Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002187.1 Hibiscus syriacus cultivar Beakdansim tig00004455_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: 70129
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:684 original size:19 final size:19
Alignment explanation
Indices: 662--706 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
652 AACTTTTAAA
*
662 TATTTAAATATTTGTTAG-T
1 TATTTAAATAATT-TTAGTT
681 TA-TTAAATAATTTTAGTT
1 TATTTAAATAATTTTAGTT
699 TATTTAAA
1 TATTTAAA
707 AATATTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 4 0.17
18 12 0.52
19 7 0.30
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (19 bp):
TATTTAAATAATTTTAGTT
Found at i:1177 original size:13 final size:15
Alignment explanation
Indices: 1159--1199 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
1149 TTAAAAAAAT
1159 TAAA-TTTATTT-TA
1 TAAATTTTATTTATA
1172 TAAATTTTATTTATA
1 TAAATTTTATTTATA
1187 TACTAATTTTATT
1 TA--AATTTTATT
1200 ATGGTAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.17
14 7 0.29
15 4 0.17
17 9 0.38
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
TAAATTTTATTTATA
Found at i:4974 original size:13 final size:12
Alignment explanation
Indices: 4940--4980 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
4930 ACTTTTAATC
4940 TATATTTTATG-
1 TATATTTTATGA
*
4951 TTTATTTTATGA
1 TATATTTTATGA
4963 TATATATTTATGA
1 TATAT-TTTATGA
4976 -ATATT
1 TATATT
4981 GTTTTTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 11 0.42
12 8 0.31
13 7 0.27
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (12 bp):
TATATTTTATGA
Found at i:6346 original size:2 final size:2
Alignment explanation
Indices: 6339--6378 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
6329 TTTTATAACC
6339 AT AT 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 AT AT
6379 TTCTTCATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11085 original size:15 final size:16
Alignment explanation
Indices: 11065--11097 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
11055 GTCGAGTGTA
*
11065 ATAAAAATAA-AATTT
1 ATAAAAAAAATAATTT
11080 ATAAAAAAAATAATTT
1 ATAAAAAAAATAATTT
11096 AT
1 AT
11098 TTTCACATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAAAAAAAATAATTT
Found at i:11284 original size:12 final size:13
Alignment explanation
Indices: 11247--11281 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
11237 ATAATGCTAG
11247 ATTTTTATTTAA-
1 ATTTTTATTTAAT
11259 ATTTTTATTTTAAT
1 ATTTTTA-TTTAAT
11273 ATTTTTATT
1 ATTTTTATT
11282 AATTTAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.33
13 7 0.33
14 7 0.33
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTTTTATTTAAT
Found at i:16967 original size:29 final size:29
Alignment explanation
Indices: 16934--17015 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
16924 AATTAAATTA
16934 ATGTCATTGTTTACATCATTTAAGTAAAG
1 ATGTCATTGTTTACATCATTTAAGTAAAG
* * *
16963 ATGTCATTGTTTACACCATTAAAGTAATG
1 ATGTCATTGTTTACATCATTTAAGTAAAG
* *
16992 ATGACATTGCTTACATCAATTTAA
1 ATGTCATTGTTTACATC-ATTTAA
17016 TTAAGTGAGA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 40 0.89
30 5 0.11
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.39
Consensus pattern (29 bp):
ATGTCATTGTTTACATCATTTAAGTAAAG
Found at i:18206 original size:15 final size:15
Alignment explanation
Indices: 18183--18212 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18173 ACCAGGCTGG
18183 AATTACAACAACAAC
1 AATTACAACAACAAC
*
18198 AATTCCAACAACAAC
1 AATTACAACAACAAC
18213 TATAAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.13
Consensus pattern (15 bp):
AATTACAACAACAAC
Found at i:19835 original size:18 final size:18
Alignment explanation
Indices: 19814--19854 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
19804 GCAACTCCAC
19814 CCACTTCACCAACATCAA
1 CCACTTCACCAACATCAA
*
19832 CCACTTCACCAATATCAA
1 CCACTTCACCAACATCAA
19850 CCACT
1 CCACT
19855 CAAGGAGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.44, G:0.00, T:0.20
Consensus pattern (18 bp):
CCACTTCACCAACATCAA
Found at i:21629 original size:29 final size:29
Alignment explanation
Indices: 21587--21667 Score: 144
Period size: 29 Copynumber: 2.8 Consensus size: 29
21577 AACTAAATTA
21587 ATGTCATTGCTTACATCATTTAAGTAAAG
1 ATGTCATTGCTTACATCATTTAAGTAAAG
*
21616 ATGTCATTGCTTACATCATTTAAGTAATG
1 ATGTCATTGCTTACATCATTTAAGTAAAG
21645 ATGTCATTGCTTACATCAATTTA
1 ATGTCATTGCTTACATC-ATTTA
21668 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (29 bp):
ATGTCATTGCTTACATCATTTAAGTAAAG
Found at i:22087 original size:30 final size:29
Alignment explanation
Indices: 22053--22126 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 29
