Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008439.1 Corchorus capsularis cultivar CVL-1 contig08460, 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: 17500
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:4333 original size:16 final size:16
Alignment explanation
Indices: 4314--4351 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
4304 GGGTGAATAC
4314 TTGATAGGGTTATTAT
1 TTGATAGGGTTATTAT
4330 TTGATAGGGTTATTAT
1 TTGATAGGGTTATTAT
4346 TTGATA
1 TTGATA
4352 ATTGAGTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (16 bp):
TTGATAGGGTTATTAT
Found at i:5663 original size:19 final size:18
Alignment explanation
Indices: 5639--5674 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5629 TGAAGATTTC
5639 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
5658 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
5675 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:8277 original size:30 final size:30
Alignment explanation
Indices: 8243--8305 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
8233 CATCTTCAAG
*
8243 TCCATGATAAGTCCTTGG-CGCTTCATTCCC
1 TCCATGATAAG-CCTTGGACGCATCATTCCC
8273 TCCATGATAAGCCTTGGACGCATCATTCCC
1 TCCATGATAAGCCTTGGACGCATCATTCCC
8303 TCC
1 TCC
8306 CCCTTGAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 6 0.19
30 25 0.81
ACGTcount: A:0.19, C:0.35, G:0.16, T:0.30
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGACGCATCATTCCC
Found at i:10554 original size:21 final size:21
Alignment explanation
Indices: 10530--10572 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
10520 CTTGCTCTTG
* *
10530 TCAACGGACCTAATGGCATCT
1 TCAAAGGACCAAATGGCATCT
*
10551 TCAAAGGATCAAATGGCATCT
1 TCAAAGGACCAAATGGCATCT
10572 T
1 T
10573 AATGGCATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (21 bp):
TCAAAGGACCAAATGGCATCT
Found at i:10804 original size:4 final size:4
Alignment explanation
Indices: 10797--10966 Score: 51
Period size: 4 Copynumber: 45.0 Consensus size: 4
10787 ATTAGGTAGG
* ** * *
10797 TAAA TAAA -AAGA TAAA TAAA TAGA T-AA TAGC TGAA TAGA TAAA TAAA
1 TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * * * *
10844 -AGGA TAAA T-AG TAAA TAAA TAAA T-AG TAGA TAAA TAGA T-AA T-AA
1 TA-AA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * * * *
10888 TAAA T-AA T-AA T-AA CAAA TAGA TAAG TAAG TAAA TAAA -AAA AAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * * *
10932 CTAAG TAGA TAGA TAGA T-AA T-AA TAAA TAAA TAAA
1 -TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
10967 GAAAATAACT
Statistics
Matches: 123, Mismatches: 31, Indels: 24
0.69 0.17 0.13
Matches are distributed among these distances:
3 30 0.24
4 88 0.72
5 5 0.04
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:10836 original size:27 final size:26
Alignment explanation
Indices: 10761--10894 Score: 93
Period size: 27 Copynumber: 5.2 Consensus size: 26
10751 AAAAATATAT
10761 ATAAATAGAT-AATAGCATAATAGATAA
1 ATAAATAGATAAATAG--TAATAGATAA
* ** * *
10788 TTAGGTAGGTAAATA--AAAAGATAA
1 ATAAATAGATAAATAGTAATAGATAA
10812 ATAAATAGAT-AATAGCTGAATAGATAA
1 ATAAATAGATAAATAG-T-AATAGATAA
*
10839 ATAAA-AGGATAAATAGTAAATAAATAA
1 ATAAATA-GATAAATAGT-AATAGATAA
*
10866 AT-AGTAGATAAATAGATAATA-ATAA
1 ATAAATAGATAAATAG-TAATAGATAA
10891 ATAA
1 ATAA
10895 TAATAACAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
23 4 0.05
24 14 0.17
25 6 0.07
26 16 0.19
27 35 0.42
