Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006730.1 Hibiscus syriacus cultivar Beakdansim tig00016860_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: 46646
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:8327 original size:18 final size:18
Alignment explanation
Indices: 8292--8329 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
8282 CGTTGGAGGT
*
8292 GGGACGACAGGAGGGAAA
1 GGGACGACAGGAGAGAAA
8310 GGGACGAC-GAGAGAGAAA
1 GGGACGACAG-GAGAGAAA
8328 GG
1 GG
8330 AGTTTGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.39, C:0.11, G:0.50, T:0.00
Consensus pattern (18 bp):
GGGACGACAGGAGAGAAA
Found at i:8870 original size:15 final size:15
Alignment explanation
Indices: 8842--8881 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
8832 AGTGGAACAC
8842 GTGTCAA-A-GACTT
1 GTGTCAATATGACTT
8855 GTGTCAATATGACTT
1 GTGTCAATATGACTT
8870 GTGTCAATATGA
1 GTGTCAATATGA
8882 ACATAGATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 7 0.28
14 1 0.04
15 17 0.68
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (15 bp):
GTGTCAATATGACTT
Found at i:15802 original size:11 final size:11
Alignment explanation
Indices: 15786--15818 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
15776 TAATTTTATT
15786 TTTTTATAAAA
1 TTTTTATAAAA
15797 TTTTTAT-AAA
1 TTTTTATAAAA
15807 TTTTT-TAAAA
1 TTTTTATAAAA
15817 TT
1 TT
15819 ATCAGGTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 1 0.05
10 13 0.62
11 7 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTTATAAAA
Found at i:15817 original size:10 final size:11
Alignment explanation
Indices: 15785--15818 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
15775 GTAATTTTAT
15785 TTTTTTATAAA
1 TTTTTTATAAA
*
15796 ATTTTTATAAA
1 TTTTTTATAAA
15807 TTTTTTA-AAA
1 TTTTTTATAAA
15817 TT
1 TT
15819 ATCAGGTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTTTATAAA
Found at i:16128 original size:32 final size:31
Alignment explanation
Indices: 16086--16154 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
16076 CAAAAATTAT
* *
16086 AAAATTGTCATTAAATTTTATCAAAATATAAC
1 AAAATGGTCATTAAA-CTTATCAAAATATAAC
* *
16118 AAAATGGTCATTAAACTTATCAAATTATAAT
1 AAAATGGTCATTAAACTTATCAAAATATAAC
16149 AAAATG
1 AAAATG
16155 CTCTTTGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
31 19 0.58
32 14 0.42
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.35
Consensus pattern (31 bp):
AAAATGGTCATTAAACTTATCAAAATATAAC
Found at i:32095 original size:3 final size:3
Alignment explanation
Indices: 32082--32154 Score: 92
Period size: 3 Copynumber: 24.0 Consensus size: 3
32072 GTAATATTTA
* * *
32082 AAT AAT AAAT AAT ATT ACT ATT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
32128 AAT AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
32155 TTAAAATGAA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 58 0.95
4 3 0.05
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:32411 original size:76 final size:76
Alignment explanation
Indices: 32280--33222 Score: 1635
Period size: 76 Copynumber: 12.5 Consensus size: 76
32270 GATGGAAATG
*
32280 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
32345 CCCGAAGGCTT
66 CCCGAAGGCTT
*
32356 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
32421 CCCGAAGGCTT
66 CCCGAAGGCTT
32432 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTG-AGGCTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC-GAAGGCTTTGAAAACATCAAAAAGC
*
32496 TCCTGAAGGCTT
65 TCCCGAAGGCTT
* *
32508 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
32573 CCTGAAGGCTT
66 CCCGAAGGCTT
* *
32584 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
32649 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
32660 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
32725 CCCGAAGGCTT
66 CCCGAAGGCTT
* * *
32736 TTTGGAAACATCATGCATTGAAGGGCTTACAGATGACCCGAAGGCTTTGACAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
32801 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
32812 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
32877 CCCGAAGGCTC
66 CCCGAAGGCTT
* *
32888 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTT-AAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
32952 CCCGAAGGCTT
66 CCCGAAGGCTT
*
32963 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTT-AAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
33027 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
33038 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTT-AAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
33102 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
33113 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTT-AAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
33177 CCCGAAGGCTT
66 CCCGAAGGCTT
33188 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
33223 TGGGAAATAG
Statistics
Matches: 841, Mismatches: 24, Indels: 5
0.97 0.03 0.01
Matches are distributed among these distances:
75 284 0.34
76 556 0.66
77 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:33765 original size:112 final size:113
