Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008495.1 Hibiscus syriacus cultivar Beakdansim tig00111338_pilon, whole genome shotgun sequence
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: 5120959
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 21
Found at i:2323940 original size:14 final size:14
Alignment explanation
Indices: 2323909--2323983 Score: 64
Period size: 14 Copynumber: 5.4 Consensus size: 14
2323899 AAACTAATAT
*
2323909 AACTATAT-T-TTT
1 AACTATATGTATTA
*
2323921 AACTATATGTATTG
1 AACTATATGTATTA
* *
2323935 AACTATAATAATATAA
1 AACTAT-AT-GTATTA
2323951 AACTATATGTATTA
1 AACTATATGTATTA
* *
2323965 AACTACATGTATTG
1 AACTATATGTATTA
2323979 AACTA
1 AACTA
2323984 ATATAATATA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
12 8 0.16
13 1 0.02
14 29 0.57
15 4 0.08
16 9 0.18
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (14 bp):
AACTATATGTATTA
Found at i:2324037 original size:8 final size:8
Alignment explanation
Indices: 2324024--2324149 Score: 50
Period size: 8 Copynumber: 16.0 Consensus size: 8
2324014 TAAACTACAT
2324024 ACTATAAA
1 ACTATAAA
*
2324032 ACTATATA
1 ACTATAAA
*
2324040 A-TATGAA
1 ACTATAAA
*
2324047 ACTAGAAA
1 ACTATAAA
*
2324055 ACTAGAAA
1 ACTATAAA
2324063 ACTATATAA
1 ACTATA-AA
*
2324072 AATATATAA
1 ACTATA-AA
*
2324081 A-TAATTAA
1 ACT-ATAAA
2324089 A-TAT--A
1 ACTATAAA
* *
2324094 AGTATTAA
1 ACTATAAA
2324102 ACTATATTAA
1 ACTATA--AA
* *
2324112 ACTACATA
1 ACTATAAA
2324120 A-TATAAA
1 ACTATAAA
*
2324127 ACTATAAT
1 ACTATAAA
*
2324135 ACTATATA
1 ACTATAAA
2324143 A-TATAAA
1 ACTATAAA
2324150 GTATTAAAAT
Statistics
Matches: 91, Mismatches: 18, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
5 2 0.02
6 3 0.03
7 17 0.19
8 49 0.54
9 13 0.14
10 7 0.08
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (8 bp):
ACTATAAA
Found at i:2324041 original size:95 final size:92
Alignment explanation
Indices: 2323838--2324050 Score: 248
Period size: 95 Copynumber: 2.3 Consensus size: 92
2323828 AAGTATATAA
* * * *
2323838 TATAAAACTATATAATATAAAGTATATATATATATATATATATATTGAACTGCATAATATAAAAC
1 TATAAAACTATATAATATAAACTATATATATATAAATACATATATTGAACTACATAATATAAAAC
* * * *
2323903 TAATATAACTATATTTTTAACTATATG
66 TAATATAAATATATTTTAAACTACATC
** * * *
2323930 TATTGAACTATAATAATATAAAACTATATGTAT-TAAACTACATGTATTGAACTAATATAATATA
1 TATAAAACTAT-ATAATAT-AAACTATATATATATAAA-TACATATATTGAACT-ACATAATATA
2323994 AAACTAATATAAATATATTTTAAACTACATAC
62 AAACTAATATAAATATATTTTAAACTACAT-C
2324026 TATAAAACTATATAATATGAAACTA
1 TATAAAACTATATAATAT-AAACTA
2324051 GAAAACTAGA
Statistics
Matches: 100, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
92 9 0.09
93 10 0.10
94 24 0.24
95 48 0.48
96 9 0.09
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (92 bp):
TATAAAACTATATAATATAAACTATATATATATAAATACATATATTGAACTACATAATATAAAAC
TAATATAAATATATTTTAAACTACATC
Found at i:2324110 original size:23 final size:22
Alignment explanation
Indices: 2324061--2324179 Score: 80
Period size: 25 Copynumber: 5.7 Consensus size: 22
2324051 GAAAACTAGA
2324061 AAACTATA-TAAA-AT-ATA-T
1 AAACTATATTAAATATAATATT
2324079 AAA-TA-ATTAAATATAAGTATT
1 AAACTATATTAAATATAA-TATT
*
2324100 AAACTATATTAAACTACATAATATA
1 AAACTATATTAAA-T--ATAATATT
* *
2324125 AAACTATAATACTATATAATA-T
1 AAACTATATTA-AATATAATATT
*
2324147 AAA--GTATTAAA-ATAATATT
1 AAACTATATTAAATATAATATT
2324166 AAACTATA-TAAATA
1 AAACTATATTAAATA
2324180 ATTAAATAAG
Statistics
Matches: 78, Mismatches: 8, Indels: 27
0.69 0.07 0.24
Matches are distributed among these distances:
16 1 0.01
17 6 0.08
18 11 0.14
19 6 0.08
20 10 0.13
21 7 0.09
22 5 0.06
23 12 0.15
24 1 0.01
25 14 0.18
26 5 0.06
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (22 bp):
AAACTATATTAAATATAATATT
Found at i:2324130 original size:25 final size:23
Alignment explanation
Indices: 2324091--2324149 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 23
2324081 ATAATTAAAT
*
2324091 ATAAGTATTAAACTATATTAAACTAC
1 ATAA-TATAAAACTATA--AAACTAC
* *
2324117 ATAATATAAAACTATAATACTAT
1 ATAATATAAAACTATAAAACTAC
2324140 ATAATATAAA
1 ATAATATAAA
2324150 GTATTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.50
25 11 0.37
26 4 0.13
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.34
Consensus pattern (23 bp):
ATAATATAAAACTATAAAACTAC
Found at i:2324174 original size:28 final size:26
Alignment explanation
Indices: 2324061--2324195 Score: 70
Period size: 28 Copynumber: 5.1 Consensus size: 26
2324051 GAAAACTAGA
*
2324061 AAACTATATAAAATATATAAAT-A-ATT
1 AAACTATATAATAT-TA-AAATAATATT
* *
2324087 AAA-TATA-AGTATTAAACT-ATATT
1 AAACTATATAATATTAAAATAATATT
* *
2324110 AAACTACATAATATAAAACTATAATACTAT
1 AAACTATATAATATTAAA--ATAATA-T-T
2324140 ATAA-TATA-AAGTATTAAAATAATATT
1 A-AACTATATAA-TATTAAAATAATATT
2324166 AAACTATATAAATAATT-AAATAAGTATT
1 AAACTATAT-AAT-ATTAAAATAA-TATT
2324194 AA
1 AA
2324196 GTAATAAATT
Statistics
Matches: 85, Mismatches: 9, Indels: 28
0.70 0.07 0.23
Matches are distributed among these distances:
22 4 0.05
23 8 0.09
24 6 0.07
25 13 0.15
26 9 0.11
27 9 0.11
28 20 0.24
29 3 0.04
30 11 0.13
31 2 0.02
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (26 bp):
AAACTATATAATATTAAAATAATATT
Found at i:2324276 original size:21 final size:21
Alignment explanation
Indices: 2324250--2324292 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2324240 AATGTAACCA
*
2324250 AAATT-AATACATTTTAAGACT
1 AAATTAAATA-ATTTTAAAACT
2324271 AAATTAAATAATTTTAAAACT
1 AAATTAAATAATTTTAAAACT
2324292 A
1 A
2324293 TGGGAAAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.37
Consensus pattern (21 bp):
AAATTAAATAATTTTAAAACT
Found at i:2324580 original size:28 final size:28
Alignment explanation
Indices: 2324540--2324596 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
2324530 TTATTCATCG
2324540 CTTGATCATCCCTTGTTCATCCATAACA
1 CTTGATCATCCCTTGTTCATCCATAACA
2324568 CTTGATCATCCCTTGTTCATCCATAACA
1 CTTGATCATCCCTTGTTCATCCATAACA
2324596 C
1 C
2324597 CCTGTTTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.33, G:0.07, T:0.35
Consensus pattern (28 bp):
CTTGATCATCCCTTGTTCATCCATAACA
Found at i:2325171 original size:162 final size:162
Alignment explanation
Indices: 2324797--2325278 Score: 696
Period size: 163 Copynumber: 3.0 Consensus size: 162
2324787 CCTGTTCCTC
* * * * *
2324797 GTTTAATCCTTACAAACACCCAAATACTTTTCCCCGATATGTTTTTCAAGATCA-AAACCCCCAA
1 GTTTGATCCTTACAAACA-CTAAATACTTTTCCCCAATCTATTTTTCAAGAT-ATAAACCCCCAA
* *
2324861 ATCAAAGTACTATTCATCTTCTTCCCTAACCCTAAATCCCAAATCCCATTGTTCATCCCCCTTCC
64 ATCAAAGCACTATTCATCTTATTCCCTAACCCTAAATCCCAAATCCCATTGTTCAT-CCCCTTCC
* * *
2324926 ACTTCTTCAACTGATACTCTTCCTCTTCCCCTTCT
128 CCTTCTTCAACTAAGACTCTTCCTCTTCCCCTTCT
* *
2324961 GTTTGATCCTTAAAAACACTAAATACTCTTCCCCAATCTATTTTTCAAGATATAAACCCCCAAAT
1 GTTTGATCCTTACAAACACTAAATACTTTTCCCCAATCTATTTTTCAAGATATAAACCCCCAAAT
* *
2325026 CAAAGCACTATTCATCTTATTCCCTAACCTTAAATCCCAAATCCCACTGTTCATCCCCTTCCCCT
66 CAAAGCACTATTCATCTTATTCCCTAACCCTAAATCCCAAATCCCATTGTTCATCCCCTTCCCCT
* *
2325091 TCTTCAACTAAGACTCTTCCTCTTCCCTTTTT
131 TCTTCAACTAAGACTCTTCCTCTTCCCCTTCT
** * *
2325123 GTTTGATCCTTACAAACACTAAGCACTTTTCCCCAATCTATTTTTCAAGATCTAAACCCCCAAAC
1 GTTTGATCCTTACAAACACTAAATACTTTTCCCCAATCTATTTTTCAAGATATAAACCCCCAAAT
* *
2325188 CAAAGCACTATTCATCTTATTCTCATAACCCTAAATCCCAAATCCCATTATTCATCCCTCTTCCC
66 CAAAGCACTATTCATCTTATTC-CCTAACCCTAAATCCCAAATCCCATTGTTCATCCC-CTTCCC
* *
2325253 ATTCTTCAACGAAGACTCTTCCTCTT
129 CTTCTTCAACTAAGACTCTTCCTCTT
2325279 TCTCCCATAA
Statistics
Matches: 287, Mismatches: 28, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
162 120 0.42
163 121 0.42
164 46 0.16
ACGTcount: A:0.28, C:0.34, G:0.04, T:0.34
Consensus pattern (162 bp):
GTTTGATCCTTACAAACACTAAATACTTTTCCCCAATCTATTTTTCAAGATATAAACCCCCAAAT
CAAAGCACTATTCATCTTATTCCCTAACCCTAAATCCCAAATCCCATTGTTCATCCCCTTCCCCT
TCTTCAACTAAGACTCTTCCTCTTCCCCTTCT
Found at i:2325645 original size:12 final size:13
Alignment explanation
Indices: 2325628--2325656 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2325618 GGTTTATATT
2325628 TTTTTGTTTT-TG
1 TTTTTGTTTTCTG
2325640 TTTTTGTTTTCTG
1 TTTTTGTTTTCTG
2325653 TTTT
1 TTTT
2325657 GTATATGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.00, C:0.03, G:0.14, T:0.83
Consensus pattern (13 bp):
TTTTTGTTTTCTG
Found at i:2326380 original size:25 final size:25
Alignment explanation
Indices: 2326333--2326405 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 25
2326323 TAAAATTTTC
*
2326333 TTTTTTTATATATATTT-TGTTTTGTA
1 TTTTTTTTTAT-TATTTGT-TTTTGTA
*
2326359 TTTTTTTTTATTATTTGTTTTTTTA
1 TTTTTTTTTATTATTTGTTTTTGTA
* *
2326384 TTTCTTTTCATT-TTATGTTTTT
1 TTTTTTTTTATTATT-TGTTTTT
2326406 TAGTGCATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 2 0.05
25 28 0.68
26 11 0.27
ACGTcount: A:0.14, C:0.03, G:0.05, T:0.78
Consensus pattern (25 bp):
TTTTTTTTTATTATTTGTTTTTGTA
Found at i:2326391 original size:24 final size:22
Alignment explanation
Indices: 2326347--2326406 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 22
2326337 TTTATATATA
2326347 TTTTGTTTTGTATTTTTTTTT-AT
1 TTTTGTTTT-T-TTTTTTTTTCAT
2326370 TATTTGTTTTTTTATTTCTTTTCAT
1 T-TTTGTTTTTTT-TTT-TTTTCAT
2326395 TTTATGTTTTTT
1 TTT-TGTTTTTT
2326407 AGTGCATTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
22 2 0.06
23 5 0.16
24 14 0.44
25 11 0.34
ACGTcount: A:0.10, C:0.03, G:0.07, T:0.80
Consensus pattern (22 bp):
TTTTGTTTTTTTTTTTTTTCAT
Found at i:2326697 original size:5 final size:5
Alignment explanation
Indices: 2326689--2326731 Score: 50
Period size: 5 Copynumber: 7.8 Consensus size: 5
2326679 ATGTTTTTGT
2326689 TTTTA TTTTA TTTTA TGTTTTA TTTTA TTTTA TATGTTA TTTT
1 TTTTA TTTTA TTTTA --TTTTA TTTTA TTTTA T-T-TTA TTTT
2326732 CTGTTTTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
5 23 0.68
6 2 0.06
7 9 0.26
