Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009384.1 Corchorus capsularis cultivar CVL-1 contig09405, 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: 11753
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:232 original size:11 final size:11
Alignment explanation
Indices: 216--241 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
206 CGTTTTTAGC
216 AAATTGCCACG
1 AAATTGCCACG
227 AAATTGCCACG
1 AAATTGCCACG
238 AAAT
1 AAAT
242 ATTTCTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.19
Consensus pattern (11 bp):
AAATTGCCACG
Found at i:1146 original size:331 final size:329
Alignment explanation
Indices: 227--1972 Score: 2678
Period size: 331 Copynumber: 5.3 Consensus size: 329
217 AATTGCCACG
* *
227 AAATTGCCACGAAATATTTCTCCTCAATTTTTGGCTAAAAGT-CTCATAAAAAATATGTAATTCA
1 AAATTGCCACGAAAGATTTCTCCTCAATTTTTGGCTAAAA-TACTCATAAAAAATATATAATTCA
*
291 ACGCCAAAAAGATTGAAGGGATTTTAACGTTTCTAATATCGTTCTTCCTA-TTTTCCAAATTAAT
65 ACGCCAAAAAGATTGAAGGGATTTTAACGTTTCTAATATCGTTCTTCCTATTTTTCCGAATTAAT
* *
355 TTCTAATTAAATCAAATCAAGATTCACATGCTCGGAAAAACAAATCCTTAAGTCCAATTTGACTG
130 TTCTAATTAAATCAAAACAAGATTCACATGCTCGGAAAAACAAATCCTTAAGTCCAATGTGACTG
* *
420 AGATTGGATTAGAGGAATATAGATATTTCTAGTAGTCTCGGAGCCAAAAATCATGCAAAATTGAG
195 AGATTTGATTAGATGAATATAGATATTTCTAGTAGTCTCGGAGCCAAAAATCATGCAAAATTGAG
* *
485 CCGTGTACCCGAAACGCGTTTTTACTTTTTAGCCAAAACCTTGATGGCTAGTACACGATTTCGGC
260 CCGGGTACCCG-AACGCG-------TTTTTAGCCAAAACCGTGATGGCTAGTACACGATTTCGGC
550 TAAAATTTTGTAA
317 TAAAATTTTGTAA
563 AAATTGCCACGAAAGATTTCTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAA
1 AAATTGCCACGAAAGATTTCTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAA
* *
628 TGCCAAAAAGATTGAAGGGATTTTAACGTTTCTAATATCGTTTTTCCTATTTTTCCG-ATTAATT
66 CGCCAAAAAGATTGAAGGGATTTTAACGTTTCTAATATCGTTCTTCCTATTTTTCCGAATTAATT
* * *
692 TCTAATTAAATCAAAACAAGTTTCAGATGCTCGGAAAAACAAATGCTTAAGTCCAATGTGACTGA
131 TCTAATTAAATCAAAACAAGATTCACATGCTCGGAAAAACAAATCCTTAAGTCCAATGTGACTGA
757 GATTTGATTAGATGAATATAGATATTTCTAGTAGTCTCGGAG-CACAAAATCATGCAAAATTGAG
196 GATTTGATTAGATGAATATAGATATTTCTAGTAGTCTCGGAGCCA-AAAATCATGCAAAATTGAG
*
821 CCGGGTACCCAGAACACGTTTTTAGCCAAAACCGTGATGGCTAGTACACGATTTCGGCTAAAATT
260 CCGGGTACCC-GAACGCGTTTTTAGCCAAAACCGTGATGGCTAGTACACGATTTCGGCTAAAATT
886 TTGTAA
324 TTGTAA
892 AAATTGCCACGAAAGATTTCTCCTCAATTTTTGGCTAAAAGT-CTCATAAAAAAATATATAATTC
1 AAATTGCCACGAAAGATTTCTCCTCAATTTTTGGCTAAAA-TACTCAT-AAAAAATATATAATTC
* *
956 AACGCCAAAAAGATTGAAAGGATTTTAACGTTTCTAATATCGTTCTTCCTATTTTTCTGAATTAA
