Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 157 of 311
Found at i:53488889 original size:13 final size:13
Alignment explanation
Indices: 53488871--53488899 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
53488861 TTTAGTTTAA
53488871 TTAGTTAATTAGT
1 TTAGTTAATTAGT
53488884 TTAGTTAATTAGT
1 TTAGTTAATTAGT
53488897 TTA
1 TTA
53488900 ATGAACAACC
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:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:53491949 original size:7 final size:7
Alignment explanation
Indices: 53491927--53491964 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
53491917 CACTAACATA
*
53491927 TTTTGAT
1 TTTTTAT
53491934 TTCTTTAT
1 TT-TTTAT
53491942 TTTTTAT
1 TTTTTAT
53491949 TTTTTAT
1 TTTTTAT
53491956 TTTTTAT
1 TTTTTAT
53491963 TT
1 TT
53491965 CTAACACTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
7 23 0.79
8 6 0.21
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.82
Consensus pattern (7 bp):
TTTTTAT
Found at i:53491959 original size:14 final size:15
Alignment explanation
Indices: 53491927--53491966 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
53491917 CACTAACATA
*
53491927 TTTTGATTTCTTTAT
1 TTTTTATTTCTTTAT
53491942 TTTTTATTT-TTTAT
1 TTTTTATTTCTTTAT
53491956 TTTTTATTTCT
1 TTTTTATTTCT
53491967 AACACTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.12, C:0.05, G:0.03, T:0.80
Consensus pattern (15 bp):
TTTTTATTTCTTTAT
Found at i:53493242 original size:174 final size:174
Alignment explanation
Indices: 53492946--53493295 Score: 583
Period size: 174 Copynumber: 2.0 Consensus size: 174
53492936 GATTTAGTTA
*
53492946 AATGTTAACACATCTTGGACCTACTATATCAATGCTCATACATATTCAAGTACATTATGTCATCA
1 AATGTTAACACATCTTAGACCTACTATATCAATGCTCATACATATTCAAGTACATTATGTCATCA
* *
53493011 TCGAGAGGCAAGAAGTCCATGGTCCCATCCTCAAAGAGACGTAGGGGACCGGGTTCTTCCTCTAT
66 TCGAGAGGCAAGAAGGCCATGGTCCCATCCTCAAAGAGACGTAGGGGACCAGGTTCTTCCTCTAT
* *
53493076 ATGTGCTACAACCGAAGTTCGGCACCCATTCCTTGAGTTTTTGC
131 ACGTGCTACAACCGAAGTTCGGCACCCATTCCTTGAGTTTTCGC
53493120 AATGTTAACACATCTTAGACCTACTATATCAATGCTCATACATATTCAAGTACATTATGTCATCA
1 AATGTTAACACATCTTAGACCTACTATATCAATGCTCATACATATTCAAGTACATTATGTCATCA
* * * * *
53493185 TTGAGAGGCAAGAAGGCCGTGGTCCCATCTTCAAAGAGACGTAGGGGATCAGGTTCTTCCTCTGT
66 TCGAGAGGCAAGAAGGCCATGGTCCCATCCTCAAAGAGACGTAGGGGACCAGGTTCTTCCTCTAT
* * *
53493250 ACGTGCTACAGCTGAAGTTCGGCACCCGTTCCTTGAGTTTTCGC
131 ACGTGCTACAACCGAAGTTCGGCACCCATTCCTTGAGTTTTCGC
53493294 AA
1 AA
53493296 GCTTCATAGG
Statistics
Matches: 163, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
174 163 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (174 bp):
AATGTTAACACATCTTAGACCTACTATATCAATGCTCATACATATTCAAGTACATTATGTCATCA
TCGAGAGGCAAGAAGGCCATGGTCCCATCCTCAAAGAGACGTAGGGGACCAGGTTCTTCCTCTAT
ACGTGCTACAACCGAAGTTCGGCACCCATTCCTTGAGTTTTCGC
Found at i:53495985 original size:37 final size:37
Alignment explanation
Indices: 53495923--53496068 Score: 177
Period size: 37 Copynumber: 3.9 Consensus size: 37
53495913 AGCTCAGACG
* *
53495923 AAATCTCCACACGA-AGTTATCGGGTCTTACCCGGGCA
1 AAATCTCCACAC-ATAGTCATCGGGTCTTACCCGGACA
*
53495960 AAATCTCCACACATAGTCATTGGGTCTTACCCGGACA
1 AAATCTCCACACATAGTCATCGGGTCTTACCCGGACA
* * * *
53495997 TACTCTCCACACGTAGTCATCGGGTCTTACCCAGACA
1 AAATCTCCACACATAGTCATCGGGTCTTACCCGGACA
* * * *
53496034 TAATCTCCATACGTAGTCATCGGGTCTCACCCGGA
1 AAATCTCCACACATAGTCATCGGGTCTTACCCGGA
53496069 ATATATTTCC
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
36 1 0.01
37 95 0.99
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACATAGTCATCGGGTCTTACCCGGACA
Found at i:53496051 original size:74 final size:74
Alignment explanation
Indices: 53495926--53496068 Score: 205
Period size: 74 Copynumber: 1.9 Consensus size: 74
53495916 TCAGACGAAA
* * * * *
53495926 TCTCCACACGAAGTTATCGGGTCTTACCCGGGCAAAATCTCCACACATAGTCATTGGGTCTTACC
1 TCTCCACACGAAGTCATCGGGTCTTACCCAGACAAAATCTCCACACATAGTCATCGGGTCTCACC
53495991 CGGACATAC
66 CGGACATAC
* * * *
53496000 TCTCCACACGTAGTCATCGGGTCTTACCCAGACATAATCTCCATACGTAGTCATCGGGTCTCACC
1 TCTCCACACGAAGTCATCGGGTCTTACCCAGACAAAATCTCCACACATAGTCATCGGGTCTCACC
53496065 CGGA
66 CGGA
53496069 ATATATTTCC
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.24
Consensus pattern (74 bp):
TCTCCACACGAAGTCATCGGGTCTTACCCAGACAAAATCTCCACACATAGTCATCGGGTCTCACC
CGGACATAC
Found at i:53496352 original size:47 final size:47
Alignment explanation
Indices: 53496273--53496560 Score: 396
Period size: 47 Copynumber: 6.1 Consensus size: 47
53496263 TATATATATT
* * * * *
53496273 TCACATTGACCATTCGACTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * *
53496320 CCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
53496367 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCGCATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
53496414 TCACATAGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * * *
53496461 CCACATTGGCCATTTGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * * **
53496508 TCACATTGGTCATTCGACCTTATCACATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
53496555 TCACAT
1 TCACAT
53496561 AAAATCCTAA
Statistics
Matches: 211, Mismatches: 30, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 211 1.00
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:53496442 original size:22 final size:22
Alignment explanation
Indices: 53496366--53496442 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
53496356 GCTCACATTC
*
53496366 ATCACATTGGCCATTCGGCCTT
1 ATCACATAGGCCATTCGGCCTT
* *
53496388 ATCACATATATG-CATGTTC-GCATT
1 ATCAC--ATAGGCCA--TTCGGCCTT
53496412 CATCACATAGGCCATTCGGCCTT
1 -ATCACATAGGCCATTCGGCCTT
53496435 ATCACATA
1 ATCACATA
53496443 TATGCATGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
22 16 0.37
23 10 0.23
24 9 0.21
25 8 0.19
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (22 bp):
ATCACATAGGCCATTCGGCCTT
Found at i:53496444 original size:141 final size:141
Alignment explanation
Indices: 53496273--53496561 Score: 470
Period size: 141 Copynumber: 2.0 Consensus size: 141
53496263 TATATATATT
* *
53496273 TCACATTGACCATTCGACTTTACCACATATATGCATGTTCATATTCACCACATTGGCCATTCGGC
1 TCACATAGACCATTCGACCTTACCACATATATGCATGTTCATATTCACCACATTGGCCATTCGGC
* * *
53496338 CTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
66 CTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGACCTTATCACATATATACAC
* *
53496403 GTTCGCATTCA
131 ATTCACATTCA
* * * *
53496414 TCACATAGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCACCACATTGGCCATTTGGC
1 TCACATAGACCATTCGACCTTACCACATATATGCATGTTCATATTCACCACATTGGCCATTCGGC
*
53496479 CTTATCACACATATGCATGCTCACATTCATCACATTGGTCATTCGACCTTATCACATATATACAC
66 CTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGACCTTATCACATATATACAC
53496544 ATTCACATTCA
131 ATTCACATTCA
53496555 TCACATA
1 TCACATA
53496562 AAATCCTAAA
Statistics
Matches: 136, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
141 136 1.00
ACGTcount: A:0.28, C:0.29, G:0.11, T:0.33
Consensus pattern (141 bp):
TCACATAGACCATTCGACCTTACCACATATATGCATGTTCATATTCACCACATTGGCCATTCGGC
CTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGACCTTATCACATATATACAC
ATTCACATTCA
Found at i:53509126 original size:13 final size:13
Alignment explanation
Indices: 53509108--53509136 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
53509098 TTTAGTTTAA
53509108 TTAGTTAATTAGT
1 TTAGTTAATTAGT
53509121 TTAGTTAATTAGT
1 TTAGTTAATTAGT
53509134 TTA
1 TTA
53509137 ACGAACAACC
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:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:53514036 original size:17 final size:19
Alignment explanation
Indices: 53513994--53514037 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
53513984 ATGAAATTTT
*
53513994 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
53514013 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
53514031 AA-TATTA
1 AATTATTA
53514038 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:53527770 original size:24 final size:24
Alignment explanation
Indices: 53527741--53527788 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
53527731 ACTCAAAGGA
53527741 AGAAATTATTTTTATGCATTTAAG
1 AGAAATTATTTTTATGCATTTAAG
53527765 AGAAATTATTTTTATGCATTTAAG
1 AGAAATTATTTTTATGCATTTAAG
53527789 GTTCGGCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (24 bp):
AGAAATTATTTTTATGCATTTAAG
Found at i:53528043 original size:29 final size:29
Alignment explanation
Indices: 53528011--53528071 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
53528001 TAAAGTGATT
* *
53528011 TTGAGTAAAAATGTATATT-AGGGATTAAA
1 TTGAG-AAAAATATAAATTGAGGGATTAAA
* *
53528040 TTGAGAAAAGTATAAATTGAGGGGTTAAA
1 TTGAGAAAAATATAAATTGAGGGATTAAA
53528069 TTG
1 TTG
53528072 TGAGATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.43, C:0.00, G:0.25, T:0.33
Consensus pattern (29 bp):
TTGAGAAAAATATAAATTGAGGGATTAAA
Found at i:53529729 original size:8 final size:8
Alignment explanation
Indices: 53529716--53529740 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
53529706 AATTTTGAGT
53529716 ATTTTGTG
1 ATTTTGTG
53529724 ATTTTGTG
1 ATTTTGTG
53529732 ATTTTGTG
1 ATTTTGTG
53529740 A
1 A
53529741 ACAAGGGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (8 bp):
ATTTTGTG
Found at i:53530256 original size:43 final size:43
Alignment explanation
Indices: 53530216--53530314 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 43
53530206 CTTGAGATAT
*
53530216 CATGTAAGACCATGTTTGAGACACTGACATCGATTAGAGATTA
1 CATGTAAGACCATATTTGAGACACTGACATCGATTAGAGATTA
* * * * * **
53530259 CGTGTAAGACCCTATTTGGGACAGTGGCATCGA-TATTTGATTA
1 CATGTAAGACCATATTTGAGACACTGACATCGATTA-GAGATTA
53530302 CATGTAAGACCAT
1 CATGTAAGACCAT
53530315 GTCATGGACG
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
42 2 0.04
43 43 0.96
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29
Consensus pattern (43 bp):
CATGTAAGACCATATTTGAGACACTGACATCGATTAGAGATTA
Found at i:53533030 original size:28 final size:28
Alignment explanation
Indices: 53532990--53533105 Score: 155
Period size: 28 Copynumber: 4.2 Consensus size: 28
53532980 GGAGGAAGCA
53532990 TTCTGGTGGCTCTGCCACAAATATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
*
53533018 TTCTAGTGGCTCTGCCACAAATATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
* * *
53533046 TTCTGGTGGCCCTGCCACAATTATCTCT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
