Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004123.1 Corchorus capsularis cultivar CVL-1 contig04131, 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: 7074
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:1267 original size:30 final size:29
Alignment explanation
Indices: 1211--1268 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1201 CCACCAATGC
* * *
1211 CCAAATAAGCCCATGAGCATCAATTTTGG
1 CCAAATAACCCCATGAACACCAATTTTGG
1240 CCAAATAACCCCATGAACTACCAATTTTG
1 CCAAATAACCCCATGAAC-ACCAATTTTG
1269 ACCAGATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.24
Consensus pattern (29 bp):
CCAAATAACCCCATGAACACCAATTTTGG
Found at i:2262 original size:22 final size:21
Alignment explanation
Indices: 2201--2401 Score: 125
Period size: 22 Copynumber: 9.2 Consensus size: 21
2191 ACCAAAACTA
*
2201 CATAGGAATGTTATCAAAATTT
1 CATATGAA-GTTATCAAAATTT
* ** **
2223 AATAATGTGGTTCCCAAAATTT
1 CAT-ATGAAGTTATCAAAATTT
* *
2245 CATATGAAGATCATCAAAACTT
1 CATATGAAG-TTATCAAAATTT
*
2267 CATAATGTAGTTATCAAAATTT
1 CAT-ATGAAGTTATCAAAATTT
* * *
2289 CACAAGAAGGTTACCAAAATTT
1 CATATGAA-GTTATCAAAATTT
**
2311 CATAAAAAGGTTATCAAAATTT
1 CATATGAA-GTTATCAAAATTT
* *
2333 CTTATGGAAGTTATCGAAATTT
1 CATAT-GAAGTTATCAAAATTT
* *
2355 TATAGTGTAGTTATCAAAATTT
1 CATA-TGAAGTTATCAAAATTT
** *
2377 CGCA-GAAGGTTAACAAAATTT
1 CATATGAA-GTTATCAAAATTT
2398 CATA
1 CATA
2402 GGGAAGGAAT
Statistics
Matches: 134, Mismatches: 38, Indels: 15
0.72 0.20 0.08
Matches are distributed among these distances:
20 2 0.01
21 21 0.16
22 101 0.75
23 10 0.07
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (21 bp):
CATATGAAGTTATCAAAATTT
Found at i:2307 original size:44 final size:44
Alignment explanation
Indices: 2210--2401 Score: 147
Period size: 44 Copynumber: 4.4 Consensus size: 44
2200 ACATAGGAAT
* * * ** * *
2210 GTTATCAAAATTTAATAATGTGGTTCCCAAAATTTCATATGAAG
1 GTTAACAAAATTTCATAATGTAGTTATCAAAATTTCACAAGAAG
* * * *
2254 ATCATCAAAACTTCATAATGTAGTTATCAAAATTTCACAAGAAG
1 GTTAACAAAATTTCATAATGTAGTTATCAAAATTTCACAAGAAG
* ** ** *
2298 GTTACCAAAATTTCATAA-AAAGGTTATCAAAATTTCTTATGGAA-
1 GTTAACAAAATTTCATAATGTA-GTTATCAAAATTTCACA-AGAAG
* * * * *
2342 GTTATCGAAATTTTATAGTGTAGTTATCAAAATTTCGC-AGAAG
1 GTTAACAAAATTTCATAATGTAGTTATCAAAATTTCACAAGAAG
2385 GTTAACAAAATTTCATA
1 GTTAACAAAATTTCATA
2402 GGGAAGGAAT
Statistics
Matches: 114, Mismatches: 30, Indels: 9
0.75 0.20 0.06
Matches are distributed among these distances:
42 3 0.03
43 15 0.13
44 92 0.81
45 4 0.04
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (44 bp):
GTTAACAAAATTTCATAATGTAGTTATCAAAATTTCACAAGAAG
Found at i:2345 original size:66 final size:67
Alignment explanation
Indices: 2193--2354 Score: 154
Period size: 66 Copynumber: 2.5 Consensus size: 67
2183 GACAATCAAC
* * * * **
2193 CAAAACTACAT-A-GGAATGTTATCAAAATTTAATAATGTGGTTCCCAAAATTTCATATGAAGAT
1 CAAAACTTCATAATGGAA-GTTATCAAAATTTAACAATGAGGTTACCAAAATTTCATAAAAAGAT
2256 CAT
65 CAT
* * *
2259 CAAAACTTCATAAT-GTAGTTATCAAAATTTCACAA-GAAGGTTACCAAAATTTCATAAAAAGGT
1 CAAAACTTCATAATGGAAGTTATCAAAATTTAACAATG-AGGTTACCAAAATTTCATAAAAAGAT
*
2322 TAT
65 CAT
* * *
2325 CAAAATTTC-TTATGGAAGTTATCGAAATTT
1 CAAAACTTCATAATGGAAGTTATCAAAATTT
2355 TATAGTGTAG
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
65 4 0.05
66 71 0.91
67 3 0.04
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.33
Consensus pattern (67 bp):
CAAAACTTCATAATGGAAGTTATCAAAATTTAACAATGAGGTTACCAAAATTTCATAAAAAGATC
AT
Found at i:2625 original size:22 final size:22
Alignment explanation
Indices: 2544--2685 Score: 128
Period size: 22 Copynumber: 6.5 Consensus size: 22
2534 CATATGGAGG
* *
2544 TTATCAAAATTTCAT-GTTCTGG
1 TTATCAAAATTTCATAG-TGTGA
