Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001033.1 Hibiscus syriacus cultivar Beakdansim tig00002055_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: 61415
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3790 original size:11 final size:11
Alignment explanation
Indices: 3774--3807 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
3764 ACGAGGGTGA
3774 ATACGAGCCAT
1 ATACGAGCCAT
3785 ATACGAGCCAT
1 ATACGAGCCAT
*
3796 ATACGAGTCAT
1 ATACGAGCCAT
3807 A
1 A
3808 CGAGCCAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (11 bp):
ATACGAGCCAT
Found at i:3838 original size:22 final size:22
Alignment explanation
Indices: 3807--3884 Score: 93
Period size: 22 Copynumber: 3.4 Consensus size: 22
3797 TACGAGTCAT
*
3807 ACGAGCCAATGGGGAGGATGCA
1 ACGAGCCAATGGGGAGCATGCA
*
3829 ACGAGGCAATGGGGAGCATGCAGGA
1 ACGAGCCAATGGGGAGCATGC---A
*
3854 ATAGAGCCAATGGGGAGCATGCA
1 A-CGAGCCAATGGGGAGCATGCA
3877 ACGAGCCA
1 ACGAGCCA
3885 TATACGAGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
22 25 0.53
23 2 0.04
25 2 0.04
26 18 0.38
ACGTcount: A:0.33, C:0.19, G:0.38, T:0.09
Consensus pattern (22 bp):
ACGAGCCAATGGGGAGCATGCA
Found at i:3992 original size:60 final size:60
Alignment explanation
Indices: 3829--4016 Score: 308
Period size: 60 Copynumber: 3.1 Consensus size: 60
3819 GGAGGATGCA
*
3829 ACGAGGCAATGGGGAGCATGCAGGAAT--AGAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAAT-GGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
**
3888 ACGAGCCCACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAG-CCAATGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
3949 ACGAGCCAATGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAATGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
*
4009 ACAAGCCA
1 ACGAGCCA
4017 TGCAGGAATA
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
59 21 0.17
60 62 0.52
61 37 0.31
ACGTcount: A:0.35, C:0.21, G:0.34, T:0.11
Consensus pattern (60 bp):
ACGAGCCAATGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
Found at i:4086 original size:26 final size:26
Alignment explanation
Indices: 4050--4132 Score: 139
Period size: 26 Copynumber: 3.1 Consensus size: 26
4040 GCAGCCTAGG
4050 CGACCTTGTAGGTCGCCATGTAGTCC
1 CGACCTTGTAGGTCGCCATGTAGTCC
4076 CGACCTTGTAGGTCGCCATGTAGTCCC
1 CGACCTTGTAGGTCGCCATGTAGT-CC
4103 GGCGACCTTGTAGGTCGCCATGTAGTCC
1 --CGACCTTGTAGGTCGCCATGTAGTCC
4131 CG
1 CG
4133 GCGCCATTCC
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
26 26 0.48
27 2 0.04
28 2 0.04
29 24 0.44
ACGTcount: A:0.14, C:0.31, G:0.29, T:0.25
Consensus pattern (26 bp):
CGACCTTGTAGGTCGCCATGTAGTCC
Found at i:4118 original size:29 final size:29
Alignment explanation
Indices: 4030--4135 Score: 157
Period size: 29 Copynumber: 3.8 Consensus size: 29
4020 AGGAATAGAG
* *
4030 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
4059 AGGTCGCCATGTAGT-CC--CGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
4085 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
4114 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
4136 CCATTCCATC
Statistics
Matches: 71, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
26 24 0.34
27 2 0.03
29 45 0.63
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:4253 original size:36 final size:37
Alignment explanation
Indices: 4185--4258 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
4175 CATAGATTCC
4185 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
1 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
4222 TTCACGTGCTCCCCGCTGCA-TGCCTACACCTCCCAA
1 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
4258 T
1 T
4259 GCATGCATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 17 0.46
37 20 0.54
ACGTcount: A:0.16, C:0.46, G:0.14, T:0.24
Consensus pattern (37 bp):
TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
Found at i:4286 original size:18 final size:18
Alignment explanation
Indices: 4263--4297 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
4253 CCCAATGCAT
4263 GCATGTGAACCATTTGAG
1 GCATGTGAACCATTTGAG
4281 GCATGTGAACCATTTGA
1 GCATGTGAACCATTTGA
4298 TTATTGGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (18 bp):
GCATGTGAACCATTTGAG
Found at i:4411 original size:23 final size:23
Alignment explanation
Indices: 4383--4428 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
