Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008082.1 Hibiscus syriacus cultivar Beakdansim tig00110584_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: 6025995
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 28
Found at i:2973371 original size:17 final size:16
Alignment explanation
Indices: 2973294--2973387 Score: 66
Period size: 16 Copynumber: 5.8 Consensus size: 16
2973284 TTTTAAATAG
2973294 TTATTATTTTTTAT-A
1 TTATTATTTTTTATAA
* * *
2973309 TTAATATATTTATGTAA
1 TTATTAT-TTTTTATAA
*
2973326 ATATTATTTTTTATTAA
1 TTATTATTTTTTA-TAA
* * *
2973343 -AATAATATTTTATAA
1 TTATTATTTTTTATAA
*
2973358 TTATTATTTATTTAGAA
1 TTATTATTT-TTTATAA
2973375 TTATTAATTTTTT
1 TTATT-ATTTTTT
2973388 TTGCTAATTA
Statistics
Matches: 59, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
15 9 0.15
16 23 0.39
17 23 0.39
18 4 0.07
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TTATTATTTTTTATAA
Found at i:2973532 original size:17 final size:17
Alignment explanation
Indices: 2973510--2973563 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
2973500 AATGTTAATA
2973510 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
2973527 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
2973544 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
2973561 TTT
1 TTT
2973564 TTATAATATA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:2975115 original size:21 final size:21
Alignment explanation
Indices: 2975085--2975132 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2975075 GCAGGTGTAC
* *
2975085 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
2975106 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
2975127 ATGCCA
1 ATGCCA
2975133 TCTCCGCAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:2975229 original size:21 final size:20
Alignment explanation
Indices: 2975136--2975226 Score: 110
Period size: 21 Copynumber: 4.3 Consensus size: 20
2975126 TATGCCATCT
* *
2975136 CCGCAAGGTTACATTCCGAGC
1 CCGC-AGGTTACATGCCTAGC
*
2975157 CCGCAGGGTTACATTCCTAGC
1 CCGCA-GGTTACATGCCTAGC
2975178 CCGCCAGGTTACATGCCTAGC
1 CCG-CAGGTTACATGCCTAGC
*
2975199 CCGCCAGGTTAAATGCCTAGC
1 CCG-CAGGTTACATGCCTAGC
2975220 CCGCAGG
1 CCGCAGG
2975227 GTTTTATACC
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
20 5 0.08
21 58 0.89
22 2 0.03
ACGTcount: A:0.21, C:0.35, G:0.25, T:0.19
Consensus pattern (20 bp):
CCGCAGGTTACATGCCTAGC
Found at i:2975800 original size:33 final size:34
Alignment explanation
Indices: 2975751--2975846 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
2975741 TAAATGTTTT
2975751 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATACAAATTATATTATTCGAAATTTAAAATA
* * *
2975785 AAAATA-AAATAATATTATTC-AAATTTAAATTT
1 AAAATACAAATTATATTATTCGAAATTTAAAATA
* *
2975817 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATACAAATTATATTATTCGAAATTTAA
2975847 CATTAAATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
32 16 0.29
33 25 0.45
34 14 0.25
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (34 bp):
AAAATACAAATTATATTATTCGAAATTTAAAATA
Found at i:2976466 original size:128 final size:128
Alignment explanation
Indices: 2976238--2976995 Score: 1455
Period size: 128 Copynumber: 5.9 Consensus size: 128
2976228 AGTTATTCAA
2976238 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
*
2976303 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAAGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
2976366 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
2976431 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
*
2976494 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGAGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
2976559 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
2976622 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
2976687 GACGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
*
2976749 ACTGATATATCTAGTGTCCCCGAGAGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
* *
2976814 GACGAAATAATGGAAGGCGTGCCCCCGGGAACGCGCCTTCATGTAAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
*
2976877 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
2976942 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
2976996 CCGATTATAG
Statistics
Matches: 619, Mismatches: 10, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
127 125 0.20
128 494 0.80
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
Found at i:2976874 original size:255 final size:256
Alignment explanation
Indices: 2976238--2976995 Score: 1455
Period size: 255 Copynumber: 3.0 Consensus size: 256
2976228 AGTTATTCAA
2976238 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
*
2976303 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAAGTAC
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
2976368 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
131 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
2976433 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
196 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
*
2976494 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGAGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
2976559 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
2976624 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
131 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
2976689 CGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
196 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
*
2976749 ACTGATATATCTAGTGTCCCCGAGAGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
* *
2976814 GACGAAATAATGGAAGGCGTGCCCCCGGGAACGCGCCTTCATGTAAATAGTGAAATAATAGGTAC
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
*
2976879 TGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGA
131 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
2976944 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
196 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
2976996 CCGATTATAG
Statistics
Matches: 494, Mismatches: 7, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
255 250 0.51
256 244 0.49
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.23
Consensus pattern (256 bp):
ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
Found at i:2976946 original size:383 final size:384
Alignment explanation
Indices: 2976238--2976995 Score: 1455
Period size: 383 Copynumber: 2.0 Consensus size: 384
2976228 AGTTATTCAA
2976238 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
2976303 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAAGTAC
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAAGTAC
*
2976368 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
131 TGATATATCTAGTGTCCCCGAGAGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
*
2976433 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTG
196 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTAAATAGTGAAATAATAGGTACTG
*
2976498 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGAGCAATGATAACATATTCTCTGACG
261 ATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGAGCAATGATAACATATTCTCTGACG
2976563 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
326 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
2976622 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
*
2976687 GACGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAAGTAC
2976751 TGATATATCTAGTGTCCCCGAGAGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
131 TGATATATCTAGTGTCCCCGAGAGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
*
2976816 CGAAATAATGGAAGGCGTGCCCCCGGGAACGCGCCTTCATGTAAATAGTGAAATAATAGGTACTG
196 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTAAATAGTGAAATAATAGGTACTG
*
2976881 ATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACG
261 ATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGAGCAATGATAACATATTCTCTGACG
2976946 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
326 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
2976996 CCGATTATAG
Statistics
Matches: 368, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
383 282 0.77
384 86 0.23
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.23
Consensus pattern (384 bp):
ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAAGTAC
TGATATATCTAGTGTCCCCGAGAGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTAAATAGTGAAATAATAGGTACTG
ATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGAGCAATGATAACATATTCTCTGACG
AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
Found at i:2977076 original size:8 final size:8
Alignment explanation
Indices: 2977063--2977103 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
2977053 TCATAATCTT
2977063 TCAAATTC
1 TCAAATTC
2977071 TCAAATTC
1 TCAAATTC
*
2977079 TCAAACTC
1 TCAAATTC
2977087 T-AAATTC
1 TCAAATTC
2977094 TCAAATTC
1 TCAAATTC
2977102 TC
1 TC
2977104 TGAAAATGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (8 bp):
TCAAATTC
Found at i:2977093 original size:15 final size:16
Alignment explanation
Indices: 2977063--2977103 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
2977053 TCATAATCTT
*
2977063 TCAAATTCTCAAATTC
1 TCAAACTCTCAAATTC
2977079 TCAAACTCT-AAATTC
1 TCAAACTCTCAAATTC
*
2977094 TCAAATTCTC
1 TCAAACTCTC
2977104 TGAAAATGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (16 bp):
TCAAACTCTCAAATTC
Found at i:2980120 original size:12 final size:12
Alignment explanation