* * *
53533074 ATCTGGTGACTCTGTCAC-AATATCTG-
1 TTCTGGTGGCTCTGCCACAAATATCTGT
53533100 TTCTGG
1 TTCTGG
53533106 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
26 5 0.07
27 6 0.08
28 65 0.86
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.36
Consensus pattern (28 bp):
TTCTGGTGGCTCTGCCACAAATATCTGT
Found at i:53538456 original size:47 final size:47
Alignment explanation
Indices: 53538402--53538592 Score: 274
Period size: 47 Copynumber: 4.1 Consensus size: 47
53538392 GATTTTATGA
** * * *
53538402 GATGAATGTGAATGTGTATATATGAGATAAGGCCTAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
53538449 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
* *
53538496 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAGTGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
* * ** *
53538543 GATGAATGTGAACATGCATATGTGTTATAAGGTAGAATGGCTAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
53538590 GAT
1 GAT
53538593 AAACGTGGAA
Statistics
Matches: 132, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 132 1.00
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.28
Consensus pattern (47 bp):
GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
Found at i:53538473 original size:25 final size:25
Alignment explanation
Indices: 53538445--53538523 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 25
53538435 CTAATGGCCA
53538445 ATGTGATGAATGTGAACATGCATAT
1 ATGTGATGAATGTGAACATGCATAT
* * *
53538470 ATGTGAT-AAGGCCG-A-ATGGC-CA-
1 ATGTGATGAATG-TGAACAT-GCATAT
53538492 ATGTGATGAATGTGAACATGCATAT
1 ATGTGATGAATGTGAACATGCATAT
*
53538517 GTGTGAT
1 ATGTGAT
53538524 AAGGCCGAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
22 8 0.20
23 9 0.22
24 9 0.22
25 14 0.35
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.29
Consensus pattern (25 bp):
ATGTGATGAATGTGAACATGCATAT
Found at i:53538627 original size:94 final size:94
Alignment explanation
Indices: 53538419--53538638 Score: 246
Period size: 94 Copynumber: 2.3 Consensus size: 94
53538409 GTGAATGTGT
* * * *
53538419 ATATATGAGATAAGGCCTAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGGCCG
1 ATATATGTGAGAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGGCAG
* *
53538484 AATGGCCAATGTGATGAATGTGAACATGC
66 AATGGCCAATGTGATAAACGTGAACATGC
* * * * * *
53538513 ATATGTGTGATAAGGCCGAATGGCCAGTGTGATGAATGTGAACATGCATATGTGTTATAAGGTAG
1 ATATATGTGAGAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGGCAG
* * *
53538578 AATGGCTAATGTGATAAACGTGGAA-GTGT
66 AATGGCCAATGTGATAAACGT-GAACATGC
* * *
53538607 ATATATGTGGCGAA-GTCGAATGGCTAATGTGA
1 ATATATGT-GAGAAGGCCGAATGGCCAATGTGA
53538639 GATATGTATG
Statistics
Matches: 105, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
94 99 0.94
95 6 0.06
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.27
Consensus pattern (94 bp):
ATATATGTGAGAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGGCAG
AATGGCCAATGTGATAAACGTGAACATGC
Found at i:53541761 original size:46 final size:46
Alignment explanation
Indices: 53541711--53541839 Score: 195
Period size: 46 Copynumber: 2.8 Consensus size: 46
53541701 TGGTTGAGCA
*
53541711 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
53541757 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
53541803 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53541840 GCAGGTTACG
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:53544696 original size:15 final size:15
Alignment explanation
Indices: 53544650--53544684 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
53544640 GTATCTTGGG
53544650 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
53544665 TTACTTTATTCTGGA
1 TTTCTTTATTCTGGA
53544680 TTTCT
1 TTTCT
53544685 CTATCTTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.14, C:0.14, G:0.11, T:0.60
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:53547104 original size:46 final size:46
Alignment explanation
Indices: 53547044--53547171 Score: 175
Period size: 46 Copynumber: 2.8 Consensus size: 46
53547034 GGTTGAGCAT
* * *
53547044 CCGAACTCGCTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
* * * *
53547090 CTGAACTCGTTGAGTTGAGTCTGAGTTCACTCATGGATGCGAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
* *
53547136 CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53547172 GCGGGTTACA
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 70 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
Found at i:53548955 original size:8 final size:8
Alignment explanation
Indices: 53548937--53548988 Score: 70
Period size: 8 Copynumber: 6.6 Consensus size: 8
53548927 TATGTATCGG
53548937 CAAAA-GC
1 CAAAATGC
*
53548944 CGAAATGC
1 CAAAATGC
*
53548952 CGAAATGC
1 CAAAATGC
53548960 CAAAATGC
1 CAAAATGC
53548968 CAAAATGC
1 CAAAATGC
*
53548976 CAAAAAGC
1 CAAAATGC
53548984 CAAAA
1 CAAAA
53548989 GTTTGGATAC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
7 4 0.10
8 37 0.90
ACGTcount: A:0.52, C:0.25, G:0.15, T:0.08
Consensus pattern (8 bp):
CAAAATGC
Found at i:53549250 original size:29 final size:28
Alignment explanation
Indices: 53549198--53549312 Score: 122
Period size: 29 Copynumber: 4.0 Consensus size: 28
53549188 GTGAGCATGA
* *
53549198 ATATGAATGTGACTAGGCCTAATGGGCC
1 ATATAAATGTGATTAGGCCTAATGGGCC
53549226 ATATAAATGTGATTTAGGCCTAATGGGCC
1 ATATAAATGTGA-TTAGGCCTAATGGGCC
* * *
53549255 ATATACAGGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGA-TTAGGCCTAATGGGCC
* * * * *
53549284 GTATGAATATGATTGGGCTTAATGGGCC
1 ATATAAATGTGATTAGGCCTAATGGGCC
53549312 A
1 A
53549313 GATATAAGTA
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
28 26 0.35
29 48 0.65
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.29
Consensus pattern (28 bp):
ATATAAATGTGATTAGGCCTAATGGGCC
Found at i:53552203 original size:25 final size:24
Alignment explanation
Indices: 53552143--53552243 Score: 112
Period size: 25 Copynumber: 4.1 Consensus size: 24
53552133 GCCTAGCCTC
* *
53552143 TTTTAATAACTAGGGCAAAGCCCT
1 TTTTGATAACTGGGGCAAAGCCCT
*
53552167 TTTTAATAACTGGGGCAAAGCCCT
1 TTTTGATAACTGGGGCAAAGCCCT
*
53552191 TTTTGATACACTGGGGCAAAGCTCT
1 TTTTGATA-ACTGGGGCAAAGCCCT
* * * *
53552216 TTTCGGTAAACTAGGCCAAAGCCCT
1 TTTTGAT-AACTGGGGCAAAGCCCT
53552241 TTT
1 TTT
53552244 GCACTTCCTC
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
24 30 0.45
25 36 0.54
26 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (24 bp):
TTTTGATAACTGGGGCAAAGCCCT
Found at i:53552316 original size:20 final size:21
Alignment explanation
Indices: 53552291--53552338 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
53552281 AAATGAATAC
* *
53552291 ATCATGTGCTTATCATA-CAT
1 ATCATGTGCATATCATATCAA
53552311 ATCATGTGCATATCATATCAA
1 ATCATGTGCATATCATATCAA
53552332 ATCATGT
1 ATCATGT
53552339 ATATCAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (21 bp):
ATCATGTGCATATCATATCAA
Found at i:53575908 original size:27 final size:27
Alignment explanation
Indices: 53575878--53575960 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 27
53575868 ATCATTATTC
*
53575878 TACCATACAGGGGTATTACGGTCGTTT
1 TACCATACAGGGGTATTACGGTCATTT
* * * * *
53575905 TACCTTACAGGGGCATCATGGTTATTT
1 TACCATACAGGGGTATTACGGTCATTT
* * * *
53575932 TACCCTACAAGGGTACTACGGTTATTT
1 TACCATACAGGGGTATTACGGTCATTT
53575959 TA
1 TA
53575961 TACTACCAGG
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (27 bp):
TACCATACAGGGGTATTACGGTCATTT
Found at i:53576089 original size:26 final size:27
Alignment explanation
Indices: 53575972--53576093 Score: 160
Period size: 27 Copynumber: 4.6 Consensus size: 27
53575962 ACTACCAGGT
* * *
53575972 TATTTCGATAATTTTCTAAACTGGGGG
1 TATTTCGGTAATTTTCCAAACTCGGGG
*
53575999 TATTTCGATAATTTTCCAAACT-GGAGG
1 TATTTCGGTAATTTTCCAAACTCGG-GG
53576026 TATTTCGGTAATTTTCCAAA-TCGAGGG
1 TATTTCGGTAATTTTCCAAACTCG-GGG
*
53576053 TATTTCAGTAATTTTCCAAACT-GGGG
1 TATTTCGGTAATTTTCCAAACTCGGGG
53576079 TATTTCGGTAATTTT
1 TATTTCGGTAATTTT
53576094 ACAATCTAAG
Statistics
Matches: 87, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
26 20 0.23
27 65 0.75
28 2 0.02
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (27 bp):
TATTTCGGTAATTTTCCAAACTCGGGG
Found at i:53585465 original size:42 final size:42
Alignment explanation
Indices: 53585400--53585526 Score: 146
Period size: 43 Copynumber: 3.0 Consensus size: 42
53585390 CATCAACTGG
53585400 TGATTTACGTGTAAGACCATGTCTGAGACATTGGCATCGTATA
1 TGATTT-CGTGTAAGACCATGTCTGAGACATTGGCATCGTATA
* * * * *
53585443 TGATTTCGTGTAAGACCTTGTCTGGGACAGTGGCTTCGATATT
1 TGATTTCGTGTAAGACCATGTCTGAGACATTGGCATCG-TATA
* * * * *
53585486 TGACTACATGTAAGACCACGTCTGAGACATTGGCATTGTAT
1 TGATTTCGTGTAAGACCATGTCTGAGACATTGGCATCGTAT
53585527 GAGCTTACGA
Statistics
Matches: 69, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
42 31 0.45
43 38 0.55
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCATGTCTGAGACATTGGCATCGTATA
Found at i:53586407 original size:40 final size:40
Alignment explanation
Indices: 53586299--53586434 Score: 188
Period size: 40 Copynumber: 3.4 Consensus size: 40
53586289 NNNNNNNGGC
* * *
53586299 TAAG-CCCGAAGGCACTGGTGCGAGCTACTAAAATCCGGGT
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAATCCGGGT
53586339 TAAGTCCCGAAGGCATTTGTGCGA-TTACTAAATCCGGGT
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGT
*
53586378 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGT
*
53586418 TATGTCCCGAAGGCATT
1 TAAGTCCCGAAGGCATT
53586435 GAACGAGGAG
Statistics
Matches: 88, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
39 34 0.39
40 35 0.40
41 19 0.22
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGT
Found at i:53586453 original size:79 final size:78
Alignment explanation
Indices: 53586299--53586458 Score: 180
Period size: 79 Copynumber: 2.0 Consensus size: 78
53586289 NNNNNNNGGC
* ** *
53586299 TAAGCCCGAAGGCACTGGTGCGAGCTACTAAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAT
1 TAAGCCCGAAGGCACTGGTGCGAGCTACTAAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAG
*
53586364 TACTAAATCCGGGT
66 GACTAAATCC-GGT
* * * * *
53586378 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCA-TTGAACGA
1 TAAG-CCCGAAGGCACTGGTGCGAGCTACTAAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGA
*
53586441 GGAGCTATATCCGGT
65 GGA-CTAAATCCGGT
53586456 TAA
1 TAA
53586459 ATTCTGAAGG
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
78 13 0.19
79 30 0.44
80 25 0.37
