Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000570.1 Hibiscus syriacus cultivar Beakdansim tig00001116_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: 81094
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6535 original size:2 final size:2
Alignment explanation
Indices: 6528--6553 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6518 TTTCTTTCCA
6528 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
6554 TGTTTTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12823 original size:103 final size:103
Alignment explanation
Indices: 12644--12833 Score: 292
Period size: 103 Copynumber: 1.8 Consensus size: 103
12634 TAATTCACAA
* ** *
12644 CTCATTATGAATACCATGGATGCACAAATAGTGCTGAAAGTACACAAAGTACTGATATGAAAATG
1 CTCATTATGAACACCATCAATGCACAAATAGTGCTGAAAGTACACAAAGTACTGATATAAAAATG
* * *
12709 TAACATATGCATTAAATAAAATCGATCGATAACAAGTG
66 CAACAAATGCATTAAACAAAATCGATCGATAACAAGTG
*
12747 CTCATTATGAACACCATCAATGCACACATAGTGCCT-AAAGTACACAAAGTACTGATATAAAAAT
1 CTCATTATGAACACCATCAATGCACAAATAGTG-CTGAAAGTACACAAAGTACTGATATAAAAAT
12811 GCAACAAATGCATTAAACAAAAT
65 GCAACAAATGCATTAAACAAAAT
12834 GAATCTATGA
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
103 76 0.97
104 2 0.03
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (103 bp):
CTCATTATGAACACCATCAATGCACAAATAGTGCTGAAAGTACACAAAGTACTGATATAAAAATG
CAACAAATGCATTAAACAAAATCGATCGATAACAAGTG
Found at i:19115 original size:21 final size:21
Alignment explanation
Indices: 19089--19132 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
19079 AATAAGTGTA
19089 CCAAAGTACTACATATATGTT
1 CCAAAGTACTACATATATGTT
*
19110 CCAAAGTATTACATATATGTT
1 CCAAAGTACTACATATATGTT
19131 CC
1 CC
19133 GAAGGACCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.34
Consensus pattern (21 bp):
CCAAAGTACTACATATATGTT
Found at i:21392 original size:2 final size:2
Alignment explanation
Indices: 21385--21432 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
21375 CGTTCTTCAA
21385 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21426 AT AT AT A
1 AT AT AT A
21433 ATTTAAAATC
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29396 original size:18 final size:18
Alignment explanation
Indices: 29373--29446 Score: 94
Period size: 18 Copynumber: 3.9 Consensus size: 18
29363 AAGGGATATC
29373 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
29391 AGTGGTCCATCGAGACATAT
1 AGTGGTCCTTCGGGAC--AT
29411 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
29430 AGTGGTCTTTCGGGACA
1 AGTGGTCCTTCGGGACA
29447 AATATTCAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
18 30 0.62
19 2 0.04
20 2 0.04
21 14 0.29
ACGTcount: A:0.20, C:0.22, G:0.31, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:29706 original size:2 final size:2
Alignment explanation
Indices: 29699--29734 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
29689 AATGCATTGT
*
29699 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29735 CTATGGCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:36165 original size:18 final size:18
Alignment explanation
Indices: 36142--36215 Score: 76
Period size: 18 Copynumber: 3.9 Consensus size: 18
36132 GAGGGATATC
36142 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* * *
36160 AGTGGTCATTTGAGACATAT
1 AGTGGTCCTTCGGGAC--AT
*
36180 CAGTGGTCCTTTGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
36199 AGTGGTCTTTCGGGACA
1 AGTGGTCCTTCGGGACA
36216 AATATTCAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
18 28 0.61
19 2 0.04
20 2 0.04
21 14 0.30
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:36186 original size:21 final size:21
Alignment explanation
Indices: 36160--36199 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
36150 TTCGGGACAT
36160 AGTGGTCATTTGAGACATATC
1 AGTGGTCATTTGAGACATATC
* *
36181 AGTGGTCCTTTGGGACATA
1 AGTGGTCATTTGAGACATA
