Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 106 of 345
Found at i:28544830 original size:17 final size:17
Alignment explanation
Indices: 28544808--28544880 Score: 62
Period size: 17 Copynumber: 4.2 Consensus size: 17
28544798 AAATATTTAA
28544808 AAAATATATAAAATCAT
1 AAAATATATAAAATCAT
* *
28544825 AAAATATATAAATTTTAT
1 AAAATATATAAA-ATCAT
*
28544843 AAAAGTA-A-AAAATTAT
1 AAAA-TATATAAAATCAT
28544859 AAAATAT-TAAAAGTACAT
1 AAAATATATAAAA-T-CAT
28544877 AAAA
1 AAAA
28544881 ATTTAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
15 2 0.04
16 12 0.26
17 16 0.35
18 14 0.30
19 2 0.04
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (17 bp):
AAAATATATAAAATCAT
Found at i:28546580 original size:23 final size:23
Alignment explanation
Indices: 28546550--28546595 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
28546540 GAAATAAATG
28546550 AATACAAATAATTTTGGTGGTGT
1 AATACAAATAATTTTGGTGGTGT
28546573 AATACAAATAATTTTGGTGGTGT
1 AATACAAATAATTTTGGTGGTGT
28546596 TTAAGTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (23 bp):
AATACAAATAATTTTGGTGGTGT
Found at i:28547612 original size:3 final size:3
Alignment explanation
Indices: 28547604--28547634 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
28547594 AGTGCCAGTC
*
28547604 TCA TCA TCA TCA TCA TCA TCA TCA TGA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
28547635 GGACTAGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:28548353 original size:110 final size:110
Alignment explanation
Indices: 28548160--28548376 Score: 380
Period size: 110 Copynumber: 2.0 Consensus size: 110
28548150 TTCTTTGTTT
* *
28548160 GTACTTATACAAATTGAAAGATCTCATTTTCTTTTTCTTCTATAATTCGATTTTTTTTCATGAAA
1 GTACTTATACAAATTGAAAGATCTCATTTTCCTTCTCTTCTATAATTCGATTTTTTTTCATGAAA
*
28548225 TAGTTTTGATACGTCAAATCAAAGTATAAGTTTAACGGGCGATTC
66 TAATTTTGATACGTCAAATCAAAGTATAAGTTTAACGGGCGATTC
*
28548270 GTACTTATACCAATTGAAAGATCTCATTTTCCTTCTCTTCTATAATTCGATTTTTTTTCATGAAA
1 GTACTTATACAAATTGAAAGATCTCATTTTCCTTCTCTTCTATAATTCGATTTTTTTTCATGAAA
* *
28548335 TAATTTTGATGCGTCAAATCAAAGTATAAGTTTAAGGGGCGA
66 TAATTTTGATACGTCAAATCAAAGTATAAGTTTAACGGGCGA
28548377 ATCTAGGAGC
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
110 101 1.00
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.41
Consensus pattern (110 bp):
GTACTTATACAAATTGAAAGATCTCATTTTCCTTCTCTTCTATAATTCGATTTTTTTTCATGAAA
TAATTTTGATACGTCAAATCAAAGTATAAGTTTAACGGGCGATTC
Found at i:28549908 original size:20 final size:21
Alignment explanation
Indices: 28549883--28549931 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
28549873 TGAAAATTTG
*
28549883 GAATTTTTATAAA-TATTTTT
1 GAATTTTTAAAAATTATTTTT
28549903 GAATTTTTAAAAATTATTTTT
1 GAATTTTTAAAAATTATTTTT
28549924 -ATATTTTT
1 GA-ATTTTT
28549932 TTGTTGAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (21 bp):
GAATTTTTAAAAATTATTTTT
Found at i:28549910 original size:21 final size:21
Alignment explanation
Indices: 28549885--28549931 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
28549875 AAAATTTGGA
*
28549885 ATTTTTATAAA-TATTTTTGA-
1 ATTTTTAAAAATTATTTTT-AT
28549905 ATTTTTAAAAATTATTTTTAT
1 ATTTTTAAAAATTATTTTTAT
28549926 ATTTTT
1 ATTTTT
28549932 TTGTTGAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
ATTTTTAAAAATTATTTTTAT
Found at i:28556631 original size:24 final size:24
Alignment explanation
Indices: 28556595--28556789 Score: 96
Period size: 24 Copynumber: 8.0 Consensus size: 24
28556585 TCCAGGCTGT
28556595 ATAAT-GGGAAGCTCATAAGAGCC
1 ATAATCGGGAAGCTCATAAGAGCC
**
28556618 ATAATCGGGAAGCTCATGTGAGCC
1 ATAATCGGGAAGCTCATAAGAGCC
* *
28556642 AATAA-CGGGTAGCTCAGAAGAGCC
1 -ATAATCGGGAAGCTCATAAGAGCC
* ** * *
28556666 ATTAGTCAAGAAGCT-TTGAATAGCC
1 A-TAATCGGGAAGCTCAT-AAGAGCC
* * * *
28556691 ATATATTGGAAAGTTGA-AACGAGCC
1 ATA-ATCGGGAAGCTCATAA-GAGCC
28556716 AT-ATCGGGAAGCTCATAAAGAGCC
1 ATAATCGGGAAGCTCAT-AAGAGCC
* ***
28556740 TTTAATTTAGAAGCTCATGAAGAGCC
1 -ATAATCGGGAAGCTCAT-AAGAGCC
*
28556766 ATATAAT-GGGACGCTCATAAGAGC
1 --ATAATCGGGAAGCTCATAAGAGC
28556790 TGCGGTGTGC
Statistics
Matches: 125, Mismatches: 34, Indels: 24
0.68 0.19 0.13
Matches are distributed among these distances:
23 15 0.12
24 42 0.34
25 37 0.30
26 26 0.21
27 5 0.04
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (24 bp):
ATAATCGGGAAGCTCATAAGAGCC
Found at i:28557254 original size:10 final size:11
Alignment explanation
Indices: 28557235--28557264 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
28557225 AATTTAATAA
28557235 AATTCACATTC
1 AATTCACATTC
28557246 AATTC-CATTC
1 AATTCACATTC
28557256 AATTCACAT
1 AATTCACAT
28557265 CTTAGGCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (11 bp):
AATTCACATTC
Found at i:28565743 original size:25 final size:25
Alignment explanation
Indices: 28565714--28565777 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
28565704 TCTCGAGCCA
28565714 TATAACGGGAAGCTTATCTGGGCTG
1 TATAACGGGAAGCTTATCTGGGCTG
28565739 TATAACGGGAAGCTTATCTGGGCTG
1 TATAACGGGAAGCTTATCTGGGCTG
28565764 TATAACGGGAAGCT
1 TATAACGGGAAGCT
28565778 CACAAGAGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.27
Consensus pattern (25 bp):
TATAACGGGAAGCTTATCTGGGCTG
Found at i:28566424 original size:10 final size:11
Alignment explanation
Indices: 28566405--28566434 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
28566395 AATTTAATAA
28566405 AATTCACATTC
1 AATTCACATTC
28566416 AATTC-CATTC
1 AATTCACATTC
28566426 AATTCACAT
1 AATTCACAT
28566435 CTTAGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (11 bp):
AATTCACATTC
Found at i:28571445 original size:257 final size:257
Alignment explanation
Indices: 28570989--28571506 Score: 982
Period size: 257 Copynumber: 2.0 Consensus size: 257
28570979 CCCTAACTCG
* *
28570989 AAATAATGGTAGAAATAGGTAAGCCGAGCTACGAGGATTTCAAAAATGTAAAGAACATTAAAAAC
1 AAATAATGGTAGAAATAAGTAAACCGAGCTACGAGGATTTCAAAAATGTAAAGAACATTAAAAAC
28571054 GGGGCTTGAATGCACTTACTATTGAGCTTGAAAGCTTGAAACAAACCCTAGCTATGGAGAACATG
66 GGGGCTTGAATGCACTTACTATTGAGCTTGAAAGCTTGAAACAAACCCTAGCTATGGAGAACATG
*
28571119 CAAGTTTCGGCCAAGTTAAATGAGGATGAACACATTTTTGTGTTATTTTTCCCATTTTATTTCAT
131 CAAGTTTCAGCCAAGTTAAATGAGGATGAACACATTTTTGTGTTATTTTTCCCATTTTATTTCAT
28571184 TTATTATGTAAATGACCAAAATGCCCTTACTACTAAACTTTCTAAAAATTCCATCCATGTCC
196 TTATTATGTAAATGACCAAAATGCCCTTACTACTAAACTTTCTAAAAATTCCATCCATGTCC
*
28571246 AAATAATGGTAGAAATAAGTAAACTGAGCTACGAGGATTTCAAAAATGTAAAGAACATTAAAAAC
1 AAATAATGGTAGAAATAAGTAAACCGAGCTACGAGGATTTCAAAAATGTAAAGAACATTAAAAAC
*
28571311 GGGGCTTGAATGCACTTACTATTGAGCTTGAAAGCTTGAAACAAATCCTAGCTATGGAGAACATG
66 GGGGCTTGAATGCACTTACTATTGAGCTTGAAAGCTTGAAACAAACCCTAGCTATGGAGAACATG
28571376 CAAGTTTCAGCCAAGTTAAATGAGGATGAACACATTTTTGTGTTATTTTTCCCATTTTATTTCAT
131 CAAGTTTCAGCCAAGTTAAATGAGGATGAACACATTTTTGTGTTATTTTTCCCATTTTATTTCAT
*
28571441 TTATTATGTAAATGACCAAAATGCCCTTACTACTAAACTTTCTAAAAATTTCATCCATGTCC
196 TTATTATGTAAATGACCAAAATGCCCTTACTACTAAACTTTCTAAAAATTCCATCCATGTCC
28571503 AAAT
1 AAAT
28571507 TTTTGTCCAT
Statistics
Matches: 255, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
257 255 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (257 bp):
AAATAATGGTAGAAATAAGTAAACCGAGCTACGAGGATTTCAAAAATGTAAAGAACATTAAAAAC
GGGGCTTGAATGCACTTACTATTGAGCTTGAAAGCTTGAAACAAACCCTAGCTATGGAGAACATG
CAAGTTTCAGCCAAGTTAAATGAGGATGAACACATTTTTGTGTTATTTTTCCCATTTTATTTCAT
TTATTATGTAAATGACCAAAATGCCCTTACTACTAAACTTTCTAAAAATTCCATCCATGTCC
Found at i:28585644 original size:42 final size:43
Alignment explanation
Indices: 28585574--28585745 Score: 172
Period size: 43 Copynumber: 4.1 Consensus size: 43
28585564 ACACATAGCT
* * * * *
28585574 CATA-CAATGCC-ATATCCCAGATATGGTCTTACATGTTATCA
1 CATATCAATGCCAATGTCTCAGACATGGTCTTACACGTAATCA
* * *
28585615 CATATCAATGCCACTGTCTC-GACAGGGTCTTACACGAAATCA
1 CATATCAATGCCAATGTCTCAGACATGGTCTTACACGTAATCA
* * * * *
28585657 TATAACGATGCCAATGTCTCAAACATGGTCTTACACATAATCA
1 CATATCAATGCCAATGTCTCAGACATGGTCTTACACGTAATCA
* *
28585700 CTATAT-AATGCCAATGTCCCAGACATGGTCTTACATGTAATCA
1 C-ATATCAATGCCAATGTCTCAGACATGGTCTTACACGTAATCA
28585743 CAT
1 CAT
28585746 CTCGGTAATC
Statistics
Matches: 104, Mismatches: 23, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
41 4 0.04
42 42 0.40
43 55 0.53
44 3 0.03
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.28
Consensus pattern (43 bp):
CATATCAATGCCAATGTCTCAGACATGGTCTTACACGTAATCA
Found at i:28589495 original size:29 final size:30
Alignment explanation
Indices: 28589462--28589518 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
28589452 CCTGGACTGC
*
28589462 CACATGAGCGTGTG-GCAGCCCGTGTGGCT
1 CACATGAGCATGTGCGCAGCCCGTGTGGCT
* *
28589491 CACATGGGCATGTGCTCAGCCCGTGTGG
1 CACATGAGCATGTGCGCAGCCCGTGTGG
28589519 AAATGGTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.14, C:0.28, G:0.37, T:0.21
Consensus pattern (30 bp):
CACATGAGCATGTGCGCAGCCCGTGTGGCT
Found at i:28591625 original size:27 final size:26
Alignment explanation
Indices: 28591568--28591675 Score: 126
Period size: 27 Copynumber: 4.0 Consensus size: 26
28591558 GGAAGCGTCT
* *
28591568 TGGTGGCTATGCCACAAATTATCTGATC
1 TGGTGGCTCTGCCAC--ATTATCTGTTC
28591596 TGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTCTGCCACAT-TATCTGTTC
*
28591623 TGGTGGCTTTGCCACGATTATCTGTATC
1 TGGTGGCTCTGCCAC-ATTATCTGT-TC
* *
28591651 TGGTGACTCTGTCACATTATCTGTT
1 TGGTGGCTCTGCCACATTATCTGTT
28591676 TTGGCAGCCA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
26 3 0.04
27 38 0.54
28 30 0.42
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (26 bp):
TGGTGGCTCTGCCACATTATCTGTTC
Found at i:28591652 original size:55 final size:54
Alignment explanation
Indices: 28591568--28591675 Score: 155
Period size: 55 Copynumber: 2.0 Consensus size: 54
28591558 GGAAGCGTCT
*
28591568 TGGTGGCTATGCCACAAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTATGCCACAAATTATCTGATCTGGTGACTCTGCCACAT-TATCTGTTC
* * *
28591623 TGGTGGCTTTGCCAC-GATTATCTGTATCTGGTGACTCTGTCACATTATCTGTT
1 TGGTGGCTATGCCACAAATTATCTG-ATCTGGTGACTCTGCCACATTATCTGTT
28591676 TTGGCAGCCA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
54 16 0.33
55 32 0.67
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (54 bp):
TGGTGGCTATGCCACAAATTATCTGATCTGGTGACTCTGCCACATTATCTGTTC
Found at i:28599285 original size:28 final size:26
Alignment explanation
Indices: 28599254--28599317 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 26
28599244 AATTACTGAA
28599254 ATACCCTTATGCATGCAAAATT-ACCATT
1 ATACCCTTA-G-ATG-AAAATTGACCATT
*
28599282 ATACCCTTAGATGTAAATTGACCATT
1 ATACCCTTAGATGAAAATTGACCATT
28599308 ATACCCTTAG
1 ATACCCTTAG
28599318 GGTTATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
25 5 0.15
26 19 0.56
27 1 0.03
28 9 0.26
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.33
Consensus pattern (26 bp):
ATACCCTTAGATGAAAATTGACCATT
Found at i:28599453 original size:28 final size:28
Alignment explanation
Indices: 28599421--28599527 Score: 107
Period size: 27 Copynumber: 3.9 Consensus size: 28
28599411 AGGAAGCGTC
*
28599421 CTGGTGGCTATGCCACAAATTATCTGAT
1 CTGGTGGCTCTGCCACAAATTATCTGAT
* *
28599449 CTGGTGGCTCTGCCACATA-TATCTGTT
1 CTGGTGGCTCTGCCACAAATTATCTGAT
*
28599476 CTGGTGGCTCTG-CA-ATGATTATCTGTAT
1 CTGGTGGCTCTGCCACA-AATTATCTG-AT
* *
28599504 CTGGTGACTCTGTCAC--ATTATCTG
1 CTGGTGGCTCTGCCACAAATTATCTG
