Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006943.1 Hibiscus syriacus cultivar Beakdansim tig00017844_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: 58890
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:420 original size:19 final size:19
Alignment explanation
Indices: 396--440 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
386 AAATTTGTAT
396 TGTTCTCTTTGGGAGAGAG
1 TGTTCTCTTTGGGAGAGAG
*
415 TGTTCTCTTTTGGAGAGAG
1 TGTTCTCTTTGGGAGAGAG
434 TGTTCTC
1 TGTTCTC
441 AAGAATTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.31, T:0.42
Consensus pattern (19 bp):
TGTTCTCTTTGGGAGAGAG
Found at i:5376 original size:20 final size:20
Alignment explanation
Indices: 5332--5376 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
5322 AAATTATTAT
5332 TTTATTATTTTGATGTTTTA
1 TTTATTATTTTGATGTTTTA
* *
5352 ATTATTATCTTTTATG-TTTA
1 TTTATTAT-TTTGATGTTTTA
5372 TTTAT
1 TTTAT
5377 CCTTTCGTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (20 bp):
TTTATTATTTTGATGTTTTA
Found at i:13708 original size:95 final size:95
Alignment explanation
Indices: 13598--13787 Score: 362
Period size: 95 Copynumber: 2.0 Consensus size: 95
13588 CATCTTTTAG
* *
13598 TTTCACTTATCTTGCCTATAAACAAGGGTCTTGTGTAATACTTCATCTCTCCCTTTAGATCTTTT
1 TTTCACTTATCTTGCCTATAAACAAGAGTCTTGTGTAATACTTCATCTCTCCCTTTAGATATTTT
13663 GATTTTTATAATTTTCATATTAAAAAGTCA
66 GATTTTTATAATTTTCATATTAAAAAGTCA
13693 TTTCACTTATCTTGCCTATAAACAAGAGTCTTGTGTAATACTTCATCTCTCCCTTTAGATATTTT
1 TTTCACTTATCTTGCCTATAAACAAGAGTCTTGTGTAATACTTCATCTCTCCCTTTAGATATTTT
13758 GATTTTTATAATTTTCATATTAAAAAGTCA
66 GATTTTTATAATTTTCATATTAAAAAGTCA
13788 ACAAACAAAG
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 93 1.00
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.45
Consensus pattern (95 bp):
TTTCACTTATCTTGCCTATAAACAAGAGTCTTGTGTAATACTTCATCTCTCCCTTTAGATATTTT
GATTTTTATAATTTTCATATTAAAAAGTCA
Found at i:21142 original size:13 final size:13
Alignment explanation
Indices: 21124--21160 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
21114 ACCAGAGACG
*
21124 CTTGAGTAGCAAA
1 CTTGAGCAGCAAA
21137 CTTGAGCAGCAAA
1 CTTGAGCAGCAAA
21150 CTTGAGCAGCA
1 CTTGAGCAGCA
21161 GTAGCTAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (13 bp):
CTTGAGCAGCAAA
Found at i:23215 original size:29 final size:29
Alignment explanation
Indices: 23173--23231 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
23163 GGTATATCCA
23173 AGCTTAAGGCTAAGCTTCTGAAATTATGT
1 AGCTTAAGGCTAAGCTTCTGAAATTATGT
*
23202 AGCTTAAGGTTAAGCTTCTGAAATTATGT
1 AGCTTAAGGCTAAGCTTCTGAAATTATGT
23231 A
1 A
23232 CTCCTATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (29 bp):
AGCTTAAGGCTAAGCTTCTGAAATTATGT
Found at i:24338 original size:22 final size:22
Alignment explanation
Indices: 24290--24338 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
24280 GATTGAGATA
*
24290 GATTTGTGTTTTAGAATTTAAG
1 GATTTATGTTTTAGAATTTAAG
* *
24312 AATTTATGTATTT-GAATTTAGG
1 GATTTATGT-TTTAGAATTTAAG
24334 GATTT
1 GATTT
24339 TGAAGATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (22 bp):
GATTTATGTTTTAGAATTTAAG
Found at i:28580 original size:13 final size:13
Alignment explanation
Indices: 28564--28601 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
28554 AAAACAGTAA
28564 GAAAAAAATGGAT
1 GAAAAAAATGGAT
28577 GAAAAAAATGGAT
1 GAAAAAAATGGAT
28590 GAAAAAAATGGA
1 GAAAAAAATGGA
28602 AATTTCCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.24, T:0.13
