Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000670.1 Hibiscus syriacus cultivar Beakdansim tig00001303_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: 71547
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:3602 original size:19 final size:19
Alignment explanation
Indices: 3578--3630 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
3568 AAAACTTTAA
3578 TAATAATTTTAT-ATTAATT
1 TAATAATTTTATAATT-ATT
*
3597 TAATAAATTTATAATTATT
1 TAATAATTTTATAATTATT
3616 T-ATAATTTTAATAAT
1 TAATAATTTT-ATAAT
3631 CATGAGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 7 0.23
19 20 0.67
20 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATAATTTTATAATTATT
Found at i:5901 original size:39 final size:39
Alignment explanation
Indices: 5858--5934 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
5848 GATAGTAGAA
* *
5858 AATGAGAATATATTTTAAAGAAAATAGAAAGATAATTTC
1 AATGAGAATATATTTTAAAGAAAAAAAAAAGATAATTTC
*
5897 AATGAGAATATATTTTGAAGAAAAAAAAAAGATAATTT
1 AATGAGAATATATTTTAAAGAAAAAAAAAAGATAATTT
5935 TAATAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.56, C:0.01, G:0.13, T:0.30
Consensus pattern (39 bp):
AATGAGAATATATTTTAAAGAAAAAAAAAAGATAATTTC
Found at i:13971 original size:23 final size:22
Alignment explanation
Indices: 13927--13971 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
13917 CAACCTCTCT
* **
13927 TTCAACTCCGATCTACTCGCCG
1 TTCAACTCCGATCGACGAGCCG
13949 TTCAACCTCCGATCGACGAGCCG
1 TTCAA-CTCCGATCGACGAGCCG
13972 AAACCACAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.20, C:0.40, G:0.18, T:0.22
Consensus pattern (22 bp):
TTCAACTCCGATCGACGAGCCG
Found at i:24032 original size:14 final size:14
Alignment explanation
Indices: 24013--24058 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
24003 ATTGATAACC
24013 ATAGTTGTTTACAT
1 ATAGTTGTTTACAT
*
24027 ATA---GTTTACAC
1 ATAGTTGTTTACAT
24038 ATAGTTGTTTACAT
1 ATAGTTGTTTACAT
24052 ATAGTTG
1 ATAGTTG
24059 GATGGTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 10 0.37
14 17 0.63
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (14 bp):
ATAGTTGTTTACAT
Found at i:24281 original size:6 final size:6
Alignment explanation
Indices: 24272--24328 Score: 78
Period size: 6 Copynumber: 9.5 Consensus size: 6
24262 CACTATCACT
* * *
24272 ACTCCC ACTCCC ACTCCC ACTCCC ACTCCC ACTTCC ACTTCC ACTTCC
1 ACTCCC ACTCCC ACTCCC ACTCCC ACTCCC ACTCCC ACTCCC ACTCCC
*
24320 ACTTCC ACT
1 ACTCCC ACT
24329 ACCGCTACTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.18, C:0.58, G:0.00, T:0.25
Consensus pattern (6 bp):
ACTCCC
Found at i:24295 original size:18 final size:18
Alignment explanation
Indices: 24272--24328 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
24262 CACTATCACT
*
24272 ACTCCCACTCCCACTCCC
1 ACTCCCACTCCCACTTCC
24290 ACTCCCACTCCCACTTCC
1 ACTCCCACTCCCACTTCC
* *
24308 ACTTCCACTTCCACTTCC
1 ACTCCCACTCCCACTTCC
24326 ACT
1 ACT
24329 ACCGCTACTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.18, C:0.58, G:0.00, T:0.25
Consensus pattern (18 bp):
ACTCCCACTCCCACTTCC
Found at i:28598 original size:11 final size:9
Alignment explanation
Indices: 28567--28592 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28557 TAATTAATTA
28567 ATTAAATAT
1 ATTAAATAT
28576 ATTAAATAT
1 ATTAAATAT
28585 ATTAAATA
1 ATTAAATA
28593 CATATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
