Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 144 of 276
Found at i:46960107 original size:79 final size:79
Alignment explanation
Indices: 46959942--46960118 Score: 252
Period size: 79 Copynumber: 2.2 Consensus size: 79
46959932 CGGATGATAA
* * *
46959942 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCATTTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCATTTGA
46960007 GCGAGTTACTATAT
66 GCGAGTTACTATAT
*
46960021 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAG-CCCGAAGGCATTT
46960085 GAGCGAG-TAGCTATAT
64 GAGCGAGTTA-CTATAT
* *
46960101 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
46960119 TACTTGGTTT
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
78 2 0.02
79 60 0.67
80 27 0.30
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCATTTGA
GCGAGTTACTATAT
Found at i:46966877 original size:42 final size:42
Alignment explanation
Indices: 46966838--46966920 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
46966828 TCATGTTCGG
46966838 TTGGTTGGTTTTTTAGGAGGAGGTATATTTGATGTTGTTCCA
1 TTGGTTGGTTTTTTAGGAGGAGGTATATTTGATGTTGTTCCA
*
46966880 TTGGTTGGTTTTTTAGGAGGAGGTATGTTTGATGTTGTTCC
1 TTGGTTGGTTTTTTAGGAGGAGGTATATTTGATGTTGTTCC
46966921 GTGAGATTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.14, C:0.05, G:0.33, T:0.48
Consensus pattern (42 bp):
TTGGTTGGTTTTTTAGGAGGAGGTATATTTGATGTTGTTCCA
Found at i:46972555 original size:24 final size:24
Alignment explanation
Indices: 46972528--46972573 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
46972518 AGTAACAGTT
*
46972528 GGGCCT-AGCCCATTAACAGAATCA
1 GGGCCTAAGCCCAAT-ACAGAATCA
46972552 GGGCCTAAGCCCAATACAGAAT
1 GGGCCTAAGCCCAATACAGAAT
46972574 GAATATCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.35, C:0.28, G:0.22, T:0.15
Consensus pattern (24 bp):
GGGCCTAAGCCCAATACAGAATCA
Found at i:46978483 original size:41 final size:42
Alignment explanation
Indices: 46978321--46978471 Score: 207
Period size: 42 Copynumber: 3.6 Consensus size: 42
46978311 TAATAGTGAT
*
46978321 ATATCAGGCTTATTGCCTAACAGGCTTTGATGCCGGTGTATG
1 ATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCGGTGTATG
* * *
46978363 ATATTAGGCTTATTGCCTAGCAGGATTTGATGCTGGTGTATG
1 ATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCGGTGTATG
* *
46978405 ATATCAGGTTTATTGCCTAGTAGGCTTT-ATGCCGGTGTATTG
1 ATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCGGTGTA-TG
* *
46978447 A-ATCAGGTTTATTACCTAGCAGGCT
1 ATATCAGGCTTATTGCCTAGCAGGCT
46978472 CTATGTCGGT
Statistics
Matches: 97, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
41 32 0.33
42 65 0.67
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (42 bp):
ATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCGGTGTATG
Found at i:46978500 original size:83 final size:85
Alignment explanation
Indices: 46978321--46978506 Score: 208
Period size: 83 Copynumber: 2.2 Consensus size: 85
46978311 TAATAGTGAT
* *
46978321 ATATCAGGC-TTATTGCCTAACAGGCTTTGATGCCGGTGTATGATATTAGGCTTATTGCCTAGCA
1 ATATCAGGCTTTATTGCCTAACAGGCTTTGATGCCGGTGTATGATATCAGGCTTATTACCTAGCA
*
46978385 GGATTTGATGCTGGTGTATG
66 GGATCTGATGCTGGTGTATG
** *
46978405 ATATCAGG-TTTATTGCCTAGTAGGCTTT-ATGCCGGTGTATTGA-ATCAGGTTTATTACCTAGC
1 ATATCAGGCTTTATTGCCTAACAGGCTTTGATGCCGGTGTA-TGATATCAGGCTTATTACCTAGC
* * *
46978467 AGGCTCT-ATG-TCGGTGTTTT
65 AGGATCTGATGCT-GGTGTATG
46978487 ATA-CAAGGCTTTA-TGCCTAA
1 ATATC-AGGCTTTATTGCCTAA
46978507 TGAATTTTAT
Statistics
Matches: 87, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
81 2 0.02
82 21 0.24
83 36 0.41
84 28 0.32
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (85 bp):
ATATCAGGCTTTATTGCCTAACAGGCTTTGATGCCGGTGTATGATATCAGGCTTATTACCTAGCA
GGATCTGATGCTGGTGTATG
Found at i:46981151 original size:34 final size:34
Alignment explanation
Indices: 46981077--46981164 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 34
46981067 ACTGTACTGA
* * * *
46981077 TACTGGAATGGGCTTAGGCCC-CACTGATACTAT
1 TACTGAAATGAGCTAAGGCCCAGACTGATACTAT
* *
46981110 TACTGAAATGAGCTCAGGCCCAGACTGTTACTAT
1 TACTGAAATGAGCTAAGGCCCAGACTGATACTAT
*
46981144 TATTGAAATGAGCTAAGGCCC
1 TACTGAAATGAGCTAAGGCCC
46981165 TAACTGAGAC
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 18 0.38
34 29 0.62
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (34 bp):
TACTGAAATGAGCTAAGGCCCAGACTGATACTAT
Found at i:46987927 original size:40 final size:39
Alignment explanation
Indices: 46987883--46988107 Score: 263
Period size: 40 Copynumber: 5.7 Consensus size: 39
46987873 GCCACTAGCT
*
46987883 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
**
46987923 CAAATGCCTTCGGGACTTAGCCCGGTATAACAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* * *
46987962 CAAATGCCTTCGGGACTTAGCCCGGACATAATAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * *
46988002 CAAACGCCTTCGGGACTTAGCCTGGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * ** * *
46988042 CAAATGCCTTCGGGACTTAGCCTGGAATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
46988082 CAAATG-CTCTCGGGACTTAGCCCGGT
1 CAAATGCCT-TCGGGACTTAGCCCGGT
46988108 TATCATCCGA
Statistics
Matches: 163, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
39 39 0.24
40 124 0.76
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:46987981 original size:79 final size:78
Alignment explanation
Indices: 46987883--46988107 Score: 272
Period size: 79 Copynumber: 2.8 Consensus size: 78
46987873 GCCACTAGCT
* *
46987883 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG-AATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
46987948 TATAACAACTCGCA
65 TATAACAACTCGCA
* * * * *
46987962 CAAATGCCTTCGGGACTTAGCCCGGACATAATAGCTCGCACAAACGCCTTCGGGACTTAGCCTGG
1 CAAATGCCTTCGGGACTTAGCCCGGA-ATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
** *
46988027 ATATAGTAGCTCGCA
65 -TATAACAACTCGCA
* ** *
46988042 CAAATGCCTTCGGGACTTAGCCTGGAATTAGCCACTAGCTCAAATG-CTCTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAA-TAGTAACTAGCACAAATGCCT-TCGGGACTTAGCCCG
46988106 GT
64 GT
46988108 TATCATCCGA
Statistics
Matches: 124, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
79 62 0.50
80 62 0.50
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGT
ATAACAACTCGCA
Found at i:46996111 original size:40 final size:40
Alignment explanation
Indices: 46996067--46996250 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
46996057 GCCACTAGCT
* *
46996067 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTACCTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTACCTCGCA
* * * * *
46996107 CAAATGCCTTCGGGACTTAGCCCAGACATAATAGCTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTACCTCGCA
* *
46996147 CAAACGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTACCTCGCA
* * *
46996187 CAAATGCCTT-GGGACTTAGCCCGGA-ATTAG-CCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAC-CTCGCA
46996226 CAAATG-CTCTCGGGACTTAGCCCGG
1 CAAATGCCT-TCGGGACTTAGCCCGG
46996251 TTATCATCTG
Statistics
Matches: 123, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
38 3 0.02
39 29 0.24
40 91 0.74
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTACCTCGCA
Found at i:46999758 original size:23 final size:23
Alignment explanation
Indices: 46999728--46999771 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
46999718 AATTTAGTAA
46999728 CTATAATAACTATCGTTATAGCC
1 CTATAATAACTATCGTTATAGCC
*
46999751 CTATAATAACTATCTTTATAG
1 CTATAATAACTATCGTTATAG
46999772 AAATTTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (23 bp):
CTATAATAACTATCGTTATAGCC
Found at i:47003916 original size:37 final size:37
Alignment explanation
Indices: 47003857--47003965 Score: 184
Period size: 37 Copynumber: 2.9 Consensus size: 37
47003847 AGCTCAGATG
*
47003857 AAATCTCCACACG-AGGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTA-GTCATCGGGTCTTACCCGGACA
47003894 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
47003931 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
47003966 ATATATTTCC
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
37 68 0.99
38 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:47004166 original size:48 final size:48
Alignment explanation
Indices: 47004112--47004210 Score: 164
Period size: 48 Copynumber: 2.0 Consensus size: 48
47004102 GTACATCGCC
47004112 TACATATTTCACACTAGCCATTCGGCTTTACCAC-ATATGCATGTCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACAATATGCATGT-TCA
*
47004160 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACA-ATATGCATGTTCA
47004209 TA
1 TA
47004211 TTCATCACAT
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
48 33 0.69
49 5 0.10
50 10 0.21
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.35
Consensus pattern (48 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACAATATGCATGTTCA
Found at i:47004247 original size:47 final size:47
Alignment explanation
Indices: 47004128--47004332 Score: 245
Period size: 47 Copynumber: 4.3 Consensus size: 47
47004118 TTTCACACTA
* * *
47004128 GCCATTCGGCTTTA-C-CACATATGCATGTCTCATACATAT-TTCACATTA
1 GCCATTCGGCCTTATCACACATATGCATGT-TC--ACAT-TCATCACATTG
* * * *
47004176 GCCATTCGGCTTTACCACATATATGCATGTTCATATTCATCACATTG
1 GCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
*
47004223 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
** *
47004270 TTCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
*
47004317 GCCATTCGACCTTATC
1 GCCATTCGGCCTTATC
47004333 NNNNNNNNNN
Statistics
Matches: 138, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
46 1 0.01
47 108 0.78
48 14 0.10
49 3 0.02
50 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (47 bp):
GCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
Found at i:47004276 original size:94 final size:95
Alignment explanation
Indices: 47004128--47004332 Score: 276
Period size: 94 Copynumber: 2.2 Consensus size: 95
47004118 TTTCACACTA
* * *
47004128 GCCATTCGGCTTTA-CCACATATGCATGTCTCATACATATTTCACATTAGCCATTCGGCTTTACC
1 GCCATTCGGCCTTATCCACATATGCATGTCTCA-ACATATATCACATTAGCCATTCGGCCTTACC
*
47004192 ACATATATGCATGTTCATATTCATCACATTG
65 ACATATATGCATGTTCACATTCATCACATTG
*
47004223 GCCATTCGGCCTTATCACACATATGCATG-CTC-ACAT-TCATCACATT-GTTCATTCGGCCTTA
1 GCCATTCGGCCTTATC-CACATATGCATGTCTCAACATAT-ATCACATTAG-CCATTCGGCCTTA
*
47004284 TCACATATATGCATGTTCACATTCATCACATTG
63 CCACATATATGCATGTTCACATTCATCACATTG
*
47004317 GCCATTCGACCTTATC
1 GCCATTCGGCCTTATC
47004333 NNNNNNNNNN
Statistics
Matches: 99, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
93 2 0.02
94 68 0.69
95 13 0.13
96 4 0.04
97 12 0.12
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (95 bp):
GCCATTCGGCCTTATCCACATATGCATGTCTCAACATATATCACATTAGCCATTCGGCCTTACCA
CATATATGCATGTTCACATTCATCACATTG
Found at i:47007882 original size:40 final size:40
Alignment explanation
Indices: 47007850--47008240 Score: 559
Period size: 40 Copynumber: 9.8 Consensus size: 40
47007840 CCAGCATGAT
* * * *
47007850 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * * *
47007890 TGCT-TTCGGGGTTTAGCACGGATATATCACTAGCACGGA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * * * *
47007929 TGCTTTTCAGAACTTAGTCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
47007969 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
47008009 TGCTCTTCGAGACTTAGCCTGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
47008049 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
47008089 TGCTCTTCGGGACTTAGCTCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
47008129 TGCTCTTCGGGACTTAGCCCGGGTAAATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
47008169 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
47008209 TGCCCTTCGGGACTTAGCCCGGGTATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATACATCACT
47008241 CTCAATTCTC
