Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 288 of 438
Found at i:90184109 original size:52 final size:51
Alignment explanation
Indices: 90183996--90184174 Score: 231
Period size: 52 Copynumber: 3.5 Consensus size: 51
90183986 ACGGATGCCC
* * * * * *
90183996 AGTGACCTGCACACAGTACCACCCTTGT-AGTCAAAGCTACCTTCTTCACAA
1 AGTGGCCTTCACATAGTACCACACTTGTGA-CCAAAGCTATCTTCTTCACAA
90184047 AGTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTTCTTCACAA
1 AGTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATC-TTCTTCACAA
* *
90184099 AGTGGCCTTCATATAGTACCACACTTGTGACC-AAGCTATC-TCTTCTCAA
1 AGTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTCTTCACAA
90184148 AGTGG-CTTGCACATAGTACCACACTTG
1 AGTGGCCTT-CACATAGTACCACACTTG
90184175 AGTCACTAGT
Statistics
Matches: 116, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
48 3 0.03
49 30 0.26
51 41 0.35
52 42 0.36
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.27
Consensus pattern (51 bp):
AGTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTCTTCACAA
Found at i:90186085 original size:30 final size:29
Alignment explanation
Indices: 90185991--90186092 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
90185981 TATAGTGAAT
* * *
90185991 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
90186020 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
90186048 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
90186078 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
90186093 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:90193970 original size:30 final size:29
Alignment explanation
Indices: 90193876--90193977 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
90193866 TATAGTGAAT
* * *
90193876 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
90193905 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
90193933 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
90193963 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
90193978 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:90200480 original size:47 final size:47
Alignment explanation
Indices: 90200427--90200618 Score: 294
Period size: 47 Copynumber: 4.1 Consensus size: 47
90200417 TTAGGATTTT
* *
90200427 AATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
* * *
90200474 AATGTGATGAATGTGAACATGCGTATGTGCGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
*
90200521 AATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
* * * *
90200568 GATGTGATGAATGTGAACATGTATATATGTGGTAAGGCCGAATGGCT
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
90200615 AATG
1 AATG
90200619 CGAAATGTGT
Statistics
Matches: 135, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 135 1.00
ACGTcount: A:0.32, C:0.12, G:0.31, T:0.26
Consensus pattern (47 bp):
AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
Found at i:90200728 original size:46 final size:46
Alignment explanation
Indices: 90200592--90200728 Score: 193
Period size: 46 Copynumber: 3.0 Consensus size: 46
90200582 GAACATGTAT
* *
90200592 ATATGTGGTAAGGCCGAATGGCTAATGCGAAATGTGTATGAGATAG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* * *
90200638 ATATGAGATAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* * * *
90200684 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATG
90200729 TGTATATATA
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.35, C:0.09, G:0.31, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
Found at i:90206222 original size:24 final size:23
Alignment explanation
Indices: 90206179--90206225 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
90206169 TTTATGGTCT
90206179 AAAATTTCACGGAATGATTTTGAG
1 AAAATTTCACGGAA-GATTTTGAG
90206203 AAAATTTCATTCGGAA-ATTTTGA
1 AAAATTTCA--CGGAAGATTTTGA
90206226 CGTTTGGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 16 0.76
26 5 0.24
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (23 bp):
AAAATTTCACGGAAGATTTTGAG
Found at i:90208874 original size:53 final size:54
Alignment explanation
Indices: 90208805--90209007 Score: 176
Period size: 53 Copynumber: 3.8 Consensus size: 54
90208795 TTCCTTTTTA
* * * *
90208805 AACTTACCATTTCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * * *
90208858 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGAG-ATCTTTGCCTTATCG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATG-GTATCCTTGCCTTATAG
** * * * * * * *
90208912 TAGTTTATCAATGCCATGTCTCGACATGGTCTTACATGATTTCCTTGCCTTGTAA
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * *
90208967 AACTTACCAATACCATGCCTTGGCATGATCTTACTTGGTAT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTAT
90209008 GCTTAAACCC
Statistics
Matches: 115, Mismatches: 31, Indels: 7
0.75 0.20 0.05
Matches are distributed among these distances:
53 44 0.38
54 32 0.28
55 39 0.34
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.37
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:90208960 original size:55 final size:53
Alignment explanation
Indices: 90208817--90209000 Score: 161
Period size: 55 Copynumber: 3.4 Consensus size: 53
90208807 CTTACCATTT
* * *
90208817 CCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATGAACTCACCATTG
1 CCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATGAACTCACCAATG
* * * * ** * *
90208870 CCATGCCTTGGCATGGTCTTACATGAGATCTTTGCCTTATCGTAGTTTATCAATG
1 CCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAT-G-AACTCACCAATG
* * * * * *
90208925 CCATGTCTCGACATGGTCTTACATGATTTCCTTGCCTTGTAAAACTTACCAATA
1 CCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAT-GAACTCACCAATG
* * *
90208979 CCATGCCTTGGCATGATCTTAC
1 CCATGTCTTGACATGGTCTTAC
90209001 TTGGTATGCT
Statistics
Matches: 101, Mismatches: 28, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
53 34 0.34
54 27 0.27
55 40 0.40
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (53 bp):
CCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATGAACTCACCAATG
Found at i:90211737 original size:19 final size:19
Alignment explanation
Indices: 90211713--90211750 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
90211703 GCTAAGATAG
90211713 AACCATCATCCAATAAGGT
1 AACCATCATCCAATAAGGT
90211732 AACCATCATCCAATAAGGT
1 AACCATCATCCAATAAGGT
90211751 TAAACTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (19 bp):
AACCATCATCCAATAAGGT
Found at i:90215752 original size:24 final size:24
Alignment explanation
Indices: 90215710--90215756 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
90215700 CTGTCAGGAG
***
90215710 AGGATTTAGGAGTTTATAAGGGAT
1 AGGATTTAGGAGCAGATAAGGGAT
90215734 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGCAGATAAGGGA
90215757 GGAAATCTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.36, T:0.26
Consensus pattern (24 bp):
AGGATTTAGGAGCAGATAAGGGAT
Found at i:90217205 original size:27 final size:26
Alignment explanation
Indices: 90217166--90217276 Score: 114
Period size: 27 Copynumber: 4.1 Consensus size: 26
90217156 GGAAGCGTCG
*
90217166 TGGTGGCTATGCCACAATTATCTGATC
1 TGGTGGCTCTGCCAC-ATTATCTGATC
*
90217193 TGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTCTGCCACAT-TATCTGATC
* *
90217220 TGGTGGTTCTGCCACGATTATCTATATC
1 TGGTGGCTCTGCCAC-ATTATCT-GATC
** * *
90217248 TGGTAACTCTGTCACATTATCTGTTC
1 TGGTGGCTCTGCCACATTATCTGATC
90217274 TGG
1 TGG
90217277 CAGCTAGGGT
Statistics
Matches: 70, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
26 7 0.10
27 48 0.69
28 15 0.21
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.38
Consensus pattern (26 bp):
TGGTGGCTCTGCCACATTATCTGATC
Found at i:90217269 original size:54 final size:54
Alignment explanation
Indices: 90217166--90217276 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 54
90217156 GGAAGCGTCG
**
90217166 TGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTATGCCACAATTATCTGATCTGGTAACTCTGCCACATATATCTGTTC
* * * * *
90217220 TGGTGGTTCTGCCACGATTATCTATATCTGGTAACTCTGTCACAT-TATCTGTTC
1 TGGTGGCTATGCCACAATTATCT-GATCTGGTAACTCTGCCACATATATCTGTTC
90217274 TGG
1 TGG
90217277 CAGCTAGGGT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
54 32 0.65
55 17 0.35
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.38
Consensus pattern (54 bp):
TGGTGGCTATGCCACAATTATCTGATCTGGTAACTCTGCCACATATATCTGTTC
Found at i:90218982 original size:79 final size:81
Alignment explanation
Indices: 90218881--90219065 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
90218871 ACGACTCGCT
** * *
90218881 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC
* *
90218944 GGGTTTAGTAACTT-GCA
64 GGATATAGTAACTTAGCA
* **
90218961 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
*
90219025 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
90219041 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
90219066 CATCATTCGA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:90219065 original size:40 final size:39
Alignment explanation
Indices: 90218874--90219065 Score: 163
Period size: 40 Copynumber: 4.8 Consensus size: 39
90218864 GGATATAACG
* ** * *
90218874 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
90218914 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* * *
90218954 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
90218993 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
90219033 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
90219066 CATCATTCGA
Statistics
Matches: 121, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 79 0.65
41 10 0.08
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:90227026 original size:79 final size:81
Alignment explanation
Indices: 90226925--90227109 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
90226915 ACGACTCGCT
** * *
90226925 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC
* *
90226988 GGGTTTAGTAACTT-GCA
64 GGATATAGTAACTTAGCA
* **
90227005 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
*
90227069 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