Consensus pattern (13 bp):
GAAAAAAATGGAT
Found at i:30005 original size:12 final size:12
Alignment explanation
Indices: 29988--30042 Score: 60
Period size: 12 Copynumber: 4.5 Consensus size: 12
29978 ATATACAATA
29988 AAAAAATATAAT
1 AAAAAATATAAT
30000 -AAAAA-ATAAT
1 AAAAAATATAAT
*
30010 AGAAATATATACAAT
1 A-AAA-A-ATATAAT
30025 AAAAAATATAAT
1 AAAAAATATAAT
30037 AAAAAA
1 AAAAAA
30043 CAATTTAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
10 5 0.14
11 5 0.14
12 15 0.42
13 2 0.06
14 4 0.11
15 5 0.14
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (12 bp):
AAAAAATATAAT
Found at i:30038 original size:37 final size:38
Alignment explanation
Indices: 29961--30042 Score: 139
Period size: 38 Copynumber: 2.2 Consensus size: 38
29951 AATTTAAGAT
* *
29961 TAAAAAGTATTAGAAATATATACAATAAAAAAATATAA
1 TAAAAAATAATAGAAATATATACAATAAAAAAATATAA
29999 TAAAAAATAATAGAAATATATACAAT-AAAAAATATAA
1 TAAAAAATAATAGAAATATATACAATAAAAAAATATAA
30036 TAAAAAA
1 TAAAAAA
30043 CAATTTAGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
37 18 0.43
38 24 0.57
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (38 bp):
TAAAAAATAATAGAAATATATACAATAAAAAAATATAA
Found at i:34552 original size:18 final size:19
Alignment explanation
Indices: 34524--34560 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
34514 AAAAAGTTTG
34524 TCTCATTCTTTCTTCTCCA
1 TCTCATTCTTTCTTCTCCA
34543 TCTC-TTCTTTCTTCTCCA
1 TCTCATTCTTTCTTCTCCA
34561 AGAATTAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.08, C:0.38, G:0.00, T:0.54
Consensus pattern (19 bp):
TCTCATTCTTTCTTCTCCA
Found at i:36300 original size:82 final size:81
Alignment explanation
Indices: 36194--36532 Score: 241
Period size: 82 Copynumber: 4.1 Consensus size: 81
36184 GATACTTTAA
* * * * * * * * *
36194 TGGCATTTTCCAATAAACGCCGTAATAGAGTGGTAATTTAGAGGCGTTTATAGCACAAACACCGG
1 TGGCATTTTTCAACAAACGACGTAATACAGTAGTAATTTAGCGGCGTTTATA-AACAAACGCCGA
*
36259 AATAGAGTTGTTTATAG
65 AATAGGGTTGTTTATAG
* * * * * * * **
36276 TGGCTTTTTTCAACAAACGTCGTAATATAATAGTAATTTAGCGGTGTTTTTATACAAACGCCTCA
1 TGGCATTTTTCAACAAACGACGTAATACAGTAGTAATTTAGCGGCGTTTATAAACAAACGCCGAA
*
36341 ACAGGGTTGTTTATAG
66 ATAGGGTTGTTTATAG
* * * * *
36357 TGGCGTTTGTCAAACAAACGACGCT-ATACAGAAGTAATTTAGCGGCATTTATCAAACAAACGTC
1 TGGCATTTTTC-AACAAACGACG-TAATACAGTAGTAATTTAGCGGCGTTTAT-AAACAAACGCC
36421 GAAATAGGGTTGTTTATAG
63 GAAATAGGGTTGTTTATAG
* * * * * * * * ** * *
36440 TGGCATTTATACAAAAAAAGGTCATTATAAAGTAGTAATTTAGCGGTGTTT-TCCTACAAATGTC
1 TGGCATTT-TTC-AACAAACGACGTAATACAGTAGTAATTTAGCGGCGTTTAT-AAACAAACGCC
* * *
36504 GTAATATGGTTATTTATAG
63 GAAATAGGGTTGTTTATAG
36523 TGGCATTTTT
1 TGGCATTTTT
36533 AGAAAAAATG
Statistics
Matches: 204, Mismatches: 48, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
81 32 0.16
82 74 0.36
83 68 0.33
84 30 0.15
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (81 bp):
TGGCATTTTTCAACAAACGACGTAATACAGTAGTAATTTAGCGGCGTTTATAAACAAACGCCGAA
ATAGGGTTGTTTATAG
Found at i:36439 original size:83 final size:81
Alignment explanation
Indices: 36248--36443 Score: 207
Period size: 81 Copynumber: 2.4 Consensus size: 81
36238 CGTTTATAGC
* * * * * * *
36248 ACAAACACCGGAATAGAGTTGTTTATAGTGGCTTTTTTCAACAAACGTCGTAATATAATAGTAAT
1 ACAAACGCCGAAATAGGGTTGTTTATAGTGGCGTTTGTCAACAAACGACGTAATACAATAGTAAT
** * *
36313 TTAGCGGTGTTTTTAT
66 TTAGCGGCATTTTCAA
** *
36329 ACAAACGCCTCAACAGGGTTGTTTATAGTGGCGTTTGTCAAACAAACGACGCT-ATACAGA-AGT
