Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001864.1 Hibiscus syriacus cultivar Beakdansim tig00003772_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: 56122
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:532 original size:147 final size:147
Alignment explanation
Indices: 252--551 Score: 568
Period size: 147 Copynumber: 2.0 Consensus size: 147
242 CGAAGTGCCC
252 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
317 CATATACATATACTATGGATCAAGTGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATACA
66 CATATACATATACTATGGATCAAGTGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATACA
382 TATGTCCTAAAGAACCG
131 TATGTCCTAAAGAACCG
399 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
464 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTT-CAAAGGATATA
66 CATATACATATACTATGGATCAAG--TGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
528 -ATATGTCCTAAAGAACCG
129 CATATGTCCTAAAGAACCG
546 CGTAGA
1 CGTAGA
552 CCCTCTACCC
Statistics
Matches: 151, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
147 113 0.75
148 11 0.07
149 27 0.18
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (147 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTATGGATCAAGTGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATACA
TATGTCCTAAAGAACCG
Found at i:1145 original size:66 final size:67
Alignment explanation
Indices: 1017--1167 Score: 225
Period size: 66 Copynumber: 2.3 Consensus size: 67
1007 TTTTTCTCAT
* * *
1017 GGGGGAATCGGTTCCCCCCCTTGGGGGTATCGGTTCCCCTCTAGCATTCTAGAATTTCATATCCG
1 GGGGGTATCGGTT-CCCCCCTTGGGGGTATCGATTCCCCTCTAGCATTCTAGAAATTCATATCCG
1082 TTGA
65 -TGA
* *
1086 GGGGGTATCGGTTCCCCCC-TGGGGGTATCGATT-CCCTCTAGTATTCTGGAAATTCATATCCGT
1 GGGGGTATCGGTTCCCCCCTTGGGGGTATCGATTCCCCTCTAGCATTCTAGAAATTCATATCCGT
1149 GA
66 GA
1151 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
1168 TTGAATGGGT
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
65 20 0.26
66 26 0.34
67 13 0.17
68 6 0.08
69 12 0.16
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTTGGGGGTATCGATTCCCCTCTAGCATTCTAGAAATTCATATCCGT
GA
Found at i:2563 original size:24 final size:24
Alignment explanation
Indices: 2529--2580 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
2519 ATTTATTATC
*
2529 TAATTTTGCAC-CCCTAAAATTTT
1 TAATTTCGCACTCCCTAAAATTTT
*
2552 ATAATTTCGCACTCTCTAAAATTTT
1 -TAATTTCGCACTCCCTAAAATTTT
2577 TAAT
1 TAAT
2581 ATACTCTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (24 bp):
TAATTTCGCACTCCCTAAAATTTT
Found at i:11190 original size:16 final size:16
Alignment explanation
Indices: 11169--11219 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
11159 AATTTAATCG
11169 GTCAAATCAAATTCGA
1 GTCAAATCAAATTCGA
*
11185 GTCAAAT---ATT-TA
1 GTCAAATCAAATTCGA
*
11197 TTCAAATCAAATTCGA
1 GTCAAATCAAATTCGA
11213 GTCAAAT
1 GTCAAAT
11220 ATTTATTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
12 7 0.26
13 3 0.11
15 3 0.11
16 14 0.52
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (16 bp):
GTCAAATCAAATTCGA
Found at i:11210 original size:28 final size:28
Alignment explanation
Indices: 11170--11227 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
11160 ATTTAATCGG
11170 TCAAATCAAATTCGAGTCAAATATTTAT
1 TCAAATCAAATTCGAGTCAAATATTTAT
11198 TCAAATCAAATTCGAGTCAAATATTTAT
1 TCAAATCAAATTCGAGTCAAATATTTAT
11226 TC
1 TC
11228 TATGAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (28 bp):
TCAAATCAAATTCGAGTCAAATATTTAT
Found at i:22747 original size:17 final size:19
Alignment explanation
Indices: 22725--22761 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
22715 TATTAATTAA
22725 TTAATAATTT-A-TTTATT
1 TTAATAATTTGATTTTATT
*
22742 TTAATATTTTGATTTTATT
1 TTAATAATTTGATTTTATT
22761 T
1 T
22762 ATTTTACCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 1 0.06
19 7 0.41
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TTAATAATTTGATTTTATT
Found at i:44651 original size:2 final size:2
Alignment explanation
Indices: 44644--44675 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
44634 ATTACAAGTT
44644 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
44676 CTGATATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49236 original size:37 final size:37
Alignment explanation
Indices: 49181--49255 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
