Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006149.1 Corchorus capsularis cultivar CVL-1 contig06167, 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: 31457
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:410 original size:41 final size:41
Alignment explanation
Indices: 354--434 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
344 TCCTTTCTTA
354 TTTCTTTCTTCGAGTTTATGTATTCCTAAGCCTCGTAATAC
1 TTTCTTTCTTCGAGTTTATGTATTCCTAAGCCTCGTAATAC
* * *
395 TTTCTTTCTTTGAGTTTATGTATTTCTAAGCCTGGTAATA
1 TTTCTTTCTTCGAGTTTATGTATTCCTAAGCCTCGTAATA
435 AGGAAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (41 bp):
TTTCTTTCTTCGAGTTTATGTATTCCTAAGCCTCGTAATAC
Found at i:3736 original size:31 final size:32
Alignment explanation
Indices: 3675--3736 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
3665 ATTGAAGATG
**
3675 ATAACTAAGTTGTAAGCCCTTTTATCTGCTAC
1 ATAACTAAGTTGTAAGCCCTTTTAAATGCTAC
*
3707 ATAATTAAGTTGTAAG-CCTTTTAAATGCTA
1 ATAACTAAGTTGTAAGCCCTTTTAAATGCTA
3737 GGTATCTCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 12 0.44
32 15 0.56
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (32 bp):
ATAACTAAGTTGTAAGCCCTTTTAAATGCTAC
Found at i:7234 original size:27 final size:28
Alignment explanation
Indices: 7155--7234 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
7145 GCTTAATACC
* *
7155 CAAATTAGTCCCTTAACTATTCATTTTGGGA
1 CAAATTGGCCCCTTAACT-TT--TTTTGGGA
*
7186 TAAATTGGCCCCTTAACTTTTTTTGGGA
1 CAAATTGGCCCCTTAACTTTTTTTGGGA
7214 CAAATTGGCCCCTTAACTTTT
1 CAAATTGGCCCCTTAACTTTT
7235 AAAAACGAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 28 0.62
30 2 0.04
31 15 0.33
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (28 bp):
CAAATTGGCCCCTTAACTTTTTTTGGGA
Found at i:7957 original size:29 final size:29
Alignment explanation
Indices: 7921--7978 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
7911 TCTCGTTTTT
*
7921 AAAAGTTAAGGGGTCAATTTGTCCCAAAA
1 AAAAGTTAAGGGGTCAATTTATCCCAAAA
7950 AAAAGTTAAGGGGTCAATTTATCCCAAAA
1 AAAAGTTAAGGGGTCAATTTATCCCAAAA
7979 TGGATAGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (29 bp):
AAAAGTTAAGGGGTCAATTTATCCCAAAA
Found at i:9203 original size:14 final size:12
Alignment explanation
Indices: 9179--9258 Score: 71
Period size: 12 Copynumber: 7.0 Consensus size: 12
9169 GAACCGTTTA
9179 ATAATTATATAT
1 ATAATTATATAT
*
9191 ATCATTATATAT
1 ATAATTATATAT
9203 ATAATTATATAT
1 ATAATTATATAT
*
9215 AT--CTA-ATAT
1 ATAATTATATAT
9224 -T-ATTATATAT
1 ATAATTATATAT
**
9234 ATAAAAAATATAT
1 AT-AATTATATAT
*
9247 TTAATTATATAT
1 ATAATTATATAT
9259 TAACTAAACG
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
8 1 0.02
9 6 0.11
10 6 0.11
11 1 0.02
12 32 0.59
13 8 0.15
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (12 bp):
ATAATTATATAT
Found at i:9369 original size:9 final size:8
Alignment explanation
Indices: 9346--9385 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
9336 TTTGGCGGTT
9346 CAAACCGC
1 CAAACCGC
9354 CAAACCGAC
1 CAAACCG-C
*
9363 TAAACCGC
1 CAAACCGC
9371 CAAACCGC
1 CAAACCGC
9379 CAAACCG
1 CAAACCG
9386 AAGAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 22 0.76
9 7 0.24
ACGTcount: A:0.40, C:0.45, G:0.12, T:0.03
Consensus pattern (8 bp):
CAAACCGC
Found at i:13582 original size:31 final size:30
Alignment explanation
Indices: 13544--13740 Score: 165
Period size: 31 Copynumber: 6.5 Consensus size: 30
13534 TTAGGCTAAT
*
13544 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTT-CGAAAA
* * * **
13575 TGCTCAAATAAGGGCTTTATC-TTT-TAATT
1 TGCTCAAATAAGGGC-CTAACGTTTCGAAAA
13604 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTT-TCGAAAA
* **
13635 TGCTCAAATAAGGGCC---CGATCTTCTAATT
1 TGCTCAAATAAGGGCCTAACG-T-TTCGAAAA
*
13664 TGGC-CAAATAAGGGCCTAACGTTATTGAAAA
1 T-GCTCAAATAAGGGCCTAACGTT-TCGAAAA
*
13695 TGTTCAAATAAGGGCCTAACGTTATCGAAAA
1 TGCTCAAATAAGGGCCTAACGTT-TCGAAAA
13726 TGCTCAAATAAGGGC
1 TGCTCAAATAAGGGC
13741 TTGGTTTCAG
Statistics
Matches: 132, Mismatches: 20, Indels: 28
0.73 0.11 0.16
Matches are distributed among these distances:
28 5 0.04
29 34 0.26
30 10 0.08
31 78 0.59
32 5 0.04
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTCGAAAA
Found at i:13641 original size:60 final size:60