Indices: 2980098--2980134 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
2980088 TTAATACATA
2980098 AATATTTTAATAT
1 AATA-TTTAATAT
*
2980111 ATTATTTAATAT
1 AATATTTAATAT
2980123 AATATTTAATAT
1 AATATTTAATAT
2980135 TTAGTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 19 0.86
13 3 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AATATTTAATAT
Found at i:2986178 original size:13 final size:13
Alignment explanation
Indices: 2986141--2986180 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
2986131 TCGATATTGA
2986141 AAAATAAATA-TT
1 AAAATAAATATTT
*
2986153 AAAATAATTTATTT
1 AAAATAA-ATATTT
2986167 AAAATAAATATTT
1 AAAATAAATATTT
2986180 A
1 A
2986181 TTTATTACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:2987703 original size:3 final size:3
Alignment explanation
Indices: 2987685--2987756 Score: 108
Period size: 3 Copynumber: 23.7 Consensus size: 3
2987675 TATATGTATT
* *
2987685 TAA TATA TAT TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2987731 TAA TAA TAA TAG TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
2987757 TGGATAAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
3 59 0.95
4 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2988211 original size:116 final size:116
Alignment explanation
Indices: 2988073--2988633 Score: 812
Period size: 116 Copynumber: 4.9 Consensus size: 116
2988063 TGATAGAATT
* *
2988073 ATTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTA
1 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTA
*
2988138 TGAACTCTATTTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAG
66 TGAACTCTATCTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAG
2988189 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTA
1 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTA
* * *
2988254 TGAACTCTACCCGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAA-
66 TGAACTCTATCTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAG
2988304 AGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATT
1 A-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATT
*
2988369 ATGAACTCTATTTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAG
65 ATGAACTCTATCTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAG
* *
2988421 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTA
1 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTA
* *** * * *
2988483 TGAACT-TCTCTGGCAAAAATAATCCATCAAGTGATGAATTC-AGATAAAAG
66 TGAACTCTATCTGGCAATGTTGATCCATCAAATGATGAATTCAAG-CAAAAG
* * * * *
2988533 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCCTTCAAATGATGAGTTCTTCTCATTA
1 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTA
* * * * *
2988598 TGAAC-CTTCTCTGGAAAAGATAATCCATCAAATGAT
66 TGAACTC-TATCTGGCAATGTTGATCCATCAAATGAT
2988634 AGATTTGAAT
Statistics
Matches: 412, Mismatches: 25, Indels: 16
0.91 0.06 0.04
Matches are distributed among these distances:
111 2 0.00
112 78 0.19
113 21 0.05
115 21 0.05
116 290 0.70
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (116 bp):
ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTA
TGAACTCTATCTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAG
Found at i:2989443 original size:83 final size:83
Alignment explanation
Indices: 2989304--2989774 Score: 761
Period size: 83 Copynumber: 5.7 Consensus size: 83
2989294 CATACCAAAC
* * * *
2989304 CAGATCAAATAACTCAAAGAATACTTCCAGAAGATGCTA-TGAGCACATTCATCTTCTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAATTCA
2989368 ATGATTGGTTCTGCTAAAT
65 ATGATTGGTTCTGCTAAAT
2989387 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAA
*
2989452 TGATT-GTTCTG-TCCAAT
66 TGATTGGTTCTGCT-AAAT
*
2989469 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTCAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAA
*
2989534 TGATTGGTTCTGCTAAAC
66 TGATTGGTTCTGCTAAAT
* * *
2989552 CAGGTCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATCTTCTCAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAA
*
2989617 TGATTGGTTCTGCTAAAC
66 TGATTGGTTCTGCTAAAT
* *
2989635 CAGGTCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAA
* *
2989700 TGATT-GTTCTGTTCAAT
66 TGATTGGTTCTGCTAAAT
2989717 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTA
2989775 TTTAATGTTT
Statistics
Matches: 368, Mismatches: 16, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
81 1 0.00
82 143 0.39
83 221 0.60
84 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAA
TGATTGGTTCTGCTAAAT
Found at i:2989488 original size:165 final size:166
Alignment explanation
Indices: 2989300--2989774 Score: 769
Period size: 165 Copynumber: 2.9 Consensus size: 166
2989290 GGTTCATACC
* * *
2989300 AAACCAGATCAAATAACTCAAAGAATACTTCCAGAAGATGCTA-TGAGCACATTCATCTTCTAAA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAA
*
2989364 CTCAATGATTGGTTCTGCTAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
65 TTCAATGATTGGTTCTGCTAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
2989429 GCAAATTCATCTTCTAAATTCAATGATT-GTTCTG-T
130 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCT
* * *
2989464 CCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTCAA
1 -AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAA
* * *
2989529 TTCAATGATTGGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTG
65 TTCAATGATTGGTTCTGCTAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
*
2989594 GCAAATTCATCTTCTCAATTCAATGATTGGTTCTGCT
130 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCT
* *
2989631 AAACCAGGTCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGCAAATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAAT
* *
2989696 TCAATGATT-GTTCTGTTCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGG
66 TCAATGATTGGTTCTGCTAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGG
2989760 CAAATTCATCTTCTA
131 CAAATTCATCTTCTA
2989775 TTTAATGTTT
Statistics
Matches: 285, Mismatches: 22, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
165 207 0.73
166 77 0.27
167 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (166 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAAT
TCAATGATTGGTTCTGCTAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGG
CAAATTCATCTTCTAAATTCAATGATTGGTTCTGCT
Found at i:2989701 original size:248 final size:248
Alignment explanation
Indices: 2989300--2989773 Score: 833
Period size: 248 Copynumber: 1.9 Consensus size: 248
2989290 GGTTCATACC
* *
2989300 AAACCAGATCAAATAACTCAAAGAATACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAAC
1 AAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAAC
*
2989365 TCAATGATTGGTTCTGCTAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGG
66 TCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGG
2989430 CAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACTT
131 CAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACTT
2989495 CCAGAAGATGCTATTGGCAAATTCATCTTCTCAATTCAATGATTGGTTCTGCT
196 CCAGAAGATGCTATTGGCAAATTCATCTTCTCAATTCAATGATTGGTTCTGCT
* * * *
2989548 AAACCAGGTCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTG-GCAAATTCATCTTCTCAA
1 AAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCAAATTCATCTTCTAAA
* * *
2989612 TTCAATGATTGGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTG
65 CTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
*
2989677 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGTTCAATCAGATCAGATAACTCAAAGAACACT
130 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACT
2989742 TCCAGAAGATGCTATTGGCAAATTCATCTTCT
195 TCCAGAAGATGCTATTGGCAAATTCATCTTCT
2989774 ATTTAATGTT
Statistics
Matches: 214, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
248 212 0.99
249 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.30
Consensus pattern (248 bp):
AAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAAC
TCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGG
CAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACTT
CCAGAAGATGCTATTGGCAAATTCATCTTCTCAATTCAATGATTGGTTCTGCT
Found at i:3001577 original size:17 final size:16
Alignment explanation
Indices: 3001535--3001579 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
3001525 AAATACTTGC
3001535 AAATAAAACATATAAAT
1 AAATAAAA-ATATAAAT
*
3001552 ATTATAAAAATAATAAAT
1 A-AATAAAAAT-ATAAAT
3001570 AAATAAAAAT
1 AAATAAAAAT
3001580 TTGAAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATAAAAATATAAAT
Found at i:3002268 original size:13 final size:13
Alignment explanation
Indices: 3002231--3002270 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
3002221 TCGATATTGA
3002231 AAAATAAATA-TT
1 AAAATAAATATTT
*
3002243 AAAATAATTTATTT
1 AAAATAA-ATATTT
3002257 AAAATAAATATTT
1 AAAATAAATATTT
3002270 A
1 A
3002271 TTTATTACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:3003775 original size:3 final size:3
Alignment explanation
Indices: 3003757--3003831 Score: 114
Period size: 3 Copynumber: 24.7 Consensus size: 3
3003747 TATATGTATT
* *
3003757 TAA TATA TAT TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3003803 TAA TAA TAA TAA TAG TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3003832 TGGATAAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
3 62 0.95
4 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3025421 original size:17 final size:17
Alignment explanation
Indices: 3025401--3025463 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 17
3025391 ATATAAATAT
3025401 AAAAAAATAGTAAATTA
1 AAAAAAATAGTAAATTA
3025418 AAAAAAATTA-TAAA-TA
1 AAAAAAA-TAGTAAATTA
*
