Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003553.1 Hibiscus syriacus cultivar Beakdansim tig00007498_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: 85636
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:463 original size:2 final size:2
Alignment explanation
Indices: 456--503 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
446 ACCAACAATA
456 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
498 AT AT AT
1 AT AT AT
504 TTTAATCTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7275 original size:15 final size:14
Alignment explanation
Indices: 7242--7275 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
7232 ATGCTTGTGA
7242 AGTAAATTGGTGGG
1 AGTAAATTGGTGGG
*
7256 TGTAAATTGGTTGGG
1 AGTAAATTGG-TGGG
7271 AGTAA
1 AGTAA
7276 GAGCTAACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.29, C:0.00, G:0.38, T:0.32
Consensus pattern (14 bp):
AGTAAATTGGTGGG
Found at i:13227 original size:12 final size:12
Alignment explanation
Indices: 13212--13240 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
13202 AGATTTTAAA
13212 AAATATTTTTTT
1 AAATATTTTTTT
13224 AAATA-TTTTTT
1 AAATATTTTTTT
13235 AAATAT
1 AAATAT
13241 ATATATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
AAATATTTTTTT
Found at i:14482 original size:2 final size:2
Alignment explanation
Indices: 14475--14522 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
14465 TATTGAATTA
14475 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14517 AT AT AT
1 AT AT AT
14523 GTTTTAAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14691 original size:32 final size:32
Alignment explanation
Indices: 14650--14711 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
14640 AAAGCTTAAG
14650 CTAATAGCATGCAACATATGCCATTGAATAAC
1 CTAATAGCATGCAACATATGCCATTGAATAAC
14682 CTAATAGCATGCAACATATGCCATTGAATA
1 CTAATAGCATGCAACATATGCCATTGAATA
14712 GCAGGTGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (32 bp):
CTAATAGCATGCAACATATGCCATTGAATAAC
Found at i:16154 original size:2 final size:2
Alignment explanation
Indices: 16087--16135 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
16077 GTCAGGTCAG
16087 TA TA TA TA TA 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 TA TA TA TA TA
16129 TA TA TA T
1 TA TA TA T
16136 GATTCATGGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30108 original size:26 final size:25
Alignment explanation
Indices: 30043--30108 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 25
30033 CATTTTAATC
30043 AAAATATTAATTATTATTAAAATATTT
1 AAAATA-TAA-TATTATTAAAATATTT
*
30070 AAAATAT-AT-TTATTAACAT-TTCT
1 AAAATATAATATTATTAAAATATT-T
30093 AATAATATAATATTAT
1 AA-AATATAATATTAT
30109 ATTTTTAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
22 2 0.06
23 12 0.35
24 6 0.18
25 3 0.09
26 5 0.15
27 6 0.18
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (25 bp):
AAAATATAATATTATTAAAATATTT
Found at i:30199 original size:31 final size:33
Alignment explanation
Indices: 30111--30199 Score: 89
Period size: 34 Copynumber: 2.8 Consensus size: 33
30101 AATATTATAT
*
30111 TTTTAAT-AT-TATAATAAAATAATCAATTTTA
1 TTTTAATAATATATAATAAAATTATCAATTTTA
* *
30142 TTATAATAATATA-ATATAAGATATTAT-ATTTTTA
1 TTTTAATAATATATA-ATAA-A-ATTATCAATTTTA
30176 TTTTAATAATATATAAT-AAATTAT
1 TTTTAATAATATATAATAAAATTAT
30200 TAATAAAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
31 11 0.23
32 4 0.08
33 7 0.15
34 21 0.44
35 5 0.10
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (33 bp):
TTTTAATAATATATAATAAAATTATCAATTTTA
Found at i:30288 original size:24 final size:24
Alignment explanation
Indices: 30211--30290 Score: 63
Period size: 27 Copynumber: 3.1 Consensus size: 24
30201 AATAAAATTT
* *
30211 ATATTATTTATTAATTTCATAGAAATA
1 ATATTATTTA-T-ATTTAATA-TAATA
*
30238 ATATTA-TTAAATTATTAATAATGAATA
1 ATATTATTTATA-T-TTAAT-AT-AATA
