Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004023.1 Corchorus capsularis cultivar CVL-1 contig04031, 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: 9292
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Found at i:409 original size:27 final size:27
Alignment explanation
Indices: 357--410 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
347 GATTTTCTGA
*
357 CTTTTCTTCTTTTTGTTTCGGTTTTTT
1 CTTTTCTTCTTTTTGTTTCGGATTTTT
* *
384 CTTTTCTT-TTTTTTTTTGCTGATTTTT
1 CTTTTCTTCTTTTTGTTT-CGGATTTTT
411 TATAATAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.02, C:0.13, G:0.09, T:0.76
Consensus pattern (27 bp):
CTTTTCTTCTTTTTGTTTCGGATTTTT
Found at i:830 original size:15 final size:15
Alignment explanation
Indices: 810--839 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
800 GTTCTAATTA
810 TTGGGAAGTAAGCTT
1 TTGGGAAGTAAGCTT
825 TTGGGAAGTAAGCTT
1 TTGGGAAGTAAGCTT
840 CTCGAGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.33, T:0.33
Consensus pattern (15 bp):
TTGGGAAGTAAGCTT
Found at i:1131 original size:43 final size:43
Alignment explanation
Indices: 1066--1147 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
1056 GCAGACCTCT
*
1066 GAAAATTGACAAGAAGACAATTCAA-AGATCAACTTAGATCTCC
1 GAAAATTGACAAGAAGACAATTCAAGA-ATCAACATAGATCTCC
**
1109 GAAAATTGACAAGAAGGTAATTCAAGAATCAACATAGAT
1 GAAAATTGACAAGAAGACAATTCAAGAATCAACATAGAT
1148 TTCTAAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
43 34 0.97
44 1 0.03
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.21
Consensus pattern (43 bp):
GAAAATTGACAAGAAGACAATTCAAGAATCAACATAGATCTCC
Found at i:1395 original size:47 final size:48
Alignment explanation
Indices: 1279--1447 Score: 205
Period size: 48 Copynumber: 3.5 Consensus size: 48
1269 TGCAGATTCG
* *
1279 CGTGGAAGCGAGAAAATACCAACTGTGGTCAAAGAAATAGCAAACTCA
1 CGTGGAAGTGAGAAAAGACCAACTGTGGTCAAAGAAATAGCAAACTCA
* * * ** * * *
1327 CGTGGAAGTGAGGAAAGACCAACTGTTG-CCATTAAATTGTAGACTCA
1 CGTGGAAGTGAGAAAAGACCAACTGTGGTCAAAGAAATAGCAAACTCA
* *
1374 CGTGGAAGCGAGAAAATACCAACTGTGGTCAAAGAAATAGCAAACTCA
1 CGTGGAAGTGAGAAAAGACCAACTGTGGTCAAAGAAATAGCAAACTCA
* *
1422 CGTGGAAGTGAGGAAAGACTAACTGT
1 CGTGGAAGTGAGAAAAGACCAACTGT
1448 TGCCATTAAA
Statistics
Matches: 96, Mismatches: 24, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
47 37 0.39
48 59 0.61
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (48 bp):
CGTGGAAGTGAGAAAAGACCAACTGTGGTCAAAGAAATAGCAAACTCA
Found at i:1446 original size:95 final size:95
Alignment explanation
Indices: 1279--1481 Score: 379
Period size: 95 Copynumber: 2.1 Consensus size: 95
1269 TGCAGATTCG
1279 CGTGGAAGCGAGAAAATACCAACTGTGGTCAAAGAAATAGCAAACTCACGTGGAAGTGAGGAAAG
1 CGTGGAAGCGAGAAAATACCAACTGTGGTCAAAGAAATAGCAAACTCACGTGGAAGTGAGGAAAG
1344 ACCAACTGTTGCCATTAAATTGTAGACTCA
66 ACCAACTGTTGCCATTAAATTGTAGACTCA
1374 CGTGGAAGCGAGAAAATACCAACTGTGGTCAAAGAAATAGCAAACTCACGTGGAAGTGAGGAAAG
1 CGTGGAAGCGAGAAAATACCAACTGTGGTCAAAGAAATAGCAAACTCACGTGGAAGTGAGGAAAG
* *
1439 ACTAACTGTTGCCATTAAATTGTAGACTCG
66 ACCAACTGTTGCCATTAAATTGTAGACTCA
*
1469 CGTGGAAGTGAGA
1 CGTGGAAGCGAGA
