Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_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: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 64 of 65
Found at i:12599968 original size:23 final size:23
Alignment explanation
Indices: 12599934--12599979 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
12599924 GGACATTATA
*
12599934 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
*
12599957 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
12599980 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:12600017 original size:143 final size:141
Alignment explanation
Indices: 12599664--12599967 Score: 387
Period size: 143 Copynumber: 2.1 Consensus size: 141
12599654 GGGTAGAGGG
* * ** * *
12599664 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGG-ACTTCGGGATATATATA-A-GCTGTGGAACATGCAT-AAGTC-TATAACACACAT
*
12599729 ACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATAT
61 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATAT
12599794 GGCACTACGGTGCAAT
126 GGCACTACGGTGCAAT
* ** ** * *
12599810 TCTACGCGGTCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATACT
1 TCTACGCGGACTTCGGGATATATATAAGCTGTGGAACATGCAT-AAGTC-TATAACACACATACT
12599875 TGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCC-T-TGGACATTATATGGC
64 TGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATATGGC
12599938 ACTACGGTGCAAT
129 ACTACGGTGCAAT
*
12599951 TCTACGTGGCACTTCGG
1 TCTACGCGG-ACTTCGG
12599968 TGCAATTATA
Statistics
Matches: 152, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
141 36 0.24
142 7 0.05
143 84 0.55
145 16 0.11
146 9 0.06
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (141 bp):
TCTACGCGGACTTCGGGATATATATAAGCTGTGGAACATGCATAAGTCTATAACACACATACTTG
ATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATATGGCAC
TACGGTGCAAT
Found at i:12603802 original size:43 final size:45
Alignment explanation
Indices: 12603729--12603817 Score: 164
Period size: 43 Copynumber: 2.0 Consensus size: 45
12603719 CTATGGATGC
12603729 AAGATTATCTTTAACTGGAGATGGTGGTCTATGTGCAGAGTTAAA
1 AAGATTATCTTTAACTGGAGATGGTGGTCTATGTGCAGAGTTAAA
12603774 AAGATTATCTTTAA-T-GAGATGGTGGTCTATGTGCAGAGTTAAA
1 AAGATTATCTTTAACTGGAGATGGTGGTCTATGTGCAGAGTTAAA
12603817 A
1 A
12603818 CTTAAACCAG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 29 0.66
44 1 0.02
45 14 0.32
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.34
Consensus pattern (45 bp):
AAGATTATCTTTAACTGGAGATGGTGGTCTATGTGCAGAGTTAAA
Found at i:12606789 original size:139 final size:144
Alignment explanation
Indices: 12606612--12606902 Score: 495
Period size: 143 Copynumber: 2.0 Consensus size: 144
12606602 GGGTAGAGGG
12606612 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAG-ACATA
1 TCTACGCGGTCCTTCGGGA-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGAACATA
*
12606676 CTTGAT-CTTAGTATATGTAT-ATTCTTAAGGAATAATATG-GGTCCTTATGGACATTATTATAT
65 CTTGATCCCTAGTATATGTATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATAT
12606738 GGCACTACGGTGCAAT
130 -GCACTACGGTGCAAT
*
12606754 TCTACGC-GTCCTTTGGG-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
1 TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGA-ACATA
12606817 CTTGATCCCTAGTATATGTATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATAT
65 CTTGATCCCTAGTATATGTATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATAT
12606882 GCACTACGGTGCAAT
130 GCACTACGGTGCAAT
12606897 TCTACG
1 TCTACG
12606903 TGGCACTTCG
Statistics
Matches: 142, Mismatches: 2, Indels: 9
0.93 0.01 0.06
Matches are distributed among these distances:
139 39 0.27
141 20 0.14
142 20 0.14
143 40 0.28
144 23 0.16
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (144 bp):
TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGAACATAC
TTGATCCCTAGTATATGTATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATG
CACTACGGTGCAAT
Found at i:12606918 original size:22 final size:23
Alignment explanation
Indices: 12606882--12606924 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
12606872 ATTATTATAT
*
12606882 GCACTACGGTGCAATTCTACGTG
1 GCACTACGGTGCAATTATACGTG
*
12606905 GCACTTCGG-GCAATTATACG
1 GCACTACGGTGCAATTATACG
12606925 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GCACTACGGTGCAATTATACGTG
Found at i:12611260 original size:29 final size:30
Alignment explanation
Indices: 12611227--12611307 Score: 87
Period size: 29 Copynumber: 2.7 Consensus size: 30
12611217 ACTAATGACT
*
12611227 AAAATATAATTTTTG-AAAGTTT-GGTGATC
1 AAAATATAATTTTTGAAAAGTTTAGG-GACC
**
12611256 AAAATA-AAACTTTGAAAAGTTTAGGGACC
1 AAAATATAATTTTTGAAAAGTTTAGGGACC
*
12611285 AAAAGTATAATTTTTAAAAAGTT
1 AAAA-TATAATTTTTGAAAAGTT
12611308 ATATTTTGAC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 6 0.14
29 20 0.48
30 4 0.10
31 12 0.29
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.35
Consensus pattern (30 bp):
AAAATATAATTTTTGAAAAGTTTAGGGACC
Found at i:12616009 original size:35 final size:35
Alignment explanation
Indices: 12615962--12616047 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
12615952 AAAACAGTCA
* * *
12615962 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
12615997 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
12616032 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
12616048 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:12616041 original size:21 final size:21
Alignment explanation
Indices: 12616016--12616058 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
12616006 TTCTAAACCC
12616016 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
12616037 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
12616058 T
1 T
12616059 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:12616216 original size:14 final size:16
Alignment explanation
Indices: 12616180--12616216 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
12616170 ATATTATGTA
12616180 TGAATCATTTATATTTT
1 TGAAT-ATTTATATTTT
12616197 TGAATATTT-TATTTT
1 TGAATATTTATATTTT
12616212 T-AATA
1 TGAATA
12616217 AGAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TGAATATTTATATTTT
Found at i:12616748 original size:21 final size:22
Alignment explanation
Indices: 12616703--12616748 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
12616693 GTGTCACCAA
*
12616703 TAACACATATCATGATCATGTT
1 TAACACATATCATGATCATGAT
* *
12616725 TAACACATGTCA-GATCCTGAT
1 TAACACATATCATGATCATGAT
12616746 TAA
1 TAA
12616749 ATGATTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.33
Consensus pattern (22 bp):
TAACACATATCATGATCATGAT
Found at i:12616896 original size:128 final size:128
Alignment explanation
Indices: 12616676--12616919 Score: 400
Period size: 128 Copynumber: 1.9 Consensus size: 128
12616666 AATTTTCTTC
* * *
12616676 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTTTAACACATGTCAGATC
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTCTAACACATGTCAGATC
*
12616741 CTGATTAAATGATTAATTTATTAAATTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CTAATTAAATGATTAATTTATTAAATTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
12616804 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGT-CTAACACATGTCAGAT
12616869 CCTAATTAAATGATTAATTTATT-AATTTATTTAATTTAGGACCAAATTGAT
65 CCTAATTAAATGATTAATTTATTAAATTTATTTAATTTAGGACCAAATTGAT
12616920 TATATAAATA
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
128 70 0.65
129 37 0.35
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (128 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTCTAACACATGTCAGATC
CTAATTAAATGATTAATTTATTAAATTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:12626879 original size:60 final size:60
Alignment explanation
Indices: 12626789--12626901 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
12626779 GGCTGCGGGC
* * *
12626789 GTTCCTCTTGAGGTTGTATCTGCCGAGGCTGTTGGTCTTGATGTCCAAGTGGCTGCAGAT
1 GTTCCTCTTGAGGTTGTATCTGCCGAGGCTGTTGATCTCGAGGTCCAAGTGGCTGCAGAT
* *
12626849 GTTCCTCTTGAGGTTGTCTCT-CCTGCGGCTGTTGATCTCGAGGTCCAAGTGGC
1 GTTCCTCTTGAGGTTGTATCTGCC-GAGGCTGTTGATCTCGAGGTCCAAGTGGC
12626902 AGGACACGCT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 2 0.04
60 45 0.96
ACGTcount: A:0.12, C:0.23, G:0.31, T:0.35
Consensus pattern (60 bp):
GTTCCTCTTGAGGTTGTATCTGCCGAGGCTGTTGATCTCGAGGTCCAAGTGGCTGCAGAT
Found at i:12626915 original size:60 final size:60
Alignment explanation
Indices: 12626791--12626927 Score: 159
Period size: 60 Copynumber: 2.3 Consensus size: 60
12626781 CTGCGGGCGT
* * * * * * * *
12626791 TCCTCTTGAGGTTGTATCTGCCGAGGCTGTTGGTCTTGATGTCCAAGTGGCTGCAGATGT
1 TCCTCTTGAGGTTGTCTCTGCCGAGGCTGTTGATCTCGAGGTCCAAGTGGCAGCACACGC
* *
12626851 TCCTCTTGAGGTTGTCTCT-CCTGCGGCTGTTGATCTCGAGGTCCAAGTGGCAGGACACGC
1 TCCTCTTGAGGTTGTCTCTGCC-GAGGCTGTTGATCTCGAGGTCCAAGTGGCAGCACACGC
*
12626911 TCCTCTTGGGGTTGTCT
1 TCCTCTTGAGGTTGTCT
12626928 TTGCTGTTGG
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 2 0.03
60 63 0.97
ACGTcount: A:0.12, C:0.24, G:0.31, T:0.34
Consensus pattern (60 bp):
TCCTCTTGAGGTTGTCTCTGCCGAGGCTGTTGATCTCGAGGTCCAAGTGGCAGCACACGC
Found at i:12627994 original size:19 final size:20
Alignment explanation
