Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 190 of 259
Found at i:60938737 original size:30 final size:28
Alignment explanation
Indices: 60938675--60938738 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
60938665 TAGTATTTAC
* *
60938675 AATTTTTTTCAATTTAGTCCCGTCTTAC
1 AATTTTTTTCAATTTAGTCCCATCTTAA
*
60938703 AATTTTTTTCAATTTAGTCCTATCTCTAA
1 AATTTTTTTCAATTTAGTCCCATCT-TAA
*
60938732 AAATTTT
1 AATTTTT
60938739 AAAAATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 23 0.74
29 8 0.26
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.52
Consensus pattern (28 bp):
AATTTTTTTCAATTTAGTCCCATCTTAA
Found at i:60953259 original size:25 final size:25
Alignment explanation
Indices: 60953201--60953250 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
60953191 TAAGTTGGGA
60953201 AGTTGTTTCTTAAAACGTACTTCAT
1 AGTTGTTTCTTAAAACGTACTTCAT
60953226 AGTTGTTTCTTAAAACGTACTTCAT
1 AGTTGTTTCTTAAAACGTACTTCAT
60953251 TTCTGTTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (25 bp):
AGTTGTTTCTTAAAACGTACTTCAT
Found at i:60956928 original size:35 final size:35
Alignment explanation
Indices: 60956809--60956930 Score: 120
Period size: 35 Copynumber: 3.4 Consensus size: 35
60956799 GATTTATTCG
* * *
60956809 ACTAGCGCTGGGCGTAAATATCGTTGGTTTATCCA
1 ACTAGAGCTAGGCGCAAATATCGTTGGTTTATCCA
* * *
60956844 ACTAGAGCTGGGCTCACTAATTATTTCGTT-GTTTATCTA
1 ACTAGAGCTAGGCGCA--AA-TA--TCGTTGGTTTATCCA
* *
60956883 ACTAGCGCTAGGCGCAAATATCATTGGTTTATCCA
1 ACTAGAGCTAGGCGCAAATATCGTTGGTTTATCCA
60956918 ACTAGAGCTAGGC
1 ACTAGAGCTAGGC
60956931 TAACTAATTA
Statistics
Matches: 71, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
34 4 0.06
35 33 0.46
36 2 0.03
37 4 0.06
38 2 0.03
39 21 0.30
40 5 0.07
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (35 bp):
ACTAGAGCTAGGCGCAAATATCGTTGGTTTATCCA
Found at i:60957064 original size:74 final size:75
Alignment explanation
Indices: 60956808--60957048 Score: 351
Period size: 74 Copynumber: 3.2 Consensus size: 75
60956798 CGATTTATTC
* * *
60956808 GACTAGCGCTGGGCGTAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGT
1 GACTAGCGCTGGGCGCAAATATCATTGGTTTATCCAACTAGAGCTAGGCTCACTAATTATTTCGT
*
60956873 -TGTTTATCT
66 CCGTTTATCT
* * *
60956882 AACTAGCGCTAGGCGCAAATATCATTGGTTTATCCAACTAGAGCTAGGCTAACTAATTATTTCGT
1 GACTAGCGCTGGGCGCAAATATCATTGGTTTATCCAACTAGAGCTAGGCTCACTAATTATTTCGT
60956947 CCGTTTATCT
66 CCGTTTATCT
* * * *
60956957 GACTAGCACTGGACACAAATATCATTGGTTTATCGAACTAGAGCTAGGCTCACTAATTA-TTCGT
1 GACTAGCGCTGGGCGCAAATATCATTGGTTTATCCAACTAGAGCTAGGCTCACTAATTATTTCGT
* *
60957021 CGGTTTATCC
66 CCGTTTATCT
60957031 GACTAGCGCTGGGCGCAA
1 GACTAGCGCTGGGCGCAA
60957049 CTTCCACCAT
Statistics
Matches: 147, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
74 87 0.59
75 60 0.41
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (75 bp):
GACTAGCGCTGGGCGCAAATATCATTGGTTTATCCAACTAGAGCTAGGCTCACTAATTATTTCGT
CCGTTTATCT
Found at i:60957816 original size:18 final size:18
Alignment explanation
Indices: 60957793--60957830 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
60957783 TTTGGTTGTT
60957793 AGTTGTTTTGTGAATGTG
1 AGTTGTTTTGTGAATGTG
60957811 AGTTGTTTTGTGAATGTG
1 AGTTGTTTTGTGAATGTG
60957829 AG
1 AG
60957831 GTAAATTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.47
Consensus pattern (18 bp):
AGTTGTTTTGTGAATGTG
Found at i:60963108 original size:3 final size:3
Alignment explanation
Indices: 60963097--60963215 Score: 104
Period size: 3 Copynumber: 41.0 Consensus size: 3
60963087 CTTGGGTAGT
* * *
60963097 AGA ATA AGA AGA A-A AAA AGA AGA ATA AG- AGA AGA A-A CAG- AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA
* *
60963139 AGA AGA AGA AGA AGA AAA AGA AGA AGA AGA AGA AGA AGA AAA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * * * *
60963187 AAA AG- AGG AGG AGG AGA AGA AGA ATA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
60963216 GAAAATGGAA
Statistics
Matches: 96, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
2 9 0.09
3 87 0.91
ACGTcount: A:0.67, C:0.01, G:0.29, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:60963235 original size:29 final size:32
Alignment explanation
Indices: 60963103--60963229 Score: 125
Period size: 33 Copynumber: 4.0 Consensus size: 32
60963093 TAGTAGAATA
* * *
60963103 AGAAGAA-AAAAAGAAGAATAAGAGAAGAAACAG
1 AGAAGAAGAAAAAGAAGAAAAAGAGAAG-GA-GG
* * *
60963136 AGAAGAAGAAGAAGAAGAAAAAGAAGAAGAAGA
1 AGAAGAAGAAAAAGAAGAAAAAG-AGAAGGAGG
*
60963169 AGAAGAAGAAAAAGAAGAAAAAGAGGAGGAGG
1 AGAAGAAGAAAAAGAAGAAAAAGAGAAGGAGG
* *
60963201 AGAAGAAGAATAAG-AGAAAATG-GAAGGAG
1 AGAAGAAGAAAAAGAAGAAAAAGAGAAGGAG
60963230 ATAAGACTAG
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
30 6 0.07
31 7 0.09
32 19 0.23
33 29 0.36
34 15 0.19
35 5 0.06
ACGTcount: A:0.65, C:0.01, G:0.31, T:0.02
Consensus pattern (32 bp):
AGAAGAAGAAAAAGAAGAAAAAGAGAAGGAGG
Found at i:60964208 original size:16 final size:16
Alignment explanation
Indices: 60964187--60964271 Score: 161
Period size: 16 Copynumber: 5.2 Consensus size: 16
60964177 TTTGGTTCGC
60964187 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
60964203 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
60964219 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
60964235 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
60964252 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
60964268 TGTA
1 TGTA
60964272 ATAGCTAATC
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
16 52 0.76
17 16 0.24
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:60964251 original size:33 final size:32
Alignment explanation
Indices: 60964187--60964271 Score: 161
Period size: 33 Copynumber: 2.6 Consensus size: 32
60964177 TTTGGTTCGC
60964187 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
60964219 TGTATTGGATTAGAGGTGTATTGGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATT-GGATTAGAGG
60964252 TGTATTGGATTAGAGGTGTA
1 TGTATTGGATTAGAGGTGTA
60964272 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 22 0.42
33 30 0.58
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:60964336 original size:44 final size:45
Alignment explanation
Indices: 60964252--60964342 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
60964242 GGATTAGAGG
* * *
60964252 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
60964297 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
60964341 TG
1 TG
60964343 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:60964528 original size:18 final size:19
Alignment explanation
Indices: 60964507--60964543 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
60964497 TTATTATTAA
60964507 ATAT-ATTT-TAATTAAAAT
1 ATATAATTTATAA-TAAAAT
60964525 ATATAATTTATAATAAAAT
1 ATATAATTTATAATAAAAT
60964544 TCTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 10 0.59
20 3 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATAATTTATAATAAAAT
Found at i:60964602 original size:61 final size:59
Alignment explanation
Indices: 60964537--60964724 Score: 163
Period size: 61 Copynumber: 3.1 Consensus size: 59
60964527 ATAATTTATA
*
60964537 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTCTTAATAATAAATATTCTTATATGAATTT-CT-AAATCATAATATATGATACT
* ** * * *
60964598 ATAAAATATAATTTGAAATAATAAATATT-AAATAT--ATTT-T-AATTAAAATATATGAT-TT
1 ATAAAAT-T--CTT--AATAATAAATATTCTTATATGAATTTCTAAATCATAATATATGATACT
* *
60964656 AATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACT
1 -ATAAAATTCTTAATAATAAATATTCTTATATGAA-TTTCT-AAATCATAATATATGATACT
60964718 ATAAAAT
1 ATAAAAT
60964725 ATAATTTAAC
Statistics
Matches: 98, Mismatches: 15, Indels: 28
0.70 0.11 0.20
Matches are distributed among these distances:
54 12 0.12
55 4 0.04
56 2 0.02
57 1 0.01
58 5 0.05
59 22 0.22
61 28 0.29
62 2 0.02
63 4 0.04
64 2 0.02
65 4 0.04
66 12 0.12
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (59 bp):
ATAAAATTCTTAATAATAAATATTCTTATATGAATTTCTAAATCATAATATATGATACT
Found at i:60964708 original size:120 final size:120
Alignment explanation
Indices: 60964487--60964776 Score: 429
Period size: 120 Copynumber: 2.4 Consensus size: 120
60964477 TTAATCATAT
* *
60964487 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTATAATAAAATTCTTAATA
1 TTTAACATAATAAATATTAAATATATTTTAATTAAAATATATAA-TT-TAATAAAATTCTTAATA
* * *
60964552 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
64 ATAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* *
60964609 TTTGAA-ATAATAAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAT
1 TTT-AACATAATAAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
60964673 TAAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
65 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* * ** *
60964729 TTTAACATAATTATTATTAAATATAAGTTAATAAAAATATATAATTTA
1 TTTAACATAATAAATATTAAATATATTTTAATTAAAATATATAATTTA
60964777 TCATCATACT
Statistics
Matches: 152, Mismatches: 14, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
119 2 0.01
120 108 0.71
121 2 0.01
122 38 0.25
123 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
TTTAACATAATAAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:60970059 original size:14 final size:15
Alignment explanation
Indices: 60970033--60970061 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
60970023 GCTTCATCAT
60970033 CTTCTTCTTCCTCTG
1 CTTCTTCTTCCTCTG
60970048 CTTCTT-TTCCTCTG
1 CTTCTTCTTCCTCTG
60970062 GTTTTTGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.00, C:0.38, G:0.07, T:0.55
Consensus pattern (15 bp):
CTTCTTCTTCCTCTG
Found at i:60970478 original size:21 final size:21
Alignment explanation
Indices: 60970452--60970492 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
60970442 CAACGTGGCA
60970452 AGTTAACTGGCCACATCAGCT
1 AGTTAACTGGCCACATCAGCT
* *
60970473 AGTTAACTTGCCACGTCAGC
1 AGTTAACTGGCCACATCAGC
60970493 GTTCCTGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (21 bp):
AGTTAACTGGCCACATCAGCT
Found at i:60976867 original size:15 final size:15
Alignment explanation
Indices: 60976847--60976905 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
