Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012337.1 Corchorus olitorius cultivar O-4 contig12370, 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: 14105
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:4664 original size:20 final size:20
Alignment explanation
Indices: 4639--4678 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4629 ACGTGATTTA
* *
4639 ACTATCAAACTTTGTGGTTT
1 ACTATCAAAATTTGGGGTTT
4659 ACTATCAAAATTTGGGGTTT
1 ACTATCAAAATTTGGGGTTT
4679 GACCATGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.42
Consensus pattern (20 bp):
ACTATCAAAATTTGGGGTTT
Found at i:4821 original size:55 final size:53
Alignment explanation
Indices: 4727--4904 Score: 142
Period size: 54 Copynumber: 3.2 Consensus size: 53
4717 ACTATCGAAC
* * * * * ** *
4727 TTTGCGGTTTGAGCATCATTATCTGAGTTTTGACTATGCATGTGTAATGATTTTT
1 TTTGTGGTTTGACCATCATTATTTGGGGTTTGAC-ATGCATGTACAAT-AATTTT
*
4782 TTTGTGGTTTGACCATCATTTTTTGGGGTTTGATCATGCATGTACAATAATTTT
1 TTTGTGGTTTGACCATCATTATTTGGGGTTTGA-CATGCATGTACAATAATTTT
* * ** * **
4836 TTTATGGTTTGACTAT-AAAACTTTGGGGTTTGACCATGCATATACAATGAAATACT
1 TTTGTGGTTTGACCATCATTA-TTTGGGGTTTGA-CATGCATGTACAAT--AATTTT
4892 TTTGTGGTTTGAC
1 TTTGTGGTTTGAC
4905 TTTCGAATTT
Statistics
Matches: 100, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
53 1 0.01
54 44 0.44
55 38 0.38
56 17 0.17
ACGTcount: A:0.23, C:0.11, G:0.21, T:0.45
Consensus pattern (53 bp):
TTTGTGGTTTGACCATCATTATTTGGGGTTTGACATGCATGTACAATAATTTT
Found at i:4861 original size:54 final size:55
Alignment explanation
Indices: 4803--4928 Score: 155
Period size: 56 Copynumber: 2.3 Consensus size: 55
4793 ACCATCATTT
* * **
4803 TTTGGGGTTTGATCATGCATGTACAAT-AATTTTTTTATGGTTTGACTATAAAAC
1 TTTGGGGTTTGACCATGCATATACAATAAATACTTTTATGGTTTGACTATAAAAC
* * ** *
4857 TTTGGGGTTTGACCATGCATATACAATGAAATACTTTTGTGGTTTGACTTTCGAAT
1 TTTGGGGTTTGACCATGCATATACAAT-AAATACTTTTATGGTTTGACTATAAAAC
4913 TTTGGGGTTTGACCAT
1 TTTGGGGTTTGACCAT
4929 CATCCTTTGT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 25 0.41
56 36 0.59
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (55 bp):
TTTGGGGTTTGACCATGCATATACAATAAATACTTTTATGGTTTGACTATAAAAC
Found at i:4943 original size:131 final size:132
Alignment explanation
Indices: 4781--5563 Score: 1030
Period size: 131 Copynumber: 6.0 Consensus size: 132
4771 TAATGATTTT
* * * * * * * *
4781 TTTTGTGGTTTGACCATCATTTTTTGGGGTTTGATCATGCATGTACAATAATTTTTTTATGGTTT
