Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016037.1 Corchorus capsularis cultivar CVL-1 contig16058, 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: 75702
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3799 original size:42 final size:42
Alignment explanation
Indices: 3753--4001 Score: 157
Period size: 42 Copynumber: 5.9 Consensus size: 42
3743 GGTCACGTTG
* * * *
3753 CTTCTG-TCCAGGCCCAAACTCAGCCTCAACAAGGTCCCAGCA
1 CTTCTGTTCCA-GCCAAAAATCAGCCTCAACAAGGTCCAAACA
* *
3795 CTTCTGTTTCAGCCAAAAATCAGCCTCAGA-AAGGTCCAAATA
1 CTTCTGTTCCAGCCAAAAATCAGCCTCA-ACAAGGTCCAAACA
* * * ** * * *
3837 CTGCTCTACCCTCCCAAAATCAGCCTCAACAAGGTCCTACCA
1 CTTCTGTTCCAGCCAAAAATCAGCCTCAACAAGGTCCAAACA
* * * *
3879 CTTCTGTTTCAGCCAAAAATCAGCCTCAAAAAGGTCCTAATA
1 CTTCTGTTCCAGCCAAAAATCAGCCTCAACAAGGTCCAAACA
* * * ** * * * * *
3921 CTGCTCTACCCTCCCAAAATCAGCCTCAACAAGGCCCTATCG
1 CTTCTGTTCCAGCCAAAAATCAGCCTCAACAAGGTCCAAACA
*
3963 CTTCTGATTTGCC--CC-AAAATCAGCCTCAAAAAGGTCCAA
1 CTTCTG--TT-CCAGCCAAAAATCAGCCTCAACAAGGTCCAA
4002 TTACTGCTCT
Statistics
Matches: 157, Mismatches: 44, Indels: 12
0.74 0.21 0.06
Matches are distributed among these distances:
41 1 0.01
42 147 0.94
43 6 0.04
44 1 0.01
45 2 0.01
ACGTcount: A:0.31, C:0.35, G:0.13, T:0.21
Consensus pattern (42 bp):
CTTCTGTTCCAGCCAAAAATCAGCCTCAACAAGGTCCAAACA
Found at i:3869 original size:84 final size:84
Alignment explanation
Indices: 3765--4117 Score: 378
Period size: 84 Copynumber: 4.2 Consensus size: 84
3755 TCTGTCCAGG
* * *
3765 CCCAAACTCAGCCTCAACAAGGTCCCAGCACTTCTGTTTCAGCCAAAAATCAGCCTCAGAAAGGT
1 CCCAAAATCAGCCTCAACAAGGTCCCACCACTTCTGTTTCAGCCAAAAATCAGCCTCAAAAAGGT
3830 CCAAATACTGCTCTACCCT
66 CCAAATACTGCTCTACCCT
*
3849 CCCAAAATCAGCCTCAACAAGGTCCTACCACTTCTGTTTCAGCCAAAAATCAGCCTCAAAAAGGT
1 CCCAAAATCAGCCTCAACAAGGTCCCACCACTTCTGTTTCAGCCAAAAATCAGCCTCAAAAAGGT
*
3914 CCTAATACTGCTCTACCCT
66 CCAAATACTGCTCTACCCT
* * *
3933 CCCAAAATCAGCCTCAACAAGG-CCCTATCGCTTCTGATTT--GCCCCAAAATCAGCCTCAAAAA
1 CCCAAAATCAGCCTCAACAAGGTCCC-ACCACTTCTG-TTTCAG-CCAAAAATCAGCCTCAAAAA
*
3995 GGTCCAATTACTGCTCT-CCCT
63 GGTCCAAATACTGCTCTACCCT
* * * ** * * ** * * *
4016 GCCCAAACTCACCCTCAGA-AAGGTCCAATTACTGCTCTCCCTGCCCAAACTCAGCCTCAAAAAG
1 -CCCAAAATCAGCCTCA-ACAAGGTCCCACCACTTCTGTTTCAGCCAAAAATCAGCCTCAAAAAG
*
4080 GTAC-AATAACTGCTCT-CCCT
64 GTCCAAAT-ACTGCTCTACCCT
* *
4100 GCCCAGACTCAGCCTCAA
1 -CCCAAAATCAGCCTCAA
4118 AAAGTTGCAA
Statistics
Matches: 235, Mismatches: 25, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
83 11 0.05
84 217 0.92
85 7 0.03
ACGTcount: A:0.30, C:0.37, G:0.12, T:0.21
Consensus pattern (84 bp):
CCCAAAATCAGCCTCAACAAGGTCCCACCACTTCTGTTTCAGCCAAAAATCAGCCTCAAAAAGGT
CCAAATACTGCTCTACCCT
Found at i:4021 original size:42 final size:42
