Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007274.1 Hibiscus syriacus cultivar Beakdansim tig00019287_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: 81102
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:23382 original size:24 final size:24
Alignment explanation
Indices: 23355--23409 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
23345 TATGTTATAG
**
23355 TTGATTTGAATCGTTTTGTTTCAC
1 TTGATTTGAATAATTTTGTTTCAC
*
23379 TTGATTTGAGTAATTTTGTTTCAC
1 TTGATTTGAATAATTTTGTTTCAC
*
23403 TTTATTT
1 TTGATTT
23410 TATGATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.18, C:0.09, G:0.15, T:0.58
Consensus pattern (24 bp):
TTGATTTGAATAATTTTGTTTCAC
Found at i:34471 original size:31 final size:31
Alignment explanation
Indices: 34436--34495 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
34426 GCGGATATCT
34436 TCACTAAAGTCTGACATTGATGTCACAAACC
1 TCACTAAAGTCTGACATTGATGTCACAAACC
34467 TCACTAAAGTCTGACATTGATGTCACAAA
1 TCACTAAAGTCTGACATTGATGTCACAAA
34496 ACTTTTAGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (31 bp):
TCACTAAAGTCTGACATTGATGTCACAAACC
Found at i:34801 original size:16 final size:16
Alignment explanation
Indices: 34760--34804 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
34750 GGGTCTCCAA
*
34760 CGTTTATGTACGTGTT
1 CGTTTATGTTCGTGTT
34776 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
34792 TGTTTATGTTCGT
1 CGTTTATGTTCGT
34805 TTATTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.09, C:0.11, G:0.24, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:39385 original size:17 final size:17
Alignment explanation
Indices: 39344--39388 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
39334 CACTATTTAA
39344 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** **
39361 TTTTATATTTTTTAAAT
1 TTAAATATTTAATAAAT
39378 TTAAATATTTA
1 TTAAATATTTA
39389 TTTTTACATA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:40826 original size:2 final size:2
Alignment explanation
Indices: 40819--40854 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40809 GAACTTGTCC
40819 AT AT AT AT 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 AT AT AT AT
40855 CAACTTTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48267 original size:174 final size:174
Alignment explanation
Indices: 47970--48311 Score: 612
Period size: 174 Copynumber: 2.0 Consensus size: 174
47960 CAAAACCCTT
*
47970 ACTAAGATTAGTACGAGCACAGGTCATGCGAAACAAGACTGGCCTATGATCCGAACCAAGACGAT
1 ACTAAGATTAGTACGAGAACAGGTCATGCGAAACAAGACTGGCCTATGATCCGAACCAAGACGAT
*
48035 CCAGGTGAAAAATAGAAGAATCGGGATAAGCACTCAACCAACAAGAATTGACAAGGCATCGATCT
66 CCAGGTGAAAAATAGAAGAATCGAGATAAGCACTCAACCAACAAGAATTGACAAGGCATCGATCT
48100 AGCCTTTGTTGCAAGTTACCTCGACACCAAGTAAAAGGCTTTTG
131 AGCCTTTGTTGCAAGTTACCTCGACACCAAGTAAAAGGCTTTTG
*
48144 ACTAAGATTAGTACGAGAACAGGTCATGCGAAACAAGACTGGCCTATGGTCCGAACCAAGACGAT
1 ACTAAGATTAGTACGAGAACAGGTCATGCGAAACAAGACTGGCCTATGATCCGAACCAAGACGAT
* ** * *
48209 CCAGGTGTATGATAGAAGAATCGAGATAAGTACTCAACCAACAAGAATTGATAAGGCATCGATCT
66 CCAGGTGAAAAATAGAAGAATCGAGATAAGCACTCAACCAACAAGAATTGACAAGGCATCGATCT
48274 AGCCTTTGTTGCAAGTTACCTCGACACCAAGTAAAAGG
131 AGCCTTTGTTGCAAGTTACCTCGACACCAAGTAAAAGG
48312 AGGGCCATGG
Statistics
Matches: 160, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
174 160 1.00
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (174 bp):
ACTAAGATTAGTACGAGAACAGGTCATGCGAAACAAGACTGGCCTATGATCCGAACCAAGACGAT
CCAGGTGAAAAATAGAAGAATCGAGATAAGCACTCAACCAACAAGAATTGACAAGGCATCGATCT
AGCCTTTGTTGCAAGTTACCTCGACACCAAGTAAAAGGCTTTTG
Found at i:50405 original size:23 final size:23
Alignment explanation
Indices: 50343--50403 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
50333 TTGTTACATG
* *
50343 TTTTACCTCTTCCTTTATGACAC
1 TTTTATCTCTTCCTTTGTGACAC
*
50366 GTTTATCTCTGT-CTTTGTGACA-
1 TTTTATCTCT-TCCTTTGTGACAC
50388 TTTTATCTCTTCCTTT
1 TTTTATCTCTTCCTTT
50404 TGGTAGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
21 1 0.03
22 13 0.41
23 17 0.53
24 1 0.03
ACGTcount: A:0.13, C:0.25, G:0.08, T:0.54
Consensus pattern (23 bp):
TTTTATCTCTTCCTTTGTGACAC
Found at i:55130 original size:18 final size:18
Alignment explanation
Indices: 55107--55147 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
55097 TTATGTCAAC
55107 TTCATTTACATGTTTTTG
1 TTCATTTACATGTTTTTG
*
55125 TTCA-TTATATGTTTTTG
1 TTCATTTACATGTTTTTG
55142 TTCATT
1 TTCATT
55148 ATATATTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.63
Consensus pattern (18 bp):
TTCATTTACATGTTTTTG
Found at i:55136 original size:17 final size:17
Alignment explanation
