Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009334.1 Hibiscus syriacus cultivar Beakdansim tig00113101_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: 36627
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:9336 original size:7 final size:7
Alignment explanation
Indices: 9324--9360 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
9314 GTCAAAGAAA
9324 GTCAACG
1 GTCAACG
9331 GTCAACG
1 GTCAACG
9338 GTC-ACG
1 GTCAACG
9344 GTCAACG
1 GTCAACG
9351 GTCAACG
1 GTCAACG
9358 GTC
1 GTC
9361 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:9346 original size:13 final size:14
Alignment explanation
Indices: 9324--9360 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
9314 GTCAAAGAAA
9324 GTCAACGGTCAACG
1 GTCAACGGTCAACG
9338 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
9351 GTCAACGGTC
1 GTCAACGGTC
9361 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:9372 original size:17 final size:17
Alignment explanation
Indices: 9350--9390 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
9340 CACGGTCAAC
*
9350 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
9367 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
9384 GGTCAAC
1 GGTCAAC
9391 CCGGTTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:9408 original size:19 final size:19
Alignment explanation
Indices: 9384--9436 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
9374 AGTCGGGTCG
*
9384 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
9403 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
9422 GGTCAAACCGGTTCA
1 GGTCAAACCGGTTCA
9437 AAATTGGTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.25, C:0.32, G:0.26, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:9414 original size:9 final size:9
Alignment explanation
Indices: 9384--9453 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
9374 AGTCGGGTCG
*
9384 GGTCAACCC
1 GGTCAAACC
*
9393 GGTTCAGACC
1 GG-TCAAACC
9403 GGTCAAACC
1 GGTCAAACC
*
9412 GGTTCAGACC
1 GG-TCAAACC
9422 GGTCAAACC
1 GGTCAAACC
**
9431 GGTTCAAAATT
1 GG-TC-AAACC
9442 GGTCAAACC
1 GGTCAAACC
9451 GGT
1 GGT
9454 TTTCCAGCAG
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
9 24 0.50
10 19 0.40
11 5 0.10
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.19
Consensus pattern (9 bp):
GGTCAAACC
Found at i:9422 original size:10 final size:10
Alignment explanation
Indices: 9386--9438 Score: 65
Period size: 10 Copynumber: 5.5 Consensus size: 10
9376 TCGGGTCGGG
*
9386 TCAACCCGGT
1 TCAAACCGGT
*
9396 TCAGACCGG-
1 TCAAACCGGT
9405 TCAAACCGGT
1 TCAAACCGGT
*
9415 TCAGACCGG-
1 TCAAACCGGT
9424 TCAAACCGGT
1 TCAAACCGGT
9434 TCAAA
1 TCAAA
9439 ATTGGTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 16 0.44
10 20 0.56
ACGTcount: A:0.28, C:0.32, G:0.23, T:0.17
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:16647 original size:6 final size:7
Alignment explanation
Indices: 16625--16671 Score: 64
Period size: 7 Copynumber: 7.0 Consensus size: 7
16615 GTCAAAGAAA
16625 GTCAACG
1 GTCAACG
16632 GTCAACG
1 GTCAACG
16639 GTC-ACG
1 GTCAACG
16645 GTCAACG
1 GTCAACG
16652 GTC-ACG
1 GTCAACG
16658 G-CAAACG
1 GTC-AACG
16665 GTCAACG
1 GTCAACG
16672 CTCGGGTCGG
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
5 1 0.03
6 10 0.28
7 24 0.67
8 1 0.03
ACGTcount: A:0.28, C:0.30, G:0.30, T:0.13
Consensus pattern (7 bp):
GTCAACG
Found at i:16647 original size:13 final size:13
Alignment explanation
Indices: 16629--16668 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
16619 AAGAAAGTCA
16629 ACGGTCAACGGTC
1 ACGGTCAACGGTC
16642 ACGGTCAACGGTC
1 ACGGTCAACGGTC
16655 ACGG-CAAACGGTC
1 ACGGTC-AACGGTC
16668 A
1 A
16669 ACGCTCGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 1 0.04
13 25 0.96
ACGTcount: A:0.28, C:0.30, G:0.30, T:0.12
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:16686 original size:17 final size:16
Alignment explanation
Indices: 16664--16720 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 16
16654 CACGGCAAAC
16664 GGTCAACGCTCGGGTCG
1 GGTCAACG-TCGGGTCG
16681 GGTCAACGATCGGGTCG
1 GGTCAACG-TCGGGTCG
*
16698 AGTCAACAGTCGGGTCG
1 GGTCAAC-GTCGGGTCG
16715 GGTCAA
1 GGTCAA
16721 ACCGGTTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
17 35 0.97
18 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.39, T:0.18
Consensus pattern (16 bp):
GGTCAACGTCGGGTCG
Found at i:17433 original size:17 final size:17
Alignment explanation
Indices: 17411--17444 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17401 TCAATTTTCA
*
17411 CAATTAACGTCCAATTT
1 CAATTAAAGTCCAATTT
*
17428 CAATTAAATTCCAATTT
1 CAATTAAAGTCCAATTT
17445 TGTAAACAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (17 bp):
CAATTAAAGTCCAATTT
Found at i:28524 original size:33 final size:33
Alignment explanation
Indices: 28482--28550 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
28472 GTTGATGAAT
*
28482 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
28515 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
28548 GAA
1 GAA
28551 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:28972 original size:19 final size:20
Alignment explanation
Indices: 28925--28975 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
28915 GAAATCCCTT
**
28925 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
28945 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
28964 TGAAGATACATG
1 TGAAAATACATG
28976 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:31883 original size:24 final size:24
Alignment explanation
Indices: 31844--31892 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
31834 TAGAAAATGG
* *
31844 TAAGAAAAGGATAAAGTAATGAAA
1 TAAGAAAAGGATAAAGAAAGGAAA
31868 TAAGAAAA-GATGAAAGAAAGGAAA
1 TAAGAAAAGGAT-AAAGAAAGGAAA
31892 T
1 T
31893 GAAATAGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.14
Consensus pattern (24 bp):
TAAGAAAAGGATAAAGAAAGGAAA
Found at i:32537 original size:33 final size:33
Alignment explanation
Indices: 32495--32563 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
32485 GTTGATGAAT
*
32495 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
32528 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
32561 GAA
1 GAA
32564 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:32983 original size:19 final size:20
Alignment explanation
Indices: 32936--32986 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
32926 TGAATCCCTT
**
32936 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
32956 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
32975 TGAAGATACATG
1 TGAAAATACATG
32987 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Done.