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.24
Consensus pattern (78 bp):
TAAGCCCGAAGGCACTGGTGCGAGCTACTAAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAG
GACTAAATCCGGT
Found at i:53591130 original size:47 final size:47
Alignment explanation
Indices: 53590847--53591116 Score: 387
Period size: 47 Copynumber: 5.9 Consensus size: 47
53590837 TGTGATGTGT
*
53590847 ATATATGAGATAAGGCCGAATGG-CAATGTGATGAATGTGAACATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
* *
53590893 ATATGTGTGATAAGGCCGACATGGCCAATGTGATGAA--TGAGCATGC
1 ATATATGTGATAAGGCCGA-ATGGCCAATGTGATGAATGTGAACATGC
*
53590939 ATATGTGTGATAAGG-CGAATGGCC-ATGTGATGAA--T-AACATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
* *
53590981 ATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAGCATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
*
53591028 -TATGATGTGATAAGGCCGAATCGCCAATGTGATGAATGTGAACATGC
1 ATAT-ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
*
53591075 ATATATGTGATAAGGCAGAATGGCCAATGTGATGAATGTGAA
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
53591117 AAGTGTAATA
Statistics
Matches: 203, Mismatches: 12, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
42 20 0.10
43 19 0.09
44 16 0.08
45 3 0.01
46 44 0.22
47 86 0.42
48 15 0.07
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.26
Consensus pattern (47 bp):
ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
Found at i:53591593 original size:40 final size:40
Alignment explanation
Indices: 53591526--53591661 Score: 192
Period size: 40 Copynumber: 3.5 Consensus size: 40
53591516 TCAAACCGGC
*
53591526 TAAG-CCCGAAGGCA--TGTGCGAGCTACTAAATCCGGGT
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGT
53591563 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGT
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGT
*
53591603 TAAGTCCCGAAGGCAATTTGTGCG-GTTACTATAA-CCGGGC
1 TAAGTCCCGAAGGC-ATTTGTGCGAGTTACTA-AATCCGGGT
*
53591643 TATGTCCCGAAGGCATTTG
1 TAAGTCCCGAAGGCATTTG
53591662 AACGAGGAGC
Statistics
Matches: 91, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
37 4 0.04
38 10 0.11
39 5 0.05
40 61 0.67
41 11 0.12
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGT
Found at i:53591679 original size:80 final size:77
Alignment explanation
Indices: 53591521--53591694 Score: 176
Period size: 80 Copynumber: 2.2 Consensus size: 77
53591511 AGATATCAAA
* * **
53591521 CCGGCTAAG-CCCGAAGGCATGTGCGAGCTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGC
1 CCGGTTAAGTCCCGAAGGCATGTGCGAGCTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAAC
*
53591585 GAGTTACTAAAT
66 GAGTGACTAAAT
* *
53591597 CCGGGTTAAGTCCCGAAGGCAATTTGTGCG-GTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 CC-GGTTAAGTCCCGAAGGC-A--TGTGCGAGCTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
*
53591660 TGAACGAG-GAGCTATAT
61 TGAACGAGTGA-CTAAAT
* *
53591677 CCGGTTAAATTCCGAAGG
1 CCGGTTAAGTCCCGAAGG
53591695 TACGTGATTT
Statistics
Matches: 81, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
76 2 0.02
77 6 0.07
78 9 0.11
79 16 0.20
80 40 0.49
81 8 0.10
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (77 bp):
CCGGTTAAGTCCCGAAGGCATGTGCGAGCTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAAC
GAGTGACTAAAT
Found at i:53599486 original size:40 final size:40
Alignment explanation
Indices: 53599402--53599626 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
53599392 TTGAATGATG
* * * *
53599402 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
53599442 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
53599482 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
53599521 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
53599561 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
53599602 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53599627 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:53599648 original size:119 final size:119
Alignment explanation
Indices: 53599402--53599659 Score: 283
Period size: 119 Copynumber: 2.2 Consensus size: 119
53599392 TTGAATGATG
* *
53599402 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* ** *
53599467 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
* * * **
53599521 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
53599584 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTGA-CTAAA
* *
53599641 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
53599660 TACGTGATTT
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 83 0.71
120 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
Found at i:53609924 original size:43 final size:43
Alignment explanation
Indices: 53609858--53609941 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
53609848 AAATTGTACA
*
53609858 ATGCCAATGTCCCAGACGTGGTCTTACATGTAACCACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGTAAACACATATCG
* *
53609901 ATGCCACTGTCCCAGACAG-GGTCTTACTTGTAAACACATAT
1 ATGCCAATGTCCCAGAC-GTGGTCTTACATGTAAACACATAT
53609942 TGGAATCACA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 36 0.97
44 1 0.03
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACATGTAAACACATATCG
Found at i:53612894 original size:34 final size:33
Alignment explanation
Indices: 53612856--53612936 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 33
53612846 GTAAATAGTT
*
53612856 TGGGCCTAAGCCC-TTATCAGTAGAAATATCAGTG
1 TGGGCCTAAGCCCATTA-CAGTA-AAAGATCAGTG
* * *
53612890 TGGGCCTTAGCCCATTACGGTAATAGATCAGTG
1 TGGGCCTAAGCCCATTACAGTAAAAGATCAGTG
* *
53612923 TGGGCTTTAGCCCA
1 TGGGCCTAAGCCCA
53612937 ATTTAGTACA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 22 0.54
34 16 0.39
35 3 0.07
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (33 bp):
TGGGCCTAAGCCCATTACAGTAAAAGATCAGTG
Found at i:53615202 original size:30 final size:30
Alignment explanation
Indices: 53615168--53615250 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
53615158 CGTTTGCAGT
53615168 AAAGGCTTCGGCCTAGTGATATG-ATAATGA
1 AAAGGCTTCGGCC-AGTGATATGAATAATGA
* * *
53615198 AAAGGCTTTGGTCCAGTGACATGAATAATGC
1 AAAGGCTTCGG-CCAGTGATATGAATAATGA
*
53615229 AAAGGCTTCAGCCCAGT-ATATG
1 AAAGGCTTC-GGCCAGTGATATG
53615251 TTGAGATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
30 22 0.50
31 21 0.48
32 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (30 bp):
AAAGGCTTCGGCCAGTGATATGAATAATGA
Found at i:53615245 original size:31 final size:30
Alignment explanation
Indices: 53615168--53615245 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 30
53615158 CGTTTGCAGT
* *
53615168 AAAGGCTTCGGCCTAGTGATATGATAATGA
1 AAAGGCTTCGGCCCAGTGACATGATAATGA
* * *
53615198 AAAGGCTTTGGTCCAGTGACATGAATAATGC
1 AAAGGCTTCGGCCCAGTGACATG-ATAATGA
*
53615229 AAAGGCTTCAGCCCAGT
1 AAAGGCTTCGGCCCAGT
53615246 ATATGTTGAG
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 19 0.49
31 20 0.51
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (30 bp):
AAAGGCTTCGGCCCAGTGACATGATAATGA
Found at i:53618196 original size:43 final size:41
Alignment explanation
Indices: 53618140--53618266 Score: 103
Period size: 43 Copynumber: 3.0 Consensus size: 41
53618130 ATGTTGTACA
** * *
53618140 ATGCCAACCTCCCATACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAATATCCCAAACGTGGTCTTACAAG-AA-CACATATCG
* * *
53618183 ATGCCACTATCCCAGACAG-GGTCTTACACAAGAACACATATTG
1 ATGCCAATATCCCAAAC-GTGGTCTT--ACAAGAACACATATCG
* *
53618226 ATTCCAATGTCCCAAACGTGGTCTTACACGAGAACACATAT
1 ATGCCAATATCCCAAACGTGGTCTTACA--AGAACACATAT
53618267 AAAAAATCCT
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
41 3 0.04
42 1 0.01
43 57 0.84
44 3 0.04
45 4 0.06
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.24
Consensus pattern (41 bp):
ATGCCAATATCCCAAACGTGGTCTTACAAGAACACATATCG
Found at i:53618870 original size:15 final size:15
Alignment explanation
Indices: 53618850--53618878 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
53618840 CAAAAATTCC
53618850 AATACAAAACATATT
1 AATACAAAACATATT
53618865 AATACAAAACATAT
1 AATACAAAACATAT
53618879 CTTTCATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (15 bp):
AATACAAAACATATT
Found at i:53624118 original size:22 final size:24
Alignment explanation
Indices: 53624093--53624137 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
53624083 GTTTTTGGCT
*
53624093 TATGGAATG-ACATGA-ATTGGTA
1 TATGCAATGAACATGAGATTGGTA
*
53624115 TATGCTATGAACATGAGATTGGT
1 TATGCAATGAACATGAGATTGGT
53624138 TGATGCCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 6 0.32
24 6 0.32
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (24 bp):
TATGCAATGAACATGAGATTGGTA
Found at i:53624143 original size:24 final size:23
Alignment explanation
Indices: 53624102--53624149 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
53624092 TTATGGAATG
*
53624102 ACATGAATTGGTATATGCTATGA
1 ACATGAATTGGTATATGCCATGA
53624125 ACATGAGATTGGT-TGATGCCATGA
1 ACATGA-ATTGGTAT-ATGCCATGA
53624149 A
1 A
53624150 TGTTGAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.31
Consensus pattern (23 bp):
ACATGAATTGGTATATGCCATGA
Found at i:53634025 original size:50 final size:49
Alignment explanation
Indices: 53633852--53634089 Score: 289
Period size: 49 Copynumber: 4.8 Consensus size: 49
53633842 TAGCCAAAGC
* * * * *
53633852 TATCTGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* *
53633901 TATCCGGTACACGTAGTAGCCTACACTTAGTACTACACACGTGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* *
53633950 TATCTGGTACACGTAGTACCCTGCACTTAGTACTACACACGTGACCTAAC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC-AAT
* * * *
53634000 CATCTGATACACGTAGTAGCCTGCACTTAGTACTACACAAGTGATCACAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAAT
* * *
53634051 T-TTTGGGTACGCATAGTAGCCTGCACTTAGTACTACACA
1 TATCT-GGTACACGTAGTAGCCTGCACTTAGTACTACACA
53634090 TGCGACCTCA
Statistics
Matches: 163, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
49 85 0.52
50 44 0.27
51 33 0.20
52 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
Found at i:53636368 original size:43 final size:42
Alignment explanation
Indices: 53636238--53636399 Score: 132
Period size: 43 Copynumber: 3.8 Consensus size: 42
53636228 CGATATGTGT
* *
53636238 TTTCGTGTAAGACCACATCTGGAACGTTGGG-ATCGACT-TATGA
1 TTTCGTGTAAGACCATATCTGGGACG-TGGGCATC-A-TATATGA
* *
53636281 TTTACGTGTAAGACCATATCTGGGACGTTGGCATCATATTTGA
1 TTT-CGTGTAAGACCATATCTGGGACGTGGGCATCATATATGA
* * *
