Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 5 of 144
Found at i:1198659 original size:31 final size:31
Alignment explanation
Indices: 1198618--1198684 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
1198608 TTCAAAATGG
* *
1198618 TCAAACAAGGACCAAAGATTTTCGAAAGTGC
1 TCAAAAAAGGACCAAACATTTTCGAAAGTGC
* **
1198649 TCAAAAAAGGACCAAACCTTTTCGGTAGTGC
1 TCAAAAAAGGACCAAACATTTTCGAAAGTGC
1198680 TCAAA
1 TCAAA
1198685 TAAGTGCTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (31 bp):
TCAAAAAAGGACCAAACATTTTCGAAAGTGC
Found at i:1201230 original size:20 final size:20
Alignment explanation
Indices: 1201205--1201251 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
1201195 TACTATTTTC
1201205 TTGTTGTTTTTTTCACTATT
1 TTGTTGTTTTTTTCACTATT
1201225 TTGTTG-TTTTTTCACTATT
1 TTGTTGTTTTTTTCACTATT
*
1201244 ATGTTGTT
1 TTGTTGTT
1201252 ACTATTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.11, C:0.09, G:0.13, T:0.68
Consensus pattern (20 bp):
TTGTTGTTTTTTTCACTATT
Found at i:1201251 original size:22 final size:20
Alignment explanation
Indices: 1201180--1201243 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 20
1201170 TTTTTATTTT
*
1201180 TTTTTATTGTTTTGTT-ACTA
1 TTTTTGTTGTTTT-TTCACTA
1201200 TTTTCTTGTTGTTTTTTTCACTA
1 -TTT-TTGTTG-TTTTTTCACTA
1201223 -TTTTGTTGTTTTTTCACTA
1 TTTTTGTTGTTTTTTCACTA
1201242 TT
1 TT
1201244 ATGTTGTTAC
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 11 0.29
20 7 0.18
21 5 0.13
22 7 0.18
23 8 0.21
ACGTcount: A:0.11, C:0.09, G:0.09, T:0.70
Consensus pattern (20 bp):
TTTTTGTTGTTTTTTCACTA
Found at i:1201263 original size:13 final size:13
Alignment explanation
Indices: 1201238--1201272 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1201228 TTGTTTTTTC
1201238 ACTATTATGTTGTT
1 ACTATT-TGTTGTT
1201252 ACTATTTGTTGTT
1 ACTATTTGTTGTT
*
1201265 ATTATTTG
1 ACTATTTG
1201273 GATATTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.20, C:0.06, G:0.14, T:0.60
Consensus pattern (13 bp):
ACTATTTGTTGTT
Found at i:1203002 original size:245 final size:245
Alignment explanation
Indices: 1202565--1203051 Score: 803
Period size: 245 Copynumber: 2.0 Consensus size: 245
1202555 TTTAATGGTT
* *
1202565 AAAATGCTAGAGCCCCTCAAGTGACCCGAGTTTGAGCCATGCATCTCCCTTCCATTTCCTTTTAA
1 AAAACGCTAGAGCCCCCCAAGTGACCCGAGTTTGAGCCATGCATCTCCCTTCCATTTCCTTTTAA
* * * * *
1202630 TTTCGGCCAAAAATAGAGGAATTTGCAAATTGCTGCCCCTTGCTTCTAATTTTGGAAATTTGCAT
66 ATTCGACCAAAAATAGAGGAATTTGCAAATTGCCGCCCCTTGCTCCTAATTTGGGAAATTTGCAT
* *
1202695 TTGTAGCCCTTAGGGTTTGCAAACCCTAGGAATTTACCAAATTCCTTCCTAATTAGAATTCATAA
131 GTGTAGCCCTTAGGGTTTACAAACCCTAGGAATTTACCAAATTCCTTCCTAATTAGAATTCATAA
* * *
1202760 CTTGCCCCTTTTCAAAATTCCAACAAAATTAGCATTCCACCATCTTTGGG
196 CTTGCCCCTTCTCAAAATTCCAACAAAATCAACATTCCACCATCTTTGGG
1202810 AAAACGCTAGAGCCCCCCAAGTGACCCGAGTTTGAGCCATGCATCTCCCTTCCATTTCCTTTTAA
1 AAAACGCTAGAGCCCCCCAAGTGACCCGAGTTTGAGCCATGCATCTCCCTTCCATTTCCTTTTAA
*
1202875 ATTCGACCAAAAATAGGGGAATTTGCAAATTGCCGCCCCTTGCTCCTAATTTGGGAAATTTGCAT
66 ATTCGACCAAAAATAGAGGAATTTGCAAATTGCCGCCCCTTGCTCCTAATTTGGGAAATTTGCAT
* * * *
1202940 GTGTAGCCCTTAGGGTTTACAAATCTTAGGAATTTACCCAATTCCTTCCTAATTATAATTCATAA
131 GTGTAGCCCTTAGGGTTTACAAACCCTAGGAATTTACCAAATTCCTTCCTAATTAGAATTCATAA
* *
1203005 CTTGCCCCTTCTCAAAATTCCAATAGAATCAACATTCCACCATCTTT
196 CTTGCCCCTTCTCAAAATTCCAACAAAATCAACATTCCACCATCTTT
1203052 TTCTCTTTTT
Statistics
Matches: 223, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
245 223 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (245 bp):
AAAACGCTAGAGCCCCCCAAGTGACCCGAGTTTGAGCCATGCATCTCCCTTCCATTTCCTTTTAA
ATTCGACCAAAAATAGAGGAATTTGCAAATTGCCGCCCCTTGCTCCTAATTTGGGAAATTTGCAT
GTGTAGCCCTTAGGGTTTACAAACCCTAGGAATTTACCAAATTCCTTCCTAATTAGAATTCATAA
CTTGCCCCTTCTCAAAATTCCAACAAAATCAACATTCCACCATCTTTGGG
Found at i:1204141 original size:40 final size:38
Alignment explanation
Indices: 1204031--1204156 Score: 162
Period size: 38 Copynumber: 3.3 Consensus size: 38
1204021 ACATGATTTG
* * *
1204031 CATGTCTACTGTTAATAATGAATTGAGTACGTGTTAAA
1 CATGTTTACTATTAATAATGAATTGAGTACATGTTAAA
* *
1204069 CATGCTTACTATTAATGATGAATTGAGTACATGTTAAA
1 CATGTTTACTATTAATAATGAATTGAGTACATGTTAAA
* *
1204107 CATGTTTACTATTATAATAATGAATTGAGCACATGTTATA
1 CATGTTTACTA-T-TAATAATGAATTGAGTACATGTTAAA
*
1204147 CATGTCTACT
1 CATGTTTACT
1204157 GCTAGTGTTG
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
38 43 0.57
39 1 0.01
40 32 0.42
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (38 bp):
CATGTTTACTATTAATAATGAATTGAGTACATGTTAAA
Found at i:1205718 original size:53 final size:53
Alignment explanation
Indices: 1205651--1205877 Score: 292
Period size: 53 Copynumber: 4.3 Consensus size: 53
1205641 CAAGAGCTCT
* *
1205651 GTCATCGGACCTTTAATCCATAATAGGATTCATATAACTCACGATGAAACAGA
1 GTCATCGGACCTTTAATCCATAATAAGATTCATATAACTCACGATGACACAGA
* * *
1205704 GTCATCGAATCTTTAATCCATAATAAGATTTCATATAACTCACGATGACATAGA
1 GTCATCGGACCTTTAATCCATAATAAGA-TTCATATAACTCACGATGACACAGA
* * * * * * *
1205758 GTCATCGGACCTTTAATCCATGATAGGATTCATATAAATTATGGTGACACTGA
1 GTCATCGGACCTTTAATCCATAATAAGATTCATATAACTCACGATGACACAGA
* * * *
1205811 GTCATTGGACCTTTAATCCGTAATAAGATTCATATAACTTACGATGACACAAA
1 GTCATCGGACCTTTAATCCATAATAAGATTCATATAACTCACGATGACACAGA
*
1205864 GTCATTGGACCTTT
1 GTCATCGGACCTTT
1205878 TTGCATTTAC
Statistics
Matches: 149, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
53 102 0.68
54 47 0.32
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (53 bp):
GTCATCGGACCTTTAATCCATAATAAGATTCATATAACTCACGATGACACAGA
Found at i:1205837 original size:107 final size:106
Alignment explanation
Indices: 1205651--1205877 Score: 310
Period size: 107 Copynumber: 2.1 Consensus size: 106
1205641 CAAGAGCTCT
* *
1205651 GTCATCGGACCTTTAATCCATAATAGGATTCATATAACTCACGATGAAACAGAGTCATCGAATCT
1 GTCATCGGACCTTTAATCCATAATAGGATTCATATAAATCACGATGAAACAGAGTCATCGAACCT
* *
1205716 TTAATCCATAATAAGATTTCATATAACTCACGATGACATAGA
66 TTAATCCATAATAAGA-TTCATATAACTCACGATGACACAAA
* * * * * * * *
1205758 GTCATCGGACCTTTAATCCATGATAGGATTCATATAAATTATGGTGACACTGAGTCATTGGACCT
1 GTCATCGGACCTTTAATCCATAATAGGATTCATATAAATCACGATGAAACAGAGTCATCGAACCT
* *
1205823 TTAATCCGTAATAAGATTCATATAACTTACGATGACACAAA
66 TTAATCCATAATAAGATTCATATAACTCACGATGACACAAA
*
1205864 GTCATTGGACCTTT
1 GTCATCGGACCTTT
1205878 TTGCATTTAC
Statistics
Matches: 105, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
106 35 0.33
107 70 0.67
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (106 bp):
GTCATCGGACCTTTAATCCATAATAGGATTCATATAAATCACGATGAAACAGAGTCATCGAACCT
TTAATCCATAATAAGATTCATATAACTCACGATGACACAAA
Found at i:1214719 original size:13 final size:13
Alignment explanation
Indices: 1214703--1214727 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1214693 TTAAATTAAG
1214703 AAATTAAAATGTC
1 AAATTAAAATGTC
1214716 AAATTAAAATGT
1 AAATTAAAATGT
1214728 TGTTACAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (13 bp):
AAATTAAAATGTC
Found at i:1214976 original size:18 final size:19
Alignment explanation
Indices: 1214955--1214991 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1214945 TTAAAAAATA
1214955 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
1214973 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
1214992 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:1214992 original size:18 final size:19
Alignment explanation
Indices: 1214955--1215005 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
1214945 TTAAAAAATA
*
1214955 TATAAAT-TTTGGAATTTT
1 TATAAATATTTTGAATTTT
1214973 TATAAATATTTTGAA-TTT
1 TATAAATATTTTGAATTTT
*
1214991 TAAAAATTATTTTGA
1 TATAAA-TATTTTGA
1215006 TTTGTTGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:1215008 original size:18 final size:18
Alignment explanation
Indices: 1214960--1215005 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
1214950 AAATATATAA
*
1214960 ATTTTGGAATTTTTATAAAT
1 ATTTT-GAA-TTTTAAAAAT
1214980 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTAAAAA-T
1214999 ATTTTGA
1 ATTTTGA
1215006 TTTGTTGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 8 0.33
19 11 0.46
20 5 0.21
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (18 bp):
ATTTTGAATTTTAAAAAT
Found at i:1220792 original size:90 final size:89
Alignment explanation
Indices: 1220688--1220947 Score: 490
Period size: 90 Copynumber: 2.9 Consensus size: 89
1220678 TCGAATGATA
1220688 ATATATATATTGCTTAACCGTGGATAGCTTTTCAAAAGCATAAGGATAAATTCAGCTCTTAACGT
1 ATATATATATTGCTTAACCGTGGATAGCTTTTCAAAAGCATAAGGATAAATTCAGCTCTTAACGT
1220753 TTACATCTTTTGTCAATATATATAT
66 TTACATCTTTTGTCAA-ATATATAT
1220778 ATATATATATTGCTTAACCGTGGATAGCTTTTCAAAAGCATAAGGATAAATTCAGCTCTTAACGT
1 ATATATATATTGCTTAACCGTGGATAGCTTTTCAAAAGCATAAGGATAAATTCAGCTCTTAACGT
1220843 TTACATCTTTTGTC-AATATATAT
66 TTACATCTTTTGTCAAATATATAT
1220866 ATATATAT-TT-CTTAACCGTGGATAGCTTTTCAAAAGCATAAGGATAAATTCAGCTCTTAACGT
1 ATATATATATTGCTTAACCGTGGATAGCTTTTCAAAAGCATAAGGATAAATTCAGCTCTTAACGT
1220929 TTACATCTTTTGTCAAATA
66 TTACATCTTTTGTCAAATA
1220948 GGTCTTTTTT
Statistics
Matches: 169, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
86 67 0.40
87 6 0.04
88 16 0.09
89 1 0.01
90 79 0.47
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (89 bp):
ATATATATATTGCTTAACCGTGGATAGCTTTTCAAAAGCATAAGGATAAATTCAGCTCTTAACGT
TTACATCTTTTGTCAAATATATAT
