Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008591.1 Hibiscus syriacus cultivar Beakdansim tig00111540_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: 1730314
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1081896 original size:19 final size:19
Alignment explanation
Indices: 1081872--1081935 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
1081862 CCTCGAGTTG
*
1081872 CTGTTCAAACAGTGATTTA
1 CTGTTCAAACAGTAATTTA
*
1081891 CTGTTCAAATAGTAATTTA
1 CTGTTCAAACAGTAATTTA
* *
1081910 CTGTTCAAATAGTAAATTA
1 CTGTTCAAACAGTAATTTA
*
1081929 CTATTCA
1 CTGTTCA
1081936 TAAAAACATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (19 bp):
CTGTTCAAACAGTAATTTA
Found at i:1082032 original size:29 final size:31
Alignment explanation
Indices: 1082000--1082059 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1081990 AAATTTTGAA
*
1082000 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1082029 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1082060 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1082305 original size:30 final size:30
Alignment explanation
Indices: 1082240--1082320 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 30
1082230 GAACAATTTG
* *
1082240 ATATTTTATATAAAGTTTAAATGTTAAATTA
1 ATATTTTATATAAA-TTTAAATGTCAAAATA
*
1082271 ATATTTTATGTAGAATTTAAA-GTCAAAATA
1 ATATTTTATATA-AATTTAAATGTCAAAATA
*
1082301 ATATTTTATTTAAAATTTAA
1 ATATTTTATAT-AAATTTAA
1082321 CTACTTTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
30 24 0.55
31 18 0.41
32 2 0.05
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (30 bp):
ATATTTTATATAAATTTAAATGTCAAAATA
Found at i:1084292 original size:149 final size:149
Alignment explanation
Indices: 1084022--1084325 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
1084012 CAAAGTGCCC
1084022 CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1084087 CATATACATATGCTAAGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAAGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
1084152 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
*
1084171 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
* *
1084236 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCATACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAAGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
1084301 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
1084320 CGTAGA
1 CGTAGA
1084326 CCCTCGACTC
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.28
Consensus pattern (149 bp):
CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAAGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:1084869 original size:2 final size:2
Alignment explanation
Indices: 1084862--1084889 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1084852 TCTCTTAGAC
1084862 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
1084890 TCACATGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1085238 original size:18 final size:18
Alignment explanation
Indices: 1085217--1085251 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1085207 TCCCATCTAG
1085217 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
1085235 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
1085252 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:1085859 original size:21 final size:21
Alignment explanation
Indices: 1085835--1085879 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1085825 TCTTGTTCAT
* *
1085835 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1085856 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1085877 TTG
1 TTG
1085880 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1107353 original size:36 final size:36
Alignment explanation
Indices: 1107298--1107520 Score: 220
Period size: 36 Copynumber: 6.2 Consensus size: 36
1107288 CTCTCCTGGT
* * * * *
1107298 ATTTGTGGAATCTGAGGGATCTGTGGGATTTGAGGA
1 ATTTGTGGGATCTGTGGGATTTGTGGGATTTGTGGG
1107334 ATTTGTGGGATGCT-TGGGATTTGTGGGATTCT-TGGG
1 ATTTGTGGGAT-CTGTGGGATTTGTGGGATT-TGTGGG
* *
1107370 ATTTGTGGGATCTGTGGGATTTGTGGTATCTGTGGG
1 ATTTGTGGGATCTGTGGGATTTGTGGGATTTGTGGG
* * * * *
1107406 ATTTGTGGGATATTTGGGATTTCTGGTATCTGTGGG
1 ATTTGTGGGATCTGTGGGATTTGTGGGATTTGTGGG
* *
1107442 ATTTGTGGGATCTGTGGGATTCT-TGGGATTTCTGGT
1 ATTTGTGGGATCTGTGGGATT-TGTGGGATTTGTGGG
* * *
1107478 ATCTGTGGGATTTGTGGAATTAT-TGGGATTTGTGGG
1 ATTTGTGGGATCTGTGGGATT-TGTGGGATTTGTGGG
*
1107514 ACTTGTG
1 ATTTGTG
1107521 CACATGGTGG
Statistics
Matches: 158, Mismatches: 24, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
35 3 0.02
36 151 0.96
37 4 0.03
ACGTcount: A:0.14, C:0.06, G:0.39, T:0.41
Consensus pattern (36 bp):
ATTTGTGGGATCTGTGGGATTTGTGGGATTTGTGGG
Found at i:1107513 original size:9 final size:9
Alignment explanation
Indices: 1107298--1107520 Score: 195
Period size: 9 Copynumber: 24.8 Consensus size: 9
1107288 CTCTCCTGGT
*
1107298 ATTTGTGGA
1 ATTTGTGGG
* *
1107307 ATCTGAGGG
1 ATTTGTGGG
*
1107316 ATCTGTGGG
1 ATTTGTGGG
* *
1107325 ATTTGAGGA
1 ATTTGTGGG
1107334 ATTTGTGGG
1 ATTTGTGGG
*
1107343 ATGCT-TGGG
1 AT-TTGTGGG
1107352 ATTTGTGGG
1 ATTTGTGGG
1107361 ATTCT-TGGG
1 ATT-TGTGGG
1107370 ATTTGTGGG
1 ATTTGTGGG
*
1107379 ATCTGTGGG
1 ATTTGTGGG
*
1107388 ATTTGTGGT
1 ATTTGTGGG
*
1107397 ATCTGTGGG
1 ATTTGTGGG
1107406 ATTTGTGGG
1 ATTTGTGGG
1107415 ATATT-TGGG
1 AT-TTGTGGG
* *
1107424 ATTTCTGGT
1 ATTTGTGGG
*
1107433 ATCTGTGGG
1 ATTTGTGGG
1107442 ATTTGTGGG
1 ATTTGTGGG
*
1107451 ATCTGTGGG
1 ATTTGTGGG
1107460 ATTCT-TGGG
1 ATT-TGTGGG
* *
1107469 ATTTCTGGT
1 ATTTGTGGG
*
1107478 ATCTGTGGG
1 ATTTGTGGG
*
1107487 ATTTGTGGA
1 ATTTGTGGG
1107496 ATTAT-TGGG
1 ATT-TGTGGG
1107505 ATTTGTGGG
1 ATTTGTGGG
*
1107514 ACTTGTG
1 ATTTGTG
1107521 CACATGGTGG
Statistics
Matches: 172, Mismatches: 32, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
8 6 0.03
9 160 0.93
10 6 0.03
ACGTcount: A:0.14, C:0.06, G:0.39, T:0.41
Consensus pattern (9 bp):
ATTTGTGGG
Found at i:1108786 original size:23 final size:23
Alignment explanation
Indices: 1108760--1108807 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1108750 ATAAAGTACA
*
1108760 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1108783 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1108806 AT
1 AT
1108808 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1109557 original size:18 final size:18
Alignment explanation
Indices: 1109534--1109570 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1109524 CGAAATATAT
1109534 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1109552 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1109570 A
1 A
1109571 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1109800 original size:23 final size:23
Alignment explanation
Indices: 1109774--1109838 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
1109764 ATGCGAGATA
1109774 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
**
1109797 GATACCTATTACATTATATAAGG
1 GATACCTATTACATTATATAAAC
* *
1109820 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
1109839 GTTTACCTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:1110222 original size:21 final size:22
Alignment explanation
Indices: 1110197--1110248 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1110187 ACACTTTACA
*
1110197 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
1110220 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
1110243 ATATAA
1 ATATAA
1110249 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:1110233 original size:23 final size:23
Alignment explanation
Indices: 1110207--1110269 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1110197 ATATAACCAC
1110207 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1110230 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1110253 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1110270 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1110652 original size:21 final size:22
Alignment explanation
Indices: 1110627--1110678 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1110617 ACACTTTACA
*
1110627 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
1110650 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
1110673 ATATAA
1 ATATAA
1110679 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:1110663 original size:23 final size:23
Alignment explanation
Indices: 1110637--1110699 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1110627 ATATAACCAC
1110637 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1110660 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1110683 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1110700 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1111083 original size:21 final size:22
Alignment explanation
Indices: 1111058--1111109 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1111048 ACACTTTACA
*
1111058 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
1111081 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
1111104 ATATAA
1 ATATAA
1111110 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:1111094 original size:23 final size:23
Alignment explanation
Indices: 1111068--1111130 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1111058 ATATAACCAC
1111068 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1111091 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1111114 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1111131 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1111125 original size:431 final size:431
Alignment explanation
Indices: 1109776--1111229 Score: 2892
Period size: 431 Copynumber: 3.4 Consensus size: 431
1109766 GCGAGATAGA
1109776 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
*
1109841 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
1109906 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
1109971 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
1110036 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
261 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
1110101 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
