Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 144 of 182
Found at i:44313948 original size:39 final size:39
Alignment explanation
Indices: 44313850--44314243 Score: 358
Period size: 39 Copynumber: 10.1 Consensus size: 39
44313840 AATAGAAATA
* * *
44313850 CGGTGATTATACGGGCTATGCGCCTAGCAGGCTTTGTGC
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
** * *
44313889 CAATG-TTATTCGGGTTAAGTGCCTAGTAGGCTTTGTGC
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
* * * * * *
44313927 CGGTGATTATTCAGGTTAAGTGCCTGGCCGTCTTTGTGT
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
* * * *
44313966 CAGTGACTATTCCGGCTAAGTGCCTAGCAGGCATTGTGC
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
* * * * * *
44314005 TGTTGATTATTCAGGCTATGTGCCTAGCAGGCATTATGC
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
* * * *
44314044 CGGTGATTATTCGAGCTAAGTGCCCAACAGGCTTTGTGT
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
* * * *
44314083 TGCTGATTATTCGGGCTCAGTGCCTAGCAGGCTTTGTGT
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
** * * * *
44314122 CAATGATTATTTGGGCTAAGTACCTAGCAAGCTTTGTGT
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
* * * * *
44314161 CGGTGAGTATTTGGGCTATGTGCCTAGCAGGCTTTATAC
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
* * **
44314200 AGGTGATTATTCAGGCTTTGTGCCTAGCAGGCTTTGTGC
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
*
44314239 TGGTG
1 CGGTG
44314244 TATTGCAAGT
Statistics
Matches: 283, Mismatches: 71, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
38 31 0.11
39 252 0.89
ACGTcount: A:0.18, C:0.19, G:0.29, T:0.34
Consensus pattern (39 bp):
CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
Found at i:44321100 original size:17 final size:17
Alignment explanation
Indices: 44321080--44321130 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
44321070 GCTTAGTATT
44321080 TTTGGATAAATTATTGA
1 TTTGGATAAATTATTGA
*
44321097 TTTGAGA-AAATTAGTTAA
1 TTTG-GATAAATTA-TTGA
44321115 TTT-GATAAATT-TTGA
1 TTTGGATAAATTATTGA
44321130 T
1 T
44321131 AAGGGACTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 4 0.14
16 2 0.07
17 15 0.52
18 8 0.28
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (17 bp):
TTTGGATAAATTATTGA
Found at i:44321486 original size:39 final size:39
Alignment explanation
Indices: 44321440--44321867 Score: 531
Period size: 39 Copynumber: 11.0 Consensus size: 39
44321430 AATAGAAATA
* * *
44321440 CGGTGATTATTCGGGCTAAGCGCCTAGCAGGCTTTATGC
1 CGGTGATTATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
* * *
44321479 CGATGATTATTCGGGATATGTGCCTAGTAGGCTTTGTGC
1 CGGTGATTATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
* * *
44321518 TGGTGATTATTTGGGCTAAGTGCCTAGCAGGCTTTGTGC
1 CGGTGATTATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
* *
44321557 TGGTGATTATTCGGGCTATGTGCCTAGCTGGCTTTGTGC
1 CGGTGATTATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
* * * *
44321596 TGGTGATTATTCAGACTAAGTGCCTAGCAGGCTTTGTGC
1 CGGTGATTATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
* * * *
44321635 TGCTAATTATTCAGGCT-TAGTGCCTAGCAGGCTTTGTGC
1 CGGTGATTATTCGGGCTAT-GTGCCTAGCAGGCTTTGTGC
*
44321674 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
1 CGGTGATTATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
* * * *
44321713 CGGAT-ATTATTTGAGCTATGTACCTAGTAGGCTTTGTGC
1 CGG-TGATTATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
*
44321752 CGGTGATTATTCGGGCTATGTGCCTAGCAGGCTTTGT-T
1 CGGTGATTATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
* * **
44321790 AGGTGATTATTCGGGCTTTGTGCCTAAAAGG-TTTGTGC
1 CGGTGATTATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
* *
44321828 CGGTGATTATTCGGGCTTTGTGCCTAGCAGGCTATGTGC
1 CGGTGATTATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
44321867 C
1 C
44321868 AGTGTATTGG
Statistics
Matches: 336, Mismatches: 47, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
37 5 0.01
38 56 0.17
39 274 0.82
40 1 0.00
ACGTcount: A:0.16, C:0.18, G:0.31, T:0.35
Consensus pattern (39 bp):
CGGTGATTATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
Found at i:44325540 original size:18 final size:16
Alignment explanation
Indices: 44325507--44325546 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 16
44325497 TTCAATATGG
44325507 ATTTTACTTTTATTTT
1 ATTTTACTTTTATTTT
44325523 ATTTTACTATTGTATTTT
1 ATTTTACT-TT-TATTTT
44325541 ATTTTA
1 ATTTTA
44325547 ATAAGGATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 8 0.36
17 2 0.09
18 12 0.55
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (16 bp):
ATTTTACTTTTATTTT
Found at i:44327688 original size:22 final size:22
Alignment explanation
Indices: 44327647--44327702 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
44327637 GATATTATAT
** *
44327647 GATATGATATGTTATAAGATGC
1 GATATGATATGACATAAGATCC
*
44327669 GATATGATATGACATGAGATCC
1 GATATGATATGACATAAGATCC
*
44327691 GATTTGATATGA
1 GATATGATATGA
44327703 TATGTTATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.34
Consensus pattern (22 bp):
GATATGATATGACATAAGATCC
Found at i:44328939 original size:19 final size:19
Alignment explanation
Indices: 44328915--44328952 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
44328905 CCTTCAGTTG
44328915 GAATCTTCGTAAAATAATT
1 GAATCTTCGTAAAATAATT
44328934 GAATCTTCGTAAAATAATT
1 GAATCTTCGTAAAATAATT
44328953 TTGCATCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (19 bp):
GAATCTTCGTAAAATAATT
Found at i:44332789 original size:13 final size:13
Alignment explanation
Indices: 44332771--44332795 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44332761 TGTCGTTCCA
44332771 GTGACTTAATTTG
1 GTGACTTAATTTG
44332784 GTGACTTAATTT
1 GTGACTTAATTT
44332796 CATGGTTGTG
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:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (13 bp):
GTGACTTAATTTG
Found at i:44333176 original size:63 final size:60
Alignment explanation
Indices: 44333098--44333240 Score: 186
Period size: 61 Copynumber: 2.4 Consensus size: 60
44333088 TTTTTCTAAT
* * *
44333098 ATTATATATTTTTATTTTTATTAATTCATATTTTAATAATAATTATATTAAGAATTTTATTAA
1 ATTATATATTTTTATTTTTATTAATT-ATA-TTTAATAATAATTAGATTAA-AATATAATTAA
44333161 ATTATATATTTTTA-TTTTATTAAATTATATTTAATAATAATTAGATTAAAATATAATTAA
1 ATTATATATTTTTATTTTTATT-AATTATATTTAATAATAATTAGATTAAAATATAATTAA
*
44333221 A--ATAT-TTATTATTTTTATTA
1 ATTATATATTTTTATTTTTATTA
44333241 CATTTAATAA
Statistics
Matches: 74, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
57 6 0.08
58 11 0.15
60 10 0.14
61 19 0.26
62 10 0.14
63 18 0.24
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (60 bp):
ATTATATATTTTTATTTTTATTAATTATATTTAATAATAATTAGATTAAAATATAATTAA
Found at i:44333910 original size:12 final size:12
Alignment explanation
Indices: 44333893--44333918 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44333883 CAAAATAGGC
44333893 TTTTAGCGGCAT
1 TTTTAGCGGCAT
44333905 TTTTAGCGGCAT
1 TTTTAGCGGCAT
44333917 TT
1 TT
44333919 GGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCAT
Found at i:44334018 original size:38 final size:40
Alignment explanation
Indices: 44333924--44334019 Score: 142
Period size: 39 Copynumber: 2.4 Consensus size: 40
44333914 CATTTGGATA
*
44333924 AAAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTAC
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTAC
*
44333964 AAAAACGCCGCTAAAAAT-AAGCATTAGCGGCG-TTTTCC
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTAC
*
44334002 AAAAAGCGCCGCAAAAAA
1 AAAAA-CGCCGCTAAAAA
44334020 CCTAAGCTCA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
38 10 0.19
39 25 0.48
40 17 0.33
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.17
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTAC
Found at i:44334113 original size:41 final size:41
Alignment explanation
Indices: 44334053--44334218 Score: 190
Period size: 41 Copynumber: 4.0 Consensus size: 41
44334043 CAGAGTTTTG
*
44334053 GGGGCATTTAGTGGCGTTTTTGAAAAAGCACCGCTAATGCTC
1 GGGGC-TTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTC
** ** *
44334095 GGGGCTTTAGCGAAGTTTTTGAAAAAGTGCCGCTAATGCTT
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTC
* * *
44334136 GGGGATTTAGCGGCGTTTTTTAAAAAG-AGCCCCTAATGCTC
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCA-CCGCTAATGCTC
* * * *
44334177 GAGCCTTTAGCGGCGTTTTTGGAAAAGCACTGCTAATGCTC
1 GGGGCTTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTC
44334218 G
1 G
44334219 TACCTTTTGC
Statistics
Matches: 102, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
41 96 0.94
42 6 0.06
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (41 bp):
GGGGCTTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTC
Found at i:44334225 original size:41 final size:41
Alignment explanation
Indices: 44334059--44334243 Score: 167
Period size: 41 Copynumber: 4.5 Consensus size: 41
44334049 TTTGGGGGCA
* **
44334059 TTTAGTGGCGTTTTTGAAAAAGCACCGCTAATGCTCGGGGC
1 TTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTCGGACC
** ** * ***
44334100 TTTAGCGAAGTTTTTGAAAAAGTGCCGCTAATGCTTGGGGA
1 TTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTCGGACC
* *
44334141 TTTAGCGGCGTTTTTTAAAAAG-AGCCCCTAATGCTC-GAGCC
1 TTTAGCGGCGTTTTTGAAAAAGCA-CCGCTAATGCTCGGA-CC
* * *
44334182 TTTAGCGGCGTTTTTGGAAAAGCACTGCTAATGCTCGTACC
1 TTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTCGGACC
* *
44334223 TTTTGCGGCATTTTTAGAAAA
1 TTTAGCGGCGTTTTT-GAAAA
44334244 GCGTCGGCGT
Statistics
Matches: 115, Mismatches: 24, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
40 1 0.01
41 108 0.94
42 6 0.05
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTCGGACC
Found at i:44334231 original size:82 final size:82
Alignment explanation
Indices: 44334057--44334243 Score: 187
Period size: 82 Copynumber: 2.3 Consensus size: 82
44334047 GTTTTGGGGG
* * * *
44334057 CATTTAGTGGCGTTTTTGAAAAAGCACCGCTAATGCTCGGGGCTTTAGCGAAGTTTTTGAAAAAG
1 CATTTAGCGGCGTTTTTGAAAAAGCACCCCTAATGCTCGAGCCTTTAGCGAAGTTTTTGAAAAAG
** * *
44334122 TGCCGCTAATGCTTGGG
66 CACCGCTAATGCTCGGA
* * ** *
44334139 GATTTAGCGGCGTTTTTTAAAAAG-AGCCCCTAATGCTCGAGCCTTTAGCGGCGTTTTTGGAAAA
