Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005897.1 Hibiscus syriacus cultivar Beakdansim tig00013848_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: 70922
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:857 original size:22 final size:21
Alignment explanation
Indices: 828--884 Score: 98
Period size: 21 Copynumber: 2.7 Consensus size: 21
818 TCAATTCGAG
828 TCAGTTTTT-GAGTCGAAAAAT
1 TCAGTTTTTCGAGTCG-AAAAT
849 TCAGTTTTTCGAGTCGAAAAT
1 TCAGTTTTTCGAGTCGAAAAT
870 TCAGTTTTTCGAGTC
1 TCAGTTTTTCGAGTC
885 AAGTCGAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 29 0.83
22 6 0.17
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.40
Consensus pattern (21 bp):
TCAGTTTTTCGAGTCGAAAAT
Found at i:11705 original size:10 final size:10
Alignment explanation
Indices: 11690--11715 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
11680 TTCTATAAAA
11690 TATATATAGT
1 TATATATAGT
11700 TATATATAGT
1 TATATATAGT
11710 TATATA
1 TATATA
11716 ATTTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (10 bp):
TATATATAGT
Found at i:12874 original size:3 final size:3
Alignment explanation
Indices: 12866--12893 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12856 AAAGGTGAGT
12866 CTC CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC C
12894 ACTTATCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:28606 original size:22 final size:22
Alignment explanation
Indices: 28578--28626 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
28568 TGTGATTGTA
*
28578 ATTTTTTGTTATAATTTGAGAT
1 ATTTTTTATTATAATTTGAGAT
28600 ATTTTTTATTATAATTTGAGAT
1 ATTTTTTATTATAATTTGAGAT
28622 ATTTT
1 ATTTT
28627 AATTGCTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (22 bp):
ATTTTTTATTATAATTTGAGAT
Found at i:29366 original size:17 final size:17
Alignment explanation
Indices: 29346--29389 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
29336 TGAAATTTAG
*
29346 TGGATTATTTTGATGTT
1 TGGAATATTTTGATGTT
29363 TGGAATATTTTGATGTT
1 TGGAATATTTTGATGTT
29380 TGGAATATTT
1 TGGAATATTT
29390 CATTCTCTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (17 bp):
TGGAATATTTTGATGTT
Found at i:37432 original size:65 final size:64
Alignment explanation
Indices: 37342--37521 Score: 193
Period size: 65 Copynumber: 2.8 Consensus size: 64
37332 TGGAATACTT
* * * ** *
37342 AGTGCATCGGTGCACCA-AGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAA-AATAGTCT
1 AGTGCATCGATGCA-TAGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAA-AACCC
*
37405 G
64 A
* * ** * *
37406 AGTGCATCGGGTGCATTGTTTGTGCATCGATACATGAAATGCATTCGATGTTTTAATAAAACCCA
1 AGTGCATC-GATGCATAGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
*
37471 AGTGCATCGATGCATAGAGAGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATAGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
37522 CAATTTATTC
Statistics
Matches: 96, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
64 45 0.47
65 49 0.51
66 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (64 bp):
AGTGCATCGATGCATAGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
Found at i:37539 original size:64 final size:64
Alignment explanation
Indices: 37427--37549 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 64
37417 TGCATTGTTT
* *
37427 GTGCATCGATACATGAAATGCATTCGATGTTTTAATAAAACCCAAGTGCATCGATGCATAGAGA
1 GTGCATCGATACATGAAATGCATTCGATGTTTCAATAAAACCAAAGTGCATCGATGCATAGAGA
* ** **
37491 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCAATAGTGCATCGATGCAT
1 GTGCATCGATACATGAAATGCATTCGATGTTTCAATAAAACCAA-AGTGCATCGATGCAT
37550 GCCTTTGAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 8 0.16
64 43 0.84
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (64 bp):
GTGCATCGATACATGAAATGCATTCGATGTTTCAATAAAACCAAAGTGCATCGATGCATAGAGA
Found at i:37922 original size:19 final size:20
Alignment explanation
Indices: 37884--37923 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
37874 TTTGAAATTA
*
37884 CTCCCCCTTACTATAACATTT
1 CTCCCCCTTA-TAAAACATTT
37905 CTCCCCCTT-TAAAACATTT
1 CTCCCCCTTATAAAACATTT
37924 TGCACTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.38
Consensus pattern (20 bp):
CTCCCCCTTATAAAACATTT
Found at i:39275 original size:44 final size:44
Alignment explanation
Indices: 39191--39293 Score: 138
Period size: 43 Copynumber: 2.3 Consensus size: 44
39181 AAAACCTGAC
* *
39191 GGATGCATCGATGCATGACCATGTGCATCGATGCACATTC-AAG
1 GGATGCATCGATGCATGAACATGTGAATCGATGCACATTCAAAG
* *
39234 GCG-TGCATCGGTGCATGAACATGATGAATCGATGCGCATTCAAAG
1 G-GATGCATCGATGCATGAACATG-TGAATCGATGCACATTCAAAG
39279 GGATGCATCGATGCA
1 GGATGCATCGATGCA
39294 CTGTTAAGTG
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
43 19 0.37
44 17 0.33
45 15 0.29
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.22
Consensus pattern (44 bp):
GGATGCATCGATGCATGAACATGTGAATCGATGCACATTCAAAG
Found at i:45145 original size:64 final size:63
Alignment explanation
Indices: 45077--45255 Score: 209
Period size: 64 Copynumber: 2.8 Consensus size: 63
45067 TGGAACACTT
* * ** **
45077 AGTGCATCGGTGCACCAAGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAA-AATAGTCTG
1 AGTGCATCGGTGCA-TAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAA-AACCCA
* *
45141 AGTGCATCGGTGCAT-TGCTTGTGCATCGATGCATGAAATGCATTCGATGTTTTAATAAAACCCA
1 AGTGCATCGGTGCATAAG--TGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
* *
45205 AGTGCATCGATGCATAGAGAGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGGTGCATA-AGTGTGCATCGATGCATGAAATGCATTCGATGTT
45256 CAATTTATTC
Statistics
