Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007301.1 Hibiscus syriacus cultivar Beakdansim tig00019433_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: 57223
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:9343 original size:21 final size:21
Alignment explanation
Indices: 9316--9375 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
9306 CGTCCGAGTT
9316 ACCCGCGACGGCCGCAATAGC
1 ACCCGCGACGGCCGCAATAGC
* ** *
9337 ATCCGCGGTGGCCGTAATAGC
1 ACCCGCGACGGCCGCAATAGC
*
9358 GCCCGCGACGGCCGCAAT
1 ACCCGCGACGGCCGCAAT
9376 CACGGTAAAT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.38, G:0.32, T:0.10
Consensus pattern (21 bp):
ACCCGCGACGGCCGCAATAGC
Found at i:29696 original size:26 final size:26
Alignment explanation
Indices: 29666--29731 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
29656 ATTGCTGAGT
29666 TCGACTCGAAAACTCTGAAATGGAGC
1 TCGACTCGAAAACTCTGAAATGGAGC
*
29692 TCGACTCGAACACTCTGAAATGGAGC
1 TCGACTCGAAAACTCTGAAATGGAGC
29718 TCGACTCGAAAACT
1 TCGACTCGAAAACT
29732 TGCGAGCTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (26 bp):
TCGACTCGAAAACTCTGAAATGGAGC
Found at i:31490 original size:32 final size:32
Alignment explanation
Indices: 31449--31509 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
31439 AAATAATACC
31449 CTATTCACGATGGGTTGAGATAATTATACACT
1 CTATTCACGATGGGTTGAGATAATTATACACT
31481 CTATTCACGATGGGTTGAGATAATTATAC
1 CTATTCACGATGGGTTGAGATAATTATAC
31510 TTTAGAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (32 bp):
CTATTCACGATGGGTTGAGATAATTATACACT
Found at i:32629 original size:2 final size:2
Alignment explanation
Indices: 32622--32666 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
32612 GAAAGCAAGC
32622 AT 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 AT
32664 AT A
1 AT A
32667 GAGAAAAGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42565 original size:29 final size:29
Alignment explanation
Indices: 42532--42616 Score: 134
Period size: 29 Copynumber: 2.9 Consensus size: 29
42522 TCCCCAAGCA
*
42532 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
* * *
42561 TAGGTCGCAATGCAATCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
42590 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
42617 ACCCTTGCTC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.15, C:0.34, G:0.29, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:42704 original size:14 final size:14
Alignment explanation
Indices: 42685--42730 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
42675 CTCACATAAT
42685 TCGGTCGGATGGCC
1 TCGGTCGGATGGCC
*
42699 TCGGTCGGATGCCC
1 TCGGTCGGATGGCC
*
42713 TTGGTCGGATGGCC
1 TCGGTCGGATGGCC
42727 TCGG
1 TCGG
42731 ATGCTCTCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.07, C:0.28, G:0.41, T:0.24
Consensus pattern (14 bp):
TCGGTCGGATGGCC
Found at i:42732 original size:10 final size:11
Alignment explanation
Indices: 42717--42765 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 11
42707 ATGCCCTTGG
42717 TCGGATGGC-C
1 TCGGATGGCTC
42727 TCGGAT-GCTC
1 TCGGATGGCTC
* *
42737 TCGCATAGCTTC
1 TCGGATGGC-TC
42749 TCGGATGGC-C
1 TCGGATGGCTC
42759 TCGGATG
1 TCGGATG
42766 CCCACCGTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 2 0.06
10 20 0.61
11 2 0.06
12 9 0.27
ACGTcount: A:0.12, C:0.29, G:0.33, T:0.27
Consensus pattern (11 bp):
TCGGATGGCTC
Found at i:42904 original size:29 final size:29
Alignment explanation
Indices: 42862--42917 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
42852 CCCCAACACA
**
42862 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCCAGCGACCTTG
42891 TAGGTCGCCATGCCCTCCCAGCGACCT
1 TAGGTCGCCATGCCCTCCCAGCGACCT
42918 ACGACAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.12, C:0.41, G:0.27, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCCAGCGACCTTG
Found at i:44913 original size:9 final size:9