36200 GTGGTCTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
AGTGGTCATTTGAGACATATC
Found at i:42078 original size:16 final size:15
Alignment explanation
Indices: 42005--42089 Score: 64
Period size: 16 Copynumber: 5.5 Consensus size: 15
41995 TCGCATAGAT
*
42005 ATTTTCACGTAAAAC
1 ATTTTCACGTATAAC
* *
42020 AATTTT-ACATATATC
1 -ATTTTCACGTATAAC
* * *
42035 ATATTCACGTAGATC
1 ATTTTCACGTATAAC
42050 ATTTTTCACGTATAAC
1 A-TTTTCACGTATAAC
*
42066 ACTTTTCACGTATGAC
1 A-TTTTCACGTATAAC
*
42082 ATATTCAC
1 ATTTTCAC
42090 CACTATCATA
Statistics
Matches: 55, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
14 4 0.07
15 20 0.36
16 31 0.56
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (15 bp):
ATTTTCACGTATAAC
Found at i:43914 original size:16 final size:16
Alignment explanation
Indices: 43893--43923 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
43883 TATATATATA
43893 ATATAATGGATTATTT
1 ATATAATGGATTATTT
43909 ATATAATGGATTATT
1 ATATAATGGATTATT
43924 AGATTTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (16 bp):
ATATAATGGATTATTT
Found at i:44079 original size:22 final size:22
Alignment explanation
Indices: 44044--44149 Score: 151
Period size: 22 Copynumber: 4.9 Consensus size: 22
44034 AATGAAAAAA
44044 AGGTATC-GGTACCCGAAATCT
1 AGGTATCGGGTACCCGAAATCT
* *
44065 GGGTATCGGGTACCCGAAATCC
1 AGGTATCGGGTACCCGAAATCT
* * *
44087 AGGTACCGGGAACCTGAAATCT
1 AGGTATCGGGTACCCGAAATCT
44109 AGGTATCGGGTACCCGAAATCT
1 AGGTATCGGGTACCCGAAATCT
*
44131 GGGTATCGGGTACCCGAAA
1 AGGTATCGGGTACCCGAAA
44150 CATCCGGGTT
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
21 6 0.08
22 67 0.92
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (22 bp):
AGGTATCGGGTACCCGAAATCT
Found at i:46528 original size:20 final size:20
Alignment explanation
Indices: 46503--46542 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
46493 TTAACATTAT
*
46503 AAAAGAAAATACTATAGGTG
1 AAAAGAAAATACTAGAGGTG
46523 AAAAGAAAATACTAGAGGTG
1 AAAAGAAAATACTAGAGGTG
46543 TCTAACATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.23, T:0.17
Consensus pattern (20 bp):
AAAAGAAAATACTAGAGGTG
Found at i:52299 original size:19 final size:20
Alignment explanation
Indices: 52261--52300 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
52251 TTGACCACCG
52261 ATGCTACTCAACAAAGCTCTC
1 ATGCTACT-AACAAAGCTCTC
*
52282 ATGCTACT-ACAGAGCTCTC
1 ATGCTACTAACAAAGCTCTC
52301 TATCGAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.30, C:0.33, G:0.12, T:0.25
Consensus pattern (20 bp):
ATGCTACTAACAAAGCTCTC
Found at i:53050 original size:50 final size:50
Alignment explanation
Indices: 52967--53068 Score: 177
Period size: 50 Copynumber: 2.0 Consensus size: 50
52957 ATCCAATCAC
*
52967 TACTTAGCTAATTTAGAAAAGTTCGATCCTACTCAATTAATGATTTTCAA
1 TACTTAGCTAATTTAGAAAAGTTCGATCATACTCAATTAATGATTTTCAA
* *
53017 TACTTAGCTAATTTAGAAAAGTTTGATCATACTCAATTAATTATTTTCAA
1 TACTTAGCTAATTTAGAAAAGTTCGATCATACTCAATTAATGATTTTCAA
53067 TA
1 TA
53069 TTGTAGTAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (50 bp):
TACTTAGCTAATTTAGAAAAGTTCGATCATACTCAATTAATGATTTTCAA
Found at i:56188 original size:11 final size:11
Alignment explanation
Indices: 56166--56201 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
56156 GTTTGATGCT
56166 TTCTCT-TTGA
1 TTCTCTCTTGA
56176 TTCTCTCTTGA
1 TTCTCTCTTGA
56187 TTCTCTCTTGA
1 TTCTCTCTTGA
56198 TTCT
1 TTCT
56202 TGTTTCTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.08, C:0.25, G:0.08, T:0.58
Consensus pattern (11 bp):
TTCTCTCTTGA
Found at i:56423 original size:19 final size:19
Alignment explanation
Indices: 56399--56507 Score: 209
Period size: 19 Copynumber: 5.7 Consensus size: 19
56389 TTGGACCCTT
56399 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
56418 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
56437 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
