Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020516.1 Corchorus olitorius cultivar O-4 contig20549, 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: 17808
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1000 original size:36 final size:36
Alignment explanation
Indices: 958--1027 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
948 TTGTTAATGA
958 AAAAAGGAGAAAACTTTCTTAGGAATTAATGTTGTG
1 AAAAAGGAGAAAACTTTCTTAGGAATTAATGTTGTG
994 AAAAAGGAGAAAACTTTCTTAGGAATTAATGTTG
1 AAAAAGGAGAAAACTTTCTTAGGAATTAATGTTG
1028 CAAAAGTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.30
Consensus pattern (36 bp):
AAAAAGGAGAAAACTTTCTTAGGAATTAATGTTGTG
Found at i:2075 original size:7 final size:7
Alignment explanation
Indices: 2060--2117 Score: 75
Period size: 7 Copynumber: 8.6 Consensus size: 7
2050 TATGCAAAAA
*
2060 AAAAATG
1 AAAATTG
2067 AAAATTG
1 AAAATTG
*
2074 -AAAGT-
1 AAAATTG
*
2079 AAAAGTG
1 AAAATTG
2086 AAAATTG
1 AAAATTG
2093 AAAATTG
1 AAAATTG
2100 AAAATTG
1 AAAATTG
2107 AAAATTG
1 AAAATTG
2114 AAAA
1 AAAA
2118 AATAAGATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
6 9 0.20
7 37 0.80
ACGTcount: A:0.62, C:0.00, G:0.16, T:0.22
Consensus pattern (7 bp):
AAAATTG
Found at i:2082 original size:21 final size:19
Alignment explanation
Indices: 2055--2117 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
2045 ATAAATATGC
*
2055 AAAAAAAAAATGAAAATTG
1 AAAATAAAAATGAAAATTG
* *
2074 AAAGTAAAAGTGAAAATTG
1 AAAATAAAAATGAAAATTG
*
2093 AAAATTGAAAATTGAAAATTG
1 AAAA-T-AAAAATGAAAATTG
2114 AAAA
1 AAAA
2118 AATAAGATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 19 0.51
20 1 0.03
21 17 0.46
ACGTcount: A:0.65, C:0.00, G:0.14, T:0.21
Consensus pattern (19 bp):
AAAATAAAAATGAAAATTG
Found at i:3651 original size:145 final size:142
Alignment explanation
Indices: 3340--3748 Score: 565
Period size: 145 Copynumber: 2.9 Consensus size: 142
3330 TCTATACTTA
* ** *
3340 GAGTTTGCATCTGTAAGACCTCCGGGCACGATTTCAGAAACCTCCAAGTATTAATTCTAATAAAT
1 GAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
3405 CCTCCGGGTATCA-TC--TT-ATCAAGTTTTTAATCAAAGTTGCGTTTAAATTTCAAAAAAAACC
66 CCTCCGGGTATCATTCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAATTTCAAAAAAAACC
*
3466 TTGCTCAAGGTT
131 ATGCTCAAGGTT
* * * *
3478 GAGTTTGCATTTGTAAGACCTCCCGGCACGATTTTAGAAACTTCCGGGTATTAATTATGATAAAT
1 GAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
* * * **
3543 CCTCAGGGTATCATTTCATTTCATCAAGTTTTTAGTCGAAGTTGCGTTTAAGCTTCAAAATCAAA
66 CCTCCGGGTATCA-TTCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAATTTCAAAA--AAA
3608 ACCATGCTCAAGGTT
128 ACCATGCTCAAGGTT
* * *
3623 GAGTTTGCATTTGTAAGACCTCTGGGCACAACTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
1 GAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
* * * *
3688 CCTCCGGGTGTCATCTCATTTCGTCAAATTTTTAATCAAAATTGCGTTTAAATTTCAAAAA
66 CCTCCGGGTATCAT-TCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAATTTCAAAAA
3749 CCTTGCTCAA
Statistics
Matches: 233, Mismatches: 30, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
138 69 0.30
140 2 0.01
142 2 0.01
143 35 0.15
144 1 0.00
145 124 0.53
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (142 bp):
GAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
CCTCCGGGTATCATTCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAATTTCAAAAAAAACC
ATGCTCAAGGTT
Found at i:3949 original size:15 final size:16
Alignment explanation
Indices: 3925--3964 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
3915 AGAGGTTGAA
*
3925 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
3940 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