1 ACAAACGCCGAAATAGGGTTGTTTATAGTGGCGTTTGTC-AACAAACGACG-TAATACA-ATAGT
36392 AATTTAGCGGCATTTATCAA
63 AATTTAGCGGCATTT-TCAA
*
36412 ACAAACGTCGAAATAGGGTTGTTTATAGTGGC
1 ACAAACGCCGAAATAGGGTTGTTTATAGTGGC
36444 ATTTATACAA
Statistics
Matches: 94, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
81 32 0.34
82 30 0.32
83 32 0.34
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (81 bp):
ACAAACGCCGAAATAGGGTTGTTTATAGTGGCGTTTGTCAACAAACGACGTAATACAATAGTAAT
TTAGCGGCATTTTCAA
Found at i:36499 original size:83 final size:83
Alignment explanation
Indices: 36259--36540 Score: 266
Period size: 83 Copynumber: 3.4 Consensus size: 83
36249 CAAACACCGG
* * * *
36259 AATAGAGTTGTTTATAGTGGC-TTTTTTC-AACAAACGTCGTAATATAA-TAGTAATTTAGCGGT
1 AATAGGGTTGTTTATAGTGGCATTTTTACAAAAAAACGTCGTTATA-AAGTAGTAATTTAGCGGT
* * **
36321 GTTTTTATACAAACGCCTC
65 GTTTTCATACAAACGTCGA
* * * * * * * * **
36340 AACAGGGTTGTTTATAGTGGCGTTTGT-CAAACAAACGACGCTATACAGAAGTAATTTAGCGGCA
1 AATAGGGTTGTTTATAGTGGCATTTTTACAAAAAAACGTCGTTATAAAGTAGTAATTTAGCGGTG
*
36404 TTTATCAAACAAACGTCGA
66 TTT-TCATACAAACGTCGA
* * *
36423 AATAGGGTTGTTTATAGTGGCATTTATACAAAAAAAGGTCATTATAAAGTAGTAATTTAGCGGTG
1 AATAGGGTTGTTTATAGTGGCATTTTTACAAAAAAACGTCGTTATAAAGTAGTAATTTAGCGGTG
* * *
36488 TTTTCCTACAAATGTCGT
66 TTTTCATACAAACGTCGA
* * *
36506 AATATGGTTATTTATAGTGGCATTTTTAGAAAAAA
1 AATAGGGTTGTTTATAGTGGCATTTTTACAAAAAA
36541 TGCCATAATA
Statistics
Matches: 161, Mismatches: 35, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
81 21 0.13
82 33 0.20
83 76 0.47
84 31 0.19
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (83 bp):
AATAGGGTTGTTTATAGTGGCATTTTTACAAAAAAACGTCGTTATAAAGTAGTAATTTAGCGGTG
TTTTCATACAAACGTCGA
Found at i:36982 original size:22 final size:22
Alignment explanation
Indices: 36954--36998 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
36944 ATATATATAC
36954 ATAGGAAAATAATAACTTTTGA
1 ATAGGAAAATAATAACTTTTGA
*
36976 ATAGGAAAATAATAGCTTTTGA
1 ATAGGAAAATAATAACTTTTGA
36998 A
1 A
36999 AACCCGAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.04, G:0.16, T:0.31
Consensus pattern (22 bp):
ATAGGAAAATAATAACTTTTGA
Found at i:39183 original size:43 final size:43
Alignment explanation
Indices: 39121--39318 Score: 238
Period size: 43 Copynumber: 4.6 Consensus size: 43
39111 GAAGGATATA
*
39121 TCGCGCCTTCAGTCGCCACCATTCACTCAGTCGGTTCCTTGCG
1 TCGCGCCTTCAGTCGCCACCATTCACTCAGTCGGTTCCTTACG
** *
39164 TCGCGCCTTCAGTTTCCACCATTCACTCCG-CTGGTTCCTTACG
1 TCGCGCCTTCAGTCGCCACCATTCACTCAGTC-GGTTCCTTACG
** *
39207 TCGCATCTTCAGTCGCCACCATTCACTCAGTCGGTTCCTTGCG
1 TCGCGCCTTCAGTCGCCACCATTCACTCAGTCGGTTCCTTACG
** *
39250 TCGCGCCTTCAGTTTCCACCATTCACTTC-GCCGGTTCCTTACG
1 TCGCGCCTTCAGTCGCCACCATTCAC-TCAGTCGGTTCCTTACG
** * *
39293 TCGCATCTTCAGTCACCACTATTCAC
1 TCGCGCCTTCAGTCGCCACCATTCAC
39319 GCCGTTCAAA
Statistics
Matches: 131, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
42 1 0.01
43 127 0.97
44 3 0.02
ACGTcount: A:0.14, C:0.39, G:0.17, T:0.31
Consensus pattern (43 bp):
TCGCGCCTTCAGTCGCCACCATTCACTCAGTCGGTTCCTTACG
Found at i:39272 original size:86 final size:86
Alignment explanation
Indices: 39127--39318 Score: 348
Period size: 86 Copynumber: 2.2 Consensus size: 86
39117 TATATCGCGC
39127 CTTCAGTCGCCACCATTCACTCAGTCGGTTCCTTGCGTCGCGCCTTCAGTTTCCACCATTCACTC
1 CTTCAGTCGCCACCATTCACTCAGTCGGTTCCTTGCGTCGCGCCTTCAGTTTCCACCATTCACTC
*
39192 CGCTGGTTCCTTACGTCGCAT
66 CGCCGGTTCCTTACGTCGCAT
*
39213 CTTCAGTCGCCACCATTCACTCAGTCGGTTCCTTGCGTCGCGCCTTCAGTTTCCACCATTCACTT