22043 ATATAATTAT
22053 TTTATATTTATTTTTTTATCT-TTTAAAGTA
1 TTTATATTTATTTTTTTATCTATTTAAA--A
*
22083 TTTATA--TA-TTTTTTATTTATTTAAAA
1 TTTATATTTATTTTTTTATCTATTTAAAA
22109 TTTAGTATTATATTTTTT
1 TTTA-TATT-TATTTTTT
22127 GTTTATTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
26 5 0.14
27 11 0.30
28 8 0.22
30 8 0.22
31 5 0.14
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (29 bp):
TTTATATTTATTTTTTTATCTATTTAAAA
Found at i:22888 original size:83 final size:85
Alignment explanation
Indices: 22791--23012 Score: 403
Period size: 83 Copynumber: 2.6 Consensus size: 85
22781 TGGTAGTAAA
22791 TTTTAGCGATATTAAGAGTGGGTTGTATATATATAGCTACTACTGAACCAGCTGGTATGGAAGAT
1 TTTTAGCGATATTAAGAGTGGGTTGTATATATATAGCTACTACTGAACCAGCTGGTATGGAAGAT
22856 AGGG-T-CATGCAATGGTGG
66 AGGGTTCCATGCAATGGTGG
*
22874 TTTTAGCGATATTAAGAGTGGGTTGTATATATATAGCTACTACTGAACCAGATGGTATGGAAGAT
1 TTTTAGCGATATTAAGAGTGGGTTGTATATATATAGCTACTACTGAACCAGCTGGTATGGAAGAT
22939 AGGGTTCCCATGCAATGGTGG
66 AGGGTT-CCATGCAATGGTGG
*
22960 TTTTAGCGATATTAAGAGTGGGTTGTATATATATAGCTACCACTGAACCAGCT
1 TTTTAGCGATATTAAGAGTGGGTTGTATATATATAGCTACTACTGAACCAGCT
23013 TCATATTTGA
Statistics
Matches: 133, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
83 68 0.51
84 1 0.01
86 64 0.48
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (85 bp):
TTTTAGCGATATTAAGAGTGGGTTGTATATATATAGCTACTACTGAACCAGCTGGTATGGAAGAT
AGGGTTCCATGCAATGGTGG
Found at i:50739 original size:24 final size:24
Alignment explanation
Indices: 50712--50761 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
50702 AGGTTACTCA
*
50712 AATTTGTATTAGTTTTTGAATTGT
1 AATTTGTATTACTTTTTGAATTGT
*
50736 AATTTGTATTACTTTTTGAGTTGT
1 AATTTGTATTACTTTTTGAATTGT
50760 AA
1 AA
50762 CAAAACATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.26, C:0.02, G:0.16, T:0.56
Consensus pattern (24 bp):
AATTTGTATTACTTTTTGAATTGT
Found at i:52907 original size:23 final size:23
Alignment explanation
Indices: 52858--52913 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
52848 TGTTCGTTCG
* * * *
52858 TTTAACGTTCGTGAACGTATTCG
1 TTTAACGTTCATGAACATACTCA
*
52881 TTTAACGTTCATGAATATACTCA
1 TTTAACGTTCATGAACATACTCA
*
52904 TTTAATGTTC
1 TTTAACGTTC
52914 GTTTAATGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (23 bp):
TTTAACGTTCATGAACATACTCA
Found at i:57199 original size:19 final size:19
Alignment explanation
Indices: 57177--57218 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
57167 TATACCCCAA
57177 ACCCTAAATCCCAAATTAT
1 ACCCTAAATCCCAAATTAT
57196 ACCCTAAATCCCAAATTAT
1 ACCCTAAATCCCAAATTAT
57215 ACCC
1 ACCC
57219 CCTTACCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (19 bp):
ACCCTAAATCCCAAATTAT
Found at i:57211 original size:26 final size:26
Alignment explanation
Indices: 57147--57211 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
57137 AAATTTAGAT
* *
57147 CTAAACCCTAAACCCCGAATTATACC
1 CTAAACCCTAAATCCCAAATTATACC
*
57173 CCAAACCCTAAATCCCAAATTATACC
1 CTAAACCCTAAATCCCAAATTATACC
57199 CTAAATCCC-AAAT
1 CTAAA-CCCTAAAT
57212 TATACCCCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 31 0.91
27 3 0.09
ACGTcount: A:0.42, C:0.37, G:0.02, T:0.20
Consensus pattern (26 bp):
CTAAACCCTAAATCCCAAATTATACC
Found at i:64104 original size:2 final size:2
Alignment explanation
Indices: 64097--64124 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
64087 AACTTATTAA
64097 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
64125 ACATATTCAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:64249 original size:2 final size:2
Alignment explanation
Indices: 64242--64266 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
64232 ATAATTGACT
64242 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
64267 TTCTAAGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64467 original size:21 final size:21
Alignment explanation
Indices: 64425--64467 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
64415 GTATCCGCAC
* *
64425 TCTTGTATAGGGTATTCATTA
1 TCTTGTAGAGGGTATGCATTA
* *
64446 TCTTGTAGATGGTATGCCTTA
1 TCTTGTAGAGGGTATGCATTA
64467 T
1 T
64468 TTAGATAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (21 bp):
TCTTGTAGAGGGTATGCATTA
Found at i:65563 original size:23 final size:20
Alignment explanation
Indices: 65514--65571 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 20
65504 CAATTTGTGA
*
65514 TATAATTTTTATATTTAATT
1 TATAATTTTTAAATTTAATT
*
65534 TAAAATTTTTACAATTTATAATT
1 TATAATTTTTA-AA-TT-TAATT
65557 TATAATTTTTTAAAT
1 TATAA-TTTTTAAAT
65572 ACATTAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 10 0.32
21 1 0.03
22 3 0.10
23 11 0.35
24 6 0.19
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TATAATTTTTAAATTTAATT
Done.