Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 91
Found at i:5505938 original size:19 final size:20
Alignment explanation
Indices: 5505895--5505942 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
5505885 TCTAAATCCT
*
5505895 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATATCATTTTGG
* *
5505915 CTTTCAAAATAT-ATTTTTG
1 TTTTCAAAATATCATTTTGG
5505934 TTTTCAAAA
1 TTTTCAAAA
5505943 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATATCATTTTGG
Found at i:5507178 original size:21 final size:21
Alignment explanation
Indices: 5507152--5507193 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5507142 CTACGATAGG
5507152 GGGTATCAGTAC-CTCTTCATA
1 GGGTATCAGTACTC-CTTCATA
*
5507173 GGGTATCGGTACTCCTTCATA
1 GGGTATCAGTACTCCTTCATA
5507194 AAATTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.33
Consensus pattern (21 bp):
GGGTATCAGTACTCCTTCATA
Found at i:5507265 original size:18 final size:19
Alignment explanation
Indices: 5507224--5507312 Score: 98
Period size: 20 Copynumber: 4.8 Consensus size: 19
5507214 GTTGCAGCCA
5507224 GGGGGTATAGATACCCCTGG
1 GGGGGTATAGATACCCCT-G
5507244 GGGGGTATAGATACCCCTGG
1 GGGGGTATAGATACCCCT-G
*
5507264 GGGGGTATCGATA---CT-
1 GGGGGTATAGATACCCCTG
* *
5507279 CGGGGTATGGATACCCCT-
1 GGGGGTATAGATACCCCTG
5507297 GGGGGTATAGATACCC
1 GGGGGTATAGATACCC
5507313 TCCGAGCAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
15 11 0.18
17 2 0.03
18 16 0.26
20 32 0.52
ACGTcount: A:0.20, C:0.20, G:0.38, T:0.21
Consensus pattern (19 bp):
GGGGGTATAGATACCCCTG
Found at i:5507471 original size:29 final size:29
Alignment explanation
Indices: 5507450--5507507 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
5507440 AAACTTTGAA
*
5507450 TAAATTCAATT-AAGTCTAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
5507479 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
5507508 TACCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 13 0.50
31 2 0.08
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:5507501 original size:30 final size:30
Alignment explanation
Indices: 5507450--5507508 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
5507440 AAACTTTGAA
*
5507450 TAAATTCAATTAAGTCTAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
5507479 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATT-AAGTCCAAAAACCATTTT
5507509 ACCTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 10 0.37
31 6 0.22
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:5508960 original size:39 final size:39
Alignment explanation
Indices: 5508917--5509034 Score: 166
Period size: 39 Copynumber: 3.0 Consensus size: 39
5508907 GAGACCATTT
* *
5508917 CAACCTAATACATAGTCTTGTCAAAACTCATTGGGAAGA
1 CAACCTAATACATAGTCTTATCAAAACTCCTTGGGAAGA
*
5508956 CAACCTAATTAC-TAGTCTTATCAAAACTCCTTGAGAAGA
1 CAACCTAA-TACATAGTCTTATCAAAACTCCTTGGGAAGA
* * *
5508995 CAACCGAATATATAGTCTTCTCAAAACTCCTTGGGAAGA
1 CAACCTAATACATAGTCTTATCAAAACTCCTTGGGAAGA
5509034 C
1 C
5509035 CACTTGATGT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
38 2 0.03
39 65 0.93
40 3 0.04
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (39 bp):
CAACCTAATACATAGTCTTATCAAAACTCCTTGGGAAGA
Found at i:5512898 original size:12 final size:12
Alignment explanation
Indices: 5512881--5512905 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5512871 TTGAGATTTT
5512881 ATTATGTTTTAA
1 ATTATGTTTTAA
5512893 ATTATGTTTTAA
1 ATTATGTTTTAA
5512905 A
1 A
5512906 CTAAGAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (12 bp):
ATTATGTTTTAA
Found at i:5513510 original size:28 final size:28
Alignment explanation
Indices: 5513448--5513532 Score: 91
Period size: 29 Copynumber: 3.0 Consensus size: 28
5513438 TTATCCAAAG
* *
5513448 TATTTTTTTATCAAGATAAGTA-TATAAT
1 TATTTTTTTATCAAAATAAGTACTA-AAA
5513476 TATTTTTTTATCAAAATAAGTACTTAAAA
1 TATTTTTTTATCAAAATAAGTAC-TAAAA
* * *
5513505 TATTTTTTAATTAAAATATGTACATAAA
1 TATTTTTTTATCAAAATAAGTAC-TAAA
5513533 GTATACAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
28 21 0.43
29 26 0.53
30 2 0.04
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (28 bp):
TATTTTTTTATCAAAATAAGTACTAAAA
Found at i:5520923 original size:2 final size:2
Alignment explanation
Indices: 5520916--5520975 Score: 79
Period size: 2 Copynumber: 30.5 Consensus size: 2
5520906 TTATACTTTC
5520916 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
5520956 AT AT GAT AG AT AA AT AT AT A
1 AT AT -AT AT AT AT AT AT AT A
5520976 AAAAAACGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
1 2 0.04
2 47 0.92
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5521574 original size:20 final size:19
Alignment explanation
Indices: 5521535--5521576 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
5521525 TTTCCTCGAT
5521535 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
5521554 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
5521574 ATT
1 ATT
5521577 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:5521687 original size:120 final size:120
Alignment explanation
Indices: 5521448--5521681 Score: 287
Period size: 120 Copynumber: 2.0 Consensus size: 120
5521438 TATATTAATT
* *
5521448 TATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTACCT
1 TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCTAGGTACCT
* *
5521513 TAAGACAACTCTTTTCCTCGATATTAAAAAATAAATAAATAATTAAAACAATTAA
66 TAAGACAACTCCTTTCCTCAATATTAAAAAATAAATAAATAATTAAAACAATTAA
** * * **
5521568 TATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATTAGAAAATGGACATCTAGTTGT
1 TATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCTAGGTAC
* ** * *
5521632 TTTAAGACTGC-CCTTT-CTTAATATTGAAAAATAAATAAAT-ATTAAAACAA
64 CTTAAGACAACTCCTTTCCTCAATATTAAAAAATAAATAAATAATTAAAACAA
5521682 GATTAAAATA
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
118 10 0.10
119 27 0.28
120 42 0.43
121 18 0.19
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.37
Consensus pattern (120 bp):
TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCTAGGTACCT
TAAGACAACTCCTTTCCTCAATATTAAAAAATAAATAAATAATTAAAACAATTAA
Found at i:5523096 original size:3 final size:3
Alignment explanation
Indices: 5523088--5523140 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
5523078 TGTAATTATT
* *
5523088 TAA TAA TAA TATA TAA TAA TAAA TAA -AA TTA TAA TAA T-A TAT TAA
1 TAA TAA TAA TA-A TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
5523133 TAA TAA TA
1 TAA TAA TA
5523141 TTAAAAACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 4 0.10
3 32 0.76
4 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:5523103 original size:10 final size:10
Alignment explanation
Indices: 5523090--5523137 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
5523080 TAATTATTTA
5523090 ATAATAATAT
1 ATAATAATAT
*
5523100 ATAATAATAA
1 ATAATAATAT
5523110 ATAA-AAT-T
1 ATAATAATAT
5523118 ATAATAATAT
1 ATAATAATAT
5523128 ATTAATAATA
1 A-TAATAATA
5523138 ATATTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 4 0.12
9 6 0.18
10 15 0.45
11 8 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATAATAATAT
Found at i:5523121 original size:25 final size:25
Alignment explanation
Indices: 5523093--5523143 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
5523083 TTATTTAATA
5523093 ATAAT-ATATAATAATAAATAAAATT
1 ATAATAATATAATAAT-AATAAAATT
* *
5523118 ATAATAATATATTAATAATAATATT
1 ATAATAATATAATAATAATAAAATT
5523143 A
1 A
5523144 AAAACAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
ATAATAATATAATAATAATAAAATT
Found at i:5525638 original size:8 final size:8
Alignment explanation
Indices: 5525629--5525663 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
5525619 TAATTAATAT
*
5525629 ATATATAT
1 ATATATAC
5525637 ATATATAC
1 ATATATAC
*
5525645 ACATATAC
1 ATATATAC
5525653 ATATATAC
1 ATATATAC
5525661 ATA
1 ATA
5525664 AAAATGTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (8 bp):
ATATATAC
Found at i:5525845 original size:2 final size:2
Alignment explanation
Indices: 5525840--5525874 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5525830 ACACACACAC
5525840 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5525875 AACCAATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5526280 original size:22 final size:21
Alignment explanation
Indices: 5526255--5526296 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5526245 GGATTCTACC
5526255 TAAAAATCAC-AAAATATATATA
1 TAAAAAT-ACTAAAATA-ATATA
5526277 TAAAAATACTAAAATAATAT
1 TAAAAATACTAAAATAATAT
5526297 CATTTGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAATACTAAAATAATATA
Found at i:5528280 original size:28 final size:25
Alignment explanation
Indices: 5528249--5528310 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 25
5528239 ATTACTAATC
5528249 TATTAATTTTATAATAAATAATTAAAAA
1 TATTAATTTTAT--TAAATAA-TAAAAA
* *
5528277 TATTAA-ATTATTAAATAATAATAA
1 TATTAATTTTATTAAATAATAAAAA
*
5528301 TAATAATTTT
1 TATTAATTTT
5528311 GTAACACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
24 10 0.34
25 9 0.31
27 4 0.14
28 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TATTAATTTTATTAAATAATAAAAA
Found at i:5528289 original size:17 final size:18
Alignment explanation
Indices: 5528263--5528296 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5528253 AATTTTATAA
5528263 TAAATAATTAAA-AATAT
1 TAAATAATTAAATAATAT
*
5528280 TAAATTATTAAATAATA
1 TAAATAATTAAATAATA
5528297 ATAATAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAATAATTAAATAATAT
Found at i:5528587 original size:38 final size:37
Alignment explanation
Indices: 5528536--5528665 Score: 123
Period size: 38 Copynumber: 3.6 Consensus size: 37
5528526 AACAACGAAC
* * *
5528536 TTAATGAGTTTAACGAGCGACGGGTCGAGCAACAAATT
1 TTAACGAGCTTAACGAGC-ACGAGTCGAGCAACAAATT
* *
5528574 TTAACGAGCTTAACAAACAACGAGTCGAGCAACAAATT
1 TTAACGAGCTTAACGAGC-ACGAGTCGAGCAACAAATT
*
5528612 TT------CTTAATGAGCACGAGTCGAGC-A-AAATT
1 TTAACGAGCTTAACGAGCACGAGTCGAGCAACAAATT
5528641 TTAACGAGCTTAACGAGCAACGAGT
1 TTAACGAGCTTAACGAGC-ACGAGT
5528666 AGAGTCGAGC
Statistics
Matches: 75, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
29 7 0.09
30 1 0.01
31 11 0.15
32 7 0.09
35 9 0.12
36 6 0.08
38 34 0.45
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (37 bp):
TTAACGAGCTTAACGAGCACGAGTCGAGCAACAAATT
Found at i:5529517 original size:15 final size:13
Alignment explanation
Indices: 5529460--5529521 Score: 76
Period size: 12 Copynumber: 4.8 Consensus size: 13
5529450 ATTTTTCGTT
5529460 TATTATTATTAAA
1 TATTATTATTAAA
5529473 -ATTATTATTATAAA
1 TATTATTA-T-TAAA
*