60976837 GAATTCTAAT
*
60976847 ATAAATAATCATAAC
1 ATAAATAATAATAAC
*
60976862 ATAAATAATAATAAT
1 ATAAATAATAATAAC
*
60976877 A-ATAATAATAATAAT
1 ATA-AATAATAATAAC
60976892 A-ATAATAATAATAA
1 ATA-AATAATAATAA
60976906 TAGGGGTGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
14 1 0.02
15 40 0.98
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAAATAATAATAAC
Found at i:60976873 original size:3 final size:3
Alignment explanation
Indices: 60976865--60976907 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
60976855 TCATAACATA
60976865 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
60976908 GGGGTGACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:60981941 original size:14 final size:14
Alignment explanation
Indices: 60981922--60981950 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
60981912 TTTCCTTTCA
60981922 AATCTATTATGCAT
1 AATCTATTATGCAT
60981936 AATCTATTATGCAT
1 AATCTATTATGCAT
60981950 A
1 A
60981951 TAGTTTACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (14 bp):
AATCTATTATGCAT
Found at i:60982952 original size:127 final size:125
Alignment explanation
Indices: 60982739--60983038 Score: 417
Period size: 127 Copynumber: 2.4 Consensus size: 125
60982729 AATATTTGAT
60982739 GTTTGGAAATTC-AGGAAATCGTGCCCTACCGTGCTGGGTTTCGATTTCCCGTTTGATCAAAATA
1 GTTTGGAAATTCGAGG-AATCGTGCCCTA-CGTGCTGGGTTTCGATTTCCCGTTTGATCAAAATA
*
60982803 ATTGAATATTCCTTTAGAATTTCACTCGTGTTTTCCAAATTCTAAAACAAGGCAATGTTCAA
64 ATTGAATATTCCTTTAGAATTTCACTCGTGTTTTACAAATTCTAAAACAAGGCAATGTTCAA
* * *
60982865 GGTTTGGAAATTCGAGGAATCGTGCCCTATCGTGCTAGGTTTCGATTTCCGGTTT-ATTCCAAAT
1 -GTTTGGAAATTCGAGGAATCGTGCCCTA-CGTGCTGGGTTTCGATTTCCCGTTTGA-TCAAAAT
* * * *
60982929 AATTGAATGTTCCTTTAGTATTTCACTCGTGTTTTATAAATTCTAAAGCAAGGCAATGTTCAA
63 AATTGAATATTCCTTTAGAATTTCACTCGTGTTTTACAAATTCTAAAACAAGGCAATGTTCAA
* * *
60982992 -TAATGGAAGTTCGAGGAATCGTGCCCTACTGTGCCGGGTTTCGATTT
1 GT-TTGGAAATTCGAGGAATCGTGCCCTAC-GTGCTGGGTTTCGATTT
60983039 TTCGTTGGAC
Statistics
Matches: 156, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
125 2 0.01
126 40 0.26
127 111 0.71
128 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (125 bp):
GTTTGGAAATTCGAGGAATCGTGCCCTACGTGCTGGGTTTCGATTTCCCGTTTGATCAAAATAAT
TGAATATTCCTTTAGAATTTCACTCGTGTTTTACAAATTCTAAAACAAGGCAATGTTCAA
Found at i:60985181 original size:30 final size:30
Alignment explanation
Indices: 60985147--60985203 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
60985137 TCCTTAAGTC
60985147 AAACTTTAGCAAAATTACAATTTTGCCTAT
1 AAACTTTAGCAAAATTACAATTTTGCCTAT
* * * *
60985177 AAACTTTTGCATATTTACACTTTTGCC
1 AAACTTTAGCAAAATTACAATTTTGCC
60985204 CCTAGGCTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.40
Consensus pattern (30 bp):
AAACTTTAGCAAAATTACAATTTTGCCTAT
Found at i:60987617 original size:19 final size:19
Alignment explanation
Indices: 60987593--60987639 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
60987583 ATTTCTTTCC
60987593 TTTGCATT-CATCCCATGCA
1 TTTGCATTACATCCCAT-CA
**
60987612 TTTGCATTACATTGCATCA
1 TTTGCATTACATCCCATCA
60987631 TTTGCATTA
1 TTTGCATTA
60987640 GATTTTCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (19 bp):
TTTGCATTACATCCCATCA
Found at i:61010570 original size:26 final size:26
Alignment explanation
Indices: 61010534--61010615 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
61010524 TGAAATTCCA
61010534 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
61010560 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
61010586 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
61010612 ATCA
1 ATCA
61010616 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:61016525 original size:50 final size:51
Alignment explanation
Indices: 61016450--61016570 Score: 183
Period size: 50 Copynumber: 2.4 Consensus size: 51
61016440 CCATGGCAAC
61016450 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAA-GAGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA-A
* *
61016500 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATGAC
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGAA
* *
61016551 AAGTGAAAAGTGGTAGCTTC
1 AAGTGATAAGTGATAGCTTC
61016571 AACTACCTGA
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
50 42 0.65
51 21 0.32
52 2 0.03
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (51 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGAA
Found at i:61016590 original size:31 final size:31
Alignment explanation
Indices: 61016552--61016731 Score: 290
Period size: 31 Copynumber: 5.8 Consensus size: 31
61016542 ACAAATGACA
* **
61016552 AGTGAAAAGTGGTAGCTTCAACTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
61016583 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
*
61016614 AATGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
*
61016645 AATGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
61016676 AGTGAAAAGTGGTAG-TACCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCT-CCGGCTACCTGATC
*
61016707 AGTGAAAAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTCCGGCTAC
61016732 AAGTGACAAG
Statistics
Matches: 141, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
30 1 0.01
31 139 0.99
32 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
Found at i:61016823 original size:47 final size:47
Alignment explanation
Indices: 61016754--61016962 Score: 189
Period size: 47 Copynumber: 4.5 Consensus size: 47
61016744 ATTTCCGTAC
* * * *
61016754 AAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACTGTAT
1 AAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATACTGTGT
* * * *
61016801 AAGACCATATCTGGGATATGGCATCAGTGAGATATGTGAT-TTGTGT
1 AAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATACTGTGT
* * * *
61016847 ACGACCATAGCTGGGCTATGGTATCGATATGTGATATGTGATTAC-GTGT
1 AAGACCATAGCTGGGATATGGCATCG--GTGTGATATGTGA-TACTGTGT
* * *
61016896 AAGACCATAGCTGGGCTATGGCATC-G-AT-ATATG-AATA-TGTGT
1 AAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATACTGTGT
* *
61016938 AAGACCATAGTTGGGCTATGGCATC
1 AAGACCATAGCTGGGATATGGCATC
61016963 ATTATGTGAA
Statistics
Matches: 137, Mismatches: 20, Indels: 15
0.80 0.12 0.09
Matches are distributed among these distances:
42 30 0.22
43 1 0.01
44 5 0.04
45 1 0.01
46 25 0.18
47 36 0.26
48 11 0.08
49 28 0.20
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (47 bp):
AAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATACTGTGT
Found at i:61016903 original size:49 final size:48
Alignment explanation
Indices: 61016754--61017006 Score: 189
Period size: 42 Copynumber: 5.6 Consensus size: 48
61016744 ATTTCCGTAC
* * * * * * *
61016754 AAGACCATATCTGGGATATGGCATCG--GTGTGATATATGCTACTGTAT
1 AAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTC-GTGT
* * * * *
61016801 AAGACCATATCTGGGATATGGCATC-A-GTGAGATATGTGATTTGTGT
1 AAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTCGTGT
* *
61016847 ACGACCATAGCTGGGCTATGGTATCGATATGTGATATGTGATTACGTGT
1 AAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATT-CGTGT
*
61016896 AAGACCATAGCTGGGCTATGGCATCGATATATGA-A--T-A-T-GTGT
1 AAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTCGTGT
*
61016938 AAGACCATAGTTGGGCTATGGCATC-ATTATGTGA-A---GA-T-GTGT
1 AAGACCATAGCTGGGCTATGGCATCGA-TATGTGATATGTGATTCGTGT
* **
61016980 AAGACCATAGTTGAACTATGGCATCGA
1 AAGACCATAGCTGGGCTATGGCATCGA
61017007 GAAAACGAAG
Statistics
Matches: 179, Mismatches: 20, Indels: 18
0.82 0.09 0.08
Matches are distributed among these distances:
41 1 0.01
42 64 0.36
43 1 0.01
44 1 0.01
45 1 0.01
46 25 0.14
47 37 0.21
48 14 0.08
49 35 0.20
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (48 bp):
AAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTCGTGT
Found at i:61020637 original size:5 final size:5
Alignment explanation
Indices: 61020629--61020662 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
61020619 AACCTAAATT
*
61020629 AATAA AATAAA AATAA AATAA AACAA AATAA AAT
1 AATAA AAT-AA AATAA AATAA AATAA AATAA AAT
61020663 CTTTCTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:61020645 original size:11 final size:11
Alignment explanation
Indices: 61020629--61020661 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
61020619 AACCTAAATT
61020629 AATAAAATAAA
1 AATAAAATAAA
61020640 AATAAAAT-AA
1 AATAAAATAAA
*
61020650 AACAAAATAAA
1 AATAAAATAAA
61020661 A
1 A
61020662 TCTTTCTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:61029101 original size:28 final size:28
Alignment explanation
Indices: 61029047--61029101 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
61029037 ACTGGGGTTT
*
61029047 TCACACGGCTTGACACATGCCCGTGTCCC
1 TCACACGGCATGACACA-GCCCGTGTCCC
61029076 TCACACGGCCATGACAC-GCCCGTGTC
1 TCACACGG-CATGACACAGCCCGTGTC
61029102 TTAGCCCGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 9 0.38
29 8 0.33
30 7 0.29
ACGTcount: A:0.18, C:0.42, G:0.22, T:0.18
Consensus pattern (28 bp):
TCACACGGCATGACACAGCCCGTGTCCC
Found at i:61029621 original size:58 final size:58
Alignment explanation
Indices: 61029557--61029675 Score: 211
Period size: 58 Copynumber: 2.1 Consensus size: 58
61029547 TTTCATAGAA
*
61029557 TAACTTTCAATATTAGCAATTTACCATGGCCTTATACAAAATGAATCAAATGTTAAAG
1 TAACTTTCAATATTAGCAATTTACCATGGCCTTATACAAAATGAATCAAATGCTAAAG
* *
61029615 TAACTTTCAATATTAGCCATTTACCATGGTCTTATACAAAATGAATCAAATGCTAAAG
1 TAACTTTCAATATTAGCAATTTACCATGGCCTTATACAAAATGAATCAAATGCTAAAG
61029673 TAA
1 TAA
61029676 GCTAACACAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (58 bp):
TAACTTTCAATATTAGCAATTTACCATGGCCTTATACAAAATGAATCAAATGCTAAAG
Found at i:61030387 original size:46 final size:46
Alignment explanation
Indices: 61030294--61030464 Score: 143
Period size: 46 Copynumber: 3.7 Consensus size: 46
61030284 TCTCGTAGCC
* * *
61030294 GATGCATGTCCCAGACATGTCTTACATTGGCTTACGTCACGAGGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCTTACGTCACAAGGCT
* * *
61030340 GATGCATGTCCCAAACATGTCTTACACTAGCTCT-CGTCTCAATGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCT-TACGTCACAAGGCT
* * * * * *
