Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001313.1 Corchorus capsularis cultivar CVL-1 contig01313, 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: 8035
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Found at i:1740 original size:19 final size:19
Alignment explanation
Indices: 1716--1762 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
1706 CAATATATTT
1716 AAATTTTAAATGAAAATTA
1 AAATTTTAAATGAAAATTA
1735 AAATTTTAAATGAAAATTA
1 AAATTTTAAATGAAAATTA
1754 AAATTTTAA
1 AAATTTTAA
1763 GCAACTCACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (19 bp):
AAATTTTAAATGAAAATTA
Found at i:2017 original size:16 final size:15
Alignment explanation
Indices: 1996--2030 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1986 ATATTTAAAT
1996 GATCCGAATCCGAAAA
1 GATCCGAATCC-AAAA
2012 GATCCGAATCCAAAA
1 GATCCGAATCCAAAA
2027 -ATCC
1 GATCC
2031 AAAACTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 4 0.21
16 11 0.58
ACGTcount: A:0.43, C:0.29, G:0.14, T:0.14
Consensus pattern (15 bp):
GATCCGAATCCAAAA
Found at i:4980 original size:6 final size:6
Alignment explanation
Indices: 4969--5003 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
4959 CACCAGATAC
4969 ATTCAT ATTCAT ATTCAATT ATTCAT ATTCAT ATT
1 ATTCAT ATTCAT ATTC-A-T ATTCAT ATTCAT ATT
5004 TCTATAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 20 0.74
7 2 0.07
8 5 0.19
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (6 bp):
ATTCAT
Found at i:6690 original size:325 final size:326
Alignment explanation
Indices: 5944--6694 Score: 838
Period size: 328 Copynumber: 2.3 Consensus size: 326
5934 ATATTTTTTG
*
5944 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * * * ** *
6009 GAGGCTGAGATTTGATTAGATGAATAAAAATATTTCTAGGAGTCTCGGTGCCAAAAATTATACAA
66 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCACCAAAAATCATACAA
* * *
6074 ACAGAGCCGTGGCTCGGAACATGTTTGCAGCCAAAAACTATGATGGTTAGTACACGATTTCGGCT
131 ACAGAGCCGTGGCTCAGAACACGTTTGCAGCCAAAAACCATGATGG-T-GTACACGATTTCGGCT
* * * * * *
6139 AAAATTTTGTAAAAATTTACCCAAAAGATACTTCCTAAATTTTTGGCTAAAATATAAGAAAATAT
194 AAAATTTTGCAAAAATTGACCCAAAAGATACTTCCTAAATTTCTAGCGAAAATATAAAAAAATAT
* * * * * *
6204 ATAATTCGAAGTTAAAAAGATTGAAGGAATTTTAGTGCTTCTAATATTGTTTTTCTTATTTCTTT
259 ATAATTCAAAGTCAAAAAGATTGAAAGAATTTTAGCGCTGCT-ATATTGTTTTTCCTATTTCTTT
6269 CCGA
323 CCGA
* *
6273 AA-TAATTTCTTATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* *
6337 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAA
66 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCACCAAAAATCATAC-A
