Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003510.1 Hibiscus syriacus cultivar Beakdansim tig00007418_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: 63668
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5823 original size:23 final size:24
Alignment explanation
Indices: 5796--5845 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
5786 GATCATAAAT
* *
5796 AAATATTTTAA-ATTTAATTTTTA
1 AAATAGTTTAATATTGAATTTTTA
*
5819 AAATAGTTTAATATTGATTTTTTA
1 AAATAGTTTAATATTGAATTTTTA
5843 AAA
1 AAA
5846 AACATATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
AAATAGTTTAATATTGAATTTTTA
Found at i:6581 original size:27 final size:27
Alignment explanation
Indices: 6549--6606 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
6539 GACCCAAATC
*
6549 AAAACATAACATAAATCATGAAAATAT
1 AAAACATAACATAAAACATGAAAATAT
6576 AAAACATAACATAAAACATGAAAATAT
1 AAAACATAACATAAAACATGAAAATAT
6603 AAAA
1 AAAA
6607 TATACAAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.67, C:0.10, G:0.03, T:0.19
Consensus pattern (27 bp):
AAAACATAACATAAAACATGAAAATAT
Found at i:6606 original size:15 final size:15
Alignment explanation
Indices: 6559--6606 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
6549 AAAACATAAC
*
6559 ATAAATCATGAAAAT
1 ATAAAACATGAAAAT
*
6574 ATAAAACAT---AAC
1 ATAAAACATGAAAAT
6586 ATAAAACATGAAAAT
1 ATAAAACATGAAAAT
6601 ATAAAA
1 ATAAAA
6607 TATACAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
12 11 0.41
15 16 0.59
ACGTcount: A:0.67, C:0.08, G:0.04, T:0.21
Consensus pattern (15 bp):
ATAAAACATGAAAAT
Found at i:7017 original size:31 final size:31
Alignment explanation
Indices: 6982--7083 Score: 159
Period size: 31 Copynumber: 3.3 Consensus size: 31
6972 AAAACATAAA
6982 TTTTGGTCACTTATGTTATCATTTTATTAAG
1 TTTTGGTCACTTATGTTATCATTTTATTAAG
* * *
7013 TTTTGATCACTCATGTTATCGTTTTATTAAG
1 TTTTGGTCACTTATGTTATCATTTTATTAAG
* *
7044 TTTTGGTCACTTATATTATCTTTTTATTAAG
1 TTTTGGTCACTTATGTTATCATTTTATTAAG
7075 TTTTGGTCA
1 TTTTGGTCA
7084 TTTAGATGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 64 1.00
ACGTcount: A:0.22, C:0.11, G:0.13, T:0.55
Consensus pattern (31 bp):
TTTTGGTCACTTATGTTATCATTTTATTAAG
Found at i:7788 original size:22 final size:22
Alignment explanation
Indices: 7748--7790 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
7738 CTAAAGCGCC
*
7748 TTAGCACTGATATGGAAGTGTG
1 TTAGCACTGATATGAAAGTGTG
7770 TTAGCACTGATACT-AAAGTGT
1 TTAGCACTGATA-TGAAAGTGT
7791 CTTTACACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.33
Consensus pattern (22 bp):
TTAGCACTGATATGAAAGTGTG
Found at i:8097 original size:20 final size:21
Alignment explanation
Indices: 8057--8100 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
8047 CAATATGATG
* *
8057 GTATCGATATTGATCCCTTCA
1 GTATCAATATAGATCCCTTCA
8078 GTATCAATATAGAT-CCTTCA
1 GTATCAATATAGATCCCTTCA
8098 GTA
1 GTA
8101 CTGATACCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (21 bp):
GTATCAATATAGATCCCTTCA
Found at i:9007 original size:19 final size:19
Alignment explanation
Indices: 8967--9007 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
8957 TTCTGCACAC
* *
8967 AAAGTTTTGAAACTCTAGG
1 AAAGTTTTGAAACTATACG
*
8986 AAAGTTTTGAAACTATTCG
1 AAAGTTTTGAAACTATACG
9005 AAA
1 AAA
9008 AAGCCATTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (19 bp):
AAAGTTTTGAAACTATACG
Found at i:9085 original size:19 final size:19
Alignment explanation
Indices: 9038--9091 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
9028 ATTGGAGCCC
*
9038 AAGTATCAAAACTTTAGGGA
1 AAGTATCAAAACTTTA-GAA
*
9058 AAGTTTCAAAACTCTT-GAA
1 AAGTATCAAAACT-TTAGAA
9077 AAGTATCAAAACTTT
1 AAGTATCAAAACTTT
9092 TTGGGAAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 2 0.07
19 14 0.47
20 12 0.40
21 2 0.07
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (19 bp):
AAGTATCAAAACTTTAGAA
Found at i:13357 original size:19 final size:21
Alignment explanation
Indices: 13312--13357 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
