Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022013.1 Corchorus olitorius cultivar O-4 contig22046, 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: 35976
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:75 original size:7 final size:7
Alignment explanation
Indices: 65--108 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
55 AATAGCAAAG
65 TTCTTTT
1 TTCTTTT
72 TTCTTTT
1 TTCTTTT
*
79 TCTTTTTT
1 T-TCTTTT
*
87 TTCTGTT
1 TTCTTTT
94 TTCTTTT
1 TTCTTTT
*
101 TTATTTT
1 TTCTTTT
108 T
1 T
109 AAGAAACAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.02, C:0.11, G:0.02, T:0.84
Consensus pattern (7 bp):
TTCTTTT
Found at i:88 original size:15 final size:16
Alignment explanation
Indices: 68--102 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
58 AGCAAAGTTC
68 TTTTTTCT-TTTTCTT
1 TTTTTTCTGTTTTCTT
83 TTTTTTCTGTTTTCTT
1 TTTTTTCTGTTTTCTT
99 TTTT
1 TTTT
103 ATTTTTAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (16 bp):
TTTTTTCTGTTTTCTT
Found at i:352 original size:16 final size:15
Alignment explanation
Indices: 325--355 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
315 GATTCTCTGC
325 ATTTTCTTTTTTTTT
1 ATTTTCTTTTTTTTT
*
340 ATTTTCATTTTTTTT
1 ATTTTCTTTTTTTTT
355 A
1 A
356 GAAACCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (15 bp):
ATTTTCTTTTTTTTT
Found at i:4722 original size:16 final size:16
Alignment explanation
Indices: 4695--4733 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
4685 GAGTAAGTGA
*
4695 ATGAATTATGAATTATT
1 ATGAA-TATGAATGATT
4712 ATGAATATGAATGATT
1 ATGAATATGAATGATT
4728 -TGAATA
1 ATGAATA
4734 ATTAGAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.29
16 10 0.48
17 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (16 bp):
ATGAATATGAATGATT
Found at i:5179 original size:13 final size:12
Alignment explanation
Indices: 5151--5178 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5141 CGATAAGCTC
5151 TTTTCTTTTTTT
1 TTTTCTTTTTTT
5163 TTTTCTTTTTTT
1 TTTTCTTTTTTT
5175 TTTT
1 TTTT
5179 TGAAAATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:10456 original size:24 final size:24
Alignment explanation
Indices: 10424--10471 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
10414 AGCCAAAAAG
10424 AAAAAAAATAATTTTCTTTAAATT
1 AAAAAAAATAATTTTCTTTAAATT
10448 AAAAAAAATAATTTTCTTTAAATT
1 AAAAAAAATAATTTTCTTTAAATT
10472 GTGATGTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
AAAAAAAATAATTTTCTTTAAATT
Found at i:13338 original size:34 final size:34
Alignment explanation
Indices: 13295--13381 Score: 165
Period size: 34 Copynumber: 2.6 Consensus size: 34
13285 GCAGGTGTTC
13295 TGAGCCATGTGGCAAGTGTTACTTAAAGAGGGTA
1 TGAGCCATGTGGCAAGTGTTACTTAAAGAGGGTA
13329 TGAGCCATGTGGCAAGTGTTACTTAAAGAGGGTA
1 TGAGCCATGTGGCAAGTGTTACTTAAAGAGGGTA
*
13363 TGAGCCATGTGGAAAGTGT
1 TGAGCCATGTGGCAAGTGT
13382 GGGTTAGAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 52 1.00
ACGTcount: A:0.29, C:0.11, G:0.33, T:0.26
Consensus pattern (34 bp):
TGAGCCATGTGGCAAGTGTTACTTAAAGAGGGTA
Found at i:26891 original size:3 final size:3
Alignment explanation
