Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016158.1 Corchorus olitorius cultivar O-4 contig16191, 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: 12430
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:3547 original size:58 final size:58
Alignment explanation
Indices: 3457--3572 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
3447 TCTATTCAAC
3457 TCATTTGTTCACTCATCTCATAGAGAGGTGAAATAATTATTTTAACTCGAAGTAAATA
1 TCATTTGTTCACTCATCTCATAGAGAGGTGAAATAATTATTTTAACTCGAAGTAAATA
3515 TCATTTGTTCACTCATCTCATAGAGAGGTGAAATAATTATTTTAACTCGAAGTAAATA
1 TCATTTGTTCACTCATCTCATAGAGAGGTGAAATAATTATTTTAACTCGAAGTAAATA
3573 GTGACTCTGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (58 bp):
TCATTTGTTCACTCATCTCATAGAGAGGTGAAATAATTATTTTAACTCGAAGTAAATA
Found at i:3651 original size:33 final size:33
Alignment explanation
Indices: 3585--3649 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
3575 GACTCTGATG
*
3585 AATATGTAAGTGAAAGGTATTTCTAGTTATTTT
1 AATATGTAAGTGAAAGGTACTTCTAGTTATTTT
3618 AATATGTAAGTG-AAGGTACTTCTAGTTATTTT
1 AATATGTAAGTGAAAGGTACTTCTAGTTATTTT
3650 TACTTGATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.61
33 12 0.39
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (33 bp):
AATATGTAAGTGAAAGGTACTTCTAGTTATTTT
Found at i:4250 original size:49 final size:49
Alignment explanation
Indices: 4176--4273 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
4166 GATTTTTTTT
4176 TTTCTATTTCCATGTATTATCGTGGCTAGAACTTGCAATTTCATTGATC
1 TTTCTATTTCCATGTATTATCGTGGCTAGAACTTGCAATTTCATTGATC
* *
4225 TTTCTTTTTCCATGTATTATTGTGGCTAGAACTTGCAATTTCATTGATC
1 TTTCTATTTCCATGTATTATCGTGGCTAGAACTTGCAATTTCATTGATC
4274 AAACTCGTAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.47
Consensus pattern (49 bp):
TTTCTATTTCCATGTATTATCGTGGCTAGAACTTGCAATTTCATTGATC
Found at i:6671 original size:22 final size:22
Alignment explanation
Indices: 6640--7188 Score: 126
Period size: 22 Copynumber: 24.6 Consensus size: 22
6630 GTATAGCTAC
*
6640 CAAAAATTCATATGGAGGTTAT
1 CAAAATTTCATATGGAGGTTAT
* *
6662 CAACACTTCAT-TGTGTA-GTTAT
1 CAAAATTTCATATG-G-AGGTTAT
**
6684 CAAAATTTCATACAGAGGTTAT
1 CAAAATTTCATATGGAGGTTAT
*** **
6706 CAAAATTTCATAAAAACTTTAT
1 CAAAATTTCATATGGAGGTTAT
* * *
6728 CAAAATTTCTTAGGGAGGTTAA
1 CAAAATTTCATATGGAGGTTAT
* * * **
6750 CAAAATCTCATACGAATATTAT
1 CAAAATTTCATATGGAGGTTAT
** * *
6772 TGAAATTTTATA-GTGTGGTTAT
1 CAAAATTTCATATG-GAGGTTAT
*
6794 CAAAATTTCATAGGGAGGGAGGTTAT
1 CAAAATTTCAT----ATGGAGGTTAT
* *
6820 CAAAA--T--T-T-GTGCTTAT
1 CAAAATTTCATATGGAGGTTAT
*
6836 CAAAATTTCATAGGGAGGTTAATT
1 CAAAATTTCATATGGAGGTT-A-T
*
6860 AACCAAATTTCATATGGAGGTTAT
1 --CAAAATTTCATATGGAGGTTAT
*
6884 GAAAATTT--TATGGAGAGGTTAT
1 CAAAATTTCATAT-G-GAGGTTAT
* *
6906 CAAAATTACATA-GAGAGGATAT
1 CAAAATTTCATATG-GAGGTTAT
* * *
6928 CACAGTTTTATTCTCATAAGAAGGTTAT
1 CA-A----AATT-TCATATGGAGGTTAT
* *
6956 CGAAATTTC--ATGGTGTGTTTAT
1 CAAAATTTCATATGGAG-G-TTAT
6978 CATAATATTT--TGA-GGAGGTTAT
1 CA-AA-ATTTCAT-ATGGAGGTTAT
**
7000 CAAAATTTTCAT-TGTGTTGTTA-
1 CAAAA-TTTCATATG-GAGGTTAT
* * * **
