Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 17 of 143
Found at i:5259268 original size:24 final size:24
Alignment explanation
Indices: 5259238--5259316 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 24
5259228 CATGAGTGGT
5259238 GAAAGGAGAAGGGAGAAGGAGCGA
1 GAAAGGAGAAGGGAGAAGGAGCGA
* * *
5259262 GAGAGGAGTAGGGAAAGAGAACTGGAGAGA
1 GAAAGGAG-AAGG---GAGAA--GGAGCGA
5259292 GAAAGGAGAAGGGAGAAGGAGCGA
1 GAAAGGAGAAGGGAGAAGGAGCGA
5259316 G
1 G
5259317 GGAAGAGCCG
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
24 14 0.33
25 3 0.07
26 5 0.12
28 5 0.12
29 3 0.07
30 13 0.30
ACGTcount: A:0.44, C:0.04, G:0.49, T:0.03
Consensus pattern (24 bp):
GAAAGGAGAAGGGAGAAGGAGCGA
Found at i:5276279 original size:3 final size:3
Alignment explanation
Indices: 5276271--5276301 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5276261 GAAACCATAT
5276271 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5276302 AAGATAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5276400 original size:20 final size:20
Alignment explanation
Indices: 5276351--5276401 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
5276341 AAAAATAAAA
*
5276351 TTTTATTTTTTAATATATTT
1 TTTTATTTTTTAATAAATTT
* *
5276371 TTTGA-ATTTTAA-AAATTAT
1 TTTTATTTTTTAATAAATT-T
5276390 TTTTATTTTTTA
1 TTTTATTTTTTA
5276402 TTTTTTGTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
18 4 0.17
19 11 0.46
20 9 0.38
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTATTTTTTAATAAATTT
Found at i:5280723 original size:65 final size:65
Alignment explanation
Indices: 5280647--5280821 Score: 234
Period size: 66 Copynumber: 2.7 Consensus size: 65
5280637 AGGTAAGAGC
* *
5280647 ATAGAGTAATTCCTTGATGAGGAAGTATCATAGAATGTAAGGGTTTTTAATGCTGGTAATGTATT
1 ATAGAGTAATTCCTTGATAAGGAAGTATCATAGAATGTAAGGGTTTTTAACGCTGGTAATGTATT
** * *
5280712 ATAGAGTAATTCCTCAATAAGGAAGTATCATAGAAAT-TAAGGTTTTTTTAACGCTGTTAATGTA
1 ATAGAGTAATTCCTTGATAAGGAAGTATCATAG-AATGTAAGG-GTTTTTAACGCTGGTAATGTA
5280776 TT
64 TT
*
5280778 ACAGAGTAATTCCTTGATAAGGAAGTATC--A-AA-GTAAGGGTTTTT
1 ATAGAGTAATTCCTTGATAAGGAAGTATCATAGAATGTAAGGGTTTTT
5280822 TTGGCTGGTA
Statistics
Matches: 97, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
61 5 0.05
62 7 0.07
64 1 0.01
65 35 0.36
66 49 0.51
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.36
Consensus pattern (65 bp):
ATAGAGTAATTCCTTGATAAGGAAGTATCATAGAATGTAAGGGTTTTTAACGCTGGTAATGTATT
Found at i:5295342 original size:55 final size:55
Alignment explanation
Indices: 5295258--5295368 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
5295248 GAAGTTCGTA
*
5295258 AATTTTCTTGATTTATCAATGAATAAATCATAAAACGAATCTCGGTATTGCACCC
1 AATTTTCTTGATTTATCAATGAATAAATCATAAAACGAATCTCGGTATCGCACCC
*
5295313 AATTTTCTTGATTTATCAATGAATAAATCATAAAGCGAATCTCGGTATCGCACCC
1 AATTTTCTTGATTTATCAATGAATAAATCATAAAACGAATCTCGGTATCGCACCC
5295368 A
1 A
5295369 CTTCGCTTAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (55 bp):
AATTTTCTTGATTTATCAATGAATAAATCATAAAACGAATCTCGGTATCGCACCC
Found at i:5309348 original size:16 final size:14
Alignment explanation
Indices: 5309311--5309353 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
5309301 TATAATTAGT
5309311 TTAATTAATCACTAA
1 TTAATTAA-CACTAA
*
5309326 TTTATTAACACTAA
1 TTAATTAACACTAA
5309340 CCTTAATTAACACT
1 --TTAATTAACACT
5309354 TTTGGTGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.25
15 7 0.29
16 11 0.46
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.40
Consensus pattern (14 bp):
TTAATTAACACTAA
Found at i:5314559 original size:69 final size:68
Alignment explanation
Indices: 5314479--5314613 Score: 234
Period size: 69 Copynumber: 2.0 Consensus size: 68
5314469 AGGTTAATTT
*
5314479 AGTTAATACTAGTTCAATTCAATTAACCGATCGATTAACTGTTTGAACATCCCCTAATTTGAAAC
1 AGTTAATACTAGTTCAATTCAATTAACCGATCGATTAACTGTTTAAACA-CCCCTAATTTGAAAC
5314544 TTTC
65 TTTC
* *
5314548 AGTTAATACTAGTTCAGTTCAATTAACCGATTGATTAACTGTTTAAACACCCCTAATTTGAAACT
1 AGTTAATACTAGTTCAATTCAATTAACCGATCGATTAACTGTTTAAACACCCCTAATTTGAAACT
5314613 T
66 T
5314614 GATTCTCTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
68 17 0.27
69 46 0.73
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.36
Consensus pattern (68 bp):
AGTTAATACTAGTTCAATTCAATTAACCGATCGATTAACTGTTTAAACACCCCTAATTTGAAACT
TTC
Found at i:5315076 original size:20 final size:20
Alignment explanation
Indices: 5315051--5315090 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5315041 TTGATCTAGG
5315051 GTCAAAACAATCACTCAACT
1 GTCAAAACAATCACTCAACT
*
5315071 GTCAAAACAGTCACTCAACT
1 GTCAAAACAATCACTCAACT
5315091 TTCTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.30, G:0.07, T:0.20
Consensus pattern (20 bp):
GTCAAAACAATCACTCAACT
