Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 136 of 218
Found at i:41441538 original size:101 final size:101
Alignment explanation
Indices: 41441402--41441614 Score: 309
Period size: 101 Copynumber: 2.1 Consensus size: 101
41441392 CATAGCCTTG
* * * *
41441402 CCATGGTCTTATGTTCATAGTGCCATAACCCAGTTATAGTCTTACCATCAGAATGCCATAGCCCA
1 CCATGGTCTTACGTCCATAGTGCCATAACCCAGTTATAGTCTTACCATCAAAATGCCATAACCCA
* *
41441467 GCTATGGTCTTACATATAAACACTACCATGGTCTAA
66 GCAATGGTCTTACATATAAACACTACCATGGTCCAA
* ** * *
41441503 CCATTGTCTTACGTCCATAGTGTTATAACTCAGTTATGGTCTTACCATCAAAATGCCATAACCCA
1 CCATGGTCTTACGTCCATAGTGCCATAACCCAGTTATAGTCTTACCATCAAAATGCCATAACCCA
* *
41441568 GCAATGGTCTTACATATATACACTGCCATGGTCCAA
66 GCAATGGTCTTACATATAAACACTACCATGGTCCAA
41441604 CCATGGTCTTA
1 CCATGGTCTTA
41441615 AATACTTCAA
Statistics
Matches: 98, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 98 1.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.31
Consensus pattern (101 bp):
CCATGGTCTTACGTCCATAGTGCCATAACCCAGTTATAGTCTTACCATCAAAATGCCATAACCCA
GCAATGGTCTTACATATAAACACTACCATGGTCCAA
Found at i:41441650 original size:27 final size:27
Alignment explanation
Indices: 41441610--41441684 Score: 141
Period size: 27 Copynumber: 2.8 Consensus size: 27
41441600 CCAACCATGG
41441610 TCTTAAATACTTCAATTTTTTTATTAT
1 TCTTAAATACTTCAATTTTTTTATTAT
*
41441637 TTTTAAATACTTCAATTTTTTTATTAT
1 TCTTAAATACTTCAATTTTTTTATTAT
41441664 TCTTAAATACTTCAATTTTTT
1 TCTTAAATACTTCAATTTTTT
41441685 AATTTCTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (27 bp):
TCTTAAATACTTCAATTTTTTTATTAT
Found at i:41451591 original size:24 final size:25
Alignment explanation
Indices: 41451564--41451678 Score: 90
Period size: 25 Copynumber: 4.6 Consensus size: 25
41451554 GTACATGTAT
*
41451564 GCTCATATGAGCTGTA-AACGGTAA
1 GCTCATATGAGCTGAATAACGGTAA
* * *
41451588 GCTCCTCTGAGTTGAATAACGGTAA
1 GCTCATATGAGCTGAATAACGGTAA
* ** *
41451613 GCTCCT-TCGAGAGGAATAATGGTAA
1 GCTCATAT-GAGCTGAATAACGGTAA
* * * *
41451638 GCTCATACGAGTTGAGTAATGGTAA
1 GCTCATATGAGCTGAATAACGGTAA
*
41451663 GCTCATAAGAGCTGAA
1 GCTCATATGAGCTGAA
41451679 ATTGGTAACC
Statistics
Matches: 73, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
24 13 0.18
25 60 0.82
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (25 bp):
GCTCATATGAGCTGAATAACGGTAA
Found at i:41451667 original size:25 final size:25
Alignment explanation
Indices: 41451583--41451686 Score: 95
Period size: 25 Copynumber: 4.2 Consensus size: 25
41451573 AGCTGTAAAC
* *
41451583 GGTAAGCTCCT-CTGAGTTGAATAAC
1 GGTAAGCTCATAC-GAGTTGAATAAT
* * **
41451608 GGTAAGCTCCTTCGAGAGGAATAAT
1 GGTAAGCTCATACGAGTTGAATAAT
*
41451633 GGTAAGCTCATACGAGTTGAGTAAT
1 GGTAAGCTCATACGAGTTGAATAAT
* * *
41451658 GGTAAGCTCATAAGAGCTGAA-ATT
1 GGTAAGCTCATACGAGTTGAATAAT
41451682 GGTAA
1 GGTAA
41451687 CCCTAATGAC
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
24 7 0.11
25 58 0.88
26 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.26
Consensus pattern (25 bp):
GGTAAGCTCATACGAGTTGAATAAT
Found at i:41455329 original size:122 final size:123
Alignment explanation
Indices: 41455112--41455416 Score: 405
Period size: 122 Copynumber: 2.5 Consensus size: 123
41455102 TCGCGGTGTT
* * * * *
41455112 TATGGAAAAAATACTGCTATTACTTTACCTTTTATGGCGTTTATGGGCAAAACGCCACTATTGCT
1 TATGGGAAAAATACCGCTATTACTTTACCTTTTGTGGCATTTATGGGCAAAATGCCACTATTGCT
*
41455177 TTACCTTTTGTGGCGTTTATGGGAAAAATGCCGCTATTGC-TTACCTTTTACAGCGTG
66 TTACCTTTTGTGGCATTTATGGGAAAAATGCCGCTATTGCTTTACCTTTTACAGCGTG
* * *
41455234 TATGGGAAAAACACCGCTATTGCTTTACCTTTTGTGGCATTTATGGGCAAAATGCCGCTATTGCT
1 TATGGGAAAAATACCGCTATTACTTTACCTTTTGTGGCATTTATGGGCAAAATGCCACTATTGCT
* * * * *
41455299 TTACCTTTTGTGGCATTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGCGGTGTT
66 TTACCTTTTGTGGCATTTATGGGAAAAATGCCGCTATTGCTTTACCTTTTACAGCGTG
* * * * * * * *
41455357 TATGGGCAATATACCACTATTTCTTTACCTTTTGCGGCATTTATAGGAAAAATTCCACTA
1 TATGGGAAAAATACCGCTATTACTTTACCTTTTGTGGCATTTATGGGCAAAATGCCACTA
41455417 ATGGTATATA
Statistics
Matches: 158, Mismatches: 24, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
122 95 0.60
123 63 0.40
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37
Consensus pattern (123 bp):
TATGGGAAAAATACCGCTATTACTTTACCTTTTGTGGCATTTATGGGCAAAATGCCACTATTGCT
TTACCTTTTGTGGCATTTATGGGAAAAATGCCGCTATTGCTTTACCTTTTACAGCGTG
Found at i:41455416 original size:41 final size:41
Alignment explanation
Indices: 41455109--41455409 Score: 343
Period size: 41 Copynumber: 7.4 Consensus size: 41
41455099 AATTCGCGGT
** * * * *
41455109 GTTTATGGAAAAAATACTGCTATTACTTTACCTTTTATGGC
1 GTTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGTGGC
* *
41455150 GTTTATGGGCAAAACGCCACTATTGCTTTACCTTTTGTGGC
1 GTTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGTGGC
* ***
41455191 GTTTATGGGAAAAATGCCGCTATTGC-TTACCTTTTACAGC
1 GTTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGTGGC
* * **
41455231 GTGTATGGGAAAAACACCGCTATTGCTTTACCTTTTGTGGC
1 GTTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGTGGC
*
41455272 ATTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGTGGC
1 GTTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGTGGC
* * *
41455313 ATTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGCGGT
1 GTTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGTGGC
* * * * *
41455354 GTTTATGGGCAATATACCACTATTTCTTTACCTTTTGCGGC
1 GTTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGTGGC
* * *
41455395 ATTTATAGGAAAAAT
1 GTTTATGGGCAAAAT
41455410 TCCACTAATG
Statistics
Matches: 222, Mismatches: 37, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
40 34 0.15
41 188 0.85
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.38
Consensus pattern (41 bp):
GTTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGTGGC
Found at i:41467001 original size:40 final size:39
Alignment explanation
Indices: 41466957--41467139 Score: 199
Period size: 40 Copynumber: 4.6 Consensus size: 39
41466947 TGACCATATT
*
41466957 CGGACTAAGATCCAAAGGCATTTGTGCGAGATACTAAATC
1 CGGACTAAG-TCCGAAGGCATTTGTGCGAGATACTAAATC
* *
41466997 CGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTT
1 CGGACTAAG-TCCGAAGGCATTTGTGCGAGATACTAAATC
* * *
41467037 CGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATC
1 CGGACTAAGTCCGAAGGCATTTGTGCGAGATACTAAATC
* ** *
41467076 TGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-C
1 CGGACTAAGT-CCGAAGGCATTTGTGCGAGATACTA-AATC
*
41467116 CAGG-CTATGTCCCGAAGGCATTTG
1 C-GGACTAAGT-CCGAAGGCATTTG
41467140 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
39 33 0.26
40 89 0.71
41 4 0.03
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (39 bp):
CGGACTAAGTCCGAAGGCATTTGTGCGAGATACTAAATC
Found at i:41467062 original size:39 final size:39
Alignment explanation
Indices: 41466917--41467139 Score: 191
Period size: 40 Copynumber: 5.6 Consensus size: 39
41466907 GAATGATGTC
* * *
41466917 CGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATATT
1 CGGGCTAAGACCCGAAGGCATTTGTGCGAGA-T-ACTA-ATT
* * * *
41466957 CGGACTAAGATCCAAAGGCATTTGTGCGAGATACTAAATC
1 CGGGCTAAGACCCGAAGGCATTTGTGCGAGATACT-AATT
* *
41466997 CGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTT
1 CGGGCTAAGACCCGAAGGCATTTGTGCGAGATACTAA-TT
* *
41467037 CGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CGGGCTAAGACCCGAAGGCATTTGTGCGAGATACTAATT
* * * **
41467075 CTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAC
1 C-GGGCTAAGACCCGAAGGCATTTGTGCGAGATACTA-ATT
* * *
41467116 CAGGCTATGTCCCGAAGGCATTTG
1 CGGGCTAAGACCCGAAGGCATTTG
41467140 AACGAGGAGC
Statistics
Matches: 158, Mismatches: 18, Indels: 14
0.83 0.09 0.07
Matches are distributed among these distances:
38 2 0.01
39 34 0.22
40 108 0.68
41 13 0.08
42 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (39 bp):
CGGGCTAAGACCCGAAGGCATTTGTGCGAGATACTAATT
Found at i:41467122 original size:79 final size:80
Alignment explanation
Indices: 41466971--41467139 Score: 218
Period size: 79 Copynumber: 2.1 Consensus size: 80
41466961 CTAAGATCCA
*
41466971 AAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATT
1 AAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATA
* *
41467036 TCGGGCTAAG-CCCG
66 CCAGGCTAAGTCCCG
* * ** *
41467050 AAGGCATTTGTGCGAGTTACTAAATCTGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACT-AT
1 AAGGCATTTGTGCGAGATACTAAATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
*
41467113 AACCAGGCTATGTCCCG
65 -ACCAGGCTAAGTCCCG
41467130 AAGGCATTTG
1 AAGGCATTTG
41467140 AACGAGGAGC
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
78 3 0.04
79 61 0.78
80 14 0.18
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (80 bp):
AAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATA
CCAGGCTAAGTCCCG
Found at i:41467161 original size:79 final size:79
Alignment explanation
Indices: 41467008--41467162 Score: 172
Period size: 79 Copynumber: 2.0 Consensus size: 79
41466998 GGACTAAGAT
** * ** *
41467008 CCGAAGGCATTTGTGCGAGATACTAATTTCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCAGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
41467073 ATCTGGGTTAAGTC
66 ATCTCGGTTAAGTC
* *
41467087 CCGAAGGCATTTGTGCGAGTTACT-ATAACCAGGCTATGTCCCGAAGGCATTTGAACGAG-GAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCAGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-C
*
41467150 TATATC-CGGTTAA
63 TAAATCTCGGTTAA
41467163 ATTTCGAAGG
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
78 2 0.03
79 37 0.59
80 24 0.38
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCAGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCTCGGTTAAGTC
Found at i:41483099 original size:40 final size:40
Alignment explanation
Indices: 41483015--41483198 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
41483005 TTGAATGCTG
* * * *
41483015 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
41483054 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
41483095 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
41483135 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
41483175 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
41483199 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:41483152 original size:80 final size:81
Alignment explanation
Indices: 41483015--41483195 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
41483005 TTGAATGCTG
* * *
41483015 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
41483079 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
41483095 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