5529487 TATTATTATT-AT
1 TATTATTATTAAA
5529499 TATTATTATTAAA
1 TATTATTATTAAA
5529512 TA-TATTATTA
1 TATTATTATTA
5529522 CAAGCCCAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
12 26 0.60
13 5 0.12
14 5 0.12
15 7 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTATTATTAAA
Found at i:5529521 original size:3 final size:3
Alignment explanation
Indices: 5529459--5529509 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
5529449 AATTTTTCGT
** * *
5529459 TTA TTA TTA TTA AAA TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5529507 TTA
1 TTA
5529510 AATATATTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:5531144 original size:126 final size:126
Alignment explanation
Indices: 5531037--5531273 Score: 300
Period size: 126 Copynumber: 1.9 Consensus size: 126
5531027 TATAAATTAC
* * *
5531037 TTTTAAGAAAAATAATCATATTTT-GATATTTATTTATTTTT-AATATCGAAGAAAAGAGCTGTC
1 TTTTAAGAAAAAGAA-AATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTC
* *
5531100 TTAAGGCACCTAAAAGC-CATTTTTTGATATTTTTAAATAAATAAATATCTTATTAAAATAAA
65 TTAAGGCACCTAAAAGCTC-TTTTCTGATATTTTTAAATAAATAAATATATTATTAAAATAAA
* **** * *
5531162 TTTTTATTTTAAGAAAATGTTTTGGTTATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCT
1 TTTTAAGAAAAAGAAAATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCT
* * *
5531227 TAAGGTACCTAGAAGCTCTTTTCTGATATTTTTGAATAAATAAATAT
66 TAAGGCACCTAAAAGCTCTTTTCTGATATTTTTAAATAAATAAATAT
5531274 CTTACTATAT
Statistics
Matches: 95, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
124 6 0.06
125 25 0.26
126 63 0.66
127 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (126 bp):
TTTTAAGAAAAAGAAAATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCT
TAAGGCACCTAAAAGCTCTTTTCTGATATTTTTAAATAAATAAATATATTATTAAAATAAA
Found at i:5534268 original size:21 final size:22
Alignment explanation
Indices: 5534242--5534291 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
5534232 AGTAAACACC
5534242 TTTGCATATATGCA-TTTTCAT
1 TTTGCATATATGCATTTTTCAT
* *
5534263 TTTGCATCTTTGCATTTTTCAT
1 TTTGCATATATGCATTTTTCAT
5534285 TTTGCAT
1 TTTGCAT
5534292 TCATACTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.56
Consensus pattern (22 bp):
TTTGCATATATGCATTTTTCAT
Found at i:5534287 original size:7 final size:7
Alignment explanation
Indices: 5534242--5534292 Score: 59
Period size: 7 Copynumber: 7.1 Consensus size: 7
5534232 AGTAAACACC
5534242 TTTGCAT
1 TTTGCAT
*
5534249 ATATGCAT
1 -TTTGCAT
5534257 TTT-CAT
1 TTTGCAT
5534263 TTTGCAT
1 TTTGCAT
5534270 CTTTGCAT
1 -TTTGCAT
*
5534278 TTTTCAT
1 TTTGCAT
5534285 TTTGCAT
1 TTTGCAT
5534292 T
1 T
5534293 CATACTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 6 0.16
7 18 0.49
8 13 0.35
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.57
Consensus pattern (7 bp):
TTTGCAT
Found at i:5538695 original size:114 final size:114
Alignment explanation
Indices: 5538495--5538831 Score: 557
Period size: 114 Copynumber: 3.0 Consensus size: 114
5538485 GTGCCATGTT
* * *
5538495 CTCGTAGTAGAAATATAGAGACCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATGTGATCTG
1 CTCGTAGTAGAAATAAAGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
5538560 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
66 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
5538609 CTCGTAGTAGAAATAAAGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCGTAGTAGAAATAAAGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
5538674 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
66 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
* * * * *
5538723 CTCATGGTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTG
1 CTCGTAGTAGAAATAAAGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * * * *
5538788 GTTCGGTAGGAACCACAAAACCAATCATTGGAATTAAAAGATGA
66 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGA
5538832 GCTGCATGAT
Statistics
Matches: 210, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 210 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (114 bp):
CTCGTAGTAGAAATAAAGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
Found at i:5540094 original size:75 final size:75
Alignment explanation
Indices: 5539930--5540096 Score: 212
Period size: 75 Copynumber: 2.2 Consensus size: 75
5539920 ATTAACAAAA
5539930 AGCAAATGTTGGGGCATGTTGAAAACCCTTTTCAATCAGAATCAGGAATGTTGATGTATCATGAA
1 AGCAAATGTTGGGGCATGTTGAAAACCCTTTTCAATCAGAATCAGGAATGTTGATGTATCATGAA
* *
5539995 TGTTTATATC
66 CGTTCATATC
* * * * **
5540005 AGCAAAATG-CGGGGCATGTTGAAAGCCTTTTTCAATCAGAATGA-GAATGTTGATGTATTTTTG
1 AGC-AAATGTTGGGGCATGTTGAAAACCCTTTTCAATCAGAATCAGGAATGTTGATGTA-TCATG
*
5540068 AACGTTCGTATC
64 AACGTTCATATC
*
5540080 AGCAATTGTTGGGGCAT
1 AGCAAATGTTGGGGCAT
5540097 ACTGAGGCCC
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
74 17 0.22
75 56 0.72
76 5 0.06
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGTTGAAAACCCTTTTCAATCAGAATCAGGAATGTTGATGTATCATGAA
CGTTCATATC
Found at i:5541418 original size:24 final size:23
Alignment explanation
Indices: 5541386--5541464 Score: 108
Period size: 22 Copynumber: 3.5 Consensus size: 23
5541376 ATCTACACTC
5541386 TTCAAAGATGATAAATTCTCTTTT
1 TTCAAAGATGATAAATTCTC-TTT
**
5541410 TTCAAAGATGATGGATTCTCTTT
1 TTCAAAGATGATAAATTCTCTTT
*
5541433 TT-AAAGATGATATATTCTC-TT
1 TTCAAAGATGATAAATTCTCTTT
5541454 TTCAAAGATGA
1 TTCAAAGATGA
5541465 AAGCTTTATT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.08
22 23 0.46
23 5 0.10
24 18 0.36
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (23 bp):
TTCAAAGATGATAAATTCTCTTT
Found at i:5542290 original size:165 final size:167
Alignment explanation
Indices: 5541978--5542303 Score: 507
Period size: 165 Copynumber: 2.0 Consensus size: 167
5541968 AAAATGAGCA
*
5541978 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAACATAATGAGAAAAC
1 TTATCTTAAGATTGGGGCATGTTACCCAATCAACATGTTATTT-AAAAAAACATAATGAGAAAAC
* **
5542043 GATTTTCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACCATTT
65 GATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACCATTT
* *
5542108 TCTTAGTTTTTTTACTTAGTAAACTATTTCCAACAACC
130 TCATAGTTTTCTTACTTAGTAAACTATTTCCAACAACC
* **
5542146 TTATCTTAAGATTGGGGCATTTTACCCAATCAACATGTTATTT-TGAAAA-ATAATGAGAAAACG
1 TTATCTTAAGATTGGGGCATGTTACCCAATCAACATGTTATTTAAAAAAACATAATGAGAAAACG
*
5542209 ATTTCCATAGTTTCTCATTCAATCTTTTTTAAAAATGAAATTGTTGAAAAGTAAG-AAACCGATT
66 ATTTCCATAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAACC-ATT
5542273 TTCATAG-TTTCTTACTTAGTAAACTATTTCC
129 TTCATAGTTTTCTTACTTAGTAAACTATTTCC
5542304 CACATCTGTA
Statistics
Matches: 146, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
165 68 0.47
166 37 0.25
168 41 0.28
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (167 bp):
TTATCTTAAGATTGGGGCATGTTACCCAATCAACATGTTATTTAAAAAAACATAATGAGAAAACG
ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACCATTTT
CATAGTTTTCTTACTTAGTAAACTATTTCCAACAACC
Found at i:5542568 original size:75 final size:75
Alignment explanation
Indices: 5542306--5543091 Score: 1365
Period size: 76 Copynumber: 10.4 Consensus size: 75
5542296 CTATTTCCCA
5542306 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
5542371 AACCTTAGGGT
65 AACCTTAGGGT
*
5542382 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5542447 AGCCTTAGGGT
66 A-CCTTAGGGT
*
5542458 CATCTGTAAGTCCTGCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
5542523 ACCTTCGGGT
66 ACCTTAGGGT
* * *
5542533 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5542598 AGCCTTAGGGT
66 A-CCTTAGGGT
*
5542609 CATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
5542674 ACCTTCGGGT
66 ACCTTAGGGT
*
5542684 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
5542749 ACCTTCGGGT
66 ACCTTAGGGT
*
5542759 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
5542824 ACCTTCGGGT
66 ACCTTAGGGT
* *
5542834 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
5542899 AACTTTAGGGT
65 AACCTTAGGGT
*
5542910 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
5542975 AACCTTAGGGT
65 AACCTTAGGGT
5542986 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5543051 AGCCTTAGGGT
66 A-CCTTAGGGT
*
5543062 CATCTGTAAGTCCTGTAGTGCATGATGTTT
1 CATCTGTAAGTCCTGCAGTGCATGATGTTT
5543092 TTAAGACCTC
Statistics
Matches: 681, Mismatches: 25, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
75 294 0.43
76 387 0.57
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (75 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ACCTTAGGGT
Found at i:5542587 original size:151 final size:151
Alignment explanation
Indices: 5542306--5543091 Score: 1421
Period size: 151 Copynumber: 5.2 Consensus size: 151
5542296 CTATTTCCCA
5542306 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
5542371 AACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
65 AACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
5542436 GATGTTTTCAAAGCCTTAGGGT
130 GATGTTTTCAAAGCCTTAGGGT
*
5542458 CATCTGTAAGTCCTGCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
5542523 ACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTG
66 ACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
*
5542588 ATGTTTTTAAAGCCTTAGGGT
131 ATGTTTTCAAAGCCTTAGGGT
*
5542609 CATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5542674 ACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
66 ACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
*
5542739 ATGTTTTCAAA-CCTTCGGGT
131 ATGTTTTCAAAGCCTTAGGGT
*
5542759 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
5542824 ACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTG
66 ACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
* *
5542889 ATGTTTTCAAAACTTTAGGGT
131 ATGTTTTCAAAGCCTTAGGGT
*
5542910 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
* *
5542975 AACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
65 AACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
5543040 GATGTTTTCAAAGCCTTAGGGT
130 GATGTTTTCAAAGCCTTAGGGT
*
5543062 CATCTGTAAGTCCTGTAGTGCATGATGTTT
1 CATCTGTAAGTCCTGCAGTGCATGATGTTT
5543092 TTAAGACCTC
Statistics
Matches: 610, Mismatches: 22, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
150 146 0.24
151 290 0.48
152 174 0.29
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (151 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
ATGTTTTCAAAGCCTTAGGGT
Found at i:5543259 original size:12 final size:12
Alignment explanation
Indices: 5543242--5543341 Score: 90
Period size: 12 Copynumber: 8.8 Consensus size: 12
5543232 TTTTTCGTTT
5543242 ATTATTATTAAA
1 ATTATTATTAAA
5543254 ATTATTATTATAA
