Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 14 of 378
Found at i:3968336 original size:68 final size:68
Alignment explanation
Indices: 3968252--3968450 Score: 287
Period size: 68 Copynumber: 2.9 Consensus size: 68
3968242 TCTTCTTCCA
* * * *
3968252 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCTCTCCAATGCCATTTCTGGAAGAAGAGGT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCAGGAAGAAAAGAT
*
3968317 -TT
66 CCT
*
3968319 GCTGAAACTTCAAGGAGATCTGTTGTGGCTTTTAGCCGCTCC-ATCGCCATTTCAGGAAGAAAAG
1 -CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAAT-GCCATTTCAGGAAGAAAAG
3968383 ATCCT
64 ATCCT
* *
3968388 CTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAATGCCATTTCAGGGA-AAAAGA
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCAGGAAGAAAAGA
3968451 AATTTGTAAT
Statistics
Matches: 119, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
67 8 0.07
68 108 0.91
69 3 0.03
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.28
Consensus pattern (68 bp):
CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCAGGAAGAAAAGAT
CCT
Found at i:3968618 original size:88 final size:89
Alignment explanation
Indices: 3968512--3969323 Score: 413
Period size: 87 Copynumber: 9.3 Consensus size: 89
3968502 CATCTTCGAT
* * * *
3968512 CTATTTCCCAACTGCTTAAGGGGTTAAGATC-TGTAAATTCAACCTGTTACCCTACTGGTTAGGG
1 CTATTACCCTACTGCTTAAGGGGTTAAGATCTTGTAAATTCGACCTGTTACCCTACTGCTTAGGG
*
3968576 GGTTAAGATTTGTAAATCTTCAGC
66 GGTTAAGATCTGTAAATCTTCAGC
* * * * *
3968600 CTGTTACCCTACTGCTTAAGGGTTTAAGGT-TTGTAAATTCGGCTTGTTACCCTACTGCTTAGGG
1 CTATTACCCTACTGCTTAAGGGGTTAAGATCTTGTAAATTCGACCTGTTACCCTACTGCTTAGGG
* ** * * * * *
3968664 GGTTAA-AGCCCATCATTTTTTA-T
66 GGTTAAGA-TCTGTAAATCTTCAGC
* ** * * ** * * *
3968687 CTATTTCCCTACTGCTT-AGGGGTTAAAGCCCAT-CATCTTTGATCTGTTTCCCTACTGCTTAGG
1 CTATTACCCTACTGCTTAAGGGGTT-AAGATCTTGTAAATTCGACCTGTTACCCTACTGCTTAGG
*
3968750 AGGTTAAGATCTGTAAATCTTCAGC
65 GGGTTAAGATCTGTAAATCTTCAGC
* * * * *
3968775 CTATTACCCTACTGCTTAGGGGGTTAAG-GCTTGTAAATTTGGCTTGTTACCCTACTGCTTAGGG
1 CTATTACCCTACTGCTTAAGGGGTTAAGATCTTGTAAATTCGACCTGTTACCCTACTGCTTAGGG
* ** * *
3968839 GGTTAA-AGC-CCATCATCTTC-GAT
66 GGTTAAGATCTGTA-AATCTTCAG-C
* * * ** * * *
3968862 CTATTTCCCTACTGCTTAGGGGGTTAAGATCTT-CATCTTCGATCTGTTTCCCTACTTCTTAGGG
1 CTATTACCCTACTGCTTAAGGGGTTAAGATCTTGTAAATTCGACCTGTTACCCTACTGCTTAGGG
* * * * *
3968926 AGATAAGATCTG-CAA--TTCGGT
66 GGTTAAGATCTGTAAATCTTCAGC
* * * * * * *
3968947 CTGTTACCCTACCGATT-AGGGGTTTAAGACCCTTCGT--CTTCGATCTGTTTCCCTACTGCTTA
1 CTATTACCCTACTGCTTAAGGGG-TTAAGA-TCTT-GTAAATTCGACCTGTTACCCTACTGCTTA
*
3969009 -GGGGTTAAGATCTATAAATCTTCAGC
63 GGGGGTTAAGATCTGTAAATCTTCAGC
* * * * * * *
3969035 CTGTTACCCTACTGCTTAGGGGGTTAAG-GCTTGTAAATTTGGCTTGTTACCCTACTACTTAGGG
1 CTATTACCCTACTGCTTAAGGGGTTAAGATCTTGTAAATTCGACCTGTTACCCTACTGCTTAGGG
* ** * *
3969099 GGTTAA-AGC-CCATCATCTTC-GAT
66 GGTTAAGATCTGTA-AATCTTCAG-C
* * * * ** * * *
3969122 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTT-CATCTTCGATCTGTTTCCCTACCGCTTAGGG
1 CTATTACCCTACTGCTTAAGGGGTTAAGATCTTGTAAATTCGACCTGTTACCCTACTGCTTAGGG
* * * * * *
3969186 AGATGAGATCTG-CAA--TTCCGT
66 GGTTAAGATCTGTAAATCTTCAGC
* * * * * ** * **
3969207 CTGTTACCCTACCGATT-AGGGGTTTAAGACCCTT-CATCTTCGATCTGTTTGCCTACTGCTTAG
1 CTATTACCCTACTGCTTAAGGGG-TTAAGA-TCTTGTAAATTCGACCTGTTACCCTACTGCTTAG
*
3969270 GGGGTTAAGATCTATAAATCTTCAGC
64 GGGGTTAAGATCTGTAAATCTTCAGC
* *
3969296 CTGTTACCCTATTGCTT-AGGGGCTTAAG
1 CTATTACCCTACTGCTTAAGGGG-TTAAG
3969324 GCTTGTGAAT
Statistics
Matches: 546, Mismatches: 142, Indels: 71
0.72 0.19 0.09
Matches are distributed among these distances:
84 8 0.01
85 60 0.11
86 84 0.15
87 198 0.36
88 158 0.29
89 38 0.07
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (89 bp):
CTATTACCCTACTGCTTAAGGGGTTAAGATCTTGTAAATTCGACCTGTTACCCTACTGCTTAGGG
GGTTAAGATCTGTAAATCTTCAGC
Found at i:3968767 original size:175 final size:172
Alignment explanation
Indices: 3968469--3968937 Score: 632
Period size: 175 Copynumber: 2.7 Consensus size: 172
3968459 ATTTCCAGCC
* * * *
3968469 TGTTACCCTACTACTTAGGGGTTTAAGGCCCATCATCTTCGATCTATTTCCCAACTGCTTAAGGG
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCTACTGCTT-AGGG
* ** * * * * *
3968534 GTTAAGATCTGTAAATTCAACCTGTTACCCTACTGGTTAGGGGGTTAAGATTTGTAAATCTTCAG
65 GTTAAGATCT-CATCTTCGATCTGTTTCCCTACTGCTTA-GGGGTTAAGATCTGTAAATCTTCAG
* * *
3968599 CCTGTTACCCTACTGCTTAAGGGTTTAAGGTTTGTAAATTCGGCT
128 CCTATTACCCTACTGCTTAAGGGGTTAAGGCTTGTAAATTCGGCT
* **
3968644 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATTTTTTATCTATTTCCCTACTGCTTAGGGG
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCTACTGCTTAGGGG
** *
3968709 TTAAAGCCCATCATCTTTGATCTGTTTCCCTACTGCTTAGGAGGTTAAGATCTGTAAATCTTCAG
66 TT-AAGATC-TCATCTTCGATCTGTTTCCCTACTGCTTAGG-GGTTAAGATCTGTAAATCTTCAG
* *
3968774 CCTATTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTGGCT
128 CCTATTACCCTACTGCTTAAGGGGTTAAGGCTTGTAAATTCGGCT
3968819 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCTACTGCTTAGGGG
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCTACTGCTTA-GGG
* *
3968884 GTTAAGATCTTCATCTTCGATCTGTTTCCCTACTTCTTAGGGAGATAAGATCTG
65 GTTAAGATC-TCATCTTCGATCTGTTTCCCTACTGCTTAGGG-GTTAAGATCTG
3968938 CAATTCGGTC
Statistics
Matches: 257, Mismatches: 32, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
174 10 0.04
175 240 0.93
176 7 0.03
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (172 bp):
TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCTACTGCTTAGGGG
TTAAGATCTCATCTTCGATCTGTTTCCCTACTGCTTAGGGGTTAAGATCTGTAAATCTTCAGCCT
ATTACCCTACTGCTTAAGGGGTTAAGGCTTGTAAATTCGGCT
Found at i:3969053 original size:260 final size:260
Alignment explanation
Indices: 3968693--3969334 Score: 1097
Period size: 260 Copynumber: 2.5 Consensus size: 260
3968683 TTATCTATTT
* * * * *
3968693 CCCTACTGCTTAGGGGTTAAAG-CCCATCATCTTTGATCTGTTTCCCTACTGCTTAGGAGGTTAA
1 CCCTACCGATTAGGGGTTTAAGACCCTTCATCTTCGATCTGTTTCCCTACTGCTTAGG-GGTTAA
* *
3968757 GATCTGTAAATCTTCAGCCTATTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTGGCTTGT
65 GATCTATAAATCTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTGGCTTGT
*
3968822 TACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCTACTGCTTAGGGGGTT
130 TACCCTACTACTTAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCTACTGCTTAGGGGGTT
** *
3968887 AAGATCTTCATCTTCGATCTGTTTCCCTACTTCTTAGGGAGATAAGATCTGCAATTCGGTCTGTT
195 AAGATCTTCATCTTCGATCTGTTTCCCTACCGCTTAGGGAGATAAGATCTGCAATTCCGTCTGTT
3968952 A
260 A
*
3968953 CCCTACCGATTAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGTTAAG
1 CCCTACCGATTAGGGGTTTAAGACCCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGGTTAAG
3969018 ATCTATAAATCTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTGGCTTGTT
66 ATCTATAAATCTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTGGCTTGTT
*
3969083 ACCCTACTACTTAGGGGGTTAAAGCCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTA
131 ACCCTACTACTTAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCTACTGCTTAGGGGGTTA
*
3969148 AGATCTTCATCTTCGATCTGTTTCCCTACCGCTTAGGGAGATGAGATCTGCAATTCCGTCTGTTA
196 AGATCTTCATCTTCGATCTGTTTCCCTACCGCTTAGGGAGATAAGATCTGCAATTCCGTCTGTTA
*
3969213 CCCTACCGATTAGGGGTTTAAGACCCTTCATCTTCGATCTGTTTGCCTACTGCTTAGGGGGTTAA
1 CCCTACCGATTAGGGGTTTAAGACCCTTCATCTTCGATCTGTTTCCCTACTGCTTA-GGGGTTAA
* * *
3969278 GATCTATAAATCTTCAGCCTGTTACCCTATTGCTTAGGGGCTTAAGGCTTGTGAATT
65 GATCTATAAATCTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATT
3969335 CACTGATTCT
Statistics
Matches: 361, Mismatches: 19, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
260 267 0.74
261 94 0.26
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.35
Consensus pattern (260 bp):
CCCTACCGATTAGGGGTTTAAGACCCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGGTTAAG
ATCTATAAATCTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTGGCTTGTT
ACCCTACTACTTAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCTACTGCTTAGGGGGTTA
AGATCTTCATCTTCGATCTGTTTCCCTACCGCTTAGGGAGATAAGATCTGCAATTCCGTCTGTTA
Found at i:3969195 original size:43 final size:43
Alignment explanation
Indices: 3968468--3969323 Score: 488
Period size: 43 Copynumber: 19.7 Consensus size: 43
3968458 AATTTCCAGC
* * * ** *
3968468 CTGTTACCCTACTACTTAGGGGTTTAAGGCCCATCATCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGGTTAA-GATCTTCATCTTCGAT
* * * ** * *
3968512 CTATTTCCCAACTGCTTAAGGGGTTAAGATCTGT-AAATTCAAC
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-TCATCTTCGAT
* * * * *
3968555 CTGTTACCCTACTGGTTAGGGGGTTAAGATTTGTAAATCTTC-AGC
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-T-CATCTTCGA-T
* * * * * ** *
3968600 CTGTTACCCTACTGCTTAAGGGTTTAAGGT-TTGTAAATTCG-G
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTT-CATCTTCGAT
* ** * * **
3968642 CTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATTTTTTAT
1 C-TGTTTCCCTACTGCTTAGGGGGTT-AAGATCTTCATCTTCGAT
* ** * *
3968687 CTATTTCCCTACTGCTTA-GGGGTTAAAGCCCATCATCTTTGAT
1 CTGTTTCCCTACTGCTTAGGGGGTT-AAGATCTTCATCTTCGAT
* * *
3968730 CTGTTTCCCTACTGCTTAGGAGGTTAAGATCTGTAAATCTTC-AGC
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-T-CATCTTCGA-T
* * * * * *
3968775 CTATTACCCTACTGCTTAGGGGGTTAAG-GCTTGTAAAT-TTGGCT
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATC-T-T-CATCTTCGAT
* ** *
3968819 -TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGGTT-AAGATCTTCATCTTCGAT
*
3968862 CTATTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGAT
* * * * * *
3968905 CTGTTTCCCTACTTCTTAGGGAGATAAGATCTGCA-ATTCGGT
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGAT
* * * * * *
3968947 CTGTTACCCTACCGATTAGGGGTTTAAGACCCTTCGTCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGA-TCTTCATCTTCGAT
* *
3968991 CTGTTTCCCTACTGCTTA-GGGGTTAAGATCTATAAATCTTC-AGC
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-T-CATCTTCGA-T
* * * * *
3969035 CTGTTACCCTACTGCTTAGGGGGTTAAG-GCTTGTAAAT-TTGGCT
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATC-T-T-CATCTTCGAT
* * ** *
3969079 -TGTTACCCTACTACTTAGGGGGTTAAAGCCCATCATCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGGTT-AAGATCTTCATCTTCGAT
3969122 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGAT
* * * * * *
3969165 CTGTTTCCCTACCGCTTAGGGAGATGAGATCTGCAAT-TCCG-T
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTC-ATCTTCGAT
* * * * *
3969207 CTGTTACCCTACCGATTAGGGGTTTAAGACCCTTCATCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGA-TCTTCATCTTCGAT
* * *
3969251 CTGTTTGCCTACTGCTTAGGGGGTTAAGATCTATAAATCTTC-AGC
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-T-CATCTTCGA-T
* * *
3969296 CTGTTACCCTATTGCTTAGGGGCTTAAG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAG
3969324 GCTTGTGAAT
Statistics
Matches: 632, Mismatches: 142, Indels: 75
0.74 0.17 0.09
Matches are distributed among these distances:
42 60 0.09
43 276 0.44
44 179 0.28
45 117 0.19
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (43 bp):
CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGAT
Found at i:3969493 original size:66 final size:66
Alignment explanation
Indices: 3969387--3969513 Score: 236
Period size: 66 Copynumber: 1.9 Consensus size: 66
3969377 TCTATGCTTA
*
3969387 TGTCAAATGATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
1 TGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
3969452 G
66 G
*
3969453 TGTCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAGATGTGTTAT
1 TGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTAT
3969514 TATATGAATG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (66 bp):
TGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
G
Found at i:3973230 original size:20 final size:20
Alignment explanation
Indices: 3973205--3973242 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3973195 GTTTATTCGC
*
3973205 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
3973225 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
3973243 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:3981137 original size:20 final size:20
Alignment explanation
Indices: 3981112--3981149 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3981102 GTTTATTCGC
*
3981112 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
3981132 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
3981150 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:3984256 original size:19 final size:20
