Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 152 of 328
Found at i:44401699 original size:35 final size:35
Alignment explanation
Indices: 44401644--44401713 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
44401634 CTTACTTGTA
44401644 AACACATATCAGAATCATATAACGATGCCATGGTC
1 AACACATATCAGAATCATATAACGATGCCATGGTC
* *
44401679 AACACATATCATAATTATATAACGATGCCATGGTC
1 AACACATATCAGAATCATATAACGATGCCATGGTC
44401714 TTACTCGCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (35 bp):
AACACATATCAGAATCATATAACGATGCCATGGTC
Found at i:44406085 original size:35 final size:35
Alignment explanation
Indices: 44406045--44406248 Score: 210
Period size: 35 Copynumber: 5.8 Consensus size: 35
44406035 AGGTAAGTAT
* *
44406045 ATGTGAGGTTATATTGAACTTGTATATTCGGCTGC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
* *
44406080 ATGTGAGGTTATATTGAACTTGTTTATTCGATTAC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
*
44406115 ATGTGAGCTTATATTGAACTTGTATATTCGGTTAC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
** ** * * * *
44406150 ACATGAGAATATATTGAATTTGTATATTTGGTCAT
1 ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
* * * * * *
44406185 ATGAGATGTTTTATTGAACTTGAACATTAGGTTAC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
* * *
44406220 ATGTGATGATATATTGAACTTATATATTC
1 ATGTGAGGTTATATTGAACTTGTATATTC
44406249 AGCCATATGA
Statistics
Matches: 134, Mismatches: 35, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 134 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.43
Consensus pattern (35 bp):
ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
Found at i:44406236 original size:105 final size:105
Alignment explanation
Indices: 44406054--44406248 Score: 243
Period size: 105 Copynumber: 1.9 Consensus size: 105
44406044 TATGTGAGGT
* *** *
44406054 TATATTGAACTTGTATATTCGGCTGCATGTGAGGTTATATTGAACTTGTTTATTCGATTACATGT
1 TATATTGAACTTGTATATTCGGCTGCATATGAGGTTATATTGAACTTGAACATTAGATTACATGT
* *
44406119 GAGCTTATATTGAACTTGTATATTCGGTTACACATGAGAA
66 GAGCATATATTGAACTTATATATTCGGTTACACATGAGAA
* * * *
44406159 TATATTGAATTTGTATATTTGG-T-CATATGAGATGTTTTATTGAACTTGAACATTAGGTTACAT
1 TATATTGAACTTGTATATTCGGCTGCATATGAG--GTTATATTGAACTTGAACATTAGATTACAT
44406222 GTGATG-ATATATTGAACTTATATATTC
64 GTGA-GCATATATTGAACTTATATATTC
44406249 AGCCATATGA
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
103 7 0.09
104 1 0.01
105 67 0.88
106 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.43
Consensus pattern (105 bp):
TATATTGAACTTGTATATTCGGCTGCATATGAGGTTATATTGAACTTGAACATTAGATTACATGT
GAGCATATATTGAACTTATATATTCGGTTACACATGAGAA
Found at i:44407053 original size:2 final size:2
Alignment explanation
Indices: 44407046--44407077 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
44407036 TGTCAGTGTC
44407046 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44407078 TTAAAGTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44433828 original size:38 final size:38
Alignment explanation
Indices: 44433785--44433939 Score: 121
Period size: 38 Copynumber: 3.8 Consensus size: 38
44433775 TTTCAGATTA
44433785 ACATGTATAACCGTGGCATATCCACTTAGCACCATGTT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCATGTT
* * * ** *
44433823 ACATGTTTAACCGTGGTATATCCACTTACCATTACGTTAAT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCATG-T--T
* *
44433864 GAATCAATATATGTAACCGTGGCATATCCACTTATCACCATGTT
1 --A-C-ATGTA--TAACCGTGGCATATCCACTTAGCACCATGTT
* * * *
44433908 ATATGTTTAGCCGTGGTATATCCACTTAGCAC
1 ACATGTATAACCGTGGCATATCCACTTAGCAC
44433940 AACGTTAATG
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 52 0.58
39 1 0.01
40 3 0.03
41 1 0.01
42 1 0.01
43 1 0.01
44 2 0.02
45 3 0.03
46 1 0.01
47 24 0.27
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (38 bp):
ACATGTATAACCGTGGCATATCCACTTAGCACCATGTT
Found at i:44433884 original size:47 final size:48
Alignment explanation
Indices: 44433830--44434043 Score: 218
Period size: 47 Copynumber: 4.7 Consensus size: 48
44433820 GTTACATGTT
* **
44433830 TAACCGTGGTATATCCACTTACCATTACGTTA-ATGAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
* * * *
44433877 TAACCGTGGCATATCCACTTATCACCATGTTATATG--T---T-TA-G
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
*
44433918 ---CCGTGGTATATCCACTTAGCACAACGTTA-ATGAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
* * * *
44433962 TAACCGTGGCATATCCACTTAGCACCACGTTACGTGTATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
* *
44434010 TAATCGTGGTATATCCACTTAGCACCACATTACA
1 TAACCGTGGTATATCCACTTAGCACCACGTTACA
44434044 CATATAACCG
Statistics
Matches: 137, Mismatches: 18, Indels: 23
0.77 0.10 0.13
Matches are distributed among these distances:
37 3 0.02
38 25 0.18
39 1 0.01
41 1 0.01
42 3 0.02
43 3 0.02
44 1 0.01
46 1 0.01
47 54 0.39
48 45 0.33
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (48 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
Found at i:44433885 original size:85 final size:85
Alignment explanation
Indices: 44433792--44433994 Score: 343
Period size: 85 Copynumber: 2.4 Consensus size: 85
44433782 TTAACATGTA
**
44433792 TAACCGTGGCATATCCACTTAGCACCATGTTACATGTTTAACCGTGGTATATCCACTTACCATTA
1 TAACCGTGGCATATCCACTTAGCACCATGTTACATGTTTAACCGTGGTATATCCACTTACCACAA
44433857 CGTTAATGAATCAATATATG
66 CGTTAATGAATCAATATATG
* * * *
44433877 TAACCGTGGCATATCCACTTATCACCATGTTATATGTTTAGCCGTGGTATATCCACTTAGCACAA
1 TAACCGTGGCATATCCACTTAGCACCATGTTACATGTTTAACCGTGGTATATCCACTTACCACAA
44433942 CGTTAATGAATCAATATATG
66 CGTTAATGAATCAATATATG
*
44433962 TAACCGTGGCATATCCACTTAGCACCACGTTAC
1 TAACCGTGGCATATCCACTTAGCACCATGTTAC
44433995 GTGTATCAAT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 109 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.32
Consensus pattern (85 bp):
TAACCGTGGCATATCCACTTAGCACCATGTTACATGTTTAACCGTGGTATATCCACTTACCACAA
CGTTAATGAATCAATATATG
Found at i:44434005 original size:48 final size:48
Alignment explanation
Indices: 44433918--44434043 Score: 182
Period size: 48 Copynumber: 2.6 Consensus size: 48
44433908 ATATGTTTAG
*
44433918 CCGTGGTATATCCACTTAGCACAACGTTA-ATGAATCAATATATGTAA
1 CCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATGTAA
* * * *
44433965 CCGTGGCATATCCACTTAGCACCACGTTACGTGTATCAATATGTGTAA
1 CCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATGTAA
* *
44434013 TCGTGGTATATCCACTTAGCACCACATTACA
1 CCGTGGTATATCCACTTAGCACCACGTTACA
44434044 CATATAACCG
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
47 27 0.39
48 42 0.61
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (48 bp):
CCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATGTAA
Found at i:44434067 original size:133 final size:132
Alignment explanation
Indices: 44433830--44434070 Score: 311
Period size: 133 Copynumber: 1.8 Consensus size: 132
44433820 GTTACATGTT
* **
44433830 TAACCGTGGTATATCCACTTACCATTACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
1 TAACCGTGGCATATCCACTTACCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
* ** * ** * *
44433895 TTATCACCATGTTATATGTTTAGCCGTGGTATATCCACTTAGCACAACGTTAATGAATCAATATA
66 TTAGCACCACATTACACATATAACCGTGGTATATCCACTTAGCACAACGTTAATGAATCAATATA
44433960 TG
131 TG
* * * * * *
44433962 TAACCGTGGCATATCCACTTAGCACCACGTTACGTGTATCAATATGTGTAATCGTGGTATATCCA
1 TAACCGTGGCATATCCACTTACCACCACGTTA-ATGAATCAATATATGTAACCGTGGCATATCCA
*
44434027 CTTAGCACCACATTACACATATAACCGTGGTATTTCCACTTAGC
65 CTTAGCACCACATTACACATATAACCGTGGTATATCCACTTAGC
44434071 GCCACATTTT
Statistics
Matches: 90, Mismatches: 18, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
132 28 0.31
133 62 0.69
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (132 bp):
TAACCGTGGCATATCCACTTACCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
TTAGCACCACATTACACATATAACCGTGGTATATCCACTTAGCACAACGTTAATGAATCAATATA
TG
Found at i:44441368 original size:40 final size:40
Alignment explanation
Indices: 44441164--44441368 Score: 211
Period size: 40 Copynumber: 5.1 Consensus size: 40
44441154 CGAAGTTTAA
** *
44441164 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
44441204 CCGGTTATAGTAACTCGCGCAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
44441244 CCGGATTTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * * *
44441284 CCGAATTTAGTAACTCGCACGAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
44441324 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTGAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
44441364 CCGGA
1 CCGGA
44441369 CATCATTCGA
Statistics
Matches: 142, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
39 4 0.03
40 128 0.90
41 10 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:44449219 original size:40 final size:40
Alignment explanation
Indices: 44449175--44449358 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
44449165 TACTCGTTCC
* *
44449175 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCGCA
1 AATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACA
*
44449215 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACA
* *
44449255 AATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCACG
1 AATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCACA
* * * * *
44449295 AATTCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCACA
*
44449336 AA-GCCTTCGGGACTGAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
44449359 CATCATTCAA
Statistics
Matches: 126, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
39 3 0.02
40 111 0.88
41 12 0.10
