Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013807.1 Corchorus olitorius cultivar O-4 contig13840, 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: 50933
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1871 original size:12 final size:12
Alignment explanation
Indices: 1856--1886 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1846 CCTTGAATAA
1856 TTAATTTTACTT
1 TTAATTTTACTT
*
1868 TTAATTTTATTT
1 TTAATTTTACTT
1880 TTAATTT
1 TTAATTT
1887 ATACACTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (12 bp):
TTAATTTTACTT
Found at i:3937 original size:30 final size:29
Alignment explanation
Indices: 3894--3950 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
3884 TTAGGATTAG
3894 TTATTTATGCTTTAATTTTCAA-TTTCCT
1 TTATTTATGCTTTAATTTTCAAGTTTCCT
3922 TTATCTTATGTCTTTAATTTTCAAGTTTC
1 TTAT-TTATG-CTTTAATTTTCAAGTTTC
3951 ATTAATAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.15
29 5 0.19
30 13 0.50
31 4 0.15
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (29 bp):
TTATTTATGCTTTAATTTTCAAGTTTCCT
Found at i:8429 original size:22 final size:22
Alignment explanation
Indices: 8360--8527 Score: 121
Period size: 22 Copynumber: 7.5 Consensus size: 22
8350 AGGAGATTAA
* * *
8360 CAAAATCTCATAGGGAAAGTTA-
1 CAAAATTTCATA-GGTAGGTTAT
* *
8382 CAAAATTTCATAGGAAGATTTAT
1 CAAAATTTCATAGGTAG-GTTAT
*
8405 CAAAATTTCATAGTTAGGTTAT
1 CAAAATTTCATAGGTAGGTTAT
* **
8427 CAAAGTTTCATATGG-AATTTAT
1 CAAAATTTCATA-GGTAGGTTAT
* **
8449 CACAATTTCATAGG-AAATTAT
1 CAAAATTTCATAGGTAGGTTAT
8470 CAAAATTTTTCATAGCGT-GGTTAT
1 CAAAA--TTTCATAG-GTAGGTTAT
*
8494 CAAAATTTAATAGGATA-GTTAT
1 CAAAATTTCATAGG-TAGGTTAT
8516 CAAAATTTCATA
1 CAAAATTTCATA
8528 AAAATATTCA
Statistics
Matches: 119, Mismatches: 18, Indels: 18
0.77 0.12 0.12
Matches are distributed among these distances:
21 17 0.14
22 68 0.57
23 24 0.20
24 10 0.08
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATAGGTAGGTTAT
Found at i:8463 original size:67 final size:66
Alignment explanation
Indices: 8377--8527 Score: 184
Period size: 67 Copynumber: 2.3 Consensus size: 66
8367 TCATAGGGAA
* * *
8377 AGTTA-CAAAATTTCATAGGAAGATTTATCAAAA-TTTCATAG-TTAGGTTATCAAAGTTTCATA
1 AGTTATCAAAATTTCATAGGAA-A-TTATCAAAATTTTCATAGCGT-GGTTATCAAAATTTAATA
8439 TGGA-
63 -GGAT
* *
8443 ATTTATCACAATTTCATAGGAAATTATCAAAATTTTTCATAGCGTGGTTATCAAAATTTAATAGG
1 AGTTATCAAAATTTCATAGGAAATTATCAAAA-TTTTCATAGCGTGGTTATCAAAATTTAATAGG
8508 AT
65 AT
8510 AGTTATCAAAATTTCATA
1 AGTTATCAAAATTTCATA
8528 AAAATATTCA
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
65 9 0.12
66 8 0.11
67 55 0.75
68 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.38
Consensus pattern (66 bp):
AGTTATCAAAATTTCATAGGAAATTATCAAAATTTTCATAGCGTGGTTATCAAAATTTAATAGGA
T
Found at i:8481 original size:45 final size:46
Alignment explanation
Indices: 8432--8523 Score: 107
Period size: 45 Copynumber: 2.0 Consensus size: 46
8422 GTTATCAAAG
* * *
8432 TTTCATATG-GAATTTATCACAATTTCATAGGA-AATTATCAAAATT
1 TTTCATA-GCGAAGTTATCAAAATTTAATAGGATAATTATCAAAATT
** *
8477 TTTCATAGCGTGGTTATCAAAATTTAATAGGATAGTTATCAAAATT
1 TTTCATAGCGAAGTTATCAAAATTTAATAGGATAATTATCAAAATT
8523 T
1 T
8524 CATAAAAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