53636324 TTTCGTGTAAGACCCTGTCTGGGACAGTGGG-ACTGATATATGA
1 TTTCGTGTAAGACCATATCTGGGAC-GTGGGCA-TCATATATGA
* * ** * *
53636367 TTACATGTAAGACCACGTTTGGGACGTTGGCAT
1 TTTCGTGTAAGACCATATCTGGGACGTGGGCAT
53636400 TGTACGAGCT
Statistics
Matches: 98, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
42 27 0.28
43 47 0.48
44 24 0.24
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (42 bp):
TTTCGTGTAAGACCATATCTGGGACGTGGGCATCATATATGA
Found at i:53641661 original size:53 final size:54
Alignment explanation
Indices: 53641479--53641685 Score: 200
Period size: 53 Copynumber: 3.8 Consensus size: 54
53641469 ATTAGGGTTT
* * * * * *
53641479 AAGGATGCCAAGTAAGGCCATGACAAGGCATGGCATTGGTAAGTTCTACAAGGC
1 AAGGATACCAAGTAAGACCATGTCAAGACATGGCAATGGTAAGTTCTATAAGGC
* * * * * * *
53641533 AAGGAAATCAAGTAAAACCATGTCAAGACATGGCATTGATAAACTACTATAAGGC
1 AAGGATACCAAGTAAGACCATGTCAAGACATGGCAATGGT-AAGTTCTATAAGGC
* * * * * * *
53641588 AAAGATCCCATGTAACACCATGCCAAGGCATGGCAATGGTGAGTTC-ATAAGGC
1 AAGGATACCAAGTAAGACCATGTCAAGACATGGCAATGGTAAGTTCTATAAGGC
* *
53641641 AAGGATACCACGTAAGACCATGTCAAGACATGCCAATGGTAAGTT
1 AAGGATACCAAGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
53641686 TAAAAAGGAA
Statistics
Matches: 120, Mismatches: 32, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
53 44 0.37
54 35 0.29
55 41 0.34
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (54 bp):
AAGGATACCAAGTAAGACCATGTCAAGACATGGCAATGGTAAGTTCTATAAGGC
Found at i:53643174 original size:27 final size:27
Alignment explanation
Indices: 53643120--53643230 Score: 127
Period size: 27 Copynumber: 4.1 Consensus size: 27
53643110 AGCTTGGCTG
* * *
53643120 CCAGAACAGATAA-TGTGACAGGGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
53643146 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
* *
53643173 CCAAAATAGAT-ATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* * *
53643200 CTAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
53643227 CCAG
1 CCAG
53643231 GACGCTTCCT
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
26 15 0.21
27 54 0.76
28 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:53651200 original size:27 final size:27
Alignment explanation
Indices: 53651170--53651343 Score: 197
Period size: 27 Copynumber: 6.4 Consensus size: 27
53651160 TGAGTCCGCT
* * * *
53651170 CACTCAGTGCTATATAATCAACTCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
* *
53651197 CACTTAGTGCTACGTAATCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
53651224 CACTTAGTGCTACATAGTCAAACTCGCA
1 CACTTAGTGCTACATAGTCAAA-TCGCA
** * *
53651252 CACTTAGTGCCGCATGGTCAATTCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
* **
53651279 CACTTAGTGC-ATCATATTCATTTCGCA
1 CACTTAGTGCTA-CATAGTCAAATCGCA
*
53651306 CACTTAGTGCAACATAGTCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
53651333 CACTTAGTGCT
1 CACTTAGTGCT
53651344 GTACAATTTA
Statistics
Matches: 126, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 102 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CACTTAGTGCTACATAGTCAAATCGCA
Found at i:53651312 original size:82 final size:81
Alignment explanation
Indices: 53651187--53651342 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
53651177 TGCTATATAA
* *
53651187 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
53651252 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
53651269 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
53651333 CACTTAGTGC
65 CACTTAGTGC
53651343 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:53654381 original size:53 final size:54
Alignment explanation
Indices: 53654254--53654508 Score: 220
Period size: 55 Copynumber: 4.8 Consensus size: 54
53654244 ACACGGGTAC
* * * * *
53654254 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTA---TT--CTTTTGAAA
1 CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * *** *
53654303 CTTACCATTGCCATGTCTCAACATGGTCTTGCATGGTATCCTTGCCTTATG-AA
1 CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATGAAA
* *
53654356 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTCTGCCTTATAGAAA
1 CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCT-TGCCTTAT-GAAA
* ** * * *
53654411 CTTATCAATGCCATGTTTTGACATGGTATTACATGATATCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * *
53654464 CCTTACCAATTTCCATGCCTTGGTATGGTCTTGCATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
53654509 AAACCCTAAT
Statistics
Matches: 163, Mismatches: 32, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
49 32 0.20
52 5 0.03
53 44 0.27
54 13 0.08
55 66 0.40
56 3 0.02
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (54 bp):
CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATGAAA
Found at i:53654451 original size:108 final size:110
Alignment explanation
Indices: 53654299--53654501 Score: 268
Period size: 108 Copynumber: 1.9 Consensus size: 110
53654289 GTATTCTTTT
* * * *
53654299 GAAACTTACCATTGCCATGTCTCAACATGGTCTTGCATGGTATCCTTGCCTTATG-AA-CTCACC
1 GAAACTTACCAATGCCATGTCTCAACATGGTATTACATGATATCCTTGCCTTA-GAAACCTCACC
53654362 AA-TGCCATGCCTTGGCATGGTCTTACATGGGACCTCTGCCTTATA
65 AATTGCCATGCCTTGGCATGGTCTTACATGGGACCTCTGCCTTATA
* * ** *
53654407 GAAACTTATCAATGCCATGTTTTGACATGGTATTACATGATATCCTTGCCTTAGAAACCTTACCA
1 GAAACTTACCAATGCCATGTCTCAACATGGTATTACATGATATCCTTGCCTTAGAAACCTCACCA
* * *
53654472 ATTTCCATGCCTTGGTATGGTCTTGCATGG
66 ATTGCCATGCCTTGGCATGGTCTTACATGG
53654502 TATCCTTAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
107 1 0.01
108 47 0.59
109 7 0.09
110 25 0.31
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (110 bp):
GAAACTTACCAATGCCATGTCTCAACATGGTATTACATGATATCCTTGCCTTAGAAACCTCACCA
ATTGCCATGCCTTGGCATGGTCTTACATGGGACCTCTGCCTTATA
Found at i:53659062 original size:11 final size:11
Alignment explanation
Indices: 53659026--53659081 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
53659016 CATGGTATGT
53659026 ATGATATGCAC
1 ATGATATGCAC
* *
53659037 ATGACATG--T
1 ATGATATGCAC
53659046 ATGATATGCAC
1 ATGATATGCAC
*
53659057 ATGATATG--T
1 ATGATATGCAC
53659066 ATGATATGCAC
1 ATGATATGCAC
53659077 ATGAT
1 ATGAT
53659082 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:53659081 original size:20 final size:20
Alignment explanation
Indices: 53659015--53659081 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
53659005 ATTTTGATAA
*
53659015 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
53659035 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
53659055 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
53659075 ACATGAT
1 ACATGAT
53659082 GTATTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:53659430 original size:31 final size:31
Alignment explanation
Indices: 53659395--53659456 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
53659385 CGTTTACCGT
53659395 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
53659426 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
53659457 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:53667117 original size:11 final size:11
Alignment explanation
Indices: 53667063--53667119 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
53667053 ACATGGTATG
53667063 TATGATATGCA
1 TATGATATGCA
* *
53667074 CATGACATG--
1 TATGATATGCA
*
53667083 TATGATATACA
1 TATGATATGCA
*
53667094 CATGATATG--
1 TATGATATGCA
53667103 TATGATATGCA
1 TATGATATGCA
53667114 TATGAT
1 TATGAT
53667120 GTATTCATAA
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
9 14 0.41
11 20 0.59
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.35
Consensus pattern (11 bp):
TATGATATGCA
Found at i:53667119 original size:20 final size:20
Alignment explanation
Indices: 53667053--53667119 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
53667043 ATTTTGATAA
*
53667053 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
* *
53667073 ACATGACATGTATGATATAC
1 ACATGATATGTATGATATGC
53667093 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
53667113 ATATGAT
1 ACATGAT
53667120 GTATTCATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:53667269 original size:24 final size:24
Alignment explanation
Indices: 53667168--53667268 Score: 150
Period size: 24 Copynumber: 4.2 Consensus size: 24
53667158 GGAGGAAGTG
53667168 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
53667192 GATAAAGGGCTTATGCCCCAGTTAT
1 TA-AAAGGGCTTATGCCCCAGTTAT
53667217 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
* * *
53667241 TAAAATGGCTT-TGCCACAATTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
53667264 TAAAA
1 TAAAA
53667269 AAGACTAGGC
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
23 15 0.21
24 33 0.46
25 23 0.32
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:53667271 original size:49 final size:49
Alignment explanation
Indices: 53667168--53667268 Score: 152
Period size: 49 Copynumber: 2.1 Consensus size: 49
53667158 GGAGGAAGTG
* *
53667168 TAAAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCACAATTAT
* *
53667217 TAAAAGGGCTTATGCCCCAGTTATTA-AAATGGCTT-TGCCACAATTAT
1 TAAAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCACAATTAT
53667264 TAAAA
1 TAAAA
53667269 AAGACTAGGC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 15 0.31
48 8 0.17
49 25 0.52
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (49 bp):
TAAAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCACAATTAT
Found at i:53668829 original size:25 final size:25
Alignment explanation
Indices: 53668786--53668856 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
53668776 GAGGAAGTGC
*
53668786 AAAAGGGCTTTTGCCCCAGTTTACCG
1 AAAAGGGC-TTTGCCCCAGTTTACCA
*
53668812 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
53668837 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
53668857 ATTAAAAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
25 35 0.81
26 8 0.19
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:53668869 original size:24 final size:24
Alignment explanation
Indices: 53668785--53668869 Score: 109
Period size: 25 Copynumber: 3.4 Consensus size: 24
53668775 GGAGGAAGTG
*
53668785 CAAAAGGGCTTTTGCCCCAGTTTAC
1 CAAAAGGGC-TTTGCCCCAGTTTAT
53668810 CGAAAAGGGCTTTGCCCCAGTTTAT
1 C-AAAAGGGCTTTGCCCCAGTTTAT
53668835 CAAAAAGGGCTTTGCCCCAG-TTAT
1 C-AAAAGGGCTTTGCCCCAGTTTAT
*
53668859 TAAAAGAGGCT
1 CAAAAG-GGCT
53668870 AGGCGTCCAG
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
23 5 0.09
24 8 0.15
25 34 0.62
26 8 0.15
