Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 122 of 344
Found at i:41292235 original size:15 final size:15
Alignment explanation
Indices: 41292207--41292240 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
41292197 TGGACCCACT
41292207 ACATAATAAAAATTA
1 ACATAATAAAAATTA
* *
41292222 ACATATTAATAATTA
1 ACATAATAAAAATTA
41292237 ACAT
1 ACAT
41292241 GAAAATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (15 bp):
ACATAATAAAAATTA
Found at i:41299526 original size:15 final size:15
Alignment explanation
Indices: 41299506--41299543 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
41299496 TCAAGATAAG
*
41299506 GAAATCCATAATAGA
1 GAAATCCAGAATAGA
*
41299521 GAAATCCAGAATATA
1 GAAATCCAGAATAGA
41299536 GAAATCCA
1 GAAATCCA
41299544 ACATAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.53, C:0.16, G:0.13, T:0.18
Consensus pattern (15 bp):
GAAATCCAGAATAGA
Found at i:41300347 original size:46 final size:45
Alignment explanation
Indices: 41300280--41300447 Score: 196
Period size: 46 Copynumber: 3.6 Consensus size: 45
41300270 GGACAATACG
* *
41300280 ATGCATGTCCCAGACATGTCTTACACTGACTATCATCTCGTA-GCCA
1 ATGCATGTCCCAAACATGTCTTACACTGACT-TCGTCTCG-AGGCCA
* * *
41300326 ATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTCGAGGCCG
1 ATGCATGTCCCAAACATGTCTTACACTGACTT-CGTCTCGAGGCCA
*
41300372 ATGCATGTCCCAAACATGTCTTACACTAGTACTT-GTCTCGATGCCA
1 ATGCATGTCCCAAACATGTCTTACACT-G-ACTTCGTCTCGAGGCCA
*
41300418 ATGCCATATCCCAAACATGGTCTTACACTG
1 ATG-CATGTCCCAAACAT-GTCTTACACTG
41300448 GTCCTCATAA
Statistics
Matches: 108, Mismatches: 8, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
45 2 0.02
46 78 0.72
47 15 0.14
48 13 0.12
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (45 bp):
ATGCATGTCCCAAACATGTCTTACACTGACTTCGTCTCGAGGCCA
Found at i:41305687 original size:15 final size:16
Alignment explanation
Indices: 41305667--41305696 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41305657 GAAAATTGCC
41305667 AAAATGGG-CTAAATA
1 AAAATGGGACTAAATA
41305682 AAAATGGGACTAAAT
1 AAAATGGGACTAAAT
41305697 TGGAATATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (16 bp):
AAAATGGGACTAAATA
Found at i:41310451 original size:25 final size:25
Alignment explanation
Indices: 41310381--41310454 Score: 112
Period size: 25 Copynumber: 3.0 Consensus size: 25
41310371 CCATTAGGGT
* *
41310381 TACCGATTTATAGCTCGTGAAAGCA
1 TACCGATTTATAGCTCATGAGAGCA
41310406 TACCGATTTATAGCTCATGAGAGCA
1 TACCGATTTATAGCTCATGAGAGCA
* *
41310431 TACTGATTGATAGCTCATGAGAGC
1 TACCGATTTATAGCTCATGAGAGC
41310455 GTACGGATCT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (25 bp):
TACCGATTTATAGCTCATGAGAGCA
Found at i:41310472 original size:25 final size:24
Alignment explanation
Indices: 41310388--41310462 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 24
41310378 GGTTACCGAT
* * *
41310388 TTATAGCTCGTGAAAGCATACCGA
1 TTATAGCTCATGAGAGCATACGGA
*
41310412 TTTATAGCTCATGAGAGCATACTGA
1 -TTATAGCTCATGAGAGCATACGGA
*
41310437 TTGATAGCTCATGAGAGCGTACGGA
1 TT-ATAGCTCATGAGAGCATACGGA
41310462 T
1 T
41310463 CTTCAGCTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
24 2 0.05
25 42 0.95
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (24 bp):
TTATAGCTCATGAGAGCATACGGA
Found at i:41311928 original size:30 final size:30
Alignment explanation
Indices: 41311892--41311959 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
41311882 CCTAAGACAT
* *
41311892 GGGCATGTCTATTGGTCGTGTGAGTCACAC
1 GGGCATGTCTATTGGTCGTGTGAGGCACAA
*
41311922 GGGCATGTCTCTTGGTCGTGTGAGGCACAA
1 GGGCATGTCTATTGGTCGTGTGAGGCACAA
*
41311952 GGCCATGT
1 GGGCATGT
41311960 GACCCCTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.16, C:0.21, G:0.35, T:0.28
Consensus pattern (30 bp):
GGGCATGTCTATTGGTCGTGTGAGGCACAA
Found at i:41317160 original size:27 final size:27
Alignment explanation
Indices: 41317130--41317274 Score: 130
Period size: 27 Copynumber: 5.4 Consensus size: 27
41317120 GTGGCATTTC
*
41317130 AGTCATTTTACCACATAAGGGCAAAGT
1 AGTCATTTTACCACATAAGGGCAAAAT
* * * *
41317157 AGTCATTTTACCTCAAAAGGGTAGAAT
1 AGTCATTTTACCACATAAGGGCAAAAT
* * * * * *
41317184 AGTCATTTTATCATATAGGGGTGAGACT
1 AGTCATTTTACCACATAAGGG-CAAAAT
* *
41317212 -GTCATTTTACCACATAAAGGCAAAAC
1 AGTCATTTTACCACATAAGGGCAAAAT
** *
41317238 AGTCATTTTACCTTATAAGGGGAAAAT
1 AGTCATTTTACCACATAAGGGCAAAAT
41317265 AGTCATTTTA
1 AGTCATTTTA
41317275 TCGATTAAGG
Statistics
Matches: 91, Mismatches: 25, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
26 2 0.02
27 85 0.93
28 4 0.04
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (27 bp):
AGTCATTTTACCACATAAGGGCAAAAT
Found at i:41317188 original size:54 final size:54
Alignment explanation
Indices: 41317129--41317274 Score: 152
Period size: 54 Copynumber: 2.7 Consensus size: 54
41317119 AGTGGCATTT
* * * * * *
41317129 CAGTCATTTTACCACATAAGGGCAAAGTAGTCATTTTACCTCA-AAAGGGTAGAA
1 CAGTCATTTTACCATATAAGGGGAAAATAGTCATTTTACCACATAAA-GGCAAAA
* * * * *
41317183 TAGTCATTTTATCATATAGGGGTGAGACT-GTCATTTTACCACATAAAGGCAAAA
1 CAGTCATTTTACCATATAAGGG-GAAAATAGTCATTTTACCACATAAAGGCAAAA
*
41317237 CAGTCATTTTACCTTATAAGGGGAAAATAGTCATTTTA
1 CAGTCATTTTACCATATAAGGGGAAAATAGTCATTTTA
41317275 TCGATTAAGG
Statistics
Matches: 73, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
53 4 0.05
54 63 0.86
55 6 0.08
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (54 bp):
CAGTCATTTTACCATATAAGGGGAAAATAGTCATTTTACCACATAAAGGCAAAA
Found at i:41320860 original size:27 final size:27
Alignment explanation
Indices: 41320830--41321001 Score: 188
Period size: 27 Copynumber: 6.4 Consensus size: 27
41320820 GGGGCATTTT
41320830 AGTCATTTTAGCAT-ATAAGGGCAAAAC
1 AGTCATTTTA-CATCATAAGGGCAAAAC
* *
41320857 AGTCATTTTACCTCATAAGGGCAAAAT
1 AGTCATTTTACATCATAAGGGCAAAAC
*
41320884 AGTCATTTTACCAT-ATAAGGGCAAGAC
1 AGTCATTTTA-CATCATAAGGGCAAAAC
*
41320911 TGTCATTTTACCA-CATAAGGGCAAAAC
1 AGTCATTTTA-CATCATAAGGGCAAAAC
* * * *
41320938 AATCATTTCACCTCATAAGGCCAAAAC
1 AGTCATTTTACATCATAAGGGCAAAAC
* * * *
41320965 AATTATTTTACCTCATAAGGGCAAAAT
1 AGTCATTTTACATCATAAGGGCAAAAC
41320992 AGTCATTTTA
1 AGTCATTTTA
41321002 TCGATTAAAG
Statistics
Matches: 123, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
26 3 0.02
27 118 0.96
28 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.28
Consensus pattern (27 bp):
AGTCATTTTACATCATAAGGGCAAAAC
Found at i:41320887 original size:54 final size:53
Alignment explanation
Indices: 41320829--41321001 Score: 229
Period size: 54 Copynumber: 3.2 Consensus size: 53
41320819 AGGGGCATTT
41320829 TAGTCATTTTAGCATATAAGGGCAAAACAGTCATTTTACCTCATAAGGGCAAAA
1 TAGTCATTTTA-CATATAAGGGCAAAACAGTCATTTTACCTCATAAGGGCAAAA
* * *
41320883 TAGTCATTTTACCATATAAGGGCAAGACTGTCATTTTACCACATAAGGGCAAAA
1 TAGTCATTTTA-CATATAAGGGCAAAACAGTCATTTTACCTCATAAGGGCAAAA
* * * * * * *
41320937 CAATCATTTCACCTCATAAGGCCAAAACAATTATTTTACCTCATAAGGGCAAAA
1 TAGTCATTTTACAT-ATAAGGGCAAAACAGTCATTTTACCTCATAAGGGCAAAA
41320991 TAGTCATTTTA
1 TAGTCATTTTA
41321002 TCGATTAAAG
Statistics
Matches: 101, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
53 2 0.02
54 99 0.98
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (53 bp):
TAGTCATTTTACATATAAGGGCAAAACAGTCATTTTACCTCATAAGGGCAAAA
Found at i:41320956 original size:81 final size:81
Alignment explanation
Indices: 41320829--41321001 Score: 233
Period size: 81 Copynumber: 2.1 Consensus size: 81
41320819 AGGGGCATTT
* * * * * * *
41320829 TAGTCATTTTAGCATATAAGGGCAAAACAGTCATTTTACCTCATAAGGGCAAAATAGTCATTTTA
1 TAGTCATTTTACCACATAAGGGCAAAACAATCATTTCACCTCATAAGGCCAAAACAATCATTTTA
*
41320894 CCAT-ATAAGGGCAAGAC
66 CC-TCATAAGGGCAA-AA
*
41320911 T-GTCATTTTACCACATAAGGGCAAAACAATCATTTCACCTCATAAGGCCAAAACAATTATTTTA
1 TAGTCATTTTACCACATAAGGGCAAAACAATCATTTCACCTCATAAGGCCAAAACAATCATTTTA
41320975 CCTCATAAGGGCAAAA
66 CCTCATAAGGGCAAAA
41320991 TAGTCATTTTA
1 TAGTCATTTTA
41321002 TCGATTAAAG
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
80 3 0.04
81 76 0.95
82 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (81 bp):
TAGTCATTTTACCACATAAGGGCAAAACAATCATTTCACCTCATAAGGCCAAAACAATCATTTTA
CCTCATAAGGGCAAAA
Found at i:41324251 original size:18 final size:18
Alignment explanation
Indices: 41324218--41324252 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41324208 ATGATATGCT
**
41324218 AAACTATTTTTGTGCTTG
1 AAACTATTTTAATGCTTG
41324236 AAACTATTTTAATGCTT
1 AAACTATTTTAATGCTT
41324253 CCTGTTCTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (18 bp):
AAACTATTTTAATGCTTG
Found at i:41327100 original size:39 final size:39
Alignment explanation
Indices: 41327046--41327202 Score: 255
Period size: 39 Copynumber: 4.0 Consensus size: 39
41327036 CAAGACACTA
*
41327046 GAAATGTATTCGGGCTAAAGT-CTCGCAGGCTTCGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCT-GCAGGCTTCGTGCTG
41327085 GAAATGTATCCGGGCTAAAGTCCTGCAGGCTTCGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCTGCAGGCTTCGTGCTG
*
41327124 GAAATGTATCCGGGCTAAAGT-CTCGTAGGCTTCGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCT-GCAGGCTTCGTGCTG
*
41327163 GAAATGTATCCGGGCTAAAGTCCTGCAGGCTTTGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCTGCAGGCTTCGTGCTG
41327202 G
1 G
41327203 TAATATAATA
Statistics
Matches: 111, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
38 2 0.02
39 105 0.95
40 4 0.04
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.27
Consensus pattern (39 bp):
GAAATGTATCCGGGCTAAAGTCCTGCAGGCTTCGTGCTG
Found at i:41327145 original size:78 final size:78
Alignment explanation
Indices: 41327046--41327202 Score: 287
Period size: 78 Copynumber: 2.0 Consensus size: 78
41327036 CAAGACACTA
*
41327046 GAAATGTATTCGGGCTAAAGTCTCGCAGGCTTCGTGCTGGAAATGTATCCGGGCTAAAGTCCTGC
1 GAAATGTATCCGGGCTAAAGTCTCGCAGGCTTCGTGCTGGAAATGTATCCGGGCTAAAGTCCTGC
41327111 AGGCTTCGTGCTG
66 AGGCTTCGTGCTG
*
41327124 GAAATGTATCCGGGCTAAAGTCTCGTAGGCTTCGTGCTGGAAATGTATCCGGGCTAAAGTCCTGC
1 GAAATGTATCCGGGCTAAAGTCTCGCAGGCTTCGTGCTGGAAATGTATCCGGGCTAAAGTCCTGC
*
41327189 AGGCTTTGTGCTG
66 AGGCTTCGTGCTG
41327202 G
1 G
41327203 TAATATAATA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.27
Consensus pattern (78 bp):
GAAATGTATCCGGGCTAAAGTCTCGCAGGCTTCGTGCTGGAAATGTATCCGGGCTAAAGTCCTGC
AGGCTTCGTGCTG
Found at i:41329939 original size:12 final size:12
Alignment explanation
Indices: 41329922--41329951 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
41329912 CCACAAATGT
*
41329922 CCATGTGCTAGG
1 CCATGTGCGAGG
41329934 CCATGTGCGAGG
1 CCATGTGCGAGG
41329946 CCATGT
1 CCATGT
41329952 AATAGCCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.27, G:0.33, T:0.23
Consensus pattern (12 bp):
CCATGTGCGAGG
Found at i:41338850 original size:45 final size:45
Alignment explanation
Indices: 41338734--41338837 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 45
41338724 ATCTAATACG
* * * *
41338734 ATGCCAGTGTCCCAGACATGGTCTTACACATAACCACATATATCA
1 ATGCCAATGTCCCAAACATGGTCTTACACAAAAACACATATATCA
*
41338779 ATGCCAACGTCCCAAACATGGTCTTACACAAAAACACATATATCA
1 ATGCCAATGTCCCAAACATGGTCTTACACAAAAACACATATATCA
41338824 ATGCCAATGTCCCA
1 ATGCCAATGTCCCA