30265 ATATTATTTATATTTAATATAATA
1 ATATTATTTATATTTAATATAATA
30289 AT
1 AT
30291 CTAATAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
24 7 0.16
25 3 0.07
26 12 0.27
27 18 0.41
28 4 0.09
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (24 bp):
ATATTATTTATATTTAATATAATA
Found at i:30336 original size:34 final size:33
Alignment explanation
Indices: 30292--30372 Score: 96
Period size: 34 Copynumber: 2.5 Consensus size: 33
30282 TATAATAATC
30292 TAAT-AAATATACTAAT-TTATAATATTTTTATT
1 TAATAAAATATACTAATATTATAATATTTTTA-T
* * *
30324 TCAATAAAATATACCAATATTATTATTTTTTTAT
1 T-AATAAAATATACTAATATTATAATATTTTTAT
30358 TAATAAAAT-TACTAA
1 TAATAAAATATACTAA
30373 ATAATAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
32 6 0.14
33 11 0.26
34 13 0.31
35 12 0.29
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (33 bp):
TAATAAAATATACTAATATTATAATATTTTTAT
Found at i:30596 original size:15 final size:14
Alignment explanation
Indices: 30569--30602 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
30559 AAATATAATT
30569 CATTTTACGAAAAA
1 CATTTTACGAAAAA
*
30583 CATTTTTCGAAAAA
1 CATTTTACGAAAAA
30597 CATTTT
1 CATTTT
30603 CAGTGAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (14 bp):
CATTTTACGAAAAA
Found at i:40859 original size:29 final size:28
Alignment explanation
Indices: 40802--40859 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
40792 AATTGAAACG
* **
40802 AAAATTAAAGTTCAGTGTTATAATTGAT
1 AAAATTAAAGTTCAGTGGTATAAACGAT
*
40830 AAAATTAAAAGTTTAGTGGTATAAACGAT
1 AAAATT-AAAGTTCAGTGGTATAAACGAT
40859 A
1 A
40860 CAACTATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.34
Consensus pattern (28 bp):
AAAATTAAAGTTCAGTGGTATAAACGAT
Found at i:41118 original size:2 final size:2
Alignment explanation
Indices: 41111--41153 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
41101 TTGTCCTTAT
41111 TA TA TA TA TA 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 TA TA TA TA TA
41153 T
1 T
41154 TTATTTAACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46897 original size:42 final size:42
Alignment explanation
Indices: 46850--46975 Score: 144
Period size: 42 Copynumber: 3.0 Consensus size: 42
46840 CCGTGCAAGG
* * ** *
46850 TCAAGATCCAAATCAAAATCACCCCTTAGTTACCGGAGAAGA
1 TCAAGATCCAAGTCAAGATCACCAATTAGTTACAGGAGAAGA
* * *
46892 TCAAGATCCAAGTCAAGATCACCAATTATTTATAGGAGAAGG
1 TCAAGATCCAAGTCAAGATCACCAATTAGTTACAGGAGAAGA
* * * *
46934 TCAAGGTCCAAGTCAAGATCACCAATCAGTTATAGGCGAAGA
1 TCAAGATCCAAGTCAAGATCACCAATTAGTTACAGGAGAAGA
46976 AGGAGGTCTC
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (42 bp):
TCAAGATCCAAGTCAAGATCACCAATTAGTTACAGGAGAAGA
Found at i:47758 original size:45 final size:46
Alignment explanation
Indices: 47692--47873 Score: 240
Period size: 45 Copynumber: 4.2 Consensus size: 46
47682 TAAGAAATCT
* * *
47692 AAGCATC-GGGATAGAAGGCGGTCGAGGTCGAGATCTGCTGATGGC
1 AAGCATCAGCGATAGAAAGCGGTCAAGGTCGAGATCTGCTGATGGC
47737 AAGCATCAG-GATAGAAA---G-C--GGTCGAGATCTGCTGATGGC
1 AAGCATCAGCGATAGAAAGCGGTCAAGGTCGAGATCTGCTGATGGC
47776 AAGCATC-GCGATAGAAAGCGGTCAAGGTCGAGATCTGCTGATGGC
1 AAGCATCAGCGATAGAAAGCGGTCAAGGTCGAGATCTGCTGATGGC
* * *
47821 AAGCAT-TGTGATAGAAAGCGGTCAAGGTCAAGATCTGCTGATGGC
1 AAGCATCAGCGATAGAAAGCGGTCAAGGTCGAGATCTGCTGATGGC
47866 AAGCATCA
1 AAGCATCA
47874 CAGAGGAAGC
Statistics
Matches: 123, Mismatches: 4, Indels: 19
0.84 0.03 0.13
Matches are distributed among these distances:
38 1 0.01
39 35 0.28
41 1 0.01
42 2 0.02
43 1 0.01
45 82 0.67
46 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.34, T:0.19
Consensus pattern (46 bp):
AAGCATCAGCGATAGAAAGCGGTCAAGGTCGAGATCTGCTGATGGC
Found at i:47834 original size:84 final size:86
Alignment explanation
Indices: 47692--47872 Score: 260
Period size: 84 Copynumber: 2.1 Consensus size: 86
47682 TAAGAAATCT
* * *
47692 AAGCATCGGGATAGAAGGCGGTCGAGGTCGAGATCTGCTGATGGCAAGCATCAGGATAGAAAGCG
