Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017702.1 Corchorus olitorius cultivar O-4 contig17735, 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: 35626
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:2765 original size:76 final size:76
Alignment explanation
Indices: 2615--2758 Score: 177
Period size: 76 Copynumber: 1.9 Consensus size: 76
2605 ACAAGGATCC
* * *
2615 CGACTCTACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
2680 GGGCAGTGTCA
66 GGGCAGTGTCA
* * **
2691 CGACTCCAGCTGGGCGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
2753 GATGGG
63 GATGGG
2759 TTGTGTCTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
75 4 0.07
76 48 0.83
77 6 0.10
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:12293 original size:51 final size:51
Alignment explanation
Indices: 12197--12295 Score: 119
Period size: 51 Copynumber: 1.9 Consensus size: 51
12187 CTTCATATTT
** ***
12197 TCTTGTTTAGATCTTGTCTCAGGACATCCAAACACTCTTTTAGTGTTTTTC
1 TCTTGTTTAGATCTTGTCTCAGGACATAAAAACACTCTACAAGTGTTTTTC
* *
12248 TCTTGTTTCA-ATCTTGTCTCCGGACATAAAAACACTGTACAAGTGTTT
1 TCTTGTTT-AGATCTTGTCTCAGGACATAAAAACACTCTACAAGTGTTT
12296 CTCTTTCAGA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 39 0.98
52 1 0.03
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.41
Consensus pattern (51 bp):
TCTTGTTTAGATCTTGTCTCAGGACATAAAAACACTCTACAAGTGTTTTTC
Found at i:13912 original size:2 final size:2
Alignment explanation
Indices: 13905--13934 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
13895 TGGGCAACAG
*
13905 AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13935 GCGATGGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15735 original size:67 final size:66
Alignment explanation
Indices: 15660--16217 Score: 396
Period size: 67 Copynumber: 8.4 Consensus size: 66
15650 TCAGTTCTTT
*
15660 TTTCCAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGCATTTAAGTTTATTATTTTC
1 TTTCCAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTAGTATTTTC
15724 AAA
66 --A
* *
15727 TTTCCAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGTATTTAAGTGTAGTATTTTC
1 TTTCCAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTAGTATTTTC
15791 A
66 A
* ** * * *
15792 TTTCCAAAAATACCTTTTCGGTTAAAGGGTCAGTCTT-GTCTTTTTGCATTCAATTTTAGTATTT
1 TTTCC-AAAATACCCTTTCGGTCGAAGGGTCA-TTTTCGTCTTTTTGCATTTAAGTTTAGTATTT
*
15856 TGA
64 TCA
* * * * * *
15859 TTTCTAGAAATACCCTTTCGGTCAAAGGGTCGGTTTT-GTCTTTTTGCATTCATGTTTAGTGTTT
1 TTTCCA-AAATACCCTTTCGGTCGAAGGGTC-ATTTTCGTCTTTTTGCATTTAAGTTTAGTATTT
*
15923 TCG
64 TCA
* * ** * * *
15926 TTTCCAGAGATATCCTTTCGGTCGAAGGGTCGGTTTCGTCTTTTTGCATTCAGGTTTAGT-TTTA
1 TTTCCA-AAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTAGTATTTT
15990 C-
65 CA
* * * * * * *
15991 TTTCCAAAAATACCCTTCCGGTCGAAAGGTCAGTTTCATCAGGTTGTTGCATTTAAGTCTAAT-T
1 TTTCC-AAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC---TTTTTGCATTTAAGTTTAGTAT
16055 TTTC-
62 TTTCA
** * * * *
16059 TTTCCAAAGAATACCCTTTCTATCAAAGGGTCAATTTT-GTCATTCTTGCATTTGAGTTTACTGA
1 TTTCC-AA-AATACCCTTTCGGTCGAAGGGTC-ATTTTCGTC-TTTTTGCATTTAAGTTTAGT-A
16123 -TTTC-
61 TTTTCA
* * * * * * *
16127 ---CAAAAATACCCTTTCGGT-GAAAGGGTCAGTTCCATCATTTCTGCATTTCAGTTTA-T-TCT
1 TTTCCAAAATACCCTTTCGGTCG-AAGGGTCATTTTCGTC-TTTTTGCATTTAAGTTTAGTATTT
*
16186 AC-
64 TCA
* *
16188 TTTCCAAAAATGCCCTTTCGGTCCAAGGGT
1 TTTCC-AAAATACCCTTTCGGTCGAAGGGT
16218 GAACTTTGTC
Statistics
Matches: 401, Mismatches: 68, Indels: 46
0.78 0.13 0.09
Matches are distributed among these distances:
61 2 0.00
62 4 0.01
63 37 0.09
64 3 0.01
65 60 0.15
66 36 0.09
67 204 0.51
68 31 0.08
69 20 0.05
70 4 0.01
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.42
Consensus pattern (66 bp):
TTTCCAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTAGTATTTTC
A
Found at i:23034 original size:18 final size:19
Alignment explanation
Indices: 23013--23051 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
23003 GAGTGGACTA
23013 AGCTAGGTGAGC-GGGCTG
1 AGCTAGGTGAGCAGGGCTG
23031 AGCTAGGTGAGCAGGGCTG
1 AGCTAGGTGAGCAGGGCTG
23050 AG
1 AG
23052 GAAAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.21, C:0.15, G:0.49, T:0.15
Consensus pattern (19 bp):
AGCTAGGTGAGCAGGGCTG
Found at i:24507 original size:27 final size:27
Alignment explanation
Indices: 24477--24559 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
24467 GAATACTGGG
24477 TCTAGTGGTTAAAGTGTTGTATTTTCA
1 TCTAGTGGTTAAAGTGTTGTATTTTCA
*** * * * *
24504 TCTACAAGAT-AA--GTTGAATACTTGA
1 TCTAGTGGTTAAAGTGTTGTAT-TTTCA
*
24529 CCTAGTGGTTAAAGTGTTGTATTTTCA
1 TCTAGTGGTTAAAGTGTTGTATTTTCA
24556 TCTA
1 TCTA
24560 CAAGACCAAG
Statistics
Matches: 36, Mismatches: 16, Indels: 8
0.60 0.27 0.13
Matches are distributed among these distances:
24 6 0.17
25 8 0.22
26 4 0.11
27 12 0.33
28 6 0.17
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (27 bp):
TCTAGTGGTTAAAGTGTTGTATTTTCA
Found at i:24519 original size:52 final size:52
Alignment explanation
Indices: 24460--24564 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
24450 ATAAATTTGC
**
24460 ATAAGTTGAATACTGGGTCTAGTGGTTAAAGTGTTGTATTTTCATCTACAAG
1 ATAAGTTGAATACTGGACCTAGTGGTTAAAGTGTTGTATTTTCATCTACAAG
*
24512 ATAAGTTGAATACTTGACCTAGTGGTTAAAGTGTTGTATTTTCATCTACAAG
1 ATAAGTTGAATACTGGACCTAGTGGTTAAAGTGTTGTATTTTCATCTACAAG
24564 A
1 A
24565 CCAAGGTTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.38
Consensus pattern (52 bp):
ATAAGTTGAATACTGGACCTAGTGGTTAAAGTGTTGTATTTTCATCTACAAG
Found at i:25346 original size:43 final size:42
Alignment explanation
Indices: 25264--25346 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
25254 AATTTTATTA
* *
25264 AAAACAAAAACATGTTTGGATACACAATGTTTTATAAAACAT
1 AAAACAAAAACATGTTTGGATACAAAATGTGTTATAAAACAT
* * *
25306 AAAACATAAACATGTTTGGTTAACATAAAT-TGTTGTAAAAC
1 AAAACAAAAACATGTTTGGAT-ACA-AAATGTGTTATAAAAC
25347 TCTACATCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
42 19 0.56
43 12 0.35
44 3 0.09
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (42 bp):
AAAACAAAAACATGTTTGGATACAAAATGTGTTATAAAACAT
Found at i:26751 original size:11 final size:11
Alignment explanation
Indices: 26722--26766 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
26712 ATTAACAAAC
26722 ATAAACGAACTA
1 ATAAACGAAC-A
*
26734 TTAAACGAACA
1 ATAAACGAACA
26745 ATAAACGAACA
1 ATAAACGAACA
* *
26756 CTAAATGAACA
1 ATAAACGAACA
26767 TTAATCGAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.58, C:0.18, G:0.09, T:0.16
Consensus pattern (11 bp):
ATAAACGAACA
Found at i:28019 original size:16 final size:15
Alignment explanation
Indices: 27999--28056 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
27989 TTCTTTTATC
27999 TTTTTTTTTTTAAGG
1 TTTTTTTTTTTAAGG
*
28014 TATTTTTTGTTTT-TGG
1 T-TTTTTT-TTTTAAGG
**
28030 TTTTTTTTTTTAATC
1 TTTTTTTTTTTAAGG
28045 TTTTTTCTTTTT
1 TTTTTT-TTTTT
28057 CAAATGCCAG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
14 4 0.11
15 13 0.37
16 14 0.40
17 4 0.11
ACGTcount: A:0.09, C:0.03, G:0.09, T:0.79
Consensus pattern (15 bp):
TTTTTTTTTTTAAGG
Done.