61030386 GATGCCATGTCCTAGGCATGGTCTTACACTGGC--AC-TCATAGTGTGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTTACGTCACA---AGGCT
*
61030434 GATGTATGTCCCAGACATGTCTTACACTAGC
1 GATGCATGTCCCAGACATGTCTTACACTAGC
61030465 ACACAAATAA
Statistics
Matches: 99, Mismatches: 19, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
45 3 0.03
46 55 0.56
47 23 0.23
48 18 0.18
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTTACGTCACAAGGCT
Found at i:61035364 original size:27 final size:27
Alignment explanation
Indices: 61035334--61035423 Score: 94
Period size: 28 Copynumber: 3.3 Consensus size: 27
61035324 AAAAAAAATC
61035334 AAATAAAGCCATTAATGGAAAAATAGT
1 AAATAAAGCCATTAATGGAAAAATAGT
* * * *
61035361 AAATAAATTG-AAATAA-GAAAAAAATAAT
1 AAATAAA--GCCATTAATG-GAAAAATAGT
61035389 CAAATAAAGCCATTAATGGAAAAATAGT
1 -AAATAAAGCCATTAATGGAAAAATAGT
61035417 AAATAAA
1 AAATAAA
61035424 TTGAAATTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
27 16 0.33
28 24 0.49
29 9 0.18
ACGTcount: A:0.62, C:0.06, G:0.11, T:0.21
Consensus pattern (27 bp):
AAATAAAGCCATTAATGGAAAAATAGT
Found at i:61035390 original size:56 final size:55
Alignment explanation
Indices: 61035319--61035430 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 55
61035309 GCGGCATAAG
61035319 TAAGAAAAAAAAATCAAATAAAGCCATTAATGGAAAAATAGTAAATAAATTGAAA
1 TAAGAAAAAAAAATCAAATAAAGCCATTAATGGAAAAATAGTAAATAAATTGAAA
61035374 TAAGAAAAAAATAATCAAATAAAGCCATTAATGGAAAAATAGTAAATAAATTGAAA
1 TAAGAAAAAAA-AATCAAATAAAGCCATTAATGGAAAAATAGTAAATAAATTGAAA
61035430 T
1 T
61035431 TAAAAACAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 11 0.20
56 45 0.80
ACGTcount: A:0.62, C:0.05, G:0.11, T:0.21
Consensus pattern (55 bp):
TAAGAAAAAAAAATCAAATAAAGCCATTAATGGAAAAATAGTAAATAAATTGAAA
Found at i:61036405 original size:25 final size:24
Alignment explanation
Indices: 61036377--61036430 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
61036367 CATCCCGTTA
61036377 TATGGATCTCACGAGCTTCCTAATT
1 TATGGATCTCACGAGCTTCCT-ATT
* **
61036402 TATGGCTCTCTTGAGCTTCCTATT
1 TATGGATCTCACGAGCTTCCTATT
61036426 TATGG
1 TATGG
61036431 CCCGTATAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.41
Consensus pattern (24 bp):
TATGGATCTCACGAGCTTCCTATT
Found at i:61036483 original size:25 final size:24
Alignment explanation
Indices: 61036442--61036527 Score: 66
Period size: 25 Copynumber: 3.4 Consensus size: 24
61036432 CCGTATAAGC
*
61036442 TTCCCGATAATTA-GCTCTCCAGAGT
1 TTCCCGATAA-AAGGCTCTCCAGA-T
* *
61036467 TTCCCGATAAAAGGCTCTTTCATGACC
1 TTCCCGATAAAAGGCTC-TCCA-GA-T
* *
61036494 TTCCCGATTAATGGCTCTCCAGAT
1 TTCCCGATAAAAGGCTCTCCAGAT
61036518 TTACCCGATA
1 TT-CCCGATA
61036528 TTGGTTTACA
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
24 3 0.06
25 22 0.46
26 6 0.12
27 17 0.35
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.31
Consensus pattern (24 bp):
TTCCCGATAAAAGGCTCTCCAGAT
Found at i:61036583 original size:25 final size:25
Alignment explanation
Indices: 61036561--61036608 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
61036551 TGTGGCTCTT
61036561 ATGAGCTTCCCGTTACATGGCTCAC
1 ATGAGCTTCCCGTTACATGGCTCAC
* *
61036586 ATGAGCTTCCTGTTATATGGCTC
1 ATGAGCTTCCCGTTACATGGCTC
61036609 GAAAGAGCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (25 bp):
ATGAGCTTCCCGTTACATGGCTCAC
Found at i:61036641 original size:25 final size:25
Alignment explanation
Indices: 61036561--61036641 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
61036551 TGTGGCTCTT
* * *
61036561 ATGAGCTTCCCGTTACATGGCTCAC
1 ATGAGCTACCTGTTATATGGCTCAC
*
61036586 ATGAGCTTCCTGTTATATGGCTCGA-
1 ATGAGCTACCTGTTATATGGCTC-AC
* *
61036611 AAGAGCTACCTATTTATAT-GCTCAC
1 ATGAGCTACCT-GTTATATGGCTCAC
61036636 ATGAGC
1 ATGAGC
61036642 ATTCCTGAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
24 1 0.02
25 39 0.83
26 7 0.15
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31
Consensus pattern (25 bp):
ATGAGCTACCTGTTATATGGCTCAC
Found at i:61060714 original size:36 final size:36
Alignment explanation
Indices: 61060667--61060739 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
61060657 CTTCTTTTTG
61060667 TTGCATCTTCCCAATGTCAAGCTTCTATTCTCCGCA
1 TTGCATCTTCCCAATGTCAAGCTTCTATTCTCCGCA
61060703 TTGCATCTTCCCAATGTCAAGCTTCTATTCTCCGCA
1 TTGCATCTTCCCAATGTCAAGCTTCTATTCTCCGCA
61060739 T
1 T
61060740 CCTATATGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.19, C:0.33, G:0.11, T:0.37
Consensus pattern (36 bp):
TTGCATCTTCCCAATGTCAAGCTTCTATTCTCCGCA
Found at i:61064274 original size:28 final size:28
Alignment explanation
Indices: 61064242--61064297 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
61064232 AAATTAAAAG
61064242 TCTATTAACTTTGCAGTCTATGTCAGTA
1 TCTATTAACTTTGCAGTCTATGTCAGTA
61064270 TCTATTAACTTTGCAGTCTATGTCAGTA
1 TCTATTAACTTTGCAGTCTATGTCAGTA
61064298 ATTAATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (28 bp):
TCTATTAACTTTGCAGTCTATGTCAGTA
Found at i:61067579 original size:16 final size:16
Alignment explanation
Indices: 61067552--61067592 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
61067542 TAGAAGGGAC
61067552 TTTGTATTTGTTTTTGT
1 TTTGT-TTTGTTTTTGT
*
61067569 TTTGTTTTGTTTTTTT
1 TTTGTTTTGTTTTTGT
*
61067585 TTTCTTTT
1 TTTGTTTT
61067593 TGTGTCTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.83
Consensus pattern (16 bp):
TTTGTTTTGTTTTTGT
Found at i:61077516 original size:37 final size:37
Alignment explanation
Indices: 61077466--61077544 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
61077456 TTATTACGAA
* * *
61077466 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
61077503 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
61077540 GTCTT
1 GTCTT
61077545 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:61077837 original size:49 final size:47
Alignment explanation
Indices: 61077663--61077945 Score: 431
Period size: 47 Copynumber: 5.9 Consensus size: 47
61077653 CCCTTCGGGA
* * * * * * *
61077663 CTTATCACATTTGTACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
61077710 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
61077757 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
61077804 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
61077853 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
61077900 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTA
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTA
61077946 CGCCATACTA
Statistics
Matches: 218, Mismatches: 14, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
47 136 0.62
49 82 0.38
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:61077858 original size:96 final size:96
Alignment explanation
Indices: 61077663--61077945 Score: 462
Period size: 96 Copynumber: 3.0 Consensus size: 96
61077653 CCCTTCGGGA
* * * * * * * *
61077663 CTTATCACATTTGTACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
61077726 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* *
61077757 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGACCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
61077822 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
61077853 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
61077918 ACTTTCACATTCATCACATCGGCCATTA
66 ACTTTCACATTCATCACATCGGCCATTA
61077946 CGCCATACTA
Statistics
Matches: 175, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
94 45 0.26
96 130 0.74
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (96 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:61085731 original size:36 final size:36
Alignment explanation
Indices: 61085684--61085755 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
61085674 TTCTTTCTGC
61085684 CGTTCCAAATTCCC-ACCTCCTCCCCCAATTTTTCCT
1 CGTTCCAAATTCCCAACC-CCTCCCCCAATTTTTCCT
*
61085720 CGTTCCAAATTCCCAACCCCTTCCCCAATTTTTCCT
1 CGTTCCAAATTCCCAACCCCTCCCCCAATTTTTCCT
61085756 TTGTTCTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 31 0.91
37 3 0.09
ACGTcount: A:0.18, C:0.46, G:0.03, T:0.33
Consensus pattern (36 bp):
CGTTCCAAATTCCCAACCCCTCCCCCAATTTTTCCT
Found at i:61086420 original size:45 final size:45
Alignment explanation
Indices: 61086356--61086446 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
61086346 AATTAAATTA
* *
61086356 ACCATTATTAGCAGGTTTAATTTCATTTAAGTCATGCATATATAT
1 ACCATTATTAGCAGGTTTAACTTCATTTAAGTCAAGCATATATAT
61086401 ACCATTATTAGCAGGTTTAACTTCATTTAAGTCAAGCATATATAT
1 ACCATTATTAGCAGGTTTAACTTCATTTAAGTCAAGCATATATAT
61086446 A
1 A
61086447 TATGCATTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (45 bp):
ACCATTATTAGCAGGTTTAACTTCATTTAAGTCAAGCATATATAT
Found at i:61086462 original size:43 final size:43
Alignment explanation
Indices: 61086362--61086493 Score: 122
Period size: 45 Copynumber: 3.0 Consensus size: 43
61086352 ATTAACCATT
* * * *
61086362 ATTAGCAGGTTTAATTTCATTTAAGTCATGCATATATATACCATT
1 ATTA-CAGGTTTAACTTCATTTAAGTCAAGCATATATATA-TATC
61086407 ATTAGCAGGTTTAACTTCATTTAAGTCAAGCATATATATATATGC
1 ATTA-CAGGTTTAACTTCATTTAAGTCAAGCATATATATATAT-C
** * * *
61086452 ATTA-TTGTTTAGCTTCATTTAATATTAATGCATATATATATA
1 ATTACAGGTTTAACTTCATTTAA-GTCAA-GCATATATATATA
61086494 ATGTTTTGCT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
43 15 0.20
44 5 0.07
45 55 0.73
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (43 bp):
ATTACAGGTTTAACTTCATTTAAGTCAAGCATATATATATATC
Found at i:61086683 original size:36 final size:36
Alignment explanation
Indices: 61086623--61086695 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
61086613 GCATATATAT
* *
61086623 ATATTAATGCATATGTATACTGTTTAGCTTCATTTA
1 ATATTAATGCATATATATAATGTTTAGCTTCATTTA
* *
61086659 ATATTAATGGATATATATAATGTTTTGCTTCATTTA
1 ATATTAATGCATATATATAATGTTTAGCTTCATTTA
61086695 A
1 A
61086696 GTCATGCGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.48
Consensus pattern (36 bp):
ATATTAATGCATATATATAATGTTTAGCTTCATTTA
Found at i:61086709 original size:177 final size:171
Alignment explanation
Indices: 61086390--61086712 Score: 436
Period size: 177 Copynumber: 1.8 Consensus size: 171
61086380 ATTTAAGTCA
* * *
61086390 TGCATATATATACCATTATTAGCAGGTTTAACTTCATTTAAGTCAAGCATATATATATATGCATT