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:2326702 original size:17 final size:17
Alignment explanation
Indices: 2326689--2326731 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
2326679 ATGTTTTTGT
2326689 TTTTATTTTATTTTATG
1 TTTTATTTTATTTTATG
*
2326706 TTTTATTTTATTTTATA
1 TTTTATTTTATTTTATG
*
2326723 TGTTATTTT
1 TTTTATTTT
2326732 CTGTTTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (17 bp):
TTTTATTTTATTTTATG
Found at i:2326803 original size:27 final size:27
Alignment explanation
Indices: 2326743--2326804 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
2326733 TGTTTTCTTT
*
2326743 TTTTTTCTGTATGACTGTATACATTATA
1 TTTTTT-TATATGACTGTATACATTATA
* * *
2326771 TGTTTTTATATGACTGTATGCATTATG
1 TTTTTTTATATGACTGTATACATTATA
2326798 TTTTTTT
1 TTTTTTT
2326805 TATTATATAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 24 0.83
28 5 0.17
ACGTcount: A:0.21, C:0.08, G:0.13, T:0.58
Consensus pattern (27 bp):
TTTTTTTATATGACTGTATACATTATA
Found at i:2326846 original size:18 final size:18
Alignment explanation
Indices: 2326825--2326859 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2326815 TTTCTATTTT
* *
2326825 TTTATTTGTTTTCTGTTA
1 TTTATTTATTTCCTGTTA
2326843 TTTATTTATTTCCTGTT
1 TTTATTTATTTCCTGTT
2326860 TTCTGTATGC
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:0.11, C:0.09, G:0.09, T:0.71
Consensus pattern (18 bp):
TTTATTTATTTCCTGTTA
Found at i:2326883 original size:15 final size:15
Alignment explanation
Indices: 2326862--2326905 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
2326852 TTCCTGTTTT
2326862 CTGTATGCATTATGA
1 CTGTATGCATTATGA
*
2326877 TTGTATGCATTATGA
1 CTGTATGCATTATGA
*
2326892 CTGGATGCATTATG
1 CTGTATGCATTATG
2326906 TTATTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.41
Consensus pattern (15 bp):
CTGTATGCATTATGA
Found at i:2330197 original size:16 final size:16
Alignment explanation
Indices: 2330158--2330191 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2330148 TTATAACTTA
2330158 CAAGTCAGATAAATAT
1 CAAGTCAGATAAATAT
*
2330174 CAAGTCAGGTAAATAT
1 CAAGTCAGATAAATAT
2330190 CA
1 CA
2330192 GTTCAGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (16 bp):
CAAGTCAGATAAATAT
Found at i:2330261 original size:16 final size:16
Alignment explanation
Indices: 2330242--2330272 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2330232 CAGTAACATA
*
2330242 TCAGGTTTATAACAGG
1 TCAGGTTAATAACAGG
2330258 TCAGGTTAATAACAG
1 TCAGGTTAATAACAG
2330273 ATCGGGTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (16 bp):
TCAGGTTAATAACAGG
Found at i:2331867 original size:2 final size:2
Alignment explanation
Indices: 2331860--2331912 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
2331850 TGAACCCTCT
2331860 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2331901 TA TA TA TA TA TA
1 TA TA TA TA TA TA
2331913 GAGAGAGAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2331917 original size:2 final size:2
Alignment explanation
Indices: 2331912--2331951 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2331902 ATATATATAT
2331912 AG AG AG AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2331952 TTGTGGTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2332505 original size:49 final size:49
Alignment explanation
Indices: 2332429--2332527 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
2332419 GATGAACTCT
*
2332429 TGGAATATGGCTAGTGGTATCATAACAGTATGGTAATTGAGATACCCCC
1 TGGAATATGGCTAGTGGTATCAAAACAGTATGGTAATTGAGATACCCCC
*
2332478 TGGAATATGGCTAGTGGTATCAAAACAGTATGGTAATTGAGATATCCCC
1 TGGAATATGGCTAGTGGTATCAAAACAGTATGGTAATTGAGATACCCCC
2332527 T
1 T
2332528 ATCATGTATC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.29
Consensus pattern (49 bp):
TGGAATATGGCTAGTGGTATCAAAACAGTATGGTAATTGAGATACCCCC
Found at i:2333842 original size:43 final size:43
Alignment explanation
Indices: 2333781--2333866 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
2333771 AATTATCTTC
2333781 TACTTGATAGAGTAGAAAGTACAACATAGTGCTTGAAATTGAT
1 TACTTGATAGAGTAGAAAGTACAACATAGTGCTTGAAATTGAT
2333824 TACTTGATAGAGTAGAAAGTACAACATAGTGCTTGAAATTGAT
1 TACTTGATAGAGTAGAAAGTACAACATAGTGCTTGAAATTGAT
2333867 CTCTCGACCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (43 bp):
TACTTGATAGAGTAGAAAGTACAACATAGTGCTTGAAATTGAT
Found at i:2353548 original size:16 final size:15
Alignment explanation
Indices: 2353527--2353602 Score: 75
Period size: 15 Copynumber: 4.9 Consensus size: 15
2353517 ATTCAATCAG
2353527 AACAAAAAGATAAAAA
1 AACAAAAAGA-AAAAA
*
2353543 AACAAAAAAGAAAAGA
1 AAC-AAAAAGAAAAAA
*
2353559 AACAAAAA-AGAAGAA
1 AACAAAAAGA-AAAAA
2353574 AA-AAAAAGAACAAAA
1 AACAAAAAGAA-AAAA
*
2353589 ATCAAAAAGAAAAA
1 AACAAAAAGAAAAA
2353603 GGGACAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
14 7 0.14
15 18 0.36
16 18 0.36
17 7 0.14
ACGTcount: A:0.82, C:0.07, G:0.09, T:0.03
Consensus pattern (15 bp):
AACAAAAAGAAAAAA
Found at i:2353552 original size:17 final size:16
Alignment explanation
Indices: 2353530--2353602 Score: 73
Period size: 16 Copynumber: 4.7 Consensus size: 16
2353520 CAATCAGAAC
2353530 AAAAAGATAAAAAAACA
1 AAAAAGA-AAAAAAACA
*
2353547 AAAAAGAAAAGAAACA
1 AAAAAGAAAAAAAACA
*
2353563 AAAAAG--AAGAAA-A
1 AAAAAGAAAAAAAACA
*
2353576 AAAAAGAACAAAAATC-
1 AAAAAGAA-AAAAAACA
2353592 AAAAAGAAAAA
1 AAAAAGAAAAA
2353603 GGGACAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
13 7 0.14
14 6 0.12
15 3 0.06
16 26 0.53
17 7 0.14
ACGTcount: A:0.82, C:0.05, G:0.10, T:0.03
Consensus pattern (16 bp):
AAAAAGAAAAAAAACA
Found at i:2353602 original size:23 final size:23
Alignment explanation
Indices: 2353530--2353613 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 23
2353520 CAATCAGAAC
2353530 AAAAAGATA-AAAAAACAAAAA-A
1 AAAAAGA-ACAAAAAACAAAAAGA
* *
2353552 GAAAAGAAACAAAAAAGAAGAAA-A
1 AAAAAG-AACAAAAAACAA-AAAGA
*
2353576 AAAAAGAACAAAAATCAAAAAGA
1 AAAAAGAACAAAAAACAAAAAGA
* *
2353599 AAAAGGGACAAAAAA
1 AAAAAGAACAAAAAA
2353614 ACACATGCAA
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
22 9 0.18
23 32 0.64
24 9 0.18
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.02
Consensus pattern (23 bp):
AAAAAGAACAAAAAACAAAAAGA
Found at i:2355279 original size:106 final size:106
Alignment explanation
Indices: 2355153--2356228 Score: 1625
Period size: 106 Copynumber: 10.2 Consensus size: 106
2355143 ATATCGTGCC
* * * * * *
2355153 ACTCGAGACAACACAAGTTCAACTCCACAACGAAGGGACGGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
**
2355218 AATTTCAGAGCCAATTTCAACTTCACAGCGATTGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
2355259 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCACTGGTTGTCAGCAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2355324 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
2355365 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTATCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2355430 AATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
2355471 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
2355536 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
2355577 ACTCGAGACAAAGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
2355642 AATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
2355683 ACTCCAGACAATGCAAGTTCAACTTCACGACGATGGGACCGCTGGTTGTCAACAAACAATTTACC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
2355748 AATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
2355789 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2355854 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
2355895 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
2355960 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
2356001 ACTCGAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
2356066 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
2356107 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
2356172 GA-TTCTAGAGCAAATTTCAACTTCAC-GACGTAGGATATTGG
66 AATTTC-AGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
* * *
2356213 CCTCAAAACAACGCAA
1 ACTCCAGACAACGCAA
2356229 CTTACATTGG
Statistics
Matches: 893, Mismatches: 75, Indels: 4
0.92 0.08 0.00
Matches are distributed among these distances:
105 3 0.00
106 890 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:2358080 original size:2 final size:2
Alignment explanation
Indices: 2358073--2358110 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2358063 TCTCATACCA
2358073 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2358111 TGTTGTTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2358234 original size:24 final size:27
Alignment explanation
Indices: 2358179--2358239 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 27
2358169 GCATTTATAA
*
2358179 TTTATTTTGATTTCTTTCTCCTTTTCACT
1 TTTATTTTGATTTCATTCTCCTTTT--CT
2358208 TTTATTTT-ATTTCATT-TCCTTTT-T
1 TTTATTTTGATTTCATTCTCCTTTTCT
2358232 TTTATTTT
1 TTTATTTT
2358240 TTACTAGATC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 9 0.29
27 7 0.23
28 7 0.23
29 8 0.26
ACGTcount: A:0.11, C:0.15, G:0.02, T:0.72
Consensus pattern (27 bp):
TTTATTTTGATTTCATTCTCCTTTTCT
Found at i:2364441 original size:31 final size:29
Alignment explanation
Indices: 2364385--2364476 Score: 94
Period size: 31 Copynumber: 3.0 Consensus size: 29
2364375 AACTCTAATA
*
2364385 GCTTATCAAAGCCCATGGCCACCTATCACCTT
1 GCTTATC-AAG-CC-TGGCCGCCTATCACCTT
* *
2364417 TCTTATCACAAGCTTGGCCGCCTATCACCTT
1 GCTTAT--CAAGCCTGGCCGCCTATCACCTT
**
2364448 GCTTATCAAGCCTAACCGCCTATCACCTT
1 GCTTATCAAGCCTGGCCGCCTATCACCTT
2364477 CAAGAAGACT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
29 20 0.39
31 21 0.41
32 6 0.12
33 3 0.06
34 1 0.02
ACGTcount: A:0.23, C:0.37, G:0.12, T:0.28
Consensus pattern (29 bp):
GCTTATCAAGCCTGGCCGCCTATCACCTT
Found at i:2364467 original size:29 final size:30
Alignment explanation
