Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016899.1 Corchorus olitorius cultivar O-4 contig16932, 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: 56671
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:6518 original size:13 final size:13
Alignment explanation
Indices: 6496--6540 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
6486 GGAACTGTTT
*
6496 TATAACTGCTTTA
1 TATAAATGCTTTA
6509 TATAAATGCTTTA
1 TATAAATGCTTTA
*
6522 TA-AAATGTTTTA
1 TATAAATGCTTTA
6534 -ATAAATG
1 TATAAATG
6541 TTTTGGGTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 1 0.03
12 14 0.48
13 14 0.48
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (13 bp):
TATAAATGCTTTA
Found at i:11817 original size:17 final size:17
Alignment explanation
Indices: 11795--11828 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
11785 CTACTATTCA
11795 AAATAGATTCTTCTTTT
1 AAATAGATTCTTCTTTT
11812 AAATAGATTCTTCTTTT
1 AAATAGATTCTTCTTTT
11829 TCGAAGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (17 bp):
AAATAGATTCTTCTTTT
Found at i:26729 original size:14 final size:13
Alignment explanation
Indices: 26710--26756 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
26700 CTGCAAAATT
26710 AACAAAAACACAAA
1 AACAAAAACA-AAA
26724 AACAAAAACAAAA
1 AACAAAAACAAAA
* *
26737 TACGAAAAA-TAAA
1 AAC-AAAAACAAAA
26750 AACAAAA
1 AACAAAA
26757 CTAAAGGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 4 0.14
13 10 0.34
14 15 0.52
ACGTcount: A:0.79, C:0.15, G:0.02, T:0.04
Consensus pattern (13 bp):
AACAAAAACAAAA
Found at i:26735 original size:20 final size:20
Alignment explanation
Indices: 26710--26756 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
26700 CTGCAAAATT
26710 AACAAAA-ACACAAAAACAAA
1 AACAAAATAC-CAAAAACAAA
* *
26730 AACAAAATACGAAAAATAAA
1 AACAAAATACCAAAAACAAA
26750 AACAAAA
1 AACAAAA
26757 CTAAAGGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.79, C:0.15, G:0.02, T:0.04
Consensus pattern (20 bp):
AACAAAATACCAAAAACAAA
Found at i:26736 original size:5 final size:6
Alignment explanation
Indices: 26714--26756 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
26704 AAAATTAACA
*
26714 AAAACAC AAAAAC AAAAAC AAAATAC GAAAAAT AAAAAC AAAA
1 AAAA-AC AAAAAC AAAAAC AAAA-AC -AAAAAC AAAAAC AAAA
26757 CTAAAGGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 21 0.66
7 7 0.22
8 4 0.12
ACGTcount: A:0.79, C:0.14, G:0.02, T:0.05
Consensus pattern (6 bp):
AAAAAC
Found at i:31379 original size:42 final size:43
Alignment explanation
Indices: 31332--31414 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
31322 CGTGTTTGGC
*
31332 TTATCGTGTCTCGTGT-CTGAATCGTGTC-GGACACGATTAAGA
1 TTATCGTGTCTCGTGTCCT-AATCGTGTCAAGACACGATTAAGA
*
31374 TTATCGTGTTTCGTGTCCTAATCGTGTCAAGACACGATTAA
1 TTATCGTGTCTCGTGTCCTAATCGTGTCAAGACACGATTAA
31415 CACGTTTAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 24 0.65
43 13 0.35
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (43 bp):
TTATCGTGTCTCGTGTCCTAATCGTGTCAAGACACGATTAAGA
Found at i:31427 original size:20 final size:20
Alignment explanation
Indices: 31402--31441 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
