Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017506.1 Corchorus olitorius cultivar O-4 contig17539, 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: 48402
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:6713 original size:2 final size:2
Alignment explanation
Indices: 6706--6739 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6696 TGATATCTCG
6706 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6740 CTGTAATTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7336 original size:17 final size:17
Alignment explanation
Indices: 7293--7352 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
7283 CTGTTTCAAT
7293 TATGGGTTTCAACTTAA-
1 TATGGGTTTCAA-TTAAG
***
7310 TATCCATTTCAATTAAG
1 TATGGGTTTCAATTAAG
7327 TATGGGTTTCAATTAAG
1 TATGGGTTTCAATTAAG
*
7344 TCTGGGTTT
1 TATGGGTTT
7353 TGGTTATCTC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
16 4 0.11
17 31 0.89
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (17 bp):
TATGGGTTTCAATTAAG
Found at i:7477 original size:19 final size:19
Alignment explanation
Indices: 7453--7494 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
7443 AAATGTATGA
*
7453 TTAAATTAGTATATTTGAT
1 TTAAATTACTATATTTGAT
7472 TTAAATTACTATATTTGAT
1 TTAAATTACTATATTTGAT
7491 TTAA
1 TTAA
7495 TATTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (19 bp):
TTAAATTACTATATTTGAT
Found at i:7540 original size:31 final size:26
Alignment explanation
Indices: 7470--7520 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
7460 AGTATATTTG
*
7470 ATTTAAATTACTATATTTGATTTAAT
1 ATTTAAATTAGTATATTTGATTTAAT
7496 ATTTAAATTAGTATATTTGATTTAA
1 ATTTAAATTAGTATATTTGATTTAA
7521 ATGTATGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (26 bp):
ATTTAAATTAGTATATTTGATTTAAT
Found at i:7545 original size:13 final size:14
Alignment explanation
Indices: 7523--7552 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
7513 TGATTTAAAT
7523 GTATGATTAAATTA
1 GTATGATTAAATTA
7537 GTATG-TTAAATTA
1 GTATGATTAAATTA
7550 GTA
1 GTA
7553 CACATATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (14 bp):
GTATGATTAAATTA
Found at i:7743 original size:13 final size:13
Alignment explanation
Indices: 7712--7746 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
7702 TTATTATAAC
7712 TTCGATATATCCG
1 TTCGATATATCCG
*
7725 -TCGATATATCGG
1 TTCGATATATCCG
7737 TTCGATATAT
1 TTCGATATAT
7747 TTATGGATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (13 bp):
TTCGATATATCCG
Found at i:10630 original size:5 final size:5
Alignment explanation
Indices: 10620--10649 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
10610 TAGTTTCGTA
10620 TACAC TACAC TACAC TACAC TACAC TACAC
1 TACAC TACAC TACAC TACAC TACAC TACAC
10650 CATTCATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (5 bp):
TACAC
Found at i:15489 original size:20 final size:21
Alignment explanation
Indices: 15461--15500 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
15451 TATTGACAAA
15461 AGACAAAG-AGAAAATTAAAT
1 AGACAAAGAAGAAAATTAAAT
* *
15481 AGACCAAGAAGAAAGTTAAA
1 AGACAAAGAAGAAAATTAAA
15501 AGTAATTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.62, C:0.07, G:0.17, T:0.12
Consensus pattern (21 bp):
AGACAAAGAAGAAAATTAAAT
