Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 113 of 297
Found at i:40611127 original size:96 final size:96
Alignment explanation
Indices: 40610948--40611373 Score: 561
Period size: 96 Copynumber: 4.4 Consensus size: 96
40610938 GGTAAGATGT
* * * * * ** *
40610948 CGATGCCATGTCCTAGACATGGTCTTACACTGGCTTTTATATATCGGTGCCAATGCCATGTTCCA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGC-TCT-CATCTCAATGCCGATGCCATGTTCCA
* *
40611013 AACATGGTCTTA-ACCTAGC-C-TATAAGTCGAGGT
64 AACATGGTCTTACA-CTAGCTCACAT-A-TCGAGGC
* *
40611046 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATCTCAATGTCGATGCCATGTTCCAAA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGCCGATGCCATGTTCCAAA
*
40611111 CATGGTCTTACACTAGCTCACATATCCAGGC
66 CATGGTCTTACACTAGCTCACATATCGAGGC
*
40611142 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGCCGATGTCATGTTCCAAA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGCCGATGCCATGTTCCAAA
*
40611207 CATGGTCTTACACTAGCTCACATATCAAGGC
66 CATGGTCTTACACTAGCTCACATATCGAGGC
* * * **
40611238 CGATGCAATGTCCCAGACATGGTCTTATATTAGCTCTCATCTCAATGTTGATGCCATGTTCCAAA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGCCGATGCCATGTTCCAAA
*
40611303 CATGGTCTTACACTGGCTCACATATCGAGGC
66 CATGGTCTTACACTAGCTCACATATCGAGGC
* * **
40611334 TGATACCATGTTTCAGACATGGTCTTACACTAGCTCTCAT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT
40611374 TGTAACACCC
Statistics
Matches: 293, Mismatches: 32, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
96 255 0.87
97 5 0.02
98 33 0.11
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (96 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGCCGATGCCATGTTCCAAA
CATGGTCTTACACTAGCTCACATATCGAGGC
Found at i:40611206 original size:144 final size:144
Alignment explanation
Indices: 40611000--40611373 Score: 412
Period size: 144 Copynumber: 2.6 Consensus size: 144
40610990 ATCGGTGCCA
* * * * *
40611000 ATGCCATGTTCCAAACATGGTCTTA-ACCTAGC-C-TATAAGTCGAGGTCGATGCCATGTCCCAA
1 ATGCCATGTCCCAAACATGGTCTTACA-CTAGCTCACAT-A-TCAAGGCCGATGCCATGTTCCAA
* * * * *
40611062 ACATGGTCTTACACTAGCTCTCATCTCAATGTCGATGCCATGTTCCAAACATGGTCTTACACTAG
63 ACATGGTCTTACACTAGCTCTCATATCAAGGCCGATGCAATGTCCCAAACATGGTCTTACACTAG
*
40611127 CTCACATATCCAGGCCG
128 CTCACATATCAAGGCCG
* * * * *
40611144 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGCCGATGTCATGTTCCAAACA
1 ATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCAAGGCCGATGCCATGTTCCAAACA
* * * *
40611209 TGGTCTTACACTAGCTCACATATCAAGGCCGATGCAATGTCCCAGACATGGTCTTATATTAGCTC
66 TGGTCTTACACTAGCTCTCATATCAAGGCCGATGCAATGTCCCAAACATGGTCTTACACTAGCTC
* * * **
40611274 TCATCTCAATGTTG
131 ACATATCAAGGCCG
* * * * * * *
40611288 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCTGATACCATGTTTCAGACA
1 ATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCAAGGCCGATGCCATGTTCCAAACA
40611353 TGGTCTTACACTAGCTCTCAT
66 TGGTCTTACACTAGCTCTCAT
40611374 TGTAACACCC
Statistics
Matches: 190, Mismatches: 37, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
144 186 0.98
145 2 0.01
146 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (144 bp):
ATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCAAGGCCGATGCCATGTTCCAAACA
TGGTCTTACACTAGCTCTCATATCAAGGCCGATGCAATGTCCCAAACATGGTCTTACACTAGCTC
ACATATCAAGGCCG
Found at i:40613591 original size:50 final size:50
Alignment explanation
Indices: 40613482--40613755 Score: 239
Period size: 50 Copynumber: 5.4 Consensus size: 50
40613472 TACGCATAGC
* * * *
40613482 AGCCTGCACTTAGTACTACACATGCGACC-AACAATC-CAGTACACGTAGT
1 AGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGA-TACACGTAGT
*
40613531 AGCCTACACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGT
1 AGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGT
* * * * *** * * * *
40613581 ATCCCGCACTTAGTACTACACACATGA-TTGAAGTTGTCGGGTACGCATAGT
1 AGCCTGCACTTAGTACTACACACGTGACCT-AA-CCATCTGATACACGTAGT
* * * * * *
40613632 ATCCTGCACTTAGTACTACACATGCGACCTAACTATCTGGTACATGTAGT
1 AGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGT
* * * *
40613682 AGCCTGCACTTAGTACTACACACGTGACCTAAAACCATTTTAAACACATAGT
1 AGCCTGCACTTAGTACTACACACGTGACCT--AACCATCTGATACACGTAGT
*
40613734 AGCCTGCACATAGTACTACACA
1 AGCCTGCACTTAGTACTACACA
40613756 TGTGTTCTCA
Statistics
Matches: 179, Mismatches: 39, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
49 27 0.15
50 80 0.45
51 37 0.21
52 35 0.20
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (50 bp):
AGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGT
Found at i:40620620 original size:13 final size:13
Alignment explanation
Indices: 40620602--40620627 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40620592 ATATTATAAT
40620602 TATTTTATGTTAA
1 TATTTTATGTTAA
40620615 TATTTTATGTTAA
1 TATTTTATGTTAA
40620628 AAATAAAAAT
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:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTTATGTTAA
Found at i:40622053 original size:40 final size:40
Alignment explanation
Indices: 40622005--40622290 Score: 434
Period size: 40 Copynumber: 7.2 Consensus size: 40
40621995 AGACTAAGAT
40622005 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
*
40622045 CCGAAGGCATTTCTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
* *
40622085 CCGAAGGCATTTGTGCTAGTTACTATAACCGGACTAAGAT-
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAG-TC
* * *
40622125 CTGAAGGCATTTGTGCTAGTTACTATAACCGGACTAAGAT-
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAG-TC
40622165 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
* *
40622205 CCGAAGGCATTTGTGCTAGTTACTATATCTGGGCTAACTC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
* * *
40622245 CCGAAGGCATTTGTGCGAGTTGCTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
40622284 CCGAAGG
1 CCGAAGG
40622291 TACTTGGGTT
Statistics
Matches: 230, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
39 16 0.07
40 213 0.93
41 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
Found at i:40628566 original size:13 final size:13
Alignment explanation
Indices: 40628548--40628573 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40628538 ATATTATAAT
40628548 TATTTTATGTTAA
1 TATTTTATGTTAA
40628561 TATTTTATGTTAA
1 TATTTTATGTTAA
40628574 AAATAAAAAT
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:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTTATGTTAA
Found at i:40638428 original size:29 final size:28
Alignment explanation
Indices: 40638392--40638469 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
40638382 TCATGAGATT
40638392 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
40638422 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
40638449 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
40638470 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:40638744 original size:173 final size:174
Alignment explanation
Indices: 40638422--40638748 Score: 557
Period size: 173 Copynumber: 1.9 Consensus size: 174
40638412 AAATTGTACA
* *
40638422 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
* * *
40638487 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTATCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
*
40638552 TTTTGGACAGTGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * * *
40638596 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
40638661 TGTGC-AACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
40638725 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
40638749 ACCTTGAGTT
Statistics
Matches: 143, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
173 79 0.55
174 64 0.45
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:40642084 original size:179 final size:179
Alignment explanation
Indices: 40641784--40642137 Score: 665
Period size: 179 Copynumber: 2.0 Consensus size: 179
40641774 AGATGTCCCC
* *
40641784 TAGTAATTCGAGGTTCTTGTTTTTCGGCGGACTTGATGCTTTTTCCGTTTGATGAATTTGATGTT
1 TAGTAATTCGAGGTTCTTGTTTTCCGGCGGACTTGATGCTTTTGCCGTTTGATGAATTTGATGTT
40641849 ATTCTTGGTTTGGATTGGCTGACCGCACATGATGCGGTTGTGAATTGCAAAAGCAAGACTATTGA
66 ATTCTTGGTTTGGATTGGCTGACCGCACATGATGCGGTTGTGAATTGCAAAAGCAAGACTATTGA
*
40641914 TTTGAGGTGCGCAAATAACG-AGATAATCCGAGTTGAGTCTGCGGACTTT
131 TTTGAGGTGCGCAAATAACGAAG-TAATCCGAGTTGAGTCTACGGACTTT
40641963 TAGTAATTCGAGGTTCTTGTTTTCCGGCGGACTTGATGCTTTTGCCGTTTGATGAATTTGATGTT
1 TAGTAATTCGAGGTTCTTGTTTTCCGGCGGACTTGATGCTTTTGCCGTTTGATGAATTTGATGTT
40642028 ATTCTTGGTTTGGATTGGCTGACCGCACATGATGCGGTTGTGAATTGCAAAAGCAAGACTATTGA
66 ATTCTTGGTTTGGATTGGCTGACCGCACATGATGCGGTTGTGAATTGCAAAAGCAAGACTATTGA
40642093 TTTGAGGTGCGCAAATAACGAAGTAATCCGAGTTGAGTCTACGGA
131 TTTGAGGTGCGCAAATAACGAAGTAATCCGAGTTGAGTCTACGGA
40642138 TTTGGAGGGG
Statistics
Matches: 171, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
179 169 0.99
180 2 0.01
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (179 bp):
TAGTAATTCGAGGTTCTTGTTTTCCGGCGGACTTGATGCTTTTGCCGTTTGATGAATTTGATGTT
ATTCTTGGTTTGGATTGGCTGACCGCACATGATGCGGTTGTGAATTGCAAAAGCAAGACTATTGA
TTTGAGGTGCGCAAATAACGAAGTAATCCGAGTTGAGTCTACGGACTTT
Found at i:40646892 original size:79 final size:81
Alignment explanation
Indices: 40646756--40646940 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
40646746 TTGAATGATG
*
40646756 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
40646820 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
40646835 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
40646897 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
40646915 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40646941 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:40646954 original size:40 final size:40
Alignment explanation
Indices: 40646757--40646940 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
40646747 TGAATGATGT
* * * *
40646757 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
40646797 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
40646837 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
40646875 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
40646916 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
40646941 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:40646962 original size:79 final size:79
Alignment explanation
Indices: 40646809--40646973 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
40646799 GGACTAAGAT
* **
40646809 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
40646874 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
40646888 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
40646951 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
40646967 CCGAAGG
1 CCGAAGG
40646974 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:40653869 original size:79 final size:81
Alignment explanation
Indices: 40653734--40653917 Score: 234
Period size: 79 Copynumber: 2.3 Consensus size: 81
40653724 TGAATGATGT
*
40653734 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
*
40653798 GTGCGAGATACTA-ATT
66 GTGCGAGATACTATA-A
* * * **
40653814 TCGGGCTAAG-CCCGAAGGCATTTGTGC-AAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATT
*
40653876 TGTGCGAGTTACTATAA
65 TGTGCGAGATACTATAA
*
40653893 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
40653918 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.64
