Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004922.1 Hibiscus syriacus cultivar Beakdansim tig00011083_pilon, 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: 48668
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:3530 original size:36 final size:36
Alignment explanation
Indices: 3483--3588 Score: 144
Period size: 35 Copynumber: 3.0 Consensus size: 36
3473 CTACCTAAAC
3483 ATCACCATCTTCCATCACCATTTTCACGCCTATAAT-
1 ATCACCATCTTCCATCACCA-TTTCACGCCTATAATG
* *
3519 ATCACCATCTTCCATTACCATTGCACGCCTAT-ATG
1 ATCACCATCTTCCATCACCATTTCACGCCTATAATG
* * *
3554 ATTACCATCTTCTAGCACCATTTCACGCCTATAAT
1 ATCACCATCTTCCATCACCATTTCACGCCTATAAT
3589 TGCCAATCCC
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
34 2 0.03
35 38 0.62
36 21 0.34
ACGTcount: A:0.27, C:0.34, G:0.06, T:0.33
Consensus pattern (36 bp):
ATCACCATCTTCCATCACCATTTCACGCCTATAATG
Found at i:9048 original size:13 final size:13
Alignment explanation
Indices: 9030--9088 Score: 61
Period size: 13 Copynumber: 4.8 Consensus size: 13
9020 ATAGGCGTGC
9030 AATGGTGATGGAA
1 AATGGTGATGGAA
**
9043 AATGGTGATGTTA
1 AATGGTGATGGAA
*
9056 TA-GGTG-T-GAA
1 AATGGTGATGGAA
9066 AATGGTGATGGAA
1 AATGGTGATGGAA
*
9079 GATGGTGATG
1 AATGGTGATG
9089 AATAGATAGT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
10 2 0.06
11 5 0.14
12 5 0.14
13 24 0.67
ACGTcount: A:0.32, C:0.00, G:0.39, T:0.29
Consensus pattern (13 bp):
AATGGTGATGGAA
Found at i:9048 original size:35 final size:36
Alignment explanation
Indices: 8994--9093 Score: 141
Period size: 35 Copynumber: 2.8 Consensus size: 36
8984 TATATAAGTG
*
8994 AAATGGTGATAGAAGATGGTGATGATATAGGCGTG-
1 AAATGGTGATGGAAGATGGTGATGATATAGGCGTGA
* * * *
9029 CAATGGTGATGGAAAATGGTGATGTTATAGGTGTGA
1 AAATGGTGATGGAAGATGGTGATGATATAGGCGTGA
9065 AAATGGTGATGGAAGATGGTGATGA-ATAG
1 AAATGGTGATGGAAGATGGTGATGATATAG
9094 ATAGTATCTT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
35 34 0.61
36 22 0.39
ACGTcount: A:0.34, C:0.02, G:0.37, T:0.27
Consensus pattern (36 bp):
AAATGGTGATGGAAGATGGTGATGATATAGGCGTGA
Found at i:15186 original size:24 final size:22
Alignment explanation
Indices: 15159--15205 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
15149 AGAATTGTTG
15159 TTGAGTGCTTACAAATTTCTTCTT
1 TTGAGTG-TTAC-AATTTCTTCTT
* *
15183 TTGAGTGTTTCAATTTTTTCTT
1 TTGAGTGTTACAATTTCTTCTT
15205 T
1 T
15206 GCTGAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.52
23 3 0.14
24 7 0.33
ACGTcount: A:0.17, C:0.13, G:0.13, T:0.57
Consensus pattern (22 bp):
TTGAGTGTTACAATTTCTTCTT
Found at i:17988 original size:22 final size:22
Alignment explanation
Indices: 17962--18003 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17952 TATTTATAGT
*
17962 TATGATGATGATATTATGAATG
1 TATGAAGATGATATTATGAATG
* *
17984 TATGAAGTTGTTATTATGAA
1 TATGAAGATGATATTATGAA
18004 CCACATATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (22 bp):
TATGAAGATGATATTATGAATG
Found at i:31430 original size:15 final size:14
Alignment explanation
Indices: 31403--31433 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
31393 TATAACATGG
31403 ATATATTCATCTAT
1 ATATATTCATCTAT
31417 ATATATTACATCTAT
1 ATATATT-CATCTAT
31432 AT
1 AT
31434 CTATGATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATATTCATCTAT
Found at i:33219 original size:32 final size:31
Alignment explanation
Indices: 33183--33271 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 31
33173 CACCTATTCC
33183 TTCTTTTCTTTCATTCATTTTCTTAAAACCAT
1 TTCTTTTCTTTCATTCATTTTCTT-AAACCAT
* *
33215 TTCTTTTATTTTCATTCATTTCCTTAAACCAT
1 TTCTTTT-CTTTCATTCATTTTCTTAAACCAT
*
33247 TTATTTATCTTTCCATTC-TTTTCTT
1 TTCTTT-TCTTT-CATTCATTTTCTT
33272 CTTCCAGCTA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
32 28 0.57
33 21 0.43
ACGTcount: A:0.19, C:0.21, G:0.00, T:0.60
Consensus pattern (31 bp):
TTCTTTTCTTTCATTCATTTTCTTAAACCAT
Found at i:37386 original size:23 final size:23
Alignment explanation
Indices: 37359--37423 Score: 98
Period size: 22 Copynumber: 2.9 Consensus size: 23
37349 AACAAAGTGA
37359 AGCACTCAAAAGAAAGAAAAATC
1 AGCACTCAAAAGAAAGAAAAATC
37382 AGCACTCAAAAGAAAG-AAAATC
1 AGCACTCAAAAGAAAGAAAAATC
*
37404 AGCGCTCAAAA-AGAAGAAAA
1 AGCACTCAAAAGA-AAGAAAA
37424 GCAAAGAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
21 1 0.03
22 19 0.49
23 19 0.49
ACGTcount: A:0.60, C:0.17, G:0.15, T:0.08
Consensus pattern (23 bp):
AGCACTCAAAAGAAAGAAAAATC
Found at i:38755 original size:24 final size:21
Alignment explanation
Indices: 38721--38763 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
38711 TTTTGGTGAT
*
38721 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
38743 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
38764 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Done.