4373 AAAAGAAAGA
4383 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
4406 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
4429 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:4443 original size:25 final size:23
Alignment explanation
Indices: 4383--4443 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
4373 AAAAGAAAGA
**
4383 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
4406 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
4429 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
4444 AGAAAGGGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 23 0.70
25 10 0.30
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:4467 original size:21 final size:21
Alignment explanation
Indices: 4431--4489 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
4421 GATTGCAGCC
4431 GAGAAA-GAAAGAAAGAAAGG
1 GAGAAAGGAAAGAAAGAAAGG
*
4451 GAGAAAGGAAAGGAAGAAAGG
1 GAGAAAGGAAAGAAAGAAAGG
*
4472 GAGAAAGGAAAGTAAGAA
1 GAGAAAGGAAAGAAAGAA
4490 GAAGAAAGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 6 0.17
21 30 0.83
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (21 bp):
GAGAAAGGAAAGAAAGAAAGG
Found at i:4749 original size:46 final size:48
Alignment explanation
Indices: 4685--4776 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 48
4675 AGTTATAGTT
4685 AAAAAATAATTAATTAGTTTGTATT-GTT-AATAGTT-AGTTATATAA
1 AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
* *
4730 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATAT
4777 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 6 0.15
46 17 0.41
47 3 0.07
48 7 0.17
49 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (48 bp):
AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
Found at i:7087 original size:26 final size:24
Alignment explanation
Indices: 7029--7087 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
7019 CTAATAAACC
*
7029 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
7053 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
7081 TAATAAT
1 TAATAAT
7088 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:7914 original size:8 final size:8
Alignment explanation
Indices: 7901--7943 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
7891 TAATATAACT
7901 TAAACTAA
1 TAAACTAA
7909 TAAACTAA
1 TAAACTAA
*
7917 TATA-TAA
1 TAAACTAA
7924 CTAAACTAA
1 -TAAACTAA
*
7933 CAAACTAA
1 TAAACTAA
7941 TAA
1 TAA
7944 TTTATACTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 3 0.10
8 23 0.79
9 3 0.10
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (8 bp):
TAAACTAA
Found at i:8604 original size:29 final size:29
Alignment explanation
Indices: 8572--8651 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
8562 TATACCTTGG
*
8572 AGGTCGCCCGGATTGCATGGCGACCTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
8601 AGGTCGCCTGGATTGCATGGCGACCTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
8630 AGGTCGCCTGGATTGCATGGCG
1 AGGTCGCCTGGATTGCATGGCG
8652 TCCTATGGCG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.16, C:0.30, G:0.34, T:0.20
Consensus pattern (29 bp):
AGGTCGCCTGGATTGCATGGCGACCTCCA
Found at i:20559 original size:35 final size:35
Alignment explanation
Indices: 20501--20600 Score: 182
Period size: 35 Copynumber: 2.8 Consensus size: 35
20491 CGCGTTGATA
20501 ACTTTTATCAAGGTGTTTTAGTTTAGAGACAAGAAG
1 ACTTTTATCAA-GTGTTTTAGTTTAGAGACAAGAAG
20537 ACTTTTATCAAGTGTTTTAGTTTAGAGACAAGAAG
1 ACTTTTATCAAGTGTTTTAGTTTAGAGACAAGAAG
20572 ACTTTTATCAAGTGGTTTTAGTTTAGAGA
1 ACTTTTATCAAGT-GTTTTAGTTTAGAGA
20601 GGAGAAGAAG
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
35 37 0.59
36 26 0.41
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (35 bp):
ACTTTTATCAAGTGTTTTAGTTTAGAGACAAGAAG
Found at i:22960 original size:2 final size:2
Alignment explanation
Indices: 22953--22983 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
22943 TTTTTAAAAC
22953 AT AT 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 AT AT A
22984 CCCCTATCCG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23224 original size:24 final size:24
Alignment explanation
Indices: 23197--23330 Score: 162
Period size: 24 Copynumber: 5.6 Consensus size: 24
23187 CATAATTCAT
* *
23197 GTCAAATATCATATCAAAATCCAG
1 GTCAAATATCATATCAGAATCCAA
* *