3025434 AATAAAATTTAGTAAATTA
1 AA-AAAA-ATAGTAAATTA
3025453 ATAAAATAATA
1 A-AAAA-AATA
3025464 TTTATCGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
16 4 0.11
17 17 0.46
18 6 0.16
19 8 0.22
20 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAAAAATAGTAAATTA
Found at i:3025422 original size:18 final size:18
Alignment explanation
Indices: 3025401--3025463 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
3025391 ATATAAATAT
3025401 AAAAAAATAGTAAATTAA
1 AAAAAAATAGTAAATTAA
*
3025419 AAAAAATTA-TAAA-TAA
1 AAAAAAATAGTAAATTAA
**
3025435 ATAAAATTTAGTAAATTAA
1 A-AAAAAATAGTAAATTAA
*
3025454 TAAAATAATA
1 -AAAAAAATA
3025464 TTTATCGCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
16 4 0.11
17 11 0.31
18 12 0.33
19 8 0.22
20 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAAAAATAGTAAATTAA
Found at i:3033645 original size:6 final size:6
Alignment explanation
Indices: 3033634--3033661 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3033624 GGGTGCTGCC
3033634 CCAGCT CCAGCT CCAGCT CCAGCT CCAG
1 CCAGCT CCAGCT CCAGCT CCAGCT CCAG
3033662 TAGCTCCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.50, G:0.18, T:0.14
Consensus pattern (6 bp):
CCAGCT
Found at i:3040179 original size:20 final size:20
Alignment explanation
Indices: 3040156--3040197 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3040146 ACACTGCACG
3040156 TGCAATCATTCGGGGCAGGA
1 TGCAATCATTCGGGGCAGGA
3040176 TGCAATCATTCGGGGCAGGA
1 TGCAATCATTCGGGGCAGGA
3040196 TG
1 TG
3040198 ATGGAGATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (20 bp):
TGCAATCATTCGGGGCAGGA
Found at i:3041196 original size:33 final size:32
Alignment explanation
Indices: 3041159--3041268 Score: 96
Period size: 33 Copynumber: 3.3 Consensus size: 32
3041149 GATGAAGTTG
* *
3041159 AAAAGATAAAATAAAATAAAT-AATTATAATTTA
1 AAAAGATAAAATAAAA-AAATAAATAATAA-TAA
* *
3041192 AAAAGAAAAAATAATAAAATAAATAATAATAA
1 AAAAGATAAAATAAAAAAATAAATAATAATAA
** * *
3041224 AAAAGAATAATAATAAACTAATAAATAATAGTAG
1 AAAAG-ATAA-AATAAAAAAATAAATAATAATAA
*
3041258 TAAAGATAAAA
1 AAAAGATAAAA
3041269 AAAGATTTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
32 13 0.21
33 28 0.44
34 22 0.35
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.24
Consensus pattern (32 bp):
AAAAGATAAAATAAAAAAATAAATAATAATAA
Found at i:3041225 original size:31 final size:31
Alignment explanation
Indices: 3041159--3041253 Score: 79
Period size: 31 Copynumber: 3.0 Consensus size: 31
3041149 GATGAAGTTG
* * *
3041159 AAAAGATAAAATAAAATAAATAATTATAAT-TTA
1 AAAAGAAAAAATAATA-AAATAA--ATAATAATA
3041192 AAAAGAAAAAATAATAAAATAAATAATAATA
1 AAAAGAAAAAATAATAAAATAAATAATAATA
* *
3041223 AAAA-AGAATAATAATAAACT-AATAAATAATA
1 AAAAGA-AAAAATAATAAAATAAAT-AATAATA
3041254 GTAGTAAAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
30 9 0.17
31 25 0.46
32 6 0.11
33 14 0.26
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (31 bp):
AAAAGAAAAAATAATAAAATAAATAATAATA
Found at i:3042997 original size:24 final size:25
Alignment explanation
Indices: 3042922--3042999 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 25
3042912 CATAATATAT
* *
3042922 ATCAGAATAGAA-TCCAGATCA-GAA
1 ATCAGAACAGAATTCAAG-TCAGGAA
* * *
3042946 ATCAGAACAGAATTCAGGTCATG-T
1 ATCAGAACAGAATTCAAGTCAGGAA
*
3042970 ATCAGAACATAATTCAAGTC-GGAA
1 ATCAGAACAGAATTCAAGTCAGGAA
3042994 ATCAGA
1 ATCAGA
3043000 TAAAATATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
23 1 0.02
24 38 0.88
25 4 0.09
ACGTcount: A:0.45, C:0.17, G:0.18, T:0.21
Consensus pattern (25 bp):
ATCAGAACAGAATTCAAGTCAGGAA
Found at i:3047671 original size:24 final size:23
Alignment explanation
Indices: 3047644--3047720 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 23
3047634 AAAACATAAT
*
3047644 TCAGAACAGAATCCATATCAGAAA
1 TCAGAACAGAATTCA-ATCAGAAA
* * *
3047668 TCAGAACAAAATTCAGGTCATG-TA
1 TCAGAACAGAATTCA-ATCA-GAAA
3047692 TCAGAACAGAATTCAAGTCAGAAA
1 TCAGAACAGAATTCAA-TCAGAAA
3047716 TCAGA
1 TCAGA
3047721 TAAAATATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
23 1 0.02
24 40 0.95
25 1 0.02
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.19
Consensus pattern (23 bp):
TCAGAACAGAATTCAATCAGAAA
Found at i:3051480 original size:28 final size:28
Alignment explanation
Indices: 3051440--3051504 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
3051430 TTACACATAT
*
3051440 CCGCTCAAAGTGTTTGGGGTAAATGAAA
1 CCGCTCAAAGTGTTTGGGGTAAATAAAA
3051468 CCGCTCAAAGTGTTTGGGGTAAATAAAA
1 CCGCTCAAAGTGTTTGGGGTAAATAAAA
*
3051496 TCGCTCAAA
1 CCGCTCAAA
3051505 CCGAAACTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (28 bp):
CCGCTCAAAGTGTTTGGGGTAAATAAAA
Found at i:3051725 original size:66 final size:66
Alignment explanation
Indices: 3051646--3051779 Score: 178
Period size: 66 Copynumber: 2.0 Consensus size: 66
3051636 AAAAGGCTGA
* * * * **
3051646 AAAGAAAGGTTTAAAATACCAAAACAAGAGATCAAAATAATTAAGAACAATCCATGAATTAACAT
1 AAAGAAAGATTTAAAATAACAAAACAAGAGATCAAAATAATTAAAAAAAATCCACAAATTAACAT
3051711 G
66 G
* * * *
3051712 AAAGAAATATTTAAAATAACGAAACAAGAGGTCAAAGTAATTAAAAAAAATCCACAAATTAACAT
1 AAAGAAAGATTTAAAATAACAAAACAAGAGATCAAAATAATTAAAAAAAATCCACAAATTAACAT
3051777 G
66 G
3051778 AA
1 AA
3051780 GCACAATGAA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.19
Consensus pattern (66 bp):
AAAGAAAGATTTAAAATAACAAAACAAGAGATCAAAATAATTAAAAAAAATCCACAAATTAACAT
G
Found at i:3059721 original size:20 final size:20
Alignment explanation
Indices: 3059672--3059721 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
3059662 AAAAGTTGAT
*
3059672 TTTGAAAAACAAAATGAATA
1 TTTGAAAAATAAAATGAATA
*
3059692 TTTAAAAAATAAAATGAATA
1 TTTGAAAAATAAAATGAATA
3059712 TTTGAAAAAT
1 TTTGAAAAAT
3059722 GATTTAGAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (20 bp):
TTTGAAAAATAAAATGAATA
Found at i:3066499 original size:16 final size:16
Alignment explanation
Indices: 3066471--3066503 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3066461 AAAAGGAAAG
3066471 GGAGGAGGAGAGGGGA
1 GGAGGAGGAGAGGGGA
3066487 GGAGAGAGG-GAGGGGA
1 GGAG-GAGGAGAGGGGA
3066503 G
1 G
3066504 CACAGACTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (16 bp):
GGAGGAGGAGAGGGGA
Found at i:3069268 original size:18 final size:17
Alignment explanation
Indices: 3069225--3069268 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
3069215 ATTAGGATAA
3069225 TATTTTATTATTATTTT
1 TATTTTATTATTATTTT
*
3069242 TATTGTTATTATTTTCTTT
1 TATT-TTATTATTAT-TTT
*
3069261 TGTTTTAT
1 TATTTTAT
3069269 ACAATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.17
18 13 0.57
19 6 0.26
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.75
Consensus pattern (17 bp):
TATTTTATTATTATTTT
Found at i:3076899 original size:42 final size:42
Alignment explanation
Indices: 3076801--3076941 Score: 149
Period size: 42 Copynumber: 3.3 Consensus size: 42
3076791 TTTAGTGATG
* * *
3076801 TTTTCTACACAAACACTGCTAAAAGTCATGATATATAGTGGTG
1 TTTTC-ACCCAAACACTGCTAATAGTCATGATATATAGTGGTA
** * *
3076844 TTTTCACATAAACACTGCTAATAGTTATGATATATAGTGGCA
1 TTTTCACCCAAACACTGCTAATAGTCATGATATATAGTGGTA
* ** *
3076886 TTTTAACCCAAACACCACTAATACTGC-TGATATATAGTGGTA
1 TTTTCACCCAAACACTGCTAATAGT-CATGATATATAGTGGTA
3076928 TTTTTCACCCAAAC
1 -TTTTCACCCAAAC
3076942 GCCGCTATTG
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
42 65 0.79
43 17 0.21
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (42 bp):
TTTTCACCCAAACACTGCTAATAGTCATGATATATAGTGGTA
Found at i:3080079 original size:2 final size:2
Alignment explanation
Indices: 3080072--3080096 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3080062 GGATTTAATT
3080072 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 T
3080097 GAATATGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3089255 original size:11 final size:11
Alignment explanation
Indices: 3089236--3089274 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
3089226 CGATGACCAA
3089236 TCAACGGTCGG
1 TCAACGGTCGG
*
3089247 TCAAAGGTCCGG
1 TCAACGGT-CGG
3089259 TCAACGGT-GG
1 TCAACGGTCGG
3089269 TCAACG
1 TCAACG
3089275 ACGGTCAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 8 0.32
11 7 0.28
12 10 0.40
ACGTcount: A:0.23, C:0.26, G:0.33, T:0.18
Consensus pattern (11 bp):
TCAACGGTCGG
Found at i:3089384 original size:23 final size:23
Alignment explanation
Indices: 3089347--3089393 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
3089337 GCAGTCGAGT
*
3089347 CGGGTCGGGTCAACCTGGGTCAAA
1 CGGGTCGGGTCAACC-AGGTCAAA
3089371 CGGGTC-GGTCAACCAGGTCAAA
1 CGGGTCGGGTCAACCAGGTCAAA
3089393 C
1 C
3089394 TGCTCAGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
23 8 0.36
24 6 0.27
ACGTcount: A:0.23, C:0.28, G:0.34, T:0.15
Consensus pattern (23 bp):
CGGGTCGGGTCAACCAGGTCAAA
Found at i:3093012 original size:17 final size:17
Alignment explanation
Indices: 3092990--3093030 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
3092980 AATTCGGAGA
3092990 TTTTCAGGTCAATTACC
1 TTTTCAGGTCAATTACC
*
3093007 TTTTCAGGTCAATTGCC
1 TTTTCAGGTCAATTACC
3093024 TTTTCAG
1 TTTTCAG
3093031 AAGTTACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.44
Consensus pattern (17 bp):
TTTTCAGGTCAATTACC
Found at i:3095005 original size:17 final size:17
Alignment explanation
Indices: 3094985--3095057 Score: 65
Period size: 17 Copynumber: 4.0 Consensus size: 17
3094975 TTTATCCGGA
3094985 TAAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
*
3095002 TAAAAAACTGGATTTTTAT
1 TAAAAAACCGG-TTTTT-T
*
3095021 CCGAAAAAATCCGGTTTTTT
1 --TAAAAAA-CCGGTTTTTT