Found at i:1220917 original size:86 final size:86
Alignment explanation
Indices: 1220688--1220944 Score: 469
Period size: 86 Copynumber: 2.9 Consensus size: 86
1220678 TCGAATGATA
*
1220688 ATATATATATTGCTTAACCGTGGATAGCTTTTCAAAAGCATAAGGATAAATTCAGCTCTTAACGT
1 ATATATATATTTCTTAACCGTGGATAGCTTTTCAAAAGCATAAGGATAAATTCAGCTCTTAACGT
1220753 TTACATCTTTTGTCAATATATAT
66 TTACATCTTTTGTC-A-ATATAT
1220776 ATATATATATATTGCTTAACCGTGGATAGCTTTTCAAAAGCATAAGGATAAATTCAGCTCTTAAC
1 ATATATATAT-TT-CTTAACCGTGGATAGCTTTTCAAAAGCATAAGGATAAATTCAGCTCTTAAC
1220841 GTTTACATCTTTTGTCAATATAT
64 GTTTACATCTTTTGTCAATATAT
1220864 ATATATATATTTCTTAACCGTGGATAGCTTTTCAAAAGCATAAGGATAAATTCAGCTCTTAACGT
1 ATATATATATTTCTTAACCGTGGATAGCTTTTCAAAAGCATAAGGATAAATTCAGCTCTTAACGT
1220929 TTACATCTTTTGTCAA
66 TTACATCTTTTGTCAA
1220945 ATAGGTCTTT
Statistics
Matches: 166, Mismatches: 1, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
86 69 0.42
87 2 0.01
88 26 0.16
89 2 0.01
90 67 0.40
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (86 bp):
ATATATATATTTCTTAACCGTGGATAGCTTTTCAAAAGCATAAGGATAAATTCAGCTCTTAACGT
TTACATCTTTTGTCAATATAT
Found at i:1221197 original size:18 final size:17
Alignment explanation
Indices: 1221145--1221205 Score: 68
Period size: 19 Copynumber: 3.4 Consensus size: 17
1221135 CTTTATATAT
*
1221145 ATATTTTTTAATTTTTA
1 ATATTTTTTAATTTTGA
*
1221162 ATTTTTTTTAATTTTTTGA
1 ATATTTTTTAA--TTTTGA
1221181 ATATTTTTATAATTTTGA
1 ATATTTTT-TAATTTTGA
1221199 ATTATTT
1 A-TATTT
1221206 CTTGATGTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 10 0.27
18 7 0.19
19 17 0.46
20 3 0.08
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
ATATTTTTTAATTTTGA
Found at i:1221897 original size:2 final size:2
Alignment explanation
Indices: 1221890--1221923 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1221880 TCATCATTTA
* *
1221890 AT AT AT AT AT AT AT AT AT AT AA AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1221924 TTGATAATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1222142 original size:10 final size:10
Alignment explanation
Indices: 1222129--1222175 Score: 67
Period size: 10 Copynumber: 4.5 Consensus size: 10
1222119 AAAACTATTC
1222129 AAAATAATAT
1 AAAATAATAT
1222139 AAAATAATAT
1 AAAATAATAT
1222149 AAAATAATAT
1 AAAATAATAT
*
1222159 ATTAATAATATT
1 A-AAATAATA-T
1222171 AAAAT
1 AAAAT
1222176 TATAAACATG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
10 21 0.64
11 10 0.30
12 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAATAATAT
Found at i:1239396 original size:60 final size:60
Alignment explanation
Indices: 1239292--1239410 Score: 152
Period size: 60 Copynumber: 2.0 Consensus size: 60
1239282 CATTTGAAAA
* * * *
1239292 GGTTTGGCCTTTATTTGAGCACTTTCAAAAAGGTTAGGTCCTTATCTGACCGTTTTGAAC
1 GGTTTGCCCTTCATTTGAGCACTTTCAAAAAGGTTAGGTCCTTATATGACCATTTTGAAC
* *
1239352 GGTTTGCCCTTCATTTGAGCACTTTTATAAAA-GTTTGG-CTCTTATATGACCATTTTGAA
1 GGTTTGCCCTTCATTTGAGCACTTTCA-AAAAGGTTAGGTC-CTTATATGACCATTTTGAA
1239411 AGGTGTGGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
59 1 0.02
60 46 0.90
61 4 0.08
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (60 bp):
GGTTTGCCCTTCATTTGAGCACTTTCAAAAAGGTTAGGTCCTTATATGACCATTTTGAAC
Found at i:1241519 original size:16 final size:18
Alignment explanation
Indices: 1241500--1241541 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1241490 AAAAATTCAG
1241500 AATAA-AAAA-ATAATAA
1 AATAATAAAAGATAATAA
*
1241516 AATAATAAAAGCTAATAA
1 AATAATAAAAGATAATAA
1241534 ATATAATA
1 A-ATAATA
1241542 TTGAACTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 4 0.18
18 7 0.32
19 6 0.27
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (18 bp):
AATAATAAAAGATAATAA
Found at i:1246210 original size:49 final size:49
Alignment explanation
Indices: 1246153--1246313 Score: 148
Period size: 49 Copynumber: 3.2 Consensus size: 49
1246143 ATGCTACACC
* * *
1246153 ATGTCTCGAGACTTGCTTTCTCAGCTTCAAACTTTAGCTTCGAAGTTCT
1 ATGTCTCGAGACTTGCATCCTCAGCTTCAAACTTTAGCTTCGAAGTTTT
* * * *
1246202 ATGTCTCGAAACAT-CACCCTCCAAG-TCTCAAGACTTTAGCTTAGAAGTTTT
1 ATGTCTCGAGACTTGCATCCT-C-AGCT-TCAA-ACTTTAGCTTCGAAGTTTT
* * * *
1246253 ATGTCTC-AGGACTTGCCTCCTCAGCTTCAAATTTTACCTTCAAAGTTTT
1 ATGTCTCGA-GACTTGCATCCTCAGCTTCAAACTTTAGCTTCGAAGTTTT
*
1246302 ATGTCTTGAGAC
1 ATGTCTCGAGAC
1246314 ATAGGAGTTA
Statistics
Matches: 88, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
48 3 0.03
49 38 0.43
50 14 0.16
51 29 0.33
52 4 0.05
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (49 bp):
ATGTCTCGAGACTTGCATCCTCAGCTTCAAACTTTAGCTTCGAAGTTTT
Found at i:1246370 original size:22 final size:22
Alignment explanation
Indices: 1246329--1246370 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1246319 AGTTATGTCT
*
1246329 CAAGACTTTACCCTCTAAGTCC
1 CAAGACTTTACCCTCGAAGTCC
* *
1246351 CAAGACTTTAGCTTCGAAGT
1 CAAGACTTTACCCTCGAAGT
1246371 TTTATGTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (22 bp):
CAAGACTTTACCCTCGAAGTCC
Found at i:1249840 original size:15 final size:15
Alignment explanation
Indices: 1249822--1249918 Score: 77
Period size: 15 Copynumber: 6.5 Consensus size: 15
1249812 TGCTGCTATG
*
1249822 CCAAATGTTGGGGTA
1 CCAAATGTTGCGGTA
* *
1249837 CCAAATGCTGCGATA
1 CCAAATGTTGCGGTA
** **
1249852 CCAAATGCGGTTGTA
1 CCAAATGTTGCGGTA
* *
1249867 CCAAATATTGCCGTA
1 CCAAATGTTGCGGTA
**
1249882 CCAAATGTTGCTATA
1 CCAAATGTTGCGGTA
* *
1249897 CCAAATGCTACGGTA
1 CCAAATGTTGCGGTA
1249912 CCAAATG
1 CCAAATG
1249919 CAGAAGATAA
Statistics
Matches: 63, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 63 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (15 bp):
CCAAATGTTGCGGTA
Found at i:1249868 original size:30 final size:29
Alignment explanation
Indices: 1249803--1249919 Score: 92
Period size: 30 Copynumber: 3.9 Consensus size: 29
1249793 CCTATGCCGA
* * *
1249803 TGTACCAAATGCTGCTATGCCAAATGTTGG
1 TGTACCAAATGCTGCGATACCAAATG-CGG
*
1249833 GGTACCAAATGCTGCGATACCAAATGCGG
1 TGTACCAAATGCTGCGATACCAAATGCGG
** * *
1249862 TTGTACCAAATATTGCCG-TACCAAATGTTGC
1 -TGTACCAAATGCTG-CGATACCAAATG-CGG
* * *
1249893 TATACCAAATGCTACGGTACCAAATGC
1 TGTACCAAATGCTGCGATACCAAATGC
1249920 AGAAGATAAA
Statistics
Matches: 69, Mismatches: 14, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
29 4 0.06
30 62 0.90
31 3 0.04
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (29 bp):
TGTACCAAATGCTGCGATACCAAATGCGG
Found at i:1255525 original size:15 final size:15
Alignment explanation
Indices: 1255507--1255607 Score: 121
Period size: 15 Copynumber: 6.7 Consensus size: 15
1255497 CCTATGCCGA
*
1255507 TGTACCAAATGTTGT
1 TGTACCAAATGTTGC
* *
1255522 TGTACCGAATGCTGC
1 TGTACCAAATGTTGC
* *
1255537 TGTACCAAATGTGGT
1 TGTACCAAATGTTGC
1255552 TGTACCAAATGTTGC
1 TGTACCAAATGTTGC
* * *
1255567 CGTACCAAATGCTGT
1 TGTACCAAATGTTGC
1255582 TGTACCAAATGTTGC
1 TGTACCAAATGTTGC
*
1255597 GGTACCAAATG
1 TGTACCAAATG
1255608 CGGAAGATAA
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 70 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.31
Consensus pattern (15 bp):
TGTACCAAATGTTGC
Found at i:1255543 original size:30 final size:30
Alignment explanation
Indices: 1255507--1255607 Score: 148
Period size: 30 Copynumber: 3.4 Consensus size: 30
1255497 CCTATGCCGA
* *
1255507 TGTACCAAATGTTGTTGTACCGAATGCTGC
1 TGTACCAAATGTTGTTGTACCAAATGTTGC
*
1255537 TGTACCAAATGTGGTTGTACCAAATGTTGC
1 TGTACCAAATGTTGTTGTACCAAATGTTGC
* *
1255567 CGTACCAAATGCTGTTGTACCAAATGTTGC
1 TGTACCAAATGTTGTTGTACCAAATGTTGC
*
1255597 GGTACCAAATG
1 TGTACCAAATG
1255608 CGGAAGATAA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.31
Consensus pattern (30 bp):
TGTACCAAATGTTGTTGTACCAAATGTTGC
Found at i:1255557 original size:45 final size:45
Alignment explanation
Indices: 1255507--1255607 Score: 139
Period size: 45 Copynumber: 2.2 Consensus size: 45
1255497 CCTATGCCGA
** * *
1255507 TGTACCAAATGTTGTTGTACCGAATGCTGCTGTACCAAATGTGGT
1 TGTACCAAATGTTGCCGTACCAAATGCTGCTGTACCAAATGTGGC
* *
1255552 TGTACCAAATGTTGCCGTACCAAATGCTGTTGTACCAAATGTTGC
1 TGTACCAAATGTTGCCGTACCAAATGCTGCTGTACCAAATGTGGC
*
1255597 GGTACCAAATG
1 TGTACCAAATG
1255608 CGGAAGATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.31
Consensus pattern (45 bp):
TGTACCAAATGTTGCCGTACCAAATGCTGCTGTACCAAATGTGGC
Found at i:1256918 original size:20 final size:20
Alignment explanation
Indices: 1256893--1256959 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
1256883 AAGGACATTT
1256893 AAATCAATTTGATTAGAATA
1 AAATCAATTTGATTAGAATA
*** *
1256913 AAATCAAATCAAATCA-AATTA
1 AAATC-AATTTGATTAGAA-TA
*
1256934 AAATCAATTTGATTGGAATA
1 AAATCAATTTGATTAGAATA
1256954 AAATCA
1 AAATCA
1256960 TATTGAGATA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (20 bp):
AAATCAATTTGATTAGAATA
Found at i:1270746 original size:22 final size:22
Alignment explanation
Indices: 1270701--1270746 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1270691 CACAGGCGTA
*
1270701 TGGATGAGGGCACACAACCGTG
1 TGGATGAGGGCACACAACCATG
* **
1270723 TGGATGAGGGTACACGGCCATG
1 TGGATGAGGGCACACAACCATG
1270745 TG
1 TG
1270747 ACCCCTGCAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.20, G:0.39, T:0.17
Consensus pattern (22 bp):
TGGATGAGGGCACACAACCATG
Found at i:1273542 original size:29 final size:29
Alignment explanation
Indices: 1273507--1273624 Score: 135
