Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022990.1 Corchorus olitorius cultivar O-4 contig23023, 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: 13798
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:157 original size:17 final size:16
Alignment explanation
Indices: 135--180 Score: 67
Period size: 17 Copynumber: 2.9 Consensus size: 16
125 CCTTCCTCCA
135 TATTTCCTTTCTCTTAC
1 TATTTCCTTTC-CTTAC
*
152 TATTTCCTTTCCTTCC
1 TATTTCCTTTCCTTAC
168 TATTT-CTTTCCTT
1 TATTTCCTTTCCTT
181 CCTACCAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 8 0.29
16 9 0.32
17 11 0.39
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTCCTTTCCTTAC
Found at i:178 original size:15 final size:16
Alignment explanation
Indices: 121--184 Score: 78
Period size: 16 Copynumber: 4.0 Consensus size: 16
111 TGTGACTTCC
*
121 TTTCCCTTCC-TCCATA
1 TTTCCTTTCCTTCC-TA
*
137 TTTCCTTTCTCTTACTA
1 TTTCCTTTC-CTTCCTA
154 TTTCCTTTCCTTCCTA
1 TTTCCTTTCCTTCCTA
170 TTT-CTTTCCTTCCTA
1 TTTCCTTTCCTTCCTA
185 CCAAACATAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
15 12 0.28
16 17 0.40
17 12 0.28
18 2 0.05
ACGTcount: A:0.09, C:0.36, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTCCTTTCCTTCCTA
Found at i:4995 original size:18 final size:18
Alignment explanation
Indices: 4956--4998 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
4946 TAAAAGGATG
*
4956 GGAAAGTTAACTTTCGCG
1 GGAAAGTTAACTTTCGCA
4974 GGAAAGTTAACTTTC-CTA
1 GGAAAGTTAACTTTCGC-A
4992 GGAAAGT
1 GGAAAGT
4999 GTTATTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (18 bp):
GGAAAGTTAACTTTCGCA
Found at i:7250 original size:132 final size:131
Alignment explanation
Indices: 7034--7298 Score: 503
Period size: 132 Copynumber: 2.0 Consensus size: 131
7024 ATTTATTTGT
7034 TTATTTGGTAGGTATGTAGTTTATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTTAAA
1 TTATTTGGTAGGTATGTAGTTTATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTTAAA
*
7099 TGTTTGGGTATAGAGATTTATTTGAATTGTAATGAGATTTCACTGGGTTTGTTTGTTGGGGAAGG
66 TGTTTGGGTATAGAGATTTATTTG-ATTGTAATGAGATTTCACTGGCTTTGTTTGTTGGGGAAGG
7164 GG
130 GG
7166 TTATTTGGTAGGTATGTAGTTTATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTTAAA
1 TTATTTGGTAGGTATGTAGTTTATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTTAAA
*
7231 TGTTTGGGTATAGAGATTTATTTGATTGTAATTAGATTTCACTGGCTTTGTTTGTTGGGGAAGGG
66 TGTTTGGGTATAGAGATTTATTTGATTGTAATGAGATTTCACTGGCTTTGTTTGTTGGGGAAGGG
7296 G
131 G
7297 TT
1 TT
7299 TGTTGGCTCA
Statistics
Matches: 131, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
131 42 0.32
132 89 0.68
ACGTcount: A:0.22, C:0.04, G:0.27, T:0.47
Consensus pattern (131 bp):
TTATTTGGTAGGTATGTAGTTTATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTTAAA
TGTTTGGGTATAGAGATTTATTTGATTGTAATGAGATTTCACTGGCTTTGTTTGTTGGGGAAGGG
G
Found at i:7648 original size:165 final size:164
Alignment explanation
Indices: 7370--7699 Score: 581
Period size: 165 Copynumber: 2.0 Consensus size: 164
7360 CCTGTGCGTT
7370 TGTAATCCCAATCTCTTTAAGAAATAAAAATGATTCTTATCTCAAAAAAGTGTAATGATTGCATA
1 TGTAATCCCAATCTCTTTAAGAAATAAAAATGATTCTTATCTCAAAAAAGTGTAATGATTGCATA
* * * *
7435 AAAAGTGGGTATAAAATTTTTAAATAATATTGTTCATAGAAGAGAGAATTTGTATGTCAAAACTA
66 AAAAGTGGGTATAAAATTTCTAAATAATACTCTTCATAGAAGAGAGAATTTGCATGTCAAAACTA
7500 CCTTTATACCCAAATAAGGGATATAAAATCATTA
131 CCTTTATACCCAAATAAGGGATATAAAATCATTA
* *
7534 TGTAATTCCAATCTCTTTAAGAAATGAAAATGATTCTTATCTCAAAAAAAGTGTAATGATTGCAT
1 TGTAATCCCAATCTCTTTAAGAAATAAAAATGATTCTTATCTC-AAAAAAGTGTAATGATTGCAT
7599 AAAAAGTGGGTATAGAAA-TTCTAAATAATACTCTTCATAGAAGAGAGAATTTGCATGTCAAAAC
