Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013079.1 Corchorus olitorius cultivar O-4 contig13112, 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: 19644
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Found at i:9 original size:2 final size:2
Alignment explanation
Indices: 3--40 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1 TA
3 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41 GAAGAGACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1806 original size:5 final size:5
Alignment explanation
Indices: 1793--1826 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
1783 TATAACACCA
*
1793 AAATC AAATT AAATT AAATT AAATT AAATT AAAT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAAT
1827 ATGATATGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (5 bp):
AAATT
Found at i:2679 original size:12 final size:12
Alignment explanation
Indices: 2664--2693 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2654 CCTTGTGGAT
2664 CCCAATCCCAAC
1 CCCAATCCCAAC
*
2676 CCCAACCCCAAC
1 CCCAATCCCAAC
2688 CCCAAT
1 CCCAAT
2694 TCGAATTTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.33, C:0.60, G:0.00, T:0.07
Consensus pattern (12 bp):
CCCAATCCCAAC
Found at i:4541 original size:7 final size:7
Alignment explanation
Indices: 4529--4562 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
4519 TAATACTCAA
4529 TCACATT
1 TCACATT
4536 TCACATT
1 TCACATT
4543 TCACATT
1 TCACATT
4550 TCACATT
1 TCACATT
4557 TCACAT
1 TCACAT
4563 AGTGAGTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.41
Consensus pattern (7 bp):
TCACATT
Found at i:5805 original size:2 final size:2
Alignment explanation
Indices: 5798--5823 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5788 TAAAATGTGG
5798 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5824 GGTTATAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7541 original size:23 final size:23
Alignment explanation
Indices: 7498--7541 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
7488 AAGTTTTTTT
*
7498 AATAAAATTAGTAAAATGATAAA
1 AATAAAATTAGTAAAAGGATAAA
*
7521 AATAAAA-TAGGTATAAGGATA
1 AATAAAATTA-GTAAAAGGATA
7542 TTAGATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (23 bp):
AATAAAATTAGTAAAAGGATAAA
Found at i:7614 original size:102 final size:104
Alignment explanation
Indices: 7494--7703 Score: 273
Period size: 111 Copynumber: 2.0 Consensus size: 104
7484 GTCTAAGTTT
*
7494 TTTTAATAAAATTAGTAAAATGATAAAAATAAAATAG-GTATAAGG-ATATTAGATTTAATTAAA
1 TTTTAATAAAATTAGTAAAATGATAAAAATAAAATAGAGTATAAGGAATATTAGATTTAATCAAA
* *
7557 TAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTA
66 TAAAAATAAAGTTTTCAGTTGAGTAAAACTATAAAAGTA
* *
7596 TTTTAATTAAAA-TAGTAAAATGGTAAAAATAAAATAGTACTTATAAGGATATATATATTAGATT
1 TTTTAA-TAAAATTAGTAAAATGATAAAAATAAAATAG-A-GTATAAGG----A-ATATTAGATT
*
7660 TAATCAAATAAAAATAAAGTTTTCAGTTGAGTAAAACTTTAAAA
58 TAATCAAATAAAAATAAAGTTTTCAGTTGAGTAAAACTATAAAA
7704 ATTTAAACAA
Statistics
Matches: 92, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
