Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_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: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 64
Found at i:2721623 original size:59 final size:58
Alignment explanation
Indices: 2721544--2721697 Score: 211
Period size: 59 Copynumber: 2.6 Consensus size: 58
2721534 ATGAATTTGG
** * * *
2721544 AGATAAAATTGGAATATTCAAAAGTTTAGGGTCTAATTTAGAAAGAGGGTCATAGTTT
1 AGATAAAATTAAAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGAGTCATAGTTT
*
2721602 AGGGATAAAATT-AAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTT
1 A--GATAAAATTAAAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGAGTCATAGTTT
* *
2721661 AGAGAAAATTAAAATATTTAAAAGTTTAAGGACTAAT
1 AGATAAAATTAAAATATTCAAAAGTTTAAGGACTAAT
2721698 CTAAAATAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
57 8 0.09
58 26 0.30
59 43 0.50
60 9 0.10
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.32
Consensus pattern (58 bp):
AGATAAAATTAAAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGAGTCATAGTTT
Found at i:2721716 original size:58 final size:57
Alignment explanation
Indices: 2721556--2721720 Score: 172
Period size: 58 Copynumber: 2.8 Consensus size: 57
2721546 ATAAAATTGG
* * * * * *
2721556 AATATTCAAAAGTTTAGGGTCTAATTTAGAAA-GAGGGTCATAGTTTAGGGATAAAATTA
1 AATATTCAAAAGTTTAAGGACTAATCTA-AAATAAGAGTCATAGTTTA--GAGAAAATTA
* * *
2721615 AATATTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTAGAGAAAATTAA
1 AATATTCAAAAGTTTAAGGACTAATCTAAAATAAGAGTCATAGTTTAGAGAAAATT-A
* *
2721673 AATATTTAAAAGTTTAAGGACTAATCTAAAATAA-AGATTATAGTTTAG
1 AATATTCAAAAGTTTAAGGACTAATCTAAAATAAGAG-TCATAGTTTAG
2721721 GTACAGATGA
Statistics
Matches: 93, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
57 10 0.11
58 43 0.46
59 40 0.43
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.33
Consensus pattern (57 bp):
AATATTCAAAAGTTTAAGGACTAATCTAAAATAAGAGTCATAGTTTAGAGAAAATTA
Found at i:2722059 original size:21 final size:21
Alignment explanation
Indices: 2722035--2722074 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2722025 AGATATAATA
2722035 ATTAAGAAT-TTAAATATATGT
1 ATTAA-AATATTAAATATATGT
*
2722056 ATTAAAATATTTAATATAT
1 ATTAAAATATTAAATATAT
2722075 TTTAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (21 bp):
ATTAAAATATTAAATATATGT
Found at i:2722925 original size:35 final size:35
Alignment explanation
Indices: 2722884--2722951 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
2722874 TTTACATTTA
2722884 ATATGCATAGGTGCTAATAAAACTTAAAACTTTTT
1 ATATGCATAGGTGCTAATAAAACTTAAAACTTTTT
* * * *
2722919 ATATGCATATGTGTTATTAAAATTTAAAACTTT
1 ATATGCATAGGTGCTAATAAAACTTAAAACTTT
2722952 CCATAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (35 bp):
ATATGCATAGGTGCTAATAAAACTTAAAACTTTTT
Found at i:2723759 original size:60 final size:60
Alignment explanation
Indices: 2723695--2723878 Score: 158
Period size: 60 Copynumber: 3.1 Consensus size: 60
2723685 GTATTACATG
* * * *
2723695 TCCCTAAACTAT-ATCTCTCATTTTAAATTGGTCCTTAAACTTTTTAATATT-TCAATTTCA
1 TCCCTAAACTATGA-CTCCCATTCTAAATTAGTCCTTAAACTTTTGAATATTCT-AATTTCA
* * *
2723755 TCCCTAAATTATGACTCCCATTCTAAATTATTCCTTAAACTTTTGAATATTCTAATTTTA
1 TCCCTAAACTATGACTCCCATTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCA
* * * * * ** * * * *
2723815 TCTCTAAACCATGACACTCTTTCTAAACAAATCTCCT-AACTTTTGAATATTCCAATTCCA
1 TCCCTAAACTATGACTCCCATTCTAAATTAGTC-CTTAAACTTTTGAATATTCTAATTTCA
2723875 TCCC
1 TCCC
2723879 CAAGTTCATC
Statistics
Matches: 100, Mismatches: 21, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
60 96 0.96
61 4 0.04
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.42
Consensus pattern (60 bp):
TCCCTAAACTATGACTCCCATTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCA
Found at i:2724441 original size:23 final size:23
Alignment explanation
Indices: 2724414--2724457 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
2724404 ATATAAAAAT
2724414 AAGGGTAAATCACACAAGTGAAA
1 AAGGGTAAATCACACAAGTGAAA
2724437 AAGGGTAAATCACACAAGTGA
1 AAGGGTAAATCACACAAGTGA
2724458 TCTTTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.14, G:0.23, T:0.14
Consensus pattern (23 bp):
AAGGGTAAATCACACAAGTGAAA
Found at i:2724592 original size:13 final size:13
Alignment explanation
Indices: 2724574--2724598 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2724564 TAATGAAAAT
2724574 CAGAATTGATAAC
1 CAGAATTGATAAC
2724587 CAGAATTGATAA
1 CAGAATTGATAA
2724599 TTAAAATAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
CAGAATTGATAAC
Found at i:2728013 original size:22 final size:20
Alignment explanation
Indices: 2727982--2728065 Score: 73
Period size: 22 Copynumber: 3.9 Consensus size: 20
2727972 ATATTAAAGT
2727982 ATATAAGTATTAAAGTATATA
1 ATATAAGTATTAAA-TATATA
*
2728003 CA-ATAATGTATAAAATTATATA
1 -ATATAA-GTATTAAA-TATATA
2728025 ATATAAGTATTAAATATA-A
1 ATATAAGTATTAAATATATA
2728044 AGTATTAAAGTATATAAATATA
1 A-TA-T-AAGTAT-TAAATATA
2728066 AAGTATTAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
19 2 0.04
20 6 0.11
21 13 0.25
22 24 0.45
23 8 0.15
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (20 bp):
ATATAAGTATTAAATATATA
Found at i:2728063 original size:23 final size:23
Alignment explanation
Indices: 2728029--2728082 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
2728019 TATATAATAT
2728029 AAGTAT-TAAATATAAAGTATTA
1 AAGTATATAAATATAAAGTATTA
2728051 AAGTATATAAATATAAAGTATTA
1 AAGTATATAAATATAAAGTATTA
*
2728074 AAATATATA
1 AAGTATATA
2728083 CTTTAAAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 6 0.20
23 24 0.80
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (23 bp):
AAGTATATAAATATAAAGTATTA
Found at i:2728075 original size:8 final size:8
Alignment explanation
Indices: 2728029--2728075 Score: 57
Period size: 8 Copynumber: 6.2 Consensus size: 8
2728019 TATATAATAT
2728029 AAGTATTA
1 AAGTATTA
2728037 AA-TA-TA
1 AAGTATTA
2728043 AAGTATTA
1 AAGTATTA
2728051 AAGTATATA
1 AAGTAT-TA
2728060 AA-TA-TA
1 AAGTATTA
2728066 AAGTATTA
1 AAGTATTA
2728074 AA
1 AA
2728076 ATATATACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
6 8 0.24
7 6 0.18
8 16 0.47
9 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (8 bp):
AAGTATTA
Found at i:2728160 original size:26 final size:24
Alignment explanation
Indices: 2727893--2728205 Score: 88
Period size: 26 Copynumber: 13.0 Consensus size: 24
2727883 ATAAAGTTTT
2727893 AGTATAAAGTATATATATATATACA
1 AGTATAAAGTATATATATATATA-A
* *
2727918 CACTATAAACTATA-AGTATATATAA
1 -AGTATAAAGTATATA-TATATATAA
* *** *
2727943 ACTATAGTCTATAAAGTGTATAATATAA
1 AGTATAAAGTAT--A-TATAT-ATATAA
*
2727971 AATATTAAAGTATATA-AGTAT-TAA
1 AGTA-TAAAGTATATATA-TATATAA
* ** *
2727995 AGTATATACAATA-ATGTATA-AA
1 AGTATAAAGTATATATATATATAA
* *
2728017 ATTATATAA-TATAAGTATTAAATATAA
1 AGTATA-AAGTAT-A-TA-TATATATAA
2728044 AGTATTAAAGTATATA-A-ATATAA
1 AGTA-TAAAGTATATATATATATAA
* * *
2728067 AGTATTAAAATATATACTTTAAAGTAA
1 AGTA-TAAAGTATATA-TATATA-TAA
* *
2728094 AGTAT-ATGTATGAATATATATATAT
1 AGTATAAAGTAT--ATATATATATAA
*
2728119 A-TATAAAGT-T-T-TA-GTATAA
1 AGTATAAAGTATATATATATATAA
*
2728138 AGTAT--A---TATACATATATAA
1 AGTATAAAGTATATATATATATAA
*
2728157 AGTATAAAGTGTATATATATATAA
1 AGTATAAAGTATATATATATATAA
* *
2728181 ACTATAAACTATAAGTATATATATA
1 AGTATAAAGTAT-A-TATATATATA
2728206 TTGTAACACC
Statistics
Matches: 213, Mismatches: 38, Indels: 72
0.66 0.12 0.22
Matches are distributed among these distances:
16 1 0.00
17 1 0.00
18 2 0.01
19 15 0.07
20 5 0.02
21 2 0.01
22 13 0.06
23 29 0.14
24 42 0.20
25 17 0.08
26 45 0.21
27 22 0.10
28 14 0.07
29 5 0.02
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (24 bp):
AGTATAAAGTATATATATATATAA
Found at i:2728176 original size:24 final size:25
Alignment explanation
Indices: 2728131--2728193 Score: 83
Period size: 24 Copynumber: 2.5 Consensus size: 25
2728121 ATAAAGTTTT
2728131 AGTATAAAGTATATATACATATATAA
1 AGTATAAAGTATATATA-ATATATAA
*
2728157 AGTATAAAGTGTATAT-ATATATAA
1 AGTATAAAGTATATATAATATATAA
* *
2728181 ACTATAAACTATA
1 AGTATAAAGTATA
2728194 AGTATATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 18 0.55
26 15 0.45
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (25 bp):
AGTATAAAGTATATATAATATATAA
Found at i:2728199 original size:24 final size:24
Alignment explanation
Indices: 2728142--2728205 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
2728132 GTATAAAGTA
* * *
2728142 TATATACATATATAAAGTATAAAG
1 TATATATATATATAAACTATAAAC
*
2728166 TGTATATATATATAAACTATAAAC
1 TATATATATATATAAACTATAAAC
2728190 TATAAGTATATATATA
1 TAT-A-TATATATATA
2728206 TTGTAACACC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
24 22 0.67
25 1 0.03
26 10 0.30
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.38
Consensus pattern (24 bp):
TATATATATATATAAACTATAAAC
Found at i:2729027 original size:13 final size:13
Alignment explanation
Indices: 2728980--2729016 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2728970 GTTCTAACCC
2728980 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
2728993 TACCCGACTCGTT
1 GACCCGACCCGTT
2729006 GACCCGACCCG
1 GACCCGACCCG
2729017 ACCCGTTGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2731688 original size:57 final size:57
Alignment explanation
Indices: 2731599--2731706 Score: 137
Period size: 57 Copynumber: 1.9 Consensus size: 57
2731589 GGAAGAATAC
* *
2731599 TTGCAGGTTCCTCGACTTTGTGCTGAGAGCCTTACTATTCGTGACGAGGTTGATTAT
1 TTGCAGGTTCATCGACTTTGTGCTAAGAGCCTTACTATTCGTGACGAGGTTGATTAT
* * * * *
2731656 TTGCAGGTTCATTGGCTTTGTGCTCAAG-GCCTTACTGTTTGTGACGGGGTT
1 TTGCAGGTTCATCGACTTTGTGCT-AAGAGCCTTACTATTCGTGACGAGGTT
2731707 TTATGGTTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
57 41 0.95
58 2 0.05
ACGTcount: A:0.15, C:0.19, G:0.29, T:0.38
Consensus pattern (57 bp):
TTGCAGGTTCATCGACTTTGTGCTAAGAGCCTTACTATTCGTGACGAGGTTGATTAT
Found at i:2734592 original size:3 final size:3
Alignment explanation
Indices: 2734578--2734621 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
2734568 AGAGATATTC
* *
2734578 TCT TCA TCT TCT TCT TCT TCT TCT TCT TTT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
2734622 ATGTACGAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:2736245 original size:23 final size:23
Alignment explanation
Indices: 2736169--2736246 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
2736159 CCTTATGGAC
*
2736169 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
2736193 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
2736216 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
2736239 ATTATATG
1 ATTATATG
2736247 AGTTGTGGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 42 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:2739714 original size:22 final size:22
Alignment explanation
Indices: 2739689--2739807 Score: 107
Period size: 22 Copynumber: 5.4 Consensus size: 22
2739679 GTATATAATA
2739689 TAAAGTAT-TAAATAAAAAGTAT
1 TAAAGTATAT-AATAAAAAGTAT
*
2739711 TAAAGTATATAATATAAAGTAT
1 TAAAGTATATAATAAAAAGTAT
*
2739733 TAAAGTATATAAGTATATAAGTAT
1 TAAAGTATATAA-TA-AAAAGTAT
* * *