1 ATTATTATTA-AA
5543267 A-TATTATT---
1 ATTATTATTAAA
5543275 ATTATTATT---
1 ATTATTATTAAA
5543284 ATTATTATTAAA
1 ATTATTATTAAA
**
5543296 ATTATTATTATT
1 ATTATTATTAAA
**
5543308 ATTATTATTATT
1 ATTATTATTAAA
5543320 ATTATTATT-AA
1 ATTATTATTAAA
5543331 ATATATTATTA
1 AT-TATTATTA
5543342 CAAGCCCAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 13
0.82 0.04 0.14
Matches are distributed among these distances:
8 1 0.01
9 16 0.21
11 2 0.03
12 55 0.71
13 3 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTATTATTAAA
Found at i:5543337 original size:15 final size:16
Alignment explanation
Indices: 5543240--5543341 Score: 117
Period size: 15 Copynumber: 6.6 Consensus size: 16
5543230 AATTTTTCGT
5543240 TTATTATTATTAAA-A
1 TTATTATTATTAAATA
5543255 TTATTATTA-TAAATA
1 TTATTATTATTAAATA
*
5543270 TTATTATTATT-ATTA
1 TTATTATTATTAAATA
5543285 TTATTATTA--AAATTA
1 TTATTATTATTAAA-TA
*
5543300 TTATTATTATTATTATTA
1 TTATTATTATTA--AATA
5543318 TTATTATTATTAAATA
1 TTATTATTATTAAATA
5543334 -TATTATTA
1 TTATTATTA
5543342 CAAGCCCAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
14 5 0.07
15 50 0.67
16 4 0.05
17 1 0.01
18 14 0.19
19 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATTATTATTAAATA
Found at i:5543341 original size:3 final size:3
Alignment explanation
Indices: 5543240--5543329 Score: 126
Period size: 3 Copynumber: 30.0 Consensus size: 3
5543230 AATTTTTCGT
** * *
5543240 TTA TTA TTA TTA AAA TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
**
5543288 TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5543330 AATATATTAT
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:5545256 original size:111 final size:111
Alignment explanation
Indices: 5545022--5545256 Score: 285
Period size: 111 Copynumber: 2.1 Consensus size: 111
5545012 GGTTATTTAT
** * * * *
5545022 TTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGCTCTTTTCTGATATTTTT
1 TTATTTTGAAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTTTTCTGATATTTCT
* * * *
5545087 GAATAAATAAATATCTTACTATATTAAAATAAAATGTTTTTGATAT
66 AAATAAATAAATATCTTACTATATTAAAATAAAATATTTTTGAAAA
*
5545133 TTATTTTTAAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTTTTCTGATATTTCT
1 TTATTTTGAAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTTTTCTGATATTTCT
* * * * * *
5545198 AAATAAGTAAATATCTTA-TTTATGTATATTAATATATTTTCTTAAAA
66 AAATAAATAAATATCTTACTATAT-TAAAATAAAATATTTT-TGAAAA
5545245 TTA-TTTGAAATA
1 TTATTTTGAAATA
5545257 GTAGAATTAT
Statistics
Matches: 106, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
110 4 0.04
111 96 0.91
112 6 0.06
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (111 bp):
TTATTTTGAAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTTTTCTGATATTTCT
AAATAAATAAATATCTTACTATATTAAAATAAAATATTTTTGAAAA
Found at i:5547852 original size:2 final size:2
Alignment explanation
Indices: 5547845--5547869 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5547835 ATGTTATGTT
5547845 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5547870 TTAATTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5566491 original size:27 final size:27
Alignment explanation
Indices: 5566453--5566544 Score: 166
Period size: 27 Copynumber: 3.4 Consensus size: 27
5566443 CCCACATCTT
*
5566453 TTACTAATTCGCAAAGAATGGAATGAG
1 TTACTAACTCGCAAAGAATGGAATGAG
5566480 TTACTAACTCGCAAAGAATGGAATGAG
1 TTACTAACTCGCAAAGAATGGAATGAG
*
5566507 TTACTAAGTCGCAAAGAATGGAATGAG
1 TTACTAACTCGCAAAGAATGGAATGAG
5566534 TTACTAACTCG
1 TTACTAACTCG
5566545 TCTAGAGGCT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (27 bp):
TTACTAACTCGCAAAGAATGGAATGAG
Found at i:5571423 original size:9 final size:9
Alignment explanation
Indices: 5571409--5571434 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5571399 AACAGTAGGA
5571409 GCGGGTGGT
1 GCGGGTGGT
5571418 GCGGGTGGT
1 GCGGGTGGT
5571427 GCGGGTGG
1 GCGGGTGG
5571435 AGTGATGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.69, T:0.19
Consensus pattern (9 bp):
GCGGGTGGT
Found at i:5572934 original size:20 final size:21
Alignment explanation
Indices: 5572888--5572941 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
5572878 TTTGGAAAAT
*
5572888 ATTATCGATACTCTTACCAGG
1 ATTATCGATACTCTTACCAGC
* **
5572909 AGTATCGATACTC-TACCTTC
1 ATTATCGATACTCTTACCAGC
5572929 ATTATCGATACTC
1 ATTATCGATACTC
5572942 CTATGAGTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (21 bp):
ATTATCGATACTCTTACCAGC
Found at i:5578125 original size:24 final size:24
Alignment explanation
Indices: 5578093--5578149 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
5578083 AACAAATCCT
5578093 TTAGCCACCAGCCGAGCTTTATAC
1 TTAGCCACCAGCCGAGCTTTATAC
*
5578117 TTAGCCACCATCCGAGCTTTATAC
1 TTAGCCACCAGCCGAGCTTTATAC
5578141 TTAGCCACC
1 TTAGCCACC
5578150 GATCCATCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.35, G:0.14, T:0.26
Consensus pattern (24 bp):
TTAGCCACCAGCCGAGCTTTATAC
Found at i:5579968 original size:17 final size:17
Alignment explanation
Indices: 5579946--5579985 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
5579936 ATGGTCGAAT
* *
5579946 GTTGACTGTTAACCTGC
1 GTTGACAGTTAACCGGC
*
5579963 GTTGACAGTTGACCGGC
1 GTTGACAGTTAACCGGC
5579980 GTTGAC
1 GTTGAC
5579986 CACAATTGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (17 bp):
GTTGACAGTTAACCGGC
Found at i:5582435 original size:24 final size:24
Alignment explanation
Indices: 5582408--5582522 Score: 133
Period size: 24 Copynumber: 4.8 Consensus size: 24
5582398 TTGATTTGAT
*
5582408 TTCTAATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
*
5582432 TTCTGATCTGATA-TCTGATATGGA
1 TTCTGATCTGATACT-TGACATGGA
* *
5582456 TTCTGATCTGATACTTAACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* * *
5582480 TTTTGATATGATACTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
5582504 TTTTGATATGATACTTGAC
1 TTCTGATCTGATACTTGAC
5582523 GTGAATTATG
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 1 0.01
24 78 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:5587228 original size:24 final size:24
Alignment explanation
Indices: 5587201--5587315 Score: 133
Period size: 24 Copynumber: 4.8 Consensus size: 24
5587191 TTGATTTGAT
*
5587201 TTCTAATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
*
5587225 TTCTGATCTGATA-TCTGATATGGA
1 TTCTGATCTGATACT-TGACATGGA
* *
5587249 TTCTGATCTGATACTTAACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* * *
5587273 TTTTGATATGATACTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
5587297 TTTTGATATGATACTTGAC
1 TTCTGATCTGATACTTGAC
5587316 GTGAATTATA
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 1 0.01
24 78 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:5587332 original size:24 final size:24
Alignment explanation
Indices: 5587278--5587332 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
5587268 TTGGATTTTG
* * *
5587278 ATATGATACTTGACCTGGATTTTG
1 ATATGATACTTGACCTGAATTATA
*
5587302 ATATGATACTTGACGTGAATTATA
1 ATATGATACTTGACCTGAATTATA
*
5587326 ATTTGAT
1 ATATGAT
5587333 TTTTGATATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (24 bp):
ATATGATACTTGACCTGAATTATA
Found at i:5589418 original size:22 final size:23
Alignment explanation
Indices: 5589390--5589438 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
5589380 TTAATTTCTT
5589390 TTTGGGTGCTA-TTTGTGTAAA-A
1 TTTGGGTGCTAGTTT-TGTAAATA
*
5589412 TTTGGGTGTTAGTTTTGTAAATA
1 TTTGGGTGCTAGTTTTGTAAATA
5589435 TTTG
1 TTTG
5589439 TAGAAGGTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.20, C:0.02, G:0.27, T:0.51
Consensus pattern (23 bp):
TTTGGGTGCTAGTTTTGTAAATA
Found at i:5592033 original size:48 final size:48
Alignment explanation
Indices: 5591972--5592136 Score: 242
Period size: 48 Copynumber: 3.4 Consensus size: 48
5591962 TTTCGATTTA
* *
5591972 ATTTCTGATCTGATACTTGACATAGATTCTGATATGATATCTAACATGG
1 ATTT-TGATCTGATACTTGACTTGGATTCTGATATGATATCTAACATGG
5592021 ATTTTGATCTGATACTTGACTTGGATTCTGATATGATATCTAACATGG
1 ATTTTGATCTGATACTTGACTTGGATTCTGATATGATATCTAACATGG
* * * *
5592069 ATTTTGATCTGATACTTGACTTGGATTCTGATCTGATA-CTTGACCTTG
1 ATTTTGATCTGATACTTGACTTGGATTCTGATATGATATC-TAACATGG
*
5592117 ATTTTGATATGATACTTGAC
1 ATTTTGATCTGATACTTGAC
5592137 GTGAATTATG
Statistics
Matches: 108, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
47 1 0.01
48 103 0.95
49 4 0.04
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.42
Consensus pattern (48 bp):
ATTTTGATCTGATACTTGACTTGGATTCTGATATGATATCTAACATGG
Found at i:5592051 original size:72 final size:72
Alignment explanation
Indices: 5591974--5592136 Score: 197
Period size: 72 Copynumber: 2.3 Consensus size: 72
5591964 TCGATTTAAT
* *
5591974 TTCTGATCTGATACTTGACATAGATTCTGATATGATA-TCTAACATGGATTTTGATCTGATACTT
1 TTCTGATATGATACTTGACATAGATTCTGATATGATACT-TAACATGGATTCTGATCTGATACTT
5592038 GA-CTTGGA
65 GACCTT-GA
* * * * * *
5592046 TTCTGATATGATA-TCTAACATGGATTTTGATCTGATACTTGACTTGGATTCTGATCTGATACTT
1 TTCTGATATGATACT-TGACATAGATTCTGATATGATACTTAACATGGATTCTGATCTGATACTT
5592110 GACCTTGA
65 GACCTTGA
*
5592118 TTTTGATATGATACTTGAC
1 TTCTGATATGATACTTGAC
5592137 GTGAATTATG
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
71 1 0.01
72 71 0.92
73 5 0.06
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (72 bp):
TTCTGATATGATACTTGACATAGATTCTGATATGATACTTAACATGGATTCTGATCTGATACTTG
ACCTTGA
Found at i:5592148 original size:24 final size:24
Alignment explanation
Indices: 5591974--5592136 Score: 177
Period size: 24 Copynumber: 6.8 Consensus size: 24
5591964 TCGATTTAAT
*
5591974 TTCTGATCTGATACTTGACATAGA
1 TTCTGATCTGATACTTGACATGGA
* *
5591998 TTCTGATATGATA-TCTAACATGGA
1 TTCTGATCTGATACT-TGACATGGA
* *
5592022 TTTTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
5592046 TTCTGATATGATA-TCTAACATGGA
1 TTCTGATCTGATACT-TGACATGGA
* *
5592070 TTTTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
5592094 TTCTGATCTGATACTTGACCTTGA
1 TTCTGATCTGATACTTGACATGGA
* *
5592118 TTTTGATATGATACTTGAC
1 TTCTGATCTGATACTTGAC
5592137 GTGAATTATG
Statistics
Matches: 115, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
23 2 0.02
24 111 0.97
25 2 0.02
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:5595730 original size:3 final size:3
Alignment explanation
Indices: 5595724--5595866 Score: 214
Period size: 3 Copynumber: 47.7 Consensus size: 3
5595714 TTTTTATCTA
* ** *
5595724 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
** * *
5595772 TAT TAT CCT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5595820 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5595867 ATTTATATTA
