Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003737.1 Hibiscus syriacus cultivar Beakdansim tig00007996_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: 61133
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1520 original size:2 final size:2
Alignment explanation
Indices: 1513--1543 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1503 AGTGTTGGCT
1513 TA TA 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 TA TA T
1544 CTCTCACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4143 original size:11 final size:13
Alignment explanation
Indices: 4113--4144 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
4103 GCCGAAATCG
4113 AATATATCTAGAA
1 AATATATCTAGAA
4126 AATATATCTAGAA
1 AATATATCTAGAA
4139 AATATA
1 AATATA
4145 GATTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.31
Consensus pattern (13 bp):
AATATATCTAGAA
Found at i:7610 original size:264 final size:260
Alignment explanation
Indices: 6971--7841 Score: 1162
Period size: 259 Copynumber: 3.4 Consensus size: 260
6961 CTTATTCATA
* * * *
6971 TATTAAATAAAAATATTTTTTTATTATTTCGGGTTAGGTTGGGGTTT-TAATTTATATATTC--G
1 TATTAAATAAAAATATTTTTTTATTATTTCGGG-TCGGGTCGGGTTTCTAATTCATATATTCAGG
* * * *
7033 ---GGTCGGGTGAAACTTTATTTTGATCGAGTCGGGTCGTTTTTTTAAGTGTGATATTCGGGTTG
65 TCAGGTCAGGTGAAACTTTATTTTGGTCGGGTCGGGTCATTTTTTTAAGTGTGATATTC-----G
*
7095 GGTCGAGTTCGGGTTTAGGGTG-AAAA-A--T-----ACCCGACCCGAAAATATATATAATTTTA
125 GGTCGGGTTCGGGTTTAGGGTGAAAAATACCTACCCGACCCGACCCGAAAATATATATAATTTTA
*
7151 CCTTATATATTTACGAATAATTACAATAATACCCCTCTATATATAA-TTTTTTCAATTAAGTCAC
190 CCTTATATATTTAAGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCAC
*
7215 TGTTTT
255 TATTTT
*
7221 TATTAAATAAAAATAATTTTTTTATTA-TT----TCGGGTCGGGTTTCTACTTCATATATTCAGG
1 TATTAAATAAAAAT-ATTTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATTCAGG
*
7281 TCAGGTCAGGTGAAACTTTATTTTGGTCGGGTCGGGTTGATTTTTTTAAGTGTGATATTCGGGTC
65 TCAGGTCAGGTGAAACTTTATTTTGGTCGGGTCGGG-TCATTTTTTTAAGTGTGATATTCGGGTC
7346 GGGTTCGGGTTTAGGGTGAAAAATACCTGACCCGACCCGACCCGAAAATATATATAATTTTACCT
129 GGGTTCGGGTTTAGGGTGAAAAATACCT-ACCCGACCCGACCCGAAAATATATATAATTTTACCT
* *
7411 TATATATTTATGAATAATTATAATAATACCCCTCTATATATAATTTTTTTTCAATTAAGTCACTA
193 TATATATTTAAGAATAATTACAATAATACCCCTCTATATATAA-TTTTTTTCAATTAAGTCACTA
7476 TTTT
257 TTTT
* *
7480 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGGTTTCTACTTCATATATTCAGG
1 TATTAAATAAAAAT-ATTTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATTCAGG
* * *
7545 TCAGGTTAGGTGAAACTTTATTTTGGTCGGGCCGGGTCAATTTTTTTAAATGTGATATTCGGGTC
65 TCAGGTCAGGTGAAACTTTATTTTGGTCGGGTCGGGTC-ATTTTTTTAAGTGTGATATTCGGGTC
* * *
7610 GGGTTCGAGTTTAGGGTGAAAAATACCTA----ACCCGACCCCAAAAAAATATATAATTTTACCT
129 GGGTTCGGGTTTAGGGTGAAAAATACCTACCCGACCCGA-CCCGAAAATATATATAATTTTACCT
*
7671 TATATATTTAAAAATAATTACAATAATACCCCTCTATATATAACTTTTTTTCAATTAAGTCACTA
193 TATATATTTAAGAATAATTACAATAATACCCCTCTATATATAA-TTTTTTTCAATTAAGTCACTA
7736 TTTT
257 TTTT
* * *
7740 TATTGAATAAAAATATTTTTTTATTATTTCGGATCGGGTCGGGTTTCTAATTCATATATTCGGGT
1 TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATTCAGGT
* * * *
7805 CGGGCCGGGTGAAACTTTATTTTTGTCGGGTCGGGTC
66 CAGGTCAGGTGAAACTTTATTTTGGTCGGGTCGGGTC
7842 GGGTAGACCA
Statistics
Matches: 559, Mismatches: 35, Indels: 45
0.87 0.05 0.07
Matches are distributed among these distances:
245 10 0.02
246 12 0.02
247 22 0.04
248 5 0.01
249 1 0.00
250 16 0.03
251 43 0.08
252 21 0.04
257 72 0.13
259 134 0.24
260 104 0.19
263 2 0.00
264 117 0.21
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (260 bp):
TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATTCAGGT
CAGGTCAGGTGAAACTTTATTTTGGTCGGGTCGGGTCATTTTTTTAAGTGTGATATTCGGGTCGG
GTTCGGGTTTAGGGTGAAAAATACCTACCCGACCCGACCCGAAAATATATATAATTTTACCTTAT
ATATTTAAGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCACTATTTT
Found at i:8533 original size:35 final size:35
Alignment explanation
Indices: 8487--8557 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
