Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023034.1 Corchorus olitorius cultivar O-4 contig23067, 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: 52333
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:640 original size:9 final size:9
Alignment explanation
Indices: 622--650 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
612 TTAAACCCCA
622 ATAC-TCTT
1 ATACATCTT
630 ATACATCTT
1 ATACATCTT
639 ATACATCTT
1 ATACATCTT
648 ATA
1 ATA
651 ATGGGCACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (9 bp):
ATACATCTT
Found at i:3054 original size:111 final size:111
Alignment explanation
Indices: 2860--3081 Score: 426
Period size: 111 Copynumber: 2.0 Consensus size: 111
2850 CTTCTGCTTG
* *
2860 CCCATTGACCTTTGTTTTGGCGTTGAATTAGATGGGAGGGTCAAACCTGGGTTTGAAACATATTG
1 CCCATTGACCTTTGTTTTGGCATTGAATTAGATGGGAGGGTCAAACCCGGGTTTGAAACATATTG
2925 TCCTCCTCTACTTGGTAGACAACTCGGATTCATTCAGCAAATCCCT
66 TCCTCCTCTACTTGGTAGACAACTCGGATTCATTCAGCAAATCCCT
2971 CCCATTGACCTTTGTTTTGGCATTGAATTAGATGGGAGGGTCAAACCCGGGTTTGAAACATATTG
1 CCCATTGACCTTTGTTTTGGCATTGAATTAGATGGGAGGGTCAAACCCGGGTTTGAAACATATTG
3036 TCCTCCTCTACTTGGTAGACAACTCGGATTCATTCAGCAAATCCCT
66 TCCTCCTCTACTTGGTAGACAACTCGGATTCATTCAGCAAATCCCT
3082 TCACCTCCTC
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 109 1.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (111 bp):
CCCATTGACCTTTGTTTTGGCATTGAATTAGATGGGAGGGTCAAACCCGGGTTTGAAACATATTG
TCCTCCTCTACTTGGTAGACAACTCGGATTCATTCAGCAAATCCCT
Found at i:14441 original size:19 final size:18
Alignment explanation
Indices: 14408--14443 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
14398 TTGAAATAAT
14408 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
14426 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
14444 TGAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:14451 original size:11 final size:10
Alignment explanation
Indices: 14408--14454 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
14398 TTGAAATAAT
14408 TCTTCAATGA
1 TCTTCAATGA
14418 TCTTCAA--A
1 TCTTCAATGA
*
14426 TCTTCAAATTA
1 TCTTC-AATGA
14437 TCTTCAATGA
1 TCTTCAATGA
14447 GTCTTCAA
1 -TCTTCAA
14455 ACACGAACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 11 0.34
11 13 0.41
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (10 bp):
TCTTCAATGA
Found at i:18763 original size:17 final size:18
Alignment explanation
Indices: 18730--18765 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
18720 CTCCTCTTGC
*
18730 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
18748 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTCTTTTT
18765 A
1 A
18766 ACTACCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:19447 original size:16 final size:14
Alignment explanation
Indices: 19426--19465 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 14
19416 AATAGGCAAG
19426 CAATCAAAGCAATAA
1 CAATCAAAGCAA-AA
19441 TCAATCAAAGCAAAA
1 -CAATCAAAGCAAAA
19456 CAATGCAAAG
1 CAAT-CAAAG
19466 GAAATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.17
15 7 0.30
16 12 0.52
ACGTcount: A:0.57, C:0.20, G:0.10, T:0.12
Consensus pattern (14 bp):
CAATCAAAGCAAAA
Found at i:19638 original size:6 final size:6
Alignment explanation
Indices: 19627--19666 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
19617 ATGAAACCCT
* *
19627 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAT AGAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
19667 TTAAAATGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:27431 original size:18 final size:19
Alignment explanation
Indices: 27394--27442 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
27384 ATAAATAAAT
27394 AAAAGAAAAAAGAGATAAGG
1 AAAAGAAAAAA-AGATAAGG
27414 AAAAGAAAAAAAGA-AAGG
1 AAAAGAAAAAAAGATAAGG
*
27432 -AAGGAAAAAAA
1 AAAAGAAAAAAA
