Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012471.1 Corchorus olitorius cultivar O-4 contig12504, 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: 36481
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:2579 original size:35 final size:35
Alignment explanation
Indices: 2539--2609 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
2529 GGGATGTGAG
*
2539 ATCATTTCATTTGAAAAAATTAAAAAGACGAGCTC
1 ATCATTTCATTTGAAAAAATTAAAAAGAAGAGCTC
* *
2574 ATCATTTCATTTGGATAAATTAAAAAGAAGAGCTC
1 ATCATTTCATTTGAAAAAATTAAAAAGAAGAGCTC
2609 A
1 A
2610 GGATGCAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.30
Consensus pattern (35 bp):
ATCATTTCATTTGAAAAAATTAAAAAGAAGAGCTC
Found at i:12039 original size:18 final size:19
Alignment explanation
Indices: 12001--12043 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
11991 ATTGAGACTC
12001 AAACT-AACTGACTCAACA
1 AAACTGAACTGACTCAACA
12019 AAACTGAACTGACTCAA-A
1 AAACTGAACTGACTCAACA
12037 AAACTGA
1 AAACTGA
12044 CTAAACCCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.51, C:0.23, G:0.09, T:0.16
Consensus pattern (19 bp):
AAACTGAACTGACTCAACA
Found at i:20740 original size:22 final size:22
Alignment explanation
Indices: 20712--20904 Score: 142
Period size: 22 Copynumber: 8.7 Consensus size: 22
20702 TGTCTCTGTG
*
20712 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
20734 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
* *
20757 -GGTTATCAAAATTCCATAATG-
1 TGGTTATCAAAATTTCAT-AGGA
*
20778 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
* * *
20801 -AGTTATCAAAAATTCATGGGA
1 TGGTTATCAAAATTTCATAGGA
*
20822 AGGTTATCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* ** *
20844 TCAGGTTATTAAAATTTTTTAGAA
1 T--GGTTATCAAAATTTCATAGGA
* **
20868 AGGTTATTGAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
20890 TGGTTATCACAATTT
1 TGGTTATCAAAATTT
20905 TATTGAAAGT
Statistics
Matches: 131, Mismatches: 32, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
21 4 0.03
22 107 0.82
23 3 0.02
24 17 0.13
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:20817 original size:66 final size:66
Alignment explanation
Indices: 20710--20840 Score: 167
Period size: 66 Copynumber: 2.0 Consensus size: 66
20700 CTTGTCTCTG
* * * * *
20710 TGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCCAT
1 TGTGGTTACCAAAATTTCATAAGATAGTTATCAAAAATTCATG-GGAAGGTTATCAAAATTCCAT
20774 AA
65 AA
* *
20776 TGTGGTTACCAAAATTTCATATGGA-AGTTATCAAAAATTCATGGGAAGGTTATCAAAATTTCAT
1 TGTGGTTACCAAAATTTCATA-AGATAGTTATCAAAAATTCATGGGAAGGTTATCAAAATTCCAT
20840 A
65 A
20841 GGATCAGGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 2 0.04
66 52 0.93
67 2 0.04
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (66 bp):
TGTGGTTACCAAAATTTCATAAGATAGTTATCAAAAATTCATGGGAAGGTTATCAAAATTCCATA
A
Found at i:20913 original size:44 final size:45
Alignment explanation
Indices: 20779--20922 Score: 118
Period size: 44 Copynumber: 3.2 Consensus size: 45
20769 TCCATAATGT
* * ** * *
20779 GGTTACCAAAATTTCATATGGA-A-GTTATCAAAAATTCATGGGAA
1 GGTTATCAAAATTTCATA-GGATAGGTTATCAAAATTTTTTAGAAA
*
20823 GGTTATCAAAATTTCATAGGATCAGGTTATTAAAATTTTTTAGAAA
1 GGTTATCAAAATTTCATAGGAT-AGGTTATCAAAATTTTTTAGAAA