1 CATTTAGCGGCGTTTTTGAAAAAGCA-CCCCTAATGCTCGAGCCTTTAGCGAAGTTTTTGAAAAA
* *
44334203 GCACTGCTAATGCTCGTA
65 GCACCGCTAATGCTCGGA
* * *
44334221 CCTTTTGCGGCATTTTTAGAAAA
1 CATTTAGCGGCGTTTTT-GAAAA
44334244 GCGTCGGCGT
Statistics
Matches: 83, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
81 1 0.01
82 78 0.94
83 4 0.05
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (82 bp):
CATTTAGCGGCGTTTTTGAAAAAGCACCCCTAATGCTCGAGCCTTTAGCGAAGTTTTTGAAAAAG
CACCGCTAATGCTCGGA
Found at i:44335382 original size:6 final size:7
Alignment explanation
Indices: 44335358--44335417 Score: 50
Period size: 7 Copynumber: 8.7 Consensus size: 7
44335348 ATAGTTTTGA
44335358 GTTTAGG
1 GTTTAGG
44335365 GTTTAGG
1 GTTTAGG
44335372 GTTTA-G
1 GTTTAGG
44335378 GTTTAGG
1 GTTTAGG
* *
44335385 GCTTGGG
1 GTTTAGG
* *
44335392 GATTGGG
1 GTTTAGG
* *
44335399 GTTAAAG
1 GTTTAGG
*
44335406 GTTTAGA
1 GTTTAGG
44335413 GTTTA
1 GTTTA
44335418 CATTTTAGTG
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
6 6 0.14
7 36 0.86
ACGTcount: A:0.18, C:0.02, G:0.40, T:0.40
Consensus pattern (7 bp):
GTTTAGG
Found at i:44335866 original size:24 final size:25
Alignment explanation
Indices: 44335830--44335877 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
44335820 TTAAAATGAA
44335830 TTTTAAAAGATTT-TAAACTTTTAT
1 TTTTAAAAGATTTATAAACTTTTAT
* * *
44335854 TTTTATAATATTTATATACTTTTA
1 TTTTAAAAGATTTATAAACTTTTA
44335878 AAGAAAAGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (25 bp):
TTTTAAAAGATTTATAAACTTTTAT
Found at i:44336161 original size:41 final size:41
Alignment explanation
Indices: 44336099--44336185 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
44336089 AAGTTCTACG
*
44336099 ATTTTGGGCCGACTTTATTATACGGGCAAATCCATATAAAA
1 ATTTTGGGCCAACTTTATTATACGGGCAAATCCATATAAAA
* **
44336140 ATTTTGGGCCAACTTTGTTATACGGGCTTATCCATATAAAA
1 ATTTTGGGCCAACTTTATTATACGGGCAAATCCATATAAAA
44336181 ATTTT
1 ATTTT
44336186 ATCCATATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (41 bp):
ATTTTGGGCCAACTTTATTATACGGGCAAATCCATATAAAA
Found at i:44339944 original size:43 final size:43
Alignment explanation
Indices: 44339865--44340020 Score: 215
Period size: 43 Copynumber: 3.6 Consensus size: 43
44339855 AATAATTTTT
* * * ** *
44339865 TAAAGGTTAT-GTTTTTAGCGGCGTTTGTGACAAAAAGCTCCGC
1 TAAAGGTCATGGTCTTTAGCAGCGTTTGTG-GGAAAAGCACCGC
* *
44339908 TAAAGGTCATGTTCTTTAGCAGCGTTTGTGGGAAAAGCGCCGC
1 TAAAGGTCATGGTCTTTAGCAGCGTTTGTGGGAAAAGCACCGC
*
44339951 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCACCGC
1 TAAAGGTCATGGTCTTTAGCAGCGTTTGTGGGAAAAGCACCGC
44339994 TAAAGGTCATGGTCTTTAGCAGCGTTT
1 TAAAGGTCATGGTCTTTAGCAGCGTTT
44340021 ATTTCTAAAA
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
43 85 0.84
44 16 0.16
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (43 bp):
TAAAGGTCATGGTCTTTAGCAGCGTTTGTGGGAAAAGCACCGC
Found at i:44348732 original size:27 final size:27
Alignment explanation
Indices: 44348708--44348849 Score: 184
Period size: 27 Copynumber: 5.3 Consensus size: 27
44348698 AGAAGTATAA
44348708 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
*
44348735 C-GATCATTTTACCC--TGAGGGTATTT
1 CAG-TCATTTTACCCTATGGGGGTATTT
* *
44348760 CAGTCATTTTACCTTATAGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * *
44348787 CGGTCATTTTACCCTATGAGGGCATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
44348814 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
44348841 C-GATCATTT
1 CAG-TCATTT
44348850 ATTGACCGCT
Statistics
Matches: 98, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
25 21 0.21
26 3 0.03
27 74 0.76
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (27 bp):
CAGTCATTTTACCCTATGGGGGTATTT
Found at i:44348769 original size:52 final size:53
Alignment explanation
Indices: 44348708--44348849 Score: 232
Period size: 54 Copynumber: 2.7 Consensus size: 53
44348698 AGAAGTATAA
*
44348708 CAGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCC-TGAGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCATGAGGGCATTT
* * *
44348760 CAGTCATTTTACCTTATAGGGGTATTTCGGTCATTTTACCCTATGAGGGCATTT
1 CAGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCC-ATGAGGGCATTT
44348814 CAGTCATTTTACCCTATGGGGGTATTTCGATCATTT
1 CAGTCATTTTACCCTATGGGGGTATTTCGATCATTT
44348850 ATTGACCGCT
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
52 38 0.47
54 43 0.53
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (53 bp):
CAGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCATGAGGGCATTT
Found at i:44349823 original size:34 final size:37
Alignment explanation
Indices: 44349771--44349852 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 37
44349761 GGTAGAAATC
*
44349771 AAAGACAGA-AAGAGAAAG-ATATTCGGCCA-AAG-AA
1 AAAGA-AGAGAAGAGAAAGAAGATTCGGCCAGAAGAAA
* *
44349805 GAAGAAGAGAAGAGAAAGAAGATTCGGCCAGTAGAAA
1 AAAGAAGAGAAGAGAAAGAAGATTCGGCCAGAAGAAA
44349842 AAAGAAGAGAA
1 AAAGAAGAGAA
44349853 AAAGAGAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 3 0.08
34 13 0.32
35 10 0.25
36 2 0.05
37 12 0.30
ACGTcount: A:0.56, C:0.09, G:0.28, T:0.07
Consensus pattern (37 bp):
AAAGAAGAGAAGAGAAAGAAGATTCGGCCAGAAGAAA
Found at i:44349847 original size:37 final size:36
Alignment explanation
Indices: 44349762--44349852 Score: 98
Period size: 37 Copynumber: 2.5 Consensus size: 36
44349752 ATAATAGGAG
*
44349762 GTAGAAATCAAAGACAGA-AAGAGAAAGATATTCGGCCA
1 GTAGAAA--AAAGA-AGAGAAGAGAAAGAGATTCGGCCA
* *
44349800 -AAG-AAGAAGAAGAGAAGAGAAAGAAGATTCGGCCA
1 GTAGAAAAAAGAAGAGAAGAGAAAG-AGATTCGGCCA
44349835 GTAGAAAAAAGAAGAGAA
1 GTAGAAAAAAGAAGAGAA
44349853 AAAGAGAGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
33 3 0.07
34 13 0.30
35 10 0.23
36 4 0.09
37 14 0.32
ACGTcount: A:0.55, C:0.09, G:0.27, T:0.09
Consensus pattern (36 bp):
GTAGAAAAAAGAAGAGAAGAGAAAGAGATTCGGCCA
Found at i:44356136 original size:28 final size:28
Alignment explanation
Indices: 44356070--44356148 Score: 94
Period size: 28 Copynumber: 3.0 Consensus size: 28
44356060 ATATCAGTAC
**
44356070 AGTGTGGGCC-TAGCCTGATACAGTAAT
1 AGTGTGGGCCTTAGCCCAATACAGTAAT
**
44356097 AGTGTGATCCTTAGCCCAATACAGTAAT
1 AGTGTGGGCCTTAGCCCAATACAGTAAT
44356125 AGTGTGGGCCTT---CCAATACAGTAA
1 AGTGTGGGCCTTAGCCCAATACAGTAA
44356149 CAGTACAGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
25 12 0.27
27 8 0.18
28 25 0.56
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (28 bp):
AGTGTGGGCCTTAGCCCAATACAGTAAT
Found at i:44356524 original size:27 final size:27
Alignment explanation
Indices: 44356501--44356698 Score: 204
Period size: 27 Copynumber: 7.3 Consensus size: 27
44356491 AGAGGTATAA
44356501 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
**
44356528 C-GATCATTTTACCCTATAAGGGTATTT
1 CAG-TCATTTTACCCTATGGGGGTATTT
* *
44356555 CGGTTATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* **
44356582 CAGTCATTTTACCATATGAAGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* *
44356609 C-GATCATCTTACCCTATGGGGATATTT
1 CAG-TCATTTTACCCTATGGGGGTATTT
* *
44356636 AAGTCATTTTACCCTATGGGGATATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
** * * *
44356663 TGGTCATTCTACCTTATGGCGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
44356690 C-GATCATTT
1 CAG-TCATTT
44356699 ATTGATCGCT
Statistics
Matches: 141, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
26 3 0.02
27 136 0.96
28 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (27 bp):
CAGTCATTTTACCCTATGGGGGTATTT
Found at i:44356564 original size:54 final size:55
Alignment explanation
Indices: 44356503--44356698 Score: 233
Period size: 54 Copynumber: 3.6 Consensus size: 55
44356493 AGGTATAACA
44356503 GTCATTTTACCCTATGGGGGTATTTCGA-TCATTTTACCCTATAAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCGAGTCATTTTACCCTATAAGGGTATTTCG
* *
44356557 GTTATTTTACCCTATGGGGGTATTTC-AGTCATTTTACCATATGAA-GGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCGAGTCATTTTACCCTAT-AAGGGTATTTCG
* * * * * *
44356611 ATCATCTTACCCTATGGGGATATTT-AAGTCATTTTACCCTAT-GGGGATATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCGAGTCATTTTACCCTATAAGGG-TATTTCG
* * *
44356665 GTCATTCTACCTTATGGCGGTATTTCGA-TCATTT
1 GTCATTTTACCCTATGGGGGTATTTCGAGTCATTT
44356699 ATTGATCGCT
Statistics
Matches: 120, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
53 3 0.03
54 114 0.95
55 3 0.03
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.42
Consensus pattern (55 bp):
GTCATTTTACCCTATGGGGGTATTTCGAGTCATTTTACCCTATAAGGGTATTTCG
Found at i:44356606 original size:81 final size:81
Alignment explanation
Indices: 44356501--44356698 Score: 254
Period size: 81 Copynumber: 2.4 Consensus size: 81
44356491 AGAGGTATAA
* * ** *
44356501 CAGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAAGGG-TATTTCGGTTATTTT
1 CAGTCATTTTACCATATGGAGGTATTTCGATCATTTTACCCTAT-AGGGATATTTAAGTCATTTT
*
44356565 ACCCTATGGGGGTATTT
65 ACCCTATGGGGATATTT
* * *
44356582 CAGTCATTTTACCATATGAAGGTATTTCGATCATCTTACCCTATGGGGATATTTAAGTCATTTTA
1 CAGTCATTTTACCATATGGAGGTATTTCGATCATTTTACCCTATAGGGATATTTAAGTCATTTTA
44356647 CCCTATGGGGATATTT
66 CCCTATGGGGATATTT
** * * *
44356663 TGGTCATTCTACCTTATGGCGGTATTTCGATCATTT
1 CAGTCATTTTACCATATGGAGGTATTTCGATCATTT
44356699 ATTGATCGCT
Statistics
Matches: 100, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
80 3 0.03
81 97 0.97
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (81 bp):
CAGTCATTTTACCATATGGAGGTATTTCGATCATTTTACCCTATAGGGATATTTAAGTCATTTTA
CCCTATGGGGATATTT
Found at i:44357693 original size:27 final size:27
Alignment explanation
Indices: 44357663--44357725 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
44357653 GAAGAAGAAT
*
44357663 AGAAGAGAAAGAAGATTCAGCCAGCAG
1 AGAAGAGAAAGAAGATTCAGCCAACAG
** *
44357690 AGAAGAGAAAGAAGATTTGGCCAATAG
1 AGAAGAGAAAGAAGATTCAGCCAACAG
44357717 AGAAGAGAA
1 AGAAGAGAA
44357726 GAGAGAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.51, C:0.10, G:0.30, T:0.10
Consensus pattern (27 bp):
AGAAGAGAAAGAAGATTCAGCCAACAG
Found at i:44358432 original size:35 final size:35
Alignment explanation
Indices: 44358382--44358530 Score: 208
Period size: 35 Copynumber: 4.2 Consensus size: 35
44358372 CAATCCCTCA
