Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010379.1 Corchorus capsularis cultivar CVL-1 contig10400, 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: 92981
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:562 original size:3 final size:3
Alignment explanation
Indices: 554--588 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
544 AAGTTATGAA
554 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
589 GAAAATACGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:671 original size:31 final size:31
Alignment explanation
Indices: 630--766 Score: 145
Period size: 31 Copynumber: 4.5 Consensus size: 31
620 GTCAAATACT
* * *
630 CAATTTAGGATATAACATTTGTTG-CTGCAAG
1 CAATTAAGGATATAACGTTT-TTGACTTCAAG
** ***
661 CAATTAAGGATATAACG--TTACAAAACAAG
1 CAATTAAGGATATAACGTTTTTGACTTCAAG
*
690 CAATTAAGGATATAACGTTTTTGATTTCAAG
1 CAATTAAGGATATAACGTTTTTGACTTCAAG
* *
721 CAATTAAGGATATAACGTTTTCGATTTCAAG
1 CAATTAAGGATATAACGTTTTTGACTTCAAG
752 CAATTAAGGATATAA
1 CAATTAAGGATATAA
767 TCAGTTAGGG
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
28 1 0.01
29 22 0.24
31 67 0.74
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (31 bp):
CAATTAAGGATATAACGTTTTTGACTTCAAG
Found at i:723 original size:60 final size:62
Alignment explanation
Indices: 630--766 Score: 172
Period size: 60 Copynumber: 2.2 Consensus size: 62
620 GTCAAATACT
*
630 CAATTTAGGATATAACATTTGTTGCTGCAAGCAATTAAGGATATAACG-TTAC-AAAACAAG
1 CAATTAAGGATATAACATTTGTTGCTGCAAGCAATTAAGGATATAACGTTTACGAAAACAAG
* * * * ***
690 CAATTAAGGATATAACGTTT-TTGATTTCAAGCAATTAAGGATATAACGTTTTCGATTTCAAG
1 CAATTAAGGATATAACATTTGTTG-CTGCAAGCAATTAAGGATATAACGTTTACGAAAACAAG
752 CAATTAAGGATATAA
1 CAATTAAGGATATAA
767 TCAGTTAGGG
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
59 3 0.05
60 40 0.61
61 3 0.05
62 20 0.30
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (62 bp):
CAATTAAGGATATAACATTTGTTGCTGCAAGCAATTAAGGATATAACGTTTACGAAAACAAG
Found at i:951 original size:29 final size:31
Alignment explanation
Indices: 885--951 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
875 TCTAACGGAA
*
885 TATATCCTTATTTGCTCGATTTTCGTAACAT
1 TATATCCTTAATTGCTCGATTTTCGTAACAT
* *
916 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGATTTTCGTAACAT
945 TATATCC
1 TATATCC
952 CAAATTGCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 13 0.39
30 4 0.12
31 16 0.48
ACGTcount: A:0.22, C:0.18, G:0.10, T:0.49
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGATTTTCGTAACAT
Found at i:11621 original size:17 final size:17
Alignment explanation
Indices: 11594--11648 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
11584 AACCCATGTA
*
11594 ATCTTTGATCACTAGTG
1 ATCTTAGATCACTAGTG
*
11611 ATCTT-GCATCACTGGTG
1 ATCTTAG-ATCACTAGTG
*
11628 ATCTTAGATCACTAGTA
1 ATCTTAGATCACTAGTG
11645 ATCT
1 ATCT
11649 GGGGGGTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 1 0.03
17 31 0.94
18 1 0.03
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.38
Consensus pattern (17 bp):
ATCTTAGATCACTAGTG
Found at i:12265 original size:12 final size:12
Alignment explanation
Indices: 12248--12272 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12238 AATGTATATA
12248 AGGCACCCAAAC
1 AGGCACCCAAAC
12260 AGGCACCCAAAC
1 AGGCACCCAAAC
12272 A
1 A
12273 AACACTCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.40, G:0.16, T:0.00
Consensus pattern (12 bp):
