Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008916.1 Hibiscus syriacus cultivar Beakdansim tig00112220_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: 75979
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:5880 original size:19 final size:19
Alignment explanation
Indices: 5858--5936 Score: 90
Period size: 19 Copynumber: 4.2 Consensus size: 19
5848 GACCGGTTCC
*
5858 GACCGGTTCGAACCAGTTT
1 GACCGGTTCGAACCGGTTT
* *
5877 GACCGGTTTG-ACCGGTTCC
1 GACCGGTTCGAACCGGTT-T
5896 GACCGGTTCGAACCGGTTT
1 GACCGGTTCGAACCGGTTT
* *
5915 GACCGGTTTG-ACCGGTCT
1 GACCGGTTCGAACCGGTTT
5933 GACC
1 GACC
5937 CGACCCGACT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
18 17 0.33
19 27 0.53
20 7 0.14
ACGTcount: A:0.15, C:0.29, G:0.30, T:0.25
Consensus pattern (19 bp):
GACCGGTTCGAACCGGTTT
Found at i:5887 original size:9 final size:9
Alignment explanation
Indices: 5843--5936 Score: 98
Period size: 9 Copynumber: 10.0 Consensus size: 9
5833 CTGGAAAATT
5843 GGTTTGACC
1 GGTTTGACC
*
5852 GGTTCCGACC
1 GGTT-TGACC
*
5862 GGTTCGAACC
1 GGTTTG-ACC
*
5872 AGTTTGACC
1 GGTTTGACC
5881 GGTTTGACC
1 GGTTTGACC
*
5890 GGTTCCGACC
1 GGTT-TGACC
*
5900 GGTTCGAACC
1 GGTTTG-ACC
5910 GGTTTGACC
1 GGTTTGACC
5919 GGTTTGACC
1 GGTTTGACC
*
5928 GGTCTGACC
1 GGTTTGACC
5937 CGACCCGACT
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
9 43 0.58
10 31 0.42
ACGTcount: A:0.14, C:0.29, G:0.31, T:0.27
Consensus pattern (9 bp):
GGTTTGACC
Found at i:5894 original size:38 final size:38
Alignment explanation
Indices: 5843--5930 Score: 167
Period size: 38 Copynumber: 2.3 Consensus size: 38
5833 CTGGAAAATT
5843 GGTTTGACCGGTTCCGACCGGTTCGAACCAGTTTGACC
1 GGTTTGACCGGTTCCGACCGGTTCGAACCAGTTTGACC
*
5881 GGTTTGACCGGTTCCGACCGGTTCGAACCGGTTTGACC
1 GGTTTGACCGGTTCCGACCGGTTCGAACCAGTTTGACC
5919 GGTTTGACCGGT
1 GGTTTGACCGGT
5931 CTGACCCGAC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.14, C:0.27, G:0.32, T:0.27
Consensus pattern (38 bp):
GGTTTGACCGGTTCCGACCGGTTCGAACCAGTTTGACC
Found at i:5984 original size:17 final size:17
Alignment explanation
Indices: 5962--5998 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5952 GACCCGACCC
*
5962 GACCCGACCTGACCGTT
1 GACCCGACCCGACCGTT
*
5979 GACCCGACCCGTCCGTT
1 GACCCGACCCGACCGTT
5996 GAC
1 GAC
5999 TTCCTTTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.43, G:0.24, T:0.16
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:13134 original size:10 final size:10
Alignment explanation
Indices: 13121--13221 Score: 122
Period size: 10 Copynumber: 10.6 Consensus size: 10
13111 ACCGATTCCG
*
13121 ACCGGTTCGA
1 ACCGGTTTGA
13131 ACCGGTTTG-
1 ACCGGTTTGA
*
13140 ACCGGTTCGA
1 ACCGGTTTGA
13150 ACCGGTTTG-
1 ACCGGTTTGA
*
13159 ACCGGTATGA
1 ACCGGTTTGA
13169 ACCGGTTTG-
1 ACCGGTTTGA
*
13178 ACCGGTATGA
1 ACCGGTTTGA
13188 ACCGGTTTG-
1 ACCGGTTTGA
*
13197 ACCGGTATGA
1 ACCGGTTTGA
13207 ACCGGTTTG-
1 ACCGGTTTGA
13216 ACCGGT
1 ACCGGT
13222 CTGACCCGAC
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
9 38 0.49
10 40 0.51
ACGTcount: A:0.19, C:0.24, G:0.32, T:0.26
Consensus pattern (10 bp):
ACCGGTTTGA
Found at i:13142 original size:19 final size:19
Alignment explanation
Indices: 13120--13221 Score: 172
Period size: 19 Copynumber: 5.4 Consensus size: 19
13110 GACCGATTCC
13120 GACCGGT-TCGAACCGGTTT
1 GACCGGTAT-GAACCGGTTT
13139 GACCGGT-TCGAACCGGTTT
1 GACCGGTAT-GAACCGGTTT