Alignment explanation
Indices: 3984232--3984278 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
3984222 AGTGAAAGTT
3984232 TAATGCAAATGT-TGCAATG
1 TAATGCAAATGTATGCAATG
*
3984251 TAATGCAAATGTATGGAATG
1 TAATGCAAATGTATGCAATG
3984271 -AATGCAAA
1 TAATGCAAA
3984279 AGAAAGGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGTATGCAATG
Found at i:3986720 original size:2 final size:2
Alignment explanation
Indices: 3986713--3986755 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
3986703 ACAATAATAC
* *
3986713 TA TA TA TA -A TA AA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3986754 TA
1 TA
3986756 ATGAAATACA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3986723 original size:12 final size:11
Alignment explanation
Indices: 3986706--3986757 Score: 59
Period size: 12 Copynumber: 4.5 Consensus size: 11
3986696 AAAGTAAACA
3986706 ATAATACTATAT
1 ATAATA-TATAT
*
3986718 ATAATAAATAT
1 ATAATATATAT
3986729 ATATATATATAT
1 ATA-ATATATAT
*
3986741 ATATATATGTAT
1 ATA-ATATATAT
3986753 ATAAT
1 ATAAT
3986758 GAAATACACA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
11 9 0.25
12 27 0.75
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (11 bp):
ATAATATATAT
Found at i:3986845 original size:38 final size:38
Alignment explanation
Indices: 3986773--3986845 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
3986763 ACACACTACT
* *
3986773 ATATAATAATAATAATAAATATAGAAATACAAAAAGAA
1 ATATAATAAAAATAATAAATAAAGAAATACAAAAAGAA
* *
3986811 ATATAATAAAAATATTAAATTAAAGTAATA-AAAAA
1 ATATAATAAAAATAATAAA-TAAAGAAATACAAAAA
3986846 CAATACTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
38 22 0.73
39 8 0.27
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.26
Consensus pattern (38 bp):
ATATAATAAAAATAATAAATAAAGAAATACAAAAAGAA
Found at i:3987052 original size:3 final size:3
Alignment explanation
Indices: 3986986--3987033 Score: 53
Period size: 3 Copynumber: 15.0 Consensus size: 3
3986976 AATAGGGGTG
3986986 ATA ATA ATA ATA ATA ATA CA-A ATA ATA ATA CATA TATA TATA ATA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA -ATA -ATA -ATA ATA ATA
3987034 GTAGTTAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
2 1 0.02
3 29 0.71
4 11 0.27
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3987117 original size:3 final size:3
Alignment explanation
Indices: 3987104--3987186 Score: 59
Period size: 3 Copynumber: 27.3 Consensus size: 3
3987094 GAGGACATAT
3987104 ATA AT- ATA ATA ATA AT- ATAA ATA ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A -ATA ATA
* *
3987148 ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3987187 AACAAAGCTC
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
2 9 0.14
3 45 0.69
4 9 0.14
5 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:3987128 original size:12 final size:12
Alignment explanation
Indices: 3987104--3987183 Score: 76
Period size: 12 Copynumber: 6.8 Consensus size: 12
3987094 GAGGACATAT
3987104 ATAATAT-AATA
1 ATAATATAAATA
3987115 ATAATATAAATA
1 ATAATATAAATA
*
3987127 ATAATATATACATG
1 ATAATATA-A-ATA
*
3987141 AGAA-AT-AATA
1 ATAATATAAATA
3987151 ATAATATAAATA
1 ATAATATAAATA
* *
3987163 ATAGTAAAAATA
1 ATAATATAAATA
*
3987175 ATAAAATAA
1 ATAATATAA
3987184 TAAAACAAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
10 5 0.09
11 10 0.18
12 32 0.58
13 3 0.05
14 5 0.09
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (12 bp):
ATAATATAAATA
Found at i:3987552 original size:23 final size:23
Alignment explanation
Indices: 3987516--3987589 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
3987506 CCTTCTTTTC
*
3987516 CAAAAAAA-CACCTCCAAAAAAA
1 CAAAAAAACCTCCTCCAAAAAAA
3987538 CAAAAAAACCTCCTCCAAAATAAA
1 CAAAAAAACCTCCTCCAAAA-AAA
* * * *
3987562 -GAACAATCCTCCTCCAAAAAAC
1 CAAAAAAACCTCCTCCAAAAAAA
3987584 CAAAAA
1 CAAAAA
3987590 CCCACATTCA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
22 10 0.24
23 29 0.69
24 3 0.07
ACGTcount: A:0.59, C:0.30, G:0.01, T:0.09
Consensus pattern (23 bp):
CAAAAAAACCTCCTCCAAAAAAA
Found at i:3988134 original size:44 final size:44
Alignment explanation
Indices: 3988026--3988600 Score: 446
Period size: 44 Copynumber: 13.1 Consensus size: 44
3988016 CTTCAATGTT
* *
3988026 TTCAACTTGTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATC
1 TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAAT-CTGATATC
** * * * * * * *
3988069 TTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATC
1 TTCAATTTG-TTCCCTATAAGCACAGGGATGCCAAATCTGATATC
* * * * *
3988114 TTCGATTTGCTCCCTATAAGCACAGGGATGCCAAATCTGCTGTT
1 TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAATCTGATATC
* * *
3988158 TTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTT
1 TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAATCTGATATC
* *
3988202 TTCAACTTGTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATC
1 TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAAT-CTGATATC
** * * * * * * *
3988245 TTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGTTATC
1 TTCAATTTG-TTCCCTATAAGCACAGGGATGCCAAATCTGATATC
* * * * *
3988290 TTTAATTTGTTCCCTAAAAGCACAAGGATGCCAAATCTGATGTT
1 TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAATCTGATATC
* * *
3988334 TTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTT
1 TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAATCTGATATC
* *
3988378 TTCAACTTGTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATC
1 TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAAT-CTGATATC
** * * * * * * *
3988421 TTTGATCTGTTTCACTGTAAGCACAGGAATGTCAGATCTGCTATC
1 TTCAATTTG-TTCCCTATAAGCACAGGGATGCCAAATCTGATATC
* * * *
3988466 TTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTT
1 TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAATCTGATATC
* * *
3988510 TTCAACTTGTTCCCTATAAGCATAGGGATGCC--ATGCTGAAATC
1 TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAAT-CTGATATC
* * * * * * * *
3988553 TTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATC
1 TTCAATTTG-TTCCCTATAAGCACAGGGATGCCAAATCTGATATC
3988598 TTC
1 TTC
3988601 GGTCTGCTCC
Statistics
Matches: 425, Mismatches: 92, Indels: 28
0.78 0.17 0.05
Matches are distributed among these distances:
42 6 0.01
43 35 0.08
44 328 0.77
45 48 0.11
46 8 0.02
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (44 bp):
TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAATCTGATATC
Found at i:3988321 original size:176 final size:176
Alignment explanation
Indices: 3988021--3988542 Score: 963
Period size: 176 Copynumber: 3.0 Consensus size: 176
3988011 CTTCACTTCA
3988021 ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
1 ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
*
3988086 TAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGCTCCCTATAAGCACAGGGATGCCAAATC
66 TAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATC
3988151 TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTG
131 TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTG
3988197 ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
1 ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
* ** * *
3988262 TAAGCACAGGAATGTCAGATCTGTTATCTTTAATTTGTTCCCTAAAAGCACAAGGATGCCAAATC
66 TAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATC
*
3988327 TGATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTG
131 TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTG
*
3988373 ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGTTTCACTG
1 ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
3988438 TAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATC
66 TAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATC
*
3988503 TGCTGTTTTCAACTTGTTCCCTATAAGCATAGGGATGCCA
131 TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCA
3988543 TGCTGAAATC
Statistics
Matches: 331, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
176 331 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (176 bp):
ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
TAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATC
TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTG
Found at i:3989115 original size:176 final size:174
Alignment explanation
Indices: 3988803--3989309 Score: 617
Period size: 176 Copynumber: 2.9 Consensus size: 174
3988793 ATTTCCTGCC
* * * * * * *
3988803 TGTTACCCTACTACTTAGGGGTTTAAGGCCCATCATCTTCGATCTATTTCCCAACTGCTTAAGGG
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTTGATCTATTCCCCTACTGCTTAGGGG
* * * * * * * * *
3988868 GTTAAGATC-TGTAAATTCAACCTATTACCCTACTGGTTAGGGGGTTAAGATTTGTAAATCTTCA
66 GTTAAGACCAT-CATATTCGATCTGTTTCCCTACTGCTTA-GGGGTTAAGATCTGTAAATCTTCA
*
3988932 GCCTGTTACCCTACTGCTTAGGGGTTTAAGGTTTGTAAATTCGGCT
129 GCCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTGTAAATTCGGCT
* *
3988978 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATTTTTTATCTATTCCCCTACTGCTTAGGGG
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTTGATCTATTCCCCTACTGCTTAGGGG
* *
3989043 GTTAAAGCCCATCATATTTGATCTGTTTCCCTACTGCTTAGGGGTTTAAGATCTGTAAATCTTCA
66 GTT-AAGACCATCATATTCGATCTGTTTCCCTACTGCTTAGGGG-TTAAGATCTGTAAATCTTCA
* * *
3989108 GCCTGTTACCCTACTGCTTAGGGGGTTAATGCTTGTAAATTTGGCT
129 GCCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTGTAAATTCGGCT
* *
3989154 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTTGATCTGTTTCCCTACTGCTTAGGGG
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTTGATCTATTCCCCTACTGCTTAGGGG
* * * * * * *
3989219 GTTAAGATCTTCATCTTCGATCTGTTTCCCTACTTCTTAGGGAGATAAGATCTG-CAA--TTCGG
66 GTTAAGACCATCATATTCGATCTGTTTCCCTACTGCTTAGGG-GTTAAGATCTGTAAATCTTCAG
* * *
3989281 TCTGTTACCCTACCGATTAGGGGTTTAAG
130 CCTGTTACCCTACTGCTTAGGGGTTTAAG
3989310 ACCCTTCATC
Statistics
Matches: 286, Mismatches: 42, Indels: 11
0.84 0.12 0.03
Matches are distributed among these distances:
172 28 0.10
174 2 0.01
175 105 0.37
176 150 0.52
177 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (174 bp):
TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTTGATCTATTCCCCTACTGCTTAGGGG
GTTAAGACCATCATATTCGATCTGTTTCCCTACTGCTTAGGGGTTAAGATCTGTAAATCTTCAGC
CTGTTACCCTACTGCTTAGGGGTTTAAGGCTTGTAAATTCGGCT
Found at i:3989334 original size:129 final size:132
Alignment explanation
Indices: 3989040--3989652 Score: 727
Period size: 129 Copynumber: 4.7 Consensus size: 132
3989030 TACTGCTTAG
* * * *
3989040 GGGGTTAAAG-CCCATCATATTTGATCTGTTTCCCTACTGCTTAGGGGTTTAAGATCTGTAAATC
1 GGGGTTTAAGACCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
* * * * * *
3989104 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAATGCT-TGTAAATTTGGCTTGTTACCCTACTGC
66 TTCAGCCTGTTACCCTACTGCTTAGGGAGATAA-GATCTGTAAATTCGGCTTGTTACCCTACCGA
3989168 TTA
130 TTA
* * *
3989171 GGGGGTTAA-AGCCCATCATCTTTGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-T-CAT
1 GGGGTTTAAGA-CCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAAT
* * * *
3989233 CTTC-GATCTGTTTCCCTACTTCTTAGGGAGATAAGATCTG-CAATTCGG-TCTGTTACCCTACC
65 CTTCAG-CCTGTTACCCTACTGCTTAGGGAGATAAGATCTGTAAATTCGGCT-TGTTACCCTACC
3989295 GATTA
128 GATTA
*
3989300 GGGGTTTAAGACCCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
1 GGGGTTTAAGACCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
* * * * * *
3989365 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG-GCTTGTAAATTTGGCTTGTTACCCTACTGC
66 TTCAGCCTGTTACCCTACTGCTTAGGGAGATAAGATC-TGTAAATTCGGCTTGTTACCCTACCGA
3989429 TTA
130 TTA
* *
3989432 GGGGGTTAA-AGCCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-T-CAT
1 GGGGTTTAAGA-CCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAAT
* * * *
3989494 CTTC-GATCTGTTTCCCTACTGCTTAGGAAGATGAGATC--TACAATTCCGGC-TGTTACCCTAC
65 CTTCAG-CCTGTTACCCTACTGCTTAGGGAGATAAGATCTGTA-AATT-CGGCTTGTTACCCTAC
3989555 CGATTA
127 CGATTA
* * *
3989561 GGGGTTTAAGACCCTTCATCTTCGATCTCTTTCCCTACTGCTTAGGGGGTTAAGATCTATAAATC
1 GGGGTTTAAGACCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
*
3989626 TTCAGCCTGTTACCCTATTGCTTAGGG
66 TTCAGCCTGTTACCCTACTGCTTAGGG
3989653 GCTTAAGGCT
Statistics
Matches: 411, Mismatches: 50, Indels: 42
0.82 0.10 0.08
Matches are distributed among these distances:
128 3 0.01
129 150 0.36
130 68 0.17
131 67 0.16
132 122 0.30
133 1 0.00
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (132 bp):
GGGGTTTAAGACCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