90227085 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
90227110 CATCATTCGA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:90227109 original size:40 final size:39
Alignment explanation
Indices: 90226918--90227109 Score: 163
Period size: 40 Copynumber: 4.8 Consensus size: 39
90226908 GGATATAACG
* ** * *
90226918 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
90226958 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* * *
90226998 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
90227037 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
90227077 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
90227110 CATCATTCGA
Statistics
Matches: 121, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 79 0.65
41 10 0.08
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:90229898 original size:16 final size:15
Alignment explanation
Indices: 90229877--90229907 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
90229867 CGAAATGTCA
90229877 GCTTTTCGGCATTTTG
1 GCTTTTCGGC-TTTTG
90229893 GCTTTTCGGCTTTTG
1 GCTTTTCGGCTTTTG
90229908 CCGATCTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.03, C:0.19, G:0.26, T:0.52
Consensus pattern (15 bp):
GCTTTTCGGCTTTTG
Found at i:90232877 original size:80 final size:80
Alignment explanation
Indices: 90232793--90232941 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
90232783 TATGGTAACC
* * * *
90232793 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
90232857 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
90232873 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
90232938 CCGG
66 CCGG
90232942 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:90232883 original size:40 final size:38
Alignment explanation
Indices: 90232834--90232941 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
90232824 ATCACGATTT
*
90232834 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
90232874 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
90232914 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
90232942 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:90240988 original size:80 final size:80
Alignment explanation
Indices: 90240904--90241052 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
90240894 TATGGTAACC
* * * *
90240904 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
90240968 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
90240984 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
90241049 CCGG
66 CCGG
90241053 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:90240994 original size:40 final size:38
Alignment explanation
Indices: 90240945--90241052 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
90240935 ATCACGATTT
*
90240945 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
90240985 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
90241025 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
90241053 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:90246899 original size:50 final size:50
Alignment explanation
Indices: 90246780--90247068 Score: 226
Period size: 50 Copynumber: 5.7 Consensus size: 50
90246770 ATTGTAAGAA
* * ** *
90246780 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGATGGT-TTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTG--TACTA-GGTAGTTAGGT
*
90246832 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGGTAGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGGTAGTTAGGT
** * ** ** ** * * *
90246882 TGCATGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGACAATTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAG-GTAGTTAGGT
* * * *
90246933 CACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTA-TCAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACT-AGGTAGTTAGGT
* * * * * *
90246983 CACGTGTGTAGTACTTAGTGCAGGCTACTACATGTAC-CGG-ATTTTTGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGGTA-GTTAGGT
* *
90247032 CACATGTGTAGTAGTAAGTGCAGGCTACTATGTGTAC
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTAC
90247069 CAGATAGCTT
Statistics
Matches: 185, Mismatches: 47, Indels: 13
0.76 0.19 0.05
Matches are distributed among these distances:
49 41 0.22
50 78 0.42
51 35 0.19
52 31 0.17
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGGTAGTTAGGT
Found at i:90246961 original size:101 final size:101
Alignment explanation
Indices: 90246831--90247075 Score: 293
Period size: 101 Copynumber: 2.4 Consensus size: 101
90246821 TGGTTTTAGG
* **
90246831 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CTAGGTAGTTAGGTTGCATGTGTAGTA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-AGATAGTTAGGTCACATGTGTAGTA
90246895 CTAAGTGCAGGCTACTATGCATACCCGACAATTTCGA
65 CTAAGTGCAGGCTACTATGCATACCCGACAATTTCGA
* * *
90246932 TCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAGTTAGGTCACATGTGTAGTAC
* * * * *
90246997 TTAGTGCAGGCTACTA--CATGTA-CCG-GATTTTTGG
66 TAAGTGCAGGCTACTATGCA--TACCCGACAATTTCGA
* * * *
90247031 TCACATGTGTAGTAGTAAGTGCAGGCTACTATGTGTACCAGATAG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAG
90247076 CTTCGGTTAC
Statistics
Matches: 124, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
99 46 0.37
100 3 0.02
101 74 0.60
102 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (101 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAGTTAGGTCACATGTGTAGTAC
TAAGTGCAGGCTACTATGCATACCCGACAATTTCGA
Found at i:90256434 original size:43 final size:43
Alignment explanation
Indices: 90256369--90256466 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 43
90256359 TAACCCAGTT
90256369 ATGGTCTTACACGAAATCAAATAACAATACCAATGTCCCAAAC
1 ATGGTCTTACACGAAATCAAATAACAATACCAATGTCCCAAAC
* * * * ** * * *
90256412 ATGGTGTTACATGTAATTAAATAATGATGCCAATGTCTCAGAC
1 ATGGTCTTACACGAAATCAAATAACAATACCAATGTCCCAAAC
90256455 ATGGTCTTACAC
1 ATGGTCTTACAC
90256467 ATAATCACAT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACACGAAATCAAATAACAATACCAATGTCCCAAAC
Found at i:90266934 original size:49 final size:47
Alignment explanation
Indices: 90266866--90266994 Score: 134
Period size: 49 Copynumber: 2.7 Consensus size: 47
90266856 GAGGTGTGTT
* * * *
90266866 AGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATGAATG-GAGGTC
1 AGTGTAAGACCAGTTTGGGACATGGCATCGGCCTAGATG--TGAGA-GCC
* ** *
90266915 AGTGTAAAACCAGTTTGGGACATGGCATCAACTTAGATGTGAGAGCC
1 AGTGTAAGACCAGTTTGGGACATGGCATCGGCCTAGATGTGAGAGCC
*
90266962 AGTGTAAGACCATGTTTGGAACATGGCATCGGC
1 AGTGTAAGACCA-GTTTGGGACATGGCATCGGC
90266995 ATCGTACCCT
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
47 15 0.23
48 19 0.29
49 32 0.48
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACCAGTTTGGGACATGGCATCGGCCTAGATGTGAGAGCC
Found at i:90283392 original size:52 final size:50
Alignment explanation
Indices: 90283311--90283605 Score: 193
Period size: 49 Copynumber: 5.9 Consensus size: 50
90283301 ATTGTGAGAA
* * * * ** * *
90283311 CACATATGTAGTACTATGAGCAGGATACTATGTGTTTAATATGGTTTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAGATAG--TTAGGT
*
90283363 CACATGTGTAGTACTAAGTGCAGGCTACTA-GTGTACCAGATAGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAGATAGTTAGGT
** * ** * * * *
90283412 TGCATGTGTAGTACTAAGTGTAGGCTACTATGCATACCCAACA-ACTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTA--CAAGATAGTTAGGT
* ** *
90283463 CACGTGTGTAGTACTAAGTGCAGGCTACTACATGTATC-AGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTA-CAAGATAGTTAGGT
* * * * ** * *
90283513 CACGTGTTTAGTACTAAGTGCAAGCTACTACGTGTACCGGAT-TTTTGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAGATAGTTAGGT
** * * * *
90283562 TGCATGTGTGGTACTTAGTGCAGGCTACTATGCGTACTAGATAG
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAGATAG
90283606 CTTCGGTTGC
Statistics
Matches: 186, Mismatches: 51, Indels: 14
0.74 0.20 0.06
Matches are distributed among these distances:
49 72 0.39
50 44 0.24
51 41 0.22
52 29 0.16
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.32
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAGATAGTTAGGT
Found at i:90283427 original size:49 final size:50
Alignment explanation
Indices: 90283365--90283616 Score: 204
Period size: 49 Copynumber: 5.0 Consensus size: 50
90283355 TTTTAGGTCA
90283365 CATGTGTAGTACTAAGTGCAGGCTACTA-GTGTACCAGATAGTTAGGTTG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTTG
* * ** * * * * **
90283414 CATGTGTAGTACTAAGTGTAGGCTACTATGCATACCCA-ACAACTTCGATCA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCAGA-TAGTTAGGTTG
* * * * **
90283465 CGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCAGATGGTTAGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTTG
* * * * * *
90283515 CGTGTTTAGTACTAAGTGCAAGCTACTACGTGTACCGGAT-TTTTGGTTG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTTG
* * * * * *
90283564 CATGTGTGGTACTTAGTGCAGGCTACTATGCGTACTAGATAGCTTCGGTTG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG-TTAGGTTG
90283615 CA
1 CA
90283617 AGGGTGGTAA
Statistics
Matches: 156, Mismatches: 41, Indels: 10
0.75 0.20 0.05
Matches are distributed among these distances:
49 63 0.40
50 47 0.30
51 46 0.29
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (50 bp):
CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTTG
Found at i:90283510 original size:101 final size:100
Alignment explanation
Indices: 90283362--90283542 Score: 263
Period size: 101 Copynumber: 1.8 Consensus size: 100
90283352 TGGTTTTAGG
* **
90283362 TCACATGTGTAGTACTAAGTGCAGGCTACTAGTGTACCAGATAGTTAGGTTGCATGTGTAGTACT
1 TCACATGTGTAGTACTAAGTGCAGGCTACTAATGTACCAGATAGTTAGGTCACATGTGTAGTACT
* *
90283427 AAGTGTAGGCTACTATGCATACCCAACAACTTCGA
66 AAGTGCAAGCTACTATGCATACCCAACAACTTCGA
* * * * *
90283462 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCAGATGGTTAGGTCACGTGTTTAGTAC
1 TCACATGTGTAGTACTAAGTGCAGGCTACTA-ATGTACCAGATAGTTAGGTCACATGTGTAGTAC
90283527 TAAGTGCAAGCTACTA
65 TAAGTGCAAGCTACTA
90283543 CGTGTACCGG
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
100 30 0.43