80 31 0.34
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTATAA
Found at i:40653924 original size:40 final size:40
Alignment explanation
Indices: 40653733--40653917 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
40653723 TTGAATGATG
* * * *
40653733 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
40653773 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40653813 TTCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40653852 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
40653893 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40653918 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 33 0.27
40 80 0.65
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40653939 original size:79 final size:79
Alignment explanation
Indices: 40653734--40653950 Score: 192
Period size: 79 Copynumber: 2.7 Consensus size: 79
40653724 TGAATGATGT
** * * * **
40653734 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-AAGTTACTAAATCCGGGTTAA-ATCCCGAAGGCATT
*
40653797 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
* ** *
40653814 TCGGGCTAAGCCCGAAGGCATTTGTGCAAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACAAGTTACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
*
40653879 GCGAGTTACT-ATAA
66 GCGAGATACTAAT-A
* * * *
40653893 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACAAGTTA-CTAAATCCGGGTTAAATCCCGAAGG
40653951 TACGTGATTT
Statistics
Matches: 115, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
78 3 0.03
79 72 0.63
80 40 0.35
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACAAGTTACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:40662954 original size:28 final size:28
Alignment explanation
Indices: 40662891--40663016 Score: 191
Period size: 28 Copynumber: 4.5 Consensus size: 28
40662881 ATATTAAGTC
*
40662891 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
40662918 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
40662946 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
40662974 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
40663003 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40663017 CAATCTCATG
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
27 22 0.24
28 51 0.55
29 19 0.21
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:40663474 original size:2 final size:2
Alignment explanation
Indices: 40663467--40663496 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
40663457 CATACTTATG
*
40663467 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40663497 CTTCGGAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40668157 original size:62 final size:62
Alignment explanation
Indices: 40668081--40668267 Score: 374
Period size: 62 Copynumber: 3.0 Consensus size: 62
40668071 ATTTAACAAA
40668081 TTTCGTAACTTTCATAAATCAAGGGTTCCATGTTTTTCAATACACATGTTGTAACCAAACCG
1 TTTCGTAACTTTCATAAATCAAGGGTTCCATGTTTTTCAATACACATGTTGTAACCAAACCG
40668143 TTTCGTAACTTTCATAAATCAAGGGTTCCATGTTTTTCAATACACATGTTGTAACCAAACCG
1 TTTCGTAACTTTCATAAATCAAGGGTTCCATGTTTTTCAATACACATGTTGTAACCAAACCG
40668205 TTTCGTAACTTTCATAAATCAAGGGTTCCATGTTTTTCAATACACATGTTGTAACCAAACCG
1 TTTCGTAACTTTCATAAATCAAGGGTTCCATGTTTTTCAATACACATGTTGTAACCAAACCG
40668267 T
1 T
40668268 AATCATTCCA
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 125 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (62 bp):
TTTCGTAACTTTCATAAATCAAGGGTTCCATGTTTTTCAATACACATGTTGTAACCAAACCG
Found at i:40674661 original size:19 final size:19
Alignment explanation
Indices: 40674633--40674673 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
40674623 CAGGCAGCTG
*
40674633 ATTCGGGTCTAGGAATTAA
1 ATTCGAGTCTAGGAATTAA
40674652 ATTCGAGTCTAGGAATTAA
1 ATTCGAGTCTAGGAATTAA
40674671 ATT
1 ATT
40674674 TGGGAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (19 bp):
ATTCGAGTCTAGGAATTAA
Found at i:40678214 original size:29 final size:29
Alignment explanation
Indices: 40678155--40678214 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
40678145 CTACAATTTA
* *
40678155 ACTTTCTACCAGTTCTACACTTCTTATGT
1 ACTTTCTACCAGTTCTACACTTCTCACGT
40678184 ACTTTCTACCAGTTCTACACTTCTCACGT
1 ACTTTCTACCAGTTCTACACTTCTCACGT
40678213 AC
1 AC
40678215 AATTCTCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.22, C:0.32, G:0.07, T:0.40
Consensus pattern (29 bp):
ACTTTCTACCAGTTCTACACTTCTCACGT
Found at i:40692268 original size:34 final size:34
Alignment explanation
Indices: 40692221--40692287 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
40692211 ATAAAGCAGA
*
40692221 TGCAAGAGACTTCGACTTCCTCACCTGTTTAAGG
1 TGCAAAAGACTTCGACTTCCTCACCTGTTTAAGG
* *
40692255 TGCAAAAGGCTTCGACTTCCTCGCCTGTTTAAG
1 TGCAAAAGACTTCGACTTCCTCACCTGTTTAAG
40692288 AAGCTGTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (34 bp):
TGCAAAAGACTTCGACTTCCTCACCTGTTTAAGG
Found at i:40694401 original size:19 final size:18
Alignment explanation
Indices: 40694377--40694420 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
40694367 TACGTCATAC
40694377 TAATTTTTTTAACTTTTTA
1 TAATTTTTTT-ACTTTTTA
*
40694396 TAATTTTTTTATTTTTTA
1 TAATTTTTTTACTTTTTA
40694414 -AATTTTT
1 TAATTTTT
40694421 AAATTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 7 0.29
18 7 0.29
19 10 0.42
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
TAATTTTTTTACTTTTTA
Found at i:40694402 original size:9 final size:9
Alignment explanation
Indices: 40694377--40694431 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
40694367 TACGTCATAC
*
40694377 TAATTTTTT
1 TAATTTTTA
40694386 TAACTTTTTA
1 TAA-TTTTTA
*
40694396 TAATTTTTT
1 TAATTTTTA
*
40694405 TATTTTTTA
1 TAATTTTTA
40694414 -AATTTTTA
1 TAATTTTTA
40694422 -AATTATTTA
1 TAATT-TTTA
40694431 T
1 T
40694432 TGACGTAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
8 11 0.29
9 19 0.50
10 8 0.21
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (9 bp):
TAATTTTTA
Found at i:40696985 original size:25 final size:25
Alignment explanation
Indices: 40696957--40697023 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
40696947 TTATGTACAT
* *
40696957 GTATGCTCATGCGAGCTATGAATTG
1 GTATGCTCATACGAGCTATGAATCG
*
40696982 GTATGCTC-TCACGAGCTGTGAATCG
1 GTATGCTCAT-ACGAGCTATGAATCG
*
40697007 GTAAGCTCATACGAGCT
1 GTATGCTCATACGAGCT
40697024 GCAAATTCGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.03
25 34 0.94
26 1 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (25 bp):
GTATGCTCATACGAGCTATGAATCG
Found at i:40697024 original size:25 final size:25
Alignment explanation
Indices: 40696961--40697075 Score: 76
Period size: 25 Copynumber: 4.6 Consensus size: 25
40696951 GTACATGTAT
* * * *
40696961 GCTCATGCGAGCTATGAATTGGTAT
1 GCTCATACGAGCTGTGAATCGGTAA
40696986 GCTC-TCACGAGCTGTGAATCGGTAA
1 GCTCAT-ACGAGCTGTGAATCGGTAA
**
40697011 GCTCATACGAGCTGCAAATTC-G-AA
1 GCTCATACGAGCTGTGAA-TCGGTAA
** * *
40697035 GCTCATAC-ATGCTGCAAATTGGGAA
1 GCTCATACGA-GCTGTGAATCGGTAA
*
40697060 GCTCATATGAGCTGTG
1 GCTCATACGAGCTGTG
40697076 GTGTGTCTGT
Statistics
Matches: 73, Mismatches: 10, Indels: 14
0.75 0.10 0.14
Matches are distributed among these distances:
23 2 0.03
24 20 0.27
25 47 0.64
26 4 0.05
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (25 bp):
GCTCATACGAGCTGTGAATCGGTAA
Found at i:40697040 original size:24 final size:25
Alignment explanation
Indices: 40697009--40697073 Score: 89
Period size: 24 Copynumber: 2.6 Consensus size: 25
40696999 GTGAATCGGT
40697009 AAGCTCATACGAGCTGCAAATT-CG
1 AAGCTCATACGAGCTGCAAATTGCG
*
40697033 AAGCTCATAC-ATGCTGCAAATTGGG
1 AAGCTCATACGA-GCTGCAAATTGCG
*
40697058 AAGCTCATATGAGCTG
1 AAGCTCATACGAGCTG
40697074 TGGTGTGTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 1 0.03
24 20 0.56
25 14 0.39
26 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (25 bp):
AAGCTCATACGAGCTGCAAATTGCG
Found at i:40697814 original size:12 final size:12
Alignment explanation
Indices: 40697797--40697837 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
40697787 CAGTGGTATT
40697797 ACTATAATTCAA
1 ACTATAATTCAA
40697809 ACTATAA-T--A
1 ACTATAATTCAA
*
40697818 ACAATAATTCAA
1 ACTATAATTCAA
40697830 ACTATAAT
1 ACTATAAT
40697838 AACAATAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
9 7 0.29
10 1 0.04
11 1 0.04
12 15 0.62
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.32
Consensus pattern (12 bp):
ACTATAATTCAA
Found at i:40697824 original size:21 final size:21
Alignment explanation
Indices: 40697800--40697846 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
40697790 TGGTATTACT
40697800 ATAATTCAAACTATAATAACA
1 ATAATTCAAACTATAATAACA
40697821 ATAATTCAAACTATAATAACA
1 ATAATTCAAACTATAATAACA
40697842 ATAAT
1 ATAAT
40697847 GAAATATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAATTCAAACTATAATAACA
Found at i:40698971 original size:22 final size:24
Alignment explanation
Indices: 40698929--40698972 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
40698919 TAACTAAGTT
40698929 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
40698953 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
40698973 TCTTGCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:40699374 original size:2 final size:2
Alignment explanation
Indices: 40699367--40699393 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40699357 CTTTATGACT
40699367 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
40699394 TAGTTTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40702631 original size:46 final size:46
Alignment explanation
Indices: 40702578--40702670 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
40702568 ATTTGAATTG
40702578 CACTATATGATGTTTATGTTATTGAATTGTTGGTTGGTAAGTTTTA
1 CACTATATGATGTTTATGTTATTGAATTGTTGGTTGGTAAGTTTTA
40702624 CACTATATGATGTTTATGTTATTGAATTGTTGGTTGGTAAGTTTTA
1 CACTATATGATGTTTATGTTATTGAATTGTTGGTTGGTAAGTTTTA
40702670 C
1 C
40702671 TTACTTAGCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.24, C:0.05, G:0.22, T:0.49
Consensus pattern (46 bp):
CACTATATGATGTTTATGTTATTGAATTGTTGGTTGGTAAGTTTTA
Found at i:40705256 original size:22 final size:21
Alignment explanation
Indices: 40705230--40705271 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
40705220 TTTTATGTCT
*
40705230 TTTATGTTTATTTTTAGAATTA
1 TTTATGTTTATGTTTA-AATTA
*
40705252 TTTATTTTTATGTTTAAATT
1 TTTATGTTTATGTTTAAATT
40705272 GAATAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (21 bp):
TTTATGTTTATGTTTAAATTA
Found at i:40707294 original size:17 final size:17
Alignment explanation
Indices: 40707272--40707305 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40707262 TTTGGTAAGT
* *
40707272 TGTTAATTAAGTTAAAA
1 TGTTAAGTAAATTAAAA
40707289 TGTTAAGTAAATTAAAA
1 TGTTAAGTAAATTAAAA
40707306 GGTAAAAGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (17 bp):
TGTTAAGTAAATTAAAA
Found at i:40709416 original size:40 final size:40
Alignment explanation
Indices: 40709372--40709556 Score: 289
Period size: 40 Copynumber: 4.6 Consensus size: 40
40709362 GCTACTTGCT
* * *
40709372 CAAATGCCTTCAAGACTTAGCCCGGTTATAGTAACTCCCA
1 CAAATGCCTTCGAGACTTAGCCCGGATATAGTAACTCGCA
*
40709412 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGAGACTTAGCCCGGATATAGTAACTCGCA
* *
40709452 CAAATGCCTTCGACACTTAGCCCAGATATAGTAACTCGCA