TTCAGCCTGTTACCCTACTGCTTAGGGAGATAAGATCTGTAAATTCGGCTTGTTACCCTACCGAT
TA
Found at i:3989363 original size:261 final size:261
Alignment explanation
Indices: 3989040--3989670 Score: 1095
Period size: 261 Copynumber: 2.4 Consensus size: 261
3989030 TACTGCTTAG
* * * * *
3989040 GGGGTTAAAG-CCCATCATATTTGATCTGTTTCCCTACTGCTTAGGGGTTTAAGATCTGTAAATC
1 GGGGTTTAAGACCCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
*
3989104 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAATGCTTGTAAATTTGGCTTGTTACCCTACTGCT
66 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCT
*
3989169 TAGGGGGTTAAAGCCCATCATCTTTGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATC
131 TAGGGGGTTAAAGCCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATC
* * *
3989234 TTCGATCTGTTTCCCTACTTCTTAGGGAGATAAGATCTGCAATT-CGGTCTGTTACCCTACCGAT
196 TTCGATCTGTTTCCCTACTGCTTAGGAAGATAAGATCTACAATTCCGG-CTGTTACCCTACCGAT
3989298 TA
260 TA
3989300 GGGGTTTAAGACCCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
1 GGGGTTTAAGACCCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
3989365 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCT
66 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCT
3989430 TAGGGGGTTAAAGCCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATC
131 TAGGGGGTTAAAGCCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATC
*
3989495 TTCGATCTGTTTCCCTACTGCTTAGGAAGATGAGATCTACAATTCCGGCTGTTACCCTACCGATT
196 TTCGATCTGTTTCCCTACTGCTTAGGAAGATAAGATCTACAATTCCGGCTGTTACCCTACCGATT
3989560 A
261 A
* *
3989561 GGGGTTTAAGACCCTTCATCTTCGATCTCTTTCCCTACTGCTTAGGGGGTTAAGATCTATAAATC
1 GGGGTTTAAGACCCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
* * *
3989626 TTCAGCCTGTTACCCTATTGCTTAGGGGCTTAAGGCTTGTTAATT
66 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATT
3989671 CACTGATTCT
Statistics
Matches: 353, Mismatches: 16, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
260 9 0.03
261 341 0.97
262 3 0.01
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (261 bp):
GGGGTTTAAGACCCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCT
TAGGGGGTTAAAGCCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATC
TTCGATCTGTTTCCCTACTGCTTAGGAAGATAAGATCTACAATTCCGGCTGTTACCCTACCGATT
A
Found at i:3989508 original size:43 final size:43
Alignment explanation
Indices: 3988802--3989659 Score: 533
Period size: 43 Copynumber: 19.7 Consensus size: 43
3988792 AATTTCCTGC
* * ** *
3988802 CTGTTACCCTACTACTTAGGGGTTTAAGGCCCATCATCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAA-GATCTTCATCTTCGAT
* * * * ** * *
3988846 CTATTTCCCAACTGCTTAAGGGGTTAAGATCTGT-AAATTCAAC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCT-TCATCTTCGAT
* * * * *
3988889 CTATTACCCTACTGGTTAGGGGGTTAAGATTTGTAAATCTTC-AGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCT-T-CATCTTCGA-T
* * * ** *
3988934 CTGTTACCCTACTGCTTAGGGGTTTAAGGT-TTGTAAATTCG-G
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTT-CATCTTCGAT
** * * **
3988976 CTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATTTTTTAT
1 C-TGTTACCCTACTGCTTAGGGGGTT-AAGATCTTCATCTTCGAT
* * ** * * *
3989021 CTATTCCCCTACTGCTTAGGGGGTTAAAGCCCATCATATTTGAT
1 CTGTTACCCTACTGCTTAGGGGGTT-AAGATCTTCATCTTCGAT
* * * *
3989065 CTGTTTCCCTACTGCTTAGGGGTTTAAGATCTGTAAATCTTC-AGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCT-T-CATCTTCGA-T
* * * *
3989110 CTGTTACCCTACTGCTTAGGGGGTTAATGCT-TGTAAAT-TTGGCT
1 CTGTTACCCTACTGCTTAGGGGGTTAA-GATCT-T-CATCTTCGAT
** * *
3989154 -TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTTGAT
1 CTGTTACCCTACTGCTTAGGGGGTT-AAGATCTTCATCTTCGAT
*
3989197 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGAT
* * * * * * *
3989240 CTGTTTCCCTACTTCTTAGGGAGATAAGATCTGCA-ATTCGGT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGAT
* * * *
3989282 CTGTTACCCTACCGATTAGGGGTTTAAGACCCTTCATCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGA-TCTTCATCTTCGAT
* * *
3989326 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTC-AGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCT-T-CATCTTCGA-T
* * * *
3989371 CTGTTACCCTACTGCTTAGGGGGTTAAG-GCTTGTAAAT-TTGGCT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATC-T-T-CATCTTCGAT
** *
3989415 -TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGGTT-AAGATCTTCATCTTCGAT
*
3989458 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGAT
* ** * * * * *
3989501 CTGTTTCCCTACTGCTTAGGAAGATGAGATCTACAAT-TCCG-G
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTTC-ATCTTCGAT
* * * *
3989543 CTGTTACCCTACCGATTAGGGGTTTAAGACCCTTCATCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGA-TCTTCATCTTCGAT
* * * *
3989587 CTCTTTCCCTACTGCTTAGGGGGTTAAGATCTATAAATCTTC-AGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCT-T-CATCTTCGA-T
* *
3989632 CTGTTACCCTATTGCTTAGGGGCTTAAG
1 CTGTTACCCTACTGCTTAGGGGGTTAAG
3989660 GCTTGTTAAT
Statistics
Matches: 640, Mismatches: 138, Indels: 71
0.75 0.16 0.08
Matches are distributed among these distances:
42 55 0.09
43 234 0.37
44 209 0.33
45 140 0.22
46 2 0.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (43 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGAT
Found at i:3989829 original size:66 final size:66
Alignment explanation
Indices: 3989723--3989849 Score: 227
Period size: 66 Copynumber: 1.9 Consensus size: 66
3989713 TCTATGCTTA
*
3989723 TGTCAAATGATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
1 TGTCAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
3989788 G
66 G
**
3989789 TGTCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAGATGTGTTAT
1 TGTCAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAACTAGATGTGTTAT
3989850 TATATGAATG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (66 bp):
TGTCAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
G
Found at i:3991003 original size:10 final size:10
Alignment explanation
Indices: 3990966--3991026 Score: 59
Period size: 10 Copynumber: 5.9 Consensus size: 10
3990956 CTAGCTTCTC
*
3990966 TTTTTTTCTG
1 TTTTTTTTTG
3990976 CTTTTTTTTTAG
1 -TTTTTTTTT-G
**
3990988 AATTTTTTTG
1 TTTTTTTTTG
3990998 TTTTTTTTTG
1 TTTTTTTTTG
* *
3991008 TGTTTTTGTG
1 TTTTTTTTTG
3991018 TTTTTTTTT
1 TTTTTTTTT
3991027 TGCCTTTGCC
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
10 24 0.60
11 15 0.38
12 1 0.03
ACGTcount: A:0.05, C:0.03, G:0.11, T:0.80
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:3993853 original size:19 final size:20
Alignment explanation
Indices: 3993829--3993875 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
3993819 AGTGAAAGTT
3993829 TAATGCAAATGT-TGCAATG
1 TAATGCAAATGTATGCAATG
*
3993848 TAATGCAAATGTATGGAATG
1 TAATGCAAATGTATGCAATG
3993868 -AATGCAAA
1 TAATGCAAA
3993876 AGAAAGGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGTATGCAATG
Found at i:3996343 original size:2 final size:2
Alignment explanation
Indices: 3996305--3996334 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3996295 ACAATAATAC
3996305 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3996335 GTGTATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3996771 original size:26 final size:26
Alignment explanation
Indices: 3996734--3996869 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
3996724 TGATACAAAT
* *
3996734 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
3996760 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
3996786 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
3996812 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
3996838 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
3996864 TGATAA
1 TGATAA
3996870 GAATATCATG
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:3999644 original size:3 final size:3
Alignment explanation
Indices: 3999636--3999683 Score: 53
Period size: 3 Copynumber: 15.0 Consensus size: 3
3999626 AATAGGGGTG
3999636 ATA ATA ATA ATA ATA ATA CA-A ATA ATA ATA CATA TATA TATA ATA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA -ATA -ATA -ATA ATA ATA
3999684 GTAGTTAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
2 1 0.02
3 29 0.71
4 11 0.27
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3999771 original size:3 final size:3
Alignment explanation
Indices: 3999759--3999843 Score: 63
Period size: 3 Copynumber: 28.0 Consensus size: 3
3999749 AGGACATATT
3999759 TAA T-A TAA TAA TAA T-A TAAA TAA TAA TATA TACA TGAGA -AA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA-A TA-A T-A-A TAA TAA
* *
3999803 TAA TAA TAA T-A TAAA TAA TAG TAA AAA TAA TAA -AA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3999844 AACAAAGCTC
Statistics
Matches: 67, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
2 9 0.13
3 47 0.70
4 9 0.13
5 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:3999782 original size:12 final size:12
Alignment explanation
Indices: 3999759--3999840 Score: 71
Period size: 12 Copynumber: 6.7 Consensus size: 12
3999749 AGGACATATT
3999759 TAATAT-AATAA
1 TAATATAAATAA
3999770 TAATATAAATAA
1 TAATATAAATAA
3999782 TAATATATACATGAGA
1 TAATATA-A-AT-A-A
3999798 -AATA-ATAATAA
1 TAATATA-AATAA
3999809 TAATATAAATAA
1 TAATATAAATAA
* *
3999821 TAGTAAAAATAA
1 TAATATAAATAA
*
3999833 TAAAATAA
1 TAATATAA
3999841 TAAAACAAAG
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
11 7 0.12
12 37 0.63
13 4 0.07
14 5 0.08
15 5 0.08
16 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (12 bp):
TAATATAAATAA
Found at i:3999802 original size:21 final size:18
Alignment explanation
Indices: 3999763--3999843 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
3999753 CATATTTAAT
*
3999763 ATAATAATAATATAAATA
1 ATAATAATAATAGAAATA
3999781 ATAATATATACATGAGAAATA
1 ATAATA-ATA-AT-AGAAATA
*
3999802 ATAATAATAATATAAATA
1 ATAATAATAATAGAAATA
* *
3999820 ATAGTAAAAATA-ATAA-A
1 ATAATAATAATAGA-AATA
3999837 ATAATAA
1 ATAATAA
3999844 AACAAAGCTC
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
17 8 0.15
18 24 0.44
19 5 0.09
20 5 0.09
21 12 0.22
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (18 bp):
ATAATAATAATAGAAATA
Found at i:3999831 original size:27 final size:27
Alignment explanation
Indices: 3999759--3999844 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
3999749 AGGACATATT
* *
3999759 TAATAT-AATAATAATATAAATAATAA
1 TAATATAAATAATAGTAAAAATAATAA
* *
3999785 T-ATATACAT--GAG-AAATAATAATAA
1 TAATATAAATAATAGTAAA-AATAATAA
3999809 TAATATAAATAATAGTAAAAATAATAA
1 TAATATAAATAATAGTAAAAATAATAA
3999836 -AATAATAAA
1 TAAT-ATAAA
3999845 ACAAAGCTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
23 2 0.04
24 10 0.21
25 11 0.23
26 6 0.13
27 15 0.32
28 3 0.06
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (27 bp):
TAATATAAATAATAGTAAAAATAATAA
Found at i:4000213 original size:24 final size:23
Alignment explanation
Indices: 4000177--4000243 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
4000167 CTTCTTTTCC
*
4000177 AAAAAAA-CACCTCCAAAAAAACA
1 AAAAAAACCTCCTCCAAAAAAA-A
*
4000200 AAAAAAACCTCCTCCAAAATAAA
1 AAAAAAACCTCCTCCAAAAAAAA
* * *
4000223 GAACAATCCTCCTCCAAAAAA
1 AAAAAAACCTCCTCCAAAAAA
4000244 CTAAAAACCC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
23 25 0.68
24 12 0.32
ACGTcount: A:0.60, C:0.28, G:0.01, T:0.10
Consensus pattern (23 bp):
AAAAAAACCTCCTCCAAAAAAAA
Found at i:4000359 original size:13 final size:13
Alignment explanation
Indices: 4000324--4000367 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
4000314 GGGTGGTTTA
*
4000324 GGTGGCCAAGGGT
1 GGTGGCCAAGGTT
4000337 GGTGG---A-GTT
1 GGTGGCCAAGGTT
4000346 GGTGGCCAAGGTT
1 GGTGGCCAAGGTT
4000359 GGTGGCCAA
1 GGTGGCCAA
4000368 CAAAGGTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
9 7 0.27
10 1 0.04
12 1 0.04
13 17 0.65
ACGTcount: A:0.16, C:0.14, G:0.50, T:0.20
Consensus pattern (13 bp):
GGTGGCCAAGGTT
Found at i:4000797 original size:44 final size:44
Alignment explanation
Indices: 4000689--4001263 Score: 428
Period size: 44 Copynumber: 13.1 Consensus size: 44
4000679 CTTCAATGTT
* *
4000689 TTCAACTTGTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATC
1 TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAAT-CTGATATC
** * * * * * * *
4000732 TTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATC
1 TTCAATTTG-TTCCCTATAAGCACAGGGATGCCAAATCTGATATC
* * * * *
4000777 TTCGATTTGCTCCCTATAAGCACAGGGATGCCAAATCTGCTGTT
