Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014578.1 Corchorus capsularis cultivar CVL-1 contig14599, 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: 46830
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Found at i:11165 original size:177 final size:178
Alignment explanation
Indices: 10860--11216 Score: 470
Period size: 177 Copynumber: 2.0 Consensus size: 178
10850 ACCAATTTTT
* **
10860 GCTTCTTCAGTATCCCTTGCTCGGCTTCAAGATCCACCACTATTGAAGGTGCACGTTTTTTATCC
1 GCTTCTTCAGTATCCCTTGCTCGGCTTCAAGAT-C-CCACTATTGAAGGAGCACGACTTTTATCC
*
10925 TTCTTCAATGGAAGTTGATTATTTGCCAAATTCCTCCCATTCGCCTTTGGTTGCAACACTTCTTT
64 TTCTTCAATGGAAGTTGATCATTTGCCAAATTCCTCCCATTCGCCTTTGGTTGCAACACTTCTTT
* *
10990 CTCACCATTGGCTACCTT-TGTTCCTTCACCAAGGACAACATCCATCATTG
129 CTCAACATTGGCTA-CTTCTGTTCCTCCACCAAGGACAACATCCATCATTG
* * *
11040 GCTTCTTCAGTATCCCTTGCTTGGCTTCAGGAT-CCACTATTGAAGGAGCAGGACTTTTATCCTT
1 GCTTCTTCAGTATCCCTTGCTCGGCTTCAAGATCCCACTATTGAAGGAGCACGACTTTTATCCTT
* * * * * * *
11104 -TTCCATTGGACGTTGATCATTTTCCAAAATT-TTCTCATTTGCCTTTGGTTGCAAGACTTCTTT
66 CTT-CAATGGAAGTTGATCATTTGCC-AAATTCCTCCCATTCGCCTTTGGTTGCAACACTTCTTT
* * *
11167 CTCAACATTGGCTATTTCTGTTCCTCCTCCAAGGACACCATCCATCATTG
129 CTCAACATTGGCTACTTCTGTTCCTCCACCAAGGACAACATCCATCATTG
11217 TTTCTAAAAT
Statistics
Matches: 155, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
176 4 0.03
177 115 0.74
178 5 0.03
180 31 0.20
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.37
Consensus pattern (178 bp):
GCTTCTTCAGTATCCCTTGCTCGGCTTCAAGATCCCACTATTGAAGGAGCACGACTTTTATCCTT
CTTCAATGGAAGTTGATCATTTGCCAAATTCCTCCCATTCGCCTTTGGTTGCAACACTTCTTTCT
CAACATTGGCTACTTCTGTTCCTCCACCAAGGACAACATCCATCATTG
Found at i:13423 original size:1 final size:1
Alignment explanation
Indices: 13417--13445 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
13407 TCGATTATCT
13417 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
13446 CGAACCTACA
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:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:19506 original size:31 final size:31
Alignment explanation
Indices: 19468--19526 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
19458 AGGAAGTAAA
19468 TCCAATAGAATAGAATCAATATATATATTCT
1 TCCAATAGAATAGAATCAATATATATATTCT
19499 TCCAATAGAATAGAATCAATATATATAT
1 TCCAATAGAATAGAATCAATATATATAT
19527 CAGTATTGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (31 bp):
TCCAATAGAATAGAATCAATATATATATTCT
Found at i:20615 original size:6 final size:6
Alignment explanation
Indices: 20606--20631 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
20596 TGATGATGAT
20606 TCCGCC TCCGCC TCCGCC TCCGCC TC
1 TCCGCC TCCGCC TCCGCC TCCGCC TC
20632 TTCCTCTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.65, G:0.15, T:0.19
Consensus pattern (6 bp):
TCCGCC
Found at i:21242 original size:2 final size:2
Alignment explanation
Indices: 21235--21267 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
21225 AGTGGTCATC
*
21235 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21268 GTGAGATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 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):
AT
Found at i:21598 original size:2 final size:2
Alignment explanation
Indices: 21593--21713 Score: 215
Period size: 2 Copynumber: 60.5 Consensus size: 2
21583 ACCCCCATAT
**
21593 AC AC AC AC AC TG AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
21635 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
21677 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC GC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
21714 TATATATATA
