Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009265.1 Hibiscus syriacus cultivar Beakdansim tig00112919_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: 76718
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:508 original size:14 final size:15
Alignment explanation
Indices: 489--518 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
479 ATTTTGTTCG
489 ACTCG-TGCTCGTTA
1 ACTCGTTGCTCGTTA
503 ACTCGTTGCTCGTTA
1 ACTCGTTGCTCGTTA
518 A
1 A
519 GCTCATCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.37
Consensus pattern (15 bp):
ACTCGTTGCTCGTTA
Found at i:7217 original size:65 final size:65
Alignment explanation
Indices: 7113--7242 Score: 208
Period size: 65 Copynumber: 2.0 Consensus size: 65
7103 ACCAGACTAT
*
7113 TCATTATGTTCCAAACTTATCATTTTCTGTTAAAAAATTGAAGGTCGAT-TGATATGGATGTTAA
1 TCATTATGTTCCAAACTCATCATTTTCTGTTAAAAAATTGAAGGTCG-TCTGATATGGATGTTAA
7177 C
65 C
* * *
7178 TCATTTTGTTCCAAACTCGTCATTTTCTGTTAAAAAATTGGAGGTCGTCTGATATGGATGTTAAC
1 TCATTATGTTCCAAACTCATCATTTTCTGTTAAAAAATTGAAGGTCGTCTGATATGGATGTTAAC
7243 ATAATGATTG
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
64 1 0.02
65 59 0.98
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (65 bp):
TCATTATGTTCCAAACTCATCATTTTCTGTTAAAAAATTGAAGGTCGTCTGATATGGATGTTAAC
Found at i:15937 original size:47 final size:47
Alignment explanation
Indices: 15846--15937 Score: 105
Period size: 47 Copynumber: 2.0 Consensus size: 47
15836 ATACCCGAAT
* * *
15846 CGACCCGACTTATTATAGATCCAAATAAAACCAAATCCGGAATGACC
1 CGACCCGACTTACTATAGATCCAAATAAAACCAAAACCGAAATGACC
* * * *
15893 CGACCCGACTTACTATAGA-CTCGAATAAAGCTAAAACTGAAATGA
1 CGACCCGACTTACTATAGATC-CAAATAAAACCAAAACCGAAATGA
15938 ATCGAACCCA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
46 1 0.03
47 36 0.97
ACGTcount: A:0.41, C:0.25, G:0.14, T:0.20
Consensus pattern (47 bp):
CGACCCGACTTACTATAGATCCAAATAAAACCAAAACCGAAATGACC
Found at i:16514 original size:60 final size:58
Alignment explanation
Indices: 16387--16532 Score: 159
Period size: 60 Copynumber: 2.4 Consensus size: 58
16377 ATTATGATTC
* * ** *
16387 TCATTCTAAATTAATCCCTAAACTTTTAACATTCTAATTTCATCCTTAAACTATGATCA
1 TCATTCTAAATTAGTCCC-AAACTTTTAACATTCTAATTCCATCCCCAAACTATGACCA
** * *
16446 TCGCTCTAAATTAGTCCTCAAACTTTTGAACATT-TCAATTCCATCCCCAAACTATGGCCT
1 TCATTCTAAATTAGTCC-CAAACTTTT-AACATTCT-AATTCCATCCCCAAACTATGACCA
16506 TCATTCTAAATTAGTTCCCAAACTTTT
1 TCATTCTAAATTAG-TCCCAAACTTTT
16533 TAAATATTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
59 23 0.32
60 46 0.64
61 3 0.04
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (58 bp):
TCATTCTAAATTAGTCCCAAACTTTTAACATTCTAATTCCATCCCCAAACTATGACCA
Found at i:17508 original size:35 final size:35
Alignment explanation
Indices: 17462--17971 Score: 313
Period size: 35 Copynumber: 14.7 Consensus size: 35
17452 TAGGGTTCAT
*
17462 TGGATAGTGGATAAGCTCAATTATGTATGCATGTA
1 TGGATAGTGGATAAGCTCAATTATGTATGCATGCA
* * *
17497 TGGATAGTGGATAAGCTAAATTATGTCTGCATGTA
1 TGGATAGTGGATAAGCTCAATTATGTATGCATGCA
* * *
17532 TGGATAGTGGATAAGCTAAATTATGTCTGCATGTA
1 TGGATAGTGGATAAGCTCAATTATGTATGCATGCA
* *
17567 TGGATAGTGGATAAGCTC-A--A-GTATGCGTTCA
1 TGGATAGTGGATAAGCTCAATTATGTATGCATGCA
17598 TGGA-AGGATGGATAAGCTCAATTATGTATGCATACATGCA
1 TGGATA-G-TGGATAAGCTCAATTATGTATG----CATGCA
* *
17638 TGGGTAGTGGATAAGCTCAATTATGTGTGCATGCA
1 TGGATAGTGGATAAGCTCAATTATGTATGCATGCA
* * * * * *
17673 CGGATAGTGGATAAACTCAAGTATGTGTTCATGGA
1 TGGATAGTGGATAAGCTCAATTATGTATGCATGCA
* * * * *
17708 AGGAT-GATCGG-TAAGCTTAAATATTTATGCATACA
1 TGGATAG-T-GGATAAGCTCAATTATGTATGCATGCA
* **
17743 T-GA-ATTGG-T-AGCAGTGGA-TATGTATGCATGCA
1 TGGATAGTGGATAAGC--TCAATTATGTATGCATGCA
* * *
17775 TGGGA-AGCGGATAAACTCAATTATGTGTGCATGCA
1 T-GGATAGTGGATAAGCTCAATTATGTATGCATGCA
* * * * * * *
17810 CGGATAGTGGATAAACTCAAGTATTTGTTCACGC-
1 TGGATAGTGGATAAGCTCAATTATGTATGCATGCA
* * *
17844 TAGTG-TAATGGATAAGCGCAATTATGTGTGCATGCA
1 T-G-GATAGTGGATAAGCTCAATTATGTATGCATGCA
* * *
17880 -GGTATAGTGGAT-A--TGAATGCAT-AATGCATGCA
1 TGG-ATAGTGGATAAGCTCAAT-TATGTATGCATGCA
* * *
17912 TGTAGAGTGGATAAGCTCAATTATGTATGCAAGCA
1 TGGATAGTGGATAAGCTCAATTATGTATGCATGCA
* * *
17947 TGGAATACTAGATAAGCTTAATTAT
1 TGG-ATAGTGGATAAGCTCAATTAT
17972 TCTTATCCAA
Statistics
Matches: 372, Mismatches: 69, Indels: 67
0.73 0.14 0.13
Matches are distributed among these distances:
30 1 0.00
31 15 0.04
32 47 0.13
33 9 0.02
34 18 0.05
35 225 0.60
36 27 0.07
39 21 0.06
40 8 0.02
