size: 41
39480 TAAACGCCGT
* * *
39490 AAAAGGTAAAGCAATATCGGTGTTTATAAGGAAAATGCCAC
1 AAAAGGTAAAGCAATAGCGGCGTTTATAAGGAAAATACCAC
* *
39531 AAAAGGTATAGAGCAATAGCGGCGTTTATGA-GAAAATACCGC
1 AAAAGGTA-A-AGCAATAGCGGCGTTTATAAGGAAAATACCAC
39573 AAAAGGT
1 AAAAGGT
39580 CCAGACATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 8 0.19
42 17 0.40
43 17 0.40
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.20
Consensus pattern (41 bp):
AAAAGGTAAAGCAATAGCGGCGTTTATAAGGAAAATACCAC
Found at i:39685 original size:15 final size:15
Alignment explanation
Indices: 39665--39709 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
39655 CAGATTTCGA
* * *
39665 AATTTCGAAATTCTT
1 AATTTCTAAATCCCT
39680 AATTTCTAAATCCCT
1 AATTTCTAAATCCCT
39695 AATTTCTAAATCCCT
1 AATTTCTAAATCCCT
39710 CTCCTCCTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.02, T:0.42
Consensus pattern (15 bp):
AATTTCTAAATCCCT
Found at i:40698 original size:18 final size:18
Alignment explanation
Indices: 40665--40699 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40655 TGCCTCTGTA
**
40665 GTTGCTAAGATTATTGAG
1 GTTGCTAAGAAAATTGAG
40683 GTTGCTAAGAAAATTGA
1 GTTGCTAAGAAAATTGA
40700 AGTGACATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (18 bp):
GTTGCTAAGAAAATTGAG
Found at i:41049 original size:16 final size:16
Alignment explanation
Indices: 41028--41063 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41018 ACTAACTAAT
*
41028 AACTGCTTACTGCAGA
1 AACTGCTAACTGCAGA
*
41044 AACTGCTAACTGCAGT
1 AACTGCTAACTGCAGA
41060 AACT
1 AACT
41064 AACTAACTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (16 bp):
AACTGCTAACTGCAGA
Found at i:45454 original size:16 final size:17
Alignment explanation
Indices: 45429--45462 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
45419 AATTGCTTAT
45429 TGCAGAAACT-ACTAAC
1 TGCAGAAACTAACTAAC
*
45445 TGCAGTAACTAACTAAC
1 TGCAGAAACTAACTAAC
45462 T
1 T
45463 CTAATACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (17 bp):
TGCAGAAACTAACTAAC
Found at i:46691 original size:13 final size:13
Alignment explanation
Indices: 46673--46697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46663 TGTTTTGATG
46673 AAAATGGTAGTTC
1 AAAATGGTAGTTC
46686 AAAATGGTAGTT
1 AAAATGGTAGTT
46698 GACATTGAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.32
Consensus pattern (13 bp):
AAAATGGTAGTTC
Found at i:47626 original size:8 final size:8
Alignment explanation
Indices: 47613--47651 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
47603 ATCCAAATAG
47613 TTAATTAT
1 TTAATTAT
47621 TTAATTA-
1 TTAATTAT
*
47628 -TATTTAT
1 TTAATTAT
47635 TTAATTAT
1 TTAATTAT
47643 TTAATTAT
1 TTAATTAT
47651 T
1 T
47652 AAAACACCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 5 0.19
8 22 0.81
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTAATTAT
Found at i:47680 original size:14 final size:14
Alignment explanation
Indices: 47661--47754 Score: 58
Period size: 14 Copynumber: 6.9 Consensus size: 14
47651 TAAAACACCC
47661 AAATATTTAATTCA
1 AAATATTTAATTCA