2739757 AAAAGTATATATTATAAAGTAT
1 TAAAGTATATAATAAAAAGTAT
* * * *
2739779 AAAACTATAGAAT-ATAAGTAT
1 TAAAGTATATAATAAAAAGTAT
*
2739800 TCAAGTAT
1 TAAAGTAT
2739808 TAAAATATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
21 11 0.14
22 47 0.59
23 5 0.06
24 16 0.20
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (22 bp):
TAAAGTATATAATAAAAAGTAT
Found at i:2739715 original size:8 final size:7
Alignment explanation
Indices: 2739673--2740453 Score: 208
Period size: 8 Copynumber: 106.6 Consensus size: 7
2739663 AACTATAGTC
2739673 TATAAAG
1 TATAAAG
2739680 TATATAA-
1 TATA-AAG
2739687 TATAAAG
1 TATAAAG
2739694 TATTAAA-
1 TA-TAAAG
*
2739701 TAAAAAG
1 TATAAAG
2739708 TATTAAAG
1 TA-TAAAG
2739716 TATATAA-
1 TATA-AAG
2739723 TATAAAG
1 TATAAAG
2739730 TATTAAAG
1 TA-TAAAG
2739738 TATATAAG
1 TATA-AAG
2739746 TATATAAG
1 TATA-AAG
2739754 TATAAAAG
1 TAT-AAAG
* *
2739762 TATATAT
1 TATAAAG
2739769 TATAAAG
1 TATAAAG
*
2739776 TATAAAAC
1 TAT-AAAG
2739784 TATAGAA-
1 TATA-AAG
2739791 TAT-AAG
1 TATAAAG
*
2739797 TATTCAAG
1 TA-TAAAG
*
2739805 TATTAAAA
1 TA-TAAAG
* *
2739813 TATATAC
1 TATAAAG
2739820 TAT-AAG
1 TATAAAG
*
2739826 TATAATAC
1 TATAA-AG
2739834 TATAGAA-
1 TATA-AAG
*
2739841 TAT-ACG
1 TATAAAG
2739847 TATTAAAG
1 TA-TAAAG
*
2739855 TATAAAAC
1 TAT-AAAG
2739863 TATATAA-
1 TATA-AAG
2739870 TAT-AAG
1 TATAAAG
2739876 TATTAAAG
1 TA-TAAAG
2739884 TATTAAAG
1 TA-TAAAG
*
2739892 TATAAAAC
1 TAT-AAAG
2739900 TATAGAA-
1 TATA-AAG
2739907 TAT-AAG
1 TATAAAG
2739913 TATTAAAG
1 TA-TAAAG
*
2739921 TATATAG
1 TATAAAG
2739928 TATAAAG
1 TATAAAG
*
2739935 TATAAAAC
1 TAT-AAAG
2739943 TATAGAA-
1 TATA-AAG
2739950 TAT-AAG
1 TATAAAG
2739956 TATTAAAG
1 TA-TAAAG
*
2739964 TATAAAA
1 TATAAAG
*
2739971 T-TATAG
1 TATAAAG
*
2739977 AATAGAAG
1 TATA-AAG
2739985 TATGAAAG
1 TAT-AAAG
*
2739993 TTTAAAAG
1 TAT-AAAG
*
2740001 TATACATATA
1 TATA-A-A-G
*
2740011 TATAAAC
1 TATAAAG
*
2740018 TATAATG
1 TATAAAG
2740025 TAT-AAG
1 TATAAAG
2740031 TATTAAAG
1 TA-TAAAG
*
2740039 TGTACAAG
1 TATA-AAG
*
2740047 TATAAAAA
1 TAT-AAAG
*
2740055 TATTTAAG
1 TA-TAAAG
*
2740063 TATAAAAC
1 TAT-AAAG
*
2740071 TATGGAA-
1 TAT-AAAG
2740078 TAT-AAG
1 TATAAAG
2740084 TATTAAAG
1 TA-TAAAG
* *
2740092 TATATAC
1 TATAAAG
2740099 TATAAAG
1 TATAAAG
*
2740106 TATAAAAC
1 TAT-AAAG
2740114 TATATAA-
1 TATA-AAG
2740121 TAT-AAG
1 TATAAAG
2740127 TATTAAA-
1 TA-TAAAG
*
2740134 TATAAAT
1 TATAAAG
2740141 TATTAAAG
1 TA-TAAAG
*
2740149 TATATAAA
1 TATA-AAG
2740157 TAT-AAG
1 TATAAAG
2740163 TATTAAAG
1 TA-TAAAG
* *
2740171 TATATAC
1 TATAAAG
2740178 TATAAAG
1 TATAAAG
* *
2740185 TGTAAAAC
1 TAT-AAAG
2740193 TATATAA-
1 TATA-AAG
2740200 TAT-AAG
1 TATAAAG
2740206 TATTAAAG
1 TA-TAAAG
*
2740214 TGTAAAAG
1 TAT-AAAG
2740222 TATTAAAG
1 TA-TAAAG
*
2740230 TATAAAAC
1 TAT-AAAG
2740238 TATAGAA-
1 TATA-AAG
2740245 TATAAA-
1 TATAAAG
2740251 TATTAAAG
1 TA-TAAAG
*
2740259 TATTATAG
1 TA-TAAAG
* *
2740267 TTTATA-
1 TATAAAG
2740273 TAT-AAG
1 TATAAAG
*
2740279 T-TAATAT
1 TATAA-AG
2740286 TATTAAAG
1 TA-TAAAG
*
2740294 TATAAAA
1 TATAAAG
*
2740301 T-TATAG
1 TATAAAG
*
2740307 AATAGAAG
1 TATA-AAG
2740315 TATGAAAG
1 TAT-AAAG
2740323 TATAAAAG
1 TAT-AAAG
*
2740331 TATACATATA
1 TATA-A-A-G
*
2740341 TATAAAC
1 TATAAAG
*
2740348 TATAATG
1 TATAAAG
2740355 TAT-AAG
1 TATAAAG
*
2740361 TATATAAAC
1 --TATAAAG
2740370 TATATAAG
1 TATA-AAG
*
2740378 TTTATATA-
1 --TATAAAG
* *
2740386 TAAAAAC
1 TATAAAG
*
2740393 TATAATG
1 TATAAAG
*
2740400 TATAAGTG
1 TATAA-AG
*
2740408 TATAAAC
1 TATAAAG
2740415 TAT-AAG
1 TATAAAG
2740421 TATATAAG
1 TATA-AAG
2740429 TATTAAA-
1 TA-TAAAG
*
2740436 TTTAAAG
1 TATAAAG
2740443 TATAAAG
1 TATAAAG
2740450 TATA
1 TATA
2740454 TATAACTATA
Statistics
Matches: 586, Mismatches: 93, Indels: 190
0.67 0.11 0.22
Matches are distributed among these distances:
5 17 0.03
6 68 0.12
7 202 0.34
8 268 0.46
9 19 0.03
10 12 0.02
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.35
Consensus pattern (7 bp):
TATAAAG
Found at i:2739794 original size:29 final size:29
Alignment explanation
Indices: 2739774--2739924 Score: 75
Period size: 29 Copynumber: 5.2 Consensus size: 29
2739764 TATATTATAA
*
2739774 AGTATAAAACTATAGAATATA-AGTATTCA
1 AGTATAAAACTATAGAATATATAGTA-TAA
* *
2739803 AGTATTAAAA-TATATACTATA-AGTATAA
1 AGTA-TAAAACTATAGAATATATAGTATAA
* * * *
2739831 TACTATAGAA-TATACGTAT-TAAAGTATAAA
1 -AGTATAAAACTATA-GAATATATAGTAT-AA
* * * *
2739861 ACTATATAA-TATA-AGTATTAAAGTATTAA
1 AGTATAAAACTATAGAATA-TATAGTA-TAA
2739890 AGTATAAAACTATAGAATATA-AGTATTAA
1 AGTATAAAACTATAGAATATATAGTA-TAA
2739919 AGTATA
1 AGTATA
2739925 TAGTATAAAG
Statistics
Matches: 98, Mismatches: 14, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
27 1 0.01
28 12 0.12
29 68 0.69
30 14 0.14
31 3 0.03
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (29 bp):
AGTATAAAACTATAGAATATATAGTATAA
Found at i:2739814 original size:22 final size:21
Alignment explanation
Indices: 2739681--2739971 Score: 146
Period size: 21 Copynumber: 14.1 Consensus size: 21
2739671 TCTATAAAGT
*
2739681 ATATAA-TA-TAAAGTATTAA
1 ATATAAGTATTAAAGTATAAA
* *
2739700 ATAAAAAGTATTAAAGTATATA
1 AT-ATAAGTATTAAAGTATAAA
2739722 ATATAAAGTATTAAAGTATATAA
1 ATAT-AAGTATTAAAGTATA-AA
* *
2739745 GTATATAAGTATAAAAGTATATA
1 --ATATAAGTATTAAAGTATAAA
* * * *
2739768 TTATAAAGTATAAAACTATAGA
1 ATAT-AAGTATTAAAGTATAAA
*
2739790 ATATAAGTATTCAAGTATTAAA
1 ATATAAGTATTAAAGTA-TAAA
*
2739812 ATAT-A-TACTATAAGTATAATA
1 ATATAAGTATTA-AAGTATAA-A
* * *
2739833 CTAT-AG-AATATACGTAT---
1 ATATAAGTATTA-AAGTATAAA
* * *
2739850 -TA-AAGTATAAAACTATATA
1 ATATAAGTATTAAAGTATAAA
2739869 ATATAAGTATTAAAGTAT---
1 ATATAAGTATTAAAGTATAAA
* * *
2739887 -TA-AAGTATAAAACTATAGA
1 ATATAAGTATTAAAGTATAAA
*
2739906 ATATAAGTATTAAAGTATATA
1 ATATAAGTATTAAAGTATAAA
* * * *
2739927 GTATAAAGTATAAAACTATAGA
1 ATAT-AAGTATTAAAGTATAAA
2739949 ATATAAGTATTAAAGTATAAA
1 ATATAAGTATTAAAGTATAAA
2739970 AT
1 AT
2739972 TATAGAATAG
Statistics
Matches: 208, Mismatches: 39, Indels: 48
0.71 0.13 0.16
Matches are distributed among these distances:
16 20 0.10
17 4 0.02
19 2 0.01
20 13 0.06
21 81 0.39
22 68 0.33
23 2 0.01
24 14 0.07
25 4 0.02
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (21 bp):
ATATAAGTATTAAAGTATAAA
Found at i:2739850 original size:50 final size:50
Alignment explanation
Indices: 2739739--2739987 Score: 193
Period size: 50 Copynumber: 4.8 Consensus size: 50
2739729 GTATTAAAGT
* *
2739739 ATATAAGTA-TATAAGTATAAAAGTATATATTATAAAGTATAAAACTATAGA
1 ATATAAGTATTA-AAGTATAAAACTATATAATAT-AAGTATAAAACTATAGA
* * *
2739790 ATATAAGTATTCAAGTATTAAAA-TATATACTATAAGTATAATACTATAGA
1 ATATAAGTATTAAAGTA-TAAAACTATATAATATAAGTATAAAACTATAGA
* * *
2739840 ATATACGTATTAAAGTATAAAACTATATAATATAAGTATTAAAGTATTA-A
1 ATATAAGTATTAAAGTATAAAACTATATAATATAAGTATAAAACTA-TAGA
* * * *
2739890 AGTATAA-AACTATAGAA-TATAAGTATTAAAGTATATAGTATAAAGTATAAAACTATAGA
1 A-TATAAGTA-T-TA-AAGTATAA-AACTATA-TA-ATA-TA---AGTATAAAACTATAGA
* * *
2739949 ATATAAGTATTAAAGTATAAAATTATAGAATAGAAGTAT
1 ATATAAGTATTAAAGTATAAAACTATATAATATAAGTAT
2739988 GAAAGTTTAA
Statistics
Matches: 159, Mismatches: 21, Indels: 37
0.73 0.10 0.17
Matches are distributed among these distances:
49 5 0.03
50 58 0.36
51 30 0.19
52 13 0.08
53 7 0.04
54 5 0.03
55 4 0.03
56 9 0.06
57 7 0.04
58 8 0.05
59 13 0.08
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.34
Consensus pattern (50 bp):
ATATAAGTATTAAAGTATAAAACTATATAATATAAGTATAAAACTATAGA
Found at i:2739935 original size:43 final size:43
Alignment explanation
Indices: 2739873--2740261 Score: 301
Period size: 43 Copynumber: 9.1 Consensus size: 43
2739863 TATATAATAT
2739873 AAGTATTAAAGTATTAAAGTATAAAACTATAGAATATAAGTATTA
1 AAGTA-TAAAGTA-TAAAGTATAAAACTATAGAATATAAGTATTA
*
2739918 AAGTATATAGTATAAAGTATAAAACTATAGAATATAAGTATTA
1 AAGTATAAAGTATAAAGTATAAAACTATAGAATATAAGTATTA
* * * * *
2739961 AAGTATAAAAT-TATAGAATAGAAGTAT-G---A-AAGT-TTAA
1 AAGTATAAAGTATAAAGTATAAAACTATAGAATATAAGTATT-A
* * ** * *
2739998 AAGTATACATATATATAAACTAT-AATGTATA-AGTATTAAAGT-GTA
1 AAGTATA-A-A-GTATAAAGTATAAAACTATAGAATA-T-AAGTATTA
* * *
2740043 CAAGTATAAAAATATTTAAGTATAAAACTATGGAATATAAGTATTA
1 -AAGTAT-AAAGTA-TAAAGTATAAAACTATAGAATATAAGTATTA
* * *
2740089 AAGTATATACTATAAAGTATAAAACTATATAATATAAGTATTA
1 AAGTATAAAGTATAAAGTATAAAACTATAGAATATAAGTATTA
*
2740132 AA-TATAAATTATTAAAG--T---A-TATA-AATATAAGTATTA
1 AAGTATAAAGTA-TAAAGTATAAAACTATAGAATATAAGTATTA
* * * *
2740168 AAGTATATACTATAAAGTGTAAAACTATATAATATAAGTATTA
1 AAGTATAAAGTATAAAGTATAAAACTATAGAATATAAGTATTA
* *
2740211 AAGTGTAAAAGTATTAAAGTATAAAACTATAGAATATAAATATTA
1 AAGTAT-AAAGTA-TAAAGTATAAAACTATAGAATATAAGTATTA
2740256 AAGTAT
1 AAGTAT
2740262 TATAGTTTAT
Statistics
Matches: 279, Mismatches: 36, Indels: 58
0.75 0.10 0.16
Matches are distributed among these distances:
36 22 0.08
37 23 0.08
38 4 0.01
39 1 0.00
40 7 0.03
41 8 0.03
42 23 0.08
43 94 0.34
44 17 0.06
45 56 0.20
46 20 0.07
47 4 0.01
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.34
Consensus pattern (43 bp):
AAGTATAAAGTATAAAGTATAAAACTATAGAATATAAGTATTA
Found at i:2739963 original size:29 final size:29
Alignment explanation
Indices: 2739823--2739924 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 29
2739813 TATATACTAT
* *
2739823 AAGTATAATACTATAGAATATACGTATTA
1 AAGTATAAAACTATAGAATATAAGTATTA
*
2739852 AAGTATAAAACTATATAATATAAGTATTAAAGTATTA
1 AAGTATAAAAC----T-ATAGAA-TA-T-AAGTATTA
2739889 AAGTATAAAACTATAGAATATAAGTATTA
1 AAGTATAAAACTATAGAATATAAGTATTA
2739918 AAGTATA
1 AAGTATA
2739925 TAGTATAAAG
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
29 25 0.41
30 1 0.02
31 2 0.03
32 5 0.08
33 2 0.03
34 5 0.08
35 2 0.03
36 1 0.02
37 18 0.30
ACGTcount: A:0.53, C:0.04, G:0.10, T:0.33
Consensus pattern (29 bp):
AAGTATAAAACTATAGAATATAAGTATTA
Found at i:2739964 original size:29 final size:29
Alignment explanation
Indices: 2739921--2740334 Score: 113
Period size: 29 Copynumber: 14.9 Consensus size: 29
2739911 AGTATTAAAG
*
2739921 TATATAGTA-TAAAGTATAAAACTATAGAA
1 TATA-AGTATTAAAGTATAAAAGTATAGAA
*
2739950 TATAAGTATTAAAGTATAAAATTATAGAA
1 TATAAGTATTAAAGTATAAAAGTATAGAA
* * * *
2739979 TAGAAGTATGAAAGTTTAAAAGTATA-CA
1 TATAAGTATTAAAGTATAAAAGTATAGAA
*
2740007 TAT-A-TA-TAAACTAT---A--AT-G--
1 TATAAGTATTAAAGTATAAAAGTATAGAA
* *
2740025 TATAAGTATTAAAGTGTACAAGTAT--AA
1 TATAAGTATTAAAGTATAAAAGTATAGAA
* * *
2740052 -A-AA-TATTTAAGTATAAAACTATGGAA
1 TATAAGTATTAAAGTATAAAAGTATAGAA
* *
2740078 TATAAGTATTAAAGTAT-ATACTATA-AA
1 TATAAGTATTAAAGTATAAAAGTATAGAA
* * * *
2740105 GTATAA-AACTATA-TAATATAAGTATTA-AA
1 -TATAAGTATTAAAGT-ATAAAAGTA-TAGAA
* *
2740134 TATAAATTATTAAAGTATATAAA-TATA-AG
1 TAT-AAGTATTAAAGTATA-AAAGTATAGAA
* * * *
2740163 TATTAAAGTA-TATACTAT-AAAGTGTAAAA
1 TA-T-AAGTATTAAAGTATAAAAGTATAGAA
* *
2740192 CTAT-A-TAATATAAGTATTAAAG--T-G--
1 -TATAAGTATTA-AAGTATAAAAGTATAGAA
* *
2740216 TAAAAGTATTAAAGTATAAAACTATAGAA
1 TATAAGTATTAAAGTATAAAAGTATAGAA
* * * * *
2740245 TATAAATATTAAAGTATTATAGTTTATATA
1 TATAAGTATTAAAGTATAAAAGTATAGA-A
* *
2740275 TAAGTTAATATTATTAAAGTATAAAATTATAGAA
1 T-A--T-A-AGTATTAAAGTATAAAAGTATAGAA
* *
2740309 TAGAAGTATGAAAGTATAAAAGTATA
1 TATAAGTATTAAAGTATAAAAGTATA