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACA
Found at i:44452417 original size:35 final size:35
Alignment explanation
Indices: 44452377--44452509 Score: 176
Period size: 35 Copynumber: 3.8 Consensus size: 35
44452367 AGGTAAGTAT
* * *
44452377 ATGTGAGGTTATATTGAACTTGTGTATTCGGCTGC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
* *
44452412 ATGTGAGGTTATATTGAACTTGTGTATTCGATTAC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
* * *
44452447 ATGTGAGCTTGTATTGAACTTGTATATTCTGTTAC
1 ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
* *
44452482 ATGTGAGATTATATTGAATTTGTATATT
1 ATGTGAGGTTATATTGAACTTGTATATT
44452510 TAGACATATG
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 87 1.00
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (35 bp):
ATGTGAGGTTATATTGAACTTGTATATTCGGTTAC
Found at i:44452532 original size:70 final size:70
Alignment explanation
Indices: 44452388--44452581 Score: 178
Period size: 70 Copynumber: 2.8 Consensus size: 70
44452378 TGTGAGGTTA
* * * * * *
44452388 TATTGAACTTGTGTATTCGGCTGCATGTGAGGTTATATTGAACTTGTGTATTCGATTACATGTGA
1 TATTGAACTTGTATATTCGGCTACATGTGAGATTATATTGAACTTGTATATTCGATGACATATGA
44452453 GCTTG
66 GCTTG
* * * *
44452458 TATTGAACTTGTATATTCTGTTACATGTGAGATTATATTGAATTTGTATATT-TA-GACATATGA
1 TATTGAACTTGTATATTCGGCTACATGTGAGATTATATTGAACTTGTATATTCGATGACATATGA
* *
44452521 GATGTTT
66 G--CTTG
* * * * * *
44452528 TATTGAACTTGAACATTAGACTACATATGATGA-TATATTGAACTTATATATTCG
1 TATTGAACTTGTATATTCGGCTACATGTGA-GATTATATTGAACTTGTATATTCG
44452582 GCCATATGAA
Statistics
Matches: 98, Mismatches: 22, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
68 8 0.08
69 1 0.01
70 87 0.89
71 2 0.02
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (70 bp):
TATTGAACTTGTATATTCGGCTACATGTGAGATTATATTGAACTTGTATATTCGATGACATATGA
GCTTG
Found at i:44458051 original size:26 final size:26
Alignment explanation
Indices: 44458022--44458162 Score: 129
Period size: 27 Copynumber: 5.3 Consensus size: 26
44458012 ATCCCTATTT
* *
44458022 AAAATACTTTGGTTTACAAAATTACC
1 AAAATACCTTGGTTTATAAAATTACC
* * * **
44458048 AAAATACCCTGCTTTGTAAAATTATT
1 AAAATACCTTGGTTTATAAAATTACC
44458074 AAAATACCCTTGGTTTATAAAATTACC
1 AAAATA-CCTTGGTTTATAAAATTACC
* * * *
44458101 AAAATACCCCTAGTTTGTAAAATTATC
1 AAAATA-CCTTGGTTTATAAAATTACC
* * *
44458128 AAAATACCCCTAGTTTGTAAAATTACC
1 AAAATA-CCTTGGTTTATAAAATTACC
44458155 AAAATACC
1 AAAATACC
44458163 CCTAATTTGT
Statistics
Matches: 97, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
26 27 0.28
27 70 0.72
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (26 bp):
AAAATACCTTGGTTTATAAAATTACC
Found at i:44458104 original size:27 final size:27
Alignment explanation
Indices: 44458039--44458190 Score: 180
Period size: 27 Copynumber: 5.7 Consensus size: 27
44458029 TTTGGTTTAC
*
44458039 AAAATTACCAAAATA-CCCTGCTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
** * *
44458065 AAAATTATTAAAATACCCTTGGTTTAT
1 AAAATTACCAAAATACCCCTGGTTTGT
*
44458092 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* *
44458119 AAAATTATCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
**
44458146 AAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* **
44458173 GAAATTACTGAAATACCC
1 AAAATTACCAAAATACCC
44458191 TCGACCTGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
26 13 0.12
27 96 0.88
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTGGTTTGT
Found at i:44458149 original size:54 final size:54
Alignment explanation
Indices: 44458033--44458179 Score: 208
Period size: 54 Copynumber: 2.7 Consensus size: 54
44458023 AAATACTTTG
* * * *
44458033 GTTTACAAAATTACCAAAATA-CCCT-GCTTTGTAAAATTATTAAAATACCCTTG
1 GTTTATAAAATTACCAAAATACCCCTAG-TTTGTAAAATTATCAAAATACCCCTA
44458086 GTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTATCAAAATACCCCTA
1 GTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTATCAAAATACCCCTA
* * *
44458140 GTTTGTAAAATTACCAAAATACCCCTAATTTGTGAAATTA
1 GTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTA
44458180 CTGAAATACC
Statistics
Matches: 85, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
53 20 0.24
54 64 0.75
55 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.33
Consensus pattern (54 bp):
GTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTATCAAAATACCCCTA
Found at i:44458159 original size:81 final size:80
Alignment explanation
Indices: 44458039--44458261 Score: 216
Period size: 81 Copynumber: 2.8 Consensus size: 80
44458029 TTTGGTTTAC
* * ** *
44458039 AAAATTACCAAAATACCCTGCTTTGTAAAATTATTAAAATACCCTTGGTTTATAAAATTACCAAA
1 AAAATTATCAAAATACCCTGATTTGTAAAATTACCAAAATACCCTTGATTTATAAAATTACCAAA
**
44458104 ATACCCCTAG-TTTGT
66 ATA-CCCTAGACCTGT
* * * * **
44458119 AAAATTATCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCCTAATTTGTGAAATTACTG
1 AAAATTATCAAAATA-CCCTGA-TTTGTAAAATTACCAAAATACCCTTGATTTATAAAATTACCA
*
44458183 AAATACCCTCGACCTGT
64 AAATACCCTAGACCTGT
** * * * *
44458200 AAAATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTCGATTTATAGAATTAC
1 AAAATTATCAAAATACCCT-GATTTGTAAAATTACCAAAATACCCTTGATTTATAAAATTAC
44458262 TGTTTTACCC
Statistics
Matches: 114, Mismatches: 24, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
80 23 0.20
81 90 0.79
82 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (80 bp):
AAAATTATCAAAATACCCTGATTTGTAAAATTACCAAAATACCCTTGATTTATAAAATTACCAAA
ATACCCTAGACCTGT
Found at i:44458201 original size:54 final size:53
Alignment explanation
Indices: 44458039--44458261 Score: 191
Period size: 54 Copynumber: 4.2 Consensus size: 53
44458029 TTTGGTTTAC
** * * *
44458039 AAAATTACCAAAATA-CCCTGCTTTGTAAAATTATTAAAATACCCTTGGTTTAT
1 AAAATTACCAAAATACCCCTAATTTGTAAAATTA-TAAAATACCCTCGATTTGT
* *
44458092 AAAATTACCAAAATACCCCTAGTTTGTAAAATTATCAAAATACCC-CTAGTTTGT
1 AAAATTACCAAAATACCCCTAATTTGTAAAATTAT-AAAATACCCTCGA-TTTGT
* * **
44458146 AAAATTACCAAAATACCCCTAATTTGTGAAATTACTGAAATACCCTCGACCTGT
1 AAAATTACCAAAATACCCCTAATTTGTAAAATTA-TAAAATACCCTCGATTTGT
*** * * * * *
44458200 AAAATTATTGAAATA-CCCTCGACTTGTAAAATTACCAAAGTACCCTCGATTTAT
1 AAAATTACCAAAATACCCCT-AATTTGTAAAATTA-TAAAATACCCTCGATTTGT
*
44458254 AGAATTAC
1 AAAATTAC
44458262 TGTTTTACCC
Statistics
Matches: 138, Mismatches: 26, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
53 20 0.14
54 115 0.83
55 3 0.02
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (53 bp):
AAAATTACCAAAATACCCCTAATTTGTAAAATTATAAAATACCCTCGATTTGT
Found at i:44458204 original size:27 final size:27
Alignment explanation
Indices: 44458174--44458248 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
44458164 CTAATTTGTG
44458174 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACTGAAATACCCTCGACCTGTA
* *
44458201 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACTGAAATACCCTCGACCTGTA
*
44458228 AAATTAC-CAAAGTACCCTCGA
1 AAATTACTGAAA-TACCCTCGA
44458249 TTTATAGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 3 0.07
27 40 0.93
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.27
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGACCTGTA
Found at i:44458262 original size:81 final size:81
Alignment explanation
Indices: 44458116--44458287 Score: 188
Period size: 81 Copynumber: 2.1 Consensus size: 81
44458106 ACCCCTAGTT
* * *
44458116 TGTAAAATTATCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAATTTGTGAAATTAC
1 TGTAAAATTATCAAAATACCCCGAGCTTGTAAAATTACCAAAATACCCCTAATTTATGAAATTAC
44458181 TGAAATACCCTCGACC
66 TGAAATACCCTCGACC
** * *
44458197 TGTAAAATTATTGAAATACCCTCGA-CTTGTAAAATTACCAAAGTA-CCCTCGATTTAT-AGAAT
1 TGTAAAATTATCAAAATACCC-CGAGCTTGTAAAATTACCAAAATACCCCT-AATTTATGA-AAT
*** **
44458259 TACTGTTTTACCCTCGATT
63 TACTGAAATACCCTCGACC
44458278 TGTAAAATTA
1 TGTAAAATTA
44458288 CCGTTTTACC
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
80 5 0.07
81 69 0.91
82 2 0.03
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (81 bp):
TGTAAAATTATCAAAATACCCCGAGCTTGTAAAATTACCAAAATACCCCTAATTTATGAAATTAC
TGAAATACCCTCGACC
Found at i:44458298 original size:81 final size:82
Alignment explanation
Indices: 44458240--44458531 Score: 369
Period size: 81 Copynumber: 3.6 Consensus size: 82
44458230 ATTACCAAAG
* **
44458240 TACCCTCGATTTATAGAATTACTGTTTTACCCTCGATTTGTAAAATTACCGTTTTACCCTC-AAT
1 TACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGAAT
44458304 TTACAGAATTACCGTTT
66 TTACAGAATTACCGTTT
* * * *
44458321 TACCCTC-AGTTTACAGAATTACTATTTTACCCTCGATTTATAGAATTACCGTTTTACCC-CTAA
1 TACCCTCGA-TTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGAA
*
44458384 TTTACATAATTACCGTTT
65 TTTACAGAATTACCGTTT
* * * * *
44458402 TACCCCCGATTTACATAATTA-TCGTTTTACCCTCGATTTGCAGAATTACCATTTTACCCTCG-A
1 TACCCTCGATTTACAGAATTACT-GTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGAA
* *
44458465 TTTATAGAATTACTGTTT
65 TTTACAGAATTACCGTTT
** *
44458483 TACCCTTAATTTACAAAATTACTGTTTTACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTAC
44458532 TAAAATACCA
Statistics
Matches: 184, Mismatches: 21, Indels: 12
0.85 0.10 0.06
Matches are distributed among these distances:
80 3 0.02
81 178 0.97
82 3 0.02
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.40
Consensus pattern (82 bp):
TACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGAAT
TTACAGAATTACCGTTT
Found at i:44458532 original size:27 final size:27
Alignment explanation
Indices: 44458240--44458532 Score: 331
Period size: 27 Copynumber: 10.9 Consensus size: 27
44458230 ATTACCAAAG
*
44458240 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