101 40 0.57
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (100 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTAATGTACCAGATAGTTAGGTCACATGTGTAGTACT
AAGTGCAAGCTACTATGCATACCCAACAACTTCGA
Found at i:90285218 original size:40 final size:40
Alignment explanation
Indices: 90285159--90285289 Score: 172
Period size: 40 Copynumber: 3.3 Consensus size: 40
90285149 CGGGACTTTA
* * *
90285159 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
90285199 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
90285239 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
90285279 CCCGGATATAA
1 CCCGGATATAA
90285290 TTTCAGCATA
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:90285322 original size:39 final size:40
Alignment explanation
Indices: 90285176--90285326 Score: 180
Period size: 40 Copynumber: 3.8 Consensus size: 40
90285166 ATCACGATTT
* * * *
90285176 GCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAACTT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACTACTA
*
90285216 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAACTACTA
* * *
90285256 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-A
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACTACTA
* * *
90285295 GCATAATTGTCTTCGGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
90285327 CATTCAATTT
Statistics
Matches: 97, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
39 31 0.32
40 64 0.66
41 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACTACTA
Found at i:90293251 original size:40 final size:40
Alignment explanation
Indices: 90293192--90293360 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 40
90293182 CGGGACTTTA
* * *
90293192 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
90293232 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
90293272 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * *
90293312 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG
1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG
90293352 CCCGGATAT
1 CCCGGATAT
90293361 CATTCAATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 3 0.03
38 3 0.03
39 1 0.01
40 99 0.93
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:90295158 original size:16 final size:15
Alignment explanation
Indices: 90295137--90295166 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
90295127 GAATGGAGTA
90295137 AGTGAAATTATGTAAG
1 AGTGAAATT-TGTAAG
90295153 AGTGAAATTTGTAA
1 AGTGAAATTTGTAA
90295167 TAAAACAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTGAAATTTGTAAG
Found at i:90297694 original size:40 final size:40
Alignment explanation
Indices: 90297650--90297726 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
90297640 TTAGTGCCAC
* *
90297650 ATATAGCCGAAGCTAT-TCCAATTCGCACACTAAGTGCTAT
1 ATATAGCCAAAGCTATATCCAA-ACGCACACTAAGTGCTAT
*
90297690 ATATAGCCAAAGCTATATCGAAACGCACACTAAGTGC
1 ATATAGCCAAAGCTATATCCAAACGCACACTAAGTGC
90297727 CAAACGTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 29 0.88
41 4 0.12
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (40 bp):
ATATAGCCAAAGCTATATCCAAACGCACACTAAGTGCTAT
Found at i:90303850 original size:46 final size:46
Alignment explanation
Indices: 90303767--90303980 Score: 179
Period size: 46 Copynumber: 4.6 Consensus size: 46
90303757 TCTCCGTGAT
* *
90303767 GATGCCATGTCCTAGACATGGTCTTACACT-A-ACACATCTCATA-GCC
1 GATG-CATGTCCTAGACAT-GTCTTACACTGACTCTCATCTCA-AGGCC
90303813 GATGCATGTCCTAGACATGTCTTACACTGACT-TACATCTCAAGGCC
1 GATGCATGTCCTAGACATGTCTTACACTGACTCT-CATCTCAAGGCC
* * * * * *
90303859 GATGCATGTCCCAAACATGTTTTACACT-AGCTCTCGTCTCAATGTC
1 GATGCATGTCCTAGACATGTCTTACACTGA-CTCTCATCTCAAGGCC
* * * * * * *
90303905 GTTGCCATGTCCCAGACAAGGTCTTACACTGGCTCTCATAAT-ATGGCT
1 GATG-CATGTCCTAGAC-ATGTCTTACACTGACTCTCAT-CTCAAGGCC
90303953 GATGCATGTCCTAGACATGTCTTACACT
1 GATGCATGTCCTAGACATGTCTTACACT
90303981 AGCGCACAAA
Statistics
Matches: 136, Mismatches: 22, Indels: 20
0.76 0.12 0.11
Matches are distributed among these distances:
44 10 0.07
45 17 0.12
46 64 0.47
47 23 0.17
48 21 0.15
49 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.29
Consensus pattern (46 bp):
GATGCATGTCCTAGACATGTCTTACACTGACTCTCATCTCAAGGCC
Found at i:90315475 original size:17 final size:17
Alignment explanation
Indices: 90315453--90315486 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
90315443 TTGTTGGTTC
90315453 GGTTTTGAAATTCAAAA
1 GGTTTTGAAATTCAAAA
90315470 GGTTTTGAAATTCAAAA
1 GGTTTTGAAATTCAAAA
90315487 CCGTTTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (17 bp):
GGTTTTGAAATTCAAAA
Found at i:90315562 original size:21 final size:22
Alignment explanation
Indices: 90315538--90315578 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
90315528 ATATACATTT
90315538 AAACCCAAACCTAAA-ACAACC
1 AAACCCAAACCTAAATACAACC
*
90315559 AAACCCAAATCTAAATACAA
1 AAACCCAAACCTAAATACAA
90315579 TTTAAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.59, C:0.32, G:0.00, T:0.10
Consensus pattern (22 bp):
AAACCCAAACCTAAATACAACC
Found at i:90315669 original size:17 final size:18
Alignment explanation
Indices: 90315637--90315710 Score: 69
Period size: 19 Copynumber: 4.0 Consensus size: 18
90315627 AATTAGAAAT
*
90315637 TAAAAGATAATAATATTAA
1 TAAAA-ATATTAATATTAA
* *
90315656 TTAAAAT-TTAATATTCA
1 TAAAAATATTAATATTAA
*
90315673 TAAAAATATTAAACATTAA
1 TAAAAATATT-AATATTAA
*
90315692 TAAAAAATATTAAAATTAA
1 T-AAAAATATTAATATTAA
90315711 AACCTGACTT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
17 14 0.31
18 4 0.09
19 18 0.40
20 9 0.20
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (18 bp):
TAAAAATATTAATATTAA
Found at i:90315696 original size:19 final size:18
Alignment explanation
Indices: 90315637--90315710 Score: 69
Period size: 17 Copynumber: 4.0 Consensus size: 18
90315627 AATTAGAAAT
* *
90315637 TAAAAGATAATAATATTAA
1 TAAAA-ATATTAAAATTAA
* * *
90315656 TTAAAAT-TTAATATTCA
1 TAAAAATATTAAAATTAA
90315673 TAAAAATATTAAACATTAA
1 TAAAAATATTAAA-ATTAA
90315692 TAAAAAATATTAAAATTAA
1 T-AAAAATATTAAAATTAA
90315711 AACCTGACTT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
17 14 0.30
18 6 0.13
19 14 0.30
20 12 0.26
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (18 bp):
TAAAAATATTAAAATTAA
Found at i:90318518 original size:11 final size:11
Alignment explanation
Indices: 90318502--90318530 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
90318492 GTAATGTTAA
90318502 AATATATACAT
1 AATATATACAT
90318513 AATATATACAT
1 AATATATACAT
90318524 -ATATATA
1 AATATATA
90318531 AAATAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (11 bp):
AATATATACAT
Found at i:90318696 original size:24 final size:23
Alignment explanation
Indices: 90318663--90318707 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
90318653 TATGACAATA
90318663 ATACTATAT-ATAAAAGTGTATAT
1 ATACTATATAATAAAA-TGTATAT
90318686 ATACTCATATAATAAAATGTAT
1 ATACT-ATATAATAAAATGTAT
90318708 GTACTAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 5 0.25
24 9 0.45
25 6 0.30
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.38
Consensus pattern (23 bp):
ATACTATATAATAAAATGTATAT
Found at i:90319115 original size:22 final size:22
Alignment explanation
Indices: 90319041--90319115 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
90319031 ATAGTATCAG
*
90319041 AAATATACGT-ACAATAGTATAA
1 AAATATACATAACAATA-TATAA
*
90319063 AAGATATATAACTAACAATAT-TAA
1 AA-ATATA-CA-TAACAATATATAA
*
90319087 AGCATATACATAACAATATATAA
1 A-AATATACATAACAATATATAA
90319110 AAATAT
1 AAATAT
90319116 GATATTAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
22 15 0.36
23 10 0.24
24 9 0.21
25 2 0.05
26 6 0.14
ACGTcount: A:0.57, C:0.09, G:0.05, T:0.28
Consensus pattern (22 bp):
AAATATACATAACAATATATAA
Found at i:90319528 original size:3 final size:3
Alignment explanation
Indices: 90319522--90319609 Score: 56
Period size: 3 Copynumber: 29.0 Consensus size: 3
90319512 AGAAATATAC
* * *
90319522 TAA TAA TGA TAA TAA TAA TAA TAG TAA TAA T-A TAAA TAT TATA TACA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA-A TA-A
* * * *
90319569 TAA AAA T-G TAA TAA TAA CAA TAAA TAA -CA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
90319610 ATATAAAAAA
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
2 4 0.06
3 50 0.78
4 10 0.16
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:90320654 original size:13 final size:13
Alignment explanation
Indices: 90320636--90320671 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
90320626 TTCGGGATTG
90320636 GGCTTGGTTATTA
1 GGCTTGGTTATTA
*
90320649 GGCTTGGTTATTG
1 GGCTTGGTTATTA
*
90320662 GGCTAGGTTA
1 GGCTTGGTTA
90320672 ATTTTAGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.14, C:0.08, G:0.36, T:0.42
Consensus pattern (13 bp):
GGCTTGGTTATTA
Found at i:90323834 original size:46 final size:45
Alignment explanation
Indices: 90323730--90323947 Score: 183
Period size: 46 Copynumber: 4.8 Consensus size: 45
90323720 AGATTTGTGT
**
90323730 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CATTGA-GACGAA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACAGATGA-G-A
* *
90323777 GGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGA
1 -GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAG-ATGAGA
* *** **
90323824 GCCAGTGTAAGACATGTCTGGGACATGCATTGGCTTTGAGATGTTA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGC-CACAGATGAGA
* * * * *
90323870 GCCAGTGTCAGACATGTTTGGGACATGCGTCGGCTACAAGAT-A-T
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-AGATGAGA
* *
90323914 GCTAGTGTAAGACATGTCTGCGACATGCATCGGC
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGC
90323948 ATGGTTACAT
Statistics
Matches: 140, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
44 29 0.21
45 1 0.01
46 75 0.54
47 20 0.14
48 13 0.09
49 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAGATGAGA
Found at i:90323883 original size:92 final size:90
Alignment explanation
Indices: 90323730--90323984 Score: 255
