Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006549.1 Hibiscus syriacus cultivar Beakdansim tig00016003_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: 70890
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:2212 original size:13 final size:13
Alignment explanation
Indices: 2190--2219 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2180 ACTAAACACC
2190 TTTC-ACATACCT
1 TTTCAACATACCT
2202 TTTCAACATACCT
1 TTTCAACATACCT
2215 TTTCA
1 TTTCA
2220 TCTTTGGCCA
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:13906 original size:24 final size:21
Alignment explanation
Indices: 13872--13914 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
13862 TCCACAAGAT
*
13872 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
13894 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
13915 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:19541 original size:11 final size:13
Alignment explanation
Indices: 19509--19538 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
19499 TGGCCAAAGA
19509 TGAAAAGGTATGT
1 TGAAAAGGTATGT
19522 TGAAAAGGTATG-
1 TGAAAAGGTATGT
19534 TGAAA
1 TGAAA
19539 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:22180 original size:28 final size:26
Alignment explanation
Indices: 22148--22204 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
22138 TCAGAAAAAA
* *
22148 AAAGAAATTGAAGCACTCCAAAAGAAAG
1 AAAGAAAATCAAGCACT-CAAAAG-AAG
*
22176 AAAGAAAATCCAGCACTCAAAAGAAG
1 AAAGAAAATCAAGCACTCAAAAGAAG
22202 AAA
1 AAA
22205 AAGCAAGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 6 0.23
27 6 0.23
28 14 0.54
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.09
Consensus pattern (26 bp):
AAAGAAAATCAAGCACTCAAAAGAAG
Found at i:28656 original size:23 final size:25
Alignment explanation
Indices: 28630--28684 Score: 87
Period size: 23 Copynumber: 2.3 Consensus size: 25
28620 AAATCCAGCA
28630 AAGAAAATGAAAGCACTCAAA-A-G
1 AAGAAAATGAAAGCACTCAAAGAGG
*
28653 AAGAAATTGAAAGCACTCAAAGAGG
1 AAGAAAATGAAAGCACTCAAAGAGG
28678 AAGAAAA
1 AAGAAAA
28685 AAAAGAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 20 0.71
24 1 0.04
25 7 0.25
ACGTcount: A:0.60, C:0.11, G:0.20, T:0.09
Consensus pattern (25 bp):
AAGAAAATGAAAGCACTCAAAGAGG
Found at i:28697 original size:14 final size:14
Alignment explanation
Indices: 28678--28711 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
28668 CTCAAAGAGG
28678 AAGAAAA-AAAAGAA
1 AAGAAAAGAAAAG-A
28692 AAGAAAAGAAAAGA
1 AAGAAAAGAAAAGA
28706 AAGAAA
1 AAGAAA
28712 GTTGAAGCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAGAAAAGAAAAGA
Found at i:28712 original size:4 final size:5
Alignment explanation
Indices: 28678--28711 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
28668 CTCAAAGAGG
28678 AAGAA AA-AA AAGAA AAGAA AAGAA AAG-A AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
28712 GTTGAAGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 8 0.30
5 19 0.70
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:46276 original size:33 final size:33
Alignment explanation
Indices: 46234--46302 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
46224 GTTGATGAAT
*
46234 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
46267 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
46300 GAA
1 GAA
46303 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:52402 original size:91 final size:91
Alignment explanation
Indices: 52247--52429 Score: 294
Period size: 91 Copynumber: 2.0 Consensus size: 91
52237 GGTAGTTGAT
52247 GCTTGGCCAAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
1 GCTTGGCCAAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
*
52312 GGGGCTGATCACATGCAAAACACATG
66 GAGGCTGATCACATGCAAAACACATG
* * *
52338 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCACATGCAAGGCACATG
1 GCTTGGCCAAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
* * **
52403 GAGGCTGGTCATATGCAAGGCACATG
66 GAGGCTGATCACATGCAAAACACATG
52429 G
1 G
52430 GTGTTCTAGG
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (91 bp):
GCTTGGCCAAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATG
GAGGCTGATCACATGCAAAACACATG
Found at i:54179 original size:24 final size:21
Alignment explanation
Indices: 54144--54186 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
54134 GGCACATTCT
*
54144 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
