Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021041.1 Corchorus olitorius cultivar O-4 contig21074, 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: 35154
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:5936 original size:33 final size:33
Alignment explanation
Indices: 5835--5972 Score: 127
Period size: 33 Copynumber: 4.2 Consensus size: 33
5825 TTTCAAAGAG
* * * *
5835 TGTTTTAGATGTTGTTAGTGATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
** * *
5868 TAATTTAAGTGTTGTTTGTGATGACACTAAATC
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
5901 TGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTC
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAA-TC
* ** **
5934 TGTTTT-GGATGCTAATTGTGATGAAAAAAAATC
1 TGTTTTAGG-TGTTGTTTGTGATGAAACTAAATC
5967 TGTTTT
1 TGTTTT
5973 GGTTGATAAT
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
32 5 0.06
33 79 0.91
34 3 0.03
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.43
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
Found at i:7812 original size:21 final size:21
Alignment explanation
Indices: 7788--7867 Score: 151
Period size: 21 Copynumber: 3.8 Consensus size: 21
7778 ATTCGAGCAA
7788 GTTCCAAGCTCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
7809 GTTCCAAGCTCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
7830 GTTCCAAGCTCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
*
7851 GTTTCAAGCTCATTGGA
1 GTTCCAAGCTCATTGGA
7868 ATTAGCTAAG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (21 bp):
GTTCCAAGCTCATTGGAGAAG
Found at i:9665 original size:39 final size:39
Alignment explanation
Indices: 9614--9973 Score: 463
Period size: 39 Copynumber: 9.3 Consensus size: 39
9604 CCTCAGACAG
* * * *
9614 ACAGGTCATCGTTTCAATGGTTATCAAAGTTGACTGCAG
1 ACAGGTCATCTTTTCAATAGTTATCAAAGTTGACTGGAA
* *
9653 ACAGGTCATCGTTTCAATGGTTATCAAAGTTGACTGGAA
1 ACAGGTCATCTTTTCAATAGTTATCAAAGTTGACTGGAA
* *
9692 ACAGGTCATCGTTTCAATGGTTATCAAAGTTGACTGGAA
1 ACAGGTCATCTTTTCAATAGTTATCAAAGTTGACTGGAA
* ** *
9731 ACAGGTTATCTTTTCAGCAGTTATCAAAGTTGACTAGAA
1 ACAGGTCATCTTTTCAATAGTTATCAAAGTTGACTGGAA
** *
9770 ACAGGTCATCTTTTCAGCAGTAATCAAAGTTGACTGGAA
1 ACAGGTCATCTTTTCAATAGTTATCAAAGTTGACTGGAA
* *
9809 ACAGGTCATCTTTTCAGTAATTATCAAAGTTGACTGGAA
1 ACAGGTCATCTTTTCAATAGTTATCAAAGTTGACTGGAA
*
9848 ACAGGTCATCTTTCCAATAGTTATCAAAGTTGACTGGAA
1 ACAGGTCATCTTTTCAATAGTTATCAAAGTTGACTGGAA
* **
9887 ACAGGTTATCTTTTCAGCAGTTATCAAAGTTGACTAGG-A
1 ACAGGTCATCTTTTCAATAGTTATCAAAGTTGACT-GGAA
* * * * *
9926 ACAGGTCATC-TATCAGTAGTTACCAAGGTTGGCTGGAA
1 ACAGGTCATCTTTTCAATAGTTATCAAAGTTGACTGGAA
9964 ACAGGTCATC
1 ACAGGTCATC
9974 CTTCCTCAGT
Statistics
Matches: 292, Mismatches: 27, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
37 2 0.01
38 30 0.10
39 258 0.88
40 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (39 bp):
ACAGGTCATCTTTTCAATAGTTATCAAAGTTGACTGGAA
Found at i:10013 original size:21 final size:22
Alignment explanation
Indices: 9987--10029 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
9977 CCTCAGTTTT
*
9987 ATTTTC-GACCTCAGATAGGTC
1 ATTTTCAGACCTCAGACAGGTC
10008 ATTTTCAGACCTCAGACAGGTC
1 ATTTTCAGACCTCAGACAGGTC
10030 TTTCTTAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (22 bp):
ATTTTCAGACCTCAGACAGGTC
Found at i:10293 original size:17 final size:17
Alignment explanation
Indices: 10271--10308 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
10261 TGTTGTCTTC
* *
10271 CCTTTTAGAGCCCATTT
1 CCTTTTAAAGCCCATCT
10288 CCTTTTAAAGCCCATCT
1 CCTTTTAAAGCCCATCT
10305 CCTT
1 CCTT
10309 CCTATTATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.34, G:0.08, T:0.39
Consensus pattern (17 bp):