7022 C-CAATTTTATA-GTATAATTAT
1 CAAAATTTCATATGGA-GGTTAT
*
7043 CAAAATTTTAT-TGGAGGATTAT
1 CAAAATTTCATATGGAGG-TTAT
*** *
7065 CAAAATTTCATACAAAGATTAT
1 CAAAATTTCATATGGAGGTTAT
*
7087 CAAAATTTCATA-GTGTGGTTAT
1 CAAAATTTCATATG-GAGGTTAT
7109 CAAAATTTCATAGTGTGA--TTAT
1 CAAAATTTCATA-TG-GAGGTTAT
7131 CAAAATTTCATA-GGAAGGTTAT
1 CAAAATTTCATATGG-AGGTTAT
***
7153 TGGAATTTCATAAT-GAGGTTAT
1 CAAAATTTCAT-ATGGAGGTTAT
*
7175 CAATATTTCTATAT
1 CAAAATTTC-ATAT
7189 TAGAGCATGA
Statistics
Matches: 380, Mismatches: 89, Indels: 116
0.65 0.15 0.20
Matches are distributed among these distances:
16 11 0.03
18 1 0.00
19 1 0.00
20 19 0.05
21 14 0.04
22 248 0.65
23 21 0.06
24 15 0.04
25 2 0.01
26 31 0.08
27 5 0.01
28 11 0.03
29 1 0.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (22 bp):
CAAAATTTCATATGGAGGTTAT
Found at i:6672 original size:44 final size:43
Alignment explanation
Indices: 6597--6717 Score: 116
Period size: 44 Copynumber: 2.7 Consensus size: 43
6587 CAATCAAACC
* *
6597 AAAATTACATAGGAAGATTATTAACATTTCATAGTATAGCTACCA
1 AAAATT-CATAGG-AGGTTATCAACATTTCATAGTATAGCTACCA
* * * * *
6642 AAAATTCATATGGAGGTTATCAACACTTCATTGTGTAGTTATCA
1 AAAATTCATA-GGAGGTTATCAACATTTCATAGTATAGCTACCA
* * *
6686 AAATTTCATACAGAGGTTATCAAAATTTCATA
1 AAAATTCATA-GGAGGTTATCAACATTTCATA
6718 AAAACTTTAT
Statistics
Matches: 62, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
44 54 0.87
45 8 0.13
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (43 bp):
AAAATTCATAGGAGGTTATCAACATTTCATAGTATAGCTACCA
Found at i:7160 original size:44 final size:44
Alignment explanation
Indices: 6640--7183 Score: 149
Period size: 44 Copynumber: 12.2 Consensus size: 44
6630 GTATAGCTAC
* * * **
6640 CAAAAATTCATA-TGGAGGTTATCAACACTTCATTGTGTAG-TTAT
1 CAAAATTTCATAGT-GAGGTTATCAAAATTTCATAATG-AGATTAT
** ** **
6684 CAAAATTTCATACAGAGGTTATCAAAATTTCATAAAAACTTTAT
1 CAAAATTTCATAGTGAGGTTATCAAAATTTCATAATGAGATTAT
* * * * * *
6728 CAAAATTTCTTAGGGAGGTTAACAAAATCTCAT-ACGAATATTAT
1 CAAAATTTCATAGTGAGGTTATCAAAATTTCATAATG-AGATTAT
** * * * *
6772 TGAAATTTTATAGTGTGGTTATCAAAATTTCATAGGGAGGGAGGTTAT
1 CAAAATTTCATAGTGAGGTTATCAAAATTTCATA---A-TGAGATTAT
* ** *
6820 CAAAA-TT--T-GT--GCTTATCAAAATTTCATAGGGAGGTTAATTAA
1 CAAAATTTCATAGTGAGGTTATCAAAATTTCATAATGA-G---ATTAT
* * * * *
6862 CCAAATTTCATA-TGGAGGTTATGAAAATTTTATGGA-GAGGTTAT
1 CAAAATTTCATAGT-GAGGTTATCAAAATTTCAT-AATGAGATTAT
* * * * *
6906 CAAAATTACATAGAGAGGATATCACAGTTTTATTCTCATAA-GAAGGTTAT
1 CAAAATTTCATAGTGAGGTTATCA-A----AATT-TCATAATG-AGATTAT
* * * * * * *
6956 CGAAATTTCATGGTGTGTTTATCATAATATTT--TGAGGAGGTTAT
1 CAAAATTTCATAGTGAGGTTATCA-AA-ATTTCATAATGAGATTAT
* ** * *
7000 CAAAATTTTCATTGTGTTGTTA-C-CAATTTTATAGTAT-A-ATTAT
1 CAAAA-TTTCATAGTGAGGTTATCAAAATTTCATA--ATGAGATTAT
* * *
7043 CAAAATTTTATTG-GAGGATTATCAAAATTTCATACA-AAGATTAT
1 CAAAATTTCATAGTGAGG-TTATCAAAATTTCATA-ATGAGATTAT
* * *
7087 CAAAATTTCATAGTGTGGTTATCAAAATTTCATAGTGTGATTAT
1 CAAAATTTCATAGTGAGGTTATCAAAATTTCATAATGAGATTAT
*** *
7131 CAAAATTTCATAG-GAAGGTTATTGGAATTTCATAATGAGGTTAT
1 CAAAATTTCATAGTG-AGGTTATCAAAATTTCATAATGAGATTAT
*
7175 CAATATTTC
