Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006535.1 Hibiscus syriacus cultivar Beakdansim tig00015950_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: 96922
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:4030 original size:24 final size:24
Alignment explanation
Indices: 3982--4030 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
3972 GGTACAAGTT
* *
3982 CCTTACATCAAGTGGCATCAGAAG
1 CCTTACATCAAGCGGAATCAGAAG
4006 CCTTACATCAAGCGGTAATCA-AAG
1 CCTTACATCAAGCGG-AATCAGAAG
4030 C
1 C
4031 TTTGGTGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (24 bp):
CCTTACATCAAGCGGAATCAGAAG
Found at i:6889 original size:11 final size:13
Alignment explanation
Indices: 6857--6886 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
6847 TGGCCAAAGA
6857 TGAAAAGGTATGT
1 TGAAAAGGTATGT
6870 TGAAAAGGTATG-
1 TGAAAAGGTATGT
6882 TGAAA
1 TGAAA
6887 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:14011 original size:14 final size:14
Alignment explanation
Indices: 13976--14013 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
13966 TTTTCATTGA
* *
13976 GACTAGGAAGTCTC
1 GACTAGGAGGGCTC
13990 GA-TAGGAGGGCTC
1 GACTAGGAGGGCTC
14003 GACTAGGAGGG
1 GACTAGGAGGG
14014 AGATCAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.26, C:0.16, G:0.42, T:0.16
Consensus pattern (14 bp):
GACTAGGAGGGCTC
Found at i:16918 original size:21 final size:21
Alignment explanation
Indices: 16892--16946 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
16882 TTTAAAGGAT
16892 TACCTTCGTAATAGGATGAAG
1 TACCTTCGTAATAGGATGAAG
* *
16913 TACCTTTGTAATAGGATGGAG
1 TACCTTCGTAATAGGATGAAG
16934 TACCTTCGTAATA
1 TACCTTCGTAATA
16947 TTCTCTGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.33
Consensus pattern (21 bp):
TACCTTCGTAATAGGATGAAG
Found at i:28428 original size:33 final size:33
Alignment explanation
Indices: 28386--28454 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
28376 GTTGATGAAT
*
28386 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
28419 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
28452 GAA
1 GAA
28455 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:32812 original size:33 final size:33
Alignment explanation
Indices: 32770--32838 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
32760 GTTGATGAAT
*
32770 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
32803 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
32836 GAA
1 GAA
32839 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:37354 original size:13 final size:13
Alignment explanation
Indices: 37332--37361 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
37322 ACTAAACACC
37332 TTTC-ACATACCT
1 TTTCAACATACCT
37344 TTTCAACATACCT
1 TTTCAACATACCT
37357 TTTCA
1 TTTCA
37362 TCTTTGGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:43267 original size:15 final size:15
Alignment explanation
Indices: 43247--43283 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
43237 AGAAGTATCA
43247 GGGTGACATAGATAG
1 GGGTGACATAGATAG
43262 GGGTGACATAGATAG
1 GGGTGACATAGATAG
43277 GGGTGAC
1 GGGTGAC
43284 GCCACAAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.30, C:0.08, G:0.43, T:0.19
Consensus pattern (15 bp):
GGGTGACATAGATAG
Found at i:47446 original size:33 final size:33
Alignment explanation
Indices: 47404--47472 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
47394 GTTGATGAAT
*
47404 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
47437 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
47470 GAA
1 GAA
47473 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:51384 original size:33 final size:33
Alignment explanation
Indices: 51342--51410 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
51332 GTTGATGAAT
*
51342 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
51375 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
51408 GAA
1 GAA
51411 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:55291 original size:33 final size:33
Alignment explanation
Indices: 55249--55317 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
55239 GTTGATGAAT
*
55249 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
55282 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
55315 GAA
1 GAA
55318 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:62477 original size:13 final size:15
Alignment explanation
Indices: 62454--62485 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
62444 CTTCTTTGCA
62454 TTTTCATTTCTTT-G
1 TTTTCATTTCTTTAG
62468 TTTT-ATTTCTTTAG
1 TTTTCATTTCTTTAG
62482 TTTT
1 TTTT
62486 TCTTCACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.75
Consensus pattern (15 bp):
TTTTCATTTCTTTAG
Found at i:65248 original size:90 final size:90
Alignment explanation
Indices: 65085--65262 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
65075 TAATCTCGAA
* * ** * *
65085 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATTCCTGATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
65150 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
*
65175 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATATTAAAAACCCTAATATGAC
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
*
65240 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
65263 GTGTGTTAGG
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.38
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
TAGGGTAACTTGGATATAAAAGGAT
Found at i:68087 original size:15 final size:14
Alignment explanation
Indices: 68069--68109 Score: 64
Period size: 14 Copynumber: 2.8 Consensus size: 14
68059 TTCAAAAAAA
68069 AAAAACAAAAAAGGC
1 AAAAA-AAAAAAGGC
68084 AAAAAAAAAAAGGC
1 AAAAAAAAAAAGGC
68098 AAAAAAACAAAA
1 AAAAAAA-AAAA
68110 AAAGAGCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Found at i:68088 original size:21 final size:21