28599528 GCAGCCATGC
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
25 1 0.01
26 3 0.04
27 33 0.49
28 29 0.43
29 2 0.03
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.36
Consensus pattern (28 bp):
CTGGTGGCTCTGCCACAAATTATCTGAT
Found at i:28599479 original size:27 final size:28
Alignment explanation
Indices: 28599421--28599521 Score: 118
Period size: 28 Copynumber: 3.6 Consensus size: 28
28599411 AGGAAGCGTC
* * *
28599421 CTGGTGGCTATGCCACAAATTATCTGAT
1 CTGGTGGCTCTGCCACATATTATCTGTT
28599449 CTGGTGGCTCTGCCACATA-TATCTGTT
1 CTGGTGGCTCTGCCACATATTATCTGTT
28599476 CTGGTGGCTCTG-CA-ATGATTATCTGTAT
1 CTGGTGGCTCTGCCACAT-ATTATCTGT-T
* *
28599504 CTGGTGACTCTGTCACAT
1 CTGGTGGCTCTGCCACAT
28599522 TATCTGGCAG
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.03
26 3 0.05
27 26 0.41
28 29 0.45
29 2 0.03
30 2 0.03
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.36
Consensus pattern (28 bp):
CTGGTGGCTCTGCCACATATTATCTGTT
Found at i:28601407 original size:15 final size:15
Alignment explanation
Indices: 28601387--28601419 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
28601377 ATAATCGAAG
28601387 CAAGATCTAGAATAA
1 CAAGATCTAGAATAA
28601402 CAAGATCTAGAATAA
1 CAAGATCTAGAATAA
28601417 CAA
1 CAA
28601420 TTATTGACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.55, C:0.15, G:0.12, T:0.18
Consensus pattern (15 bp):
CAAGATCTAGAATAA
Found at i:28601862 original size:49 final size:49
Alignment explanation
Indices: 28601800--28601897 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
28601790 ATGTACATTG
*
28601800 TCTCTAATGTACAAAAATAGATAATCATAATAGGAATAGAATATCATAA
1 TCTCCAATGTACAAAAATAGATAATCATAATAGGAATAGAATATCATAA
28601849 TCTCCAATGTACAAAAATAGATAATCATAATAGGAATAGAATATCATAA
1 TCTCCAATGTACAAAAATAGATAATCATAATAGGAATAGAATATCATAA
28601898 GAGAGGGAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.51, C:0.11, G:0.10, T:0.28
Consensus pattern (49 bp):
TCTCCAATGTACAAAAATAGATAATCATAATAGGAATAGAATATCATAA
Found at i:28602146 original size:5 final size:5
Alignment explanation
Indices: 28602132--28602183 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
28602122 AATAAACAGA
* * *
28602132 AAAAT AAAAAT AAAAT AAAAT AATGA- AAAAT AAAAG GAAAT AAAAT AAAAT
1 AAAAT -AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT
28602183 A
1 A
28602184 GACTCAGTGG
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
4 1 0.03
5 31 0.82
6 6 0.16
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:28602166 original size:25 final size:26
Alignment explanation
Indices: 28602112--28602179 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 26
28602102 AAAGAAGTCT
*
28602112 AGAAAATAGAAATAAACAGAAAAATAAAA
1 AGAAAATA-AAAT-AA-TGAAAAATAAAA
*
28602141 ATAAAATAAAATAATGAAAAAT-AAA
1 AGAAAATAAAATAATGAAAAATAAAA
*
28602166 AGGAAATAAAATAA
1 AGAAAATAAAATAA
28602180 AATAGACTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 15 0.43
26 7 0.20
27 2 0.06
28 4 0.11
29 7 0.20
ACGTcount: A:0.75, C:0.01, G:0.09, T:0.15
Consensus pattern (26 bp):
AGAAAATAAAATAATGAAAAATAAAA
Found at i:28602172 original size:20 final size:18
Alignment explanation
Indices: 28602116--28602174 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 18
28602106 AAGTCTAGAA
*
28602116 AATAGAAATAAACAGAAA-
1 AATAAAAATAAA-AGAAAT
*
28602134 AATAAAAATAAAATAAAAT
1 AATAAAAATAAAA-GAAAT
28602153 AATGAAAAATAAAAGGAAAT
1 AAT-AAAAATAAAA-GAAAT
28602173 AA
1 AA
28602175 AATAAAATAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
17 1 0.03
18 14 0.41
19 3 0.09
20 16 0.47
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (18 bp):
AATAAAAATAAAAGAAAT
Found at i:28603703 original size:31 final size:31
Alignment explanation
Indices: 28603660--28603776 Score: 164
Period size: 31 Copynumber: 3.8 Consensus size: 31
28603650 TCAATCTCAG
28603660 CATAT-ACTGGGCCGAAGCCTTTACATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
* * *
28603690 CATATCACTGGGCCGAAACCTTTTCACTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
* *
28603721 CATATCACTAGGCCGAAGCCTTTTCATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
* *
28603752 CATATCACTGTGCTGAAGCCTTTAC
1 CATATCACTGGGCCGAAGCCTTTAC
28603777 TGTAACAATA
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
30 5 0.07
31 71 0.93
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTACATTATT
Found at i:28604013 original size:24 final size:25
Alignment explanation
Indices: 28603983--28604062 Score: 117
Period size: 25 Copynumber: 3.2 Consensus size: 25
28603973 GGAGGCCTAG
*
28603983 CCTTTTTGATAAACTGGGGCAAAGC
1 CCTTTTCGATAAACTGGGGCAAAGC
28604008 CCTTTTCGATAAACTGGGGCAAAGC
1 CCTTTTCGATAAACTGGGGCAAAGC
* * *
28604033 CCTTTTCGGT-AATTGGGGCATAGC
1 CCTTTTCGATAAACTGGGGCAAAGC
28604057 CCTTTT
1 CCTTTT
28604063 GCACTTCCTC
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
24 18 0.35
25 33 0.65
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (25 bp):
CCTTTTCGATAAACTGGGGCAAAGC
Found at i:28611825 original size:31 final size:31
Alignment explanation
Indices: 28611790--28611894 Score: 174
Period size: 31 Copynumber: 3.4 Consensus size: 31
28611780 TATACTAGGT
28611790 CGAAGCCTTTACATTATTCATATCACTGGGC
1 CGAAGCCTTTACATTATTCATATCACTGGGC
*
28611821 CGAAGCCTTTTCATTATTCATATCACTGGGC
1 CGAAGCCTTTACATTATTCATATCACTGGGC
* **
28611852 CAAAGCCTTTTTATTATTCATATCACTGGGC
1 CGAAGCCTTTACATTATTCATATCACTGGGC
28611883 CGAAGCCTTTAC
1 CGAAGCCTTTAC
28611895 TGTAACAATA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 68 1.00
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (31 bp):
CGAAGCCTTTACATTATTCATATCACTGGGC
Found at i:28612127 original size:25 final size:24
Alignment explanation
Indices: 28612099--28612207 Score: 105
Period size: 25 Copynumber: 4.4 Consensus size: 24
28612089 CTGGAGGCCT
*
28612099 AGCCTCTTTTAAT-AACTGGGGCAAA
1 AGCC-CTTTTGATAAACTGGGGC-AA
*
28612124 AGCCCTTTTTGATAAACTGGGCCAA
1 AGCCC-TTTTGATAAACTGGGGCAA
*
28612149 AGCCCTTTTCGGTAAACTGGGGCAA
1 AGCCCTTTT-GATAAACTGGGGCAA
* * *
28612174 AGCCCTTTTCGGT-AACTAGGGCAT
1 AGCCCTTTT-GATAAACTGGGGCAA
28612198 AGCCCTTTTG
1 AGCCCTTTTG
28612208 CACTTCTTCC
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
23 1 0.01
24 23 0.31
25 43 0.57
26 8 0.11
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (24 bp):
AGCCCTTTTGATAAACTGGGGCAA
Found at i:28612195 original size:24 final size:25
Alignment explanation
Indices: 28612112--28612206 Score: 129
Period size: 25 Copynumber: 3.8 Consensus size: 25
28612102 CTCTTTTAAT
* *
28612112 AACTGGGGCAAAAGCCCTTTTTGATA
1 AACTGGGGC-AAAGCCCTTTTCGGTA
*
28612138 AACTGGGCCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
28612163 AACTGGGGCAAAGCCCTTTTCGGT-
1 AACTGGGGCAAAGCCCTTTTCGGTA
* *
28612187 AACTAGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
28612207 GCACTTCTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
24 18 0.29
25 37 0.59
26 8 0.13
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGGTA
Found at i:28615092 original size:5 final size:5
Alignment explanation
Indices: 28615082--28615112 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
28615072 CAAAAGAATT
28615082 ATAAA ATAAA ATAAA ATAAA ATAATA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAA-A ATAAA
28615113 TAAGTTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
ATAAA
Found at i:28620034 original size:18 final size:19
Alignment explanation
Indices: 28620001--28620036 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28619991 TTAAATTTAG
*
28620001 TAAATTAATTGAATTATGT
1 TAAATTAAATGAATTATGT
28620020 TAAATTAAATG-ATTATG
1 TAAATTAAATGAATTATG
28620037 GTGCCAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (19 bp):
TAAATTAAATGAATTATGT
Found at i:28620628 original size:49 final size:50
Alignment explanation
Indices: 28620447--28620640 Score: 255
Period size: 50 Copynumber: 3.9 Consensus size: 50
28620437 ATGATGTAGC
* * *
28620447 TAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCTGATAACT
1 TAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T
* * * * * *
28620498 TCGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATAGT
1 TAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAAT
*
28620548 TAGGTCATATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAAT
1 TAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAAT
* * *
28620598 T-GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCA
1 TAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCA
28620641 AATAGTTTGG
Statistics
Matches: 123, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
49 38 0.31
50 45 0.37
51 40 0.33
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (50 bp):
TAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAAT
Found at i:28620658 original size:101 final size:101
Alignment explanation
Indices: 28620455--28620661 Score: 301
Period size: 101 Copynumber: 2.0 Consensus size: 101
28620445 GCTAGGTCGC
* * *
28620455 ATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCTGATAACTTCGATCACGTGTGTAGTACTAA
1 ATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACTTCGATCACATGTGTAGTACTAA
* *
28620520 GTGCAGGCTACTACGTGTATCAAATAGTTAGGTCAT
66 GTGCAGGCTACTACGCGTACCAAATAGTTAGGTCAT
* *
28620556 ATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT-GGTCGCATGTGTAGTACTAA
1 ATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACTTCGATCACATGTGTAGTACTAA
* *
28620619 GTGCAGGCTACTATGCGTACCAAATAGTTTGGCTACAT
66 GTGCAGGCTACTACGCGTACCAAATAGTTAGG-T-CAT
28620657 ATGTG
1 ATGTG
28620662 GCACTTATGT
Statistics
Matches: 95, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
99 45 0.47
100 3 0.03
101 47 0.49
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (101 bp):
ATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACTTCGATCACATGTGTAGTACTAA
GTGCAGGCTACTACGCGTACCAAATAGTTAGGTCAT
Found at i:28622572 original size:43 final size:43
Alignment explanation
Indices: 28622506--28622591 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
28622496 GTTACATGAA
* *
28622506 TCGCATCCATTATGAACTTAGACCACTCAACGAGCTCAGATGC
1 TCGCATCCATAATGAACTCAGACCACTCAACGAGCTCAGATGC
* * *
28622549 TCGCATCCATAATGAACTCAGACCTCTCAATGAGCTCCGATGC
1 TCGCATCCATAATGAACTCAGACCACTCAACGAGCTCAGATGC
28622592 CACATAGATC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.23
Consensus pattern (43 bp):
TCGCATCCATAATGAACTCAGACCACTCAACGAGCTCAGATGC
Found at i:28622746 original size:12 final size:12
Alignment explanation
Indices: 28622729--28622754 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28622719 TAAGGTTCAA
28622729 ACGGGATTTTCC
1 ACGGGATTTTCC
28622741 ACGGGATTTTCC
1 ACGGGATTTTCC
28622753 AC
1 AC
28622755 ACTTGCACAT
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:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (12 bp):
ACGGGATTTTCC
Found at i:28629480 original size:17 final size:17
Alignment explanation
Indices: 28629458--28629493 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
28629448 CATAGCAGTC
*
28629458 GTGGAGAACCTTTTCCG
1 GTGGAGAACCTTTCCCG
28629475 GTGGAGAACCTTTCCCG
1 GTGGAGAACCTTTCCCG
28629492 GT
1 GT
28629494 AGAGTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.28
Consensus pattern (17 bp):
GTGGAGAACCTTTCCCG
Found at i:28637730 original size:19 final size:19
