Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 21 of 433
Found at i:5635901 original size:46 final size:46
Alignment explanation
Indices: 5635726--5635901 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
5635716 TGTAACCCGC
***
5635726 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
5635772 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTCGCAT
* *
5635822 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* * *
5635865 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
5635902 TGCCCAAATA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.58
47 28 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:5638304 original size:15 final size:15
Alignment explanation
Indices: 5638269--5638333 Score: 80
Period size: 15 Copynumber: 4.4 Consensus size: 15
5638259 CAAAGATAAC
*
5638269 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
5638283 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
*
5638298 GAGAAATCCAGAATA
1 AAGAAATCCAGAATA
*
5638313 AATAAATCCAGAATA
1 AAGAAATCCAGAATA
5638328 AAGAAA
1 AAGAAA
5638334 CCCAAGATAC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
14 9 0.21
15 33 0.77
16 1 0.02
ACGTcount: A:0.62, C:0.12, G:0.14, T:0.12
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:5641340 original size:93 final size:93
Alignment explanation
Indices: 5641228--5641400 Score: 310
Period size: 93 Copynumber: 1.9 Consensus size: 93
5641218 CGCCCATAAG
*
5641228 CGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
5641293 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
* *
5641321 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
*
5641386 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
5641401 CAAATATCCC
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:5641396 original size:46 final size:46
Alignment explanation
Indices: 5641221--5641396 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
5641211 TGTAACCCGC
*
5641221 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* * *
5641267 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTCGCAT
* *
5641317 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
5641360 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
5641397 TGCCCAAATA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 27 0.25
48 2 0.02
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:5644878 original size:2 final size:2
Alignment explanation
Indices: 5644871--5644908 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5644861 AAATCCATCC
5644871 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5644909 CCTCCTCCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5649019 original size:21 final size:21
Alignment explanation
Indices: 5648995--5649034 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5648985 CTGCAATATC
5648995 TATTTGACTGTCTAATTGAAT
1 TATTTGACTGTCTAATTGAAT
*
5649016 TATTTGACTGTCTGATTGA
1 TATTTGACTGTCTAATTGA
5649035 CTGAGAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.47
Consensus pattern (21 bp):
TATTTGACTGTCTAATTGAAT
Found at i:5657107 original size:14 final size:14
Alignment explanation
Indices: 5657088--5657115 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5657078 GCATATAAGT
5657088 CCTACAATAAATAC
1 CCTACAATAAATAC
5657102 CCTACAATAAATAC
1 CCTACAATAAATAC
5657116 TATCAGCCAA
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:0.29, G:0.00, T:0.21
Consensus pattern (14 bp):
CCTACAATAAATAC
Found at i:5658421 original size:22 final size:23
Alignment explanation
Indices: 5658362--5658423 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
5658352 TTAGGGTCGA
*
5658362 AATTAAATTATAATTTTTACGAT
1 AATTAAATTATAATTTTTACAAT
* *
5658385 AATAAAAATATAATTTTTA-AAT
1 AATTAAATTATAATTTTTACAAT
* *
5658407 GATTAAATTAAAATTTT
1 AATTAAATTATAATTTT
5658424 ATCAATTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (23 bp):
AATTAAATTATAATTTTTACAAT
Found at i:5658854 original size:12 final size:12
Alignment explanation
Indices: 5658837--5658861 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5658827 CGAGAATAAT
5658837 TTTTTAATATTA
1 TTTTTAATATTA
5658849 TTTTTAATATTA
1 TTTTTAATATTA
5658861 T
1 T
5658862 AAAAATATTA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTAATATTA
Found at i:5659583 original size:10 final size:10
Alignment explanation
Indices: 5659570--5659616 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 10
5659560 ATTTATAAAA
5659570 ATAAAAAATT
1 ATAAAAAATT
5659580 AT-AAAAATT
1 ATAAAAAATT
*
5659589 ATTAAAAATT
1 ATAAAAAATT
*
5659599 ATGTAAAAA-T
1 AT-AAAAAATT
5659609 ATAAAAAA
1 ATAAAAAA
5659617 ATTCATTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
9 14 0.41
10 14 0.41
11 6 0.18
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:5659587 original size:9 final size:9
Alignment explanation
Indices: 5659562--5659615 Score: 60
Period size: 10 Copynumber: 6.0 Consensus size: 9
5659552 CATTTTAAAT
5659562 TTATAAAAA
1 TTATAAAAA
5659571 -TA-AAAAA
1 TTATAAAAA
5659578 TTATAAAAA
1 TTATAAAAA
5659587 TTATTAAAAA
1 TTA-TAAAAA
5659597 TTATGTAAAAA
1 TTA--TAAAAA
5659608 -TATAAAAA
1 TTATAAAAA
5659616 AATTCATTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
7 5 0.12
8 10 0.25
9 8 0.20
10 11 0.28
11 6 0.15
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (9 bp):
TTATAAAAA
Found at i:5659619 original size:21 final size:19
Alignment explanation
Indices: 5659570--5659616 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
5659560 ATTTATAAAA
5659570 ATAAAAAATTATAAAAATT
1 ATAAAAAATTATAAAAATT
*
5659589 ATTAAAAATTATGTAAAAA-T
1 ATAAAAAATTA--TAAAAATT
5659609 ATAAAAAA
1 ATAAAAAA
5659617 ATTCATTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 8 0.33
21 6 0.25
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
ATAAAAAATTATAAAAATT
Found at i:5659636 original size:21 final size:20
Alignment explanation
Indices: 5659571--5659651 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 20
5659561 TTTATAAAAA
5659571 TAAAAAATTA-TAAAAATTAT
1 TAAAAAATTATTAAAAATT-T
*
5659591 T-AAAAATTATGTAAAAATAT
1 TAAAAAATTAT-TAAAAATTT
* *
5659611 AAAAAAATTCATTGAAAATTT
1 TAAAAAATT-ATTAAAAATTT
5659632 TAAAATAATTTATATAAAAA
1 TAAAA-AA-TTAT-TAAAAA
5659652 AATCATTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
19 8 0.17
20 2 0.04
21 25 0.52
22 6 0.12
23 7 0.15
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (20 bp):
TAAAAAATTATTAAAAATTT
Found at i:5661237 original size:21 final size:21
Alignment explanation
Indices: 5661188--5661246 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
5661178 AATATGCTAG
* *
5661188 AGATATTTTGATATTTT-ATA
1 AGATATATTAATATTTTAATA
*
5661208 A-TTATTATTAATATTTTAATA
1 AGATA-TATTAATATTTTAATA
*
5661229 AGATATATTATTATTTTA
1 AGATATATTAATATTTTA
5661247 TTAGTATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.06
20 11 0.35
21 16 0.52
22 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
AGATATATTAATATTTTAATA
Found at i:5661255 original size:21 final size:21
Alignment explanation
Indices: 5661198--5661256 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
5661188 AGATATTTTG
*
5661198 ATATTTTATAATTAT-TATTA
1 ATATTTTATAAGTATATATTA
5661218 ATATTTTAATAAG-ATATATTA
1 ATATTTT-ATAAGTATATATTA
* *
5661239 TTATTTTATTAGTATATA
1 ATATTTTATAAGTATATA
5661257 AAGAAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 13 0.39
21 20 0.61
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
ATATTTTATAAGTATATATTA
Found at i:5663098 original size:23 final size:23
Alignment explanation
Indices: 5662992--5663107 Score: 83
Period size: 23 Copynumber: 5.0 Consensus size: 23
5662982 CCGAAATATA
* * *
5662992 GCTCTTTGTGAGTTTCCTGATAG
1 GCTCTTCGTGAGCTTCCCGATAG
*
5663015 GCTCTTTGTGAGCTTCCCGATAG
1 GCTCTTCGTGAGCTTCCCGATAG
* * *
5663038 TGCTC-GCTTGAACTTCCCGACATATG
1 -GCTCTTCGTGAGCTTCCCG--ATA-G
* * *
5663064 GCTATCCG-GAGCTTCTCGATAG
1 GCTCTTCGTGAGCTTCCCGATAG
*
5663086 GCTCTTCGTGAGCTTCACGATA
1 GCTCTTCGTGAGCTTCCCGATA
5663108 TGGTTCTTTG
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
22 7 0.10
23 46 0.63
24 4 0.05
25 14 0.19
26 2 0.03
ACGTcount: A:0.16, C:0.26, G:0.24, T:0.34
Consensus pattern (23 bp):
GCTCTTCGTGAGCTTCCCGATAG
Found at i:5663490 original size:46 final size:46
Alignment explanation
Indices: 5663440--5663621 Score: 240
Period size: 46 Copynumber: 4.0 Consensus size: 46
5663430 GCTCTCTGAT
* * * *
5663440 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTAAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
5663486 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
5663532 ATGAAATGAATAAAACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
5663578 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
5663622 TCAAAGATAA
Statistics
Matches: 122, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
45 1 0.01
46 121 0.99
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:5664843 original size:21 final size:20
Alignment explanation
Indices: 5664794--5664850 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
5664784 ATACTAAAAA
* *
5664794 AATAATAATAAAATAATAAT
1 AATAATTATAAAATATTAAT
*
5664814 -ATATCTTATTAAAATATTAAT
1 AATA-ATTA-TAAAATATTAAT
5664835 AATAATTATAAAATAT
1 AATAATTATAAAATAT
5664851 CAAAATATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
19 3 0.10
20 10 0.33
21 14 0.47
22 3 0.10
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AATAATTATAAAATATTAAT