1 CAAATGCCTTCGAGACTTAGCCCGGATATAGTAACTCGCA
* *
40709492 CAAATGCCTTCGACACTTAGCCCAGATATAGTAACTCGCA
1 CAAATGCCTTCGAGACTTAGCCCGGATATAGTAACTCGCA
*
40709532 CAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGAGACTTAGCCCGG
40709557 TTATCATCCG
Statistics
Matches: 135, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 135 1.00
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGAGACTTAGCCCGGATATAGTAACTCGCA
Found at i:40719416 original size:40 final size:40
Alignment explanation
Indices: 40719339--40719559 Score: 358
Period size: 40 Copynumber: 5.6 Consensus size: 40
40719329 AAACCAAGTA
** * *
40719339 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
40719378 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
40719418 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
40719458 CCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
40719498 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
40719538 CCTTCGGG-CTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
40719560 CAATCCGAAT
Statistics
Matches: 172, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
39 26 0.15
40 146 0.85
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:40729299 original size:46 final size:46
Alignment explanation
Indices: 40729210--40729474 Score: 240
Period size: 47 Copynumber: 5.7 Consensus size: 46
40729200 GCATATCTGT
* *
40729210 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCATA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCGTCTCATA
40729256 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACTCGTCTCAATA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT-G-ACTCGTCTC-ATA
* * * * * * *
40729303 -CCGATGCCATATCCTAGACATGGTCTTACACTGGCTCTTATAATGTT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCGTCTCA--TA
40729350 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACTCGTCTCAATA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT-G-ACTCGTCTC-ATA
* * * * * * *
40729397 -CCGATGCCATATCCTAGACATGGTCTTACACTGGCTCTTATAATGTT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCGTCTCA--TA
40729444 GCCGATG-CATGTCCCAGACAT-GTCTTACACT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT
40729475 AGCTCACACA
Statistics
Matches: 178, Mismatches: 25, Indels: 32
0.76 0.11 0.14
Matches are distributed among these distances:
44 10 0.06
45 17 0.10
46 56 0.31
47 57 0.32
48 37 0.21
49 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (46 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCGTCTCATA
Found at i:40729368 original size:94 final size:94
Alignment explanation
Indices: 40729211--40729477 Score: 448
Period size: 94 Copynumber: 2.9 Consensus size: 94
40729201 CATATCTGTG
* * * * * * * *
40729211 CCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCA--TAGCCGATGCATGTCCCAGA
1 CCGATGCCATATCCTAGACATGGTCTTACACTGGCTCTTATAATGTTGCCGATGCATGTCCCAGA
40729274 CATGTCTTACACTAGCACTCGTCTCAATA
66 CATGTCTTACACTAGCACTCGTCTCAATA
40729303 CCGATGCCATATCCTAGACATGGTCTTACACTGGCTCTTATAATGTTGCCGATGCATGTCCCAGA
1 CCGATGCCATATCCTAGACATGGTCTTACACTGGCTCTTATAATGTTGCCGATGCATGTCCCAGA
40729368 CATGTCTTACACTAGCACTCGTCTCAATA
66 CATGTCTTACACTAGCACTCGTCTCAATA
40729397 CCGATGCCATATCCTAGACATGGTCTTACACTGGCTCTTATAATGTTGCCGATGCATGTCCCAGA
1 CCGATGCCATATCCTAGACATGGTCTTACACTGGCTCTTATAATGTTGCCGATGCATGTCCCAGA
40729462 CATGTCTTACACTAGC
66 CATGTCTTACACTAGC
40729478 TCACACAAGT
Statistics
Matches: 165, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
92 36 0.22
94 129 0.78
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (94 bp):
CCGATGCCATATCCTAGACATGGTCTTACACTGGCTCTTATAATGTTGCCGATGCATGTCCCAGA
CATGTCTTACACTAGCACTCGTCTCAATA
Found at i:40731940 original size:48 final size:49
Alignment explanation
Indices: 40731815--40732096 Score: 245
Period size: 48 Copynumber: 5.8 Consensus size: 49
40731805 GTAAGATGCT
* * * * *
40731815 GATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATATATCAGT-GTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAG--CTCACATATCAATGGCC
* * * * *
40731865 GATGCCATGTTCCA-AAACTGATATTACACTAGCTCACATATC-ATGGCT
1 GATGCCATGTCCCAGACA-TGGTCTTACACTAGCTCACATATCAATGGCC
* * *
40731913 GATGCGATGTCCCAGACATGGTCTTACACTAGTTCTCATATCAAT-GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAATGGCC
* * * * *
40731961 GATGCTATGTTCCAAACATGATCTTACACTAGCT-AGCATATCGA-GGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCA-CATATCAATGGCC
* * * *
40732009 GATGCCATGTCCCAGACATGTTCTTACACTAACTCTCACATCAAT-GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAATGGCC
** * *
40732057 GATGCCATGTTGCAAACATGGTCTTACACTAGCTTACATA
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATA
40732097 ACCCTAGTAT
Statistics
Matches: 183, Mismatches: 41, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
47 1 0.01
48 153 0.84
49 6 0.03
50 23 0.13
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (49 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAATGGCC
Found at i:40732001 original size:96 final size:96
Alignment explanation
Indices: 40731812--40732096 Score: 369
Period size: 96 Copynumber: 2.9 Consensus size: 96
40731802 AGCGTAAGAT
* * * *
40731812 GCTGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATATATCAGTGTCGATGCCATGTTC
1 GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTC--ATATCAATGCCGATGCCATGTTC
*
40731877 CAAA-ACTGATATTACACTAGCTCACATATC-ATG
64 CAAACA-TGATCTTACACTAGCTCACATATCGA-G
* * *
40731910 GCTGATGCGATGTCCCAGACATGGTCTTACACTAGTTCTCATATCAATGCCGATGCTATGTTCCA
1 GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCA
40731975 AACATGATCTTACACTAGCT-AGCATATCGAG
66 AACATGATCTTACACTAGCTCA-CATATCGAG
* * * * *
40732006 GCCGATGCCATGTCCCAGACATGTTCTTACACTAACTCTCACATCAATGCCGATGCCATGTTGCA
1 GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCA
* *
40732071 AACATGGTCTTACACTAGCTTACATA
66 AACATGATCTTACACTAGCTCACATA
40732097 ACCCTAGTAT
Statistics
Matches: 166, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
95 1 0.01
96 126 0.76
97 3 0.02
98 36 0.22
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (96 bp):
GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCA
AACATGATCTTACACTAGCTCACATATCGAG
Found at i:40738291 original size:17 final size:17
Alignment explanation
Indices: 40738253--40738291 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
40738243 GGCATGTATA
* *
40738253 GCTAGATTCATACACAT
1 GCTAGACTCATACACAC
*
40738270 ACTAGACTCATACACAC
1 GCTAGACTCATACACAC
40738287 GCTAG
1 GCTAG
40738292 GTTAGTTCAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (17 bp):
GCTAGACTCATACACAC
Found at i:40738591 original size:20 final size:21
Alignment explanation
Indices: 40738566--40738605 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40738556 CAATGCAAAC
*
40738566 AAGGGC-ACACGCCTGTGTGG
1 AAGGGCGAAACGCCTGTGTGG
40738586 AAGGGCGAAACGCCTGTGTG
1 AAGGGCGAAACGCCTGTGTG
40738606 TCCTCTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.23, C:0.23, G:0.40, T:0.15
Consensus pattern (21 bp):
AAGGGCGAAACGCCTGTGTGG
Found at i:40739969 original size:48 final size:47
Alignment explanation
Indices: 40739836--40740004 Score: 182
Period size: 48 Copynumber: 3.5 Consensus size: 47
40739826 CATATCCTAG
* * *
40739836 ACATGGTCTTACACTAGCTCCCATATCAATGCCGATGCTATCTTCCAA
1 ACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCAT-GTCCAA
* * * *
40739884 ACATTGTCTTACACTAGCT-T-ACTAAT-AGAGGCTGATGCCATGTCCTAG
1 ACATGGTCTTACACTAGCTCTCA-T-ATCA-ATGCCGATGCCATGTCC-AA
40739932 ACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCAA
1 ACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATG-TCCAA
* *
40739980 ACATGGTCTTACACTGGCTCACATA
1 ACATGGTCTTACACTAGCTCTCATA
40740005 ACCCTAGTAT
Statistics
Matches: 100, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
46 1 0.01
47 5 0.05
48 87 0.87
49 6 0.06
50 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (47 bp):
ACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTCCAA
Found at i:40741613 original size:8 final size:8
Alignment explanation
Indices: 40741602--40741653 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
40741592 CGTAAATCCT
40741602 GAAATGTC
1 GAAATGTC
* *
40741610 GAAAAGTT
1 GAAATGTC
*
40741618 GAAATATC
1 GAAATGTC
*
40741626 GAAATGCC
1 GAAATGTC
*
40741634 GAAATGCC
1 GAAATGTC
*
40741642 AAAATGTC
1 GAAATGTC
40741650 GAAA
1 GAAA
40741654 AGCTGAAAGT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.19
Consensus pattern (8 bp):
GAAATGTC
Found at i:40741918 original size:29 final size:29
Alignment explanation
Indices: 40741876--40741949 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
40741866 CATGTATATA
40741876 AATGTGATTTGGGCCTAATGGGCCATACG
1 AATGTGATTTGGGCCTAATGGGCCATACG
**
40741905 AATGTGATTTGGGCCTAATGGGCCATGTG
1 AATGTGATTTGGGCCTAATGGGCCATACG
*
40741934 AATGAGA-TTGGGCCTA
1 AATGTGATTTGGGCCTA
40741950 GTCCGCCATA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 9 0.21
29 33 0.79
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.28
Consensus pattern (29 bp):
AATGTGATTTGGGCCTAATGGGCCATACG
Found at i:40746640 original size:12 final size:12
Alignment explanation
Indices: 40746621--40746650 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
40746611 TGTTGGCATA
40746621 TCTTTTTTT-TT
1 TCTTTTTTTCTT
40746632 TCTTTTTTTCTT
1 TCTTTTTTTCTT
40746644 TCTTTTT
1 TCTTTTT
40746651 CTCGAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TCTTTTTTTCTT
Found at i:40747706 original size:13 final size:13
Alignment explanation
Indices: 40747674--40747721 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
40747664 GTAGGACTCA
*
40747674 CTGTATCTGTTCT
1 CTGTATCTGTTAT
* *
40747687 ATTTATCTGTTAT
1 CTGTATCTGTTAT
40747700 CTGTATCTG-TAT
1 CTGTATCTGTTAT
40747712 CTGTATCTGT
1 CTGTATCTGT
40747722 AAAGGATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
12 12 0.41
13 17 0.59
ACGTcount: A:0.15, C:0.17, G:0.15, T:0.54
Consensus pattern (13 bp):
CTGTATCTGTTAT
Found at i:40747708 original size:6 final size:6
Alignment explanation
Indices: 40747690--40747722 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
40747680 CTGTTCTATT
40747690 TATCTG TTATCTG TATCTG TATCTG TATCTG TA
1 TATCTG -TATCTG TATCTG TATCTG TATCTG TA
40747723 AAGGATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.52
Consensus pattern (6 bp):
TATCTG
Found at i:40762479 original size:49 final size:49
Alignment explanation
Indices: 40762426--40762603 Score: 189
Period size: 49 Copynumber: 3.6 Consensus size: 49
40762416 CTGGTACGCA
*
40762426 TAGTAGCCTGCACTTAGTACTACATATGCAACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATCCGGTACACG
* ** * * *
40762475 TAGTAGCCTG-ACTTAGTACTACACACGTGACCTAACTATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCAACC-AATTATCCGGTACACG
* * * ** *
40762524 TAGTAGCCTGCACTTAGTACTACACACGTG-ATCGAAGTTATCGGGTATGCA
1 TAGTAGCCTGCACTTAGTACTACACA--TGCAACCAA-TTATCCGGTACACG
40762575 TAGTAGCCTGCACTTAGTACTACACATGC
1 TAGTAGCCTGCACTTAGTACTACACATGC
40762604 GACCTAGCTA
Statistics
Matches: 106, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
48 18 0.17
49 35 0.33
50 17 0.16
51 35 0.33
52 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATCCGGTACACG
Found at i:40762628 original size:98 final size:98
Alignment explanation
Indices: 40762410--40762609 Score: 249
