Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011342.1 Corchorus capsularis cultivar CVL-1 contig11363, 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: 3259
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.37
Found at i:806 original size:21 final size:22
Alignment explanation
Indices: 782--878 Score: 80
Period size: 22 Copynumber: 4.5 Consensus size: 22
772 TTACTATTTC
782 ACTGATTA-TTCTTTACTTTGT
1 ACTGATTACTTCTTTACTTTGT
803 ACTGATTACTAT-TTTACTCTTGT
1 ACTGATTACT-TCTTTACT-TTGT
*
826 --TGATTACCTTC-TTACTTTTT
1 ACTGATTA-CTTCTTTACTTTGT
* *
846 ACTGATTACCAT-TTTACTCTTTT
1 ACTGATTA-CTTCTTTACT-TTGT
869 ACTGATTACT
1 ACTGATTACT
879 ATTTTCTGCT
Statistics
Matches: 64, Mismatches: 3, Indels: 17
0.76 0.04 0.20
Matches are distributed among these distances:
20 3 0.05
21 20 0.31
22 24 0.38
23 17 0.27
ACGTcount: A:0.21, C:0.19, G:0.07, T:0.54
Consensus pattern (22 bp):
ACTGATTACTTCTTTACTTTGT
Found at i:853 original size:43 final size:43
Alignment explanation
Indices: 794--1123 Score: 140
Period size: 43 Copynumber: 7.7 Consensus size: 43
784 TGATTATTCT
*
794 TTACTTTGTACTGATTACTATTTTACTCTTGTTGATTACCTTC
1 TTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCTTC
* * *
837 TTACTTTTTACTGATTACCATTTTACTCTTTTACTGATTACTATTTTC
1 TTACTTTTTACTGATTACTATTTTACTCTTGT--TGATTAC---CTTC
* * * * * *
885 TGCTCCTTTTT-TTGATTACTCTTTTAGT-TTTTACTGATTGCCTT-
1 T--TACTTTTTACTGATTACTATTTTACTCTTGT--TGATTACCTTC
* * * * *
929 TTGCTTTTTA-TCGATTACCT-TTTTACTTTTTGCTGATTAGCTTT
1 TTACTTTTTACT-GATTA-CTATTTTAC-TCTTGTTGATTACCTTC
* * *
973 TTACTCTTTACTGATTACCT-TTTTACTCTT-TCTAATTTCCTT-
1 TTACTTTTTACTGATTA-CTATTTTACTCTTGT-TGATTACCTTC
* * * **
1015 TTGCTTCTTACTTATTACCCT-TTTTACTCTTACTGATTA----C
1 TTACTTTTTACTGATTA--CTATTTTACTCTTGTTGATTACCTTC
* *
1055 -TA---TTTACTG-TCTA-TGATTTTACTCTTGTTGACTACTTTC
1 TTACTTTTTACTGAT-TACT-ATTTTACTCTTGTTGATTACCTTC
1094 TTACTTTTTACTGATTACTATTTTACTCTT
1 TTACTTTTTACTGATTACTATTTTACTCTT
1124 TACTAATTAC
Statistics
Matches: 219, Mismatches: 37, Indels: 62
0.69 0.12 0.19
Matches are distributed among these distances:
33 1 0.00
35 16 0.07
36 7 0.03
39 2 0.01
40 2 0.01
42 21 0.10
43 94 0.43
44 28 0.13
45 12 0.05
48 16 0.07
49 13 0.06
50 7 0.03
ACGTcount: A:0.17, C:0.19, G:0.07, T:0.56
Consensus pattern (43 bp):
TTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCTTC
Found at i:929 original size:21 final size:21
Alignment explanation
Indices: 897--1173 Score: 116
Period size: 22 Copynumber: 13.2 Consensus size: 21
887 CTCCTTTTTT
*
897 TGATTACTCTTTTAGTTTTTAC
1 TGATTAC-CTTTTACTTTTTAC
* *
919 TGATTGCCTTTTGCTTTTTA-
1 TGATTACCTTTTACTTTTTAC
*
939 TCGATTACCTTTTTACTTTTTGC
1 T-GATTACC-TTTTACTTTTTAC
* *
962 TGATTAGCTTTTTACTCTTTAC
1 TGATTA-CCTTTTACTTTTTAC
*
984 TGATTACCTTTTTACTCTTT-C
1 TGATTACC-TTTTACTTTTTAC
* * * *
1005 TAATTTCCTTTTGCTTCTTAC
1 TGATTACCTTTTACTTTTTAC
* *
1026 TTATTACCCTTTTTAC-TCTTAC
1 TGATTA-CC-TTTTACTTTTTAC
*
1048 TGATTA-CTATTTAC--TGT-C
1 TGATTACCT-TTTACTTTTTAC
* *
1066 T-ATGA--TTTTACTCTTGT--
1 TGATTACCTTTTACT-TTTTAC
* *
1083 TGACTACTTTCTTACTTTTTAC
1 TGATTACCTT-TTACTTTTTAC
* *
1105 TGATTACTATTTTACTCTTTAC
1 TGATTAC-CTTTTACTTTTTAC
* *
1127 TAATTACCATTTTACCCTTTTA-
1 TGATTACC-TTTTA-CTTTTTAC
*
1149 -GA-TACCTTTGCACTTTTTAC
1 TGATTACCTTT-TACTTTTTAC
1169 TGATT
1 TGATT
1174 GCATGCTATT
Statistics
Matches: 195, Mismatches: 35, Indels: 50
0.70 0.12 0.18
Matches are distributed among these distances:
15 5 0.03
16 1 0.01
17 4 0.02
18 7 0.04
19 11 0.06
20 25 0.13
21 38 0.19
22 90 0.46
23 14 0.07
ACGTcount: A:0.18, C:0.20, G:0.07, T:0.55
Consensus pattern (21 bp):
TGATTACCTTTTACTTTTTAC
Found at i:1358 original size:22 final size:24
Alignment explanation
Indices: 1333--1376 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