** *
20869 GGTTATTGAAATTTCATAGTG-T-GGTTATCACAATTTTATT-GAAA
1 GGTTATCAAAATTTCATAG-GATAGGTTATCAAAATTTT-TTAGAAA
*
20913 GTTTATCAAA
1 GGTTATCAAA
20923 GAGATTATCA
Statistics
Matches: 81, Mismatches: 14, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
43 3 0.04
44 41 0.51
45 3 0.04
46 33 0.41
47 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (45 bp):
GGTTATCAAAATTTCATAGGATAGGTTATCAAAATTTTTTAGAAA
Found at i:21007 original size:22 final size:22
Alignment explanation
Indices: 20927--21363 Score: 106
Period size: 22 Copynumber: 19.7 Consensus size: 22
20917 ATCAAAGAGA
*
20927 TTATCAAAATGTCAT-AGCGA-G
1 TTATCAAAATTTCATAAG-GAGG
*
20948 TATAT-AAGAATTTCAT-AGTGTGG
1 T-TATCAA-AATTTCATAAG-GAGG
* *
20971 TTAAC-AAATCTCATAAGGAGG
1 TTATCAAAATTTCATAAGGAGG
* *
20992 TTA-CTAATATTTCATAGGGAGG
1 TTATC-AAAATTTCATAAGGAGG
* **
21014 TTATCAAAATTTCATAATGTCG
1 TTATCAAAATTTCATAAGGAGG
* * * **
21036 TTATTAAAA-TTCTTTAGTGTTG
1 TTATCAAAATTTCATAAG-GAGG
* *
21058 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATAAGGAGG
*
21080 TTATAAAAGTCTTAATTTCATAAGGA-G
1 TTAT-CAA-----AATTTCATAAGGAGG
* *
21107 -TACCAAAATTTGAT--GGAAGG
1 TTATCAAAATTTCATAAGG-AGG
* *
21127 CTATC-AAATCTCAT-A-GAGTG
1 TTATCAAAATTTCATAAGGAG-G
* *
21147 ATTATCGAAATTTCAT-AGAGATCGAA
1 -TTATCAAAATTTCATAAG-GA--G-G
* *
21173 TTATCAAAATTT-AT-AGAAAGA
1 TTATCAAAATTTCATAAG-GAGG
* ***
21194 TCATCAAAATTTCAT-AGTGTTC
1 TTATCAAAATTTCATAAG-GAGG
21216 TTATCAAAATTTCA-AAGCGAGG
1 TTATCAAAATTTCATAAG-GAGG
* * **
21238 TTATCAAAATTACATAATGAAA
1 TTATCAAAATTTCATAAGGAGG
*
21260 ATATCAAAATTTCATAGAGG-GG
1 TTATCAAAATTTCATA-AGGAGG
* * * *
21282 TCAACAAAATTTTAT-AGAGAAG
1 TTATCAAAATTTCATAAG-GAGG
*
21304 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAAGGAGG
* * * * *
21326 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAAGGAGG
*
21348 TTACCAAAATTTCATA
1 TTATCAAAATTTCATA
21364 GTGGTATTTC
Statistics
Matches: 303, Mismatches: 79, Indels: 67
0.67 0.18 0.15
Matches are distributed among these distances:
18 2 0.01
19 3 0.01
20 20 0.07
21 41 0.14
22 186 0.61
23 15 0.05
24 8 0.03
25 13 0.04
26 3 0.01
27 1 0.00
28 11 0.04
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGGAGG
Found at i:21490 original size:22 final size:22
Alignment explanation
Indices: 21464--21981 Score: 135
Period size: 22 Copynumber: 23.5 Consensus size: 22
21454 TCAGGGAGGA
21464 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
*
21486 TATCAAAATTTCATAGTTTAA--T
1 TATCAAAATTTCATA--TGAAGGT
* * *
21508 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* * *
21530 TATCAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATATGAAGGT
*
21552 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
21574 TATCAAAA-ACCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
21595 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
21611 TATCAAGATTTCATAAGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * *
21633 TATTAAAATTTTATATGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
21656 TATTAAAATTTTATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
21678 TATCACAATTTTATAGTGTGATTAATGAT
1 TATCAAAATTTCATA---TG---AA-GGT
* * *
21707 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