27443 AGAAGAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 10 0.36
18 4 0.14
19 3 0.11
20 11 0.39
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (19 bp):
AAAAGAAAAAAAGATAAGG
Found at i:27459 original size:17 final size:16
Alignment explanation
Indices: 27415--27467 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
27405 GAGATAAGGA
27415 AAAG-AAAAAAAGAAAGG
1 AAAGAAAAAAAAG-AA-G
*
27432 AAGGAAAAAAAAGAAG
1 AAAGAAAAAAAAGAAG
27448 AAAGAAATAAAAAGAAG
1 AAAGAAA-AAAAAGAAG
27465 AAA
1 AAA
27468 ATAGGAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 7 0.22
17 17 0.53
18 8 0.25
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (16 bp):
AAAGAAAAAAAAGAAG
Found at i:27460 original size:21 final size:20
Alignment explanation
Indices: 27374--27460 Score: 57
Period size: 20 Copynumber: 4.2 Consensus size: 20
27364 GGGCCCAAAC
* * * *
27374 AAAAAAATAAATAAATAAAT
1 AAAAAAAAAAAGAAAGAAAG
* * * *
27394 AAAAGAAAAAAGAGATAAGG
1 AAAAAAAAAAAGAAAGAAAG
*
27414 AAAAGAAAAAAAGAAAGGAAGG
1 AAAA-AAAAAAAGAAA-GAAAG
* *
27436 AAAAAAAAGAAGAAAGAAAT
1 AAAAAAAAAAAGAAAGAAAG
27456 AAAAA
1 AAAAA
27461 GAAGAAAATA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
20 26 0.49
21 19 0.36
22 8 0.15
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (20 bp):
AAAAAAAAAAAGAAAGAAAG
Found at i:30244 original size:50 final size:50
Alignment explanation
Indices: 30181--30316 Score: 211
Period size: 50 Copynumber: 2.7 Consensus size: 50
30171 TCTCAAGATT
*
30181 GAATGGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAAGTC
1 GAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAAGTC
*
30231 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAAGTC
1 GAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAAGTC
* ** *
30281 AAATTGGAAGACAG-TCTGAGGATGAGCGGGAGACGG
1 GAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGG
30317 CTCTCTTAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
49 18 0.23
50 61 0.77
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.19
Consensus pattern (50 bp):
GAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAAGTC
Found at i:32857 original size:49 final size:48
Alignment explanation
Indices: 32757--32885 Score: 127
Period size: 49 Copynumber: 2.7 Consensus size: 48
32747 TTACATTTCC
* ** *
32757 TGCACTTTTCCTCAATTTTTACTACAAAATTGAACCTTTATTTTTCCT
1 TGCACTTTTTCTCAATTTTTAAGACAAAATTGAACCTTTATTTTTCAT
* * *
32805 TGCACCTTTTTCTCAATTTTTAAGATAAAATTGATCTTTTACTTTTT-AT
1 TGCA-CTTTTTCTCAATTTTTAAGACAAAATTGAACCTTTA-TTTTTCAT
* * * *
32854 TGCACTTTATATCAATTTGT-GGACAAAATTGA
1 TGCACTTTTTCTCAATTTTTAAGACAAAATTGA
32886 TCGGCACGCT
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
47 10 0.15
48 17 0.25
49 35 0.52
50 5 0.07
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.47
Consensus pattern (48 bp):
TGCACTTTTTCTCAATTTTTAAGACAAAATTGAACCTTTATTTTTCAT
Found at i:33462 original size:36 final size:36
Alignment explanation
Indices: 33422--33517 Score: 95
Period size: 36 Copynumber: 2.7 Consensus size: 36
33412 GCAGCAAATG
*
33422 GCGCCACACCAAGTGGCCGCACTGCACCAAATAGCC
1 GCGCCACACCAAGTAGCCGCACTGCACCAAATAGCC
* * * *
33458 GCGCCACACCCAA-TAGTCGCACCGTACCAAATGGCC
1 GCGCCACA-CCAAGTAGCCGCACTGCACCAAATAGCC
* * * *
33494 ACACCACACCAAGTTGCCACACTG
1 GCGCCACACCAAGTAGCCGCACTG
33518 GTTCAACCAC
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
35 4 0.09
36 39 0.83
37 4 0.09
ACGTcount: A:0.29, C:0.42, G:0.19, T:0.10
Consensus pattern (36 bp):
GCGCCACACCAAGTAGCCGCACTGCACCAAATAGCC
Found at i:33467 original size:18 final size:18
Alignment explanation
Indices: 33425--33505 Score: 63
Period size: 18 Copynumber: 4.5 Consensus size: 18
33415 GCAAATGGCG
* *
33425 CCACACCAAGTGGCCGCA
1 CCACACCAAATAGCCGCA
** *
33443 CTGCACCAAATAGCCGCG
1 CCACACCAAATAGCCGCA
* *
33461 CCACACCCAATAGTCGCA