41338838 TATGTGGTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.37, C:0.30, G:0.12, T:0.22
Consensus pattern (45 bp):
ATGCCAATGTCCCAAACATGGTCTTACACAAAAACACATATATCA
Found at i:41340675 original size:27 final size:26
Alignment explanation
Indices: 41340619--41340729 Score: 132
Period size: 27 Copynumber: 4.2 Consensus size: 26
41340609 AGCATGGCTG
* * *
41340619 CCAGAATAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
41340645 CCAGAACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAAT-GTGGCAGAGCCA
41340672 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * * *
41340699 CTAGATCTGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
41340726 CCAG
1 CCAG
41340730 GACGCTTCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
26 14 0.19
27 58 0.78
28 2 0.03
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:41344750 original size:6 final size:6
Alignment explanation
Indices: 41344732--41344819 Score: 65
Period size: 6 Copynumber: 14.3 Consensus size: 6
41344722 AAGAAACATT
* *
41344732 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATTAG- GTGACAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * *
41344781 ATCAGA ATCAGT ATCAGGTA A-CCGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
41344820 GTGAATGCAA
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
5 4 0.06
6 53 0.83
7 5 0.08
8 2 0.03
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:41344777 original size:31 final size:31
Alignment explanation
Indices: 41344741--41344819 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
41344731 TATCAGAACT
* *
41344741 AGAATCAGAATCAGAATCAGAATTAGGTGAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
*
41344772 AGAATCAGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
* *
41344803 CGAATCAAAATCAGAAT
1 AGAATCAGAATCAGAAT
41344820 GTGAATGCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGAATCAGGTAAC
Found at i:41345278 original size:27 final size:27
Alignment explanation
Indices: 41345239--41345442 Score: 291
Period size: 27 Copynumber: 7.6 Consensus size: 27
41345229 TACCTCACAA
*
41345239 GGTATCTCGGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
41345266 GGTATTTCAGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
** *
41345293 GGTATTTCGGTGTTTCTACCCTACAAG
1 GGTATTTCGGTAATTCTACCCTACAGG
41345320 GGTATTTCGGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
41345347 GGTATTTCAGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* ** *
41345374 GGTATTGCCATAATTCTACCCTATAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* *
41345401 GGTATTTCGGTAATTCTACCCTATAGA
1 GGTATTTCGGTAATTCTACCCTACAGG
*
41345428 GGTGTTTCGGTAATT
1 GGTATTTCGGTAATT
41345443 TTACAAGTCA
Statistics
Matches: 158, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 158 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (27 bp):
GGTATTTCGGTAATTCTACCCTACAGG
Found at i:41345467 original size:27 final size:27
Alignment explanation
Indices: 41345437--41345525 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 27
41345427 AGGTGTTTCG
*
41345437 GTAATTTTAC-AAGTCAAGGGTATTTTA
1 GTAATTTTACAAACT-AAGGGTATTTTA
* *
41345464 GTAATTTTACAAACTAGGGGTATTTTG
1 GTAATTTTACAAACTAAGGGTATTTTA
** *
41345491 GTAATTTTGTAAACTAAGGGTATTTCA
1 GTAATTTTACAAACTAAGGGTATTTTA
*
41345518 ATAATTTT
1 GTAATTTT
41345526 GTAAATCGAG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
27 49 0.94
28 3 0.06
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (27 bp):
GTAATTTTACAAACTAAGGGTATTTTA
Found at i:41345526 original size:27 final size:27
Alignment explanation
Indices: 41345452--41345530 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
41345442 TTTACAAGTC
**
41345452 AAGGGTATTTTAGTAATTTTACAAACT
1 AAGGGTATTTTAGTAATTTTGTAAACT
* *
41345479 AGGGGTATTTTGGTAATTTTGTAAACT
1 AAGGGTATTTTAGTAATTTTGTAAACT
* *
41345506 AAGGGTATTTCAATAATTTTGTAAA
1 AAGGGTATTTTAGTAATTTTGTAAA
41345531 TCGAGGATAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.42
Consensus pattern (27 bp):
AAGGGTATTTTAGTAATTTTGTAAACT
Found at i:41345546 original size:27 final size:27
Alignment explanation
Indices: 41345519--41345741 Score: 277
Period size: 27 Copynumber: 8.3 Consensus size: 27
41345509 GGTATTTCAA
* * *
41345519 TAATTTTGTAAATCGAGGATAAAACAA
1 TAATTCTGTAAATCGAGGGTAAAACAG
* *
41345546 TAATTCTATAAATCGAGGGTAAAACGG
1 TAATTCTGTAAATCGAGGGTAAAACAG
* **
41345573 TAATTCTATAAATCGAGGGTAAAATGG
1 TAATTCTGTAAATCGAGGGTAAAACAG
*
41345600 TAATTCTGTAAATCGAGGGTAAAATAG
1 TAATTCTGTAAATCGAGGGTAAAACAG
* * *
41345627 TAATTCTATAAGTTGAGGGTAAAAC-G
1 TAATTCTGTAAATCGAGGGTAAAACAG
* *
41345653 ATAATTTTGTAAATCGAGGGTAAAATAG
1 -TAATTCTGTAAATCGAGGGTAAAACAG
**
41345681 TAATTCTGTAAATCGAGGGTAAAATGG
1 TAATTCTGTAAATCGAGGGTAAAACAG
*
41345708 TAATTCTGTAAATCGAGGGTAAAACGG
1 TAATTCTGTAAATCGAGGGTAAAACAG
41345735 TAATTCT
1 TAATTCT
41345742 ATCTTATTTT
Statistics
Matches: 174, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 1 0.01
27 172 0.99
28 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (27 bp):
TAATTCTGTAAATCGAGGGTAAAACAG
Found at i:41345575 original size:81 final size:81
Alignment explanation
Indices: 41345519--41345739 Score: 334
Period size: 81 Copynumber: 2.7 Consensus size: 81
41345509 GGTATTTCAA
* * * * * *
41345519 TAATTTTGTAAATCGAGGATAAAACAATAATTCTATAAATCGAGGGTAAAACGGTAATTCTATAA
1 TAATTCTGTAAATCGAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTGTAA
*
41345584 ATCGAGGGTAAAATGG
66 ATCGAGGGTAAAATAG
* * *
41345600 TAATTCTGTAAATCGAGGGTAAAATAGTAATTCTATAAGTTGAGGGTAAAACGATAATTTTGTAA
1 TAATTCTGTAAATCGAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTGTAA
41345665 ATCGAGGGTAAAATAG
66 ATCGAGGGTAAAATAG
* *
41345681 TAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAACGGTAATT
1 TAATTCTGTAAATCGAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGGTAATT
41345740 CTATCTTATT
Statistics
Matches: 125, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 125 1.00
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (81 bp):
TAATTCTGTAAATCGAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTGTAA
ATCGAGGGTAAAATAG
Found at i:41345786 original size:27 final size:25
Alignment explanation
Indices: 41345756--41345840 Score: 80
Period size: 27 Copynumber: 3.2 Consensus size: 25
41345746 TATTTTAGTG
41345756 ATTTTACAAATCGAGGATATTTGGGTA
1 ATTTTACAAATCGAGG-TATTT-GGTA
* *
41345783 ATTTTATAAATCGGGGGTACTTTGGTA
1 ATTTTACAAATC-GAGGTA-TTTGGTA
* *
41345810 ATTTTACAAGTCGAAGGTATTTCAGTA
1 ATTTTACAAATCG-AGGTATTT-GGTA
41345837 ATTT
1 ATTT
41345841 GGTAAACTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
26 4 0.08
27 38 0.79
28 6 0.12
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (25 bp):
ATTTTACAAATCGAGGTATTTGGTA
Found at i:41352364 original size:27 final size:26
Alignment explanation
Indices: 41352285--41352395 Score: 105
Period size: 27 Copynumber: 4.2 Consensus size: 26
41352275 AGCATGGCTG
* *
41352285 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
* * * * *
41352311 CCAGGACTGATATTCATGGCAGTGCCA
1 CCAGAACAGATAAT-GTGGCAGAGCCA
*
41352338 CCAGAACAGATATATGTGGTAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
41352365 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
41352392 CCAG
1 CCAG
41352396 GACGCTTCCT
Statistics
Matches: 66, Mismatches: 16, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
26 12 0.18
27 53 0.80
28 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:41352385 original size:54 final size:53
Alignment explanation
Indices: 41352285--41352395 Score: 120
Period size: 54 Copynumber: 2.1 Consensus size: 53
41352275 AGCATGGCTG
* *
41352285 CCAGAACAGATAATGTGACAGAGTCACCAGGACTGATATTCATGGCAGT-GCCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGGACAGATATTCATGGCA-TAGCCA
** *
41352338 CCAGAACAGATATATGTGGTAGAGCCACCA-GATCAGATAATT-GTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCACCAGGA-CAGAT-ATTCATGGCATAGCCA
41352392 CCAG
1 CCAG
41352396 GACGCTTCCT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
53 15 0.31
54 31 0.63
55 3 0.06
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (53 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGGACAGATATTCATGGCATAGCCA
Found at i:41352913 original size:17 final size:18
Alignment explanation
Indices: 41352874--41352915 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
41352864 TCCACGTACG
*
41352874 AACTACCTACATTTATAT
1 AACTACCTACATTAATAT
* *
41352892 TACTACC-ACATTAATCT
1 AACTACCTACATTAATAT
41352909 AACTACC
1 AACTACC
41352916 GAAATAGAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.38, C:0.29, G:0.00, T:0.33
Consensus pattern (18 bp):
AACTACCTACATTAATAT
Found at i:41353828 original size:24 final size:24
Alignment explanation
Indices: 41353790--41353890 Score: 166
Period size: 24 Copynumber: 4.2 Consensus size: 24
41353780 CCAACACCGT
* *
41353790 TCTCCCTAATTAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
41353814 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
*
41353838 TCTCCCTTATCAGCTTCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
*
41353862 TCTCCCTTATCAGCTCCTAAATCT
1 TCTCCCTTATCAGCTCCTAAATCC
41353886 TCTCC
1 TCTCC
41353891 TGACAGCCTT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.21, C:0.40, G:0.04, T:0.36
Consensus pattern (24 bp):
TCTCCCTTATCAGCTCCTAAATCC
Found at i:41363418 original size:12 final size:12
Alignment explanation
Indices: 41363401--41363425 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41363391 ATGTAAGTGA
41363401 TCTTGATGATTT
1 TCTTGATGATTT
41363413 TCTTGATGATTT
1 TCTTGATGATTT
41363425 T
1 T
41363426 TACATTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TCTTGATGATTT
Found at i:41368208 original size:40 final size:40
Alignment explanation
Indices: 41368153--41368371 Score: 336
Period size: 40 Copynumber: 5.5 Consensus size: 40
41368143 TTCAGATGAC
41368153 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
41368193 ATCCGGGCTAAGTCCCGAAGGCA-TTGTGCTAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
* * *
41368232 ATCCAGGCTAAGCCCCGAAGGCATTTGTGCTATTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
*
41368272 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
* * *
41368312 ATCTGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTG-CTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTAT
*
41368352 ATCC-GGCTAAATCCCGAAGG
1 ATCCGGGCTAAGTCCCGAAGG
41368372 TACTTGGGTT
Statistics
Matches: 165, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
39 51 0.31
40 112 0.68
41 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
Found at i:41368289 original size:79 final size:80
Alignment explanation
Indices: 41368153--41368371 Score: 336
Period size: 79 Copynumber: 2.8 Consensus size: 80
41368143 TTCAGATGAC
*
41368153 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCA-T
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTATATCCGGGCTAAGTCCCGAAGGCATT
41368217 TGTGCTAGTGACTAT
66 TGTGCTAGTGACTAT
* *
41368232 ATCCAGGCTAAGCCCCGAAGGCATTTGTGCTATTGACTATATCCGGGCTAAGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTATATCCGGGCTAAGTCCCGAAGGCATT
*
41368297 TGTGCTATTGACTAT