31392 TAATCGTGTC
*
31402 AAGACACGATTAACACGTTT
1 AAGACACGAGTAACACGTTT
*
31422 AAGACACGAGTGACACGTTT
1 AAGACACGAGTAACACGTTT
31442 TAATTAACGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
AAGACACGAGTAACACGTTT
Found at i:31919 original size:12 final size:12
Alignment explanation
Indices: 31902--31932 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
31892 TACCCTATAT
31902 AAACACGACACG
1 AAACACGACACG
31914 AAACACGACACG
1 AAACACGACACG
31926 AAACACG
1 AAACACG
31933 GATTGCCAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.52, C:0.32, G:0.16, T:0.00
Consensus pattern (12 bp):
AAACACGACACG
Found at i:38174 original size:13 final size:13
Alignment explanation
Indices: 38156--38184 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
38146 TCATTCTGTC
38156 CCAAAACATGTGT
1 CCAAAACATGTGT
38169 CCAAAACATGTGT
1 CCAAAACATGTGT
38182 CCA
1 CCA
38185 CTTATAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.21
Consensus pattern (13 bp):
CCAAAACATGTGT
Found at i:39633 original size:3 final size:3
Alignment explanation
Indices: 39625--39680 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
39615 TTCTTTTTCC
39625 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
39673 ATA GTA AT
1 ATA ATA AT
39681 TTTAAAATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:39814 original size:2 final size:2
Alignment explanation
Indices: 39807--39844 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
39797 ACATACATAC
*
39807 AT AT AT AT AT AT AA 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
39845 TAAGTTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:41324 original size:25 final size:26
Alignment explanation
Indices: 41296--41358 Score: 110
Period size: 25 Copynumber: 2.5 Consensus size: 26
41286 AAATGGAAGG
41296 AAATATTATTAGAAATCTAATGTTT-
1 AAATATTATTAGAAATCTAATGTTTA
*
41321 AAATATTATTAGAAATCTAATTTTTA
1 AAATATTATTAGAAATCTAATGTTTA
41347 AAATATTATTAG
1 AAATATTATTAG
41359 TAATTAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 24 0.67
26 12 0.33
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.44
Consensus pattern (26 bp):
AAATATTATTAGAAATCTAATGTTTA
Found at i:46966 original size:3 final size:3
Alignment explanation
Indices: 46958--46982 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
46948 GGTTCTCAAT
46958 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
46983 TGAAGAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:47708 original size:162 final size:162
Alignment explanation
Indices: 47441--48120 Score: 1146
Period size: 162 Copynumber: 4.2 Consensus size: 162
47431 TATTTCCTTT
* * * * *
47441 AGACAACCTATTGTTCTCACCGTGTCTTCATTTACAAAAGCCTACTATGTGGCAAAGCATTGGTG
1 AGACAACCTATAGTTCTCACCGTGTCTTTATTTACAAAAGCCCACTATGCGGCAAGGCATTGGTG
*
47506 ATTGAGAAACCCACTATAGCTCACACCTAGTCTTCCTTGTATGATGCATTATTTACCATCATCAA
66 ATTGAGAAACCCACTATAGCTCACACCTAGTCTTCCTTGTATGATGCATTGTTTACCATCATCAA
*
47571 GGTATGGCAAGGCATTATGCCGCCGGTGATTG
131 GGCATGGCAAGGCATTATGCCGCCGGTGATTG
*
47603 AGACAACCTATAGTTCTCACCGTGTCTTTATTTACAAAAGCTCACTATGTC-GCAAGGCATTGGT
1 AGACAACCTATAGTTCTCACCGTGTCTTTATTTACAAAAGCCCACTATG-CGGCAAGGCATTGGT
