Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 164 of 320
Found at i:53980358 original size:81 final size:81
Alignment explanation
Indices: 53980223--53980371 Score: 201
Period size: 81 Copynumber: 1.8 Consensus size: 81
53980213 ACATTGAGCC
* * *
53980223 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAG
1 CGCACACTCAGTGCTATATAATCAACTCGCACACTGAGTGCAACATAATCAAATCGCACACTTAG
53980288 TGCCGCATGGTCAATT
66 TGCCGCATGGTCAATT
* * ** * *
53980304 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTGAGTGCAACATAGTCAAATCGCACCCTTA
1 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTGAGTGCAACATAATCAAATCGCACACTTA
53980368 GTGC
65 GTGC
53980372 TGTACAATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
80 2 0.03
81 56 0.97
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.26
Consensus pattern (81 bp):
CGCACACTCAGTGCTATATAATCAACTCGCACACTGAGTGCAACATAATCAAATCGCACACTTAG
TGCCGCATGGTCAATT
Found at i:53990656 original size:13 final size:13
Alignment explanation
Indices: 53990638--53990666 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
53990628 GGTTGTTTAT
53990638 TAAACTAATTAAC
1 TAAACTAATTAAC
53990651 TAAACTAATTAAC
1 TAAACTAATTAAC
53990664 TAA
1 TAA
53990667 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:53999920 original size:27 final size:27
Alignment explanation
Indices: 53999890--54000101 Score: 280
Period size: 27 Copynumber: 7.9 Consensus size: 27
53999880 GGCATAATTA
* * * *
53999890 TCATTTTACCATATAGGGGTATTACGG
1 TCATTTTACCCTACAAGGGCATTACGG
*
53999917 TCATTTTACCCTACACGGGCATTACGG
1 TCATTTTACCCTACAAGGGCATTACGG
* *
53999944 TCATTTTACCTTACAAGGGTATTACGG
1 TCATTTTACCCTACAAGGGCATTACGG
*
53999971 TTATTTTACCCTACAAGGGCATTACGG
1 TCATTTTACCCTACAAGGGCATTACGG
* * *
53999998 TCATTTTAACCTACAAGGGTATTACGA
1 TCATTTTACCCTACAAGGGCATTACGG
* *
54000025 TTATTTTACCCTACAGGGGCATTACGG
1 TCATTTTACCCTACAAGGGCATTACGG
*
54000052 TCATTTTACCCTACATGGGCATTACGG
1 TCATTTTACCCTACAAGGGCATTACGG
* *
54000079 TCATTTTATCCTACAACGGCATT
1 TCATTTTACCCTACAAGGGCATT
54000102 GATCGCAGTG
Statistics
Matches: 161, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 161 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.34
Consensus pattern (27 bp):
TCATTTTACCCTACAAGGGCATTACGG
Found at i:54004476 original size:40 final size:40
Alignment explanation
Indices: 54004430--54004654 Score: 234
Period size: 40 Copynumber: 5.6 Consensus size: 40
54004420 CTTGCACAAG
* * *
54004430 GCCTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * * *
54004470 GCCTTCGGGACTTAGCCCGGATATAATCGCTAGAACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * * *
54004510 GCCTTCGAGTTTTAGCCCGGATATAATCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * ** * *
54004550 GCCTTCAGGTCTTAGCCCAGATATAGAAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * * *
54004590 GCCTTCGGATCTTAGTCCGGTTATAGTCACCTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAAT
* *
54004631 GCCTTCTGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
54004655 CATTCGAATA
Statistics
Matches: 148, Mismatches: 36, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
40 121 0.82
41 27 0.18
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:54013990 original size:41 final size:41
Alignment explanation
Indices: 54013924--54014021 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 41
54013914 ACGGGCCTGA
* *
54013924 TCACACAAGCTATCAACCAAAATGTAGCTACACGGTGCTAC
1 TCACACAAGCTGTCAACCAAAATGTAGCTACACGATGCTAC
** * * *
54013965 TCACACAAGCTGTCAGTCAAGATGTAGCTACATGATGCTGC
1 TCACACAAGCTGTCAACCAAAATGTAGCTACACGATGCTAC
54014006 TCACACAAGCTGTCAA
1 TCACACAAGCTGTCAA
54014022 GTAATGCCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (41 bp):
TCACACAAGCTGTCAACCAAAATGTAGCTACACGATGCTAC
Found at i:54034951 original size:42 final size:43
Alignment explanation
Indices: 54034883--54035028 Score: 111
Period size: 44 Copynumber: 3.4 Consensus size: 43
54034873 GCTCGGATGT
* * *
54034883 GGTCTTACATGTAATCAAATATCGATGCC-ACTGTCTTAGA-AA
1 GGTCTTACACGAAATCAAATATCGATGCCGA-TGTCCTAGACAA
* *
54034925 GGTTCTTACACGAAATCATATA-CGATGCCGATGTCCTAGACAT
1 GG-TCTTACACGAAATCAAATATCGATGCCGATGTCCTAGACAA
* * * * * * *
54034968 GGTCTTACACGTATATCTCAA-GTCGATGCCAATGTCCCAAACAT
1 GGTCTTACACG-AAATC-AAATATCGATGCCGATGTCCTAGACAA
*
54035012 GGTCTTACACGATATCA
1 GGTCTTACACGAAATCA
54035029 CACCTCAAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
42 26 0.31
43 29 0.34
44 30 0.35
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (43 bp):
GGTCTTACACGAAATCAAATATCGATGCCGATGTCCTAGACAA
Found at i:54035571 original size:15 final size:15
Alignment explanation
Indices: 54035551--54035581 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
54035541 AATTTCTCAT
54035551 TTAACCCAACACATA
1 TTAACCCAACACATA
54035566 TTAACCCAACACATA
1 TTAACCCAACACATA
54035581 T
1 T
54035582 CTTTCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (15 bp):
TTAACCCAACACATA
Found at i:54040965 original size:40 final size:40
Alignment explanation
Indices: 54040912--54041107 Score: 261
Period size: 40 Copynumber: 4.9 Consensus size: 40
54040902 GGATATAGCT
* * * *
54040912 ACTCGCTCGAATGCCTTCGGGACATAGCCCGGTTATGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* *
54040952 ACTCGCACAAATGCCTTCGGGGCTTAGCCCGGATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* *
54040992 ACTCGCACGAATGCCTTCGGGACATAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* *
54041032 ACTCGCACAAATGCCTTCGAGG-CTTAGCCCGG-AATTAGTC
1 ACTCGCACAAATGCCTTCG-GGACTTAGCCCGGTTA-TAGTA
*
54041072 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
54041108 CACCCGAATA
Statistics
Matches: 136, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.02
40 130 0.96
41 3 0.02
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:54041033 original size:80 final size:79
Alignment explanation
Indices: 54040900--54041107 Score: 319
Period size: 80 Copynumber: 2.6 Consensus size: 79
54040890 CGGAATTTAA
* *
54040900 CCGGATATAGCTACTCGCTCGAATGCCTTCGGGACATAGCCCGGTTATGGTAACTCGCACAAATG
1 CCGGATATAG-TACTCGCACGAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATG
*
54040965 CCTTCGGGGCTTAGC
65 CCTTCGAGGCTTAGC
54040980 CCGGATATAGTAACTCGCACGAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATG
1 CCGGATATAGT-ACTCGCACGAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATG
54041045 CCTTCGAGGCTTAGC
65 CCTTCGAGGCTTAGC
* * *
54041060 CCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CCGGATA-TAGT-ACTCGCACGAATGCCTTCGGGACATAGCCCGGTTAT
54041108 CACCCGAATA
Statistics
Matches: 119, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
79 2 0.02
80 117 0.98
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.24
Consensus pattern (79 bp):
CCGGATATAGTACTCGCACGAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGC
CTTCGAGGCTTAGC
Found at i:54045825 original size:22 final size:21
Alignment explanation
Indices: 54045793--54045835 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
54045783 GTTGTTACAC
*
54045793 AACATATAGCATACATTTCTCA
1 AACATAAAGCATACA-TTCTCA
*
54045815 AACATAAAGCATCCATTCTCA
1 AACATAAAGCATACATTCTCA
54045836 TAAATCATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.42, C:0.26, G:0.05, T:0.28
Consensus pattern (21 bp):
AACATAAAGCATACATTCTCA
Found at i:54053198 original size:46 final size:45
Alignment explanation
Indices: 54053131--54053305 Score: 181
Period size: 46 Copynumber: 3.8 Consensus size: 45
54053121 TGTAACCCGC
* *
54053131 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGGC-TTCGCAT
* * * *
54053177 CCATAAGTGAACTCAGACTCAACTCAACAAGTTCGGATGCCTAG-TT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGG--GCTTCGCAT
* *** * *
54053223 ACATCTCTCGAACTCAGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGT-GAACTCAGACTCAACTCAACGAGTTCGGGC-TTCGCAT
*
54053270 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGG
54053306 ATGCCCAAAT
Statistics
Matches: 102, Mismatches: 22, Indels: 10
0.76 0.16 0.07
Matches are distributed among these distances:
45 1 0.01
46 66 0.65
47 33 0.32
48 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGGCTTCGCAT
Found at i:54053247 original size:93 final size:93
Alignment explanation
Indices: 54053139--54053310 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
54053129 GCCCATAAGT
* * * *
54053139 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
54053204 CAAGTTCGGATGCCTAGTTACATCTCTC
66 CAAGTTCGGATGCCTAGTTACATCTCTC
* *
54053232 GAACTCAGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
54053297 CGAGTTCGGATGCC
66 CAAGTTCGGATGCC
54053311 CAAATATCCT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CAAGTTCGGATGCCTAGTTACATCTCTC
Found at i:54055267 original size:15 final size:16
Alignment explanation
Indices: 54055241--54055296 Score: 82
Period size: 15 Copynumber: 3.7 Consensus size: 16
54055231 CAAGGAAACC
54055241 GAATAAAGAAATCCAA
1 GAATAAAGAAATCCAA
*
54055257 G-ATAGAGAAATCC-A
1 GAATAAAGAAATCCAA
54055271 GAATAAAGAAATCC-A
1 GAATAAAGAAATCCAA
54055286 GAATAAAGAAA
1 GAATAAAGAAA
54055297 CCTAAGATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 2 0.05
15 34 0.92
16 1 0.03
ACGTcount: A:0.61, C:0.11, G:0.16, T:0.12
Consensus pattern (16 bp):
GAATAAAGAAATCCAA
Found at i:54058311 original size:46 final size:45
Alignment explanation
Indices: 54058244--54058418 Score: 199
Period size: 46 Copynumber: 3.8 Consensus size: 45
54058234 TGTAACCCGC
54058244 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGTAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGTAT
* * *
54058290 CCATAAGTGAACTCGGACTCAACTTAACGAGTTCGGATGCCTAGT-T
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--GCTTCGTAT
* *** * * *
54058336 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGTAT
*
54058383 CCATAAGTGAACTCGGACTCAACTCAACAAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