21729 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
21751 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * * *
21773 TATCAATATATGATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
21795 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
21818 TATCAAAATTTCAT-TCGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
21840 TATCAAAATTTCATAGTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
21862 TTTCAAAA-TTCCTTTAGGAGGT
1 TATCAAAATTTCATAT-GAAGGT
* *
21884 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** *
21906 TAAAAAAATTT-ATA-AAAGGGT
1 TATCAAAATTTCATATGAA-GGT
* * * **
21927 TCTCGAAATTTGATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* * *
21949 TATTAAAGTTTCATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
*
21971 TATTAAAATTT
1 TATCAAAATTT
21982 TGTAAGGAGG
Statistics
Matches: 368, Mismatches: 87, Indels: 82
0.69 0.16 0.15
Matches are distributed among these distances:
16 9 0.02
17 2 0.01
18 2 0.01
20 7 0.02
21 43 0.12
22 232 0.63
23 50 0.14
24 4 0.01
26 1 0.00
27 3 0.01
28 1 0.00
29 14 0.04
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:21520 original size:44 final size:44
Alignment explanation
Indices: 21456--21898 Score: 178
Period size: 44 Copynumber: 10.0 Consensus size: 44
21446 TCAAAGTTTC
21456 AGGGAGGA-TATCAAAATTTCATATGAAGGTTATCAAAATTTCAT
1 AGGGA-GATTATCAAAATTTCATATGAAGGTTATCAAAATTTCAT
** * * *
21500 AGTTTA-ATTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCAT
1 AG-GGAGATTATCAAAATTTCATATGAAGGTTATCAAAATTTCAT
* **
21544 AGGGAGATTAACAAAATTTCATAATG-AGGTTATCAAAA-ACCAT
1 AGGGAGATTATCAAAATTTCAT-ATGAAGGTTATCAAAATTTCAT
* * *
21587 AGGGAGGTTATCAAAA--T--T-TGTA-GTTATCAAGATTTCAT
1 AGGGAGATTATCAAAATTTCATATGAAGGTTATCAAAATTTCAT
* * * * * * *
21625 AAGGAGGTTATTAAAATTTTATATGGAGGTTTATTAAAATTTTAT
1 AGGGAGATTATCAAAATTTCATATGAAGG-TTATCAAAATTTCAT
* * * * * *
21670 AGCGAGGTTATCACAATTTTATAGTGTGATTAATGATTATCAAAATTTCAG
1 AGGGAGATTATCAAAATTTCATA---TG---AA-GGTTATCAAAATTTCAT
* * * * * *
21721 AGTGTGATTA-CTAACAA-TTCATATGGAGGTTTTTAAATTTTCAT
1 AGGGAGATTATC-AA-AATTTCATATGAAGGTTATCAAAATTTCAT
** * * * * * * * *
21765 AACGTGGTTATCAATATATGATATGGAGGTTATCAACATCTCAT
1 AGGGAGATTATCAAAATTTCATATGAAGGTTATCAAAATTTCAT
** *
21809 AGTGTTGGTTATCAAAATTTCAT-TCGGAA-GTTATCAAAATTTCAT
1 AG-GGAGATTATCAAAATTTCATAT--GAAGGTTATCAAAATTTCAT
* * * * * * *
21854 AGTGAGGTTTTCAAAA-TTCCTTTAGGAGGTTAACAAAATTTCAT
1 AGGGAGATTATCAAAATTTCATAT-GAAGGTTATCAAAATTTCAT
21898 A
1 A
21899 AGAAGGTTAA
Statistics
Matches: 298, Mismatches: 72, Indels: 58
0.70 0.17 0.14
Matches are distributed among these distances:
37 11 0.04
38 18 0.06
39 1 0.00
40 1 0.00
41 1 0.00
42 1 0.00
43 29 0.10
44 133 0.45
45 67 0.22
46 2 0.01
48 4 0.01
50 1 0.00
51 26 0.09
52 3 0.01
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (44 bp):
AGGGAGATTATCAAAATTTCATATGAAGGTTATCAAAATTTCAT
Found at i:22934 original size:21 final size:20
Alignment explanation
Indices: 22897--22935 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
22887 TTTAAAAGCA
*
22897 ATTAATTAAAAGCATTAAAC
1 ATTAATTAAAAACATTAAAC
22917 ATTAATTAAAAACAATTAA
1 ATTAATTAAAAAC-ATTAA
22936 GGAAGGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (20 bp):