Indices: 2364406--2364476 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
2364396 CCCATGGCCA
* * **
2364406 CCTATCACCTTTCTTATCACAAGCTTGGCCG
1 CCTATCACCTTGCTTAT-ACAAGCCTAACCG
2364437 CCTATCACCTTGCTTAT-CAAGCCTAACCG
1 CCTATCACCTTGCTTATACAAGCCTAACCG
2364466 CCTATCACCTT
1 CCTATCACCTT
2364477 CAAGAAGACT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 20 0.56
31 16 0.44
ACGTcount: A:0.21, C:0.38, G:0.10, T:0.31
Consensus pattern (30 bp):
CCTATCACCTTGCTTATACAAGCCTAACCG
Found at i:2366134 original size:18 final size:19
Alignment explanation
Indices: 2366099--2366135 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2366089 CACGGAATGT
2366099 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
2366119 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
2366136 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:2366313 original size:34 final size:34
Alignment explanation
Indices: 2366282--2366345 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
2366272 TACAAATTGT
*
2366282 AAAATATTTATAT-TTTCTTTA-AAATTTAAATTC
1 AAAATATTTATATATTT-TTTACAAAATTAAATTC
*
2366315 ATAATATTTATATATTTTTTACAAAATTAAA
1 AAAATATTTATATATTTTTTACAAAATTAAA
2366346 AAGAGAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 16 0.59
34 11 0.41
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (34 bp):
AAAATATTTATATATTTTTTACAAAATTAAATTC
Found at i:2366589 original size:20 final size:20
Alignment explanation
Indices: 2366566--2366629 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 20
2366556 GAATATGTAA
2366566 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
2366586 ATCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
2366606 AATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
2366627 ATC
1 ATC
2366630 ACGTTGCGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
19 2 0.05
20 18 0.49
21 15 0.41
22 2 0.05
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:2366610 original size:41 final size:41
Alignment explanation
Indices: 2366564--2366661 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 41
2366554 ACGAATATGT
*
2366564 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCACAACGCGATAATACA
* ***
2366605 TAATCGCAACGCGATTCTGACTATCACGTTGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCACAACGCGATAATACA
* *
2366646 AAATCACAATGCGATT
1 AAATCGCAACGCGATT
2366662 TTCAAAGCGC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.23
Consensus pattern (41 bp):
AAATCGCAACGCGATTCTGACTATCACAACGCGATAATACA
Found at i:2366826 original size:22 final size:22
Alignment explanation
Indices: 2366798--2366848 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2366788 CTACGGCGAC
* * *
2366798 ATCCGTCCCCATCTTCGATGAA
1 ATCCGTCCCCACCTCCGACGAA
*
2366820 ATCCGTCCCCACCTCCGGCGAA
1 ATCCGTCCCCACCTCCGACGAA
2366842 ATCCGTC
1 ATCCGTC
2366849 TATCTCCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCACCTCCGACGAA
Found at i:2367221 original size:19 final size:19
Alignment explanation
Indices: 2367197--2367298 Score: 79
Period size: 19 Copynumber: 5.5 Consensus size: 19
2367187 AGGATCGCAA
2367197 CGATAGTCAATTCGCGTTG
1 CGATAGTCAATTCGCGTTG
* *
2367216 CGATAGTCATTTTCGTGTTG
1 CGATAGTCA-ATTCGCGTTG
* ** *
2367236 CAATTTTCATTTCGCGTTG
1 CGATAGTCAATTCGCGTTG
*
2367255 CGAT--T--A-TCTCGTTG
1 CGATAGTCAATTCGCGTTG
2367269 CGATAGTCAAATTCGCGTTGG
1 CGATAGTC-AATTCGCGTT-G
2367290 CGATAGTCA
1 CGATAGTCA
2367299 TTTTCATGTT
Statistics
Matches: 65, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
14 11 0.17
16 1 0.02
17 1 0.02
19 22 0.34
20 21 0.32
21 9 0.14
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (19 bp):
CGATAGTCAATTCGCGTTG
Found at i:2367235 original size:20 final size:19
Alignment explanation
Indices: 2367197--2367301 Score: 85
Period size: 20 Copynumber: 5.6 Consensus size: 19
2367187 AGGATCGCAA
*
2367197 CGATAGTCAATTCGCGTTG
1 CGATAGTCATTTCGCGTTG
*
2367216 CGATAGTCATTTTCGTGTTG
1 CGATAGTCA-TTTCGCGTTG
* **
2367236 CAATTTTCATTTCGCGTTG
1 CGATAGTCATTTCGCGTTG
*
2367255 CGAT--T-A--TCTCGTTG
1 CGATAGTCATTTCGCGTTG
*
2367269 CGATAGTCAAATTCGCGTTGG
1 CGATAGTC-ATTTCGCGTT-G
2367290 CGATAGTCATTT
1 CGATAGTCATTT
2367302 TCATGTTGCG
Statistics
Matches: 68, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 1 0.01
18 1 0.01
19 21 0.31
20 23 0.34
21 9 0.13
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (19 bp):
CGATAGTCATTTCGCGTTG
Found at i:2369015 original size:19 final size:20
Alignment explanation
Indices: 2368955--2369022 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
2368945 AAACTTAAAA
* *
2368955 ATCGCAACGTGAAAATGACT
1 ATCGCAACGCGGAAATGACT
*
2368975 ATCGCAACGCGGAAAGGACT
1 ATCGCAACGCGGAAATGACT
* *
2368995 ATCGCAATGC-GAATTGACT
1 ATCGCAACGCGGAAATGACT
2369014 ATCGCAACG
1 ATCGCAACG
2369023 GATAATCGTA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 15 0.37
20 26 0.63
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:2369127 original size:19 final size:19
Alignment explanation
Indices: 2369105--2369150 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2369095 TAGTTTCACG
*
2369105 TTGCGATTTTGGTTTCGCA
1 TTGCGATTTTGATTTCGCA
*
2369124 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTGATTTCGCA
2369143 TTGCGATT
1 TTGCGATT
2369151 ATCCCGTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.15, G:0.22, T:0.50
Consensus pattern (19 bp):
TTGCGATTTTGATTTCGCA
Found at i:2369209 original size:20 final size:19
Alignment explanation
Indices: 2369155--2369223 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 19
2369145 GCGATTATCC
*
2369155 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-ATTTCG
*
2369175 TGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
2369195 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
*
2369215 CATTGCGAT
1 CGTTGCGAT
2369224 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.07
20 37 0.86
21 3 0.07
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:2369233 original size:20 final size:20
Alignment explanation
Indices: 2369210--2369253 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2369200 CGATAGTCAT
*
2369210 TTTCGCATTGCGATTTTAAG
1 TTTCGCATTGCAATTTTAAG
**
2369230 TTTCGTGTTGCAATTTTAAG
1 TTTCGCATTGCAATTTTAAG
2369250 TTTC
1 TTTC
2369254 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.50
Consensus pattern (20 bp):
TTTCGCATTGCAATTTTAAG
Found at i:2369835 original size:42 final size:42
Alignment explanation
Indices: 2369736--2369856 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 42
2369726 CCGACTCACC
* * * *
2369736 TGTCATCGTTCAAGAGGCCTCTCCTA-TCGTTCAAGAGGCCCC
1 TGTCATCGTTCAAGAGTCCCCTCCCACT-GTTCAAGAGGCCCA
* **
2369778 TATCATCCCTCAAGAGTCCCCTCCCACTGTTCAAGAGGCCCA
1 TGTCATCGTTCAAGAGTCCCCTCCCACTGTTCAAGAGGCCCA
* **
2369820 TGTCATCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TGTCATCGTTCAAGA-GTCCCCTCCCACTGTTCAAGAG
2369857 CCTGATTCAT
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
42 61 0.95
43 3 0.05
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (42 bp):
TGTCATCGTTCAAGAGTCCCCTCCCACTGTTCAAGAGGCCCA
Found at i:2371475 original size:63 final size:63
Alignment explanation
Indices: 2371397--2371559 Score: 258
Period size: 61 Copynumber: 2.6 Consensus size: 63
2371387 TAGCATTTTT
2371397 TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTG
1 TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTG
2371460 TGCTTGTTTAATTGATTTGTAAAAGTTGATTTG--TAATTGATGTGTAAATAATTCTTATTTG
1 TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTG
* *
2371521 TTCTTATTTAATTGATTGAAATGTAAAAGTTGATTTGTT
1 TGCTTGTTTAATTGATT----TGTAAAAGTTGATTTGTT
2371560 GATTTCAATC
Statistics
Matches: 92, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
61 43 0.47
63 33 0.36
65 16 0.17
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.52
Consensus pattern (63 bp):
TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTG
Found at i:2371648 original size:20 final size:20
Alignment explanation
Indices: 2371613--2371664 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2371603 GTACACTTTT
* *
2371613 GCAACGCTAAATTCAAAATC
1 GCAACGCGAAAGTCAAAATC
*
2371633 GCAATGCGAAAGTCAAAATC
1 GCAACGCGAAAGTCAAAATC
2371653 GCAACGCGAAAG
1 GCAACGCGAAAG
2371665 CCAATTCGCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.44, C:0.23, G:0.19, T:0.13
Consensus pattern (20 bp):
GCAACGCGAAAGTCAAAATC
Found at i:2371737 original size:20 final size:20
Alignment explanation
Indices: 2371712--2371774 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
2371702 TTCTCTTTGT
*
2371712 GATAGTCAAATTCCCGTTGC
1 GATAGTCAAATTCACGTTGC
2371732 GATAGTCAAATTCACGTTGC
1 GATAGTCAAATTCACGTTGC
*
2371752 GATAGTCAAATTCGCGTTGC
1 GATAGTCAAATTCACGTTGC
2371772 GAT
1 GAT
2371775 TTTTGCGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (20 bp):
GATAGTCAAATTCACGTTGC
Found at i:2371875 original size:20 final size:20
Alignment explanation
Indices: 2371836--2371875 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2371826 GATTTTTGAG
**
2371836 TGCGATAGTCAAATTCATGT
1 TGCGATAGTCAAATGAATGT
*
2371856 TGCGATATTCAAATGAATGT
1 TGCGATAGTCAAATGAATGT
2371876 ATAATAAGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (20 bp):
TGCGATAGTCAAATGAATGT
Found at i:2372046 original size:138 final size:137
Alignment explanation
Indices: 2371840--2372117 Score: 470
Period size: 138 Copynumber: 2.0 Consensus size: 137
2371830 TTTGAGTGCG
**
2371840 ATAGTCAAATTCATGTTGCGATATTCAAATGAATGTATAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCACATTGCGATATTCAAATGAATGTATAATAAGTGATAACAACTGAACAGATCA
2371905 TAGCAATGTTCAAACTCAAGTTACTAATACATGCATAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACT-ATACATGCATAACTGAAAATGTTAAAAGTTT--ACATAA
2371970 AA-A-ACATA
128 AATACACATA
* *
2371978 ATAGTCAAATTCGCATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCACATTGCGATATTCAAATGAATGTATAATAAGTGATAACAACTGAACAGATCA