Found at i:5671672 original size:15 final size:16
Alignment explanation
Indices: 5671652--5671698 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
5671642 AATAATAGAA
5671652 TATATAAAAAATATAT
1 TATATAAAAAATATAT
5671668 T-TATAAGAATAATAT-T
1 TATATAA-AA-AATATAT
*
5671684 TATATGAAAAATATA
1 TATATAAAAAATATA
5671699 AAATATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
15 10 0.38
16 7 0.27
17 9 0.35
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (16 bp):
TATATAAAAAATATAT
Found at i:5671978 original size:15 final size:16
Alignment explanation
Indices: 5671942--5672192 Score: 76
Period size: 16 Copynumber: 16.1 Consensus size: 16
5671932 TTAAAACCTT
5671942 TAATGATAATAATATA
1 TAATGATAATAATATA
5671958 T-A-GATAA-AATATA
1 TAATGATAATAATATA
5671971 TAATGAT-ATAA-A-A
1 TAATGATAATAATATA
* *
5671984 -AATGA-CATAATGTA
1 TAATGATAATAATATA
* * * *
5671998 AAATAATTATAATTTA
1 TAATGATAATAATATA
* *
5672014 TAAT-ATGAA-AGTGTA
1 TAATGAT-AATAATATA
*
5672029 TATATG-TAAAAAATATA
1 TA-ATGAT-AATAATATA
5672046 TATAT-ATATATAATATA
1 TA-ATGATA-ATAATATA
*
5672063 -AATAATTAATAAATATA
1 TAATGA-TAAT-AATATA
* *
5672080 TAAT-ACAAGTAAAATA
1 TAATGATAA-TAATATA
*
5672096 TAATAATAATAA-ATAA
1 TAATGATAATAATAT-A
5672112 TAATGTAAAATAATAATATA
1 TAATG----ATAATAATATA
*
5672132 TAAT-A-AATAATAATG
1 TAATGATAATAAT-ATA
*
5672147 TAA-AATAATAATATA
1 TAATGATAATAATATA
*
5672162 TAATAAATAATAATA-A
1 TAAT-GATAATAATATA
5672178 T-ATGA-AATAATATA
1 TAATGATAATAATATA
5672192 T
1 T
5672193 TGTTAAAATG
Statistics
Matches: 184, Mismatches: 19, Indels: 66
0.68 0.07 0.25
Matches are distributed among these distances:
12 9 0.05
13 15 0.08
14 18 0.10
15 36 0.20
16 49 0.27
17 40 0.22
18 3 0.02
20 12 0.07
21 2 0.01
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.35
Consensus pattern (16 bp):
TAATGATAATAATATA
Found at i:5672103 original size:30 final size:30
Alignment explanation
Indices: 5672032--5672175 Score: 171
Period size: 30 Copynumber: 5.1 Consensus size: 30
5672022 AAGTGTATAT
*
5672032 ATGTAAAA-AAT-ATATAT-ATATAT-ATA
1 ATGTAAAATAATAATATATAATAAATAATA
* * *
5672058 ATAT-AAATAATTA-ATA-AATATATAATA
1 ATGTAAAATAATAATATATAATAAATAATA
*
5672085 CAAGTAAAAT-ATAATA-ATAATAAATAATA
1 -ATGTAAAATAATAATATATAATAAATAATA
5672114 ATGTAAAATAATAATATATAATAAATAATA
1 ATGTAAAATAATAATATATAATAAATAATA
5672144 ATGTAAAATAATAATATATAATAAATAATA
1 ATGTAAAATAATAATATATAATAAATAATA
5672174 AT
1 AT
5672176 AATATGAAAT
Statistics
Matches: 102, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
25 3 0.03
26 15 0.15
27 4 0.04
28 14 0.14
29 21 0.21
30 45 0.44
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (30 bp):
ATGTAAAATAATAATATATAATAAATAATA
Found at i:5672113 original size:13 final size:13
Alignment explanation
Indices: 5672055--5672179 Score: 83
Period size: 15 Copynumber: 8.7 Consensus size: 13
5672045 ATATATATAT
5672055 ATAAT-ATAAATA
1 ATAATAATAAATA
*
5672067 ATTAATAAATATATA
1 A-TAAT-AATAAATA
5672082 ATACAAGTAA-AATATA
1 AT--AA-TAATAA-ATA
5672098 ATAATAATAAATA
1 ATAATAATAAATA
*
5672111 ATAATGTAAAATAATA
1 ATAA--TAATA-AATA
5672127 ATATATAATAAATA
1 ATA-ATAATAAATA
*
5672141 ATAATGTAAAATAATA
1 ATAA--TAATA-AATA
5672157 ATATATAATAAATA
1 ATA-ATAATAAATA
5672171 ATAATAATA
1 ATAATAATA
5672180 TGAAATAATA
Statistics
Matches: 91, Mismatches: 6, Indels: 31
0.71 0.05 0.24
Matches are distributed among these distances:
12 1 0.01
13 21 0.23
14 19 0.21
15 24 0.26
16 23 0.25
17 3 0.03
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (13 bp):
ATAATAATAAATA
Found at i:5672135 original size:33 final size:33
Alignment explanation
Indices: 5672055--5672189 Score: 133
Period size: 33 Copynumber: 4.2 Consensus size: 33
5672045 ATATATATAT
*
5672055 ATAAT-ATAAATAATTAATAAATATATAA--TACAA
1 ATAATAATATATAA-TAATAAATA-ATAATGTA-AA
*
5672088 GTAA-AATATAATAATAATAAATAATAATGTAAA
1 ATAATAATAT-ATAATAATAAATAATAATGTAAA
5672121 ATAAT-A-ATAT-ATAATAAATAATAATGTAAA
1 ATAATAATATATAATAATAAATAATAATGTAAA
* *
5672151 ATAATAATATATAATAA-ATAATAATAATATGAA
1 ATAATAATATATAATAATA-AATAATAATGTAAA
5672184 ATAATA
1 ATAATA
5672190 TATTGTTAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 18
0.79 0.05 0.16
Matches are distributed among these distances:
30 25 0.28
31 3 0.03
32 11 0.12
33 43 0.49
34 6 0.07
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.33
Consensus pattern (33 bp):
ATAATAATATATAATAATAAATAATAATGTAAA
Found at i:5672186 original size:13 final size:12
Alignment explanation
Indices: 5672035--5672189 Score: 97
Period size: 10 Copynumber: 13.8 Consensus size: 12
5672025 TGTATATATG
*
5672035 TAAAAAATATATA
1 TAAATAATA-ATA
*
5672048 TATATATATAATA
1 TAAATA-ATAATA
*
5672061 TAAATAATTA-A
1 TAAATAATAATA
5672072 TAAATATATAATA
1 TAAATA-ATAATA
* *
5672085 CAAGTAA-AATA
1 TAAATAATAATA
5672096 T-AATAAT-A-A
1 TAAATAATAATA
*
5672105 TAAATAATAATG
1 TAAATAATAATA
5672117 TAAAATAATAATA
1 T-AAATAATAATA
5672130 T--ATAATAA-A
1 TAAATAATAATA
*
5672139 T-AATAAT-GTA
1 TAAATAATAATA
5672149 -AAATAATAATA
1 TAAATAATAATA
5672160 T--ATAATAA-A
1 TAAATAATAATA
5672169 T-AATAATAATA
1 TAAATAATAATA
5672180 TGAAATAATA
1 T-AAATAATA
5672190 TATTGTTAAA
Statistics
Matches: 112, Mismatches: 13, Indels: 34
0.70 0.08 0.21
Matches are distributed among these distances:
9 6 0.05
10 44 0.39
11 16 0.14
12 8 0.07
13 35 0.31
14 3 0.03
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.34
Consensus pattern (12 bp):
TAAATAATAATA
Found at i:5672187 original size:30 final size:29
Alignment explanation
Indices: 5672040--5672192 Score: 149
Period size: 30 Copynumber: 5.2 Consensus size: 29
5672030 ATATGTAAAA
*
5672040 AATATAT-ATATATATATAA-TATAAATAATT
1 AATATATAATAAATA-ATAAGTA-AAATAA-T
* *
5672070 AATAAAT-ATATAAT-ACAAGTAAAAT-AT
1 AATATATAATA-AATAATAAGTAAAATAAT
5672097 AATA-ATAATAAATAATAATGTAAAATAAT
1 AATATATAATAAATAATAA-GTAAAATAAT
5672126 AATATATAATAAATAATAATGTAAAATAAT
1 AATATATAATAAATAATAA-GTAAAATAAT
*
5672156 AATATATAATAAATAATAA-TAATATGAAAT
1 AATATATAATAAATAATAAGTAAAAT--AAT
5672186 AATATAT
1 AATATAT
5672193 TGTTAAAATG
Statistics
Matches: 109, Mismatches: 5, Indels: 18
0.83 0.04 0.14
Matches are distributed among these distances:
26 5 0.05
27 11 0.10
28 13 0.12
29 13 0.12
30 65 0.60
31 2 0.02
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.35
Consensus pattern (29 bp):
AATATATAATAAATAATAAGTAAAATAAT
Found at i:5672189 original size:3 final size:3
Alignment explanation
Indices: 5672095--5672179 Score: 79
Period size: 3 Copynumber: 28.0 Consensus size: 3
5672085 CAAGTAAAAT
*
5672095 ATA ATA ATA ATAA ATA ATA AT- GTA A-A ATA ATA ATA TATA ATAA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA -ATA AT-A ATA
*
5672141 ATA AT- GTA A-A ATA ATA ATA TATA ATAA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA AT-A ATA ATA ATA ATA
5672180 TGAAATAATA
Statistics
Matches: 69, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
2 6 0.09
3 48 0.70
4 15 0.22
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5684316 original size:18 final size:18
Alignment explanation
Indices: 5684279--5684331 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
5684269 TATAAATCCA
*
5684279 AAATATATATTAAAAATTAT
1 AAATA-ATATT-ATAATTAT
5684299 AAATAATATTATAATTAT
1 AAATAATATTATAATTAT
** *
5684317 TTATACTATTATAAT
1 AAATAATATTATAAT
5684332 AGTTTTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 19 0.66
19 5 0.17
20 5 0.17
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATAATATTATAATTAT
Found at i:5686075 original size:26 final size:27
Alignment explanation
Indices: 5686023--5686075 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
5686013 AATTAAGTAT
*
5686023 TTAATAATTTAATATATTTTTTATTTA
1 TTAATAATTTAATATATATTTTATTTA
*
5686050 TTAA-AATTTTATATATAATTTT-TTTA
1 TTAATAATTTAATATAT-ATTTTATTTA
5686076 AAAGAATACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TTAATAATTTAATATATATTTTATTTA
Found at i:5691090 original size:48 final size:48
Alignment explanation
Indices: 5691011--5691163 Score: 243
Period size: 48 Copynumber: 3.2 Consensus size: 48
5691001 CAGAGACTCG
* * * *
5691011 GAAGTCTCGCACCCTAGGTGCCAATATCATGGCCCGAAGCCAAATTAAT
1 GAAG-CTCGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAAT
*
5691060 GAAGCTTGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAAT
1 GAAGCTCGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAAT
*
5691108 GAAGCTCGCACCCGAAGTACTAATATCATGGCCCGAAGCCAAATCAAT
1 GAAGCTCGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAAT
5691156 GAAGCTCG
1 GAAGCTCG
5691164 TAATGACATG
Statistics
Matches: 97, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
48 93 0.96
49 4 0.04
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (48 bp):
GAAGCTCGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAAT
Found at i:5693578 original size:19 final size:19
Alignment explanation
Indices: 5693554--5693621 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
5693544 TTATTTTAAA
*
5693554 TATTTATATATATATATAT
1 TATTTATATATATAAATAT
* *
5693573 TATTTATTTTTATAAATAT
1 TATTTATATATATAAATAT
* * *
5693592 TATTTATACATGTAAAAAT
1 TATTTATATATATAAATAT
5693611 TA-TTATATATA
1 TATTTATATATA
5693622 ATATTTTTAT
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
18 7 0.18
19 32 0.82
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (19 bp):
TATTTATATATATAAATAT
Found at i:5693674 original size:7 final size:7
Alignment explanation
