Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015099.1 Corchorus capsularis cultivar CVL-1 contig15120, 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: 9403
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Found at i:612 original size:52 final size:52
Alignment explanation
Indices: 551--677 Score: 182
Period size: 52 Copynumber: 2.4 Consensus size: 52
541 AAGAGAGTTT
*
551 CATCAAGTTTTCAAAGCATTCAATTTAGGTCTTCTCAAATTGGAAAAGTTCC
1 CATCAAGTTTTCAAAGCATTCAATTTAGGTCTTCTCAAAGTGGAAAAGTTCC
* *** * *
603 CATTAAGTTTTCAAAGTGCTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCC
1 CATCAAGTTTTCAAAGCATTCAATTTAGGTCTTCTCAAAGTGGAAAAGTTCC
*
655 CATCAAGTTTTCAAAACATTCAA
1 CATCAAGTTTTCAAAGCATTCAA
678 ACAACTTTTT
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (52 bp):
CATCAAGTTTTCAAAGCATTCAATTTAGGTCTTCTCAAAGTGGAAAAGTTCC
Found at i:5220 original size:10 final size:10
Alignment explanation
Indices: 5191--5227 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
5181 GTCCAAAAAA
5191 AAAAATGATG
1 AAAAATGATG
*
5201 AATGAATGATG
1 AA-AAATGATG
5212 AAAAATGATG
1 AAAAATGATG
5222 AAAAAT
1 AAAAAT
5228 AAATAAAGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.59, C:0.00, G:0.19, T:0.22
Consensus pattern (10 bp):
AAAAATGATG
Found at i:5322 original size:14 final size:13
Alignment explanation
Indices: 5293--5329 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
5283 AGAGTCATGA
*
5293 TTTTCAAAAATGT
1 TTTTAAAAAATGT
5306 TTTTAAAAAATGT
1 TTTTAAAAAATGT
5319 TTTTCAAAAAA
1 TTTT-AAAAAA
5330 ATAATAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (13 bp):
TTTTAAAAAATGT
Found at i:6018 original size:19 final size:18
Alignment explanation
Indices: 5991--6034 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
5981 AAGTGCAATG
*
5991 GAAAAAAAAAGAAAGAAT
1 GAAAAAAAAAGAAAAAAT
*
6009 GAAAATAAAAATAAAAAAT
1 GAAAA-AAAAAGAAAAAAT
6028 GAAAAAA
1 GAAAAAA
6035 TGAAAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (18 bp):
GAAAAAAAAAGAAAAAAT
Found at i:6035 original size:15 final size:15
Alignment explanation
Indices: 6015--6048 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
6005 GAATGAAAAT
6015 AAAAATAAAAAATGA
1 AAAAATAAAAAATGA
*
6030 AAAAATGAAAAATGA
1 AAAAATAAAAAATGA
6045 AAAA
1 AAAA
6049 TGAAGGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAAATAAAAAATGA
Found at i:6040 original size:22 final size:21
Alignment explanation
Indices: 6010--6052 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
6000 AGAAAGAATG
6010 AAAATAAAAATAAAAAATGAA
1 AAAATAAAAATAAAAAATGAA
*
6031 AAAATGAAAAATGAAAAATGAA
1 AAAAT-AAAAATAAAAAATGAA
6053 GGGAAAAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (21 bp):
AAAATAAAAATAAAAAATGAA
Found at i:6050 original size:7 final size:7
Alignment explanation
Indices: 5995--6052 Score: 66
Period size: 7 Copynumber: 8.3 Consensus size: 7
5985 GCAATGGAAA
*
5995 AAAAAAG
1 AAAAATG
6002 AAAGAATG
1 AAA-AATG
6010 -AAAAT-
1 AAAAATG
*
6015 AAAAATA
1 AAAAATG
6022 AAAAATG
1 AAAAATG
6029 AAAAAATG
1 -AAAAATG
6037 AAAAATG
1 AAAAATG
6044 AAAAATG