Found at i:15980 original size:101 final size:99
Alignment explanation
Indices: 15773--15963 Score: 235
Period size: 101 Copynumber: 1.9 Consensus size: 99
15763 ATTGTTTGAT
* *
15773 AGAATGGTTAGGCATGCAGTTTCTAGTGACTGGAGCAATAAAAGAGGCTCACTAACAAAACATAG
1 AGAATGGTGAGGCATGCAGTTTCTAGTGACCGGAGCAATAAAAGAGGCTCAC--ACAAAACATAG
* * * * * *
15838 ATATTAATTTGCCTTCAGACTACATTAAATGCCTTC
64 ATATTAATTTGCCTGCAAACTAAATCAAATGCATAC
* *
15874 AGAATGGTGATGCATGCTGTTTCTAGTGACCGGAGCAATAAAA-AGTGCTCAC-CAATAACATAG
1 AGAATGGTGAGGCATGCAGTTTCTAGTGACCGGAGCAATAAAAGAG-GCTCACACAA-AACATAG
15937 ATATTAA-TTGCCTGCAAACTAAATCAA
64 ATATTAATTTGCCTGCAAACTAAATCAA
15964 CTATTCATGA
Statistics
Matches: 80, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
98 19 0.24
99 14 0.17
100 2 0.03
101 45 0.56
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.27
Consensus pattern (99 bp):
AGAATGGTGAGGCATGCAGTTTCTAGTGACCGGAGCAATAAAAGAGGCTCACACAAAACATAGAT
ATTAATTTGCCTGCAAACTAAATCAAATGCATAC
Found at i:16617 original size:17 final size:17
Alignment explanation
Indices: 16595--16627 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16585 ACCCCAAATT
*
16595 AGGATTTCCCATTTTCG
1 AGGATTCCCCATTTTCG
16612 AGGATTCCCCATTTTC
1 AGGATTCCCCATTTTC
16628 TAGCTTCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.39
Consensus pattern (17 bp):
AGGATTCCCCATTTTCG
Found at i:22743 original size:29 final size:30
Alignment explanation
Indices: 22693--22751 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
22683 CAGAAAAATC
*
22693 CCTTATGTTTTGCTTTTGGGACAAAATAATT
1 CCTTATGTTTT-CTTTCGGGACAAAATAATT
*
22724 CCTTATGTTTT-TTTCGGGACAAATTAAT
1 CCTTATGTTTTCTTTCGGGACAAAATAAT
22752 CTCTTACGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 15 0.58
31 11 0.42
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (30 bp):
CCTTATGTTTTCTTTCGGGACAAAATAATT
Found at i:22757 original size:29 final size:30
Alignment explanation
Indices: 22689--22762 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
22679 TATCCAGAAA
* *
22689 AATCCCTTATGTTTTGCTTTTGGGACAAAAT
1 AATCTCTTATGTTTT-CTTTCGGGACAAAAT
*
22720 AAT-TCCTTATGTTTT-TTTCGGGACAAATT
1 AATCT-CTTATGTTTTCTTTCGGGACAAAAT
*
22749 AATCTCTTACGTTT
1 AATCTCTTATGTTT
22763 CAAAAATGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
29 23 0.62
30 1 0.03
31 13 0.35
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (30 bp):
AATCTCTTATGTTTTCTTTCGGGACAAAAT
Found at i:22956 original size:31 final size:31
Alignment explanation
Indices: 22906--23000 Score: 149
Period size: 31 Copynumber: 3.1 Consensus size: 31
22896 AAGGGACCAA
22906 TTTGTCTCC-AAA-AAAAACATAAGGGATTTT
1 TTTGTC-CCAAAAGAAAAACATAAGGGATTTT
*
22936 TTTGTCCCAAAAGAAAAACATAAGAGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
*
22967 TTTGTCCCAAAAGAAAAACATTAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
22998 TTT
1 TTT
23001 AGTATTTAGT
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
29 2 0.03
30 9 0.15
31 49 0.82
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.34
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTTT
Found at i:23277 original size:128 final size:125
Alignment explanation
Indices: 23133--23373 Score: 340
