Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002873.1 Hibiscus syriacus cultivar Beakdansim tig00005924_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: 76492
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:979 original size:23 final size:22
Alignment explanation
Indices: 949--1010 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 22
939 TCGATCCCCT
949 AGGGGGAATCGGTTCCCCTTTAA
1 AGGGGGAATCGGTTCCCCTTT-A
* *
972 AGGGGGAATCAGTTCACCTTTA
1 AGGGGGAATCGGTTCCCCTTTA
* *
994 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
1011 TCTGCCCTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.42
23 19 0.58
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.26
Consensus pattern (22 bp):
AGGGGGAATCGGTTCCCCTTTA
Found at i:4821 original size:22 final size:21
Alignment explanation
Indices: 4779--4818 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4769 TAAGTTTATT
*
4779 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
4800 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
4819 ATAATTTCTC
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:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:17081 original size:16 final size:16
Alignment explanation
Indices: 17042--17108 Score: 62
Period size: 16 Copynumber: 4.2 Consensus size: 16
17032 GACTGATACA
*
17042 AATTTGAACCAAAAAT
1 AATTTGAACCAAAAGT
** *
17058 AACATGAAGCAAAAGT
1 AATTTGAACCAAAAGT
*
17074 AATTTGAACCGAAAGT
1 AATTTGAACCAAAAGT
* **
17090 AACTTGAATAAAAAGT
1 AATTTGAACCAAAAGT
17106 AAT
1 AAT
17109 CTAAATCGAA
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.22
Consensus pattern (16 bp):
AATTTGAACCAAAAGT
Found at i:17083 original size:32 final size:32
Alignment explanation
Indices: 17042--17108 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
17032 GACTGATACA
*
17042 AATTTGAACCAAAAATAACATGAAGCAAAAGT
1 AATTTGAACCAAAAATAACATGAAGAAAAAGT
* * * *
17074 AATTTGAACCGAAAGTAACTTGAATAAAAAGT
1 AATTTGAACCAAAAATAACATGAAGAAAAAGT
17106 AAT
1 AAT
17109 CTAAATCGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.22
Consensus pattern (32 bp):
AATTTGAACCAAAAATAACATGAAGAAAAAGT
Found at i:17119 original size:32 final size:31
Alignment explanation
Indices: 17068--17138 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 31
17058 AACATGAAGC
* * *
17068 AAAAGTAATTTGAACCGAAAGTAACTTGAATA
1 AAAAGTAATCTAAACCGAAAGTAACCTGAA-A
* *
17100 AAAAGTAATCTAAATCGAAAGTAACCTGAAC
1 AAAAGTAATCTAAACCGAAAGTAACCTGAAA
17131 AAAAGTAA
1 AAAAGTAA
17139 CCTGACACAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 8 0.24
32 26 0.76
ACGTcount: A:0.54, C:0.11, G:0.14, T:0.21
Consensus pattern (31 bp):
AAAAGTAATCTAAACCGAAAGTAACCTGAAA
Found at i:28535 original size:16 final size:16
Alignment explanation
Indices: 28496--28562 Score: 62
Period size: 16 Copynumber: 4.2 Consensus size: 16
28486 GACTGATACA
*
28496 AATTTGAACCAAAAAT
1 AATTTGAACCAAAAGT
** *
28512 AACATGAAGCAAAAGT
1 AATTTGAACCAAAAGT
*
28528 AATTTGAACCGAAAGT
1 AATTTGAACCAAAAGT
* **
28544 AACTTGAATAAAAAGT
1 AATTTGAACCAAAAGT
28560 AAT
1 AAT
28563 CTAAATCGAA
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.22
Consensus pattern (16 bp):
AATTTGAACCAAAAGT
Found at i:28537 original size:32 final size:32
Alignment explanation
Indices: 28496--28562 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
28486 GACTGATACA
*
28496 AATTTGAACCAAAAATAACATGAAGCAAAAGT
1 AATTTGAACCAAAAATAACATGAAGAAAAAGT
* * * *
28528 AATTTGAACCGAAAGTAACTTGAATAAAAAGT
1 AATTTGAACCAAAAATAACATGAAGAAAAAGT
28560 AAT
1 AAT
28563 CTAAATCGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.22
Consensus pattern (32 bp):
AATTTGAACCAAAAATAACATGAAGAAAAAGT
Found at i:28573 original size:32 final size:32
Alignment explanation
Indices: 28522--28593 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
28512 AACATGAAGC
* * * *
28522 AAAAGTAATTTGAACCGAAAGTAACTTGAATA