Period size: 98 Copynumber: 2.0 Consensus size: 98
40762400 TATGTAGCCA
* * * * *
40762410 AACTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACATATGCAACCAATTATCCGGTACACG
1 AACTATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATCCGGTACACA
*
40762475 TAGTAGCCTGACTTAGTACTACACACGTGACCT
66 TAGTAGCCTGACTTAGTACTACACACGCGACCT
* * * *
40762508 AACTATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTG-ATCGAAGTTATCGGGTAT
1 AACTATCTGATACACGTAGTAGCCTGCACTTAGTACTACACA--TGCAACCAA-TTATCCGGTAC
* *
40762572 GCATAGTAGCCTGCACTTAGTACTACACATGCGACCT
63 ACATAGTAGCCTG-ACTTAGTACTACACACGCGACCT
40762609 A
1 A
40762610 GCTACATATA
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
98 38 0.44
99 4 0.05
100 22 0.26
101 22 0.26
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (98 bp):
AACTATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATCCGGTACACA
TAGTAGCCTGACTTAGTACTACACACGCGACCT
Found at i:40763448 original size:30 final size:30
Alignment explanation
Indices: 40763414--40763474 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
40763404 TCCTTAACTC
40763414 AAACTTTTACAAATTTACAATTTTGCCCCT
1 AAACTTTTACAAATTTACAATTTTGCCCCT
* * *
40763444 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTACAAATTTACAATTTTGCCCCT
40763474 A
1 A
40763475 GGCTCGGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.41
Consensus pattern (30 bp):
AAACTTTTACAAATTTACAATTTTGCCCCT
Found at i:40766074 original size:28 final size:28
Alignment explanation
Indices: 40766034--40766129 Score: 129
Period size: 28 Copynumber: 3.4 Consensus size: 28
40766024 ATATTAAGTC
* *
40766034 CGCACACTCAGTGCTATGTAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
40766062 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
40766090 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
40766119 CGCACACTTAG
1 CGCACACTTAG
40766130 CGCCAATCTC
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
28 45 0.74
29 16 0.26
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:40768525 original size:40 final size:40
Alignment explanation
Indices: 40768425--40768689 Score: 261
Period size: 40 Copynumber: 6.7 Consensus size: 40
40768415 GCTCCTCGTT
* * * *
40768425 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* **
40768465 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
40768504 CGAATGCCTTCAGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
40768544 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
* *
40768584 CAAATGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
40768624 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
40768665 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
40768690 CAGCATTCAA
Statistics
Matches: 195, Mismatches: 24, Indels: 12
0.84 0.10 0.05
Matches are distributed among these distances:
39 39 0.20
40 141 0.72
41 15 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:40768698 original size:41 final size:41
Alignment explanation
Indices: 40768621--40768698 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
40768611 TTTGTATCTC
* * *
40768621 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
40768662 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
40768699 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:40777723 original size:47 final size:47
Alignment explanation
Indices: 40777663--40777784 Score: 190
Period size: 47 Copynumber: 2.6 Consensus size: 47
40777653 ACATTGGCAC
*
40777663 TAAGACAAGGATACCATGAAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* * *
40777710 TAAGACAATGATACCATGTAAGACCATGTTTGGAACATTGTATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* *
40777757 TAAGATAAGGATATCATGTAAGACCATG
1 TAAGACAAGGATACCATGTAAGACCATG
40777785 CCAAGGCATG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 68 1.00
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:40784589 original size:33 final size:33
Alignment explanation
Indices: 40784542--40784631 Score: 146
Period size: 33 Copynumber: 2.7 Consensus size: 33
40784532 AGTTTATTTT
40784542 GGATTA-CAAGTCCAGGCTAAATCCAGTCAATTA
1 GGATTACCAA-TCCAGGCTAAATCCAGTCAATTA
*
40784575 GGATTACCAATCCAGGTTAAATCCAGTCAATTA
1 GGATTACCAATCCAGGCTAAATCCAGTCAATTA
*
40784608 GGATTACCAGTCCAGGCTAAATCC
1 GGATTACCAATCCAGGCTAAATCC
40784632 TAATTGAAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
33 50 0.94
34 3 0.06
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (33 bp):
GGATTACCAATCCAGGCTAAATCCAGTCAATTA
Found at i:40793688 original size:47 final size:46
Alignment explanation
Indices: 40793348--40793688 Score: 158
Period size: 47 Copynumber: 7.3 Consensus size: 46
40793338 GGGATATATT
* * *
40793348 GCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATACGCG
1 GCTGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATA-ATGTG
* * * *
40793397 TGCTGATGCATGTCCCAGACATGTCTTACACTAG--CACA-ACTCTTA
1 -GCTGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAAT-GTG
* ** * * * * * * *
40793442 GCCGATGTGTGTTCCAGGCACGTTTTACACTGGCTATCTC-T-GTCGGG
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGC--TCTCATAAT-GTG
** * * * * *
40793489 GCCAATGCATGTCCCAGACATGTCTTACATTGGCACTCAT-CTCTG
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAATGTG
* * * * * *
40793534 TGCCGCTGCCATGTCCCAGACATGGTCTTACATTAGCTATCATAGTATG
1 -GCTGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATAATGTG
* ** *
40793583 GCTGATGCATGTCCCAGACATGTCTTACACTAGCCCTTGT-TTGGATG
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAAT-G-TG
* *
40793630 TC-GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTG
1 GCTGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATAATGTG
*
40793677 GCTGAAGCATGT
1 GCTGATGCATGT
40793689 TGTAACACCC
Statistics
Matches: 218, Mismatches: 56, Indels: 37
0.70 0.18 0.12
Matches are distributed among these distances:
44 25 0.11
45 6 0.03
46 28 0.13
47 81 0.37
48 53 0.24
49 18 0.08
50 7 0.03
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.30
Consensus pattern (46 bp):
GCTGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAATGTG
Found at i:40794435 original size:31 final size:31
Alignment explanation
Indices: 40794394--40794457 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
40794384 CCTTTTCATA
*
40794394 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
40794425 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
40794456 TT
1 TT
40794458 ATTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:40794703 original size:24 final size:24
Alignment explanation
Indices: 40794651--40794816 Score: 239
Period size: 24 Copynumber: 7.0 Consensus size: 24
40794641 GCTTTATCAT
*
40794651 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
40794676 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
40794700 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
40794723 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
40794747 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
40794771 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
40794794 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
40794817 TCACTTCCTC
Statistics
Matches: 129, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
23 43 0.33
24 74 0.57
25 12 0.09
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:40794727 original size:47 final size:48
Alignment explanation
Indices: 40794650--40794816 Score: 241
Period size: 47 Copynumber: 3.5 Consensus size: 48
40794640 TGCTTTATCA
* *
40794650 TATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTT
1 TATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTT
*
40794699 TATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCGTAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
* *
40794746 GATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC-TTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
*
40794793 AATAACTGGGGCATAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTT
40794817 TCACTTCCTC
Statistics
Matches: 109, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
47 70 0.64
48 26 0.24
49 13 0.12
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (48 bp):
TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
Found at i:40794751 original size:71 final size:71
Alignment explanation
Indices: 40794651--40794816 Score: 262
Period size: 71 Copynumber: 2.3 Consensus size: 71
40794641 GCTTTATCAT
* *
40794651 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAA
40794715 GCCCTTTA
64 GCCCTTTA
* * *
40794723 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGC
40794788 CCTTTA
66 CCTTTA
40794794 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
40794817 TCACTTCCTC
Statistics
Matches: 88, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
71 76 0.86
72 12 0.14
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (71 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGC
CCTTTA
Found at i:40794891 original size:20 final size:20
Alignment explanation
Indices: 40794866--40794926 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
40794856 TGATGAATAC
40794866 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
40794886 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
40794906 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
40794926 A
1 A
40794927 CCGTGTTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:40794897 original size:11 final size:11
Alignment explanation
Indices: 40794866--40794921 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
40794856 TGATGAATAC
40794866 ATCATGTGCAT
1 ATCATGTGCAT
*
40794877 ATCA--TACAT
1 ATCATGTGCAT
40794886 ATCATGTGCAT
1 ATCATGTGCAT
*
40794897 ATCA--TACAT
1 ATCATGTGCAT
*
40794906 GTCATGTGCAT
1 ATCATGTGCAT
40794917 ATCAT
1 ATCAT
40794922 ACATACCGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:40796084 original size:27 final size:27
Alignment explanation
Indices: 40796054--40796106 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
40796044 GGGTGTTTTG
40796054 GTAAATCTGCAAACCAAAGGTATTTCA
1 GTAAATCTGCAAACCAAAGGTATTTCA
* * * *
40796081 GTAATTTTGTAAACCAATGGTATTTC
1 GTAAATCTGCAAACCAAAGGTATTTC
40796107 CATAATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (27 bp):
GTAAATCTGCAAACCAAAGGTATTTCA
Found at i:40796112 original size:27 final size:26
Alignment explanation
Indices: 40796064--40796119 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
40796054 GTAAATCTGC
40796064 AAACCAAAGGTATTTCAGTAATTTTGT
1 AAACCAAAGGTATTTCAGTAATTTT-T
*
40796091 AAACCAATGGTATTTCCA-TAATTTTT
1 AAACCAAAGGTATTT-CAGTAATTTTT
40796117 AAA
1 AAA
40796120 AAGTCAAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 4 0.15
27 21 0.78
28 2 0.07
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (26 bp):
AAACCAAAGGTATTTCAGTAATTTTT
Found at i:40796167 original size:27 final size:26
Alignment explanation
Indices: 40796127--40796258 Score: 99
Period size: 27 Copynumber: 4.9 Consensus size: 26
40796117 AAAAAGTCAA
*
40796127 GGGTATTTCT-GTAACTTTGTAAATCAG
1 GGGTATTT-TGGTAA-TTTATAAATCAG
* *
40796154 GGGTATTTTGGTAATTTTACAAAT-TG
1 GGGTATTTTGGTAA-TTTATAAATCAG
* * *
40796180 AGGGTATTTCGGTAATTTCACAAACCAG
1 -GGGTATTTTGGTAATTT-ATAAATCAG
* *
40796208 TGGTATTTTGGTAATTT-TACAAACTAG