** * *
44458267 TACCCTCGATTTGTAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
44458294 TACCCTCAATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
44458321 TACCCTC-AGTTTACAGAATTACTATTT
1 TACCCTCGA-TTTACAGAATTACTGTTT
* *
44458348 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
44458375 TACCC-CTAATTTACATAATTACCGTTT
1 TACCCTC-GATTTACAGAATTACTGTTT
* *
44458402 TACCCCCGATTTACATAATTA-TCGTTT
1 TACCCTCGATTTACAGAATTACT-GTTT
* **
44458429 TACCCTCGATTTGCAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
44458456 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
** *
44458483 TACCCTTAATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
44458510 TACCCTCGATTTACAAAATTACT
1 TACCCTCGATTTACAGAATTACT
44458533 AAAATACCAT
Statistics
Matches: 228, Mismatches: 32, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
26 2 0.01
27 224 0.98
28 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:44459797 original size:25 final size:25
Alignment explanation
Indices: 44459769--44459816 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
44459759 TTATACCATG
* * *
44459769 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
44459794 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
44459817 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:44459883 original size:20 final size:20
Alignment explanation
Indices: 44459860--44459943 Score: 150
Period size: 20 Copynumber: 4.2 Consensus size: 20
44459850 TAAACATGGT
44459860 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
44459880 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
44459900 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
44459920 ATGTATGATATGCACATGAG
1 ATGTATGATATGCACATGAC
44459940 ATGT
1 ATGT
44459944 TCATAAATGC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:44459900 original size:11 final size:11
Alignment explanation
Indices: 44459864--44459938 Score: 63
Period size: 11 Copynumber: 7.4 Consensus size: 11
44459854 CATGGTATGT
44459864 ATGATATGCAC
1 ATGATATGCAC
* *
44459875 ATGACATG--T
1 ATGATATGCAC
44459884 ATGATATGCAC
1 ATGATATGCAC
*
44459895 ATGATATG--T
1 ATGATATGCAC
44459904 ATGATATGCAC
1 ATGATATGCAC
* *
44459915 ATGACATG--T
1 ATGATATGCAC
44459924 ATGATATGCAC
1 ATGATATGCAC
44459935 ATGA
1 ATGA
44459939 GATGTTCATA
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
9 22 0.46
11 26 0.54
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:44460045 original size:24 final size:24
Alignment explanation
Indices: 44459989--44460130 Score: 200
Period size: 24 Copynumber: 6.0 Consensus size: 24
44459979 GAGGAAGTGA
44459989 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
44460012 TAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
44460036 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
*
44460060 -AAAGGGCTTATGCCCCAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATC
* *
44460083 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
44460107 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
44460131 ATGATAAAGC
Statistics
Matches: 108, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
23 44 0.41
24 53 0.49
25 11 0.10
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:44460058 original size:47 final size:47
Alignment explanation
Indices: 44459988--44460131 Score: 218
Period size: 47 Copynumber: 3.0 Consensus size: 47
44459978 GGAGGAAGTG
44459988 AAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* *
44460035 CAAAAGGGCTTATGCCCCAGTTATCAAAGGGCTTATGCCCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* *
44460082 AAAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTATT-AAAG-GGCTTATGCC-CCAGTTAT
44460131 A
1 A
44460132 TGATAAAGCA
Statistics
Matches: 88, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
47 67 0.76
48 9 0.10
49 12 0.14
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (47 bp):
AAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
Found at i:44462896 original size:46 final size:46
Alignment explanation
Indices: 44462843--44462973 Score: 190
Period size: 46 Copynumber: 2.8 Consensus size: 46
44462833 AGGATATGGG
* *
44462843 CATCTGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGGGAA
1 CATCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
** *
44462889 TGTCTGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* **
44462935 CATCTGAGCTCGTTCAGTTGAGTCCGAGTTTGCTTATGG
1 CATCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
44462974 GCAGGTTACA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.34
Consensus pattern (46 bp):
CATCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
Found at i:44468104 original size:37 final size:37
Alignment explanation
Indices: 44468054--44468128 Score: 125
Period size: 37 Copynumber: 2.0 Consensus size: 37
44468044 ACAGATTGAC
44468054 TAAATCAGCCCATTTTATT-TCGGTACGCACTGATTAT
1 TAAATCAGCCCATTTTATTCT-GGTACGCACTGATTAT
*
44468091 TAAATCAGTCCATTTTATTCTGGTACGCACTGATTAT
1 TAAATCAGCCCATTTTATTCTGGTACGCACTGATTAT
44468128 T
1 T
44468129 CTCTTGATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 35 0.97
38 1 0.03
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (37 bp):
TAAATCAGCCCATTTTATTCTGGTACGCACTGATTAT
Found at i:44474437 original size:25 final size:25
Alignment explanation
Indices: 44474402--44474451 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
44474392 AGTTGTCAAG
44474402 AAAAAATTTTCTAAAGAAATTATTTC
1 AAAAAATTTTCTAAAGAAATT-TTTC
*
44474428 AAAAAA-TTTCTAAAGATATTTTTC
1 AAAAAATTTTCTAAAGAAATTTTTC
44474452 TTATTTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.17
25 13 0.57
26 6 0.26
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (25 bp):
AAAAAATTTTCTAAAGAAATTTTTC
Found at i:44474897 original size:2 final size:2
Alignment explanation
Indices: 44474886--44474918 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
44474876 AATGAATGTG
44474886 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44474919 TTTCCAAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:44477647 original size:40 final size:40
Alignment explanation
Indices: 44477588--44477775 Score: 270
Period size: 40 Copynumber: 4.7 Consensus size: 40
44477578 TGAATGATAC
* * * *
44477588 CCGGGCTAAGCCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
* *
44477628 CCGGGTTAAGACCCAAAGGCATTTGTGAGAGTTGTTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
44477668 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * *
44477708 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
44477748 CCGGGTTAAGACCCGAAGGCAATTGTGC
1 CCGGGTTAAGACCCGAAGGCATTTGTGC
44477776 TTGCGGTTAT
Statistics
Matches: 134, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 132 0.99
41 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:44477785 original size:80 final size:80
Alignment explanation
Indices: 44477584--44477795 Score: 291
Period size: 80 Copynumber: 2.7 Consensus size: 80
44477574 CATTTGAATG
* * * * *
44477584 ATACCCGGGCTAAGCCCCGAAGGCATTTATGCTAGTGATTATATCCGGGTTAAGACCCAAAGGCA
1 ATACCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAAGACCCAAAGGCA
*
44477649 TTTGTGAGAGTTGTT
66 TTTGTGAGAGTTGCT
* * * *
44477664 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCA
1 ATACCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAAGACCCAAAGGCA
*
44477729 TTTGTGCGAGTTGCT
66 TTTGTGAGAGTTGCT
* * *
44477744 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGCGGTTATATCC-GGCTAA
1 ATACCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAA
44477796 ATTCTGAAGA
Statistics
Matches: 115, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
79 6 0.05
80 109 0.95
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
ATACCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAAGACCCAAAGGCA
TTTGTGAGAGTTGCT
Found at i:44505869 original size:29 final size:31
Alignment explanation
Indices: 44505809--44505868 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
44505799 TTAAAAATAA
* *
44505809 AAATTATTTAATAATATTTTTTATACTTTTT
1 AAATAATTTAATAATATTTTATATACTTTTT
44505840 AAATAATTCTAATAA-ATTTTATAT-CTTTT
1 AAATAATT-TAATAATATTTTATATACTTTT
44505869 AGAATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 5 0.19
31 15 0.58
32 6 0.23
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (31 bp):
AAATAATTTAATAATATTTTATATACTTTTT
Found at i:44506254 original size:2 final size:2
Alignment explanation
Indices: 44506249--44506284 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
44506239 TAAATCACAC
44506249 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44506285 GAGAATCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44506586 original size:13 final size:13
Alignment explanation
Indices: 44506568--44506596 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
44506558 TGAATTCTCC
44506568 TTTCTTTTTTTTT
1 TTTCTTTTTTTTT
44506581 TTTCTTTTTTTTT
1 TTTCTTTTTTTTT
44506594 TTT
1 TTT
44506597 TTTGTTGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTCTTTTTTTTT
Found at i:44506592 original size:17 final size:17
Alignment explanation
Indices: 44506567--44506599 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
44506557 ATGAATTCTC
44506567 CTTTCTTTTTTTTTTTT
1 CTTTCTTTTTTTTTTTT
44506584 CTTT-TTTTTTTTTTTT
1 CTTTCTTTTTTTTTTTT
44506600 GTTGAGGGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (17 bp):
CTTTCTTTTTTTTTTTT
Found at i:44511117 original size:22 final size:22