1 TTTTGGGGTTTGACCATCATCTTTTGTGGTTTGACCATGTAAGTATAATAATTTTTTTGTGGTTT
*
4846 GACTATAAAACTTTGGGGTTTGACCATGCATATACAATGAAATAC-TTTTGTGGTTTGACTTTCG
66 GACTATAAAACTTTGGGGTTTGACCATGCATATACAATGAAATACTTTTTGTGGTTTGACTATCG
4910 AA
131 AA
* * * * *
4912 TTTTGGGGTTTGACCATCATCCTTTGTGGTTTGACCATGTAAATATAATGATTTTATTGTGATTT
1 TTTTGGGGTTTGACCATCATCTTTTGTGGTTTGACCATGTAAGTATAATAATTTTTTTGTGGTTT
* * *
4977 GACTATAAAACTTTAGGGTTTGACCATGCATATAAAATAAAATACTTTTTGTGGTTTGACTATCG
66 GACTATAAAACTTTGGGGTTTGACCATGCATATACAATGAAATACTTTTTGTGGTTTGACTATCG
5042 AA
131 AA
* ** * ** **
5044 TTTTGTGGTTTGACCATCATCTTTTGTAATTTGACCATGTAAATATAA-AGATTTTAATGTAATT
1 TTTTGGGGTTTGACCATCATCTTTTGTGGTTTGACCATGTAAGTATAATA-ATTTTTTTGTGGTT
*
5108 TGACTATAAAACTTTGGGGTTTCACCATGCATATACAATGAAATACTTTTTGTGGTTTGACTATC
65 TGACTATAAAACTTTGGGGTTTGACCATGCATATACAATGAAATACTTTTTGTGGTTTGACTATC
5173 GAA
130 GAA
* *
5176 TTTTGGGGTTTGACCATCATCTTTTGTGGTTTGACAATGTAAGTATAAT-ATTTTTTTGTGGTCT
1 TTTTGGGGTTTGACCATCATCTTTTGTGGTTTGACCATGTAAGTATAATAATTTTTTTGTGGTTT
* * * * *
5240 GA-TAATCAAACTTTGGGCTTTGACCATGCATATACATTGAAATATTTTTTGTGGTTTGGCTATC
66 GACT-ATAAAACTTTGGGGTTTGACCATGCATATACAATGAAATACTTTTTGTGGTTTGACTATC
5304 GAA
130 GAA
5307 TTTTGGGGTTTGACCATCATCTTTTGTGGTTTGACCATGTAAGTATAATAA-TTTTTTGTGGTTT
1 TTTTGGGGTTTGACCATCATCTTTTGTGGTTTGACCATGTAAGTATAATAATTTTTTTGTGGTTT
* *
5371 GATTATCAAACTTTGGGGTTTGACCATGCATATACAATGAAATACTTTTTGTGGTTTGACTATCG
66 GACTATAAAACTTTGGGGTTTGACCATGCATATACAATGAAATACTTTTTGTGGTTTGACTATCG
5436 AA
131 AA
* * *
5438 TTTTGGGGTTTGAGCATCATCCTTTGTGGTTTGGCCAT-TAAAGTAT-A-AATGGTTTTTTGTGG
1 TTTTGGGGTTTGACCATCATCTTTTGTGGTTTGACCATGT-AAGTATAATAAT--TTTTTTGTGG
* * * * * * * *
5500 TTTGACTATTAAAGTTTTGGGTTTGACAATGCATGTAGAATG--AT-GTTTTTGTGATTTGACTA
63 TTTGACTATAAAACTTTGGGGTTTGACCATGCATATACAATGAAATACTTTTTGTGGTTTGACTA
5562 TC
128 TC
5564 AAACTTTTTA
Statistics
Matches: 580, Mismatches: 62, Indels: 22
0.87 0.09 0.03
Matches are distributed among these distances:
129 20 0.03
130 5 0.01
131 325 0.56
132 230 0.40
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (132 bp):
TTTTGGGGTTTGACCATCATCTTTTGTGGTTTGACCATGTAAGTATAATAATTTTTTTGTGGTTT
GACTATAAAACTTTGGGGTTTGACCATGCATATACAATGAAATACTTTTTGTGGTTTGACTATCG
AA
Found at i:5034 original size:188 final size:187
Alignment explanation
Indices: 4649--5060 Score: 447
Period size: 188 Copynumber: 2.2 Consensus size: 187
4639 ACTATCAAAC
*
4649 TTTGTGGTTT-ACTATCAAAATTTGGGGTTTGACCATGCATATACAATGAAAATGCTTTTTGGGT
