Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005417.1 Corchorus capsularis cultivar CVL-1 contig05435, 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: 21738
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1594 original size:139 final size:139
Alignment explanation
Indices: 1344--1761 Score: 827
Period size: 139 Copynumber: 3.0 Consensus size: 139
1334 CTTCCCATTT
*
1344 AATGTCAATTTCCTTCTTTAGCCATATCTTGTTTTTTAAATCCTTAAATCATCTCAAATTCTGTG
1 AATGTCAGTTTCCTTCTTTAGCCATATCTTGTTTTTTAAATCCTTAAATCATCTCAAATTCTGTG
1409 TCATTTCGATCCTTATTTCCTTTCATTCTATTTATCTTGTTTTTCTTATTTGCACATTTGTTACA
66 TCATTTCGATCCTTATTTCCTTTCATTCTATTTATCTTGTTTTTCTTATTTGCACATTTGTTACA
1474 CTAGGAGTG
131 CTAGGAGTG
1483 AATGTCAGTTTCCTTCTTTAGCCATATCTTGTTTTTTAAATCCTTAAATCATCTCAAATTCTGTG
1 AATGTCAGTTTCCTTCTTTAGCCATATCTTGTTTTTTAAATCCTTAAATCATCTCAAATTCTGTG
1548 TCATTTCGATCCTTATTTCCTTTCATTCTATTTATCTTGTTTTTCTTATTTGCACATTTGTTACA
66 TCATTTCGATCCTTATTTCCTTTCATTCTATTTATCTTGTTTTTCTTATTTGCACATTTGTTACA
1613 CTAGGAGTG
131 CTAGGAGTG
1622 AATGTCAGTTTCCTTCTTTAGCCATATCTTGTTTTTTAAATCCTTAAATCATCTCAAATTCTGTG
1 AATGTCAGTTTCCTTCTTTAGCCATATCTTGTTTTTTAAATCCTTAAATCATCTCAAATTCTGTG
1687 TCATTTCGATCCTTATTTCCTTTCATTCTATTTATCTTGTTTTTCTTATTTGCACATTTGTTACA
66 TCATTTCGATCCTTATTTCCTTTCATTCTATTTATCTTGTTTTTCTTATTTGCACATTTGTTACA
1752 CTAGGAGTG
131 CTAGGAGTG
1761 A
1 A
1762 TGAAGTTCTT
Statistics
Matches: 278, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 278 1.00
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.50
Consensus pattern (139 bp):
AATGTCAGTTTCCTTCTTTAGCCATATCTTGTTTTTTAAATCCTTAAATCATCTCAAATTCTGTG
TCATTTCGATCCTTATTTCCTTTCATTCTATTTATCTTGTTTTTCTTATTTGCACATTTGTTACA
CTAGGAGTG
Found at i:4596 original size:16 final size:16
Alignment explanation
Indices: 4577--4615 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
4567 TTTTTTCTTT
*
4577 TTCTTT-TTCTTTTCAC
1 TTCTTTCTTCTTCTC-C
4593 TTCTTTCTTCTTCTCC
1 TTCTTTCTTCTTCTCC
4609 TTCTTTC
1 TTCTTTC
4616 GGCCAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.67
Consensus pattern (16 bp):
TTCTTTCTTCTTCTCC
Found at i:6445 original size:60 final size:60
Alignment explanation
Indices: 6351--6471 Score: 206
Period size: 60 Copynumber: 2.0 Consensus size: 60
6341 AGTGTATCAA
* * *
6351 ATAATTATCCATAAAACAAAAGGATAATATATTAATGATTGAAAAGATCAAACACAACAT
1 ATAATTATCCATAAAACAAAAGGATAATACATTAATGATAGAAAAGATCAAACAAAACAT
*
6411 ATAATTATCCGTAAAACAAAAGGATAATACATTAATGATAGAAAAGATCAAACAAAACAT
1 ATAATTATCCATAAAACAAAAGGATAATACATTAATGATAGAAAAGATCAAACAAAACAT
6471 A
1 A
6472 ATGTTTAGTT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.56, C:0.12, G:0.09, T:0.23
Consensus pattern (60 bp):
ATAATTATCCATAAAACAAAAGGATAATACATTAATGATAGAAAAGATCAAACAAAACAT
Found at i:7081 original size:11 final size:11
Alignment explanation
Indices: 7067--7108 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