Period size: 128 Copynumber: 1.9 Consensus size: 125
23123 ATTCCCTAAA
* *
23133 AAAATGGTAAAGATAAAATAGTTATAAAAATATT-GAATTTAATTAAATAAAAATAGAATTTTTG
1 AAAATGGTAAAAATAAAATAGTTATAAAAATATTAG-ATTTAATTAAATAAAAATAGAATTTTTA
* *
23197 GTAAAATAAAACTGTAAAAGTTTAAATAATGTGTCATTTAAGAAATATATTTAATCAAAATAGT
65 ATAAAATAAAACTGTAAAAGTTTAAA-AA--TGCCATTTAAGAAATATATTTAATCAAAATAGT
* * *
23261 AAAATGGTAAAAATAAAATAGTTATAAATATATTAGATTTGATTAAATAAAAATAGAGTTTTTAA
1 AAAATGGTAAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGAATTTTTAA
** * *
23326 TTGAGTAAAATTGTAAAAGTTTAAAAATGCCATTTAAGAAATATATTT
66 TAAAATAAAACTGTAAAAGTTTAAAAATGCCATTTAAGAAATATATTT
23374 GAAAAATAAG
Statistics
Matches: 101, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
125 20 0.20
127 2 0.02
128 78 0.77
129 1 0.01
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.35
Consensus pattern (125 bp):
AAAATGGTAAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGAATTTTTAA
TAAAATAAAACTGTAAAAGTTTAAAAATGCCATTTAAGAAATATATTTAATCAAAATAGT
Found at i:24104 original size:31 final size:31
Alignment explanation
Indices: 23968--24094 Score: 211
Period size: 31 Copynumber: 4.1 Consensus size: 31
23958 GACTAAATCT
*
23968 AAAAAAATTCTCTTATATTTTTCTTTTGGGAC
1 AAAAAAA-TCCCTTATATTTTTCTTTTGGGAC
24000 -AAAAAATCCCTTATATTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATATTTTTCTTTTGGGAC
*
24030 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATATTTTTCTTTTGGGAC
*
24061 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATATTTTTCTTTTGGGAC
24092 AAA
1 AAA
24095 TCAGTCCCTT
Statistics
Matches: 92, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
30 23 0.25
31 69 0.75
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (31 bp):
AAAAAAATCCCTTATATTTTTCTTTTGGGAC
Found at i:24268 original size:29 final size:30
Alignment explanation
Indices: 24226--24296 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 30
24216 TGAACGTAAT
* *
24226 GGATTAATTTGTCCCGAAA-AAAACATAAG
1 GGATTATTTTGTCCCAAAACAAAACATAAG
24255 GGATTATTTTGTCCCAAAAGCAAAACATAAG
1 GGATTATTTTGTCCCAAAA-CAAAACATAAG
* *
24286 AGATTTTTTTG
1 GGATTATTTTG
24297 GGTATTTAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 17 0.47
31 19 0.53
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (30 bp):
GGATTATTTTGTCCCAAAACAAAACATAAG
Found at i:26365 original size:45 final size:45
Alignment explanation
Indices: 26315--26404 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
26305 AAATATTCCC
26315 AACTTAAAGAGAATGTATACAGAAAATACCAGTTCTAAACTAATT
1 AACTTAAAGAGAATGTATACAGAAAATACCAGTTCTAAACTAATT
*
26360 AACTTAAAGAGAATGTATACAGAAAATACCGGTTCTAAACTAATT
1 AACTTAAAGAGAATGTATACAGAAAATACCAGTTCTAAACTAATT
26405 CCAAGATGTG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (45 bp):
AACTTAAAGAGAATGTATACAGAAAATACCAGTTCTAAACTAATT
Found at i:42081 original size:27 final size:27
Alignment explanation
Indices: 42051--42131 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
42041 TACCAAAATA
42051 TTATGAGATTAGAGCAAATCATAACAC
1 TTATGAGATTAGAGCAAATCATAACAC
* * *
42078 TTATGA-ATCA-A-TACAA--A-AATA-
1 TTATGAGATTAGAGCA-AATCATAACAC
42099 TTATGAGATTAGAGCAAATCATAACAC
1 TTATGAGATTAGAGCAAATCATAACAC
*
42126 TCATGA
1 TTATGA
42132 ATCAAAATAG
Statistics