13302 CTTATAAAAA
*
13312 AATCTTTTATTTCTGTTTATC
1 AATCTCTTATTTCTGTTTATC
*
13333 -AGCTCTTATTT-TGTTT-TC
1 AATCTCTTATTTCTGTTTATC
13351 AATCTCT
1 AATCTCT
13358 CGCAATAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
18 2 0.10
19 10 0.48
20 9 0.43
ACGTcount: A:0.17, C:0.17, G:0.07, T:0.59
Consensus pattern (21 bp):
AATCTCTTATTTCTGTTTATC
Found at i:16969 original size:50 final size:50
Alignment explanation
Indices: 16894--16992 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
16884 ACTTAGTGTT
*
16894 GCTACTTGGATTAAATTATTTGTTGTGTTTGATTGTATTTCTTATGTTTC
1 GCTACTTGGATTAAATTATTTGTTGTGGTTGATTGTATTTCTTATGTTTC
16944 GCTACTTGGATTAAATTATTTGTTGTGGTTGATTGTATTTCTTATGTTT
1 GCTACTTGGATTAAATTATTTGTTGTGGTTGATTGTATTTCTTATGTTT
16993 TCGAAACAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.18, C:0.07, G:0.19, T:0.56
Consensus pattern (50 bp):
GCTACTTGGATTAAATTATTTGTTGTGGTTGATTGTATTTCTTATGTTTC
Found at i:30100 original size:2 final size:2
Alignment explanation
Indices: 30088--30122 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
30078 TCCTTTGAAT
*
30088 GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
30123 TATTTGTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:33251 original size:38 final size:38
Alignment explanation
Indices: 33209--33323 Score: 167
Period size: 38 Copynumber: 3.0 Consensus size: 38
33199 AAAAGACGCC
*
33209 ATCAATAAAAAATTTATTATTACTTATTTATTTAAGTT
1 ATCAATAAAAAATTTATTAATACTTATTTATTTAAGTT
* * **
33247 ATCAATAAAAAATCTGTTAATACTTATTTATTTAACCT
1 ATCAATAAAAAATTTATTAATACTTATTTATTTAAGTT
* *
33285 ATCAATAAAAAAATTATTAATATTTATTTATTTAAGTT
1 ATCAATAAAAAATTTATTAATACTTATTTATTTAAGTT
33323 A
1 A
33324 ATAAACTAAC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 66 1.00
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (38 bp):
ATCAATAAAAAATTTATTAATACTTATTTATTTAAGTT
Found at i:40218 original size:22 final size:21
Alignment explanation
Indices: 40193--40234 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
40183 GTTTTTATAA
*
40193 AAGTTTTCTCTTTTTACTTTTC
1 AAGTTTTCTATTTTT-CTTTTC
*
40215 AAGTTTTTTATTTTTCTTTT
1 AAGTTTTCTATTTTTCTTTT
40235 ATTTTCAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (21 bp):
AAGTTTTCTATTTTTCTTTTC
Found at i:44279 original size:18 final size:18
Alignment explanation
Indices: 44256--44302 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
44246 CAATGGAATT
44256 ATTTTGTTCACACTTGAC
1 ATTTTGTTCACACTTGAC
* *
44274 ATTTTGGTCACATTTGAC
1 ATTTTGTTCACACTTGAC
44292 ATTTTGATTCA
1 ATTTTG-TTCA
44303 TGATACAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.47
Consensus pattern (18 bp):
ATTTTGTTCACACTTGAC
Found at i:51673 original size:2 final size:2
Alignment explanation
Indices: 51666--51693 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
51656 ATACTAACTC
51666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51694 TACACAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52717 original size:20 final size:19
Alignment explanation
Indices: 52686--52756 Score: 133
Period size: 19 Copynumber: 3.7 Consensus size: 19
52676 CTATTTCATA
52686 GCATGGACTCATGGAGCTG
1 GCATGGACTCATGGAGCTG
52705 GCATGGAACTCATGGAGCTG
1 GCATGG-ACTCATGGAGCTG
52725 GCATGGACTCATGGAGCTG
1 GCATGGACTCATGGAGCTG
52744 GCATGGACTCATG
1 GCATGGACTCATG
52757 TGTTTTATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
19 32 0.63
20 19 0.37
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.21
Consensus pattern (19 bp):
GCATGGACTCATGGAGCTG
Found at i:56510 original size:26 final size:25
Alignment explanation
Indices: 56478--56528 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
56468 CCAAAAATCC
56478 AAGTTCAAGGACCAATGTGGAGAAAA
1 AAGTTCAAGGACCAA-GTGGAGAAAA
*
56504 AAGTTCAAGGACCAAGTTGAGAAAA
1 AAGTTCAAGGACCAAGTGGAGAAAA
56529 GTTTCCAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.47, C:0.12, G:0.25, T:0.16
Consensus pattern (25 bp):
AAGTTCAAGGACCAAGTGGAGAAAA
Done.