65 AAAAAGTGGGTATA-AAATTTCTAAATAATACTCTTCATAGAAGAGAGAATTTGCATGTCAAAAC
7663 TACCTTTATACCCAAATAAGGGATATAAAATCATTA
129 TACCTTTATACCCAAATAAGGGATATAAAATCATTA
7699 T
1 T
7700 TATGATTATT
Statistics
Matches: 158, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
164 41 0.26
165 114 0.72
166 3 0.02
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (164 bp):
TGTAATCCCAATCTCTTTAAGAAATAAAAATGATTCTTATCTCAAAAAAGTGTAATGATTGCATA
AAAAGTGGGTATAAAATTTCTAAATAATACTCTTCATAGAAGAGAGAATTTGCATGTCAAAACTA
CCTTTATACCCAAATAAGGGATATAAAATCATTA
Found at i:8408 original size:19 final size:18
Alignment explanation
Indices: 8380--8423 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
8370 TATTTTATTA
*
8380 TTTTTAAAAAATTAAAAT
1 TTTTTAAAAAAATAAAAT
*
8398 TTTTATAAAAAAATATAAT
1 TTTT-TAAAAAAATAAAAT
8417 TTTTTAA
1 TTTTTAA
8424 GGACATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTTTAAAAAAATAAAAT
Found at i:11369 original size:53 final size:52
Alignment explanation
Indices: 11304--11471 Score: 144
Period size: 53 Copynumber: 3.3 Consensus size: 52
11294 CTCTATTTCA
* *
11304 GGAATGATTTTTGGAACAATTATTTATCATTGCTAAACTCATTCCTCCACTTT
1 GGAATGACTTTTGAAACAATTATTTATCATTGCTAAA-TCATTCCTCCACTTT
* *
11357 GGAATGACTTTTGAAAC-ATCTAAAATTTA-CA--GCCAAA-AATT--T-CA----
1 GGAATGACTTTTGAAACAAT-T---ATTTATCATTGCTAAATCATTCCTCCACTTT
* *
11401 GGAATGATTTTTGGAACAATTATTTATCATTGCTAAATTCATTCCTCCACTTT
1 GGAATGACTTTTGAAACAATTATTTATCATTGCTAAA-TCATTCCTCCACTTT
11454 GGAATGACTTTTGAAACA
1 GGAATGACTTTTGAAACA
11472 TCTAAAATTT
Statistics
Matches: 88, Mismatches: 10, Indels: 34
0.67 0.08 0.26
Matches are distributed among these distances:
41 5 0.06
42 2 0.02
44 21 0.24
45 2 0.02
46 3 0.03
48 3 0.03
49 3 0.03
51 3 0.03
52 2 0.02
53 37 0.42
55 2 0.02
56 5 0.06
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (52 bp):
GGAATGACTTTTGAAACAATTATTTATCATTGCTAAATCATTCCTCCACTTT
Found at i:11464 original size:97 final size:97
Alignment explanation
Indices: 11298--11494 Score: 376
Period size: 97 Copynumber: 2.0 Consensus size: 97
11288 GAACGACTCT
11298 ATTTCAGGAATGATTTTTGGAACAATTATTTATCATTGCTAAACTCATTCCTCCACTTTGGAATG
1 ATTTCAGGAATGATTTTTGGAACAATTATTTATCATTGCTAAACTCATTCCTCCACTTTGGAATG
*
11363 ACTTTTGAAACATCTAAAATTTACAGCCAAAA
66 ACTTTTGAAACATCTAAAATTTACAGCAAAAA
*
11395 ATTTCAGGAATGATTTTTGGAACAATTATTTATCATTGCTAAATTCATTCCTCCACTTTGGAATG
1 ATTTCAGGAATGATTTTTGGAACAATTATTTATCATTGCTAAACTCATTCCTCCACTTTGGAATG
11460 ACTTTTGAAACATCTAAAATTTACAGCAAAAA
66 ACTTTTGAAACATCTAAAATTTACAGCAAAAA
11492 ATT
1 ATT
11495 ATAATTGTTC
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (97 bp):
ATTTCAGGAATGATTTTTGGAACAATTATTTATCATTGCTAAACTCATTCCTCCACTTTGGAATG
ACTTTTGAAACATCTAAAATTTACAGCAAAAA
Found at i:11674 original size:31 final size:31
Alignment explanation
Indices: 11636--11696 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
11626 TATATTAAAA
11636 TTCAAGGTTTGTAAATTAAAATTTACAATAC
1 TTCAAGGTTTGTAAATTAAAATTTACAATAC
*
11667 TTCAAGGTTTGTAAATTTAAATTTACAATA
1 TTCAAGGTTTGTAAATTAAAATTTACAATA
11697 TGTCAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (31 bp):
TTCAAGGTTTGTAAATTAAAATTTACAATAC
Found at i:11776 original size:26 final size:26
Alignment explanation
Indices: 11740--11802 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
11730 TCAGTTTCCT
11740 TTCCTCAAAAATAAAGGAATTAGAGC
1 TTCCTCAAAAATAAAGGAATTAGAGC
11766 TTCCTCAAAAATAAAGGAATTAGAGC
1 TTCCTCAAAAATAAAGGAATTAGAGC
11792 TTCCTCAAAAA
1 TTCCTCAAAAA
11803 GATTAGATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (26 bp):
TTCCTCAAAAATAAAGGAATTAGAGC
Done.