Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011557.1 Corchorus capsularis cultivar CVL-1 contig11578, 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: 27568
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1207 original size:14 final size:14
Alignment explanation
Indices: 1177--1225 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
1167 TATTATAAAA
*
1177 ATATAT-ATTAAATT
1 ATATATAATTATA-T
*
1191 ATATTTAATTATAT
1 ATATATAATTATAT
1205 ATATATAATTATAT
1 ATATATAATTATAT
1219 ATATATA
1 ATATATA
1226 TAATTTAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 26 0.84
15 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATATAATTATAT
Found at i:1221 original size:12 final size:12
Alignment explanation
Indices: 1162--1223 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
1152 ATATACCCAA
1162 ATAATTAT-TAT
1 ATAATTATATAT
* *
1173 AAAAATATATAT
1 ATAATTATATAT
1185 -TAAATTATAT-T
1 AT-AATTATATAT
1196 -TAATTATATATAT
1 ATAA-T-TATATAT
1209 ATAATTATATAT
1 ATAATTATATAT
1221 ATA
1 ATA
1224 TATAATTTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
10 2 0.05
11 9 0.22
12 25 0.61
13 2 0.05
14 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATAATTATATAT
Found at i:2089 original size:17 final size:17
Alignment explanation
Indices: 2058--2091 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2048 ACCCAAAATT
*
2058 AAAAAAAAAGAAAAACG
1 AAAAAAAAACAAAAACG
*
2075 AAAAAAAAACCAAAACG
1 AAAAAAAAACAAAAACG
2092 TCCAAAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.12, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAAAAACAAAAACG
Found at i:3840 original size:29 final size:29
Alignment explanation
Indices: 3798--3888 Score: 112
Period size: 29 Copynumber: 3.2 Consensus size: 29
3788 TGGGCATACG
*
3798 ACGTGGCATGCCACGTGTATAAAAATGCC
1 ACGTGGCATGCCACGTGTACAAAAATGCC
* * *
3827 ACGTGGCATGCCACGTTTACAAAAAGGAC
1 ACGTGGCATGCCACGTGTACAAAAATGCC
* * *
3856 ACATGGCGTGCCACATGT-CAAAAATGCC
1 ACGTGGCATGCCACGTGTACAAAAATGCC
3884 ACGTG
1 ACGTG
3889 CTATGTGTCA
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
28 12 0.24
29 39 0.76
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.19
Consensus pattern (29 bp):
ACGTGGCATGCCACGTGTACAAAAATGCC
Found at i:4331 original size:16 final size:16
Alignment explanation
Indices: 4310--4341 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4300 GACATAAAAA
4310 AGGATTAGTTATAAAT
1 AGGATTAGTTATAAAT
*
4326 AGGATTAGTTGTAAAT
1 AGGATTAGTTATAAAT
4342 TATTAAATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (16 bp):
AGGATTAGTTATAAAT
Found at i:7286 original size:6 final size:6
Alignment explanation
Indices: 7277--7301 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
7267 GTGGTTCAGG
7277 TTCAAC TTCAAC TTCAAC TTCAAC T
1 TTCAAC TTCAAC TTCAAC TTCAAC T
7302 GCATCCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (6 bp):
TTCAAC
Found at i:20067 original size:6 final size:6
Alignment explanation
Indices: 20038--20077 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
20028 TAAAAACGTT
* *
20038 AAAGAA AAAAAA AGAAGAA CAAGAA AAAGAA AAAGAA AAA
1 AAAGAA AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAA
20078 AGAACGTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 25 0.86
7 4 0.14
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:25678 original size:17 final size:16
Alignment explanation
Indices: 25638--25688 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
25628 CATGTAATCT
*
25638 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
*
25654 TTGCATCACTGGTGATT
1 TTG-ATCACTGGTGATC
*
25671 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
25688 T
1 T
25689 GGGGGGTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Done.