Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004351.1 Hibiscus syriacus cultivar Beakdansim tig00009533_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: 89537
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:31869 original size:23 final size:23
Alignment explanation
Indices: 31842--31885 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
31832 ATTGACGTTA
*
31842 TTGGTCAAAGTCAATAGTCAACC
1 TTGGTCAAACTCAATAGTCAACC
*
31865 TTGGTCAAACTCAATGGTCAA
1 TTGGTCAAACTCAATAGTCAA
31886 GTCAAAGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (23 bp):
TTGGTCAAACTCAATAGTCAACC
Found at i:39990 original size:20 final size:20
Alignment explanation
Indices: 39967--40004 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39957 CGCCATTCAT
*
39967 GAATGGTACATGCCATCTAA
1 GAATGGCACATGCCATCTAA
*
39987 GAATGGCCCATGCCATCT
1 GAATGGCACATGCCATCT
40005 TCTATATCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (20 bp):
GAATGGCACATGCCATCTAA
Found at i:45385 original size:56 final size:56
Alignment explanation
Indices: 45298--45544 Score: 325
Period size: 56 Copynumber: 4.4 Consensus size: 56
45288 GAAATGAATA
* * * * *
45298 CACTTAGTATGCATTTCCT-AGTTTTTGCACATATAGTGCCCATATAGAAATTCGTC
1 CACTTAGTATGAATTTCTTAAG-TTTTACACATATAGTGCCCATACAGAAATTCATC
* *
45354 CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAAAAATCCATC
1 CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAGAAATTCATC
** *
45410 CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGTGCATACGGAAATTCATC
1 CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAGAAATTCATC
* * * * * *
45466 CACTCAGTTTGAATTTCTTAAGGTTTACACATACAGCGCCCATACGGAAATTCATC
1 CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAGAAATTCATC
*
45522 CACTTAGTATGAATTTATTAAGT
1 CACTTAGTATGAATTTCTTAAGT
45545 CATTGCACAC
Statistics
Matches: 167, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
56 165 0.99
57 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.36
Consensus pattern (56 bp):
CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAGAAATTCATC
Found at i:45997 original size:20 final size:20
Alignment explanation
Indices: 45972--46020 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
45962 TGTTTTGAAT
45972 GGTATCGATAC-CTTCCCTTC
1 GGTATCGATACTC-TCCCTTC
* *
45992 GGTATCGATACTCTCTCTTT
1 GGTATCGATACTCTCCCTTC
46012 GGTATCGAT
1 GGTATCGAT
46021 GCTGATTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.16, C:0.27, G:0.18, T:0.39
Consensus pattern (20 bp):
GGTATCGATACTCTCCCTTC
Found at i:49690 original size:53 final size:53
Alignment explanation
Indices: 49610--49716 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
49600 TAGGATTATG
* *
49610 TTTTGTCTGATAATATCATAATCTAATGTACGCTCAAGTATTCGGGTCTATCT
1 TTTTGTCTGACAATATCATAATCTAATGTACGCTCAAGTATTCGGGTATATCT
49663 TTTTGTCTGACAATATCATAATCTAATGTACGCTCAAGTATTCGGGTATATCT
1 TTTTGTCTGACAATATCATAATCTAATGTACGCTCAAGTATTCGGGTATATCT
49716 T
1 T
49717 CTATACCAGG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (53 bp):
TTTTGTCTGACAATATCATAATCTAATGTACGCTCAAGTATTCGGGTATATCT
Found at i:52683 original size:90 final size:88
Alignment explanation
Indices: 52575--52748 Score: 276
Period size: 90 Copynumber: 2.0 Consensus size: 88
52565 TCCAGAATAT
* * *
52575 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCAAATATGACTAG
52640 GATAACTTAGATATAAAAGGATTA
65 GATAACTTAGATATAAAAGGATTA
52664 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCAAATATGACTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCAAATATGACTAG
* * *
52729 GGTAACTTGGCTATAAAAGG
65 GATAACTTAGATATAAAAGG
52749 GTGTGTTAGG
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 37 0.47
90 41 0.53
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCAAATATGACTAGG
ATAACTTAGATATAAAAGGATTA
Found at i:55947 original size:20 final size:20