1 AAAAGTAATCTAAACCGAAAGTAACCTGAACA
*
28554 AAAAGTAATCTAAATCGAAAGTAACCTGAACA
1 AAAAGTAATCTAAACCGAAAGTAACCTGAACA
28586 AAAAGTAA
1 AAAAGTAA
28594 CCTGACACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.54, C:0.11, G:0.14, T:0.21
Consensus pattern (32 bp):
AAAAGTAATCTAAACCGAAAGTAACCTGAACA
Found at i:28590 original size:16 final size:17
Alignment explanation
Indices: 28500--28598 Score: 57
Period size: 16 Copynumber: 6.2 Consensus size: 17
28490 GATACAAATT
*
28500 TGAACCAAAAA-TAACA
1 TGAACCAAAAAGTAACC
* **
28516 TGAAGC-AAAAGTAATT
1 TGAACCAAAAAGTAACC
* *
28532 TGAACC-GAAAGTAACT
1 TGAACCAAAAAGTAACC
* *
28548 TGAA-TAAAAAGTAATC
1 TGAACCAAAAAGTAACC
* * *
28564 TAAATC-GAAAGTAACC
1 TGAACCAAAAAGTAACC
28580 TGAA-CAAAAAGTAACC
1 TGAACCAAAAAGTAACC
28596 TGA
1 TGA
28599 CACATGTCAA
Statistics
Matches: 63, Mismatches: 16, Indels: 8
0.72 0.18 0.09
Matches are distributed among these distances:
15 5 0.08
16 58 0.92
ACGTcount: A:0.53, C:0.14, G:0.14, T:0.19
Consensus pattern (17 bp):
TGAACCAAAAAGTAACC
Found at i:40511 original size:16 final size:17
Alignment explanation
Indices: 40484--40518 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
40474 TATCGCCGAC
40484 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
40501 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
40517 CG
1 CG
40519 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:45285 original size:2 final size:2
Alignment explanation
Indices: 45264--45318 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
45254 AGTGTAATCA
* * *
45264 AT AT AT AA AT AA AT AA 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 AT
45306 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
45319 AAAGATAAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:47430 original size:22 final size:23
Alignment explanation
Indices: 47384--47431 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
47374 ATATGAAGGT
*
47384 TTTTTTTCAATTAAGTATCTGAA
1 TTTTTTTCAATTAAGTATCTAAA
*
47407 TTTTTTT-AATTAAGTATTTAAA
1 TTTTTTTCAATTAAGTATCTAAA
47429 TTT
1 TTT
47432 GAATTGTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.58
Consensus pattern (23 bp):
TTTTTTTCAATTAAGTATCTAAA
Found at i:47572 original size:2 final size:2
Alignment explanation
Indices: 47567--47593 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47557 TATATCAGAT
47567 TA 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 TA T
47594 TGAATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49794 original size:2 final size:2
Alignment explanation
Indices: 49787--49822 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
49777 TGCATCTTTC
49787 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
49823 CCACGCATAC
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:50132 original size:29 final size:30
Alignment explanation
Indices: 50090--50171 Score: 103
Period size: 30 Copynumber: 2.8 Consensus size: 30
50080 CCCAAAGGAC
*
50090 CTATCCAGAGGTCACAAAG-ACCCCGGTAA
1 CTATCCAGAGGTCACAAAGAACCCCGGCAA
*
50119 CTATCCAGAGGTCACAAAGAACCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCCCGGCAA
* * * *
50149 CTGTCCATAGGTCTCGAAGAACC
1 CTATCCAGAGGTCACAAAGAACC
50172 TAGGTAAACT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 19 0.41
30 27 0.59
ACGTcount: A:0.33, C:0.30, G:0.21, T:0.16
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCCCGGCAA
Found at i:51125 original size:20 final size:22
Alignment explanation
Indices: 51100--51157 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
51090 TTCCCCTTGA
51100 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
*
51120 AGTGCATCGATACATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
51143 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
51158 CTACCCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:51257 original size:64 final size:63
Alignment explanation
