Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021682.1 Corchorus olitorius cultivar O-4 contig21715, 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: 22797
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:766 original size:19 final size:19
Alignment explanation
Indices: 744--781 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
734 GTTTTGCATT
744 CTGTTGATAATTTTCCATC
1 CTGTTGATAATTTTCCATC
*
763 CTGTTGGTAATTTTCCATC
1 CTGTTGATAATTTTCCATC
782 TACTAAACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.47
Consensus pattern (19 bp):
CTGTTGATAATTTTCCATC
Found at i:3413 original size:16 final size:16
Alignment explanation
Indices: 3392--3433 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
3382 AAAGTCAAGT
3392 CCCGAACCCGTAATTA
1 CCCGAACCCGTAATTA
3408 CCCGAACCCGTAATTA
1 CCCGAACCCGTAATTA
3424 CCCGAACCCG
1 CCCGAACCCG
3434 ACCCGAGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.29, C:0.43, G:0.14, T:0.14
Consensus pattern (16 bp):
CCCGAACCCGTAATTA
Found at i:4254 original size:13 final size:12
Alignment explanation
Indices: 4218--4264 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
4208 TCAATCTTTA
*
4218 TATATATTGATAA
1 TATATATT-ATAT
*
4231 TA-ATGTTATAT
1 TATATATTATAT
4242 TATATTATTATAT
1 TATA-TATTATAT
4255 TATATATTAT
1 TATATATTAT
4265 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:4410 original size:23 final size:23
Alignment explanation
Indices: 4384--4427 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
4374 ATCGAATCGA
*
4384 AATCAAACCCGAGCCCGAACCCG
1 AATCAAACCCGAGACCGAACCCG
**
4407 AATCCTACCCGAGACCGAACC
1 AATCAAACCCGAGACCGAACC
4428 TGAAAATACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.34, C:0.43, G:0.16, T:0.07
Consensus pattern (23 bp):
AATCAAACCCGAGACCGAACCCG
Found at i:4467 original size:32 final size:32
Alignment explanation
Indices: 4429--4509 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
4419 GACCGAACCT
*
4429 GAAAATACCCGAACCCGACATAAGCC-AAGTCC
1 GAAAATACCCGAACCCGACATAA-CCTAAGCCC
* * *
4461 GAAAATACCCGAATCCGACTTAACCTGAGCCC
1 GAAAATACCCGAACCCGACATAACCTAAGCCC
*
4493 GAAAATACCGGAACCCG
1 GAAAATACCCGAACCCG
4510 CCCAATTGCC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 2 0.05
32 40 0.95
ACGTcount: A:0.38, C:0.33, G:0.17, T:0.11
Consensus pattern (32 bp):
GAAAATACCCGAACCCGACATAACCTAAGCCC
Found at i:4568 original size:29 final size:29
Alignment explanation
Indices: 4526--4581 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
4516 TGCCAGCTCT
4526 ACCGGAGATCTAAGGCTTAAATATTGAGA
1 ACCGGAGATCTAAGGCTTAAATATTGAGA
4555 ACCGGAGATCTAAGGCTTAAATATTGA
1 ACCGGAGATCTAAGGCTTAAATATTGA
4582 TTCTCAAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (29 bp):
ACCGGAGATCTAAGGCTTAAATATTGAGA
Found at i:9539 original size:19 final size:18
Alignment explanation
Indices: 9515--9554 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
9505 TTGAAGATCT
*
9515 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
9534 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
9552 ATT
1 ATT
9555 ATTTCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:9564 original size:30 final size:30
Alignment explanation
Indices: 9504--9564 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
9494 GAAGTTCGTG
* *
9504 ATTGAAGATCTATTGAAGATAATTTGAAGA
1 ATTGAAGATCCATTGAAGATAATTTCAAGA
*
9534 ATTGAAGA-CCATTGAAGAATTATTTCAAGA
1 ATTGAAGATCCATTGAAG-ATAATTTCAAGA
9564 A
1 A
9565 GCAAGAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.31
Consensus pattern (30 bp):
ATTGAAGATCCATTGAAGATAATTTCAAGA
Found at i:11828 original size:6 final size:6
Alignment explanation
Indices: 11817--11846 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
11807 ACACGTCAGA
*
11817 AATGGC AATGGC AATGGA AATGGC AATGGC
1 AATGGC AATGGC AATGGC AATGGC AATGGC
11847 GTCAGGAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.33, T:0.17
Consensus pattern (6 bp):
AATGGC
Found at i:15387 original size:29 final size:29
Alignment explanation