Statistics
Matches: 124, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 124 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:5597335 original size:21 final size:22
Alignment explanation
Indices: 5597305--5597346 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
5597295 AATATTTTTA
5597305 TTTTATTATATTGT-TAAATATT
1 TTTTATTATATT-TATAAATATT
5597327 TTTTA-TATATTTATAAATAT
1 TTTTATTATATTTATAAATAT
5597347 ACTTATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.05
21 13 0.68
22 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTATTATATTTATAAATATT
Found at i:5608669 original size:5 final size:5
Alignment explanation
Indices: 5608659--5608738 Score: 73
Period size: 5 Copynumber: 16.6 Consensus size: 5
5608649 GCTTGAAGAA
5608659 AAAAG AAAAG AAAAAG AAAAG -AAAG AAAAG -AAA- AAAAG AAAAG AAAA-
1 AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
* *
5608706 AAATAG AAATG -AAA- AAAAG AGAAG AAAAAG AAA
1 AAA-AG AAAAG AAAAG AAAAG AAAAG -AAAAG AAA
5608739 GGGGGTCAAG
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
4 18 0.29
5 32 0.52
6 12 0.19
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:5608694 original size:33 final size:32
Alignment explanation
Indices: 5608657--5608738 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 32
5608647 ATGCTTGAAG
5608657 AAAAAAGAAAAGAAAAAGAAAAGAAA-GAAAAGA
1 AAAAAAGAAAAGAAAAA-AAAAGAAATGAAAA-A
*
5608690 AAAAAAGAAAAGAAAAAAATAGAAATGAAAAA
1 AAAAAAGAAAAGAAAAAAAAAGAAATGAAAAA
*
5608722 AAGAGAAGAAAAAGAAA
1 AA-AAAAG-AAAAGAAA
5608739 GGGGGTCAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
32 10 0.23
33 26 0.59
34 8 0.18
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (32 bp):
AAAAAAGAAAAGAAAAAAAAAGAAATGAAAAA
Found at i:5608706 original size:28 final size:28
Alignment explanation
Indices: 5608654--5608739 Score: 106
Period size: 28 Copynumber: 3.1 Consensus size: 28
5608644 ATTATGCTTG
*
5608654 AAGAAAA-AAGAAAAGAAAA-AGAAAAGA
1 AAGAAAAGAAAAAAAGAAAAGA-AAAAGA
5608681 AAGAAAAGAAAAAAAGAAAAGAAAAA-A
1 AAGAAAAGAAAAAAAGAAAAGAAAAAGA
* *
5608708 ATAGAAATGAAAAAAAGAGAAGAAAAAGA
1 A-AGAAAAGAAAAAAAGAAAAGAAAAAGA
5608737 AAG
1 AAG
5608740 GGGGTCAAGG
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
27 9 0.17
28 40 0.77
29 3 0.06
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (28 bp):
AAGAAAAGAAAAAAAGAAAAGAAAAAGA
Found at i:5608739 original size:15 final size:14
Alignment explanation
Indices: 5608672--5608739 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
5608662 AGAAAAGAAA
* *
5608672 AAGAAAAGAAAGAA
1 AAGAAAAAAAAGAG
*
5608686 AAG-AAAAAAAGAA
1 AAGAAAAAAAAGAG
5608699 AAGAAAAAAATAGA-
1 AAGAAAAAAA-AGAG
5608713 AATG-AAAAAAAGAG
1 AA-GAAAAAAAAGAG
5608727 AAGAAAAAGAAAG
1 AAGAAAAA-AAAG
5608740 GGGGTCAAGG
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
13 16 0.34
14 23 0.49
15 8 0.17
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (14 bp):
AAGAAAAAAAAGAG
Found at i:5610047 original size:83 final size:81
Alignment explanation
Indices: 5609856--5610278 Score: 629
Period size: 82 Copynumber: 5.2 Consensus size: 81
5609846 AAACATTAAA
* *
5609856 TGGAAGATGAATTTACCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTA-C
5609921 AGAACAATCATTGAATT
65 AGAACAATCATTGAATT
* * * * *
5609938 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTATAT
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTT-TAC
*
5610003 AGAACCAAGCATTGAATT
65 AGAA-CAATCATTGAATT
5610021 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTA-C
5610086 AGAACAATCATTGAATT
65 AGAACAATCATTGAATT
* * * *
5610103 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAGGTGTTCTTTGAGTTAT-TGA--TGATTTATA
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTACA
*
5610165 GAACCAAGCATTGAATT
66 GAA-CAATCATTGAATT
* *
5610182 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTT-TTTGAGTTATCTGATCTGGTTGGAC
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTT-TAC
5610246 AGAACAATCATTGAATT
65 AGAACAATCATTGAATT
5610263 TGGAAGATGAATTTGC
1 TGGAAGATGAATTTGC
5610279 TCATAGTAAA
Statistics
Matches: 308, Mismatches: 25, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
78 14 0.05
79 58 0.19
81 35 0.11
82 126 0.41
83 75 0.24
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.36
Consensus pattern (81 bp):
TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTACA
GAACAATCATTGAATT
Found at i:5610128 original size:165 final size:161
Alignment explanation
Indices: 5609856--5610278 Score: 733
Period size: 165 Copynumber: 2.6 Consensus size: 161
5609846 AAACATTAAA
* *
5609856 TGGAAGATGAATTTACCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
5609921 AGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTT
66 AGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTT
5609986 ATTTGATCTGATTATATAGAACCAAGCATTGAATT
131 A-TTGA--TGATT-TATAGAACCAAGCATTGAATT
5610021 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
*
5610086 AGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAGGTGTTCTTTGAGTT
66 AGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTT
5610151 ATTGATGATTTATAGAACCAAGCATTGAATT
131 ATTGATGATTTATAGAACCAAGCATTGAATT
* *
5610182 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTT-TTTGAGTTATCTGATCTGG-TTGGA
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAG-
*
5610245 CAGAACAATCATTGAATTTGGAAGATGAATTTGC
65 CAGAACAATCATTGAATTTAGAAGATGAATTTGC
5610279 TCATAGTAAA
Statistics
Matches: 251, Mismatches: 6, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
159 3 0.01
160 51 0.20
161 60 0.24
162 5 0.02
164 4 0.02
165 128 0.51
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.36
Consensus pattern (161 bp):
TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
AGAACAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTT
ATTGATGATTTATAGAACCAAGCATTGAATT
Found at i:5611384 original size:113 final size:113
Alignment explanation
Indices: 5610891--5611536 Score: 980
Period size: 113 Copynumber: 5.8 Consensus size: 113
5610881 GATTTGAATC
* * * * *
5610891 CATTTGATGGAACAGCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 CATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
*
5610956 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCGT
66 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCAT
*
5611004 CATTTGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAA--CATCTGAAGAAGGAAGA
1 CATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
*
5611067 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCGT
66 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCAT
* *
5611115 CATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGA
1 CATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
* * ** * *
5611180 AGAAGTTCATAATG-GAAGAACTTGTTCAACTTTTTGTTTAAATTCAT
66 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCAT
* * *
5611227 CATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 CATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
* *
5611292 AGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCAT
66 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCAT
* * *
5611340 CATTTGGTGAATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 CATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
* *
5611405 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCAT
66 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCAT
* * *
5611453 CA-TTGATGGATCAACATTGCCAG-GTAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-
1 CATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
5611515 AGAAAGTTCATAATGAGAAGAA
66 AG-AAGTTCATAATGAGAAGAA
5611537 CTCATCAAGA
Statistics
Matches: 484, Mismatches: 45, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
110 2 0.00
111 166 0.34
112 115 0.24
113 201 0.42
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (113 bp):
CATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCAT
Found at i:5611504 original size:336 final size:337
Alignment explanation
Indices: 5610891--5611538 Score: 1088
Period size: 336 Copynumber: 1.9 Consensus size: 337
5610881 GATTTGAATC
*
5610891 CATTTGATGGAACAGCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 CATTTGATGGAACAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
* * * * *
5610956 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCGTCATTTGATGGATTAACT
66 AGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGAATCAACT
5611021 TTTCCAGAGAAAGTTCATAATGAGAAGAACATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
131 TTTCCAGAGAAAGTTCATAATGAGAAGAACATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
* * * *
5611086 AATTTGTTCAACCTTTTACTTGAATCCGTCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATA
196 AATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATA
5611151 ATGAGAAGAACTCATCTGAAGAAAGAAGA-AGAAGTTCATAATG-GAAGAACTTGTTCAACTTTT
261 ATGAGAAGAACTCATCTGAAGAAAGAAGAGA-AAGTTCATAATGAGAAGAACTTGTTCAACTTTT
5611214 TGTTTAAATTCAT
325 TGTTTAAATTCAT
*
5611227 CATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 CATTTGATGGAACAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
* *
5611292 AGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGAATCATCT
66 AGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGAATCAACT
5611357 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
131 TTTCCAGAGAAAGTTCATAATGAGAAGAA--CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * *
5611422 AGAATTTGTTCAACCTTTTGCTTGAATTCATCA-TTGATGGATCAACATTGCCAG-GTAAGTTCA
194 AGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCA
*
5611485 TAATGAGAAGAACTCATCTGAAGAAGGAAGAGAAAGTTCATAATGAGAAGAACT
259 TAATGAGAAGAACTCATCTGAAGAAAGAAGAGAAAGTTCATAATGAGAAGAACT
5611539 CATCAAGAGC
Statistics
Matches: 291, Mismatches: 17, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
336 200 0.69
337 27 0.09
338 64 0.22
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (337 bp):
CATTTGATGGAACAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
AGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGAATCAACT
TTTCCAGAGAAAGTTCATAATGAGAAGAACATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
AATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATA
ATGAGAAGAACTCATCTGAAGAAAGAAGAGAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTT
GTTTAAATTCAT
Found at i:5611793 original size:3 final size:3
Alignment explanation
Indices: 5611787--5611925 Score: 158
Period size: 3 Copynumber: 47.3 Consensus size: 3
5611777 TTTTTATCCA
* ** *
5611787 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