54058419 ATGCCCAAAT
Statistics
Matches: 105, Mismatches: 19, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
45 1 0.01
46 68 0.65
47 34 0.32
48 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCTTCGTAT
Found at i:54058359 original size:93 final size:93
Alignment explanation
Indices: 54058252--54058423 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
54058242 GCCCATAAGT
* * * * *
54058252 GAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGTATCCATAAGTGAACTCGGACTCAACTTAA
1 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
54058317 CGAGTTCGGATGCCTAGTTACATCTCTC
66 CAAGTTCGGATGCCTAGTTACATCTCTC
54058345 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54058410 CAAGTTCGGATGCC
66 CAAGTTCGGATGCC
54058424 CAAATATCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CAAGTTCGGATGCCTAGTTACATCTCTC
Found at i:54061141 original size:16 final size:17
Alignment explanation
Indices: 54061122--54061155 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
54061112 AAATTTTATG
54061122 AAATAAAAAT-AAACAA
1 AAATAAAAATCAAACAA
*
54061138 AAATAAACATCAAACAA
1 AAATAAAAATCAAACAA
54061155 A
1 A
54061156 CGCCATCCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (17 bp):
AAATAAAAATCAAACAA
Found at i:54064953 original size:23 final size:23
Alignment explanation
Indices: 54064927--54064976 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
54064917 GCTGGCTGAA
54064927 TCTTCAAACCATTTTCATCGCTT
1 TCTTCAAACCATTTTCATCGCTT
*
54064950 TCTTCAAACCATTTTCATGGCTT
1 TCTTCAAACCATTTTCATCGCTT
54064973 TCTT
1 TCTT
54064977 TGCCCTAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.20, C:0.28, G:0.06, T:0.46
Consensus pattern (23 bp):
TCTTCAAACCATTTTCATCGCTT
Found at i:54067608 original size:26 final size:26
Alignment explanation
Indices: 54067564--54067614 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
54067554 TTTATAGGTG
* *
54067564 GAAAATTTACAGATTTACCCCTAGGA
1 GAAAAATTACAGATATACCCCTAGGA
*
54067590 GAAAAATTACTGATATACCCCTAGG
1 GAAAAATTACAGATATACCCCTAGG
54067615 GTTAAGGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (26 bp):
GAAAAATTACAGATATACCCCTAGGA
Found at i:54079121 original size:33 final size:33
Alignment explanation
Indices: 54079079--54079142 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
54079069 CATTTCAGTA
* *
54079079 ATAGTTCAAT-TTAGTTAGGGCCCTAGCCCATT
1 ATAGTTCAATATCAGTGAGGGCCCTAGCCCATT
*
54079111 ATAGTATCAATATCAGTGAGGGCCTTAGCCCA
1 ATAGT-TCAATATCAGTGAGGGCCCTAGCCCA
54079143 ATTCAGTAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 5 0.19
33 5 0.19
34 17 0.63
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (33 bp):
ATAGTTCAATATCAGTGAGGGCCCTAGCCCATT
Found at i:54088067 original size:46 final size:47
Alignment explanation
Indices: 54088000--54088169 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 47
54087990 TGTAACCCGC
54088000 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAGACGTTCGCAT
* *
54088046 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GA-GAC--GTTCGCAT
* * * * * *
54088096 --TTCA-CGAACTCGGACTCAACTCAACGAGTTTG-GACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAGACGTTCGCAT
54088139 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
54088170 TTCGGATGCT
Statistics
Matches: 103, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 58 0.56
47 26 0.25
48 3 0.03
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (47 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAGACGTTCGCAT
Found at i:54088120 original size:93 final size:93
Alignment explanation
Indices: 54088008--54088178 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
54087998 GCCCATAAGT
*
54088008 GAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGA-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54088072 ACGAGCTCGGATGCCTAGTTACATTTCAC
65 ACGAGCTCGGATGCCTAGTTACATTTCAC
* *
54088101 GAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
54088166 CGAGTTCGGATGC
66 CGAGCTCGGATGC
54088179 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
93 71 0.97
94 2 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATTTCAC
Found at i:54092147 original size:46 final size:46
Alignment explanation
Indices: 54092094--54092269 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
54092084 TATTTGGGCA
54092094 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * * *
54092140 TCCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
54092187 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
54092233 CCCGAGCTCGTTGAGTTGAGCCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54092270 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 66 0.61
47 31 0.28
48 2 0.02
50 4 0.04
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:54092249 original size:93 final size:93
Alignment explanation
Indices: 54092090--54092262 Score: 301
Period size: 93 Copynumber: 1.9 Consensus size: 93
54092080 GGGGTATTTG
*
54092090 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGCCCGAACTCGTTGAG
* *
54092155 TTGAGTCTGAGTTCGTGAGATGTAACTA
66 TTGAGCCCGAGTTCGTGAGATGTAACTA
* *
54092183 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGCCCGAACTCGTTGAG
54092248 TTGAGCCCGAGTTCG
66 TTGAGCCCGAGTTCG
54092263 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.19, C:0.22, G:0.32, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGCCCGAACTCGTTGAG
TTGAGCCCGAGTTCGTGAGATGTAACTA
Found at i:54095218 original size:15 final size:15
Alignment explanation
Indices: 54095198--54095275 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
54095188 CATAGTATGG
*
54095198 TATCTTGGGTTTCTT
1 TATCTTGGATTTCTT
* *
54095213 TATCTTAGATCTCTT
1 TATCTTGGATTTCTT
54095228 TAT-TCTGGATTTCTT
1 TATCT-TGGATTTCTT
* * *
54095243 TAT-TCCGGGTTTCTC
1 TATCT-TGGATTTCTT
*
54095258 TATCATGGATTTCTT
1 TATCTTGGATTTCTT
54095273 TAT
1 TAT
54095276 TCGGTTTTCT
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
14 1 0.02
15 48 0.98
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:54097724 original size:46 final size:46
Alignment explanation
Indices: 54097671--54097846 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
54097661 TATTTAGGCA
54097671 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
54097717 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
* * * * *
54097764 TACGAGCCCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
54097810 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54097847 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 17, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
43 4 0.04
45 3 0.03
46 63 0.60
47 29 0.28
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:54104532 original size:40 final size:40
Alignment explanation
Indices: 54104477--54104706 Score: 331
Period size: 40 Copynumber: 5.8 Consensus size: 40
54104467 GATGATAATG
* *
54104477 GGGCTAAGTCCCGAAGGCATCTGTGCTAGTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCC
* *
54104517 GGGCTAAGTCCCGAAGGCATCTGTGCTAGTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCC
* *
54104557 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCC
*
54104597 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-TCC
*
54104637 GGGCTAAGTCCCGAAGGCATTTGTGCGAACT-ACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCG-AGTGACTAAT-TCC
*
54104677 GGGCTAAGTCCCGAAGGCATTTGAGCGAGT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGT
54104707 AGCTATATCC
Statistics
Matches: 180, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
39 4 0.02
40 174 0.97
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCC
Found at i:54112625 original size:40 final size:40
Alignment explanation
Indices: 54112570--54112797 Score: 313
Period size: 40 Copynumber: 5.8 Consensus size: 40
54112560 GATGATAACG
* *
54112570 GGGCTAAGTCCCGAAGGCATCTGTGCTAGTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCC
* *
54112610 GGGCTAAGTCCCGAAGGCATCT-TGCTAGTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCC
* *
54112649 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCC
*
54112689 GGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-TCC
*
54112728 GGGCTAAGTCCCGAAGGCATTTGTGCGAACT-ACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCG-AGTGACTAAT-TCC
*
54112768 GGGCTAAGTCCCGAAGGCATTTGAGCGAGT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGT
54112798 AGCTATATCC
Statistics
Matches: 176, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
38 2 0.01
39 75 0.43
40 97 0.55
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCC
Found at i:54112729 original size:79 final size:80
Alignment explanation
Indices: 54112570--54112823 Score: 331
Period size: 79 Copynumber: 3.2 Consensus size: 80
54112560 GATGATAACG
* * * *
54112570 GGGCTAAGTCCCGAAGGCATCTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATCT-TG
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
* *
54112634 CTAGTGACTA-ATTCC
66 CGAGTTACTATA-TCC
*
54112649 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGT-CCGAAGGCATTTGTG
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
54112713 CGAGTTACTATATCC
66 CGAGTTACTATATCC
** *
54112728 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACT-ATATCCGGGCTAAGTCCCGAAGGCATTTGA
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGCTAAGTCCCGAAGGCATTTGT
54112792 GCGAG-TAGCTATATCC
65 GCGAGTTA-CTATATCC
* *
54112808 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
54112824 TACTTGGTTT
Statistics
Matches: 157, Mismatches: 13, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
78 13 0.08
79 117 0.75
80 27 0.17
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (80 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
CGAGTTACTATATCC
Found at i:54112804 original size:40 final size:39
Alignment explanation
