Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012260.1 Corchorus olitorius cultivar O-4 contig12293, 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: 26448
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:2027 original size:37 final size:35
Alignment explanation
Indices: 1901--2286 Score: 344
Period size: 37 Copynumber: 10.6 Consensus size: 35
1891 AATCAGTCAG
* * * * *
1901 AGACTTAGTTTCAAGGAAACTAGGTAAATCAGTCAA
1 AGACTTAATTTCAAGGAAATTAGGAAAAACA-ACAA
* * ** *
1937 AGGCTTAATTTCAAGGAAATTAGGTAACATGAGCAA
1 AGACTTAATTTCAAGGAAATTAGG-AAAAACAACAA
* *
1973 AGAGTTAATTTCAAGGAAATTAGGAAAAATCCAACAG
1 AGACTTAATTTCAAGGAAATTAGGAAAAA--CAACAA
* *
2010 AGACTTAATTTCAAGGAAATTTGGAAAAATCCAGCAA
1 AGACTTAATTTCAAGGAAATTAGGAAAAA--CAACAA
* *
2047 AGACTTAATTTCAAGGAAATTAGGTAAGAACAAGTAA
1 AGACTTAATTTCAAGGAAATTAGG-AAAAACAA-CAA
* *
2084 AGACTTAATTTCAAGGAAATTAGGTAAGAACAAGTAA
1 AGACTTAATTTCAAGGAAATTAGG-AAAAACAA-CAA
*
2121 AGACTTAATTTCAAGGAAATTAGGTAAGAACAAGCAA
1 AGACTTAATTTCAAGGAAATTAGG-AAAAACAA-CAA
* *
2158 AGACTTAATTTGAAGGAAATTAGGTAAGAACAAGCAA
1 AGACTTAATTTCAAGGAAATTAGG-AAAAACAA-CAA
* * * * *
2195 AGACTTAATTCCAAGGAAATTAAGTAAATCAGCAA
1 AGACTTAATTTCAAGGAAATTAGGAAAAACAACAA
* *
2230 AGACTTAA-TTCAAGGTAATTAAGCAAAAACAAACAA
1 AGACTTAATTTCAAGGAAATT-AGGAAAAAC-AACAA
* *
2266 AAACTTAA-TTCAAGGTAATTA
1 AGACTTAATTTCAAGGAAATTA
2287 AGTAAAAGTA
Statistics
Matches: 304, Mismatches: 39, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
34 10 0.03
35 20 0.07
36 75 0.25
37 195 0.64
38 4 0.01
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.24
Consensus pattern (35 bp):
AGACTTAATTTCAAGGAAATTAGGAAAAACAACAA
Found at i:2065 original size:74 final size:73
Alignment explanation
Indices: 1901--2286 Score: 392
Period size: 74 Copynumber: 5.3 Consensus size: 73
1891 AATCAGTCAG
* * * * *
1901 AGACTTAGTTTCAAGGAAACTAGG-TAAATCAGTCAAAGGCTTAATTTCAAGGAAATTAGGT-AA
1 AGACTTAATTTCAAGGAAATTAGGAAAAATCA-ACAAAGACTTAATTTCAAGGAAATTAGGTAAA
* **
1964 CATGAGCAA
65 AACAAGCAA
* * *
1973 AGAGTTAATTTCAAGGAAATTAGGAAAAATCCAACAGAGACTTAATTTCAAGGAAATTTGG-AAA
1 AGACTTAATTTCAAGGAAATTAGGAAAAAT-CAACAAAGACTTAATTTCAAGGAAATTAGGTAAA
*
2037 AATCCAGCAA
65 AA-CAAGCAA
* *
2047 AGACTTAATTTCAAGGAAATTAGGTAAGAA-CAAGTAAAGACTTAATTTCAAGGAAATTAGGTAA
1 AGACTTAATTTCAAGGAAATTAGG-AAAAATCAA-CAAAGACTTAATTTCAAGGAAATTAGGTAA
* *
2111 GAACAAGTAA
64 AAACAAGCAA
* *
2121 AGACTTAATTTCAAGGAAATTAGGTAAGAA-CAAGCAAAGACTTAATTTGAAGGAAATTAGGTAA
1 AGACTTAATTTCAAGGAAATTAGG-AAAAATCAA-CAAAGACTTAATTTCAAGGAAATTAGGTAA
*
2185 GAACAAGCAA
64 AAACAAGCAA
* * * * * * *
2195 AGACTTAATTCCAAGGAAATTAAG-TAAATCAGCAAAGACTTAA-TTCAAGGTAATTAAGCAAAA
1 AGACTTAATTTCAAGGAAATTAGGAAAAATCAACAAAGACTTAATTTCAAGGAAATTAGGTAAAA