* *
3095041 TTAAAAACCAGTTTTTT
1 TAAAAAACCGGTTTTTT
3095058 GCAAACCGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
17 19 0.42
18 10 0.22
19 1 0.02
20 1 0.02
21 11 0.24
22 3 0.07
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (17 bp):
TAAAAAACCGGTTTTTT
Found at i:3095057 original size:39 final size:41
Alignment explanation
Indices: 3094975--3095057 Score: 107
Period size: 39 Copynumber: 2.1 Consensus size: 41
3094965 GGATAAAAAA
**
3094975 TTTATCCGGATAAAAAACCGGTTTTTTTAAAAAACTGGATT
1 TTTATCCGGATAAAAAACCGGTTTTTTTAAAAAACCAGATT
* * *
3095016 TTTATCC-GA-AAAAATCCGGTTTTTTTTAAAAACCAGTTT
1 TTTATCCGGATAAAAAACCGGTTTTTTTAAAAAACCAGATT
3095055 TTT
1 TTT
3095058 GCAAACCGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 28 0.76
40 2 0.05
41 7 0.19
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (41 bp):
TTTATCCGGATAAAAAACCGGTTTTTTTAAAAAACCAGATT
Found at i:3095698 original size:12 final size:12
Alignment explanation
Indices: 3095678--3095728 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
3095668 TATTAACAAT
3095678 TTTAA-AATATA
1 TTTAATAATATA
* *
3095689 TTTATTAATATT
1 TTTAATAATATA
3095701 TTTAATAATATAA
1 TTTAATAATAT-A
*
3095714 TATAATAATAATA
1 TTTAATAAT-ATA
3095727 TT
1 TT
3095729 ATTATTACAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 4 0.13
12 15 0.48
13 10 0.32
14 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TTTAATAATATA
Found at i:3095703 original size:23 final size:23
Alignment explanation
Indices: 3095657--3095714 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
3095647 TATTTTAATA
3095657 AAAATATTAATTATTAACAATTTT
1 AAAATA-TAATTATTAACAATTTT
* * *
3095681 AAAATATATTTATTAATATTTTT
1 AAAATATAATTATTAACAATTTT
3095704 AATAATATAAT
1 AA-AATATAAT
3095715 ATAATAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATATAATTATTAACAATTTT
Found at i:3095719 original size:22 final size:23
Alignment explanation
Indices: 3095668--3095723 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
3095658 AAATATTAAT
* * *
3095668 TATTAACAATTTTAAAATATATT
1 TATTAATATTTTTAAAATATATA
3095691 TATTAATATTTTTAATAATATAATA
1 TATTAATATTTTTAA-AATAT-ATA
*
3095716 TAATAATA
1 TATTAATA
3095724 ATATTATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 13 0.48
24 5 0.19
25 9 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTAATATTTTTAAAATATATA
Found at i:3095757 original size:23 final size:25
Alignment explanation
Indices: 3095726--3095783 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 25
3095716 TAATAATAAT
3095726 ATTATTATTACAATAATATAC-T-CA
1 ATTA-TATTACAATAATATACATACA
*
3095750 ATTATATTATAATAATATACGATACA
1 ATTATATTACAATAATATAC-ATACA
3095776 ATTATATT
1 ATTATATT
3095784 CTTATTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 15 0.50
24 4 0.13
25 1 0.03
26 10 0.33
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTATATTACAATAATATACATACA
Found at i:3096057 original size:29 final size:33
Alignment explanation
Indices: 3095993--3096059 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 33
3095983 AATTTATCAC
* *
3095993 ATTTTTATTTTAATAGAATATACTAGAATTAAT
1 ATTTTTATTTTAATAAAATATACTAGAAATAAT
*
3096026 ATTTTTA-TTT-ATAAAAT-TA-TAGAAATACT
1 ATTTTTATTTTAATAAAATATACTAGAAATAAT
3096055 ATTTT
1 ATTTT
3096060 AATAATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 13 0.42
30 2 0.06
31 6 0.19
32 3 0.10
33 7 0.23
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (33 bp):
ATTTTTATTTTAATAAAATATACTAGAAATAAT
Found at i:3096143 original size:23 final size:21
Alignment explanation
Indices: 3096105--3096146 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
3096095 TATTCTAATA
3096105 TTTTTAAAAAATAATATTAAG
1 TTTTTAAAAAATAATATTAAG
3096126 TTTTTATAATAAATAATATTA
1 TTTTTA-AA-AAATAATATTA
3096147 TTTATTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 2 0.11
23 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TTTTTAAAAAATAATATTAAG
Found at i:3096251 original size:13 final size:13
Alignment explanation
Indices: 3096233--3096267 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3096223 CCTAACACCA
*
3096233 AAAAAATTTTTTC
1 AAAAAATATTTTC
3096246 AAAAAATATTTTC
1 AAAAAATATTTTC
*
3096259 CAAAAATAT
1 AAAAAATAT
3096268 AATTCATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAAAATATTTTC
Found at i:3096291 original size:14 final size:14
Alignment explanation
Indices: 3096280--3096315 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3096270 TTCATTTTAC
3096280 GTAAAACATTTTCTA
1 GTAAAACATTTTC-A
3096295 -TAAAACATTTTCA
1 GTAAAACATTTTCA
3096308 GTAAAACA
1 GTAAAACA
3096316 AACGAACCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 1 0.05
14 19 0.95
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (14 bp):
GTAAAACATTTTCA
Found at i:3096864 original size:24 final size:24
Alignment explanation
Indices: 3096826--3096882 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
3096816 CTATTGTGGT
* * *
3096826 TGGCTGCTGCTGAGGCTGAGATTG
1 TGGCTGCTGCCGAGGCCGAGACTG
*
3096850 TGGCTGTTGCCGAGGCCGAGACTG
1 TGGCTGCTGCCGAGGCCGAGACTG
*
3096874 TGGCGGCTG
1 TGGCTGCTG
3096883 TAGTGGCTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.11, C:0.21, G:0.44, T:0.25
Consensus pattern (24 bp):
TGGCTGCTGCCGAGGCCGAGACTG
Found at i:3099629 original size:2 final size:2
Alignment explanation
Indices: 3099624--3099654 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3099614 ACATATAGAT
3099624 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3099655 GCACAGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3105204 original size:64 final size:64
Alignment explanation
Indices: 3105103--3105226 Score: 212
Period size: 64 Copynumber: 1.9 Consensus size: 64
3105093 AATTGGATGC
* *
3105103 TCCAACTCCATCCAATCTCCGATTTAGAACCGAAATCCGCCACATAACCTGCTATGTTTAATGG
1 TCCAACTCCATCCAATCTCCGATTTAGAACCAAAATCCGCCACACAACCTGCTATGTTTAATGG
* *
3105167 TCCAACTCCATCCCATCTCCGATTTAGAACCAAAATCCGCCACACAACCTGCTTTGTTTA
1 TCCAACTCCATCCAATCTCCGATTTAGAACCAAAATCCGCCACACAACCTGCTATGTTTA
3105227 TTGCAAGCGT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.29, C:0.34, G:0.10, T:0.27
Consensus pattern (64 bp):
TCCAACTCCATCCAATCTCCGATTTAGAACCAAAATCCGCCACACAACCTGCTATGTTTAATGG
Found at i:3110408 original size:3 final size:3
Alignment explanation
Indices: 3110400--3110460 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
3110390 AAGTAGAAAG
3110400 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3110448 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
3110461 CAACAACAAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3113452 original size:21 final size:22
Alignment explanation
Indices: 3113402--3113454 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
3113392 ACGAATAAAT
3113402 ATAAATTAGTTAAAAATTTAAAGG
1 ATAAATTA-TTAAAAA-TTAAAGG
*
3113426 -TAAATTATTTAAAA-TAAAGG
1 ATAAATTATTAAAAATTAAAGG
3113446 ATAAATTAT
1 ATAAATTAT
3113455 ACCAGTTACC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 6 0.22
21 8 0.30
22 6 0.22
23 7 0.26
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (22 bp):
ATAAATTATTAAAAATTAAAGG
Found at i:3114973 original size:24 final size:24
Alignment explanation
Indices: 3114946--3115003 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
3114936 GAAATTATCG
*
3114946 CGTAGAATTTGCACCGAAGTGCCA
1 CGTAGAATTTGCACCAAAGTGCCA
* *
3114970 CGTAGAATATACACCAAAGTGCCA
1 CGTAGAATTTGCACCAAAGTGCCA
*
3114994 CATAG-ATTTG
1 CGTAGAATTTG
3115004 TCCCAAGGGA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (24 bp):
CGTAGAATTTGCACCAAAGTGCCA
Found at i:3115037 original size:23 final size:23
Alignment explanation
Indices: 3115001--3115089 Score: 108
Period size: 23 Copynumber: 3.9 Consensus size: 23
3114991 CCACATAGAT
*
3115001 TTGTCCC-AAGGGACCGCGTAGAA
1 TTGTCCCGAA-GGACCGCGTAAAA
* *
3115024 TTGTCTCGAAGGACCGCATAAAA
1 TTGTCCCGAAGGACCGCGTAAAA
* *
3115047 TTGTCCCGAATGACTGCGTAAAA
1 TTGTCCCGAAGGACCGCGTAAAA
*
3115070 TTATCCCGAAGGACCGCGTA
1 TTGTCCCGAAGGACCGCGTA
3115090 GAACCCTTGA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 53 0.96
24 2 0.04
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (23 bp):
TTGTCCCGAAGGACCGCGTAAAA
Found at i:3115265 original size:15 final size:15
Alignment explanation
Indices: 3115195--3115264 Score: 77
Period size: 15 Copynumber: 4.7 Consensus size: 15
3115185 AAGTATCTCT
*
3115195 TATTCACATAGATCA
1 TATTCACATAGAACA
* *
3115210 CATTCACAAAGAACA
1 TATTCACATAGAACA
*
3115225 TTTTCACATAGAACA
1 TATTCACATAGAACA
* * *
3115240 TATTCATATATATCA
1 TATTCACATAGAACA
3115255 TATTCACATA
1 TATTCACATA
3115265 TTAATAAAAT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.33
Consensus pattern (15 bp):
TATTCACATAGAACA
Found at i:3128263 original size:17 final size:17
Alignment explanation
Indices: 3128225--3128266 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3128215 ATGGGGTTTT
3128225 GTAAAAATGATTAAATA
1 GTAAAAATGATTAAATA
* *
3128242 ATAAAAAGTGATTTAA-A
1 GTAAAAA-TGATTAAATA
3128259 GTAAAAAT
1 GTAAAAAT
3128267 AAAGAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 1 0.05
17 13 0.62
18 7 0.33
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.29
Consensus pattern (17 bp):
GTAAAAATGATTAAATA
Found at i:3128889 original size:29 final size:28
Alignment explanation
Indices: 3128848--3128907 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
3128838 AGCATGTTTA
*
3128848 AAAATAAAACTTAAAAA-AAATGAAAATG
1 AAAATAAAACTTAAAAAGAAAAGAAAA-G
3128876 AAAATGAAAACTTAAAAAGAAAAGAAAAG