1 TGCATATATATACCATAATTAACAGGTTTAACTTCATTTAAGCCAAGCATATATATATATGCATT
*
61086455 ATTGTTTAGCTTCATTTAATATTAATGCATATATATATAATGTTTTGCTTCATTTAAGTCATGCG
66 ATTGTTTAGCTTCATTTAATATTAATG-AGATATATATAATGTTTTGCTTCATTTAAGTCAT-CG
61086520 CATAATGCATATATATTCCATTTAACTTCATTTAAGTCATGCATAAT
129 C---A-GCATATATATTCCATTTAACTTCATTTAAGTCATGCATAAT
* *
61086567 TGCATATATATACCATAATTAACAGGTTTAGCTTGATTTAAGCCAAGCATATATATATATTAATG
1 TGCATATATATACCATAATTAACAGGTTTAACTTCATTTAAGCCAAGC--ATATATATA-T-ATG
61086632 CATATGTATACTGTTTAGCTTCATTTAATATTAATG-GATATATATAATGTTTTGCTTCATTTAA
62 C--AT-TAT--TGTTTAGCTTCATTTAATATTAATGAGATATATATAATGTTTTGCTTCATTTAA
61086696 GTCAT-GC-GCATATATAT
122 GTCATCGCAGCATATATAT
61086713 ATATTAATGC
Statistics
Matches: 131, Mismatches: 6, Indels: 18
0.85 0.04 0.12
Matches are distributed among these distances:
177 53 0.40
179 9 0.07
180 1 0.01
181 4 0.03
182 2 0.02
183 2 0.02
184 35 0.27
186 25 0.19
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (171 bp):
TGCATATATATACCATAATTAACAGGTTTAACTTCATTTAAGCCAAGCATATATATATATGCATT
ATTGTTTAGCTTCATTTAATATTAATGAGATATATATAATGTTTTGCTTCATTTAAGTCATCGCA
GCATATATATTCCATTTAACTTCATTTAAGTCATGCATAAT
Found at i:61087336 original size:36 final size:32
Alignment explanation
Indices: 61087289--61087358 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 32
61087279 TTTTATAAGT
61087289 AAGTTACTCCATTGTTTTTGTTTTGAGTTAATTTTG
1 AAGTTACTCCA---TTTTT-TTTTGAGTTAATTTTG
*
61087325 AAGTTGCTCCATTTTTTTTTGAGTTAATTTTG
1 AAGTTACTCCATTTTTTTTTGAGTTAATTTTG
61087357 AA
1 AA
61087359 CGCTTTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 18 0.55
33 5 0.15
36 10 0.30
ACGTcount: A:0.21, C:0.09, G:0.16, T:0.54
Consensus pattern (32 bp):
AAGTTACTCCATTTTTTTTTGAGTTAATTTTG
Found at i:61090273 original size:21 final size:22
Alignment explanation
Indices: 61090249--61090291 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
61090239 TTACATGTAA
* *
61090249 TTATTTAG-TAAATTATATTGT
1 TTATGTAGTTAAATAATATTGT
61090270 TTATGTAGTTAAATAATATTGT
1 TTATGTAGTTAAATAATATTGT
61090292 ACTTTGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TTATGTAGTTAAATAATATTGT
Found at i:61099291 original size:40 final size:40
Alignment explanation
Indices: 61099236--61099334 Score: 162
Period size: 40 Copynumber: 2.5 Consensus size: 40
61099226 TGTGCATAGC
61099236 ATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGA
1 ATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGA
* *
61099276 ATTCGTGCGGGTTATTATAACCGGGTTAAGTCCTGAAGGC
1 ATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGA
* *
61099316 ATTCGTGCTGGTTGTTATA
1 ATTCGTGCGGGTTATTATA
61099335 TCCGAGCCAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.32
Consensus pattern (40 bp):
ATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGA
Found at i:61104055 original size:17 final size:18
Alignment explanation
Indices: 61104019--61104055 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
61104009 TCCAGACTAG
61104019 TTACAAACCCAAATAAAA
1 TTACAAACCCAAATAAAA
61104037 TTACAAACCCAAA-AAAA
1 TTACAAACCCAAATAAAA
61104054 TT
1 TT
61104056 TAAAGCCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.59, C:0.22, G:0.00, T:0.19
Consensus pattern (18 bp):
TTACAAACCCAAATAAAA
Found at i:61105356 original size:3 final size:3
Alignment explanation
Indices: 61105348--61105395 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
61105338 TTATGCCTTC
* *
61105348 ATT ATT ATT ACT ATT -TT ATT ATCT ATT ATT ATT ACT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT
61105393 ATT
1 ATT
61105396 TATTCATCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:61105385 original size:12 final size:12
Alignment explanation
Indices: 61105348--61105393 Score: 76
Period size: 12 Copynumber: 3.8 Consensus size: 12
61105338 TTATGCCTTC
61105348 ATTATTATTACT
1 ATTATTATTACT
61105360 ATT-TTATTATCT
1 ATTATTATTA-CT
61105372 ATTATTATTACT
1 ATTATTATTACT
61105384 ATTATTATTA
1 ATTATTATTA
61105394 TTTATTCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 6 0.19
12 20 0.62
13 6 0.19
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTATTATTACT
Found at i:61105478 original size:3 final size:3
Alignment explanation
Indices: 61105467--61105560 Score: 95
Period size: 3 Copynumber: 30.3 Consensus size: 3
61105457 TTTTTTTTAC
*
61105467 TTA TATA TTA TTA TTA TTA CTA TTA TTA TTA TTA TT- TTA TCTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
*
61105513 TTA TT- TTA TCTA TTA TTA TTT TTA TTA TTTA TTTA TGTA TT- TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA -TTA -TTA T-TA TTA TTA TTA
61105560 T
1 T
61105561 AAATTGTACC
Statistics
Matches: 79, Mismatches: 4, Indels: 16
0.80 0.04 0.16
Matches are distributed among these distances:
2 6 0.08
3 54 0.68
4 19 0.24
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:61105513 original size:36 final size:36
Alignment explanation
Indices: 61105467--61105557 Score: 116
Period size: 36 Copynumber: 2.5 Consensus size: 36
61105457 TTTTTTTTAC
61105467 TTATATATTATTATTATTA-CTATTATTATTATTATT
1 TTATATATTATTATT-TTATCTATTATTATTATTATT
* *
61105503 TTATCTATTATTATTTTATCTATTATTATTTTTATT
1 TTATATATTATTATTTTATCTATTATTATTATTATT
61105539 ATT-TAT-TTATGTATTTTAT
1 -TTATATATTAT-TATTTTAT
61105558 TATAAATTGT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
35 7 0.14
36 40 0.82
37 2 0.04
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (36 bp):
TTATATATTATTATTTTATCTATTATTATTATTATT
Found at i:61105724 original size:3 final size:3
Alignment explanation
Indices: 61105716--61105750 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
61105706 ATATTTTGTC
*
61105716 ATT ATT ATT ATT ATT ATT -TT ATC ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
61105751 CACTTCATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:61105734 original size:23 final size:23
Alignment explanation
Indices: 61105707--61105750 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
61105697 TTCATATGCA
*
61105707 TATTTTGTCATTATTATTATTAT
1 TATTTTATCATTATTATTATTAT
61105730 TATTTTATCATTATTATTATT
1 TATTTTATCATTATTATTATT
61105751 CACTTCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (23 bp):
TATTTTATCATTATTATTATTAT
Found at i:61105737 original size:17 final size:17
Alignment explanation
Indices: 61105717--61105750 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
61105707 TATTTTGTCA
*
61105717 TTATTATTATTATTATT
1 TTATCATTATTATTATT
61105734 TTATCATTATTATTATT
1 TTATCATTATTATTATT
61105751 CACTTCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATCATTATTATTATT
Found at i:61109934 original size:11 final size:11
Alignment explanation
Indices: 61109918--61109953 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
61109908 TAGGGTGGCA
61109918 TTTTTCTTTTT
1 TTTTTCTTTTT
61109929 TTTTTCTTTTT
1 TTTTTCTTTTT
*
61109940 CTTTTCTTTCTT
1 TTTTTCTTT-TT
61109952 TT
1 TT
61109954 CACTTGTGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 19 0.86
12 3 0.14
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:61111293 original size:25 final size:25
Alignment explanation
Indices: 61111250--61111297 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
61111240 TTATAATATG
* * *
61111250 AAAATGACTATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
61111275 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
61111298 GTTTAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:61111358 original size:20 final size:21
Alignment explanation
Indices: 61111323--61111379 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
61111313 TGATACATGG
61111323 GATATGATAT--ACATGA-AT
1 GATATGATATGCACATGATAT
61111341 GATATGATATGCACATGATAT
1 GATATGATATGCACATGATAT
*
61111362 G-TATGAAATGCACATGAT
1 GATATGATATGCACATGAT
61111380 GTAATCATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
18 10 0.29
20 22 0.63
21 3 0.09
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (21 bp):
GATATGATATGCACATGATAT
Found at i:61111458 original size:27 final size:26
Alignment explanation
Indices: 61111428--61111526 Score: 146
Period size: 26 Copynumber: 3.8 Consensus size: 26
61111418 GAGGAAGTGC
61111428 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* **
61111454 AAAAAGGGCTTATGCCCTAGTTTATTG
1 -AAAAGGGCTTATGCCCCAGTTTACCG
61111481 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
61111507 AAAAGGGCTT-TGCTCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
61111527 ATTAAAGAGG
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
25 9 0.14
26 33 0.51
27 23 0.35
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:61115781 original size:44 final size:44
Alignment explanation
Indices: 61115710--61115880 Score: 144
Period size: 44 Copynumber: 3.7 Consensus size: 44
61115700 ATGACAAATT
** * * *
61115710 TTATCTCATTGAAATTGTAGTGAAGCAGATTGAAGCCACTAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAATC
* * ** *
61115754 TTATCTCTCTGAAGTTACAGTGGAGCAGATATTGAAGTTATTATGGCGAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAG--ATTGAAG---CCA---CTAATC
* * *
61115806 TTATCTCCCTGAAGTTGCAGTGGAACATATTGAAGCCACTAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAATC
*
61115850 TTATCTCCCTGAAGTTGCAGTAGAGCAGATT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATT
61115881 AAAAATAGCG
Statistics
Matches: 99, Mismatches: 20, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
44 54 0.55
46 7 0.07
47 1 0.01
49 1 0.01
50 7 0.07
52 29 0.29
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAATC
Found at i:61116122 original size:145 final size:146
Alignment explanation
Indices: 61115564--61116208 Score: 496
Period size: 145 Copynumber: 4.5 Consensus size: 146
61115554 GCCACTAGCA
* * * * * ** **
61115564 TTATCTCCCTGAAGTTGCATTAGAACAGATTGAAGATAGTGAATCTTATTTCCCTGAAGTTGTAG
1 TTATCTCCCTAAAATTGCAGTGGAGCAGATTGAAGCCAGTGAATCTTATTTCCCTGAAGTTACAG
* * * *
61115629 TGGAATAGATTAAAGCTACAAGTCACAAATCCTGTACTTCTGAAGTTGTAGTAGGTCGGATCAAA
66 TGGAATAGATTAAAGCTACAAGTCACAAATCCTATACCTCTGAAGTTGCAGTAGGTTGGATCAAA
* ** *
61115694 TCTACCATGACAAATT
131 TCTACCACGATGAATC
