Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009092.1 Hibiscus syriacus cultivar Beakdansim tig00112539_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: 50849
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:76 original size:32 final size:31
Alignment explanation
Indices: 40--115 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
30 CGGGGCCGTG
*
40 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
72 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
103 GAGCCTACCTAAG
1 GGGCCTACCTAAG
116 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:2938 original size:7 final size:7
Alignment explanation
Indices: 2926--2964 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
2916 GGTCAACGTG
2926 GGTCAAC
1 GGTCAAC
2933 GGTCAAC
1 GGTCAAC
2940 GGGTCAAC
1 -GGTCAAC
2948 GGTCAAC
1 GGTCAAC
2955 GGGTCAAC
1 -GGTCAAC
2963 GG
1 GG
2965 GTCGGGTCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:2945 original size:15 final size:15
Alignment explanation
Indices: 2925--2964 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
2915 TGGTCAACGT
2925 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
2940 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
2955 GGGTCAACGG
1 GGGTCAACGG
2965 GTCGGGTCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.38, T:0.12
Consensus pattern (15 bp):
GGGTCAACGGTCAAC
Found at i:2946 original size:8 final size:8
Alignment explanation
Indices: 2925--2967 Score: 72
Period size: 8 Copynumber: 5.6 Consensus size: 8
2915 TGGTCAACGT
2925 GGGTCAAC
1 GGGTCAAC
2933 -GGTCAAC
1 GGGTCAAC
2940 GGGTCAAC
1 GGGTCAAC
2948 -GGTCAAC
1 GGGTCAAC
2955 GGGTCAAC
1 GGGTCAAC
2963 GGGTC
1 GGGTC
2968 GGGTCGGGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.42
8 19 0.58
ACGTcount: A:0.23, C:0.26, G:0.37, T:0.14
Consensus pattern (8 bp):
GGGTCAAC
Found at i:2972 original size:13 final size:13
Alignment explanation
Indices: 2967--3002 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
2957 GTCAACGGGT
2967 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
2980 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
2993 CGGGTCGGGT
1 CGGGTCGGGT
3003 CGGGTATGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.50, T:0.17
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:2981 original size:18 final size:18
Alignment explanation
Indices: 2954--3008 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
2944 CAACGGTCAA
*
2954 CGGGTCAACGGGTCGGGT
1 CGGGTAAACGGGTCGGGT
2972 CGGGTAAA-----CGGGT
1 CGGGTAAACGGGTCGGGT
2985 CGGGTAAACGGGTCGGGT
1 CGGGTAAACGGGTCGGGT
3003 CGGGTA
1 CGGGTA
3009 TGACCGGTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
13 13 0.42
18 18 0.58
ACGTcount: A:0.16, C:0.18, G:0.49, T:0.16
Consensus pattern (18 bp):
CGGGTAAACGGGTCGGGT
Found at i:5136 original size:32 final size:31
Alignment explanation
Indices: 5100--5175 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
5090 CGGGGCCGTG
*
5100 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
5132 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
5163 GAGCCTACCTAAG
1 GGGCCTACCTAAG
5176 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:5159 original size:63 final size:63
Alignment explanation
Indices: 5053--5175 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
5043 ACCTAAGGGA
* * ** *
5053 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
5116 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
5176 TGTCACATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:8022 original size:15 final size:15
Alignment explanation
Indices: 8002--8033 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
7992 GGTCAACGTG
8002 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
8017 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
8032 GG
