Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013972.1 Corchorus capsularis cultivar CVL-1 contig13993, 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: 6663
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:790 original size:43 final size:43
Alignment explanation
Indices: 735--1087 Score: 224
Period size: 43 Copynumber: 8.4 Consensus size: 43
725 TGATTATTCT
* * *
735 TTACTTTGTACTGATTACTATTTTACTCTTGTTGACTACCTTC
1 TTACTTTTTACTGATTACTATTTTACTCTTGCTGATTACCTTC
*
778 TTACTTTTTACTGATTA-TCATTTTACTCTTTTACTGATTA-C-TC
1 TTACTTTTTACTGATTACT-ATTTTACTC--TTGCTGATTACCTTC
* ** *
821 TTTACTATTTT-CTGCTCCCCT-TTTT-CT-TTACTGATTACTCTT-
1 -TTACT-TTTTACTGAT-TACTATTTTACTCTTGCTGATTAC-CTTC
* * * * *
863 TTACTTTTTACTGATTGC-CTTTTGCTTCTTGCTGATTAGCTTT
1 TTACTTTTTACTGATTACTATTTTAC-TCTTGCTGATTACCTTC
* * * * * *
906 TTACTCTTTACTCATCACCT-TTTTACTCTTACCGATTTCCTT-
1 TTACTTTTTACTGATTA-CTATTTTACTCTTGCTGATTACCTTC
* * *
948 TTACTTCTTACTTATTAC---TTT--T-TTACTGATTA-CTAT-
1 TTACTTTTTACTGATTACTATTTTACTCTTGCTGATTACCT-TC
* *
984 TTACTTTTTACTGACTACTATTTTACTCTTGTTGATTACCTTC
1 TTACTTTTTACTGATTACTATTTTACTCTTGCTGATTACCTTC
* *
1027 TTACTTTTTACTGATTACTGTTTTACTCCTTACTGATTACCTTC
1 TTACTTTTTACTGATTACTATTTTACT-CTTGCTGATTACCTTC
*
1071 TTAC-TCTTACTGATTAC
1 TTACTTTTTACTGATTAC
1088 CCTTTACTCT
Statistics
Matches: 245, Mismatches: 37, Indels: 56
0.72 0.11 0.17
Matches are distributed among these distances:
35 2 0.01
36 24 0.10
37 1 0.00
39 6 0.02
40 19 0.08
41 12 0.05
42 28 0.11
43 103 0.42
44 38 0.16
45 11 0.04
46 1 0.00
ACGTcount: A:0.18, C:0.22, G:0.07, T:0.54
Consensus pattern (43 bp):
TTACTTTTTACTGATTACTATTTTACTCTTGCTGATTACCTTC
Found at i:824 original size:22 final size:21
Alignment explanation
Indices: 719--1100 Score: 133
Period size: 21 Copynumber: 18.2 Consensus size: 21
709 AGCATCACTA
*
719 TTTTACTGATTATTCTTTACT
1 TTTTACTGATTACTCTTTACT
* *
740 TTGTACTGATTACTATTTTACT
1 TTTTACTGATTACT-CTTTACT
* *
762 CTTGT--TGACTAC-CTTCTTACT
1 -TTTTACTGATTACTC-T-TTACT
783 TTTTACTGATTA-TCATTTTACT
1 TTTTACTGATTACTC--TTTACT
805 CTTTTACTGATTACTCTTTACT
1 -TTTTACTGATTACTCTTTACT
* * *
827 ATTTT-CTG-CTCCCCTTT--T
1 -TTTTACTGATTACTCTTTACT
845 TCTTTACTGATTACTCTTTTACT
1 T-TTTACTGATTACTC-TTTACT
* *
868 TTTTACTGATTGC-CTTTTGCT
1 TTTTACTGATTACTC-TTTACT
* * *
889 TCTTGCTGATTAGCTTTTTACT
1 TTTTACTGATTA-CTCTTTACT
* * * *
911 CTTTACTCATCACCTTTTTAC-
1 TTTTACTGATTA-CTCTTTACT
* * *
932 TCTTACCGATTTC-CTTTTACT
1 TTTTACTGATTACTC-TTTACT
* *
953 TCTTACTTATTA--C--T--T
1 TTTTACTGATTACTCTTTACT
*
968 TTTTACTGATTACTATTTACT
1 TTTTACTGATTACTCTTTACT
* *
989 TTTTACTGACTACTATTTTACT
1 TTTTACTGATTACT-CTTTACT
*