Found at i:5315414 original size:19 final size:18
Alignment explanation
Indices: 5315390--5315431 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
5315380 CAATGTTAAC
* *
5315390 TTCAATTTTAATATAAATA
1 TTCAATTATAAT-TAAAAA
5315409 TTCAA-TATAATTAAAAA
1 TTCAATTATAATTAAAAA
5315426 TTCAAT
1 TTCAAT
5315432 AATATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 10 0.50
18 5 0.25
19 5 0.25
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (18 bp):
TTCAATTATAATTAAAAA
Found at i:5315428 original size:17 final size:18
Alignment explanation
Indices: 5315398--5315432 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5315388 ACTTCAATTT
*
5315398 TAATATAAATATTCAATA
1 TAATATAAAAATTCAATA
5315416 TAAT-TAAAAATTCAATA
1 TAATATAAAAATTCAATA
5315433 ATATAAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATATAAAAATTCAATA
Found at i:5315452 original size:36 final size:36
Alignment explanation
Indices: 5315412--5315480 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
5315402 ATAAATATTC
5315412 AATAT-AATTAAAAATTCAATAATATAAATAGTACAA
1 AATATGAATT-AAAATTCAATAATATAAATAGTACAA
** *
5315448 AATATGAATTTTAATTTAATAATATAAATAGTA
1 AATATGAATTAAAATTCAATAATATAAATAGTA
5315481 GATATAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 25 0.86
37 4 0.14
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (36 bp):
AATATGAATTAAAATTCAATAATATAAATAGTACAA
Found at i:5316646 original size:20 final size:22
Alignment explanation
Indices: 5316605--5316647 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
5316595 TAGTAAGAGG
*
5316605 GATGGTGGGGAAGAGCGGGAGA
1 GATGGTGGGGAAGAGAGGGAGA
5316627 GATGGT-GGGAA-AGAGGGAGA
1 GATGGTGGGGAAGAGAGGGAGA
5316647 G
1 G
5316648 GGATGGGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 5 0.25
22 6 0.30
ACGTcount: A:0.30, C:0.02, G:0.58, T:0.09
Consensus pattern (22 bp):
GATGGTGGGGAAGAGAGGGAGA
Found at i:5316652 original size:22 final size:23
Alignment explanation
Indices: 5316600--5316653 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
5316590 TTTCATAGTA
*
5316600 AGAGGGATGGTGGGGAAGAGCGG
1 AGAGGGATGGTGGGAAAGAGCGG
*
5316623 -GAGAGATGGTGGGAAAGAG-GG
1 AGAGGGATGGTGGGAAAGAGCGG
5316644 AGAGGGATGG
1 AGAGGGATGG
5316654 GAGGGGGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.30, C:0.02, G:0.59, T:0.09
Consensus pattern (23 bp):
AGAGGGATGGTGGGAAAGAGCGG
Found at i:5316790 original size:20 final size:20
Alignment explanation
Indices: 5316765--5316807 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5316755 TTTTGTTATT
*
5316765 TTTTGAAAGTTGAATGATTG
1 TTTTGAAAGTTGAATGACTG
* *
5316785 TTTTGACAGTTGAGTGACTG
1 TTTTGAAAGTTGAATGACTG
5316805 TTT
1 TTT
5316808 ATTTCCCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.26, T:0.47
Consensus pattern (20 bp):
TTTTGAAAGTTGAATGACTG
Found at i:5322864 original size:21 final size:20
Alignment explanation
Indices: 5322827--5322877 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
5322817 TTATTTATTC
* *
5322827 ATTTTTCTTTCTTTTTTGTTT
1 ATTTTTCTTTCTCTTTT-TCT
5322848 ATTTTTCTTT-TACTTTTTCT
1 ATTTTTCTTTCT-CTTTTTCT
5322868 ATGTTTTCTT
1 AT-TTTTCTT
5322878 AATAAAACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.76
Consensus pattern (20 bp):
ATTTTTCTTTCTCTTTTTCT
Found at i:5324567 original size:20 final size:21
Alignment explanation
Indices: 5324542--5324582 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
5324532 TAAAACGTTT
5324542 TATAATAAATATTT-ATAATA
1 TATAATAAATATTTAATAATA
5324562 TATAATAAATATTTAATAATA
1 TATAATAAATATTTAATAATA
5324583 AAAAGGGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TATAATAAATATTTAATAATA
Found at i:5325695 original size:30 final size:29
Alignment explanation
Indices: 5325659--5325759 Score: 103
Period size: 30 Copynumber: 3.3 Consensus size: 29
5325649 CACAAAAGGT
5325659 CCCTAAACTTTCCAAAAATCATATTTTGAC
1 CCCTAAACTTTCCAAAAATCA-ATTTTGAC
* * *
5325689 CCCTAAACTTTTCTAAAAATGAATTTGGAC
1 CCCTAAAC-TTTCCAAAAATCAATTTTGAC
* * * *
5325719 CCCTCAAAATTTCCTAAAATTACATTTTTAC
1 CCCT-AAACTTTCCAAAAATCA-ATTTTGAC
5325750 CCCTAAACTT
1 CCCTAAACTT
5325760 CTCAAAATTA
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
30 34 0.59
31 24 0.41
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAAATCAATTTTGAC
Found at i:5325768 original size:29 final size:29
Alignment explanation
Indices: 5325734--5325962 Score: 123
Period size: 29 Copynumber: 7.7 Consensus size: 29
5325724 AAAATTTCCT
5325734 AAAATTACATTTTTACCCCTAAACTTCTC
1 AAAATTACATTTTTACCCCTAAACTTCTC
*
5325763 AAAATTACATTTTTA-CCCTCGAACTTCCCAACTTCC
1 AAAATTACATTTTTACCCCT-AAACTT-----C-T-C
* * * *
5325799 AAAAATCACATTTTCA-CCCTAAACTTTTTT
1 -AAAATTACATTTTTACCCCTAAAC-TTCTC
* * **
5325829 GAAATTGCA-TTTTACCCCCGAACTTC-C