Statistics
Matches: 314, Mismatches: 36, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
39 32 0.10
40 282 0.90
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:47008146 original size:23 final size:23
Alignment explanation
Indices: 47008040--47008146 Score: 58
Period size: 23 Copynumber: 5.2 Consensus size: 23
47008030 GATACATCAC
47008040 TAGCACGAATGCTCTTCGGGACT
1 TAGCACGAATGCTCTTCGGGACT
* * * *
47008063 TAGCCCGGAT-AT-ATC---AC-
1 TAGCACGAATGCTCTTCGGGACT
47008080 TAGCACGAATGCTCTTCGGGACT
1 TAGCACGAATGCTCTTCGGGACT
* * * *
47008103 TAGCTCGGAT--ACATC---AC-
1 TAGCACGAATGCTCTTCGGGACT
47008120 TAGCACGAATGCTCTTCGGGACT
1 TAGCACGAATGCTCTTCGGGACT
47008143 TAGC
1 TAGC
47008147 CCGGGTAAAT
Statistics
Matches: 56, Mismatches: 16, Indels: 24
0.58 0.17 0.25
Matches are distributed among these distances:
17 16 0.29
18 5 0.09
19 5 0.09
21 5 0.09
22 5 0.09
23 20 0.36
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (23 bp):
TAGCACGAATGCTCTTCGGGACT
Found at i:47009544 original size:37 final size:37
Alignment explanation
Indices: 47009494--47009606 Score: 199
Period size: 37 Copynumber: 3.1 Consensus size: 37
47009484 CTTTAGCTCA
* *
47009494 GACAAAATCTCCACACGAAGTTATCGGGTCTTACCCG
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
47009531 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
*
47009568 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
47009605 GA
1 GA
47009607 ATATATTTCC
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.22
Consensus pattern (37 bp):
GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
Found at i:47009807 original size:48 final size:48
Alignment explanation
Indices: 47009753--47009851 Score: 164
Period size: 48 Copynumber: 2.0 Consensus size: 48
47009743 GCACATCGCC
47009753 TACATATTTCACACTAGCCATTCGGCTTTACCAC-ATATGCATGTCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACAATATGCATGT-TCA
*
47009801 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACA-ATATGCATGTTCA
47009850 TA
1 TA
47009852 TTCATCACAT
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
48 33 0.69
49 5 0.10
50 10 0.21
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.35
Consensus pattern (48 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACAATATGCATGTTCA
Found at i:47010112 original size:56 final size:56
Alignment explanation
Indices: 47010021--47010137 Score: 207
Period size: 56 Copynumber: 2.1 Consensus size: 56
47010011 GACTTTGACT
* *
47010021 AATAAACTGTACTAATTGGCCCGACCAAAAATTCTAGAAAAAAATATGTAGATGGG
1 AATATACTGTACTAATTGGCACGACCAAAAATTCTAGAAAAAAATATGTAGATGGG
47010077 AATATACTGTACTAATTGGCACGACCAAAAATTCTAGAAAAAAATATGTAGATGGG
1 AATATACTGTACTAATTGGCACGACCAAAAATTCTAGAAAAAAATATGTAGATGGG
*
47010133 CATAT
1 AATAT
47010138 GAGTCTAGTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (56 bp):
AATATACTGTACTAATTGGCACGACCAAAAATTCTAGAAAAAAATATGTAGATGGG
Found at i:47016695 original size:48 final size:48
Alignment explanation
Indices: 47016618--47017085 Score: 398
Period size: 48 Copynumber: 9.8 Consensus size: 48
47016608 TGGTACATGT
* * * * *
47016618 GAGCCTGTGTAAGACCATGTTTGGAACATGGCATTGGCATTGTTATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTATTATGA
* * * * * * * * *
47016666 AAGCTAGTGTAAAACCATGTCTAGGACATGGCATCGGCCTCAATAGGT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTATTATGA
* * * *
47016714 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGTATTGTTGTGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTATTATGA
* ** * * * *
47016762 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATTAGCCTCAATATGT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTATTATGA
* * * *
47016810 GAGCCAGTGTACGACCATGTTTGGAACATGGCATCGGCATTGTTATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTATTATGA
* * * * * * **
47016858 GAGCTACTGTAAAACCATGTCTGGGACATGGGATCGGCCTCAATT-TCT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT-TATTATGA
* * *
47016906 GAGCCAGTGTAAGACCATGTTTTGAACATGGCATCGGCATTATTATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTATTATGA
* * * * * * * *
47016954 AAGCTAGTGTAAGACCATGTTTGGGACATGGCATTGGCCTCAATATGT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTATTATGA
* * * * * **
47017002 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATTGGCTTTGTTACAA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTATTATGA
* * *
47017050 AAACCATTGTAAGACCATGTCTGGGACATGGCATCG
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
47017086 ACATCTTACT
Statistics
Matches: 321, Mismatches: 97, Indels: 4
0.76 0.23 0.01
Matches are distributed among these distances:
47 3 0.01
48 316 0.98
49 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (48 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTATTATGA
Found at i:47016780 original size:96 final size:96
Alignment explanation
Indices: 47016614--47017085 Score: 683
Period size: 96 Copynumber: 4.9 Consensus size: 96
47016604 GTTATGGTAC
* * *
47016614 ATGTGAGCCTGTGTAAGACCATGTTTGGAACATGGCATTGGCATTGTTATGAAAGCTAGTGTAAA
1 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGAAAGCTAGTGTAAG
*
47016679 ACCATGTCTAGGACATGGCATCGGCCTCAAT
66 ACCATGTCTGGGACATGGCATCGGCCTCAAT
* * * * *
47016710 AGGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGTATTGTTGTGAGAGCTAGTGTAAG
1 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGAAAGCTAGTGTAAG
**
47016775 ACCATGTCTGGGACATGGCATTAGCCTCAAT
66 ACCATGTCTGGGACATGGCATCGGCCTCAAT
* * * *
47016806 ATGTGAGCCAGTGTACGACCATGTTTGGAACATGGCATCGGCATTGTTATGAGAGCTACTGTAAA
1 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGAAAGCTAGTGTAAG
*
47016871 ACCATGTCTGGGACATGGGATCGGCCTCAAT
66 ACCATGTCTGGGACATGGCATCGGCCTCAAT
* * * *
47016902 TTCTGAGCCAGTGTAAGACCATGTTTTGAACATGGCATCGGCATTATTATGAAAGCTAGTGTAAG
1 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGAAAGCTAGTGTAAG
* *
47016967 ACCATGTTTGGGACATGGCATTGGCCTCAAT
66 ACCATGTCTGGGACATGGCATCGGCCTCAAT
* * ** * * *
47016998 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATTGGCTTTGTTACAAAAACCATTGTAAG
1 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGAAAGCTAGTGTAAG
47017063 ACCATGTCTGGGACATGGCATCG
66 ACCATGTCTGGGACATGGCATCG
47017086 ACATCTTACT
Statistics
Matches: 331, Mismatches: 45, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 331 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (96 bp):
ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGAAAGCTAGTGTAAG
ACCATGTCTGGGACATGGCATCGGCCTCAAT
Found at i:47020291 original size:47 final size:46
Alignment explanation
Indices: 47020222--47020350 Score: 147
Period size: 47 Copynumber: 2.8 Consensus size: 46
47020212 GTTATTGTGA
* *
47020222 GCTAGTGTAAGACATGTCTGGGATATGCATCGGCCACATT-ATGAGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCC-CATTGACGAGT
* * *
47020268 GCTAGTGTAAAACCATGTTTGGGACATGGCACCGG--CATTGAGACGAGT
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCCATT--GACGAGT
47020316 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCC
47020351 TTGAGACATA
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
45 4 0.06
46 17 0.25
47 25 0.37
48 22 0.32
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCCATTGACGAGT
Found at i:47020321 original size:48 final size:46
Alignment explanation
Indices: 47020222--47020357 Score: 134
Period size: 46 Copynumber: 2.9 Consensus size: 46
47020212 GTTATTGTGA
* * * *
47020222 GCTAGTGTAAGACATGTCTGGGATATGCATCGGCCACATT---ATGAGT
1 GCTAGTGTAAAACATGTCTGGGACATGCACCGG---CATTGAGACGAGT
*
47020268 GCTAGTGTAAAACCATGTTTGGGACATGGCACCGGCATTGAGACGAGT
1 GCTAGTGTAAAA-CATGTCTGGGACAT-GCACCGGCATTGAGACGAGT
* * *
47020316 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGAC
1 GCTAGTGTAAAACATGTCTGGGACATGCACCGGCATTGAGAC
47020358 ATAAGTCAGT
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
45 4 0.05
46 25 0.33
47 25 0.33
48 22 0.29
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (46 bp):
GCTAGTGTAAAACATGTCTGGGACATGCACCGGCATTGAGACGAGT
Found at i:47024701 original size:10 final size:10
Alignment explanation
Indices: 47024688--47024720 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
47024678 AAAACGAGAA
47024688 AAAAAGGGAC
1 AAAAAGGGAC
47024698 AAAAAGGGAC
1 AAAAAGGGAC
*
47024708 -AAAACGGAC
1 AAAAAGGGAC
47024717 AAAA
1 AAAA
47024721 TCGAGAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.64, C:0.12, G:0.24, T:0.00
Consensus pattern (10 bp):
AAAAAGGGAC
Found at i:47025762 original size:13 final size:13
Alignment explanation
Indices: 47025744--47025768 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47025734 GTTTAATTAG
47025744 TTAATTAGTTTAT
1 TTAATTAGTTTAT
47025757 TTAATTAGTTTA
1 TTAATTAGTTTA
47025769 ATAAACAACC
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:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
TTAATTAGTTTAT
Found at i:47033768 original size:14 final size:14
Alignment explanation
Indices: 47033749--47033778 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
47033739 GATAAATACT
47033749 TGATTTGTTCTTAA
1 TGATTTGTTCTTAA
47033763 TGATTTGTTCTTAA
1 TGATTTGTTCTTAA
47033777 TG
1 TG
47033779 CTTTAGTTAC
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:0.20, C:0.07, G:0.17, T:0.57
Consensus pattern (14 bp):
TGATTTGTTCTTAA
Found at i:47034227 original size:13 final size:13
Alignment explanation
Indices: 47034209--47034233 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47034199 AGTTTAATTA
47034209 GTTAATTAGTTTG
1 GTTAATTAGTTTG
47034222 GTTAATTAGTTT
1 GTTAATTAGTTT
47034234 AATAAACAAC
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:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (13 bp):
GTTAATTAGTTTG
Found at i:47037781 original size:47 final size:47
Alignment explanation
Indices: 47037730--47038345 Score: 926
Period size: 47 Copynumber: 13.1 Consensus size: 47
47037720 TTCCACGTTT
* **
47037730 ATCACATTAGCCATTCTACCTTATCACACATATGCATGTTCACATTC
1 ATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC
47037777 ATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC
1 ATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC
47037824 ATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC
1 ATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC
47037871 ATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC
1 ATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC
47037918 ATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC
1 ATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC
*
47037965 ATCACATTGGCTATTCGGCCTTATCACACATATGCATGTTCACATTC
1 ATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC
*
47038012 ATCACATTGGCCATTCGGCATTATCACACATATGCATGTTCACATTC
1 ATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC
* *
47038059 ATCACATTGGCCATTCGGCATTATCTAGGCCTTATCACATATACACT-TTCACATTC
1 ATCACATTGGCCATTCGGCCTTA--T----C--A-CACATATGCA-TGTTCACATTC
* * * *
47038115 ATCACATCGGCCATTAGGCCTTATCACATATATACACT-TTCACATTC
1 ATCACATTGGCCATTCGGCCTTATCACACATATGCA-TGTTCACATTC
*
47038162 ATCACATCGGCCA-------TTATCACACATATGCATGTTCACATTC
1 ATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC
47038202 ATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC
1 ATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC
47038249 ATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC
1 ATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC
* * **
47038296 ATCACATTGGCCATTCGGCCTTATCACATATATACACATTCACATTC
1 ATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC
47038343 ATC
1 ATC
47038346 TCATAAAATC
Statistics
Matches: 533, Mismatches: 18, Indels: 36
0.91 0.03 0.06
Matches are distributed among these distances:
39 1 0.00
40 35 0.07
47 452 0.85
48 1 0.00
49 1 0.00
50 1 0.00
53 1 0.00
54 1 0.00
55 1 0.00
