Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022996.1 Corchorus olitorius cultivar O-4 contig23029, 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: 30701
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:434 original size:51 final size:50
Alignment explanation
Indices: 333--434 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 50
323 GTTCTTCATA
* **
333 TTTTTCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
1 TTTTTCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
*
383 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTT-TCTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT
434 T
1 T
435 CTTCATTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
50 6 0.13
51 38 0.84
52 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42
Consensus pattern (50 bp):
TTTTTCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
Found at i:2616 original size:33 final size:33
Alignment explanation
Indices: 2574--2648 Score: 150
Period size: 33 Copynumber: 2.3 Consensus size: 33
2564 ATGGTCCGCC
2574 AATCAAGTCTAACTACTAGCTAGTAAACCACCA
1 AATCAAGTCTAACTACTAGCTAGTAAACCACCA
2607 AATCAAGTCTAACTACTAGCTAGTAAACCACCA
1 AATCAAGTCTAACTACTAGCTAGTAAACCACCA
2640 AATCAAGTC
1 AATCAAGTC
2649 ATACGTACTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.43, C:0.27, G:0.09, T:0.21
Consensus pattern (33 bp):
AATCAAGTCTAACTACTAGCTAGTAAACCACCA
Found at i:2767 original size:12 final size:13
Alignment explanation
Indices: 2739--2794 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
2729 TAATGCACCC
2739 AAAATCATTTAAT
1 AAAATCATTTAAT
*
2752 AAAATCATTTATAA
1 AAAATCATTTA-AT
**
2766 AAAAAAATTTAAT
1 AAAATCATTTAAT
*
2779 AAAA-CA-GTAAT
1 AAAATCATTTAAT
2790 AAAAT
1 AAAAT
2795 AGTTCCTCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
11 8 0.23
12 1 0.03
13 16 0.46
14 10 0.29
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.30
Consensus pattern (13 bp):
AAAATCATTTAAT
Found at i:7909 original size:30 final size:31
Alignment explanation
Indices: 7857--7917 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
7847 TTTTTGATCG
7857 ATTTTCTTCTTTTAATTTTAGAATTGAAGAT
1 ATTTTCTTCTTTTAATTTTAGAATTGAAGAT
7888 ATTTTCTTCTTTTAA-TTTAGAATTGAAGAT
1 ATTTTCTTCTTTTAATTTTAGAATTGAAGAT
7918 CTTATATGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.54
Consensus pattern (31 bp):
ATTTTCTTCTTTTAATTTTAGAATTGAAGAT
Found at i:8222 original size:9 final size:9
Alignment explanation
Indices: 8182--8263 Score: 60
Period size: 9 Copynumber: 8.8 Consensus size: 9
8172 CATACCACTA
8182 ATAATAATT
1 ATAATAATT
* *
8191 ATTATTATT
1 ATAATAATT
8200 ATAATAAGTT
1 ATAATAA-TT
8210 -TAATAATT
1 ATAATAATT
*
8218 ATAATACCACTA
1 ATAATA--A-TT
8230 ATAATAAGTT
1 ATAATAA-TT
8240 -TAATAATT
1 ATAATAATT
* *
8248 ATTATAATA
1 ATAATAATT
8257 ATAATAA
1 ATAATAA
8264 GTCTAAATTA
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
8 4 0.07
9 41 0.72
10 4 0.07
11 1 0.02
12 7 0.12
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (9 bp):
ATAATAATT
Found at i:8258 original size:27 final size:27
Alignment explanation
Indices: 8183--8265 Score: 112
Period size: 30 Copynumber: 3.0 Consensus size: 27
8173 ATACCACTAA
* *
8183 TAATAATTATTATTATTATAATAAGTT
1 TAATAATTATTATAATAATAATAAGTT
*
8210 TAATAATTATAATACCACTAATAATAAGTT
1 TAATAATTATTATA--A-TAATAATAAGTT
8240 TAATAATTATTATAATAATAATAAGT
1 TAATAATTATTATAATAATAATAAGT
8266 CTAAATTAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 23 0.47
28 1 0.02
29 1 0.02
30 24 0.49
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (27 bp):
TAATAATTATTATAATAATAATAAGTT
Found at i:12939 original size:27 final size:27
Alignment explanation
Indices: 12893--12957 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
12883 TTCACCCCAA
*
12893 AAAATTTATATTTTAGAACAATCAATAAC
1 AAAATTTAT-TTTGAGAACAA-CAATAAC
* *
12922 AAAATTTATTTTGA-AACAACCATAAT
1 AAAATTTATTTTGAGAACAACAATAAC
*
12948 AAAATGTATT
1 AAAATTTATT
12958 CATGGTGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 14 0.44
27 5 0.16
28 4 0.12
29 9 0.28
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (27 bp):
AAAATTTATTTTGAGAACAACAATAAC
Found at i:13433 original size:27 final size:30
Alignment explanation
Indices: 13395--13454 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
13385 AATTGTCTTC
*
13395 TTTTTTTTTTT-G-C-AGAAATCAAAATTG
1 TTTTTTTTTTTGGCCAAAAAATCAAAATTG
13422 TTTTTTTTTTTGGCCAAAAAATCAAAATTG
1 TTTTTTTTTTTGGCCAAAAAATCAAAATTG
13452 TTT
1 TTT
13455 ATGTACCCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 11 0.38
28 1 0.03
29 1 0.03
30 16 0.55
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52
Consensus pattern (30 bp):
TTTTTTTTTTTGGCCAAAAAATCAAAATTG
Found at i:21261 original size:8 final size:8
Alignment explanation
Indices: 21248--21278 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
21238 CTTCTTGAAC
*
21248 TTTCTCTG
1 TTTCTCTA
21256 TTTCTCTA
1 TTTCTCTA
21264 TTTCTCTA
1 TTTCTCTA
21272 TTTCTCT
1 TTTCTCT
21279 TCAGTCTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.06, C:0.26, G:0.03, T:0.65
Consensus pattern (8 bp):
TTTCTCTA
Found at i:25292 original size:3 final size:3
Alignment explanation
Indices: 25277--25306 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
25267 ATGCCTAAAG
*
25277 TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25307 ATTCGTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:26242 original size:21 final size:21
Alignment explanation
Indices: 26218--26259 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
26208 GAAATAATAC
26218 GATACAAAGAGTATCCAATTG
1 GATACAAAGAGTATCCAATTG
26239 GATACAAAGAGTATCCAATTG
1 GATACAAAGAGTATCCAATTG
26260 CATCAAGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (21 bp):
GATACAAAGAGTATCCAATTG
Done.