41483156 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
41483175 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
41483196 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:41483219 original size:39 final size:38
Alignment explanation
Indices: 41483096--41483245 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
41483086 GTTATTAATT
* ** * *
41483096 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
41483136 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
41483175 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
41483215 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
41483246 GAGCTATCCG
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:41490935 original size:40 final size:40
Alignment explanation
Indices: 41490851--41491034 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
41490841 TTGAATGCTG
* * * *
41490851 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
41490890 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
41490931 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
41490971 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
41491011 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
41491035 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:41490988 original size:80 final size:81
Alignment explanation
Indices: 41490851--41491031 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
41490841 TTGAATGCTG
* * *
41490851 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
41490915 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
41490931 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
41490992 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
41491011 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
41491032 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:41491055 original size:39 final size:38
Alignment explanation
Indices: 41490932--41491081 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
41490922 GTTATTAATT
* ** * *
41490932 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
41490972 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
41491011 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
41491051 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
41491082 GAGCTAATCC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:41493131 original size:22 final size:22
Alignment explanation
Indices: 41493100--41493163 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
41493090 GCCAGTAACC
*
41493100 AGAATGGCTAAGAGCCATAAAT
1 AGAATAGCTAAGAGCCATAAAT
* *
41493122 AGGATAGCTATA-AGCTATAAAT
1 AGAATAGCTA-AGAGCCATAAAT
* *
41493144 AGAATGGCTACGAGCCATAA
1 AGAATAGCTAAGAGCCATAA
41493164 GTTCAGTAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
22 32 0.97
23 1 0.03
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (22 bp):
AGAATAGCTAAGAGCCATAAAT
Found at i:41493334 original size:27 final size:27
Alignment explanation
Indices: 41493298--41493364 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
41493288 GTATCGCAAT
*
41493298 AAAGCTACCAGTAACAGT-ATATGTGGC
1 AAAGCCACCAGTAACAGTGAT-TGTGGC
*
41493325 CAAGCCACCAGTAACAGTGATTGTGGC
1 AAAGCCACCAGTAACAGTGATTGTGGC
*
41493352 AAAACCACCAGTA
1 AAAGCCACCAGTA
41493365 TAGTACTTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 33 0.94
28 2 0.06
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (27 bp):
AAAGCCACCAGTAACAGTGATTGTGGC
Found at i:41493546 original size:27 final size:26
Alignment explanation
Indices: 41493485--41493550 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
41493475 AAAAAAATCA
* *
41493485 ATCATTTACCCTTCAGGGGCATTACGG
1 ATCATTTACCCTCCAGAGGCATTAC-G
* *
41493512 TTAATTTACCCTCCAGAGGCATTACG
1 ATCATTTACCCTCCAGAGGCATTACG
41493538 ATCATTTTACCCT
1 ATCA-TTTACCCT
41493551 ATAAGGGCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 3 0.09
27 29 0.91
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.33
Consensus pattern (26 bp):
ATCATTTACCCTCCAGAGGCATTACG
Found at i:41493571 original size:27 final size:27
Alignment explanation
Indices: 41493541--41493655 Score: 126
Period size: 27 Copynumber: 4.3 Consensus size: 27
41493531 CATTACGATC
*
41493541 ATTTTACCCTATAAGGGCATTTCAGTA
1 ATTTTACCCTATAAGGGTATTTCAGTA
*
41493568 ATTTTA-CCTAGTGAGGGTATTTCAGTA
1 ATTTTACCCTA-TAAGGGTATTTCAGTA
* * **
41493595 ATCTTACCC-ATCAGGGGTATTTTTGTA
1 ATTTTACCCTAT-AAGGGTATTTCAGTA
* *
41493622 ATTTTACCCTTTAAGGGTATTTTAGTA
1 ATTTTACCCTATAAGGGTATTTCAGTA
41493649 ATTTTAC
1 ATTTTAC
41493656 AACCTTTCCG
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
26 5 0.07
27 65 0.89
28 3 0.04
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTATAAGGGTATTTCAGTA
Found at i:41497949 original size:9 final size:9
Alignment explanation
Indices: 41497932--41497968 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
41497922 TGAGTTTTCG
41497932 AATTCGAAT
1 AATTCGAAT
*
41497941 AACTCGAAT
1 AATTCGAAT
41497950 AATTCGAAT
1 AATTCGAAT
41497959 AATTCGAAT
1 AATTCGAAT
41497968 A
1 A
41497969 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:41498216 original size:30 final size:31
Alignment explanation
Indices: 41498182--41498241 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
41498172 AAACCTTTTA
*
41498182 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
41498212 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
41498242 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:41498368 original size:21 final size:21
Alignment explanation
Indices: 41498339--41498378 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
41498329 TCCCTCAAAC
41498339 TTTTATTCCCCAAAACTTTTTA
1 TTTTATT-CCCAAAACTTTTTA
*
41498361 TTTT-TTCCCTAAACTTTT
1 TTTTATTCCCAAAACTTTT
41498379 ACTTCTCACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTATTCCCAAAACTTTTTA
Found at i:41509460 original size:18 final size:18
Alignment explanation
Indices: 41509437--41509476 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41509427 GATGTGTGCT
* * *
41509437 TTTGTCCTATCTCCTATC
1 TTTGTCCAAACTCCTATA
41509455 TTTGTCCAAACTCCTATA
1 TTTGTCCAAACTCCTATA
41509473 TTTG
1 TTTG
41509477 AACATCTGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.28, G:0.07, T:0.47
Consensus pattern (18 bp):
TTTGTCCAAACTCCTATA
Found at i:41511552 original size:12 final size:12
Alignment explanation
Indices: 41511514--41511555 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
41511504 ATTGGTCATA
41511514 GAGAGATTTGAG
1 GAGAGATTTGAG
* *
41511526 GAGGGATATT-TG
1 GAGAGAT-TTGAG
41511538 GAGAGATTTGAG
1 GAGAGATTTGAG
41511550 GAGAGA
1 GAGAGA
41511556 ATATTGGGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.24
Consensus pattern (12 bp):
GAGAGATTTGAG
Found at i:41511562 original size:24 final size:24
Alignment explanation
Indices: 41511514--41511560 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
41511504 ATTGGTCATA
*
41511514 GAGAGATTTGAGGAGGGATATTTG
1 GAGAGATTTGAGGAGGAATATTTG
41511538 GAGAGATTTGAGGAGAGAATATT
1 GAGAGATTTGAGGAG-GAATATT
41511561 GGGATTTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.38, T:0.28
Consensus pattern (24 bp):
GAGAGATTTGAGGAGGAATATTTG
Found at i:41514411 original size:25 final size:25
Alignment explanation
Indices: 41514383--41514461 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 25
41514373 CTAATGGCCG
41514383 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* *** ****
41514408 ATGTGAT-AAGGCCTAA-TG-GCCG
1 ATGTGATGAATGTGAAAGTGTATAT
41514430 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
41514455 ATGTGAT
1 ATGTGAT
41514462 AAGGCCTAAT
Statistics
Matches: 35, Mismatches: 16, Indels: 6
0.61 0.28 0.11
Matches are distributed among these distances:
22 7 0.20
23 7 0.20
24 7 0.20
25 14 0.40
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:41514416 original size:47 final size:47
Alignment explanation
Indices: 41514335--41514647 Score: 521
Period size: 47 Copynumber: 6.7 Consensus size: 47
41514325 TTAGGATTCT
* * *
41514335 ATGTGATGGATGATGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATG-TGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
41514383 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
41514430 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
41514477 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
41514524 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
41514571 ATGTGATGAATGTGAAAGTG--TATA--T-ATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
41514613 ATGTGATGAATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
41514648 TCCCGAAGGG
Statistics
Matches: 253, Mismatches: 6, Indels: 13
0.93 0.02 0.05
Matches are distributed among these distances:
42 37 0.15
43 1 0.00
44 3 0.01
45 4 0.02
46 2 0.01
47 195 0.77
48 11 0.04
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:41514822 original size:37 final size:37
Alignment explanation
Indices: 41514766--41514844 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
41514756 CCGAGCTCTA
* * *
41514766 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
41514803 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
41514840 AAGAC
1 AAGAC
41514845 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:41516038 original size:14 final size:15
Alignment explanation
Indices: 41516011--41516049 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
41516001 AATGTAAATG
41516011 ATATGCTA-ATGTGT
1 ATATGCTACATGTGT
41516025 AT-TGCTACATGTGT
1 ATATGCTACATGTGT
41516039 ATATG-TACATG
1 ATATGCTACATG
41516050 AGAATTGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.22
14 16 0.70
15 2 0.09
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (15 bp):
ATATGCTACATGTGT
Found at i:41516302 original size:40 final size:40
Alignment explanation
Indices: 41516059--41516290 Score: 311
Period size: 40 Copynumber: 5.8 Consensus size: 40
41516049 GAGAATTGAG
*
41516059 AGTGATATATCCGGGCTATGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
41516099 AGTGATATATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
41516139 AGTGATATATCCAGGTTAAATCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * * * *
41516179 AATGATGTATCCGGACTAAGTTCCAAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* **
41516219 AGTGATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
41516259 GGTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCA
41516291 ATCATGCTGG
Statistics
Matches: 162, Mismatches: 30, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 162 1.00