Alignment explanation
Indices: 3810--4167 Score: 332
Period size: 42 Copynumber: 8.5 Consensus size: 42
3800 GTTTCAGCCA
* *
3810 AAAATCAGCCTCAGAAAGGTCCAAATACTGCTCTACCCT-CCC
1 AAAATCAGCCTCAAAAAGGTCCAATTACTGCTCT-CCCTGCCC
* * ** * * ** * *
3852 AAAATCAGCCTCAACAAGGTCCTACCACTTCTGTTTCAGCCA
1 AAAATCAGCCTCAAAAAGGTCCAATTACTGCTCTCCCTGCCC
3894 AAAATCAGCCTCAAAAAGGTCCTAA-TACTGCTCTACCCT-CCC
1 AAAATCAGCCTCAAAAAGGTCC-AATTACTGCTCT-CCCTGCCC
* * * ***
3936 AAAATCAGCCTCAACAAGGCCCTA-T-C-GCTTCTGATTTGCCCC
1 AAAATCAGCCTCAAAAAGGTCCAATTACTGC-TCT-CCCTG-CCC
3978 AAAATCAGCCTCAAAAAGGTCCAATTACTGCTCTCCCTGCCC
1 AAAATCAGCCTCAAAAAGGTCCAATTACTGCTCTCCCTGCCC
* * *
4020 AAACTCACCCTCAGAAAGGTCCAATTACTGCTCTCCCTGCCC
1 AAAATCAGCCTCAAAAAGGTCCAATTACTGCTCTCCCTGCCC
* * *
4062 AAACTCAGCCTCAAAAAGGTACAATAACTGCTCTCCCTGCCC
1 AAAATCAGCCTCAAAAAGGTCCAATTACTGCTCTCCCTGCCC
* * * * * *
4104 AGACTCAGCCTCAAAAAGTTGCAACTACTGCTCTCCCTGGCC
1 AAAATCAGCCTCAAAAAGGTCCAATTACTGCTCTCCCTGCCC
* *
4146 AAAGTCAGCCTCAACAAGGTCC
1 AAAATCAGCCTCAAAAAGGTCC
4168 TAGCACTTCT
Statistics
Matches: 256, Mismatches: 51, Indels: 18
0.79 0.16 0.06
Matches are distributed among these distances:
39 2 0.01
40 5 0.02
41 3 0.01
42 235 0.92
43 5 0.02
44 4 0.02
45 2 0.01
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (42 bp):
AAAATCAGCCTCAAAAAGGTCCAATTACTGCTCTCCCTGCCC
Found at i:14116 original size:3 final size:3
Alignment explanation
Indices: 14103--14159 Score: 82
Period size: 3 Copynumber: 19.0 Consensus size: 3
14093 TCTGTCCATA
14103 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
14150 TAT ATAT TAT
1 TAT -TAT TAT
14160 GTGTGTGTAC
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.08
3 40 0.80
4 6 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:14751 original size:15 final size:15
Alignment explanation
Indices: 14731--14762 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
14721 AACATATGGA
14731 GATGGATTTTGAATT
1 GATGGATTTTGAATT
14746 GATGGATTTTGAATT
1 GATGGATTTTGAATT
14761 GA
1 GA
14763 CTTAAGGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (15 bp):
GATGGATTTTGAATT
Found at i:22813 original size:1 final size:1
Alignment explanation
Indices: 22807--22839 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
22797 TATAATAATT
22807 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
22840 CCTTCTATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:30021 original size:1 final size:1
Alignment explanation
Indices: 30015--30044 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
30005 AACTTCATTT
30015 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
30045 GACTAACCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:49600 original size:21 final size:20