3956 AGAAAACAA
1 AGAAAACAA
3965 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:11142 original size:28 final size:28
Alignment explanation
Indices: 11083--11145 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
11073 AGAAAAACTT
***** *
11083 TTTTTTTGTATGACGCAAAAACTCTCTT
1 TTTTTTTGTATGACGCAAAAAAAAAATC
11111 TTTTTTTGTATGACGCAAAAAAAAAATC
1 TTTTTTTGTATGACGCAAAAAAAAAATC
11139 TTTTTTT
1 TTTTTTT
11146 TTTCAAAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.48
Consensus pattern (28 bp):
TTTTTTTGTATGACGCAAAAAAAAAATC
Found at i:11499 original size:15 final size:16
Alignment explanation
Indices: 11479--11518 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
11469 AGAGGTTGAA
11479 AGAAAACAATTAAAC-
1 AGAAAACAATTAAACT
*
11494 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
11510 AGAAAACAA
1 AGAAAACAA
11519 AGCAAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:12301 original size:11 final size:12
Alignment explanation
Indices: 12275--12301 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12265 ACCCTTGCCT
12275 AAAACTAGAAGA
1 AAAACTAGAAGA
12287 AAAACTAGAAGA
1 AAAACTAGAAGA
12299 AAA
1 AAA
12302 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.07, G:0.15, T:0.07
Consensus pattern (12 bp):
AAAACTAGAAGA
Found at i:13514 original size:149 final size:143
Alignment explanation
Indices: 13164--13532 Score: 467
Period size: 146 Copynumber: 2.5 Consensus size: 143
13154 AGCTCAATCA
*
13164 TCGAGTTTGCATTTGTAAGAACTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAA
1 TCGAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAA
* *
13229 ATCCTCCAGGTATCTTCTTATTTCATCAAAATGTTAATCAAAGTTGCTTTTTAAATTTAAAAAAA
66 ATCCTCCAGGTATCATCTTATTTCATCAAAATGTTAATCAAAGTTGCTGTTTAAATTT---AAAA
13294 AAAACCTTGCCCAAGG
128 AAAACCTTGCCCAAGG
* *
13310 TCGAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAACCTCCGAGTATTAATTCTGATAA
1 TCGAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAA
** * *
13375 ATCCTCC-GGATATCATCTTATTTCATCAAGTTGTTAATCAAAGTTGC-GTTTAAATTT-CAATA
66 ATCCTCCAGG-TATCATCTTATTTCATCAAAATGTTAATCAAAGTTGCTGTTTAAATTTAAAAAA
* *
13437 AACCTTGCTCATGG
130 AACCTTGCCCAAGG
* * *
13451 TCTTTACTCATAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAATCTCCGGGAATTAAT
1 -------TC-GAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAAT
*
13516 TCTGACAAATCC-CCAGG
58 TCTGATAAATCCTCCAGG
13533 GCATCTAACA
Statistics
Matches: 196, Mismatches: 17, Indels: 17
0.85 0.07 0.07
Matches are distributed among these distances:
141 15 0.08
145 11 0.06
146 103 0.53
148 4 0.02
149 63 0.32
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (143 bp):
TCGAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAA
ATCCTCCAGGTATCATCTTATTTCATCAAAATGTTAATCAAAGTTGCTGTTTAAATTTAAAAAAA
ACCTTGCCCAAGG
Found at i:13695 original size:40 final size:40
Alignment explanation
Indices: 13611--13945 Score: 335
Period size: 40 Copynumber: 8.5 Consensus size: 40
13601 ATAATCCTGC
* * *
13611 TCAGGATCATTTCTTTACCAG-TCAA--TCACAATCCTAT
1 TCAGGATCATTGCTTTATCAGATCAATTTCAAAATCCTAT
* * *
13648 TCAGGATCATTGCTTTATCAAATTAATTTCAGAAA-CCTAC
1 TCAGGATCATTGCTTTATCAGATCAATTTCA-AAATCCTAT
* ** *
13688 TCAGGATCATTGCCTTATCAG-TTTATTTCAAAGTCCTAT
1 TCAGGATCATTGCTTTATCAGATCAATTTCAAAATCCTAT
*
13727 TCAGGATCATTGCCTTATCAGATCAATTTCAAAATCCTAT
1 TCAGGATCATTGCTTTATCAGATCAATTTCAAAATCCTAT
* *
13767 TCAAGATCATTGCTTTATCAGATAAATTTCAAAATCCTAT
1 TCAGGATCATTGCTTTATCAGATCAATTTCAAAATCCTAT
** * * * *
13807 TTGGGATCATTGTTTTATTAGATCAATTTCACAATCTTAT
1 TCAGGATCATTGCTTTATCAGATCAATTTCAAAATCCTAT
* * *
13847 TCAGGATCATTGCATCATCAG-TCAACTTT-GAAATCCTAT
