Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003978.1 Hibiscus syriacus cultivar Beakdansim tig00008642_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: 46783
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:5158 original size:8 final size:8
Alignment explanation
Indices: 5146--5192 Score: 67
Period size: 8 Copynumber: 5.9 Consensus size: 8
5136 TACTTACGTT
*
5146 ATATATAT
1 ATATATAC
5154 ATATATAC
1 ATATATAC
5162 ATATATAC
1 ATATATAC
*
5170 ATACATAC
1 ATATATAC
*
5178 ATACATAC
1 ATATATAC
5186 ATATATA
1 ATATATA
5193 TGGATGCGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATATAC
Found at i:5165 original size:12 final size:12
Alignment explanation
Indices: 5145--5193 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
5135 TTACTTACGT
*
5145 TATATATATATA
1 TATACATATATA
5157 TATACATATATA
1 TATACATATATA
* *
5169 CATACATACATA
1 TATACATATATA
*
5181 CATACATATATA
1 TATACATATATA
5193 T
1 T
5194 GGATGCGATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (12 bp):
TATACATATATA
Found at i:6996 original size:2 final size:2
Alignment explanation
Indices: 6989--7014 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6979 CGTAATTTAA
6989 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
7015 TTCATGAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7975 original size:18 final size:19
Alignment explanation
Indices: 7952--7988 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
7942 TCAATAATCC
7952 TATTCTC-TGATAATCTTT
1 TATTCTCATGATAATCTTT
7970 TATTCTCATTGATAATCTT
1 TATTCTCA-TGATAATCTT
7989 ACATTTCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.24, C:0.16, G:0.05, T:0.54
Consensus pattern (19 bp):
TATTCTCATGATAATCTTT
Found at i:11284 original size:27 final size:27
Alignment explanation
Indices: 11251--11311 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
11241 GTTTCCTTAA
11251 GATCTATTCAGTGATGAATCCGAAGAT
1 GATCTATTCAGTGATGAATCCGAAGAT
*
11278 GATCTATTCAGTGATGAGTCCGAAGAT
1 GATCTATTCAGTGATGAATCCGAAGAT
11305 GATCTAT
1 GATCTAT
11312 GAATAAGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (27 bp):
GATCTATTCAGTGATGAATCCGAAGAT
Found at i:11715 original size:24 final size:24
Alignment explanation
Indices: 11688--11734 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
11678 TCCGATCTAA
*
11688 ATTCTATTCTGATA-TCTGACCTGG
1 ATTCTATTATGATATTC-GACCTGG
*
11712 ATTCTGTTATGATATTCGACCTG
1 ATTCTATTATGATATTCGACCTG
11735 AATTATGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (24 bp):
ATTCTATTATGATATTCGACCTGG
Found at i:11743 original size:24 final size:23
Alignment explanation
Indices: 11697--11753 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
11687 AATTCTATTC
* *
11697 TGATATCTGACCTGGATTCTGTT
1 TGATATCTGACCTGAATTATGTT
11720 ATGATAT-TCGACCTGAATTATGTT
1 -TGATATCT-GACCTGAATTATGTT
*
11744 TGATTTCTGA
1 TGATATCTGA
11754 TATCTCCGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 8 0.29
24 20 0.71
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (23 bp):
TGATATCTGACCTGAATTATGTT
Found at i:17084 original size:44 final size:44
Alignment explanation
Indices: 17021--17105 Score: 170
Period size: 44 Copynumber: 1.9 Consensus size: 44
17011 AAGCTGTGAA
17021 ACAACTTCAGATGGTGTAATTAAGTCCCGATTTTGGAGCAATTC
1 ACAACTTCAGATGGTGTAATTAAGTCCCGATTTTGGAGCAATTC
17065 ACAACTTCAGATGGTGTAATTAAGTCCCGATTTTGGAGCAA
1 ACAACTTCAGATGGTGTAATTAAGTCCCGATTTTGGAGCAA
17106 CAAATTAACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (44 bp):
ACAACTTCAGATGGTGTAATTAAGTCCCGATTTTGGAGCAATTC
Found at i:21509 original size:21 final size:21
Alignment explanation
Indices: 21476--21522 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
21466 AAGCCTCGGC
* * *
21476 TCTTCTTCATCGTCCTCTTCT
1 TCTTCATCATCGTCCACGTCT
*
21497 TCTTCATCGTCGTCCACGTCT
1 TCTTCATCATCGTCCACGTCT
21518 TCTTC
1 TCTTC
21523 TTCTTCTTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.06, C:0.38, G:0.09, T:0.47
Consensus pattern (21 bp):
TCTTCATCATCGTCCACGTCT
Found at i:23004 original size:2 final size:2
Alignment explanation
Indices: 22997--23024 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22987 TATGAAAAAG
22997 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
23025 TATGGTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24132 original size:12 final size:12
Alignment explanation
Indices: 24117--24159 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
24107 ATGTATATTT
*
24117 TATTATATTTAA
1 TATTTTATTTAA
*
24129 TATTTTA-TTAG
1 TATTTTATTTAA
24140 TATTTTATTTAA
1 TATTTTATTTAA
24152 CTATTTTA
1 -TATTTTA
24160 ATTTTTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 10 0.38
12 9 0.35
13 7 0.27
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (12 bp):
TATTTTATTTAA
Found at i:24133 original size:17 final size:18
Alignment explanation
Indices: 24111--24144 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
24101 TCTTTAATGT
