Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000906.1 Hibiscus syriacus cultivar Beakdansim tig00001788_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: 46660
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:7752 original size:24 final size:24
Alignment explanation
Indices: 7725--7790 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
7715 AAATTCAAAA
7725 CAGATATCAGAACAGAATCCAGAT
1 CAGATATCAGAACAGAATCCAGAT
* * * ** *
7749 CAGAAACCATAACAGAATTTAGGT
1 CAGATATCAGAACAGAATCCAGAT
7773 CATG-TATCAGAACAGAAT
1 CA-GATATCAGAACAGAAT
7791 TCAAGTAGGA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
24 31 0.97
25 1 0.03
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.20
Consensus pattern (24 bp):
CAGATATCAGAACAGAATCCAGAT
Found at i:12273 original size:24 final size:24
Alignment explanation
Indices: 12202--12291 Score: 83
Period size: 24 Copynumber: 3.8 Consensus size: 24
12192 AGATATCAGA
* *
12202 AAATCAAAATAGAATTCAGAACAG
1 AAATCAAAATAGAATTCAGATCAT
*
12226 ATATCAAAATAGAA-TCTAGATCAT
1 AAATCAAAATAGAATTC-AGATCAT
* *
12250 AAATCAGAATAGAATTCAGGTCAT
1 AAATCAAAATAGAATTCAGATCAT
** * *
12274 GCATCAGAACAGAATTCA
1 AAATCAAAATAGAATTCA
12292 AGTAGGAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
23 2 0.04
24 51 0.93
25 2 0.04
ACGTcount: A:0.50, C:0.14, G:0.13, T:0.22
Consensus pattern (24 bp):
AAATCAAAATAGAATTCAGATCAT
Found at i:16969 original size:24 final size:24
Alignment explanation
Indices: 16898--16987 Score: 81
Period size: 24 Copynumber: 3.8 Consensus size: 24
16888 AGATATCAGA
* * * *
16898 AAATCAAAATAGAATTCAGAACAG
1 AAATCAGAACAGAATTCAGATCAT
* * *
16922 ATATCAAAACAGAATCCAGATCAT
1 AAATCAGAACAGAATTCAGATCAT
* *
16946 AAATCAGAACAGAATTTAGGTCAT
1 AAATCAGAACAGAATTCAGATCAT
**
16970 GTATCAGAACAGAATTCA
1 AAATCAGAACAGAATTCA
16988 AGTAGGAAAT
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.50, C:0.16, G:0.13, T:0.21
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAGATCAT
Found at i:16999 original size:24 final size:25
Alignment explanation
Indices: 16946--16999 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
16936 TCCAGATCAT
* * *
16946 AAATCAGAACAGAATTTAGGTCATG
1 AAATCAGAACAGAATTCAAGTCAGG
*
16971 -TATCAGAACAGAATTCAAGT-AGG
1 AAATCAGAACAGAATTCAAGTCAGG
16994 AAATCA
1 AAATCA
17000 TATAAAACAT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.46, C:0.13, G:0.19, T:0.22
Consensus pattern (25 bp):
AAATCAGAACAGAATTCAAGTCAGG
Found at i:19193 original size:17 final size:17
Alignment explanation
Indices: 19173--19205 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19163 AAATTTTAAC
*
19173 TTTTCGGTCTAAATCAT
1 TTTTCGGTCAAAATCAT
19190 TTTTCGGTCAAAATCA
1 TTTTCGGTCAAAATCA
19206 AAGTCAACGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (17 bp):
TTTTCGGTCAAAATCAT
Found at i:26992 original size:2 final size:2
Alignment explanation
Indices: 26985--27013 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
26975 TATTTAAAAT
26985 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27014 TTCAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27580 original size:26 final size:26
Alignment explanation
Indices: 27541--27599 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
27531 AAAATATAAT
*