Alignment explanation
Indices: 28637708--28637750 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
28637698 ACACCCAAGA
28637708 TGCATAAT-GGAGCACGAAG
1 TGCATAATGGGA-CACGAAG
* *
28637727 TGCATCATGGGACACGAGG
1 TGCATAATGGGACACGAAG
28637746 TGCAT
1 TGCAT
28637751 TCTGGCACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.30, C:0.19, G:0.33, T:0.19
Consensus pattern (19 bp):
TGCATAATGGGACACGAAG
Found at i:28640264 original size:23 final size:23
Alignment explanation
Indices: 28640215--28640346 Score: 133
Period size: 23 Copynumber: 5.7 Consensus size: 23
28640205 ATCACCCACT
* *
28640215 AAACATAACCA-ATTTACCCTCC
1 AAACACAACCATATATACCCTCC
*
28640237 AAACACAACCATATATACCATCC
1 AAACACAACCATATATACCCTCC
* * * *
28640260 GAACACAACCAAATATACCTTTC
1 AAACACAACCATATATACCCTCC
*
28640283 AAACACAACCATATGTATAACCTCC
1 AAACACAACCATA--TATACCCTCC
*
28640308 GAACACAACCA-AGTATACCCTCC
1 AAACACAACCATA-TATACCCTCC
28640331 AAACACAACCAGTATA
1 AAACACAACCA-TATA
28640347 CCTTTCAACA
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
22 10 0.11
23 59 0.66
24 3 0.03
25 18 0.20
ACGTcount: A:0.45, C:0.33, G:0.04, T:0.18
Consensus pattern (23 bp):
AAACACAACCATATATACCCTCC
Found at i:28640319 original size:48 final size:46
Alignment explanation
Indices: 28640216--28640346 Score: 167
Period size: 48 Copynumber: 2.8 Consensus size: 46
28640206 TCACCCACTA
* *
28640216 AACATAACC-AATTTACCCTCCAAACACAACCATATATACCATCCG
1 AACACAACCAAATATACCCTCCAAACACAACCATATATACCATCCG
* *
28640261 AACACAACCAAATATACCTTTCAAACACAACCATATGTATAACC-TCCG
1 AACACAACCAAATATACCCTCCAAACACAACCATA--TAT-ACCATCCG
*
28640309 AACACAACCAAGTATACCCTCCAAACACAACCAGTATA
1 AACACAACCAAATATACCCTCCAAACACAACCA-TATA
28640347 CCTTTCAACA
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
45 8 0.11
46 22 0.30
47 2 0.03
48 37 0.50
49 5 0.07
ACGTcount: A:0.44, C:0.34, G:0.04, T:0.18
Consensus pattern (46 bp):
AACACAACCAAATATACCCTCCAAACACAACCATATATACCATCCG
Found at i:28644750 original size:49 final size:50
Alignment explanation
Indices: 28644582--28644718 Score: 231
Period size: 50 Copynumber: 2.8 Consensus size: 50
28644572 TAAGATGCTG
*
28644582 ATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCATATAGCGGGGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCATATAGCGAGGCCA
* *
28644632 ATGTCATGTCTCAGACATGGTCTTACACTGGCTTTCATATAGCGAGGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCATATAGCGAGGCCA
*
28644682 ATGCCATGTCCCAGACA-GGTCTTACACTGGCTCTCAT
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCAT
28644719 CTATCAATGT
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
49 19 0.23
50 62 0.77
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCATATAGCGAGGCCA
Found at i:28644756 original size:49 final size:49
Alignment explanation
Indices: 28644582--28644759 Score: 203
Period size: 50 Copynumber: 3.6 Consensus size: 49
28644572 TAAGATGCTG
* * **
28644582 ATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCATATAGCGGGGCCA
1 ATGCCATGTCTCAGACA-GGTCTTACACTGGCTCTCATATAGCAAGGCCA
* * *
28644632 ATGTCATGTCTCAGACATGGTCTTACACTGGCTTTCATATAGCGAGGCCA
1 ATGCCATGTCTCAGACA-GGTCTTACACTGGCTCTCATATAGCAAGGCCA
* * * * * *
28644682 ATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATCTATCAATGTCG
1 ATGCCATGTCTCAGACAGGTCTTACACTGGCTCTCATATAGCAAGGCCA
* *
28644731 ATGCCATGTCTCAAACAGGTTTTACACTG
1 ATGCCATGTCTCAGACAGGTCTTACACTG
28644760 ATACACCACA
Statistics
Matches: 113, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
49 51 0.45
50 62 0.55
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.29
Consensus pattern (49 bp):
ATGCCATGTCTCAGACAGGTCTTACACTGGCTCTCATATAGCAAGGCCA
Found at i:28644833 original size:48 final size:46
Alignment explanation
Indices: 28644779--28644899 Score: 120
Period size: 46 Copynumber: 2.6 Consensus size: 46
28644769 AAGCTGACGC
* * *
28644779 CATGTCCCAGACAAGTCTTACACTAGCTTGTATATCGC-GAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGC-TCT-CAT-GCTGAGGCCGATG
* * * * *
28644827 CATGTCCCGGACATGT-TTGACATTGGCTCTCATGCTGTGGCTGATG
1 CATGTCCCAGACATGTCTT-ACACTAGCTCTCATGCTGAGGCCGATG
28644873 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
28644900 ACACATATCA
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
45 2 0.03
46 31 0.53
47 6 0.10
48 20 0.34
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCATGCTGAGGCCGATG
Found at i:28654123 original size:23 final size:23
Alignment explanation
Indices: 28654097--28654166 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 23
28654087 CAAAGGCAGC
28654097 CAAAAAGAAAA-ACAAAAAAAGTA
1 CAAAAAGAAAATA-AAAAAAAGTA
*
28654120 CAAAAAGAAAATAAAAAAAAGGAAA
1 CAAAAAGAAAATAAAAAAAA-G-TA
*
28654145 GAAAAAGAAGAATAAAAAAAAG
1 CAAAAAGAA-AATAAAAAAAAG
28654167 GTCATAGTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
23 18 0.44
24 2 0.05
25 10 0.24
26 11 0.27
ACGTcount: A:0.79, C:0.04, G:0.13, T:0.04
Consensus pattern (23 bp):
CAAAAAGAAAATAAAAAAAAGTA
Found at i:28655920 original size:64 final size:64
Alignment explanation
Indices: 28655846--28655972 Score: 209
Period size: 64 Copynumber: 2.0 Consensus size: 64
28655836 CGTTCATAAT
* **
28655846 ACATCTAGTTAGGAGTATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATAAGCATC
1 ACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCATC
* *
28655910 ACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTACTTATTTGGCATAAGCAT
1 ACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
28655973 AGATACATGA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (64 bp):
ACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCATC
Found at i:28656265 original size:44 final size:44
Alignment explanation
Indices: 28656043--28657007 Score: 318
Period size: 44 Copynumber: 21.9 Consensus size: 44
28656033 AATTTACAAC
* * *** *
28656043 CTTATCTCTCTGAAGTAGCAAGAGAGCAGGCCG-A-ATTGAAGT
1 CTTATCTCTCTGAGGTAGCAAGGGAGCAGATTGAAGATTGTAGT
* * * *
28656085 CTTATCTTTCTGAGGTAGCAAGGAAGCAGACTGAAGATTGAAGAT
1 CTTATCTCTCTGAGGTAGCAAGGGAGCAGATTGAAGATTGTAG-T
* * * ** * * * *
28656130 CTTATCTCTCT-AAGCAG-TAGTGGAATAGATCGAAGATGGCAAAT
1 CTTATCTCTCTGAGGTAGCAAG-GGAGCAGATTGAAGATTG-TAGT
* * **** *
28656174 ATTATCT-TCTCGAGGTAGC-AGGGAGCAGATTTAAGCCACTAGC
1 CTTATCTCTCT-GAGGTAGCAAGGGAGCAGATTGAAGATTGTAGT
* *
28656217 CTTATCTCTCTGAGGTAGCAAGGGAGCAGGTTGACGATTGTAGT
1 CTTATCTCTCTGAGGTAGCAAGGGAGCAGATTGAAGATTGTAGT
* * * * *
28656261 CTTATCT-TCCTGAAGTAGCAAGGAAGCAGACTAAAGATTGAAGAT
1 CTTATCTCT-CTGAGGTAGCAAGGGAGCAGATTGAAGATTGTAG-T
* * * * * *
28656306 CTTATCTCCCT-AAGTAG-TAGTGGAGCAGATCGAAAATGGTAAGT
1 CTTATCTCTCTGAGGTAGCAAG-GGAGCAGATTGAAGATTGT-AGT
** * * ***** *
28656350 CTTATCT-TCCCAAGGTAGCAGGGGAGCAGATTTAAGCCACCAGC
1 CTTATCTCT-CTGAGGTAGCAAGGGAGCAGATTGAAGATTGTAGT
* *
28656394 CTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGT
1 CTTATCTCTCTGAGGTAGCAAGGGAGCAGATTGAAGATTGTAGT
* ** * * * *
28656438 CTTATCTTTCTGAGGTAGCAAGAAAACAGACTGAACATTAAATA-T
1 CTTATCTCTCTGAGGTAGCAAGGGAGCAGATTGAAGATT--GTAGT
* * * * * * *
28656483 CTTATCTCCCT-AAGCAG-TAGTGAAGCAGATCGAAGA-TGGAGAAT
1 CTTATCTCTCTGAGGTAGCAAG-GGAGCAGATTGAAGATTGTAG--T
* * * ** **** *
28656527 CTTATC-CTTTCGAGGTAGCAGGGGAGCATATTTTAGCCACTAGC
1 CTTATCTCTCT-GAGGTAGCAAGGGAGCAGATTGAAGATTGTAGT
* * *
28656571 CTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAAATTGTAGT
1 CTTATCTCTCTGAGGTAGCAAGGGAGCAGATTGAAGATTGTAGT
* * * * * * *
28656615 ATTATCT-TACTGGGGTAGCAAGGAAGTAAACTGAAGATTGAAGAT
1 CTTATCTCT-CTGAGGTAGCAAGGGAGCAGATTGAAGATTGTAG-T
* * * * * * *
28656660 CTTATCTCCCT-AAGCAG-TAGTGGAGCAGATCGAAGATGGT-GAA
1 CTTATCTCTCTGAGGTAGCAAG-GGAGCAGATTGAAGATTGTAG-T
* * ** **** *
28656703 CTTATCTTTCTGAGGTAGCAGGGGAGCAGATTTTAGCCACTAGC
1 CTTATCTCTCTGAGGTAGCAAGGGAGCAGATTGAAGATTGTAGT
* * *
28656747 CTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGT
1 CTTATCTCTCTGAGGTAGCAAGGGAGCAGATTGAAGATTGTAGT
* * * * * **
28656791 CTTATCTTTCTGAGGTAGCAAGGAACCAGACTGAGGATTAAAGAT
1 CTTATCTCTCTGAGGTAGCAAGGGAGCAGATTGAAGATTGTAG-T
* * * * ** * *
28656836 CTTATCTCCCT-AAGTAGTAATGGAGCAGATCAAAGATGGTGAAT
1 CTTATCTCTCTGAGGTAGCAAGGGAGCAGATTGAAGATTGT-AGT
* * * * * ** **** *
28656880 CTCATCT-TCCCGAAGTAGTAGGGGAGCAGATTTTAGCCACTAGC
1 CTTATCTCT-CTGAGGTAGCAAGGGAGCAGATTGAAGATTGTAGT
* * **
28656924 CTTATCTCCCTGGGGTAGCAAGGGAGCAGGCTGAAGATTGTAGT
1 CTTATCTCTCTGAGGTAGCAAGGGAGCAGATTGAAGATTGTAGT
* * * *
28656968 CTTATCT-TCCTAAGGTAGCAAGGAAGCAGACTAAAGATTG
1 CTTATCTCT-CTGAGGTAGCAAGGGAGCAGATTGAAGATTG
28657008 AAGACCTTAT
Statistics
Matches: 639, Mismatches: 241, Indels: 84
0.66 0.25 0.09
Matches are distributed among these distances:
41 1 0.00
42 27 0.04
43 43 0.07
44 446 0.70
45 116 0.18
46 6 0.01
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (44 bp):
CTTATCTCTCTGAGGTAGCAAGGGAGCAGATTGAAGATTGTAGT
Found at i:28656379 original size:45 final size:44
Alignment explanation
Indices: 28656258--28656380 Score: 117
Period size: 45 Copynumber: 2.8 Consensus size: 44
28656248 TGACGATTGT
* * * * *
28656258 AGTCTTATCTTCCTGAAGTAGCAAGGAAGCAGA-CTAAAGATTGA
1 AGTCTTATCTTCC-CAAGTAGCAGGGGAGCAGATCGAAAGATGGA
* *
28656302 AGATCTTATC-TCCCTAAGTAGTAGTGGAGCAGATCGAAA-ATGGTA
1 AG-TCTTATCTTCCC-AAGTAGCAGGGGAGCAGATCGAAAGATGG-A
28656347 AGTCTTATCTTCCCAAGGTAGCAGGGGAGCAGAT
1 AGTCTTATCTTCCCAA-GTAGCAGGGGAGCAGAT
28656381 TTAAGCCACC
Statistics
Matches: 64, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
44 31 0.48
45 33 0.52
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (44 bp):
AGTCTTATCTTCCCAAGTAGCAGGGGAGCAGATCGAAAGATGGA
Found at i:28656458 original size:177 final size:176
Alignment explanation
Indices: 28656042--28657025 Score: 1375
Period size: 177 Copynumber: 5.6 Consensus size: 176
28656032 GAATTTACAA
* ** *
28656042 CCTTATCTCTCTGAAGTAGCAAGAGAGCAGGCCG-A-ATTGAAGTCTTATCTTTCTGAGGTAGCA
1 CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTTCTGAGGTAGCA
* **
28656105 AGGAAGCAGACTGAAGATTGAAGATCTTATCTCTCTAAGCAGTAGTGGAATAGATCGAAGATGGC
66 AGGAAGCAGACTGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG-
* * * *
28656170 AAATATTATCTTCTCGAGGTAGCA-GGGAGCAGATTTAAGCCACTAG
130 TAATCTTATCTTCCCGAGGTAGCAGGGGAGCAGATTTTAGCCACTAG
* * * *
28656216 CCTTATCTCTCTGAGGTAGCAAGGGAGCAGGTTGACGATTGTAGTCTTATCTTCCTGAAGTAGCA
1 CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTTCTGAGGTAGCA
* * *
28656281 AGGAAGCAGACTAAAGATTGAAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAAATGGT
66 AGGAAGCAGACTGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGT
* * *
28656346 AAGTCTTATCTTCCCAAGGTAGCAGGGGAGCAGATTTAAGCCACCAG
131 AA-TCTTATCTTCCCGAGGTAGCAGGGGAGCAGATTTTAGCCACTAG
28656393 CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTTCTGAGGTAGCA
1 CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTTCTGAGGTAGCA
* * * * * *
28656458 AGAAAACAGACTGAACATTAAATATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCGAAGATGGA
66 AGGAAGCAGACTGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG-
* * *
28656523 GAATCTTATCCTT-TCGAGGTAGCAGGGGAGCATATTTTAGCCACTAG
130 TAATCTTAT-CTTCCCGAGGTAGCAGGGGAGCAGATTTTAGCCACTAG
* * * *
28656570 CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAAATTGTAGTATTATCTTACTGGGGTAGCA
1 CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTTCTGAGGTAGCA
* *
28656635 AGGAAGTAAACTGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGT
66 AGGAAGCAGACTGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGT
* *
28656700 GAA-CTTATCTTTCTGAGGTAGCAGGGGAGCAGATTTTAGCCACTAG
131 -AATCTTATCTTCCCGAGGTAGCAGGGGAGCAGATTTTAGCCACTAG
*
28656746 CCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTTCTGAGGTAGCA
1 CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTTCTGAGGTAGCA
* * * * * *
28656811 AGGAACCAGACTGAGGATTAAAGATCTTATCTCCCTAAGTAGTAATGGAGCAGATCAAAGATGGT
66 AGGAAGCAGACTGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGT
* * *
28656876 GAATCTCATCTTCCCGAAGTAGTAGGGGAGCAGATTTTAGCCACTAG
131 -AATCTTATCTTCCCGAGGTAGCAGGGGAGCAGATTTTAGCCACTAG
* * * * * *
28656923 CCTTATCTCCCTGGGGTAGCAAGGGAGCAGGCTGAAGATTGTAGTCTTATCTTCCTAAGGTAGCA
1 CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTTCTGAGGTAGCA
* *
28656988 AGGAAGCAGACTAAAGATTGAAGACCTTATCTCCCTAA
66 AGGAAGCAGACTGAAGATTGAAGATCTTATCTCCCTAA
28657026 AGTTGCAGTG
Statistics
Matches: 717, Mismatches: 84, Indels: 15
0.88 0.10 0.02
Matches are distributed among these distances:
174 30 0.04
175 5 0.01
176 257 0.36
177 420 0.59
178 5 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (176 bp):
CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTTCTGAGGTAGCA
AGGAAGCAGACTGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGT
AATCTTATCTTCCCGAGGTAGCAGGGGAGCAGATTTTAGCCACTAG
Found at i:28656750 original size:353 final size:353
Alignment explanation
Indices: 28656042--28657025 Score: 1442
Period size: 353 Copynumber: 2.8 Consensus size: 353
28656032 GAATTTACAA
* ** *
28656042 CCTTATCTCTCTGAAGTAGCAAGAGAGCAGGCCG-A-ATTGAAGTCTTATCTTTCTGAGGTAGCA
1 CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTTCTGAGGTAGCA
* * * *
28656105 AGGAAGCAGACTGAAGATTGAAGATCTTATCTCTCTAAGCAGTAGTGGAA-TAGATCGAAGATGG
66 AGGAAACAGACTGAAGATTAAAGATCTTATCTCCCTAAGCAGTAGT-GAAGCAGATCGAAGATGG
* *
28656169 CA-AATATTATCTTCTCGAGGTAGCA-GGGAGCAGATTTAAGCCACTAGCCTTATCTCTCTGAGG
130 -AGAATCTTATCTTCTCGAGGTAGCAGGGGAGCAGATTTTAGCCACTAGCCTTATCTCTCTGAGG
* *
28656232 TAGCAAGGGAGCAGGTTGACGATTGTAGTCTTATCTTCCTGAAGTAGCAAGGAAGCAGACTAAAG
194 TAGCAAGGGAGCAGGTTGAAGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAAG
*
28656297 ATTGAAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAAATGGTAAGTCTTATCTTCCCA
259 ATTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAAATGGTAAG-CTTATCTTCCCA
28656362 AGGTAGCAGGGGAGCAGATTTAAGCCACCAG
323 AGGTAGCAGGGGAGCAGATTTAAGCCACCAG
28656393 CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTTCTGAGGTAGCA
1 CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTTCTGAGGTAGCA
* * *
28656458 AGAAAACAGACTGAACATTAAATATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCGAAGATGGA
66 AGGAAACAGACTGAAGATTAAAGATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCGAAGATGGA
*
28656523 GAATCTTATCCTT-TCGAGGTAGCAGGGGAGCATATTTTAGCCACTAGCCTTATCTCTCTGAGGT
131 GAATCTTAT-CTTCTCGAGGTAGCAGGGGAGCAGATTTTAGCCACTAGCCTTATCTCTCTGAGGT
* * * * * * * *
28656587 AGCAAGAGAGCAGGTTGAAAATTGTAGTATTATCTTACTGGGGTAGCAAGGAAGTAAACTGAAGA
195 AGCAAGGGAGCAGGTTGAAGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAAGA
* * **
28656652 TTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAA-CTTATCTTTCTGA
260 TTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAAATGGT-AAGCTTATCTTCCCAA
* *
28656716 GGTAGCAGGGGAGCAGATTTTAGCCACTAG
324 GGTAGCAGGGGAGCAGATTTAAGCCACCAG
*
28656746 CCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTTCTGAGGTAGCA
1 CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTTCTGAGGTAGCA
* * * * * * *
28656811 AGGAACCAGACTGAGGATTAAAGATCTTATCTCCCTAAGTAGTAATGGAGCAGATCAAAGATGGT
66 AGGAAACAGACTGAAGATTAAAGATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCGAAGATGGA
* * * * * *
28656876 GAATCTCATCTTCCCGAAGTAGTAGGGGAGCAGATTTTAGCCACTAGCCTTATCTCCCTGGGGTA
131 GAATCTTATCTTCTCGAGGTAGCAGGGGAGCAGATTTTAGCCACTAGCCTTATCTCTCTGAGGTA
* *
28656941 GCAAGGGAGCAGGCTGAAGATTGTAGTCTTATCTTCCTAAGGTAGCAAGGAAGCAGACTAAAGAT
196 GCAAGGGAGCAGGTTGAAGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAAGAT
*
28657006 TGAAGACCTTATCTCCCTAA
261 TGAAGATCTTATCTCCCTAA
28657026 AGTTGCAGTG
Statistics
Matches: 565, Mismatches: 60, Indels: 14
0.88 0.09 0.02
Matches are distributed among these distances:
351 31 0.05
352 8 0.01
353 383 0.68
354 141 0.25
355 2 0.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (353 bp):
CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTTCTGAGGTAGCA
AGGAAACAGACTGAAGATTAAAGATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCGAAGATGGA
GAATCTTATCTTCTCGAGGTAGCAGGGGAGCAGATTTTAGCCACTAGCCTTATCTCTCTGAGGTA
GCAAGGGAGCAGGTTGAAGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAAGAT
TGAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAAATGGTAAGCTTATCTTCCCAAGG
TAGCAGGGGAGCAGATTTAAGCCACCAG
Found at i:28657089 original size:13 final size:13
Alignment explanation
Indices: 28657071--28657096 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28657061 TCTCCTTAAA
28657071 GTTGCAGTGGAGT
1 GTTGCAGTGGAGT
28657084 GTTGCAGTGGAGT
1 GTTGCAGTGGAGT
28657097 AGACTGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.46, T:0.31
Consensus pattern (13 bp):
GTTGCAGTGGAGT
Found at i:28657140 original size:45 final size:45
Alignment explanation
Indices: 28657084--28657189 Score: 160
Period size: 45 Copynumber: 2.4 Consensus size: 45
28657074 GCAGTGGAGT
* *
28657084 GTTGCAGTGGAGTAGACTGAAGATAGCA-AGTCTTATCTCCCTGAA
1 GTTGCAGTGGAGCAGACTAAAGATAGCAGA-TCTTATCTCCCTGAA
* *
28657129 GTTGTAGTGGAGCAGACTAAAGATGGCAGATCTTATCTCCCTGAA
1 GTTGCAGTGGAGCAGACTAAAGATAGCAGATCTTATCTCCCTGAA
28657174 GTTGCAGTGGAGCAGA
1 GTTGCAGTGGAGCAGA
28657190 TCAAAGCCAT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 54 0.98
46 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.25
Consensus pattern (45 bp):
GTTGCAGTGGAGCAGACTAAAGATAGCAGATCTTATCTCCCTGAA
Found at i:28657962 original size:18 final size:20
Alignment explanation
Indices: 28657936--28657978 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
28657926 AATTCGAATC
28657936 TTTCAATT-A-CAAGTAGAT
1 TTTCAATTAATCAAGTAGAT
*
28657954 TTTCGATTAAATCAAGTAGAT
1 TTTCAATT-AATCAAGTAGAT
28657975 TTTC
1 TTTC
28657979 CTTCTTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 7 0.33
20 1 0.05
21 13 0.62
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (20 bp):
TTTCAATTAATCAAGTAGAT
Found at i:28658887 original size:252 final size:252
Alignment explanation
Indices: 28658442--28658933 Score: 824
Period size: 252 Copynumber: 2.0 Consensus size: 252
28658432 CAAATCCGCA
* * *
28658442 CCTTTTCACCTAAAAGGGTCGATTTGTTTACGTGGTCCTCTTTCTTTGTTGAGCCATTCAATCGA
1 CCTTTTCACCTAAAAGGGTCGATTTGCTCACGTGGTCATCTTTCTTTGTTGAGCCATTCAATCGA
* * *
28658507 GCCTTATTTATATTTTCTTTGATTCTTTTAAATTATCCCTGGAATTTGCGCATATGATCATTTCA
66 GCCCTATTTATATTTCCTTTGATTCTTTTAAATTATCCCTGGAATTTGCACATATGATCATTTCA
* * *
28658572 GTCCGCGTTGAAATGATTCGTTTTCGGGTTTGGTTTATTTGCTTTTTTAATCCCTATTGGTTTAT
131 GTCCACGTTGAAACGATTCGTTTTCGGGTTTGGTTTATTTACTTTTTTAATCCCTATTGGTTTAT
* *
28658637 GTGCATTGTATTTTAGTCCTCCATGTTGCTTAATAGTTTTTATTTGTTGGATCCACG
196 GCGCATTGTATTTTAGTCCTCCATGTTGCTTAACAGTTTTTATTTGTTGGATCCACG
* *
28658694 CCTTTTCACCTAAAAGGGTCGATTTGCTCGCGTGGTCATCTTTCTTTGTTGAGCCATTCAATTGA
1 CCTTTTCACCTAAAAGGGTCGATTTGCTCACGTGGTCATCTTTCTTTGTTGAGCCATTCAATCGA
* * *
28658759 GCCCTATTTATGTTTCCTTTGATTCTTTTAAATTATCCCTGGAATTTGCACATTTGCTCATTTCA
66 GCCCTATTTATATTTCCTTTGATTCTTTTAAATTATCCCTGGAATTTGCACATATGATCATTTCA
28658824 GTCCACGTTGAAACGATTCGTTTT-GAGGTTTGGTTTATTTACTTTTTTAATCCCTATTGGTTTA
131 GTCCACGTTGAAACGATTCGTTTTCG-GGTTTGGTTTATTTACTTTTTTAATCCCTATTGGTTTA
28658888 TGCGCATTGTATTTTAGTCCTCCATGTTGCTTAACAGTTTTTATTT
195 TGCGCATTGTATTTTAGTCCTCCATGTTGCTTAACAGTTTTTATTT
28658934 CTTTACAAAT
Statistics
Matches: 223, Mismatches: 16, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
251 1 0.00
252 222 1.00
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.46
Consensus pattern (252 bp):
CCTTTTCACCTAAAAGGGTCGATTTGCTCACGTGGTCATCTTTCTTTGTTGAGCCATTCAATCGA
GCCCTATTTATATTTCCTTTGATTCTTTTAAATTATCCCTGGAATTTGCACATATGATCATTTCA
GTCCACGTTGAAACGATTCGTTTTCGGGTTTGGTTTATTTACTTTTTTAATCCCTATTGGTTTAT
GCGCATTGTATTTTAGTCCTCCATGTTGCTTAACAGTTTTTATTTGTTGGATCCACG
Found at i:28659556 original size:30 final size:30
Alignment explanation
Indices: 28659522--28659581 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
28659512 ACTTAACAAG
*
28659522 CAAATACCTCTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
28659552 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
28659582 TAATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:28659994 original size:15 final size:16
Alignment explanation
Indices: 28659971--28660004 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
28659961 CTAAAATAAA
*
28659971 TTTATATATTATT-AT
1 TTTACATATTATTAAT
28659986 TTTACATATTATTAAT
1 TTTACATATTATTAAT
28660002 TTT
1 TTT
28660005 TATTTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTACATATTATTAAT
Found at i:28666106 original size:2 final size:2
Alignment explanation
Indices: 28666101--28666134 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28666091 TTACACACGC
28666101 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
28666135 TAAAGAAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28671662 original size:21 final size:22
Alignment explanation
Indices: 28671623--28671663 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
28671613 ATAACAATCT
28671623 AATAATATAAATGAAATTTTCA
1 AATAATATAAATGAAATTTTCA
* *
28671645 AATAAT-TTAATGATATTTT
1 AATAATATAAATGAAATTTT
28671664 ATAATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
AATAATATAAATGAAATTTTCA
Found at i:28679362 original size:19 final size:20
Alignment explanation
Indices: 28679340--28679386 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
28679330 ACATAACAAT
28679340 AAACATAAAAAT-AGAAA-TA
1 AAAC-TAAAAATAAGAAATTA
28679359 AAACTAAAAATAAGAAATTA
1 AAACTAAAAATAAGAAATTA
*
28679379 AAATTAAA
1 AAACTAAA
28679387 TGATAAATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 7 0.28
19 9 0.36
20 9 0.36
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.19
Consensus pattern (20 bp):
AAACTAAAAATAAGAAATTA
Found at i:28681087 original size:17 final size:17
Alignment explanation
Indices: 28681059--28681100 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
28681049 AAAGACTAAT
*
28681059 TAAATAAGTAAAG-AAA
1 TAAATAATTAAAGAAAA
*
28681075 TATAATAATTAAATAAAA
1 TA-AATAATTAAAGAAAA
28681093 TAAATAAT
1 TAAATAAT
28681101 AATAATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 15 0.68
18 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (17 bp):
TAAATAATTAAAGAAAA
Found at i:28681101 original size:3 final size:3
Alignment explanation
Indices: 28681076--28681123 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
28681066 GTAAAGAAAT
* *
28681076 ATA ATA ATT A-A ATA A-A ATAA ATA ATA ATA ATA ATA CTA ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
28681120 ATA A
1 ATA A
28681124 AGTAAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 3 0.08
3 32 0.84
4 3 0.08
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:28681101 original size:25 final size:26
Alignment explanation
Indices: 28681055--28681109 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