1 GGGTATTTTGGTAATTTATA-AATC-AG
40796235 GGGTATTTTGGTAATTTTATAAAT
1 GGGTATTTTGGTAA-TTTATAAAT
40796259 TGAGGGTATT
Statistics
Matches: 84, Mismatches: 13, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
25 1 0.01
26 8 0.10
27 67 0.80
28 6 0.07
29 2 0.02
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (26 bp):
GGGTATTTTGGTAATTTATAAATCAG
Found at i:40796247 original size:81 final size:81
Alignment explanation
Indices: 40796152--40796346 Score: 293
Period size: 81 Copynumber: 2.4 Consensus size: 81
40796142 TTTGTAAATC
* *
40796152 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTT
1 AGGGGTATTTTGGTAATTTTATAAATTGAGGGTATTTCGGTAATTTCACAAACCAATGGTATTTT
*
40796217 GGTAATTTTACAAACT
66 AGTAATTTTACAAACT
* *
40796233 AGGGGTATTTTGGTAATTTTATAAATTGAGGGTATTTCTGTAATTTTACAAACCAATGGTATTTT
1 AGGGGTATTTTGGTAATTTTATAAATTGAGGGTATTTCGGTAATTTCACAAACCAATGGTATTTT
*
40796298 AGTAATTTTACAGACT
66 AGTAATTTTACAAACT
* * * *
40796314 A-GGGTATTTTAGTGATTTTGTAAATCGAGGGTA
1 AGGGGTATTTTGGTAATTTTATAAATTGAGGGTA
40796347 AAACAGTAAT
Statistics
Matches: 104, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
80 28 0.27
81 76 0.73
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.41
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTATAAATTGAGGGTATTTCGGTAATTTCACAAACCAATGGTATTTT
AGTAATTTTACAAACT
Found at i:40796265 original size:27 final size:27
Alignment explanation
Indices: 40796154--40796332 Score: 186
Period size: 27 Copynumber: 6.7 Consensus size: 27
40796144 TGTAAATCAG
*
40796154 GGGTATTTTGGTAATTTTACAAATTGA
1 GGGTATTTTGGTAATTTTACAAACTGA
* * *
40796181 GGGTATTTCGGTAATTTCACAAAC-CA
1 GGGTATTTTGGTAATTTTACAAACTGA
40796207 GTGGTATTTTGGTAATTTTACAAACT-A
1 G-GGTATTTTGGTAATTTTACAAACTGA
* *
40796234 GGGGTATTTTGGTAATTTTATAAATTGA
1 -GGGTATTTTGGTAATTTTACAAACTGA
**
40796262 GGGTATTTCT-GTAATTTTACAAACCAA
1 GGGTATTT-TGGTAATTTTACAAACTGA
* * *
40796289 TGGTATTTTAGTAATTTTACAGACT-A
1 GGGTATTTTGGTAATTTTACAAACTGA
* *
40796315 GGGTATTTTAGTGATTTT
1 GGGTATTTTGGTAATTTT
40796333 GTAAATCGAG
Statistics
Matches: 129, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
26 20 0.16
27 106 0.82
28 3 0.02
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACTGA
Found at i:40796535 original size:27 final size:27
Alignment explanation
Indices: 40796332--40796528 Score: 241
Period size: 27 Copynumber: 7.3 Consensus size: 27
40796322 TTAGTGATTT
* *
40796332 TGTAAATCGAGGGTAAAACAGTAATTC
1 TGTAAATCAAGGGTAAAACGGTAATTC
**
40796359 TGTAAATCAAGGGTAAAATAGTAATTC
1 TGTAAATCAAGGGTAAAACGGTAATTC
* * *
40796386 TATAAATCAAGGGTAAAACAGTACTTC
1 TGTAAATCAAGGGTAAAACGGTAATTC
40796413 TGTAAATCAAGGGTAAAACGGTAATTC
1 TGTAAATCAAGGGTAAAACGGTAATTC
* * * * *
40796440 TATAAGTCAATGGTAAAACGATAATTA
1 TGTAAATCAAGGGTAAAACGGTAATTC
* *
40796467 TGTAAATCAGGGGTAAAACGGTAATTA
1 TGTAAATCAAGGGTAAAACGGTAATTC
** *
40796494 TGTAAATCGGGGGTAAAACGGTAATTT
1 TGTAAATCAAGGGTAAAACGGTAATTC
40796521 TGTAAATC
1 TGTAAATC
40796529 GGGGGTACTC
Statistics
Matches: 150, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 150 1.00
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.28
Consensus pattern (27 bp):
TGTAAATCAAGGGTAAAACGGTAATTC
Found at i:40797984 original size:30 final size:30
Alignment explanation
Indices: 40797943--40798000 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
40797933 AAATTTACAT
* * *
40797943 CTTTGGTAAAATGACCATTTTGCCCCTAAA
1 CTTTGGCAAAATAACCATTTTACCCCTAAA
*
40797973 CTTTGGCAAAATAACTATTTTACCCCTA
1 CTTTGGCAAAATAACCATTTTACCCCTA
40798001 TGCCCAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (30 bp):
CTTTGGCAAAATAACCATTTTACCCCTAAA
Found at i:40798855 original size:27 final size:27
Alignment explanation
Indices: 40798825--40798896 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
40798815 GCTGTTACAG
*
40798825 CCCTTGTGTGGTAAAATGACAATTTTT
1 CCCTTATGTGGTAAAATGACAATTTTT
*
40798852 CCCTTATGTGGTAAAATGACAGTTTTT
1 CCCTTATGTGGTAAAATGACAATTTTT
* *
40798879 CCCTTATATGGTAGAATG
1 CCCTTATGTGGTAAAATG
40798897 GTTGTTTTGC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.39
Consensus pattern (27 bp):
CCCTTATGTGGTAAAATGACAATTTTT
Found at i:40798903 original size:27 final size:27
Alignment explanation
Indices: 40798847--40798969 Score: 97
Period size: 27 Copynumber: 4.6 Consensus size: 27
40798837 AAAATGACAA
* * * * *
40798847 TTTTTCCCTTATGTGGTAAAATGACAG
1 TTTTGCCCTTATATGGTAGAATGGCTG
* *
40798874 TTTTTCCCTTATATGGTAGAATGGTTG
1 TTTTGCCCTTATATGGTAGAATGGCTG
*
40798901 TTTTGCCCTTA-AGTGGTAGAATGGCTA
1 TTTTGCCCTTATA-TGGTAGAATGGCTG
* * * *
40798928 TATTGCCCTTATATGCTCAG-ATGACTA
1 TTTTGCCCTTATATGGT-AGAATGGCTG
*
40798955 TTTTGCCCCTATATG
1 TTTTGCCCTTATATG
40798970 ATGTATGTTT
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
26 1 0.01
27 76 0.95
28 3 0.04
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (27 bp):
TTTTGCCCTTATATGGTAGAATGGCTG
Found at i:40806430 original size:49 final size:49
Alignment explanation
Indices: 40806358--40806745 Score: 479
Period size: 49 Copynumber: 7.8 Consensus size: 49
40806348 TGAGGTCACG
*
40806358 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGGTCGCA
* * * * *
40806407 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTATGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAA-T-TGGTCGCA
*
40806458 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGGTCGCA
* * * * *
40806507 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTATGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAA-T-TGGTCGCA
*** * *
40806558 TGTGTAGTACTAAGTGCAGGCTACTACAAGGACCAGATTATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGGTCGCA
* * * * *
40806607 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTATGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAA-T-TGGTCGCA
*** * *
40806658 TGTGTAGTACTAAGTGCAGGCTACTACAAGGACCAGATTATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGGTCGCA
40806707 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
40806746 GCTTCGGCTA
Statistics
Matches: 280, Mismatches: 53, Indels: 12
0.81 0.15 0.03
Matches are distributed among these distances:
49 156 0.56
50 6 0.02
51 118 0.42
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGGTCGCA
Found at i:40806526 original size:100 final size:100
Alignment explanation
Indices: 40806353--40806740 Score: 686
Period size: 100 Copynumber: 3.9 Consensus size: 100
40806343 TATTGTGAGG
*** *
40806353 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACAAGGACCAGATAATTGGTCGCATGTGTAGTACT
40806418 AAGTGCAGGCTACTATGCGTACCCGAAAACTATGA
66 AAGTGCAGGCTACTATGCGTACCCGAAAACTATGA
*** *
40806453 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACAAGGACCAGATAATTGGTCGCATGTGTAGTACT
40806518 AAGTGCAGGCTACTATGCGTACCCGAAAACTATGA
66 AAGTGCAGGCTACTATGCGTACCCGAAAACTATGA
*
40806553 TCACGTGTGTAGTACTAAGTGCAGGCTACTACAAGGACCAGATTATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACAAGGACCAGATAATTGGTCGCATGTGTAGTACT
40806618 AAGTGCAGGCTACTATGCGTACCCGAAAACTATGA
66 AAGTGCAGGCTACTATGCGTACCCGAAAACTATGA
*
40806653 TCACGTGTGTAGTACTAAGTGCAGGCTACTACAAGGACCAGATTATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACAAGGACCAGATAATTGGTCGCATGTGTAGTACT
40806718 AAGTGCAGGCTACTATGCGTACC
66 AAGTGCAGGCTACTATGCGTACC
40806741 AGATAGCTTC
Statistics
Matches: 283, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 283 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACAAGGACCAGATAATTGGTCGCATGTGTAGTACT
AAGTGCAGGCTACTATGCGTACCCGAAAACTATGA
Found at i:40808750 original size:37 final size:37
Alignment explanation
Indices: 40808700--40808778 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
40808690 TTATTACGAA
* * *
40808700 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
40808737 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
40808774 GTCTT
1 GTCTT
40808779 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:40808975 original size:47 final size:47
Alignment explanation
Indices: 40808897--40809072 Score: 228
Period size: 47 Copynumber: 3.7 Consensus size: 47
40808887 CCCTTCGGGA
* * * * * *
40808897 CTTATCACATTTATACACTTTCACACCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGC
* * *
40808944 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGC
* *
40808991 CTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGC
*
40809038 CTTATCACATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATCCATCACAT
40809073 AGAATCTTAA
Statistics
Matches: 113, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
46 1 0.01
47 112 0.99
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGC
Found at i:40813144 original size:27 final size:29
Alignment explanation
Indices: 40813099--40813158 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
40813089 TATTCAGTAT
40813099 CAGT-ATAGTCTGGGCCTT-AGCCC-TATA
1 CAGTAATAGTCTGGGCCTTAAGCCCAT-TA
*
40813126 CAGTAATAGTGTGGG-CTTAAGCCCATTA
1 CAGTAATAGTCTGGGCCTTAAGCCCATTA
40813154 CAGTA
1 CAGTA
40813159 TCAGTACCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 7 0.24
28 21 0.72
29 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (29 bp):
CAGTAATAGTCTGGGCCTTAAGCCCATTA
Found at i:40813373 original size:27 final size:27
Alignment explanation
Indices: 40813314--40813378 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
40813304 AGCATAGCTG
* *
40813314 CCAGAAACAGTAAATGTGGCAAAGCCA
1 CCAGTAACAGTAAATGTGACAAAGCCA
* * *
40813341 CCAGTAACAGTGAATGTGACATAGTCA
1 CCAGTAACAGTAAATGTGACAAAGCCA
*
40813368 CTAGT-ACAGTA
1 CCAGTAACAGTA
40813379 TTTCATCCAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 5 0.16
27 26 0.84
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (27 bp):
CCAGTAACAGTAAATGTGACAAAGCCA
Found at i:40813544 original size:27 final size:27
Alignment explanation
Indices: 40813514--40813630 Score: 144
Period size: 27 Copynumber: 4.3 Consensus size: 27
40813504 GGCATAATCG
* * *
40813514 TCATTCTACCATACAGGGGTATTACAA
1 TCATTTTACCCTACAGGGGTATTACGA
* *
40813541 TCATTTTACCCTATAGGGGTATTACGG
1 TCATTTTACCCTACAGGGGTATTACGA
*
40813568 TCATTTTACCCTATAGGGGTATTACGA
1 TCATTTTACCCTACAGGGGTATTACGA
* * * *
40813595 CCATTTTACCCTACAGGGATATTATGG
1 TCATTTTACCCTACAGGGGTATTACGA
40813622 TCATTTTAC
1 TCATTTTAC
40813631 AAATTAGGGG
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 78 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGTATTACGA
Found at i:40813600 original size:54 final size:54
Alignment explanation
Indices: 40813513--40813630 Score: 164
Period size: 54 Copynumber: 2.2 Consensus size: 54
40813503 GGGCATAATC
* * * *
40813513 GTCATTCTACCATACAGGGGTATTACAATCATTTTACCCTATAGGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACAACCATTTTACCCTACAGGGATATTACG
* * * *
40813567 GTCATTTTACCCTATAGGGGTATTACGACCATTTTACCCTACAGGGATATTATG
1 GTCATTTTACCATACAGGGGTATTACAACCATTTTACCCTACAGGGATATTACG
40813621 GTCATTTTAC
1 GTCATTTTAC
40813631 AAATTAGGGG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (54 bp):
GTCATTTTACCATACAGGGGTATTACAACCATTTTACCCTACAGGGATATTACG
Found at i:40813639 original size:27 final size:26
Alignment explanation
Indices: 40813609--40813753 Score: 128
Period size: 27 Copynumber: 5.4 Consensus size: 26
40813599 TTTACCCTAC
* *
40813609 AGGGATATTATGGTCATTTTACAAATT
1 AGGGGTATT-TGGTAATTTTACAAATT
40813636 AGGGGTATTTTGGTAATTTTACAAATT