*
2372043 TAGCAATGTTCAAACTCAAGTTACTATACATGCCTAACTGAAAATGTTAAAAGTTTACATAAAAT
66 TAGCAATGTTCAAACTCAAGTTACTATACATGCATAACTGAAAATGTTAAAAGTTTACATAAAAT
2372108 ACACATA
131 ACACATA
2372115 ATA
1 ATA
2372118 CAACGTTTGC
Statistics
Matches: 133, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
135 8 0.06
136 1 0.01
137 38 0.29
138 86 0.65
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (137 bp):
ATAGTCAAATTCACATTGCGATATTCAAATGAATGTATAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTATACATGCATAACTGAAAATGTTAAAAGTTTACATAAAAT
ACACATA
Found at i:2374745 original size:20 final size:20
Alignment explanation
Indices: 2374720--2374790 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
2374710 TTGAAATTCA
*
2374720 GCGTTGCGACAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
**
2374740 GCGTTGCGATTATGT-ATTATC
1 GCGTTGCGA-TA-GTCAGAATC
2374761 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
2374781 GCGTTGCGAT
1 GCGTTGCGAT
2374791 TTACATATTC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.05
20 25 0.58
21 14 0.33
22 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAATC
Found at i:2374867 original size:20 final size:19
Alignment explanation
Indices: 2374844--2374889 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2374834 GGAAACTGAT
* *
2374844 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
2374864 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
2374883 TTGCGAT
1 TTGCGAT
2374890 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:2374879 original size:19 final size:19
Alignment explanation
Indices: 2374855--2374891 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2374845 TGCGATACTG
*
2374855 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
2374874 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
2374892 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:2377386 original size:114 final size:112
Alignment explanation
Indices: 2377228--2377459 Score: 383
Period size: 114 Copynumber: 2.1 Consensus size: 112
2377218 ACTCACCCGA
* *
2377228 TGGCCAGAGCTATAGCAAAAATCACGAAGAACTTGTTGAATTACATCTAGTTGATCCAAAGAAAC
1 TGGCCCGAGCTATAGCAAAAATCACAAAGAACTTGTTGAATTACATCTAGTTGATCCAAAGAAAC
*
2377293 CTTAGCAAACAATACGAAATCATCAACAAAAAAATAGGTGAGTCAAAGG
66 CTCAGCAAACAATACGAAATCATC-AC-AAAAAATAGGTGAGTCAAAGG
* * *
2377342 TGGCCCGAGCTATAGCAGAAATCACAAAGAACTTGTTGGATTACATCTAGTTGATCCAAAGAAGC
1 TGGCCCGAGCTATAGCAAAAATCACAAAGAACTTGTTGAATTACATCTAGTTGATCCAAAGAAAC
*
2377407 CTCAGCAAACAATACGAGATCATCACAAAAAATAGGTGAGTCAAAGG
66 CTCAGCAAACAATACGAAATCATCACAAAAAATAGGTGAGTCAAAGG
2377454 TGGCCC
1 TGGCCC
2377460 TCCCCGAGAT
Statistics
Matches: 111, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
112 27 0.24
113 2 0.02
114 82 0.74
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.20
Consensus pattern (112 bp):
TGGCCCGAGCTATAGCAAAAATCACAAAGAACTTGTTGAATTACATCTAGTTGATCCAAAGAAAC
CTCAGCAAACAATACGAAATCATCACAAAAAATAGGTGAGTCAAAGG
Found at i:2382572 original size:19 final size:19
Alignment explanation
Indices: 2382534--2382573 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2382524 CGAATAATTG
* *
2382534 AATCGAATATAATATTTTA
1 AATCGAATATAAAATCTTA
2382553 AATCGAATATAAAATCTTA
1 AATCGAATATAAAATCTTA
2382572 AA
1 AA
2382574 ATACTTAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (19 bp):
AATCGAATATAAAATCTTA
Found at i:2393467 original size:22 final size:21
Alignment explanation
Indices: 2393439--2393486 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
2393429 AAAAATGTTG
* *
2393439 AAAAAAATAGCAGTTCGAAAA
1 AAAAAAAAAACAGTTCGAAAA
*
2393460 AGAAAAAAAAACTGTTCGAAAA
1 A-AAAAAAAAACAGTTCGAAAA
2393482 AAAAA
1 AAAAA
2393487 GACATGAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.67, C:0.08, G:0.12, T:0.12
Consensus pattern (21 bp):
AAAAAAAAAACAGTTCGAAAA
Found at i:2395796 original size:13 final size:13
Alignment explanation
Indices: 2395780--2395804 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2395770 TGAAAACTAT
2395780 TTTGAAAAATAAG
1 TTTGAAAAATAAG
2395793 TTTGAAAAATAA
1 TTTGAAAAATAA
2395805 TTGTATGTAT
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:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (13 bp):
TTTGAAAAATAAG
Found at i:2395855 original size:18 final size:18
Alignment explanation
Indices: 2395834--2395868 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2395824 GAAAACAATG
2395834 TAATTAAATA-AAAAACAC
1 TAATTAAA-ACAAAAACAC
2395852 TAATTAAAACAAAAACA
1 TAATTAAAACAAAAACA
2395869 TTTTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 15 0.94
ACGTcount: A:0.69, C:0.11, G:0.00, T:0.20
Consensus pattern (18 bp):
TAATTAAAACAAAAACAC
Found at i:2399600 original size:17 final size:17
Alignment explanation
Indices: 2399578--2399616 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2399568 CCCCCTTGGG
2399578 TATCCATTTGTTTAGGA
1 TATCCATTTGTTTAGGA
2399595 TATCCATTTGTTTAGGA
1 TATCCATTTGTTTAGGA
2399612 TATCC
1 TATCC
2399617 TTATCTTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (17 bp):
TATCCATTTGTTTAGGA
Found at i:2399625 original size:17 final size:17
Alignment explanation
Indices: 2399578--2399626 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
2399568 CCCCCTTGGG
*
2399578 TATCCATTTGTTTAGGA
1 TATCCATTTCTTTAGGA
*
2399595 TATCCATTTGTTTAGGA
1 TATCCATTTCTTTAGGA
2399612 TATCC-TTATCTTTAG
1 TATCCATT-TCTTTAG
2399627 TAGTATTGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 2 0.07
17 28 0.93
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.49
Consensus pattern (17 bp):
TATCCATTTCTTTAGGA
Found at i:2403009 original size:48 final size:49
Alignment explanation
Indices: 2402916--2403009 Score: 129
Period size: 48 Copynumber: 1.9 Consensus size: 49
2402906 ATAGTGCCAA
* *
2402916 GAGTAGATGAATGTACTAAATACAGGAATGCACAAATGCACTAATATAG
1 GAGTACATGAATGTACTAAATACAGGAATGCACAAATGCAATAATATAG
* *
2402965 GAGTACATGAATGTACT-AATAC-GAGAGTTCACAAATGCAATAATA
1 GAGTACATGAATGTACTAAATACAG-GAATGCACAAATGCAATAATA
2403010 CAAGATCGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
47 1 0.03
48 23 0.57
49 16 0.40
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (49 bp):
GAGTACATGAATGTACTAAATACAGGAATGCACAAATGCAATAATATAG
Found at i:2403258 original size:61 final size:62
Alignment explanation
Indices: 2403145--2403265 Score: 165
Period size: 61 Copynumber: 2.0 Consensus size: 62
2403135 CTAACATGCC
* * *
2403145 AAAATATCGTATAAAAATACAATAGGCTAATTCATACCCGAAATCATCCATAAATCATTTAT
1 AAAATATCATATAAAAATACAATAGGATAATTCATACCCAAAATCATCCATAAATCATTTAT
* * *
2403207 AAAATATCATATAAAAATA-TATTGGATAACTT-ATACCCAAAATCATTCATAAATCATTT
1 AAAATATCATATAAAAATACAATAGGATAA-TTCATACCCAAAATCATCCATAAATCATTT
2403266 CCAAATATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
61 32 0.62
62 20 0.38
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (62 bp):
AAAATATCATATAAAAATACAATAGGATAATTCATACCCAAAATCATCCATAAATCATTTAT
Found at i:2412010 original size:40 final size:40
Alignment explanation
Indices: 2411961--2412040 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
2411951 ATTGTAAGAG
*
2411961 ATGAATGAAAAATGATATTCTTATTAGTTGAATCAGATGT
1 ATGAATGAAAAATGATACTCTTATTAGTTGAATCAGATGT
2412001 ATGAATGAAAAATGATACTCTTATTAGTTGAATCAGATGT
1 ATGAATGAAAAATGATACTCTTATTAGTTGAATCAGATGT
2412041 GTTGAAAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.36
Consensus pattern (40 bp):
ATGAATGAAAAATGATACTCTTATTAGTTGAATCAGATGT
Found at i:2412132 original size:29 final size:30
Alignment explanation
Indices: 2412099--2412169 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
2412089 CAAATTTTGG
*
2412099 TTAGTGACCAAAATGCAAATTTT-AAAAGT
1 TTAGTGACCAAAATACAAATTTTAAAAAGT
** * *
2412128 TTAGTTTCCAAAGTATAAATTTTAAAAAGT
1 TTAGTGACCAAAATACAAATTTTAAAAAGT
*
2412158 TTAG-GAACAAAA
1 TTAGTGACCAAAA
2412170 AATGTAACTT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.32
Consensus pattern (30 bp):
TTAGTGACCAAAATACAAATTTTAAAAAGT
Found at i:2414430 original size:23 final size:23
Alignment explanation
Indices: 2414354--2414464 Score: 91
Period size: 23 Copynumber: 4.8 Consensus size: 23
2414344 GAGTCGAGGG
* * * *
2414354 ATTCTATGCGGTCCTCCGAGACA
1 ATTCTATGTGGTCCTTCGGGATA
*
2414377 ATTCTACGCT-GTCCTTCGGGATA
1 ATTCTATG-TGGTCCTTCGGGATA
*
2414400 ATTTTATGTGGTCCTTCGGGATA
1 ATTCTATGTGGTCCTTCGGGATA
* * * *
2414423 ATTCTATGTTGTTCTTTGGGAGA
1 ATTCTATGTGGTCCTTCGGGATA
*
2414446 AATCTATGTGG-CACTTCGG
1 ATTCTATGTGGTC-CTTCGG
2414465 TGCATATTCT
Statistics
Matches: 69, Mismatches: 16, Indels: 6
0.76 0.18 0.07
Matches are distributed among these distances:
22 1 0.01
23 68 0.99
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (23 bp):
ATTCTATGTGGTCCTTCGGGATA
Found at i:2415093 original size:64 final size:65
Alignment explanation
Indices: 2414985--2415105 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 65
2414975 GAATGCATTT
* * *
2414985 CATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATGCATTTGATGCATCGATTCACCAGC
1 CATGCATCGATGCACTCAGACTTTTATGAAAACATCAAATGCATTTCATGCATCGATTCACCAGC
2415050 CATGCATCGATGCACTCTAG-CTATTT-TG-AAACATCAAATGCATTTCATGCATCGAT
1 CATGCATCGATGCACTC-AGACT-TTTATGAAAACATCAAATGCATTTCATGCATCGAT
2415106 ACACTCTTAG
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
64 26 0.51
65 20 0.39
66 5 0.10
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (65 bp):
CATGCATCGATGCACTCAGACTTTTATGAAAACATCAAATGCATTTCATGCATCGATTCACCAGC
Found at i:2420981 original size:23 final size:23
Alignment explanation
Indices: 2420903--2420983 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 23
2420893 ACACTTAACA
* *
2420903 GTGCATCGATGCATCTCTTTGAAT
1 GTGCATCGATGCA-CACCTTGAAT
* *
2420927 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
2420948 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
*