Indices: 54112570--54112823 Score: 304
Period size: 40 Copynumber: 6.4 Consensus size: 39
54112560 GATGATAACG
* *
54112570 GGGCTAAGTCCCGAAGGCATCTGTGCTAGTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTAATTCC
* *
54112610 GGGCTAAGTCCCGAAGGCATCT-TGCTAGTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTAATTCC
*
54112649 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTAATTCC
54112689 GGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTAAT-TCC
*
54112728 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCG-AGTACTAAT-TCC
*
54112768 GGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGCT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTA-CTAAT-TCC
* *
54112808 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
54112824 TACTTGGTTT
Statistics
Matches: 199, Mismatches: 9, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
38 2 0.01
39 90 0.45
40 105 0.53
41 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (39 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTAATTCC
Found at i:54113776 original size:1 final size:1
Alignment explanation
Indices: 54113770--54113861 Score: 184
Period size: 1 Copynumber: 92.0 Consensus size: 1
54113760 TAAGTCCGTA
54113770 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
54113835 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
54113862 ACTGTGTTGA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 91 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:54118948 original size:25 final size:26
Alignment explanation
Indices: 54118920--54118968 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
54118910 CAATGATAAC
* *
54118920 CTTTATGGCGTAATATG-AAGAAAGA
1 CTTTATCGAGTAATATGAAAGAAAGA
*
54118945 CTTTGTCGAGTAATATGAAAGAAA
1 CTTTATCGAGTAATATGAAAGAAA
54118969 AACCTTTGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (26 bp):
CTTTATCGAGTAATATGAAAGAAAGA
Found at i:54132650 original size:38 final size:38
Alignment explanation
Indices: 54132607--54132759 Score: 225
Period size: 38 Copynumber: 4.0 Consensus size: 38
54132597 AACATATGAT
*
54132607 GTATTATATCCGGGTTAAATTCCGCAAGCTTAATGCTG
1 GTATTATATCCGGGTTAAATCCCGCAAGCTTAATGCTG
54132645 GTATTATATCCGGGTTAAATCCCGCAAGCTTAATGCTG
1 GTATTATATCCGGGTTAAATCCCGCAAGCTTAATGCTG
* *
54132683 GTATTATATCCGGGTTAAATCCCGCAGGCTTAACGCTG
1 GTATTATATCCGGGTTAAATCCCGCAAGCTTAATGCTG
* * * *
54132721 GTATTATATTCGGGTTTAAAGTCTCGCAGGCTTTATGCT
1 GTATTATATCCGGG-TTAAA-TCCCGCAAGCTTAATGCT
54132760 AGTGACTAGA
Statistics
Matches: 106, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
38 86 0.81
39 5 0.05
40 15 0.14
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (38 bp):
GTATTATATCCGGGTTAAATCCCGCAAGCTTAATGCTG
Found at i:54148783 original size:40 final size:40
Alignment explanation
Indices: 54148739--54148868 Score: 197
Period size: 40 Copynumber: 3.2 Consensus size: 40
54148729 ATAATTATTG
*
54148739 CTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
1 CTGAATGCACATACGTGCCCCTGTTTGTTCTTCGGTACCC
* *
54148779 CTGAATGCACATATGTGCCCCTGTTTGTTCTTCGATACCC
1 CTGAATGCACATACGTGCCCCTGTTTGTTCTTCGGTACCC
* * *
54148819 GTGGATGCACATACGTGCCCCTGTTTGTTCTTCTGTACCC
1 CTGAATGCACATACGTGCCCCTGTTTGTTCTTCGGTACCC
*
54148859 CTGGATGCAC
1 CTGAATGCAC
54148869 TAGCATGTGA
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.16, C:0.31, G:0.21, T:0.32
Consensus pattern (40 bp):
CTGAATGCACATACGTGCCCCTGTTTGTTCTTCGGTACCC
Found at i:54148799 original size:20 final size:20
Alignment explanation
Indices: 54148739--54148801 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
54148729 ATAATTATTG
54148739 CTGAATGCACATACGTGCCC
1 CTGAATGCACATACGTGCCC
** * * *
54148759 CTGTTTGTAC-TTCGGTACCC
1 CTGAATGCACATAC-GTGCCC
*
54148779 CTGAATGCACATATGTGCCC
1 CTGAATGCACATACGTGCCC
54148799 CTG
1 CTG
54148802 TTTGTTCTTC
Statistics
Matches: 30, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
19 2 0.07
20 27 0.90
21 1 0.03
ACGTcount: A:0.19, C:0.32, G:0.21, T:0.29
Consensus pattern (20 bp):
CTGAATGCACATACGTGCCC
Found at i:54151027 original size:31 final size:31
Alignment explanation
Indices: 54150989--54151052 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
54150979 TAAGTAGATT
54150989 TCCCATATAAATACATCATTTAATTCATCAA
1 TCCCATATAAATACATCATTTAATTCATCAA
54151020 TCCCATATAAATACATCATTTAATTCATCAA
1 TCCCATATAAATACATCATTTAATTCATCAA
54151051 TC
1 TC
54151053 TTTTTATAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.41, C:0.23, G:0.00, T:0.36
Consensus pattern (31 bp):
TCCCATATAAATACATCATTTAATTCATCAA
Found at i:54153250 original size:30 final size:30
Alignment explanation
Indices: 54153214--54153279 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
54153204 GTCACACGGT
*
54153214 CGTGTGACACGCACGACCTGACGACACAAC
1 CGTGTGACACACACGACCTGACGACACAAC
* **
54153244 CGTGTGACACACACGGCCTGGTGACACAAC
1 CGTGTGACACACACGACCTGACGACACAAC
*
54153274 TGTGTG
1 CGTGTG
54153280 TCATTTAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.32, G:0.27, T:0.15
Consensus pattern (30 bp):
CGTGTGACACACACGACCTGACGACACAAC
Found at i:54159598 original size:13 final size:13
Alignment explanation
Indices: 54159580--54159604 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54159570 ATCAGCAAAA
54159580 ATTTTAAAATATT
1 ATTTTAAAATATT
54159593 ATTTTAAAATAT
1 ATTTTAAAATAT
54159605 AAATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTAAAATATT
Found at i:54160041 original size:4 final size:4
Alignment explanation
Indices: 54160024--54160054 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
54160014 TTTTTTTACT
54160024 TAAA TAATA TAAA TAAA TAAA TAAA TAAA TA
1 TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TA
54160055 TTGAAACAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
TAAA
Found at i:54171380 original size:15 final size:15
Alignment explanation
Indices: 54171362--54171391 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54171352 AAGCAAATAA
54171362 AGAAATCCAAGATAG
1 AGAAATCCAAGATAG
*
54171377 AGAAATCCGAGATAG
1 AGAAATCCAAGATAG
54171392 GATACCATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.23, T:0.13
Consensus pattern (15 bp):
AGAAATCCAAGATAG
Found at i:54171843 original size:20 final size:20
Alignment explanation
Indices: 54171818--54171857 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
54171808 TTCACTGTGA
54171818 TTACCACATTCTTTCAATAT
1 TTACCACATTCTTTCAATAT
*
54171838 TTACCACATTCTTTTAATAT
1 TTACCACATTCTTTCAATAT
54171858 CGTATCCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (20 bp):
TTACCACATTCTTTCAATAT
Found at i:54181152 original size:25 final size:25
Alignment explanation
Indices: 54181123--54181364 Score: 189
Period size: 25 Copynumber: 9.7 Consensus size: 25
54181113 AAGATAATAC
* *
54181123 GATCGGCACAAATCCATCGATAACA
1 GATCGGCACAAAGCCATCAATAACA
* * *
54181148 GATCGACACATAGCCATCAATATCA
1 GATCGGCACAAAGCCATCAATAACA
* **
54181173 TATCGGCACAAAGCCATTGATAACA
1 GATCGGCACAAAGCCATCAATAACA
* * *
54181198 GATCGACACATAGCCATCAATATCA
1 GATCGGCACAAAGCCATCAATAACA
* * **
54181223 TATCAGCACAAAGCCATCGTTAACA
1 GATCGGCACAAAGCCATCAATAACA
* * *
54181248 AATCGACACATAGCCATCAATAACA
1 GATCGGCACAAAGCCATCAATAACA
* * *
54181273 TATCGGCACAAAGCCATGAATAGCA
1 GATCGGCACAAAGCCATCAATAACA
* * * * *
54181298 TA-CTGGCACGAAGCCTTCAGTAGCA
1 GATC-GGCACAAAGCCATCAATAACA
* ** *
54181323 TATCGGCACAAAGCTTTCAATAGCA
1 GATCGGCACAAAGCCATCAATAACA
*
54181348 TATCGGCACAAAGCCAT
1 GATCGGCACAAAGCCAT
54181365 AATTAGAATA
Statistics
Matches: 171, Mismatches: 44, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
24 1 0.01
25 169 0.99
26 1 0.01
ACGTcount: A:0.39, C:0.27, G:0.15, T:0.19
Consensus pattern (25 bp):
GATCGGCACAAAGCCATCAATAACA
Found at i:54181199 original size:50 final size:50
Alignment explanation
Indices: 54181124--54181289 Score: 278
Period size: 50 Copynumber: 3.3 Consensus size: 50
54181114 AGATAATACG
*
54181124 ATCGGCACAAATCCATCGATAACAGATCGACACATAGCCATCAATATCAT
1 ATCGGCACAAAGCCATCGATAACAGATCGACACATAGCCATCAATATCAT
*
54181174 ATCGGCACAAAGCCATTGATAACAGATCGACACATAGCCATCAATATCAT
1 ATCGGCACAAAGCCATCGATAACAGATCGACACATAGCCATCAATATCAT
* * * *
54181224 ATCAGCACAAAGCCATCGTTAACAAATCGACACATAGCCATCAATAACAT
1 ATCGGCACAAAGCCATCGATAACAGATCGACACATAGCCATCAATATCAT
54181274 ATCGGCACAAAGCCAT
1 ATCGGCACAAAGCCAT
54181290 GAATAGCATA
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 108 1.00
ACGTcount: A:0.41, C:0.28, G:0.13, T:0.19
Consensus pattern (50 bp):
ATCGGCACAAAGCCATCGATAACAGATCGACACATAGCCATCAATATCAT
Found at i:54181332 original size:100 final size:100
Alignment explanation
Indices: 54181124--54181336 Score: 279
Period size: 100 Copynumber: 2.1 Consensus size: 100
54181114 AGATAATACG
* * *
54181124 ATCGGCACAAATCCATCGATAACAGATCGACACATAGCCATCAATATCATATCGGCACAAAGCCA
1 ATCGGCACAAAGCCATCGATAACAAATCGACACATAGCCATCAATAACATATCGGCACAAAGCCA
*
54181189 TTGATAACAGATCGACACATAGCCATCAATATCAT
66 TTGATAACAGATCGACACATAGCCATCAATAGCAT
* *
54181224 ATCAGCACAAAGCCATCGTTAACAAATCGACACATAGCCATCAATAACATATCGGCACAAAGCCA
1 ATCGGCACAAAGCCATCGATAACAAATCGACACATAGCCATCAATAACATATCGGCACAAAGCCA
* * * * *
54181289 -TGAATAGCATA-CTGGCACGA-AGCCTTCAGTAGCAT
66 TTG-ATAACAGATC-GACAC-ATAGCCATCAATAGCAT
54181324 ATCGGCACAAAGC
1 ATCGGCACAAAGC
54181337 TTTCAATAGC
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
99 3 0.03
100 94 0.96
101 1 0.01
ACGTcount: A:0.39, C:0.27, G:0.15, T:0.18
Consensus pattern (100 bp):
ATCGGCACAAAGCCATCGATAACAAATCGACACATAGCCATCAATAACATATCGGCACAAAGCCA
TTGATAACAGATCGACACATAGCCATCAATAGCAT
Found at i:54181645 original size:26 final size:26
Alignment explanation
Indices: 54181616--54181673 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
54181606 AAAACGTCAT
54181616 TTTACCCTACAAGGGTATTTCAGTAA
1 TTTACCCTACAAGGGTATTTCAGTAA
*
54181642 TTTACCCTACAGGGGTATTTCAGTAA
1 TTTACCCTACAAGGGTATTTCAGTAA
54181668 TCTTAC
