Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023365.1 Corchorus olitorius cultivar O-4 contig23398, 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: 9525
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:62 original size:33 final size:32
Alignment explanation
Indices: 4--172 Score: 169
Period size: 33 Copynumber: 5.1 Consensus size: 32
1 GCA
* * *
4 ATGACACGAAATCTGTTTTGAGTGTTGTTAGTG
1 ATGACACTAAATCT-ATTTGAGTGTTGTTTGTG
* * *
37 ATGATACTAAACCTAATTTGAGTGTTGTTTGCG
1 ATGACACTAAATCT-ATTTGAGTGTTGTTTGTG
* *
70 ATGACACTAAATCTGTTCT-AGATGTTGTTAGTG
1 ATGACACTAAATCTATT-TGAG-TGTTGTTTGTG
* *
103 ATGATACTAAAACTAATTTGAGTGTTGTTTGTG
1 ATGACACTAAATCT-ATTTGAGTGTTGTTTGTG
* *
136 ATGACACTAAATCTGTTTTAGGTGTTGTTTGTG
1 ATGACACTAAATCTATTTGA-GTGTTGTTTGTG
169 ATGA
1 ATGA
173 AACAAATTCT
Statistics
Matches: 111, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
32 8 0.07
33 99 0.89
34 4 0.04
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (32 bp):
ATGACACTAAATCTATTTGAGTGTTGTTTGTG
Found at i:110 original size:66 final size:65
Alignment explanation
Indices: 4--172 Score: 257
Period size: 66 Copynumber: 2.6 Consensus size: 65
1 GCA
* * *
4 ATGACACGAAATCTGTTTTGAGTGTTGTTAGTGATGATACTAAACCTAATTTGAGTGTTGTTTGC
1 ATGACACTAAATCTGTTTAGA-TGTTGTTAGTGATGATACTAAAACTAATTTGAGTGTTGTTTGC
69 G
65 G
*
70 ATGACACTAAATCTGTTCTAGATGTTGTTAGTGATGATACTAAAACTAATTTGAGTGTTGTTTGT
1 ATGACACTAAATCTGTT-TAGATGTTGTTAGTGATGATACTAAAACTAATTTGAGTGTTGTTTGC
135 G
65 G
* *
136 ATGACACTAAATCTGTTTTAGGTGTTGTTTGTGATGA
1 ATGACACTAAATCTG-TTTAGATGTTGTTAGTGATGA
173 AACAAATTCT
Statistics
Matches: 95, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
66 90 0.95
67 5 0.05
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (65 bp):
ATGACACTAAATCTGTTTAGATGTTGTTAGTGATGATACTAAAACTAATTTGAGTGTTGTTTGCG
Found at i:184 original size:33 final size:32
Alignment explanation
Indices: 12--215 Score: 160
Period size: 33 Copynumber: 6.2 Consensus size: 32
2 CAATGACACG
* *
12 AAATCTGTTTTGAGTGTTGTTAGTGATGATACT
1 AAATCTGTTTTG-GTGTTGTTTGTGATGAAACT
* ** * *
45 AAACCTAATTTGAGTGTTGTTTGCGATGACACT
1 AAATCTGTTTTG-GTGTTGTTTGTGATGAAACT
* * * *
78 AAATCTGTTCTAGATGTTGTTAGTGATGATACT
1 AAATCTGTT-TTGGTGTTGTTTGTGATGAAACT
* ** *
111 AAAACTAATTTGAGTGTTGTTTGTGATGACACT
1 AAATCTGTTTTG-GTGTTGTTTGTGATGAAACT
144 AAATCTGTTTTAGGTGTTGTTTGTGATGAAAC-
1 AAATCTGTTTT-GGTGTTGTTTGTGATGAAACT
* **
176 AAATTCTGTTTTGGATGCTAATTGTGATGAAAAC-
1 AAA-TCTGTTTTGG-TGTTGTTTGTGATG-AAACT
210 AAATCT
1 AAATCT
216 CTTGAAAATA
Statistics
Matches: 137, Mismatches: 28, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
32 7 0.05
33 120 0.88
34 10 0.07
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (32 bp):
AAATCTGTTTTGGTGTTGTTTGTGATGAAACT
Found at i:201 original size:66 final size:66
Alignment explanation
Indices: 4--205 Score: 194
Period size: 66 Copynumber: 3.1 Consensus size: 66
1 GCA
* * * * * **
4 ATGACACGAAATCTGTT-TTGAGTGTTGTTAGTGATGATACTAAACCTAATTTGAGTGTTGTTTG
1 ATGACACTAAATCTGTTCTAGA-TGTTGTTAGTGATGAAACTAAAACTAATTTGAGTGCTAATTG
*
68 CG
65 TG
* * **
70 ATGACACTAAATCTGTTCTAGATGTTGTTAGTGATGATACTAAAACTAATTTGAGTGTTGTTTGT
1 ATGACACTAAATCTGTTCTAGATGTTGTTAGTGATGAAACTAAAACTAATTTGAGTGCTAATTGT
135 G
66 G
* * * * **
136 ATGACACTAAATCTGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTCTGTTTTG-GATGCTAATT
1 ATGACACTAAATCTGTTCTAGATGTTGTTAGTGATGAAACTAAA-ACTAATTTGAG-TGCTAATT
199 GTG
64 GTG
202 ATGA
1 ATGA
206 AAACAAATCT
Statistics
Matches: 119, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
65 4 0.03
66 112 0.94
67 3 0.03
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (66 bp):
ATGACACTAAATCTGTTCTAGATGTTGTTAGTGATGAAACTAAAACTAATTTGAGTGCTAATTGT
G
Found at i:203 original size:99 final size:99
Alignment explanation
Indices: 20--205 Score: 225
