Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013316.1 Corchorus olitorius cultivar O-4 contig13349, 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: 32709
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:7963 original size:2 final size:2
Alignment explanation
Indices: 7956--7997 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
7946 TTACTGATTT
7956 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7998 CTAGATCTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10520 original size:28 final size:28
Alignment explanation
Indices: 10482--10537 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
10472 CATGCATTAA
10482 ATATAAAATTAGTTAAGGAAATGAGTAT
1 ATATAAAATTAGTTAAGGAAATGAGTAT
*
10510 ATATAAAATTAGTTAAGGAAATGGGTAT
1 ATATAAAATTAGTTAAGGAAATGAGTAT
10538 GTATCAACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (28 bp):
ATATAAAATTAGTTAAGGAAATGAGTAT
Found at i:22415 original size:51 final size:51
Alignment explanation
Indices: 22327--22430 Score: 163
Period size: 51 Copynumber: 2.0 Consensus size: 51
22317 CTGTAACATA
* * *
22327 TAAAGTAATGACCTGTTGCAGTTTTCAAACAAGAATTACATCATCCAATAC
1 TAAAGTAAGGACCTGTTGCAATTTTCAAACAAAAATTACATCATCCAATAC
* *
22378 TAAAGTAAGGACCTGTTGCAATTTTTAAGCAAAAATTACATCATCCAATAC
1 TAAAGTAAGGACCTGTTGCAATTTTCAAACAAAAATTACATCATCCAATAC
22429 TA
1 TA
22431 GGCTCAAAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (51 bp):
TAAAGTAAGGACCTGTTGCAATTTTCAAACAAAAATTACATCATCCAATAC
Found at i:24011 original size:58 final size:58
Alignment explanation
Indices: 23939--24056 Score: 200
Period size: 58 Copynumber: 2.0 Consensus size: 58
23929 TATGAGATAA
* * *
23939 AAGACAACACAAAATACTTTCAACTTCAAGAAATTTGTCCACTGCATTAATTAATTTG
1 AAGACAACAAAAAATACTTTCAACTTCAAGAAATGTGTCCACTGCAGTAATTAATTTG
*
23997 AAGACAACAAAAAATACTTTCAACTTCAAGAAATGTGTTCACTGCAGTAATTAATTTG
1 AAGACAACAAAAAATACTTTCAACTTCAAGAAATGTGTCCACTGCAGTAATTAATTTG
24055 AA
1 AA
24057 AGAATTCCAC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (58 bp):
AAGACAACAAAAAATACTTTCAACTTCAAGAAATGTGTCCACTGCAGTAATTAATTTG
Found at i:24420 original size:21 final size:21
Alignment explanation
Indices: 24386--24430 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
24376 GGCTTCCTTT
*
24386 TGTTACGAAGCATGATAAACA
1 TGTTACGAAACATGATAAACA
*
24407 TGTTATGAAACATGATAAACA
1 TGTTACGAAACATGATAAACA
24428 TGT
1 TGT
24431 CAGATTGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (21 bp):
TGTTACGAAACATGATAAACA
Found at i:24486 original size:67 final size:68
Alignment explanation
Indices: 24407--24537 Score: 201
Period size: 72 Copynumber: 1.9 Consensus size: 68
24397 ATGATAAACA
24407 TGTTATGAAACATGATAAACATGTCAGA-TTGCTTGATACTACATGTTTTTGCATTATTACTTCC
1 TGTTATGAAACATGATAAACATGTCAGATTTGCTTGATACTACATGTTTTTGCATTATTACTTCC
24471 TTT
66 TTT
* *
24474 TGTTATGAAACATGATAAACATGTCAGATTTGGTTGCTTGGTACTACATTTTTTTGCATTATTA
1 TGTTATGAAACATGATAAACATGTCAGA--T--TTGCTTGATACTACATGTTTTTGCATTATTA