326 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
1110166 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
391 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
1110207 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1110272 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTAAAACTTA
66 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
1110336 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
1110401 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
1110466 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
261 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
1110531 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
326 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
1110596 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
391 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
1110637 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1110702 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
1110767 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
1110832 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
1110897 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
261 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
1110962 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
326 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
1111027 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
391 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
1111068 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1111133 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
1111198 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
1111230 ACTGCGAATT
Statistics
Matches: 1021, Mismatches: 1, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
430 430 0.42
431 591 0.58
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (431 bp):
TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
Found at i:1112657 original size:199 final size:200
Alignment explanation
Indices: 1112213--1112840 Score: 1177
Period size: 200 Copynumber: 3.1 Consensus size: 200
1112203 TTTAAATTTG
* *
1112213 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1112278 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1112343 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
1112408 AAAAA
196 AAAAA
*
1112413 TATCGACACAAATTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
1112478 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
1112543 CGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
1112607 AAAAA
196 AAAAA
1112612 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
1112677 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1112742 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
1112807 AAAAA
196 AAAAA
*
1112812 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
1112841 TGACCCTTAA
Statistics
Matches: 416, Mismatches: 11, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
199 194 0.47
200 222 0.53
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (200 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
AAAAA
Found at i:1112948 original size:19 final size:19
Alignment explanation
Indices: 1112921--1112965 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1112911 TATTCACATA
*
1112921 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
1112940 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
1112959 AAAATTA
1 AAAATTA
1112966 ACTCGACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:1114791 original size:33 final size:33
Alignment explanation
Indices: 1114754--1114819 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1114744 CATCTTAATA
*
1114754 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
1114787 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
1114820 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:1116963 original size:24 final size:24
Alignment explanation
Indices: 1116926--1116978 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1116916 CCGTTCTATC
1116926 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
1116950 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
1116974 TATTT
1 TATTT
1116979 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:1117169 original size:20 final size:19
Alignment explanation
Indices: 1117123--1117169 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1117113 TCCGGTATCA
*
1117123 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
1117142 TTGGTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
1117163 TTTTACC
1 TTTTACC
1117170 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1118348 original size:22 final size:20
Alignment explanation
Indices: 1118317--1118358 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
1118307 GTGATGAGTC
1118317 AATTAAAAAATATTAAAAAATA
1 AATTAAAAAATA--AAAAAATA
*
1118339 AATTAGAAAATAAAAAAATA
1 AATTAAAAAATAAAAAAATA
1118359 TTCGATGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (20 bp):
AATTAAAAAATAAAAAAATA
Found at i:1121450 original size:29 final size:27
Alignment explanation
Indices: 1121417--1121470 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
1121407 TGCAATTATG
*
1121417 TAATACTTTTAATTTTTTTAAATATATAT
1 TAATA-TTTT-ATTTTTATAAATATATAT
*
1121446 TAATATTTTATTTTTATAATTATAT
1 TAATATTTTATTTTTATAAATATAT
1121471 GATATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 14 0.61
28 4 0.17
29 5 0.22
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (27 bp):
TAATATTTTATTTTTATAAATATATAT
Found at i:1121460 original size:25 final size:24
Alignment explanation
Indices: 1121410--1121478 Score: 66
Period size: 27 Copynumber: 2.7 Consensus size: 24
1121400 TTAAATATGC
* *
1121410 AATTATGTAATACTTTTAATTTTTTT
1 AATTATATAATA-TTTT-ATTTTTAT
1121436 AAATATATATTAATATTTTATTTTTAT
1 -AAT-TATA-TAATATTTTATTTTTAT
*
1121463 AATTATATGATATTTT
1 AATTATATAATATTTT
1121479 TAGAAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
24 8 0.22
25 4 0.11
26 3 0.08
27 10 0.27
28 7 0.19
29 5 0.14
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.59
Consensus pattern (24 bp):
AATTATATAATATTTTATTTTTAT
Found at i:1121765 original size:20 final size:20
Alignment explanation
Indices: 1121717--1121778 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
1121707 AACTTAAATC
*
1121717 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
1121737 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
1121755 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
1121774 AAAAT
1 AAAAT
1121779 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:1121860 original size:63 final size:64
Alignment explanation
Indices: 1121773--1121932 Score: 234
Period size: 63 Copynumber: 2.5 Consensus size: 64
1121763 TTATATGATA
**
1121773 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTT-AAAAATTAATAT
1 TAAAATT-AATATAAATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1121837 TAAAATTAATATAAATAATATAATATT-AAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAATATAAATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
* *
1121900 TAAAATTAAAATCAAATATAATATAAAATTAAA
1 TAAAATTAATAT--AA-ATAATATAATATTAAA
1121933 TATAAAACCT
Statistics
Matches: 87, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
62 23 0.26
63 41 0.47
64 7 0.08
65 2 0.02
66 12 0.14
67 2 0.02
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (64 bp):
TAAAATTAATATAAATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:1121875 original size:27 final size:24
Alignment explanation
Indices: 1121770--1121939 Score: 93
Period size: 24 Copynumber: 6.9 Consensus size: 24
1121760 AATTTATATG
*
1121770 ATAT-AAAATTAAATATCTATAATATA
1 ATATAAAAATT-AATAT-TAAAAT-TA
* *
1121796 ATATTAAAAAATTAATATT-TAATTT
1 ATA-T-AAAAATTAATATTAAAATTA
*
1121821 ATTTAAAAATTAATATTAAAATTA
1 ATATAAAAATTAATATTAAAATTA
1121845 ATATAAATAATATAATATTAAAAATTA
1 ATATAAA-AAT-TAATATT-AAAATTA
** *
1121872 ATAT-TTAATTTAT-TTAAAAAATTA
1 ATATAAAAATTAATATT--AAAATTA
* * *
1121896 ATATTAAAATTAA-AATCAAATATA
1 ATATAAAAATTAATATTAAAAT-TA
1121920 ATAT-AAAATTAA-ATATAAAA
1 ATATAAAAATTAATAT-TAAAA
1121940 CCTCCTTGAA
Statistics
Matches: 117, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
23 28 0.24
24 36 0.31
25 15 0.13
26 14 0.12
27 13 0.11
28 5 0.04
29 6 0.05
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (24 bp):
ATATAAAAATTAATATTAAAATTA
Found at i:1121934 original size:12 final size:12
Alignment explanation
Indices: 1121889--1121939 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
1121879 ATTTATTTAA
1121889 AAAATT-AATATT
1 AAAATTAAATA-T
1121901 AAAATTAAA-AT
1 AAAATTAAATAT
*
1121912 CAAA-TATAATAT
1 AAAATTA-AATAT
1121924 AAAATTAAATAT
1 AAAATTAAATAT
1121936 AAAA
1 AAAA
1121940 CCTCCTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 2 0.06
11 6 0.18
12 21 0.64
13 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:1122369 original size:20 final size:20
Alignment explanation
Indices: 1122321--1122382 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
1122311 AACTTAAATC
*
1122321 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
1122341 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
1122359 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
1122378 AAAAT
1 AAAAT
1122383 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:1122380 original size:604 final size:593
Alignment explanation
Indices: 1121483--1122684 Score: 2269
Period size: 604 Copynumber: 2.0 Consensus size: 593
1121473 TATTTTTAGA
1121483 AAATATTTTTTAATTTATCAAATTATTTTATGATTATTTTTTATTTAATTGTGATTATATTTTAA
1 AAATATTTTTTAATTTATCAAATTATTTTATGATTATTTTTTATTTAATTGTGATTATATTTTAA
1121548 AATTTTAAAAACATAATTTATAATTTTTTATATTTTAAAATCTTAATTATCAAAAAATGAAATTA
66 AATTTTAAAAACATAATTTATAATTTTTTATATTTTAAAATCTTAATTATCAAAAAATGAAATTA
1121613 TTTTTTATTAAGCAATGTGGTTTAAATACTTACATTTTGTATAAAAAGTTTAAATATAATTTAAA
131 TTTTTTATTAAGCAATGTGGTTTAAATACTTACATTTTGTATAAAAAGTTTAAATATAATTTAAA
1121678 AATAACAAATCCAAAAAATATTATATTTAAACTTAAATCAAAATAATTAAAATAAATATAAAATT