Period size: 99 Copynumber: 1.9 Consensus size: 99
10 CGAAATCTGT
* *
20 TTTGAGTGTTGTTAGTGATGATACTAAACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTG
1 TTTGAGTGTTGTTAGTGATGACACTAAACCTAATTTGAGTGTTGTTTGCGATGAAACTAAATCTG
**
85 TTCTAGATGTTGTTAGTGATGATACTAAAACTAA
66 TTCTAGATGTAATTAGTGATGATACTAAAACTAA
* * * * *
119 TTTGAGTGTTGTTTGTGATGACACTAAATCT-GTTTTAGGTGTTGTTTGTGATGAAAC-AAATTC
1 TTTGAGTGTTGTTAGTGATGACACTAAACCTAATTTGA-GTGTTGTTTGCGATGAAACTAAA-TC
* *
182 TGTTTTGGATGCTAATT-GTGATGA
64 TGTTCTAGATG-TAATTAGTGATGA
206 AAACAAATCT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
98 7 0.10
99 63 0.86
100 3 0.04
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42
Consensus pattern (99 bp):
TTTGAGTGTTGTTAGTGATGACACTAAACCTAATTTGAGTGTTGTTTGCGATGAAACTAAATCTG
TTCTAGATGTAATTAGTGATGATACTAAAACTAA
Found at i:2193 original size:21 final size:20
Alignment explanation
Indices: 2156--2197 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2146 TCTTGAAGAG
*
2156 TTTGAAGCCATCGGAGATCA
1 TTTGAAGCCATCAGAGATCA
*
2176 TTTGAAGCCCATTAGAGATCA
1 TTTGAAG-CCATCAGAGATCA
2197 T
1 T
2198 CAACAAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (20 bp):
TTTGAAGCCATCAGAGATCA
Found at i:5564 original size:36 final size:36
Alignment explanation
Indices: 5524--5611 Score: 158
Period size: 36 Copynumber: 2.4 Consensus size: 36
5514 TAGTATCCAC
*
5524 ATTAGTAACTAGGCATCATCATTCACATTAGTAATT
1 ATTAGTAATTAGGCATCATCATTCACATTAGTAATT
*
5560 ATTAGTAATTAGGCATCATCGTTCACATTAGTAATT
1 ATTAGTAATTAGGCATCATCATTCACATTAGTAATT
5596 ATTAGTAATTAGGCAT
1 ATTAGTAATTAGGCAT
5612 TGCATTCACA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (36 bp):
ATTAGTAATTAGGCATCATCATTCACATTAGTAATT
Found at i:7688 original size:41 final size:40
Alignment explanation
Indices: 7630--7809 Score: 189
Period size: 41 Copynumber: 4.4 Consensus size: 40
7620 TGTTTTCGTG
* * *
7630 TTCAATATGGTCCCTGATTAAGGATTTCAATTATTTAATTGA
1 TTCAAT-TTGTCCCTGATTTAGGATTTCAATTA-CTAATTGA
* *
7672 TTCAATTTGTCCCTGATTTAGGATTTCATTTATTAATTGA
1 TTCAATTTGTCCCTGATTTAGGATTTCAATTACTAATTGA
* * * *
7712 TGCAATTTGGTCCCTGATTTAGGATTTTAGTTACTATTTGA
1 TTCAATTT-GTCCCTGATTTAGGATTTCAATTACTAATTGA
* * * * *
7753 TGCGATTTAGTCCCTGATTTAGGATTTTACTTACTATTTGA
1 TTCAATTT-GTCCCTGATTTAGGATTTCAATTACTAATTGA
7794 TTCAATTTGTTCCCTG
1 TTCAATTTG-TCCCTG
7810 GTTTTAGAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
40 16 0.13
41 101 0.82
42 6 0.05
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.47
Consensus pattern (40 bp):
TTCAATTTGTCCCTGATTTAGGATTTCAATTACTAATTGA
Found at i:7736 original size:82 final size:82
Alignment explanation
Indices: 7632--7809 Score: 214
Period size: 82 Copynumber: 2.2 Consensus size: 82
7622 TTTTCGTGTT
* * *
7632 CAATATGGTCCCTGATTAAGGATTTCAATTATTTAATTGATTCAATTT-GTCCCTGATTTAGGAT
1 CAATTTGGTCCCTGATTAAGGATTTCAATTA-CTAATTGATGCAATTTAGTCCCTGATTTAGGAT
* *
7696 TTCATTTATTAATTGATG
65 TTCACTTACTAATTGATG
* * * * *
7714 CAATTTGGTCCCTGATTTAGGATTTTAGTTACTATTTGATGCGATTTAGTCCCTGATTTAGGATT
1 CAATTTGGTCCCTGATTAAGGATTTCAATTACTAATTGATGCAATTTAGTCCCTGATTTAGGATT
* * *
7779 TTACTTACTATTTGATT
66 TCACTTACTAATTGATG
*
7796 CAATTTGTTCCCTG
1 CAATTTGGTCCCTG
7810 GTTTTAGAAA
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
81 12 0.15
82 69 0.85
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (82 bp):
CAATTTGGTCCCTGATTAAGGATTTCAATTACTAATTGATGCAATTTAGTCCCTGATTTAGGATT
TCACTTACTAATTGATG
Found at i:9321 original size:21 final size:21
Alignment explanation
Indices: 9291--9330 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9281 CTAAAAACAG
* *
9291 GACAAGTCCTGCCCAGGACTT
1 GACAACTCCTACCCAGGACTT
9312 GACAACTCCTACCCAGGAC
1 GACAACTCCTACCCAGGAC
9331 CTGGTCTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.38, G:0.20, T:0.15
Consensus pattern (21 bp):
GACAACTCCTACCCAGGACTT
Done.