Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 172 of 356
Found at i:55991022 original size:25 final size:25
Alignment explanation
Indices: 55990994--55991046 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
55990984 GATAAATGTG
55990994 ATTGCCTTATAAAATGAGATCTTAC
1 ATTGCCTTATAAAATGAGATCTTAC
55991019 ATTGCCTTATAAAATGAGATCTTAC
1 ATTGCCTTATAAAATGAGATCTTAC
55991044 ATT
1 ATT
55991047 TGTTGCTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (25 bp):
ATTGCCTTATAAAATGAGATCTTAC
Found at i:55994833 original size:49 final size:47
Alignment explanation
Indices: 55994773--55995323 Score: 841
Period size: 47 Copynumber: 11.6 Consensus size: 47
55994763 GATAATTGTG
* * *
55994773 ATGTGAATGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
55994820 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * *
55994867 ATGTGAAAGTGTATATATGAGATAAGGCCGAATCGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
55994914 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
55994963 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
55995010 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
55995059 ATATGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
55995108 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
55995157 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
55995204 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
55995251 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
55995298 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
55995324 TCCCGAAGGG
Statistics
Matches: 470, Mismatches: 30, Indels: 8
0.93 0.06 0.02
Matches are distributed among these distances:
47 286 0.61
49 184 0.39
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:55994880 original size:96 final size:95
Alignment explanation
Indices: 55994773--55995323 Score: 847
Period size: 96 Copynumber: 5.8 Consensus size: 95
55994763 GATAATTGTG
* * * * *
55994773 ATGTGAATGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG-TATATA
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGATATATA
*
55994837 TGTGATAAGGCCTAATAGCCGATGTGATGA
66 TGTGATAAGGCCTAATGGCCGATGTGATGA
* *
55994867 ATGTGAAAGTGTATATATGAGATAAGGCCGAATCGCCAATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG-ATATAT
55994932 ATGTGATAAGGCCTAATGGCCGATGTGATGA
65 ATGTGATAAGGCCTAATGGCCGATGTGATGA
55994963 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG-ATATAT
55995028 ATGTGATAAGGCCTAATGGCCGATGTGATGA
65 ATGTGATAAGGCCTAATGGCCGATGTGATGA
* * *
55995059 ATATGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG-ATAT
55995124 ATATGTGATAAGGCCTAATGGCCGATGTGATGA
63 ATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * *
55995157 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG-TATATA
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGATATATA
*
55995221 TGTGATGAGGCCTAATGGCCGATGTGATGA
66 TGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * *
55995251 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTG-TATAAA
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGATATATA
55995315 TGTGATAAG
66 TGTGATAAG
55995324 TCCCGAAGGG
Statistics
Matches: 428, Mismatches: 25, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
94 150 0.35
96 185 0.43
98 93 0.22
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (95 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGATATATA
TGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:56005855 original size:46 final size:45
Alignment explanation
Indices: 56005773--56006088 Score: 152
Period size: 46 Copynumber: 6.9 Consensus size: 45
56005763 CCCATCCACG
* * * * * *
56005773 GTCTTATTTATCTT-TGACATGATGCCATAGTGTCTTTCAACTACA
1 GTCTTATTAATTTTCTGTCATGTTGCCATGGTATCTTTCAAC-ACA
* *
56005818 GTCTTACTAATTTTCTGTCATGTTGCCAAGGTATCTTTCAA-ACA
1 GTCTTATTAATTTTCTGTCATGTTGCCATGGTATCTTTCAACACA
* * *
56005862 TGGTCTTATTCA-TTTCATGTCACGCTGCCATGGTATCTTTCAAC-CA
1 --GTCTTATTAATTTTC-TGTCATGTTGCCATGGTATCTTTCAACACA
* * *
56005908 TGGTCTTATTTATTTCCCGTCATGTTGCCATGGTATCTTTCAAC-CA
1 --GTCTTATTAATTTTCTGTCATGTTGCCATGGTATCTTTCAACACA
* ** * *
56005954 TGGTCTTA-CACGTTTCATATCA-GGTGCCATGGTATCTTTCAAC-CA
1 --GTCTTATTAATTTTC-TGTCATGTTGCCATGGTATCTTTCAACACA
* ** * * *
56005999 TGGTCTTA-CACGTTTCATATCAGGCTGCCATGGTATCTTTCAAC-CA
1 --GTCTTATTAATTTTC-TGTCATGTTGCCATGGTATCTTTCAACACA
* * *
56006045 TGGTCTTA-CACA-TTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 --GTCTTATTA-ATTTTC-TGTCATGTTGCCATGGTATCTTTCAAC
56006089 CATGGTCTTA
Statistics
Matches: 233, Mismatches: 29, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
44 3 0.01
45 62 0.27
46 165 0.71
47 3 0.01
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (45 bp):
GTCTTATTAATTTTCTGTCATGTTGCCATGGTATCTTTCAACACA
Found at i:56005915 original size:92 final size:91
Alignment explanation
Indices: 56005795--56006099 Score: 378
Period size: 92 Copynumber: 3.3 Consensus size: 91
56005785 TTTGACATGA
* * * ** * *
56005795 TGCCATAGTGTCTTTCAACTACAGTCTTACTAATTTTCTGTCATGTTGCCAAGGTATCTTTCAAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACTAATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
** *
56005860 CATGGTCTTATTCATTTCATGTCACGC
66 CATGGTCTTACACATTTCATATCA-GC
* * * *
56005887 TGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCCCGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTAATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
* *
56005952 CATGGTCTTACACGTTTCATATCAGG
66 CATGGTCTTACACATTTCATATCAGC
** * * *
56005978 TGCCATGGTATCTTTCAACCATGGTCTTAC-ACGTTTCATATCAGGCTGCCATGGTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACTAATTTTC-TGTCATGTTGCCATGGTATCTTTCAA
*
56006042 CCATGGTCTTACACATTTCATATCAGGT
65 CCATGGTCTTACACATTTCATATCA-GC
56006070 TGCCATGGTATCTTTCAACCATGGTCTTAC
1 TGCCATGGTATCTTTCAACCATGGTCTTAC
56006100 ACATTTCATA
Statistics
Matches: 184, Mismatches: 27, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
90 3 0.02
91 76 0.41
92 105 0.57
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (91 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTAATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTCATATCAGC
Found at i:56006001 original size:137 final size:137
Alignment explanation
Indices: 56005841--56006113 Score: 411
Period size: 137 Copynumber: 2.0 Consensus size: 137
56005831 TCTGTCATGT
** *
56005841 TGCCAAGGTATCTTTCAAACATGGTCTTATTCATTTCATGTCACGCTGCCATGGTATCTTTCAAC
1 TGCCAAGGTATCTTTCAAACATGGTCTTACACATTTCATATCACGCTGCCATGGTATCTTTCAAC
*** * * * *
56005906 CATGGTCTTATTTATTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCA
66 CATGGTCTTACACATTTCACATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
56005971 TATCAGG
131 TATCAGG
* * * *
56005978 TGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCAGGCTGCCATGGTATCTTTCAAC
1 TGCCAAGGTATCTTTCAAACATGGTCTTACACATTTCATATCACGCTGCCATGGTATCTTTCAAC
*
56006043 CATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
66 CATGGTCTTACACATTTCACATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
56006108 TATCAG
131 TATCAG
56006114 AGAGCACACT
Statistics
Matches: 121, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
137 121 1.00
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (137 bp):
TGCCAAGGTATCTTTCAAACATGGTCTTACACATTTCATATCACGCTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTCACATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
TATCAGG
Found at i:56006029 original size:91 final size:91
Alignment explanation
Indices: 56005841--56006113 Score: 384
Period size: 91 Copynumber: 3.0 Consensus size: 91
56005831 TCTGTCATGT
* * ** * *
56005841 TGCCAAGGTATCTTTCAAACATGGTCTTATTCATTTCATGTCACGCTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA-GGTGCCATGGTATCTTTCAAC
*** *** * *
56005906 CATGGTCTTATTTATTTCCCGTCATGT
65 CATGGTCTTACACATTTCATATCAGGC
*
56005933 TGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCAGGTGCCATGGTATCTTTCAACC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTGCCATGGTATCTTTCAACC
*
56005998 ATGGTCTTACACGTTTCATATCAGGC
66 ATGGTCTTACACATTTCATATCAGGC
56006024 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGG-TGCCATGGTATCTTTCAAC
56006089 CATGGTCTTACACATTTCATATCAG
65 CATGGTCTTACACATTTCATATCAG
56006114 AGAGCACACT
Statistics
Matches: 162, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
91 82 0.51
92 80 0.49
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (91 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTGCCATGGTATCTTTCAACC
ATGGTCTTACACATTTCATATCAGGC
Found at i:56006089 original size:46 final size:46
Alignment explanation
Indices: 56005839--56006113 Score: 390
Period size: 46 Copynumber: 6.0 Consensus size: 46
56005829 TTTCTGTCAT
* * ** * *
56005839 GTTGCCAAGGTATCTTTCAAACATGGTCTTATTCATTTCATGTCAC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
* *** *** *
56005885 GCTGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCCCGTCAT
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
*
56005931 GTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
*
56005977 G-TGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
*
56006022 GCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
56006068 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
56006114 AGAGCACACT
Statistics
Matches: 210, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 45 0.21
46 165 0.79
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.37
Consensus pattern (46 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
Found at i:56034367 original size:5 final size:5
Alignment explanation
Indices: 56034357--56034388 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
56034347 TTGTGTGTTC
56034357 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
56034389 TCACATGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:56034371 original size:9 final size:9
Alignment explanation
Indices: 56034357--56034387 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
56034347 TTGTGTGTTC
56034357 TTTATTTTA
1 TTTATTTTA
56034366 TTTATTTTA
1 TTTATTTTA
56034375 TTTTATTTTA
1 -TTTATTTTA
56034385 TTT
1 TTT
56034388 TTCACATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:56036745 original size:27 final size:27
Alignment explanation
Indices: 56036714--56036829 Score: 151
Period size: 27 Copynumber: 4.3 Consensus size: 27
56036704 CCAAAATAGC
*
56036714 TAAAATGACCGTAATACCCCTATAGGG
1 TAAAATGATCGTAATACCCCTATAGGG
* * * *
56036741 TAAAATGATCGTAACACTCTTGTAGGG
1 TAAAATGATCGTAATACCCCTATAGGG
*
56036768 TAAAATGATCGTAATGCCCCTATAGGG
