Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017844.1 Corchorus olitorius cultivar O-4 contig17877, 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: 52112
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1340 original size:29 final size:29
Alignment explanation
Indices: 1272--1343 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
1262 ATTTGAGGGG
*
1272 CAAAACGTCCCAAAATTAAGAGTTCGGGAA
1 CAAAACAT-CCAAAATTAAGAGTTCGGGAA
* * * *
1302 TAGAATATCCAAAATT-ATAGTTCGGGAGA
1 CAAAACATCCAAAATTAAGAGTTCGGGA-A
1331 CAAAACATCCAAA
1 CAAAACATCCAAA
1344 CACTATAAGT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
28 10 0.30
29 19 0.58
30 4 0.12
ACGTcount: A:0.46, C:0.18, G:0.17, T:0.19
Consensus pattern (29 bp):
CAAAACATCCAAAATTAAGAGTTCGGGAA
Found at i:11882 original size:120 final size:117
Alignment explanation
Indices: 11559--11912 Score: 584
Period size: 117 Copynumber: 3.0 Consensus size: 117
11549 CAAATGCTCA
* * *
11559 AACGCTACTGTTAACTGGGATGCTTTCATTCTTAAGAGACTCGTTGCACTCAATTTTCTGTTCTT
1 AACGCTACTGTTAACTGGGATGCTTTCTTTCTTGAGAGACTTGTTGCACTCAATTTTCTGTTCTT
11624 TGGGTTCTTCAATCTCCAATTTCTTGGCGACTTCCTTTTCCTCAACTTCTTT
66 TGGGTTCTTCAATCTCCAATTTCTTGGCGACTTCCTTTTCCTCAACTTCTTT
*
11676 AACGCTACTGTTAACTGGGATGCTTTCTTTCTCGAGAGACTTGTTGCACTCAATTTTCTGTTCTT
1 AACGCTACTGTTAACTGGGATGCTTTCTTTCTTGAGAGACTTGTTGCACTCAATTTTCTGTTCTT
*
11741 TGGGTTCTTCAATCTCCAATTTCTTAGCGACTTCCTTTTCCTCAACTTCTTT
66 TGGGTTCTTCAATCTCCAATTTCTTGGCGACTTCCTTTTCCTCAACTTCTTT
*
11793 AACGCTACTGTTAATTACGGGGATGCTTTCTTTCTTGAGAGACTTGTTGCACTCAATTTTCTGTT
1 AACGCTACTGTT-A--ACTGGGATGCTTTCTTTCTTGAGAGACTTGTTGCACTCAATTTTCTGTT
* * *
11858 CTTTGAGTTCCTT-AATCTCCAATTTCTTGGCGGCTTCCTTTTCCTCAGCTTCTTT
63 CTTTGGGTT-CTTCAATCTCCAATTTCTTGGCGACTTCCTTTTCCTCAACTTCTTT
11913 TTGTTCTAAT
Statistics
Matches: 222, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
117 124 0.56
118 1 0.00
120 94 0.42
121 3 0.01
ACGTcount: A:0.17, C:0.24, G:0.15, T:0.44
Consensus pattern (117 bp):
AACGCTACTGTTAACTGGGATGCTTTCTTTCTTGAGAGACTTGTTGCACTCAATTTTCTGTTCTT
TGGGTTCTTCAATCTCCAATTTCTTGGCGACTTCCTTTTCCTCAACTTCTTT
Found at i:13755 original size:13 final size:12
Alignment explanation
Indices: 13738--13771 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
13728 CAAAAGATTA
13738 AAAAAAGGAAAC
1 AAAAAAGGAAAC
*
13750 AAAAAAGGAAAG
1 AAAAAAGGAAAC
*
13762 AATAAAGGAA
1 AAAAAAGGAA
13772 GTGGTTAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.03
Consensus pattern (12 bp):
AAAAAAGGAAAC
Found at i:19535 original size:30 final size:30
Alignment explanation
Indices: 19501--19561 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
19491 ATTTTTATCT
*
19501 TGACTTTTCTCTTAT-ACTCTCAAATTTTAA
1 TGACTTTCCTCTTATAACT-TCAAATTTTAA
19531 TGACTTTCCTCTTATAACTTCAAATTTTAA
1 TGACTTTCCTCTTATAACTTCAAATTTTAA
19561 T
1 T
19562 ATCTTACTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.28, C:0.20, G:0.03, T:0.49
Consensus pattern (30 bp):
TGACTTTCCTCTTATAACTTCAAATTTTAA
Found at i:25547 original size:21 final size:20
Alignment explanation
Indices: 25503--25554 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
25493 GACAAATTCT
* *
25503 TTTTTCTTTCTCCTATTGTC
1 TTTTTCTTCCTCCTAATGTC
25523 TTTTTCTTCCTCAC-AATGTC
1 TTTTTCTTCCTC-CTAATGTC
25543 TTTTTCTTCCTC
1 TTTTTCTTCCTC
25555 GCAAATCAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.08, C:0.29, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTTTCTTCCTCCTAATGTC
Found at i:27273 original size:11 final size:11
Alignment explanation
Indices: 27259--27301 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
