Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007255.1 Corchorus capsularis cultivar CVL-1 contig07276, 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: 23827
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Found at i:63 original size:16 final size:15
Alignment explanation
Indices: 23--62 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
13 CAACTAAGGT
*
23 TTTTGAAATCTAGGG
1 TTTTGAAAACTAGGG
38 TTCTTGAAAACTAGGG
1 TT-TTGAAAACTAGGG
54 TTTTGAAAA
1 TTTTGAAAA
63 AAAGAAGGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.38
Consensus pattern (15 bp):
TTTTGAAAACTAGGG
Found at i:906 original size:49 final size:48
Alignment explanation
Indices: 829--1009 Score: 193
Period size: 49 Copynumber: 3.7 Consensus size: 48
819 AGCTTGTAAA
*
829 TAAAAGATTGAATTTTTAGCAATTAGTAAGTAAAAATGTCATCTTTAGG
1 TAAAAGATTGAATTTTTAGTAATTAGTAAGTAAAAATGTCATCTTT-GG
*
878 TAAAAGATTGAATTTTTAGTAATCAGTAAGTAAAAATGTCATCTTTGGG
1 TAAAAGATTGAATTTTTAGTAATTAGTAAGTAAAAATGTCATCTTT-GG
* * * * * * * * *
927 TAAGAGATGGAAACTTTTAATGATTAGTGAGTAAAACTGTCACCCTTGAG
1 TAAAAGATTG-AATTTTTAGTAATTAGTAAGTAAAAATGTCATCTTTG-G
*
977 CAAAAGATTG-ATTTTTAGAGTAATTAGTAAGTA
1 TAAAAGATTGAATTTTT--AGTAATTAGTAAGTA
1010 GAGATGTACC
Statistics
Matches: 108, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
48 5 0.05
49 55 0.51
50 48 0.44
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.35
Consensus pattern (48 bp):
TAAAAGATTGAATTTTTAGTAATTAGTAAGTAAAAATGTCATCTTTGG
Found at i:1916 original size:55 final size:55
Alignment explanation
Indices: 1851--2112 Score: 427
Period size: 55 Copynumber: 4.8 Consensus size: 55
1841 AGTCCGAATC
* * *
1851 GTAATAAGTAAATCAGTAATTAACTGAAAAGAGATTAATCAGAGTTAAAGTAATA
1 GTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAAGTAATA
*
1906 GTAATCAGTAAATCAGTAATTAAGTGAAAATAGATTAATCAGAGTCAAAGTAATA
1 GTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAAGTAATA
1961 GTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAAGTAATA
1 GTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAAGTAATA
* *
2016 GTAATCAGTAAATCAGTAGTTAAGT-AAGAAGAGATTAATCAGAGTCAAGGTAATA
1 GTAATCAGTAAATCAGTAATTAAGTGAA-AAGAGATTAATCAGAGTCAAAGTAATA
* * *
2071 GTAATCAGTGAATCAGTAGTTAAGTAAAAAGAGATTAATCAG
1 GTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAG
2113 TAAATTGATA
Statistics
Matches: 197, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
54 2 0.01
55 193 0.98
56 2 0.01
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (55 bp):
GTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAAGTAATA
Found at i:2128 original size:34 final size:33
Alignment explanation
Indices: 2090--2200 Score: 91
Period size: 34 Copynumber: 3.2 Consensus size: 33
2080 GAATCAGTAG
2090 TTAAGTAAAAAGAGATTAATCAGTAAATTGATAA
1 TTAAGTAAAAAGA-ATTAATCAGTAAATTGATAA
* *
2124 TTAAG-AGTCAAAGTAATAGTAATCAGTAAA-TCAGTAA
1 TTAAGTA--AAAAG-AAT--TAATCAGTAAATTGA-TAA
* * *
2161 TCAAGTAAAAAGATAGTAATTAGTAAATTGATAA
1 TTAAGTAAAAAGA-ATTAATCAGTAAATTGATAA
2195 TTAAGT
1 TTAAGT
2201 GTCAAGGTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
33 1 0.02
34 23 0.38
35 9 0.15
36 8 0.13
37 18 0.30
38 1 0.02
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.30
Consensus pattern (33 bp):
TTAAGTAAAAAGAATTAATCAGTAAATTGATAA
Found at i:2131 original size:71 final size:70
Alignment explanation
Indices: 2056--2271 Score: 240
Period size: 71 Copynumber: 3.0 Consensus size: 70
2046 GAGATTAATC
2056 AGAGTCAAGGTAATAGTAATCAGTGAATCAGTAGTTAAGTAAAAAGAGATTAATCAGTAAATTGA
1 AGAGTCAAGGTAATAGTAATCAGTGAATCAGTAGTTAAGTAAAAAGAGA-TAATCAGTAAATTGA
2121 TAATTA
65 TAATTA
* * * * * *
2127 AGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGATAGTAATTAGTAAATTGA
1 AGAGTCAAGGTAATAGTAATCAGTGAATCAGTAGTTAAGTAAAAAGAGA-TAATCAGTAAATTGA
2192 TAATTA
65 TAATTA
* * * *
2198 AGTGTCAAGGTAAGAGATTAATCAGTG-ATCAAAG-AGTTAAGGTAAAAATAG-TAATCAGTGAA
1 AGAGTCAAGGTAATAG--TAATCAGTGAATC--AGTAGTTAA-GTAAAAAGAGATAATCAGTAAA
**
2260 TCAATAATTA
61 TTGATAATTA
2270 AG
1 AG
2272 GGTTAAAGTG
Statistics
Matches: 121, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
71 77 0.64
72 22 0.18
73 12 0.10
74 10 0.08
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (70 bp):
AGAGTCAAGGTAATAGTAATCAGTGAATCAGTAGTTAAGTAAAAAGAGATAATCAGTAAATTGAT
AATTA
Found at i:2729 original size:31 final size:33
Alignment explanation
Indices: 2691--2759 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 33
2681 GATATAAATG
*
2691 GTAAAAAAAAAGAAAGT-AAAAATGG-CATTAA
1 GTAAAAAAAAAGAAAGTAAAAAATGGTAATTAA
* *
2722 GT--AAAAAAGGAGAGTAAAAAATGGTAATTAA
1 GTAAAAAAAAAGAAAGTAAAAAATGGTAATTAA
2753 GTAAAAA
1 GTAAAAA
2760 GAGTAAAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
29 11 0.35
30 8 0.26
31 9 0.29
33 3 0.10
ACGTcount: A:0.62, C:0.01, G:0.19, T:0.17
Consensus pattern (33 bp):
GTAAAAAAAAAGAAAGTAAAAAATGGTAATTAA
Found at i:2737 original size:29 final size:31
Alignment explanation
Indices: 2695--2759 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
2685 TAAATGGTAA
*
2695 AAAAAAAGAAAGT-AAAAATGG-CATTAAGT
1 AAAAAAAGAAAGTAAAAAATGGTAATTAAGT
* *
2724 AAAAAAGGAGAGTAAAAAATGGTAATTAAGT
1 AAAAAAAGAAAGTAAAAAATGGTAATTAAGT
2755 AAAAA
1 AAAAA
2760 GAGTAAAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 11 0.35
30 8 0.26
31 12 0.39
ACGTcount: A:0.63, C:0.02, G:0.18, T:0.17
Consensus pattern (31 bp):
AAAAAAAGAAAGTAAAAAATGGTAATTAAGT
Found at i:2857 original size:29 final size:26
Alignment explanation
Indices: 2611--2847 Score: 155
Period size: 26 Copynumber: 8.9 Consensus size: 26
2601 CTGAAAAAGA
* *
2611 GTAATTAGTAAATAAGAGTAAGAAATG
1 GTAATCAGTAAA-AAGAGTAAAAAATG
* *
2638 GTGATCAGTAAAAAAGAGTAAAAAGTG
1 GTAATCAGT-AAAAAGAGTAAAAAATG
* *
2665 GTATTCAGTAAAAAGAG-ATATAAATG
1 GTAATCAGTAAAAAGAGTA-AAAAATG
*
2691 GTAA--A-AAAAAAGAAAGT-AAAAATG
1 GTAATCAGTAAAAAG--AGTAAAAAATG
* * *
2715 GCATTAAGTAAAAAAGGAGAGTAAAAAATG
1 GTAATCAGT--AAAA--AGAGTAAAAAATG
*
2745 GTAATTAAGTAAAAAGAGT--AAAATG
1 GTAA-TCAGTAAAAAGAGTAAAAAATG
* * * * *
2770 GTATTCAGTCAAAACAGAAAGAAAAGGG
1 GTAATCAGTAAAAAGAGTAA-AAAA-TG
*
2798 GTAATCAGTAAAAAGAGTAAAATATG
1 GTAATCAGTAAAAAGAGTAAAAAATG
*
2824 GTAATCAGTACAAAGAGTAAAAAA
1 GTAATCAGTAAAAAGAGTAAAAAA
2848 GAATGGTAAT
Statistics
Matches: 162, Mismatches: 30, Indels: 37
0.71 0.13 0.16
Matches are distributed among these distances:
23 6 0.04
24 19 0.12
25 12 0.07
26 40 0.25
27 38 0.23
28 20 0.12
29 11 0.07
30 9 0.06
31 7 0.04
ACGTcount: A:0.55, C:0.04, G:0.21, T:0.20
Consensus pattern (26 bp):
GTAATCAGTAAAAAGAGTAAAAAATG
Found at i:15332 original size:28 final size:28
Alignment explanation
Indices: 15257--15331 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 28
15247 AGGGTCGCCC
* * *
15257 AGGGACATTTTGGTCATTTTCTGCATTT
1 AGGGGCATTTTGGTCATTTTCTACATCT
*
15285 AGGGGCATTTTCGTCATTTTC-ACATCT
1 AGGGGCATTTTGGTCATTTTCTACATCT
*
15312 AGGGGCATTTAGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
15332 TTTTTTGCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.43
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTCTACATCT
Found at i:15535 original size:21 final size:21
Alignment explanation
Indices: 15493--15536 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
15483 CATTATGGTG
*
15493 TTTTCAATTAGTATTGTTGCA
1 TTTTCAATTAGTATTGTGGCA
*
15514 TTTTCATTTAGTAATT-TGGCA
1 TTTTCAATTAGT-ATTGTGGCA
15535 TT
1 TT
15537 GTTACACTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.55
Consensus pattern (21 bp):
TTTTCAATTAGTATTGTGGCA
Done.