AGGCACCCAAAC
Found at i:15590 original size:78 final size:78
Alignment explanation
Indices: 15507--15752 Score: 323
Period size: 78 Copynumber: 3.1 Consensus size: 78
15497 GGTTTTTATA
* * *
15507 ATTTTACTCAACTAAAAACTCTATTTTTATTTAATTGAATATAATAT-CTTCATAACTATTTTAT
1 ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTT-ATAACTATTATAT
*
15571 TTTACCATGTTACT
65 TTTACCATTTTACT
* * *
15585 ATTTTATTCAAATAAAAACTCTATTTTTATATAATTAAATATAATGAGTGAATCCTTATGACTAT
1 ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATAT-A--A-T--ATCCTTATAACTAT
15650 TATATTTTACCATTTTACT
60 TATATTTTACCATTTTACT
* *
15669 ATTTTACTCAACTAAAAAATCTATTTTTATATAATTAAATTTAATATCCTTATAACTATTATATT
1 ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTATTATATT
**
15734 TTAAAATTTTACT
66 TTACCATTTTACT
15747 ATTTTA
1 ATTTTA
15753 ATTAAAAAAC
Statistics
Matches: 147, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
78 74 0.50
79 1 0.01
80 1 0.01
81 2 0.01
82 1 0.01
83 1 0.01
84 64 0.44
85 3 0.02
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.48
Consensus pattern (78 bp):
ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTATTATATT
TTACCATTTTACT
Found at i:16645 original size:9 final size:9
Alignment explanation
Indices: 16631--16691 Score: 58
Period size: 9 Copynumber: 7.2 Consensus size: 9
16621 AAATTTACTT
*
16631 ATGATGATA
1 ATGATAATA
*
16640 ATGATGATA
1 ATGATAATA
16649 AT---AATA
1 ATGATAATA
*
16655 ATTATAATA
1 ATGATAATA
*
16664 ATAATAATA
1 ATGATAATA
16673 ATGATAATA
1 ATGATAATA
16682 ATGAT-ATA
1 ATGATAATA
16690 AT
1 AT
16692 TTCCAGTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
6 5 0.11
8 5 0.11
9 36 0.78
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (9 bp):
ATGATAATA
Found at i:16652 original size:3 final size:3
Alignment explanation
Indices: 16646--16683 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
16636 GATAATGATG
* *
16646 ATA ATA ATA ATT ATA ATA ATA ATA ATA ATG ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
16684 GATATAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:18363 original size:45 final size:45
Alignment explanation
Indices: 18299--18395 Score: 185
Period size: 45 Copynumber: 2.2 Consensus size: 45
18289 AGTATTACTT
18299 AGGAGGATAGCCGGATGGCGGGTAAGCAGCTGGAGGGTACTGGGC
1 AGGAGGATAGCCGGATGGCGGGTAAGCAGCTGGAGGGTACTGGGC
*
18344 AGGAGGATAGCTGGATGGCGGGTAAGCAGCTGGAGGGTACTGGGC
1 AGGAGGATAGCCGGATGGCGGGTAAGCAGCTGGAGGGTACTGGGC
18389 AGGAGGA
1 AGGAGGA
18396 GGATATCCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.24, C:0.13, G:0.49, T:0.13
Consensus pattern (45 bp):
AGGAGGATAGCCGGATGGCGGGTAAGCAGCTGGAGGGTACTGGGC
Found at i:38796 original size:46 final size:44
Alignment explanation
Indices: 38700--38787 Score: 151
Period size: 43 Copynumber: 2.0 Consensus size: 44
38690 CCCATGTTAG
38700 CTTTTTTGCTTTCAGTCTTTACAAAGATCGAAGAAGATCGAAGTCA
1 CTTTTTTGCTTTCAGTCTTT--AAAGATCGAAGAAGATCGAAGTCA
38746 CTTTTTTGCTTTCAGTCTTT-AAGATCGAAGAAGATCGAAGTC
1 CTTTTTTGCTTTCAGTCTTTAAAGATCGAAGAAGATCGAAGTC
38788 CAAACTTTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
43 22 0.52
46 20 0.48
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.36
Consensus pattern (44 bp):
CTTTTTTGCTTTCAGTCTTTAAAGATCGAAGAAGATCGAAGTCA
Found at i:38801 original size:43 final size:44
Alignment explanation
Indices: 38703--38801 Score: 130
Period size: 43 Copynumber: 2.2 Consensus size: 44