2740335 CATATATATA
Statistics
Matches: 281, Mismatches: 59, Indels: 90
0.65 0.14 0.21
Matches are distributed among these distances:
18 3 0.01
19 1 0.00
20 4 0.01
21 6 0.02
22 1 0.00
23 2 0.01
24 26 0.09
25 11 0.04
26 11 0.04
27 18 0.06
28 33 0.12
29 118 0.42
30 20 0.07
31 4 0.01
33 2 0.01
34 3 0.01
35 18 0.06
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.35
Consensus pattern (29 bp):
TATAAGTATTAAAGTATAAAAGTATAGAA
Found at i:2740106 original size:22 final size:22
Alignment explanation
Indices: 2740081--2740173 Score: 88
Period size: 22 Copynumber: 4.3 Consensus size: 22
2740071 TATGGAATAT
*
2740081 AAGTATTAAAGTATATACTA-TA
1 AAGTATTAAA-TATATAATATTA
*
2740103 AAGTATAAAACTATATAATA-T-
1 AAGTATTAAA-TATATAATATTA
2740124 AAGTATTAAATATA-AATTATTA
1 AAGTATTAAATATATAA-TATTA
*
2740146 AAGTATATAAATATA-AGTATTA
1 AAGTAT-TAAATATATAATATTA
2740168 AAGTAT
1 AAGTAT
2740174 ATACTATAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
19 2 0.03
20 6 0.10
21 10 0.16
22 35 0.56
23 9 0.15
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.37
Consensus pattern (22 bp):
AAGTATTAAATATATAATATTA
Found at i:2740161 original size:79 final size:80
Alignment explanation
Indices: 2740076--2740241 Score: 273
Period size: 79 Copynumber: 2.1 Consensus size: 80
2740066 AAAACTATGG
2740076 AATATAAGTATTAAAGTATATACTATAAAGTATAAAACTATATAATATAAGTATTAAA-TAT-AA
1 AATATAAGTATTAAAGTATATACTATAAAGTATAAAACTATATAATATAAGTATTAAAGTATAAA
*
2740139 ATTATTAAAGTATATA
66 AGTATTAAAGTATA-A
* *
2740155 AATATAAGTATTAAAGTATATACTATAAAGTGTAAAACTATATAATATAAGTATTAAAGTGTAAA
1 AATATAAGTATTAAAGTATATACTATAAAGTATAAAACTATATAATATAAGTATTAAAGTATAAA
2740220 AGTATTAAAGTATAA
66 AGTATTAAAGTATAA
2740235 AACTATA
1 AA-TATA
2740242 GAATATAAAT
Statistics
Matches: 81, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
79 57 0.70
80 5 0.06
81 19 0.23
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (80 bp):
AATATAAGTATTAAAGTATATACTATAAAGTATAAAACTATATAATATAAGTATTAAAGTATAAA
AGTATTAAAGTATAA
Found at i:2740185 original size:22 final size:22
Alignment explanation
Indices: 2740124--2740261 Score: 122
Period size: 22 Copynumber: 6.3 Consensus size: 22
2740114 TATATAATAT
*
2740124 AAGTAT-TAAATATAAATTATTA
1 AAGTATAT-AATATAAAGTATTA
2740146 AAGTATATAA-ATATAAGTATTA
1 AAGTATATAATATA-AAGTATTA
* * *
2740168 AAGTATATACTATAAAGTGTAA
1 AAGTATATAATATAAAGTATTA
*
2740190 AACTATATAATAT-AAGTATTA
1 AAGTATATAATATAAAGTATTA
* * *
2740211 AAGTGTAAAAGTATTAAAGTATAA
1 AAGTATATAA-TA-TAAAGTATTA
* *
2740235 AACTATAGAATATAAA-TATTA
1 AAGTATATAATATAAAGTATTA
2740256 AAGTAT
1 AAGTAT
2740262 TATAGTTTAT
Statistics
Matches: 93, Mismatches: 17, Indels: 13
0.76 0.14 0.11
Matches are distributed among these distances:
21 25 0.27
22 47 0.51
23 7 0.08
24 14 0.15
ACGTcount: A:0.54, C:0.02, G:0.09, T:0.35
Consensus pattern (22 bp):
AAGTATATAATATAAAGTATTA
Found at i:2740193 original size:330 final size:328
Alignment explanation
Indices: 2739747--2740368 Score: 872
Period size: 330 Copynumber: 1.9 Consensus size: 328
2739737 GTATATAAGT
* *
2739747 ATATAAGTATAAAAGTATATATTATAAAGTATAAAACTATAGAATATAAGTATTCAAGTATTAAA
1 ATATAAGTATAAAAGTATATACTATAAAGTATAAAACTATAGAATATAAGTATTCAAATATTAAA
* * *
2739812 ATATATACTATAAGTATAATACTATAGAATATACGTATTAAAGTATAAAACTATATAATATAAG-
66 ATAAATACTATAAATATAATACTAAAGAATATACGTATTAAAGTATAAAACTATATAATATAAGT
*
2739876 T-A-T-T-AAAGTATTAAAGTATAAAACTATAGAATATAAGTATTAAAGTA-TATAGTATAAAGT
131 TAAGTGTAAAAGTATTAAAGTATAAAACTATAGAATATAAATATTAAAGTATTATAGT-T-AA-T
*
2739936 ATAAAACTATAGAATATAAGTATTAAAGTATAAAATTATAGAATAGAAGTATGAAAGTTTAAAAG
193 ATAAAACT-T--AATAT---TATTAAAGTATAAAATTATAGAATAGAAGTATGAAAGTATAAAAG
2740001 TATACATATATATAAACTATAATGTATAAGTAT-TAAAGTGTACAAGTATAAAAATATTTAAGTA
252 TATACATATATATAAACTATAATGTATAAGTATATAAAGTGTACAAGTATAAAAATATTTAAGTA
2740065 TAAAACTATGGA
317 TAAAACTATGGA
* *
2740077 ATATAAGTATTAAAGTATATACTATAAAGTATAAAACTATATAATATAAGTATT-AAATA-TAAA
1 ATATAAGTATAAAAGTATATACTATAAAGTATAAAACTATAGAATATAAGTATTCAAATATTAAA
* * *
2740140 TTATTAAAGTA-TATAAATATAAGTATTAAAGTATATAC-TA-TAAAGTGTAAAACTATATAATA
66 --A-TAAA-TACTATAAATATAA-TACTAAAGAATATACGTATTAAAGTATAAAACTATATAATA
2740202 TAAGTATTAAAGTGTAAAAGTATTAAAGTATAAAACTATAGAATATAAATATTAAAGTATTATAG
126 TAAG--TT-AAGTGTAAAAGTATTAAAGTATAAAACTATAGAATATAAATATTAAAGTATTATAG
* * *
2740267 TTTATATATAAGTTAATATTATTAAAGTATAAAATTATAGAATAGAAGTATGAAAGTATAAAAGT
188 TTAATATAAAACTTAATATTATTAAAGTATAAAATTATAGAATAGAAGTATGAAAGTATAAAAGT
2740332 ATACATATATATAAACTATAATGTATAAGTATATAAA
253 ATACATATATATAAACTATAATGTATAAGTATATAAA
2740369 CTATATAAGT
Statistics
Matches: 262, Mismatches: 15, Indels: 29
0.86 0.05 0.09
Matches are distributed among these distances:
328 4 0.02
329 4 0.02
330 154 0.59
331 19 0.07
332 14 0.05
333 6 0.02
335 2 0.01
336 8 0.03
337 2 0.01
338 43 0.16
339 6 0.02
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.34
Consensus pattern (328 bp):
ATATAAGTATAAAAGTATATACTATAAAGTATAAAACTATAGAATATAAGTATTCAAATATTAAA
ATAAATACTATAAATATAATACTAAAGAATATACGTATTAAAGTATAAAACTATATAATATAAGT
TAAGTGTAAAAGTATTAAAGTATAAAACTATAGAATATAAATATTAAAGTATTATAGTTAATATA
AAACTTAATATTATTAAAGTATAAAATTATAGAATAGAAGTATGAAAGTATAAAAGTATACATAT
ATATAAACTATAATGTATAAGTATATAAAGTGTACAAGTATAAAAATATTTAAGTATAAAACTAT
GGA
Found at i:2740367 original size:22 final size:22
Alignment explanation
Indices: 2740339--2740513 Score: 148
Period size: 22 Copynumber: 7.9 Consensus size: 22
2740329 AGTATACATA
*
2740339 TATATAAACTATAATGTATAAG
1 TATATAAACTATAAAGTATAAG
*
2740361 TATATAAACTATATAAGTTTATA-
1 TATATAAACTATA-AAGTATA-AG
* *
2740384 TATAAAAACTATAATGTATAAG
1 TATATAAACTATAAAGTATAAG
*
2740406 TGTATAAACTAT-AAGTATATAAG
1 TATATAAACTATAAAG--TATAAG
*
2740429 TAT-TAAA-TTTAAAGTATAAAG
1 TATATAAACTATAAAGTAT-AAG
2740450 TATATATAACTATAAAAGTATAAG
1 TATATA-AACTAT-AAAGTATAAG
* * *
2740474 TATGTTAA-TATAAAGTATTAAT
1 TATATAAACTATAAAGTA-TAAG
2740496 TAT-TAAA-TATAAAGTATA
1 TATATAAACTATAAAGTATA
2740514 TAAATATATA
Statistics
Matches: 126, Mismatches: 15, Indels: 26
0.75 0.09 0.16
Matches are distributed among these distances:
20 5 0.04
21 29 0.23
22 46 0.37
23 29 0.23
24 10 0.08
25 7 0.06
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.38
Consensus pattern (22 bp):
TATATAAACTATAAAGTATAAG
Found at i:2740454 original size:68 final size:66
Alignment explanation
Indices: 2740423--2740561 Score: 97
Period size: 67 Copynumber: 2.1 Consensus size: 66
2740413 ACTATAAGTA
* * * * * *
2740423 TATAAGTATTAAATTTAAAGTATAAAGTATAT-ATAACTATAAAAGTATAAGTATGTTAATATAA
1 TATAAGTATTAAATATAAAGTATAAA-TATATAAAAACTAT-AATGTATAAGTGTATAAATAT-A
2740487 AGTA
63 AGTA
* * * *
2740491 T-TAATTATTAAATATAAAGTATATAAATATATATAAA-TAAATATGTATAA-AGTATTAAATAT
1 TATAAGTATTAAATATAAAG--TATAAATATATAAAAACTATA-ATGTATAAGTGTA-TAAATAT
2740553 AAGTA
62 AAGTA
2740558 TATA
1 TATA
2740562 TAAATATGTA
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
67 24 0.44
68 23 0.42
69 8 0.15
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (66 bp):
TATAAGTATTAAATATAAAGTATAAATATATAAAAACTATAATGTATAAGTGTATAAATATAAGT
A
Found at i:2740532 original size:14 final size:14
Alignment explanation
Indices: 2740499--2740541 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2740489 TATTAATTAT
* *
2740499 TAAATATAAAGTATA
1 TAAATATATA-TAAA
2740514 TAAATATATATAAA
1 TAAATATATATAAA
*
2740528 TAAATATGTATAAA
1 TAAATATATATAAA
2740542 GTATTAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (14 bp):
TAAATATATATAAA
Found at i:2740570 original size:34 final size:32
Alignment explanation
Indices: 2740503--2740585 Score: 121
Period size: 34 Copynumber: 2.5 Consensus size: 32
2740493 AATTATTAAA
2740503 TATAAAGTATATAAATATATATAAATAAATATG
1 TATAAAGTAT-TAAATATATATAAATAAATATG
*
2740536 TATAAAGTATTAAATATAAGTATATATAAATATG
1 TATAAAGTATTAAATAT-A-TATAAATAAATATG
*
2740570 TATAAAATATTAAATA
1 TATAAAGTATTAAATA
2740586 AAACATTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
32 7 0.15
33 11 0.24
34 28 0.61
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (32 bp):
TATAAAGTATTAAATATATATAAATAAATATG
Found at i:2740572 original size:14 final size:14
Alignment explanation
Indices: 2740510--2740573 Score: 56
Period size: 14 Copynumber: 4.1 Consensus size: 14
2740500 AAATATAAAG
*
2740510 TATATAAATATATA
1 TATATAAATATGTA
*
2740524 TAAATAAATATGTA
1 TATATAAATATGTA
2740538 TAAAGTATTAAATATAAGTA
1 T--A-TA-TAAATAT--GTA
2740558 TATATAAATATGTA
1 TATATAAATATGTA
2740572 TA
1 TA
2740574 AAATATTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 18 0.44
16 8 0.20
17 3 0.07
18 8 0.20
20 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (14 bp):
TATATAAATATGTA
Found at i:2740790 original size:2 final size:2
Alignment explanation
Indices: 2740783--2740824 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2740773 ATTTTCTAAA
2740783 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
2740825 TCATTTTCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2741308 original size:22 final size:23
Alignment explanation
Indices: 2741283--2741332 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
2741273 CTGTAACCCT
*
2741283 AATCCCCAAATCCTAAATCC-CA
1 AATCCCCAAATACTAAATCCTCA
*
2741305 AATCCCCAAATATTAAATCCTCA
1 AATCCCCAAATACTAAATCCTCA
2741328 AATCC
1 AATCC
2741333 TTAACTCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.42, C:0.36, G:0.00, T:0.22
Consensus pattern (23 bp):
AATCCCCAAATACTAAATCCTCA
Found at i:2741879 original size:27 final size:27
Alignment explanation
Indices: 2741843--2742052 Score: 179
Period size: 27 Copynumber: 7.8 Consensus size: 27
2741833 TGATATTTGT
* *
2741843 TTTGTGTATGGTTTCTGATATTTATGA
1 TTTGAGTATGGTTACTGATATTTATGA
*
2741870 TTTGAATATGGTTACTGATATTT-T--
1 TTTGAGTATGGTTACTGATATTTATGA
** *
2741894 TTTCTGTATGGTTACTGATGTTTATGA
1 TTTGAGTATGGTTACTGATATTTATGA
*
2741921 TTTCAGTATGGTTACTGAT-TTT-T--
1 TTTGAGTATGGTTACTGATATTTATGA
*
2741944 TTTGTGTATGGTTACTGATATTTATGATTTGCGA
1 TTTGAGTATGGTTACTGATA-TT-T-A--T--GA
*
2741978 TTTTGAGTATGGCTACTGATATTT-T--
1 -TTTGAGTATGGTTACTGATATTTATGA
*
2742003 TTGTGTGTATGGTTACTGATATTTATGA
1 TT-TGAGTATGGTTACTGATATTTATGA
2742031 TTTGAGTATGGTTACTGATATT
1 TTTGAGTATGGTTACTGATATT
2742053 CTGAAAGATG
Statistics
Matches: 149, Mismatches: 15, Indels: 38
0.74 0.07 0.19
Matches are distributed among these distances:
23 17 0.11
24 21 0.14
25 23 0.15
26 6 0.04
27 57 0.38
28 2 0.01
29 1 0.01
30 1 0.01
33 1 0.01
34 2 0.01
35 18 0.12
ACGTcount: A:0.20, C:0.06, G:0.21, T:0.52
Consensus pattern (27 bp):
TTTGAGTATGGTTACTGATATTTATGA
Found at i:2742013 original size:25 final size:26
Alignment explanation
Indices: 2741979--2742052 Score: 98
Period size: 25 Copynumber: 2.8 Consensus size: 26
2741969 GATTTGCGAT
*
2741979 TTTGAGTATGGCTACTGATATTT-T-
1 TTTGAGTATGGTTACTGATATTTATA
*
2742003 TTGTGTGTATGGTTACTGATATTTATGA
1 TT-TGAGTATGGTTACTGATATTTAT-A
2742031 TTTGAGTATGGTTACTGATATT
1 TTTGAGTATGGTTACTGATATT
2742053 CTGAAAGATG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
24 2 0.05
25 19 0.44
26 1 0.02
27 19 0.44
28 2 0.05
ACGTcount: A:0.22, C:0.05, G:0.23, T:0.50
Consensus pattern (26 bp):