23221 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAATATCATATCAGAATCCAA
* *
23245 GTCAAGTATCATATCAGAATCCAT
1 GTCAAATATCATATCAGAATCCAA
* *
23269 GTCATATATCATATCAGAATCCAT
1 GTCAAATATCATATCAGAATCCAA
* *
23293 GTCAAGTATCATATCAGAATTCAA
1 GTCAAATATCATATCAGAATCCAA
23317 GTCGAAA-ATCATAT
1 GTC-AAATATCATAT
23331 AAAATATCAT
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
24 94 0.98
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (24 bp):
GTCAAATATCATATCAGAATCCAA
Found at i:23328 original size:72 final size:72
Alignment explanation
Indices: 23194--23330 Score: 204
Period size: 72 Copynumber: 1.9 Consensus size: 72
23184 AAGCATAATT
*
23194 CATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGTATCATAT
1 CATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGAATCATAT
23259 CAGAATC
66 CAGAATC
* * * * *
23266 CATGTCATATATCATATCAGAATCCATGTCAAGTATCATATCAGAATTCAAGTCGAA-AATCATA
1 CATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTC-AAGAATCATA
23330 T
65 T
23331 AAAATATCAT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 56 0.97
73 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.28
Consensus pattern (72 bp):
CATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGAATCATAT
CAGAATC
Found at i:23342 original size:72 final size:72
Alignment explanation
Indices: 23190--23342 Score: 202
Period size: 72 Copynumber: 2.1 Consensus size: 72
23180 ATTAAAGCAT
*
23190 AATTCATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGTATC
1 AATTCATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGAATC
*
23255 ATATCAG
66 ATATCAA
* * * * * *
23262 AATCCATGTCATATATCATATCAGAATCCATGTCAAGTATCATATCAGAATTCAAGTCGAA-AAT
1 AATTCATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTC-AAGAAT
23326 CATAT-AA
65 CATATCAA
23333 AATATCATGT
1 AAT-TCATGT
23343 GAGTAGGAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
71 4 0.06
72 64 0.91
73 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (72 bp):
AATTCATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGAATC
ATATCAA
Found at i:31253 original size:24 final size:24
Alignment explanation
Indices: 31226--31273 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
31216 GCTTTACGTT
31226 GATTATTAATTCAATTACCACGGC
1 GATTATTAATTCAATTACCACGGC
*
31250 GATTATTAATTCAATTACCTCGGC
1 GATTATTAATTCAATTACCACGGC
31274 AATGATGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.35
Consensus pattern (24 bp):
GATTATTAATTCAATTACCACGGC
Found at i:41014 original size:14 final size:15
Alignment explanation
Indices: 40995--41027 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40985 ACGTTTGTGA
*
40995 AAAAAG-AAGAAAAG
1 AAAAAGAAAAAAAAG
41009 AAAAAGAAAAAAAAG
1 AAAAAGAAAAAAAAG
41024 AAAA
1 AAAA
41028 TGTTTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:43544 original size:18 final size:18
Alignment explanation
Indices: 43518--43571 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
43508 TTGTCACCAT
* *
43518 TGTCGTCATTGCCGCCAC
1 TGTCATCATCGCCGCCAC
*
43536 TGTCATCATCGTCGCCAC
1 TGTCATCATCGCCGCCAC
*
43554 TGTCATCATCGTCGCCAC
1 TGTCATCATCGCCGCCAC
43572 CGATATCATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.15, C:0.39, G:0.19, T:0.28
Consensus pattern (18 bp):
TGTCATCATCGCCGCCAC
Found at i:43839 original size:22 final size:22
Alignment explanation
Indices: 43814--43855 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
43804 AATTTTTAAC
43814 TAATTTATAA-TTACATGTTTAG
1 TAATTTATAATTTA-ATGTTTAG
*
43836 TAATTTTTAATTTAATGTTT
1 TAATTTATAATTTAATGTTT
43856 TATAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (22 bp):
TAATTTATAATTTAATGTTTAG
Found at i:44811 original size:13 final size:14
Alignment explanation
Indices: 44789--44820 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
44779 GGTATTTGAG
44789 AAAATAAAATATTA
1 AAAATAAAATATTA
44803 AAAAT-AAATATTA
1 AAAATAAAATATTA
44816 AAAAT
1 AAAAT
44821 TAATTAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATAAAATATTA
Found at i:56629 original size:23 final size:23
Alignment explanation
Indices: 56600--56644 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
56590 ATGTATTTAT
*
56600 TAATAATTCTAATTTTCTAAGTC
1 TAATAATTCTAACTTTCTAAGTC
*
56623 TAATAATTTTAACTTTCTAAGT
1 TAATAATTCTAACTTTCTAAGT
56645 ATATTTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (23 bp):
TAATAATTCTAACTTTCTAAGTC
Done.