Indices: 5693662--5693698 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
5693652 TATTTGTATT
5693662 TTATATA
1 TTATATA
5693669 TTATATA
1 TTATATA
*
5693676 TTATATC
1 TTATATA
5693683 TT-T-TA
1 TTATATA
5693688 TTATATA
1 TTATATA
5693695 TTAT
1 TTAT
5693699 TCCCTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
5 3 0.12
6 2 0.08
7 21 0.81
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (7 bp):
TTATATA
Found at i:5693708 original size:19 final size:19
Alignment explanation
Indices: 5693665--5693710 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
5693655 TTGTATTTTA
*
5693665 TATATTATATATTATATCT
1 TATATTATATATTATATCC
*
5693684 TTTATTATATATTAT-TCCC
1 TATATTATATATTATAT-CC
5693703 TATATTAT
1 TATATTAT
5693711 CTTCATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.59
Consensus pattern (19 bp):
TATATTATATATTATATCC
Found at i:5693913 original size:20 final size:18
Alignment explanation
Indices: 5693882--5693936 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
5693872 ATATTATTAT
*
5693882 TTTTATAAATATATTAAG
1 TTTTATATATATATTAAG
* *
5693900 TTATTATATCATATAGTATG
1 TT-TTATAT-ATATATTAAG
5693920 TTTTATATATATATTAA
1 TTTTATATATATATTAA
5693937 TCGTTTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 9 0.30
19 11 0.37
20 10 0.33
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (18 bp):
TTTTATATATATATTAAG
Found at i:5693942 original size:20 final size:19
Alignment explanation
Indices: 5693882--5693944 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
5693872 ATATTATTAT
*
5693882 TTTTATAAATATATTAA-G
1 TTTTATATATATATTAATG
*
5693900 TTATTATATCATATAGT-ATG
1 TT-TTATAT-ATATATTAATG
5693920 TTTTATATATATATTAATCG
1 TTTTATATATATATTAAT-G
5693940 TTTTA
1 TTTTA
5693945 AAAAATTCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 8 0.22
19 14 0.38
20 15 0.41
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (19 bp):
TTTTATATATATATTAATG
Found at i:5694042 original size:14 final size:13
Alignment explanation
Indices: 5694002--5694044 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5693992 ACCTCATCTA
*
5694002 TTTTTAATTATAT
1 TTTTTACTTATAT
* *
5694015 TTTTTATTTTTAT
1 TTTTTACTTATAT
5694028 TTTTTGACTTATAT
1 TTTTT-ACTTATAT
5694042 TTT
1 TTT
5694045 ATATATGTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTTTACTTATAT
Found at i:5694160 original size:18 final size:18
Alignment explanation
Indices: 5694139--5694173 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5694129 ATCTCATAAA
*
5694139 TTATTTGTTATTTTTATG
1 TTATTTATTATTTTTATG
*
5694157 TTATTTATTGTTTTTAT
1 TTATTTATTATTTTTAT
5694174 ATATTCGCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (18 bp):
TTATTTATTATTTTTATG
Found at i:5694202 original size:45 final size:43
Alignment explanation
Indices: 5694146--5694263 Score: 129
Period size: 43 Copynumber: 2.7 Consensus size: 43
5694136 AAATTATTTG
*
5694146 TTATT-TTTATGTTATTTATTGTTTTTATATATTCGCATGAAA-A
1 TTATTATTTATGTTATTTATTGTTGTTATAT-TT-GCATGAAATA
5694189 TTGATTATTTATGTTA-TTATT-TTAAGTTATATTTGCATGAAATA
1 TT-ATTATTTATGTTATTTATTGTT--GTTATATTTGCATGAAATA
* *
5694233 TTATTATATATGTAATTTA-TGTTGTTATATT
1 TTATTATTTATGTTATTTATTGTTGTTATATT
5694264 CATCATTTTC
Statistics
Matches: 65, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
42 8 0.12
43 24 0.37
44 18 0.28
45 15 0.23
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.58
Consensus pattern (43 bp):
TTATTATTTATGTTATTTATTGTTGTTATATTTGCATGAAATA
Found at i:5697691 original size:2 final size:2
Alignment explanation
Indices: 5697684--5697738 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
5697674 TTAAAATCAC
*
5697684 AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5697726 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
5697739 AAAAACCTAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5706304 original size:40 final size:40
Alignment explanation
Indices: 5706259--5706462 Score: 261
Period size: 40 Copynumber: 5.1 Consensus size: 40
5706249 CGAGATTTAA
* * *
5706259 CCGGATATAGCT-ACTCACTCGAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCACACAAATGCCTTCGGGACTTAGC
* *
5706299 CCGGATATAGTAACTCGCACCAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAGC
5706339 CCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAGC
*
5706379 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAGC
* * ** *
5706419 CCAGA-ACTAGTCACT-AGTGCAAATGCCTTCGGGACTTAAC
1 CCGGATA-TAGTAACTCA-CACAAATGCCTTCGGGACTTAGC
5706459 CCGG
1 CCGG
5706463 TTATCATCCA
Statistics
Matches: 147, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
39 2 0.01
40 145 0.99
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (40 bp):
CCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAGC
Found at i:5707732 original size:6 final size:6
Alignment explanation
Indices: 5707714--5707750 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
5707704 CATGAGAGCC
*
5707714 TTTCTT TTT-TT TTTCTT TTTCTT TCTC-T TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
5707751 TTCATCATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 9 0.33
6 18 0.67
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTCTT
Found at i:5707736 original size:17 final size:17
Alignment explanation
Indices: 5707714--5707750 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5707704 CATGAGAGCC
* *
5707714 TTTCTTTTTTTTTTCTT
1 TTTCTTTCTCTTTTCTT
5707731 TTTCTTTCTCTTTTCTT
1 TTTCTTTCTCTTTTCTT
5707748 TTT
1 TTT
5707751 TTCATCATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTCTTTCTCTTTTCTT
Found at i:5709188 original size:90 final size:90
Alignment explanation
Indices: 5709075--5709329 Score: 384
Period size: 90 Copynumber: 2.8 Consensus size: 90
5709065 CAAATCAAAT
* * * *
5709075 ATGACAGATTTGGCGTCTTTGTATTAGACGGAGAGTAGATCGAAGATAGCAGATCTGATATTCGT
1 ATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGT
*
5709140 GTGTTTACATCAAAGCAGATTGAAG
66 GTGTTTACATCAAAGCAGATCGAAG
* *
5709165 ATGACAGATTTGGTGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGT
1 ATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGT
**
5709230 GTGTTTACATTGAAGCAGATCGAAG
66 GTGTTTACATCAAAGCAGATCGAAG
* * * * *
5709255 ATGATAGATTTAGCGACTCTGTATTAGACGGGGAGCAGGTCGAAGATAGCAGATCTGAGATTCGT
1 ATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGT
5709320 GTGTTTACAT
66 GTGTTTACAT
5709330 AGCAGGTCGA
Statistics
Matches: 149, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 149 1.00
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.29
Consensus pattern (90 bp):
ATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGT
GTGTTTACATCAAAGCAGATCGAAG
Found at i:5709335 original size:42 final size:42
Alignment explanation
Indices: 5709288--5709371 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
5709278 TTAGACGGGG
*
5709288 AGCAGGTCGAAGATAGCAGATCTGAGATTCGTGTGTTTACAT
1 AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACAT
5709330 AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACAT
1 AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACAT
5709372 CGAAGCAGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (42 bp):
AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACAT
Found at i:5709358 original size:132 final size:132
Alignment explanation
Indices: 5709198--5709725 Score: 442
Period size: 132 Copynumber: 4.0 Consensus size: 132
5709188 TTAGACGGGG
* * *
5709198 AGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATTGAAGCAGATCGAA-GATGATAG
1 AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATC-AAGGATGACAG
* * *
5709262 ATTTAGCG-A-CTCTGTATTAGACGGGGAGCAGGTCGAAGATAGCAGATCTGAGATTCGTGTGTT
65 ATTT-G-GTATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCATGTGTT
5709325 TACAT
128 TACAT
*
5709330 AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCAAGGATGACAGA
1 AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCAAGGATGACAGA
*
5709395 TTTGGTATCTCTGTATTAGATGGGGAGCAGATCGAAGATAGCAGATCTGACATTCATGTGTTTAC
66 TTTGGTATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCATGTGTTTAC
5709460 AT
131 AT
* * * * * * * *
5709462 CGAGACAGATCGAAGAT-GACAGATTTGGCGTCTC-TAT-ATTAGA-CG--G-GGAGC-AGGAT-
1 --AG-CAGATCGAAGATAG-CAGATCTGACAT-TCGTGTGTTTACATCGAAGCAGATCAAGGATG
* ** * * * * * * *
5709518 AGCAGATCTGACAT-TCGTGTGTTTACATC--GAAGTAGATCGAAGAT-GACAGATTTGGCGTCT
61 A-CAGATTTGGTATCTC-TGT-ATTAGA-CGGGGAGCAGATCGAAGATAG-CAGATCTGACAT-T
* * **
5709579 C-TGTATTAGACGGGG
120 CATGTGTT-TAC--AT
* * * *
5709594 AGCAGATCGAAGGTAGCAGATCTGACATTCGTGTGTTTATATCGAAGTAGATCAAAGATGACAGA
1 AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCAAGGATGACAGA
** * *
5709659 TTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGGTAGCAAATCTGACATTCATGTGTTTAC
66 TTTGGTATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCATGTGTTTAC
5709724 AT
131 AT
5709726 CGAAGCAAAT
Statistics
Matches: 307, Mismatches: 58, Indels: 62
0.72 0.14 0.15
Matches are distributed among these distances:
128 6 0.02
129 67 0.22
130 19 0.06
131 7 0.02
132 116 0.38
133 4 0.01
134 18 0.06
135 64 0.21
136 6 0.02
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (132 bp):
AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCAAGGATGACAGA
TTTGGTATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCATGTGTTTAC
AT
Found at i:5709444 original size:90 final size:90
Alignment explanation
Indices: 5709330--5709884 Score: 802
