Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012838.1 Corchorus capsularis cultivar CVL-1 contig12859, 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: 153662
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:8865 original size:7 final size:7
Alignment explanation
Indices: 8853--8877 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
8843 ATAAAGCAAT
8853 TAAACCC
1 TAAACCC
8860 TAAACCC
1 TAAACCC
8867 TAAACCC
1 TAAACCC
8874 TAAA
1 TAAA
8878 AATGGACGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAACCC
Found at i:17439 original size:67 final size:67
Alignment explanation
Indices: 17331--17469 Score: 278
Period size: 67 Copynumber: 2.1 Consensus size: 67
17321 TAAACCTTAC
17331 AAAATATTGAAAGGGGTGAAAAAGAGGCAAATGCAGACAATCTTCCCTGACCTACTGGTATACTA
1 AAAATATTGAAAGGGGTGAAAAAGAGGCAAATGCAGACAATCTTCCCTGACCTACTGGTATACTA
17396 AG
66 AG
17398 AAAATATTGAAAGGGGTGAAAAAGAGGCAAATGCAGACAATCTTCCCTGACCTACTGGTATACTA
1 AAAATATTGAAAGGGGTGAAAAAGAGGCAAATGCAGACAATCTTCCCTGACCTACTGGTATACTA
17463 AG
66 AG
17465 AAAAT
1 AAAAT
17470 GCAATGCAGG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 72 1.00
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.21
Consensus pattern (67 bp):
AAAATATTGAAAGGGGTGAAAAAGAGGCAAATGCAGACAATCTTCCCTGACCTACTGGTATACTA
AG
Found at i:28622 original size:2 final size:2
Alignment explanation
Indices: 28615--28640 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28605 CTTTTTAATC
28615 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
28641 CTTAATCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28894 original size:9 final size:9
Alignment explanation
Indices: 28882--28922 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
28872 TAAAAATAAT
28882 TATTATATA
1 TATTATATA
28891 TATTATATA
1 TATTATATA
*
28900 TATCATAAATA
1 TAT--TATATA
28911 TATTATATA
1 TATTATATA
28920 TAT
1 TAT
28923 AATACCATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 20 0.71
11 8 0.29
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (9 bp):
TATTATATA
Found at i:76607 original size:5 final size:5
Alignment explanation
Indices: 76593--76623 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
76583 CTATAGGAAG
*
76593 TATGT AATGT TATGT TATGT TATGT TATGT T
1 TATGT TATGT TATGT TATGT TATGT TATGT T
76624 TCTTCATTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (5 bp):
TATGT
Found at i:81325 original size:15 final size:15
Alignment explanation
Indices: 81305--81334 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
81295 ACCTTGGAAG
81305 CCAGATCATTATTAT
1 CCAGATCATTATTAT
81320 CCAGATCATTATTAT
1 CCAGATCATTATTAT
81335 TCATTAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (15 bp):
CCAGATCATTATTAT
Found at i:88365 original size:15 final size:15
Alignment explanation
Indices: 88342--88384 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
88332 ATAACATGGG
88342 TTTGGTTTGGTTTGT
1 TTTGGTTTGGTTTGT
* *
88357 TTTGTTTTGTTTTGT
1 TTTGGTTTGGTTTGT
88372 TATTCGGTTTGGT
1 T-TT-GGTTTGGT
88385 CTTTTTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 14 0.64
16 2 0.09
17 6 0.27
ACGTcount: A:0.02, C:0.02, G:0.28, T:0.67
Consensus pattern (15 bp):
TTTGGTTTGGTTTGT
Found at i:89187 original size:22 final size:22
Alignment explanation
Indices: 89160--89201 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
89150 AATTTAATTC
89160 TATATAATTTTATTACAAAAAA
1 TATATAATTTTATTACAAAAAA
* *
89182 TATATAATTTTTTTTCAAAA
1 TATATAATTTTATTACAAAA
89202 CATGATTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
TATATAATTTTATTACAAAAAA
Found at i:89963 original size:2 final size:2
Alignment explanation
Indices: 89956--89985 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
89946 GTAAAATAGC
89956 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
89986 GCATATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:90557 original size:25 final size:22
Alignment explanation
Indices: 90506--90558 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 22
90496 ACTCTCCAAT
90506 GAAATAATGTACTTAAGAAAAA
1 GAAATAATGTACTTAAGAAAAA
* *
90528 AAAATAATGTACTAACTAGGAAAAA
1 GAAATAATGTACT---TAAGAAAAA
90553 GAAATA
1 GAAATA
90559 TAAAAGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 12 0.48
25 13 0.52
ACGTcount: A:0.60, C:0.06, G:0.13, T:0.21
Consensus pattern (22 bp):
GAAATAATGTACTTAAGAAAAA
Found at i:92560 original size:99 final size:102
Alignment explanation
Indices: 92368--92560 Score: 275
Period size: 99 Copynumber: 1.9 Consensus size: 102
92358 TCGTAGGTGA
* * * *
92368 AGAAGGAGGCCCGTATGGGTCTAGACCATCCACTGGCCATGATCGGTTGGCCATGCGAAAGATCT
1 AGAAGGAGGCCCATATGGGTCTAGACCATCCACTGGCCATGATCAGCTGGCCATGCGAAAGACCT