24111 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
24128 ATATTTTATTAGTATTT
1 ATATTTTATTAGTATTT
24145 TATTTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:25605 original size:14 final size:14
Alignment explanation
Indices: 25586--25641 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
25576 CGTTCGTGAA
25586 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
25600 CGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
25613 --TT-GTTTATGTT
1 CGTTCGATTATGTT
25624 CGTTCGATTATGTT
1 CGTTCGATTATGTT
25638 CGTT
1 CGTT
25642 TATGTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 3 0.09
13 3 0.09
14 23 0.66
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:25620 original size:24 final size:24
Alignment explanation
Indices: 25593--25662 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
25583 GAACGTTCGA
*
25593 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGATTATGTTTGT
*
25617 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTTGT
*
25641 TTATGTTCATTC-ATTTATGTTT
1 TTATGTTCGTTCGA-TTATGTTT
25663 AACTCAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTTGT
Found at i:26403 original size:10 final size:10
Alignment explanation
Indices: 26388--26462 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
26378 GGGTCTCCAA
26388 CGTTTATGTT
1 CGTTTATGTT
26398 CGTTTATGTT
1 CGTTTATGTT
26408 CGTATTCAT-TT
1 CGT-TT-ATGTT
* **
26419 ATGTTCGTGTT
1 -CGTTTATGTT
26430 CGTTTATGTT
1 CGTTTATGTT
26440 CG----TGTT
1 CGTTTATGTT
26446 CGTTTATGTT
1 CGTTTATGTT
26456 CGTTTAT
1 CGTTTAT
26463 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.11, C:0.12, G:0.20, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:26421 original size:16 final size:16
Alignment explanation
Indices: 26394--26466 Score: 96
Period size: 16 Copynumber: 4.7 Consensus size: 16
26384 CCAACGTTTA
*
26394 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
*
26410 TATTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
26426 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
*
26442 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
26458 T-TT-ATTTAT
1 TGTTCATTTAT
26467 TAAATGAACG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 45 0.87
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:26435 original size:32 final size:32
Alignment explanation
Indices: 26394--26458 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
26384 CCAACGTTTA
26394 TGTTCGTTTATGTTCGTATTCATTTATGTTCG
1 TGTTCGTTTATGTTCGTATTCATTTATGTTCG
* *
26426 TGTTCGTTTATGTTCGTGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCGTATTCATTTATGTTCG
26458 T
1 T
26459 TTATTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.57
Consensus pattern (32 bp):
TGTTCGTTTATGTTCGTATTCATTTATGTTCG
Found at i:26549 original size:16 final size:16
Alignment explanation
Indices: 26528--26560 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
26518 AAAAAAAATT
26528 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
26544 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
26560 T
1 T
26561 CTATTTATTA
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:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:31322 original size:39 final size:39
Alignment explanation
Indices: 31257--31355 Score: 135
Period size: 39 Copynumber: 2.5 Consensus size: 39
31247 TAATTGCATG
* * *
31257 AAGGCGCGGCCCATGCTCCGCTTTATACCTTACGTGACAT
1 AAGGCGCGG-CCATGCACCGCGTTATACCCTACGTGACAT
*
31297 AAGGCGCGGCCATGCACCGCGTTATACCCTACGTGGCAT
1 AAGGCGCGGCCATGCACCGCGTTATACCCTACGTGACAT
*
31336 AAGGCGCGCCCTATGCACCG
1 AAGGCGCGGCC-ATGCACCG
31356 TGTCTTAGCC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
39 36 0.68
40 17 0.32
ACGTcount: A:0.20, C:0.34, G:0.26, T:0.19
Consensus pattern (39 bp):
AAGGCGCGGCCATGCACCGCGTTATACCCTACGTGACAT
Found at i:43935 original size:15 final size:15
Alignment explanation
Indices: 43907--43984 Score: 93
Period size: 15 Copynumber: 5.2 Consensus size: 15
43897 ATTTATATAA
* *
43907 GAATATGTTATATGC
1 GAATATGTTCTATGT
43922 GAATATGTTCTATGT
1 GAATATGTTCTATGT
* *
43937 GAAAATGTTTTATGT
1 GAATATGTTCTATGT
* *
43952 GAATATGTACTAAGT
1 GAATATGTTCTATGT
*
43967 GAATATGTTCAATGT
1 GAATATGTTCTATGT
43982 GAA
1 GAA
43985 CAAATGATAC
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 52 1.00
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.40
Consensus pattern (15 bp):
GAATATGTTCTATGT
Found at i:45777 original size:26 final size:27
Alignment explanation
Indices: 45713--45778 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 27
45703 CCTTTTTTTT
*
45713 TCAAAGTCAACAGTTAACTGTTAGACTGG
1 TCAAAGTCAACAGTTAACGGTTAGA--GG
*
45742 TCAAATTCAACAGTTAACGGGTT-G-GG
1 TCAAAGTCAACAGTTAAC-GGTTAGAGG
45768 TCAAAGTCAAC
1 TCAAAGTCAAC
45779 GGTCATATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 12 0.36
29 18 0.55
30 3 0.09
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (27 bp):
TCAAAGTCAACAGTTAACGGTTAGAGG
Done.