Indices: 12627957--12627994 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
12627947 ACTATTGATA
*
12627957 ATTATAAAATTTTAAAATAT
1 ATTATAAAATTCTAAAATAT
*
12627977 ATTA-AAAATTCTATAATA
1 ATTATAAAATTCTAAAATA
12627995 CAACTACCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTATAAAATTCTAAAATAT
Found at i:12628053 original size:14 final size:14
Alignment explanation
Indices: 12628036--12628074 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
12628026 CAGTAAACCC
12628036 TAAACTCTAAATCT
1 TAAACTCTAAATCT
12628050 TAAAC-CATAAATCT
1 TAAACTC-TAAATCT
*
12628064 TATACTCTAAA
1 TAAACTCTAAA
12628075 CTATAAACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAACTCTAAATCT
Found at i:12629980 original size:16 final size:16
Alignment explanation
Indices: 12629956--12629993 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
12629946 GAATGAGCTC
* *
12629956 TTGAATTTTTTTGAGT
1 TTGAGTTTTTTCGAGT
12629972 TTGAGTTTTTTCGAGT
1 TTGAGTTTTTTCGAGT
12629988 TTGAGT
1 TTGAGT
12629994 CGAGTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.16, C:0.03, G:0.24, T:0.58
Consensus pattern (16 bp):
TTGAGTTTTTTCGAGT
Found at i:12630040 original size:31 final size:31
Alignment explanation
Indices: 12629980--12630040 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
12629970 GTTTGAGTTT
* * * *
12629980 TTTCGAGTTTGAGTCGAGTTTTAATATTTTC
1 TTTCGAGTTCGAGTCGAGCTTAAAAATTTTC
*
12630011 TTTCGAGTTCGAGTTGAGCTTAAAAATTTT
1 TTTCGAGTTCGAGTCGAGCTTAAAAATTTT
12630041 AGACTCTCGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.23, C:0.10, G:0.20, T:0.48
Consensus pattern (31 bp):
TTTCGAGTTCGAGTCGAGCTTAAAAATTTTC
Found at i:12630911 original size:10 final size:10
Alignment explanation
Indices: 12630896--12630920 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12630886 AGAACTTAAT
12630896 TTTTTTTTTA
1 TTTTTTTTTA
12630906 TTTTTTTTTA
1 TTTTTTTTTA
12630916 TTTTT
1 TTTTT
12630921 CTTTCAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:12634103 original size:31 final size:31
Alignment explanation
Indices: 12634065--12634168 Score: 81
Period size: 31 Copynumber: 3.4 Consensus size: 31
12634055 CCGTTAAAAT
12634065 TTTAGGTACTAAAATGAAACAAAAAGTAAAC
1 TTTAGGTACTAAAATGAAACAAAAAGTAAAC
**** * *
12634096 TTTAGGTA-TGGTTTTGAAA-AAAATG-AAAG
1 TTTAGGTACT-AAAATGAAACAAAAAGTAAAC
* *
12634125 TTTAGGTACTAAAACGAAAC-AAAAGTGATAC
1 TTTAGGTACTAAAATGAAACAAAAAGT-AAAC
*
12634156 TTTAAGTACTAAA
1 TTTAGGTACTAAA
12634169 CATGTAGGAT
Statistics
Matches: 53, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
29 19 0.36
30 7 0.13
31 27 0.51
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (31 bp):
TTTAGGTACTAAAATGAAACAAAAAGTAAAC
Found at i:12645397 original size:23 final size:23
Alignment explanation
Indices: 12645370--12645415 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
12645360 ATAATTTTTA
*
12645370 TTTCATTTTAGTA-CATTTTAGTT
1 TTTCATTCTAGTACCA-TTTAGTT
12645393 TTTCATTCTAGTACCATTTAGTT
1 TTTCATTCTAGTACCATTTAGTT
12645416 AAAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.57
Consensus pattern (23 bp):
TTTCATTCTAGTACCATTTAGTT
Found at i:12647988 original size:2 final size:2
Alignment explanation
Indices: 12647981--12648005 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12647971 ATTTGTTTAA
12647981 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12648006 AATTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12648597 original size:18 final size:19
Alignment explanation
Indices: 12648563--12648602 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
12648553 TAAATTTAAG
12648563 ATAAAATTGATTGAAT-GT
1 ATAAAATTGATTGAATGGT
12648581 ATAAATATTGATT-AATGGT
1 ATAAA-ATTGATTGAATGGT
12648600 ATA
1 ATA
12648603 GTTTATCCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (19 bp):
ATAAAATTGATTGAATGGT
Found at i:12652063 original size:32 final size:31
Alignment explanation
Indices: 12652000--12652103 Score: 86
Period size: 31 Copynumber: 3.4 Consensus size: 31
12651990 GGGCCTGAGA
* * **
12652000 GCCTACCCAAGAAA-AT-TCGGGGCCATGGG
1 GCCTACCTAAGAAACATCTCAGGGCCACAGG
* *
12652029 GCCTACCTAAGAACACATCTTAGGGCCGCAGG
1 GCCTACCTAAGAA-ACATCTCAGGGCCACAGG
** ** *
12652061 GCCTACCCGAGAATGATCTCAGGGCCACAGA
1 GCCTACCTAAGAAACATCTCAGGGCCACAGG
12652092 GCCTACCTAAGA
1 GCCTACCTAAGA
12652104 GTCACATTAG
Statistics
Matches: 57, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
29 12 0.21
30 1 0.02
31 25 0.44
32 19 0.33
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GCCTACCTAAGAAACATCTCAGGGCCACAGG
Found at i:12663276 original size:17 final size:17
Alignment explanation
Indices: 12663256--12663288 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12663246 TTATTAACAA
*
12663256 TAAATTTTTTTTTATTT
1 TAAAATTTTTTTTATTT
12663273 TAAAATTTTTTTTATT
1 TAAAATTTTTTTTATT
12663289 AAAATTACTA
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:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TAAAATTTTTTTTATTT
Found at i:12663283 original size:15 final size:15
Alignment explanation
Indices: 12663256--12663294 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
12663246 TTATTAACAA
*
12663256 TAAATTTTTTTTTATTT
1 TAAAATTTTTTTTA--T
12663273 TAAAATTTTTTTTAT
1 TAAAATTTTTTTTAT
12663288 TAAAATT
1 TAAAATT
12663295 ACTAGAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
17 13 0.62
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TAAAATTTTTTTTAT
Found at i:12664503 original size:16 final size:17
Alignment explanation
Indices: 12664466--12664505 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
12664456 AATGTAAACT
12664466 TTTTTTCTTTGTTTCAA
1 TTTTTTCTTTGTTTCAA
*
12664483 TTTTTTCTTTGTTTTAA
1 TTTTTTCTTTGTTTCAA
12664500 TTTTTT
1 TTTTTT
12664506 TTCTTTTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (17 bp):
TTTTTTCTTTGTTTCAA
Found at i:12664522 original size:20 final size:19
Alignment explanation
Indices: 12664465--12664523 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 19
12664455 GAATGTAAAC
12664465 TTTTTTTCTTTGTT-TCAA-
1 TTTTTTTCTTTGTTCT-AAT
*
12664483 -TTTTTTCTTTGTTTTAAT
1 TTTTTTTCTTTGTTCTAAT
*
12664501 TTTTTTTCTTTTGTTCTGAT
1 TTTTTTTC-TTTGTTCTAAT
12664521 TTT
1 TTT
12664524 GATTGTTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 15 0.43
18 1 0.03
19 7 0.20
20 12 0.34
ACGTcount: A:0.08, C:0.08, G:0.07, T:0.76
Consensus pattern (19 bp):
TTTTTTTCTTTGTTCTAAT
Found at i:12664660 original size:13 final size:14
Alignment explanation
Indices: 12664642--12664670 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12664632 GTTAATAAAA
12664642 AATAATAAAAT-TT
1 AATAATAAAATATT
12664655 AATAATAAAATATT
1 AATAATAAAATATT
12664669 AA
1 AA
12664671 CTATCACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AATAATAAAATATT
Found at i:12669498 original size:112 final size:109
Alignment explanation
Indices: 12669370--12669570 Score: 305
Period size: 112 Copynumber: 1.8 Consensus size: 109
12669360 TTTTTAAAAT
* **
12669370 ATATTAACTTAAAAATA-AATTGTATAAAAAATATATTTTTATACGAATTTATATTTTAAAATAT
1 ATATTAACTTAAAAATACAATTATATAAAAAATATATTTCAATACGAA-TTATATTTT-AAA-AT
*
12669434 ATTAACTTAAAATATTTTATTATTATACGAATATAAAAAAATATTAAA
63 ATTAACCTAAAATA-TTTATTATTATACGAATATAAAAAAATATTAAA
* *
12669482 ATATTAACTTAAAAATACAATTATATAAAATATATATTTCAATACGAATTATATTTTTAAATATT
1 ATATTAACTTAAAAATACAATTATATAAAAAATATATTTCAATACGAATTATATTTTAAAATATT
12669547 AACCTAAAATATTTATTATTATAC
66 AACCTAAAATATTTATTATTATAC
12669571 AATGTAGTAC
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
109 13 0.16
110 15 0.18
111 2 0.02
112 26 0.32
113 26 0.32
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.42
Consensus pattern (109 bp):
ATATTAACTTAAAAATACAATTATATAAAAAATATATTTCAATACGAATTATATTTTAAAATATT
AACCTAAAATATTTATTATTATACGAATATAAAAAAATATTAAA
Found at i:12669741 original size:56 final size:56
Alignment explanation
Indices: 12669423--12669775 Score: 290
Period size: 54 Copynumber: 6.4 Consensus size: 56
12669413 CGAATTTATA
* *
12669423 TTTTAAAATATATTAACTTAAAATATTTTATTATTATACGAATATAA-A--AA-AA
1 TTTTAAAATATATTAACTTAAAATATTTTATTATTATACAAATATAATACTAATAT
* ** ** * * * *
12669475 TATT-AAA-ATATTAACTTAAAAATACAATTATATAAAATATATATTTCAATACGAATTAT
1 TTTTAAAATATATTAACTT-AAAATA-TTTTAT-TATTATACAAATAT-AATACTAA-TAT
* * * *
12669534 ATTTT-TAA-ATATTAACCTAAAATA-TTTATTATTATAC-AATGTAGTACT-ATAT
1 -TTTTAAAATATATTAACTTAAAATATTTTATTATTATACAAATATAATACTAATAT
* * *
12669586 ATTT-AAATAT-TTAAATTAAAATATTTTATT-TTATACAAATATAATACGAATAT
1 TTTTAAAATATATTAACTTAAAATATTTTATTATTATACAAATATAATACTAATAT
* *
12669639 TTTTAAAATATA-TAACTTAAAATATTTTATTA-TATAAAAATATAATATTAATATT
1 TTTTAAAATATATTAACTTAAAATATTTTATTATTATACAAATATAATACTAATA-T
* *
12669694 TTTTAAAATATATTAACGTAAAATATTTTATTATTATACAAAT-TAATATGTATATATTT
1 TTTTAAAATATATTAACTTAAAATATTTTATTATTATACAAATATAATA-CTA-ATA--T
12669753 TTTTAAAATATATTAACTTAAAA
1 TTTTAAAATATATTAACTTAAAA
12669776 ATAAAATTAT
Statistics
Matches: 241, Mismatches: 37, Indels: 39
0.76 0.12 0.12
Matches are distributed among these distances:
50 10 0.04
51 31 0.13
52 26 0.11
53 16 0.07
54 48 0.20
55 17 0.07
56 29 0.12
57 16 0.07
58 3 0.01
59 31 0.13
60 14 0.06
