Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019818.1 Corchorus olitorius cultivar O-4 contig19851, 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: 23009
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:1101 original size:12 final size:13
Alignment explanation
Indices: 1070--1107 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
1060 CGGTACTGCA
1070 ATTTATATATTATCT
1 ATTTATAT-TTA-CT
1085 ATTTATATTTA-T
1 ATTTATATTTACT
1097 ATTTATATTTA
1 ATTTATATTTA
1108 GGAATATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.52
14 3 0.13
15 8 0.35
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTTATATTTACT
Found at i:6885 original size:432 final size:432
Alignment explanation
Indices: 5911--7071 Score: 1472
Period size: 433 Copynumber: 2.7 Consensus size: 432
5901 GGTTATTGCA
* *
5911 TGATCTACGACTTTCATGAA---TTCAAAAGGAAATTTTTATGTTTCAAGATCTCCATCAACGAA
1 TGATCTACGAGTTTCATGAAGGGTTCAAAAGGAAATTTTTATGTTTCAAGATCTCCATCAACAAA
* * * * *
5973 CATTTTCTTAATTGGATTATTTATCAAATGACCCTCATATTTTTCTACTTTATACAACTTAGTCC
66 TATTTTCTTATTTGAATTA-TTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAGTCC
** * * * *
6038 TTTATTAATTCTATTTTTAATCGATTTAACGCTTCAGCTTTAATTTTTTATTTCTTT-TTCTATT
130 TTTACAAATTCTA-TCTTAATC----TAATGTTTAAGCTTT-ATTTTTTA-TTCTTTGTTCTATT
* *
6102 TGTCCGATTAAGGTGATTCAGGTGC-CTATTACAAGGTAATTTCATTATCTACAACTTTCATAAA
188 TGTCCGATTAAGGTGATTCAGGT-CTCTATTAAAAGGTAATTTC---ATCTACAACTTTCATGAA
* *
6166 GGACTCAAAAGCCAATTTTTATGTTTCAATT-AAACAAAATGCTTCCCAAATTTGGTGGGTTCGA
249 GGACT-AAAAGCAAATTTTTATGTTTCAATTCAAA-AAAATGCTTCCCAAATTTGGTCGGTTCGA
* * * *
6230 TTGCCAGTCTATTTAATACCATATGATTTTCAATCCACATGTCCGATTAAATTTATTAAAGTGTT
312 TTGCCAGTCTATTTAATACCATATAATTTTCAATACACATGTCCGATTAAAGTTATTAAAGTGTC
* * * * *
6295 GGTTAAAAGGTTATTGCATGATTTATGACTTTCATGAAGGACCTGAAAGCTAAATT
377 GGTTAAAAGGTTACTGCATGATCTACGACTTTCATGAAGAACCCGAAAGCTAAATT
* * * *
6351 TGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTCCAAGATCTCCATTAACAAT
1 TGATCTACGAGTTTCATGAAGGGTTCAAAAGGAAATTTTTATGTTTCAAGATCTCCATCAACAAA
*
6416 TATTTTCTTATTTGAATTATTAATCAAATGACCCTCATACTTTTCTACTTCATACTACTTAGTCC
66 TATTTTCTTATTTGAATTATT-ATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAGTCC
*
6481 TTTACAAATTCTATCTTAATCTAATGTTTAAGCTTTATTTTTTATTCTTTGTTCTATTTGTCTGA
130 TTTACAAATTCTATCTTAATCTAATGTTTAAGCTTTATTTTTTATTCTTTGTTCTATTTGTCCGA
* *
6546 TTAAGTTGATTCATGTCTCTATTAAAAGGTAATTTCATCTACAACTTTCATGAAGGACTAAAAGC
195 TTAAGGTGATTCAGGTCTCTATTAAAAGGTAATTTCATCTACAACTTTCATGAAGGACTAAAAGC
* * * ***
6611 AAATTTTTATTTTTCAATTCAAAAAAATG-TGTCCTAAATTTGGTCGTTTCGATTGTTGGTCTAT
260 AAATTTTTATGTTTCAATTCAAAAAAATGCT-TCCCAAATTTGGTCGGTTCGATTGCCAGTCTAT
* *
6675 TTAATACCATATAATTTTCGATACACATGTCCGATTAAAGTTATTCAAGTGTCGGTTAAAAGGTT
324 TTAATACCATATAATTTTCAATACACATGTCCGATTAAAGTTATTAAAGTGTCGGTTAAAAGGTT
* *
6740 ACTGTATGATCTACGACTTTCATGAAGAACCCGAAAG-TTAATT
389 ACTGCATGATCTACGACTTTCATGAAGAACCCGAAAGCTAAATT
6783 TGATCTACGAGTTTCATGAAGGGTTCAAAAGGAAATTTTTATGTTTCAAGATCTCCATCAACAAA
1 TGATCTACGAGTTTCATGAAGGGTTCAAAAGGAAATTTTTATGTTTCAAGATCTCCATCAACAAA
* * *
6848 TATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTATTTTATGCTACTTAGTCC
66 TATTTTCTTATTTGAATTA-TTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAGTCC
* * * *
6913 TTTACAAATTCTATCTTACTC-GAT-TTAAAGC-TTA---TTT-TT-TTTGTTCTATTTGTCCAA
130 TTTACAAATTCTATCTTAATCTAATGTTTAAGCTTTATTTTTTATTCTTTGTTCTATTTGTCCGA
* * * * * *
6970 TTAAGGTAATTCAGGTGTCTATTAAAATGTAATTTTATAATCTACAACTTTCATGAAAGAGTCAA
195 TTAAGGTGATTCAGGTCTCTATTAAAAGGTAA--TT-TCATCTACAACTTTCATG-AAG-GACTA