2420971 GTGCATTGATGCA
1 GTGCATCGATGCA
2420984 TCCGTCGGGT
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
21 15 0.33
22 1 0.02
23 19 0.42
24 10 0.22
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:2430482 original size:23 final size:23
Alignment explanation
Indices: 2430456--2430540 Score: 71
Period size: 23 Copynumber: 3.7 Consensus size: 23
2430446 CGATCCTCTC
2430456 GGACAATTCTATGTGGTTCTTCG
1 GGACAATTCTATGTGGTTCTTCG
* * *** *
2430479 GGACAATTATACGCAATTCTTCA
1 GGACAATTCTATGTGGTTCTTCG
* **
2430502 GGAAAATTCTATGTGGACCTTCG
1 GGACAATTCTATGTGGTTCTTCG
* *
2430525 GGATAAATCTATGTGG
1 GGACAATTCTATGTGG
2430541 CACTTCGGTG
Statistics
Matches: 45, Mismatches: 17, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (23 bp):
GGACAATTCTATGTGGTTCTTCG
Found at i:2431569 original size:65 final size:65
Alignment explanation
Indices: 2431434--2431594 Score: 195
Period size: 65 Copynumber: 2.5 Consensus size: 65
2431424 GTGCACTAAG
* *
2431434 TGTGCATCAATGCA-TAAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGTC
1 TGTGCATCGATGCATTAAA-TGCATTCGATGTTTTCAAAATACCCAGAGTGCATCGATGCATGTC
*
2431497 T
65 A
* * *
2431498 TATGCATCGATGCATTAAATACATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATGGT
1 TGTGCATCGATGCATTAAATGCATTCGATGTTTTCA-AAATACCCAGAGTGCATCGATGCAT-GT
2431562 -A
64 CA
* *
2431563 TGTGCATCGATGCATAAAATGCATTTGATGTT
1 TGTGCATCGATGCATTAAATGCATTCGATGTT
2431595 CAAATTATTA
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
64 22 0.27
65 56 0.67
66 5 0.06
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (65 bp):
TGTGCATCGATGCATTAAATGCATTCGATGTTTTCAAAATACCCAGAGTGCATCGATGCATGTCA
Found at i:2434259 original size:20 final size:20
Alignment explanation
Indices: 2434234--2434285 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
2434224 CCCAACGGAC
2434234 GCATCGATGCATGGCCTTGT
1 GCATCGATGCATGGCCTTGT
2434254 GCATCGATGCATGGCCTTGT
1 GCATCGATGCATGGCCTTGT
2434274 GCATCGATGCAT
1 GCATCGATGCAT
2434286 ATTCAAGGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29
Consensus pattern (20 bp):
GCATCGATGCATGGCCTTGT
Found at i:2439854 original size:65 final size:65
Alignment explanation
Indices: 2439722--2439881 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
2439712 TGCAATAAGA
* * ** *
2439722 GTGCAGCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGTCTGAGTGCATCGATGCATGTCTT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGTCAT
*
2439786 GTGCATCGATGCGTCAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATGGT-
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATACCCTGAGTGCATCGATGCAT-GTC
2439849 AT
64 AT
*
2439851 GTGCATCGATGCATAAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
2439882 CAATTTATTC
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 26 0.31
65 54 0.64
66 5 0.06
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGTCAT
Found at i:2439920 original size:65 final size:64
Alignment explanation
Indices: 2439722--2439923 Score: 191
Period size: 65 Copynumber: 3.1 Consensus size: 64
2439712 TGCAATAAGA
* * ** * *
2439722 GTGCAGCGATGCATCAAGTGCATTCGATGTTTCAAAATAGTC--TGAGTGCATCGATGCATGTCT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTCAATTTATTCAATGAGTGCATCGATGCATG-GT
2439785 T
64 T
* * **
2439786 GTGCATCGATGCGTCAAATGCATTCGATGTT---TTCATAAAACCCTGAGTGCATCGATGCATGG
1 GTGCATCGATGCATCAAATGCATTCGATGTTCAATTTATTCAA---TGAGTGCATCGATGCATGG
2439848 TAT
63 T-T
*
2439851 GTGCATCGATGCATAAAATGCATTCGATGTTCAATTTATTCAATG-GTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTCAATTTATTCAATGAGTGCATCGATGCATGG-TT
2439915 GGTGCATCG
1 -GTGCATCG
2439924 GTGTATCCCT
Statistics
Matches: 112, Mismatches: 15, Indels: 21
0.76 0.10 0.14
Matches are distributed among these distances:
60 1 0.01
63 2 0.02
64 44 0.39
65 59 0.53
68 6 0.05
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTCAATTTATTCAATGAGTGCATCGATGCATGGTT
Found at i:2451236 original size:81 final size:80
Alignment explanation
Indices: 2451092--2451313 Score: 300
Period size: 81 Copynumber: 2.7 Consensus size: 80
2451082 ATGTTCTTCA
* * * * * *
2451092 TCTAACTTGCATTAGTGGCACCTTTATACCATATTGCACCATTAGGCGTTAGTATTTTATCCTAA
1 TCTAACTTGCATTATTGGCACCTTTCTACCA-AATGCA-CATTATGCATTAGTCTTTTATCCTAA
2451157 AGGCATTTAACCTTTCT
64 AGGCATTTAACCTTTCT
* * *
2451174 TTTAACTTGTATTATTAGCACCTTTCTACCAAATGCACAGTTATGCATTAGTCTTTTATCCTAAA
1 TCTAACTTGCATTATTGGCACCTTTCTACCAAATGCACA-TTATGCATTAGTCTTTTATCCTAAA
2451239 GGCATTTAACCTTTCT
65 GGCATTTAACCTTTCT
* * *
2451255 TCTAACTTGCATTATTGGTACCTTTCTGCCAAATACACAATTATGCATTAGTCTTTTAT
1 TCTAACTTGCATTATTGGCACCTTTCTACCAAATGCAC-ATTATGCATTAGTCTTTTAT
2451314 TTTAGAACAA
Statistics
Matches: 123, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
80 2 0.02
81 94 0.76
82 27 0.22
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (80 bp):
TCTAACTTGCATTATTGGCACCTTTCTACCAAATGCACATTATGCATTAGTCTTTTATCCTAAAG
GCATTTAACCTTTCT
Found at i:2451633 original size:54 final size:54
Alignment explanation
Indices: 2451568--2451942 Score: 421
Period size: 54 Copynumber: 6.9 Consensus size: 54
2451558 TAGTGTCTGT
* * ** *
2451568 ACGGTTGTTCATCAAC-TCCTGATGAATTCCGTGCGTTCCACACTTAGTGCCGAA
1 ACGGTTATTCATCAACAT-ATGATGAATTCCGTGAATTGCACACTTAGTGCCGAA
* * * * * *
2451622 ATGGTTATTCATCAATATATGATGAATTTCTTGAATTGTACACTTAGTGTCGAA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAA
** ** *
2451676 ACATTTATTCATCAACATATGATGAATTATGTGAATTGCACACTTAGTGCCAAA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAA
** * * *
2451730 ACGGTTATTCATCAATGTATGAAGAATTCCTTGAATTGCACACTTAGTGTCGAA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAA
* * * *
2451784 ACAGTTATTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTACTGAA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAA
* * * *
2451838 ATGATTATTCATCAACATATGATGAATTTCATGAATTGCACACTTAGTGCCGAA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAA
* * * *
2451892 ATGGTTATTCATCAACATATGACGAATTTCGT-ACTTTGCACACTTAGTGCC
1 ACGGTTATTCATCAACATATGATGAATTCCGTGA-ATTGCACACTTAGTGCC
2451943 TATTTAGTAA
Statistics
Matches: 267, Mismatches: 52, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
53 1 0.00
54 265 0.99
55 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (54 bp):
ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAA
Found at i:2451722 original size:108 final size:107
Alignment explanation
Indices: 2451606--2451942 Score: 478
Period size: 108 Copynumber: 3.1 Consensus size: 107
2451596 CCGTGCGTTC
*
2451606 CACACTTAGTGCCGAAATGGTTATTCATCAATATATGATGAATTTCTTGAATTGTACACTTAGTG
1 CACACTTAGTGCCGAAATGGTTATTCATCAATATATGATGAATTTCTTGAATTGCACACTTAGTG
*
2451671 TCGAAACATTTATTCATCAACATATGATGAATTATGTGAATTG
66 TCGAAACAGTTATTCATCAACATATGATGAATT-TGTGAATTG
* * * * *
2451714 CACACTTAGTGCCAAAACGGTTATTCATCAATGTATGAAGAATTCCTTGAATTGCACACTTAGTG
1 CACACTTAGTGCCGAAATGGTTATTCATCAATATATGATGAATTTCTTGAATTGCACACTTAGTG
2451779 TCGAAACAGTTATTCATCAACATATGATGAATTCTGTGAATTG
66 TCGAAACAGTTATTCATCAACATATGATGAATT-TGTGAATTG
* * * * *
2451822 CACACTTAGTACTGAAATGATTATTCATCAACATATGATGAATTTCATGAATTGCACACTTAGTG
1 CACACTTAGTGCCGAAATGGTTATTCATCAATATATGATGAATTTCTTGAATTGCACACTTAGTG
* ** * *
2451887 CCGAAATGGTTATTCATCAACATATGACGAATTTCGT-ACTTTG
66 TCGAAACAGTTATTCATCAACATATGATGAATTT-GTGA-ATTG
2451930 CACACTTAGTGCC
1 CACACTTAGTGCC
2451943 TATTTAGTAA
Statistics
Matches: 202, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
107 2 0.01
108 200 0.99
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (107 bp):
CACACTTAGTGCCGAAATGGTTATTCATCAATATATGATGAATTTCTTGAATTGCACACTTAGTG
TCGAAACAGTTATTCATCAACATATGATGAATTTGTGAATTG
Found at i:2462355 original size:21 final size:21
Alignment explanation
Indices: 2462329--2462384 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
2462319 TTAATACAAG
2462329 GGGTATTGGTACCTTTGGGCT
1 GGGTATTGGTACCTTTGGGCT
2462350 GGGTATTGGTACCTTTGGGCT
1 GGGTATTGGTACCTTTGGGCT
* *
2462371 AGGTATCGGTACCT
1 GGGTATTGGTACCT
2462385 CTATATAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.12, C:0.16, G:0.36, T:0.36
Consensus pattern (21 bp):
GGGTATTGGTACCTTTGGGCT
Found at i:2466177 original size:81 final size:81
Alignment explanation
Indices: 2466038--2466259 Score: 291
Period size: 81 Copynumber: 2.7 Consensus size: 81
2466028 ATGTTCTTCA
* * * * * * * * * *
2466038 TCTAACTTGCATTAGTGGCACCTTTATACCATATTGCACCATTAGGCGTTAGTATTTTATCCTAA
1 TCTAACTTGCATTATTAGCACCTTTCTGCCA-AATACACAATTATGCATTAGTCTTTTATCCTAA
*
2466103 AGGCATTTAACCTTTCT
65 AGGCATTTAACATTTCT
* * * *
2466120 TTTAACTTGTATTATTAGCACCTTTCTGCCAAATGCACAGTTATGCATTAGTCTTTTATCCTAAA
1 TCTAACTTGCATTATTAGCACCTTTCTGCCAAATACACAATTATGCATTAGTCTTTTATCCTAAA
2466185 GGCATTTAACATTTCT
66 GGCATTTAACATTTCT
*
2466201 TCTAACTTGCATTATTGGCACCTTTCTGCCAAATACACAATTATGCATTAGTCTTTTAT
1 TCTAACTTGCATTATTAGCACCTTTCTGCCAAATACACAATTATGCATTAGTCTTTTAT
2466260 TTTAGAACAA
Statistics
Matches: 122, Mismatches: 18, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
81 97 0.80
82 25 0.20
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.41
Consensus pattern (81 bp):
TCTAACTTGCATTATTAGCACCTTTCTGCCAAATACACAATTATGCATTAGTCTTTTATCCTAAA
GGCATTTAACATTTCT
Found at i:2466500 original size:46 final size:46
Alignment explanation
Indices: 2466433--2466523 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
2466423 CATCAACACA
** *
2466433 TGATGAATTTTTTGGGTTGCACACATATTG-CATGTACGGTTGTTCG
1 TGATGAATTTCGTGGGTTGCACACATAGTGTC-TGTACGGTTGTTCG
2466479 TGATGAATTTCGTGGGTTGCACACATAGTGTCTGTACGGTTGTTC
1 TGATGAATTTCGTGGGTTGCACACATAGTGTCTGTACGGTTGTTC
2466524 ATCAACTCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 40 0.98
47 1 0.02
ACGTcount: A:0.19, C:0.14, G:0.27, T:0.40
Consensus pattern (46 bp):
TGATGAATTTCGTGGGTTGCACACATAGTGTCTGTACGGTTGTTCG
Found at i:2466579 original size:54 final size:54
Alignment explanation
Indices: 2466514--2466888 Score: 456