Period size: 90 Copynumber: 6.2 Consensus size: 90
5709320 GTGTTTACAT
*
5709330 AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATC-AAGGATGACAG
1 AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAA-GATGACAG
** *
5709394 ATTTGGTATCTCTGTATTAGATGGGG
65 ATTTGGCGTCTCTGTATTAGACGGGG
*
5709420 AGCAGATCGAAGATAGCAGATCTGACATTCATGTGTTTACATCG-AGACAGATCGAAGATGACAG
1 AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAG-CAGATCGAAGATGACAG
*
5709484 ATTTGGCGTCTCTATATTAGACGGGG
65 ATTTGGCGTCTCTGTATTAGACGGGG
*
5709510 AGC--A--G--GATAGCAGATCTGACATTCGTGTGTTTACATCGAAGTAGATCGAAGATGACAGA
1 AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGA
5709569 TTTGGCGTCTCTGTATTAGACGGGG
66 TTTGGCGTCTCTGTATTAGACGGGG
* * * *
5709594 AGCAGATCGAAGGTAGCAGATCTGACATTCGTGTGTTTATATCGAAGTAGATCAAAGATGACAGA
1 AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGA
5709659 TTTGGCGTCTCTGTATTAGACGGGG
66 TTTGGCGTCTCTGTATTAGACGGGG
* * * *
5709684 AGCAGATCGAAGGTAGCAAATCTGACATTCATGTGTTTACATCGAAGCAAATCGAAGATGACAGA
1 AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGA
5709749 TTTGGCGTCTCTGTATTAGACGGGG
66 TTTGGCGTCTCTGTATTAGACGGGG
* * * *
5709774 AGCAGATCGAAGATAGTAGATTTGACCTTCGTGTGTTTACATCGAAGCAGATCAAAGATGACAGA
1 AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGA
* * * * *
5709839 TTTGACGTGTCTATATTAGACAGAG
66 TTTGGCGTCTCTGTATTAGACGGGG
* *
5709864 AGCAGATTGAAAATAGCAGAT
1 AGCAGATCGAAGATAGCAGAT
5709885 TTGGTGTCTC
Statistics
Matches: 422, Mismatches: 34, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
84 76 0.18
85 2 0.00
86 2 0.00
88 2 0.00
89 2 0.00
90 336 0.80
91 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (90 bp):
AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGA
TTTGGCGTCTCTGTATTAGACGGGG
Found at i:5709504 original size:222 final size:216
Alignment explanation
Indices: 5709114--5709545 Score: 661
Period size: 222 Copynumber: 2.0 Consensus size: 216
5709104 GGAGAGTAGA
* *
5709114 TCGAAGATAGCAGATCTGATATTCGTGTGTTTACATCAAAGCAGATTGAAGATGACAGATTTGGT
1 TCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATTCAAGATGACAGATTTGGT
* * * *
5709179 GTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATTGAA
66 ATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCATGTGTTTACATCGAA
* *
5709244 GCAGATCGAAGATGATAGATTTAGCGACTCTGTATTAGACGGGGAGCAGGTCGAAGATAGCAGAT
131 GCAGATCGAAGATGACAGATTTAGCGACTCTATATTAGACGGGGAGCA----G--GATAGCAGAT
*
5709309 CTGAGATTCGTGTGTTTACATAGCAGG
190 CTGACATTCGTGTGTTTACATAGCAGG
*
5709336 TCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGA-TCAAGGATGACAGATTTGG
1 TCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATTCAA-GATGACAGATTTGG
*
5709400 TATCTCTGTATTAGATGGGGAGCAGATCGAAGATAGCAGATCTGACATTCATGTGTTTACATCG-
65 TATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCATGTGTTTACATCGA
* *
5709464 AGACAGATCGAAGATGACAGATTTGGCGTCTCTATATTAGACGGGGAGCAGGATAGCAGATCTGA
130 AG-CAGATCGAAGATGACAGATTTAGCGACTCTATATTAGACGGGGAGCAGGATAGCAGATCTGA
5709529 CATTCGTGTGTTTACAT
194 CATTCGTGTGTTTACAT
5709546 CGAAGTAGAT
Statistics
Matches: 195, Mismatches: 13, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
216 30 0.15
218 1 0.01
221 5 0.03
222 159 0.82
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (216 bp):
TCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATTCAAGATGACAGATTTGGT
ATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCATGTGTTTACATCGAA
GCAGATCGAAGATGACAGATTTAGCGACTCTATATTAGACGGGGAGCAGGATAGCAGATCTGACA
TTCGTGTGTTTACATAGCAGG
Found at i:5709544 original size:174 final size:175
Alignment explanation
Indices: 5709340--5709869 Score: 796
Period size: 174 Copynumber: 3.0 Consensus size: 175
5709330 AGCAGGTCGA
**
5709340 AGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATC-AAGGATGACAGATTTGGTATC
1 AGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAA-GATGACAGATTTGGCGTC
* *
5709404 TCTGTATTAGATGGGGAGCAGATCGAAGATAGCAGATCTGACATTCATGTGTTTACATCG-AGAC
65 TCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAG-C
*
5709468 AGATCGAAGATGACAGATTTGGCGTCTCTATATTAGACGGGGAGCAG
129 AGATCAAAGATGACAGATTTGGCGTCTCTATATTAGACGGGGAGCAG
*
5709515 -GATAGCAGATCTGACATTCGTGTGTTTACATCGAAGTAGATCGAAGATGACAGATTTGGCGTCT
1 AGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGATTTGGCGTCT
* * *
5709579 CTGTATTAGACGGGGAGCAGATCGAAGGTAGCAGATCTGACATTCGTGTGTTTATATCGAAGTAG
66 CTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAG
*
5709644 ATCAAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAG
131 ATCAAAGATGACAGATTTGGCGTCTCTATATTAGACGGGGAGCAG
* * *
5709689 ATCGAAGGTAGCAAATCTGACATTCATGTGTTTACATCGAAGCAAATCGAAGATGACAGATTTGG
1 A--G-A--TAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGATTTGG
* * *
5709754 CGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATTTGACCTTCGTGTGTTTACATCGA
61 CGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGA
* * * *
5709819 AGCAGATCAAAGATGACAGATTTGACGTGTCTATATTAGACAGAGAGCAG
126 AGCAGATCAAAGATGACAGATTTGGCGTCTCTATATTAGACGGGGAGCAG
5709869 A
1 A
5709870 TTGAAAATAG
Statistics
Matches: 322, Mismatches: 25, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
174 158 0.49
175 4 0.01
177 1 0.00
178 1 0.00
180 158 0.49
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.27
Consensus pattern (175 bp):
AGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGATTTGGCGTCT
CTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAG
ATCAAAGATGACAGATTTGGCGTCTCTATATTAGACGGGGAGCAG
Found at i:5709840 original size:45 final size:44
Alignment explanation
Indices: 5709111--5709844 Score: 308
Period size: 45 Copynumber: 16.5 Consensus size: 44
5709101 GACGGAGAGT
* * *
5709111 AGATCGAAGATAGCAGATCTGATATTCGTGTGTTTACATCAAAGC
1 AGATCGAAGATAGCAGATTTGACATTC-TGTGTTTACATCGAAGC
* * * * *
5709156 AGATTGAAGAT-GACAGATTTG--GTGTCTCTGTATTAGA-CGGGGAGC
1 AGATCGAAGATAG-CAGATTTGACAT-TCTGTGT-TTACATC--GAAGC
* * *
5709201 AGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATTGAAGC
1 AGATCGAAGATAGCAGATTTGACATTC-TGTGTTTACATCGAAGC
* * * * *
5709246 AGATCGAAGAT-GATAGATTT-AGCGACTCTGT-ATTAGA-CGGGGAGC
1 AGATCGAAGATAG-CAGATTTGA-C-ATTCTGTGTTTACATC--GAAGC
* * *
5709291 AGGTCGAAGATAGCAGATCTGAGATTCGTGTGTTTACAT---AGC
1 AGATCGAAGATAGCAGATTTGACATTC-TGTGTTTACATCGAAGC
* *
5709333 AGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGC
1 AGATCGAAGATAGCAGATTTGACATTC-TGTGTTTACATCGAAGC
** * * * *
5709378 AGATC-AAGGAT-GACAGATTTGGTATCTCTGT-ATTAGATGGGGAGC
1 AGATCGAA-GATAG-CAGATTTGACAT-TCTGTGTTTACAT-CGAAGC
*
5709423 AGATCGAAGATAGCAGATCTGACATTCATGTGTTTACATCG-AGAC
1 AGATCGAAGATAGCAGATTTGACATTC-TGTGTTTACATCGAAG-C
* * * * *
5709468 AGATCGAAGAT-GACAGATTTGGCGTCTCTAT-ATTAGA-CG--G-
1 AGATCGAAGATAG-CAGATTTGACAT-TCTGTGTTTACATCGAAGC
* * * * *
5709508 GGAGC-AGGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGT
1 AGATCGAAGATAGCAGATTTGACATTC-TGTGTTTACATCGAAGC
* * * * *
5709552 AGATCGAAGAT-GACAGATTTGGCGTCTCTGT-ATTAGA-CGGGGAGC
1 AGATCGAAGATAG-CAGATTTGACAT-TCTGTGTTTACATC--GAAGC
* * * *
5709597 AGATCGAAGGTAGCAGATCTGACATTCGTGTGTTTATATCGAAGT
1 AGATCGAAGATAGCAGATTTGACATTC-TGTGTTTACATCGAAGC
* * * * * *
5709642 AGATCAAAGAT-GACAGATTTGGCGTCTCTGT-ATTAGA-CGGGGAGC
1 AGATCGAAGATAG-CAGATTTGACAT-TCTGTGTTTACATC--GAAGC
* * *
5709687 AGATCGAAGGTAGCAAATCTGACATTCATGTGTTTACATCGAAGC
1 AGATCGAAGATAGCAGATTTGACATTC-TGTGTTTACATCGAAGC
* * * * * *
5709732 AAATCGAAGAT-GACAGATTTGGCGTCTCTGT-ATTAGA-CGGGGAGC
1 AGATCGAAGATAG-CAGATTTGACAT-TCTGTGTTTACATC--GAAGC
* *
5709777 AGATCGAAGATAGTAGATTTGACCTTCGTGTGTTTACATCGAAGC
1 AGATCGAAGATAGCAGATTTGACATTC-TGTGTTTACATCGAAGC
*
5709822 AGATCAAAGAT-GACAGATTTGAC
1 AGATCGAAGATAG-CAGATTTGAC
5709845 GTGTCTATAT
Statistics
Matches: 510, Mismatches: 112, Indels: 134
0.67 0.15 0.18
Matches are distributed among these distances:
38 2 0.00
39 15 0.03
40 8 0.02
41 2 0.00
42 42 0.08
43 12 0.02
44 58 0.11
45 314 0.62
46 49 0.10
47 8 0.02
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (44 bp):
AGATCGAAGATAGCAGATTTGACATTCTGTGTTTACATCGAAGC
Found at i:5711438 original size:19 final size:20
Alignment explanation
Indices: 5711404--5711445 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
5711394 TTATTTTAAA
*
5711404 TATTTTATATATATATTATT
1 TATTTTATATAAATATTATT
5711424 TATTTT-TATAAATATTATT
1 TATTTTATATAAATATTATT
5711443 TAT
1 TAT
5711446 ACATGTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTTTATATAAATATTATT
Found at i:5711538 original size:12 final size:13
Alignment explanation
Indices: 5711507--5711541 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
5711497 TTATTTGTAT
5711507 TTTATATATTTTA
1 TTTATATATTTTA
*
5711520 TTTATATCTTTTA
1 TTTATATATTTTA
5711533 -TTATATATT
1 TTTATATATT
5711542 ATATATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATATATTTTA
Found at i:5711543 original size:7 final size:7
Alignment explanation
Indices: 5711508--5711562 Score: 57
Period size: 7 Copynumber: 8.6 Consensus size: 7
5711498 TATTTGTATT
5711508 TTATATA
1 TTATATA
*
5711515 TTTTAT-
1 TTATATA
*
5711521 TTATATC
1 TTATATA
5711528 TT-T-TA
1 TTATATA
5711533 TTATATA
1 TTATATA
5711540 TTATATA
1 TTATATA
5711547 TT-T-TA
1 TTATATA
5711552 TTATATA
1 TTATATA
5711559 TTAT
1 TTAT
5711563 TCCCTATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
5 7 0.17
6 9 0.22
7 24 0.60
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (7 bp):
TTATATA
Found at i:5711545 original size:19 final size:19
Alignment explanation