1 AAAATTACATTTTTACCCCTAAACTTCTC
*
5325856 AAAAATACATTTTTA-CCCTCAAACTTCTC
1 AAAATTACATTTTTACCCCT-AAACTTCTC
*
5325885 AAAAATTACA-TTTTACCCCCAAACTTC-C
1 -AAAATTACATTTTTACCCCTAAACTTCTC
* * *
5325913 AAAAATCACATTTTCACCGCC-AAACTTTTCC
1 -AAAATTACATTTTTACC-CCTAAACTTCT-C
* *
5325944 AAAATTGCATTTTTGCCCC
1 AAAATTACATTTTTACCCC
5325963 CGAACATTCA
Statistics
Matches: 152, Mismatches: 28, Indels: 40
0.69 0.13 0.18
Matches are distributed among these distances:
27 9 0.06
28 31 0.20
29 59 0.39
30 26 0.17
31 2 0.01
34 1 0.01
35 1 0.01
36 4 0.03
37 19 0.12
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATTACATTTTTACCCCTAAACTTCTC
Found at i:5325824 original size:36 final size:37
Alignment explanation
Indices: 5325755--5325824 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
5325745 TTTACCCCTA
* * *
5325755 AACTTCTCAAAATTACATTTTTACCCTCGAACTTCCC
1 AACTTCTCAAAATCACATTTTCACCCTCAAACTTCCC
5325792 AACTTC-CAAAAATCACATTTTCACCCT-AAACTT
1 AACTTCTC-AAAATCACATTTTCACCCTCAAACTT
5325825 TTTTGAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 6 0.21
37 23 0.79
ACGTcount: A:0.34, C:0.31, G:0.01, T:0.33
Consensus pattern (37 bp):
AACTTCTCAAAATCACATTTTCACCCTCAAACTTCCC
Found at i:5325851 original size:65 final size:66
Alignment explanation
Indices: 5325729--5325967 Score: 171
Period size: 57 Copynumber: 3.9 Consensus size: 66
5325719 CCCTCAAAAT
* * * *
5325729 TTCCTAAAATTACATTTTTACCCCTAAACTTCTCAAAATTACATTTTTACCCTCGAACTTCCCAA
1 TTCCAAAAATCACATTTTCACCCCTAAACTTCTCAAAATTACATTTTTACCCCCGAACTTCCCAA
5325794 C
66 C
* ** *
5325795 TTCCAAAAATCACATTTTCA-CCCTAAACTTTTTTGAAATTGCA-TTTTACCCCCG--------A
1 TTCCAAAAATCACATTTTCACCCCTAAAC-TTCTCAAAATTACATTTTTACCCCCGAACTTCCCA
5325850 AC
65 AC
*
5325852 TTCCAAAAAT-ACATTTTTA-CCCTCAAACTTCTCAAAAATTACA-TTTTACCCCC--A------
1 TTCCAAAAATCACATTTTCACCCCT-AAACTTCTC-AAAATTACATTTTTACCCCCGAACTTCCC
5325906 AAC
64 AAC
* * *
5325909 TTCCAAAAATCACATTTTCACCGCC-AAACTTTTCCAAAATTGCATTTTTGCCCCCGAAC
1 TTCCAAAAATCACATTTTCACC-CCTAAACTTCT-CAAAATTACATTTTTACCCCCGAAC
5325968 ATTCAAAAAT
Statistics
Matches: 144, Mismatches: 17, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
56 15 0.10
57 47 0.33
58 23 0.16
59 11 0.08
60 2 0.01
61 1 0.01
65 18 0.12
66 27 0.19
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.33
Consensus pattern (66 bp):
TTCCAAAAATCACATTTTCACCCCTAAACTTCTCAAAATTACATTTTTACCCCCGAACTTCCCAA
C
Found at i:5325861 original size:57 final size:57
Alignment explanation
Indices: 5325792--5325986 Score: 232
Period size: 57 Copynumber: 3.4 Consensus size: 57
5325782 CGAACTTCCC
***
5325792 AACTTCCAAAAATCACATTTTCACCCTAAACTTTTTTGAAATTGCATTTTACCCCCG
1 AACTTCCAAAAATCACATTTTCACCCTAAACTTTTCAAAAATTGCATTTTACCCCCG
* * * *
5325849 AACTTCCAAAAAT-ACATTTTTACCCTCAAACTTCTCAAAAATTACATTTTACCCCCA
1 AACTTCCAAAAATCACATTTTCACCCT-AAACTTTTCAAAAATTGCATTTTACCCCCG
* * *
5325906 AACTTCCAAAAATCACATTTTCACCGCCAAACTTTTCCAAAATTGCATTTTTGCCCCCG
1 AACTTCCAAAAATCACATTTTCACC-CTAAACTTTTCAAAAATTGCA-TTTTACCCCCG
*
5325965 AACATT-CAAAAATTATCATTTT
1 AAC-TTCCAAAAATCA-CATTTT
5325987 GCCCTCAAAT
Statistics
Matches: 117, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
56 12 0.10
57 50 0.43
58 26 0.22
59 21 0.18
60 8 0.07
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (57 bp):
AACTTCCAAAAATCACATTTTCACCCTAAACTTTTCAAAAATTGCATTTTACCCCCG
Found at i:5325986 original size:29 final size:27
Alignment explanation
Indices: 5325830--5326014 Score: 129
Period size: 29 Copynumber: 6.4 Consensus size: 27
5325820 AACTTTTTTG
* *
5325830 AAATTGCATTTTACCCCCGAACTTCCAA
1 AAATTACATTTTACCCCCAAACTT-CAA
*
5325858 AAA-TACATTTTTACCCTCAAACTTCTCAA
1 AAATTACA-TTTTACCCCCAAAC-T-TCAA
5325887 AAATTACATTTTACCCCCAAACTTCCAA
1 AAATTACATTTTACCCCCAAACTT-CAA
* * *
5325915 AAATCACATTTTCACCGCCAAACTTTTCCA
1 AAATTACATTTT-ACCCCCAAAC--TTCAA
* * *
5325945 AAATTGCATTTTTGCCCCCGAACATTCAA
1 AAATTACA-TTTTACCCCCAAAC-TTCAA
* * *
5325974 AAATTATCATTTTGCCCTCAAATTTCCAA
1 AAATTA-CATTTTACCCCCAAACTT-CAA
* *
5326003 AAGTCACATTTT
1 AAATTACATTTT
5326015 CGACCTCGAA
Statistics
Matches: 126, Mismatches: 20, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
27 4 0.03
28 38 0.30
29 56 0.44
30 22 0.17
31 6 0.05
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (27 bp):
AAATTACATTTTACCCCCAAACTTCAA
Found at i:5326115 original size:29 final size:30
Alignment explanation
Indices: 5326030--5326115 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
5326020 TCGAATTTCA
* *
5326030 AAAAATTCGATTTTAATCCCAAATT-TTCC
1 AAAAATTCAATTTTAATCCCAAATTCCTCC
*
5326059 AAAAATCTCAATTTTGATCCCCAAATTCCT-C
1 AAAAAT-TCAATTTTAAT-CCCAAATTCCTCC
* * *
5326090 AAAAATTCTATTTTCATCCCTAATTC
1 AAAAATTCAATTTTAATCCCAAATTC