Alignment explanation
Indices: 13548--13710 Score: 247
Period size: 60 Copynumber: 2.7 Consensus size: 60
13538 GCTAATTGCT
* *** *
13548 CAAATAAGGGCCTAACGTT-TGCCAAAATGCTCAAATAAGGGCTTTATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGCCCGATCTTCTAATTTGGC
13608 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTCTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTCTAATTTGGC
* *
13668 CAAATAAGGGCCTAACGTTATTGAAAATGTTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
13711 TAACGTTATC
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
60 94 0.99
61 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTCTAATTTGGC
Found at i:13804 original size:31 final size:31
Alignment explanation
Indices: 13769--13937 Score: 147
Period size: 31 Copynumber: 5.6 Consensus size: 31
13759 ACGTATGAGA
13769 TAGGCCCTTATTTGAGCATTTTGGCAAACGT
1 TAGGCCCTTATTTGAGCATTTTGGCAAACGT
** *
13800 TAGGCCCTTATTTG-GCCAAATT--CAAA-GAC
1 TAGGCCCTTATTTGAG-CATTTTGGCAAACG-T
* * *
13829 CAAGCCCTTCTTTGAGCATTTTGGCAAACGT
1 TAGGCCCTTATTTGAGCATTTTGGCAAACGT
** *
13860 TAGGCCCTTATTT-AGCCAAATT---AAAAGAT
1 TAGGCCCTTATTTGAG-CATTTTGGCAAACG-T
* *
13889 CAGGCCCTTATTTGAGCATTTTGGTAAACGT
1 TAGGCCCTTATTTGAGCATTTTGGCAAACGT
13920 TAGGCCCTTATTTGAGCA
1 TAGGCCCTTATTTGAGCA
13938 ATTAGCCTTT
Statistics
Matches: 106, Mismatches: 20, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
28 5 0.05
29 36 0.34
30 6 0.06
31 54 0.51
32 5 0.05
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (31 bp):
TAGGCCCTTATTTGAGCATTTTGGCAAACGT
Found at i:13846 original size:60 final size:60
Alignment explanation
Indices: 13772--13933 Score: 270
Period size: 60 Copynumber: 2.7 Consensus size: 60
13762 TATGAGATAG
*
13772 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGACCAA
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACCAA
* * * *
13832 GCCCTTCTTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTAGCCAAATTAAAAGATCAG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACCAA
*
13892 GCCCTTATTTGAGCATTTTGGTAAACGTTAGGCCCTTATTTG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
13934 AGCAATTAGC
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 94 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACCAA
Found at i:15058 original size:24 final size:25
Alignment explanation
Indices: 15031--15080 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
15021 TTCTTCTTCA
15031 GCAAT-CAAGTGCTTTCGGTTGCTG
1 GCAATCCAAGTGCTTTCGGTTGCTG
*
15055 GCAATCCAAGTGCTTTTGGTTGCTG
1 GCAATCCAAGTGCTTTCGGTTGCTG
15080 G
1 G
15081 TTTTCCTAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.16, C:0.20, G:0.30, T:0.34
Consensus pattern (25 bp):
GCAATCCAAGTGCTTTCGGTTGCTG
Found at i:18220 original size:14 final size:14
Alignment explanation
Indices: 18175--18234 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 14
18165 CTTACCCTTA
*
18175 TCTTTTTTTTTCGT
1 TCTTTTTTTTTCTT
*
18189 TCGTTTTTCCTCTTCTT
1 TC-TTTTT--TTTTCTT
18206 T-TTTTTTTTTGCTT
1 TCTTTTTTTTT-CTT
18220 TCTTTTTTTTTCTT
1 TCTTTTTTTTTCTT
18234 T
1 T
18235 AGATTGCTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
13 3 0.08
14 10 0.26
15 19 0.50
17 6 0.16
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (14 bp):
TCTTTTTTTTTCTT
Found at i:21177 original size:21 final size:21
Alignment explanation
Indices: 21153--21193 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21143 ACCCTGTTCC
21153 TGCCTCATCTCTTCCTGTGAA
1 TGCCTCATCTCTTCCTGTGAA
* *
21174 TGCCTCATTTCTTCTTGTGA
1 TGCCTCATCTCTTCCTGTGA
21194 CTGCATCAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.29, G:0.15, T:0.44
Consensus pattern (21 bp):
TGCCTCATCTCTTCCTGTGAA
Found at i:22701 original size:3 final size:3
Alignment explanation
Indices: 22693--22718 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
22683 ATCAATTAAT
22693 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
22719 TATATATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:25937 original size:2 final size:2
Alignment explanation
Indices: 25930--25959 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25920 TGAATACTAG
25930 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25960 CTTAGTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.