Indices: 51145--51285 Score: 153
Period size: 64 Copynumber: 2.2 Consensus size: 63
51135 TCTTTAACAT
* * *
51145 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * *
51208 GATGCATCGATGCACT-CCTTATGCATCGATGCATC-AATTGCATTTGATGTTTCTTCTTTAAAG
1 G-TGCATCGATGCACTACC-CATGCATCGATACA-CAAATTACATTCGATGTTTCATCTTTAAAG
51271 A
63 A
51272 GTGCATCGATGCAC
1 GTGCATCGATGCAC
51286 ATTGAATATG
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
63 21 0.32
64 44 0.67
65 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:52183 original size:2 final size:2
Alignment explanation
Indices: 52176--52211 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
52166 CTTTTTCCCT
52176 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
52212 CATGTCACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52517 original size:20 final size:19
Alignment explanation
Indices: 52492--52531 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
52482 ACTCATCCCT
*
52492 TTCATTTCTTTATTCCATTA
1 TTCATTTATTTATTCC-TTA
52512 TTCATTTATTTATTCCTTA
1 TTCATTTATTTATTCCTTA
52531 T
1 T
52532 ACCCAAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.62
Consensus pattern (19 bp):
TTCATTTATTTATTCCTTA
Found at i:55628 original size:20 final size:22
Alignment explanation
Indices: 55603--55660 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
55593 TTCCCCTTGA
55603 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
*
55623 AGTGCATCGATACATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
55646 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
55661 CTACCCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:55726 original size:64 final size:63
Alignment explanation
Indices: 55648--55788 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
55638 TCTTTAACAT
* * * *
55648 GTGCATCGATGCACTACCCATGCATCGATACA-CAAATTACCTTCGATGTTTTCAT-TTTAAGGG
1 GTGCATCGATGCACTACCAATGCATCGATACATC-AATTACATTCGATG-TTTCATCTTTAAAGA
* * * * *
55711 GTTGCATCGATGCACTTCTAATGCATCGATGCATCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACCAATGCATCGATACATCAATTACATTCGATGTTTCATCTTTAAAGA
55775 GTGCATCGATGCAC
1 GTGCATCGATGCAC
55789 ATTGAATATG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
63 19 0.29
64 46 0.70
65 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCAATGCATCGATACATCAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:58494 original size:14 final size:14
Alignment explanation
Indices: 58475--58502 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
58465 TTCAATCTGT
58475 TGTGGAATTATCTA
1 TGTGGAATTATCTA
58489 TGTGGAATTATCTA
1 TGTGGAATTATCTA
58503 CAACTGAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (14 bp):
TGTGGAATTATCTA
Found at i:59884 original size:2 final size:2
Alignment explanation
Indices: 59877--59923 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
59867 TGTCGTAAAT
59877 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59919 TA TA T
1 TA TA T
59924 TGTAAATGAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:68795 original size:38 final size:38
Alignment explanation
Indices: 68744--68821 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
68734 CGTGATTCTC
68744 TGGTGATGCATGTAATGTTCTCCATTTTCAATCTTCAT
1 TGGTGATGCATGTAATGTTCTCCATTTTCAATCTTCAT
*
68782 TGGTGATGCATGTAATGTTCTCCCTTTTCAATCTTCAT
1 TGGTGATGCATGTAATGTTCTCCATTTTCAATCTTCAT
68820 TG
1 TG
68822 TTTTCCATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (38 bp):
TGGTGATGCATGTAATGTTCTCCATTTTCAATCTTCAT
Found at i:73988 original size:21 final size:21
Alignment explanation
Indices: 73963--74004 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
73953 CATACAGGCA
73963 TGCAAATCTAAACAACCGAAC
1 TGCAAATCTAAACAACCGAAC
73984 TGCAAATCTAAACAACCGAAC
1 TGCAAATCTAAACAACCGAAC
74005 GCGGAGTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.29, G:0.10, T:0.14
Consensus pattern (21 bp):
TGCAAATCTAAACAACCGAAC
Done.