1 CTTCAGTCGCCACCATTCACTCAGTCGGTTCCTTGCGTCGCGCCTTCAGTTTCCACCATTCACTC
39278 CGCCGGTTCCTTACGTCGCAT
66 CGCCGGTTCCTTACGTCGCAT
* *
39299 CTTCAGTCACCACTATTCAC
1 CTTCAGTCGCCACCATTCAC
39319 GCCGTTCAAA
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 102 1.00
ACGTcount: A:0.14, C:0.39, G:0.16, T:0.31
Consensus pattern (86 bp):
CTTCAGTCGCCACCATTCACTCAGTCGGTTCCTTGCGTCGCGCCTTCAGTTTCCACCATTCACTC
CGCCGGTTCCTTACGTCGCAT
Found at i:40448 original size:5 final size:5
Alignment explanation
Indices: 40424--40571 Score: 273
Period size: 5 Copynumber: 30.0 Consensus size: 5
40414 ATCCTATACT
*
40424 TATCA T-TCA TA-CA CATCA TATCA TATCA TATCA TATCA TATCA TATCA
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
40472 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
40522 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
40572 CCAAACAAAC
Statistics
Matches: 139, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
4 7 0.05
5 132 0.95
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.39
Consensus pattern (5 bp):
TATCA
Found at i:49296 original size:40 final size:40
Alignment explanation
Indices: 49240--49361 Score: 217
Period size: 40 Copynumber: 3.0 Consensus size: 40
49230 TGTAGGTTTA
*
49240 TAATACACTTCTGTGTATATGGTGGGCATGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCATGACCTTATGTG
*
49280 TAATAAACTTCGGTGTATATGGTGGGCATGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCATGACCTTATGTG
*
49320 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCATGACCTTATGTG
49360 TA
1 TA
49362 GCACTACGGT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCATGACCTTATGTG
Found at i:49560 original size:47 final size:45
Alignment explanation
Indices: 49466--49590 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
49456 GTAACCATGT
* * *
49466 AAATAAGCTTACTAGCTTAGGGGAT-AATGGCAAGTATATGAGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATGAGTA
* *
49510 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTG-GTA
1 AAATAAGCTTACGAGCTTATGGGA--TAAATGGTAAGTA-TATGAGTA
*
49557 AAATGAGCTTACGAGCTTATGGGATAAATGGTAA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAA
49591 AAGATTTTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
44 21 0.30
45 10 0.14
46 1 0.01
47 35 0.50
48 3 0.04
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATGAGTA
Found at i:55575 original size:26 final size:26
Alignment explanation
Indices: 55528--55577 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
55518 GCTGCAAGGA
* *
55528 ATTTTTTTAACTTCATTTATTTAACC
1 ATTTTTTGAACTTCATTAATTTAACC
* *
55554 ATTTTTTGAATTTGATTAATTTAA
1 ATTTTTTGAACTTCATTAATTTAA
55578 TTTTTTTTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.30, C:0.08, G:0.04, T:0.58
Consensus pattern (26 bp):
ATTTTTTGAACTTCATTAATTTAACC
Found at i:55580 original size:23 final size:22
Alignment explanation
Indices: 55554--55605 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
55544 TTATTTAACC
55554 ATTTTTTGAATTTGATTAATTT
1 ATTTTTTGAATTTGATTAATTT
** *
55576 AATTTTTTTTATTTGTTTAATTT
1 -ATTTTTTGAATTTGATTAATTT
55599 -TTTTTTG
1 ATTTTTTG
55606 TTTTTAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 6 0.24
23 19 0.76
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (22 bp):
ATTTTTTGAATTTGATTAATTT
Found at i:56692 original size:16 final size:17
Alignment explanation
Indices: 56655--56695 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