196 AATAACAAATCCAAAAAATATTATATTTAAACTTAAATCAAAATAATTAAAATAAATATAAAATT
1121743 TTAATAATATATAAAATAATTTATATGATATAAAATTAAATATCTATAATATAATATTAAAAAAT
261 TTAATAATATATAAAATAATTTATATGATATAAAATTAAATATCTATAATATAATATTAAAAAAT
1121808 TAATATTTAATTTATTTAAAAATTAATATTAAAATTAATATAAATAATATAATATTAAAAATTAA
326 TAATATTTAATTTATTTAAAAATTAATATTAAAATTAATATAAATAATATAATATTAAAAATTAA
1121873 TATTTAATTTATTTAAAAAATTAATATTAAAATTAAAATCAAATATAATATAAAATTAAATATAA
391 TATTTAATTTATTTAAAAAATTAATATTAAAATTAAAATCAAATATAATATAAAATTAAATATAA
*
1121938 AACCTCCTTGAAGAGGTTAGAAGAAGTCTGCAGACATAAGGCCACGTCTACGTCGCGCAGACCAC
456 AACCTCCTTGAAAAGGTTAGAAGAAGTCTGCAGACATAAGGCCACGTCTACGT-----------C
1122003 GCGCAGACGTTAAAAGAGCTTATGTCTTATAAAAAACAAATGGTCTGTGAAGCACAATGTTTGCG
510 GCGCAGACGTTAAAAGAGCTTATGTCTTATAAAAAACAAATGGTCTGTGAAGCACAATGTTTGCG
*
1122068 CGTGGTCTGTGCGGCGCAG
575 CGTGGTCTGTGCGGCACAG
1122087 AAATATTTTTTAATTTATCAAATTATTTTATGATTATTTTTTATTTAATTGTGATTATATTTTAA
1 AAATATTTTTTAATTTATCAAATTATTTTATGATTATTTTTTATTTAATTGTGATTATATTTTAA
1122152 AATTTTAAAAACATAATTTATAATTTTTTATATTTTAAAATCTTAATTATCAAAAAATGAAATTA
66 AATTTTAAAAACATAATTTATAATTTTTTATATTTTAAAATCTTAATTATCAAAAAATGAAATTA
1122217 TTTTTTATTAAGCAATGTGGTTTAAATACTTACATTTTGTATAAAAAGTTTAAATATAATTTAAA
131 TTTTTTATTAAGCAATGTGGTTTAAATACTTACATTTTGTATAAAAAGTTTAAATATAATTTAAA
1122282 AATAACAAATCCAAAAAATATTATATTTAAACTTAAATCAAAATAATTAAAATAAATATAAAATT
196 AATAACAAATCCAAAAAATATTATATTTAAACTTAAATCAAAATAATTAAAATAAATATAAAATT
1122347 TTAATAATATATAAAATAATTTATATGATATAAAATTAAATATCTATAATATAATATTAAAAAAT
261 TTAATAATATATAAAATAATTTATATGATATAAAATTAAATATCTATAATATAATATTAAAAAAT
1122412 TAATATTTAATTTATTTAAAAATTAATATTAAAATTAATATAAATAATATAATATTAAAAATTAA
326 TAATATTTAATTTATTTAAAAATTAATATTAAAATTAATATAAATAATATAATATTAAAAATTAA
*
1122477 TATTTAATTTATTTAAAAAATTAATATTAAAATTAAAATCAAATATAATATATAATTAAATATAA
391 TATTTAATTTATTTAAAAAATTAATATTAAAATTAAAATCAAATATAATATAAAATTAAATATAA
*
1122542 AACCTCCTTGAAAAGGTTAGAATAAGTCTGCAGACATAAGGCCACGTCTACGTCGCGCAGACGTT
456 AACCTCCTTGAAAAGGTTAGAAGAAGTCTGCAGACATAAGGCCACGTCTACGTCGCGCAGACGTT
1122607 AAAAGAGCTTATGTCTTATAAAAAACAAATGGTCTGTGAAGCACAATGTTTGCGCGTGGTCTGTG
521 AAAAGAGCTTATGTCTTATAAAAAACAAATGGTCTGTGAAGCACAATGTTTGCGCGTGGTCTGTG
1122672 CGGCACAG
586 CGGCACAG
1122680 AAATA
1 AAATA
1122685 AGAGCTTTAC
Statistics
Matches: 594, Mismatches: 4, Indels: 11
0.98 0.01 0.02
Matches are distributed among these distances:
593 89 0.15
604 505 0.85
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (593 bp):
AAATATTTTTTAATTTATCAAATTATTTTATGATTATTTTTTATTTAATTGTGATTATATTTTAA
AATTTTAAAAACATAATTTATAATTTTTTATATTTTAAAATCTTAATTATCAAAAAATGAAATTA
TTTTTTATTAAGCAATGTGGTTTAAATACTTACATTTTGTATAAAAAGTTTAAATATAATTTAAA
AATAACAAATCCAAAAAATATTATATTTAAACTTAAATCAAAATAATTAAAATAAATATAAAATT
TTAATAATATATAAAATAATTTATATGATATAAAATTAAATATCTATAATATAATATTAAAAAAT
TAATATTTAATTTATTTAAAAATTAATATTAAAATTAATATAAATAATATAATATTAAAAATTAA
TATTTAATTTATTTAAAAAATTAATATTAAAATTAAAATCAAATATAATATAAAATTAAATATAA
AACCTCCTTGAAAAGGTTAGAAGAAGTCTGCAGACATAAGGCCACGTCTACGTCGCGCAGACGTT
AAAAGAGCTTATGTCTTATAAAAAACAAATGGTCTGTGAAGCACAATGTTTGCGCGTGGTCTGTG
CGGCACAG
Found at i:1122464 original size:63 final size:63
Alignment explanation
Indices: 1122377--1122521 Score: 229
Period size: 63 Copynumber: 2.3 Consensus size: 63
1122367 TTATATGATA
**
1122377 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTT-AAAAATTAATAT
1 TAAAATT-AATATAAATAATATAATATT-AAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1122441 TAAAATTAATATAAATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAATATAAATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
*
1122504 TAAAATTAAAATCAAATA
1 TAAAATTAATAT-AAATA
1122522 TAATATATAA
Statistics
Matches: 76, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
62 23 0.30
63 41 0.54
64 12 0.16
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (63 bp):
TAAAATTAATATAAATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:1122476 original size:39 final size:37
Alignment explanation
Indices: 1122427--1122528 Score: 116
Period size: 39 Copynumber: 2.7 Consensus size: 37
1122417 TTTAATTTAT
*
1122427 TTAAAAATTAATATTAAAATTAATATAAATAATATAATA
1 TTAAAAATTAATATT-AAATTAATATAAAAAAT-TAATA
* * *
1122466 TTAAAAATTAATATTTAATTTATTTAAAAAATTAATA
1 TTAAAAATTAATATTAAATTAATATAAAAAATTAATA
* *
1122503 TT-AAAATTAAAATCAAATATAATATA
1 TTAAAAATTAATATTAAAT-TAATATA
1122529 TAATTAAATA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
36 13 0.25
37 12 0.23
38 13 0.25
39 15 0.28
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (37 bp):
TTAAAAATTAATATTAAATTAATATAAAAAATTAATA
Found at i:1122479 original size:27 final size:24
Alignment explanation
Indices: 1122374--1122479 Score: 90
Period size: 26 Copynumber: 4.2 Consensus size: 24
1122364 AATTTATATG
*
1122374 ATAT-AAAATTAAATATCTATAATATA
1 ATATAAAAATT-AATAT-TAAAAT-TA
* *
1122400 ATATTAAAAAATTAATATT-TAATTT
1 ATA-T-AAAAATTAATATTAAAATTA
*
1122425 ATTTAAAAATTAATATTAAAATTA
1 ATATAAAAATTAATATTAAAATTA
1122449 ATATAAATAATATAATATTAAAAATTA
1 ATATAAA-AAT-TAATATT-AAAATTA
1122476 ATAT
1 ATAT
1122480 TTAATTTATT
Statistics
Matches: 68, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
23 13 0.19
24 11 0.16
25 6 0.09
26 14 0.21
27 13 0.19
28 5 0.07
29 6 0.09
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.42
Consensus pattern (24 bp):
ATATAAAAATTAATATTAAAATTA
Found at i:1137844 original size:22 final size:20
Alignment explanation
Indices: 1137818--1137858 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1137808 TTCACCTTTA
1137818 ATTTAAATTACATATTTTTTTT
1 ATTT-AATTA-ATATTTTTTTT
*
1137840 ATTTAATTAATCTTTTTTT
1 ATTTAATTAATATTTTTTT
1137859 ATATGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 5 0.28
22 4 0.22
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTTAATTAATATTTTTTTT
Found at i:1139163 original size:27 final size:27
Alignment explanation
Indices: 1139125--1139216 Score: 130
Period size: 27 Copynumber: 3.4 Consensus size: 27
1139115 CACCTTGCGG
* * * *
1139125 AGGTGCTGGTGGACTTGAACTGGTTGA
1 AGGTGCCGGTGGACTTAAACCGGTAGA
1139152 AGGTGCCGGTGGACTTAAACCGGTAGA
1 AGGTGCCGGTGGACTTAAACCGGTAGA
*
1139179 CGGTGCCGGTGGACTTAAACCGGTAGA
1 AGGTGCCGGTGGACTTAAACCGGTAGA
*
1139206 CGGTGCCGGTG
1 AGGTGCCGGTG
1139217 AGGAATCAGA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.20, C:0.18, G:0.40, T:0.22
Consensus pattern (27 bp):
AGGTGCCGGTGGACTTAAACCGGTAGA
Found at i:1166766 original size:23 final size:24
Alignment explanation
Indices: 1166718--1166766 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
1166708 TCATGTATCA
*
1166718 TTAATTATTTAAATTTATTTTGAT
1 TTAATTATTTAAATTTAATTTGAT
*
1166742 TTAATT-TTTTAATTTAGATTT-AT
1 TTAATTATTTAAATTTA-ATTTGAT
1166765 TT
1 TT
1166767 TAATCATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
TTAATTATTTAAATTTAATTTGAT
Found at i:1168112 original size:20 final size:20
Alignment explanation
Indices: 1168087--1168136 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1168077 CAATACTTTG
*
1168087 GTATCGATACTGGC-CTTACA
1 GTATCGATACTGCCTCTTA-A
1168107 GTATCGATACTGCCTCTTAA
1 GTATCGATACTGCCTCTTAA
*
1168127 GTATTGATAC
1 GTATCGATAC
1168137 CCTAGTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (20 bp):
GTATCGATACTGCCTCTTAA
Found at i:1169034 original size:12 final size:12
Alignment explanation
Indices: 1169017--1169059 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
1169007 CTTGAAGGAG
1169017 GAAGAAAAAGAA
1 GAAGAAAAAGAA
*
1169029 GAAGAATAAGAA
1 GAAGAAAAAGAA
*
1169041 G-AGAAAAAAAA
1 GAAGAAAAAGAA
*
1169052 AAAGAAAA
1 GAAGAAAA
1169060 TATGGAAGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 8 0.31
12 18 0.69
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (12 bp):
GAAGAAAAAGAA
Found at i:1172612 original size:26 final size:26
Alignment explanation
Indices: 1172582--1172640 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
1172572 GGTTCAAGAG
*
1172582 TATTCTCTCTTAGAGATATAATCAAA
1 TATTCTCTCTTAGAGATATAATAAAA
* * *
1172608 TATTCTTTTTTAGAGGTATAATAAAA
1 TATTCTCTCTTAGAGATATAATAAAA
1172634 TATTCTC
1 TATTCTC
1172641 AACGGTATCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (26 bp):
TATTCTCTCTTAGAGATATAATAAAA
Found at i:1172865 original size:14 final size:14
Alignment explanation
Indices: 1172834--1172870 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1172824 TTACAACAAC
*
1172834 CTAAC-AACTTCAA
1 CTAACTAACTGCAA
1172847 C-AACTAACTGCAA
1 CTAACTAACTGCAA
1172860 CTAACTAACTG
1 CTAACTAACTG
1172871 ACTACACCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 3 0.14
13 9 0.43
14 9 0.43
ACGTcount: A:0.43, C:0.30, G:0.05, T:0.22
Consensus pattern (14 bp):
CTAACTAACTGCAA
Found at i:1183215 original size:20 final size:21
Alignment explanation
Indices: 1183190--1183246 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
1183180 GGTACAGAGA
1183190 GAATCGATTCCCCCTTT-AGG
1 GAATCGATTCCCCCTTTAAGG
1183210 GAATCGATTCCCCCTTTGAAAGG
1 GAATCGATTCCCCCTTT--AAGG
*
1183233 GAACCGATTCCCCC
1 GAATCGATTCCCCC
1183247 CACAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 17 0.52
23 16 0.48
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.25
Consensus pattern (21 bp):
GAATCGATTCCCCCTTTAAGG
Found at i:1183240 original size:23 final size:20
Alignment explanation
Indices: 1183194--1183246 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 20
1183184 CAGAGAGAAT
*
1183194 CGATTCCCCCTTTAGGGAAT
1 CGATTCCCCCTTTAGGGAAC
1183214 CGATTCCCCCTTTGAAAGGGAAC
1 CGATTCCCCCTTT---AGGGAAC
1183237 CGATTCCCCC
1 CGATTCCCCC
1183247 CACAGGGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 13 0.45
23 16 0.55
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.25
Consensus pattern (20 bp):
CGATTCCCCCTTTAGGGAAC
Found at i:1190068 original size:21 final size:21
Alignment explanation
Indices: 1190042--1190081 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1190032 CAGAACCCCA
*
1190042 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1190063 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1190082 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1190111 original size:21 final size:21
Alignment explanation
