Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011360.1 Corchorus capsularis cultivar CVL-1 contig11381, 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: 17137
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Found at i:639 original size:15 final size:17
Alignment explanation
Indices: 607--643 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
597 TGGATTGATT
607 TTTTTTTCATTTCCTCA
1 TTTTTTTCATTTCCTCA
*
624 TTTTTTTC-TTT-TTCA
1 TTTTTTTCATTTCCTCA
639 TTTTT
1 TTTTT
644 CCTTTCATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 3 0.16
17 8 0.42
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTTCATTTCCTCA
Found at i:1781 original size:42 final size:42
Alignment explanation
Indices: 1638--1783 Score: 202
Period size: 42 Copynumber: 3.5 Consensus size: 42
1628 AGTTTGATAC
*
1638 TTGAATGACATAACACTTAAAAGGTAGGAAACATATATATTA
1 TTGAATGACATAACACTGAAAAGGTAGGAAACATATATATTA
*
1680 TTGAATGACATAACACTAAAAAGGTAGGAAACATATATATTA
1 TTGAATGACATAACACTGAAAAGGTAGGAAACATATATATTA
** ** * *
1722 TTGAACAACATTGCACTGAAAAGGTAGGAAACATATTTATCA
1 TTGAATGACATAACACTGAAAAGGTAGGAAACATATATATTA
* *
1764 TTGAATGGCATTACACTGAA
1 TTGAATGACATAACACTGAA
1784 TGTCAATACA
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 92 1.00
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (42 bp):
TTGAATGACATAACACTGAAAAGGTAGGAAACATATATATTA
Found at i:2230 original size:137 final size:136
Alignment explanation
Indices: 1984--2609 Score: 812
Period size: 137 Copynumber: 4.6 Consensus size: 136
1974 GGTTGGATTT
*
1984 GTGAGATTCTCTGAAATTGATTGGATAATGTGTTAGATTTTATGACTTTTCTTGGATATGTAGTG
1 GTGAGATTCTCTGAAATTGATTGGATATTGTGTTAGATTTT-TGACTTTTCTTGGATATGTAGTG
* * *
2049 GAAGAGATAAGGATTCAATTCAACGGTCACATTTAAATCTCAATTTTAATCCAATAGTTGGATAG
65 GAAGAGATAAGGATTCAATTCAACAGTCACATTTAAATCTCAATTTTAATCCAACAGTTAGATAG
2114 AGATAAA
130 AGATAAA
2121 GTGAGATTCT-TCGAAATTGATTGGATATTGTGTTAGATTTTTAGACTTTTCTTGGATATGTAGT
1 GTGAGATTCTCT-GAAATTGATTGGATATTGTGTTAGATTTTT-GACTTTTCTTGGATATGTAGT
* * *
2185 GGAAGAGATAAGGATTCAATTCAACAGTCATATTTGAATCTCAATTTTAATTCAA-AGGTTAGAT
64 GGAAGAGATAAGGATTCAATTCAACAGTCACATTTAAATCTCAATTTTAATCCAACA-GTTAGAT
2249 AGAGATAAA
128 AGAGATAAA
*
2258 GTGAGATTCTCTGAAATTGATTGCATATTGTGTTAGATTTTTTGACTTTTCTTGGATATGGT-GT
1 GTGAGATTCTCTGAAATTGATTGGATATTGTGTTAGA-TTTTTGACTTTTCTTGGATAT-GTAGT
* *
2322 GGAAGAGATAAGGATTCAATTCAA-TGATCACATTTAAATCTCAATTTTAATCCAACGGTTAGAT