1 TAAAATGATCGTAATACCCCTATAGGG
* *
56036795 TAAAATGATCGTGATACCCCTATATGG
1 TAAAATGATCGTAATACCCCTATAGGG
*
56036822 AAAAATGA
1 TAAAATGA
56036830 CGAGTAACCC
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 75 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (27 bp):
TAAAATGATCGTAATACCCCTATAGGG
Found at i:56037058 original size:27 final size:27
Alignment explanation
Indices: 56036967--56037067 Score: 105
Period size: 27 Copynumber: 3.8 Consensus size: 27
56036957 ATGGAGGAAG
* *
56036967 TACTG-TACTGGTGACTATGTCACATT
1 TACTGTTACTGGTGGCTATGCCACATT
* *
56036993 CACTGTTACTGGTGGCTATGCCACAAT
1 TACTGTTACTGGTGGCTATGCCACATT
* *
56037020 TACTGATACTGGTGGCTTTGCCACATT
1 TACTGTTACTGGTGGCTATGCCACATT
* * **
56037047 TAGTGTTTCTGGAAGCTATGC
1 TACTGTTACTGGTGGCTATGC
56037068 TGCACTATTA
Statistics
Matches: 60, Mismatches: 14, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
26 4 0.07
27 56 0.93
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTATGCCACATT
Found at i:56037273 original size:32 final size:33
Alignment explanation
Indices: 56037231--56037295 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
56037221 CCCACACTAT
*
56037231 TACTGTATAGGGCTAAGGCCCAGACTG-TACTG
1 TACTGAATAGGGCTAAGGCCCAGACTGTTACTG
*
56037263 TACTGAATAGGGCTCAGGCCCAGACTGTTACTG
1 TACTGAATAGGGCTAAGGCCCAGACTGTTACTG
56037296 CATGCACTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 25 0.83
33 5 0.17
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (33 bp):
TACTGAATAGGGCTAAGGCCCAGACTGTTACTG
Found at i:56040211 original size:18 final size:18
Alignment explanation
Indices: 56040188--56040223 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
56040178 TTTGCAGACG
56040188 TTAGGAAATTGAACTGCA
1 TTAGGAAATTGAACTGCA
56040206 TTAGGAAATTGAACTGCA
1 TTAGGAAATTGAACTGCA
56040224 CAAACAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (18 bp):
TTAGGAAATTGAACTGCA
Found at i:56040696 original size:9 final size:9
Alignment explanation
Indices: 56040682--56040759 Score: 86
Period size: 9 Copynumber: 8.7 Consensus size: 9
56040672 ATAAGTATAA
56040682 AATTAACCG
1 AATTAACCG
56040691 AATTAACCG
1 AATTAACCG
**
56040700 AATTAGTCG
1 AATTAACCG
56040709 AATT-ACTCG
1 AATTAAC-CG
*
56040718 AATTATCCG
1 AATTAACCG
*
56040727 AATTACCCG
1 AATTAACCG
* *
56040736 AATTAGCCA
1 AATTAACCG
56040745 AATTAACCG
1 AATTAACCG
56040754 AATTAA
1 AATTAA
56040760 ACAAATTATT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
9 56 0.98
10 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:56040802 original size:5 final size:6
Alignment explanation
Indices: 56040787--56040827 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
56040777 AATTATATGT
*
56040787 TTTTTA TTTTTA TTTTTA GTTTTAAA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
56040828 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 22 0.71
7 8 0.26
8 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:56040815 original size:20 final size:21
Alignment explanation
Indices: 56040792--56040835 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
56040782 TATGTTTTTT
56040792 ATTTTTATTTTTAGTT-TTAA
1 ATTTTTATTTTTAGTTATTAA
*
56040812 ATTTTTATTTTTATTTATTAA
1 ATTTTTATTTTTAGTTATTAA
56040833 ATT
1 ATT
56040836 ATTTGTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
ATTTTTATTTTTAGTTATTAA
Found at i:56042656 original size:6 final size:6
Alignment explanation
Indices: 56042645--56042706 Score: 61
Period size: 6 Copynumber: 9.8 Consensus size: 6
56042635 GTTAGCGAAC
* * * *
56042645 AAATAT AAATAT AAATAC AAATAT AAATATT AAATAT AAGATTT GAATAA
1 AAATAT AAATAT AAATAT AAATAT AAATA-T AAATAT AA-ATAT AAATAT
56042695 ATAATAT AAATA
1 A-AATAT AAATA
56042707 AATATTTATT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
6 30 0.67
7 15 0.33
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:56042666 original size:12 final size:12
Alignment explanation
Indices: 56042645--56042706 Score: 61
Period size: 13 Copynumber: 4.9 Consensus size: 12
56042635 GTTAGCGAAC
56042645 AAATATAAATAT
1 AAATATAAATAT
*
56042657 AAATACAAATAT
1 AAATATAAATAT
56042669 AAATATTAAATAT
1 AAATA-TAAATAT
* * *
56042682 AAGATTTGAATAA
1 AA-ATATAAATAT
56042695 ATAATATAAATA
1 A-AATATAAATA
56042707 AATATTTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
12 16 0.40
13 21 0.52
14 3 0.08
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (12 bp):
AAATATAAATAT
Found at i:56042666 original size:18 final size:19
Alignment explanation
Indices: 56042643--56042680 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
56042633 ATGTTAGCGA
56042643 ACAAATATAAATA-TAAAT
1 ACAAATATAAATATTAAAT
56042661 ACAAATATAAATATTAAAT
1 ACAAATATAAATATTAAAT
56042680 A
1 A
56042681 TAAGATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (19 bp):
ACAAATATAAATATTAAAT
Found at i:56044889 original size:87 final size:87
Alignment explanation
Indices: 56044738--56044912 Score: 332
Period size: 87 Copynumber: 2.0 Consensus size: 87
56044728 ACCCCTTATG
*
56044738 TTAAAAGAGATTTTGAGAGGTGGGATCGTTCAAATCAGAGGATGAGTTTTATGATCCCAAAATTA
1 TTAAAAGAGATTTTGAGAGGTGGGATCATTCAAATCAGAGGATGAGTTTTATGATCCCAAAATTA
56044803 AAACTATTTTTGAGACAAGAAT
66 AAACTATTTTTGAGACAAGAAT
*
56044825 TTAAAAGAGATTTTGAGAGGTGGGATCATTCAAATCAGAGGATGAGTTTTATGATCCCAGAATTA
1 TTAAAAGAGATTTTGAGAGGTGGGATCATTCAAATCAGAGGATGAGTTTTATGATCCCAAAATTA
56044890 AAACTATTTTTGAGACAAGAAT
66 AAACTATTTTTGAGACAAGAAT
56044912 T
1 T
56044913 GCAACATTTT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (87 bp):
TTAAAAGAGATTTTGAGAGGTGGGATCATTCAAATCAGAGGATGAGTTTTATGATCCCAAAATTA
AAACTATTTTTGAGACAAGAAT
Found at i:56053318 original size:7 final size:6
Alignment explanation
Indices: 56053297--56053330 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
56053287 TAAATAAAGG
*
56053297 AAAATA AAAATA AAAATAA AAAATA ATAATA AAA
1 AAAATA AAAATA AAAAT-A AAAATA AAAATA AAA
56053331 GGGTTTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:56053320 original size:13 final size:13
Alignment explanation
Indices: 56053282--56053330 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
56053272 ATAAGTCTTG
*
56053282 AAAAATAAATAAAG
1 AAAAATAAA-AAAT
*
56053296 GAAAAT-AAAAAT
1 AAAAATAAAAAAT
56053308 AAAAATAAAAAAT
1 AAAAATAAAAAAT
*
56053321 AATAATAAAA
1 AAAAATAAAA
56053331 GGGTTTCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 8 0.27
13 17 0.57
14 5 0.17
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:56054792 original size:28 final size:28
Alignment explanation
Indices: 56054750--56054807 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
56054740 GGGCTAAAGT
* *
56054750 ACGAAATCAACACCGCTTGGACCTCCTC
1 ACGAAATCAAAACCGCCTGGACCTCCTC
56054778 ACGAAATCAAAACCGCCTGGACCTCCTC
1 ACGAAATCAAAACCGCCTGGACCTCCTC
56054806 AC
1 AC
56054808 ACGGGCAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.31, C:0.40, G:0.14, T:0.16
Consensus pattern (28 bp):
ACGAAATCAAAACCGCCTGGACCTCCTC
Found at i:56057829 original size:5 final size:5
Alignment explanation
Indices: 56057821--56057865 Score: 90
Period size: 5 Copynumber: 9.0 Consensus size: 5
56057811 TTTTATTTAG
56057821 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
56057866 TGATTATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:56057891 original size:16 final size:15
Alignment explanation
Indices: 56057825--56057891 Score: 57
Period size: 15 Copynumber: 4.4 Consensus size: 15
56057815 ATTTAGATTA
*
56057825 TATTATATTA-TATT
1 TATTATATTATTAAT
*
56057839 ATATTATATTA-TATT
1 -TATTATATTATTAAT
*
56057854 ATATTATATTATTGAT
1 -TATTATATTATTAAT
56057870 TATTATAATTATTAAT
1 TATTAT-ATTATTAAT
*
56057886 TGTTAT
1 TATTAT
56057892 GGTTTTATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
15 31 0.67
16 15 0.33
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
TATTATATTATTAAT
Found at i:56059552 original size:45 final size:45
Alignment explanation
Indices: 56059488--56059594 Score: 153
Period size: 45 Copynumber: 2.4 Consensus size: 45
56059478 CAACTACTGT
*
56059488 TACTGTTACCGTTACTGTTACGGATTC-GACACTTTGTGTGTCAAA
1 TACTGTTACCGTTACTGTTACAGATTCAG-CACTTTGTGTGTCAAA
**
56059533 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCAAA
**
56059578 TACTGTTATTGTTACTG
1 TACTGTTACCGTTACTG
56059595 CTACTGCTAC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 55 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCAAA
Found at i:56062163 original size:55 final size:55
Alignment explanation
Indices: 56062102--56062212 Score: 134
Period size: 55 Copynumber: 2.0 Consensus size: 55
56062092 GGTGTCAATC
* * *
56062102 TAACAGGTTTGACC-ACGGGTGTTAGACACGGGCGTGTCACACGCCCGTGTTGTTT
1 TAACAGG-TTCACCTACGGGTCTTAGACACGGGCGTGTCACACCCCCGTGTTGTTT
* ** **
56062157 TAACAGGTTCACCTACGGTTCTTCTACACGGGCGTGTCGTACCCCCGTGTTGTTT
1 TAACAGGTTCACCTACGGGTCTTAGACACGGGCGTGTCACACCCCCGTGTTGTTT
56062212 T
1 T
56062213 GGCAGTCTCG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
54 5 0.11
55 42 0.89
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.31
Consensus pattern (55 bp):
TAACAGGTTCACCTACGGGTCTTAGACACGGGCGTGTCACACCCCCGTGTTGTTT
Found at i:56079991 original size:358 final size:358
Alignment explanation
Indices: 56079334--56080033 Score: 1159
Period size: 358 Copynumber: 2.0 Consensus size: 358
56079324 AAGGCGGTGT
* * ** * *
56079334 AGAAAATATTGCCCTAAAAACAAGAAATCTTAAGTACCGATACACTTTTACTATAGCATGTATCT
1 AGAAAATATTGCCCTAAAAACAAGAAATCTTAAGTACCCATAAACTTCCACTATAGAAAGTATCT
* *
56079399 CCTAATTTACCTAGTTCATTTTTTAACTAAACCCAGTTTCATTTTTTCCTCTCTATTTTGCTAGC
66 CCTAATTTACCCAGTTCATCTTTTAACTAAACCCAGTTTCATTTTTTCCTCTCTATTTTGCTAGC
* *
56079464 CTTATACATACTCAAATACATACATATCTATTTATTATATTTTTTATTAGGGGATTCAACTTTTC
131 CTTATACATACTCAAATACATACATATATATTTATTACATTTTTTATTAGGGGATTCAACTTTTC
* * * * *
56079529 ATATGATTTTTTGACTCGACAATCATAGTGGAGCATAAACTGAATTGCCAGATACTCAATCATGT
196 ATATGATTTTTTGACTCAACAATCACAATGGAGCATAAACTAAATTGCCAAATACTCAATCATGT
* *
56079594 CACAATATGAATGGGACTCACTCATGAAGCTAAGGCTTTTGACTAAAAGGATGGATGAAGTAAAC
261 CACAATATGAATGGGACTCACTCATGAAGCTAAGGCTTTTGACTAAAAAGATGGATGAAGCAAAC
*
56079659 AGCTAACCCCTTAGCTATAGAGGAAAGGAGTGC
326 AACTAACCCCTTAGCTATAGAGGAAAGGAGTGC
*
56079692 AGAAAATATTGCCCTAAAAACAAGAAATTTTAAGTACCCATAAACTTCCACTATAGAAAGTATCT
1 AGAAAATATTGCCCTAAAAACAAGAAATCTTAAGTACCCATAAACTTCCACTATAGAAAGTATCT
* * * *
56079757 CCTATTTTACCCAGTTCATCTTTTAACTAAGCCCAGTTTCATTTTTTCCTCTCTTTTTTGCTGGC
66 CCTAATTTACCCAGTTCATCTTTTAACTAAACCCAGTTTCATTTTTTCCTCTCTATTTTGCTAGC
56079822 CTTATACATACTCAAATACATACATATATATTTATTACATTTTTTATTAGGGGATTCAACTTTTC