1 TTTGTGGTTTGACTAT-AAAATTTGGGGTTTGACCATGCATATACAATGAAAATACTTTTTGGGT
* * * * ** *
4713 TTTGACTATCGAACTTTGCGGTTTGAGCATCATTATCTGAGTTTTGACTATGCATGTGTAATGAT
65 TTTGACTATCGAACTTTGCGGTTTGACCATCATCATCTGAGGTTTGACCATGCAAATATAATGAT
* * * *** * * * * *
4778 TTTTTTTGTGGTTTGACCATCATTTTTTGGGGTTTGATCATGCATGTACAATAATTTT
130 TTTTATTGTGATTTGACCATAAAACTTTAGGGTTTGACCATGCATATAAAATAATCTT
*
4836 TTTATGGTTTGACTATAAAACTTTGGGGTTTGACCATGCATATACAATG-AAATAC-TTTTGTGG
1 TTTGTGGTTTGACTATAAAA-TTTGGGGTTTGACCATGCATATACAATGAAAATACTTTTTG-GG
* * * * * * *
4899 -TTTGACTTTCGAATTTTGGGGTTTGACCATCATCCTTTGTGGTTTGACCATGTAAATATAATGA
64 TTTTGACTATCGAACTTTGCGGTTTGACCATCATCATCTGAGGTTTGACCATGCAAATATAATGA
*
4963 -TTTTATTGTGATTTGACTATAAAACTTTAGGGTTTGACCATGCATATAAAATAAAATACTT
129 TTTTTATTGTGATTTGACCATAAAACTTTAGGGTTTGACCATGCATATAAAAT--AAT-CTT
* * *
5024 TTTGTGGTTTGACTATCGAATTTTGTGGTTTGACCAT
1 TTTGTGGTTTGACTAT-AAAATTTGGGGTTTGACCAT
5061 CATCTTTTGT
Statistics
Matches: 186, Mismatches: 32, Indels: 13
0.81 0.14 0.06
Matches are distributed among these distances:
185 41 0.22
186 55 0.30
187 23 0.12
188 65 0.35
189 2 0.01
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (187 bp):
TTTGTGGTTTGACTATAAAATTTGGGGTTTGACCATGCATATACAATGAAAATACTTTTTGGGTT
TTGACTATCGAACTTTGCGGTTTGACCATCATCATCTGAGGTTTGACCATGCAAATATAATGATT
TTTATTGTGATTTGACCATAAAACTTTAGGGTTTGACCATGCATATAAAATAATCTT
Found at i:5253 original size:263 final size:261
Alignment explanation
Indices: 4843--5533 Score: 1005
Period size: 263 Copynumber: 2.6 Consensus size: 261
4833 TTTTTTATGG
*
4843 TTTGACTATAAAACTTTGGGGTTTGACCATGCATATACAATGAAATAC-TTTTGTGGTTTGACTT
1 TTTGACTATAAAACTTTGGGGTTTGACCATGCATATACAATGAAATACTTTTTGTGGTTTGACTA
* *
4907 TCGAATTTTGGGGTTTGACCATCATCCTTTGTGGTTTGACCATGTAAATATAATGATTTTATTGT
66 TCGAATTTTGGGGTTTGACCATCATCCTTTGTGGTTTGACCATGTAAGTATAAT-ATTTTTTTGT
*
4972 GATTTGACTATAAAACTTTAGGGTTTGACCATGCATATAAAATAAAATACTTTTTGTGGTTTGAC
130 GGTTTGACTATAAAACTTT-GGGTTTGACCATGCATATAAAATAAAATACTTTTTGTGGTTTGAC
*
5037 TATCGAATTTTGTGGTTTGACCATCATCTTTTGTAATTTGACCATGTAAATATAA-AGATTTTAA
194 TATCGAATTTTGGGGTTTGACCATCATCTTTTGTAATTTGACCATGTAAATATAATA-ATTTT-A
5101 TGTAA
257 TGTAA
*
5106 TTTGACTATAAAACTTTGGGGTTTCACCATGCATATACAATGAAATACTTTTTGTGGTTTGACTA
1 TTTGACTATAAAACTTTGGGGTTTGACCATGCATATACAATGAAATACTTTTTGTGGTTTGACTA
* *
5171 TCGAATTTTGGGGTTTGACCATCATCTTTTGTGGTTTGACAATGTAAGTATAATATTTTTTTGTG
66 TCGAATTTTGGGGTTTGACCATCATCCTTTGTGGTTTGACCATGTAAGTATAATATTTTTTTGTG
