Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000415.1 Hibiscus syriacus cultivar Beakdansim tig00000762_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: 66459
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1128 original size:21 final size:22
Alignment explanation
Indices: 1093--1149 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
1083 ACTCAAAAAA
1093 ATTCAAGAGCTCAATTCAAGC-TC
1 ATTCAA-A-CTCAATTCAAGCTTC
* *
1116 ATTCAAACTCAATTTAAGCTTG
1 ATTCAAACTCAATTCAAGCTTC
*
1138 ATACAAACTCAA
1 ATTCAAACTCAA
1150 GTGCTCACCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 6 0.20
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (22 bp):
ATTCAAACTCAATTCAAGCTTC
Found at i:2394 original size:18 final size:18
Alignment explanation
Indices: 2371--2407 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2361 AACTTTAGTA
2371 CTAATGACTAAGGTACTC
1 CTAATGACTAAGGTACTC
2389 CTAATGACTAAGGTACTC
1 CTAATGACTAAGGTACTC
2407 C
1 C
2408 ATAACCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (18 bp):
CTAATGACTAAGGTACTC
Found at i:2820 original size:21 final size:21
Alignment explanation
Indices: 2796--2848 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2786 CATAATCAGA
*
2796 TTTAGATTTTAGGGTTTAAT-G
1 TTTAGAGTTTAGGGTTT-ATGG
* *
2817 TTTATAGTTTATGGTTTATGG
1 TTTAGAGTTTAGGGTTTATGG
2838 TTTAGAGTTTA
1 TTTAGAGTTTA
2849 AGATTTATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (21 bp):
TTTAGAGTTTAGGGTTTATGG
Found at i:2855 original size:21 final size:21
Alignment explanation
Indices: 2816--2856 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2806 AGGGTTTAAT
* * *
2816 GTTTATAGTTTATGGTTTATG
1 GTTTAGAGTTTAAGATTTATG
2837 GTTTAGAGTTTAAGATTTAT
1 GTTTAGAGTTTAAGATTTAT
2857 TGTAAAGACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (21 bp):
GTTTAGAGTTTAAGATTTATG
Found at i:2967 original size:21 final size:21
Alignment explanation
Indices: 2903--2968 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
2893 ATGAGGTAAG
* * *
2903 TATAATTTAGGGTTTATGGCT
1 TATAGTTTAGGGTTTAGGGTT
* *
2924 TATAGTTTAAGGTTTAGGATT
1 TATAGTTTAGGGTTTAGGGTT
2945 TATAGTTTAGGGTTTAGGGTT
1 TATAGTTTAGGGTTTAGGGTT
2966 TAT
1 TAT
2969 TGCAAGGACA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.24, C:0.02, G:0.26, T:0.48
Consensus pattern (21 bp):
TATAGTTTAGGGTTTAGGGTT
Found at i:4089 original size:30 final size:31
Alignment explanation
Indices: 4053--4114 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
4043 ACTCTTGATA
*
4053 TTTAGATATAATA-CTATTTTGATCA-TAAAC
1 TTTAGATATAATATC-ATTTTGACCACTAAAC
*
4083 TTTAGATGTAATATCATTTTGACCACTAAAC
1 TTTAGATATAATATCATTTTGACCACTAAAC
4114 T
1 T
4115 AAAGATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 21 0.75
31 7 0.25
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (31 bp):
TTTAGATATAATATCATTTTGACCACTAAAC
Found at i:15096 original size:14 final size:14
Alignment explanation
Indices: 15077--15105 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
15067 TAGTATTGAG
15077 TTTAGAAAAAATAC
1 TTTAGAAAAAATAC
15091 TTTAGAAAAAATAC
1 TTTAGAAAAAATAC
15105 T
1 T
15106 ACATATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (14 bp):
TTTAGAAAAAATAC
Found at i:23410 original size:118 final size:118
Alignment explanation
Indices: 23202--23438 Score: 449
Period size: 118 Copynumber: 2.0 Consensus size: 118
23192 TAGTCCTAGA
23202 ATTGATTGTTGTTGATGAGTTGACAAAGATAGATCCAACTATTAGATAGGAAACTAATAATGGGA
1 ATTGATTGTTGTTGATGAGTTGACAAAGATAGATCCAACTATTAGATAGGAAACTAATAATGGGA
23267 TTGACAGCGATCATGTCGAGAGACTATAGTACGAC-AAAGGACATAAAACTTCG
66 TTGACAGCGATCATGTCGAGAGACTATAGTACGACGAAA-GACATAAAACTTCG
*
23320 ATTGATTGTTGTTGATGAGTTGACAAAGATAGATCCAACTATTAGATAGTAAACTAATAATGGGA
1 ATTGATTGTTGTTGATGAGTTGACAAAGATAGATCCAACTATTAGATAGGAAACTAATAATGGGA
23385 TTGACAGCGATCATGTCGAGAGACTATAGTACGACGAAAGACATAAAACTTCG
66 TTGACAGCGATCATGTCGAGAGACTATAGTACGACGAAAGACATAAAACTTCG