1 T-TTAC
54181674 AAACTTAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.36
Consensus pattern (26 bp):
TTTACCCTACAAGGGTATTTCAGTAA
Found at i:54184858 original size:25 final size:25
Alignment explanation
Indices: 54184819--54185060 Score: 180
Period size: 25 Copynumber: 9.7 Consensus size: 25
54184809 ACAACAATAC
* * *
54184819 GATCTGCATAAAGCCATCGATAACA
1 GATCGGCACAAAGCCATCAATAACA
* *
54184844 GATCGGCACATAGCCATCAATATCA
1 GATCGGCACAAAGCCATCAATAACA
* * * *
54184869 TATCGACACAAAGCCATCGATAATA
1 GATCGGCACAAAGCCATCAATAACA
* *
54184894 GATCGGCACATAGCCATCAATATCA
1 GATCGGCACAAAGCCATCAATAACA
* * **
54184919 TATCAGCACAAAGCCATCGTTAACA
1 GATCGGCACAAAGCCATCAATAACA
* *
54184944 GATCGGCACATAGCCATCAATATCA
1 GATCGGCACAAAGCCATCAATAACA
* * *
54184969 TATCGGCACAAAGCCATGAATAGCA
1 GATCGGCACAAAGCCATCAATAACA
* * * * * *
54184994 TA-CTGGCACGAGGCCTTCAGTAGCA
1 GATC-GGCACAAAGCCATCAATAACA
* * ** *
54185019 TATCGACACAAAGCTTTCAATAGCA
1 GATCGGCACAAAGCCATCAATAACA
*
54185044 TATCGGCACAAAGCCAT
1 GATCGGCACAAAGCCAT
54185061 AATTAGAATA
Statistics
Matches: 169, Mismatches: 46, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
24 1 0.01
25 167 0.99
26 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (25 bp):
GATCGGCACAAAGCCATCAATAACA
Found at i:54184887 original size:50 final size:50
Alignment explanation
Indices: 54184828--54184985 Score: 273
Period size: 50 Copynumber: 3.2 Consensus size: 50
54184818 CGATCTGCAT
54184828 AAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCATATCGACAC
1 AAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCATATCGACAC
*
54184878 AAAGCCATCGATAATAGATCGGCACATAGCCATCAATATCATATC-AGCAC
1 AAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCATATCGA-CAC
* *
54184928 AAAGCCATCGTTAACAGATCGGCACATAGCCATCAATATCATATCGGCAC
1 AAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCATATCGACAC
54184978 AAAGCCAT
1 AAAGCCAT
54184986 GAATAGCATA
Statistics
Matches: 102, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
49 1 0.01
50 101 0.99
ACGTcount: A:0.39, C:0.27, G:0.15, T:0.19
Consensus pattern (50 bp):
AAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCATATCGACAC
Found at i:54185002 original size:50 final size:49
Alignment explanation
Indices: 54184828--54185032 Score: 247
Period size: 50 Copynumber: 4.1 Consensus size: 49
54184818 CGATCTGCAT
*
54184828 AAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCATATCGACAC
1 AAAGCCATCG-TAATAGATCGGCACATAGCCATCAATATCATATCGACAC
54184878 AAAGCCATCGATAATAGATCGGCACATAGCCATCAATATCATATC-AGCAC
1 AAAGCCATCG-TAATAGATCGGCACATAGCCATCAATATCATATCGA-CAC
* *
54184928 AAAGCCATCGTTAACAGATCGGCACATAGCCATCAATATCATATCGGCAC
1 AAAGCCATCG-TAATAGATCGGCACATAGCCATCAATATCATATCGACAC
* * * *
54184978 AAAGCCAT-G-AATAGCATACTGGCACGA-GGCCTTCAGTAGCATATCGACAC
1 AAAGCCATCGTAATAG-AT-C-GGCAC-ATAGCCATCAATATCATATCGACAC
54185028 AAAGC
1 AAAGC
54185033 TTTCAATAGC
Statistics
Matches: 139, Mismatches: 10, Indels: 12
0.86 0.06 0.07
Matches are distributed among these distances:
47 4 0.03
48 2 0.01
49 3 0.02
50 129 0.93
51 1 0.01
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.19
Consensus pattern (49 bp):
AAAGCCATCGTAATAGATCGGCACATAGCCATCAATATCATATCGACAC
Found at i:54185021 original size:100 final size:99
Alignment explanation
Indices: 54184828--54185060 Score: 276
Period size: 100 Copynumber: 2.3 Consensus size: 99
54184818 CGATCTGCAT
54184828 AAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCATATCGACACAAAGCCATCGATAAT
1 AAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCATATCGACACAAAGCCATCGA-AAT
*
54184893 AGATCGGCACATAGCCATCAATATCATATC-AGCAC
65 AGATCGGCACATAGCCATCAATAGCATATCGA-CAC
* *
54184928 AAAGCCATCGTTAACAGATCGGCACATAGCCATCAATATCATATCGGCACAAAGCCAT-G-AATA
1 AAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCATATCGACACAAAGCCATCGAAATA
* * *
54184991 GCATACTGGCACGA-GGCCTTCAGTAGCATATCGACAC
66 G-AT-C-GGCAC-ATAGCCATCAATAGCATATCGACAC
** * * * *
54185028 AAAGCTTTCAATAGCATATCGGCACAAAGCCAT
1 AAAGCCATCGATAACAGATCGGCACATAGCCAT
54185061 AATTAGAATA
Statistics
Matches: 115, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
97 5 0.04
98 2 0.02
99 2 0.02
100 104 0.90
101 2 0.02
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19
Consensus pattern (99 bp):
AAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCATATCGACACAAAGCCATCGAAATA
GATCGGCACATAGCCATCAATAGCATATCGACAC
Found at i:54185347 original size:26 final size:27
Alignment explanation
Indices: 54185290--54185348 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 27
54185280 GTAAAACATC
54185290 ATTTTACCCTACAAGGGTATTTCGGTA
1 ATTTTACCCTACAAGGGTATTTCGGTA
* *
54185317 A-TTTACCTTAC-AGGGTATTTTGGTA
1 ATTTTACCCTACAAGGGTATTTCGGTA
54185342 ATTTTAC
1 ATTTTAC
54185349 AAACCTGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 14 0.48
26 14 0.48
27 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (27 bp):
ATTTTACCCTACAAGGGTATTTCGGTA
Found at i:54193045 original size:26 final size:26
Alignment explanation
Indices: 54193010--54193080 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
54193000 TTCATTAATA
* *
54193010 CAAAACATACCATATA-TCATGCATAT
1 CAAAATATACCATAAACT-ATGCATAT
**
54193036 CAAAATATACTTTAAACTATGCATAT
1 CAAAATATACCATAAACTATGCATAT
**
54193062 CAAAATATACTTTAAACTA
1 CAAAATATACCATAAACTA
54193081 ACTTAACATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 39 0.98
27 1 0.03
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.31
Consensus pattern (26 bp):
CAAAATATACCATAAACTATGCATAT
Found at i:54195872 original size:30 final size:30
Alignment explanation
Indices: 54195838--54195898 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
54195828 TCCTTAACTC
54195838 AAACTTTGGAAAAATTACAATTTTGTCCCT
1 AAACTTTGGAAAAATTACAATTTTGTCCCT
* * * * *
54195868 AAACTTTTGCATATTTACATTTTTGTCCCT
1 AAACTTTGGAAAAATTACAATTTTGTCCCT
54195898 A
1 A
54195899 GGCTCGAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.43
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGTCCCT
Found at i:54203571 original size:40 final size:40
Alignment explanation
Indices: 54203523--54203749 Score: 427
Period size: 40 Copynumber: 5.7 Consensus size: 40
54203513 GCAAACACAT
* *
54203523 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
54203563 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
54203603 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
54203643 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
54203683 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
54203723 TTGCCTTCGGGTCTTAGCCCGGATATA
1 TTGCCTTCGGGTCTTAGCCCGGATATA
54203750 ATCCAATGCT
Statistics
Matches: 183, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 183 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:54210813 original size:40 final size:40
Alignment explanation
Indices: 54210765--54210951 Score: 347
Period size: 40 Copynumber: 4.7 Consensus size: 40
54210755 GCAAACACAT
* *
54210765 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
54210805 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
54210845 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
54210885 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
54210925 TTGCCTTCGGGTCTTAGCCCGGATATA
1 TTGCCTTCGGGTCTTAGCCCGGATATA
54210952 ATCCAATGCT
Statistics
Matches: 143, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 143 1.00
ACGTcount: A:0.21, C:0.28, G:0.20, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:54214413 original size:21 final size:21
Alignment explanation
Indices: 54214384--54214436 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
54214374 TTTTGGATAT
54214384 TTTCC-CCCA-TAATCCTCTAA
1 TTTCCTCCCACTAATCC-CTAA
*
54214404 TTTCCTCCCACTTATCCCTAA
1 TTTCCTCCCACTAATCCCTAA
*
54214425 ATTCACTCCCAC
1 TTTC-CTCCCAC
54214437 ACTTCCCCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.18
21 11 0.39
22 12 0.43
ACGTcount: A:0.23, C:0.43, G:0.00, T:0.34
Consensus pattern (21 bp):
TTTCCTCCCACTAATCCCTAA
Found at i:54218753 original size:25 final size:26
Alignment explanation
Indices: 54218725--54218776 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
54218715 GAGAATTTCG
54218725 ATTAAA-GGTTCTTTATGAACTTCCC
1 ATTAAATGGTTCTTTATGAACTTCCC
* *
54218750 ATTAAATTGGTTCTTTGTGAGCTTCCC
1 ATTAAA-TGGTTCTTTATGAACTTCCC
54218777 GATCGTGCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
27 17 0.74
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.42
Consensus pattern (26 bp):
ATTAAATGGTTCTTTATGAACTTCCC
Found at i:54218842 original size:24 final size:24
Alignment explanation
Indices: 54218815--54218870 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
54218805 TGGCTATCAA
54218815 GAGCTTCCTGACATGG-TCTTTTGT
1 GAGCTTCCTGACATGGTTC-TTTGT
*
54218839 GAGCTTCCTGATATGGTTCTTTGT
1 GAGCTTCCTGACATGGTTCTTTGT
*
54218863 GAACTTCC
1 GAGCTTCC
54218871 CAATTATTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.14, C:0.21, G:0.23, T:0.41
Consensus pattern (24 bp):
GAGCTTCCTGACATGGTTCTTTGT
Found at i:54227314 original size:18 final size:18
Alignment explanation
Indices: 54227291--54227351 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
54227281 ATTATACGAA
54227291 CTTACTAAGCATTAAATG
1 CTTACTAAGCATTAAATG
* * *
54227309 CTTACT-AG-GTTATACG
1 CTTACTAAGCATTAAATG
54227325 AACTTACTAAGCATTAAATG
1 --CTTACTAAGCATTAAATG
54227345 CTTACTA
1 CTTACTA
54227352 GGTTTTCTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 5 0.15
17 2 0.06
18 19 0.58
19 2 0.06
20 5 0.15
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (18 bp):
CTTACTAAGCATTAAATG
Found at i:54227329 original size:36 final size:36
Alignment explanation
Indices: 54227282--54227355 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
54227272 TAAATTCCTA
54227282 TTATACGAACTTACTAAGCATTAAATGCTTACTAGG