TTTGAGTATGGTTACTGATATTTATA
Found at i:2742114 original size:110 final size:107
Alignment explanation
Indices: 2741860--2742114 Score: 255
Period size: 110 Copynumber: 2.3 Consensus size: 107
2741850 ATGGTTTCTG
* * *
2741860 ATATTTATGATTTGAATATGGTTACTGATATTTTTTTCTGTATGGTTACTGATGTTTATGATTTC
1 ATATTTATGATTTGAGTATGGTTACTGATATTTTTGTCTGTATGGTTACTGATATTTATGATTTC
**** *
2741925 AGTATGGTTACTGATTTTTTTTGTGTATGGTTACTGATATTT
66 AGTATGGTTACTGATTTTGAAAGTGCATGGTTACTGATATTT
** * *
2741967 ATGATTTGCGATTTTGAGTATGGCTACTGATATTTTTTGTGTGTATGGTTACTGATATTTATGAT
1 AT-ATTTATGA-TTTGAGTATGGTTACTGATA-TTTTTGTCTGTATGGTTACTGATATTTATGAT
* * **
2742032 TTGAGTATGGTTACTGATATTCTGAAAGATGAACACT-TTTTTTG-T-TTT
63 TTCAGTATGGTTACTGAT-TT-TGAAAG-TG--CA-TGGTTACTGATATTT
*
2742080 ATATTTATGATTTGAGTATGATTACTGATATTTTT
1 ATATTTATGATTTGAGTATGGTTACTGATATTTTT
2742115 TTATTTCCTG
Statistics
Matches: 119, Mismatches: 20, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
107 2 0.02
108 6 0.05
109 18 0.15
110 51 0.43
111 20 0.17
112 8 0.07
113 7 0.06
114 1 0.01
115 5 0.04
116 1 0.01
ACGTcount: A:0.23, C:0.06, G:0.19, T:0.52
Consensus pattern (107 bp):
ATATTTATGATTTGAGTATGGTTACTGATATTTTTGTCTGTATGGTTACTGATATTTATGATTTC
AGTATGGTTACTGATTTTGAAAGTGCATGGTTACTGATATTT
Found at i:2744379 original size:5 final size:5
Alignment explanation
Indices: 2744369--2744393 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2744359 TTCACTAATA
2744369 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
2744394 GTAGGGTGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:2744966 original size:21 final size:21
Alignment explanation
Indices: 2744940--2744985 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2744930 TCTCTCTCTG
*
2744940 CTTCTCTCTCTGCTTCTCTCA
1 CTTCTCTCTCTGCTTCACTCA
* *
2744961 CTTCTCTTTCTGCTTCACTCG
1 CTTCTCTCTCTGCTTCACTCA
2744982 CTTC
1 CTTC
2744986 AACTTTGACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.04, C:0.41, G:0.07, T:0.48
Consensus pattern (21 bp):
CTTCTCTCTCTGCTTCACTCA
Found at i:2744976 original size:12 final size:12
Alignment explanation
Indices: 2744926--2744959 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
2744916 TCTGATATGT
2744926 TGCTTCTCTCTC
1 TGCTTCTCTCTC
2744938 TGCTTCTCTCTC
1 TGCTTCTCTCTC
2744950 TGCTTCTCTC
1 TGCTTCTCTC
2744960 ACTTCTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.41, G:0.09, T:0.50
Consensus pattern (12 bp):
TGCTTCTCTCTC
Found at i:2763401 original size:42 final size:42
Alignment explanation
Indices: 2763297--2763402 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
2763287 CTGATTGTAG
*
2763297 CGTTTTCTACACAAACGCCACTAATGTAAGGTGAAACTGTGA
1 CGTTTTCTACACAAACGCCACTAATGTAAGGAGAAACTGTGA
* * * * * * *
2763339 CATTTTATGCACAAATGCCACTAATGTAAGGAGCAATTGTGC
1 CGTTTTCTACACAAACGCCACTAATGTAAGGAGAAACTGTGA
* *
2763381 CGTTTTCTATAAAAACGCCACT
1 CGTTTTCTACACAAACGCCACT
2763403 TTGGTACGAG
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (42 bp):
CGTTTTCTACACAAACGCCACTAATGTAAGGAGAAACTGTGA
Found at i:2772952 original size:21 final size:21
Alignment explanation
Indices: 2772926--2772967 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2772916 CAGGTAAAAA
* *
2772926 ATACCTACAACATTATTATTT
1 ATACCTAAAACATTAATATTT
2772947 ATACCTAAAACATTAATATTT
1 ATACCTAAAACATTAATATTT
2772968 TTTAACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (21 bp):
ATACCTAAAACATTAATATTT
Found at i:2774553 original size:2 final size:2
Alignment explanation
Indices: 2774548--2774573 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2774538 AAAAATTAAA
2774548 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
2774574 TAAGTACAAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2776463 original size:29 final size:29
Alignment explanation
Indices: 2776431--2776528 Score: 69
Period size: 29 Copynumber: 3.4 Consensus size: 29
2776421 TGTGGTTTAT
2776431 AAAAAGTTTTGTATTTTATTGTAAATTCC
1 AAAAAGTTTTGTATTTTATTGTAAATTCC
* ** * *
2776460 AAAAAAATTACG--CTTTATAGTAAATTCC
1 -AAAAAGTTTTGTATTTTATTGTAAATTCC
** *
2776488 AATTA-TTTT-TATCCTTTATTGTAAATTTC
1 AAAAAGTTTTGTAT--TTTATTGTAAATTCC
2776517 AAAAAGTTTTGT
1 AAAAAGTTTTGT
2776529 CTTTATTATA
Statistics
Matches: 48, Mismatches: 14, Indels: 11
0.66 0.19 0.15
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 14 0.29
29 16 0.33
30 12 0.25
31 1 0.02
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.46
Consensus pattern (29 bp):
AAAAAGTTTTGTATTTTATTGTAAATTCC
Found at i:2776826 original size:9 final size:9
Alignment explanation
Indices: 2776812--2776851 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
2776802 AAATGGAAAT
2776812 AAGAAATGA
1 AAGAAATGA
2776821 AAGAAA-GA
1 AAGAAATGA
2776829 AATGAAATGA
1 AA-GAAATGA
2776839 TAAGAAATGA
1 -AAGAAATGA
2776849 AAG
1 AAG
2776852 GGATAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 4 0.14
9 13 0.46
10 9 0.32
11 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.23, T:0.12
Consensus pattern (9 bp):
AAGAAATGA
Found at i:2776845 original size:15 final size:14
Alignment explanation
Indices: 2776810--2776851 Score: 68
Period size: 13 Copynumber: 3.0 Consensus size: 14
2776800 TTAAATGGAA
2776810 ATAAGAAATGAAAG
1 ATAAGAAATGAAAG
2776824 A-AAGAAATGAAATG
1 ATAAGAAATGAAA-G
2776838 ATAAGAAATGAAAG
1 ATAAGAAATGAAAG
2776852 GGATAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 11 0.42
14 4 0.15
15 11 0.42
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.14
Consensus pattern (14 bp):
ATAAGAAATGAAAG
Found at i:2778538 original size:32 final size:29
Alignment explanation
Indices: 2778478--2778550 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
2778468 CTTCTTGCAA
*
2778478 CTTCTTTTTTCTTTTTGCAGCACTTTCTT
1 CTTCTTCTTTCTTTTTGCAGCACTTTCTT
* *
2778507 CTTCTTCTTTCTTTTTGTAGCACATTCTT
1 CTTCTTCTTTCTTTTTGCAGCACTTTCTT
2778536 CTTCTTC-TTCTTTTT
1 CTTCTTCTTTCTTTTT
2778551 CAAAACTCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 8 0.20
29 33 0.80
ACGTcount: A:0.07, C:0.25, G:0.05, T:0.63
Consensus pattern (29 bp):
CTTCTTCTTTCTTTTTGCAGCACTTTCTT
Found at i:2779810 original size:26 final size:25
Alignment explanation
Indices: 2779780--2779836 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
2779770 AGTTTCAAAG
*
2779780 AAGAAGCTGCAAAAATAAAGAAGAAA
1 AAGAAACTGCAAAAA-AAAGAAGAAA
* *
2779806 AAGAAACTGCAAGAAGAAGAAG-AA
1 AAGAAACTGCAAAAAAAAGAAGAAA
2779830 AAGAAAC
1 AAGAAAC
2779837 GGCCACATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 9 0.32
25 6 0.21
26 13 0.46
ACGTcount: A:0.65, C:0.09, G:0.21, T:0.05
Consensus pattern (25 bp):
AAGAAACTGCAAAAAAAAGAAGAAA
Found at i:2781492 original size:15 final size:16
Alignment explanation
Indices: 2781467--2781502 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
2781457 TTTTTTGGTA
2781467 TTTTATAATTTCTATT
1 TTTTATAATTTCTATT
*
2781483 TTTTAT-ATTTTTATT
1 TTTTATAATTTCTATT
2781498 TTTTA
1 TTTTA
2781503 AAACATATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTATAATTTCTATT
Found at i:2781691 original size:2 final size:2
Alignment explanation
Indices: 2781686--2781761 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
2781676 AGTTACTAGT
2781686 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
2781728 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
2781762 GGGCAAGATT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2784545 original size:26 final size:26
Alignment explanation
Indices: 2784509--2784562 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
2784499 ATCGAGATAT
*
2784509 ATTTGCTCCACTGCTGTTTAGGGAAG
1 ATTTGCTCCACTGCTCTTTAGGGAAG
*
2784535 ATTTGCTCCACTTCTCTTTAGGGAAG
1 ATTTGCTCCACTGCTCTTTAGGGAAG
2784561 AT
1 AT
2784563 CAAATCTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (26 bp):
ATTTGCTCCACTGCTCTTTAGGGAAG
Found at i:2784765 original size:131 final size:130
Alignment explanation
Indices: 2784528--2784874 Score: 338
Period size: 131 Copynumber: 2.6 Consensus size: 130
2784518 ACTGCTGTTT
** **
2784528 AGGGAAGATTTGCTCCACTTCTCTTTAGGGAAGATCAAATCTCAAAAAGGGATATGTTTTGCTAC
1 AGGGAAGATTTGCTCCACTTCTCTTTAGGGAAGATCAAATCTCAAAAAGGGATATACTCCGCTAC
* * * *
2784593 TCTTCAGGGTAGATCAGATCTGGAATCGTTGATTCAATTCACTGCTCTTCAGGGAAGATTGAATC
66 TCTTCAGGGTAGATCAGATCTGGAATAGTTGATTCAATTCACTACGCTTCAGGAAAGATTGAATC
* * * * * *
2784658 AGGGAATATTTGCTCCACTTTTCTTTAGGGAAGATCAAATCTGGAAAAAGGGATCTACTCCGTTG
1 AGGGAAGATTTGCTCCACTTCTCTTTAGGGAAGATCAAATCT-CAAAAAGGGATATACTCCGCTA
* * * *
2784723 CTCTTCAGGGTAGATTAGATCTTGAA-AGTTTGATTCACTTCACTACGCTTCAGGAAAGATTTAA
65 CTCTTCAGGGTAGATCAGATCTGGAATAG-TTGATTCAATTCACTACGCTTCAGGAAAGATTGAA
2784787 TC
129 TC
** * * * * * ** * *
2784789 -GAGGTTGATTTGCTTCACTGCTCTTCAGAGAAGATTAAATCGGGAAAAATGAGATATGCTCCGC
1 AG-GGAAGATTTGCTCCACTTCTCTTTAGGGAAGATCAAATC-TCAAAAA-GGGATATACTCCGC
** * *
2784853 TGTTCTTCAAGGTATATCAGAT
63 TACTCTTCAGGGTAGATCAGAT
2784875 ATGTATATCA
Statistics
Matches: 176, Mismatches: 36, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
130 42 0.24
131 106 0.60
132 28 0.16
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (130 bp):
AGGGAAGATTTGCTCCACTTCTCTTTAGGGAAGATCAAATCTCAAAAAGGGATATACTCCGCTAC
TCTTCAGGGTAGATCAGATCTGGAATAGTTGATTCAATTCACTACGCTTCAGGAAAGATTGAATC
Found at i:2786177 original size:45 final size:45
Alignment explanation
Indices: 2785473--2786176 Score: 663
Period size: 45 Copynumber: 16.0 Consensus size: 45
2785463 AGATAACATT
* * * * * *
2785473 ACTAAAATATCGAATCCTCTTAACAAGAAAGTCAGGAATGACAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * * * *
2785518 ACTAAAAGGTTAGA-TTCTCTTCACGAGAAAGTTAAGAAGGAAAAC
1 ACTAAAAGATT-GACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * *
2785563 ACTAAAAGATCGACTCCTCTTTGA-GAGAAAGTCAAG---GAAAAC
1 ACTAAAAGATTGACTCCTC-TTCACGAGAAAGTCAAGAATGACAAC
* *
2785605 ACTAAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAA-GAATAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATG-ACAAC
* * *
2785650 ACCAAAAGGTTGACTCCTATTCACGAGAAAGTCAAGAA-GAACAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATG-ACAAC
* * *
2785695 ACTAAAAGATTTACTCCTCTTCATGAGAAAGTCAAGAATAACAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
*
2785740 ACTAAAAGATCGACT-C-C-T--CGAGAAAGTCAAG---GACAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * * *
2785777 ACTAAAAGATTGACTCCTCTTCGCGAGAAAGTTAAGAATAACATC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * * * * * *
2785822 ACTAAATGGTTAACTCCTCTTCACAAGAAAGTTAAGAAGGATAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * *
2785867 ACTAAAAGATTGACTTCTCTTCATGAGAAAGTCAAGAAGGACAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * * *
2785912 TCTGAAAGATTGACTCCTCTTCATGAGAAAGTCAAGAA-GAAAAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATG-ACAAC
* ** *
2785957 ACTAAAAGATCGACTCCTCTTTGCGAGAAAGTGAAG-A--ACAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * ** * * *
2785999 ACTAAAATATTGACTCATCTTCGTGAGAAAGTTAAGAATAACATC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * * * *
2786044 ACTAAAAGGTTGACTTCTTTTCACAAGAAAGTCAAGAATGAAAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * *
2786089 ACTAAAAGATCGACTCTTCTTCACGAGAAAGTCAAGAATGACATC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
* * *
2786134 ACTAAAAGGTTGACTCCTCTTGACGAGAAATTCAAGAATGACA
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACA
2786177 TGTAACACCC
Statistics
Matches: 540, Mismatches: 99, Indels: 40
0.80 0.15 0.06
Matches are distributed among these distances:
37 19 0.04
38 1 0.00
39 1 0.00
40 13 0.02
41 2 0.00
42 83 0.15
43 2 0.00
44 6 0.01
45 408 0.76
46 5 0.01
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.22
Consensus pattern (45 bp):
ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAAC
Found at i:2786780 original size:23 final size:23
Alignment explanation
Indices: 2786754--2786821 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
2786744 GTGCCATATA
2786754 TTTGTCCCTAAGGACCACATAGT
1 TTTGTCCCTAAGGACCACATAGT
* *
2786777 TTTGT-CCTGAATGACAACATAGT
1 TTTGTCCCT-AAGGACCACATAGT
* * *
2786800 TTTCTCTCGAAGGACCACATAG
1 TTTGTCCCTAAGGACCACATAG
2786822 AATCCTCGTC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
22 3 0.08
23 32 0.89
24 1 0.03
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (23 bp):
TTTGTCCCTAAGGACCACATAGT
Found at i:2794720 original size:20 final size:19
Alignment explanation
Indices: 2794691--2794729 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
2794681 GATAAAGGAA
2794691 AAAAAGAAAAATAAACAAAT
1 AAAAAGAAAAATAAA-AAAT
*
2794711 AAAAATAAAAATAAAAAAT
1 AAAAAGAAAAATAAAAAAT
2794730 GGTGTTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (19 bp):
AAAAAGAAAAATAAAAAAT
Found at i:2795377 original size:136 final size:134
Alignment explanation
Indices: 2795134--2795474 Score: 504
Period size: 136 Copynumber: 2.5 Consensus size: 134
2795124 TTGAACCAAT
* * *
2795134 TCTTCTCATTATGAACTTCTTCTCCCTTATCGGATAAGTTCTTCTCATTATGAACTCTCCACTGG
1 TCTTCTCATTATGAACTTCTTCTCCCTTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGG
** * * * *
2795199 AAATGTTGATCGCTCGAGTGAGGTGTTACTGATTTGAAATGTCGTGAATCGAGTGATAGGTCGAA
66 AAATGTCAATCCCTCAAGCGAGGTGTCACTGATTTGAAATGTCGTGAATCGAGTGATAGGTCGAA
2795264 CAAG
131 CAAG
* * *
2795268 CTCTTCTCATTATGAACTTCTTCTCTCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTTCATT
1 -TCTTCTCATTATGAACTTCTTCTCCCT-TGTCGGATGAGTTCTTCTCATTATGAACTCTCCATT
**
2795333 TTAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTTGAAATGTCGTGAATCGAGTGATAGGTCG
64 GGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTTGAAATGTCGTGAATCGAGTGATAGGTCG
2795398 AACAAG
129 AACAAG
* *
2795404 -CTTCTCATTATAAACTTCTTCTCCCTTTGTCGGATGAGTTATTCTCATTATGAACTCTCCATTG
1 TCTTCTCATTATGAACTTCTTCTCCC-TTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
2795468 GAAATGT
65 GAAATGT
2795475 TGATTGGTTT
Statistics
Matches: 183, Mismatches: 21, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
134 62 0.34
135 27 0.15
136 94 0.51
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (134 bp):
TCTTCTCATTATGAACTTCTTCTCCCTTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGG
AAATGTCAATCCCTCAAGCGAGGTGTCACTGATTTGAAATGTCGTGAATCGAGTGATAGGTCGAA
CAAG
Found at i:2797951 original size:29 final size:28
Alignment explanation
Indices: 2797909--2797998 Score: 112
Period size: 28 Copynumber: 3.2 Consensus size: 28
2797899 TATAAAGCTT
*
2797909 AGGTTGACTT-GGGAAGATAATGTGTTTC
1 AGGTTAACTTGGGGAAG-TAATGTGTTTC
* *
2797937 AAGTTAA-TCTGGGGAAGTAATGTGTTTT
1 AGGTTAACT-TGGGGAAGTAATGTGTTTC
*
2797965 AGGTTAACTTGGGGAGGTAATGTGTTTC
1 AGGTTAACTTGGGGAAGTAATGTGTTTC
2797993 AGGTTA
1 AGGTTA
2797999 GCTTCTCGCG
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
27 1 0.02
28 45 0.85
29 7 0.13
ACGTcount: A:0.26, C:0.06, G:0.32, T:0.37
Consensus pattern (28 bp):
AGGTTAACTTGGGGAAGTAATGTGTTTC
Found at i:2798670 original size:7 final size:7
Alignment explanation
Indices: 2798620--2798718 Score: 56
Period size: 7 Copynumber: 13.0 Consensus size: 7
2798610 ATTTGATCAA
2798620 TTTTTCT
1 TTTTTCT
2798627 TTCTTTCT
1 TT-TTTCT
*
2798635 TCTTTCT
1 TTTTTCT
*
2798642 TTCTTTTT
1 TT-TTTCT
2798650 ATTTTTCACAT
1 -TTTTT--C-T
2798661 TTTTTCTT
1 TTTTTC-T
2798669 TTTTTCT
1 TTTTTCT
2798676 CATTTTTCT
1 --TTTTTCT
*
2798685 GTTTTCT
1 TTTTTCT
*
2798692 ATTTT-T
1 TTTTTCT
* *
2798698 TTTCTAT
1 TTTTTCT
2798705 TTTTTCT
1 TTTTTCT
2798712 TTTTTCT
1 TTTTTCT
2798719 ATATCTTTTC
Statistics
Matches: 72, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
6 4 0.06
7 32 0.44
8 21 0.29
9 9 0.12
10 5 0.07
11 1 0.01
ACGTcount: A:0.06, C:0.16, G:0.01, T:0.77
Consensus pattern (7 bp):
TTTTTCT
Found at i:2798697 original size:27 final size:27
Alignment explanation
Indices: 2798667--2798729 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
2798657 ACATTTTTTC
2798667 TTTTTTTCTCA-TTTTTCTGTTTTCTAT
1 TTTTTTTCT-ATTTTTTCTGTTTTCTAT
*
2798694 TTTTTTTCTATTTTTTCTTTTTTCTAT
1 TTTTTTTCTATTTTTTCTGTTTTCTAT
* *
2798721 ATCTTTTCT
1 TTTTTTTCT
2798730 TCTTTCTCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 1 0.03
27 31 0.97
ACGTcount: A:0.08, C:0.14, G:0.02, T:0.76
Consensus pattern (27 bp):
TTTTTTTCTATTTTTTCTGTTTTCTAT
Found at i:2798714 original size:18 final size:18
Alignment explanation
Indices: 2798660--2798740 Score: 65
Period size: 18 Copynumber: 4.6 Consensus size: 18
2798650 ATTTTTCACA
*
2798660 TTTTTTCT-TTTTTTCTC
1 TTTTTTCTATTTTTTCTT
* * * *
2798677 ATTTTTCTGTTTTCTATT
1 TTTTTTCTATTTTTTCTT
2798695 TTTTTTCTATTTTTTCTT
1 TTTTTTCTATTTTTTCTT
* * *
2798713 TTTTCTATATCTTTTCTT
1 TTTTTTCTATTTTTTCTT
* *
2798731 CTTTCTCTAT
1 TTTTTTCTAT
2798741 ATGTCGTCAA
Statistics
Matches: 50, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
17 7 0.14
18 43 0.86
ACGTcount: A:0.07, C:0.16, G:0.01, T:0.75
Consensus pattern (18 bp):
TTTTTTCTATTTTTTCTT
Found at i:2798739 original size:20 final size:18
Alignment explanation
Indices: 2798695--2798742 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 18
2798685 GTTTTCTATT
2798695 TTTTTTCTAT-T-TTTTC
1 TTTTTTCTATATCTTTTC
2798711 TTTTTTCTATATCTTTTC
1 TTTTTTCTATATCTTTTC
2798729 TTCTTTCTCTATAT
1 TT-TTT-TCTATAT
2798743 GTCGTCAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.36
17 1 0.04
18 7 0.25
19 3 0.11
20 7 0.25
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTTCTATATCTTTTC
Found at i:2799186 original size:3 final size:3
Alignment explanation
Indices: 2799180--2799207 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2799170 TATTTTTTTA
2799180 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
2799208 ATTTGCTCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:2802432 original size:49 final size:50
Alignment explanation
Indices: 2802368--2802463 Score: 167
Period size: 49 Copynumber: 1.9 Consensus size: 50
2802358 CATAATATGT
*
2802368 GGTCACTTCTCGTGCTTCTAATAACTTATTGCTTAAATCT-CATATGCAG
1 GGTCACTTCTCGTGCTTCTAACAACTTATTGCTTAAATCTCCATATGCAG
*
2802417 GGTCACTTCTCGTGCTTCTAACAACTTATTGTTTAAATCTCCATATG
1 GGTCACTTCTCGTGCTTCTAACAACTTATTGCTTAAATCTCCATATG
2802464 AGATAGGAGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 38 0.86
50 6 0.14
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.40
Consensus pattern (50 bp):
GGTCACTTCTCGTGCTTCTAACAACTTATTGCTTAAATCTCCATATGCAG
Found at i:2807484 original size:22 final size:22
Alignment explanation
Indices: 2807459--2807576 Score: 98
Period size: 23 Copynumber: 5.3 Consensus size: 22
2807449 CACCACAACT
2807459 CACATAATTTG-CACCGAAGTG-C
1 CACATAATTTGTC-CCGAAG-GAC
2807481 CACAT-ATTTGTCCCGAAGGAC
1 CACATAATTTGTCCCGAAGGAC
* *
2807502 CACATAGGTTTGTCCCTAAGGAC
1 CACATA-ATTTGTCCCGAAGGAC
* *
2807525 CACATAGTTTTTTCCCGAAGGAC
1 CACATA-ATTTGTCCCGAAGGAC
* * * *
2807548 CACATAGTTTTTTCCTGAATGAC
1 CACATA-ATTTGTCCCGAAGGAC
2807571 CACATA
1 CACATA
2807577 GAACCCTCGA
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
20 1 0.01
21 17 0.20
22 6 0.07
23 61 0.72
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (22 bp):
CACATAATTTGTCCCGAAGGAC
Found at i:2807517 original size:23 final size:23
Alignment explanation
Indices: 2807472--2807577 Score: 128
Period size: 23 Copynumber: 4.7 Consensus size: 23
2807462 ATAATTTGCA
2807472 CCGAAGTG-CCACATA--TTTGTC
1 CCGAAG-GACCACATAGTTTTGTC
*
2807493 CCGAAGGACCACATAGGTTTGTC
1 CCGAAGGACCACATAGTTTTGTC
* *
2807516 CCTAAGGACCACATAGTTTTTTC
1 CCGAAGGACCACATAGTTTTGTC
*
2807539 CCGAAGGACCACATAGTTTTTTC
1 CCGAAGGACCACATAGTTTTGTC
* *
2807562 CTGAATGACCACATAG
1 CCGAAGGACCACATAG
2807578 AACCCTCGAC
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
20 1 0.01
21 13 0.17
23 62 0.82
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.27
Consensus pattern (23 bp):
CCGAAGGACCACATAGTTTTGTC
Found at i:2819343 original size:45 final size:45
Alignment explanation
Indices: 2819279--2819896 Score: 513
Period size: 45 Copynumber: 13.9 Consensus size: 45
2819269 ACACTTTAGT
* * * * *
2819279 CACTAAAAGGTTGACTCCTCTTCATGAGAATGTCATGAAGGAAAA
1 CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAA
* * * * **
2819324 CACTAAAAGGTTGACTCCTCTTCAAGAGAATGTTAAGAAATA-AA
1 CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAA
* * *
2819368 AACTAAAAGATTTACTCCTCTTCATGAGAAAGTC---AAGGACAA
1 CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAA
* ** *
2819410 CTCTAAAAGATTGACTCCTCTTTGCGAGAAAGTC---AAGGACGA
1 CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAA
* * * ** *
2819452 CACTAAAAGATTGACTCCACTT-GCGAGGAAGTCAAGAATAACAT
1 CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAA
* * * *
2819496 CACTAAAAGGTTAACTCCTCTTCACAAGAAAGTCAAGAATGACAA
1 CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAA
* * * *
2819541 CACTAAAAGATTGATTCCTCTTCATGAGAAAGTCAAGAATGACAT
1 CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAA
* * * * * ** *
2819586 CACTGAAAGGTTGACTCCTTTTGACGAGAAAGTTAAGAATAACAT
1 CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAA
* ** * **
2819631 CACTAAAAGATTTACTCCTCTTCGTGATAAAGTTGAG-AGAGACAA
1 CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAG-GACAA
* * * * *
2819676 CACTAAAAGATTGAAT-TTTTTCATGAGAAAGTCAAGAATGACAA
1 CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAA
* * *
2819720 GACAAAAAGATTGACTCCTCTTCGCGA-AAATGTCAAGAAGGACAA
1 CACTAAAAGATTGACTCCTCTTCACGAGAAA-GTCAAGAAGGACAA
* * * * ** *
2819765 CACTAAAAGATCGAATTCTCTTCATGAGAAAGTCAAGAATAACAT
1 CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAA
* * ** * *
2819810 CATTAAAAGATCGACTTATCTTCACGAGAAATTCAAGGATGGA-AA
1 CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAA-GAAGGACAA
*
2819855 CACTAAAAGATTTACTCCTCTTCACGAGAAAGTCAAGAAGGA
1 CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGA
2819897 TAAAAATGAA
Statistics
Matches: 458, Mismatches: 104, Indels: 23
0.78 0.18 0.04
Matches are distributed among these distances:
41 13 0.03
42 57 0.12
44 94 0.21
45 288 0.63
46 6 0.01
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (45 bp):
CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAA
Found at i:2819859 original size:179 final size:180
Alignment explanation
Indices: 2819278--2819893 Score: 460
Period size: 179 Copynumber: 3.5 Consensus size: 180
2819268 TACACTTTAG
* * * * * * * * * *