5326116 TCTGAAACTT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
29 14 0.29
30 18 0.38
31 15 0.31
32 1 0.02
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.37
Consensus pattern (30 bp):
AAAAATTCAATTTTAATCCCAAATTCCTCC
Found at i:5328530 original size:29 final size:30
Alignment explanation
Indices: 5328498--5328556 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
5328488 TATAATTTAA
5328498 TGTGTAATTGTATACAT-AAACTTTGATTT
1 TGTGTAATTGTATACATGAAACTTTGATTT
* *
5328527 TGTGTAATTTTATACATGAAATTTTGATTT
1 TGTGTAATTGTATACATGAAACTTTGATTT
5328557 GATCTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.51
Consensus pattern (30 bp):
TGTGTAATTGTATACATGAAACTTTGATTT
Found at i:5328565 original size:30 final size:29
Alignment explanation
Indices: 5328502--5328571 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
5328492 ATTTAATGTG
* *
5328502 TAATTGTATACATAAACTTTGATTTTGTG
1 TAATTTTATACATAAACTTTGATTTTGTC
*
5328531 TAATTTTATACATGAAATTTTGA-TTTGATC
1 TAATTTTATACAT-AAACTTTGATTTTG-TC
5328561 TAATTATTATA
1 TAATT-TTATA
5328572 ACTTATTAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 16 0.46
30 14 0.40
31 5 0.14
ACGTcount: A:0.34, C:0.06, G:0.10, T:0.50
Consensus pattern (29 bp):
TAATTTTATACATAAACTTTGATTTTGTC
Found at i:5330131 original size:21 final size:22
Alignment explanation
Indices: 5330093--5330133 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5330083 TACTTTTACA
*
5330093 ACCTTTTGGGATTTTTTTAAAC
1 ACCTTTTGGGATTGTTTTAAAC
*
5330115 ACCTTTT-GTATTGTTTTAA
1 ACCTTTTGGGATTGTTTTAA
5330134 TATTGATGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.54
Consensus pattern (22 bp):
ACCTTTTGGGATTGTTTTAAAC
Found at i:5334402 original size:205 final size:205
Alignment explanation
Indices: 5334043--5334454 Score: 700
Period size: 205 Copynumber: 2.0 Consensus size: 205
5334033 TTGAGAAATC
5334043 ATGAATGTTACATTTCTAAATAGTTTACTACTCAATTTACACTATTTCTGAAATCCAAATTCAAA
1 ATGAATGTTACATTTCTAAATAGTTTACTACTCAATTTACACTATTTCTGAAATCCAAA-TCAAA
* * *
5334108 TTGTAAAATCTTAGCTCCCAAATCCTACCTAAGGGGTGAATTAGATAAAATTTTATAGGAGCTTA
65 TTGTAAAATCTTAGCTCCCAAACCCTACCTAAGGGGTGAATTAGATAAAATTGTATAAGAGCTTA
* * *
5334173 TTTAGGATATTTGGAAACGGAAAGGGCTTTTTAGTATTTAGGCTTTTTACTAACATTTTAAGATT
130 TTTAGGATATTTGGAAAAGGAAAGGGC-TTTTAGTATTTAGCCTTTTTAATAACATTTTAAGATT
5334238 ATGAAGACATTT
194 ATGAAGACATTT
* *
5334250 ATGAATGTTACATTTGTAAATAGTTTACTACTCGATTTACACTATTTCTGAAATCCAAA-CAAAT
1 ATGAATGTTACATTTCTAAATAGTTTACTACTCAATTTACACTATTTCTGAAATCCAAATCAAAT
*
5334314 TGTAAAATCTTAGCTCCGAAACCCTACCTAAGGGGTGAATTAGATAAAATTGTATAAGAGCTTAT
66 TGTAAAATCTTAGCTCCCAAACCCTACCTAAGGGGTGAATTAGATAAAATTGTATAAGAGCTTAT
*
5334379 TTAGGATATTTGGAAAAGGAAAGGGCTTTTAGTGTTTAGCCTTTTTAATAACATTTTAAGATTAT
131 TTAGGATATTTGGAAAAGGAAAGGGCTTTTAGTATTTAGCCTTTTTAATAACATTTTAAGATTAT
*
5334444 GAAGATATTT
196 GAAGACATTT
5334454 A
1 A
5334455 ACTGTTCCCT
Statistics
Matches: 194, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
204 46 0.24
205 91 0.47
207 57 0.29
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (205 bp):
ATGAATGTTACATTTCTAAATAGTTTACTACTCAATTTACACTATTTCTGAAATCCAAATCAAAT
TGTAAAATCTTAGCTCCCAAACCCTACCTAAGGGGTGAATTAGATAAAATTGTATAAGAGCTTAT
TTAGGATATTTGGAAAAGGAAAGGGCTTTTAGTATTTAGCCTTTTTAATAACATTTTAAGATTAT
GAAGACATTT
Found at i:5341091 original size:19 final size:19
Alignment explanation
Indices: 5341067--5341104 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
5341057 AAAAATTGAG
5341067 TTATTT-TATCTTTTTAATT
1 TTATTTGTAT-TTTTTAATT
5341086 TTATTTGTATTTTTTAATT
1 TTATTTGTATTTTTTAATT
5341105 AAATCGAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (19 bp):
TTATTTGTATTTTTTAATT
Found at i:5341147 original size:15 final size:15
Alignment explanation
Indices: 5341127--5341159 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5341117 ATAAAATTTG
*
5341127 AATCAAATCGAATAA
1 AATCAAATAGAATAA
5341142 AATCAAATAGAATAA
1 AATCAAATAGAATAA
5341157 AAT
1 AAT
5341160 TATTTGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.09, G:0.06, T:0.21
Consensus pattern (15 bp):
AATCAAATAGAATAA
Found at i:5341283 original size:22 final size:21
Alignment explanation
Indices: 5341265--5341305 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5341255 AATTTTTACT
5341265 ATAATAAAAATT-AAATTTTAA
1 ATAAT-AAAATTAAAATTTTAA
*
5341286 ATAATTAAATTAAAATTTTA
1 ATAATAAAATTAAAATTTTA
5341306 TCACTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAATAAAATTAAAATTTTAA
Found at i:5350832 original size:24 final size:24
Alignment explanation
Indices: 5350805--5350865 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
5350795 TGCTGCAGTT
5350805 GCTGCTGCTGCTGCAGCTG-GGAAA
1 GCTGCTGCTGCTGCAGCTGTGG-AA
* *
5350829 GCTGCTGCTGTTGCAGCTGTGGTA
1 GCTGCTGCTGCTGCAGCTGTGGAA