ATTAAATAT
Found at i:35332 original size:15 final size:15
Alignment explanation
Indices: 35284--35337 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
35274 ATGAATCCAA
35284 AATTATATAATTAAC
1 AATTATATAATTAAC
* *
35299 AATTAAAAAGTAATAAAC
1 AATT--ATA-TAATTAAC
*
35317 AGTTATATAATTAAC
1 AATTATATAATTAAC
35332 AATTAT
1 AATTAT
35338 GTCTGTAGAC
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 16 0.53
16 2 0.07
17 2 0.07
18 10 0.33
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (15 bp):
AATTATATAATTAAC
Found at i:35376 original size:17 final size:17
Alignment explanation
Indices: 35354--35389 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
35344 AGACACCCAT
35354 TTTCATACAGATTCTAA
1 TTTCATACAGATTCTAA
* *
35371 TTTCATCCGGATTCTAA
1 TTTCATACAGATTCTAA
35388 TT
1 TT
35390 ACAATCCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.44
Consensus pattern (17 bp):
TTTCATACAGATTCTAA
Found at i:36850 original size:10 final size:10
Alignment explanation
Indices: 36821--36908 Score: 85
Period size: 10 Copynumber: 9.1 Consensus size: 10
36811 GCTGCTGGAA
36821 AACCGGTTTG
1 AACCGGTTTG
*
36831 -ACCAGTTTTG
1 AACC-GGTTTG
*
36841 AATCGGTTTG
1 AACCGGTTTG
*
36851 -ACCGGTTCG
1 AACCGGTTTG
36860 AACCGGTTTG
1 AACCGGTTTG
*
36870 -ACCGGTCTG
1 AACCGGTTTG
36879 AACCGGTTTG
1 AACCGGTTTG
*
36889 -ACCGGTCTG
1 AACCGGTTTG
*
36898 AACCGGGTTG
1 AACCGGTTTG
36908 A
1 A
36909 CCCGACCCGA
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
9 26 0.42
10 34 0.55
11 2 0.03
ACGTcount: A:0.18, C:0.23, G:0.31, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:36868 original size:19 final size:19
Alignment explanation
Indices: 36821--36910 Score: 119
Period size: 19 Copynumber: 4.7 Consensus size: 19
36811 GCTGCTGGAA
* *
36821 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
*
36841 AATCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
36860 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
36879 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
36898 AACCGGGTTGACC
1 AACCGGTTTGACC
36911 CGACCCGACT
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
18 1 0.02
19 50 0.78
20 13 0.20
ACGTcount: A:0.18, C:0.24, G:0.30, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:36926 original size:17 final size:17
Alignment explanation
Indices: 36904--36949 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
36894 TCTGAACCGG
36904 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
36921 GTTGACCTGACCCGACT
1 GTTGACCCGACCCGACT
36938 GTTGACCCGACC
1 GTTGACCCGACC
36950 GTTGACCGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.17, C:0.39, G:0.24, T:0.20
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:36943 original size:12 final size:12
Alignment explanation
Indices: 36928--36970 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
36918 ACTGTTGACC
*
36928 TGACCCGACTGT
1 TGACCCGACCGT
36940 TGACCCGACCGT
1 TGACCCGACCGT
*
36952 TGACCGTTGACCGT
1 TGACC--CGACCGT
36966 TGACC
1 TGACC
36971 GTGATCGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 16 0.59
14 11 0.41
ACGTcount: A:0.16, C:0.35, G:0.26, T:0.23
Consensus pattern (12 bp):
TGACCCGACCGT
Found at i:36958 original size:7 final size:7
Alignment explanation
Indices: 36946--36989 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
36936 CTGTTGACCC
36946 GACCGTT
1 GACCGTT
36953 GACCGTT