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.45
Consensus pattern (56 bp):
TTTTAAAATATATTAACTTAAAATATTTTATTATTATACAAATATAATACTAATAT
Found at i:12670735 original size:19 final size:20
Alignment explanation
Indices: 12670711--12670750 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
12670701 TGAAAGATTT
*
12670711 TAAATTGTTTA-AAATAAAA
1 TAAATTGTTTATAAAGAAAA
*
12670730 TAAATTTTTTATAAAGAAAA
1 TAAATTGTTTATAAAGAAAA
12670750 T
1 T
12670751 TACAAGGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (20 bp):
TAAATTGTTTATAAAGAAAA
Found at i:12680917 original size:21 final size:20
Alignment explanation
Indices: 12680831--12680988 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
12680821 AAATGACCAA
**
12680831 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
12680850 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
12680870 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
12680890 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
12680911 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
12680932 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
12680952 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
12680973 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
12680989 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:12681017 original size:20 final size:20
Alignment explanation
Indices: 12680955--12681148 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
12680945 CGATTTTCCA
* ** *
12680955 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
12680975 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
12680995 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
12681015 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
12681035 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
12681055 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
12681075 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTATCCGT
* * *
12681095 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
12681115 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
12681136 AAATCGCAACGCG
1 AAATCGCAACGCG
12681149 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:12681039 original size:60 final size:60
Alignment explanation
Indices: 12680955--12681148 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
12680945 CGATTTTCCA
* ** * *
12680955 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
12681015 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * **
12681075 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
12681136 AAATCGCAACGCG
1 AAATCGCAACGCG
12681149 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:12681570 original size:33 final size:33
Alignment explanation
Indices: 12681531--12681601 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
12681521 TTCACTTAGA
*
12681531 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
12681564 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
12681597 TTTCA
1 TTTCA
12681602 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:12681738 original size:41 final size:41
Alignment explanation
Indices: 12681680--12681757 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
12681670 TTGCAGAAGA
*
12681680 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
12681721 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
12681758 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:12681754 original size:21 final size:21
Alignment explanation
Indices: 12681681--12681756 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
12681671 TGCAGAAGAG
*
12681681 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
12681702 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
12681722 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
12681743 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
12681757 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:12681760 original size:14 final size:14
Alignment explanation
Indices: 12681741--12681797 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
12681731 GAGAAATGAA
12681741 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
12681755 AATCGCAACGCGATATGAA
1 AATCGCAA--CG--A-GAG
12681774 AATCGCAACGAGAG
1 AATCGCAACGAGAG
12681788 AATCGCAACG
1 AATCGCAACG
12681798 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:12681776 original size:33 final size:33
Alignment explanation
Indices: 12681736--12681800 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
12681726 AACGAGAGAA
12681736 ATGAAAATCGCAACGAGAGAATCGCAACGCGAT
1 ATGAAAATCGCAACGAGAGAATCGCAACGCGAT
12681769 ATGAAAATCGCAACGAGAGAATCGCAACGCGA
1 ATGAAAATCGCAACGAGAGAATCGCAACGCGA
12681801 AACCAAAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.11
Consensus pattern (33 bp):
ATGAAAATCGCAACGAGAGAATCGCAACGCGAT
Found at i:12681809 original size:33 final size:33
Alignment explanation
Indices: 12681739--12681813 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
12681729 GAGAGAAATG
* **
12681739 AAAATCGCAACGAGAGAATCGCAACGCGATATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
12681772 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
12681805 AAAATCGCA
1 AAAATCGCA
12681814 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.45, C:0.24, G:0.21, T:0.09
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:12681831 original size:19 final size:19
Alignment explanation
Indices: 12681809--12681906 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
12681799 GAAACCAAAA
*
12681809 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
12681828 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
12681842 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
12681861 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
12681875 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
12681894 TCGCGTTGCGATT
1 TCGCGTTGCGATT
12681907 ATCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:12681850 original size:14 final size:14
Alignment explanation
Indices: 12681831--12681920 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
12681821 TTTCATTTCG
12681831 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
12681845 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
12681864 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
12681878 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
*
12681897 CGTTGCGATTATCT
1 CGTTGCGATTCTCT
12681911 CGTTGCGATT
1 CGTTGCGATT
12681921 TTCATTTCAA
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
14 30 0.49
15 1 0.02
16 5 0.08
17 4 0.07
18 1 0.02
19 20 0.33
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:12681856 original size:33 final size:33
Alignment explanation
Indices: 12681814--12681928 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
12681804 CAAAATCGCA
12681814 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
12681847 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
12681880 TTGCGATTGTCATTTCGCGTTGCGATTATCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
12681913 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
12681929 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:12683783 original size:93 final size:93
Alignment explanation
Indices: 12683624--12683906 Score: 541
Period size: 93 Copynumber: 3.1 Consensus size: 93
12683614 TAGATTGCTT
*
12683624 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
12683689 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
12683717 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
12683782 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
12683810 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
12683875 TTTGTCTTTGTTTTGTATTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
12683902 AGTAA
1 AGTAA
12683907 TGCAATCCAT
Statistics
Matches: 188, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 6 0.03
93 182 0.97
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:12684014 original size:33 final size:32
Alignment explanation
Indices: 12683971--12684063 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
12683961 ACGAAACTTA
**
12683971 AAATCGCAACGCGAAATAAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
12684003 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
12684036 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
12684064 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:12684029 original size:19 final size:19
Alignment explanation
Indices: 12683954--12684063 Score: 87
Period size: 19 Copynumber: 6.3 Consensus size: 19
12683944 TAGTTTACTT
* *
12683954 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
**
12683974 TCGCAACGCGAAATAAAAA
1 TCGCAACGCGAAACCAAAA
*
12683993 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
12684007 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
12684026 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
12684040 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
12684059 TCGCA
1 TCGCA
12684064 TTGCGATTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.26
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 29 0.40