131 CTTATACATACTCAAATACATACATATATATTTATTACATTTTTTATTAGGGGATTCAACTTTTC
56079887 ATATGATTTTTTGACTCAACAATCACAATGGAGCATAAAAC-AAATTGCCAAATACTCAATCATG
196 ATATGATTTTTTGACTCAACAATCACAATGGAGCAT-AAACTAAATTGCCAAATACTCAATCATG
* *
56079951 TCACAATTTGAATGGGACTCACTCATGAAGCTAAGGCTTTTGACTAAAAAGATGGATGGAGCAAA
260 TCACAATATGAATGGGACTCACTCATGAAGCTAAGGCTTTTGACTAAAAAGATGGATGAAGCAAA
56080016 CAACTAACCCCTTAGCTA
325 CAACTAACCCCTTAGCTA
56080034 CTCAGTCTAT
Statistics
Matches: 316, Mismatches: 25, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
358 312 0.99
359 4 0.01
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (358 bp):
AGAAAATATTGCCCTAAAAACAAGAAATCTTAAGTACCCATAAACTTCCACTATAGAAAGTATCT
CCTAATTTACCCAGTTCATCTTTTAACTAAACCCAGTTTCATTTTTTCCTCTCTATTTTGCTAGC
CTTATACATACTCAAATACATACATATATATTTATTACATTTTTTATTAGGGGATTCAACTTTTC
ATATGATTTTTTGACTCAACAATCACAATGGAGCATAAACTAAATTGCCAAATACTCAATCATGT
CACAATATGAATGGGACTCACTCATGAAGCTAAGGCTTTTGACTAAAAAGATGGATGAAGCAAAC
AACTAACCCCTTAGCTATAGAGGAAAGGAGTGC
Found at i:56086467 original size:48 final size:48
Alignment explanation
Indices: 56086350--56086583 Score: 263
Period size: 48 Copynumber: 4.8 Consensus size: 48
56086340 GTAAGATGCA
* * * **
56086350 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATATATC-AGTGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTAG--CTCACATATCGAG-GCC
* * * * *
56086400 GATGCCATGTTCCAAACATGGTTTTACACTAGCCCACATGTCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCC
* *
56086448 GATGCCATGTCCCAGACATGGTTTTACACTGGCTCACATATCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCC
* * * * * * *
56086496 GATGTCATGTCCCAGAGATGGTCTTACACCAGCTCTCATATCAATGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCC
56086544 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATA
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATA
56086584 ACCCTAGTAT
Statistics
Matches: 155, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
48 126 0.81
49 2 0.01
50 27 0.17
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCC
Found at i:56097638 original size:29 final size:29
Alignment explanation
Indices: 56097598--56097653 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
56097588 ATACAACAAG
56097598 AAAGAAACTGTAAACTGAAGAGAAAATGA
1 AAAGAAACTGTAAACTGAAGAGAAAATGA
*
56097627 AAAGAAGCTGTAAACTGAAGAGAAAAT
1 AAAGAAACTGTAAACTGAAGAGAAAAT
56097654 AAACTTCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (29 bp):
AAAGAAACTGTAAACTGAAGAGAAAATGA
Found at i:56099216 original size:17 final size:17
Alignment explanation
Indices: 56099194--56099226 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
56099184 TCCCTTTTCC
56099194 AAGTTGATATATTATTA
1 AAGTTGATATATTATTA
56099211 AAGTTGATATATTATT
1 AAGTTGATATATTATT
56099227 TTTATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (17 bp):
AAGTTGATATATTATTA
Found at i:56100312 original size:40 final size:40
Alignment explanation
Indices: 56100240--56100364 Score: 144
Period size: 40 Copynumber: 3.1 Consensus size: 40
56100230 AAGGAGGAAA
* * * *
56100240 TACTAGCAGCTTGTCTGCAATTCTT-GTCGCTTGTCCATAT
1 TACTGGCAACTTGTTTGCAATT-TTGGTGGCTTGTCCATAT
*
56100280 TACTGGCAACTTGTTTGCAATTTTGGTGGCTTGTCCATAA
1 TACTGGCAACTTGTTTGCAATTTTGGTGGCTTGTCCATAT
* * ** *
56100320 TATTGGCAATTTGTTTGCAATCCTGGTGGCTTGTCCACAT
1 TACTGGCAACTTGTTTGCAATTTTGGTGGCTTGTCCATAT
56100360 TACTG
1 TACTG
56100365 ATAGTTTATA
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 2 0.03
40 70 0.97
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (40 bp):
TACTGGCAACTTGTTTGCAATTTTGGTGGCTTGTCCATAT
Found at i:56110088 original size:19 final size:20
Alignment explanation
Indices: 56110051--56110094 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
56110041 CCTTAAATTG
56110051 TTTTATTTGTAAGATTATTA
1 TTTTATTTGTAAGATTATTA
56110071 TTTTATTATG-AA-ATTATTA
1 TTTTATT-TGTAAGATTATTA
56110090 TTTTA
1 TTTTA
56110095 ATAAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 12 0.52
20 9 0.39
21 2 0.09
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (20 bp):
TTTTATTTGTAAGATTATTA
Found at i:56111070 original size:25 final size:24
Alignment explanation
Indices: 56111042--56111088 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
56111032 GCTAAATTTG
* *
56111042 ATTTTTGAATTTTATTTATTTTTTT
1 ATTTTAGAATTTTAATT-TTTTTTT
*
56111067 ATTTTAGTATTTTAATTTTTTT
1 ATTTTAGAATTTTAATTTTTTT
56111089 CTCAATTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 5 0.26
25 14 0.74
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.74
Consensus pattern (24 bp):
ATTTTAGAATTTTAATTTTTTTTT
Found at i:56113534 original size:34 final size:33
Alignment explanation
Indices: 56113496--56113563 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
56113486 TCTTTTCTTT
*
56113496 TCTTTCATTTTTCTCTTGTGTTTTTACCTCATTC
1 TCTTT-ATTTTTCTCTTGTGTTTTTAACTCATTC
* *
56113530 TCTTTGTTTTTCTCTTTTGTTTTTAACTCATTC
1 TCTTTATTTTTCTCTTGTGTTTTTAACTCATTC
56113563 T
1 T
56113564 TTACTTTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.09, C:0.21, G:0.06, T:0.65
Consensus pattern (33 bp):
TCTTTATTTTTCTCTTGTGTTTTTAACTCATTC
Found at i:56113577 original size:31 final size:32
Alignment explanation
Indices: 56113505--56113585 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 32
56113495 TTCTTTCATT
* * **
56113505 TTTC-TCTTGTGTTTTTACCTCATTCTCTTTG
1 TTTCTTCTTTTGTTTTTAACTCATTCTCTTAC
*
56113536 TTTTTCTCTTTTGTTTTTAACTCATTCT-TTAC
1 TTTCT-TCTTTTGTTTTTAACTCATTCTCTTAC
56113568 TTTCTTCTTTTGTATTTT
1 TTTCTTCTTTTGT-TTTT
56113586 CTTATTTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
31 11 0.27
32 10 0.24
33 20 0.49
ACGTcount: A:0.09, C:0.19, G:0.06, T:0.67
Consensus pattern (32 bp):
TTTCTTCTTTTGTTTTTAACTCATTCTCTTAC
Found at i:56114709 original size:14 final size:14
Alignment explanation
Indices: 56114692--56114723 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
56114682 CAAAGAGGTA
*
56114692 AAAATAAAATAAAG
1 AAAAGAAAATAAAG
56114706 AAAAGAAAATAAAG
1 AAAAGAAAATAAAG
56114720 AAAA
1 AAAA
56114724 AAATTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (14 bp):
AAAAGAAAATAAAG
Found at i:56120623 original size:28 final size:28
Alignment explanation
Indices: 56120583--56120639 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
56120573 TTGAGCATTT
* * *
56120583 CGAACCCCTTGATCGCTTTTCGACTTCC
1 CGAACCCCTTGATCCCTTCTCAACTTCC
*
56120611 CGAACCTCTTGATCCCTTCTCAACTTCC
1 CGAACCCCTTGATCCCTTCTCAACTTCC
56120639 C
1 C
56120640 AATCACAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.16, C:0.42, G:0.11, T:0.32
Consensus pattern (28 bp):
CGAACCCCTTGATCCCTTCTCAACTTCC
Found at i:56131746 original size:27 final size:27
Alignment explanation
Indices: 56131716--56131784 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 27
56131706 TGCAACACAT
* *
56131716 TGCATCAAATGTATGGGTTGCATGGAA
1 TGCATCAAATGCATGGGTTGCATAGAA
* **
56131743 TGCATGAAATGCATGTTTTGCATAGAA
1 TGCATCAAATGCATGGGTTGCATAGAA
* *
56131770 TGCATGAAGTGCATG
1 TGCATCAAATGCATG
56131785 CCCAAAATCG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (27 bp):
TGCATCAAATGCATGGGTTGCATAGAA
Found at i:56139278 original size:13 final size:13
Alignment explanation
Indices: 56139262--56139291 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
56139252 TTTTTACCTT
*
56139262 TTAATTTTCTTAG
1 TTAATCTTCTTAG
56139275 TTAATCTTCTTAG
1 TTAATCTTCTTAG
56139288 TTAA
1 TTAA
56139292 AATCTAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.57
Consensus pattern (13 bp):
TTAATCTTCTTAG
Found at i:56141449 original size:25 final size:24
Alignment explanation
Indices: 56141420--56141482 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
56141410 ACACCATAGA
* *
56141420 TCGCATGAGCTTCTTGATATTTAGC
1 TCGCATGAGCTTC-CGATACTTAGC
*
56141445 TCGCATGAGCTTCCGCTACTTAGC
1 TCGCATGAGCTTCCGATACTTAGC
*
56141469 TCACATGAGCTTCC
1 TCGCATGAGCTTCC
56141483 TATTATTCAG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 21 0.62
25 13 0.38
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (24 bp):
TCGCATGAGCTTCCGATACTTAGC
Found at i:56142126 original size:25 final size:26
Alignment explanation
Indices: 56142080--56142131 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
56142070 GGTCAATGTT
*
56142080 GGTATATAAATGTTTTTTTGAAACTA
1 GGTATATAAATGTTTTGTTGAAACTA
56142106 GGTATATAAAT-TTTTGTTGAAACTA
1 GGTATATAAATGTTTTGTTGAAACTA
56142131 G
1 G
56142132 CCATTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (26 bp):
GGTATATAAATGTTTTGTTGAAACTA
Found at i:56142140 original size:25 final size:26
Alignment explanation
Indices: 56142083--56142142 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
56142073 CAATGTTGGT
* **
56142083 ATATAAATGTTTTTTTGAAACTAGGT
1 ATATAAATGTTTTGTTGAAACTAGCC
56142109 ATATAAAT-TTTTGTTGAAACTAGCC
1 ATATAAATGTTTTGTTGAAACTAGCC
*
56142134 ATTTAAATG
1 ATATAAATG
56142143 GCTTGTGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 21 0.72
26 8 0.28
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (26 bp):
ATATAAATGTTTTGTTGAAACTAGCC
Found at i:56144941 original size:16 final size:17
Alignment explanation
Indices: 56144912--56144943 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
56144902 GAAAATAATA
56144912 TATAAAATTTAAAAAAC
1 TATAAAATTTAAAAAAC
56144929 TATAAAA-TTAAAAAA
1 TATAAAATTTAAAAAA
56144944 AGTATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
TATAAAATTTAAAAAAC
Found at i:56144944 original size:17 final size:17
Alignment explanation
Indices: 56144912--56144944 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
56144902 GAAAATAATA
*
56144912 TATAAAATTTAAAAAAC
1 TATAAAATTAAAAAAAC
56144929 TATAAAATTAAAAAAA
1 TATAAAATTAAAAAAA
56144945 GTATTTAAAT
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:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
TATAAAATTAAAAAAAC
Found at i:56147157 original size:80 final size:79
Alignment explanation
Indices: 56147073--56147244 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
56147063 GGACTAAGAT
*
56147073 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
56147137 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
56147153 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
56147218 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
56147232 CCGAAGGCATTTG
1 CCGAAGGCATTTG
56147245 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:56147224 original size:39 final size:39
Alignment explanation
Indices: 56147020--56147242 Score: 209
