Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015100.1 Corchorus capsularis cultivar CVL-1 contig15121, 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: 25560
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:555 original size:18 final size:19
Alignment explanation
Indices: 507--557 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
497 TAAAAAACTA
507 AAATTAAT-TAAATTGTTC
1 AAATTAATCTAAATTGTTC
*
525 AAAGTTAAACTAAA-T-TTC
1 AAA-TTAATCTAAATTGTTC
543 TAAATTAATCTAAAT
1 -AAATTAATCTAAAT
558 CTAACATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 15 0.56
19 8 0.30
20 4 0.15
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (19 bp):
AAATTAATCTAAATTGTTC
Found at i:3853 original size:14 final size:15
Alignment explanation
Indices: 3825--3853 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3815 GTGTGAATTC
3825 AAATTGATCTTTTGA
1 AAATTGATCTTTTGA
3840 AAATTGAT-TTTTGA
1 AAATTGATCTTTTGA
3854 TTAACTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (15 bp):
AAATTGATCTTTTGA
Found at i:4173 original size:19 final size:18
Alignment explanation
Indices: 4149--4184 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4139 TGAAGATTTC
4149 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
4168 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
4185 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:12478 original size:17 final size:17
Alignment explanation
Indices: 12456--12493 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
12446 GTTATCCAGC
12456 ACCTCATGC-TACCTAGT
1 ACCTCAT-CATACCTAGT
*
12473 ACCTCATCATACCTGGT
1 ACCTCATCATACCTAGT
12490 ACCT
1 ACCT
12494 TGAGAGGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 1 0.05
17 18 0.95
ACGTcount: A:0.24, C:0.37, G:0.11, T:0.29
Consensus pattern (17 bp):
ACCTCATCATACCTAGT
Found at i:13688 original size:30 final size:30
Alignment explanation
Indices: 13652--13713 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
13642 ATTGTTAAGT
13652 TGTAATCATATTAATGGTTGGTTCCATAGC
1 TGTAATCATATTAATGGTTGGTTCCATAGC
13682 TGTAATCATATTAATGGTTGGTTCCATAGC
1 TGTAATCATATTAATGGTTGGTTCCATAGC
13712 TG
1 TG
13714 ACATGGTCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (30 bp):
TGTAATCATATTAATGGTTGGTTCCATAGC
Found at i:15601 original size:17 final size:17
Alignment explanation
Indices: 15579--15612 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
15569 ATCGCCCACT
15579 GATTTCATTCCAAGCTA
1 GATTTCATTCCAAGCTA
15596 GATTTCATTCCAAGCTA
1 GATTTCATTCCAAGCTA
15613 CTGATGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (17 bp):
GATTTCATTCCAAGCTA
Found at i:22864 original size:16 final size:16
Alignment explanation
Indices: 22843--22914 Score: 65
Period size: 16 Copynumber: 4.5 Consensus size: 16
22833 AAATCCGAAT
22843 CCGAAAAATCTCAAAC
1 CCGAAAAATCTCAAAC
*
22859 CCGAAAAA-ATCAGAAC
1 CCGAAAAATCTCA-AAC
** *
22875 TTGAAAAATCTGAAAC
1 CCGAAAAATCTCAAAC
* * *
22891 CCGAAAAAACCCGAAC
1 CCGAAAAATCTCAAAC
22907 CCGAAAAA
1 CCGAAAAA
22915 CCCGAACTCA
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
15 3 0.07
16 38 0.88
17 2 0.05
ACGTcount: A:0.53, C:0.26, G:0.11, T:0.10
Consensus pattern (16 bp):
CCGAAAAATCTCAAAC
Found at i:22869 original size:32 final size:31
Alignment explanation
Indices: 22824--22914 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 31
22814 TCCGAACCCC
22824 AACCC-AAAGAAATCCGAATCCGAAAAATCTCA
1 AACCCGAAA-AAATCCGAA-CCGAAAAATCTCA
* * *
22856 AACCCGAAAAAATCAGAACTTGAAAAATCTGA
1 AACCCGAAAAAATCCGAAC-CGAAAAATCTCA
*
22888 AACCCGAAAAAACCCGAACCCGAAAAA
1 AACCCGAAAAAATCCGAA-CCGAAAAA