* * *
44358382 AAACACACCAAATGCTCACAAGATCTAGTCGAACCG
1 AAACACGCC-AATGCTCACAAGAGCTAGTCCAACCG
*
44358418 AAACACGCCAATGCTCACAAGAACTAGTCCAACCG
1 AAACACGCCAATGCTCACAAGAGCTAGTCCAACCG
* * * *
44358453 AAACATGCTAATGCTCATAAGAGGTAGTCCAACCG
1 AAACACGCCAATGCTCACAAGAGCTAGTCCAACCG
*
44358488 AAACACGCCAATGCTCATAAGAGCTAGTCCAACCG
1 AAACACGCCAATGCTCACAAGAGCTAGTCCAACCG
44358523 AAACACGC
1 AAACACGC
44358531 AAAACAGAGA
Statistics
Matches: 102, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 94 0.92
36 8 0.08
ACGTcount: A:0.40, C:0.30, G:0.16, T:0.14
Consensus pattern (35 bp):
AAACACGCCAATGCTCACAAGAGCTAGTCCAACCG
Found at i:44360145 original size:18 final size:19
Alignment explanation
Indices: 44360104--44360150 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
44360094 TATTGAACAT
* *
44360104 AAAAATAAAATTCAAATTG
1 AAAATTAAAATTCAAAATG
*
44360123 GAAATTAAAATT-AAAATG
1 AAAATTAAAATTCAAAATG
*
44360141 AAAATGAAAA
1 AAAATTAAAA
44360151 ATTTCTTTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AAAATTAAAATTCAAAATG
Found at i:44364348 original size:36 final size:36
Alignment explanation
Indices: 44364296--44364369 Score: 112
Period size: 36 Copynumber: 2.1 Consensus size: 36
44364286 AGTAAACTCT
* * *
44364296 ATTCATTTCAGTAGCCTTTGGGATCTATTATGACTG
1 ATTCATTTCAATAGCCTTTCGAATCTATTATGACTG
*
44364332 ATTCCTTTCAATAGCCTTTCGAATCTATTATGACTG
1 ATTCATTTCAATAGCCTTTCGAATCTATTATGACTG
44364368 AT
1 AT
44364370 GCGCTCCTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (36 bp):
ATTCATTTCAATAGCCTTTCGAATCTATTATGACTG
Found at i:44366595 original size:20 final size:20
Alignment explanation
Indices: 44366570--44366634 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
44366560 CAATTAGATA
44366570 ACTGAGGAAAAGAGAAAGTT
1 ACTGAGGAAAAGAGAAAGTT
* *
44366590 ACTGAGTAACAAGTAG--A-TA
1 ACTGAGGAA-AAG-AGAAAGTT
**
44366609 ACCAAGGAAAAGAGAAAGTT
1 ACTGAGGAAAAGAGAAAGTT
44366629 ACTGAG
1 ACTGAG
44366635 TAGTCCTTGA
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
17 2 0.06
18 3 0.09
19 8 0.25
20 14 0.44
21 3 0.09
22 2 0.06
ACGTcount: A:0.49, C:0.09, G:0.26, T:0.15
Consensus pattern (20 bp):
ACTGAGGAAAAGAGAAAGTT
Found at i:44366617 original size:39 final size:39
Alignment explanation
Indices: 44366558--44366636 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
44366548 ATAGATCAAG
* **
44366558 AACAATTAGATAACTGAGGAAAAGAGAAAGTTACTGAGT
1 AACAAGTAGATAACCAAGGAAAAGAGAAAGTTACTGAGT
44366597 AACAAGTAGATAACCAAGGAAAAGAGAAAGTTACTGAGT
1 AACAAGTAGATAACCAAGGAAAAGAGAAAGTTACTGAGT
44366636 A
1 A
44366637 GTCCTTGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.51, C:0.09, G:0.23, T:0.18
Consensus pattern (39 bp):
AACAAGTAGATAACCAAGGAAAAGAGAAAGTTACTGAGT
Found at i:44368201 original size:54 final size:54
Alignment explanation
Indices: 44368143--44368255 Score: 201
Period size: 54 Copynumber: 2.1 Consensus size: 54
44368133 TTTTTCTATT
*
44368143 TGAAGTTAAATGTTATGAATTGTACTATAATACTCTATAACCTTAA-TCTGATGA
1 TGAAGTTAAATGTTATGAATTGTACTATAATACTCTATAACCCTAATTC-GATGA
44368197 TGAAGTTAAATGTTATGAATTGTACTATAATACTCTATAACCCTAATTCGATGA
1 TGAAGTTAAATGTTATGAATTGTACTATAATACTCTATAACCCTAATTCGATGA
44368251 TGAAG
1 TGAAG
44368256 ATAGGTTAGG
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
54 55 0.96
55 2 0.04
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (54 bp):
TGAAGTTAAATGTTATGAATTGTACTATAATACTCTATAACCCTAATTCGATGA
Found at i:44380640 original size:20 final size:22
Alignment explanation
Indices: 44380596--44380643 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
44380586 CCTATATGTA
* *
44380596 TAAATTAACCTATATTAATAAC
1 TAAATTAACCTATATAAAAAAC
44380618 TAAATTAACC-AT-TAAAAAAC
1 TAAATTAACCTATATAAAAAAC
44380638 TAAATT
1 TAAATT
44380644 TAATAGTTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.50
21 2 0.08
22 10 0.42
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAATTAACCTATATAAAAAAC
Found at i:44392175 original size:27 final size:26
Alignment explanation
Indices: 44392144--44392321 Score: 142
Period size: 27 Copynumber: 6.6 Consensus size: 26
44392134 TAAATTGTAC
*
44392144 AGCACTAAGTGTGCGATTCTACTTTGT
1 AGCACTAAGTGTGCGATT-TACTATGT
* * * *
44392171 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTTACTATGT
* * *
44392197 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTTACTATGT
*
44392225 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTT-ACTATGT
* *
44392253 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTT-ACTATGT
* * *
44392280 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTTACTATGT
*
44392307 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
44392322 GGCTCAATAT
Statistics
Matches: 125, Mismatches: 20, Indels: 12
0.80 0.13 0.08
Matches are distributed among these distances:
26 1 0.01
27 100 0.80
28 24 0.19
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTTACTATGT
Found at i:44392205 original size:54 final size:54
Alignment explanation
Indices: 44392144--44392321 Score: 166
Period size: 54 Copynumber: 3.3 Consensus size: 54
44392134 TAAATTGTAC
* *
44392144 AGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATT-TACTTTGTAGCACTAAGTGTGCGAATTGAATATGAT
* ** ** * *
44392199 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATG-T
1 AGCACTAAGTGTGCG-ATTTACTTTGTAGCACTAAGTGTGCGA-ATTGAATATGAT
* * *
44392253 AGCACTAAGTGTGCGATTTGA-TTACGTAGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGATTT-ACTT-TGTAGCACTAAGTGTGCGAATTGAATATGAT
*
44392307 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
44392322 GGCTCAATAT
Statistics
Matches: 100, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
54 59 0.59
55 41 0.41
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTTACTTTGTAGCACTAAGTGTGCGAATTGAATATGAT
Found at i:44392268 original size:55 final size:54
Alignment explanation
Indices: 44392172--44392321 Score: 167
Period size: 55 Copynumber: 2.8 Consensus size: 54
44392162 CTACTTTGTT
** * *
44392172 GCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGTTGAATATGTA-GCACTAAGTGTGCGAATTGACCACGCA
* * ** *
44392226 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAG-TTGAATATGTAGCACTAAGTGTGCGAATTGACCACGCA
* * *
44392281 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCG
44392322 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
54 37 0.45
55 44 0.54
56 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAATTGACCACGCA
Found at i:44392268 original size:82 final size:81
Alignment explanation
Indices: 44392145--44392300 Score: 208
Period size: 82 Copynumber: 1.9 Consensus size: 81
44392135 AAATTGTACA
* * *
44392145 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
44392209 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
44392226 GCACTAAGTGTGCGAGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGT
1 GCACTAAGTGTGCGA-TTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGT
*
44392290 GTGCGAGTTGA
64 GTGCGAATTGA
44392301 TTATATAGCA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
81 16 0.25
82 48 0.74
83 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:44392312 original size:82 final size:81
Alignment explanation
Indices: 44392141--44392321 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
44392131 GATTAAATTG
* * *
44392141 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
44392206 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
44392222 TGCGGCACTAAGTGTGCGAGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCAC
1 TACAGCACTAAGTGTGCGA-TTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCAC
* **
44392285 TAAGTGTGCGAGTTGATTA
63 TAAGTGTGCGAATTGACCA
* *
44392304 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
44392322 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
81 19 0.23
82 63 0.77
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:44392332 original size:27 final size:27
Alignment explanation
Indices: 44392226--44392332 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
44392216 TGACCATGCG
* * * *
44392226 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
44392254 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
44392281 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
44392308 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
44392333 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:44394190 original size:12 final size:12
Alignment explanation
Indices: 44394173--44394201 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
44394163 AAAGGAAAAA
44394173 ATTTTCAAAATT
1 ATTTTCAAAATT
44394185 ATTTTCAAAATT
1 ATTTTCAAAATT
44394197 ATTTT
1 ATTTT
44394202 TCTGAATCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTTCAAAATT
Found at i:44405824 original size:92 final size:92
Alignment explanation
Indices: 44405667--44405853 Score: 365
Period size: 92 Copynumber: 2.0 Consensus size: 92
44405657 TATGACCATT
44405667 AGAACTTAAACACAAACATACAATTTAGTCACTTAAACATGCACCATAACTTAGCCATATTCACA
1 AGAACTTAAACACAAACATACAATTTAGTCACTTAAACATGCACCATAACTTAGCCATATTCACA
*
44405732 CACATCACTAAGGCGCCAAAACTACCA
66 CACATCACTAAGGCACCAAAACTACCA
44405759 AGAACTTAAACACAAACATACAATTTAGTCACTTAAACATGCACCATAACTTAGCCATATTCACA
1 AGAACTTAAACACAAACATACAATTTAGTCACTTAAACATGCACCATAACTTAGCCATATTCACA
44405824 CACATCACTAAGGCACCAAAACTACCA
66 CACATCACTAAGGCACCAAAACTACCA
44405851 AGA
1 AGA
44405854 TTACGTAAAC
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 94 1.00
ACGTcount: A:0.44, C:0.28, G:0.07, T:0.20
Consensus pattern (92 bp):
AGAACTTAAACACAAACATACAATTTAGTCACTTAAACATGCACCATAACTTAGCCATATTCACA
CACATCACTAAGGCACCAAAACTACCA
Found at i:44406341 original size:20 final size:20
Alignment explanation
Indices: 44406302--44406369 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 20
44406292 TGTGAAGCAC
* *
44406302 TCAATTT-CTTACTTACCAT
1 TCAATTTACATACTTTCCAT
*
44406321 TCAATTTACATACTTTTCAT
1 TCAATTTACATACTTTCCAT
** * *
44406341 TTTATTTACTTTCTTTCCAT
1 TCAATTTACATACTTTCCAT
*
44406361 TCCATTTAC
1 TCAATTTAC
44406370 CTAGCATAAG
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 7 0.18
20 31 0.82
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (20 bp):