** * ** *
5611835 TAT TAT CCT TAT TAT TAT TAA TA- TAT TAT TAT CCT TAT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
5611882 TAT TAT TAT TAT CA- TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5611926 TTTAATTTAT
Statistics
Matches: 112, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
2 5 0.04
3 107 0.96
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:5613380 original size:20 final size:20
Alignment explanation
Indices: 5613357--5613397 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5613347 AATATTTTTA
5613357 TTTTATTATATTGT-TAAATAT
1 TTTTA-TATATT-TATAAATAT
5613378 TTTTATATATTTATAAATAT
1 TTTTATATATTTATAAATAT
5613398 ACTTATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.05
20 13 0.68
21 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTTATATATTTATAAATAT
Found at i:5613382 original size:38 final size:36
Alignment explanation
Indices: 5613315--5613389 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 36
5613305 TATGTCTTCA
*
5613315 TTTATTTTATTGTTTTTAAATATTGTTTTAGTAATATT
1 TTTATTTTATTATTTTTAAATATTGTTTTA-T-ATATT
5613353 TTTATTTTATTATATTGTTAAATA-T-TTTTATATATT
1 TTTATTTTATTAT-TT-TTAAATATTGTTTTATATATT
5613389 T
1 T
5613390 ATAAATATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
36 6 0.18
37 1 0.03
38 17 0.50
39 3 0.09
40 7 0.21
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (36 bp):
TTTATTTTATTATTTTTAAATATTGTTTTATATATT
Found at i:5622090 original size:32 final size:33
Alignment explanation
Indices: 5622054--5622131 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 33
5622044 GGTAAGAAAT
* *
5622054 TTATTTTTATGTTAGTATTTT-T-TAAATAGTTA
1 TTATTTTTATATTAATATTTTATGTAAATA-TTA
5622086 TTATTTTTATATTAATATTTTATGTAAATATTA
1 TTATTTTTATATTAATATTTTATGTAAATATTA
5622119 TT-TTTTT-TATTAA
1 TTATTTTTATATTAA
5622132 AATAATATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
31 6 0.14
32 24 0.57
33 6 0.14
34 6 0.14
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (33 bp):
TTATTTTTATATTAATATTTTATGTAAATATTA
Found at i:5622322 original size:17 final size:17
Alignment explanation
Indices: 5622300--5622353 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
5622290 AATGTTAATA
5622300 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
5622317 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
5622334 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
5622351 TTT
1 TTT
5622354 TTATAATATA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:5623901 original size:21 final size:21
Alignment explanation
Indices: 5623871--5623918 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
5623861 GCAGGGGTAC
* *
5623871 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
5623892 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
5623913 ATGCCA
1 ATGCCA
5623919 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:5623948 original size:21 final size:21
Alignment explanation
Indices: 5623922--5624015 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
5623912 TATGCCATCT
* *
5623922 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
5623943 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
5623964 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
5623985 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
*
5624006 CTGCAGGGTT
1 CCGCAGGGTT
5624016 TTATACCATA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 2 0.03
21 64 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:5624572 original size:32 final size:34
Alignment explanation
Indices: 5624524--5624625 Score: 138
Period size: 32 Copynumber: 3.1 Consensus size: 34
5624514 AAATGTTTTT
5624524 AAAATACAAATTATATTATTCGAAATTTAAA-TA
1 AAAATACAAATTATATTATTCGAAATTTAAATTA
* *
5624557 AAAATA-AAATAATATTATTC-AAATTTAAATTT
1 AAAATACAAATTATATTATTCGAAATTTAAATTA
* *
5624589 AAAATATAAATTATAGTATTCGAAATTTAACATTA
1 AAAATACAAATTATATTATTCGAAATTTAA-ATTA
5624624 AA
1 AA
5624626 TTTCAACTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
31 9 0.15
32 20 0.33
33 18 0.30
34 8 0.13
35 5 0.08
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATACAAATTATATTATTCGAAATTTAAATTA
Found at i:5625354 original size:126 final size:128
Alignment explanation
Indices: 5625011--5626007 Score: 1791
Period size: 127 Copynumber: 7.9 Consensus size: 128
5625001 TTACCTGATT
5625011 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
5625076 TGACGAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCATGTGAATACTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
5625139 TACTGATATATCTAGTGTCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
1 TACTGATATATCTAGTGT-CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
*
5625204 CTGACGAAATAATGGAAGGTGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTG-AA-AATAGG
65 CTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
5625266 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
5625331 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
5625394 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
5625459 TGACGAAATAATAGAA-G-GCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
5625519 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
5625584 TGACG-AATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
5625646 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGAC---ATAGGGC-ATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
5625707 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
5625770 TACTGATATA-CTA--GTCCCCGAGGGACATGAGTGAC--AATAGGGCAATGAT-ACATA-T-TC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
5625827 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
5625890 TACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
5625955 TGACG-AATAATGGAAGGCGCGCCCCCGGGAACGC-CCTTCATGTGAATAGTGAA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
5626008 CCGATTATAG
Statistics
Matches: 843, Mismatches: 9, Indels: 36
0.95 0.01 0.04
Matches are distributed among these distances:
120 75 0.09
121 26 0.03
122 12 0.01
123 50 0.06
124 82 0.10
125 125 0.15
126 128 0.15
127 135 0.16
128 113 0.13
129 97 0.12
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:5625930 original size:371 final size:378
Alignment explanation
Indices: 5625011--5626007 Score: 1768
Period size: 371 Copynumber: 2.6 Consensus size: 378
5625001 TTACCTGATT
5625011 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAG-GTCCCCGAGGGACATGAGTGACA-AATAGGGCAATGATAACATATTCTC
* *
5625076 TGACGAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCATGTGAATACTGAAATAATAGGTA
64 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
5625141 CTGATATATCTAGTGTCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
129 CTGATATATCTAGTGT-CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
*
5625206 GACGAAATAATGGAAGGTGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTG-AAAATAGGTACT
193 GACG-AATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAAAATAGGTACT
5625270 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
257 GATATATCTAGTGTCCCCGAGGGACATGAGTGAC--AATAGGGCAATGATAACATATTCTCTGAC
5625335 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
320 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
5625394 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAG-GTCCCCGAGGGACATGAGTGACA-AATAGGGCAATGATAACATATTCTC
*
5625459 TGACGAAATAATAGAA-G-GCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
64 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
5625521 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
129 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
*
5625586 ACGAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTG
194 ACGAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAA-AATAGGTACTG
5625651 ATATATCTAGTGTCCCCGAGGGACATGAGTGAC-ATAGGGC-ATGATAACATATTCTCTGACGAA
258 ATATATCTAGTGTCCCCGAGGGACATGAGTGACAATAGGGCAATGATAACATATTCTCTGACGAA
5625714 ATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
323 ATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
5625770 TACTGATATA-CTA-GTCCCCGAGGGACATGAGTGAC-AATAGGGCAATGAT-ACATA-T-TCTG
1 TACTGATATATCTAGGTCCCCGAGGGACATGAGTGACAAATAGGGCAATGATAACATATTCTCTG
5625829 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
66 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
*
5625894 GATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGAC
131 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
5625959 GAATAATGGAAGGCGCGCCCCCGGGAACGC-CCTTCATGTGAATAGTGAA
196 GAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
5626008 CCGATTATAG
Statistics
Matches: 601, Mismatches: 8, Indels: 23
0.95 0.01 0.04
Matches are distributed among these distances:
368 17 0.03
369 2 0.00
370 27 0.04
371 151 0.25
373 22 0.04
375 3 0.00
376 89 0.15
377 7 0.01
378 45 0.07
379 54 0.09
380 101 0.17
381 2 0.00
382 1 0.00
383 80 0.13
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (378 bp):
TACTGATATATCTAGGTCCCCGAGGGACATGAGTGACAAATAGGGCAATGATAACATATTCTCTG
ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
GAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAAAATAGGTACTGATA
TATCTAGTGTCCCCGAGGGACATGAGTGACAATAGGGCAATGATAACATATTCTCTGACGAAATA
ATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:5632283 original size:10 final size:10
Alignment explanation
Indices: 5632268--5632298 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5632258 TTTATCCCAA
5632268 AAAGAGAGAG
1 AAAGAGAGAG
5632278 AAAGAGAGAG
1 AAAGAGAGAG
*
5632288 AGAGAGAGAG
1 AAAGAGAGAG
5632298 A
1 A
5632299 TGATGATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (10 bp):
AAAGAGAGAG
Found at i:5634006 original size:17 final size:16
Alignment explanation
Indices: 5633979--5634019 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
5633969 CCGGGTTTTC
*
5633979 ATTATATTATTATATT
1 ATTATATTATTAGATT
5633995 ATTATGATTATTAGATT
1 ATTAT-ATTATTAGATT
5634012 ATATATAT
1 AT-TATAT
5634020 ATATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 14 0.64
18 3 0.14
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (16 bp):
ATTATATTATTAGATT
Found at i:5634018 original size:2 final size:2
Alignment explanation
Indices: 5634011--5634062 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
5634001 ATTATTAGAT
5634011 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5634053 TA TA TA TA TA
1 TA TA TA TA TA
5634063 AGATCCAAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5634261 original size:18 final size:19
Alignment explanation
Indices: 5634221--5634264 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