20 12 0.17
ACGTcount: A:0.46, C:0.28, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:12684081 original size:19 final size:19
Alignment explanation
Indices: 12684059--12684193 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
12684049 GAAACCAAAA
*
12684059 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
12684078 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
12684094 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
12684111 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
12684127 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
12684144 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
12684163 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
12684183 TCGTGTTGCGA
1 TCGCGTTGCGA
12684194 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:12684100 original size:14 final size:14
Alignment explanation
Indices: 12684081--12684137 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
12684071 TTTCATTTCG
12684081 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
12684095 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
12684112 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
12684128 CGTTGCGATT
1 CGTTGCGATT
12684138 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:12684106 original size:33 final size:33
Alignment explanation
Indices: 12684064--12684156 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
12684054 CAAAATCGCA
*
12684064 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
12684097 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
12684130 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
12684157 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:12686136 original size:14 final size:14
Alignment explanation
Indices: 12686117--12686152 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
12686107 ATTGTTTAAT
12686117 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
12686131 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
12686145 TGATTTGT
1 TGATTTGT
12686153 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:12686275 original size:19 final size:19
Alignment explanation
Indices: 12686259--12686356 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
12686249 AAAAATGACT
12686259 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
12686278 ATAGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
12686297 ATCGCAA--CG--A-GATA
1 ATCGCAATGCGAAATGAAA
12686311 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
12686330 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
12686350 ATCGCAA
1 ATCGCAA
12686357 CGAGAGAATC
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 37 0.54
20 16 0.23
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:12686388 original size:53 final size:53
Alignment explanation
Indices: 12686259--12686374 Score: 207
Period size: 53 Copynumber: 2.2 Consensus size: 53
12686249 AAAAATGACT
* *
12686259 ATCGCAATGCGAAATGAAAATAGCAATGC-GAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
12686311 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
12686364 ATCGCAATGCG
1 ATCGCAATGCG
12686375 TTTATAATTT
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 28 0.46
53 33 0.54
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:12686418 original size:33 final size:33
Alignment explanation
Indices: 12686381--12686533 Score: 159
Period size: 33 Copynumber: 4.5 Consensus size: 33
12686371 TGCGTTTATA
12686381 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
12686414 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
12686454 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
12686485 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
12686518 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
12686534 TTCATTTCGC
Statistics
Matches: 97, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 52 0.54
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:12686427 original size:19 final size:19
Alignment explanation
Indices: 12686403--12686619 Score: 240
Period size: 19 Copynumber: 12.4 Consensus size: 19
12686393 GATTCTCTCG
12686403 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
12686422 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
12686441 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
12686455 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
12686474 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
12686493 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
12686507 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
12686526 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
12686545 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
12686559 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
12686579 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
12686593 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
12686612 TTGCGATT
1 TTGCGATT
12686620 GTAATTTCCG
Statistics
Matches: 169, Mismatches: 8, Indels: 42
0.77 0.04 0.19
Matches are distributed among these distances:
14 29 0.17
16 23 0.14
17 20 0.12
18 3 0.02
19 82 0.49
20 12 0.07
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:12686438 original size:52 final size:52
Alignment explanation
Indices: 12686381--12686591 Score: 413
Period size: 52 Copynumber: 4.0 Consensus size: 52
12686371 TGCGTTTATA
12686381 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
12686433 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
12686485 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
12686537 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
12686590 AT
1 AT
12686592 GTTGGGATTT
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 141 0.89
53 17 0.11
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:12686563 original size:33 final size:33
Alignment explanation
Indices: 12686422--12686619 Score: 197
Period size: 33 Copynumber: 5.8 Consensus size: 33
12686412 TCATTTCGCA
12686422 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
12686455 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
12686491 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
12686526 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
12686559 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
12686593 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
12686620 GTAATTTCCG
Statistics
Matches: 137, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
31 9 0.07
32 5 0.04
33 62 0.45
34 29 0.21
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.06
39 3 0.02
40 9 0.07
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:12688859 original size:12 final size:12
Alignment explanation
Indices: 12688842--12688866 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12688832 TCTTCGGGGA
12688842 CTTTTTCTTCTT
1 CTTTTTCTTCTT
12688854 CTTTTTCTTCTT
1 CTTTTTCTTCTT
12688866 C
1 C
12688867 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:12689798 original size:20 final size:20
Alignment explanation
Indices: 12689770--12689979 Score: 215
Period size: 20 Copynumber: 10.5 Consensus size: 20
12689760 AAATTTCAGT
* * *
12689770 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
12689790 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
12689810 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
12689830 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
12689850 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
12689870 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
12689890 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
*
12689910 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
12689930 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
12689950 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
12689970 GTTGCGATTT
1 GTTGCGATTT
12689980 TGGAAAATCG
Statistics
Matches: 164, Mismatches: 24, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
20 163 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:12689996 original size:21 final size:21
Alignment explanation
Indices: 12689966--12690048 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
12689956 ATTTTCATAT
*
12689966 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
12689987 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
12690008 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
12690029 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
12690049 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:12690039 original size:42 final size:43
Alignment explanation
Indices: 12689946--12690044 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
12689936 ATTTATGTGT
* *
12689946 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
12689987 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
12690029 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
12690045 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:12693662 original size:21 final size:22
Alignment explanation
Indices: 12693634--12693683 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
12693624 ATTTTTTAAA
