Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020909.1 Corchorus olitorius cultivar O-4 contig20942, 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: 45560
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Found at i:4380 original size:31 final size:31
Alignment explanation
Indices: 4345--4422 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
4335 GGGAGCGTAT
*
4345 CAATTGGTTCC-GATATATCGTCAGGACCCAA
1 CAATTGG-TCCTGATATACCGTCAGGACCCAA
*
4376 CAATTGATCCTGATATACCGTCAGGACCCAA
1 CAATTGGTCCTGATATACCGTCAGGACCCAA
*
4407 TAATTGGTCCTGATAT
1 CAATTGGTCCTGATAT
4423 TAGATTGTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 3 0.07
31 39 0.93
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (31 bp):
CAATTGGTCCTGATATACCGTCAGGACCCAA
Found at i:4547 original size:2 final size:2
Alignment explanation
Indices: 4540--4587 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
4530 GGTGCTCTTT
* *
4540 TA TA TA TA CA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4582 TA TA TA
1 TA TA TA
4588 ATAAAGTACG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:4559 original size:14 final size:14
Alignment explanation
Indices: 4540--4587 Score: 87
Period size: 14 Copynumber: 3.4 Consensus size: 14
4530 GGTGCTCTTT
4540 TATATATACATATA
1 TATATATACATATA
4554 TATATATACATATA
1 TATATATACATATA
*
4568 TATATATATATATA
1 TATATATACATATA
4582 TATATA
1 TATATA
4588 ATAAAGTACG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (14 bp):
TATATATACATATA
Found at i:13893 original size:3 final size:3
Alignment explanation
Indices: 13885--13934 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
13875 AAATAACTAC
13885 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13933 AT
1 AT
13935 ATATATATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:14637 original size:16 final size:16
Alignment explanation
Indices: 14618--14666 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
14608 GAGATTTTTT
14618 TAATTATAATATAAAC
1 TAATTATAATATAAAC
*
14634 TAATT-TGAACA-AAA-
1 TAATTAT-AATATAAAC
*
14648 AAATTATAATATAAAC
1 TAATTATAATATAAAC
14664 TAA
1 TAA
14667 CAAAATCTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
14 7 0.28
15 8 0.32
16 10 0.40
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (16 bp):
TAATTATAATATAAAC
Found at i:17774 original size:49 final size:49
Alignment explanation
Indices: 17721--17814 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
17711 TTTTATCACC
*
17721 TTTGAAAGA-ATATTGTCCT-TGTGTTATATGTGTTTAGGGACTTTGTGTG
1 TTTGAAAGAGA-ATTG-CCTATCTGTTATATGTGTTTAGGGACTTTGTGTG
* * *
17770 TTTGAGAGAGAGTTGCCTATCTGTTATATGTGTTTTGGGACTTTG
1 TTTGAAAGAGAATTGCCTATCTGTTATATGTGTTTAGGGACTTTG
17815 GCTATTGGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
48 3 0.08
49 35 0.90
50 1 0.03
ACGTcount: A:0.19, C:0.07, G:0.28, T:0.46
Consensus pattern (49 bp):
TTTGAAAGAGAATTGCCTATCTGTTATATGTGTTTAGGGACTTTGTGTG
Found at i:20164 original size:55 final size:55
Alignment explanation
Indices: 20076--20184 Score: 173
Period size: 55 Copynumber: 2.0 Consensus size: 55
20066 TATTGAATGA
* * *
20076 CCACCAAACTACAACAGCCGCATAATCAGAATTGCAGCAAAATCAACCAAGAAAG
1 CCACCAAACTACAACAGCCACATAATCAAAATTGCAACAAAATCAACCAAGAAAG
* *