Period size: 40 Copynumber: 5.6 Consensus size: 39
56147010 TTGAATGCTG
* * * * *
56147020 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
56147060 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
56147099 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
56147140 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
56147180 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
56147219 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
56147243 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
39 40 0.25
40 103 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:56147262 original size:79 final size:80
Alignment explanation
Indices: 56147100--56147277 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
56147090 AGATACAAAT
* * * *
56147100 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
56147165 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
56147180 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
56147244 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
56147259 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
56147278 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:56149171 original size:20 final size:19
Alignment explanation
Indices: 56149134--56149179 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
56149124 TAGATTTTTT
*
56149134 TAAAAATTTTATAAATTTG
1 TAAAAATTTTATAAATTTA
56149153 TAAAACATTATTA-AAATTTA
1 TAAAA-ATT-TTATAAATTTA
56149173 TAAAAAT
1 TAAAAAT
56149180 ATATATAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.29
20 14 0.58
21 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
TAAAAATTTTATAAATTTA
Found at i:56149197 original size:16 final size:16
Alignment explanation
Indices: 56149176--56149206 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56149166 AAATTTATAA
56149176 AAATATATATAGTTTC
1 AAATATATATAGTTTC
*
56149192 AAATATATATTGTTT
1 AAATATATATAGTTT
56149207 GACATGTTTA
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:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (16 bp):
AAATATATATAGTTTC
Found at i:56154001 original size:55 final size:53
Alignment explanation
Indices: 56153914--56154168 Score: 227
Period size: 55 Copynumber: 4.8 Consensus size: 53
56153904 ATTAGGGTTT
* *
56153914 AAGGATACGATGTAAGACCATG-CTAAGGCATGGCAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGTC-AAGACATGGC-ATTGGTAA-GTTTCTAAGGC
* * * *
56153969 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTT--TCTAAGGC
* * * * *
56154024 AAAGG-TCCCATGTAAAACCATGCCAAGGCATGGCATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTTC-TAAGGC
* * *
56154077 AAGGATACCATGTAAGACCATGTCAAGACATGGTAATGGTAACTTTC-AA---
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTTCTAAGGC
** * * *
56154126 AAGGATACCACATAAGACCATGACAAGTCATGGCAATGGTAAG
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAG
56154169 GTACCCATGT
Statistics
Matches: 164, Mismatches: 29, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
49 37 0.23
52 7 0.04
53 39 0.24
54 11 0.07
55 65 0.40
56 5 0.03
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTTCTAAGGC
Found at i:56157046 original size:8 final size:8
Alignment explanation
Indices: 56157033--56157057 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
56157023 AATCTTTAGC
56157033 GCAAAGAG
1 GCAAAGAG
56157041 GCAAAGAG
1 GCAAAGAG
56157049 GCAAAGAG
1 GCAAAGAG
56157057 G
1 G
56157058 ATGTCTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.12, G:0.40, T:0.00
Consensus pattern (8 bp):
GCAAAGAG
Found at i:56159972 original size:54 final size:53
Alignment explanation
Indices: 56159842--56160036 Score: 153
Period size: 54 Copynumber: 3.6 Consensus size: 53
56159832 CTTACCATTG
* * *
56159842 CCATGTCTTGATATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATG
1 CCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAATA
* * * * * *
56159895 CCATGCCTCGGCATGGTCTTACATGGGA-CTTTGCCTTATAGTAACTTATCAATA
1 CCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTAT-G-AACTCACCAATA
* *** * * *
56159949 CCATGTCTTGACATTGTCTTACATGATTTCCTTGCCTTA-GAAACCTTACTAATTT
1 CCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG-AA-CTCACCAA-TA
* *
56160004 CCATGCCTT-AGCATGGTCTTACATGGTATCCTT
1 CCATGTCTTGA-CATGGTCTTACATGGGATCCTT
56160037 AAACCCTAAT
Statistics
Matches: 111, Mismatches: 25, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
52 10 0.09
53 27 0.24
54 37 0.33
55 37 0.33
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.37
Consensus pattern (53 bp):
CCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAATA
Found at i:56163298 original size:37 final size:37
Alignment explanation
Indices: 56163246--56163324 Score: 142
Period size: 37 Copynumber: 2.2 Consensus size: 37
56163236 ACTATGCACA
56163246 ATTTA-TTATTTCCGTAAGTTGTACCTATATACTATT
1 ATTTACTTATTTCCGTAAGTTGTACCTATATACTATT
*
56163282 ATTTACTTATTTCCGTAAGTTGTATCTATATACTATT
1 ATTTACTTATTTCCGTAAGTTGTACCTATATACTATT
56163319 ATTTAC
1 ATTTAC
56163325 ACTTTTGATT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 5 0.12
37 36 0.88
ACGTcount: A:0.28, C:0.14, G:0.08, T:0.51
Consensus pattern (37 bp):
ATTTACTTATTTCCGTAAGTTGTACCTATATACTATT
Found at i:56166398 original size:64 final size:64
Alignment explanation
Indices: 56166317--56166499 Score: 174
Period size: 67 Copynumber: 2.8 Consensus size: 64
56166307 AGACATTATG
* * *
56166317 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGAGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * * *
56166381 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGTTACGAGAT
1 ATGTAGCTAGGTCGCATGAGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
56166446 AA
63 AA
* * * *
56166448 ACTG--GCTAGGTCACATGAGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAG
1 A-TGTAGCTAGGTCGCATGAGTGATACTATGTGTACACCATGTAG-ACAAGAGAG
56166500 TCGAACTATA
Statistics
Matches: 96, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 18 0.19
64 21 0.22
65 8 0.08
66 16 0.17
67 30 0.31
68 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGAGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:56169978 original size:15 final size:14
Alignment explanation
Indices: 56169944--56169988 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 14
56169934 AAATAAATCA
*
56169944 AAATAATAA-AAAT
1 AAATAATAATATAT
56169957 AAA-AATAATATAT
1 AAATAATAATATAT
56169970 GAAATAATAATATAT
1 -AAATAATAATATAT
56169985 AAAT
1 AAAT
56169989 GATATTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 5 0.18
13 6 0.21
14 7 0.25
15 10 0.36
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (14 bp):
AAATAATAATATAT
Found at i:56170310 original size:21 final size:20
Alignment explanation
Indices: 56170285--56170323 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
56170275 AAAAAAATCA
56170285 AAACAATATAGATGATATACC
1 AAACAATATAGAT-ATATACC
*
56170306 AAACAATATATATATATA
1 AAACAATATAGATATATA
56170324 TATGAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.28
Consensus pattern (20 bp):
AAACAATATAGATATATACC
Found at i:56171977 original size:177 final size:177
Alignment explanation
Indices: 56171766--56172149 Score: 662
Period size: 177 Copynumber: 2.2 Consensus size: 177
56171756 CTTAAATATG
*
56171766 CTCCATAGCCGATACATGGAGATAAGATCTACAATTTTCAGTCTGCTT-TCTGCAACTTCAGGAA
1 CTCCATAGCCGATACATGGAGATAAGATCTACAATTTTCAGTCTACTTCT-TGCAACTTCAGGAA
56171830 GATAAGACCTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAAT
65 GATAAGACCTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAAT
*
56171895 CTACTCCATAGCTGATACATGGAGATAAGACTCGCCATTTTCGATCTA
130 CTACTCCATAGCCGATACATGGAGATAAGACTCGCCATTTTCGATCTA
*
56171943 CTCCATAGCCGATACATGGATATAAGATCTACAATTTTCAGTCTACTTCTTGCAACTTCAGGAAG
1 CTCCATAGCCGATACATGGAGATAAGATCTACAATTTTCAGTCTACTTCTTGCAACTTCAGGAAG
* * * *
56172008 ATAAGACTTGTATCTTCAACTTGCTCTTTTGCTACCTCAGAGAGATAAGGTTGGTGGCTAAAATC
66 ATAAGACCTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATC
* *
56172073 TGCTCCATAGCCGATACATGGAGATAAGACTCGCCATTTTCGATCTG
131 TACTCCATAGCCGATACATGGAGATAAGACTCGCCATTTTCGATCTA
*
56172120 CTCCATAGCCGATACATAGAGATAAGATCT
1 CTCCATAGCCGATACATGGAGATAAGATCT
56172150 GTAACTTTCA
Statistics
Matches: 195, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
177 194 0.99
178 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (177 bp):
CTCCATAGCCGATACATGGAGATAAGATCTACAATTTTCAGTCTACTTCTTGCAACTTCAGGAAG
ATAAGACCTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATC
TACTCCATAGCCGATACATGGAGATAAGACTCGCCATTTTCGATCTA
Found at i:56171980 original size:45 final size:44
Alignment explanation
Indices: 56171893--56171989 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 44
56171883 GGTGGCTAAA
* * *
56171893 ATCTACTCCATAGCTGATACATGGAGATAAGACTCGCCATTTTC
1 ATCTACTCCATAGCCGATACATGGAGATAAGACTCACAATTTTC
*
56171937 GATCTACTCCATAGCCGATACATGGATATAAGA-TCTACAATTTTC
1 -ATCTACTCCATAGCCGATACATGGAGATAAGACTC-ACAATTTTC
56171982 AGTCTACT
1 A-TCTACT
56171990 TCTTGCAACT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
44 3 0.07
45 43 0.93
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (44 bp):
ATCTACTCCATAGCCGATACATGGAGATAAGACTCACAATTTTC
Found at i:56184093 original size:18 final size:19
Alignment explanation
Indices: 56184072--56184112 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
56184062 AAAATAATAA
*
56184072 AAATAAAAATA-ATATATG
1 AAATAAAAATATATAGATG
*
56184090 AAATAATAATATATAGATG
1 AAATAAAAATATATAGATG
56184109 AAAT
1 AAAT
56184113 TTCAAAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (19 bp):
AAATAAAAATATATAGATG
Found at i:56184097 original size:15 final size:14
Alignment explanation
Indices: 56184063--56184104 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
56184053 AAATAAATCA
*
56184063 AAATAATAA-AAAT
1 AAATAATAATATAT
56184076 AAA-AATAATATAT
1 AAATAATAATATAT
56184089 GAAATAATAATATAT
1 -AAATAATAATATAT
56184104 A
1 A
56184105 GATGAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 5 0.20
13 6 0.24
14 4 0.16
15 10 0.40
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (14 bp):
AAATAATAATATAT
Found at i:56184433 original size:21 final size:20
Alignment explanation
Indices: 56184408--56184446 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
56184398 AAAAATAACA
56184408 AAACAATATAGATGATATACC
1 AAACAATATAGAT-ATATACC
*
56184429 AAACAATATATATATATA
1 AAACAATATAGATATATA
56184447 TGTGAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.28
Consensus pattern (20 bp):
AAACAATATAGATATATACC
Found at i:56184466 original size:29 final size:29