Indices: 5711521--5711562 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
5711511 TATATTTTAT
*
5711521 TTATATCTTTTATTATATA
1 TTATATATTTTATTATATA
5711540 TTATATATTTTATTATATA
1 TTATATATTTTATTATATA
5711559 TTAT
1 TTAT
5711563 TCCCTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATATATTTTATTATATA
Found at i:5711553 original size:12 final size:12
Alignment explanation
Indices: 5711508--5711560 Score: 60
Period size: 12 Copynumber: 4.8 Consensus size: 12
5711498 TATTTGTATT
5711508 TTATATATTTTA
1 TTATATATTTTA
*
5711520 TT-TATATCTT-
1 TTATATATTTTA
*
5711530 TTAT-TA-TATA
1 TTATATATTTTA
5711540 TTATATATTTTA
1 TTATATATTTTA
5711552 TTATATATT
1 TTATATATT
5711561 ATTCCCTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
9 1 0.03
10 8 0.24
11 10 0.30
12 14 0.42
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATATATTTTA
Found at i:5711571 original size:33 final size:34
Alignment explanation
Indices: 5711504--5711596 Score: 81
Period size: 33 Copynumber: 2.9 Consensus size: 34
5711494 ATGTTATTTG
* *
5711504 TATT-TTATATATTTTATT-TATATCT-TTTATTA
1 TATTATTATATATTTTATTATATAT-TATTCACTA
*
5711536 TA-TATTATATATTTTATTATATATTATTCCCTA
1 TATTATTATATATTTTATTATATATTATTCACTA
* *
5711569 TATTATCT-T-CATTTTATTATATACTATT
1 TATTAT-TATATATTTTATTATATATTATT
5711597 TTATCATTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
31 1 0.02
32 17 0.33
33 28 0.55
34 4 0.08
35 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (34 bp):
TATTATTATATATTTTATTATATATTATTCACTA
Found at i:5711777 original size:20 final size:18
Alignment explanation
Indices: 5711746--5711795 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
5711736 ATATTATTAT
* *
5711746 TTTTATAAATATATTAAG
1 TTTTATATATATAGTAAG
*
5711764 TTATTATATCATATAGTATG
1 TT-TTATAT-ATATAGTAAG
5711784 TTTTATATATAT
1 TTTTATATATAT
5711796 TAATCGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 6 0.22
19 11 0.41
20 10 0.37
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (18 bp):
TTTTATATATATAGTAAG
Found at i:5711881 original size:14 final size:13
Alignment explanation
Indices: 5711841--5711883 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5711831 ACCTCATCTA
*
5711841 TTTTTAATTATAT
1 TTTTTACTTATAT
* *
5711854 TTTTTATTTTTAT
1 TTTTTACTTATAT
5711867 TTTTTGACTTATAT
1 TTTTT-ACTTATAT
5711881 TTT
1 TTT
5711884 ATATATGTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTTTACTTATAT
Found at i:5711947 original size:21 final size:21
Alignment explanation
Indices: 5711910--5711953 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5711900 TGTTTATTTG
* *
5711910 TTTATTTATTTTTGTATTTTT
1 TTTATTTATTTTAGTATTGTT
5711931 TTTATCTTA-TTTAGTATTGTT
1 TTTAT-TTATTTTAGTATTGTT
5711952 TT
1 TT
5711954 AGTAGGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.75
Consensus pattern (21 bp):
TTTATTTATTTTAGTATTGTT
Found at i:5712000 original size:18 final size:18
Alignment explanation
Indices: 5711979--5712013 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5711969 ATCTCATAAA
*
5711979 TTATTTGTTATTTTTATG
1 TTATTTATTATTTTTATG
5711997 TTATTTATTATTTTTAT
1 TTATTTATTATTTTTAT
5712014 ATATTCGCAT
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:0.00, G:0.06, T:0.74
Consensus pattern (18 bp):
TTATTTATTATTTTTATG
Found at i:5712043 original size:45 final size:43
Alignment explanation
Indices: 5711991--5712103 Score: 115
Period size: 43 Copynumber: 2.6 Consensus size: 43
5711981 ATTTGTTATT
*
5711991 TTTATGTTATTTATTATT-TTTATATATTCGCATGAAAATTGATTA
1 TTTATGTTATTTATT-TTAGTTATAT-TT-GCATGAAAATTGATTA
* *
5712036 TTTATGTTA-TTATTTTAAGTTATATTTGCATGAAATTTTATTA
1 TTTATGTTATTTATTTT-AGTTATATTTGCATGAAAATTGATTA
* * *
5712079 TATATGTAATTTATGTT-GTTATATT
1 TTTATGTTATTTATTTTAGTTATATT
5712104 CATCATTTTC
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
42 8 0.14
43 23 0.39
44 13 0.22
45 15 0.25
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.58
Consensus pattern (43 bp):
TTTATGTTATTTATTTTAGTTATATTTGCATGAAAATTGATTA
Found at i:5713460 original size:2 final size:2
Alignment explanation
Indices: 5713455--5713488 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5713445 ACACACACAC
5713455 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
5713489 CCTTATAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5714252 original size:133 final size:133
Alignment explanation
Indices: 5714021--5714412 Score: 387
Period size: 133 Copynumber: 3.0 Consensus size: 133
5714011 GTGAAATCCC
* * ** * *
5714021 AAAGAGATATTCGGTTGTTTTGAACAAACGAGAGATTGCAACCCAGCGCGATAGGGCACGATTCT
1 AAAGAGATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACGATTCC
* * *
5714086 CGAATTGCCAAACATCGAACATAGCCTTTGTTTTAAAGGGTTTTCTTAAAAGACATGAGTGAAAA
66 CAAATTGCCAAACATCGAACATAGCCTTAGTTTTAAAGGATTTT-TTAAAAGACATGAGTGAAAA
5714151 CCTA
130 CCTA
*
5714155 AAAGA-ATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCATGATTCC
1 AAAGAGATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACGATTCC
* ** * * * * * * *
5714219 CAAATTGTCAAACATCGAGTATTGCCTTAGTTTTAGAGGATTTTTTAGAAGACCTGAATG-GAAT
66 CAAATTGCCAAACATCGAACATAGCCTTAGTTTTAAAGGATTTTTTAAAAGACATGAGTGAAAAC
*
5714283 CTC
131 CTA
* * * * * * ** * *
5714286 GAAGGGATATTTGATTATCTTGAGC-AACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCC
1 AAAGAGATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACGATTCC
* * * * * * * *
5714350 GCGAATTGCCAAATATCAAACTTTGCCTTCGTTTTAAA-GAATTTTTAAAAGGCATGAGTGAAA
66 -CAAATTGCCAAACATCGAACATAGCCTTAGTTTTAAAGGATTTTTTAAAAGACATGAGTGAAA
5714413 GTTTGAAGGA
Statistics
Matches: 208, Mismatches: 47, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
131 58 0.28
132 57 0.27
133 88 0.42
134 5 0.02
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (133 bp):
AAAGAGATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACGATTCC
CAAATTGCCAAACATCGAACATAGCCTTAGTTTTAAAGGATTTTTTAAAAGACATGAGTGAAAAC
CTA
Found at i:5714394 original size:132 final size:133
Alignment explanation
Indices: 5714039--5714527 Score: 440
Period size: 132 Copynumber: 3.7 Consensus size: 133
5714029 ATTCGGTTGT
* * * * *
5714039 TTTGAACAAACGAGAGATTGCAACCCAGCGCGATAGGGCACGATT-CTCGAATTGCCAAACATCG
1 TTTGAGCAAACGAGAAATTGCAACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAACATCG
** * * *
5714103 AAC-ATAGCCTTTGTTTTAAAGGGTTTTCTTAAAAGACATGAGTGAAAAC-CTAAAAGAATATTC
66 AACTATAGCCTTTGTTTTAAAGAATTTT-TTAAAAGACATGAGTGAAATCTC-GAAGGAATATTC
*
5714166 GATTGT
129 GATT-A
* ** * * * *
5714172 TTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCATGATTCC-CAAATTGTCAAACATCG
1 TTTGAGCAAACGAGAAATTGCAACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAACATCG
* * * * * * * * * * *
5714236 -AGTATTGCCTTAGTTTTAGAGGATTTTTTAGAAGACCTGAATGGAATCTCGAAGGGATATTTGA
66 AACTATAGCCTTTGTTTTAAAGAATTTTTTAAAAGACATGAGTGAAATCTCGAAGGAATATTCGA
5714300 TTA
131 TTA
* *
5714303 TCTTGAGC-AACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAATATC
1 T-TTGAGCAAACGAGAAATTGCAACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAACATC
* * * * *
5714367 AAACT-TTGCCTTCGTTTTAAAGAA-TTTTTAAAAGGCATGAGTGAAAGT-TTGAAGGAATATTC
65 GAACTATAGCCTTTGTTTTAAAGAATTTTTTAAAAGACATGAGTGAAA-TCTCGAAGGAATATTC
5714429 GATTA
129 GATTA
* * * * * * * *
5714434 TTTCGAGCAAACGCGAAATTGCAACCCAACATGTTAGAGCACTATTCCGTGAGTTGCCAAATATC
1 TTT-GAGCAAACGAGAAATTGCAACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAACATC
* *
5714499 GAA-TCTAGTCTTTGTTTTAAAGAATTTTT
65 GAACTATAGCCTTTGTTTTAAAGAATTTTT
5714528 AAATGAATGA
Statistics
Matches: 291, Mismatches: 54, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
130 2 0.01
131 74 0.25
132 132 0.45
133 82 0.28
134 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (133 bp):
TTTGAGCAAACGAGAAATTGCAACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAACATCG
AACTATAGCCTTTGTTTTAAAGAATTTTTTAAAAGACATGAGTGAAATCTCGAAGGAATATTCGA
TTA
Found at i:5716626 original size:2 final size:2
Alignment explanation
Indices: 5716621--5716663 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5716611 TATATATATA
5716621 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
5716663 T
1 T
5716664 ATTATACTCG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:5717814 original size:20 final size:19
Alignment explanation
Indices: 5717745--5717835 Score: 67
Period size: 20 Copynumber: 4.6 Consensus size: 19
5717735 CATAACAAGA
* **
5717745 GCACCAAAGTGCTGACAGG
1 GCACCGAAGTGCAAACAGG
*
5717764 GCA-CAAATGTGCAAACAGGG
1 GCACCGAA-GTGCAAACA-GG
* * **
5717784 GCATCGTAGTGTGAACAGG
1 GCACCGAAGTGCAAACAGG
5717803 GACACCGAAGTGCAAACAGAG
1 G-CACCGAAGTGCAAACAG-G
5717824 GCACCGAAGTGC
1 GCACCGAAGTGC
5717836 GAATCCCATA
Statistics
Matches: 57, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
18 4 0.07
19 13 0.23
20 36 0.63
21 4 0.07
ACGTcount: A:0.34, C:0.23, G:0.32, T:0.11
Consensus pattern (19 bp):
GCACCGAAGTGCAAACAGG
Found at i:5719127 original size:39 final size:41
Alignment explanation
Indices: 5719050--5719130 Score: 139
Period size: 39 Copynumber: 2.0 Consensus size: 41
5719040 AATGGAGAAG
5719050 AAAACCATTATATTTTCGTTTTCTTCTTTTTTTTTTTACTTT
1 AAAACCATTATATTTTCG-TTTCTTCTTTTTTTTTTTACTTT
5719092 AAAACCATTATATTTTC-TTT-TTCTTTTTTTTTTTACTTT
1 AAAACCATTATATTTTCGTTTCTTCTTTTTTTTTTTACTTT
5719131 TTAACCTTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
39 19 0.49
40 3 0.08
42 17 0.44
ACGTcount: A:0.20, C:0.14, G:0.01, T:0.65
Consensus pattern (41 bp):