41 1 0.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (35 bp):
TGGATAGTGGATAAGCTCAATTATGTATGCATGCA
Found at i:17669 original size:106 final size:102
Alignment explanation
Indices: 17462--17713 Score: 306
Period size: 106 Copynumber: 2.4 Consensus size: 102
17452 TAGGGTTCAT
* * * * * *
17462 TGGATAGTGGATAAGCTCAATTATGTATGCATGTATGGATAGTGGATAAGCTAAATTATGTCTGC
1 TGGATAGTGGATAAGCTCAAGTATGTGTTCATGGAAGG--A-TGGATAAGCTAAATTATGTCTAC
* *
17527 ATGTATGGATAGTGGATAAGCTAAATTATGTCTGCATGTA
63 ATGCATGGATAGTGGATAAGCTAAATTATGTCTGCATGCA
* *
17567 TGGATAGTGGATAAGCTCAAGTATGCGTTCATGGAAGGATGGATAAGCTCAATTATGTATGCATA
1 TGGATAGTGGATAAGCTCAAGTATGTGTTCATGGAAGGATGGATAAGCTAAATTATG--T-C-TA
* * *
17632 CATGCATGGGTAGTGGATAAGCTCAATTATGTGTGCATGCA
62 CATGCATGGATAGTGGATAAGCTAAATTATGTCTGCATGCA
* *
17673 CGGATAGTGGATAAACTCAAGTATGTGTTCATGGAAGGATG
1 TGGATAGTGGATAAGCTCAAGTATGTGTTCATGGAAGGATG
17714 ATCGGTAAGC
Statistics
Matches: 127, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
102 17 0.13
103 1 0.01
104 1 0.01
105 33 0.26
106 75 0.59
ACGTcount: A:0.31, C:0.10, G:0.28, T:0.31
Consensus pattern (102 bp):
TGGATAGTGGATAAGCTCAAGTATGTGTTCATGGAAGGATGGATAAGCTAAATTATGTCTACATG
CATGGATAGTGGATAAGCTAAATTATGTCTGCATGCA
Found at i:17723 original size:141 final size:138
Alignment explanation
Indices: 17469--17840 Score: 369
Period size: 141 Copynumber: 2.7 Consensus size: 138
17459 CATTGGATAG
* * * * * *
17469 TGGATAAGCTCAATTATGTATGCATGTATGGATAGTGGATAAGCTAAATTATGTCTGCATGTATG
1 TGGATAAGCTCAATTATGTATGCATGCATGGGTAGTGGATAAGCTCAATTATGTGTGCATGCACG
* * * * * * * * * *
17534 GATAGTGGATAAGCTAAATTATGTCTGCATGTATGGATAGTGGATAAGCTCAAGTATGCGTTCAT
66 GATAGTGGATAAACTCAAGTATGTGTTCATGGAAGGATAGTGGATAAGCTCAAATATGCATGCAT
** *
17599 GGAAGGA-
131 ACAAGAAT
17606 TGGATAAGCTCAATTATGTATGCATACATGCATGGGTAGTGGATAAGCTCAATTATGTGTGCATG
1 TGGATAAGCTCAATTATGTATG----CATGCATGGGTAGTGGATAAGCTCAATTATGTGTGCATG
* **
17671 CACGGATAGTGGATAAACTCAAGTATGTGTTCATGGAAGGAT-GATCGG-TAAGCTTAAATATTT
62 CACGGATAGTGGATAAACTCAAGTATGTGTTCATGGAAGGATAG-T-GGATAAGCTCAAATATGC
*
17734 ATGCATACATGAAT
125 ATGCATACAAGAAT
** * * *
17748 TGG-T-AGCAGTGGA-TATGTATGCATGCATGGGAAGCGGATAAACTCAATTATGTGTGCATGCA
1 TGGATAAGC--TCAATTATGTATGCATGCATGGGTAGTGGATAAGCTCAATTATGTGTGCATGCA
*
17810 CGGATAGTGGATAAACTCAAGTATTTGTTCA
64 CGGATAGTGGATAAACTCAAGTATGTGTTCA
17841 CGCTAGTGTA
Statistics
Matches: 197, Mismatches: 29, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
137 90 0.46
140 4 0.02
141 96 0.49
142 7 0.04
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.31
Consensus pattern (138 bp):
TGGATAAGCTCAATTATGTATGCATGCATGGGTAGTGGATAAGCTCAATTATGTGTGCATGCACG
GATAGTGGATAAACTCAAGTATGTGTTCATGGAAGGATAGTGGATAAGCTCAAATATGCATGCAT
ACAAGAAT
Found at i:17775 original size:106 final size:103
Alignment explanation
Indices: 17541--17807 Score: 231
Period size: 106 Copynumber: 2.5 Consensus size: 103
17531 ATGGATAGTG
* * *
17541 GATAAGCTAAATTATGTC-TGCATGTATGGATAGTGGATAAGCTCAAGTATGCGTTCATGGAAGG
1 GATAAGAT-AATTATG-CATGCATG-A-GGATAGTGGATAAACTCAAGTATGTGTTCATGGAAGG
* * **
17605 ATGGATAAGCTCAATTATGTATGCATACATGCATGGGTAGTG
62 ATGGATAAGCTCAAATATGTATGCATACATGAATGGGTAGCA
* **
17647 GATAAGCTCAATTATGTGTGCATGCACGGATAGTGGATAAACTCAAGTATGTGTTCATGGAAGGA
1 GATAAGAT-AATTATGCATGCATG-A-GGATAGTGGATAAACTCAAGTATGTGTTCATGGAAGGA
* * * *
17712 TGATCGGTAAGCTTAAATATTTATGCATACATGAATTGGTAGCA
63 TG---GATAAGCTCAAATATGTATGCATACATGAATGGGTAGCA
* * * *
17756 G-T-GGAT-ATGTATGCATGCATG-GGA-AGCGGATAAACTCAATTATGTGTGCATG
1 GATAAGATAAT-TATGCATGCATGAGGATAGTGGATAAACTCAAGTATGTGTTCATG
17808 CACGGATAGT
Statistics
Matches: 135, Mismatches: 21, Indels: 14
0.79 0.12 0.08
Matches are distributed among these distances:
102 25 0.19
103 3 0.02
105 2 0.01
106 70 0.52
107 2 0.01
108 1 0.01
109 32 0.24
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (103 bp):
GATAAGATAATTATGCATGCATGAGGATAGTGGATAAACTCAAGTATGTGTTCATGGAAGGATGG
ATAAGCTCAAATATGTATGCATACATGAATGGGTAGCA
Found at i:17907 original size:137 final size:135
Alignment explanation
Indices: 17632--17942 Score: 326
Period size: 137 Copynumber: 2.3 Consensus size: 135
17622 TGTATGCATA
*
17632 CATGCATGGGTAGTGGATAAGCTCAATTATGTGTGCATGCACGGATAGTGGATAAACTCAAGTAT
1 CATGCATGGGAAGTGGATAAGCTCAATTATGTGTGCATGCACGGATAGTGGATAAACTCAAGTAT
* * * ** * * * * *
17697 GTGTTCATGGAAGGATGATCGGTAAGCTTAAATATTTATGCATACATGAATTGGTAGCAGTGGAT
66 GTGTTCACGCAAGGATAATCGGTAAGCGCAAATATGTATGCATACAGGAAGTGGTAGCAATGCAT