27541 TTATTTTATTATAAAATATAAACATA
1 TTATTTTATAATAAAATATAAACATA
*
27567 TTGTTTTATAATAAAATATAAACATA
1 TTATTTTATAATAAAATATAAACATA
27593 TTATTTT
1 TTATTTT
27600 TGTTATGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (26 bp):
TTATTTTATAATAAAATATAAACATA
Found at i:27610 original size:27 final size:26
Alignment explanation
Indices: 27544--27617 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
27534 ATATAATTTA
27544 TTTTATTATAAAATATAAACATATTG
1 TTTTATTATAAAATATAAACATATTG
* *
27570 TTTTATAATAAAATATAAACATATTAT
1 TTTTATTATAAAATATAAACATATT-G
* * *
27597 TTTTGTTATGAAATGTAAACA
1 TTTTATTATAAAATATAAACA
27618 CAAATTTATG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
26 24 0.59
27 17 0.41
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (26 bp):
TTTTATTATAAAATATAAACATATTG
Found at i:28184 original size:29 final size:30
Alignment explanation
Indices: 28147--28205 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
28137 ATTTTTTTTT
*
28147 AAAGTTTTAA-TGCTTATTTAATTTTTTAAA
1 AAAGTTTTAAGGGCTTATTT-ATTTTTTAAA
*
28177 AAAG-TTTAAGGGTTTATTTATTTTTTAAA
1 AAAGTTTTAAGGGCTTATTTATTTTTTAAA
28206 TAAATTAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.53
Consensus pattern (30 bp):
AAAGTTTTAAGGGCTTATTTATTTTTTAAA
Found at i:28282 original size:21 final size:20
Alignment explanation
Indices: 28229--28301 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 20
28219 TATTTAAATT
28229 AAAAA-TATTAAAAATA-AA
1 AAAAATTATTAAAAATATAA
**
28247 AAAAGAACA-TAAAAATA-AA
1 AAAA-ATTATTAAAAATATAA
28266 AACTAAATTATTAAAAATATAA
1 AA--AAATTATTAAAAATATAA
*
28288 AAACATTATTAAAA
1 AAAAATTATTAAAA
28302 TTTCCAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.09
19 13 0.29
20 14 0.31
21 10 0.22
22 4 0.09
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.23
Consensus pattern (20 bp):
AAAAATTATTAAAAATATAA
Found at i:30933 original size:24 final size:26
Alignment explanation
Indices: 30901--30950 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
30891 ACCACACATA
* *
30901 TTAACATATAAT-GTACAAACATGAC
1 TTAACATATAATAATAAAAACATGAC
30926 TTAA-ATATAATAATAAAAACATGAC
1 TTAACATATAATAATAAAAACATGAC
30951 ATGCAAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.28
Consensus pattern (26 bp):
TTAACATATAATAATAAAAACATGAC
Found at i:33618 original size:109 final size:109
Alignment explanation
Indices: 33484--33857 Score: 366
Period size: 109 Copynumber: 3.4 Consensus size: 109
33474 CTTCTGCAAA
*
33484 CGGGTTCTCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTTTGAAAACGTGTATGCTC
1 CGGGTTCTCTCCCTCTTTCTCCAGGGAGTATAGAACTCGAAAATCTTTTGAAAACGTGTATGCTC
* *
33549 CTTATTCCTTCAGAGAGTATGAGACTCAAACAATCTTCAACAAT
66 CCTATTCCTTCAGAGAGTATGAGACTCAAACAAACTTCAACAAT
*
33593 CGGGTTCGT-TCCCTCTTTCTCCAGGGAGTATAGAACTTGAAAATCTTTTGAAAACGTGTATGCT
1 CGGGTTC-TCTCCCTCTTTCTCCAGGGAGTATAGAACTCGAAAATCTTTTGAAAACGTGTATGCT
* *
33657 CCCTATTCCTTCAGAGAGTATGAGACTCGAATAAACTTCAACAAT
65 CCCTATTCCTTCAGAGAGTATGAGACTCAAACAAACTTCAACAAT
* * * * * * * * * * * **
33702 TGCG-TCTGCCCCCTATTTCTTCAGAGAGTATA-AGAC-CCATAATCTTCAT-CAATCGCATATG
1 CGGGTTCT-CTCCCTCTTTCTCCAGGGAGTATAGA-ACTCGAAAATCTT-TTGAAAACGTGTATG
* * * * * *
33763 CCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGAT
63 CTCCCTATTCCTTCAGAGAGTATGAGACTCAAACAAACTTCAACAAT