TCAATTTACATACTTTCCAT
Found at i:44407738 original size:12 final size:12
Alignment explanation
Indices: 44407721--44407750 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
44407711 GTCTCGATTC
44407721 AGAACTCATATT
1 AGAACTCATATT
*
44407733 AGAACTCGTATT
1 AGAACTCATATT
44407745 AGAACT
1 AGAACT
44407751 TGATACTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (12 bp):
AGAACTCATATT
Found at i:44411439 original size:20 final size:20
Alignment explanation
Indices: 44411402--44411477 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 20
44411392 AAGACTATGA
*
44411402 ACCACTCCATTT-CTTACTT
1 ACCATTCCATTTACTTACTT
44411421 ACCATTCCATTTACTTACTT
1 ACCATTCCATTTACTTACTT
* * *
44411441 TCCATTTCATTTACTTATTT
1 ACCATTCCATTTACTTACTT
* *
44411461 TCAATTCCATTTACTTA
1 ACCATTCCATTTACTTA
44411478 TAATAAGCTT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
19 11 0.22
20 39 0.78
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.49
Consensus pattern (20 bp):
ACCATTCCATTTACTTACTT
Found at i:44411445 original size:15 final size:16
Alignment explanation
Indices: 44411415--44411447 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
44411405 ACTCCATTTC
44411415 TTACTTACCATTCCAT
1 TTACTTACCATTCCAT
*
44411431 TTACTTA-CTTTCCAT
1 TTACTTACCATTCCAT
44411446 TT
1 TT
44411448 CATTTACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.21, C:0.27, G:0.00, T:0.52
Consensus pattern (16 bp):
TTACTTACCATTCCAT
Found at i:44414884 original size:6 final size:6
Alignment explanation
Indices: 44414863--44414896 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
44414853 AAATAAAGAC
44414863 AATTAA AATTGCAA AATTAA AATTAA AATTAA AA
1 AATTAA AATT--AA AATTAA AATTAA AATTAA AA
44414897 GCTTTTGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 20 0.77
8 6 0.23
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (6 bp):
AATTAA
Found at i:44425237 original size:15 final size:15
Alignment explanation
Indices: 44425217--44425324 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
44425207 TTTATGGAAA
44425217 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
44425232 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
44425246 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
44425262 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
44425276 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
44425292 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
44425306 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
44425322 ATC
1 ATC
44425325 GAGATATTGG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:44425254 original size:30 final size:30
Alignment explanation
Indices: 44425211--44425334 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
44425201 TCCACATTTA
* *
44425211 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
44425241 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
44425271 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
44425301 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
44425332 TGG
1 TGG
44425335 CATAATAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 80 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:44427668 original size:474 final size:474
Alignment explanation
Indices: 44426775--44427723 Score: 1702
Period size: 474 Copynumber: 2.0 Consensus size: 474
44426765 GACTGGTTTT
* *
44426775 CTAGTCTTAAAGAACTAGAAGGTGGAGTTGTTTTTATGGGCAATGATAGCGCTTATAAGACAATG
1 CTAGTCTTAAAGAACTAGAAGGTGGAATTGTTCTTATGGGCAATGATAGCGCTTATAAGACAATG
44426840 GGAGTAGGTACAATCCAATTGAAGAATCACGACGGCTCAATCCAAGTCTTGACAGATGTTCGCTA
66 GGAGTAGGTACAATCCAATTGAAGAATCACGACGGCTCAATCCAAGTCTTGACAGATGTTCGCTA
44426905 CGTACCTAGCCTGAAGAAAAATCTCATCTCATTAGGGGCCCTAGAATCTAAAGGGCTCACAATCA
131 CGTACCTAGCCTGAAGAAAAATCTCATCTCATTAGGGGCCCTAGAATCTAAAGGGCTCACAATCA
*
44426970 CTTTGAGAGATGGATTACTAAAGGTAGTAGCTGGGGTATTGACGGTGATGAAAGGCACTAGAAGA
196 CTTTGAGAGATGGATTACTAAAGGTAGTAGCTGGGGTATTGACGGTGATGAAAGGCACAAGAAGA
44427035 AATAACTTGTACTATTTAAATGGAAGTACAGTTATTGGATCAACATCAACAACTTCTGCGAAAGA
261 AATAACTTGTACTATTTAAATGGAAGTACAGTTATTGGATCAACATCAACAACTTCTGCGAAAGA
44427100 TGCAGATTCAGAGGCTACCAGGTTATGGCATAGGCGATTGGGACATGCTGGTGAAAAAGCTTTGC
326 TGCAGATTCAGAGGCTACCAGGTTATGGCATAGGCGATTGGGACATGCTGGTGAAAAAGCTTTGC
*
44427165 AGACATTGGTGAAGCAAGGCTTATTGAAAGGTGCAAATTCTTGCAAAATGGAATTCTGTGAACAT
391 AGACATTGGCGAAGCAAGGCTTATTGAAAGGTGCAAATTCTTGCAAAATGGAATTCTGTGAACAT
*
44427230 TGTTTTCTGGGCAAGCAGA
456 TGTGTTCTGGGCAAGCAGA
* * *
44427249 CTAGTCTTAAAGAGCTAGAAGGTGGAATTGTTCTTATGGGCAATGATAGTGCTTGTAAGACAATG
1 CTAGTCTTAAAGAACTAGAAGGTGGAATTGTTCTTATGGGCAATGATAGCGCTTATAAGACAATG
* * * *
44427314 GGAGTGGGTACAGTCCACTTGAAGAATCACGACGGCTCAATCCAAGTCTTGACAGGTGTTCGCTA
66 GGAGTAGGTACAATCCAATTGAAGAATCACGACGGCTCAATCCAAGTCTTGACAGATGTTCGCTA
*
44427379 CGTACCTAGCCTGAAGAAAAATCTCATCTCATTAGGTGCCCTAGAATCTAAAGGGCTCACAATCA
131 CGTACCTAGCCTGAAGAAAAATCTCATCTCATTAGGGGCCCTAGAATCTAAAGGGCTCACAATCA
*
44427444 CTTTGAGAGATGGATTACTAAAGGTAGTAGCTGGGGTATTGACGGTGATGAAAGGCACAAGAAGG
196 CTTTGAGAGATGGATTACTAAAGGTAGTAGCTGGGGTATTGACGGTGATGAAAGGCACAAGAAGA
*
44427509 AATAA-TCTGTACTATTTAAATGGAAGTACAGTTATTGGATCAACATCAACAGCTTCTGCGAAAG
261 AATAACT-TGTACTATTTAAATGGAAGTACAGTTATTGGATCAACATCAACAACTTCTGCGAAAG
*
44427573 ATGCAGATTCAGAGGCTACCAGGTTATGGCATATGCGATTGGGACATGCTGGTGAAAAAGCTTTG
325 ATGCAGATTCAGAGGCTACCAGGTTATGGCATAGGCGATTGGGACATGCTGGTGAAAAAGCTTTG
** * *
44427638 CAGAGTTTGGCGAAGCAAGGCTTGTTGAAAGGTGCAAATTCTTGCAAATTGGAATTCTGTGAACA
390 CAGACATTGGCGAAGCAAGGCTTATTGAAAGGTGCAAATTCTTGCAAAATGGAATTCTGTGAACA
44427703 TTGTGTTCTGGGCAAGCAGA
455 TTGTGTTCTGGGCAAGCAGA
44427723 C
1 C
44427724 GAGGATAAAA
Statistics
Matches: 454, Mismatches: 20, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
473 1 0.00
474 453 1.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (474 bp):
CTAGTCTTAAAGAACTAGAAGGTGGAATTGTTCTTATGGGCAATGATAGCGCTTATAAGACAATG
GGAGTAGGTACAATCCAATTGAAGAATCACGACGGCTCAATCCAAGTCTTGACAGATGTTCGCTA
CGTACCTAGCCTGAAGAAAAATCTCATCTCATTAGGGGCCCTAGAATCTAAAGGGCTCACAATCA
CTTTGAGAGATGGATTACTAAAGGTAGTAGCTGGGGTATTGACGGTGATGAAAGGCACAAGAAGA
AATAACTTGTACTATTTAAATGGAAGTACAGTTATTGGATCAACATCAACAACTTCTGCGAAAGA
TGCAGATTCAGAGGCTACCAGGTTATGGCATAGGCGATTGGGACATGCTGGTGAAAAAGCTTTGC
AGACATTGGCGAAGCAAGGCTTATTGAAAGGTGCAAATTCTTGCAAAATGGAATTCTGTGAACAT
TGTGTTCTGGGCAAGCAGA
Found at i:44430404 original size:15 final size:15
Alignment explanation
Indices: 44430384--44430491 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
44430374 TTTATGGAAA
44430384 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
44430399 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
44430413 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
44430429 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
44430443 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
44430459 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
44430473 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
44430489 ATC
1 ATC
44430492 GAGATATTGG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:44430421 original size:30 final size:30
Alignment explanation
Indices: 44430378--44430501 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
44430368 TCCATATTTA
* *
44430378 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
44430408 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
44430438 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
44430468 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
44430499 TGG
1 TGG
44430502 CATAATAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 80 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:44431676 original size:40 final size:40
Alignment explanation
Indices: 44431595--44431792 Score: 197
Period size: 40 Copynumber: 5.0 Consensus size: 40
44431585 GTGCATTCAA
* * * * *
44431595 GGGTACCAAAGTACAAATA-AGGCACATATGTGCATTTAG
1 GGGTACCAAAGTACAAACAGGGGCACATATGTGTAATCAG
* *
44431634 GGGTACCAAACTACAAACAGGGGCACATATGTGTAACCAG
1 GGGTACCAAAGTACAAACAGGGGCACATATGTGTAATCAG
* * *
44431674 GGGTACCGAATTACAAACATGGGTGC-C-TATGTATAATCAG
1 GGGTACCAAAGTACAAACA-GGG-GCACATATGTGTAATCAG
*
44431714 GGGTACCAAAGTACAAACAGGGGCACGTATGT-TCAATCAG
1 GGGTACCAAAGTACAAACAGGGGCACATATGTGT-AATCAG
** * * *
44431754 GGGTACTGAAGTACAAATAGGGGCACCTATGTGCAATCA
1 GGGTACCAAAGTACAAACAGGGGCACATATGTGTAATCA
44431793 TCAATAATTA
Statistics
Matches: 134, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 22 0.16
40 104 0.78
41 4 0.03
42 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.20
Consensus pattern (40 bp):
GGGTACCAAAGTACAAACAGGGGCACATATGTGTAATCAG
Found at i:44431734 original size:20 final size:20
Alignment explanation
Indices: 44431632--44431736 Score: 68
Period size: 20 Copynumber: 5.2 Consensus size: 20
44431622 ATGTGCATTT
*
44431632 AGGGGTACCAAACTACAAAC
1 AGGGGTACCAAAGTACAAAC
* * ** *
44431652 AGGGGCA-CATATGTGTAACC
1 AGGGGTACCA-AAGTACAAAC
* *
44431672 AGGGGTACCGAATTACAAAC
1 AGGGGTACCAAAGTACAAAC
* * * * * *
44431692 ATGGGTGCCTATGTATAATC
1 AGGGGTACCAAAGTACAAAC
44431712 AGGGGTACCAAAGTACAAAC
1 AGGGGTACCAAAGTACAAAC
44431732 AGGGG
1 AGGGG
44431737 CACGTATGTT
Statistics
Matches: 57, Mismatches: 26, Indels: 4
0.66 0.30 0.05
Matches are distributed among these distances:
19 2 0.04
20 54 0.95
21 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.17
Consensus pattern (20 bp):
AGGGGTACCAAAGTACAAAC
Found at i:44431792 original size:80 final size:79
Alignment explanation
Indices: 44431595--44431792 Score: 227
Period size: 80 Copynumber: 2.5 Consensus size: 79
44431585 GTGCATTCAA
* * * * *
44431595 GGGTACCAAAGTACAAATAAGGCACATATGTGCATTTAGGGGTACCAAACTACAAACAGGGGCAC
1 GGGTACCGAAGTACAAATAGGGCACCTATGTGCAATCAGGGGTACCAAACTACAAACAGGGGCAC
44431660 ATATGTGTAACCAG
66 ATATGTGTAACCAG
* * ** ** *
44431674 GGGTACCGAATTACAAACATGGGTGCCTATGTATAATCAGGGGTACCAAAGTACAAACAGGGGCA
1 GGGTACCGAAGTACAAATA-GGGCACCTATGTGCAATCAGGGGTACCAAACTACAAACAGGGGCA
* *
44431739 CGTATGT-TCAATCAG
65 CATATGTGT-AACCAG
*
44431754 GGGTACTGAAGTACAAATAGGGGCACCTATGTGCAATCA
1 GGGTACCGAAGTACAAATA-GGGCACCTATGTGCAATCA
44431793 TCAATAATTA
Statistics