* *
92433 AAACGCTTCTTATCAGAAACATCGATGATCTTGAACC
66 AAACGCTCCTTATCAGAAACATCAATGATCTTGAACC
*
92470 AGAAGGAGGCCCATATGGGTCTAGACTATCCACTGG-C-T-ATCAGCTGGCCATGCGAAAGACCT
1 AGAAGGAGGCCCATATGGGTCTAGACCATCCACTGGCCATGATCAGCTGGCCATGCGAAAGACCT
* * *
92532 AAACGCTCCTTATCGGAAATATTAATGAT
66 AAACGCTCCTTATCAGAAACATCAATGAT
92561 TGAACCGGTA
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
99 45 0.56
100 1 0.01
101 1 0.01
102 34 0.42
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.23
Consensus pattern (102 bp):
AGAAGGAGGCCCATATGGGTCTAGACCATCCACTGGCCATGATCAGCTGGCCATGCGAAAGACCT
AAACGCTCCTTATCAGAAACATCAATGATCTTGAACC
Found at i:92928 original size:126 final size:126
Alignment explanation
Indices: 92718--92971 Score: 472
Period size: 126 Copynumber: 2.0 Consensus size: 126
92708 ATATATATAC
*
92718 GATTGGGACGGGGTAGCGGTTATATATGATATATATACGATTGGGACGGGGTAGCGGCTAGGGTT
1 GATTGGGACGAGGTAGCGGTTATATATGATATATATACGATTGGGACGGGGTAGCGGCTAGGGTT
* *
92783 ACAGTATAATGGGCTTAAGTTGACTAATGCTTGTGCTTCAAACCTTTTACAAAGCAGACAT
66 ACAGTATAATGGGCCTAAGTTGACTAATGCTTGTGCTTCAAACCATTTACAAAGCAGACAT
92844 GATTGGGACGAGGTAGCGGTTATATATGATATATATACGATTGGGACGGGGTAGCGGCTAGGGTT
1 GATTGGGACGAGGTAGCGGTTATATATGATATATATACGATTGGGACGGGGTAGCGGCTAGGGTT
*
92909 ACAGTATAATGGGCCTAAGTTGACTAATGCTTGTGCTTCAAATCATTTACAAAGCAGACAT
66 ACAGTATAATGGGCCTAAGTTGACTAATGCTTGTGCTTCAAACCATTTACAAAGCAGACAT
92970 GA
1 GA
92972 GTGATCTGAG
Statistics
Matches: 124, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 124 1.00
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (126 bp):
GATTGGGACGAGGTAGCGGTTATATATGATATATATACGATTGGGACGGGGTAGCGGCTAGGGTT
ACAGTATAATGGGCCTAAGTTGACTAATGCTTGTGCTTCAAACCATTTACAAAGCAGACAT
Found at i:93775 original size:2 final size:2
Alignment explanation
Indices: 93770--93802 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
93760 ATATGTGTGC
93770 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
93803 GTATGAAATG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:94629 original size:3 final size:3
Alignment explanation
Indices: 94623--94649 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
94613 ACTCATCATC
94623 CAG CAG CAG CAG CAG CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG
94650 GGTCGTGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:97319 original size:30 final size:30
Alignment explanation
Indices: 97266--97332 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
97256 CTGTGTCTTC
* *
97266 TCATCTGACAAAACAAACCCATCATCGTCA
1 TCATCTGACAAAACAAAACCATCATCATCA
* *
97296 TCATC-GACAAAACAAAAATCATCATCATCT
1 TCATCTGACAAAAC-AAAACCATCATCATCA
97326 TCATCTG
1 TCATCTG
97333 TGTCGGATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 8 0.26
30 22 0.71
31 1 0.03
ACGTcount: A:0.40, C:0.30, G:0.06, T:0.24
Consensus pattern (30 bp):
TCATCTGACAAAACAAAACCATCATCATCA
Found at i:109609 original size:1 final size:1
Alignment explanation
Indices: 109603--109632 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
109593 GGCTTCGAGG
109603 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
109633 AAAGGACGTT
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:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:117632 original size:1 final size:1
Alignment explanation
Indices: 117626--117654 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
117616 TTACAAGAGT
117626 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
117655 CCCAAATCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:127645 original size:3 final size:3
Alignment explanation
Indices: 127637--127671 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
127627 CCCACTTTCT
127637 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
127672 GTCCAAATTA
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:129864 original size:15 final size:16
Alignment explanation
Indices: 129844--129874 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
129834 AAAGAAGTCT
129844 TTGTTACTGTT-ATTG
1 TTGTTACTGTTCATTG
129859 TTGTTACTGTTCATTG
1 TTGTTACTGTTCATTG
129875 GCTTTGAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.58
Consensus pattern (16 bp):
TTGTTACTGTTCATTG
Found at i:152346 original size:31 final size:31
Alignment explanation
Indices: 152311--152375 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
152301 TTGGGTTATC
***
152311 AGTCTCCAAATGTTTAGATCTTGGATGTTTG
1 AGTCTCCAAATCCCTAGATCTTGGATGTTTG
152342 AGTCTCCAAATCCCTAGATCTTGGATGTTTG
1 AGTCTCCAAATCCCTAGATCTTGGATGTTTG
152373 AGT
1 AGT
152376 TAGTTCAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (31 bp):
AGTCTCCAAATCCCTAGATCTTGGATGTTTG
Done.