1011 CTTGT--TGATTAC-CTTCTTACT
1 -TTTTACTGATTACTC-T-TTACT
*
1032 TTTTACTGATTACTGTTTTACT
1 TTTTACTGATTACT-CTTTACT
**
1054 CCTTACTGATTAC-CTTCTTAC-
1 TTTTACTGATTACTC-T-TTACT
* *
1075 TCTTACTGATTACCCTTTACT
1 TTTTACTGATTACTCTTTACT
*
1096 CTTTA
1 TTTTA
1101 TCATTCTTCC
Statistics
Matches: 270, Mismatches: 53, Indels: 76
0.68 0.13 0.19
Matches are distributed among these distances:
15 11 0.04
17 2 0.01
18 4 0.01
19 4 0.01
20 28 0.10
21 102 0.38
22 93 0.34
23 24 0.09
24 2 0.01
ACGTcount: A:0.18, C:0.22, G:0.06, T:0.54
Consensus pattern (21 bp):
TTTTACTGATTACTCTTTACT
Found at i:1053 original size:65 final size:65
Alignment explanation
Indices: 962--1088 Score: 159
Period size: 65 Copynumber: 2.0 Consensus size: 65
952 TTCTTACTTA
** * **
962 TTACTTTTTTACTGATTACTATTTACTTTTTACTGACTA-CTATTTTACTCTTGTTGATTACCTT
1 TTACTTTTTTACTGATTACTATTTACTCCTTACTGACTACCT-TCTTACTCTTACTGATTACCTT
1026 C
65 C
* *
1027 TTAC-TTTTTACTGATTACTGTTTTACTCCTTACTGATTACCTTCTTACTCTTACTGATTACC
1 TTACTTTTTTACTGATTACT-ATTTACTCCTTACTGACTACCTTCTTACTCTTACTGATTACC
1089 CTTTACTCTT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
64 15 0.28
65 36 0.68
66 2 0.04
ACGTcount: A:0.20, C:0.21, G:0.06, T:0.53
Consensus pattern (65 bp):
TTACTTTTTTACTGATTACTATTTACTCCTTACTGACTACCTTCTTACTCTTACTGATTACCTTC
Found at i:1191 original size:14 final size:14
Alignment explanation
Indices: 1174--1214 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1164 TTTGCCATTT
1174 TTACTTTTTACTGA
1 TTACTTTTTACTGA
* *
1188 TTACTCTTTATTGA
1 TTACTTTTTACTGA
1202 TTACTATTTTACT
1 TTACT-TTTTACT
1215 CTCTTGAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.22, C:0.15, G:0.05, T:0.59
Consensus pattern (14 bp):
TTACTTTTTACTGA
Found at i:1237 original size:26 final size:26
Alignment explanation
Indices: 1201--1254 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
1191 CTCTTTATTG
1201 ATTACTATTTT-ACTCTCTTGAATTTA
1 ATTACTATTTTCACTCT-TTGAATTTA
1227 ATTACTATTTTCACTCTTTGAATTTA
1 ATTACTATTTTCACTCTTTGAATTTA
1253 AT
1 AT
1255 CACCATTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 22 0.81
27 5 0.19
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.54
Consensus pattern (26 bp):
ATTACTATTTTCACTCTTTGAATTTA
Found at i:1262 original size:26 final size:26
Alignment explanation
Indices: 1207--1262 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
1197 ATTGATTACT
* *
1207 ATTTTACTCTCTTGAATTTAATTACT
1 ATTTTACTCTCTTGAATTTAATCACC
1233 ATTTTCACTCT-TTGAATTTAATCACC
1 ATTTT-ACTCTCTTGAATTTAATCACC
1259 ATTT
1 ATTT
1263 GTCATTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 22 0.81
27 5 0.19