** * * * * * *
61115710 TTATCTCATTGAAATTGTAGTGAAGCAGATTGAAGCCACT-AATCTTATCTCTCTGAAGTTACAG
1 TTATCTCCCTAAAATTGCAGTGGAGCAGATTGAAGCCAGTGAATCTTATTTCCCTGAAGTTACAG
* * * * ** ** * * * *
61115774 TGGAGCAGATATTGAAGTTATTA-TGGCGAATCTTAT-CTCCCTGAAGTTGC---A-G-TGGAAC
66 TGGA--ATAGATTAAAGCTACAAGTCACAAATCCTATAC-CTCTGAAGTTGCAGTAGGTTGGATC
* *
61115832 ATAT-TGAAGCCAC--T-AACC
128 AAATCT--A-CCACGATGAATC
* * * * *** * *
61115850 TTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAAATAGCGAATCTTATTTCCCTGAAGTTATAG
1 TTATCTCCCTAAAATTGCAGTGGAGCAGATTGAAGCCAGTGAATCTTATTTCCCTGAAGTTACAG
* ** *
61115915 TGGAATAGATTAAAGCTACAAGTCACAAATCAC-ATACTTCTGAAGTTATAGTAGGTTAGATCAA
66 TGGAATAGATTAAAGCTACAAGTCACAAATC-CTATACCTCTGAAGTTGCAGTAGGTTGGATCAA
61115979 ATCTACCACGATGAATC
130 ATCTACCACGATGAATC
* * * *
61115996 TTTTCTCCCTAAAATTGCAGTGGAGCAGATTGAAGCCA-TGAATCTTATTTCCCCGAAGTTGCAA
1 TTATCTCCCTAAAATTGCAGTGGAGCAGATTGAAGCCAGTGAATCTTATTTCCCTGAAGTTACAG
61116060 TGGAATAGATTAAAGCTACAAGTCACAAATCCTATACCTCTGAAGTTGCAGTAGGTTGGATCAAG
66 TGGAATAGATTAAAGCTACAAGTCACAAATCCTATACCTCTGAAGTTGCAGTAGGTTGGATCAA-
* * ** *
61116125 GTC-ATCGTGGTGAATC
130 ATCTACCACGATGAATC
* * * * *
61116141 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCA--CAAGTCTTATCTCCTTGAAGTTACA
1 TTATCTCCCTAAAATTGCAGTGGAGCAGATTGAAGCCAGTGAA-TCTTATTTCCCTGAAGTTACA
61116204 GTGGA
65 GTGGA
61116209 GCAGACTGAA
Statistics
Matches: 377, Mismatches: 100, Indels: 45
0.72 0.19 0.09
Matches are distributed among these distances:
139 11 0.03
140 47 0.12
141 33 0.09
142 2 0.01
143 9 0.02
144 5 0.01
145 177 0.47
146 82 0.22
147 11 0.03
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (146 bp):
TTATCTCCCTAAAATTGCAGTGGAGCAGATTGAAGCCAGTGAATCTTATTTCCCTGAAGTTACAG
TGGAATAGATTAAAGCTACAAGTCACAAATCCTATACCTCTGAAGTTGCAGTAGGTTGGATCAAA
TCTACCACGATGAATC
Found at i:61116419 original size:89 final size:88
Alignment explanation
Indices: 61116261--61116465 Score: 239
Period size: 89 Copynumber: 2.3 Consensus size: 88
61116251 TATTATTTTT
* * * * *
61116261 CTGAAGTTGCAGTGGAGCAAATTGAAGCCACTAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGG
1 CTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAACCTTATCTCCCCGAAGTTACAGTGGAGCAGA
* *
61116326 TTGAAGTTACAAGTTTTATCTCC
66 TTGAAGCTACAAATTTTATCTCC
* ** * ** *
61116349 CTGAAGTTGCAGTAGAGCAGATTGAAGGTAGTGAATTTTATCTCCCCGAAGTTATAGTGGAGCAG
1 CTGAAGTTGCAGTGGAGCAGATTGAAGCCACT-AACCTTATCTCCCCGAAGTTACAGTGGAGCAG
*
61116414 ATTGAAGCTACAAATTTTATCTTC
65 ATTGAAGCTACAAATTTTATCTCC
* **
61116438 CTGAGGTTGCAGTGGAGTGGATTGAAGC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGC
61116466 AACAAATTCT
Statistics
Matches: 96, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
88 27 0.28
89 69 0.72
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (88 bp):
CTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAACCTTATCTCCCCGAAGTTACAGTGGAGCAGA
TTGAAGCTACAAATTTTATCTCC
Found at i:61116452 original size:44 final size:44
Alignment explanation
Indices: 61116261--61116473 Score: 228
Period size: 44 Copynumber: 4.8 Consensus size: 44
61116251 TATTATTTTT
* * * ** *
61116261 CTGAAGTTGCAGTGGAGCAAATTGAAGCCACTAACCTTATCTCT
1 CTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATTTTATCTCC
* * *
61116305 CTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGTTTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATTTTATCTCC
* * **
61116349 CTGAAGTTGCAGTAGAGCAGATTGAAGGTAGTGAATTTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGCTA-CAAATTTTATCTCC
* ** *
61116394 CCGAAGTTATAGTGGAGCAGATTGAAGCTACAAATTTTATCTTC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATTTTATCTCC
* ** *
61116438 CTGAGGTTGCAGTGGAGTGGATTGAAGCAACAAATT
1 CTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATT
61116474 CTATACCTTT
Statistics
Matches: 138, Mismatches: 30, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
44 102 0.74
45 36 0.26
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (44 bp):
CTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATTTTATCTCC
Found at i:61117406 original size:5 final size:5
Alignment explanation
Indices: 61117387--61117420 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
61117377 AGAATTTTTA
61117387 TTTGTT TTTGTT TTTGT TTTGT TTTGT TTTGT TT
1 TTTG-T TTTG-T TTTGT TTTGT TTTGT TTTGT TT
61117421 CACTTAGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.64
6 10 0.36
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (5 bp):
TTTGT
Found at i:61117819 original size:4 final size:4
Alignment explanation
Indices: 61117799--61117923 Score: 72
Period size: 4 Copynumber: 30.2 Consensus size: 4
61117789 TTTTAATTCT
* * * * * *
61117799 TTTA TGTA TTCA TTTA TTTA TTTA CTTG TTTA TTTA TTCA -TTA TTTCT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A
* * * * * * * *
61117847 TTTA TTTTA TTCA TTTG TTTG TTCA TTTA CTTA TCTA TTGA TATA TTGCTCA
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT--T-A
61117899 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
61117924 ATTTTTTAAA
Statistics
Matches: 89, Mismatches: 26, Indels: 12
0.70 0.20 0.09
Matches are distributed among these distances:
3 2 0.02
4 75 0.84
5 8 0.09
6 1 0.01
7 3 0.03
ACGTcount: A:0.22, C:0.08, G:0.05, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:61118037 original size:3 final size:3
Alignment explanation
Indices: 61118022--61118077 Score: 85
Period size: 3 Copynumber: 18.3 Consensus size: 3
61118012 ATACCTTCAC
* *
61118022 TAT TAT TAC TAT TAT TAT TAC TAT TAT TAT TAT TAT CTAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
61118068 TAT TAT TAT T
1 TAT TAT TAT T
61118078 TATCTATTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:61118087 original size:8 final size:7
Alignment explanation
Indices: 61118031--61118089 Score: 54
Period size: 6 Copynumber: 8.6 Consensus size: 7
61118021 CTATTATTAC
61118031 TATTA-T
1 TATTATT
61118037 TATTACTAT
1 TATTA-T-T
61118046 TATTA-T
1 TATTATT
*
61118052 TATTATC
1 TATTATT
61118059 TATTA-T
1 TATTATT
61118065 TATTA-T
1 TATTATT
61118071 TATTATT
1 TATTATT
61118078 TATCTATT
1 TAT-TATT
61118086 TATT
1 TATT
61118090 TATTACCCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
6 22 0.49
7 10 0.22
8 7 0.16
9 6 0.13
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (7 bp):
TATTATT
Found at i:61120463 original size:75 final size:76
Alignment explanation
Indices: 61120375--61120527 Score: 236
Period size: 77 Copynumber: 2.0 Consensus size: 76
61120365 TTATTTTTCA
* *
61120375 TACTAATGTATAAAAACAAAAAA-AAATAAATTGAAAGTATAATATAAAAGAAAATGAGATAGGA
1 TACTAATGTATAAAAACAAAAAAGAAATAAATTGAAAGTATAAGAGAAAAGAAAATGAGATAGGA
61120439 GTATATGTTAG
66 GTATATGTTAG
* ** *
61120450 TACTAATGTATAAAAATAAAAAAGTATCTAAATTGAAATTATAAGAGAAAAGAAAATGAGATAGG
1 TACTAATGTATAAAAACAAAAAAG-AAATAAATTGAAAGTATAAGAGAAAAGAAAATGAGATAGG
61120515 AGTATATGTTAG
65 AGTATATGTTAG
61120527 T
1 T
61120528 TCAAAATTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
75 22 0.31
77 48 0.69
ACGTcount: A:0.55, C:0.03, G:0.16, T:0.27
Consensus pattern (76 bp):
TACTAATGTATAAAAACAAAAAAGAAATAAATTGAAAGTATAAGAGAAAAGAAAATGAGATAGGA
GTATATGTTAG
Found at i:61122805 original size:13 final size:13
Alignment explanation
Indices: 61122773--61122797 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61122763 TAAAGATATA
61122773 TAAAACTTATGTG
1 TAAAACTTATGTG
61122786 TAAAACTTATGT
1 TAAAACTTATGT
61122798 TAATAACTCT
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:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
TAAAACTTATGTG
Found at i:61125357 original size:16 final size:16
Alignment explanation
Indices: 61125331--61125379 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
61125321 TAAAATTGAG
61125331 TTGAGAAAATTATTTAA
1 TTGA-AAAATTATTTAA
*
61125348 TTGAAAAATTAATTAA
1 TTGAAAAATTATTTAA
61125364 TT--AAAATTAATTTAA
1 TTGAAAAATT-ATTTAA
61125379 T
1 T
61125380 GAATAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 6 0.21
15 6 0.21
16 13 0.45
17 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (16 bp):
TTGAAAAATTATTTAA
Found at i:61131176 original size:14 final size:14
Alignment explanation
Indices: 61131157--61131184 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
61131147 AAGAATTATA
61131157 ATTATTTAAATAAT
1 ATTATTTAAATAAT
61131171 ATTATTTAAATAAT
1 ATTATTTAAATAAT
61131185 TATAATTAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTATTTAAATAAT
Found at i:61131700 original size:13 final size:13
Alignment explanation
Indices: 61131678--61131715 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
61131668 AATTTCATTG
61131678 AAAATAAATTTTAA
1 AAAAT-AATTTTAA
*
61131692 AAAATAATTTTGA
1 AAAATAATTTTAA
61131705 AAAAT-ATTTTA
1 AAAATAATTTTA
61131716 CATAAAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 5 0.23
13 12 0.55
14 5 0.23
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (13 bp):
AAAATAATTTTAA
Found at i:61131801 original size:13 final size:14
Alignment explanation
Indices: 61131768--61131799 Score: 55
Period size: 14 Copynumber: 2.2 Consensus size: 14
61131758 AAAAAATCTA
61131768 TTTTCTAAAAATTGT
1 TTTTC-AAAAATTGT
61131783 TTTTCAAAAATTGT
1 TTTTCAAAAATTGT
61131797 TTT
1 TTT
61131800 CAGTACAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (14 bp):
TTTTCAAAAATTGT
Found at i:61144073 original size:25 final size:26
Alignment explanation
Indices: 61144013--61144061 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
61144003 ATTTGTTTTA
*
61144013 ATATTTG-TTT-TTATGTTTTTAAAT
1 ATATTTGATTTATTATATTTTTAAAT
61144037 ATATTTGATTTATTATATTTTTAAA
1 ATATTTGATTTATTATATTTTTAAA
61144062 ATTTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (26 bp):
ATATTTGATTTATTATATTTTTAAAT
Found at i:61149344 original size:4 final size:4
Alignment explanation
Indices: 61149335--61149375 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
61149325 TAGATAAGGC
61149335 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
61149376 CTTTTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:61154352 original size:43 final size:43
Alignment explanation