1 TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAATCTGATATC
* * *
4000821 TTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTT
1 TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAATCTGATATC
* *
4000865 TTCAACTTGTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATC
1 TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAAT-CTGATATC
** * * * * * * *
4000908 TTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGTTATC
1 TTCAATTTG-TTCCCTATAAGCACAGGGATGCCAAATCTGATATC
** * * * *
4000953 TTTGATTTGTTCCCTAAAAGCACAAGGATGCCAAATCTGATGTT
1 TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAATCTGATATC
* * *
4000997 TTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTT
1 TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAATCTGATATC
* * *
4001041 TTCAACTTGTTCCCTATAAGCACATGGATGCC--ATGCTGAAATC
1 TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAAT-CTGATATC
** * * * ** * * *
4001084 TTTGATCTGCTTCACTGTAAGCACAGAAATGTCAGATCTGCTATC
1 TTCAATTTG-TTCCCTATAAGCACAGGGATGCCAAATCTGATATC
* * * * *
4001129 TTCGATTTGTTCCCTGTAAGCACAGGGATGCCAAATCTGCTGTT
1 TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAATCTGATATC
* *
4001173 TTCAACTTGTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATC
1 TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAAT-CTGATATC
* * * * * * *
4001216 TTCAATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATC
1 TTCAATTTG-TTCCCTATAAGCACAGGGATGCCAAATCTGATATC
4001261 TTC
1 TTC
4001264 GATCTGCTCC
Statistics
Matches: 424, Mismatches: 93, Indels: 28
0.78 0.17 0.05
Matches are distributed among these distances:
42 6 0.01
43 36 0.08
44 325 0.77
45 49 0.12
46 8 0.02
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (44 bp):
TTCAATTTGTTCCCTATAAGCACAGGGATGCCAAATCTGATATC
Found at i:4000984 original size:176 final size:176
Alignment explanation
Indices: 4000684--4001205 Score: 963
Period size: 176 Copynumber: 3.0 Consensus size: 176
4000674 CTTCACTTCA
4000684 ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
1 ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
*
4000749 TAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGCTCCCTATAAGCACAGGGATGCCAAATC
66 TAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATC
4000814 TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTG
131 TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTG
4000860 ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
1 ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
* * * *
4000925 TAAGCACAGGAATGTCAGATCTGTTATCTTTGATTTGTTCCCTAAAAGCACAAGGATGCCAAATC
66 TAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATC
*
4000990 TGATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTG
131 TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTG
*
4001036 ATGTTTTCAACTTGTTCCCTATAAGCACATGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
1 ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
* *
4001101 TAAGCACAGAAATGTCAGATCTGCTATCTTCGATTTGTTCCCTGTAAGCACAGGGATGCCAAATC
66 TAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATC
4001166 TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCA
131 TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCA
4001206 TGCTGAAATC
Statistics
Matches: 332, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
176 332 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (176 bp):
ATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTG
TAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATC
TGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCTG
Found at i:4001207 original size:132 final size:132
Alignment explanation
Indices: 4001003--4001266 Score: 474
Period size: 132 Copynumber: 2.0 Consensus size: 132
4000993 TGTTTTCAAC
*
4001003 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACATGG
1 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGG
**
4001068 ATGCCATGCTGAAATCTTTGATCTGCTTCACTGTAAGCACAGAAATGTCAGATCTGCTATCTTCG
66 ATGCCATGCTGAAATCTTCAATCTGCTTCACTGTAAGCACAGAAATGTCAGATCTGCTATCTTCG
4001133 AT
131 AT
* *
4001135 TTGTTCCCTGTAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGG
1 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGG
*
4001200 ATGCCATGCTGAAATCTTCAATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
66 ATGCCATGCTGAAATCTTCAATCTGCTTCACTGTAAGCACAGAAATGTCAGATCTGCTATCTTCG
4001265 AT
131 AT
4001267 CTGCTCCTCT
Statistics
Matches: 126, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 126 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (132 bp):
TTGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGG
ATGCCATGCTGAAATCTTCAATCTGCTTCACTGTAAGCACAGAAATGTCAGATCTGCTATCTTCG
AT
Found at i:4001399 original size:68 final size:68
Alignment explanation
Indices: 4001317--4001515 Score: 262
Period size: 68 Copynumber: 2.9 Consensus size: 68
4001307 TCTTCTTCCA
* * *
4001317 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCTCTCCAATGCCATTTCTGGAAGAAGAGGT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCTCTCCAATGCCATTTCAGGAAGAAAAGAT
*
4001382 -TT
66 CCT
*
4001384 GCTGAAACTTCAAGGAGATCTGTTGTGGCTTTTAGCCGT-TCC-ATCGCCATTTCAGGAAGAAAA
1 -CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCC-TCTCCAAT-GCCATTTCAGGAAGAAAA
4001447 GATCCT
63 GATCCT
* * * *
4001453 CTAAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAATGCCATTTCAGGGA-AAAAGA
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCTCTCCAATGCCATTTCAGGAAGAAAAGA
4001516 AATTTGTAAT
Statistics
Matches: 116, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
67 8 0.07
68 104 0.90
69 4 0.03
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (68 bp):
CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCTCTCCAATGCCATTTCAGGAAGAAAAGAT
CCT
Found at i:4001645 original size:43 final size:43
Alignment explanation
Indices: 4001571--4002390 Score: 442
Period size: 43 Copynumber: 18.8 Consensus size: 43
4001561 GCCCATCATC
* * * *
4001571 TTCGATCTATTTCCCAACTGCTTAAGGGGTTAAGATCTGTAAA
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA
* * * *
4001614 TTCAACCTGTTACCCTACTGGTTAGGGGGTTAAGATTTGTAAA
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA
* * * *
4001657 TCTTC-AGCCTGTTACCCTACTGCTTAGGGGTTTAAGGTTTGTAAA
1 --TTCGA-TCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA
* ** * **
4001702 TTCG-GCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCAT-CATT
1 TTCGATC-TGTTACCCTACTGCTTAGGGGGTT-AAGATC-TGTAAA
** * * ** * **
4001746 TTTTATCTATTTCCCTACTGCTTAGGGGGTTAAAGCCCAT-CATC
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTT-AAGATC-TGTAAA
* * *
4001790 TTTGATCTGTTTCCCTACTGCTTAGGAGGTTAAGATCTGTAAA
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA
* *
4001833 TCTTC-AGCCTGTTACCCTACTGCTTAGGGGGTTAAG-GCTTGTAAA
1 --TTCGA-TCTGTTACCCTACTGCTTAGGGGGTTAAGATC-TGTAAA
* * ** * **
4001878 TTTG-GCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCAT-CATC
1 TTCGATC-TGTTACCCTACTGCTTAGGGGGTT-AAGATC-TGTAAA
* * **
4001922 TTCGATCTATTTCCCTACTGCTTAGGGGGTTAAGATCT-TCATC
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGT-AAA
* * * * *
4001965 TTCGATCTGTTTCCCTACTTCTTAGGGAGATAAGATCTG-CAA
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA
* * * * * *
4002007 TTCGGTCTGTTACCCTACCGATTAGGGGTTTAAGACCCTTCGT--C
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGA-TC-T-GTAAA
*
4002051 TTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAA
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA
* *
4002094 TCTTC-AGCCTGTTACCCTACTGCTTAGGGGGTTAAG-GCTTGTAAA
1 --TTCGA-TCTGTTACCCTACTGCTTAGGGGGTTAAGATC-TGTAAA
* * * ** * **
4002139 TTTG-GCTTGTTACCCTACTTCTTAGGGGGTTAAAGCCCAT-CATC
1 TTCGATC-TGTTACCCTACTGCTTAGGGGGTT-AAGATC-TGTAAA
* **
4002183 TTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-TCATC
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGT-AAA
* * * *
4002226 TTCGATCTGTTTCCCTACTGCTTAGGGAGATGAGATC--TACAA
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTA-AA
* * * * * *
4002268 TTCGGTCTGTTACCCTACCGATTAGGGGTTTAAGACCCTTCGT--C
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGA-TC-T-GTAAA
*
4002312 TTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAA
1 TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA
* * *
4002355 TCTTC-AGCCTGTTACCCTATTGCTTAGGGGCTTAAG
1 --TTCGA-TCTGTTACCCTACTGCTTAGGGGGTTAAG
4002391 GCTTGTGAAT
Statistics
Matches: 610, Mismatches: 120, Indels: 92
0.74 0.15 0.11
Matches are distributed among these distances:
41 5 0.01
42 63 0.10
43 203 0.33
44 193 0.32
45 145 0.24
47 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (43 bp):
TTCGATCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA
Found at i:4001851 original size:176 final size:173
Alignment explanation
Indices: 4001534--4002402 Score: 685
Period size: 176 Copynumber: 5.0 Consensus size: 173
4001524 ATTTCTAGCC
* * * * *
4001534 TGTTACCCTACTACTTAGGGGTTTAAGGCCCATCATCTTCGATCTATTTCCCAACTGCTTAAGGG
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCTACTGCTTAGGGG
* ** * * * * *
4001599 GTTAAGATCTGTAAATTCAACCTGTTACCCTACTGGTTAGGGGGTTAAGATTTGTAAATCTTCAG
66 GTTAAGATCT-CATCTTCGATCTGTTTCCCTACTGCTTA-GGGGTTAAGATCTGTAAATCTTCAG
*
4001664 CCTGTTACCCTACTGCTTAGGGGTTTAAGGTTTGTAAATTCGGCT
129 CCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTGTAAATTCGGCT
* **
4001709 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATTTTTTATCTATTTCCCTACTGCTTAGGGG
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCTACTGCTTAGGGG
** *
4001774 GTTAAAGCCCATCATCTTTGATCTGTTTCCCTACTGCTTAGGAGGTTAAGATCTGTAAATCTTCA
66 GTT-AAGATC-TCATCTTCGATCTGTTTCCCTACTGCTTAGG-GGTTAAGATCTGTAAATCTTCA
* *
4001839 GCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTGGCT
128 GCCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTGTAAATTCGGCT
4001885 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCTACTGCTTAGGGG
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCTACTGCTTAGGGG
* * * *
4001950 GTTAAGATCTTCATCTTCGATCTGTTTCCCTACTTCTTAGGGAGATAAGATCTG-CAA--TTCGG
66 GTTAAGATC-TCATCTTCGATCTGTTTCCCTACTGCTTAGGG-GTTAAGATCTGTAAATCTTCAG
* * * * * *
4002012 TCTGTTACCCTACCGATTAGGGGTTTAAGACCCTTCGT--CTTC-GAT
129 CCTGTTACCCTACTGCTTAGGGGTTTAAG--GCTT-GTAAATTCGGCT
* * ** * * * *
4002057 CTGTTTCCCTACTGCTTAGGGGGTT-AAGATCTGTAAATCTTC-AGCCTGTTACCCTACTGCTTA
1 -TGTTACCCTACTGCTTAGGGGGTTAAAG-CCCAT-CATCTTCGA-TCTATTTCCCTACTGCTTA
* * * * * * * * ** *
4002120 GGGGGTTAAGGCTTGTAAAT-TTGGCT-TGTTACCCTACTTCTTAGGGGGTTAA-AGC-CCATCA
62 GGGGGTTAA-G-ATCT-CATCTTCGATCTGTTTCCCTACTGCTTA-GGGGTTAAGATCTGTA-AA
* * * * * ** *
4002181 TCTTC-GATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTT-CATCTTC-GAT
122 TCTTCAG-CCTGTTACCCTACTGCTTAGGGGTTTAAG-GCTTGTAAATTCGGCT
* * * * ** * * * * * *
4002232 CTGTTTCCCTACTGCTTAGGGAGAT-GAGATC-TACA-ATTCGGTCTGTTACCCTACCGATTAGG
1 -TGTTACCCTACTGCTTAGGGGGTTAAAGCCCAT-CATCTTCGATCTATTTCCCTACTGCTTAGG
* * *
4002294 GGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTT
64 GGGTTAAGA-TC-TCATCTTCGATCTGTTTCCCTACTGCTTA-GGGGTTAAGATCTGTAAATCTT
* * *
4002359 CAGCCTGTTACCCTATTGCTTAGGGGCTTAAGGCTTGTGAATTC
126 CAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTGTAAATTC
4002403 ACTGATTCTA
Statistics
Matches: 561, Mismatches: 102, Indels: 63
0.77 0.14 0.09
Matches are distributed among these distances:
171 2 0.00
172 66 0.12
173 60 0.11
174 94 0.17
175 154 0.27
176 184 0.33
177 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (173 bp):
TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCTACTGCTTAGGGG
GTTAAGATCTCATCTTCGATCTGTTTCCCTACTGCTTAGGGGTTAAGATCTGTAAATCTTCAGCC
TGTTACCCTACTGCTTAGGGGTTTAAGGCTTGTAAATTCGGCT
Found at i:4002064 original size:129 final size:132
Alignment explanation
Indices: 4001771--4002402 Score: 747
Period size: 129 Copynumber: 4.8 Consensus size: 132
4001761 TACTGCTTAG
* * *
4001771 GGGGTTAAAG-CCCATCATCTTTGATCTGTTTCCCTACTGCTTAGGAGGTTAAGATCTGTAAATC
1 GGGGTTTAAGACCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
* * * * *
4001835 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCT
66 TTCAGCCTGTTACCCTACTGCTTAGGGAGATAAGGCTTGTAAATTCGGCTTGTTACCCTACCGAT
4001900 TA
131 TA
* * *
4001902 GGGGGTTAA-AGCCCATCATCTTCGATCTATTTCCCTACTGCTTAGGGGGTTAAGATCT-T-CAT
1 GGGGTTTAAGA-CCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAAT
* * * * *
4001964 CTTC-GATCTGTTTCCCTACTTCTTAGGGAGATAA-GATCTG-CAATTCGG-TCTGTTACCCTAC