Period size: 54 Copynumber: 6.9 Consensus size: 54
2466504 TAGTGTCTGT
* * ** *
2466514 ACGGTTGTTCATCAAC-TCCTGATGAATTCTGTGCGTTCCACACTTAGTGCCGAA
1 ACGGTTATTCATCAACAT-ATGATGAATTCTGTGAATTGCACACTTAGTGCCGAA
* * * *
2466568 ATGGTTATTCATCAATATATGATGAATTTCT-TGAATTGTACACTTAGTGTCGAA
1 ACGGTTATTCATCAACATATGATGAA-TTCTGTGAATTGCACACTTAGTGCCGAA
* *
2466622 ACAGTTATTCATCAACATATGATGAATTATGTGAATTGCACACTTAGTGCCGAA
1 ACGGTTATTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAA
** * *
2466676 ACGGTTATTCATCAATGTATGAAGAATTCCT-TGAATTGCACACTTAGTGTCGAA
1 ACGGTTATTCATCAACATATGATGAATT-CTGTGAATTGCACACTTAGTGCCGAA
* *
2466730 ACGGTTATTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTACTGAA
1 ACGGTTATTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAA
*
2466784 ACGGTTATTCATCAACATATGATGAATT-TCATGAATTGCACACTTAGTGCCGAA
1 ACGGTTATTCATCAACATATGATGAATTCT-GTGAATTGCACACTTAGTGCCGAA
* * * *
2466838 ATGGTTATTCATTAACATATGACGAATT-TCGT-ACTTTGCACACTTAGTGCC
1 ACGGTTATTCATCAACATATGATGAATTCT-GTGA-ATTGCACACTTAGTGCC
2466889 TATTTAGTAA
Statistics
Matches: 279, Mismatches: 35, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
53 7 0.03
54 266 0.95
55 6 0.02
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (54 bp):
ACGGTTATTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAA
Found at i:2466668 original size:108 final size:108
Alignment explanation
Indices: 2466479--2466888 Score: 522
Period size: 108 Copynumber: 3.8 Consensus size: 108
2466469 CGGTTGTTCG
* ** * * * *
2466479 TGATGAATTTCGTGGGTTGCACACATAGTGTCTG-TACGGTTGTTCATCAAC-TCCTGATGAATT
1 TGATGAATTTCTTGAATTGCACACTTAGTGTC-GAAACGGTTATTCATCAACAT-ATGATGAATT
** * *
2466542 CTGTGCGTTCCACACTTAGTGCCGAAATGGTTATTCATCAATATA
64 CTGTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAATATA
* * *
2466587 TGATGAATTTCTTGAATTGTACACTTAGTGTCGAAACAGTTATTCATCAACATATGATGAATTAT
1 TGATGAATTTCTTGAATTGCACACTTAGTGTCGAAACGGTTATTCATCAACATATGATGAATTCT
*
2466652 GTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAATGTA
66 GTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAATATA
* *
2466695 TGAAGAATTCCTTGAATTGCACACTTAGTGTCGAAACGGTTATTCATCAACATATGATGAATTCT
1 TGATGAATTTCTTGAATTGCACACTTAGTGTCGAAACGGTTATTCATCAACATATGATGAATTCT
* * *
2466760 GTGAATTGCACACTTAGTACTGAAACGGTTATTCATCAACATA
66 GTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAATATA
* * * * *
2466803 TGATGAATTTCATGAATTGCACACTTAGTGCCGAAATGGTTATTCATTAACATATGACGAATT-T
1 TGATGAATTTCTTGAATTGCACACTTAGTGTCGAAACGGTTATTCATCAACATATGATGAATTCT
*
2466867 CGT-ACTTTGCACACTTAGTGCC
66 -GTGA-ATTGCACACTTAGTGCC
2466889 TATTTAGTAA
Statistics
Matches: 264, Mismatches: 34, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
107 3 0.01
108 260 0.98
109 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (108 bp):
TGATGAATTTCTTGAATTGCACACTTAGTGTCGAAACGGTTATTCATCAACATATGATGAATTCT
GTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAATATA
Found at i:2466809 original size:26 final size:26
Alignment explanation
Indices: 2466727--2466809 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 26
2466717 ACTTAGTGTC
2466727 GAAACGGTTATTCATCAACATATGAT
1 GAAACGGTTATTCATCAACATATGAT
* * * *
2466753 GAATTCTGTGAATTGCA-C-ACTTA-GTACT
1 GAA-ACGGT-TATT-CATCAACATATG-A-T
2466781 GAAACGGTTATTCATCAACATATGAT
1 GAAACGGTTATTCATCAACATATGAT
2466807 GAA
1 GAA
2466810 TTTCATGAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 16
0.63 0.12 0.25
Matches are distributed among these distances:
25 2 0.05
26 12 0.29
27 16 0.39
28 9 0.22
29 2 0.05
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (26 bp):
GAAACGGTTATTCATCAACATATGAT
Found at i:2469349 original size:24 final size:21
Alignment explanation
Indices: 2469320--2469379 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 21
2469310 CCTTTGGGCT
2469320 AGGTATCGATACCTCTATATA-A
1 AGGTATCGATACCTCT-TA-AGA
*
2469342 AGGGGTATCGGTACCTCTTAAGA
1 A--GGTATCGATACCTCTTAAGA
2469365 AGGTATCGATACCTC
1 AGGTATCGATACCTC
2469380 CCTATTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
21 13 0.39
22 2 0.06
23 4 0.12
24 14 0.42
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (21 bp):
AGGTATCGATACCTCTTAAGA
Found at i:2469550 original size:17 final size:18
Alignment explanation
Indices: 2469530--2469566 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2469520 TTATATTCAA
2469530 ATAA-TTGAATCGAATAT
1 ATAATTTGAATCGAATAT
2469547 ATAATTTTGAATCGAATAT
1 ATAA-TTTGAATCGAATAT
2469566 A
1 A
2469567 AAATATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
19 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (18 bp):
ATAATTTGAATCGAATAT
Found at i:2477297 original size:21 final size:21
Alignment explanation
Indices: 2477271--2477326 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
2477261 TTAATACAAG
2477271 GGGTATTGGTACCTTTGGGCT
1 GGGTATTGGTACCTTTGGGCT
2477292 GGGTATTGGTACCTTTGGGCT
1 GGGTATTGGTACCTTTGGGCT
* *
2477313 AGGTATCGGTACCT
1 GGGTATTGGTACCT
2477327 CTATATAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.12, C:0.16, G:0.36, T:0.36
Consensus pattern (21 bp):
GGGTATTGGTACCTTTGGGCT
Found at i:2477593 original size:17 final size:18
Alignment explanation
Indices: 2477573--2477609 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2477563 TGATATTCGA
2477573 ATAA-TTGAATCGAATAT
1 ATAATTTGAATCGAATAT
2477590 ATAATTTTGAATCGAATAT
1 ATAA-TTTGAATCGAATAT
2477609 A
1 A
2477610 AAATCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
19 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (18 bp):
ATAATTTGAATCGAATAT
Found at i:2481122 original size:81 final size:81
Alignment explanation
Indices: 2481031--2481204 Score: 285
Period size: 81 Copynumber: 2.1 Consensus size: 81
2481021 CCATTAGGCG
* * * *
2481031 TTAGTATTTTATCCTAAAGGCATTTAACCTTTCTTTTAACTTGTATTATTAGCACCTTCCTGCCA
1 TTAGTCTTTTATCCTAAAGGCATTTAACCTTTCTTCTAACTTGCATTATTAGCACATTCCTGCCA
2481096 AATGCACAGTTATGAA
66 AATGCACAGTTATGAA
* *
2481112 TTAGTCTTTTATCCTAAAGGCATTTAACCTTTCTTCTAACTTGCATTATTGGCACATTTCTGCCA
1 TTAGTCTTTTATCCTAAAGGCATTTAACCTTTCTTCTAACTTGCATTATTAGCACATTCCTGCCA
*
2481177 AATGCACAGTTATGCA
66 AATGCACAGTTATGAA
2481193 TTAGTCTTTTAT
1 TTAGTCTTTTAT
2481205 TTTAGAATAA
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 86 1.00
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.42
Consensus pattern (81 bp):
TTAGTCTTTTATCCTAAAGGCATTTAACCTTTCTTCTAACTTGCATTATTAGCACATTCCTGCCA
AATGCACAGTTATGAA
Found at i:2481531 original size:54 final size:54
Alignment explanation
Indices: 2481413--2481870 Score: 485
Period size: 54 Copynumber: 8.5 Consensus size: 54
2481403 TAGTGCATGT
* ** * *
2481413 ACGGTTGTTCATCAAC-TCATGATGAATTTTGTG--TTGCACACATAGTGGCGAA
1 ACGGTTATTCATCAACAT-ATGATGAATTCCGTGAATTGCACACTTAGTGTCGAA
* * ** ** * *
2481465 ACGGTTGTTCATCAAC-TCATGATAAATTTTGTGGGTTACACACTTAGCGTCGAA
1 ACGGTTATTCATCAACAT-ATGATGAATTCCGTGAATTGCACACTTAGTGTCGAA
* * * * *
2481519 ATGGTTATTCATCAACATATGATGAATTTCGTGAATTGTACACTTAGTGCCAAA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGTCGAA
* * * * *
2481573 ATGGTAATTCATCAACATATGATGAATTCTGTGAACTGCACACTTAGTGTCAAA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGTCGAA
*
2481627 ACAGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGTCGAA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGTCGAA
* * * *
2481681 ACAGTTGTTCATTAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGTCGAA
* * * * * *
2481735 ACGGTTATTCATCAATATATGATTAATTCCATGAATTGTACACTTAGTGCCAAA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGTCGAA
* * * **
2481789 ACGGTTATTCATCAACATTTGATGAATTCCAT-ACTTTGCACACTTAGTACCGAA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGA-ATTGCACACTTAGTGTCGAA
* *
2481843 ATGGTTATTCTTCAACATATGATGAATT
1 ACGGTTATTCATCAACATATGATGAATT
2481871 TTGTACTTTG
Statistics
Matches: 353, Mismatches: 49, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
52 32 0.09
53 1 0.00
54 319 0.90
55 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (54 bp):
ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGTCGAA
Found at i:2481967 original size:15 final size:15
Alignment explanation
Indices: 2481947--2481978 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2481937 TGACTAGTAT
2481947 AACATATAGTTACAC
1 AACATATAGTTACAC
2481962 AACATATAGTTACAC
1 AACATATAGTTACAC
2481977 AA
1 AA
2481979 TTAAATGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (15 bp):
AACATATAGTTACAC
Found at i:2490675 original size:15 final size:16
Alignment explanation
Indices: 2490633--2490675 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
2490623 TTTAGGGTTT
2490633 TTAATTCTAAA-TTAA
1 TTAATTCTAAATTTAA
* *
2490648 TTAAATCTGAATTTAA
1 TTAATTCTAAATTTAA
2490664 TTAATTC-AAATT
1 TTAATTCTAAATT
2490676 AAAAATATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (16 bp):
TTAATTCTAAATTTAA
Found at i:2490768 original size:2 final size:2
Alignment explanation
Indices: 2490761--2490820 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
2490751 ATTTCGGATA
2490761 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2490803 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
2490821 TAATCTTAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2495774 original size:23 final size:23
Alignment explanation
Indices: 2495748--2495805 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 23
2495738 GGGAAAATTT
2495748 AGTATCGATACCATAAAAAGGGG
1 AGTATCGATACCATAAAAAGGGG
* *
2495771 AGTATTGATACC----CAAGGGG
1 AGTATCGATACCATAAAAAGGGG
*
2495790 AGTATCAATACCATAA
1 AGTATCGATACCATAA
2495806 TGAATTCTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
19 16 0.59
23 11 0.41
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (23 bp):
AGTATCGATACCATAAAAAGGGG
Found at i:2503072 original size:24 final size:24
Alignment explanation
Indices: 2503045--2503097 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