64 AACGCCAAAAAGATTGAAGGGATTTTAACGTTTCTAATATCGTTCTTCCTATTTTTCCGAATTAA
*
1021 TTTCTAATTAAATCAAAACAAGA-TCTACATGCTCGGAAAAACAAATCCTTAAGTCCAACGTGAC
129 TTTCTAATTAAATCAAAACAAGATTC-ACATGCTCGGAAAAACAAATCCTTAAGTCCAATGTGAC
* *
1085 TGAGATTTGATTAGATGAATATAGATATATCAAGTAGTACT-GGAGCCAAAAATCATGCAAAATT
193 TGAGATTTGATTAGATGAATATAGATATTTCTAGTAGT-CTCGGAGCCAAAAATCATGCAAAATT
* *
1149 GAGCTGGGTACCCGAAACGCATTTTTAGCCAAAACCGTGATGGCTAGTACACGATTTCGGCTAAA
257 GAGCCGGGTACCCG-AACGCGTTTTTAGCCAAAACCGTGATGGCTAGTACACGATTTCGGCTAAA
1214 ATTTTGTAA
321 ATTTTGTAA
* * *
1223 AAGTTGCCACGAAAGATTTCTCCTCAATTTTTGCCTAAAATACTAATAAAAAATATATAATTCAA
1 AAATTGCCACGAAAGATTTCTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAA
* * *
1288 TGCCAAAAAGATTGAAGGGATTTTAACGTTTCTAATATCGTTTTTCCCATTTTTTCCGAATTAAT
66 CGCCAAAAAGATTGAAGGGATTTTAACGTTTCTAATATCGTTCTTCCTA-TTTTTCCGAATTAAT
* * * *
1353 CTTCTAATTAAATCAAAACAAGTTTCAGATGCTC-GAAAAAAAAATCCTTAAGTCCAATGTGACC
130 -TTCTAATTAAATCAAAACAAGATTCACATGCTCGGAAAAACAAATCCTTAAGTCCAATGTGACT
* * *
1417 GAGATTTCATTAGATGAATATATATATTTCTAGTAGTCTCGGAGCAAAAAATCATGCAAAATTGA
194 GAGATTTGATTAGATGAATATAGATATTTCTAGTAGTCTCGGAGCCAAAAATCATGCAAAATTGA
** *
1482 GCCGGGTACATGGAACGCGTTTTTAGCCAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAT
259 GCCGGGTAC-CCGAACGCGTTTTTAGCCAAAACCGTGATGGCTAGTACACGATTTCGGCTAAAAT
*
1547 TTTGTAC
323 TTTGTAA
1554 AAATTGCCACGAAAGATTTCTCCTCAATTTTTGGCTAAAAGT-CTCATAAAAAATATATAATTCA
1 AAATTGCCACGAAAGATTTCTCCTCAATTTTTGGCTAAAA-TACTCATAAAAAATATATAATTCA
* * *
1618 ACGCCAAAAAGATTGAAGGGATTTTAACGTTTCTAATATCGTTCTTCTTATTTTTCCAAATTAAA
65 ACGCCAAAAAGATTGAAGGGATTTTAACGTTTCTAATATCGTTCTTCCTATTTTTCCGAATTAAT
* * * *
1683 TTCTTATTAAACCAAAACAAGATTGAAATGCTCGGAAAAACAAATCCTTAAGTCCAATGTGACTG
130 TTCTAATTAAATCAAAACAAGATTCACATGCTCGGAAAAACAAATCCTTAAGTCCAATGTGACTG
* **
1748 AGATTTGATTAGATGAATATAGATA-TTCAAGTAGTCTCAAAGCCAAAAATCATGC---A---AG
195 AGATTTGATTAGATGAATATAGATATTTCTAGTAGTCTCGGAGCCAAAAATCATGCAAAATTGAG
* * * * * *
1806 CTGGGTACCCGGAACGTGTTTTTTGTCAAAACCGTGATGGTTAGTAGACGATTTCGGCTAAAATT
260 CCGGGTACCC-GAACGCGTTTTTAGCCAAAACCGTGATGGCTAGTACACGATTTCGGCTAAAATT
*
1871 TTGCAA
324 TTGTAA
*
1877 AAATTGCCACGAAAGATTTCTCCTCAATTTTTGGTTAAAATACTCATAAAAAATATATAATTCAA
1 AAATTGCCACGAAAGATTTCTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAA
1942 CGCCAAAAAGATTGAAGGGATTTTAACGTTT
66 CGCCAAAAAGATTGAAGGGATTTTAACGTTT
1973 TAAAATTTTA
Statistics
Matches: 1305, Mismatches: 84, Indels: 55
0.90 0.06 0.04
Matches are distributed among these distances:
322 1 0.00
323 156 0.12
326 1 0.00