1 AAAAT-AAAACTTAAAAAGAAAAGAAAAG
3128905 AAA
1 AAA
3128908 GAACTTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 5 0.17
29 16 0.55
30 8 0.28
ACGTcount: A:0.73, C:0.03, G:0.10, T:0.13
Consensus pattern (28 bp):
AAAATAAAACTTAAAAAGAAAAGAAAAG
Found at i:3136509 original size:64 final size:64
Alignment explanation
Indices: 3136408--3136572 Score: 258
Period size: 64 Copynumber: 2.6 Consensus size: 64
3136398 CAGCTTTTAA
* *
3136408 AGTCAATTTCAACTTCACAATAAAGGATATTGGACTCAACAAACAACTTTTCAGTTTCATTCAG
1 AGTCAATTTCAACTTCACAACAAAGGATATTGGACTCAACAAACAACTTTTCAGATTCATTCAG
* *
3136472 AGTCAATTTCAACTTCACAGCAAAGGATATTGGACTCAACAAACAACTTTTCAGATTCATTCAT
1 AGTCAATTTCAACTTCACAACAAAGGATATTGGACTCAACAAACAACTTTTCAGATTCATTCAG
* * * *
3136536 AGTCAATTTTAACTTCACATCGAATGATATTGGACTC
1 AGTCAATTTCAACTTCACAACAAAGGATATTGGACTC
3136573 GAAGCGACAC
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 93 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.32
Consensus pattern (64 bp):
AGTCAATTTCAACTTCACAACAAAGGATATTGGACTCAACAAACAACTTTTCAGATTCATTCAG
Found at i:3136627 original size:22 final size:22
Alignment explanation
Indices: 3136598--3136670 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 22
3136588 ACTCGAGATT
3136598 GGAT-TTCAACTTCACGATGAA
1 GGATATTCAACTTCACGATGAA
* *
3136619 GGATATTCAAC-TCAAGAT--T
1 GGATATTCAACTTCACGATGAA
* *
3136638 GGATCTT-AACTTCACGACGAA
1 GGATATTCAACTTCACGATGAA
*
3136659 GGATATCCAACT
1 GGATATTCAACT
3136671 CAAAACCAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
18 3 0.08
19 11 0.28
21 15 0.38
22 10 0.26
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (22 bp):
GGATATTCAACTTCACGATGAA
Found at i:3136649 original size:40 final size:40
Alignment explanation
Indices: 3136588--3136673 Score: 129
Period size: 40 Copynumber: 2.1 Consensus size: 40
3136578 GACACAATTT
* * *
3136588 ACTCGAGATTGGATTTCAACTTCACGATGAAGGATATTCA
1 ACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCA
3136628 ACTCAAGATTGGATCTT-AACTTCACGACGAAGGATATCCA
1 ACTCAAGATTGGAT-TTCAACTTCACGACGAAGGATATCCA
3136668 ACTCAA
1 ACTCAA
3136674 AACCAATTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
40 40 0.95
41 2 0.05
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (40 bp):
ACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCA
Found at i:3137127 original size:124 final size:124
Alignment explanation
Indices: 3136696--3137129 Score: 503
Period size: 124 Copynumber: 3.5 Consensus size: 124
3136686 GAAAGAACCC
* * * * *
3136696 TTGGATTTCAACTTCACAACGAAGGATATCCAATTTAAGGCTAAACTTCACAACAAAGGGGCTAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAATGAGCCAT
* * * * * *
3136761 GTACGATTTCAACTTCTCGAAGAAGGATATCGTGCTCACCAGCAACATTCATCTTTAGA
66 CTACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAATATCCATCTTTAGA
*
3136820 TTGGATTTCAACTTCACAATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAATG-GCCA
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAGGCTCAACTTCACAAC-AAATGAGCCA
* ** * *
3136884 TCCACGATTTCAACTTCATAACGAATGATATCGTGTCCACCAGCAATATCCATCTTTAGA
65 TCTACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAATATCCATCTTTAGA
* * * * ** * * * **
3136944 TTGGATTTCAACTTTACGATGAAGGATATCTAATTTGAGGTTTAACTTTACAATGAATGAGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAATGAGCCAT
* * * * *
3137009 CTATGATTTCAAATTCACGACGAAGGATATCGTGCCCACAAGCAGTATCCAAT-TATAGA
66 CTACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAATATCC-ATCTTTAGA
* * * *
3137068 TTAGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCATAGCAAATGAGC
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAATGAGC
3137130 TTTCCAGTTT
Statistics
Matches: 256, Mismatches: 51, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
123 4 0.02
124 246 0.96
125 6 0.02
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (124 bp):
TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAATGAGCCAT
CTACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAATATCCATCTTTAGA
Found at i:3141462 original size:45 final size:46
Alignment explanation
Indices: 3141377--3141464 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
3141367 AAATAGCCTG
* * *
3141377 AGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTA
1 AGTGCATCGATGCATGGTCATGTGCATAGATGCATAAAATGCACTA
3141423 AGTGCATCGATGCATGGT-ATGTGCATAGATGCATAAAATGCA
1 AGTGCATCGATGCATGGTCATGTGCATAGATGCATAAAATGCA
3141465 TTCGATGTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.54
46 18 0.46
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (46 bp):
AGTGCATCGATGCATGGTCATGTGCATAGATGCATAAAATGCACTA
Found at i:3142641 original size:21 final size:21
Alignment explanation
Indices: 3142617--3142660 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3142607 GAGGAGGAGG
*
3142617 AGGAGGAGCACGAGAGGAGCT
1 AGGAGGAGCACGAGAGGAACT
* * *
3142638 AGGAGTAGCTCGTGAGGAACT
1 AGGAGGAGCACGAGAGGAACT
3142659 AG
1 AG
3142661 CTCCCGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.43, T:0.11
Consensus pattern (21 bp):
AGGAGGAGCACGAGAGGAACT
Found at i:3148162 original size:22 final size:21
Alignment explanation
Indices: 3148120--3148159 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3148110 GAGTTTATTT
*
3148120 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3148141 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3148160 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3150237 original size:45 final size:46
Alignment explanation
Indices: 3150152--3150239 Score: 124
Period size: 45 Copynumber: 1.9 Consensus size: 46
3150142 AAATAGCCTG
* * *
3150152 AGTGCATCGATGCATGGTCTTGTGCATCAATGCATCAAATGCACTA
1 AGTGCATCGATGCATGGTCATGTGCATCAATACATAAAATGCACTA
**
3150198 AGTGCATCGATGCATGGT-ATGTGCATCGTTACATAAAATGCA
1 AGTGCATCGATGCATGGTCATGTGCATCAATACATAAAATGCA
3150240 TTCGATGTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 19 0.51
46 18 0.49
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (46 bp):
AGTGCATCGATGCATGGTCATGTGCATCAATACATAAAATGCACTA
Found at i:3153375 original size:2 final size:2
Alignment explanation
Indices: 3153368--3153429 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
3153358 TTCTTAAAGG
3153368 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3153410 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
3153430 CCAGCATATT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3156681 original size:6 final size:6
Alignment explanation
Indices: 3156664--3156699 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
3156654 TGAATCGAGT
3156664 ATTTTAA ATTTTA ATTTTA ATTTTA ATTTTA ATTTT
1 ATTTT-A ATTTTA ATTTTA ATTTTA ATTTTA ATTTT
3156700 CGCAATTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTTA
Found at i:3158537 original size:131 final size:130
Alignment explanation
Indices: 3158292--3158654 Score: 501
Period size: 131 Copynumber: 2.8 Consensus size: 130
3158282 ATAATTCTAA
* * * * * *
3158292 GAGAGAAAACGATAAGATCTAATTATTTCCAATTGATAATAAATGACCTCTTATGCCTTAAACCA
1 GAGAGAAAACGATAATATCTAATT-TTTTCAATAGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * * * *
3158357 GTCATTTATTACTCCGATTTAAATGAATAGATATCACTATTTCGACTTAAAATTCAATATTGATT
65 GTCATTTATTACTCCAATTGAAATGAAGAGATATCACCATTTCGACTTAAAAATAAATATTGATT
3158422 C
130 C
*
3158423 GAGAGAAAACGATAATATCTAATTGTTTTCAATAGAGAATAACTGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATT-TTTTCAATAGAGAATAAATGACCTCTCATGCCTTAAAGCA
* *
3158488 GTCATTTATTACTCCAATTGAAATGAAGAGATATCACCATTTTGTCTTAAAAATAAATATTGATT
65 GTCATTTATTACTCCAATTGAAATGAAGAGATATCACCATTTCGACTTAAAAATAAATATTGATT
*
3158553 T
130 C
* * * * *
3158554 GAGAGAAAATGATGATATCTAATTATCTCTAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTTTTTC-AATAGAGAATAAATGACCTCTCATGCCTTAAAGCA
*
3158619 GCCATTTATTACTCCAATTGAAATGAAGAGATATCA
65 GTCATTTATTACTCCAATTGAAATGAAGAGATATCA
3158655 TTATTATCAA
Statistics
Matches: 207, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
130 3 0.01
131 204 0.99
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.33
Consensus pattern (130 bp):
GAGAGAAAACGATAATATCTAATTTTTTCAATAGAGAATAAATGACCTCTCATGCCTTAAAGCAG
TCATTTATTACTCCAATTGAAATGAAGAGATATCACCATTTCGACTTAAAAATAAATATTGATTC
Found at i:3162202 original size:27 final size:28
Alignment explanation
Indices: 3162172--3162229 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
3162162 TTATTGCTAG
3162172 AAATATTAAATTTAT-TATTAAAATA-AA
1 AAATATT-AATTTATGTATTAAAATATAA
* *
3162199 AAATATTAATTTTTGTTTTAAAATATAA
1 AAATATTAATTTATGTATTAAAATATAA
3162227 AAA
1 AAA
3162230 AATTCAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 6 0.22
27 16 0.59
28 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (28 bp):
AAATATTAATTTATGTATTAAAATATAA
Found at i:3162282 original size:2 final size:2
Alignment explanation
Indices: 3162275--3162307 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3162265 TTACTATTTA
3162275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3162308 ATGTATTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3164214 original size:18 final size:18
Alignment explanation
Indices: 3164177--3164210 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3164167 ATTTAAGATT
*
3164177 TTATATTCGATTCAAATA
1 TTATATTCCATTCAAATA
3164195 TTATATTCCATT-AAAT
1 TTATATTCCATTCAAAT
3164211 TATTCGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (18 bp):
TTATATTCCATTCAAATA
Found at i:3171024 original size:65 final size:65
Alignment explanation
Indices: 3170937--3171101 Score: 203