12693634 ATATATTAACTTAAAATATTTT
1 ATATATTAACTTAAAATATTTT
* * *
12693656 AT-TATTAATTTAATATGTTTT
1 ATATATTAACTTAAAATATTTT
12693677 ATATATT
1 ATATATT
12693684 TATATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATATTAACTTAAAATATTTT
Found at i:12696206 original size:4 final size:4
Alignment explanation
Indices: 12696197--12696227 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
12696187 TACATTTTAA
12696197 AAAT AAAT AAAT AAAT AAAT AAAT AATAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AA
12696228 CCATCGATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:12708239 original size:32 final size:33
Alignment explanation
Indices: 12708193--12708259 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 33
12708183 GGAGAAGCAT
*
12708193 AAAAATTTTATATTAGATCAGTGAACTTATAAA
1 AAAAAATTTATATTAGATCAGTGAACTTATAAA
12708226 AAAAAATTT-TATTAGATCAGTGAACTTATAAA
1 AAAAAATTTATATTAGATCAGTGAACTTATAAA
12708258 AA
1 AA
12708260 TTTTAAGATA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 25 0.76
33 8 0.24
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (33 bp):
AAAAAATTTATATTAGATCAGTGAACTTATAAA
Found at i:12711860 original size:2 final size:2
Alignment explanation
Indices: 12711853--12711878 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12711843 AACGCGGGAG
12711853 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
12711879 ATCGTTTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12712295 original size:33 final size:35
Alignment explanation
Indices: 12712231--12712296 Score: 84
Period size: 33 Copynumber: 1.9 Consensus size: 35
12712221 AAAATATTTA
*
12712231 TATATTTTCTTTAAAAAAATTAAATTAATAAAATT
1 TATATTTTCTTTAAAAAAATTAAAATAATAAAATT
*
12712266 TATATTTT-TTT-ACAAAATTCAAAAT-ATAAAA
1 TATATTTTCTTTAAAAAAATT-AAAATAATAAAA
12712297 AGGTTTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 13 0.46
34 7 0.25
35 8 0.29
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (35 bp):
TATATTTTCTTTAAAAAAATTAAAATAATAAAATT
Found at i:12713021 original size:2 final size:2
Alignment explanation
Indices: 12713014--12713059 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
12713004 ACTCGACCTG
12713014 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12713056 AT AT
1 AT AT
12713060 TAGTTTAAAT
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):
AT
Found at i:12715152 original size:18 final size:18
Alignment explanation
Indices: 12715129--12715164 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12715119 ACTGAGATTT
* *
12715129 ATTATTTTTTATTAGTAA
1 ATTATTTTATAATAGTAA
12715147 ATTATTTTATAATAGTAA
1 ATTATTTTATAATAGTAA
12715165 TGATAAGAAA
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:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
ATTATTTTATAATAGTAA
Found at i:12718072 original size:2 final size:2
Alignment explanation
Indices: 12718065--12718135 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
12718055 CATTCGACTT
12718065 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
12718107 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
12718136 CTTTACTTGC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12726713 original size:103 final size:103
Alignment explanation
Indices: 12726534--12726737 Score: 282
Period size: 103 Copynumber: 2.0 Consensus size: 103
12726524 GTGAAGTGAT
* ** * * *
12726534 TGATATGCCATGGTGTTATTGGTGGGTACACTAGTATATTTTCGATATGACTGCACTTTATGTGC
1 TGATATACCATGGTGTTACCGGTAGGTACACTAATATATTTTAGATATGACTGCACTTTATGTGC
*
12726599 ATATTATGATTCTGATGTGATACCACTGTGTGTGCTTA
66 ATATTATGATTCTGATATGATACCACTGTGTGTGCTTA
* ** * *
12726637 TGATATACGATGGTGTTACCGGTAGGTACACTAATATATTTTAGATATGGTTGTACTTTGTGTGC
1 TGATATACCATGGTGTTACCGGTAGGTACACTAATATATTTTAGATATGACTGCACTTTATGTGC
* *
12726702 ATATTATGATTCTGATATGATAGCACTGTGTTTGCT
66 ATATTATGATTCTGATATGATACCACTGTGTGTGCT
12726738 AATATGTTCC
Statistics
Matches: 87, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
103 87 1.00
ACGTcount: A:0.24, C:0.12, G:0.23, T:0.41
Consensus pattern (103 bp):
TGATATACCATGGTGTTACCGGTAGGTACACTAATATATTTTAGATATGACTGCACTTTATGTGC
ATATTATGATTCTGATATGATACCACTGTGTGTGCTTA
Found at i:12727998 original size:48 final size:48
Alignment explanation
Indices: 12727936--12728075 Score: 218
Period size: 48 Copynumber: 3.0 Consensus size: 48
12727926 TCACACATTT
* *
12727936 ATTTTGGAGGGTAAGTCTATCAAACAAGATTTGCTACATACACAAAAA
1 ATTTTGGAAGGTAAGTCTCTCAAACAAGATTTGCTACATACACAAAAA
12727984 ATTTTGGAAGGTAAGTCTCTCAAACAAGATTTGCTACATACACAAAAA
1 ATTTTGGAAGGTAAGTCTCTCAAACAAGATTTGCTACATACACAAAAA
12728032 ATTTTGGAA-G---G-CTCTCAAACAAAGATTTGCTACATACACAAAAA
1 ATTTTGGAAGGTAAGTCTCTCAAAC-AAGATTTGCTACATACACAAAAA
12728076 TTCAAACTTA
Statistics
Matches: 89, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
43 9 0.10
44 24 0.27
47 1 0.01
48 55 0.62
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.26
Consensus pattern (48 bp):
ATTTTGGAAGGTAAGTCTCTCAAACAAGATTTGCTACATACACAAAAA
Found at i:12733037 original size:21 final size:22
Alignment explanation
Indices: 12733008--12733048 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
12732998 TTATTTATTT
12733008 AAGAGTGCATCGATACACATTG
1 AAGAGTGCATCGATACACATTG
*
12733030 AAGA-TGCATCGATGCACAT
1 AAGAGTGCATCGATACACAT
12733049 AACCCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (22 bp):
AAGAGTGCATCGATACACATTG
Found at i:12733947 original size:18 final size:19
Alignment explanation
Indices: 12733924--12733963 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
12733914 AAACTTTTAT
12733924 AACATTT-AAATTATTCAA
1 AACATTTAAAATTATTCAA
12733942 AACATTTACAAAATTATTCAA
1 AACATTT--AAAATTATTCAA
12733963 A
1 A
12733964 GCTTATACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
21 12 0.63
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (19 bp):
AACATTTAAAATTATTCAA
Found at i:12734492 original size:31 final size:31
Alignment explanation
Indices: 12734454--12734578 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
12734444 CACGAAGGAC
* * **
12734454 CAGTCCATA-GATTCCGAAGAACCTAGGTACT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
12734485 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
12734516 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
12734547 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
12734578 C
1 C
12734579 CCTCGACCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:12738789 original size:31 final size:31
Alignment explanation
Indices: 12738750--12738861 Score: 188
Period size: 31 Copynumber: 3.6 Consensus size: 31
12738740 TAAATAGATT
* *
12738750 TCGAAGAACCTAGGTAATCAGTCCATATGTC
1 TCGAAGAACATAGGTAAACAGTCCATATGTC
*
12738781 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 TCGAAGAACATAGGTAAACAGTCCATATGTC
*
12738812 TCGAAGAACATAGGTAAACAGTCTATATGTC
1 TCGAAGAACATAGGTAAACAGTCCATATGTC
12738843 TCGAAGAACATAGGTAAAC
1 TCGAAGAACATAGGTAAAC
12738862 CCTCGACCCT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (31 bp):
TCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:12741070 original size:76 final size:74
Alignment explanation
Indices: 12740931--12741072 Score: 180
Period size: 76 Copynumber: 1.9 Consensus size: 74
12740921 TAATCACAAT
* * *
12740931 TGGTTGTCATGATCAACTCACATTATGGACATCGATATGGTCGACTCGTCTAAGCACAGATTCAC
1 TGGTTGTCATGATCAACTCACATTATGGACAACGAAATGGTCGACTCGTCTAAGCACACATTCAC
12740996 ACTTAGAGA
66 ACTTAGAGA
* * *
12741005 TGGTTGTCATGATCAACCTCACACTTATGGATAACGAGAATGTTCG-CTCGTAC-AATCACACAT
1 TGGTTGTCATGATCAA-CTCACA-TTATGGACAACGA-AATGGTCGACTCGT-CTAAGCACACAT
12741068 TCACA
62 TCACA
12741073 TTATATATAG
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
74 16 0.28
75 6 0.10
76 29 0.50
77 7 0.12
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (74 bp):
TGGTTGTCATGATCAACTCACATTATGGACAACGAAATGGTCGACTCGTCTAAGCACACATTCAC
ACTTAGAGA
Found at i:12747114 original size:4 final size:4
Alignment explanation
Indices: 12747105--12747214 Score: 62
Period size: 4 Copynumber: 26.0 Consensus size: 4
12747095 ATATCCCTTC
**
12747105 AAAT AAAT AAAT AAATTT GAAAT AAAT AAAT CCA- AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAA--T -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * * * *
12747155 GAGA- AAAT AAATTT GAAAT AAAT AAAT CAATT AAAC AAAT TATT AAAG
1 -AAAT AAAT AAA--T -AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT
12747203 AAAT AAAT AAAT
1 AAAT AAAT AAAT
12747215 TATTCAAAAT
Statistics
Matches: 80, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
3 3 0.04
4 62 0.77
5 7 0.09
6 2 0.03
7 6 0.08
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:12747129 original size:15 final size:15
Alignment explanation
Indices: 12747109--12747181 Score: 76
Period size: 15 Copynumber: 4.8 Consensus size: 15
12747099 CCCTTCAAAT
12747109 AAATAAATAAATTTG
1 AAATAAATAAATTTG
***
12747124 AAATAAATAAATCCA
1 AAATAAATAAATTTG
*
12747139 AAATAAATAAATAAATG
1 AAATAAATAAAT--TTG
*
12747156 AGA-AAATAAATTTG
1 AAATAAATAAATTTG
12747170 AAATAAATAAAT
1 AAATAAATAAAT
12747182 CAATTAAACA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
14 4 0.09
15 32 0.70
16 8 0.17