1 AGGGGTA-TTTGGTAATTTTACAAATT
* * *
40813663 GGGGGTATTTCGGTAATTTCACAAATA
1 AGGGGTATTT-GGTAATTTTACAAATT
* * **
40813690 AAGGGTATTTCAGTAATTTTACAACCT
1 AGGGGTATTT-GGTAATTTTACAAATT
* * * *
40813717 AGGAGTATTTCAGTAATTTCACAAATC
1 AGGGGTATTT-GGTAATTTTACAAATT
40813744 AGGGGTATTT
1 AGGGGTATTT
40813754 CAATAATTTC
Statistics
Matches: 97, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
26 3 0.03
27 92 0.95
28 2 0.02
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.38
Consensus pattern (26 bp):
AGGGGTATTTGGTAATTTTACAAATT
Found at i:40813639 original size:54 final size:54
Alignment explanation
Indices: 40813513--40813644 Score: 158
Period size: 54 Copynumber: 2.4 Consensus size: 54
40813503 GGGCATAATC
* * * * * *
40813513 GTCATTCTACCATACAGGGGTATTACAATCATTTTACCCTATAGGGGTATTACG
1 GTCATTTTACAATATAGGGGTATTACAACCATTTTACCCTACAGGGATATTACG
** * *
40813567 GTCATTTTACCCTATAGGGGTATTACGACCATTTTACCCTACAGGGATATTATG
1 GTCATTTTACAATATAGGGGTATTACAACCATTTTACCCTACAGGGATATTACG
40813621 GTCATTTTACAA-ATTAGGGGTATT
1 GTCATTTTACAATA-TAGGGGTATT
40813645 TTGGTAATTT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
53 1 0.01
54 66 0.99
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (54 bp):
GTCATTTTACAATATAGGGGTATTACAACCATTTTACCCTACAGGGATATTACG
Found at i:40813687 original size:54 final size:54
Alignment explanation
Indices: 40813624--40813768 Score: 173
Period size: 54 Copynumber: 2.7 Consensus size: 54
40813614 TATTATGGTC
* * ** * * * *
40813624 ATTTTACAAATTAGGGGTATTTTGGTAATTTTACAAATTGGGGGTATTTCGGTA
1 ATTTCACAAATAAGGGGTATTTCAGTAATTTTACAAACTAGGAGTATTTCAGTA
* *
40813678 ATTTCACAAATAAAGGGTATTTCAGTAATTTTACAACCTAGGAGTATTTCAGTA
1 ATTTCACAAATAAGGGGTATTTCAGTAATTTTACAAACTAGGAGTATTTCAGTA
* * *
40813732 ATTTCACAAATCAGGGGTATTTCAATAATTTCACAAA
1 ATTTCACAAATAAGGGGTATTTCAGTAATTTTACAAA
40813769 TCGGGGTCTT
Statistics
Matches: 76, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 76 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (54 bp):
ATTTCACAAATAAGGGGTATTTCAGTAATTTTACAAACTAGGAGTATTTCAGTA
Found at i:40813754 original size:27 final size:27
Alignment explanation
Indices: 40813624--40813775 Score: 155
Period size: 27 Copynumber: 5.7 Consensus size: 27
40813614 TATTATGGTC
* * **
40813624 ATTTTACAAATTAGGGGTATTTTGGTA
1 ATTTCACAAATCAGGGGTATTTCAGTA
* ** *
40813651 ATTTTACAAATTGGGGGTATTTCGGTA
1 ATTTCACAAATCAGGGGTATTTCAGTA
* *
40813678 ATTTCACAAATAAAGGGTATTTCAGTA
1 ATTTCACAAATCAGGGGTATTTCAGTA
* * *
40813705 ATTTTAC-AACCTAGGAGTATTTCAGTA
1 ATTTCACAAATC-AGGGGTATTTCAGTA
*
40813732 ATTTCACAAATCAGGGGTATTTCAATA
1 ATTTCACAAATCAGGGGTATTTCAGTA
40813759 ATTTCACAAATC-GGGGT
1 ATTTCACAAATCAGGGGT
40813776 CTTAACGACC
Statistics
Matches: 107, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.07
27 97 0.91
28 3 0.03
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (27 bp):
ATTTCACAAATCAGGGGTATTTCAGTA
Found at i:40817681 original size:27 final size:27
Alignment explanation
Indices: 40817650--40817799 Score: 155
Period size: 27 Copynumber: 5.6 Consensus size: 27
40817640 TTAGTTTACC
*
40817650 AAATTACTGAAATACCCTCGACTTATA
1 AAATTACTGAAATACCCTCGATTTATA
*
40817677 AAATTAC-CAAAGTACCC-CTGATTTATA
1 AAATTACTGAAA-TACCCTC-GATTTATA
** * *
40817704 AAATTACCCAAATATCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTATA
**
40817731 AAATTA-TCGAAATACCCTC-AGTTTGCA
1 AAATTACT-GAAATACCCTCGA-TTTATA
*
40817758 AAATTACTGAAATACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTATA
40817785 AAATTACTGAAATAC
1 AAATTACTGAAATAC
40817800 TCCTGTAAGA
Statistics
Matches: 106, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
26 5 0.05
27 94 0.89
28 7 0.07
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGATTTATA
Found at i:40817733 original size:54 final size:53
Alignment explanation
Indices: 40817642--40817791 Score: 176
Period size: 54 Copynumber: 2.8 Consensus size: 53
40817632 AGAATACTTT
* * *
40817642 AGTTTACCAAATTACTGAAATACCCTCGACTTATAAAATTACCAAAGTACCC-C
1 AGTTTACAAAATTACTGAAATACCCTCGATTTGTAAAATTACCAAA-TACCCTC
* * ** * *
40817695 TGATTTATAAAATTACCCAAATATCCTCGATTTGTAAAATTATCGAAATACCCTC
1 AG-TTTACAAAATTACTGAAATACCCTCGATTTGTAAAATTA-CCAAATACCCTC
*
40817750 AGTTTGCAAAATTACTGAAATACCCTCGATTTGTAAAATTAC
1 AGTTTACAAAATTACTGAAATACCCTCGATTTGTAAAATTAC
40817792 TGAAATACTC
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
53 2 0.03
54 71 0.90
55 6 0.08
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (53 bp):
AGTTTACAAAATTACTGAAATACCCTCGATTTGTAAAATTACCAAATACCCTC
Found at i:40817817 original size:54 final size:52
Alignment explanation
Indices: 40817650--40817818 Score: 139
Period size: 54 Copynumber: 3.1 Consensus size: 52
40817640 TTAGTTTACC
* * * *
40817650 AAATTACTGAAATACCCTCGACTTATAAAATTAC-CAAAGTACCCCTG-ATTTAT
1 AAATTACTGAAATACCCTCGATTTGTAAAATTACTGAAA-TA-CCCTGTA-TGAT
** * *
40817703 AAAATTACCCAAATATCCTCGATTTGTAAAATTA-TCGAAATACCCTCAGTTTGCA-
1 -AAATTACTGAAATACCCTCGATTTGTAAAATTACT-GAAATACCCT--GTATG-AT
*
40817758 AAATTACTGAAATACCCTCGATTTGTAAAATTACTGAAATACTCCTGTAAGAT
1 AAATTACTGAAATACCCTCGATTTGTAAAATTACTGAAATAC-CCTGTATGAT
40817811 AGAATTAC
1 A-AATTAC
40817819 CATTTTACCC
Statistics
Matches: 92, Mismatches: 13, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
52 1 0.01
53 8 0.09
54 73 0.79
55 9 0.10
56 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (52 bp):
AAATTACTGAAATACCCTCGATTTGTAAAATTACTGAAATACCCTGTATGAT
Found at i:40817841 original size:27 final size:27
Alignment explanation
Indices: 40817811--40817979 Score: 257
Period size: 27 Copynumber: 6.3 Consensus size: 27
40817801 CCTGTAAGAT
*
40817811 AGAATTACCATTTTACCCTTGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
* *
40817838 AGAATTACCGTTTTACCCTCGATTTAT
1 AGAATTACCATTTTACCCTCGATTTAC
40817865 AGAATTACCATTTTACCCTCGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
** *
40817892 AGAATTACTGTCTTACCCTCGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
*
40817919 AGAATTACCATTTTACCTTCGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
*
40817946 ATAATTACCATTTTACCCTCGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
*
40817973 AAAATTA
1 AGAATTA
40817980 TTGAAATACC
Statistics
Matches: 127, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 127 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (27 bp):
AGAATTACCATTTTACCCTCGATTTAC
Found at i:40817844 original size:54 final size:54
Alignment explanation
Indices: 40817770--40817953 Score: 174
Period size: 54 Copynumber: 3.4 Consensus size: 54
40817760 ATTACTGAAA
** *
40817770 TACCCTCGATTTGTAAAATTACTGAAATACTCCT-G-TAAGATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACTGAAATAC-CCTCGAT-AGATAGAATTACCATTT
* * *** **
40817824 TACCCTTGATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACTGAAATACCCTCGATAGATAGAATTACCATTT
*** ** *
40817878 TACCCTCGATTTACAGAATTACTGTCTTACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACTGAAATACCCTCGATAGATAGAATTACCATTT
* *
40817932 TACCTTCGATTTACATAATTAC
1 TACCCTCGATTTACAGAATTAC
40817954 CATTTTACCC
Statistics
Matches: 112, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
53 3 0.03
54 108 0.96
55 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.38
Consensus pattern (54 bp):
TACCCTCGATTTACAGAATTACTGAAATACCCTCGATAGATAGAATTACCATTT
Found at i:40817990 original size:81 final size:81
Alignment explanation
Indices: 40817824--40818009 Score: 264
Period size: 81 Copynumber: 2.3 Consensus size: 81
40817814 ATTACCATTT
* *
40817824 TACCCTTGATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATT
1 TACCCTTGATTTACAGAATTACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATT
* ***
40817889 TACAGAATTACTGTCT
66 TACAAAATTACTGAAA
* * *
40817905 TACCCTCGATTTACAGAATTACCATTTTACCTTCGATTTACATAATTACCATTTTACCCTCGATT
1 TACCCTTGATTTACAGAATTACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATT
*
40817970 TACAAAATTATTGAAA
66 TACAAAATTACTGAAA
* *
40817986 TACCCTTGGTTTACAAAATTACCA
1 TACCCTTGATTTACAGAATTACCA
40818010 AAATACCCCT
Statistics
Matches: 92, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 92 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (81 bp):
TACCCTTGATTTACAGAATTACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATT
TACAAAATTACTGAAA
Found at i:40818013 original size:27 final size:27
Alignment explanation
Indices: 40817644--40818044 Score: 119
Period size: 27 Copynumber: 14.9 Consensus size: 27
40817634 AATACTTTAG
* ** *
40817644 TTTACCAAATTACTGAAATACCCTCGA
1 TTTACAAAATTACCAAAATACCCTTGA
* * * *
40817671 CTTATAAAATTACCAAAGTACCCCTGA
1 TTTACAAAATTACCAAAATACCCTTGA
* * * *
40817698 TTTATAAAATTACCCAAATATCCTCGA
1 TTTACAAAATTACCAAAATACCCTTGA
** * * *
40817725 TTTGTAAAATTATCGAAATACCC-TCA
1 TTTACAAAATTACCAAAATACCCTTGA
* ** *
40817751 GTTTGCAAAATTACTGAAATACCCTCGA
1 -TTTACAAAATTACCAAAATACCCTTGA
** **
40817779 TTTGTAAAATTACTGAAATACTCC-TG-
1 TTTACAAAATTACCAAAATAC-CCTTGA
* * ***
40817805 -TAAGATAGAATTACCATTTTACCCTTGA
1 TTTACA-A-AATTACCAAAATACCCTTGA
* **** *
40817833 TTTACAGAATTACCGTTTTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTTGA
* * *** *
40817860 TTTATAGAATTACCATTTTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTTGA
* ***** *
40817887 TTTACAGAATTACTGTCTTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTTGA
* ***
40817914 TTTACAGAATTACCATTTTA-CCTTCGA
1 TTTACAAAATTACCAAAATACCCTT-GA
* *** *
40817941 TTTACATAATTACCATTTTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTTGA
*** *
40817968 TTTACAAAATTATTGAAATACCCTTGG
1 TTTACAAAATTACCAAAATACCCTTGA
* *
40817995 TTTACAAAATTACCAAAATACCCCTAA
1 TTTACAAAATTACCAAAATACCCTTGA
***
40818022 TTTGTGAAATTACCAAAATACCC
1 TTTACAAAATTACCAAAATACCC
40818045 CTCTAGGGTA
Statistics
Matches: 294, Mismatches: 70, Indels: 20
0.77 0.18 0.05
Matches are distributed among these distances:
25 2 0.01
26 7 0.02
27 276 0.94
28 6 0.02
29 3 0.01
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.34
Consensus pattern (27 bp):
TTTACAAAATTACCAAAATACCCTTGA
Found at i:40818059 original size:27 final size:27
Alignment explanation
Indices: 40818029--40818197 Score: 203
Period size: 27 Copynumber: 6.3 Consensus size: 27
40818019 TAATTTGTGA
* * *
40818029 AATTACCAAAATACCCCTCTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
40818056 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* * *
40818083 AATTACTGAAATACCCTTATAGGGTAA
1 AATTACCGAAATACCCTTGTAGGGTAG
* * *
40818110 AATTATCGAAATACCCTTGTAAGGTAT
1 AATTACCGAAATACCCTTGTAGGGTAG
* *
40818137 AAATATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* * * *
40818164 AATTACTGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCCTTGTAGGGTAG
40818191 AATTACC
1 AATTACC
40818198 ATTTTGCCCC
Statistics
Matches: 121, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 121 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (27 bp):
AATTACCGAAATACCCTTGTAGGGTAG
Found at i:40818087 original size:81 final size:81
Alignment explanation
Indices: 40818002--40818198 Score: 198
Period size: 81 Copynumber: 2.4 Consensus size: 81
40817992 TGGTTTACAA
** * * *
40818002 AATTACCAAAATACCCCTAAT-TTGTGAAATTACCAAAATACCCCTCTAGGGTAGAATTACCGAA
1 AATTACCAAAATA-CCCTAATAGGGTAAAATTACCAAAATACCCCTCTAAGGTAGAAATACCGAA
40818066 ATACCCTTGTAGGGTAG
65 ATACCCTTGTAGGGTAG