Period size: 65 Copynumber: 2.6 Consensus size: 65
3170927 TACACTTGGG
* * *
3170937 GTGCATTGGTACACT-AATTGCATTCGATGTTTCAA-AAGAGCC-AGGAGTGCATCGACGCATGG
1 GTGCATCGGTACA-TAAAATGCATTCGATGTTTCAATAA-AACCTA-GAGTGCATCGACGCATGG
*
3170999 TCT
63 TAT
*
3171002 GTGCATCGGTACATAAAATGCATTCGATGTTTCAATAAAACCTAGAGTGCATCGATGCATGGTAT
1 GTGCATCGGTACATAAAATGCATTCGATGTTTCAATAAAACCTAGAGTGCATCGACGCATGGTAT
* * *
3171067 GTGCATCGGTAAACATAATGCATTCGATG-TTCAAT
1 GTGCATCGGTACATAAAATGCATTCGATGTTTCAAT
3171102 TAAATTAGGT
Statistics
Matches: 89, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
64 7 0.08
65 79 0.89
66 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (65 bp):
GTGCATCGGTACATAAAATGCATTCGATGTTTCAATAAAACCTAGAGTGCATCGACGCATGGTAT
Found at i:3171141 original size:65 final size:65
Alignment explanation
Indices: 3170937--3171142 Score: 170
Period size: 65 Copynumber: 3.2 Consensus size: 65
3170927 TACACTTGGG
* * * * *
3170937 GTGCATTGGTACAC-TAATTGCATTCGATGTTTCAA-AAGAGCC-AGGAGTGCATCGACGCATGG
1 GTGCATCGGTAAACATAA-TGCATTCGATGTTTCAATAA-AACCTA-GAGTGCATCGATGCATGC
**
3170999 TCT
63 AAT
* * * **
3171002 GTGCATCGGTACATAAAATGCATTCGATGTTTCAATAAAACCTAGAGTGCATCGATGCATGGTAT
1 GTGCATCGGTAAACATAATGCATTCGATGTTTCAATAAAACCTAGAGTGCATCGATGCATGCAAT
* * * * *
3171067 GTGCATCGGTAAACATAATGCATTCGATG-TTCAATTAAA-TTAGGTGTGTATCGATGCATTCAA
1 GTGCATCGGTAAACATAATGCATTCGATGTTTCAATAAAACCTA-GAGTGCATCGATGCATGCAA
3171130 T
65 T
*
3171131 AGTGCCTCGGTA
1 -GTGCATCGGTA
3171143 CATCCCTTGA
Statistics
Matches: 119, Mismatches: 17, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
63 2 0.02
64 25 0.21
65 87 0.73
66 5 0.04
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (65 bp):
GTGCATCGGTAAACATAATGCATTCGATGTTTCAATAAAACCTAGAGTGCATCGATGCATGCAAT
Found at i:3173160 original size:13 final size:14
Alignment explanation
Indices: 3173142--3173174 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3173132 GGGCAAAATA
*
3173142 TGAAAACTAAT-TT
1 TGAAAAATAATGTT
3173155 TGAAAAATAATGTT
1 TGAAAAATAATGTT
3173169 TGAAAA
1 TGAAAA
3173175 TCAATATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33
Consensus pattern (14 bp):
TGAAAAATAATGTT
Found at i:3173234 original size:20 final size:21
Alignment explanation
Indices: 3173189--3173236 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
3173179 TATGTAGTTT
3173189 TCAAAACAACATAATTAAAAC
1 TCAAAACAACATAATTAAAAC
*
3173210 -AAAAACAACA-ATATT-AAAC
1 TCAAAACAACATA-ATTAAAAC
3173229 TCAAAACA
1 TCAAAACA
3173237 TTTTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.65, C:0.19, G:0.00, T:0.17
Consensus pattern (21 bp):
TCAAAACAACATAATTAAAAC
Found at i:3179226 original size:65 final size:64
Alignment explanation
Indices: 3179157--3179321 Score: 167
Period size: 65 Copynumber: 2.5 Consensus size: 64
3179147 TACACTTGGG
* *
3179157 GTGCATTGGTACACTAATTGCATTCGATGTTTCAA-AAGAGC-TAAGAGTGCATCGATGCATGGT
1 GTGCATCGGTACACTAA-TGCATTCGATGTTTCAATAA-AACAT-AGAGTGCATCGATGCATGGT
*
3179220 CT
63 AT
* * *
3179222 GTGCATCGGTACA-TAAAATACACTCGATGTTTCAATAAAACATGGAGTGCATCGATGCATGGTA
1 GTGCATCGGTACACT--AATGCATTCGATGTTTCAATAAAACATAGAGTGCATCGATGCATGGTA
3179286 T
64 T
* * *
3179287 GAGCATCGGTATACATAATGCATTCAATG-TTCAAT
1 GTGCATCGGTACAC-TAATGCATTCGATGTTTCAAT
3179322 TAAATTTGGT
Statistics
Matches: 83, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
64 7 0.08
65 70 0.84
66 5 0.06
67 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.30
Consensus pattern (64 bp):
GTGCATCGGTACACTAATGCATTCGATGTTTCAATAAAACATAGAGTGCATCGATGCATGGTAT
Found at i:3183461 original size:17 final size:17
Alignment explanation
Indices: 3183439--3183471 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3183429 AACTAACAAA
3183439 GCCATTGAATCATTCAG
1 GCCATTGAATCATTCAG
3183456 GCCATTGAATCATTCA
1 GCCATTGAATCATTCA
3183472 ACGTTTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (17 bp):
GCCATTGAATCATTCAG
Found at i:3184164 original size:31 final size:31
Alignment explanation
Indices: 3184102--3184166 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
3184092 TTTAATAATT
* * *
3184102 AAAACACTTAATAAAATAATAATTTATAATC
1 AAAAAACTTAATAAAATAATAATATACAATC
3184133 AAAAAACTTAATAAAATAAT-ATCATACAATC
1 AAAAAACTTAATAAAATAATAAT-ATACAATC
3184164 AAA
1 AAA
3184167 CTATTATCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.28
Consensus pattern (31 bp):
AAAAAACTTAATAAAATAATAATATACAATC
Found at i:3197713 original size:36 final size:36
Alignment explanation
Indices: 3197663--3197734 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
3197653 TATTAAATGG
3197663 TAAACCAGAATGAATCAATTATTTTCTCCTAGAAGT
1 TAAACCAGAATGAATCAATTATTTTCTCCTAGAAGT
*
3197699 TAAACCAGACTGAATCAATTATTTTCTCCTAGAAGT
1 TAAACCAGAATGAATCAATTATTTTCTCCTAGAAGT
3197735 ATTATTCAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (36 bp):
TAAACCAGAATGAATCAATTATTTTCTCCTAGAAGT
Found at i:3202843 original size:16 final size:16
Alignment explanation
Indices: 3202818--3202853 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
3202808 TAAATAAATT
3202818 TTAT-TAATATTATAA
1 TTATATAATATTATAA
*
3202833 TTATATAATATTCTAA
1 TTATATAATATTATAA
3202849 TTATA
1 TTATA
3202854 AAAATTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATATAATATTATAA
Found at i:3203001 original size:13 final size:13
Alignment explanation
Indices: 3202983--3203007 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3202973 CAGTATAATG
3202983 TTTATTATATTAA
1 TTTATTATATTAA
3202996 TTTATTATATTA
1 TTTATTATATTA
3203008 GATCTTATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTATTATATTAA
Found at i:3207415 original size:3 final size:3
Alignment explanation
Indices: 3207407--3207446 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
3207397 ACCCTTTCCG
*
3207407 ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3207447 ATAATAAGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:3208079 original size:21 final size:22
Alignment explanation
Indices: 3208037--3208095 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
3208027 TCATTTCATC
3208037 AAAATATAATTATTAAAATATTT
1 AAAATATAATTATT-AAATATTT
*
3208060 AAAATATATTTATT-AATATTT
1 AAAATATAATTATTAAATATTT
*
3208081 ATAATAATAA-TATTA
1 AAAAT-ATAATTATTA
3208096 TACTTTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 15 0.48
22 3 0.10
23 13 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAAATATAATTATTAAATATTT
Found at i:3208149 original size:18 final size:17
Alignment explanation
Indices: 3208116--3208151 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
3208106 ATTATAATAA
*
3208116 AATAATAAATATATTAT
1 AATAATAAAGATATTAT
3208133 AATAATATAAGATATTAT
1 AATAATA-AAGATATTAT
3208151 A
1 A
3208152 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAATAAAGATATTAT
Found at i:3208172 original size:25 final size:25
Alignment explanation
Indices: 3208061--3208172 Score: 68
Period size: 25 Copynumber: 4.3 Consensus size: 25
3208051 AAAATATTTA
*
3208061 AAATATATT-TATTAATATTTATAAT
1 AAATATATTATATTATTA-TTATAAT
*
3208086 -AATAATATTATACTTTTAATATTATAAT
1 AAAT-ATATTATA---TTATTATTATAAT
* * *
3208114 AAA-ATAATAAATATATTATAATAAT
1 AAATATATTATAT-TATTATTATAAT
* * *
3208139 ATAAGATATTATATTTTTATTTTAAT
1 A-AATATATTATATTATTATTATAAT
3208165 AAATATAT
1 AAATATAT
3208173 AATAAAAATT
Statistics
Matches: 68, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
24 4 0.06
25 22 0.32
26 14 0.21
27 13 0.19
28 7 0.10
29 8 0.12
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (25 bp):
AAATATATTATATTATTATTATAAT
Found at i:3208669 original size:30 final size:29
Alignment explanation
Indices: 3208617--3208693 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 29
3208607 TTCCAGAAAT
*
3208617 GTAATTTATTTTCCAGAATTCAAATTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
* *
3208646 GTAATTCATTTTCCTGTAATTCAAATTTCA
1 GTAATTCATTTTCCAG-AATTCAAATTCCA
*
3208676 GTAATTCATTTTTCAGAA
1 GTAATTCATTTTCCAGAA
3208694 AACCAATTGC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAATTCAAATTCCA
Found at i:3208691 original size:15 final size:15
Alignment explanation
Indices: 3208617--3208687 Score: 74
Period size: 15 Copynumber: 4.8 Consensus size: 15
3208607 TTCCAGAAAT
*
3208617 GTAATTTATTTTCCA
1 GTAATTCATTTTCCA
**
3208632 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
*
3208646 GTAATTCATTTTCCT
1 GTAATTCATTTTCCA
*
3208661 GTAATTCAAATTT-CA
1 GTAATTC-ATTTTCCA
3208676 GTAATTCATTTT
1 GTAATTCATTTT
3208688 TCAGAAAACC
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
14 15 0.33
15 26 0.58
16 4 0.09
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.46
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:3216651 original size:20 final size:20
Alignment explanation
Indices: 3216626--3216671 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
3216616 CCACAGCTCG
3216626 TATAAATTCCCACTAAGGCA
1 TATAAATTCCCACTAAGGCA
*
3216646 TATAAATTCTCACTAAGGCA
1 TATAAATTCCCACTAAGGCA
*
3216666 TGTAAA
1 TATAAA
3216672 AATTATCCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (20 bp):
TATAAATTCCCACTAAGGCA
Found at i:3222128 original size:39 final size:39
Alignment explanation
Indices: 3222056--3222161 Score: 133
Period size: 39 Copynumber: 2.7 Consensus size: 39
3222046 TTATACATAT
* * *
3222056 AGCATAAGGA-CCTGCAGCAAGGACTTACCCTGAGTACAA
1 AGCA-AAGGAGCCTACAGTAAGGACTTACCCTGAGGACAA
* *
3222095 AGCAGATGAGCCTACAGTAAGGACTTACCCTGAGGACAA
1 AGCAAAGGAGCCTACAGTAAGGACTTACCCTGAGGACAA
* *
3222134 AGCAAAGGAGCCTACTGTAAGGTCTTAC
1 AGCAAAGGAGCCTACAGTAAGGACTTAC