AAAACCATTATATTTTCGTTTCTTCTTTTTTTTTTTACTTT
Found at i:5719549 original size:23 final size:23
Alignment explanation
Indices: 5719502--5719549 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
5719492 TAATTATTCG
*
5719502 ATCAAAATAACATTAATTACCAT
1 ATCAAAATAACATTAATTACAAT
5719525 ATCAAAATCAA-ATATAA-TACAAT
1 ATCAAAAT-AACAT-TAATTACAAT
5719548 AT
1 AT
5719550 TTGAATCGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (23 bp):
ATCAAAATAACATTAATTACAAT
Found at i:5719983 original size:13 final size:13
Alignment explanation
Indices: 5719944--5720007 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
5719934 AATTTGGCAA
5719944 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
5719957 TG-TTGTGGAAAAG
1 TGCTT-TTGAAAAG
*
5719970 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
5719983 TGATTTTGAGAAG
1 TGCTTTTGAAAAG
*
5719996 TACTTTTGAAAA
1 TGCTTTTGAAAA
5720008 TTTTGGTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
12 2 0.05
13 38 0.90
14 2 0.05
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:5719996 original size:26 final size:26
Alignment explanation
Indices: 5719944--5720007 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
5719934 AATTTGGCAA
5719944 TGCTTTTGAAAAGTGTTGTGGAAAAG
1 TGCTTTTGAAAAGTGTTGTGGAAAAG
* * *
5719970 TGCTTTTGAGAAGTGATT-TTGAGAAG
1 TGCTTTTGAAAAGTG-TTGTGGAAAAG
*
5719996 TACTTTTGAAAA
1 TGCTTTTGAAAA
5720008 TTTTGGTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 30 0.94
27 2 0.06
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.38
Consensus pattern (26 bp):
TGCTTTTGAAAAGTGTTGTGGAAAAG
Found at i:5724432 original size:45 final size:45
Alignment explanation
Indices: 5724382--5724467 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
5724372 AAAAGATCTA
*
5724382 AGTTCCACGAGCCATCCTCAGTAGCCATCTTGTGCAGAAGGTAAT
1 AGTTCCACGAGCCATCCTCAGTAACCATCTTGTGCAGAAGGTAAT
5724427 AGTTCCACGAGCCATCCTCAGTAACCATCTTGTGCAGAAGG
1 AGTTCCACGAGCCATCCTCAGTAACCATCTTGTGCAGAAGG
5724468 CAATCACGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (45 bp):
AGTTCCACGAGCCATCCTCAGTAACCATCTTGTGCAGAAGGTAAT
Found at i:5731377 original size:27 final size:27
Alignment explanation
Indices: 5731312--5731370 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
5731302 TGATTTAATG
5731312 ACATAACATTTTTTTTCTATGTCATTA
1 ACATAACATTTTTTTTCTATGTCATTA
5731339 ACATAACATTTTTTTTCTATGTCATTA
1 ACATAACATTTTTTTTCTATGTCATTA
5731366 ACATA
1 ACATA
5731371 TAATTTTGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.49
Consensus pattern (27 bp):
ACATAACATTTTTTTTCTATGTCATTA
Found at i:5733484 original size:22 final size:22
Alignment explanation
Indices: 5733459--5733501 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5733449 TATCTAAACA
5733459 ATAACAACAAAAT-ATTAGCAAT
1 ATAACAACAAAATGA-TAGCAAT
*
5733481 ATAATAACAAAATGATAGCAA
1 ATAACAACAAAATGATAGCAA
5733502 AATAGCAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.60, C:0.12, G:0.07, T:0.21
Consensus pattern (22 bp):
ATAACAACAAAATGATAGCAAT
Found at i:5734230 original size:11 final size:10
Alignment explanation
Indices: 5734187--5734226 Score: 50
Period size: 9 Copynumber: 4.2 Consensus size: 10
5734177 ATTACTTAAT
5734187 TATTATTTTA
1 TATTATTTTA
5734197 T-TTATTTTA
1 TATTATTTTA
5734206 TA-T-TTTTA
1 TATTATTTTA
5734214 TCATTATTTTA
1 T-ATTATTTTA
5734225 TA
1 TA
5734227 ATTAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
8 6 0.23
9 11 0.42
10 3 0.12
11 6 0.23
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (10 bp):
TATTATTTTA
Found at i:5741140 original size:18 final size:18
Alignment explanation
Indices: 5741117--5741160 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5741107 TAATTTGATA
5741117 TGGATTCTGTTGTACCAT
1 TGGATTCTGTTGTACCAT
* **
5741135 TGGATTCTGTTTTTTCAT
1 TGGATTCTGTTGTACCAT
5741153 TGGATTCT
1 TGGATTCT
5741161 AAATTTCCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (18 bp):
TGGATTCTGTTGTACCAT
Found at i:5747423 original size:13 final size:13
Alignment explanation
Indices: 5747405--5747432 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5747395 GCAGTGTAAG
5747405 GTTCTAGAAATGA
1 GTTCTAGAAATGA
5747418 GTTCTAGAAATGA
1 GTTCTAGAAATGA
5747431 GT
1 GT
5747433 GGGCCTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (13 bp):
GTTCTAGAAATGA
Found at i:5748863 original size:20 final size:20
Alignment explanation
Indices: 5748821--5748874 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
5748811 GAATCATTGT
* *
5748821 AAAATTAATTGAACTAATAA
1 AAAAATAATTGAATTAATAA
* *
5748841 AAAAATAATTGAATTGATTA
1 AAAAATAATTGAATTAATAA
* *
5748861 AAAACTATTTGAAT
1 AAAAATAATTGAAT
5748875 AGGATTTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (20 bp):
AAAAATAATTGAATTAATAA
Found at i:5750329 original size:40 final size:40
Alignment explanation
Indices: 5750270--5750350 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
5750260 GGACTCTTTG
* *
5750270 TTGGTTCAAGTAAAGAGTGTTATATTAGCAATCAATTAGA
1 TTGGTTCAAGTAAAAAGTGTTATATTAACAATCAATTAGA
5750310 TTGGTTCAAGTAAAAAGTGTTATATTAACAATCAATTAGA
1 TTGGTTCAAGTAAAAAGTGTTATATTAACAATCAATTAGA
5750350 T
1 T
5750351 AGATTCCAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (40 bp):
TTGGTTCAAGTAAAAAGTGTTATATTAACAATCAATTAGA
Found at i:5751745 original size:2 final size:2
Alignment explanation
Indices: 5751738--5751778 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
5751728 AATTGATGAC
*
5751738 AT AT AT AT AT AT GT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5751779 TTTTCATGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5752920 original size:2 final size:2
Alignment explanation
Indices: 5752913--5752948 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5752903 TTAATAGTTA
5752913 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5752949 ACAATAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5765194 original size:3 final size:3
Alignment explanation
Indices: 5765188--5765219 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5765178 TATTATTATT
5765188 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
5765220 TATTATTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:5765588 original size:32 final size:32
Alignment explanation
Indices: 5765550--5765612 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
5765540 GAGAGGGCTA
*
5765550 CAATTAAAGAAGATAGAAATTTA-AAA-GTTAAT
1 CAATTAAA-AAG-TACAAATTTATAAATGTTAAT
5765582 CAATTAAAAAGTACAAATTTATAAATGTTAA
1 CAATTAAAAAGTACAAATTTATAAATGTTAA
5765613 CGAACCATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 9 0.32
31 6 0.21
32 13 0.46
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.30
Consensus pattern (32 bp):
CAATTAAAAAGTACAAATTTATAAATGTTAAT
Found at i:5771217 original size:37 final size:37
Alignment explanation
Indices: 5771129--5771223 Score: 129
Period size: 37 Copynumber: 2.6 Consensus size: 37
5771119 ATTACACAAG
*
5771129 TAATCCAACCGA-AACACGCCAACTGCTCATAAGAGC
1 TAATCCAACCGATAACACGCCAAATGCTCATAAGAGC
* * * *
5771165 TAATCTACCCAATAACACGTCAAATGCTCATAAGAGC
1 TAATCCAACCGATAACACGCCAAATGCTCATAAGAGC
*
5771202 TAATCCAATCGATAACACGCCA
1 TAATCCAACCGATAACACGCCA
5771224 CGGCAGTAAG
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
36 9 0.19
37 39 0.81
ACGTcount: A:0.40, C:0.31, G:0.12, T:0.18
Consensus pattern (37 bp):
TAATCCAACCGATAACACGCCAAATGCTCATAAGAGC
Found at i:5775113 original size:27 final size:27
Alignment explanation
Indices: 5775081--5775146 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
5775071 TAGTTGAACT
5775081 ATGGCAAAGTGATAAAGTGTGCCAAAC
1 ATGGCAAAGTGATAAAGTGTGCCAAAC
*
5775108 ATGGCAAAGTGATAAAGTGTGCCAAAT
1 ATGGCAAAGTGATAAAGTGTGCCAAAC
5775135 ATGGCAAAGTGA
1 ATGGCAAAGTGA
5775147 AATGTGACAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (27 bp):
ATGGCAAAGTGATAAAGTGTGCCAAAC
Found at i:5775385 original size:33 final size:33
Alignment explanation
Indices: 5775348--5775418 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
5775338 GTATAAGTGT
5775348 ATGAATGTTTGGTAAGATTTATGTTTTATGCCA
1 ATGAATGTTTGGTAAGATTTATGTTTTATGCCA
5775381 ATGAATGTTTGGTAAGATTTATGTTTTATGCCA
1 ATGAATGTTTGGTAAGATTTATGTTTTATGCCA
5775414 ATGAA
1 ATGAA
5775419 CTTACTAAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.44
Consensus pattern (33 bp):
ATGAATGTTTGGTAAGATTTATGTTTTATGCCA
Found at i:5776709 original size:16 final size:16
Alignment explanation
Indices: 5776688--5776719 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5776678 TTTATATGTT
*
5776688 TAAATAATATAATATA
1 TAAATAACATAATATA
5776704 TAAATAACATAATATA
1 TAAATAACATAATATA
5776720 ATACATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAATAACATAATATA
Found at i:5780614 original size:26 final size:26
Alignment explanation
Indices: 5780577--5780660 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
5780567 TGATACAAAT
*
5780577 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5780603 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
5780629 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5780655 TGATAA
1 TGATAA
5780661 AAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:5782167 original size:26 final size:28
Alignment explanation
Indices: 5782112--5782176 Score: 89
Period size: 26 Copynumber: 2.4 Consensus size: 28
5782102 AATTACTATA
* *
5782112 ATACCCCTATGTATGAAAATTTACTGTT
1 ATACCCCTAGGTATGAAAATTTACCGTT
*
5782140 ATACCCCTAGGTGT-AAAA-TTACCGTT