** * * * * * * *
40818083 AATTACTGAAATACCCTTATAGGGTAAAATTATCGAAATACCCTTGTAAGGTATAAATATCGAAA
1 AATTACCAAAATACCCTAATAGGGTAAAATTACCAAAATACCCCTCTAAGGTAGAAATACCGAAA
40818148 TACCCTTGTAGGGTAG
66 TACCCTTGTAGGGTAG
** * ** *
40818164 AATTACTGAGATACCCTTGTGGGGTAAAATTACCA
1 AATTACCAAAATACCCTAATAGGGTAAAATTACCA
40818199 TTTTGCCCCT
Statistics
Matches: 96, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
80 6 0.06
81 90 0.94
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (81 bp):
AATTACCAAAATACCCTAATAGGGTAAAATTACCAAAATACCCCTCTAAGGTAGAAATACCGAAA
TACCCTTGTAGGGTAG
Found at i:40818623 original size:6 final size:6
Alignment explanation
Indices: 40818592--40818679 Score: 74
Period size: 6 Copynumber: 14.3 Consensus size: 6
40818582 TTGCATTCAC
* *
40818592 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* *
40818641 -TCACCTG ATTCTG ATTCTA ATTCTG ATTCT- AGTTCTG AT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
40818680 AATGTTTCTT
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
5 4 0.06
6 53 0.80
7 7 0.11
8 2 0.03
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:40818627 original size:31 final size:31
Alignment explanation
Indices: 40818592--40818670 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
40818582 TTGCATTCAC
* *
40818592 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTCACCTGATACTG
*
40818623 ATTCTGATTCTGATTCTGTCACCTGATTCTG
1 ATTCTGATTCTGATTCTGTCACCTGATACTG
*
40818654 ATTCTAATTCTGATTCT
1 ATTCTGATTCTGATTCT
40818671 AGTTCTGATA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.48
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTCACCTGATACTG
Found at i:40819875 original size:27 final size:27
Alignment explanation
Indices: 40819836--40819954 Score: 166
Period size: 27 Copynumber: 4.4 Consensus size: 27
40819826 TGGATAAGTT
40819836 GTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * *
40819863 ATAGAATTACCGAAATACCCTTGTAAG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
40819890 GTAGAAATACTGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
40819917 GTAGAATTACCGAGATACCCCTGTGGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
40819944 GTAAAATTACC
1 GTAGAATTACC
40819955 ATTTTGCCCC
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 79 1.00
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Found at i:40821415 original size:18 final size:18
Alignment explanation
Indices: 40821394--40821446 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
40821384 CAATCACTTA
40821394 AACCAGCGAATGCATACT
1 AACCAGCGAATGCATACT
40821412 AACCA-C-AAT-C--ACTT
1 AACCAGCGAATGCATAC-T
40821426 AAACCAGCGAATGCATACT
1 -AACCAGCGAATGCATACT
40821445 AA
1 AA
40821447 GTCGTAAGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 14
0.67 0.00 0.33
Matches are distributed among these distances:
13 2 0.07
14 1 0.04
15 6 0.21
16 4 0.14
17 4 0.14
18 8 0.29
19 1 0.04
20 2 0.07
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.17
Consensus pattern (18 bp):
AACCAGCGAATGCATACT
Found at i:40821422 original size:33 final size:33
Alignment explanation
Indices: 40821384--40821446 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
40821374 AAGACCACCC
40821384 CAATCACTTAAACCAGCGAATGCATACTAACCA
1 CAATCACTTAAACCAGCGAATGCATACTAACCA
40821417 CAATCACTTAAACCAGCGAATGCATACTAA
1 CAATCACTTAAACCAGCGAATGCATACTAA
40821447 GTCGTAAGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.29, G:0.10, T:0.19
Consensus pattern (33 bp):
CAATCACTTAAACCAGCGAATGCATACTAACCA
Found at i:40838815 original size:28 final size:27
Alignment explanation
Indices: 40838783--40838842 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
40838773 GTATACATAG
40838783 ACCCTCAAATTGATAAAATGACTATTTT
1 ACCCTCAAA-TGATAAAATGACTATTTT
* * *
40838811 ACCCTTATATGGTAAAATGACTATTTT
1 ACCCTCAAATGATAAAATGACTATTTT
*
40838838 GCCCT
1 ACCCT
40838843 TATGTGGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (27 bp):
ACCCTCAAATGATAAAATGACTATTTT
Found at i:40838873 original size:27 final size:27
Alignment explanation
Indices: 40838796--40838875 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 27
40838786 CTCAAATTGA
* *
40838796 TAAAATGACTATTTTACCCTTATATGG
1 TAAAATGACTATTTTGCCCTTATGTGG
40838823 TAAAATGACTATTTTGCCCTTATGTGG
1 TAAAATGACTATTTTGCCCTTATGTGG
* *
40838850 TGAGATGACTCA-TTTGCCCTTATGTG
1 TAAAATGACT-ATTTTGCCCTTATGTG
40838876 AGGTATTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 47 0.98
28 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.40
Consensus pattern (27 bp):
TAAAATGACTATTTTGCCCTTATGTGG
Found at i:40841927 original size:38 final size:38
Alignment explanation
Indices: 40841883--40842041 Score: 93
Period size: 47 Copynumber: 3.7 Consensus size: 38
40841873 TTCACATTCA
40841883 TCACATTGACCATTCGGCCTTATCACACATACACATGTTCACATT
1 TCACATTGACCATTCGGCCTTATCACACATACACATG-------T
* * * **
40841928 CATCACATTGGCCATTCGGCCTTATCTCATATATGCATGT
1 --TCACATTGACCATTCGGCCTTATCACACATACACATGT
*
40841968 TCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGT
1 TCACATTGA-C-CATT---C----GGCCTTATCACACATACACATGT
*
40842015 TCACATTGGCCATTCGGCCTTATCACA
1 TCACATTGACCATTCGGCCTTATCACA
40842042 TATATATACA
Statistics
Matches: 90, Mismatches: 13, Indels: 27
0.69 0.10 0.21
Matches are distributed among these distances:
38 19 0.21
39 1 0.01
40 5 0.06
42 1 0.01
43 1 0.01
45 4 0.04
46 1 0.01
47 58 0.64
ACGTcount: A:0.26, C:0.31, G:0.12, T:0.31
Consensus pattern (38 bp):
TCACATTGACCATTCGGCCTTATCACACATACACATGT
Found at i:40842073 original size:49 final size:49
Alignment explanation
Indices: 40842015--40843037 Score: 1973
Period size: 49 Copynumber: 21.0 Consensus size: 49
40842005 ATACACATGT
* *
40842015 TCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
* *
40842064 TCACATTGGCCATTCGGCCTTATCAC--ATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
40842111 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
40842160 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
40842209 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
40842258 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
40842307 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
40842356 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
40842405 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
40842454 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
40842503 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
40842552 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
40842601 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
40842650 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
40842699 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
40842748 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
40842797 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
40842846 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
40842895 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
40842944 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
*
40842993 TCACATTGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATT
1 TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATT
40843038 TATTCAAATA
Statistics
Matches: 969, Mismatches: 3, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
47 64 0.07
49 905 0.93
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (49 bp):
TCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
Found at i:40844563 original size:56 final size:56
Alignment explanation
Indices: 40844496--40844615 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
40844486 TATTAGTTTA
40844496 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
40844552 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
40844608 TTGCCCAT
1 TTGCCCAT
40844616 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:40854437 original size:5 final size:5
Alignment explanation
Indices: 40854427--40854456 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
40854417 AGATGAAGAT
40854427 AAAAG AAAAG AAAAG AAAAG AAGAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AA-AAG AAAA
40854457 AACTGAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:40863360 original size:39 final size:40
Alignment explanation
Indices: 40863339--40863482 Score: 211
Period size: 40 Copynumber: 3.6 Consensus size: 40
40863329 ACTACTTGCT
*
40863339 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
40863379 CAAATGCTTTCGGGACTTAGCCCGGATATAGTAGCTCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
40863419 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
40863458 CAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
40863483 TTATCATCCA
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
38 1 0.01
39 33 0.35
40 59 0.63
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:40865552 original size:20 final size:20
Alignment explanation
Indices: 40865529--40865611 Score: 112
Period size: 20 Copynumber: 4.2 Consensus size: 20
40865519 TAGTGGCTCG
*
40865529 AAGCCATCAGTAGCGACACA
1 AAGCCATCAATAGCGACACA
* *
40865549 AAGCCATTAATAGCGGCACA
1 AAGCCATCAATAGCGACACA
*
40865569 AAGCCATTAATAGCGACACA
1 AAGCCATCAATAGCGACACA
* *
40865589 AAGCCATCAATAGTGGCACA
1 AAGCCATCAATAGCGACACA
40865609 AAG
1 AAG
40865612 TTATAAATAT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.13
Consensus pattern (20 bp):
AAGCCATCAATAGCGACACA
Found at i:40865573 original size:40 final size:40
Alignment explanation
Indices: 40865529--40865611 Score: 130
Period size: 40 Copynumber: 2.1 Consensus size: 40
40865519 TAGTGGCTCG
* *
40865529 AAGCCATCAGTAGCGACACAAAGCCATTAATAGCGGCACA
1 AAGCCATCAATAGCGACACAAAGCCATCAATAGCGGCACA
* *
40865569 AAGCCATTAATAGCGACACAAAGCCATCAATAGTGGCACA
1 AAGCCATCAATAGCGACACAAAGCCATCAATAGCGGCACA
40865609 AAG
1 AAG
40865612 TTATAAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.13
Consensus pattern (40 bp):
AAGCCATCAATAGCGACACAAAGCCATCAATAGCGGCACA
Found at i:40867037 original size:40 final size:39
Alignment explanation
Indices: 40866976--40867197 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 39
40866966 AGATGATAAT
* *
40866976 CGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTAATTC
1 CGGGCTAAGTCCCGAAG-GCATTTGTGCTAGT-ACTAATTC
* * *
40867016 CGGGCTAAGTCCCAAAGGCATTTGTGCGAGCTACTAATTT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TACTAATTC
* * *
40867056 CGAGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTACTTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TACTAATTC
* *
40867096 CGGGCTAAGTCCCGAAGGCATTTGTG-TGAGTTA-TTATAC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCT-AG-TACTAATTC
* *
40867135 CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT-ATAGC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TACTAAT-TC
40867175 CGGGCTAAGTCCCGAAGGCATTT
1 CGGGCTAAGTCCCGAAGGCATTT
40867198 AAGCTAGTGG
Statistics
Matches: 159, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
39 36 0.23
40 120 0.75
41 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26
Consensus pattern (39 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTACTAATTC
Found at i:40867170 original size:79 final size:79
Alignment explanation
Indices: 40866976--40867197 Score: 268
Period size: 79 Copynumber: 2.8 Consensus size: 79
40866966 AGATGATAAT