Period size: 29 Copynumber: 4.3 Consensus size: 29
1273497 GCGGAATACG
1273507 AAATAATTTATTTAATTTAAAATCAATCA
1 AAATAATTTATTTAATTTAAAATCAATCA
*
1273536 GAATAATTTATTTAATTTAAAATCAAT--
1 AAATAATTTATTTAATTTAAAATCAATCA
* *
1273563 AAA-AA-TAATTT-A-TT-CAATCAATCA
1 AAATAATTTATTTAATTTAAAATCAATCA
*
1273587 AAATAATTTATTCAATTTAAAAGT-AATCA
1 AAATAATTTATTTAATTTAAAA-TCAATCA
1273616 AAATAATTT
1 AAATAATTT
1273625 TAAAGATTGA
Statistics
Matches: 74, Mismatches: 7, Indels: 16
0.76 0.07 0.16
Matches are distributed among these distances:
22 7 0.09
23 2 0.03
24 4 0.05
25 7 0.09
26 6 0.08
27 3 0.04
28 2 0.03
29 42 0.57
30 1 0.01
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.40
Consensus pattern (29 bp):
AAATAATTTATTTAATTTAAAATCAATCA
Found at i:1273584 original size:22 final size:22
Alignment explanation
Indices: 1273556--1273602 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1273546 TTTAATTTAA
1273556 AATCAATAAAAATAATTTATTC
1 AATCAATAAAAATAATTTATTC
*
1273578 AATCAATCAAAATAATTTATTC
1 AATCAATAAAAATAATTTATTC
1273600 AAT
1 AAT
1273603 TTAAAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (22 bp):
AATCAATAAAAATAATTTATTC
Found at i:1273584 original size:51 final size:51
Alignment explanation
Indices: 1273527--1273624 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
1273517 TTTAATTTAA
* *
1273527 AATCAATCAGAATAATTTATTTAATTTAAAA-TCAATAAAAATAATTTATTC
1 AATCAATCAAAATAATTTATTCAATTTAAAAGT-AATAAAAATAATTTATTC
*
1273578 AATCAATCAAAATAATTTATTCAATTTAAAAGTAATCAAAATAATTT
1 AATCAATCAAAATAATTTATTCAATTTAAAAGTAATAAAAATAATTT
1273625 TAAAGATTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (51 bp):
AATCAATCAAAATAATTTATTCAATTTAAAAGTAATAAAAATAATTTATTC
Found at i:1286390 original size:29 final size:27
Alignment explanation
Indices: 1286344--1286400 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
1286334 AAAAAGTGTC
* *
1286344 AAGTTCAGGTACCGAATTAGGCCAAAAAA
1 AAGTTCAGATACCAAATTAGG--AAAAAA
*
1286373 AAGTTTAGATACCAAATTAGGAAAAAA
1 AAGTTCAGATACCAAATTAGGAAAAAA
1286400 A
1 A
1286401 TGTAAGTTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 7 0.28
29 18 0.72
ACGTcount: A:0.51, C:0.12, G:0.18, T:0.19
Consensus pattern (27 bp):
AAGTTCAGATACCAAATTAGGAAAAAA
Found at i:1286417 original size:31 final size:30
Alignment explanation
Indices: 1286319--1286420 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 30
1286309 AAAAAAGCTA
* *
1286319 AGGTACCAAATTAAGAAAAAGTGTCAAGTTC
1 AGGTACCAAATTAGGAAAAAATGT-AAGTTC
* *
1286350 AGGTACCGAATTAGGCCAAAAAA---AAGTTT
1 AGGTACCAAATTAGG--AAAAAATGTAAGTTC
*
1286379 AGATACCAAATTAGGAAAAAAATGTAAGTTC
1 AGGTACCAAATTAGG-AAAAAATGTAAGTTC
*
1286410 GGGTACCAAAT
1 AGGTACCAAAT
1286421 GTAATATTAA
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
28 6 0.11
29 18 0.32
31 27 0.48
33 5 0.09
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.22
Consensus pattern (30 bp):
AGGTACCAAATTAGGAAAAAATGTAAGTTC
Found at i:1296182 original size:26 final size:27
Alignment explanation
Indices: 1296142--1296217 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 27
1296132 ATATAAAAAA
*
1296142 ATTTTAATGTATTTTAAATTTATTT-AT
1 ATTTTAATAT-TTTTAAATTTATTTGAT
* * *
1296169 TTTTTAATATTTTTAAGTGTATTTGAT
1 ATTTTAATATTTTTAAATTTATTTGAT
*
1296196 ATATTATATATTTTTTAAATTT
1 ATTTTA-ATA-TTTTTAAATTT
1296218 GTTGTATGTA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
26 12 0.32
27 14 0.37
28 3 0.08
29 9 0.24
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (27 bp):
ATTTTAATATTTTTAAATTTATTTGAT
Found at i:1296191 original size:37 final size:36
Alignment explanation
Indices: 1296143--1296217 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 36
1296133 TATAAAAAAA
* *
1296143 TTTTAATGTATTTTAAAT-TTATTTATTTTTTAATAT
1 TTTTAATGTATTTGAAATATTATATATTTTTTAA-AT
*
1296179 TTTTAAGTGTATTTGATATATTATATATTTTTTAAAT
1 TTTTAA-TGTATTTGAAATATTATATATTTTTTAAAT
1296216 TT
1 TT
1296218 GTTGTATGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 6 0.18
37 14 0.41
38 14 0.41
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (36 bp):
TTTTAATGTATTTGAAATATTATATATTTTTTAAAT
Found at i:1298029 original size:16 final size:15
Alignment explanation
Indices: 1298008--1298060 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 15
1297998 TTCTTAATGA
*
1298008 TTTTTATAATTTATAT
1 TTTTTA-AATTTAAAT
* *
1298024 TTTTTAAAATTAGAT
1 TTTTTAAATTTAAAT
1298039 TTTTTAAAAATTTAAAT
1 TTTTT--AAATTTAAAT
1298056 TTTTT
1 TTTTT
1298061 TACTTAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
15 12 0.39
16 6 0.19
17 13 0.42
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (15 bp):
TTTTTAAATTTAAAT
Found at i:1298040 original size:15 final size:15
Alignment explanation
Indices: 1298008--1298047 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1297998 TTCTTAATGA
* *
1298008 TTTTTATAATTTATAT
1 TTTTTA-AAATTAGAT
1298024 TTTTTAAAATTAGAT
1 TTTTTAAAATTAGAT
1298039 TTTTTAAAA
1 TTTTTAAAA
1298048 ATTTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
TTTTTAAAATTAGAT
Found at i:1298043 original size:17 final size:17
Alignment explanation
Indices: 1298015--1298060 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 17
1298005 TGATTTTTAT
*
1298015 AATTTATATTTTTT-AA
1 AATTTAAATTTTTTAAA
*
1298031 AA-TTAGATTTTTTAAA
1 AATTTAAATTTTTTAAA
1298047 AATTTAAATTTTTT
1 AATTTAAATTTTTT
1298061 TACTTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 10 0.38
16 6 0.23
17 10 0.38
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
AATTTAAATTTTTTAAA
Found at i:1303472 original size:37 final size:37
Alignment explanation
Indices: 1303393--1303472 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 37
1303383 TAGATAAAAG
* * * *
1303393 ATGTTATTGACAGAATGGCCAAACAGTTACACGTGGT
1 ATGTTATTGACAGAATAGCCAAACACTTACAAGTGAT
*
1303430 ATGTTATTGACAGAATAGTCAAACACTTACAAGTGAT
1 ATGTTATTGACAGAATAGCCAAACACTTACAAGTGAT
*
1303467 GTGTTA
1 ATGTTA
1303473 AAAATTGGCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (37 bp):
ATGTTATTGACAGAATAGCCAAACACTTACAAGTGAT
Found at i:1304491 original size:237 final size:237
Alignment explanation
Indices: 1304076--1304552 Score: 945
Period size: 237 Copynumber: 2.0 Consensus size: 237
1304066 TTCTGTTAAA
1304076 AATTTCATCAATTTTTATTGTTAAAAATGGATTTTTGTAAACATGACACATCATATGCCACTGTT
1 AATTTCATCAATTTTTATTGTTAAAAATGGATTTTTGTAAACATGACACATCATATGCCACTGTT
1304141 TGATTATTTTTTCAACCACGTCAATTTTTAACAATACAAATGAATGAAATTTTTAACAGAAATGA
66 TGATTATTTTTTCAACCACGTCAATTTTTAACAATACAAATGAATGAAATTTTTAACAGAAATGA
1304206 TAACTTACTTTTCGATCTAATGTATATAGATTAATTTATTCATTTTTATAAAGGAAGTAAAGTGC
131 TAACTTACTTTTCGATCTAATGTATATAGATTAATTTATTCATTTTTATAAAGGAAGTAAAGTGC
1304271 AATCTAACTTTTAATGCATGAATCTACTGATACTTTGATTTG
196 AATCTAACTTTTAATGCATGAATCTACTGATACTTTGATTTG
1304313 AATTTCATCAATTTTTATTGTTAAAAATGGATTTTTGTAAACATGACACATCATATGCCACTGTT
1 AATTTCATCAATTTTTATTGTTAAAAATGGATTTTTGTAAACATGACACATCATATGCCACTGTT
*
1304378 TGATTATTTTTTCAACCACGTCAATTTTTAACAATACAAATGGATGAAATTTTTAACAGAAATGA
66 TGATTATTTTTTCAACCACGTCAATTTTTAACAATACAAATGAATGAAATTTTTAACAGAAATGA
1304443 TAACTTACTTTTCGATCTAATGTATATAGATTAATTTATTCATTTTTATAAAGGAAGTAAAGTGC
131 TAACTTACTTTTCGATCTAATGTATATAGATTAATTTATTCATTTTTATAAAGGAAGTAAAGTGC
1304508 AATCTAACTTTTAATGCATGAATCTACTGATACTTTGATTTG
196 AATCTAACTTTTAATGCATGAATCTACTGATACTTTGATTTG
1304550 AAT
1 AAT
1304553 ATTAATTCAT
Statistics
Matches: 239, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
237 239 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (237 bp):
AATTTCATCAATTTTTATTGTTAAAAATGGATTTTTGTAAACATGACACATCATATGCCACTGTT
TGATTATTTTTTCAACCACGTCAATTTTTAACAATACAAATGAATGAAATTTTTAACAGAAATGA
TAACTTACTTTTCGATCTAATGTATATAGATTAATTTATTCATTTTTATAAAGGAAGTAAAGTGC
AATCTAACTTTTAATGCATGAATCTACTGATACTTTGATTTG
Found at i:1305548 original size:16 final size:16
Alignment explanation
Indices: 1305518--1305547 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1305508 CTTTTTAAAT
1305518 AATTTTTATAATTTTG
1 AATTTTTATAATTTTG
1305534 AATTTTTA-AATTTT
1 AATTTTTATAATTTT
1305548 TAAATATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
AATTTTTATAATTTTG
Found at i:1307875 original size:26 final size:26
Alignment explanation
Indices: 1307839--1307905 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
1307829 ATTATCGGGG
1307839 TGCTAACACTAGCTTTGGATCAGAGT
1 TGCTAACACTAGCTTTGGATCAGAGT
1307865 TGCTAACACTAGCTTTGGATCAGAGT
1 TGCTAACACTAGCTTTGGATCAGAGT
*
1307891 TGCTAACATTAGCTT
1 TGCTAACACTAGCTT
1307906 GGTTTGATGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (26 bp):
TGCTAACACTAGCTTTGGATCAGAGT
Found at i:1310277 original size:23 final size:25
Alignment explanation
Indices: 1310248--1310293 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1310238 TTGTTGGAAA
1310248 ATATTT-ATTT-TAATATTTTTAGT
1 ATATTTAATTTATAATATTTTTAGT
*
1310271 ATATTTAATTTATTATATTTTTA
1 ATATTTAATTTATAATATTTTTA
1310294 AATTTACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 4 0.20
25 10 0.50
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
ATATTTAATTTATAATATTTTTAGT
Found at i:1318086 original size:7 final size:7
Alignment explanation
Indices: 1318070--1318105 Score: 63
Period size: 7 Copynumber: 5.0 Consensus size: 7
1318060 ATTTTCAATT
1318070 TAATACAA
1 TAATA-AA
1318078 TAATAAA
1 TAATAAA
1318085 TAATAAA