56 38 0.07
57 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.32
Consensus pattern (47 bp):
ATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC
Found at i:47038229 original size:22 final size:22
Alignment explanation
Indices: 47038202--47038324 Score: 60
Period size: 23 Copynumber: 5.3 Consensus size: 22
47038192 GTTCACATTC
47038202 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* *
47038224 ATCACACATAT-G-CATGTTC-ACATT
1 AT--CACAT-TGGCCA--TTCGGCCTT
47038248 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* *
47038271 ATCACACATAT-G-CATGTTC-ACATT
1 AT--CACAT-TGGCCA--TTCGGCCTT
47038295 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
47038318 ATCACAT
1 ATCACAT
47038325 ATATACACAT
Statistics
Matches: 75, Mismatches: 8, Indels: 36
0.63 0.07 0.30
Matches are distributed among these distances:
22 19 0.25
23 22 0.29
24 22 0.29
25 12 0.16
ACGTcount: A:0.25, C:0.30, G:0.13, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:47048712 original size:46 final size:46
Alignment explanation
Indices: 47048587--47048747 Score: 143
Period size: 46 Copynumber: 3.5 Consensus size: 46
47048577 GTGCGAATGC
* * * *
47048587 CATGTCCCAGACATGGTCTTACACTGACATA--TCTCGTA-GCCGATG
1 CATGTCCCAGACAT-GTCTTACACTGACTTACGTCTC-AAGGCCAACG
* *
47048632 CATGTCCCAAACATGTCTTACACTGACTTACGTCTCGAGGCCAACG
1 CATGTCCCAGACATGTCTTACACTGACTTACGTCTCAAGGCCAACG
* * * *
47048678 CATGTCCCAGACATGTCTTATACTAGCAC-T-CGTCTCAATGCCGATG
1 CATGTCCCAGACATGTCTTACACT-G-ACTTACGTCTCAAGGCCAACG
47048724 CCATGTCCCAGACATGGTCTTACA
1 -CATGTCCCAGACAT-GTCTTACA
47048748 ATGGCTCTCA
Statistics
Matches: 97, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
44 15 0.15
45 14 0.14
46 43 0.44
47 16 0.16
48 9 0.09
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGACTTACGTCTCAAGGCCAACG
Found at i:47049962 original size:25 final size:25
Alignment explanation
Indices: 47049921--47049972 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
47049911 TGTGTACTAA
47049921 TGAATGAATAAGAGCACTATGTGTG
1 TGAATGAATAAGAGCACTATGTGTG
* *
47049946 TGAATG-ATTAGAGGCACTGTGTGTG
1 TGAATGAATAAGA-GCACTATGTGTG
47049971 TG
1 TG
47049973 CGAATTCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.29, C:0.08, G:0.33, T:0.31
Consensus pattern (25 bp):
TGAATGAATAAGAGCACTATGTGTG
Found at i:47052607 original size:47 final size:47
Alignment explanation
Indices: 47052538--47052655 Score: 182
Period size: 47 Copynumber: 2.5 Consensus size: 47
47052528 GTGTGTATAC
* * *
47052538 GTGAAAGTGTATATATGTGATAAGGCTTAATAGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATAGCCAACGTGATGAAT
* *
47052585 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAACGTGATGGAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATAGCCAACGTGATGAAT
*
47052632 GTGAAAGTGTATAAATGTGATAAG
1 GTGAAAGTGTATATATGTGATAAG
47052656 TCCCGAAGGG
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 65 1.00
ACGTcount: A:0.35, C:0.07, G:0.29, T:0.30
Consensus pattern (47 bp):
GTGAAAGTGTATATATGTGATAAGGCCTAATAGCCAACGTGATGAAT
Found at i:47052882 original size:162 final size:162
Alignment explanation
Indices: 47052615--47052928 Score: 628
Period size: 162 Copynumber: 1.9 Consensus size: 162
47052605 TAAGGCCTAA
47052615 TGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGTA
1 TGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGTA
47052680 CTATATCCGGGTTAAAACCCCGCAGGCTTTATGCGAGAATATTATCACTGATTAATGTCCGTAAG
66 CTATATCCGGGTTAAAACCCCGCAGGCTTTATGCGAGAATATTATCACTGATTAATGTCCGTAAG
47052745 CTTCGTGCTCGTACTATATCCGCAGGGCCGAG
131 CTTCGTGCTCGTACTATATCCGCAGGGCCGAG
47052777 TGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGTA
1 TGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGTA
47052842 CTATATCCGGGTTAAAACCCCGCAGGCTTTATGCGAGAATATTATCACTGATTAATGTCCGTAAG
66 CTATATCCGGGTTAAAACCCCGCAGGCTTTATGCGAGAATATTATCACTGATTAATGTCCGTAAG
47052907 CTTCGTGCTCGTACTATATCCG
131 CTTCGTGCTCGTACTATATCCG
47052929 AGCTCTAAAG
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
162 152 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (162 bp):
TGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAGTCCCGAAGGGCATTTGTGTCAGTA
CTATATCCGGGTTAAAACCCCGCAGGCTTTATGCGAGAATATTATCACTGATTAATGTCCGTAAG
CTTCGTGCTCGTACTATATCCGCAGGGCCGAG
Found at i:47052992 original size:37 final size:37
Alignment explanation
Indices: 47052936--47053014 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
47052926 CCGAGCTCTA
* * *
47052936 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
47052973 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
47053010 AAGAC
1 AAGAC
47053015 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:47054586 original size:34 final size:34
Alignment explanation
Indices: 47054548--47054617 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 34
47054538 TTAACCCCTC
* *
47054548 TTTCAATAGCAGTAGCAGTCTCGGCCTGAGCCCA
1 TTTCAATAACAATAGCAGTCTCGGCCTGAGCCCA
* * * *
47054582 TTTCAGTAACAATGGCAGTCTGGGCCTTAGCCCA
1 TTTCAATAACAATAGCAGTCTCGGCCTGAGCCCA
47054616 TT
1 TT
47054618 ACATTACAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (34 bp):
TTTCAATAACAATAGCAGTCTCGGCCTGAGCCCA
Found at i:47055080 original size:18 final size:19
Alignment explanation
Indices: 47055040--47055080 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
47055030 CATATCGCAG
47055040 GCCCATGTGGACCTACACA
1 GCCCATGTGGACCTACACA
*
47055059 -CCCATGTGG-CCTACATA
1 GCCCATGTGGACCTACACA
47055076 GCCCA
1 GCCCA
47055081 AACATGGCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.24, C:0.39, G:0.20, T:0.17
Consensus pattern (19 bp):
GCCCATGTGGACCTACACA
Found at i:47057418 original size:93 final size:93
Alignment explanation
Indices: 47057303--47057473 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
47057293 GCCCCTAAGT
* * *
47057303 GAACTCGGACTCAACTGAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
47057368 TGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
47057396 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
47057461 CGAGTTCGGATGC
66 CGAGTTCGGATGC
47057474 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:47057461 original size:46 final size:45
Alignment explanation
Indices: 47057300--47057470 Score: 179
Period size: 46 Copynumber: 3.7 Consensus size: 45
47057290 CCCGCCCCTA
* * * *
47057300 AGTGAACTCGGACTCAACTGAACGAGCTCGGGCGTTCGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT
* *
47057345 AAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACAT-C-T
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCAT
*
47057393 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT
47057438 AGGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 A-GTGAACTCGGACTCAACTCAACGAGTTCGGA
47057471 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 11, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 3 0.03
45 1 0.01
46 57 0.55
47 28 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT
Found at i:47057927 original size:30 final size:30
Alignment explanation
Indices: 47057893--47057952 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
47057883 ATTTAATACG
47057893 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
47057923 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
47057953 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:47064884 original size:46 final size:46
Alignment explanation
Indices: 47064812--47064983 Score: 172
Period size: 46 Copynumber: 3.7 Consensus size: 46
47064802 AACCCGCCCC
* * * *
47064812 TAAGTGAACTCAGACGCAACTGAACGAGCTT-GGGCGTTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAG-TTCGGGCATTTGCATCCA
* *
47064858 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C-ATTTGCATCCA
* * * *
47064906 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCATCCA
*
47064951 TAGGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
47064984 ATGCTCAACC
Statistics
Matches: 103, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
43 5 0.05
44 2 0.02
45 3 0.03
46 55 0.53
47 28 0.27
48 3 0.03
49 2 0.02
50 5 0.05
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCATCCA
Found at i:47064931 original size:93 final size:93
Alignment explanation
Indices: 47064817--47064987 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
47064807 GCCCCTAAGT
* * * *
47064817 GAACTCAGACGCAACTGAACGAGCTT-GGGCGTTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCAGACGCAACTCAACGAG-TTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
47064881 ACGAGTTCGGATGCCTAGTTACATCTCAC
65 ACGAGTTCGGATGCCTAGTTACATCTCAC
* * *
47064910 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCAGACGCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
47064975 CGAGTTCGGATGC
66 CGAGTTCGGATGC
47064988 TCAACCATCT
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
92 2 0.03
93 68 0.97
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (93 bp):
GAACTCAGACGCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:47068613 original size:11 final size:11
Alignment explanation
Indices: 47068594--47068623 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
47068584 GACTCAGGTA
47068594 CATACGAGATT
1 CATACGAGATT
*
47068605 CATATGAGATT
1 CATACGAGATT
47068616 CATACGAG
1 CATACGAG
47068624 TATTGAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (11 bp):
CATACGAGATT
Found at i:47069636 original size:27 final size:26
Alignment explanation
Indices: 47069596--47069646 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
47069586 CGAGGCTGCT
*
47069596 AGATATTATGGCGAAGTCACCAGAAC
1 AGATATTATGGCGAAGCCACCAGAAC
* *
47069622 AGATATATGTGGCGAGGCCACCAGA
1 AGATAT-TATGGCGAAGCCACCAGA
47069647 TTGCAGCGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (26 bp):
AGATATTATGGCGAAGCCACCAGAAC
Found at i:47069915 original size:8 final size:8
Alignment explanation
Indices: 47069902--47069930 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
47069892 TACCAAAGTG
47069902 GGCCCATT
1 GGCCCATT
47069910 GGCCCATT
1 GGCCCATT
47069918 GGCCCATT
1 GGCCCATT
47069926 GGCCC
1 GGCCC
47069931 TTTTTCGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.41, G:0.28, T:0.21
Consensus pattern (8 bp):
GGCCCATT
Found at i:47072634 original size:27 final size:27
Alignment explanation
Indices: 47072604--47072781 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
47072594 ATATTGAGCC
* *
47072604 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
47072631 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
47072658 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
47072686 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
47072713 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
47072740 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
47072767 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
47072782 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:47072716 original size:55 final size:54
Alignment explanation
Indices: 47072604--47072781 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
47072594 ATATTGAGCC
* * * * *
47072604 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
47072658 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
47072713 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
47072767 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
47072782 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:47081973 original size:8 final size:8
Alignment explanation
Indices: 47081956--47081995 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
47081946 TACCAAAGTG
*
47081956 GGCCCGTT
1 GGCCCATT
47081964 GGCCCATT
1 GGCCCATT
*
47081972 GGCCCGTT
1 GGCCCATT
47081980 GGCCCATT
1 GGCCCATT
47081988 GGCCCATT
1 GGCCCATT