56645 AAAATATAAA
*
56655 TAAA-TTTATTTTTCTT
1 TAAATTTTAATTTTCTT
*
56671 TTAATTTTAATTTT-TT
1 TAAATTTTAATTTTCTT
56687 TAAATTTTA
1 TAAATTTTA
56696 TCCAATCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
TAAATTTTAATTTTCTT
Found at i:57240 original size:4 final size:4
Alignment explanation
Indices: 57231--58890 Score: 3050
Period size: 4 Copynumber: 421.0 Consensus size: 4
57221 TGGTCACCAA
57231 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
57279 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
57327 -CAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT -CAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
57373 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
57421 ACAT ACAT ACAT -CAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
57468 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
57516 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC--
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
57562 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
57609 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT -ACAT ACAT
57658 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
57706 ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
57752 ACAT ACAT ACAT ACAT ACAT ACAT ACAAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT AC-AT ACAT ACAT ACAT ACAT ACAT
57801 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
57849 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
57897 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
57945 ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
57992 ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
58039 ACAT ACAT ACAT ACAT ACAT ACA- ACAT ACAT ACAC ATAC ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
58086 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
58134 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
58182 ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
58229 ACAT ACAT ACAT ACAT ACAT -CAAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT AC-AT ACAT ACAT ACAT ACAT ACAT ACAT
58277 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A-AT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
58324 ACAT ACAT ACAT AC-- ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
58368 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
58416 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
58464 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA- ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
58511 AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
58558 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
58604 ACAT ACAT ACAT ACAT ATAC ACAT ACAT -CAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
58651 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAC ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
58699 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
58747 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
58795 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
58843 ACAT ACAT --AT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACA- ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
58887 ACAT
1 ACAT
Statistics
Matches: 1616, Mismatches: 10, Indels: 60
0.96 0.01 0.04
Matches are distributed among these distances:
2 12 0.01
3 43 0.03
4 1552 0.96
5 9 0.01
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Done.