Matches: 95, Mismatches: 22, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
79 17 0.18
80 78 0.82
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.20
Consensus pattern (79 bp):
GGGTACCGAAGTACAAATAGGGCACCTATGTGCAATCAGGGGTACCAAACTACAAACAGGGGCAC
ATATGTGTAACCAG
Found at i:44434145 original size:23 final size:25
Alignment explanation
Indices: 44434104--44434151 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
44434094 ATGAAATATG
44434104 TAATATAATATAAAGGAAAAGAAAT
1 TAATATAATATAAAGGAAAAGAAAT
* *
44434129 TAATA-AATA-AAATGAAATGAAAT
1 TAATATAATATAAAGGAAAAGAAAT
44434152 AAACACTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.57
24 4 0.19
25 5 0.24
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (25 bp):
TAATATAATATAAAGGAAAAGAAAT
Found at i:44438029 original size:21 final size:21
Alignment explanation
Indices: 44438004--44438044 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
44437994 TGCAGGTTGA
44438004 TGTGGCTCAACACAAGGCTGT
1 TGTGGCTCAACACAAGGCTGT
*
44438025 TGTGGCTCAATACAAGGCTG
1 TGTGGCTCAACACAAGGCTG
44438045 CATGTTGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (21 bp):
TGTGGCTCAACACAAGGCTGT
Found at i:44438480 original size:11 final size:11
Alignment explanation
Indices: 44438464--44438489 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
44438454 TTCCTTAAGC
44438464 AAACAAAATAA
1 AAACAAAATAA
44438475 AAACAAAATAA
1 AAACAAAATAA
44438486 AAAC
1 AAAC
44438490 TGAAACTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.12, G:0.00, T:0.08
Consensus pattern (11 bp):
AAACAAAATAA
Found at i:44440339 original size:17 final size:17
Alignment explanation
Indices: 44440317--44440349 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
44440307 AATGAAAAAT
*
44440317 AAAATTTAAAATCAAAC
1 AAAATTTAAAAGCAAAC
44440334 AAAATTTAAAAGCAAA
1 AAAATTTAAAAGCAAA
44440350 ATCCTTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.09, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAATTTAAAAGCAAAC
Found at i:44457176 original size:27 final size:24
Alignment explanation
Indices: 44457122--44457176 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 24
44457112 TATCTCATTG
44457122 AAATTATTGCTTTCTTTCAATTTT
1 AAATTATTGCTTTCTTTCAATTTT
44457146 -AATTATTGCTTTCTTTGCTAAGTTTT
1 AAATTATTGCTTTCTTT-C-AA-TTTT
44457172 AAATT
1 AAATT
44457177 TAATTTTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 16 0.59
24 1 0.04
25 2 0.07
26 4 0.15
27 4 0.15
ACGTcount: A:0.25, C:0.11, G:0.07, T:0.56
Consensus pattern (24 bp):
AAATTATTGCTTTCTTTCAATTTT
Found at i:44457656 original size:13 final size:13
Alignment explanation
Indices: 44457638--44457664 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
44457628 CAGCCATGGG
44457638 TACATTTTCATAA
1 TACATTTTCATAA
44457651 TACATTTTCATAA
1 TACATTTTCATAA
44457664 T
1 T
44457665 TTCCTACCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (13 bp):
TACATTTTCATAA
Found at i:44459164 original size:40 final size:40
Alignment explanation
Indices: 44459072--44459171 Score: 121
Period size: 41 Copynumber: 2.5 Consensus size: 40
44459062 GACCCCCACG
**
44459072 TATTGCTTCCCATACACATGTTTTGTTTACCTCCACGTGAA
1 TATTGCTTCCCATACATTTGTTTTGTTTACCTCCAC-TGAA
***
44459113 TATTGCTTCCCATACATTTGTTTTGTTTTTTTACCA-TGAA
1 TATTGCTTCCCATACATTTGTTTTGTTTACCT-CCACTGAA
*
44459153 TATTGCTTCCCAAACATTT
1 TATTGCTTCCCATACATTT
44459172 TTATACTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
40 22 0.42
41 27 0.52
42 3 0.06
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.45
Consensus pattern (40 bp):
TATTGCTTCCCATACATTTGTTTTGTTTACCTCCACTGAA
Found at i:44465885 original size:23 final size:23
Alignment explanation
Indices: 44465822--44465885 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
44465812 ATAGACACAT
* *
44465822 AGGTTCGCATGTAACAACATGAA
1 AGGTTCGTATGTAACAATATGAA
* *
44465845 AGGTTCGTATCTAACAATATG-T
1 AGGTTCGTATGTAACAATATGAA
44465867 AGAGTTCGTATGTAACAAT
1 AG-GTTCGTATGTAACAAT
44465886 GTTTAGGGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 2 0.06
23 33 0.94
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (23 bp):
AGGTTCGTATGTAACAATATGAA
Found at i:44465941 original size:22 final size:22
Alignment explanation
Indices: 44465916--44465967 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
44465906 ATAGGATTCG
*
44465916 CATAGTACAAATAAATGGTTCA
1 CATAGTACAAATAAAGGGTTCA
*
44465938 CATAGTACAAATAAAGGGTTCG
1 CATAGTACAAATAAAGGGTTCA
44465960 CAT-GTACA
1 CATAGTACA
44465968 TATGTATAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (22 bp):
CATAGTACAAATAAAGGGTTCA
Found at i:44468323 original size:31 final size:29
Alignment explanation
Indices: 44468275--44468340 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
44468265 TAATTATGTT
*
44468275 TTTAATTTTTACACTTTTTGGATTTTAAAAA
1 TTTAATTTTTACAC-TTTT-AATTTTAAAAA
* *
44468306 TTTAATATTTT-CTCTTTTAATTTTATAAA
1 TTTAAT-TTTTACACTTTTAATTTTAAAAA
44468335 TTTAAT
1 TTTAAT
44468341 CAGTATACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 15 0.48
30 4 0.13
31 8 0.26
32 4 0.13
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (29 bp):
TTTAATTTTTACACTTTTAATTTTAAAAA
Found at i:44468783 original size:18 final size:18
Alignment explanation
Indices: 44468748--44468783 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
44468738 AAATAATTTA
*
44468748 TTTTTTAAATTAAATAAT
1 TTTTTTAAAATAAATAAT
*
44468766 TTTTTTAAAATAACTAAT
1 TTTTTTAAAATAAATAAT
44468784 AAAAAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTTTAAAATAAATAAT
Found at i:44468905 original size:9 final size:10
Alignment explanation
Indices: 44468891--44468939 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
44468881 ACTAAAAAAA
44468891 ATTAAAAATT
1 ATTAAAAATT
* *
44468901 ATAAAAAAAT
1 ATTAAAAATT
*
44468911 ATTAATAATT
1 ATTAAAAATT
*
44468921 ATTTAAAATT
1 ATTAAAAATT
44468931 -TTAAAAATT
1 ATTAAAAATT
44468940 TGAAAAACAT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
9 8 0.26
10 23 0.74
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:44468928 original size:20 final size:20
Alignment explanation
Indices: 44468884--44468922 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
44468874 CTTCAAAACT
44468884 AAAAAAAATTAAAAATTATA
1 AAAAAAAATTAAAAATTATA
* *
44468904 AAAAAATATTAATAATTAT
1 AAAAAAAATTAAAAATTAT
44468923 TTAAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAAAAATTAAAAATTATA
Found at i:44474141 original size:23 final size:22
Alignment explanation
Indices: 44474075--44474153 Score: 110
Period size: 21 Copynumber: 3.7 Consensus size: 22
44474065 TCAATAAACA
44474075 ACACAT-AAGTGCCTGAA-ACG
1 ACACATAAAGTGCCTGAATACG
* *
44474095 ACACACAAGGTGCCT-AATACG
1 ACACATAAAGTGCCTGAATACG
44474116 ACACATAAAGTGCCTGAGATACG
1 ACACATAAAGTGCCTGA-ATACG
44474139 ACACATAAAGTGCCT
1 ACACATAAAGTGCCT
44474154 AATCGGCAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
20 7 0.14
21 23 0.45
22 1 0.02
23 20 0.39
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.16
Consensus pattern (22 bp):
ACACATAAAGTGCCTGAATACG
Found at i:44474154 original size:44 final size:41
Alignment explanation
Indices: 44474075--44474156 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
44474065 TCAATAAACA
*
44474075 ACACATAAGTGCCTGAAACGACACACAAGGTGCCTAATACG
1 ACACATAAGTGCCTGAAACGACACACAAAGTGCCTAATACG
*
44474116 ACACATAAAGTGCCTGAGATACGACACATAAAGTGCCTAAT
1 ACACAT-AAGTGCCTGA-A-ACGACACACAAAGTGCCTAAT
44474157 CGGCAAAGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 6 0.17
42 10 0.28
43 1 0.03
44 19 0.53
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.17
Consensus pattern (41 bp):
ACACATAAGTGCCTGAAACGACACACAAAGTGCCTAATACG
Found at i:44475153 original size:16 final size:16
Alignment explanation
Indices: 44475132--44475162 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44475122 ATTTTCCCTT
*
44475132 TTCTTTCTTTCTTTTC
1 TTCTTTCCTTCTTTTC
44475148 TTCTTTCCTTCTTTT
1 TTCTTTCCTTCTTTT
44475163 GCTCTCTGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TTCTTTCCTTCTTTTC
Found at i:44475370 original size:5 final size:5
Alignment explanation
Indices: 44475362--44475389 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
44475352 TTTTTACATA
44475362 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
44475390 TTTAAAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:44485775 original size:68 final size:69
Alignment explanation
Indices: 44485697--44485829 Score: 214
Period size: 69 Copynumber: 1.9 Consensus size: 69
44485687 ATATTAATAG
* *
44485697 AATATTAAATTTAATTTAATACTTATCTTGAT-AGTATTTTATTAATTTAACATTAAAGTGATTA
1 AATATTAAATTTAATCTAATACTTATCTTGATAAGTATTATATTAATTTAACATTAAAGTGATTA
44485761 TCTT
66 TCTT
* * *
44485765 AATATTAAATTTAATCTAATATTTATTTTGATAAGTATTATATTAATTTAATATTAAAGTGATTA
1 AATATTAAATTTAATCTAATACTTATCTTGATAAGTATTATATTAATTTAACATTAAAGTGATTA
44485830 AGTTTAATCA
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
68 29 0.49
69 30 0.51
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (69 bp):
AATATTAAATTTAATCTAATACTTATCTTGATAAGTATTATATTAATTTAACATTAAAGTGATTA
TCTT
Found at i:44485832 original size:32 final size:32
Alignment explanation
Indices: 44485729--44485832 Score: 75
Period size: 32 Copynumber: 3.1 Consensus size: 32
44485719 TTATCTTGAT
* *
44485729 AGTATTTTATTAATTTAACATTAAAGTGATTA
1 AGTATTATATTAATTTAATATTAAAGTGATTA
* * * ***
44485761 TCTTAATATTAAATTTAATCTAATATTTATTTTGA-TA
1 ----AGTATTATA-TTAATTTAATA-TTAAAGTGATTA
44485798 AGTATTATATTAATTTAATATTAAAGTGATTA
1 AGTATTATATTAATTTAATATTAAAGTGATTA
44485830 AGT
1 AGT
44485833 TTAATCATAG
Statistics
Matches: 51, Mismatches: 14, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
31 6 0.12
32 15 0.29
33 7 0.14
36 6 0.12
37 11 0.22
38 6 0.12
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (32 bp):
AGTATTATATTAATTTAATATTAAAGTGATTA
Found at i:44486231 original size:65 final size:65
Alignment explanation
Indices: 44486127--44486253 Score: 227
Period size: 65 Copynumber: 2.0 Consensus size: 65
44486117 CGTGTTCATC
*
44486127 CTAGACGAATCAAAAATGTACAATTTTGATTAGGTGTTTATTACTTTAGATATAACAACCAAATT