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.52
Consensus pattern (26 bp):
ATTTTACTCTCTTGAATTTAATCACC
Found at i:2273 original size:51 final size:49
Alignment explanation
Indices: 2216--2471 Score: 237
Period size: 51 Copynumber: 5.0 Consensus size: 49
2206 AGGGTGACAT
*
2216 TTTATTTACTAATTACTTAAGAAATCCAATCTTTTATTCAATGGTTAAATC
1 TTTATTTACTAATTACTTAA-AAATTCAATCTTTTATTCAA-GGTTAAATC
* * * * * * *
2267 TTTATTTATTAACTACCCTAAAAATTCAATCTTTTACTCAAAGATAACATT
1 TTTATTTACTAATTA-CTTAAAAATTCAATCTTTTATTCAAGGTTAA-ATC
* ** *
2318 TTTGTTTACCGATTACTTAAAAATTCAATCTTTTGTTCAAAGGTTAAATC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTC-AAGGTTAAATC
* * * * *
2368 TTTATTTACTAATTACCCTAAAAATTCAATCTTTTACTCAAAGATAATATT
1 TTTATTTACTAATTA-CTTAAAAATTCAATCTTTTATTCAAGGTTAA-ATC
*
2419 TTTATTTA-TCAATTTACTTAAAAATTCAAT-TTTTCATTCAAAGGTTACATC
1 TTTATTTACT-AA-TTACTTAAAAATTCAATCTTTT-ATTC-AAGGTTAAATC
2470 TT
1 TT
2472 CTAGCAAAAG
Statistics
Matches: 162, Mismatches: 34, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
50 49 0.30
51 101 0.62
52 12 0.07
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.45
Consensus pattern (49 bp):
TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAGGTTAAATC
Found at i:2333 original size:102 final size:101
Alignment explanation
Indices: 2215--2471 Score: 381
Period size: 101 Copynumber: 2.5 Consensus size: 101
2205 AAGGGTGACA
* * * *
2215 TTTTATTTACTAATTACTTAAGAAATCCAATCTTTTATTCAATGGTTAAATCTTTATTTATTAAC
1 TTTTATTTACCAATTACTTAA-AAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAAC
2280 TACCCTAAAAATTCAATCTTTTACTCAAAGATAACAT
65 TACCCTAAAAATTCAATCTTTTACTCAAAGATAACAT
* * * *
2317 TTTTGTTTACCGATTACTTAAAAATTCAATCTTTTGTTCAAAGGTTAAATCTTTATTTACTAATT
1 TTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAACT
*
2382 ACCCTAAAAATTCAATCTTTTACTCAAAGATAATAT
66 ACCCTAAAAATTCAATCTTTTACTCAAAGATAACAT
* *
2418 TTTTATTTATCAATTTACTTAAAAATTCAAT-TTTTCATTCAAAGGTTACATCTT
1 TTTTATTTACCAA-TTACTTAAAAATTCAATCTTTT-ATTCAAAGGTTAAATCTT
2472 CTAGCAAAAG
Statistics
Matches: 139, Mismatches: 14, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
101 88 0.63
102 51 0.37
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.45
Consensus pattern (101 bp):
TTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAACT
ACCCTAAAAATTCAATCTTTTACTCAAAGATAACAT
Found at i:2521 original size:20 final size:20
Alignment explanation
Indices: 2458--2516 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
2448 TTTTTCATTC
*
2458 AAAGGTTACATCTTCTAGCA
1 AAAGGTTACATCTTTTAGCA
2478 AAAGGTTACATCTTTTAGCA
1 AAAGGTTACATCTTTTAGCA
*
2498 AAATGTTACATCTTTTAGC
1 AAAGGTTACATCTTTTAGC