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (24 bp):
CAAAAGGGCTTTGCCCCAGTTTAT
Found at i:53669113 original size:30 final size:31
Alignment explanation
Indices: 53669077--53669159 Score: 100
Period size: 30 Copynumber: 2.7 Consensus size: 31
53669067 CATTTACAAT
* *
53669077 AAAGGCTTCAGCCCAGTGATATG-ATAACGA-
1 AAAGGCTTCGGCCCAGTGACATGAATAA-GAC
* *
53669107 AAAGGCTTCGGCCTAGTGACATGAATAATAC
1 AAAGGCTTCGGCCCAGTGACATGAATAAGAC
53669138 AAAGGCTTCGGCCCAGT-ACATG
1 AAAGGCTTCGGCCCAGTGACATG
53669160 TTGAGATTGA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 26 0.57
31 20 0.43
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGACATGAATAAGAC
Found at i:53674347 original size:40 final size:40
Alignment explanation
Indices: 53674303--53674526 Score: 217
Period size: 40 Copynumber: 5.6 Consensus size: 40
53674293 GCTCCTCGTT
*
53674303 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
53674343 CAAATTCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* *
53674383 CAAATGCCTTCGGGACTTAACTCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* * * *
53674423 CCAATGCCTTCGGG-CTTAGCCCAG-AATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* * * * * *
53674462 CAAATACCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
*
53674503 CAAA-GCCTTCGGGACATAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
53674527 ACATCATTCA
Statistics
Matches: 153, Mismatches: 23, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.01
39 27 0.18
40 110 0.72
41 14 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:53674511 original size:79 final size:79
Alignment explanation
Indices: 53674303--53674524 Score: 207
Period size: 79 Copynumber: 2.8 Consensus size: 79
53674293 GCTCCTCGTT
* * * * * * * * *
53674303 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATTCCTTCGGGACTTAACCCGG
1 CAAATACCTTCGGGACTTAACTCGGATATAGTAACTAGCACAAA-GCCTTCGGGACTTAGCCCAG
*
53674368 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
* * * *
53674383 CAAATGCCTTCGGGACTTAACTCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCAG
1 CAAATACCTTCGGGACTTAACTCGGATATAGTAACTAGCA-CAAAGCCTTCGGGACTTAGCCCAG
*
53674447 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
* * * *
53674462 CAAATACCTTC-GGATCTT-AGTCCGGATATGGTCACTTAGCACAAAGCCTTCGGGACATAGCCC
1 CAAATACCTTCGGGA-CTTAACT-CGGATATAGTAAC-TAGCACAAAGCCTTCGGGACTTAGCCC
53674525 GGACATCATT
Statistics
Matches: 118, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
78 5 0.04
79 56 0.47
80 54 0.46
81 3 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (79 bp):
CAAATACCTTCGGGACTTAACTCGGATATAGTAACTAGCACAAAGCCTTCGGGACTTAGCCCAGA
ATTAGTAACTCGCA
Found at i:53681592 original size:40 final size:40
Alignment explanation
Indices: 53681537--53681709 Score: 278
Period size: 40 Copynumber: 4.3 Consensus size: 40
53681527 TGATAACCGA
53681537 GCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGG
1 GCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGG
*
53681577 GCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCTGG
1 GCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGG
* *
53681617 GCTAAGACCCGAAGACATTTGTGCGAGTTGCTGTATCCGG
1 GCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGG
* *
53681657 GCTAGGACCCGAAGGCATTTGTGCGAGTTGTTATATCC-G
1 GCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGG
53681696 GCTAA-ATCCCGAAG
1 GCTAAGA-CCCGAAG
53681710 ATACTTGGGT
Statistics
Matches: 123, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
38 1 0.01
39 12 0.10
40 110 0.89
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
GCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGG
Found at i:53689749 original size:40 final size:40
Alignment explanation
Indices: 53689694--53689855 Score: 261
Period size: 40 Copynumber: 4.0 Consensus size: 40
53689684 CGGATGATAA
53689694 CCGGGCTAAGACCCAAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCAAAGGCATTTGTGCGAGTTGCTATAT
53689734 CCGGGCTAAGACCCAAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCAAAGGCATTTGTGCGAGTTGCTATAT
* * * *
53689774 CCTGGCTAAGACCCGAAGGCATTTGTCCGAGTTGCTGTAT
1 CCGGGCTAAGACCCAAAGGCATTTGTGCGAGTTGCTATAT
* * *
53689814 CCGGGCTAGGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCAAAGGCATTTGTGCGAGTTGCTATAT
53689854 CC
1 CC
53689856 AGCTAAATCC
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 113 1.00
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCAAAGGCATTTGTGCGAGTTGCTATAT
Found at i:53690139 original size:22 final size:22
Alignment explanation
Indices: 53690097--53690140 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
53690087 AAAGTGTGCA
* *
53690097 TATATGAAGTTATTCATTTAGC
1 TATATGAAGTTATACACTTAGC
53690119 TATATGAATGTTATAC-CTTAGC
1 TATATGAA-GTTATACACTTAGC
53690141 CGAAACTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATATGAAGTTATACACTTAGC
Found at i:53691399 original size:25 final size:25
Alignment explanation
Indices: 53691356--53691426 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
53691346 GAGGAAGTGC
* *
53691356 AAAAGGGCTTTTGTCCCAGTTTACCG
1 AAAAGGGC-TTTGCCCCAGTTTACCA
* *
53691382 AAAAGGACTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
53691407 AAAAGGGCTTTACCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
53691427 ATTAAAAGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
25 32 0.82
26 7 0.18
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:53691681 original size:30 final size:31
Alignment explanation
Indices: 53691647--53691729 Score: 125
Period size: 30 Copynumber: 2.7 Consensus size: 31
53691637 CGTTTACAGT
53691647 AAAGGCTTCGGCCCAGTGATATG-ATAATGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
* *
53691677 AAAGGCTTCGGCCCAGTGACATGAATAATGC
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
*
53691708 AAAGGCTTCGGCCTAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
53691730 TTGAGATTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 26 0.54
31 22 0.46
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGA
Found at i:53697133 original size:46 final size:46
Alignment explanation
Indices: 53697057--53697321 Score: 334
Period size: 46 Copynumber: 5.7 Consensus size: 46
53697047 TGATGTCACA
* * * * *
53697057 GTATCTTTCAACTACGGTTTTACTCGTTTTC-TATCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATATCAGGTTGCCATG
* *** *
53697103 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGTTGCCATG
* *
53697150 GCATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
53697196 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* * *
53697242 GTATCTTTCAACCACGGTCTTACACATTTCATATCAGGTTGCCATC
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
53697288 GTATCTTTCAACCATGGTCTTACACATTCCATAT
1 GTATCTTTCAACCATGGTCTTACTCATTTCATAT
53697322 TAGAGAGCAC
Statistics
Matches: 194, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
46 157 0.81
47 37 0.19
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.40
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
Found at i:53700528 original size:16 final size:16
Alignment explanation
Indices: 53700509--53700539 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53700499 CTTCTTCACT
53700509 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
53700525 TACTTACTTACTTAA
1 TACTCACTTACTTAA
53700540 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:53700545 original size:20 final size:20
Alignment explanation
Indices: 53700506--53700545 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
53700496 AAACTTCTTC
* *
53700506 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
53700526 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
53700546 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:53700898 original size:55 final size:53
Alignment explanation
Indices: 53700755--53700913 Score: 167
Period size: 53 Copynumber: 3.0 Consensus size: 53
53700745 ATCCTTTTAA
* * * *
53700755 AACTTACCATTGCCATGTCTCAACATGGTCTTACATGGTATCCTTGCCTTATG
1 AACTCACCAATGCCATGTCTTAACATGGTCTTACATGGGATCCTTGCCTTATG
* **
53700808 AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAG
1 AACTCACCAATGCCATGTCTTAACATGGTCTTACATGGGATCC-TTGCCTTAT-G
* ** ** *
53700862 AAACTTATTAATGCCATGTCTTAACATGGTCTTACATGATATCCTTTCCTTA
1 -AACTCACCAATGCCATGTCTTAACATGGTCTTACATGGGATCCTTGCCTTA
53700914 GAAACCTTAC
Statistics
Matches: 86, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
52 2 0.02
53 42 0.49
54 1 0.01
55 39 0.45
56 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (53 bp):
AACTCACCAATGCCATGTCTTAACATGGTCTTACATGGGATCCTTGCCTTATG
Found at i:53700945 original size:55 final size:53
Alignment explanation
Indices: 53700708--53700962 Score: 225
Period size: 55 Copynumber: 4.8 Consensus size: 53
53700698 ACACGGGTAC
* * * *
53700708 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCC-TT--TTA-AAA
1 CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTTCCTTAGAAA
* * *** *
53700757 CTTACCATTGCCATGTCTCAACATGGTCTTACATGGTATCCTTGCCTTATG-AA
1 CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTTCCTTA-GAAA
* *
53700810 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGAAA
1 CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTT-CC-T-TAGAAA
** * ** *
53700865 CTTATTAATGCCATGTCTTAACATGGTCTTACATGATATCCTTTCCTTAGAAA
1 CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTTCCTTAGAAA
** *
53700918 CCTTACCAATTTTCATGCCTTGGCATGGTCTTGCATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
53700963 AAACCCTAAT
Statistics
Matches: 163, Mismatches: 31, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
49 36 0.22
50 1 0.01
52 7 0.04
53 41 0.25
54 9 0.06
55 64 0.39
56 5 0.03
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (53 bp):
CTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTTCCTTAGAAA
Found at i:53705262 original size:53 final size:54
Alignment explanation
Indices: 53705082--53705288 Score: 220
Period size: 53 Copynumber: 3.8 Consensus size: 54
53705072 ATTAGGGTTT
* * *
53705082 AAGGATACC-TAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCTACAAGGC
1 AAGGATACCAT-GTAAGACCATGCCAAGACATGGCAATGGTAAGTTCTATAAGGC
* * ** * * * *
53705136 AAGGAAATCATGTAAGACCATGTTAAGACATGGCATTGATAAACTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTCTATAAGGC
** * * *
53705191 AAATATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTC-ATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCTATAAGGC
* *
