Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018194.1 Corchorus olitorius cultivar O-4 contig18227, 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: 15689
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Found at i:208 original size:10 final size:10
Alignment explanation
Indices: 195--222 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
185 TCCCATCCCG
195 TCCCGTCCTA
1 TCCCGTCCTA
205 TCCCGTCCTA
1 TCCCGTCCTA
215 TCCCGTCC
1 TCCCGTCC
223 CTTACTGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.07, C:0.54, G:0.11, T:0.29
Consensus pattern (10 bp):
TCCCGTCCTA
Found at i:464 original size:32 final size:32
Alignment explanation
Indices: 423--486 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
413 TTTGGAGGTT
*
423 TTTCTTTTTTCTTTTTCCTTTAAATTATCAAA
1 TTTCTTTTTTCTTTTTCCTTCAAATTATCAAA
455 TTTCTTTTTTCTTTTTCCTTCAAATTATCAAA
1 TTTCTTTTTTCTTTTTCCTTCAAATTATCAAA
487 GGAACAAGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.61
Consensus pattern (32 bp):
TTTCTTTTTTCTTTTTCCTTCAAATTATCAAA
Found at i:3670 original size:52 final size:52
Alignment explanation
Indices: 3604--3704 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
3594 AGAGTTGCAA
* *
3604 CGTTGTTATGATAAAATAATGATACTAACGGGCATCCATTTTGACTCTGACC
1 CGTTATTATAATAAAATAATGATACTAACGGGCATCCATTTTGACTCTGACC
3656 CGTTATTATAATAAAATAATGATACTAACGGGCATCCATTTTGACTCTG
1 CGTTATTATAATAAAATAATGATACTAACGGGCATCCATTTTGACTCTG
3705 GCACGTGTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Consensus pattern (52 bp):
CGTTATTATAATAAAATAATGATACTAACGGGCATCCATTTTGACTCTGACC
Found at i:3859 original size:73 final size:73
Alignment explanation
Indices: 3772--3917 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
3762 GCGATTGAAA
3772 AGGAGATTATGATTAAGGTTCCGTTTGACCGATGTACCAGTGCACTGACCCAAACAGTGATGAAC
1 AGGAGATTATGATTAAGGTTCCGTTTGACCGATGTACCAGTGCACTGACCCAAACAGTGATGAAC
3837 CAGTTTCG
66 CAGTTTCG
*
3845 AGGAGATTATGATTAAGGTTCCGTTTGACCGATGTACCAGTGTACTGACCCAAACAGTGATGAAC
1 AGGAGATTATGATTAAGGTTCCGTTTGACCGATGTACCAGTGCACTGACCCAAACAGTGATGAAC
3910 CAGTTTCG
66 CAGTTTCG
3918 TTTGACTGGT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (73 bp):
AGGAGATTATGATTAAGGTTCCGTTTGACCGATGTACCAGTGCACTGACCCAAACAGTGATGAAC
CAGTTTCG
Found at i:4043 original size:33 final size:33
Alignment explanation
Indices: 4006--4073 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
3996 AAATATATAG
4006 AAAAACAAAATAACATGCATTTTAAATAAAGTA
1 AAAAACAAAATAACATGCATTTTAAATAAAGTA
*
4039 AAAAACAAAATAACATGCATTTTAAGTAAAGTA
1 AAAAACAAAATAACATGCATTTTAAATAAAGTA
4072 AA
1 AA
4074 CTAAACCTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.60, C:0.09, G:0.07, T:0.24
Consensus pattern (33 bp):
AAAAACAAAATAACATGCATTTTAAATAAAGTA
Found at i:5555 original size:16 final size:16
Alignment explanation
Indices: 5534--5567 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5524 AACCGATTAC
*
5534 TAATATATATTATATA
1 TAATATATATTAAATA
*
5550 TAATATATCTTAAATA
1 TAATATATATTAAATA
5566 TA
1 TA
5568 TTTAATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATATATATTAAATA
Found at i:11891 original size:21 final size:21
Alignment explanation
Indices: 11865--11906 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
11855 TAAGGAAGAA
11865 GTTTCAACCTCATCGGAGTTG
1 GTTTCAACCTCATCGGAGTTG
*
11886 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAACCTCATCGGAGTTG
11907 CCTAAGATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.33
Consensus pattern (21 bp):
GTTTCAACCTCATCGGAGTTG