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Found at i:41518391 original size:19 final size:19
Alignment explanation
Indices: 41518359--41518399 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
41518349 CATGGGCTTA
* *
41518359 GGCCGTAATGGGCCATATG
1 GGCCGAAATAGGCCATATG
*
41518378 GGCCGAAATAGGCCATGTG
1 GGCCGAAATAGGCCATATG
41518397 GGC
1 GGC
41518400 TCAATGGGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.39, T:0.17
Consensus pattern (19 bp):
GGCCGAAATAGGCCATATG
Found at i:41518662 original size:27 final size:27
Alignment explanation
Indices: 41518632--41518847 Score: 270
Period size: 27 Copynumber: 8.0 Consensus size: 27
41518622 GATAAATTAT
*
41518632 CGAAATACCCCCATAAGGTAAAATGAC
1 CGAAATACCCCCATAGGGTAAAATGAC
* *
41518659 CGAAATACCTCCATAGGGTAAAATGAT
1 CGAAATACCCCCATAGGGTAAAATGAC
* *
41518686 TGAAATACCCCCATAGTGTAAAATGAC
1 CGAAATACCCCCATAGGGTAAAATGAC
* * *
41518713 CAAAATACCCTCATAGGGTAGAATGAC
1 CGAAATACCCCCATAGGGTAAAATGAC
*
41518740 CGAAATACCCCCATAGGGTAGAATGAC
1 CGAAATACCCCCATAGGGTAAAATGAC
* ** *
41518767 CAAAATACCCTTAATAGGGTAAAATGAT
1 CGAAATACCC-CCATAGGGTAAAATGAC
*
41518795 CGAAATACCCTCATAGGGTAAAATGAC
1 CGAAATACCCCCATAGGGTAAAATGAC
* * *
41518822 CAAAATAACCCCATAAGGTAAAATGA
1 CGAAATACCCCCATAGGGTAAAATGA
41518848 TTTTTATACC
Statistics
Matches: 162, Mismatches: 26, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
27 140 0.86
28 22 0.14
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (27 bp):
CGAAATACCCCCATAGGGTAAAATGAC
Found at i:41518719 original size:54 final size:53
Alignment explanation
Indices: 41518625--41518848 Score: 304
Period size: 54 Copynumber: 4.1 Consensus size: 53
41518615 AGAGGTCGAT
* * *
41518625 AAATTATCGAAATACCCCCATAAGGTAAAATGACCGAAATACCTCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTAAAATGACCAAAATACC-CCATAGGGTA
* *
41518679 AAATGATTGAAATACCCCCATAGTGTAAAATGACCAAAATACCCTCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTAAAATGACCAAAATACCC-CATAGGGTA
* * * *
41518733 GAATGACCGAAATACCCCCATAGGGTAGAATGACCAAAATACCCTTAATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTAAAATGACCAAAATACCC--CATAGGGTA
* *
41518788 AAATGATCGAAATACCCTCATAGGGTAAAATGACCAAAATAACCCCATAAGGTA
1 AAATGATCGAAATACCCCCATAGGGTAAAATGACCAAAAT-ACCCCATAGGGTA
41518842 AAATGAT
1 AAATGAT
41518849 TTTTATACCC
Statistics
Matches: 150, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
53 1 0.01
54 100 0.67
55 45 0.30
56 4 0.03
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (53 bp):
AAATGATCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCATAGGGTA
Found at i:41518888 original size:109 final size:109
Alignment explanation
Indices: 41518632--41518847 Score: 319
Period size: 109 Copynumber: 2.0 Consensus size: 109
41518622 GATAAATTAT
* * * ** *
41518632 CGAAATACCCCCATAAGGTAAAATGACCGAAATA-CCTCCATAGGGTAAAATGATTGAAATACCC
1 CGAAATACCCCCATAGGGTAGAATGACCAAAATACCCTTAATAGGGTAAAATGATCGAAATACCC
* * *
41518696 CCATAGTGTAAAATGACCAAAATACCCTCATAGGGTAGAATGAC
66 CCATAGGGTAAAATGACCAAAATACCCTCATAAGGTAAAATGAC
41518740 CGAAATACCCCCATAGGGTAGAATGACCAAAATACCCTTAATAGGGTAAAATGATCGAAATACCC
1 CGAAATACCCCCATAGGGTAGAATGACCAAAATACCCTTAATAGGGTAAAATGATCGAAATACCC
*
41518805 TCATAGGGTAAAATGACCAAAATAACCC-CATAAGGTAAAATGA
66 CCATAGGGTAAAATGACCAAAAT-ACCCTCATAAGGTAAAATGA
41518848 TTTTTATACC
Statistics
Matches: 96, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
108 31 0.32
109 61 0.64
110 4 0.04
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (109 bp):
CGAAATACCCCCATAGGGTAGAATGACCAAAATACCCTTAATAGGGTAAAATGATCGAAATACCC
CCATAGGGTAAAATGACCAAAATACCCTCATAAGGTAAAATGAC
Found at i:41519261 original size:28 final size:28
Alignment explanation
Indices: 41519216--41519363 Score: 201
Period size: 28 Copynumber: 5.3 Consensus size: 28
41519206 TGCACTGCAT
41519216 TGTTACTGTATTGGGCTAAGGCCCACAC
1 TGTTACTGTATTGGGCTAAGGCCCACAC
*
41519244 TGATT-CTGTACTGGGCTAAGGCCCACAC
1 TG-TTACTGTATTGGGCTAAGGCCCACAC
* * *
41519272 TAATT-CTGTATTGGGCTAAGTCCCATAC
1 T-GTTACTGTATTGGGCTAAGGCCCACAC
* *
41519300 TGTTACTCTATTGGGCTAAGGCCCACAT
1 TGTTACTGTATTGGGCTAAGGCCCACAC
*
41519328 TGTTACTGTATTGGGCTAAGGCCCAGAC
1 TGTTACTGTATTGGGCTAAGGCCCACAC
41519356 TGTTACTG
1 TGTTACTG
41519364 CATGCTGTTT
Statistics
Matches: 104, Mismatches: 13, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
27 2 0.02
28 100 0.96
29 2 0.02
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (28 bp):
TGTTACTGTATTGGGCTAAGGCCCACAC
Found at i:41521077 original size:14 final size:13
Alignment explanation
Indices: 41521054--41521088 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
41521044 TCTAATATAT
41521054 TTTAATTTTAAAA
1 TTTAATTTTAAAA
*
41521067 TTTAATATTTATAA
1 TTTAAT-TTTAAAA
41521081 TTTAATTT
1 TTTAATTT
41521089 CTAAGATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTAATTTTAAAA
Found at i:41552764 original size:20 final size:20
Alignment explanation
Indices: 41552741--41552783 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
41552731 GGGCACAAAT
* *
41552741 GTGCAAATAGGGGCACCGTA
1 GTGCAAATAGGGACACCGAA
*
41552761 GTGCGAATAGGGACACCGAA
1 GTGCAAATAGGGACACCGAA
41552781 GTG
1 GTG
41552784 TATACAGGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.19, G:0.37, T:0.14
Consensus pattern (20 bp):
GTGCAAATAGGGACACCGAA
Found at i:41560274 original size:39 final size:39
Alignment explanation
Indices: 41560170--41560280 Score: 107
Period size: 39 Copynumber: 2.8 Consensus size: 39
41560160 TTAAAACATG
* * * *
41560170 TATTAAAGATGTCCTAAACTATGACATAATT-AAAACCCT
1 TATTAATGATGTTC-AAATTATGACATAATTAAAAACCCA
* * * ** *
41560209 TGTTAATGTTGTTCAGATTACCACATAATTAAAAACTCA
1 TATTAATGATGTTCAAATTATGACATAATTAAAAACCCA
41560248 TATTAATGATGTTCAAATTATGACATAAATTAA
1 TATTAATGATGTTCAAATTATGACAT-AATTAA
41560281 CTAAAGTAAC
Statistics
Matches: 55, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
38 12 0.22
39 37 0.67
40 6 0.11
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (39 bp):
TATTAATGATGTTCAAATTATGACATAATTAAAAACCCA
Found at i:41568239 original size:27 final size:26
Alignment explanation
Indices: 41568209--41568369 Score: 169
Period size: 27 Copynumber: 6.0 Consensus size: 26
41568199 CGAATCGTGC
**
41568209 GTAAAATGACCGTATTACCCCCGAAAG
1 GTAAAATGACCAAATTACCCCC-AAAG
*
41568236 GTAAAATGACCATATTACCCCCAAAGG
1 GTAAAATGACCAAATTACCCCCAAA-G
* *
41568263 GTAAAATCACCAAATTACCCCCTAAAA
1 GTAAAATGACCAAATTACCCCC-AAAG
*
41568290 GTAAAATGACCAAATTACCCCCGAAGG
1 GTAAAATGACCAAATTACCCCC-AAAG
* * *
41568317 GTAAAATGATCGAATTACCCCCAAGG
1 GTAAAATGACCAAATTACCCCCAAAG
* * * *
41568343 GTAAAATTACTAAAATACCCTCAAAG
1 GTAAAATGACCAAATTACCCCCAAAG
41568369 G
1 G
41568370 GTTAAATTAC
Statistics
Matches: 115, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
26 27 0.23
27 85 0.74
28 3 0.03
ACGTcount: A:0.42, C:0.25, G:0.14, T:0.19
Consensus pattern (26 bp):
GTAAAATGACCAAATTACCCCCAAAG
Found at i:41568268 original size:54 final size:54
Alignment explanation
Indices: 41568209--41568465 Score: 221
Period size: 54 Copynumber: 4.8 Consensus size: 54
41568199 CGAATCGTGC
* *
41568209 GTAAAATGACCGTATTACCCCCGAAAGGTAAAATGACCATATTACCCCCAAAGG
1 GTAAAATGACCGAATTACCCCCGAAAGGTAAAATGACCAAATTACCCCCAAAGG
* * * * *
41568263 GTAAAATCACCAAATTACCCCCTAAAAGTAAAATGACCAAATTACCCCCGAAGG
1 GTAAAATGACCGAATTACCCCCGAAAGGTAAAATGACCAAATTACCCCCAAAGG
* * * * * *
41568317 GTAAAATGATCGAATTACCCCC-AAGGGTAAAATTACTAAAATACCCTCAAAGG
1 GTAAAATGACCGAATTACCCCCGAAAGGTAAAATGACCAAATTACCCCCAAAGG
* * * * * * * * *
41568370 GTTAAATTACCGAAATACCCTCGAAGGGTAAAAATTATCGAAA-TACCCTCGAAGG
1 GTAAAATGACCGAATTACCCCCGAAAGGT-AAAATGA-CCAAATTACCCCCAAAGG
* * * * * * *
41568425 GTAAAATTATCAAAATACCCTCGAAGGGTAAAATTACCAAA
1 GTAAAATGACCGAATTACCCCCGAAAGGTAAAATGACCAAA
41568466 AACCCCTAAG
Statistics
Matches: 172, Mismatches: 28, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
53 45 0.26
54 79 0.46
55 44 0.26
56 4 0.02
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.20
Consensus pattern (54 bp):
GTAAAATGACCGAATTACCCCCGAAAGGTAAAATGACCAAATTACCCCCAAAGG
Found at i:41568325 original size:81 final size:80
Alignment explanation
Indices: 41568209--41568465 Score: 241
Period size: 81 Copynumber: 3.2 Consensus size: 80
41568199 CGAATCGTGC
** *
41568209 GTAAAATGACCGTATTACCCCCGAAAGGTAAAATGA-CCATATTACCCCCAAAGGGTAAAATCAC
1 GTAAAATGACCAAATTACCCCCGAAGGGTAAAATGATCCA-ATTACCCCC-AAGGGTAAAATCAC
*
41568273 CAAATTACCCCCTAAA-A
64 CAAAATACCCCC-AAAGA
* * *
41568290 GTAAAATGACCAAATTACCCCCGAAGGGTAAAATGATCGAATTACCCCCAAGGGTAAAATTACTA
1 GTAAAATGACCAAATTACCCCCGAAGGGTAAAATGATCCAATTACCCCCAAGGGTAAAATCACCA
* *
41568355 AAATACCCTCAAAGG
66 AAATACCCCCAAAGA
* * * * * * * *
41568370 GTTAAATTACCGAAA-TACCCTCGAAGGGTAAAAATTATCGAAATACCCTCGAAGGGTAAAATTA
1 GTAAAATGACC-AAATTACCCCCGAAGGGT-AAAATGATCCAATTACCC-CCAAGGGTAAAATCA
* * * *
41568434 TCAAAATACCCTCGAAGG
63 CCAAAATACCCCCAAAGA
*
41568452 GTAAAATTACCAAA
1 GTAAAATGACCAAA
41568466 AACCCCTAAG
Statistics
Matches: 152, Mismatches: 19, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
79 3 0.02
80 44 0.29
81 64 0.42
82 41 0.27
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.20
Consensus pattern (80 bp):
GTAAAATGACCAAATTACCCCCGAAGGGTAAAATGATCCAATTACCCCCAAGGGTAAAATCACCA
AAATACCCCCAAAGA
Found at i:41568413 original size:28 final size:27
Alignment explanation
Indices: 41568305--41568510 Score: 206
Period size: 27 Copynumber: 7.7 Consensus size: 27
41568295 ATGACCAAAT
* * *
41568305 TACCCCCGAAGGGTAAAATGATCGAAT
1 TACCCTCGAAGGGTAAAATTATCGAAA
* *
41568332 TACCC-CCAAGGGTAAAATTA-CTAAAA
1 TACCCTCGAAGGGTAAAATTATC-GAAA
* * *
41568358 TACCCTCAAAGGGTTAAATTACCGAAA
1 TACCCTCGAAGGGTAAAATTATCGAAA
41568385 TACCCTCGAAGGGTAAAAATTATCGAAA
1 TACCCTCGAAGGGT-AAAATTATCGAAA
*
41568413 TACCCTCGAAGGGTAAAATTATCAAAA
1 TACCCTCGAAGGGTAAAATTATCGAAA
*
41568440 TACCCTCGAAGGGTAAAATTA-CCAAA
1 TACCCTCGAAGGGTAAAATTATCGAAA
* * * *
41568466 AACCC-CTAAGAGTAAAATTA-CTATAA
1 TACCCTCGAAGGGTAAAATTATCGA-AA
* *
41568492 TACCCCCTAAGGGTAAAAT
1 TACCCTCGAAGGGTAAAAT
41568511 GATCTTTATA
Statistics
Matches: 155, Mismatches: 18, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
25 16 0.10
26 34 0.22
27 79 0.51
28 26 0.17
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (27 bp):
TACCCTCGAAGGGTAAAATTATCGAAA
Found at i:41568415 original size:55 final size:55
Alignment explanation
Indices: 41568313--41568509 Score: 201
Period size: 55 Copynumber: 3.7 Consensus size: 55
41568303 ATTACCCCCG
* * *
41568313 AAGGGTAAAATGATCGAATTACCC-CCAAGGGT-AAAATTACTAAAATACCCTCA
1 AAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAAATTACTAAAATACCCTCA
* * * *
41568366 AAGGGTTAAATTACCGAAATACCCTCGAAGGGTAAAAATTA-TCGAAATACCCTCG
1 AAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAAATTACT-AAAATACCCTCA
* * *
41568421 AAGGGTAAAATTATCAAAATACCCTCGAAGGGT-AAAATTACCAAAA-ACCC-CT
1 AAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAAATTACTAAAATACCCTCA
* * * *
41568473 AAGAGTAAAATTA-CTATAATACCCCCTAAGGGTAAAA
1 AAGGGTAAAATTATCGA-AATACCCTCGAAGGGTAAAA
41568510 TGATCTTTAT
Statistics
Matches: 121, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
51 2 0.02
52 27 0.22
53 27 0.22
54 18 0.15
55 47 0.39
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (55 bp):
AAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAAATTACTAAAATACCCTCA
Found at i:41568521 original size:27 final size:27
Alignment explanation
Indices: 41568209--41568543 Score: 82
Period size: 27 Copynumber: 12.5 Consensus size: 27
41568199 CGAATCGTGC
** * *
41568209 GTAAAATGACCGTATTACCCCCGAA-A
1 GTAAAATGACTATAATACCCCCTAAGA
* * * *
41568235 GGTAAAATGACCATATTACCCCCAAAGG
1 -GTAAAATGACTATAATACCCCCTAAGA
* * *
41568263 GTAAAATCACCA-AATTACCCCCTAAAA
1 GTAAAATGACTATAA-TACCCCCTAAGA
* * *
41568290 GTAAAATGACCA-AATTACCCCCGAAGG
1 GTAAAATGACTATAA-TACCCCCTAAGA
* * *
41568317 GTAAAATGATCGA-ATTACCCCC-AAGG
1 GTAAAATGA-CTATAATACCCCCTAAGA
* * * * *
41568343 GTAAAATTACTAAAATACCCTCAAAGG
1 GTAAAATGACTATAATACCCCCTAAGA
* * * * * *
41568370 GTTAAATTACCGA-AATACCCTCGAAGG
1 GTAAAATGA-CTATAATACCCCCTAAGA
* * * * *
41568397 GTAAAAATTATCGA-AATACCCTCGAAGG
1 GT-AAAATGA-CTATAATACCCCCTAAGA
* * * * *
41568425 GTAAAATTA-TCAAAATACCCTCGAAGG
1 GTAAAATGACT-ATAATACCCCCTAAGA
* * *
41568452 GTAAAATTACCA-AA-AACCCCTAAGA
1 GTAAAATGACTATAATACCCCCTAAGA
* *
41568477 GTAAAATTACTATAATACCCCCTAAGG
1 GTAAAATGACTATAATACCCCCTAAGA
* *
41568504 GTAAAATGATCT-TTATA-CCCCTAGGA
1 GTAAAATGA-CTATAATACCCCCTAAGA
*
41568530 GATGAAATGACTAT
1 G-TAAAATGACTAT
41568544 TATGGCCTTA
Statistics
Matches: 256, Mismatches: 37, Indels: 30
0.79 0.11 0.09
Matches are distributed among these distances:
25 20 0.08
26 35 0.14
27 169 0.66
28 32 0.12
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.21
Consensus pattern (27 bp):
GTAAAATGACTATAATACCCCCTAAGA
Found at i:41572170 original size:13 final size:13
Alignment explanation
Indices: 41572154--41572183 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41572144 ATATAACTGA
41572154 TTCATATAGCCAT
1 TTCATATAGCCAT
*
41572167 TTCATATAGTCAT
1 TTCATATAGCCAT
41572180 TTCA
1 TTCA
41572184 AAGTGCTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (13 bp):
TTCATATAGCCAT
Found at i:41572172 original size:26 final size:25
Alignment explanation
Indices: 41572112--41572174 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
41572102 TCCATGTAAT
*
41572112 CATTTCATATAACACTTCATATAAT
1 CATTTCATATAACACTTCATATAAC
* *
41572137 TATTTCCATATAACTGA-TTCATATAGC
1 CATTT-CATATAAC--ACTTCATATAAC
41572164 CATTTCATATA
1 CATTTCATATA
41572175 GTCATTTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
25 4 0.13
26 14 0.45
27 12 0.39
28 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.03, T:0.41
Consensus pattern (25 bp):
CATTTCATATAACACTTCATATAAC
Found at i:41576881 original size:19 final size:19
Alignment explanation
Indices: 41576857--41576895 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41576847 AAATTAGCGG
41576857 TAATTATCGAC-TTAGTTAA
1 TAATTA-CGACTTTAGTTAA
*
41576876 TAATTACTACTTTAGTTAA
1 TAATTACGACTTTAGTTAA
41576895 T
1 T
41576896 TCTAGGCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (19 bp):
TAATTACGACTTTAGTTAA
Found at i:41590721 original size:27 final size:27
Alignment explanation
Indices: 41590616--41590727 Score: 138
Period size: 27 Copynumber: 4.1 Consensus size: 27
41590606 TATAACAGTC
* *
41590616 ATTTTACCCTAT-GAGGGTAATTCGGTA
1 ATTTTACCCT-TCGAGGGTATTTCGATA
* *
41590643 ATTTTACCCATCGAGGGTATTGT-GGTA
1 ATTTTACCCTTCGAGGGTATT-TCGATA
*
41590670 AATTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
*
41590697 ATTTTACCCTTCGAGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGATA
41590724 ATTT
1 ATTT
41590728 AACAATCTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
26 2 0.03
27 72 0.96
28 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGATA
Found at i:41593320 original size:25 final size:25
Alignment explanation
Indices: 41593266--41593340 Score: 98
Period size: 25 Copynumber: 3.0 Consensus size: 25
41593256 GGTTATCGAT
*
41593266 TTCAGCTCTTATGAGCTTACCGA-TA
1 TTCAGCTCATATGAGCTTACC-ATTA
*
41593291 CTCAGCTCATATGAGCTTACCATTA
1 TTCAGCTCATATGAGCTTACCATTA
* *
41593316 TTCAGCTCAGAGGAGCTTACCATTA
1 TTCAGCTCATATGAGCTTACCATTA
41593341 ATCATCTCGG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
24 1 0.02
25 43 0.98
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (25 bp):
TTCAGCTCATATGAGCTTACCATTA
Found at i:41593353 original size:25 final size:25
Alignment explanation
Indices: 41593278--41593361 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 25
41593268 CAGCTCTTAT
* * *
41593278 GAGCTTACCGA-TACTCAGCTCATAT
1 GAGCTTACC-ATTAATCAGCTCAGAG
*
41593303 GAGCTTACCATTATTCAGCTCAGAG
1 GAGCTTACCATTAATCAGCTCAGAG
* *
41593328 GAGCTTACCATTAATCATCTCGGAG
1 GAGCTTACCATTAATCAGCTCAGAG
41593353 GAGCTTACC
1 GAGCTTACC
41593362 GTTTACAGCT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
24 1 0.02
25 51 0.98
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.27
Consensus pattern (25 bp):
GAGCTTACCATTAATCAGCTCAGAG
Found at i:41595303 original size:14 final size:14
Alignment explanation
Indices: 41595284--41595323 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
41595274 GATTCAAAGA
41595284 TAAATAAAATATCC
1 TAAATAAAATATCC
41595298 TAAATAAAATATCC
1 TAAATAAAATATCC
*
41595312 CAAATAAAATAT
1 TAAATAAAATAT
41595324 ATTAATAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (14 bp):
TAAATAAAATATCC
Found at i:41596629 original size:30 final size:30
Alignment explanation
Indices: 41596595--41596656 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
41596585 CTTTACTTTA
*
41596595 AACTTCTCAATATGACCATTTAAAGAGTTG
1 AACTTCTCAATATGACCAGTTAAAGAGTTG
*
41596625 AACTTCTCAATATGACCGGTTAAAGAGTTG
1 AACTTCTCAATATGACCAGTTAAAGAGTTG
41596655 AA
1 AA
41596657 GAATCCTAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (30 bp):
AACTTCTCAATATGACCAGTTAAAGAGTTG
Found at i:41603179 original size:21 final size:20
Alignment explanation
Indices: 41603149--41603191 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
41603139 TTATGTTCAG
*
41603149 TCTCAATTTCGTCTTTCTTTT
1 TCTCAATTTC-ACTTTCTTTT
*
41603170 TCTCACTTTCACTTTCTTTT
1 TCTCAATTTCACTTTCTTTT
41603190 TC
1 TC
41603192 AATTTCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.09, C:0.28, G:0.02, T:0.60
Consensus pattern (20 bp):
TCTCAATTTCACTTTCTTTT
Found at i:41603197 original size:12 final size:12
Alignment explanation
Indices: 41603176--41603214 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
41603166 TTTTTCTCAC
*
41603176 TTTCACTTTCTT
1 TTTCAATTTCTT
41603188 TTTCAATTTCTT
1 TTTCAATTTCTT
**
41603200 TTTCGTTTTCTT
1 TTTCAATTTCTT
41603212 TTT
1 TTT
41603215 AACAATCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.18, G:0.03, T:0.72
Consensus pattern (12 bp):
TTTCAATTTCTT
Found at i:41603203 original size:18 final size:18
Alignment explanation
Indices: 41603182--41603284 Score: 64
Period size: 18 Copynumber: 5.6 Consensus size: 18
41603172 TCACTTTCAC
41603182 TTTCTTTTTCAATTTCTT
1 TTTCTTTTTCAATTTCTT
* ** ***
41603200 TTTCGTTTTCTTTTTAAC
1 TTTCTTTTTCAATTTCTT
** *
41603218 AATCTTTTTCGA-TTCTT
1 TTTCTTTTTCAATTTCTT
* *
41603235 TTCTCTCTTTCAATTTTTT
1 TT-TCTTTTTCAATTTCTT
*
41603254 TTCCTCTTTTTCAATCTCTT
1 TT--TCTTTTTCAATTTCTT
41603274 TTTCTTTTTCA
1 TTTCTTTTTCA
41603285 TTACAACATG
Statistics
Matches: 60, Mismatches: 22, Indels: 6
0.68 0.25 0.07
Matches are distributed among these distances:
17 2 0.03
18 36 0.60
19 6 0.10
20 16 0.27
ACGTcount: A:0.12, C:0.20, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTCTTTTTCAATTTCTT
Found at i:41603203 original size:24 final size:24
Alignment explanation
Indices: 41603176--41603277 Score: 63
Period size: 24 Copynumber: 4.2 Consensus size: 24
41603166 TTTTTCTCAC
41603176 TTTCACTTTCTTTTTCAATTTCTT
1 TTTCACTTTCTTTTTCAATTTCTT
**
41603200 TTTCGTTTTCTTTTTAACAA--TCTT
1 TTTCACTTTCTTTTT--CAATTTCTT
41603224 TTTCGATTCTTTTCTCTCTTTCAATTT-TT
1 TTTC-A--C-TTTCT-T-TTTCAATTTCTT
*
41603253 TTTC-C--TCTTTTTCAATCTCTT
1 TTTCACTTTCTTTTTCAATTTCTT
41603274 TTTC
1 TTTC
41603278 TTTTTCATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 25
0.67 0.05 0.27
Matches are distributed among these distances:
20 8 0.13
21 7 0.11
22 3 0.05
24 21 0.34
25 1 0.02
26 3 0.05
28 8 0.13
29 7 0.11
30 4 0.06
ACGTcount: A:0.12, C:0.22, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTCACTTTCTTTTTCAATTTCTT
Found at i:41603275 original size:20 final size:18
Alignment explanation
Indices: 41603220--41603284 Score: 69
Period size: 18 Copynumber: 3.5 Consensus size: 18
41603210 TTTTTAACAA
*
41603220 TCTTTTTCGATTCTTTTC
1 TCTTTTTCAATTCTTTTC
* *
41603238 TCTCTTTCAATTTTTTTTCC
1 TCTTTTTCAA-TTCTTTT-C
41603258 TCTTTTTCAATCTCTTTT-
1 TCTTTTTCAAT-TCTTTTC
41603276 TCTTTTTCA
1 TCTTTTTCA
41603285 TTACAACATG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 17 0.44
19 7 0.18
20 15 0.38
ACGTcount: A:0.09, C:0.23, G:0.02, T:0.66
Consensus pattern (18 bp):
TCTTTTTCAATTCTTTTC
Found at i:41608690 original size:47 final size:47
Alignment explanation
Indices: 41608615--41609203 Score: 1054
Period size: 47 Copynumber: 12.5 Consensus size: 47
41608605 TTCGGGACTC
* * * * * * *
41608615 ATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
*
41608662 GTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
41608709 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
*
41608756 ATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
41608803 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
*
41608850 ATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
*
41608897 ATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
41608944 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
41608991 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
41609038 ATCACATATATACACTTTCACATTCATCACATCGG-CATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
41609084 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
41609131 ATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
41609180 ATCACATATATACACTTTCACATT
1 ATCACATATATACACTTTCACATT
41609204 TATTCAAATA
Statistics