5634211 TTTGGTTCAC
* *
5634221 GGAATATAAGATTATCAGTG
1 GGAATAAAAGATTACCAG-G
5634241 GGAATAAAAGATTACCA-G
1 GGAATAAAAGATTACCAGG
5634259 GGAATA
1 GGAATA
5634265 GGATTACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.45, C:0.07, G:0.25, T:0.23
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:5634486 original size:36 final size:36
Alignment explanation
Indices: 5634415--5634487 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
5634405 GTTGAAAAAT
*
5634415 ATTTATATATTTTCTTTAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
*
5634451 ATTTATATAATTTT-TTTACAAAATTTAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAAATTAAAATCATAAA
5634487 A
1 A
5634488 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 18 0.55
37 15 0.45
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
Found at i:5635205 original size:38 final size:38
Alignment explanation
Indices: 5635133--5635205 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
5635123 TTATTTTCAC
*
5635133 TTTTATAAAAAAAATTATATAAATTTTATGAATTTAAA
1 TTTTATAAAAAAAATTATATAAATTTTATCAATTTAAA
* * *
5635171 TTTTTTAAAGAAAA-TATATAAATATTTTTCAATTT
1 TTTTATAAAAAAAATTATATAAAT-TTTATCAATTT
5635206 GTTAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 9 0.30
38 21 0.70
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (38 bp):
TTTTATAAAAAAAATTATATAAATTTTATCAATTTAAA
Found at i:5635358 original size:16 final size:16
Alignment explanation
Indices: 5635337--5635373 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
5635327 AACATTTTCA
5635337 GTAATCCTATTCCCTT
1 GTAATCCTATTCCCTT
5635353 GTAATCCTATTCCCTT
1 GTAATCCTATTCCCTT
5635369 GTAAT
1 GTAAT
5635374 ATTTTATTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.22, C:0.27, G:0.08, T:0.43
Consensus pattern (16 bp):
GTAATCCTATTCCCTT
Found at i:5638916 original size:3 final size:3
Alignment explanation
Indices: 5638910--5638943 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
5638900 GAAATGAAAC
*
5638910 TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5638944 CATCACCATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:5642169 original size:4 final size:5
Alignment explanation
Indices: 5642073--5643279 Score: 1605
Period size: 5 Copynumber: 249.6 Consensus size: 5
5642063 GTGTGTTAAT
* *
5642073 TAACA TAACA GAACA TAA-A TAACA -AGAGA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TA-ACA TAACA TAACA TAACA TAACA
* *
5642122 TAACA TAACA GAACA -AACA TAAC- -AACA GAACA TAACA T-ACA TAA-A
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
* *
5642167 TAACA TAACA CAACA TAACA TAACA TAACA TAACA TAACA AAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
*
5642217 GAACA TAACA TAACA -AACA TAACA TAACA TAACA TAAC- -AACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
5642264 TAACA TAACA TAACA TAAAACA TAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA T--AACA TAACA TAACA TAACA TAACA TAACA TAACA
5642316 -AACAA TAACA TAACA TAACA TAACACA TAACA TAACA TAACA -AACA
1 TAAC-A TAACA TAACA TAACA T-A-ACA TAACA TAACA TAACA TAACA
5642362 TAACA TAAC- -AACA TAACA TAACA TAACA TAA-A TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
* *
5642409 TAACA GAACA TAACA AAACA TAACA TAACA TAACA TAACA TAACA T-ACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
*
5642458 -AACA TAACA TAACA TAAC- TAACA TAACA TAAC- -AACA GAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
* * *
5642504 TAACA TAACA TAACA TAACA GAAACA GAAC- -AACA TAACA TAACA GAACA
1 TAACA TAACA TAACA TAACA -TAACA TAACA TAACA TAACA TAACA TAACA
*
5642553 TAAC- -AACA AAACA TAACA TAACA TAACA -AACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
5642600 TAACA TAACA TAACA TAACA TAACA -AACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
*
5642649 -AACA TAAAACA TAACA T-A-A TAACA TAACA TAACA -AACA TAACA TAAAA
1 TAACA T--AACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
*
5642697 TAACA TAACA TAACA TAAC- -AACA TAACA -AACA TAACA TAA-A GAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
*
5642743 TAACA -AACA TAACA TAACA TAACA TAACA TAACA TAACA AAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
* * *
5642792 AAAAA AAACA TAAC- TAACA TAACA TAACCA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAA-CA TAACA TAACA TAACA TAACA
* *
5642842 TAAAA TAACA TAACA GAACA TAACA T-ACA -AACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
5642890 TAACA TAACA TAACA TAACA -AACA TAAC- TAACATA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAAC--A TAACA TAACA TAACA
*
5642940 TAACA TAACA TAACA -AACA TAACA GAACA TAACATA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAAC--A TAACA TAACA TAACA
5642991 TAACA TAACA TAACA TAACA TAACA TAACA TAAC- -AACA T-ACA -AACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
*
5643037 -AACA -AACA TAACA TAACA TAACA TAACA TAACA GAACA T-ACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
*
5643084 TAACA -AACA T-ACA TAACA TAACA -ACCA TAACA TAACA TAAACA -AACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA T-AACA TAACA
5643131 TAACA TAACA TAAC- -AACA TTAACA TAAACA TAACA TAAC- -AACA TAACA
1 TAACA TAACA TAACA TAACA -TAACA T-AACA TAACA TAACA TAACA TAACA
*
5643179 TAACA TAACA TAACA AAACA TAAC- -AACA TAACA TAAC- TAACA TAACA
1 TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA TAACA
5643226 TAACA TAACA TAACA TAACA TAAACA TAACA TAACA TAACA TAACA TAACA
1 TAACA TAACA TAACA TAACA T-AACA TAACA TAACA TAACA TAACA TAACA
5643277 TAA
1 TAA
5643280 TATATATGTA
Statistics
Matches: 1083, Mismatches: 44, Indels: 150
0.85 0.03 0.12
Matches are distributed among these distances:
3 35 0.03
4 130 0.12
5 862 0.80
6 33 0.03
7 23 0.02
ACGTcount: A:0.62, C:0.20, G:0.01, T:0.17
Consensus pattern (5 bp):
TAACA
Found at i:5644382 original size:20 final size:19
Alignment explanation
Indices: 5644337--5644388 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
5644327 CCGATTCAAG
*
5644337 TGGTATCGATACCAAGAGG
1 TGGTATCGATACCAAGAGA
* *
5644356 GGAGTATCGATACCATGAGAA
1 TG-GTATCGATACCAAGAG-A
5644377 TGGTATCGATAC
1 TGGTATCGATAC
5644389 TGTAACATCC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (19 bp):
TGGTATCGATACCAAGAGA
Found at i:5645896 original size:18 final size:18
Alignment explanation
Indices: 5645873--5645907 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5645863 AGAGATTATC
5645873 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
*
5645891 AGTGGTCCTTCGGGACA
1 AGTGGTCATTCGGGACA
5645908 AATTTTAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:5647068 original size:55 final size:55
Alignment explanation
Indices: 5646954--5647086 Score: 151
Period size: 55 Copynumber: 2.4 Consensus size: 55
5646944 GCACTAAGTG
* * * * * * * *
5646954 TGTAAAAAGCTAAGGAATTCATACTAATTGTATGGATTTCCATATGGGTACTATG
1 TGTACAAATCTAAGAAATTCATACTAAGTGTATGAATTTCCATATGGGAAATATA
*
5647009 TGTACAGAA-CTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGAAATATA
1 TGTACA-AATCTAAGAAATTCATACTAAGTGTATGAATTTCCATATGGGAAATATA
* *
5647064 TGTACAAATATAAGAAGTTCATA
1 TGTACAAATCTAAGAAATTCATA
5647087 ATAATTAGGC
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
54 2 0.03
55 62 0.94
56 2 0.03
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (55 bp):
TGTACAAATCTAAGAAATTCATACTAAGTGTATGAATTTCCATATGGGAAATATA
Found at i:5647469 original size:68 final size:68
Alignment explanation
Indices: 5647265--5647454 Score: 301
Period size: 68 Copynumber: 2.8 Consensus size: 68
5647255 CAAGATTAAT
*
5647265 GGCCTAATTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
5647330 TGA
66 TGA
* *
5647333 GGCCTAACTGTGCATTTGATAGAAAGGTGCCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
5647398 TGA
66 TGA
* * * *
5647401 GGCCTGACTGTGCATTTGACCAG-AAGGTGTTAATTATGCTAGTTAGATGAAAGG
1 GGCCTAACTGTGCATTTGA-CAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGG
5647455 TCAAATACCT
Statistics
Matches: 112, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
68 110 0.98
69 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (68 bp):
GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
TGA
Found at i:5647662 original size:45 final size:45
Alignment explanation
Indices: 5647591--5647976 Score: 520
Period size: 45 Copynumber: 8.6 Consensus size: 45
5647581 TTGTAAAAAA
* * * * *
5647591 GGCATGAAATGATGTCATAATCGAAATGTATATGGGTTCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * * * *
5647636 GGTATGAAAGAATGCCATAATTGAAATGTATATGTGTGTATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* *
5647681 AGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATCATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* *
5647726 GGCGTGAAAGGATGTCATAATTGAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
*
5647771 GGCATGAAAGGATGCCATAATTTAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * *
5647816 AGCATGAAAGGATGCCATAATCGAAATGCATATAGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* *
5647861 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTTCATTATA
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
*** *
5647906 GGCATGAAAGGATTTAATAATTTAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * * *
5647951 GGTATGAAAAGATGCTATAAATGAAA
1 GGCATGAAAGGATGCCATAATTGAAA
5647977 AGGCATAATA
Statistics
Matches: 297, Mismatches: 44, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 297 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (45 bp):
GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
Found at i:5649459 original size:2 final size:2
Alignment explanation
Indices: 5649452--5649512 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
5649442 TGTCAGAAAG
5649452 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5649493 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
5649513 CTTTTATGGT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5651674 original size:20 final size:19
Alignment explanation
Indices: 5651628--5651683 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
5651618 ACCGATTCAA
*
5651628 GTGGTATCGATACCAAGAG
1 GTGGTATCGATACCATGAG
* *
5651647 GGGAGTATCAATACCATGAG
1 GTG-GTATCGATACCATGAG
5651667 GATGGTATCGATACCAT
1 G-TGGTATCGATACCAT
5651684 TGAACACAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.07
20 27 0.90
21 1 0.03
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (19 bp):
GTGGTATCGATACCATGAG
Found at i:5652531 original size:68 final size:68
Alignment explanation
Indices: 5652412--5652601 Score: 263
Period size: 68 Copynumber: 2.8 Consensus size: 68