66 TGTGCTAGTGACTAT
* * * *
41368312 ATCTGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAGG
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-TTGACTATATCCGGGCTAAGTCCCGAAGG
41368372 TACTTGGGTT
Statistics
Matches: 128, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
79 75 0.59
80 50 0.39
81 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTATATCCGGGCTAAGTCCCGAAGGCATT
TGTGCTAGTGACTAT
Found at i:41368368 original size:119 final size:119
Alignment explanation
Indices: 41368153--41368371 Score: 352
Period size: 119 Copynumber: 1.8 Consensus size: 119
41368143 TTCAGATGAC
*
41368153 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCAAAGGCATT
* *
41368218 GTGCTAGTGACTATATCCAGGCTAAGCCCCGAAGGCATTTGTGCTATTGACTAT
66 GTGCGAGTGACTATATCCAGGCTAAACCCCGAAGGCATTTGTGCTATTGACTAT
* *
41368272 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTATATCTGGGCTAAGTCCCAAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCAAAGGCA-T
*
41368337 TGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAGG
65 TGTGCGAG-TGACTATATCCAGGCTAAACCCCGAAGG
41368372 TACTTGGGTT
Statistics
Matches: 92, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
119 74 0.80
120 16 0.17
121 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (119 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCAAAGGCATT
GTGCGAGTGACTATATCCAGGCTAAACCCCGAAGGCATTTGTGCTATTGACTAT
Found at i:41390366 original size:40 final size:39
Alignment explanation
Indices: 41390268--41390490 Score: 241
Period size: 40 Copynumber: 5.6 Consensus size: 39
41390258 TCCTCGTTCA
* * * * *
41390268 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* *
41390307 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
41390346 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* *
41390386 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* * * * * *
41390426 AAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCAC
* *
41390467 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41390491 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
Found at i:41390490 original size:120 final size:119
Alignment explanation
Indices: 41390268--41390490 Score: 272
Period size: 120 Copynumber: 1.9 Consensus size: 119
41390258 TCCTCGTTCA
* * * *
41390268 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
* *
41390333 TAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
66 TAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * *
41390387 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAATCCGGA
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGA-CATAACCCGGA
* *
41390451 TATATTC-ACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
64 TATA-ACAAC-TAGCACGAAAGCCTTCGGGACTTAACCCGGA
41390491 CAGCATTCAA
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
119 37 0.43
120 44 0.51
121 6 0.07
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
TAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:41392241 original size:25 final size:25
Alignment explanation
Indices: 41392213--41392272 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
41392203 TCACATTCTG
*
41392213 ATTCTGATTCTGTTACCTGATACTA
1 ATTCTGATTCTGTCACCTGATACTA
* ** *
41392238 ATTCTGATTTTGTCACCTGATTTTG
1 ATTCTGATTCTGTCACCTGATACTA
41392263 ATTCTGATTC
1 ATTCTGATTC
41392273 ACATTTTGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.48
Consensus pattern (25 bp):
ATTCTGATTCTGTCACCTGATACTA
Found at i:41397016 original size:55 final size:55
Alignment explanation
Indices: 41396926--41397105 Score: 252
Period size: 55 Copynumber: 3.2 Consensus size: 55
41396916 CTTCTCCCAT
* * *
41396926 GCCCATGTTCAATTGACAGGTTCACCTACGGTTTCAAAACACGGGCGTGTTACAC
1 GCCCGTGTTCAATTGACAGGTTCACCCACGATTTCAAAACACGGGCGTGTTACAC
*
41396981 ACCCGTGTTCAATTGACAGGTTCACCCACGATTTCAAAACACGGGCGTGCCCGTGTTACAC
1 GCCCGTGTTCAATTGACAGGTTCACCCACGATTTCAAAACAC--G-G-G--CGTGTTACAC
* *
41397042 GCCCGTGTTAAATTGACAGGTTCACCCACGATTTCAAAACACGGGCGTGTTGCAC
1 GCCCGTGTTCAATTGACAGGTTCACCCACGATTTCAAAACACGGGCGTGTTACAC
41397097 GCCCGTGTT
1 GCCCGTGTT
41397106 ATTTTGGCAG
Statistics
Matches: 112, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
55 56 0.50
57 2 0.02
58 2 0.02
59 2 0.02
61 50 0.45
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (55 bp):
GCCCGTGTTCAATTGACAGGTTCACCCACGATTTCAAAACACGGGCGTGTTACAC
Found at i:41397066 original size:61 final size:59
Alignment explanation
Indices: 41396926--41397090 Score: 239
Period size: 61 Copynumber: 2.8 Consensus size: 59
41396916 CTTCTCCCAT
* * *
41396926 GCCCATGTTCAATTGACAGGTTCACCTACGGTTTCAAAACAC--G-G-GCGTGTTACAC
1 GCCCGTGTTCAATTGACAGGTTCACCCACGATTTCAAAACACGGGCGTGCGTGTTACAC
*
41396981 ACCCGTGTTCAATTGACAGGTTCACCCACGATTTCAAAACACGGGCGTGCCCGTGTTACAC
1 GCCCGTGTTCAATTGACAGGTTCACCCACGATTTCAAAACACGGGCGTG--CGTGTTACAC
*
41397042 GCCCGTGTTAAATTGACAGGTTCACCCACGATTTCAAAACACGGGCGTG
1 GCCCGTGTTCAATTGACAGGTTCACCCACGATTTCAAAACACGGGCGTG
41397091 TTGCACGCCC
Statistics
Matches: 98, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
55 38 0.39
57 1 0.01
58 1 0.01
59 1 0.01
61 57 0.58
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (59 bp):
GCCCGTGTTCAATTGACAGGTTCACCCACGATTTCAAAACACGGGCGTGCGTGTTACAC
Found at i:41398735 original size:47 final size:47
Alignment explanation
Indices: 41398664--41399068 Score: 544
Period size: 47 Copynumber: 8.6 Consensus size: 47
41398654 CCCTTCGGGA
** * *
41398664 CTTATCACATTTATACACT-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACACATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
* * * *
41398711 CTTATCTCACATACACATGCTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
41398758 CTTATCACACATACACCTGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
41398805 CTTATCACACATATACATGTTCACTTTCATCACATTGGCCATTCGAC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
41398852 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
41398899 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
41398946 CCTATTCACACATACACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTA-TCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
41398994 CTTATCACACATATACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
41399041 CCTATTCACACATATACACT-TTCACATT
1 CTTA-TCACACATATACA-TGTTCACATT
41399069 TATTCAATTA
Statistics
Matches: 323, Mismatches: 31, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
46 1 0.00
47 260 0.80
48 61 0.19
49 1 0.00
ACGTcount: A:0.26, C:0.31, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
Found at i:41403736 original size:40 final size:40
Alignment explanation
Indices: 41403679--41404535 Score: 1428
Period size: 40 Copynumber: 21.6 Consensus size: 40
41403669 CCAGCATGAT
* *
41403679 TGCTCTTCGGGATTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
41403719 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
41403759 TGCTCTTCGAGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
41403799 TGCTC-TCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
41403838 TGCTCTTC-GGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
41403877 TGCTC-TCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
41403916 TGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
41403956 TGCTC-TCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
41403995 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
41404035 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
41404074 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
41404114 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
41404154 TGCTC-TCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
41404193 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
41404233 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
41404273 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
41404313 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
41404353 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
41404393 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * * *
41404433 TGCTCTTTGGGACTTAGCCCGGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATATA-TCACTAGCACGAA
* * *
41404474 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAACAC-AA
1 TGCTCTTCGGGA-CTTAGCCCGGATAT-ATCAC-TAGCACGAA
*
41404514 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
41404536 CATCATTCAA
Statistics
Matches: 772, Mismatches: 34, Indels: 22
0.93 0.04 0.03
Matches are distributed among these distances:
38 2 0.00
39 228 0.30
40 522 0.68
41 20 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:41406440 original size:47 final size:47
Alignment explanation
Indices: 41406369--41406773 Score: 544
Period size: 47 Copynumber: 8.6 Consensus size: 47
41406359 CCCTTCGGGA
** ** *
41406369 CTTATCACATTTATACACT-TTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACACATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
* * * *
41406416 CTTATCTCACATACACATGCTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
41406463 CTTATCACACATACACCTGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
41406510 CTTATCACACATATACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
41406557 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
41406604 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
41406651 CCTATTCACACATACACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTA-TCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
41406699 CTTATCACACATATACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
41406746 CCTATTCACACATATACACT-TTCACATT
1 CTTA-TCACACATATACA-TGTTCACATT
41406774 TATTCAATTA
Statistics
Matches: 324, Mismatches: 30, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
46 1 0.00
47 261 0.81
48 61 0.19
49 1 0.00
ACGTcount: A:0.26, C:0.31, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
Found at i:41416022 original size:12 final size:13
Alignment explanation
Indices: 41415997--41416025 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41415987 AGGGAAAAAG
41415997 AAAAATTAGTAAT
1 AAAAATTAGTAAT
41416010 AAAAATTAG-AAT
1 AAAAATTAGTAAT
41416022 AAAA
1 AAAA
41416026 TTTAAATTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (13 bp):
AAAAATTAGTAAT
Found at i:41423342 original size:17 final size:19
Alignment explanation
Indices: 41423311--41423345 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
41423301 ATAGTACCAC
41423311 TTATACATTTATACCAAAA
1 TTATACATTTATACCAAAA
41423330 TTAT-CATTT-TACCAAA
1 TTATACATTTATACCAAA
41423346 TATCTTTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 5 0.31
19 4 0.25
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (19 bp):
TTATACATTTATACCAAAA
Found at i:41425525 original size:30 final size:30
Alignment explanation
Indices: 41425491--41425547 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
41425481 TCCTTAACTC
41425491 AAACTTTGGCAAAATTACAATTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
* * * *
41425521 AAACTTTTGCATATTTACACTTTTGCC
1 AAACTTTGGCAAAATTACAATTTTGCC
41425548 TCTAGGCTCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.39