Indices: 55116--55151 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
55106 CTTCATTTAC
55116 ATGTTTTTGTTCATTAT
1 ATGTTTTTGTTCATTAT
55133 ATGTTTTTGTTCATTAT
1 ATGTTTTTGTTCATTAT
55150 AT
1 AT
55152 ATTGCTAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.06, G:0.11, T:0.64
Consensus pattern (17 bp):
ATGTTTTTGTTCATTAT
Found at i:71408 original size:55 final size:55
Alignment explanation
Indices: 70968--71445 Score: 508
Period size: 55 Copynumber: 8.8 Consensus size: 55
70958 TGATAAGTCT
* *
70968 GCTCCCTATTCCTTCAGGGAGTATA-AGACTCGAACAATCTTCAACAAACGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGTGTCC
* * * * *
71023 GCTCCCTATTCATTCAGGGAGTATA-AGACTCGAACAATCTTCAGCAAATGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGTGTCC
* * * *
71078 GCTCCCTATTCGTTCAGGGAGTATA-AGACTCGAACAATCTTCAATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAA-CAAACGTGTCC
* * ** *
71134 GCTCTCTATTCCTTCAGAGTGTATAGAACTCGAACAATCTTCAACAAATATGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
* * *
71189 GCTCCCTATTTCTTCAGAGAGTATAGGACTTG----ATCTTCAACAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
* * * *
71240 GCTCCCTATTTCTTCAGAGAGTATAGGACTCGAACAATCTTTATA-AAACGAGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACGTGTCC
* * *
71295 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGCCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
* * * * *
71350 GCTCTCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCAACAAATGGGTTC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
* * * * *
71405 GCTCCCTCTTTC-TCTAGGGAGTATGGAACTCAAAC-ATCTTC
1 GCTCCCTATTCCTTC-AGAGAGTATAGAACTCGAACAATCTTC
71446 TTCTTACGGG
Statistics
Matches: 370, Mismatches: 44, Indels: 19
0.85 0.10 0.04
Matches are distributed among these distances:
51 47 0.13
54 9 0.02
55 267 0.72
56 46 0.12
57 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
Found at i:71463 original size:54 final size:54
Alignment explanation
Indices: 71399--71557 Score: 282
Period size: 54 Copynumber: 2.9 Consensus size: 54
71389 TTCAACAAAT
* *
71399 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAAACATCTTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTAC
71453 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTAC
* *
71507 AGGTTCGCTCCCTCTTTCTCTAGGGAGTATGAAACTCGAACATTTTCTTCT
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCT
71558 GCTTTACTAC
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 101 1.00
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.36
Consensus pattern (54 bp):
GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTAC
Found at i:72055 original size:37 final size:36
Alignment explanation
Indices: 71961--72056 Score: 129
Period size: 36 Copynumber: 2.6 Consensus size: 36
71951 TAAAAAAATA
* * * *
71961 TGCTTCACTACTCTTCGATGAAGGCTTAAGATGGTT
1 TGCTTCACTACTCTTTGGTGAAGGCTCAAAATGGTT
* *
71997 TGCTTCACTACTCGTTAGTGAAGGCTCAAAATGGATT
1 TGCTTCACTACTCTTTGGTGAAGGCTCAAAATGG-TT
72034 TGCTTCACTACTCTTTGGTGAAG
1 TGCTTCACTACTCTTTGGTGAAG
72057 ACTTGGATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 28 0.55
37 23 0.45
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (36 bp):
TGCTTCACTACTCTTTGGTGAAGGCTCAAAATGGTT
Found at i:76801 original size:72 final size:72
Alignment explanation
Indices: 76684--76834 Score: 257
Period size: 72 Copynumber: 2.1 Consensus size: 72
76674 CCCCTAATAG
*
76684 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1 GTTCTTGATCAGTTGATATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
*
76749 TTCATCT
66 TTCATAT
* *
76756 GTTCTTGATCATTTGATATCATCACATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1 GTTCTTGATCAGTTGATATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
76821 TTCATAT
66 TTCATAT
*
76828 TTTCTTG
1 GTTCTTG
76835 TGTATAGGGT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.36
Consensus pattern (72 bp):
GTTCTTGATCAGTTGATATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
TTCATAT
Found at i:77601 original size:53 final size:55
Alignment explanation
Indices: 77500--77610 Score: 154
Period size: 53 Copynumber: 2.1 Consensus size: 55
77490 TTCTTTGTGG
**
77500 ATCGGTCTTCAATCAGTTTCAAATTTCTTCATTCATCGGATGTCCTTCTTCATGA
1 ATCGGTCTTCAATCAGTTTCAAATTTCTTCATTCATCAAATGTCCTTCTTCATGA
* * * *
77555 ATCGTTCTTCAGTCAG-TTC-AATTTCTTCATTCGTCAAATGTTCTTCTTCATGA
1 ATCGGTCTTCAATCAGTTTCAAATTTCTTCATTCATCAAATGTCCTTCTTCATGA
77608 ATC
1 ATC
77611 ATCTGAATGC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
53 33 0.66
54 3 0.06
55 14 0.28
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (55 bp):
ATCGGTCTTCAATCAGTTTCAAATTTCTTCATTCATCAAATGTCCTTCTTCATGA
Done.