Indices: 26879--26928 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
26869 TAAAGTTTTA
*
26879 ATT A-T ATT ATT ATT ATC ATT A-T ATT ATT A-T ATT ATT ATGT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
26921 ATT ATT AT
1 ATT ATT AT
26929 ACTGTCAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 7 0.17
3 32 0.80
4 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:26901 original size:17 final size:17
Alignment explanation
Indices: 26879--26928 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
26869 TAAAGTTTTA
26879 ATTATATTATTATTATC
1 ATTATATTATTATTATC
*
26896 ATTATATTATTA-TATT
1 ATTATATTATTATTATC
*
26912 ATTATGTTTATTATTAT
1 ATTAT-ATTATTATTAT
26929 ACTGTCAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 8 0.28
17 18 0.62
18 3 0.10
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
ATTATATTATTATTATC
Found at i:26907 original size:8 final size:8
Alignment explanation
Indices: 26879--26916 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
26869 TAAAGTTTTA
26879 ATTATATT
1 ATTATATT
*
26887 ATTATTATC
1 ATTA-TATT
26896 ATTATATT
1 ATTATATT
26904 ATTATATT
1 ATTATATT
26912 ATTAT
1 ATTAT
26917 GTTTATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (8 bp):
ATTATATT
Found at i:28358 original size:23 final size:24
Alignment explanation
Indices: 28332--28376 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
28322 GCATTGGATT
*
28332 TTTGGCATTTTC-TTTGTTTTTCC
1 TTTGGAATTTTCTTTTGTTTTTCC
*
28355 TTTGTAATTTTCTTTTGTTTTT
1 TTTGGAATTTTCTTTTGTTTTT
28377 GTCCCAAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.07, C:0.11, G:0.11, T:0.71
Consensus pattern (24 bp):
TTTGGAATTTTCTTTTGTTTTTCC
Found at i:28791 original size:52 final size:52
Alignment explanation
Indices: 28724--28826 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
28714 AACCCTTATG
*
28724 TATACTATATTTTATTTTTAGTGGCTATAGAAATTACTTAAAGGCCAAATTA
1 TATACTATATATTATTTTTAGTGGCTATAGAAATTACTTAAAGGCCAAATTA
*
28776 TATACTATATATTATTTTTAGTGGCTATGGAAATTACTTAAAGGCCAAATT
1 TATACTATATATTATTTTTAGTGGCTATAGAAATTACTTAAAGGCCAAATT
28827 GAGAATTAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.42
Consensus pattern (52 bp):
TATACTATATATTATTTTTAGTGGCTATAGAAATTACTTAAAGGCCAAATTA
Found at i:31154 original size:22 final size:22
Alignment explanation
Indices: 31126--31167 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
31116 AATGATTGAT
31126 TAATTATGGACAAACACAAAAC
1 TAATTATGGACAAACACAAAAC
*
31148 TAATTATGGGCAAACACAAA
1 TAATTATGGACAAACACAAA
31168 CCATGCAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.17, G:0.12, T:0.19
Consensus pattern (22 bp):
TAATTATGGACAAACACAAAAC
Found at i:31595 original size:16 final size:16
Alignment explanation
Indices: 31574--31605 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
31564 TATATATATT
31574 TTTCATATTAAGCTAG
1 TTTCATATTAAGCTAG
31590 TTTCATATTAAGCTAG
1 TTTCATATTAAGCTAG
31606 AAATATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (16 bp):
TTTCATATTAAGCTAG
Found at i:33747 original size:194 final size:193
Alignment explanation
Indices: 33402--33789 Score: 670