Period size: 90 Copynumber: 2.8 Consensus size: 90
90323720 AGATTTGTGT
*
90323730 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAAGGCTAGTGTAAGACATGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGACGAAGGCCAGTGTAAGACATGT
90323795 CTGGGACATGCATCAGCCAC-AGTATGAGA
64 CTGGGACATGCATCAGCCACAAG-AT-A-A
* * * * * *
90323824 GCCAGTGTAAGACATGTCTGGGACATGCATTGGCTTTGAGATGTTA-GCCAGTGTCAGACATGTT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACG-AAGGCCAGTGTAAGACATGTC
* * * *
90323888 TGGGACATGCGTCGGCTACAAGATAT
65 TGGGACATGCATCAGCCACAAGATAA
* * * ** * * *
90323914 GCTAGTGTAAGACATGTCTGCGACATGCATCGGCATGGTTAC-ATGTGTCAGTGTAAGACCTGTC
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACGAAG-GCCAGTGTAAGACATGTC
90323978 TGGGACA
65 TGGGACA
90323985 CAGCATCAAC
Statistics
Matches: 132, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
90 55 0.42
91 1 0.01
92 47 0.36
93 17 0.13
94 12 0.09
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (90 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACGAAGGCCAGTGTAAGACATGTCT
GGGACATGCATCAGCCACAAGATAA
Found at i:90327032 original size:30 final size:31
Alignment explanation
Indices: 90326973--90327036 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
90326963 ACTTAACAAG
*
90326973 CAAATGCTTCTAAAATAGTAATAAAAATTAA
1 CAAATGCTTCTAAAATAATAATAAAAATTAA
*
90327004 CAAATGCCTT-TAAAATAATAA-GAAAATTAA
1 CAAATG-CTTCTAAAATAATAATAAAAATTAA
90327034 CAA
1 CAA
90327037 TAAAATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 11 0.37
31 16 0.53
32 3 0.10
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.27
Consensus pattern (31 bp):
CAAATGCTTCTAAAATAATAATAAAAATTAA
Found at i:90340533 original size:26 final size:27
Alignment explanation
Indices: 90340485--90340552 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
90340475 CAATTTAATC
90340485 CTTTACTAAAA-AC-CTAACAAAAACCA
1 CTTTA-TAAAATACTCTAACAAAAACCA
90340511 CTTTATAAAATACTCTAACAAAAACCA
1 CTTTATAAAATACTCTAACAAAAACCA
90340538 CTTTATAAAATACTC
1 CTTTATAAAATACTC
90340553 ATAATCAACA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
25 5 0.12
26 7 0.17
27 28 0.70
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (27 bp):
CTTTATAAAATACTCTAACAAAAACCA
Found at i:90341364 original size:40 final size:40
Alignment explanation
Indices: 90341297--90341406 Score: 159
Period size: 40 Copynumber: 2.7 Consensus size: 40
90341287 AAAAAGGTTT
*
90341297 TTAGCGGCG-TTTGAATGAAAAACGCCGCTAAAGAACGAGCA
1 TTAGCGGCGCTTTTAA--AAAAACGCCGCTAAAGAACGAGCA
* *
90341338 TTAGCGGTGCTTTTAAAAAAATGCCGCTAAAGAACGAGCA
1 TTAGCGGCGCTTTTAAAAAAACGCCGCTAAAGAACGAGCA
*
90341378 TTAGCGGCGCTTTTTAAAAAACGCCGCTA
1 TTAGCGGCGCTTTTAAAAAAACGCCGCTA
90341407 TAAGTTCACC
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
40 49 0.79
41 8 0.13
42 5 0.08
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22
Consensus pattern (40 bp):
TTAGCGGCGCTTTTAAAAAAACGCCGCTAAAGAACGAGCA
Found at i:90341422 original size:40 final size:40
Alignment explanation
Indices: 90341314--90341438 Score: 144
Period size: 40 Copynumber: 3.1 Consensus size: 40
90341304 CGTTTGAATG
* * *
90341314 AAAAACGCCGCTAAAGAACGAGCATTAGCGGTGCTTTTAA
1 AAAAACGCCGCTAAAGAACGACCATTAGCGGCGCTTTTTA
* *
90341354 AAAAATGCCGCTAAAGAACGAGCATTAGCGGCGCTTTTTA
1 AAAAACGCCGCTAAAGAACGACCATTAGCGGCGCTTTTTA
** * **
90341394 AAAAACGCCGCTATAAGTTC-ACCTTTAGCCACGCTTTTTA
1 AAAAACGCCGCTA-AAGAACGACCATTAGCGGCGCTTTTTA
90341434 AAAAA
1 AAAAA
90341439 AGGCCGCAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 70 0.95
41 4 0.05
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (40 bp):
AAAAACGCCGCTAAAGAACGACCATTAGCGGCGCTTTTTA
Found at i:90342202 original size:15 final size:14
Alignment explanation
Indices: 90342182--90342216 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
90342172 ACTATTTTAA
*
90342182 GGTTTATGGATTAT
1 GGTTTAGGGATTAT
90342196 GGGTTTAGGGATTAT
1 -GGTTTAGGGATTAT
90342211 GGTTTA
1 GGTTTA
90342217 AAGGTGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:90342276 original size:14 final size:14
Alignment explanation
Indices: 90342225--90342298 Score: 69
Period size: 14 Copynumber: 5.2 Consensus size: 14
90342215 TAAAGGTGGT
90342225 TTAAGGGTT-GGGG
1 TTAAGGGTTAGGGG
* *
90342238 TTTAAGGTTTAGGTG
1 -TTAAGGGTTAGGGG
*
90342253 TTACGGGTTAGGGG
1 TTAAGGGTTAGGGG
*
90342267 TTAAGGGTTAGGTG
1 TTAAGGGTTAGGGG
* *
90342281 TTCATGGTTCAGGGG
1 TTAAGGGTT-AGGGG
90342296 TTA
1 TTA
90342299 TATTTTAGGA
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
14 38 0.81
15 9 0.19
ACGTcount: A:0.18, C:0.04, G:0.42, T:0.36
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:90342289 original size:28 final size:28
Alignment explanation
Indices: 90342229--90342282 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
90342219 GGTGGTTTAA
*
90342229 GGGTT-GGGGTTTAAGGTTTAGGTGTTAC
1 GGGTTAGGGG-TTAAGGGTTAGGTGTTAC
90342257 GGGTTAGGGGTTAAGGGTTAGGTGTT
1 GGGTTAGGGGTTAAGGGTTAGGTGTT
90342283 CATGGTTCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.15, C:0.02, G:0.46, T:0.37
Consensus pattern (28 bp):
GGGTTAGGGGTTAAGGGTTAGGTGTTAC
Found at i:90342466 original size:14 final size:14
Alignment explanation
Indices: 90342447--90342479 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
90342437 TATCATTATA
90342447 GTTTAGGGTTTAAG
1 GTTTAGGGTTTAAG
90342461 GTTTAGGGTTTAAG
1 GTTTAGGGTTTAAG
*
90342475 CTTTA
1 GTTTA
90342480 AGAGTTACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.03, G:0.30, T:0.45
Consensus pattern (14 bp):
GTTTAGGGTTTAAG
Found at i:90342509 original size:7 final size:7
Alignment explanation
Indices: 90342491--90342545 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
90342481 GAGTTACTAT
*
90342491 TTTAAGG
1 TTTATGG
90342498 TTTATGG
1 TTTATGG
*
90342505 ATTATGGG
1 TTTAT-GG
*
90342513 TTTAGGG
1 TTTATGG
*
90342520 ATTATGG
1 TTTATGG
90342527 TTTTATGG
1 -TTTATGG
90342535 TTTATGG
1 TTTATGG
90342542 TTTA
1 TTTA
90342546 AAGGTTGGGG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
7 28 0.72
8 11 0.28
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (7 bp):
TTTATGG
Found at i:90342514 original size:15 final size:15
Alignment explanation
Indices: 90342496--90342545 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
90342486 ACTATTTTAA
90342496 GGTTTATGGATTATG
1 GGTTTATGGATTATG
*
90342511 GGTTTAGGGATTATG
1 GGTTTATGGATTATG
* *
90342526 GTTTTATGGTTTAT-
1 GGTTTATGGATTATG
90342540 GGTTTA
1 GGTTTA
90342546 AAGGTTGGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 5 0.17
15 25 0.83
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (15 bp):
GGTTTATGGATTATG
Found at i:90342516 original size:22 final size:22
Alignment explanation
Indices: 90342491--90342545 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
90342481 GAGTTACTAT
90342491 TTTAAGGTTTATGG-ATTATGGG
1 TTTAAGGTTTATGGTATTAT-GG
* * *
90342513 TTTAGGGATTATGGTTTTATGG
1 TTTAAGGTTTATGGTATTATGG
*
90342535 TTTATGGTTTA
1 TTTAAGGTTTA
90342546 AAGGTTGGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 23 0.85
23 4 0.15
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (22 bp):
TTTAAGGTTTATGGTATTATGG
Found at i:90343030 original size:21 final size:21
Alignment explanation
Indices: 90343000--90343050 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
90342990 GGGTTTAGGG
90343000 TTTA-GGTTTATTG-TCTACGA
1 TTTAGGGTTTA-TGATCTACGA
*
90343020 TTTAGGGTTTATGATCTAGGA
1 TTTAGGGTTTATGATCTACGA
*
90343041 TTTGGGGTTT
1 TTTAGGGTTT
90343051 GGAGTTTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.18, C:0.06, G:0.27, T:0.49
Consensus pattern (21 bp):
TTTAGGGTTTATGATCTACGA
Found at i:90343495 original size:41 final size:41
Alignment explanation
Indices: 90343439--90343567 Score: 156
Period size: 41 Copynumber: 3.1 Consensus size: 41
90343429 AAAGAAAATT
* **
90343439 AAAATTGAGCAATAGTGGCGTTTTTGGGT-AAAACGCTGCA
1 AAAATTGAGCTATAGTGGCGTTTTTGGGTAAAAACGCCACA
*
90343479 AAAATTTGAGCTATAGTGGCGTTTTT-GGTAAAAACGCCATA
1 AAAA-TTGAGCTATAGTGGCGTTTTTGGGTAAAAACGCCACA
**
90343520 AAAAGTTGAGCTATAGTGGCGTTTTT-GGTGGAAACGCCACA
1 AAAA-TTGAGCTATAGTGGCGTTTTTGGGTAAAAACGCCACA
90343561 ACAAATT
1 A-AAATT
90343568 CGAGAATTAC
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
40 7 0.09
41 68 0.87
42 3 0.04
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (41 bp):
AAAATTGAGCTATAGTGGCGTTTTTGGGTAAAAACGCCACA
Found at i:90343593 original size:82 final size:82
Alignment explanation
Indices: 90343439--90343599 Score: 186
Period size: 82 Copynumber: 2.0 Consensus size: 82
90343429 AAAGAAAATT
** * * *
90343439 AAAATTGAGCAATAGTGGCGTTTTTGGGTAAAACGCTGCAAAAATTTGAGCTATAGTGGCGTTTT
1 AAAATTGAGCAATAGTGGCGTTTTTGGGTAAAACGCCACAAAAATTCGAGATATACTGGCGTTTT
90343504 TGGTAAAAA-CGCCATA
66 TGGTAAAAATCGCCATA
* *
90343520 AAAAGTTGAGCTATAGTGGCGTTTTT-GGTGGAAACGCCACAACAAATTCGAGA-ATTACTGGCG
1 AAAA-TTGAGCAATAGTGGCGTTTTTGGGT-AAAACGCCACAA-AAATTCGAGATA-TACTGGCG
*
90343583 TTTTT-TTAAAAATCGCC
62 TTTTTGGTAAAAATCGCC
90343600 GCAAAAGGCC
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
81 7 0.10
82 36 0.54
83 24 0.36
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (82 bp):
AAAATTGAGCAATAGTGGCGTTTTTGGGTAAAACGCCACAAAAATTCGAGATATACTGGCGTTTT
TGGTAAAAATCGCCATA
Found at i:90343873 original size:3 final size:3
Alignment explanation
Indices: 90343847--90343932 Score: 138
Period size: 3 Copynumber: 28.7 Consensus size: 3
90343837 AATGGAAGTT
* *
90343847 GAA G-A GAA GGA GAA TGAG GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
90343892 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
90343933 GAGTGAAGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.03
3 73 0.95
4 2 0.03
ACGTcount: A:0.63, C:0.00, G:0.36, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:90347673 original size:8 final size:8
Alignment explanation
Indices: 90347660--90347689 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
90347650 CCATTTTTGA
90347660 TAATCTCG
1 TAATCTCG
90347668 TAATCTCG