1 AAAAATG
6051 AA
1 AA
6053 GGGAAAAGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
6 8 0.18
7 27 0.60
8 10 0.22
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:7019 original size:16 final size:16
Alignment explanation
Indices: 6998--7028 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6988 TTTCAATTAA
*
6998 CTTCAATTCTTCAATC
1 CTTCAATGCTTCAATC
7014 CTTCAATGCTTCAAT
1 CTTCAATGCTTCAAT
7029 TTATATCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.29, G:0.03, T:0.42
Consensus pattern (16 bp):
CTTCAATGCTTCAATC
Found at i:7076 original size:24 final size:25
Alignment explanation
Indices: 7049--7103 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
7039 ATAATCTCTT
7049 TCTTCAACTATTCAATGCTTCAA-A
1 TCTTCAACTATTCAATGCTTCAACA
* * *
7073 TCTTCCATTATTCAATTCTTCAACA
1 TCTTCAACTATTCAATGCTTCAACA
7098 -CTTCAA
1 TCTTCAA
7104 TTTATCTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.31, C:0.27, G:0.02, T:0.40
Consensus pattern (25 bp):
TCTTCAACTATTCAATGCTTCAACA
Found at i:7094 original size:8 final size:8
Alignment explanation
Indices: 7048--7188 Score: 57
Period size: 8 Copynumber: 18.4 Consensus size: 8
7038 AATAATCTCT
7048 TTCTTCAA
1 TTCTTCAA
* *
7056 CTATTCAA
1 TTCTTCAA
*
7064 TGCTTCAA
1 TTCTTCAA
* *
7072 ATCTTCCA
1 TTCTTCAA
*
7080 TTATTCAA
1 TTCTTCAA
7088 TTCTTCAA
1 TTCTTCAA
**
7096 CACTTCAA
1 TTCTTCAA
7104 -T-TT--A
1 TTCTTCAA
*
7108 TCTCTTCGA
1 T-TCTTCAA
* * *
7117 CTCTTTAG
1 TTCTTCAA
*
7125 TTATTCAA
1 TTCTTCAA
7133 TTCTTCAA
1 TTCTTCAA
*
7141 TACTTCAA
1 TTCTTCAA
7149 -T-TT--A
1 TTCTTCAA
7153 TTCCTTCAA
1 TT-CTTCAA
7162 TTCTTCAA
1 TTCTTCAA
7170 TTAC-TCAA
1 TT-CTTCAA
*
7178 TGCTTCAA
1 TTCTTCAA
7186 TTC
1 TTC
7189 ACTTCAATGA
Statistics
Matches: 93, Mismatches: 28, Indels: 24
0.64 0.19 0.17
Matches are distributed among these distances:
4 2 0.02
5 1 0.01
6 5 0.05
7 5 0.05
8 75 0.81
9 5 0.05
ACGTcount: A:0.27, C:0.25, G:0.03, T:0.45
Consensus pattern (8 bp):
TTCTTCAA
Found at i:7178 original size:45 final size:45
Alignment explanation
Indices: 7066--7196 Score: 147
Period size: 45 Copynumber: 2.9 Consensus size: 45
7056 CTATTCAATG
* *
7066 CTTCAAATCTTCCATTATTCAATTCTTCAACACTTCAATTTATCT
1 CTTCAAATCTTCAATTATTCAATTCTTCAATACTTCAATTTATCT
* * * *
7111 CTTCGACTCTTTAGTTATTCAATTCTTCAATACTTCAATTTAT-T
1 CTTCAAATCTTCAATTATTCAATTCTTCAATACTTCAATTTATCT
* * *
7155 CCTTCAATTCTTCAATTACTCAATGCTTCAATTCACTTCAAT
1 -CTTCAAATCTTCAATTATTCAATTCTTCAA-T-ACTTCAAT
7197 GACCCAGGGT
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
44 1 0.01
45 61 0.86
46 1 0.01
47 8 0.11
ACGTcount: A:0.27, C:0.25, G:0.02, T:0.45
Consensus pattern (45 bp):
CTTCAAATCTTCAATTATTCAATTCTTCAATACTTCAATTTATCT
Found at i:7224 original size:58 final size:58
Alignment explanation
Indices: 7162--7304 Score: 193
Period size: 58 Copynumber: 2.5 Consensus size: 58
7152 ATTCCTTCAA
* *
7162 TTCTTCAATTACTCAATGCTTCAATTCACTTCAATGACCCAG-GGTGGTCTTT-TTTCG
1 TTCTTCAATTATTCAATGCTTCAATTCACTTCAATGACAC-GTGGTGGTCTTTCTTTCG
* *
7219 TTTCTTCAATTATTCAATGCTTCAATTTACTTCAATGATACGTGGTGGTCTTTCTTTCG
