Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005838.1 Corchorus capsularis cultivar CVL-1 contig05856, 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: 4658
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:2036 original size:22 final size:22
Alignment explanation
Indices: 2001--2238 Score: 141
Period size: 22 Copynumber: 10.8 Consensus size: 22
1991 GCTGCGTCAG
*
2001 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGAGTGA
*
2022 TTATCGAAATTTCATAGAGATCAGA
1 TTATCAAAATTTCATAGAG-T--GA
*
2047 TTATCAAAATTT-ATAG-GAAGA
1 TTATCAAAATTTCATAGAG-TGA
*
2068 TTATCAAAATTTCATAGTGTTG-
1 TTATCAAAATTTCATAGAG-TGA
* * * *
2090 TTATCAAAATCTCA-ACGCGAGG
1 TTATCAAAATTTCATA-GAGTGA
*
2112 TTATCAAAATTACATA-ATGTGA
1 TTATCAAAATTTCATAGA-GTGA
* * *
2134 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGAGTGA
* * * * *
2156 TCAACAAAATTTTATAAAGTGG
1 TTATCAAAATTTCATAGAGTGA
* * *
2178 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGAGTGA
* *
2200 TTATCAAATTTTCA-AAATGTGA
1 TTATCAAAATTTCATAGA-GTGA
2222 TTA-CAAAAATTTCATAG
1 TTATC-AAAATTTCATAG
2239 TGGTATTTCT
Statistics
Matches: 171, Mismatches: 32, Indels: 26
0.75 0.14 0.11
Matches are distributed among these distances:
21 25 0.15
22 121 0.71
23 8 0.05
24 4 0.02
25 13 0.08
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGAGTGA
Found at i:2068 original size:21 final size:24
Alignment explanation
Indices: 2020--2084 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 24
2010 CTCATAGAGT
*
2020 GATTATCGAAATTTCATAGAGATCA
1 GATTATCAAAATTTCATAGAGA-CA
2045 GATTATCAAAATTT-ATAG-GA-A
1 GATTATCAAAATTTCATAGAGACA
2066 GATTATCAAAATTTCATAG
1 GATTATCAAAATTTCATAG
2085 TGTTGTTATC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
21 15 0.39
22 4 0.11
23 2 0.05
24 4 0.11
25 13 0.34
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (24 bp):
GATTATCAAAATTTCATAGAGACA
Found at i:2514 original size:25 final size:25
Alignment explanation
Indices: 2486--2556 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
2476 ATAAGAAAGT
2486 TATCAAAATTTTATAGGGAGGTTTA
1 TATCAAAATTTTATAGGGAGGTTTA
* *
2511 TATCAAAATTTTATAGGAAGATTTA
1 TATCAAAATTTTATAGGGAGGTTTA
* *
2536 T-T-AAAATTTCATAGCGAGGTT
1 TATCAAAATTTTATAGGGAGGTT
2557 ATCATAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.38
24 1 0.03
25 24 0.60
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (25 bp):
TATCAAAATTTTATAGGGAGGTTTA
Found at i:2549 original size:23 final size:23
Alignment explanation
Indices: 2471--2549 Score: 70
Period size: 25 Copynumber: 3.4 Consensus size: 23
2461 AGTTATCAAG
* * *
2471 ATTTCATAAGAA-AGTTATCAAA
1 ATTTCATAGGAAGATTTATTAAA
* * *
2493 ATTTTATAGGGAGGTTTATATCAAA
1 ATTTCATAGGAAGATTTAT-T-AAA
*
2518 ATTTTATAGGAAGATTTATTAAA
1 ATTTCATAGGAAGATTTATTAAA
2541 ATTTCATAG
1 ATTTCATAG
2550 CGAGGTTATC
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
22 9 0.20
23 15 0.33
24 1 0.02
25 20 0.44
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (23 bp):
ATTTCATAGGAAGATTTATTAAA
Found at i:2565 original size:22 final size:22
Alignment explanation
Indices: 2338--2590 Score: 96
Period size: 22 Copynumber: 11.6 Consensus size: 22
2328 TTAGGGAGGA
**
2338 TATCAAAATTTCATAGTTTAG-T
1 TATCAAAATTTCATAG-AGAGAT
* * *
2360 TTTCAAAATTTCATA-AAAGGGT
1 TATCAAAATTTCATAGAGA-GAT
*
2382 TATCAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATAGAGAGAT
* * * *
2404 TA-AAACAATTTCATAAAAAGGT
1 TATCAA-AATTTCATAGAGAGAT
** * *
2426 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAGAGAGAT
* * *
2448 GATTAAAA-TT--T-G-TAG-T
1 TATCAAAATTTCATAGAGAGAT
* *
2464 TATCAAGATTTCATA-AGAAAGT
1 TATCAAAATTTCATAGAGAGA-T
* * *
2486 TATCAAAATTTTATAGGGAGGTTT
1 TATCAAAATTTCATAGAGA-G-AT
*
2510 ATATCAAAATTTTATAG-GAAGATT
1 -TATCAAAATTTCATAGAG-AGA-T
* * *
2534 TATTAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAGAGAGAT
* *
2556 TATCATAATTTCATAGAGTGAT
1 TATCAAAATTTCATAGAGAGAT
2578 TATCAAAATTTCA
1 TATCAAAATTTCA
2591 GAGTGTGGTT
Statistics
Matches: 170, Mismatches: 42, Indels: 38
0.68 0.17 0.15
Matches are distributed among these distances:
16 6 0.04
17 4 0.02
18 1 0.01
19 2 0.01
20 2 0.01
21 4 0.02
22 108 0.64
23 21 0.12
24 5 0.03
25 17 0.10
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGAGAGAT
Found at i:2595 original size:20 final size:21
Alignment explanation
Indices: 2555--2595 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2545 CATAGCGAGG
*
2555 TTATCATAATTTCATAGAGTGA
1 TTATCAAAATTTCA-AGAGTGA
2577 TTATCAAAATTTC-AGAGTG
1 TTATCAAAATTTCAAGAGTG
2596 TGGTTACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (21 bp):
TTATCAAAATTTCAAGAGTGA
Found at i:2716 original size:22 final size:22
Alignment explanation
Indices: 2654--2717 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
2644 GTGTTGGTTA
* **
2654 TCAAAATTTCATTGGGAAAT-T
1 TCAAAATTTCATAGGGAGGTGT
**
2675 ATCAAAATTTCATATTGAGGTGT
1 -TCAAAATTTCATAGGGAGGTGT
*
2698 TCAAAATTTCTTAGGGAGGT
1 TCAAAATTTCATAGGGAGGT
2718 TAACTAAATT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
22 32 0.97
23 1 0.03
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (22 bp):
TCAAAATTTCATAGGGAGGTGT
Done.