1 TAATCTCG
90347676 TAATCTCG
1 TAATCTCG
90347684 TAATCT
1 TAATCT
90347690 TCTTCTACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (8 bp):
TAATCTCG
Found at i:90348706 original size:43 final size:43
Alignment explanation
Indices: 90348637--90348791 Score: 177
Period size: 43 Copynumber: 3.6 Consensus size: 43
90348627 AATATTTTTT
* * * * *
90348637 TAAAGGTCATGTTCTCTAGCGGCGTTTGTGAGAAAAGCGCCGC
1 TAAAAGTCATGGTCTTTAGCAGCGTTTGTCAGAAAAGCGCCGC
* * * * *
90348680 TAAAAGTCATGGTATTTAGCATCGTTTTTTAGAAAAGCGCTGC
1 TAAAAGTCATGGTCTTTAGCAGCGTTTGTCAGAAAAGCGCCGC
* * * *
90348723 TAAAAGTCATAGTCTTTAGCGGCATTTG-CAAAAAAGCGCCGC
1 TAAAAGTCATGGTCTTTAGCAGCGTTTGTCAGAAAAGCGCCGC
90348765 TAAAAGTCATGGTCTTTAGCAGCGTTT
1 TAAAAGTCATGGTCTTTAGCAGCGTTT
90348792 TTTTAAATAA
Statistics
Matches: 91, Mismatches: 21, Indels: 1
0.81 0.19 0.01
Matches are distributed among these distances:
42 35 0.38
43 56 0.62
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (43 bp):
TAAAAGTCATGGTCTTTAGCAGCGTTTGTCAGAAAAGCGCCGC
Found at i:90348771 original size:42 final size:43
Alignment explanation
Indices: 90348669--90348788 Score: 152
Period size: 42 Copynumber: 2.8 Consensus size: 43
90348659 CGTTTGTGAG
* * * ** *
90348669 AAAAGCGCCGCTAAAAGTCATGGTATTTAGCATCGTTTTTTAG
1 AAAAGCGCCGCTAAAAGTCATGGTCTTTAGCAGCGATTTGCAA
* * *
90348712 AAAAGCGCTGCTAAAAGTCATAGTCTTTAGCGGC-ATTTGCAA
1 AAAAGCGCCGCTAAAAGTCATGGTCTTTAGCAGCGATTTGCAA
90348754 AAAAGCGCCGCTAAAAGTCATGGTCTTTAGCAGCG
1 AAAAGCGCCGCTAAAAGTCATGGTCTTTAGCAGCG
90348789 TTTTTTTAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 35 0.55
43 29 0.45
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAAGTCATGGTCTTTAGCAGCGATTTGCAA
Found at i:90355905 original size:31 final size:31
Alignment explanation
Indices: 90355870--90355935 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
90355860 AAAAATAACC
** * * *
90355870 ATTTGACTTTTTTTGAAAAATTAATGGTCAA
1 ATTTGACTCCTTTTAAAAAATTAACGATCAA
90355901 ATTTGACTCCTTTTAAAAAATTAACGATCAA
1 ATTTGACTCCTTTTAAAAAATTAACGATCAA
90355932 ATTT
1 ATTT
90355936 AGCTAAAAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (31 bp):
ATTTGACTCCTTTTAAAAAATTAACGATCAA
Found at i:90357985 original size:6 final size:6
Alignment explanation
Indices: 90357974--90357998 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
90357964 TTGTATGCTC
90357974 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
90357999 CTCTTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:90370687 original size:46 final size:46
Alignment explanation
Indices: 90370571--90370687 Score: 162
Period size: 46 Copynumber: 2.5 Consensus size: 46
90370561 CATCGGCAGG
* * **
90370571 AAGCTTACTAGGCACAAGGCTCGATACATTATAGTACACCGGCATA
1 AAGCTTGCTAGGCACAAGGCCCGATACATTATAGTACACCAACATA
* *
90370617 AAGCCTGCTAGGCACAAGGACCGATACATTATAGTACACCAACATA
1 AAGCTTGCTAGGCACAAGGCCCGATACATTATAGTACACCAACATA
* *
90370663 AAGCTTGCTAGGCTCAAGCCCCGAT
1 AAGCTTGCTAGGCACAAGGCCCGAT
90370688 TCAATACACT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 61 1.00
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (46 bp):
AAGCTTGCTAGGCACAAGGCCCGATACATTATAGTACACCAACATA
Found at i:90385449 original size:41 final size:41
Alignment explanation
Indices: 90385404--90385482 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
90385394 GTCAGGTAAC
90385404 CCTCCTAATTATTCCAATCTTAGAATTTTCAGTTGTCTGAT
1 CCTCCTAATTATTCCAATCTTAGAATTTTCAGTTGTCTGAT
90385445 CCTCCTAATTATTCCAATCTTAGAATTTTCAGTTGTCT
1 CCTCCTAATTATTCCAATCTTAGAATTTTCAGTTGTCT
90385483 TACTTATGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.44
Consensus pattern (41 bp):
CCTCCTAATTATTCCAATCTTAGAATTTTCAGTTGTCTGAT
Found at i:90387821 original size:7 final size:7
Alignment explanation
Indices: 90387811--90387839 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
90387801 GTTAAAAAAT
90387811 ATTTAAA
1 ATTTAAA
90387818 ATTTAAA
1 ATTTAAA
90387825 ATTTAAA
1 ATTTAAA
90387832 ATTTAAA
1 ATTTAAA
90387839 A
1 A
90387840 AGAAACATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
ATTTAAA
Found at i:90389944 original size:40 final size:40
Alignment explanation
Indices: 90389898--90390105 Score: 204
Period size: 40 Copynumber: 5.2 Consensus size: 40
90389888 CGGAATACAA
* *
90389898 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGC
* * * * *
90389938 TCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGC
*
90389978 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGC
*** * *
90390018 CCGGATGAGGTC-ACTGGCAC-AATGGCCTTCGGGTCTTAAC
1 CCGGAT-ATAACAACTTGCACGAAT-GCCTTCGGGTCTTAGC
** * ** * *
90390058 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGC
90390098 CCGGATAT
1 CCGGATAT
90390106 CATTCAATTG
Statistics
Matches: 137, Mismatches: 27, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
39 4 0.03
40 129 0.94
41 4 0.03
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGC
Found at i:90390038 original size:80 final size:80
Alignment explanation
Indices: 90389898--90390104 Score: 238
Period size: 80 Copynumber: 2.6 Consensus size: 80
90389888 CGGAATACAA
* * * *
90389898 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCTCGGATAGAACGACTTGCACAAAT-
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTGGCAC-AATG
*
90389962 GCCTTCGGGTATTAGC
65 GCCTTCGGGTATTAAC
* **
90389978 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGAGGTC-ACTGGCACAATG
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-AGAACGACTGGCACAATG
*
90390042 GCCTTCGGGTCTTAAC
65 GCCTTCGGGTATTAAC
** * ** * *
90390058 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA
90390105 TCATTCAATT
Statistics
Matches: 108, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
79 4 0.04
80 101 0.94
81 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTGGCACAATGG
CCTTCGGGTATTAAC
Found at i:90393637 original size:40 final size:40
Alignment explanation
Indices: 90393592--90393758 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
90393582 CGGAATATAA
90393592 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
90393632 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
90393672 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
90393712 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
90393751 CCGGATAT
1 CCGGATAT
90393759 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:90393742 original size:80 final size:79
Alignment explanation
Indices: 90393592--90393758 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
90393582 CGGAATATAA
* *
90393592 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
90393657 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
90393672 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
90393734 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
90393751 CCGGATAT
1 CCGGATAT
90393759 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:90401650 original size:40 final size:40
Alignment explanation
Indices: 90401605--90401771 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
90401595 CGGAATATAA
90401605 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
90401645 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
90401685 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
90401725 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
90401764 CCGGATAT
1 CCGGATAT
90401772 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:90401755 original size:80 final size:79
Alignment explanation
Indices: 90401605--90401771 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
90401595 CGGAATATAA
* *
90401605 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
90401670 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
90401685 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
90401747 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
90401764 CCGGATAT
1 CCGGATAT
90401772 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:90402620 original size:17 final size:19
Alignment explanation
Indices: 90402597--90402642 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
90402587 AAGAAGCATG
90402597 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
90402615 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
90402633 AATCATGCTC
1 AATCATGCTC
90402643 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:90403716 original size:27 final size:26
Alignment explanation
Indices: 90403656--90403717 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
90403646 ATAAGACTCC
90403656 ATTTTATTAGGATAATTAATATTAAG
1 ATTTTATTAGGATAATTAATATTAAG
* * * *
90403682 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGA-TAATTAATATTAAG
90403710 ATTTTATT
1 ATTTTATT
90403718 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 14 0.48
28 13 0.45
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:90408733 original size:40 final size:40
Alignment explanation
Indices: 90408689--90408864 Score: 273
Period size: 40 Copynumber: 4.4 Consensus size: 40
90408679 CCGGGCTAAG
* *
90408689 CCGAAGGCATTTATGCTAG-TGATTATATCCGGGTTAAGAC
1 CCGAAGGCATTTGTGCGAGTTG-TTATATCCGGGTTAAGAC
*
90408729 CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGTTAAGAC
1 CCGAAGGCATTTGTGCGAGTTGTTATATCCGGGTTAAGAC
*
90408769 CCGAAGGCATTTGTGCGAGTTGTTATATCCGGGCTAAGAC
1 CCGAAGGCATTTGTGCGAGTTGTTATATCCGGGTTAAGAC
* *
90408809 CCGAAGGCATTTGTGCGAGTTGCTATACCCGGGTTAAGAC
1 CCGAAGGCATTTGTGCGAGTTGTTATATCCGGGTTAAGAC
*
90408849 CCGAAGGCAATTGTGC
1 CCGAAGGCATTTGTGC
90408865 TTGTGGTTAT
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 124 0.98
41 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTGTTATATCCGGGTTAAGAC
Found at i:90408874 original size:80 final size:80
Alignment explanation
Indices: 90408675--90408877 Score: 311
Period size: 80 Copynumber: 2.6 Consensus size: 80
90408665 CAATTGAATG
* * * *
90408675 ATACCCGGGCTAAG--CCGAAGGCATTTATGCTAGTGATTATATCCGGGTTAAGACCCGAAGGCA
1 ATACCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCA
90408738 TTTGTGCGAGTTGCT