1 TAATAAA
1318092 TAATAAA
1 TAATAAA
1318099 TAATAAA
1 TAATAAA
1318106 AGATATTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 23 0.82
8 5 0.18
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (7 bp):
TAATAAA
Found at i:1318267 original size:24 final size:26
Alignment explanation
Indices: 1318214--1318275 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 26
1318204 TATCGTCCTA
1318214 TAAAAA-TAAAATATATTATTAAATT
1 TAAAAATTAAAATATATTATTAAATT
1318239 T-AAAATTAAAATAT-TTA-T-AATT
1 TAAAAATTAAAATATATTATTAAATT
*
1318261 TAAAAAATCAAAATA
1 T-AAAAATTAAAATA
1318276 ATTTGAATCC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
22 5 0.15
23 1 0.03
24 18 0.55
25 9 0.27
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
TAAAAATTAAAATATATTATTAAATT
Found at i:1318896 original size:24 final size:24
Alignment explanation
Indices: 1318863--1318912 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1318853 ATTTAAGAAT
1318863 ATAATATATAATAAAATT-ATATTA
1 ATAATATATAA-AAAATTAATATTA
* *
1318887 ATAATTTATAAATAATTAATATTA
1 ATAATATATAAAAAATTAATATTA
1318911 AT
1 AT
1318913 TTCTTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATATATAAAAAATTAATATTA
Found at i:1321441 original size:30 final size:30
Alignment explanation
Indices: 1321361--1321452 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
1321351 CATTATAATA
1321361 AATGTTAACATTATCTCTTTTAATTT-CAC
1 AATGTTAACATTATCTCTTTTAATTTCCAC
* * *
1321390 -AT-TT--CCTCATCTCACATTTAATTTCCAC
1 AATGTTAACATTATCT--CTTTTAATTTCCAC
1321418 AATGTTAACATTATCTCTTTTAATTTCCAC
1 AATGTTAACATTATCTCTTTTAATTTCCAC
1321448 AATGT
1 AATGT
1321453 GAAAAATACA
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
25 6 0.12
27 11 0.22
28 5 0.10
29 2 0.04
30 20 0.40
32 6 0.12
ACGTcount: A:0.29, C:0.22, G:0.03, T:0.46
Consensus pattern (30 bp):
AATGTTAACATTATCTCTTTTAATTTCCAC
Found at i:1325159 original size:24 final size:25
Alignment explanation
Indices: 1325067--1325160 Score: 131
Period size: 24 Copynumber: 3.9 Consensus size: 25
1325057 CTGGATAAAA
* *
1325067 TTAGCTCATACGAGCCCAG-ATAGA
1 TTAGCTCTTACGAGCCCAGAATAGG
* *
1325091 TTAGCTCTCACGAGCCCA-AATAAG
1 TTAGCTCTTACGAGCCCAGAATAGG
1325115 TTAGCTCTTACGAGCCCAGAAT-GG
1 TTAGCTCTTACGAGCCCAGAATAGG
1325139 TTAGCTCTTACGAGCCCAGAAT
1 TTAGCTCTTACGAGCCCAGAAT
1325161 CAGAATAATG
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
24 59 0.95
25 3 0.05
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (25 bp):
TTAGCTCTTACGAGCCCAGAATAGG
Found at i:1325201 original size:27 final size:27
Alignment explanation
Indices: 1325142--1325277 Score: 146
Period size: 27 Copynumber: 5.0 Consensus size: 27
1325132 AGAATGGTTA
* *
1325142 GCTCTTACGAGCCCAGAATCAGAATAAT
1 GCTCTTTCGAG-CCAGAATCAGAATAAC
* *
1325170 GCTCTTTCGAGCCAAAATCAAAATAAC
1 GCTCTTTCGAGCCAGAATCAGAATAAC
* * *
1325197 ACTCTTTCAAGCCAAAATCAGAATAAC
1 GCTCTTTCGAGCCAGAATCAGAATAAC
* * *
1325224 GCTATTTCAAGCCAGAATCAGAATAAT
1 GCTCTTTCGAGCCAGAATCAGAATAAC
* * *
1325251 GCTCTTTTGAGGCAGAATCAAAATAAC
1 GCTCTTTCGAGCCAGAATCAGAATAAC
1325278 TCCTCAAGCT
Statistics
Matches: 91, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
27 81 0.89
28 10 0.11
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.24
Consensus pattern (27 bp):
GCTCTTTCGAGCCAGAATCAGAATAAC
Found at i:1327695 original size:13 final size:13
Alignment explanation
Indices: 1327677--1327703 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1327667 TTTGGTCTTA
1327677 TAAGTTTCCACTT
1 TAAGTTTCCACTT
1327690 TAAGTTTCCACTT
1 TAAGTTTCCACTT
1327703 T
1 T
1327704 TTCGTCCGCA
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:0.22, C:0.22, G:0.07, T:0.48
Consensus pattern (13 bp):
TAAGTTTCCACTT
Found at i:1336764 original size:19 final size:19
Alignment explanation
Indices: 1336742--1336782 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1336732 TTTACATTTT
1336742 TTTAATATTTT-TAAATAAA
1 TTTAA-ATTTTCTAAATAAA
*
1336761 TTTAAATTTTCTAAATTAA
1 TTTAAATTTTCTAAATAAA
1336780 TTT
1 TTT
1336783 TTACTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTAAATTTTCTAAATAAA
Found at i:1343465 original size:2 final size:2
Alignment explanation
Indices: 1343460--1343490 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1343450 TTTATCCCTT
*
1343460 TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1343491 CTTTTCCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1349476 original size:15 final size:16
Alignment explanation
Indices: 1349456--1349497 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1349446 AATTCAAAAA
1349456 AAAAATTTAAAAAT-T
1 AAAAATTTAAAAATAT
1349471 AAAAA-TTATAAAATAT
1 AAAAATTTA-AAAATAT
*
1349487 ATAAATTTAAA
1 AAAAATTTAAA
1349498 TTTAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 7 0.30
17 3 0.13
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAATTTAAAAATAT
Found at i:1349506 original size:23 final size:23
Alignment explanation
Indices: 1349455--1349507 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1349445 TAATTCAAAA
*
1349455 AAAAAATTTAAAAATTAAAAATT
1 AAAAAATATAAAAATTAAAAATT
* * * *
1349478 ATAAAATATATAAATTTAAATTT
1 AAAAAATATAAAAATTAAAAATT
1349501 AAAAAAT
1 AAAAAAT
1349508 CAAAATATTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
AAAAAATATAAAAATTAAAAATT
Found at i:1349527 original size:13 final size:14
Alignment explanation
Indices: 1349509--1349556 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1349499 TTAAAAAATC
1349509 AAAATA-TTATATA
1 AAAATATTTATATA
*
1349522 AAAATATTTTTATA
1 AAAATATTTATATA
1349536 AAAAT-TTTA-A-A
1 AAAATATTTATATA
*
1349547 AATATATTTA
1 AAAATATTTA
1349557 ATTTAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 5 0.17
12 5 0.17
13 9 0.30
14 11 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATATTTATATA
Found at i:1349564 original size:25 final size:23
Alignment explanation
Indices: 1349520--1349573 Score: 54
Period size: 25 Copynumber: 2.3 Consensus size: 23
1349510 AAATATTATA
* **
1349520 TAAAAATATTTTTATAAAAATTT
1 TAAAAATATTTTAATAAAAAAAT
*
1349543 TAAAAATATATTTAATTTAAAAAAT
1 TAAAAATAT-TTTAA-TAAAAAAAT
1349568 TAAAAA
1 TAAAAA
1349574 AAAACTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 9 0.36
24 4 0.16
25 12 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAAAATATTTTAATAAAAAAAT
Found at i:1349825 original size:29 final size:28
Alignment explanation
Indices: 1349789--1349843 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
1349779 CATTTCAAAT
* *
1349789 TTTTTATATAACTTTTTAATTTTTTAAAA
1 TTTTTATATAA-TATTTAAATTTTTAAAA
1349818 TTTTTATATAATATTTAAATTTTTAA
1 TTTTTATATAATATTTAAATTTTTAA
1349844 TTTAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTTTATATAATATTTAAATTTTTAAAA
Found at i:1349876 original size:16 final size:16
Alignment explanation
Indices: 1349819--1349888 Score: 65
Period size: 18 Copynumber: 4.2 Consensus size: 16
1349809 TTTTTAAAAT
1349819 TTTTATATAATATTTAAA
1 TTTTATAT-AT-TTTAAA
1349837 TTTT-TA-A-TTTAAA
1 TTTTATATATTTTAAA
1349850 TTTTATATATTTTAGAA
1 TTTTATATATTTTA-AA
*
1349867 TTTTACTATTTTTTAAA
1 TTTTA-TATATTTTAAA
1349884 CTTTT
1 -TTTT
1349889 TTAATTTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
13 10 0.22
14 2 0.04
15 2 0.04
16 4 0.09
17 11 0.24
18 16 0.36
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (16 bp):
TTTTATATATTTTAAA
Found at i:1355332 original size:13 final size:13
Alignment explanation
Indices: 1355314--1355340 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1355304 ATATGTTTTA
1355314 GGCAACTTGATTT
1 GGCAACTTGATTT
1355327 GGCAACTTGATTT
1 GGCAACTTGATTT
1355340 G
1 G
1355341 TACAAGGCTT
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:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (13 bp):
GGCAACTTGATTT
Found at i:1356380 original size:18 final size:20
Alignment explanation
Indices: 1356348--1356385 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1356338 CATCCAAACA
*
1356348 CAAAAAATATTAACT-TTTT
1 CAAAAAATATAAACTATTTT
1356367 CAAAAAA-ATAAACTATTTT
1 CAAAAAATATAAACTATTTT
1356386 TCAGAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (20 bp):
CAAAAAATATAAACTATTTT
Found at i:1357564 original size:84 final size:84
Alignment explanation
Indices: 1357228--1358280 Score: 816
Period size: 84 Copynumber: 12.6 Consensus size: 84
1357218 CCTATCATTC
* * * * *
1357228 ATTTATGTCATGGTGTTACTGAAAGTTAGGCTTTGTATAAGCTGCATTTGTTAGTCCGAGTTCGG
1 ATTTATGTTATTGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTG-TAATCCGAGTTCGG
*
1357293 CTTCAGCTCTCATATAATAG
65 GTTCAGCTCTCATATAATAG
*
1357313 A-TT-TGTTA-TGTTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCTC-AGTTCA
1 ATTTATGTTATTG-TGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATC-CGAGTTCG
* *
1357374 AGTTCAGCTCTCATATAATGG
64 GGTTCAGCTCTCATATAATAG
* * ** *
1357395 ATTTATGTTA-TGTTGTCATTGAAAGTTAAGACTTTGTATAAGCTGTATTTGCGATCCGAGTTCT
1 ATTTATGTTATTG-TGTCACTGAAAGTT-AGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCG
* * * * *
1357459 GGTTTAGCCCTCATTTGATAT
64 GGTTCAGCTCTCATATAATAG
* *
1357480 ATTTATGTTATTGTGTCACTGAAAGTTAGACATTGTATAAGCTGCATTTGTAATCTGAGTTCGGG
1 ATTTATGTTATTGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
* *
1357545 TTCGGCTCTCATATAATAT
66 TTCAGCTCTCATATAATAG
* * * *