65 CTTCAG-CCTGTTACCCTACTGCTTAGGGAGATAAGGCT-TGTAAATTCGGCT-TGTTACCCTAC
4002025 CGATTA
127 CGATTA
* *
4002031 GGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
1 GGGGTTTAAGACCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
* * * ***
4002096 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTTCT
66 TTCAGCCTGTTACCCTACTGCTTAGGGAGATAAGGCTTGTAAATTCGGCTTGTTACCCTACCGAT
4002161 TA
131 TA
* *
4002163 GGGGGTTAA-AGCCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-T-CAT
1 GGGGTTTAAGA-CCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAAT
* * * * *
4002225 CTTC-GATCTGTTTCCCTACTGCTTAGGGAGATGA-G-ATCTACAATTCGG-TCTGTTACCCTAC
65 CTTCAG-CCTGTTACCCTACTGCTTAGGGAGATAAGGCTTGTA-AATTCGGCT-TGTTACCCTAC
4002286 CGATTA
127 CGATTA
* *
4002292 GGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
1 GGGGTTTAAGACCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
* * *
4002357 TTCAGCCTGTTACCCTATTGCTTAGGG-GCTTAAGGCTTGTGAATTC
66 TTCAGCCTGTTACCCTACTGCTTAGGGAG-ATAAGGCTTGTAAATTC
4002403 ACTGATTCTA
Statistics
Matches: 419, Mismatches: 59, Indels: 45
0.80 0.11 0.09
Matches are distributed among these distances:
128 5 0.01
129 151 0.36
130 65 0.16
131 68 0.16
132 127 0.30
133 3 0.01
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.36
Consensus pattern (132 bp):
GGGGTTTAAGACCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
TTCAGCCTGTTACCCTACTGCTTAGGGAGATAAGGCTTGTAAATTCGGCTTGTTACCCTACCGAT
TA
Found at i:4002097 original size:261 final size:261
Alignment explanation
Indices: 4001771--4002401 Score: 1138
Period size: 261 Copynumber: 2.4 Consensus size: 261
4001761 TACTGCTTAG
* * * * *
4001771 GGGGTTAAAG-CCCATCATCTTTGATCTGTTTCCCTACTGCTTAGGAGGTTAAGATCTGTAAATC
1 GGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
4001835 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCT
66 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCT
4001900 TAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCTACTGCTTAGGGGGTTAAGATCTTCATC
131 TAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCTACTGCTTAGGGGGTTAAGATCTTCATC
* *
4001965 TTCGATCTGTTTCCCTACTTCTTAGGGAGATAAGATCTGCAATTCGGTCTGTTACCCTACCGATT
196 TTCGATCTGTTTCCCTACTGCTTAGGGAGATAAGATCTACAATTCGGTCTGTTACCCTACCGATT
4002030 A
261 A
4002031 GGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
1 GGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
*
4002096 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTTCT
66 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCT
*
4002161 TAGGGGGTTAAAGCCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATC
131 TAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCTACTGCTTAGGGGGTTAAGATCTTCATC
*
4002226 TTCGATCTGTTTCCCTACTGCTTAGGGAGATGAGATCTACAATTCGGTCTGTTACCCTACCGATT
196 TTCGATCTGTTTCCCTACTGCTTAGGGAGATAAGATCTACAATTCGGTCTGTTACCCTACCGATT
4002291 A
261 A
4002292 GGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
1 GGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
* * *
4002357 TTCAGCCTGTTACCCTATTGCTTAGGGGCTTAAGGCTTGTGAATT
66 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATT
4002402 CACTGATTCT
Statistics
Matches: 357, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
260 9 0.03
261 348 0.97
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.36
Consensus pattern (261 bp):
GGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATC
TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAATTTGGCTTGTTACCCTACTGCT
TAGGGGGTTAAAGCCCATCATCTTCGATCTATTTCCCTACTGCTTAGGGGGTTAAGATCTTCATC
TTCGATCTGTTTCCCTACTGCTTAGGGAGATAAGATCTACAATTCGGTCTGTTACCCTACCGATT
A
Found at i:4002560 original size:66 final size:66
Alignment explanation
Indices: 4002454--4002580 Score: 236
Period size: 66 Copynumber: 1.9 Consensus size: 66
4002444 TCTATGCTTA
*
4002454 TGTCAAATGATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
1 TGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
4002519 G
66 G
*
4002520 TGTCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAGATGTGTTAT
1 TGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTAT
4002581 TATATGAATG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (66 bp):
TGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
G
Found at i:4003732 original size:21 final size:21
Alignment explanation
Indices: 4003708--4003758 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
4003698 TTTTTTCCGC
*
4003708 TTTTTTTTTAGAATTTTTTTG
1 TTTTTTTTTAGAATTTTTGTG
* **
4003729 TTTTTTTTTTGTGTTTTTGTG
1 TTTTTTTTTAGAATTTTTGTG
4003750 TTTTTTTTT
1 TTTTTTTTT
4003759 TTTTTGCCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.06, C:0.00, G:0.12, T:0.82
Consensus pattern (21 bp):
TTTTTTTTTAGAATTTTTGTG
Found at i:4006584 original size:19 final size:20
Alignment explanation
Indices: 4006560--4006606 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
4006550 AGTGAAAGTT
4006560 TAATGCAAATGT-TGCAATG
1 TAATGCAAATGTATGCAATG
*
4006579 TAATGCAAATGTATGGAATG
1 TAATGCAAATGTATGCAATG
4006599 -AATGCAAA
1 TAATGCAAA
4006607 AGAAAGGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGTATGCAATG
Found at i:4009048 original size:2 final size:2
Alignment explanation
Indices: 4009041--4009074 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
4009031 ACAATAATAC
* *
4009041 TA TA TA TA AA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4009075 ATAGAAATAC
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:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4009177 original size:39 final size:40
Alignment explanation
Indices: 4009089--4009191 Score: 97
Period size: 39 Copynumber: 2.6 Consensus size: 40
4009079 AAATACACAC
* * *
4009089 TACTATATAATAATAATAAATATAGAAATATAAAAAGCAA
1 TACTATATAAAAATATTAAATATAGAAATATAAAAAACAA
*
4009129 -A-TATAATAAAAATATTAAAT-TA-AAGTAATAAAAAACAA
1 TACTAT-ATAAAAATATTAAATATAGAAAT-ATAAAAAACAA
* *
4009167 TACTATATAAATATATATATATATA
1 TACTATATAAAAATAT-TAAATATA
4009192 CATAAAAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
37 3 0.06
38 15 0.29
39 24 0.47
40 7 0.14
41 2 0.04
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (40 bp):
TACTATATAAAAATATTAAATATAGAAATATAAAAAACAA
Found at i:4009313 original size:3 final size:3
Alignment explanation
Indices: 4009305--4009360 Score: 51
Period size: 3 Copynumber: 17.0 Consensus size: 3
4009295 AATAGGGGTG
4009305 ATA ATA ATA ATA ATA ATA CA-A ATA ATA ATA CATA TATA TATA TATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA -ATA -ATA -ATA -ATA
4009351 TATA ATA ATA
1 -ATA ATA ATA
4009361 GTAGTTAGAA
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
2 1 0.02
3 29 0.59
4 19 0.39
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:4009320 original size:12 final size:13
Alignment explanation
Indices: 4009305--4009360 Score: 62
Period size: 12 Copynumber: 4.2 Consensus size: 13
4009295 AATAGGGGTG
4009305 ATAATA-ATAATA
1 ATAATACATAATA
4009317 ATAATACA-AATA
1 ATAATACATAATA
4009329 ATAATACATATATA
1 ATAATACATA-ATA
*
4009343 TATATATATATAATA
1 -ATA-ATACATAATA
4009358 ATA
1 ATA
4009361 GTAGTTAGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
12 18 0.47
13 2 0.05
14 6 0.16
15 6 0.16
16 6 0.16
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAATACATAATA
Found at i:4009447 original size:3 final size:3
Alignment explanation
Indices: 4009434--4009519 Score: 65
Period size: 3 Copynumber: 28.3 Consensus size: 3
4009424 GAGGGCATAT
4009434 ATA AT- ATA ATA ATA AT- ATAA ATA ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A -ATA ATA
* *
4009478 ATA ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4009520 AACAAAGCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
2 9 0.13
3 48 0.71
4 9 0.13
5 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:4009458 original size:12 final size:12
Alignment explanation
Indices: 4009434--4009516 Score: 73
Period size: 12 Copynumber: 6.8 Consensus size: 12
4009424 GAGGGCATAT
4009434 ATAATAT-AATA
1 ATAATATAAATA
4009445 ATAATATAAATA
1 ATAATATAAATA
4009457 ATAATATATACATGA
1 ATAATATA-A-AT-A
4009472 GA-AATA-ATAATA
1 -ATAATATA-AATA
4009484 ATAATATAAATA
1 ATAATATAAATA
* *
4009496 ATAGTAAAAATA
1 ATAATATAAATA
*
4009508 ATAAAATAA
1 ATAATATAA
4009517 TAAAACAAAG
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
11 8 0.13
12 37 0.62
13 4 0.07
14 5 0.08
15 5 0.08
16 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (12 bp):
ATAATATAAATA
Found at i:4009507 original size:27 final size:27
Alignment explanation
Indices: 4009434--4009520 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 27
4009424 GAGGGCATAT
* *
4009434 ATAATAT-AATAATAATATAAATAATA
1 ATAATATAAATAATAGTAAAAATAATA
* *
4009460 AT-ATATACAT--GAG-AAATAATAATA
1 ATAATATAAATAATAGTAAA-AATAATA
4009484 ATAATATAAATAATAGTAAAAATAATA
1 ATAATATAAATAATAGTAAAAATAATA
4009511 A-AATAATAAA
1 ATAAT-ATAAA
4009521 ACAAAGCTCT
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
23 2 0.04
24 10 0.21
25 11 0.23
26 7 0.15
27 15 0.31
28 3 0.06
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (27 bp):
ATAATATAAATAATAGTAAAAATAATA
Found at i:4009872 original size:21 final size:22
Alignment explanation
Indices: 4009848--4009927 Score: 76
Period size: 22 Copynumber: 3.6 Consensus size: 22
4009838 ACCTTCTTTC
4009848 CAAAAAAA-CACCTCCAAAAAA
1 CAAAAAAACCACCTCCAAAAAA
*
4009869 CAAAAAAACCTCCTCC--AAAA
1 CAAAAAAACCACCTCCAAAAAA
*
4009889 CAAAGAACAATCCTCCTCCAAAAAA
1 CAAA-AA-AA-CCACCTCCAAAAAA
* *
4009914 CCAAAAACCCACCT
1 CAAAAAAACCACCT
4009928 AAAAACAAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
20 8 0.16
21 10 0.20
22 13 0.27
23 9 0.18
24 2 0.04
25 7 0.14
ACGTcount: A:0.55, C:0.35, G:0.01, T:0.09
Consensus pattern (22 bp):
CAAAAAAACCACCTCCAAAAAA
Found at i:4009888 original size:20 final size:23
Alignment explanation
Indices: 4009865--4009911 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
4009855 ACACCTCCAA
4009865 AAAACAAA-AA-AA-CCTCCTCC
1 AAAACAAAGAACAATCCTCCTCC
4009885 AAAACAAAGAACAATCCTCCTCC
1 AAAACAAAGAACAATCCTCCTCC
4009908 AAAA
1 AAAA
4009912 AACCAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 8 0.33
21 2 0.08
22 2 0.08
23 12 0.50
ACGTcount: A:0.55, C:0.32, G:0.02, T:0.11
Consensus pattern (23 bp):
AAAACAAAGAACAATCCTCCTCC
Found at i:4010489 original size:2 final size:2
Alignment explanation
Indices: 4010482--4010508 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4010472 CATAAGATAA
4010482 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
4010509 TTTGCAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4012498 original size:25 final size:25
Alignment explanation
Indices: 4012436--4012599 Score: 99
Period size: 24 Copynumber: 6.6 Consensus size: 25
4012426 ACACACTACA
* * * *
4012436 GCTCTTATGAGCATCTCGTTATTTG
1 GCTCTTATGAGCTTCCCGATAATTG
* * *
4012461 GCTTCTCACGAGCTTCCCGATAATTA
1 GC-TCTTATGAGCTTCCCGATAATTG
**
4012487 GCTCTTATGAGCTTCTTGATTAA-TG
1 GCTCTTATGAGCTTCCCGA-TAATTG
***
4012512 GCTCTCCGGAGCTTCCCGAT-ATTG
1 GCTCTTATGAGCTTCCCGATAATTG
**
4012536 GCTCGCATGAGCTTCCC-A-AATTTG
1 GCTCTTATGAGCTTCCCGATAA-TTG
*
4012560 GCTCTCT-TGAGCTTCCCGTTAA-TG
1 GCTCT-TATGAGCTTCCCGATAATTG
4012584 GCT-TGTATGAGCTTCC
1 GCTCT-TATGAGCTTCC
4012600 TGATGATTAG
Statistics
Matches: 106, Mismatches: 24, Indels: 19
0.71 0.16 0.13
Matches are distributed among these distances:
23 5 0.05
24 48 0.45
25 30 0.28
26 23 0.22
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (25 bp):
GCTCTTATGAGCTTCCCGATAATTG
Found at i:4012514 original size:51 final size:49
Alignment explanation
Indices: 4012435--4012550 Score: 128
Period size: 51 Copynumber: 2.3 Consensus size: 49
4012425 GACACACTAC
* *
4012435 AGCTCTTATGAGCATCTCGTTATTTGGCTTCTCAC-GAGCTTCCCGATAATT
1 AGCTCTTATGAGCTTCTCGTTATATGGC-TCTC-CGGAGCTTCCCGAT-ATT
*
4012486 AGCTCTTATGAGCTTCTTGATTA-ATGGCTCTCCGGAGCTTCCCGATATT
1 AGCTCTTATGAGCTTCTCG-TTATATGGCTCTCCGGAGCTTCCCGATATT
* **
4012535 GGCTCGCATGAGCTTC
1 AGCTCTTATGAGCTTC
4012551 CCAAATTTGG
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
49 17 0.30
50 16 0.28
51 21 0.37
52 3 0.05
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (49 bp):
AGCTCTTATGAGCTTCTCGTTATATGGCTCTCCGGAGCTTCCCGATATT
Found at i:4012547 original size:24 final size:24
Alignment explanation
Indices: 4012458--4012623 Score: 102