Indices: 15346--15401 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
15336 GTGTTCATGA
*
15346 TTTGGGTTACTAACCCT-TTTATTTTTAT
1 TTTGGGTTACTAACACTCTTTATTTTTAT
15374 TTTGAGGTTACTAACACTCTTTATTTTT
1 TTTG-GGTTACTAACACTCTTTATTTTT
15402 TCAGAGGGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 4 0.16
29 12 0.48
30 9 0.36
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.55
Consensus pattern (29 bp):
TTTGGGTTACTAACACTCTTTATTTTTAT
Found at i:18145 original size:6 final size:7
Alignment explanation
Indices: 18096--18126 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
18086 TCAAGTTAGG
18096 AATTAAA
1 AATTAAA
18103 AATTAAA
1 AATTAAA
18110 AATTAAA
1 AATTAAA
*
18117 AATTGAA
1 AATTAAA
18124 AAT
1 AAT
18127 AAGTAGGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (7 bp):
AATTAAA
Found at i:18791 original size:25 final size:25
Alignment explanation
Indices: 18757--18832 Score: 152
Period size: 25 Copynumber: 3.0 Consensus size: 25
18747 GGCTTCCAAT
18757 AAAATAAGACAGGAAGAAGAAATTC
1 AAAATAAGACAGGAAGAAGAAATTC
18782 AAAATAAGACAGGAAGAAGAAATTC
1 AAAATAAGACAGGAAGAAGAAATTC
18807 AAAATAAGACAGGAAGAAGAAATTC
1 AAAATAAGACAGGAAGAAGAAATTC
18832 A
1 A
18833 TTCAAAAATC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.61, C:0.08, G:0.20, T:0.12
Consensus pattern (25 bp):
AAAATAAGACAGGAAGAAGAAATTC
Found at i:19872 original size:47 final size:47
Alignment explanation
Indices: 19820--19911 Score: 157
Period size: 47 Copynumber: 2.0 Consensus size: 47
19810 AATCTTTTAA
*
19820 CCAAACCACATCCTCTCAAAAGAAGAATGAAACAGATTTGAAGGAAT
1 CCAAACCACATCCTCTCAAAAGAAGAATGAAACAAATTTGAAGGAAT
* *
19867 CCAAACCCCATCCTCTTAAAAGAAGAATGAAACAAATTTGAAGGA
1 CCAAACCACATCCTCTCAAAAGAAGAATGAAACAAATTTGAAGGA
19912 GCGAGAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.47, C:0.22, G:0.14, T:0.17
Consensus pattern (47 bp):
CCAAACCACATCCTCTCAAAAGAAGAATGAAACAAATTTGAAGGAAT
Found at i:19995 original size:24 final size:24
Alignment explanation
Indices: 19963--20012 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
19953 TTTGAATACT
*
19963 GAAGAAACAAATTTGAAGAGGAGA
1 GAAGAAACAAATGTGAAGAGGAGA
* *
19987 GAAGAAACATATGTGAAGGGGAGA
1 GAAGAAACAAATGTGAAGAGGAGA
20011 GA
1 GA
20013 CGTCAGAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.04, G:0.34, T:0.12
Consensus pattern (24 bp):
GAAGAAACAAATGTGAAGAGGAGA
Found at i:20653 original size:5 final size:5
Alignment explanation
Indices: 20643--20693 Score: 66
Period size: 5 Copynumber: 9.8 Consensus size: 5
20633 ATATAAACCC
* *
20643 ATATT ATATT ATATT ATGTT ATGTT ATATT ATATT ATATAT ATATAT ATAT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATAT-T ATAT-T ATAT
20694 CCTATATATT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
5 32 0.74
6 11 0.26
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:20690 original size:20 final size:19
Alignment explanation
Indices: 20643--20705 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 19
20633 ATATAAACCC
*
20643 ATATTATATTATATTATGTT
1 ATATTATATTATATTAT-AT
*
20663 ATGTTATATTATATTATAT
1 ATATTATATTATATTATAT
**
20682 ATA-TATA-TATATCCTAT
1 ATATTATATTATATTATAT
20699 ATATTAT
1 ATATTAT
20706 TTTTGTAACC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 11 0.30
18 7 0.19
19 3 0.08
20 16 0.43
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
ATATTATATTATATTATAT
Found at i:22044 original size:17 final size:18
Alignment explanation
Indices: 22012--22046 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
22002 TATATTTATA
*
22012 TAATTCATTAATATAATT
1 TAATTCATTAAAATAATT
22030 TAATTC-TTAAAATAATT
1 TAATTCATTAAAATAATT
22047 ATTAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTCATTAAAATAATT
Found at i:22520 original size:13 final size:12
Alignment explanation
Indices: 22499--22533 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
22489 AATAAAGTAA
22499 TAATACTATTAT
1 TAATACTATTAT
22511 TAATTACTATTAT
1 TAA-TACTATTAT
22524 TAATACTATT
1 TAATACTATT
22534 TCAATGTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (12 bp):
TAATACTATTAT
Done.