Alignment explanation
Indices: 56184434--56184494 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
56184424 ATACCAAACA
56184434 ATATATATATATATGTGAATAAATAATAT
1 ATATATATATATATGTGAATAAATAATAT
*
56184463 ATATATATATATGTGTGAATAAATAATAT
1 ATATATATATATATGTGAATAAATAATAT
56184492 ATA
1 ATA
56184495 CATAAAAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (29 bp):
ATATATATATATATGTGAATAAATAATAT
Found at i:56184991 original size:25 final size:27
Alignment explanation
Indices: 56184952--56185002 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
56184942 TTAAAAACCC
*
56184952 TTTGTTTTTTGCTTTT-AAAGAAAACT
1 TTTGTTCTTTGCTTTTAAAAGAAAACT
56184978 TTTGTTCTTT-CTTTTAAAAGAAAAC
1 TTTGTTCTTTGCTTTTAAAAGAAAAC
56185003 CCTTAATGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (27 bp):
TTTGTTCTTTGCTTTTAAAAGAAAACT
Found at i:56188298 original size:21 final size:21
Alignment explanation
Indices: 56188265--56188304 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
56188255 TTAATGAATA
* * *
56188265 ATAGCTCATACTTATCATAAT
1 ATAGATCACACTTAACATAAT
56188286 ATAGATCACACTTAACATA
1 ATAGATCACACTTAACATA
56188305 TAACATATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (21 bp):
ATAGATCACACTTAACATAAT
Found at i:56190411 original size:5 final size:5
Alignment explanation
Indices: 56190403--56190432 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
56190393 AGGAAATAAG
56190403 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
56190433 TGTTGGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:56206663 original size:10 final size:10
Alignment explanation
Indices: 56206650--56206688 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
56206640 ATATATGAAT
56206650 ATATCATGGC
1 ATATCATGGC
56206660 ATATCATGTGC
1 ATATCATG-GC
*
56206671 ATATCATTGC
1 ATATCATGGC
56206681 ATATCATG
1 ATATCATG
56206689 TACAGAACAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (10 bp):
ATATCATGGC
Found at i:56206676 original size:21 final size:21
Alignment explanation
Indices: 56206650--56206689 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
56206640 ATATATGAAT
56206650 ATATCATGGCATATCATGTGC
1 ATATCATGGCATATCATGTGC
*
56206671 ATATCATTGCATATCATGT
1 ATATCATGGCATATCATGT
56206690 ACAGAACAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
ATATCATGGCATATCATGTGC
Found at i:56206756 original size:25 final size:25
Alignment explanation
Indices: 56206728--56206778 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
56206718 ATAGCATATC
* *
56206728 CCTAAGGGTATAATGGTCATTTTCA
1 CCTAAGGGCAAAATGGTCATTTTCA
*
56206753 CCTAGGGGCAAAATGGTCATTTTCA
1 CCTAAGGGCAAAATGGTCATTTTCA
56206778 C
1 C
56206779 ATTATAGGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (25 bp):
CCTAAGGGCAAAATGGTCATTTTCA
Found at i:56210205 original size:40 final size:40
Alignment explanation
Indices: 56210157--56210290 Score: 124
Period size: 40 Copynumber: 3.4 Consensus size: 40
56210147 CTTTTCAGGT
* * *
56210157 CAAATCCTACCCGCCTTAAGTTACCGTAGTGAATCAGGAA
1 CAAATCCTACCCACCTTAAATTACCATAGTGAATCAGGAA
* ** *
56210197 TAAATCCTATTCACTTTAAATTACCATAGTGAATCAGGAA
1 CAAATCCTACCCACCTTAAATTACCATAGTGAATCAGGAA
* * * ** **
56210237 CAAATCCTATCCACTTTGAGGTATTATAGTGAATCAGGAA
1 CAAATCCTACCCACCTTAAATTACCATAGTGAATCAGGAA
* *
56210277 CGAATCCTATCCAC
1 CAAATCCTACCCAC
56210291 TTTATATTCT
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (40 bp):
CAAATCCTACCCACCTTAAATTACCATAGTGAATCAGGAA
Found at i:56210291 original size:40 final size:40
Alignment explanation
Indices: 56210178--56210294 Score: 153
Period size: 40 Copynumber: 2.9 Consensus size: 40
56210168 CGCCTTAAGT
* * * *
56210178 TACCGTAGTGAATCAGGAATAAATCCTATTCACTTTAAAT
1 TACCATAGTGAATCAGGAACAAATCCTATCCACTTTAAAG
* *
56210218 TACCATAGTGAATCAGGAACAAATCCTATCCACTTTGAGG
1 TACCATAGTGAATCAGGAACAAATCCTATCCACTTTAAAG
** *
56210258 TATTATAGTGAATCAGGAACGAATCCTATCCACTTTA
1 TACCATAGTGAATCAGGAACAAATCCTATCCACTTTA
56210295 TATTCTCGAG
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.30
Consensus pattern (40 bp):
TACCATAGTGAATCAGGAACAAATCCTATCCACTTTAAAG
Found at i:56215417 original size:5 final size:5
Alignment explanation
Indices: 56215409--56215441 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
56215399 AAATAAAAAA
*
56215409 TATTT TATTT TATTT TATTT TATTA TATTT TAT
1 TATTT TATTT TATTT TATTT TATTT TATTT TAT
56215442 AGTTGGCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:56220544 original size:46 final size:46
Alignment explanation
Indices: 56220393--56220667 Score: 231
Period size: 46 Copynumber: 5.8 Consensus size: 46
56220383 ACTATCGAAA
* *
56220393 TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATA
1 TCGAGGCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCT--CATC
* * * * *
56220443 TCCGTGTCAACG-T-CATGTCCCAGACATGGCCTTACACT-G-ACACATC
1 T-CGAGGC--CGATGCATGTCCCAGACAT-GTCTTACACTGGCTCTCATC
* * *
56220489 TTGTA-GCCGATGCATATCCCAGACATGTCTTACATTGGCT-TACATC
1 TCG-AGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCT-CATC
* *
56220535 TCGAGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTC
1 TCGAGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATC
* * *
56220581 TCAATGCCGATGCCATGTCCCAGACATTGTCTTACACTGGCTCTCATAA
1 TCGAGGCCGATG-CATGTCCCAGACA-TGTCTTACACTGGCTCTCAT-C
* *
56220630 T-GTGGCCGATGCATGTCCCAGACATGTTTTACACTGGC
1 TCGAGGCCGATGCATGTCCCAGACATGTCTTACACTGGC
56220668 ACACAAATAA
Statistics
Matches: 183, Mismatches: 28, Indels: 32
0.75 0.12 0.13
Matches are distributed among these distances:
43 2 0.01
44 9 0.05
45 17 0.09
46 68 0.37
47 27 0.15
48 26 0.14
49 2 0.01
50 25 0.14
51 4 0.02
52 1 0.01
53 2 0.01
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.27
Consensus pattern (46 bp):
TCGAGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATC
Found at i:56220614 original size:94 final size:92
Alignment explanation
Indices: 56220494--56220664 Score: 247
Period size: 94 Copynumber: 1.8 Consensus size: 92
56220484 ACATCTTGTA
* *
56220494 GCCGATGCATATCCCAGACATGTCTTACATTGGCT-TACAT-CTCGAGGCCGATGCATGTCCCAG
1 GCCGATGCATATCCCAGACATGTCTTACACTGGCTCT-CATAAT-GAGGCCGATGCATGTCCCAG
56220557 ACATGTCTTACACTAGCTCTCGTCTCAAT
64 ACATGTCTTACACTAGCTCTCGTCTCAAT
* *
56220586 GCCGATGCCATGTCCCAGACATTGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAG
1 GCCGATG-CATATCCCAGACA-TGTCTTACACTGGCTCTCATAATGAGGCCGATGCATGTCCCAG
*
56220651 ACATGTTTTACACT
64 ACATGTCTTACACT
56220665 GGCACACAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
92 7 0.10
93 12 0.17
94 49 0.70
95 2 0.03
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.29
Consensus pattern (92 bp):
GCCGATGCATATCCCAGACATGTCTTACACTGGCTCTCATAATGAGGCCGATGCATGTCCCAGAC
ATGTCTTACACTAGCTCTCGTCTCAAT
Found at i:56220639 original size:140 final size:144
Alignment explanation
Indices: 56220303--56220667 Score: 376
Period size: 140 Copynumber: 2.6 Consensus size: 144
56220293 GGGTATAATA
* *
56220303 CCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCCATCAA-GT--CAATGCCATGTCCC
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-CAT-AATGTGCCGATG-CATGTCCC
* * *
56220365 GGGCATGGTCTTACATTGACTATCGAAATCGAGGCCGATGCCATGTCCCAGACATGGTCTTACAC
63 AGACAT-GTCTTACATTGGCTATCGAAATCGAGGCCGATGCCATGTCCCAGACATGGTCTTACAC
**
56220430 TAGCTCTCACATATCCGTG
127 TAGCTCT-ACATATCAATG
* * * * * * * *
56220449 TCAACGTCATGTCCCAGACATGGCCTTACACTGACACATC-T--TGTAGCCGATGCATATCCCAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATAATGT-GCCGATGCATGTCCCAG
**
56220511 ACATGTCTTACATTGGCT-TAC-ATCTCGAGGCCGATG-CATGTCCCAGACAT-GTCTTACACTA
65 ACATGTCTTACATTGGCTAT-CGAAATCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTA
* *
56220572 GCTCT-CGTCTCAATG
129 GCTCTACATATCAATG
*
56220587 CCGATGCCATGTCCCAGACATTGTCTTACACTGGCTC-TCATAATGTGGCCGATGCATGTCCCAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATAATGT-GCCGATGCATGTCCCAG
* *
56220651 ACATGTTTTACACTGGC
65 ACATGTCTTACATTGGC
56220668 ACACAAATAA
Statistics
Matches: 180, Mismatches: 31, Indels: 22
0.77 0.13 0.09
Matches are distributed among these distances:
137 2 0.01
138 36 0.20
140 50 0.28
141 14 0.08
142 16 0.09
143 14 0.08
144 12 0.07
145 5 0.03
146 31 0.17
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.27
Consensus pattern (144 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATAATGTGCCGATGCATGTCCCAGA
CATGTCTTACATTGGCTATCGAAATCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGC
TCTACATATCAATG
Found at i:56222360 original size:25 final size:25
Alignment explanation
Indices: 56222315--56222363 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
56222305 TGGTTGACAC
* * *
56222315 GGCCTTGAACATGGGCGTGTTACAT
1 GGCCTTGAACACGAGCATGTTACAT
56222340 GGCCTTGAACACGAGCATGTTACA
1 GGCCTTGAACACGAGCATGTTACA
56222364 CGTCCATGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (25 bp):
GGCCTTGAACACGAGCATGTTACAT
Found at i:56228312 original size:49 final size:49
Alignment explanation
Indices: 56228223--56228379 Score: 224
Period size: 49 Copynumber: 3.2 Consensus size: 49
56228213 TCACGTGTGT
* * **
56228223 AGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAGTGC
1 AGGCTACTACGTGTACCGGATAATT-GGTCACGTGTGTAGTACTAAGTGC
56228273 AGGCTACTACGTGTACCGGATAATTGGTCACGTGTGTAGTACTAAGTGC
1 AGGCTACTACGTGTACCGGATAATTGGTCACGTGTGTAGTACTAAGTGC
* * * * *
56228322 AGGCTACTATGTGTACTGGATAATTGGTCGCATGTGTAGTACTATGTGC
1 AGGCTACTACGTGTACCGGATAATTGGTCACGTGTGTAGTACTAAGTGC
56228371 AGGCTACTA
1 AGGCTACTA
56228380 TGCGTACCAG
Statistics
Matches: 98, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
49 77 0.79
50 21 0.21
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.31
Consensus pattern (49 bp):
AGGCTACTACGTGTACCGGATAATTGGTCACGTGTGTAGTACTAAGTGC
Found at i:56228334 original size:26 final size:26
Alignment explanation
Indices: 56228256--56228336 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
56228246 TTAGGTCACG
56228256 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
* * * * *
56228282 CGTGTACCGGA-TAATTG--GTC-AC-G
1 TGTGTA--GTACTAAGTGCAGGCTACTA
56228305 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
56228331 TGTGTA
1 TGTGTA
56228337 CTGGATAATT
Statistics
Matches: 38, Mismatches: 10, Indels: 14
0.61 0.16 0.23
Matches are distributed among these distances:
21 2 0.05
22 5 0.13
23 5 0.13
24 4 0.11
25 4 0.11
26 11 0.29
27 5 0.13
28 2 0.05
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (26 bp):
TGTGTAGTACTAAGTGCAGGCTACTA
Found at i:56231402 original size:15 final size:16