1 -TTCTTCAATTATTCAATGCTTCAATTCACTTCAATGACACGTGGTGGTCTTTCTTTCG
*
7278 TTCCTCAATTATTCAATGCGTT-AATTC
1 TTCTTCAATTATTCAATGC-TTCAATTC
7305 CAAATCTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
57 1 0.01
58 68 0.89
59 7 0.09
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.44
Consensus pattern (58 bp):
TTCTTCAATTATTCAATGCTTCAATTCACTTCAATGACACGTGGTGGTCTTTCTTTCG
Found at i:7243 original size:16 final size:18
Alignment explanation
Indices: 7222--7255 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
7212 TTTTTCGTTT
7222 CTTCAA-TTA-TTCAATG
1 CTTCAATTTACTTCAATG
7238 CTTCAATTTACTTCAATG
1 CTTCAATTTACTTCAATG
7256 ATACGTGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (18 bp):
CTTCAATTTACTTCAATG
Found at i:7325 original size:22 final size:22
Alignment explanation
Indices: 7289--7670 Score: 148
Period size: 22 Copynumber: 17.2 Consensus size: 22
7279 TCCTCAATTA
*
7289 TTCAATGCGTT-AATTCCAAATC
1 TTCAATGC-TTCAATTTCAAATC
**
7311 TTCAATGCTTCAATTTCATTTC
1 TTCAATGCTTCAATTTCAAATC
* *
7333 TTCAATGTTTC--TTTCAATTC
1 TTCAATGCTTCAATTTCAAATC
* *
7353 TTTAATGCTTCAGTTTCAATAT-
1 TTCAATGCTTCAATTTCAA-ATC
*
7375 TTCAATGCTTCAATTTCAGTAT-
1 TTCAATGCTTCAATTTCA-AATC
* * *
7397 TTCAATGTTTCAAATTCAATTC
1 TTCAATGCTTCAATTTCAAATC
*
7419 TTCAATGTTTCAATGCTTC-AAT-
1 TTCAATGCTTCAAT--TTCAAATC
* * * *
7441 TTCAATTCTTCGATATTCCTATTCC
1 TTCAATGCTTC-A-ATTTCAAAT-C
* * *
7466 TATTCCTATTCTTCAAATTCAAA--
1 --TT-CAATGCTTCAATTTCAAATC
7489 TTCAAT-CTTTCAATGCTTC-AAT-
1 TTCAATGC-TTCAAT--TTCAAATC
* * **
7511 TTCAATCCTTCAAATTCAACCC
1 TTCAATGCTTCAATTTCAAATC
* * *
7533 ATCAATGTTTCAATTTCAATTC
1 TTCAATGCTTCAATTTCAAATC
* *
7555 TTCAATGTTTCAGTTTCAATAT-
1 TTCAATGCTTCAATTTCAA-ATC
* *
7577 TTCAATGTTTCAATTTCAATTC
1 TTCAATGCTTCAATTTCAAATC
* * *
7599 TTTCAGTTCTTCCAA-TTC-GATCC
1 -TTCAATGCTT-CAATTTCAAAT-C
*
7622 TTCAATGTTTCAATTTCAACAT-
1 TTCAATGCTTCAATTTCAA-ATC
* * *
7644 TCCAATGCTTCAGTTTCAATTC
1 TTCAATGCTTCAATTTCAAATC
7666 TTCAA
1 TTCAA
7671 ATTCTACTCT
Statistics
Matches: 272, Mismatches: 56, Indels: 64
0.69 0.14 0.16
Matches are distributed among these distances:
19 1 0.00
20 28 0.10
21 13 0.05
22 186 0.68
23 19 0.07
24 10 0.04
26 4 0.01
27 3 0.01
28 8 0.03
ACGTcount: A:0.27, C:0.22, G:0.06, T:0.45
Consensus pattern (22 bp):
TTCAATGCTTCAATTTCAAATC
Found at i:7360 original size:64 final size:65
Alignment explanation
Indices: 7282--7432 Score: 175
Period size: 64 Copynumber: 2.3 Consensus size: 65
7272 CTTTCGTTCC
* *
7282 TCAATTATTCAATGCGTT-AATTCCAA-ATCTTCAATGCTTCAATTTCA-TTTCTTCAATGTTTC
1 TCAATTCTTCAATGC-TTCAATTCCAATAT-TTCAATGCTTCAATTTCAGTAT-TTCAATGTTTC
*
7344 -TT
63 AAT
* * *
7346 TCAATTCTTTAATGCTTCAGTTTCAATATTTCAATGCTTCAATTTCAGTATTTCAATGTTTCAAA
1 TCAATTCTTCAATGCTTCAATTCCAATATTTCAATGCTTCAATTTCAGTATTTCAATGTTTC-AA
7411 T
65 T
*
7412 TCAATTCTTCAATGTTTCAAT
1 TCAATTCTTCAATGCTTCAAT
7433 GCTTCAATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
63 2 0.03
64 48 0.66
65 4 0.05
66 19 0.26
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.47
Consensus pattern (65 bp):
TCAATTCTTCAATGCTTCAATTCCAATATTTCAATGCTTCAATTTCAGTATTTCAATGTTTCAAT