47675 AAATATTTAATT-A
1 AAATATTTAATTCA
* *
47688 TTTAATTATATAATT--
1 ---AAATATTTAATTCA
47703 AAATATTTAATTACTA
1 AAATATTTAATT-C-A
* *
47719 AAA-A--CAA-TCC
1 AAATATTTAATTCA
47729 AAATATTTAATTCA
1 AAATATTTAATTCA
47743 AAATATTTAATT
1 AAATATTTAATT
47755 ATTTATGTTG
Statistics
Matches: 61, Mismatches: 8, Indels: 22
0.67 0.09 0.24
Matches are distributed among these distances:
10 3 0.05
11 2 0.03
12 11 0.18
13 5 0.08
14 26 0.43
15 1 0.02
16 13 0.21
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATATTTAATTCA
Found at i:47685 original size:68 final size:68
Alignment explanation
Indices: 47607--47759 Score: 229
Period size: 68 Copynumber: 2.2 Consensus size: 68
47597 AAAATAATCC
* * * *
47607 AAATAGTTAATTATTTAATTATATTTATTTAATTATTTAATTA-TTAAAAC-ACCCAAATATTTA
1 AAATATTTAATTATTTAATTATA--TAATTAAATATTTAATTACTAAAAACAACCCAAATATTTA
47670 ATTCA
64 ATTCA
*
47675 AAATATTTAATTATTTAATTATATAATTAAATATTTAATTACTAAAAACAATCCAAATATTTAAT
1 AAATATTTAATTATTTAATTATATAATTAAATATTTAATTACTAAAAACAACCCAAATATTTAAT
47740 TCA
66 TCA
47743 AAATATTTAATTATTTA
1 AAATATTTAATTATTTA
47760 TGTTGTACTC
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
66 16 0.21
67 6 0.08
68 56 0.72
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.46
Consensus pattern (68 bp):
AAATATTTAATTATTTAATTATATAATTAAATATTTAATTACTAAAAACAACCCAAATATTTAAT
TCA
Found at i:47689 original size:54 final size:55
Alignment explanation
Indices: 47578--47703 Score: 141
Period size: 54 Copynumber: 2.3 Consensus size: 55
47568 ACCAAATCAG
* * *
47578 TTTAATTATTTAATTATTAAAAATAATCCAAATAGTTAATTATTTAATTATATTTA
1 TTTAATTATTTAATTATTAAAAATAACCCAAATAGTTAATTA-TAAATTATAATTA
* * *
47634 TTTAATTATTTAATTATT-AAAA-CACCCAAATATTTAATTCA-AAATATTTAATTA
1 TTTAATTATTTAATTATTAAAAATAACCCAAATAGTTAATT-ATAAAT-TATAATTA
*
47688 TTTAATTATATAATTA
1 TTTAATTATTTAATTA
47704 AATATTTAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
53 3 0.05
54 35 0.57
55 5 0.08
56 18 0.30
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (55 bp):
TTTAATTATTTAATTATTAAAAATAACCCAAATAGTTAATTATAAATTATAATTA
Found at i:50056 original size:43 final size:43
Alignment explanation
Indices: 50003--50142 Score: 181
Period size: 43 Copynumber: 3.3 Consensus size: 43
49993 CTGTTAATGT
* * **
50003 TAGTAGCGTTTGTGAGAAAAATGCCATTAAAGAACATGATCTA
1 TAGTGGCGTTTGTGAGAAAAACGCCGCTAAAGAACATGATCTA
* * * *
50046 TAGCGGCGTTTGTGGGAAATACGCCGCTAAAGAACATGCTCTA
1 TAGTGGCGTTTGTGAGAAAAACGCCGCTAAAGAACATGATCTA
* * *
50089 TAGTGGCGTTTGTGAGAAAAGCGCCGCTAAAGATCATGTTCTA
1 TAGTGGCGTTTGTGAGAAAAACGCCGCTAAAGAACATGATCTA
50132 TAGTGGCGTTT
1 TAGTGGCGTTT
50143 TTACGCATAA
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 83 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (43 bp):
TAGTGGCGTTTGTGAGAAAAACGCCGCTAAAGAACATGATCTA
Found at i:50275 original size:39 final size:39
Alignment explanation
Indices: 50211--50286 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
50201 TAGTGATTCA
* *
50211 AATATTTATTAATAGTAAAGATTATTGAATAATATTATT
1 AATATTTATTAATAATAAAGATTATTGAAAAATATTATT