Indices: 61154302--61154452 Score: 146
Period size: 43 Copynumber: 3.5 Consensus size: 43
61154292 TATCTCATAT
* * *
61154302 ATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAAAC
1 ATGGTCTTACATGTAATCACATATCGATGCCAATGTCCCAGAC
* * * * *
61154345 AGGGTCTTACACT-AAATCGA-TTAACGATGCCAATGTCCCCGAC
1 ATGGTCTTACA-TGTAATC-ACATATCGATGCCAATGTCCCAGAC
* * * *
61154388 ATGGTCTTACACGTGATCTCA-ATACAATGCCAATGTCCCAGAC
1 ATGGTCTTACATGTAATCACATAT-CGATGCCAATGTCCCAGAC
61154431 ATGGTCTTACATGTAATCACAT
1 ATGGTCTTACATGTAATCACAT
61154453 CTCGGTAACC
Statistics
Matches: 82, Mismatches: 20, Indels: 11
0.73 0.18 0.10
Matches are distributed among these distances:
42 1 0.01
43 79 0.96
44 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCACATATCGATGCCAATGTCCCAGAC
Found at i:61157831 original size:25 final size:27
Alignment explanation
Indices: 61157803--61157853 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 27
61157793 CCATTTTTTT
61157803 AATAATA-TAGTTTTATT-T-TTTTAAA
1 AATAATATTA-TTTTATTATATTTTAAA
*
61157828 AATATTATTATTTTATTATATTTTAA
1 AATAATATTATTTTATTATATTTTAA
61157854 TAATTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 13 0.59
26 3 0.14
27 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (27 bp):
AATAATATTATTTTATTATATTTTAAA
Found at i:61159227 original size:11 final size:11
Alignment explanation
Indices: 61159192--61159219 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
61159182 GAGAGTAAGA
61159192 AATTTTAATGT
1 AATTTTAATGT
61159203 AATTTTAATGT
1 AATTTTAATGT
61159214 AATTTT
1 AATTTT
61159220 GATATAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (11 bp):
AATTTTAATGT
Found at i:61160853 original size:12 final size:12
Alignment explanation
Indices: 61160833--61160899 Score: 73
Period size: 12 Copynumber: 5.6 Consensus size: 12
61160823 TGCACCAACT
61160833 CCGGAGCCAGAG
1 CCGGAGCCAGAG
*
61160845 CCAGAGCCAGAG
1 CCGGAGCCAGAG
* *
61160857 CCGGAGGCAGTG
1 CCGGAGCCAGAG
*
61160869 CCGGACCCAGAG
1 CCGGAGCCAGAG
*
61160881 -CGGCGGCCAGAG
1 CCGG-AGCCAGAG
61160893 CCGGAGC
1 CCGGAGC
61160900 TACACTCAGG
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 3 0.07
12 37 0.86
13 3 0.07
ACGTcount: A:0.22, C:0.34, G:0.42, T:0.01
Consensus pattern (12 bp):
CCGGAGCCAGAG
Found at i:61164944 original size:6 final size:6
Alignment explanation
Indices: 61164933--61164961 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
61164923 TGCAAGGCTG
61164933 GGGGGT GGGGGT GGGGGT GGGGGT GGGGG
1 GGGGGT GGGGGT GGGGGT GGGGGT GGGGG
61164962 GGCAGGGACA
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:0.00, C:0.00, G:0.86, T:0.14
Consensus pattern (6 bp):
GGGGGT
Found at i:61165119 original size:24 final size:23
Alignment explanation
Indices: 61165081--61165138 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
61165071 ATTTAAAAAT
*
61165081 TATTAAAATATAATAAAATAATAA
1 TATTAAAA-AAAATAAAATAATAA
* *
61165105 TATTTAAAAAAAATAAAATTATAT
1 TA-TTAAAAAAAATAAAATAATAA
61165129 TATTAAAAAA
1 TATTAAAAAA
61165139 TAGGTCGCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.27
24 16 0.53
25 6 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
TATTAAAAAAAATAAAATAATAA
Found at i:61171669 original size:29 final size:30
Alignment explanation
Indices: 61171632--61171689 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
61171622 AAATTGATCC
* *
61171632 AATCAAAATTTCATGTGTAAAATTACACAA
1 AATCAAAATTTCAAGTATAAAATTACACAA
61171662 AATC-AAATTTCAAGTATAAAATTACACA
1 AATCAAAATTTCAAGTATAAAATTACACA
61171690 TTAGATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (30 bp):
AATCAAAATTTCAAGTATAAAATTACACAA
Found at i:61172997 original size:17 final size:17
Alignment explanation
Indices: 61172975--61173008 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
61172965 TTAAAAAAAA
61172975 GAGATAAACAGTTCTTT
1 GAGATAAACAGTTCTTT
61172992 GAGATAAACAGTTCTTT
1 GAGATAAACAGTTCTTT
61173009 TAGTTAAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
GAGATAAACAGTTCTTT
Found at i:61182210 original size:35 final size:35
Alignment explanation
Indices: 61182171--61182237 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 35
61182161 GGTTTTAAGG
61182171 TTAGGGTATTGCCAAAATAAGTTAAGGTTTAGTAT
1 TTAGGGTATTGCCAAAATAAGTTAAGGTTTAGTAT
* * ** * *
61182206 TTAGGTTTTTGTTAAAATAGGTTAGGGTTTAG
1 TTAGGGTATTGCCAAAATAAGTTAAGGTTTAG
61182238 AGTTTTAGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 26 1.00
ACGTcount: A:0.30, C:0.03, G:0.25, T:0.42
Consensus pattern (35 bp):
TTAGGGTATTGCCAAAATAAGTTAAGGTTTAGTAT
Found at i:61182329 original size:34 final size:34
Alignment explanation
Indices: 61182291--61182412 Score: 94
Period size: 34 Copynumber: 3.6 Consensus size: 34
61182281 AAAAATTATT
61182291 TAAATTAAGGTTTAAGGTTTATAAATAAATTAAA
1 TAAATTAAGGTTTAAGGTTTATAAATAAATTAAA
* * *
61182325 TAAATTAAGATTTTTAGGGTTT-TAAATAAATTAAGG
1 TAAATTAAG--GTTTAAGGTTTATAAATAAATTAA-A
* *
61182361 T---TTAGGGTTTATA-GTTTTTAAATAAATT-AA
1 TAAATTAAGGTTTA-AGGTTTATAAATAAATTAAA
* *
61182391 TCAAATTAGGGTTTAAAGTTTA
1 T-AAATTAAGGTTTAAGGTTTA
61182413 AGGTTAAATT
Statistics
Matches: 70, Mismatches: 8, Indels: 20
0.71 0.08 0.20
Matches are distributed among these distances:
30 1 0.01
31 9 0.13
32 10 0.14
33 5 0.07
34 23 0.33
35 12 0.17
36 10 0.14
ACGTcount: A:0.42, C:0.01, G:0.15, T:0.43
Consensus pattern (34 bp):
TAAATTAAGGTTTAAGGTTTATAAATAAATTAAA
Found at i:61182369 original size:24 final size:25
Alignment explanation
Indices: 61182320--61182370 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
61182310 TATAAATAAA
*
61182320 TTAAATAAATTAAGATTTTTAGGGTT
1 TTAAATAAATTAAGA-GTTTAGGGTT
61182346 TTAAATAAATTAAG-GTTTAGGGTT
1 TTAAATAAATTAAGAGTTTAGGGTT
61182370 T
1 T
61182371 ATAGTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 10 0.42
26 14 0.58
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (25 bp):
TTAAATAAATTAAGAGTTTAGGGTT
Found at i:61182757 original size:126 final size:126
Alignment explanation
Indices: 61182500--61182872 Score: 529
Period size: 127 Copynumber: 3.0 Consensus size: 126
61182490 TTGTACCCTA
* * * *
61182500 AAAAAATTATTTTGAGAAA-ACATTTCTGAATAAATAGTGTCAAAAACGCTTGAAGCAGGATGCA
1 AAAAAATAATTTTGA-AAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCA
* *
61182564 CTGTCAGCAAAATTACAGAAAAAAGCTACCACGTGGACGCTCTTTTTCTACAGTAATTCCTG
65 CTGTCAGCAAAATTACAGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCCTG
**
61182626 AAAAAATAATTTTGAAAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGTGC
1 AAAAAATAATTTTGAAAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCAC
*
61182691 TGTCAGCAAAAATCACAGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCCTG
66 TGTCAGC-AAAATTACAGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCCTG
* * * * * * *
61182753 AAAAAATAATTTTGAGAAGATGTTTCTAAACAAGTAGTGT--TAAA-GCTTCAAGTAGGATGCAA
1 AAAAAATAATTTTGAAAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCAC
* * *
61182815 TGTCAGCAAAATTTCTGAAAAAAGCTCTCACGTGGACGCTCTTTTTCTACAGTAGTTC
66 TGTCAGCAAAATTACAGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTC
61182873 ATGATTGGCC
Statistics
Matches: 223, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
123 47 0.21
124 21 0.09
125 6 0.03
126 62 0.28
127 87 0.39
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (126 bp):
AAAAAATAATTTTGAAAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCAC
TGTCAGCAAAATTACAGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCCTG
Found at i:61186407 original size:18 final size:18
Alignment explanation
Indices: 61186381--61186423 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
61186371 GACTGAAAAA
* *
61186381 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
61186399 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
61186417 AGGATAC
1 AGGATAC
61186424 GCACCTAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:61186538 original size:30 final size:30
Alignment explanation
Indices: 61186495--61186573 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
61186485 ATGATTGTAG
* *
61186495 GGCACTATTGATGGGCC-AGGTGATTGTTTA
1 GGCACTGTTGATGGGCCTA-ATGATTGTTTA
* *
61186525 GGCCCTGTTGATGGGCCTAATGATTGTTTG
1 GGCACTGTTGATGGGCCTAATGATTGTTTA
*
61186555 GGCACTGTTGATAGGCCTA
1 GGCACTGTTGATGGGCCTA
61186574 TGCCATCATC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 41 0.98
31 1 0.02
ACGTcount: A:0.18, C:0.16, G:0.33, T:0.33
Consensus pattern (30 bp):
GGCACTGTTGATGGGCCTAATGATTGTTTA
Found at i:61192580 original size:27 final size:27
Alignment explanation
Indices: 61192550--61192603 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
61192540 ATTTTTAATT
61192550 ATTTA-TAATGATAATAATTGAAAAATA
1 ATTTATTAAT-ATAATAATTGAAAAATA
* *
61192577 ATTTATTAATTTAATAATTTAAAAATA
1 ATTTATTAATATAATAATTGAAAAATA
61192604 TATTCACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (27 bp):
ATTTATTAATATAATAATTGAAAAATA
Found at i:61192614 original size:27 final size:27
Alignment explanation
Indices: 61192561--61192617 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
61192551 TTTATAATGA
* *
61192561 TAATAATTGAAAAATAATTTATTAATT
1 TAATAATTGAAAAATAATTCATCAATT
*
61192588 TAATAATTTAAAAATATATTCA-CAATT
1 TAATAATTGAAAAATA-ATTCATCAATT
61192615 TAA
1 TAA
61192618 AAATATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (27 bp):
TAATAATTGAAAAATAATTCATCAATT
Found at i:61195195 original size:18 final size:18
Alignment explanation
Indices: 61195153--61195196 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
61195143 AAATCATCCC
* *
61195153 TAAAATCACTTGTAAAAT
1 TAAAATTACATGTAAAAT
61195171 TAAAATTACATGTATAAA-
1 TAAAATTACATGTA-AAAT
61195189 TAAAATTA
1 TAAAATTA
61195197 AAAACATACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.34
Consensus pattern (18 bp):
TAAAATTACATGTAAAAT
Found at i:61204748 original size:3 final size:3
Alignment explanation
Indices: 61204740--61204764 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
61204730 CACTATAATC
61204740 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