54167 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
54187 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:58188 original size:23 final size:23
Alignment explanation
Indices: 58160--58280 Score: 83
Period size: 23 Copynumber: 5.1 Consensus size: 23
58150 ACAATCTGTC
*
58160 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCACC-ATAT
58183 CATCACCA-TAGTCTATCACCAT-T
1 CATCACCATTA-TC-ATCACCATAT
*
58206 -ATCACGCCTATATCATCACCATATT
1 CATCAC-CAT-TATCATCACCATA-T
*
58231 CCATCACCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
58255 CATCACCA-TATTCCATCACCATAT
1 CATCACCATTA-T-CATCACCATAT
58279 CA
1 CA
58281 CGCCTATATT
Statistics
Matches: 79, Mismatches: 5, Indels: 27
0.71 0.05 0.24
Matches are distributed among these distances:
22 9 0.11
23 29 0.37
24 17 0.22
25 17 0.22
26 2 0.03
27 5 0.06
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (23 bp):
CATCACCATTATCATCACCATAT
Found at i:58208 original size:36 final size:36
Alignment explanation
Indices: 58158--58297 Score: 246
Period size: 36 Copynumber: 3.9 Consensus size: 36
58148 ATACAATCTG
*
58158 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
58194 TCTATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
58230 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
58266 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
58298 ACTTATAAAT
Statistics
Matches: 100, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
35 21 0.21
36 79 0.79
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.30
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:58237 original size:13 final size:12
Alignment explanation
Indices: 58182--58278 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
58172 CACGCCTATA
*
58182 TCATCACCATAG
1 TCATCACCATAT
58194 TCTATCACC--AT
1 TC-ATCACCATAT
*
58205 T-ATCACGCCTAT
1 TCATCAC-CATAT
58217 ATCATCACCATAT
1 -TCATCACCATAT
58230 TCCATCACC--AT
1 T-CATCACCATAT
*
58241 T-ATCACGCCTAT
1 TCATCAC-CATAT
58253 ATCATCACCATAT
1 -TCATCACCATAT
58266 TCCATCACCATAT
1 T-CATCACCATAT
58279 CACGCCTATA
Statistics
Matches: 69, Mismatches: 3, Indels: 25
0.71 0.03 0.26
Matches are distributed among these distances:
9 10 0.14
10 2 0.03
11 5 0.07
12 8 0.12
13 34 0.49
14 10 0.14
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.31
Consensus pattern (12 bp):
TCATCACCATAT
Found at i:62419 original size:13 final size:11
Alignment explanation
Indices: 62378--62485 Score: 78
Period size: 11 Copynumber: 9.2 Consensus size: 11
62368 ACAATCTGTC
62378 CATCACCATTAT
1 CATCACCA-TAT
*
62390 CA-CGCCTATAT
1 CATCACC-ATAT
62401 CATCACCATAGT
1 CATCACCATA-T
62413 CCATCACCATTAT
1 -CATCACCA-TAT
*
62426 CA-CGCCTATAT
1 CATCACC-ATAT
62437 CATCACCATATT
1 CATCACCATA-T
62449 CCATCACCATTAT
1 -CATCACCA-TAT
*
62462 CA-CGCCTATAT
1 CATCACC-ATAT
62473 CATCACCATAT
1 CATCACCATAT
62484 CA
1 CA
62486 CGCCTATATT
Statistics
Matches: 78, Mismatches: 6, Indels: 25
0.72 0.06 0.23
Matches are distributed among these distances:
11 36 0.46
12 20 0.26
13 18 0.23
14 4 0.05
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:62483 original size:36 final size:36
Alignment explanation
Indices: 62376--62483 Score: 207
Period size: 36 Copynumber: 3.0 Consensus size: 36
62366 ATACAATCTG
*
62376 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
62412 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
62448 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
62484 CACGCCTATA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.30
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:62484 original size:22 final size:22
Alignment explanation
Indices: 62378--62502 Score: 103
Period size: 23 Copynumber: 5.4 Consensus size: 22
62368 ACAATCTGTC
62378 CATCACCATTATCACGCCTATAT
1 CATCACCA-TATCACGCCTATAT
*
62401 CATCACCATAGTCCATCACC-ATTAT
1 CATCACCATA-T-CA-CGCCTA-TAT
* *
62426 CA-CGCCTATATCATCACC-ATATT
1 CATCACC-ATATCA-CGCCTATA-T
62449 CCATCACCATTATCACGCCTATAT
1 -CATCACCA-TATCACGCCTATAT
62473 CATCACCATATCACGCCTATAT
1 CATCACCATATCACGCCTATAT
*
62495 TATCACCA
1 CATCACCA
62503 ACTTATAAAT
Statistics
Matches: 87, Mismatches: 5, Indels: 21
0.77 0.04 0.19
Matches are distributed among these distances:
22 25 0.29
23 26 0.30
24 14 0.16
25 22 0.25
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (22 bp):
CATCACCATATCACGCCTATAT
Done.