53705244 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGCAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
53705289 TAAAAAGAAA
Statistics
Matches: 122, Mismatches: 29, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
53 45 0.37
54 35 0.29
55 42 0.34
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCTATAAGGC
Found at i:53709710 original size:28 final size:29
Alignment explanation
Indices: 53709670--53709782 Score: 142
Period size: 29 Copynumber: 4.0 Consensus size: 29
53709660 CCTGTATCTA
* *
53709670 GCCCATTAAGCCC-AATCATATTCATATG
1 GCCCATTAGGCCCAAATCACATTCATATG
*
53709698 GCCCATTAGGCCCAAATCACCTGT-ATATG
1 GCCCATTAGGCCCAAATCACAT-TCATATG
*
53709727 GCCCATTAGGCCCAAATCACATTTATATG
1 GCCCATTAGGCCCAAATCACATTCATATG
* *
53709756 GCCCGTTAGGCCC-AGTCACATTCATAT
1 GCCCATTAGGCCCAAATCACATTCATAT
53709783 TGATGCTCAC
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
28 25 0.33
29 49 0.65
30 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.27
Consensus pattern (29 bp):
GCCCATTAGGCCCAAATCACATTCATATG
Found at i:53709768 original size:58 final size:57
Alignment explanation
Indices: 53709659--53709769 Score: 159
Period size: 58 Copynumber: 1.9 Consensus size: 57
53709649 AATTTCACAT
* *
53709659 ACCTGTATCTAGCCCATTAAGCCCAATCATATTCATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATAGCCCATTAAGCCCAATCACATTCATATGGCCCATTAGGCCCAAATC
* * * *
53709716 ACCTGTATATGGCCCATTAGGCCCAAATCACATTTATATGGCCCGTTAGGCCCA
1 ACCTGTATATAGCCCATTAAGCCC-AATCACATTCATATGGCCCATTAGGCCCA
53709770 GTCACATTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 21 0.45
58 26 0.55
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (57 bp):
ACCTGTATATAGCCCATTAAGCCCAATCACATTCATATGGCCCATTAGGCCCAAATC
Found at i:53711154 original size:16 final size:16
Alignment explanation
Indices: 53711133--53711166 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
53711123 AGAAAATTCA
53711133 GGATTTCGAGATTTTT
1 GGATTTCGAGATTTTT
53711149 GGATTTCGAGATTTTT
1 GGATTTCGAGATTTTT
53711165 GG
1 GG
53711167 GCAGTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.06, G:0.29, T:0.47
Consensus pattern (16 bp):
GGATTTCGAGATTTTT
Found at i:53712672 original size:28 final size:27
Alignment explanation
Indices: 53712587--53712676 Score: 83
Period size: 27 Copynumber: 3.2 Consensus size: 27
53712577 GTGACAGAGT
* *
53712587 CACCAGATATAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
* * * *
53712616 CACTAGAACAAAT-ATATGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
53712643 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
53712671 CACCAG
1 CACCAG
53712677 GACCCTTCCT
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
27 22 0.45
28 21 0.43
29 6 0.12
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.22
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Found at i:53712829 original size:28 final size:28
Alignment explanation
Indices: 53712782--53712846 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
53712772 AAATTAACCC
*
53712782 TAGGGGTATAAAGGTCATTTTGCACACA
1 TAGGGGTATAAAGGTAATTTTGCACACA
* *
53712810 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCACACA
53712838 TAGGGGTAT
1 TAGGGGTAT
53712847 TCTAGTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.31, C:0.09, G:0.28, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCACACA
Found at i:53712967 original size:19 final size:19
Alignment explanation
Indices: 53712943--53712996 Score: 108
Period size: 19 Copynumber: 2.8 Consensus size: 19
53712933 AATTGGGCCC
53712943 TTTGGCCCATTAACCCAGT
1 TTTGGCCCATTAACCCAGT
53712962 TTTGGCCCATTAACCCAGT
1 TTTGGCCCATTAACCCAGT
53712981 TTTGGCCCATTAACCC
1 TTTGGCCCATTAACCC
53712997 CTAAATATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.20, C:0.33, G:0.15, T:0.31
Consensus pattern (19 bp):
TTTGGCCCATTAACCCAGT
Found at i:53724714 original size:40 final size:40
Alignment explanation
Indices: 53724670--53724792 Score: 210
Period size: 40 Copynumber: 3.1 Consensus size: 40
53724660 CCCGGATGTC
*
53724670 ATTCCAGCACGAAGCCTACGGGTCTTTAAGCCCGGATACA
1 ATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACA
* * *
53724710 ATTCCAGCACAAAGCCTGCGGGTTTTTCAGCCCGGATACA
1 ATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACA
53724750 ATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACA
1 ATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACA
53724790 ATT
1 ATT
53724793 TCACATCAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 76 1.00
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (40 bp):
ATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACA
Found at i:53731082 original size:17 final size:17
Alignment explanation
Indices: 53731060--53731102 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
53731050 TTCAAGTGAC
53731060 TGAATTTACATCCTAGG
1 TGAATTTACATCCTAGG
53731077 TGAATTTACATCCTAGG
1 TGAATTTACATCCTAGG
*
53731094 TAAATTTAC
1 TGAATTTAC
53731103 TATTTTGCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (17 bp):
TGAATTTACATCCTAGG
Found at i:53734657 original size:6 final size:6
Alignment explanation
Indices: 53734627--53734701 Score: 73
Period size: 6 Copynumber: 12.3 Consensus size: 6
53734617 AAGAAACATT
* * *
53734627 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATCAG- GTGCTAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT-C-AGA
*
53734676 ATCAAA ATCAGA ATCAGA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA ATCAGA AT
53734702 GAAGCCCATA
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
5 2 0.04
6 49 0.88
7 4 0.07
8 1 0.02
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:53735094 original size:27 final size:27
Alignment explanation
Indices: 53735064--53735196 Score: 171
Period size: 27 Copynumber: 5.0 Consensus size: 27
53735054 AGGGCAAAAT
*
53735064 GGTAATTTTACCCTACAAGGGTATCTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* *
53735091 GGTAATTTTACCCTATAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
53735118 GGT-ATTTCTACCCTACAAGGGTATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
*
53735145 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* * * *
53735172 AGTAATTCTA-CCTATAGGGGTATTT
1 GGTAATTTTACCCTACAAGGGTATTT
53735197 TAATAATTTT
Statistics
Matches: 95, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
26 17 0.18
27 75 0.79
28 3 0.03
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.37
Consensus pattern (27 bp):
GGTAATTTTACCCTACAAGGGTATTTC
Found at i:53735220 original size:53 final size:54
Alignment explanation
Indices: 53735162--53735285 Score: 124
Period size: 54 Copynumber: 2.3 Consensus size: 54
53735152 CTACCCTACA
** * **
53735162 AGGGTATTTCAGTAATTCTACCTATAGGGG-TATTTTAATAATTTTGTAAATCG
1 AGGGTATTTCAGTAATTCTACAAATAGGGGATACTTTAATAATTTTACAAATCG
* *** * * * *
53735215 CGGGTAAAACGGTAATTCTACAAATCGGGGATACTTTAGTAATTTTACAAGTCG
1 AGGGTATTTCAGTAATTCTACAAATAGGGGATACTTTAATAATTTTACAAATCG
53735269 AGGGTATTTCAGTAATT
1 AGGGTATTTCAGTAATT
53735286 TGGTAAACTA
Statistics
Matches: 52, Mismatches: 18, Indels: 1
0.73 0.25 0.01
Matches are distributed among these distances:
53 22 0.42
54 30 0.58
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.36
Consensus pattern (54 bp):
AGGGTATTTCAGTAATTCTACAAATAGGGGATACTTTAATAATTTTACAAATCG
Found at i:53735286 original size:27 final size:27
Alignment explanation
Indices: 53735226--53735286 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
53735216 GGGTAAAACG
*
53735226 GTAATTCTACAAATCGGGGATACTTTA
1 GTAATTTTACAAATCGGGGATACTTTA
*
53735253 GTAATTTTACAAGTCGAGGG-TA-TTTCA
1 GTAATTTTACAAATCG-GGGATACTTT-A
53735280 GTAATTT
1 GTAATTT
53735287 GGTAAACTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 3 0.10
27 24 0.80
28 3 0.10
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (27 bp):
GTAATTTTACAAATCGGGGATACTTTA
Found at i:53740095 original size:49 final size:50
Alignment explanation
Indices: 53740014--53740246 Score: 272
Period size: 49 Copynumber: 4.7 Consensus size: 50
53740004 ATCTGTTGTG
* * *
53740014 AGGTCACGTGTGTAGTACTAAGTGTAGACTACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* * ** *
53740064 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCATACCTGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT
* * * * * * **
53740114 CGATCACGTGTGTAGTACTAAGTGCAGGCTATTACGTGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
*
53740164 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
**
53740214 -GGTTGCATGTGTAGTACTAAGTGCAGGCTACTA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTA
53740247 TACGTACCAG
Statistics
Matches: 152, Mismatches: 29, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
49 69 0.45
50 47 0.31
51 36 0.24
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
Found at i:53740211 original size:101 final size:99
Alignment explanation
Indices: 53740017--53740246 Score: 284
Period size: 100 Copynumber: 2.3 Consensus size: 99
53740007 TGTTGTGAGG
* * * *
53740017 TCACGTGTGTAGTACTAAGTGTAGACTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACATGTGTAGTACT
* *
53740082 AAGTGCAGGCTACTATGCATACCTGATAACTTCGA
66 AAGTGCAGGCTACTACGCATACCGGATAA-TTCGA
* * ** *
53740117 TCACGTGTGTAGTACTAAGTGCAGGCTATTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCACATGTGTAGTAC
** * *
53740182 TAAGTGCAGGCTACTACGTGTACCGGATAATTGGT
65 TAAGTGCAGGCTACTACGCATACCGGATAATTCGA
53740217 TGCA--TGTGTAGTACTAAGTGCAGGCTACTA
1 T-CACGTGTGTAGTACTAAGTGCAGGCTACTA
53740247 TACGTACCAG
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
99 25 0.22
100 44 0.39
101 43 0.38
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (99 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACATGTGTAGTACT
AAGTGCAGGCTACTACGCATACCGGATAATTCGA
Found at i:53740251 original size:101 final size:100
Alignment explanation
Indices: 53740017--53740259 Score: 273
Period size: 101 Copynumber: 2.4 Consensus size: 100
53740007 TGTTGTGAGG
* * * *
53740017 TCACGTGTGTAGTACTAAGTGTAGACTAC-TACGTGTACCGGATAATTGGTCGCATGTGTAGTAC
1 TCAC-TGTGTAGTACTAAGTGCAGGCTACTTACGTGTACCAGATAATTGGTCACATGTGTAGTAC
* *
53740081 TAAGTGCAGGCTACTATGCATACCTGATAACTTCGA
65 TAAGTGCAGGCTACTACGCATACCGGATAACTTCGA
* ** *
53740117 TCACGTGTGTAGTACTAAGTGCAGGCTA-TTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTA
1 TCAC-TGTGTAGTACTAAGTGCAGGCTACTTACGTGTACCAGATAATT-GGTCACATGTGTAGTA
** * *
53740181 CTAAGTGCAGGCTACTACGTGTACCGGATAA-TTGGT