Alignment explanation
Indices: 55918--55958 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
55908 AACCAGATTG
55918 CCCAGAGGGTACAGATACCC
1 CCCAGAGGGTACAGATACCC
*
55938 CCCAGGGGGTACAGATACCC
1 CCCAGAGGGTACAGATACCC
55958 C
1 C
55959 ATGAATGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.37, G:0.27, T:0.10
Consensus pattern (20 bp):
CCCAGAGGGTACAGATACCC
Found at i:56024 original size:23 final size:23
Alignment explanation
Indices: 55992--56036 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
55982 AAACAGAATG
55992 TCCAGAGGGTACAGATACCCCCC
1 TCCAGAGGGTACAGATACCCCCC
* * *
56015 TCCAGGGGGTACCGATTCCCCC
1 TCCAGAGGGTACAGATACCCCC
56037 TTTTGTAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.40, G:0.24, T:0.16
Consensus pattern (23 bp):
TCCAGAGGGTACAGATACCCCCC
Found at i:57484 original size:117 final size:118
Alignment explanation
Indices: 57270--57485 Score: 253
Period size: 117 Copynumber: 1.8 Consensus size: 118
57260 ATCATCTTTT
* * * *
57270 GAAAGCTAAAACAGATTTAGAAAATCAAAATGAAATGTTGAGAAAGGAGTTAGAGCGTTTAAAAA
1 GAAAGCTAAAACAGATTTAGAAAATCAAAACGAAATATTGAGAAAGAAGTTAGAACGTTTAAAAA
* * *
57335 TGAAATCTGAAAAATTTGAAAAAGGAATTTTCGAATTAAACAAACTTCTTCTA
66 TGAAATCTGAAAAATTGGAAAAAGAAAATTTCGAATTAAACAAACTTCTTCTA
* * *
57388 GAAA-CTAAAA-AGGATTTTGAAAATCAAAACGAAATATTGA-AGGAGAATTTAGAAC-TTTCAA
1 GAAAGCTAAAACA-GATTTAGAAAATCAAAACGAAATATTGAGA-AAGAAGTTAGAACGTTT-AA
* *
57449 AAATGAAATTTG-AAAGTATGGAAAAAGAAAATTTCGA
63 AAATGAAATCTGAAAAAT-TGGAAAAAGAAAATTTCGA
57486 TTTGAAAGTT
Statistics
Matches: 82, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
116 9 0.11
117 69 0.84
118 4 0.05
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.25
Consensus pattern (118 bp):
GAAAGCTAAAACAGATTTAGAAAATCAAAACGAAATATTGAGAAAGAAGTTAGAACGTTTAAAAA
TGAAATCTGAAAAATTGGAAAAAGAAAATTTCGAATTAAACAAACTTCTTCTA
Found at i:63865 original size:19 final size:20
Alignment explanation
Indices: 63831--63868 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
63821 GGGCAGATTG
63831 CCCAGAGGGAACCGATTCCA
1 CCCAGAGGGAACCGATTCCA
*
63851 CCCAG-GGGTACCGATTCC
1 CCCAGAGGGAACCGATTCC
63869 CCCTGAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.24, C:0.37, G:0.26, T:0.13
Consensus pattern (20 bp):
CCCAGAGGGAACCGATTCCA
Found at i:72450 original size:11 final size:12
Alignment explanation
Indices: 72412--72443 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
72402 AGGAGTAGTA
72412 ATTTCAAATTTG
1 ATTTCAAATTTG
72424 ATTTCAAATTTG
1 ATTTCAAATTTG
72436 ATTTCAAA
1 ATTTCAAA
72444 ATGATTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (12 bp):
ATTTCAAATTTG
Found at i:79292 original size:17 final size:17
Alignment explanation
Indices: 79270--79320 Score: 102
Period size: 17 Copynumber: 3.0 Consensus size: 17
79260 TGACTTGCAT
79270 GTCTTAGAATAAAATGG
1 GTCTTAGAATAAAATGG
79287 GTCTTAGAATAAAATGG
1 GTCTTAGAATAAAATGG
79304 GTCTTAGAATAAAATGG
1 GTCTTAGAATAAAATGG
79321 AAATGGCACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (17 bp):
GTCTTAGAATAAAATGG
Found at i:88534 original size:3 final size:3
Alignment explanation
Indices: 88526--88574 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
88516 TTTAGAAGAT
* *
88526 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTT TTA TTA ATA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
88572 TTA
1 TTA
88575 GTGATTCATG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:89173 original size:18 final size:17
Alignment explanation
Indices: 89146--89179 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
89136 TATTACATAT
*
89146 TTATTTCTTTGTATTTAA
1 TTATTACTTTGT-TTTAA
89164 TTATTACTTTGTTTTA
1 TTATTACTTTGTTTTA
89180 TCTTGTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.68
Consensus pattern (17 bp):
TTATTACTTTGTTTTAA
Done.