Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000373.1 Hibiscus syriacus cultivar Beakdansim tig00000681_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: 59859
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:7224 original size:18 final size:17
Alignment explanation
Indices: 7201--7254 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 17
7191 ACATTTTTCA
7201 AAGATGATAGATATCTTC
1 AAGATGATAGAT-TCTTC
7219 AAGATGATAGATTCTTTTTC
1 AAGATGATAGATTC---TTC
7239 AAAGATGATAGATTCT
1 -AAGATGATAGATTCT
7255 CTTTTCAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 2 0.06
18 13 0.41
20 3 0.09
21 14 0.44
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (17 bp):
AAGATGATAGATTCTTC
Found at i:7921 original size:20 final size:20
Alignment explanation
Indices: 7892--7944 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
7882 CTCACAAATT
*
7892 TGTAAATCCTTCGGGTCATC
1 TGTAAGTCCTTCGGGTCATC
7912 TGTAAGTCCTTCGGGTCATC
1 TGTAAGTCCTTCGGGTCATC
*
7932 TGTAAGTCTTTCG
1 TGTAAGTCCTTCG
7945 AGCATGATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
TGTAAGTCCTTCGGGTCATC
Found at i:8219 original size:12 final size:13
Alignment explanation
Indices: 8202--8269 Score: 61
Period size: 14 Copynumber: 5.3 Consensus size: 13
8192 TGTTCGTTTT
8202 TATTATTA-ATTA
1 TATTATTATATTA
8214 TATTATTATTATTA
1 TATTATTA-TATTA
**
8228 TATTA-CGTATT-
1 TATTATTATATTA
*
8239 TATTATATATAATA
1 TATTAT-TATATTA
*
8253 TATTATTATATAA
1 TATTATTATATTA
8266 TATT
1 TATT
8270 TGCATTTACA
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
11 5 0.11
12 12 0.27
13 12 0.27
14 15 0.34
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (13 bp):
TATTATTATATTA
Found at i:8224 original size:18 final size:18
Alignment explanation
Indices: 8201--8261 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 18
8191 TTGTTCGTTT
8201 TTATTATTAATTATATTA
1 TTATTATTAATTATATTA
8219 TTATTATTATATTACGTATTTA
1 TTATTATTA-ATTA--TA-TTA
8241 TTA-TATATAA-TATATTA
1 TTATTAT-TAATTATATTA
8258 TTAT
1 TTAT
8262 ATAATATTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
17 6 0.16
18 11 0.30
19 4 0.11
20 2 0.05
21 6 0.16
22 8 0.22
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (18 bp):
TTATTATTAATTATATTA
Found at i:8264 original size:15 final size:14
Alignment explanation
Indices: 8239--8268 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
8229 ATTACGTATT
8239 TATTATATATAATA
1 TATTATATATAATA
8253 TATTATTATATAATA
1 TATTA-TATATAATA
8268 T
1 T
8269 TTGCATTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTATATATAATA
Found at i:15485 original size:2 final size:2
Alignment explanation
Indices: 15480--15506 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15470 TAATAAAAGA
15480 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
15507 GTTATAGAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20804 original size:3 final size:3
Alignment explanation
Indices: 20798--20904 Score: 142
Period size: 3 Copynumber: 35.7 Consensus size: 3
20788 AATAATAATA
*
20798 ATT ATT ATT ATT ATT ATT ATT ATT ATT CTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
20846 ATT ATT ATT ATT ATT ATT ATT ATT ATC ATC ATC ATC ATC ATC ATC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20894 ATT ATT ATT AT
1 ATT ATT ATT AT
20905 GTGTTTCATT
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 100 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:24286 original size:23 final size:24
Alignment explanation
Indices: 24248--24299 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
24238 ACCGAAGTGT
24248 CACATAGAATTTGTCCCGAAGGAC
1 CACATAGAATTTGTCCCGAAGGAC
* *
24272 CACATAG-ATTTGTCCTGAATGAC
1 CACATAGAATTTGTCCCGAAGGAC
24295 CACAT
1 CACAT
24300 GGAACCCCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (24 bp):
CACATAGAATTTGTCCCGAAGGAC
Found at i:28790 original size:23 final size:21
Alignment explanation
Indices: 28743--28822 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
28733 AGAACCCCAG
* ***
28743 GGGGGTATCGATTCCCCTGTG
1 GGGGGAATCGATTCCCCTCAA
28764 GGGGGAATCGATTCCCCTTCAAA
1 GGGGGAATCGATTCCCC-TC-AA
* *
28787 GGGGGAATCGGTT-CCCTCAT
1 GGGGGAATCGATTCCCCTCAA
*
28807 GGGGGGATCGATTCCC
1 GGGGGAATCGATTCCC
28823 TCTGCACCCA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 12 0.25
21 20 0.42
22 4 0.08
23 12 0.25
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
GGGGGAATCGATTCCCCTCAA
Found at i:28816 original size:20 final size:20
Alignment explanation
Indices: 28764--28824 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
28754 TTCCCCTGTG
*
28764 GGGGGAATCGATTCCCCTTCAAA
1 GGGGGAATCGATT-CCC-TC-AT
*
28787 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