1 TTATACGAACTTACTAAGCATTAAATGCTTACTAGG
54227318 TTATACGAACTTACTAAGCATTAAATGCTTACTAGG
1 TTATACGAACTTACTAAGCATTAAATGCTTACTAGG
54227354 TT
1 TT
54227356 TTCTTTTCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (36 bp):
TTATACGAACTTACTAAGCATTAAATGCTTACTAGG
Found at i:54232656 original size:41 final size:41
Alignment explanation
Indices: 54232551--54232659 Score: 130
Period size: 43 Copynumber: 2.6 Consensus size: 41
54232541 CGATGATAAA
* * * *
54232551 TCAGATATATGTGGCACTTAGTATGCGAGATCGAGATATAT
1 TCAGCTATATATGGCACTTAGTGTGCAAGATCGAGATATAT
**
54232592 TTGGCTATATATATGGCACTTAGTGTGCAAGATCGAGATA-ACT
1 TCAGC--TATATATGGCACTTAGTGTGCAAGATCGAGATATA-T
54232635 TCAGCTATATATGGCACTTAGTGTG
1 TCAGCTATATATGGCACTTAGTGTG
54232660 TGATTTAAGA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
41 22 0.39
42 1 0.02
43 34 0.60
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (41 bp):
TCAGCTATATATGGCACTTAGTGTGCAAGATCGAGATATAT
Found at i:54232682 original size:40 final size:39
Alignment explanation
Indices: 54232599--54232702 Score: 109
Period size: 40 Copynumber: 2.6 Consensus size: 39
54232589 TATTTGGCTA
* *
54232599 TATATATGGCACTTAGTGTGCAAGATCGAGATAACTTCAGC
1 TATATATGGCACTTAGTGTG--TGATCAAGATAACTTCAGC
* * *
54232640 TATATATGGCACTTAGTGTGTGATTTAAGATAGCTTCGGC
1 TATATATGGCACTTAGTGTGTGA-TCAAGATAACTTCAGC
* * *
54232680 TATGTACGACACTTAGTGTGTGA
1 TATATATGGCACTTAGTGTGTGA
54232703 GATATTGAGT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.04
40 32 0.59
41 20 0.37
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (39 bp):
TATATATGGCACTTAGTGTGTGATCAAGATAACTTCAGC
Found at i:54232740 original size:28 final size:28
Alignment explanation
Indices: 54232689--54232742 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
54232679 CTATGTACGA
* * *
54232689 CACTTAGTGTGTGAGATATTGAGTATGG
1 CACTTAGTGTCTGAGACATGGAGTATGG
*
54232717 CACTTAGTGTCTGAGGCATGGAGTAT
1 CACTTAGTGTCTGAGACATGGAGTAT
54232743 TCAACGGCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.24, C:0.11, G:0.31, T:0.33
Consensus pattern (28 bp):
CACTTAGTGTCTGAGACATGGAGTATGG
Found at i:54238839 original size:22 final size:20
Alignment explanation
Indices: 54238809--54238853 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
54238799 CATTTATGAG
*
54238809 AATGAATGCTTTATGTTTGATA
1 AATGAATGCTATAT-TTTG-TA
*
54238831 AATGTATGCTATATTTTGTA
1 AATGAATGCTATATTTTGTA
54238851 AAT
1 AAT
54238854 TGATCGGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 4 0.19
22 12 0.57
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (20 bp):
AATGAATGCTATATTTTGTA
Found at i:54239220 original size:12 final size:11
Alignment explanation
Indices: 54239187--54239219 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
54239177 ACCCCTAATA
*
54239187 AAAATTATTTT
1 AAAATTCTTTT
54239198 AAAATTCTTTT
1 AAAATTCTTTT
54239209 AAAATTCTTTT
1 AAAATTCTTTT
54239220 TCGACCCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (11 bp):
AAAATTCTTTT
Found at i:54240154 original size:16 final size:16
Alignment explanation
Indices: 54240133--54240165 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
54240123 TTGTAACACC
54240133 CCAAAAATCTCGAAAT
1 CCAAAAATCTCGAAAT
54240149 CCAAAAATCTCGAAAT
1 CCAAAAATCTCGAAAT
54240165 C
1 C
54240166 TTGAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.27, G:0.06, T:0.18
Consensus pattern (16 bp):
CCAAAAATCTCGAAAT
Found at i:54241685 original size:29 final size:29
Alignment explanation
Indices: 54241646--54241757 Score: 129
Period size: 29 Copynumber: 3.9 Consensus size: 29
54241636 ATGAGTATAA
*
54241646 ATGATTTGGGCCTAATGGGCCATATGAAT
1 ATGAATTGGGCCTAATGGGCCATATGAAT
* *
54241675 GTGAATTGGGCCTAATGGGCCATAAGAAT
1 ATGAATTGGGCCTAATGGGCCATATGAAT
*
54241704 ATGAACTGGGCC-AGATGGGCCATATGAAT
1 ATGAATTGGGCCTA-ATGGGCCATATGAAT
* * * *
54241733 AAG-ATTGGGCCCAGTGGACCATATG
1 ATGAATTGGGCCTAATGGGCCATATG
54241758 CATGTATGTA
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
28 18 0.25
29 53 0.75
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.24
Consensus pattern (29 bp):
ATGAATTGGGCCTAATGGGCCATATGAAT
Found at i:54243921 original size:14 final size:14
Alignment explanation
Indices: 54243902--54243929 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54243892 ATACTTAAGA
54243902 CTCTTATGATCAGT
1 CTCTTATGATCAGT
54243916 CTCTTATGATCAGT
1 CTCTTATGATCAGT
54243930 GTATATCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (14 bp):
CTCTTATGATCAGT
Found at i:54246519 original size:14 final size:14
Alignment explanation
Indices: 54246500--54246529 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
54246490 ATGGCATATT
54246500 GGTTAGTTGAATTA
1 GGTTAGTTGAATTA
54246514 GGTTAGTTGAATTA
1 GGTTAGTTGAATTA
54246528 GG
1 GG
54246530 GTATTGGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.40
Consensus pattern (14 bp):
GGTTAGTTGAATTA
Found at i:54249050 original size:19 final size:20
Alignment explanation
Indices: 54249007--54249052 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
54248997 ATTGGGCATT
54249007 GCCCATATTAACACAGTTGG
1 GCCCATATTAACACAGTTGG
* *
54249027 GCCCATTTTAATACAGTT-G
1 GCCCATATTAACACAGTTGG
54249046 GCCCATA
1 GCCCATA
54249053 ACAAAATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (20 bp):
GCCCATATTAACACAGTTGG
Found at i:54254765 original size:24 final size:24
Alignment explanation
Indices: 54254738--54254785 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
54254728 TAGTGAATAT
54254738 ATATATGAG-GTTATAATATGGTTA
1 ATATATGAGTGTT-TAATATGGTTA
* *
54254762 ATATATGTGTGTTTGATATGGTTA
1 ATATATGAGTGTTTAATATGGTTA
54254786 TATTGAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (24 bp):
ATATATGAGTGTTTAATATGGTTA
Found at i:54257519 original size:53 final size:53
Alignment explanation
Indices: 54257337--54257543 Score: 191
Period size: 53 Copynumber: 3.8 Consensus size: 53
54257327 ATTAGGGTTT
* * * *
54257337 AAGGATACCA-AGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTTTACAAGGC
1 AAGGATACCATA-TAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGC
* * * ** * * * *
54257391 AAGGAAATCATGTAAGACCATGTTAAGACATGGCATTGATAAACTACTATAAGGC
1 AAGGATACCATATAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* * * * *
54257446 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATATAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* *
54257499 AAGGATACCACATAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATATAAGACCATGCCAAGACATGGCAATGGTAAGTT
54257544 TAAAAATGAA
Statistics
Matches: 120, Mismatches: 30, Indels: 7
0.76 0.19 0.04
Matches are distributed among these distances:
53 45 0.38
54 36 0.30
55 39 0.32
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.21
Consensus pattern (53 bp):
AAGGATACCATATAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:54261290 original size:27 final size:27
Alignment explanation
Indices: 54261260--54261437 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 27
54261250 ATATTGAGCC
* *
54261260 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
54261287 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
54261314 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
54261342 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
54261369 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
54261396 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
54261423 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54261438 GTACAATTTA
Statistics
Matches: 127, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
27 102 0.80
28 25 0.20
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:54261399 original size:82 final size:81
Alignment explanation
Indices: 54261281--54261436 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
54261271 TGCTATATAA
* * *
54261281 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTC-GAATCGCA
54261346 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54261363 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCA
54261427 CACTTAGTGC
65 CACTTAGTGC
54261437 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 19 0.29
82 47 0.71
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54276743 original size:27 final size:27
Alignment explanation
Indices: 54276712--54276889 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
54276702 TAAATTGTAC
54276712 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
54276739 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
54276765 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
54276793 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
54276821 AGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
54276848 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
54276875 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
54276890 GACTCGATAT
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 108 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:54276826 original size:82 final size:81
Alignment explanation
Indices: 54276713--54276868 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
54276703 AAATTGTACA
*
54276713 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTA-GCACTAAGTG
54276777 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
54276794 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTG
*
54276859 TGCGAGTTGA
65 TGCGAATTGA
54276869 TTATATAGCA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 15 0.22
82 52 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:54276880 original size:82 final size:81
Alignment explanation
Indices: 54276709--54276889 Score: 238
Period size: 82 Copynumber: 2.2 Consensus size: 81
54276699 GATTAAATTG
*
54276709 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
54276774 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