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 113 1.00
ACGTcount: A:0.49, C:0.49, G:0.02, T:0.01
Consensus pattern (2 bp):
AC
Found at i:22027 original size:109 final size:109
Alignment explanation
Indices: 21831--22105 Score: 455
Period size: 109 Copynumber: 2.5 Consensus size: 109
21821 ACTATTATAG
* *
21831 TTTTATTCTACTAAAAATTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
21896 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
21945 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
22010 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
22054 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA
22106 TAGTTTTTTT
Statistics
Matches: 157, Mismatches: 3, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
108 7 0.04
109 124 0.79
110 3 0.02
111 2 0.01
114 21 0.13
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.49
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:22903 original size:2 final size:2
Alignment explanation
Indices: 22896--22930 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
22886 AGCGAAAAAC
22896 TA 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 TA T
22931 TTCCCAATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23782 original size:6 final size:6
Alignment explanation
Indices: 23771--23802 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
23761 AACACAAACT
23771 TTGGCA TTGGCA TTGGCA TTGGCA TTTGGCA T
1 TTGGCA TTGGCA TTGGCA TTGGCA -TTGGCA T
23803 GACATGAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.16, C:0.16, G:0.31, T:0.38
Consensus pattern (6 bp):
TTGGCA
Found at i:41343 original size:14 final size:14
Alignment explanation
Indices: 41324--41353 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
41314 GGTTATCTTG
41324 GAGGATCTGCAATT
1 GAGGATCTGCAATT
41338 GAGGATCTGCAATT
1 GAGGATCTGCAATT
41352 GA
1 GA
41354 TATAGGTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.27
Consensus pattern (14 bp):
GAGGATCTGCAATT
Found at i:41556 original size:22 final size:22
Alignment explanation
Indices: 41528--41578 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
41518 AACCACAGAT
41528 GTGTGCAGATATTGCGTCATTA
1 GTGTGCAGATATTGCGTCATTA
41550 GTGTGCAGATATTGCGTCATTA
1 GTGTGCAGATATTGCGTCATTA
41572 GTGTGCA
1 GTGTGCA
41579 TTCCGTCAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.22, C:0.14, G:0.29, T:0.35
Consensus pattern (22 bp):
GTGTGCAGATATTGCGTCATTA
Found at i:43789 original size:21 final size:21
Alignment explanation
Indices: 43763--43803 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
43753 GTTATGTTGA
43763 GGGAAGGTTCAAGGTGAGTGT
1 GGGAAGGTTCAAGGTGAGTGT
*
43784 GGGAAGGTTCTAGGTGAGTG
1 GGGAAGGTTCAAGGTGAGTG
43804 CGTCGTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.05, G:0.49, T:0.24
Consensus pattern (21 bp):
GGGAAGGTTCAAGGTGAGTGT
Found at i:44896 original size:21 final size:21
Alignment explanation
Indices: 44872--44914 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
44862 TCCAAATGAG
44872 AGTGCATTAAGGCCCAATAAC
1 AGTGCATTAAGGCCCAATAAC
* *
44893 AGTGCATTCAGGTCCAATAAC
1 AGTGCATTAAGGCCCAATAAC
44914 A
1 A
44915 TTCAGGCCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTGCATTAAGGCCCAATAAC
Found at i:44918 original size:16 final size:16
Alignment explanation
Indices: 44897--44929 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
44887 AATAACAGTG
*
44897 CATTCAGGTCCAATAA
1 CATTCAGGCCCAATAA
44913 CATTCAGGCCCAATAA
1 CATTCAGGCCCAATAA
44929 C
1 C
44930 CATATTAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.21
Consensus pattern (16 bp):
CATTCAGGCCCAATAA