1482 GAGGATTACC
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 105 1.00
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (95 bp):
CGTGGAAGCGAGAAAATACCAACTGTGGTCAAAGAAATAGCAAACTCACGTGGAAGTGAGGAAAG
ACCAACTGTTGCCATTAAATTGTAGACTCA
Found at i:1477 original size:47 final size:47
Alignment explanation
Indices: 1322--1480 Score: 201
Period size: 47 Copynumber: 3.4 Consensus size: 47
1312 GAAATAGCAA
1322 ACTCACGTGGAAGTGAGGAAAGACCAACTGTTGCCATTAAATTGTAG
1 ACTCACGTGGAAGTGAGGAAAGACCAACTGTTGCCATTAAATTGTAG
* * * * * ** * * *
1369 ACTCACGTGGAAGCGAGAAAATACCAACTGTGGTCAAAGAAATAGCAA
1 ACTCACGTGGAAGTGAGGAAAGACCAACTGTTG-CCATTAAATTGTAG
*
1417 ACTCACGTGGAAGTGAGGAAAGACTAACTGTTGCCATTAAATTGTAG
1 ACTCACGTGGAAGTGAGGAAAGACCAACTGTTGCCATTAAATTGTAG
*
1464 ACTCGCGTGGAAGTGAG
1 ACTCACGTGGAAGTGAG
1481 AGAGGATTAC
Statistics
Matches: 89, Mismatches: 22, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
47 53 0.60
48 36 0.40
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (47 bp):
ACTCACGTGGAAGTGAGGAAAGACCAACTGTTGCCATTAAATTGTAG
Found at i:1717 original size:70 final size:71
Alignment explanation
Indices: 1599--1735 Score: 197
Period size: 70 Copynumber: 1.9 Consensus size: 71
1589 TCATTGAACA
* * * * * *
1599 TGGCTTATGGAAAAGCCCCTTGATGTTTGGGTGGAACCAAGGGCTAAACTGACTCGTATGGAAAC
1 TGGCTTATGGAAAAGCCCCTAGATGTTTAGATGGAACCAAGAGCTAAACTAACTCGTATAGAAAC
1664 GAACTT
66 GAACTT
1670 TGGCTTATGGAAAAGCCCC-AGATGTTTAGATGGAACCAA-AGCTTAAACTAACTCGTATAGAAA
1 TGGCTTATGGAAAAGCCCCTAGATGTTTAGATGGAACCAAGAGC-TAAACTAACTCGTATAGAAA
1733 CGA
65 CGA
1736 GTTTGGTCTT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
69 2 0.03
70 38 0.64
71 19 0.32
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (71 bp):
TGGCTTATGGAAAAGCCCCTAGATGTTTAGATGGAACCAAGAGCTAAACTAACTCGTATAGAAAC
GAACTT
Found at i:1986 original size:105 final size:105
Alignment explanation
Indices: 1825--2179 Score: 493
Period size: 102 Copynumber: 3.4 Consensus size: 105
1815 CCCCAAATGT
* * * * *
1825 TTGGATGGAACCAAAG-CTTAAACTTACTTGTATAGAAACAAGCTTAGTCTTAGAAGACTGAATT
1 TTGGATGGAACC-AAGTCTTAAACTGACTCGTATGGAAACGAGCTTAGTCTTGGAAGACTGAATT
*
1889 CATGCGGAAATGAACTTGGCTTATGAAAAAACCCATGTTGC
65 CATGTGGAAATGAACTTGGCTTATGAAAAAACCCATGTTGC
* *
1930 TTGGATGGAATCAAGTCTTAAACTGACTCGTATGGAAACGAGTTTAGTCTTGGAAGACTGAATTC
1 TTGGATGGAACCAAGTCTTAAACTGACTCGTATGGAAACGAGCTTAGTCTTGGAAGACTGAATTC
* * * *
1995 ATGTTGAAAT---CTTGGCTTATGGAAAAGCGCATGTTGC
66 ATGTGGAAATGAACTTGGCTTATGAAAAAACCCATGTTGC
* * *
2032 TTGGATGGAACCAAGACTTAAACTGACTCGTATGGAAACGAGCTTAGTCCTGGAAGACTGAGTTC
1 TTGGATGGAACCAAGTCTTAAACTGACTCGTATGGAAACGAGCTTAGTCTTGGAAGACTGAATTC
** *
2097 ATGTGGAAATGAACTTGGCTTATGGAAAAGCCCCCTGTTGC
66 ATGTGGAAATGAACTTGGCTTAT-GAAAAAACCCATGTTGC
*
2138 TTGGATGGAACCAAGTCTTAAACTGACTCGTAGGGAAACGAG
1 TTGGATGGAACCAAGTCTTAAACTGACTCGTATGGAAACGAG
2180 TTTGACTTAT
Statistics
Matches: 220, Mismatches: 25, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
102 93 0.42
104 3 0.01
105 72 0.33
106 52 0.24
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (105 bp):
TTGGATGGAACCAAGTCTTAAACTGACTCGTATGGAAACGAGCTTAGTCTTGGAAGACTGAATTC