*
2258 ACAAACAA
66 ACAAGCAA
* *
2266 AAACTTAA-TTCAAGGTAATTA
1 AGACTTAATTTCAAGGAAATTA
2287 AGTAAAAGTA
Statistics
Matches: 270, Mismatches: 36, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
70 11 0.04
71 29 0.11
72 34 0.13
73 36 0.13
74 152 0.56
75 8 0.03
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.24
Consensus pattern (73 bp):
AGACTTAATTTCAAGGAAATTAGGAAAAATCAACAAAGACTTAATTTCAAGGAAATTAGGTAAAA
ACAAGCAA
Found at i:2129 original size:111 final size:110
Alignment explanation
Indices: 1901--2291 Score: 431
Period size: 111 Copynumber: 3.6 Consensus size: 110
1891 AATCAGTCAG
* * * *
1901 AGACTTAGTTTCAAGGAAACTAGG-TAAAT-CAGTCAAAGGCTTAATTTCAAGGAAATTAGGTAA
1 AGACTTAATTTCAAGGAAATTAGGAAAAATCCAG-CAAAGACTTAATTTCAAGGAAATTAGGTAA
* ** * * *
1964 -CATGAGCAAAGAGTTAATTTCAAGGAAATTAGGAAAAATCCAA-CAG
65 GAACAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAAA--CAAGCAA
*
2010 AGACTTAATTTCAAGGAAATTTGGAAAAATCCAGCAAAGACTTAATTTCAAGGAAATTAGGTAAG
1 AGACTTAATTTCAAGGAAATTAGGAAAAATCCAGCAAAGACTTAATTTCAAGGAAATTAGGTAAG
* *
2075 AACAAGTAAAGACTTAATTTCAAGGAAATTAGGTAAGAACAAGTAA
66 AACAAGCAAAGACTTAATTTCAAGGAAATTAGGTAA-AACAAGCAA
* * *
2121 AGACTTAATTTCAAGGAAATTAGGTAAGAA-CAAGCAAAGACTTAATTTGAAGGAAATTAGGTAA
1 AGACTTAATTTCAAGGAAATTAGG-AAAAATCCAGCAAAGACTTAATTTCAAGGAAATTAGGTAA
* * *
2185 GAACAAGCAAAGACTTAATTCCAAGGAAATTAAGTAAATC-AGCAA
65 GAACAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAAACAAGCAA
* * * * * * *
2230 AGACTTAA-TTCAAGGTAATTAAGCAAAAA-CAAACAAAAACTTAA-TTCAAGGTAATTAAGTAA
1 AGACTTAATTTCAAGGAAATT-AGGAAAAATCCAGCAAAGACTTAATTTCAAGGAAATTAGGTAA
2292 AAGTAGTCAA
Statistics
Matches: 245, Mismatches: 30, Indels: 16
0.84 0.10 0.05
Matches are distributed among these distances:
107 15 0.06
108 28 0.11
109 35 0.14
110 38 0.16
111 123 0.50
112 6 0.02
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.24
Consensus pattern (110 bp):
AGACTTAATTTCAAGGAAATTAGGAAAAATCCAGCAAAGACTTAATTTCAAGGAAATTAGGTAAG
AACAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAAACAAGCAA
Found at i:2349 original size:35 final size:34
Alignment explanation
Indices: 2266--2443 Score: 157
Period size: 35 Copynumber: 5.1 Consensus size: 34
2256 AAACAAACAA
*
2266 AAACTTAATTCAAGGTAATTAAGTAAAAGTAGTCAA-
1 AAACTTAATTCAGGGTAATTAAG--AAAG-AGTCAAT
**
2302 GGACTTAATTCAGGGTAATTAAGCAAAGAGTCAAT
1 AAACTTAATTCAGGGTAATTAAG-AAAGAGTCAAT
* *
2337 AAACTTAATTCAGGGTAATTAAGTAA-AGCCAAT
1 AAACTTAATTCAGGGTAATTAAGAAAGAGTCAAT
*
2370 AAGAACTTAATTCAGGGTAATTAAG-TAGAGTCAAT
1 -A-AACTTAATTCAGGGTAATTAAGAAAGAGTCAAT
* * * *
2405 AAAGAACTTAATTCAGCGAAATTAAG-TATAGTCAAT
1 --A-AACTTAATTCAGGGTAATTAAGAAAGAGTCAAT
2441 AAA
1 AAA