1 CTAGACGAATCAAAAAGGTACAATTTTGATTAGGTGTTTATTACTTTAGATATAACAACCAAATT
* *
44486192 CTAGACGAATCGAAAAGGTACAATTTTGATTAGGTGTTTATTACTTTAGTTATAACAACCAA
1 CTAGACGAATCAAAAAGGTACAATTTTGATTAGGTGTTTATTACTTTAGATATAACAACCAA
44486254 GTTATAGTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (65 bp):
CTAGACGAATCAAAAAGGTACAATTTTGATTAGGTGTTTATTACTTTAGATATAACAACCAAATT
Found at i:44490788 original size:18 final size:17
Alignment explanation
Indices: 44490755--44490793 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
44490745 TTGTATAAAT
44490755 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
44490773 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
44490790 TGTG
1 TGTG
44490794 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:44491033 original size:23 final size:23
Alignment explanation
Indices: 44491005--44491080 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
44490995 AGTGTTATTG
44491005 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
44491028 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
44491051 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
44491074 ATCAGTG
1 ATCAGTG
44491081 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:44495054 original size:16 final size:16
Alignment explanation
Indices: 44495030--44495060 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44495020 TTGAATATAT
44495030 ATTAAATTTATATTTA
1 ATTAAATTTATATTTA
*
44495046 ATTATATTTATATTT
1 ATTAAATTTATATTT
44495061 TTAAAATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTAAATTTATATTTA
Found at i:44497128 original size:19 final size:19
Alignment explanation
Indices: 44497106--44497168 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 19
44497096 ATTACAAAAT
44497106 AATTCAAAATATTTTTTAA
1 AATTCAAAATATTTTTTAA
* * *
44497125 AATTTAAAATATTTATAAA
1 AATTCAAAATATTTTTTAA
44497144 AATTCTAAAATTTATATTTTTAA
1 AATTC-AAAA--TAT-TTTTTAA
44497167 AA
1 AA
44497169 AATTATAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 20 0.59
20 4 0.12
22 3 0.09
23 7 0.21
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
AATTCAAAATATTTTTTAA
Found at i:44498752 original size:24 final size:25
Alignment explanation
Indices: 44498719--44498769 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
44498709 ACACTTGGCC
*
44498719 TTCCTCTTATATTTAGAA-TTTAGT
1 TTCCTCTTATATTTAAAATTTTAGT
* *
44498743 TTCCTTTTATTTTTAAAATTTTAGT
1 TTCCTCTTATATTTAAAATTTTAGT
44498768 TT
1 TT
44498770 TATATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.61
Consensus pattern (25 bp):
TTCCTCTTATATTTAAAATTTTAGT
Found at i:44499701 original size:13 final size:13
Alignment explanation
Indices: 44499683--44499707 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44499673 TATTTTAATA
44499683 TTATTTTGTGTGT
1 TTATTTTGTGTGT
44499696 TTATTTTGTGTG
1 TTATTTTGTGTG
44499708 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:44501168 original size:75 final size:75
Alignment explanation
Indices: 44501034--44501175 Score: 169
Period size: 75 Copynumber: 1.9 Consensus size: 75
44501024 TGCAAATCTA
* * ** * *
44501034 CATGTATATGTTCTTGTATTAAATTTAGGTATGCCATTTATACAAGTTTATATGGGGTTCGACTA
1 CATGTATATGTTCTTGTAATAAATTTAAGTATGAAATTTATACAAGTATATAGGGGGTTCGACTA
44501099 TGCAATTATG
66 TGCAATTATG
* * * * *
44501109 CATGTATATGTTCTTGTAATGAGTTTAAGTATGAAATTTATATATGTATA-AGGGAGGTTCGATT
1 CATGTATATGTTCTTGTAATAAATTTAAGTATGAAATTTATACAAGTATATAGGG-GGTTCGACT
44501173 ATG
65 ATG
44501176 TATGTATGTT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
74 3 0.05
75 52 0.95
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (75 bp):
CATGTATATGTTCTTGTAATAAATTTAAGTATGAAATTTATACAAGTATATAGGGGGTTCGACTA
TGCAATTATG
Found at i:44501553 original size:41 final size:42
Alignment explanation
Indices: 44501491--44501602 Score: 158
Period size: 41 Copynumber: 2.7 Consensus size: 42
44501481 ATTGTCAGTG
*
44501491 ACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGA-
1 ACAT-ATTCAGACTATACGTCTAGCAGGCTTAATGCCGGTGAT
44501533 A-ATTATTCAGACTATACGTCTAGCAGGCTTAATGCCGGTGAT
1 ACA-TATTCAGACTATACGTCTAGCAGGCTTAATGCCGGTGAT
* *
44501575 ACAT-TTCGGACTATAAGTCTAGCAGGCT
1 ACATATTCAGACTATACGTCTAGCAGGCT
44501603 CAAGAGCTGG
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
41 59 0.92
42 4 0.06
43 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (42 bp):
ACATATTCAGACTATACGTCTAGCAGGCTTAATGCCGGTGAT
Found at i:44501862 original size:33 final size:33
Alignment explanation
Indices: 44501820--44501980 Score: 173
Period size: 33 Copynumber: 4.6 Consensus size: 33
44501810 ATAGATAAAT
*
44501820 ATATATGTATGCATTCGGCATAGGTGGATATAA
1 ATATATGTATGCATTCGGCATAGGTGAATATAA
*
44501853 ATATATGTATGCATTCGGCATAGGTGGATAT--
1 ATATATGTATGCATTCGGCATAGGTGAATATAA
*
44501884 ATATATGTATGCATTCGGCATAGGTGAAAATAAGGGTAT
1 ATATATGTATGCATTCGGCATAGGTG--AAT-A---TAA
* *
44501923 ATATATGTATGCATTTGGCATAGGTGAAAATAA
1 ATATATGTATGCATTCGGCATAGGTGAATATAA
44501956 GTGTATATATGTATGCATTCGGCAT
1 ----ATATATGTATGCATTCGGCAT
44501981 TTATGGTTGA
Statistics
Matches: 111, Mismatches: 5, Indels: 20
0.82 0.04 0.15
Matches are distributed among these distances:
31 26 0.23
33 35 0.32
34 1 0.01
36 1 0.01
37 23 0.21
39 25 0.23
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.34
Consensus pattern (33 bp):
ATATATGTATGCATTCGGCATAGGTGAATATAA
Found at i:44501935 original size:39 final size:37
Alignment explanation
Indices: 44501818--44501980 Score: 193
Period size: 39 Copynumber: 4.6 Consensus size: 37
44501808 TGATAGATAA
*
44501818 ATATATATGTATGCATTCGGCATAGGTG--GAT-A-T
1 ATATATATGTATGCATTCGGCATAGGTGAAAATAAGT
* *
44501851 AAATATATGTATGCATTCGGCATAGGTG-----GA-T
1 ATATATATGTATGCATTCGGCATAGGTGAAAATAAGT
44501882 ATATATATGTATGCATTCGGCATAGGTGAAAATAAGGGT
1 ATATATATGTATGCATTCGGCATAGGTGAAAATAA--GT
*
44501921 ATATATATGTATGCATTTGGCATAGGTGAAAATAAGT
1 ATATATATGTATGCATTCGGCATAGGTGAAAATAAGT
*
44501958 GTATATATGTATGCATTCGGCAT
1 ATATATATGTATGCATTCGGCAT
44501981 TTATGGTTGA
Statistics
Matches: 115, Mismatches: 6, Indels: 14
0.85 0.04 0.10
Matches are distributed among these distances:
31 29 0.25
33 27 0.23
36 1 0.01
37 23 0.20
39 35 0.30
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.34
Consensus pattern (37 bp):
ATATATATGTATGCATTCGGCATAGGTGAAAATAAGT
Found at i:44507370 original size:13 final size:13
Alignment explanation
Indices: 44507352--44507376 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44507342 TATTTTAATA
44507352 TTATTTTGTGTGT
1 TTATTTTGTGTGT
44507365 TTATTTTGTGTG
1 TTATTTTGTGTG
44507377 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:44509226 original size:41 final size:42
Alignment explanation
Indices: 44509164--44509275 Score: 149
Period size: 41 Copynumber: 2.7 Consensus size: 42
44509154 ATTGTCAGTG
*
44509164 ACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCAGGTGA-
1 ACAT-ATTCAGACTATACGTCTAGCAGGCTTAATGCAGGTGAT
*
44509206 A-ATTATTCAGACTATACGTCTAGCAGGCTTAATGCCGGTGAT
1 ACA-TATTCAGACTATACGTCTAGCAGGCTTAATGCAGGTGAT
* *
44509248 ACAT-TTCGGACTATAAGTCTAGCAGGCT
1 ACATATTCAGACTATACGTCTAGCAGGCT
44509276 CAAGAGCTGG
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
41 58 0.92
42 4 0.06
43 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (42 bp):
ACATATTCAGACTATACGTCTAGCAGGCTTAATGCAGGTGAT
Found at i:44509535 original size:33 final size:33
Alignment explanation
Indices: 44509493--44509653 Score: 182
Period size: 33 Copynumber: 4.6 Consensus size: 33
44509483 ATAGATAAAT
*
44509493 ATATATGTATGCATTCGGCATAGGTGGATATAA
1 ATATATGTATGCATTCGGCATAGGTGAATATAA
*
44509526 ATATATGTATGCATTCGGCATAGGTGGATAT--
1 ATATATGTATGCATTCGGCATAGGTGAATATAA
*
44509557 ATATATGTATGCATTCGGCATAGGTGAAAATAAGGGTAT
1 ATATATGTATGCATTCGGCATAGGTG--AAT-A---TAA
*
44509596 ATATATGTATGCATTCGGCATAGGTGAAAATAA
1 ATATATGTATGCATTCGGCATAGGTGAATATAA
44509629 GTGTATATATGTATGCATTCGGCAT
1 ----ATATATGTATGCATTCGGCAT
44509654 TTATGGTTGA
Statistics
Matches: 113, Mismatches: 3, Indels: 20
0.83 0.02 0.15
Matches are distributed among these distances:
31 26 0.23
33 35 0.31
34 1 0.01
36 1 0.01
37 24 0.21
39 26 0.23
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.34
Consensus pattern (33 bp):
ATATATGTATGCATTCGGCATAGGTGAATATAA
Found at i:44509608 original size:39 final size:37
Alignment explanation
Indices: 44509491--44509653 Score: 202
Period size: 39 Copynumber: 4.6 Consensus size: 37
44509481 TGATAGATAA
*
44509491 ATATATATGTATGCATTCGGCATAGGTG--GAT-A-T
1 ATATATATGTATGCATTCGGCATAGGTGAAAATAAGT
* *
44509524 AAATATATGTATGCATTCGGCATAGGTG-----GA-T
1 ATATATATGTATGCATTCGGCATAGGTGAAAATAAGT
44509555 ATATATATGTATGCATTCGGCATAGGTGAAAATAAGGGT
1 ATATATATGTATGCATTCGGCATAGGTGAAAATAA--GT
44509594 ATATATATGTATGCATTCGGCATAGGTGAAAATAAGT
1 ATATATATGTATGCATTCGGCATAGGTGAAAATAAGT
*
44509631 GTATATATGTATGCATTCGGCAT
1 ATATATATGTATGCATTCGGCAT
44509654 TTATGGTTGA
Statistics
Matches: 117, Mismatches: 4, Indels: 14
0.87 0.03 0.10
Matches are distributed among these distances:
31 29 0.25
33 27 0.23
36 1 0.01
37 24 0.21
39 36 0.31
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.34
Consensus pattern (37 bp):
ATATATATGTATGCATTCGGCATAGGTGAAAATAAGT
Found at i:44515001 original size:138 final size:138
Alignment explanation
Indices: 44514833--44515112 Score: 438
Period size: 138 Copynumber: 2.0 Consensus size: 138
44514823 ATATAGATAA
* * *
44514833 AATTAATATATGAATTTGATTTATATAAAATATTAATTGTATATATTTTA-CGAAATTTATTAAT
1 AATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACCG-AATTTATTAAT
*
44514897 ATAAACAATTATATTGATTAATTTCAATCAAAATATAAAAGACATAAAAATTAATATTCTTTT-A
65 ATAAACAATTATATTAATTAATTTCAATCAAAATATAAAAGACATAAAAATTAATATTCTTTTGA
44514961 GAAATAATAT
130 -AAATAATAT
44514971 AATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
1 AATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
* *** * *
44515036 TAAACAGTTATATTAATTAATTTTGGTCAAAATATAAAAGACATGAGAATTAATATTCTTTTGAA
66 TAAACAATTATATTAATTAATTTCAATCAAAATATAAAAGACATAAAAATTAATATTCTTTTGAA
44515101 AATAATAT
131 AATAATAT
44515109 AATT
1 AATT
44515113 CCTTTTTACT
Statistics
Matches: 130, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
138 127 0.98
139 3 0.02
