Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005326.1 Corchorus capsularis cultivar CVL-1 contig05344, 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: 4797
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Found at i:298 original size:36 final size:36
Alignment explanation
Indices: 251--322 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
241 TATTTACTTC
251 TTAATCATGAGGGGGAAGACCCAGCTGTTGGAAAAA
1 TTAATCATGAGGGGGAAGACCCAGCTGTTGGAAAAA
287 TTAATCATGAGGGGGAAGACCCAGCTGTTGGAAAAA
1 TTAATCATGAGGGGGAAGACCCAGCTGTTGGAAAAA
323 CCTATAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.14, G:0.31, T:0.19
Consensus pattern (36 bp):
TTAATCATGAGGGGGAAGACCCAGCTGTTGGAAAAA
Found at i:2107 original size:45 final size:44
Alignment explanation
Indices: 2056--2190 Score: 189
Period size: 45 Copynumber: 3.0 Consensus size: 44
2046 GATTACTTTT
** *
2056 CCAGCTCATCATTAATCTGGGGTAGAAATCTTTTAATAATTCCAC
1 CCAGCTCATCATTAAT-TGGGGTAGGGATCTTTTAGTAATTCCAC
*
2101 CCAGCTCATCATTAATTCGGGGTAGGGATCTTTTAGTAATTTCAC
1 CCAGCTCATCATTAATT-GGGGTAGGGATCTTTTAGTAATTCCAC
* *
2146 CCAGCTCATCAATAATTTCGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAA-TTGGGGTAGGGATCTTTTAGTAATTCCAC
2191 TACTCTATTA
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
44 1 0.01
45 78 0.96
46 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.34
Consensus pattern (44 bp):
CCAGCTCATCATTAATTGGGGTAGGGATCTTTTAGTAATTCCAC
Found at i:2476 original size:17 final size:17
Alignment explanation
Indices: 2454--2503 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
2444 TTAAAATGGT
2454 AAAATAAAATATTTTTA
1 AAAATAAAATATTTTTA
2471 AAAATATAAA-ATTTAATTA
1 AAAATA-AAATATTT--TTA
*
2490 AATA-AAAATATTTT
1 AAAATAAAATATTTT
2504 AGTCAAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
16 1 0.04
17 13 0.46
18 8 0.29
19 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATAAAATATTTTTA
Found at i:4049 original size:17 final size:17
Alignment explanation
Indices: 4027--4059 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4017 CTGAGTATAA
*
4027 AATTTCATCTATATTAG
1 AATTTCATCCATATTAG
4044 AATTTCATCCATATTA
1 AATTTCATCCATATTA
4060 ATGTATAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.45
Consensus pattern (17 bp):
AATTTCATCCATATTAG
Found at i:4341 original size:109 final size:108
Alignment explanation
Indices: 4117--4332 Score: 364
Period size: 109 Copynumber: 2.0 Consensus size: 108
4107 ATTAATCGGA
* * *
4117 TATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAATTTTTAAGGCTGGGATATTCGGA
1 TATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATATTCGGA
*
4182 AAAAAGAAAACAAAAAAATTGATTTAAGGATATTGTTAATTAAT
66 AAAAAGAAAACAAAAAAATTGA-TTAAGAATATTGTTAATTAAT
*
4226 TATATTAATTCTTGAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATATTCGGA
1 TATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATATTCGGA
4291 AAAAA-AAAACAAAAAAATTGA-TAAGAATATTGTTAATTAAT
66 AAAAAGAAAACAAAAAAATTGATTAAGAATATTGTTAATTAAT
4332 T
1 T
4333 TTTATATTAT
Statistics
Matches: 102, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
106 20 0.20
108 16 0.16
109 66 0.65
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (108 bp):
TATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATATTCGGA
AAAAAGAAAACAAAAAAATTGATTAAGAATATTGTTAATTAAT
Done.