Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017671.1 Corchorus olitorius cultivar O-4 contig17704, 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: 31329
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3043 original size:6 final size:6
Alignment explanation
Indices: 3032--3058 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3022 GAAGACCTTA
3032 TCCCCG TCCCCG TCCCCG TCCCCG TCC
1 TCCCCG TCCCCG TCCCCG TCCCCG TCC
3059 TCGGCTGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.67, G:0.15, T:0.19
Consensus pattern (6 bp):
TCCCCG
Found at i:3232 original size:22 final size:22
Alignment explanation
Indices: 3207--3269 Score: 65
Period size: 25 Copynumber: 2.7 Consensus size: 22
3197 CATAGATTAA
3207 TACAAGTTTACAACACCACAAT
1 TACAAGTTTACAACACCACAAT
**
3229 TACAAGTAACAATCAACACCACAAT
1 TACAAGT--TTA-CAACACCACAAT
3254 TACAAGCTTT-CAACAC
1 TACAAG-TTTACAACAC
3270 TGTGCAAGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
22 13 0.39
24 1 0.03
25 18 0.55
26 1 0.03
ACGTcount: A:0.46, C:0.29, G:0.05, T:0.21
Consensus pattern (22 bp):
TACAAGTTTACAACACCACAAT
Found at i:4919 original size:57 final size:57
Alignment explanation
Indices: 4801--4912 Score: 147
Period size: 57 Copynumber: 2.0 Consensus size: 57
4791 CCTTTCACAC
* * * *
4801 AATAAATGTTATAATAAATCATATCTCTCCTATCTCTACTTAATTATTCTTTCACAC
1 AATAAATGTTATAATAAATCATATCTCCCCTATCTCTACTTAATTATTCTTACAAAA
* * *
4858 AATAAATGTTATATTAAATCCTATC-CCCCTATTTCTACTTAATTATTC-TACAAAA
1 AATAAATGTTATAATAAATCATATCTCCCCTATCTCTACTTAATTATTCTTACAAAA
4913 TAAATAATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
55 4 0.08
56 21 0.44
57 23 0.48
ACGTcount: A:0.37, C:0.21, G:0.02, T:0.41
Consensus pattern (57 bp):
AATAAATGTTATAATAAATCATATCTCCCCTATCTCTACTTAATTATTCTTACAAAA
Found at i:6929 original size:124 final size:126
Alignment explanation
Indices: 6771--7022 Score: 436
Period size: 124 Copynumber: 2.0 Consensus size: 126
6761 ACCTACCCAT
* *
6771 GCCTAGTCTAGCTTTTGCCGTCTGAGAACAGAAATTTGATATTCTTAGTGTGAGGCAT-GAATGA
1 GCCTAGTCTAGCTTTTGCCATCTGAGAACAGAAATTAGATATTCTTAGTGTGAGGCATGGAATGA
* * *
6835 TATATATTTCCACTTTC-TCTTCTTCGTATATCTAATGCACGCATCTAGCTATGTTTTGGG
66 TATATATATCCACCTTCTTCTTCTTCGTATATCTAATGCACACATCTAGCTATGTTTTGGG
*
6895 GCCTAGTCTAGCTTTTGCCATCTGAGAACTGAAATTAGATATTCTTAGTGTGAGGCATGGAATGA
1 GCCTAGTCTAGCTTTTGCCATCTGAGAACAGAAATTAGATATTCTTAGTGTGAGGCATGGAATGA
6960 TATATATATCCACCTTCTTCTTCTTCGTATATCTAATGCACACATCTAGCTATGTTTTGGG
66 TATATATATCCACCTTCTTCTTCTTCGTATATCTAATGCACACATCTAGCTATGTTTTGGG
7021 GC
1 GC
7023 TTTGACTGCT
Statistics
Matches: 120, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
124 55 0.46
125 21 0.17
126 44 0.37
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (126 bp):
GCCTAGTCTAGCTTTTGCCATCTGAGAACAGAAATTAGATATTCTTAGTGTGAGGCATGGAATGA
TATATATATCCACCTTCTTCTTCTTCGTATATCTAATGCACACATCTAGCTATGTTTTGGG
Found at i:16237 original size:40 final size:39
Alignment explanation
Indices: 16182--16260 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 39
16172 GAGATCAACA
16182 ACTAAAATATGGTAATAACTCATAATTTTTTAAAAATCCT
1 ACTAAAATATGGTAATAACTCATAA-TTTTTAAAAATCCT
16222 ACTAAAATATGGTAATAACTCATAATTTTTAAAAATCCT