* * * * *
33810 CGCG-TCTGCCCCCTATTTCTTCAGAGAGTATA-AGACTCGAACAATCTT
1 CGGGTTCT-CTCCCTCTTTCTCCAGGGAGTATAGA-ACTCGAA-AATCTT
33858 CAACAAATGG
Statistics
Matches: 229, Mismatches: 29, Indels: 13
0.85 0.11 0.05
Matches are distributed among these distances:
107 1 0.00
108 94 0.41
109 127 0.55
110 7 0.03
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (109 bp):
CGGGTTCTCTCCCTCTTTCTCCAGGGAGTATAGAACTCGAAAATCTTTTGAAAACGTGTATGCTC
CCTATTCCTTCAGAGAGTATGAGACTCAAACAAACTTCAACAAT
Found at i:33772 original size:53 final size:55
Alignment explanation
Indices: 33494--33863 Score: 312
Period size: 55 Copynumber: 6.8 Consensus size: 55
33484 CGGGTTCTCT
* * * * *
33494 CCCTCTTTCTTCAGGGAGTAT-AGAACTCGAA-AATCTTTTGAA-AA-CGTGTATGCT
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCGAATAATC--TTCAACAATCGCGTATGCC
* * * * * * **
33548 CCTTATTCCTTCAGAGAGTATGAGACTCAAACAATCTTCAACAATCGGGT-TCGTT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAATAATCTTCAACAATCGCGTAT-GCC
* * * * * * *
33603 CCCTCTTTCTCCAGGGAGTAT-AGAACTTGAA-AATCTTTTGAA-AA-CGTGTATGCT
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCGAATAATC--TTCAACAATCGCGTATGCC
* * * * *
33657 CCCTATTCCTTCAGAGAGTATGAGACTCGAATAAACTTCAACAATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAATAATCTTCAACAATCGCGTATGCC
* * *
33712 CCCTATTTCTTCAGAGAGTATAAGAC-C-CATAATCTTCATCAATCGCATATGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAATAATCTTCAACAATCGCGTATGCC
* * *
33765 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAATAATCTTCAACAATCGCGTATGCC
*
33820 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAA
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAATAATCTTCAACAA
33864 ATGGGTTCGC
Statistics
Matches: 257, Mismatches: 44, Indels: 29
0.78 0.13 0.09
Matches are distributed among these distances:
53 54 0.21
54 65 0.25
55 134 0.52
56 4 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (55 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAATAATCTTCAACAATCGCGTATGCC
Found at i:33826 original size:55 final size:55
Alignment explanation
Indices: 33551--33863 Score: 316
Period size: 55 Copynumber: 5.7 Consensus size: 55
33541 GTATGCTCCT
* * * * **
33551 TATTCCTTCAGAGAGTATGAGACTCAAACAATCTTCAACAATCGGGT-TCGTTCCC
1 TATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCT-GCCCCC
* * * * * * * *
33606 TCTTTCTCCAGGGAGTAT-AGAACTTGAA-AATCTTTTGAA-AA-CGTGTATGCTCCC
1 TATTTCTTCAGAGAGTATAAG-ACTCGAACAATC--TTCAACAATCGCGTCTGCCCCC
* * * * *
33660 TATTCCTTCAGAGAGTATGAGACTCGAATAAACTTCAACAATTGCGTCTGCCCCC
1 TATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCC
* * * * *
33715 TATTTCTTCAGAGAGTATAAGAC-C-CATAATCTTCATCAATCGCATATGCCCCC
1 TATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCC
*
33768 TATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCC
1 TATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCC
33823 TATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAA
1 TATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAA
33864 ATGGGTTCGC
Statistics
Matches: 213, Mismatches: 35, Indels: 20
0.79 0.13 0.07
Matches are distributed among these distances:
53 50 0.23
54 39 0.18
55 120 0.56
56 4 0.02
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29
Consensus pattern (55 bp):
TATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCC
Found at i:33884 original size:55 final size:55
Alignment explanation
Indices: 33429--34383 Score: 567
Period size: 51 Copynumber: 17.9 Consensus size: 55
33419 TCTTTTGCCT
* * **
33429 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTTGAA-AATCTTCTGCAA
1 ACGGGTTCGCTCCCTCTTTCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
* * **
33483 ACGGGTTCTCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-AATCTTTTGA-AA
1 ACGGGTTCGCTCCCTCTTTCTTCAGAGAGTATAGAACTCGAACAATC-TTCAACAA
* * * * *
33537 ACGTGTAT-GCTCCTTATTCCTTCAGAGAGTAT-GAGACTCAAACAATCTTCAACAA
1 ACGGGT-TCGCTCCCTCTTTCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAA
* * * * * **
33592 TCGGGTTCGTTCCCTCTTTCTCCAGGGAGTATAGAACTTGAA-AATCTTTTGA-AA
1 ACGGGTTCGCTCCCTCTTTCTTCAGAGAGTATAGAACTCGAACAATC-TTCAACAA
* * * * *
33646 ACGTGTAT-GCTCCCTATTCCTTCAGAGAGTAT-GAGACTCGAATAAACTTCAACAA
1 ACGGGT-TCGCTCCCTCTTTCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAA
** * * * * * *
33701 TTGCG-TCTGCCCCCTATTTCTTCAGAGAGTATA-AGAC-C-CATAATCTTCATCAA
1 ACGGGTTC-GCTCCCTCTTTCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAA
* ** * * *
33754 TCGCATAT-GCCCCCTATTTCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACGA
1 ACGGGT-TCGCTCCCTCTTTCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAA
* * * *
33809 TCGCG-TCTGCCCCCTATTTCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAA
1 ACGGGTTC-GCTCCCTCTTTCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAA
* * * **
33864 ATGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAAC-ATC-TCTTC--
1 ACGGGTTCGCTCCCTCTTTCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
* *
33915 ACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAACTCGAAC-ATCTTCAAC--
1 ACGGGTTCGCTCCCTCTTTCTTC-AGAGAGTATAGAACTCGAACAATCTTCAACAA
* * * ** **
33967 -TGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTC-AAGAATCTTCTTCTT
1 ACGGGTTCGCTCCCTCTTTCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
* * * *
34020 ACGGGTTCGCTCCTTCTCTCTTTAAAGAGTATAGAACTCGAAC-ATCTT---CAA
1 ACGGGTTCGCTCCCTCTTTCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
* * * * *
34071 ACGGGTTCGCTCCTTCTTTCATTAAG-GAGTATGGAACTCGGA-TATCTTC-AC--
1 ACGGGTTCGCTCCCTCTTTC-TTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
* * **
34122 ACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAACTC-AGAC-ATC-TCTTCAA
1 ACGGGTTCGCTCCCTCTTTCTTC-AGAGAGTATAGAACTCGA-ACAATCTTCAACAA
* *
34175 ACGGGTTCGCTCCTTCTTTCTTTA-AGGAGTATAGAACTCG--CATATCTTC-AC--
1 ACGGGTTCGCTCCCTCTTTCTTCAGA-GAGTATAGAACTCGAACA-ATCTTCAACAA
* * * ** *
34226 ACGGGTTCGCTCCCGCTTTCTTTA-AGGAAGTATAGAACTTGAATGATCTTCTGA-AA
1 ACGGGTTCGCTCCCTCTTTCTTCAGA-G-AGTATAGAACTCGAACAATCTTC-AACAA
* * *
34282 ATGGGTTCTCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-AATCTT---CAA
1 ACGGGTTCGCTCCCTCTTTCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
* * * * *
34333 ACGGGTTCGCTCCTTCTTTC-TCTAGGGAGTATGGAACTCAAATAATCTTCA
1 ACGGGTTCGCTCCCTCTTTCTTC-AGAGAGTATAGAACTCGAACAATCTTCA
34384 TTTGCTTCAC
Statistics
Matches: 728, Mismatches: 112, Indels: 122
0.76 0.12 0.13
Matches are distributed among these distances:
49 1 0.00
50 9 0.01
51 219 0.30
52 26 0.04
53 96 0.13
54 168 0.23
55 183 0.25