Alignment explanation
Indices: 56231379--56231426 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
56231369 TAGTATCGTA
56231379 TCTTGGGTTTCTTTAT
1 TCTTGGGTTTCTTTAT
56231395 TC-TGGGTTT-TTCTA-
1 TCTTGGGTTTCTT-TAT
*
56231409 TCTTGGATTTCTTTAT
1 TCTTGGGTTTCTTTAT
56231425 TC
1 TC
56231427 AGTTTTCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
14 4 0.15
15 17 0.63
16 6 0.22
ACGTcount: A:0.08, C:0.15, G:0.17, T:0.60
Consensus pattern (16 bp):
TCTTGGGTTTCTTTAT
Found at i:56233688 original size:49 final size:49
Alignment explanation
Indices: 56233573--56233746 Score: 258
Period size: 49 Copynumber: 3.5 Consensus size: 49
56233563 TGAGGTCGCA
* * **
56233573 TGTGTAGTACTAAGTGCAGGCTACTGCGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGATAATT-GGTCACG
*
56233623 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGATAATTGGTCACG
* *
56233672 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGATAATTGGTCACG
* *
56233721 TGTGTAGTACTATGAGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
56233747 TGCGTACCAT
Statistics
Matches: 114, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
49 77 0.68
50 37 0.32
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGATAATTGGTCACG
Found at i:56240273 original size:9 final size:9
Alignment explanation
Indices: 56240259--56240293 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
56240249 TTTAATAAGT
56240259 TAAATTAAC
1 TAAATTAAC
*
56240268 TAAATTAAT
1 TAAATTAAC
*
56240277 TAAACTAAC
1 TAAATTAAC
56240286 TAAATTAA
1 TAAATTAA
56240294 TTTCTTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (9 bp):
TAAATTAAC
Found at i:56240285 original size:18 final size:18
Alignment explanation
Indices: 56240258--56240295 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
56240248 ATTTAATAAG
*
56240258 TTAAATTAACTAAATTAA
1 TTAAACTAACTAAATTAA
56240276 TTAAACTAACTAAATTAA
1 TTAAACTAACTAAATTAA
56240294 TT
1 TT
56240296 TCTTAATTAA
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:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAACTAACTAAATTAA
Found at i:56240970 original size:15 final size:15
Alignment explanation
Indices: 56240950--56240980 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
56240940 TTCATATGTC
56240950 ATGTAATGCCAATGA
1 ATGTAATGCCAATGA
*
56240965 ATGTAATGTCAATGA
1 ATGTAATGCCAATGA
56240980 A
1 A
56240981 GGGACATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (15 bp):
ATGTAATGCCAATGA
Found at i:56241919 original size:17 final size:17
Alignment explanation
Indices: 56241894--56241928 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
56241884 TATTGTATTT
56241894 TCAGAACAATCTAAAAC
1 TCAGAACAATCTAAAAC
*
56241911 TCAGTACAATCTAAAAC
1 TCAGAACAATCTAAAAC
56241928 T
1 T
56241929 TTTCCAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.23, G:0.06, T:0.23
Consensus pattern (17 bp):
TCAGAACAATCTAAAAC
Found at i:56242868 original size:7 final size:7
Alignment explanation
Indices: 56242858--56242928 Score: 60
Period size: 7 Copynumber: 10.3 Consensus size: 7
56242848 GTAATTAGAG
56242858 TTTAATA
1 TTTAATA
56242865 TTTAATA
1 TTTAATA
56242872 TTTAA-A
1 TTTAATA
56242878 CTTTAATA
1 -TTTAATA
*
56242886 -CTAATA
1 TTTAATA
56242892 TTT-ATA
1 TTTAATA
*
56242898 GTTGAA-A
1 -TTTAATA
56242905 GTTTAATA
1 -TTTAATA
56242913 TTTAATA
1 TTTAATA
*
56242920 TTTAGTA
1 TTTAATA
56242927 TT
1 TT
56242929 AGAGCTTAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
6 9 0.17
7 41 0.77
8 3 0.06
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (7 bp):
TTTAATA
Found at i:56242990 original size:14 final size:14
Alignment explanation
Indices: 56242973--56243011 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
56242963 AAATTTAGAA
*
56242973 TTTAATATTTAATG
1 TTTAATATTTAAAG
56242987 TTTAA-ATTTTAAAG
1 TTTAATA-TTTAAAG
56243001 TTTAATATTTA
1 TTTAATATTTA
56243012 TATTTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (14 bp):
TTTAATATTTAAAG
Found at i:56244231 original size:20 final size:20
Alignment explanation
Indices: 56244203--56244244 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
56244193 AAGTATGAGG
* *
56244203 AATCGTTACCCTTATGGAGC
1 AATCATTACCCTTACGGAGC
56244223 AATCATTACCCTTACGGAGC
1 AATCATTACCCTTACGGAGC
56244243 AA
1 AA
56244245 CAACAACTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (20 bp):
AATCATTACCCTTACGGAGC
Found at i:56244715 original size:265 final size:263
Alignment explanation
Indices: 56244223--56245871 Score: 1827
Period size: 265 Copynumber: 6.3 Consensus size: 263
56244213 CTTATGGAGC
* *
56244223 AATCATTACCCTTACGGAGCAACAACAACTAGCAAAAAAGGATTAGAAT-GGTATTTGTAATGAT
1 AATCATTACCCTTATGGAGCAACAACAACTAGCAAAAAA-GATTAGAATAAG-ATTTGTAATGAT
* * * * * *
56244287 CAACGTGAAGGCATGTATGTTTTGGACTATAAATCATGCTTACACAATATTTGGCCTCAGGAAGT
64 CAACATGAAGGCACGTATGTCTTGGACTATAAATCATGCTTGCACAACATTTGGCCTCAAGAAGT
* * * * * *
56244352 TATCAATACTTAATTTCTCCTGTGGATTTACATTCTTCTTCACTCAAATTTCAGTTGAACGTGTG
129 TATCAATACTTAATTTCACCTGTGTAATTACGTTCTTCTTCCCTCAAATTTCGGTTGAACGTGTG
* *** * * * *
56244417 AAAAGAAAAATAAGGTTCTTTCAGTATTATGTTAGGGGCAAATACGAAAACACACTACATAAAGT
194 AAAAGCAAAGGGAGGTTCCTTCAGTATTATGTTAAGGGCAAATACGTAAACACACTGCATAAAGT
56244482 ATGAG
259 ATGAG
* * * *
56244487 AAATCATTACCCTTCTGGAGCAACAACAACTGGCAAAAAATGATTAAAACAAGATTTGTAATGAT
1 -AATCATTACCCTTATGGAGCAACAACAACTAGCAAAAAA-GATTAGAATAAGATTTGTAATGAT
* * * * * * * *
56244552 CGACATGAAGGTACATATTTATTGTACTATAATTCATGCTTGCATAACATTTGGCCTCAAGAAGT
64 CAACATGAAGGCACGTATGTCTTGGACTATAAATCATGCTTGCACAACATTTGGCCTCAAGAAGT
56244617 TATCAATACTTAATTTCACCTGTGTAATTACGTTCTTCTTCCCTCAAATTTCGGTTGAACGTGTG
129 TATCAATACTTAATTTCACCTGTGTAATTACGTTCTTCTTCCCTCAAATTTCGGTTGAACGTGTG
* * * * *
56244682 AAAAGCAAAGGGAGGTTCCTTTAATAATATGTTAAGGGCAAATGCGTAAACACATTGCATAAAGT
194 AAAAGCAAAGGGAGGTTCCTTCAGTATTATGTTAAGGGCAAATACGTAAACACACTGCATAAAGT
56244747 ATGACG
259 ATGA-G
* * * *
56244753 AATCATTACCCTTCTAGAGCAACAACAACTAGTAAAAAAAGATTAGAACAAGATTTGTAATGATC
1 AATCATTACCCTTATGGAGCAACAACAACTAG-CAAAAAAGATTAGAATAAGATTTGTAATGATC
* * *
56244818 AACATGAAAGCACATATGTCTTGGACTATAAATCATGCTTGCACAACATTTGGCCTTAAGAAGTT
65 AACATGAAGGCACGTATGTCTTGGACTATAAATCATGCTTGCACAACATTTGGCCTCAAGAAGTT
* * *
56244883 ATCAATACTTAATTTCACCTGTGTAATTACGTTCTTCTTCCCACAAATTTCGATTGACCGTGTGA
130 ATCAATACTTAATTTCACCTGTGTAATTACGTTCTTCTTCCCTCAAATTTCGGTTGAACGTGTGA
* *
56244948 AAAACAAAGGGAGGTTCCTTCAGTATTATGTTAAAGGG-AAATATGTAAACACA-TCGCATAAAG
195 AAAGCAAAGGGAGGTTCCTTCAGTATTATGTT-AAGGGCAAATACGTAAACACACT-GCATAAAG
*
56245011 TATAAG
258 TATGAG
* * * *
56245017 TAATCATCACCCTTATGAAGCAACAACAACTGGCAAAAAAAGATTAGAATAGGATTTGTAATGAT
1 -AATCATTACCCTTATGGAGCAACAACAACTAGC-AAAAAAGATTAGAATAAGATTTGTAATGAT
* *
56245082 CAACGTGAAGGCACGTATGTCTTGGACTATAAATCATGCTTGCACAACATTTGGCCTCAAGAACT
64 CAACATGAAGGCACGTATGTCTTGGACTATAAATCATGCTTGCACAACATTTGGCCTCAAGAAGT
* * ** * * ** *
56245147 TATCAATACTTAATTTCACATGTGTAATTACGTTCTTTTTCTTTTAAATTTTGGTTGAATATGTC
129 TATCAATACTTAATTTCACCTGTGTAATTACGTTCTTCTTCCCTCAAATTTCGGTTGAACGTGTG
* * **
56245212 AAAAGCAATA-GGAGGTTCCCTCAGTATTATGTTAAGGGGAAATATATAAACACA-TCGCATAAA
194 AAAAGCAA-AGGGAGGTTCCTTCAGTATTATGTTAAGGGCAAATACGTAAACACACT-GCATAAA
56245275 GTATGAGG
257 GTATGA-G
* * * * * * * * *
56245283 AATCATAATCCTTATGAAGGAACAACAACTAGTAAAGAAAGATTAGAAAAAAAATTGTAATGATT
1 AATCATTACCCTTATGGAGCAACAACAACTAGCAAA-AAAGATTAGAATAAGATTTGTAATGATC
* ** * *
56245348 AACATGAAGGTACGTATGTCTCAGACTATAAATCATGCTTACACAACATTTGGCCTTAAGAAGTT
65 AACATGAAGGCACGTATGTCTTGGACTATAAATCATGCTTGCACAACATTTGGCCTCAAGAAGTT
* * * ** ** *
56245413 ATCAATACCTAATTTCACCTGTGGATTTATATTCTTCTTTGCTCAAAGTTT-GGTTGAACCTGTG
130 ATCAATACTTAATTTCACCTGTGTAATTACGTTCTTCTTCCCTCAAA-TTTCGGTTGAACGTGTG
** * * ** ** *
56245477 AAAAGCAAAAAGAGGTTTCC-TCAGTATTATGTTAAGAGCAAATATGTAAACATGCCACAAAAAG
194 AAAAGCAAAGGGAGG-TTCCTTCAGTATTATGTTAAGGGCAAATACGTAAACACACTGCATAAAG
56245541 TATGATG
258 TATGA-G
* * * * * *
56245548 AATCATTACCCTTATAGAGGAACAACAACTAGAAAAAAAATATTAAAATAAGATTTCTAATGATC
1 AATCATTACCCTTATGGAGCAACAACAACTAG-CAAAAAAGATTAGAATAAGATTTGTAATGATC
* *
56245613 AACATGAAGGCATGTATGTCTTAGACTATAAATCA----TG-----C--TT-G-CTCAAGAAGTT
65 AACATGAAGGCACGTATGTCTTGGACTATAAATCATGCTTGCACAACATTTGGCCTCAAGAAGTT
* * * *
56245665 ATCAATACTTAATTTCACATGTGTAATTATGTTCTTCTTCCATCAAATTTTGGTTGAACGTGT--
130 ATCAATACTTAATTTCACCTGTGTAATTACGTTCTTCTTCCCTCAAATTTCGGTTGAACGTGTGA
* * * * *
56245728 -AA--AAAGGGAGGTTCCCTCATTATTATGTTAAGGGCAAATACGTAAGCACACCGTATAAAGTA
195 AAAGCAAAGGGAGGTTCCTTCAGTATTATGTTAAGGGCAAATACGTAAACACACTGCATAAAGTA
56245790 TGAGG
260 TGA-G
* * * *
56245795 AATTATTACCCTTATGGAGCAACAAAAACTAGCAAAACAAGATTAGAATAACATTTGTAAAGATC
1 AATCATTACCCTTATGGAGCAACAACAACTAGCAAAA-AAGATTAGAATAAGATTTGTAATGATC
*
56245860 AACCTGAAGGCA
65 AACATGAAGGCA
56245872 TAACATTTGG
Statistics
Matches: 1184, Mismatches: 181, Indels: 56
0.83 0.13 0.04
Matches are distributed among these distances:
246 8 0.01
247 109 0.09
249 2 0.00
251 3 0.00
252 60 0.05
253 1 0.00
254 2 0.00
256 1 0.00
261 1 0.00
264 11 0.01
265 961 0.81
266 25 0.02
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (263 bp):
AATCATTACCCTTATGGAGCAACAACAACTAGCAAAAAAGATTAGAATAAGATTTGTAATGATCA
ACATGAAGGCACGTATGTCTTGGACTATAAATCATGCTTGCACAACATTTGGCCTCAAGAAGTTA
TCAATACTTAATTTCACCTGTGTAATTACGTTCTTCTTCCCTCAAATTTCGGTTGAACGTGTGAA
AAGCAAAGGGAGGTTCCTTCAGTATTATGTTAAGGGCAAATACGTAAACACACTGCATAAAGTAT
GAG
Found at i:56245862 original size:247 final size:251
Alignment explanation
Indices: 56245405--56245872 Score: 586
Period size: 247 Copynumber: 1.9 Consensus size: 251
56245395 ATTTGGCCTT
* * *
56245405 AAGAAGTTATCAATACCTAATTTCACCTGTGGATTTATATTCTTCTTTGCTCAAAGTTTGGTTGA
1 AAGAAGTTATCAATACCTAATTTCACATGTGGAATTATATTCTTCTTTCCTCAAAGTTTGGTTGA
* * **
56245470 ACCTGTGAAAAGCAAAAAGAGGTTTCCTCAGTATTATGTTAAGAGCAAATATGTAAACATGCCAC
66 ACCTGTGAAAA-CAAAAAGAGGTTCCCTCAGTATTATGTTAAGAGCAAATACGTAAACACACCAC
* * * * *
56245535 AAAAAGTATGATGAATCATTACCCTTATAGAGGAACAACAACTAGAAAAAAAATATTAAAATAAG
130 AAAAAGTATGAGGAATCATTACCCTTATAGAGCAACAAAAACTAGAAAAAAAAGATTAAAATAAC
*
56245600 ATTTCTAATGATCAACATGAAGGCATGTATGTCTTAGACTATAAATCATGCTTGCTC
195 ATTTCTAAAGATCAACATGAAGGCATGTATGTCTTAGACTATAAATCATGCTTGCTC
* * * *
56245657 AAGAAGTTATCAATACTTAATTTCACATGTGTAATTATGTTCTTC-TTCCATCAAATTTTGGTTG
1 AAGAAGTTATCAATACCTAATTTCACATGTGGAATTATATTCTTCTTTCC-TCAAAGTTTGGTTG
* ** * * * **
56245721 AA-C-GTG-TAA-AAAGGGAGGTTCCCTCATTATTATGTTAAGGGCAAATACGTAAGCACACCGT
65 AACCTGTGAAAACAAAAAGAGGTTCCCTCAGTATTATGTTAAGAGCAAATACGTAAACACACCAC
* * * * * *
56245782 ATAAAGTATGAGGAATTATTACCCTTATGGAGCAACAAAAACTAGCAAAACAAGATTAGAATAAC
