Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000994.1 Hibiscus syriacus cultivar Beakdansim tig00001988_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: 45462
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:803 original size:19 final size:19
Alignment explanation
Indices: 776--812 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
766 ATTAACATTT
*
776 TATAATATAATAATATATC
1 TATAATATAAGAATATATC
*
795 TATAGTATAAGAATATAT
1 TATAATATAAGAATATAT
813 TATTTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (19 bp):
TATAATATAAGAATATATC
Found at i:3043 original size:113 final size:112
Alignment explanation
Indices: 2591--3167 Score: 911
Period size: 112 Copynumber: 5.1 Consensus size: 112
2581 TTGTCAGTTT
* *
2591 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
*
2656 GGTATATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
** * *
2703 GTGTCGATACTTTATAAAAATGTATTTATCTATAACAATATAACAAGTAAAAAAATGACAAAACA
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
*
2768 GATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
2815 GTGTCGATACTTTATAAAAATGTATCTATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
* *
2880 GGTCTATAAATGACAAAACAGGTAAAACGCTACCAGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
2927 GTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAACGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGT-AAAAAAATGACAAAAC
* * * * *
2992 CGGTATATAAATGACAAAACAGATAAAGCGCTACCAGATATGTTGATA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
3040 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACAGGTAAAAAAAATGACAAAAT
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGT-AAAAAAATGACAAAAC
* * *
3105 CGGTCTATAAATGACAAAACAAGTAAAGCGCTACCGGATATGTTGATA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
3153 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
3168 TATAATTATC
Statistics
Matches: 435, Mismatches: 29, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
112 257 0.59
113 178 0.41
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:3364 original size:182 final size:182
Alignment explanation
Indices: 3039--3493 Score: 716
Period size: 182 Copynumber: 2.5 Consensus size: 182
3029 ATATGTTGAT
* *
3039 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACAGGTAAAAAAAATGACAAAA
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAATATGACAAAA
** * *
3104 TCGGTCT-ATAAATGACAAAACAAGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTAT
65 TCGGTCTCA-AAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTAT
* *
3168 TATAATTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCG-CTAATAA
129 TATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTC-AATAA
* * * *
3222 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAGTATGATAAAAC
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
*
3287 CGGTCTCAAAATGATAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTATTA
66 CGGTCTCAAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTATTA
3352 TAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTCAATAA
131 TAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTCAATAA
* *
3404 AATGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATAACAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
* *
3469 CGATCTCGAAATGACAAAACCGGTA
66 CGGTCTCAAAATGACAAAACCGGTA
3494 GTAAAAAAGT
Statistics
Matches: 248, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
182 199 0.80
183 49 0.20
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.28
Consensus pattern (182 bp):
AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
CGGTCTCAAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTATTA
TAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTCAATAA
Found at i:4452 original size:17 final size:17
Alignment explanation
Indices: 4424--4465 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
4414 GAACTTTAAA
*
4424 AAAATATAAAGAAATAGT
1 AAAAT-TAAAGAAAGAGT
*
4442 AAAATTAAAGAGAGAGT
1 AAAATTAAAGAAAGAGT
4459 AAAATTA
1 AAAATTA
4466 TAAAATGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (17 bp):
AAAATTAAAGAAAGAGT
Found at i:5892 original size:2 final size:2
Alignment explanation
Indices: 5880--5910 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
5870 CCAACTTTCT
5880 TC TC GTC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC -TC TC TC TC TC TC TC TC TC TC TC TC TC
5911 ATTTAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.00, C:0.48, G:0.03, T:0.48
Consensus pattern (2 bp):
TC
Found at i:9278 original size:11 final size:12
Alignment explanation
Indices: 9257--9289 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
9247 ATAAAAAAAA
*
9257 ATATGTATTTGT