Indices: 1190063--1190125 Score: 90
Period size: 21 Copynumber: 2.9 Consensus size: 21
1190053 ATTCCCCTGT
1190063 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
*
1190086 AGGGGGAATCGGTTCCCTCAA
1 GGGGGGAATCGGTTCCCTCAA
*
1190107 GGGGGGAATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
1190126 TGCACCAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 21 0.57
22 3 0.08
23 13 0.35
ACGTcount: A:0.19, C:0.25, G:0.35, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:1198101 original size:19 final size:19
Alignment explanation
Indices: 1198073--1198146 Score: 85
Period size: 19 Copynumber: 3.7 Consensus size: 19
1198063 CAGGCAAAGT
*
1198073 GTATCCATACTTTCCAAGA
1 GTATCGATACTTTCCAAGA
* *
1198092 GTATCGATACATTAACCTAGAA
1 GTATCGATAC-TT-TCCAAG-A
*
1198114 GTATGGATACTTTCCAAGA
1 GTATCGATACTTTCCAAGA
1198133 GTATCGATACTTTC
1 GTATCGATACTTTC
1198147 AGCAACATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 23 0.51
20 6 0.13
21 6 0.13
22 10 0.22
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (19 bp):
GTATCGATACTTTCCAAGA
Found at i:1200076 original size:23 final size:23
Alignment explanation
Indices: 1200041--1200098 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
1200031 ACAATTATGA
* *
1200041 AAATTATGTTTTGTAATTTATTAG
1 AAATTAT-CTTTGCAATTTATTAG
*
1200065 AAATTATCTTTGCAATTTTTTAG
1 AAATTATCTTTGCAATTTATTAG
* *
1200088 GAATCATCTTT
1 AAATTATCTTT
1200099 TAGGGTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 22 0.76
24 7 0.24
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.52
Consensus pattern (23 bp):
AAATTATCTTTGCAATTTATTAG
Found at i:1201782 original size:2 final size:2
Alignment explanation
Indices: 1201775--1201815 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1201765 CAATCAACTT
1201775 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1201816 TGAATCTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1202589 original size:209 final size:209
Alignment explanation
Indices: 1202229--1202647 Score: 838
Period size: 209 Copynumber: 2.0 Consensus size: 209
1202219 AAAAGTAACC
1202229 CATGCACTTGCTGTCCTTGGTACATTTCTTGCCACATTCTTCTTCTTTTATGGCATTCCCTCTGG
1 CATGCACTTGCTGTCCTTGGTACATTTCTTGCCACATTCTTCTTCTTTTATGGCATTCCCTCTGG
1202294 TGTAACGAGTCATGAAATGATCAACCCCTTCAAGCTTGTAATAGTAGAAATCCTTGTCGTTGCAG
66 TGTAACGAGTCATGAAATGATCAACCCCTTCAAGCTTGTAATAGTAGAAATCCTTGTCGTTGCAG
1202359 CTCGGTAACTTTTGGACATCGCAATCTTTACTCCAACTCATCAGCCCGTTCGGCGACGGGCAAGC
131 CTCGGTAACTTTTGGACATCGCAATCTTTACTCCAACTCATCAGCCCGTTCGGCGACGGGCAAGC
1202424 CACACATTGGCTGT
196 CACACATTGGCTGT
1202438 CATGCACTTGCTGTCCTTGGTACATTTCTTGCCACATTCTTCTTCTTTTATGGCATTCCCTCTGG
1 CATGCACTTGCTGTCCTTGGTACATTTCTTGCCACATTCTTCTTCTTTTATGGCATTCCCTCTGG
1202503 TGTAACGAGTCATGAAATGATCAACCCCTTCAAGCTTGTAATAGTAGAAATCCTTGTCGTTGCAG
66 TGTAACGAGTCATGAAATGATCAACCCCTTCAAGCTTGTAATAGTAGAAATCCTTGTCGTTGCAG
1202568 CTCGGTAACTTTTGGACATCGCAATCTTTACTCCAACTCATCAGCCCGTTCGGCGACGGGCAAGC
131 CTCGGTAACTTTTGGACATCGCAATCTTTACTCCAACTCATCAGCCCGTTCGGCGACGGGCAAGC
1202633 CACACATTGGCTGT
196 CACACATTGGCTGT
1202647 C
1 C
1202648 CTCACAAAGC
Statistics
Matches: 210, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
209 210 1.00
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.32
Consensus pattern (209 bp):
CATGCACTTGCTGTCCTTGGTACATTTCTTGCCACATTCTTCTTCTTTTATGGCATTCCCTCTGG
TGTAACGAGTCATGAAATGATCAACCCCTTCAAGCTTGTAATAGTAGAAATCCTTGTCGTTGCAG
CTCGGTAACTTTTGGACATCGCAATCTTTACTCCAACTCATCAGCCCGTTCGGCGACGGGCAAGC
CACACATTGGCTGT
Found at i:1203484 original size:20 final size:20
Alignment explanation
Indices: 1203459--1203496 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1203449 TTTGGTTCAC
1203459 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
1203479 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
1203497 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:1203726 original size:37 final size:37
Alignment explanation
Indices: 1203653--1203727 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
1203643 GTTGGAAAAT
* *
1203653 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
1203690 ATTTATATAATATTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-AT-TTTCTTTAAAAAATTGAAAATCATAAA
1203727 A
1 A
1203728 ATGTTTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 16 0.48
39 3 0.09
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:1206316 original size:2 final size:2
Alignment explanation
Indices: 1206309--1206348 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1206299 AAAACACATC
1206309 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
1206349 CAAAACTCGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1213721 original size:2 final size:2
Alignment explanation
Indices: 1213714--1213756 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1213704 TTGCGCACTC
1213714 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1213756 T
1 T
1213757 TAAAGTACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1215536 original size:6 final size:6
Alignment explanation
Indices: 1215491--1215535 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
1215481 GACACGTATT
*
1215491 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCCCG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1215536 CGAGACAGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1216322 original size:23 final size:21
Alignment explanation
Indices: 1216265--1216383 Score: 93
Period size: 21 Copynumber: 5.7 Consensus size: 21
1216255 ATTTTAGACT
*
1216265 ATCGCAACGAATTTAGAATAA
1 ATCGCAACGAACTTAGAATAA
*
1216286 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTAGAATAA
* *
1216307 ATCGCAACACGAACTTCGACT--
1 ATCGC-A-ACGAACTTAGAATAA
* *
1216328 ATCGTAACGAAATTAGAATAA
1 ATCGCAACGAACTTAGAATAA
* * *
1216349 ATCCCAACGCGAATTTAGACT--
1 ATCGCAA--CGAACTTAGAATAA
1216370 ATCGCAACGAACTT
1 ATCGCAACGAACTT
1216384 GATAACAACA
Statistics
Matches: 78, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
19 16 0.21
20 1 0.01
21 39 0.50
22 1 0.01
23 21 0.27
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAACTTAGAATAA
Found at i:1216337 original size:42 final size:42
Alignment explanation
Indices: 1216286--1216384 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
1216276 TTTAGAATAA
* *
1216286 ATCGCAACGAACTTGGAATAAATCGCAACACGAACTTCGACT
1 ATCGCAACGAACTTGGAATAAATCCCAACACGAACTTAGACT
* * * * *
1216328 ATCGTAACGAAATTAGAATAAATCCCAACGCGAATTTAGACT
1 ATCGCAACGAACTTGGAATAAATCCCAACACGAACTTAGACT
1216370 ATCGCAACGAACTTG
1 ATCGCAACGAACTTG
1216385 ATAACAACAT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.21
Consensus pattern (42 bp):
ATCGCAACGAACTTGGAATAAATCCCAACACGAACTTAGACT
Found at i:1228256 original size:20 final size:20
Alignment explanation
Indices: 1228231--1228269 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1228221 TAAAATCCCA
1228231 TAAATACAATATATATATAT
1 TAAATACAATATATATATAT
1228251 TAAATACAATATATATATA
1 TAAATACAATATATATATA
1228270 AAGTAAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATACAATATATATATAT
Found at i:1228753 original size:15 final size:16
Alignment explanation
Indices: 1228734--1228797 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 16
1228724 TTTTAATAGA
1228734 AATATTAATTATTAA-
1 AATATTAATTATTAAT
1228749 AATATTCAATATATATATAT
1 AATATT-AAT-TAT-TA-AT
1228769 AATA-TAATT-TTAAT
1 AATATTAATTATTAAT
1228783 AATATT-A-TATTAAT
1 AATATTAATTATTAAT
1228797 A
1 A
1228798 TGTACTCAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
13 1 0.02
14 13 0.31
15 9 0.21
16 4 0.10
17 4 0.10
18 5 0.12
19 2 0.05
20 4 0.10
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATTAATTATTAAT
Found at i:1230553 original size:17 final size:16
Alignment explanation
Indices: 1230502--1230553 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
1230492 TAACCTCAAA
*
1230502 TTTATTTTTTAATTA-
1 TTTATTATTTAATTAT
*
1230517 TTT-TTATATAATTAT
1 TTTATTATTTAATTAT
1230532 ATTTATTATTTAATATAT
1 -TTTATTATTTAAT-TAT
1230550 TTTA
1 TTTA
1230554 CCTTAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 9 0.30
15 3 0.10
16 3 0.10
17 12 0.40
18 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATTATTTAATTAT
Found at i:1230696 original size:22 final size:22
Alignment explanation
Indices: 1230653--1230693 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1230643 AAAAAATTAT
1230653 TTTTTATTAAATATTTTTAATA
1 TTTTTATTAAATATTTTTAATA
*
1230675 TTTTTATTTAAT-TTTTTAA
1 TTTTTATTAAATATTTTTAA
1230694 ATAATTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTATTAAATATTTTTAATA
Found at i:1236710 original size:17 final size:18
Alignment explanation
Indices: 1236688--1236721 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1236678 ATATTATAAA
1236688 ATATTAACAT-TATTTTT
1 ATATTAACATGTATTTTT
*
1236705 ATATTAATATGTATTTT
1 ATATTAACATGTATTTT
1236722 ATAATTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (18 bp):
ATATTAACATGTATTTTT
Found at i:1237257 original size:42 final size:42
Alignment explanation
Indices: 1237202--1237281 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
1237192 AACGCGATAG
* *
1237202 TCCAAGTTTGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
1237244 TCCAAATTCGTTGCGATAGTCTAAGTTCGCGTTGCGAT
1 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGAT
1237282 AGTCGAAGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (42 bp):
TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:1237279 original size:63 final size:63
Alignment explanation
Indices: 1237195--1237344 Score: 241
Period size: 63 Copynumber: 2.4 Consensus size: 63
1237185 GATTCGCAAC
*
1237195 GCGATAGTCCAAGTT--TGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTT
1 GCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTT
* * *
1237256 GCGATAGTCTAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTTCAAGTTCGTT
1 GCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTT
*
1237319 GCGATAGTCGAAGTTCGCGTTGCGAT
1 GCGATAGTCCAAGTTCGCGTTGCGAT
1237345 TTATTCCAAA
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
61 14 0.17
63 68 0.83
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (63 bp):
GCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTT
Found at i:1237298 original size:42 final size:40
Alignment explanation
Indices: 1237252--1237411 Score: 160
Period size: 42 Copynumber: 3.8 Consensus size: 40
1237242 ATTCCAAATT
1237252 CGTTGCGATAGTCTAAGTTCGCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCTAAGTT--CGTTGCGATAGTCGAAGTTCG
*
1237294 CGTTGCGATTTA-TTTCAAGTTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGA--TAGTCT-AAGTTCGTTGCGATAGTCGAAGTTCG
* * *
1237336 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGA--TAGTCTAAGTTCGTTGCGATAGTCGAAGTTCG
* * **
1237378 CATTGCGATTTATTCTAAAATCGTTGCGATAGTC
1 CGTTGCGA--TAGTCTAAGTTCGTTGCGATAGTC
1237412 CAAAATCGCA
Statistics
Matches: 107, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
42 97 0.91
43 3 0.03
44 7 0.07
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (40 bp):
CGTTGCGATAGTCTAAGTTCGTTGCGATAGTCGAAGTTCG
Found at i:1237361 original size:63 final size:62
Alignment explanation
Indices: 1237195--1237365 Score: 195
Period size: 63 Copynumber: 2.7 Consensus size: 62
1237185 GATTCGCAAC
* * * *
1237195 GCGATAGTCCAAGTT--TGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAATTC-CGTTGCGATTTATTCCAAATTCGTT
* * * * *
1237256 GCGATAGTCTAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTTCAAGTTCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAATTC-CGTTGCGATTTATTCCAAATTCGTT
*
1237319 GCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT-CGTTGCGAT
1 GCGATAGTCGAAGTTCGCGTTGCGA--TAGTCCAAATTCCGTTGCGAT
1237366 AGTCGAAGTT
Statistics
Matches: 98, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
61 14 0.14
63 76 0.78
65 8 0.08
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (62 bp):
GCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAATTCCGTTGCGATTTATTCCAAATTCGTT
Found at i:1237384 original size:63 final size:61
Alignment explanation
Indices: 1237195--1237386 Score: 162
Period size: 63 Copynumber: 3.1 Consensus size: 61
1237185 GATTCGCAAC
* * * * *
1237195 GCGATAGTCCAAGTT--TGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT-TCCAAATTCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAATTC-CGTTGCGA-TTATGT-CAAGTTCGTT
* * * *
1237256 GCGATAGTCTAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTTCAAGTTCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAATTC-CGTTGCGA-TTATGTCAAGTTCGTT
*
1237319 GCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT-CGTTGCGA-TA-GTCGAAGTTCGCAT
1 GCGATAGTCGAAGTTCGCGTTGCGA--TAGTCCAAATTCCGTTGCGATTATGTC-AAGTTCG--T
1237381 T
61 T
1237382 GCGAT
1 GCGAT
1237387 TTATTCTAAA
Statistics
Matches: 115, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
60 2 0.02
61 23 0.20
63 81 0.70
64 1 0.01
65 8 0.07
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (61 bp):
GCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAATTCCGTTGCGATTATGTCAAGTTCGTT
Found at i:1237404 original size:21 final size:21
Alignment explanation
Indices: 1237231--1237407 Score: 82
Period size: 21 Copynumber: 8.4 Consensus size: 21
1237221 TCGAAGTTCG
1237231 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT
* * *
1237252 CGTTGCGA--TAGTCTAAGTT
1 CGTTGCGATTTATTCCAAATT
* * *
1237271 CGCGTTGCGA--TAGTCGAAGTT
1 --CGTTGCGATTTATTCCAAATT
* *
1237292 CGCGTTGCGATTTATTTCAAGTT
1 --CGTTGCGATTTATTCCAAATT
* * *
1237315 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
1237334 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
* * *
1237357 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
* *
1237376 CGCATTGCGATTTATTCTAAAAT
1 CG--TTGCGATTTATTCCAAATT
1237399 CGTTGCGAT
1 CGTTGCGAT
1237408 AGTCCAAAAT
Statistics
Matches: 124, Mismatches: 20, Indels: 24
0.74 0.12 0.14
Matches are distributed among these distances:
19 26 0.21
21 73 0.59
23 25 0.20
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:1237421 original size:42 final size:42
Alignment explanation
Indices: 1237273--1237411 Score: 217
Period size: 42 Copynumber: 3.3 Consensus size: 42
1237263 TCTAAGTTCG
* *
1237273 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATT-TCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCATTGCGATTTATTCT-AAATT
* *
1237315 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCATTGCGATTTATTCTAAATT
*
1237357 CGTTGCGATAGTCGAAGTTCGCATTGCGATTTATTCTAAAAT
1 CGTTGCGATAGTCGAAGTTCGCATTGCGATTTATTCTAAATT
1237399 CGTTGCGATAGTC
1 CGTTGCGATAGTC
1237412 CAAAATCGCA
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCATTGCGATTTATTCTAAATT
Found at i:1239718 original size:72 final size:72
Alignment explanation
Indices: 1239640--1239776 Score: 220
Period size: 72 Copynumber: 1.9 Consensus size: 72
1239630 ATAACATTGT
* * *
1239640 TTTTTATAAGATAAATATAAATAAAATGTTCAAATAAATATAATAAATAAAATAAATAACTAATT
1 TTTTTATAAGATAAATATAAATAAAATATTAAAACAAATATAATAAATAAAATAAATAACTAATT
1239705 ACATTAC
66 ACATTAC
* * *
1239712 TTTTTATAAGATAAATATAAATAAAATATTAAAACAAATATAATCAATAAAATAATTAATTAATT
1 TTTTTATAAGATAAATATAAATAAAATATTAAAACAAATATAATAAATAAAATAAATAACTAATT
1239777 GAAAATTTTG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (72 bp):
TTTTTATAAGATAAATATAAATAAAATATTAAAACAAATATAATAAATAAAATAAATAACTAATT
ACATTAC
Found at i:1244356 original size:24 final size:24
Alignment explanation
Indices: 1244311--1244358 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1244301 GTTCATGAGA
** *
1244311 AAACTCGTTTATTGGGTTGTTTAT
1 AAACTCGTTTATTGACTCGTTTAT
*
1244335 AAACTTGTTTATTGACTCGTTTAT
1 AAACTCGTTTATTGACTCGTTTAT
1244359 CCGGTTCTCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.10, G:0.17, T:0.50
Consensus pattern (24 bp):
AAACTCGTTTATTGACTCGTTTAT
Found at i:1254101 original size:10 final size:10
Alignment explanation
Indices: 1254086--1254111 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1254076 TTTTCCCCTT
1254086 GTTTTGGAGA
1 GTTTTGGAGA
1254096 GTTTTGGAGA
1 GTTTTGGAGA
1254106 GTTTTG
1 GTTTTG
1254112 ATTGGGATCT
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:0.00, G:0.38, T:0.46
Consensus pattern (10 bp):
GTTTTGGAGA
Found at i:1267111 original size:22 final size:23
Alignment explanation
Indices: 1267073--1267117 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1267063 CTTATTTTTC
*
1267073 GATTTTTGTCTC-CTTTTATGTG
1 GATTTTTGTCTCATTTTTATGTG
*
1267095 GATTTTTGTCTTATTTTTATGTG
1 GATTTTTGTCTCATTTTTATGTG
1267118 AAGTATTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.62
Consensus pattern (23 bp):
GATTTTTGTCTCATTTTTATGTG
Found at i:1268702 original size:15 final size:16
Alignment explanation
Indices: 1268682--1268711 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1268672 TGGTTAGTCA
1268682 GTAA-TTTTATTCTCG
1 GTAATTTTTATTCTCG
1268697 GTAATTTTTATTCTC
1 GTAATTTTTATTCTC
1268712 AACAATAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.13, G:0.10, T:0.57
Consensus pattern (16 bp):
GTAATTTTTATTCTCG
Found at i:1280950 original size:35 final size:34
Alignment explanation
Indices: 1280911--1281008 Score: 83
Period size: 35 Copynumber: 2.8 Consensus size: 34
1280901 AAGTTTTTGA
1280911 CGAAATATAATATATAATTTTCAGAAAACGA-TTTT
1 CGAAATATAATATATAATTTT-AGAAAAC-ATTTTT
* * *
1280946 CGAAAATTTATATTATATAGTTTTTGAAAACATTTTT
1 CG-AAA--TATAATATATAATTTTAGAAAACATTTTT
**
1280983 AAAATATATAATATATAATTTT-GAAA
1 CGAA-ATATAATATATAATTTTAGAAA
1281009 TATTTATATT
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
34 4 0.08
35 16 0.31
36 6 0.12
37 11 0.22
38 14 0.27
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (34 bp):
CGAAATATAATATATAATTTTAGAAAACATTTTT
Found at i:1281097 original size:38 final size:37
Alignment explanation
Indices: 1281001--1281119 Score: 161
Period size: 37 Copynumber: 3.2 Consensus size: 37
1280991 TAATATATAA
* * * *
1281001 TTTTGAAATATT-TATATTATATAGTTTTTAAAACAA
1 TTTTGAAAAATTATATAATATATAGTTTTTAAAATAT
* *
1281037 TTTTAAAAAACTTATATAATATAGA-TTTTTAAAATAT
1 TTTTGAAAAA-TTATATAATATATAGTTTTTAAAATAT
1281074 TTTTGAAAAATTATATAATATATAGTTTTTAAAATAT
1 TTTTGAAAAATTATATAATATATAGTTTTTAAAATAT
1281111 TTTTGAAAA
1 TTTTGAAAA
1281120 CATCTATAAT
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
36 21 0.29
37 42 0.58
38 9 0.12
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (37 bp):
TTTTGAAAAATTATATAATATATAGTTTTTAAAATAT
Found at i:1281128 original size:37 final size:37
Alignment explanation
Indices: 1281013--1281131 Score: 143
Period size: 37 Copynumber: 3.2 Consensus size: 37
1281003 TTGAAATATT
* * ** *
1281013 TATATTATATAGTTTTTAAAACAATTTTAAAAAACTTA
1 TATAATATATAGTTTTTAAAA-TATTTTTGAAAACATA
*
1281051 TATAATATAGA-TTTTTAAAATATTTTTGAAAA-ATTA
1 TATAATATATAGTTTTTAAAATATTTTTGAAAACA-TA
*
1281087 TATAATATATAGTTTTTAAAATATTTTTGAAAACATC
1 TATAATATATAGTTTTTAAAATATTTTTGAAAACATA
1281124 TATAATAT
1 TATAATAT
1281132 TTTTAAAACA
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
36 21 0.30
37 39 0.56
38 10 0.14
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (37 bp):
TATAATATATAGTTTTTAAAATATTTTTGAAAACATA
Found at i:1282590 original size:2 final size:2
Alignment explanation
Indices: 1282585--1282622 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1282575 TTTTTCTTTG
1282585 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
1282623 TTTCTATTTA
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:1286108 original size:2 final size:2
Alignment explanation
Indices: 1286097--1286141 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1286087 GTCATTTTTT
*
1286097 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1286139 TA T
1 TA T
1286142 TCCTCTGATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1287885 original size:14 final size:14
Alignment explanation
Indices: 1287866--1287916 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
1287856 CGTTCGGTAA
1287866 ATGTTCGTTCGTTT
1 ATGTTCGTTCGTTT
1287880 ATGTTCGTTCGTTT
1 ATGTTCGTTCGTTT
* *
1287894 ATGTTCATTCATTT
1 ATGTTCGTTCGTTT
*
1287908 ATGTCCGTT
1 ATGTTCGTT
1287917 TATGTGCGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.12, C:0.16, G:0.18, T:0.55
Consensus pattern (14 bp):
ATGTTCGTTCGTTT
Found at i:1296203 original size:18 final size:19