2503035 TAGCGTGGTT
*
2503045 GTGTTTGTAAATTAGCCGCATCTA
1 GTGTTTGTAAATTAGCCGCAACTA
2503069 GTGTTTGTAAATTAGCCGCAACTA
1 GTGTTTGTAAATTAGCCGCAACTA
2503093 GTGTT
1 GTGTT
2503098 GTAGTTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (24 bp):
GTGTTTGTAAATTAGCCGCAACTA
Found at i:2506721 original size:13 final size:13
Alignment explanation
Indices: 2506703--2506728 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2506693 CCAAGGCGTA
2506703 TTGGGGATAGTTG
1 TTGGGGATAGTTG
2506716 TTGGGGATAGTTG
1 TTGGGGATAGTTG
2506729 ACCTAAGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (13 bp):
TTGGGGATAGTTG
Found at i:2510995 original size:20 final size:20
Alignment explanation
Indices: 2510969--2511020 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2510959 TGATTCAATC
*
2510969 GGTATCGATACCGAAGGG-G
1 GGTATCGATACCGAAGGGAA
2510988 GAGTATCGATACCGAAGGGAA
1 G-GTATCGATACCGAAGGGAA
2511009 GGTATCGATACC
1 GGTATCGATACC
2511021 ATTCAAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.31, C:0.17, G:0.35, T:0.17
Consensus pattern (20 bp):
GGTATCGATACCGAAGGGAA
Found at i:2511805 original size:54 final size:54
Alignment explanation
Indices: 2511242--2511795 Score: 750
Period size: 54 Copynumber: 10.3 Consensus size: 54
2511232 ATGTATTTAA
** *
2511242 TGGATGAATAACTTTTTCGGCACTAAGTGTGCATTTCACAGAATTCATCCTATG
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATG
2511296 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATG
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATG
* * *
2511350 TGGATGAATAACTGCTT-GGCACTAAGTGTACATTTCACGGAATTCATCCTATG
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATG
* *
2511403 TGGATGAATAACCGTTTCAGCACTGAGTGTGCATTTCACGGAATTCATCCTATG
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATG
** * * * *
2511457 TGGATGAATAATTGTTTCGGCACTAAGTGAGCATTTCACAGAATTCATACTATA
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATG
* * *
2511511 TGGAGGAATAACCGTTTCGGCACTGAGTGTGCATTTCATGGAATTCATCCTATG
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATG
* * * * * *
2511565 TGGATGAATAACCATTTTGGTACTGAGCGTGCATTTCACAGAATTCATCCTATG
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATG
* * * *
2511619 TGGATGAATAATCGTTTCAGCACTAAGTGTGCATTTCATGGAATTTATCCTATG
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATG
** * *
2511673 TGGATGAATAATTGTTTCGACACTAAGTGTGCATTTCACGGAATTCATCTTATG
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATG
* * * * **
2511727 TGGATGAATAACCGTTTCAGTACTAAATGTGCATTTCACGAAATTCATAATATG
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATG
**
2511781 TTTATGAATAACCGT
1 TGGATGAATAACCGT
2511796 ATGGGTACTA
Statistics
Matches: 437, Mismatches: 62, Indels: 2
0.87 0.12 0.00
Matches are distributed among these distances:
53 50 0.11
54 387 0.89
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (54 bp):
TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATG
Found at i:2515490 original size:29 final size:29
Alignment explanation
Indices: 2515437--2515496 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 29
2515427 CATACTTAGC
*
2515437 ATAAAAATAAAACTTGAAAATAAAGA-AAA
1 ATAAAAAT-AAACTTGAAAAAAAAGAGAAA
2515466 ATAAAAAT-AACTTGAAAAGGAAAAGAGAAA
1 ATAAAAATAAACTTGAAAA--AAAAGAGAAA
2515496 A
1 A
2515497 CTTTTATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 10 0.37
29 13 0.48
30 4 0.15
ACGTcount: A:0.70, C:0.03, G:0.12, T:0.15
Consensus pattern (29 bp):
ATAAAAATAAACTTGAAAAAAAAGAGAAA
Found at i:2516576 original size:18 final size:17
Alignment explanation
Indices: 2516555--2516611 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 17
2516545 TTTCATGTCT
2516555 TTTTTTTCTTTCGAACAG
1 TTTTTTT-TTTCGAACAG
*
2516573 -TTTTTTTTTCGAACTG
1 TTTTTTTTTTCGAACAG
2516589 CTATTTTTTTTTC-AACA-
1 -T-TTTTTTTTTCGAACAG
2516606 TTTTTT
1 TTTTTT
2516612 GTGATGGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 5 0.15
16 10 0.29
17 6 0.18
18 3 0.09
19 10 0.29
ACGTcount: A:0.16, C:0.14, G:0.07, T:0.63
Consensus pattern (17 bp):
TTTTTTTTTTCGAACAG
Found at i:2521523 original size:29 final size:29
Alignment explanation
Indices: 2521470--2521529 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 29
2521460 CATACTTAGC
*
2521470 ATAAAAATAAAACTTGAAAATAAAGA-AAA
1 ATAAAAAT-AAACTTGAAAAAAAAGAGAAA
2521499 ATAAAAAT-AACTTGAAAAGGAAAAGAGAAA
1 ATAAAAATAAACTTGAAAA--AAAAGAGAAA
2521529 A
1 A
2521530 CTTTTATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 10 0.37
29 13 0.48
30 4 0.15
ACGTcount: A:0.70, C:0.03, G:0.12, T:0.15
Consensus pattern (29 bp):
ATAAAAATAAACTTGAAAAAAAAGAGAAA
Found at i:2525256 original size:45 final size:46
Alignment explanation
Indices: 2525169--2525260 Score: 141
Period size: 45 Copynumber: 2.0 Consensus size: 46
2525159 TTGAAAAGCC
* * *
2525169 TGAGTGCATCGATGCATAGTCTTGTGCATCGATGCATCAAATGCAT
1 TGAGTGCATAGATGCATAGTCATGTGCATCGATGCATAAAATGCAT
*
2525215 TGAGTGCATAGATGCATGGT-ATGTGCATCGATGCATAAAATGCAT
1 TGAGTGCATAGATGCATAGTCATGTGCATCGATGCATAAAATGCAT
2525260 T
1 T
2525261 CGATGTTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 24 0.57
46 18 0.43
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (46 bp):
TGAGTGCATAGATGCATAGTCATGTGCATCGATGCATAAAATGCAT
Found at i:2530119 original size:19 final size:19
Alignment explanation
Indices: 2530092--2530138 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
2530082 CTCTCAATGC
*
2530092 ATCGGTGCACTAAGAGTGA
1 ATCGATGCACTAAGAGTGA
2530111 ATCGATGCACTAAGAGTGA
1 ATCGATGCACTAAGAGTGA
2530130 ATCGATGCA
1 ATCGATGCA
2530139 TAAAATGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (19 bp):
ATCGATGCACTAAGAGTGA
Found at i:2530254 original size:45 final size:46
Alignment explanation
Indices: 2530166--2530256 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
2530156 TTTGAAAAAC
* * *
2530166 CTGAGTGCATCGATGCATAGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATAGTCATCTGCATCGATGCATAAAATGCA
*
2530212 CTGAGTGCATCGATGCATGGT-ATCTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATAGTCATCTGCATCGATGCATAAAATGCA
2530257 TTCGATGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 21 0.51
46 20 0.49
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATAGTCATCTGCATCGATGCATAAAATGCA
Found at i:2530304 original size:20 final size:20
Alignment explanation
Indices: 2530276--2530313 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2530266 TGAAAAATTA
2530276 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
* *
2530296 ATTGTTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
2530314 CACTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:2531309 original size:18 final size:18
Alignment explanation
Indices: 2531286--2531326 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
2531276 AGTGATAAAT
2531286 AGAGCGAAGGCGATTGAA
1 AGAGCGAAGGCGATTGAA
2531304 AGAGCGAAGGCGATTGAA
1 AGAGCGAAGGCGATTGAA
2531322 AGAGC
1 AGAGC
2531327 TCAAGAGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.12, G:0.39, T:0.10
Consensus pattern (18 bp):
AGAGCGAAGGCGATTGAA
Found at i:2536332 original size:54 final size:54
Alignment explanation
Indices: 2536268--2536842 Score: 738
Period size: 54 Copynumber: 10.6 Consensus size: 54
2536258 ATGTATTTAA
*
2536268 TGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCACGAAATTCATCCTATG
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCCTATG
* ** * * *
2536322 TGGATGAATAAACGTTTCAACAATAAGTGTGTATTTCACGAAATTTATCCTATG
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCCTATG
* * *
2536376 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCAGGGAATTCATCATATG
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCCTATG
* * *
2536430 TGGATGAATAACCGTTTAGGCACTAAGTGTGCATTTCAGGGAATTCATCCTATG
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCCTATG
2536484 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCCTATG
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCCTATG
* * * ** *
2536538 TAGACGAATAATCGTTTCAACACTAAGTGTGCATTTCACGAAATTTATCCTATG
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCCTATG
* * *
2536592 TGGATGAATAACCGTTTCGGCACTGAGTGTACATTTCACGGAATTCATCCTATG
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCCTATG
* *
2536646 TGGATGAATAACCGTTTCGGCACTAAGTGTACATTTCACGGAATTCATCCTATG
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCCTATG
* * * * * * * **
2536700 TAGATGAAGAATCATTTCGGCAATAAGTGTGCATTTCATGGAATTCATAATATG
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCCTATG
** * **
2536754 TTTATGAATAACCGTTTCGGCACTAAGTGTGCATTTCA-TAGAATTCATAATATG
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGA-AATTCATCCTATG
** * * * *
2536808 TTTATGAATAACCGTATGGGCACTACGAGTGCATT
1 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATT
2536843 ATAAAGAAAT
Statistics
Matches: 464, Mismatches: 56, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
54 464 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (54 bp):
TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCCTATG
Found at i:2545470 original size:21 final size:20
Alignment explanation
Indices: 2545424--2545478 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
2545414 AGGGATGGAA
*
2545424 AAGCA-AGTGGTGCAATGGG
1 AAGCATAGTGGTGGAATGGG
2545443 AAGCATAGTGGTGGAATGAGG
1 AAGCATAGTGGTGGAATG-GG
*
2545464 GAGCATAGTGGTGGA
1 AAGCATAGTGGTGGA
2545479 CATATATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.16
20 11 0.34
21 16 0.50
ACGTcount: A:0.31, C:0.07, G:0.44, T:0.18
Consensus pattern (20 bp):
AAGCATAGTGGTGGAATGGG
Found at i:2545848 original size:16 final size:17
Alignment explanation
Indices: 2545829--2545861 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2545819 GAAAATTTAT
*
2545829 AAATAAGAAT-AATAAA
1 AAATAACAATAAATAAA
2545845 AAATAACAATAAATAAA
1 AAATAACAATAAATAAA
2545862 TATAAATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (17 bp):
