Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016381.1 Corchorus capsularis cultivar CVL-1 contig16402, 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: 50488
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Found at i:3217 original size:23 final size:23
Alignment explanation
Indices: 3187--3241 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
3177 TAATTAGAAG
3187 GAAGCAAGACCGTGGTGCCCTCT
1 GAAGCAAGACCGTGGTGCCCTCT
3210 GAAGCAAGACCGTGGTGCCCTCT
1 GAAGCAAGACCGTGGTGCCCTCT
**
3233 TTAGCAAGA
1 GAAGCAAGA
3242 TTGCTGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.18
Consensus pattern (23 bp):
GAAGCAAGACCGTGGTGCCCTCT
Found at i:4434 original size:57 final size:58
Alignment explanation
Indices: 4367--4476 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 58
4357 TAGAAATATA
* *
4367 TTTGAC-AAAAAATGGTATAA-TCGAAAAACATAAAGTTTCCCCTTATTCGTGCGTTTG
1 TTTGACAAAAAAAAGGTATAATTCG-AAAACATAAAGTTTACCCTTATTCGTGCGTTTG
* *
4424 TTTGACAAAAAAAAGGTATAATTTGAAAACATAAAGTTTACTCTTATTCGTGC
1 TTTGACAAAAAAAAGGTATAATTCGAAAACATAAAGTTTACCCTTATTCGTGC
4477 TTTTATATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
57 6 0.13
58 39 0.83
59 2 0.04
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.34
Consensus pattern (58 bp):
TTTGACAAAAAAAAGGTATAATTCGAAAACATAAAGTTTACCCTTATTCGTGCGTTTG
Found at i:9421 original size:102 final size:102
Alignment explanation
Indices: 9245--9446 Score: 377
Period size: 102 Copynumber: 2.0 Consensus size: 102
9235 TGGGTTTTAG
9245 CCTTTGGCTTGCAAAGGGGATAAAGTAATCTAACCATGCCATTGATGTGCCATGAGATTCCATCT
1 CCTTTGGCTTGCAAAGGGGATAAAGTAATCTAACCATGCCATTGATGTGCCATGAGATTCCATCT
*
9310 TCATAGCCCTACCTCTTTTTTGCATGACTGGTTATCC
66 TCATAGCCCTAACTCTTTTTTGCATGACTGGTTATCC
* *
9347 CCTTTGGTTTGCAAAGGGGATAAAGTAATCTAACCATGCCATTGATGTGCCATGTGATTCCATCT
1 CCTTTGGCTTGCAAAGGGGATAAAGTAATCTAACCATGCCATTGATGTGCCATGAGATTCCATCT
9412 TCATAGCCCTAACTCTTTTTTGCATGACTGGTTAT
66 TCATAGCCCTAACTCTTTTTTGCATGACTGGTTAT
9447 TAAGCTCATA
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 97 1.00
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.35
Consensus pattern (102 bp):
CCTTTGGCTTGCAAAGGGGATAAAGTAATCTAACCATGCCATTGATGTGCCATGAGATTCCATCT
TCATAGCCCTAACTCTTTTTTGCATGACTGGTTATCC
Found at i:23395 original size:21 final size:21
Alignment explanation
Indices: 23369--23419 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
23359 TTGAAGCCGA
*
23369 AAATCATGTTGCCGTGTCCCC
1 AAATCATGTTACCGTGTCCCC
**
23390 AAATCATGTTACCGTGTCTGC
1 AAATCATGTTACCGTGTCCCC
23411 AAATCATGT
1 AAATCATGT
23420 AGATTGATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (21 bp):
AAATCATGTTACCGTGTCCCC
Found at i:24734 original size:29 final size:29
Alignment explanation
Indices: 24666--24757 Score: 105
Period size: 31 Copynumber: 3.1 Consensus size: 29
24656 GCCACGTGGT
* *
24666 ACGTGGCATTTTTG-ACACTTGGCGTGCC
1 ACGTGGCATTTTTGTACACATGGCATGCC
* * * *
24694 ATGTGTCCTTTTTGTACACGTGGCATGCC
1 ACGTGGCATTTTTGTACACATGGCATGCC
24723 ACGTGGCATTTTTTGATACACATGGCATGCC
1 ACGTGGCA-TTTTTG-TACACATGGCATGCC
24754 ACGT
1 ACGT
24758 CGGATGCCCG
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
28 11 0.21
29 17 0.33
30 6 0.12
31 18 0.35
ACGTcount: A:0.17, C:0.24, G:0.25, T:0.34
Consensus pattern (29 bp):
ACGTGGCATTTTTGTACACATGGCATGCC
Found at i:32684 original size:21 final size:21
Alignment explanation
Indices: 32660--32700 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
32650 AACTGGCGGG
32660 TTTTACTTGCTGAGGAAGGCA
1 TTTTACTTGCTGAGGAAGGCA
*
32681 TTTTGCTTGCTGAGGAAGGC
1 TTTTACTTGCTGAGGAAGGC
32701 GAACTCTTCT
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:0.20, C:0.15, G:0.32, T:0.34
Consensus pattern (21 bp):