47081996 TTCGGCCCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.07, C:0.38, G:0.30, T:0.25
Consensus pattern (8 bp):
GGCCCATT
Found at i:47081977 original size:16 final size:16
Alignment explanation
Indices: 47081956--47081992 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
47081946 TACCAAAGTG
47081956 GGCCCGTTGGCCCATT
1 GGCCCGTTGGCCCATT
47081972 GGCCCGTTGGCCCATT
1 GGCCCGTTGGCCCATT
47081988 GGCCC
1 GGCCC
47081993 ATTTTCGGCC
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:0.05, C:0.41, G:0.32, T:0.22
Consensus pattern (16 bp):
GGCCCGTTGGCCCATT
Found at i:47090980 original size:13 final size:13
Alignment explanation
Indices: 47090962--47090987 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47090952 GCCTAGTGAG
47090962 GTATGTAGGAAAA
1 GTATGTAGGAAAA
47090975 GTATGTAGGAAAA
1 GTATGTAGGAAAA
47090988 AAATAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (13 bp):
GTATGTAGGAAAA
Found at i:47092471 original size:40 final size:39
Alignment explanation
Indices: 47092303--47092509 Score: 310
Period size: 39 Copynumber: 5.3 Consensus size: 39
47092293 CAAAGATCCA
47092303 AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCG
1 AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCG
*
47092342 AAGGCATTTGTGTGAGATACTAATTCCGGGCTAAGCCCG
1 AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCG
47092381 AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCG
1 AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCG
* * *
47092420 AAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCG
1 AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-CCCG
* *
47092460 AAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCG
1 AAGGCATTTGTGCGAGA-TACTAAT-TCCGGGCTAAG-CCCG
47092500 AAGGCATTTG
1 AAGGCATTTG
47092510 AACGAGGAGC
Statistics
Matches: 155, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
39 109 0.70
40 46 0.30
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCG
Found at i:47092523 original size:40 final size:40
Alignment explanation
Indices: 47092248--47092509 Score: 260
Period size: 39 Copynumber: 6.7 Consensus size: 40
47092238 TTGAATGATG
* *
47092248 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAAT-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGT-ACTATAA
* * * *
47092287 TCCGGACAAAGAT-CCAAAGGCATTTGTGCGAGATACTA-AT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TACTATAA
* *
47092327 TCCGGGCTAAG-CCCGAAGGCATTTGTGTGAGATACTA-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAA
*
47092366 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTA-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAA
47092405 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAA
* *
47092444 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTACTATAA
*
47092485 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
47092510 AACGAGGAGC
Statistics
Matches: 197, Mismatches: 17, Indels: 17
0.85 0.07 0.07
Matches are distributed among these distances:
39 126 0.64
40 61 0.31
41 10 0.05
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAA
Found at i:47092532 original size:79 final size:79
Alignment explanation
Indices: 47092303--47092542 Score: 249
Period size: 78 Copynumber: 3.1 Consensus size: 79
47092293 CAAAGATCCA
* *** *
47092303 AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGTGAGAT-ACTAATT
1 AAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAG-TGACTAAAT
* *
47092367 CCGGGCTAAG-CCCG
65 CCGAGTTAAGTCCCG
* ** *
47092381 AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATC
1 AAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATC
*
47092446 CGGGTTAAGTCCCG
66 CGAGTTAAGTCCCG
*
47092460 AAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTA
1 AAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTA
* * *
47092522 TATCC-AGTTAAATTCCG
62 AATCCGAGTTAAGTCCCG
47092539 AAGG
1 AAGG
47092543 TACGTGATTT
Statistics
Matches: 144, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
77 1 0.01
78 72 0.50
79 46 0.32
80 25 0.17
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
AAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATC
CGAGTTAAGTCCCG
Found at i:47100390 original size:79 final size:79
Alignment explanation
Indices: 47100258--47100770 Score: 920
Period size: 79 Copynumber: 6.5 Consensus size: 79
47100248 TTGAATGATG
* * * *
47100258 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGACTAAGATCCGAAGGCATT
47100322 TGTGCGAGATACTAAT
64 TGTGCGAGATACTAAT
47100338 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTG
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTG
47100403 TGCGAGATACTAAT
66 TGCGAGATACTAAT
47100417 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTG
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTG
47100482 TGCGAGATACTAAT
66 TGCGAGATACTAAT
47100496 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTG
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTG
47100561 TGCGAGATACTAAT
66 TGCGAGATACTAAT
47100575 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTG
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTG
47100640 TGCGAGATACTAAT
66 TGCGAGATACTAAT
47100654 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTG
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTG
* *
47100719 TGCGAGTTACTAAA
66 TGCGAGATACTAAT
* *
47100733 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA
47100771 TAACCAGGCT
Statistics
Matches: 423, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
79 380 0.90
80 43 0.10
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTG
TGCGAGATACTAAT
Found at i:47100787 original size:40 final size:40
Alignment explanation
Indices: 47100258--47100798 Score: 623
Period size: 40 Copynumber: 13.7 Consensus size: 40
47100248 TTGAATGATG
* * * *
47100258 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAA-TTACTAAA
* *
47100298 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGA-TACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGA-ATTACTAAA
*
47100338 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATTACTAAA
* *
47100377 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGA-TACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGA-ATTACTAAA
*
47100417 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATTACTAAA
* *
47100456 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGA-TACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGA-ATTACTAAA
*
47100496 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATTACTAAA
* *
47100535 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGA-TACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGA-ATTACTAAA
*
47100575 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATTACTAAA
* *
47100614 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGA-TACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGA-ATTACTAAA
*
47100654 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATTACTAAA
* *
47100693 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAATTACTAAA
*
47100733 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATTACTA-AA
* *
47100774 -CCAGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
47100799 AACGAGGAGC
Statistics
Matches: 432, Mismatches: 40, Indels: 58
0.82 0.08 0.11
Matches are distributed among these distances:
39 171 0.40
40 249 0.58
41 11 0.03
42 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATTACTAAA
Found at i:47105605 original size:23 final size:24
Alignment explanation
Indices: 47105570--47105621 Score: 97
Period size: 23 Copynumber: 2.2 Consensus size: 24
47105560 AACATTTGTA
47105570 AAAAGTGTTAGCATGAAAACACCT
1 AAAAGTGTTAGCATGAAAACACCT
47105594 AAAAGT-TTAGCATGAAAACACCT
1 AAAAGTGTTAGCATGAAAACACCT
47105617 AAAAG
1 AAAAG
47105622 GATTAATGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.19
Consensus pattern (24 bp):
AAAAGTGTTAGCATGAAAACACCT
Found at i:47111243 original size:86 final size:86
Alignment explanation
Indices: 47111027--47111338 Score: 312
Period size: 86 Copynumber: 3.6 Consensus size: 86
47111017 ACTAAATCCC
* * * * * **
47111027 GAAACAAAATTATATCAAAATAAAATCTATTAAATGGTGGGAATAACTCCTGAAACATATTTTAT
1 GAAACAAAA-TAAAACAAAATAAAATCTATTAAATGGCGAGAATAAATCCCAAAACATATTTTAT
*
47111092 TTAATTTAA-TTCT-A-ATTTG
65 TTAATTTAATTTCTCATTTTTG
* *** *
47111111 TAAACAAAATAAAATC-AAATAAAATCTTATTAAACAACGAGAATAAATCCCAAAACATATTTAA
1 GAAACAAAATAAAA-CAAAATAAAATC-TATTAAATGGCGAGAATAAATCCCAAAACATATTTTA
47111175 TTTAATTTAATTTCTCATTTTTG
64 TTTAATTTAATTTCTCATTTTTG
* *
47111198 GAAACAAAATAAAACAAAAT-AAATCTTATTAAATGGCGAGAATAAATCCCAAAATAGATTTTAT
1 GAAACAAAATAAAACAAAATAAAATC-TATTAAATGGCGAGAATAAATCCCAAAACATATTTTAT
*
47111262 TTAATTTAATTTCTCGTTTTTG
65 TTAATTTAATTTCTCATTTTTG
* *** * * * * *
47111284 GCAACAAAATCAAAATGTAAT-AAATCTGTTGAATTGCGAGAATCAATCCCGAAAC
1 GAAACAAAAT-AAAACAAAATAAAATCTATTAAATGGCGAGAATAAATCCCAAAAC
47111339 GGATATTATT
Statistics
Matches: 190, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
83 13 0.07
84 47 0.25
85 4 0.02
86 93 0.49
87 33 0.17
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (86 bp):
GAAACAAAATAAAACAAAATAAAATCTATTAAATGGCGAGAATAAATCCCAAAACATATTTTATT
TAATTTAATTTCTCATTTTTG
Found at i:47111444 original size:62 final size:63
Alignment explanation
Indices: 47111324--47111449 Score: 173
Period size: 63 Copynumber: 2.0 Consensus size: 63
47111314 GAATTGCGAG
* *
47111324 AATCAATCCCGAAACGGATATTATTTTACTCATTTTTGGAAATAAAAAAAAATTTGGAAGAAA
1 AATCAATCCCAAAACGGATATTATTTTACTCATTTTCGGAAATAAAAAAAAATTTGGAAGAAA
* * * ** *
47111387 AATCATTCCCAAAATGGATTTTATTTTACTCA-TTTCGGAAATAAAATCAAATTTGGAATAAA
1 AATCAATCCCAAAACGGATATTATTTTACTCATTTTCGGAAATAAAAAAAAATTTGGAAGAAA
47111449 A
1 A
47111450 TCGTTGAACG
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
62 27 0.49
63 28 0.51
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (63 bp):
AATCAATCCCAAAACGGATATTATTTTACTCATTTTCGGAAATAAAAAAAAATTTGGAAGAAA
Found at i:47111512 original size:78 final size:80
Alignment explanation
Indices: 47111386--47111571 Score: 238
Period size: 80 Copynumber: 2.4 Consensus size: 80
47111376 TTTGGAAGAA
* *
47111386 AAATCATTCCCAAAATGGATTTTATTTTACTCATTTCGGAAATAAAATC-AAA-TTTGGAATAA-
1 AAATCAATCCCAAAACGGATTTTATTTTACTCATTTCGGAAATAAAATCAAAATTTTGGAA-AAG
*
47111448 AATCGTTGAACGGCGG
65 AATCGTTGAACAGCGG
* * *
47111464 GAATCAATCCCAAAACGGATTTTATTTTACTCGTTTTTGGAAAT-AAATCAAAATTTTGGAAAAG
1 AAATCAATCCCAAAACGGATTTTATTTTACTC-ATTTCGGAAATAAAATCAAAATTTTGGAAAAG
*
47111528 AATCGTTGAACAGTGG
65 AATCGTTGAACAGCGG
**
47111544 AAATCAATCCTGAAACGGA-TTTATTTTA
1 AAATCAATCCCAAAACGGATTTTATTTTA
47111572 TCTTTAATTT
Statistics
Matches: 94, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
78 34 0.36
79 23 0.24
80 37 0.39
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (80 bp):
AAATCAATCCCAAAACGGATTTTATTTTACTCATTTCGGAAATAAAATCAAAATTTTGGAAAAGA
ATCGTTGAACAGCGG
Found at i:47111960 original size:4 final size:4
Alignment explanation
Indices: 47111951--47111979 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
47111941 TATCAAAACA
47111951 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
47111980 TATTTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:47118526 original size:27 final size:27
Alignment explanation
Indices: 47118493--47118756 Score: 178
Period size: 27 Copynumber: 9.7 Consensus size: 27
47118483 CCTCAAATTG
*
47118493 TAAAATTACCAAAGTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* ****
47118520 TAGAATTACCGTTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* ***
47118547 TAGAATTACCATTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* ***** *
47118574 TAGAATTACTGTTTTACCCTTGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* *