8477 ACATTTACTA
* *
8487 ACAACTAAACATTTAATAATATTAAATTTTATCAT
1 ACAACTAAACATTTAATAATACTAAAATTTATCAT
8522 ACAACTAAACATTTAATAATACTAAAATTTATCAT
1 ACAACTAAACATTTAATAATACTAAAATTTATCAT
8557 A
1 A
8558 TTTACGATGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.37
Consensus pattern (35 bp):
ACAACTAAACATTTAATAATACTAAAATTTATCAT
Found at i:8547 original size:17 final size:16
Alignment explanation
Indices: 8490--8552 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 16
8480 TTTACTAACA
8490 ACTAAACATTTAATAAT
1 ACTAAA-ATTTAATAAT
* *
8507 ATTAAATTTTATCATACA-
1 ACTAAAATTTA--ATA-AT
8525 ACTAAACATTTAATAAT
1 ACTAAA-ATTTAATAAT
8542 ACTAAAATTTA
1 ACTAAAATTTA
8553 TCATATTTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
16 10 0.27
17 14 0.38
18 8 0.22
19 5 0.14
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (16 bp):
ACTAAAATTTAATAAT
Found at i:13640 original size:18 final size:18
Alignment explanation
Indices: 13599--13651 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
13589 AACGGTTAAG
13599 ATAATATATTTTATAATTAA
1 ATAATATATTTTA-AA-TAA
13619 ATAATATATTTTAAA-AA
1 ATAATATATTTTAAATAA
*
13636 TATAAAATATTATTAA
1 -ATAATATATT-TTAA
13652 CCGTGTCAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 2 0.07
18 9 0.30
19 6 0.20
20 13 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATATATTTTAAATAA
Found at i:13645 original size:20 final size:20
Alignment explanation
Indices: 13599--13637 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13589 AACGGTTAAG
* *
13599 ATAATATATTTTATAATTAA
1 ATAATATATTTTAAAAATAA
13619 ATAATATATTTTAAAAATA
1 ATAATATATTTTAAAAATA
13638 TAAAATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAATATATTTTAAAAATAA
Found at i:15540 original size:24 final size:24
Alignment explanation
Indices: 15513--15626 Score: 158
Period size: 24 Copynumber: 4.8 Consensus size: 24
15503 ATAATCAAAT
15513 ACAAATGAACGAACATAAACGAAC
1 ACAAATGAACGAACATAAACGAAC
*
15537 ACAAATGAACGAACGTAAACGAAC
1 ACAAATGAACGAACATAAACGAAC
* *
15561 ACAAATGAACGAACGTAAACGAAT
1 ACAAATGAACGAACATAAACGAAC
* *
15585 AC-AATAAACGAATATAAACGAAC
1 ACAAATGAACGAACATAAACGAAC
* *
15608 ACAAACGAACCAACATAAA
1 ACAAATGAACGAACATAAA
15627 TGCAAATATT
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
23 19 0.24
24 60 0.76
ACGTcount: A:0.58, C:0.20, G:0.12, T:0.10
Consensus pattern (24 bp):
ACAAATGAACGAACATAAACGAAC
Found at i:16465 original size:31 final size:31
Alignment explanation
Indices: 16420--16484 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
16410 AGGAGGAATG
*
16420 GTCCCTAATATTATCAAGCCATTCAATTTTA
1 GTCCCTAACATTATCAAGCCATTCAATTTTA
* * * **
16451 GTCCCTAACCTTATCGATCCATTCGCTTTTA
1 GTCCCTAACATTATCAAGCCATTCAATTTTA
16482 GTC
1 GTC
16485 ACTCAACCAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.28, G:0.09, T:0.38
Consensus pattern (31 bp):
GTCCCTAACATTATCAAGCCATTCAATTTTA
Found at i:16767 original size:3 final size:3
Alignment explanation
Indices: 16759--16808 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
16749 TAGAAGCAAT
16759 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16807 AT
1 AT
16809 TGTATTTTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:18267 original size:37 final size:37
Alignment explanation
Indices: 18197--18271 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 37
18187 CATTAAACTT
*
18197 TTTTATATTTTAAATTTTGTAAAAAATATTATATAAA
1 TTTTATAATTTAAATTTTGTAAAAAATATTATATAAA
*
18234 TTTTATGAATTTAAATTTTTTAAATAAA-A-TATATAAA
1 TTTTAT-AATTTAAATTTTGTAAA-AAATATTATATAAA
18271 T
1 T
18272 ATTTTCCAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 15 0.44
38 16 0.47
39 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (37 bp):
TTTTATAATTTAAATTTTGTAAAAAATATTATATAAA
Found at i:36781 original size:28 final size:29
Alignment explanation
Indices: 36727--36783 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
36717 AAATTGTTAC
**
36727 TTCAAAGCATTGACTCGACGATGTAATAT