Alignment explanation
Indices: 68063--68130 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
68053 TTGTTTTTCA
*
68063 AAAAAAAAAAACAAAAAAGGC
1 AAAAAAAAAAACAAAAAAGAC
68084 AAAAAAAAAAAGGCAAAAAA-AC
1 AAAAAAAAAAA--CAAAAAAGAC
* ** *
68106 AAAAAAAGAGCCAAAAAAGCC
1 AAAAAAAAAAACAAAAAAGAC
68127 AAAA
1 AAAA
68131 TTTCAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 7 0.18
21 16 0.41
22 9 0.23
23 7 0.18
ACGTcount: A:0.78, C:0.12, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAACAAAAAAGAC
Found at i:68089 original size:22 final size:22
Alignment explanation
Indices: 68061--68112 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
68051 TTTTGTTTTT
*
68061 CAAAAAAAAAAA-ACAAAAAAGG
1 CAAAAAAAAAAAGACAAAAAA-A
*
68083 CAAAAAAAAAAAGGCAAAAAAA
1 CAAAAAAAAAAAGACAAAAAAA
68105 CAAAAAAA
1 CAAAAAAA
68113 GAGCCAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.83, C:0.10, G:0.08, T:0.00
Consensus pattern (22 bp):
CAAAAAAAAAAAGACAAAAAAA
Found at i:68092 original size:23 final size:22
Alignment explanation
Indices: 68062--68112 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
68052 TTTGTTTTTC
*
68062 AAAAAAAAAAAACAAAAAAGGCA
1 AAAAAAAAAAAACAAAAAA-ACA
**
68085 AAAAAAAAAAGGCAAAAAAACA
1 AAAAAAAAAAAACAAAAAAACA
68107 AAAAAA
1 AAAAAA
68113 GAGCCAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAAACAAAAAAACA
Found at i:68130 original size:20 final size:20
Alignment explanation
Indices: 68086--68123 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
68076 AAAAAGGCAA
*
68086 AAAAAAAAAGGCAAAAAAAC
1 AAAAAAAAAGCCAAAAAAAC
*
68106 AAAAAAAGAGCCAAAAAA
1 AAAAAAAAAGCCAAAAAA
68124 GCCAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGCCAAAAAAAC
Found at i:76087 original size:24 final size:23
Alignment explanation
Indices: 76060--76114 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
76050 TTCAATTGGA
76060 ACATTCTTTTG-AATTTCAAGAGG
1 ACATTCTTTTGAAATTTCAA-AGG
*
76083 TACA-TCCTTTGAAATTTCAAAGG
1 -ACATTCTTTTGAAATTTCAAAGG
76106 ACATGTCTT
1 ACAT-TCTT
76115 GTGGATCACC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 3 0.12
23 9 0.35
24 14 0.54
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (23 bp):
ACATTCTTTTGAAATTTCAAAGG
Found at i:77379 original size:23 final size:22
Alignment explanation
Indices: 77339--77389 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
77329 TTACTTTTTC
* * *
77339 TTCTTTTTTGAGTTCTTTTAAT
1 TTCTTTTTTAAGTGCTTTGAAT
*
77361 TTCTTCTTTTAAGTGCTTTGATT
1 TTCTT-TTTTAAGTGCTTTGAAT
77384 TTCTTT
1 TTCTTT
77390 GCTAGATTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.12, C:0.12, G:0.10, T:0.67
Consensus pattern (22 bp):
TTCTTTTTTAAGTGCTTTGAAT
Found at i:79122 original size:15 final size:16
Alignment explanation
Indices: 79102--79135 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
79092 TATATTGGAA
*
79102 ATAAGAAATTAAA-GG
1 ATAAGAAATAAAATGG
79117 ATAAGAAATAAAATGG
1 ATAAGAAATAAAATGG
79133 ATA
1 ATA
79136 GAGATGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.62, C:0.00, G:0.18, T:0.21
Consensus pattern (16 bp):
ATAAGAAATAAAATGG
Found at i:79708 original size:19 final size:20
Alignment explanation
Indices: 79661--79711 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
79651 GAAACCCCTT
**
79661 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
79681 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
79700 TGAAGATACATG
1 TGAAAATACATG
79712 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:80664 original size:22 final size:23
Alignment explanation
Indices: 80620--80665 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
80610 TTGGTGTTGG
80620 AAACAAGATAAGAAATAAGATTA
1 AAACAAGATAAGAAATAAGATTA
80643 AAACAAGATAA-AGAA-AAGATTA
1 AAACAAGATAAGA-AATAAGATTA
80665 A
1 A
80666 TGAATTGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.67, C:0.04, G:0.13, T:0.15
Consensus pattern (23 bp):
AAACAAGATAAGAAATAAGATTA
Found at i:86603 original size:12 final size:13
Alignment explanation
Indices: 86580--86606 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
86570 TTTTTTGAAA
86580 TTTTGGCTTTTTT
1 TTTTGGCTTTTTT
86593 TTTTGGCTTTTTT
1 TTTTGGCTTTTTT
86606 T
1 T
86607 GGTTTTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.15, T:0.78
Consensus pattern (13 bp):
TTTTGGCTTTTTT
Found at i:86990 original size:22 final size:23
Alignment explanation
Indices: 86946--86991 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
86936 TTGGTGTTGG
86946 AAACAAGATAAGAAATAAGATTA
1 AAACAAGATAAGAAATAAGATTA
86969 AAACAAGATAA-AGAA-AAGATTA
1 AAACAAGATAAGA-AATAAGATTA
86991 A
1 A
86992 GGAATTGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.67, C:0.04, G:0.13, T:0.15
Consensus pattern (23 bp):
AAACAAGATAAGAAATAAGATTA
Found at i:90625 original size:19 final size:21
Alignment explanation
Indices: 90582--90633 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
90572 GAAACCCCTT
90582 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
90603 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
90622 TGAAGATACATG
1 TGAAAATACATG
90634 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:91583 original size:30 final size:31
Alignment explanation
Indices: 91543--91602 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
91533 ACATGCTGCC
**
91543 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
91574 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
91603 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:95748 original size:30 final size:31
Alignment explanation
Indices: 95708--95767 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
95698 ACATGCTGCC
**
95708 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
95739 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
95768 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Done.