Period size: 194 Copynumber: 2.0 Consensus size: 193
33392 AAGAAAGAAT
33402 TATCTTTCATTGGTTTCTTAATTGATTCAAAATCACGTTATTTGAAATATGGAAAAGAAAAAAAC
1 TATCTTTCATTGGTTTCTTAATTGATTCAAAATCACGTTATTTGAAATATGGAAAAGAAAAAAAC
* *
33467 AGCTGATTATGGCTCTGTTTAGTAGAGCTGTGAGATTAATGTGGGGAAGATTGGAATTGGAAGAT
66 AGCTGATTATGGCTCTGTTTAGTAGAGCTGTGAGATTAATGTGGGGAAGATTGAAATGGGAAGAT
*
33532 TAGTTACTGTATATGTGAGATTAGAATTGTAACTGTAAAAACTTAACCATCGATTAAAAAATA
131 TAGTTACTGTATATGTGAGATTAGAATTGTAACTGTAAAAACTTAACCAGCGATTAAAAAATA
*
33595 TATCTTTCATTGGTTTCCTTAATTGATTCAAAATCACGTTATTTGAAATATGGAAAAGAGAAAAA
1 TATCTTTCATTGGTTT-CTTAATTGATTCAAAATCACGTTATTTGAAATATGGAAAAGAAAAAAA
* *
33660 CAGCTGATTATGGCTCTGTTTGGTAGAGCTGTGAGATTAGTGTAGGGG-AGATTGAAATGGGAAG
65 CAGCTGATTATGGCTCTGTTTAGTAGAGCTGTGAGATTAATGT-GGGGAAGATTGAAATGGGAAG
* * *
33724 ATTAGTTACTGTATATGTGAGATTAGAATTGTAGCTGTGAAAACTTAACCAGCGATTAAAAGATA
129 ATTAGTTACTGTATATGTGAGATTAGAATTGTAACTGTAAAAACTTAACCAGCGATTAAAAAATA
33789 T
1 T
33790 GTGTTTGGTG
Statistics
Matches: 184, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
193 16 0.09
194 164 0.89
195 4 0.02
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (193 bp):
TATCTTTCATTGGTTTCTTAATTGATTCAAAATCACGTTATTTGAAATATGGAAAAGAAAAAAAC
AGCTGATTATGGCTCTGTTTAGTAGAGCTGTGAGATTAATGTGGGGAAGATTGAAATGGGAAGAT
TAGTTACTGTATATGTGAGATTAGAATTGTAACTGTAAAAACTTAACCAGCGATTAAAAAATA
Found at i:34041 original size:22 final size:22
Alignment explanation
Indices: 34010--34174 Score: 119
Period size: 22 Copynumber: 7.6 Consensus size: 22
34000 TATTTTTATG
34010 GAAA-TTTGATAACTACCCTAT
1 GAAATTTTGATAACTACCCTAT
* *
34031 TAAATTTTGATAACCACCCTAT
1 GAAATTTTGATAACTACCCTAT
* *
34053 AAAATTTTGATAATTA-CCTAT
1 GAAATTTTGATAACTACCCTAT
* *
34074 GAAATTATGATAAACT-CCATAT
1 GAAATTTTGAT-AACTACCCTAT
* *
34096 GAAACTTTGATAATCTA-ACTAT
1 GAAATTTTGATAA-CTACCCTAT
* * * *
34118 GAAATTTTAATAAACCATCATAT
1 GAAATTTTGAT-AACTACCCTAT
*
34141 GAAATTTTG-TAATCT-TCCTAT
1 GAAATTTTGATAA-CTACCCTAT
*
34162 G-ATTTTTGATAAC
1 GAAATTTTGATAAC
34175 ATCCCCGTGA
Statistics
Matches: 113, Mismatches: 22, Indels: 19
0.73 0.14 0.12
Matches are distributed among these distances:
20 7 0.06
21 30 0.27
22 63 0.56
23 13 0.12
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (22 bp):
GAAATTTTGATAACTACCCTAT
Found at i:34131 original size:44 final size:43
Alignment explanation
Indices: 34010--34173 Score: 160
Period size: 43 Copynumber: 3.8 Consensus size: 43
34000 TATTTTTATG
*
34010 GAAA-TTTGATAA-CTACCCTATTAAATTTTGATAACCACCC-TAT
1 GAAATTTTGATAATCTA-CCTATGAAATTTTGATAA--ACCCATAT
* *
34053 AAAATTTTGATAAT-TACCTATGAAATTATGATAAACTCCATAT
1 GAAATTTTGATAATCTACCTATGAAATTTTGATAAAC-CCATAT
* * *
34096 GAAACTTTGATAATCTAACTATGAAATTTTAATAAACCATCATAT
1 GAAATTTTGATAATCTACCTATGAAATTTTGATAAACC--CATAT
* *
34141 GAAATTTTG-TAATCTTCCTATG-ATTTTTGATAA
1 GAAATTTTGATAATCTACCTATGAAATTTTGATAA
34174 CATCCCCGTG
Statistics
Matches: 101, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
41 2 0.02
42 2 0.02
43 44 0.44
44 40 0.40
45 13 0.13
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (43 bp):
GAAATTTTGATAATCTACCTATGAAATTTTGATAAACCCATAT
Done.