20131 CCACCAAACTACAACAGCCACATAATCAAAATTGCAACAAATTCAAGCAAGAAA
1 CCACCAAACTACAACAGCCACATAATCAAAATTGCAACAAAATCAACCAAGAAA
20185 ACAAATCACA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.50, C:0.28, G:0.10, T:0.12
Consensus pattern (55 bp):
CCACCAAACTACAACAGCCACATAATCAAAATTGCAACAAAATCAACCAAGAAAG
Found at i:32337 original size:92 final size:91
Alignment explanation
Indices: 32169--32385 Score: 217
Period size: 92 Copynumber: 2.4 Consensus size: 91
32159 ATTTAAAATA
* * ** * *
32169 TTTAAGTTAAAATTAACTTAAAAATTGATTCTTTGATCATTTTTGGGTTAAGCTTAGCTTAAAAA
1 TTTAGGTT-AAATTAACTTGAAAATTGATTCTTTGATCATTTTTAAGTAAAGCTTAACTTAAAAA
** * * *
32234 TGGATTCTTTAATTTAAAGTTTGGGATT
65 TCCATTCTTTAACTTAAAGTCT-AGATT
*
32262 TTTGGGTTAAAGTTAACTTGAAAATTGATTCCTTT-AT-ATTTTTAAGTCAAAG-TTAACTTAAA
1 TTTAGGTTAAA-TTAACTTGAAAATTGATT-CTTTGATCATTTTTAAGT-AAAGCTTAACTTAAA
*
32324 AATCCATTCTTTAACTTGAAGTCTAGATT
63 AATCCATTCTTTAACTTAAAGTCTAGATT
* *
32353 TTTAGGTTGAAATTAACCTG-AAATTGAGTCTTT
1 TTTAGGTT-AAATTAACTTGAAAATTGATTCTTT
32386 AATTTAAAAA
Statistics
Matches: 104, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
89 4 0.04
90 8 0.08
91 18 0.17
92 42 0.40
93 28 0.27
94 4 0.04
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (91 bp):
TTTAGGTTAAATTAACTTGAAAATTGATTCTTTGATCATTTTTAAGTAAAGCTTAACTTAAAAAT
CCATTCTTTAACTTAAAGTCTAGATT
Found at i:35737 original size:42 final size:44
Alignment explanation
Indices: 35686--35779 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
35676 AGTGCATTAC
*
35686 CTAA-ATTCTA-T-TCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
*
35727 TTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACT-CTCCATCTCTAGATAATTCATCAAAATAAAG
35772 CTAATATT
1 CTAATATT
35780 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 3 0.07
42 6 0.13
43 1 0.02
45 36 0.78
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.36
Consensus pattern (44 bp):
CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:36543 original size:7 final size:7
Alignment explanation
Indices: 36528--36578 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 7
36518 ATCACTAGAA
36528 ATAATAT
1 ATAATAT
*
36535 ATAAGAT
1 ATAATAT
36542 AT-ATAT
1 ATAATAT
36548 ATAATAT
1 ATAATAT
36555 AT-AT-T
1 ATAATAT
*
36560 ATATTAT
1 ATAATAT
36567 ATAATA-
1 ATAATAT
36573 ATAATA
1 ATAATA
36579 CAATGAAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
5 3 0.08
6 14 0.38
7 20 0.54
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (7 bp):
ATAATAT
Found at i:37750 original size:107 final size:104
Alignment explanation
Indices: 37522--37783 Score: 393
Period size: 107 Copynumber: 2.5 Consensus size: 104
37512 AATTTTTCTA
** *
37522 ACCCTTAAAATAAAATTTTAATTTTAATTT-AGGCTAAACTTAGTG-AATTAGTTATATATTTTA
1 ACCCTTAAAATAAAA-TAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
37585 CTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
65 CTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
* *
37625 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAAT-AAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
* *
37690 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
65 CTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTT
*
37732 ACCCTTAAAATGAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTA
1 ACCCTTAAAAT-AAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
37784 AGGCTAAACT
Statistics
Matches: 145, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
103 23 0.16
104 18 0.12
105 36 0.25
107 68 0.47
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (104 bp):
ACCCTTAAAATAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTAC
TTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
Found at i:39410 original size:16 final size:16
Alignment explanation
Indices: 39389--39420 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39379 ATATTTAAAT
*
39389 GACCCGAATCCGAAAA
1 GACCCGAACCCGAAAA
39405 GACCCGAACCCGAAAA
1 GACCCGAACCCGAAAA
39421 TCCGAGGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.34, G:0.19, T:0.03
Consensus pattern (16 bp):
GACCCGAACCCGAAAA
Found at i:40258 original size:177 final size:180
Alignment explanation
Indices: 39916--40270 Score: 522
Period size: 177 Copynumber: 2.0 Consensus size: 180
39906 GTACAAAAAT
* * *
39916 ATAATTATAAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAACTGTACA
1 ATAATTATAAAAATATTGAATTTAATAAAATGAAAATAAAGTTTTTAGAAGAATAAAACTGTACA
*
39981 TTAAATTTTTTTTTCAAATATCCAAGTTTTTAATGAAAAATAGTAAAAGGAAAGTAATATTATAA
66 TTAAA--TTTTTTTCAAATATCCAAGTTTTTAATGAAAAATAGTAAAAAGAAAGTAATATTATAA
* *
40046 AGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGTAGAATAAAATAAA
129 AGATATTAGATTTAATTAAATAAAAAAAGAGTTTTTAGTAGAATAAAATAAA
* *
40098 ATAATTATAAAAATATTGAATTTAAATAAAAT-AAAATAAAG-TTTTAGAAGAATAAACCTGTAT
1 ATAATTATAAAAATATTGAATTT-AATAAAATGAAAATAAAGTTTTTAGAAGAATAAAACTGTAC
* * * * *
40161 ATTAAA-TTTTTTGAATATATCCAAGTTTTTAGTGATAAATAGTAAAAATAAAGT-A-ATTATAT
65 ATTAAATTTTTTTCAA-ATATCCAAGTTTTTAATGAAAAATAGTAAAAAGAAAGTAATATTATAA
40223 AGATATTAGATTTAATTAAATAAAAAAAGAGTTTTTAGTAGAATAAAA
129 AGATATTAGATTTAATTAAATAAAAAAAGAGTTTTTAGTAGAATAAAA
40271 CTATATCAAT
Statistics
Matches: 158, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
177 52 0.33
178 9 0.06
179 34 0.22
181 25 0.16
182 31 0.20
183 7 0.04
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.37
Consensus pattern (180 bp):
ATAATTATAAAAATATTGAATTTAATAAAATGAAAATAAAGTTTTTAGAAGAATAAAACTGTACA
TTAAATTTTTTTCAAATATCCAAGTTTTTAATGAAAAATAGTAAAAAGAAAGTAATATTATAAAG
ATATTAGATTTAATTAAATAAAAAAAGAGTTTTTAGTAGAATAAAATAAA
Found at i:41010 original size:11 final size:11
Alignment explanation
Indices: 40967--41004 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
40957 TTCCTATATA
*
40967 AAATAAATTAT
1 AAATTAATTAT
40978 CAAA-TAATTAT
1 -AAATTAATTAT
40989 AAATTAATTAT
1 AAATTAATTAT
41000 AAATT
1 AAATT
41005 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:44334 original size:27 final size:28
Alignment explanation
Indices: 44270--44344 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 28
44260 AGGGTCATCT
44270 AGGGGCATTTTGGTCATTTCCAAAAATTC
1 AGGGGCATTTTGGTCATTT-CAAAAATTC
* **
44299 AGGGGCATTTTGGTCATTT-GAATGTTC
1 AGGGGCATTTTGGTCATTTCAAAAATTC
* *
44326 AGTGGCATTTAGGTCATTT
1 AGGGGCATTTTGGTCATTT
44345 TAGGTTCACT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
27 22 0.54
29 19 0.46
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.39
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTCAAAAATTC
Done.