1 ATACCCCTAGGTATGAAAATTTACCGTT
5782166 ATACCCCTAGG
1 ATACCCCTAGG
5782177 GTTAATTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 18 0.53
27 4 0.12
28 12 0.35
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (28 bp):
ATACCCCTAGGTATGAAAATTTACCGTT
Found at i:5782320 original size:27 final size:27
Alignment explanation
Indices: 5782279--5782394 Score: 178
Period size: 27 Copynumber: 4.3 Consensus size: 27
5782269 GAGGAAGCAT
*
5782279 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
5782306 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
5782333 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
5782360 TCTAGTGGCTCTGCCACAATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
5782388 TCTGGTG
1 TCTGGTG
5782395 AATCTGTCAC
Statistics
Matches: 80, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
27 74 0.93
28 6 0.08
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:5782368 original size:54 final size:55
Alignment explanation
Indices: 5782279--5782416 Score: 190
Period size: 54 Copynumber: 2.5 Consensus size: 55
5782269 GAGGAAGCAT
* * * *
5782279 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACATATATCTGTTCTAGTGGCTCTGCCACAAATATCTGTA
*
5782333 TCTGGTGGCTCTGCCACATATATCTGTTCTAGTGGCTCTGCCACAATTATCTGTA
1 TCTGGTGGCTCTGCCACATATATCTGTTCTAGTGGCTCTGCCACAAATATCTGTA
** *
5782388 TCTGGTGAATCTGTCACAT-TATCTGTTCT
1 TCTGGTGGCTCTGCCACATATATCTGTTCT
5782417 GGCAGCCATG
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
54 58 0.77
55 17 0.23
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (55 bp):
TCTGGTGGCTCTGCCACATATATCTGTTCTAGTGGCTCTGCCACAAATATCTGTA
Found at i:5782408 original size:27 final size:28
Alignment explanation
Indices: 5782279--5782418 Score: 166
Period size: 27 Copynumber: 5.2 Consensus size: 28
5782269 GAGGAAGCAT
* *
5782279 TCTGGTGGCTATGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACAATTATCTGTA
*
5782306 TCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACAATTATCTGTA
5782333 TCTGGTGGCTCTGCCAC-ATATATCTGT-
1 TCTGGTGGCTCTGCCACAAT-TATCTGTA
*
5782360 TCTAGTGGCTCTGCCACAATTATCTGTA
1 TCTGGTGGCTCTGCCACAATTATCTGTA
** *
5782388 TCTGGTGAATCTGTCAC-ATTATCTGT-
1 TCTGGTGGCTCTGCCACAATTATCTGTA
5782414 TCTGG
1 TCTGG
5782419 CAGCCATGCT
Statistics
Matches: 102, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
26 6 0.06
27 81 0.79
28 15 0.15
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (28 bp):
TCTGGTGGCTCTGCCACAATTATCTGTA
Found at i:5783968 original size:10 final size:10
Alignment explanation
Indices: 5783949--5783998 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
5783939 TTAAATTTTA
5783949 AAAGATAAAT
1 AAAGATAAAT
5783959 ACAA-ATAAAT
1 A-AAGATAAAT
*
5783969 AAAGATAATT
1 AAAGATAAAT
5783979 AAAGATAAAT
1 AAAGATAAAT
*
5783989 AAAAATAAAT
1 AAAGATAAAT
5783999 CCTAAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 2 0.06
10 31 0.89
11 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:5785660 original size:15 final size:15
Alignment explanation
Indices: 5785640--5785687 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
5785630 TTAATATCTG
*
5785640 AAAATAATAAATAAT
1 AAAATAATAAATAAA
5785655 AAAATAATAAGATAAA
1 AAAATAATAA-ATAAA
5785671 ATAAATAA-AAATAAA
1 A-AAATAATAAATAAA
5785686 AA
1 AA
5785688 TTGGGTTGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
16 7 0.23
17 6 0.20
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (15 bp):
AAAATAATAAATAAA
Found at i:5789388 original size:10 final size:10
Alignment explanation
Indices: 5789369--5789418 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
5789359 TTAAATTCTA
5789369 AAAGATAAAT
1 AAAGATAAAT
5789379 ACAA-ATAAAT
1 A-AAGATAAAT
*
5789389 AAAGATAATT
1 AAAGATAAAT
5789399 AAAGATAAAT
1 AAAGATAAAT
*
5789409 AAAAATAAAT
1 AAAGATAAAT
5789419 CCTAAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 2 0.06
10 31 0.89
11 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:5796274 original size:23 final size:23
Alignment explanation
Indices: 5796248--5796292 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5796238 TGGGTATGTG
* *
5796248 ATGACGTTATCTTATAAATATGC
1 ATGAAGTTATCTTAAAAATATGC
*
5796271 ATGAATTTATCTTAAAAATATG
1 ATGAAGTTATCTTAAAAATATG
5796293 TTGAATTGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTAAAAATATGC
Found at i:5803583 original size:2 final size:2
Alignment explanation
Indices: 5803576--5803609 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5803566 ATAAATATCA
5803576 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
5803610 GAGGAAATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5804549 original size:25 final size:25
Alignment explanation
Indices: 5804521--5804626 Score: 61
Period size: 25 Copynumber: 4.2 Consensus size: 25
5804511 AAGCTCTTCC
*
5804521 GAGCCATATAACGGGAAGCTCATGT
1 GAGCCATATAACAGGAAGCTCATGT
* * * * **
5804546 GAGCTA-AGTAACGGGTAGTTCATAC
1 GAGCCATA-TAACAGGAAGCTCATGT
** * *
5804571 GAGCTGTATATCAGGAAGCTCTTGT
1 GAGCCATATAACAGGAAGCTCATGT
* * * *
5804596 GAGCCAAATATCAGGAAGCTCAAGA
1 GAGCCATATAACAGGAAGCTCATGT
5804621 GAGCCA
1 GAGCCA
5804627 AGTGTCGGAA
Statistics
Matches: 60, Mismatches: 19, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
24 1 0.02
25 58 0.97
26 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (25 bp):
GAGCCATATAACAGGAAGCTCATGT
Found at i:5804627 original size:25 final size:25
Alignment explanation
Indices: 5804578--5804627 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5804568 TACGAGCTGT
** *
5804578 ATATCAGGAAGCTCTTGTGAGCCAA
1 ATATCAGGAAGCTCAAGAGAGCCAA
5804603 ATATCAGGAAGCTCAAGAGAGCCAA
1 ATATCAGGAAGCTCAAGAGAGCCAA
5804628 GTGTCGGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (25 bp):
ATATCAGGAAGCTCAAGAGAGCCAA
Found at i:5819166 original size:19 final size:19
Alignment explanation
Indices: 5819142--5819178 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5819132 GAAACAAGGG
*
5819142 AAGGAAAGAAGGAAAAAGA
1 AAGGAAAGAAAGAAAAAGA
5819161 AAGGAAAGAAAGAAAAAG
1 AAGGAAAGAAAGAAAAAG
5819179 GAAAAATTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAGGAAAGAAAGAAAAAGA
Found at i:5819700 original size:16 final size:18
Alignment explanation
Indices: 5819679--5819711 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
5819669 GAATATAATA
5819679 ATTATTT-GT-TGAATTT
1 ATTATTTAGTATGAATTT
5819695 ATTATTTAGTATGAATT
1 ATTATTTAGTATGAATT
5819712 GTAATAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (18 bp):
ATTATTTAGTATGAATTT
Found at i:5820100 original size:6 final size:6
Alignment explanation
Indices: 5820086--5820120 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
5820076 TGTGTACCGC
* *
5820086 TACTGT TACTAT TACTGT TACTGT TACCGT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG
5820121 ACACAGTGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (6 bp):
TACTGT
Found at i:5820273 original size:18 final size:18
Alignment explanation
Indices: 5820250--5820309 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
5820240 AACTGTTTGC
*
5820250 TACTGAATAATTGACTGT
1 TACTGAATAAATGACTGT
* * *
5820268 TACTGAATAAACGGCTGA
1 TACTGAATAAATGACTGT
*
5820286 TACTGAATAAATGATTGT
1 TACTGAATAAATGACTGT
5820304 TACTGA
1 TACTGA
5820310 TTAACCGATT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (18 bp):
TACTGAATAAATGACTGT
Found at i:5827101 original size:209 final size:209
Alignment explanation
Indices: 5826741--5827368 Score: 1202
Period size: 209 Copynumber: 3.0 Consensus size: 209
5826731 TTCGACCAAC
*
5826741 CAATTATAGTGTATGTAAAGGGTGTTGTCAAAGGGCCTTAAGATACAAAAAATTTTATGTTTCAA
1 CAATTATAGTGTATGTAAAGGGTGTTGTCAAAGGGCCTTAAGATACAACAAATTTTATGTTTCAA
*
5826806 ATCAAAATCAAACTACTAAATACCTTTCATAAGAGCCATTCTTATACTTGGTTTTCTACAGCAGA
66 ATCAAAATCAAACCACTAAATACCTTTCATAAGAGCCATTCTTATACTTGGTTTTCTACAGCAGA
5826871 CAAAGACTAAGGGACTTACATTTACTTGAGAATGATACCAAAGAGAGTGATTCAAAAATTGTATT
131 CAAAGACTAAGGGACTTACATTTACTTGAGAATGATACCAAAGAGAGTGATTCAAAAATTGTATT
5826936 TATCTTTTCATATT
196 TATCTTTTCATATT
*
5826950 CAATTATAGTGTATGTAAAGGGTGTTGTCAAAGAGCCTTAAGATACAACAAATTTTATGTTTCAA
1 CAATTATAGTGTATGTAAAGGGTGTTGTCAAAGGGCCTTAAGATACAACAAATTTTATGTTTCAA
5827015 ATCAAAATCAAACCACTAAATACCTTTCATAAGAGCCATTCTTATACTTGGTTTTCTACAGCAGA
66 ATCAAAATCAAACCACTAAATACCTTTCATAAGAGCCATTCTTATACTTGGTTTTCTACAGCAGA
**
5827080 CAAAGACTAAGGGACTTACATTTACTTGAGAATGATACCAAAGAGAGAAATTCAAAAATTGTATT
131 CAAAGACTAAGGGACTTACATTTACTTGAGAATGATACCAAAGAGAGTGATTCAAAAATTGTATT
*
5827145 TATTTTTTCATATT
196 TATCTTTTCATATT
5827159 CAATTATAGTGTATGTAAAGGGTGTTGTCAAAGGGCCTTAAGATACAACAAATTTTATGTTTCAA
1 CAATTATAGTGTATGTAAAGGGTGTTGTCAAAGGGCCTTAAGATACAACAAATTTTATGTTTCAA
5827224 ATCAAAATCAAACCACTAAATACCTTTCATAAGAGCCATTCTTATACTTGGTTTTCTACAGCAGA
66 ATCAAAATCAAACCACTAAATACCTTTCATAAGAGCCATTCTTATACTTGGTTTTCTACAGCAGA
5827289 CAAAGACTAAGGGACTTACATTTACTTGAGAATGATACCAAAGAGAGTGATTCAAAAATTGTATT
131 CAAAGACTAAGGGACTTACATTTACTTGAGAATGATACCAAAGAGAGTGATTCAAAAATTGTATT
5827354 TATCTTTTCATATT
196 TATCTTTTCATATT
5827368 C
1 C
5827369 TATGTTGGAA
Statistics
Matches: 409, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
209 409 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (209 bp):
CAATTATAGTGTATGTAAAGGGTGTTGTCAAAGGGCCTTAAGATACAACAAATTTTATGTTTCAA
ATCAAAATCAAACCACTAAATACCTTTCATAAGAGCCATTCTTATACTTGGTTTTCTACAGCAGA
CAAAGACTAAGGGACTTACATTTACTTGAGAATGATACCAAAGAGAGTGATTCAAAAATTGTATT
TATCTTTTCATATT