28 9 0.11
ACGTcount: A:0.60, C:0.01, G:0.13, T:0.25
Consensus pattern (26 bp):
ATAAATAGATAAATAGTAATAGATAA
Found at i:10852 original size:51 final size:50
Alignment explanation
Indices: 10749--10869 Score: 138
Period size: 51 Copynumber: 2.4 Consensus size: 50
10739 AATGGGTAGG
* **
10749 TAAAAAATATATATAAATAGATAATAGCATAATAGATAATTAGGTAGGTAAA
1 TAAAAAATA-A-ATAAATAGATAATAGCATAATAGATAAATAGAAAGGTAAA
10801 TAAAAAGATAAATAAATAGATAATAGC-TGAATAGATAAATA-AAAGGATAAA
1 TAAAAA-ATAAATAAATAGATAATAGCAT-AATAGATAAATAGAAAGG-TAAA
**
10852 TAGTAAATAAATAAATAG
1 TAAAAAATAAATAAATAG
10870 TAGATAAATA
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
50 16 0.26
51 35 0.57
52 7 0.11
53 3 0.05
ACGTcount: A:0.60, C:0.02, G:0.13, T:0.26
Consensus pattern (50 bp):
TAAAAAATAAATAAATAGATAATAGCATAATAGATAAATAGAAAGGTAAA
Found at i:10865 original size:15 final size:15
Alignment explanation
Indices: 10847--10924 Score: 63
Period size: 15 Copynumber: 5.3 Consensus size: 15
10837 AAATAAAAGG
10847 ATAAATAGTAAATAA
1 ATAAATAGTAAATAA
*
10862 ATAAATAGTAGATAA
1 ATAAATAGTAAATAA
* *
10877 ATAGATAAT-AATAA
1 ATAAATAGTAAATAA
* *
10891 AT-AATAAT-AACAA
1 ATAAATAGTAAATAA
* *
10904 ATAGATAAGTAAGTAA
1 ATAAAT-AGTAAATAA
10920 ATAAA
1 ATAAA
10925 AAAAAAACTA
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
13 11 0.22
14 8 0.16
15 23 0.47
16 7 0.14
ACGTcount: A:0.64, C:0.01, G:0.09, T:0.26
Consensus pattern (15 bp):
ATAAATAGTAAATAA
Found at i:10984 original size:13 final size:14
Alignment explanation
Indices: 10968--10998 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
10958 ATAAATAAAG
10968 AAAATAAC-TTAAT
1 AAAATAACTTTAAT
10981 AAAATAACTTTAAT
1 AAAATAACTTTAAT
10995 AAAA
1 AAAA
10999 GCAAAATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATAACTTTAAT
Found at i:13172 original size:97 final size:96
Alignment explanation
Indices: 13070--13245 Score: 237
Period size: 97 Copynumber: 1.8 Consensus size: 96
13060 TCGATCAATG
* * * * * *
13070 CTTACATTCGGCACT-AAGACCCCTAGTTGGGCAGTAAGGCCGACCGACATCATTTTCTCCAATA
1 CTTACATTCGACAATGAA-ACCCCTAGTTGGGAAGTAAGGCCAACCAACATCATTTTCGCCAATA
*
13134 AGTGCCCTAGTCGGGCGATAAGTCTGACCGACA
65 AG-ACCCTAGTCGGGCGATAAGTCTGACCGACA
* * *
13167 CTTACATTCGACAATGAAACCCCTAGTTGGGAAGTAAGGTCAATCAACATCATTTTCGGCAATAA
1 CTTACATTCGACAATGAAACCCCTAGTTGGGAAGTAAGGCCAACCAACATCATTTTCGCCAATAA
13232 GACCCTAGTCGGGC
66 GACCCTAGTCGGGC
13246 AGCAAGGCCG
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
96 12 0.18
97 54 0.79
98 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (96 bp):
CTTACATTCGACAATGAAACCCCTAGTTGGGAAGTAAGGCCAACCAACATCATTTTCGCCAATAA
GACCCTAGTCGGGCGATAAGTCTGACCGACA
Found at i:16859 original size:13 final size:13
Alignment explanation
Indices: 16841--16874 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
16831 TAATTATTGT
16841 TTGCTTTATTAAA
1 TTGCTTTATTAAA
*
16854 TTGCTTTATTAAT
1 TTGCTTTATTAAA
16867 TTGCTTTA
1 TTGCTTTA
16875 GATTTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.59
Consensus pattern (13 bp):
TTGCTTTATTAAA
Found at i:16882 original size:6 final size:6
Alignment explanation
Indices: 16871--16897 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
16861 ATTAATTTGC
16871 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
16898 GCTTTGCTTT
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:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Done.