28681045 AATGAAAGAC
*
28681055 TAATTAAATAAGTAAAGAAAT-ATAA
1 TAATTAAATAAATAAAGAAATAATAA
*
28681080 TAATTAAATAAAATAAA-TAATAATAA
1 TAATTAAAT-AAATAAAGAAATAATAA
28681106 TAAT
1 TAAT
28681110 ACTAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (26 bp):
TAATTAAATAAATAAAGAAATAATAA
Found at i:28684978 original size:18 final size:18
Alignment explanation
Indices: 28684955--28684993 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
28684945 AAAAGTTAGT
* *
28684955 AAACAAGAATTAAAATAA
1 AAACAAAAAATAAAATAA
28684973 AAACAAAAAATAAAATAA
1 AAACAAAAAATAAAATAA
28684991 AAA
1 AAA
28684994 TGGCTAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.79, C:0.05, G:0.03, T:0.13
Consensus pattern (18 bp):
AAACAAAAAATAAAATAA
Found at i:28686094 original size:11 final size:11
Alignment explanation
Indices: 28686078--28686104 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
28686068 TAGGAAATTC
28686078 TATTTTAAGTT
1 TATTTTAAGTT
28686089 TATTTTAAGTT
1 TATTTTAAGTT
28686100 TATTT
1 TATTT
28686105 ATTTTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (11 bp):
TATTTTAAGTT
Found at i:28686137 original size:17 final size:16
Alignment explanation
Indices: 28686088--28686143 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
28686078 TATTTTAAGT
*
28686088 TTATTTTAAGTTTAT-
1 TTATTTTAATTTTATA
*
28686103 TTATTTTTAATTAT-TA
1 TTA-TTTTAATTTTATA
28686119 TTATTTTAGATTTTATA
1 TTATTTTA-ATTTTATA
28686136 TTAATTTT
1 TT-ATTTT
28686144 CTTAAGCTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 9 0.27
16 15 0.45
17 4 0.12
18 5 0.15
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (16 bp):
TTATTTTAATTTTATA
Found at i:28687039 original size:17 final size:19
Alignment explanation
Indices: 28687008--28687046 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
28686998 TTCCTTTAAA
28687008 TTATTTCACTATTTA-TTT
1 TTATTTCACTATTTACTTT
*
28687026 TTATTTCA-TCTTTACTTT
1 TTATTTCACTATTTACTTT
28687044 TTA
1 TTA
28687047 CTTTTTACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTCACTATTTACTTT
Found at i:28696363 original size:16 final size:15
Alignment explanation
Indices: 28696338--28696385 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
28696328 CTATTTTAAG
28696338 TTTATTTTAATTTTA
1 TTTATTTTAATTTTA
28696353 TTTATTTTTAATTATTA
1 TTTA-TTTTAATT-TTA
28696370 -TTATTTTAGATTTTA
1 TTTATTTTA-ATTTTA
28696385 T
1 T
28696386 ATTAATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.41
16 14 0.48
17 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTTTAATTTTA
Found at i:28697282 original size:17 final size:19
Alignment explanation
Indices: 28697251--28697289 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
28697241 TTCCTTTAAA
28697251 TTATTTCACTATTTA-TTT
1 TTATTTCACTATTTACTTT
*
28697269 TTATTTCA-TCTTTACTTT
1 TTATTTCACTATTTACTTT
28697287 TTA
1 TTA
28697290 CTTTTTACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTCACTATTTACTTT
Found at i:28700721 original size:4 final size:4
Alignment explanation
Indices: 28700712--28700744 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
28700702 CAAAGCAAGG
28700712 GCAT GCAT GCAT GCAT GCAT GCA- GACAT GCAT G
1 GCAT GCAT GCAT GCAT GCAT GCAT G-CAT GCAT G
28700745 ATGTTGTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 1 0.04
4 25 0.93
5 1 0.04
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.21
Consensus pattern (4 bp):
GCAT
Found at i:28703217 original size:3 final size:3
Alignment explanation
Indices: 28703209--28703241 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
28703199 TGGAAAGTTT
28703209 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28703242 ATAAGCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:28705539 original size:18 final size:19
Alignment explanation
Indices: 28705516--28705554 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
28705506 ATATATTCAC
28705516 ACATTTTCA-CAATTCAAT
1 ACATTTTCATCAATTCAAT
28705534 ACATTTTCATTCAATTCAAT
1 ACATTTTCA-TCAATTCAAT
28705554 A
1 A
28705555 TCAATACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (19 bp):
ACATTTTCATCAATTCAAT
Found at i:28706476 original size:3 final size:3
Alignment explanation
Indices: 28706468--28706510 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
28706458 TTATTTTATT
28706468 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
28706511 TTTATTGGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:28707491 original size:22 final size:22
Alignment explanation
Indices: 28707466--28707526 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
28707456 AATACTTGAA
28707466 CTTTCAAAATGTATAAAAAGAC
1 CTTTCAAAATGTATAAAAAGAC
28707488 CTTTCAAAATGTATAAAAAGAC
1 CTTTCAAAATGTATAAAAAGAC
*
28707510 ATTTCAAAAT-TA-AAAAA
1 CTTTCAAAATGTATAAAAA
28707527 TAAAAAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 5 0.13
21 2 0.05
22 31 0.82
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (22 bp):
CTTTCAAAATGTATAAAAAGAC
Found at i:28707735 original size:19 final size:19
Alignment explanation
Indices: 28707713--28707855 Score: 96
Period size: 20 Copynumber: 7.3 Consensus size: 19
28707703 TTTTTGTTGC
28707713 ATTTTATAATTTTTTTATGA
1 ATTTTATAATTTTTTTAT-A
* ** *
28707733 TTTTTATAA-AATTTTACA
1 ATTTTATAATTTTTTTATA
*
28707751 ATTTTTATAAATCTTTTTTTCTA
1 A-TTTTAT-AA--TTTTTTTATA
*
28707774 ATTTTAATAATTTTTTAATA
1 ATTTT-ATAATTTTTTTATA
*
28707794 ATTTTAT-ATTTTTATTAAA
1 ATTTTATAATTTTT-TTATA
* *
28707813 ATTTAAT-A-CTTTTTATA
1 ATTTTATAATTTTTTTATA
28707830 ACTTTTATTAATTTTTTTATA
1 A-TTTTA-TAATTTTTTTATA
28707851 ATTTT
1 ATTTT
28707856 TTGTCACATG
Statistics
Matches: 94, Mismatches: 18, Indels: 22
0.70 0.13 0.16
Matches are distributed among these distances:
17 5 0.05
18 14 0.15
19 24 0.26
20 28 0.30
21 9 0.10
22 6 0.06
23 8 0.09
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (19 bp):
ATTTTATAATTTTTTTATA
Found at i:28707737 original size:20 final size:20
Alignment explanation
Indices: 28707714--28707856 Score: 100
Period size: 19 Copynumber: 7.2 Consensus size: 20
28707704 TTTTGTTGCA
*
28707714 TTTTATAATTTTTTTATGAT
1 TTTTATAATTTTTTTATAAT
** *
28707734 TTTTATAA-AATTTTACAAT
1 TTTTATAATTTTTTTATAAT
*
28707753 TTTTATAAATCTTTTTTTCTAAT
1 TTTTAT-AA--TTTTTTTATAAT
* *
28707776 TTTAATAATTTTTTAATAA-
1 TTTTATAATTTTTTTATAAT
*
28707795 TTTTAT-ATTTTTATTA-AAA
1 TTTTATAATTTTT-TTATAAT
* * *
28707814 TTTAAT-A-CTTTTTATAAC
1 TTTTATAATTTTTTTATAAT
28707832 TTTTATTAATTTTTTTATAAT
1 TTTTA-TAATTTTTTTATAAT
28707853 TTTT
1 TTTT
28707857 TGTCACATGT
Statistics
Matches: 94, Mismatches: 19, Indels: 19
0.71 0.14 0.14
Matches are distributed among these distances:
17 3 0.03
18 17 0.18
19 27 0.29
20 20 0.21
21 13 0.14
22 2 0.02
23 12 0.13
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (20 bp):
TTTTATAATTTTTTTATAAT
Found at i:28709939 original size:16 final size:17
Alignment explanation
Indices: 28709918--28709952 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
28709908 CTTTGGATAT
28709918 CTAAATCCCGG-TAATG
1 CTAAATCCCGGTTAATG
28709934 CTAAATCCCGGTTAATG
1 CTAAATCCCGGTTAATG
28709951 CT
1 CT
28709953 CCATTGTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (17 bp):
CTAAATCCCGGTTAATG
Found at i:28712783 original size:20 final size:20
Alignment explanation
Indices: 28712742--28712783 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28712732 ACTAAAGCGA
*
28712742 TAAAAAAAGTAAATTAATAT
1 TAAAAAAAGTAAATGAATAT
28712762 TAAAAAAA-TAAATGAATGAT
1 TAAAAAAAGTAAATGAAT-AT
28712782 TA
1 TA
28712784 TTCCACAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (20 bp):
TAAAAAAAGTAAATGAATAT
Found at i:28713734 original size:2 final size:2
Alignment explanation
Indices: 28713727--28713764 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
28713717 TTACAGCCAA
28713727 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28713765 TTTGAGACCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28715614 original size:2 final size:2
Alignment explanation
Indices: 28715609--28715640 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
28715599 GTATATACAC
*
28715609 AT AT AT AC 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
28715641 TTGAATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28715615 original size:10 final size:10
Alignment explanation
Indices: 28715600--28715640 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
28715590 CTTTTATGTG
*
28715600 TATATACACA
1 TATATACATA
28715610 TATATACATA
1 TATATACATA
*
28715620 TATATATATA
1 TATATACATA
*
28715630 TATATATATA
1 TATATACATA
28715640 T
1 T
28715641 TTGAATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (10 bp):
TATATACATA
Found at i:28715618 original size:8 final size:8
Alignment explanation
Indices: 28715601--28715639 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
28715591 TTTTATGTGT
*
28715601 ATATACAC
1 ATATATAC
28715609 ATATATAC
1 ATATATAC
*
28715617 ATATATAT
1 ATATATAC
*
28715625 ATATATAT
1 ATATATAC
28715633 ATATATA
1 ATATATA
28715640 TTTGAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATATAC
Found at i:28721066 original size:61 final size:60
Alignment explanation
Indices: 28720997--28721131 Score: 141
Period size: 60 Copynumber: 2.2 Consensus size: 60
28720987 TCTGACTATA
* ** *
28720997 AAAT-ATTCAACAAAATTAG-CCTTCAATGTTTGTAAAATTTGT-ATTTTTAGTTCGAATTCT
1 AAATAATTCAACAAAATTAGTCC-TCAA-ATTTACAAAATTTGTCA-ATTTAGTTCGAATTCT
* * * *
28721057 AAATAATTCAACAAAGTTTGTCCTCAAATTTACAAATTTTGTCAATTTAGTTCTAATTCT
1 AAATAATTCAACAAAATTAGTCCTCAAATTTACAAAATTTGTCAATTTAGTTCGAATTCT
*
28721117 AAAAAATTCAACAAA
1 AAATAATTCAACAAA
28721132 GTAATTTTTG
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
60 43 0.68
61 18 0.29
62 2 0.03
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.39
Consensus pattern (60 bp):
AAATAATTCAACAAAATTAGTCCTCAAATTTACAAAATTTGTCAATTTAGTTCGAATTCT
Found at i:28725166 original size:46 final size:47
Alignment explanation
Indices: 28725096--28725316 Score: 160
Period size: 46 Copynumber: 4.9 Consensus size: 47
28725086 ATAGGGAGAC
*
28725096 CAAAATTCGAATCTGCTCCGCTCCTGCTCAGCGAAGATAAGATTCAT
1 CAAAATTCGAATCTGCTCCACTCCTGCTCAGCGAAGATAAGATTCAT
* *
28725143 CAAAATTCG-ATCTGCTTCACTCCTGCTCAGTGAAGATAAGA-TC-T
1 CAAAATTCGAATCTGCTCCACTCCTGCTCAGCGAAGATAAGATTCAT
** * ** * *
28725187 -AGTATT-TAGCCTGCTCCACTCCTGCTCAGTGAAGATAAG--GC-T
1 CAAAATTCGAATCTGCTCCACTCCTGCTCAGCGAAGATAAGATTCAT
* ** * * * * * *
28725229 GATGATTGGAATCTGCTCCA-TCGCCGGT-ACGTGGAGATAAAATTCAT
1 CAAAATTCGAATCTGCTCCACTC-CTGCTCA-GCGAAGATAAGATTCAT
*
28725276 CAAAATTCG-ATCTGCTCCACTCCTG-TCAGTGAAGATAAGAT
1 CAAAATTCGAATCTGCTCCACTCCTGCTCAGCGAAGATAAGAT
28725317 CTGGTGTTTA
Statistics
Matches: 137, Mismatches: 27, Indels: 22
0.74 0.15 0.12
Matches are distributed among these distances:
42 2 0.01
43 39 0.28
44 22 0.16
45 14 0.10
46 43 0.31
47 17 0.12
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (47 bp):
CAAAATTCGAATCTGCTCCACTCCTGCTCAGCGAAGATAAGATTCAT
Found at i:28725351 original size:132 final size:132
Alignment explanation
Indices: 28725130--28725630 Score: 779
Period size: 132 Copynumber: 3.8 Consensus size: 132
28725120 TGCTCAGCGA
* * * *
28725130 AGATAAGATTCATCAAAATTCGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATTTA
1 AGATAAAATTCATCAAAATTCGATCTGCTCCACTCCTG-TCAGTGAAGATAAGATCTAGTCTATA
28725195 GCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACG
65 GCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACG
28725260 TGG
130 TGG
* * *
28725263 AGATAAAATTCATCAAAATTCGATCTGCTCCACTCCTGTCAGTGAAGATAAGATCTGGTGTTTAG
1 AGATAAAATTCATCAAAATTCGATCTGCTCCACTCCTGTCAGTGAAGATAAGATCTAGTCTATAG
* ** * * * *
28725328 CCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACAT
66 CCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGT
28725393 GG
131 GG
* * * * *
28725395 AGATAAGACTT-GTCAAAATTTGATCTGCTTCACTCCTGTCAGTGAAGGTAAGATCTAGTCTATA
1 AGATAA-AATTCATCAAAATTCGATCTGCTCCACTCCTGTCAGTGAAGATAAGATCTAGTCTATA
28725459 GCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACG
65 GCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACG
28725524 TGG
130 TGG
* *
28725527 AGATAAGATTCATCAAAATTCGATCTACTCCACTCCTGTCAGTGAAGATAAGATCTAGTCTATAG
1 AGATAAAATTCATCAAAATTCGATCTGCTCCACTCCTGTCAGTGAAGATAAGATCTAGTCTATAG
*
28725592 CCTGCTCCACTCCTGCTCAGTGGAGATAAGGCTGATGAT
66 CCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGAT
28725631 ATCTGTAATC
Statistics
Matches: 332, Mismatches: 34, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
131 2 0.01
132 291 0.88
133 39 0.12
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (132 bp):
AGATAAAATTCATCAAAATTCGATCTGCTCCACTCCTGTCAGTGAAGATAAGATCTAGTCTATAG
CCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGT
GG
Found at i:28725479 original size:264 final size:265
Alignment explanation
Indices: 28725142--28725625 Score: 871
Period size: 264 Copynumber: 1.8 Consensus size: 265
28725132 ATAAGATTCA
*
28725142 TCAAAATTCGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATTTAGCCTGCTCCACT
1 TCAAAATTCGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATATAGCCTGCTCCACT
28725207 CCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAAAT
66 CCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAAAT
* * * *
28725272 TCATCAAAATTCGATCTGCTCCACTCCTGTCAGTGAAGATAAGATCTGGTGTTTAGCCTGCTCCA
131 TCATCAAAATTCGATCTACTCCACTCCTGTCAGTGAAGATAAGATCTAGTCTATAGCCTGCTCCA
28725337 CTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAG
196 CTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAG
28725402 ACTTG
261 ACTTG
* * *
28725407 TCAAAATTTGATCTGCTTCACTCCTG-TCAGTGAAGGTAAGATCTAGTCTATAGCCTGCTCCACT
1 TCAAAATTCGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATATAGCCTGCTCCACT
*
28725471 CCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGAT
66 CCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAAAT
28725536 TCATCAAAATTCGATCTACTCCACTCCTGTCAGTGAAGATAAGATCTAGTCTATAGCCTGCTCCA
131 TCATCAAAATTCGATCTACTCCACTCCTGTCAGTGAAGATAAGATCTAGTCTATAGCCTGCTCCA
*
28725601 CTCCTGCTCAGTGGAGATAAGGCTG
196 CTCCTGCTCAGTGAAGATAAGGCTG
28725626 ATGATATCTG
Statistics
Matches: 209, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
264 184 0.88
265 25 0.12
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (265 bp):
TCAAAATTCGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATATAGCCTGCTCCACT
CCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAAAT
TCATCAAAATTCGATCTACTCCACTCCTGTCAGTGAAGATAAGATCTAGTCTATAGCCTGCTCCA
CTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAG
ACTTG
Found at i:28749708 original size:46 final size:47
Alignment explanation
Indices: 28749638--28749857 Score: 160
Period size: 43 Copynumber: 4.9 Consensus size: 47
28749628 ATAGGGAGAC
*
28749638 CAAAATTCGAATCTGCTCCGCTCCTGCTCAGCGAAGATAAGATTCAT
1 CAAAATTCGAATCTGCTCCACTCCTGCTCAGCGAAGATAAGATTCAT
* *
28749685 CAAAATTCG-ATCTGCTTCACTCCTGCTCAGTGAAGATAAGA-TC-T
1 CAAAATTCGAATCTGCTCCACTCCTGCTCAGCGAAGATAAGATTCAT
** * ** * *
28749729 -AGTATT-TAGCCTGCTCCACTCCTGCTCAGTGAAGATAAG--GC-T
1 CAAAATTCGAATCTGCTCCACTCCTGCTCAGCGAAGATAAGATTCAT
* ** * * * * *
28749771 GATGATTGGAATCTGCTCCA-TGCC-GGT-ACGTGGAGATAAAATTCAT
1 CAAAATTCGAATCTGCTCCACT-CCTGCTCA-GCGAAGATAAGATTCAT
*
28749817 CAAAATTCG-ATCTGCTCCACTCCTG-TCAGTGAAGATAAGAT
1 CAAAATTCGAATCTGCTCCACTCCTGCTCAGCGAAGATAAGAT
28749858 CTGGTGTTTA
Statistics
Matches: 137, Mismatches: 25, Indels: 24
0.74 0.13 0.13
Matches are distributed among these distances:
42 3 0.02
43 48 0.35
44 12 0.09
45 27 0.20
46 38 0.28
47 9 0.07
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (47 bp):
CAAAATTCGAATCTGCTCCACTCCTGCTCAGCGAAGATAAGATTCAT
Found at i:28749838 original size:132 final size:131
Alignment explanation
Indices: 28749672--28750171 Score: 768
Period size: 132 Copynumber: 3.8 Consensus size: 131
28749662 TGCTCAGCGA
* * * *
28749672 AGATAAGATTCATCAAAATTCGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATTTA
1 AGATAAAATTCATCAAAATTCGATCTGCTCCACTCCTG-TCAGTGAAGATAAGATCTAGTCTATA
28749737 GCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATGCCGGTACGT
65 GCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATGCCGGTACGT
28749802 GG
130 GG
* * *
28749804 AGATAAAATTCATCAAAATTCGATCTGCTCCACTCCTGTCAGTGAAGATAAGATCTGGTGTTTAG
1 AGATAAAATTCATCAAAATTCGATCTGCTCCACTCCTGTCAGTGAAGATAAGATCTAGTCTATAG
* ** * * *
28749869 CCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACAT
66 CCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCA-TGCCGGTACGT
28749934 GG
130 GG
* * * * *
28749936 AGATAAGACTT-GTCAAAATTTGATCTGCTTCACTCCTGTCAGTGAAGGTAAGATCTAGTCTATA
1 AGATAA-AATTCATCAAAATTCGATCTGCTCCACTCCTGTCAGTGAAGATAAGATCTAGTCTATA
28750000 GCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACG
65 GCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCAT-GCCGGTACG
28750065 TGG
129 TGG
* *
28750068 AGATAAGATTCATCAAAATTCGATCTACTCCACTCCTGTCAGTGAAGATAAGATCTAGTCTATAG
1 AGATAAAATTCATCAAAATTCGATCTGCTCCACTCCTGTCAGTGAAGATAAGATCTAGTCTATAG
*
28750133 CCTGCTCCACTCCTGCTCAGTGGAGATAAGGCTGATGAT
66 CCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGAT
28750172 ATCTGTAATC
Statistics
Matches: 332, Mismatches: 32, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
131 77 0.23
132 252 0.76
133 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (131 bp):
AGATAAAATTCATCAAAATTCGATCTGCTCCACTCCTGTCAGTGAAGATAAGATCTAGTCTATAG
CCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATGCCGGTACGTG
G
Found at i:28750020 original size:263 final size:265
Alignment explanation
Indices: 28749684--28750166 Score: 862
Period size: 264 Copynumber: 1.8 Consensus size: 265
28749674 ATAAGATTCA
*
28749684 TCAAAATTCGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATTTAGCCTGCTCCACT
1 TCAAAATTCGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATATAGCCTGCTCCACT
28749749 CCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCAT-GCCGGTACGTGGAGATAAAAT
66 CCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAAAT
* * * *
28749813 TCATCAAAATTCGATCTGCTCCACTCCTGTCAGTGAAGATAAGATCTGGTGTTTAGCCTGCTCCA
131 TCATCAAAATTCGATCTACTCCACTCCTGTCAGTGAAGATAAGATCTAGTCTATAGCCTGCTCCA
28749878 CTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAG
196 CTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAG
28749943 ACTTG
261 ACTTG
* * *
28749948 TCAAAATTTGATCTGCTTCACTCCTG-TCAGTGAAGGTAAGATCTAGTCTATAGCCTGCTCCACT
1 TCAAAATTCGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATATAGCCTGCTCCACT
*
28750012 CCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGAT
66 CCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAAAT
28750077 TCATCAAAATTCGATCTACTCCACTCCTGTCAGTGAAGATAAGATCTAGTCTATAGCCTGCTCCA
131 TCATCAAAATTCGATCTACTCCACTCCTGTCAGTGAAGATAAGATCTAGTCTATAGCCTGCTCCA
*
28750142 CTCCTGCTCAGTGGAGATAAGGCTG
196 CTCCTGCTCAGTGAAGATAAGGCTG
28750167 ATGATATCTG
Statistics
Matches: 208, Mismatches: 10, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
263 78 0.38
264 130 0.62
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (265 bp):
TCAAAATTCGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATATAGCCTGCTCCACT
CCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAAAT
TCATCAAAATTCGATCTACTCCACTCCTGTCAGTGAAGATAAGATCTAGTCTATAGCCTGCTCCA
CTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAG
ACTTG
Found at i:28767484 original size:2 final size:2
Alignment explanation
Indices: 28767477--28767508 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28767467 GGCTATTATA
28767477 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
28767509 AATTCATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:28770219 original size:16 final size:16
Alignment explanation
Indices: 28770198--28770268 Score: 99
Period size: 16 Copynumber: 4.4 Consensus size: 16
28770188 GTTTGGTTCA
28770198 CTGTAATGGAATA-AGG
1 CTGTAATGGAATAGA-G
*
28770214 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
*
28770230 TTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
28770246 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
28770262 TTGTAAT
1 CTGTAAT
28770269 CAGTAATTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
16 48 0.98
17 1 0.02
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.31
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:28770240 original size:32 final size:32
Alignment explanation
Indices: 28770199--28770268 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
28770189 TTTGGTTCAC
*
28770199 TGTAATGGAATA-AGGCTGTAATTGAATAGAGT
1 TGTAATGGAATAGA-GCTGTAATGGAATAGAGT
28770231 TGTAATGGAATAGAGCTGTAATGGAATAGAGT
1 TGTAATGGAATAGAGCTGTAATGGAATAGAGT
28770263 TGTAAT
1 TGTAAT
28770269 CAGTAATTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 35 0.97
33 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.29, T:0.31
Consensus pattern (32 bp):
TGTAATGGAATAGAGCTGTAATGGAATAGAGT
Found at i:28770306 original size:46 final size:44
Alignment explanation
Indices: 28770250--28770338 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
28770240 ATAGAGCTGT
**
28770250 AATGGAATAGAGTTGTAATCAGTAATTC-AACTGTTTGGTTGAATGA
1 AATGGAATAGAACTGTAAT-AGT-ATTCTAA-TGTTTGGTTGAATGA
*
28770296 AATGGAATAGAACTGTAATAGTATTCTTATGTTTGGTTGAATG
1 AATGGAATAGAACTGTAATAGTATTCTAATGTTTGGTTGAATG
28770339 GAATAATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
44 18 0.46
45 4 0.10
46 17 0.44
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCTAATGTTTGGTTGAATGA
Found at i:28770559 original size:58 final size:57
Alignment explanation
Indices: 28770428--28770586 Score: 162
Period size: 58 Copynumber: 2.8 Consensus size: 57
28770418 TATTGTTATT
* * * * * *
28770428 AAATTTTAATAAAATTACTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACC
1 AAATTTTAACATAATTATTATTAAATATAAATTAAT-AAAATAATAAATAATTTAACA
* * * *
28770486 ATATTTTAACATAATTATTATTAAATATAACTTAATAAAATAATATATAATTTAATA
1 AAATTTTAACATAATTATTATTAAATATAAATTAATAAAATAATAAATAATTTAACA
** *
28770543 AAATTCTTAATGTAATTATTATT--ATATAAATTAA-AAAATCATAA
1 AAATT-TTAACATAATTATTATTAAATATAAATTAATAAAATAATAA
28770587 CTATTATTAT
Statistics
Matches: 85, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
55 8 0.09
56 10 0.12
57 22 0.26
58 45 0.53
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (57 bp):
AAATTTTAACATAATTATTATTAAATATAAATTAATAAAATAATAAATAATTTAACA
Found at i:28776386 original size:25 final size:25
Alignment explanation
Indices: 28776352--28776403 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
28776342 TTCATATATG