54276790 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGAT-GCACT
* **
54276854 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
54276872 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
54276890 GACTCGATAT
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 18 0.21
82 67 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:54284772 original size:27 final size:27
Alignment explanation
Indices: 54284742--54284917 Score: 201
Period size: 27 Copynumber: 6.5 Consensus size: 27
54284732 AAATTGTACA
54284742 GCACTAAGTGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTT
** * *
54284769 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGATTTGACTATGTT
* * **
54284796 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGTT
54284823 GCACTAAGTGTGCGAGTTTGACTATG-T
1 GCACTAAGTGTGCGA-TTTGACTATGTT
* *
54284850 GCACTAAGTGTGCGATTTGATTATGTA
1 GCACTAAGTGTGCGATTTGACTATGTT
* * * *
54284877 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGATTTGACTATGTT
*
54284904 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
54284918 GACTCGATAT
Statistics
Matches: 130, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
26 9 0.07
27 113 0.87
28 8 0.06
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGTT
Found at i:54284853 original size:81 final size:81
Alignment explanation
Indices: 54284742--54284896 Score: 242
Period size: 81 Copynumber: 1.9 Consensus size: 81
54284732 AAATTGTACA
54284742 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGTA-GCACTAAGTG
54284806 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
54284823 GCACTAAGTGTGCGAGTTTGACTATG-TGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTG
*
54284887 TGCGAGTTGA
65 TGCGAATTGA
54284897 TTATATAGCA
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
81 57 0.84
82 11 0.16
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:54284908 original size:81 final size:81
Alignment explanation
Indices: 54284738--54284917 Score: 238
Period size: 81 Copynumber: 2.2 Consensus size: 81
54284728 GATTAAATTG
54284738 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
54284803 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
54284819 TGCGGCACTAAGTGTGCGAGTTTGACTATG-TGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACT
* **
54284882 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
54284900 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
54284918 GACTCGATAT
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
80 1 0.01
81 74 0.87
82 10 0.12
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.31
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:54292781 original size:27 final size:26
Alignment explanation
Indices: 54292750--54292927 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 26
54292740 TAAATTGTAC
54292750 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
54292777 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
54292803 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
54292831 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
54292859 GGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
54292886 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
54292913 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
54292928 GACTCGATAT
Statistics
Matches: 131, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.01
27 104 0.79
28 26 0.20
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:54292866 original size:82 final size:81
Alignment explanation
Indices: 54292751--54292906 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54292741 AAATTGTACA
*
54292751 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGTA-GCACTAAGTG
54292815 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
54292832 GCACTAAGTGTGCGAGTTTGACTATGTGGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTG
*
54292897 TGCGAGTTGA
65 TGCGAATTGA
54292907 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:54292918 original size:82 final size:81
Alignment explanation
Indices: 54292747--54292927 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
54292737 GATTAAATTG
*
54292747 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGATGCACTAA
54292812 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
54292828 TGCGGCACTAAGTGTGCGAGTTTGACTATGTGGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGAT-GCACT
* **
54292892 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
54292910 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
54292928 GACTCGATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:54294916 original size:36 final size:36
Alignment explanation
Indices: 54294869--54294942 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
54294859 TTGAATCAGT
54294869 ATCCTGGGATATCAAAACAAGAATTAAGAACACATA
1 ATCCTGGGATATCAAAACAAGAATTAAGAACACATA
54294905 ATCCTGGGATATCAAAACAAGAATTAAGAACACATA
1 ATCCTGGGATATCAAAACAAGAATTAAGAACACATA
54294941 AT
1 AT
54294943 TAAGAACAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (36 bp):
ATCCTGGGATATCAAAACAAGAATTAAGAACACATA
Found at i:54298423 original size:21 final size:21
Alignment explanation
Indices: 54298397--54298436 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54298387 TAATATAAAC
54298397 AATAATAGTAATAGATAAATG
1 AATAATAGTAATAGATAAATG
* *
54298418 AATAATAGTGATAGGTAAA
1 AATAATAGTAATAGATAAA
54298437 CAAATTCGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (21 bp):
AATAATAGTAATAGATAAATG
Found at i:54299535 original size:40 final size:39
Alignment explanation
Indices: 54299480--54299638 Score: 212
Period size: 40 Copynumber: 4.0 Consensus size: 39
54299470 CCGAATCCAG
* * *
54299480 TTACTAGCACAAAGCCTGCGGGACTTTAGGCCCGGATATA-
1 TTACCAGCACGAAGCCTGCGGGA-TTTA-ACCCGGATATAC
* *
54299520 GTACCAGCACTAAGCCTGCGGGATTTAACCCGGATATAC
1 TTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAC
*
54299559 TTTACCAGCACGAAGCCTGCGGGCTTTAACCCGGATATAC
1 -TTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAC
*
54299599 TTTACCAGCACGAAGCCTGCAGGATTTAACCCGGATATAC
1 -TTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAC
54299639 AATATAGCGA
Statistics
Matches: 108, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
38 10 0.09
39 4 0.04
40 94 0.87
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.22
Consensus pattern (39 bp):
TTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAC
Found at i:54302105 original size:13 final size:13
Alignment explanation
Indices: 54302087--54302111 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54302077 TGTGGGTGCA
54302087 CACGGCCATGTCG
1 CACGGCCATGTCG
54302100 CACGGCCATGTC
1 CACGGCCATGTC
54302112 TGGCGTTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.28, T:0.16
Consensus pattern (13 bp):
CACGGCCATGTCG
Found at i:54308490 original size:42 final size:42
Alignment explanation
Indices: 54308429--54308595 Score: 226
Period size: 42 Copynumber: 4.0 Consensus size: 42
54308419 GAAAATATTT
*
54308429 GAGATAGCTTCGACTATGCATTGGCACTTAGTGTGCAAGATC
1 GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCAAGATC
* *
54308471 GGGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCGAGATC
1 GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCAAGATC
* * * ** *
54308513 AAGATAGCTTCAGCTATGCATTGGCACTTAGTATGCGTGATT
1 GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCAAGATC
* * *
54308555 GAGTTAGCTTCGGCTACGTATTGGCACTTAGTGTGCAAGAT
1 GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCAAGAT
54308596 TCCCGAGTAA
Statistics
Matches: 108, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 108 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (42 bp):
GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCAAGATC
Found at i:54308727 original size:32 final size:32
Alignment explanation
Indices: 54308665--54308727 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
54308655 TATGAGATTG
* * *
54308665 GTACGATATGGTACAAGTATGTATGGAAATTT
1 GTACGAGATGGTACAAGTATGTACGAAAATTT
*
54308697 GTACGAGATGGTACAGGTATGTACGAAAATT
1 GTACGAGATGGTACAAGTATGTACGAAAATT
54308728 CAATTGAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.30
Consensus pattern (32 bp):
GTACGAGATGGTACAAGTATGTACGAAAATTT
Found at i:54312436 original size:19 final size:20
Alignment explanation
Indices: 54312409--54312448 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
54312399 ATGATTATGT
*
54312409 CAATGCATATTTTGT-AAAA
1 CAATACATATTTTGTGAAAA
54312428 CAATACATATTTTGTGAAAA
1 CAATACATATTTTGTGAAAA
54312448 C
1 C
54312449 GGACCTACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (20 bp):
CAATACATATTTTGTGAAAA
Found at i:54312647 original size:49 final size:51
Alignment explanation
Indices: 54312514--54312654 Score: 196
Period size: 51 Copynumber: 2.8 Consensus size: 51
54312504 CTAAACACCA
* *
54312514 TTTGTGGACAAGCTACCACTGATTTGCAGATAAATTGCCAGTGATAACACT
1 TTTGTGGACAAGCTACCACTGATTTGCAGATATATTGCCACTGATAACACT
* * * *
54312565 TTTGTAGACAAGCCACCATTGATATGCAGATATATTGCCACTGATAA-A-T
1 TTTGTGGACAAGCTACCACTGATTTGCAGATATATTGCCACTGATAACACT
* *
54312614 TTTGTGGACAAGCTACCACTGATTTGCAAATATACTGCCAC
1 TTTGTGGACAAGCTACCACTGATTTGCAGATATATTGCCAC
54312655 AGCTTCAACC
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 36 0.46
50 1 0.01
51 41 0.53
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (51 bp):
TTTGTGGACAAGCTACCACTGATTTGCAGATATATTGCCACTGATAACACT
Found at i:54316132 original size:46 final size:46
Alignment explanation
Indices: 54315964--54316141 Score: 157
Period size: 46 Copynumber: 3.8 Consensus size: 46
54315954 TGTAACCCAC
* * *
54315964 CCATAAGCGAACTCAGACTCAACTCAATGAGATCGGGTGTTCCCA-T
1 CCATAAGCGAACTCAGACTCAACTCAACGAGTTCGGATGTT-CCATT
* *
54316010 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATG--CCTAGTT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGTTCGGATGTTCC-A-TT
* * * * * *