130 AAAAAGTATGAGGAATCATTACCCTTATAGAGCAACAAAAACTAGAAAAAAAAGATTAAAATAAC
* *
56245847 ATTTGTAAAGATCAACCTGAAGGCAT
195 ATTTCTAAAGATCAACATGAAGGCAT
56245873 AACATTTGGC
Statistics
Matches: 182, Mismatches: 33, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
247 118 0.65
249 2 0.01
250 3 0.02
251 4 0.02
252 55 0.30
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (251 bp):
AAGAAGTTATCAATACCTAATTTCACATGTGGAATTATATTCTTCTTTCCTCAAAGTTTGGTTGA
ACCTGTGAAAACAAAAAGAGGTTCCCTCAGTATTATGTTAAGAGCAAATACGTAAACACACCACA
AAAAGTATGAGGAATCATTACCCTTATAGAGCAACAAAAACTAGAAAAAAAAGATTAAAATAACA
TTTCTAAAGATCAACATGAAGGCATGTATGTCTTAGACTATAAATCATGCTTGCTC
Found at i:56246391 original size:2 final size:2
Alignment explanation
Indices: 56246384--56246412 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
56246374 ATGCTTTAAA
56246384 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
56246413 AGACATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:56249406 original size:50 final size:50
Alignment explanation
Indices: 56249352--56249447 Score: 156
Period size: 50 Copynumber: 1.9 Consensus size: 50
56249342 GACAAATAAA
* * *
56249352 TACAAGAAAGAAGTAAAAACTATCAAGCCATGGACATAATGATAAAAAAT
1 TACAAGAAAGAAGTAAAAACTATAAAACCATGAACATAATGATAAAAAAT
*
56249402 TACAAGAAAGACGTAAAAACTATAAAACCATGAACATAATGATAAA
1 TACAAGAAAGAAGTAAAAACTATAAAACCATGAACATAATGATAAA
56249448 TAAGGCCCTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.18
Consensus pattern (50 bp):
TACAAGAAAGAAGTAAAAACTATAAAACCATGAACATAATGATAAAAAAT
Found at i:56251111 original size:19 final size:19
Alignment explanation
Indices: 56251087--56251128 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
56251077 TTGAACTTGA
* * *
56251087 AAATTGGATCTGAGATCGT
1 AAATTGGACCCGAGATCAT
56251106 AAATTGGACCCGAGATCAT
1 AAATTGGACCCGAGATCAT
56251125 AAAT
1 AAAT
56251129 GGGGTCCAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.26
Consensus pattern (19 bp):
AAATTGGACCCGAGATCAT
Found at i:56251536 original size:16 final size:18
Alignment explanation
Indices: 56251488--56251538 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
56251478 AAGAGTACTA
56251488 TATTAATTTAATATTAAAG
1 TATT-ATTTAATATTAAAG
56251507 TGATTATCTTAATATTAAA-
1 T-ATTAT-TTAATATTAAAG
56251526 T-TTATTTAATATT
1 TATTATTTAATATT
56251539 TATCTTATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.27
17 4 0.13
19 4 0.13
20 14 0.47
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (18 bp):
TATTATTTAATATTAAAG
Found at i:56251578 original size:71 final size:68
Alignment explanation
Indices: 56251447--56251583 Score: 179
Period size: 71 Copynumber: 2.0 Consensus size: 68
56251437 TTTAATAGAT
* *
56251447 TTAATATTAAATTAAATTTAATATTTATCTTAAGAGTACTATATTAATTTAATATTAAAGTGATT
1 TTAATATTAAATTAAATTTAATATTTATCTTAAGAGTAATATATTAATTTAATAATAAAGTGATT
56251512 ATC
66 ATC
* *
56251515 TTAATATTAAATT-TATTTAATATTTATCTTATAGA-TAAATATTCTTTTAATTTAATAATAAAG
1 TTAATATTAAATTAAATTTAATATTTATCTTA-AGAGT-AATA---TATTAATTTAATAATAAAG
56251578 TGATTA
61 TGATTA
56251584 AATTTAACCA
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
67 18 0.30
68 19 0.32
71 23 0.38
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (68 bp):
TTAATATTAAATTAAATTTAATATTTATCTTAAGAGTAATATATTAATTTAATAATAAAGTGATT
ATC
Found at i:56256472 original size:50 final size:50
Alignment explanation
Indices: 56256395--56256491 Score: 133
Period size: 50 Copynumber: 1.9 Consensus size: 50
56256385 CATAAGCATG
** * * *
56256395 TGTCCAGGCTGTGTAACTTACTTTTTTGGCTTTGGGGTCACACGGGCGTA
1 TGTCCAGGCCATGTAACTCACTTTTTTGGCTTTAGGGCCACACGGGCGTA
56256445 TGTCCAGGCCATGTAACTCA-TTGTTTTGGCTTTAGGGCCACACGGGC
1 TGTCCAGGCCATGTAACTCACTT-TTTTGGCTTTAGGGCCACACGGGC
56256492 CAGGGACACG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
49 2 0.05
50 39 0.95
ACGTcount: A:0.15, C:0.23, G:0.29, T:0.33
Consensus pattern (50 bp):
TGTCCAGGCCATGTAACTCACTTTTTTGGCTTTAGGGCCACACGGGCGTA
Found at i:56256537 original size:113 final size:112
Alignment explanation
Indices: 56256339--56256549 Score: 271
Period size: 113 Copynumber: 1.9 Consensus size: 112
56256329 CGTATGGCAA
* * * *
56256339 GCCATGTAACTCACTGTATTGGCTTTAGGGTCTCACGGGCCAAGGACATAAGCATGTGTCCAGGC
1 GCCATGTAACTCACTGTATTGGCTTTAGGGCCACACGGGCCAAGGACAGAAG-ATGTGTCCAGAC
* * * *
56256404 TGTGTAACTTACTTTTTTGGCTTTGGGGTCACACGGGCGTATGTCCAG
65 TGTGTAACTCACTATTTTGGCTTTAGAGTCACACGGGCGTATGTCCAG
* * * *
56256452 GCCATGTAACTCATTGTTTTGGCTTTAGGGCCACACGGGCCAGGGACACGGATG-TGTGTCCAGA
1 GCCATGTAACTCACTGTATTGGCTTTAGGGCCACACGGGCCAAGGACA--GAAGATGTGTCCAGA
*
56256516 TTGTGTAACTCACTATTTTGGCTTTAGAGTCACA
64 CTGTGTAACTCACTATTTTGGCTTTAGAGTCACA
56256550 TGACTCGAGC
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
113 81 0.98
115 2 0.02
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.30
Consensus pattern (112 bp):
GCCATGTAACTCACTGTATTGGCTTTAGGGCCACACGGGCCAAGGACAGAAGATGTGTCCAGACT
GTGTAACTCACTATTTTGGCTTTAGAGTCACACGGGCGTATGTCCAG
Found at i:56257675 original size:20 final size:20
Alignment explanation
Indices: 56257650--56257707 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
56257640 AATGCTTCGA
56257650 ATTAATCGACTACATTTCAG
1 ATTAATCGACTACATTTCAG
56257670 ATTAATCGACTACATTTCAG
1 ATTAATCGACTACATTTCAG
*
56257690 ATTAATCAACTACATTTC
1 ATTAATCGACTACATTTC
56257708 TACTTTTATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (20 bp):
ATTAATCGACTACATTTCAG
Found at i:56257881 original size:30 final size:30
Alignment explanation
Indices: 56257847--56258042 Score: 109
Period size: 30 Copynumber: 6.6 Consensus size: 30
56257837 CTAATGGAAG
* *
56257847 GGGATAGCCTCGACTATCAAATTGTGAAAA
1 GGGATAGCTTCGACTATCAAATTATGAAAA
* * * ** *
56257877 GGGAT-GGTGACGACCAT-AAACAATGGAAA
1 GGGATAGCT-TCGACTATCAAATTATGAAAA
* *
56257906 GGGATAGCTTCGACTATCGAATAATGAAAA
1 GGGATAGCTTCGACTATCAAATTATGAAAA
**
56257936 CAGATAGCTTC-ACCTATCAAATTATGAAAA
1 GGGATAGCTTCGA-CTATCAAATTATGAAAA
* * * *
56257966 GGGAT-GGTGACAAATATCAACA--ATGAAAA
1 GGGATAGCT-TCGACTATCAA-ATTATGAAAA
* * * *
56257995 GAGAT-GGTGACGACTATCAAATAATGAAAA
1 GGGATAGCT-TCGACTATCAAATTATGAAAA
*
56258025 GGGATAGCTTCGGCTATC
1 GGGATAGCTTCGACTATC
56258043 GAGCTAGGAA
Statistics
Matches: 126, Mismatches: 30, Indels: 20
0.72 0.17 0.11
Matches are distributed among these distances:
28 1 0.01
29 47 0.37
30 74 0.59
31 4 0.03
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (30 bp):
GGGATAGCTTCGACTATCAAATTATGAAAA
Found at i:56258042 original size:89 final size:89
Alignment explanation
Indices: 56257832--56258042 Score: 237
Period size: 89 Copynumber: 2.4 Consensus size: 89
56257822 ATCAACGATC
* * * * * * *
56257832 ATCAACTAATGGAAGGGGATAGCCTCGACTATCAAATTGTGAAAAGGGATGGTGACGACCATAAA
1 ATCAAATAATGAAAAGGGATAGCTTCGACTATCAAATTATGAAAAGGGATGGTGACAAACATAAA
* * *
56257897 CAATGGAAAGGGATAGCTTCGACT
66 CAATGAAAAGAGATAGCTACGACT
* ** * *
56257921 ATCGAATAATGAAAACAGATAGCTTC-ACCTATCAAATTATGAAAAGGGATGGTGACAAATATCA
1 ATCAAATAATGAAAAGGGATAGCTTCGA-CTATCAAATTATGAAAAGGGATGGTGACAAACATAA
*
56257985 ACAATGAAAAGAGAT-GGTGACGACT
65 ACAATGAAAAGAGATAGCT-ACGACT
*
56258010 ATCAAATAATGAAAAGGGATAGCTTCGGCTATC
1 ATCAAATAATGAAAAGGGATAGCTTCGACTATC
56258043 GAGCTAGGAA
Statistics
Matches: 99, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
88 3 0.03
89 96 0.97
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (89 bp):
ATCAAATAATGAAAAGGGATAGCTTCGACTATCAAATTATGAAAAGGGATGGTGACAAACATAAA
CAATGAAAAGAGATAGCTACGACT
Found at i:56260162 original size:22 final size:23
Alignment explanation
Indices: 56260136--56260179 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
56260126 TATATCTGAA
*
56260136 TCTGTATTTGTATCTG-ATATGT
1 TCTGTATTCGTATCTGAATATGT
*
56260158 TCTGTATTCGTTTCTGAATATG
1 TCTGTATTCGTATCTGAATATG
56260180 ATATTTGACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.52
Consensus pattern (23 bp):
TCTGTATTCGTATCTGAATATGT
Found at i:56262627 original size:21 final size:21
Alignment explanation
Indices: 56262603--56262650 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
56262593 TTTAATCTAA
*
56262603 AATAAATGCTATTATATAATC
1 AATAAATACTATTATATAATC
* * *
56262624 AATAAATATTATTATGTACTC
1 AATAAATACTATTATATAATC
56262645 AATAAA
1 AATAAA
56262651 GTTAGCAGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (21 bp):
AATAAATACTATTATATAATC
Found at i:56263111 original size:3 final size:3
Alignment explanation
Indices: 56263103--56263140 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
56263093 AATTAATCAC
56263103 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
56263141 CTCAATACGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:56271672 original size:69 final size:69
Alignment explanation
Indices: 56271315--56271674 Score: 348
Period size: 69 Copynumber: 5.2 Consensus size: 69
56271305 ACAACATTTA
** * * * *
56271315 TGTCATATTAAGGCTCACAGGTGAAGAGCTACAGCCTTCAACATAGTTAGCGAGAGCAAAG-TTC
1 TGTCATATTAAGGCTTGCAGGTGAAAAGCTACAGCCTCCAACATAGTTAGCGAGAACAAAGCTCC
* *
56271379 CTAG
66 CAAC
* * * * * *
56271383 TAGTCATATTAAGGCTCGCAGGTGAAGAGCCACAGCCTCCAACACAGTTAGCAAGAGCAAAGCTC
1 T-GTCATATTAAGGCTTGCAGGTGAAAAGCTACAGCCTCCAACATAGTTAGCGAGAACAAAGCTC
*
56271448 CTAGA-
65 CCA-AC
* * * * * * * *
56271453 TGTCATATTAAGCCTTACAGGAGAAAAGCCACAGCCTCTAACACAGTTAGCTAAAACAAAGCTCC
1 TGTCATATTAAGGCTTGCAGGTGAAAAGCTACAGCCTCCAACATAGTTAGCGAGAACAAAGCTCC
* *
56271518 TAGC
66 CAAC
* * *
56271522 TGTCATATTAAGGCTTGTAGGTGAAGAG-TCACAACCTCCAACATAGTTAGCGAGAACAAAGCTC
1 TGTCATATTAAGGCTTGCAGGTGAAAAGCT-ACAGCCTCCAACATAGTTAGCGAGAACAAAGCTC
56271586 CCAAC
65 CCAAC
* * * * * *
56271591 TGTCACACTAGGGCTTGTAGGTGAAAAACTACAACCTCCAACATAGTTAGCGAGAACAAAGCTCC
1 TGTCATATTAAGGCTTGCAGGTGAAAAGCTACAGCCTCCAACATAGTTAGCGAGAACAAAGCTCC
56271656 CAAC
66 CAAC
* *
56271660 TGGCATATTAGGGCT
1 TGTCATATTAAGGCT
56271675 CTTAAGATAA
Statistics
Matches: 247, Mismatches: 39, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
68 1 0.00
69 241 0.98
70 4 0.02
71 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (69 bp):
TGTCATATTAAGGCTTGCAGGTGAAAAGCTACAGCCTCCAACATAGTTAGCGAGAACAAAGCTCC
CAAC
Found at i:56273701 original size:26 final size:26
Alignment explanation
Indices: 56273671--56273721 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
56273661 CGTTGGAAAG
56273671 AACACACGTCCTGGCTCTGTGAAAAA
1 AACACACGTCCTGGCTCTGTGAAAAA
*
56273697 AACACACGTCTTGGCTCTGTGAAAA
1 AACACACGTCCTGGCTCTGTGAAAA
56273722 CTACCTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (26 bp):
AACACACGTCCTGGCTCTGTGAAAAA