ATGTGGAAATGAACTTGGCTTATGAAAAAACCCATGTTGC
Found at i:2058 original size:102 final size:104
Alignment explanation
Indices: 1799--2179 Score: 493
Period size: 105 Copynumber: 3.7 Consensus size: 104
1789 GAAGCGAACT
** * * * *
1799 TTGGCTTATGGAAAAGCCCCA-AATGTTTGGATGGAACCAA-AGCTTAAACTTACTTGTATAGAA
1 TTGGCTTATGGAAAAGCCCCATGTTGCTTGGATGGAACCAAGA-CTTAAACTGACTCGTATGGAA
* * *
1862 ACAAGCTTAGTCTTAGAAGACTGAATTCATGCGGAAATGAAC
65 ACGAGCTTAGTCTTGGAAGACTGAATTCATGTGGAAAT--AC
** * *
1904 TTGGCTTAT-GAAAAAACCCATGTTGCTTGGATGGAATCAAGTCTTAAACTGACTCGTATGGAAA
1 TTGGCTTATGGAAAAGCCCCATGTTGCTTGGATGGAACCAAGACTTAAACTGACTCGTATGGAAA
* *
1968 CGAGTTTAGTCTTGGAAGACTGAATTCATGTTGAAAT-C
66 CGAGCTTAGTCTTGGAAGACTGAATTCATGTGGAAATAC
*
2006 TTGGCTTATGGAAAAG-CGCATGTTGCTTGGATGGAACCAAGACTTAAACTGACTCGTATGGAAA
1 TTGGCTTATGGAAAAGCCCCATGTTGCTTGGATGGAACCAAGACTTAAACTGACTCGTATGGAAA
* *
2070 CGAGCTTAGTCCTGGAAGACTGAGTTCATGTGGAAATGAAC
66 CGAGCTTAGTCTTGGAAGACTGAATTCATGTGGAAAT--AC
* * *
2111 TTGGCTTATGGAAAAGCCCCCTGTTGCTTGGATGGAACCAAGTCTTAAACTGACTCGTAGGGAAA
1 TTGGCTTATGGAAAAGCCCCATGTTGCTTGGATGGAACCAAGACTTAAACTGACTCGTATGGAAA
2176 CGAG
66 CGAG
2180 TTTGACTTAT
Statistics
Matches: 242, Mismatches: 27, Indels: 13
0.86 0.10 0.05
Matches are distributed among these distances:
102 88 0.36
103 5 0.02
104 9 0.04
105 92 0.38
106 48 0.20
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (104 bp):
TTGGCTTATGGAAAAGCCCCATGTTGCTTGGATGGAACCAAGACTTAAACTGACTCGTATGGAAA
CGAGCTTAGTCTTGGAAGACTGAATTCATGTGGAAATAC
Found at i:2693 original size:53 final size:53
Alignment explanation
Indices: 2542--2693 Score: 191
Period size: 53 Copynumber: 2.9 Consensus size: 53
2532 AACAGAAGAT
* * * * * *
2542 TTTGAAAGGCCACCTAGGACCATCAGAAGATCAACATAGATTTCTG-AAATTG
1 TTTGAAAGGTCACCTAGGACCATCAGAATATCATCTTAGACTTCTGAAAATTC
* * * *
2594 ATTGAAAGGTCACCCAAGATCATCAGAATATCATCTTAGAAC-TCTGAAAATTC
1 TTTGAAAGGTCACCTAGGACCATCAGAATATCATCTTAG-ACTTCTGAAAATTC
2647 TTTGAAAGGTCACCTAGGACCATCAGAATATCATCTTAGACTTCTGA
1 TTTGAAAGGTCACCTAGGACCATCAGAATATCATCTTAGACTTCTGA
2694 TTTTGTGCCC
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
52 37 0.45
53 46 0.55
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (53 bp):
TTTGAAAGGTCACCTAGGACCATCAGAATATCATCTTAGACTTCTGAAAATTC
Found at i:5565 original size:14 final size:13
Alignment explanation
Indices: 5546--5589 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
5536 ACCCAAAACC
5546 TTTTGAAAACTCAT
1 TTTTGAAAAC-CAT
*
5560 TTTTGAAAACCTT
1 TTTTGAAAACCAT
*
5573 TTCTTGAAAACAAT
1 TT-TTGAAAACCAT
5587 TTT
1 TTT
5590 CTTGAAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 5 0.19
14 21 0.81
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (13 bp):
TTTTGAAAACCAT
Found at i:5591 original size:15 final size:14
Alignment explanation
Indices: 5562--5597 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
5552 AAACTCATTT
*
5562 TTGAAAACCTTTTC
1 TTGAAAACATTTTC
5576 TTGAAAACAATTTTC
1 TTGAAAAC-ATTTTC
5591 TTGAAAA
1 TTGAAAA
5598 ACGTCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (14 bp):
TTGAAAACATTTTC
Done.