47118601 TACAAAATTACTAAAATACCATC-AGTTTA
1 T--AAAATTACCAAAATACCCTCGA-TTTA
* *
47118630 CAAAATTACCAAAATACCCTCGA-TCA
1 TAAAATTACCAAAATACCCTCGATTTA
* *
47118656 GTAAAATTACCAAAATACCCTAG-TTTG
1 -TAAAATTACCAAAATACCCTCGATTTA
* * * *
47118683 TAAAATTGCTAAAATACCCTCAATTTG
1 TAAAATTACCAAAATACCCTCGATTTA
47118710 TAAAATTACCAAAATACCC-CTGATTTA
1 TAAAATTACCAAAATACCCTC-GATTTA
* *
47118737 CAAAGTTA-CAGAAATACCCT
1 TAAAATTACCA-AAATACCCT
47118757 TAACTTTCTA
Statistics
Matches: 193, Mismatches: 34, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
26 23 0.12
27 151 0.78
28 2 0.01
29 17 0.09
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.33
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCTCGATTTA
Found at i:47118697 original size:53 final size:54
Alignment explanation
Indices: 47118604--47118756 Score: 168
Period size: 53 Copynumber: 2.9 Consensus size: 54
47118594 TGATTTATAC
* * *
47118604 AAAATTACTAAAATACCATCAGTTTACAAAATTACCAAAATACCCTCGATCAGT
1 AAAATTACCAAAATACCCTCAGTTTACAAAATTACCAAAATACCCTCAATCAGT
** * * **
47118658 AAAATTACCAAAATACCCT-AGTTTGTAAAATTGCTAAAATACCCTCAATTTGT
1 AAAATTACCAAAATACCCTCAGTTTACAAAATTACCAAAATACCCTCAATCAGT
* *
47118711 AAAATTACCAAAATACCC-CTGATTTACAAAGTTA-CAGAAATACCCT
1 AAAATTACCAAAATACCCTCAG-TTTACAAAATTACCA-AAATACCCT
47118757 TAACTTTCTA
Statistics
Matches: 81, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
53 47 0.58
54 34 0.42
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.27
Consensus pattern (54 bp):
AAAATTACCAAAATACCCTCAGTTTACAAAATTACCAAAATACCCTCAATCAGT
Found at i:47118828 original size:27 final size:27
Alignment explanation
Indices: 47118767--47118819 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
47118757 TAACTTTCTA
47118767 AAAATTA-TGGAAATACCATTGGTTTAC
1 AAAATTACT-GAAATACCATTGGTTTAC
*
47118794 AAAATTACTGAAATACCCTTGGTTTA
1 AAAATTACTGAAATACCATTGGTTTA
47118820 TAGATTTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (27 bp):
AAAATTACTGAAATACCATTGGTTTAC
Found at i:47118901 original size:26 final size:26
Alignment explanation
Indices: 47118872--47118962 Score: 94
Period size: 27 Copynumber: 3.4 Consensus size: 26
47118862 ACCCCTATTA
*
47118872 GGTAAAAAGACCGAAAGCCCCTGTAG
1 GGTAAAATGACCGAAAGCCCCTGTAG
* * *
47118898 GGTAAAGTCACCACAAAGCCCCTGTAG
1 GGTAAAATGACC-GAAAGCCCCTGTAG
* *
47118925 GGTAAAGTGACCGTAATA-CCCCTGTAT
1 GGTAAAATGACCG-AA-AGCCCCTGTAG
47118952 GGTAAAATGAC
1 GGTAAAATGAC
47118963 GAATATGCCC
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
26 9 0.17
27 44 0.81
28 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (26 bp):
GGTAAAATGACCGAAAGCCCCTGTAG
Found at i:47118946 original size:27 final size:27
Alignment explanation
Indices: 47118885--47118962 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
47118875 AAAAAGACCG
*
47118885 AAAGCCCCTGTAGGGTAAAGTCACCAC
1 AAAGCCCCTGTAGGGTAAAGTGACCAC
**
47118912 AAAGCCCCTGTAGGGTAAAGTGACCGT
1 AAAGCCCCTGTAGGGTAAAGTGACCAC
* *
47118939 AATA-CCCCTGTATGGTAAAATGAC
1 AA-AGCCCCTGTAGGGTAAAGTGAC
47118963 GAATATGCCC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
27 44 0.98
28 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.19
Consensus pattern (27 bp):
AAAGCCCCTGTAGGGTAAAGTGACCAC
Found at i:47119793 original size:26 final size:26
Alignment explanation
Indices: 47119764--47119961 Score: 256
Period size: 26 Copynumber: 7.7 Consensus size: 26
47119754 GAGGAAGTGC
* *
47119764 AAAAAGGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
47119790 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* *
47119816 AAAGGGGCTTATGCCCCAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
47119842 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
47119868 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* ** **
47119894 AAAATGGCTTATGCCTTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
47119920 AAAAGGGCTT-TGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
47119945 AAAAGGGCTT-TGCCCCA
1 AAAAGGGCTTATGCCCCA
47119962 ATTATTAAAG
Statistics
Matches: 148, Mismatches: 24, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
25 28 0.19
26 120 0.81
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:47119846 original size:52 final size:52
Alignment explanation
Indices: 47119764--47119961 Score: 310
Period size: 52 Copynumber: 3.8 Consensus size: 52
47119754 GAGGAAGTGC
* *
47119764 AAAAAGGCTTATGCCCTAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
* *
47119816 AAAGGGGCTTATGCCCCAGTTTACCAAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
* **
47119868 AAAAGGGCTTATGCCCCAGTTTACCGAAAATGGCTTATGCCTTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
*
47119920 AAAAGGGCTT-TGCCCTAGTTTACCGAAAAGGGCTT-TGCCCCA
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCA
47119962 ATTATTAAAG
Statistics
Matches: 133, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
50 5 0.04
51 23 0.17
52 105 0.79
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
Found at i:47120168 original size:42 final size:42
Alignment explanation
Indices: 47120109--47120200 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
47120099 TAGTCTCCCC
* ** *
47120109 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
47120151 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
47120193 AAATGGGC
1 AAATGGGC
47120201 CTAAGGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:47120301 original size:31 final size:31
Alignment explanation
Indices: 47120224--47120307 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
47120214 CGTTTGCAGT
*
47120224 AAAGGCTTCAGCCCAATGATATGATTTATGA
1 AAAGGCTTCAGCCCAGTGATATGATTTATGA
*
47120255 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCAGCCCAGTGATATGATTTATGA
47120286 AAAGGCTTCAGCCCAGT-ATATG
1 AAAGGCTTCAGCCCAGTGATATG
47120308 TCAAGACTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
30 5 0.10
31 45 0.90
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCAGCCCAGTGATATGATTTATGA
Found at i:47143915 original size:32 final size:34
Alignment explanation
Indices: 47143874--47143938 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 34
47143864 CCACATTATC
* *
47143874 ACTGTATAGGGCTAAGG-CCAGACTG-TACTGTT
1 ACTGAATAGGGCTAAGGCCCAGACCGTTACTGTT
*
47143906 ACTGAATAGGGCTCAGGCCCAGACCGTTACTGT
1 ACTGAATAGGGCTAAGGCCCAGACCGTTACTGT
47143939 ATGCACTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 15 0.54
33 7 0.25
34 6 0.21
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (34 bp):
ACTGAATAGGGCTAAGGCCCAGACCGTTACTGTT
Found at i:47146974 original size:29 final size:29
Alignment explanation
Indices: 47146920--47146979 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
47146910 AAAAGGAAGT
47146920 TTTGGCACAAGTGTAAGATTTAAACTAGC
1 TTTGGCACAAGTGTAAGATTTAAACTAGC
**
47146949 TTTGGCACTAAGTGTGCGATTT-AACTAGC
1 TTTGGCAC-AAGTGTAAGATTTAAACTAGC
47146978 TT
1 TT
47146980 CGGCTACTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (29 bp):
TTTGGCACAAGTGTAAGATTTAAACTAGC
Found at i:47160258 original size:13 final size:13
Alignment explanation
Indices: 47160240--47160266 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
47160230 TGAATTAGTA
47160240 TGTGTGAAAATTT
1 TGTGTGAAAATTT
47160253 TGTGTGAAAATTT
1 TGTGTGAAAATTT
47160266 T
1 T
47160267 ATGGTTTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:47178302 original size:40 final size:40
Alignment explanation
Indices: 47178213--47178476 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
47178203 TTGAATGATG
* *
47178213 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
* * *
47178252 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
47178292 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
47178331 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
47178371 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
47178411 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
47178452 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
47178477 AACGAGGAGC
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
39 53 0.26
40 143 0.69
41 10 0.05
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:47178494 original size:120 final size:118
Alignment explanation
Indices: 47178213--47178509 Score: 338
Period size: 119 Copynumber: 2.5 Consensus size: 118
47178203 TTGAATGATG
* *
47178213 TCCGGGCTAAGTCCCGAAGGC-TTGTG--CTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
1 TCCGGGCTAAGTCCCGAAGGCATT-TGAAC-GAGTGACTAA-ATCCGG-TTAA-ATCCCGAAGGC
* *
47178273 ATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
61 ATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAATTACTAAA
* ** * *
47178331 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCC-GGTTAAATCCCGAAGGCATTT
* *
47178396 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
65 GTGCGAGATACTAAATCCGGGCTAAG-CCCGAAGGCATTTGTGCGAATTACTA-AA
* * *
47178452 -CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCCGGTTAAATTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGTTAAATCCCGAAGG
47178510 TACGTGATTT
Statistics
Matches: 153, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
118 23 0.15
119 64 0.42
120 64 0.42
121 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (118 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCCGGTTAAATCCCGAAGGCATTTG
TGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAATTACTAAA
Found at i:47190806 original size:13 final size:13
Alignment explanation
Indices: 47190788--47190814 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
47190778 TGAATTAGTA
47190788 TGTGTGAAAATTT
1 TGTGTGAAAATTT
47190801 TGTGTGAAAATTT
1 TGTGTGAAAATTT
47190814 T
1 T
47190815 ATGGTTTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:47199864 original size:46 final size:46
Alignment explanation
Indices: 47199814--47199939 Score: 209
Period size: 46 Copynumber: 2.7 Consensus size: 46
47199804 TGGTTGAGCA
* *
47199814 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
47199860 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*
47199906 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
47199940 GGGGCGGGTT
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
45 2 0.03
46 74 0.97
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:47214769 original size:28 final size:29
Alignment explanation
Indices: 47214737--47214835 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 29
47214727 ATAATAAGCC
*
47214737 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* *
47214765 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* * *
47214793 CGCACACTTAGTGCTATACA-ATTTGAACC
1 CGCACACTTAGTGCT-TACATAATCGAACT
47214822 CGCACACTTAGTGC
1 CGCACACTTAGTGC
47214836 CAAACTCATG
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
27 2 0.03
28 37 0.61
29 19 0.31
30 3 0.05
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCGAACT
Found at i:47216852 original size:39 final size:40
Alignment explanation
Indices: 47216751--47216895 Score: 165
Period size: 40 Copynumber: 3.6 Consensus size: 40
47216741 TTGAATGTTG
* *
47216751 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
47216790 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
* *
47216831 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
47216870 TCCGGGTTAAGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
47216896 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
39 35 0.38
40 44 0.48
41 12 0.13
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:47216913 original size:40 final size:40
Alignment explanation
Indices: 47216751--47216928 Score: 116
Period size: 40 Copynumber: 4.5 Consensus size: 40
47216741 TTGAATGTTG
* ** * * *