1 ATATTTATTTGT
9269 -TATTTATTTGT
1 ATATTTATTTGT
9280 ATATTTATTT
1 ATATTTATTT
9290 CTAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (12 bp):
ATATTTATTTGT
Found at i:11730 original size:6 final size:6
Alignment explanation
Indices: 11720--11749 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
11710 AACAGGGGTT
*
11720 TGAAAT TGAAAC TGAAAC TGAAAC TGAAAC
1 TGAAAC TGAAAC TGAAAC TGAAAC TGAAAC
11750 AGAGTTTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (6 bp):
TGAAAC
Found at i:20748 original size:31 final size:30
Alignment explanation
Indices: 20656--20749 Score: 127
Period size: 30 Copynumber: 3.1 Consensus size: 30
20646 GAAGGACCTA
* * * *
20656 TCCAGAGGTCACACAGA-CCCCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
20685 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
20715 TCCAGAGGTCATAAAGGTCCTCGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
20746 TCCA
1 TCCA
20750 TATGTTCCTT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 15 0.26
30 34 0.59
31 9 0.16
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:20777 original size:31 final size:31
Alignment explanation
Indices: 20737--20837 Score: 132
Period size: 31 Copynumber: 3.2 Consensus size: 31
20727 AAAGGTCCTC
*
20737 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCATAGAACATA
* * *
20768 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCATAGAACATA
*
20799 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT-AAACTGTCCATATGTTCCATAGAACATA
20831 GGTAAAC
1 GGTAAAC
20838 CCTCGACTCT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
31 33 0.56
32 26 0.44
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCATAGAACATA
Found at i:21693 original size:21 final size:21
Alignment explanation
Indices: 21663--21707 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
21653 ATTCTATCGT
* *
21663 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
21684 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
21705 TTG
1 TTG
21708 CCCATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:24700 original size:31 final size:30
Alignment explanation
Indices: 24608--24701 Score: 127
Period size: 30 Copynumber: 3.1 Consensus size: 30
24598 GAAGGACCTA
* * * *
24608 TCCAGAGGTCACACAGA-CCCCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
24637 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
24667 TCCAGAGGTCATAAAGGTCCTCGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
24698 TCCA
1 TCCA
24702 TATGTTCCTT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 15 0.26
30 34 0.59
31 9 0.16
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:24729 original size:31 final size:31
Alignment explanation
Indices: 24689--24789 Score: 132
Period size: 31 Copynumber: 3.2 Consensus size: 31
24679 AAAGGTCCTC
*
24689 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCATAGAACATA
* * *
24720 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCATAGAACATA
*
24751 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT-AAACTGTCCATATGTTCCATAGAACATA
24783 GGTAAAC
1 GGTAAAC
24790 CCTCGACTCT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
31 33 0.56
32 26 0.44
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCATAGAACATA
Found at i:25566 original size:2 final size:2
Alignment explanation
Indices: 25559--25583 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25549 ATACAATTCC
25559 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
25584 CTAACTCATG
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:25670 original size:29 final size:29
Alignment explanation
Indices: 25616--25671 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
25606 TTTCTCTTGT
* *
25616 TATCATATAAATCATTGCCATATAACACA
1 TATCATATAAATCATTACCACATAACACA
*
25645 TATCATATAAATTCA-TACCACCTAACA
1 TATCATATAAA-TCATTACCACATAACA
25672 TGTAATACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.45, C:0.23, G:0.02, T:0.30
Consensus pattern (29 bp):
TATCATATAAATCATTACCACATAACACA
Found at i:26088 original size:21 final size:21
Alignment explanation
Indices: 26058--26102 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
26048 ATTCTGTCGT
* *
26058 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
26079 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
26100 TTG
1 TTG
26103 CCCGTAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:37172 original size:18 final size:17
Alignment explanation
Indices: 37132--37165 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
37122 TCTTGCAAAA
37132 ATTTTAAATTTTTATAT
1 ATTTTAAATTTTTATAT
*
37149 AATTTAAATATTTTATA
1 ATTTTAAAT-TTTTATA
37166 GTTTTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTAAATTTTTATAT
Done.