54316056 ACATCTCA-CAAACTCGGACTCAACTCAACGAGTTCGGACGTTCGATT
1 CCA--TAAGCGAACTCAGACTCAACTCAACGAGTTCGGATGTTCCATT
* * *
54316103 CCATAAGTGAACTCGGACTCAACTCAACGAGTTAGGATG
1 CCATAAGCGAACTCAGACTCAACTCAACGAGTTCGGATG
54316142 CCCAAATATC
Statistics
Matches: 106, Mismatches: 18, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
43 2 0.02
44 1 0.01
45 2 0.02
46 66 0.62
47 31 0.29
48 3 0.03
49 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCAGACTCAACTCAACGAGTTCGGATGTTCCATT
Found at i:54316132 original size:93 final size:93
Alignment explanation
Indices: 54315973--54316143 Score: 245
Period size: 93 Copynumber: 1.8 Consensus size: 93
54315963 CCCATAAGCG
* **
54315973 AACTCAGACTCAACTCAATGAGATCGGGTGTTCCCATCCATAAGTGAACTCAGACTCAACTCAAC
1 AACTCAGACTCAACTCAACGAGATCGGACGTTCCCATCCATAAGTGAACTCAGACTCAACTCAAC
*
54316038 GAGCTCGGATGCCTAGTTACATCTCACA
66 GAGCTAGGATGCCTAGTTACATCTCACA
* * * *
54316066 AACTCGGACTCAACTCAACGAGTTCGGACGTT-CGATTCCATAAGTGAACTCGGACTCAACTCAA
1 AACTCAGACTCAACTCAACGAGATCGGACGTTCCCA-TCCATAAGTGAACTCAGACTCAACTCAA
*
54316130 CGAGTTAGGATGCC
65 CGAGCTAGGATGCC
54316144 CAAATATCCG
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
92 2 0.03
93 66 0.97
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (93 bp):
AACTCAGACTCAACTCAACGAGATCGGACGTTCCCATCCATAAGTGAACTCAGACTCAACTCAAC
GAGCTAGGATGCCTAGTTACATCTCACA
Found at i:54318915 original size:30 final size:29
Alignment explanation
Indices: 54318873--54318929 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
54318863 AAAGATAACA
54318873 AGAAAACCGAATAAAGAAATCCAAGATTG
1 AGAAAACCGAATAAAGAAATCCAAGATTG
*
54318902 AGAAACCCAGAATAAAGAAATCCAAGAT
1 AGAAAACC-GAATAAAGAAATCCAAGAT
54318930 ACGATACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.56, C:0.16, G:0.16, T:0.12
Consensus pattern (29 bp):
AGAAAACCGAATAAAGAAATCCAAGATTG
Found at i:54334379 original size:20 final size:19
Alignment explanation
Indices: 54334333--54334370 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
54334323 ATATTAATAC
54334333 ATTTTTATATAAAATTTAA
1 ATTTTTATATAAAATTTAA
54334352 ATATTTTA-ACTAAAATTTA
1 AT-TTTTATA-TAAAATTTA
54334371 TTATTTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTTTATATAAAATTTAA
Found at i:54338186 original size:3 final size:3
Alignment explanation
Indices: 54338178--54338207 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
54338168 TATGAGTGGT
54338178 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54338208 GAAAAACTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:54339362 original size:3 final size:3
Alignment explanation
Indices: 54339356--54339389 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
54339346 CTCTATTTTT
54339356 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
54339390 GAGATAAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:54341784 original size:16 final size:16
Alignment explanation
Indices: 54341763--54341799 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
54341753 ATAGTGAATG
54341763 AATGCTCATAGTTATA
1 AATGCTCATAGTTATA
54341779 AATGCTCATAGTTATA
1 AATGCTCATAGTTATA
54341795 AATGC
1 AATGC
54341800 ATTTGTAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (16 bp):
AATGCTCATAGTTATA
Found at i:54352808 original size:30 final size:30
Alignment explanation
Indices: 54352774--54352834 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
54352764 TCCTTAACTC
54352774 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
54352804 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
54352834 A
1 A
54352835 GGCTTGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:54360982 original size:61 final size:58
Alignment explanation
Indices: 54360887--54361028 Score: 230
Period size: 61 Copynumber: 2.4 Consensus size: 58
54360877 GAAAATGGTT
*
54360887 TTAATTTGATTGAACCACTTATAATTAACATGTCTTGTATCAATCTCATACATATCCATAA
1 TTAATTTGATTGAACCACTTATAATTAACATGTCTTGTATCAATCTCATACACAT--AT-A
* *
54360948 TTAATTTGATTGAACCACTTATAATTAACATGTCTTGTATCAATCTCATACACATGTT
1 TTAATTTGATTGAACCACTTATAATTAACATGTCTTGTATCAATCTCATACACATATA
54361006 TTAATTTGATTGAACCACTTATA
1 TTAATTTGATTGAACCACTTATA
54361029 TGATTCAACC
Statistics
Matches: 78, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
58 23 0.29
59 1 0.01
61 54 0.69
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.41
Consensus pattern (58 bp):
TTAATTTGATTGAACCACTTATAATTAACATGTCTTGTATCAATCTCATACACATATA
Found at i:54376313 original size:27 final size:27
Alignment explanation
Indices: 54376283--54376460 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
54376273 ATATTGAGCC
* *
54376283 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
54376310 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
54376337 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
54376365 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
54376392 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
54376419 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
54376446 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54376461 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:54376395 original size:55 final size:54
Alignment explanation
Indices: 54376283--54376460 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
54376273 ATATTGAGCC
* * * * *
54376283 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
54376337 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
54376392 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
54376446 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54376461 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:54379050 original size:15 final size:15
Alignment explanation
Indices: 54379030--54379062 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
54379020 TTATTTATTT
54379030 TATATAATA-ATATAA
1 TATATAATATA-ATAA
54379045 TATATAATATAATAA
1 TATATAATATAATAA
54379060 TAT
1 TAT
54379063 TAAATATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.94
16 1 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TATATAATATAATAA
Found at i:54381761 original size:21 final size:20
Alignment explanation
Indices: 54381714--54381777 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
54381704 CCAATTATTC
*
54381714 CATAAATCAATAATAATTAATA
1 CATAAAT-AAT-ATAATTAAAA
*
54381736 TATAAATAATATAATTAAAAA
1 CATAAATAATATAATT-AAAA
*
54381757 CATAAATAACATAATTCAAAA
1 CATAAATAATATAATT-AAAA
54381778 GAAGAAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.17
21 24 0.67
22 6 0.17
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (20 bp):
CATAAATAATATAATTAAAA
Found at i:54384314 original size:38 final size:38
Alignment explanation
Indices: 54384265--54384340 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
54384255 CAAGTTAGTG
54384265 GTGGCATGATTTCGTTGAAATTAGTATATAAGTGTATA
1 GTGGCATGATTTCGTTGAAATTAGTATATAAGTGTATA
54384303 GTGGCATGATTTCGTTGAAATTAGTATATAAGTGTATA
1 GTGGCATGATTTCGTTGAAATTAGTATATAAGTGTATA
54384341 TTAGGATCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (38 bp):
GTGGCATGATTTCGTTGAAATTAGTATATAAGTGTATA
Found at i:54384721 original size:33 final size:35
Alignment explanation
Indices: 54384655--54384732 Score: 108
Period size: 33 Copynumber: 2.3 Consensus size: 35
54384645 GACGGCAGCA
* * *
54384655 ATTAGAGTTTTACTTTTATTTATTTTCTTTATTAT
1 ATTAGAGTTTTACGTTTACTTATTTTCTCTATTAT
54384690 A-TAGAGTTTTA-GTTTACTTATTTTCTCTATTAT
1 ATTAGAGTTTTACGTTTACTTATTTTCTCTATTAT
54384723 ATTA-AGTTTT
1 ATTAGAGTTTT
54384733 TATTTCCTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
33 26 0.67
34 12 0.31
35 1 0.03
ACGTcount: A:0.24, C:0.06, G:0.08, T:0.62
Consensus pattern (35 bp):
ATTAGAGTTTTACGTTTACTTATTTTCTCTATTAT
Found at i:54393202 original size:25 final size:25
Alignment explanation
Indices: 54393161--54393210 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
54393151 TTTTAAAAAA
* *
54393161 TAAATATATTAATTTATTTTTATAT
1 TAAATAAATTAATTTATTTGTATAT
54393186 TAAATAAATATAA-TTATTTGTATAT
1 TAAATAAAT-TAATTTATTTGTATAT
54393211 ATAATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TAAATAAATTAATTTATTTGTATAT
Found at i:54393213 original size:29 final size:29
Alignment explanation
Indices: 54393158--54393213 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
54393148 ATGTTTTAAA
* *
54393158 AAATAAATATATTAATTTATTTTTATATT
1 AAATAAATATATTAATTTATATATATATT
*
54393187 AAATAAATATAATT-ATTTGTATATATA
1 AAATAAATAT-ATTAATTTATATATATA
54393214 ATATATAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
AAATAAATATATTAATTTATATATATATT
Found at i:54394104 original size:42 final size:42
Alignment explanation
Indices: 54394045--54394128 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
54394035 AAATTTTTGA
* *
54394045 ATAAAGAGTGTAAATTGCAATCTATCTTCTAGTACATGGGGC
1 ATAAAGAGTGTAAATTGCAATCTATCTTCTAATACATAGGGC
54394087 ATAAAGAGTGTAAATTGCAATCTATCTTCTAATACATAGGGC
1 ATAAAGAGTGTAAATTGCAATCTATCTTCTAATACATAGGGC
54394129 CTCCATGATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (42 bp):
ATAAAGAGTGTAAATTGCAATCTATCTTCTAATACATAGGGC
Found at i:54402410 original size:79 final size:80
Alignment explanation
Indices: 54402274--54402465 Score: 230
Period size: 79 Copynumber: 2.4 Consensus size: 80
54402264 TTGAATGATG
* * *
54402274 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTAC-GAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
54402338 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * **
54402353 TTCCGGGCTAAG-CCCGAAGGCATTTGTACGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
*
54402416 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* * *
54402433 ACCGGGCTATGTCCCGAAGGCATTTGAACGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGT
54402466 AGCTATATCT
Statistics
Matches: 97, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.60
80 38 0.39