Matches: 39, Mismatches: 7, Indels: 16
0.63 0.11 0.26
Matches are distributed among these distances:
21 6 0.15
22 6 0.15
23 4 0.10
24 2 0.05
25 4 0.10
26 6 0.15
27 11 0.28
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (27 bp):
TTATGAGATTAGAGCAAATCATAACAC
Found at i:42091 original size:48 final size:48
Alignment explanation
Indices: 42039--42136 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
42029 ACGTTAATTT
* *
42039 AATACCAAAATATTATGAGATTAGAGCAAATCATAACACTTATGAATC
1 AATACAAAAATATTATGAGATTAGAGCAAATCATAACACTCATGAATC
42087 AATACAAAAATATTATGAGATTAGAGCAAATCATAACACTCATGAATC
1 AATACAAAAATATTATGAGATTAGAGCAAATCATAACACTCATGAATC
42135 AA
1 AA
42137 AATAGTTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (48 bp):
AATACAAAAATATTATGAGATTAGAGCAAATCATAACACTCATGAATC
Found at i:42629 original size:67 final size:69
Alignment explanation
Indices: 42557--42696 Score: 230
Period size: 72 Copynumber: 2.0 Consensus size: 69
42547 TATATCATAA
*
42557 TAATAATATGTTGTTTAACGTAATATCT-AAAAAAA-ATGTACTTTAACTTAAAAATAATGAGTA
1 TAATAATATGTTGTTCAACGTAATATCTAAAAAAAAGATGTACTTTAACTTAAAAATAATGAGTA
42620 TTAT
66 TTAT
42624 TAATAATATGTTGTTCAACGTAATATCTAAAAAAAAAAAGATGTACTTTAACTTAAAAATAATGA
1 TAATAATATGTTGTTCAACGTAATATCT---AAAAAAAAGATGTACTTTAACTTAAAAATAATGA
42689 GTATTAT
63 GTATTAT
42696 T
1 T
42697 TTAGACATTT
Statistics
Matches: 67, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
67 27 0.40
71 7 0.10
72 33 0.49
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.37
Consensus pattern (69 bp):
TAATAATATGTTGTTCAACGTAATATCTAAAAAAAAGATGTACTTTAACTTAAAAATAATGAGTA
TTAT
Found at i:43271 original size:3 final size:3
Alignment explanation
Indices: 43258--43286 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
43248 TAGATGCTAT
43258 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
43287 CATTAGAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:47690 original size:15 final size:15
Alignment explanation
Indices: 47670--47713 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
47660 CTTCCAGTTG
47670 GATGCAGCTTGGTTA
1 GATGCAGCTTGGTTA
*
47685 GATGCAGCTTGGTTT
1 GATGCAGCTTGGTTA
**
47700 GATGTTGCTTGGTT
1 GATGCAGCTTGGTT
47714 GGAGGTTGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.14, C:0.11, G:0.34, T:0.41
Consensus pattern (15 bp):
GATGCAGCTTGGTTA
Found at i:47712 original size:30 final size:30
Alignment explanation
Indices: 47676--47734 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
47666 GTTGGATGCA
*
47676 GCTTGGTTAGATGCAGCTTGGTTTGATGTT
1 GCTTGGTTAGAGGCAGCTTGGTTTGATGTT
* **
47706 GCTTGGTTGGAGGTTGCTTGGTTTGATGT
1 GCTTGGTTAGAGGCAGCTTGGTTTGATGT
47735 GGATGCAGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.10, C:0.08, G:0.37, T:0.44
Consensus pattern (30 bp):
GCTTGGTTAGAGGCAGCTTGGTTTGATGTT
Found at i:47721 original size:15 final size:15
Alignment explanation
Indices: 47691--47728 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
47681 GTTAGATGCA
* *
47691 GCTTGGTTTGATGTT
1 GCTTGGTTGGAGGTT
47706 GCTTGGTTGGAGGTT
1 GCTTGGTTGGAGGTT
47721 GCTTGGTT
1 GCTTGGTT
47729 TGATGTGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.08, G:0.39, T:0.47
Consensus pattern (15 bp):
GCTTGGTTGGAGGTT
Done.