5350853 GCTGCTGCTGCTG
1 GCTGCTGCTGCTG
5350866 TTGTTGTAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.10, C:0.25, G:0.38, T:0.28
Consensus pattern (24 bp):
GCTGCTGCTGCTGCAGCTGTGGAA
Found at i:5350856 original size:21 final size:21
Alignment explanation
Indices: 5350808--5350877 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
5350798 TGCAGTTGCT
*
5350808 GCTGCTGCTGCAGCTG-GGAAA
1 GCTGCTGCTGCAGCTGTGG-TA
5350829 GCTGCTGCTGTTGCAGCTGTGGTA
1 GCTGCTGC---TGCAGCTGTGGTA
* * *
5350853 GCTGCTGCTGCTGTTGTTGTA
1 GCTGCTGCTGCAGCTGTGGTA
5350874 GCTG
1 GCTG
5350878 AGGGAGTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
21 22 0.54
24 17 0.41
25 2 0.05
ACGTcount: A:0.10, C:0.21, G:0.37, T:0.31
Consensus pattern (21 bp):
GCTGCTGCTGCAGCTGTGGTA
Found at i:5350863 original size:30 final size:30
Alignment explanation
Indices: 5350829--5350896 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
5350819 AGCTGGGAAA
* *
5350829 GCTGCTGCTGTTGCAGCTGTGGTAGCTGCT
1 GCTGCTGCTGTTGCAGCTGAGGGAGCTGCT
* * * *
5350859 GCTGCTGTTGTTGTAGCTGAGGGAGTTGTT
1 GCTGCTGCTGTTGCAGCTGAGGGAGCTGCT
5350889 GCTGCTGC
1 GCTGCTGC
5350897 AAGTGCGGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.07, C:0.19, G:0.38, T:0.35
Consensus pattern (30 bp):
GCTGCTGCTGTTGCAGCTGAGGGAGCTGCT
Found at i:5350935 original size:24 final size:24
Alignment explanation
Indices: 5350908--5350964 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
5350898 AGTGCGGAAG
*
5350908 CTGCTGTTGTTGCAGTTGTGGATT
1 CTGCTGTTGTTGCAGTTGTGAATT
*
5350932 CTGCTGCTGTTGCAGTTGTGAATT
1 CTGCTGTTGTTGCAGTTGTGAATT
5350956 CTGCTGTTG
1 CTGCTGTTG
5350965 CTGCTGCTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.09, C:0.16, G:0.32, T:0.44
Consensus pattern (24 bp):
CTGCTGTTGTTGCAGTTGTGAATT
Found at i:5355243 original size:22 final size:22
Alignment explanation
Indices: 5355218--5355262 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5355208 GCAAGCAGAG
5355218 TGAAGATAAATCTGAATTTTTC
1 TGAAGATAAATCTGAATTTTTC
5355240 TGAAGATAAATCTGAATTTTTC
1 TGAAGATAAATCTGAATTTTTC
5355262 T
1 T
5355263 TCTTCTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (22 bp):
TGAAGATAAATCTGAATTTTTC
Found at i:5364243 original size:26 final size:26
Alignment explanation
Indices: 5364213--5364266 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
5364203 TGTTAAAAAT
5364213 TTTAAAATT-T-TGTTTATGTATGTTTA
1 TTTAAAATTATATGTTT-T-TATGTTTA
5364239 TTTAAAATTATATGTTTTTATGTTTA
1 TTTAAAATTATATGTTTTTATGTTTA
5364265 TT
1 TT
5364267 CGTTTGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 19 0.73
27 2 0.08
28 5 0.19
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (26 bp):
TTTAAAATTATATGTTTTTATGTTTA
Found at i:5364931 original size:29 final size:29
Alignment explanation
Indices: 5364898--5364958 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
5364888 ATTTTTACGA
* *
5364898 TTACGATTACTATAGTAAAAATATAATTT
1 TTACGATTACGATAATAAAAATATAATTT
5364927 TTACGATTACGATAATAAAAATATAATTT
1 TTACGATTACGATAATAAAAATATAATTT
5364956 TTA
1 TTA
5364959 AAGGATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.41
Consensus pattern (29 bp):
TTACGATTACGATAATAAAAATATAATTT
Found at i:5368305 original size:2 final size:2
Alignment explanation
Indices: 5368298--5368324 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5368288 GGTCTAAATT
5368298 TA 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 TA T
5368325 GTGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5372713 original size:28 final size:28
Alignment explanation
Indices: 5372682--5372735 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
5372672 TCTTTCTTTA
5372682 TCACTGAATTATGAATTTTATTAAATGG
1 TCACTGAATTATGAATTTTATTAAATGG
* * *
5372710 TCACTTAATTGTGAATTTTTTTAAAT
1 TCACTGAATTATGAATTTTATTAAAT
5372736 TGATTATCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.48
Consensus pattern (28 bp):
TCACTGAATTATGAATTTTATTAAATGG
Found at i:5372975 original size:17 final size:18
Alignment explanation
Indices: 5372955--5372992 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5372945 TATATAATAC
5372955 ATAA-ATATTTTAAAAAT
1 ATAATATATTTTAAAAAT
* *
5372972 ATAATATTTTTTAAAATT
1 ATAATATATTTTAAAAAT
5372990 ATA
1 ATA
5372993 TAAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAATATATTTTAAAAAT
Found at i:5373004 original size:17 final size:16
Alignment explanation
Indices: 5372983--5373049 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 16
5372973 TAATATTTTT
*
5372983 TAAAATTATATAAAAA
1 TAAAAATATATAAAAA
*
5372999 TAAAAAATATTATTAACAA
1 T-AAAAATA-TA-TAAAAA
* * *
5373018 CAATAATATATAAAATT
1 TAAAAATATATAAAA-A
5373035 TAAAAATATATAAAA
1 TAAAAATATATAAAA
