Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005076.1 Hibiscus syriacus cultivar Beakdansim tig00011399_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: 87272
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1058 original size:19 final size:16
Alignment explanation
Indices: 1034--1084 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 16
1024 AATGCATTTT
1034 ATGCATCGATGCACATACC
1 ATGCATCGATGCAC-T--C
*
1053 ATGCATCGACGCACTC
1 ATGCATCGATGCACTC
1069 AGTGCATCGATGCACT
1 A-TGCATCGATGCACT
1085 TAGGCTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 2 0.07
17 13 0.45
18 1 0.03
19 13 0.45
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (16 bp):
ATGCATCGATGCACTC
Found at i:7915 original size:23 final size:23
Alignment explanation
Indices: 7866--7915 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
7856 AATATTTTAT
* * *
7866 TTTAATTAAATTATATTTAAATT
1 TTTAACTAAATTATAATTAAATG
* *
7889 TTTAACTAATTTATAATTATATG
1 TTTAACTAAATTATAATTAAATG
7912 TTTA
1 TTTA
7916 GTACTTCATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTAACTAAATTATAATTAAATG
Found at i:8191 original size:56 final size:56
Alignment explanation
Indices: 8130--8243 Score: 151
Period size: 56 Copynumber: 2.0 Consensus size: 56
8120 TTAAAATACA
*
8130 TAAATGAT-TCCCGACTATAGGATACTACTTTGTTGAGTCTC-CCGGCTATTAAAAGT
1 TAAATGATCTCCCGACTATAAG-TACTACTTTGTTGAGTC-CACCGGCTATTAAAAGT
* * * *
8186 TAAATGATCTCTCGATTATAAGTATTACTTTGTTGAGTCCATCGGCTATTAAAAGT
1 TAAATGATCTCCCGACTATAAGTACTACTTTGTTGAGTCCACCGGCTATTAAAAGT
8242 TA
1 TA
8244 TAAAATGACC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
55 1 0.02
56 40 0.78
57 10 0.20
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (56 bp):
TAAATGATCTCCCGACTATAAGTACTACTTTGTTGAGTCCACCGGCTATTAAAAGT
Found at i:9498 original size:16 final size:17
Alignment explanation
Indices: 9460--9504 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
9450 TGTTTATGAG
*
9460 GGAATTGGAATCTGTGAA
1 GGAATTGGAATATGT-AA
9478 GGAATTGGAATATGT-A
1 GGAATTGGAATATGTAA
9494 GGAATTGGAAT
1 GGAATTGGAAT
9505 CCAATTTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.36, C:0.02, G:0.33, T:0.29
Consensus pattern (17 bp):
GGAATTGGAATATGTAA
Found at i:10196 original size:31 final size:31
Alignment explanation
Indices: 10104--10197 Score: 82
Period size: 31 Copynumber: 2.9 Consensus size: 31
10094 CACTTAAAAA
* ** *
10104 ACCCGACCCGACCCGAACAAAATAAAGTTTC
1 ACCCGACCCGACCCGAACATAATAAAAATCC
* *
10135 ATCCGACCCGACCCGAATATATGAATTAAAAATCC
1 ACCCGACCCGACCCG-A-ACAT-AA-TAAAAATCC
10170 GACCCGACCCGACCCGAA-ATAATAAAAA
1 -ACCCGACCCGACCCGAACATAATAAAAA
10198 ATTATTTTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
31 20 0.39
32 3 0.06
33 4 0.08
34 3 0.06
35 7 0.14
36 14 0.27
ACGTcount: A:0.41, C:0.32, G:0.13, T:0.14
Consensus pattern (31 bp):
ACCCGACCCGACCCGAACATAATAAAAATCC
Found at i:10342 original size:37 final size:37
Alignment explanation
Indices: 10285--10377 Score: 159
Period size: 37 Copynumber: 2.5 Consensus size: 37
10275 TCTTCACCCT
10285 AAACCCGAACCCGACCCGACCCGAATATCACACTTAAA
1 AAACCCG-ACCCGACCCGACCCGAATATCACACTTAAA
*
10323 AAACCCGACCCGACTCGACCCGAATATCACACTTAAA
1 AAACCCGACCCGACCCGACCCGAATATCACACTTAAA
*
10360 AAACCTGACCCGACCCGA
1 AAACCCGACCCGACCCGA
10378 ACAAAATAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 45 0.87
38 7 0.13
ACGTcount: A:0.38, C:0.40, G:0.12, T:0.11
Consensus pattern (37 bp):
AAACCCGACCCGACCCGACCCGAATATCACACTTAAA
Found at i:10352 original size:258 final size:254
Alignment explanation
Indices: 10068--10570 Score: 769
Period size: 258 Copynumber: 1.9 Consensus size: 254
10058 TAAACCCGAT
10068 CCCGACCCGACCTAACCCGAATATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAGTT
1 CCCGACCCGACCTAACCCGAATATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAGTT
10133 TCAT-CCGACCCGACCCGAATATATGAATTAAAAATCCGACCCGACCCGACCCGAAATAATAAAA
66 TCATCCCGACCCGACCCGAATATATGAATTAAAAAT-----CCGACCCGACCCGAAATAATAAAA
* * * *
10197 AATTATTTTTATTTAATAAAAACAATTACTTAATCCGACCCGACCCGAATTATATATATTTTCGG
126 AAATATTTTTATTTAATAAAAACAATGACTTAATCCAACCCGACCCGAATTATATATATATTCGG
10262 GTCGG-TCTGGTTTTCTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAA
191 GTCGGTTC-GGTTTTCTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAA
* *
10326 CCCGACCCGA-CTCGACCCGAATATCACACTTAAAAAACCTGACCCGACCCGAACAAAATAAAGT
1 CCCGACCCGACCT-AACCCGAATATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAGT
* *
10390 TTCATCCGACCCGACCCGACCCGAATATATGAATTAGAAATCCGATCCGACCCGAAATAATAAAA
65 TTCAT----CCCGACCCGACCCGAATATATGAATTAAAAATCCGACCCGACCCGAAATAATAAAA
* * *
10455 AAATATTTTTATTTAATAAAAACAGTGACTTAATCCAACCTGACCTGAATTATATATATATTCGG
126 AAATATTTTTATTTAATAAAAACAATGACTTAATCCAACCCGACCCGAATTATATATATATTCGG
* *
10520 GTTGGTTCGGTTTTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATAT
191 GTCGGTTCGGTTTTCTTCACCCTAAACCCGAACCCGACCCGACCCGAATAT
10571 ATGAATTAGA
Statistics
Matches: 225, Mismatches: 13, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
257 2 0.01
258 191 0.85
259 2 0.01
263 30 0.13
ACGTcount: A:0.36, C:0.29, G:0.12, T:0.23
Consensus pattern (254 bp):
CCCGACCCGACCTAACCCGAATATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAGTT
TCATCCCGACCCGACCCGAATATATGAATTAAAAATCCGACCCGACCCGAAATAATAAAAAAATA
TTTTTATTTAATAAAAACAATGACTTAATCCAACCCGACCCGAATTATATATATATTCGGGTCGG
TTCGGTTTTCTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAA
Found at i:11128 original size:23 final size:24
Alignment explanation
Indices: 11102--11156 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
11092 AATATCTCTT
* *
11102 TTGTGACACAT-TTTTCTTTGCCC
1 TTGTGACACATATTTTATCTGCCC
* *
11125 TTGTGACACTTATTTTATCTGCTC
1 TTGTGACACATATTTTATCTGCCC
11149 TTGTGACA
1 TTGTGACA
11157 TGATTCTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.16, C:0.22, G:0.15, T:0.47
Consensus pattern (24 bp):
TTGTGACACATATTTTATCTGCCC
Found at i:11151 original size:24 final size:23
Alignment explanation
Indices: 11094--11156 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
11084 TGAATAAGAA
*
11094 TATCT-CTTTTGTGACACATTTT
1 TATCTGCTCTTGTGACACATTTT
* * * *
11116 TCTTTGCCCTTGTGACACTTATTT
1 TATCTGCTCTTGTGACACAT-TTT
11140 TATCTGCTCTTGTGACA
1 TATCTGCTCTTGTGACA
11157 TGATTCTTAT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
22 3 0.10
23 11 0.35
24 17 0.55
ACGTcount: A:0.16, C:0.22, G:0.13, T:0.49
Consensus pattern (23 bp):
TATCTGCTCTTGTGACACATTTT
Found at i:11503 original size:21 final size:21
Alignment explanation
Indices: 11474--11526 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
11464 ATTCTGACTA
11474 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
11495 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
* *
11516 TCACAATGCGA
1 TCGCATTGCGA
11527 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:11548 original size:20 final size:20
Alignment explanation
Indices: 11519--11644 Score: 146
Period size: 20 Copynumber: 6.2 Consensus size: 20
11509 TCCTAATTCA
11519 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
* ** *
11539 CAACGCGAATTTGGAAAATCG
1 CAATGCGAA-TACGTAAATCG
11560 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
* *
11580 CAATGCGATTACACATAAATCG
1 CAATGCGA--ATACGTAAATCG
*
11602 CAATGCGAATACGTAAATCT
1 CAATGCGAATACGTAAATCG
11622 CAATGCGAAT-CTGTAAATCG
1 CAATGCGAATAC-GTAAATCG
11642 CAA
1 CAA
11645 CGAGATTCTG
Statistics
Matches: 88, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.01
20 53 0.60
21 16 0.18