Alignment explanation
Indices: 1296162--1296205 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
1296152 AAGTACGATT
1296162 ATATAATATAAAAATATTA
1 ATATAATATAAAAATATTA
* *
1296181 A-ATAATAT-ACATTATTA
1 ATATAATATAAAAATATTA
1296198 ATATAATA
1 ATATAATA
1296206 ATGTTCTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 8 0.36
18 13 0.59
19 1 0.05
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATAATATAAAAATATTA
Found at i:1296235 original size:20 final size:19
Alignment explanation
Indices: 1296197--1296237 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
1296187 ATACATTATT
*
1296197 AATATAATAATGTTCTATA
1 AATATAATAATGTTATATA
*
1296216 AATATATATAATTTTATATA
1 AATATA-ATAATGTTATATA
1296236 AA
1 AA
1296238 GCTATAATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
AATATAATAATGTTATATA
Found at i:1336516 original size:106 final size:106
Alignment explanation
Indices: 1336055--1337357 Score: 2094
Period size: 106 Copynumber: 12.3 Consensus size: 106
1336045 CTCGAGAGTA
* * * * * * *
1336055 AATTTCAACTTCTCAACGAAGGATCTT-GAATCCAAGACAACACAAGCTCAACTTCATGACGAAG
1 AATTTCAACTTCACAACGAAGGATATTGGACT-CGAGACAACGCAAGTTCAACTTCACGACGAAG
* * * * * *
1336119 GGGCGGCTGATTGTCAACAAACAACTTCTCAATCTCAGAGTC
65 GGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
*
1336161 AATTTCAAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAG
1 AATTTC-AACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAG
* * *
1336226 GGACCGCTGGTTGTCAACGAAC-ATTTCTCGATTTCAGAGTC
65 GGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
*
1336267 AATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
1336332 GACCGCTGGTTGTCAACAAAC-ATTTCTCGATTTCAGAGTC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
*
1336372 AATTTCAACTTCACAACGAAGGATATTGGACTTC-AGACAACGTAAGTTCAACTTCACGACGAAG
1 AATTTCAACTTCACAACGAAGGATATTGGAC-TCGAGACAACGCAAGTTCAACTTCACGACGAAG
*
1336436 GGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCC
65 GGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
*
1336478 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCATGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
1336543 GACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
* * *
1336584 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
1336649 GACCGCCGGTTGTCAACAAACAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
*
1336690 AATTTCAACTTCACAACGAAGGATATTGGTCTCGAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
1336755 GACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
* * *
1336796 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGG
*
1336861 GACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
*
1336902 AATTTTAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGG
1336967 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
1337008 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGG
1337073 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
1337114 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
1337179 GACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
* * *
1337220 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGG
* * * *
1337285 GA-CGACTGGTTGTCAACAAACAATTTCCCAGTTCCAAAGCC
66 GACCG-CTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
* *
1337326 AATTTCAACTTCACGACGGAGGATATTGGACT
1 AATTTCAACTTCACAACGAAGGATATTGGACT
1337358 TGGAACAATA
Statistics
Matches: 1126, Mismatches: 65, Indels: 12
0.94 0.05 0.01
Matches are distributed among these distances:
105 184 0.16
106 874 0.78
107 65 0.06
108 3 0.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
Found at i:1356411 original size:13 final size:13
Alignment explanation
Indices: 1356393--1356419 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1356383 TTGATATCGT
1356393 TTAAATAATATTA
1 TTAAATAATATTA
1356406 TTAAATAATATTA
1 TTAAATAATATTA
1356419 T
1 T
1356420 AAGTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAATAATATTA
Found at i:1358270 original size:23 final size:23
Alignment explanation
Indices: 1358215--1358270 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
1358205 TTTATTTTTA
* *
1358215 TGACACATTTCTTCTCTACCTTT
1 TGACACATTTCTTCTCTACCCTC
* * * *
1358238 TAACATATTTCTTTTCTGCCCTC
1 TGACACATTTCTTCTCTACCCTC
1358261 TGACACATTT
1 TGACACATTT
1358271 TTGGTCTTCG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.20, C:0.29, G:0.05, T:0.46
Consensus pattern (23 bp):
TGACACATTTCTTCTCTACCCTC
Found at i:1363705 original size:26 final size:27
Alignment explanation
Indices: 1363654--1363703 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
1363644 ATGTATATAA
*
1363654 TATATATATATATATTTTTTGAAAACG
1 TATATATATATATATGTTTTGAAAACG
1363681 TATATA-ATATATA-GTTTTGAAAA
1 TATATATATATATATGTTTTGAAAA
1363704 ACATTTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
26 7 0.32
27 6 0.27
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (27 bp):
TATATATATATATATGTTTTGAAAACG
Found at i:1363723 original size:38 final size:37
Alignment explanation
Indices: 1363593--1363889 Score: 180
Period size: 38 Copynumber: 7.9 Consensus size: 37
1363583 GTTTTTTTCG
* *
1363593 AAAACATTTTAAAAATATATATAATATATAATCTTTG-
1 AAAACATTTTGAAAATATATATAATATATAGT-TTTGA
* *
1363630 AAAACATTTTGAAAATGTATATAATATATA--TAT-A
1 AAAACATTTTGAAAATATATATAATATATAGTTTTGA
* * ** **
1363664 TATATTTTTTGAAAACGTATATAATATATAGTTTTGA
1 AAAACATTTTGAAAATATATATAATATATAGTTTTGA
* *
1363701 AAAACATTTTTGAAAATTTATATGATATATAGTTTTG-
1 AAAACA-TTTTGAAAATATATATAATATATAGTTTTGA
* * *
1363738 AAAACATTTTGAAAACATTTATATATTATATAGTTTTTTTA
1 AAAACATTTTG-AAA-ATATATATAATATATAG--TTTTGA
* * **
1363779 AAAA-ATATTTTAAAA-ATATATAATATATAATTTTTTTT
1 AAAACAT-TTTGAAAATATATATAATATAT-A-GTTTTGA
** * * **
1363817 AAAACATTTTTTAAATATATATATTATATAATTTAAAAAA
1 AAAACATTTTGAAAATATATATAATATATAGTTT---TGA
* *
1363857 AAAACATTTTGGAAAT-TATATATTATAT-GTTTT
1 AAAACATTTTGAAAATATATATAATATATAGTTTT
1363890 TTAAAATATT
Statistics
Matches: 208, Mismatches: 34, Indels: 38
0.74 0.12 0.14
Matches are distributed among these distances:
34 27 0.13
36 7 0.03
37 43 0.21
38 73 0.35
39 28 0.13
40 23 0.11
41 7 0.03
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.45
Consensus pattern (37 bp):
AAAACATTTTGAAAATATATATAATATATAGTTTTGA
Found at i:1363749 original size:11 final size:11
Alignment explanation
Indices: 1363733--1363757 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1363723 TGATATATAG
1363733 TTTTGAAAACA
1 TTTTGAAAACA
1363744 TTTTGAAAACA
1 TTTTGAAAACA
1363755 TTT
1 TTT
1363758 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:1363849 original size:39 final size:39
Alignment explanation
Indices: 1363757--1363850 Score: 136
Period size: 39 Copynumber: 2.4 Consensus size: 39
1363747 TGAAAACATT
*
1363757 TATATATTATAT-AGTTTTTTTAAAAAATATTTTAAAAA
1 TATATATTATATAATTTTTTTTAAAAAATATTTTAAAAA
* * * *
1363795 TATATAATATATAATTTTTTTTAAAACATTTTTTAAATA
1 TATATATTATATAATTTTTTTTAAAAAATATTTTAAAAA
1363834 TATATATTATATAATTT
1 TATATATTATATAATTT
1363851 AAAAAAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
38 11 0.22
39 38 0.78
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (39 bp):
TATATATTATATAATTTTTTTTAAAAAATATTTTAAAAA
Found at i:1363921 original size:3 final size:3
Alignment explanation
Indices: 1363908--1363982 Score: 93
Period size: 3 Copynumber: 25.3 Consensus size: 3
1363898 TTTATATATA
1363908 TAT TA- TAT TAT TA- TAT TAT TAT TAT TATT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA-T TAT
* *
1363953 TAT TAT TGT AAT TAT T-T TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1363983 TCTTATTTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
2 6 0.10
3 51 0.81
4 6 0.10
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1363924 original size:13 final size:13
Alignment explanation
Indices: 1363906--1363997 Score: 77
Period size: 13 Copynumber: 7.1 Consensus size: 13
1363896 TATTTATATA
1363906 TATATTATATTAT
1 TATATTATATTAT
1363919 TATATTATTATTAT
1 TATATTA-TATTAT
1363933 TAT-TTATTATTAT
1 TATATTA-TATTAT
1363946 TAT-TTATTATTAT
1 TATATTA-TATTAT
* *
1363959 TGTAATTATTTTAT
1 TAT-ATTATATTAT
*
1363973 TATTATTAT-TTCT
1 TA-TATTATATTAT
1363986 TAT-TTA-ATTAT
1 TATATTATATTAT
1363997 T
1 T
1363998 TTGTTATTGT
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
11 7 0.10
12 1 0.01
13 37 0.54
14 20 0.29
15 4 0.06
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (13 bp):
TATATTATATTAT
Found at i:1364004 original size:29 final size:29
Alignment explanation
Indices: 1363939--1364013 Score: 98
Period size: 30 Copynumber: 2.6 Consensus size: 29
1363929 TTATTATTTA
*
1363939 TTATTATTATTTATTATTATTGTAATTATT
1 TTATTATTATTT-TTCTTATTGTAATTATT
1363969 TTATTATTATTATTTCTTATT-TAATTATT
1 TTATTATTATT-TTTCTTATTGTAATTATT
* *
1363998 TTGTTATTGTTTTTCT
1 TTATTATTATTTTTCT
1364014 GTTCAGGGTC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
28 5 0.12
29 17 0.41
30 18 0.44
31 1 0.02
ACGTcount: A:0.24, C:0.03, G:0.04, T:0.69
Consensus pattern (29 bp):
TTATTATTATTTTTCTTATTGTAATTATT
Found at i:1367078 original size:18 final size:19
Alignment explanation
Indices: 1367057--1367101 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1367047 ATTTAGACAT
1367057 TTTGCATTTT-TTATTTTC
1 TTTGCATTTTGTTATTTTC
1367075 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
1367094 TTTGCATT
1 TTTGCATT
1367102 CACATTAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.11, C:0.11, G:0.09, T:0.69
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTC
Found at i:1370629 original size:84 final size:84
Alignment explanation
Indices: 1370447--1371232 Score: 1000
Period size: 84 Copynumber: 9.4 Consensus size: 84
1370437 CAAACAAACT
* * * ** * *
1370447 ATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* ***
1370508 CTCTGCCTCGGGGGCACATC
66 CTCAG-CTCCAAGGCACATC
1370528 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
1370593 CTCAGCTCCAAGGCATATC
66 CTCAGCTCCAAGGCACATC
* * * * *
1370612 ATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1370677 CTCAGCT-CAACGGCACATC
66 CTCAGCTCCAA-GGCACATC
* * * * *