Matches: 524, Mismatches: 15, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
46 46 0.09
47 431 0.82
49 47 0.09
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
Found at i:41612175 original size:22 final size:25
Alignment explanation
Indices: 41612127--41612175 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
41612117 TGATTTTTTA
*
41612127 CTTTTTCTTTTTCTTCTCCAACGTTC
1 CTTTTTCTTATTCTTCTCCAAC-TTC
41612153 CTTTTTC-TATTCTT-TCCAA-TTC
1 CTTTTTCTTATTCTTCTCCAACTTC
41612175 C
1 C
41612176 AATTTCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 4 0.18
24 5 0.23
25 6 0.27
26 7 0.32
ACGTcount: A:0.10, C:0.31, G:0.02, T:0.57
Consensus pattern (25 bp):
CTTTTTCTTATTCTTCTCCAACTTC
Found at i:41612748 original size:21 final size:21
Alignment explanation
Indices: 41612699--41612755 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
41612689 CATGGGCTGC
*
41612699 TCACACGGGCATGTGTCCCCT
1 TCACACGGGCATGTGGCCCCT
* * **
41612720 CCATACGGGCATGTGGGGCCT
1 TCACACGGGCATGTGGCCCCT
*
41612741 TCACACGGGTATGTG
1 TCACACGGGCATGTG
41612756 TAGACCCCTA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.16, C:0.30, G:0.32, T:0.23
Consensus pattern (21 bp):
TCACACGGGCATGTGGCCCCT
Found at i:41612795 original size:19 final size:19
Alignment explanation
Indices: 41612771--41612807 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41612761 CCCTACATGG
41612771 CTTGGGCACTTCCACACGA
1 CTTGGGCACTTCCACACGA
*
41612790 CTTGGGCACTTCTACACG
1 CTTGGGCACTTCCACACG
41612808 GCCAGGGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.35, G:0.22, T:0.24
Consensus pattern (19 bp):
CTTGGGCACTTCCACACGA
Found at i:41612815 original size:19 final size:19
Alignment explanation
Indices: 41612774--41612817 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
41612764 TACATGGCTT
**
41612774 GGGCACTTCCACACGACTT
1 GGGCACTTCCACACGACCA
* *
41612793 GGGCACTTCTACACGGCCA
1 GGGCACTTCCACACGACCA
41612812 GGGCAC
1 GGGCAC
41612818 ACGGCCATGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.36, G:0.27, T:0.16
Consensus pattern (19 bp):
GGGCACTTCCACACGACCA
Found at i:41624237 original size:25 final size:26
Alignment explanation
Indices: 41624195--41624243 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
41624185 AGTTGTAAAT
*
41624195 TAGAAAAATGTCTCTAGA-AATTTTC
1 TAGAAAAATCTCTCTAGAGAATTTTC
* *
41624220 TAGAATAATCTCTTTAGAGAATTT
1 TAGAAAAATCTCTCTAGAGAATTT
41624244 CTCTTTACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (26 bp):
TAGAAAAATCTCTCTAGAGAATTTTC
Found at i:41626166 original size:12 final size:13
Alignment explanation
Indices: 41626142--41626170 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
41626132 GAGCTATAAC
41626142 TATTGCATTTATT
1 TATTGCATTTATT
41626155 TATTGC-TTTATT
1 TATTGCATTTATT
41626167 TATT
1 TATT
41626171 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:41632614 original size:2 final size:2
Alignment explanation
Indices: 41632603--41632631 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
41632593 AGTACGTATG
41632603 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
41632632 TTCACGAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:41638455 original size:16 final size:15
Alignment explanation
Indices: 41638396--41638455 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
41638386 CACTTTTCAT
41638396 AATT-AATTAA-TAA
1 AATTAAATTAATTAA
* * *
41638409 TAATTTATTTAATTCA
1 -AATTAAATTAATTAA
41638425 AATTAAATTAGATTAA
1 AATTAAATTA-ATTAA
41638441 AATTAAAATTAATTA
1 AATT-AAATTAATTA
41638456 TATTATGAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
14 4 0.11
15 13 0.35
16 14 0.38
17 6 0.16
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
AATTAAATTAATTAA
Found at i:41638466 original size:22 final size:21
Alignment explanation
Indices: 41638399--41638468 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
41638389 TTTTCATAAT
41638399 TAATTAATAA-TAATT-TATT-
1 TAATTAA-AATTAATTATATTA
* *
41638418 TAATTCAAATTAAATTAGATTA
1 TAATTAAAATT-AATTATATTA
*
41638440 AAATTAAAATTAATTATATTA
1 TAATTAAAATTAATTATATTA
41638461 TGAATTAA
1 T-AATTAA
41638469 TACAAATAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
18 2 0.05
19 7 0.17
20 4 0.10
21 12 0.30
22 15 0.38
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (21 bp):
TAATTAAAATTAATTATATTA
Found at i:41643567 original size:21 final size:18
Alignment explanation
Indices: 41643528--41643599 Score: 64
Period size: 18 Copynumber: 4.2 Consensus size: 18
41643518 TTAATACAAT
41643528 TTAATTATTTTATAAAAA
1 TTAATTATTTTATAAAAA
* *
41643546 TTAATTATTTTATGACAA
1 TTAATTATTTTATAAAAA
*
41643564 --AA--ATTCTATCAAAAA
1 TTAATTATTTTAT-AAAAA
41643579 TTAATTATTTTA-AATAAA
1 TTAATTATTTTATAA-AAA
41643597 TTA
1 TTA
41643600 GGTATGAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
14 6 0.14
15 3 0.07
16 2 0.05
17 4 0.10
18 22 0.52
19 5 0.12
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (18 bp):
TTAATTATTTTATAAAAA
Found at i:41645356 original size:31 final size:31
Alignment explanation
Indices: 41645293--41645348 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
41645283 TATATATCAC
*
41645293 AATTATAAAAT---TATATAATATTATAAAT
1 AATTATAAAATAAATATATAATAATATAAAT
41645321 AATTATAAAATAAATATATAATAATATA
1 AATTATAAAATAAATATATAATAATATA
41645349 GGTAATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 11 0.46
31 13 0.54
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (31 bp):
AATTATAAAATAAATATATAATAATATAAAT
Found at i:41646358 original size:20 final size:18
Alignment explanation
Indices: 41646311--41646401 Score: 65
Period size: 17 Copynumber: 5.3 Consensus size: 18
41646301 CAAGATAAAC
41646311 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
41646328 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
*
41646348 ATTAAATTAATA--AAAT
1 ATTAAATTAATATTTAAT
*
41646364 ATT--ATTAAGA--TAAGT
1 ATTAAATTAATATTTAA-T
41646379 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
41646396 ATTAAA
1 ATTAAA
41646402 CTATTAAAGT
Statistics
Matches: 61, Mismatches: 3, Indels: 20
0.73 0.04 0.24
Matches are distributed among these distances:
14 8 0.13
15 4 0.07
16 7 0.11
17 20 0.33
18 4 0.07
19 3 0.05
20 15 0.25
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:41647180 original size:35 final size:35
Alignment explanation
Indices: 41647134--41647203 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
41647124 CATTAACTCT
41647134 TTAATTGAGCTATGAATTCCACTGTTGCTAGTAAA
1 TTAATTGAGCTATGAATTCCACTGTTGCTAGTAAA
41647169 TTAATTGAGCTATGAATTCCACTGTTGCTAGTAAA
1 TTAATTGAGCTATGAATTCCACTGTTGCTAGTAAA
41647204 GTCATGCCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (35 bp):
TTAATTGAGCTATGAATTCCACTGTTGCTAGTAAA
Found at i:41650479 original size:33 final size:33
Alignment explanation
Indices: 41650437--41650502 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
41650427 TTAAAGAGAA
41650437 AATTAAAATCTTGAGTAATTTTATTTTATTACT
1 AATTAAAATCTTGAGTAATTTTATTTTATTACT
41650470 AATTAAAATCTTGAGTAATTTTATTTTATTACT
1 AATTAAAATCTTGAGTAATTTTATTTTATTACT
41650503 CTAACATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (33 bp):
AATTAAAATCTTGAGTAATTTTATTTTATTACT
Found at i:41650783 original size:18 final size:20
Alignment explanation
Indices: 41650743--41650787 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
41650733 ATAATATAAT
41650743 TATATTTAAAAATTAAAATA
1 TATATTTAAAAATTAAAATA
41650763 TATATTTAAAAATTAAAATA
1 TATATTTAAAAATTAAAATA
41650783 T-TATT
1 TATATT
41650788 ATTGTATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TATATTTAAAAATTAAAATA
Found at i:41651487 original size:31 final size:31
Alignment explanation
Indices: 41651422--41651496 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
41651412 TACAAAATCA
*
41651422 TCACTAAATTATTTGAAAATTTTCATTTAAG
1 TCACTAAATTATTTGAAAATTTTCATTCAAG
* * *
41651453 TCACTGAATTATTTGAAAATTTTTATTCATG
1 TCACTAAATTATTTGAAAATTTTCATTCAAG
* *
41651484 TCACCAAACTATT
1 TCACTAAATTATT
41651497 AAGTTTTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (31 bp):
TCACTAAATTATTTGAAAATTTTCATTCAAG
Found at i:41651898 original size:3 final size:3
Alignment explanation
Indices: 41651890--41651951 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
41651880 AGGTTACCTC
41651890 ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41651937 ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT
41651952 TATCTGCAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:41654244 original size:100 final size:103
Alignment explanation
Indices: 41654099--41654285 Score: 218
Period size: 100 Copynumber: 1.8 Consensus size: 103
41654089 TTTCTTGTAC
* * * ** * * *
41654099 TGCCAATGCCATATCCCAGATATGGTCTTACACGATAGTTCTCAT-A-TC-GGTGCCCATGCCAT
1 TGCCAACGCCATATCCCAGACATGGTCTTACACGAGACCTATCATAACTCAGATGCCAATGCCAT
41654161 GTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
66 GTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
* * *
41654199 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTATCATAACCTCAATGATGCCAATGC
1 TGCCAACGCCATATCCCAGACATGGTCTTACACGAGACCTATCATAA-CTC-A-GATGCCAATGC
*
41654264 CATGTCCTAGACATGGTCTTAC
63 CATGTCCCAGACATGGTCTTAC
41654286 ATGGGATCTC
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
100 36 0.52
101 1 0.01
103 2 0.03
106 30 0.43
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (103 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACACGAGACCTATCATAACTCAGATGCCAATGCCAT
GTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
Found at i:41654266 original size:56 final size:50
Alignment explanation
Indices: 41654049--41654291 Score: 186
Period size: 50 Copynumber: 4.8 Consensus size: 50
41654039 TGATAATAAC
* * * * * *
41654049 ATGCCAAAGCCATGTCCCAAACATGGTCTTACATAGGA--TGT-TTCTTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTATCATCTCG
* * * ** ** * *
41654096 TACTGCCAATGCCATATCCCAGATATGGTCTTACACGATAGTTCTCATATCG
1 -A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTATCATCTCG
* * ** *
41654148 GTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTATCATCTCG
* *
41654198 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTATCATAACCTCAATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTATCAT---CTC---G
*
41654254 ATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
41654292 TCTCTTTACC
Statistics
Matches: 154, Mismatches: 31, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
48 1 0.01
49 29 0.19
50 80 0.52
51 2 0.01
52 3 0.02
53 3 0.02
56 36 0.23
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTATCATCTCG
Found at i:41654667 original size:30 final size:30
Alignment explanation
Indices: 41654633--41654690 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
41654623 CCTTGACTCG
41654633 AACTTTGGCAAAATTACA-TTTTTACCCCTA
1 AACTTTGGCAAAATTACACTTTTT-CCCCTA
* * *
41654663 AACTTTTGCATATTTACACTTTTTCCCC
1 AACTTTGGCAAAATTACACTTTTTCCCC
41654691 AAAGCTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.28, C:0.26, G:0.05, T:0.41
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTTCCCCTA
Found at i:41657194 original size:20 final size:20
Alignment explanation
Indices: 41657166--41657218 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
41657156 TTAACTTTTG
* *
41657166 GAATCATAAAAATCCAACAA
1 GAATTATAAAAATCCAAAAA
* * *
41657186 GAATTATAAGATTTCAAAAA
1 GAATTATAAAAATCCAAAAA
*
41657206 GAATTCTAAAAAT
1 GAATTATAAAAAT
41657219 AGTCAATTTT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.57, C:0.11, G:0.08, T:0.25
Consensus pattern (20 bp):
GAATTATAAAAATCCAAAAA
Found at i:41663132 original size:23 final size:23
Alignment explanation
Indices: 41663106--41663151 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
41663096 AATTGTTAAC
* * *
41663106 TTTACATCTCAAAAATTATAAAT
1 TTTACATATAAAAAATTAAAAAT
*
41663129 TTTATATATAAAAAATTAAAAAT
1 TTTACATATAAAAAATTAAAAAT
41663152 ATATATAGCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (23 bp):
TTTACATATAAAAAATTAAAAAT
Found at i:41663156 original size:22 final size:23
Alignment explanation
Indices: 41663116--41663158 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
41663106 TTTACATCTC
* *
41663116 AAAAATTATAAATTTTATATATA
1 AAAAATTATAAAATATATATATA
41663139 AAAAATTA-AAAATATATATA
1 AAAAATTATAAAATATATATA
41663159 GCAAACCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAAATTATAAAATATATATATA
Found at i:41666673 original size:139 final size:138
Alignment explanation
Indices: 41666252--41666728 Score: 408
Period size: 139 Copynumber: 3.4 Consensus size: 138
41666242 GGGTGTTACA
*
41666252 GTACCCATCCACGATACA-ACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTACCCAT
1 GTACCTATCCACGATA-AGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTA-CCAT
* * * ** * **
41666316 CCACGATACAACTCTGAAAGGTACCTATCCATGGTATGACTTCTAACGGTACCATCCACGACATG
64 CCACGACACAACTCTTAAAGGTACCTATCCATGGTATGACTCCTAATAGTACCATCCACGATACA
* *
41666381 ACTCCTAATA
129 ACTCCTATTG
* * * * * * * *
41666391 GTAGCC-ATCCACAATAAAATTCCTAATGGTTCCCCTCCATGGTACAACTTCTAGTGGTATCCAT
1 GTA-CCTATCCACGATAAGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTA-CCAT
* ** * * *
41666455 CTACGACATGACTCTTAAAGGTACCTATCCATGGTATGACTCATAATAGTATTCATCCATGGCAT
64 CCACGACACAACTCTTAAAGGTACCTATCCATGGTATGACTCCTAATAGTA-CCATCCA-CG-AT
* *
41666520 -GAA-TCCTATAG
126 ACAACTCCTATTG
* * * * * * *
41666531 GTACCTACCCACGGTATGACTCCTAAAGGTACGCATCTACGGTAAAACTCCTAATGGTACCTATC
1 GTACCTATCCACGATAAGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTACC-ATC
* * * *
41666596 CACTACACAACTCTTAAAGGTATC-ATCCATGGTATGGCTCCTAATAGTACCCCTCCACGATACA
65 CACGACACAACTCTTAAAGGTACCTATCCATGGTATGACTCCTAATAGTA-CCATCCACGATACA
41666660 ACTCCTATTG
129 ACTCCTATTG
* * * * * ** *
41666670 GTA-CTCATCCACGATACGACTCTTAAAGGTATCTATCTATTATACAACTCCTACTGGTA
1 GTACCT-ATCCACGATAAGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTA
41666729 TTCTTTACGG
Statistics
Matches: 263, Mismatches: 65, Indels: 20
0.76 0.19 0.06
Matches are distributed among these distances:
137 2 0.01
138 6 0.02
139 176 0.67
140 76 0.29
141 2 0.01
142 1 0.00
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (138 bp):
GTACCTATCCACGATAAGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTACCATCC
ACGACACAACTCTTAAAGGTACCTATCCATGGTATGACTCCTAATAGTACCATCCACGATACAAC
TCCTATTG
Found at i:41666773 original size:28 final size:28
Alignment explanation
Indices: 41666252--41666791 Score: 208
Period size: 28 Copynumber: 19.4 Consensus size: 28
41666242 GGGTGTTACA
* * *
41666252 GTACCCATCCACGATACAACTCCTAAAG
1 GTACCCATCCACGGTACGACTCCTAATG
* *
41666280 GTACCCATCCATGGTACAACTCCTAATG
1 GTACCCATCCACGGTACGACTCCTAATG
* * *
41666308 GTACCCATCCACGATACAACT-CTGAAAG
1 GTACCCATCCACGGTACGACTCCT-AATG
* * * * *
41666336 GTACCTATCCATGGTATGACTTCTAACG
1 GTACCCATCCACGGTACGACTCCTAATG
** * *
41666364 GTA-CCATCCACGACATGACTCCTAATA
1 GTACCCATCCACGGTACGACTCCTAATG
* ** ** *
41666391 GTAGCCATCCACAATAAAATTCCTAATG
1 GTACCCATCCACGGTACGACTCCTAATG
* * * * * *
41666419 GTTCCCCTCCATGGTACAACTTCTAGTG
1 GTACCCATCCACGGTACGACTCCTAATG
* * ** * * *
41666447 GTATCCATCTACGACATGACTCTTAAAG
1 GTACCCATCCACGGTACGACTCCTAATG
* * * * *
41666475 GTACCTATCCATGGTATGACTCATAATA
1 GTACCCATCCACGGTACGACTCCTAATG
** * * * *
41666503 GTATTCATCCATGGCATGAATCCT-ATAG
1 GTACCCATCCACGGTACGACTCCTAAT-G
* * * *
41666531 GTACCTACCCACGGTATGACTCCTAAAG
1 GTACCCATCCACGGTACGACTCCTAATG
* * **
41666559 GTACGCATCTACGGTAAAACTCCTAATG
1 GTACCCATCCACGGTACGACTCCTAATG
* *** * * *
41666587 GTACCTATCCACTACACAACTCTTAAAG
1 GTACCCATCCACGGTACGACTCCTAATG
* * * * *
41666615 GTA-TCATCCATGGTATGGCTCCTAATA
1 GTACCCATCCACGGTACGACTCCTAATG
* * * *
41666642 GTACCCCTCCACGATACAACTCCTATTG
1 GTACCCATCCACGGTACGACTCCTAATG
* * * *
41666670 GTACTCATCCACGATACGACTCTTAAAG
1 GTACCCATCCACGGTACGACTCCTAATG
* * * *** * *
41666698 GTATCTATCTATTATACAACTCCTACTG
1 GTACCCATCCACGGTACGACTCCTAATG
** ** * *
41666726 GTATTC-TTTACGGTATGACTCATAATG
1 GTACCCATCCACGGTACGACTCCTAATG
41666753 GTACCCATCCACGGTACGACTCCTAATG
1 GTACCCATCCACGGTACGACTCCTAATG
* *
41666781 ATACCTATCCA
1 GTACCCATCCA
41666792 TGAAACGACT
Statistics
Matches: 362, Mismatches: 143, Indels: 14
0.70 0.28 0.03
Matches are distributed among these distances:
27 56 0.15
28 303 0.84
29 3 0.01
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (28 bp):
GTACCCATCCACGGTACGACTCCTAATG
Found at i:41669416 original size:30 final size:30
Alignment explanation
Indices: 41669381--41669440 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
41669371 CTAAACTTAA
41669381 ATAAACTCTAATCACTTAATTAGAAAACAT
1 ATAAACTCTAATCACTTAATTAGAAAACAT
41669411 ATAAACTCTAATCACTTAATTAGAAAACAT
1 ATAAACTCTAATCACTTAATTAGAAAACAT
41669441 GAAAGAGACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.30
Consensus pattern (30 bp):
ATAAACTCTAATCACTTAATTAGAAAACAT
Found at i:41675965 original size:346 final size:347
Alignment explanation
Indices: 41675328--41676025 Score: 1263
Period size: 346 Copynumber: 2.0 Consensus size: 347
41675318 GTGGAGATTT
* *
41675328 GTTAAGTATGACTCCTATTTTCAGTCAAATTTGAGAAATAATCTTTTAATTAAACTTTGTTTATT
1 GTTAAGTATGACTCCTATTTTCAGTCAAATTTGAAAAATAATCTTTTAATTAAACTCTGTTTATT
*
41675393 TGTTTCAGTCAAACACTGATTAGTTTAGATTATTTTATTATTATTTGACATATGAATTTAGCCTA
66 TATTTCAGTCAAACACTGATTAGTTTAGATTATTTTATTATTATTTGACATATGAATTTAGCCTA
* *
41675458 TAAATAGGCTCTTTTACAACCTTAGTAAAAACATCAATTAGATTAGAACTCATAACACATTCAGA
131 TAAATAGGCTCTTTTACAACCTTAGAAAAAACACCAATTAGATTAGAACTCATAACACATTCAGA
* *
41675523 GAATTTTGTGTTTACGTTTTGAGGGTTCTTTGTTTTTCGGGTTTTCGGGGTTTAATTTTATCTCC
196 GAATTTTGTGTTTACGTTTTGAGGGTTCTTTATTTTTCGAGTTTTCGGGGTTTAATTTTATCTCC
*
41675588 ATCTTTTGTACTCTTCATTCTTTTTCCATTATAGTAAAATTATCTTTGCCCGTGG-TTTTTTATC
261 ATCTTTTGTACTCTTCATTCTTTTGCCATTATAGTAAAATTATCTTTGCCCGTGGTTTTTTTATC
41675652 CTCTTTGGAGGGGGTTTTCCAC
326 CTCTTTGGAGGGGGTTTTCCAC
*
41675674 GTTAAGTATGACTCCTATTTTCAGTCAAATTTGAAAAATAATCTTTTAGTTAAACTCTGTTTATT
1 GTTAAGTATGACTCCTATTTTCAGTCAAATTTGAAAAATAATCTTTTAATTAAACTCTGTTTATT
41675739 TATTTCAGTCAAACACTGATTAGTTTAGATTATTTTATTATTATTTGACATATGAATTTAGCCTA
66 TATTTCAGTCAAACACTGATTAGTTTAGATTATTTTATTATTATTTGACATATGAATTTAGCCTA
*
41675804 TAAATAGGCTCTTTTACAACCTTAGAAAAAACACCCATTAGATTAGAACTCATAACACATTCAGA
131 TAAATAGGCTCTTTTACAACCTTAGAAAAAACACCAATTAGATTAGAACTCATAACACATTCAGA
* *
41675869 GAATTTTGTGTTTACGTTTTGAGGGTTCTTTATTTTTCGAGTTTTTGGGGTTTAGTTTTATCTCC
196 GAATTTTGTGTTTACGTTTTGAGGGTTCTTTATTTTTCGAGTTTTCGGGGTTTAATTTTATCTCC
41675934 ATCTTTTGTACTCTTCATTCTTTTGCCATTATAGTAAAATTATCTTTGCCCGTGGTTTTTTTATC
261 ATCTTTTGTACTCTTCATTCTTTTGCCATTATAGTAAAATTATCTTTGCCCGTGGTTTTTTTATC
**
41675999 CTCTTTGGAGGGTTTTTTCCAC
326 CTCTTTGGAGGGGGTTTTCCAC
41676021 GTTAA
1 GTTAA
41676026 ATTTGTGTGT
Statistics
Matches: 337, Mismatches: 14, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
346 303 0.90
347 34 0.10
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (347 bp):
GTTAAGTATGACTCCTATTTTCAGTCAAATTTGAAAAATAATCTTTTAATTAAACTCTGTTTATT
TATTTCAGTCAAACACTGATTAGTTTAGATTATTTTATTATTATTTGACATATGAATTTAGCCTA
TAAATAGGCTCTTTTACAACCTTAGAAAAAACACCAATTAGATTAGAACTCATAACACATTCAGA
GAATTTTGTGTTTACGTTTTGAGGGTTCTTTATTTTTCGAGTTTTCGGGGTTTAATTTTATCTCC
ATCTTTTGTACTCTTCATTCTTTTGCCATTATAGTAAAATTATCTTTGCCCGTGGTTTTTTTATC
CTCTTTGGAGGGGGTTTTCCAC
Found at i:41680032 original size:27 final size:27
Alignment explanation
Indices: 41679977--41680033 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
41679967 ATATACAATG
*
41679977 TATTGAATGAATGTGAAAATGATTATAT
1 TATTGAATGAATGT-AAAATGATGATAT
*
41680005 TATTGAATGATATGT-ATATGATGATAT
1 TATTGAATGA-ATGTAAAATGATGATAT
41680032 TA
1 TA
41680034 CAATATTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 12 0.46
28 10 0.38
29 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (27 bp):
TATTGAATGAATGTAAAATGATGATAT
Found at i:41688052 original size:9 final size:9
Alignment explanation
Indices: 41688040--41688101 Score: 61
Period size: 9 Copynumber: 6.7 Consensus size: 9
41688030 TATTAAAAGC
41688040 GAGAGAGTT
1 GAGAGAGTT
*
41688049 GAGAGACTT
1 GAGAGAGTT
*
41688058 GAGAGTGTTT
1 GAGAGAG-TT
*
41688068 GAGAGAATTT
1 GAGAG-AGTT
* *
41688078 GAAAGAATT
1 GAGAGAGTT
41688087 GAGAGAGTT
1 GAGAGAGTT
41688096 GAGAGA
1 GAGAGA
41688102 AGGATGTGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
9 29 0.69
10 13 0.31
ACGTcount: A:0.37, C:0.02, G:0.37, T:0.24
Consensus pattern (9 bp):
GAGAGAGTT
Found at i:41692273 original size:18 final size:16
Alignment explanation
Indices: 41692231--41692273 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 16
41692221 TGTCGTTCTT
41692231 TTTCAAAATATTATTCA
1 TTTC-AAATATTATTCA
41692248 TTTACAAATCATTATTCAA
1 TTT-CAAAT-ATTATTC-A
41692267 TTTCAAA
1 TTTCAAA
41692274 ATGTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.30
18 12 0.52
19 4 0.17
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTCAAATATTATTCA
Found at i:41692275 original size:19 final size:17
Alignment explanation
Indices: 41692231--41692275 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 17
41692221 TGTCGTTCTT
41692231 TTTCAAAATATTATTCA
1 TTTCAAAATATTATTCA
41692248 TTT-ACAAATCATTATTCAA
1 TTTCA-AAAT-ATTATTC-A
41692267 TTTCAAAAT