1 CCACACCAAATAGCCGCA
** * *
33479 CCGTACCAAATGGCCACA
1 CCACACCAAATAGCCGCA
33497 CCACACCAA
1 CCACACCAA
33506 GTTGCCACAC
Statistics
Matches: 45, Mismatches: 18, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.32, C:0.43, G:0.16, T:0.09
Consensus pattern (18 bp):
CCACACCAAATAGCCGCA
Found at i:34765 original size:15 final size:15
Alignment explanation
Indices: 34745--34811 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
34735 AGATGATGGT
34745 ACCAAAATCGACGGC
1 ACCAAAATCGACGGC
*
34760 ACCAAAGAT-GATGGC
1 ACCAAA-ATCGACGGC
34775 ACCAAAATCGACGGC
1 ACCAAAATCGACGGC
* ** *
34790 ACCGAAATTTATGGC
1 ACCAAAATCGACGGC
34805 ACCAAAA
1 ACCAAAA
34812 GTGTTTACTA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
14 2 0.05
15 39 0.91
16 2 0.05
ACGTcount: A:0.42, C:0.27, G:0.19, T:0.12
Consensus pattern (15 bp):
ACCAAAATCGACGGC
Found at i:34768 original size:30 final size:30
Alignment explanation
Indices: 34734--34811 Score: 113
Period size: 30 Copynumber: 2.6 Consensus size: 30
34724 GTCATGGAAG
*
34734 AAGATGATGGTACCAAAATCGACGGCACCA
1 AAGATGATGGCACCAAAATCGACGGCACCA
34764 AAGATGATGGCACCAAAATCGACGGCACCGA
1 AAGATGATGGCACCAAAATCGACGGCACC-A
* *
34795 AA-TTTATGGCACCAAAA
1 AAGATGATGGCACCAAAA
34812 GTGTTTACTA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 41 0.93
31 3 0.07
ACGTcount: A:0.41, C:0.23, G:0.22, T:0.14
Consensus pattern (30 bp):
AAGATGATGGCACCAAAATCGACGGCACCA
Found at i:37481 original size:49 final size:49
Alignment explanation
Indices: 37411--37544 Score: 159
Period size: 49 Copynumber: 2.8 Consensus size: 49
37401 ATCATTTACA
* **
37411 TTTCC-TGCACTTTTTCTCAATTTTTACTACAAAATTGAACCTTTA-TT
1 TTTCCTTGCACTTTTTATCAATTTTTAAGACAAAATTGAACCTTTACTT
* * *
37458 TTTCCTTGCACCTTTTTTTCAATTTTTAAGACAAAATTGATCTTTTACTT
1 TTTCCTTGCA-CTTTTTATCAATTTTTAAGACAAAATTGAACCTTTACTT
* *
37508 TTT-ATTGCACTTTTTATCAATTTTT-GGACAAAATTGA
1 TTTCCTTGCACTTTTTATCAATTTTTAAGACAAAATTGA
37545 TTGGCACGCT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
47 16 0.21
48 19 0.25
49 36 0.47
50 5 0.07
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (49 bp):
TTTCCTTGCACTTTTTATCAATTTTTAAGACAAAATTGAACCTTTACTT
Found at i:39042 original size:21 final size:20
Alignment explanation
Indices: 39007--39047 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
38997 TGATTAAATG
*
39007 AATTTTTTTTGTTTTTTTCC
1 AATTTTTTTTGTTTTATTCC
*
39027 AATTTTTTATTTTTTTATTCC
1 AATTTTTT-TTGTTTTATTCC
39048 GAAAAAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (20 bp):
AATTTTTTTTGTTTTATTCC
Found at i:44659 original size:29 final size:30
Alignment explanation
Indices: 44615--44696 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 30
44605 TGCATCTTGA
** ** *
44615 AAAGGTTTAGGTTCAATTTGGTTCAACT-T
1 AAAGGTTTAGACTCAATTTGGAACAACTCG
*
44644 AAAGGTTTAGACTCAAATT-GAACAACTCGCG
1 AAAGGTTTAGACTCAATTTGGAACAACT--CG
44675 AAAGGTTTAGACTCAATTTGGA
1 AAAGGTTTAGACTCAATTTGGA
44697 CATTTGGCCG
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
28 6 0.14
29 16 0.38
31 18 0.43
32 2 0.05
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (30 bp):
AAAGGTTTAGACTCAATTTGGAACAACTCG
Found at i:44780 original size:2 final size:2
Alignment explanation
Indices: 44773--44800 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44763 GGTATAGTTG
44773 TA TA TA 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
44801 AATACGAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48539 original size:2 final size:2
Alignment explanation
Indices: 48534--48562 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
48524 TGTGTGTGTG
48534 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 T
48563 TCGATATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50569 original size:43 final size:42
Alignment explanation