22 18 0.20
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (20 bp):
CAATGCGAATACGTAAATCG
Found at i:11613 original size:42 final size:40
Alignment explanation
Indices: 11519--11629 Score: 150
Period size: 42 Copynumber: 2.7 Consensus size: 40
11509 TCCTAATTCA
* ***
11519 CAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAATCG
1 CAATGCGAATACGTAAATCGCAATGCG-ATTCACAAAATCG
11560 CAATGCGAATACGTAAATCGCAATGCGATTACACATAAATCG
1 CAATGCGAATACGTAAATCGCAATGCGATT-CACA-AAATCG
*
11602 CAATGCGAATACGTAAATCTCAATGCGA
1 CAATGCGAATACGTAAATCGCAATGCGA
11630 ATCTGTAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
40 3 0.05
41 27 0.43
42 33 0.52
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (40 bp):
CAATGCGAATACGTAAATCGCAATGCGATTCACAAAATCG
Found at i:12530 original size:24 final size:24
Alignment explanation
Indices: 12503--12556 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
12493 GTATTCGAAA
12503 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
12527 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
12551 TTTGAT
1 TTTGAT
12557 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:15016 original size:20 final size:20
Alignment explanation
Indices: 14991--15079 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
14981 CAATGCGGAA
14991 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAATATGACT
* * *
15011 ATCGCAACACAAAAATGACT
1 ATCGCAACGCGAATATGACT
* *
15031 ATCACAATGCGGAAT-TGACT
1 ATCGCAACGC-GAATATGACT
15051 ATCGCAACATG-GAA-ATGACT
1 ATCGCAAC--GCGAATATGACT
15071 ATCGCAACG
1 ATCGCAACG
15080 AGAGAATCGC
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
18 1 0.02
20 51 0.93
21 2 0.04
22 1 0.02
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAATATGACT
Found at i:15101 original size:33 final size:33
Alignment explanation
Indices: 15062--15145 Score: 123
Period size: 33 Copynumber: 2.5 Consensus size: 33
15052 TCGCAACATG
**
15062 GAAATGACTATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
*
15095 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
*
15128 GAAAATGAAAATTGCAAC
1 G-AAATGAAAATCGCAAC
15146 ACGAAATTAG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 31 0.67
34 15 0.33
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:15342 original size:14 final size:14
Alignment explanation
Indices: 15323--15359 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
15313 CACCAATTAA
15323 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
15337 ACAAATCATCTTTT
1 ACAAATCAACATTT
15351 ACAAATCAA
1 ACAAATCAA
15360 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:17384 original size:33 final size:33
Alignment explanation
Indices: 17305--17385 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
17295 GCAAATGACT
** * * *
17305 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCG-AAATGAAAATCGCAACAACAAA
* *
17339 ATTGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACAACAAA
17372 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
17386 ATGACTATCG
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
33 29 0.76
34 9 0.24
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACAACAAA
Found at i:17490 original size:20 final size:20
Alignment explanation
Indices: 17465--17608 Score: 183
Period size: 20 Copynumber: 7.5 Consensus size: 20
17455 GATTCTTTCG
**
17465 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
17485 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
17505 TTGAGATAGTAATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
17525 TTGTGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
17545 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
17559 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