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCCT
Found at i:41429928 original size:27 final size:26
Alignment explanation
Indices: 41429861--41429975 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
41429851 TGGAGGAAGC
*
41429861 GTTCAGGTGGCTCTGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
41429888 GTTTCTGGTGGCTCTGCCACAAATATCT
1 G-TTCTGGTGGCTCTGCCAC-AATATCT
*
41429916 GTTCTGGTGGCTCCGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * *
41429942 GTATTTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
41429969 GTTCTGG
1 GTTCTGG
41429976 CAGCCATGCT
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
26 13 0.16
27 40 0.51
28 26 0.33
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:41430485 original size:16 final size:16
Alignment explanation
Indices: 41430464--41430496 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
41430454 GATTTAAATG
*
41430464 TTTGAAATTGAATAGC
1 TTTGAAATTAAATAGC
41430480 TTTGAAATTAAATAGC
1 TTTGAAATTAAATAGC
41430496 T
1 T
41430497 CTAGGGCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.39
Consensus pattern (16 bp):
TTTGAAATTAAATAGC
Found at i:41436427 original size:39 final size:39
Alignment explanation
Indices: 41436376--41436465 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 39
41436366 GGTATTGGAA
* * * *
41436376 AAATATATCCGGACTTGAAGTCCGCGGGCTTTA-TGCTGG
1 AAATATATCCGGACTTAAAGTCCACAGGC-TAAGTGCTGG
41436415 AAATATATCCGGACTTAAAGTCCACAGGCTAAGTGCTGG
1 AAATATATCCGGACTTAAAGTCCACAGGCTAAGTGCTGG
*
41436454 AAAAATATCCGG
1 AAATATATCCGG
41436466 GCTAAGTCCC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
38 2 0.04
39 43 0.96
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (39 bp):
AAATATATCCGGACTTAAAGTCCACAGGCTAAGTGCTGG
Found at i:41436490 original size:39 final size:39
Alignment explanation
Indices: 41436458--41436790 Score: 423
Period size: 39 Copynumber: 8.5 Consensus size: 39
41436448 TGCTGGAAAA
* *
41436458 ATATCCGGGCTAAGTCCCGATGGCATTCGTGCTGGTGTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
* * *
41436497 ATATCCGGGCTAATTCCTGAAGGCATTCGTACTGGTATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
* *
41436536 ATATCCAGGCTAAGTCCTGAAGGCATTCGTGCTGGTATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
* * **
41436575 ATATCCGGGCTAAGTCCCAAAGGCATTCGCGCTGGTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
* *
41436614 ATATTCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
* * **
41436653 ATGTCCGGGCTAAGTCCCGAAGGCATTCGTGTTGGTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
* * * * *
41436692 ATATCTGGGCTAAGTCCCGATGGTATTCGTGCTGCTGTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
* * *
41436731 ATATCCAGGCTAAGTCCTGAAGGCATTCGTGCTAGTATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
41436770 ATATCCGGGCTTAAAGTCCCG
1 ATATCCGGGC-T-AAGTCCCG
41436791 CATGCTTTGT
Statistics
Matches: 249, Mismatches: 43, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
39 241 0.97
40 1 0.00
41 7 0.03
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.30
Consensus pattern (39 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
Found at i:41436502 original size:78 final size:77
Alignment explanation
Indices: 41436409--41436790 Score: 358
Period size: 78 Copynumber: 4.9 Consensus size: 77
41436399 GCGGGCTTTA
* * * ** * **
41436409 TGCTGGAAATATATCCGGACTTAAAGTCCACAGGC-TAAGTGCTGGAAAAATATCCGGGCTAAGT
1 TGCTGGTATTATATCCGGGC-T-AAGTCCACAGGCATTCGTGCTGGTACTATATCCGGGCTAAGT
*
41436473 CCCGATGGCATTCG
64 CCCGAAGGCATTCG
* * * * *
41436487 TGCTGGTGTTATATCCGGGCTAATTCCTGA-AGGCATTCGTACTGGTATTATATCCAGGCTAAGT
1 TGCTGGTATTATATCCGGGCTAAGTCC--ACAGGCATTCGTGCTGGTACTATATCCGGGCTAAGT
*
41436551 CCTGAAGGCATTCG
64 CCCGAAGGCATTCG
* * * *
41436565 TGCTGGTATTATATCCGGGCTAAGTCCCAAAGGCATTCGCGCTGGTGCTATATTCGGGCTAAGTC
1 TGCTGGTATTATATCCGGGCTAAGT-CCACAGGCATTCGTGCTGGTACTATATCCGGGCTAAGTC
*
41436630 CTGAAGGCATTCG
65 CCGAAGGCATTCG
* * * *
41436643 TGCTGGTATTATGTCCGGGCTAAGTCC-CGAAGGCATTCGTGTTGGTGCTATATCTGGGCTAAGT
1 TGCTGGTATTATATCCGGGCTAAGTCCAC--AGGCATTCGTGCTGGTACTATATCCGGGCTAAGT
* *
41436707 CCCGATGGTATTCG
64 CCCGAAGGCATTCG
* * * * *
41436721 TGCTGCTGTTATATCCAGGCTAAGTCCTGA-AGGCATTCGTGCTAGTATTATATCCGGGCTTAAA
1 TGCTGGTATTATATCCGGGCTAAGTCC--ACAGGCATTCGTGCTGGTACTATATCCGGGC-T-AA
41436785 GTCCCG
62 GTCCCG
41436791 CATGCTTTGT
Statistics
Matches: 252, Mismatches: 40, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
76 5 0.02
77 8 0.03
78 228 0.90
79 3 0.01
80 8 0.03
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (77 bp):
TGCTGGTATTATATCCGGGCTAAGTCCACAGGCATTCGTGCTGGTACTATATCCGGGCTAAGTCC
CGAAGGCATTCG
Found at i:41436592 original size:117 final size:117
Alignment explanation
Indices: 41436458--41436790 Score: 486
Period size: 117 Copynumber: 2.8 Consensus size: 117
41436448 TGCTGGAAAA
*
41436458 ATATCCGGGCTAAGTCCCGATGGCATTCGTGCTGGTGTTATATCCGGGCTAATTCCTGAAGGCAT
1 ATATCCGGGCTAAGTCCCGATGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCTGAAGGCAT
* * * *
41436523 TCGTACTGGTATTATATCCAGGCTAAGTCCTGAAGGCATTCGTGCTGGTATT
66 TCGTGCTGGTATTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTACT
* * * * *
41436575 ATATCCGGGCTAAGTCCCAAAGGCATTCGCGCTGGTGCTATATTCGGGCTAAGTCCTGAAGGCAT
1 ATATCCGGGCTAAGTCCCGATGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCTGAAGGCAT
* * *
41436640 TCGTGCTGGTATTATGTCCGGGCTAAGTCCCGAAGGCATTCGTGTTGGTGCT
66 TCGTGCTGGTATTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTACT
* * * *
41436692 ATATCTGGGCTAAGTCCCGATGGTATTCGTGCTGCTGTTATATCCAGGCTAAGTCCTGAAGGCAT
1 ATATCCGGGCTAAGTCCCGATGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCTGAAGGCAT
*
41436757 TCGTGCTAGTATTATATCCGGGCTTAAAGTCCCG
66 TCGTGCTGGTATTATATCCGGGC-T-AAGTCCCG
41436791 CATGCTTTGT
Statistics
Matches: 190, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
117 181 0.95
118 1 0.01
119 8 0.04
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.30
Consensus pattern (117 bp):
ATATCCGGGCTAAGTCCCGATGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCTGAAGGCAT
TCGTGCTGGTATTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTACT
Found at i:41439298 original size:42 final size:42
Alignment explanation
Indices: 41439227--41439328 Score: 143
Period size: 42 Copynumber: 2.4 Consensus size: 42
41439217 GCAGATACTA
41439227 GACAGCTTGTGTGAGCAGCATCATGTAGCTTACATT-TCGACC
1 GACAGCTTGTGTGAGCAGCATCATGTAGCTTACATTCT-GACC
* ** *
41439269 GACAACTTGTGTGAGCAGCATTGTTTAGCTTACATTCTGACC
1 GACAGCTTGTGTGAGCAGCATCATGTAGCTTACATTCTGACC
*
41439311 GACAGCTTGTGTTAGCAG
1 GACAGCTTGTGTGAGCAG
41439329 ACCCATTCTA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 52 0.98
43 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.30
Consensus pattern (42 bp):
GACAGCTTGTGTGAGCAGCATCATGTAGCTTACATTCTGACC
Found at i:41447370 original size:17 final size:17
Alignment explanation
Indices: 41447348--41447382 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
41447338 TTGCTACGGG
41447348 TTGAAATTTACTCTAAC
1 TTGAAATTTACTCTAAC
41447365 TTGAAATTTACTCTAAC
1 TTGAAATTTACTCTAAC
41447382 T
1 T
41447383 AAAGAGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (17 bp):
TTGAAATTTACTCTAAC
Found at i:41451234 original size:95 final size:95
Alignment explanation
Indices: 41451060--41451239 Score: 227
Period size: 95 Copynumber: 1.9 Consensus size: 95
41451050 GCTGTGATTC
* * *
41451060 AGACATTAACCATTACACAATGCTGCTCACACAATAAGTGAAGAATCCACAACACATGCATAATC
1 AGACATTAACCATTACACAATGCTACTCACACAAGAAGTGAAGAATCCACAACACATGCAAAATC
**
41451125 TTAGACATTGGTAAGGTATCTAGTAAATGA
66 TTAGACATCAGTAAGGTATCTAGTAAATGA
* * ** ** * *
41451155 AGACATTAATCATTACACAATGCTATTCACATGAGCTGTGAAGAATCCACAATATATGCAAAATC
1 AGACATTAACCATTACACAATGCTACTCACACAAGAAGTGAAGAATCCACAACACATGCAAAATC
41451220 TTA-ACCATCAGTAAGGTATC
66 TTAGA-CATCAGTAAGGTATC
41451240 CACCACCGAT
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
94 1 0.01
95 70 0.99
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.26
Consensus pattern (95 bp):
AGACATTAACCATTACACAATGCTACTCACACAAGAAGTGAAGAATCCACAACACATGCAAAATC
TTAGACATCAGTAAGGTATCTAGTAAATGA
Found at i:41458847 original size:40 final size:40
Alignment explanation
Indices: 41458763--41458848 Score: 93
Period size: 40 Copynumber: 2.2 Consensus size: 40
41458753 AACTCCATAC
* * *
41458763 CAGA-TTCAGATTATATCAGAATAGGAGCCTAAGTTAGAA
1 CAGACTTCAGACTATATCAGAACAGGAGCCTAAGTCAGAA
* * * * *
41458802 TAGACTTCAGACTGTATGAGAACAGGTGCCTGAGTCAGAA
1 CAGACTTCAGACTATATCAGAACAGGAGCCTAAGTCAGAA
41458842 CAGACTT
1 CAGACTT
41458849 TAGCTTTTCA
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
39 3 0.08
40 34 0.92
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.24
Consensus pattern (40 bp):
CAGACTTCAGACTATATCAGAACAGGAGCCTAAGTCAGAA
Found at i:41460243 original size:37 final size:37
Alignment explanation
Indices: 41460188--41460262 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
41460178 AAAGTTCAGA
*
41460188 TACAGTACTAGCTACGTAGGAGTGCGTAGAACCTATG
1 TACAATACTAGCTACGTAGGAGTGCGTAGAACCTATG
41460225 TACAATACTAGCTACGTAGGAGTGCGTAGAACCTATG
1 TACAATACTAGCTACGTAGGAGTGCGTAGAACCTATG
41460262 T
1 T
41460263 CTATCAGAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (37 bp):
TACAATACTAGCTACGTAGGAGTGCGTAGAACCTATG
Found at i:41467567 original size:47 final size:47
Alignment explanation
Indices: 41467509--41468082 Score: 722
Period size: 47 Copynumber: 12.4 Consensus size: 47
41467499 CAGCCAAGAG
41467509 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
41467556 AGTGTATATATGTGATAAGG-CTAATGG-CGATGTGATGAATGTG-A
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
41467600 A--G------TGT-ATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
41467638 AGTGTATGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
41467689 AGTGTATGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
41467740 AGTGTATATATGTGATAAGGCCTAAT-G-CGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
41467785 AGTGTATGTATATATGTGATAAGGCCTAAT-GCCGATGTGATGAATGTG-A
1 A--G--TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
41467834 AGTGTATAT-TGT-AT-A-GCCTAATAG-CGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * *
41467876 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * *
41467923 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
41467970 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * * *
41468017 AGTGTATATACGTGACAAGGCCGAGTGGCCAACGTAATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
41468064 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
41468083 TCCCGAAAGG
Statistics
Matches: 480, Mismatches: 19, Indels: 56
0.86 0.03 0.10
Matches are distributed among these distances:
35 6 0.01
36 10 0.02
37 16 0.03
38 2 0.00
41 23 0.05
42 13 0.03
43 5 0.01
44 8 0.02
45 43 0.09
46 17 0.04
47 207 0.43
49 28 0.06
50 19 0.04
51 83 0.17
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:41467627 original size:37 final size:36
Alignment explanation
Indices: 41467570--41467644 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 36
41467560 TATATATGTG
41467570 ATAAGGCTAATGGCGATGTGATGAATGTG-AAGTGT