56 26 0.04
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (55 bp):
ACGGGTTCGCTCCCTCTTTCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
Found at i:34130 original size:207 final size:204
Alignment explanation
Indices: 33834--34372 Score: 647
Period size: 207 Copynumber: 2.6 Consensus size: 204
33824 ATTTCTTCAG
33834 AGAGTATA-AGACTCGAACAATCTTCAACAAATGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAG
1 AGAGTATAGA-ACTCGAAC-ATCTT---CAAATGGGTTCGCTCCCTCTTTC-TTAGGGAGTATAG
* *
33898 AACTCGAACATC-TCTTCACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC-GA-ACAT
60 AACTCGAAAATCTTC-ACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAGACAC-T
* * **
33960 CTTC-AACTGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCAAGAATCTTCTTCTTACGG
123 CTTCAAAC-GGGTTCGCTCCCTCTTTCTTCAAGGAGTATAGAACTC--GAAT-ATCTTCACACGG
**
34024 GTTCGCTCCTTCTCTCTTTAA
184 GTTCGCTCCCGCTCTCTTTAA
* * * *
34045 AGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCATTAAGGAGTATGGAACTC
1 AGAGTATAGAACTCGAACATCTTCAAATGGGTTCGCTCCCTCTTTC-TTAGGGAGTATAGAACTC
* *
34110 GGATATCTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAGACATCTCTTCAA
65 GAAAATCTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAGACA-CTCTTCAA
* * *
34175 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGCATATCTTCACACGGGTTCGCTCCC
129 ACGGGTTCGCTCCCTCTTTCTTCAAGGAGTATAGAACTCGAATATCTTCACACGGGTTCGCTCCC
*
34240 GCTTTCTTTAA
194 GCTCTCTTTAA
* * * *
34251 GGAAGTATAGAACTTGAATGATCTTCTGAAAATGGGTTCTCTCCCTCTTTCTTCAGGGAGTATAG
1 AG-AGTATAGAACTCGAA-CATCTTC---AAATGGGTTCGCTCCCTCTTTCTT-AGGGAGTATAG
* *
34316 AACTCGAAAATCTTCAAACGGGTTCGCTCCTTCTTTCTCTAGGGAGTATGGAACTCA
60 AACTCGAAAATCTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCA
34373 AATAATCTTC
Statistics
Matches: 286, Mismatches: 30, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
206 28 0.10
207 99 0.35
208 10 0.03
209 40 0.14
210 11 0.04
211 97 0.34
212 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (204 bp):
AGAGTATAGAACTCGAACATCTTCAAATGGGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCG
AAAATCTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAGACACTCTTCAAAC
GGGTTCGCTCCCTCTTTCTTCAAGGAGTATAGAACTCGAATATCTTCACACGGGTTCGCTCCCGC
TCTCTTTAA
Found at i:34136 original size:156 final size:153
Alignment explanation
Indices: 33820--34371 Score: 618
Period size: 156 Copynumber: 3.5 Consensus size: 153
33810 CGCGTCTGCC
* * * ** * *
33820 CCCTATTTCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAAATGGGTTCGCTCCCTCTTTC
1 CCCTCTTTCTTCAGGGAGTATAGA-ACTC-AAGAATCTTCTTCAAACGGGTTCGCTCCTTCTTTC
* *
33884 TTTAGGGAGTATAGAACTCGAACATCTCTTC-ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATG
64 TTTAAGGAGTATAGAACTCGAACA--TCTTCAACGGGTTCGCTCCCTCTTTCT-TAAGGAGTATG
*
33948 GAACTCGAACATCTTCAACTGGGTTCGCT
126 GAACTCGAATATCTTCAAC-GGGTTCGCT
** *
33977 CCCTCTTTCTTCAGGGAGTATAGAACTCAAGAATCTTCTTCTTACGGGTTCGCTCCTTCTCTCTT
1 CCCTCTTTCTTCAGGGAGTATAGAACTCAAGAATCTTCTTCAAACGGGTTCGCTCCTTCTTTCTT
* *
34042 TAAAGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCATTAAGGAGTATGGAA
66 TAAGGAGTATAGAACTCGAACATCTTC-AACGGGTTCGCTCCCTCTTTC-TTAAGGAGTATGGAA
*
34107 CTCGGATATCTTCACACGGGTTCGCT
129 CTCGAATATCTTCA-ACGGGTTCGCT
*
34133 CCCTCTTTC-TCTAGGGAGTATGGAACTC-AGACATC-TCTTCAAACGGGTTCGCTCCTTCTTTC
