Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005761.1 Corchorus capsularis cultivar CVL-1 contig05779, 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: 23982
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:1828 original size:198 final size:197
Alignment explanation
Indices: 1202--1865 Score: 850
Period size: 198 Copynumber: 3.4 Consensus size: 197
1192 GCTTTATAAT
* * * **
1202 AAGGATCATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGTGGGTTAAGAAGTTGA
1 AAGGATTATTATACAATACACTGTCAGTATAAATTTTGGACTCCATAAGCAGGTTAAGAAGTTGA
* * * *
1267 AACATACCACATTTCATAATTAATTAAATACTTAAAATTAATACATATTCCTTAAGGGGACACAT
66 CACATACCCCATTTCATAATTAATT-AATA-TTTAAATTAATACATATTCCCTAAGGGGACACAT
* * * *
1332 GTCAACCCCTAAACCGTGCACGTGCAGTATGCTAAACTCCACTGACGGTGTATTGTCTAATTTTT
129 GTCAACCCTTAAACCATGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTT
1397 -TTA
194 CTTA
* * * * * * *
1400 TAGGATTATTATACAACACACTATCATTATAAATTTTGGACTTCATAAGCACGTTAAGGAGTTGA
1 AAGGATTATTATACAATACACTGTCAGTATAAATTTTGGACTCCATAAGCAGGTTAAGAAGTTGA
* * * *
1465 CACATACCCTATTTCATAATTAATTAA-ATATAAAAT-ATACATATTCCCTAAGGGGATACATGT
66 CACATACCCCATTTCATAATTAATTAATATTTAAATTAATACATATTCCCTAAGGGGACACATGT
** ** ** * * *
1528 CAACCCTCCAACCCCGCGTGTGCAGTCTGCTAAACTCCGCTAACGGTATATTGTATAATTTTTCT
131 CAACCCTTAAACCATGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTCT
1593 TA
196 TA
* * * *
1595 CATGATTATTATACAATACACTGTCAGTATAAATTTTGGACGCCATAAGCTGGTTAAGAAGTTGA
1 AAGGATTATTATACAATACACTGTCAGTATAAATTTTGGACTCCATAAGCAGGTTAAGAAGTTGA
*
1660 CACATGCCCCATTTCATAATTAATTATATATTTAATATTAATACATATTCCCTAAGGGGACACAT
66 CACATACCCCATTTCATAATTAATTA-ATATTTAA-ATTAATACATATTCCCTAAGGGGACACAT
* * * *
1725 GTCAACTCTTAAATCATGCACGTGCAGTCTACTAAAATCCACTGACGG-GTATTGTATAATTTTT
129 GTCAACCCTTAAACCATGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTT
1789 CTTA
194 CTTA
* * *
1793 AAGGATTATTATACAATACATTGTCAGTGTAAATTTTGGACTCCATAAGCAGATTAAGAAGTTGA
1 AAGGATTATTATACAATACACTGTCAGTATAAATTTTGGACTCCATAAGCAGGTTAAGAAGTTGA
*
1858 TACATACC
66 CACATACC
1866 TCTATATTCC
Statistics
Matches: 393, Mismatches: 68, Indels: 10
0.83 0.14 0.02
Matches are distributed among these distances:
194 76 0.19
195 87 0.22
196 2 0.01
197 7 0.02
198 161 0.41
199 60 0.15
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (197 bp):
AAGGATTATTATACAATACACTGTCAGTATAAATTTTGGACTCCATAAGCAGGTTAAGAAGTTGA
CACATACCCCATTTCATAATTAATTAATATTTAAATTAATACATATTCCCTAAGGGGACACATGT
CAACCCTTAAACCATGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTCT
TA
Found at i:1894 original size:165 final size:164
Alignment explanation
Indices: 1704--2033 Score: 466
Period size: 168 Copynumber: 2.0 Consensus size: 164
1694 ATATTAATAC
* *
1704 ATATTCCCTAAGGGGACACATGTCAACTCTTAAA-T-CATGCACGTGCAGTCTACTAAAATCCAC
1 ATATTCCCTAAGGGGACACATGTCAACCCTTAAAGTACACGCACGTGCAGTCTACTAAAATCCAC
* * *
1767 TGACGGGTATTGTATAATTTTTCTTAAAGGATTATTATACAATACATTGTCAGTGTAAATTTTGG
66 TGAC-GG--TTGTATAAATTTTCTTAAAGGATTATTATACAATACACTGTCAGTGTAAATTTTGA
*
1832 ACTCCATAAGCAGATTAAGAAGTTGATACATACCTCT
128 ACTCCATAAGCAGATTAAGAAGTTGACACATACCTCT