* * *
7035 AAAGCTAATTTTTATGTTTCAGTTCTAAAAAATGCTT
255 AAAGCAAATTTTTATGTTTCAATTCAAAAAAATGCTT
7072 TTGAAATTTT
Statistics
Matches: 637, Mismatches: 69, Indels: 41
0.85 0.09 0.05
Matches are distributed among these distances:
424 43 0.07
425 2 0.00
426 5 0.01
427 17 0.03
428 3 0.00
429 37 0.06
430 7 0.01
431 2 0.00
432 145 0.23
433 148 0.23
434 25 0.04
436 7 0.01
437 52 0.08
438 12 0.02
440 19 0.03
442 9 0.01
443 104 0.16
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.42
Consensus pattern (432 bp):
TGATCTACGAGTTTCATGAAGGGTTCAAAAGGAAATTTTTATGTTTCAAGATCTCCATCAACAAA
TATTTTCTTATTTGAATTATTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAGTCCT
TTACAAATTCTATCTTAATCTAATGTTTAAGCTTTATTTTTTATTCTTTGTTCTATTTGTCCGAT
TAAGGTGATTCAGGTCTCTATTAAAAGGTAATTTCATCTACAACTTTCATGAAGGACTAAAAGCA
AATTTTTATGTTTCAATTCAAAAAAATGCTTCCCAAATTTGGTCGGTTCGATTGCCAGTCTATTT
AATACCATATAATTTTCAATACACATGTCCGATTAAAGTTATTAAAGTGTCGGTTAAAAGGTTAC
TGCATGATCTACGACTTTCATGAAGAACCCGAAAGCTAAATT
Found at i:8687 original size:21 final size:20
Alignment explanation
Indices: 8657--8697 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
8647 GTGTTTTAGA
8657 TATTTTGTTGGATAATTGTT
1 TATTTTGTTGGATAATTGTT
8677 TATTTCTGTTGGATAATTGTT
1 TATTT-TGTTGGATAATTGTT
8698 CAATTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.20, C:0.02, G:0.20, T:0.59
Consensus pattern (20 bp):
TATTTTGTTGGATAATTGTT
Found at i:9230 original size:39 final size:39
Alignment explanation
Indices: 9172--9250 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
9162 TTCAACTACA
9172 AATACACAAAAACAATTTAAGTTGCCTACTTTAATAAGT
1 AATACACAAAAACAATTTAAGTTGCCTACTTTAATAAGT
* *
9211 AATACACAAAAAGAGTTTAAGTTGCCTACTTTAATAAGT
1 AATACACAAAAACAATTTAAGTTGCCTACTTTAATAAGT
9250 A
1 A
9251 GGCAAACAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (39 bp):
AATACACAAAAACAATTTAAGTTGCCTACTTTAATAAGT
Found at i:10672 original size:26 final size:26
Alignment explanation
Indices: 10643--10720 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
10633 AGGGTAACAA
10643 AAAATTAACTCTAATGGTACAACATG
1 AAAATTAACTCTAATGGTACAACATG
* * *
10669 AAAACTCA-TAC-AA--G-A-AATCAAG
1 AAAATTAACT-CTAATGGTACAA-CATG
10691 AAAATTAACTCTAATGGTACAACATG
1 AAAATTAACTCTAATGGTACAACATG
10717 AAAA
1 AAAA
10721 CTCATACAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
21 2 0.05
22 11 0.29
23 4 0.11
25 4 0.11
26 15 0.39
27 2 0.05
ACGTcount: A:0.53, C:0.15, G:0.10, T:0.22
Consensus pattern (26 bp):
AAAATTAACTCTAATGGTACAACATG
Found at i:10741 original size:48 final size:47
Alignment explanation
Indices: 10638--10743 Score: 176
Period size: 48 Copynumber: 2.2 Consensus size: 47
10628 TTCAAAGGGT
*
10638 AACAAAAAATTAACTCTAATGGTACAACATGAAAACTCATACAAGAA
1 AACAGAAAATTAACTCTAATGGTACAACATGAAAACTCATACAAGAA
*
10685 ATCAAGAAAATTAACTCTAATGGTACAACATGAAAACTCATACAAGAAA
1 AAC-AGAAAATTAACTCTAATGGTACAACATGAAAACTCATACAAG-AA
10734 AACAGAAAAT
1 AACAGAAAAT
10744 GTTTCATACA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
47 2 0.04
48 48 0.89
49 4 0.07
ACGTcount: A:0.56, C:0.16, G:0.09, T:0.19
Consensus pattern (47 bp):
AACAGAAAATTAACTCTAATGGTACAACATGAAAACTCATACAAGAA
Found at i:21554 original size:19 final size:18
Alignment explanation
Indices: 21530--21565 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
21520 TGAAGACTTA
21530 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
21549 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
21566 ATAATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Done.