Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011258.1 Corchorus capsularis cultivar CVL-1 contig11279, 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: 16822
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:902 original size:21 final size:21
Alignment explanation
Indices: 876--921 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
866 ATTTCAAAAA
876 AAAGGAAAAATAATGGTCTGC
1 AAAGGAAAAATAATGGTCTGC
897 AAAGGAAAAATAATGGTCTGC
1 AAAGGAAAAATAATGGTCTGC
918 AAAG
1 AAAG
922 TTATCCCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.50, C:0.09, G:0.24, T:0.17
Consensus pattern (21 bp):
AAAGGAAAAATAATGGTCTGC
Found at i:1612 original size:16 final size:16
Alignment explanation
Indices: 1593--1664 Score: 67
Period size: 16 Copynumber: 4.5 Consensus size: 16
1583 CTACCCGAGA
*
1593 CCGAACCTGAAAATAC
1 CCGAACCCGAAAATAC
*
1609 CCGAACCCG-ACATAAC
1 CCGAACCCGAAAAT-AC
* * *
1625 CCGAGCCTGAATATAC
1 CCGAACCCGAAAATAC
1641 CCGAACCCGAAAA-AGC
1 CCGAACCCGAAAATA-C
1657 CCGAACCC
1 CCGAACCC
1665 ACCCAATTAC
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
15 4 0.09
16 38 0.84
17 3 0.07
ACGTcount: A:0.38, C:0.39, G:0.15, T:0.08
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:1660 original size:32 final size:32
Alignment explanation
Indices: 1593--1663 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
1583 CTACCCGAGA
*
1593 CCGAACCTGAAAATACCCGAACCCGACATAAC
1 CCGAACCTGAAAATACCCGAACCCGACAAAAC
* *
1625 CCGAGCCTGAATATACCCGAACCCGA-AAAAGC
1 CCGAACCTGAAAATACCCGAACCCGACAAAA-C
1657 CCGAACC
1 CCGAACC
1664 CACCCAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 3 0.09
32 31 0.91
ACGTcount: A:0.38, C:0.38, G:0.15, T:0.08
Consensus pattern (32 bp):
CCGAACCTGAAAATACCCGAACCCGACAAAAC
Found at i:2590 original size:27 final size:27
Alignment explanation
Indices: 2553--2621 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
2543 AATCCTAGGG
* * *
2553 AACTAATTTTGAATGGGGAACTGTTTT
1 AACTAACTTTGAATGGAGAACTGTCTT
* *
2580 GACTAACTTTGAGTGGAGAACTGTCTT
1 AACTAACTTTGAATGGAGAACTGTCTT
*
2607 AACTAACTTGGAATG
1 AACTAACTTTGAATG
2622 AGAGTCTGAC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (27 bp):
AACTAACTTTGAATGGAGAACTGTCTT
Found at i:3382 original size:3 final size:3
Alignment explanation
Indices: 3374--3434 Score: 77
Period size: 3 Copynumber: 19.0 Consensus size: 3
3364 GTTCGCATCA
3374 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATAT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T AT-T AT-T
*
3422 ACT ATAT ATT ATT
1 ATT AT-T ATT ATT
3435 TTTAATTACT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
3 41 0.76
4 13 0.24
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:5987 original size:427 final size:433
Alignment explanation
Indices: 5369--6254 Score: 1022
Period size: 442 Copynumber: 2.0 Consensus size: 433
5359 TAATTTTTTG
* * * * * * *
5369 TCCACAGGTCCGATTGAAGTTGTTGAAGTGTCAATTAAAAGGTTATTGCATGATTTACGACTTCC
1 TCCACATGTCCGATTAAAGTTATTCAAGTGTCAATTAAAAGGTTACTGCATAATCTACGACTTCC
* * * *
5434 ATGAAGGACCCGAAAACTAAATTTGATCTACGAGTTTCGTTAAGGGTTCAAAAGGGAATTTTTAT
66 ATGAAGAACCCGAAAACTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGAAATTTTTAT
*
5499 GTTTCAAGATCTCCATTAACAAACATTTTCTTATTTAGATTATTGATCAAATGACCCTCATAATT
131 GTTTCAAGATCTCCATTAACAAACATTTTCTTATTTAGATTATTGATCAAATCACCCTCATAATT
* *
5564 TTATACTTTA-TACTAAGTCCTTTACAAATTCTATCTTA-A-TT-ACTTTATTTTTT-TAAAA-T
196 TTATACTTTACTACTAAGTCCTTTACAAATTCTATCTTATATTTAACTTCATTTTTTAAAAAATT
* ** * * * *
5623 CTTTTTTCTATTTGTCTGATTAAGTTGATTCATG-TGTCTATTAAAAGGTAATTTCATAATGTAC
261 CTTTGTTCTATTTGTCCAATTAAGATAATTCA-GATGTATATTAAAAGGTAATTTCATAATCTAC
* * *
5687 ATCTTTCATGAAAGATTCAAAAGCAAATTTTTATGTTTCAATTCAAAAAAATACTTCCT-AAATG
325 AACTTTCATGAAAGACTCAAAAGCAAATTTTTATATTTCAATTCAAAAAAATACTT-CTGAAATG
*** *
5751 TGGTCG-TTTCGATTGTTGATCTATTTAATACCATATAATTTTCGA
389 TGGT-GATTTCGATTGACAATCTATTTAATACCATATAATTTTCAA
* ** * *
