Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005159.1 Corchorus capsularis cultivar CVL-1 contig05177, 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: 2577
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:946 original size:2 final size:2
Alignment explanation
Indices: 939--1017 Score: 54
Period size: 2 Copynumber: 44.5 Consensus size: 2
929 GTTCGTTTAT
*
939 TA TA TA TA T- TA TA TA T- TA TA TA -A TA T- TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
977 T- TA -A CA -A T- TA -A TA -A TA TA TA TCA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
1013 TA TA T
1 TA TA T
1018 TATTACTACC
Statistics
Matches: 63, Mismatches: 2, Indels: 24
0.71 0.02 0.27
Matches are distributed among these distances:
1 11 0.17
2 50 0.79
3 2 0.03
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:953 original size:7 final size:7
Alignment explanation
Indices: 941--1020 Score: 51
Period size: 7 Copynumber: 11.4 Consensus size: 7
931 TCGTTTATTA
941 TATATAT
1 TATATAT
948 TATATAT
1 TATATAT
*
955 TATATAA
1 TATATAT
*
962 TATTATTT
1 TA-TATAT
970 ATATATAT
1 -TATATAT
*
978 TA-ACAAT
1 TATA-TAT
*
985 TA-ATAA
1 TATATAT
991 TATATAT
1 TATATAT
*
998 CAT-TA-
1 TATATAT
1003 TATATAT
1 TATATAT
1010 ATATATAT
1 -TATATAT
1018 TAT
1 TAT
1021 TACTACCAGA
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
5 2 0.04
6 8 0.14
7 30 0.54
8 14 0.25
9 2 0.04
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (7 bp):
TATATAT
Found at i:957 original size:16 final size:16
Alignment explanation
Indices: 936--1020 Score: 74
Period size: 16 Copynumber: 5.4 Consensus size: 16
926 AACGTTCGTT
936 TATTATATATATTATA
1 TATTATATATATTATA
952 TATTATATA-A-TAT-
1 TATTATATATATTATA
965 TATTTATATATATTA-A
1 TA-TTATATATATTATA
*
981 CAATTA-ATA-ATATATA
1 -TATTATATATAT-TATA
997 TCATTATATATATATATA
1 T-ATTATATATAT-TATA
1015 TATTAT
1 TATTAT
1021 TACTACCAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 19
0.73 0.03 0.24
Matches are distributed among these distances:
13 2 0.04
14 12 0.21
15 7 0.12
16 19 0.33
17 9 0.16
18 8 0.14
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTATATATATTATA
Found at i:972 original size:30 final size:32
Alignment explanation
Indices: 936--1020 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 32
926 AACGTTCGTT
936 TATTATATATATTATATATTATATAATAT-TA
1 TATTATATATATTATATATTATATAATATATA
*
967 T-TTATATATATTA-ACAATTA-ATAATATATA
1 TATTATATATATTATA-TATTATATAATATATA
997 TCATTATATATATATATATATTAT
1 T-ATTATATATAT-TATATATTAT
1021 TACTACCAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
29 8 0.18
30 19 0.42
31 1 0.02
32 10 0.22
33 6 0.13
34 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (32 bp):
TATTATATATATTATATATTATATAATATATA
Found at i:1013 original size:20 final size:19
Alignment explanation
Indices: 939--1022 Score: 72
Period size: 18 Copynumber: 4.6 Consensus size: 19
929 GTTCGTTTAT
939 TATATATATTATATAT-TA
1 TATATATATTATATATATA
*
957 TATA-ATATTATTTATATA
1 TATATATATTATATATATA
*
975 TAT-TAACAATTA-ATA-ATA
1 TATAT-A-TATTATATATATA
*
993 TATAT-CATTATATATATA
1 TATATATATTATATATATA
1011 TATATATTATTA
1 TATATA-TATTA
1023 CTACCAGAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
16 4 0.08
17 13 0.25
18 23 0.44
19 4 0.08
20 8 0.15
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TATATATATTATATATATA
Found at i:1077 original size:14 final size:14
Alignment explanation
Indices: 1058--1084 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1048 CGGGAAAATT
1058 TTCTGTTACAAAAA
1 TTCTGTTACAAAAA
1072 TTCTGTTACAAAA
1 TTCTGTTACAAAA
1085 CTTGGTAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (14 bp):
TTCTGTTACAAAAA
Found at i:1510 original size:42 final size:43
Alignment explanation
Indices: 1463--1545 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
1453 GTTGTAACAA
1463 TTATTT-AGAGGGAAAAATTTTGGAAAAT-AAAAATAGGCGGGT
1 TTATTTGAG-GGGAAAAATTTTGGAAAATGAAAAATAGGCGGGT
* **
1505 TTATTTGAGGGGGAAAATTTTGTTAAATGAAAAATAGGCGG
1 TTATTTGAGGGGAAAAATTTTGGAAAATGAAAAATAGGCGG
1546 CATTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 22 0.61
43 14 0.39
ACGTcount: A:0.40, C:0.02, G:0.28, T:0.30
Consensus pattern (43 bp):
TTATTTGAGGGGAAAAATTTTGGAAAATGAAAAATAGGCGGGT
Done.