17579 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
17599 TTGCGATAGT
1 TTGCGATAGT
17609 AAACTATTCT
Statistics
Matches: 108, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
14 7 0.06
16 6 0.06
18 6 0.06
20 89 0.82
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:19504 original size:20 final size:20
Alignment explanation
Indices: 19481--19535 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
19471 CTGAAACTTT
19481 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
19501 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
19521 CTATCGCAACGCGAA
1 AAATCGCAACACGAA
19536 TTTGACTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:19541 original size:20 final size:20
Alignment explanation
Indices: 19483--19552 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
19473 GAAACTTTAA
* **
19483 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
19503 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
19523 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
19543 ATCGTAACGC
1 ATCGCAACGC
19553 AAGAATCGCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:19621 original size:20 final size:20
Alignment explanation
Indices: 19596--19642 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
19586 GATTCTCTCG
19596 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
19616 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
19636 TTGCGAT
1 TTGCGAT
19643 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:20308 original size:21 final size:20
Alignment explanation
Indices: 20232--20308 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
20222 CGATAGTCAG
*
20232 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCAATTTACGT
* * **
20252 AATCGCATTGCAATTTTCCAA
1 ATTCGCATTGCAA-TTTACGT
*
20273 ATTCGCGTTGCAATTTACGT
1 ATTCGCATTGCAATTTACGT
20293 ATTCGCATTGCGAATT
1 ATTCGCATTGC-AATT
20309 AGGAAAATCG
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
20 25 0.57
21 19 0.43
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCAATTTACGT
Found at i:20319 original size:21 final size:21
Alignment explanation
Indices: 20295--20347 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
20285 ATTTACGTAT
*
20295 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* * *
20316 TCGCAACGCGAATTTGGGAAA
1 TCGCAATGCGAATTAGGAAAA
20337 TCGCAATGCGA
1 TCGCAATGCGA
20348 TAGTCAGAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:24198 original size:2 final size:2
Alignment explanation
Indices: 24191--24236 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
24181 ATCATTTGTG
24191 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24233 TA TA
1 TA TA
24237 GCATCCTCGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26081 original size:87 final size:88
Alignment explanation
Indices: 25920--26091 Score: 319
Period size: 87 Copynumber: 2.0 Consensus size: 88
25910 AACATGAAAA
*
25920 AACTTTCATCTCAAAATCAACTATCCATTTACCAGAAAAATAAATTATAGTTTAGAACCTAATCA
1 AACTTTCATCTCAAAATCAACTATCCATTTACCAGAAAAATAAAATATAGTTTAGAACCTAATCA
25985 AGTAAATTAAATCTTCTTGGAAC
66 AGTAAATTAAATCTTCTTGGAAC
*
26008 AACTTTCATCTCAAAATCAACTATCCATTTGCCAG-AAAATAAAATATAGTTTAGAACCTAATCA
1 AACTTTCATCTCAAAATCAACTATCCATTTACCAGAAAAATAAAATATAGTTTAGAACCTAATCA
26072 AGTAAATTAAATCTTCTTGG
66 AGTAAATTAAATCTTCTTGG
26092 GTTTATTGTA
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
87 48 0.59
88 34 0.41
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (88 bp):
AACTTTCATCTCAAAATCAACTATCCATTTACCAGAAAAATAAAATATAGTTTAGAACCTAATCA
AGTAAATTAAATCTTCTTGGAAC
Found at i:27583 original size:24 final size:24
Alignment explanation
Indices: 27551--27631 Score: 99
Period size: 24 Copynumber: 3.4 Consensus size: 24
27541 GATATTAGAA