17762 ATGTATG
131 A--TATG
* *
17769 CATGCATGGGAAGCGGATAAACTCAATTATGTGTGCATGCACGGATAGTGGATAAACTCAAGTAT
1 CATGCATGGGAAGTGGATAAGCTCAATTATGTGTGCATGCACGGATAGTGGATAAACTCAAGTAT
* * * * *
17834 TTGTTCACGCTAGTG-TAAT-GGATAAGCGCAATTATGTGTGCATGCAGGTATAGTGGATATG-A
66 GTGTTCACGCAAG-GATAATCGG-TAAGCGCAAATATGTATGCATACAGG-A-AGTGG-TA-GCA
17896 ATGCATA-ATG
125 ATGCATATATG
* *
17906 CATGCAT-GTAGAGTGGATAAGCTCAATTATGTATGCA
1 CATGCATGGGA-AGTGGATAAGCTCAATTATGTGTGCA
17943 AGCATGGAAT
Statistics
Matches: 145, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
136 4 0.03
137 126 0.87
138 2 0.01
139 4 0.03
140 8 0.06
141 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (135 bp):
CATGCATGGGAAGTGGATAAGCTCAATTATGTGTGCATGCACGGATAGTGGATAAACTCAAGTAT
GTGTTCACGCAAGGATAATCGGTAAGCGCAAATATGTATGCATACAGGAAGTGGTAGCAATGCAT
ATATG
Found at i:19051 original size:23 final size:23
Alignment explanation
Indices: 19021--19067 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
19011 AAAGATAAAA
* *
19021 ATATCTTGATCTCTAAGGTATTG
1 ATATCTTGAACTCTAAGGCATTG
19044 ATATCTTGAACTCTAAGGCATTG
1 ATATCTTGAACTCTAAGGCATTG
19067 A
1 A
19068 GTCATAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (23 bp):
ATATCTTGAACTCTAAGGCATTG
Found at i:19071 original size:62 final size:60
Alignment explanation
Indices: 18983--19105 Score: 201
Period size: 62 Copynumber: 2.0 Consensus size: 60
18973 AAAGATAAAA
* *
18983 ATATCTTGAACTCAAGGCAGTGAGTCATAAAGATAAAAATATCTTGATCTCTAAGGTATTG
1 ATATCTTGAACTCAAGGCAGTGAGTCATAAAGATAAAAATATCTTGAACTC-AAGGCATTG
*
19044 ATATCTTGAACTCTAAGGCATTGAGTCATAAAGATAAAAATATCTTGAACTCAAGGCATTG
1 ATATCTTGAACTC-AAGGCAGTGAGTCATAAAGATAAAAATATCTTGAACTCAAGGCATTG
19105 A
1 A
19106 GTCATAAAGA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 22 0.38
62 36 0.62
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (60 bp):
ATATCTTGAACTCAAGGCAGTGAGTCATAAAGATAAAAATATCTTGAACTCAAGGCATTG
Found at i:19108 original size:38 final size:38
Alignment explanation
Indices: 19044--19151 Score: 200
Period size: 38 Copynumber: 2.8 Consensus size: 38
19034 TAAGGTATTG
19044 ATATCTTGAACTCTAAGGCATTGAGTCATAAAGATAAAA
1 ATATCTTGAACTC-AAGGCATTGAGTCATAAAGATAAAA
19083 ATATCTTGAACTCAAGGCATTGAGTCATAAAGATAAAA
1 ATATCTTGAACTCAAGGCATTGAGTCATAAAGATAAAA
19121 ATATCTTGAACTCAAGGCATTGAGTCA-AAAG
1 ATATCTTGAACTCAAGGCATTGAGTCATAAAG
19152 CCCAATCCTC
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
37 4 0.06
38 52 0.75
39 13 0.19
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.27
Consensus pattern (38 bp):
ATATCTTGAACTCAAGGCATTGAGTCATAAAGATAAAA
Found at i:24680 original size:35 final size:35
Alignment explanation
Indices: 24631--24926 Score: 231
Period size: 35 Copynumber: 8.7 Consensus size: 35
24621 TAGGGTTCCT
*
24631 TGGATAGTGGATAAGCTCAATTATGTGTGCATGCC
1 TGGATAGTGGATAAGCTCAATTATGTGTGCATGCA
* * * *
24666 TGGATAGTGTATAAGCTTAATTGTGTATGCATGCA
1 TGGATAGTGGATAAGCTCAATTATGTGTGCATGCA
* * * *
24701 TGGATAGTGGATAAACTCAAGTATGTGTTCATGGA
1 TGGATAGTGGATAAGCTCAATTATGTGTGCATGCA
* *
24736 -GGCAAAATGGATAAGCTCAATTATGTGTGCATGCA
1 TGG-ATAGTGGATAAGCTCAATTATGTGTGCATGCA
* * * **
24771 TGGATAGTGGATATG-T-ACTGCAT-AATGCATGCA
1 TGGATAGTGGATAAGCTCAAT-TATGTGTGCATGCA
* * * ** *
24804 TGTAGAGTGGATAAGCTC-GTTATGCATGCATGGATA
1 TGGATAGTGGATAAGCTCAATTATGTGTGCAT-G-CA
* *
24840 CTGGATACTGGATACGCTCAATTA----TGCATGCA
1 -TGGATAGTGGATAAGCTCAATTATGTGTGCATGCA
24872 TGGATAGTGGATAAGCTCAATTA----TGCATGCA
1 TGGATAGTGGATAAGCTCAATTATGTGTGCATGCA
*
24903 TGGATAGTGGATAAGCTCGATTAT
1 TGGATAGTGGATAAGCTCAATTAT
24927 TCTCATCCAA
Statistics
Matches: 208, Mismatches: 42, Indels: 25
0.76 0.15 0.09
Matches are distributed among these distances:
31 51 0.25
32 1 0.00
33 25 0.12
34 18 0.09
35 93 0.45
36 3 0.01
37 14 0.07
38 3 0.01
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.31
Consensus pattern (35 bp):
TGGATAGTGGATAAGCTCAATTATGTGTGCATGCA
Found at i:24869 original size:38 final size:36
Alignment explanation
Indices: 24811--24915 Score: 123
Period size: 31 Copynumber: 3.0 Consensus size: 36
24801 GCATGTAGAG
*
24811 TGGATAAGCTC-GTTATGCATGCATGGATACTGGATA
1 TGGATAAGCTCAATTATGCATGCATGGATA-TGGATA
*
24847 CTGGATACGCTCAATTATGCATGCATGGATA--G---
1 -TGGATAAGCTCAATTATGCATGCATGGATATGGATA
24879 TGGATAAGCTCAATTATGCATGCATGGATAGTGGATA
1 TGGATAAGCTCAATTATGCATGCATGGATA-TGGATA
24916 AGCTCGATTA
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
31 29 0.50
34 1 0.02
35 1 0.02