Alignment explanation
Indices: 49561--49605 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
49551 AGAAATTAAT
* *
49561 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
49581 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
49602 TAAA
1 TAAA
49606 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:50342 original size:17 final size:17
Alignment explanation
Indices: 50320--50354 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
50310 CGACACCCTT
*
50320 AACCTAAAACTAGAGAA
1 AACCTAAAACTAAAGAA
50337 AACCTAAAACTAAAGAA
1 AACCTAAAACTAAAGAA
50354 A
1 A
50355 GGTAGAAAAT
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:0.63, C:0.17, G:0.09, T:0.11
Consensus pattern (17 bp):
AACCTAAAACTAAAGAA
Found at i:55006 original size:2 final size:2
Alignment explanation
Indices: 54999--55042 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
54989 TAGTAGCTAT
54999 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
55041 CA
1 CA
55043 AATATATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:55812 original size:13 final size:13
Alignment explanation
Indices: 55796--55820 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55786 ACTTTTGTTG
55796 TTGACTGTTGACT
1 TTGACTGTTGACT
55809 TTGACTGTTGAC
1 TTGACTGTTGAC
55821 CTCCGCGAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (13 bp):
TTGACTGTTGACT
Found at i:56005 original size:27 final size:27
Alignment explanation
Indices: 55975--56094 Score: 131
Period size: 27 Copynumber: 4.5 Consensus size: 27
55965 CGTGATTCCG
55975 TTCCGTTGTCCGTTGTCTGCTATCTGA
1 TTCCGTTGTCCGTTGTCTGCTATCTGA
* *
56002 TTCCGTTGTTCGTTGTCTGCTGTCTGA
1 TTCCGTTGTCCGTTGTCTGCTATCTGA
* *
56029 TTCCGTTATCCCG-T-TCCGCTATCTGA
1 TTCCGTTGT-CCGTTGTCTGCTATCTGA
*
56055 TTCCG-T-TCCGTTGTCTGTCTGTCTGA
1 TTCCGTTGTCCGTTGTCTG-CTATCTGA
* *
56081 TTCTGCTGTCCGTT
1 TTCCGTTGTCCGTT
56095 TTATCTCCAT
Statistics
Matches: 78, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
23 3 0.04
24 2 0.03
25 4 0.05
26 26 0.33
27 35 0.45
28 8 0.10
ACGTcount: A:0.06, C:0.28, G:0.22, T:0.45
Consensus pattern (27 bp):
TTCCGTTGTCCGTTGTCTGCTATCTGA
Found at i:60080 original size:15 final size:15
Alignment explanation
Indices: 60015--60081 Score: 98
Period size: 15 Copynumber: 4.5 Consensus size: 15
60005 AATGATGAAA
* *
60015 AGGAGACAAGTAAGG
1 AGGAGGCAAGTGAGG
*
60030 AGGAGACAAGTGAGG
1 AGGAGGCAAGTGAGG
*
60045 AGGAAGCAAGTGAGG
1 AGGAGGCAAGTGAGG
60060 AGGAGGCAAGTGAGG
1 AGGAGGCAAGTGAGG
60075 AGGAGGC
1 AGGAGGC
60082 GGTATCTTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 48 1.00
ACGTcount: A:0.39, C:0.07, G:0.48, T:0.06
Consensus pattern (15 bp):
AGGAGGCAAGTGAGG
Found at i:61201 original size:2 final size:2
Alignment explanation