5796 TCCACATGTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAAGGTTACTGTATAATCTACGACTTT
1 TCCACATGTCCGATTAAAGTTATTCAAGTGTCAATT-AAAAGGTTACTGCATAATCTACGACTTC
* * * *
5861 CATGAAGAACCCG-AAAGTTAATTTGATCTATGAGTTTCATGAAGGGTTTAAAAGGAAATTTTTA
65 CATGAAGAACCCGAAAACTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGAAATTTTTA
* * * * *
5925 TGTTTCGAGATCTCCATTAACAAATATTTTCTTATTT-GAATTAGTT-TTCAAGTCATCCTCATA
130 TGTTTCAAGATCTCCATTAACAAACATTTTCTTATTTAG-ATTA-TTGATCAAATCACCCTCATA
* * * *
5988 CTTTTCTATTTTATGCTACTTAGTCCTTTACAAATTCTATCTTACTTGATTTAACACTTCATTTT
193 ATTTTATACTTTA--CTACTAAGTCCTTTACAAATTCTATCTTA--T-ATTT-A-ACTTCATTTT
6053 TTAAAAAATTTTCTTTGTTCTATTTGTCCAATTAAGATAATTCAGATGTATATTAAAAGGTAATT
251 TTAAAAAA--TTCTTTGTTCTATTTGTCCAATTAAGATAATTCAGATGTATATTAAAAGGTAATT
* * * * **
6118 TTATGATCTACAACTTTCATGAAAGACTCAAAAGCTAATTTTTATATTTCATTTCTGAAAAATAC
314 TCATAATCTACAACTTTCATGAAAGACTCAAAAGCAAATTTTTATATTTCAATTCAAAAAAATAC
* * * * * *
6183 TTTTGAAATTTTGTGATTTCGATTGACAATCTATTTAATATCATATTATTTTTAA
379 TTCTGAAATGTGGTGATTTCGATTGACAATCTATTTAATACCATATAATTTTCAA
*
6238 TCCAGATGTCCGATTAA
1 TCCACATGTCCGATTAA
6255 CAAAGATTCA
Statistics
Matches: 378, Mismatches: 60, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
426 1 0.00
427 135 0.36
428 37 0.10
430 27 0.07
434 1 0.00
435 2 0.01
438 11 0.03
439 4 0.01
441 3 0.01
442 157 0.42
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (433 bp):
TCCACATGTCCGATTAAAGTTATTCAAGTGTCAATTAAAAGGTTACTGCATAATCTACGACTTCC
ATGAAGAACCCGAAAACTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGAAATTTTTAT
GTTTCAAGATCTCCATTAACAAACATTTTCTTATTTAGATTATTGATCAAATCACCCTCATAATT
TTATACTTTACTACTAAGTCCTTTACAAATTCTATCTTATATTTAACTTCATTTTTTAAAAAATT
CTTTGTTCTATTTGTCCAATTAAGATAATTCAGATGTATATTAAAAGGTAATTTCATAATCTACA
ACTTTCATGAAAGACTCAAAAGCAAATTTTTATATTTCAATTCAAAAAAATACTTCTGAAATGTG
GTGATTTCGATTGACAATCTATTTAATACCATATAATTTTCAA
Found at i:6327 original size:2 final size:2
Alignment explanation
Indices: 6322--6358 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6312 AAAAAACTAG
6322 TA 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 TA T
6359 GATAGAGATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10091 original size:17 final size:17
Alignment explanation
Indices: 10041--10092 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
10031 ATCTTTCTCA
*
10041 TTCTCCATATTCTCTTC
1 TTCTCCATATTCTCTTG
10058 TTCTCCATATTCTCTTG
1 TTCTCCATATTCTCTTG
10075 TTCTCTCA-ATTCTCTTG
1 TTCTC-CATATTCTCTTG
10092 T
1 T
10093 CTTTTCCATA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 31 0.94
18 2 0.06
ACGTcount: A:0.12, C:0.31, G:0.04, T:0.54
Consensus pattern (17 bp):
TTCTCCATATTCTCTTG
Found at i:10450 original size:33 final size:33
Alignment explanation
Indices: 10408--10498 Score: 164
Period size: 33 Copynumber: 2.8 Consensus size: 33
10398 TTGAATATTT
*
10408 GTGGCACCTGAAGTTGTCACATCAAGTATATCA
1 GTGGCACCTGAAGTTGTCACATCAAGCATATCA
*
10441 GTGGCACCTGAAGTTGTCACATCAAGCATATTA
1 GTGGCACCTGAAGTTGTCACATCAAGCATATCA
10474 GTGGCACCTGAAGTTGTCACATCAA
1 GTGGCACCTGAAGTTGTCACATCAA
10499 AAATATAGAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (33 bp):
GTGGCACCTGAAGTTGTCACATCAAGCATATCA
Found at i:10572 original size:51 final size:53
Alignment explanation
Indices: 10513--10642 Score: 142
Period size: 54 Copynumber: 2.5 Consensus size: 53
10503 ATAGAATTAC
* ** * *
10513 TTTGACACCCGAAGTTGTCATTATTAAGGA-TGGAAA-TATTTGTTGCCAAAG
1 TTTGACACCCGAAGTTGTCATTACTAACCACTGAAAATTAATTGTTGCCAAAG
* * *
10564 TTTGACACCTGAAGTTGTCA-TACTATCCACTTAAAACTTTAATTGTTGCCAAAG
1 TTTGACACCCGAAGTTGTCATTACTAACCACTGAAAA--TTAATTGTTGCCAAAG
10618 TTTGACACCCGAAGTTGTCA-TACTA
1 TTTGACACCCGAAGTTGTCATTACTA
10643 TCAACTTTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
50 5 0.08
51 23 0.35
54 38 0.58
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (53 bp):
TTTGACACCCGAAGTTGTCATTACTAACCACTGAAAATTAATTGTTGCCAAAG
Done.