* * * * * * *
5236 GTCTGA-TAATCAAACTTTGGGCTTTGACCATGCATATACATTGAAATATTTTTTGTGGTTTGGC
131 GTTTGACT-ATAAAACTTTGGG-TTTGACCATGCATATAAAATAAAATACTTTTTGTGGTTTGAC
** * *
5300 TATCGAATTTTGGGGTTTGACCATCATCTTTTGTGGTTTGACCATGTAAGTATAATAATTTTTTG
194 TATCGAATTTTGGGGTTTGACCATCATCTTTTGTAATTTGACCATGTAAATATAATAATTTTATG
**
5365 TGG
259 TAA
* *
5368 TTTGATTATCAAACTTTGGGGTTTGACCATGCATATACAATGAAATACTTTTTGTGGTTTGACTA
1 TTTGACTATAAAACTTTGGGGTTTGACCATGCATATACAATGAAATACTTTTTGTGGTTTGACTA
* *
5433 TCGAATTTTGGGGTTTGAGCATCATCCTTTGTGGTTTGGCCAT-TAAAGTATAA-ATGGTTTTTT
66 TCGAATTTTGGGGTTTGACCATCATCCTTTGTGGTTTGACCATGT-AAGTATAATAT--TTTTTT
** *
5496 GTGGTTTGACTATTAAAGTTTTGGGTTTGACAATGCAT
128 GTGGTTTGACTA-TAAAACTTTGGGTTTGACCATGCAT
5534 GTAGAATGAT
Statistics
Matches: 386, Mismatches: 33, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
261 3 0.01
262 116 0.30
263 190 0.49
264 77 0.20
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (261 bp):
TTTGACTATAAAACTTTGGGGTTTGACCATGCATATACAATGAAATACTTTTTGTGGTTTGACTA
TCGAATTTTGGGGTTTGACCATCATCCTTTGTGGTTTGACCATGTAAGTATAATATTTTTTTGTG
GTTTGACTATAAAACTTTGGGTTTGACCATGCATATAAAATAAAATACTTTTTGTGGTTTGACTA
TCGAATTTTGGGGTTTGACCATCATCTTTTGTAATTTGACCATGTAAATATAATAATTTTATGTA
A
Found at i:7740 original size:31 final size:31
Alignment explanation
Indices: 7697--7764 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
7687 ATCCCGCTAA
* *
7697 AGGTAATTCCCCACGTGGTTAAACATGTTAC
1 AGGTAATACCCCACGTGGTTAAACACGTTAC
* **
7728 AGGTAATACCCCACTTGGTTGCACACGTTAC
1 AGGTAATACCCCACGTGGTTAAACACGTTAC
7759 AGGTAA
1 AGGTAA
7765 CACCTTGTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (31 bp):
AGGTAATACCCCACGTGGTTAAACACGTTAC
Found at i:7800 original size:30 final size:30
Alignment explanation
Indices: 7760--7820 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
7750 ACACGTTACA
*
7760 GGTAACACCTTGTAACTAGTTATACATGTT
1 GGTAACACCTTGTAACTAGTAATACATGTT
* * *
7790 GGTAATACCTTGTGACTGGTAATACATGTT
1 GGTAACACCTTGTAACTAGTAATACATGTT
7820 G
1 G
7821 TTGGTAATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (30 bp):
GGTAACACCTTGTAACTAGTAATACATGTT
Found at i:13883 original size:13 final size:13
Alignment explanation
Indices: 13865--13890 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13855 CTGACTCGTC
13865 CCTCAACATTTCT
1 CCTCAACATTTCT
13878 CCTCAACATTTCT
1 CCTCAACATTTCT
13891 TTTTCTGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (13 bp):
CCTCAACATTTCT
Done.