Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024294.1 Corchorus olitorius cultivar O-4 contig24327, 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: 33496
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Found at i:821 original size:20 final size:21
Alignment explanation
Indices: 798--840 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
788 ATCTTGAAGA
798 ATTTAAAG-CCATCGGAGATC
1 ATTTAAAGCCCATCGGAGATC
* *
818 ATTTGAAGCCCATTGGAGATC
1 ATTTAAAGCCCATCGGAGATC
839 AT
1 AT
841 CAACAAAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (21 bp):
ATTTAAAGCCCATCGGAGATC
Found at i:15496 original size:3 final size:3
Alignment explanation
Indices: 15488--15546 Score: 82
Period size: 3 Copynumber: 19.0 Consensus size: 3
15478 TTTCCAACTC
* *
15488 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TATT ATA TTA TATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA -ATA ATA
15535 ATA ATA ATA ATA
1 ATA ATA ATA ATA
15547 CTAGCTAGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
3 46 0.92
4 4 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:21101 original size:28 final size:29
Alignment explanation
Indices: 21060--21119 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
21050 GCCTTTCTTT
21060 TTGTATTTATTCAAGTG-CGGTTGTGCAC
1 TTGTATTTATTCAAGTGTCGGTTGTGCAC
* * *
21088 TTGTGTTTGTTCAAGTGTGGGTTGTGCAC
1 TTGTATTTATTCAAGTGTCGGTTGTGCAC
21117 TTG
1 TTG
21120 GGATTGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.13, C:0.12, G:0.30, T:0.45
Consensus pattern (29 bp):
TTGTATTTATTCAAGTGTCGGTTGTGCAC
Found at i:21140 original size:30 final size:29
Alignment explanation
Indices: 21069--21127 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
21059 TTTGTATTTA
* * *
21069 TTCAAGTG-CGGTTGTGCACTTGTGTTTG
1 TTCAAGTGTGGGTTGTGCACTTGGGATTG
21097 TTCAAGTGTGGGTTGTGCACTTGGGATTG
1 TTCAAGTGTGGGTTGTGCACTTGGGATTG
21126 TT
1 TT
21128 TTGAGTGTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.12, C:0.12, G:0.34, T:0.42
Consensus pattern (29 bp):
TTCAAGTGTGGGTTGTGCACTTGGGATTG
Found at i:22348 original size:23 final size:23
Alignment explanation
Indices: 22321--22405 Score: 63
Period size: 23 Copynumber: 3.7 Consensus size: 23
22311 TATCCTTGAA
22321 AAATAAA-CAAAACCCAGATATGC
1 AAATAAATCAAAACCCAGAT-TGC
* *
22344 AAATAAATCAAATTATCC---TTGAA
1 AAATAAATCAAA--ACCCAGATTG-C
22367 AAATAAA-CAAAACCCAGATCTGC
1 AAATAAATCAAAACCCAGAT-TGC
22390 AAATAAATCAACAACC
1 AAATAAATCAA-AACC
22406 AAAAAAAAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 18
0.69 0.06 0.26
Matches are distributed among these distances:
20 3 0.06
22 6 0.12
23 23 0.48
24 9 0.19
25 4 0.08
26 3 0.06
ACGTcount: A:0.55, C:0.21, G:0.06, T:0.18
Consensus pattern (23 bp):
AAATAAATCAAAACCCAGATTGC
Found at i:22365 original size:46 final size:46
Alignment explanation
Indices: 22311--22400 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
22301 AACCCATCAC
22311 TATCCTTGAAAAATAAACAAAACCCAGATATGCAAATAAATCAAAT
1 TATCCTTGAAAAATAAACAAAACCCAGATATGCAAATAAATCAAAT
*
22357 TATCCTTGAAAAATAAACAAAACCCAGATCTGCAAATAAATCAA
1 TATCCTTGAAAAATAAACAAAACCCAGATATGCAAATAAATCAA
22401 CAACCAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.53, C:0.19, G:0.07, T:0.21
Consensus pattern (46 bp):
TATCCTTGAAAAATAAACAAAACCCAGATATGCAAATAAATCAAAT
Found at i:22538 original size:5 final size:5
Alignment explanation
Indices: 22505--22537 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
22495 AATCACTCTT
*
22505 CTTCC CTTCC CTTCC CTTCC CTTCC CTTTC CTT
1 CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CTT
22538 TGTCTTCTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (5 bp):
CTTCC
Found at i:24725 original size:17 final size:17
Alignment explanation
Indices: 24703--24737 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
24693 AAAAGGAGAA
24703 ACATCTAAAACGAAGAG
1 ACATCTAAAACGAAGAG
*
24720 ACATCTAAAGCGAAGAG
1 ACATCTAAAACGAAGAG
24737 A
1 A
24738 AAGCTCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.17, G:0.20, T:0.11
Consensus pattern (17 bp):
ACATCTAAAACGAAGAG
Found at i:26275 original size:15 final size:15
Alignment explanation
Indices: 26255--26285 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
26245 AGATGATGAG
26255 AAAGTTGAAGAAGAA
1 AAAGTTGAAGAAGAA
*
26270 AAAGTTGAGGAAGAA
1 AAAGTTGAAGAAGAA
26285 A
1 A
26286 GGCAAACAGA
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:0.58, C:0.00, G:0.29, T:0.13
Consensus pattern (15 bp):
AAAGTTGAAGAAGAA
Found at i:27225 original size:2 final size:2
Alignment explanation
Indices: 27218--27246 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27208 TGAACTTAAC
27218 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27247 TAATGCCACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28322 original size:29 final size:29
Alignment explanation
Indices: 28274--28342 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
28264 TTTAAGTGCA
* *
28274 GGTTATGCACTTGTGTTTG-TTCAAGTGTG
1 GGTT-TGCACTTGGGATTGTTTCAAGTGTG
**
28303 GGTTGTGCACTTGGGATTGTTTTGAGTGTG
1 GGTT-TGCACTTGGGATTGTTTCAAGTGTG
28333 GGTTTGCACT
1 GGTTTGCACT
28343 CGTGTCAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 22 0.65
30 12 0.35
ACGTcount: A:0.12, C:0.10, G:0.35, T:0.43
Consensus pattern (29 bp):
GGTTTGCACTTGGGATTGTTTCAAGTGTG
Found at i:32747 original size:39 final size:40
Alignment explanation
Indices: 32691--32771 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
32681 TTTAATTCCT
32691 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* * *
32731 ATGTAATA-CTATAATAACTGAAATACTTATATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
32770 AT
1 AT
32772 TCTTAGGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:32761 original size:18 final size:18
Alignment explanation
Indices: 32701--32761 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 18
32691 ATGTAATATA
*
32701 TATAATAACTAAAATACT
1 TATAATAACTGAAATACT
* *
32719 TACATTAATTAAATGTAATAC-
1 T--A-TAA-TAACTGAAATACT
32740 TATAATAACTGAAATACT
1 TATAATAACTGAAATACT
32758 TATA
1 TATA
32762 TTAATTAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
17 10 0.30
18 8 0.24
19 1 0.03
20 1 0.03
21 4 0.12
22 9 0.27
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (18 bp):
TATAATAACTGAAATACT
Done.