27249 TAACTATTAC
27259 TTAACCATAGA
1 TTAACCATAGA
*
27270 TTAACCATATA
1 TTAACCATAGA
* *
27281 TTAACTATAGC
1 TTAACCATAGA
*
27292 TTGACCATAG
1 TTAACCATAG
27302 TTGGTAACAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.33
Consensus pattern (11 bp):
TTAACCATAGA
Found at i:27284 original size:22 final size:22
Alignment explanation
Indices: 27259--27300 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
27249 TAACTATTAC
27259 TTAACCATAGATTAACCATATA
1 TTAACCATAGATTAACCATATA
* * *
27281 TTAACTATAGCTTGACCATA
1 TTAACCATAGATTAACCATA
27301 GTTGGTAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.33
Consensus pattern (22 bp):
TTAACCATAGATTAACCATATA
Found at i:31459 original size:11 final size:11
Alignment explanation
Indices: 31432--31462 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
31422 TAACTATTAC
*
31432 TTAACCATAGA
1 TTAACTATAGA
31443 TTAACTATAGA
1 TTAACTATAGA
31454 TTAACTATA
1 TTAACTATA
31463 ACTTGACCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (11 bp):
TTAACTATAGA
Found at i:31459 original size:33 final size:33
Alignment explanation
Indices: 31409--31474 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
31399 CTTATATACA
*
31409 ATTAACCTATAACTAACTATTACTTAACCATAG
1 ATTAACCTATAACTAACTATAACTTAACCATAG
* *
31442 ATTAA-CTATAGATTAACTATAACTTGACCATAG
1 ATTAACCTATA-ACTAACTATAACTTAACCATAG
31475 GTTAGTAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 5 0.17
33 24 0.83
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.33
Consensus pattern (33 bp):
ATTAACCTATAACTAACTATAACTTAACCATAG
Found at i:45563 original size:26 final size:28
Alignment explanation
Indices: 45496--45563 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
45486 TTGAATTTTC
*
45496 CAACTAATTAATTATTCTTCTTATTTTCCT
1 CAACTAA-TAATTATTCTTCTTA-TTACCT
** *
45526 CAAAAAAAAATTATTCTTCTTA-TACCT
1 CAACTAATAATTATTCTTCTTATTACCT
45553 -AACTAATAATT
1 CAACTAATAATT
45564 GTATGATTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
26 8 0.26
27 4 0.13
29 14 0.45
30 5 0.16
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (28 bp):
CAACTAATAATTATTCTTCTTATTACCT
Found at i:45696 original size:11 final size:11
Alignment explanation
Indices: 45652--45698 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
45642 TGTCATAAAA
45652 TTATTCCTTTT
1 TTATTCCTTTT
45663 TTA-TCCTTTT
1 TTATTCCTTTT
*
45673 CTTATTGCATTTT
1 -TTATT-CCTTTT
*
45686 TTATTTCTTTT
1 TTATTCCTTTT
45697 TT
1 TT
45699 TGTACTGTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
10 7 0.23
11 12 0.40
12 6 0.20
13 5 0.17
ACGTcount: A:0.11, C:0.15, G:0.02, T:0.72
Consensus pattern (11 bp):
TTATTCCTTTT
Found at i:45790 original size:2 final size:2
Alignment explanation
Indices: 45783--45807 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45773 AGCAAAATTA
45783 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 A
45808 ATAAAAGGTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47718 original size:13 final size:13
Alignment explanation
Indices: 47702--47726 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47692 GATTTTATCA
47702 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
47715 AAAAAGAAAAAA
1 AAAAAGAAAAAA
47727 ACTTATACCA
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:48596 original size:28 final size:27
Alignment explanation
Indices: 48554--48608 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
48544 ACTGAGATTA
*
48554 GACTCGAAACTGACTCGAAAAAACAAACT
1 GACTCGAAACCGACTC--AAAAACAAACT
48583 GACTC-AAACCGACTCAAAAACAAACT
1 GACTCGAAACCGACTCAAAAACAAACT
48609 CAAATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 11 0.44
