Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016361.1 Corchorus olitorius cultivar O-4 contig16394, 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: 37812
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1743 original size:52 final size:51
Alignment explanation
Indices: 1657--1763 Score: 151
Period size: 52 Copynumber: 2.1 Consensus size: 51
1647 CCAAAATACC
* *
1657 ATAAAATGCCATAAAAAACCCATTAGAAACCAACAATAAACATAACAGAAG
1 ATAAAATACCATAAAAAACCCACTAGAAACCAACAATAAACATAACAGAAG
* * * *
1708 ATAAAATACCATAAAAGAACCCACTAGAAAGCAACAGTAAACCTAGCAGAAG
1 ATAAAATACCATAAAA-AACCCACTAGAAACCAACAATAAACATAACAGAAG
1760 ATAA
1 ATAA
1764 CCCTAAACAA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
51 15 0.31
52 34 0.69
ACGTcount: A:0.57, C:0.20, G:0.10, T:0.13
Consensus pattern (51 bp):
ATAAAATACCATAAAAAACCCACTAGAAACCAACAATAAACATAACAGAAG
Found at i:4445 original size:191 final size:192
Alignment explanation
Indices: 4184--4532 Score: 558
Period size: 191 Copynumber: 1.8 Consensus size: 192
4174 GAGACTTGTC
* * *
4184 ACAATAAAAATGGTTTATTTACAAAATAATCCTCAAAACATTTATACTTCATGCTATTTAATCCC
1 ACAATAAAAATAGTTTATTTAAAAAATAATCCTCAAAACATTTATACTTCATACTATTTAATCCC
* * *
4249 TTAGACATCTTTATTATATACGATTTAACCCTCCAACTTTAATTATTTTATAG-GAAAGCCCTCG
66 TTAGACATCTTTATTATATACAATTTAACCCTCCAACTTTAATTATTTTATAGAGAAA-CCATCA
4313 TACATTTCTATTTTATGCAATTCCCTTGATATTTTATAGGAAAGCCTTCATACATTTCTATTT
130 TACATTTCTATTTTATGCAATTCCCTTGATATTTTATAGGAAAGCCTTCATACATTTCTATTT
* * *
4376 ACAATAAAAATAGTTTATTTAAAAAATAGTCCTC-AAATATTTATACTTCATACTATTTAATCTC
1 ACAATAAAAATAGTTTATTTAAAAAATAATCCTCAAAACATTTATACTTCATACTATTTAATCCC
* * * *
4440 TTAGACATCTTTATTCTATACAATTTAGCCCTTCAACTTTAATTATTTTATAGAGAAATCATCAT
66 TTAGACATCTTTATTATATACAATTTAACCCTCCAACTTTAATTATTTTATAGAGAAACCATCAT
4505 ACATTTCTATTTTATGCAATTCCCTTGA
131 ACATTTCTATTTTATGCAATTCCCTTGA
4533 CATTCTATTA
Statistics
Matches: 143, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
191 108 0.76
192 35 0.24
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (192 bp):
ACAATAAAAATAGTTTATTTAAAAAATAATCCTCAAAACATTTATACTTCATACTATTTAATCCC
TTAGACATCTTTATTATATACAATTTAACCCTCCAACTTTAATTATTTTATAGAGAAACCATCAT
ACATTTCTATTTTATGCAATTCCCTTGATATTTTATAGGAAAGCCTTCATACATTTCTATTT
Found at i:6956 original size:22 final size:22
Alignment explanation
Indices: 6901--6957 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
6891 TTTGTTTTCT
*
6901 AATTTGGCCCCTTTTTTTGTTG
1 AATTTGGCCCCTTTTTTTGTTA
* *
6923 AATGT-GCTCCCTTTTTTTTTTA
1 AATTTGGC-CCCTTTTTTTGTTA
6945 AATTTGGCCCCTT
1 AATTTGGCCCCTT
6958 GATAAAACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 2 0.07
22 25 0.86
23 2 0.07
ACGTcount: A:0.12, C:0.21, G:0.14, T:0.53
Consensus pattern (22 bp):
AATTTGGCCCCTTTTTTTGTTA
Found at i:7419 original size:30 final size:30
Alignment explanation
Indices: 7383--7473 Score: 155
Period size: 30 Copynumber: 3.0 Consensus size: 30
7373 CGTGATTATA
*
7383 GATTATAGGGTACCTGACACTACCCGACCC
1 GATTATAGGGTACCTGGCACTACCCGACCC
*
7413 GATTATAGGGTGCCTGGCACTACCCGACCC
1 GATTATAGGGTACCTGGCACTACCCGACCC
*
7443 GATTATAGGGTACCTGGCACTACCCGTCCC
1 GATTATAGGGTACCTGGCACTACCCGACCC
7473 G
1 G
7474 GTTAAGTAGG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.22, C:0.33, G:0.24, T:0.21
Consensus pattern (30 bp):
GATTATAGGGTACCTGGCACTACCCGACCC
Found at i:10196 original size:6 final size:6
Alignment explanation
Indices: 10185--10221 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
10175 ATAAAATTAG