1357564 ATTTATGTTATGGTGTCACTGAAAGTTCGACTTTGCA-AAGCTGCATTTGTAATCCAAGTTCGGG
1 ATTTATGTTATTGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
* *
1357628 TTCAGCTCTCACATAATAT
66 TTCAGCTCTCATATAATAG
* * * * *
1357647 ATTTATGTTATGGTGCCACTGAAAGTTAGACTTTGTATAAGTTGCATTTGTAATCCAAGTTCAGG
1 ATTTATGTTATTGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
* * * * *
1357712 TTTAGCCCTCGTTTGATAG
66 TTCAGCTCTCATATAATAG
* * * * *
1357731 ATTTATGTTATTGTGTCACTGAAAGTTAGACTTTGCATGAGCTGCATTTATAA-CCTCAGTTCAG
1 ATTTATGTTATTGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCC-GAGTTCGG
* * * * *
1357795 GTTTAGCCCTCTTTTGATAG
65 GTTCAGCTCTCATATAATAG
* * * * * *
1357815 ATTTATGTTATTGTGTTACTGAAAGTTAAACTTTGCATGAGCTGCATTTATAACCCGAGTTCGGG
1 ATTTATGTTATTGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
*
1357880 CTT-AGCTCT-ATTGTAATAG
66 -TTCAGCTCTCA-TATAATAG
* * * ** * * * * * * * *
1357899 ATTTATATTATGGTTTTGCTGAATGTAAGACTTTTTATGAGTTGTATTTGTAATCCAAGTTCAGG
1 ATTTATGTTATTGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
* * *
1357964 TTTAGCTCTTGA-ATTATAG
66 TTCAGCTC-TCATATAATAG
* ** * * * * * * *
1357983 ATTTTATGTTATGGTGTTGCTGACAGTTAGACTCTGTGTGAGCTGCATTTGCAATCCGATTTTGG
1 A-TTTATGTTATTGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGG
*
1358048 GATT-AGCTCTCGA-ATCATAG
65 G-TTCAGCTCTC-ATATAATAG
* * * *
1358068 ATTTATGTTA-TG-G----TG-AAGTTAGACTTTGTATGAGCTGCATTTGTAATCTGACTTTGGG
1 ATTTATGTTATTGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
* * *
1358126 TTCAGCCCTCATGTCATAG
66 TTCAGCTCTCATATAATAG
* ** * ** * * * * * * *
1358145 ATTTGTCATATGGTGTCACTGCCACTTGGACTTTGTTTGAGCTGCATTTCTAA-CCTTAGTTCAG
1 ATTTATGTTATTGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCC-GAGTTCGG
* * *
1358209 GTTTAGCTCTCAAATCATAG
65 GTTCAGCTCTCATATAATAG
* * ** * **
1358229 ATTTATATTA-TGTTTTTGCTGAAAGTTAGATTTTGTATGTGCTGCATTTGTA
1 ATTTATGTTATTG-TGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTA
1358281 CTAAGAGGAG
Statistics
Matches: 794, Mismatches: 145, Indels: 59
0.80 0.15 0.06
Matches are distributed among these distances:
76 3 0.00
77 56 0.07
78 3 0.00
79 1 0.00
82 30 0.04
83 127 0.16
84 434 0.55
85 135 0.17
86 5 0.01
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (84 bp):
ATTTATGTTATTGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
TTCAGCTCTCATATAATAG
Found at i:1358157 original size:77 final size:77
Alignment explanation
Indices: 1358007--1358159 Score: 184
Period size: 77 Copynumber: 2.0 Consensus size: 77
1357997 TGTTGCTGAC
* * *
1358007 AGTTAGACTCTGTGTGAGCTGCATTTGCAATCCGATTTTGGGATTAGCTCTCGAATCATAGATTT
1 AGTTAGACTCTGTATGAGCTGCATTTGCAATCCGACTTTGGGATTAGCCCTCGAATCATAGATTT
**
1358072 ATGTTATGGTGA
66 ATCATATGGTGA
* * * *
1358084 AGTTAGACTTTGTATGAGCTGCATTTGTAATCTGACTTTGGG-TTCAGCCCTC-ATGTCATAGAT
1 AGTTAGACTCTGTATGAGCTGCATTTGCAATCCGACTTTGGGATT-AGCCCTCGA-ATCATAGAT
*
1358147 TTGTCATATGGTG
64 TTATCATATGGTG
1358160 TCACTGCCAC
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
76 3 0.05
77 61 0.95
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (77 bp):
AGTTAGACTCTGTATGAGCTGCATTTGCAATCCGACTTTGGGATTAGCCCTCGAATCATAGATTT
ATCATATGGTGA
Found at i:1387575 original size:30 final size:31
Alignment explanation
Indices: 1387506--1387582 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 31
1387496 CATCATTATT
1387506 TTAGTGACTGTTTTGTCACTTTTCGATAACG
1 TTAGTGACTGTTTTGTCACTTTTCGATAACG
1387537 TTAGTGACTGTTTTGTCACGTTTTC-A-AA-G
1 TTAGTGACTGTTTTGTCAC-TTTTCGATAACG
1387566 TTGAGTGACTGTTTTGT
1 TT-AGTGACTGTTTTGT
1387583 TAAATGTAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
29 3 0.07
30 16 0.36
31 20 0.45
32 5 0.11
ACGTcount: A:0.18, C:0.13, G:0.22, T:0.47
Consensus pattern (31 bp):
TTAGTGACTGTTTTGTCACTTTTCGATAACG
Found at i:1387940 original size:6 final size:6
Alignment explanation
Indices: 1387920--1387998 Score: 78
Period size: 6 Copynumber: 13.8 Consensus size: 6
1387910 TTGATTAATG
*
1387920 TTTAAA -TTAAT TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA
* * *
1387966 TTT-AC TTTAAA TTTAAA ATTGAA -TTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
1387999 TTAAATGAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
4 2 0.03
5 14 0.23
6 42 0.70
7 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:1387946 original size:23 final size:23
Alignment explanation
Indices: 1387920--1388004 Score: 84
Period size: 23 Copynumber: 3.8 Consensus size: 23
1387910 TTGATTAATG
*
1387920 TTTAAATTAATTTTAAATTTAAA
1 TTTAAATTAAATTTAAATTTAAA
**
1387943 TTTATCTTAAATTTAAATTTAAA
1 TTTAAATTAAATTTAAATTTAAA
** * *
1387966 TTTACTTTAAATTTAAAATTGAA
1 TTTAAATTAAATTTAAATTTAAA
*
1387989 -TTAAATTTAA-TTAAAT
1 TTTAAATTAAATTTAAAT
1388005 GAATATCCAT
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
21 5 0.10
22 7 0.14
23 39 0.76
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (23 bp):
TTTAAATTAAATTTAAATTTAAA
Found at i:1387962 original size:17 final size:17
Alignment explanation
Indices: 1387920--1387963 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
1387910 TTGATTAATG
* *
1387920 TTTAAATTAATTTTAAA
1 TTTAAATTTATCTTAAA
1387937 TTTAAATTTATCTTAAA
1 TTTAAATTTATCTTAAA
1387954 TTTAAATTTA
1 TTTAAATTTA
1387964 AATTTACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATCTTAAA
Found at i:1387974 original size:11 final size:10
Alignment explanation
Indices: 1387936--1387980 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 10
1387926 TTAATTTTAA
1387936 ATTTAAATTT
1 ATTTAAATTT
1387946 ATCTTAAATTT
1 AT-TTAAATTT
1387957 AAATTTAAATTT
1 --ATTTAAATTT
1387969 ACTTTAAATTT
1 A-TTTAAATTT
1387980 A
1 A
1387981 AAATTGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
10 3 0.10
11 18 0.58
12 8 0.26
13 2 0.06
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:1388071 original size:14 final size:14
Alignment explanation
Indices: 1388052--1388092 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
1388042 AGCCCGAATG
1388052 AAAGGCCCAATTAC
1 AAAGGCCCAATTAC
* *
1388066 AAAGG-CCAAATAG
1 AAAGGCCCAATTAC
1388079 AAA-GCCCAATTAC
1 AAAGGCCCAATTAC
1388092 A
1 A
1388093 TCAGCCCCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
12 1 0.05
13 16 0.73
14 5 0.23
ACGTcount: A:0.49, C:0.24, G:0.15, T:0.12
Consensus pattern (14 bp):
AAAGGCCCAATTAC
Found at i:1388085 original size:26 final size:26
Alignment explanation
Indices: 1388018--1388092 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
1388008 TATCCATTTA
* *
1388018 CAAAAAGAAAGTCCATATTACAAAAGCC
1 CAAATAGAAAGCCCA-ATTAC-AAAGCC
* *
1388046 CGAAT-GAAAGGCCCAATTACAAAGGC
1 CAAATAGAAA-GCCCAATTACAAAGCC
1388072 CAAATAGAAAGCCCAATTACA
1 CAAATAGAAAGCCCAATTACA
1388093 TCAGCCCCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 20 0.50
27 13 0.32
28 7 0.17
ACGTcount: A:0.49, C:0.23, G:0.15, T:0.13
Consensus pattern (26 bp):
CAAATAGAAAGCCCAATTACAAAGCC
Found at i:1388808 original size:7 final size:7
Alignment explanation
Indices: 1388796--1388837 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
1388786 TCAATATTTG
1388796 TTAATAA
1 TTAATAA
1388803 TTAATAA
1 TTAATAA
1388810 -TAATAA
1 TTAATAA
*
1388816 TTAATAT
1 TTAATAA
1388823 TATAATAA
1 T-TAATAA
1388831 TTAATAA
1 TTAATAA
1388838 AAAGGAAGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 6 0.19
7 19 0.61
8 6 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TTAATAA
Found at i:1388829 original size:15 final size:13
Alignment explanation
Indices: 1388797--1388837 Score: 64
Period size: 13 Copynumber: 3.0 Consensus size: 13
1388787 CAATATTTGT
1388797 TAATAATTAATAA
1 TAATAATTAATAA
1388810 TAATAATTAATATTA
1 TAATAATTAATA--A
1388825 TAATAATTAATAA
1 TAATAATTAATAA
1388838 AAAGGAAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 13 0.50
15 13 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAATAATTAATAA
Found at i:1389904 original size:30 final size:30
Alignment explanation
Indices: 1389870--1389978 Score: 122
Period size: 29 Copynumber: 3.7 Consensus size: 30
1389860 CCCGGTTTCA
* *
1389870 CCAAAAATTACCGTTTTACTCTC-AAACTTT
1 CCAAAAATTACCATTTTAC-CCCAAAACTTT
1389900 CC-AAAATT-CCATTTTAACCCCAAAAC-TT
1 CCAAAAATTACCATTTT-ACCCCAAAACTTT
*
1389928 CCAAAAATTACCATTTTACCCCTAAACTTT
1 CCAAAAATTACCATTTTACCCCAAAACTTT
1389958 CC-AAAATT-CCATTTTAACCCC
1 CCAAAAATTACCATTTT-ACCCC
1389979 GGTTTCACCA
Statistics
Matches: 70, Mismatches: 3, Indels: 13
0.81 0.03 0.15
Matches are distributed among these distances:
28 19 0.27
29 38 0.54
30 13 0.19
ACGTcount: A:0.36, C:0.31, G:0.01, T:0.32
Consensus pattern (30 bp):
CCAAAAATTACCATTTTACCCCAAAACTTT
Found at i:1389925 original size:29 final size:29
Alignment explanation
Indices: 1389893--1389978 Score: 131
Period size: 29 Copynumber: 3.0 Consensus size: 29
1389883 TTTTACTCTC
1389893 AAACTTTCCAAAATTCCATTTTAACCCCA
1 AAACTTTCCAAAATTCCATTTTAACCCCA
*
1389922 AAAC-TTCCAAAAATTACCATTTT-ACCCCT
1 AAACTTTCC-AAAATT-CCATTTTAACCCCA
1389951 AAACTTTCCAAAATTCCATTTTAACCCC
1 AAACTTTCCAAAATTCCATTTTAACCCC
1389979 GGTTTCACCA
Statistics
Matches: 52, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
28 11 0.21
29 30 0.58
30 11 0.21
ACGTcount: A:0.37, C:0.31, G:0.00, T:0.31
Consensus pattern (29 bp):
AAACTTTCCAAAATTCCATTTTAACCCCA
Found at i:1389990 original size:58 final size:58
Alignment explanation
Indices: 1389829--1390006 Score: 213