64 GGAAGAGATAAGGATTCAATTCAACAG-TCACATTTAAATCTCAATTTTAATCCAACAGTTAGAT
2386 AGAGATAAA
128 AGAGATAAA
* * *
2395 GTGAGATTCTCTGAAATTGATTGGATATTTTGTTAGACTGTCTGACTTTTCTTGGAT-TG-ATGT
1 GTGAGATTCTCTGAAATTGATTGGATATTGTGTTAGA-TTTTTGACTTTTCTTGGATATGTA-GT
* * * * * *
2458 GGAAGAGATAAGG-----ATT-AACAGTCACATTTAAATCTTACTTTCAATCCAACGGTTGGATT
64 GGAAGAGATAAGGATTCAATTCAACAGTCACATTTAAATCTCAATTTTAATCCAACAGTTAGATA
2517 GAGATAAA
129 GAGATAAA
* * * * **
2525 GTTAGGTTCTCTTAAATTGATTGGATATTGTGTTAGGTTTTCTGA-TAAATCTTGGATATGGT-G
1 GTGAGATTCTCTGAAATTGATTGGATATTGTGTTAGATTTT-TGACT-TTTCTTGGATAT-GTAG
*
2588 TGGAATAGATAAGGATTCAATT
63 TGGAAGAGATAAGGATTCAATT
2610 TGGCTATTGC
Statistics
Matches: 435, Mismatches: 33, Indels: 43
0.85 0.06 0.08
Matches are distributed among these distances:
129 3 0.01
130 86 0.20
131 19 0.04
132 1 0.00
135 1 0.00
136 23 0.05
137 294 0.68
138 8 0.02
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (136 bp):
GTGAGATTCTCTGAAATTGATTGGATATTGTGTTAGATTTTTGACTTTTCTTGGATATGTAGTGG
AAGAGATAAGGATTCAATTCAACAGTCACATTTAAATCTCAATTTTAATCCAACAGTTAGATAGA
GATAAA
Found at i:7043 original size:42 final size:42
Alignment explanation
Indices: 6994--7139 Score: 211
Period size: 42 Copynumber: 3.5 Consensus size: 42
6984 AGTTTGATAC
6994 TTGAATGACATAACACTGAAAAGGTAGGAAACATATATATTA
1 TTGAATGACATAACACTGAAAAGGTAGGAAACATATATATTA
* *
7036 TTAAATGACATAACACTAAAAAGGTAGGAAACATATATATTA
1 TTGAATGACATAACACTGAAAAGGTAGGAAACATATATATTA
* ** * *
7078 TTGAACGACATTGCACTGAAAAGGTAGGAAATATATTTATTA
1 TTGAATGACATAACACTGAAAAGGTAGGAAACATATATATTA
* *
7120 TCGAATGACATTACACTGAA
1 TTGAATGACATAACACTGAA
7140 TGACACTACA
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 92 1.00
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (42 bp):
TTGAATGACATAACACTGAAAAGGTAGGAAACATATATATTA
Found at i:7433 original size:137 final size:136
Alignment explanation
Indices: 7268--7899 Score: 808
Period size: 137 Copynumber: 4.6 Consensus size: 136
7258 GGTTGGATTT
* * *
7268 GTGAGATTCTTTGAAATTGATTGGATATTGTGTTAGATTTTATGACTTTTCATGGATATGTAGAG
1 GTGAGATTCTCTGAAATTGATT-GATATTGTGTTAGATTTTATGACTTTTCTTGGATATGTAGTG
* * * * *
7333 GAAGAGATAAAGATTCAATTCAACGGTCAAATTTGAATCTCAATTTTAATCCAACAGTTGGATAG
65 GAAGAGATAAGGATTCAATTCAACAGTCACATTTAAATCTCAATTTTAATCCAACAGTTAGATAG
7398 AGATAAA
130 AGATAAA
* *
7405 GTGAGATTCTCCGAAATTGATTAGATATTGTGTTAGATTTTCTGACTTTTCTTGGATATGTAGTG
1 GTGAGATTCTCTGAAATTGATT-GATATTGTGTTAGATTTTATGACTTTTCTTGGATATGTAGTG