37 10 0.17
38 17 0.29
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (36 bp):
TGGATAAGCTCAATTATGCATGCATGGATATGGATA
Found at i:34063 original size:21 final size:21
Alignment explanation
Indices: 34037--34081 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
34027 AAATTACAAA
34037 TTTAGTATATAAACTATT-AAT
1 TTTAGTATATAAACT-TTAAAT
*
34058 TTTAGTATTTAAACTTTAAAT
1 TTTAGTATATAAACTTTAAAT
34079 TTT
1 TTT
34082 TTTAAAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTAGTATATAAACTTTAAAT
Found at i:34466 original size:23 final size:23
Alignment explanation
Indices: 34440--34487 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
34430 ATAAAGTACA
*
34440 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
34463 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
34486 AT
1 AT
34488 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:34894 original size:21 final size:20
Alignment explanation
Indices: 34864--34917 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
34854 GATAGACACT
*
34864 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
34885 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
34908 TTACATTATA
1 TTACATTATA
34918 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:34905 original size:23 final size:23
Alignment explanation
Indices: 34879--34941 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
34869 ATATAACCAT
34879 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
34902 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
34925 TACCTATTACATCATAT
1 TACCTATTACATTATAT
34942 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:37811 original size:184 final size:184
Alignment explanation
Indices: 37498--38727 Score: 2309
Period size: 184 Copynumber: 6.7 Consensus size: 184
37488 TTTTAAATGG
*
37498 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
37563 TAA-ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
* *
37627 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
37681 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
37746 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
37811 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
37865 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
37930 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
37995 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
38049 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
38114 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
38179 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACAATTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
38233 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
38298 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
38363 GATGTGTAAAATTTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
38417 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
38482 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
* *
38547 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
38601 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGGTTGTAGACCTAT
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCG--ATA-----TAGGTTGTAGACCTAT
**
38666 TCGCGCATAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
59 TCGCGCATAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
38728 ATGTTGAAAG
Statistics
Matches: 1028, Mismatches: 11, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
183 67 0.07
184 882 0.86
186 3 0.00
191 76 0.07
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
Found at i:40097 original size:3 final size:3
Alignment explanation
Indices: 40089--40139 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
40079 ACTTGTTTGG
* * * *
40089 ATC ATC ATC TTC ATC ATC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
40137 ATC
1 ATC
40140 GTCAGCTTCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.25, C:0.33, G:0.04, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:40106 original size:12 final size:12
Alignment explanation
Indices: 40089--40151 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
40079 ACTTGTTTGG
40089 ATCATCATCTTC
1 ATCATCATCTTC
*
40101 ATCATCATCGTC
1 ATCATCATCTTC
*
40113 ATCATCATCATC
1 ATCATCATCTTC
*
40125 ATCGTCATCTTC
1 ATCATCATCTTC
* *
40137 ATCGTCAGCTTC
1 ATCATCATCTTC
40149 ATC
1 ATC
40152 TTCTGCGACC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.37