* *
50250 AATATTTGTTAATAATAAA-ATTTATTTAAAAATATTA
1 AATATTTATTAATAATAAAGA-TTATTGAAAAATATTA
50287 AAATACATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.03
39 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (39 bp):
AATATTTATTAATAATAAAGATTATTGAAAAATATTATT
Found at i:51506 original size:31 final size:31
Alignment explanation
Indices: 51470--51586 Score: 118
Period size: 31 Copynumber: 3.9 Consensus size: 31
51460 TTAATATAAC
*
51470 ATTTGGTATCTAAATTTGACACTTTTTCTTA
1 ATTTGGTACCTAAATTTGACACTTTTTCTTA
* *
51501 ATTTGGCACCTAAATTT-----TTTTTGGTCTA
1 ATTTGGTACCTAAATTTGACACTTTTT-CT-TA
* * * *
51529 ATTTGGTACTTAAACTTGACAATTTTTCCTA
1 ATTTGGTACCTAAATTTGACACTTTTTCTTA
51560 ATTTGGTACCTAAATTTGACACTTTTT
1 ATTTGGTACCTAAATTTGACACTTTTT
51587 TTTTAAGTTA
Statistics
Matches: 68, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
26 5 0.07
27 1 0.01
28 16 0.24
31 41 0.60
33 5 0.07
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.49
Consensus pattern (31 bp):
ATTTGGTACCTAAATTTGACACTTTTTCTTA
Found at i:51637 original size:91 final size:91
Alignment explanation
Indices: 51470--51664 Score: 232
Period size: 91 Copynumber: 2.1 Consensus size: 91
51460 TTAATATAAC
* * * * * *
51470 ATTTGGTATCTAAATTTGACACTTTTTCTTAATTTGGCACCTAAATTTTTTTTGGTCTAATTTGG
1 ATTTGGTACCTAAATTTGACACTTTTTCTTAAGTTAGCACCTAAATTTTTTGTGGTCAAATTTGA
51535 TACTTAAACTTGA-CAATTTTTCCTA
66 TACTTAAACTTGATCAATTTTTCCTA
* * **
51560 ATTTGGTACCTAAATTTGACACTTTTTTTTTAAGTTAGTATTTAAATTTTTTG-GTGTCAAATTT
1 ATTTGGTACCTAAATTTGACAC-TTTTTCTTAAGTTAGCACCTAAATTTTTTGTG-GTCAAATTT
* ***
51624 GATACTTGAACTTGATTTTTTTTTCCTA
64 GATACTTAAACTTGATCAATTTTTCCTA
51652 ATTTGGTACCTAA
1 ATTTGGTACCTAA
51665 TCTTTTTAAT
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
90 22 0.25
91 44 0.50
92 22 0.25
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (91 bp):
ATTTGGTACCTAAATTTGACACTTTTTCTTAAGTTAGCACCTAAATTTTTTGTGGTCAAATTTGA
TACTTAAACTTGATCAATTTTTCCTA
Found at i:51892 original size:30 final size:30
Alignment explanation
Indices: 51846--51914 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
51836 AAGCTTAATA
* * *
51846 ACCAAATTAGAAAAAAAT-TCAAATTTAAGT
1 ACCAAA-TAAAAAAAAATATCAAATTCAAGC
51876 ACCTAAATAAAAAAAAATATCAAATTCAAGC
1 ACC-AAATAAAAAAAAATATCAAATTCAAGC
51907 ACCAAATA
1 ACCAAATA
51915 TTATATTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 18 0.53
31 16 0.47
ACGTcount: A:0.59, C:0.14, G:0.04, T:0.22
Consensus pattern (30 bp):
ACCAAATAAAAAAAAATATCAAATTCAAGC
Found at i:54114 original size:33 final size:34
Alignment explanation
Indices: 54077--54145 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 34
54067 AGAAAATCGA
* * *
54077 AAGATCCTGTTTGAAAAATA-TATATTGAAAAGT
1 AAGATCCAGTTTGAAAAAAAGAATATTGAAAAGT
*
54110 AAGATCCAGTTTTAAAAAAAGAATATTGAAAAGT
1 AAGATCCAGTTTGAAAAAAAGAATATTGAAAAGT
54144 AA
1 AA
54146 AACCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 17 0.55
34 14 0.45
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (34 bp):
AAGATCCAGTTTGAAAAAAAGAATATTGAAAAGT
Done.