Period size: 58 Copynumber: 3.1 Consensus size: 58
1389819 GCTTATAGGT
* *
1389829 CCCTAAACTGTTCCAAAATTCCATTTTTGACCCCGGTTTCACCAAAAATTACCGTTTTA-
1 CCCTAAACT-TTCCAAAATTCCA-TTTTAACCCCGGTTTCACCAAAAATTACCATTTTAC
* ***
1389888 CTCTCAAACTTTCCAAAATTCCATTTTAACCCCAAAACTT--CCAAAAATTACCATTTTAC
1 CCCT-AAACTTTCCAAAATTCCATTTTAACCCC--GGTTTCACCAAAAATTACCATTTTAC
1389947 CCCTAAACTTTCCAAAATTCCATTTTAACCCCGGTTTCACC-AAAATT-CCATTTTTAC
1 CCCTAAACTTTCCAAAATTCCATTTTAACCCCGGTTTCACCAAAAATTACCA-TTTTAC
1390004 CCC
1 CCC
1390007 CGGAAGTCAA
Statistics
Matches: 102, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
56 5 0.05
57 15 0.15
58 56 0.55
59 19 0.19
60 7 0.07
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.33
Consensus pattern (58 bp):
CCCTAAACTTTCCAAAATTCCATTTTAACCCCGGTTTCACCAAAAATTACCATTTTAC
Found at i:1402460 original size:200 final size:200
Alignment explanation
Indices: 1402115--1402719 Score: 924
Period size: 200 Copynumber: 3.0 Consensus size: 200
1402105 GAAGTAGTTT
* *** * * *
1402115 AACAAGCGAGGCGGTCATCTTCCTGATGAGATGCAGAGAAGAGCGCCAACTCAGCACTCAAACAC
1 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCT-TAACAC
* * * * * * *
1402180 GAACAAATCTTTGTACCCAGCTTCCAGAGGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGT
65 GAGCAAATCTTCGAACCAAGCTTCCAGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAATGGT
*
1402245 TAGCTTCCTGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGTG
130 TAGCTTCCTGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGAG
1402310 AATTAA
195 AATTAA
* * * *
1402316 AACAAGCAAGGCGGTCATCTTCCTAATGAGATACAGAGAAGAATACCAACTCAACGCTTAGCTCG
1 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTTAACACG
* *
1402381 AGCAAATCTTCGAACCAAGCTTCCGGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTT
66 AGCAAATCTTCGAACCAAGCTTCCAGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAATGGTT
*
1402446 AGCTTCCGGATGAGATACAGAGAAGT-AGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGAG
131 AGCTTCCTGATGAGATACAGAGAAGTGA-ACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGAG
1402510 AATTAA
195 AATTAA
*
1402516 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTTAACGCG
1 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTTAACACG
* * *
1402581 AGCAAACCTTCGAACCAAGCTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAATAGTT
66 AGCAAATCTTCGAACCAAGCTTCCAGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAATGGTT
* * *
1402646 AGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAAAGAAGCGA
131 AGCTTCCTGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGAGA
1402711 ATTAA
196 ATTAA
1402716 AACA
1 AACA
1402720 GATGATTGCA
Statistics
Matches: 368, Mismatches: 34, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
199 1 0.00
200 317 0.86
201 50 0.14
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (200 bp):
AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTTAACACG
AGCAAATCTTCGAACCAAGCTTCCAGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAATGGTT
AGCTTCCTGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGAGA
ATTAA
Found at i:1403116 original size:11 final size:11
Alignment explanation
Indices: 1403093--1403153 Score: 59
Period size: 11 Copynumber: 5.3 Consensus size: 11
1403083 TGAACTTTTG
1403093 ATTAATGTTTAA
1 ATTAAT-TTTAA
1403105 ATTAATTTTAA
1 ATTAATTTTAA
1403116 ATTAATTTTTAA
1 ATTAA-TTTTAA
* *
1403128 ATTTAAATTTAT
1 A-TTAATTTTAA
* *
1403140 CTTAAATTTAA
1 ATTAATTTTAA
1403151 ATT
1 ATT
1403154 TATCTATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
11 21 0.50
12 17 0.40
13 4 0.10
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (11 bp):
ATTAATTTTAA
Found at i:1403132 original size:6 final size:6
Alignment explanation
Indices: 1403100--1403205 Score: 73
Period size: 6 Copynumber: 18.0 Consensus size: 6
1403090 TTGATTAATG
* *
1403100 TTTAAA -TTAAT TTTAAA -TTAATT TTTAAA TTTAAA TTT--A TCTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA T-TTAAA
* * *
1403146 TTTAAA TTTATCTAT TTTAAA TTTAAA TTT-AC TTTAAA TTTAAA ATT-AA
1 TTTAAA TTTA---AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
1403195 -TTAAA TTTAAA
1 TTTAAA TTTAAA
1403206 ATTGAATTAA
Statistics
Matches: 79, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
4 4 0.05
5 18 0.23
6 46 0.58
7 6 0.08
9 5 0.06
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:1403146 original size:17 final size:17
Alignment explanation
Indices: 1403123--1403205 Score: 89
Period size: 17 Copynumber: 4.7 Consensus size: 17
1403113 TAAATTAATT
1403123 TTTAAATTTAAATTTA-
1 TTTAAATTTAAATTTAC
1403139 TCTTAAATTTAAATTTATC
1 T-TTAAATTTAAATTTA-C
1403158 TATTTTAAATTTAAATTTAC
1 ---TTTAAATTTAAATTTAC
*
1403178 TTTAAATTTAAAATTA-
1 TTTAAATTTAAATTTAC
*
1403194 ATTAAATTTAAA
1 TTTAAATTTAAA
1403206 ATTGAATTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
16 12 0.20
17 30 0.51
20 1 0.02
21 15 0.25
22 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAAATTTAAATTTAC
Found at i:1403155 original size:29 final size:29
Alignment explanation
Indices: 1403100--1403155 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1403090 TTGATTAATG
* *
1403100 TTTAAATTAATTTTAAATTAATTTTTAAA
1 TTTAAATTAATCTTAAATTAATATTTAAA
*
1403129 TTTAAATTTATCTTAAATTTAA-ATTTA
1 TTTAAATTAATCTTAAA-TTAATATTTA
1403156 TCTATTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTAAATTAATCTTAAATTAATATTTAAA
Found at i:1403215 original size:17 final size:16
Alignment explanation
Indices: 1403162--1403221 Score: 75
Period size: 17 Copynumber: 3.6 Consensus size: 16
1403152 TTTATCTATT
* *
1403162 TTAAATTTAAATTTACT
1 TTAAATTTAAAATTA-A
1403179 TTAAATTTAAAATTAA
1 TTAAATTTAAAATTAA
1403195 TTAAATTTAAAATTGAA
1 TTAAATTTAAAATT-AA
*
1403212 TTAAACTTAA
1 TTAAATTTAA
1403222 TTAAATGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
16 14 0.36
17 25 0.64
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (16 bp):
TTAAATTTAAAATTAA
Found at i:1403294 original size:14 final size:14
Alignment explanation
Indices: 1403275--1403315 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
1403265 ATCCCGAATG
1403275 AAAGGCCCAATTAC
1 AAAGGCCCAATTAC
* *
1403289 AAAGG-CCAAATAG
1 AAAGGCCCAATTAC
1403302 AAA-GCCCAATTAC
1 AAAGGCCCAATTAC
1403315 A
1 A
1403316 TTAGCCCAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
12 1 0.05
13 16 0.73
14 5 0.23
ACGTcount: A:0.49, C:0.24, G:0.15, T:0.12
Consensus pattern (14 bp):
AAAGGCCCAATTAC
Found at i:1403932 original size:9 final size:9
Alignment explanation
Indices: 1403920--1403971 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
1403910 TTTCAATATT
*
1403920 ATTAATATC
1 ATTAATAAC
1403929 ATTAATAAC
1 ATTAATAAC
1403938 ATTAAATAAC
1 ATT-AATAAC
*
1403948 ATTAATGAC
1 ATTAATAAC
*
1403957 AGTT-ATAAT
1 A-TTAATAAC
1403966 ATTAAT
1 ATTAAT
1403972 TGCTAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 2 0.06
9 23 0.64
10 11 0.31
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (9 bp):
ATTAATAAC
Found at i:1404027 original size:7 final size:7
Alignment explanation
Indices: 1404015--1404059 Score: 54
Period size: 7 Copynumber: 6.0 Consensus size: 7
1404005 TCAATATTTG
1404015 TTAATAA
1 TTAATAA
1404022 TTAATAA
1 TTAATAA
1404029 TAATAATAA
1 T--TAATAA
*
1404038 TTAATAT
1 TTAATAA
1404045 TATAATAA
1 T-TAATAA
1404053 TTAATAA
1 TTAATAA
1404060 AAAGGAAGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 20 0.61
8 6 0.18
9 7 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TTAATAA
Found at i:1404051 original size:15 final size:15
Alignment explanation
Indices: 1404016--1404058 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
1404006 CAATATTTGT
1404016 TAATAATTAATAATAA
1 TAATAATTAAT-ATAA
*
1404032 TAATAATTAATATTA
1 TAATAATTAATATAA
1404047 TAATAATTAATA
1 TAATAATTAATA
1404059 AAAAGGAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATAATTAATATAA
Found at i:1405127 original size:29 final size:29
Alignment explanation
Indices: 1405095--1405254 Score: 175
Period size: 29 Copynumber: 5.6 Consensus size: 29
1405085 CCCAGTTTCA
*
1405095 CCAAAATTACCGTTTTACCCCTAAACTTC
1 CCAAAATTACCATTTTACCCCTAAACTTC
** *
1405124 CCAAAATT-CCATTTTAACCCAAAAACTAC
1 CCAAAATTACCATTTT-ACCCCTAAACTTC
* *
1405153 CAAAAATTACCATTTTA-CCCTAAACTTT
1 CCAAAATTACCATTTTACCCCTAAACTTC
* *
1405181 CCAAAATT-CCATTTTTGGCCCCGAAACTTC
1 CCAAAATTACCA-TTTT-ACCCCTAAACTTC
* *
1405211 CAAAAATTACCATTTTACCCCTAAACTTT
1 CCAAAATTACCATTTTACCCCTAAACTTC
1405240 CCAAAATT-CCATTTT
1 CCAAAATTACCATTTT
1405255 TAACCCCGGT
Statistics
Matches: 107, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
27 3 0.03
28 31 0.29
29 43 0.40
30 27 0.25
31 3 0.03
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.32
Consensus pattern (29 bp):
CCAAAATTACCATTTTACCCCTAAACTTC
Found at i:1405255 original size:29 final size:29
Alignment explanation
Indices: 1405054--1405261 Score: 173
Period size: 29 Copynumber: 7.1 Consensus size: 29
1405044 GCTTATAGGT
1405054 CCCTAAACTGTTCCAAAATTCCATTTTTGAC
1 CCCTAAACT-TTCCAAAATTCCATTTTT-AC
* *
1405085 CCC---AGTTTCACCAAAATTACC-GTTTTAC
1 CCCTAAACTTT--CCAAAATT-CCATTTTTAC
* *
1405113 CCCTAAACTTCCCAAAATTCCATTTTAAC
1 CCCTAAACTTTCCAAAATTCCATTTTTAC
** *
1405142 CCAAAAAC-TACCAAAAATTACCA-TTTTA-
1 CCCTAAACTTTCC-AAAATT-CCATTTTTAC
*
1405170 CCCTAAACTTTCCAAAATTCCATTTTTGGC
