Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024214.1 Corchorus olitorius cultivar O-4 contig24247, 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: 35804
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:836 original size:104 final size:105
Alignment explanation
Indices: 648--908 Score: 418
Period size: 106 Copynumber: 2.5 Consensus size: 105
638 AATTTTTCTA
* ** *
648 ACCCTTAAAATAAAATTTTAATTTTAATTTGGACTAAACTTAGTG-AATTAGTTATATATTTTAT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTAT
*
712 TTCTAAAACCCTATAACAAT-ATTATTAATTATGGAATTT
66 TTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
* *
751 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTAT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTAT
*
816 TTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTCTAAAACCCTATAACAAT-AATTATTAATTATGAAATTT
857 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGG-CTAAACTTAGTGAAATTA
909 AGGCTAAACT
Statistics
Matches: 146, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
103 41 0.28
104 37 0.25
106 50 0.34
107 18 0.12
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.41
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTAT
TTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
Found at i:2035 original size:106 final size:104
Alignment explanation
Indices: 1864--2124 Score: 425
Period size: 106 Copynumber: 2.5 Consensus size: 104
1854 AATTTAGCCT
*
1864 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
1929 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
65 AATAA--TATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
1971 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTA
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
* *
2036 ATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 ATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
** *
2075 TAA-TTCACTAAGTTTAGCCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
2125 TAGAAAAATT
Statistics
Matches: 147, Mismatches: 7, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
103 44 0.30
104 36 0.24
106 49 0.33
107 18 0.12
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (104 bp):
TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
ATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:2462 original size:13 final size:14
Alignment explanation
Indices: 2436--2468 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2426 ATCATTATGG
*
2436 AAAACAAAGTTTGA
1 AAAAAAAAGTTTGA
2450 AAAAAAAAG-TTGA
1 AAAAAAAAGTTTGA
2463 AAAAAA
1 AAAAAA
2469 GGTTTAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.70, C:0.03, G:0.12, T:0.15
Consensus pattern (14 bp):
AAAAAAAAGTTTGA
Found at i:3806 original size:23 final size:23
Alignment explanation
Indices: 3775--3828 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
3765 GATTTACAAA
3775 AGAGATTTGAAAGCCAAGG-GCTTG
1 AGAG-TTTGAAAG-CAAGGAGCTTG
*
3799 AGAGTTTGAAAGCACGGAGCTTG
1 AGAGTTTGAAAGCAAGGAGCTTG
3822 AGA-TTTG
1 AGAGTTTG
3829 CTTTGCGCGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 8 0.29
23 16 0.57
24 4 0.14
ACGTcount: A:0.31, C:0.11, G:0.33, T:0.24
Consensus pattern (23 bp):
AGAGTTTGAAAGCAAGGAGCTTG
Found at i:3855 original size:28 final size:27
Alignment explanation
Indices: 3823--3880 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 27
3813 CGGAGCTTGA
3823 GATTTGCTTTGCGCGGAGCAAGTTTGTT
1 GATTTG-TTTGCGCGGAGCAAGTTTGTT
3851 GA----TTTGCGCGGAGCAAGTTTGTT
1 GATTTGTTTGCGCGGAGCAAGTTTGTT
3874 G-TTTGTT
1 GATTTGTT
3881 CTCTCGGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
23 22 0.85
26 2 0.08
28 2 0.08
ACGTcount: A:0.14, C:0.12, G:0.33, T:0.41
Consensus pattern (27 bp):
GATTTGTTTGCGCGGAGCAAGTTTGTT
Found at i:3856 original size:23 final size:22
Alignment explanation
Indices: 3830--3878 Score: 89
Period size: 23 Copynumber: 2.2 Consensus size: 22
3820 TGAGATTTGC
3830 TTTGCGCGGAGCAAGTTTGTTG
1 TTTGCGCGGAGCAAGTTTGTTG
3852 ATTTGCGCGGAGCAAGTTTGTTG
1 -TTTGCGCGGAGCAAGTTTGTTG
3875 TTTG
1 TTTG
3879 TTCTCTCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.14, C:0.12, G:0.35, T:0.39
Consensus pattern (22 bp):
TTTGCGCGGAGCAAGTTTGTTG
Found at i:18335 original size:11 final size:11
Alignment explanation
Indices: 18319--18344 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
18309 CTAGCCCTAA
18319 AAAACTAGAAG
1 AAAACTAGAAG
18330 AAAACTAGAAG
1 AAAACTAGAAG
18341 AAAA
1 AAAA
18345 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:21340 original size:23 final size:23
Alignment explanation
Indices: 21309--21363 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
21299 GATTTACAAA
21309 AGAGATTTGAAAGCCAAGG-GCTTG
1 AGAG-TTTGAAAG-CAAGGAGCTTG
*
21333 AGAGTTTGAAAGCACGGAGCTTG
1 AGAGTTTGAAAGCAAGGAGCTTG
21356 AGA-TTTGA
1 AGAGTTTGA
21364 TTTGCGCGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 9 0.31
23 16 0.55
24 4 0.14
ACGTcount: A:0.33, C:0.11, G:0.33, T:0.24
Consensus pattern (23 bp):
AGAGTTTGAAAGCAAGGAGCTTG
Found at i:21386 original size:23 final size:23
Alignment explanation
Indices: 21360--21412 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
21350 AGCTTGAGAT
21360 TTGATTTGCGCGGAGCAAGTTTA
1 TTGATTTGCGCGGAGCAAGTTTA
* *
21383 TTGATTTACGCGGAGCAAGTTTG
1 TTGATTTGCGCGGAGCAAGTTTA
21406 TTG-TTTG
1 TTGATTTG
21413 TTCTCTCGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 3 0.11
23 24 0.89
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.40
Consensus pattern (23 bp):
TTGATTTGCGCGGAGCAAGTTTA
Found at i:23226 original size:24 final size:24
Alignment explanation
Indices: 23193--23238 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
23183 CAATCATTTC
23193 TGCATCCTCTCTTCCAACTCTTTT
1 TGCATCCTCTCTTCCAACTCTTTT
* *
23217 TGCATTCTCTCTTGCAACTCTT
1 TGCATCCTCTCTTCCAACTCTT
23239 CAACTTGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.13, C:0.35, G:0.07, T:0.46
Consensus pattern (24 bp):
TGCATCCTCTCTTCCAACTCTTTT
Found at i:30770 original size:29 final size:29
Alignment explanation
Indices: 30728--30786 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
30718 CATGCATTGA
30728 CATCTTCTGTTTTGGTACGTAATTATTTC
1 CATCTTCTGTTTTGGTACGTAATTATTTC
30757 CATCTTCTGTTTTGGTACGTAATTATTTC
1 CATCTTCTGTTTTGGTACGTAATTATTTC
30786 C
1 C
30787 TTTTGAGAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.14, T:0.51
Consensus pattern (29 bp):
CATCTTCTGTTTTGGTACGTAATTATTTC
Found at i:33372 original size:14 final size:15
Alignment explanation
Indices: 33353--33382 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
33343 TGATAAAAGG
33353 AAAAAGAGA-AGAAA
1 AAAAAGAGAGAGAAA
33367 AAAAAGAGAGAGAAA
1 AAAAAGAGAGAGAAA
33382 A
1 A
33383 GTTAGATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAAAGAGAGAGAAA
Done.