Alignment explanation
Indices: 44901--44929 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
44891 TAATTTTAAG
44901 TTTTTTTCT
1 TTTTTTTCT
44910 TTTTTTTCT
1 TTTTTTTCT
44919 TTTTTTTCT
1 TTTTTTTCT
44928 TT
1 TT
44930 GCACTTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:50898 original size:13 final size:13
Alignment explanation
Indices: 50876--50909 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
50866 GTGTCCTCTA
50876 TTTTTCTCTTCTTC
1 TTTTT-TCTTCTTC
50890 TTTTTTCTTCTTC
1 TTTTTTCTTCTTC
50903 TTTTTTC
1 TTTTTTC
50910 ACCCTCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTCTTCTTC
Found at i:51097 original size:28 final size:27
Alignment explanation
Indices: 51048--51106 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
51038 ATACTTAAAA
* * * *
51048 TAAATTATTTTTTTTCATTTAAGCACC
1 TAAAGTATTTTTTTTAAATTAAACACC
*
51075 TAAAGTATTTTTTATTAAATTAAATACC
1 TAAAGTATTTTTT-TTAAATTAAACACC
51103 TAAA
1 TAAA
51107 ATCATCTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.47
Consensus pattern (27 bp):
TAAAGTATTTTTTTTAAATTAAACACC
Found at i:51166 original size:29 final size:30
Alignment explanation
Indices: 51130--51198 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
51120 TCAAAATAGG
51130 TACCTAAAGTTTTCAA-TCTTTAATCTAAA
1 TACCTAAAGTTTTCAATTCTTTAATCTAAA
*
51159 TACCTAAAGTTTTCAATTTTTTAATCTAAA
1 TACCTAAAGTTTTCAATTCTTTAATCTAAA
51189 TACCTAAAGT
1 TACCTAAAGT
51199 ATTCTTTAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 16 0.42
30 22 0.58
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (30 bp):
TACCTAAAGTTTTCAATTCTTTAATCTAAA
Found at i:55411 original size:80 final size:81
Alignment explanation
Indices: 55320--55481 Score: 206
Period size: 81 Copynumber: 2.0 Consensus size: 81
55310 GTAGAAAAAT
* * * * * *
55320 AACATTTTAGGT-GACGCCCAATATTAATA-TTTCTTGTAG-AAAAAAATAATGTTTTAGGTAGC
1 AACATTATAGGTAG-CGCACAATATTAACATTTTC-GGTAGAAAAAAAATAATATTTTAGGTAAC
*
55382 GTTTTACCTG-AAATGTTA
64 GCTTTA-CTGAAAATGTTA
55400 AACATTATAGGTAGCGCACAATATTAACATTTTCGGTAGAAAAAAAATAATATTTTAGGTAACGC
1 AACATTATAGGTAGCGCACAATATTAACATTTTCGGTAGAAAAAAAATAATATTTTAGGTAACGC
55465 TTTACTGAAAATGTTA
66 TTTACTGAAAATGTTA
55481 A
1 A
55482 TATTTTTATT
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
80 31 0.44
81 40 0.56
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (81 bp):
AACATTATAGGTAGCGCACAATATTAACATTTTCGGTAGAAAAAAAATAATATTTTAGGTAACGC
TTTACTGAAAATGTTA
Found at i:56671 original size:29 final size:29
Alignment explanation
Indices: 56605--56732 Score: 165
Period size: 29 Copynumber: 4.5 Consensus size: 29
56595 TTTCATTTAA
* *
56605 GTACCT-AAGTA-TTTTTGGTCAAAATAA
1 GTACCTAAAGTATTTTTTGATCAAAATAG
*
56632 GTACCTAAAAGTATATTTTGATCAAAATAG
1 GTACCT-AAAGTATTTTTTGATCAAAATAG
*
56662 GTACCTAAAGTCTTTTTTGATC-AAATAG
1 GTACCTAAAGTATTTTTTGATCAAAATAG
*
56690 G-ACCTAAAGTATTTTTTGATCAAAATAT
1 GTACCTAAAGTATTTTTTGATCAAAATAG
*
56718 GTACCTAAAGCATTT
1 GTACCTAAAGTATTT
56733 AATTTCTTTT
Statistics
Matches: 88, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
27 25 0.28
28 13 0.15
29 31 0.35
30 19 0.22
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (29 bp):
GTACCTAAAGTATTTTTTGATCAAAATAG
Found at i:56710 original size:56 final size:59
Alignment explanation
Indices: 56616--56727 Score: 167
Period size: 56 Copynumber: 1.9 Consensus size: 59
56606 TACCTAAGTA
* *
56616 TTTTTGGTCAAAATAAGTACCTAAAAGTATATTTTGATCAAAATAGGTACCTAAAGTCT
1 TTTTTGATCAAAATAAGGACCTAAAAGTATATTTTGATCAAAATAGGTACCTAAAGTCT
* *
56675 TTTTTGATC-AAAT-AGGACCT-AAAGTATTTTTTGATCAAAATATGTACCTAAAG
1 TTTTTGATCAAAATAAGGACCTAAAAGTATATTTTGATCAAAATAGGTACCTAAAG
56728 CATTTAATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 31 0.63
57 6 0.12
58 4 0.08
59 8 0.16
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (59 bp):
TTTTTGATCAAAATAAGGACCTAAAAGTATATTTTGATCAAAATAGGTACCTAAAGTCT
Done.