49171 ACTTACATAG
49181 CCCATCCGCGCAACCCTGTCCTTAGAAGGCAGGCCAT
1 CCCATCCGCGCAACCCTGTCCTTAGAAGGCAGGCCAT
*
49218 CCCATCCGCGCAAGCCTGTCCTTAGAAGGCAGGCCAT
1 CCCATCCGCGCAACCCTGTCCTTAGAAGGCAGGCCAT
49255 C
1 C
49256 TAAGCAATCG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.21, C:0.40, G:0.23, T:0.16
Consensus pattern (37 bp):
CCCATCCGCGCAACCCTGTCCTTAGAAGGCAGGCCAT
Found at i:49866 original size:89 final size:89
Alignment explanation
Indices: 49715--49886 Score: 265
Period size: 89 Copynumber: 1.9 Consensus size: 89
49705 TAACACACTA
* * * *
49715 TTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTATA-
1 TTTTATAGCCAAGTTACCCTAATCATATCAGGGGTTCTATTATTTCAAATTAATTAAATCTATAT
*
49779 TTAATTAATTAGAATTTAATAATCC
66 TTAATTAATT-GAAATTAATAATCC
* *
49804 TTTTATATCCAAGTTACCCTAATCATATCAGGGGTTCTATTATTTTAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATCAGGGGTTCTATTATTTCAAATTAATTAAATCTATAT
49869 TTAATTAATTGAAATTAA
66 TTAATTAATTGAAATTAA
49887 ATATTCGGGA
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
89 65 0.87
90 10 0.13
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (89 bp):
TTTTATAGCCAAGTTACCCTAATCATATCAGGGGTTCTATTATTTCAAATTAATTAAATCTATAT
TTAATTAATTGAAATTAATAATCC
Found at i:50151 original size:15 final size:17
Alignment explanation
Indices: 50131--50163 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
50121 GATTAACTCT
50131 TTTATGT-A-TTATATC
1 TTTATGTCATTTATATC
50146 TTTATGTCATTTATATC
1 TTTATGTCATTTATATC
50163 T
1 T
50164 AGAATAGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.24, C:0.09, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTATGTCATTTATATC
Found at i:53532 original size:66 final size:66
Alignment explanation
Indices: 53426--53614 Score: 324
Period size: 66 Copynumber: 2.9 Consensus size: 66
53416 TAGGGAGATG
* *
53426 CCTCCAAATCAGGGCATGCAGAATGCAGCAGGTGGAATGCCTCCAAACAATATGGGAGGTATGCA
1 CCTCCATACCAGGGCATGCAGAATGCAGCAGGTGGAATGCCTCCAAACAATATGGGAGGTATGCA
53491 T
66 T
53492 CCTCCATACCAGGGCATGCAGAATGCAGCAGGTGGAATGCCTCCAAACAATATGGGAGGTATGCA
1 CCTCCATACCAGGGCATGCAGAATGCAGCAGGTGGAATGCCTCCAAACAATATGGGAGGTATGCA
53557 T
66 T
* * * *
53558 CCTCCATACCAGGGCATGCAGAATGCAGCAGGAGGAATGCCACCCAACAACATGGGA
1 CCTCCATACCAGGGCATGCAGAATGCAGCAGGTGGAATGCCTCCAAACAATATGGGA
53615 AGGATGCCAC
Statistics
Matches: 117, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 117 1.00
ACGTcount: A:0.32, C:0.25, G:0.27, T:0.16
Consensus pattern (66 bp):
CCTCCATACCAGGGCATGCAGAATGCAGCAGGTGGAATGCCTCCAAACAATATGGGAGGTATGCA
T
Found at i:53621 original size:24 final size:24
Alignment explanation
Indices: 53594--53676 Score: 112
Period size: 24 Copynumber: 3.3 Consensus size: 24
53584 AGCAGGAGGA
53594 ATGCCACCCAACAACATGGGAAGG
1 ATGCCACCCAACAACATGGGAAGG
53618 ATGCCACCCAACAACATGGGAAGG
1 ATGCCACCCAACAACATGGGAAGG
* * *
53642 ATGCCACCACCAAGCAATACGGGAGGG
1 ATGCCA-C-CCAA-CAACATGGGAAGG
53669 ATGCCACC
1 ATGCCACC
53677 ACCAAACAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
24 30 0.57
25 2 0.04
26 5 0.09
27 16 0.30
ACGTcount: A:0.35, C:0.31, G:0.25, T:0.08
Consensus pattern (24 bp):
ATGCCACCCAACAACATGGGAAGG
Found at i:53651 original size:27 final size:27
Alignment explanation
Indices: 53597--53685 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 27
53587 AGGAGGAATG
53597 CCACCCAACAACATGGGAAGGATG---
1 CCACCCAACAACATGGGAAGGATGCCA
53621 CCACCCAACAACATGGGAAGGATGCCA
1 CCACCCAACAACATGGGAAGGATGCCA
* * *
53648 CCA-CCAAGCAATACGGGAGGGATGCCA
1 CCACCCAA-CAACATGGGAAGGATGCCA
*
53675 CCACCAAACAA
1 CCACCCAACAA
53686 TACGGGAGGG
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
24 24 0.43
26 4 0.07
27 25 0.45
28 3 0.05
ACGTcount: A:0.38, C:0.33, G:0.22, T:0.07
Consensus pattern (27 bp):
CCACCCAACAACATGGGAAGGATGCCA
Found at i:53686 original size:27 final size:27
Alignment explanation
Indices: 53621--53701 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 27
53611 GGGAAGGATG
* * * *
53621 CCACCCAACAACATGGGAAGGATGCCA
1 CCACCAAACAATACGGGAGGGATGCCA
*
53648 CCACCAAGCAATACGGGAGGGATGCCA
1 CCACCAAACAATACGGGAGGGATGCCA
*
53675 CCACCAAACAATACGGGAGGGCTGCCA
1 CCACCAAACAATACGGGAGGGATGCCA
53702 TCAAACAGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.35, C:0.32, G:0.26, T:0.07
Consensus pattern (27 bp):
CCACCAAACAATACGGGAGGGATGCCA
Done.