13158 GACCGGTATGAACCGGTTT
1 GACCGGTATGAACCGGTTT
13177 GACCGGTATGAACCGGTTT
1 GACCGGTATGAACCGGTTT
13196 GACCGGTATGAACCGGTTT
1 GACCGGTATGAACCGGTTT
13215 GACCGGT
1 GACCGGT
13222 CTGACCCGAC
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
19 81 0.99
20 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.32, T:0.25
Consensus pattern (19 bp):
GACCGGTATGAACCGGTTT
Found at i:13143 original size:29 final size:27
Alignment explanation
Indices: 13101--13227 Score: 116
Period size: 29 Copynumber: 4.5 Consensus size: 27
13091 GCTGTTGGAA
*
13101 AACCGGTTTGACCGATTCCGACCGGTTCG
1 AACCGGTTTGACCGGTT-CGACCGGTT-G
13130 AACCGGTTTGACCGGTTCGAACCGGTTTG
1 AACCGGTTTGACCGGTTCG-ACCGG-TTG
* *
13159 -ACCGGTATGAACCGGTTTGACCGGTATG
1 AACCGGTTTG-ACCGGTTCGACCGGT-TG
13187 AACCGGTTTGACCGGTAT-GAACCGGTTTG
1 AACCGGTTTGACCGGT-TCG-ACCGG-TTG
*
13216 -ACCGGTCTGACC
1 AACCGGTTTGACC
13228 CGACCCAACC
Statistics
Matches: 85, Mismatches: 5, Indels: 17
0.79 0.05 0.16
Matches are distributed among these distances:
27 1 0.01
28 35 0.41
29 46 0.54
30 3 0.04
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.25
Consensus pattern (27 bp):
AACCGGTTTGACCGGTTCGACCGGTTG
Found at i:20289 original size:9 final size:9
Alignment explanation
Indices: 20275--20343 Score: 57
Period size: 9 Copynumber: 7.3 Consensus size: 9
20265 CTGCTGGAAA
20275 ACCGGTTTG
1 ACCGGTTTG
20284 ACCGGTTTTG
1 ACCGG-TTTG
*
20294 ACCGGTTCG
1 ACCGGTTTG
* *
20303 AATCGGTTTA
1 -ACCGGTTTG
*
20313 ACCGGTCTG
1 ACCGGTTTG
*
20322 AACTGGTTTG
1 -ACCGGTTTG
*
20332 ACCGGTCTG
1 ACCGGTTTG
20341 ACC
1 ACC
20344 CGACCCGACC
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
9 24 0.52
10 22 0.48
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:22539 original size:5 final size:5
Alignment explanation
Indices: 22529--22577 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
22519 AACGGTCAAC
*
22529 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC- GGTC- GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
22578 AGACCGGTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 8 0.21
5 27 0.69
7 4 0.10
ACGTcount: A:0.04, C:0.22, G:0.53, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:22547 original size:22 final size:22
Alignment explanation
Indices: 22522--22566 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
22512 GAAAGTCAAC
22522 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
22544 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
22566 G
1 G
22567 TCGGTCGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.09, C:0.22, G:0.51, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:22621 original size:19 final size:19
Alignment explanation
Indices: 22574--22623 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
22564 CGGTCGGTCG
*
22574 GGTCAGACCGGTCAAATCT
1 GGTCAGACCGGTCAAATCC
*
22593 GTTCAGACCGGTCAAA-CC
1 GGTCAGACCGGTCAAATCC
22611 GGTCAGAACCGGT
1 GGTCAG-ACCGGT
22624 TGAACCGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (19 bp):
GGTCAGACCGGTCAAATCC
Found at i:35462 original size:22 final size:22
Alignment explanation
Indices: 35437--35480 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
35427 GTCAAAGAAA
*
35437 GTCAACGGTCGGGTCGGGTCGG
1 GTCAACGGTCGGGTCAGGTCGG
35459 GTCAACGGTCGGGTCAGGTCGG
1 GTCAACGGTCGGGTCAGGTCGG
35481 TCGGTCGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (22 bp):