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTATA
Found at i:54402472 original size:40 final size:41
Alignment explanation
Indices: 54402274--54402465 Score: 209
Period size: 40 Copynumber: 4.8 Consensus size: 41
54402264 TTGAATGATG
* * * *
54402274 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAT-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTAC-GAGTTACTATAA
* * * *
54402314 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-AT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTACGAGTTACTATAA
54402354 TCCGGGCTAAG-CCCGAAGGCATTTGTACGAGTTACTA-AA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAA
* *
54402393 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAA
* *
54402434 -CCGGGCTATGTCCCGAAGGCATTTGAACGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGT
54402466 AGCTATATCT
Statistics
Matches: 130, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
39 34 0.26
40 86 0.66
41 10 0.08
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAA
Found at i:54402480 original size:79 final size:79
Alignment explanation
Indices: 54402327--54402491 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
54402317 GGACTAAGAT
* *
54402327 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTACGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
54402392 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
54402406 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* * *
54402469 TATAT-CTGGTTAAATT
63 TAAATCCGGGTTAAATC
54402485 CCGAAGG
1 CCGAAGG
54402492 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 49 0.65
80 24 0.32
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:54410478 original size:40 final size:40
Alignment explanation
Indices: 54410240--54410464 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
54410230 TTGAATGATG
* * * * *
54410240 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * * *
54410280 TCCGGACTAAGAT-CCGAAGGCATTTGTGTGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
54410320 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
54410359 TCCAGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
54410399 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
54410440 -CCGGGTTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
54410465 AACGAGTAGC
Statistics
Matches: 164, Mismatches: 16, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
39 33 0.20
40 122 0.74
41 9 0.05
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54410486 original size:119 final size:119
Alignment explanation
Indices: 54410247--54410487 Score: 276
Period size: 119 Copynumber: 2.0 Consensus size: 119
54410237 ATGTCCGGGC
* *
54410247 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGTGAG
1 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
* **
54410312 ATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCAGGT
66 ATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAATCCAGGT
* * * **
54410366 TAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGTGCG
1 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATTTGTGCG
* * * *
54410429 AGTTACT-ATAACCGGGTTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGT
64 AGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-CTAAATCCAGGT
54410485 TAA
1 TAA
54410488 ATTCTGAAGG
Statistics
Matches: 103, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
118 3 0.03
119 68 0.66
120 32 0.31
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (119 bp):
TAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
ATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAATCCAGGT
Found at i:54412046 original size:16 final size:17
Alignment explanation
Indices: 54412015--54412047 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54412005 TTCATAAGTA
54412015 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
54412032 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
54412048 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:54412393 original size:46 final size:46
Alignment explanation
Indices: 54412328--54413152 Score: 1231
Period size: 46 Copynumber: 18.0 Consensus size: 46
54412318 TTATCTTTGA
* * * * * *
54412328 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
* *** *
54412374 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* ** ** ***
54412420 TACATTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
54412465 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
54412511 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
54412557 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
54412603 CCTATTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
54412649 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* * *
54412695 CCTGTTGCCGTGGTATCTTTCAACCATGGTCTTACATATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
54412741 CATGTTGCCGTGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
54412787 CCTGTTGCCGTGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
54412833 CGTGTTGCCGTGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
54412879 CATGTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* * *
54412925 CCTGTTGCCATGGTGTCTTTCAACCACGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
54412971 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
54413017 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
54413063 CCTGTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
54413109 CATGTTGCCATGGTGTCTTTCAACCATGATCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
54413153 TTCAGAAAGC
Statistics
Matches: 719, Mismatches: 58, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
45 42 0.06
46 677 0.94
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:54417217 original size:21 final size:24
Alignment explanation
Indices: 54417169--54417217 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 24
54417159 CTAAATAGGA
*
54417169 AACTCATAAGAGTTTTAATCAGGG
1 AACTCATAAGAGTCTTAATCAGGG
*
54417193 AACTCAT-AGAG-CTTAA-CAGGT
1 AACTCATAAGAGTCTTAATCAGGG
54417214 AACT
1 AACT
54417218 TCGAATAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.35
22 4 0.17
23 4 0.17
24 7 0.30
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (24 bp):
AACTCATAAGAGTCTTAATCAGGG
Found at i:54420861 original size:40 final size:40
Alignment explanation
Indices: 54420806--54420889 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
54420796 AATTGAATTT
54420806 ATGAAAGAATAATTTATGAGTTAAAGGAGCTCATTAAAAC
1 ATGAAAGAATAATTTATGAGTTAAAGGAGCTCATTAAAAC
54420846 ATGAAAGAATAATTTATGAGTTAAAGGAGCTCATTAAAAC
1 ATGAAAGAATAATTTATGAGTTAAAGGAGCTCATTAAAAC
54420886 ATGA
1 ATGA
54420890 TATTCAATCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (40 bp):
ATGAAAGAATAATTTATGAGTTAAAGGAGCTCATTAAAAC
Found at i:54430032 original size:184 final size:184
Alignment explanation
Indices: 54429695--54430049 Score: 419
Period size: 184 Copynumber: 1.9 Consensus size: 184
54429685 AAGAATAAAC
* * * *
54429695 TATAACGGTAACAACTAGAGTAATCCGAGGAGGATACGGCAGTCCCAGATTTAAATAATATTTTA
1 TATAACGGTAACAACTAAAGTAATCCAAGGAGGATACGGCAGTCCCAGAATTAAATAATAGTTTA
* * * *
54429760 CTCAAAGTCATGTAGAAAACAAATCCATGTATTTAAAAGGTCCTAATTCTCCCAATCATAATCAG
66 CACAAAGTCATGTAGAAAACAAATCCAAGTATTTAAAAGATCCTAATTCTCCCAATCATAACCAG
* * *
54429825 GTCCAAAATGTATGGAAAAATATATTTCCCCCTAATCATATCAAATAATAAAGT
131 GGCCAAAATCTAAGGAAAAATATATTTCCCCCTAATCATATCAAATAATAAAGT
* * * * *
54429879 TATAATGGTAACAATTAAAGTATTCCAAGGAGGATAGGGC-GTTCCAGAATTAAATAAT-GTTTA
1 TATAACGGTAACAACTAAAGTAATCCAAGGAGGATACGGCAGTCCCAGAATTAAATAATAGTTTA
* * * * **
54429942 GACAAAGTCACATGTAG-TAACAAATCCAAGTATTTAACAGAATCTTAATTCTCCTTATCATAAC
66 CACAAAGT--CATGTAGAAAACAAATCCAAGTATTTAAAAG-ATCCTAATTCTCCCAATCATAAC
* ** * *
54430006 CAGGGCTAAAATCTAAGGTCAAATATATTTTCTCCTAATCATAT
128 CAGGGCCAAAATCTAAGGAAAAATATATTTCCCCCTAATCATAT
54430050 TGAACATTTG
Statistics
Matches: 141, Mismatches: 27, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
182 10 0.07
183 36 0.26
184 95 0.67
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (184 bp):
TATAACGGTAACAACTAAAGTAATCCAAGGAGGATACGGCAGTCCCAGAATTAAATAATAGTTTA
CACAAAGTCATGTAGAAAACAAATCCAAGTATTTAAAAGATCCTAATTCTCCCAATCATAACCAG
GGCCAAAATCTAAGGAAAAATATATTTCCCCCTAATCATATCAAATAATAAAGT
Found at i:54435246 original size:47 final size:46
Alignment explanation
Indices: 54435160--54435259 Score: 116
Period size: 47 Copynumber: 2.2 Consensus size: 46
54435150 TATCTTAATC
*
54435160 TAAGACACATTAAAAAGTTGTACCTATTATAACATATTAATTAAACT
1 TAAGACACATTAAAAAGTTGTACCTAATATAACATATTAA-TAAACT
* *
54435207 TAAGACACATTAAAATGCTT-TA-CTAAT-TAACATGCATTAATAGACT
1 TAAGACACATTAAAAAG-TTGTACCTAATATAACAT--ATTAATAAACT
54435253 TAAGACA
1 TAAGACA
54435260 TATTTAAGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
45 6 0.13
46 16 0.34
47 23 0.49
48 2 0.04
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (46 bp):
TAAGACACATTAAAAAGTTGTACCTAATATAACATATTAATAAACT
Found at i:54437019 original size:10 final size:9
Alignment explanation
Indices: 54436997--54437032 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
54436987 TAGGTTTTTT
54436997 GGTTGTTTAG
1 GGTT-TTTAG
54437007 GGTTTTTAG
1 GGTTTTTAG
*
54437016 GGGTTTTAG
1 GGTTTTTAG
54437025 GGTTTTTA
1 GGTTTTTA
54437033 ATTGATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 20 0.83
10 4 0.17
ACGTcount: A:0.11, C:0.00, G:0.36, T:0.53
Consensus pattern (9 bp):
GGTTTTTAG
Found at i:54438812 original size:16 final size:16
Alignment explanation
Indices: 54438791--54438821 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54438781 TTCACTATTA
*
54438791 TGTCTTTCGTATTTTC
1 TGTCTTTCATATTTTC
54438807 TGTCTTTCATATTTT
1 TGTCTTTCATATTTT
54438822 GCATGAATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.16, G:0.10, T:0.65
Consensus pattern (16 bp):
TGTCTTTCATATTTTC
Done.