* * ** ** * *
6402 AACTGAGCCG-GGTTTCAGAATGCGTTTTTAGCCAAAAACCGTGATGG-GTACACGATTTTGGCT
130 AACAGAGCCGTGG-CTCAGAACACGTTTGCAGCCAAAAACCATGATGGTGTACACGATTTCGGCT
** * *
6465 AAAATTTTGCAAAAATTGACCTGAAAGAT-TTTCCTCAATTTCTAGCGAAAATACTCATAAAAAA
194 AAAATTTTGCAAAAATTGACCCAAAAGATACTTCCTAAATTTCTAGCGAAAATA-T-A-AAAAAA
**
6529 TATATAATT-AAACGTCAGAAAA-ATTGAAAGCCTTTT-GCGC-GCT-TATTGTTTTTCCTATTT
256 TATATAATTCAAA-GTCA-AAAAGATTGAAAGAATTTTAGCGCTGCTATATTGTTTTTCCTATTT
* *
6589 -TATTTCTA
319 CT-TTCCGA
* * * * * * * * *
6597 AATTAATTTATGATTAAATCGAAACAAAATTTAGATACTTGTAAAAACAAATCCTCAAATACAAC
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
** *
6662 GTGTATGAGATTTGGTTAGATGAATATAGATAT
66 GTGGCTGAGATTTGATTAGATGAATATAGATAT
6695 ATCCTCAAAT
Statistics
Matches: 357, Mismatches: 56, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
323 1 0.00
324 22 0.06
325 101 0.28
326 43 0.12
327 6 0.02
328 143 0.40
329 41 0.11
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (326 bp):
AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCACCAAAAATCATACAA
ACAGAGCCGTGGCTCAGAACACGTTTGCAGCCAAAAACCATGATGGTGTACACGATTTCGGCTAA
AATTTTGCAAAAATTGACCCAAAAGATACTTCCTAAATTTCTAGCGAAAATATAAAAAAATATAT
AATTCAAAGTCAAAAAGATTGAAAGAATTTTAGCGCTGCTATATTGTTTTTCCTATTTCTTTCCG
A
Found at i:7623 original size:339 final size:338
Alignment explanation
Indices: 6828--8024 Score: 1063
Period size: 338 Copynumber: 3.6 Consensus size: 338
6818 CATGCTTCTA
* * * * * * * *
6828 ATATCATTTTTCCTATTTTTT-TCAAATAAATTTCTAATTAAATCGAAACATGATTCAAATGCTC
1 ATATCGTTTTTCATATTTTTTCT-GAATTAATTTATAATTAAATCGAAAAAAGATTCAGATGCTC
* * * * * * * * *
6892 CTAAAAATAAATCCTTAAATCCAATGTGGCTAAG-TTTCGGTTAGATGAATATAGATATTTCACG
65 GTAAAAACAAATCCTTAAATGCAACGTGCCTGAGATTT-GATTAGATGGATATAGATATTTCATG
* * * * * * * *** *
6956 GAGTTTTG-CAACCAAAAATCATTCAAAACTGA-CCTAGGGACCTGGAACGCGTTTTTAGAAAAA
129 AAGTCTCGAC-ACCAAAAATCATGCAAAACTGAGTC-GGGGCCCCAAAACGCGTTTTTAG---CA
** * * * * *
7019 AAAAAAAAAAGCCATGATGG-TA-CAC-GA-TTTCGGCTAAAATTTTGC--AAAATTGA-ACCGA
189 AATCAAAAAA-CCGTGATGGTTAGTACAAAGTTTCGACTAAAATTTTGCAAAAAAATGACA-CGA
* * ** * * * * * *
7077 AATATTTTTCATCAATTTTTAACCACAATACTCAT-AATAT-ATATATAATTCAATGCCAAAAAG
252 AATATTTTTCCTCAAATTTTGGCAAAAATATTCATGAA-ATGA-ATAAAATTGAACGCCAAAAAG
* * *
7140 ATTAGAGGAATTTTTACGCTTTTA
315 ATTGGAGGACTTTTTACGCTTTTC
* * * *
7164 ATATCGTTTTTCATA-TTTTTCTGTATTAATTTCTAATTAAATCGAAAAAACATTTAGATGCTCG
1 ATATCGTTTTTCATATTTTTTCTGAATTAATTTATAATTAAATCGAAAAAAGATTCAGATGCTCG
* * *
7228 TAAAAACAAATCCTTAAATGCAACGTGGCTGAGATTTGATTGGATGGATATAGATATTTCATGGA
