Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006317.1 Corchorus capsularis cultivar CVL-1 contig06338, 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: 26392
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:1402 original size:2 final size:2
Alignment explanation
Indices: 1395--1422 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1385 AAATAAATAA
1395 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1423 TAGTTGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2670 original size:6 final size:6
Alignment explanation
Indices: 2659--2685 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2649 ATTTAATCAC
2659 AAATAT AAATAT AAATAT AAATAT AAA
1 AAATAT AAATAT AAATAT AAATAT AAA
2686 AGAGACTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATAT
Found at i:3610 original size:31 final size:30
Alignment explanation
Indices: 3572--3739 Score: 123
Period size: 31 Copynumber: 5.6 Consensus size: 30
3562 ATAGGCTAAT
*
3572 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAAC-TTTGCCAAAA
* * * **
3603 TGCTCAAATAAGGGTCTGATCTTT--TAATT
1 TGCTCAAATAAGGGCCT-AACTTTGCCAAAA
*
3632 TGGC-CAAATAAGGGCCTAATGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAA-CTTTGCCAAAA
* * * **
3663 TGCTCAAATAAGAGTCTCATCTTTG--AATT
1 TGCTCAAATAAGGGCCT-AACTTTGCCAAAA
3692 TGGC-CAAATAAGGGCCTAACATTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAAC-TTTGCCAAAA
3723 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
3740 GTCTCATGCG
Statistics
Matches: 103, Mismatches: 22, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
28 3 0.03
29 36 0.35
30 8 0.08
31 53 0.51
32 3 0.03
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACTTTGCCAAAA
Found at i:3669 original size:60 final size:60
Alignment explanation
Indices: 3576--3736 Score: 268
Period size: 60 Copynumber: 2.7 Consensus size: 60
3566 GCTAATTGCT
* * *
3576 CAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTCATCTTTGAATTTGGC
* *
3636 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGAGTCTCATCTTTGAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTCATCTTTGAATTTGGC
*
3696 CAAATAAGGGCCTAACATTTGCCAAAATGCTCAAATAAGGG
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
3737 CCTGTCTCAT
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTCATCTTTGAATTTGGC
Found at i:3703 original size:29 final size:29
Alignment explanation
Indices: 3607--3710 Score: 93
Period size: 29 Copynumber: 3.5 Consensus size: 29
3597 TCAAAATGCT
* *
3607 CAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGTCTAATCTTTGAATTTGGC
* * **
3636 CAAATAAGGGCCTAATGTTTGCCAAAAT-GC
1 CAAATAAGGGTCTAATCTTTG--AATTTGGC
* *
3666 TCAAATAAGAGTCTCATCTTTGAATTTGGC
1 -CAAATAAGGGTCTAATCTTTGAATTTGGC
*
3696 CAAATAAGGGCCTAA
1 CAAATAAGGGTCTAA
3711 CATTTGCCAA
Statistics
Matches: 56, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
29 32 0.57
30 4 0.07
31 20 0.36
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (29 bp):
CAAATAAGGGTCTAATCTTTGAATTTGGC
Found at i:8995 original size:15 final size:16
Alignment explanation
Indices: 8975--9009 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
8965 TTTTAGCGGC
8975 AAAAGAAAAAAAAG-A
1 AAAAGAAAAAAAAGTA
*
8990 AAAAGAAAATAAAGTA
1 AAAAGAAAAAAAAGTA
9006 AAAA
1 AAAA
9010 CCCATTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (16 bp):
AAAAGAAAAAAAAGTA
Found at i:10205 original size:12 final size:12
Alignment explanation
Indices: 10183--10304 Score: 136
Period size: 12 Copynumber: 10.2 Consensus size: 12
10173 CTCCAGATCC