Alignment explanation
Indices: 44511092--44511145 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
44511082 TTGTTTGGTT
*
44511092 ACATCACAATGTAGAAGAGATG
1 ACATCACAACGTAGAAGAGATG
***
44511114 ACATCATGGCGTAGAAGAGATG
1 ACATCACAACGTAGAAGAGATG
*
44511136 ACACCACAAC
1 ACATCACAAC
44511146 TTCAGACCTA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (22 bp):
ACATCACAACGTAGAAGAGATG
Found at i:44513465 original size:13 final size:13
Alignment explanation
Indices: 44513431--44513465 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
44513421 GTTATTCGTT
*
44513431 ATTCTCATAAATA
1 ATTCTCAAAAATA
44513444 ATGTCTCAAAAATA
1 AT-TCTCAAAAATA
44513458 ATTCTCAA
1 ATTCTCAA
44513466 GCAATCATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (13 bp):
ATTCTCAAAAATA
Found at i:44515159 original size:25 final size:26
Alignment explanation
Indices: 44515121--44515172 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
44515111 CCCACTAAAG
44515121 ACCCAAACACCCCAAA-ACAACCCAA
1 ACCCAAACACCCCAAATACAACCCAA
* *
44515146 ACCCACACAGCCCAAATACAACCCAA
1 ACCCAAACACCCCAAATACAACCCAA
44515172 A
1 A
44515173 ATCAAAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.50, C:0.46, G:0.02, T:0.02
Consensus pattern (26 bp):
ACCCAAACACCCCAAATACAACCCAA
Found at i:44516298 original size:6 final size:7
Alignment explanation
Indices: 44516286--44516330 Score: 62
Period size: 6 Copynumber: 7.0 Consensus size: 7
44516276 ACTACTATAG
44516286 TTTATTA
1 TTTATTA
44516293 -TTATTA
1 TTTATTA
44516299 -TTATTA
1 TTTATTA
44516305 -TTA-TA
1 TTTATTA
44516310 TTTATTA
1 TTTATTA
44516317 TTTATTA
1 TTTATTA
44516324 TTTATTA
1 TTTATTA
44516331 GCATTGGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 2 0.06
6 18 0.50
7 16 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTATTA
Found at i:44516299 original size:25 final size:25
Alignment explanation
Indices: 44516271--44516325 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
44516261 ACCATTATCG
44516271 TTATTACTACTATAGTTTATTA-TTA
1 TTATTACTACTATA-TTTATTATTTA
* *
44516296 TTATTATTATTATATTTATTATTTA
1 TTATTACTACTATATTTATTATTTA
44516321 TTATT
1 TTATT
44516326 TATTAGCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.64
Consensus pattern (25 bp):
TTATTACTACTATATTTATTATTTA
Found at i:44516344 original size:3 final size:3
Alignment explanation
Indices: 44516287--44516330 Score: 54
Period size: 3 Copynumber: 14.0 Consensus size: 3
44516277 CTACTATAGT
44516287 TTA TTA TTA TTA TTA TTA TTA -TA TTTA TTA TTTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA -TTA TTA
44516331 GCATTGGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 2 0.05
3 27 0.73
4 8 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:44516365 original size:2 final size:2
Alignment explanation
Indices: 44516358--44516390 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
44516348 ATTTAATGCT
44516358 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44516391 GTATTATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44516395 original size:10 final size:9
Alignment explanation
Indices: 44516357--44516397 Score: 57
Period size: 10 Copynumber: 4.4 Consensus size: 9
44516347 CATTTAATGC
44516357 TTATATATA
1 TTATATATA
44516366 -TATATATA
1 TTATATATA
44516374 TATATATATA
1 T-TATATATA
44516384 TTATATAGTA
1 TTATATA-TA
44516394 TTAT
1 TTAT
44516398 TAATAGTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.28
9 6 0.21
10 15 0.52
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
TTATATATA
Found at i:44516541 original size:29 final size:30
Alignment explanation
Indices: 44516492--44516558 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
44516482 ATGCATATAC
*
44516492 ATATTA-ACATTATTATGTATG-TTTTTAA
1 ATATTATACATTATTATATATGATTTTTAA
*
44516520 ATATTATACA-TATATATATATGTATTTTTAT
1 ATATTATACATTAT-TATATATG-ATTTTTAA
44516551 ATATTATA
1 ATATTATA
44516559 TCGTGTACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 9 0.27
29 10 0.30
31 14 0.42
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (30 bp):
ATATTATACATTATTATATATGATTTTTAA
Found at i:44517171 original size:3 final size:3
Alignment explanation
Indices: 44517163--44517199 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
44517153 ATCTCACTTT
* *
44517163 TTA TTA TTA TTA CTA TTA TTA TTA TTA TCA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
44517200 CGTTCGCGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:44519573 original size:24 final size:24
Alignment explanation
Indices: 44519540--44519597 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
44519530 ATAGAAATAC
*
44519540 TAATACGACTCATAATCATAACAA
1 TAATAAGACTCATAATCATAACAA
44519564 TAATAAGACTCATAATCATAACAA
1 TAATAAGACTCATAATCATAACAA
44519588 TAATAAGACT
1 TAATAAGACT
44519598 AAGTAATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.52, C:0.17, G:0.05, T:0.26
Consensus pattern (24 bp):
TAATAAGACTCATAATCATAACAA
Found at i:44519614 original size:24 final size:24
Alignment explanation
Indices: 44519540--44519609 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
44519530 ATAGAAATAC
* * *
44519540 TAATACGACTCATAATCATAACAA
1 TAATAAGACTAATAATAATAACAA
* *
44519564 TAATAAGACTCATAATCATAACAA
1 TAATAAGACTAATAATAATAACAA
44519588 TAATAAGACTAAGTAATAATAA
1 TAATAAGACTAA-TAATAATAA
44519610 TATAAGAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
24 34 0.81
25 8 0.19
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.26
Consensus pattern (24 bp):
TAATAAGACTAATAATAATAACAA
Found at i:44519621 original size:16 final size:13
Alignment explanation
Indices: 44519605--44519638 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
44519595 ACTAAGTAAT
44519605 AATAATATAA-GAA
1 AATAATA-AATGAA
44519618 AATAATAAATGAA
1 AATAATAAATGAA
44519631 AATAATAA
1 AATAATAA
44519639 CAATAACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 2 0.10
13 18 0.90
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (13 bp):
AATAATAAATGAA
Found at i:44519719 original size:14 final size:14
Alignment explanation
Indices: 44519700--44519731 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
44519690 ACTAAAACTA
44519700 AAAATAATAACAAT
1 AAAATAATAACAAT
*
44519714 AAAATAATAATAAT
1 AAAATAATAACAAT
44519728 AAAA
1 AAAA
44519732 CTAAGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATAATAACAAT
Found at i:44519791 original size:25 final size:24
Alignment explanation
Indices: 44519749--44519802 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
44519739 ATATAGGAAA
44519749 AATAAAACAAATAATAAT-AAATAT
1 AATAAAACAAATAATAATGAAA-AT
*
44519773 AATAACAATAAATAATAATGAAAAT
1 AATAA-AACAAATAATAATGAAAAT
44519798 AATAA
1 AATAA
44519803 TAAATAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 19 0.70
26 3 0.11
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (24 bp):
AATAAAACAAATAATAATGAAAAT
Found at i:44519811 original size:15 final size:15
Alignment explanation
Indices: 44519700--44519811 Score: 58
Period size: 15 Copynumber: 7.3 Consensus size: 15
44519690 ACTAAAACTA
*
44519700 AAAATAATAA-CAAT
1 AAAATAATAATAAAT
44519714 AAAATAATAAT-AAT
1 AAAATAATAATAAAT
* *
44519728 AAAACTAAGAA-ATAT
1 AAAA-TAATAATAAAT
44519743 AGGAAA-AATAA-AACA-
1 A--AAATAATAATAA-AT
44519758 AATAATAATAAATATAAT
1 AA-AATAAT-AATA-AAT
44519776 AACAATAAATAAT-AAT
1 AA-AAT-AATAATAAAT
44519792 GAAAATAATAATAAAT
1 -AAAATAATAATAAAT
44519808 AAAA
1 AAAA
44519812 AGAAACAAAG
Statistics
Matches: 78, Mismatches: 5, Indels: 29
0.70 0.04 0.26
Matches are distributed among these distances:
13 1 0.01
14 19 0.24
15 27 0.35
16 12 0.15
17 7 0.09
18 9 0.12
19 3 0.04
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.22
Consensus pattern (15 bp):
AAAATAATAATAAAT
Found at i:44522351 original size:93 final size:93
Alignment explanation
Indices: 44522239--44522410 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
44522229 CGCCCATAAG
* *
44522239 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
44522304 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
44522332 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
44522397 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
44522411 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:44522407 original size:46 final size:46
Alignment explanation
Indices: 44522232--44522407 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
44522222 TGTAACCCGC
* * *
44522232 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
44522278 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
44522328 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
44522371 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
44522408 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:44529886 original size:93 final size:93
Alignment explanation
Indices: 44529774--44529945 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
44529764 CGCCCATAAG
* *
44529774 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
44529839 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
44529867 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
44529932 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
44529946 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:44529942 original size:46 final size:46
Alignment explanation
Indices: 44529767--44529942 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
44529757 TGTAACCCGC
* * *
44529767 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