1 AAGCATCGCGATAGAAAGCGGTCAAGGTCGAGATCTGCTGATGGCAAGCATCAGGATAGAAAGCG
47757 GTC-G-AGATCTGCTGATGGC
66 GTCAGAAGATCTGCTGATGGC
*
47776 AAGCATCGCGATAGAAAGCGGTCAAGGTCGAGATCTGCTGATGGCAAGCAT-TGTGATAGAAAGC
1 AAGCATCGCGATAGAAAGCGGTCAAGGTCGAGATCTGCTGATGGCAAGCATCAG-GATAGAAAGC
47840 GGTCAAGGTCAAGATCTGCTGATGGC
65 GGTC-A-G--AAGATCTGCTGATGGC
47866 AAGCATC
1 AAGCATC
47873 ACAGAGGAAG
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
83 1 0.01
84 62 0.72
87 1 0.01
90 22 0.26
ACGTcount: A:0.29, C:0.18, G:0.34, T:0.19
Consensus pattern (86 bp):
AAGCATCGCGATAGAAAGCGGTCAAGGTCGAGATCTGCTGATGGCAAGCATCAGGATAGAAAGCG
GTCAGAAGATCTGCTGATGGC
Found at i:50193 original size:18 final size:18
Alignment explanation
Indices: 50167--50203 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
50157 TGGGTATGTG
50167 AATGAGTCGGATACGGAT
1 AATGAGTCGGATACGGAT
* *
50185 AATGTGTCGGATGCGGAT
1 AATGAGTCGGATACGGAT
50203 A
1 A
50204 TATAGACAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.11, G:0.35, T:0.24
Consensus pattern (18 bp):
AATGAGTCGGATACGGAT
Found at i:51502 original size:23 final size:23
Alignment explanation
Indices: 51476--51520 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
51466 TTCAGTCTCA
*
51476 AATCTCTTAAATTATTCTCATTG
1 AATCTCTTAAATTATTCCCATTG
51499 AATCTCTTAAATTATTCCCATT
1 AATCTCTTAAATTATTCCCATT
51521 TTCATATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.31, C:0.20, G:0.02, T:0.47
Consensus pattern (23 bp):
AATCTCTTAAATTATTCCCATTG
Found at i:51770 original size:17 final size:18
Alignment explanation
Indices: 51748--51788 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
51738 ATTAATATTG
51748 TTATG-TAA-ATTATTGAT
1 TTATGTTAAGATTATT-AT
51765 TTATGTTAATGATTATTAT
1 TTATGTTAA-GATTATTAT
51784 TTATG
1 TTATG
51789 CCACATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.24
18 3 0.14
19 7 0.33
20 6 0.29
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (18 bp):
TTATGTTAAGATTATTAT
Found at i:52155 original size:2 final size:2
Alignment explanation
Indices: 52148--52174 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52138 GTATAAAATT
52148 TA 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 TA T
52175 TTCTATTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58651 original size:24 final size:25
Alignment explanation
Indices: 58593--58655 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
58583 AGTTATTACT
*
58593 TCTGTCCTTTT-CTTTTTCTTTATC
1 TCTGTCCTTTTCCTTCTTCTTTATC
* *
58617 TCGGCCCTTTTCCTTCTT-TTTATC
1 TCTGTCCTTTTCCTTCTTCTTTATC
*
58641 TCTGTCTTTTTCCTT
1 TCTGTCCTTTTCCTT
58656 TTTGTCTTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 27 0.84
25 5 0.16
ACGTcount: A:0.03, C:0.29, G:0.06, T:0.62
Consensus pattern (25 bp):
TCTGTCCTTTTCCTTCTTCTTTATC
Found at i:60694 original size:17 final size:17
Alignment explanation
Indices: 60672--60706 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
60662 AAGAAACAAA
60672 ATAGTCCAGTAAAATCT
1 ATAGTCCAGTAAAATCT
60689 ATAGTCCAGTAAAATCT
1 ATAGTCCAGTAAAATCT
60706 A
1 A
60707 ACACGCTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (17 bp):
ATAGTCCAGTAAAATCT
Found at i:66859 original size:8 final size:8
Alignment explanation
Indices: 66846--66870 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
66836 GGCAAGAACA
66846 CCCAAAAC
1 CCCAAAAC
66854 CCCAAAAC
1 CCCAAAAC
66862 CCCAAAAC
1 CCCAAAAC
66870 C
1 C
66871 TATTCCACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (8 bp):
CCCAAAAC
Found at i:73643 original size:13 final size:13
Alignment explanation
Indices: 73625--73649 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
73615 GTCAATGGTT
73625 AACGGGTCGGGTA
1 AACGGGTCGGGTA
73638 AACGGGTCGGGT
1 AACGGGTCGGGT
73650 CGAAACCGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.48, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Done.