3222162 AAGTCATAGA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 3 0.05
39 54 0.95
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.17
Consensus pattern (39 bp):
AGCAAAGGAGCCTACAGTAAGGACTTACCCTGAGGACAA
Found at i:3222944 original size:14 final size:14
Alignment explanation
Indices: 3222925--3222952 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3222915 GGTTAACAGT
3222925 CAGTCAATGGTCAA
1 CAGTCAATGGTCAA
3222939 CAGTCAATGGTCAA
1 CAGTCAATGGTCAA
3222953 TGGTTGATCG
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:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (14 bp):
CAGTCAATGGTCAA
Found at i:3229898 original size:17 final size:17
Alignment explanation
Indices: 3229876--3229947 Score: 126
Period size: 17 Copynumber: 4.2 Consensus size: 17
3229866 TCGTTGATCC
*
3229876 GACCCGACCCGACTGTT
1 GACCCGACCCGACCGTT
3229893 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
3229910 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
*
3229927 GACCCGACCCGACAGTT
1 GACCCGACCCGACCGTT
3229944 GACC
1 GACC
3229948 GTTGACCGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 53 1.00
ACGTcount: A:0.19, C:0.44, G:0.24, T:0.12
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:3230087 original size:30 final size:29
Alignment explanation
Indices: 3230021--3230087 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
3230011 TTCGAAATGA
* *
3230021 TGCTATTTTGGTAATTAATTTGAAAAGGG
1 TGCTATTTTGGTAACTAATTTAAAAAGGG
* * *
3230050 TGATATTTTGGTTACTATTTTAAAAAGGGG
1 TGCTATTTTGGTAACTAATTTAAAAA-GGG
3230080 TGCTATTT
1 TGCTATTT
3230088 ATGTAAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.45
Consensus pattern (29 bp):
TGCTATTTTGGTAACTAATTTAAAAAGGG
Found at i:3230854 original size:15 final size:15
Alignment explanation
Indices: 3230834--3230866 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3230824 TGATACGTGA
3230834 TTCCTGAATAT-TGAT
1 TTCCTG-ATATCTGAT
3230849 TTCCTGATATCTGAT
1 TTCCTGATATCTGAT
3230864 TTC
1 TTC
3230867 TGTATTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.48
Consensus pattern (15 bp):
TTCCTGATATCTGAT
Found at i:3231360 original size:19 final size:18
Alignment explanation
Indices: 3231321--3231354 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3231311 ATTTGCTGTC
3231321 GTTTTGGATATATATTTT
1 GTTTTGGATATATATTTT
*
3231339 GTTTTGTAT-TATATTT
1 GTTTTGGATATATATTT
3231355 AATGTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.65
Consensus pattern (18 bp):
GTTTTGGATATATATTTT
Found at i:3234662 original size:20 final size:20
Alignment explanation
Indices: 3234637--3234676 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3234627 TCATAAGAGT
3234637 CTGAAGTATCTGCTTACTCA
1 CTGAAGTATCTGCTTACTCA
3234657 CTGAAGTATCTGCTTACTCA
1 CTGAAGTATCTGCTTACTCA
3234677 GAAAGAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (20 bp):
CTGAAGTATCTGCTTACTCA
Found at i:3237133 original size:22 final size:22
Alignment explanation
Indices: 3237108--3237161 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
3237098 ACCGATCTGA
*
3237108 ACCGTTGATCCGACCCGACCCG
1 ACCGTTGACCCGACCCGACCCG
3237130 ACCGTTGACCCGACCCGACCCG
1 ACCGTTGACCCGACCCGACCCG
*
3237152 ACAGTTGACC
1 ACCGTTGACC
3237162 GTTGAACGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.44, G:0.22, T:0.13
Consensus pattern (22 bp):
ACCGTTGACCCGACCCGACCCG
Found at i:3237289 original size:30 final size:28
Alignment explanation
Indices: 3237198--3237293 Score: 102
Period size: 28 Copynumber: 3.4 Consensus size: 28
3237188 ATTCGATTTT
* * ** *
3237198 GGTGCTATTCTGGGAATTAATTCGAAAT
1 GGTGCTATTTTGGTAATTAATTTAAAAG
*
3237226 GATGCTATTTTGGTAATTAATTTAAAAG
1 GGTGCTATTTTGGTAATTAATTTAAAAG
* *
3237254 GGTGCTATTTTGGTTATTATTTTAAAAAGG
1 GGTGCTATTTTGGTAATTAATTT-AAAA-G
3237284 GGTGCTATTT
1 GGTGCTATTT
3237294 ATGTAAAATG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
28 42 0.74
29 4 0.07
30 11 0.19
ACGTcount: A:0.28, C:0.06, G:0.23, T:0.43
Consensus pattern (28 bp):
GGTGCTATTTTGGTAATTAATTTAAAAG
Found at i:3238061 original size:15 final size:15
Alignment explanation
Indices: 3238041--3238073 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3238031 TGATACGTGA
3238041 TTCCTGA-ATATTGAT
1 TTCCTGATAT-TTGAT
3238056 TTCCTGATATTTGAT
1 TTCCTGATATTTGAT
3238071 TTC
1 TTC
3238074 TGTATTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.21, C:0.15, G:0.12, T:0.52
Consensus pattern (15 bp):
TTCCTGATATTTGAT
Found at i:3238568 original size:19 final size:18
Alignment explanation
Indices: 3238529--3238562 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3238519 ATTTGCTGTC
3238529 GTTTTGGATATATATTTT
1 GTTTTGGATATATATTTT
*
3238547 GTTTTGTAT-TATATTT
1 GTTTTGGATATATATTT
3238563 AATGTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.65
Consensus pattern (18 bp):
GTTTTGGATATATATTTT
Found at i:3239887 original size:31 final size:31
Alignment explanation
Indices: 3239775--3239938 Score: 179
Period size: 31 Copynumber: 5.3 Consensus size: 31
3239765 GCCTATAGGT
* * *
3239775 CTACCCAAGAAAGTTCTCAAGGCCATAGGGC
1 CTACCCAAGAAAGATCTCAGGGCCACAGGGC
* * * * *
3239806 TTAACCAAGAAAGATCTGAGGGACACAAGGC
1 CTACCCAAGAAAGATCTCAGGGCCACAGGGC
*
3239837 CTA-CCAA-AAATGATCTCAGGGCCACGGGGC
1 CTACCCAAGAAA-GATCTCAGGGCCACAGGGC
*
3239867 CTACCCAAGAAAAATCTCAGGGCCACAGGGC
1 CTACCCAAGAAAGATCTCAGGGCCACAGGGC
* * * *
3239898 TTACCCAAGAATGATCTCAGGGCCGCAGAGC
1 CTACCCAAGAAAGATCTCAGGGCCACAGGGC
3239929 CTACCCAAGA
1 CTACCCAAGA
3239939 GTCACATTAG
Statistics
Matches: 109, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
29 3 0.03
30 22 0.20
31 81 0.74
32 3 0.03
ACGTcount: A:0.34, C:0.29, G:0.24, T:0.13
Consensus pattern (31 bp):
CTACCCAAGAAAGATCTCAGGGCCACAGGGC
Found at i:3241716 original size:20 final size:20
Alignment explanation
Indices: 3241691--3241745 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
3241681 TCAATGTTCG
*
3241691 GTCAACGACAGTCAGCGGTA
1 GTCAACGACAGTCAACGGTA
3241711 GTCAACGAC-GATCAACGGTA
1 GTCAACGACAG-TCAACGGTA
*
3241731 GTCAACGCCAGTCAA
1 GTCAACGACAGTCAA
3241746 TGGTCAACGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.15
Consensus pattern (20 bp):
GTCAACGACAGTCAACGGTA
Found at i:3241753 original size:17 final size:16
Alignment explanation
Indices: 3241731--3241779 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
3241721 ATCAACGGTA
3241731 GTCAACGCCAGTCAATG
1 GTCAACGCC-GTCAATG
*
3241748 GTCAACGCCGATCAACG
1 GTCAACGCCG-TCAATG
3241765 GTCAAC-CCGGTCAAT
1 GTCAACGCC-GTCAAT
3241780 TGCTCAATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 7 0.25
17 21 0.75
ACGTcount: A:0.29, C:0.33, G:0.22, T:0.16
Consensus pattern (16 bp):
GTCAACGCCGTCAATG
Found at i:3255484 original size:29 final size:29
Alignment explanation
Indices: 3255441--3255594 Score: 141
Period size: 29 Copynumber: 5.4 Consensus size: 29
3255431 AACATTTGAA
*
3255441 AATTCCCAAAATGTCACATTTTTTAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* * * * *
3255470 AATTCCCAGAGTGTCAC-CTTTACGAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* * * *
3255498 AATTCCCAATATGTTACCTTTTTCCAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* * **
3255527 ATTTCCCATAATGTCACCCTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* *
3255556 AATTCCCAAAATGTCACATTTATCGAAA-
1 AATTCCCAAAATGTCACATTTTTCAAAAT
*
3255584 AATTTCCAAAA
1 AATTCCCAAAA
3255595 ATTATTTTAA
Statistics
Matches: 98, Mismatches: 26, Indels: 3
0.77 0.20 0.02
Matches are distributed among these distances:
28 30 0.31
29 68 0.69
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (29 bp):
AATTCCCAAAATGTCACATTTTTCAAAAT
Found at i:3255520 original size:57 final size:58
Alignment explanation
Indices: 3255441--3255576 Score: 175
Period size: 57 Copynumber: 2.4 Consensus size: 58
3255431 AACATTTGAA
* * *
3255441 AATTCCCAAAATGTCACATTTTTTAAAATAATTCCCAGAGTGTCA-CCTTTACGAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAATAATTCCCAGAATGTCACCCTTTACAAAAT
* * * * * * *
3255498 AATTCCCAATATGTTACCTTTTTCCAAATATTTCCCATAATGTCACCCTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAATAATTCCCAGAATGTCACCCTTTACAAAAT
3255556 AATTCCCAAAATGTCACATTT
1 AATTCCCAAAATGTCACATTT
3255577 ATCGAAAAAT
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
57 37 0.57
58 28 0.43
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.36
Consensus pattern (58 bp):
AATTCCCAAAATGTCACATTTTTCAAAATAATTCCCAGAATGTCACCCTTTACAAAAT
Found at i:3261366 original size:29 final size:27
Alignment explanation
Indices: 3261292--3261426 Score: 153
Period size: 29 Copynumber: 4.8 Consensus size: 27
3261282 AACATTTGAA
3261292 AATTCCCAAAATGTCACCTTTTAAAAT
1 AATTCCCAAAATGTCACCTTTTAAAAT
* *
3261319 AATTCCCAGAGTGTCACCTTTTAAGAAAT
1 AATTCCCAAAATGTCACCTTTT-A-AAAT
* * *
3261348 AATTCCCAATATGTTACCTTTTTCCAAAT
1 AATTCCCAAAATGTCACC-TTTT-AAAAT
* *
3261377 ATTTCCCATAATGTCACCCTTTTCAAAAT
1 AATTCCCAAAATGTCA-CCTTTT-AAAAT
3261406 AATTCCCAAAATGTCACCTTT
1 AATTCCCAAAATGTCACCTTT
3261427 ATCGAAAAAT
Statistics
Matches: 89, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
27 20 0.22
28 6 0.07
29 57 0.64
30 6 0.07
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.36
Consensus pattern (27 bp):
AATTCCCAAAATGTCACCTTTTAAAAT
Found at i:3261392 original size:58 final size:58
Alignment explanation
Indices: 3261292--3261440 Score: 180
Period size: 58 Copynumber: 2.6 Consensus size: 58
3261282 AACATTTGAA
* *
3261292 AATTCCCAAAATGTCACC-TTTT-AAAATAATTCCCAGAGTGTCA-CCTTTTAAGAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAATATTTCCCAGAATGTCACCCTTTTAA-AAAT