2517 CAAATATCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.36
Consensus pattern (20 bp):
AAAGGTTACATCTTTTAGCA
Found at i:3255 original size:24 final size:26
Alignment explanation
Indices: 3208--3256 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3198 TTTTTTTTTC
3208 GAAAAGAAGAAAAAAAAACCCAAGAGA
1 GAAAAGAAGAAAAAAAAA-CCAAGAGA
*
3235 GAAAAG-AGAAAAAAGAA-CAAGA
1 GAAAAGAAGAAAAAAAAACCAAGA
3257 ACCCTAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
26 10 0.48
27 6 0.29
ACGTcount: A:0.71, C:0.08, G:0.20, T:0.00
Consensus pattern (26 bp):
GAAAAGAAGAAAAAAAAACCAAGAGA
Found at i:5031 original size:27 final size:27
Alignment explanation
Indices: 5001--5070 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
4991 AAGGTGAACC
*
5001 CAAAAATGACTAAAATGCCCCTGAGTA
1 CAAAAATGACCAAAATGCCCCTGAGTA
* *
5028 CAAAAATGACCAAAATGCCCCTGGGTG
1 CAAAAATGACCAAAATGCCCCTGAGTA
5055 CAAAAATGACCAAAAT
1 CAAAAATGACCAAAAT
5071 ACCCTTGGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.46, C:0.23, G:0.16, T:0.16
Consensus pattern (27 bp):
CAAAAATGACCAAAATGCCCCTGAGTA
Found at i:6295 original size:14 final size:14
Alignment explanation
Indices: 6276--6302 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6266 TTATTCACTT
6276 TTTACTGATTACTC
1 TTTACTGATTACTC
6290 TTTACTGATTACT
1 TTTACTGATTACT
6303 AATTAATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTACTGATTACTC
Found at i:6379 original size:35 final size:35
Alignment explanation
Indices: 6276--6405 Score: 106
Period size: 35 Copynumber: 3.7 Consensus size: 35
6266 TTATTCACTT
** ** *
6276 TTTACTGATTACTCTTTACTGATTACTAATTAATAT-
1 TTTACTGATTACTCTTTACTCTTTAC--ATTTTTTTC
*
6312 TTTACTGATT--TCTTCTCACTCCTTAC-TATTTTTTC
1 TTTACTGATTACTCTT-T-ACTCTTTACAT-TTTTTTC
6347 TTTACTGATTACTCTTTACTCTTTACATTTTTTTC
1 TTTACTGATTACTCTTTACTCTTTACATTTTTTTC
* * *
6382 TTTATTGGTTACTCTTTGCTCTTT
1 TTTACTGATTACTCTTTACTCTTT
6406 TACTCTTACT
Statistics
Matches: 78, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
33 1 0.01
34 7 0.09
35 47 0.60
36 19 0.24
37 4 0.05
ACGTcount: A:0.18, C:0.19, G:0.05, T:0.57
Consensus pattern (35 bp):
TTTACTGATTACTCTTTACTCTTTACATTTTTTTC
Found at i:6456 original size:22 final size:22
Alignment explanation
Indices: 6403--6456 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
6393 CTCTTTGCTC
* *
6403 TTTTACTC-TTACTGATTACTA
1 TTTTACTCTTTACTAATTACCA
*
6424 TTTCACTCTTTACTAATTACCA
1 TTTTACTCTTTACTAATTACCA
*
6446 TTTTACCCTTT
1 TTTTACTCTTT
6457 CAGATACCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.22, C:0.24, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTTACTCTTTACTAATTACCA
Done.