Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013974.1 Corchorus olitorius cultivar O-4 contig14007, 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: 19842
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Found at i:707 original size:11 final size:11
Alignment explanation
Indices: 691--732 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
681 AAGTGTGCCA
*
691 GACACAAGCTT
1 GACACAAGCAT
702 GACACAAGCAT
1 GACACAAGCAT
713 -ACACAAGACA-
1 GACACAAG-CAT
723 GACACAAGCA
1 GACACAAGCA
733 GTGGACAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.48, C:0.29, G:0.17, T:0.07
Consensus pattern (11 bp):
GACACAAGCAT
Found at i:2020 original size:20 final size:19
Alignment explanation
Indices: 1978--2022 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
1968 AGGCCCCTGG
*
1978 ATTA-GTTTAATTTGGTCC
1 ATTAGGTTTAATTTGGTCA
*
1996 CTTAGGTTTAAATTTGGTCA
1 ATTAGGTTT-AATTTGGTCA
2016 ATTAGGT
1 ATTAGGT
2023 GCCTGTCAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.24, C:0.09, G:0.20, T:0.47
Consensus pattern (19 bp):
ATTAGGTTTAATTTGGTCA
Found at i:2750 original size:29 final size:29
Alignment explanation
Indices: 2708--2769 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
2698 GGGCTTTTGT
2708 TTGGATATATGGGTTTCATTTTCATGGGC
1 TTGGATATATGGGTTTCATTTTCATGGGC
2737 TTGGATATATGGGTTTCATTTTCATGGGC
1 TTGGATATATGGGTTTCATTTTCATGGGC
2766 TTGG
1 TTGG
2770 TTTCATTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.16, C:0.10, G:0.29, T:0.45
Consensus pattern (29 bp):
TTGGATATATGGGTTTCATTTTCATGGGC
Found at i:2773 original size:20 final size:20
Alignment explanation
Indices: 2748--2797 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
2738 TGGATATATG
*
2748 GGTTTCATTTTCATGGGCTT
1 GGTTTCATTTTCATGGACTT
2768 GGTTTCATTTTCATGGACTT
1 GGTTTCATTTTCATGGACTT
2788 GGTTT-ATTTT
1 GGTTTCATTTT
2798 AAGATGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 5 0.17
20 24 0.83
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.54
Consensus pattern (20 bp):
GGTTTCATTTTCATGGACTT
Found at i:8951 original size:46 final size:46
Alignment explanation
Indices: 8895--8986 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
8885 TAGAATGTTA
8895 TTATTTCCACAACTTTTGGATTAGGCGACTCCCTTAATTTTAATTC
1 TTATTTCCACAACTTTTGGATTAGGCGACTCCCTTAATTTTAATTC
*
8941 TTATTTCCACAACTTTTGGATTAGGCGGCTCCCTTAATTTTAATTC
1 TTATTTCCACAACTTTTGGATTAGGCGACTCCCTTAATTTTAATTC
8987 AGGTCTATCG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (46 bp):
TTATTTCCACAACTTTTGGATTAGGCGACTCCCTTAATTTTAATTC
Found at i:9430 original size:20 final size:18
Alignment explanation
Indices: 9388--9431 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
9378 GAGGAAAGAG
9388 AAGAGAAAAGAGGATGGA
1 AAGAGAAAAGAGGATGGA
* *
9406 GAGAGACAAAGAGAGCTGGA
1 AAGAGA-AAAGAG-GATGGA
9426 AAGAGA
1 AAGAGA
9432 GATCGAGTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 5 0.24
19 6 0.29
20 10 0.48
ACGTcount: A:0.52, C:0.05, G:0.39, T:0.05
Consensus pattern (18 bp):
AAGAGAAAAGAGGATGGA
Found at i:11898 original size:30 final size:30
Alignment explanation
Indices: 11862--11919 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
11852 TTGTTGCCCA
*
11862 AACATGCCACCCCAACCATAAATTTCAATG
1 AACATGCCACCCCAACCATAAAGTTCAATG
* *
11892 AACATGCCTCCCCAACCATGAAGTTCAA
1 AACATGCCACCCCAACCATAAAGTTCAA
11920 GGATGTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.38, C:0.34, G:0.09, T:0.19
Consensus pattern (30 bp):
AACATGCCACCCCAACCATAAAGTTCAATG
Found at i:13279 original size:2 final size:2
Alignment explanation
Indices: 13272--13296 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13262 ATATGCAGTT
13272 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
13297 TTACTTATAC
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:13410 original size:17 final size:18
Alignment explanation
Indices: 13390--13431 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
13380 AAGAGGTCAC
*
13390 AAATATTCAATTAA-AAT
1 AAATATTCAAATAATAAT
*
13407 AAATATTTAAATAATAAT
1 AAATATTCAAATAATAAT
13425 AAATATT
1 AAATATT
13432 AAACATTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATTCAAATAATAAT
Found at i:15506 original size:21 final size:21
Alignment explanation