61204765 TTTCCTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:61205547 original size:159 final size:158
Alignment explanation
Indices: 61205254--61205547 Score: 434
Period size: 159 Copynumber: 1.9 Consensus size: 158
61205244 TTTTTTTCTC
**
61205254 GTTCAATTTAGTTTGATTATAAGCTTATGAAGAAATTAAACGATTTCGCAGTAGCATTTTAGTTG
1 GTTCAATTTAGTTTGATTATAAGCTTATGAAGAAATTAAACGATTTCGCAGTAGCATTTTAGGCG
*
61205319 ATATCCTAATGCTTAATTTCGTCATTCTTATGCTGAATTATTTGTGGTTTAATGGATTTTACTCT
66 ATATCCTAATGCTTAATTTCGTCATTCTTATGCTGAATGATTTGTGGTTTAATGGATTTTACTCT
61205384 CTATTCAATGCTACTTTTTGTGTTCATT
131 CTATTCAATGCTACTTTTTGTGTTCATT
* * * * **
61205412 GTTCCATTTAGTTTGATTATAAGCTTATGATGGAA-TAAGGGCGATTTCG-AGTTTTCATTTTAG
1 GTTCAATTTAGTTTGATTATAAGCTTATGAAGAAATTAA--ACGATTTCGCAG-TAGCATTTTAG
61205475 GCGATATCCTGAA-GCTTAATTTCGT-ATTTCTTATGCTGAATGATTTGTGGTTTAATGGATTTT
63 GCGATATCCT-AATGCTTAATTTCGTCA-TTCTTATGCTGAATGATTTGTGGTTTAATGGATTTT
61205538 ACTCTCTATT
126 ACTCTCTATT
61205548 TGCAAATTAG
Statistics
Matches: 122, Mismatches: 9, Indels: 9
0.87 0.06 0.06
Matches are distributed among these distances:
157 3 0.02
158 35 0.29
159 82 0.67
160 2 0.02
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (158 bp):
GTTCAATTTAGTTTGATTATAAGCTTATGAAGAAATTAAACGATTTCGCAGTAGCATTTTAGGCG
ATATCCTAATGCTTAATTTCGTCATTCTTATGCTGAATGATTTGTGGTTTAATGGATTTTACTCT
CTATTCAATGCTACTTTTTGTGTTCATT
Found at i:61209185 original size:28 final size:28
Alignment explanation
Indices: 61209151--61209303 Score: 155
Period size: 28 Copynumber: 5.5 Consensus size: 28
61209141 CAAACCAAAA
* **
61209151 AAGTGCAAGCCAAAGTGGCGGACAATTT
1 AAGTGCAAGCCAAAATGGCGGACAATCC
* * *
61209179 AAGTGCAAGCCAAAATGGCGGATAGTTC
1 AAGTGCAAGCCAAAATGGCGGACAATCC
* **
61209207 AAGT-AAAGCCAAAATGATGGACAATCC
1 AAGTGCAAGCCAAAATGGCGGACAATCC
* * * *
61209234 AAGTACAAGCTAAAATGGTGGACAGTCC
1 AAGTGCAAGCCAAAATGGCGGACAATCC
* * *
61209262 AAGTACAAGCTAAAATGGCGGGCAATCC
1 AAGTGCAAGCCAAAATGGCGGACAATCC
61209290 AAGTGCAAGCCAAA
1 AAGTGCAAGCCAAA
61209304 GCGTCAGACA
Statistics
Matches: 105, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
27 21 0.20
28 84 0.80
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.16
Consensus pattern (28 bp):
AAGTGCAAGCCAAAATGGCGGACAATCC
Found at i:61209229 original size:55 final size:56
Alignment explanation
Indices: 61209151--61209303 Score: 173
Period size: 55 Copynumber: 2.8 Consensus size: 56
61209141 CAAACCAAAA
* * * ** * *
61209151 AAGTGCAAGCCAAAGTGGCGGACAATTTAAGTGCAAGCCAAAATGGCGGATAGTTC
1 AAGTACAAGCCAAAATGACGGACAATCCAAGTGCAAGCCAAAATGGCGGACAGTCC
* * * *
61209207 AAGTA-AAGCCAAAATGATGGACAATCCAAGTACAAGCTAAAATGGTGGACAGTCC
1 AAGTACAAGCCAAAATGACGGACAATCCAAGTGCAAGCCAAAATGGCGGACAGTCC
* * *
61209262 AAGTACAAGCTAAAATGGCGGGCAATCCAAGTGCAAGCCAAA
1 AAGTACAAGCCAAAATGACGGACAATCCAAGTGCAAGCCAAA
61209304 GCGTCAGACA
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
55 45 0.57
56 34 0.43
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.16
Consensus pattern (56 bp):
AAGTACAAGCCAAAATGACGGACAATCCAAGTGCAAGCCAAAATGGCGGACAGTCC
Found at i:61209520 original size:73 final size:73
Alignment explanation
Indices: 61209385--61209520 Score: 175
Period size: 73 Copynumber: 1.9 Consensus size: 73
61209375 AAATGAGGGC
* * * * * *
61209385 AAGCCAAAGTGGTGGATGATCTAAATGTAAGCTAAAAGTGGGTGCAAGCCAAAATTGCAGACAAC
1 AAGCCAAAGTGGCGGAAGATCTAAATGCAAGCCAAAAGTAGGTGCAAGCCAAAATGGCAGACAAC
61209450 CCAAGTGT
66 CCAAGTGT
* * *
61209458 AAGCCAAAGTGGCGGACAG-TCTAAATGCAAGCCAAAAGTAGGTGCAAGCTAAAGTGGTAGACA
1 AAGCCAAAGTGGCGGA-AGATCTAAATGCAAGCCAAAAGTAGGTGCAAGCCAAAATGGCAGACA
61209521 GTCTAAATAC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
73 52 0.98
74 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (73 bp):
AAGCCAAAGTGGCGGAAGATCTAAATGCAAGCCAAAAGTAGGTGCAAGCCAAAATGGCAGACAAC
CCAAGTGT
Found at i:61209534 original size:101 final size:100
Alignment explanation
Indices: 61209429--61209624 Score: 268
Period size: 101 Copynumber: 1.9 Consensus size: 100
61209419 AAAGTGGGTG
* * *** *
61209429 CAAGCCAAAATTGCAGACAACCCAAGTGTAAGCCAAAGTGGCGGACAGTCTAAATGCAAGCCAAA
1 CAAGCCAAAATGGCAGACAACCCAAGTGCAAGCCAAAGCAACGAACAGTCTAAATGCAAGCCAAA
61209494 AGTAGGTG-CAAGCTAAAGTGGTAGACAGTCTAAATA
66 A-TAGGTGAC-AGCTAAAGTGGTAGACAGTCTAAATA
* * *
61209530 CAAGCCAAAATGGTAGACAACCCAAGTGCAAGCCAAAGCAATGAACAGTCTAAATTCAAGCCAAA
1 CAAGCCAAAATGGCAGACAACCCAAGTGCAAGCCAAAGCAACGAACAGTCTAAATGCAAGCCAAA
* *
61209595 ATTGGTGACAGCTAAAGTGGTGGACAGTCT
66 ATAGGTGACAGCTAAAGTGGTAGACAGTCT
61209625 GTCACACCCC
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
100 25 0.30
101 58 0.70
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.16
Consensus pattern (100 bp):
CAAGCCAAAATGGCAGACAACCCAAGTGCAAGCCAAAGCAACGAACAGTCTAAATGCAAGCCAAA
ATAGGTGACAGCTAAAGTGGTAGACAGTCTAAATA
Found at i:61215491 original size:28 final size:28
Alignment explanation
Indices: 61215459--61215517 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
61215449 AAATGGGTGT
*
61215459 AAGCCAATGTAGC-GAACAATCCAAGTGC
1 AAGCCAAAGTAGCAG-ACAATCCAAGTGC
* *
61215487 AAGCCAAAGTGGCAGACACTCCAAGTGC
1 AAGCCAAAGTAGCAGACAATCCAAGTGC
61215515 AAG
1 AAG
61215518 ATATTTCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.39, C:0.25, G:0.24, T:0.12
Consensus pattern (28 bp):
AAGCCAAAGTAGCAGACAATCCAAGTGC
Found at i:61218516 original size:20 final size:19
Alignment explanation
Indices: 61218493--61218541 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
61218483 TCCATTAAAA
*
61218493 ATTTTAGTATTTGATTAGAG
1 ATTTTAGTATCTG-TTAGAG
* *
61218513 ATTTTTGCATCTGTTAGAG
1 ATTTTAGTATCTGTTAGAG
*
61218532 ATTTTGGTAT
1 ATTTTAGTAT
61218542 AGCATTTGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.24, C:0.04, G:0.20, T:0.51
Consensus pattern (19 bp):
ATTTTAGTATCTGTTAGAG
Found at i:61218691 original size:19 final size:19
Alignment explanation
Indices: 61218664--61218753 Score: 83
Period size: 19 Copynumber: 4.7 Consensus size: 19
61218654 ATTTAGTTAG
61218664 GAAATTTTGGTATTCCTTA
1 GAAATTTTGGTATTCCTTA
* * **
61218683 GAGATTTTGATATTTGTTA
1 GAAATTTTGGTATTCCTTA
*
61218702 GAAATTTTGGTA-TCAGTTA
1 GAAATTTTGGTATTC-CTTA
* *
61218721 AAAATTTTGGTACTCCTTCA
1 GAAATTTTGGTATTCCTT-A
*
61218741 AAAATTTTGGTAT
1 GAAATTTTGGTAT
61218754 GCCACGTAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
18 1 0.02
19 42 0.72
20 15 0.26
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.46
Consensus pattern (19 bp):
GAAATTTTGGTATTCCTTA
Found at i:61218728 original size:38 final size:40
Alignment explanation
Indices: 61218654--61218729 Score: 95
Period size: 38 Copynumber: 1.9 Consensus size: 40
61218644 TTCGTTAGAG
* *
61218654 ATTTAGTTAGGAAATTTTGGTATTCCTTAGAGATTTTGAT
1 ATTTAGTTAGGAAATTTTGGTATTCCTTAAAAATTTTGAT
*
61218694 ATTT-GTTA-GAAATTTTGGTA-TCAGTTAAAAATTTTG
1 ATTTAGTTAGGAAATTTTGGTATTC-CTTAAAAATTTTG
61218730 GTACTCCTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 2 0.06
38 22 0.69
39 4 0.12
40 4 0.12
ACGTcount: A:0.30, C:0.04, G:0.18, T:0.47
Consensus pattern (40 bp):
ATTTAGTTAGGAAATTTTGGTATTCCTTAAAAATTTTGAT
Found at i:61218745 original size:20 final size:19
Alignment explanation
Indices: 61218703--61218753 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
61218693 TATTTGTTAG
*
61218703 AAATTTTGGTATCAGTTAA
1 AAATTTTGGTATCACTTAA
61218722 AAATTTTGGTACTC-CTTCAA
1 AAATTTTGGTA-TCACTT-AA
61218742 AAATTTTGGTAT
1 AAATTTTGGTAT
61218754 GCCACGTAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (19 bp):
AAATTTTGGTATCACTTAA
Found at i:61218864 original size:23 final size:23
Alignment explanation
Indices: 61218809--61218864 Score: 55
Period size: 23 Copynumber: 2.4 Consensus size: 23
61218799 CCATAAAAAC
61218809 ATATAATT-AATAAAAATACTAAA
1 ATAT-ATTAAATAAAAATACTAAA
*
61218832 ATGT-TATAAATAAAATATAC-AAA
1 ATATAT-TAAATAAAA-ATACTAAA
61218855 ATATATTAAA
1 ATATATTAAA
61218865 AGTGCACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
21 1 0.04
22 1 0.04
23 20 0.74
24 5 0.19
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (23 bp):
ATATATTAAATAAAAATACTAAA
Found at i:61218911 original size:20 final size:19
Alignment explanation
Indices: 61218886--61218979 Score: 64
Period size: 19 Copynumber: 4.8 Consensus size: 19
61218876 TTATAAAAAT
61218886 TTAGAAATTTTGGTATTCAA
1 TTAGAAATTTTGGTATTC-A
* *
61218906 TTAGAAATATTGGCA-TCTA
1 TTAGAAATTTTGGTATTC-A
* * *
61218925 TTAAAAATATTGGTATTTGA
1 TTAGAAATTTTGGTA-TTCA
** **
61218945 TTAGGGATTTTTATATTCA
1 TTAGAAATTTTGGTATTCA
*
61218964 TTAGAAATTTTAGTAT
1 TTAGAAATTTTGGTAT
61218980 ATTATTTGCC
Statistics
Matches: 55, Mismatches: 17, Indels: 5
0.71 0.22 0.06
Matches are distributed among these distances:
19 31 0.56
20 23 0.42
21 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (19 bp):
TTAGAAATTTTGGTATTCA
Found at i:61222306 original size:41 final size:41
Alignment explanation
Indices: 61222239--61222581 Score: 481
Period size: 41 Copynumber: 8.4 Consensus size: 41
61222229 CGTTCTAGAA
*
61222239 AAAACGCCGC-TAAAACCAGAGCATTAGCGGCGCTTTTCCT
1 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCCT
** * *
61222279 AAAACGCAACAAAAAACTAGAGCATTAGCGGCGCTTTTCGT
1 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCCT
* **
61222320 AAAATGCCGTTAAAAACCAGAGCATTAGCGGCGCTTTTCCT
1 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCCT
* *
61222361 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTCTCGT
1 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCCT
* * * *
61222402 AAAATGCTGCTAAAAACTAGAGCATTAGCGGCGCTTTTCCT
1 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCCT
* *
61222443 AAAACGCCGTAAAAAACCAGAGCATTAGCGTCGCTTTTCCT
1 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCCT
*
61222484 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCGT
1 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCCT
* * * *
61222525 AAAACGCCGCTAAATACCAGAGCATCAGCGGCGCTTTTCGT
1 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCCT
*
61222566 AAAACGCCGCTAAAAA
1 AAAACGCCGCAAAAAA
61222582 TCTCATAACC
Statistics
Matches: 266, Mismatches: 36, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
40 8 0.03
41 258 0.97