1 CCCTCTTTCTTC-AGGGAGTATAGAACTCAAGA-ATCTTCTTCAAACGGGTTCGCTCCTTCTTTC
* * * *
34195 TTTAAGGAGTATAGAACTCGCATATCTTCACACGGGTTCGCTCCCGCTTTCTTTAAGGAAGTATA
64 TTTAAGGAGTATAGAACTCGAACATCTTCA-ACGGGTTCGCTCCCTCTTTC-TTAAGG-AGTATG
* * *
34260 GAACTTGAATGATCTTCTGAAAATGGGTTCTCT
126 GAACTCGAAT-ATCTTC----AACGGGTTCGCT
34293 CCCTCTTTCTTCAGGGAGTATAGAACTCGAA-AA---TCTTCAAACGGGTTCGCTCCTTCTTTCT
1 CCCTCTTTCTTCAGGGAGTATAGAACTC-AAGAATCTTCTTCAAACGGGTTCGCTCCTTCTTTCT
* * *
34354 CTAGGGAGTATGGAACTC
65 TTAAGGAGTATAGAACTC
34372 AAATAATCTT
Statistics
Matches: 343, Mismatches: 35, Indels: 33
0.83 0.09 0.08
Matches are distributed among these distances:
154 6 0.02
155 79 0.23
156 142 0.41
157 33 0.10
158 44 0.13
160 34 0.10
161 4 0.01
162 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (153 bp):
CCCTCTTTCTTCAGGGAGTATAGAACTCAAGAATCTTCTTCAAACGGGTTCGCTCCTTCTTTCTT
TAAGGAGTATAGAACTCGAACATCTTCAACGGGTTCGCTCCCTCTTTCTTAAGGAGTATGGAACT
CGAATATCTTCAACGGGTTCGCT
Found at i:34811 original size:36 final size:36
Alignment explanation
Indices: 34753--34982 Score: 275
Period size: 36 Copynumber: 6.4 Consensus size: 36
34743 ACTCTTCTGA
* * **
34753 GAAGGCTTAAAATGGATCTGCTTCACTACTT-TTTGGT
1 GAAGGCTTAAGATGG-TTTGCTTCACTA-TTCTCCGGT
* * *
34790 GAAGACTTAAGATGGTTTGCTTCACTACTCTCTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* * *
34826 GAAGACTTATGATTGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* * *
34862 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
*
34898 GAAGGCTTCAGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
34934 GAAGGCTTAGGATGGTTTGCTTCACT-TCTCTTCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTAT-TCTCCGGT
34970 GAAGGCTTAAGAT
1 GAAGGCTTAAGAT
34983 TGACTTGCTC
Statistics
Matches: 172, Mismatches: 19, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
35 2 0.01
36 157 0.91
37 13 0.08
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.37
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
Found at i:34921 original size:108 final size:109
Alignment explanation
Indices: 34753--34991 Score: 306
Period size: 108 Copynumber: 2.2 Consensus size: 109
34743 ACTCTTCTGA
* * **
34753 GAAGGCTTAAAATGGA-TCTGCTTCACTACTT-TTTGGTGAAGACTTAAGATGGTTTGCTTCACT
1 GAAGGCTTAAGATTGACT-TGCTTCACTA-TTCTCCGGTGAAGACTTAAGATGGTTTGCTTCACT
* * *
34816 ACTCTCTGGTGAAGACTTATGATTGTTTGCTTCACTAT-TCTCCGGT
64 ACTCTCCGGTGAAGACTTAGGATGGTTTGCTTCACT-TCTCTCCGGT
* * * *
34862 GAAGGCTTCAGATTGA-TTGCTTCACTATTCTCCGGTGAAGGCTTCAGATGGTTTGCTTCACTAT
1 GAAGGCTTAAGATTGACTTGCTTCACTATTCTCCGGTGAAGACTTAAGATGGTTTGCTTCACTAC
* *
34926 TCTCCGGTGAAGGCTTAGGATGGTTTGCTTCACTTCTCTTCGGT
66 TCTCCGGTGAAGACTTAGGATGGTTTGCTTCACTTCTCTCCGGT
34970 GAAGGCTTAAGATTGACTTGCT
1 GAAGGCTTAAGATTGACTTGCT
34992 CCAATCTCAT
Statistics
Matches: 113, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
107 3 0.03
108 91 0.81
109 19 0.17
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.37
Consensus pattern (109 bp):
GAAGGCTTAAGATTGACTTGCTTCACTATTCTCCGGTGAAGACTTAAGATGGTTTGCTTCACTAC
TCTCCGGTGAAGACTTAGGATGGTTTGCTTCACTTCTCTCCGGT
Found at i:36395 original size:125 final size:125
Alignment explanation
Indices: 36173--36425 Score: 355
Period size: 125 Copynumber: 2.0 Consensus size: 125
36163 ACTAATGTCG