66 TTTGTGCGAGTTGCT
* * *
90408753 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCA
1 ATACCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCA
90408818 TTTGTGCGAGTTGCT
66 TTTGTGCGAGTTGCT
* *
90408833 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATC
1 ATACCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATC
90408878 TGGCTAAATT
Statistics
Matches: 111, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
78 12 0.11
80 99 0.89
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.28
Consensus pattern (80 bp):
ATACCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCA
TTTGTGCGAGTTGCT
Found at i:90410713 original size:15 final size:14
Alignment explanation
Indices: 90410693--90410739 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
90410683 GCAACCTAAT
90410693 TTTTATTTTTATTTA
1 TTTTATTTTTA-TTA
*
90410708 TTTTA-TCTTATTA
1 TTTTATTTTTATTA
90410721 TTTTATTATTTATTA
1 TTTTATT-TTTATTA
90410736 TTTT
1 TTTT
90410740 CAGATATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 8 0.29
14 5 0.18
15 15 0.54
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTATTTTTATTA
Found at i:90412370 original size:27 final size:26
Alignment explanation
Indices: 90412310--90412371 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
90412300 ATAAGACTCC
90412310 ATTTTATTAGGATAATTAATATTAAG
1 ATTTTATTAGGATAATTAATATTAAG
* * * *
90412336 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGA-TAATTAATATTAAG
90412364 ATTTTATT
1 ATTTTATT
90412372 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 14 0.48
28 13 0.45
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:90412386 original size:10 final size:10
Alignment explanation
Indices: 90412367--90412398 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
90412357 TTTTAGGATT
90412367 TTAT-TTTAA
1 TTATCTTTAA
90412376 TTATCTTTAA
1 TTATCTTTAA
90412386 TTATCTTTAA
1 TTATCTTTAA
90412396 TTA
1 TTA
90412399 ATTGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:90417773 original size:21 final size:21
Alignment explanation
Indices: 90417733--90417774 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
90417723 TAAGGTGGTA
* *
90417733 TTAAAGTTTTGTTAAGAAATT
1 TTAAAGTTTCGATAAGAAATT
*
90417754 TTAAAGTTTCGATAATAAATT
1 TTAAAGTTTCGATAAGAAATT
90417775 AATTAAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.45
Consensus pattern (21 bp):
TTAAAGTTTCGATAAGAAATT
Found at i:90418418 original size:25 final size:25
Alignment explanation
Indices: 90418390--90418514 Score: 136
Period size: 25 Copynumber: 5.2 Consensus size: 25
90418380 CTTAGCGCGT
90418390 TCTCTGATTATTAGCACATCAGTGC
1 TCTCTGATTATTAGCACATCAGTGC
**
90418415 TCTCTGATTATTAGCATGTCAGTGC
1 TCTCTGATTATTAGCACATCAGTGC
* *
90418440 TCTCTGATTATTAGCACGTTAGTGC
1 TCTCTGATTATTAGCACATCAGTGC
* *
90418465 TCTCTG---ATTAGCACATCTGTGT
1 TCTCTGATTATTAGCACATCAGTGC
* *
90418487 TCTCTG--TA-TAGCACTTCAGTGT
1 TCTCTGATTATTAGCACATCAGTGC
90418509 TCTCTG
1 TCTCTG
90418515 CTCATTAGTG
Statistics
Matches: 89, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
22 36 0.40
23 1 0.01
25 52 0.58
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.40
Consensus pattern (25 bp):
TCTCTGATTATTAGCACATCAGTGC
Found at i:90418626 original size:18 final size:18
Alignment explanation
Indices: 90418603--90418657 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
90418593 AATATGAGAT
90418603 TGTGAATTGAAAATAGAA
1 TGTGAATTGAAAATAGAA
*
90418621 TGTG-A---AATAT-G-A
1 TGTGAATTGAAAATAGAA
90418633 TAGTGAATTGAAAATAGAA
1 T-GTGAATTGAAAATAGAA
90418652 TGTGAA
1 TGTGAA
90418658 ATATGTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 14
0.64 0.05 0.32
Matches are distributed among these distances:
12 2 0.07
13 4 0.14
14 5 0.18
17 5 0.18
18 10 0.36
19 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (18 bp):
TGTGAATTGAAAATAGAA
Found at i:90418641 original size:31 final size:31
Alignment explanation
Indices: 90418604--90418662 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
90418594 ATATGAGATT
90418604 GTGAATTGAAAATAGAATGTGAAATATGATA
1 GTGAATTGAAAATAGAATGTGAAATATGATA
90418635 GTGAATTGAAAATAGAATGTGAAATATG
1 GTGAATTGAAAATAGAATGTGAAATATG
90418663 TTGTAAATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (31 bp):
GTGAATTGAAAATAGAATGTGAAATATGATA
Found at i:90419210 original size:18 final size:19
Alignment explanation
Indices: 90419172--90419210 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
90419162 GATGATATGA
*
90419172 TTAAATTATGATGTGAATG
1 TTAAATAATGATGTGAATG
*
90419191 TTAAATAATTATGT-AATG
1 TTAAATAATGATGTGAATG
90419209 TT
1 TT
90419211 TGTATTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (19 bp):
TTAAATAATGATGTGAATG
Found at i:90421548 original size:19 final size:19
Alignment explanation
Indices: 90421524--90421569 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
90421514 TGTATTATCG
*
90421524 CTATGTATTCCTATAATCA
1 CTATGTATTCCTACAATCA
90421543 CTATGTATTCCTACAATCA
1 CTATGTATTCCTACAATCA
*
90421562 CCATGTAT
1 CTATGTAT
90421570 GCAAATGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (19 bp):
CTATGTATTCCTACAATCA
Found at i:90421599 original size:3 final size:3
Alignment explanation
Indices: 90421591--90421644 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
90421581 CTAGTTAGAT
90421591 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
90421639 GAA GAA
1 GAA GAA
90421645 AATAGTAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:90425236 original size:46 final size:47
Alignment explanation
Indices: 90425179--90425397 Score: 180
Period size: 46 Copynumber: 4.6 Consensus size: 47
90425169 TATATGTGCT
* *
90425179 AGTGTAGGACATGTCTGGGACATGCATCGGCTACA-ATATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGACTACAGATATGAGAGCC
** * *
90425225 AGTGTAAGACATGTCTGGGACATGCATCGACGTTGAGACA--AGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGAC-TACAGATATGAGAGCC
* * * * * * *
90425271 AGTGTATGACATGTTTGGGACATGCATCAGCCT-CGCGAT-GGACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATC-GACTAC-AGATATGA-GAGCC
* *
90425319 AGTGTAAGACCTGTCTGGGACATGGCATCGAC-ACCGATAGATGAGAGCC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGACTACAGAT--ATGAGAGCC
90425368 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATC
90425398 AGTATCTTAG
Statistics
Matches: 139, Mismatches: 21, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
46 63 0.45
47 9 0.06
48 29 0.21
49 17 0.12
50 21 0.15
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACTACAGATATGAGAGCC
Found at i:90428395 original size:39 final size:40
Alignment explanation
Indices: 90428261--90428398 Score: 131
Period size: 40 Copynumber: 3.5 Consensus size: 40
90428251 GGATATAACG
* * * **
90428261 ACTCGCTCAAATGCCTTCGGGAC-GAAGCCCGG-TTATAGCG
1 ACTCGCACGAATGCCTTCGGGACTTAA-CCCGGATT-TAGTA
* *
90428301 ACTTGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAGTA
* * * *
90428341 ACTTGCAC-AAAGCCTTCGGGA-TTAGCCCGGATTTATTA
1 ACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAGTA
90428379 ACTCGCACGAATGCCTTCGG
1 ACTCGCACGAATGCCTTCGG
90428399 ATCCTAGTCT
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
38 21 0.25
39 22 0.27
40 36 0.43
41 4 0.05
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
ACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAGTA
Found at i:90428398 original size:78 final size:80
Alignment explanation
Indices: 90428305--90428451 Score: 201
Period size: 78 Copynumber: 1.9 Consensus size: 80
90428295 ATAGCGACTT
* * *
90428305 GCACGAATGCCTTCGGGA-CTTAACCCGGGTTTAGTAACTT-GCACAAAGCCTTCGGGA-TTAGC
1 GCACGAATGCCTTC-GGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGATTTAGC
90428367 CCGGATTTATTAACTC
65 CCGGATTTATTAACTC
** * *
90428383 GCACGAATGCCTTCGGATCCTAGTCTGGATATAGTCACTTAGCACAAAGCCTTCGGGATTTAGCC
1 GCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGATTTAGCC
90428448 CGGA
66 CGGA
90428452 CATCATTCGA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
77 3 0.05
78 29 0.49
79 17 0.29
80 10 0.17
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (80 bp):
GCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGATTTAGCC
CGGATTTATTAACTC
Found at i:90434625 original size:48 final size:48
Alignment explanation
Indices: 90434505--90434984 Score: 368
Period size: 48 Copynumber: 9.9 Consensus size: 48
90434495 AGGCTAAGAT
* * * * * *
90434505 GCCGATGCCATGTCCCAGACATGGTCTTGCATTGGCTCTCATATATCGAT
1 GCCGATGCCATGT-CCAAACATGGTCTTACACTAGC-CTCACATATCGAG
* * *
90434555 GCTGATGTCATGTTCCAAACATGATCTTACACTAGCCT-ACATATCGAG
1 GCCGATGCCATG-TCCAAACATGGTCTTACACTAGCCTCACATATCGAG
* * * ** *
90434603 GCCGATGCCATGTCCAAGACATGGACTTACAGTAG-CTCTA-GTATAAAT
1 GCCGATGCCATGTCCAA-ACATGGTCTTACACTAGCCTC-ACATATCGAG
* * * *
90434651 GCCAATGCCATACTCCAAACATGGTCTTACACT-GGCTCACATATTGAG
1 GCCGATGCCAT-GTCCAAACATGGTCTTACACTAGCCTCACATATCGAG
* * * *
90434699 GCTGATGCCATGTCCCAGATATGGTCTTACACTAGCC-CACATATCAAG
1 GCCGATGCCATGT-CCAAACATGGTCTTACACTAGCCTCACATATCGAG
** * ** *
90434747 GCCGATGCCATGTCCCAAACATGGTCTTACACTAG-CTTTCGTATAAAAT
1 GCCGATGCCATGT-CCAAACATGGTCTTACACTAGCCTCACATAT-CGAG
* *
90434796 GCTGATGCCATGCTCCAAACATGGTCTTACACT-GGCTCACATATCGAG
1 GCCGATGCCATG-TCCAAACATGGTCTTACACTAGCCTCACATATCGAG
* * * * * ** *
90434844 GCTGATGCCATGTCCCAGACATGGTCTTACACTA-ACTCTCGTATAAAT
1 GCCGATGCCATGT-CCAAACATGGTCTTACACTAGCCTCACATATCGAG
* * * * *
90434892 GTCTATGCCATACTCTAAACATGGTCTTACACT-GGCTCACATATCGAG
1 GCCGATGCCAT-GTCCAAACATGGTCTTACACTAGCCTCACATATCGAG
*
90434940 GCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCACATATC
1 GCCGATGCCATGT-CCAAACATGGTCTTACACTAGCCTCACATATC
90434985 CCTAGTATCA
Statistics
Matches: 338, Mismatches: 73, Indels: 40
0.75 0.16 0.09
Matches are distributed among these distances:
47 13 0.04
48 246 0.73
49 50 0.15
50 28 0.08
51 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (48 bp):
GCCGATGCCATGTCCAAACATGGTCTTACACTAGCCTCACATATCGAG
Found at i:90434837 original size:97 final size:96
Alignment explanation