28 9 0.36
29 5 0.20
ACGTcount: A:0.49, C:0.27, G:0.11, T:0.13
Consensus pattern (27 bp):
GACTCGAAACCGACTCAAAAACAAACT
Found at i:49713 original size:46 final size:46
Alignment explanation
Indices: 49660--49748 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
49650 CTTTTAACCA
* *
49660 AACCCCATCCTCTCAAAAGAAGGATGAAACATATTTGAAGGAATCC
1 AACCCCATCCTCTCAAAAGAAGAATGAAACAGATTTGAAGGAATCC
* *
49706 AACCCCATCCTGTTAAAAGAAGAATGAAACAGATTTGAAGGAA
1 AACCCCATCCTCTCAAAAGAAGAATGAAACAGATTTGAAGGAA
49749 CCAGAGAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.19
Consensus pattern (46 bp):
AACCCCATCCTCTCAAAAGAAGAATGAAACAGATTTGAAGGAATCC
Found at i:51985 original size:333 final size:322
Alignment explanation
Indices: 51210--52038 Score: 870
Period size: 333 Copynumber: 2.5 Consensus size: 322
51200 TAAATGACAA
** * * * * ** *
51210 GAAAGATTTTTCCTCAATTT-TTGACAAAAATACTCATAAAATAGAT-AATTCAATGCAAAAAAG
1 GAAAGATACTTCCTCAATTTCTAG-CGAAAATACACATAAAATATATAAATTCAACACCAAAAAG
* * *
51273 ATTG-GAGTACTTTTCACGCTTTTAATATA-ATTTTTC-ATATTTTTTCTGAATTAATGTT-TAA
65 ATTGAAAG-CCTTTTCACGCTTCTAATATATATTTTTCTAT-TTTTTTCTGAATTAAT-TTCTAA
* * ** *
51334 TTAAATCAAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
127 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTAACTGAGAATT
*
51399 GATTAGATGAATAAAGATATTTCAAAGAGTCTCGACACAAAAAATCATGCAATACAGAGTCGTGG
192 GATTAGATGAATAAAGATATTTCAAAGAGTCTCGACACAAAAAATCATGCAAAACAGAGTCGTGG
** * *
51464 CTTCGGAACGCGTTTTTTAGCCAAAAACTTGTACGATTTCGGTTAAAATTTTGCAAAAATTGACC
257 CCCCGGAACGCGTTTTTTAGCCAAAAACTAGTACGATTTCGGTTAAAATTTTACAAAAATTGACC
51529 C
322 C
* * * * * *
51530 GAAAGATACTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATAGAATTCGACATCAAAAAG
1 GAAAGATACTTCCTCAATTTCTAGCGAAAATACACATAAAATATATA-AATTCAACACCAAAAAG
* * * * * * *
51595 ATTGAAGGGCTTTTAACGCTTCTAATATTGTATTTCCTCTTTTTTTTTCCGAATTAATTTCTAAT
65 ATTGAAAGCCTTTTCACGCTTCTAATA-TATATTT-TTCTATTTTTTTCTGAATTAATTTCTAAT
* *
51660 TAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTAACTGATAATTG
128 TAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTAACTGAGAATTG
* * * * * * * *
51725 GTTAGATGAATATAGATATTTC-AAGGGTCTTGGCACAAAAAATCATGTAAAACTGATTCG-GGC
193 ATTAGATGAATAAAGATATTTCAAAGAGTCTCGACACAAAAAATCATGCAAAACAGAGTCGTGGC
51788 CCCGGAACGCG-TTTTTAGCCGAAAACCGTGATGGCTAGTACACGATTTCGGTTAAAATTTTACA
258 CCCGGAACGCGTTTTTTAGCC-AAAA-----A---CTAGT--ACGATTTCGGTTAAAATTTTACA
51852 AAAATTGACCC
312 AAAATTGACCC
** * *
51863 GAAAGATTTTTCCTCAATTTCTAGCGAAAATACAGATACAAATATAT-AATTTAACACCAAAACA
1 GAAAGATACTTCCTCAATTTCTAGCGAAAATACACATA-AAATATATAAATTCAACACCAAAA-A
* * *
51927 -ATTGAAAGCCTTTTTCACGCTTCTAATATCATCTTTTTCTATTTTATTTCTAAATTAATTTCTG
64 GATTGAAAGCC-TTTTCACGCTTCTAATAT-ATATTTTTCTATTTT-TTTCTGAATTAATTTCTA
* * * *
51991 ATTAAATCGAAATATGATTTAGATGCTCGTAAAAACAAATCGTTAAAT
126 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT
52039 ATGGCTGAGA
Statistics
Matches: 420, Mismatches: 64, Indels: 37
0.81 0.12 0.07
Matches are distributed among these distances:
320 38 0.09
321 2 0.00
322 41 0.10
323 18 0.04
324 37 0.09
325 99 0.24
326 1 0.00
328 1 0.00
331 4 0.01
332 28 0.07
333 143 0.34
334 8 0.02
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.34
Consensus pattern (322 bp):
GAAAGATACTTCCTCAATTTCTAGCGAAAATACACATAAAATATATAAATTCAACACCAAAAAGA
TTGAAAGCCTTTTCACGCTTCTAATATATATTTTTCTATTTTTTTCTGAATTAATTTCTAATTAA
ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTAACTGAGAATTGATT
AGATGAATAAAGATATTTCAAAGAGTCTCGACACAAAAAATCATGCAAAACAGAGTCGTGGCCCC
GGAACGCGTTTTTTAGCCAAAAACTAGTACGATTTCGGTTAAAATTTTACAAAAATTGACCC
Done.