Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010077.1 Corchorus capsularis cultivar CVL-1 contig10098, 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: 17761
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2924 original size:31 final size:30
Alignment explanation
Indices: 2889--2964 Score: 102
Period size: 28 Copynumber: 2.6 Consensus size: 30
2879 ATACCGTAGA
*
2889 GGTCCCTCTACTTACAAAAAGGGATCAATTT
1 GGTCCCTCTACTTACAAAAACGG-TCAATTT
* *
2920 GGTCCCCCTAC-TAC-AAAACTGTCAATTT
1 GGTCCCTCTACTTACAAAAACGGTCAATTT
2948 GGTCCCTCTACTTACAA
1 GGTCCCTCTACTTACAA
2965 TTTGGTGTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
28 17 0.44
29 8 0.21
30 4 0.10
31 10 0.26
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (30 bp):
GGTCCCTCTACTTACAAAAACGGTCAATTT
Found at i:2977 original size:31 final size:29
Alignment explanation
Indices: 2889--2992 Score: 97
Period size: 31 Copynumber: 3.5 Consensus size: 29
2879 ATACCGTAGA
2889 GGTCCCTCTACTTACAAAAAGG-GATCAATTT
1 GGTCCCTCTACTTAC--AAAGGTG-TCAATTT
* **
2920 GGTCCCCCTAC-TACAAAACTGTCAATTT
1 GGTCCCTCTACTTACAAAGGTGTCAATTT
*
2948 GGTCCCTCTACTTACAATTTGGTGTCAA-TT
1 GGTCCCTCTACTTACAA--AGGTGTCAATTT
2978 GAGTCCCTCTACTTA
1 G-GTCCCTCTACTTA
2993 ACAACAAACT
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
28 20 0.33
29 6 0.10
30 6 0.10
31 29 0.48
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (29 bp):
GGTCCCTCTACTTACAAAGGTGTCAATTT
Found at i:3104 original size:29 final size:31
Alignment explanation
Indices: 3060--3136 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 31
3050 TGACACCAAA
* * *
3060 TTGTAAGTAGAAGGACCAAATTGA-CAGTTT
1 TTGTAAGTAGAGGGACCAAAGTGATCACTTT
* *
3090 TTGT-AGTAGGGGGACCAAAGTGATCCCTTT
1 TTGTAAGTAGAGGGACCAAAGTGATCACTTT
3120 TTGTAAGTAGAGGGACC
1 TTGTAAGTAGAGGGACC
3137 TGTACGGTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 16 0.41
30 12 0.31
31 11 0.28
ACGTcount: A:0.30, C:0.13, G:0.29, T:0.29
Consensus pattern (31 bp):
TTGTAAGTAGAGGGACCAAAGTGATCACTTT
Found at i:9104 original size:2 final size:2
Alignment explanation
Indices: 9097--9124 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9087 TTTAAGAAAT
9097 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
9125 CTCATTTCGT
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):
TA
Found at i:10163 original size:21 final size:21
Alignment explanation
Indices: 10137--10177 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10127 ACCCTAGTTG
10137 GAAAATG-CAGAAATATATATC
1 GAAAATGACA-AAATATATATC
*
10158 GAAAATGACAAGATATATAT
1 GAAAATGACAAAATATATAT
10178 GTTCACTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.54, C:0.07, G:0.15, T:0.24
Consensus pattern (21 bp):
GAAAATGACAAAATATATATC
Found at i:10240 original size:14 final size:13
Alignment explanation
Indices: 10221--10259 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
10211 ATTTACCGAC
10221 TTTCTTTTTCTTTT
1 TTTCTTTTT-TTTT
10235 TTTCTTTTTTTCTT
1 TTTCTTTTTTT-TT
10249 TTTCCTTTTTT
1 TTT-CTTTTTT
10260 GGTATCGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 14 0.61
15 7 0.30
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTCTTTTTTTTT
Found at i:10259 original size:8 final size:8
Alignment explanation
Indices: 10225--10251 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
10215 ACCGACTTTC
10225 TTTTTCTT
1 TTTTTCTT
10233 TTTTTCTT
1 TTTTTCTT
10241 TTTTTCTT
1 TTTTTCTT
10249 TTT
1 TTT
10252 CCTTTTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTCTT
Found at i:11947 original size:14 final size:14
Alignment explanation
Indices: 11910--11947 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
11900 CTACATAGCA
*
11910 TTTTTTTTGCTCTT
1 TTTTTTTTCCTCTT
*
11924 TTTTTCTTCCTCTT
1 TTTTTTTTCCTCTT
11938 TTTTTTTTCC
1 TTTTTTTTCC
11948 CCCCTCTCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (14 bp):
TTTTTTTTCCTCTT
Found at i:12516 original size:23 final size:22
Alignment explanation
Indices: 12488--12545 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
12478 ATTTATATGA
* *
12488 ATAAATATATAAATTAAAAAATT
1 ATAAATACATAAA-TAAAAAAGT
* *
12511 ATAAATAGAGAAATAAAAAAGT
1 ATAAATACATAAATAAAAAAGT
12533 ATAAATACATAAA
1 ATAAATACATAAA
12546 AATCTTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (22 bp):
ATAAATACATAAATAAAAAAGT
Done.