Alignment explanation
Indices: 33632--34430 Score: 1060
Period size: 112 Copynumber: 7.0 Consensus size: 113
33622 ATAGAATTAT
* *
33632 GCAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
33697 ATTATGAAC-TTCTCTGGAAAAGCTGCTCCATCA-AGTGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGA-TGATGGATTTGA
* *
33744 GTAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
33809 ATTATGAACTTTCTCTGGAAAAACTGATCCATCA-AGTGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGA-TGATGGATTTGA
** *
33857 GC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
33921 ATTATGAGCTTTTTTTTTTTTTTTGGAAAAGCTGATCCATCAGAAGATGGATTTGA
66 ATTATGAAC--------TTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
**
33977 GC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTT-TT-TT--TT-TTCCAGATGAGTTCTTCT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTT-CAGATGAGTTCTTCT
* *
34036 CATTATGAACTTTTTTTTTTGGAAAAGCTGATCCATCAGAAGATGGATTTGA
65 CATTATGAAC---TTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
*
34088 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
* * * * * * * **
34153 CTCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
63 CTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATT-TGA
* * *
34205 CCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
34270 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
* * *
34318 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGCTCTTCTA
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
34383 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
34431 ATCTTTGCTA
Statistics
Matches: 618, Mismatches: 48, Indels: 41
0.87 0.07 0.06
Matches are distributed among these distances:
111 44 0.07
112 168 0.27
113 147 0.24
114 51 0.08
115 2 0.00
116 60 0.10
117 53 0.09
118 2 0.00
119 22 0.04
120 68 0.11
121 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
Found at i:37550 original size:93 final size:93
Alignment explanation
Indices: 37436--37674 Score: 469
Period size: 93 Copynumber: 2.6 Consensus size: 93
37426 GACTTTAGAG
*
37436 TTCATACCAAACCATATCAGATAATTCAAAGAACACTTTCAGAAGATGCTATGAGCACATCCATC
1 TTCATACCAAACCATATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATGAGCACATCCATC
37501 TTCCAAATTCAATGATTGATTCTGTGGT
66 TTCCAAATTCAATGATTGATTCTGTGGT
37529 TTCATACCAAACCATATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATGAGCACATCCATC
1 TTCATACCAAACCATATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATGAGCACATCCATC
37594 TTCCAAATTCAATGATTGATTCTGTGGT
66 TTCCAAATTCAATGATTGATTCTGTGGT
37622 TTCATACCAAACCATATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCATACCAAACCATATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATG
37675 GGTCTCCTTA
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 145 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (93 bp):
TTCATACCAAACCATATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATGAGCACATCCATC
TTCCAAATTCAATGATTGATTCTGTGGT
Found at i:37557 original size:45 final size:45
Alignment explanation
Indices: 37506--37650 Score: 107
Period size: 45 Copynumber: 3.2 Consensus size: 45
37496 CCATCTTCCA
37506 AATTCAATGATTGATTCTGTGGTTTCATACCAAACCATATCAGAT
1 AATTCAATGATTGATTCTGTGGTTTCATACCAAACCATATCAGAT
* ** * ** * * * * * *
37551 AATTCAAAGA-ACACTTCCAGAAGATGCTATGAGCACATCCATCTTC-CA-
1 AATTCAATGATTGA-TT-CTGTGGTTTC-AT-ACCA-AACCAT-ATCAGAT
37599 AATTCAATGATTGATTCTGTGGTTTCATACCAAACCATATCAGAT
1 AATTCAATGATTGATTCTGTGGTTTCATACCAAACCATATCAGAT
37644 AATTCAA
1 AATTCAA
37651 AGAACACTTC
Statistics
Matches: 67, Mismatches: 24, Indels: 18
0.61 0.22 0.17
Matches are distributed among these distances:
43 2 0.03
44 7 0.10
45 21 0.31
46 7 0.10
47 7 0.10
48 14 0.21
49 7 0.10
50 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (45 bp):
AATTCAATGATTGATTCTGTGGTTTCATACCAAACCATATCAGAT
Found at i:39621 original size:16 final size:17
Alignment explanation
Indices: 39600--39631 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
39590 TCAATTTTCC
39600 TTTTTCTTC-TTCTTTT
1 TTTTTCTTCTTTCTTTT
39616 TTTTTCTTCTTTCTTT
1 TTTTTCTTCTTTCTTT
39632 GTTGGATGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTCTTCTTTCTTTT
Found at i:42199 original size:21 final size:21
Alignment explanation
Indices: 42174--42214 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
42164 AAAGATATAA
42174 AAATACAAAATGAAAATGCAC
1 AAATACAAAATGAAAATGCAC
*
42195 AAATACAAAATGTAAATGCA
1 AAATACAAAATGAAAATGCA
42215 TGTATGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.61, C:0.12, G:0.10, T:0.17
Consensus pattern (21 bp):
AAATACAAAATGAAAATGCAC
Found at i:46523 original size:3 final size:3
Alignment explanation
Indices: 46510--46572 Score: 63
Period size: 3 Copynumber: 20.0 Consensus size: 3
46500 GTAATATTTA
* *
46510 AAT AAT AAAT AAT ATT ACT ATAT ATAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT
**
46558 TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
46573 TTAAAATGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
3 42 0.82
4 9 0.18
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Done.