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:40150 original size:18 final size:18
Alignment explanation
Indices: 40093--40154 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
40083 GTTTGGATCA
40093 TCATCTTCATCATCATCG
1 TCATCTTCATCATCATCG
*
40111 TCATCATCATCATCATCG
1 TCATCTTCATCATCATCG
* * *
40129 TCATCTTCATCGTCAGCT
1 TCATCTTCATCATCATCG
40147 TCATCTTC
1 TCATCTTC
40155 TGCGACCGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.39
Consensus pattern (18 bp):
TCATCTTCATCATCATCG
Found at i:40154 original size:6 final size:6
Alignment explanation
Indices: 40093--40154 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
40083 GTTTGGATCA
* * * * * *
40093 TCATCT TCATCA TCATCG TCATCA TCATCA TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
*
40141 TCAGCT TCATCT TC
1 TCATCT TCATCT TC
40155 TGCGACCGAT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:42103 original size:198 final size:198
Alignment explanation
Indices: 41617--43230 Score: 2878
Period size: 198 Copynumber: 8.1 Consensus size: 198
41607 TTTAAATTAG
* * *
41617 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
41682 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * **** *
41747 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTTATTCATTCTGG--GA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGGAAAA
41810 AAAA
195 AAAA
*
41814 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTTATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
41879 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
41944 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
42009 AAA
196 AAA
*
42012 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTTTTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
42077 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * **** *
42142 CGACACTTGTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTTATTCATTCTGG--G
131 CGACACTT-TTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGGAAA
42205 AAAAA
194 AAAAA
42210 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
42275 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
42340 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGG-AAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
42404 AAA
196 AAA
42407 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
42472 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
42537 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
42602 AAA
196 AAA
42605 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
42670 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * ***
42735 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGGAAA
42800 AAAAA
194 AAAAA
42805 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
42870 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
42935 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
43000 AAA
196 AAA
43003 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
43068 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
43133 CGACACTTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAA
43198 AAAA
195 AAAA
*
43202 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
43231 TGACCCTTAA
Statistics
Matches: 1364, Mismatches: 44, Indels: 16
0.96 0.03 0.01
Matches are distributed among these distances:
196 24 0.02
197 396 0.29
198 580 0.43
199 196 0.14
200 168 0.12
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
AAA
Found at i:42750 original size:593 final size:594
Alignment explanation
Indices: 41617--43230 Score: 3025
Period size: 593 Copynumber: 2.7 Consensus size: 594
41607 TTTAAATTAG
* * *
41617 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
41682 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * **** *
41747 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTTATTCATTCTGG-GAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGGAAAA
*
41811 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTTATAAAACCGGT
195 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
41876 ATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
260 ATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
41941 GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAA
325 GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAA
*
42006 AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTTTTCTCTCATAAAACC
390 AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACC
42071 GGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
455 GGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
*
42136 TGGGATCGACACTTGTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTTATTCATTC
520 TGGGATCGACACTTGTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
*
42201 TGG-GAAAAA
585 TGGAAAAAAA
42210 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
42275 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
42340 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
42405 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTA
196 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTA
*
42470 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
261 TAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
42535 ATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAA
326 ATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAA
42600 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
391 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
42665 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
456 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
*
42730 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
521 GGGATCGACACTTGTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
42795 GGAAAAAAAA
586 GG-AAAAAAA
42805 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
42870 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
42935 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGG-AAAA
43000 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
195 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
43065 ATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
260 ATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
43130 GATCGACACTTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGA
325 GATCGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGA
*
43195 AAAAAAATATCGACACAAACTATATTAGTATCGACA
389 AAAAAAATATCGACACAAACTATATTAGTGTCGACA
43231 TGACCCTTAA
Statistics
Matches: 998, Mismatches: 18, Indels: 6
0.98 0.02 0.01
Matches are distributed among these distances:
592 12 0.01
593 559 0.56
595 195 0.20
596 142 0.14
597 90 0.09
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (594 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTA
TAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAA
AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
GGGATCGACACTTGTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
GGAAAAAAA
Found at i:43340 original size:19 final size:19
Alignment explanation
Indices: 43318--43373 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
43308 TAAAAAAATA
43318 AAATCGTATACAAAATTAT
1 AAATCGTATACAAAATTAT
43337 AAATCGTATACAAAATTAT
1 AAATCGTATACAAAATTAT
*
43356 AAATCTTATACAAAATTA
1 AAATCGTATACAAAATTA
43374 ACTCGACATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.32
Consensus pattern (19 bp):
AAATCGTATACAAAATTAT
Found at i:45203 original size:33 final size:33
Alignment explanation
Indices: 45166--45231 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
45156 CATCTTAATA
*
45166 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
45199 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
45232 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:47373 original size:24 final size:24
Alignment explanation
Indices: 47336--47388 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
47326 CCGTTCTATC
47336 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
47360 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
47384 TATTT
1 TATTT
47389 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:47579 original size:20 final size:19
Alignment explanation
Indices: 47533--47579 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
47523 TCCGGTATCA
*
47533 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
47552 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
47573 TTTTACC
1 TTTTACC
47580 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:47734 original size:19 final size:20
Alignment explanation
Indices: 47700--47745 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
47690 ACACTTTTAA
47700 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
47719 TTGTTACCGG-TTTATCATAT
1 TT-TTACCGGTTTTATCATAT
47739 TTTTACC
1 TTTTACC
47746 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:60128 original size:51 final size:52
Alignment explanation