* * ** *
40866976 CGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTAATTCCGGGCTAAGTCCCAAAGGCATTTG
1 CGGGCTAAGTCCCGAAG-GCATTTGTGCAAGTTACT-ATTCCGGGCTAAGTCCCGAAGGCATTTG
**
40867040 TGCGAGCTACTAATTT
64 TGCGAGCTACTAATAC
* * *
40867056 CGAGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTACTTCCGGGCTAAGTCCCGAAGGCATTTGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTA-TTCCGGGCTAAGTCCCGAAGGCATTTGT
* * *
40867121 GTGAGTTA-TTATAC
65 GCGAGCTACTAATAC
*
40867135 CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAGCCGGGCTAAGTCCCGAAGGCATTT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTAT-TCCGGGCTAAGTCCCGAAGGCATTT
40867198 AAGCTAGTGG
Statistics
Matches: 123, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
78 1 0.01
79 61 0.50
80 59 0.48
81 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26
Consensus pattern (79 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATTCCGGGCTAAGTCCCGAAGGCATTTGTG
CGAGCTACTAATAC
Found at i:40875353 original size:40 final size:40
Alignment explanation
Indices: 40875301--40875524 Score: 242
Period size: 40 Copynumber: 5.6 Consensus size: 40
40875291 TAACTCATAC
* *
40875301 AATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAGAAACTCGCACA
* *
40875341 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGAAACTCGCACA
* * *
40875381 AAGGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGAAACTCGCACA
*
40875421 AAGGCCTTCGGGACTTAACCCGGAATTA-ATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGA-AACTCGCACA
** ** *
40875461 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAGAAAC-TCGCACA
*
40875502 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
40875525 CAGCATTCAA
Statistics
Matches: 162, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
39 8 0.05
40 143 0.88
41 11 0.07
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAGAAACTCGCACA
Found at i:40875363 original size:79 final size:79
Alignment explanation
Indices: 40875264--40875524 Score: 228
Period size: 80 Copynumber: 3.3 Consensus size: 79
40875254 CTCGTTCAAG
* * * * *
40875264 TGCCTTCGGGACATAGCCCGGTTAA-AGTAACTCATAC-AATGCCTTCGGGACTTAACCCGGATT
1 TGCCTTCGGGACTTAACCCGG--AATAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGA-A
*
40875327 TTA-AAACTCGCACGAA
63 TTAGAAACTCGCACAAA
* *
40875343 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAGGCCTTCGGGACTTAACCCGGAATT
1 TGCCTTCGGGACTTAACCCGGAA-TAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
* *
40875408 AGTATCTCGCACAAA
65 AGAAACTCGCACAAA
* * * * **
40875423 GGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATGCCTTC-GGATCTTAGTCCGG-AT
1 TGCCTTCGGGACTTAACCCGGAA-TAGTAACTCACACAAAGGCCTTCGGGA-CTTAACCCGGAAT
** *
40875486 ATAGTCACTTAGCACAAA
64 -TAGAAAC-TCGCACAAA
*
40875504 -GCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGACTTAACCCGGA
40875525 CAGCATTCAA
Statistics
Matches: 155, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
77 2 0.01
79 36 0.23
80 109 0.70
81 8 0.05
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (79 bp):
TGCCTTCGGGACTTAACCCGGAATAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATTA
GAAACTCGCACAAA
Found at i:40875444 original size:120 final size:120
Alignment explanation
Indices: 40875304--40875524 Score: 308
Period size: 120 Copynumber: 1.8 Consensus size: 120
40875294 CTCATACAAT
* *
40875304 GCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-A
1 GCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATGCCTTC-GGATCTTAACCCGGATA
*
40875366 TTAGT-A-TCTCGCACAAAGGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAG
64 -TAGTCACT-TAGCACAAA-GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAG
**
40875424 GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATATA
1 GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATA
*
40875489 GTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
66 GTCACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
40875525 CAGCATTCAA
Statistics
Matches: 90, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
119 7 0.08
120 72 0.80
121 10 0.11
122 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (120 bp):
GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAAGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAG
Found at i:40881880 original size:52 final size:52
Alignment explanation
Indices: 40881802--40881903 Score: 177
Period size: 52 Copynumber: 2.0 Consensus size: 52
40881792 CCGTTCTGGC
* *
40881802 CCTGTCTCACGAGAACCTGAATATCTCTTAACATACTGTCCATATGATTGGA
1 CCTGTCTCACAAGAACCTGAATATCTCTTAACATACTGTCCATATAATTGGA
*
40881854 CCTGTCTCACAAGAACCTGAATATCTCTTAACATACTGTCCGTATAATTG
1 CCTGTCTCACAAGAACCTGAATATCTCTTAACATACTGTCCATATAATTG
40881904 TTTCGTTACT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.31
Consensus pattern (52 bp):
CCTGTCTCACAAGAACCTGAATATCTCTTAACATACTGTCCATATAATTGGA
Found at i:40882839 original size:40 final size:40
Alignment explanation
Indices: 40882787--40882930 Score: 152
Period size: 40 Copynumber: 3.6 Consensus size: 40
40882777 TAACTCATAC
* *
40882787 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
40882827 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
40882867 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
40882908 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
40882931 CAGCATTCAA
Statistics
Matches: 90, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
39 9 0.10
40 70 0.78
41 11 0.12
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:40884966 original size:40 final size:39
Alignment explanation
Indices: 40884911--40885137 Score: 255
Period size: 40 Copynumber: 5.7 Consensus size: 39
40884901 CGGATGATAA
* *
40884911 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTAATT
1 CCGGGCTAAGTCCCGAAG-GCATTTGAGCGAGT-ACTAATT
*
40884951 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TACTAATT
* *
40884991 CCGGGCTAAGTCCCGAAGGCATTTGGGAGAGCTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TACTAATT
* *
40885031 CCGGGCTAAGTCCCGAAGGCATTTGTA-CGAGTTA-TTATA
1 CCGGGCTAAGTCCCGAAGGCATTTG-AGCGAG-TACTAATT
* * *
40885070 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT-ATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TACTAAT-T
*
40885110 CCGGGCTAAGTCCCGAAAGCATTTGAGC
1 CCGGGCTAAGTCCCGAAGGCATTTGAGC
40885138 TAGTGGCTAT
Statistics
Matches: 167, Mismatches: 14, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
39 36 0.22
40 128 0.77
41 3 0.02
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTACTAATT
Found at i:40885156 original size:79 final size:79
Alignment explanation
Indices: 40884911--40885157 Score: 242
Period size: 79 Copynumber: 3.1 Consensus size: 79
40884901 CGGATGATAA
* * *
40884911 CCGGGCTAAGTCCCG-AGAGCATTTGAGC-TAG-TGGCTAATTCCGGGCTAAGTCCCGAAGGCAT
1 CCGGGCTAAGTCCCGAAG-GCATTTG-GCAGAGCT-ACTAATACCGGGCTAAGTCCCGAAGGCAT
*
40884973 TTGTGCGAGCTACTA-ATT
63 TTGAGCGAG-TACTATA-T
* *
40884991 CCGGGCTAAGTCCCGAAGGCATTTGGGAGAGCTACTAATTCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGGCAGAGCTACTAATACCGGGCTAAGTCCCGAAGGCATTTG
*
40885056 TA-CGAGTTATTATA-
66 -AGCGAG-TACTATAT
* *
40885070 CCGGGCTAAGTCCCGAAGGCATTTGTGCA-AGTTACT-ATAACCGGGCTAAGTCCCGAAAGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTG-GCAGAGCTACTAAT-ACCGGGCTAAGTCCCGAAGGCATT
* *
40885133 TGAGCTAGTGGCTATAT
64 TGAGCGAGT-ACTATAT
40885150 CC-GGCTAA
1 CCGGGCTAA
40885158 ACTCCGAAGG
Statistics
Matches: 144, Mismatches: 13, Indels: 21
0.81 0.07 0.12
Matches are distributed among these distances:
78 4 0.03
79 69 0.48
80 67 0.47
81 4 0.03
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGGCAGAGCTACTAATACCGGGCTAAGTCCCGAAGGCATTTG
AGCGAGTACTATAT
Found at i:40887306 original size:20 final size:20
Alignment explanation
Indices: 40887283--40887414 Score: 201
Period size: 20 Copynumber: 6.6 Consensus size: 20
40887273 TAGCGGCTTG
*
40887283 AAGCCATCAATAGCGGCACA
1 AAGCCATCAATAGTGGCACA
40887303 AAGCCATCAATAGTGGCACA
1 AAGCCATCAATAGTGGCACA
* **
40887323 AAGCCATCAATAGTGTCATG
1 AAGCCATCAATAGTGGCACA
40887343 AAGCCATCAATAGTGGCACA
1 AAGCCATCAATAGTGGCACA
*
40887363 AAGCCATCAATAGTGGTACA
1 AAGCCATCAATAGTGGCACA
*
40887383 AAGCCATCAATAGCGGCACA
1 AAGCCATCAATAGTGGCACA
*
40887403 AAGCCATAAATA
1 AAGCCATCAATA
40887415 TTGCAGCAAT
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 101 1.00
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
AAGCCATCAATAGTGGCACA
Found at i:40887327 original size:40 final size:40
Alignment explanation
Indices: 40887256--40887414 Score: 201
Period size: 40 Copynumber: 4.0 Consensus size: 40
40887246 TATCAGTATA
* * * ***
40887256 TGGCACAAAGCCATGAGTAGCGGCTTGAAGCCATCAATAG
1 TGGCACAAAGCCATCAATAGTGGCACAAAGCCATCAATAG
*
40887296 CGGCACAAAGCCATCAATAGTGGCACAAAGCCATCAATAG
1 TGGCACAAAGCCATCAATAGTGGCACAAAGCCATCAATAG
* **
40887336 TGTCATGAAGCCATCAATAGTGGCACAAAGCCATCAATAG
1 TGGCACAAAGCCATCAATAGTGGCACAAAGCCATCAATAG
* * *
40887376 TGGTACAAAGCCATCAATAGCGGCACAAAGCCATAAATA
1 TGGCACAAAGCCATCAATAGTGGCACAAAGCCATCAATA
40887415 TTGCAGCAAT
Statistics
Matches: 102, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 102 1.00
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.16
Consensus pattern (40 bp):
TGGCACAAAGCCATCAATAGTGGCACAAAGCCATCAATAG
Found at i:40887349 original size:60 final size:60
Alignment explanation
Indices: 40887256--40887414 Score: 228
Period size: 60 Copynumber: 2.6 Consensus size: 60
40887246 TATCAGTATA
* * *
40887256 TGGCACAAAGCCATGAGTAGCGGCTTGAAGCCATCAATAGCGGCACAAAGCCATCAATAG
1 TGGCACAAAGCCATCAATAGCGGCATGAAGCCATCAATAGCGGCACAAAGCCATCAATAG
* * *
40887316 TGGCACAAAGCCATCAATAGTGTCATGAAGCCATCAATAGTGGCACAAAGCCATCAATAG
1 TGGCACAAAGCCATCAATAGCGGCATGAAGCCATCAATAGCGGCACAAAGCCATCAATAG
* ** *
40887376 TGGTACAAAGCCATCAATAGCGGCACAAAGCCATAAATA
1 TGGCACAAAGCCATCAATAGCGGCATGAAGCCATCAATA
40887415 TTGCAGCAAT
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 87 1.00
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.16
Consensus pattern (60 bp):
TGGCACAAAGCCATCAATAGCGGCATGAAGCCATCAATAGCGGCACAAAGCCATCAATAG
Found at i:40892277 original size:16 final size:16
Alignment explanation
Indices: 40892256--40892287 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40892246 ATAACTCCTT
40892256 GAACCGCTCCCATGCC
1 GAACCGCTCCCATGCC
40892272 GAACCGCTCCCATGCC
1 GAACCGCTCCCATGCC
40892288 TCATATAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.50, G:0.19, T:0.12
Consensus pattern (16 bp):
GAACCGCTCCCATGCC
Found at i:40895739 original size:42 final size:43
Alignment explanation
Indices: 40895638--40895774 Score: 111
Period size: 43 Copynumber: 3.2 Consensus size: 43
40895628 TGAGATATTG
* * * * *
40895638 TGTAAGACCGTGTCTGGGACACAGGCTTC-A-ATTGATATTTACT
1 TGTAAGACCATATCTGGGACAGAGGCATCGATATTGA-A-TTACA
* * ** * *
40895681 TATAAGACCATGTCTGGGACATCGGCATCG-TATGTG-ATTTCG
1 TGTAAGACCATATCTGGGACAGAGGCATCGATAT-TGAATTACA
*
40895723 TGTAAGACCCTATCTGGGACAGAGGCATCGATATTGAATTACA
1 TGTAAGACCATATCTGGGACAGAGGCATCGATATTGAATTACA
40895766 TGTAAGACC
1 TGTAAGACC
40895775 GCGTCAGGAA
Statistics
Matches: 75, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
42 30 0.40
43 41 0.55
44 2 0.03
45 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (43 bp):
TGTAAGACCATATCTGGGACAGAGGCATCGATATTGAATTACA
Done.