2444 TAACTTAATC
Statistics
Matches: 124, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
33 8 0.06
34 11 0.09
35 53 0.43
36 52 0.42
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (34 bp):
AAACTTAATTCAGGGTAATTAAGAAAGAGTCAAT
Found at i:2362 original size:71 final size:70
Alignment explanation
Indices: 2197--2432 Score: 225
Period size: 71 Copynumber: 3.3 Consensus size: 70
2187 ACAAGCAAAG
* * *
2197 ACTTAATTCCAAGGAAATTAAGTAAA-TCAG-CAAAGACTTAATTCAAGGTAATTAAGCAAAAAC
1 ACTTAATT-CAAGGAAATTAAGTAAAGT-AGTCAAGGACTTAATTCAGGGTAATTAAGC--AAAG
**
2260 AAACAA-AA
62 AGTCAATAA
*
2268 ACTTAATTCAAGGTAATTAAGTAAAAGTAGTCAAGGACTTAATTCAGGGTAATTAAGCAAAGAGT
1 ACTTAATTCAAGGAAATTAAGT-AAAGTAGTCAAGGACTTAATTCAGGGTAATTAAGCAAAGAGT
2333 CAATAA
65 CAATAA
* * * * * *
2339 ACTTAATTCAGGGTAATTAAGTAAAGCCAAT-AAGAACTTAATTCAGGGTAATTAAG--TAGAGT
1 ACTTAATTCAAGGAAATTAAGTAAAG-TAGTCAAGGACTTAATTCAGGGTAATTAAGCAAAGAGT
2401 CAATAAAGA
65 CAAT--A-A
2410 ACTTAATTC-AGCGAAATTAAGTA
1 ACTTAATTCAAG-GAAATTAAGTA
2433 TAGTCAATAA
Statistics
Matches: 143, Mismatches: 13, Indels: 18
0.82 0.07 0.10
Matches are distributed among these distances:
68 9 0.06
70 50 0.35
71 58 0.41
72 26 0.18
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.25
Consensus pattern (70 bp):
ACTTAATTCAAGGAAATTAAGTAAAGTAGTCAAGGACTTAATTCAGGGTAATTAAGCAAAGAGTC
AATAA
Found at i:2414 original size:106 final size:107
Alignment explanation
Indices: 2232--2430 Score: 258
Period size: 106 Copynumber: 1.9 Consensus size: 107
2222 ATCAGCAAAG
2232 ACTTAATTCAAGGTAATTAAGCAAAAACAAACAAAAACTTAATTCAAGGTAATTAAGTAAAAGTA
1 ACTTAATTCAAGGTAATTAAGCAAAAACAAACAAAAACTTAATTCAAGGTAATTAAGTAAAAGTA
* * * * *
2297 GTCAAGGACTTAATTCAGGGTAATTAAGCAAAGAGTCAATAA
66 ATAAAGAACTTAATTCAGCGAAATTAAGCAAAGAGTCAATAA
* * * * * * * *
2339 ACTTAATTCAGGGTAATTAAG-TAAAGCCAATAAGAACTTAATTCAGGGTAATTAAGT-AGAGTC
1 ACTTAATTCAAGGTAATTAAGCAAAAACAAACAAAAACTTAATTCAAGGTAATTAAGTAAAAGT-
2402 AATAAAGAACTTAATTCAGCGAAATTAAG
65 AATAAAGAACTTAATTCAGCGAAATTAAG
2431 TATAGTCAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
105 4 0.05
106 54 0.69
107 20 0.26
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (107 bp):
ACTTAATTCAAGGTAATTAAGCAAAAACAAACAAAAACTTAATTCAAGGTAATTAAGTAAAAGTA
ATAAAGAACTTAATTCAGCGAAATTAAGCAAAGAGTCAATAA
Found at i:2417 original size:36 final size:36
Alignment explanation
Indices: 2193--2452 Score: 232
Period size: 36 Copynumber: 7.3 Consensus size: 36
2183 AAGAACAAGC
* * **
2193 AAAG-ACTTAATTCCAAGGAAATTAAGTAAA-TCAGC
1 AAAGAACTTAATT-CAGGGTAATTAAGTAAAGTCAAT
* * **
2228 AAAG-ACTTAATTCAAGGTAATTAAGCAAAAACAA-
1 AAAGAACTTAATTCAGGGTAATTAAGTAAAGTCAAT
* * *
2262 ACAAAAACTTAATTCAAGGTAATTAAGTAAAAGT-AGT