TTTTACTTGCTGAGGAAGGCA
Found at i:32888 original size:17 final size:17
Alignment explanation
Indices: 32850--32882 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
32840 CTCATAGTAC
32850 CTAGGTAGCATGAGGTA
1 CTAGGTAGCATGAGGTA
*
32867 CTAGGTAGTATGAGGT
1 CTAGGTAGCATGAGGT
32883 GATAGGCTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.27
Consensus pattern (17 bp):
CTAGGTAGCATGAGGTA
Found at i:33660 original size:155 final size:156
Alignment explanation
Indices: 33234--33746 Score: 806
Period size: 156 Copynumber: 3.3 Consensus size: 156
33224 TTCTCACCTT
* * * *
33234 AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTTATTCTAAGTCTGAATG-AGCTGAAATTT
1 AAACTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAAGCTG--ATTT
* * * * *
33298 TGCCA--AG-GGTCTTAGAATATC-CACAT-GAGACTATGGAAAAAATTCTAAGTAAAACCGAAC
63 T-CCACCAGTAGACTTAGATTATCAC-CATAAAG-CTATGGGAAAAATTCTAAGTAAAACCGAAC
33358 TCTCTAGCATAGAGAAGTTGGTTTGACTCCTC
125 TCTCTAGCATAGAGAAGTTGGTTTGACTCCTC
33390 AAACTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAACGAAGCTGATTTTCC
1 AAACTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAACGAAGCTGATTTTCC
*
33455 ACCAGTAGACTTAGATTATCACCATAAAGCTATGGGGAAAATTCTAAGTAAAACCGAACTCTCTA
66 ACCAGTAGACTTAGATTATCACCATAAAGCTATGGGAAAAATTCTAAGTAAAACCGAACTCTCTA
33520 GCATAGAGAAGTTGGTTTGACTCCTC
131 GCATAGAGAAGTTGGTTTGACTCCTC
33546 AAACTGTCCTTAACTGAAAAACTAGCATAA-TTTTTCATTCTAAGTCCAACGAAGCTGATTTTCC
1 AAACTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAACGAAGCTGATTTTCC
*
33610 ACCAGTAGACTTAGATTATCACCATAAAGCTATGGGAAAAATTCTAAGTAAAACTGAACTCTCTA
66 ACCAGTAGACTTAGATTATCACCATAAAGCTATGGGAAAAATTCTAAGTAAAACCGAACTCTCTA
33675 GCATAGAGAAGTTGGTTTGACTCCTC
131 GCATAGAGAAGTTGGTTTGACTCCTC
* *
33701 AAACTGTCCTTAACTGAAAAACTAGAATAAGTTTTTCATACTAAGT
1 AAACTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCATTCTAAGT
33747 TTGTTTGAGA
Statistics
Matches: 336, Mismatches: 14, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
153 3 0.01
154 5 0.01
155 157 0.47
156 168 0.50
157 3 0.01
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (156 bp):
AAACTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAACGAAGCTGATTTTCC
ACCAGTAGACTTAGATTATCACCATAAAGCTATGGGAAAAATTCTAAGTAAAACCGAACTCTCTA
GCATAGAGAAGTTGGTTTGACTCCTC
Found at i:46787 original size:200 final size:200
Alignment explanation
Indices: 46068--46881 Score: 1049
Period size: 200 Copynumber: 4.1 Consensus size: 200
46058 ATTTTATCTC
* * * * * * * *
46068 AATACATATTCCTTAA-GGGACACATTTCAATCTTTAAA-CCCTGCACATGCAATCTGCTAAATT
1 AATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGGCACGTGCAGTCTGCTAAACT
* * * * *
46131 CGACTAACGGTGTATAGTATAATTTTTCTTATAAGATTATTATACAATCCACTGTCAGCGTAAAT
66 CCACTGACGGTGTATAATATAATTTTTCTTATAAGATTATTATACAATACACTGTCAGTGTAAAT
* * *
46196 TTTGGACTCCATAAGCGGGTTAAGAAGTTGACATATACC-CAATTTCATAATTAATTCAATATTT
131 TTTGGACTCCATAAGCAGGTTAAGAAGTTGACACATACCTC-ATTTCATAATTAATTAAATATTT
46260 AATATT
195 AATATT
* *
46266 AATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCC-GCACGTGCAGTTTGCTAAAAT
1 AATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGGCACGTGCAGTCTGCTAAACT
* * * * *
46330 CCACCGACGGTGTATTATATAATTTTT-TTATATGATTATTATACAACACGCTGTCAGTGTAAAT
66 CCACTGACGGTGTATAATATAATTTTTCTTATAAGATTATTATACAATACACTGTCAGTGTAAAT
** * * * **
46394 TTTAAACTCTATAAGCAGGTTAAGAAGTTGACACATACCTCATTTCATCATCAATTAAATAGATA
131 TTTGGACTCCATAAGCAGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATTTA
46459 ATA-T
196 ATATT
* * *
46463 --TACATATTCCTTAAAGGAACACATGTCAACCCTTAAA-CCCGGCACGTGCAGTCTGCTAAACT
1 AATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGGCACGTGCAGTCTGCTAAACT
* * * *