CCTTTTAAAGCCCATCT
Found at i:17795 original size:21 final size:21
Alignment explanation
Indices: 17749--17796 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
17739 TCCCGACCCA
* *
17749 AAAGTGATTAGTCTCCAGTCC
1 AAAGGGATTAGTCTCCAGCCC
*
17770 GAAGGGATTAGTCT-CAGGCCC
1 AAAGGGATTAGTCTCCA-GCCC
17791 AAAGGG
1 AAAGGG
17797 TTTGGCGATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (21 bp):
AAAGGGATTAGTCTCCAGCCC
Found at i:18602 original size:82 final size:84
Alignment explanation
Indices: 18462--18654 Score: 228
Period size: 82 Copynumber: 2.3 Consensus size: 84
18452 GCCTATGTCA
* * * * * * * *
18462 CATTAGAATTAGTTTAAGCTACCTAAATCTATATATAATATGTGTGATATGAAATTTAAACCTTA
1 CATTAAAATTAGCTTAAGATACCTAAATCCATACATAAAATGTGTGACATGAAATTTAAACCATA
*
18527 GGTGAAAAAAAATGAATAC
66 AGTGAAAAAAAATGAATAC
* *
18546 CATTAAAATTAGCTTAA-ATACCTAAATCCATACATAAAATG-GTGACATGAAATTTAAGCGATA
1 CATTAAAATTAGCTTAAGATACCTAAATCCATACATAAAATGTGTGACATGAAATTTAAACCATA
* * *
18609 AGTGAGAGAGAATGAATAC
66 AGTGAAAAAAAATGAATAC
* *
18628 CATTAAAATTAGCTTAAGGTATCTAAA
1 CATTAAAATTAGCTTAAGATACCTAAA
18655 CCTGTATTAT
Statistics
Matches: 92, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
82 50 0.54
83 27 0.29
84 15 0.16
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (84 bp):
CATTAAAATTAGCTTAAGATACCTAAATCCATACATAAAATGTGTGACATGAAATTTAAACCATA
AGTGAAAAAAAATGAATAC
Found at i:19815 original size:45 final size:45
Alignment explanation
Indices: 19764--19860 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 45
19754 AGCAACAATT
** *
19764 AATATTAGCTTTATTTTAATGAATTATGTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTAATGAATTACCTAGAGATGGAGGACTAG
* * *
19809 AATATTAGCTTTATTTTGATGAATTACCTATAGATGGAGTACTAG
1 AATATTAGCTTTATTTTAATGAATTACCTAGAGATGGAGGACTAG
19854 AAT-TTAG
1 AATATTAG
19861 GTAATGCACT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 4 0.09
45 42 0.91
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (45 bp):
AATATTAGCTTTATTTTAATGAATTACCTAGAGATGGAGGACTAG
Found at i:20987 original size:16 final size:17
Alignment explanation
Indices: 20958--20989 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
20948 GTTAGCAAAA
20958 AAATTAATATAAGAAAC
1 AAATTAATATAAGAAAC
20975 AAATTAA-ATAAGAAA
1 AAATTAATATAAGAAA
20990 AACAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.22
Consensus pattern (17 bp):
AAATTAATATAAGAAAC
Found at i:20992 original size:18 final size:18
Alignment explanation
Indices: 20954--20995 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
20944 TCTAGTTAGC
20954 AAAA-AAATTAATATAAG
1 AAAACAAATTAATATAAG
20971 -AAACAAATTAA-ATAAG
1 AAAACAAATTAATATAAG
20987 AAAAACAAA
1 -AAAACAAA
20996 AAATAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.36
17 7 0.32
18 7 0.32
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.17
Consensus pattern (18 bp):
AAAACAAATTAATATAAG
Found at i:28604 original size:21 final size:21
Alignment explanation
Indices: 28580--28627 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
28570 GCCACTGGGT
28580 GCCCAGGC-AAAATGCCTCAGC
1 GCCCAGGCGAAAA-GCCTCAGC
* *
28601 GCCCAGGCGACAAGGCTCAGC
1 GCCCAGGCGAAAAGCCTCAGC
28622 GCCCAG
1 GCCCAG
28628 CTCGATCCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.25, C:0.40, G:0.29, T:0.06
Consensus pattern (21 bp):
GCCCAGGCGAAAAGCCTCAGC
Found at i:34399 original size:5 final size:5
Alignment explanation
Indices: 34386--34415 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
34376 ACTTTCCTCC
*
34386 CCTTC CCTTT CCTTT CCTTT CCTTT CCTTT
1 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT
34416 AAAAACTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (5 bp):
CCTTT
Done.