5373050 GTACATAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
16 5 0.13
17 21 0.54
18 8 0.21
19 5 0.13
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAAAATATATAAAAA
Found at i:5373590 original size:17 final size:18
Alignment explanation
Indices: 5373549--5373595 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 18
5373539 AAGCTAGTAG
*
5373549 AGGTGGCAAGCTAGCGGA
1 AGGTGGCGAGCTAGCGGA
5373567 A--TGGCGAGCTAGC-GA
1 AGGTGGCGAGCTAGCGGA
5373582 AGGTGGCGAGCTAG
1 AGGTGGCGAGCTAG
5373596 ATGGCATCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 3 0.12
16 11 0.42
17 11 0.42
18 1 0.04
ACGTcount: A:0.26, C:0.17, G:0.45, T:0.13
Consensus pattern (18 bp):
AGGTGGCGAGCTAGCGGA
Found at i:5375165 original size:52 final size:52
Alignment explanation
Indices: 5375085--5375190 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 52
5375075 AAGGCTAACG
*
5375085 TATTCAGTGTATAACATCCGCCCGATGAAAACCCTAGTGTTTGAATACTGGT
1 TATTCAGTGTATAACATCCGCCCAATGAAAACCCTAGTGTTTGAATACTGGT
*
5375137 TATTCAGTGTATAACATCCGCCCAATGAAAACCTTAGTGTTTGAATACTGGT
1 TATTCAGTGTATAACATCCGCCCAATGAAAACCCTAGTGTTTGAATACTGGT
5375189 TA
1 TA
5375191 AGGAAATAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (52 bp):
TATTCAGTGTATAACATCCGCCCAATGAAAACCCTAGTGTTTGAATACTGGT
Found at i:5376693 original size:60 final size:60
Alignment explanation
Indices: 5376527--5376755 Score: 230
Period size: 60 Copynumber: 3.8 Consensus size: 60
5376517 TGGAGAATTC
* * * * *** * *
5376527 GGGGTCAAAATGTGATTTTGGAAAAGTTTAGGGATGAAAATGCAATTTT-TGAATAGTTTG
1 GGGGTTAAAATGTGATTTTTGAAAAGTTTAGAGATCAAAATATGATTTTGGGAA-AGTTTA
* * *
5376587 GGGGTT-AAATGTGATTTTTGAAAAGTTTGGAGGTTAAAATATGATTTTGGGAAAGTTTA
1 GGGGTTAAAATGTGATTTTTGAAAAGTTTAGAGATCAAAATATGATTTTGGGAAAGTTTA
* ** * *
5376646 GGGGTTAAAATATGA-TTTTGAAAAAGTTTAGAGATCAAAATGGGATTTTAGGAAAGTTCA
1 GGGGTTAAAATGTGATTTTTG-AAAAGTTTAGAGATCAAAATATGATTTTGGGAAAGTTTA
** * *
5376706 ATGGTTAAAATGTGATTTTTGAAAAGTTTAAAGGTCAAAATATGATTTTG
1 GGGGTTAAAATGTGATTTTTGAAAAGTTTAGAGATCAAAATATGATTTTG
5376756 TAAGAGTTTG
Statistics
Matches: 138, Mismatches: 27, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
59 50 0.36
60 83 0.60
61 5 0.04
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (60 bp):
GGGGTTAAAATGTGATTTTTGAAAAGTTTAGAGATCAAAATATGATTTTGGGAAAGTTTA
Found at i:5376746 original size:30 final size:30
Alignment explanation
Indices: 5376529--5376791 Score: 194
Period size: 30 Copynumber: 8.8 Consensus size: 30
5376519 GAGAATTCGG
*
5376529 GGTCAAAATGTGATTTTGGAAAAGTTTAG-
1 GGTCAAAATGTGATTTTTGAAAAGTTTAGA
* ** * * *
5376558 GGATGAAAATGCAATTTTTGAATAGTTTGGG
1 GG-TCAAAATGTGATTTTTGAAAAGTTTAGA
* *
5376589 GGT-TAAATGTGATTTTTGAAAAGTTTGGA
1 GGTCAAAATGTGATTTTTGAAAAGTTTAGA
* * * * *
5376618 GGTTAAAATATGATTTTGGGAAAGTTTAGG
1 GGTCAAAATGTGATTTTTGAAAAGTTTAGA
* *
5376648 GGTTAAAATATGA-TTTTGAAAAAGTTTAGA
1 GGTCAAAATGTGATTTTTG-AAAAGTTTAGA
* * * * *
5376678 GATCAAAATGGGATTTTAGGAAAGTTCA-A
1 GGTCAAAATGTGATTTTTGAAAAGTTTAGA
* *
5376707 TGGTTAAAATGTGATTTTTGAAAAGTTTAAA
1 -GGTCAAAATGTGATTTTTGAAAAGTTTAGA
* * *
5376738 GGTCAAAATATGA-TTTTGTAAGAGTTTGGA
1 GGTCAAAATGTGATTTTTG-AAAAGTTTAGA
* * *
5376768 CGTCAAAATATAATTTTTGAAAAG
1 GGTCAAAATGTGATTTTTGAAAAG
5376792 CTCAGGAGCC
Statistics
Matches: 184, Mismatches: 41, Indels: 17
0.76 0.17 0.07
Matches are distributed among these distances:
29 36 0.20
30 136 0.74
31 12 0.07
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (30 bp):
GGTCAAAATGTGATTTTTGAAAAGTTTAGA
Found at i:5379229 original size:22 final size:21
Alignment explanation
Indices: 5379204--5379246 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5379194 TATTTCTTTC
5379204 AATTCTGTTTTCTTTTATTTTT
1 AATTCTG-TTTCTTTTATTTTT
*
5379226 AATTTTGTTTCTTTTATTTTT
1 AATTCTGTTTCTTTTATTTTT
5379247 CCTTAGATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.74
Consensus pattern (21 bp):
AATTCTGTTTCTTTTATTTTT
Found at i:5381394 original size:6 final size:6
Alignment explanation
Indices: 5381383--5381408 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5381373 GACAATCCAA
5381383 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
5381409 TCTCTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:5381433 original size:17 final size:16
Alignment explanation
Indices: 5381383--5381435 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
5381373 GACAATCCAA
*
5381383 TTATTTTTATTTTTATTT
1 TTATTTTT-TATTTA-TT
* *
5381401 TTATTTTTTCTCTATT
1 TTATTTTTTATTTATT
5381417 TTATTTATTTATTTATT
1 TTATTT-TTTATTTATT
5381434 TT
1 TT
5381436 GTGTTCAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 8 0.27
17 14 0.47
18 8 0.27
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATTTTTTATTTATT
Found at i:5382862 original size:5 final size:5
