Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014444.1 Corchorus capsularis cultivar CVL-1 contig14465, 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: 17730
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:959 original size:2 final size:2
Alignment explanation
Indices: 952--1013 Score: 57
Period size: 2 Copynumber: 34.0 Consensus size: 2
942 CCGTTTAGTA
*
952 AT AT AT AT AT AT A- AT AT AT AT A- AT A- AT AT CAG 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
992 A- AT -T AT AT AT A- AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1014 TATTATTAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
1 7 0.14
2 42 0.84
3 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1015 original size:19 final size:20
Alignment explanation
Indices: 953--1016 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
943 CGTTTAGTAA
*
953 TATATATATATAATATATAT
1 TATATATAGATAATATATAT
*
973 AATAATATCAGAT-ATATATAAT
1 TAT-ATAT-AGATAATATAT-AT
995 TATATATA-ATAATATATAT
1 TATATATAGATAATATATAT
1014 TAT
1 TAT
1017 TATTAAATGG
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 7 0.19
20 9 0.24
21 14 0.38
22 7 0.19
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
TATATATAGATAATATATAT
Found at i:2952 original size:3 final size:3
Alignment explanation
Indices: 2946--2978 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2936 CAAAAACAAT
*
2946 AAG AAG AAG AAG AAG AAG AAG AAG AAG GAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
2979 TCTTCCTGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12838 original size:34 final size:34
Alignment explanation
Indices: 12800--12872 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
12790 AATACTTCAA
12800 TAATTTGACCCAATCATCCATCCCTTACCAATAT
1 TAATTTGACCCAATCATCCATCCCTTACCAATAT
*
12834 TAATTTGACCCAATCATCCATCCCTTACCGATAT
1 TAATTTGACCCAATCATCCATCCCTTACCAATAT
12868 TAATT
1 TAATT
12873 ACTCCCTCCG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (34 bp):
TAATTTGACCCAATCATCCATCCCTTACCAATAT
Found at i:17380 original size:21 final size:21
Alignment explanation
Indices: 17356--17398 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
17346 TAAATCTGGA
17356 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCGCCCCATTT
*
17377 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
17398 T
1 T
17399 GACGTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.19, C:0.35, G:0.09, T:0.37
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:17655 original size:33 final size:33
Alignment explanation
Indices: 17583--17669 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 33
17573 GATGACCCAT
** *
17583 GCCGCCCCAAAAGGGCGGCTT-ACCATGGTCAG
1 GCCGCCCCACTAGGGCGGCTTCACCATGATCAG
*
17615 GCCGCCCCACTAGGGCGGCTTCACTATGAAT-AG
1 GCCGCCCCACTAGGGCGGCTTCACCATG-ATCAG
*
17648 GCCGCCCCACTGGGGCGGCTTC
1 GCCGCCCCACTAGGGCGGCTTC
17670 GCCACGGCAG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
32 19 0.40
33 28 0.58
34 1 0.02
ACGTcount: A:0.17, C:0.37, G:0.31, T:0.15
Consensus pattern (33 bp):
GCCGCCCCACTAGGGCGGCTTCACCATGATCAG
Done.