44 1 0.03
45 25 0.64
46 13 0.33
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (46 bp):
TTTCATAGCGAAGTTATCAAAATTTAATAGGATAATTATCAAAATT
Found at i:18889 original size:48 final size:48
Alignment explanation
Indices: 18815--18911 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
18805 TAACTTGTAA
* *
18815 AAGATGGATAAATTAGTCTTTGAACTTCTAAATTTGTCAATCACACAT
1 AAGATGGATAAATTAGTCTTTAAACTTCTAAATTTATCAATCACACAT
*
18863 AAGATGGATAAATTAGTCTTTAAACTTCTAAATTTATCAATTACACAT
1 AAGATGGATAAATTAGTCTTTAAACTTCTAAATTTATCAATCACACAT
18911 A
1 A
18912 TGAACTTGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.36
Consensus pattern (48 bp):
AAGATGGATAAATTAGTCTTTAAACTTCTAAATTTATCAATCACACAT
Found at i:30390 original size:2 final size:2
Alignment explanation
Indices: 30385--30444 Score: 54
Period size: 2 Copynumber: 30.5 Consensus size: 2
30375 TATATACTCC
* *
30385 TA TA TA TA TA TCA GA TA TA TA T- TA TGA TA TA TA AA TA TA TA T-
1 TA TA TA TA TA T-A TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
*
30427 TA TA AA TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
30445 TAGGCGGTCG
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
1 3 0.06
2 41 0.87
3 3 0.06
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:30432 original size:13 final size:14
Alignment explanation
Indices: 30403--30440 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 14
30393 TATCAGATAT
30403 ATATTATGATATATAA
1 ATATTAT-AT-TATAA
30419 ATA-TATATTATAA
1 ATATTATATTATAA
30432 ATATTATAT
1 ATATTATAT
30441 ATATTAGGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 8 0.38
14 7 0.33
15 3 0.14
16 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
ATATTATATTATAA
Found at i:30439 original size:22 final size:20
Alignment explanation
Indices: 30357--30446 Score: 67
Period size: 20 Copynumber: 4.2 Consensus size: 20
30347 ATTTATAAAT
*
30357 TATTATTAATATAATAATTATA
1 TATTA-TAATAT-ATAAATATA
*
30379 TACTCCTATATATATATCAGATATA
1 TA-T--TATA-ATATAT-AAATATA
*
30404 TATTATGATATATAAATATA
1 TATTATAATATATAAATATA
*
30424 TATTATAA-ATAT-TATATA
1 TATTATAATATATAAATATA
30442 TATTA
1 TATTA
30447 GGCGGTCGGT
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
18 10 0.18
19 4 0.07
20 13 0.23
21 6 0.11
22 5 0.09
23 1 0.02
24 5 0.09
25 13 0.23
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
TATTATAATATATAAATATA
Found at i:31136 original size:11 final size:11
Alignment explanation
Indices: 31093--31130 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
31083 TTCCTATATA
*
31093 AAATAAATTAT
1 AAATTAATTAT
31104 CAAA-TAATTAT
1 -AAATTAATTAT
31115 AAATTAATTAT
1 AAATTAATTAT
31126 AAATT
1 AAATT
31131 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:33047 original size:31 final size:29
Alignment explanation
Indices: 33012--33082 Score: 79
Period size: 31 Copynumber: 2.4 Consensus size: 29
33002 GCTCAATTAA
*
33012 GGGCAAAACGTTTTAGTTTCAGTCTAATTTG
1 GGGCAAAACGTTTTAATTT-AGTC-AATTTG
* * * *
33043 GGGCAAGACCTTTTAATTTGGTCGATTTG
1 GGGCAAAACGTTTTAATTTAGTCAATTTG
33072 GGGCAAAACGT
1 GGGCAAAACGT
33083 CCTGAAATCG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
29 14 0.42
30 3 0.09
31 16 0.48
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (29 bp):