1 GG
8034 GTCGGGTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.25, G:0.38, T:0.12
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:8041 original size:13 final size:13
Alignment explanation
Indices: 8036--8072 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
8026 GTCAACGGGT
8036 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
* *
8049 CTGGTCGGGTAAA
1 CGGGTCGGGTCAA
8062 CGGGTCGGGTC
1 CGGGTCGGGTC
8073 GGGTTATGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.22, G:0.46, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:8046 original size:18 final size:18
Alignment explanation
Indices: 8023--8076 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
8013 CAACGGTCAA
8023 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
8041 CGGGTCAAC---T--GGT
1 CGGGTCAACGGGTCGGGT
*
8054 CGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
8072 CGGGT
1 CGGGT
8077 TATGACCGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
13 11 0.37
15 1 0.03
16 1 0.03
18 17 0.57
ACGTcount: A:0.13, C:0.20, G:0.48, T:0.19
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:8054 original size:8 final size:8
Alignment explanation
Indices: 8001--8036 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
7991 TGGTCAACGT
8001 GGGTCAAC
1 GGGTCAAC
8009 GGGTCAAC
1 GGGTCAAC
8017 -GGTCAAC
1 GGGTCAAC
8024 GGGTCAAC
1 GGGTCAAC
8032 GGGTC
1 GGGTC
8037 GGGTCGGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.22, C:0.25, G:0.39, T:0.14
Consensus pattern (8 bp):
GGGTCAAC
Found at i:10200 original size:75 final size:75
Alignment explanation
Indices: 10121--10295 Score: 208
Period size: 75 Copynumber: 2.3 Consensus size: 75
10111 GGCGATTGGC
* * * *
10121 ATTCTAATTTTTTGTTCCTGGTACC-AGACCGACCCACATTCATGATAAAATTTGTTCATACAAA
1 ATTCTAATTTTTCGTTCCTAGTACCGA-ACCGACCCACATTCATGATAAAATGTGTGCATACAAA
* *
10185 TAGTGATTTAT
65 TAATAATTTAT
* * * * * * *
10196 ATTCTAATTTTTCATTTCTAGTACCGAATCGATCCACATTCATGGTAAAATGTGTGCATACGAGT
1 ATTCTAATTTTTCGTTCCTAGTACCGAACCGACCCACATTCATGATAAAATGTGTGCATACAAAT
*
10261 AATAATTTGT
66 AATAATTTAT
10271 ATTCTAATTTTTCGTTCCTAGTACC
1 ATTCTAATTTTTCGTTCCTAGTACC
10296 TATCCACATT
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
75 82 0.99
76 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (75 bp):
ATTCTAATTTTTCGTTCCTAGTACCGAACCGACCCACATTCATGATAAAATGTGTGCATACAAAT
AATAATTTAT
Found at i:14390 original size:25 final size:25
Alignment explanation
Indices: 14360--14409 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
14350 ATCTCCTTTG
14360 TATTTCTTGTTCCCTCATCTTAATC
1 TATTTCTTGTTCCCTCATCTTAATC
14385 TATTTCTTGTTCCCTCATCTTAATC
1 TATTTCTTGTTCCCTCATCTTAATC
14410 ATCATCATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.28, G:0.04, T:0.52
Consensus pattern (25 bp):
TATTTCTTGTTCCCTCATCTTAATC
Found at i:14615 original size:111 final size:111
Alignment explanation
Indices: 14421--14642 Score: 444
Period size: 111 Copynumber: 2.0 Consensus size: 111
14411 TCATCATCGT
14421 TATTTAGTTTGAGTTGTGATAGATTTTGTGGTATATGTTTTACAGCTTATGGTGTTGATATGTTG
1 TATTTAGTTTGAGTTGTGATAGATTTTGTGGTATATGTTTTACAGCTTATGGTGTTGATATGTTG
14486 AATACAATTGGTTACATCTATTCAAGACAAGCAGCGAAAGAACTTG
66 AATACAATTGGTTACATCTATTCAAGACAAGCAGCGAAAGAACTTG
14532 TATTTAGTTTGAGTTGTGATAGATTTTGTGGTATATGTTTTACAGCTTATGGTGTTGATATGTTG
1 TATTTAGTTTGAGTTGTGATAGATTTTGTGGTATATGTTTTACAGCTTATGGTGTTGATATGTTG
14597 AATACAATTGGTTACATCTATTCAAGACAAGCAGCGAAAGAACTTG
66 AATACAATTGGTTACATCTATTCAAGACAAGCAGCGAAAGAACTTG
14643 GGAAGAAAGC
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 111 1.00
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.40
Consensus pattern (111 bp):
TATTTAGTTTGAGTTGTGATAGATTTTGTGGTATATGTTTTACAGCTTATGGTGTTGATATGTTG
AATACAATTGGTTACATCTATTCAAGACAAGCAGCGAAAGAACTTG
Found at i:17187 original size:6 final size:6