* * * **
1869 ATATTCCCTAAGGGTACACATGTCAACCCTTAAAGTTAAACCCCGCACGTGCAGTCTGCTAAGCT
1 ATATTCCCTAAGGGGACACATGTCAACCCTTAAAG-T--A-CACGCACGTGCAGTCTACTAAAAT
**
1934 CCACTGACGGTTGTATAAATTTTCTTGTAGGATTATTATACAATACACTGTCAGTGTAAATTTTG
62 CCACTGACGGTTGTATAAATTTTCTTAAAGGATTATTATACAATACACTGTCAGTGTAAATTTTG
1999 AACTCCATAAGCAGATTAAGAAGTTGACACATACC
127 AACTCCATAAGCAGATTAAGAAGTTGACACATACC
2034 CCATTTTATG
Statistics
Matches: 146, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
165 32 0.22
167 1 0.01
168 84 0.58
170 2 0.01
171 27 0.18
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (164 bp):
ATATTCCCTAAGGGGACACATGTCAACCCTTAAAGTACACGCACGTGCAGTCTACTAAAATCCAC
TGACGGTTGTATAAATTTTCTTAAAGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACT
CCATAAGCAGATTAAGAAGTTGACACATACCTCT
Found at i:3366 original size:22 final size:21
Alignment explanation
Indices: 3333--3390 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
3323 CTTCTAAACT
*
3333 TTAAGTTTTTTAATAACCTTA
1 TTAAGTTTTTTAATAACCATA
**
3354 TTAAGTTTTTTTAGGAACCATA
1 TTAAG-TTTTTTAATAACCATA
*
3376 TTAAGGTTTTTAATA
1 TTAAGTTTTTTAATA
3391 TACAACCTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 12 0.40
22 18 0.60
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (21 bp):
TTAAGTTTTTTAATAACCATA
Found at i:3531 original size:21 final size:19
Alignment explanation
Indices: 3505--3545 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3495 TTTAGTTACT
3505 TTATTATAAAATTTTTAGAAA
1 TTATTAT-AAATTTTT-GAAA
*
3526 TTATTATGAATTTTTGAAA
1 TTATTATAAATTTTTGAAA
3545 T
1 T
3546 CATATTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 7 0.37
21 7 0.37
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (19 bp):
TTATTATAAATTTTTGAAA
Found at i:10758 original size:87 final size:86
Alignment explanation
Indices: 10607--10783 Score: 302
Period size: 87 Copynumber: 2.0 Consensus size: 86
10597 CACATCAATT
*
10607 CAAAACTCGTGGGTTAGGGAACAAATAAAAAAAATTGGAGAAGAAAACAATGTAAAATTAAAATA
1 CAAAACTCGTGGGTTAGAGAACAAATAAAAAAAATTGGAGAAGAAAACAATGTAAAATTAAAATA
*
10672 GACAAAAGTGAGAAAACAACC
66 GACAAAAGTGAGAAAACAAAC
10693 CAAAAGCTCGTGGGTTAGAGAACAAATAAAAAAAAATTGGAGAAGAAAACAATGTAAAATT-AAA
1 CAAAA-CTCGTGGGTTAGAGAACAAAT-AAAAAAAATTGGAGAAGAAAACAATGTAAAATTAAAA
*
10757 TAGACAAAAGTGAGAGAACAAAC
64 TAGACAAAAGTGAGAAAACAAAC
10780 CAAA
1 CAAA
10784 GAATAGTCAT
Statistics
Matches: 86, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
86 5 0.06
87 48 0.56
88 33 0.38
ACGTcount: A:0.56, C:0.10, G:0.19, T:0.15
Consensus pattern (86 bp):
CAAAACTCGTGGGTTAGAGAACAAATAAAAAAAATTGGAGAAGAAAACAATGTAAAATTAAAATA
GACAAAAGTGAGAAAACAAAC
Found at i:11680 original size:5 final size:5
Alignment explanation
Indices: 11670--11702 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
11660 TCCTTTTAAG
11670 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAG
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAG
11703 GGTGTTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:13403 original size:13 final size:13
Alignment explanation
Indices: 13385--13413 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