17 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (15 bp):
AAATAAATAAATTTG
Found at i:12747215 original size:29 final size:30
Alignment explanation
Indices: 12747138--12747239 Score: 80
Period size: 30 Copynumber: 3.3 Consensus size: 30
12747128 AAATAAATCC
* *
12747138 AAAATAAATAAATAAATGAGAAAATAAATTTGAAA
1 AAAATAAATAAATTAA--ACAAAAT-AA-TT-AAA
* * *
12747173 TAAATAAATCAATTAAAC-AAATTATTAAA
1 AAAATAAATAAATTAAACAAAATAATTAAA
* **
12747202 GAAATAAATAAATTATTCAAAATAATTAAA
1 AAAATAAATAAATTAAACAAAATAATTAAA
12747232 AAAATAAA
1 AAAATAAA
12747240 ACAAAAGAAT
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
29 17 0.31
30 19 0.35
31 1 0.02
32 4 0.07
33 1 0.02
35 13 0.24
ACGTcount: A:0.67, C:0.03, G:0.04, T:0.26
Consensus pattern (30 bp):
AAAATAAATAAATTAAACAAAATAATTAAA
Found at i:12747352 original size:14 final size:15
Alignment explanation
Indices: 12747326--12747354 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12747316 GTCTCACCAT
12747326 AATAATATGAGAGAG
1 AATAATATGAGAGAG
12747341 AATAAT-TGAGAGAG
1 AATAATATGAGAGAG
12747355 TTTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.52, C:0.00, G:0.28, T:0.21
Consensus pattern (15 bp):
AATAATATGAGAGAG
Found at i:12747691 original size:46 final size:46
Alignment explanation
Indices: 12747638--12747729 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
12747628 CATGTCCTAC
12747638 GTGTGCTCTTTGGGGATATTCTTCTAAGAAATATGCTAAGGGGTTA
1 GTGTGCTCTTTGGGGATATTCTTCTAAGAAATATGCTAAGGGGTTA
12747684 GTGTGCTCTTTGGGGATATTCTTCTAAGAAATATGCTAAGGGGTTA
1 GTGTGCTCTTTGGGGATATTCTTCTAAGAAATATGCTAAGGGGTTA
12747730 TTGTTCAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.24, C:0.11, G:0.28, T:0.37
Consensus pattern (46 bp):
GTGTGCTCTTTGGGGATATTCTTCTAAGAAATATGCTAAGGGGTTA
Found at i:12750537 original size:10 final size:10
Alignment explanation
Indices: 12750519--12750567 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
12750509 TCACACCAAA
* *
12750519 TTCTTTCAAT
1 TTCTCTCAAC
12750529 TTCTCTCAAC
1 TTCTCTCAAC
* *
12750539 TTCTCTTAAT
1 TTCTCTCAAC
12750549 TTCTCTCAAC
1 TTCTCTCAAC
12750559 TTCTCTCAA
1 TTCTCTCAA
12750568 ATACTCTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.20, C:0.31, G:0.00, T:0.49
Consensus pattern (10 bp):
TTCTCTCAAC
Found at i:12750549 original size:20 final size:20
Alignment explanation
Indices: 12750526--12750564 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
12750516 AAATTCTTTC
12750526 AATTTCTCTCAACTTCTCTT
1 AATTTCTCTCAACTTCTCTT
12750546 AATTTCTCTCAACTTCTCT
1 AATTTCTCTCAACTTCTCT
12750565 CAAATACTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.31, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTTCTCTCAACTTCTCTT
Found at i:12750563 original size:30 final size:30
Alignment explanation
Indices: 12750519--12750576 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
12750509 TCACACCAAA
* * * *
12750519 TTCTTTCAATTTCTCTCAACTTCTCTTAAT
1 TTCTCTCAACTTCTCTCAAATACTCTTAAT
12750549 TTCTCTCAACTTCTCTCAAATACTCTTA
1 TTCTCTCAACTTCTCTCAAATACTCTTA
12750577 TAATCTCTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.48
Consensus pattern (30 bp):
TTCTCTCAACTTCTCTCAAATACTCTTAAT
Found at i:12750574 original size:20 final size:20
Alignment explanation
Indices: 12750531--12750574 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
12750521 CTTTCAATTT
* * *
12750531 CTCTCAACTTCTCTTAATTT
1 CTCTCAACTTCTCTCAAATA
12750551 CTCTCAACTTCTCTCAAATA
1 CTCTCAACTTCTCTCAAATA
12750571 CTCT
1 CTCT
12750575 TATAATCTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.34, G:0.00, T:0.43
Consensus pattern (20 bp):
CTCTCAACTTCTCTCAAATA
Found at i:12750584 original size:30 final size:30
Alignment explanation
Indices: 12750524--12750584 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
12750514 CCAAATTCTT
* * * *
12750524 TCAATTTCTCTCAACTTCTCTTAATTTCTC
1 TCAACTTCTCTCAAATACTCTTAATATCTC
12750554 TCAACTTCTCTCAAATACTCTT-ATAATCTC
1 TCAACTTCTCTCAAATACTCTTAAT-ATCTC
12750584 T
1 T
12750585 GTCTAAGGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.46
Consensus pattern (30 bp):
TCAACTTCTCTCAAATACTCTTAATATCTC
Found at i:12750633 original size:9 final size:9
Alignment explanation
Indices: 12750621--12750654 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
12750611 TAATATTTTG
12750621 TATTTAATT
1 TATTTAATT
*
12750630 TATTTAA-G
1 TATTTAATT
12750638 TATTTAATT
1 TATTTAATT
12750647 TATTTAAT
1 TATTTAAT
12750655 AGTTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:12750642 original size:17 final size:17
Alignment explanation
Indices: 12750620--12750653 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12750610 TTAATATTTT
12750620 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
12750637 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
12750654 TAGTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:12750660 original size:17 final size:16
Alignment explanation
Indices: 12750621--12750670 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
12750611 TAATATTTTG
12750621 TATTTAATTTATTTAA
1 TATTTAATTTATTTAA
12750637 GTATTTAATTTATTTAA
1 -TATTTAATTTATTTAA
*
12750654 TAGTTT-ATTTAATTAA
1 TA-TTTAATTTATTTAA
12750670 T
1 T
12750671 TTTTTTTTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (16 bp):
TATTTAATTTATTTAA
Found at i:12752928 original size:25 final size:25
Alignment explanation
Indices: 12752888--12752948 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
12752878 AGATTTTGTT
* * *
12752888 TTTTTATTATATTTGTATT-TAGTAC
1 TTTTTATTGTAGTTGT-TTATAGGAC
*
12752913 TTTTTATTGTAGTTGTTTATTGGAC
1 TTTTTATTGTAGTTGTTTATAGGAC
12752938 TTTTTATTGTA
1 TTTTTATTGTA
12752949 ATTTTTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 2 0.06
25 29 0.94
ACGTcount: A:0.20, C:0.03, G:0.13, T:0.64
Consensus pattern (25 bp):
TTTTTATTGTAGTTGTTTATAGGAC
Found at i:12752933 original size:13 final size:12
Alignment explanation
Indices: 12752909--12752954 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
12752899 TTTGTATTTA
12752909 GTACTTTTTATT
1 GTACTTTTTATT
*
12752921 GTAGTTGTTTATT
1 GTACTT-TTTATT
*
12752934 GGACTTTTTATT
1 GTACTTTTTATT
*
12752946 GTAATTTTT
1 GTACTTTTT
12752955 TTATTTATCA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.17, C:0.04, G:0.15, T:0.63
Consensus pattern (12 bp):
GTACTTTTTATT
Found at i:12757448 original size:2 final size:2
Alignment explanation
Indices: 12757432--12757466 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
12757422 TTTAAGTAAT
12757432 TA TA TCA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12757467 TAATGATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12760993 original size:16 final size:17
Alignment explanation
Indices: 12760969--12761003 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12760959 TTTATTACCA
12760969 AATAATAAC-TTTTTTT
1 AATAATAACATTTTTTT
*
12760985 AATAGTAACATTTTTTT
1 AATAATAACATTTTTTT
12761002 AA
1 AA
12761004 GTTAAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (17 bp):
AATAATAACATTTTTTT
Found at i:12761239 original size:16 final size:17
Alignment explanation
Indices: 12761201--12761241 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
12761191 GAGTATTTAA
* *
12761201 AATTATTTTATATTTTT
1 AATTATTTAATATTGTT
12761218 AA-TATTTAATA-TGTT
1 AATTATTTAATATTGTT
12761233 AATTATTTA
1 AATTATTTA
12761242 TAATTTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 5 0.24
16 14 0.67
17 2 0.10
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
AATTATTTAATATTGTT
Found at i:12765048 original size:13 final size:13
Alignment explanation
Indices: 12765030--12765058 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
12765020 ACACCACAAA
12765030 AGAATAGCGTAGC
1 AGAATAGCGTAGC
12765043 AGAATAGCGTAGC
1 AGAATAGCGTAGC
12765056 AGA
1 AGA
12765059 GCGCATGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.14, G:0.31, T:0.14
Consensus pattern (13 bp):
AGAATAGCGTAGC
Found at i:12773079 original size:89 final size:89
Alignment explanation
Indices: 12772967--12773145 Score: 322
Period size: 89 Copynumber: 2.0 Consensus size: 89
12772957 AGCCCGGTCC
*
12772967 TTTTTGATATTCACATTTTAAAAAAGGGTGAATTTCAATGTTAGTCACTTGATATTTAGAATCCT
1 TTTTTGATATTCACATTTTAAAAAAGGGTGAATTTCAATGTTAGTCACTTAATATTTAGAATCCT
12773032 TTCATTTTAGTTACAAAACTTTAA
66 TTCATTTTAGTTACAAAACTTTAA
* *
12773056 TTTTTGGTATTCACATTTTAAAAAAGGGTGAATTTCAATGTTAGTCACTTAATATTTAGCATCCT
1 TTTTTGATATTCACATTTTAAAAAAGGGTGAATTTCAATGTTAGTCACTTAATATTTAGAATCCT
*
12773121 TTCATTTTAGTTACAATACTTTAA
66 TTCATTTTAGTTACAAAACTTTAA
12773145 T
1 T
12773146 ACTTATATTA
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (89 bp):
TTTTTGATATTCACATTTTAAAAAAGGGTGAATTTCAATGTTAGTCACTTAATATTTAGAATCCT
TTCATTTTAGTTACAAAACTTTAA
Found at i:12778515 original size:23 final size:23
Alignment explanation
Indices: 12778471--12778515 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
12778461 AACATATTAG
**
12778471 GTAGCGCTTATATAATGTAATAA
1 GTAGCGCTTATATAATAAAATAA
12778494 GTAGCGCTTATATAATAAAATA
1 GTAGCGCTTATATAATAAAATA
12778516 TGCATTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (23 bp):
GTAGCGCTTATATAATAAAATAA