Indices: 15480--15521 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
15470 GAAGGCCTAA
15480 AATTACCAGTGAAATGGGTAT
1 AATTACCAGTGAAATGGGTAT
15501 AATTACCAGTGAAATGGGTAT
1 AATTACCAGTGAAATGGGTAT
15522 TCCAAAAGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (21 bp):
AATTACCAGTGAAATGGGTAT
Found at i:16931 original size:437 final size:438
Alignment explanation
Indices: 16128--17133 Score: 1168
Period size: 437 Copynumber: 2.3 Consensus size: 438
16118 AATCTAATTA
* * * *
16128 ACAAAATTTCAAAAGCATTTTTTAGAACTGAAACATAAAAATTAGCTTTTGAGTCTTTCATGAAA
1 ACAAACTTTCAGAAGCATTTTTTAGAATTGAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAA
* * * * * * * * *
16193 GTTGCAGATCATAAAATTATCTTTTAATAGACACCTCAATTACCTTAATTGGACACATAAAACAA
66 GTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCACTTTAATCGGACAAATAAAACAA
* * * *
16258 AGAAAATAAAAAAAATTTGAAGTGTTAAATCGAGTAAGATATAATTTGTAAAGGACTAAGTAGCA
131 AG-AAATAAAAAAAA-TTAAAGTGTAAAATAGAGTAAGATAGAATTTGTAAAGGACTAAGTAGCA
* * * * * *
16323 TAAAATAAAAAAGTATGAGGGTGATTTGATAACTAATTCAAGTAAGAACATATTTGTTAATGGAG
194 TAAAATAAAAAAGTATGACGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAATGGAG
* * *
16388 ATCTTAAAACATAAAAATTCCATTTTGAACTCTTCATGAAACTCGTGGATCAAATTAACTTTCGG
259 ATCTTAAAACATAAAAATTCCATTTTGAACCCTTCACGAAACTCGTAGATCAAATTAACTTTCGG
* * * * * * * *
16453 GTTATTCATGAAAGTCGTAGATCATACAGTAACCTTTTAACCGACAGTTGAATAACTTTAATTGG
324 ATCATTCATGAAAGTCGTAAATCATACAGTAACCATTTAACCGACACTTCAATAACTTCAATCGG
* * * *
16518 ACATGTGGATC-GAAAATTATATGGTATTAAA-TAGACCAGCAACCAAAACG
389 ACATGTGGA-CAAAAAATTATACGATATTAAATTA-ACCAGCAACCAAAACC
* *
16568 ACCAAA-TTT-AGGAAGCATTTTTTTGAATTGAAACATAAAAATTTGCTTTTGAGTCCTTCATGA
1 A-CAAACTTTCA-GAAGCATTTTTTAGAATTGAAACATAAAAATTAGCTTTTGAGTCCTTCATGA
* * * *
16631 AAGTTATAGATCATGAAATTACCTTTTGATAGACACATGAATCAATTTAATCGGACAAATAGAAC
64 AAGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCACTTTAATCGGACAAATAAAAC
* *
16696 AAAG-AAT-AAAAAAA-TAAAGCT-TAAACATTAGATTAAGGTAGAATTTGTAAAGGACTAAGTA
129 AAAGAAATAAAAAAAATTAAAG-TGTAAA-A-TAGAGTAAGATAGAATTTGTAAAGGACTAAGTA
* * * *
16757 GTATAAATTAGAAAAGTATGACGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATG
191 GCATAAAATAAAAAAGTATGACGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAATG
* * * *
16822 GAGATCTTGAAACATAAAAATTCCCTTTTGAACCCTTCACGAAACTCGTAGATCAAGTTTAGCTT
256 GAGATCTTAAAACATAAAAATTCCATTTTGAACCCTTCACGAAACTCGTAGATCAA-ATTAACTT
* * *
16887 TCGGATCCTT-ATTAAAGTCGTAAATCATGCCA-TAACCATTTAACCGACACTTCAATAACTTCA
320 TCGGATCATTCATGAAAGTCGTAAATCAT-ACAGTAACCATTTAACCGACACTTCAATAACTTCA
* **
16950 ATCGGACATGTGGACAAAAAATTATACGATATTAAATTAACCGGCAATTAAAACC
384 ATCGGACATGTGGACAAAAAATTATACGATATTAAATTAACCAGCAACCAAAACC
* ** * * * * * *
17005 ACAAACTTTCAGAAGCAATTTTTAGAATCAAAACATTATAATTGGCTTTTAAGTTCTTAATGAAA
1 ACAAACTTTCAGAAGCATTTTTTAGAATTGAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAA
* * * *
17070 CTTGTAGATCATGAAATAACCTTTTAATAGACACTTGAATCACCTTCTAATCGGATAAATAAAA
66 GTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCA-CTT-TAATCGGACAAATAAAA
17134 AAAAACAAAA
Statistics
Matches: 476, Mismatches: 77, Indels: 27
0.82 0.13 0.05
Matches are distributed among these distances:
435 7 0.01
436 7 0.01
437 312 0.66
438 23 0.05
439 16 0.03
440 107 0.22
441 4 0.01
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (438 bp):
ACAAACTTTCAGAAGCATTTTTTAGAATTGAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAA
GTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCACTTTAATCGGACAAATAAAACAA
AGAAATAAAAAAAATTAAAGTGTAAAATAGAGTAAGATAGAATTTGTAAAGGACTAAGTAGCATA
AAATAAAAAAGTATGACGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAATGGAGAT
CTTAAAACATAAAAATTCCATTTTGAACCCTTCACGAAACTCGTAGATCAAATTAACTTTCGGAT
CATTCATGAAAGTCGTAAATCATACAGTAACCATTTAACCGACACTTCAATAACTTCAATCGGAC
ATGTGGACAAAAAATTATACGATATTAAATTAACCAGCAACCAAAACC
Found at i:18229 original size:27 final size:27
Alignment explanation
Indices: 18199--18250 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
18189 AAATACTTTT
18199 ATTAATTA-ATTAATTGTATAATGGCAG
1 ATTAATTATA-TAATTGTATAATGGCAG
* *
18226 ATTAATTGTATAATTGTATATTGGC
1 ATTAATTATATAATTGTATAATGGC
18251 TATTTGAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (27 bp):
ATTAATTATATAATTGTATAATGGCAG
Done.