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (138 bp):
AATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
TAAACAATTATATTAATTAATTTCAATCAAAATATAAAAGACATAAAAATTAATATTCTTTTGAA
AATAATAT
Found at i:44517085 original size:27 final size:27
Alignment explanation
Indices: 44517055--44517117 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
44517045 TCAGGTAGGT
44517055 GCCAATGAAGGTGCCTCACAGAGAGAC
1 GCCAATGAAGGTGCCTCACAGAGAGAC
* *
44517082 GCCAATGAAGGTGCCTCATAGAGAGGC
1 GCCAATGAAGGTGCCTCACAGAGAGAC
44517109 GCCAATGAA
1 GCCAATGAA
44517118 TATTGTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.33, C:0.24, G:0.30, T:0.13
Consensus pattern (27 bp):
GCCAATGAAGGTGCCTCACAGAGAGAC
Found at i:44517140 original size:19 final size:19
Alignment explanation
Indices: 44517116--44517246 Score: 81
Period size: 19 Copynumber: 6.6 Consensus size: 19
44517106 GGCGCCAATG
44517116 AATATTGTAATTTTGTATT
1 AATATTGTAATTTTGTATT
*
44517135 AATATTGTAATTAT-T-TT
1 AATATTGTAATTTTGTATT
* *
44517152 -ATAAT-TAAATTTGTATTT
1 AATATTGTAATTTTGTA-TT
* *
44517170 ATAGTTTTGGATTAGTATTTTGTATG
1 A-A-TATT-G--TA--ATTTTGTATT
*
44517196 AATATTGTAATTTTTTATAT
1 AATATTGTAATTTTGTAT-T
*
44517216 GAATATTGTAATTTTGTATG
1 -AATATTGTAATTTTGTATT
44517236 AATATTGTAAT
1 AATATTGTAAT
44517247 ATTATAATTT
Statistics
Matches: 85, Mismatches: 13, Indels: 28
0.67 0.10 0.22
Matches are distributed among these distances:
15 5 0.06
16 5 0.06
17 2 0.02
18 3 0.04
19 32 0.38
20 1 0.01
21 21 0.25
23 1 0.01
24 3 0.04
25 3 0.04
26 2 0.02
27 7 0.08
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (19 bp):
AATATTGTAATTTTGTATT
Found at i:44517216 original size:21 final size:20
Alignment explanation
Indices: 44517187--44517246 Score: 95
Period size: 19 Copynumber: 3.0 Consensus size: 20
44517177 TGGATTAGTA
44517187 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAA-T
*
44517208 TTTTATATGAATATTGTAA-
1 TTTTGTATGAATATTGTAAT
44517227 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
44517247 ATTATAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 18 0.50
21 18 0.50
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (20 bp):
TTTTGTATGAATATTGTAAT
Found at i:44517498 original size:21 final size:21
Alignment explanation
Indices: 44517467--44517515 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
44517457 CTAATTAATA
44517467 ATAATAAAATTACAATATTCAT
1 ATAA-AAAATTACAATATTCAT
44517489 ATAAAAAATTACAATATTCAT
1 ATAAAAAATTACAATATTCAT
*
44517510 ACAAAA
1 ATAAAA
44517516 TACTAATCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAAAAAATTACAATATTCAT
Found at i:44517568 original size:19 final size:19
Alignment explanation
Indices: 44517549--44517586 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
44517539 AAATTTAATT
44517549 ATAAAATAATTACAATATTA
1 ATAAAA-AATTACAATATTA
*
44517569 ATACAAAATTACAATATT
1 ATAAAAAATTACAATATT
44517587 CATTGGCGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAAAAATTACAATATTA
Found at i:44517623 original size:27 final size:27
Alignment explanation
Indices: 44517585--44517651 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
44517575 AATTACAATA
*
44517585 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATAAGGCACC
* *
44517612 TTCATTAGCGCCTCTCTGTAAGGCACC
1 TTCATTGGCGCCTCTCTATAAGGCACC
44517639 TTCATTGGCGCCT
1 TTCATTGGCGCCT
44517652 ACCTGATAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.15, C:0.33, G:0.21, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATAAGGCACC
Found at i:44517662 original size:27 final size:28
Alignment explanation
Indices: 44517585--44517659 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
44517575 AATTACAATA
*
44517585 TTCATTGGCGCCTCTCT-ATGAGGCACC
1 TTCATTGGCGCCTCTCTGATAAGGCACC
*
44517612 TTCATTAGCGCCTCTCTG-TAAGGCACC
1 TTCATTGGCGCCTCTCTGATAAGGCACC
44517639 TTCATTGGCGCCTAC-CTGATA
1 TTCATTGGCGCCT-CTCTGATA
44517660 GGCGCCACCC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 39 0.93
28 3 0.07
ACGTcount: A:0.17, C:0.32, G:0.20, T:0.31
Consensus pattern (28 bp):
TTCATTGGCGCCTCTCTGATAAGGCACC
Found at i:44517728 original size:13 final size:13
Alignment explanation
Indices: 44517712--44517765 Score: 60
Period size: 12 Copynumber: 4.2 Consensus size: 13
44517702 TCGTATTTTT
44517712 TTAAAAAAAATTA
1 TTAAAAAAAATTA
44517725 TT-AAAAAAA-TA
1 TTAAAAAAAATTA
*
44517736 -TAAAAAATATTTTA
1 TTAAAAAA-A-ATTA
44517750 TTAAAAAAAATTA
1 TTAAAAAAAATTA
44517763 TTA
1 TTA
44517766 TTTTTTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
10 1 0.03
11 7 0.21
12 8 0.24
13 8 0.24
14 3 0.09
15 7 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TTAAAAAAAATTA
Found at i:44519985 original size:23 final size:24
Alignment explanation
Indices: 44519959--44520009 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
44519949 TTATTTATTT
*
44519959 GCTTGGGCGGTGCTCAG-TTATCC
1 GCTTGGACGGTGCTCAGTTTATCC
* *
44519982 GCTTTGACGGTGGTCAGTTTATCC
1 GCTTGGACGGTGCTCAGTTTATCC
44520006 GCTT
1 GCTT
44520010 CAGCGGTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.10, C:0.24, G:0.31, T:0.35
Consensus pattern (24 bp):
GCTTGGACGGTGCTCAGTTTATCC
Found at i:44520016 original size:24 final size:22
Alignment explanation
Indices: 44519965--44520017 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
44519955 ATTTGCTTGG
*
44519965 GCGGTGCTCAGTTATCCGCTTT
1 GCGGTGCTCAGTTATCCGCTTA
*
44519987 GACGGTGGTCAGTTTATCCGCTTCA
1 G-CGGTGCTCAG-TTATCCGCTT-A
44520012 GCGGTG
1 GCGGTG
44520018 TTTATTCGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 1 0.04
23 9 0.35
24 15 0.58
25 1 0.04
ACGTcount: A:0.11, C:0.25, G:0.32, T:0.32
Consensus pattern (22 bp):
GCGGTGCTCAGTTATCCGCTTA
Found at i:44526763 original size:23 final size:23
Alignment explanation
Indices: 44526737--44526783 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
44526727 AGAGAAAATC
* *
44526737 ATACACTATGAAGGATGTGTCTA
1 ATACAATATGAAAGATGTGTCTA
44526760 ATACAATATGAAAGATGTGTCTA
1 ATACAATATGAAAGATGTGTCTA
44526783 A
1 A
44526784 CATGTGCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (23 bp):
ATACAATATGAAAGATGTGTCTA
Found at i:44552901 original size:3 final size:3
Alignment explanation
Indices: 44552895--44553029 Score: 71
Period size: 3 Copynumber: 45.0 Consensus size: 3
44552885 TTTTATTCAT
* * *
44552895 TTA TTA TTA -TA TTG TTT TTA CTT- TTA TTA TTA TTTA TTA TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA
* * ** * * * *
44552940 TTA TTA ATA TTA TTT TTA TTA TTA ACA TTA GTA TTC TTA GTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * *
44552988 GGA TTA CTA TTA TT- TTA CTGTA TT- TTA TTA TTC TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -T-TA TTA TTA TTA TTA TTA TTA TTA
44553030 GTTTATTAGT
Statistics
Matches: 95, Mismatches: 29, Indels: 16
0.68 0.21 0.11
Matches are distributed among these distances:
2 8 0.08
3 78 0.82
4 7 0.07
5 2 0.02
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:44560389 original size:17 final size:17
Alignment explanation
Indices: 44560367--44560422 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
44560357 ACTCAAGAAT
44560367 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
44560384 CATATCATATCTAAGATTA
1 CATATC-T-TCTAAGATTA
**
44560403 CATATCTTAGAAGATTA
1 CATATCTTCTAAGATTA
44560420 CAT
1 CAT
44560423 TCCATATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 17 0.49
18 2 0.06
19 16 0.46
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:44563256 original size:19 final size:17
Alignment explanation
Indices: 44563229--44563288 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
44563219 TTTAGAAATT
*
44563229 ATATATTTAGAATATAGAA
1 ATATATTTA-AAAATA-AA
*
44563248 ATATGTTTAAAAATAAA
1 ATATATTTAAAAATAAA
*
44563265 ATATA-ATAAATAATAAA
1 ATATATTTAAA-AATAAA
*
44563282 ACATATT
1 ATATATT
44563289 AGTTGAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
16 4 0.12
17 16 0.48
18 5 0.15
19 8 0.24
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (17 bp):
ATATATTTAAAAATAAA
Found at i:44563766 original size:308 final size:305
Alignment explanation
Indices: 44563246--44563964 Score: 719
Period size: 308 Copynumber: 2.4 Consensus size: 305
44563236 TAGAATATAG
* * * * *
44563246 AAATATGT-TTAAAAATAAAATATAATAAATAATAAAACATATTAGTTGAAATAATTAACAATAA
1 AAATATGTGTTAAAAATAAAATACAATAAATAATGAAACTTA-TGGTTGAAATAATTAATAATAA
* **
44563310 CACATGAAATATGTACGTTACTAAAAT----AAAAT--ATTAAATTGTGAGTAAAACAAAATTTA
65 CACATGAAATATGTATGTTGTTAAAATAAAAAAAATAGATTAAATTGTGAGTAAAACAAAATTTA
* ** * * * * * ** * *
44563369 AAAATATAAATACGTTAGATTTAGAATACTTAATGAATATAATTGTTTATCATGGTGTTGTCATC
130 AAAACATAAATAAATCAAATTAAAAATACTTAATGAATACAATCATTGATCAAGGTGTTGTCATC
* * * * * *
44563434 AATCCTTAGTTTGTTTTAAGTTAATTTAGTGACACCAACTCAATCAACAGCATTATTTATA-AGA
195 AATCCTGAGTTTGTGTCAAGTTAATTCA-TGACACCAACTCAATCAACAACATTATTAATACAGA
** * * ** * *
44563498 ATA-TCTATCAA-TTGTGTATATGTGTGGAAACCACATATTTAGAACAC
259 A-ACTCTAT-AACACGCGTAGACATATGAAAACCACATATTTAGAACAC
*
44563545 AAATATGTGTTAAAAATAAAATACAATAAATAATGAAACTTATGGTCTAAAACTAATTAATAATA
1 AAATATGTGTTAAAAATAAAATACAATAAATAATGAAACTTATGGT-TGAAA-TAATTAATAATA
* * *
44563610 GCACATGAAATATGTATGTTGTTAAAATGAAAAAAAATAGATTAAATTGTGAGTAAAACGAATTT
64 ACACATGAAATATGTATGTTGTTAAAAT-AAAAAAAATAGATTAAATTGTGAGTAAAACAAAATT
**
44563675 TAAGCACATAAATAAATCAAATTAAAAATA-TTAAATGAATACAATCATTGATCAAGGTGTTGTC
128 TAAAAACATAAATAAATCAAATTAAAAATACTT-AATGAATACAATCATTGATCAAGGTGTTGTC
* * * * *
44563739 ATCAA-CCATGA-TTTGGTGTCGAGTTAATTCATGATACCAATTCAATTAACAATATTATTAATA
192 ATCAATCC-TGAGTTT-GTGTCAAGTTAATTCATGACACCAACTCAATCAACAACATTATTAATA
* ** ***
44563802 CTAGAAACTCTATAACACGCGTAGGCATATGAAAACCATGTATTTAGAATGT
255 C-AGAAACTCTATAACACGCGTAGACATATGAAAACCACATATTTAGAACAC
* *
44563854 AAATTTGTGTTTAAAAATAACATACAATAAATAATGAAA-TGTATGGTTTGAAATTAATTAATAA
1 AAATATGTG-TTAAAAATAAAATACAATAAATAATGAAACT-TATGG-TTGAAA-TAATTAATAA
*
44563918 TAACACATGAAATATGTATGGTGTTAAAATAAAAAAAATAGATTAAA
62 TAACACATGAAATATGTATGTTGTTAAAATAAAAAAAATAGATTAAA
44563965 ATGCGCATAA
Statistics
Matches: 343, Mismatches: 57, Indels: 30
0.80 0.13 0.07
Matches are distributed among these distances:
299 11 0.03