2819278 TCACTAAAAGGTTGACTCCTCTTCATGAGAATGTCATGA-AGGAAAACACTAAAAGGTTGACTCC
1 TCACTAAAAGATCGACTCATCTTCACGAGAAAGTTAAGAGA-GACAACACTAAAAGATTGAATCC
* * * * * * *
2819342 TCTTCAAGAGAATGTTAAGAAAT-A-AAAACTAAAAGATTTACTCCTCTTCATGAGAAAGTC---
65 TCTTCACGAGAAAGTCAAG-AATGACAACACAAAAAGATTGACTCCTCTTCACGAGAAAGTCAAG
* * * ** *
2819402 AAGGACAACTCTAAAAGATTGACTCCTCTTTGCGAGAAAGTCAAG---GACGA
129 AAGGACAACACTAAAAGATCGAATCCTCTTCACGAGAAAGTCAAGAATAAC-A
* * * * * * *
2819452 -CACTAAAAGATTGACTCCA-CTT-GCGAGGAAGTCAAGA-ATAACATCACTAAAAGGTT-AACT
1 TCACTAAAAGATCGACT-CATCTTCACGAGAAAGTTAAGAGA-GACAACACTAAAAGATTGAA-T
* * * *
2819512 CCTCTTCACAAGAAAGTCAAGAATGACAACACTAAAAGATTGATTCCTCTTCATGAGAAAGTCAA
63 CCTCTTCACGAGAAAGTCAAGAATGACAACACAAAAAGATTGACTCCTCTTCACGAGAAAGTCAA
* * * * * * * * *
2819577 GAATGACATCACTGAAAGGTTGACTCCTTTTGACGAGAAAGTTAAGAATAACA
128 GAAGGACAACACTAAAAGATCGAATCCTCTTCACGAGAAAGTCAAGAATAACA
** * ** * * *
2819630 TCACTAAAAGATTTACTCCTCTTCGTGATAAAGTTGAGAGAGACAACACTAAAAGATTGAAT-TT
1 TCACTAAAAGATCGACTCATCTTCACGAGAAAGTTAAGAGAGACAACACTAAAAGATTGAATCCT
* * * *
2819694 TTTCATGAGAAAGTCAAGAATGACAAGACAAAAAGATTGACTCCTCTTCGCGA-AAATGTCAAGA
66 CTTCACGAGAAAGTCAAGAATGACAACACAAAAAGATTGACTCCTCTTCACGAGAAA-GTCAAGA
* *
2819758 AGGACAACACTAAAAGATCGAATTCTCTTCATGAGAAAGTCAAGAATAACA
130 AGGACAACACTAAAAGATCGAATCCTCTTCACGAGAAAGTCAAGAATAACA
* * * *
2819809 TCATTAAAAGATCGACTTATCTTCACGAGAAA-TTCAAG-GATGGA-AACACTAAAAGATTTACT
1 TCACTAAAAGATCGACTCATCTTCACGAGAAAGTT-AAGAGA--GACAACACTAAAAGATTGAAT
2819871 CCTCTTCACGAGAAAGTCAAGAA
63 CCTCTTCACGAGAAAGTCAAGAA
2819894 GGATAAAAAT
Statistics
Matches: 349, Mismatches: 73, Indels: 34
0.77 0.16 0.07
Matches are distributed among these distances:
171 4 0.01
172 44 0.13
173 51 0.15
174 1 0.00
176 36 0.10
178 9 0.03
179 155 0.44
180 46 0.13
181 3 0.01
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (180 bp):
TCACTAAAAGATCGACTCATCTTCACGAGAAAGTTAAGAGAGACAACACTAAAAGATTGAATCCT
CTTCACGAGAAAGTCAAGAATGACAACACAAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAA
GGACAACACTAAAAGATCGAATCCTCTTCACGAGAAAGTCAAGAATAACA
Found at i:2820100 original size:15 final size:16
Alignment explanation
Indices: 2820072--2820105 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2820062 AAAATTTATC
*
2820072 ATGTATGTATGAAATG
1 ATGTATGTATGAAAAG
2820088 ATGTATG-ATGAAAAG
1 ATGTATGTATGAAAAG
2820103 ATG
1 ATG
2820106 CAACTTCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.32
Consensus pattern (16 bp):
ATGTATGTATGAAAAG
Found at i:2821386 original size:6 final size:6
Alignment explanation
Indices: 2821375--2821452 Score: 74
Period size: 6 Copynumber: 13.3 Consensus size: 6
2821365 ATTTGATATG
* *
2821375 TTCTTT TTCTTT TTCTTCTT TTCCTT TTC-TT CT-TTT TTC-TT TTCTTT
1 TTCTTT TTCTTT TTC-T-TT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
* *
2821422 TTATTT TT-TCT TTCTTT TTCTTT TTCTTT TT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TT
2821453 TATCTTTTCA
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
5 15 0.25
6 39 0.65
7 1 0.02
8 5 0.08
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (6 bp):
TTCTTT
Found at i:2821402 original size:14 final size:15
Alignment explanation
Indices: 2821375--2821470 Score: 80
Period size: 14 Copynumber: 6.6 Consensus size: 15
2821365 ATTTGATATG
*
2821375 TTCTTTTTCTTTTTC
1 TTCTTTTTCCTTTTC
2821390 TTC-TTTTCCTTTTC
1 TTCTTTTTCCTTTTC
*
2821404 TTCTTTTTTCTTTTC
1 TTCTTTTTCCTTTTC
2821419 TT-TTTATT--TTTTC
1 TTCTTT-TTCCTTTTC
*
2821432 TTTCTTTTTCTTTTTC
1 -TTCTTTTTCCTTTTC
2821448 TT-TTTTAT-CTTTTC
1 TTCTTTT-TCCTTTTC
2821462 ATT-TTTTTC
1 -TTCTTTTTC
2821471 TTGAATATGA
Statistics
Matches: 69, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
13 5 0.07
14 30 0.43
15 29 0.42
16 5 0.07
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (15 bp):
TTCTTTTTCCTTTTC
Found at i:2821417 original size:29 final size:27
Alignment explanation
Indices: 2821378--2821472 Score: 102
Period size: 29 Copynumber: 3.3 Consensus size: 27
2821368 TGATATGTTC
2821378 TTTTTCTTTTTCTTCTTTTCCTTTTCTTCT
1 TTTTTCTTTTTCTT-TTTT-CTTTTCTT-T
*
2821408 TTTTTC-TTTTCTTTTTATTTTTTCTTT
1 TTTTTCTTTTTCTTTTT-TCTTTTCTTT
*
2821435 CTTTTTCTTTTTCTTTTTTATCTTTTCATT
1 -TTTTTCTTTTTC-TTTTT-TCTTTTCTTT
2821465 TTTTTCTT
1 TTTTTCTT
2821473 GAATATGAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
27 1 0.02
28 16 0.28
29 21 0.36
30 20 0.34
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (27 bp):
TTTTTCTTTTTCTTTTTTCTTTTCTTT
Found at i:2821460 original size:9 final size:8
Alignment explanation
Indices: 2821384--2821460 Score: 59
Period size: 9 Copynumber: 9.2 Consensus size: 8
2821374 GTTCTTTTTC
2821384 TTTTTCTT
1 TTTTTCTT
*
2821392 CTTTTCCTT
1 -TTTTTCTT
*
2821401 TTCTTC-T
1 TTTTTCTT
2821408 TTTTTCTT
1 TTTTTCTT
*
2821416 TTCTTTTTAT
1 TT-TTTCT-T
2821426 TTTTTCTT
1 TTTTTCTT
*
2821434 TCTTTT-TC
1 T-TTTTCTT
2821442 TTTTTCTT
1 TTTTTCTT
2821450 TTTTATCTT
1 TTTT-TCTT
2821459 TT
1 TT
2821461 CATTTTTTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
7 10 0.19
8 16 0.30
9 25 0.46
10 3 0.06
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTCTT
Found at i:2821467 original size:16 final size:15
Alignment explanation
Indices: 2821385--2821469 Score: 65
Period size: 15 Copynumber: 5.8 Consensus size: 15
2821375 TTCTTTTTCT
* *
2821385 TTTTCTTCTTTT-CC
1 TTTTCTTTTTTTATC
2821399 TTTTCTTCTTTTT-TC
1 TTTTCTT-TTTTTATC
*
2821414 TTTTC--TTTTTATT
1 TTTTCTTTTTTTATC
2821427 TTTTCTTTCTTTT-TC
1 TTTTCTTT-TTTTATC
2821442 TTTT-TCTTTTTTATC
1 TTTTCT-TTTTTTATC
2821457 TTTTCATTTTTTT
1 TTTTC-TTTTTTT
2821470 CTTGAATATG
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
12 5 0.09
13 6 0.10
14 12 0.21
15 24 0.41
16 10 0.17
17 1 0.02
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTCTTTTTTTATC
Found at i:2826333 original size:15 final size:15
Alignment explanation
Indices: 2826313--2826342 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2826303 TGTTTCTTTT
2826313 TCATTATCTAATCCA
1 TCATTATCTAATCCA
2826328 TCATTATCTAATCCA
1 TCATTATCTAATCCA
2826343 AATACGTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (15 bp):
TCATTATCTAATCCA
Found at i:2826994 original size:20 final size:20
Alignment explanation
Indices: 2826969--2827016 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
2826959 TGTAGTTTTC
*
2826969 AAAACAACATAATTAAATCA
1 AAAACAAAATAATTAAATCA
**
2826989 AAAACAAAAATTTTTAAATCA
1 AAAAC-AAAATAATTAAATCA
2827010 AAAACAA
1 AAAACAA
2827017 TTTTTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAACAAAATAATTAAATCA
Found at i:2827018 original size:18 final size:19
Alignment explanation
Indices: 2826981--2827021 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
2826971 AACAACATAA
2826981 TTAAATCAAAAACAAAAATTT
1 TTAAATCAAAAAC--AAATTT
2827002 TTAAATCAAAAAC-AATTT
1 TTAAATCAAAAACAAATTT
2827020 TT
1 TT
2827022 TTATTATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
21 13 0.65
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (19 bp):
TTAAATCAAAAACAAATTT
Found at i:2833246 original size:73 final size:73
Alignment explanation
Indices: 2833163--2833298 Score: 172
Period size: 73 Copynumber: 1.9 Consensus size: 73
2833153 GTTAAATGAC
* *
2833163 TAGGGGTATCGATACCTCCA-G-GGGGTATC-GATACCC-ATAGGGCATTCTATTTTTCTCGAAG
1 TAGGGGTATCGATACC-CCATGAGGGGTATCAG-TACCCTATA-GGCAATCT-GTTTTCTCGAAG
2833224 CCAAATATTGCA
62 CCAAATATTGCA
* *
2833236 TAGGGGTATCGGTACCCTATGAGGGGTATCAGTACCCTATAGGCAATCTGTTTTCTCGAAGCC
1 TAGGGGTATCGATACCCCATGAGGGGTATCAGTACCCTATAGGCAATCTGTTTTCTCGAAGCC
2833299 CTTCCTATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
72 2 0.04
73 29 0.53
74 20 0.36
75 4 0.07
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (73 bp):
TAGGGGTATCGATACCCCATGAGGGGTATCAGTACCCTATAGGCAATCTGTTTTCTCGAAGCCAA
ATATTGCA
Found at i:2833262 original size:20 final size:20
Alignment explanation
Indices: 2833237--2833275 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2833227 AATATTGCAT
*
2833237 AGGGGTATCGGTACCCTATG
1 AGGGGTATCAGTACCCTATG
2833257 AGGGGTATCAGTACCCTAT
1 AGGGGTATCAGTACCCTAT
2833276 AGGCAATCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.26
Consensus pattern (20 bp):
AGGGGTATCAGTACCCTATG
Found at i:2834029 original size:18 final size:19
Alignment explanation
Indices: 2834006--2834046 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
2833996 TTGGGAACCC
**
2834006 AAAAATATTTTTTTTAA-T
1 AAAAATATTAATTTTAATT
2834024 AAAAATATTAATTTTAATT
1 AAAAATATTAATTTTAATT
2834043 AAAA
1 AAAA
2834047 CATAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAAAATATTAATTTTAATT
Found at i:2834038 original size:19 final size:19
Alignment explanation
Indices: 2834006--2834056 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
2833996 TTGGGAACCC
*
2834006 AAAAATATT-TTTTTTAAT
1 AAAAATATTAATTTTTAAT
2834024 AAAAATATTAA-TTTTAAT
1 AAAAATATTAATTTTTAAT
* * *
2834042 TAAAACATAAATTTT
1 AAAAATATTAATTTT
2834057 ATGATATGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 24 0.89
19 3 0.11
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAAATATTAATTTTTAAT
Found at i:2834054 original size:18 final size:18
Alignment explanation
Indices: 2834017--2834057 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2834007 AAAATATTTT
* *
2834017 TTTTAATAAAAATATTAA
1 TTTTAATAAAAACATAAA
*
2834035 TTTTAATTAAAACATAAA
1 TTTTAATAAAAACATAAA
2834053 TTTTA
1 TTTTA
2834058 TGATATGTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTTAATAAAAACATAAA
Found at i:2834845 original size:13 final size:13
Alignment explanation
Indices: 2834822--2834851 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2834812 CTATGACACA
2834822 CATTTATGACGCG
1 CATTTATGACGCG
*
2834835 CATTTATGACGCT
1 CATTTATGACGCG
2834848 CATT
1 CATT
2834852 GCGCGTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (13 bp):
CATTTATGACGCG
Found at i:2839910 original size:14 final size:14
Alignment explanation
Indices: 2839891--2839922 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2839881 TGACATGGAA
2839891 ATATATATCTATAT
1 ATATATATCTATAT
2839905 ATATATATCTATAT
1 ATATATATCTATAT
2839919 ATAT
1 ATAT
2839923 GTACATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATATATCTATAT
Found at i:2840098 original size:37 final size:36
Alignment explanation
Indices: 2840057--2840265 Score: 210
Period size: 39 Copynumber: 5.7 Consensus size: 36
2840047 ACATATATAG
* *
2840057 TATATAACATATAGTTTTTTATAAAATTTTTAAAACATA
1 TATATAATATATAGTTTTTGA-AAAA-TTTTAAAA-ATA
* *
2840096 TATATAATATATAGTTTTTGAGAACATTTTAAAAACA
1 TATATAATATATAGTTTTTGA-AAAATTTTAAAAATA
* * * * *
2840133 TATAT-ATATATA--ATAT-ATAAGTTTTGAAAATA
1 TATATAATATATAGTTTTTGAAAAATTTTAAAAATA
2840165 TATATAATATATAGTTTTTGAAAACATTTTGAAAAAATA
1 TATATAATATATAGTTTTTGAAAA-ATTTT--AAAAATA
*
2840204 TATATAATATATAGTTTTTGAAAATATTTTGAAAATA
1 TATATAATATATAGTTTTTGAAAA-ATTTTAAAAATA
* *
2840241 TATATATTATATAGTTTTTTAAAAA
1 TATATAATATATAGTTTTTGAAAAA
2840266 ATATATATAT
Statistics
Matches: 142, Mismatches: 21, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
32 15 0.11
33 8 0.06
34 2 0.01
35 2 0.01
36 11 0.08
37 39 0.27