GTCAACGGTCGGGTCAGGTCGG
Found at i:35470 original size:12 final size:12
Alignment explanation
Indices: 35437--35474 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
35427 GTCAAAGAAA
35437 GTCAACGGTCGG
1 GTCAACGGTCGG
*
35449 GTC--GGGTCGG
1 GTCAACGGTCGG
35459 GTCAACGGTCGG
1 GTCAACGGTCGG
35471 GTCA
1 GTCA
35475 GGTCGGTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.13, C:0.24, G:0.45, T:0.18
Consensus pattern (12 bp):
GTCAACGGTCGG
Found at i:35487 original size:18 final size:18
Alignment explanation
Indices: 35442--35493 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
35432 AGAAAGTCAA
*
35442 CGGTCGGGTCGGGTCGGGT
1 CGGTC-GGTCGGGTCAGGT
**
35461 C-AACGGTCGGGTCAGGT
1 CGGTCGGTCGGGTCAGGT
35478 CGGTCGGTCGGGTCAG
1 CGGTCGGTCGGGTCAG
35494 ACCGGTCAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 13 0.48
18 13 0.48
19 1 0.04
ACGTcount: A:0.08, C:0.23, G:0.50, T:0.19
Consensus pattern (18 bp):
CGGTCGGTCGGGTCAGGT
Found at i:35499 original size:18 final size:18
Alignment explanation
Indices: 35464--35500 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
35454 GTCGGGTCAA
**
35464 CGGTCGGGTCAGGTCGGT
1 CGGTCGGGTCAGACCGGT
35482 CGGTCGGGTCAGACCGGT
1 CGGTCGGGTCAGACCGGT
35500 C
1 C
35501 AAACCGGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.27, G:0.46, T:0.19
Consensus pattern (18 bp):
CGGTCGGGTCAGACCGGT
Found at i:35500 original size:9 final size:9
Alignment explanation
Indices: 35488--35547 Score: 66
Period size: 10 Copynumber: 6.3 Consensus size: 9
35478 CGGTCGGTCG
*
35488 GGTCAGACC
1 GGTCAAACC
35497 GGTCAAACC
1 GGTCAAACC
*
35506 GGTTCGAACC
1 GG-TCAAACC
35516 GGTCGAAACC
1 GGTC-AAACC
*
35526 AGTCAAACC
1 GGTCAAACC
35535 GGTCAGAACC
1 GGTCA-AACC
35545 GGT
1 GGT
35548 TGAACCGGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
9 21 0.49
10 22 0.51
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.13
Consensus pattern (9 bp):
GGTCAAACC
Found at i:35517 original size:10 final size:9
Alignment explanation
Indices: 35494--35556 Score: 63
Period size: 9 Copynumber: 6.7 Consensus size: 9
35484 GTCGGGTCAG
*
35494 ACCGGTCAA
1 ACCGGTCGA
35503 ACCGGTTCGA
1 ACCGG-TCGA
35513 ACCGGTCGAA
1 ACCGGTCG-A
* *
35523 ACCAGTCAA
1 ACCGGTCGA
35532 ACCGGTCAGA
1 ACCGGTC-GA
*
35542 ACCGGTTGA
1 ACCGGTCGA
35551 ACCGGT
1 ACCGGT
35557 TTCCAGCAGC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
9 23 0.51
10 22 0.49
ACGTcount: A:0.29, C:0.30, G:0.27, T:0.14
Consensus pattern (9 bp):
ACCGGTCGA
Found at i:35518 original size:19 final size:19
Alignment explanation
Indices: 35494--35556 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
35484 GTCGGGTCAG
35494 ACCGGTCAAACCGGTTCGA
1 ACCGGTCAAACCGGTTCGA
* *
35513 ACCGGTCGAAACCAG-TCAA
1 ACCGGTC-AAACCGGTTCGA
35532 ACCGGTCAGAACCGGTT-GA
1 ACCGGTCA-AACCGGTTCGA
35551 ACCGGT
1 ACCGGT
35557 TTCCAGCAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
18 1 0.03
19 29 0.78
20 7 0.19
ACGTcount: A:0.29, C:0.30, G:0.27, T:0.14
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:58244 original size:12 final size:12
Alignment explanation
Indices: 58227--58252 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58217 AATTTCTAAG
58227 TATTTTAATCAA
1 TATTTTAATCAA
58239 TATTTTAATCAA
1 TATTTTAATCAA
58251 TA
1 TA
58253 GAGAACTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (12 bp):
TATTTTAATCAA
Done.