Found at i:5832587 original size:65 final size:65
Alignment explanation
Indices: 5832508--5832638 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
5832498 ATAGAATAAG
*
5832508 AAAGAAAGAAAAATGGAATAATAAAATAGACCTCCCTATTCATGAAAATTAAGATTGAAAATTAA
1 AAAGAAAGAAAAATGAAATAATAAAATAGACCTCCCTATTCATGAAAATTAAGATTGAAAATTAA
* *
5832573 AAAGAAAGAAAAATGAAATAATAAAATAGACCTTCGTATTCATGAAAATTAAGATTGAAAATTAA
1 AAAGAAAGAAAAATGAAATAATAAAATAGACCTCCCTATTCATGAAAATTAAGATTGAAAATTAA
5832638 A
1 A
5832639 TTGTAAAACT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (65 bp):
AAAGAAAGAAAAATGAAATAATAAAATAGACCTCCCTATTCATGAAAATTAAGATTGAAAATTAA
Found at i:5836949 original size:87 final size:87
Alignment explanation
Indices: 5836803--5836974 Score: 335
Period size: 87 Copynumber: 2.0 Consensus size: 87
5836793 TTCACCCCAT
*
5836803 TGTTGAAATGATTAATTACCTTTGTCTGAAAAACTAGTCACTGTTGGTGGTAGGATTAGCATAAA
1 TGTTGAAATGATTAATTACCTTTGTCTGAAAAACTAGTCACTGTCGGTGGTAGGATTAGCATAAA
5836868 TCCAATGAATTATGGTACACAC
66 TCCAATGAATTATGGTACACAC
5836890 TGTTGAAATGATTAATTACCTTTGTCTGAAAAACTAGTCACTGTCGGTGGTAGGATTAGCATAAA
1 TGTTGAAATGATTAATTACCTTTGTCTGAAAAACTAGTCACTGTCGGTGGTAGGATTAGCATAAA
5836955 TCCAATGAATTATGGTACAC
66 TCCAATGAATTATGGTACAC
5836975 TTTTTTACGA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (87 bp):
TGTTGAAATGATTAATTACCTTTGTCTGAAAAACTAGTCACTGTCGGTGGTAGGATTAGCATAAA
TCCAATGAATTATGGTACACAC
Found at i:5837295 original size:27 final size:27
Alignment explanation
Indices: 5837264--5837315 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
5837254 TTAAACTTCA
5837264 ACTTTGTAATATAATTACAGCGAGGTG
1 ACTTTGTAATATAATTACAGCGAGGTG
5837291 ACTTTGTAATATAATTACAGCGAGG
1 ACTTTGTAATATAATTACAGCGAGG
5837316 CGATACTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (27 bp):
ACTTTGTAATATAATTACAGCGAGGTG
Found at i:5840010 original size:13 final size:13
Alignment explanation
Indices: 5839994--5840029 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
5839984 TAATTCTAAA
*
5839994 TTTTGTAATTTAT
1 TTTTATAATTTAT
*
5840007 TTTTTTAATTTAT
1 TTTTATAATTTAT
5840020 TTTTATAATT
1 TTTTATAATT
5840030 GCAATTCCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTATAATTTAT
Found at i:5844835 original size:6 final size:6
Alignment explanation
Indices: 5844824--5844856 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
5844814 GAAGATTCAA
5844824 TTGTGT TTGTGT TTGTGT TTGTGT TTGTGT TTG
1 TTGTGT TTGTGT TTGTGT TTGTGT TTGTGT TTG
5844857 AGGGAGACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (6 bp):
TTGTGT
Found at i:5846280 original size:58 final size:56
Alignment explanation
Indices: 5846218--5846336 Score: 134
Period size: 57 Copynumber: 2.1 Consensus size: 56
5846208 AGAAATGGTG
5846218 AAATGGAGAAATAAAAAAC-ATTTGGAAATGATTATGT-TTTTCTCCAAAATAAAAATGA
1 AAATGGAGAAAT--AAAACTATTTGGAAATGA--ATGTATTTTCTCCAAAATAAAAATGA
* * ** *
5846276 AAATGGTGAAATGAAACTATTTGGGCATGAATGTAGTTTTCTCCAAAATGAAAATGA
1 AAATGGAGAAATAAAACTATTTGGAAATGAATGTA-TTTTCTCCAAAATAAAAATGA
5846333 AAAT
1 AAAT
5846337 AAAAAATGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
55 4 0.08
56 4 0.08
57 34 0.64
58 11 0.21
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (56 bp):
AAATGGAGAAATAAAACTATTTGGAAATGAATGTATTTTCTCCAAAATAAAAATGA
Found at i:5852505 original size:13 final size:14
Alignment explanation
Indices: 5852489--5852521 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
5852479 TAAATAGCAT
5852489 TATTAATATTTT-A
1 TATTAATATTTTAA
5852502 TATTAATATTTTAA
1 TATTAATATTTTAA
5852516 TATTAA
1 TATTAA
5852522 CAAATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATTAATATTTTAA
Found at i:5855147 original size:30 final size:31
Alignment explanation
Indices: 5855086--5855147 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
5855076 AGAGGTGGGA
* *
5855086 TGAGAGGGGAGTAAAAGTTTTTAGGGAAAAG
1 TGAGAGGGGAATAAAAGTTTTGAGGGAAAAG
* *
5855117 TGAGA-GGGAATAAAAGTTTTGGGGGGAAAG
1 TGAGAGGGGAATAAAAGTTTTGAGGGAAAAG
5855147 T
1 T
5855148 AAAAAGGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.40, T:0.23
Consensus pattern (31 bp):
TGAGAGGGGAATAAAAGTTTTGAGGGAAAAG
Found at i:5858425 original size:9 final size:9
Alignment explanation
Indices: 5858411--5858438 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
5858401 TGACGTTTTC
5858411 TTCTTCTTT
1 TTCTTCTTT
5858420 TTCTTCTTT
1 TTCTTCTTT
5858429 TTCTTCTTT
1 TTCTTCTTT
5858438 T
1 T
5858439 CTCTCATCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTCTTCTTT
Found at i:5878291 original size:21 final size:21
Alignment explanation
Indices: 5878265--5878305 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5878255 GTACATCATC
5878265 AACAGAAGCTCATAAGAGCTT
1 AACAGAAGCTCATAAGAGCTT
* *
5878286 AACAGAAGCTCGTTAGAGCT
1 AACAGAAGCTCATAAGAGCT
5878306 AATCCACCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.20
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTT
Found at i:5881789 original size:3 final size:3
Alignment explanation
Indices: 5881783--5881820 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
5881773 AAAAAAAAAA
5881783 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG A
5881821 GAAAACCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5881823 original size:12 final size:12
Alignment explanation
Indices: 5881786--5881824 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
5881776 AAAAAAAAAG
5881786 AAGAAGAAGA-A
1 AAGAAGAAGAGA
5881797 GAAGAAGAAGAAGA
1 -AAGAAGAAG-AGA
5881811 AAGAAGAAGAGA
1 AAGAAGAAGAGA
5881823 AA
1 AA
5881825 ACCCAAACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 14 0.56
13 10 0.40
14 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (12 bp):
AAGAAGAAGAGA
Found at i:5881927 original size:47 final size:47
Alignment explanation
Indices: 5881858--5881950 Score: 150
Period size: 47 Copynumber: 2.0 Consensus size: 47
5881848 GAGATAGTTT
* *
5881858 TACGGCCCTTTCCGATTCCTATCACAACTTCCAAGTCACAAACACCC
1 TACGGCCCTTTCCCATTCCTATCACAACTCCCAAGTCACAAACACCC
* *
5881905 TACGGCCCTTTCCCATTCCTATCAGAACTCCCAAGTCACCAACACC
1 TACGGCCCTTTCCCATTCCTATCACAACTCCCAAGTCACAAACACC
5881951 ATCAATCTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.27, C:0.42, G:0.09, T:0.23
Consensus pattern (47 bp):
TACGGCCCTTTCCCATTCCTATCACAACTCCCAAGTCACAAACACCC
Found at i:5882514 original size:13 final size:14
Alignment explanation
Indices: 5882493--5882531 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
5882483 ATTTATTTTT
5882493 ATATAAAAATTAAA
1 ATATAAAAATTAAA
*
5882507 AT-TAAAAATAAAA
1 ATATAAAAATTAAA
5882520 ATATATAAAATT
1 ATATA-AAAATT
5882532 TAATTACGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 12 0.57
14 4 0.19
15 5 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
ATATAAAAATTAAA
Found at i:5882862 original size:3 final size:3
Alignment explanation
Indices: 5882854--5882882 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5882844 ATATTTATAT
5882854 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5882883 TGTTTGATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5884804 original size:22 final size:23
Alignment explanation
Indices: 5884770--5884818 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
5884760 TAAAGCTATG
*
5884770 ATTTTAATGAAAA-GTTCATTTA
1 ATTTTAATAAAAATGTTCATTTA
* * *
5884792 ATTTTATTAAAAATTTTCATTTC
1 ATTTTAATAAAAATGTTCATTTA
5884815 ATTT
1 ATTT
5884819 GGTGAGGTCC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (23 bp):
ATTTTAATAAAAATGTTCATTTA
Found at i:5887006 original size:15 final size:16
Alignment explanation
Indices: 5886988--5887024 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
5886978 ATTTAATTAA
5886988 AAAATTATTAAAAATA-
1 AAAATTA-TAAAAATAT
5887004 AAAA-TATAAAAATAT
1 AAAATTATAAAAATAT
5887019 AAAATT
1 AAAATT
5887025 TGAGTCAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.42
15 6 0.32
16 5 0.26
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATTATAAAAATAT
Found at i:5887625 original size:25 final size:25
Alignment explanation
Indices: 5887544--5887626 Score: 60
Period size: 25 Copynumber: 3.2 Consensus size: 25
5887534 AATTTCTTCC
* * *
5887544 ATTAAAACAAACGTTCACTTTCAAT
1 ATTAAAATAAACCTTCATTTTCAAT
* **
5887569 ATTAAAATAAACCCTCATATTT-TTT
1 ATTAAAATAAACCTTCAT-TTTCAAT
*
5887594 GCCATTAAAATAAACTTTCATTTTCAAT
1 ---ATTAAAATAAACCTTCATTTTCAAT
5887622 ATTAA
1 ATTAA
5887627 GAACCCAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
25 20 0.47
26 3 0.07
27 3 0.07
28 17 0.40
ACGTcount: A:0.42, C:0.17, G:0.02, T:0.39
Consensus pattern (25 bp):
ATTAAAATAAACCTTCATTTTCAAT
Found at i:5890942 original size:41 final size:39
Alignment explanation
Indices: 5890820--5890955 Score: 118
Period size: 40 Copynumber: 3.5 Consensus size: 39
5890810 ACCAGTTTGG
*
5890820 CACCCAGTGCCTCATCGGA-TAAT-TCAAAGTAATAATTTGA
1 CACCCAGTGCCTCATCGAATTAATCT-AAAGT-ATAA-TTGA
* * * ** *
5890860 CACCCAGTGTCTTATCG-ATTAAACCGAAGTA-AATTGG
1 CACCCAGTGCCTCATCGAATTAATCTAAAGTATAATTGA
*
5890897 CACCCAATGCCTCATCGAATTAATCTAAAGTAGTAAGTTGA
1 CACCCAGTGCCTCATCGAATTAATCTAAAGTA-TAA-TTGA
*
5890938 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
5890956 CTCAAAGTCG
Statistics
Matches: 75, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
37 17 0.23
38 13 0.17
39 2 0.03
40 24 0.32
41 19 0.25
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.26
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGAATTAATCTAAAGTATAATTGA
Done.