*
10183 AGTTGATGAAAG
1 AGTTGAAGAAAG
* *
10195 GGTTGTAGAAAG
1 AGTTGAAGAAAG
* *
10207 GGTTCAAGAAAG
1 AGTTGAAGAAAG
10219 AGTTGAAGAAAG
1 AGTTGAAGAAAG
* *
10231 AGTTCAAGAAAC
1 AGTTGAAGAAAG
*
10243 TGTTGAAGAAAG
1 AGTTGAAGAAAG
10255 AGTTGAAGAAAG
1 AGTTGAAGAAAG
*
10267 ATTTGAAGAAAG
1 AGTTGAAGAAAG
*
10279 GGTTGAAGAAAG
1 AGTTGAAGAAAG
* *
10291 AGCTGCAGAAAG
1 AGTTGAAGAAAG
10303 AG
1 AG
10305 ATGGTGAAGA
Statistics
Matches: 91, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 91 1.00
ACGTcount: A:0.44, C:0.04, G:0.33, T:0.19
Consensus pattern (12 bp):
AGTTGAAGAAAG
Found at i:10230 original size:36 final size:36
Alignment explanation
Indices: 10183--10304 Score: 154
Period size: 36 Copynumber: 3.4 Consensus size: 36
10173 CTCCAGATCC
* * * *
10183 AGTTGATGAAAGGGTTGTAGAAAGGGTTCAAGAAAG
1 AGTTGAAGAAAGAGTTGAAGAAAGGGTTGAAGAAAG
* **
10219 AGTTGAAGAAAGAGTTCAAGAAACTGTTGAAGAAAG
1 AGTTGAAGAAAGAGTTGAAGAAAGGGTTGAAGAAAG
*
10255 AGTTGAAGAAAGATTTGAAGAAAGGGTTGAAGAAAG
1 AGTTGAAGAAAGAGTTGAAGAAAGGGTTGAAGAAAG
* *
10291 AGCTGCAGAAAGAG
1 AGTTGAAGAAAGAG
10305 ATGGTGAAGA
Statistics
Matches: 72, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 72 1.00
ACGTcount: A:0.44, C:0.04, G:0.33, T:0.19
Consensus pattern (36 bp):
AGTTGAAGAAAGAGTTGAAGAAAGGGTTGAAGAAAG
Found at i:13731 original size:8 final size:8
Alignment explanation
Indices: 13718--13751 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
13708 CTCTGTTTTA
13718 TGCCTTTG
1 TGCCTTTG
13726 TGCCTTTG
1 TGCCTTTG
13734 TGCCTTTG
1 TGCCTTTG
13742 TGCCTTTG
1 TGCCTTTG
13750 TG
1 TG
13752 ATACTGGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.00, C:0.24, G:0.26, T:0.50
Consensus pattern (8 bp):
TGCCTTTG
Found at i:13914 original size:24 final size:24
Alignment explanation
Indices: 13887--13960 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
13877 ATACATTTAA
13887 CAGAAACAGAGCATGCCTAAAACT
1 CAGAAACAGAGCATGCCTAAAACT
*
13911 CAGAAACATAGCATGCCTAAAACT
1 CAGAAACAGAGCATGCCTAAAACT
*
13935 CAGAAACAGAGCAAGCCTAAAA-T
1 CAGAAACAGAGCATGCCTAAAACT
13958 CAG
1 CAG
13961 GGCAATGCCT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
23 4 0.09
24 43 0.91
ACGTcount: A:0.47, C:0.24, G:0.16, T:0.12
Consensus pattern (24 bp):
CAGAAACAGAGCATGCCTAAAACT
Found at i:16573 original size:27 final size:27
Alignment explanation
Indices: 16542--16605 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
16532 ATGATACGAG
*
16542 ATCAAGCCCAGCTGCAAGCAGCACTCC
1 ATCAAGCCCAGCTACAAGCAGCACTCC
16569 ATCAAGCCCAGCTACAAGCAGCACTCC
1 ATCAAGCCCAGCTACAAGCAGCACTCC
16596 ATCAAGCCCA
1 ATCAAGCCCA
16606 TCATCTAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.33, C:0.41, G:0.16, T:0.11
Consensus pattern (27 bp):
ATCAAGCCCAGCTACAAGCAGCACTCC
Found at i:17916 original size:19 final size:19
Alignment explanation
Indices: 17892--17930 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
17882 TTGGGTTTAG
17892 TCAGTTTTTTT-AGTTCAGT
1 TCAGTTTTTTTGAG-TCAGT
17911 TCAGTTTTTTTGAGTCAGT
1 TCAGTTTTTTTGAGTCAGT
17930 T
1 T
17931 AGTCTAAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.15, C:0.10, G:0.18, T:0.56
Consensus pattern (19 bp):
TCAGTTTTTTTGAGTCAGT
Found at i:23051 original size:16 final size:18
Alignment explanation
Indices: 23032--23064 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23022 ATATATATAA
23032 ATAT-AATTT-AGTTAAT
1 ATATGAATTTGAGTTAAT
23048 ATATGAATTTGAGTTAA
1 ATATGAATTTGAGTTAA
23065 GAAATTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (18 bp):
ATATGAATTTGAGTTAAT
Done.