1 ATAAGGCTAATGGCGATGTGATGAATGTGAAAGTGT
41467605 ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATAAGG-CTAATGG-CGATGTGATGAATGTGAAAGTGT
41467643 AT
1 AT
41467645 GTATATATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
35 6 0.16
36 7 0.19
37 16 0.43
38 8 0.22
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.28
Consensus pattern (36 bp):
ATAAGGCTAATGGCGATGTGATGAATGTGAAAGTGT
Found at i:41468257 original size:37 final size:37
Alignment explanation
Indices: 41468201--41468279 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
41468191 CCGAGCTCTA
* * *
41468201 AAGACCCGATGATTACGTGTGGGGATTTTGTCAGGGT
1 AAGACCCGATAATTACGTGTGGAGATTATGTCAGGGT
*
41468238 AAGACCCGATAACTT-CGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAA-TTACGTGTGGAGATTATGTCAGGGT
41468275 AAGAC
1 AAGAC
41468280 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 35 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAATTACGTGTGGAGATTATGTCAGGGT
Found at i:41470178 original size:43 final size:43
Alignment explanation
Indices: 41470130--41470232 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
41470120 TTGGTTTTCA
41470130 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
41470173 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
41470216 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
41470233 TTGAAATGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:41470249 original size:29 final size:29
Alignment explanation
Indices: 41470214--41470287 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
41470204 GTTGTGAGAT
* * *
41470214 TGGCACTAAGTGTGCGGGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTAAAATACA
*
41470243 TGGCACTAAGTGTGCGAGTTTAAAATACA
1 TGGCACTAAGTGTGCGAGCTTAAAATACA
41470272 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
41470288 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTAAAATACA
Found at i:41470721 original size:40 final size:40
Alignment explanation
Indices: 41470598--41470873 Score: 272
Period size: 40 Copynumber: 6.9 Consensus size: 40
41470588 TTGAATGATG
** *
41470598 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TATA
* ** * * *
41470638 TCCGGACTAAGAT-CCGAAG-GCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGAGCATTCATGCTAGTGA-TATA
* *
41470678 TCCGGGCTAAGTCTCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* *
41470718 TCCGGGCTAAGTCCCGAGGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* *
41470758 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* ** * * *
41470798 TCCGTGCTAAACCCCGAAGAGCATTCATGCTGGTGTTATG
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * *
41470838 TCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
41470874 CGTGTATTCG
Statistics
Matches: 198, Mismatches: 34, Indels: 8
0.82 0.14 0.03
Matches are distributed among these distances:
39 1 0.01
40 178 0.90
41 19 0.10
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
Found at i:41472164 original size:269 final size:269
Alignment explanation
Indices: 41471685--41472220 Score: 1054
Period size: 269 Copynumber: 2.0 Consensus size: 269
41471675 ATATGTGGGT
41471685 TGATGATGTGAATTATACATGTTAATATGTGTTTGAAATGCATTTATGAATTAAGTTAAGTGATT
1 TGATGATGTGAATTATACATGTTAATATGTGTTTGAAATGCATTTATGAATTAAGTTAAGTGATT
41471750 ATTGCTTATGAAATCAAGAAAATGAGATATTTGTGCATACTTGTAGAAATGTTTATGTATTTGTT
66 ATTGCTTATGAAATCAAGAAAATGAGATATTTGTGCATACTTGTAGAAATGTTTATGTATTTGTT
41471815 TTAAGATAAGAAAATGATTTTATAGACCGATGCAAAATCAATAATGAATTACAATTGCTATCAAT
131 TTAAGATAAGAAAATGATTTTATAGACCGATGCAAAATCAATAATGAATTACAATTGCTATCAAT
41471880 GAGCTAATGTCTTTGTGGATGTAATTCAATAAGAGGACGTTATCCTAAACTATGCATCGGTAGAA
196 GAGCTAATGTCTTTGTGGATGTAATTCAATAAGAGGACGTTATCCTAAACTATGCATCGGTAGAA
41471945 ATTTTCGTC
261 ATTTTCGTC
*
41471954 TGATGATGTGAATTATACATGTTAATATGTGTTTGAAATGCATTTGTGAATTAAGTTAAGTGATT
1 TGATGATGTGAATTATACATGTTAATATGTGTTTGAAATGCATTTATGAATTAAGTTAAGTGATT
41472019 ATTGCTTATGAAATCAAGAAAATGAGATATTTGTGCATACTTGTAGAAATGTTTATGTATTTGTT
66 ATTGCTTATGAAATCAAGAAAATGAGATATTTGTGCATACTTGTAGAAATGTTTATGTATTTGTT
*
41472084 TTAAGATAAGAAAATGATTTTATAGACCGATGCGAAATCAATAATGAATTACAATTGCTATCAAT
131 TTAAGATAAGAAAATGATTTTATAGACCGATGCAAAATCAATAATGAATTACAATTGCTATCAAT
41472149 GAGCTAATGTCTTTGTGGATGTAATTCAATAAGAGGACGTTATCCTAAACTATGCATCGGTAGAA
196 GAGCTAATGTCTTTGTGGATGTAATTCAATAAGAGGACGTTATCCTAAACTATGCATCGGTAGAA
41472214 ATTTTCG
261 ATTTTCG
41472221 GGGACGAAAA
Statistics
Matches: 265, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
269 265 1.00
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (269 bp):
TGATGATGTGAATTATACATGTTAATATGTGTTTGAAATGCATTTATGAATTAAGTTAAGTGATT
ATTGCTTATGAAATCAAGAAAATGAGATATTTGTGCATACTTGTAGAAATGTTTATGTATTTGTT
TTAAGATAAGAAAATGATTTTATAGACCGATGCAAAATCAATAATGAATTACAATTGCTATCAAT
GAGCTAATGTCTTTGTGGATGTAATTCAATAAGAGGACGTTATCCTAAACTATGCATCGGTAGAA
ATTTTCGTC
Found at i:41474719 original size:47 final size:47
Alignment explanation
Indices: 41474661--41475212 Score: 753
Period size: 47 Copynumber: 11.4 Consensus size: 47
41474651 CAGCCAAGAG
*
41474661 AGTGTATATATGTGATAAGGCCTAATGGCTGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
41474708 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
41474755 AGTGTATGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAACGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
41474806 AGTGTATGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
41474857 AGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
41474904 AGTGTATGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
41474955 AGTGTATGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * *
41475006 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * *
41475053 AGTGTATATGTGTGATAAGGCCGAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
41475100 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * * *
41475147 AGTGTATATACGTGACAAGGCCGAGTGGCCAACGTAATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
41475194 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
41475213 TCCCGAAGGC
Statistics
Matches: 466, Mismatches: 31, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
47 275 0.59
49 4 0.01
51 187 0.40
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:41474933 original size:149 final size:149
Alignment explanation
Indices: 41474663--41475197 Score: 825
Period size: 149 Copynumber: 3.6 Consensus size: 149
41474653 GCCAAGAGAG
* * *
41474663 TGTATATATGTGATAAGGCCTAATGGCTGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
1 TGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
*
41474728 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATATATGTGATAAGGCCTAATGGCCGATG
66 CCTAATGGCCGACGTGATGAATGTGAAAGTGTATGTATATATGTGATAAGGCCTAATGGCCGATG
*
41474793 TGATGAACGTGAAAGTGTA
131 TGATGAATGTGAAAGTGTA
*
41474812 TGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTATATATATGTGATAAGG
1 TGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
*
41474877 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATATATGTGATAAGGCCTAATGGCCGATG
66 CCTAATGGCCGACGTGATGAATGTGAAAGTGTATGTATATATGTGATAAGGCCTAATGGCCGATG
41474942 TGATGAATGTGAAAGTGTA
131 TGATGAATGTGAAAGTGTA
*
41474961 TGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGG
1 TGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
* * * *
41475026 CCTAATAGCCGACGTGATGAATGTGAAA--G--TGTATATGTGTGATAAGGCCGAATAGCCGATG
66 CCTAATGGCCGACGTGATGAATGTGAAAGTGTATGTATATATGTGATAAGGCCTAATGGCCGATG
41475087 TGATGAATGTGAAA--G--
131 TGATGAATGTGAAAGTGTA
* * * *
41475102 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGACAAGG
1 TGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
* * * * *
41475167 CCGAGTGGCCAACGTAATGGATGTGAAAGTG
66 CCTAATGGCCGACGTGATGAATGTGAAAGTG
41475198 CATAAATGTG
Statistics
Matches: 361, Mismatches: 23, Indels: 10
0.92 0.06 0.03
Matches are distributed among these distances:
141 82 0.23
143 2 0.01
145 43 0.12
147 1 0.00
149 233 0.65
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (149 bp):
TGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
CCTAATGGCCGACGTGATGAATGTGAAAGTGTATGTATATATGTGATAAGGCCTAATGGCCGATG
TGATGAATGTGAAAGTGTA
Found at i:41475388 original size:37 final size:37
Alignment explanation
Indices: 41475330--41475408 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
41475320 CCGAGCTCTA
* * *
41475330 AAGACCCGATGATTACATGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAATTACATGTGGAGATTATGTCCGGGT
*
41475367 AAGACCCGATAACTT-CGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAA-TTACATGTGGAGATTATGTCCGGGT
41475404 AAGAC
1 AAGAC
41475409 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 35 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAATTACATGTGGAGATTATGTCCGGGT
Found at i:41477445 original size:49 final size:49
Alignment explanation
Indices: 41477373--41477604 Score: 293
Period size: 49 Copynumber: 4.7 Consensus size: 49
41477363 CAGGTATGCA
* * *
41477373 TAGTAGCCTGCACTTAGTACTACATATGCGACCAATTATGTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCTGGTACACG
* ** * *
41477422 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATATGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACC-AATTATCTGGTACACG
* * * * *
41477472 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCTGGTACACG
*
41477523 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCTGGTACACG
* *
41477572 TAGTAGCCTACACTTAGTACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGCGACC
41477605 TCACAATAGC
Statistics
Matches: 156, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
49 71 0.46
50 48 0.31
51 37 0.24
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCTGGTACACG
Found at i:41477546 original size:101 final size:98
Alignment explanation
Indices: 41477373--41477604 Score: 302
Period size: 100 Copynumber: 2.3 Consensus size: 98
41477363 CAGGTATGCA
* * * ** *
41477373 TAGTAGCCTGCACTTAGTACTACATATGCGACCAATTATGTGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCAGGTACACATAGTAGCCTGCACTTA
*
41477438 GTACTACACACGTGACCTAACCATATGATACACG
66 GTACTACACACGCGACC-AACCATATGATACACG
* *
41477472 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCAGGTACACATAGTAGCCTGCACT
* ** * *
41477537 TAGTACTACACATGCGACCAATTATCTGGTACACG
64 TAGTACTACACACGCGACCAACCATATGATACACG
*
41477572 TAGTAGCCTACACTTAGTACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC
41477605 TCACAATAGC
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
99 29 0.25
100 45 0.39
101 41 0.36
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (98 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCAGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCAACCATATGATACACG
Found at i:41504768 original size:8 final size:8
Alignment explanation
Indices: 41504755--41504779 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
41504745 AATTTTAATG
41504755 ATGTTTAT
1 ATGTTTAT
41504763 ATGTTTAT
1 ATGTTTAT
41504771 ATGTTTAT
1 ATGTTTAT
41504779 A
1 A
41504780 AAGTTAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (8 bp):
ATGTTTAT
Found at i:41516785 original size:48 final size:47
Alignment explanation