10185 GAGGCA GAGGCA GAGGCA GAGGCA GAGGCA GAGGCA G
1 GAGGCA GAGGCA GAGGCA GAGGCA GAGGCA GAGGCA G
10222 GTAATTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.16, G:0.51, T:0.00
Consensus pattern (6 bp):
GAGGCA
Found at i:15543 original size:21 final size:21
Alignment explanation
Indices: 15517--15562 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
15507 AGCGGGAGGA
* * *
15517 GAACCATGTAGTGAAGGTGGT
1 GAACCAGGCAGTGAAGGCGGT
*
15538 GAACCAGGCAGTGACGGCGGT
1 GAACCAGGCAGTGAAGGCGGT
15559 GAAC
1 GAAC
15563 ATGGCGGTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.17, G:0.39, T:0.15
Consensus pattern (21 bp):
GAACCAGGCAGTGAAGGCGGT
Found at i:17850 original size:26 final size:26
Alignment explanation
Indices: 17769--17851 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
17759 TTCTGCTAGG
*
17769 TTTATTGTTGGTTTCTAGTGGGGTCT
1 TTTATTGTTGGTTTCTAGTGGGTTCT
* * **
17795 TTTATTGTAT-TTTATCT--TCGGTGAT
1 TTTATTGT-TGGTT-TCTAGTGGGTTCT
17820 GTTTATTGTTGGTTTCTAGTGGGTTCT
1 -TTTATTGTTGGTTTCTAGTGGGTTCT
17847 TTTAT
1 TTTAT
17852 GGCATTTTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
25 8 0.19
26 25 0.60
27 9 0.21
ACGTcount: A:0.11, C:0.07, G:0.24, T:0.58
Consensus pattern (26 bp):
TTTATTGTTGGTTTCTAGTGGGTTCT
Found at i:19870 original size:30 final size:30
Alignment explanation
Indices: 19805--19863 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
19795 TCGTCCATTC
* * *
19805 CAACCACACCTCATGATTATGCACCCATCT
1 CAACCACACCTCAAGATTATGCAACAATCT
*
19835 CAACCACACCTCAAGGTTATGCAACAATC
1 CAACCACACCTCAAGATTATGCAACAATC
19864 CAAACCAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.34, C:0.37, G:0.08, T:0.20
Consensus pattern (30 bp):
CAACCACACCTCAAGATTATGCAACAATCT
Found at i:20155 original size:45 final size:45
Alignment explanation
Indices: 20091--20176 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
20081 GAGAGATGCG
* *
20091 TTGGAGTAGTTTATTTCTTTTGCTATGTTAGGGAGGAAGGGGGCA
1 TTGGAGTAGTTTATATCTTTTGATATGTTAGGGAGGAAGGGGGCA
20136 TTGGAGTAGTTTATATCTTTTGATATGTTAGGGAGGAAGGG
1 TTGGAGTAGTTTATATCTTTTGATATGTTAGGGAGGAAGGG
20177 TGGTTTATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.22, C:0.05, G:0.35, T:0.38
Consensus pattern (45 bp):
TTGGAGTAGTTTATATCTTTTGATATGTTAGGGAGGAAGGGGGCA
Found at i:24924 original size:11 final size:11
Alignment explanation
Indices: 24908--24932 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24898 TTTATGCAAG
24908 TTTCTTCCTTT
1 TTTCTTCCTTT
24919 TTTCTTCCTTT
1 TTTCTTCCTTT
24930 TTT
1 TTT
24933 TTATAGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTCTTCCTTT
Found at i:25936 original size:7 final size:7
Alignment explanation
Indices: 25924--25950 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
25914 CGGTGTTCTC
25924 TTACGAG
1 TTACGAG
25931 TTACGAG
1 TTACGAG
25938 TTACGAG
1 TTACGAG
25945 TTACGA
1 TTACGA
25951 CTGACTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (7 bp):
TTACGAG
Found at i:26303 original size:2 final size:2
Alignment explanation
Indices: 26296--26333 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
26286 CCCTGACCTC
26296 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26334 GGTAAATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26342 original size:23 final size:21
Alignment explanation
Indices: 26297--26344 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
26287 CCTGACCTCA
*
26297 TATATATATATATATATATAT
1 TATATATATATATATATAAAT
26318 TATATATATATATATAGGTAAAT