102 30 0.33
103 5 0.05
105 7 0.08
111 50 0.54
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.35
Consensus pattern (104 bp):
TTTTAATAAAATTAGTAAAATGATAAAAATAAAATAGAGTATAAGGAATATTAGATTTAATCAAA
TAAAAATAAAGTTTTCAGTTGAGTAAAACTATAAAAGTA
Found at i:9530 original size:21 final size:23
Alignment explanation
Indices: 9485--9542 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
9475 ACAAGTGTAA
*
9485 TTACCAAAATTTCAGAGGGGAGG
1 TTACCAAAATTTCAGAGGAGAGG
*
9508 TTACC-AAATTTCA-TGGAGAGG
1 TTACCAAAATTTCAGAGGAGAGG
**
9529 TTAATAAAATTTCA
1 TTACCAAAATTTCA
9543 TAAGTTATAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 9 0.30
22 16 0.53
23 5 0.17
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (23 bp):
TTACCAAAATTTCAGAGGAGAGG
Found at i:9607 original size:44 final size:44
Alignment explanation
Indices: 9559--9759 Score: 147
Period size: 44 Copynumber: 4.6 Consensus size: 44
9549 ATAGACTTTT
* * *
9559 ATAGGGAGATTATCAAAATTTCATAATATGGTTACCAAACTTTC
1 ATAGGGAGATTATCAAAATTTCATAATGTAGTTACCAAAATTTC
* * ** ** * *
9603 ATAGGAAGTTTATCAAAATTTCATTCTGGGGTAATCAAAATTTC
1 ATAGGGAGATTATCAAAATTTCATAATGTAGTTACCAAAATTTC
* * * * * * *
9647 TTAGTGAGGGTTAACAAAATTTGATAA-GCTAGTTATCGAAATTTC
1 ATAGGGA-GATTATCAAAATTTCATAATG-TAGTTACCAAAATTTC
* * * *
9692 AAAGGGAGATTATCGAAAATTT-ATAGTGTAGTTATCAAAATCTC
1 ATAGGGAGATTATC-AAAATTTCATAATGTAGTTACCAAAATTTC
*
9736 ATAGGG-GGTTATCAAAATTTCATA
1 ATAGGGAGATTATCAAAATTTCATA
9760 GTATAAATTT
Statistics
Matches: 121, Mismatches: 31, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
42 7 0.06
43 9 0.07
44 67 0.55
45 38 0.31
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.34
Consensus pattern (44 bp):
ATAGGGAGATTATCAAAATTTCATAATGTAGTTACCAAAATTTC
Found at i:9619 original size:22 final size:22
Alignment explanation
Indices: 9559--9891 Score: 87
Period size: 22 Copynumber: 15.2 Consensus size: 22
9549 ATAGACTTTT
*
9559 ATAGGGAGATTATCAAAATTTC
1 ATAGGAAGATTATCAAAATTTC
** * * * *
9581 ATAATATGGTTACCAAACTTTC
1 ATAGGAAGATTATCAAAATTTC
*
9603 ATAGGAAGTTTATCAAAATTTC
1 ATAGGAAGATTATCAAAATTTC
* * *
9625 ATTCTGG--GGTAATCAAAATTTC
1 A-T-AGGAAGATTATCAAAATTTC
* * * * *
9647 TTAGTGAGGGTTAACAAAATTTG
1 ATAG-GAAGATTATCAAAATTTC
** *
9670 ATAAGCTAG-TTATCGAAATTTC
1 AT-AGGAAGATTATCAAAATTTC
* *
9692 AAAGGGAGATTATCGAAAATTT-
1 ATAGGAAGATTATC-AAAATTTC
* *
9714 ATAGTGTAG-TTATCAAAATCTC
1 ATAG-GAAGATTATCAAAATTTC
* *
9736 ATAGG-GGGTTATCAAAATTTC
1 ATAGGAAGATTATCAAAATTTC
* * **
9757 ATAGTATAAATT-TTTAAATTTC
1 ATAGGA-AGATTATCAAAATTTC
* * *
9779 GTAGGGTA-ATTAACAAAATTTC
1 ATA-GGAAGATTATCAAAATTTC
* *
9801 GTAAGGAA-ATTATCAAAAAATT-
1 AT-AGGAAGATTATC-AAAATTTC
* * *
9823 ATA-GAAAAGTTATTAAAATTTT
1 ATAGGAAGA-TTATCAAAATTTC
** * *
9845 ATAGGGTGGTTATCAAAATTTT
1 ATAGGAAGATTATCAAAATTTC
* * *
9867 ACAGGGAGGTT-TCAAAATTTC
1 ATAGGAAGATTATCAAAATTTC
9888 ATAG
1 ATAG
9892 TAAGTGTAGA
Statistics
Matches: 226, Mismatches: 64, Indels: 43
0.68 0.19 0.13
Matches are distributed among these distances:
20 5 0.02
21 52 0.23
22 130 0.58
23 35 0.15