Period size: 24 Copynumber: 6.8 Consensus size: 24
4012448 ATCTCGTTAT
*
4012458 TTGGCTTCTCACGAGCTTCCCGATAA
1 TTGGC-TCTCATGAGCTTCCCGAT-A
* * **
4012484 TTAGCTCTTATGAGCTTCTTGATTA
1 TTGGCTCTCATGAGCTTCCCGA-TA
* **
4012509 ATGGCTCTCCGGAGCTTCCCGATA
1 TTGGCTCTCATGAGCTTCCCGATA
* *
4012533 TTGGCTCGCATGAGCTTCCC-AAA
1 TTGGCTCTCATGAGCTTCCCGATA
* *
4012556 TTTGGCTCTCTTGAGCTTCCCGTTA
1 -TTGGCTCTCATGAGCTTCCCGATA
* * *
4012581 ATGGCT-TGTATGAGCTTCCTGATGA
1 TTGGCTCT-CATGAGCTTCCCGAT-A
* * *
4012606 TTAGCTCACAAGAGCTTC
1 TTGGCTCTCATGAGCTTC
4012624 TAGTTATACA
Statistics
Matches: 103, Mismatches: 31, Indels: 13
0.70 0.21 0.09
Matches are distributed among these distances:
23 3 0.03
24 52 0.50
25 43 0.42
26 5 0.05
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (24 bp):
TTGGCTCTCATGAGCTTCCCGATA
Found at i:4013020 original size:19 final size:19
Alignment explanation
Indices: 4012996--4013058 Score: 126
Period size: 19 Copynumber: 3.3 Consensus size: 19
4012986 TAAGTATTCA
4012996 ATGTTTGAATGTGCCTTGC
1 ATGTTTGAATGTGCCTTGC
4013015 ATGTTTGAATGTGCCTTGC
1 ATGTTTGAATGTGCCTTGC
4013034 ATGTTTGAATGTGCCTTGC
1 ATGTTTGAATGTGCCTTGC
4013053 ATGTTT
1 ATGTTT
4013059 ATCTTACATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.16, C:0.14, G:0.25, T:0.44
Consensus pattern (19 bp):
ATGTTTGAATGTGCCTTGC
Found at i:4017156 original size:38 final size:38
Alignment explanation
Indices: 4017059--4017186 Score: 123
Period size: 40 Copynumber: 3.3 Consensus size: 38
4017049 CGAGGTATAA
* * * *
4017059 AACCCGAATATAACACCAGCACGAAGCCTACGGGACTTT
1 AACCCGGATATAATACCAGCACTAAGCCTGCGGGA-TTT
* * *
4017098 AAACTCAGATATAATACCAGCACTAGGCCTGCGGGATTT
1 -AACCCGGATATAATACCAGCACTAAGCCTGCGGGATTT
* *
4017137 AACCCGGATATAATTCCAGCA-TATAGCCTGCGGGTCTTT
1 AACCCGGATATAATACCAGCACTA-AGCCTGCGGG-ATTT
4017176 AAGCCCGGATA
1 AA-CCCGGATA
4017187 CACATCAAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
37 2 0.03
38 27 0.37
39 8 0.11
40 36 0.49
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (38 bp):
AACCCGGATATAATACCAGCACTAAGCCTGCGGGATTT
Found at i:4021387 original size:2 final size:2
Alignment explanation
Indices: 4021382--4021420 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4021372 ATAAATACAA
4021382 AT AT AT 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 AT AT AT A
4021421 AGGAAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4025581 original size:26 final size:26
Alignment explanation
Indices: 4025552--4025601 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
4025542 AAATAATAAA
4025552 TATTATTTTGAGAGTATTTAGGAATT
1 TATTATTTTGAGAGTATTTAGGAATT
4025578 TATTATTTTGAGAGTATTTAGGAA
1 TATTATTTTGAGAGTATTTAGGAA
4025602 CAAAGTTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (26 bp):
TATTATTTTGAGAGTATTTAGGAATT
Found at i:4028667 original size:21 final size:21
Alignment explanation
Indices: 4028643--4028694 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
4028633 TGAAGGTCTC
4028643 ACACGCCCGTGTGCCCACAAA-
1 ACACGCCCGTGTGCCCA-AAAT
** *
4028664 ACACGGTCGTGTGTCCAAAAT
1 ACACGCCCGTGTGCCCAAAAT
*
4028685 ACATGCCCGT
1 ACACGCCCGT
4028695 ATGGGATCTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.27, C:0.35, G:0.21, T:0.17
Consensus pattern (21 bp):
ACACGCCCGTGTGCCCAAAAT
Found at i:4029313 original size:3 final size:3
Alignment explanation
Indices: 4029305--4029365 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
4029295 AAGTTCTAAA
4029305 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4029353 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
4029366 TAAATGGTTA
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):
AAT
Found at i:4032270 original size:19 final size:19
Alignment explanation
Indices: 4032246--4032351 Score: 198
Period size: 19 Copynumber: 5.7 Consensus size: 19
4032236 AATCTTTAAG
4032246 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
4032265 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
4032284 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
4032301 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
4032320 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
4032339 GATATGCAATCTT
1 GATATGCAATCTT
4032352 GAAGATATAA
Statistics
Matches: 85, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
17 17 0.20
19 68 0.80
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:4032276 original size:36 final size:35
Alignment explanation
Indices: 4032236--4032359 Score: 162
Period size: 36 Copynumber: 3.4 Consensus size: 35
4032226 ATGGAAATAT
*
4032236 AATCTTTAAGGATATGCAATCTTAGATATGATATGC
1 AATCTTGAA-GATATGCAATCTTAGATATGATATGC
4032272 AATCTT--AGATATGATACAATCTTAGATATGATATGC
1 AATCTTGAAGATATG---CAATCTTAGATATGATATGC
4032308 AATCTTAGATATGATATGCAATCTTAGATATGATATGC
1 AATCTT-GA-A-GATATGCAATCTTAGATATGATATGC
4032346 AATCTTGAAGATAT
1 AATCTTGAAGATAT
4032360 AATCTTGTAA
Statistics
Matches: 80, Mismatches: 0, Indels: 17
0.82 0.00 0.18
Matches are distributed among these distances:
33 6 0.08
34 1 0.01
35 5 0.06
36 33 0.41
37 2 0.03
38 26 0.32
40 1 0.01
41 6 0.08
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (35 bp):
AATCTTGAAGATATGCAATCTTAGATATGATATGC
Found at i:4032309 original size:55 final size:56
Alignment explanation
Indices: 4032246--4032351 Score: 196
Period size: 55 Copynumber: 1.9 Consensus size: 56
4032236 AATCTTTAAG
4032246 GATATGCAATCTTAGATATGATATGCAATCTTAGATATGATA-CAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCTTAGATATGATAGCAATCTTAGATAT
4032301 GATATGCAATCTTAGATATGATATGCAATCTTAGATATGATATGCAATCTT
1 GATATGCAATCTTAGATATGATATGCAATCTTAGATATGATA-GCAATCTT
4032352 GAAGATATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
55 42 0.86
57 7 0.14
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (56 bp):
GATATGCAATCTTAGATATGATATGCAATCTTAGATATGATAGCAATCTTAGATAT
Found at i:4032373 original size:22 final size:21
Alignment explanation
Indices: 4032346--4032389 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
4032336 TATGATATGC
4032346 AATCTTGAAGATATAATCTTGT
1 AATCTTGAAGATATAAT-TTGT
* *
4032368 AATCTTGGAGATTTAATTTGT
1 AATCTTGAAGATATAATTTGT
4032389 A
1 A
4032390 GATATCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (21 bp):
AATCTTGAAGATATAATTTGT
Found at i:4037820 original size:28 final size:28
Alignment explanation
Indices: 4037751--4037851 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
4037741 GACAAGATTG
* * * *
4037751 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
4037781 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
4037809 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
4037838 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
4037852 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:4044966 original size:28 final size:28
Alignment explanation
Indices: 4044897--4044997 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
4044887 GACAAGATTG
* * * *
4044897 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
4044927 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
4044955 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
4044984 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
4044998 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:4047226 original size:28 final size:28
Alignment explanation
Indices: 4047173--4047256 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
4047163 CACTTTGTGC
4047173 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
* *
4047202 TATTCTAGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* *
4047230 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
4047257 CTGGTGTGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 32 0.65
29 17 0.35
ACGTcount: A:0.20, C:0.04, G:0.30, T:0.46
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:4047491 original size:23 final size:22
Alignment explanation
Indices: 4047461--4047547 Score: 65
Period size: 21 Copynumber: 4.0 Consensus size: 22
4047451 GCTTTACTGA
4047461 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCAC-TTATGTGTCGTATT
* *
4047484 TCAGGCACGTTGTGTGTCGCA--
1 TCAGGCAC-TTATGTGTCGTATT
* * **
4047505 GCAGACACCTCGTGTGTCG--TT
1 TCAGGCA-CTTATGTGTCGTATT
4047526 TCAGGCACTTATGTGTCGTATT
1 TCAGGCACTTATGTGTCGTATT
4047548 CTGATCAGGT
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
20 9 0.18
21 19 0.39
22 3 0.06
23 18 0.37
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (22 bp):
TCAGGCACTTATGTGTCGTATT
Found at i:4058523 original size:21 final size:20
Alignment explanation
Indices: 4058477--4058523 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
4058467 GTGATGAATT
4058477 TATTGAAATTATATTGATTA
1 TATTGAAATTATATTGATTA
*
4058497 -AGTTGATATATATATTGATTA
1 TA-TTGAAAT-TATATTGATTA
4058518 TATTGA
1 TATTGA
4058524 CTAATTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 6 0.26
21 15 0.65
22 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (20 bp):
TATTGAAATTATATTGATTA
Found at i:4063911 original size:4 final size:4
Alignment explanation
Indices: 4063904--4063929 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4063894 GTATGTGTCC
4063904 ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
4063930 AGCTGTTTAA
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:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:4064348 original size:2 final size:2
Alignment explanation
Indices: 4064341--4064387 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
4064331 AAGATACTTT
4064341 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4064383 TA TA T
1 TA TA T
4064388 GGAAAAATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4068833 original size:37 final size:37
Alignment explanation
Indices: 4068721--4068833 Score: 106
Period size: 37 Copynumber: 3.1 Consensus size: 37
4068711 TTAACCTTCT
*
4068721 TTTTTTTACTAAATTAATATTTAGATACTACTTTGTA
1 TTTTTTTACTAAATTAATATTTAGATACTACTTTATA
** * * ***
4068758 TTAGTTTA-TCAAATTAA-ACTAAGA-ACGTTACCAAATA
1 TTTTTTTACT-AAATTAATATTTAGATAC--TACTTTATA
4068795 TTTTTTTACTAAATTAATATTTAGATACTACTTTATA
1 TTTTTTTACTAAATTAATATTTAGATACTACTTTATA
4068832 TT
1 TT
4068834 AGTTTATTAA
Statistics
Matches: 55, Mismatches: 15, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
35 2 0.04
36 6 0.11
37 39 0.71
38 6 0.11
39 2 0.04
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.48
Consensus pattern (37 bp):
TTTTTTTACTAAATTAATATTTAGATACTACTTTATA
Found at i:4068951 original size:59 final size:61
Alignment explanation
Indices: 4068857--4068998 Score: 191
Period size: 59 Copynumber: 2.3 Consensus size: 61
4068847 GTTAAATATA
* * *
4068857 AAATTGGTACCCGAACTTGTCCACTTCTCCTAGATTGATACTTAT-ATTTTTT-TTGTC-C
1 AAATTGGTACCCGAACTTTTTCACTTCTCCCAGATTGATACTTATGATTTTTTGTTGTCTC
* *
4068915 TAGATTGGTACCCGAACTTTTTCACTTCTCCCAGATTGATACTTATGGTTTTTTTGTTGTCTC
1 -AAATTGGTACCCGAACTTTTTCACTTCTCCCAGATTGATACTTAT-GATTTTTTGTTGTCTC
*
4068978 AAATTGGTGCCCGAACTTTTT
1 AAATTGGTACCCGAACTTTTT
4068999 TTCTATCCAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
59 41 0.57
61 6 0.08
62 24 0.33
63 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.44
Consensus pattern (61 bp):
AAATTGGTACCCGAACTTTTTCACTTCTCCCAGATTGATACTTATGATTTTTTGTTGTCTC
Found at i:4069168 original size:19 final size:19
Alignment explanation
Indices: 4069102--4069168 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 19
4069092 TTTATGCCTC
*
4069102 TTTTTTCTTTTTCTTTTCTT
1 TTTTTTC-TTTCCTTTTCTT
* *
4069122 TTTTATT-TTCCCTCCTCTTCCT
1 TTTT-TTCTT---TCCTTTTCTT
4069144 TTTTTTCTTTCCTTTTCTT
1 TTTTTTCTTTCCTTTTCTT
4069163 TTTTTT
1 TTTTTT
4069169 TCCTTTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 11
0.70 0.09 0.21
Matches are distributed among these distances:
19 16 0.43
20 4 0.11
21 4 0.11
22 13 0.35
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTTCTTTCCTTTTCTT
Found at i:4074560 original size:17 final size:18
Alignment explanation
Indices: 4074538--4074572 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4074528 GATATGATAC
*
4074538 TAAAAT-TATTAAAAAAT
1 TAAAATATATAAAAAAAT
4074555 TAAAATATATAAAAAAAT
1 TAAAATATATAAAAAAAT
4074573 CAGGGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATATATAAAAAAAT
Found at i:4074869 original size:23 final size:22
Alignment explanation
Indices: 4074826--4074883 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
4074816 AAAAGGTATC