Found at i:12783413 original size:21 final size:23
Alignment explanation
Indices: 12783380--12783429 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
12783370 AGAAAAACAC
12783380 ACACATAATTTTAAAAAGTATCG
1 ACACATAATTTTAAAAAGTATCG
*
12783403 ACAC-TAA-TTTAAAAAGTGTCG
1 ACACATAATTTTAAAAAGTATCG
*
12783424 ATACAT
1 ACACAT
12783430 TATGTAGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 16 0.67
22 4 0.17
23 4 0.17
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (23 bp):
ACACATAATTTTAAAAAGTATCG
Found at i:12783806 original size:198 final size:197
Alignment explanation
Indices: 12783394--12784749 Score: 1725
Period size: 198 Copynumber: 6.8 Consensus size: 197
12783384 ATAATTTTAA
* * * * * * * * *
12783394 AAAGTATCGACACTAATTTAAAAAGTGTCGATACATTATGTAGACATATTTTCTCATAA-AATCG
1 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCT-TTTT-T-TTAATAACCG
* * * * * *
12783458 GTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTT
63 ATATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTT
* *
12783523 TAGGATCGACACATTTTCTAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTAT
128 TGGGATCGACAC-TTTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTAT
12783588 GGACAT
192 GGACAT
* *
12783594 AAAGTGTCGACACAAATGTATAAAGTATCGATATATTATGTATACCTTTTTTTTAATAACCGGTA
1 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAACCGATA
* *
12783659 TTTTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTTGA
66 TATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTTGG
*
12783724 GATCGACACTTATTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATAGA
131 GATCGACACTT-TTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGA
12783789 CAT
195 CAT
*
12783792 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAATCGATA
1 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAACCGATA
* * * *
12783857 TATTTAGACCGATTACATTGTTATGTTACCTATTACATTATAATTATGTGTTTCGAAGTTTTTGG
66 TATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTTGG
12783922 GATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGA
131 GATCGACACTT-TTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGA
12783987 CAT
195 CAT
* * *
12783990 AAAGTGTCAACACAAATGTATAAAGTATCGATACATTATGTATACCTTTCTTTTTTAATAACTGG
1 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACC-TT-TTTTTTAATAACCGA
*
12784055 TATATTTAGACCGGTTACATTGTTATGTTACCTATTACATT-T-A-T--GTGTTTCGATGTTTTT
64 TATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTT
* *
12784115 GGGATCGACACTTGTAT-AA--TATTGACACTTTTTCGTGAACTTGTTTGGAAAATTTA-TATGG
129 GGGATCGACACTTTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGG
12784176 ACAT
194 ACAT
12784180 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTCTTTTTTAATAACCGA
1 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACC-TT-TTTTTTAATAACCGA
* *
12784245 TATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTT
64 TATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTT
* * ** *
12784310 GGGATCGACATTTGTTATAAATGTATCGACACTTTTTTCGTGCACTTGGTTTGG-AAATACATTC
129 GGGATCGACACTT-TTATAAATGTATCGACAC-TTTTTCGTGAACTT-GTTTGGAAAATTTATTA
12784374 TGGACA-
191 TGGACAT
* * * * * * * *
12784380 ACATGTATCTACACAAATGAATAAAGTGTTGATACA-TATTGTAGACCTATTTTCTCATAA-AAC
1 A-AAGTGTCGACACAAATGTATAAAGTATCGATACATTA-TGTATACCT-TTTT-T-TTAATAAC
* * * * * * * *
12784443 CGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTATATTATAGTTACGGGTTTCGATGTT
61 CGATATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGTT
*
12784508 TTTGGGATCGACACTTGATATAAATGTATCGACACTTATTT-GTGAACTTGTTTTGGTTGGAAAA
126 TTTGGGATCGACACTT-TTATAAATGTATCGACACTT-TTTCGTGAACTTG---T--TTGGAAAA
** *
12784572 TACATTATGGACAC
184 TTTATTATGGACAT
* * * ** * *
12784586 AAAGTATCGACACAAATGTATAAAGTGTCGATACTTTATGTATACCCCTTTTCTCATAAACCGAT
1 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAAT-AACCGAT
* * *
12784651 ATATTTAGACCGGTTACATTGTTATTTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTG
65 ATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTTG
*
12784716 GGATCGATACTTTTTATAAATGTATCGACACTTT
130 GGATCGACAC-TTTTATAAATGTATCGACACTTT
12784750 GTTAGTGCAA
Statistics
Matches: 1029, Mismatches: 94, Indels: 63
0.87 0.08 0.05
Matches are distributed among these distances:
190 112 0.11
191 37 0.04
192 1 0.00
193 3 0.00
194 3 0.00
195 56 0.05
196 3 0.00
197 8 0.01
198 361 0.35
199 16 0.02
200 125 0.12
201 144 0.14
202 6 0.01
203 2 0.00
204 96 0.09
205 53 0.05
206 3 0.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (197 bp):
AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAACCGATA
TATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTTGG
GATCGACACTTTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGAC
AT
Found at i:12785748 original size:22 final size:24
Alignment explanation
Indices: 12785720--12785775 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
12785710 AACCTGAATT
12785720 TATAATAAAAT-TA-ATCATTTTA
1 TATAATAAAATATACATCATTTTA
*
12785742 TATAAT-AACTATACCATCATTTTA
1 TATAATAAAATATA-CATCATTTTA
*
12785766 TATAAAAAAA
1 TATAATAAAA
12785776 CAAAAACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 3 0.11
22 8 0.30
24 14 0.52
25 2 0.07
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (24 bp):
TATAATAAAATATACATCATTTTA
Found at i:12787691 original size:20 final size:20
Alignment explanation
Indices: 12787645--12787691 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
12787635 ACCGGTAGTG
12787645 CTTTACCAGTTTTGTCATTT
1 CTTTACCAGTTTTGTCATTT
** *
12787665 CGATACCGGTTTTGTCATATT
1 CTTTACCAGTTTTGTCAT-TT
12787686 -TTTACC
1 CTTTACC
12787692 TATTATATTG
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.17, C:0.21, G:0.13, T:0.49
Consensus pattern (20 bp):
CTTTACCAGTTTTGTCATTT
Found at i:12787871 original size:182 final size:180
Alignment explanation
Indices: 12787619--12788268 Score: 793
Period size: 182 Copynumber: 3.6 Consensus size: 180
12787609 ATTAAAGTAC
* * * * *
12787619 CGACACTTTCAACATAACCGGTAG-TGCTTTACCAGTTTTGTCATTTCGATACCGGTTTTGTCAT
1 CGACACTTTCAATATATCCGGTAGCT-CTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCAT
* * * * * *
12787683 ATTTTTACCTATTATATTGTTATAGATCGATATATTTTCATAAAGTATCGATACTTTTTAGGCGC
65 ATTTTTACCTGTTATATTGCTATGGATCGATACATTTT-ATAAAGTATCGACACTTTATAGGCGC
*
12787748 TATAACTTCTTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
129 TATAACTTCTTCTCTTTTAAATT-CAAAAGTGTCGATACTTATATTAATTTAT
* * **
12787801 CGACATTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACATGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
* *
12787866 TTTTTACCTGTTATATTACTATGGATCGATAAATTTGTATAAAGTATCGACACTTTATAGGCGCT
66 TTTTTACCTGTTATATTGCTATGGATCGATACATTT-TATAAAGTATCGACACTTTATAGGCGCT
**
12787931 ATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAACGTAT
130 ATAACTTCTTCTCTTTTAAATTC-AAAAGTGTCGATACTTATATTAATTTAT
** * *
12787983 CGACACTTTCAATATATCCGGTAGCTCTTTACTTGTTTTATAATTTCGTGACCGGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
* * * *
12788048 CTTATACCTGTTATATTGTTATGGATCGATACGTTTTTATAAAGTATCGACACTTTATAGGCGCT
66 TTTTTACCTGTTATATTGCTATGGATCGATAC-ATTTTATAAAGTATCGACACTTTATAGGCGCT
* * * * *
12788113 ATTACTTTTTCTCTTTTAAATTCTAAAGGTGTCTATACTTAT-TTAAATCTAAT
130 ATAACTTCTTCTCTTTTAAATTC-AAAAGTGTCGATACTTATATT-AAT-TTAT
* * * ** * * * *
12788166 CGATACTTTCGATATATCCAGTAGCGGTTTACCGATTTTATCATAAT-GAAACCGGTTTTTATCA
1 CGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCAT-TTCGAGACCGG-TTTTGTCA
*
12788230 TATTTTTACCTGTTATATTGCTATGGAGCGATACATTTT
64 TATTTTTACCTGTTATATTGCTATGGATCGATACATTTT
12788269 TTATTTGTAT
Statistics
Matches: 401, Mismatches: 59, Indels: 15
0.84 0.12 0.03
Matches are distributed among these distances:
181 3 0.01
182 308 0.77
183 52 0.13
184 38 0.09
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.43
Consensus pattern (180 bp):
CGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
TTTTTACCTGTTATATTGCTATGGATCGATACATTTTATAAAGTATCGACACTTTATAGGCGCTA
TAACTTCTTCTCTTTTAAATTCAAAAGTGTCGATACTTATATTAATTTAT
Found at i:12810463 original size:20 final size:20
Alignment explanation
Indices: 12810438--12810479 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
12810428 ATTTGAAAAG
12810438 CTTGCCTTTTATTCGATAAT
1 CTTGCCTTTTATTCGATAAT
12810458 CTTGCCTTTTATTCGATAAT
1 CTTGCCTTTTATTCGATAAT
12810478 CT
1 CT
12810480 CTTCTCCTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.21, G:0.10, T:0.50
Consensus pattern (20 bp):
CTTGCCTTTTATTCGATAAT
Found at i:12815141 original size:48 final size:48
Alignment explanation
Indices: 12815085--12815181 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
12815075 TCGTCATGTT
12815085 TCCTCTGTTAAATTTAGCCGGTCTTATGTTTCTGTCTATATGCAGAGA
1 TCCTCTGTTAAATTTAGCCGGTCTTATGTTTCTGTCTATATGCAGAGA
12815133 TCCTCTGTTAAATTTAGCCGGTCTTATGTTTCTGTCTATATGCAGAGA
1 TCCTCTGTTAAATTTAGCCGGTCTTATGTTTCTGTCTATATGCAGAGA
12815181 T
1 T
12815182 TCTTTCGCAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (48 bp):
TCCTCTGTTAAATTTAGCCGGTCTTATGTTTCTGTCTATATGCAGAGA
Found at i:12818087 original size:20 final size:20
Alignment explanation
Indices: 12818062--12818101 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