1370696 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1370760 CTCAGCTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* * ** *
1370779 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCAAGTTCGA-TCAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT-AC
* ***
1370839 ACTCAGCTTCGGGGGCACATC
65 GCTCAGC-TCCAAGGCACATC
1370860 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
1370925 CTCAGCTCCAAGGCATATC
66 CTCAGCTCCAAGGCACATC
* * * * * * * *
1370944 ATTTACAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAACAAAAGGCCTTCGAGTTCGACTCCG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1371009 CTCAGCTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
1371028 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
1371093 CTCAGCTCCAAGGCATATC
66 CTCAGCTCCAAGGCACATC
* * * * * * * *
1371112 ATTTACAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAACAAAAGGCCTTCGAGTTCGACTCCG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1371177 CTCAGCTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* *
1371196 ATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTGC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGC
1371233 TAAAGACCCT
Statistics
Matches: 610, Mismatches: 82, Indels: 23
0.85 0.11 0.03
Matches are distributed among these distances:
79 1 0.00
80 25 0.04
81 77 0.13
83 72 0.12
84 384 0.63
85 50 0.08
86 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (84 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATC
Found at i:1371056 original size:332 final size:332
Alignment explanation
Indices: 1370447--1371232 Score: 1209
Period size: 332 Copynumber: 2.4 Consensus size: 332
1370437 CAAACAAACT
* *
1370447 ATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCT
1 ATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATCACACTCA
1370512 GCCTCGGGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
66 G-CTCGGGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
*
1370577 TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGT
130 TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCACAACTTAAGTCTAGAAGGGT
*
1370642 TGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTACAGCAT
195 TGTCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTACAGCAT
* *
1370707 AACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA
260 AACTCAAGGCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA
1370771 GGCACATC
325 GGCACATC
* *
1370779 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATCACACTCA
1 ATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATCACACTCA
1370844 GCTTCGGGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
66 GC-TCGGGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
1370909 TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCACAACTTAAGTCTAGAAGGGT
130 TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCACAACTTAAGTCTAGAAGGGT
* * * *
1370974 TGTCTGGCAACAAAAGGCCTTCGAGTTCGACTCCGCTCAGCTCCAA-GGCACATCATTTGCAGCA
195 TGTCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAACGGCACATCATTTACAGCA
* *
1371038 TAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCA
259 TAACTCAAGGCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCA
*
1371103 AGGCATATC
324 AGGCACATC
* * * * * * * **
1371112 ATTTACAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAACAAAAGGCCTTCGAGTTCGACTC-C
1 ATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCT-GC--C-AAAGACCCCCGAGTTCGA-TCAC
* *** * *
1371176 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTGC
61 ACTCAGCTCGGGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGC
1371233 TAAAGACCCT
Statistics
Matches: 415, Mismatches: 31, Indels: 12
0.91 0.07 0.03
Matches are distributed among these distances:
331 1 0.00
332 267 0.64
333 76 0.18
334 2 0.00
336 46 0.11
337 21 0.05
338 2 0.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (332 bp):
ATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATCACACTCA
GCTCGGGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCT
TCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCACAACTTAAGTCTAGAAGGGTT
GTCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTACAGCATA
ACTCAAGGCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
GCACATC
Found at i:1372007 original size:39 final size:37
Alignment explanation
Indices: 1371986--1372238 Score: 155
Period size: 37 Copynumber: 6.9 Consensus size: 37
1371976 TGTTTTTTTC
1371986 GAAAACATTTTAAAAATATATATAATATATAATCTTT
1 GAAAACATTTTAAAAATATATATAATATATAATCTTT
* * *
1372023 GAAAACATTTTGAAAATGTATATAATATAT-A--TAT
1 GAAAACATTTTAAAAATATATATAATATATAATCTTT
* ** * ** *
1372057 --ATATTTTTTGAAAACGTATATAATATATAGT-TTT
1 GAAAACATTTTAAAAATATATATAATATATAATCTTT
* * * *
1372091 GAAAAACATTTTTGAAAATTTATATGATATATAGT-TTT
1 G-AAAACA-TTTTAAAAATATATATAATATATAATCTTT
* * * *
1372129 GAAAACATTTTGAAAACATTTATATATTATATAGTTTTTT
1 GAAAACATTTT-AAAA-ATATATATAATATATA-ATCTTT
* * *
1372169 TAAAA-ATATTTTAAAA-ATATATAATATATAATTTTTT
1 GAAAACAT-TTTAAAAATATATATAATATATAA-TCTTT
* ** *
1372206 TAAAACATTTTTTAAATATATATATTATATAAT
1 GAAAACATTTTAAAAATATATATAATATATAAT
1372239 TTAAAAAAAA
Statistics
Matches: 176, Mismatches: 26, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
32 24 0.14
34 4 0.02
36 5 0.03
37 69 0.39
38 58 0.33
39 6 0.03
40 10 0.06
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (37 bp):
GAAAACATTTTAAAAATATATATAATATATAATCTTT
Found at i:1372121 original size:38 final size:36
Alignment explanation
Indices: 1371981--1372236 Score: 147
Period size: 38 Copynumber: 7.0 Consensus size: 36
1371971 ATATATGTTT
* * *
1371981 TTTTCGAAAACA-TTTTAAAAATATATATAATATATAA
1 TTTT-GAAAACATTTTTGAAAATTTATAT-ATATATAG
*
1372018 TCTTTGAAAACA-TTTTGAAAATGTATATA-ATATA-
1 T-TTTGAAAACATTTTTGAAAATTTATATATATATAG
* * * **
1372052 -TAT-ATATA-TTTTTTGAAAACGTATATAATATATAG
1 TTTTGA-AAACATTTTTGAAAATTTATAT-ATATATAG
1372087 TTTTGAAAAACATTTTTGAAAATTTATATGATATATAG
1 TTTTG-AAAACATTTTTGAAAATTTATAT-ATATATAG
1372125 TTTTGAAAACA-TTTTGAAAACATTTATATATTATATAG
1 TTTTGAAAACATTTTTG-AAA-ATTTATATA-TATATAG
* * * *
1372163 TTTTTTTAAAA-ATATTTTAAAAATATATA-ATATATAATT
1 --TTTTGAAAACAT-TTTTGAAAATTTATATATATAT-A-G
* * *
1372202 TTTTTAAAACATTTTT-TAAATATATATATTATATA
1 TTTTGAAAACATTTTTGAAAATTTATATA-TATATA
1372237 ATTTAAAAAA
Statistics
Matches: 180, Mismatches: 17, Indels: 44
0.75 0.07 0.18
Matches are distributed among these distances:
31 1 0.01
32 19 0.11
33 1 0.01
34 5 0.03
35 5 0.03
36 17 0.09
37 54 0.30
38 56 0.31
39 7 0.04
40 11 0.06
41 4 0.02
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (36 bp):
TTTTGAAAACATTTTTGAAAATTTATATATATATAG
Found at i:1372141 original size:11 final size:11
Alignment explanation
Indices: 1372125--1372149 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1372115 TGATATATAG
1372125 TTTTGAAAACA
1 TTTTGAAAACA
1372136 TTTTGAAAACA
1 TTTTGAAAACA
1372147 TTT
1 TTT
1372150 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:1372310 original size:3 final size:3
Alignment explanation
Indices: 1372298--1372364 Score: 100
Period size: 3 Copynumber: 22.3 Consensus size: 3
1372288 TTTATATATA
*
1372298 TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1372344 AAT TAT T-T TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
1372365 TCTTATTTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 53 0.91
4 3 0.05
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1376834 original size:19 final size:22
Alignment explanation
Indices: 1376802--1376844 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 22
1376792 GGGATAATAT
1376802 ATATATATATATGGATGGA-GG
1 ATATATATATATGGATGGATGG
*
1376823 ATATAT-TA-ATGGGTGGATGG
1 ATATATATATATGGATGGATGG
1376843 AT
1 AT
1376845 GATGCGGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 6 0.30
21 6 0.30
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (22 bp):
ATATATATATATGGATGGATGG
Found at i:1378957 original size:27 final size:26
Alignment explanation
Indices: 1378919--1378995 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 26
1378909 TCATTTAAAT
1378919 TTATTATTATTATTAAA-T-TTATTA
1 TTATTATTATTATTAAATTATTATTA
1378943 TTATTATTATTATTAAA-TATTATTA
1 TTATTATTATTATTAAATTATTATTA
*
1378968 TTAGTATATTATTATTAAATAATTATTA
1 TTA-T-TATTATTATTAAATTATTATTA
1378996 CAAACCCATT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
24 18 0.38
25 9 0.19
26 1 0.02
27 13 0.27
28 7 0.15
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (26 bp):
TTATTATTATTATTAAATTATTATTA
Found at i:1378995 original size:3 final size:3
Alignment explanation
Indices: 1378919--1378984 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
1378909 TCATTTAAAT
* *
1378919 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTA TTA TTA TTAA ATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
1378965 TTA TTA GTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
1378985 AATAATTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
2 3 0.06
3 48 0.89
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1379390 original size:16 final size:16
Alignment explanation
Indices: 1379369--1379403 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1379359 CGGGGAGACA
1379369 AAAAACA-GAAAAGAAG
1 AAAAACAGGAAAA-AAG
1379385 AAAAACAGGAAAAAAG
1 AAAAACAGGAAAAAAG
1379401 AAA
1 AAA
1379404 GAAAGAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAACAGGAAAAAAG
Found at i:1379407 original size:20 final size:19
Alignment explanation
Indices: 1379377--1379416 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
1379367 CAAAAAACAG
1379377 AAAAGAAGAAA-AACAGGAA
1 AAAAGAAGAAAGAA-AGGAA
1379396 AAAAGAAAGAAAGAAAGGAA
1 AAAAG-AAGAAAGAAAGGAA
1379416 A
1 A
1379417 GCTTACCGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 12 0.63
21 2 0.11
ACGTcount: A:0.75, C:0.03, G:0.23, T:0.00
Consensus pattern (19 bp):
AAAAGAAGAAAGAAAGGAA
Found at i:1380195 original size:19 final size:18
Alignment explanation
Indices: 1380171--1380223 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 18
1380161 TAATTTAGTC
1380171 ATTTATTTTATATGTTTTA
1 ATTTATTTTAT-TGTTTTA
1380190 ATTTATTTTATTGTTTT-
