Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023275.1 Corchorus olitorius cultivar O-4 contig23308, 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: 49552
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1280 original size:76 final size:76
Alignment explanation
Indices: 1143--1294 Score: 175
Period size: 76 Copynumber: 2.0 Consensus size: 76
1133 ACAAGGACCC
* * *
1143 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGATCTGCTTGAGGACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGATCTGCCTGAGCACCCAGAT
1208 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * * *
1219 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGTG-TTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGATCT-GCCTGAGCACCCA
*
1281 GATGGGCTGTGTCA
63 GATGGGCAGTGTCA
1295 TAGTTCATCA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 2 0.03
76 56 0.88
77 6 0.09
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGATCTGCCTGAGCACCCAGAT
GGGCAGTGTCA
Found at i:4054 original size:22 final size:21
Alignment explanation
Indices: 4002--4055 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
3992 TGCTTCTTGA
4002 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
4023 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
4042 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
4056 AATGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:4928 original size:21 final size:21
Alignment explanation
Indices: 4899--4944 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
4889 TCTTCTCCTC
4899 TTATCATGAAAAC-ACCTTTTTT
1 TTATCATGAAAACTA--TTTTTT
4921 TTAT-ATGAAAACTATTTTTT
1 TTATCATGAAAACTATTTTTT
4941 TTAT
1 TTAT
4945 TACCCTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 10 0.43
21 8 0.35
22 5 0.22
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.52
Consensus pattern (21 bp):
TTATCATGAAAACTATTTTTT
Found at i:5649 original size:24 final size:24
Alignment explanation
Indices: 5604--5650 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
5594 AATGAAACTT
* * *
5604 GAAAAATAAAGACATAAGATAAAG
1 GAAAAATAAAGAAAAAACATAAAG
*
5628 GAAAATTAAAGAAAAAACATAAA
1 GAAAAATAAAGAAAAAACATAAA
5651 CTAGATAACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.70, C:0.04, G:0.13, T:0.13
Consensus pattern (24 bp):
GAAAAATAAAGAAAAAACATAAAG
Found at i:6705 original size:33 final size:33
Alignment explanation
Indices: 6668--6745 Score: 147
Period size: 33 Copynumber: 2.4 Consensus size: 33
6658 AATTCCTCTT
6668 CAAAAATTGCTTATCTTATCGAAATTGTTCCTC
1 CAAAAATTGCTTATCTTATCGAAATTGTTCCTC
*
6701 CAAAAATTGCTTATCTTATTGAAATTGTTCCTC
1 CAAAAATTGCTTATCTTATCGAAATTGTTCCTC
6734 CAAAAATTGCTT
1 CAAAAATTGCTT
6746 CTAGTCTACT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (33 bp):
CAAAAATTGCTTATCTTATCGAAATTGTTCCTC
Found at i:17214 original size:43 final size:42
Alignment explanation
Indices: 17161--17248 Score: 106
Period size: 43 Copynumber: 2.1 Consensus size: 42
17151 ATTACTTAAA
* *
17161 TCAAGTCATCTCCCTTACTTTTGAATAA-ATAAATAAATTTGT
1 TCAAGTCATCTCCCTTACTTTTGAATAAGA-AAACAAATTGGT
** *
17203 TCAAGTTCATCTCTTTTACTTTTGCATAAGAAAACAAATTGGT
1 TCAAG-TCATCTCCCTTACTTTTGAATAAGAAAACAAATTGGT
17246 TCA
1 TCA
17249 GAGTACTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 5 0.13
43 33 0.85
44 1 0.03
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (42 bp):
TCAAGTCATCTCCCTTACTTTTGAATAAGAAAACAAATTGGT
Found at i:17527 original size:3 final size:3
Alignment explanation
Indices: 17519--17561 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
17509 CTGCCATACT
17519 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
17562 ATATAATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17583 original size:9 final size:9
Alignment explanation
Indices: 17520--17585 Score: 50
Period size: 9 Copynumber: 7.3 Consensus size: 9
17510 TGCCATACTT
17520 TATTAT-TA
1 TATTATATA
17528 TTATTAT-TA
1 -TATTATATA
17537 TTATTAT-TA
1 -TATTATATA
17546 TTATTAT-TA
1 -TATTATATA
17555 TTATTATATA
1 -TATTATATA
*
17565 TAATATATA
1 TATTATATA
*
17574 TATTACATA
1 TATTATATA
17583 TAT
1 TAT
17586 CGAAAAATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
9 51 0.96
10 2 0.04
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATATA
Found at i:18329 original size:6 final size:6
Alignment explanation
Indices: 18315--18378 Score: 53
Period size: 6 Copynumber: 10.8 Consensus size: 6
18305 AATCAATAAA
* *
18315 AATCAT AATCTT AATCAT AATCAT AA-CTAT AATC-- AATCAA ATATCAT
1 AATCAT AATCAT AATCAT AATCAT AATC-AT AATCAT AATCAT A-ATCAT
* *
18362 AATCAT GATCAT CATCA
1 AATCAT AATCAT AATCA
18379 CATGGATTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.08
5 1 0.02
6 37 0.77
7 6 0.12
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.33
Consensus pattern (6 bp):
AATCAT
Found at i:21673 original size:13 final size:14
Alignment explanation
Indices: 21644--21687 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
21634 AGTTGACTTT
21644 AATACATGGATAATA
1 AATA-ATGGATAATA
21659 AATAATGGA-AATA
1 AATAATGGATAATA
*
21672 AATAAATAGATAATA
1 AAT-AATGGATAATA
21687 A
1 A
21688 TAGAATTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 7 0.27
14 10 0.38
15 9 0.35
ACGTcount: A:0.61, C:0.02, G:0.11, T:0.25
Consensus pattern (14 bp):
AATAATGGATAATA
Found at i:22612 original size:17 final size:19
Alignment explanation
Indices: 22579--22622 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
22569 TATTAGTTGT
*
22579 AAATAATGGGATTTTAAAG
1 AAATAGTGGGATTTTAAAG
*
22598 -AATAGTGGG-TTTTAATG
1 AAATAGTGGGATTTTAAAG
22615 AAATAGTG
1 AAATAGTG
22623 CCCTCTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.41, C:0.00, G:0.25, T:0.34
Consensus pattern (19 bp):
AAATAGTGGGATTTTAAAG
Found at i:29818 original size:15 final size:15
Alignment explanation
Indices: 29795--29829 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
29785 GGGGAATAAT
*
29795 CAATCCAAAAACAAA
1 CAATTCAAAAACAAA
29810 CAATTCAAAAACAAA
1 CAATTCAAAAACAAA
29825 CAATT
1 CAATT
29830 TTCTATCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.63, C:0.23, G:0.00, T:0.14
Consensus pattern (15 bp):
CAATTCAAAAACAAA
Done.