ATTAATTAAAAACATTAAAC
Found at i:23521 original size:255 final size:254
Alignment explanation
Indices: 23080--23588 Score: 745
Period size: 255 Copynumber: 2.0 Consensus size: 254
23070 CAATTTGGCC
*
23080 TTTTAGTAATTACCCTGGGTACTGAATTGGTGAGAGGAAAAAAGAAAAGGGGGGAGGGGAGAAAT
1 TTTTAGTAATTACCCTGGGAACTGAATTGGTGAGAGGAAAAAAGAAAAGGGGGGAGGGGAGAAAT
* * * * **
23145 ATTAATTAAAAGCAATTAAGGAAGTGAAATGAGCAATTACAAAAAATGGTAGCAGGATAAGGAAG
66 ATTAATTAAAAGCAATTAAAGAAGTAAAATGAGCAATTACAAAAAAGGGTAGCAGGAAAAAAAAG
* *
23210 AAGGGAAACTCATAGAGGGACTTTTTAGTCATCCAAAAAGTGAAAAAAGACAAAAAAAAAAGCCA
131 AAGGAAAACTCATAGAGGGACTTTTTAGCCATCCAAAAAGTGAAAAAAGAC--AAAAAAAAGCCA
*
23275 AAAAGTGGCACTACATTAATCCTCAATTCGACCTTCTAGTAATTTCCCTGGTAACTAAAAAT
194 AAAAGTGGCACCACATTAAT-CTCAATTCGACCTTCTAGTAATTTCCCTGGTAACTAAAAAT
* * * * **
23337 TTTTAGTAATTACCCTGGGAACTGAATTGGTGTGAGGAAAAAAG-AAGGGGGGGGGGGGGGGGA-
1 TTTTAGTAATTACCCTGGGAACTGAATTGGTGAGAGGAAAAAAGAAAAGGGGGGAGGGGAGAAAT
*
23400 ATTAATTAAAAGCAATTAAAGAAGTAAAATGAGTAATTACAAAAAAGGGTAGCAGGAAAAAAAAG
66 ATTAATTAAAAGCAATTAAAGAAGTAAAATGAGCAATTACAAAAAAGGGTAGCAGGAAAAAAAAG
*
23465 -AGGAAAACTCATAGAGGGACTTTTTAGCCATCCAAAAAGTGAGAAAAGACCAAAAAAAAGCCAA
131 AAGGAAAACTCATAGAGGGACTTTTTAGCCATCCAAAAAGTGAAAAAAGA-CAAAAAAAAGCCAA
* * ** * *
23529 AAGGTGGCACCACATTAATCTCAATTTGGTCTTTTAGTAATTTTCCTGGTAACTAAAAAT
195 AAAGTGGCACCACATTAATCTCAATTCGACCTTCTAGTAATTTCCCTGGTAACTAAAAAT
23589 AATATATAGT
Statistics
Matches: 227, Mismatches: 24, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
252 36 0.16
253 30 0.13
254 46 0.20
255 59 0.26
256 14 0.06
257 42 0.19
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (254 bp):
TTTTAGTAATTACCCTGGGAACTGAATTGGTGAGAGGAAAAAAGAAAAGGGGGGAGGGGAGAAAT
ATTAATTAAAAGCAATTAAAGAAGTAAAATGAGCAATTACAAAAAAGGGTAGCAGGAAAAAAAAG
AAGGAAAACTCATAGAGGGACTTTTTAGCCATCCAAAAAGTGAAAAAAGACAAAAAAAAGCCAAA
AAGTGGCACCACATTAATCTCAATTCGACCTTCTAGTAATTTCCCTGGTAACTAAAAAT
Found at i:23777 original size:21 final size:21
Alignment explanation
Indices: 23749--23788 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
23739 ATGCACGTAT
23749 ATTTTATATT-TCAATTACTA
1 ATTTTATATTATCAATTACTA
*
23769 ATTTCTATATTATTAATTAC
1 ATTT-TATATTATCAATTAC
23789 ATTAAGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 6 0.35
22 7 0.41
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTTATATTATCAATTACTA
Found at i:26243 original size:13 final size:13
Alignment explanation
Indices: 26225--26252 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
26215 TATAGATTTC
26225 AAGAGGTGTGTTA
1 AAGAGGTGTGTTA
26238 AAGAGGTGTGTTA
1 AAGAGGTGTGTTA
26251 AA
1 AA
26253 CACCCTTTGA
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:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (13 bp):
AAGAGGTGTGTTA
Found at i:30492 original size:12 final size:14
Alignment explanation
Indices: 30470--30501 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
30460 GTAATGCCTG
30470 CTTGTGTTCCAAA-
1 CTTGTGTTCCAAAT
30483 CTTG-GTTCCAAAT
1 CTTGTGTTCCAAAT
30496 CTTGTG
1 CTTGTG
30502 CTCTCTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.47
13 8 0.47
14 1 0.06
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.41
Consensus pattern (14 bp):
CTTGTGTTCCAAAT
Done.