1 ATTTATTTTATTGTTTTA
* *
1380207 TTTTA-TATATTGTTTTA
1 ATTTATTTTATTGTTTTA
1380224 GTAGAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 10 0.32
17 4 0.13
18 6 0.19
19 11 0.35
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.72
Consensus pattern (18 bp):
ATTTATTTTATTGTTTTA
Found at i:1380274 original size:20 final size:21
Alignment explanation
Indices: 1380237--1380277 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1380227 GAATTTTTTC
**
1380237 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
1380258 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
1380278 ATATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:1380956 original size:20 final size:21
Alignment explanation
Indices: 1380933--1380984 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
1380923 AGAAATTAAA
1380933 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
1380953 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
1380975 -ATT-ATTTATT
1 AATTCATTTATT
1380985 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:1380990 original size:16 final size:16
Alignment explanation
Indices: 1380969--1381014 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1380959 TTTCTTTCAA
1380969 ATTTTTATTATTTATT
1 ATTTTTATTATTTATT
*
1380985 ATTTTTA-TATTAATAT
1 ATTTTTATTATTTAT-T
1381001 ATTTTT-TT-TTTATT
1 ATTTTTATTATTTATT
1381015 CAGGTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 1 0.04
15 10 0.38
16 15 0.58
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTTTATTATTTATT
Found at i:1387041 original size:81 final size:81
Alignment explanation
Indices: 1386890--1387053 Score: 312
Period size: 82 Copynumber: 2.0 Consensus size: 81
1386880 AGATTCCAAA
1386890 AGTTGAGATAACCAGTTTACCATCAACTAAACCTTTCCCTGGTTAGGGAAGAGTGGGATATGACA
1 AGTTGAGATAACCAGTTTACCATCAACTAAACCTTTCCCTGGTTAGGGAAGAGTGGGATATGACA
1386955 ATATGTATTTTGGAGT
66 ATATGTATTTTGGAGT
1386971 AGTTGAGATAACCAGTTTTACCATCAACTAAACCTTTCCCTGGTTAGGGAAGAGTGGGAT-TGAC
1 AGTTGAGATAACCAG-TTTACCATCAACTAAACCTTTCCCTGGTTAGGGAAGAGTGGGATATGAC
1387035 AATATGTATTTTGGAGT
65 AATATGTATTTTGGAGT
1387052 AG
1 AG
1387054 CCAAAGAGAC
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
81 38 0.46
82 44 0.54
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (81 bp):
AGTTGAGATAACCAGTTTACCATCAACTAAACCTTTCCCTGGTTAGGGAAGAGTGGGATATGACA
ATATGTATTTTGGAGT
Found at i:1391361 original size:76 final size:76
Alignment explanation
Indices: 1391155--1391633 Score: 873
Period size: 76 Copynumber: 6.4 Consensus size: 76
1391145 ACTATTCTCA
1391155 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1391219 AGCCTTC-GGT
66 ATCCTTCGGGT
1391229 CATCTGTAAGTCCTTCA-TGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1391293 ATCCTTCGGGT
66 ATCCTTCGGGT
1391304 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1391369 ATCCTTCGGGT
66 ATCCTTCGGGT
1391380 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTT--TGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1391442 A-GCTTCGGGT
66 ATCCTTCGGGT
1391452 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1391517 ATCCTTCGGGT
66 ATCCTTCGGGT
1391528 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
1391593 AGCCTTCGAGT
66 ATCCTTCGGGT
1391604 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1391634 TCAACATTTC
Statistics
Matches: 393, Mismatches: 5, Indels: 12
0.96 0.01 0.03
Matches are distributed among these distances:
72 57 0.15
73 28 0.07
74 55 0.14
75 34 0.09
76 219 0.56
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ATCCTTCGGGT
Found at i:1391488 original size:148 final size:150
Alignment explanation
Indices: 1391155--1391633 Score: 860
Period size: 148 Copynumber: 3.2 Consensus size: 150
1391145 ACTATTCTCA
1391155 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1391219 AGCCTTC-GGTCATCTGTAAGTCCTTCA-TGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 ATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
1391282 GATGTTTTCAAATCCTTCGGGT
131 -ATGTTTTCAAA-GCTTCGGGT
1391304 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1391369 ATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTT
66 ATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
1391433 -TGTTTTCAAAGCTTCGGGT
131 ATGTTTTCAAAGCTTCGGGT
1391452 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1391517 ATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 ATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
1391582 GATGTTTTCAAAGCCTTCGAGT
131 -ATGTTTTCAAAG-CTTCGGGT
1391604 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1391634 TCAACATTTC
Statistics
Matches: 320, Mismatches: 3, Indels: 11
0.96 0.01 0.03
Matches are distributed among these distances:
148 133 0.42
149 46 0.14
150 38 0.12
151 35 0.11
152 68 0.21
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (150 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
ATGTTTTCAAAGCTTCGGGT
Found at i:1391546 original size:224 final size:224
Alignment explanation
Indices: 1391155--1391633 Score: 883
Period size: 224 Copynumber: 2.1 Consensus size: 224
1391145 ACTATTCTCA
1391155 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGGGAGCTTTTT-ATGTTTTCAAA
1391220 GCCTTCGGTCATCTGTAAGTCCTTCATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAT
65 GCCTTCGGTCATCTGTAAGTCCTTCATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAT
1391285 GTTTTCAAATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
130 GTTTTCAAATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
* *
1391350 AGCTTTTTGATGTTTTCAAATCCTTCGGGT
195 AGCTTTTTGATGTTTTCAAAGCCTTCGAGT
1391380 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTT-TGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTATGTTTTCAAA
1391443 G-CTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
65 GCCTTC-GGTCATCTGTAAGTCCTTCA-TGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
1391507 ATGTTTTCAAATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCG
128 ATGTTTTCAAATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCG
1391572 GGAGCTTTTTGATGTTTTCAAAGCCTTCGAGT
193 GGAGCTTTTTGATGTTTTCAAAGCCTTCGAGT
1391604 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1391634 TCAACATTTC
Statistics
Matches: 249, Mismatches: 2, Indels: 7
0.97 0.01 0.03
Matches are distributed among these distances:
222 4 0.02
223 31 0.12
224 162 0.65
225 36 0.14
226 16 0.06
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (224 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGGGAGCTTTTTATGTTTTCAAAG
CCTTCGGTCATCTGTAAGTCCTTCATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG
TTTTCAAATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGA
GCTTTTTGATGTTTTCAAAGCCTTCGAGT
Found at i:1391807 original size:27 final size:26
Alignment explanation
Indices: 1391769--1391845 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 26
1391759 TCATTTAAAT
1391769 TTATTATTATTATTAAA-T-TTATTA
1 TTATTATTATTATTAAATTATTATTA
1391793 TTATTATTATTATTAAA-TATTATTA
1 TTATTATTATTATTAAATTATTATTA
*
1391818 TTAGTATATTATTATTAAATAATTATTA
1 TTA-T-TATTATTATTAAATTATTATTA
1391846 CAAACCCATT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
24 18 0.38
25 9 0.19
26 1 0.02
27 13 0.27
28 7 0.15
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (26 bp):
TTATTATTATTATTAAATTATTATTA
Found at i:1391845 original size:3 final size:3
Alignment explanation
Indices: 1391769--1391834 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
1391759 TCATTTAAAT
* *
1391769 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTA TTA TTA TTAA ATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
1391815 TTA TTA GTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
1391835 AATAATTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
2 3 0.06
3 48 0.89
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1392247 original size:15 final size:16
Alignment explanation
Indices: 1392216--1392249 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1392206 CGGGGAGACA
1392216 AAAAACAGAAAAGAAG
1 AAAAACAGAAAAGAAG
*
1392232 AAAAACAGGAAA-AAG
1 AAAAACAGAAAAGAAG
1392247 AAA
1 AAA
1392250 GAAAGAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAACAGAAAAGAAG
Found at i:1392253 original size:19 final size:18
Alignment explanation
Indices: 1392216--1392262 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
1392206 CGGGGAGACA
1392216 AAAAACA-G-AAAAGAAG
1 AAAAACAGGAAAAAGAAG
1392232 AAAAACAGGAAAAAGAAAG
1 AAAAACAGGAAAAAG-AAG
1392251 AAAGAA-AGGAAA
1 AAA-AACAGGAAA
1392263 GCTTACCGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 7 0.26
17 1 0.04
18 5 0.19
19 12 0.44
20 2 0.07
ACGTcount: A:0.74, C:0.04, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAACAGGAAAAAGAAG
Found at i:1393041 original size:19 final size:18
Alignment explanation
Indices: 1393017--1393069 Score: 65
Period size: 16 Copynumber: 3.0 Consensus size: 18
1393007 TAATTTAGTC
1393017 ATTTATTTTATATGTTTTA
1 ATTTATTTTAT-TGTTTTA
1393036 ATTTATTTTATTGTTTT-
1 ATTTATTTTATTGTTTTA
* *
1393053 -TTTAATATATTGTTTTA
1 ATTTATTTTATTGTTTTA
1393070 GTAGAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 14 0.45
18 6 0.19
19 11 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.70
Consensus pattern (18 bp):
ATTTATTTTATTGTTTTA
Found at i:1393120 original size:20 final size:21
Alignment explanation
Indices: 1393083--1393123 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1393073 GAATTTTTTC
**
1393083 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
1393104 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
1393124 ATATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:1394618 original size:31 final size:31
Alignment explanation
Indices: 1394580--1394641 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1394570 CTATCAACGG
1394580 TTCCTTCCGTTTTACATACCCAGATATTAAA
1 TTCCTTCCGTTTTACATACCCAGATATTAAA
1394611 TTCCTTCCGTTTTACATACCCAGATATTAAA
1 TTCCTTCCGTTTTACATACCCAGATATTAAA
1394642 GCCGACCACG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.39
Consensus pattern (31 bp):
TTCCTTCCGTTTTACATACCCAGATATTAAA
Done.