Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015667.1 Corchorus olitorius cultivar O-4 contig15700, 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: 44747
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:904 original size:19 final size:20
Alignment explanation
Indices: 875--932 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
865 CTGTTTAGTA
*
875 ACTGCACAGATGAGATTAC-
1 ACTGTACAGATGAGATTACG
* *
894 ACTGTATAGATTAGATTACG
1 ACTGTACAGATGAGATTACG
*
914 TACTGTACATATGAGATTA
1 -ACTGTACAGATGAGATTA
933 TAATAGCAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 16 0.52
21 15 0.48
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (20 bp):
ACTGTACAGATGAGATTACG
Found at i:2751 original size:14 final size:14
Alignment explanation
Indices: 2732--2766 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2722 GGGTAAACTA
*
2732 TTTTACTTTATTTT
1 TTTTACTTTACTTT
2746 TTTTACTTTACTTT
1 TTTTACTTTACTTT
*
2760 ATTTACT
1 TTTTACT
2767 ACTACTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTACTTTACTTT
Found at i:6869 original size:59 final size:59
Alignment explanation
Indices: 6803--6918 Score: 173
Period size: 59 Copynumber: 2.0 Consensus size: 59
6793 TTCCCTCCGG
* *
6803 ACTTTTAATTTGGAACTTT-ACC-CCTCTAACTATCAAAATCGGGATAATTTCTCCCTTAA
1 ACTTTTAATTTGGAACTTTCACCTCCT-AAACTATCAAAATCAGGATAATTT-TCCCTTAA
*
6862 ACTTTTAATTTGGAACTTTCACCTCCTAAACTATCAAAATCAGGATGATTTTCCCTT
1 ACTTTTAATTTGGAACTTTCACCTCCTAAACTATCAAAATCAGGATAATTTTCCCTT
6919 TTAAGTTGGC
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
59 25 0.48
60 24 0.46
61 3 0.06
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (59 bp):
ACTTTTAATTTGGAACTTTCACCTCCTAAACTATCAAAATCAGGATAATTTTCCCTTAA
Found at i:8383 original size:296 final size:295
Alignment explanation
Indices: 7747--8631 Score: 1314
Period size: 296 Copynumber: 3.0 Consensus size: 295
7737 AATCTTGATT
* * *
7747 GCAATTGTTAAATTAATGAACTCGGGTAGACACATTTACAGCACTAATCCTTTGGAATTCCGGCC
1 GCAATTGTTAAATTAATGAACTCGGGTAGACACATTTATAGCACCAATCCTTTGGAATTCCGGCA
* * * *
7812 GAGGAGTTGAACTGATAAATCCTAATATCCACACACAATCAATATGTAATTAAAACACACTTAAC
66 GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATTTCTAATTAAAACACACTTAA-
7877 TCATAAATATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGAAAATTCATC
130 TCATAAATATAAAAATAGTAAATTACAAAAAA-GGCAGCAGGAAAAGTAAGGGAGAAAATTCATC
* *
7942 GAAGGCCTTTTTAGTCACCTGAAAAGTGAGAAAAGACAAAAAAAAAAAGTCAAAAGGAAGCACCA
194 GAAGGCCTTTTTAGTCACC-GAAAAGTGAGAAAAGATAAAAAAAAAAAGCCAAAAGGAAGCACCA
*
8007 CATTAATCCTCAATTTGGCCTTTTAAGTAATTTCCATA
258 CATTAATCCTCAATTTGGCCTTTTAAGTAATTTCCAAA
* *
8045 GCAATTGTTAAATTAATGAACTCGGGTAGACACATTTATAGCACCAATCCTTTTGAATTCCGACA
1 GCAATTGTTAAATTAATGAACTCGGGTAGACACATTTATAGCACCAATCCTTTGGAATTCCGGCA
* * * * *
8110 GAGGACTTAAACCGGGAAATTCTAATATCCACACACAATCAATTTCTAATTAAAAAACACTTAAT