47216751 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGAAC-GAGTGACTAAA
** ** *
47216791 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGAT-ACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGAACGAG-TGACTAAA
* ** *
47216831 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGAACGAGTGACTAAA
*
47216870 TCCGGGTTAAGTCCCGAAGGCATTTGAACGAG-GAGCTATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGAACGAGTGA-CTAAA
* *
47216910 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
47216929 TACGTGATTT
Statistics
Matches: 117, Mismatches: 14, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
38 1 0.01
39 49 0.42
40 58 0.50
41 9 0.08
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGAACGAGTGACTAAA
Found at i:47216914 original size:79 final size:80
Alignment explanation
Indices: 47216751--47216901 Score: 191
Period size: 79 Copynumber: 1.9 Consensus size: 80
47216741 TTGAATGTTG
*
47216751 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
**
47216816 GTGCGAGATACTAAT
66 GAACGAGATACTAAT
* * * **
47216831 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
47216893 TTGAACGAG
64 TTGAACGAG
47216902 GAGCTATATC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
78 1 0.02
79 42 0.69
80 18 0.30
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GAACGAGATACTAAT
Found at i:47216928 original size:39 final size:40
Alignment explanation
Indices: 47216804--47216928 Score: 105
Period size: 39 Copynumber: 3.2 Consensus size: 40
47216794 GGACTAAGAT
** * * *
47216804 CCGAAGGCATTTGTGCGAGAT-ACTAATTCCGGGCT-AAGC
1 CCGAAGGCATTTGAACGAG-TGACTAAATCCGGGTTAAATC
** * *
47216843 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATC
* *
47216883 CCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATT
1 CCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATC
47216922 CCGAAGG
1 CCGAAGG
47216929 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
38 1 0.01
39 46 0.63
40 26 0.36
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATC
Found at i:47224356 original size:40 final size:40
Alignment explanation
Indices: 47224299--47224481 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 40
47224289 CCAGCATGAT
* *
47224299 TGCTCTTCGGGATTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
47224339 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * * *
47224379 TGCTCTTCGGGACTTAGCCCAGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATATA-TCACTAGCACGAA
* *
47224420 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AA
1 TGCTCTTCGGGA-CTTAGCCCGGATAT-ATCAC-TAGCACGAA
*
47224460 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
47224482 CATCATTCGA
Statistics
Matches: 119, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
39 3 0.03
40 96 0.81
41 20 0.17
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:47224826 original size:29 final size:29
Alignment explanation
Indices: 47224787--47224865 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
47224777 CTTAATAATC
*
47224787 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
* *
47224817 AACTCGCACACTTAGTGTCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
47224846 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
47224866 ATCTCACAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 3 0.07
29 36 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:47224911 original size:43 final size:43
Alignment explanation
Indices: 47224847--47224949 Score: 197
Period size: 43 Copynumber: 2.4 Consensus size: 43
47224837 TGCATTTCAA
47224847 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
*
47224890 GCCCACACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
47224933 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
47224950 TGAAAACCAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.27, C:0.36, G:0.15, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:47226865 original size:37 final size:37
Alignment explanation
Indices: 47226815--47226893 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
47226805 TTATTACGAA
* *
47226815 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
47226852 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
47226889 GTCTT
1 GTCTT
47226894 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:47227090 original size:47 final size:47
Alignment explanation
Indices: 47227012--47227467 Score: 826
Period size: 47 Copynumber: 9.7 Consensus size: 47
47227002 CCCTTCGGGA
* * * * * *
47227012 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
47227059 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
47227106 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
47227153 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
47227200 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
47227247 CTTATCAC--ATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
47227292 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
47227339 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
47227386 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
47227433 CTTATCACATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
47227468 AGAATCCTAA
Statistics
Matches: 397, Mismatches: 10, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
45 45 0.11
47 352 0.89
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:47227256 original size:22 final size:22
Alignment explanation
Indices: 47227228--47227301 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
47227218 TTTCACATTC
47227228 ATCACATCGGCCATTAGGCCTT
1 ATCACATCGGCCATTAGGCCTT
*** * *
47227250 ATCACATATACACTTTCA--CATT
1 ATCACATCGGC-CATT-AGGCCTT
47227272 CATCACATCGGCCATTAGGCCTT
1 -ATCACATCGGCCATTAGGCCTT
47227295 ATCACAT
1 ATCACAT
47227302 ATATACACTT
Statistics
Matches: 37, Mismatches: 10, Indels: 10
0.65 0.18 0.18
Matches are distributed among these distances:
21 1 0.03
22 21 0.57
23 14 0.38
24 1 0.03
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.30
Consensus pattern (22 bp):
ATCACATCGGCCATTAGGCCTT
Found at i:47227430 original size:233 final size:234
Alignment explanation
Indices: 47227012--47227467 Score: 833
Period size: 233 Copynumber: 1.9 Consensus size: 234
47227002 CCCTTCGGGA
* * * *
47227012 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACA-TTATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
47227077 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
65 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
47227142 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
130 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
47227207 CATATATACACTTTCACATTCATCACATCGGCCATTAGGC
195 CATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
47227247 CTTATCACA-TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
1 CTTATCACATTATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACACT
47227311 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
66 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
47227376 GCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
131 GCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
47227441 ATATATACACTTTCACATTCATCACAT
196 ATATATACACTTTCACATTCATCACAT
47227468 AGAATCCTAA
Statistics
Matches: 214, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
233 205 0.96
235 9 0.04
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (234 bp):
CTTATCACATTATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACACT
TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
GCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:47228629 original size:18 final size:18
Alignment explanation
Indices: 47228606--47228647 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
47228596 CATATGCATT
47228606 TTTAATCACATCAAGCAA
1 TTTAATCACATCAAGCAA
47228624 TTTAATCACATCAAGCAA
1 TTTAATCACATCAAGCAA
47228642 TTTAAT
1 TTTAAT
47228648 ACAATTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (18 bp):
TTTAATCACATCAAGCAA
Found at i:47236026 original size:11 final size:11
Alignment explanation
Indices: 47236010--47236038 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
47236000 TTATGAAATG
47236010 ATTTCGTGAAA
1 ATTTCGTGAAA
47236021 ATTTCGTGAAA
1 ATTTCGTGAAA
47236032 ATTTCGT
1 ATTTCGT
47236039 TTAAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41
Consensus pattern (11 bp):
ATTTCGTGAAA
Found at i:47239035 original size:46 final size:44
Alignment explanation
Indices: 47238895--47239105 Score: 169
Period size: 46 Copynumber: 4.6 Consensus size: 44
47238885 TGAGCTAGTA
** * *
47238895 TAAGACATGTCTGGGACATGCATCGGACATATTATGA-GAGCCAGTG
1 TAAGACATGTCTGGGACATGCATCGG-C-TACGA-GATGTGTCAGTG
* * * *
47238941 TAAGGCCATGTCTGGAACATGGCATCGGC-ATTGAGATGAGTGCTAGTG
1 TAA-GACATGTCTGGGACAT-GCATCGGCTA-CGAGATGTGT-C-AGTG
*
47238989 TAAGACATGTCTGGGTCATGCATCGGCCT-CGAGACT-TAAGTCAGTG
1 TAAGACATGTCTGGGACATGCATCGG-CTACGAGA-TGT--GTCAGTG
* *
47239035 TAAGACATGTCTGGGACATGTATCGGCTATGAGATGTGTCAGTG
1 TAAGACATGTCTGGGACATGCATCGGCTACGAGATGTGTCAGTG
47239079 TAAGACCATGTCTGGGACATGGCATCG
1 TAAGA-CATGTCTGGGACAT-GCATCG
47239106 ACACATATAT
Statistics
Matches: 137, Mismatches: 13, Indels: 30
0.76 0.07 0.17
Matches are distributed among these distances:
44 12 0.09
45 20 0.15
46 57 0.42
47 32 0.23
48 16 0.12
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (44 bp):
TAAGACATGTCTGGGACATGCATCGGCTACGAGATGTGTCAGTG
Found at i:47247495 original size:27 final size:27
Alignment explanation
Indices: 47247465--47247568 Score: 115
Period size: 27 Copynumber: 3.8 Consensus size: 27
47247455 GGCTGCCAAA
* * *
47247465 ACAGATAATGCGACAGAGTCACCAGAT
1 ACAGATAATGTGGCAGAGCCACCAGAT
47247492 ACAGATAATCGTGGCAGAGCCACCAGA-
1 ACAGATAAT-GTGGCAGAGCCACCAGAT
47247519 ACAGATATATGTGGCAGAGCCACCAGAT
1 ACAGATA-ATGTGGCAGAGCCACCAGAT
*
47247547 -CACATAATTGTGGC-GTAGCCAC
1 ACAGATAA-TGTGGCAG-AGCCAC
47247569 TAGGACACTT
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
26 2 0.03
27 50 0.74
28 16 0.24
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (27 bp):
ACAGATAATGTGGCAGAGCCACCAGAT
Found at i:47247554 original size:54 final size:54
Alignment explanation
Indices: 47247464--47247568 Score: 133
Period size: 54 Copynumber: 1.9 Consensus size: 54
47247454 TGGCTGCCAA
* *
47247464 AACAGATAATGCGACAGAGTCACCAGATACAGATAATCGTGGCAG-AGCCACCAG
1 AACAGATAATGCGACAGAGCCACCAGATACACATAATCGTGGC-GTAGCCACCAG
* * *
47247518 AACAGATATATGTGGCAGAGCCACCAGAT-CACATAATTGTGGCGTAGCCAC
1 AACAGATA-ATGCGACAGAGCCACCAGATACACATAATCGTGGCGTAGCCAC
47247569 TAGGACACTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
53 1 0.02
54 26 0.59
55 17 0.39
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (54 bp):
AACAGATAATGCGACAGAGCCACCAGATACACATAATCGTGGCGTAGCCACCAG
Found at i:47252726 original size:46 final size:45
Alignment explanation
Indices: 47252557--47252726 Score: 180
Period size: 46 Copynumber: 3.7 Consensus size: 45
47252547 GGCTTCTGAA
* ** *
47252557 CTCGTTGAGTTGAGTCCGAGTTCACTTATGAATTCGAATGTCCGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATT-GAACATCCGAG
*** * * *
47252603 CTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACT-AGGCATCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GATTGA-ACATCCGAG
* *
47252650 CTCGTTGAGTTGAGTCCGAGTTAACTTATGGATGTGAACACCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT-TGAACATCCGAG
47252696 CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
47252727 GCGGGTTACA
Statistics
Matches: 102, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
45 1 0.01
46 66 0.65
47 32 0.31
48 3 0.03
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (45 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATTGAACATCCGAG
Found at i:47254594 original size:15 final size:15