Found at i:56277723 original size:25 final size:26
Alignment explanation
Indices: 56277686--56277738 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
56277676 TATATCCTAG
* *
56277686 AAAATATCTATAATAATT-TTTTTTA
1 AAAATATCCATAATAATTATTCTTTA
* *
56277711 AAAATTTCCATAATCATTATTCTTTA
1 AAAATATCCATAATAATTATTCTTTA
56277737 AA
1 AA
56277739 CACAAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.47
Consensus pattern (26 bp):
AAAATATCCATAATAATTATTCTTTA
Found at i:56280049 original size:32 final size:32
Alignment explanation
Indices: 56280005--56280073 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
56279995 AAATTTGCTT
* * * **
56280005 TTTTTTTAATATTTTCTTGTTGTTTTTTTTTA
1 TTTTGTTAATATTTTCATGTTGCTTTTTACTA
56280037 TTTTGTTAATATTTTCATGTTGCTTTTTACTA
1 TTTTGTTAATATTTTCATGTTGCTTTTTACTA
56280069 TTTTG
1 TTTTG
56280074 CTACCATTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.14, C:0.06, G:0.09, T:0.71
Consensus pattern (32 bp):
TTTTGTTAATATTTTCATGTTGCTTTTTACTA
Found at i:56280297 original size:20 final size:20
Alignment explanation
Indices: 56280272--56280313 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
56280262 ATGTTTTTAG
*
56280272 TATTTTTAATGTAT-TATATA
1 TATTTTTAA-ATATGTATATA
56280292 TATTTTTAAATATGTATATA
1 TATTTTTAAATATGTATATA
56280312 TA
1 TA
56280314 AAAATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
TATTTTTAAATATGTATATA
Found at i:56283841 original size:30 final size:30
Alignment explanation
Indices: 56283805--56283865 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
56283795 AAGACTAGGC
56283805 CTACATTCTATCAACAACTCTCAGTCTGTA
1 CTACATTCTATCAACAACTCTCAGTCTGTA
*
56283835 CTACATTCTATCAACAACTCTTAGTCTGTA
1 CTACATTCTATCAACAACTCTCAGTCTGTA
56283865 C
1 C
56283866 ATTCTCTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.34
Consensus pattern (30 bp):
CTACATTCTATCAACAACTCTCAGTCTGTA
Found at i:56293802 original size:27 final size:27
Alignment explanation
Indices: 56293649--56293806 Score: 74
Period size: 27 Copynumber: 5.7 Consensus size: 27
56293639 AATGATACAT
56293649 AAAATATTTTAA-AATTTTAAATATAATAATA
1 AAAATATTTTAATAA-TTT--ATAT-A-AATA
*
56293680 AATAATATTTAAATAATTTATATAAAATA
1 AA-AATATTTTAATAATTTATAT-AAATA
* * * * * *
56293709 TAAATTAATCTGAT-TTTTATATAAATTT
1 -AAAATATTTTAATAATTTATATAAA-TA
* * * *
56293737 TAAATA-TTTAAT-ATTTAAATTAATCT
1 AAAATATTTTAATAATTTATATAAAT-A
* *
56293763 AAAGT-TTTAAATAATTTATATAAATA
1 AAAATATTTTAATAATTTATATAAATA
56293789 AAAATATTTTAATAATTT
1 AAAATATTTTAATAATTT
56293807 GAGCTTCTAA
Statistics
Matches: 96, Mismatches: 23, Indels: 20
0.69 0.17 0.14
Matches are distributed among these distances:
25 1 0.01
26 25 0.26
27 28 0.29
28 8 0.08
29 10 0.10
30 8 0.08
31 2 0.02
32 12 0.12
33 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (27 bp):
AAAATATTTTAATAATTTATATAAATA
Found at i:56294716 original size:17 final size:18
Alignment explanation
Indices: 56294694--56294732 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
56294684 ATAACTTATT
*
56294694 ATTAATATAATTTA-AAA
1 ATTAATACAATTTATAAA
56294711 ATTAATACAATTTATAAA
1 ATTAATACAATTTATAAA
56294729 ATTA
1 ATTA
56294733 TCTAGTGCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTAATACAATTTATAAA
Found at i:56301091 original size:43 final size:42
Alignment explanation
Indices: 56301019--56301169 Score: 169
Period size: 42 Copynumber: 3.6 Consensus size: 42
56301009 TACCAATGTC
* * * *
56301019 ATATCCCATATATGGTCTTACATGTAATCTCATATCGATGCTA
1 ATATCCTAGATATGGTCTTACACGAAATCTCATATCGATGC-A
* * * *
56301062 ATAACCTAGCTATGGTCTTACACGAAATCTTATATCGATGCC
1 ATATCCTAGATATGGTCTTACACGAAATCTCATATCGATGCA
* * *
56301104 ATATCCTAGATATGGTCTTATA-AAAAGTCTCATATCGATACA
1 ATATCCTAGATATGGTCTTACACGAAA-TCTCATATCGATGCA
*
56301146 ATATCCCAGATATGGTCTTACACG
1 ATATCCTAGATATGGTCTTACACG
56301170 TAAACTAAGT
Statistics
Matches: 88, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
41 3 0.03
42 51 0.58
43 34 0.39
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.33
Consensus pattern (42 bp):
ATATCCTAGATATGGTCTTACACGAAATCTCATATCGATGCA
Found at i:56306940 original size:43 final size:42
Alignment explanation
Indices: 56306878--56307041 Score: 195
Period size: 42 Copynumber: 3.9 Consensus size: 42
56306868 TACTATACCA
* * *
56306878 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* *
56306920 ATGCCAATAGCCCAGCTATGGTCTTACACGAAATCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * * *
56306963 ATGCCATATCCCAAATATGGTCTTATAC-AAAGTTTCATACCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAA-TCTCATATCG
* * *
56307005 AAGCCATATCCTAGATATGGTCTTACACGTAATCTCA
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCA
56307042 GTAACCCTAA
Statistics
Matches: 102, Mismatches: 17, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
41 3 0.03
42 60 0.59
43 39 0.38
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:56311667 original size:13 final size:13
Alignment explanation
Indices: 56311649--56311674 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56311639 TCTTTCGTGA
56311649 GCATTAGCATATT
1 GCATTAGCATATT
56311662 GCATTAGCATATT
1 GCATTAGCATATT
56311675 TTCTCTTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
GCATTAGCATATT
Found at i:56311974 original size:17 final size:15
Alignment explanation
Indices: 56311952--56312003 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
56311942 TCTTCATAAA
56311952 CATATATCATTCATTT
1 CATATATCA-TCATTT
56311968 CATTATATCAAT-ATTT
1 CA-TATATC-ATCATTT
*
56311984 CATATACCATCATTTT
1 CATATATCATCA-TTT
56312000 CATA
1 CATA
56312004 AATTTCATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
14 2 0.06
15 6 0.19
16 15 0.48
17 7 0.23
18 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.46
Consensus pattern (15 bp):
CATATATCATCATTT
Found at i:56314930 original size:79 final size:80
Alignment explanation
Indices: 56314821--56315082 Score: 381
Period size: 79 Copynumber: 3.3 Consensus size: 80
56314811 TACTCGTTCA
* * **
56314821 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGG
*
56314884 ATTTAGTGACTCGCACC
64 ATTTAGTGACTAGCACC
56314901 AATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
56314965 TTAGTGACTAGCACC
66 TTAGTGACTAGCACC
*
56314980 AATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTGGTCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
* *
56315044 ATAGTCACTTAGCA-C
66 TTAGTGAC-TAGCACC
*
56315059 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
56315083 CATCATTCGA
Statistics
Matches: 169, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
78 3 0.02
79 137 0.81
80 29 0.17
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
TTAGTGACTAGCACC
Found at i:56315042 original size:119 final size:121
Alignment explanation
Indices: 56314819--56315082 Score: 326
Period size: 119 Copynumber: 2.2 Consensus size: 121
56314809 GCTACTCGTT
* *
56314819 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCG
* * * *
56314883 GATTTAGTGACTCGCACCAATGCCTTCGGGCTTAGCCCGGA-ATTAGTAAC-TCGCA
66 GAATTAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGATA-TAGTAACTTAGCA
* * * *
56314938 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGTGACTAGCACCAATGCCTTCGGG-CTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTATAGTAACTAGCACAAATGCCTTCGGGACTTAACCC
* * * *
56315000 GGAATTAGTAACTCGCACAAATGCCTTCGGATCTTGGTCCGGATATAGTCACTTAGCA
65 GGAATTAGTAACTCGCACAAATGCCTTCGG-GCTTAGCCCGGATATAGTAACTTAGCA
56315058 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
56315083 CATCATTCGA
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
118 37 0.30
119 73 0.59
120 14 0.11
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (121 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCG
GAATTAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGATATAGTAACTTAGCA
Found at i:56315082 original size:40 final size:40
Alignment explanation
Indices: 56314800--56315082 Score: 303
Period size: 40 Copynumber: 7.1 Consensus size: 40
56314790 CGGAATTTAA
** *
56314800 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
56314840 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
56314880 CCGGATTTAGTGACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
56314919 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * * *
56314959 CCGGATTTAGTGACTAGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
56314998 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTGGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
56315038 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
56315078 CCGGA
1 CCGGA
56315083 CATCATTCGA
Statistics
Matches: 202, Mismatches: 29, Indels: 24
0.79 0.11 0.09
Matches are distributed among these distances:
38 4 0.02
39 62 0.31
40 122 0.60
41 14 0.07
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:56323119 original size:40 final size:40
Alignment explanation
Indices: 56323043--56323224 Score: 214
Period size: 39 Copynumber: 4.6 Consensus size: 40
56323033 GCTACTCGTT
*
56323043 CAAATGCCTTC-GGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
56323082 CAAATGCCTTCGGGACTTAACCCGGATTTAGTGACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
56323122 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * *
56323161 CAAATGCCTTC-GGATCTT-GTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
56323201 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
56323225 CCCGGACATC
Statistics
Matches: 122, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
38 2 0.02
39 64 0.52
40 54 0.44
41 2 0.02
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:56323142 original size:79 final size:78
Alignment explanation
Indices: 56323045--56323224 Score: 213
Period size: 79 Copynumber: 2.3 Consensus size: 78
56323035 TACTCGTTCA
* * *
56323045 AATGCCTTCGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGA
1 AATGCCTTCGGGCTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTT-ACCCGGA
* * *
56323108 TTTAGTGAC-TCGCACC
63 TATAGTCACTTAGCA-C
**
56323124 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTGTCCGGATAT
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTACCCGGATAT
56323189 AGTCACTTAGCAC
66 AGTCACTTAGCAC
*
56323202 AAAGCCTTCGGGACTTAGCCCGG
1 AATGCCTTCGGG-CTTAGCCCGG
56323225 CCCGGACATC
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
78 27 0.31
79 60 0.68
80 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.24
Consensus pattern (78 bp):
AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTACCCGGATAT
AGTCACTTAGCAC
Done.