Found at i:14387 original size:33 final size:33
Alignment explanation
Indices: 14350--14560 Score: 178
Period size: 33 Copynumber: 6.4 Consensus size: 33
14340 AAGAGTAATT
* ** *
14350 CTAAATCTGTTTTAGATTTTGTAAGTGATGATA
1 CTAAATCTGTTTTAGATGTTGTTTGTGATGACA
* ** *
14383 CTAAACCTAATTT-GAGTATTGTTTGTGATGACA
1 CTAAATCTGTTTTAGA-TGTTGTTTGTGATGACA
* *
14416 CTAAATCTGTTTTAGATGTTGTTTGCGATGATA
1 CTAAATCTGTTTTAGATGTTGTTTGTGATGACA
* **
14449 CTAAACCTAATTT-GAGTGTTGTTTGTGATGACA
1 CTAAATCTGTTTTAGA-TGTTGTTTGTGATGACA
* *
14482 CTAAATCTGTTTTAGGTGTTGTTTGTGATGAAA
1 CTAAATCTGTTTTAGATGTTGTTTGTGATGACA
* * ** *
14515 C-AAATTCTGTTTTGGATGCTAATTGTGATGAAAA
1 CTAAA-TCTGTTTTAGATGTTGTTTGTGATG-ACA
14549 C-AAATCTGTTTT
1 CTAAATCTGTTTT
14561 GGTTGATCAT
Statistics
Matches: 144, Mismatches: 28, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
32 7 0.05
33 127 0.88
34 10 0.07
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (33 bp):
CTAAATCTGTTTTAGATGTTGTTTGTGATGACA
Found at i:14456 original size:66 final size:66
Alignment explanation
Indices: 14350--14512 Score: 272
Period size: 66 Copynumber: 2.5 Consensus size: 66
14340 AAGAGTAATT
* **
14350 CTAAATCTGTTTTAGATTTTGTAAGTGATGATACTAAACCTAATTTGAGTATTGTTTGTGATGAC
1 CTAAATCTGTTTTAGATGTTGTTTGTGATGATACTAAACCTAATTTGAGTATTGTTTGTGATGAC
14415 A
66 A
* *
14416 CTAAATCTGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGTGATGAC
1 CTAAATCTGTTTTAGATGTTGTTTGTGATGATACTAAACCTAATTTGAGTATTGTTTGTGATGAC
14481 A
66 A
*
14482 CTAAATCTGTTTTAGGTGTTGTTTGTGATGA
1 CTAAATCTGTTTTAGATGTTGTTTGTGATGA
14513 AACAAATTCT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 90 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (66 bp):
CTAAATCTGTTTTAGATGTTGTTTGTGATGATACTAAACCTAATTTGAGTATTGTTTGTGATGAC
A
Found at i:14541 original size:66 final size:66
Alignment explanation
Indices: 14350--14560 Score: 203
Period size: 66 Copynumber: 3.2 Consensus size: 66
14340 AAGAGTAATT
* ** * * ** **
14350 CTAAATCTGTTTTAGATTTTGTAAGTGATGATACTAAACCTAATTTGAGTATTGTTTGTGATGAC
1 CTAAATCTGTTTTAGATGTTGTTTGCGATGAAACTAAACCTAATTTGAGTGCTAATTGTGATGAC
14415 A
66 A
* * **
14416 CTAAATCTGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGTGATGAC
1 CTAAATCTGTTTTAGATGTTGTTTGCGATGAAACTAAACCTAATTTGAGTGCTAATTGTGATGAC
14481 A
66 A
* * * **
14482 CTAAATCTGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTCTGTTTTG-GATGCTAATTGTGATG
1 CTAAATCTGTTTTAGATGTTGTTTGCGATGAAACTAAA-CCTAATTTGAG-TGCTAATTGTGATG
*
14545 AAAA
64 -ACA
14549 C-AAATCTGTTTT
1 CTAAATCTGTTTT
14561 GGTTGATCAT
Statistics
Matches: 127, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
65 4 0.03
66 120 0.94
67 3 0.02
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (66 bp):
CTAAATCTGTTTTAGATGTTGTTTGCGATGAAACTAAACCTAATTTGAGTGCTAATTGTGATGAC
A
Found at i:14943 original size:33 final size:31
Alignment explanation
Indices: 14870--15015 Score: 123
Period size: 33 Copynumber: 4.5 Consensus size: 31
14860 GCTATGATCA
** *
14870 ACCAAAACAGATTTGTTTTCATCACAATTAGC
1 ACCAAAACAGATTTG-TTTCATCACAAACAAC
14902 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC
*
14935 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC
** * *
14968 ACTCAAATTAGGTTTAGTATT-ATCGCAAACAAC
1 AC-CAAAACAGATTT-GT-TTCATCACAAACAAC
*
15001 ATCTAAAACAGATTT
1 A-CCAAAACAGATTT
15016 AGAATTACTC
Statistics
Matches: 94, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
32 7 0.07
33 79 0.84
34 8 0.09
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27
Consensus pattern (31 bp):
ACCAAAACAGATTTGTTTCATCACAAACAAC
Done.