22915 CCCGAACTCA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
31 1 0.02
32 45 0.90
33 4 0.08
ACGTcount: A:0.53, C:0.26, G:0.11, T:0.10
Consensus pattern (31 bp):
AACCCGAAAAAATCCGAACCGAAAAATCTCA
Found at i:22913 original size:15 final size:16
Alignment explanation
Indices: 22888--22921 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
22878 AAAAATCTGA
22888 AACCCGAAAAAACCCG
1 AACCCGAAAAAACCCG
22904 AACCCG-AAAAACCCG
1 AACCCGAAAAAACCCG
22919 AAC
1 AAC
22922 TCAAACCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.50, C:0.38, G:0.12, T:0.00
Consensus pattern (16 bp):
AACCCGAAAAAACCCG
Found at i:23356 original size:41 final size:41
Alignment explanation
Indices: 23299--23381 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
23289 TAATTCACAT
*
23299 TCCGTGAGAGTAGAACCCAAGACCTCATGATCTAGGTATAC
1 TCCGTGAGAGTAGAACCCAAGACCTCATGATCCAGGTATAC
* *
23340 TCCGTGAGAGTAGAACCCAATACCTCATGGTCCAGGTATAC
1 TCCGTGAGAGTAGAACCCAAGACCTCATGATCCAGGTATAC
23381 T
1 T
23382 GGAACTAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (41 bp):
TCCGTGAGAGTAGAACCCAAGACCTCATGATCCAGGTATAC
Found at i:23511 original size:32 final size:30
Alignment explanation
Indices: 23475--23576 Score: 87
Period size: 32 Copynumber: 3.2 Consensus size: 30
23465 TCTAACCAAA
*
23475 ACCCAATCCGAGCCCGAACCCGAATTAACCTG
1 ACCCAAT-CGA-CCCGAACCCGAATCAACCTG
* *
23507 ACCCAAAATTGACCTGAACCCGAATCAACCTG
1 ACCC--AATCGACCCGAACCCGAATCAACCTG
** * *
23539 ACCCAAATTTAACCTGAACCCGAATCAACCCG
1 ACCC-AA-TCGACCCGAACCCGAATCAACCTG
23571 ACCCAA
1 ACCCAA
23577 ATTTAACCCG
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
31 5 0.08
32 52 0.84
33 2 0.03
34 3 0.05
ACGTcount: A:0.36, C:0.38, G:0.12, T:0.14
Consensus pattern (30 bp):
ACCCAATCGACCCGAACCCGAATCAACCTG
Found at i:23577 original size:32 final size:32
Alignment explanation
Indices: 23490--23593 Score: 163
Period size: 32 Copynumber: 3.2 Consensus size: 32
23480 ATCCGAGCCC
* * *
23490 GAACCCGAATTAACCTGACCCAAAATTGACCT
1 GAACCCGAATCAACCTGACCCAAATTTAACCT
23522 GAACCCGAATCAACCTGACCCAAATTTAACCT
1 GAACCCGAATCAACCTGACCCAAATTTAACCT
* *
23554 GAACCCGAATCAACCCGACCCAAATTTAACCC
1 GAACCCGAATCAACCTGACCCAAATTTAACCT
23586 GAACCCGA
1 GAACCCGA
23594 CTTAAGCCTG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 67 1.00
ACGTcount: A:0.38, C:0.36, G:0.12, T:0.15
Consensus pattern (32 bp):
GAACCCGAATCAACCTGACCCAAATTTAACCT
Found at i:23598 original size:16 final size:16
Alignment explanation
Indices: 23487--23610 Score: 83
Period size: 16 Copynumber: 7.7 Consensus size: 16
23477 CCAATCCGAG
23487 CCCGAACCCGAATTAA
1 CCCGAACCCGAATTAA
* * *
23503 CCTG-ACCCAAAATTGA
1 CCCGAACCC-GAATTAA
* *
23519 CCTGAACCCGAATCAA
1 CCCGAACCCGAATTAA
* *
23535 CCTG-ACCCAAATTTAA
1 CCCGAACCCGAA-TTAA
* *
23551 CCTGAACCCGAATCAA
1 CCCGAACCCGAATTAA
*
23567 CCCG-ACCCAAATTTAA
1 CCCGAACCCGAA-TTAA
*
23583 CCCGAACCCGACTTAA
1 CCCGAACCCGAATTAA
*
23599 GCCTGAACCCGA
1 -CCCGAACCCGA
23611 TGACCTGAAA
Statistics
Matches: 85, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
15 16 0.19
16 44 0.52
17 25 0.29
ACGTcount: A:0.35, C:0.37, G:0.12, T:0.15
Consensus pattern (16 bp):
CCCGAACCCGAATTAA
Found at i:23619 original size:14 final size:14
Alignment explanation
Indices: 23600--23638 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
23590 CCGACTTAAG
*
23600 CCTGAACCCGATGA
1 CCTGAACCCAATGA
*
23614 CCTGAAACCAATGA
1 CCTGAACCCAATGA
*
23628 CCCGAACCCAA
1 CCTGAACCCAA
23639 CATGACTCGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.38, G:0.15, T:0.10
Consensus pattern (14 bp):
CCTGAACCCAATGA
Done.