28776352 TTGTTGCTGTAGAAAGGTCAGGGGT
1 TTGTTGCTGTAGAAAGGTCAGGGGT
28776377 TTGTTGCTGTAGAAAGGTCAGGGGT
1 TTGTTGCTGTAGAAAGGTCAGGGGT
28776402 TT
1 TT
28776404 TATTGACGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.08, G:0.38, T:0.35
Consensus pattern (25 bp):
TTGTTGCTGTAGAAAGGTCAGGGGT
Found at i:28776891 original size:19 final size:20
Alignment explanation
Indices: 28776863--28776901 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
28776853 TCCCATTATT
28776863 TATTTATTTTT-TGTTTTAA
1 TATTTATTTTTATGTTTTAA
*
28776882 TATTTGTTTTTATGTTTTAA
1 TATTTATTTTTATGTTTTAA
28776902 ATGTATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (20 bp):
TATTTATTTTTATGTTTTAA
Found at i:28776919 original size:25 final size:23
Alignment explanation
Indices: 28776882--28776927 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
28776872 TTTGTTTTAA
*
28776882 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
28776905 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
28776928 GTTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:28782509 original size:18 final size:18
Alignment explanation
Indices: 28782486--28782539 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
28782476 CCACCACCAA
28782486 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
*
28782504 CTCCACT----AC-C-TA
1 CTCCACTAGCCACACTTG
28782516 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
28782534 CTCCAC
1 CTCCAC
28782540 CACCACTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 8 0.29
13 1 0.04
14 2 0.07
16 2 0.07
17 1 0.04
18 14 0.50
ACGTcount: A:0.22, C:0.48, G:0.07, T:0.22
Consensus pattern (18 bp):
CTCCACTAGCCACACTTG
Found at i:28782519 original size:30 final size:30
Alignment explanation
Indices: 28782476--28782544 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
28782466 CTAGCCTTTG
28782476 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
28782506 CCACTACCTACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
28782536 CCACCACCA
1 CCACCACCA
28782545 CTTGTACCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.26, C:0.51, G:0.06, T:0.17
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:28783049 original size:23 final size:23
Alignment explanation
Indices: 28783012--28783093 Score: 62
Period size: 23 Copynumber: 3.5 Consensus size: 23
28783002 TTTTTTTTGT
28783012 TATTAT-TATATTTCTTAATATTA
1 TATTATATATA-TTCTTAATATTA
* *
28783035 TATTATATATATTCTT-TTAATA
1 TATTATATATATTCTTAATATTA
** *
28783057 TATTAGGTATATTCTAAAT-TCTA
1 TATTATATATATTCTTAATAT-TA
28783080 TATTACGTATATAT
1 TATTA--TATATAT
28783094 ATATATATTA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
22 17 0.38
23 19 0.42
24 4 0.09
25 5 0.11
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (23 bp):
TATTATATATATTCTTAATATTA
Found at i:28783094 original size:2 final size:2
Alignment explanation
Indices: 28783087--28783163 Score: 63
Period size: 2 Copynumber: 39.5 Consensus size: 2
28783077 CTATATTACG
* * * *
28783087 TA TA TA TA TA TA TA T- TA TA CTA T- TT TA TG TA TA TA TC TT TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
*
28783128 -A TA CTA TA T- TA TT TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28783164 TTTACATGTT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
1 4 0.07
2 53 0.87
3 4 0.07
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (2 bp):
TA
Found at i:28783122 original size:54 final size:54
Alignment explanation
Indices: 28783054--28783167 Score: 144
Period size: 54 Copynumber: 2.1 Consensus size: 54
28783044 TATTCTTTTA
* * *
28783054 ATATATTAGGTATAT-TC-TAAATTCTATATTACGTATATATATATATAT-TAT
1 ATATTTTATGTATATATCTTAAATACTATATTACGTATATATATATATATATAT
* **
28783105 ACTATTTTATGTATATATCTTTAATACTATATTATTTATATATATATATATATAT
1 A-TATTTTATGTATATATCTTAAATACTATATTACGTATATATATATATATATAT
28783160 ATATTTTA
1 ATATTTTA
28783168 CATGTTATCT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
51 1 0.02
52 12 0.23
53 2 0.04
54 34 0.64
55 4 0.08
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.53
Consensus pattern (54 bp):
ATATTTTATGTATATATCTTAAATACTATATTACGTATATATATATATATATAT
Found at i:28783160 original size:25 final size:26
Alignment explanation
Indices: 28783089--28783165 Score: 88
Period size: 25 Copynumber: 3.0 Consensus size: 26
28783079 ATATTACGTA
* *
28783089 TATATATATATATTATACTATTTTATG
1 TATATATATATA-TATACTATATTATT
* *
28783116 TATATATCTTTA-ATACTATATTATT
1 TATATATATATATATACTATATTATT
28783141 TATATATATATATATA-TATA-TATT
1 TATATATATATATATACTATATTATT
28783165 T
1 T
28783166 TACATGTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
24 5 0.12
25 25 0.58
26 3 0.07
27 10 0.23
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (26 bp):
TATATATATATATATACTATATTATT
Found at i:28783167 original size:25 final size:25
Alignment explanation
Indices: 28783087--28783213 Score: 84
Period size: 25 Copynumber: 5.0 Consensus size: 25
28783077 CTATATTACG
28783087 TATATATATATATAT-TATACTATTT
1 TATATATATATATATATATA-TATTT
* * *
28783112 TATGTATATATCTTTAATACTATATTATT
1 TATATATATATATAT-ATA-TATA-T-TT
28783141 TATATATATATATATATATATATTT
1 TATATATATATATATATATATATTT
* * * *
28783166 TACATGT-TATCTTATGTATATATTT
1 TATATATATAT-ATATATATATATTT
* *
28783191 TA-AT-TATAT-TATGTATGTATTT
1 TATATATATATATATATATATATTT
28783213 T
1 T
28783214 TTTACACTAT
Statistics
Matches: 84, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
22 13 0.15
23 1 0.01
24 8 0.10
25 33 0.39
26 1 0.01
27 8 0.10
28 6 0.07
29 14 0.17
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (25 bp):
TATATATATATATATATATATATTT
Found at i:28783202 original size:22 final size:24
Alignment explanation
Indices: 28783147--28783239 Score: 75
Period size: 25 Copynumber: 3.8 Consensus size: 24
28783137 TATTTATATA
*
28783147 TATATATATATATATATTTTACATGT
1 TATAT-TATGTATATATTTTACA-GT
*
28783173 TATCTTATGTATATATTTTA-A-T
1 TATATTATGTATATATTTTACAGT
* *
28783195 TATATTATGTATGTATTTTTTTACA-C
1 TATATTATGTA--TA-TATTTTACAGT
*
28783221 TATATTATGTACATATTTT
1 TATATTATGTATATATTTT
28783240 TAATATTATC
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
22 11 0.20
23 5 0.09
24 4 0.07
25 20 0.36
26 16 0.29
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57
Consensus pattern (24 bp):
TATATTATGTATATATTTTACAGT
Found at i:28783224 original size:26 final size:25
Alignment explanation
Indices: 28783178--28783240 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
28783168 CATGTTATCT
* *
28783178 TATGTATATATTTTAATTATATTATG
1 TATGTAT-TTTTTTAACTATATTATG
28783204 TATGTATTTTTTTACACTATATTATG
1 TATGTATTTTTTTA-ACTATATTATG
**
28783230 TACATATTTTT
1 TATGTATTTTT
28783241 AATATTATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 6 0.19
26 26 0.81
ACGTcount: A:0.30, C:0.05, G:0.06, T:0.59
Consensus pattern (25 bp):
TATGTATTTTTTTAACTATATTATG
Found at i:28783247 original size:20 final size:20
Alignment explanation
Indices: 28783222--28783280 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 20
28783212 TTTTTACACT
28783222 ATATTATGTACATATTTTTA
1 ATATTATGTACATATTTTTA
** *
28783242 ATATTATCACGTATTTATTTTTT
1 ATATTAT---GTACATATTTTTA
28783265 ATA-TATGTACATATTT
1 ATATTATGTACATATTT
28783281 ATGTAGTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 3 0.10
23 13 0.42
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (20 bp):
ATATTATGTACATATTTTTA
Found at i:28783419 original size:16 final size:15
Alignment explanation
Indices: 28783395--28783429 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
28783385 TAATTATTAT
28783395 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
28783411 TATTTTAATATTTTA
1 TATTCTAATATTTTA
28783426 TATT
1 TATT
28783430 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:28784704 original size:27 final size:27
Alignment explanation
Indices: 28784672--28784724 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
28784662 TCCCCCCAAA
28784672 AAAAACCTAACCCAAAAAAAAAAAAAG
1 AAAAACCTAACCCAAAAAAAAAAAAAG
*
28784699 AAAAACCTAACCCCAAAAAAAAAAAA
1 AAAAACCTAACCCAAAAAAAAAAAAA
28784725 CCAAGAAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.74, C:0.21, G:0.02, T:0.04
Consensus pattern (27 bp):
AAAAACCTAACCCAAAAAAAAAAAAAG
Found at i:28785563 original size:2 final size:2
Alignment explanation
Indices: 28785556--28785583 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28785546 TATTATATGC
28785556 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
28785584 GTATTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28787258 original size:12 final size:12
Alignment explanation
Indices: 28787241--28787276 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
28787231 ATTCATTTGA
28787241 CATTCATGCATT
1 CATTCATGCATT
28787253 CATTCATGCATT
1 CATTCATGCATT
*
28787265 CATTCATACATT
1 CATTCATGCATT
28787277 GCATATCCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:28795625 original size:76 final size:74
Alignment explanation
Indices: 28795525--28795685 Score: 218
Period size: 76 Copynumber: 2.1 Consensus size: 74
28795515 TGATATTTTT
**
28795525 ATTTCTG-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGAG
1 ATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAG
28795589 GTATTTTCA
66 GTATTTTCA
* * * *
28795598 ATTTCTGCTTTTCAAAAAAAATCAACTCATACTGCGAGAGGTAAGTTGAGCCTCAAGGCACGTTG
1 ATTTCTG-TTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTG
28795663 AGGTAATTTT-A
64 AGGT-ATTTTCA
28795674 ATTTCTGCTTTT
1 ATTTCTG-TTTT
28795686 AAATTTATAT
Statistics
Matches: 80, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
73 7 0.09
75 4 0.05
76 64 0.80
77 5 0.06
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (74 bp):
ATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAG
GTATTTTCA
Found at i:28795766 original size:89 final size:90
Alignment explanation
Indices: 28795606--28795769 Score: 251
Period size: 89 Copynumber: 1.8 Consensus size: 90
28795596 CAATTTCTGC
* *
28795606 TTTTCAAAAAAAATCAACTCATACTGCGAGAGGTAAGTTGAGCCTCAAGGCACGTTGAGGTAATT
1 TTTTCAAAAAAAATCAACTCATACTGCGAGAGGTAAGTTGACCCTCAAGGCACGCTGAGGTAATT
*
28795671 TTAATTTCTGCTTTTAAATTTATAT
66 TCAATTTCTGCTTTTAAATTTATAT
* * *
28795696 TTTTCAAAAAAATTCAACTCATATTGCGAGAGGT-GGTTGACCCTC-AGGACACGCTGAGGTAAT
1 TTTTCAAAAAAAATCAACTCATACTGCGAGAGGTAAGTTGACCCTCAAGG-CACGCTGAGGTAAT
28795759 TTCAATTTCTG
65 TTCAATTTCTG
28795770 TTGTAAAAAC
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
88 3 0.04
89 32 0.48
90 32 0.48
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (90 bp):
TTTTCAAAAAAAATCAACTCATACTGCGAGAGGTAAGTTGACCCTCAAGGCACGCTGAGGTAATT
TCAATTTCTGCTTTTAAATTTATAT
Found at i:28795778 original size:72 final size:73
Alignment explanation
Indices: 28795696--28796038 Score: 467
Period size: 75 Copynumber: 4.6 Consensus size: 73
28795686 AAATTTATAT
*
28795696 TTTTCAAAAAAATTCAACTCATATTGCGAGAGGTG-GTTGACCCTCAGGACACGCTGAGGTAATT
1 TTTT-AAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATT
28795760 TCAATTTCTG
64 TCAATTTCTG
* ** * * *
28795770 TTGTAAAAACAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATT
1 TT-T-TAAA-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAAT
*
28795835 TTCAATTTTTG
63 TTCAATTTCTG
*
28795846 TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATT
1 -TTTT-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATT
28795911 TCAATTTCTG
64 TCAATTTCTG
* * *
28795921 TTTT-CAAAAATCAACTCATATTACGAGAGGTGAATTGAGCCTC-GAGACACGCTGAGGTAATTT
1 TTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG-GACACGCTGAGGTAATTT
28795984 CAATTTCTG
65 CAATTTCTG
* *
28795993 TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 TTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
28796039 ATCACACATG
Statistics
Matches: 237, Mismatches: 23, Indels: 18
0.85 0.08 0.06
Matches are distributed among these distances:
71 1 0.00
72 67 0.28
73 35 0.15
74 7 0.03
75 83 0.35
76 42 0.18
77 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (73 bp):
TTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
AATTTCTG
Found at i:28795812 original size:165 final size:161
Alignment explanation
Indices: 28795532--28795996 Score: 557
Period size: 165 Copynumber: 2.9 Consensus size: 161
28795522 TTTATTTCTG
* ** *
28795532 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTATTTTC
1 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
* * * *
28795597 AATTTCTGCTTTTCAAAAAAAATCAACTCATACTGCGAGAGGTAAGTTGAGCCTCAAGGCACGTT
66 AATTTCTG--TTT-AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCT
28795662 GAGGTAATTTTAATTTCTGCTTTTAAATTTATATT
128 GAGGTAATTTTAATTTCTGCTTTT-AATTTATATT
*
28795697 TTTCAAAAAAATTCAACTCATATTGCGAGAGGTG-GTTGACCCTCAGGACACGCTGAGGTAATTT
1 TTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTT
** *
28795761 CAATTTCTGTTGTAAAAACAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGC
65 CAATTTCTGTT-T-AAAA-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGC
* *
28795826 TGAGG------T-ATTT-T-C----AATTTTTGTT
127 TGAGGTAATTTTAATTTCTGCTTTTAATTTATATT
*
28795848 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTC
1 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
** * * *
28795913 AATTTCTGTTT-TCAAAAATCAACTCATATTACGAGAGGTGAATTGAGCCTCGAGACACGCTGAG
66 AATTTCTGTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAG
*
28795977 GTAATTTCAATTTCTG-TTTT
131 GTAATTTTAATTTCTGCTTTT
28795997 CAAAAAATCA
Statistics
Matches: 257, Mismatches: 26, Indels: 40
0.80 0.08 0.12
Matches are distributed among these distances:
147 45 0.18
148 1 0.00
150 23 0.09
151 58 0.23
154 4 0.02
155 1 0.00
156 1 0.00
157 1 0.00
158 4 0.02
159 1 0.00
163 2 0.01
164 5 0.02
165 89 0.35
166 22 0.09
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (161 bp):
TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
AATTTCTGTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAG
GTAATTTTAATTTCTGCTTTTAATTTATATT
Found at i:28795995 original size:147 final size:150
Alignment explanation
Indices: 28795695--28796038 Score: 511
Period size: 147 Copynumber: 2.3 Consensus size: 150
28795685 TAAATTTATA
*
28795695 TTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTG-GTTGACCCTCAGGACACGCTGAGGTAAT
1 TTTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAAT
* * *
28795759 TTCAATTTCTGTTGTAAAAACAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAT
65 TTCAATTTCTGTTGT-AAAACAAAATCAACTCATATTACGAGAAATGAATTGAGCCTCAAGACAC
* *
28795824 GCTGAGGTATTTTCAATTTTTG
129 GCTGAGGTAATTTCAATTTCTG
*
28795846 TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATT
1 TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATT
** ** *
28795911 TCAATTTCTGTT-T-TCA-AAAATCAACTCATATTACGAGAGGTGAATTGAGCCTCGAGACACGC
66 TCAATTTCTGTTGTAAAACAAAATCAACTCATATTACGAGAAATGAATTGAGCCTCAAGACACGC
28795973 TGAGGTAATTTCAATTTCTG
131 TGAGGTAATTTCAATTTCTG
*
28795993 -TTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
28796039 ATCACACATG
Statistics
Matches: 178, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
145 39 0.22
146 5 0.03
147 58 0.33
148 1 0.01
150 23 0.13
151 52 0.29
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (150 bp):
TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATT
TCAATTTCTGTTGTAAAACAAAATCAACTCATATTACGAGAAATGAATTGAGCCTCAAGACACGC
TGAGGTAATTTCAATTTCTG
Found at i:28796939 original size:24 final size:24
Alignment explanation
Indices: 28796893--28796957 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
28796883 CCCTCCCAAA
**
28796893 AAAAAAAAGAAAAAAACCTAACCC
1 AAAAAAAAGAAAAAAACAAAACCC
*
28796917 AAAAAAAAGAAAAAAGA-AAAACCT
1 AAAAAAAAGAAAAAA-ACAAAACCC
*
28796941 AACCAAAAA-AAAAAAAC
1 AA-AAAAAAGAAAAAAAC
28796958 CAAGAAACCC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 1 0.03
24 27 0.79
25 6 0.18
ACGTcount: A:0.77, C:0.15, G:0.05, T:0.03
Consensus pattern (24 bp):
AAAAAAAAGAAAAAAACAAAACCC
Found at i:28796964 original size:29 final size:28
Alignment explanation
Indices: 28796887--28796956 Score: 108
Period size: 27 Copynumber: 2.5 Consensus size: 28
28796877 ATTAAGCCCT
*
28796887 CCCAAAAAAAAAAAGAA-AAAAACCTAA
1 CCCAAAAAAAAAAAAAAGAAAAACCTAA
28796914 CCCAAAAAAAAGAAAAAAGAAAAACCTAA
1 CCCAAAAAAAA-AAAAAAGAAAAACCTAA
28796943 -CCAAAAAAAAAAAA
1 CCCAAAAAAAAAAAA
28796957 CCAAGAAACC
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 15 0.38
28 15 0.38
29 10 0.25
ACGTcount: A:0.76, C:0.17, G:0.04, T:0.03
Consensus pattern (28 bp):
CCCAAAAAAAAAAAAAAGAAAAACCTAA
Found at i:28797703 original size:14 final size:14
Alignment explanation
Indices: 28797668--28797709 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
28797658 ATCATTATTT
*
28797668 TATATTATTATTGTA
1 TATATTTTTA-TGTA
*
28797683 AAT-TTTTTATGTA
1 TATATTTTTATGTA
28797696 TATATTTTTATGTA
1 TATATTTTTATGTA
28797710 CGTTTCCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 6 0.26
14 15 0.65
15 2 0.09
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (14 bp):
TATATTTTTATGTA
Found at i:28797812 original size:19 final size:19
Alignment explanation
Indices: 28797742--28797816 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 19
28797732 TTGTAGATAT
28797742 TATTATTATTATTAT-TACA
1 TATTATTATT-TTATGTACA
* *
28797761 TACTT-TTATTATATGCATATA
1 TA-TTATTATTTTATG--TACA
28797782 TATATATGTATTTTATGTACA
1 TAT-TAT-TATTTTATGTACA
28797803 TATTATTATTTTAT
1 TATTATTATTTTAT
28797817 ATTATTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
18 3 0.07
19 15 0.33
20 6 0.13
21 12 0.27
22 1 0.02
23 8 0.18
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.57
Consensus pattern (19 bp):
TATTATTATTTTATGTACA
Found at i:28804481 original size:15 final size:15
Alignment explanation
Indices: 28804449--28804482 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28804439 CGCTGAGGTA
* *
28804449 TTTTCAATTTCTGTT
1 TTTTCAATTTATGCT
28804464 TTTTCAATTTATGCT
1 TTTTCAATTTATGCT
28804479 TTTT
1 TTTT
28804483 AAAAAATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTCAATTTATGCT
Found at i:28804585 original size:73 final size:73
Alignment explanation
Indices: 28804465--28805123 Score: 873
Period size: 73 Copynumber: 9.0 Consensus size: 73
28804455 ATTTCTGTTT
* * * * *
28804465 TTTCAATTTATGCTTTTTAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACG
1 TTTCAATTTTTG-TTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
28804530 CTGAGGTAA
65 CTGAGGTAA
* * *
28804539 TTTCAATTTTTGTTTGTCAAAACTCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGT
1 TTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGC
*
28804604 TGAGGTAT
66 TGAGGTAA
* * *
28804612 TTTCAATTTTTGTTTTTCAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACACG
1 TTTCAATTTTTGTTTGTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
28804677 CTGAGGTAA
65 CTGAGGTAA
* *
28804686 TTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAAGACACGT
1 TTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGC
*
28804751 TGAGGTAT
66 TGAGGTAA
* * *
28804759 TTTCAATTTCTGTCTT-TCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
1 TTTCAATTTTTGT-TTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
28804823 CGCTGAGGTAA
63 CGCTGAGGTAA
*
28804834 TTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGT
1 TTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGC
*
28804899 TGAGGTAT
66 TGAGGTAA
* * * *
28804907 TTTCAATTTCTATCTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACTTCAA-A-A
1 TTTCAATTTTTGT-TTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
28804969 CGCTGAGGAAA
63 CGCTGAGGTAA
*
28804980 TTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGT
1 TTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGC
* *
28805045 TGAAGTAT
66 TGAGGTAA
* * * * *
28805053 TTTCAATTTCTGTCTT-TCAAAAAAACCAGCTCATATTGCAAGAGGTGAGTTGAACCTCAAG--A
1 TTTCAATTTTTGT-TTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
28805115 CGCTGAGGT
63 CGCTGAGGT
28805124 GTTTTCCATT
Statistics
Matches: 516, Mismatches: 55, Indels: 29
0.86 0.09 0.05
Matches are distributed among these distances:
71 38 0.07
72 3 0.01
73 250 0.48
74 86 0.17
75 139 0.27
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (73 bp):
TTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGC
TGAGGTAA
Found at i:28804854 original size:148 final size:148
Alignment explanation
Indices: 28804464--28805123 Score: 1080
Period size: 148 Copynumber: 4.5 Consensus size: 148
28804454 AATTTCTGTT
* ** * * *
28804464 TTTTCAATTTATG-CTTTTTAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
* *
28804528 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAACTCAACTCATATTGCAAGAGGTGAGTTGAGCC
66 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
28804593 TCAAGACACGTTGAGGTA
131 TCAAGACACGTTGAGGTA
* * * * *
28804611 TTTTCAATTTTTGTTTTTC-AAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
28804675 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
66 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
*
28804740 TTAAGACACGTTGAGGTA
131 TCAAGACACGTTGAGGTA
*
28804758 TTTTCAATTTCTGTCTTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
1 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
28804823 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
66 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
28804888 TCAAGACACGTTGAGGTA
131 TCAAGACACGTTGAGGTA
* *
28804906 TTTTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACTTCAA-A-A
1 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
*
28804969 CGCTGAGGAAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
66 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
*
28805034 TCAAGACACGTTGAAGTA
131 TCAAGACACGTTGAGGTA
* * *
28805052 TTTTCAATTTCTGTCTTTCAAAAAAACCAGCTCATATTGCAAGAGGTGAGTTGAACCTCAAG--A
1 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
28805115 CGCTGAGGT
66 CGCTGAGGT
28805124 GTTTTCCATT
Statistics
Matches: 484, Mismatches: 26, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
146 147 0.30
147 153 0.32
148 184 0.38
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (148 bp):
TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
TCAAGACACGTTGAGGTA
Found at i:28805248 original size:13 final size:14
Alignment explanation
Indices: 28805218--28805250 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28805208 CGCTGAGGTA
28805218 TTTTCAAATTCTGT
1 TTTTCAAATTCTGT
28805232 TTTTCAAATAT-TGT
1 TTTTCAAAT-TCTGT
28805246 TTTTC
1 TTTTC
28805251 CAAAAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.94
15 1 0.06
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.61
Consensus pattern (14 bp):
TTTTCAAATTCTGT
Done.