7057 ATTCATAACA
7067 AATTTATAATT
1 AATTTATAATT
7078 AATTTATAATT
1 AATTTATAATT
7089 -ATTTGATAAGTT
1 AATTT-ATAA-TT
*
7101 ATTTTATA
1 AATTTATA
7109 TGGGAAAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 4 0.15
11 15 0.56
12 5 0.19
13 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (11 bp):
AATTTATAATT
Found at i:10831 original size:45 final size:41
Alignment explanation
Indices: 10746--10829 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
10736 CTCACGGAAT
*
10746 GTGAATTTAGTTTGTAATTTATTTATTTGTGTACTTGGTAG
1 GTGAGTTTAGTTTGTAATTTATTTATTTGTGTACTTGGTAG
10787 GTGAGTTTAGTTTGTAATTTATTTATTTGTGTACTTGGTAG
1 GTGAGTTTAGTTTGTAATTTATTTATTTGTGTACTTGGTAG
10828 GT
1 GT
10830 AGATGGTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.20, C:0.02, G:0.24, T:0.54
Consensus pattern (41 bp):
GTGAGTTTAGTTTGTAATTTATTTATTTGTGTACTTGGTAG
Found at i:11425 original size:29 final size:28
Alignment explanation
Indices: 11392--11447 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
11382 ACACTCTTGT
* * *
11392 AAGTAGATGGACTAAAATGGAGCATTTCA
1 AAGTAGATGAACCAAAAT-GAACATTTCA
*
11421 AAGTATATGAACCAAAATGAACATTTC
1 AAGTAGATGAACCAAAATGAACATTTC
11448 GTGTAAGTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (28 bp):
AAGTAGATGAACCAAAATGAACATTTCA
Found at i:12699 original size:62 final size:61
Alignment explanation
Indices: 12603--12723 Score: 215
Period size: 62 Copynumber: 2.0 Consensus size: 61
12593 TCCAGTGTAA
*
12603 TTTTTTTTTTGGAAAATTTATTGGTATAAGTGAAATCTCATTACAATTAGAATAAATATGG
1 TTTTTTTTTTGGAAAATTTATTGGTACAAGTGAAATCTCATTACAATTAGAATAAATATGG
*
12664 TTTTTTTTTTGGGAAAATTTATTGTTACAAGTGAAATCTCATTACAATTAGAATAAATAT
1 TTTTTTTTTT-GGAAAATTTATTGGTACAAGTGAAATCTCATTACAATTAGAATAAATAT
12724 CCATATGTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
61 10 0.18
62 47 0.82
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (61 bp):
TTTTTTTTTTGGAAAATTTATTGGTACAAGTGAAATCTCATTACAATTAGAATAAATATGG
Found at i:12861 original size:57 final size:57
Alignment explanation
Indices: 12793--12907 Score: 185
Period size: 57 Copynumber: 2.0 Consensus size: 57
12783 CCTACTTAAC
*
12793 AAACTATCTAACAAACAAACAAATAAATAAACGAAACTCACATTCCGTAACATTTGA
1 AAACTATCTAACAAACAAACAAATAAATAAACGAAACGCACATTCCGTAACATTTGA
* * * *
12850 AAACTATCTAACAAACAAACAAATAGATAAACGAAACGCACATTTCGTGAGATTTGA
1 AAACTATCTAACAAACAAACAAATAAATAAACGAAACGCACATTCCGTAACATTTGA
12907 A
1 A
12908 CCTATGACTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.51, C:0.19, G:0.09, T:0.21
Consensus pattern (57 bp):
AAACTATCTAACAAACAAACAAATAAATAAACGAAACGCACATTCCGTAACATTTGA
Found at i:12952 original size:1 final size:1
Alignment explanation
Indices: 12946--12981 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
12936 CACTCACCAG
12946 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12982 ATCCCAGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.