38 8 0.06
39 57 0.40
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.44
Consensus pattern (36 bp):
TATATAATATATAGTTTTTGAAAAATTTTAAAAATA
Found at i:2840171 original size:69 final size:65
Alignment explanation
Indices: 2840083--2840230 Score: 208
Period size: 69 Copynumber: 2.2 Consensus size: 65
2840073 TTTTATAAAA
* *
2840083 TTTTTAAAACATATATATAATATATAGTTTTTGAGAACATTTTAAAAACATATATATATATAATA
1 TTTTTGAAA-ATATATATAATATATAGTTTTTGAAAACATTTT-AAAA-A-A-ATATATATAATA
2840148 TATAAG
61 TAT-AG
*
2840154 -TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAAAATATATATAATATATAG
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTAAAAAAATATATATAATATATAG
2840218 TTTTTGAAAATAT
1 TTTTTGAAAATAT
2840231 TTTGAAAATA
Statistics
Matches: 73, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
64 2 0.03
65 27 0.37
66 1 0.01
67 1 0.01
68 3 0.04
69 32 0.44
70 7 0.10
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (65 bp):
TTTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTAAAAAAATATATATAATATATAG
Found at i:2840172 original size:26 final size:26
Alignment explanation
Indices: 2840136--2840188 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
2840126 AAAAACATAT
2840136 ATATATATAATATATAAG-TTTTGAAA
1 ATATATATAATATAT-AGTTTTTGAAA
2840162 ATATATATAATATATAGTTTTTGAAA
1 ATATATATAATATATAGTTTTTGAAA
2840188 A
1 A
2840189 CATTTTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (26 bp):
ATATATATAATATATAGTTTTTGAAA
Found at i:2840179 original size:108 final size:109
Alignment explanation
Indices: 2840057--2840253 Score: 299
Period size: 108 Copynumber: 1.8 Consensus size: 109
2840047 ACATATATAG
* * * *
2840057 TATATAACATATAGTTTTTTATAAA-ATTTTTAAAACATATATATAATATATAGTTTTTGAGAAC
1 TATATAACATATAGTTTTTGA-AAACATTTTGAAAAAATATATATAATATATAGTTTTTGAAAAC
2840121 ATTTTAAAAACATATATA-TATATAATATATAAGTTTTGAAAATA
65 ATTTTAAAAACATATATATTATATAATATATAAGTTTTGAAAATA
* *
2840165 TATATAATATATAGTTTTTGAAAACATTTTGAAAAAATATATATAATATATAGTTTTTGAAAATA
1 TATATAACATATAGTTTTTGAAAACATTTTGAAAAAATATATATAATATATAGTTTTTGAAAACA
* *
2840230 TTTTGAAAATATATATATTATATA
66 TTTTAAAAACATATATATTATATA
2840254 GTTTTTTAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
107 3 0.04
108 70 0.89
109 6 0.08
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (109 bp):
TATATAACATATAGTTTTTGAAAACATTTTGAAAAAATATATATAATATATAGTTTTTGAAAACA
TTTTAAAAACATATATATTATATAATATATAAGTTTTGAAAATA
Found at i:2840222 original size:28 final size:28
Alignment explanation
Indices: 2840191--2840283 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 28
2840181 TTTGAAAACA
*
2840191 TTTTGAAAAAATATATATAATATATAGT
1 TTTTGAAAAAATATATATATTATATAGT
2840219 TTTTGAAAATATTTTGAAAATATATATATTATATAGT
1 TTTTG--AA-A-----A-AATATATATATTATATAGT
*
2840256 TTTTTAAAAAATATATATATTATATAGT
1 TTTTGAAAAAATATATATATTATATAGT
2840284 ATAATATATT
Statistics
Matches: 54, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
28 24 0.44
29 1 0.02
30 2 0.04
31 1 0.02
34 1 0.02
35 2 0.04
36 1 0.02
37 22 0.41
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.47
Consensus pattern (28 bp):
TTTTGAAAAAATATATATATTATATAGT
Found at i:2851266 original size:40 final size:40
Alignment explanation
Indices: 2851188--2851267 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
2851178 AATATTTCGC
* * * * *
2851188 TTAGGGTGAAAAGCTGAAAGGGCGCCCTAAGTTGAAAAAA
1 TTAGGGTGAAAACCCGAAAGGGCACCCTAAATTAAAAAAA
**
2851228 TTAGGGTGAAAACCCGAAAGGGCACTTTAAATTAAAAAAA
1 TTAGGGTGAAAACCCGAAAGGGCACCCTAAATTAAAAAAA
2851268 AAAAAGTGGG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (40 bp):
TTAGGGTGAAAACCCGAAAGGGCACCCTAAATTAAAAAAA
Found at i:2852869 original size:37 final size:37
Alignment explanation
Indices: 2852791--2853061 Score: 230
Period size: 37 Copynumber: 7.2 Consensus size: 37
2852781 ACATATATAG
* *
2852791 TATATAATATATAGTTTTTTATAAAT-TTTGAAAACATA
1 TATATAATATATAGTTTTTGA-AAATATTTTAAAA-ATA
*
2852829 TATATAATATATAGTTTTTGAAAACATTTTAAAAACATA
1 TATATAATATATAGTTTTTGAAAATATTTT-AAAA-ATA
2852868 TATATAATATATAGTTTTTGAAAATA-TTTAGAAAATA
1 TATATAATATATAGTTTTTGAAAATATTTTA-AAAATA
* *
2852905 TATATATATAAAATATAGTTTTTGAAAATA-TAT-ATAATA
1 TATATA-AT---ATATAGTTTTTGAAAATATTTTAAAAATA
* * * ** * * * *
2852944 TATA-ATTTTTGAAAACATTTTGAATATA-TATATATATA
1 TATATA-ATAT--ATAGTTTTTGAAAATATTTTAAAAATA
*
2852982 TATATAATATATAGTTTTTGAAAATATTCTAAAAATA
1 TATATAATATATAGTTTTTGAAAATATTTTAAAAATA
* * *
2853019 TACATAATATATAGTTTTTGAAAATATTTTGAATATA
1 TATATAATATATAGTTTTTGAAAATATTTTAAAAATA
2853056 TATATA
1 TATATA
2853062 GTTTTTTAAA
Statistics
Matches: 192, Mismatches: 29, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
35 1 0.01
36 12 0.06
37 73 0.38
38 43 0.22
39 43 0.22
41 20 0.10
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (37 bp):
TATATAATATATAGTTTTTGAAAATATTTTAAAAATA
Found at i:2852869 original size:39 final size:38
Alignment explanation
Indices: 2852791--2852932 Score: 194
Period size: 39 Copynumber: 3.6 Consensus size: 38
2852781 ACATATATAG
* * *
2852791 TATATAATATATAGTTTTTTATAAATTTTGAAAACATA
1 TATATAATATATAGTTTTTGAAAAATTTTAAAAACATA
2852829 TATATAATATATAGTTTTTGAAAACATTTTAAAAACATA
1 TATATAATATATAGTTTTTGAAAA-ATTTTAAAAACATA
* *
2852868 TATATAATATATAGTTTTTGAAAATATTTAGAAAATATATA
1 TATATAATATATAGTTTTTGAAAA-ATTT-TAAAA-ACATA
*
2852909 TATATAAAATATAGTTTTTGAAAA
1 TATATAATATATAGTTTTTGAAAA
2852933 TATATATAAT
Statistics
Matches: 94, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
38 22 0.23
39 41 0.44
40 4 0.04
41 27 0.29
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (38 bp):
TATATAATATATAGTTTTTGAAAAATTTTAAAAACATA
Found at i:2852906 original size:67 final size:67
Alignment explanation
Indices: 2852810--2852981 Score: 186
Period size: 67 Copynumber: 2.6 Consensus size: 67
2852800 TATAGTTTTT
* * * * * * *
2852810 TATAAATTTTGAAAACATATATATAATATATAGTTTTTGAAA-ACA-TTTTAAAAACATATATAT
1 TATAATTTTTGAAAACATTTAGAAAATATATA-TATATAAAATACAGTTTTAAAAA-ATATATAT
2852873 AATA
64 AATA
* * * **
2852877 TATAGTTTTTGAAAATATTTAGAAAATATATATATATAAAATATAGTTTTTGAAAATATATATAA
1 TATAATTTTTGAAAACATTTAGAAAATATATATATATAAAATACAGTTTTAAAAAATATATATAA
2852942 TA
66 TA
* *
2852944 TATAATTTTTGAAAACATTTTGAATATATATATATATA
1 TATAATTTTTGAAAACATTTAGAAAATATATATATATA
2852982 TATATAATAT
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
66 6 0.07
67 74 0.85
68 7 0.08
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (67 bp):
TATAATTTTTGAAAACATTTAGAAAATATATATATATAAAATACAGTTTTAAAAAATATATATAA
TA
Found at i:2852909 original size:15 final size:15
Alignment explanation
Indices: 2852891--2852939 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
2852881 GTTTTTGAAA
2852891 ATATTTAGAAAATAT
1 ATATTTAGAAAATAT
* *
2852906 ATATATATAAAATAT
1 ATATTTAGAAAATAT
*
2852921 AGT-TTTTGAAAATAT
1 A-TATTTAGAAAATAT
2852936 ATAT
1 ATAT
2852940 AATATATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
14 1 0.04
15 25 0.93
16 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (15 bp):
ATATTTAGAAAATAT
Found at i:2852935 original size:26 final size:26
Alignment explanation
Indices: 2852906--2853008 Score: 90
Period size: 26 Copynumber: 4.2 Consensus size: 26
2852896 TAGAAAATAT
2852906 ATATATATAAAATATAGTTTTTGAAA
1 ATATATATAAAATATAGTTTTTGAAA
* *
2852932 ATATATATAATATATAATTTTTGAAA
1 ATATATATAAAATATAGTTTTTGAAA
* ** * * *
2852958 ACAT-T-TTGAATATA-TATAT--AT
1 ATATATATAAAATATAGTTTTTGAAA
*
2852979 ATATATATAATATATAGTTTTTGAAA
1 ATATATATAAAATATAGTTTTTGAAA
2853005 ATAT
1 ATAT
2853009 TCTAAAAATA
Statistics
Matches: 56, Mismatches: 16, Indels: 10
0.68 0.20 0.12
Matches are distributed among these distances:
21 4 0.07
22 1 0.02
23 9 0.16
24 9 0.16
25 1 0.02
26 32 0.57
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.46
Consensus pattern (26 bp):
ATATATATAAAATATAGTTTTTGAAA
Found at i:2852989 original size:47 final size:46
Alignment explanation
Indices: 2852931--2853031 Score: 139
Period size: 47 Copynumber: 2.2 Consensus size: 46
2852921 AGTTTTTGAA
* * * *
2852931 AATATATATAATATATAATTTTTGAAAACATTTTGAATATATATAT
1 AATATATATAATATATAATTTTTGAAAACATTCTAAAAATATACAT
* *
2852977 ATATATATATAATATATAGTTTTTGAAAATATTCTAAAAATATACAT
1 A-ATATATATAATATATAATTTTTGAAAACATTCTAAAAATATACAT
2853024 AATATATA
1 AATATATA
2853032 GTTTTTGAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
46 8 0.17
47 40 0.83
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (46 bp):
AATATATATAATATATAATTTTTGAAAACATTCTAAAAATATACAT
Found at i:2853080 original size:26 final size:26
Alignment explanation
Indices: 2853011--2853087 Score: 73
Period size: 30 Copynumber: 2.7 Consensus size: 26
2853001 GAAAATATTC
* *
2853011 TAAAAATATACATAATATATAGTTTTT
1 TAAAAATTTATAT-ATATATAGTTTTT
*
2853038 GAAAATATTTTGAATATATATATAGTTTTT
1 TAAAA-A-TTT--ATATATATATAGTTTTT
2853068 TAAAAATTTATATATTATAT
1 TAAAAATTTATATA-TATAT
2853088 GGTATTATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
26 5 0.12
27 9 0.22
28 4 0.10
29 3 0.07
30 17 0.41
31 3 0.07
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.48
Consensus pattern (26 bp):
TAAAAATTTATATATATATAGTTTTT
Found at i:2853087 original size:7 final size:7
Alignment explanation
Indices: 2853075--2853137 Score: 81
Period size: 7 Copynumber: 8.6 Consensus size: 7
2853065 TTTTAAAAAT
2853075 TTATATA
1 TTATATA
2853082 TTATATGGTA
1 TTATA---TA
2853092 TTATATA
1 TTATATA
2853099 TTATATA
1 TTATATA
2853106 TTATATA
1 TTATATA
*
2853113 TTATTTA
1 TTATATA
*
2853120 TTATTTA
1 TTATATA
2853127 TTATATA
1 TTATATA
2853134 TTAT
1 TTAT
2853138 TTTCATTTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
7 44 0.86
10 7 0.14
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (7 bp):
TTATATA
Found at i:2853173 original size:6 final size:6
Alignment explanation
Indices: 2853136--2853164 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2853126 ATTATATATT
2853136 ATTTTC ATTTTC ATTTTC ATTTTC ATTTT
1 ATTTTC ATTTTC ATTTTC ATTTTC ATTTT
2853165 TTTCTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (6 bp):
ATTTTC
Found at i:2853173 original size:15 final size:15
Alignment explanation
Indices: 2853137--2853194 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
2853127 TTATATATTA
2853137 TTTTCATTTTCA---
1 TTTTCATTTTCATTT
2853149 TTTTCATTTTCATTT
1 TTTTCATTTTCATTT
* *
2853164 TTTTCTTTTTTATTT
1 TTTTCATTTTCATTT
* *
2853179 ATTT-ATTTTCGTTT
1 TTTTCATTTTCATTT
2853193 TT
1 TT
2853195 CTTTCGTTGG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
12 12 0.33
14 8 0.22
15 16 0.44
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTTCATTTTCATTT
Found at i:2853173 original size:21 final size:20
Alignment explanation
Indices: 2853142--2853195 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
2853132 TATTATTTTC
*
2853142 ATTTTCATTTTCATTTTCATTT
1 ATTTTCTTTTTCA-TTT-ATTT
*
2853164 -TTTTCTTTTTTATTTATTT
1 ATTTTCTTTTTCATTTATTT
2853183 ATTTTCGTTTTTC
1 ATTTTC-TTTTTC
2853196 TTTCGTTGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 4 0.15
20 8 0.30
21 15 0.56
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.74
Consensus pattern (20 bp):
ATTTTCTTTTTCATTTATTT