13375 ATTAATTAAG
13385 GGGATTTCATCAT
1 GGGATTTCATCAT
13398 GGGATTTCATCAT
1 GGGATTTCATCAT
13411 GGG
1 GGG
13414 GCCTAATACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.34
Consensus pattern (13 bp):
GGGATTTCATCAT
Found at i:13739 original size:10 final size:10
Alignment explanation
Indices: 13726--13751 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
13716 AAATCTCGAT
13726 ATATCCGTAA
1 ATATCCGTAA
13736 ATATCCGTAA
1 ATATCCGTAA
13746 ATATCC
1 ATATCC
13752 ATATTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:16019 original size:18 final size:18
Alignment explanation
Indices: 15996--16031 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
15986 TAATATCATC
15996 CAGCAATATTGTTCTTAA
1 CAGCAATATTGTTCTTAA
16014 CAGCAATATTGTTCTTAA
1 CAGCAATATTGTTCTTAA
16032 TTCATTTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (18 bp):
CAGCAATATTGTTCTTAA
Found at i:21485 original size:16 final size:16
Alignment explanation
Indices: 21464--21494 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
21454 GTGTACATTC
21464 ATAAAATTTATTGAGA
1 ATAAAATTTATTGAGA
21480 ATAAAATTTATTGAG
1 ATAAAATTTATTGAG
21495 TAATGTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (16 bp):
ATAAAATTTATTGAGA
Found at i:23091 original size:14 final size:14
Alignment explanation
Indices: 23044--23093 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
23034 TTCAATAACT
23044 ATTAATTATAAGTA
1 ATTAATTATAAGTA
** * *
23058 ATTTTTTTTGAAGAA
1 ATTAATTAT-AAGTA
23073 ATTAATTATAAGTA
1 ATTAATTATAAGTA
23087 ATTAATT
1 ATTAATT
23094 GGGTTTAGCT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 17 0.63
15 10 0.37
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (14 bp):
ATTAATTATAAGTA
Found at i:23402 original size:20 final size:20
Alignment explanation
Indices: 23359--23399 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
23349 AAAAAGCTAC
*
23359 TAAAATCTTAAAATATTATT
1 TAAAATCTTAAAAGATTATT
*
23379 TAAAATCTTATAAGACTTATT
1 TAAAATCTTAAAAGA-TTATT
23400 AAAGAAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (20 bp):
TAAAATCTTAAAAGATTATT
Found at i:23930 original size:21 final size:22
Alignment explanation
Indices: 23904--23960 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
23894 CAAAAGGTGT
* *
23904 TAAAAAAT-TTTATAAGGTTAC
1 TAAAAAATGCTTATAAGATTAC
23925 TAAAAAAATGCTTATAAGATTAC
1 T-AAAAAATGCTTATAAGATTAC
*
23948 T-AAAAGTGCTTAT
1 TAAAAAATGCTTAT
23961 GAACTTCCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 12 0.39
22 7 0.23
23 12 0.39
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (22 bp):
TAAAAAATGCTTATAAGATTAC
Found at i:23933 original size:22 final size:23
Alignment explanation
Indices: 23905--23952 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
23895 AAAAGGTGTT
* *
23905 AAAAAAT-TTTATAAGGTTACTA
1 AAAAAATGCTTATAAGATTACTA
23927 AAAAAATGCTTATAAGATTACTA
1 AAAAAATGCTTATAAGATTACTA
23950 AAA
1 AAA
23953 GTGCTTATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.31
Consensus pattern (23 bp):
AAAAAATGCTTATAAGATTACTA
Done.