46525 CCACTTACGGTGTATAATATAACTTTTCTTATAAGATTATTATACAATAAACTTTCAGTGTAAAT
66 CCACTGACGGTGTATAATATAATTTTTCTTATAAGATTATTATACAATACACTGTCAGTGTAAAT
* * *
46590 TTTGGACTCCATAAGCGGGTTAAAAAGTTGACACATACCTCATTTCATAAGTAATTAAATATTTA
131 TTTGGACTCCATAAGCAGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATTTA
46655 ATATT
196 ATATT
* * * *
46660 AATACATATTTCTTAAGGGGCCACATGTCAACCCTTAAACCCCGGGACGT-CTAGTCTGCTAAAC
1 AATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGGCACGTGC-AGTCTGCTAAAC
* * * *
46724 TCGACTGACGGTGTATAATATAATTTTTCTTATAGGATTATTATGCAATACACAT-TTAGTGTAA
65 TCCACTGACGGTGTATAATATAATTTTTCTTATAAGATTATTATACAATACAC-TGTCAGTGTAA
* * *
46788 ATTTTGGACTCCATAAGCAGGTTAAGAAGTTGACAGATACCTCATTTCATATTTAATAAAATATT
129 ATTTTGGACTCCATAAGCAGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATT
46853 TAACT-TT
194 TAA-TATT
46860 AATACATATTCCCTAAGGGGAC
1 AATACATATTCCCTAAGGGGAC
46882 TGATCGGTCG
Statistics
Matches: 531, Mismatches: 73, Indels: 22
0.85 0.12 0.04
Matches are distributed among these distances:
194 3 0.01
195 76 0.14
196 90 0.17
197 2 0.00
198 103 0.19
199 93 0.18
200 162 0.31
201 2 0.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.34
Consensus pattern (200 bp):
AATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGGCACGTGCAGTCTGCTAAACT
CCACTGACGGTGTATAATATAATTTTTCTTATAAGATTATTATACAATACACTGTCAGTGTAAAT
TTTGGACTCCATAAGCAGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATTTA
ATATT
Found at i:49341 original size:201 final size:198
Alignment explanation
Indices: 48867--49410 Score: 725
Period size: 203 Copynumber: 2.7 Consensus size: 198
48857 TGGTCCGATC
* *
48867 AGGGACACATGTCAACCCTTAAACCCTGCACGCGCAGTCTGCTAAACTCCACTAACGGTGTATTG
1 AGGGACACATGTCAACCCTTAAACCC-GCACGTGCAGTCTGCTAAACTCCACTAACGGTGTATTA
* * * * *
48932 TATAATTGTTCTTATAGGAATATTATACAATAAACTGTCAATGCAAATTTTGGAGTACTCCATAA
65 TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTT-G-G-ACTCCATAA
* *
48997 GCGGGTTAAGAAGTTGACGCATACCCCATTTCATAATTAATTAAATATATTTAATATTAATACAT
127 GCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATT-AAGATATTTAATATTAATACAT
49062 ATTCCCTA
191 ATTCCCTA
* * *
49070 AGGGACACATGTCAACCCTTAAACCTCGCACGTGCAGTCTGCTAAACTCAACTGACGGTGTATAA
1 AGGGACACATGTCAACCCTTAAACC-CGCACGTGCAGTCTGCTAAACTCCACTAACGGTGTATTA
49135 TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAGAA-TTTGGACTCCATAAGC
65 TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTA-AATTTTGGACTCCATAAGC
* * *
49199 GGGTTAAGAAGTTGACATATACCTCATTTTCATAAATTAATT-AGATATTTAATATTAATACATC
129 GGGTTAAGAAGTTGACACATACCCCA-TTTCAT-AATTAATTAAGATATTTAATATTAATACATA
49263 TTCCCTA
192 TTCCCTA
* * * *
49270 AGGGGACACATGTCAACCCTTAAATTCCGCACGTGCAGTCCGCTAAAATCCACTTACGGTGTATT
1 A-GGGACACATGTCAACCCTTAAA-CCCGCACGTGCAGTCTGCTAAACTCCACTAACGGTGTATT
* * * * *
49335 ATATAATTTTTTCTTATAGAATTATTATACAACACGCTATCAGTGTAAATTTTTGAC-CCTATAA
64 ATATAA-TTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCC-ATAA
*
49399 GTGGGTTAAGAA
127 GCGGGTTAAGAA
49411 CACACATACT
Statistics
Matches: 305, Mismatches: 27, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
200 62 0.20
201 72 0.24
202 67 0.22
203 101 0.33
204 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (198 bp):
AGGGACACATGTCAACCCTTAAACCCGCACGTGCAGTCTGCTAAACTCCACTAACGGTGTATTAT
ATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGG
GTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAGATATTTAATATTAATACATATTCC
CTA
Found at i:49441 original size:2 final size:2
Alignment explanation
Indices: 49430--49459 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
49420 TCATTCATTC
49430 AT AT -T 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 A
49460 CTACATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.