1 TCAGGATCATTGCTTTATCAGATCAA-TTTCAAAATCCTAT
* * * * * *
13886 TCAGGATTATTGCTTTA-CCGGTTAATTTCGAAATCTTAT
1 TCAGGATCATTGCTTTATCAGATCAATTTCAAAATCCTAT
*
13925 TCAGGATCATTGCCTTATCAG
1 TCAGGATCATTGCTTTATCAG
13946 TTAGTTTCAT
Statistics
Matches: 245, Mismatches: 43, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
37 18 0.07
38 10 0.04
39 85 0.35
40 130 0.53
41 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (40 bp):
TCAGGATCATTGCTTTATCAGATCAATTTCAAAATCCTAT
Found at i:13795 original size:119 final size:119
Alignment explanation
Indices: 13611--13954 Score: 380
Period size: 119 Copynumber: 2.9 Consensus size: 119
13601 ATAATCCTGC
* * * * *
13611 TCAGGATCATTTCTTTACCAGTCAA--TCACAATCCTATTCAGGATCATTGCTTTATCAAATTAA
1 TCAGGATCATTGCATTATCAGTCAATTTCAAAATCCTATTCAGGATCATTGCTTTATCAGATTAA
* *
13674 TTTCAGAAA-CCTACTCAGGATCATTGCCTTATCAGTTTATTTCA-AAGTCCTAT
66 TTTCAGAAATCCTATTCAGGATCATTGCCTTATCAGTTAATTTCACAA-TCCTAT
* * *
13727 TCAGGATCATTGCCTTATCAGATCAATTTCAAAATCCTATTCAAGATCATTGCTTTATCAGATAA
1 TCAGGATCATTGCATTATCAG-TCAATTTCAAAATCCTATTCAGGATCATTGCTTTATCAGATTA
** ** * * *
13792 ATTTCA-AAATCCTATTTGGGATCATTGTTTTATTAGATCAATTTCACAATCTTAT
65 ATTTCAGAAATCCTATTCAGGATCATTGCCTTATCAG-TTAATTTCACAATCCTAT
* * * * *
13847 TCAGGATCATTGCATCATCAGTCAACTTT-GAAATCCTATTCAGGATTATTGCTTTA-CCGGTTA
1 TCAGGATCATTGCATTATCAGTCAA-TTTCAAAATCCTATTCAGGATCATTGCTTTATCAGATTA
* *
13910 ATTTC-GAAATCTTATTCAGGATCATTGCCTTATCAGTTAGTTTCA
65 ATTTCAGAAATCCTATTCAGGATCATTGCCTTATCAGTTAATTTCA
13955 TTACTCTATC
Statistics
Matches: 188, Mismatches: 32, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
116 18 0.10
117 11 0.06
118 36 0.19
119 87 0.46
120 34 0.18
121 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.39
Consensus pattern (119 bp):
TCAGGATCATTGCATTATCAGTCAATTTCAAAATCCTATTCAGGATCATTGCTTTATCAGATTAA
TTTCAGAAATCCTATTCAGGATCATTGCCTTATCAGTTAATTTCACAATCCTAT
Found at i:13830 original size:80 final size:79
Alignment explanation
Indices: 13640--13946 Score: 341
Period size: 79 Copynumber: 3.9 Consensus size: 79
13630 AGTCAATCAC
* * *
13640 AATCCTATTCAGGATCATTGCTTTATCAAATTAATTTCAGAAA-CCTACTCAGGATCATTGCCTT
1 AATCCTATTCAGGATCATTGCTTTATCAGATCAATTTCA-AAATCCTATTCAGGATCATTGCCTT
**
13704 ATCAGTTTATTTCAA
65 ATCAGTAAATTTCAA
* * * *
13719 AGTCCTATTCAGGATCATTGCCTTATCAGATCAATTTCAAAATCCTATTCAAGATCATTGCTTTA
1 AATCCTATTCAGGATCATTGCTTTATCAGATCAATTTCAAAATCCTATTCAGGATCATTGCCTTA
13784 TCAGATAAATTTCAA
66 TCAG-TAAATTTCAA
** * * * * * *
13799 AATCCTATTTGGGATCATTGTTTTATTAGATCAATTTCACAATCTTATTCAGGATCATTGCATCA
1 AATCCTATTCAGGATCATTGCTTTATCAGATCAATTTCAAAATCCTATTCAGGATCATTGCCTTA
* *
13864 TCAGTCAACTTT-GA
66 TCAGT-AAATTTCAA
* * * * * *
13878 AATCCTATTCAGGATTATTGCTTTA-CCGGTTAATTTCGAAATCTTATTCAGGATCATTGCCTTA
1 AATCCTATTCAGGATCATTGCTTTATCAGATCAATTTCAAAATCCTATTCAGGATCATTGCCTTA
13942 TCAGT
66 TCAGT
13947 TAGTTTCATT
Statistics
Matches: 191, Mismatches: 34, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
78 39 0.20
79 81 0.42
80 71 0.37
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (79 bp):
AATCCTATTCAGGATCATTGCTTTATCAGATCAATTTCAAAATCCTATTCAGGATCATTGCCTTA
TCAGTAAATTTCAA
Found at i:16463 original size:13 final size:13
Alignment explanation
Indices: 16441--16491 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
16431 AGAGGCGGTG
*
16441 AAGAAGAAAAAAA
1 AAGAAAAAAAAAA
*
16454 AAGAAAAAAAAAT
1 AAGAAAAAAAAAA
**
16467 CTG-AAAAAAAAA
1 AAGAAAAAAAAAA
16479 AAGAAAAAGAAAA
1 AAGAAAAA-AAAA
16492 TAGAGTTCGA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
12 9 0.31
13 16 0.55
14 4 0.14
ACGTcount: A:0.82, C:0.02, G:0.12, T:0.04
Consensus pattern (13 bp):
AAGAAAAAAAAAA
Done.