1 GACCGTT
36960 GACCGTT
1 GACCGTT
36967 GACCG-T
1 GACCGTT
*
36973 GATCGTT
1 GACCGTT
36980 GACCGTT
1 GACCGTT
36987 GAC
1 GAC
36990 TTTCTTTGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 5 0.15
7 29 0.85
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (7 bp):
GACCGTT
Found at i:36981 original size:13 final size:13
Alignment explanation
Indices: 36946--36985 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
36936 CTGTTGACCC
36946 GACCGTTGACCGTT
1 GACCGTTGACCG-T
36960 GACCGTTGACCGT
1 GACCGTTGACCGT
*
36973 GATCGTTGACCGT
1 GACCGTTGACCGT
36986 TGACTTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.15, C:0.28, G:0.30, T:0.28
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:36981 original size:20 final size:21
Alignment explanation
Indices: 36946--36989 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
36936 CTGTTGACCC
36946 GACCGTTGACCGTTGACCGTT
1 GACCGTTGACCGTTGACCGTT
*
36967 GACCG-TGATCGTTGACCGTT
1 GACCGTTGACCGTTGACCGTT
36987 GAC
1 GAC
36990 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (21 bp):
GACCGTTGACCGTTGACCGTT
Found at i:44173 original size:10 final size:10
Alignment explanation
Indices: 44144--44231 Score: 76
Period size: 10 Copynumber: 9.1 Consensus size: 10
44134 GCTGCTGGAA
44144 AACCGGTTTG
1 AACCGGTTTG
*
44154 -ACCAGTTTTG
1 AACC-GGTTTG
44164 AACCGGTTTG
1 AACCGGTTTG
* *
44174 -ACCGATTCG
1 AACCGGTTTG
44183 AACCGGTTTG
1 AACCGGTTTG
*
44193 -ACCGGTCTG
1 AACCGGTTTG
44202 AACCGGTTTG
1 AACCGGTTTG
* *
44212 -ACTGGTCTG
1 AACCGGTTTG
*
44221 AACCGGGTTG
1 AACCGGTTTG
44231 A
1 A
44232 CCCGACTCGA
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
9 25 0.42
10 32 0.53
11 3 0.05
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:44187 original size:19 final size:18
Alignment explanation
Indices: 44144--44233 Score: 90
Period size: 19 Copynumber: 4.7 Consensus size: 18
44134 GCTGCTGGAA
*
44144 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-G-TTCG
44164 AACCGGTTTGACCGATTCG
1 AACCGGTTTGACCG-TTCG
*
44183 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGTTC-G
* *
44202 AACCGGTTTGACTGGTCTG
1 AACCGGTTTGACCGTTC-G
*
44221 AACCGGGTTGACC
1 AACCGGTTTGACC
44234 CGACTCGACT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
18 2 0.03
19 48 0.76
20 13 0.21
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.28
Consensus pattern (18 bp):
AACCGGTTTGACCGTTCG
Found at i:44249 original size:17 final size:17
Alignment explanation
Indices: 44227--44267 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
44217 TCTGAACCGG
* *
44227 GTTGACCCGACTCGACT
1 GTTGACCCGACCCGACC
44244 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
44261 GTTGACC
1 GTTGACC
44268 GTGACCGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.17, C:0.39, G:0.24, T:0.20
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:44274 original size:6 final size:7
Alignment explanation
Indices: 44257--44286 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
44247 GACCCGACCC
44257 GACCGTT
1 GACCGTT
44264 GACCG-T
1 GACCGTT
44270 GACCGTT
1 GACCGTT
44277 GACCGTT
1 GACCGTT
44284 GAC
1 GAC
44287 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:44275 original size:13 final size:13
Alignment explanation
Indices: 44257--44282 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44247 GACCCGACCC
44257 GACCGTTGACCGT
1 GACCGTTGACCGT