1 ACTAAAATATGGTAATAACTCATAATTTTTAAAAATCCT
16261 TTTTTTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
39 14 0.36
40 25 0.64
ACGTcount: A:0.46, C:0.13, G:0.05, T:0.37
Consensus pattern (39 bp):
ACTAAAATATGGTAATAACTCATAATTTTTAAAAATCCT
Found at i:18877 original size:10 final size:10
Alignment explanation
Indices: 18862--18896 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
18852 ATTTAATATA
18862 GATATTTACG
1 GATATTTACG
*
18872 GATATTTATG
1 GATATTTACG
18882 GATATTTACG
1 GATATTTACG
18892 GATAT
1 GATAT
18897 ATCGAGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (10 bp):
GATATTTACG
Found at i:18905 original size:20 final size:20
Alignment explanation
Indices: 18861--18906 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
18851 AATTTAATAT
18861 AGATATTTACGGATATTTATG
1 AGATATTTACGGATA-TTATG
18882 -GATATTTACGGATA-TATCG
1 AGATATTTACGGATATTAT-G
18901 AGATAT
1 AGATAT
18907 CGATAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 3 0.13
19 1 0.04
20 19 0.83
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.39
Consensus pattern (20 bp):
AGATATTTACGGATATTATG
Found at i:18925 original size:20 final size:19
Alignment explanation
Indices: 18890--18947 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
18880 TGGATATTTA
18890 CGGATATATCGA--GATAT
1 CGGATATATCGACGGATAT
*
18907 C-GATAAATATCGACGGATACA
1 CGGAT--ATATCGACGGATA-T
18928 CGGATATATCGACGGATAT
1 CGGATATATCGACGGATAT
18947 C
1 C
18948 CGATGACATT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
16 3 0.09
17 1 0.03
18 7 0.21
19 1 0.03
20 17 0.52
21 1 0.03
22 3 0.09
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.24
Consensus pattern (19 bp):
CGGATATATCGACGGATAT
Found at i:26424 original size:22 final size:22
Alignment explanation
Indices: 26399--26443 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
26389 ACCTTAATAG
26399 AAATCTAAGAACCATCCTGGAA
1 AAATCTAAGAACCATCCTGGAA
26421 AAATCTAAGAACCATCCTGGAA
1 AAATCTAAGAACCATCCTGGAA
26443 A
1 A
26444 CTCTGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.22, G:0.13, T:0.18
Consensus pattern (22 bp):
AAATCTAAGAACCATCCTGGAA
Found at i:29490 original size:6 final size:6
Alignment explanation
Indices: 29462--29513 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
29452 GCAAGGGGAG
* * * * *
29462 GAGGAA GAGGAA GAGATA GAGGTA GAGGTG GAGGTA GAGGTG GAGGTA
1 GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA
29510 GAGG
1 GAGG
29514 ATTTGGTATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.35, C:0.00, G:0.54, T:0.12
Consensus pattern (6 bp):
GAGGTA
Found at i:31252 original size:58 final size:58
Alignment explanation
Indices: 31152--31270 Score: 175
Period size: 58 Copynumber: 2.1 Consensus size: 58
31142 AAGGATCACA
*
31152 CTTCATAGGGGAAACAATATTTGATGAGCTTGTCAATTGTCAGTGGTTATTCATTAAC
1 CTTCATAGGGGAAACAATATTTGATGAGCTTGTCAATGGTCAGTGGTTATTCATTAAC
* * ** * *
31210 CTTCGTAGGGGAAACAATATTTGATGTGCTTGTCGCTGGTCAGTTGTTATTCATTCAC
1 CTTCATAGGGGAAACAATATTTGATGAGCTTGTCAATGGTCAGTGGTTATTCATTAAC
31268 CTT
1 CTT
31271 ATGGTAGATC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (58 bp):
CTTCATAGGGGAAACAATATTTGATGAGCTTGTCAATGGTCAGTGGTTATTCATTAAC
Done.