Indices: 41516673--41516843 Score: 172
Period size: 46 Copynumber: 3.7 Consensus size: 47
41516663 GTATATCACG
* *
41516673 AGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT-CGTCTCA
1 AGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTATGTCTCA
** * * *
41516719 A-TACGAATGTATGTCCCAGACATGTCTTACATTGGCT-TAAATATCTCA
1 AGGCCG-ATGCATGTCCCAGACATGTCTTACACTGGCTCT--ATGTCTCA
*
41516767 AGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATGT-T-G
1 AGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCT-ATGTCTCA
* * *
41516813 TGGCTGATACATGTCCCAGACATGTCTTACA
1 AGGCCGATGCATGTCCCAGACATGTCTTACA
41516844 TTAGCACGCA
Statistics
Matches: 102, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
45 3 0.03
46 57 0.56
47 1 0.01
48 38 0.37
49 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (47 bp):
AGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTATGTCTCA
Found at i:41516827 original size:94 final size:94
Alignment explanation
Indices: 41516673--41516845 Score: 242
Period size: 94 Copynumber: 1.8 Consensus size: 94
41516663 GTATATCACG
* **
41516673 AGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATACGAATGTATGTCCCAG
1 AGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAATACGAATACATGTCCCAG
41516738 ACATGTCTTACATTGGCTTAAATATCTCA
66 ACATGTCTTACATTGGCTTAAATATCTCA
* * ** *
41516767 AGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATGT-TGTGGCTG-ATACATGTCCC
1 AGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAAT-AC-GAATACATGTCCC
41516830 AGACATGTCTTACATT
64 AGACATGTCTTACATT
41516846 AGCACGCATA
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
93 1 0.01
94 67 0.97
95 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (94 bp):
AGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAATACGAATACATGTCCCAG
ACATGTCTTACATTGGCTTAAATATCTCA
Found at i:41518928 original size:29 final size:29
Alignment explanation
Indices: 41518865--41518932 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
41518855 TAATCAACCG
*
41518865 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
41518894 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
41518923 CGCACACTTA
1 CGCACACTTA
41518933 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:41519102 original size:29 final size:29
Alignment explanation
Indices: 41519039--41519106 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
41519029 TAATCAACCG
41519039 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
41519068 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
41519097 CGCACACTTA
1 CGCACACTTA
41519107 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:41519247 original size:29 final size:30
Alignment explanation
Indices: 41519208--41519286 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
41519198 CTTAATAATC
41519208 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
41519238 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
41519267 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
41519287 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:41519280 original size:174 final size:174
Alignment explanation
Indices: 41518754--41519255 Score: 941
Period size: 174 Copynumber: 2.9 Consensus size: 174
41518744 AACTCAAGGT
* * *
41518754 ACTTACCTTTTCCGCTGTCCAAAATTGATTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
41518819 GAAAATATATATTGAGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
41518884 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
41518928 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
41518993 GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
41519058 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
41519102 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
41519167 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
*
41519232 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
41519256 TGTACAATTT
Statistics
Matches: 319, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 319 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:41527231 original size:29 final size:29
Alignment explanation
Indices: 41527165--41527232 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
41527155 TAATCAACCG
*
41527165 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* * **
41527194 CACATACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
41527223 CGCACACTTA
1 CGCACACTTA
41527233 CCTTTTCCGC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
28 3 0.10
29 28 0.90
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:41527402 original size:29 final size:29
Alignment explanation
Indices: 41527339--41527406 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
41527329 TAATCAACCG
41527339 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
41527368 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
41527397 CGCACACTTA
1 CGCACACTTA
41527407 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:41527547 original size:29 final size:30
Alignment explanation
Indices: 41527508--41527586 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
41527498 CTTAATAATC
41527508 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
41527538 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
*
41527567 AACCCACACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
41527587 ATCTCATGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 32 0.76
30 4 0.10
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:41527580 original size:174 final size:174
Alignment explanation
Indices: 41527054--41527555 Score: 923
Period size: 174 Copynumber: 2.9 Consensus size: 174
41527044 GAACTAAGGT
* *
41527054 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
41527119 GAAAATATATATTGAGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
*
41527184 ACTTTAAACTCACATACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
41527228 ACTTACCTTTTCCGCTGTCCAAATTCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
41527293 GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
41527358 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
41527402 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
41527467 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
*
41527532 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
41527556 TGTACAATTT
Statistics
Matches: 316, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 316 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:41536122 original size:49 final size:47
Alignment explanation
Indices: 41536016--41536150 Score: 146
Period size: 49 Copynumber: 2.8 Consensus size: 47
41536006 ACATGGGTTA
* * *
41536016 AGATGCCGACGCCATGTCCCAAACATGGTCTTACACTGGCTTTCGTAT
1 AGATGTCGATGCCATGTCCCAAACA-GGTCTTACACTGGCTATCGTAT
** *
41536064 AGGCGGTCGATGCCATGTCCCATACAGGTCTTACACTGGCTCGCATC-TAT
1 A-GATGTCGATGCCATGTCCCAAACAGGTCTTACACTGGCT---ATCGTAT
* *
41536114 AGATGTCGATGCCATGTCCCAGACAGGTTTTACACTG
1 AGATGTCGATGCCATGTCCCAAACAGGTCTTACACTG
41536151 ACACACAATA
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
48 16 0.22
49 51 0.70
50 4 0.05
51 2 0.03
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (47 bp):
AGATGTCGATGCCATGTCCCAAACAGGTCTTACACTGGCTATCGTAT
Found at i:41536311 original size:46 final size:43
Alignment explanation
Indices: 41536210--41536336 Score: 137
Period size: 46 Copynumber: 2.8 Consensus size: 43
41536200 TATATCGCGA
* *
41536210 GGCTGATGCATGTCCCAAACATTTCTTACACTAGCTCTTGTCT
1 GGCTAATGCATGTCCCAAACATGTCTTACACTAGCTCTTGTCT
*** *
41536253 CAATACAGATGCATGTCCCAAACATGTCTTACACTAGCTCTCATGATGT
1 GGCT--A-ATGCATGTCCCAAACATGTCTTACACTAGCTCT--TG-TCT
*
41536302 GGCTAATGCATGTCCCAGACATGTCTTACACTAGC
1 GGCTAATGCATGTCCCAAACATGTCTTACACTAGC
41536337 ACACATATCA
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
43 1 0.01
46 61 0.90
47 1 0.01
48 2 0.03
49 3 0.04
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.30
Consensus pattern (43 bp):
GGCTAATGCATGTCCCAAACATGTCTTACACTAGCTCTTGTCT
Found at i:41537603 original size:8 final size:8
Alignment explanation
Indices: 41537590--41537619 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
41537580 AATTTTGATG
41537590 ATGTTTAT
1 ATGTTTAT
41537598 ATGTTTAT
1 ATGTTTAT
41537606 ATGTTTAT
1 ATGTTTAT
41537614 AATGTT
1 -ATGTT
41537620 AAGTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.27, C:0.00, G:0.13, T:0.60
Consensus pattern (8 bp):
ATGTTTAT
Found at i:41538579 original size:18 final size:19
Alignment explanation
Indices: 41538555--41538597 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
41538545 GTAACGCCCT
*
41538555 AATTTTCGGGATCTTC-GAG
1 AATTTTCAGGAT-TTCTGAG
41538574 -ATTTTCAGGATTTCTGAG
1 AATTTTCAGGATTTCTGAG
41538592 AATTTT
1 AATTTT
41538598 AGTGAATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 3 0.14
18 13 0.62
19 5 0.24
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (19 bp):
AATTTTCAGGATTTCTGAG
Found at i:41539182 original size:25 final size:25
Alignment explanation
Indices: 41539151--41539200 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
41539141 CTAGCAATTC
41539151 CTTTTCCTTCTATTTCACATTTATT
1 CTTTTCCTTCTATTTCACATTTATT
41539176 CTTTTCCTTCTATTTCACATTTATT
1 CTTTTCCTTCTATTTCACATTTATT
41539201 TTCTTTGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (25 bp):
CTTTTCCTTCTATTTCACATTTATT
Found at i:41540467 original size:27 final size:26
Alignment explanation
Indices: 41540429--41540514 Score: 109
Period size: 27 Copynumber: 3.2 Consensus size: 26
41540419 ATAGGAAGTA
* *
41540429 TTCTGGTGGCTCTACCATAAATATCTG
1 TTCTGGTGGCTCTGCCA-CAATATCTG
*
41540456 TTCTGGTGGCTCTGCCACAATATTTG
1 TTCTGGTGGCTCTGCCACAATATCTG
* *
41540482 TATCTGGTGACTCTGTCACAATATCTG
1 T-TCTGGTGGCTCTGCCACAATATCTG
41540509 TTCTGG
1 TTCTGG
41540515 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
26 13 0.25
27 39 0.75
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (26 bp):
TTCTGGTGGCTCTGCCACAATATCTG
Found at i:41542991 original size:37 final size:37
Alignment explanation
Indices: 41542941--41543019 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
41542931 TTATTACGAA
* * *
41542941 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
41542978 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
41543015 GTCTT
1 GTCTT
41543020 TAGAGCTCGG
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:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:41543170 original size:19 final size:19
Alignment explanation
Indices: 41543146--41543184 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
41543136 GACTTATCAC
*
41543146 ATTCATCACATTGGCCATT
1 ATTCATCACATCGGCCATT
*
41543165 ATTCATCATATCGGCCATT
1 ATTCATCACATCGGCCATT
41543184 A
1 A
41543185 GGCCCTATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.36
Consensus pattern (19 bp):
ATTCATCACATCGGCCATT
Found at i:41543267 original size:47 final size:47
Alignment explanation
Indices: 41543165--41543566 Score: 723
Period size: 47 Copynumber: 8.5 Consensus size: 47
41543155 ATTGGCCATT
* * *
41543165 ATTCATCATATCGGCCATTAGGCCCTATCATATATATATACACTTTCAC
1 ATTCATCACATCGGCCATTAGGCCTTATC--ACATATATACACTTTCAC