66 GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATTTCTAATTAAAACACACTTAAT
* *
8175 AATAACTATAAAAATAGTAAATTACAAAAAATGGCAGCAGGAAAAGTAAGGGAGAAAATTCATCG
131 CATAAATATAAAAATAGTAAATTACAAAAAA-GGCAGCAGGAAAAGTAAGGGAGAAAATTCATCG
* * * *
8240 AAGGCCTTTTTAGTCATCCAAAAAGTGAGAAAAGA-ACAAAAAAAAGGGCAAAAGGAAGCACCAC
195 AAGGCCTTTTTAGTCA-CCGAAAAGTGAGAAAAGATAAAAAAAAAAAGCCAAAAGGAAGCACCAC
* *
8304 ATTAATTCTCAATTTGGCCTTTTAGGTAATTTCCAAA
259 ATTAATCCTCAATTTGGCCTTTTAAGTAATTTCCAAA
* * *
8341 GCAATTGTTAAATTAATGAATTTGGGTAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCA
1 GCAATTGTTAAATTAATGAACTCGGGTAGACACATTTATAGCACCAATCCTTTGGAATTCCGGCA
* * *
8406 GAGGAGTTGAATCGGTAAATCCTAATATCCACACACAATTAA-TACATAATTAAAACACACTTAA
66 GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATTTC-TAATTAAAACACACTTAA
* * * *
8470 TCATAAATACAAAAATATTAAATTACAAAAAAGGCAGGAGGAAAAGTAAGGGATG-AAATTTATC
130 TCATAAATATAAAAATAGTAAATTACAAAAAAGGCAGCAGGAAAAGTAAGGGA-GAAAATTCATC
8534 -AAGGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGATTAAAAAAAAAAAGCCAAAAGG-AGACA
194 GAA-GGCCTTTTTAGTCA-CCGAAAAGTGAGAAAAGA-TAAAAAAAAAAAGCCAAAAGGAAG-CA
8597 CCACATTAATCCTCAATTTGGCC-TTTAAGTAATTT
255 CCACATTAATCCTCAATTTGGCCTTTTAAGTAATTT
8632 TCATAATCAC
Statistics
Matches: 530, Mismatches: 50, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
294 2 0.00
295 61 0.12
296 215 0.41
297 135 0.25
298 117 0.22
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (295 bp):
GCAATTGTTAAATTAATGAACTCGGGTAGACACATTTATAGCACCAATCCTTTGGAATTCCGGCA
GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATTTCTAATTAAAACACACTTAAT
CATAAATATAAAAATAGTAAATTACAAAAAAGGCAGCAGGAAAAGTAAGGGAGAAAATTCATCGA
AGGCCTTTTTAGTCACCGAAAAGTGAGAAAAGATAAAAAAAAAAAGCCAAAAGGAAGCACCACAT
TAATCCTCAATTTGGCCTTTTAAGTAATTTCCAAA
Found at i:15459 original size:31 final size:32
Alignment explanation
Indices: 15402--15481 Score: 99
Period size: 31 Copynumber: 2.5 Consensus size: 32
15392 GGCGGGTTCA
*
15402 GGTATTTTCAGGCTCGGGTTAAGTTGGATTCG
1 GGTATTTTCGGGCTCGGGTTAAGTTGGATTCG
* *
15434 GGTATTTTCGGGCT-GGGTTATGTTGGGTTCG
1 GGTATTTTCGGGCTCGGGTTAAGTTGGATTCG
** *
15465 AATATTTTCGGGTTCGG
1 GGTATTTTCGGGCTCGG
15482 TCTCGGGTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 26 0.63
32 15 0.37
ACGTcount: A:0.12, C:0.11, G:0.36, T:0.40
Consensus pattern (32 bp):
GGTATTTTCGGGCTCGGGTTAAGTTGGATTCG
Found at i:15500 original size:6 final size:6
Alignment explanation
Indices: 15471--15548 Score: 72
Period size: 6 Copynumber: 13.3 Consensus size: 6
15461 TTCGAATATT
* * *
15471 TTCGGG TTC-GG TCTCGGG -TAGGG TTCGGG TTCAGG TTCGGG TTCGAG
1 TTCGGG TTCGGG T-TCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
* * *
15518 TTCGAG TTCGGG -TCAGG TTCGGG CTCGGG TT
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TT
15549 TTATTTCGAT
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