28807 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
28825 TGCACCCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 12 0.35
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:32679 original size:22 final size:21
Alignment explanation
Indices: 32637--32676 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
32627 GAGTTTGTTT
*
32637 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
32658 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
32677 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:35733 original size:24 final size:27
Alignment explanation
Indices: 35688--35739 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 27
35678 TAAATTTTAT
* *
35688 TATTCAGTTTTGTTTTATTTTAGTCAC
1 TATTCAGTTTTGTTTGATTTTAGCCAC
35715 TATT-AGTTTT-TTTGA-TTTAGCCAC
1 TATTCAGTTTTGTTTGATTTTAGCCAC
35739 T
1 T
35740 GTTTTTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 9 0.39
25 4 0.17
26 6 0.26
27 4 0.17
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.58
Consensus pattern (27 bp):
TATTCAGTTTTGTTTGATTTTAGCCAC
Found at i:36560 original size:22 final size:23
Alignment explanation
Indices: 36532--36587 Score: 98
Period size: 22 Copynumber: 2.5 Consensus size: 23
36522 TATACCCACA
36532 GTACCGATACT-TCTCTTCTAAG
1 GTACCGATACTCTCTCTTCTAAG
36554 GTACCGATA-TCTCTCTTCTAAG
1 GTACCGATACTCTCTCTTCTAAG
36576 GTACCGATACTC
1 GTACCGATACTC
36588 ACTTCAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.03
22 29 0.91
23 2 0.06
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (23 bp):
GTACCGATACTCTCTCTTCTAAG
Found at i:36720 original size:14 final size:14
Alignment explanation
Indices: 36701--36732 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
36691 GTTCATACGG
36701 TTCAAACCATTTAT
1 TTCAAACCATTTAT
36715 TTCAAACCATTTAT
1 TTCAAACCATTTAT
36729 TTCA
1 TTCA
36733 GTACCAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.22, G:0.00, T:0.44
Consensus pattern (14 bp):
TTCAAACCATTTAT
Found at i:41746 original size:6 final size:6
Alignment explanation
Indices: 41735--41792 Score: 107
Period size: 6 Copynumber: 9.7 Consensus size: 6
41725 CTTAAAAAGA
41735 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
*
41783 AGAAGA AGAA
1 AGAAGG AGAA
41793 TTGGGGAGGA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:43628 original size:19 final size:18
Alignment explanation
Indices: 43592--43633 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
43582 AATATATAAC
*
43592 TTATCTTTAATTTCAATA
1 TTATTTTTAATTTCAATA
43610 TATATTTTTATATTT-AATA
1 T-TATTTTTA-ATTTCAATA
43629 TTATT
1 TTATT
43634 AATAAATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.24
19 12 0.57
20 4 0.19
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTTTTAATTTCAATA
Found at i:44427 original size:15 final size:15
Alignment explanation
Indices: 44409--44459 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
44399 CGATTATAAG
*
44409 ATATTACTTTATTAA
1 ATATTGCTTTATTAA
*
44424 ATATATGGTTTA-TAGA
1 ATAT-TGCTTTATTA-A
*
44440 ATATTGTTTTATTAA
1 ATATTGCTTTATTAA
44455 ATATT
1 ATATT
44460 TTGACTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 18 0.60
16 12 0.40
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (15 bp):
ATATTGCTTTATTAA
Found at i:45472 original size:14 final size:15
Alignment explanation
Indices: 45446--45487 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
45436 TATATGTAAT
45446 ACATAGTTTTTGAAA
1 ACATAGTTTTTGAAA
45461 ACATAG-TTTTGAAA
1 ACATAGTTTTTGAAA
45475 AC---GTTTTTGAAA
1 ACATAGTTTTTGAAA
45487 A
1 A
45488 TATGTATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 1 0.04
12 9 0.35
14 10 0.38
15 6 0.23
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (15 bp):
ACATAGTTTTTGAAA
Found at i:45534 original size:38 final size:37
Alignment explanation
Indices: 45463--45563 Score: 157
Period size: 38 Copynumber: 2.7 Consensus size: 37
45453 TTTTGAAAAC
*
45463 ATAGTTTTGAAAACGTTTTTGAAAATATGTATAATAT
1 ATAGTTTTGAAAACATTTTTGAAAATATGTATAATAT
45500 ATAGTTTTGAAAACATTTTTCGAAAATATGTATAATAT
1 ATAGTTTTGAAAACATTTTT-GAAAATATGTATAATAT
**
45538 ATAGTTTTTGAAAACCCTTTTGAAAA
1 ATAG-TTTTGAAAACATTTTTGAAAA
45564 CACACACACA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
37 19 0.32
38 26 0.44
39 14 0.24
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.42
Consensus pattern (37 bp):
ATAGTTTTGAAAACATTTTTGAAAATATGTATAATAT
Found at i:45594 original size:2 final size:2
Alignment explanation
Indices: 45583--45643 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
45573 ACACACACAC
*
45583 AT AT AC 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
45625 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
45644 GTTTTTGAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.