329 151 0.12
330 206 0.16
331 496 0.38
332 34 0.03
333 2 0.00
335 3 0.00
336 248 0.19
337 7 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (329 bp):
AAATTGCCACGAAAGATTTCTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAA
CGCCAAAAAGATTGAAGGGATTTTAACGTTTCTAATATCGTTCTTCCTATTTTTCCGAATTAATT
TCTAATTAAATCAAAACAAGATTCACATGCTCGGAAAAACAAATCCTTAAGTCCAATGTGACTGA
GATTTGATTAGATGAATATAGATATTTCTAGTAGTCTCGGAGCCAAAAATCATGCAAAATTGAGC
CGGGTACCCGAACGCGTTTTTAGCCAAAACCGTGATGGCTAGTACACGATTTCGGCTAAAATTTT
GTAA
Found at i:2172 original size:3 final size:3
Alignment explanation
Indices: 2164--2197 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2154 ATGGTATAGT
2164 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2198 GATAAGATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2204 original size:5 final size:5
Alignment explanation
Indices: 2194--2240 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
2184 AATAATAATA
*
2194 ATAAG ATAAG ATAAT ATAAG AT-AG -TAAG ATAAG ATCAA- ATAAG ATAA
1 ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG AT-AAG ATAAG ATAA
2241 AATTTAACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
3 1 0.03
4 6 0.17
5 27 0.75
6 2 0.06
ACGTcount: A:0.60, C:0.02, G:0.15, T:0.23
Consensus pattern (5 bp):
ATAAG
Found at i:2221 original size:23 final size:23
Alignment explanation
Indices: 2195--2239 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2185 ATAATAATAA
2195 TAAGATAAGAT-AATATAAGATAG
1 TAAGATAAGATCAA-ATAAGATAG
2218 TAAGATAAGATCAAATAAGATA
1 TAAGATAAGATCAAATAAGATA
2240 AAATTTAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.58, C:0.02, G:0.16, T:0.24
Consensus pattern (23 bp):
TAAGATAAGATCAAATAAGATAG
Found at i:7773 original size:70 final size:67
Alignment explanation
Indices: 7645--7780 Score: 184
Period size: 70 Copynumber: 2.0 Consensus size: 67
7635 TTTACTTGAA
* ** * *
7645 ATGCATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATTAATGGTGTTTCTACCATTTTTTT
1 ATGCATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATTAATGATACTCCCACCATTTTTTT
7710 CT
66 CT
7712 ATGCATTGTCTTTATATATGCTAATTTTAGCA-TTGAGATGTAATTAATGATACTCCCACCATTT
1 ATGCATTGTC-TT-TATATG-TAATTTTAGCATTTG-GATGTAATTAATGATACTCCCACCATTT
7776 TTTTC
62 TTTTC
7781 CTTAGTTGTT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
67 10 0.17
68 2 0.03
69 9 0.15
70 39 0.65
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (67 bp):
ATGCATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATTAATGATACTCCCACCATTTTTTT
CT
Done.