300 34 0.10
301 35 0.10
306 5 0.01
307 33 0.10
308 92 0.27
309 57 0.17
310 75 0.22
311 1 0.00
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (305 bp):
AAATATGTGTTAAAAATAAAATACAATAAATAATGAAACTTATGGTTGAAATAATTAATAATAAC
ACATGAAATATGTATGTTGTTAAAATAAAAAAAATAGATTAAATTGTGAGTAAAACAAAATTTAA
AAACATAAATAAATCAAATTAAAAATACTTAATGAATACAATCATTGATCAAGGTGTTGTCATCA
ATCCTGAGTTTGTGTCAAGTTAATTCATGACACCAACTCAATCAACAACATTATTAATACAGAAA
CTCTATAACACGCGTAGACATATGAAAACCACATATTTAGAACAC
Found at i:44576728 original size:41 final size:41
Alignment explanation
Indices: 44576671--44576753 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
44576661 GTCTGCCTAG
44576671 CCTCATTCTGATTAGCACCTCTGCCTAATGCTCTCTAACCC
1 CCTCATTCTGATTAGCACCTCTGCCTAATGCTCTCTAACCC
* *
44576712 CCTCATTCTGATTAGCACCTCTGCCTGATGCTCTCTGACCC
1 CCTCATTCTGATTAGCACCTCTGCCTAATGCTCTCTAACCC
44576753 C
1 C
44576754 TACCCGTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.17, C:0.40, G:0.12, T:0.31
Consensus pattern (41 bp):
CCTCATTCTGATTAGCACCTCTGCCTAATGCTCTCTAACCC
Found at i:44581603 original size:29 final size:27
Alignment explanation
Indices: 44581571--44581638 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 27
44581561 TAAATTTCAA
*
44581571 AATTATATATGAACTTTAATTTAATGTAT
1 AATTATACATGAACTTTAATTT-A-GTAT
*
44581600 AATTTAATACATGAATTTTAATTTAGTAT
1 AA-TT-ATACATGAACTTTAATTTAGTAT
44581629 AATTATACAT
1 AATTATACAT
44581639 ATAAAACTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 6 0.17
28 2 0.06
29 8 0.23
30 3 0.09
31 16 0.46
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (27 bp):
AATTATACATGAACTTTAATTTAGTAT
Found at i:44587829 original size:18 final size:18
Alignment explanation
Indices: 44587806--44587843 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
44587796 CGCCGTAGAC
*
44587806 TGCCTTTAGCTTACTTTT
1 TGCCTTTACCTTACTTTT
44587824 TGCCTTTACCTTACTTTT
1 TGCCTTTACCTTACTTTT
44587842 TG
1 TG
44587844 TCTCGCCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.24, G:0.11, T:0.55
Consensus pattern (18 bp):
TGCCTTTACCTTACTTTT
Found at i:44590472 original size:2 final size:2
Alignment explanation
Indices: 44590465--44590490 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44590455 ATTCCTGCAG
44590465 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
44590491 TCTTTTTAGG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:44599356 original size:29 final size:30
Alignment explanation
Indices: 44599323--44599432 Score: 111
Period size: 30 Copynumber: 3.7 Consensus size: 30
44599313 TTTTTAAAAA
*
44599323 AAATTGTATTTTGACTCCT-AACTTTTATG
1 AAATTATATTTTGACTCCTAAACTTTTATG
* *
44599352 AAATTATATTTT-AATCCCTAAACTTTTTTG
1 AAATTATATTTTGACT-CCTAAACTTTTATG
* * * *
44599382 AAATTATATTTTAACTCTTGAACTTTTCT-
1 AAATTATATTTTGACTCCTAAACTTTTATG
44599411 AGAATTATATTTTGACT-CTAAA
1 A-AATTATATTTTGACTCCTAAA
44599433 ATTTCGCAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
28 2 0.03
29 18 0.27
30 45 0.67
31 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (30 bp):
AAATTATATTTTGACTCCTAAACTTTTATG
Found at i:44599871 original size:6 final size:6
Alignment explanation
Indices: 44599820--44599871 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
44599810 AATCGCAAGC
* * *
44599820 AAAAGA AAAA-A AAAAGA GAAAGA AAAAGA GGAAAGA AGAA-A AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA -AAAAGA AAAAGA AAAAGA
44599867 AAAAG
1 AAAAG
44599872 GGGGAAAGGG
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 9 0.24
6 23 0.62
7 5 0.14
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:44599871 original size:17 final size:17
Alignment explanation
Indices: 44599822--44599871 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
44599812 TCGCAAGCAA
*
44599822 AAGAAAAAAA-AAAGAG
1 AAGAAAAAAAGAAAAAG
* *
44599838 AA-AGAAAAAGAGGAAAG
1 AAGAAAAAAAGA-AAAAG
44599855 AAGAAAAAAAGAAAAAG
1 AAGAAAAAAAGAAAAAG
44599872 GGGGAAAGGG
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
15 6 0.23
16 3 0.12
17 9 0.35
18 8 0.31
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAGAAAAAG
Found at i:44600273 original size:14 final size:15
Alignment explanation
Indices: 44600250--44600354 Score: 58
Period size: 14 Copynumber: 7.1 Consensus size: 15
44600240 CCAGCCCAGC
44600250 AGAGAAGAAAAAA-A
1 AGAGAAGAAAAAAGA
*
44600264 AGAGAGGAAAAAAGA
1 AGAGAAGAAAAAAGA
* *
44600279 AGAAAAAACAAAAAGA
1 AGAGAAGA-AAAAAGA
* * * *
44600295 AAACAAAAAGAAAACA
1 AGAGAAGAA-AAAAGA
44600311 A-A-AAGAAAAAAGA
1 AGAGAAGAAAAAAGA
* * *
44600324 AAAAAAGGAAAAA-A
1 AGAGAAGAAAAAAGA
44600338 A-AGAAGAAAAAAAGA
1 AGAGAAG-AAAAAAGA
44600353 AG
1 AG
44600355 GGAAAAAAGG
Statistics
Matches: 71, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
13 10 0.14
14 24 0.34
15 18 0.25
16 19 0.27
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (15 bp):
AGAGAAGAAAAAAGA
Found at i:44600276 original size:12 final size:10
Alignment explanation
Indices: 44600254--44600354 Score: 74
Period size: 9 Copynumber: 10.6 Consensus size: 10
44600244 CCCAGCAGAG
44600254 AAGAA-AAAA
1 AAGAAGAAAA
44600263 AAGAGAGGAAAA
1 AAGA-A-GAAAA
44600275 AAGAAGAAAA
1 AAGAAGAAAA
* *
44600285 AACAA-AAAG
1 AAGAAGAAAA
*
44600294 AA-AA-CAAA
1 AAGAAGAAAA
*
44600302 AAGAA-AACA
1 AAGAAGAAAA
44600311 AA-AAGAAAA
1 AAGAAGAAAA
44600320 AAGAA-AAAA
1 AAGAAGAAAA
*
44600329 AGGAA-AAAA
1 AAGAAGAAAA
44600338 AAGAAGAAAAA
1 AAGAAG-AAAA
44600349 AAGAAG
1 AAGAAG
44600355 GGAAAAAAGG
Statistics
Matches: 75, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
8 8 0.11
9 36 0.48
10 12 0.16
11 11 0.15
12 8 0.11
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (10 bp):
AAGAAGAAAA
Found at i:44600283 original size:24 final size:23
Alignment explanation
Indices: 44600252--44600363 Score: 84
Period size: 24 Copynumber: 4.6 Consensus size: 23
44600242 AGCCCAGCAG
*
44600252 AGAAGAAAAAAAAGAGAGGAAAAA
1 AGAAGAAAAAAAAGA-AAGAAAAA
44600276 AGAAGAAAAAACAA-AAAGAAAACA
1 AGAAGAAAAAA-AAGAAAGAAAA-A
* *
44600300 AAAAGAAAACAAAAAGAAAAAAGAAA
1 AGAAG-AAA-AAAAAGAAAGAA-AAA
*
44600326 AAAAGGAAAAAAAAG-AAGAAAAAA
1 AGAA-GAAAAAAAAGAAAG-AAAAA
**
44600350 AGAAGGGAAAAAAG
1 AGAAGAAAAAAAAG
44600364 GGGTTCAATT
Statistics
Matches: 73, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
23 14 0.19
24 25 0.34
25 15 0.21
26 16 0.22
27 3 0.04
ACGTcount: A:0.79, C:0.03, G:0.19, T:0.00
Consensus pattern (23 bp):
AGAAGAAAAAAAAGAAAGAAAAA
Found at i:44600297 original size:22 final size:21
Alignment explanation
Indices: 44600272--44600349 Score: 74
Period size: 21 Copynumber: 3.7 Consensus size: 21
44600262 AAAGAGAGGA
44600272 AAAAAGAAGAAAAAACAAAAAG
1 AAAAA-AAGAAAAAACAAAAAG
44600294 AAAACAAA-AAGAAAACAAAAAG
1 AAAA-AAAGAA-AAAACAAAAAG
44600316 -AAAAAAGAAAAAA-AGGAAAA-
1 AAAAAAAGAAAAAACA--AAAAG
*
44600336 AAAAGAAGAAAAAA
1 AAAAAAAGAAAAAA
44600350 AGAAGGGAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 13
0.78 0.02 0.21
Matches are distributed among these distances:
19 1 0.02
20 7 0.14
21 23 0.47
22 17 0.35
23 1 0.02
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (21 bp):
AAAAAAAGAAAAAACAAAAAG
Found at i:44600303 original size:29 final size:29
Alignment explanation
Indices: 44600272--44600349 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 29
44600262 AAAGAGAGGA
* *
44600272 AAAAAGAAGA-AAAAA-CAAAAAGAAAAC
1 AAAAAGAAAACAAAAAGAAAAAAGAAAAC
44600299 AAAAAGAAAACAAAAAGAAAAAAG-AAA-
1 AAAAAGAAAACAAAAAGAAAAAAGAAAAC
* *
44600326 AAAAGGAAAAAAAAGAAGAAAAAA
1 AAAAAGAAAACAAA-AAGAAAAAA
44600350 AGAAGGGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
27 21 0.48
28 17 0.39
29 6 0.14
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (29 bp):
AAAAAGAAAACAAAAAGAAAAAAGAAAAC
Found at i:44600350 original size:29 final size:30
Alignment explanation
Indices: 44600268--44600353 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 30
44600258 AAAAAAAGAG
*
44600268 AGGAAAAAAGAAGAAAAAACAAAAAGAAAACAAA
1 AGGAAAAAA-AAG-AAGAA-AAAAAG-AAACAAA
* *
44600302 AAGAAAACAAA-AAG-AAAAAAGAAA-AAA
1 AGGAAAAAAAAGAAGAAAAAAAGAAACAAA
44600329 AGGAAAAAAAAGAAGAAAAAAAGAA
1 AGGAAAAAAAAGAAGAAAAAAAGAA
44600354 GGGAAAAAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
27 12 0.27
28 6 0.13
29 15 0.33
30 1 0.02
31 2 0.04
33 2 0.04
34 7 0.16
ACGTcount: A:0.81, C:0.03, G:0.15, T:0.00
Consensus pattern (30 bp):
AGGAAAAAAAAGAAGAAAAAAAGAAACAAA
Found at i:44600359 original size:13 final size:13
Alignment explanation
Indices: 44600323--44600362 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
44600313 AAGAAAAAAG
*
44600323 AAAAA-AAGGAAA
1 AAAAAGAAGGGAA
44600335 AAAAAGAA--GAA
1 AAAAAGAAGGGAA
44600346 AAAAAGAAGGGAA
1 AAAAAGAAGGGAA
44600359 AAAA
1 AAAA
44600363 GGGGTTCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
11 10 0.42
12 5 0.21
13 9 0.38
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAGAAGGGAA
Found at i:44600363 original size:12 final size:11
Alignment explanation
Indices: 44600252--44600354 Score: 76
Period size: 11 Copynumber: 9.5 Consensus size: 11
44600242 AGCCCAGCAG
44600252 AGAAGAAAAAAA
1 AGAAG-AAAAAA
*
44600264 AGAGAGGAAAAA
1 AGA-AGAAAAAA
44600276 AGAAGAAAAAACA
1 AGAAG-AAAAA-A
*
44600289 AAAAGAAAACAA
1 AGAAGAAAA-AA
44600301 A-AAGAAAACAA
1 AGAAGAAAA-AA
44600312 A-AAG---AAA
1 AGAAGAAAAAA
44600319 A-AAGAAAAAA
1 AGAAGAAAAAA
*
44600329 AGGA-AAAAAA
1 AGAAGAAAAAA
44600339 AGAAGAAAAAA
1 AGAAGAAAAAA
44600350 AGAAG
1 AGAAG
44600355 GGAAAAAAGG
Statistics
Matches: 77, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
7 6 0.08
8 1 0.01
10 13 0.17
11 28 0.36
12 21 0.27
13 8 0.10
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (11 bp):
AGAAGAAAAAA
Found at i:44600541 original size:16 final size:16
Alignment explanation
Indices: 44600515--44600561 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
44600505 TTTTTGTATT
*
44600515 TATATTTTTAATTTAA
1 TATAATTTTAATTTAA
44600531 T-TCAATTTTAATTTAA
1 TAT-AATTTTAATTTAA
*
44600547 TATAATTTTATTTTA
1 TATAATTTTAATTTA
44600562 TTTTAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 25 0.93
17 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAATTTTAATTTAA
Done.