1 TTTCAAAAT
41692276 GTTTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 1 0.04
17 7 0.29
18 7 0.29
19 8 0.33
20 1 0.04
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTCAAAATATTATTCA
Found at i:41694019 original size:13 final size:13
Alignment explanation
Indices: 41693985--41694022 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 13
41693975 ATCTCGAAAT
41693985 CAAAATACTTACC
1 CAAAATACTTACC
41693998 CATAAAATACTTACC
1 C--AAAATACTTACC
41694013 CAAAATACTT
1 CAAAATACTT
41694023 CAAATCGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.43
15 13 0.57
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (13 bp):
CAAAATACTTACC
Found at i:41702977 original size:114 final size:114
Alignment explanation
Indices: 41702836--41703066 Score: 390
Period size: 114 Copynumber: 2.0 Consensus size: 114
41702826 TCAAACATAA
* * *
41702836 AAAAAAAACCTTGGATAAAGATTATATAAGTTCAATCTAATCCAATCCGAATTACTATTTAATGA
1 AAAAAAAACCTTGGATAAAGATTATATAAATTAAATCTAATCCAATCCGAATTACCATTTAATGA
41702901 TATTTTAATTTTTATTTAAATTTAAATATAAAATATAAAAATTTAATAT
66 TATTTTAATTTTTATTTAAATTTAAATATAAAATATAAAAATTTAATAT
* *
41702950 AAAAAAGACCTTGGATAAAGATTATATAAATTAAATTTAATCCAATCCGAATTACCATTTAATGA
1 AAAAAAAACCTTGGATAAAGATTATATAAATTAAATCTAATCCAATCCGAATTACCATTTAATGA
* * *
41703015 TATTTTAATTTTTATTTCAATTTAATTATAAAATATATAAATTTAATAT
66 TATTTTAATTTTTATTTAAATTTAAATATAAAATATAAAAATTTAATAT
41703064 AAA
1 AAA
41703067 TTTAGTTTAA
Statistics
Matches: 109, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 109 1.00
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (114 bp):
AAAAAAAACCTTGGATAAAGATTATATAAATTAAATCTAATCCAATCCGAATTACCATTTAATGA
TATTTTAATTTTTATTTAAATTTAAATATAAAATATAAAAATTTAATAT
Found at i:41706002 original size:49 final size:49
Alignment explanation
Indices: 41705892--41706004 Score: 174
Period size: 49 Copynumber: 2.3 Consensus size: 49
41705882 ATTTTTGTAG
* *
41705892 GCCATGTGGGTAAGCCTTGTAGGACACACGGTCCTTTGAAATAATGCAA
1 GCCATGTGGGTAGGCCTTGTAGGACACACGGTCCTTTGAAATAAAGCAA
* *
41705941 GCCATGTGGGTAGGCCTTGTAGGGCACATGG-CCGTTTGAAATAAAGCAA
1 GCCATGTGGGTAGGCCTTGTAGGACACACGGTCC-TTTGAAATAAAGCAA
41705990 GCCATGTGGGTAGGC
1 GCCATGTGGGTAGGC
41706005 GTGTGGGGCA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
48 2 0.03
49 57 0.97
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (49 bp):
GCCATGTGGGTAGGCCTTGTAGGACACACGGTCCTTTGAAATAAAGCAA
Found at i:41706718 original size:27 final size:27
Alignment explanation
Indices: 41706688--41706740 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
41706678 CATTGCATGA
*
41706688 TATGATATGTTATGATTTATAATATGG
1 TATGATATGGTATGATTTATAATATGG
41706715 TATGATATGGTATGATTTATAATATG
1 TATGATATGGTATGATTTATAATATG
41706741 CTTTTATATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (27 bp):
TATGATATGGTATGATTTATAATATGG
Found at i:41707718 original size:87 final size:87
Alignment explanation
Indices: 41707534--41707740 Score: 202
Period size: 87 Copynumber: 2.4 Consensus size: 87
41707524 CAGACACTCC
* * * * **
41707534 AATTTGTAGATGAACCACCAGTGTTTGCAGATAAACTATCAGTAGGTTATGAATACACAATGTGT
1 AATTTGTGGATGAACCACTAGTGTTTGCAGATAAACTACCAGTAGGATATGAATACACAACATGT
**
41707599 TTGCAAATAAAAGTTTTCAATA
66 TTGCAAATAAAAGTGCTCAATA
* * * * * * * *
41707621 AGTTTTTGGATGAACCACTAGTGTTTGTAGATAAATTACCAGTGGGATGTGATTGCACAACATGT
1 AATTTGTGGATGAACCACTAGTGTTTGCAGATAAACTACCAGTAGGATATGAATACACAACATGT
* *
41707686 TTGCAAATAAGAGCTGCT-AGTA
66 TTGCAAATAAAAG-TGCTCAATA
* * *
41707708 AATTTGTGGATAAACCATTAGTG-TTGCAAATAA
1 AATTTGTGGATGAACCACTAGTGTTTGCAGATAA
41707741 TTAAACTGCC
Statistics
Matches: 95, Mismatches: 24, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
86 8 0.08
87 85 0.89
88 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.32
Consensus pattern (87 bp):
AATTTGTGGATGAACCACTAGTGTTTGCAGATAAACTACCAGTAGGATATGAATACACAACATGT
TTGCAAATAAAAGTGCTCAATA
Found at i:41719932 original size:29 final size:31
Alignment explanation
Indices: 41719899--41719965 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 31
41719889 ATAGGGATTT
41719899 GATCAAATTTG-TCGC-TCTACTATT-AAATG
1 GATCAAATTTGATC-CTTCTACTATTAAAATG
*
41719928 GATC-AATTTGATCCTTGTACTATTAAAATG
1 GATCAAATTTGATCCTTCTACTATTAAAATG
*
41719958 AATCAAAT
1 GATCAAAT
41719966 AAGACCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 7 0.22
29 14 0.44
30 8 0.25
31 3 0.09
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (31 bp):
GATCAAATTTGATCCTTCTACTATTAAAATG
Found at i:41720166 original size:30 final size:30
Alignment explanation
Indices: 41720132--41720225 Score: 93
Period size: 29 Copynumber: 3.1 Consensus size: 30
41720122 GTTACAATAT
* ** * *
41720132 GGACTTATTTGATTCTTTTTAATAGTATAG
1 GGACTAATTTGATTCCATTTAATAATAGAG
*
41720162 GGACTAAATTGA-TCCATTTAATAATAGAG
1 GGACTAATTTGATTCCATTTAATAATAGAG
*
41720191 GGACTAATTTGA-TCCAGTTTCAATAATATAG
1 GGACTAATTTGATTCCA-TTT-AATAATAGAG
41720222 GGAC
1 GGAC
41720226 CTCCTAATAC
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 28 0.52
30 13 0.24
31 13 0.24
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (30 bp):
GGACTAATTTGATTCCATTTAATAATAGAG
Found at i:41720192 original size:29 final size:30
Alignment explanation
Indices: 41720149--41720225 Score: 111
Period size: 29 Copynumber: 2.6 Consensus size: 30
41720139 TTTGATTCTT
*
41720149 TTTAATAGTATAGGGACTAAATTGATCCA-
1 TTTAATAATATAGGGACTAAATTGATCCAG
* *
41720178 TTTAATAATAGAGGGACTAATTTGATCCAG
1 TTTAATAATATAGGGACTAAATTGATCCAG
41720208 TTTCAATAATATAGGGAC
1 TTT-AATAATATAGGGAC
41720226 CTCCTAATAC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 26 0.62
30 3 0.07
31 13 0.31
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (30 bp):
TTTAATAATATAGGGACTAAATTGATCCAG
Found at i:41721719 original size:45 final size:45
Alignment explanation
Indices: 41721655--41721842 Score: 229
Period size: 45 Copynumber: 4.2 Consensus size: 45
41721645 TACTACGTGT
* * *
41721655 ACCGGGTACCATTGATTATAAAGGCGGTTGTTGTGTACTGATTCC
1 ACCGGGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCC
*
41721700 ACCGGGTATCATTGATTATAAAGGTGGTTGTTGTGTGTTGATTCC
1 ACCGGGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCC
* * * *
41721745 ACCGGTTA-CTATTGATTATGAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGGGTATC-ATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCC
* * * *
41721790 ACCGAGTATCATTGACTATAAAGGTGG-TGCTATGTGCTGA-TCC
1 ACCGGGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCC
*
41721833 ACCGTGTATC
1 ACCGGGTATC
41721843 TGTTATTATT
Statistics
Matches: 127, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
43 12 0.09
44 14 0.11
45 100 0.79
46 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (45 bp):
ACCGGGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCC
Found at i:41723957 original size:69 final size:68
Alignment explanation
Indices: 41723847--41723980 Score: 250
Period size: 69 Copynumber: 2.0 Consensus size: 68
41723837 TTGTTTTTGT
*
41723847 GAAATTTGTCATAAATAAGTATCTACTTCGGTGGTTAAGTGTTCTGATTGTGTGTTTAAAGTCTT
1 GAAATTTGTCATAAATAAGTATCTACTTCGATGGTTAAGTGTTCTGATTGTGTGTTTAAAGTCTT
41723912 GGG
66 GGG
41723915 GAAATTTGTCATAAATAAGTAATCTACTTCGATGGTTAAGTGTTCTGATTGTGTGTTTAAAGTCT
1 GAAATTTGTCATAAATAAGT-ATCTACTTCGATGGTTAAGTGTTCTGATTGTGTGTTTAAAGTCT
41723980 T
65 T
41723981 CGGTTCAAGT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
68 20 0.31
69 44 0.69
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (68 bp):
GAAATTTGTCATAAATAAGTATCTACTTCGATGGTTAAGTGTTCTGATTGTGTGTTTAAAGTCTT
GGG
Found at i:41728440 original size:18 final size:19
Alignment explanation
Indices: 41728397--41728442 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
41728387 AAAAATCTCT
* *
41728397 TAAATTTTTTCCTAAATTC
1 TAAATTTTATCCTAAATTA
*
41728416 T-ATTTTTAT-CTAAATTA
1 TAAATTTTATCCTAAATTA
41728433 TAAATTTTAT
1 TAAATTTTAT
41728443 TATTTTTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 8 0.36
18 13 0.59
19 1 0.05
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.57
Consensus pattern (19 bp):
TAAATTTTATCCTAAATTA
Found at i:41728599 original size:31 final size:31
Alignment explanation
Indices: 41728564--41728622 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
41728554 TCTGTCAACT
41728564 AATTGCAAATGGTAAGAATAAATTTTAAACC
1 AATTGCAAATGGTAAGAATAAATTTTAAACC
41728595 AATTGCAAATGGTAAGAATAAATTTTAA
1 AATTGCAAATGGTAAGAATAAATTTTAA
41728623 TCTTTTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.31
Consensus pattern (31 bp):
AATTGCAAATGGTAAGAATAAATTTTAAACC
Found at i:41734206 original size:3 final size:3
Alignment explanation
Indices: 41734198--41734223 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41734188 TTCCATTTCT
41734198 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
41734224 TTAGAATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:41740328 original size:31 final size:29
Alignment explanation
Indices: 41740291--41740356 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
41740281 TAAAAGTTAC
*
41740291 TATTAAAATAA-AATTTAAATATTAAATAATT
1 TATTAAAATAATAAATT--ATATT-AATAATT
41740322 TATTAAAAATAATAAATTATATTAATAATT
1 TATT-AAAATAATAAATTATATTAATAATT
41740352 TATTA
1 TATTA
41740357 TATGACTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 1 0.03
30 11 0.34
31 9 0.28
32 7 0.22
33 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
TATTAAAATAATAAATTATATTAATAATT
Found at i:41741003 original size:19 final size:18
Alignment explanation
Indices: 41740976--41741011 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
41740966 CATGTTAATT
*
41740976 TTTTAAATTTTTTAATAC
1 TTTTAAATTTTTAAATAC
41740994 TTTTATAATTTTTAAATA
1 TTTTA-AATTTTTAAATA
41741012 TTTAATGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTAAATTTTTAAATAC
Found at i:41745899 original size:9 final size:9
Alignment explanation
Indices: 41745880--41745952 Score: 112
Period size: 9 Copynumber: 8.2 Consensus size: 9
41745870 TCGGGTATTT
41745880 TTCGG-TAA
1 TTCGGTTAA
41745888 TTCGGTTAA
1 TTCGGTTAA
41745897 TTCGGTTAA
1 TTCGGTTAA
41745906 TTCGGTTAA
1 TTCGGTTAA
41745915 TTCGGTTAA
1 TTCGGTTAA
*
41745924 TTCGGGTAA
1 TTCGGTTAA
*
41745933 TTCGGGTAA
1 TTCGGTTAA
*
41745942 TTCGGGTAA
1 TTCGGTTAA
41745951 TT
1 TT
41745953 TTTAACCAAA
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
8 5 0.08
9 58 0.92
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.41
Consensus pattern (9 bp):
TTCGGTTAA
Found at i:41747881 original size:138 final size:139
Alignment explanation
Indices: 41747589--41748117 Score: 670
Period size: 140 Copynumber: 3.8 Consensus size: 139