*
47667 AATTGAGAAACCCACTATAGCTCACACCTAGTCTTCCTTGTATGATGCATTGTTTACCATCATCA
65 GATTGAGAAACCCACTATAGCTCACACCTAGTCTTCCTTGTATGATGCATTGTTTACCATCATCA
47732 AGGCATGGCAAGGCATTATGCCGCCGGTGATTG
130 AGGCATGGCAAGGCATTATGCCGCCGGTGATTG
* *
47765 AGACAACCAATAGTTCTCACCGTGTCTTTATTTACAAAAGCCCACTATGCGGCAAGCCATTGGTG
1 AGACAACCTATAGTTCTCACCGTGTCTTTATTTACAAAAGCCCACTATGCGGCAAGGCATTGGTG
*
47830 ATTGAGAATCCCACTATAGCTCACACCTAGTCTTCCTTGTATGATGCATTGTTTACCATCATCAA
66 ATTGAGAAACCCACTATAGCTCACACCTAGTCTTCCTTGTATGATGCATTGTTTACCATCATCAA
* *
47895 GGTATGGTAAGGCATTATGCCGCCGGTGATTG
131 GGCATGGCAAGGCATTATGCCGCCGGTGATTG
*
47927 AGACAACCTATAGTTCTCACCGTGTCTTTATTTACAAAAACCCACTATGCGGCAAGGCATTGGTG
1 AGACAACCTATAGTTCTCACCGTGTCTTTATTTACAAAAGCCCACTATGCGGCAAGGCATTGGTG
* * **
47992 ATTGAGAAAACTACTATAGCTCACACCTAGTCTTCCTTGTATGGGGCATTGTTTACCATCATCAA
66 ATTGAGAAACCCACTATAGCTCACACCTAGTCTTCCTTGTATGATGCATTGTTTACCATCATCAA
* *
48057 GGCATGGCAAGGTATTATGCCGTCGGTGATTG
131 GGCATGGCAAGGCATTATGCCGCCGGTGATTG
*
48089 AGACAACCTATAGTTCTCACCTTGTCTTTATT
1 AGACAACCTATAGTTCTCACCGTGTCTTTATT
48121 ATTTATAAAT
Statistics
Matches: 487, Mismatches: 29, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
161 1 0.00
162 486 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (162 bp):
AGACAACCTATAGTTCTCACCGTGTCTTTATTTACAAAAGCCCACTATGCGGCAAGGCATTGGTG
ATTGAGAAACCCACTATAGCTCACACCTAGTCTTCCTTGTATGATGCATTGTTTACCATCATCAA
GGCATGGCAAGGCATTATGCCGCCGGTGATTG
Found at i:49816 original size:15 final size:15
Alignment explanation
Indices: 49798--49860 Score: 55
Period size: 15 Copynumber: 4.5 Consensus size: 15
49788 CTGCCAGGAA
49798 GCTCGCTGCTGAGAT
1 GCTCGCTGCTGAGAT
*
49813 GCT--C-GCT-A-AC
1 GCTCGCTGCTGAGAT
*
49823 GCCCGCTGCTGAGAT
1 GCTCGCTGCTGAGAT
*
49838 CCTCGCTGCTGAGAT
1 GCTCGCTGCTGAGAT
*
49853 GTTCGCTG
1 GCTCGCTG
49861 ACACCCGCTG
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
10 3 0.08
11 1 0.03
12 4 0.11
13 4 0.11
14 1 0.03
15 23 0.64
ACGTcount: A:0.13, C:0.32, G:0.30, T:0.25
Consensus pattern (15 bp):
GCTCGCTGCTGAGAT
Found at i:49859 original size:40 final size:40
Alignment explanation
Indices: 49799--49925 Score: 191
Period size: 40 Copynumber: 3.2 Consensus size: 40
49789 TGCCAGGAAG
*
49799 CTCGCTGCTGAGATGCTCGCTAACGCCCGCTGCTGAGATC
1 CTCGCTGCTGAGATGCTCGCTAACACCCGCTGCTGAGATC
* *
49839 CTCGCTGCTGAGATGTTCGCTGACACCCGCTGCTGAGATC
1 CTCGCTGCTGAGATGCTCGCTAACACCCGCTGCTGAGATC
* * * *
49879 CTCGCTGTTGAGAAGCTCGCTAACCCCCGCTGCTGAGATG
1 CTCGCTGCTGAGATGCTCGCTAACACCCGCTGCTGAGATC
49919 CTCGCTG
1 CTCGCTG
49926 ACGTTCGCTG
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.15, C:0.34, G:0.28, T:0.24
Consensus pattern (40 bp):
CTCGCTGCTGAGATGCTCGCTAACACCCGCTGCTGAGATC
Found at i:55470 original size:28 final size:27
Alignment explanation
Indices: 55438--55497 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
55428 TCATTTGTTT
* * *
55438 ATTTTAGGTCTACAGGGGCAAAATGGTA
1 ATTTTA-GTCGACAAGGGCAAAATAGTA
*
55466 ATTTTATTCGACAAGGGCAAAATAGTA
1 ATTTTAGTCGACAAGGGCAAAATAGTA
55493 ATTTT
1 ATTTT
55498 TCATGATATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (27 bp):
ATTTTAGTCGACAAGGGCAAAATAGTA
Done.