Indices: 60068--60172 Score: 194
Period size: 51 Copynumber: 2.0 Consensus size: 52
60058 TTCGGTTCGG
60068 GTGGACCGAGACCCGACCCGACCGTTG-CCTTCCTTATAAACATCTAAAAAT
1 GTGGACCGAGACCCGACCCGACCGTTGCCCTTCCTTATAAACATCTAAAAAT
*
60119 GTGGACCGAGACCCGACTCGACCGTTGCCCTTCCTTATAAACATCTAAAAAT
1 GTGGACCGAGACCCGACCCGACCGTTGCCCTTCCTTATAAACATCTAAAAAT
60171 GT
1 GT
60173 AAAGGAAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 26 0.50
52 26 0.50
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (52 bp):
GTGGACCGAGACCCGACCCGACCGTTGCCCTTCCTTATAAACATCTAAAAAT
Found at i:64963 original size:22 final size:21
Alignment explanation
Indices: 64937--64998 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
64927 AGACAAGCTG
*
64937 TTAATATCAGGAGTTATTTGAT
1 TTAAT-TCAGGAGTTATATGAT
* *
64959 TTAATTCCAGGGGTTACATGAT
1 TTAATT-CAGGAGTTATATGAT
*
64981 ATAATTTCAGGAGTTATA
1 TTAA-TTCAGGAGTTATA
64999 ACAGCTGAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.91
23 2 0.06
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.40
Consensus pattern (21 bp):
TTAATTCAGGAGTTATATGAT
Found at i:65077 original size:81 final size:81
Alignment explanation
Indices: 64942--65103 Score: 297
Period size: 81 Copynumber: 2.0 Consensus size: 81
64932 AGCTGTTAAT
* *
64942 ATCAGGAGTTATTTGATTTAATTCCAGGGGTTACATGATATAATTTCAGGAGTTATAACAGCTGA
1 ATCAGGAGTTATTTAATTTAATTCCAGGGGTTACATGAAATAATTTCAGGAGTTATAACAGCTGA
65007 ATAATGATGCAATGAA
66 ATAATGATGCAATGAA
*
65023 ATCAGGAGTTATTTAATTTAATTTCAGGGGTTACATGAAATAATTTCAGGAGTTATAACAGCTGA
1 ATCAGGAGTTATTTAATTTAATTCCAGGGGTTACATGAAATAATTTCAGGAGTTATAACAGCTGA
65088 ATAATGATGCAATGAA
66 ATAATGATGCAATGAA
65104 CTTGGACTAT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.33
Consensus pattern (81 bp):
ATCAGGAGTTATTTAATTTAATTCCAGGGGTTACATGAAATAATTTCAGGAGTTATAACAGCTGA
ATAATGATGCAATGAA
Found at i:67735 original size:11 final size:11
Alignment explanation
Indices: 67719--67760 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
67709 GAGTTTGAGT
67719 TCGAGCTTCAA
1 TCGAGCTTCAA
67730 TCGAGC-TCAA
1 TCGAGCTTCAA
67740 GTCTCGAGCTTCAA
1 ---TCGAGCTTCAA
67754 TCGAGCT
1 TCGAGCT
67761 CCTGAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 4 0.15
11 13 0.48
13 6 0.22
14 4 0.15
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (11 bp):
TCGAGCTTCAA
Found at i:72032 original size:23 final size:23
Alignment explanation
Indices: 72006--72053 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
71996 TATAAGTACA
*
72006 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
72029 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
72052 AT
1 AT
72054 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:72520 original size:23 final size:23
Alignment explanation
Indices: 72462--72533 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
72452 ACACTTTACA
* *
72462 ATATAACCACTACCTATTACA-T
1 ATATAAACGCTACCTATTACATT
*
72484 ATATAAACGATACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
72507 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
72530 ATAT
1 ATAT
72534 GTTTACCTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 18 0.42
23 25 0.58
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.33
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:72741 original size:419 final size:428
Alignment explanation
Indices: 72120--73147 Score: 1818
Period size: 419 Copynumber: 2.5 Consensus size: 428
72110 TATTACATTA
72120 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
72185 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAA--T-
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATT-ATTTAATAATTTC
72247 -TTTGCACAAAAAATTATTTGATTATTTGATATTTTAT-AAA-ATTATTTAGAATTTTTAATTTA
130 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
72309 ATAATATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCT
195 ATAATATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCT
*
72374 TAAAACTCACTC-AAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTT
260 TAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTT
72438 TATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACA-TATATAAACGATACCTATT
325 TATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATT
72502 ACATTATATAAGCGCTACCTATTACATCATATGTTTACC
390 ACATTATATAAGCGCTACCTATTACATCATATGTTTACC
72541 TATTATATTGAAAGTGTCCATAC-TTTTAT-AAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