23438 A
1 A
23439 AGGTTTTAAA
Statistics
Matches: 117, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
118 114 0.97
119 3 0.03
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (118 bp):
ATTGATTGTTGTTGATGAGTTGACAAAGATAGATCCAACTATTAGATAGGAAACTAATAATGGGA
TTGACAGCGATCATGTCGAGAGACTATAGTACGACGAAAGACATAAAACTTCG
Found at i:25647 original size:6 final size:6
Alignment explanation
Indices: 25636--25660 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
25626 CGGATGAGGC
25636 GGTGGA GGTGGA GGTGGA GGTGGA G
1 GGTGGA GGTGGA GGTGGA GGTGGA G
25661 AAGCTTGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.68, T:0.16
Consensus pattern (6 bp):
GGTGGA
Found at i:33458 original size:29 final size:29
Alignment explanation
Indices: 33422--33593 Score: 260
Period size: 29 Copynumber: 6.0 Consensus size: 29
33412 ACATTTACCG
*
33422 GGTGTTATTTTTGTAAATATTTTTAAAAA
1 GGTGTTATTTTCGTAAATATTTTTAAAAA
* *
33451 GGTTTTATTTTCGTAAATATTTTTAAAAT
1 GGTGTTATTTTCGTAAATATTTTTAAAAA
*
33480 GGTGTTATTTTCGTAAATATTTTTAAAAT
1 GGTGTTATTTTCGTAAATATTTTTAAAAA
33509 GGTGTTATTTTCGTAAATATTTTTAAAAA
1 GGTGTTATTTTCGTAAATATTTTTAAAAA
* *
33538 GATG-T-TTTT-GTAAATATTTTTAAAAG
1 GGTGTTATTTTCGTAAATATTTTTAAAAA
33564 GGTGTTATTTTCGTAAATATTTCTTAAAAA
1 GGTGTTATTTTCGTAAATATTT-TTAAAAA
33594 AAGGTGATAA
Statistics
Matches: 130, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
26 19 0.15
27 5 0.04
28 5 0.04
29 95 0.73
30 6 0.05
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (29 bp):
GGTGTTATTTTCGTAAATATTTTTAAAAA
Found at i:33576 original size:84 final size:88
Alignment explanation
Indices: 33422--33592 Score: 278
Period size: 84 Copynumber: 2.0 Consensus size: 88
33412 ACATTTACCG
* * * *
33422 GGTGTTATTTTTGTAAATATTTTTAAAAAGGTTTTATTTTCGTAAATATTTTTAAAATGGTGTTA
1 GGTGTTATTTTCGTAAATATTTTTAAAAAGGATGTATTTTCGTAAATATTTTTAAAAGGGTGTTA
33487 TTTTCGTAAATATTT-TTAAAAT
66 TTTTCGTAAATATTTCTTAAAAT
33509 GGTGTTATTTTCGTAAATATTTTTAAAAA-GATGT-TTTT-GTAAATATTTTTAAAAGGGTGTTA
1 GGTGTTATTTTCGTAAATATTTTTAAAAAGGATGTATTTTCGTAAATATTTTTAAAAGGGTGTTA
33571 TTTTCGTAAATATTTCTTAAAA
66 TTTTCGTAAATATTTCTTAAAA
33593 AAAGGTGATA
Statistics
Matches: 79, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
84 38 0.48
85 10 0.13
86 3 0.04
87 28 0.35
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (88 bp):
GGTGTTATTTTCGTAAATATTTTTAAAAAGGATGTATTTTCGTAAATATTTTTAAAAGGGTGTTA
TTTTCGTAAATATTTCTTAAAAT
Found at i:43379 original size:18 final size:19
Alignment explanation
Indices: 43356--43395 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
43346 TATATAAAAT
43356 ATCATTT-TCTTTATTTTC
1 ATCATTTCTCTTTATTTTC
*
43374 ATCATTTCTCTTTTTTTTC
1 ATCATTTCTCTTTATTTTC
43393 ATC
1 ATC
43396 TTCTTATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.65
Consensus pattern (19 bp):
ATCATTTCTCTTTATTTTC
Found at i:45705 original size:18 final size:17
Alignment explanation
Indices: 45682--45715 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
45672 ACGCTACTAG
45682 TGAACCGGTCAGAACCGC
1 TGAACCGGTCA-AACCGC
*
45700 TGAACCGTTCAAACCG
1 TGAACCGGTCAAACCG
45716 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.32, G:0.24, T:0.15
Consensus pattern (17 bp):
TGAACCGGTCAAACCGC
Found at i:45886 original size:16 final size:16
Alignment explanation
Indices: 45856--45886 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
45846 TTAAAAGTAA
*
45856 GCTTGAACTCGAAAAG
1 GCTTGAACTCAAAAAG
45872 GCTTGAACTCAAAAA
1 GCTTGAACTCAAAAA
45887 AAAATTTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (16 bp):
GCTTGAACTCAAAAAG
Found at i:50615 original size:12 final size:12
Alignment explanation
Indices: 50598--50628 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
50588 TTAACTAGTT
50598 TAATTAAACTAA
1 TAATTAAACTAA
*
50610 TAATTATACTAA
1 TAATTAAACTAA
50622 TAATTAA
1 TAATTAA
50629 GTCCTTGCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (12 bp):
TAATTAAACTAA
Done.