1 TATATATATATATATA--TAAAT
26341 TATA
1 TATA
26345 CAATACATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 16 0.67
23 8 0.33
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (21 bp):
TATATATATATATATATAAAT
Found at i:37736 original size:335 final size:333
Alignment explanation
Indices: 36862--37812 Score: 1121
Period size: 322 Copynumber: 2.9 Consensus size: 333
36852 GAATAAAAAA
* * * * *
36862 CTAATTAAATCGAAATAAGATTCAAATAG-TTGTAAAAACAAATCCTTATATCCAATATGACTGA
1 CTAATTAAATAGAAACAAAATTCAGAT-GCTCGTAAAAACAAATCCTTATATCCAATATGACTGA
* *
36926 GA-TTTGATTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAGAATCATGCAAAACTGAG
65 GATTTTG-TTCGATGAATATAGATATTTC-AGAAGTCTTTGTGCCAAAAATCATGC-AAACTGAG
* * *
36990 CCGGGGCACCGAAACGCGTTTTTAGCAAAAACCATGATGGTTAGTACACGATTTCGGCT---A--
127 CCGGGGCTCCGGAACGCGTTTTTAGCAAAAACCATGATGGTTAGTACACGATTTTGGCTAAAATT
* * * * * * *
37050 ----AAAATTGACCCG-AAATGTTTTTT-TCTCAATTTTTTGCCATAATACTCAGAAAAAAAAAA
192 TTGCAAAACTGACCCGAAAAT-TTTTTTACCTCAATTTCTTGCCACAATACTCTGAAAAAAATAT
* ** ** * * * * *
37109 AT-ATTCAACGCCAAAAATCTTGACCGG--ATTTTTACGTTTCTTATATCGTTTTTCCATTTTTT
256 ATAATTCAACGCGAAAAAGATTGAAGGGTTTTTTTTACGTTTCTAATACCGTTTTCCCATTCTTT
*
37171 TCTGAATTAATTT
321 TCCGAATTAATTT
* * * *
37184 CTAATTAAATAGAAACAAAATTCAGATGCTCTTAAAAACGAATCCTTATATCCAATGTGGCTGAG
1 CTAATTAAATAGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATATGACTGAG
* * * * * *
37249 ATTTGGTCCGATGAATATAGATATTTCAAAGAGTATTTGTGCCAAAACTCATGCAAAGTTGAGCC
66 ATTTTGTTCGATGAATATAGATATTTCAGA-AGTCTTTGTGCCAAAAATCATGCAAA-CTGAGCC
* *
37314 GGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTAATGGTTAGTACACGATTTTGGCTAAAATTT
129 GGGGCTCCGGAACGCGTTTTTAG-CAAAAACCATGATGGTTAGTACACGATTTTGGCTAAAATTT
*
37379 TGCAAGAACTAACCCGAAAATTTTTTTACCTCAATTTCTTGCCACAATACTCTGAAAAAAATATA
193 TGCAA-AACTGACCCGAAAATTTTTTTACCTCAATTTCTTGCCACAATACTCTGAAAAAAATATA
37444 TAATTCAACGCGAAAAAGATTGAAGGGTTTTTTTTCAC-TCTTCTAATACCGTTTTCCCATTCTT
257 TAATTCAACGCGAAAAAGATTGAAGGGTTTTTTTT-ACGT-TTCTAATACCGTTTTCCCATTCTT
**
37508 TTCCGAATTTTTTT
320 TTCCGAATTAATTT
* * * *
37522 CTAATT-AATCGAAACAAAATTCAGATTCTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAG
1 CTAATTAAATAGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATATGACTGAG
* * * *
37586 ATTTTGTTTGATGAATACAGATATTTCGAGAAGTCTTTTTGCCAAAAATCATGC-AACTGAGTCG
66 ATTTTGTTCGATGAATATAGATATTTC-AGAAGTCTTTGTGCCAAAAATCATGCAAACTGAGCCG
* *
37650 GGGCTCCGGAACGCGTTTTTAGCTAAAAATCATGATGGTTAGTATACGATTTTGGCTAAAATTTT
130 GGGCTCCGGAACGCGTTTTTAGC-AAAAACCATGATGGTTAGTACACGATTTTGGCTAAAATTTT
*
37715 GCAAAAGCTGACCCGAAAATTTTTTTTACCTCAATATCTTGCCACAATACTCTGAAAAAAATATA
194 GCAAAA-CTGACCCGAAAA-TTTTTTTACCTCAATTTCTTGCCACAATACTCTGAAAAAAATATA
*
37780 TAATTCAACGCGAAAGAAGATTAAAAGGGTTTT
257 TAATTCAACGCGAAA-AAGATT-GAAGGGTTTT
Statistics
Matches: 534, Mismatches: 67, Indels: 40
0.83 0.10 0.06
Matches are distributed among these distances:
321 5 0.01
322 122 0.23
323 34 0.06
326 1 0.00
332 2 0.00
333 14 0.03
334 39 0.07
335 100 0.19
336 61 0.11
337 106 0.20
338 50 0.09
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (333 bp):
CTAATTAAATAGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATATGACTGAG
ATTTTGTTCGATGAATATAGATATTTCAGAAGTCTTTGTGCCAAAAATCATGCAAACTGAGCCGG
GGCTCCGGAACGCGTTTTTAGCAAAAACCATGATGGTTAGTACACGATTTTGGCTAAAATTTTGC
AAAACTGACCCGAAAATTTTTTTACCTCAATTTCTTGCCACAATACTCTGAAAAAAATATATAAT
TCAACGCGAAAAAGATTGAAGGGTTTTTTTTACGTTTCTAATACCGTTTTCCCATTCTTTTCCGA
ATTAATTT
Done.