AAATAACAATAAATAAA
Found at i:2546353 original size:33 final size:33
Alignment explanation
Indices: 2546311--2546374 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
2546301 ATACTAAAAA
2546311 ATACATAAATTATTATAAAATAAAG-TAATTACT
1 ATACATAAATT-TTATAAAATAAAGTTAATTACT
*
2546344 ATACATAAATTTTATAAAATCAAGTTAATTA
1 ATACATAAATTTTATAAAATAAAGTTAATTA
2546375 AGTTAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (33 bp):
ATACATAAATTTTATAAAATAAAGTTAATTACT
Found at i:2546417 original size:27 final size:28
Alignment explanation
Indices: 2546311--2546422 Score: 106
Period size: 27 Copynumber: 3.9 Consensus size: 28
2546301 ATACTAAAAA
*
2546311 ATACATAAATTATTATAAAATAAAGTAATTAC
1 ATACATAAATTATTATAAAAT----CAATTAC
2546343 TATACATAAATT-TTATAAAATCAAGTTA-
1 -ATACATAAATTATTATAAAATCAA-TTAC
*
2546371 ATTA-AGTTAATTATTATAAAATCAA-TAC
1 A-TACA-TAAATTATTATAAAATCAATTAC
2546399 ATACATAAATTATTATAAAATCAA
1 ATACATAAATTATTATAAAATCAA
2546423 GTAAATTATT
Statistics
Matches: 70, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
27 24 0.34
28 11 0.16
29 15 0.21
32 9 0.13
33 11 0.16
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.37
Consensus pattern (28 bp):
ATACATAAATTATTATAAAATCAATTAC
Found at i:2546429 original size:20 final size:20
Alignment explanation
Indices: 2546404--2546490 Score: 84
Period size: 20 Copynumber: 4.0 Consensus size: 20
2546394 AATACATACA
2546404 TAAATTATTATAAAATCAAG
1 TAAATTATTATAAAATCAAG
*
2546424 TAAATTATTATAAAATCAAATATATACT
1 TAAATTATTATAAAATC------A-A-G
2546452 TAAATTATTATAAAATCAAG
1 TAAATTATTATAAAATCAAG
*
2546472 TTAATTATTATAAAATCAA
1 TAAATTATTATAAAATCAA
2546491 TATATGTACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
20 35 0.62
21 1 0.02
22 1 0.02
26 1 0.02
27 1 0.02
28 17 0.30
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (20 bp):
TAAATTATTATAAAATCAAG
Found at i:2546468 original size:48 final size:47
Alignment explanation
Indices: 2546374--2546504 Score: 208
Period size: 48 Copynumber: 2.7 Consensus size: 47
2546364 CAAGTTAATT
*
2546374 AAGTTAATTATTATAAAATCAATACATACATAAATTATTATAAAATC
1 AAGTTAATTATTATAAAATCAATATATACATAAATTATTATAAAATC
* *
2546421 AAGTAAATTATTATAAAATCAAATATATACTTAAATTATTATAAAATC
1 AAGTTAATTATTATAAAATC-AATATATACATAAATTATTATAAAATC
2546469 AAGTTAATTATTATAAAATCAATATATGTACATAAA
1 AAGTTAATTATTATAAAATCAATATA--TACATAAA
2546505 AATACATTTA
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
47 25 0.33
48 44 0.58
49 7 0.09
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (47 bp):
AAGTTAATTATTATAAAATCAATATATACATAAATTATTATAAAATC
Found at i:2552858 original size:30 final size:29
Alignment explanation
Indices: 2552799--2552858 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 29
2552789 TCTATGTCAT
**
2552799 TTCATATAACATGTAATACATATTGCATA
1 TTCATATAACATGTAATACATATCACATA
*
2552828 TTCATATAAGCATGT-ATATCATGTCACATA
1 TTCATATAA-CATGTAATA-CATATCACATA
2552858 T
1 T
2552859 ATACTATACC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (29 bp):
TTCATATAACATGTAATACATATCACATA
Found at i:2559105 original size:10 final size:10
Alignment explanation
Indices: 2559090--2559115 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2559080 TGATGTTGTG
2559090 GCCGTTTATA
1 GCCGTTTATA
2559100 GCCGTTTATA
1 GCCGTTTATA
2559110 GCCGTT
1 GCCGTT
2559116 GGGAGTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (10 bp):
GCCGTTTATA
Found at i:2559284 original size:20 final size:21
Alignment explanation
Indices: 2559254--2559293 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
2559244 AGCCGTTGGG
2559254 GCCTAATGGTATTGATACTAT
1 GCCTAATGGTATTGATACTAT
2559275 GCCT-ATGGTATTGATACTA
1 GCCTAATGGTATTGATACTA
2559294 CCATGTAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (21 bp):
GCCTAATGGTATTGATACTAT
Found at i:2560275 original size:17 final size:16
Alignment explanation
Indices: 2560247--2560298 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
2560237 ATAACTGTAA
*
2560247 AATATCTGATAATTGT
1 AATATATGATAATTGT
2560263 AATCATATGATAATTGT
1 AAT-ATATGATAATTGT
* *
2560280 ATATATCTGATAACTGT
1 A-ATATATGATAATTGT
2560297 AA
1 AA
2560299 ACATTTAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 4 0.13
17 25 0.81
18 2 0.06
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (16 bp):
AATATATGATAATTGT
Found at i:2565493 original size:35 final size:35
Alignment explanation
Indices: 2565453--2565549 Score: 149
Period size: 35 Copynumber: 2.8 Consensus size: 35
2565443 TGTCATCTCA
* *
2565453 TAATGCACTATTTTAGCAACTTTTCAGTGGTCAAT
1 TAATGCACCATTTAAGCAACTTTTCAGTGGTCAAT
* *
2565488 TAATGCACCATTTCAGTAACTTTTCAGTGGTCAAT
1 TAATGCACCATTTAAGCAACTTTTCAGTGGTCAAT
*
2565523 TAATGCACCATTTAAACAACTTTTCAG
1 TAATGCACCATTTAAGCAACTTTTCAG
2565550 AAAACTTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 56 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (35 bp):
TAATGCACCATTTAAGCAACTTTTCAGTGGTCAAT
Found at i:2567616 original size:54 final size:54
Alignment explanation
Indices: 2567534--2567641 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
2567524 GAGATCTGCG
2567534 ATGCACTTGTCTCCTGTGGATGTGCAGTCCCTCATGTTGGTCATGTTGCCAGAA
1 ATGCACTTGTCTCCTGTGGATGTGCAGTCCCTCATGTTGGTCATGTTGCCAGAA
2567588 ATGCACTTGTCTCCTGTGGATGTGCAGTCCCTCATGTTGGTCATGTTGCCAGAA
1 ATGCACTTGTCTCCTGTGGATGTGCAGTCCCTCATGTTGGTCATGTTGCCAGAA
2567642 TTCTAAAAGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (54 bp):
ATGCACTTGTCTCCTGTGGATGTGCAGTCCCTCATGTTGGTCATGTTGCCAGAA
Found at i:2576866 original size:39 final size:39
Alignment explanation
Indices: 2576823--2576933 Score: 150
Period size: 39 Copynumber: 2.8 Consensus size: 39
2576813 ACATGATGGA
* *
2576823 GCATCGAGAGCTGCAAGCCCGGGTGATGAGCATCCTACT
1 GCATCGAGAGCTGCAAGTCCGGATGATGAGCATCCTACT
** **
2576862 GCATCGAGAGCTATAAGTCCGGATGATGAGCATCCTGTT
1 GCATCGAGAGCTGCAAGTCCGGATGATGAGCATCCTACT
* *
2576901 ACATCGAGAGTTGCAAGTCCGGATGATGAGCAT
1 GCATCGAGAGCTGCAAGTCCGGATGATGAGCAT
2576934 TCTGCTGTGT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 62 1.00
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.22
Consensus pattern (39 bp):
GCATCGAGAGCTGCAAGTCCGGATGATGAGCATCCTACT
Found at i:2576950 original size:39 final size:39
Alignment explanation
Indices: 2576835--2576959 Score: 108
Period size: 39 Copynumber: 3.2 Consensus size: 39
2576825 ATCGAGAGCT
* * * * *
2576835 GCAAGCCCGGGTGATGAGCATCCTACTGCATCGAGAGCT-
1 GCAAGTCCGGATGATGAGCATCCTGCTACATCAAGAG-TG
** * * *
2576874 ATAAGTCCGGATGATGAGCATCCTGTTACATCGAGAGTT
1 GCAAGTCCGGATGATGAGCATCCTGCTACATCAAGAGTG
* ***
2576913 GCAAGTCCGGATGATGAGCATTCTGCTGTGTCAAGAGTG
1 GCAAGTCCGGATGATGAGCATCCTGCTACATCAAGAGTG
2576952 GCAAGTCC
1 GCAAGTCC
2576960 TGCTTTGGTT
Statistics
Matches: 69, Mismatches: 16, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
38 1 0.01
39 68 0.99
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (39 bp):
GCAAGTCCGGATGATGAGCATCCTGCTACATCAAGAGTG
Found at i:2581253 original size:11 final size:11
Alignment explanation
Indices: 2581237--2581275 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
2581227 CCAACAAACC
*
2581237 ATAACAGACTA
1 ATAACAAACTA
2581248 ATAACAAACTA
1 ATAACAAACTA
2581259 ATAACAAACTA
1 ATAACAAACTA
*
2581270 CTAACA
1 ATAACA
2581276 CTCTAACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.59, C:0.21, G:0.03, T:0.18
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:2581281 original size:22 final size:22
Alignment explanation
Indices: 2581229--2581275 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
2581219 TCAAGTAACC
* *
2581229 AACAAAC-CATAACAGACTAAT
1 AACAAACTAATAACAAACTAAT
*
2581250 AACAAACTAATAACAAACTACT
1 AACAAACTAATAACAAACTAAT
2581272 AACA
1 AACA
2581276 CTCTAACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.60, C:0.23, G:0.02, T:0.15
Consensus pattern (22 bp):
AACAAACTAATAACAAACTAAT
Found at i:2585046 original size:29 final size:27
Alignment explanation
Indices: 2584981--2585055 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 27
2584971 GAACCTGAAT
* *
2584981 ATGTGTTTTTATTTATTTTAATTCGGCC
1 ATGTG-TTTTATTTATTTTAATTAGCCC
2585009 ATGTAGTTTTAATTTATTTTAATTTAGTCCC
1 ATGT-GTTTT-ATTTATTTTAA-TTAG-CCC
2585040 AT-TGTTTTATTTATTT
1 ATGTGTTTTATTTATTT
2585056 CCATTATTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
28 16 0.39
29 17 0.41
30 4 0.10
31 4 0.10
ACGTcount: A:0.21, C:0.08, G:0.11, T:0.60
Consensus pattern (27 bp):
ATGTGTTTTATTTATTTTAATTAGCCC
Found at i:2585855 original size:125 final size:130
Alignment explanation
Indices: 2585713--2586017 Score: 361
Period size: 125 Copynumber: 2.4 Consensus size: 130
2585703 AAGGCATAAG
* * * * * * *
2585713 AGGTCATTTATTATCGATTGAAAATAATTTGATATTATCGTTTTCTCTCGAATTAATATCT-ATT
1 AGGTCAGTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATAT-TGAAT
* * *
2585777 TTTTAGACGGAATA-T-TATCTATTTATTTCAATTGGAGT-A-AAATGACTGTTTTAATGCACGA
65 TTTAAGACGAAATAGTATATCTATTTATTCCAATTGGAGTAATAAATGACTGTTTTAATGCACGA
2585838 A
130 A
* * ** * *
2585839 AGGTC-GTTATTCTCGATTGGAAATCATTAAATATTATTATTTTCACTTGAATCGATATTGAATT
1 AGGTCAGTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATT
* * * *
2585903 TTAAGATGAAATAGTAATATCTCTTTATTCCAATTGGAGTAATAAATGATTGTTTTAATGCATGA
66 TTAAGACGAAATAGT-ATATCTATTTATTCCAATTGGAGTAATAAATGACTGTTTTAATGCACGA
2585968 A
130 A
*
2585969 AGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTC
1 AGGTCAGTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTC
2586018 TTAAAATTAT
Statistics
Matches: 146, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
124 1 0.01
125 54 0.37
126 6 0.04
128 21 0.14
129 1 0.01
130 26 0.18
131 37 0.25
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (130 bp):
AGGTCAGTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATT
TTAAGACGAAATAGTATATCTATTTATTCCAATTGGAGTAATAAATGACTGTTTTAATGCACGAA
Done.