Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013208.1 Corchorus olitorius cultivar O-4 contig13241, 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: 16549
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:731 original size:69 final size:68
Alignment explanation
Indices: 610--799 Score: 255
Period size: 67 Copynumber: 2.8 Consensus size: 68
600 AATTAAATGA
* * *
610 CATTAATACTAATTGATTTTAATTTGATC-AATATTCAAATCAATCAATCAATCAATCAATTTAA
1 CATTAGTACTAATTGATTCTAATTGGATCAAATATTCAAATCAATCAATCAATCAATCAATTTAA
674 TAT
66 TAT
*
677 CATTAGTACTAATTGATTCTAAGTGGATCAAGATATTC--A--AATCAATCAATCAATCAATTTA
1 CATTAGTACTAATTGATTCTAATTGGATCAA-ATATTCAAATCAATCAATCAATCAATCAATTTA
738 ATAT
65 ATAT
742 CATTTTAGTACTAATTGATTCTAATTGGATCAAAATATATTCAAATCAATCAATCAAT
1 CA--TTAGTACTAATTGATTCTAATTGGATC--AA-ATATTCAAATCAATCAATCAAT
800 TTAATATATA
Statistics
Matches: 107, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
65 28 0.26
67 52 0.49
68 1 0.01
69 14 0.13
71 1 0.01
73 11 0.10
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (68 bp):
CATTAGTACTAATTGATTCTAATTGGATCAAATATTCAAATCAATCAATCAATCAATCAATTTAA
TAT
Found at i:741 original size:65 final size:67
Alignment explanation
Indices: 651--799 Score: 248
Period size: 65 Copynumber: 2.2 Consensus size: 67
641 TATTCAAATC
651 AATCAATCAATCAATCAATTTAATATCA-TTAGTACTAATTGATTCTAAGTGGATC-AAGATATT
1 AATCAATCAATCAATCAATTTAATATCATTTAGTACTAATTGATTCTAAGTGGATCAAAGATATT
714 CA
66 CA
* *
716 AATCAATCAATCAATCAATTTAATATCATTTTAGTACTAATTGATTCTAATTGGATCAAAATATA
1 AATCAATCAATCAATCAATTTAATATCA-TTTAGTACTAATTGATTCTAAGTGGATC-AAAGATA
781 TTCA
64 TTCA
785 AATCAATCAATCAAT
1 AATCAATCAATCAAT
800 TTAATATATA
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
65 28 0.36
67 26 0.33
69 24 0.31
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (67 bp):
AATCAATCAATCAATCAATTTAATATCATTTAGTACTAATTGATTCTAAGTGGATCAAAGATATT
CA
Found at i:897 original size:5 final size:5
Alignment explanation
Indices: 875--913 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
865 TCGGTAATTA
875 ATAT- ATAT- ATAT- ATATG ATATG ATATG ATATG ATATG AT
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG AT
914 GATAGACGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 12 0.35
5 22 0.65
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (5 bp):
ATATG
Found at i:2943 original size:26 final size:26
Alignment explanation
Indices: 2907--2959 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
2897 GGTTGTTCCA
2907 ATCCTACATCTATCTATTCTCATCTT
1 ATCCTACATCTATCTATTCTCATCTT
*
2933 ATCCTGCATCTATCTATTCTCATCTT
1 ATCCTACATCTATCTATTCTCATCTT
2959 A
1 A
2960 CGCCTTCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.30, G:0.02, T:0.45
Consensus pattern (26 bp):
ATCCTACATCTATCTATTCTCATCTT
Found at i:3403 original size:32 final size:32
Alignment explanation
Indices: 3367--3431 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
3357 AAAACTTTAA
*
3367 ATACAGACACTAGCTTTCATTGAGGTCATTTT
1 ATACAGACACTAACTTTCATTGAGGTCATTTT
*
3399 ATACAGACATTAACTTTCATTGAGGTCATTTT
1 ATACAGACACTAACTTTCATTGAGGTCATTTT
3431 A
1 A
3432 CATAGAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (32 bp):
ATACAGACACTAACTTTCATTGAGGTCATTTT
Found at i:6865 original size:2 final size:2
Alignment explanation
Indices: 6858--6890 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6848 ATGGTAATTA
6858 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6891 GGAAGACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11610 original size:31 final size:31
Alignment explanation
Indices: 11572--11633 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
11562 GAATTTTGTA
*
11572 AAACTTTTGAATCGTCTATTATACCCTTATT
1 AAACTTTTGAATCGCCTATTATACCCTTATT
11603 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCGCCTATTATACCCTTATT
11634 TTTTGAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATTATACCCTTATT
Found at i:11820 original size:93 final size:98
Alignment explanation
Indices: 11649--11830 Score: 248
Period size: 93 Copynumber: 1.9 Consensus size: 98
11639 AATATATTTA
* * *
11649 TAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATCAAATCTAATATCTAATATCCTTATAAC
1 TAGTTTTACTCAACTAAAAACACTAATTTTATTT-AT-AAATCTAATATCTAATATCCTTATAAC
* *
11714 TATTTTATTTTTACCATTTTACTATTTTACTTTTT
64 TATTTTACTTTTACCATATTACTATTTTACTTTTT
*
11749 TAGTTTTACTCAACTAAAAACACTAATTTTA-TT-T-AAT-TAA-ATCTAATATCCTTATACCTA
1 TAGTTTTACTCAACTAAAAACACTAATTTTATTTATAAATCTAATATCTAATATCCTTATAACTA
*
11809 TTTTACTTTTACGATATTACTA
66 TTTTACTTTTACCATATTACTA
11831 ATATAATTAA
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
93 38 0.51
94 3 0.04
95 3 0.04
97 1 0.01
99 2 0.03
100 28 0.37
ACGTcount: A:0.34, C:0.15, G:0.02, T:0.49
Consensus pattern (98 bp):
TAGTTTTACTCAACTAAAAACACTAATTTTATTTATAAATCTAATATCTAATATCCTTATAACTA
TTTTACTTTTACCATATTACTATTTTACTTTTT
Found at i:12443 original size:31 final size:31
Alignment explanation
Indices: 12405--12474 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
12395 AATTTTCTCG
12405 GGTCATTCGGATTTCGAATCATCTAGGTTCA
1 GGTCATTCGGATTTCGAATCATCTAGGTTCA
12436 GGTCATTCGGATTTCGAATCATCTAGGTTCA
1 GGTCATTCGGATTTCGAATCATCTAGGTTCA
12467 GGTCATTC
1 GGTCATTC
12475 AGCTCTCGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (31 bp):
GGTCATTCGGATTTCGAATCATCTAGGTTCA
Found at i:13638 original size:2 final size:2
Alignment explanation
Indices: 13633--13680 Score: 62
Period size: 2 Copynumber: 24.0 Consensus size: 2
13623 TTTTTAATAA
* *
13633 AT AT AT A- AT AT CAT GT AT AT AT AT TT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13675 AT AT AT
1 AT AT AT
13681 TTGTATCGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15257 original size:14 final size:14
Alignment explanation
Indices: 15238--15265 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15228 ACGTCTGTAT
15238 GTAAACTCTGACTG
1 GTAAACTCTGACTG
15252 GTAAACTCTGACTG
1 GTAAACTCTGACTG
15266 TCCGTGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (14 bp):
GTAAACTCTGACTG
Done.