1 A-AAGAACTTAATTCAGGGTAATTAAGT-AAAGTCAAT
* * *
2299 CAAGGACTTAATTCAGGGTAATTAAGCAAAGAGTCAAT
1 AAAGAACTTAATTCAGGGTAATTAAG-TAA-AGTCAAT
*
2337 --A-AACTTAATTCAGGGTAATTAAGTAAAGCCAAT
1 AAAGAACTTAATTCAGGGTAATTAAGTAAAGTCAAT
*
2370 -AAGAACTTAATTCAGGGTAATTAAGTAGAGTCAAT
1 AAAGAACTTAATTCAGGGTAATTAAGTAAAGTCAAT
* * *
2405 AAAGAACTTAATTCAGCGAAATTAAGTATAGTCAAT
1 AAAGAACTTAATTCAGGGTAATTAAGTAAAGTCAAT
*
2441 AAATAACTTAAT
1 AAAGAACTTAAT
2453 CCAAAAGGAA
Statistics
Matches: 190, Mismatches: 24, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
33 6 0.03
34 19 0.10
35 67 0.35
36 90 0.47
37 6 0.03
38 2 0.01
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26
Consensus pattern (36 bp):
AAAGAACTTAATTCAGGGTAATTAAGTAAAGTCAAT
Found at i:10751 original size:14 final size:15
Alignment explanation
Indices: 10716--10754 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
10706 TGAGGTTAAG
*
10716 TTTTGAAAAAGTTTGG
1 TTTTGAAAAAG-TTGA
10732 TTTTGAAAAAG-TGA
1 TTTTGAAAAAGTTGA
10746 TTTTGAAAA
1 TTTTGAAAA
10755 GTTCTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
16 11 0.50
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (15 bp):
TTTTGAAAAAGTTGA
Found at i:13889 original size:50 final size:50
Alignment explanation
Indices: 13826--13926 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 50
13816 TAAAATGCCC
* **
13826 TTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTAT
1 TTTGAAAAGCGAATTTTGATATCAGACTCACAAATGGAATGCAATCTTAT
*
13876 TTTGAAAATCGAATTTTGATATCAGACTCACAAATGGAATGCAATCTTAT
1 TTTGAAAAGCGAATTTTGATATCAGACTCACAAATGGAATGCAATCTTAT
13926 T
1 T
13927 ATAAAACTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.35
Consensus pattern (50 bp):
TTTGAAAAGCGAATTTTGATATCAGACTCACAAATGGAATGCAATCTTAT
Found at i:14224 original size:14 final size:14
Alignment explanation
Indices: 14205--14253 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
14195 GCTTCTTTTC
14205 TTCATTTTTTCATT
1 TTCATTTTTTCATT
*
14219 TTCATTCTTTCA-T
1 TTCATTTTTTCATT
14232 TTCATTTTTTTCATTT
1 TTCA-TTTTTTCA-TT
14248 TTCATT
1 TTCATT
14254 CTAATTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 5 0.17
14 18 0.60
15 2 0.07
16 5 0.17
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.69
Consensus pattern (14 bp):
TTCATTTTTTCATT
Found at i:14260 original size:22 final size:23
Alignment explanation
Indices: 14216--14265 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
14206 TCATTTTTTC
*
14216 ATTTTCATTCTTTCATTTCATTT
1 ATTTTCATTCTTTCATTTAATTT
14239 -TTTTCATT-TTTCATTCTAATTT
1 ATTTTCATTCTTTCATT-TAATTT
14261 ATTTT
1 ATTTT
14266 TTGTATGCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 7 0.29
22 13 0.54