Found at i:2854445 original size:7 final size:7
Alignment explanation
Indices: 2854433--2854485 Score: 63
Period size: 7 Copynumber: 7.6 Consensus size: 7
2854423 TGTTTTATTC
2854433 TTTTTTA
1 TTTTTTA
2854440 TTTTTTA
1 TTTTTTA
*
2854447 TTATTTA
1 TTTTTTA
*
2854454 TTTTATA
1 TTTTTTA
*
2854461 -TATTTA
1 TTTTTTA
2854467 TTTATTTA
1 TTT-TTTA
2854475 TTTTTTA
1 TTTTTTA
2854482 TTTT
1 TTTT
2854486 AAATTTAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
6 4 0.11
7 27 0.71
8 7 0.18
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTTA
Found at i:2854456 original size:4 final size:4
Alignment explanation
Indices: 2854436--2854484 Score: 59
Period size: 4 Copynumber: 12.8 Consensus size: 4
2854426 TTTATTCTTT
*
2854436 TTTA TTT- TTTA -TTA TTTA TTTTA TATA TTTA TTTA TTTA TTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA
2854482 TTT
1 TTT
2854485 TAAATTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 9 0.23
4 26 0.67
5 4 0.10
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:2858098 original size:43 final size:43
Alignment explanation
Indices: 2858014--2858098 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
2858004 AACGCCGTAA
* * *
2858014 TAGGTAAAGAGATATAGCGACGTTTTTGGAATAAATATCGCAG
1 TAGGTAAAGAGATATAGCAACGTTTTGGGAATAAACATCGCAG
* *
2858057 TAGGTGAAGAGATATAGCAACGTTTGTGGGAA-AAACGTCGCA
1 TAGGTAAAGAGATATAGCAACGTTT-TGGGAATAAACATCGCA
2858099 AAAGGTCGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
43 31 0.86
44 5 0.14
ACGTcount: A:0.36, C:0.11, G:0.28, T:0.25
Consensus pattern (43 bp):
TAGGTAAAGAGATATAGCAACGTTTTGGGAATAAACATCGCAG
Found at i:2864005 original size:22 final size:22
Alignment explanation
Indices: 2863977--2864025 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
2863967 CACGTTTTCA
*
2863977 AAAGCTATTATTTTCCTATTCG
1 AAAGCTATTATTTTACTATTCG
2863999 AAAGCTATTATTTTACTATTCG
1 AAAGCTATTATTTTACTATTCG
2864021 AAAGC
1 AAAGC
2864026 AGTAAAACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (22 bp):
AAAGCTATTATTTTACTATTCG
Found at i:2864567 original size:41 final size:39
Alignment explanation
Indices: 2864483--2864573 Score: 103
Period size: 41 Copynumber: 2.3 Consensus size: 39
2864473 TTTGTTAAAG
* **
2864483 AAACGCCGCTAAAGTTTCATTTTGTGGCGTTTAGATTGT
1 AAACGCCGCTAAAGTTTAATTTTGTGGCGTTTAGATTCC
* *
2864522 AAACGCCGCTATATGTTTAAATTTTGTGGCGTTTA-CTCTCC
1 AAACGCCGCTA-AAGTTT-AATTTTGTGGCGTTTAGAT-TCC
2864563 AAACGCCGCTA
1 AAACGCCGCTA
2864574 CAGAACAGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
39 11 0.25
40 6 0.14
41 27 0.61
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (39 bp):
AAACGCCGCTAAAGTTTAATTTTGTGGCGTTTAGATTCC
Found at i:2867512 original size:18 final size:19
Alignment explanation
Indices: 2867476--2867519 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
2867466 ATAAAATATT
2867476 AATAAAAATATATACACATA
1 AATAAAAATATATA-ACATA
2867496 AATAAAAATATAT-ACATA
1 AATAAAAATATATAACATA
2867514 ATATAA
1 A-ATAA
2867520 GTATAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.26
19 4 0.17
20 13 0.57
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (19 bp):
AATAAAAATATATAACATA
Found at i:2869351 original size:30 final size:30
Alignment explanation
Indices: 2869315--2869389 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
2869305 AAAGTTTTGG
2869315 TTTTTGCTATTTTGGACCTTTAAATTTATA
1 TTTTTGCTATTTTGGACCTTTAAATTTATA
* * * *
2869345 TTTTTGCTATTTTAGTCCTTTAAGTTTCTA
1 TTTTTGCTATTTTGGACCTTTAAATTTATA
*
2869375 TTATTT-TTATTTTGG
1 TT-TTTGCTATTTTGG
2869390 TCCCATAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 35 0.92
31 3 0.08
ACGTcount: A:0.19, C:0.09, G:0.11, T:0.61
Consensus pattern (30 bp):
TTTTTGCTATTTTGGACCTTTAAATTTATA
Found at i:2873008 original size:14 final size:13
Alignment explanation
Indices: 2872966--2873008 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
2872956 AGGAAAATAG
2872966 CAAAGAAAAAAAGA
1 CAAAG-AAAAAAGA
*
2872980 AAAAGAAAAAA-A
1 CAAAGAAAAAAGA
2872992 CAAAGAAAAAAGGA
1 CAAAGAAAAAA-GA
2873006 CAA
1 CAA
2873009 GAAGCACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 11 0.44
13 6 0.24
14 8 0.32
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (13 bp):
CAAAGAAAAAAGA
Found at i:2874649 original size:40 final size:40
Alignment explanation
Indices: 2874585--2874780 Score: 137
Period size: 40 Copynumber: 4.6 Consensus size: 40
2874575 TCCTAAAGAT
* * *
2874585 GACTTAACATCCTCATTACGTAGGAACCGTGTCATCCATA
1 GACTAAACCTCCTCATCACGTAGGAACCGTGTCATCCATA
* *
2874625 GACTAAACCTCCTCATCACGTAGGAGCCGTGTCA-CTCTTA
1 GACTAAACCTCCTCATCACGTAGGAACCGTGTCATC-CATA
* *
2874665 GA-TAACCAATCGTCCTCATCACGTAGGAACCGTGTTATCATCCCTAAA
1 GACT-A--AA-CCTCCTCATCACGTAGGAACCGTG---TCAT-CC-ATA
* * * **
2874713 GA-TAGTCTACCATCCTCATCACATAAGAACCGTGTCATCCACC
1 GACTA---AACC-TCCTCATCACGTAGGAACCGTGTCATCCATA
2874756 GACTAAACCTCCTCATCACGTAGGA
1 GACTAAACCTCCTCATCACGTAGGA
2874781 GCCATGTCTC
Statistics
Matches: 123, Mismatches: 19, Indels: 28
0.72 0.11 0.16
Matches are distributed among these distances:
39 2 0.02
40 50 0.41
41 3 0.02
42 2 0.02
43 25 0.20
44 4 0.03
45 4 0.03
46 3 0.02
47 3 0.02
48 27 0.22
ACGTcount: A:0.30, C:0.31, G:0.15, T:0.24
Consensus pattern (40 bp):
GACTAAACCTCCTCATCACGTAGGAACCGTGTCATCCATA
Found at i:2874810 original size:131 final size:131
Alignment explanation
Indices: 2874569--2874839 Score: 375
Period size: 131 Copynumber: 2.1 Consensus size: 131
2874559 CTCTTGAAAC
* * * * *
2874569 TATCATTCCTAAAGATGACTTAACATCCTCATTACGTAGGAACCGTGTCATCCATAGACTAAACC
1 TATCATCCCTAAAGATGACTTAACATCCTCATCACATAAGAACCGTGTCATCCACAGACTAAACC
* * * *
2874634 TCCTCATCACGTAGGAGCCGTGTCACTCTTAGATAACCAATCGTCCTCATCACGTAGGAACCGTG
66 TCCTCATCACGTAGGAGCCATGTCACTCCTAGATAACCAACCGTCCTCATCACGTAAGAACCGTG
2874699 T
131 T
* * *
2874700 TATCATCCCTAAAGAT-AGTCTACCATCCTCATCACATAAGAACCGTGTCATCCACCGACTAAAC
1 TATCATCCCTAAAGATGACT-TAACATCCTCATCACATAAGAACCGTGTCATCCACAGACTAAAC
* * * *
2874764 CTCCTCATCACGTAGGAGCCATGTCTCTCCTAGATAATCAACCGTCCTCATCGCGTAAGAATCGT
65 CTCCTCATCACGTAGGAGCCATGTCACTCCTAGATAACCAACCGTCCTCATCACGTAAGAACCGT
2874829 GT
130 GT
2874831 TATCA-CCCT
1 TATCATCCCT
2874840 CTCTAAAGAT
Statistics
Matches: 123, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
130 6 0.05
131 117 0.95
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (131 bp):
TATCATCCCTAAAGATGACTTAACATCCTCATCACATAAGAACCGTGTCATCCACAGACTAAACC
TCCTCATCACGTAGGAGCCATGTCACTCCTAGATAACCAACCGTCCTCATCACGTAAGAACCGTG
T
Found at i:2874914 original size:134 final size:131
Alignment explanation
Indices: 2874569--2874915 Score: 374
Period size: 131 Copynumber: 2.6 Consensus size: 131
2874559 CTCTTGAAAC
* * * * * *
2874569 TATCATTCCTAAAGAT-GACTTAACATCCTCATTACGTAGGAACCGTGTCATCCATAGACTAAAC
1 TATCATCCCTAAAGATAGGC-TACCATCCTCATCACGTAAGAACCGTGTCATCCATCGACTAAAC
* * * *
2874633 CTCCTCATCACGTAGGAGCCGTGTCACTCTTAGATAACCAATCGTCCTCATCACGTAGGAACCGT
65 CTCCTCATCACGTAGGAGCCATGTCACTCCTAGATAACCAACCGTCCTCATCACGTAAGAACCGT
2874698 GT
130 GT
* * *
2874700 TATCATCCCTAAAGATAGTCTACCATCCTCATCACATAAGAACCGTGTCATCCACCGACTAAACC
1 TATCATCCCTAAAGATAGGCTACCATCCTCATCACGTAAGAACCGTGTCATCCATCGACTAAACC
* * * *
2874765 TCCTCATCACGTAGGAGCCATGTCTCTCCTAGATAATCAACCGTCCTCATCGCGTAAGAATCGTG
66 TCCTCATCACGTAGGAGCCATGTCACTCCTAGATAACCAACCGTCCTCATCACGTAAGAACCGTG
2874830 T
131 T
* **** * * * *
2874831 TATCACCCTCTCTAAAGAT-GGCATGTTGTTCTCATCGCGTAAGAACAGTGTCATCCATCGACCA
1 TATCA---TCCCTAAAGATAGGC-TACCATCCTCATCACGTAAGAACCGTGTCATCCATCGACTA
* * *
2874895 GATCTCCTCATCGCGTAGGAG
62 AACCTCCTCATCACGTAGGAG
2874916 TTGTCTCACC
Statistics
Matches: 180, Mismatches: 31, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
131 117 0.65
132 2 0.01
133 2 0.01
134 59 0.33
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (131 bp):
TATCATCCCTAAAGATAGGCTACCATCCTCATCACGTAAGAACCGTGTCATCCATCGACTAAACC
TCCTCATCACGTAGGAGCCATGTCACTCCTAGATAACCAACCGTCCTCATCACGTAAGAACCGTG
T
Found at i:2875128 original size:3 final size:3
Alignment explanation
Indices: 2875120--2875146 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2875110 TATACAAAAA
2875120 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
2875147 CACTAACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2877124 original size:14 final size:14
Alignment explanation
Indices: 2877105--2877132 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2877095 GATTCAACTT
2877105 GGTCTGAGTCAACC
1 GGTCTGAGTCAACC
2877119 GGTCTGAGTCAACC
1 GGTCTGAGTCAACC
2877133 CGTTGACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.29, T:0.21
Consensus pattern (14 bp):
GGTCTGAGTCAACC
Found at i:2881562 original size:29 final size:29
Alignment explanation
Indices: 2881520--2881589 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
2881510 AGGTCTAGTC
*
2881520 ACCGAGTCAACTCGATCTAAGTCAA-CCTG
1 ACCGAGTTAACTCGATCTAAGTCAAGCC-G
* *
2881549 ACCGAGTTAACTCGGTCTGAGTCAAGCCG
1 ACCGAGTTAACTCGATCTAAGTCAAGCCG
*
2881578 TCCGAGTTAACT
1 ACCGAGTTAACT
2881590 TGTTGACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 34 0.94
30 2 0.06
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (29 bp):
ACCGAGTTAACTCGATCTAAGTCAAGCCG
Found at i:2885096 original size:30 final size:29
Alignment explanation
Indices: 2885032--2885119 Score: 88
Period size: 30 Copynumber: 3.0 Consensus size: 29
2885022 GTAGTGTAGC
* * * *
2885032 CCTTCAAATTTTTGTTTTTGCTATTTTTT
1 CCTTTAAATTTATGTTTTTGTTATTTTGT
2885061 ACCTTTAAATTTATGTTTTTGTTATTTTAGT
1 -CCTTTAAATTTATGTTTTTGTTATTTT-GT
* *
2885092 CCTTTAAGTTTCTGTTATTT-TTATTTTG
1 CCTTTAAATTTATGTT-TTTGTTATTTTG
2885120 GTCCCATAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 1 0.02
30 45 0.90
31 4 0.08
ACGTcount: A:0.17, C:0.10, G:0.09, T:0.64
Consensus pattern (29 bp):
CCTTTAAATTTATGTTTTTGTTATTTTGT
Found at i:2886995 original size:13 final size:13
Alignment explanation
Indices: 2886977--2887001 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2886967 GATCGAATTT
2886977 TTTTAACCGGTTA
1 TTTTAACCGGTTA
2886990 TTTTAACCGGTT
1 TTTTAACCGGTT
2887002 TGGAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (13 bp):
TTTTAACCGGTTA
Found at i:2889386 original size:21 final size:21
Alignment explanation
Indices: 2889362--2889403 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2889352 AGTTTATTTT
2889362 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
2889383 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
2889404 AACTTAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:2889440 original size:33 final size:33
Alignment explanation
Indices: 2889398--2889501 Score: 165
Period size: 33 Copynumber: 3.2 Consensus size: 33
2889388 TTTGTTTCAA
* *
2889398 TTATCGAACTTAGAAATTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
2889431 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
2889464 TTATCGAACTTGGAAGTATTTAAGTATTTCAA-
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
2889496 TTATCG
1 TTATCG
2889502 TAAACTTTGT
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 6 0.09
33 61 0.91
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Done.