1 CCCTAAACTTTCCAAAATTCCATTTTT-AC
*
1405200 CCCGAAAC-TTCCAAAAATTACCA-TTTTAC
1 CCCTAAACTTTCC-AAAATT-CCATTTTTAC
1405229 CCCTAAACTTTCCAAAATTCCATTTTTAAC
1 CCCTAAACTTTCCAAAATTCCATTTTT-AC
1405259 CCC
1 CCC
1405262 GGTTTCACCA
Statistics
Matches: 142, Mismatches: 17, Indels: 37
0.72 0.09 0.19
Matches are distributed among these distances:
27 5 0.04
28 31 0.22
29 66 0.46
30 31 0.22
31 9 0.06
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAATTCCATTTTTAC
Found at i:1405275 original size:58 final size:58
Alignment explanation
Indices: 1405054--1405289 Score: 266
Period size: 58 Copynumber: 4.1 Consensus size: 58
1405044 GCTTATAGGT
* * *
1405054 CCCTAAACTGTTCCAAAATTCCATTTTTGACCCCAGTTTCACCAAAATTACCGTTTTAC
1 CCCTAAACT-TTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAATTACCATTTTAC
* ***
1405113 CCCTAAACTTCCCAAAATTCCA-TTTTAA-CCCAAAAACTACCAAAAATTACCATTTTA-
1 CCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTC-ACC-AAAATTACCATTTTAC
** * *
1405170 CCCTAAACTTTCCAAAATTCCATTTTTGGCCCCGAAACTTC-CAAAAATTACCATTTTAC
1 CCCTAAACTTTCCAAAATTCCATTTTTAACCCC--AATTTCACCAAAATTACCATTTTAC
**
1405229 CCCTAAACTTTCCAAAATTCCATTTTTAACCCCGGTTTCACCAAAATT-CCATTTTTAC
1 CCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAATTACCA-TTTTAC
1405287 CCC
1 CCC
1405290 CGGAAGTCAA
Statistics
Matches: 148, Mismatches: 20, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
56 5 0.03
57 35 0.24
58 61 0.41
59 44 0.30
61 3 0.02
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (58 bp):
CCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAATTACCATTTTAC
Found at i:1405302 original size:28 final size:28
Alignment explanation
Indices: 1405241--1405311 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
1405231 CTAAACTTTC
**
1405241 CAAAATTCCATTTTTAACCCCGGTTTCA
1 CAAAATTCCATTTTTAACCCCGGAGTCA
*
1405269 CCAAAATTCCATTTTTACCCCCGGAAGTCA
1 -CAAAATTCCATTTTTAACCCCGG-AGTCA
1405299 -AAAATTACCATTT
1 CAAAATT-CCATTT
1405312 GGCTCCCGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 6 0.16
29 28 0.76
30 3 0.08
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.32
Consensus pattern (28 bp):
CAAAATTCCATTTTTAACCCCGGAGTCA
Found at i:1410356 original size:18 final size:18
Alignment explanation
Indices: 1410333--1410368 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1410323 TAAAGTGGTT
1410333 AACATAGAGTAAGACAAA
1 AACATAGAGTAAGACAAA
*
1410351 AACATAGGGTAAGACAAA
1 AACATAGAGTAAGACAAA
1410369 GAAACTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.11, G:0.19, T:0.11
Consensus pattern (18 bp):
AACATAGAGTAAGACAAA
Found at i:1413563 original size:8 final size:9
Alignment explanation
Indices: 1413522--1413566 Score: 51
Period size: 8 Copynumber: 5.3 Consensus size: 9
1413512 TATTTTATTA
1413522 TTAATAATT
1 TTAATAATT
1413531 TTAATAA-T
1 TTAATAATT
**
1413539 TTAA-AAAA
1 TTAATAATT
1413547 TTAATAATT
1 TTAATAATT
1413556 TTAA-AATT
1 TTAATAATT
1413564 TTA
1 TTA
1413567 CTGATGTGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
7 2 0.06
8 16 0.52
9 13 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TTAATAATT
Found at i:1426660 original size:102 final size:102
Alignment explanation
Indices: 1426484--1426688 Score: 383
Period size: 102 Copynumber: 2.0 Consensus size: 102
1426474 ATAGAGAAAT
1426484 TCTAGAGAAAGGTAACTAAGAAAGATTTGAATATTTTCGAAAGGATATCGGTAGCGGAAGTCAGG
1 TCTAGAGAAAGGTAACTAAGAAAGATTTGAATATTTTCGAAAGGATATCGGTAGCGGAAGTCAGG
1426549 GAGACTATAATACAAAAAGTATTTAAGAATGAAAAAC
66 GAGACTATAATACAAAAAGTATTTAAGAATGAAAAAC
*
1426586 TCTAGAGAAAGGTAACTAAGAAAGATTTGAATATTTTCGAAGGGATATCGGTAGCGGAAGTCAGG
1 TCTAGAGAAAGGTAACTAAGAAAGATTTGAATATTTTCGAAAGGATATCGGTAGCGGAAGTCAGG
* *
1426651 GGGACTATAATACAAGAAGTATTTAAGAATGAAAAAC
66 GAGACTATAATACAAAAAGTATTTAAGAATGAAAAAC
1426688 T
1 T
1426689 TTACAGAGAA
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.43, C:0.09, G:0.24, T:0.24
Consensus pattern (102 bp):
TCTAGAGAAAGGTAACTAAGAAAGATTTGAATATTTTCGAAAGGATATCGGTAGCGGAAGTCAGG
GAGACTATAATACAAAAAGTATTTAAGAATGAAAAAC
Found at i:1428060 original size:15 final size:17
Alignment explanation
Indices: 1428040--1428071 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1428030 ACTTGTTACT
1428040 TTTATA-TATT-CTAGA
1 TTTATACTATTACTAGA
1428055 TTTATACTATTACTAGA
1 TTTATACTATTACTAGA
1428072 ATTTTCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.50
Consensus pattern (17 bp):
TTTATACTATTACTAGA
Found at i:1428826 original size:21 final size:19
Alignment explanation
Indices: 1428793--1428831 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1428783 CATTGGTTCC
*
1428793 CATTTTTCTACAGGAATAG
1 CATTTTTCTACAGAAATAG
1428812 CATTTTTACCTACAGAAATA
1 CATTTTT--CTACAGAAATA
1428832 TTTGCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
21 10 0.59
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (19 bp):
CATTTTTCTACAGAAATAG
Found at i:1431939 original size:23 final size:23
Alignment explanation
Indices: 1431874--1431939 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
1431864 TGGGCAGCAA
* *
1431874 AGAGCACACACAATGCTAAACAG
1 AGAGCACACACAGTGCTAATCAG
* * *
1431897 AGAGTACACAAAGTACTAATCAG
1 AGAGCACACACAGTGCTAATCAG
1431920 AGAGCACACACAGTGCTAAT
1 AGAGCACACACAGTGCTAAT
1431940 AACAGGGAGC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.14
Consensus pattern (23 bp):
AGAGCACACACAGTGCTAATCAG
Found at i:1431949 original size:25 final size:25
Alignment explanation
Indices: 1431874--1431951 Score: 83
Period size: 23 Copynumber: 3.3 Consensus size: 25
1431864 TGGGCAGCAA
*
1431874 AGAGCACACACAATGCT-A-AACAG
1 AGAGCACACACAGTGCTAATAACAG
* * *
1431897 AGAGTACACAAAGTACTAAT--CAG
1 AGAGCACACACAGTGCTAATAACAG
1431920 AGAGCACACACAGTGCTAATAACAG
1 AGAGCACACACAGTGCTAATAACAG
*
1431945 GGAGCAC
1 AGAGCAC
1431952 GAGACGTGCT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
23 33 0.77
24 1 0.02
25 9 0.21
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.12
Consensus pattern (25 bp):
AGAGCACACACAGTGCTAATAACAG
Found at i:1432844 original size:14 final size:14
Alignment explanation
Indices: 1432825--1432852 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1432815 AAAGGGACTC
1432825 TACAAGAAAATTAA
1 TACAAGAAAATTAA
1432839 TACAAGAAAATTAA
1 TACAAGAAAATTAA
1432853 GGTGTCTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (14 bp):
TACAAGAAAATTAA
Found at i:1435168 original size:29 final size:29
Alignment explanation
Indices: 1435135--1435193 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
1435125 TTTGACTCTT
*
1435135 TTTAATAGTATAGAGACTAAATTGATCCA
1 TTTAATAATATAGAGACTAAATTGATCCA
* *
1435164 TTTAATAATATAGGGACTAATTTGATCCA
1 TTTAATAATATAGAGACTAAATTGATCCA
1435193 T
1 T
1435194 CCGTATAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (29 bp):
TTTAATAATATAGAGACTAAATTGATCCA
Found at i:1451185 original size:3 final size:3
Alignment explanation
Indices: 1451177--1451215 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
1451167 GCTTAAGTTT
* * *
1451177 TTC TTC TTC GTC TTC TTC TTC TGC TTC TTC TTC CTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1451216 AGATTCTCCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.36, G:0.05, T:0.59
Consensus pattern (3 bp):
TTC
Found at i:1458517 original size:68 final size:66
Alignment explanation
Indices: 1458399--1458524 Score: 171
Period size: 68 Copynumber: 1.9 Consensus size: 66
1458389 CAATATAATG
* * * *
1458399 GTTTTGCCTTTTAACTTAATGGGTAAATATTGATCAAAATGACATGATTTTACCTTTTAACTTTA
1 GTTTTGACTTTTAACTTAAAGGGTAAATATTGATCAAAACGACATAATTTTACCTTTTAACTTTA
1458464 T
66 T
* * *
1458465 GTTTTGACTTTTAACTTTAAAAGGGTAAATATTTATCAAAACGACGTAATTTTATCTTTT
1 GTTTTGACTTTTAAC-TT-AAAGGGTAAATATTGATCAAAACGACATAATTTTACCTTTT
1458525 CTTATTCGGA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 14 0.27
67 2 0.04
68 35 0.69
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (66 bp):
GTTTTGACTTTTAACTTAAAGGGTAAATATTGATCAAAACGACATAATTTTACCTTTTAACTTTA
T
Found at i:1460026 original size:19 final size:21
Alignment explanation
Indices: 1459988--1460032 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
1459978 CCTATTTTTT
* *
1459988 TAAAATTACACACAAAAAAAG
1 TAAAACTACACACAAAAAAAA
1460009 TAAAACTACA-AC-AAAAAAA
1 TAAAACTACACACAAAAAAAA
1460028 TAAAA
1 TAAAA
1460033 AATCAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
20 2 0.09
21 9 0.41
ACGTcount: A:0.71, C:0.13, G:0.02, T:0.13
Consensus pattern (21 bp):
TAAAACTACACACAAAAAAAA
Found at i:1460034 original size:21 final size:21
Alignment explanation
Indices: 1459988--1460032 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
1459978 CCTATTTTTT
*
1459988 TAAAATTACACACAAAAAAAG
1 TAAAACTACACACAAAAAAAG
1460009 TAAAACTACA-ACAAAAAAA-
1 TAAAACTACACACAAAAAAAG
1460028 TAAAA
1 TAAAA
1460033 AATCAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.22
20 9 0.39
21 9 0.39
ACGTcount: A:0.71, C:0.13, G:0.02, T:0.13
Consensus pattern (21 bp):
TAAAACTACACACAAAAAAAG
Found at i:1473128 original size:11 final size:11
Alignment explanation
Indices: 1473112--1473140 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1473102 AATCAAAATC
1473112 AAAATTAAAAA
1 AAAATTAAAAA
1473123 AAAATT-AAAA
1 AAAATTAAAAA
1473133 AAAATTAA
1 AAAATTAA
1473141 GTAAAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAATTAAAAA
Found at i:1473598 original size:12 final size:12
Alignment explanation
Indices: 1473576--1473604 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1473566 CAAATGCCTC
1473576 TAAAA-TAATAA
1 TAAAATTAATAA
1473587 TAAAATTAATAA
1 TAAAATTAATAA
1473599 TAAAAT
1 TAAAAT
1473605 AAGTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTAATAA
Found at i:1474790 original size:59 final size:59
Alignment explanation
Indices: 1474713--1474845 Score: 162
Period size: 59 Copynumber: 2.2 Consensus size: 59
1474703 AAACAAAGTG
* * *
1474713 AATAGTTAGGTGATCATTTTGTAACTTTTTATAGTTGTGT-GACCAAAACAAAA-TTTACC
1 AATAGTT-GGTGACCATTTTGTAACTTTTCATAGTTGAGTGGACCAAAA-AAAAGTTTACC
** *
1474772 AATAGTTGGTTGACCATTTTGTAACTTTTCATAGTTGAGTGGTGCAAAAAAAAGTTTACT
1 AATAGTTGG-TGACCATTTTGTAACTTTTCATAGTTGAGTGGACCAAAAAAAAGTTTACC
1474832 AATAGTTGGGTGAC
1 AATAGTT-GGTGAC
1474846 TACTAGTGTA
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
58 2 0.03
59 38 0.59
60 22 0.34
61 2 0.03
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.38
Consensus pattern (59 bp):
AATAGTTGGTGACCATTTTGTAACTTTTCATAGTTGAGTGGACCAAAAAAAAGTTTACC
Found at i:1480228 original size:20 final size:19
Alignment explanation
Indices: 1480199--1480248 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
1480189 AAGTATAAAA
1480199 TTTGAATTTTTATAAA-TAT
1 TTTGAATTTTTA-AAATTAT
*
1480218 TTTGAAATTTTGAAAATTAT
1 TTTG-AATTTTTAAAATTAT
1480238 TTTGAATTTTT
1 TTTGAATTTTT
1480249 TTGTTGGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (19 bp):
TTTGAATTTTTAAAATTAT
Found at i:1480319 original size:15 final size:15
Alignment explanation
Indices: 1480301--1480330 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1480291 AATCAAAAAG
1480301 ATATTTACATAAATT
1 ATATTTACATAAATT
1480316 ATATTTACATAAATT
1 ATATTTACATAAATT
1480331 TGTTATTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATTTACATAAATT
Found at i:1480619 original size:18 final size:18
Alignment explanation
Indices: 1480596--1480630 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1480586 GAATTTTAAA
1480596 TAATTTAATATTATATTG
1 TAATTTAATATTATATTG
*
1480614 TAATTTATTATTATATT
1 TAATTTAATATTATATT
1480631 TAAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TAATTTAATATTATATTG
Found at i:1480642 original size:18 final size:18
Alignment explanation
Indices: 1480590--1480644 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 18
1480580 ATACAAGAAT
1480590 TTTAAATAATTTAATATTATA
1 TTTAAAT-ATTT--TATTATA
1480611 TTGT-AAT-TTATTATTATA
1 TT-TAAATATT-TTATTATA
1480629 TTTAAATATTTTATTA
1 TTTAAATATTTTATTA
1480645 AATTAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
17 1 0.03
18 18 0.60
19 4 0.13
20 1 0.03
21 5 0.17
22 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTAAATATTTTATTATA
Found at i:1493250 original size:52 final size:52
Alignment explanation
Indices: 1493180--1493300 Score: 242
Period size: 52 Copynumber: 2.3 Consensus size: 52
1493170 TATCCATATC
1493180 AAACATATATTTGGACATAAGTATAAGTGTATAACCCTCGAATTATATCACA
1 AAACATATATTTGGACATAAGTATAAGTGTATAACCCTCGAATTATATCACA
1493232 AAACATATATTTGGACATAAGTATAAGTGTATAACCCTCGAATTATATCACA
1 AAACATATATTTGGACATAAGTATAAGTGTATAACCCTCGAATTATATCACA
1493284 AAACATATATTTGGACA
1 AAACATATATTTGGACA
1493301 CAATTCTTTG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.31
Consensus pattern (52 bp):
AAACATATATTTGGACATAAGTATAAGTGTATAACCCTCGAATTATATCACA
Found at i:1495431 original size:6 final size:6
Alignment explanation
Indices: 1495420--1495453 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1495410 TTTCAAGTCT
* *
1495420 AACTCG AACTCG AACTCG AACTCA AACTCA AACT
1 AACTCG AACTCG AACTCG AACTCG AACTCG AACT
1495454 ACCATTTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.41, C:0.32, G:0.09, T:0.18
Consensus pattern (6 bp):
AACTCG
Found at i:1502940 original size:12 final size:12
Alignment explanation
Indices: 1502909--1502943 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1502899 AAAAAGAAGT
*
1502909 ACAAGCACAAGC
1 ACAAGCATAAGC
1502921 ACAAGCATAAGC
1 ACAAGCATAAGC
*
1502933 ATAAGCATAAG
1 ACAAGCATAAG
1502944 AGCTCCATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.51, C:0.23, G:0.17, T:0.09
Consensus pattern (12 bp):
ACAAGCATAAGC
Found at i:1511707 original size:4 final size:4
Alignment explanation
Indices: 1511698--1511723 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1511688 GCATACGGAA
1511698 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
1511724 CAATTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:1512399 original size:25 final size:26
Alignment explanation
Indices: 1512369--1512419 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 26
1512359 TAAAAATTAT
*
1512369 AATTTAATTTCGTTCC-CCTAAAAAA
1 AATTTAATTTCGATCCTCCTAAAAAA
1512394 AATTTAATTTCGATCCTCCTAAAAAA
1 AATTTAATTTCGATCCTCCTAAAAAA
1512420 TCTTCTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (26 bp):
AATTTAATTTCGATCCTCCTAAAAAA
Found at i:1513198 original size:14 final size:14
Alignment explanation
Indices: 1513141--1513205 Score: 62
Period size: 14 Copynumber: 4.7 Consensus size: 14
1513131 AACTCTCAAC
*
1513141 TTATTGTTCTCGAT
1 TTATTATTCTCGAT
*
1513155 TTATTTTTCTCGAT
1 TTATTATTCTCGAT
* * *
1513169 TTCTTATTTTCAAT
1 TTATTATTCTCGAT
1513183 TT-TTAATTCTCGAT
1 TTATT-ATTCTCGAT
1513197 TT-TTATTCT
1 TTATTATTCT
1513206 AAATTTCTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
13 7 0.16
14 36 0.84
ACGTcount: A:0.17, C:0.14, G:0.06, T:0.63
Consensus pattern (14 bp):
TTATTATTCTCGAT
Found at i:1513210 original size:27 final size:28
Alignment explanation
Indices: 1513161--1513218 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
1513151 CGATTTATTT
* * *
1513161 TTCTCGATTTCTTATTTTCAATTTTTAA
1 TTCTCGATTTCTTATTCTAAATTTCTAA
1513189 TTCTCGATTT-TTATTCTAAATTTCTAA
1 TTCTCGATTTCTTATTCTAAATTTCTAA
1513216 TTC
1 TTC
1513219 CCATATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.22, C:0.16, G:0.03, T:0.59
Consensus pattern (28 bp):
TTCTCGATTTCTTATTCTAAATTTCTAA
Found at i:1514493 original size:10 final size:10
Alignment explanation
Indices: 1514435--1514494 Score: 51
Period size: 9 Copynumber: 6.5 Consensus size: 10
1514425 TAATTATTTA
1514435 TTTATAAT-T
1 TTTATAATAT
*
1514444 TTTGTATATAT
1 TTTATA-ATAT
*
1514455 TTTA-CATAT
1 TTTATAATAT
1514464 TTTA-AA-AT
1 TTTATAATAT
1514472 TTTA-AA-AT
1 TTTATAATAT
1514480 TTTATAATAT
1 TTTATAATAT
1514490 TTTAT
1 TTTAT
1514495 TTATTTTTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
8 14 0.33
9 16 0.37
10 9 0.21
11 4 0.09
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (10 bp):
TTTATAATAT
Found at i:1514675 original size:46 final size:46
Alignment explanation
Indices: 1514625--1514716 Score: 105
Period size: 46 Copynumber: 2.0 Consensus size: 46
1514615 AGTTTGGATA
* *
1514625 TCAAA-TCGAAAAGCACATTAAGTATTAATTTGATAAATAGAAAAAT
1 TCAAATTCGAAAA-CACATTAAGTACTAATTTGATAAATAAAAAAAT
* ** * *
1514671 TCAAATTCTATTATACTTTAAGTACTAATTTGATAAATAAAAAAAT
1 TCAAATTCGAAAACACATTAAGTACTAATTTGATAAATAAAAAAAT
1514717 AGAAAAATTC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
46 34 0.89
47 4 0.11
ACGTcount: A:0.50, C:0.09, G:0.08, T:0.34
Consensus pattern (46 bp):
TCAAATTCGAAAACACATTAAGTACTAATTTGATAAATAAAAAAAT
Found at i:1519076 original size:23 final size:23
Alignment explanation
Indices: 1519032--1519082 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1519022 TGAATTATTA
* *
1519032 TTTAATAATAAAAATGTTTAAAT
1 TTTAATAATAAAAATATATAAAT
* *
1519055 TTTAATTATAAAACTATATAAAT
1 TTTAATAATAAAAATATATAAAT
*
1519078 ATTAA
1 TTTAA
1519083 CATAAAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTAATAATAAAAATATATAAAT
Found at i:1542785 original size:84 final size:84
Alignment explanation
Indices: 1542644--1542853 Score: 321
Period size: 84 Copynumber: 2.5 Consensus size: 84
1542634 GTGATAAGGA
** * *
1542644 ATATTTATTTAAGCAGCATGTATTATAGAAAAATTGATAATTTTTAACATATAAAGCTAATTCTA
1 ATATTTATTTAATTAGCATGTATTATGGAAAAATTGATAATTGTTAACATATAAAGCTAATTCTA
*
1542709 TTAATTATCAATCAATTTT
66 TTAATTATCAATCAATGTT
* * * *
1542728 ATATTTATTTAATTAGCATGTACTATGGAAAAATTGATAATTGTTACCATATGAAGCTAATTTTA
1 ATATTTATTTAATTAGCATGTATTATGGAAAAATTGATAATTGTTAACATATAAAGCTAATTCTA
*
1542793 TTAATTATCAATTAATGTT
66 TTAATTATCAATCAATGTT
*
1542812 ATATTTATTTAATTAGCATGTATTATGGAAATATTGATAATT
1 ATATTTATTTAATTAGCATGTATTATGGAAAAATTGATAATT
1542854 TTTAGGCATA
Statistics
Matches: 114, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 114 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.44
Consensus pattern (84 bp):
ATATTTATTTAATTAGCATGTATTATGGAAAAATTGATAATTGTTAACATATAAAGCTAATTCTA
TTAATTATCAATCAATGTT
Found at i:1543704 original size:27 final size:28
Alignment explanation
Indices: 1543667--1543735 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
1543657 GTGTGGTCAA
*
1543667 ATTTGGGGATTTTGGGTAAGAG-TTTTG
1 ATTTGGAGATTTTGGGTAAGAGTTTTTG
* * * *
1543694 ATTTGGAGATTTTTGTTTAGGGTTTTTG
1 ATTTGGAGATTTTGGGTAAGAGTTTTTG
1543722 ATTTTGGAGATTTT
1 A-TTTGGAGATTTT
1543736 AGGTTAGTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 17 0.49
28 6 0.17
29 12 0.34
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.52
Consensus pattern (28 bp):
ATTTGGAGATTTTGGGTAAGAGTTTTTG
Done.