12818052 CGAGCCTTGT
12818062 AGAAACTATAATCATCTCGC
1 AGAAACTATAATCATCTCGC
12818082 AGAAACTATAATCATCTCGC
1 AGAAACTATAATCATCTCGC
12818102 CTAAAACTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (20 bp):
AGAAACTATAATCATCTCGC
Found at i:12821282 original size:28 final size:28
Alignment explanation
Indices: 12821228--12821282 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
12821218 TTTATGTTAA
* * * **
12821228 GGGATAAATTTGAATTTATAATTTTTAG
1 GGGACAAATTTAAACTTATAAAATTTAG
12821256 GGGACAAATTTAAACTTATAAAATTTA
1 GGGACAAATTTAAACTTATAAAATTTA
12821283 ATAATCAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.40
Consensus pattern (28 bp):
GGGACAAATTTAAACTTATAAAATTTAG
Found at i:12822132 original size:14 final size:15
Alignment explanation
Indices: 12822097--12822134 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
12822087 CCAATTCAAT
*
12822097 AAATATAATATAGTA
1 AAATATAATATAATA
12822112 AACATATAA-ATAATA
1 AA-ATATAATATAATA
12822127 AAATATAA
1 AAATATAA
12822135 GCATTGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 6 0.29
15 9 0.43
16 6 0.29
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (15 bp):
AAATATAATATAATA
Found at i:12822310 original size:17 final size:18
Alignment explanation
Indices: 12822276--12822308 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12822266 ATATTAGTAC
12822276 TAAAAATAAAGTGAAAAT
1 TAAAAATAAAGTGAAAAT
12822294 TAAAAA-AAAG-GAAAA
1 TAAAAATAAAGTGAAAA
12822309 ATAAGTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 4 0.27
18 6 0.40
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (18 bp):
TAAAAATAAAGTGAAAAT
Found at i:12828277 original size:33 final size:31
Alignment explanation
Indices: 12828240--12828311 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
12828230 AGCTCTAATA
*
12828240 GCTTATCATAAGCCCATAACTGCCTATCACCTT
1 GCTTATCACAAG--CATAACTGCCTATCACCTT
* * *
12828273 GCTTATCACAAGCTTGACTGCTTATCACCTT
1 GCTTATCACAAGCATAACTGCCTATCACCTT
12828304 GCTTATCA
1 GCTTATCA
12828312 AGCCTAGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 24 0.69
33 11 0.31
ACGTcount: A:0.25, C:0.31, G:0.11, T:0.33
Consensus pattern (31 bp):
GCTTATCACAAGCATAACTGCCTATCACCTT
Found at i:12854500 original size:60 final size:59
Alignment explanation
Indices: 12854339--12854500 Score: 184
Period size: 60 Copynumber: 2.7 Consensus size: 59
12854329 TTAAAGATCA
** * * *
12854339 AAAAGTTTTGGGACCAATTTAGAATGAGATTCATAGTTTGAAGATGAAATTAGAATGTTC
1 AAAAGTTTAAGGACCAATTTAGAATGAGAGTCATAGTTTG-AGATGAAATTAAAATATTC
* * *
12854399 AAAAGTTTAAGGACCAATTTAGAATAAGAGTCATAGCTTGAGCATGAAATTAAAATATTT
1 AAAAGTTTAAGGACCAATTTAGAATGAGAGTCATAGTTTGAG-ATGAAATTAAAATATTC
* *
12854459 AAAAGTTTAATGACCTATTT-GAAATGAG-GATCATAGTTTGAG
1 AAAAGTTTAAGGACCAATTTAG-AATGAGAG-TCATAGTTTGAG
12854501 GACATATGAT
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
59 4 0.05
60 83 0.95
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (59 bp):
AAAAGTTTAAGGACCAATTTAGAATGAGAGTCATAGTTTGAGATGAAATTAAAATATTC
Found at i:12855503 original size:37 final size:37
Alignment explanation
Indices: 12855427--12855503 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
12855417 TTTTTATATT
*
12855427 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
12855464 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
12855501 TTT
1 TTT
12855504 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:12857516 original size:28 final size:28
Alignment explanation
Indices: 12857484--12857555 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 28
12857474 AGAAGTCACG
* * *
12857484 GGTTTGAACTAATTTTTTTTATCAGTAA
1 GGTTTGAGCTAATTTTTTTGATCACTAA
* **
12857512 GGTTTGAGCT-ATATAGTTGATCACTAA
1 GGTTTGAGCTAATTTTTTTGATCACTAA
12857539 GGTTTGAGCTAATTTTT
1 GGTTTGAGCTAATTTTT
12857556 GTTTTCCCTA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
27 22 0.65
28 12 0.35
ACGTcount: A:0.26, C:0.08, G:0.19, T:0.46
Consensus pattern (28 bp):
GGTTTGAGCTAATTTTTTTGATCACTAA
Found at i:12863749 original size:23 final size:23
Alignment explanation
Indices: 12863707--12863751 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
12863697 CAAAAGGCAT
12863707 AGATAAACGTGCAACAAAGATAG
1 AGATAAACGTGCAACAAAGATAG
* *
12863730 AGATAAACGTGCCACGAAGATA
1 AGATAAACGTGCAACAAAGATA
12863752 TAATTATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.16, G:0.22, T:0.13
Consensus pattern (23 bp):
AGATAAACGTGCAACAAAGATAG
Found at i:12864810 original size:56 final size:56
Alignment explanation
Indices: 12864711--12864874 Score: 197
Period size: 56 Copynumber: 2.9 Consensus size: 56
12864701 AGATATATTT
** * * *
12864711 GATTTCGGGATACCTA-TTTTATGATTTTTAATGGCAACAACTGATAAATATACTC
1 GATTTCGGGACCCCTATTTTTATGCTTCTTAATGACAACAACTGATAAATATACTC
* *
12864766 GATTTCGGGACCCCTATTTTTATGCTTCTTAATGACAACAACTGATAGATATATTC
1 GATTTCGGGACCCCTATTTTTATGCTTCTTAATGACAACAACTGATAAATATACTC
* * * * *
12864822 GATTTCAGGG-CCTCTATTTTTATCCTTGTTAATGACAATAATTGATAAATATA
1 GATTTC-GGGACCCCTATTTTTATGCTTCTTAATGACAACAACTGATAAATATA
12864875 TATTTTTTCA
Statistics
Matches: 94, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
55 14 0.15
56 77 0.82
57 3 0.03
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (56 bp):
GATTTCGGGACCCCTATTTTTATGCTTCTTAATGACAACAACTGATAAATATACTC
Found at i:12865875 original size:20 final size:21
Alignment explanation
Indices: 12865842--12865885 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
12865832 TACGAAAAAC
12865842 AATAAAATAAATAA-ATCTATA
1 AATAAAATAAATAATAT-TATA
12865863 AATAAAA-AAATAATATTATA
1 AATAAAATAAATAATATTATA
12865883 AAT
1 AAT
12865886 CAATTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
AATAAAATAAATAATATTATA
Found at i:12866828 original size:2 final size:2
Alignment explanation
Indices: 12866823--12866854 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12866813 AAATAGACCA
12866823 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12866855 TAAGACTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12871085 original size:65 final size:65
Alignment explanation
Indices: 12871016--12871171 Score: 185
Period size: 65 Copynumber: 2.4 Consensus size: 65
12871006 TACACTTGGG
* * *
12871016 GTGCATCGGTACACT-AATTACATTCGATGTTTCAA-AAGAGCTAGGAGTGCATCGATGCATTAT
1 GTGCATCGGTACACTAAAATACATTCGATGTTTCAATAAAAGC-AGGAGTGCATCGATGCATGAT
12871079 AT
65 -T
* * * *
12871081 GTGCATCGGTACA-TAAAATGCATTCGATGTTTCAATAAAATCAGGAGTGTATCGATGCATGGTT
1 GTGCATCGGTACACTAAAATACATTCGATGTTTCAATAAAAGCAGGAGTGCATCGATGCATGATT
* *
12871145 GTGCATCGATACAC-AAAATGCATTCGA
1 GTGCATCGGTACACTAAAATACATTCGA
12871172 ACTAGGGTGT
Statistics
Matches: 80, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
64 27 0.34
65 49 0.61
66 4 0.05
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (65 bp):
GTGCATCGGTACACTAAAATACATTCGATGTTTCAATAAAAGCAGGAGTGCATCGATGCATGATT
Found at i:12874732 original size:21 final size:20
Alignment explanation
Indices: 12874692--12874774 Score: 114
Period size: 20 Copynumber: 4.1 Consensus size: 20
12874682 ATCAGATTGT
12874692 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
12874712 CCAGGGGGAACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
12874732 CCAGGGGGGTACCGATTCCCCC
1 CCA-GGGGGTACAGATT-CCCC
*
12874754 CCAGGGGGTACCGA-TCCCC
1 CCAGGGGGTACAGATTCCCC
12874773 CC
1 CC
12874775 TGTCTAACGA
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
19 6 0.10
20 23 0.40
21 22 0.38
22 7 0.12
ACGTcount: A:0.18, C:0.40, G:0.30, T:0.12
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:12874743 original size:41 final size:41
Alignment explanation
Indices: 12874695--12874774 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
12874685 AGATTGTCCA
12874695 GGGGGTACAGATT-CCCCCCAGGGGGAACAGATTCCCCCCAG
1 GGGGGTACAGATTCCCCCCCAGGGGGAACAGA-TCCCCCCAG
* * *
12874736 GGGGGTACCGATTCCCCCCCAGGGGGTACCGATCCCCCC
1 GGGGGTACAGATTCCCCCCCAGGGGGAACAGATCCCCCC
12874775 TGTCTAACGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 19 0.54
42 16 0.46
ACGTcount: A:0.17, C:0.39, G:0.31, T:0.12
Consensus pattern (41 bp):
GGGGGTACAGATTCCCCCCCAGGGGGAACAGATCCCCCCAG
Found at i:12874774 original size:22 final size:22
Alignment explanation
Indices: 12874695--12874774 Score: 78
Period size: 21 Copynumber: 3.8 Consensus size: 22
12874685 AGATTGTCCA
* *
12874695 GGGGGTACAGAT-TCCCCCCA-
1 GGGGGTACCGATCCCCCCCCAG
* * *
12874715 GGGGGAACAGAT-TCCCCCCAG
1 GGGGGTACCGATCCCCCCCCAG
*
12874736 GGGGGTACCGATTCCCCCCCA-
1 GGGGGTACCGATCCCCCCCCAG
12874757 GGGGGTACCGATCCCCCC
1 GGGGGTACCGATCCCCCC
12874775 TGTCTAACGA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 19 0.36
21 27 0.51
22 7 0.13
ACGTcount: A:0.17, C:0.39, G:0.31, T:0.12
Consensus pattern (22 bp):
GGGGGTACCGATCCCCCCCCAG
Found at i:12878721 original size:18 final size:16
Alignment explanation
Indices: 12878667--12878707 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
12878657 GTTTACTTCA
**
12878667 GAATGATT-AAGCATT
1 GAATGATTCAAGTGTT
12878682 GAATGATTCAAGTGTT
1 GAATGATTCAAGTGTT
12878698 GAATGATTCA
1 GAATGATTCA
12878708 GAGGCTCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (16 bp):
GAATGATTCAAGTGTT
Done.