38693 ATGTTAGCTT
***
38703 TTTTGCTTTCAGTCTTTACAAAGATCGAAGAAGATCGAAGTCACTT
1 TTTTGCTTTCAGTCTTT--AAAGATCGAAGAAGATCGAAGTCAAAC
38749 TTTTGCTTTCAGTCTTT-AAGATCGAAGAAGATCGAAGTCCAAAC
1 TTTTGCTTTCAGTCTTTAAAGATCGAAGAAGATCGAAGT-CAAAC
38793 TTTT-CTTTC
1 TTTTGCTTTC
38802 CTTCCGTCGC
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
43 26 0.53
44 6 0.12
46 17 0.35
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.37
Consensus pattern (44 bp):
TTTTGCTTTCAGTCTTTAAAGATCGAAGAAGATCGAAGTCAAAC
Found at i:57483 original size:28 final size:28
Alignment explanation
Indices: 57443--57497 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
57433 CTGAAAACAA
57443 TAGCAAATCTAATAGAAATACTTTCCAT
1 TAGCAAATCTAATAGAAATACTTTCCAT
57471 TAGCAAATCTAATAGAAATACTTTCCA
1 TAGCAAATCTAATAGAAATACTTTCCA
57498 AGTTGGGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (28 bp):
TAGCAAATCTAATAGAAATACTTTCCAT
Found at i:57680 original size:2 final size:2
Alignment explanation
Indices: 57675--57707 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
57665 TGTGTGTGTG
57675 TA TA 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 TA TA T
57708 TATTATGCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:65576 original size:14 final size:14
Alignment explanation
Indices: 65557--65585 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
65547 TAAGTTGCTC
65557 TGAGATCATGATTT
1 TGAGATCATGATTT
65571 TGAGATCATGATTT
1 TGAGATCATGATTT
65585 T
1 T
65586 TGCCTAGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (14 bp):
TGAGATCATGATTT
Found at i:68485 original size:215 final size:216
Alignment explanation
Indices: 68081--68512 Score: 767
Period size: 215 Copynumber: 2.0 Consensus size: 216
68071 TAGTCAAATC
* * *
68081 CCGAATCTCATAAATAAGATCTCCGCCCTCCCACCAATAAAGTTTAGAGCTATTGATCTCATTAA
1 CCGAATCTCATAAATAAGATCCCCGACCTCCCACCAAGAAAGTTTAGAGCTATTGATCTCATTAA
68146 TTGCCATTAACGAGTCACTCTCAATAACACAAATGCGTGATACCCAACTCCAATGCTATCTCAAA
66 TTGCCATTAACGAGTCACTCTCAATAACACAAATGCGTGATACCCAACTCCAATGCTATCTCAAA
* * *
68211 CGCAAACAATAAAGCATGAACCTCAGCATAGAGTGAATTGGCCACGAAATCTAACTTCCGTGCTG
131 CGCAAACAACAAAGCATGAACCTCAGCATAGAGTGAATTGACCACGAAATCTAACTTCCGTGATG
*
68276 CACTTGCAACTATTTACCCGT
196 CACTTGCAACCATTTACCCGT
*
68297 CCGAATCTCATAAATAAGATCCCCGACCTCCCACCAAGAAGGTTTAGAGCTATTGATCTCATTAA
1 CCGAATCTCATAAATAAGATCCCCGACCTCCCACCAAGAAAGTTTAGAGCTATTGATCTCATTAA
68362 TTGCCATTAACGAGTCACTCTCAATAACAC-AATGCGTGATACCCAACTCCAATGCTATCTCAAA
66 TTGCCATTAACGAGTCACTCTCAATAACACAAATGCGTGATACCCAACTCCAATGCTATCTCAAA
*
68426 CGCAAACAACAAAGCATGAACCTCAGCATAGAGTGAATTGACCATGAAATCTAACTTCCGTGATG
131 CGCAAACAACAAAGCATGAACCTCAGCATAGAGTGAATTGACCACGAAATCTAACTTCCGTGATG
*
68491 CACTTGCAACCATTTCCCCGT
196 CACTTGCAACCATTTACCCGT
68512 C
1 C
68513 AGCATTCCGT
Statistics
Matches: 206, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
215 115 0.56
216 91 0.44
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (216 bp):
CCGAATCTCATAAATAAGATCCCCGACCTCCCACCAAGAAAGTTTAGAGCTATTGATCTCATTAA
TTGCCATTAACGAGTCACTCTCAATAACACAAATGCGTGATACCCAACTCCAATGCTATCTCAAA
CGCAAACAACAAAGCATGAACCTCAGCATAGAGTGAATTGACCACGAAATCTAACTTCCGTGATG
CACTTGCAACCATTTACCCGT
Found at i:69062 original size:122 final size:121
Alignment explanation
Indices: 68762--69067 Score: 355
Period size: 122 Copynumber: 2.5 Consensus size: 121
68752 TCTTACAGTG