64 CTAAGTGCAGGCTACTACGCATACCGGATAACTTCGA
53740217 TGCA-TGTGTAGTACTAAGTGCAGGCTACTATAC--GTACCAGATA
1 T-CACTGTGTAGTACTAAGTGCAGGCTACT-TACGTGTACCAGATA
53740260 CCTTTGGCTA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
99 31 0.25
100 45 0.37
101 46 0.38
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (100 bp):
TCACTGTGTAGTACTAAGTGCAGGCTACTTACGTGTACCAGATAATTGGTCACATGTGTAGTACT
AAGTGCAGGCTACTACGCATACCGGATAACTTCGA
Found at i:53742194 original size:27 final size:26
Alignment explanation
Indices: 53742124--53742239 Score: 115
Period size: 27 Copynumber: 4.3 Consensus size: 26
53742114 CAGCATGGCT
* * *
53742124 ACCAGAATAGATATTGTGACAGAGTC
1 ACCAGAACAGATATTGTGGCAGAGCC
*
53742150 ACCAGATACAGATATTGTGGCAGAGCA
1 ACCAGA-ACAGATATTGTGGCAGAGCC
* *
53742177 ACCAGAATAGATATTTGTGGCATAGCC
1 ACCAGAACAGATA-TTGTGGCAGAGCC
* * *
53742204 ACCGGAAACATATATTTGTGGCATAGCC
1 ACCAG-AACAGATA-TTGTGGCAGAGCC
53742232 ACCAGAAC
1 ACCAGAAC
53742240 GCTTCCTCCA
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
26 12 0.16
27 40 0.53
28 24 0.32
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (26 bp):
ACCAGAACAGATATTGTGGCAGAGCC
Found at i:53742238 original size:55 final size:53
Alignment explanation
Indices: 53742124--53742238 Score: 140
Period size: 54 Copynumber: 2.1 Consensus size: 53
53742114 CAGCATGGCT
* *
53742124 ACCAGAATAGATATTGTGACAGAGTCACCAGATACAGATATTGTGGCAGAGCA
1 ACCAGAATAGATATTGTGACAGAGCCACCAGAAACAGATATTGTGGCAGAGCA
* * * * * *
53742177 ACCAGAATAGATATTTGTGGCATAGCCACCGGAAACATATATTTGTGGCATAGCC
1 ACCAGAATAGATA-TTGTGACAGAGCCACCAGAAACAGATA-TTGTGGCAGAGCA
53742232 ACCAGAA
1 ACCAGAA
53742239 CGCTTCCTCC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 13 0.25
54 21 0.40
55 18 0.35
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.22
Consensus pattern (53 bp):
ACCAGAATAGATATTGTGACAGAGCCACCAGAAACAGATATTGTGGCAGAGCA
Found at i:53742453 original size:27 final size:28
Alignment explanation
Indices: 53742391--53742454 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 28
53742381 TAGTCACTTG
* *
53742391 CCCACAAGGGCAGAATAGTCATTTAACA
1 CCCACAAGGGCAAAATAGTAATTTAACA
* * *
53742419 CCC-TAAGGGCAAAATGGTAATTTTAC-
1 CCCACAAGGGCAAAATAGTAATTTAACA
53742445 CCCACAAGGG
1 CCCACAAGGG
53742455 TATCTCGGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 3 0.10
27 23 0.79
28 3 0.10
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (28 bp):
CCCACAAGGGCAAAATAGTAATTTAACA
Found at i:53742464 original size:27 final size:27
Alignment explanation
Indices: 53742434--53742568 Score: 153
Period size: 27 Copynumber: 5.0 Consensus size: 27
53742424 AGGGCAAAAT
* * *
53742434 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
53742461 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
53742488 GGTATTTCTACCTTACAAGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
53742515 GGTAATTCTACCCTATAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
53742542 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
53742569 AATAATTTTG
Statistics
Matches: 94, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 94 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:53742551 original size:54 final size:54
Alignment explanation
Indices: 53742435--53742568 Score: 169
Period size: 54 Copynumber: 2.5 Consensus size: 54
53742425 GGGCAAAATG
* * * *
53742435 GTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
* * * * *
53742489 GTATTTCTACCTTACAAGGGTATTTTGGTAATTCTACCCTATAGGGGTATTTTA
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
* *
53742543 GTAATTCTACCCTATAGGGGTATTTC
1 GTAATTCTACCCTACAAGGGTATTTC
53742569 AATAATTTTG
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
54 66 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37
Consensus pattern (54 bp):
GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
Found at i:53742590 original size:27 final size:26
Alignment explanation
Indices: 53742560--53742664 Score: 84
Period size: 27 Copynumber: 3.9 Consensus size: 26
53742550 TACCCTATAG
*
53742560 GGGTATTTCAATAATTTTGTAAATCGA
1 GGGTATTT-AGTAATTTTGTAAATCGA
** * *
53742587 GGGTAAAATGGTAATTCTGTAAATCGA
1 GGGT-ATTTAGTAATTTTGTAAATCGA
* ** *
53742614 GGGTACTTTGGTAATTTTACAAGTCGA
1 GGGTA-TTTAGTAATTTTGTAAATCGA
*
53742641 GGGTATTTCAGTAATTTGGTAAAT
1 GGGTATTT-AGTAATTTTGTAAAT
53742665 TAAAATATTC
Statistics
Matches: 59, Mismatches: 16, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
26 4 0.07
27 53 0.90
28 2 0.03
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.37
Consensus pattern (26 bp):
GGGTATTTAGTAATTTTGTAAATCGA
Found at i:53749526 original size:27 final size:27
Alignment explanation
Indices: 53749490--53749559 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
53749480 GTCTTTAAGA
* *
53749490 CCCCAGTTTGTAAGATTACCAAAATAC
1 CCCCAATTTGTAAAATTACCAAAATAC
*
53749517 CCTCAATTTGTAAAATTACCAAAATAC
1 CCCCAATTTGTAAAATTACCAAAATAC
*
53749544 CCCCGATTTGTAAAAT
1 CCCCAATTTGTAAAAT
53749560 CATCGAGATA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.29
Consensus pattern (27 bp):
CCCCAATTTGTAAAATTACCAAAATAC
Found at i:53749582 original size:27 final size:27
Alignment explanation
Indices: 53749525--53749613 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 27
53749515 ACCCTCAATT
* * *
53749525 TGTAAAATTACCAAAATACCCCCG-ATT
1 TGTAAAATCACCAAAATACCCCTGTA-G
* * * *
53749552 TGTAAAATCATCGAGATACCCTTGTAG
1 TGTAAAATCACCAAAATACCCCTGTAG
*
53749579 TGTAAAATTACCAAAATACCCCTGTAG
1 TGTAAAATCACCAAAATACCCCTGTAG
*
53749606 GGTAAAAT
1 TGTAAAAT
53749614 GACTATTTTT
Statistics
Matches: 48, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
27 47 0.98
28 1 0.02
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.27
Consensus pattern (27 bp):
TGTAAAATCACCAAAATACCCCTGTAG
Found at i:53750139 original size:32 final size:32
Alignment explanation
Indices: 53750053--53750202 Score: 178
Period size: 32 Copynumber: 4.8 Consensus size: 32
53750043 CTTGGTACCA
* * *
53750053 ATCATATTACAG-TATTGAAGGCTTTGTGTCG
1 ATCATATTACAGCTACTGATGGCTTTGTGCCG
*
53750084 ATCATATTACAG-TACTGACGGCTTTGTGCCG
1 ATCATATTACAGCTACTGATGGCTTTGTGCCG
* * * *
53750115 ATTATATTAAAGCTACTGATGGCTTTGTGTCA
1 ATCATATTACAGCTACTGATGGCTTTGTGCCG
* * *
53750147 ATCATATTACAGCTGCTGTTGACTTTGTGCCG
1 ATCATATTACAGCTACTGATGGCTTTGTGCCG
*
53750179 ATCATATTACCGCTACTGATGGCT
1 ATCATATTACAGCTACTGATGGCT
53750203 GTAAGCCGTG
Statistics
Matches: 99, Mismatches: 19, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
31 38 0.38
32 61 0.62
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.37
Consensus pattern (32 bp):
ATCATATTACAGCTACTGATGGCTTTGTGCCG
Found at i:53754815 original size:47 final size:47
Alignment explanation
Indices: 53754752--53755061 Score: 431
Period size: 47 Copynumber: 6.6 Consensus size: 47
53754742 CCCTTCGGGA
* * *
53754752 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* * *
53754799 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* *
53754846 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* * *
53754893 CTTATCACATATATACACTTTCACATTCATCACGTTGGTCACTCGAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* *
53754940 CCTATCACATATATACACTTTCACATTCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* * *
53754987 CCTATCACATATATATATACTTTCACATTCATCACATTGGCCACTCGAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* * *
53755036 CCTATCACATATATATACTTTTACAT
1 CTTATCACATATATACACTTTCACAT
53755062 CAATTTCATC
Statistics
Matches: 242, Mismatches: 19, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
47 198 0.82
49 44 0.18
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.35
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
Found at i:53758443 original size:40 final size:40
Alignment explanation
Indices: 53758411--53758598 Score: 261
Period size: 40 Copynumber: 4.7 Consensus size: 40
53758401 CCAGCATGAT
* * * *
53758411 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * *
53758451 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
53758491 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
53758531 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
53758571 TACTCTTCGGGACTTAGCGCGGAT-CATC
1 TGCTCTTCGGGACTTAGCCCGGATACATC
53758599 GTCGAGACCT
Statistics
Matches: 132, Mismatches: 16, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
39 4 0.03
40 128 0.97
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:53761216 original size:47 final size:47
Alignment explanation
Indices: 53761153--53761381 Score: 341
Period size: 47 Copynumber: 4.9 Consensus size: 47
53761143 TCCTTCGGGA
* *
53761153 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
53761200 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
53761247 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
53761294 CTTGTCACATATATACACTTTCACATTCATCACGTTGGTCACTCGAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* **
53761341 CCTATCACATATATACACTTTCACATTCATCATGTTGGCCA
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCA
53761382 CATCATATCT
Statistics
Matches: 165, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 165 1.00
ACGTcount: A:0.27, C:0.29, G:0.09, T:0.35
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:53763538 original size:27 final size:27
Alignment explanation
Indices: 53763516--53763611 Score: 129
Period size: 27 Copynumber: 3.6 Consensus size: 27
53763506 AGTTTGTTAG
*
53763516 ATTACCAAAATACCCCCGATTTGTAAA
1 ATTATCAAAATACCCCCGATTTGTAAA
** * *
53763543 ATTAGAAAAATACCTCCAATTTGTAAA
1 ATTATCAAAATACCCCCGATTTGTAAA
*
53763570 ATTGTCAAAATACCCCCGATTTGTAAA
1 ATTATCAAAATACCCCCGATTTGTAAA
*
53763597 ATTATCGAAATACCC
1 ATTATCAAAATACCC
53763612 TTGTATGGTA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (27 bp):
ATTATCAAAATACCCCCGATTTGTAAA
Found at i:53764150 original size:32 final size:32
Alignment explanation
Indices: 53764064--53764182 Score: 161
Period size: 31 Copynumber: 3.8 Consensus size: 32
53764054 GCTTGGTACC
* *
53764064 GATCATATTACAG-TACTAATGGCTTTATGCT
1 GATCATATTACAGCTACTGATGGCTTTGTGCT
* *
53764095 GATCATATTACA-TTACTGATGGCTTTGTGTT
1 GATCATATTACAGCTACTGATGGCTTTGTGCT
* *
53764126 GATCATATTACAGCTACTGTTGGCTTTGTGCC
1 GATCATATTACAGCTACTGATGGCTTTGTGCT
*
53764158 GATCATATTACTGCTACTGATGGCT
1 GATCATATTACAGCTACTGATGGCT
53764183 GTAAGCCGTG
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
31 39 0.51
32 38 0.49
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (32 bp):