Found at i:46736 original size:330 final size:326
Alignment explanation
Indices: 45659--46775 Score: 951
Period size: 330 Copynumber: 3.3 Consensus size: 326
45649 CTCAATTTTT
* ** * * * * *
45659 TTTTCTATGATTTTTGTGTCCAAAATTTGAGGGAAAAACTTTCGGGTCAATTTTTGCAAAATCTT
1 TTTTCTATGATTATTGTGTCCAAAA--AAAGAGAAAAACTTTAGGGTCATTTTTTTCAAAATTTT
* * * * * * * ** * * *
45724 AGCCTACATCGTGTACTGTTA-CGTCACGGTATTT-GCCTAAAAACGTGTTATAGGGTCTTGGCT
64 AGCCGAAATCGTGTAC--TAACCATAACGGT-TTTCGGCTAAAAACGCGTTACGGGGCCCTGGCA
* * *
45787 CAATTTTGTATGATCTTTGGCGTTAAGAGTCCTTGAAATTTTTATATTCATCTGACAAAATCTCA
126 CAATTTTGGATGATCTTTGGCGTTAAGAGTCCTTGAAATATTTATATTCATCTAACAAAATCTCA
* * * * * *
45852 -ACTATGTTAGATTTAAGGA-TT-TTTTTACGAGCATCATAATCTTTTTTTGATTTATTATCAGA
191 GAC-ATATTAGATTTAAGGATTTGTTTTTACGAGTATTAGAATCTTTTTTCGA-TT-TTATTAGA
* * * *
45914 AATTAATTTAGAAAAAATAGGAAAAACGATAATAGAGGCGTGAAAAACCCTTCAATCTTTCTGGT
253 AAATAA-TT-GAAAAAATAGGAAAAACGATAATAGA-GCGTGAAAAGCCCTTCAATC-TTCTTGC
45979 GTTGAAGTATATA
314 GTTGAAGTATATA
* * * *
45992 TTTTCTATGATTATTGTGTCCAAAAATTGAGACAAAAACTTTTGAGTCAAATTTTTTTTTTTTTT
1 TTTTCTATGATTATTGTGTCCAAAAA--AAGAGAAAAACTTTAGGGTC--A--------TTTTTT
* * * * *
46057 TCTAAATTTTAGTCGAAATCGTGTAATAACCATAACGGTTTTTTC-GCTAAAAAGGCGTTCCGGG
54 TCAAAATTTTAGCCGAAATCGTGTACTAACCATAACGG--TTTTCGGCTAAAAACGCGTTACGGG
* * * * * * * * * *
46121 GCCCCGACCCAGTTTTGGATGAAT-TTTTGCGTCAAGACTCATTAAAATATTTATATTCATCTCA
117 GCCCTGGCACAATTTTGGATG-ATCTTTGGCGTTAAGAGTCCTTGAAATATTTATATTCATCTAA
* * * *
46185 CAAAATCTCAGACATATTGGATTTAAGGATTGGTTTATACGAGT-TTCCGAATCTTTTTTCGATT
181 CAAAATCTCAGACATATTAGATTTAAGGATTTGTTTTTACGAGTATT-AGAATCTTTTTTCGATT
* * * *
46249 TAATTAGAAAATAATTAAAAAAAT-GGAAAAACGATATTAGAAGCGTGAAAGGCCCTTCAATCTT
245 TTATTAGAAAATAATTGAAAAAATAGGAAAAACGATAATAG-AGCGTGAAAAGCCCTTCAATCTT
* *
46313 TTTGATC-TTG-AGTTATAAA
309 CTTG--CGTTGAAG-TATATA
* * * * * * * ** *
46332 TTTTTTATTATTACTGTGGCAAAAAAAATCAGCGAAAAACTTTAGGGTCAATTTTTGGAAAATCT
1 TTTTCTATGATTATTGTGTC-CAAAAAA--AGAGAAAAACTTTAGGGTCATTTTTTTCAAAATTT
* * * * * * **
46397 CAGCCGAAATCGTGTACTAACCGTTACGGTTTTCGGCAAAAAACACGTTATGGGTTCCTGGCACA
63 TAGCCGAAATCGTGTACTAACCATAACGGTTTTCGGCTAAAAACGCGTTACGGGGCCCTGGCACA
* * * *
46462 ATTTCGGATGATCTTTGGCGTTAAGAGTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGT
128 ATTTTGGATGATCTTTGGCGTTAAGAGTCCTTGAAATATTTATATTCATCTAACAAAATCTCAGA
* * *
46527 CACATTAGATTTAAGAATTTGTTTTTACGAGTATTAGAATCTTTTTTCGATTTTATTAGAAAGTA
193 CATATTAGATTTAAGGATTTGTTTTTACGAGTATTAGAATCTTTTTTCGATTTTATTAGAAAATA
*
46592 ATTCGAAAAAATAGGAAAAACGATAATAGCAGCGTGAAAAGCCCTTCGATCTTCCTTGCGTTGAA
258 ATT-GAAAAAATAGGAAAAACGATAATAG-AGCGTGAAAAGCCCTTCAATCTT-CTTGCGTTGAA
46657 GTATATA
320 GTATATA
* * *
46664 TTTTCTATGATTATTGTCTCCAAAAAAAGAGAAAAACATTCGGGTCAGTTTTTTTCAAAATTTTA
1 TTTTCTATGATTATTGTGTCCAAAAAAAGAGAAAAACTTTAGGGTCA-TTTTTTTCAAAATTTTA
* * * *
46729 ACCGAAATCGTGTACTAATCATCACGGTTTTTGGCTAAAAACGCGTT
65 GCCGAAATCGTGTACTAACCATAACGGTTTTCGGCTAAAAACGCGTT
46776 CCGAGGCCTC
Statistics
Matches: 613, Mismatches: 134, Indels: 77
0.74 0.16 0.09
Matches are distributed among these distances:
329 24 0.04
330 180 0.29
331 50 0.08
332 59 0.10
333 45 0.07
335 1 0.00
339 7 0.01
340 57 0.09
341 30 0.05
342 8 0.01
343 122 0.20
344 9 0.01
345 21 0.03
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (326 bp):
TTTTCTATGATTATTGTGTCCAAAAAAAGAGAAAAACTTTAGGGTCATTTTTTTCAAAATTTTAG
CCGAAATCGTGTACTAACCATAACGGTTTTCGGCTAAAAACGCGTTACGGGGCCCTGGCACAATT
TTGGATGATCTTTGGCGTTAAGAGTCCTTGAAATATTTATATTCATCTAACAAAATCTCAGACAT
ATTAGATTTAAGGATTTGTTTTTACGAGTATTAGAATCTTTTTTCGATTTTATTAGAAAATAATT
GAAAAAATAGGAAAAACGATAATAGAGCGTGAAAAGCCCTTCAATCTTCTTGCGTTGAAGTATAT
A
Done.