GGGCAAAACGTTTTAATTTAGTCAATTTG
Found at i:39813 original size:1 final size:1
Alignment explanation
Indices: 39802--39845 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
39792 TGTAAATTTG
* * * *
39802 TTTTTTGTTTTTTTTTTGTTTTTTTGTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
39846 CTTCTTTGTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (1 bp):
T
Found at i:39817 original size:10 final size:10
Alignment explanation
Indices: 39802--39845 Score: 72
Period size: 10 Copynumber: 4.5 Consensus size: 10
39792 TGTAAATTTG
39802 TTTTTTGTTT
1 TTTTTTGTTT
*
39812 TTTTTT-TGT
1 TTTTTTGTTT
39821 TTTTTTGTTT
1 TTTTTTGTTT
39831 TTTTTTGTTT
1 TTTTTTGTTT
39841 TTTTT
1 TTTTT
39846 CTTCTTTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 8 0.26
10 23 0.74
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:39845 original size:19 final size:18
Alignment explanation
Indices: 39798--39845 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
39788 GCATTGTAAA
*
39798 TTTGTTTTTTGTTTTTTT
1 TTTGTTTTTTTTTTTTTT
*
39816 TTTGTTTTTTTGTTTTTT
1 TTTGTTTTTTTTTTTTTT
39834 TTTGTTTTTTTT
1 TTTGTTTTTTTT
39846 CTTCTTTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (18 bp):
TTTGTTTTTTTTTTTTTT
Found at i:39853 original size:26 final size:26
Alignment explanation
Indices: 39798--39855 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
39788 GCATTGTAAA
*
39798 TTTGTTTTTTGTTTTTTTTTTGTTTT
1 TTTGTTTTTTGTTTTTTTTTTGTTTC
39824 TTTGTTTTTT-TTTGTTTTTTT-TCTTC
1 TTTGTTTTTTGTTT-TTTTTTTGT-TTC
39850 TTTGTT
1 TTTGTT
39856 ACGTATCAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.86
Consensus pattern (26 bp):
TTTGTTTTTTGTTTTTTTTTTGTTTC
Found at i:44657 original size:17 final size:17
Alignment explanation
Indices: 44635--44670 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
44625 TGATTTGTAA
44635 AGTTTGTTACACCAGAT
1 AGTTTGTTACACCAGAT
* *
44652 AGTTTGTTATACTAGAT
1 AGTTTGTTACACCAGAT
44669 AG
1 AG
44671 CTCTTTGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (17 bp):
AGTTTGTTACACCAGAT
Found at i:48667 original size:49 final size:47
Alignment explanation
Indices: 48598--48738 Score: 162
Period size: 49 Copynumber: 3.0 Consensus size: 47
48588 TCAAAGCAAT
* *
48598 CTTTTACTTTTC--TGCACTTTTTCTCAATTTTTGCTACAAAATTGAA
1 CTTTTAATTTTCTTTGCACTTTTTCTCAATTTTTG-GACAAAATTGAA
* * * *
48644 CTTTTATTTTTAC-TTGCGTCTTTTTCTCAATTTTTAAGACAAAATTGAT
1 CTTTTAATTTT-CTTTGC-ACTTTTTCTCAATTTTT-GGACAAAATTGAA
*
48693 CTTTTAATTTTCTTTGCACTTTTTATCAATTTTTGGACAAAATTGA
1 CTTTTAATTTTCTTTGCACTTTTTCTCAATTTTTGGACAAAATTGA
48739 TTGGCACGCT
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
46 10 0.12
47 12 0.15
48 19 0.23
49 40 0.49
ACGTcount: A:0.25, C:0.16, G:0.08, T:0.52
Consensus pattern (47 bp):
CTTTTAATTTTCTTTGCACTTTTTCTCAATTTTTGGACAAAATTGAA
Found at i:49601 original size:15 final size:15
Alignment explanation
Indices: 49552--49588 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
49542 TGCTAGAGTG
49552 AATGGTGCAAACAAC
1 AATGGTGCAAACAAC
49567 AATGGTGCAAACAAC
1 AATGGTGCAAACAAC
49582 AATGGTG
1 AATGGTG
49589 TGAACAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.16
Consensus pattern (15 bp):
AATGGTGCAAACAAC
Done.