*
41543214 ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCAT
1 ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCAC
*
41543261 ATTCATCACATCGGCCATTAGGCATTATCACATATATACACTTTCAC
1 ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCAC
41543308 ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCAC
1 ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCAC
*
41543355 ATTCATCACATCGGCCATTAGGCATTATCACATATATACACTTTCAC
1 ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCAC
41543402 ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCAC
1 ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCAC
41543449 ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCAC
1 ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCAC
*
41543496 ATTCATCACATCGGCCATTAGGCATTATCACATATATACACTTTCAC
1 ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCAC
41543543 ATTCATCACATCGGCCATTAGGCC
1 ATTCATCACATCGGCCATTAGGCC
41543567 ATACTATCAT
Statistics
Matches: 342, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
47 315 0.92
49 27 0.08
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (47 bp):
ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCAC
Found at i:41543316 original size:25 final size:25
Alignment explanation
Indices: 41543240--41543318 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 25
41543230 ATTAGGCCTT
*
41543240 ATCACATATATACACTTTCATATTC
1 ATCACATATATACACTTTCACATTC
**** ***
41543265 ATCACAT-CGGCCA-TTAGGCATT-
1 ATCACATATATACACTTTCACATTC
41543287 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
41543312 ATCACAT
1 ATCACAT
41543319 CGGCCATTAG
Statistics
Matches: 36, Mismatches: 15, Indels: 6
0.63 0.26 0.11
Matches are distributed among these distances:
22 7 0.19
23 7 0.19
24 8 0.22
25 14 0.39
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:41543551 original size:25 final size:25
Alignment explanation
Indices: 41543475--41543553 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 25
41543465 ATTAGGCCTT
41543475 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
**** ***
41543500 ATCACAT-CGGCCA-TTAGGCATT-
1 ATCACATATATACACTTTCACATTC
41543522 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
41543547 ATCACAT
1 ATCACAT
41543554 CGGCCATTAG
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
22 7 0.19
23 8 0.22
24 8 0.22
25 14 0.38
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:41552458 original size:27 final size:27
Alignment explanation
Indices: 41552420--41552495 Score: 118
Period size: 27 Copynumber: 2.8 Consensus size: 27
41552410 AAGTATTCTA
41552420 GTGGCTCTGCCACAAATATCTGTA-CTG
1 GTGGCTCTGCCAC-AATATCTGTATCTG
41552447 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTGTATCTG
* *
41552474 GTGACTCTGTCACAATATCTGT
1 GTGGCTCTGCCACAATATCTGT
41552496 TTTGGCAGCC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
26 10 0.22
27 36 0.78
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTATCTG
Found at i:41558346 original size:31 final size:30
Alignment explanation
Indices: 41558308--41558398 Score: 78
Period size: 31 Copynumber: 3.0 Consensus size: 30
41558298 AATTCTTTAA
41558308 ATGTATACAATTGAATCAAAATCAAAGTTTC
1 ATGTATACAATTGAA-CAAAATCAAAGTTTC
* *
41558339 ATGTATAC-ATATGAACCACAATTC-AAGTTTT
1 ATGTATACAAT-TGAA-CA-AAATCAAAGTTTC
* * * *
41558370 ATGTGTATAATTGTACCAAATCAAAGTTT
1 ATGTATACAATTGAACAAAATCAAAGTTT
41558399 ACGTATCAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
29 4 0.08
30 9 0.19
31 29 0.60
32 6 0.12
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (30 bp):
ATGTATACAATTGAACAAAATCAAAGTTTC
Found at i:41560244 original size:295 final size:297
Alignment explanation
Indices: 41559684--41560360 Score: 759
Period size: 295 Copynumber: 2.3 Consensus size: 297
41559674 ACAACAAAGC
* * *
41559684 CACCAACTTGGTTAGGAAAATTATAGG-CATACCCTTCCGTAATTAAAATAAATTAT-TTCATCC
1 CACCAACTCGGTTAGGAAAATTA-AGGACATACCCTTCCGTAATTAAAATAAGTTATATT-ATTC
* * * *
41559747 AAGGGTACTTTAGTTTTTTTATTTATTTAAAAGAATAATATAAATAAGCATATGGTGGTATTTGG
64 AAGGGTATTTTAG-TCTTTT-TTTA--TAAAAGAACAATATAAATAAGCATATGGTGGTATTTGA
** * * *
41559812 ACCCAAACTAATTGTATTAGTAAAACCTTTAATTTATCACTCAAATAACATGTTATTTTAATATA
125 ACCCAAACTAATTACATTAATAAAACCTTTAATTTACCACTCAAATAAAATGTTATTTTAATATA
* * * * *
41559877 TTTAAACATTTTAATTTTATTATGCACACTTTATCACTTTCATCATCTGTATATCTATCTATAGT
190 TTTAAACATTTTAATTTTATTATACACACTTTATCACTTACATCATCTGTATATATAACTATACT
41559942 ATTATTTAAGCTCCTTACTGAGTTGATGTCACCCTCAATCGAGT
255 ATTATTTAAGCT-CTTACTGAGTTGATGTCACCCTCAATCGAGT
* * *
41559986 TACCAACTCGGTTAGGAAAATTAAGGACATACCATTCCTTAATTAAAATAAGTTATATTATTCAA
1 CACCAACTCGGTTAGGAAAATTAAGGACATACCCTTCCGTAATTAAAATAAGTTATATTATTCAA
*
41560051 GGGTATTTTAGTCTTTTTTTA-AAAA-AACCAATA-AAA-AATGCATATTGTGAG-ATTTGAACC
66 GGGTATTTTAGTCTTTTTTTATAAAAGAA-CAATATAAATAA-GCATATGGTG-GTATTTGAACC
* ** * * *
41560111 CAAATTAATTACATTAATAAAATTTTTAATTTACCACTCAACTAAAACT-TTA-TTTGATATTTT
128 CAAACTAATTACATTAATAAAACCTTTAATTTACCACTCAAATAAAA-TGTTATTTTAATATATT
*** * * *
41560174 TATGTATTTTAATTTTATTATATACACTTTATTACTTACATCATTTGTATATATACACT-TACTA
192 TAAACATTTTAATTTTATTATACACACTTTATCACTTACATCATCTGTATATATA-ACTATACTA
* * * *
41560238 TTATTTAAGCTCTTACTGAGTTGGTGTCACCTTCAATGGGGT
256 TTATTTAAGCTCTTACTGAGTTGATGTCACCCTCAATCGAGT
** * * *
41560280 CACCAACTCGGTTA-GACAAATTATCGATATACCCTTCCGT-AGTAAAAAAAGTT-TATTATTCA
1 CACCAACTCGGTTAGGA-AAATTAAGGACATACCCTTCCGTAATTAAAATAAGTTATATTATTCA
*
41560342 AGGTTATTTTAGTCTTTTT
65 AGGGTATTTTAGTCTTTTT
41560361 ATTTTTTATT
Statistics
Matches: 321, Mismatches: 46, Indels: 26
0.82 0.12 0.07
Matches are distributed among these distances:
292 27 0.08
293 13 0.04
294 58 0.18
295 72 0.22
296 65 0.20
297 10 0.03
300 4 0.01
301 8 0.02
302 62 0.19
303 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (297 bp):
CACCAACTCGGTTAGGAAAATTAAGGACATACCCTTCCGTAATTAAAATAAGTTATATTATTCAA
GGGTATTTTAGTCTTTTTTTATAAAAGAACAATATAAATAAGCATATGGTGGTATTTGAACCCAA
ACTAATTACATTAATAAAACCTTTAATTTACCACTCAAATAAAATGTTATTTTAATATATTTAAA
CATTTTAATTTTATTATACACACTTTATCACTTACATCATCTGTATATATAACTATACTATTATT
TAAGCTCTTACTGAGTTGATGTCACCCTCAATCGAGT
Found at i:41563857 original size:12 final size:12
Alignment explanation
Indices: 41563840--41563869 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
41563830 TCAATGGATA
41563840 TTGAATTTTTTT
1 TTGAATTTTTTT
41563852 TTGAA-TTTTTT
1 TTGAATTTTTTT
41563863 TTGAATT
1 TTGAATT
41563870 ACAATATCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (12 bp):
TTGAATTTTTTT
Found at i:41567920 original size:21 final size:21
Alignment explanation
Indices: 41567896--41567935 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41567886 GCTCTCAAGA
*
41567896 AACTAGATTCTAAAGTCTCCC
1 AACTAGATTCAAAAGTCTCCC
*
41567917 AACTGGATTCAAAAGTCTC
1 AACTAGATTCAAAAGTCTC
41567936 AACGGTGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (21 bp):
AACTAGATTCAAAAGTCTCCC
Found at i:41574404 original size:38 final size:38
Alignment explanation
Indices: 41574362--41574483 Score: 138
Period size: 38 Copynumber: 3.2 Consensus size: 38
41574352 GCAGGTTATA
41574362 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
1 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
* *
41574400 TGCTGGTAA-TATATCCGGGTTAAATCCCGCAGGCCTAG
1 TGCTGG-AATTATATCCGGGTTAAATCCCGCAGGCTTCG
* ** * * *
41574438 TGCTGGTATTATATTTGAGTTTAAAGTCCTGTAGGCTTCG
1 TGCTGGAATTATATCCG-GGTTAAA-TCCCGCAGGCTTCG
41574478 TGCTGG
1 TGCTGG
41574484 TGTTATGTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
37 1 0.01
38 45 0.64
39 8 0.11
40 16 0.23
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (38 bp):
TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
Found at i:41578813 original size:30 final size:30
Alignment explanation
Indices: 41578771--41578828 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
41578761 AGAATAACTC
41578771 TTATTCGAAACAACCTCTACATTGATAACA
1 TTATTCGAAACAACCTCTACATTGATAACA
41578801 TTATT-GATAACAACCTCTACATTGATAA
1 TTATTCGA-AACAACCTCTACATTGATAA
41578829 AATGTTTCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.33
Consensus pattern (30 bp):
TTATTCGAAACAACCTCTACATTGATAACA
Found at i:41578826 original size:18 final size:18
Alignment explanation
Indices: 41578779--41578828 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
41578769 TCTTATTCGA
41578779 AACAACCTCTACATTGAT
1 AACAACCTCTACATTGAT
41578797 AAC-A--T-T--ATTGAT
1 AACAACCTCTACATTGAT
41578809 AACAACCTCTACATTGAT
1 AACAACCTCTACATTGAT
41578827 AA
1 AA
41578829 AATGTTTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
12 9 0.35
13 1 0.04
14 1 0.04
15 2 0.08
16 1 0.04
17 1 0.04
18 11 0.42
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.30
Consensus pattern (18 bp):
AACAACCTCTACATTGAT
Found at i:41581613 original size:79 final size:81
Alignment explanation
Indices: 41581471--41581653 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
41581461 TACTCGTTCA
* *
41581471 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
* *
41581535 TTTAGTAAC-TCGCACC
66 TATAGTAACTTAGCA-C
***
41581551 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTCGTCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
41581613 ATATGGTCACTTAGCAC
65 ATATAGTAACTTAGCAC
*
41581630 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
41581654 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:41581653 original size:40 final size:40
Alignment explanation
Indices: 41581450--41581653 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
41581440 CGAAATTTAA
** *
41581450 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41581490 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41581530 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41581569 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTCGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
41581609 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
41581649 CCGGA
1 CCGGA
41581654 CATCATTCGA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:41592831 original size:55 final size:52
Alignment explanation
Indices: 41592714--41592908 Score: 201
Period size: 53 Copynumber: 3.6 Consensus size: 52
41592704 GGATACCAAA
* * * *
41592714 TAAGACCATGCCAAGGCATGGCATTGGTAAGTTTTACAAGGCAAGGAAATCATG
1 TAAGACCATGCCAAGACATGGCATTGGTAAG-TTCATAAGGCAAGG-AACCATG
* * * * *
41592768 TAAGACCATGTCAAGACATGGCATTGATAAACTATGATAAGGCAAAGAACCCATG
1 TAAGACCATGCCAAGACATGGCATTGGT-AAGT-TCATAAGGCAAGGAA-CCATG
* * *
41592823 TAAGACCATGCCAAGACATGACAATGGTGAGTTCATAAGGCAAGGATACCATG
1 TAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGCAAGGA-ACCATG
* * *
41592876 TAAGACCATGTCAAGACATGGAAATGGTAAGTT
1 TAAGACCATGCCAAGACATGGCATTGGTAAGTT
41592909 TAATAAGAAA
Statistics
Matches: 117, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
53 46 0.39
54 31 0.26
55 40 0.34
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (52 bp):
TAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGCAAGGAACCATG
Found at i:41596555 original size:55 final size:53
Alignment explanation
Indices: 41596425--41596621 Score: 184