5 11 0.19
6 45 0.78
7 2 0.03
ACGTcount: A:0.06, C:0.18, G:0.44, T:0.32
Consensus pattern (6 bp):
TTCGGG
Found at i:15508 original size:29 final size:28
Alignment explanation
Indices: 15475--15547 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
15465 AATATTTTCG
*
15475 GGTTCGGTCTCGGGTAGGGTTCGGGTTCA
1 GGTTCGGTCTCGGGTAGAGTTCGGG-TCA
* *
15504 GGTTCGGGT-TCGAGTTCGAGTTCGGGTCA
1 GGTTC-GGTCTCG-GGTAGAGTTCGGGTCA
*
15533 GGTTCGGGCTCGGGT
1 GGTTCGGTCTCGGGT
15548 TTTATTTCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
28 4 0.11
29 19 0.53
30 13 0.36
ACGTcount: A:0.07, C:0.18, G:0.45, T:0.30
Consensus pattern (28 bp):
GGTTCGGTCTCGGGTAGAGTTCGGGTCA
Found at i:15684 original size:13 final size:12
Alignment explanation
Indices: 15661--15716 Score: 53
Period size: 13 Copynumber: 4.7 Consensus size: 12
15651 AAGTTTATTG
15661 ATAATATATAAT
1 ATAATATATAAT
15673 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
15686 ATAACAT-TATT
1 ATAATATATAAT
*
15697 ATCAATATGTAAT
1 AT-AATATATAAT
15710 AT-ATATA
1 ATAATATA
15717 AAGATTGAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
11 9 0.25
12 11 0.31
13 16 0.44
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:17110 original size:295 final size:293
Alignment explanation
Indices: 16577--17165 Score: 903
Period size: 295 Copynumber: 2.0 Consensus size: 293
16567 AATTTTGATT
* *
16577 GCAATTGTTAAATTAATGAATTCGGGTAAACACATTTACAGCACTAATCCTTTGGAATTCCGGCA
1 GCAATTGTTAAATTAATGAACTCGGGTAAACACATTTACAGCACCAATCCTTTGGAATTCCGGCA
** *
16642 GAGGAGTTGAACTGATAAATCCTAATATCCACACACAATCAATATGTAATTAAAACACACTTAAT
66 GAGGAGTTGAACTGATAAATCCTAATATCCACACACAATCAATACATAATCAAAACACACTTAAT
* * *
16707 CATAAATATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGCAAAGTAAGGGAGAAAATTCATCG
131 CATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGAAAATTCATCA
*
16772 AGAACCTTTTTAGTCACCTGAAAAGTGAGAAAAGACAAAAAAAAAGTCAAAAGGAAGCACCACAT
196 AGAACCTTTTTAGTCACCTGAAAAGTGAGAAAAGAC-AAAAAAAAGCCAAAAGGAAGCACCACAT
* *
16837 TAATCCTCAATATGGCCTTTTAGGTAATTTCCATA
260 TAATCCTCAATATGACC-TTTAAGTAATTTCCATA
* * * *
16872 GCAATTGTTAAATTAATGAACTCGGGTAGATACATTTATAGCACCAATCTTTTGGAATTCCGGCA
1 GCAATTGTTAAATTAATGAACTCGGGTAAACACATTTACAGCACCAATCCTTTGGAATTCCGGCA
* *
16937 GAGGAGTTGAA-TCGGTAAATCCTAATATCCACACACAATTAATACATAATCAAAACACACTTAA
66 GAGGAGTTGAACT-GATAAATCCTAATATCCACACACAATCAATACATAATCAAAACACACTTAA
* * *
17001 TCATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGGAGGAAAAGTAAGGGAGGAAATTTATC
130 TCATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGAAAATTCATC
** * *
17066 AAGGGCCTTTTTAGTCACGC-GAAAAGTGAGAAAAGACCAAAAAAAGCCAAAAGGAGGCACCACA
195 AAGAACCTTTTTAGTCAC-CTGAAAAGTGAGAAAAGACAAAAAAAAGCCAAAAGGAAGCACCACA
*
17130 TTAATCCTCAATTTGACCTTTAAGTAATTTCCATA
259 TTAATCCTCAATATGACCTTTAAGTAATTTCCATA
17165 G
1 G