1 CAAAATTTC
7184 TATATTAGAG
Statistics
Matches: 368, Mismatches: 89, Indels: 86
0.68 0.16 0.16
Matches are distributed among these distances:
38 3 0.01
39 1 0.00
41 6 0.02
42 35 0.10
43 18 0.05
44 217 0.59
45 22 0.06
46 1 0.00
47 6 0.02
48 25 0.07
49 6 0.02
50 28 0.08
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (44 bp):
CAAAATTTCATAGTGAGGTTATCAAAATTTCATAATGAGATTAT
Found at i:7160 original size:66 final size:66
Alignment explanation
Indices: 7059--7183 Score: 169
Period size: 66 Copynumber: 1.9 Consensus size: 66
7049 TTTATTGGAG
* *
7059 GATTATCAAAATTTCATACAAAGATTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGTG
1 GATTATCAAAATTTCATACAAAGATTATCAAAATTTCATAATGAGGTTATCAAAATTTCATAGTG
7124 T
66 T
** * *** *
7125 GATTATCAAAATTTCATAGGAAGGTTATTGGAATTTCATAATGAGGTTATCAATATTTC
1 GATTATCAAAATTTCATACAAAGATTATCAAAATTTCATAATGAGGTTATCAAAATTTC
7184 TATATTAGAG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 50 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (66 bp):
GATTATCAAAATTTCATACAAAGATTATCAAAATTTCATAATGAGGTTATCAAAATTTCATAGTG
T
Found at i:9619 original size:21 final size:21
Alignment explanation
Indices: 9593--9668 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
9583 TCTCACAAGG
9593 AGGTTATCAAAAATCATAGGA
1 AGGTTATCAAAAATCATAGGA
*
9614 AGGTTA-CAAAATTTCATAGGA
1 AGGTTATCAAAA-ATCATAGGA
* ***
9635 AGGTTTATTAAAAATTCATAATT
1 AGG-TTATCAAAAA-TCATAGGA
9658 AGGTTATCAAA
1 AGGTTATCAAA
9669 GTTTCATATG
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 5 0.11
21 17 0.39
22 10 0.23
23 12 0.27
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (21 bp):
AGGTTATCAAAAATCATAGGA
Found at i:9721 original size:22 final size:22
Alignment explanation
Indices: 9691--9766 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
9681 GTTTATCACA
* * *
9691 ATCACAATTTTATAGGTAAATT
1 ATCAAAATTTAATAGGTAAGTT
* *
9713 ATCAAAATTTCATAGCGT-GGTT
1 ATCAAAATTTAATAG-GTAAGTT
9735 ATCAAAATTTAATAGG-ATAGTT
1 ATCAAAATTTAATAGGTA-AGTT
9757 ATCAAAATTT
1 ATCAAAATTT
9767 CATAAAAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.02
22 42 0.93
23 2 0.04
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (22 bp):
ATCAAAATTTAATAGGTAAGTT
Found at i:9893 original size:29 final size:29
Alignment explanation
Indices: 9826--9885 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
9816 AAGCTAAAAC
9826 TAGTCTATATAAGATTAATCATGTTTGTT
1 TAGTCTATATAAGATTAATCATGTTTGTT
9855 TAGTCTATATAAGATTAATCATGTTTGTT
1 TAGTCTATATAAGATTAATCATGTTTGTT
9884 TA
1 TA
9886 TATTATATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.48
Consensus pattern (29 bp):
TAGTCTATATAAGATTAATCATGTTTGTT
Found at i:10528 original size:23 final size:23
Alignment explanation
Indices: 10502--10549 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
10492 CTGAAGTATC
*
10502 TAGACGTATAAGTGGATACAACT
1 TAGACGTAAAAGTGGATACAACT
10525 TAGACGTAAAAGTGGATACAACT
1 TAGACGTAAAAGTGGATACAACT
10548 TA
1 TA
10550 AGTTGCTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (23 bp):
TAGACGTAAAAGTGGATACAACT
Done.