41747579 TTCTAGGTTT
* * * *
41747589 GATTCCTCTCCTGCTCACATTTGTATTTTTTATTTCATGTTGCTTTAAGCTTTTTAATTTTTTAA
1 GATTCCTCTACTACTCACATTTGTATTTTTTATTTCATGTTGCTTCAAGCTTTTTAAATTTTTAA
* *
41747654 TTAATGTTTTTTAACATATTAGGTTTTTCGTTAGATGGTTAGATAGTTGTAATTACATCCTTAAG
66 TTAA-GTTTTTTAACATATTAGGTTTTTCGTTAGATGGTTAGATAGTTGTAATTACATCTTTGAG
41747719 TCTCGAGTTG
130 TCTCGAGTTG
* * * *
41747729 GATTCATCTACTACTCACATTTGTATTTTTTGTCTCATGTTGCTTCAATCTTTTTAAATTTTTAA
1 GATTCCTCTACTACTCACATTTGTATTTTTTATTTCATGTTGCTTCAAGCTTTTTAAATTTTTAA
* * * * **
41747794 TTAA-TTTGTTAACATATTA-ATTCTTTTGTTAGATGGTTAGATAGTTATTGTTACATCTTTGAG
66 TTAAGTTTTTTAACATATTAGGTT-TTTCGTTAGATGGTTAGATAGTTGTAATTACATCTTTGAG
*
41747857 TCTCGAGTTT
130 TCTCGAGTTG
* * * *
41747867 GATTTCTCTTCTACTCAAACTTGTATTTTTTATTTCATGTTGCTTCAAGCTTTTTAAATTTTTAA
1 GATTCCTCTACTACTCACATTTGTATTTTTTATTTCATGTTGCTTCAAGCTTTTTAAATTTTTAA
* *
41747932 TTAATGTTTTTTAACATATTAGTTTTTTCGTTAGATGGTTACATAGTTGTAATTACAT-TCTTGA
66 TTAA-GTTTTTTAACATATTAGGTTTTTCGTTAGATGGTTAGATAGTTGTAATTACATCT-TTGA
41747996 GTCTCGAGTTG
129 GTCTCGAGTTG
* ** * *
41748007 GATTCCTCTACTAATCACATTTGTATTTTGCATTTCATGTTGCTTCAAGCTTTTTTTATTATTTT
1 GATTCCTCTACTACTCACATTTGTATTTTTTATTTCATGTTGCTTCAAGC-TTTTTAAAT-TTTT
* * * *
41748072 AATTAA-TATTTTTAACATGTTAGCTCCTTTCGTTAGATAGTTAGAT
64 AATTAAGT-TTTTTAACATATTAGGT-TTTTCGTTAGATGGTTAGAT
41748118 GATTGCGAAT
Statistics
Matches: 333, Mismatches: 47, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
137 2 0.01
138 118 0.35
139 1 0.00
140 161 0.48
141 24 0.07
142 27 0.08
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (139 bp):
GATTCCTCTACTACTCACATTTGTATTTTTTATTTCATGTTGCTTCAAGCTTTTTAAATTTTTAA
TTAAGTTTTTTAACATATTAGGTTTTTCGTTAGATGGTTAGATAGTTGTAATTACATCTTTGAGT
CTCGAGTTG
Found at i:41748288 original size:23 final size:22
Alignment explanation
Indices: 41748231--41748289 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
41748221 TTTTGATGAT
41748231 ATTTTTTAATTATTTTTATTTTTA
1 ATTTTTT-ATT-TTTTTATTTTTA
* *
41748255 ATTAATGTATTTTTTTATTTTTA
1 ATT-TTTTATTTTTTTATTTTTA
41748278 ACTTTTTTATTT
1 A-TTTTTTATTT
41748290 ATAAAATCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
23 19 0.66
24 8 0.28
25 2 0.07
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (22 bp):
ATTTTTTATTTTTTTATTTTTA
Found at i:41748673 original size:135 final size:141
Alignment explanation
Indices: 41748387--41748691 Score: 326
Period size: 144 Copynumber: 2.2 Consensus size: 141
41748377 TTAATTAAAA
* * * *
41748387 AAAACACTTGAAGCAACATG----AAATAAAAAATACAAATGTGAGTAGTAGATGAATCAAACTC
1 AAAA-ACTTGAAGCAACATGAAACAAAAAAAAAATACAAATATGAATAGTAGAGGAATCAAACTC
* ** *
41748448 CAGACTCAATTATGTAATTACAACTATCTAACCATCTAACGAAAAACTAATATGGTAAAAAAATA
65 AAGACTCAAGGATGTAATTACAACTATCTAA-CATC-AAC-AAAAACTAATATGATAAAAAAATA
41748513 TTAATTAAAAATTTT
127 TTAATTAAAAATTTT
* *
41748528 AAAAACTTGAAGTAACATGAAACAAAAAAAAAATACAAATATGAATAGTAGAGGAATCAAACTGA
1 AAAAACTTGAAGCAACATGAAACAAAAAAAAAATACAAATATGAATAGTAGAGGAATCAAACTCA
* * * *
41748593 AGCCTCAAGGATGTAATTGCAACTATCT-A-ATC-A-AAGAACTAATAT-ATTAAAAAAT-TTAA
66 AGACTCAAGGATGTAATTACAACTATCTAACATCAACAAAAACTAATATGATAAAAAAATATTAA
*
41748652 TTATAAA-TTT
131 TTAAAAATTTT
* * *
41748662 AAAAAGTTTGAAGCAATATGAAATAAAAAA
1 AAAAA-CTTGAAGCAACATGAAACAAAAAA
41748692 TACAAATTTA
Statistics
Matches: 140, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
134 8 0.06
135 30 0.21
136 8 0.06
137 11 0.08
139 1 0.01
140 14 0.10
141 7 0.05
143 1 0.01
144 60 0.43
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.25
Consensus pattern (141 bp):
AAAAACTTGAAGCAACATGAAACAAAAAAAAAATACAAATATGAATAGTAGAGGAATCAAACTCA
AGACTCAAGGATGTAATTACAACTATCTAACATCAACAAAAACTAATATGATAAAAAAATATTAA
TTAAAAATTTT
Found at i:41753601 original size:26 final size:26
Alignment explanation
Indices: 41753572--41753623 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
41753562 CCTGGCTGAG
*
41753572 TTGTCCTTTGGATATGATCGAGTAAT
1 TTGTCCTTTGGATATGATCAAGTAAT
41753598 TTGTCCTTTGGATATGATCAAGTAAT
1 TTGTCCTTTGGATATGATCAAGTAAT
41753624 ATGCATTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (26 bp):
TTGTCCTTTGGATATGATCAAGTAAT
Found at i:41764892 original size:50 final size:50
Alignment explanation
Indices: 41764753--41764893 Score: 147
Period size: 50 Copynumber: 2.8 Consensus size: 50
41764743 TTTTCTGTAC
* * * * * **
41764753 TGCCAATGTCATATCCCAGATATGATCTTACATAAAAGTTCTCATATCGG
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
* * * ** * *
41764803 TGCCTATGCCATGTCCCAGACATAGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
*
41764853 TGCCAACGCCATATCCCAGACATGGTCTTACATGAGACCTC
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGAGACCTC
41764894 ATTCCCTTAA
Statistics
Matches: 70, Mismatches: 21, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
50 70 1.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
Found at i:41767764 original size:20 final size:20
Alignment explanation
Indices: 41767741--41767853 Score: 68
Period size: 20 Copynumber: 5.7 Consensus size: 20
41767731 GTACAGTCAT
*
41767741 GGGCACCAAAGTGCGAACAG
1 GGGCACCAAAGTGCAAACAG
* * *
41767761 GGGCA-GATACGTGCAAATAG
1 GGGCACCA-AAGTGCAAACAG
* * * * *
41767781 GGACACCGAAGTGTATATAG
1 GGGCACCAAAGTGCAAACAG
* *
41767801 GGGCACCAAAGTGCGAACAA
1 GGGCACCAAAGTGCAAACAG
*
41767821 GGGCA-CATACGTGCAAACAG
1 GGGCACCA-AAGTGCAAACAG
* *
41767841 GGACACCAGAGTG
1 GGGCACCAAAGTG
41767854 TATATAGGGG
Statistics
Matches: 66, Mismatches: 23, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
19 3 0.05
20 61 0.92
21 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.33, T:0.11
Consensus pattern (20 bp):
GGGCACCAAAGTGCAAACAG
Found at i:41767805 original size:60 final size:60
Alignment explanation
Indices: 41767741--41767926 Score: 248
Period size: 60 Copynumber: 3.1 Consensus size: 60
41767731 GTACAGTCAT
*
41767741 GGGCACCAAAGTGCGAACAGGGGCAGATACGTGCAAATAGGGACACC-GAAGTGTATATAG
1 GGGCACCAAAGTGCGAACAGGGGCACATACGTGCAAATAGGGACACCAG-AGTGTATATAG
* *
41767801 GGGCACCAAAGTGCGAACAAGGGCACATACGTGCAAACAGGGACACCAGAGTGTATATAG
1 GGGCACCAAAGTGCGAACAGGGGCACATACGTGCAAATAGGGACACCAGAGTGTATATAG
*** * ** * * *
41767861 GGGCATTGAAGTGCGAACAGGAGCACAGGCGTGCAAATAGAGACACCAGAGTGTATACAT
1 GGGCACCAAAGTGCGAACAGGGGCACATACGTGCAAATAGGGACACCAGAGTGTATATAG
41767921 GGGCAC
1 GGGCAC
41767927 GCAGGGGCAC
Statistics
Matches: 110, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
60 109 0.99
61 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.32, T:0.13
Consensus pattern (60 bp):
GGGCACCAAAGTGCGAACAGGGGCACATACGTGCAAATAGGGACACCAGAGTGTATATAG
Found at i:41767982 original size:57 final size:56
Alignment explanation
Indices: 41767913--41768030 Score: 209
Period size: 57 Copynumber: 2.1 Consensus size: 56
41767903 ACACCAGAGT
*
41767913 GTATACATGGGCACGCAGGGGCACAGTTGTGCAAACAAATGGCACTTCTTCATTTCC
1 GTATACATGGGCACGCAGGGGCACAGTTGTGCAAAC-AAGGGCACTTCTTCATTTCC
*
41767970 GTATACATGGGCACGTAGGGGCACAGTTGTGCAAACAAGGGCACTTCTTCATTTCC
1 GTATACATGGGCACGCAGGGGCACAGTTGTGCAAACAAGGGCACTTCTTCATTTCC
41768026 GTATA
1 GTATA
41768031 TAATGGAACT
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 24 0.41
57 35 0.59
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.25
Consensus pattern (56 bp):
GTATACATGGGCACGCAGGGGCACAGTTGTGCAAACAAGGGCACTTCTTCATTTCC
Found at i:41768113 original size:85 final size:85
Alignment explanation
Indices: 41767970--41768133 Score: 265
Period size: 85 Copynumber: 1.9 Consensus size: 85
41767960 CTTCATTTCC
* * * * *
41767970 GTATACATGGGCACGTAGGGGCACAGTTGTGCAAACAAGGGCACTTCTTCATTTCCGTATATAAT
1 GTATACATGAGCACGCAGGGGCACAGTCGTGCAAACAAGAGCACTTCTTCATTTCCGTATACAAT
41768035 GGAACTCATTACATCAGAGT
66 GGAACTCATTACATCAGAGT
*
41768055 GTATACATGAGCACGCAGGGGCACAGTCGTGCAAACAATAGCACTTCTTCATTTCCGTATACAAT
1 GTATACATGAGCACGCAGGGGCACAGTCGTGCAAACAAGAGCACTTCTTCATTTCCGTATACAAT
*
41768120 GGAACTCGTTACAT
66 GGAACTCATTACAT
41768134 TCATAGATAA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
85 72 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (85 bp):
GTATACATGAGCACGCAGGGGCACAGTCGTGCAAACAAGAGCACTTCTTCATTTCCGTATACAAT
GGAACTCATTACATCAGAGT
Found at i:41769126 original size:14 final size:14
Alignment explanation
Indices: 41769107--41769133 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41769097 ATGGACAAAT
41769107 TCTAAACCCTAAAC
1 TCTAAACCCTAAAC
41769121 TCTAAACCCTAAA
1 TCTAAACCCTAAA
41769134 TTTATAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (14 bp):
TCTAAACCCTAAAC
Found at i:41770259 original size:16 final size:17
Alignment explanation
Indices: 41770240--41770274 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
41770230 GGCCAAGCAA
41770240 ATCAAA-CCAAGATTCG
1 ATCAAAGCCAAGATTCG
41770256 ATCAAAGCCAAGATTCG
1 ATCAAAGCCAAGATTCG
41770273 AT
1 AT
41770275 GATGAATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.20
Consensus pattern (17 bp):
ATCAAAGCCAAGATTCG
Found at i:41786359 original size:20 final size:18
Alignment explanation
Indices: 41786330--41786383 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
41786320 TTTTAAAAAC
41786330 AATTTAACTTTGATTGAAA
1 AATTTAAC-TTGATTGAAA
41786349 AATTCTAACTTGATTGAAA
1 AATT-TAACTTGATTGAAA
*
41786368 CCATTTTAACTTGATT
1 --AATTTAACTTGATT
41786384 TAAAGGTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 14 0.45
20 14 0.45
21 3 0.10
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (18 bp):
AATTTAACTTGATTGAAA
Found at i:41786361 original size:19 final size:19
Alignment explanation
Indices: 41786326--41786383 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 19
41786316 CTTGTTTTAA
41786326 AAACAATTTAACTTTGATTG
1 AAACAATTTAAC-TTGATTG
41786346 AAA-AATTCTAACTTGATTG
1 AAACAATT-TAACTTGATTG
*
41786365 AAACCATTTTAACTTGATT
1 AAA-CAATTTAACTTGATT
41786384 TAAAGGTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 14 0.41
20 17 0.50
21 3 0.09
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (19 bp):
AAACAATTTAACTTGATTG
Found at i:41788674 original size:20 final size:20
Alignment explanation
Indices: 41788604--41788674 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
41788594 AAACCCGATA
* *
41788604 GGTATCGATATTTTTTAAGAT
1 GGTATCGATA-ATTTTAAAAT
41788625 GGTATCGATAATTTTATAAAT
1 GGTATCGATAATTTTA-AAAT
* *
41788646 -ATATTGATAATTTTAAAAT
1 GGTATCGATAATTTTAAAAT
41788665 GGTATCGATA
1 GGTATCGATA
41788675 CAAAATCACG
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
19 4 0.10
20 25 0.60
21 13 0.31
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (20 bp):
GGTATCGATAATTTTAAAAT
Done.