72604 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATA-T-TTTAATAATTTCA
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTATTTAATAATTTCA
72667 TTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
131 TTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
72732 T-A-A-ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTT
196 TAATATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTT
* *
72794 AAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACATTGGAAAAAGTATAGACACTTTT
261 AAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTT
72859 ATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTA
326 ATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTA
*
72924 CATTATATAAGCGCTACCTATTACATCATTTGTTTACC
391 CATTATATAAGCGCTACCTATTACATCATATGTTTACC
*
72962 TATTATA-TGAAAGTGTTCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
73026 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATT-ATTTAATAATTTC
73090 ATTTGCACAAAAAATTATTTG---A--T--T-TTTTATAAAATATTATTTAGAATTTTTAATTTA
130 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
73147 A
195 A
73148 CAACATTAAC
Statistics
Matches: 589, Mismatches: 5, Indels: 31
0.94 0.01 0.05
Matches are distributed among these distances:
416 42 0.07
417 1 0.00
418 2 0.00
419 154 0.26
420 152 0.26
421 135 0.23
422 70 0.12
424 33 0.06
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (428 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTATTTAATAATTTCA
TTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
TAATATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTT
AAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTT
ATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTA
CATTATATAAGCGCTACCTATTACATCATATGTTTACC
Found at i:72918 original size:23 final size:23
Alignment explanation
Indices: 72892--72949 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
72882 ATATAACCAC
72892 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
72915 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
72938 TACCTATTACAT
1 TACCTATTACAT
72950 CATTTGTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:73128 original size:22 final size:23
Alignment explanation
Indices: 73098--73141 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
73088 TCATTTGCAC
*
73098 AAAAAATTATTT-GATTTTTTAT
1 AAAAAATTATTTAGAATTTTTAT
*
73120 AAAATATTATTTAGAATTTTTA
1 AAAAAATTATTTAGAATTTTTA
73142 ATTTAACAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (23 bp):
AAAAAATTATTTAGAATTTTTAT
Found at i:73416 original size:39 final size:39
Alignment explanation
Indices: 73362--73447 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
73352 CAAGTTGTAG
*
73362 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
73401 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
73440 ATTTTGAT
1 ATTTTGAT
73448 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:73729 original size:18 final size:18
Alignment explanation
Indices: 73706--73742 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
73696 CGAAATATAT
73706 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
73724 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
73742 A
1 A
73743 CTCCAATTAC
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:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:74181 original size:21 final size:22
Alignment explanation
Indices: 74156--74234 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 22
74146 GGATAGATAC
74156 TTACA-ATATAACCACTACCTA
1 TTACATATATAACCACTACCTA
*
74177 TTACATTATATAAACGA-TACCTA
1 TTACA-TATAT-AACCACTACCTA
* *
74200 TTACATTATATAAGCGCTACCCTA
1 TTACA-TATATAACCACTA-CCTA
74224 TTACATCATAT
1 TTACAT-ATAT
74235 GTTTACCTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
21 5 0.10
22 2 0.04
23 24 0.50
24 17 0.35
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (22 bp):
TTACATATATAACCACTACCTA
Found at i:74228 original size:24 final size:23
Alignment explanation
Indices: 74171--74234 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
74161 ATATAACCAC
74171 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
74194 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
74217 TACCCTATTACATCATAT
1 TA-CCTATTACATTATAT
74235 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
23 23 0.62
24 14 0.38
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.36
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Done.