GATCATATTACAGCTACTGATGGCTTTGTGCT
Found at i:53764247 original size:26 final size:26
Alignment explanation
Indices: 53764195--53764247 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
53764185 AAGCCGTGTA
* **
53764195 TATTTCTGGCAGCTTTGCTGCTTTAT
1 TATTTCTGGCAGCTATGCTGCGATAT
*
53764221 TATTTCTGGCGGCTATGCTGCGATAT
1 TATTTCTGGCAGCTATGCTGCGATAT
53764247 T
1 T
53764248 GGTGTGCTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (26 bp):
TATTTCTGGCAGCTATGCTGCGATAT
Found at i:53768394 original size:20 final size:20
Alignment explanation
Indices: 53768369--53768410 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
53768359 GAGAAGAGGG
53768369 AAAAAGAAAAAAAAGAAGAA
1 AAAAAGAAAAAAAAGAAGAA
** *
53768389 AAAAAGTTAAAAAAGAATAA
1 AAAAAGAAAAAAAAGAAGAA
53768409 AA
1 AA
53768411 TTCCACAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (20 bp):
AAAAAGAAAAAAAAGAAGAA
Found at i:53771469 original size:17 final size:18
Alignment explanation
Indices: 53771447--53771492 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
53771437 ACTCGTTATA
53771447 GCCCGATAAATGAA-AAT
1 GCCCGATAAATGAATAAT
*
53771464 GCCCGATTAAT-AATAAT
1 GCCCGATAAATGAATAAT
* *
53771481 GCTCAATAAATG
1 GCCCGATAAATG
53771493 GTAAATGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 2 0.09
17 21 0.91
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.24
Consensus pattern (18 bp):
GCCCGATAAATGAATAAT
Found at i:53772310 original size:32 final size:32
Alignment explanation
Indices: 53772252--53772329 Score: 122
Period size: 32 Copynumber: 2.5 Consensus size: 32
53772242 AAAGTTCTGA
* * *
53772252 TATGAAATGAT-CTAGACTCGAAATGAACTAT
1 TATGAAATTATACTTGACTAGAAATGAACTAT
53772283 TATGAAATTATACTTGACTAGAAATGAACTAT
1 TATGAAATTATACTTGACTAGAAATGAACTAT
53772315 TATGAAATTATACTT
1 TATGAAATTATACTT
53772330 AAAATAATGA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
31 10 0.23
32 33 0.77
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (32 bp):
TATGAAATTATACTTGACTAGAAATGAACTAT
Found at i:53776619 original size:28 final size:28
Alignment explanation
Indices: 53776544--53776619 Score: 134
Period size: 28 Copynumber: 2.7 Consensus size: 28
53776534 TCAGCAGCAG
* *
53776544 CTAAGACACATTAAAAACAAGTATTAAA
1 CTAAGACACATTAATAACATGTATTAAA
53776572 CTAAGACACATTAATAACATGTATTAAA
1 CTAAGACACATTAATAACATGTATTAAA
53776600 CTAAGACACATTAATAACAT
1 CTAAGACACATTAATAACAT
53776620 TAATAACATG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.53, C:0.16, G:0.07, T:0.25
Consensus pattern (28 bp):
CTAAGACACATTAATAACATGTATTAAA
Found at i:53776660 original size:37 final size:38
Alignment explanation
Indices: 53776571--53776660 Score: 139
Period size: 37 Copynumber: 2.4 Consensus size: 38
53776561 CAAGTATTAA
53776571 ACTAAGACACATTAATAACATGTATTAAACTAAGACAC
1 ACTAAGACACATTAATAACATGTATTAAACTAAGACAC
* *
53776609 ATTAATA-ACATTAATAACATGTATTAAACTAAGACAC
1 ACTAAGACACATTAATAACATGTATTAAACTAAGACAC
*
53776646 ACTAA-ACACTTTAAT
1 ACTAAGACACATTAAT
53776661 TAATAGATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
36 1 0.02
37 41 0.87
38 5 0.11
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.28
Consensus pattern (38 bp):
ACTAAGACACATTAATAACATGTATTAAACTAAGACAC
Found at i:53776948 original size:23 final size:23
Alignment explanation
Indices: 53776918--53776963 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
53776908 CTAAGGCCGA
53776918 AATAGCCTCCTTGAAACATTTGG
1 AATAGCCTCCTTGAAACATTTGG
*
53776941 AATAGCCTCCTTGAAACGTTTGG
1 AATAGCCTCCTTGAAACATTTGG
53776964 CTCGTGCACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (23 bp):
AATAGCCTCCTTGAAACATTTGG
Found at i:53778208 original size:27 final size:26
Alignment explanation
Indices: 53778172--53778258 Score: 102
Period size: 27 Copynumber: 3.3 Consensus size: 26
53778162 AGCATGGTTG
* *
53778172 CCAGAACAGATATTGTGACAGAGTCA
1 CCAGAACAGATATTGTGGCAGAGCCA
* *
53778198 CCAGATACAGATACTGTGGTAGAGCCA
1 CCAGA-ACAGATATTGTGGCAGAGCCA
* *
53778225 CCAGAATAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-TTGTGGCAGAGCCA
53778252 CCAGAAC
1 CCAGAAC
53778259 GCTTCCTCTA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
26 11 0.22
27 39 0.78
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (26 bp):
CCAGAACAGATATTGTGGCAGAGCCA
Found at i:53778503 original size:27 final size:27
Alignment explanation
Indices: 53778473--53778540 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
53778463 CCCCACAATA
*
53778473 GTATCTCGGTAATTCTACCCTACAGGG
1 GTATCTCGATAATTCTACCCTACAGGG
* *
53778500 GTATTTTGATAATTCTACCCTACAGGG
1 GTATCTCGATAATTCTACCCTACAGGG
* *
53778527 GTATTTCAATAATT
1 GTATCTCGATAATT
53778541 TTTTAAATCG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (27 bp):
GTATCTCGATAATTCTACCCTACAGGG
Found at i:53781947 original size:66 final size:70
Alignment explanation
Indices: 53781818--53781947 Score: 169
Period size: 66 Copynumber: 1.9 Consensus size: 70
53781808 GGGATGTATC
* * *
53781818 CCATGTAGACAAGAGAGATACGTGAGAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGATACG-GAGAGATAAATGCAGCTAGGTCGCATGAGTGATACCAAGTGA
53781883 AGGACA
65 AGGACA
* * *
53781889 CCATGTAGACAAGAGAGCTAC-GAGA-A-AAAT-CAGCTAGGTCGCATGAGTGGTACTAAGTG
1 CCATGTAGACAAGAGAGATACGGAGAGATAAATGCAGCTAGGTCGCATGAGTGATACCAAGTG
53781948 TTCACCATGT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
66 24 0.45
67 4 0.08
68 1 0.02
69 4 0.08
71 20 0.38
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.19
Consensus pattern (70 bp):
CCATGTAGACAAGAGAGATACGGAGAGATAAATGCAGCTAGGTCGCATGAGTGATACCAAGTGAA
GGACA
Found at i:53784533 original size:40 final size:40
Alignment explanation
Indices: 53784433--53784612 Score: 174
Period size: 40 Copynumber: 4.5 Consensus size: 40
53784423 CTCATTCAAT
* * * * * *
53784433 GCCTTCGGGACTTAACCCAGATTTTA-AAACTCGCACGAAT
1 GCCTTCGGGACTTAACCCGGA-ATTAGTATCTCGCACAAAG
*
53784473 GCCTTC-GGACTTAACCCGGAATTGGTATCTCGCACAAAG
1 GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAG
53784512 GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAG
1 GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAG
** *
53784552 GCCTTC-GGATCTTAGTCCGG-ATATAGTCA-CTTAGCACAAA-
1 GCCTTCGGGA-CTTAACCCGGAAT-TAGT-ATC-TCGCACAAAG
*
53784592 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
53784613 CAGCATTCAA
Statistics
Matches: 120, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
38 2 0.02
39 34 0.28
40 72 0.60
41 12 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAG
Found at i:53784545 original size:79 final size:80
Alignment explanation
Indices: 53784433--53784612 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
53784423 CTCATTCAAT
* * * *
53784433 GCCTTCGGGACTTAACCCAGATTTTAAAACTCGCACGAATGCCTTCGGA-CTTAACCCGGA-ATT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAAGGCCTTCGGATCTTAACCCGGATA-T
* *
53784496 GGT-A-TCTCGCACAAA
65 AGTCACT-TAGCACAAA
* * **
53784511 GGCCTTCGGGACTTAACCCGGA-ATTAGTATCTCGCACAAAGGCCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTA-AAACTCGCACAAAGGCCTTCGGATCTTAACCCGGATA
53784575 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
53784592 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
53784613 CAGCATTCAA
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
78 3 0.04
79 39 0.46
80 32 0.38
81 10 0.12
82 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAAGGCCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:53792078 original size:80 final size:80
Alignment explanation
Indices: 53791968--53792147 Score: 210
Period size: 80 Copynumber: 2.3 Consensus size: 80
53791958 CTCATTCAAT
* * *
53791968 GCCTTC-GGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
53792030 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
53792046 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
53792110 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
53792127 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
53792148 CAGCATTCAA
Statistics
Matches: 88, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
79 13 0.15
80 64 0.73
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:53792107 original size:40 final size:40
Alignment explanation
Indices: 53791965--53792147 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 40
53791955 TAACTCATTC
* *
53791965 AATGCCTTC-GGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
53792004 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
53792044 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
53792084 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
53792125 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
53792148 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 17 0.14
40 93 0.77
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:53796992 original size:40 final size:40
Alignment explanation
Indices: 53796883--53797063 Score: 183
Period size: 40 Copynumber: 4.5 Consensus size: 40
53796873 CTCATTCAAT
* * * * *
53796883 GCCTTCGGGACTTAACCCGGATTTTA-AAACTCGCACGAAT
1 GCCTTCGGGACTTAACCCGGA-ATTAGTATCTCGCACAAAG
*
53796923 GCCTTCGGGACTTAACCCGGAATTGGTATCTCGCACAAAG
1 GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAG
53796963 GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAG
1 GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAG
* ** *
53797003 GCCTT-TGGATCTTAGTCCGG-ATATAGTCA-CTTAGCACAAA-
1 GCCTTCGGGA-CTTAACCCGGAAT-TAGT-ATC-TCGCACAAAG
*
53797043 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
53797064 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
39 7 0.06
40 102 0.84
41 12 0.10
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAG
Found at i:53799112 original size:27 final size:27
Alignment explanation
Indices: 53799072--53799186 Score: 162
Period size: 27 Copynumber: 4.3 Consensus size: 27
53799062 AGCATGGCTG
* *
53799072 CCAGAACAGATA-TTGTGACAGAGACA
1 CCAGAACAGATATTTGTGGCAGAGCCA
53799098 CCAGATACAGATA-TTGTGGCAGAGCCA
1 CCAGA-ACAGATATTTGTGGCAGAGCCA
*
53799125 CCAGAACAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATTTGTGGCAGAGCCA
*
53799152 CCAGAAGCAGATATTTGTGGCATAGCCA
1 CCAGAA-CAGATATTTGTGGCAGAGCCA
53799180 CCAGAAC
1 CCAGAAC
53799187 GCTTCCTACA
Statistics
Matches: 83, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
26 12 0.14
27 44 0.53
28 27 0.33
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (27 bp):
CCAGAACAGATATTTGTGGCAGAGCCA
Done.