Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021284.1 Corchorus olitorius cultivar O-4 contig21317, 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: 14805
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:219 original size:11 final size:11
Alignment explanation
Indices: 203--234 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
193 AACCGACCTA
203 GTCGGTTCCAT
1 GTCGGTTCCAT
214 GTCGGTTCCAT
1 GTCGGTTCCAT
225 GTCGGTTCCA
1 GTCGGTTCCA
235 AGCAAGCTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.28, G:0.28, T:0.34
Consensus pattern (11 bp):
GTCGGTTCCAT
Found at i:2402 original size:6 final size:6
Alignment explanation
Indices: 2387--2435 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
2377 AGCAGATTGT
* * *
2387 TGTTGC TGTTGT TGTTTC TGTTGC GGTTGC TGTTGC TGTTGC TGTTGC
1 TGTTGC TGTTGC TGTTGC TGTTGC TGTTGC TGTTGC TGTTGC TGTTGC
2435 T
1 T
2436 TGGAAGCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.00, C:0.14, G:0.33, T:0.53
Consensus pattern (6 bp):
TGTTGC
Found at i:2643 original size:3 final size:3
Alignment explanation
Indices: 2637--2661 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2627 CCACCACCAA
2637 CGC CGC CGC CGC CGC CGC CGC CGC C
1 CGC CGC CGC CGC CGC CGC CGC CGC C
2662 ACCACCACCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.32, T:0.00
Consensus pattern (3 bp):
CGC
Found at i:3175 original size:3 final size:3
Alignment explanation
Indices: 3167--3213 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
3157 CATATGATCA
* * *
3167 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG GTC TTG TTC TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
3214 TGCAGATTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.04, G:0.30, T:0.66
Consensus pattern (3 bp):
TTG
Found at i:3437 original size:15 final size:15
Alignment explanation
Indices: 3403--3440 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3393 TATTATTCCC
*
3403 ATGATGATGATCATG
1 ATGATGATGATCATA
3418 ATGATGATGATCA-A
1 ATGATGATGATCATA
3432 ATTGATGAT
1 A-TGATGAT
3441 CACCTCCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (15 bp):
ATGATGATGATCATA
Found at i:3636 original size:14 final size:15
Alignment explanation
Indices: 3619--3647 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3609 AAAATCAATC
3619 AAAAAAGAAA-AGAA
1 AAAAAAGAAATAGAA
3633 AAAAAAGAAATAGAA
1 AAAAAAGAAATAGAA
3648 TTTTGAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (15 bp):
AAAAAAGAAATAGAA
Found at i:5150 original size:10 final size:10
Alignment explanation
Indices: 5131--5181 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
5121 TAGATGAGGT
5131 AAGAAAGGAA
1 AAGAAAGGAA
*
5141 AAGGAAGGAA
1 AAGAAAGGAA
*
5151 ATGAAAGGAA
1 AAGAAAGGAA
5161 AAGAAAAGGAA
1 AAG-AAAGGAA
*
5172 ATGAAAGGAA
1 AAGAAAGGAA
5182 GGGAAGGCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
10 26 0.74
11 9 0.26
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (10 bp):
AAGAAAGGAA
Found at i:5171 original size:21 final size:20
Alignment explanation
Indices: 5133--5181 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 20
5123 GATGAGGTAA
*
5133 GAAAGGAAAAGGAAGGAAAT
1 GAAAGGAAAAGAAAGGAAAT
5153 GAAAGGAAAAGAAAAGGAAAT
1 GAAAGGAAAAG-AAAGGAAAT
5174 GAAAGGAA
1 GAAAGGAA
5182 GGGAAGGCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.04
Consensus pattern (20 bp):
GAAAGGAAAAGAAAGGAAAT
Found at i:8145 original size:25 final size:25
Alignment explanation
Indices: 8088--8164 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 25
8078 GGGTTGCTGT
*
8088 AGGAAGTGGCGCAGGGCCT-ATGAGA
1 AGGAAGTGGCGCAGGGCCTGAAGA-A
*
8113 A-GAGAGTGGTGCAGGGCCTGAAGAA
1 AGGA-AGTGGCGCAGGGCCTGAAGAA
*
8138 AGGAAGTGGCACAGGGCCTGAGAGAA
1 AGGAAGTGGCGCAGGGCCTGA-AGAA
8164 A
1 A
8165 ATAAGCACAG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
24 2 0.05
25 32 0.73
26 10 0.23
ACGTcount: A:0.32, C:0.14, G:0.43, T:0.10
Consensus pattern (25 bp):
AGGAAGTGGCGCAGGGCCTGAAGAA
Found at i:9256 original size:20 final size:20
Alignment explanation
Indices: 9231--9268 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
9221 TTATAAAATA
9231 ATTATTCAATAAATATTATT
1 ATTATTCAATAAATATTATT
9251 ATTATTCAATAAATATTA
1 ATTATTCAATAAATATTA
9269 CTAATTTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTATTCAATAAATATTATT
Found at i:13827 original size:20 final size:20
Alignment explanation
Indices: 13804--13842 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13794 ATTTCAAAGG
13804 GTTTTACTAAATACCGCCCT
1 GTTTTACTAAATACCGCCCT
**
13824 GTTTTACTAGCTACCGCCC
1 GTTTTACTAAATACCGCCC
13843 CCCCCAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (20 bp):
GTTTTACTAAATACCGCCCT
Found at i:13967 original size:22 final size:21
Alignment explanation
Indices: 13942--13990 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
13932 TCTCAACCTT
13942 AATCAATCAAAACAACATCAAA
1 AATCAA-CAAAACAACATCAAA
** *
13964 AATCAACCCAACAACATCTAA
1 AATCAACAAAACAACATCAAA
13985 AATCAA
1 AATCAA
13991 GGAGGAGCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (21 bp):
AATCAACAAAACAACATCAAA
Found at i:14544 original size:3 final size:3
Alignment explanation
Indices: 14436--14530 Score: 104
Period size: 3 Copynumber: 31.3 Consensus size: 3
14426 TATTTAGGTT
14436 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
14484 TT- TAA TTA TGTAA GTA ATG TTA TTA TTA TTA TTAA TTA -AA TTA TTA
1 TTA TTA TTA T-T-A TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
14530 T
1 T
14531 GAAAATAATT
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
2 2 0.03
3 70 0.90
4 5 0.06
5 1 0.01
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:14633 original size:20 final size:22
Alignment explanation
Indices: 14608--14656 Score: 75
Period size: 20 Copynumber: 2.3 Consensus size: 22
14598 AGAATTAGGA
14608 TTATTAAGTATTAA-TATG-TT
1 TTATTAAGTATTAATTATGATT
*
14628 TTATTAATTATTAATTATGATT
1 TTATTAAGTATTAATTATGATT
14650 TTATTAA
1 TTATTAA
14657 AATATGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 13 0.50
21 4 0.15
22 9 0.35
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (22 bp):
TTATTAAGTATTAATTATGATT
Done.