56456 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
56475 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
*
56494 AGTGCATCGATGCA
1 AGTGCATCGGTGCA
56508 TCAAGTGCAT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
19 89 1.00
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (19 bp):
AGTGCATCGGTGCACTAAG
Found at i:56529 original size:18 final size:17
Alignment explanation
Indices: 56399--56523 Score: 61
Period size: 19 Copynumber: 6.7 Consensus size: 17
56389 TTGGACCCTT
* *
56399 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
* *
56417 GAGTGCATCGGTGCACTAA
1 -AGTGCATCGATGCA-TCA
* *
56436 GAGTGCATCGGTGCACTAA
1 -AGTGCATCGATGCA-TCA
* *
56455 GAGTGCATCGGTGCACTAA
1 -AGTGCATCGATGCA-TCA
* *
56474 GAGTGCATCGGTGCACTAA
1 -AGTGCATCGATGCA-TCA
56493 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
56511 AGTGCATTCGATG
1 AGTGCA-TCGATG
56524 TTTCAAAATA
Statistics
Matches: 103, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
17 6 0.06
18 8 0.08
19 89 0.86
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.22
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:63341 original size:22 final size:21
Alignment explanation
Indices: 63299--63338 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
63289 GAGTTTATTT
*
63299 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
63320 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
63339 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:65315 original size:18 final size:17
Alignment explanation
Indices: 65261--65309 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
65251 TTGGACCCTT
* *
65261 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
65279 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
65297 AGTGCATTCGATG
1 AGTGCA-TCGATG
65310 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:65422 original size:65 final size:65
Alignment explanation
Indices: 65280--65440 Score: 195
Period size: 65 Copynumber: 2.5 Consensus size: 65
65270 GTGCACTAAG
* *
65280 AGTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
* * * *
65344 AGTGCATCAATGCATCAAATGCATTCGATGTTTTTATAAA-ATCCTCAGTGCATC-AGTGCATGG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGA-TGCATGG
65407 -T
64 CT
* *
65408 ATGTGCATCGATGCATGAAATACATTCGATGTT
1 A-GTGCATCGATGCATCAAATGCATTCGATGTT
65441 CAATTTAATT
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
64 31 0.37
65 50 0.60
66 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (65 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
Found at i:68875 original size:17 final size:17
Alignment explanation
Indices: 68855--68891 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
68845 TTAAACTAGT
68855 CTCCTAATGCAACTCTG
1 CTCCTAATGCAACTCTG
68872 CTCCTAATGCAACTCTG
1 CTCCTAATGCAACTCTG
68889 CTC
1 CTC
68892 GTCAATCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.22, C:0.38, G:0.11, T:0.30
Consensus pattern (17 bp):
CTCCTAATGCAACTCTG
Found at i:73663 original size:15 final size:15
Alignment explanation
Indices: 73640--73689 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
73630 CCACCCACAT
*
73640 CCGCACCGCATCCAC
1 CCGCCCCGCATCCAC
73655 CCGCCCCGCATCCAC
1 CCGCCCCGCATCCAC
* * *
73670 CCTCCCCACATCCGC
1 CCGCCCCGCATCCAC
73685 CCGCC
1 CCGCC
73690 AACTAAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.14, C:0.66, G:0.12, T:0.08
Consensus pattern (15 bp):
CCGCCCCGCATCCAC
Found at i:79484 original size:18 final size:19
Alignment explanation
Indices: 79461--79499 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
79451 TTTAAATAGT
79461 AATAAAAACGATTAAA-TA
1 AATAAAAACGATTAAAGTA
* *
79479 AATAAAAGCTATTAAAGTA
1 AATAAAAACGATTAAAGTA
79498 AA
1 AA
79500 AATAACAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.23
Consensus pattern (19 bp):
AATAAAAACGATTAAAGTA
Done.