* * * *
36173 CAACATTATTTTATTCTGGTACGGGCCTTCAAAATGCCTCAATATCTCAAATTATAAGGCTCATT
1 CAACATTATCTCATACTGGTACGGGCCTTCAAAATGCCTCAATACCTCAAATTATAAGGCTCATT
** * * *
36238 CTCAATGCCTTCTTGGTCTGAATCTTGTCATTTCATCATGATGTGGGTTCAGTCGCGCCC
66 CTCAATGCCTTCTTGGTCTGAATCTTGTCATTTCAAAAGGATGGGGGTTCAATCGCGCCC
* *
36298 CAACATTATCTCATACTGGTACGGGCCTTCAAAATGCC-CCATCACCTCAAATTGTAAGGCTCAT
1 CAACATTATCTCATACTGGTACGGGCCTTCAAAATGCCTCAAT-ACCTCAAATTATAAGGCTCAT
** * *
36362 TCTTGATGCCTTCTTTGTCTGAATCTTGTCATTTCAAAAGGATGGGGGTTCAATCGTGCCC
65 TCTCAATGCCTTCTTGGTCTGAATCTTGTCATTTCAAAAGGATGGGGGTTCAATCGCGCCC
36423 CAA
1 CAA
36426 TGTGGGTATT
Statistics
Matches: 112, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
124 3 0.03
125 109 0.97
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (125 bp):
CAACATTATCTCATACTGGTACGGGCCTTCAAAATGCCTCAATACCTCAAATTATAAGGCTCATT
CTCAATGCCTTCTTGGTCTGAATCTTGTCATTTCAAAAGGATGGGGGTTCAATCGCGCCC
Found at i:44804 original size:13 final size:13
Alignment explanation
Indices: 44786--44825 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
44776 GCTGCAACAA
44786 AAGAAAAGAAAAG
1 AAGAAAAGAAAAG
*
44799 AAGAAAATCAAAA-
1 AAGAAAA-GAAAAG
44812 AAGAAAAGAAAAG
1 AAGAAAAGAAAAG
44825 A
1 A
44826 CTCATACATC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 4 0.17
13 15 0.65
14 4 0.17
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.03
Consensus pattern (13 bp):
AAGAAAAGAAAAG
Found at i:45051 original size:41 final size:43
Alignment explanation
Indices: 44994--45107 Score: 142
Period size: 41 Copynumber: 2.7 Consensus size: 43
44984 TTTGTCGTTC
* * * *
44994 ACAAACGCCGCTAAAGGTGATGTTTTTTAGTGGC-ATTTT-TT
1 ACAAACGCCACTAAAGGTAATGATATTTAGTGGCGATTTTATT
* *
45035 ACAAACGCCATTAAAGGTAATGATATTTAGTGGCGTTTTTATT
1 ACAAACGCCACTAAAGGTAATGATATTTAGTGGCGATTTTATT
* *
45078 ACAAATGCCACTAAAGGTTATGATATTTAG
1 ACAAACGCCACTAAAGGTAATGATATTTAG
45108 CTGCTTTTGG
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 29 0.47
42 4 0.06
43 29 0.47
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (43 bp):
ACAAACGCCACTAAAGGTAATGATATTTAGTGGCGATTTTATT
Found at i:45201 original size:44 final size:43
Alignment explanation
Indices: 45146--45246 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 43
45136 ATTTTCTTTT
45146 GTGGTGTTTTGTGCCAAAAAAAGCCGCTAAATGTCT-TGACATATA
1 GTGGTG-TTTGTGCCAAAAAAA-CCGCTAAATGT-TATGACATATA
* * *
45191 GTGGTGTTTGTTCCCAAAAATACCGCTAAATGTTATGTCATATA
1 GTGGTGTTTG-TGCCAAAAAAACCGCTAAATGTTATGACATATA
*
45235 GTGGCGTTTGTG
1 GTGGTGTTTGTG
45247 AATGTAAAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
43 2 0.04
44 32 0.65
45 15 0.31
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (43 bp):
GTGGTGTTTGTGCCAAAAAAACCGCTAAATGTTATGACATATA
Found at i:45430 original size:22 final size:21
Alignment explanation
Indices: 45379--45438 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 21
45369 ATTATCCAAT
45379 AAACTT-AACATCCATAACAAC
1 AAACTTGAA-ATCCATAACAAC
45400 AAACTTGAAATCCATAACAA-
1 AAACTTGAAATCCATAACAAC
45420 AGATACTTGAAATCCATAA
1 A-A-ACTTGAAATCCATAA
45439 TAATAAATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
20 1 0.03
21 18 0.50
22 17 0.47
ACGTcount: A:0.52, C:0.22, G:0.05, T:0.22
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Done.