1323 TTAACCACTC
*
1333 AACTCTTAGTTAT-GA-TCACTTT
1 AACTCTTAATTATCGATTCACTTT
1355 AACTCTTAATTATCGATTCACT
1 AACTCTTAATTATCGATTCACT
1377 GATTACCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 2 0.11
24 5 0.26
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (24 bp):
AACTCTTAATTATCGATTCACTTT
Found at i:1536 original size:13 final size:13
Alignment explanation
Indices: 1518--1542 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1508 ATTACTGATT
1518 TACTGATTACTGC
1 TACTGATTACTGC
1531 TACTGATTACTG
1 TACTGATTACTG
1543 ACACTCATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (13 bp):
TACTGATTACTGC
Found at i:1581 original size:63 final size:61
Alignment explanation
Indices: 1454--1636 Score: 245
Period size: 56 Copynumber: 3.0 Consensus size: 61
1444 ATTACTATCT
* *
1454 TTTACCTGATTACTGATTACTATTACCTTAACTC-TGATTAATCTC-TTTTACTTAATTACTGA
1 TTTA-CTGATTACTG-CTACTATTA-CTGAACTCATGATTAATCTCTTTTTACTTAATTACTGA
1516 TTTACTGATTACTGCTACTGATTACTGACACTCATGATTAATCTCTTTTTACTTAATTACTGA
1 TTTACTGATTACTGCTACT-ATTACTGA-ACTCATGATTAATCTCTTTTTACTTAATTACTGA
*
1579 TTTACTGATTACTGCTAC--TT--TG-ACTCATGATTAATCTCTTTTTACTTAATTAATGA
1 TTTACTGATTACTGCTACTATTACTGAACTCATGATTAATCTCTTTTTACTTAATTACTGA
1635 TT
1 TT
1637 GCCCCCTTTC
Statistics
Matches: 114, Mismatches: 3, Indels: 14
0.87 0.02 0.11
Matches are distributed among these distances:
56 35 0.31
58 2 0.02
60 9 0.08
61 18 0.16
62 15 0.13
63 35 0.31
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (61 bp):
TTTACTGATTACTGCTACTATTACTGAACTCATGATTAATCTCTTTTTACTTAATTACTGA
Found at i:2383 original size:51 final size:49
Alignment explanation
Indices: 2290--2479 Score: 193
Period size: 51 Copynumber: 3.8 Consensus size: 49
2280 AGGGTGACAT
* * *
2290 TTTATTTACTAATTACTTAAAAATTCAATCTTTCATTTAAAGATTAAAGC
1 TTTATTTACTAATTACTTAAAGATTCAATCTTTTATTCAAAGATTAAA-C
* ** ** * *
2340 TTTATTTACTAATCACTCTAAAGATTCAATCTTTTACCCAAAGACGACAT
1 TTTATTTACTAATTACT-TAAAGATTCAATCTTTTATTCAAAGATTAAAC
* * *
2390 TCTTATTTACCAATTACTTAGAA-ATCCAAATCTTTTATTCAAAGGTTAAATC
1 T-TTATTTACTAATTACTTA-AAGATTC-AATCTTTTATTCAAAGATTAAA-C
2442 TTTATTTACTAATTACTCTAAAGATTCAATCTTTTATT
1 TTTATTTACTAATTACT-TAAAGATTCAATCTTTTATT
2480 AGAGGGAGGC
Statistics
Matches: 111, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
50 22 0.20
51 83 0.75
52 6 0.05
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (49 bp):
TTTATTTACTAATTACTTAAAGATTCAATCTTTTATTCAAAGATTAAAC
Found at i:2439 original size:102 final size:100
Alignment explanation
Indices: 2285--2477 Score: 296
Period size: 102 Copynumber: 1.9 Consensus size: 100
2275 TTCAAAGGGT
* * *
2285 GACATTTTATTTACTAATTACTTAAAAATTCAATCTTTCATTTAAAGATTAAAGCTTTATTTACT
1 GACATTTTATTTACCAATTACTTAAAAATCCAATCTTTCATTCAAAGATTAAAGCTTTATTTACT
2350 AATCACTCTAAAGATTCAATCTTTTACCCAAAGAC
66 AATCACTCTAAAGATTCAATCTTTTACCCAAAGAC
* * * *
2385 GACATTCTTATTTACCAATTACTTAGAAATCCAAATCTTTTATTCAAAGGTTAAATCTTTATTTA
1 GACATT-TTATTTACCAATTACTTAAAAATCC-AATCTTTCATTCAAAGATTAAAGCTTTATTTA
*
2450 CTAATTACTCTAAAGATTCAATCTTTTA
64 CTAATCACTCTAAAGATTCAATCTTTTA
2478 TTAGAGGGAG
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
100 6 0.07
101 22 0.27
102 55 0.66
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (100 bp):
GACATTTTATTTACCAATTACTTAAAAATCCAATCTTTCATTCAAAGATTAAAGCTTTATTTACT
AATCACTCTAAAGATTCAATCTTTTACCCAAAGAC
Found at i:2649 original size:10 final size:11
Alignment explanation
Indices: 2624--2652 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
2614 AGATTAGTCC
2624 TTTATCACCAA
1 TTTATCACCAA
2635 TTTATCACC-A
1 TTTATCACCAA
2645 TTTATCAC
1 TTTATCAC
2653 TAAAGATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.41
Consensus pattern (11 bp):
TTTATCACCAA
Done.