* * *
27551 ATCAAAACAGAATTCAGATCATAT
1 ATCAGAACAGAATCCAGATCAGAT
*
27575 ATCAGAACAGAATCCAGATCAGAA
1 ATCAGAACAGAATCCAGATCAGAT
* * *
27599 ATCAGAACAGGATCCAGGTCAGGT
1 ATCAGAACAGAATCCAGATCAGAT
27623 ATCAGAACA
1 ATCAGAACA
27632 TAATTCAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.17
Consensus pattern (24 bp):
ATCAGAACAGAATCCAGATCAGAT
Found at i:28579 original size:20 final size:20
Alignment explanation
Indices: 28554--28609 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
28544 CGAACACGCA
28554 TTCAAGTAATATCTATGTCG
1 TTCAAGTAATATCTATGTCG
28574 TTCAAGTAATATCTATGTCG
1 TTCAAGTAATATCTATGTCG
28594 TTCAAGTAATATCTAT
1 TTCAAGTAATATCTAT
28610 ATCATTAAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.41
Consensus pattern (20 bp):
TTCAAGTAATATCTATGTCG
Found at i:32011 original size:24 final size:24
Alignment explanation
Indices: 31951--32021 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
31941 GTTAACGGAG
* * * *
31951 ATATTAGAAATCAAAATAGAATTC
1 ATATAAGAAATCAGAACAGAATCC
* * *
31975 AGATCAGATATCAGAACAGAATCC
1 ATATAAGAAATCAGAACAGAATCC
31999 ATATAAGAAATCAGAACAGAATC
1 ATATAAGAAATCAGAACAGAATC
32022 TAGGTCATGT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.52, C:0.14, G:0.13, T:0.21
Consensus pattern (24 bp):
ATATAAGAAATCAGAACAGAATCC
Found at i:34323 original size:11 final size:11
Alignment explanation
Indices: 34307--34374 Score: 82
Period size: 11 Copynumber: 5.9 Consensus size: 11
34297 ACGGTTAACG
34307 GTCAACGGTCA
1 GTCAACGGTCA
34318 GTCAACGGTCA
1 GTCAACGGTCA
* *
34329 GTCAAAGTGTCG
1 GTCAACG-GTCA
34341 GTCAACGGTCA
1 GTCAACGGTCA
*
34352 GTCAACGAGTCG
1 GTCAACG-GTCA
34364 GTCAACAGGTC
1 GTCAAC-GGTC
34375 GGGTCGGACC
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
11 27 0.55
12 21 0.43
13 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.29, T:0.19
Consensus pattern (11 bp):
GTCAACGGTCA
Found at i:34328 original size:34 final size:34
Alignment explanation
Indices: 34305--34376 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
34295 GCACGGTTAA
34305 CGGTCAACGGTCAGTCAACGGTCAGTCAAAGTGT
1 CGGTCAACGGTCAGTCAACGGTCAGTCAAAGTGT
*
34339 CGGTCAACGGTCAGTCAACGAGTCGGTCAACAG-GT
1 CGGTCAACGGTCAGTCAACG-GTCAGTCAA-AGTGT
34374 CGG
1 CGG
34377 GTCGGACCAG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
34 20 0.57
35 13 0.37
36 2 0.06
ACGTcount: A:0.25, C:0.25, G:0.32, T:0.18
Consensus pattern (34 bp):
CGGTCAACGGTCAGTCAACGGTCAGTCAAAGTGT
Found at i:34345 original size:23 final size:23
Alignment explanation
Indices: 34318--34374 Score: 87
Period size: 23 Copynumber: 2.4 Consensus size: 23
34308 TCAACGGTCA
*
34318 GTCAACGGTCAGTCAAAGTGTCG
1 GTCAACGGTCAGTCAAAGAGTCG
*
34341 GTCAACGGTCAGTCAACGAGTCG
1 GTCAACGGTCAGTCAAAGAGTCG
34364 GTCAACAGGTC
1 GTCAAC-GGTC
34375 GGGTCGGACC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 27 0.87
24 4 0.13
ACGTcount: A:0.26, C:0.25, G:0.30, T:0.19
Consensus pattern (23 bp):
GTCAACGGTCAGTCAAAGAGTCG
Found at i:42426 original size:17 final size:17
Alignment explanation
Indices: 42404--42442 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
42394 TTAAGTGGTT
42404 AAAGTATAAACTTTGGA
1 AAAGTATAAACTTTGGA
42421 AAAGTATAAACTTTGGA
1 AAAGTATAAACTTTGGA
42438 AAAGT
1 AAAGT
42443 TTAGGGACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.49, C:0.05, G:0.18, T:0.28
Consensus pattern (17 bp):
AAAGTATAAACTTTGGA
Found at i:51606 original size:90 final size:89
Alignment explanation
Indices: 51444--51622 Score: 277
Period size: 90 Copynumber: 2.0 Consensus size: 89
51434 GACCTAACAC
* *
51444 ACCCTTTTATAGCCAACTTACCCTAATCATATTAGGGTTTTATTGTTTCAAATTAATTAAATCTA
1 ACCCTCTTATAGCCAACTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTA
* * *