66 TAAAAACAAATCCTTAAATGCAACGTGCCTGAGATTTGATTAGATGGATATAGATATTTCATGAA
* * *
7293 GTCTCGACAACAAAAATAATGTAAAACTGAGTCGGGGCCCCAAAACGCGTTTTTAGCAAAT-AAA
131 GTCTCGACACCAAAAATCATGCAAAACTGAGTCGGGGCCCCAAAACGCGTTTTTAGCAAATCAAA
* * *
7357 AACACTGTGATGGTTAGTACAAAGTTTTGACTAAAATTTTGCAAGAAAAATGACCCGAAA-ATTT
196 AA-ACCGTGATGGTTAGTACAAAGTTTCGACTAAAATTTTGCAA-AAAAATGACACGAAATA-TT
* *
7421 TTTCCTGAAATTTTGG-ATAAAATATTCATGAAAT-AGATAGAATTGAACGCCAAAAAGATTGGA
258 TTTCCTCAAATTTTGGCA-AAAATATTCATGAAATGA-ATAAAATTGAACGCCAAAAAGATTGGA
7484 GGACTTTTTACGCTTTTC
321 GGACTTTTTACGCTTTTC
* * * *
7502 ATATTGTTTTTCATATTTTTTCTGAATAAATTTATAATTATATCGAAAAAAGGTTCAGATGCTCG
1 ATATCGTTTTTCATATTTTTTCTGAATTAATTTATAATTAAATCGAAAAAAGATTCAGATGCTCG
* * * * * *
7567 CAAAAACGAA-CTCTTAAATGCAACGTGCCTGATATTTGACTAGATAGATATAGATATTTCAAGA
66 TAAAAACAAATC-CTTAAATGCAACGTGCCTGAGATTTGATTAGATGGATATAGATATTTCATGA
* * * * * * * *****
7631 AGTCTCGACGCCAAAAGTCATGGAAAATTGAG-CATGGGCCCCGAAACGCCTTTTT-TTTTTTGC
130 AGTCTCGACACCAAAAATCATGCAAAACTGAGTC-GGGGCCCCAAAACGCGTTTTTAGCAAAT-C
* * * *
7694 AAAAAACCGTGATGGTTAGTACATAGTTTCGGCTAAAATTTTGGAAAAAAATGATACGAAATATT
193 AAAAAACCGTGATGGTTAGTACAAAGTTTCGACTAAAATTTTGCAAAAAAATGACACGAAATATT
* * * * *
7759 TTTCCTCAATTTTTGGCAAAAATATTCCTGAAATGAATAAAATTTAACACCAAAAAAATTGGAGG
258 TTTCCTCAAATTTTGGCAAAAATATTCATGAAATGAATAAAATTGAACGCCAAAAAGATTGGAGG
* *
7824 ACTTATCACGCTTTTC
323 ACTTTTTACGCTTTTC
* * * * *
7840 ATACCGTTTTTCATATTTTTT-TCAAATTAATTTTTAATTAAATCGAAATAAGATTCAAATGCTC
1 ATATCGTTTTTCATATTTTTTCT-GAATTAATTTATAATTAAATCGAAAAAAGATTCAGATGCTC
* * * *
7904 TTAAAAACAAATCCTTAATTGCAAC-TGCCTAAGATTTGATTAGATGGATATAGATATTTGATGA
65 GTAAAAACAAATCCTTAAATGCAACGTGCCTGAGATTTGATTAGATGGATATAGATATTTCATGA
* * * * *
7968 AGCCTCGACTCCAAAAATCATGCAAAACTGAGTCGGGGCCCAAAAATGCGTTCTTAG
130 AGTCTCGACACCAAAAATCATGCAAAACTGAGTCGGGGCCCCAAAACGCGTTTTTAG
8025 TAAAAGATCA
Statistics
Matches: 699, Mismatches: 134, Indels: 54
0.79 0.15 0.06
Matches are distributed among these distances:
331 12 0.02
332 6 0.01
333 2 0.00
334 1 0.00
335 147 0.21
336 19 0.03
337 77 0.11
338 249 0.36
339 181 0.26
340 5 0.01
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (338 bp):
ATATCGTTTTTCATATTTTTTCTGAATTAATTTATAATTAAATCGAAAAAAGATTCAGATGCTCG
TAAAAACAAATCCTTAAATGCAACGTGCCTGAGATTTGATTAGATGGATATAGATATTTCATGAA
GTCTCGACACCAAAAATCATGCAAAACTGAGTCGGGGCCCCAAAACGCGTTTTTAGCAAATCAAA
AAACCGTGATGGTTAGTACAAAGTTTCGACTAAAATTTTGCAAAAAAATGACACGAAATATTTTT
CCTCAAATTTTGGCAAAAATATTCATGAAATGAATAAAATTGAACGCCAAAAAGATTGGAGGACT
TTTTACGCTTTTC
Done.