24538 ATTTAAGTCA
Statistics
Matches: 57, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
67 28 0.49
72 29 0.51
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (68 bp):
TGTTATGAAACATGATAAACATGTCAGATTTGCTTGATACTACATGTTTTTGCATTATTACTTCC
TTT
Found at i:24653 original size:32 final size:32
Alignment explanation
Indices: 24612--24676 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
24602 AGGTGAAAGC
24612 TGAGATATTGTGATGGAGCTTGAAATCGATAT
1 TGAGATATTGTGATGGAGCTTGAAATCGATAT
*
24644 TGAGATATTGTGATGGAGGTTGAAATCGATAT
1 TGAGATATTGTGATGGAGCTTGAAATCGATAT
24676 T
1 T
24677 TACCTGTCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (32 bp):
TGAGATATTGTGATGGAGCTTGAAATCGATAT
Found at i:25588 original size:22 final size:23
Alignment explanation
Indices: 25550--25595 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
25540 AATTTACTAT
25550 TTTTATATTTATGATTAAGTGTG
1 TTTTATATTTATGATTAAGTGTG
*
25573 TTTTA-ATTTCAT-ATTAATTGTG
1 TTTTATATTT-ATGATTAAGTGTG
25595 T
1 T
25596 GTGGATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.26, C:0.02, G:0.13, T:0.59
Consensus pattern (23 bp):
TTTTATATTTATGATTAAGTGTG
Found at i:26944 original size:95 final size:95
Alignment explanation
Indices: 26771--26945 Score: 289
Period size: 95 Copynumber: 1.8 Consensus size: 95
26761 TCCCATTATC
* *
26771 TTAGGGTTTTAGAAAAAAAAATATAAACAATTTTAATAAGGTTTAGCCCCAACTAGAAATGTTAT
1 TTAGGGTTTTAGAAAAAAAAATATAAACAATTTTAATAAGGTTTAGCCCCAACTAAAAATCTTAT
**
26836 AATTTTTTAAAGGGTTTAGTCCCAACTATT
66 AATTTGGTAAAGGGTTTAGTCCCAACTATT
26866 TTAGGGTTTTAGAAAAAAAAATATAAACAATTTTAATAAGGTTTAGCCCCAACTAAAAATCTT-T
1 TTAGGGTTTTAGAAAAAAAAATATAAACAATTTTAATAAGGTTTAGCCCCAACTAAAAATCTTAT
*
26930 TATTTGGTATAAGGGT
66 AATTTGGTA-AAGGGT
26946 AGTTTTGATA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
94 7 0.09
95 67 0.91
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (95 bp):
TTAGGGTTTTAGAAAAAAAAATATAAACAATTTTAATAAGGTTTAGCCCCAACTAAAAATCTTAT
AATTTGGTAAAGGGTTTAGTCCCAACTATT
Found at i:29090 original size:41 final size:41
Alignment explanation
Indices: 29039--29118 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
29029 TATAACTAGG
29039 GGCTAAACATGAATTTAATTTATTACCTTAATTATTAGGGA
1 GGCTAAACATGAATTTAATTTATTACCTTAATTATTAGGGA
* * *
29080 GGCTAAACATGGATTTTATTTATTTCCTTAATTATTAGG
1 GGCTAAACATGAATTTAATTTATTACCTTAATTATTAGG
29119 AGGGTCAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (41 bp):
GGCTAAACATGAATTTAATTTATTACCTTAATTATTAGGGA
Found at i:29135 original size:13 final size:13
Alignment explanation
Indices: 29117--29150 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
29107 TTAATTATTA
*
29117 GGAGGGTCAAGTT
1 GGAGGGTCAAATT
*
29130 GGAGGGACAAATT
1 GGAGGGTCAAATT
29143 GGAGGGTC
1 GGAGGGTC
29151 CTATTGTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.26, C:0.09, G:0.47, T:0.18
Consensus pattern (13 bp):
GGAGGGTCAAATT
Done.