Alignment explanation
Indices: 17176--17246 Score: 115
Period size: 6 Copynumber: 11.3 Consensus size: 6
17166 TGGTAGCTGG
17176 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC
17224 TCTTTCTC GTCTTCC TCTTCC TC
1 TC-TTC-C -TCTTCC TCTTCC TC
17247 GTGGCTGAAG
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
6 52 0.84
7 4 0.06
8 4 0.06
9 2 0.03
ACGTcount: A:0.00, C:0.48, G:0.01, T:0.51
Consensus pattern (6 bp):
TCTTCC
Found at i:22698 original size:60 final size:60
Alignment explanation
Indices: 22561--22698 Score: 179
Period size: 60 Copynumber: 2.3 Consensus size: 60
22551 CTGGTTATTA
* * *
22561 ATAGTCGAATGACTATTTTGTAACTTTTAATAGTCGAGTGACTCAATAAAGCAACATCTT
1 ATAGTCGAATGACCATTTTATAACTTTTAATAGTCGAGTGACTCAACAAAGCAACATCTT
* * * * *
22621 ATAGTCGAAGGATCATTTTATAACTTTTAATAGTCGA-TGGACTCAACAAAGTAATATTTT
1 ATAGTCGAATGACCATTTTATAACTTTTAATAGTCGAGT-GACTCAACAAAGCAACATCTT
*
22681 ATAGTCGGATGACCATTT
1 ATAGTCGAATGACCATTT
22699 ATGTACTTTG
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
59 1 0.02
60 65 0.98
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Consensus pattern (60 bp):
ATAGTCGAATGACCATTTTATAACTTTTAATAGTCGAGTGACTCAACAAAGCAACATCTT
Found at i:30840 original size:12 final size:12
Alignment explanation
Indices: 30823--30847 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30813 CTAAACTGTC
30823 AGGTTAATGCAA
1 AGGTTAATGCAA
30835 AGGTTAATGCAA
1 AGGTTAATGCAA
30847 A
1 A
30848 TGGGAAACGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (12 bp):
AGGTTAATGCAA
Found at i:30953 original size:21 final size:21
Alignment explanation
Indices: 30927--30967 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
30917 CGACATGCAA
30927 ATGCTTGGATATCTCGGCGTC
1 ATGCTTGGATATCTCGGCGTC
* *
30948 ATGCTTGGATCTCTTGGCGT
1 ATGCTTGGATATCTCGGCGT
30968 TATTAGGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.22, G:0.29, T:0.37
Consensus pattern (21 bp):
ATGCTTGGATATCTCGGCGTC
Found at i:31578 original size:31 final size:31
Alignment explanation
Indices: 31537--31596 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
31527 ATACTTATTT
*
31537 GATTTAAAACAAAT-AAAAAGCAAAAGAAATG
1 GATTGAAAAC-AATGAAAAAGCAAAAGAAATG
* *
31568 GATTGAAAACAATGCAAAAGTAAAAGAAA
1 GATTGAAAACAATGAAAAAGCAAAAGAAA
31597 GGTGTTGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15
Consensus pattern (31 bp):
GATTGAAAACAATGAAAAAGCAAAAGAAATG
Found at i:34182 original size:24 final size:24
Alignment explanation
Indices: 34154--34215 Score: 110
Period size: 23 Copynumber: 2.7 Consensus size: 24
34144 TTGCATGATA
34154 CAGACGTGCAGGCCCCCCCACATG
1 CAGACGTGCAGGCCCCCCCACATG
34178 CAGACGTGCAGG-CCCCCCACATG
1 CAGACGTGCAGGCCCCCCCACATG
34201 CAGACGTGCA-GCCCC
1 CAGACGTGCAGGCCCC
34216 TGCTCAACCC
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
22 1 0.03
23 24 0.65
24 12 0.32
ACGTcount: A:0.21, C:0.45, G:0.26, T:0.08
Consensus pattern (24 bp):
CAGACGTGCAGGCCCCCCCACATG
Found at i:34449 original size:30 final size:30
Alignment explanation
Indices: 34413--34475 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
34403 AAATTGTGTT
34413 AAAGACGCCGAGAGATCCAACCTTCCATGC
1 AAAGACGCCGAGAGATCCAACCTTCCATGC
* *
34443 AAAGACGCCGAGAGCTCCAAGCTTCCATGC
1 AAAGACGCCGAGAGATCCAACCTTCCATGC
34473 AAA
1 AAA
34476 TCTGCTGAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.32, G:0.21, T:0.13
Consensus pattern (30 bp):
AAAGACGCCGAGAGATCCAACCTTCCATGC
Found at i:41286 original size:13 final size:13
Alignment explanation
Indices: 41251--41289 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
41241 TTTGAGAGAA
41251 TACTTTTTTCTTTT
1 TACTTTTTT-TTTT
41265 T-CTTATTTTTTTT
1 TACTT-TTTTTTTT
41278 TACTTTTTTTTT
1 TACTTTTTTTTT
41290 AAAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (13 bp):
TACTTTTTTTTTT
Done.