Indices: 50516--50845 Score: 427
Period size: 41 Copynumber: 7.8 Consensus size: 42
50506 ATAAGGAGAA
50516 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-AATAGAG
*
50559 ATGACC-CTGTGTTATATATGTGTTTGGGGACTTTGATATA-A-
1 ATG-CCTCTGTGTTATATATGTGTTTGAGGACTTTGA-ATAGAG
50600 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-AATAGAG
* * * *
50643 TTGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGAATAGAG
*
50684 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-AATAGAG
* * * * *
50727 GTGCCTTTGTGTTATATACGTGTTTGGGGAC-TTGAATATAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGAATAGAG
* *
50768 GTGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGGG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTT-GAATAGAG
* *
50812 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTT
50846 TGGTTATTGG
Statistics
Matches: 253, Mismatches: 23, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
40 2 0.01
41 105 0.42
42 7 0.03
43 103 0.41
44 36 0.14
ACGTcount: A:0.21, C:0.10, G:0.27, T:0.42
Consensus pattern (42 bp):
ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGAATAGAG
Found at i:50610 original size:41 final size:41
Alignment explanation
Indices: 50514--50845 Score: 370
Period size: 43 Copynumber: 7.9 Consensus size: 41
50504 CCATAAGGAG
50514 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-TAAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGAT-AT
*
50555 AGAGATGACC-CTGTGTTATATATGTGTTTGGGGACTTTGATAT
1 A-A-ATG-CCTCTGTGTTATATATGTGTTTGAGGACTTTGATAT
50598 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-TAAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGAT-AT
* * *
50639 AGAGTTGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATAT
1 A-A-ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGATAT
*
50682 AGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-TAAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGAT-AT
* * *
50723 AAAGGTGCCTTTGTGTTATATACGTGTTTGGGGAC-TTGAATAT
1 AAA--TGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-ATAT
**
50766 AGGTGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGA-AT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTT-GATAT
* * *
50808 AGGGATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 A--AATGCCTCTGTGTTATATATGTGTTTGAGGACTTT
50846 TGGTTATTGG
Statistics
Matches: 251, Mismatches: 21, Indels: 36
0.81 0.07 0.12
Matches are distributed among these distances:
40 4 0.02
41 98 0.39
42 9 0.04
43 105 0.42
44 35 0.14
ACGTcount: A:0.21, C:0.10, G:0.27, T:0.42
Consensus pattern (41 bp):
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGATAT
Found at i:50628 original size:84 final size:84
Alignment explanation
Indices: 50514--50845 Score: 531
Period size: 84 Copynumber: 3.9 Consensus size: 84
50504 CCATAAGGAG
*
50514 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGACCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
50579 TGTTTGGGGACTTTGATAT
66 TGTTTGGGGACTTTGATAT
*
50598 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
50663 TGTTTGGGGACTTTGATAT
66 TGTTTGGGGACTTTGATAT
* * * ** *
50682 AGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGGTGCCTTTGTGTTATATACG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
50747 TGTTTGGGGAC-TTGAATAT
66 TGTTTGGGGACTTTG-ATAT
** * *
50766 AGGTGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGGGATGCCCCTGTGTTATATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAGATGCCCCTGTGTTATATAT
50831 GTGTTTGGGGACTTT
65 GTGTTTGGGGACTTT
50846 TGGTTATTGG
Statistics
Matches: 229, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
83 3 0.01
84 188 0.82
85 36 0.16
86 2 0.01
ACGTcount: A:0.21, C:0.10, G:0.27, T:0.42
Consensus pattern (84 bp):
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
TGTTTGGGGACTTTGATAT
Done.