Indices: 90434503--90434977 Score: 424
Period size: 96 Copynumber: 4.9 Consensus size: 96
90434493 AAAGGCTAAG
* * * * * * * *
90434503 ATGCCGATGCCATG-TCCCAGACATGGTCTTGCATTGGCTCTCATATATCGATGCTGATGTCATG
1 ATGCTGATGCCATGCT-CCAAACATGGTCTTACACTGG--CTCACATATCGAGGCCGATGCCATG
* * * * **
90434567 TTCCAAACATGATCTTACACTAGC-CTACATATCG
63 TCCCAGACATGGTCTTACACTAGCTCT-CGTATAA
* * * * * * ** * * *
90434601 AGGCCGATGCCATG-TCCAAGACATGGACTTACAGTAGCTCTA-GTATAAATGCCAATGCCAT-A
1 ATGCTGATGCCATGCTCCAA-ACATGGTCTTACACTGGCTC-ACATATCGAGGCCGATGCCATGT
* * * * **
90434663 CTCCAAACATGGTCTTACACTGGCTCACATATTG
64 C-CCAGACATGGTCTTACACTAGCTCTCGTATAA
* * * * * *
90434697 AGGCTGATGCCATG-TCCCAGATATGGTCTTACACTAGCCCACATATCAAGGCCGATGCCATGTC
1 ATGCTGATGCCATGCT-CCAAACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTC
* *
90434761 CCAAACATGGTCTTACACTAGCTTTCGTATAAA
65 CCAGACATGGTCTTACACTAGCTCTCGTAT-AA
*
90434794 ATGCTGATGCCATGCTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCTGATGCCATGTCC
1 ATGCTGATGCCATGCTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTCC
*
90434859 CAGACATGGTCTTACACTAACTCTCGTATAA
66 CAGACATGGTCTTACACTAGCTCTCGTATAA
* *
90434890 ATGTCT-ATGCCATACTCTAAACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTC
1 ATG-CTGATGCCATGCTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTC
90434954 CCAGACATGGTCTTACACTAGCTC
65 CCAGACATGGTCTTACACTAGCTC
90434978 ACATATCCCT
Statistics
Matches: 318, Mismatches: 49, Indels: 22
0.82 0.13 0.06
Matches are distributed among these distances:
95 1 0.00
96 196 0.62
97 93 0.29
98 28 0.09
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.27
Consensus pattern (96 bp):
ATGCTGATGCCATGCTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTCC
CAGACATGGTCTTACACTAGCTCTCGTATAA
Found at i:90434856 original size:145 final size:144
Alignment explanation
Indices: 90434503--90434984 Score: 515
Period size: 144 Copynumber: 3.3 Consensus size: 144
90434493 AAAGGCTAAG
* * * * * *
90434503 ATGCCGATGCCATG-TCCCAGACATGGTCTTGCATTGGCTCTCATATATCGATGCTGATGTCATG
1 ATGCCGATGCCATGCT-CCAAACATGGTCTTACACTGG--CTCACATATCGAGGCTGATGCCATG
* * * * *
90434567 TTCCAAACATGATCTTACACTAGCCTACATATCGAGGCCGATGCCATGTCCAAGACATGGACTTA
63 TCCCAGACATGGTCTTACACTAGCCCACATATCAAGGCCGATGCCATGTCCAAGACATGGACTTA
*
90434632 CAGTAGCTCTAGTATAA
128 CACTAGCTCTAGTATAA
* * *
90434649 ATGCCAATGCCATACTCCAAACATGGTCTTACACTGGCTCACATATTGAGGCTGATGCCATGTCC
1 ATGCCGATGCCATGCTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCTGATGCCATGTCC
* *
90434714 CAGATATGGTCTTACACTAGCCCACATATCAAGGCCGATGCCATGTCCCAA-ACATGGTCTTACA
66 CAGACATGGTCTTACACTAGCCCACATATCAAGGCCGATGCCATGT-CCAAGACATGGACTTACA
* *
90434778 CTAGCTTTCGTATAAA
130 CTAGCTCTAGTAT-AA
*
90434794 ATGCTGATGCCATGCTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCTGATGCCATGTCC
1 ATGCCGATGCCATGCTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCTGATGCCATGTCC
* * * * * * * * * * *
90434859 CAGACATGGTCTTACACTAACTCTCGTATAAATGTCTATGCCATACTCTAA-ACATGGTCTTACA
66 CAGACATGGTCTTACACTAGCCCACATATCAAGGCCGATGCCAT-GTCCAAGACATGGACTTACA
* * **
90434923 CTGGCTC-ACATATCG
130 CTAGCTCTA-GTATAA
* * *
90434938 AGGCCGATGCCATG-TCCCAGACATGGTCTTACACTAGCTCACATATC
1 ATGCCGATGCCATGCT-CCAAACATGGTCTTACACTGGCTCACATATC
90434985 CCTAGTATCA
Statistics
Matches: 286, Mismatches: 44, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
143 1 0.00
144 127 0.44
145 126 0.44
146 31 0.11
147 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (144 bp):
ATGCCGATGCCATGCTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCTGATGCCATGTCC
CAGACATGGTCTTACACTAGCCCACATATCAAGGCCGATGCCATGTCCAAGACATGGACTTACAC
TAGCTCTAGTATAA
Found at i:90434929 original size:241 final size:242
Alignment explanation
Indices: 90434505--90434984 Score: 712
Period size: 241 Copynumber: 2.0 Consensus size: 242
90434495 AGGCTAAGAT
* * * * ** * *
90434505 GCCGATGCCATGTCCCAGACATGGTCTTGCATTGGCTCTCATATATCGATGCTGATGTCATGTTC
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATATAAATGCTGATGCCATGCTC
*
90434570 CAAACATGATCTTACACTAGCCTACATATCGAGGCCGATGCCATGTCCAAGACATGGACTTACAG
66 CAAACATGATCTTACACTAGCCTACATATCGAGGCCGATGCCATGTCCAAGACATGGACTTACAC
* *
90434635 TAGCTCTAGTATAAATGCCAATGCCATACTCCAAACATGGTCTTACACTGGCTCACATATTGAGG
131 TAACTCTAGTATAAATGCCAATGCCATACTCCAAACATGGTCTTACACTGGCTCACATATCGAGG
* *
90434700 CTGATGCCATGTCCCAGATATGGTCTTACACTAGCCCACATATCAAG
196 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCCCACATATCAAG
* *
90434747 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTTTCGTATA-AAATGCTGATGCCATGCTC
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATATAAATGCTGATGCCATGCTC
* * * * *
90434811 CAAACATGGTCTTACACT-GGCTCACATATCGAGGCTGATGCCATGTCCCAGACATGGTCTTACA
66 CAAACATGATCTTACACTAGCCT-ACATATCGAGGCCGATGCCATGTCCAAGACATGGACTTACA
* * * *
90434875 CTAACTCTCGTATAAATGTCTATGCCATACTCTAAACATGGTCTTACACTGGCTCACATATCGAG
130 CTAACTCTAGTATAAATGCCAATGCCATACTCCAAACATGGTCTTACACTGGCTCACATATCGAG
*
90434940 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATC
195 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCCCACATATC
90434985 CCTAGTATCA
Statistics
Matches: 212, Mismatches: 25, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
240 3 0.01
241 170 0.80
242 39 0.18
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (242 bp):
GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATATAAATGCTGATGCCATGCTC
CAAACATGATCTTACACTAGCCTACATATCGAGGCCGATGCCATGTCCAAGACATGGACTTACAC
TAACTCTAGTATAAATGCCAATGCCATACTCCAAACATGGTCTTACACTGGCTCACATATCGAGG
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCCCACATATCAAG
Found at i:90439290 original size:21 final size:22
Alignment explanation
Indices: 90439261--90439301 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
90439251 TCTTCCTTGG
90439261 AAGGTGGATATCCCGATACCCA
1 AAGGTGGATATCCCGATACCCA
**
90439283 AAGG-GGATATTGCGATACC
1 AAGGTGGATATCCCGATACC
90439302 ACTGAAGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (22 bp):
AAGGTGGATATCCCGATACCCA
Found at i:90448459 original size:29 final size:29
Alignment explanation
Indices: 90448425--90448529 Score: 95
Period size: 29 Copynumber: 3.6 Consensus size: 29
90448415 TACTCGATTT
* * *
90448425 CGCACACTTAGTGCCATGCGATTTAAGCC
1 CGCACACTTAGTGCCATACCATTCAAGCC
** * *
90448454 CGCACACACAGTGCCATACCATTCGAGCT
1 CGCACACTTAGTGCCATACCATTCAAGCC
* * *
90448483 CGCACACTTAGTGCCATA-TATTTCCAGCA
1 CGCACACTTAGTGCCATACCA-TTCAAGCC
*
90448512 TGCACACTTAGTGCCATA
1 CGCACACTTAGTGCCATA
90448530 TATTTCCAGC
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
28 1 0.02
29 61 0.98
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACCATTCAAGCC
Found at i:90448517 original size:58 final size:59
Alignment explanation
Indices: 90448463--90448585 Score: 180
Period size: 58 Copynumber: 2.1 Consensus size: 59
90448453 CCGCACACAC
*
90448463 AGTGCCATACCA-TTCGAGC-TCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
1 AGTGCCATA-CATTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
* * *
90448521 AGTGCCATATATTTCCAGCAT-GCACACTCAGTGCCATATTTTTCCAGCATGCACACTT
1 AGTGCCATACATTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
90448579 AGTGCCA
1 AGTGCCA
90448586 ATCTCGTCAC
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
57 1 0.02
58 57 0.97
59 1 0.02
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.28
Consensus pattern (59 bp):
AGTGCCATACATTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
Found at i:90448530 original size:29 final size:29
Alignment explanation
Indices: 90448484--90448585 Score: 186
Period size: 29 Copynumber: 3.5 Consensus size: 29
90448474 ATTCGAGCTC
90448484 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
90448513 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
* *
90448542 GCACACTCAGTGCCATATTTTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
90448571 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
90448586 ATCTCGTCAC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:90450932 original size:27 final size:27
Alignment explanation
Indices: 90450902--90450987 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
90450892 AGTTTTCCAA
90450902 AAAGGCATTCCTTTCATATTCTACCAT
1 AAAGGCATTCCTTTCATATTCTACCAT
* * * *
90450929 AAAGACGTTCCTTCCATATTGC-GCCAT
1 AAAGGCATTCCTTTCATATT-CTACCAT
* * *
90450956 AAAGGCATTCATTTTATATTATACCAT
1 AAAGGCATTCCTTTCATATTCTACCAT
90450983 AAAGG
1 AAAGG
90450988 TTTTTCTTTC
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
27 45 0.98
28 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.34
Consensus pattern (27 bp):
AAAGGCATTCCTTTCATATTCTACCAT
Found at i:90454135 original size:11 final size:12
Alignment explanation
Indices: 90454115--90454147 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
90454105 GGACCCAAGA
90454115 TGAATTAATTT-
1 TGAATTAATTTG
*
90454126 TGAATCAATTTG
1 TGAATTAATTTG
90454138 TGAATTAATT
1 TGAATTAATT
90454148 CACTTGTGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.48
Consensus pattern (12 bp):
TGAATTAATTTG
Found at i:90456516 original size:42 final size:43
Alignment explanation
Indices: 90456459--90456588 Score: 113
Period size: 42 Copynumber: 3.0 Consensus size: 43
90456449 ACTTTAAAAC
*
90456459 AAATTTTATATAAAACTCAGTCATGCAAATTTTCATAGCAT-A
1 AAATGTTATATAAAACTCAGTCATGCAAATTTTCATAGCATAA
* * *** *
90456501 AAATGTTATATAAAACT-ATTTA-GCAAAATTGAAAATAGAATTACA
1 AAATGTTATATAAAACTCAGTCATGC-AAATT-TTCATAGCA-TA-A
*
90456546 AAATTAGTTATATAAAACTCAGTCATGTAAATTTTCATAGCAT
1 AAA-T-GTTATATAAAACTCAGTCATGCAAATTTTCATAGCAT
90456589 TTCATAACAT
Statistics
Matches: 65, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
40 2 0.03
41 8 0.12
42 21 0.32
43 1 0.02
45 4 0.06
46 2 0.03
47 18 0.28
48 8 0.12
49 1 0.02
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (43 bp):
AAATGTTATATAAAACTCAGTCATGCAAATTTTCATAGCATAA
Found at i:90457441 original size:10 final size:10
Alignment explanation
Indices: 90457426--90457453 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