* * * * *
3261348 AATTCCCAATATGTTACCTTTTTCCAAATATTTCCCATAATGTCACCCTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAATATTTCCCAGAATGTCACCCTTTTAAAAAT
*
3261406 AATTCCCAAAATGTCACCTTTATCGAAAA-ATTTCC
1 AATTCCCAAAATGTCACCTTTTTC-AAAATATTTCC
3261441 AAAAATTATT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
56 16 0.21
57 4 0.05
58 48 0.62
59 10 0.13
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (58 bp):
AATTCCCAAAATGTCACCTTTTTCAAAATATTTCCCAGAATGTCACCCTTTTAAAAAT
Found at i:3261445 original size:29 final size:27
Alignment explanation
Indices: 3261290--3261446 Score: 122
Period size: 29 Copynumber: 5.6 Consensus size: 27
3261280 CAAACATTTG
3261290 AAAA-TTCCCAAAATGTCACCTTTT-A
1 AAAATTTCCCAAAATGTCACCTTTTCA
* * *
3261315 AAATAATTCCCAGAGTGTCACCTTTT-A
1 AAA-ATTTCCCAAAATGTCACCTTTTCA
* *
3261342 AGAAATAATTCCCAATATGTTACCTTTTTCCA
1 A-AAAT--TTCCCAAAATGTCACC-TTTT-CA
* *
3261374 AATATTTCCCATAATGTCACCCTTTTCA
1 AAAATTTCCCAAAATGTCA-CCTTTTCA
*
3261402 AAATAATTCCCAAAATGTCACCTTTATCGA
1 AAA-ATTTCCCAAAATGTCACCTTT-TC-A
*
3261432 AAAATTTCCAAAAAT
1 AAAATTTCCCAAAAT
3261447 TATTTTAAGC
Statistics
Matches: 104, Mismatches: 16, Indels: 20
0.74 0.11 0.14
Matches are distributed among these distances:
25 3 0.03
26 1 0.01
27 21 0.20
28 11 0.11
29 53 0.51
30 10 0.10
31 3 0.03
32 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.34
Consensus pattern (27 bp):
AAAATTTCCCAAAATGTCACCTTTTCA
Found at i:3269158 original size:36 final size:36
Alignment explanation
Indices: 3269111--3269183 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
3269101 GTGTATGATT
*
3269111 GTTTAATATGTATGTGGTGATTACCAAATCTTCACG
1 GTTTAATATGTATATGGTGATTACCAAATCTTCACG
3269147 GTTTAATATGTATATGGTGATTACCAAATCTTCACG
1 GTTTAATATGTATATGGTGATTACCAAATCTTCACG
3269183 G
1 G
3269184 AATTCATCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (36 bp):
GTTTAATATGTATATGGTGATTACCAAATCTTCACG
Found at i:3269259 original size:54 final size:54
Alignment explanation
Indices: 3269177--3269464 Score: 240
Period size: 54 Copynumber: 5.3 Consensus size: 54
3269167 TTACCAAATC
* *
3269177 TTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGACACTAAGTGTGTAT
1 TTCACGGAATTCATCCTATGTGGATGAATAACCATTTCAACACTAAGTGTGCAT
* **
3269231 TTCACAGAATTCATCCTATGTGGATGAATAACTGTTTCAACACTAAGTGTGCAT
1 TTCACGGAATTCATCCTATGTGGATGAATAACCATTTCAACACTAAGTGTGCAT
* * * * * *
3269285 TTCACGGAATTCATCCTATGTGGATGAATAATCATTTTAGCATTATGTGTGCAAACC
1 TTCACGGAATTCATCCTATGTGGATGAATAACCATTTCAACACTAAGTGTGC--A-T
** * * * * * * *
3269342 CCCACGGAATTCATCATAAGTTGATGAATAAACA-TACAAGCACTATGTGTTCAT
1 TTCACGGAATTCATCCTATGTGGATGAATAACCATTTCAA-CACTAAGTGTGCAT
* * * * * * *
3269396 TCCACGGAATTCATCATGA-GTTGATGAATAACC-GTACAGGCACTATGTGTGCAT
1 TTCACGGAATTCATCCT-ATGTGGATGAATAACCATTTCA-ACACTAAGTGTGCAT
* *
3269450 TCCACGGAAATCATC
1 TTCACGGAATTCATC
3269465 ATGAGTTGAT
Statistics
Matches: 196, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
54 153 0.78
55 2 0.01
56 3 0.02
57 38 0.19
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (54 bp):
TTCACGGAATTCATCCTATGTGGATGAATAACCATTTCAACACTAAGTGTGCAT
Found at i:3269465 original size:54 final size:54
Alignment explanation
Indices: 3269343--3269499 Score: 217
Period size: 54 Copynumber: 2.9 Consensus size: 54
3269333 GTGCAAACCC
* * * *
3269343 CCACGGAATTCATCATAAGTTGATGAATAAACATACAAGCACTATGTGTTCATT
1 CCACGGAATTCATCATGAGTTGATGAATAACCGTACAAGCACTATGTGTGCATT
*
3269397 CCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCATT
1 CCACGGAATTCATCATGAGTTGATGAATAACCGTACAAGCACTATGTGTGCATT
* * * *
3269451 CCACGGAAATCATCATGAGTTGATGAACT-ACCGTATATGCATTATGTGT
1 CCACGGAATTCATCATGAGTTGATGAA-TAACCGTACAAGCACTATGTGT
3269500 ACATCTTAAT
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
54 92 0.99
55 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (54 bp):
CCACGGAATTCATCATGAGTTGATGAATAACCGTACAAGCACTATGTGTGCATT
Found at i:3269738 original size:29 final size:29
Alignment explanation
Indices: 3269696--3269760 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
3269686 TAGGACAGTT
** * *
3269696 AGATGAACGGTTAAAGACTGTTTAGTAAA
1 AGATGAACAATTAAACACTGTTGAGTAAA
3269725 AGATGAACAATTAAACACTGTTGAGTAAA
1 AGATGAACAATTAAACACTGTTGAGTAAA
3269754 AGATGAA
1 AGATGAA
3269761 TGGATTAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.46, C:0.08, G:0.22, T:0.25
Consensus pattern (29 bp):
AGATGAACAATTAAACACTGTTGAGTAAA
Found at i:3270027 original size:45 final size:45
Alignment explanation
Indices: 3269978--3270196 Score: 330
Period size: 45 Copynumber: 4.8 Consensus size: 45
3269968 GAACATAATG
*
3269978 GGCATGAAATGATGCCATAAATTAAATGTATAATAGTGTATAAAA
1 GGCATGAAAGGATGCCATAAATTAAATGTATAATAGTGTATAAAA
* * *
3270023 GGCATGAAAGAATCCCATAAATTAAATGTATAATTGTGTATAAAA
1 GGCATGAAAGGATGCCATAAATTAAATGTATAATAGTGTATAAAA
*
3270068 GGCATGAAAGGATGCCATAAATTAAATGCATAATAGTGTATAAAA
1 GGCATGAAAGGATGCCATAAATTAAATGTATAATAGTGTATAAAA
* *
3270113 TGCATGAAAGGATGTCATAAATTAAATGTATAATAGTGTATAAAA
1 GGCATGAAAGGATGCCATAAATTAAATGTATAATAGTGTATAAAA
* * * *
3270158 GACATGAAAGGATGTCATAAATGAAAATGCATAATAGTG
1 GGCATGAAAGGATGCCATAAAT-TAAATGTATAATAGTG
3270197 CATTATAAGC
Statistics
Matches: 158, Mismatches: 15, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
45 144 0.91
46 14 0.09
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.27
Consensus pattern (45 bp):
GGCATGAAAGGATGCCATAAATTAAATGTATAATAGTGTATAAAA
Found at i:3270110 original size:23 final size:23
Alignment explanation
Indices: 3270084--3270156 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 23
3270074 AAAGGATGCC
3270084 ATAAATTAAATGCATAATAGTGT
1 ATAAATTAAATGCATAATAGTGT
3270107 AT--A--AAATGCATGAA-AGGATGT
1 ATAAATTAAATGCAT-AATA-G-TGT
*
3270128 CATAAATTAAATGTATAATAGTGT
1 -ATAAATTAAATGCATAATAGTGT
3270152 ATAAA
1 ATAAA
3270157 AGACATGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 18
0.68 0.02 0.31
Matches are distributed among these distances:
19 9 0.22
20 3 0.08
21 4 0.10
22 2 0.05
23 7 0.17
24 4 0.10
25 3 0.08
26 8 0.20
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.32
Consensus pattern (23 bp):
ATAAATTAAATGCATAATAGTGT
Found at i:3270227 original size:46 final size:45
Alignment explanation
Indices: 3269979--3270231 Score: 253
Period size: 45 Copynumber: 5.6 Consensus size: 45
3269969 AACATAATGG
* * * *
3269979 GCATGAAATGATGCCATAAAT-TAAATGTATAATAGTGTATAAAA
1 GCATGAAAGGATGTCATAAATGAAAATGCATAATAGTGTATAAAA
* ** * * *
3270023 GGCATGAAAGAATCCCATAAAT-TAAATGTATAATTGTGTATAAAA
1 -GCATGAAAGGATGTCATAAATGAAAATGCATAATAGTGTATAAAA
* *
3270068 GGCATGAAAGGATGCCATAAAT-TAAATGCATAATAGTGTATAAAA
1 -GCATGAAAGGATGTCATAAATGAAAATGCATAATAGTGTATAAAA
* *
3270113 TGCATGAAAGGATGTCATAAAT-TAAATGTATAATAGTGTATAAAA
1 -GCATGAAAGGATGTCATAAATGAAAATGCATAATAGTGTATAAAA
* *
3270158 GACATGAAAGGATGTCATAAATGAAAATGCATAATAGTGCATTATAA
1 G-CATGAAAGGATGTCATAAATGAAAATGCATAATAGTGTA-TAAAA
* * * *
3270205 GCTTGAATGGATGTTATCAATGAAAAT
1 GCATGAAAGGATGTCATAAATGAAAAT
3270232 AAAGAATAAT
Statistics
Matches: 186, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
44 1 0.01
45 143 0.77
46 37 0.20
47 5 0.03
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (45 bp):
GCATGAAAGGATGTCATAAATGAAAATGCATAATAGTGTATAAAA
Found at i:3273287 original size:14 final size:14
Alignment explanation
Indices: 3273268--3273295 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3273258 TTTTTTATCA
3273268 AAATAAATAAAAAT
1 AAATAAATAAAAAT
3273282 AAATAAATAAAAAT
1 AAATAAATAAAAAT
3273296 GACAAATAAA
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:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:3274148 original size:47 final size:47
Alignment explanation
Indices: 3274094--3274190 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
3274084 AAAAGGAACC
3274094 TTTTAATCTTTGTATATTAATTCTAGGTCTCTCAAGAACCGACCATT
1 TTTTAATCTTTGTATATTAATTCTAGGTCTCTCAAGAACCGACCATT
3274141 TTTTAATCTTTGTATATTAATTCTAGGTCTCTCAAGAACCGACCATT
1 TTTTAATCTTTGTATATTAATTCTAGGTCTCTCAAGAACCGACCATT
3274188 TTT
1 TTT
3274191 ACATGATTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (47 bp):
TTTTAATCTTTGTATATTAATTCTAGGTCTCTCAAGAACCGACCATT
Found at i:3279209 original size:15 final size:16
Alignment explanation
Indices: 3279189--3279229 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3279179 GTTTACTTCA
*
3279189 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
3279204 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
3279220 GAATGATTCA
1 GAATGATTCA
3279230 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:3279332 original size:23 final size:23
Alignment explanation
Indices: 3279306--3279368 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
3279296 TGTACTTCTG
3279306 TGCTGAATCATTCAGCATTGTTT
1 TGCTGAATCATTCAGCATTGTTT
3279329 TGCTGAATCATTCAGCATTGTTT
1 TGCTGAATCATTCAGCATTGTTT
*
3279352 TGCTGAATCAGTCAGCA
1 TGCTGAATCATTCAGCA
3279369 CTAAATCATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (23 bp):
TGCTGAATCATTCAGCATTGTTT
Found at i:3279438 original size:22 final size:22
Alignment explanation
Indices: 3279408--3279461 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
3279398 CGCTGAATGT
*
3279408 TGAACGGTTCAACATTCAGCGC
1 TGAATGGTTCAACATTCAGCGC
*
3279430 TGAATGGTTCAGCATTCAGCGC
1 TGAATGGTTCAACATTCAGCGC
3279452 TGAATGGTTC
1 TGAATGGTTC
3279462 CATTAAGAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (22 bp):
TGAATGGTTCAACATTCAGCGC
Done.