**
2566 TTATCAAAATTTTCATAGTGCAA
1 TTATCAAAA-TTTCATAGTGTGA
* *
2589 TTA-C-CAATTTTATAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
* *
2609 TTATCAAAATTTCATAGGGAGA
1 TTATCAAAATTTCATAGTGTGA
* * **
2631 TTATCAAAATTTCACACTAAGA
1 TTATCAAAATTTCATAGTGTGA
*
2653 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGTGA
2675 TTATCAAAATT
1 TTATCAAAATT
2686 CCACAGTATG
Statistics
Matches: 95, Mismatches: 21, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
20 13 0.14
21 3 0.03
22 68 0.72
23 10 0.11
24 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGA
Found at i:2657 original size:44 final size:44
Alignment explanation
Indices: 2607--2778 Score: 146
Period size: 44 Copynumber: 3.8 Consensus size: 44
2597 TTTATAGTGT
* *
2607 GATTATCAAAATTTCATAGGGAGATTATCAAAATTTCACACTAA
1 GATTATCAAAATTTCATAGGGAGGTTATCAAAATTTCACAATAA
* * * *
2651 GATTATCAAAATTTCATAGTGTGGTTATCAAAATTCCACAGTATGCAT
1 GATTATCAAAATTTCATAGGGAGGTTATCAAAATTTCACA--AT--AA
* * * ** *
2699 GGTTATCAAATTTTCATATGGAGGTTATTGAAATTTCATAATAA
1 GATTATCAAAATTTCATAGGGAGGTTATCAAAATTTCACAATAA
* * * * * *
2743 GATTATTAAATTTTCACAGTGTGGTTATCAATATTT
1 GATTATCAAAATTTCATAGGGAGGTTATCAAAATTT
2779 TTACGTTGGA
Statistics
Matches: 99, Mismatches: 25, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
44 64 0.65
46 3 0.03
48 32 0.32
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (44 bp):
GATTATCAAAATTTCATAGGGAGGTTATCAAAATTTCACAATAA
Found at i:2725 original size:22 final size:22
Alignment explanation
Indices: 2533--2738 Score: 102
Period size: 22 Copynumber: 9.2 Consensus size: 22
2523 AGTTTCATTC
2533 TCATATGGAGGTTATCAAAATT
1 TCATATGGAGGTTATCAAAATT
* ***
2555 TCATGTTCTGGTTATCAAAATTT
1 TCATATGGAGGTTATCAAAA-TT
* * *
2578 TCATAGTGCA-ATTA-C-CAATT
1 TCATA-TGGAGGTTATCAAAATT
*
2598 TTATAGTGTGA--TTATCAAAATT
1 TCATA-TG-GAGGTTATCAAAATT
* *
2620 TCATAGGGAGATTATCAAAATT
1 TCATATGGAGGTTATCAAAATT
* * *
2642 TCACACT-AAGATTATCAAAATT
1 TCATA-TGGAGGTTATCAAAATT
*
2664 TCATA-GTGTGGTTATCAAAATT
1 TCATATG-GAGGTTATCAAAATT
* * *
2686 CCACAGTATGCATGGTTATCAAATTT
1 --TCA-TATGGA-GGTTATCAAAATT
**
2712 TCATATGGAGGTTATTGAAATT
1 TCATATGGAGGTTATCAAAATT
2734 TCATA
1 TCATA
2739 ATAAGATTAT
Statistics
Matches: 139, Mismatches: 30, Indels: 30
0.70 0.15 0.15
Matches are distributed among these distances:
20 14 0.10
21 5 0.04
22 85 0.61
23 14 0.10
24 6 0.04
25 2 0.01
26 13 0.09
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (22 bp):
TCATATGGAGGTTATCAAAATT
Found at i:2757 original size:22 final size:22
Alignment explanation
Indices: 2701--2758 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
2691 GTATGCATGG
* * *
2701 TTATCAAATTTTCATATGGAGG
1 TTATTAAATTTTCATATGAAGA
2723 TTATTGAAA-TTTCATAAT-AAGA
1 TTATT-AAATTTTCAT-ATGAAGA
2745 TTATTAAATTTTCA
1 TTATTAAATTTTCA
2759 CAGTGTGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 3 0.10
22 22 0.73
23 5 0.17
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (22 bp):
TTATTAAATTTTCATATGAAGA
Found at i:3643 original size:16 final size:16
Alignment explanation
Indices: 3619--3653 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
3609 AAAGTAGTTA
3619 AAACATTAATTTCTAT
1 AAACATTAATTTCTAT
*
3635 AAACTTTAATTTCTAT
1 AAACATTAATTTCTAT
3651 AAA
1 AAA
3654 GTAGTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (16 bp):
AAACATTAATTTCTAT
Found at i:5994 original size:18 final size:18
Alignment explanation
Indices: 5971--6007 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5961 ATTCTATGTG
5971 GATGCAAAGAGTTTTACT
1 GATGCAAAGAGTTTTACT
*
5989 GATGCAAAGGGTTTTACT
1 GATGCAAAGAGTTTTACT
6007 G
1 G
6008 TTAGCGATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (18 bp):
GATGCAAAGAGTTTTACT
Done.