90457416 ATTAGGGGAA
90457426 AAAGTAAAAC
1 AAAGTAAAAC
90457436 AAAGTAAAAC
1 AAAGTAAAAC
90457446 AAAGTAAA
1 AAAGTAAA
90457454 CATGTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.71, C:0.07, G:0.11, T:0.11
Consensus pattern (10 bp):
AAAGTAAAAC
Found at i:90459455 original size:16 final size:15
Alignment explanation
Indices: 90459434--90459463 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
90459424 GGATATTCCA
90459434 ATTTAGTTACATTTTT
1 ATTTAGTTA-ATTTTT
90459450 ATTTAGTTAATTTT
1 ATTTAGTTAATTTT
90459464 GGCAATTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (15 bp):
ATTTAGTTAATTTTT
Found at i:90474525 original size:37 final size:37
Alignment explanation
Indices: 90474475--90474567 Score: 150
Period size: 37 Copynumber: 2.5 Consensus size: 37
90474465 ACACCAATCA
* *
90474475 CTCATAAGAGCTAATCTAAACGATAACACGCTAGATG
1 CTCATAAGAGCTAATCCAAACAATAACACGCTAGATG
**
90474512 CTCATAAGAGCTAATCCATCCAATAACACGCTAGATG
1 CTCATAAGAGCTAATCCAAACAATAACACGCTAGATG
90474549 CTCATAAGAGCTAATCCAA
1 CTCATAAGAGCTAATCCAA
90474568 CCGAAAACAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.22
Consensus pattern (37 bp):
CTCATAAGAGCTAATCCAAACAATAACACGCTAGATG
Found at i:90488973 original size:24 final size:24
Alignment explanation
Indices: 90488946--90489128 Score: 332
Period size: 24 Copynumber: 7.7 Consensus size: 24
90488936 CTTATTATGT
**
90488946 TCGCACACATAGTGCCATAGCGAA
1 TCGCACACATAGTGCCATAGTAAA
90488970 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
90488994 TCGCACACATAGTGCCATAG-AAA
1 TCGCACACATAGTGCCATAGTAAA
90489017 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
90489041 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
90489065 TCGCACACATAGTGCCATGGTAAA
1 TCGCACACATAGTGCCATAGTAAA
90489089 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
90489113 TCGCACACATAGTGCC
1 TCGCACACATAGTGCC
90489129 GTATATTTCC
Statistics
Matches: 154, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
23 23 0.15
24 131 0.85
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.20
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:90489088 original size:95 final size:96
Alignment explanation
Indices: 90488946--90489128 Score: 332
Period size: 95 Copynumber: 1.9 Consensus size: 96
90488936 CTTATTATGT
*
90488946 TCGCACACATAGTGCCATAGCGAATCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCA
1 TCGCACACATAGTGCCATAGCAAATCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCA
90489011 TAG-AAATCGCACACATAGTGCCATAGTAAA
66 TAGTAAATCGCACACATAGTGCCATAGTAAA
* *
90489041 TCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCATGGTAAATCGCACACATAGTGCCA
1 TCGCACACATAGTGCCATAGCAAATCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCA
90489106 TAGTAAATCGCACACATAGTGCC
66 TAGTAAATCGCACACATAGTGCC
90489129 GTATATTTCC
Statistics
Matches: 84, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
95 65 0.77
96 19 0.23
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.20
Consensus pattern (96 bp):
TCGCACACATAGTGCCATAGCAAATCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCA
TAGTAAATCGCACACATAGTGCCATAGTAAA
Found at i:90494381 original size:17 final size:17
Alignment explanation
Indices: 90494359--90494393 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
90494349 ACCCAACATT
90494359 CACCTATGTGTCTTCTC
1 CACCTATGTGTCTTCTC
90494376 CACCTATGTGTCTTCTC
1 CACCTATGTGTCTTCTC
90494393 C
1 C
90494394 CACATTGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.37, G:0.11, T:0.40
Consensus pattern (17 bp):
CACCTATGTGTCTTCTC
Found at i:90495624 original size:29 final size:29
Alignment explanation
Indices: 90495591--90495664 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
90495581 GTGACGAGAT
90495591 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
90495620 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
90495649 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
90495665 AGCTCGAAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:90495680 original size:29 final size:29
Alignment explanation
Indices: 90495648--90495723 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
90495638 CTGGAAATAT
* *
90495648 ATGGCACTAAGTGTGCGAGCTCGAAGGGC
1 ATGGCACTAAGTGTGCGAGCTCAAAGCGC
** * * *
90495677 ATGGCACTGTGTGTGCGGGCTTAAATCGC
1 ATGGCACTAAGTGTGCGAGCTCAAAGCGC
90495706 ATGGCACTAAGTGTGCGA
1 ATGGCACTAAGTGTGCGA
90495724 AATCGAGTAT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.22, C:0.20, G:0.36, T:0.22
Consensus pattern (29 bp):
ATGGCACTAAGTGTGCGAGCTCAAAGCGC
Found at i:90495691 original size:58 final size:58
Alignment explanation
Indices: 90495591--90495723 Score: 133
Period size: 58 Copynumber: 2.3 Consensus size: 58
90495581 GTGACGAGAT
* * * * * *
90495591 TGGCACTAAGTGTGCGTGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAAAT-ATA
1 TGGCACTAAGTGTGCGAGCTCGAAAGACATGGCACTAAGTGTGCAGGCT-GAAATCACA
* * ** * * *
90495649 TGGCACTAAGTGTGCGAGCTCGAAGGGCATGGCACTGTGTGTGCGGGCTTAAATCGCA
1 TGGCACTAAGTGTGCGAGCTCGAAAGACATGGCACTAAGTGTGCAGGCTGAAATCACA
90495707 TGGCACTAAGTGTGCGA
1 TGGCACTAAGTGTGCGA
90495724 AATCGAGTAT
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
57 4 0.07
58 57 0.93
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (58 bp):
TGGCACTAAGTGTGCGAGCTCGAAAGACATGGCACTAAGTGTGCAGGCTGAAATCACA
Found at i:90498586 original size:24 final size:24
Alignment explanation
Indices: 90498558--90498670 Score: 208
Period size: 24 Copynumber: 4.7 Consensus size: 24
90498548 ACCGAATGTG
**
90498558 GCACACATAGTGCCATAGCGAATC
1 GCACACATAGTGCCATAGTAAATC
90498582 GCACACATAGTGCCATAGTAAATC
1 GCACACATAGTGCCATAGTAAATC
90498606 GCACACATAGTGCCATAGTAAATC
1 GCACACATAGTGCCATAGTAAATC
90498630 GCACACATAGTGCCATAGTAAATC
1 GCACACATAGTGCCATAGTAAATC
90498654 GCACACATAGTGCCATA
1 GCACACATAGTGCCATA
90498671 TATTTCCAGC
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 87 1.00
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (24 bp):
GCACACATAGTGCCATAGTAAATC
Found at i:90502008 original size:40 final size:41
Alignment explanation
Indices: 90501915--90502012 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
90501905 GGATGTCACA
* * ** *
90501915 ACCAGAGTGCATAACAGGGATATGAATGTGAAATCAGGGGC
1 ACCAGAGTGCAAAACAGGGACACAAATGTGAAATCAGAGGC
* * *
90501956 ACCGGAGTGCAAAACAGGGCCACAAATGTGCAATCA-AGGC
1 ACCAGAGTGCAAAACAGGGACACAAATGTGAAATCAGAGGC
90501996 ACCAGAGTGC-AAACAGG
1 ACCAGAGTGCAAAACAGG
90502013 ATAAGCGCGC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
39 7 0.15
40 12 0.25
41 29 0.60
ACGTcount: A:0.38, C:0.20, G:0.30, T:0.12
Consensus pattern (41 bp):
ACCAGAGTGCAAAACAGGGACACAAATGTGAAATCAGAGGC
Found at i:90503046 original size:14 final size:14
Alignment explanation
Indices: 90503008--90503047 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
90502998 TCTGTTTTTC
90503008 TTTT-ACTT-TAATA
1 TTTTAACTTATAA-A
90503021 TTTTAA-TTATAAA
1 TTTTAACTTATAAA
90503034 TTTTAACTTATAAA
1 TTTTAACTTATAAA
90503048 ATCACATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTTAACTTATAAA
Found at i:90506094 original size:49 final size:49
Alignment explanation
Indices: 90506022--90506122 Score: 193
Period size: 49 Copynumber: 2.1 Consensus size: 49
90506012 TATGGGAACA
*
90506022 CATATAGTGGTTGTCAATACATCAAATCTTTTATCACTCGTTAAACATT
1 CATATAGTGATTGTCAATACATCAAATCTTTTATCACTCGTTAAACATT
90506071 CATATAGTGATTGTCAATACATCAAATCTTTTATCACTCGTTAAACATT
1 CATATAGTGATTGTCAATACATCAAATCTTTTATCACTCGTTAAACATT
90506120 CAT
1 CAT
90506123 TTAGATTTCC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.39
Consensus pattern (49 bp):
CATATAGTGATTGTCAATACATCAAATCTTTTATCACTCGTTAAACATT
Found at i:90507297 original size:2 final size:2
Alignment explanation
Indices: 90507290--90507327 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
90507280 TTTGTGGGTC
*
90507290 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
90507328 GATTTGGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:90508524 original size:9 final size:9
Alignment explanation
Indices: 90508500--90508564 Score: 67
Period size: 9 Copynumber: 7.1 Consensus size: 9
90508490 TACTTAATTC
90508500 TTTTAAAAGA
1 TTTTAAAA-A
*
90508510 TATTAAAAA
1 TTTTAAAAA
* *
90508519 TTTTAATAT
1 TTTTAAAAA
90508528 TTTTAAAAA
1 TTTTAAAAA
* *
90508537 TTTTAATAT
1 TTTTAAAAA
90508546 TTTTAAAAA
1 TTTTAAAAA
*
90508555 TTTTATAAA
1 TTTTAAAAA
90508564 T
1 T
90508565 CACATTTAAT
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
9 37 0.84
10 7 0.16
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:90508535 original size:18 final size:18
Alignment explanation
Indices: 90508512--90508559 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
90508502 TTAAAAGATA
90508512 TTAAAAATTTTAATATTT
1 TTAAAAATTTTAATATTT
90508530 TTAAAAATTTTAATATTT
1 TTAAAAATTTTAATATTT
90508548 TTAAAAATTTTA
1 TTAAAAATTTTA
90508560 TAAATCACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAAAAATTTTAATATTT
Found at i:90508858 original size:18 final size:17
Alignment explanation
Indices: 90508835--90508895 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 17
90508825 TTTCAGTATC
* *
90508835 TTTTTATTATTTTTTATA
1 TTTTTAATATTATTTA-A
90508853 TTTTTAATATTATTTAA
1 TTTTTAATATTATTTAA
90508870 TTTTTAAATAATATTATTTAA
1 -TTTT---TAATATTATTTAA
90508891 TTTTT
1 TTTTT
90508896 TATAAACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 2 0.05
18 18 0.49
20 4 0.11
21 13 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTAATATTATTTAA
Found at i:90510381 original size:39 final size:39
Alignment explanation
Indices: 90510327--90510403 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
90510317 AGAATGAAGA
90510327 AGAATTTTTGAAAGATTTCATTACAAATGAATTGTGGCT
1 AGAATTTTTGAAAGATTTCATTACAAATGAATTGTGGCT
90510366 AGAATTTTTGAAAGATTTCATTACAAATGAATTGTGGC
1 AGAATTTTTGAAAGATTTCATTACAAATGAATTGTGGC
90510404 ATAAAGCCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (39 bp):
AGAATTTTTGAAAGATTTCATTACAAATGAATTGTGGCT
Done.