Indices: 61194--61231 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
61184 ACTCAAAGTA
61194 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61232 TAAACCATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61807 original size:30 final size:30
Alignment explanation
Indices: 61773--61830 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
61763 CTTCTGTTTC
61773 TGGGTTCTCATCTTTTGTTGTTATATTTTT
1 TGGGTTCTCATCTTTTGTTGTTATATTTTT
* *
61803 TGGGTTGTCCTCTTTTGTTGTTATATTT
1 TGGGTTCTCATCTTTTGTTGTTATATTT
61831 GGGTTAATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.09, C:0.10, G:0.19, T:0.62
Consensus pattern (30 bp):
TGGGTTCTCATCTTTTGTTGTTATATTTTT
Found at i:70815 original size:158 final size:158
Alignment explanation
Indices: 70527--71003 Score: 884
Period size: 158 Copynumber: 3.0 Consensus size: 158
70517 TGCTAAAAAT
** *
70527 AATTACCATAGATGACTATGTAAATAGATACGTAAGGTAGATGATCAAATTGATCACAGGCCTGA
1 AATTACCATAGATGACTATGTAAATAGATACACAAGGTAGATGATCAAATTGATCACAGACCTGA
*
70592 TATTTGGGACCTGTATTAACCCCATCATCATAAAATATCATGTATTCTCAGAGCCTTGAATCTTC
66 AATTTGGGACCTGTATTAACCCCATCATCATAAAATATCATGTATTCTCAGAGCCTTGAATCTTC
70657 CTCTTGCATGATTATCCCTTTCTAAACA
131 CTCTTGCATGATTATCCCTTTCTAAACA
**
70685 AATTATTATAGATGACTATGTAAATAGATACACAAGGTAGATGATCAAATTGATCACAGACCTGA
1 AATTACCATAGATGACTATGTAAATAGATACACAAGGTAGATGATCAAATTGATCACAGACCTGA
70750 AATTTGGGACCTGTATTAACCCCATCATCATAAAATATCATGTATTCTCAGAGCCTTGAATCTTC
66 AATTTGGGACCTGTATTAACCCCATCATCATAAAATATCATGTATTCTCAGAGCCTTGAATCTTC
70815 CTCTTGCATGATTATCCCTTTCTAAACA
131 CTCTTGCATGATTATCCCTTTCTAAACA
70843 AATTACCATAGATGACTATGTAAATAGATACACAAGGTAGATGATCAAATTGATCACAGACCTGA
1 AATTACCATAGATGACTATGTAAATAGATACACAAGGTAGATGATCAAATTGATCACAGACCTGA
*
70908 AATTTGGGACCTGTATTAACCCCATCATCATAAAAAATCATGTATTCTCAGAGCCTTGAATCTTC
66 AATTTGGGACCTGTATTAACCCCATCATCATAAAATATCATGTATTCTCAGAGCCTTGAATCTTC
70973 CTCTTGCATGATTATCCCTTTCTAAA-A
131 CTCTTGCATGATTATCCCTTTCTAAACA
71000 AATT
1 AATT
71004 TGGATATTCC
Statistics
Matches: 310, Mismatches: 9, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
157 5 0.02
158 305 0.98
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.32
Consensus pattern (158 bp):
AATTACCATAGATGACTATGTAAATAGATACACAAGGTAGATGATCAAATTGATCACAGACCTGA
AATTTGGGACCTGTATTAACCCCATCATCATAAAATATCATGTATTCTCAGAGCCTTGAATCTTC
CTCTTGCATGATTATCCCTTTCTAAACA
Found at i:74356 original size:14 final size:14
Alignment explanation
Indices: 74337--74368 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
74327 CATCATCATC
74337 TAATCCTAGACAAG
1 TAATCCTAGACAAG
74351 TAATCCTAGACAAG
1 TAATCCTAGACAAG
74365 TAAT
1 TAAT
74369 ATGAGGTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (14 bp):
TAATCCTAGACAAG
Done.