44270 GACCGTTGACCGT
1 GACCGTTGACCGT
44283 TGACTTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:50911 original size:21 final size:22
Alignment explanation
Indices: 50887--50944 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
50877 GACTATCGCA
50887 TTGCGATTTATTCCAAGTT-CG
1 TTGCGATTTATTCCAAGTTCCG
* *
50908 TTGCGA--TAGTCGAAGTTCGCG
1 TTGCGATTTATTCCAAGTTC-CG
*
50929 TTGCTATTTATTCCAA
1 TTGCGATTTATTCCAA
50945 ATTGTATTGC
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
19 9 0.32
21 13 0.46
23 6 0.21
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (22 bp):
TTGCGATTTATTCCAAGTTCCG
Found at i:53186 original size:70 final size:70
Alignment explanation
Indices: 53073--53212 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
53063 ATTTTCGACA
53073 GGTCTCCTCCATTAATCAATGACTTTGGAATTTCATATCCTACAACTTATCACCTGTTGTTGAGA
1 GGTCTCCTCCATTAATCAATGACTTTGGAATTTCATATCCTACAACTTATCACCTGTTGTTGAGA
53138 AAACC
66 AAACC
53143 GGTCTCCTCCATTAATCAATGACTTTGGAATTTCATATCCTACAACTTATCACCTGTTGTTGAGA
1 GGTCTCCTCCATTAATCAATGACTTTGGAATTTCATATCCTACAACTTATCACCTGTTGTTGAGA
53208 AAACC
66 AAACC
53213 ACTAGTAGAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (70 bp):
GGTCTCCTCCATTAATCAATGACTTTGGAATTTCATATCCTACAACTTATCACCTGTTGTTGAGA
AAACC
Found at i:56951 original size:4 final size:4
Alignment explanation
Indices: 56942--56976 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
56932 GTTTCTGTCA
56942 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
56977 TGTTTTGGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:61324 original size:50 final size:50
Alignment explanation
Indices: 61264--61389 Score: 144
Period size: 50 Copynumber: 2.5 Consensus size: 50
61254 GTAGTAGTAA
* * * * * *
61264 AGCGCGCCCCCTGAATCGTGCTATATGCTGATTTGGCGTCACGTGGGTAT
1 AGCGCGCCCCCTGAACCGCGATATACGCTGATCTGGCGCCACGTGGGTAT
* ** *
61314 AGCGCTCCCCCTGCCCCGCGATATACGGTGATCTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGAACCGCGATATACGCTGATCTGGCGCCACGTGGGTAT
* *
61364 AGCGCGCCCCCTGATCCGCGCTATAC
1 AGCGCGCCCCCTGAACCGCGATATAC
61390 CTGGGTGTCT
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.15, C:0.34, G:0.29, T:0.22
Consensus pattern (50 bp):
AGCGCGCCCCCTGAACCGCGATATACGCTGATCTGGCGCCACGTGGGTAT
Found at i:61525 original size:10 final size:10
Alignment explanation
Indices: 61510--61549 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
61500 TTTATCACAC
61510 CAAATTCTCT
1 CAAATTCTCT
61520 CAAATTCTCT
1 CAAATTCTCT
61530 -AAATTTCTCT
1 CAAA-TTCTCT
*
61540 CAAATACTCT
1 CAAATTCTCT
61550 ATTTTTTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:64991 original size:56 final size:56
Alignment explanation
Indices: 64898--65050 Score: 202
Period size: 56 Copynumber: 2.7 Consensus size: 56
64888 TTAGTGCACC
* *
64898 TATATTTTATCTGTAAGTATATAATT-AGAGAGCTCACAC-TCGAACTCTAACTTTGA
1 TATATTTTATATGTAAGTATAT-ATTCAGAGAGCTCACACAT-GAACTCGAACTTTGA
* * * *
64954 TATATTTTATATGCAAGTATATATTCAAAGAGTTCACACATGAACTCGAGCTTTGA
1 TATATTTTATATGTAAGTATATATTCAGAGAGCTCACACATGAACTCGAACTTTGA
* *
65010 TATACTATATATGTAAGTATATATTCAGAGAGCTCACACAT
1 TATATTTTATATGTAAGTATATATTCAGAGAGCTCACACAT
65051 TCCCATGCCC
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
55 3 0.04
56 80 0.95
57 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (56 bp):
TATATTTTATATGTAAGTATATATTCAGAGAGCTCACACATGAACTCGAACTTTGA
Done.