Found at i:7513 original size:14 final size:14
Alignment explanation
Indices: 7496--7529 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
7486 AAATTCAATC
*
7496 TTTCAATGCTTCAA
1 TTTCAATCCTTCAA
7510 TTTCAATCCTTCAA
1 TTTCAATCCTTCAA
*
7524 ATTCAA
1 TTTCAA
7530 CCCATCAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (14 bp):
TTTCAATCCTTCAA
Found at i:7523 original size:36 final size:36
Alignment explanation
Indices: 7483--7559 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
7473 ATTCTTCAAA
* **
7483 TTCAAATTCAATCTTTCAATGCTTCAATTTCAATCC
1 TTCAAATTCAACCCATCAATGCTTCAATTTCAATCC
* *
7519 TTCAAATTCAACCCATCAATGTTTCAATTTCAATTC
1 TTCAAATTCAACCCATCAATGCTTCAATTTCAATCC
7555 TTCAA
1 TTCAA
7560 TGTTTCAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.40
Consensus pattern (36 bp):
TTCAAATTCAACCCATCAATGCTTCAATTTCAATCC
Found at i:7545 original size:8 final size:8
Alignment explanation
Indices: 7534--7590 Score: 61
Period size: 8 Copynumber: 7.6 Consensus size: 8
7524 ATTCAACCCA
7534 TCAATGTT
1 TCAATGTT
7542 TCAA--TT
1 TCAATGTT
7548 TCAAT-TCT
1 TCAATGT-T
7556 TCAATGTT
1 TCAATGTT
7564 TC-A-GTT
1 TCAATGTT
*
7570 TCAATATT
1 TCAATGTT
7578 TCAATGTT
1 TCAATGTT
7586 TCAAT
1 TCAAT
7591 TTCAATTCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
6 11 0.26
7 3 0.07
8 27 0.64
9 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (8 bp):
TCAATGTT
Found at i:7551 original size:14 final size:14
Alignment explanation
Indices: 7534--7596 Score: 60
Period size: 14 Copynumber: 4.4 Consensus size: 14
7524 ATTCAACCCA
7534 TCAATGTTTCAATT
1 TCAATGTTTCAATT
7548 TCAAT-TCTTCAATGTT
1 TCAATGT-TTCAA--TT
7564 TC-A-GTTTCAATATT
1 TCAATGTTTC-A-ATT
7578 TCAATGTTTCAATT
1 TCAATGTTTCAATT
7592 TCAAT
1 TCAAT
7597 TCTTTCAGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
13 1 0.02
14 25 0.61
15 5 0.12
16 10 0.24
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.49
Consensus pattern (14 bp):
TCAATGTTTCAATT
Found at i:7792 original size:22 final size:21
Alignment explanation
Indices: 7714--7797 Score: 71
Period size: 22 Copynumber: 3.9 Consensus size: 21
7704 TGATCTTTCT
* *
7714 TCAATTCTTCAATTTTTC-AATT
1 TCAATGCTTCAA--TTTCAAATG
* *
7736 TCAATACTTCAAATTCCAAATG
1 TCAATGCTTC-AATTTCAAATG
* *
7758 CCAATGTTTCAATTTCAACATG
1 TCAATGCTTCAATTTCAA-ATG
7780 TCAATGCTTCAATTTCAA
1 TCAATGCTTCAATTTCAA
7798 TTCTTCCATT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
21 10 0.20
22 38 0.76
23 2 0.04
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.40
Consensus pattern (21 bp):
TCAATGCTTCAATTTCAAATG
Found at i:7797 original size:14 final size:14
Alignment explanation
Indices: 7780--7827 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
7770 TTTCAACATG
*
7780 TCAATGCTTCAATT
1 TCAATTCTTCAATT
*
7794 TCAATTCTTCCATT
1 TCAATTCTTCAATT
7808 TCAATTCTTCGAA-T
1 TCAATTCTTC-AATT
7822 TCAATT
1 TCAATT
7828 TCAATGTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
14 29 0.97
15 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.04, T:0.46
Consensus pattern (14 bp):
TCAATTCTTCAATT
Done.