23 4 0.17
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.68
Consensus pattern (23 bp):
ATTTTCATTCTTTCATTTAATTT
Found at i:14260 original size:27 final size:27
Alignment explanation
Indices: 14205--14267 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
14195 GCTTCTTTTC
*
14205 TTCA-TTTTTTCATTTTCATTCTTTCAT
1 TTCATTTTTTTCATTTTCATTC-TTAAT
14232 TTCATTTTTTTCATTTTTCATTC-TAAT
1 TTCATTTTTTTCA-TTTTCATTCTTAAT
14259 TT-ATTTTTT
1 TTCATTTTTT
14268 GTATGCACTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 7 0.21
27 9 0.27
28 8 0.24
29 9 0.27
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (27 bp):
TTCATTTTTTTCATTTTCATTCTTAAT
Found at i:14573 original size:7 final size:7
Alignment explanation
Indices: 14561--14593 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
14551 TATTATTCTT
14561 TTTTCAA
1 TTTTCAA
14568 TTTTCAA
1 TTTTCAA
14575 TTTTC-A
1 TTTTCAA
*
14581 CTTTCAA
1 TTTTCAA
14588 TTTTCA
1 TTTTCA
14594 CTTCTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTTCAA
Found at i:14587 original size:13 final size:13
Alignment explanation
Indices: 14569--14596 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
14559 TTTTTTCAAT
14569 TTTCAATTTTCAC
1 TTTCAATTTTCAC
14582 TTTCAATTTTCAC
1 TTTCAATTTTCAC
14595 TT
1 TT
14597 CTTTTTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTCAATTTTCAC
Found at i:15580 original size:75 final size:75
Alignment explanation
Indices: 15484--15635 Score: 243
Period size: 75 Copynumber: 2.0 Consensus size: 75
15474 TGGATTCAAT
* * * *
15484 CACCCCGAAATCATTGTTTTGACTAAAACTGATTTTGAAACATCTTTTGATTAAAACTCATCC-T
1 CACCCCGAAACCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTAATCAAAACTCA-CCAT
15548 TCCTTTGCTCA
65 TCCTTTGCTCA
*
15559 CACCTCGAAACCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTAATCAAAACTCACCATT
1 CACCCCGAAACCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTAATCAAAACTCACCATT
15624 CCTTTGCTCA
66 CCTTTGCTCA
15634 CA
1 CA
15636 ATCCAGATAA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
74 2 0.03
75 69 0.97
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.35
Consensus pattern (75 bp):
CACCCCGAAACCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTAATCAAAACTCACCATT
CCTTTGCTCA
Found at i:20614 original size:23 final size:22
Alignment explanation
Indices: 20580--20624 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
20570 TACCCTTTGA
* *
20580 TTTTTGAGTTTTGAACCTTTTT
1 TTTTTGAGTTTTAAAACTTTTT
*
20602 TTTTTGATTTTTTAAAACTTTTT
1 TTTTTGA-GTTTTAAAACTTTTT
20625 ATTTGTTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.18, C:0.07, G:0.09, T:0.67
Consensus pattern (22 bp):
TTTTTGAGTTTTAAAACTTTTT
Done.