Alignment explanation
Indices: 47254546--47254625 Score: 74
Period size: 15 Copynumber: 5.4 Consensus size: 15
47254536 GTATCTTGGG
*
47254546 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
* *
47254561 TCTCTTTATTCTAGA
1 TTTCTTTATTCTGGA
*
47254576 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
* *
47254591 TTTCTCTA-CCTTGGA
1 TTTCTTTATTC-TGGA
*
47254606 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
47254620 TTTCTT
1 TTTCTT
47254626 GTTATCTTTG
Statistics
Matches: 51, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
14 9 0.18
15 41 0.80
16 1 0.02
ACGTcount: A:0.11, C:0.19, G:0.12, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:47256925 original size:22 final size:22
Alignment explanation
Indices: 47256898--47256972 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
47256888 CATGCATTTG
*
47256898 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGACAA
* * *
47256920 TGTGATGAATG-TGAACATGTACATA
1 TGTGAT-AAGGCCG-A-ATGGACA-A
*
47256945 TGTGATAAGGCCGAATGGTCAA
1 TGTGATAAGGCCGAATGGACAA
47256967 TGTGAT
1 TGTGAT
47256973 GAATGTGAAC
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 14 0.35
23 9 0.22
24 9 0.22
25 8 0.20
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGACAA
Found at i:47257160 original size:22 final size:22
Alignment explanation
Indices: 47257085--47257160 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
47257075 ACATGCATAT
*
47257085 ATGTGATAAGGCAGAATGGCCA
1 ATGTGATAAGGGAGAATGGCCA
* *
47257107 ATGTGATAAATGTGA-ACAT-GCATA
1 ATGTGAT-AA-GGGAGA-ATGGC-CA
47257131 CATGTGATAAGGGAGAATGGCCA
1 -ATGTGATAAGGGAGAATGGCCA
47257154 ATGTGAT
1 ATGTGAT
47257161 GAACGTGGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
22 14 0.33
23 11 0.26
24 10 0.24
25 7 0.17
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (22 bp):
ATGTGATAAGGGAGAATGGCCA
Found at i:47257197 original size:47 final size:47
Alignment explanation
Indices: 47256825--47257163 Score: 473
Period size: 47 Copynumber: 7.2 Consensus size: 47
47256815 TTAGGATTTT
* ** * * * *
47256825 ATGTGATGGATGTGAATGTGTATATATGAGCTAAGGCCGAATGGCAA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
47256872 ATGTGATGAATGTGAACATGCATTTGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
47256919 ATGTGATGAATGTGAACATGTACATATGTGATAAGGCCGAATGGTCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
47256966 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
47257013 ATGTGATGAATATGAACATGCACATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
47257060 ATGTGA-GAAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCA
1 ATGTGATG-AATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * **
47257107 ATGTGATAAATGTGAACATGCATACATGTGATAAGGGAGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
47257154 ATGTGATGAA
1 ATGTGATGAA
47257164 CGTGGAAGTG
Statistics
Matches: 260, Mismatches: 30, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
46 1 0.00
47 259 1.00
ACGTcount: A:0.35, C:0.11, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:47257230 original size:46 final size:46
Alignment explanation
Indices: 47257177--47257267 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
47257167 GGAAGTGTAT
* * *
47257177 ATATGTGGGAAAGCCGAATGGTTAATGCGAAATGTGTATGAGATGG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
* * *
47257223 ATATGTGGTAAAGCCAAATGGCTAATGGGAGATATGTATGAGATG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATG
47257268 TGTATATACC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.34, C:0.07, G:0.33, T:0.26
Consensus pattern (46 bp):
ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
Found at i:47258769 original size:40 final size:40
Alignment explanation
Indices: 47258714--47258865 Score: 236
Period size: 40 Copynumber: 3.8 Consensus size: 40
47258704 CAGTATGTTA
47258714 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATG
* * *
47258754 TATCCGGGCTAAGTCCCGAAAATCATTCGTGCTAGTGAAG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATG
*
47258794 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATA
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATG
*
47258834 TATCCGGGCTAA-ACCTCGAAG-GCATTCGTGCT
1 TATCCGGGCTAAGTCC-CGAAGAGCATTCGTGCT
47258866 GGAATCATGA
Statistics
Matches: 103, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
39 13 0.13
40 90 0.87
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (40 bp):
TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATG
Found at i:47258940 original size:29 final size:28
Alignment explanation
Indices: 47258905--47259033 Score: 118
Period size: 29 Copynumber: 4.5 Consensus size: 28
47258895 CTTCAACCGA
* *
47258905 GCACTATGTGTGCCAGATCAGTAGTTGAG
1 GCACTATGTGTGCGAGATC-GTAATTGAG
* * *
47258934 GCACTATGTGTGCGAGTTCTTCAATCGA-
1 GCACTATGTGTGCGAGATCGT-AATTGAG
*
47258962 GCACTATGTGTGCGAGATTGGTAATTGAG
1 GCACTATGTGTGCGAGA-TCGTAATTGAG
* * *
47258991 GCACTATGTGTGCGAGTTCTTTAATCGA-
1 GCACTATGTGTGCGAGATC-GTAATTGAG
*
47259019 GCGCTATGTGTGCGA
1 GCACTATGTGTGCGA
47259034 AATCAGTCAG
Statistics
Matches: 82, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
28 37 0.45
29 45 0.55
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGTAATTGAG
Found at i:47258963 original size:57 final size:57
Alignment explanation
Indices: 47258873--47259040 Score: 246
Period size: 57 Copynumber: 2.9 Consensus size: 57
47258863 GCTGGAATCA
* * * * *
47258873 TGAGGCACTGTGTGTGCAAGTTCTTCAACCGAGCACTATGTGTGCCAGATCAGTAGT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAAT
**
47258930 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATTGGTAAT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAAT
* * *
47258987 TGAGGCACTATGTGTGCGAGTTCTTTAATCGAGCGCTATGTGTGCGAAATCAGT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGT
47259041 CAGTGGGCAC
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 99 1.00
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (57 bp):
TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAAT
Found at i:47258974 original size:28 final size:27
Alignment explanation
Indices: 47258877--47259033 Score: 143
Period size: 28 Copynumber: 5.6 Consensus size: 27
47258867 GAATCATGAG
* * *
47258877 GCACTGTGTGTGCAAGTTCTTCAACCGA
1 GCACTATGTGTGCGAGTTCTT-AATCGA
* * * * *
47258905 GCACTATGTGTGCCAGATCAGTAGTTGA
1 GCACTATGTGTGCGAGTTC-TTAATCGA
47258933 GGCACTATGTGTGCGAGTTCTTCAATCGA
1 -GCACTATGTGTGCGAGTTCTT-AATCGA
** *
47258962 GCACTATGTGTGCGAGATTGGTAATTGA
1 GCACTATGTGTGCGAG-TTCTTAATCGA
47258990 GGCACTATGTGTGCGAGTTCTTTAATCGA
1 -GCACTATGTGTGCGAGTTC-TTAATCGA
*
47259019 GCGCTATGTGTGCGA
1 GCACTATGTGTGCGA
47259034 AATCAGTCAG
Statistics
Matches: 104, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
28 57 0.55
29 47 0.45
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (27 bp):
GCACTATGTGTGCGAGTTCTTAATCGA
Found at i:47260747 original size:39 final size:40
Alignment explanation
Indices: 47260618--47260802 Score: 146
Period size: 40 Copynumber: 4.7 Consensus size: 40
47260608 GCTACTCGTT
* * * *
47260618 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAACCCGGAAT-TAGTAACTCGCA
* *
47260658 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
* * * *
47260698 CCAATGCCTTCGGG-TTTAGCCCGGAATTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
* ** * * *
47260737 CAAATACCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGAAT-TAGTAAC-TCGCA
*
47260778 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
47260803 CATCATTCGA
Statistics
Matches: 118, Mismatches: 20, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
38 2 0.02
39 31 0.26
40 73 0.62
41 12 0.10
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
Found at i:47265692 original size:22 final size:22
Alignment explanation
Indices: 47265665--47265788 Score: 76
Period size: 22 Copynumber: 5.4 Consensus size: 22
47265655 CATGCATTTG
47265665 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * **
47265687 TGTGATGAATG-TGAACATGTACATA
1 TGTGAT-AAGGCCG-A-ATGGCCA-A
47265712 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* *
47265734 TGTGATGAATG-TGAACAT-G-CATA
1 TGTGAT-AAGGCCG-A-ATGGCCA-A
47265757 TGTGTGATAAGGCCGAATGGCCAA
1 --TGTGATAAGGCCGAATGGCCAA
47265781 TGTGATAA
1 TGTGATAA
47265789 ATGTGAACAT
Statistics
Matches: 76, Mismatches: 12, Indels: 28
0.66 0.10 0.24
Matches are distributed among these distances:
22 25 0.33
23 17 0.22
24 17 0.22
25 17 0.22
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:47265866 original size:94 final size:93
Alignment explanation
Indices: 47265613--47265870 Score: 331
Period size: 94 Copynumber: 2.7 Consensus size: 93
47265603 GTGAATGTGT
* * * *
47265613 ATATATGAGCTAAGGCCGAATGGCAAATGTGATGAATGTGAACATGCAT-TTGTGTGATAAGGCC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATTGTGAGA-AA-GCC
* *
47265677 GAATGGCCAATGTGATGAATGTGAACATGT
64 GAATGGCCAATGTGATAAATGTGAACATGC
* * *
47265707 ACATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCG
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATAT-TGTGAGAAAGCCG
47265772 AATGGCCAATGTGATAAATGTGAACATGC
65 AATGGCCAATGTGATAAATGTGAACATGC
* * * * *
47265801 ATATATGTGATAAGGCAGAATGGCCAATGTGATGAACGTGGAA-GTGTATATATGTGGGAAAGCC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGT-GAACATGCATAT-TGTGAGAAAGCC
47265865 GAATGG
64 GAATGG
47265871 TTAATGCGAA
Statistics
Matches: 143, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
94 133 0.93
95 5 0.03
96 5 0.03
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (93 bp):
ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATTGTGAGAAAGCCGA
ATGGCCAATGTGATAAATGTGAACATGC
Found at i:47265870 original size:47 final size:47
Alignment explanation
Indices: 47265592--47265836 Score: 364
Period size: 47 Copynumber: 5.2 Consensus size: 47
47265582 TTAGGATTTT
* ** * * * *
47265592 ATGTGATGGATGTGAATGTGTATATATGAGCTAAGGCCGAATGGCAA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
47265639 ATGTGATGAATGTGAACATGCATTTGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
47265686 ATGTGATGAATGTGAACATGTACATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
47265733 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
47265780 ATGTGATAAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
47265827 ATGTGATGAA
1 ATGTGATGAA
47265837 CGTGGAAGTG
Statistics
Matches: 178, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 178 1.00
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:47265903 original size:46 final size:46
Alignment explanation
Indices: 47265850--47265940 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
47265840 GGAAGTGTAT
* * *
47265850 ATATGTGGGAAAGCCGAATGGTTAATGCGAAATGTGTATGAGATGG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
* * *
47265896 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATG
47265941 TGTATATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.34, C:0.07, G:0.32, T:0.27
Consensus pattern (46 bp):
ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
Found at i:47271523 original size:40 final size:40
Alignment explanation
Indices: 47271464--47271736 Score: 438
Period size: 40 Copynumber: 6.8 Consensus size: 40
47271454 GAACATTGGA
* *
47271464 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
47271504 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
47271544 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
47271584 ACATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
47271624 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
47271664 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTC
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
47271704 ATATGTCCGGGTTAAGACCCGAAGGCAAATATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATG
47271737 TTTGCGGCTG
Statistics
Matches: 215, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 215 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:47280405 original size:40 final size:40
Alignment explanation
Indices: 47280346--47280618 Score: 438
Period size: 40 Copynumber: 6.8 Consensus size: 40
47280336 GAACATTGGA
* *
47280346 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
47280386 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
47280426 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
47280466 ACATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
47280506 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
47280546 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTC
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
47280586 ATATGTCCGGGTTAAGACCCGAAGGCAAATATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATG
47280619 TTTGCGGCTG
Statistics
Matches: 215, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 215 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:47283664 original size:49 final size:49
Alignment explanation
Indices: 47283156--47284496 Score: 2292
Period size: 49 Copynumber: 27.8 Consensus size: 49
47283146 GGCTGTCACA
* * *
47283156 TAGGCCTTATCACA--TATATACACTTTCACATTCATCACATTGGCTAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
* * *
47283203 TAGGCCTTATCACA--TATATATACTCTCACATTCATCACATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
* * *
47283250 TAGGCCTTATCACA--TATATGCACTTTCACATTCATCACATCGGCTAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
*
47283297 TAGGCCTTATCACA--TATATACACTTTCACATTCATCACATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
* * *
47283344 TAGGCCTTATCACA--TATATGCACTTTCACATTCATCACATCGGCTAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
*
47283391 TAGGCCTTATCACA--TATATACACTTTCACATTCATCACATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
* * *
47283438 TAGGCCTTATCACA--TATATGCACTTTCACATTCATCACATCGGCTAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
*
47283485 TAGGCCTTATCACA--TATATACACTTTCACATTCATCACATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
* * *
47283532 TAGGCCTTATCACA--TATATGCACTTTCACATTCATCACATCGGCTAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
*
47283579 TAGGCCTTATCACA--TATATACACTTTCACATTCATCACATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
* *
47283626 TAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
47283675 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
47283724 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
47283773 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
47283822 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
47283871 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
47283920 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
47283969 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
47284018 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
47284067 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
47284116 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
47284165 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
47284214 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
47284263 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
47284312 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
47284361 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
47284410 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
1 TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
* *
47284459 TAGGCCTTATCACATATATATACA-TGTTCACATCCATC
1 TAGGCCTTATCACATGTATATACACT-TTCACATTCATC
47284497 ACATAGAATC
Statistics
Matches: 1265, Mismatches: 26, Indels: 4
0.98 0.02 0.00
Matches are distributed among these distances:
47 415 0.33
48 1 0.00
49 849 0.67
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (49 bp):
TAGGCCTTATCACATGTATATACACTTTCACATTCATCTCATCGGCCAT
Found at i:47287164 original size:50 final size:49
Alignment explanation
Indices: 47287061--47287164 Score: 111
Period size: 51 Copynumber: 2.1 Consensus size: 49
47287051 TTATGTAACT
* * * *
47287061 CTCATGTTAATTAAGTTGGCATCATAAATTATGACACGCATTATGTACT
1 CTCATGTTAATTAAGTTGGCATCATAAATTAAGACACACATTAAGTACA
* * * *
47287110 CTCATGTTAGTTAAAGTTTGCATCATTAAATTAAGTCATACATTAAGTA-A
1 CTCATGTTAATT-AAGTTGGCATCA-TAAATTAAGACACACATTAAGTACA
47287160 CTCAT
1 CTCAT
47287165 TTGTTCATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
49 11 0.24
50 16 0.36
51 18 0.40
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (49 bp):
CTCATGTTAATTAAGTTGGCATCATAAATTAAGACACACATTAAGTACA
Found at i:47288983 original size:21 final size:21
Alignment explanation
Indices: 47288958--47289001 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
47288948 TGAAATGTTT
47288958 GCCCTTCAAATCTAACATGAA
1 GCCCTTCAAATCTAACATGAA
47288979 GCCCTTCAAATCTAACATGAA
1 GCCCTTCAAATCTAACATGAA
47289000 GC
1 GC
47289002 ATGAGCAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.30, G:0.11, T:0.23
Consensus pattern (21 bp):
GCCCTTCAAATCTAACATGAA
Found at i:47291296 original size:12 final size:11
Alignment explanation
Indices: 47291279--47291350 Score: 56
Period size: 12 Copynumber: 6.2 Consensus size: 11
47291269 CACTGTTTTA
47291279 TTTATTTTGATT
1 TTTATTTT-ATT
47291291 TTTATTTTTATT
1 TTTA-TTTTATT
*
47291303 TTTATTTTCAGT
1 TTTATTTT-ATT
*
47291315 TGTACTTTTATT
1 TTTA-TTTTATT
*
47291327 TTTATTGTTAGT
1 TTTATT-TTATT
*
47291339 TGT-TTTTATT
1 TTTATTTTATT
47291349 TT
1 TT
47291351 CTTTTTGGGA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
10 5 0.10
11 8 0.17
12 27 0.56
13 8 0.17
ACGTcount: A:0.15, C:0.03, G:0.08, T:0.74
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:47291302 original size:18 final size:18
Alignment explanation
Indices: 47291279--47291350 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 18
47291269 CACTGTTTTA
47291279 TTTATTTTGATTTTTATT
1 TTTATTTTGATTTTTATT
* * *
47291297 TTTATTTTTATTTTCAGT
1 TTTATTTTGATTTTTATT
*
47291315 TGTACTTTT-ATTTTTATT
1 TTTA-TTTTGATTTTTATT
* *
47291333 GTTA-GTTG-TTTTTATT
1 TTTATTTTGATTTTTATT
47291349 TT
1 TT
47291351 CTTTTTGGGA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
16 11 0.26
18 27 0.64
19 4 0.10
ACGTcount: A:0.15, C:0.03, G:0.08, T:0.74
Consensus pattern (18 bp):
TTTATTTTGATTTTTATT
Found at i:47291310 original size:24 final size:24
Alignment explanation
Indices: 47291296--47291350 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
47291286 TGATTTTTAT
47291296 TTTTATTTTTATTTTCAGTTGTAC
1 TTTTATTTTTATTTTCAGTTGTAC
47291320 TTTTATTTTTATTGTT-AGTTGT--
1 TTTTATTTTTATT-TTCAGTTGTAC
47291342 TTTTATTTT
1 TTTTATTTT
47291351 CTTTTTGGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.30
24 19 0.63
25 2 0.07
ACGTcount: A:0.15, C:0.04, G:0.09, T:0.73
Consensus pattern (24 bp):
TTTTATTTTTATTTTCAGTTGTAC
Found at i:47291350 original size:6 final size:6
Alignment explanation
Indices: 47291279--47291332 Score: 63
Period size: 6 Copynumber: 9.0 Consensus size: 6
47291269 CACTGTTTTA
* * * * *
47291279 TTTATT TTGATT TTTATT TTTATT TTTATT TTCAGT TGTACT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
47291327 TTTATT
1 TTTATT
47291333 GTTAGTTGTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.74
Consensus pattern (6 bp):
TTTATT
Found at i:47292347 original size:21 final size:21
Alignment explanation
Indices: 47292308--47292346 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
47292298 CTTTGTTCTT
47292308 AAAAAAATGAAAGAAAAAAGG
1 AAAAAAATGAAAGAAAAAAGG
*
47292329 AAAAATATG-AAGAAAAAA
1 AAAAAAATGAAAGAAAAAA
47292347 ATTTGATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (21 bp):
AAAAAAATGAAAGAAAAAAGG
Found at i:47293832 original size:295 final size:295
Alignment explanation
Indices: 47293302--47293894 Score: 1186
Period size: 295 Copynumber: 2.0 Consensus size: 295
47293292 AAATAAGAAG
47293302 ATATGAGTGAGTCGTCATAGAATATTCAAAAAAACAACTCGAAAAACAACATTAAAACCAATTTT
1 ATATGAGTGAGTCGTCATAGAATATTCAAAAAAACAACTCGAAAAACAACATTAAAACCAATTTT
47293367 GAAGTAGACTTTCGTCAAGATTGGAGATTCTCAGTTGATTTCTTATGAAGCCATAATGAGTTTCT
66 GAAGTAGACTTTCGTCAAGATTGGAGATTCTCAGTTGATTTCTTATGAAGCCATAATGAGTTTCT
47293432 TTATTTGTTTTTTTTTTTCGGTTACACTATGTCTTGGATGTTTTTATTTTCAAGCATGAACTAAA
131 TTATTTGTTTTTTTTTTTCGGTTACACTATGTCTTGGATGTTTTTATTTTCAAGCATGAACTAAA
47293497 TTTCTAAATACTTAGGGAGATGAACCCTATGATGGATTCTGTCATTTGATTTTTATTTTACTCAA
196 TTTCTAAATACTTAGGGAGATGAACCCTATGATGGATTCTGTCATTTGATTTTTATTTTACTCAA
47293562 TAAATACTTAGTTTCTTGTTTTCAATTACGTGTGC
261 TAAATACTTAGTTTCTTGTTTTCAATTACGTGTGC
47293597 ATATGAGTGAGTCGTCATAGAATATTCAAAAAAACAACTCGAAAAACAACATTAAAACCAATTTT
1 ATATGAGTGAGTCGTCATAGAATATTCAAAAAAACAACTCGAAAAACAACATTAAAACCAATTTT
47293662 GAAGTAGACTTTCGTCAAGATTGGAGATTCTCAGTTGATTTCTTATGAAGCCATAATGAGTTTCT
66 GAAGTAGACTTTCGTCAAGATTGGAGATTCTCAGTTGATTTCTTATGAAGCCATAATGAGTTTCT
47293727 TTATTTGTTTTTTTTTTTCGGTTACACTATGTCTTGGATGTTTTTATTTTCAAGCATGAACTAAA
131 TTATTTGTTTTTTTTTTTCGGTTACACTATGTCTTGGATGTTTTTATTTTCAAGCATGAACTAAA
47293792 TTTCTAAATACTTAGGGAGATGAACCCTATGATGGATTCTGTCATTTGATTTTTATTTTACTCAA
196 TTTCTAAATACTTAGGGAGATGAACCCTATGATGGATTCTGTCATTTGATTTTTATTTTACTCAA
47293857 TAAATACTTAGTTTCTTGTTTTCAATTACGTGTGC
261 TAAATACTTAGTTTCTTGTTTTCAATTACGTGTGC
47293892 ATA
1 ATA
47293895 ATTCTTGGTT
Statistics
Matches: 298, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
295 298 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (295 bp):
ATATGAGTGAGTCGTCATAGAATATTCAAAAAAACAACTCGAAAAACAACATTAAAACCAATTTT
GAAGTAGACTTTCGTCAAGATTGGAGATTCTCAGTTGATTTCTTATGAAGCCATAATGAGTTTCT
TTATTTGTTTTTTTTTTTCGGTTACACTATGTCTTGGATGTTTTTATTTTCAAGCATGAACTAAA
TTTCTAAATACTTAGGGAGATGAACCCTATGATGGATTCTGTCATTTGATTTTTATTTTACTCAA
TAAATACTTAGTTTCTTGTTTTCAATTACGTGTGC
Found at i:47294741 original size:7 final size:7
Alignment explanation
Indices: 47294730--47294841 Score: 107
Period size: 7 Copynumber: 16.0 Consensus size: 7
47294720 TTCTTTTCAA
*
47294730 CTCAATA
1 CTCAATT
*
47294737 CTCAATC
1 CTCAATT
*
47294744 CTCAATC
1 CTCAATT
* *
47294751 CTCAGTC
1 CTCAATT
*
47294758 CTAAATT
1 CTCAATT
*
47294765 CTCAATC
1 CTCAATT
*
47294772 CTTAATT
1 CTCAATT
*
47294779 TTCAATT
1 CTCAATT
*
47294786 CTAAATT
1 CTCAATT
*
47294793 CTAAATT
1 CTCAATT
*
47294800 CTAAATT
1 CTCAATT
47294807 CTCAATT
1 CTCAATT
47294814 CTCAATT
1 CTCAATT
*
47294821 CTCAATC
1 CTCAATT
47294828 CTCAATT
1 CTCAATT
47294835 CTCAATT
1 CTCAATT
47294842 ATTATTTTTA
Statistics
Matches: 89, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 89 1.00
ACGTcount: A:0.32, C:0.28, G:0.01, T:0.39
Consensus pattern (7 bp):
CTCAATT
Found at i:47296652 original size:63 final size:63
Alignment explanation
Indices: 47296557--47296800 Score: 294
Period size: 63 Copynumber: 3.9 Consensus size: 63
47296547 GCTAACCTAG
* * * * *
47296557 TTTATTTTACACAAGCACCACAACATGCACAATCATTCCCTGCATCAACACCTTCAACTCTAG
1 TTTATTTTACACAAACACCACAACACGCACAATCATTCCCTGCATCAACACCTTCAGCTCCAA
* *
47296620 TTTATTTTACACAAACACCATAGCACGCACAATCATTCCCCT-CATCAACACCTTCAGCTCCAA
1 TTTATTTTACACAAACACCACAACACGCACAATCATT-CCCTGCATCAACACCTTCAGCTCCAA
* * * * * * *
47296683 TTTATTTTACACAAACACCACAACATGTACAATCATTCCCTACATTAATACATTCAGCACCAA
1 TTTATTTTACACAAACACCACAACACGCACAATCATTCCCTGCATCAACACCTTCAGCTCCAA
* * * *
47296746 TTTATTTTACACAAGA-ACCATAACACCCACAATCATTTCATGCATCAACACCTTC
1 TTTATTTTACACAA-ACACCACAACACGCACAATCATTCCCTGCATCAACACCTTC
47296801 TCAATAGGTA
Statistics
Matches: 153, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
62 4 0.03
63 144 0.94
64 5 0.03
ACGTcount: A:0.36, C:0.32, G:0.05, T:0.27
Consensus pattern (63 bp):
TTTATTTTACACAAACACCACAACACGCACAATCATTCCCTGCATCAACACCTTCAGCTCCAA
Done.