24 4 0.02
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (22 bp):
ATAGGAAGATTATCAAAATTTC
Found at i:11150 original size:22 final size:22
Alignment explanation
Indices: 11089--11150 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
11079 AGTGAGATTT
* **
11089 TCAAAATTTCATAAGGAAGTTA
1 TCAAAATTTCATAATGTGGTTA
* * *
11111 TCACAATTTGATAGTGTGGTTA
1 TCAAAATTTCATAATGTGGTTA
*
11133 TCAAAATATCATAATGTG
1 TCAAAATTTCATAATGTG
11151 AATACCAACA
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TCAAAATTTCATAATGTGGTTA
Found at i:11326 original size:23 final size:23
Alignment explanation
Indices: 11287--11341 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
11277 CATATGGAGC
* **
11287 TTATTAAAA-CTTCGTAGTTTCG
1 TTATCAAAATCTTCGTAGGGTCG
*
11309 TTATCAAAATCTTCGTAGGGTGG
1 TTATCAAAATCTTCGTAGGGTCG
11332 TTATCAAAAT
1 TTATCAAAAT
11342 TTCATTGGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 8 0.29
23 20 0.71
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (23 bp):
TTATCAAAATCTTCGTAGGGTCG
Found at i:11473 original size:22 final size:22
Alignment explanation
Indices: 11441--11538 Score: 69
Period size: 22 Copynumber: 4.5 Consensus size: 22
11431 AAGGAGGTTC
* *
11441 TCAAATTTTCATAGTGTTG-TTA
1 TCAAAATTTCATAATG-TGATTA
*
11463 TCAGAATTTCATAATGTGATTA
1 TCAAAATTTCATAATGTGATTA
*
11485 TCAAAATTTTAT-ATG-GATGTCA
1 TCAAAATTTCATAATGTGAT-T-A
* *
11507 TTAAAATTTCA-AGTGTGATTA
1 TCAAAATTTCATAATGTGATTA
**
11528 TCGGAATTTCA
1 TCAAAATTTCA
11539 AAAATATATT
Statistics
Matches: 60, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
20 3 0.05
21 15 0.25
22 39 0.65
23 3 0.05
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (22 bp):
TCAAAATTTCATAATGTGATTA
Found at i:12319 original size:20 final size:20
Alignment explanation
Indices: 12294--12336 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
12284 ATGCAGTATA
12294 CCTGTAAAACTTTTGAATCG
1 CCTGTAAAACTTTTGAATCG
12314 CCTGTAAAACTTTTGAATCG
1 CCTGTAAAACTTTTGAATCG
12334 CCT
1 CCT
12337 ATTATATCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (20 bp):
CCTGTAAAACTTTTGAATCG
Found at i:12881 original size:24 final size:26
Alignment explanation
Indices: 12830--12881 Score: 70
Period size: 29 Copynumber: 1.9 Consensus size: 26
12820 TACCCATTTC
12830 AATTATAATATAAACTAATTTGAAAAAAA
1 AATTATAATATAAACTAA-TT--AAAAAA
12859 AATTATAATATAAACTAA-TAAAA
1 AATTATAATATAAACTAATTAAAA
12882 GTCTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 4 0.17
27 1 0.04
29 18 0.78
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (26 bp):
AATTATAATATAAACTAATTAAAAAA
Found at i:13310 original size:16 final size:16
Alignment explanation
Indices: 13285--13330 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
13275 TTTGGTCTCA
*
13285 GGTTACTCGGGTTTTG
1 GGTTATTCGGGTTTTG
13301 GGTTATTCGGGTTTTG
1 GGTTATTCGGGTTTTG
** *
13317 AATTTTTCGGGTTT
1 GGTTATTCGGGTTT
13331 ATGACTCAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.09, C:0.09, G:0.33, T:0.50
Consensus pattern (16 bp):
GGTTATTCGGGTTTTG
Done.