Period size: 55 Copynumber: 3.6 Consensus size: 53
41596415 CTTACCATTT
*
41596425 CCATGTCTCGACATGGTCTTACATGGTATCCTTACCTTATGAACTCACCAATG
1 CCATGTCTTGACATGGTCTTACATGGTATCCTTACCTTATGAACTCACCAATG
* ** * * * *
41596478 TCATACCTTGGCATGGTCTTACATAGG-A-CCTTTGCCTTATAGTAACTTATCAATG
1 CCATGTCTTGACATGGTCTTACAT-GGTATCC-TTACCTTAT-G-AACTCACCAATG
* *
41596533 CCATGTCTTGACATGGTTTTACATGGTATCCTTACCTTA-GAAACATTACCAATTG
1 CCATGTCTTGACATGGTCTTACATGGTATCCTTACCTTATG-AAC-TCACCAA-TG
* * * *
41596588 GCATGCCTTGGCATGGTTTTACATGGTATCCTTA
1 CCATGTCTTGACATGGTCTTACATGGTATCCTTA
41596622 AACACTAATG
Statistics
Matches: 117, Mismatches: 19, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
52 2 0.02
53 32 0.27
54 11 0.09
55 70 0.60
56 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (53 bp):
CCATGTCTTGACATGGTCTTACATGGTATCCTTACCTTATGAACTCACCAATG
Found at i:41597658 original size:13 final size:13
Alignment explanation
Indices: 41597640--41597664 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41597630 TGGTCATCAT
41597640 GGTGTGAACACAA
1 GGTGTGAACACAA
41597653 GGTGTGAACACA
1 GGTGTGAACACA
41597665 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:41599900 original size:18 final size:18
Alignment explanation
Indices: 41599879--41599913 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41599869 TTTTTCTTTT
41599879 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
41599897 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
41599914 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:41600942 original size:12 final size:12
Alignment explanation
Indices: 41600925--41600949 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41600915 AAACCGTATG
41600925 CAATTTTTTTTT
1 CAATTTTTTTTT
41600937 CAATTTTTTTTT
1 CAATTTTTTTTT
41600949 C
1 C
41600950 CTTCTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:41600971 original size:14 final size:16
Alignment explanation
Indices: 41600952--41600992 Score: 59
Period size: 14 Copynumber: 2.7 Consensus size: 16
41600942 TTTTTTTCCT
*
41600952 TCTTTTTTTTTCGGA-
1 TCTTTTTTTTTCGAAC
41600967 T-TTTTTTTTTCGAAC
1 TCTTTTTTTTTCGAAC
41600982 TCTTTTTTTTT
1 TCTTTTTTTTT
41600993 TTACGCACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 12 0.52
15 2 0.09
16 9 0.39
ACGTcount: A:0.07, C:0.12, G:0.07, T:0.73
Consensus pattern (16 bp):
TCTTTTTTTTTCGAAC
Found at i:41601968 original size:13 final size:13
Alignment explanation
Indices: 41601950--41601974 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41601940 TGGTCATCAT
41601950 GGTGTGAACACAA
1 GGTGTGAACACAA
41601963 GGTGTGAACACA
1 GGTGTGAACACA
41601975 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:41604029 original size:29 final size:28
Alignment explanation
Indices: 41603972--41604057 Score: 118
Period size: 28 Copynumber: 3.0 Consensus size: 28
41603962 TACCTGTATC
* *
41603972 TGGCCCATTAAGCCCAATCATATTCATA
1 TGGCCCATTAGGCCCAATCACATTCATA
*
41604000 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCC-AATCACATTCATA
* *
41604029 TGGCTCATTAGGCCCAGTCACATTCATA
1 TGGCCCATTAGGCCCAATCACATTCATA
41604057 T
1 T
41604058 TCATGCTCAC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
28 26 0.51
29 25 0.49
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAATCACATTCATA
Found at i:41610784 original size:53 final size:53
Alignment explanation
Indices: 41610602--41610808 Score: 182
Period size: 53 Copynumber: 3.8 Consensus size: 53
41610592 ATTAGGATTT
* * * * * * *
41610602 AAGGATACCAAGTAAAACCATGCCAAGGCATGGCATTGGTAAGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATAGTAAG-TTCATAAGGC
* * * * * *
41610656 AAGGAAATCATGTAAGACCATGTCAAGACATGGC-ATTGATAAACTATGATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATAG-T-AAGT-TCATAAGGC
** * * *
41610711 AAATATCCCATGTAAGACCATGCCAAGGCATGGCAATAGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATAGTAAGTTCATAAGGC
* * *
41610764 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATAGTAAGTT
41610809 TAAAAAGAAA
Statistics
Matches: 119, Mismatches: 30, Indels: 9
0.75 0.19 0.06
Matches are distributed among these distances:
53 47 0.39
54 32 0.27
55 37 0.31
56 3 0.03
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATAGTAAGTTCATAAGGC
Found at i:41616138 original size:33 final size:33
Alignment explanation
Indices: 41616101--41616163 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
41616091 TTTCAATTAG
* *
41616101 GATTTAGCCTGGACTGGTAATCCTAATTAACTA
1 GATTTAGCCTAGACTGGTAATCCAAATTAACTA
41616134 GATTTAGCCTAGACTGGTAATCCAAATTAA
1 GATTTAGCCTAGACTGGTAATCCAAATTAA
41616164 ACTCTATAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (33 bp):
GATTTAGCCTAGACTGGTAATCCAAATTAACTA
Found at i:41616806 original size:17 final size:16
Alignment explanation
Indices: 41616780--41616811 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
41616770 AAAAGTTGAT
41616780 TGCCATTTGTTATGTG
1 TGCCATTTGTTATGTG
41616796 TGCCTATTTGTTATGT
1 TGCC-ATTTGTTATGT
41616812 CTCTTTACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.53
Consensus pattern (16 bp):
TGCCATTTGTTATGTG
Found at i:41618396 original size:24 final size:24
Alignment explanation
Indices: 41618368--41618415 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
41618358 GGTATGAAAT
41618368 AGATGATAAGAAGATGAGTTTATG
1 AGATGATAAGAAGATGAGTTTATG
41618392 AGATGATAAGAAGATGAGTTTATG
1 AGATGATAAGAAGATGAGTTTATG
41618416 TATTTGAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (24 bp):
AGATGATAAGAAGATGAGTTTATG
Found at i:41636136 original size:44 final size:44
Alignment explanation
Indices: 41636068--41636154 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
41636058 ACAAACTTTG
*
41636068 TGAGATAAGCAATTGTATGCGAAGTTTAGCAAATATGAATTTTT
1 TGAGATAAGCAACTGTATGCGAAGTTTAGCAAATATGAATTTTT
* *
41636112 TGAGATAAGCAACTGTATGTGAAGTTTAGCAAATGTGAATTTT
1 TGAGATAAGCAACTGTATGCGAAGTTTAGCAAATATGAATTTT
41636155 GGTTACGATA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.36
Consensus pattern (44 bp):
TGAGATAAGCAACTGTATGCGAAGTTTAGCAAATATGAATTTTT
Found at i:41647303 original size:40 final size:40
Alignment explanation
Indices: 41647222--41647437 Score: 312
Period size: 40 Copynumber: 5.5 Consensus size: 40
41647212 AAACCAGGTA
** *
41647222 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
41647261 CCTTCGGGACTTAGCCCGGTTGTAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
41647301 CCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
41647341 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
41647381 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
41647421 CCTTCAGG-CTTAGCCCG
1 CCTTCGGGACTTAGCCCG
41647438 ATTATCAATC
Statistics
Matches: 162, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 22 0.14
40 140 0.86
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:41651050 original size:31 final size:31
Alignment explanation
Indices: 41651006--41651072 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
41650996 AATAACTTTC
*
41651006 AATGTTAGCCATTTTTCATGGCCTTATACAA
1 AATGATAGCCATTTTTCATGGCCTTATACAA
*
41651037 AATGATAGTCATTTTTCATGGCCTTATACAA
1 AATGATAGCCATTTTTCATGGCCTTATACAA
41651068 AATGA
1 AATGA
41651073 GTCAAATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.37
Consensus pattern (31 bp):
AATGATAGCCATTTTTCATGGCCTTATACAA
Found at i:41651636 original size:47 final size:48
Alignment explanation
Indices: 41651564--41651691 Score: 152
Period size: 47 Copynumber: 2.6 Consensus size: 48
41651554 GGTATAATGC
* * *
41651564 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCCAT-CAAGT-
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCATACATAC-AGTG
* * *
41651611 CGATGCCATGTCCTAGACATAGTCTTACACTGACTCTTACATATCAGTG
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCATACATA-CAGTG
*
41651660 CTGAAGCCATGTCCCAGACATGGTCTTACACT
1 C-GATGCCATGTCCCAGACATGGTCTTACACT
41651692 AACACATCTT
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
47 36 0.53
48 3 0.04
49 2 0.03
50 27 0.40
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGACTCATACATACAGTG
Found at i:41651762 original size:46 final size:46
Alignment explanation
Indices: 41651709--41651878 Score: 179
Period size: 46 Copynumber: 3.7 Consensus size: 46
41651699 CTTGTAGCCA
* * *
41651709 ATGCATGTCCCAGACATGTTTTACACTAG-T-TTACATCTCGAGGCTG
1 ATGCATGTCCCAAACATGTCTTACACTAGCTCTT--ATCTCAAGGCTG
* *
41651755 ATGCATGTCCCAAACATGTCTTACACTAGCTCTTGTCTCAATGCTG
1 ATGCATGTCCCAAACATGTCTTACACTAGCTCTTATCTCAAGGCTG
* *
41651801 ATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCA--T-AATGTGGTCG
1 ATG-CATGTCCCAAACAT-GTCTTACACTAGCTCTTATCTCAA-G-GCT-G
41651849 ATGCATGTCCCAAACATGTCTTACACTAGC
1 ATGCATGTCCCAAACATGTCTTACACTAGC
41651879 ACATAATTAA
Statistics
Matches: 108, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
45 2 0.02
46 53 0.49
47 31 0.29
48 22 0.20
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (46 bp):
ATGCATGTCCCAAACATGTCTTACACTAGCTCTTATCTCAAGGCTG
Found at i:41651856 original size:47 final size:44
Alignment explanation
Indices: 41651559--41651878 Score: 175
Period size: 46 Copynumber: 6.8 Consensus size: 44
41651549 CTTAGGGTAT
* * *
41651559 AATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCCATC
1 AATGCTGATG-CATGTCCCAAACAT-GTCTTACACTAGCTC-TTC-TC
* *
41651607 AA-G-TCGATGCCATGTCCTAGACATAGTCTTACACT-GACTCTTACATATC
1 AATGCT-GATG-CATGTCCCAAACAT-GTCTTACACTAG-CTCTT-C---TC
* * * * * *
41651656 AGTGCTGAAGCCATGTCCCAGACATGGTCTTACACTAACACATCT-
1 AATGCTGATG-CATGTCCCAAACAT-GTCTTACACTAGCTCTTCTC
** ** * * * *
41651701 TGTAGCCAATGCATGTCCCAGACATGTTTTACACTAGTTTACATCTC
1 AAT-GCTGATGCATGTCCCAAACATGTCTTACACTAG-CT-CTTCTC
* *
41651748 GAGGCTGATGCATGTCCCAAACATGTCTTACACTAGCTCTTGTCTC
1 AATGCTGATGCATGTCCCAAACATGTCTTACACTAGCTC-T-TCTC
41651794 AATGCTGATGCCATGTCCCAAACATGGTCTTACACTAGCTC-TCAT-
1 AATGCTGATG-CATGTCCCAAACAT-GTCTTACACTAGCTCTTC-TC
*
41651839 AATGTGGTCGATGCATGTCCCAAACATGTCTTACACTAGC
1 AA--TGCT-GATGCATGTCCCAAACATGTCTTACACTAGC
41651879 ACATAATTAA
Statistics
Matches: 220, Mismatches: 32, Indels: 42
0.75 0.11 0.14
Matches are distributed among these distances:
44 11 0.05
45 21 0.10
46 67 0.30
47 63 0.29
48 21 0.10
49 5 0.02
50 31 0.14
51 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (44 bp):
AATGCTGATGCATGTCCCAAACATGTCTTACACTAGCTCTTCTC
Found at i:41660211 original size:19 final size:19
Alignment explanation
Indices: 41660183--41660220 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41660173 GGAAAAACGC
*
41660183 CGCAATAGGTAAAGCAGTA
1 CGCAAAAGGTAAAGCAGTA
*
41660202 CGCAAAAGGTCAAGCAGTA
1 CGCAAAAGGTAAAGCAGTA
41660221 GCGGCGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.18, G:0.26, T:0.13
Consensus pattern (19 bp):
CGCAAAAGGTAAAGCAGTA
Found at i:41664994 original size:23 final size:23
Alignment explanation
Indices: 41664964--41665008 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
41664954 TTGCAAACTG
*
41664964 TTAAAGCCTTTATTGTCCTATAT
1 TTAAAGCCTTCATTGTCCTATAT
41664987 TTAAAGCCTTCATTGTCCTATA
1 TTAAAGCCTTCATTGTCCTATA
41665009 CTTGCAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (23 bp):
TTAAAGCCTTCATTGTCCTATAT
Done.