** * * * * * **
68762 AATTAACCCAATTTGAACAAAATTATTCGTAAACCGTTAAAACGAAAACCAATATATGTGCCGAT
1 AATTAACTTAATTCGAACAAAACTACTCGTAAATCGTTAAAACGGATGCC-ATATATGTGCCGAT
* *
68827 ATATGTGATTTATAACAAGAATGAAGAAACTACGGTAATTTACTCATATAGTAAATT
65 ATATGTGATTTATAACAAGAATGAAGAAACTACGATAATTTACTCATATAGTAAATA
* * *
68884 AATTAACTTGATTCGAAGAAAACTATTCGTAAATCGTTAAAACGGATGCCAATATATGTGCCGAT
1 AATTAACTTAATTCGAACAAAACTACTCGTAAATCGTTAAAACGGATGCC-ATATATGTGCCGAT
* * *
68949 ATATGTGATTTATAACAAGAATGAAGAAACTACGATAATTTACTCGTACTCGTATAGTA
65 ATATGTGATTTATAACAAGAATGAAGAAACTACGATAATTTACTCATA-TAGTA-AATA
* * *
69008 AATTAA-TTCAATTCGAACAAAATTACTCGTAAA-CTGTTAAAATGGATGTCTATATATGTG
1 AATTAACTT-AATTCGAACAAAACTACTCGTAAATC-GTTAAAACGGATG-CCATATATGTG
69068 ATTTATAATT
Statistics
Matches: 158, Mismatches: 21, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
122 101 0.64
123 7 0.04
124 49 0.31
125 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (121 bp):
AATTAACTTAATTCGAACAAAACTACTCGTAAATCGTTAAAACGGATGCCATATATGTGCCGATA
TATGTGATTTATAACAAGAATGAAGAAACTACGATAATTTACTCATATAGTAAATA
Found at i:70935 original size:18 final size:20
Alignment explanation
Indices: 70909--70945 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
70899 TGCTAGAGCA
*
70909 TCATTTGAA-CTT-CTTGGG
1 TCATATGAATCTTACTTGGG
70927 TCATATGAATCTTACTTGG
1 TCATATGAATCTTACTTGG
70946 CTTTTCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 3 0.19
20 5 0.31
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (20 bp):
TCATATGAATCTTACTTGGG
Found at i:73191 original size:79 final size:79
Alignment explanation
Indices: 73052--73197 Score: 211
Period size: 79 Copynumber: 1.8 Consensus size: 79
73042 TCACTAACAC
* *
73052 TCTATTGTGCTGAATGGAAAGAGATCGATGTCCCTAATTTACGTTTGAGACTCCAATTTTGTAAT
1 TCTATTGTGCTGAATGGAAAGAGATCGATGTCCCTAAATAACGTTTGAGACTCCAATTTTGTAAT
73117 GAATCTAGTGGGAA
66 GAATCTAGTGGGAA
* ** * * * *
73131 TCTATTGTGCTGAATGGAAGGAGATCGATGTCTTTAAATAAGGTTTGAGATTCGAGTTTTGTAAT
1 TCTATTGTGCTGAATGGAAAGAGATCGATGTCCCTAAATAACGTTTGAGACTCCAATTTTGTAAT
73196 GA
66 GA
73198 TTAATATATA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 58 1.00
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.36
Consensus pattern (79 bp):
TCTATTGTGCTGAATGGAAAGAGATCGATGTCCCTAAATAACGTTTGAGACTCCAATTTTGTAAT
GAATCTAGTGGGAA
Found at i:82508 original size:2 final size:2
Alignment explanation
Indices: 82501--82531 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
82491 ACTAACCATG
82501 TA 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 TA T
82532 CTTTATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:89533 original size:16 final size:16
Alignment explanation
Indices: 89512--89542 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
89502 CAGTGGAAAA
*
89512 AGGAAGTTTTAGGTTC
1 AGGAAGGTTTAGGTTC
89528 AGGAAGGTTTAGGTT
1 AGGAAGGTTTAGGTT
89543 TATAAATTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.03, G:0.35, T:0.35
Consensus pattern (16 bp):
AGGAAGGTTTAGGTTC
Found at i:91656 original size:22 final size:22
Alignment explanation
Indices: 91631--91673 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
91621 AATTTTGTAT
91631 GGAGAATA-CTAAGATTTCATAG
1 GGAGAATATC-AAGATTTCATAG
**
91653 GGAGGTTATCAAGATTTCATA
1 GGAGAATATCAAGATTTCATA
91674 TTGAGGTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.30
Consensus pattern (22 bp):
GGAGAATATCAAGATTTCATAG
Done.