51509 TATTTAATTAATTGAAATTTAATA
66 AATTTAATTAATTAAAATTAAATA
* * *
51533 ACCCTCTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTGAAATTAATTAAATCT
1 ACCCTCTTATAGCCAACTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCT
51598 AAATTTAATTAATTAAAATTAAATA
65 AAATTTAATTAATTAAAATTAAATA
51623 TTCGGGATTA
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
89 34 0.42
90 47 0.58
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (89 bp):
ACCCTCTTATAGCCAACTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTA
AATTTAATTAATTAAAATTAAATA
Found at i:56141 original size:5 final size:5
Alignment explanation
Indices: 56131--56183 Score: 56
Period size: 5 Copynumber: 11.0 Consensus size: 5
56121 TGACCGGTCT
* * * *
56131 GACCC GACCC GACCC GACCC AAACC GACCC GA-CT GA-CC GACCC GACCT
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC
56179 GACCC
1 GACCC
56184 TTTGGCCCCT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
4 6 0.15
5 33 0.85
ACGTcount: A:0.25, C:0.53, G:0.19, T:0.04
Consensus pattern (5 bp):
GACCC
Found at i:56171 original size:13 final size:14
Alignment explanation
Indices: 56139--56182 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
56129 CTGACCCGAC
**
56139 CCGACCCGACCCAAA
1 CCGACCCGA-CCTGA
56154 CCGACCCGA-CTGA
1 CCGACCCGACCTGA
56167 CCGACCCGACCTGA
1 CCGACCCGACCTGA
56181 CC
1 CC
56183 CTTTGGCCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 11 0.42
14 6 0.23
15 9 0.35
ACGTcount: A:0.25, C:0.52, G:0.18, T:0.05
Consensus pattern (14 bp):
CCGACCCGACCTGA
Found at i:69651 original size:18 final size:18
Alignment explanation
Indices: 69628--69663 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
69618 GGATCGGTCA
*
69628 ACGGCTCGGCTCTGCTCG
1 ACGGCTCGACTCTGCTCG
*
69646 ACGGCTCGACTCTTCTCG
1 ACGGCTCGACTCTGCTCG
69664 GCAGCTCAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.08, C:0.39, G:0.28, T:0.25
Consensus pattern (18 bp):
ACGGCTCGACTCTGCTCG
Found at i:71669 original size:32 final size:32
Alignment explanation
Indices: 71623--71705 Score: 148
Period size: 32 Copynumber: 2.6 Consensus size: 32
71613 GCACCTTGGT
*
71623 GCCTAAGAGCCTACCCAAGAAAGATTATCGGG
1 GCCTCAGAGCCTACCCAAGAAAGATTATCGGG
*
71655 GCCTCAGAGCCTACCCAAGAAAGATTCTCGGG
1 GCCTCAGAGCCTACCCAAGAAAGATTATCGGG
71687 GCCTCAGAGCCTACCCAAG
1 GCCTCAGAGCCTACCCAAG
71706 GGTCGCCTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.30, C:0.31, G:0.24, T:0.14
Consensus pattern (32 bp):
GCCTCAGAGCCTACCCAAGAAAGATTATCGGG
Found at i:74883 original size:21 final size:23
Alignment explanation
Indices: 74859--74904 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
74849 TGATCGTTAC
74859 ATATGATGTT-ATCATGAAT-AT
1 ATATGATGTTAATCATGAATGAT
*
74880 ATATGATTTTAATCATGAATGAT
1 ATATGATGTTAATCATGAATGAT
74903 AT
1 AT
74905 TATGGGTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.41
22 9 0.41
23 4 0.18
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.43
Consensus pattern (23 bp):
ATATGATGTTAATCATGAATGAT
Found at i:79774 original size:66 final size:67
Alignment explanation
Indices: 79653--79785 Score: 160
Period size: 66 Copynumber: 2.0 Consensus size: 67
79643 CCTTAGGTGA
* **
79653 ATAAGGAATTACCAGTCGGTGCCGAACCTATAAAAGGAATTACCAACAATAACTAAACCTGTCAG
1 ATAAGGAATTACCAGTCGATGCAAAACCTATAAAAGGAATTACCAACAATAACTAAACCTGTCAG
79718 AG
66 AG
* ** ** * * *
79720 ATAA-GAATTACCAGTCGATGTAAAACCTATACGAGGAATTACCCGCAGTGACTAAACCTGTTAG
1 ATAAGGAATTACCAGTCGATGCAAAACCTATAAAAGGAATTACCAACAATAACTAAACCTGTCAG
79784 AG
66 AG
79786 TCTTCATACT
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
66 51 0.93
67 4 0.07
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (67 bp):
ATAAGGAATTACCAGTCGATGCAAAACCTATAAAAGGAATTACCAACAATAACTAAACCTGTCAG
AG
Done.