* * * *
7470 GAAGAGATAATGATTCAATTCAGCAGTCATATTTGAATCTCAATTTTAATCCAA-AGGTTAGATA
65 GAAGAGATAAGGATTCAATTCAACAGTCACATTTAAATCTCAATTTTAATCCAACA-GTTAGATA
7534 GAGATAAA
129 GAGATAAA
*
7542 GTGAGATTCTCTGAAATTGATTGCATATTGTGTTAGATTTTCTGACTTTTCTTGGATATGCT-GT
1 GTGAGATTCTCTGAAATTGATTG-ATATTGTGTTAGATTTTATGACTTTTCTTGGATATG-TAGT
* * *
7606 GGAAGAGATAAGGATTCTATTCAAC-GATCACATTTAAACCTCAATTTTAATCCAACGGTTAGAT
64 GGAAGAGATAAGGATTCAATTCAACAG-TCACATTTAAATCTCAATTTTAATCCAACAGTTAGAT
7670 AGAGATAAA
128 AGAGATAAA
* * * *
7679 GTGAGATTCTCTAAAAATGATTGGATATTGTGTTAGACTGTATGACTTTTCTTGGATATG-ATGT
1 GTGAGATTCTCTGAAATTGATT-GATATTGTGTTAGATTTTATGACTTTTCTTGGATATGTA-GT
* * * * *
7743 GGACGAGATAAGGATTCAATTCAACAGTCACATTTAAATCTTACTTTTAATCCAACAGTTGGATT
64 GGAAGAGATAAGGATTCAATTCAACAGTCACATTTAAATCTCAATTTTAATCCAACAGTTAGATA
7808 GAGATAAA
129 GAGATAAA
* * * * * **
7816 GTTAGGTTCTCTTAAATTGATTGAATATTGTGTTAGGTTTTCTGA-TAAATCTTGGATATGGT-G
1 GTGAGATTCTCTGAAATTGATTG-ATATTGTGTTAGATTTTATGACT-TTTCTTGGATAT-GTAG
*
7879 TGGAATAGATAAGGATTCAAT
63 TGGAAGAGATAAGGATTCAAT
7900 ATGACTATTG
Statistics
Matches: 438, Mismatches: 44, Indels: 26
0.86 0.09 0.05
Matches are distributed among these distances:
136 5 0.01
137 429 0.98
138 4 0.01
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.37
Consensus pattern (136 bp):
GTGAGATTCTCTGAAATTGATTGATATTGTGTTAGATTTTATGACTTTTCTTGGATATGTAGTGG
AAGAGATAAGGATTCAATTCAACAGTCACATTTAAATCTCAATTTTAATCCAACAGTTAGATAGA
GATAAA
Found at i:10425 original size:12 final size:13
Alignment explanation
Indices: 10397--10451 Score: 62
Period size: 13 Copynumber: 4.4 Consensus size: 13
10387 TCATGCACCC
10397 AAAATCATTTAAT
1 AAAATCATTTAAT
10410 AAAATCATTT-AT
1 AAAATCATTTAAT
*
10422 AAAAACAATTTAAT
1 AAAATC-ATTTAAT
*
10436 AAAA-CA-GTAAT
1 AAAATCATTTAAT
10447 AAAAT
1 AAAAT
10452 AGTTCCTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
11 8 0.22
12 8 0.22
13 15 0.41
14 6 0.16
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (13 bp):
AAAATCATTTAAT
Found at i:13517 original size:18 final size:18
Alignment explanation
Indices: 13494--13530 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
13484 GGATCTTGAA
13494 TCACCTAATTTGGACTTC
1 TCACCTAATTTGGACTTC
*
13512 TCACCTCATTTGGACTTC
1 TCACCTAATTTGGACTTC
13530 T
1 T
13531 AGATCAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.30, G:0.11, T:0.41
Consensus pattern (18 bp):
TCACCTAATTTGGACTTC
Done.