Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013252.1 Corchorus olitorius cultivar O-4 contig13285, 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: 31684
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:1129 original size:19 final size:18
Alignment explanation
Indices: 1096--1131 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1086 TTGAAATTAT
1096 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
1114 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
1132 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:4203 original size:91 final size:93
Alignment explanation
Indices: 4096--4273 Score: 222
Period size: 91 Copynumber: 1.9 Consensus size: 93
4086 AGTTCGATTT
* * * * * *
4096 TTTTTGGATTAAAATTAATTCAGAAATTGATCATTAAGTCTTTT-TGGGTTAATCTTAATAT-GA
1 TTTTTAGATTAAAATTAACTCAAAAATGGATCAGTAAAT-TTTTCTGGGTTAATCTTAAT-TCGA
4159 AAA-TT-AAGTCTTTGATTC-AAAGATCTGA
64 AAATTTAAAG-CTTTGATTCGAAAGATCTGA
* *
4187 TTTTTAGATTAAAATTAACTCAAAAATGGATTAGTAAATTTTTCTGGGTTAATTTTAATTCGAAA
1 TTTTTAGATTAAAATTAACTCAAAAATGGATCAGTAAATTTTTCTGGGTTAATCTTAATTCGAAA
4252 ATTTAAAGCTTTGATTCGAAAG
66 ATTTAAAGCTTTGATTCGAAAG
4274 TGAGTTTTCT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
90 5 0.07
91 51 0.69
92 11 0.15
93 7 0.09
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (93 bp):
TTTTTAGATTAAAATTAACTCAAAAATGGATCAGTAAATTTTTCTGGGTTAATCTTAATTCGAAA
ATTTAAAGCTTTGATTCGAAAGATCTGA
Found at i:4787 original size:5 final size:5
Alignment explanation
Indices: 4777--4818 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
4767 AAATGGTTTC
* *
4777 TTTGT TTTG- TTTGT TTTGG TTTGT TTTGT CTTG- TTTGT TTTG
1 TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTG
4819 ATGTTTCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 7 0.23
5 24 0.77
ACGTcount: A:0.00, C:0.02, G:0.24, T:0.74
Consensus pattern (5 bp):
TTTGT
Found at i:4810 original size:10 final size:9
Alignment explanation
Indices: 4777--4816 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
4767 AAATGGTTTC
4777 TTTGTTTTG
1 TTTGTTTTG
4786 TTTGTTTTGG
1 TTTGTTTT-G
4796 TTTGTTTTG
1 TTTGTTTTG
4805 TCTTG-TTTG
1 T-TTGTTTTG
4814 TTT
1 TTT
4817 TGATGTTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.07
9 15 0.52
10 12 0.41
ACGTcount: A:0.00, C:0.03, G:0.23, T:0.75
Consensus pattern (9 bp):
TTTGTTTTG
Found at i:4817 original size:14 final size:15
Alignment explanation
Indices: 4782--4818 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
4772 GTTTCTTTGT
*
4782 TTTG-TTTGTTTTGG
1 TTTGTTTTGTCTTGG
4796 TTTGTTTTGTCTT-G
1 TTTGTTTTGTCTTGG
4810 TTTGTTTTG
1 TTTGTTTTG
4819 ATGTTTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.00, C:0.03, G:0.24, T:0.73
Consensus pattern (15 bp):
TTTGTTTTGTCTTGG
Found at i:9970 original size:22 final size:22
Alignment explanation
Indices: 9912--9972 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
9902 ACATTAAAAA
* *
9912 TGGGTCGTGCTGCGTCGGCACG
1 TGGGTCGTGCTGTGCCGGCACG
9934 TGGGTCGTGCTGTGCCGGCACG
1 TGGGTCGTGCTGTGCCGGCACG
*
9956 TGGGTCGTGCCGTGCCG
1 TGGGTCGTGCTGTGCCG
9973 TGCCATTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.03, C:0.28, G:0.46, T:0.23
Consensus pattern (22 bp):
TGGGTCGTGCTGTGCCGGCACG
Found at i:15607 original size:19 final size:18
Alignment explanation
Indices: 15574--15609 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
15564 TTGAAATTAT
15574 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
15592 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
15610 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:18264 original size:34 final size:35
Alignment explanation
Indices: 18219--18287 Score: 131
Period size: 34 Copynumber: 2.0 Consensus size: 35
18209 CCTGAGGAGA
18219 AAAAGAAAAAAACTTGGCCTAAAAAAGAAAGAGGT
1 AAAAGAAAAAAACTTGGCCTAAAAAAGAAAGAGGT
18254 AAAA-AAAAAAACTTGGCCTAAAAAAGAAAGAGGT
1 AAAAGAAAAAAACTTGGCCTAAAAAAGAAAGAGGT
18288 TGGAAAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 30 0.88
35 4 0.12
ACGTcount: A:0.61, C:0.09, G:0.19, T:0.12