5652402 CAAGATTAAT
* * *
5652412 GGCCTAACTGTGCATTTTACAAAAATGTGTCAATCATGCCAGTTAGCTGAAAGGCTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
5652477 TGA
66 TGA
* * *
5652480 GGCCTAACTGTGCATTTGATAAAAAGGTGTCAATGATGCCAATTAGATGAAAGGCTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
5652545 TGA
66 TGA
* ** ** * *
5652548 GGCATGGCTGTGCATTTGACAGGAAGGTGTCAATTATGCCAGTTAAATGAAAGG
1 GGCCTAACTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGG
5652602 TCAAATACCT
Statistics
Matches: 107, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 107 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (68 bp):
GGCCTAACTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
TGA
Found at i:5652700 original size:81 final size:81
Alignment explanation
Indices: 5652554--5652704 Score: 212
Period size: 81 Copynumber: 1.9 Consensus size: 81
5652544 TTGAGGCATG
* * * *
5652554 GCTGTGCATTTGACAGGAAGGTGTCAATTATGCCAGTTAAATGAAAGGTCAAATACCTTTGAGTA
1 GCTGTGCAGTTGACAGAAAGGTGTCAATCATGCCAGTTAAATGAAAGGTCAAATACCTTTAAGTA
5652619 AAAGATTAATGGACTA
66 AAAGATTAATGGACTA
* * * * **
5652635 GCTGTGCAGTTGACAGAAAGGTGTCCATCATGCCAGTTAGATGAAATGTTAAATGTCTTTAAGTA
1 GCTGTGCAGTTGACAGAAAGGTGTCAATCATGCCAGTTAAATGAAAGGTCAAATACCTTTAAGTA
5652700 AAAGA
66 AAAGA
5652705 CTAGATGAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 60 1.00
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (81 bp):
GCTGTGCAGTTGACAGAAAGGTGTCAATCATGCCAGTTAAATGAAAGGTCAAATACCTTTAAGTA
AAAGATTAATGGACTA
Found at i:5652788 original size:45 final size:45
Alignment explanation
Indices: 5652739--5653169 Score: 583
Period size: 45 Copynumber: 9.6 Consensus size: 45
5652729 TTTTATAAAA
* * * *
5652739 GGCATGAAAGGATACCATAATCGAAATGCATGTGTGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * *
5652784 GGCATGAAAAGATGCCATAATTGAAATGAATATGGGTACATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* *
5652829 TGCATGAAAGGATGCAATAATTGAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* *
5652874 TGCATGAAAGGATGCCATAATTGAAATGCATATAGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * *
5652919 GGTATTAAAGGATGCCATAATCGAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * *
5652964 GACATGAAAGGATGTCATAATCGAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* *
5653009 GGCATGAAAGGATGCCATAATCGAAATGCATATGGGTTCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * * *
5653054 AGTATGAAAGGATGCCATAATTGAAATTCATATGGGTGCATTATA
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
*** *
5653099 GGCATGAAAGGATTTAATAATTGAAATGCATATAGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * * *
5653144 GGTATGAAAAGATGCTATAAATGAAA
1 GGCATGAAAGGATGCCATAATTGAAA
5653170 AGGCATAATG
Statistics
Matches: 340, Mismatches: 46, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 340 1.00
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (45 bp):
GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
Found at i:5653258 original size:13 final size:13
Alignment explanation
Indices: 5653240--5653265 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5653230 AAAAAGAGAT
5653240 AAATATAAAAGAA
1 AAATATAAAAGAA
5653253 AAATATAAAAGAA
1 AAATATAAAAGAA
5653266 GATAGGTATG
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:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
AAATATAAAAGAA
Found at i:5662189 original size:22 final size:21
Alignment explanation
Indices: 5662147--5662186 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5662137 GAGTTTATTT
*
5662147 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
5662168 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
5662187 ACAATTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:5666359 original size:20 final size:19
Alignment explanation
Indices: 5666313--5666368 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
5666303 ACCGATTCAA
*
5666313 GTGGTATCGATACCAAAAG
1 GTGGTATCGATACCATAAG
* *
5666332 GGGAGTATCGATACCATGAG
1 GTG-GTATCGATACCATAAG
5666352 GATGGTATCGATACCAT
1 G-TGGTATCGATACCAT
5666369 TGAACACAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 2 0.06
20 28 0.90
21 1 0.03
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (19 bp):
GTGGTATCGATACCATAAG
Found at i:5666909 original size:55 final size:55
Alignment explanation
Indices: 5666794--5666917 Score: 135
Period size: 55 Copynumber: 2.3 Consensus size: 55
5666784 GTGCAAAGAG
* * * * *
5666794 CTAAGGAATTCATACTAAGTGTAAGAATTTCCGTATGGGTACTATGTGTGTAGAA
1 CTAAGAAATTCATACTAAGTGTAAGAATTTCCGTATGGGAAATATATGTGCAGAA
* * *
5666849 CTAAGAAATTCATACTAAGTGTATGAAATTT-TGTGTGGGAAATATATGTGCAGATA
1 CTAAGAAATTCATACTAAGTGTAAG-AATTTCCGTATGGGAAATATATGTGCAGA-A
*
5666905 -TAAGAAGTTCATA
1 CTAAGAAATTCATA
5666918 ATAATTAGGT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
55 52 0.90
56 6 0.10
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (55 bp):
CTAAGAAATTCATACTAAGTGTAAGAATTTCCGTATGGGAAATATATGTGCAGAA
Found at i:5667211 original size:68 final size:68
Alignment explanation
Indices: 5667101--5667288 Score: 286
Period size: 68 Copynumber: 2.8 Consensus size: 68
5667091 AGATTAATGA
* * *
5667101 CCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCGAGTTAGGTGAAAGGCTAAGTGCCTTTG
1 CCTAACTGTGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
5667166 AGG
66 AGG
* *
5667169 CCTAACTGTGCATTTGATAGAAATGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTT
1 CCTAACTGTGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
5667234 AGG
66 AGG
* * * * *
5667237 CATGACTGTGCATTTGACAGGAATGTGTCAATTATGCCAGTTAGATTAAAGG
1 CCTAACTGTGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGG
5667289 TCAAATACCT
Statistics
Matches: 109, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 109 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (68 bp):
CCTAACTGTGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
AGG
Found at i:5667381 original size:81 final size:81
Alignment explanation
Indices: 5667243--5667391 Score: 228
Period size: 81 Copynumber: 1.8 Consensus size: 81
5667233 TAGGCATGAC
* * * *
5667243 TGTGCATTTGACAGGAATGTGTCAATTATGCCAGTTAGATTAAAGGTCAAATACCTTTGAGTAAA
1 TGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTCAAATACCTTTGAGTAAA
5667308 AGATTAATGGCCTAGG
66 AGATTAATGGCCTAGG
* *
5667324 TGTGCATTTGATAGAAAGGTGTCAATCATGCCAGTTAGATGAAATGGT-AAATGCCTTTGAGTAA
1 TGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAA-GGTCAAATACCTTTGAGTAA
5667388 AAGA
65 AAGA
5667392 CTAGATGAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
81 58 0.95
82 3 0.05
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.30
Consensus pattern (81 bp):
TGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTCAAATACCTTTGAGTAAA
AGATTAATGGCCTAGG
Found at i:5667411 original size:81 final size:81
Alignment explanation
Indices: 5667245--5667411 Score: 185
Period size: 81 Copynumber: 2.1 Consensus size: 81
5667235 GGCATGACTG
* * * *
5667245 TGCATTTGACAGGAATGTGTCAATTATGCCAGTTAGATTAAAGGTCAAATACCTTTGAGTAAAAG
1 TGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTCAAATACCTTTGAGTAAAAG
* ** ****
5667310 ATTAATGGCCTAGGTG
66 ACTAATGGAATAACAA
* *
5667326 TGCATTTGATAGAAAGGTGTCAATCATGCCAGTTAGATGAAATGGT-AAATGCCTTTGAGTAAAA
1 TGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAA-GGTCAAATACCTTTGAGTAAAA
5667390 GACTAGAT-GAATAACAA
65 GACTA-ATGGAATAACAA
5667407 TGCAT
1 TGCAT
5667412 AACGTTGTAT
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
81 66 0.93
82 5 0.07
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (81 bp):
TGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTCAAATACCTTTGAGTAAAAG
ACTAATGGAATAACAA
Found at i:5667766 original size:45 final size:45
Alignment explanation
Indices: 5667427--5667742 Score: 425
Period size: 45 Copynumber: 7.0 Consensus size: 45
5667417 TGTATAAAAT
* * *
5667427 GCATGAAAGGATGCCATAATCGAAATGCATGTGTGTGCATTATCG
1 GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCG
* * *
5667472 GTATGAAAGGATGCCATAATTGAAATGAATATGGGTACATTATCG
1 GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCG
** *
5667517 GCATGAAAGGATGCCATAATTGAAATTTATATGGGTGCATTATTG
1 GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCG
* * * * *
5667562 GCATTAAAGGATTCCATAATCGAAATACATATGGGTGCATTACCG
1 GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCG
* *
5667607 GCATGAAAGGATGCCATAATCGAAATGCATATGGGTGTATTATCG
1 GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCG
* *
5667652 GCATGAAAGGATGCTATAATTGAAATGCATATGGGTGCATTATAG
1 GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCG
*** * *
5667697 GCATGAAAGGATTTAATAATTGAAATGCATATGAGTACATTATCG
1 GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCG
5667742 G
1 G
5667743 TATAAAAAGA
Statistics
Matches: 238, Mismatches: 33, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 238 1.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (45 bp):
GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCG
Found at i:5668809 original size:3 final size:3
Alignment explanation
Indices: 5668803--5668858 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
5668793 AACAAAAAAT
5668803 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5668851 ATA ATA AT
1 ATA ATA AT
5668859 TAAACCTTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5669579 original size:15 final size:16
Alignment explanation
Indices: 5669559--5669590 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
5669549 ATTCTGATTT
5669559 GATTTATTA-ATTTTA
1 GATTTATTATATTTTA
5669574 GATTTATTATATTTTA
1 GATTTATTATATTTTA
5669590 G
1 G
5669591 TCCTTCGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.59
Consensus pattern (16 bp):
GATTTATTATATTTTA
Found at i:5670188 original size:4 final size:4
Alignment explanation
Indices: 5670179--5670209 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
5670169 ATTTTGTTAT
5670179 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
5670210 TCCATATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:5670751 original size:28 final size:28
Alignment explanation
Indices: 5670711--5670767 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
5670701 AAGATATTTT
5670711 TAGGTATTCGACCTACATAACCAAAAGA
1 TAGGTATTCGACCTACATAACCAAAAGA
*
5670739 TAGGTATTCGACCTACATAACCCAAAGA
1 TAGGTATTCGACCTACATAACCAAAAGA
5670767 T
1 T
5670768 TGATGGTGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (28 bp):
TAGGTATTCGACCTACATAACCAAAAGA
Found at i:5671323 original size:21 final size:22
Alignment explanation
Indices: 5671313--5671353 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5671303 CTCATTTTAT