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (41 bp):
AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCCT
Found at i:61222425 original size:123 final size:123
Alignment explanation
Indices: 61222239--61222581 Score: 535
Period size: 123 Copynumber: 2.8 Consensus size: 123
61222229 CGTTCTAGAA
* * * *
61222239 AAAACGCCGC-TAAAACCAGAGCATTAGCGGCGCTTTTCCTAAAACGCAACAAAAAACTAGAGCA
1 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCGTAAAACGCAGCTAAAAACTAGAGCA
*
61222303 TTAGCGGCGCTTTTCGTAAAATGCCGTTAAAAACCAGAGCATTAGCGGCGCTTTTCCT
66 TTAGCGGCGCTTTTCGTAAAACGCCGTTAAAAACCAGAGCATTAGCGGCGCTTTTCCT
* * *
61222361 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTCTCGTAAAATGCTGCTAAAAACTAGAGCA
1 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCGTAAAACGCAGCTAAAAACTAGAGCA
* * *
61222426 TTAGCGGCGCTTTTCCTAAAACGCCGTAAAAAACCAGAGCATTAGCGTCGCTTTTCCT
66 TTAGCGGCGCTTTTCGTAAAACGCCGTTAAAAACCAGAGCATTAGCGGCGCTTTTCCT
* * *
61222484 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCGTAAAACGCCGCTAAATACCAGAGCA
1 AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCGTAAAACGCAGCTAAAAACTAGAGCA
* *
61222549 TCAGCGGCGCTTTTCGTAAAACGCCGCTAAAAA
66 TTAGCGGCGCTTTTCGTAAAACGCCGTTAAAAA
61222582 TCTCATAACC
Statistics
Matches: 200, Mismatches: 20, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
122 10 0.05
123 190 0.95
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (123 bp):
AAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCGTAAAACGCAGCTAAAAACTAGAGCA
TTAGCGGCGCTTTTCGTAAAACGCCGTTAAAAACCAGAGCATTAGCGGCGCTTTTCCT
Found at i:61222760 original size:14 final size:14
Alignment explanation
Indices: 61222738--61222777 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
61222728 TTAATTATCA
* *
61222738 TTATAGTTTAAGGT
1 TTATGGTTTAAGAT
61222752 TTATGGTTTAAGAT
1 TTATGGTTTAAGAT
*
61222766 ATATGGTTTAAG
1 TTATGGTTTAAG
61222778 CATGTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (14 bp):
TTATGGTTTAAGAT
Found at i:61224728 original size:18 final size:17
Alignment explanation
Indices: 61224707--61224749 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
61224697 ATGATCTTAA
61224707 TGATGATGATGTTGATAC
1 TGATGATGATGTTGAT-C
*
61224725 TGATGTTGATGTTGATC
1 TGATGATGATGTTGATC
61224742 TCGATGAT
1 T-GATGAT
61224750 TATACCCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (17 bp):
TGATGATGATGTTGATC
Found at i:61225339 original size:61 final size:61
Alignment explanation
Indices: 61225196--61225377 Score: 337
Period size: 61 Copynumber: 3.0 Consensus size: 61
61225186 CCAAAATTTG
61225196 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATATTTTTGTTCTGAAATGGAAAATTC
1 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGAT-TTTTTGTTCTGAAATGGAAAATTC
61225258 ATTTCTTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATTTTTTGTTCTGAAATGGAAAATTC
1 ATTTC-TTTTTTGTCAGTTTTATGTCTGTTGTTTGGATTTTTTGTTCTGAAATGGAAAATTC
*
61225320 ATTTCCTTTTTGTCAGTTTTATGTCTGTTGTTTGGATTTTTTGTTCTGAAATGGAAAA
1 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATTTTTTGTTCTGAAATGGAAAA
61225378 ACTAGTTTGT
Statistics
Matches: 118, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
61 52 0.44
62 34 0.29
63 32 0.27
ACGTcount: A:0.19, C:0.08, G:0.18, T:0.55
Consensus pattern (61 bp):
ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATTTTTTGTTCTGAAATGGAAAATTC
Found at i:61227839 original size:288 final size:290
Alignment explanation
Indices: 61227323--61228038 Score: 1382
Period size: 288 Copynumber: 2.5 Consensus size: 290
61227313 CCAACCTTAT
61227323 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
1 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
*
61227388 GCAAGATATAATGGATCCTCCCTAAGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
66 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
61227453 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACATTAATTTATT
131 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACATTAATTTATT
*
61227518 TCCAATTTACTTATAAAAATTAAACTACGATTC-TTTTTGATATTATTATATTCAAATTACTA-T
196 TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATATTATTATATTCAAATCACTATT
61227581 TTTTTATATTAATAATGTTCGATTTTAATA
261 TTTTTATATTAATAATGTTCGATTTTAATA
61227611 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
1 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
61227676 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
66 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
61227741 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACATTAATTTATT
131 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACATTAATTTATT
61227806 TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATATTATTATATTCAAATCACTATT
196 TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATATTATTATATTCAAATCACTATT
*
61227871 TTTTTATATTAATAATGTTTGATTTTAATA
261 TTTTTATATTAATAATGTTCGATTTTAATA
*
61227901 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACTTGACGGGTTGCCTTATATCGAGCT
1 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
61227966 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
66 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
61228031 AAAGACTT
131 AAAGACTT
61228039 TTTATCACAA
Statistics
Matches: 422, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
288 227 0.54
289 28 0.07
290 167 0.40
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (290 bp):
TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACATTAATTTATT
TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATATTATTATATTCAAATCACTATT
TTTTTATATTAATAATGTTCGATTTTAATA
Found at i:61228287 original size:15 final size:15
Alignment explanation
Indices: 61228243--61228298 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
61228233 AACGACATGT
*
61228243 ATATTACTTAATTAAA
1 ATATTATTTAATT-AA
61228259 ATAATT-TTT-A-TAA
1 AT-ATTATTTAATTAA
61228272 ATATTATTTAATTAA
1 ATATTATTTAATTAA
61228287 ATATTATTTAAT
1 ATATTATTTAAT
61228299 CCTGCTACTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
12 3 0.09
13 7 0.20
14 2 0.06
15 16 0.46
16 4 0.11
17 3 0.09
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATTATTTAATTAA
Found at i:61228443 original size:9 final size:9
Alignment explanation
Indices: 61228403--61228554 Score: 171
Period size: 9 Copynumber: 17.0 Consensus size: 9
61228393 TATTTGATAT
*
61228403 CATAATTTA
1 CATAACTTA
*
61228412 TATAACTTA
1 CATAACTTA
* *
61228421 CAAAACGTA
1 CATAACTTA
61228430 CATAACTTA
1 CATAACTTA
*
61228439 TATAACTTA
1 CATAACTTA
* *
61228448 GATAA-ATA
1 CATAACTTA
*
61228456 TATAACTTA
1 CATAACTTA
*
61228465 TATAACTTA
1 CATAACTTA
*
61228474 CATAACTCA
1 CATAACTTA
* *
61228483 TATAACATA
1 CATAACTTA
61228492 CATAACTTA
1 CATAACTTA
61228501 CATAACTTA
1 CATAACTTA
*
61228510 TATAACTTA
1 CATAACTTA
61228519 CATAACTTA
1 CATAACTTA
61228528 CATAACTTA
1 CATAACTTA
*
61228537 TATAACTTA
1 CATAACTTA
61228546 CATAACTTA
1 CATAACTTA
61228555 TATGTTGTCA
Statistics
Matches: 119, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
8 6 0.05
9 113 0.95
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (9 bp):
CATAACTTA
Found at i:61234338 original size:31 final size:31
Alignment explanation
Indices: 61234292--61234358 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
61234282 TTGTTGTATT
* *
61234292 TTTTATGTTAAATTTGCTGTTTTTGGCTGCA
1 TTTTATATTAAATTTGCTGTATTTGGCTGCA
* * * *
61234323 TTTTATATTATATTTGTTGTATTTGGTTGGA
1 TTTTATATTAAATTTGCTGTATTTGGCTGCA
61234354 TTTTA
1 TTTTA
61234359 ATGCAGGAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.18, C:0.04, G:0.18, T:0.60
Consensus pattern (31 bp):
TTTTATATTAAATTTGCTGTATTTGGCTGCA
Found at i:61234457 original size:43 final size:42
Alignment explanation
Indices: 61234410--61234508 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 42
61234400 ATCTGTCAAA
* *
61234410 TTTAGCGGCGTTTGTAAAAAAAACGTCGCTAAAAGCCTTGACC
1 TTTAGCGGCGTTT-CAAAAAAAACGCCGCTAAAAGCCTTGACC
*** *
61234453 TTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAAGCCTTGACC
1 TTTAGCGGCG-TTTCAAAAAAAACGCCGCTAAAAGCCTTGACC
61234496 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
61234509 TTTTCCAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
42 3 0.06
43 43 0.88
44 3 0.06
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (42 bp):
TTTAGCGGCGTTTCAAAAAAAACGCCGCTAAAAGCCTTGACC
Found at i:61242106 original size:206 final size:208
Alignment explanation
Indices: 61241706--61242125 Score: 645
Period size: 206 Copynumber: 2.0 Consensus size: 208
61241696 TAAGAACTTG
*
61241706 CTCAATTCAGAACCATTATCTAACAAACCATTCATGAAGAATATAAAAAAATAAAATCATCATAA
1 CTCAATTCAAAACCATTATCTAACAAACCATTCATGAAGAATATAAAAAAATAAAATCATCATAA
* * *
61241771 AACCATTCCAAGTAAGTCAATCAACCGTAAAATTAGAGCTTATAGCAAATGAAACTATTTGCATT
66 AACCATTCCAAGTAAGTCAATCAACCGTAAAATTAGAGCTCATAGCAAATG-AACTACTTGCATG
*
61241836 CATGCAAATGAGGTTTCCATACTATTCTCATAATGTCACATAAGACATAAGGCTTTAACAACTAC
130 CATGCAAATGAGGTTTCCATACTATTCTCATAATGTCACATAAGACATAAGCCTTTAACAACTAC
*
61241901 ATCACAACTAATGC
195 ATCACAACCAATGC
* * *
61241915 CTCAATTCAAAACCATTATCTAACAGACCATTCATGAAGAATATTAACAAAATAAAATCATTATA
1 CTCAATTCAAAACCATTATCTAACAAACCATTCATGAAGAATA-TAAAAAAATAAAATCATCATA
* *
61241980 AAACCATTCTAAGTAAGTCAA-CTAATCGTAAAATCTA-AGCTCATAGCAAATG-A-T-CTTGCA
65 AAACCATTCCAAGTAAGTCAATC-AACCGTAAAAT-TAGAGCTCATAGCAAATGAACTACTTGCA
*
61242040 TGCATGCAAATGAGGTTTCCATA-TGATTCTCGTAATGTCACATAAGACATAAGCCTTTAACAAC
128 TGCATGCAAATGAGGTTTCCATACT-ATTCTCATAATGTCACATAAGACATAAGCCTTTAACAAC
61242104 TACATCACAACCAATGC
192 TACATCACAACCAATGC
61242121 CTCAA
1 CTCAA
61242126 GTACTGAATT
Statistics
Matches: 195, Mismatches: 12, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
205 1 0.01
206 85 0.44
207 1 0.01
208 1 0.01
209 42 0.22
210 63 0.32
211 2 0.01
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.27
Consensus pattern (208 bp):
CTCAATTCAAAACCATTATCTAACAAACCATTCATGAAGAATATAAAAAAATAAAATCATCATAA
AACCATTCCAAGTAAGTCAATCAACCGTAAAATTAGAGCTCATAGCAAATGAACTACTTGCATGC
ATGCAAATGAGGTTTCCATACTATTCTCATAATGTCACATAAGACATAAGCCTTTAACAACTACA
TCACAACCAATGC
Done.