* *
4074826 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
4074847 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
4074870 TGCATATCATATCT
1 TACAAATCATATCT
4074884 AAGATTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:4074897 original size:22 final size:19
Alignment explanation
Indices: 4074853--4074900 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
4074843 AGATTACAAA
4074853 ATCATATCTTCTAAGATTG
1 ATCATATCTTCTAAGATTG
4074872 --CATATCATATCTAAGATTG
1 ATCATATC-T-TCTAAGATTG
4074891 TATCATATCT
1 -ATCATATCT
4074901 AAGATTGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
17 6 0.25
18 1 0.04
19 10 0.42
21 1 0.04
22 6 0.25
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (19 bp):
ATCATATCTTCTAAGATTG
Found at i:4074923 original size:17 final size:19
Alignment explanation
Indices: 4074862--4074915 Score: 94
Period size: 17 Copynumber: 2.9 Consensus size: 19
4074852 AATCATATCT
4074862 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
4074881 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
4074898 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
4074916 TGAAGATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 17 0.52
19 16 0.48
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:4075334 original size:45 final size:45
Alignment explanation
Indices: 4075265--4075439 Score: 190
Period size: 45 Copynumber: 3.9 Consensus size: 45
4075255 CGATATCTAC
* * * * *
4075265 TATCTTTGATCTGCTCCCTGTCTAATACAGAGACACGAAATCTGT
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATATGT
* * * *
4075310 TATCTTCGATCTACTCCCCATCTAATATAGAGACGCCAAATATGC
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATATGT
* * * * *
4075355 T-TCTTCAATCTGTTCCCCTTCTAATACAGAGATGCCAAATTTGT
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATATGT
* * *
4075399 TATCTCCGATTTGCTCCCCGTCTAATACAGAGATGCCAAAT
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAAT
4075440 CTATCATCTT
Statistics
Matches: 107, Mismatches: 22, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
44 36 0.34
45 71 0.66
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (45 bp):
TATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATATGT
Found at i:4075603 original size:78 final size:78
Alignment explanation
Indices: 4075472--4075766 Score: 423
Period size: 78 Copynumber: 3.8 Consensus size: 78
4075462 ATGTAAACAC
* *
4075472 ATGAAGGTCAGATCTGCTATGTCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTACTATGTCTTTAATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
4075537 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* * * *
4075550 ATGAAGGTCCA-ATCTATTATGTCTTTGATCTGCTCCCCGTCTAATATATAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTACTATGTCTTTAATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
4075614 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* * * * *
4075628 ATGAAAGTCAGATCTGCTGTGTCTTCAATCTGCTCTCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTACTATGTCTTTAATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
4075693 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* * **
4075706 ATGAAGGTCAGATCTACTATGT-TTTCAATCTGCTCTCCGTCGAATATGGAGATGCCAAATC
1 ATGAAGGTCAGATCTACTATGTCTTT-AATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
4075767 TGTTTCTTCG
Statistics
Matches: 194, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
77 4 0.02
78 188 0.97
79 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (78 bp):
ATGAAGGTCAGATCTACTATGTCTTTAATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:4083767 original size:17 final size:18
Alignment explanation
Indices: 4083745--4083779 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4083735 GATATGATAC
*
4083745 TAAAAT-TATTAAAAAAT
1 TAAAATATATAAAAAAAT
4083762 TAAAATATATAAAAAAAT
1 TAAAATATATAAAAAAAT
4083780 CAGGGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATATATAAAAAAAT
Found at i:4084067 original size:22 final size:21
Alignment explanation
Indices: 4084032--4084107 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
4084022 AAAAGGTATC
* *
4084032 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
4084053 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
4084076 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
4084095 TGC-AATCATATCT
1 TACAAATCATATCT
4084108 AAGATTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:4084083 original size:17 final size:19
Alignment explanation
Indices: 4084068--4084156 Score: 134
Period size: 17 Copynumber: 4.9 Consensus size: 19
4084058 AATCATATCT
4084068 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
4084087 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
4084105 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
4084122 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
*
4084139 TCTAAGATTGTATATCAT
1 TCTAAGATTGCATATCAT
4084157 TGAAGATCAT
Statistics
Matches: 67, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 33 0.49
18 16 0.24
19 18 0.27
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:4099112 original size:12 final size:12
Alignment explanation
Indices: 4099095--4099120 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4099085 TGGTGTAATT
4099095 TTTAAAAATCAA
1 TTTAAAAATCAA
4099107 TTTAAAAATCAA
1 TTTAAAAATCAA
4099119 TT
1 TT
4099121 GAATTGATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (12 bp):
TTTAAAAATCAA
Found at i:4102290 original size:105 final size:105
Alignment explanation
Indices: 4102104--4102320 Score: 371
Period size: 105 Copynumber: 2.1 Consensus size: 105
4102094 ATCATTAGAG
4102104 TTCTCACAACTATGAACCTCCATTGATGTTTCAAGAGGAAGTTGATGGAATGGCTTAAGAGGCAT
1 TTCTCACAACTATGAACCTCCATTGATGTTTCAAGAGGAAGTTGATGGAATGGCTTAAGAGGCAT
*
4102169 CTTAAGGAGTTCAACATCAGATTCAAGCATCTTCAAGACC
66 CTCAAGGAGTTCAACATCAGATTCAAGCATCTTCAAGACC
* * * *
4102209 TTCTCACAGCTATGAACCTCCATTGATGTTTCTAGAGGAAGTTGATGGAATGGTTTAGGAGGCAT
1 TTCTCACAACTATGAACCTCCATTGATGTTTCAAGAGGAAGTTGATGGAATGGCTTAAGAGGCAT
*
4102274 CTCAAGGAGTTTAACATCAGATTCAAGCATCTTCAAGACC
66 CTCAAGGAGTTCAACATCAGATTCAAGCATCTTCAAGACC
4102314 TTACTCA
1 TT-CTCA
4102321 TTGAAGGACG
Statistics
Matches: 105, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
105 101 0.96
106 4 0.04
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (105 bp):
TTCTCACAACTATGAACCTCCATTGATGTTTCAAGAGGAAGTTGATGGAATGGCTTAAGAGGCAT
CTCAAGGAGTTCAACATCAGATTCAAGCATCTTCAAGACC
Found at i:4108203 original size:16 final size:17
Alignment explanation
Indices: 4108184--4108216 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4108174 AAAACCAACT
*
4108184 AAACCC-ACTAAGCCTA
1 AAACCCAACAAAGCCTA
4108200 AAACCCAACAAAGCCTA
1 AAACCCAACAAAGCCTA
4108217 CCCACATAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.36, G:0.06, T:0.09
Consensus pattern (17 bp):
AAACCCAACAAAGCCTA
Found at i:4111196 original size:16 final size:17
Alignment explanation
Indices: 4111177--4111209 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4111167 AAAACCAACT
*
4111177 AAACCC-ACTAAGCCTA
1 AAACCCAACAAAGCCTA
4111193 AAACCCAACAAAGCCTA
1 AAACCCAACAAAGCCTA
4111210 CCCACATAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.36, G:0.06, T:0.09
Consensus pattern (17 bp):
AAACCCAACAAAGCCTA
Found at i:4112328 original size:12 final size:12
Alignment explanation
Indices: 4112313--4112342 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4112303 ATTATCCTAT
*
4112313 TTATTATTATCA
1 TTATTATCATCA
4112325 TTATTATCATCA
1 TTATTATCATCA
4112337 TTATTA
1 TTATTA
4112343 ACATATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (12 bp):
TTATTATCATCA
Found at i:4113003 original size:12 final size:12
Alignment explanation
Indices: 4112962--4112996 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
4112952 CGTTTTATGC
4112962 TATTATTATTTA
1 TATTATTATTTA
4112974 TATTATTATTTA
1 TATTATTATTTA
4112986 TATTATTATTT
1 TATTATTATTT
4112997 TTGTTATCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTATTATTTA
Found at i:4125008 original size:87 final size:87
Alignment explanation
Indices: 4124897--4125151 Score: 289
Period size: 87 Copynumber: 2.9 Consensus size: 87
4124887 TGAACTCACA
* * * * *
4124897 AGCCTTAAACCCTTAAGCAGTAGGGTAACAGGCTAAATTCACAGATCTTGTCTCCCTAAGCAGTA
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTCATAGATCTTATCACCCTAAGCAGTA
*
4124962 GTGG-AGCAAATCAAAGACAAAG
66 G-GGAAGCAGATCAAAGACAAAG
* * * *
4124984 GGCCTTAACCCCCTAAGCAATAGGGTAACAGGCTAAATTTC-TAGATCTTAACCCCCTAAGCAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAA-TTCATAGATCTTATCACCCTAAGCAGT
* * * * *
4125048 AGGGAAACAGATCGAGGGCAACG
65 AGGGAAGCAGATCAAAGACAAAG
* * * * *
4125071 AACTTTAACCCCCTAAGCAGTAGGGTAACAAGCTGAAGTTTATAGATCTTATCACCCTAAGCAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCT-AAATTCATAGATCTTATCACCCTAAGCAGT
4125136 AGGGAAGCAGATCAAA
65 AGGGAAGCAGATCAAA
4125152 AGATGGCGAA
Statistics
Matches: 138, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
86 2 0.01
87 97 0.70
88 39 0.28
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (87 bp):
AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTCATAGATCTTATCACCCTAAGCAGTA
GGGAAGCAGATCAAAGACAAAG
Found at i:4125140 original size:88 final size:87
Alignment explanation
Indices: 4124988--4125148 Score: 250
Period size: 88 Copynumber: 1.8 Consensus size: 87
4124978 ACAAAGGGCC
* * *
4124988 TTAACCCCCTAAGCAATAGGGTAACAGGCTAAATTTCTAGATCTTAACCCCCTAAGCAGTAGGGA
1 TTAACCCCCTAAGCAATAGGGTAACAAGCTAAATTTATAGATCTTAACACCCTAAGCAGTAGGGA
4125053 AACAGATCGAGGGCAACGAACT
66 AACAGATCGAGGGCAACGAACT
* * *
4125075 TTAACCCCCTAAGCAGTAGGGTAACAAGCTGAAGTTTATAGATCTTATCACCCTAAGCAGTAGGG
1 TTAACCCCCTAAGCAATAGGGTAACAAGCT-AAATTTATAGATCTTAACACCCTAAGCAGTAGGG
*
4125140 AAGCAGATC
65 AAACAGATC
4125149 AAAAGATGGC
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
87 28 0.42
88 38 0.58
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (87 bp):
TTAACCCCCTAAGCAATAGGGTAACAAGCTAAATTTATAGATCTTAACACCCTAAGCAGTAGGGA
AACAGATCGAGGGCAACGAACT
Found at i:4125315 original size:44 final size:44
Alignment explanation
Indices: 4125252--4125417 Score: 187
Period size: 44 Copynumber: 3.8 Consensus size: 44
4125242 GATTTCCAGA
* *
4125252 TCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGACGAAGGG
1 TCTTAAACCCCTAAGCAGTAGGGAAACAGACCGAAGACGAAGGG
* * * *
4125296 TCTTAAACCCCTAAGCAGTAAGGTAACAGACCGAATTTAC-AA--A
1 TCTTAAACCCCTAAGCAGTAGGGAAACAGACCGAA--GACGAAGGG
* * *
4125339 TCTT-ATCTCCCTAAGCAGTAGGGAAACAGATCAAAGACGAAGGG
1 TCTTAAAC-CCCTAAGCAGTAGGGAAACAGACCGAAGACGAAGGG
*
4125383 TCTTAAACCCCTAAGCAGTAGGGTAACAGACCGAA
1 TCTTAAACCCCTAAGCAGTAGGGAAACAGACCGAA
4125418 TTTACAAATC
Statistics
Matches: 98, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
41 2 0.02
42 4 0.04
43 27 0.28
44 59 0.60
45 4 0.04
46 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (44 bp):
TCTTAAACCCCTAAGCAGTAGGGAAACAGACCGAAGACGAAGGG
Found at i:4125357 original size:43 final size:43
Alignment explanation
Indices: 4125304--4125442 Score: 158
Period size: 43 Copynumber: 3.2 Consensus size: 43
4125294 GGTCTTAAAC
*
4125304 CCCTAAGCAGTAAGGTAACAGACCGAATTTACAAATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGACCGAATTTACAAATCTTATCT
* * ** * *
4125347 CCCTAAGCAGTAGGGAAACAGATC-AA-AGACGAAGGGTCTTAAAC-
1 CCCTAAGCAGTAGGGTAACAGACCGAATTTAC-AA--ATCTT-ATCT
4125391 CCCTAAGCAGTAGGGTAACAGACCGAATTTACAAATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGACCGAATTTACAAATCTTATCT
4125434 CCCTAAGCA
1 CCCTAAGCA
4125443 ATAGTGGAGC
Statistics
Matches: 76, Mismatches: 13, Indels: 14
0.74 0.13 0.14
Matches are distributed among these distances:
41 2 0.03
42 6 0.08
43 34 0.45
44 26 0.34
45 6 0.08
46 2 0.03
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (43 bp):
CCCTAAGCAGTAGGGTAACAGACCGAATTTACAAATCTTATCT
Found at i:4125376 original size:87 final size:87
Alignment explanation
Indices: 4125208--4125497 Score: 395
Period size: 87 Copynumber: 3.3 Consensus size: 87
4125198 ACCACCAAGC
* *** * * * *
4125208 CTTAACCCCCTAAGCAGTAGGGTAACAGGTTGAAGATTTCCAGATCTTAACCCCCTAAGCAGTAG
1 CTTAAACCCCTAAGCAGTAGGGTAACAGACCG-A-ATTTACAAATCTTATCTCCCTAAGCAGTAG
*
4125273 GGAAACAGATCGAAGACGAAGGGT
64 GGAAACAGATCAAAGACGAAGGGT
*
4125297 CTTAAACCCCTAAGCAGTAAGGTAACAGACCGAATTTACAAATCTTATCTCCCTAAGCAGTAGGG
1 CTTAAACCCCTAAGCAGTAGGGTAACAGACCGAATTTACAAATCTTATCTCCCTAAGCAGTAGGG