44529813 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
44529863 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
44529906 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
44529943 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:44532012 original size:20 final size:20
Alignment explanation
Indices: 44531987--44532030 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
44531977 ATCTAGCATG
44531987 TCTTCAAGAATCTGAATTAT
1 TCTTCAAGAATCTGAATTAT
44532007 TCTTCAAGAATCTGAATTAT
1 TCTTCAAGAATCTGAATTAT
44532027 TCTT
1 TCTT
44532031 TCTGATTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (20 bp):
TCTTCAAGAATCTGAATTAT
Found at i:44533950 original size:39 final size:39
Alignment explanation
Indices: 44533869--44534031 Score: 272
Period size: 39 Copynumber: 4.2 Consensus size: 39
44533859 TATGGTAACC
* *
44533869 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
44533909 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
44533948 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
44533987 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
44534026 CGCACA
1 CGCACA
44534032 TTCATACACA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 99 0.85
40 17 0.15
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:44541859 original size:39 final size:39
Alignment explanation
Indices: 44541778--44541940 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
44541768 TATGGTAACC
* *
44541778 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
44541818 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
44541857 CGCACCATTGCCTTCGGGCTTAGCCCGGATATCACAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
44541896 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
44541935 CGCACA
1 CGCACA
44541941 TTCATACACA
Statistics
Matches: 114, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 97 0.85
40 17 0.15
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:44545105 original size:16 final size:16
Alignment explanation
Indices: 44545084--44545119 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
44545074 AATGTTGAAA
*
44545084 AGGCACTAGCTGATTC
1 AGGCACCAGCTGATTC
*
44545100 AGGCACCAGCTGATTT
1 AGGCACCAGCTGATTC
44545116 AGGC
1 AGGC
44545120 GCTACCATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (16 bp):
AGGCACCAGCTGATTC
Found at i:44551224 original size:17 final size:17
Alignment explanation
Indices: 44551177--44551224 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
44551167 TTTGAGTCCA
* *
44551177 TTTATTTTCACTTTGTT
1 TTTATTTTTATTTTGTT
* * *
44551194 TTTCTTTCTCTTTTGTT
1 TTTATTTTTATTTTGTT
44551211 TTTATTTTTATTTT
1 TTTATTTTTATTTT
44551225 AATTTTTCAT
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.08, C:0.10, G:0.04, T:0.77
Consensus pattern (17 bp):
TTTATTTTTATTTTGTT
Found at i:44559450 original size:6 final size:6
Alignment explanation
Indices: 44559439--44559513 Score: 105
Period size: 6 Copynumber: 12.0 Consensus size: 6
44559429 GCTTAAGGAC
*
44559439 ATAAAA ATAAAACA ACTAAAA ATAAAA ATAAAA ATAAAG ATAAAA ATAAAA
1 ATAAAA AT-AAA-A A-TAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
*
44559490 ATAAAA ATAAAA CTAAAA ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA
44559514 GAAATGAACT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
6 51 0.82
7 5 0.08
8 5 0.08
9 1 0.02
ACGTcount: A:0.79, C:0.04, G:0.01, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:44560138 original size:83 final size:83
Alignment explanation
Indices: 44559999--44560175 Score: 327
Period size: 83 Copynumber: 2.1 Consensus size: 83
44559989 CCCGTGTCCC
44559999 TCACACGGCCACAACACGCCCGTGTCCTAGCCCGTGTGCAAAAACATGGACATTCTATTTCTGAC
1 TCACACGGCCACAACACGCCCGTGTCCTAGCCCGTGTGCAAAAACATGGACATTCTATTTCTGAC
44560064 GTCAGCATGCTTAAGATG
66 GTCAGCATGCTTAAGATG
*
44560082 TCACACGGCCACAACATGCCCGTGTCCTAGCCCGTGTGCAAAAACATGGACATTCTATTTCTGAC
1 TCACACGGCCACAACACGCCCGTGTCCTAGCCCGTGTGCAAAAACATGGACATTCTATTTCTGAC
*
44560147 GTTAGCATGCTTAAGATG
66 GTCAGCATGCTTAAGATG
*
44560165 TCACATGGCCA
1 TCACACGGCCA
44560176 AGGCACACAC
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 91 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (83 bp):
TCACACGGCCACAACACGCCCGTGTCCTAGCCCGTGTGCAAAAACATGGACATTCTATTTCTGAC
GTCAGCATGCTTAAGATG
Found at i:44570851 original size:40 final size:40
Alignment explanation
Indices: 44570773--44570996 Score: 292
Period size: 40 Copynumber: 5.5 Consensus size: 40
44570763 ACCCAAGTAT
* *
44570773 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
** **
44570812 CTTCGGGTTTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
44570852 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
44570892 CTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* * *
44570935 CTTCGGGACTTAGCTCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
44570975 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
44570997 CATCCGAATA
Statistics
Matches: 164, Mismatches: 14, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
39 13 0.08
40 115 0.70
41 1 0.01
43 35 0.21
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:44570969 original size:83 final size:79
Alignment explanation
Indices: 44570773--44570996 Score: 297
Period size: 83 Copynumber: 2.8 Consensus size: 79
44570763 ACCCAAGTAT
* * * **
44570773 CTTCGGGATTTAGCCGGATATAGCAACTCGCACAAATGCCTTCGGGTTTTAGCCCGGATATAGTC
1 CTTCGGGACTTAGCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTC
**
44570838 ACTAGCATGAATGC
66 ACTAGCACAAATGC
* *
44570852 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAG-
1 CTTCGGGACTTAG-CCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
44570916 CAACTACTCGCACAAATGC
65 C-ACTA---GCACAAATGC
*
44570935 CTTCGGGACTTAGCTCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGC-CGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
44570997 CATCCGAATA
Statistics
Matches: 127, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
79 13 0.10
80 48 0.38
82 1 0.01
83 65 0.51
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (79 bp):
CTTCGGGACTTAGCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTC
ACTAGCACAAATGC
Found at i:44572755 original size:23 final size:23
Alignment explanation
Indices: 44572729--44572775 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
44572719 GCTGTCACAA
44572729 TTCTGGCCTATTTGGCCGAGTGC
1 TTCTGGCCTATTTGGCCGAGTGC
44572752 TTCTGGCCTATTTGGCCGAGTGC
1 TTCTGGCCTATTTGGCCGAGTGC
44572775 T
1 T
44572776 ACTAACACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.09, C:0.26, G:0.30, T:0.36
Consensus pattern (23 bp):
TTCTGGCCTATTTGGCCGAGTGC
Found at i:44580904 original size:30 final size:30
Alignment explanation
Indices: 44580869--44580928 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
44580859 TAAGAAAACT
*
44580869 GAATAAAGAAATCCA-AGATAGAGAAACCCA
1 GAATAAAGAAATCCAGA-ATAAAGAAACCCA
44580899 GAATAAAGAAATCCAGAATAAAGAAACCCA
1 GAATAAAGAAATCCAGAATAAAGAAACCCA
44580929 AGATACGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.58, C:0.17, G:0.15, T:0.10
Consensus pattern (30 bp):
GAATAAAGAAATCCAGAATAAAGAAACCCA
Found at i:44580908 original size:15 final size:15
Alignment explanation
Indices: 44580869--44580928 Score: 77
Period size: 15 Copynumber: 4.0 Consensus size: 15
44580859 TAAGAAAACT
*
44580869 GAATAAAGAAATCCA
1 GAATAAAGAAACCCA
*
44580884 -AGATAGAGAAACCCA
1 GA-ATAAAGAAACCCA
*
44580899 GAATAAAGAAATCCA
1 GAATAAAGAAACCCA
44580914 GAATAAAGAAACCCA
1 GAATAAAGAAACCCA
44580929 AGATACGATA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
14 1 0.03
15 36 0.95
16 1 0.03
ACGTcount: A:0.58, C:0.17, G:0.15, T:0.10
Consensus pattern (15 bp):
GAATAAAGAAACCCA
Found at i:44583965 original size:93 final size:92
Alignment explanation
Indices: 44583854--44584024 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 92
44583844 CGCCCATAAG
* *
44583854 CGAACTCGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 CGAACTCGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
44583919 CGAGTTCGGATGCCTAGTTACATTTCA
66 CGAGTTCGGATGCCTAGTTACATTTCA
*
44583946 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTC-GACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
44584011 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
44584025 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 7 0.09
93 68 0.91
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (92 bp):
CGAACTCGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCA
Found at i:44584021 original size:46 final size:46
Alignment explanation
Indices: 44583847--44584021 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
44583837 TGTAACCCGC
* * *
44583847 CCATAAGCGAACTC-GACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
44583892 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
44583942 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
44583985 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
44584022 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 12, Indels: 19
0.78 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 15 0.14
46 49 0.45
47 29 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:44584040 original size:46 final size:46
Alignment explanation
Indices: 44583895--44584033 Score: 135
Period size: 47 Copynumber: 3.0 Consensus size: 46
44583885 TTCGCATCCA
*
44583895 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATT
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC
* * * * *
44583943 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATC
44583988 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
44584034 CTAGTGACAT
Statistics
Matches: 75, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
44 8 0.11
45 2 0.03
46 28 0.37
47 30 0.40
48 2 0.03
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
Found at i:44587678 original size:40 final size:40
Alignment explanation
Indices: 44587631--44587856 Score: 255
Period size: 40 Copynumber: 5.7 Consensus size: 40
44587621 GCTACTCGTT
*
44587631 CAAATGCCTTCGGGA-CATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTC-GGATCTTAGCCCGGATT-TAGTAACTCGCA
* * * *
44587671 CAGATGCCTCCGGGA-CTTAACCCGGATTTAGTAACTTGCA
1 CAAATGCCTTC-GGATCTTAGCCCGGATTTAGTAACTCGCA
*
44587711 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGATCTTAGCCCGGATTTAGTAACTCGCA
* *
44587751 CAAATGCCTTCAGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGATCTTAGCCCGGATTTAGTAACTCGCA
* * * * *
44587791 CGAATGCCTTCGGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGATCTTAGCCCGGATTTAGTAAC-TCGCA
44587832 CAAA-GCCTTCGGGA-CTTAGCCCGGA
1 CAAATGCCTTC-GGATCTTAGCCCGGA
44587857 CATCATTCGA
Statistics
Matches: 164, Mismatches: 18, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
39 3 0.02
40 149 0.91
41 12 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGATCTTAGCCCGGATTTAGTAACTCGCA
Found at i:44589810 original size:40 final size:39
Alignment explanation
Indices: 44589645--44589828 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
44589635 AAATTGAATG
* * *
44589645 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
44589685 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
44589725 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
44589765 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
44589804 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
44589829 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:44589853 original size:80 final size:81
Alignment explanation
Indices: 44589685--44589873 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
44589675 GCTGGAAATT
* * * *
44589685 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
44589750 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
44589766 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
44589829 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
44589845 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
44589874 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:44599358 original size:39 final size:41
Alignment explanation
Indices: 44599313--44599539 Score: 251
Period size: 39 Copynumber: 5.7 Consensus size: 41
44599303 GCTACTCGTT
*
44599313 CAAATGCCTTCGGGA-CATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATT-TAGTAACTCGCA
*
44599353 C-AATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
*
44599392 CAAATGCCTTC-GGATCTTAG-TCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
*
44599431 CAAATGCCTTC-GGATCTTAGTCCGGA-TTAGTAACTCGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
* * * *
44599470 CGAATGCCTTC-GGATCTTAGTCCGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGATCTTAG--C--CCGGATTTAGTAAC-TCGCA
44599515 CAAA-GCCTTCGGGA-CTTAGCCCGGA
1 CAAATGCCTTCGGGATCTTAGCCCGGA
44599540 CATCATTCGA
Statistics
Matches: 165, Mismatches: 11, Indels: 22
0.83 0.06 0.11
Matches are distributed among these distances:
39 107 0.65
40 25 0.15
42 1 0.01
43 5 0.03
44 17 0.10
45 10 0.06
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (41 bp):
CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
Found at i:44611513 original size:93 final size:93
Alignment explanation
Indices: 44611401--44611572 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
44611391 CGCCCATAAG
* *
44611401 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
44611466 ACGAGTTCGGATGCCTAGTTACATATCA
66 ACGAGTTCGGATGCCTAGTTACATATCA
*
44611494 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
44611559 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
44611573 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATATCA
Found at i:44611569 original size:46 final size:46
Alignment explanation
Indices: 44611394--44611569 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
44611384 TGTAACCCGC
* * *
44611394 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
44611440 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
44611490 --ATCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
44611533 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
44611570 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:44615588 original size:23 final size:24
Alignment explanation
Indices: 44615533--44615590 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
44615523 AACAAAAGAC
* * *
44615533 AAATTAAAATGTAAAAATTTAATTA
1 AAATAAAAATATAAAAA-TTAAATA
*
44615558 AAACAAAAATATAAAAA-TAAATA
1 AAATAAAAATATAAAAATTAAATA
44615581 AAATAAAAAT
1 AAATAAAAAT
44615591 GGCTAAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 14 0.50
25 14 0.50
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (24 bp):
AAATAAAAATATAAAAATTAAATA
Found at i:44619854 original size:25 final size:27
Alignment explanation
Indices: 44619826--44619882 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
44619816 CAACAAAACT
*
44619826 AAAATCT-AACATAAAAA-G-AAAAGAG
1 AAAATCTAAAC-TAAAAATGAAAAAAAG
*
44619851 AAAACCTAAACTAAAAATGAAAAAAAG
1 AAAATCTAAACTAAAAATGAAAAAAAG
44619878 AAAAT
1 AAAAT
44619883 GAAAGGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 12 0.46
26 4 0.15
27 10 0.38
ACGTcount: A:0.70, C:0.09, G:0.09, T:0.12
Consensus pattern (27 bp):
AAAATCTAAACTAAAAATGAAAAAAAG
Found at i:44621427 original size:43 final size:44
Alignment explanation
Indices: 44621379--44621544 Score: 162
Period size: 43 Copynumber: 3.9 Consensus size: 44
44621369 CATGATGAGA
* *
44621379 TTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT-TGTGT
1 TTACATGTAAGACCATATCTAGGACATTGGCATCGTATATGTGT
* * *
44621422 TTACATGTAAGACCATGTCTAGGACATTAGCATCGTTATATG-AT
1 TTACATGTAAGACCATATCTAGGACATTGGCATCG-TATATGTGT
* * * * *
44621466 TT-CGTGTAAGACCACATCTGGGACATTGGCATCG-ATATATGA
1 TTACATGTAAGACCATATCTAGGACATTGGCATCGTATATGTGT
* * * *
44621508 TAACATGTAAGACCATATCTGGGATA-TGGCATTGTAT
1 TTACATGTAAGACCATATCTAGGACATTGGCATCGTAT
44621545 GAGCCCTACA
Statistics
Matches: 102, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
41 4 0.04
42 8 0.08
43 82 0.80
44 6 0.06
45 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33
Consensus pattern (44 bp):
TTACATGTAAGACCATATCTAGGACATTGGCATCGTATATGTGT
Found at i:44628385 original size:28 final size:29
Alignment explanation
Indices: 44628354--44628413 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
44628344 AAAGTGATTT
*
44628354 TTGACAAAAA-TGTCAATT-AAGGATTAAA
1 TTGA-AAAAAGTGTAAATTGAAGGATTAAA
* *
44628382 TTGAAAAAAGTGTAAATTGAGGGGTTAAA
1 TTGAAAAAAGTGTAAATTGAAGGATTAAA
44628411 TTG
1 TTG
44628414 TGAAATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 5 0.19
28 11 0.41
29 11 0.41
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.30
Consensus pattern (29 bp):
TTGAAAAAAGTGTAAATTGAAGGATTAAA
Found at i:44628958 original size:43 final size:42
Alignment explanation
Indices: 44628910--44629015 Score: 135
Period size: 43 Copynumber: 2.5 Consensus size: 42
44628900 TGAGATTACA
*
44628910 TGTAAGACCATGTCTGGGACATTGGCAT-TGTAT-TGTGTTTATG
1 TGTAAGACCATGTCTGGGACATTGGCATAT-TATATG-ATTT-TG
*
44628953 TGTAAGACCATGTCTAGGACATTGGCATCATTATATGATTTTG
1 TGTAAGACCATGTCTGGGACATTGGCAT-ATTATATGATTTTG
*
44628996 TGTAAGACCACGTCTGGGAC
1 TGTAAGACCATGTCTGGGAC
44629016 GTTAGCATCG
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
43 47 0.84
44 6 0.11
45 3 0.05
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATTGGCATATTATATGATTTTG
Found at i:44629024 original size:43 final size:43
Alignment explanation
Indices: 44628910--44629034 Score: 121
Period size: 43 Copynumber: 2.9 Consensus size: 43
44628900 TGAGATTACA
* * * * *
44628910 TGTAAGACCATGTCTGGGACATTGGCATTG-TAT-TGTGTTTATG
1 TGTAAGACCACGTCTAGGACATTAGCATCGATATATG-ATTT-TG
* *
44628953 TGTAAGACCATGTCTAGGACATTGGCATC-ATTATATGATTTTG
1 TGTAAGACCACGTCTAGGACATTAGCATCGA-TATATGATTTTG
* *
44628996 TGTAAGACCACGTCTGGGACGTTAGCATCGATATATGAT
1 TGTAAGACCACGTCTAGGACATTAGCATCGATATATGAT
44629035 AACATGTAAG
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
43 62 0.87
44 7 0.10
45 2 0.03
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (43 bp):
TGTAAGACCACGTCTAGGACATTAGCATCGATATATGATTTTG
Found at i:44630406 original size:46 final size:46
Alignment explanation
Indices: 44630260--44630430 Score: 200
Period size: 46 Copynumber: 3.7 Consensus size: 46
44630250 TTTTTGTGCT
* * * * *
44630260 AGTGTAAGACATGTCTGGGATATGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGTGACGAGAGCC
* * * * *
44630306 AGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGTGACGAGAGCC
**
44630354 AGTGTAAGACATGTCTAAGACATGCATCGGCCTCGTGACGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGTGACG-AGAGCC
44630400 AGTGTAAGACATGTCTGGGACATGCATCGGC
1 AGTGTAAGACATGTCTGGGACATGCATCGGC
44630431 TACGAGATGT
Statistics
Matches: 103, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
46 54 0.52
47 26 0.25
48 23 0.22
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGTGACGAGAGCC
Found at i:44635261 original size:19 final size:19
Alignment explanation
Indices: 44635237--44635275 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
44635227 ATACCACTTA
44635237 AATGAATGGAGGCGTGACT
1 AATGAATGGAGGCGTGACT
44635256 AATGAATGGAGGCGTGACT
1 AATGAATGGAGGCGTGACT
44635275 A
1 A
44635276 TCAACCTACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.36, T:0.21
Consensus pattern (19 bp):
AATGAATGGAGGCGTGACT
Found at i:44642002 original size:42 final size:42
Alignment explanation
Indices: 44641914--44642003 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
44641904 CCTAATTGGA
* * * **
44641914 AAAATAATTCTCTTATTCTAATATACCACTAAAACATGAGGG
1 AAAATAATTCCCTTATTCTAATAAACCACTAAAACATAAAAG
* * * *
44641956 AAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAAT
1 AAAATAATTCCCTTATTCTAATAAACCACTAAAACATAAAAG
44641998 AAAATA
1 AAAATA
44642004 TTCTTAGAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (42 bp):
AAAATAATTCCCTTATTCTAATAAACCACTAAAACATAAAAG
Found at i:44642047 original size:19 final size:18
Alignment explanation
Indices: 44642025--44642064 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
44642015 TGAATAAAAC
*
44642025 TTATCTACCTAAATAAGAT
1 TTATCTAACTAAATAA-AT
44642044 TTATCTAACTAAATAAAT
1 TTATCTAACTAAATAAAT
44642062 TTA
1 TTA
44642065 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTAACTAAATAAAT
Found at i:44644081 original size:42 final size:42
Alignment explanation
Indices: 44643992--44644082 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 42
44643982 TACTAATTAG
* * **
44643992 GAAAATAATTTCCTTATTCTAATAAACTACTAAAACATGAGG
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAAA
* *
44644034 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAAA
*
44644076 TAAAATA
1 GAAAATA
44644083 TGAATAAAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.30
Consensus pattern (42 bp):
GAAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAAA
Found at i:44644115 original size:19 final size:18
Alignment explanation
Indices: 44644093--44644132 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
44644083 TGAATAAAAC
* *
44644093 TTATCTACCTTAATAAGAT
1 TTATCTAACTAAATAA-AT
44644112 TTATCTAACTAAATAAAT
1 TTATCTAACTAAATAAAT
44644130 TTA
1 TTA
44644133 AAATATATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (18 bp):
TTATCTAACTAAATAAAT
Found at i:44649815 original size:25 final size:25
Alignment explanation
Indices: 44649781--44649831 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
44649771 TTCCTTATAA
**
44649781 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
44649806 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
44649831 A
1 A
44649832 TTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:44649830 original size:12 final size:12
Alignment explanation
Indices: 44649784--44649831 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
44649774 CTTATAAACT
44649784 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
44649796 TTCTATTAGGACT
1 TTAAATTAGGA-A
44649809 TTAAATTAGGAA
1 TTAAATTAGGAA
*
44649821 TTAGATTAGGA
1 TTAAATTAGGA
44649832 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:44654483 original size:25 final size:25
Alignment explanation
Indices: 44654449--44654499 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
44654439 TTCCTTATAA
**
44654449 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
44654474 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
44654499 A
1 A
44654500 TTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:44654498 original size:12 final size:12
Alignment explanation
Indices: 44654452--44654499 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
44654442 CTTATAAACT
44654452 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
44654464 TTCTATTAGGACT
1 TTAAATTAGGA-A
44654477 TTAAATTAGGAA
1 TTAAATTAGGAA
*
44654489 TTAGATTAGGA
1 TTAAATTAGGA
44654500 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:44658398 original size:44 final size:45
Alignment explanation
Indices: 44658331--44658415 Score: 138
Period size: 44 Copynumber: 1.9 Consensus size: 45
44658321 TGAACATTAA
*
44658331 ATTTTATTTTTAATGATTTTTAAAGTGCTT-ATAACATTCTATAAT
1 ATTTTATTTATAATGATTTTTAAAGTG-TTCATAACATTCTATAAT
44658376 ATTTTATTTAT-ATGATTTTTAAAGTGTTCATAACATTCTA
1 ATTTTATTTATAATGATTTTTAAAGTGTTCATAACATTCTA
44658416 ATTCATAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
43 2 0.05
44 26 0.68
45 10 0.26
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (45 bp):
ATTTTATTTATAATGATTTTTAAAGTGTTCATAACATTCTATAAT
Found at i:44661658 original size:21 final size:21
Alignment explanation
Indices: 44661615--44661658 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
44661605 GTCGCAATTC
* * *
44661615 AAATTTATTATAAATATTAAT
1 AAATTTATCATAAAAAATAAT
*
44661636 AAATTTATCATAAAAAATCAT
1 AAATTTATCATAAAAAATAAT
44661657 AA
1 AA
44661659 CACCATTTGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATTTATCATAAAAAATAAT
Found at i:44665129 original size:29 final size:29
Alignment explanation
Indices: 44665101--44665231 Score: 208
Period size: 29 Copynumber: 4.5 Consensus size: 29
44665091 CCTCCGAGCT
** * * *
44665101 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
44665130 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
44665159 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
44665188 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
44665217 CGCACACTTAGTGCC
1 CGCACACTTAGTGCC
44665232 GATCTCGTCA
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 95 1.00
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:44665163 original size:87 final size:86
Alignment explanation
Indices: 44665043--44665231 Score: 202
Period size: 87 Copynumber: 2.2 Consensus size: 86
44665033 TACTCGATTT
* * *
44665043 CGCACACTTAGTGCCACGTAATTTAAGCCCGCACACACAGTGCCATA-CCCTCCGAGCTCGCACA
1 CGCACACTTAGTGCCAC-TAATTTAAGCACGCACACACAGTGCCATATACCTCC-AGCACGCACA
* * *
44665107 CCCAGTGCCGTATTTTTCCAGCT
64 CCCAGTGCCATATATTTCCAGCA
* * ** **
44665130 TGCACACTTAGTGCCA-TATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCACGCACA
1 CGCACACTTAGTGCCACTA-ATTT-AAGCACGCACACACAGTGCCATATACCTCCAGCACGCACA
**
44665194 CTTAGTGCCATATATTTCCAGCA
64 CCCAGTGCCATATATTTCCAGCA
44665217 CGCACACTTAGTGCC
1 CGCACACTTAGTGCC
44665232 GATCTCGTCA
Statistics
Matches: 84, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
85 2 0.02
86 4 0.05
87 75 0.89
88 3 0.04
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (86 bp):
CGCACACTTAGTGCCACTAATTTAAGCACGCACACACAGTGCCATATACCTCCAGCACGCACACC
CAGTGCCATATATTTCCAGCA
Found at i:44671439 original size:13 final size:13
Alignment explanation
Indices: 44671423--44671483 Score: 86
Period size: 13 Copynumber: 4.7 Consensus size: 13
44671413 ACCAAATTTT
44671423 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
44671436 TCAAAAGCACTTT
1 TCAAAAGCACTTC
* *
44671449 TCCACAGCACTTC
1 TCAAAAGCACTTC
*
44671462 TCAAAAGCACTTT
1 TCAAAAGCACTTC
44671475 TCAAAAGCA
1 TCAAAAGCA
44671484 TTGCCAAACT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.38, C:0.30, G:0.08, T:0.25
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:44671483 original size:26 final size:26
Alignment explanation
Indices: 44671420--44671483 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
44671410 TAAACCAAAT
44671420 TTTTCAAAAGCACTTCTCAAAAGCAC
1 TTTTCAAAAGCACTTCTCAAAAGCAC
* *
44671446 TTTTCCACAGCACTTCTCAAAAGCAC
1 TTTTCAAAAGCACTTCTCAAAAGCAC
44671472 TTTTCAAAAGCA
1 TTTTCAAAAGCA
44671484 TTGCCAAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (26 bp):
TTTTCAAAAGCACTTCTCAAAAGCAC
Found at i:44689882 original size:43 final size:43
Alignment explanation
Indices: 44689829--44689917 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
44689819 TATAAGTTCT
*
44689829 TGTGCCATACAATTATAGCTTCGGCTAATTAATTTGCACTAAG
1 TGTGCCATACAATTATAGCTTCGGCTAATTAATTAGCACTAAG
* *
44689872 TGTGCGATACAATTATAGCTTCGGTTAATTAATTAGCACTAAG
1 TGTGCCATACAATTATAGCTTCGGCTAATTAATTAGCACTAAG
44689915 TGT
1 TGT
44689918 ACGAGTTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (43 bp):
TGTGCCATACAATTATAGCTTCGGCTAATTAATTAGCACTAAG
Found at i:44693780 original size:40 final size:40
Alignment explanation
Indices: 44693722--44693873 Score: 143
Period size: 40 Copynumber: 3.8 Consensus size: 40
44693712 GGATATAGCG
* * * *
44693722 ACTCGCTCGATTGTCTTCGGGACATT-GCCCGGTTATAGTG
1 ACTCGCACAATTGCCTTCGGGACATTAGCCCGGTT-TAGTA
* *
44693762 ATTCTCACAATTGCCTTCGGGA-ATTAGCCCGGATTTAGTA
1 ACTCGCACAATTGCCTTCGGGACATTAGCCCGG-TTTAGTA
* *
44693802 ACTCGCACGAA-TGCCTTCGGGAC-TTAACCCGGTTTTGGTA
1 ACTCGCAC-AATTGCCTTCGGGACATTAGCCCGG-TTTAGTA
* *
44693842 ACTCGCACAAATGCCTTCGGGAC-TTAACCCGG
1 ACTCGCACAATTGCCTTCGGGACATTAGCCCGG
44693874 ACTTAACCCA
Statistics
Matches: 96, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
39 5 0.05
40 87 0.91
41 4 0.04
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (40 bp):
ACTCGCACAATTGCCTTCGGGACATTAGCCCGGTTTAGTA
Found at i:44693834 original size:80 final size:80
Alignment explanation
Indices: 44693722--44693874 Score: 182
Period size: 80 Copynumber: 1.9 Consensus size: 80
44693712 GGATATAGCG
* * * * * * * *
44693722 ACTCGCTCGATTGTCTTCGGGACATTGCCCGGTTATAGTGATTCTCACAATTGCCTTCGGGAATT
1 ACTCGCACGAATGCCTTCGGGACATTACCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATT
*
44693787 AGCCCGGATTTAGTA
66 AACCCGGATTTAGTA
* * *