1 TTCAAAGCATTGACTCGACGACATAATAT
* *
36756 TTCAAA-CGTTGACTCGGCGACATAATAT
1 TTCAAAGCATTGACTCGACGACATAATAT
36784 AAACAGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (29 bp):
TTCAAAGCATTGACTCGACGACATAATAT
Found at i:36920 original size:19 final size:19
Alignment explanation
Indices: 36896--36943 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
36886 TTAAGAGTTT
*
36896 TTTTATAATTAAGGAATTA
1 TTTTATAATTAAAGAATTA
36915 TTTTATAATTAAAGAATTA
1 TTTTATAATTAAAGAATTA
36934 TTTTATAATT
1 TTTTATAATT
36944 TTTAACAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (19 bp):
TTTTATAATTAAAGAATTA
Found at i:38174 original size:47 final size:47
Alignment explanation
Indices: 38117--38221 Score: 124
Period size: 47 Copynumber: 2.3 Consensus size: 47
38107 GTGTTTATTT
* * *
38117 ATTTAT-TGTTCACGAATATGTTCATTTAATATTTGCGAA-GATGTTC
1 ATTTATATGTTCACGAACATGTTCATTTAATATTTGCAAACG-TGCTC
* * *
38163 ATTTATATGTTCATGAACATGTTCGTTTAATGTTTGCAAACGTGCTC
1 ATTTATATGTTCACGAACATGTTCATTTAATATTTGCAAACGTGCTC
*
38210 GTTTATATGTTC
1 ATTTATATGTTC
38222 GTTTATTATT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
46 6 0.12
47 43 0.86
48 1 0.02
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (47 bp):
ATTTATATGTTCACGAACATGTTCATTTAATATTTGCAAACGTGCTC
Found at i:38191 original size:24 final size:24
Alignment explanation
Indices: 38157--38221 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 24
38147 ATTTGCGAAG
*
38157 ATGTTCATTTATATGTTCATG-AAC
1 ATGTTCGTTTATATGTTC-TGAAAC
38181 ATGTTCGTTTA-ATGTT-TGCAAAC
1 ATGTTCGTTTATATGTTCTG-AAAC
* *
38204 GTGCTCGTTTATATGTTC
1 ATGTTCGTTTATATGTTC
38222 GTTTATTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 2 0.06
23 17 0.50
24 15 0.44
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.46
Consensus pattern (24 bp):
ATGTTCGTTTATATGTTCTGAAAC
Found at i:39959 original size:24 final size:25
Alignment explanation
Indices: 39927--39976 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
39917 AAATCCAATT
39927 CGATCCAAAAAA-ATAACCGAAAAC
1 CGATCCAAAAAACATAACCGAAAAC
39951 CGATCCAAAAAATCGATAACCGAAAA
1 CGATCCAAAAAA-C-ATAACCGAAAA
39977 AAAACTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 12 0.52
27 11 0.48
ACGTcount: A:0.56, C:0.24, G:0.10, T:0.10
Consensus pattern (25 bp):
CGATCCAAAAAACATAACCGAAAAC
Found at i:41044 original size:21 final size:20
Alignment explanation
Indices: 41018--41079 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
41008 TTAATATATA
41018 TTTTAAATATTTTATATAATT
1 TTTTAAA-ATTTTATATAATT
* * * *
41039 TTTTAAAACTTTATTTTCATC
1 TTTTAAAATTTTA-TATAATT
41060 TTTTAAAATTTTATA-AATT
1 TTTTAAAATTTTATATAATT
41079 T
1 T
41080 AAATTTATTC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 3 0.09
20 6 0.19
21 23 0.72
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTAAAATTTTATATAATT
Found at i:46902 original size:2 final size:2
Alignment explanation
Indices: 46895--46922 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
46885 TCCTATTCTG
46895 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
46923 TCCATACACA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:55756 original size:31 final size:31
Alignment explanation
Indices: 55718--55776 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
55708 CGAGGGTTAT
*
55718 CTATGTTCTACGGAATATATGGACAGTTTAC
1 CTATGTTCTACGGAACATATGGACAGTTTAC
*
55749 CTATGTTCTTCGGAACATATGGACAGTT
1 CTATGTTCTACGGAACATATGGACAGTT
55777 ACATAGGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (31 bp):
CTATGTTCTACGGAACATATGGACAGTTTAC
Found at i:59365 original size:18 final size:19
Alignment explanation
Indices: 59339--59377 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
59329 CATAAATAAC
*
59339 ATTATGAAAA-TACAAATA
1 ATTAAGAAAATTACAAATA
*
59357 ATTAAGAAAATTACAATTA
1 ATTAAGAAAATTACAAATA
59376 AT
1 AT
59378 AATAATGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (19 bp):
ATTAAGAAAATTACAAATA
Done.