4125362 AAACAGATCAAAGACGAAGGGT
66 AAACAGATCAAAGACGAAGGGT
*
4125384 CTTAAACCCCTAAGCAGTAGGGTAACAGACCGAATTTACAAATCTTATCTCCCTAAGCAATAGTG
1 CTTAAACCCCTAAGCAGTAGGGTAACAGACCGAATTTACAAATCTTATCTCCCTAAGCAGTAG-G
* * * *
4125449 G-AGCAGATCAAAGACGATGAGC
65 GAAACAGATCAAAGACGAAGGGT
*
4125471 CTT-GACCCCTAAGCAGTAGGGTAACAG
1 CTTAAACCCCTAAGCAGTAGGGTAACAG
4125498 GCTGAAAATT
Statistics
Matches: 183, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
86 23 0.13
87 130 0.71
88 3 0.02
89 27 0.15
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.20
Consensus pattern (87 bp):
CTTAAACCCCTAAGCAGTAGGGTAACAGACCGAATTTACAAATCTTATCTCCCTAAGCAGTAGGG
AAACAGATCAAAGACGAAGGGT
Found at i:4130669 original size:11 final size:11
Alignment explanation
Indices: 4130653--4130686 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
4130643 CTACTTCTTT
4130653 ATGTTGAT-GAC
1 ATGTTGATAG-C
4130664 ATGTTGATAGC
1 ATGTTGATAGC
4130675 ATGTTGATAGC
1 ATGTTGATAGC
4130686 A
1 A
4130687 GCAAAAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 21 0.95
12 1 0.05
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.35
Consensus pattern (11 bp):
ATGTTGATAGC
Found at i:4136702 original size:24 final size:24
Alignment explanation
Indices: 4136675--4136721 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
4136665 AAAAATAATA
*
4136675 ATATATTAAAAATATTTTTAATTG
1 ATATATTAAAAATATTTATAATTG
* *
4136699 ATATTTTAAATATATTTATAATT
1 ATATATTAAAAATATTTATAATT
4136722 AAATTTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
ATATATTAAAAATATTTATAATTG
Found at i:4136731 original size:22 final size:24
Alignment explanation
Indices: 4136680--4136731 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
4136670 TAATAATATA
* * *
4136680 TTAAAAATATTTTTAATTGATATT
1 TTAAATATATTTATAATTGATAAT
4136704 TTAAATATATTTATAATT-A-AAT
1 TTAAATATATTTATAATTGATAAT
4136726 TTAAAT
1 TTAAAT
4136732 TTAAAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 8 0.32
23 1 0.04
24 16 0.64
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTAAATATATTTATAATTGATAAT
Found at i:4136734 original size:28 final size:26
Alignment explanation
Indices: 4136703--4136764 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 26
4136693 TAATTGATAT
4136703 TTTAAATATATTTATAATTAAATTTAAA
1 TTTAAATATATTTATAATT--ATTTAAA
* * *
4136731 TTTAAAAATATTTTTTATTATTTAAA
1 TTTAAATATATTTATAATTATTTAAA
*
4136757 TTGAAATA
1 TTTAAATA
4136765 CAGAAGTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 13 0.45
28 16 0.55
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTAAATATATTTATAATTATTTAAA
Found at i:4139159 original size:2 final size:2
Alignment explanation
Indices: 4139146--4139192 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
4139136 TAAGATACTA
*
4139146 AT AT AT AA 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
4139188 AT AT A
1 AT AT A
4139193 AGACAAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4145294 original size:16 final size:17
Alignment explanation
Indices: 4145275--4145307 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4145265 AAAACCAACT
*
4145275 AAACCC-ACTAAGCCTA
1 AAACCCAACAAAGCCTA
4145291 AAACCCAACAAAGCCTA
1 AAACCCAACAAAGCCTA
4145308 CCCACATAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.36, G:0.06, T:0.09
Consensus pattern (17 bp):
AAACCCAACAAAGCCTA
Found at i:4146428 original size:12 final size:12
Alignment explanation
Indices: 4146413--4146442 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4146403 ATTATCCTAT
*
4146413 TTATTATTATCA
1 TTATTATCATCA
4146425 TTATTATCATCA
1 TTATTATCATCA
4146437 TTATTA
1 TTATTA
4146443 ACATATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (12 bp):
TTATTATCATCA
Found at i:4147020 original size:24 final size:23
Alignment explanation
Indices: 4146984--4147093 Score: 64
Period size: 24 Copynumber: 4.7 Consensus size: 23
4146974 CCCGTACATA
* *
4146984 TATTTTTAATATTATATATACTTT
1 TATTTCTATTATTATATATA-TTT
4147008 TATTTCTATTATTACGTATATATTT
1 TATTTCTATTATTA--TATATATTT
* * * *
4147033 TAATACCA-TA-TATATTATCGTTT
1 TATTTCTATTATTATA-TAT-ATTT
* *
4147056 TA-TGCTATTATTATTTATATTAT
1 TATTTCTATTATTATATATATT-T
*
4147079 TATTTATATTATTAT
1 TATTTCTATTATTAT
4147094 TTTGTTATCG
Statistics
Matches: 66, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
21 2 0.03
22 8 0.12
23 15 0.23
24 27 0.41
25 8 0.12
26 6 0.09
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (23 bp):
TATTTCTATTATTATATATATTT
Found at i:4147078 original size:12 final size:12
Alignment explanation
Indices: 4147061--4147095 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
4147051 CGTTTTATGC
4147061 TATTATTATTTA
1 TATTATTATTTA
4147073 TATTATTATTTA
1 TATTATTATTTA
4147085 TATTATTATTT
1 TATTATTATTT
4147096 TGTTATCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTATTATTTA
Found at i:4150098 original size:13 final size:13
Alignment explanation
Indices: 4150056--4150105 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
4150046 ATATAAGATA
4150056 TAAATTCTAAGTT-
1 TAAATTCTAA-TTC
**
4150069 TAAATTC-AAAAC
1 TAAATTCTAATTC
4150081 TAAATTCTAATTC
1 TAAATTCTAATTC
*
4150094 TAAATTTTAATT
1 TAAATTCTAATT
4150106 ATCCAAAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
12 9 0.30
13 21 0.70
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (13 bp):
TAAATTCTAATTC
Found at i:4150977 original size:62 final size:61
Alignment explanation
Indices: 4150900--4151032 Score: 142
Period size: 62 Copynumber: 2.2 Consensus size: 61
4150890 TGAGCTTAGG
* * * *
4150900 TTTACATATTTTATCAATTT-GGTCTTAAATATAAAAAAATTCAACAAATTTAGCCCTTAATA
1 TTTACAAAATTTATCAATTTAGTTC-TAAATATAAAAAAATT-AACAAATTTAGCCCTCAATA
* * * * * * *
4150962 TTTACAAAATTTATCATTTTAGTTCTAATTTTAAAAAAATTAATAAATTTGGTCCTCCATA
1 TTTACAAAATTTATCAATTTAGTTCTAAATATAAAAAAATTAACAAATTTAGCCCTCAATA
4151023 TTTACAAAAT
1 TTTACAAAAT
4151033 CGACCAATTT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
61 25 0.42
62 31 0.53
63 3 0.05
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.42
Consensus pattern (61 bp):
TTTACAAAATTTATCAATTTAGTTCTAAATATAAAAAAATTAACAAATTTAGCCCTCAATA
Found at i:4151081 original size:14 final size:13
Alignment explanation
Indices: 4151056--4151080 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4151046 CCTAACTCTA
4151056 ATTTTTTTAAAAT
1 ATTTTTTTAAAAT
4151069 ATTTTTTTAAAA
1 ATTTTTTTAAAA
4151081 AACTATTTTC
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTTTTTTAAAAT
Found at i:4151472 original size:22 final size:25
Alignment explanation
Indices: 4151424--4151473 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
4151414 TAATAATGAC
*
4151424 TTTTTTAAAATATATATATATTTAA
1 TTTTTTAAAATATATATATATTAAA
4151449 TTTTTT-AAATATATATA-A-TAAA
1 TTTTTTAAAATATATATATATTAAA
4151471 TTT
1 TTT
4151474 CTAACTGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 6 0.25
23 1 0.04
24 11 0.46
25 6 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTTTTAAAATATATATATATTAAA
Found at i:4152831 original size:25 final size:21
Alignment explanation
Indices: 4152769--4152833 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
4152759 TATTATTGGG
*
4152769 TAAAAAAATAATGAAAAATTTA
1 TAAATAAATAA-GAAAAATTTA
**
4152791 TAAATAAATATTAAAAATCTTA
1 TAAATAAATAAGAAAAAT-TTA
4152813 TTAATATGAAATAAGAAAAAT
1 -TAA-AT-AAATAAGAAAAAT
4152834 AATATAACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
21 6 0.18
22 12 0.35
23 3 0.09
24 2 0.06
25 11 0.32
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (21 bp):
TAAATAAATAAGAAAAATTTA
Found at i:4153183 original size:3 final size:3
Alignment explanation
Indices: 4153175--4153225 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
4153165 TTTAGACAAT
4153175 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
4153223 AGA
1 AGA
4153226 GAAAAAATGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:4155406 original size:40 final size:40
Alignment explanation
Indices: 4155362--4155548 Score: 277
Period size: 40 Copynumber: 4.7 Consensus size: 40
4155352 CCAACCCAAT
* * * *
4155362 TGCCTTCGGGATTTAGCCCGGATGTAACAACCAGCACAAA
1 TGCCTTCGGGACTTAACCCGGATATAACAACCAGCACGAA
*
4155402 TGCCTTCGGGACTTAACCCGGA-ATTAGCAACCAGCACGAA
1 TGCCTTCGGGACTTAACCCGGATA-TAACAACCAGCACGAA
* *
4155442 TGCCTTCGGGACTTAACCCGGAAATAACAACTAGCACGAA
1 TGCCTTCGGGACTTAACCCGGATATAACAACCAGCACGAA
* *
4155482 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCATGAA
1 TGCCTTCGGGACTTAACCCGGATATAACAACCAGCACGAA
4155522 TGCCTTCGGGACTTAACCCGGATATAA
1 TGCCTTCGGGACTTAACCCGGATATAA
4155549 TCCTCAATTG
Statistics
Matches: 135, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
40 134 0.99
41 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.19
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATATAACAACCAGCACGAA
Found at i:4158534 original size:21 final size:21
Alignment explanation
Indices: 4158510--4158554 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
4158500 ATTTGTGATA
*
4158510 TATT-TTTTGAATTATGTTATT
1 TATTCTTTT-AATAATGTTATT
4158531 TATTCTTTTAATAATGTTATT
1 TATTCTTTTAATAATGTTATT
4158552 TAT
1 TAT
4158555 ATTTATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (21 bp):
TATTCTTTTAATAATGTTATT
Found at i:4160223 original size:128 final size:127
Alignment explanation
Indices: 4160026--4160274 Score: 417
Period size: 128 Copynumber: 2.0 Consensus size: 127
4160016 GTGTGTGCAC
* * * *
4160026 AACTCGAGTTGGATTTTAAGATTCGCTCGTTTCAAAGGAATTAAATACCACATCCAGCACGTTAG
1 AACTCAAGTTGGATTTTAAGATTCACTCGTTTCAAAGGAATAAAATACCACATCCAGCACGTTAA
4160091 GACACGATATTTTAAACCTCCAAAAAACTGAGATCACCTCATGATTTCCAAAACACGCGAAAT
66 GACACGATATTTTAAACCTCC-AAAAACTGAGATCACCTCATGATTTCCAAAACACGCGAAAT
* * *
4160154 AACTCAAGTTGGATTTTAAGATTCACTTGTTTCAAAGGAATAAAATACCGCATCCAGCATGTTAA
1 AACTCAAGTTGGATTTTAAGATTCACTCGTTTCAAAGGAATAAAATACCACATCCAGCACGTTAA
*
4160219 GACACGATATTTTAAGCCTCCAAAAACTGAGATCACCTCATGATTTCCAAAACACG
66 GACACGATATTTTAAACCTCCAAAAACTGAGATCACCTCATGATTTCCAAAACACG
4160275 AGACGAAAAT
Statistics
Matches: 113, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
127 35 0.31
128 78 0.69
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (127 bp):
AACTCAAGTTGGATTTTAAGATTCACTCGTTTCAAAGGAATAAAATACCACATCCAGCACGTTAA
GACACGATATTTTAAACCTCCAAAAACTGAGATCACCTCATGATTTCCAAAACACGCGAAAT
Found at i:4160712 original size:2 final size:2
Alignment explanation
Indices: 4160707--4160737 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4160697 ACAATTATTA
4160707 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4160738 GCAGGAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4161945 original size:14 final size:15
Alignment explanation
Indices: 4161926--4161981 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
4161916 TCTTAGATGT
4161926 GATATG-CAATCTTA
1 GATATGACAATCTTA
4161940 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
4161957 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
4161975 GATATGA
1 GATATGA
4161982 TATGCAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:4162002 original size:17 final size:19
Alignment explanation
Indices: 4161905--4162021 Score: 150
Period size: 19 Copynumber: 6.1 Consensus size: 19
4161895 ATAATCTTCA
4161905 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
4161924 GTGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
4161943 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
4161960 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
4161978 ATGATATGCAATCTTAAAAGAT
1 ATGATATGCAATCTT---AGAT
* *
4162000 ATGATTTTGTAATCTTAGAT
1 ATGA-TATGCAATCTTAGAT
4162020 AT
1 AT
4162022 TTAATTTGTA
Statistics
Matches: 87, Mismatches: 4, Indels: 13
0.84 0.04 0.12
Matches are distributed among these distances:
17 16 0.18
18 16 0.18
19 32 0.37
20 6 0.07
22 8 0.09
23 9 0.10
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.38
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:4167145 original size:1 final size:1
Alignment explanation
Indices: 4167139--4167202 Score: 56
Period size: 1 Copynumber: 64.0 Consensus size: 1
4167129 CTTCTATTTC
* * * * * * * *
4167139 AAAAAAAAAAAAAAAAGAAAAAGAGAAAAAATAAAAAGAAAAAAGAGAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4167203 TGGAGAGGCC
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.88, C:0.00, G:0.11, T:0.02
Consensus pattern (1 bp):
A
Done.