17166 TCACTAAAAA
Statistics
Matches: 267, Mismatches: 25, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
293 17 0.06
294 41 0.15
295 208 0.78
296 1 0.00
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (293 bp):
GCAATTGTTAAATTAATGAACTCGGGTAAACACATTTACAGCACCAATCCTTTGGAATTCCGGCA
GAGGAGTTGAACTGATAAATCCTAATATCCACACACAATCAATACATAATCAAAACACACTTAAT
CATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGAAAATTCATCA
AGAACCTTTTTAGTCACCTGAAAAGTGAGAAAAGACAAAAAAAAGCCAAAAGGAAGCACCACATT
AATCCTCAATATGACCTTTAAGTAATTTCCATA
Found at i:22902 original size:29 final size:29
Alignment explanation
Indices: 22860--22930 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
22850 TTATCAAAAA
22860 CTAGATAATTATAGATCACTGATTATTTT
1 CTAGATAATTATAGATCACTGATTATTTT
22889 CTAGATAATTATAGATCACTGATTATTTT
1 CTAGATAATTATAGATCACTGATTATTTT
*
22918 CTAAATAATTATA
1 CTAGATAATTATA
22931 AAACTGAAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (29 bp):
CTAGATAATTATAGATCACTGATTATTTT
Found at i:27647 original size:18 final size:18
Alignment explanation
Indices: 27624--27667 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
27614 TTTTTGGATT
27624 ACCATTTGACTTT-ACCAC
1 ACCATTTG-CTTTCACCAC
* *
27642 ACCATTTGGTTTCACTAC
1 ACCATTTGCTTTCACCAC
27660 ACCATTTG
1 ACCATTTG
27668 GCTTCTTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.25, C:0.30, G:0.09, T:0.36
Consensus pattern (18 bp):
ACCATTTGCTTTCACCAC
Found at i:28981 original size:11 final size:11
Alignment explanation
Indices: 28965--28989 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28955 GAAATAAAAC
28965 AAACAAAAGAA
1 AAACAAAAGAA
28976 AAACAAAAGAA
1 AAACAAAAGAA
28987 AAA
1 AAA
28990 GACTTAGACA
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:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (11 bp):
AAACAAAAGAA
Found at i:31067 original size:20 final size:20
Alignment explanation
Indices: 31042--31081 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
31032 ATCTTTATTA
31042 AATGAAAGAATAATAATAAT
1 AATGAAAGAATAATAATAAT
31062 AATGAAAGAATAATAATAAT
1 AATGAAAGAATAATAATAAT
31082 TTGGTACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (20 bp):
AATGAAAGAATAATAATAAT
Found at i:41008 original size:2 final size:2
Alignment explanation
Indices: 41001--41030 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40991 TTAGGTTGTA
41001 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
41031 TTGATTTGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42266 original size:11 final size:11
Alignment explanation
Indices: 42252--42289 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
42242 ATTCATAAAA
42252 AATTTATAATT
1 AATTTATAATT
42263 AATTTATAATT
1 AATTTATAATT
42274 -ATTTGATAATT
1 AATTT-ATAATT
*
42285 TATTT
1 AATTT
42290 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Done.