Consensus pattern (35 bp):
AAAAGAAAAAAACTTGGCCTAAAAAAGAAAGAGGT
Found at i:18723 original size:20 final size:20
Alignment explanation
Indices: 18686--18743 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 20
18676 ATTATAAATC
*
18686 TTCTTTTGTTGTATATATAT
1 TTCTTTTGTTATATATATAT
18706 TTCTTTT-TTATATA-ATA-
1 TTCTTTTGTTATATATATAT
*
18723 -TCTTTT-TAATA-ATATAT
1 TTCTTTTGTTATATATATAT
18740 TTCT
1 TTCT
18744 CCTTTCATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
15 1 0.03
16 13 0.39
18 6 0.18
19 6 0.18
20 7 0.21
ACGTcount: A:0.26, C:0.07, G:0.03, T:0.64
Consensus pattern (20 bp):
TTCTTTTGTTATATATATAT
Found at i:19297 original size:59 final size:58
Alignment explanation
Indices: 19211--19603 Score: 488
Period size: 58 Copynumber: 6.7 Consensus size: 58
19201 CAAATTCCCT
* * *
19211 TTTC-TTTTCAAAATTCTGTTTGAGGTCTCTGGTAGAGAGTTTTCAATCCAAAAATATTG
1 TTTCGTTTT-AAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCC-AAAATCTTG
* ** * ** * *
19270 TTTCGTTTTAGAATCCTGTTTAAGGTCTCTGGTAGAGAGTTTCCGTTTCAAAATCTGG
1 TTTCGTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCCAAAATCTTG
*** * *
19328 TTTTAATTTAAAATCCTGTTCGTGGTCTCTGGTAGAGAGTTTTCAATCCAAAATCTCG
1 TTTCGTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCCAAAATCTTG
19386 TCTT-GTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCCAAAATCTTG
1 T-TTCG-TTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCCAAAATCTTG
* *
19445 TGTT-GTTTTAAAATCCTGTTCGATGTCTCTGGTAGAGAGTTTTCAATCCAAAAATATTG
1 T-TTCGTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCC-AAAATCTTG
* * *
19504 TTTCGTTTTAAAATCCTGTTTGAGGTCTCTGGTAGAGAGTTTCTC-TTTCAAAATCTTG
1 TTTCGTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTT-TCAATCCAAAATCTTG
* *
19562 TTTCATTTTAAAATCCTGTTCGAGGTCTCTGGTGGAGAGTTT
1 TTTCGTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTT
19604 CTGTTTCAAA
Statistics
Matches: 292, Mismatches: 36, Indels: 13
0.86 0.11 0.04
Matches are distributed among these distances:
58 146 0.50
59 140 0.48
60 6 0.02
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (58 bp):
TTTCGTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCCAAAATCTTG
Found at i:19355 original size:58 final size:58
Alignment explanation
Indices: 19211--19693 Score: 450
Period size: 58 Copynumber: 8.2 Consensus size: 58
19201 CAAATTCCCT
* * * * * *
19211 TTTC-TTTTCAAAATTCTGTTTGAGGTCTCTGGTAGAGAGTTTTCAATCCAAAAATATTG
1 TTTCATTTT-AAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTCCATTTC-AAAATCTTG
* * ** * *
19270 TTTCGTTTTAGAATCCTGTTTAAGGTCTCTGGTAGAGAGTTTCCGTTTCAAAATCTGG
1 TTTCATTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTCCATTTCAAAATCTTG
* * * * * * *
19328 TTTTAATTTAAAATCCTGTTCGTGGTCTCTGGTAGAGAGTTTTCAATCCAAAATCTCG
1 TTTCATTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTCCATTTCAAAATCTTG
** * * *
19386 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCCAAAATCTTG
1 T-TTCATTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTCCATTTCAAAATCTTG
* * * * * *
19445 TGTT-GTTTTAAAATCCTGTTCGATGTCTCTGGTAGAGAGTTTTCAATCCAAAAATATTG
1 T-TTCATTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTCCATTTC-AAAATCTTG
* *
19504 TTTCGTTTTAAAATCCTGTTTGAGGTCTCTGGTAGAGAGTTTCTC-TTTCAAAATCTTG
1 TTTCATTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTC-CATTTCAAAATCTTG
* ** *
19562 TTTCATTTTAAAATCCTGTTCGAGGTCTCTGGTGGAGAGTTTCTGTTTCAAAGTCTTG
1 TTTCATTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTCCATTTCAAAATCTTG
* *** * * ** * *
19620 TTTAAAAAAATATATATCTTGTTCGAGGTCTCTGGTAGAGAGTTTCTGTTTCGAAATCTGG
1 TTT--CATTTTA-AAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTCCATTTCAAAATCTTG
19681 TTTCATTTTAAAA
1 TTTCATTTTAAAA
19694 AATCTTGTTT
Statistics
Matches: 359, Mismatches: 56, Indels: 19
0.83 0.13 0.04
Matches are distributed among these distances:
58 164 0.46
59 142 0.40
60 8 0.02
61 45 0.13
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (58 bp):
TTTCATTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTCCATTTCAAAATCTTG
Found at i:19355 original size:117 final size:116
Alignment explanation
Indices: 19210--19603 Score: 549
Period size: 117 Copynumber: 3.4 Consensus size: 116
19200 TCAAATTCCC
* * *
19210 TTTTCTTTTCAAAATTCTGTTTGAGGTCTCTGGTAGAGAGTTTTCAATCCAAAAATATTGTTTCG
1 TTTTATTTT-AAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCCAAAAATATTGTTTCG
* * *
19275 TTTTAGAATCCTGTTTAAGGTCTCTGGTAGAGAGTTTCCGTTTCAAAATCTGG
65 TTTTAAAATCCTGTTTGAGGTCTCTGGTAGAGAGTTTCC-TTTCAAAATCTTG
* * * *
19328 TTTTAATTTAAAATCCTGTTCGTGGTCTCTGGTAGAGAGTTTTCAATCC-AAAATCTCGTCTT-G
1 TTTTATTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCCAAAAATATTGT-TTCG
* ** *
19391 TTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCCAAAATCTTG
65 -TTTTAAAATCCTGTTTGAGGTCTCTGGTAGAGAG-TTTCCTTTCAAAATCTTG
* * *
19445 TGTTGTTTTAAAATCCTGTTCGATGTCTCTGGTAGAGAGTTTTCAATCCAAAAATATTGTTTCGT
1 TTTTATTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCCAAAAATATTGTTTCGT
19510 TTTAAAATCCTGTTTGAGGTCTCTGGTAGAGAGTTTCTCTTTCAAAATCTTG
66 TTTAAAATCCTGTTTGAGGTCTCTGGTAGAGAGTTTC-CTTTCAAAATCTTG
* *
19562 TTTCATTTTAAAATCCTGTTCGAGGTCTCTGGTGGAGAGTTT
1 TTTTATTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTT
19604 CTGTTTCAAA
Statistics
Matches: 240, Mismatches: 30, Indels: 13
0.85 0.11 0.05
Matches are distributed among these distances:
116 13 0.05
117 207 0.86
118 20 0.08
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (116 bp):
TTTTATTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATCCAAAAATATTGTTTCGT
TTTAAAATCCTGTTTGAGGTCTCTGGTAGAGAGTTTCCTTTCAAAATCTTG
Found at i:24553 original size:1 final size:1
Alignment explanation
Indices: 24547--24571 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
24537 CAACAATTGG
24547 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
24572 ACAGAAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:24632 original size:18 final size:18
Alignment explanation
Indices: 24597--24631 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
24587 CTCCTCTATC
*
24597 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
24615 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTCTTTTT
24632 TTTGTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:27657 original size:67 final size:68
Alignment explanation
Indices: 27568--27704 Score: 258
Period size: 67 Copynumber: 2.0 Consensus size: 68
27558 AATACACAAT
*
27568 CTCCTTGGCAACGGCGCCAAAATTTATGATTGGTCGTCAGCAAATCATAAAAATAATCCCAACAA
1 CTCCTTGGCAACGGCGCCAAAATTTATGATCGGTCGTCAGCAAATCATAAAAATAATCCCAACAA
27633 TTA
66 TTA
27636 CTCC-TGGCAACGGCGCCAAAATTTATGATCGGTCGTCAGCAAATCATAAAAATAATCCCAACAA
1 CTCCTTGGCAACGGCGCCAAAATTTATGATCGGTCGTCAGCAAATCATAAAAATAATCCCAACAA
27700 TTA
66 TTA
27703 CT
1 CT
27705 AACTAAAAGT
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
67 64 0.94
68 4 0.06
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (68 bp):
CTCCTTGGCAACGGCGCCAAAATTTATGATCGGTCGTCAGCAAATCATAAAAATAATCCCAACAA
TTA
Found at i:27854 original size:22 final size:23
Alignment explanation
Indices: 27827--27879 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
27817 AAATCAAACT
* *
27827 AACAATTAAA-ATAATTTAAGAA
1 AACAATTAAAGAAAATTAAAGAA
*
27849 AGCAA-TAAAGAAAATTAAAGAA
1 AACAATTAAAGAAAATTAAAGAA
27871 AACAATTAA
1 AACAATTAA
27880 TCAGAAAGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 4 0.16
22 18 0.72
23 3 0.12
ACGTcount: A:0.66, C:0.06, G:0.08, T:0.21
Consensus pattern (23 bp):
AACAATTAAAGAAAATTAAAGAA
Found at i:30316 original size:40 final size:40
Alignment explanation
Indices: 30245--30321 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
30235 ATTAATTAAG
*
30245 AAATAAACCTTAAATCAGGGACTATGATGCAT-AAATCAA
1 AAATAAACCTTAAATCAGGGACTATAATGCATCAAATCAA
* *
30284 AAATAAAATCTTAAATCAGGGGCTA-AATTGCATCAAAT
1 AAAT-AAACCTTAAATCAGGGACTATAA-TGCATCAAAT
30322 AGTGAATATC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 5 0.16
40 23 0.72
41 4 0.12
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.25
Consensus pattern (40 bp):
AAATAAACCTTAAATCAGGGACTATAATGCATCAAATCAA
Done.