5671313 ATTAAATTTATATAATTATATG
1 ATTAAATTTATATAATTATATG
5671335 ATTAAATTT-TA-AATTATAT
1 ATTAAATTTATATAATTATAT
5671354 TAGGGCTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTAAATTTATATAATTATATG
Found at i:5674535 original size:16 final size:16
Alignment explanation
Indices: 5674498--5674540 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
5674488 TAAAGTCAAT
5674498 CTAATCAAAACTAACAAA
1 CTAA-CAAAA-TAACAAA
5674516 -TAACAAAATAACAAA
1 CTAACAAAATAACAAA
*
5674531 CTAACTAAAT
1 CTAACAAAAT
5674541 GTATTCACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 7 0.30
16 13 0.57
17 3 0.13
ACGTcount: A:0.63, C:0.19, G:0.00, T:0.19
Consensus pattern (16 bp):
CTAACAAAATAACAAA
Found at i:5676990 original size:15 final size:17
Alignment explanation
Indices: 5676965--5676998 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5676955 TGCCAGAAAG
5676965 TTAAAATGTTGG-GAGT
1 TTAAAATGTTGGTGAGT
5676981 TTAAAA-GTTGGTGAGT
1 TTAAAATGTTGGTGAGT
5676997 TT
1 TT
5676999 GCAGGTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.41
Consensus pattern (17 bp):
TTAAAATGTTGGTGAGT
Found at i:5687292 original size:18 final size:18
Alignment explanation
Indices: 5687269--5687322 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
5687259 CTATGTGTAA
5687269 AAAACAGACTGTAGAAAG
1 AAAACAGACTGTAGAAAG
* *
5687287 AAAACAGATTGTATTG-TAG
1 AAAACAGACTGTA--GAAAG
*
5687306 AAAACATACTGTAGAAA
1 AAAACAGACTGTAGAAA
5687323 ACAAACAAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
17 1 0.04
18 13 0.46
19 13 0.46
20 1 0.04
ACGTcount: A:0.52, C:0.09, G:0.19, T:0.20
Consensus pattern (18 bp):
AAAACAGACTGTAGAAAG
Found at i:5689292 original size:36 final size:36
Alignment explanation
Indices: 5689244--5689315 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
5689234 TTACCTTCTG
* * *
5689244 TTTCAGATGCAACAGGGTCCGAATCTGGTTCTTGGC
1 TTTCAGAGGCAACAAGATCCGAATCTGGTTCTTGGC
5689280 TTTCAGAGGCAACAAGATCCGAATCTGGTTCTTGGC
1 TTTCAGAGGCAACAAGATCCGAATCTGGTTCTTGGC
5689316 AAATGCTAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.29
Consensus pattern (36 bp):
TTTCAGAGGCAACAAGATCCGAATCTGGTTCTTGGC
Found at i:5691437 original size:14 final size:14
Alignment explanation
Indices: 5691418--5691445 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5691408 CAGACTGTAT
5691418 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
5691432 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
5691446 AAGTCTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (14 bp):
TGTAGAAAACAGAC
Found at i:5695459 original size:16 final size:16
Alignment explanation
Indices: 5695438--5695469 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5695428 GGCCAATTAT
5695438 CTTCAGATTAATGAGG
1 CTTCAGATTAATGAGG
5695454 CTTCAGATTAATGAGG
1 CTTCAGATTAATGAGG
5695470 GTTATGGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (16 bp):
CTTCAGATTAATGAGG
Found at i:5696721 original size:81 final size:81
Alignment explanation
Indices: 5696563--5696727 Score: 206
Period size: 81 Copynumber: 2.0 Consensus size: 81
5696553 AATTAGAGTT
* ** *
5696563 GTTCTGGTAAAAGTATTTATGGATTAGAGGAAGGTTGCTGGTCTAGAGGTAATGATGTAGTAGGA
1 GTTCTGGAAAAAGTATTTATAAATTAGAGGAAGGTTGCTCGTCTAGAGGTAATGATGTAGTAGGA
* * *
5696628 TTATCCGGTTGGGAGG
66 TTAGCCGATTGGGAAG
* * *
5696644 GTTCTGGAAAAAGTATTTCTAAATTAGAGGAAGGTTGTTCGTCT-GAAGGTAATGATGTTGTAGG
1 GTTCTGGAAAAAGTATTTATAAATTAGAGGAAGGTTGCTCGTCTAG-AGGTAATGATGTAGTAGG
* *
5696708 ATTGGGCGATTGGGAAG
65 ATTAGCCGATTGGGAAG
5696725 GTT
1 GTT
5696728 GTTGGTTGGG
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
80 1 0.01
81 70 0.99
ACGTcount: A:0.27, C:0.06, G:0.35, T:0.33
Consensus pattern (81 bp):
GTTCTGGAAAAAGTATTTATAAATTAGAGGAAGGTTGCTCGTCTAGAGGTAATGATGTAGTAGGA
TTAGCCGATTGGGAAG
Found at i:5700284 original size:36 final size:37
Alignment explanation
Indices: 5700244--5700319 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 37
5700234 CGGGGAGACA
*
5700244 TTCACACCCATAGAAAAGCTT-ATACATTACGAGTAC
1 TTCACACCCATAGAAAAGCTTCATACAGTACGAGTAC
*
5700280 TTCACACCCATAGAAAAGCTTCATACAGTATGAGTAC
1 TTCACACCCATAGAAAAGCTTCATACAGTACGAGTAC
5700317 TTC
1 TTC
5700320 TCTCTCTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
36 21 0.57
37 16 0.43
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (37 bp):
TTCACACCCATAGAAAAGCTTCATACAGTACGAGTAC
Found at i:5705507 original size:48 final size:48
Alignment explanation
Indices: 5705440--5705531 Score: 184
Period size: 48 Copynumber: 1.9 Consensus size: 48
5705430 CTATGCTTTA
5705440 TATCATTTAAACTTGTTTATGGTAAGATTAGGGTTATGACGACCATGC
1 TATCATTTAAACTTGTTTATGGTAAGATTAGGGTTATGACGACCATGC
5705488 TATCATTTAAACTTGTTTATGGTAAGATTAGGGTTATGACGACC
1 TATCATTTAAACTTGTTTATGGTAAGATTAGGGTTATGACGACC
5705532 GTGGCGTGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (48 bp):
TATCATTTAAACTTGTTTATGGTAAGATTAGGGTTATGACGACCATGC
Found at i:5713807 original size:22 final size:23
Alignment explanation
Indices: 5713776--5713836 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
5713766 ATAGGGCAGA
* *
5713776 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
5713798 TGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
5713821 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
5713837 CCAAGGGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.20
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:5715998 original size:2 final size:2
Alignment explanation
Indices: 5715991--5716020 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5715981 GCAGCGTATT
*
5715991 TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5716021 ATCAATTGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5720817 original size:19 final size:19
Alignment explanation
Indices: 5720778--5720833 Score: 105
Period size: 19 Copynumber: 3.0 Consensus size: 19
5720768 CCCTCCCCTG
5720778 CACACGCTCTCCTTT-TTC
1 CACACGCTCTCCTTTCTTC
5720796 CACACGCTCTCCTTTCTTC
1 CACACGCTCTCCTTTCTTC
5720815 CACACGCTCTCCTTTCTTC
1 CACACGCTCTCCTTTCTTC
5720834 ATCATTTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 15 0.41
19 22 0.59
ACGTcount: A:0.11, C:0.46, G:0.05, T:0.38
Consensus pattern (19 bp):
CACACGCTCTCCTTTCTTC
Found at i:5732504 original size:23 final size:22
Alignment explanation
Indices: 5732462--5732522 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 22
5732452 ATAGGGCAGA
* *
5732462 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
5732484 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
5732507 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
5732523 CCCAGGGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:5732531 original size:21 final size:22
Alignment explanation
Indices: 5732462--5732542 Score: 65
Period size: 23 Copynumber: 3.7 Consensus size: 22
5732452 ATAGGGCAGA
* * **
5732462 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTCCAAG
**
5732484 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TCCAAG
*
5732507 GGGAACCGATTCCCCC-CCCAG
1 GGGAACCGATTCCCCCTCCAAG
* *
5732528 GGGAATCGATACCCC
1 GGGAACCGATTCCCC
5732543 TTGAGGGTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 15 0.29
22 14 0.27
23 22 0.43
ACGTcount: A:0.23, C:0.35, G:0.26, T:0.16
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTCCAAG
Found at i:5739479 original size:19 final size:19
Alignment explanation
Indices: 5739451--5739508 Score: 98
Period size: 19 Copynumber: 3.1 Consensus size: 19
5739441 TCCCTCCCTG
*
5739451 CACACACTCTCCTTTCTTC
1 CACACGCTCTCCTTTCTTC
5739470 CACACGCTCTCCTTTCTTC
1 CACACGCTCTCCTTTCTTC
*
5739489 CACATGCTCTCCTTTCTTC
1 CACACGCTCTCCTTTCTTC
5739508 C
1 C
5739509 TCATTTCTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.12, C:0.47, G:0.03, T:0.38
Consensus pattern (19 bp):
CACACGCTCTCCTTTCTTC
Found at i:5749210 original size:2 final size:2
Alignment explanation
Indices: 5749203--5749238 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5749193 ATACGAAAAC
5749203 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
5749239 CAATATTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5755538 original size:18 final size:18
Alignment explanation
Indices: 5755515--5755550 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5755505 CCTGCCCAAC
5755515 CACAGTTATCTTACAGTT
1 CACAGTTATCTTACAGTT
5755533 CACAGTTATCTTACAGTT
1 CACAGTTATCTTACAGTT
5755551 AGCTGACCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (18 bp):
CACAGTTATCTTACAGTT
Found at i:5768639 original size:26 final size:26
Alignment explanation
Indices: 5768610--5768665 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
5768600 AAGTAAGTAG
5768610 TACTTGATTAAAATCATGCATGTACC
1 TACTTGATTAAAATCATGCATGTACC
5768636 TACTTGATTAAAATCATGCATGTACC
1 TACTTGATTAAAATCATGCATGTACC
5768662 TACT
1 TACT
5768666 ACTTAGTACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.36
Consensus pattern (26 bp):
TACTTGATTAAAATCATGCATGTACC
Found at i:5769083 original size:110 final size:111
Alignment explanation
Indices: 5768868--5769087 Score: 354
Period size: 110 Copynumber: 2.0 Consensus size: 111
5768858 TTTTAGTGGG
*
5768868 CATATGTATTCATAAGACTTTACTCATGTATTTGGTTTATCAACTCTGAGTTTGTACTATTTTGA
1 CATATGTATTCATAAGACTTTACTCATGTATTTGGTTTATCAACTCTGAGTTTGTACGATTTTGA
* * *
5768933 TTTTACATTATGTGTTAGGGAGCTTTGGTTTATAATATGTTTTTAT
66 TTTTACATTATGTGTCAGGGAGCTTCGGTTTATAAAATGTTTTTAT
* *
5768979 CATATGTATT-ATAGGA-TCTTACTCATGTATTTTGTTTATCAACTCTGAGTTTGTACGATTTTG
1 CATATGTATTCATAAGACT-TTACTCATGTATTTGGTTTATCAACTCTGAGTTTGTACGATTTTG
*
5769042 GTTTTACATTATGTGTCAGGGAGCTTCGGTTTATAAAATGTTTTTA
65 ATTTTACATTATGTGTCAGGGAGCTTCGGTTTATAAAATGTTTTTA
5769088 AAATTATTCA
Statistics
Matches: 101, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
109 1 0.01
110 90 0.89
111 10 0.10
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.48
Consensus pattern (111 bp):
CATATGTATTCATAAGACTTTACTCATGTATTTGGTTTATCAACTCTGAGTTTGTACGATTTTGA
TTTTACATTATGTGTCAGGGAGCTTCGGTTTATAAAATGTTTTTAT
Found at i:5775715 original size:35 final size:35
Alignment explanation
Indices: 5775650--5775720 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 35
5775640 CCTTAGATTC
* *
5775650 ATAAGGAATTACCAGTTTGATCGGTTTGAACCTAT
1 ATAAGGAATTACCAGTTTAATCGGTATGAACCTAT
5775685 ATAAGGAATTACCAGTTTAA-CTGAG-ATGAACCTAT
1 ATAAGGAATTACCAGTTTAATC-G-GTATGAACCTAT
5775720 A
1 A
5775721 GAGACTTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 1 0.03
35 30 0.94
36 1 0.03
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (35 bp):
ATAAGGAATTACCAGTTTAATCGGTATGAACCTAT
Done.