Matches: 99, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
62 1 0.01
64 95 0.96
65 2 0.02
66 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (63 bp):
AGTGCATCGGTGCATAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
Found at i:45274 original size:64 final size:65
Alignment explanation
Indices: 45097--45283 Score: 195
Period size: 64 Copynumber: 2.9 Consensus size: 65
45087 TGCACCAAGT
* * * * * * **
45097 GTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAGTC--TGAGTGCATCGGTGCATTGCT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATATACTCAATG-GTGCATCGATGCATAGAG
*
45160 T
65 A
* * *
45161 GTGCATCGATGCATGAAATGCATTCGATGTTTTAATAAAACCCAA--GTGCATCGATGCATAGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAT-ATACTCAATGGTGCATCGATGCATAGAG
45224 A
65 A
* *
45225 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCAATGGTGCATCGATGCAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATATACTCAATGGTGCATCGATGCAT
45284 GCCTTTGAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
62 4 0.04
63 5 0.05
64 90 0.88
65 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATATACTCAATGGTGCATCGATGCATAGAGA
Found at i:53166 original size:21 final size:21
Alignment explanation
Indices: 53153--53225 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
53143 TATGTCATCT
53153 CCGCAGGGTTATATTCCTAGC
1 CCGCAGGGTTATATTCCTAGC
53174 CCGCAGGGTTATATTCCTAGC
1 CCGCAGGGTTATATTCCTAGC
* *
53195 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTATATTCCTAGC
*
53216 CTGCAGGGTT
1 CCGCAGGGTT
53226 TTATACCATA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
20 2 0.04
21 43 0.91
22 2 0.04
ACGTcount: A:0.18, C:0.30, G:0.26, T:0.26
Consensus pattern (21 bp):
CCGCAGGGTTATATTCCTAGC
Found at i:53811 original size:34 final size:34
Alignment explanation
Indices: 53738--53804 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
53728 AATAAATGTT
53738 TTTAAAACACAAATTATAGTATTCAAAATTTAAA
1 TTTAAAACACAAATTATAGTATTCAAAATTTAAA
* * *
53772 TTTAAAATATAAATTATAGTATTCGAAATTTAA
1 TTTAAAACACAAATTATAGTATTCAAAATTTAA
53805 CATTAAATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (34 bp):
TTTAAAACACAAATTATAGTATTCAAAATTTAAA
Found at i:54460 original size:127 final size:127
Alignment explanation
Indices: 54234--54813 Score: 1007
Period size: 127 Copynumber: 4.6 Consensus size: 127
54224 GCGCTTTAAA
*
54234 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
* *
54299 TAATGATAACATATTATCTGACAAAATAATGGAAGGCGCGCACCCGGGAACGCGCCTTCACG
66 TAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
* *
54361 GTCCCCTAAGGAATAATAGGTATTGACATAAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
54426 TAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
66 TAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
* * * * *
54488 GTCACCTAAGGAATAATATGTATTGACATAAATAGTTTTCGGGAGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
* *
54553 TAATGATAACATATTCTCTGACAAAATAATAGAAGGCGCGCCCCCGGGAACACGCCTTCACG
66 TAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
* *
54615 GTCCCCTAGGGAATAATAGGTATTGACATGAATAGTTATCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
* * *
54680 TAATGATAACATATTCTCTGACTAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCGTCACA
66 TAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
54742 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
54807 TAATGAT
66 TAATGAT
54814 GTAACATCCC
Statistics
Matches: 430, Mismatches: 23, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
127 430 1.00
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (127 bp):
GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
TAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
Found at i:56462 original size:31 final size:31
Alignment explanation
Indices: 56424--56548 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
56414 AGGGTCGAGG
56424 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
56455 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
56486 GTTTTCCTACGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
56517 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
56548 G
1 G
56549 GTCCTTCGGG
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:61016 original size:16 final size:16
Alignment explanation
Indices: 60995--61027 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
60985 GGTCAAATCG
60995 CCCAAAATGTGTGCAA
1 CCCAAAATGTGTGCAA
61011 CCCAAAATGTGTGCAA
1 CCCAAAATGTGTGCAA
61027 C
1 C
61028 TGAAGGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.18
Consensus pattern (16 bp):
CCCAAAATGTGTGCAA
Found at i:61901 original size:32 final size:31
Alignment explanation
Indices: 61837--61909 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 31
61827 CATATTAAGA
** *
61837 TTATTAAATTATTATAAAACGATTGTTTAATT
1 TTATTAAATTATTATAAAACGA-TCATTAAAT
61869 TTATTAAATTATTATAAAAC-AGTCATTAAAT
1 TTATTAAATTATTATAAAACGA-TCATTAAAT
*
61900 TTAATAAATT
1 TTATTAAATT
61910 CCACATTTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 16 0.44
32 20 0.56
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (31 bp):
TTATTAAATTATTATAAAACGATCATTAAAT
Found at i:67126 original size:23 final size:23
Alignment explanation
Indices: 67096--67147 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
67086 AACCCTAATT
67096 AAGCTTGTAAACATTTTTTCTCA
1 AAGCTTGTAAACATTTTTTCTCA
67119 AAGCTTGTAAACATTTTTTCTCA
1 AAGCTTGTAAACATTTTTTCTCA
67142 AAGCTT
1 AAGCTT
67148 TTGAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (23 bp):
AAGCTTGTAAACATTTTTTCTCA
Done.