44693802 ACTCGCACGAATGCCTTCGGGAC-TTAACCCGGTTTTGGTAACTCGCACAAATGCCTTCGGGACT
1 ACTCGCACGAATGCCTTCGGGACATT-ACCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAAT
44693866 TAACCCGGA
65 TAACCCGGA
44693875 CTTAACCCAG
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 2 0.03
80 58 0.97
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.28
Consensus pattern (80 bp):
ACTCGCACGAATGCCTTCGGGACATTACCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATT
AACCCGGATTTAGTA
Found at i:44693902 original size:51 final size:51
Alignment explanation
Indices: 44693821--44693925 Score: 174
Period size: 51 Copynumber: 2.1 Consensus size: 51
44693811 AATGCCTTCG
* * *
44693821 GGACTTAACCCGGTTTTGGTAACTCGCACAAATGCCTTCGGGACTTAACCC
1 GGACTTAACCCAGTTTTGGTAACTCACACAAATGCCTTCGGGAATTAACCC
*
44693872 GGACTTAACCCAGTTTTGGTAACTCACACAAATGCCTTCGGGAATTGACCC
1 GGACTTAACCCAGTTTTGGTAACTCACACAAATGCCTTCGGGAATTAACCC
44693923 GGA
1 GGA
44693926 TTTAGTCACT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (51 bp):
GGACTTAACCCAGTTTTGGTAACTCACACAAATGCCTTCGGGAATTAACCC
Found at i:44694683 original size:2 final size:2
Alignment explanation
Indices: 44694676--44694701 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44694666 ATGTGCAAAC
44694676 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
44694702 GCTAGAGCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44699548 original size:43 final size:43
Alignment explanation
Indices: 44699496--44699596 Score: 166
Period size: 43 Copynumber: 2.3 Consensus size: 43
44699486 GGTTTAATCT
* *
44699496 ATTGGCACTAAGTGTGTGATACAATTATAGCTTCGGCTAATTA
1 ATTGGCACTAAGTGTGCGATACAATTATAGCTTCAGCTAATTA
*
44699539 ATTGGCACTAAGTGTGCGATACAATTATAGCTTCAGTTAATTA
1 ATTGGCACTAAGTGTGCGATACAATTATAGCTTCAGCTAATTA
*
44699582 ATTAGCACTAAGTGT
1 ATTGGCACTAAGTGT
44699597 ACGAGTTTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.35
Consensus pattern (43 bp):
ATTGGCACTAAGTGTGCGATACAATTATAGCTTCAGCTAATTA
Found at i:44711098 original size:7 final size:7
Alignment explanation
Indices: 44711081--44711124 Score: 74
Period size: 7 Copynumber: 6.6 Consensus size: 7
44711071 ATGGGGGTAA
44711081 GATTT-T
1 GATTTCT
44711087 GATTTCT
1 GATTTCT
44711094 GATTTCT
1 GATTTCT
44711101 GATTTCT
1 GATTTCT
44711108 GATTTCT
1 GATTTCT
44711115 GATTT-T
1 GATTTCT
44711121 GATT
1 GATT
44711125 AACACATCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 10 0.27
7 27 0.73
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.59
Consensus pattern (7 bp):
GATTTCT
Found at i:44717182 original size:16 final size:15
Alignment explanation
Indices: 44717161--44717191 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
44717151 AGACTGTTTA
44717161 TCTGTATTTGTATATT
1 TCTGTATTTG-ATATT
44717177 TCTGTATTTGATATT
1 TCTGTATTTGATATT
44717192 GGGGATGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TCTGTATTTGATATT
Found at i:44717408 original size:6 final size:7
Alignment explanation
Indices: 44717382--44717410 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
44717372 TGGGGTAAGA
44717382 TTCTGAT
1 TTCTGAT
44717389 TTCTGAT
1 TTCTGAT
44717396 TTCTGAT
1 TTCTGAT
44717403 TT-TGAT
1 TTCTGAT
44717409 TT
1 TT
44717411 GCACATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.14, C:0.10, G:0.14, T:0.62
Consensus pattern (7 bp):
TTCTGAT
Found at i:44722718 original size:29 final size:29
Alignment explanation
Indices: 44722686--44722816 Score: 235
Period size: 29 Copynumber: 4.5 Consensus size: 29
44722676 ATAGTGAATC
44722686 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
44722715 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATAT-ATTTTCAGCT
*
44722745 CGCACACTTAGTGCTATATATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCT
*
44722774 CGCACACTTAGTGCTATATATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCT
44722803 CGCACACTTAGTGC
1 CGCACACTTAGTGC
44722817 CAATCTTGTC
Statistics
Matches: 100, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
29 71 0.71
30 29 0.29
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAGCT
Found at i:44722778 original size:59 final size:58
Alignment explanation
Indices: 44722686--44722816 Score: 235
Period size: 59 Copynumber: 2.2 Consensus size: 58
44722676 ATAGTGAATC
44722686 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATAT-ATTTTCAGCT
* *
44722745 CGCACACTTAGTGCTATATATTTTCAGTTCGCACACTTAGTGCTATATATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATATTTTCAGCT
44722803 CGCACACTTAGTGC
1 CGCACACTTAGTGC
44722817 CAATCTTGTC
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
58 23 0.33
59 47 0.67
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (58 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATATTTTCAGCT
Found at i:44723271 original size:2 final size:2
Alignment explanation
Indices: 44723264--44723291 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44723254 CATACTTATG
44723264 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44723292 GGCATCACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44724159 original size:19 final size:18
Alignment explanation
Indices: 44724135--44724170 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
44724125 CCCCCTTTTT
*
44724135 CTTTTCTTATTTTATTCCC
1 CTTTTCTT-TTTAATTCCC
44724154 CTTTTCTTTTTAATTCC
1 CTTTTCTTTTTAATTCC
44724171 TTTCTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.11, C:0.25, G:0.00, T:0.64
Consensus pattern (18 bp):
CTTTTCTTTTTAATTCCC
Found at i:44726915 original size:20 final size:20
Alignment explanation
Indices: 44726877--44726924 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
44726867 TTAAATTCTA
* **
44726877 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
44726897 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
44726917 AAA-ATAAA
1 AAAGATAAA
44726925 ATCCTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:44733086 original size:27 final size:27
Alignment explanation
Indices: 44733043--44733095 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
44733033 TAAAATAATG
* *
44733043 TTTTTCCTATTTGAATCACTCTAAATT
1 TTTTTCCAATTTGAATCACTCCAAATT
44733070 TTTTTCTCAATTT-AATCACTCCAAAT
1 TTTTTC-CAATTTGAATCACTCCAAAT
44733096 AAAATTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.28, C:0.21, G:0.02, T:0.49
Consensus pattern (27 bp):
TTTTTCCAATTTGAATCACTCCAAATT
Found at i:44733877 original size:44 final size:44
Alignment explanation
Indices: 44733810--44733898 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
44733800 AGCATTAACC
44733810 AACTTAGCTCATTTAATTCGATCCTCTTAGGATGCAAGATACTT
1 AACTTAGCTCATTTAATTCGATCCTCTTAGGATGCAAGATACTT
* * * *
44733854 AACTTAGCTCATTTAGTTTGATCCTCTTAGGATGGAAGATCCTT
1 AACTTAGCTCATTTAATTCGATCCTCTTAGGATGCAAGATACTT
44733898 A
1 A
44733899 GTATCCCTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (44 bp):
AACTTAGCTCATTTAATTCGATCCTCTTAGGATGCAAGATACTT
Found at i:44741311 original size:2 final size:2
Alignment explanation
Indices: 44741304--44741345 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
44741294 TAGACCTCAG
44741304 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44741346 TATGGATTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44743642 original size:28 final size:27
Alignment explanation
Indices: 44743556--44743645 Score: 92
Period size: 27 Copynumber: 3.2 Consensus size: 27
44743546 GTGATAGAGT
* *
44743556 CACCAGATACAGATATTTTGTGACAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
** *
44743585 CACCAGAACAGAT-ATACGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
44743612 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
44743640 CACCAG
1 CACCAG
44743646 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 22 0.43
28 22 0.43
29 7 0.14
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.19
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Found at i:44751461 original size:40 final size:39
Alignment explanation
Indices: 44751343--44751468 Score: 121
Period size: 40 Copynumber: 3.2 Consensus size: 39
44751333 TTCGAATGAT
*
44751343 ATCCGGGCTAAG-TCCCGAAGGCTTT-GTGCTAAGTGACTAA
1 ATCCGGACTAAGAT-CCGAAGGCTTTCGTGC-AAGT-ACTAA
** * * * *
44751383 ATATGGACTAAGATCCGACGGCATACGTGCGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCTTTCGTGCAAG-TACTAA
*
44751423 ATCCGGACTAAGATCCGAAGGCTTTCGAGCAAGCTACTAA
1 ATCCGGACTAAGATCCGAAGGCTTTCGTGCAAG-TACTAA
44751463 ATCCGG
1 ATCCGG
44751469 GTTGAGTCCC
Statistics
Matches: 68, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
40 62 0.91
41 6 0.09
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.22
Consensus pattern (39 bp):
ATCCGGACTAAGATCCGAAGGCTTTCGTGCAAGTACTAA
Found at i:44763189 original size:40 final size:40
Alignment explanation
Indices: 44763110--44763267 Score: 151
Period size: 40 Copynumber: 4.0 Consensus size: 40
44763100 TTCGAATGAT
* * * *
44763110 ATCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTAA
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGC-GAGTTACTAA
* *
44763150 ATCCGGACTAAGATCCGACGGCATACGTGCGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
* * * *
44763190 ATCCGGACTAAGATCCGAAGGCTTTCGAGCAAGCTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
** *
44763230 ATCCGGGTTGAG-TCCCGAAGGCATTCGTGCGAGTTACT
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACT
44763268 GTAACCGGGC
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 89 0.93
41 6 0.06
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
Done.