Alignment explanation
Indices: 5382852--5382877 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5382842 AAAAGACTTG
5382852 ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT A
5382878 AAATATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:5383784 original size:22 final size:22
Alignment explanation
Indices: 5383759--5383802 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5383749 TATTTCTTTC
5383759 AATTCTGTTTTCTTTTATTTTT
1 AATTCTGTTTTCTTTTATTTTT
5383781 AATTCTGTTTTCTTTTATTTTT
1 AATTCTGTTTTCTTTTATTTTT
5383803 CCTCAGATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.09, G:0.05, T:0.73
Consensus pattern (22 bp):
AATTCTGTTTTCTTTTATTTTT
Found at i:5384338 original size:17 final size:17
Alignment explanation
Indices: 5384272--5384343 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 17
5384262 TATTTGGACT
5384272 TTTAAATTTAAA-TAAA
1 TTTAAATTTAAAGTAAA
5384288 TTTAAATTTAAAATGTATTGGACA
1 TTTAAATTT-AAA-GTA----A-A
5384312 TTTAAAATTTAAAGTAAA
1 TTT-AAATTTAAAGTAAA
5384330 TTTAAATTTAAAGT
1 TTTAAATTTAAAGT
5384344 TTATTTTGGG
Statistics
Matches: 47, Mismatches: 0, Indels: 17
0.73 0.00 0.27
Matches are distributed among these distances:
16 9 0.19
17 14 0.30
18 4 0.09
19 3 0.06
23 4 0.09
24 7 0.15
25 6 0.13
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAGTAAA
Found at i:5385132 original size:85 final size:85
Alignment explanation
Indices: 5384989--5385153 Score: 222
Period size: 85 Copynumber: 1.9 Consensus size: 85
5384979 CTTCATTGAA
* * * * * *
5384989 TTGGTCTACTTTTCTGTATCTCATTAAGAAGATAATCGCTTCATTGTTTTAATCCACTTCTCTAT
1 TTGGTCTACTTCTCTGTACCTCATCAAGAAGATAACCGCTTCATTGCTTTAACCCACTTCTCTAT
*
5385054 ATCTCATCAGGAATACGGAT
66 ATCTCATCAAGAATACGGAT
* * * * *
5385074 TTGGTCTACTTCTCTGTACCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTCTGT
1 TTGGTCTACTTCTCTGTACCTCATCAAGAAGATAACCGCTTCATTGCTTTAACCCACTTCTCTAT
5385139 ATCTCATCAAGAATA
66 ATCTCATCAAGAATA
5385154 TGAGGTTTGA
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
85 68 1.00
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (85 bp):
TTGGTCTACTTCTCTGTACCTCATCAAGAAGATAACCGCTTCATTGCTTTAACCCACTTCTCTAT
ATCTCATCAAGAATACGGAT
Found at i:5385163 original size:209 final size:209
Alignment explanation
Indices: 5384571--5385163 Score: 728
Period size: 209 Copynumber: 2.8 Consensus size: 209
5384561 GCTTCATTTC
* * ** * * *
5384571 TTGATCTACTTCTCTGTATCTCA-TGAGAAAGATGTTCGCTTTATTATTTTAATCCATTTCTCTG
1 TTGATCTACTTTTCTGTATCTCATTAAG-AAGATAATCGCTTCATTGTTTTAATCCACTTCTCTG
* * * *
5384635 TATCTCATCTGGAAGAGGGATTTGGT-TCACTTCTCTGTATTTCATCAGGGAA-ATGAACACTTT
65 TATCTCATCAGGAAGACGGATTTGGTCT-ACTTCTCTGTATCTCATCA-GGAAGATGACCACTTT
** * * * *
5384698 ATTGCTTCAACCCACTTTTTTGTACCTCATCAGGAAGAT-AGGGTTTGGAAGTTTCACGCACATT
128 ATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGA-GGTTTGAAAGTTTCACGCACATT
**
5384762 GAGCTTCACTTTGTTGAA
192 GAGCTTCACTTCATTGAA
* * * *
5384780 TTGATCTACTTTTCTATATCTCATCAGGAAGATGAA-CGCTTCATTGATTTAATCCACTTCTCTG
1 TTGATCTACTTTTCTGTATCTCATTAAGAAGAT-AATCGCTTCATTGTTTTAATCCACTTCTCTG
* * * * * * **
5384844 TATCTTATCACGAAGACGAATTTGGTCTACTTCTCTCTATCTTATCAAGAAGATGACCTTTTTAT
65 TATCTCATCAGGAAGACGGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTTAT
* * *
5384909 TGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAAGTTTCACTCTCATTGAG
130 TGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAAGTTTCACGCACATTGAG
*
5384974 CTTCGCTTCATTGAA
195 CTTCACTTCATTGAA
* *
5384989 TTGGTCTACTTTTCTGTATCTCATTAAGAAGATAATCGCTTCATTGTTTTAATCCACTTCTCTAT
1 TTGATCTACTTTTCTGTATCTCATTAAGAAGATAATCGCTTCATTGTTTTAATCCACTTCTCTGT
* * *
5385054 ATCTCATCAGGAATACGGATTTGGTCTACTTCTCTGTACCTCATCAGGAAGATGACCGCTTTATT
66 ATCTCATCAGGAAGACGGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATT
* *
5385119 GCTTTGACCCACTTCTCTGTATCTCATCAAGAATATGAGGTTTGA
131 GCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGA
5385164 TCCACTTAAT
Statistics
Matches: 324, Mismatches: 54, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
208 5 0.02
209 317 0.98
210 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (209 bp):
TTGATCTACTTTTCTGTATCTCATTAAGAAGATAATCGCTTCATTGTTTTAATCCACTTCTCTGT
ATCTCATCAGGAAGACGGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATT
GCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAAGTTTCACGCACATTGAGC
TTCACTTCATTGAA
Found at i:5390904 original size:17 final size:18
Alignment explanation
Indices: 5390884--5390923 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5390874 CTTTTTCATC
5390884 TTTTATTC-TTTATTTCT
1 TTTTATTCATTTATTTCT
* *
5390901 TTTTCTTCATTTTTTTCT
1 TTTTATTCATTTATTTCT
5390919 TTTTA
1 TTTTA
5390924 AAACAAAACC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTATTCATTTATTTCT
Found at i:5390952 original size:16 final size:16
Alignment explanation
Indices: 5390928--5390958 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5390918 TTTTTAAAAC
5390928 AAAACCCAGATCTGGG
1 AAAACCCAGATCTGGG
*
5390944 AAAATCCAGATCTGG
1 AAAACCCAGATCTGG
5390959 AAATATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.16
Consensus pattern (16 bp):
AAAACCCAGATCTGGG
Found at i:5391622 original size:25 final size:26
Alignment explanation
Indices: 5391594--5391647 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
5391584 GCAATTGTTT
*
5391594 AAAAAGGTTCT-TGTCTT-AATTTCCA
1 AAAAAGGGTCTGTGT-TTCAATTTCCA
*
5391619 AAAAAGGGTGTGTGTTTCAATTTCCA
1 AAAAAGGGTCTGTGTTTCAATTTCCA
5391645 AAA
1 AAA
5391648 CAATGGTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (26 bp):
AAAAAGGGTCTGTGTTTCAATTTCCA
Found at i:5392094 original size:14 final size:14
Alignment explanation
Indices: 5392075--5392102 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5392065 AATTTGATTA
5392075 AAGTAAATTTAAAT
1 AAGTAAATTTAAAT
5392089 AAGTAAATTTAAAT
1 AAGTAAATTTAAAT
5392103 TTAAAATAAA
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:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AAGTAAATTTAAAT
Found at i:5395866 original size:29 final size:30
Alignment explanation
Indices: 5395783--5395869 Score: 108
Period size: 28 Copynumber: 3.0 Consensus size: 30
5395773 GGAGAATTCG
* *
5395783 GGGTCAAAATAAGATTTTTGAAAAGTTTGA
1 GGGTCAAAATATGATTTTGGAAAAGTTTGA
*
5395813 GGGTTAAAATATGATTTTTGG--AAGTTT-A
1 GGGTCAAAATATGA-TTTTGGAAAAGTTTGA
*
5395841 GGGTCAAAATGTGATTTTGGAAAAGTTTG
1 GGGTCAAAATATGATTTTGGAAAAGTTTG
5395870 GAATTTTTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
27 6 0.12
28 13 0.27
29 12 0.25
30 12 0.25
31 5 0.10
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.37
Consensus pattern (30 bp):
GGGTCAAAATATGATTTTGGAAAAGTTTGA
Found at i:5395914 original size:47 final size:46
Alignment explanation
Indices: 5395826--5395917 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 46
5395816 TTAAAATATG
*
5395826 ATTTTTGGAAGTTTAGGGTCAAAATGTGATTTTGGAAAAGTTTGGA
1 ATTTTTGAAAGTTTAGGGTCAAAATGTGATTTTGGAAAAGTTTGGA
* *
5395872 ATTTTTGAAAAGTTTAGGGATTAAAATGTGATTTTGG-GAAGTTTGG
1 ATTTTTG-AAAGTTTAGGG-TCAAAATGTGATTTTGGAAAAGTTTGG
5395918 GGTCAAAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
46 7 0.17
47 18 0.44
48 16 0.39
ACGTcount: A:0.30, C:0.01, G:0.28, T:0.40
Consensus pattern (46 bp):
ATTTTTGAAAGTTTAGGGTCAAAATGTGATTTTGGAAAAGTTTGGA
Found at i:5395915 original size:29 final size:28
Alignment explanation
Indices: 5395874--5396176 Score: 275
Period size: 30 Copynumber: 10.3 Consensus size: 28
5395864 AGTTTGGAAT
*
5395874 TTTTGAAAAGTTTAGGGATTAAAATGTGA
1 TTTTGAAAAGTTTAGGG-TCAAAATGTGA
** *
5395903 TTTTGGGAAGTTTGGGGTCAAAATGTGA
1 TTTTGAAAAGTTTAGGGTCAAAATGTGA
* * *
5395931 TTTTAAGAAAGTTTAAGGGTTAAAATATGA
1 TTTTGA-AAAGTTT-AGGGTCAAAATGTGA
*
5395961 TTTTTGAAAAGTTTAGGTGCCAAAATGTGA
1 -TTTTGAAAAGTTTAGG-GTCAAAATGTGA
* *
5395991 TTTTGAAAAGTTTGAGGGTTAAAATTTGA
1 TTTTGAAAAGTTT-AGGGTCAAAATGTGA
* * *
5396020 TTTTTGGAAAGATTAAGGTCAAAATGTGA
1 -TTTTGAAAAGTTTAGGGTCAAAATGTGA
* *
5396049 TTTTAGAAAAGTTTAAGGGTTAAAATGGGA
1 TTTT-GAAAAGTTT-AGGGTCAAAATGTGA
* * *
5396079 TTTTGGGAAAGTTCGAGGGTCAAAATATGA
1 TTTT-GAAAAGTT-TAGGGTCAAAATGTGA
5396109 TTTTTGAAAAGTTTAGGGGTCAAAATGTGA
1 -TTTTGAAAAGTTTA-GGGTCAAAATGTGA
* *
5396139 TTTTGAAAGAG-TTGGGAGTCAAAATATGA
1 TTTTGAAA-AGTTTAGG-GTCAAAATGTGA
*
5396168 TTTTTAAAA
1 TTTTGAAAA
5396177 AGTTCGAAAG
Statistics
Matches: 222, Mismatches: 39, Indels: 27
0.77 0.14 0.09
Matches are distributed among these distances:
28 21 0.09
29 93 0.42
30 99 0.45
31 9 0.04
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (28 bp):
TTTTGAAAAGTTTAGGGTCAAAATGTGA
Found at i:5395942 original size:76 final size:76
Alignment explanation
Indices: 5395796--5395944 Score: 230
Period size: 76 Copynumber: 2.0 Consensus size: 76
5395786 TCAAAATAAG
* *
5395796 ATTTTTGAAAAGTTTGAGGGTTAAAATATGATTTTTGGAAGTTTAGGGTCAAAATGTGATTTTGG
1 ATTTTTGAAAAGTTTGAGGGTTAAAATATGATTTTGGGAAGTTTAGGGTCAAAATGTGATTTTAG
5395861 AAAAGTTTGGA
66 AAAAGTTTGGA
* *
5395872 ATTTTTGAAAAGTTT-AGGGATTAAAATGTGATTTTGGGAAGTTTGGGGTCAAAATGTGATTTTA
1 ATTTTTGAAAAGTTTGAGGG-TTAAAATATGATTTTGGGAAGTTTAGGGTCAAAATGTGATTTTA
5395936 -AGAAAGTTT
65 GA-AAAGTTT
5395945 AAGGGTTAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
75 5 0.07
76 62 0.93
ACGTcount: A:0.33, C:0.01, G:0.26, T:0.40
Consensus pattern (76 bp):
ATTTTTGAAAAGTTTGAGGGTTAAAATATGATTTTGGGAAGTTTAGGGTCAAAATGTGATTTTAG
AAAAGTTTGGA
Found at i:5396003 original size:59 final size:59
Alignment explanation
Indices: 5395874--5396176 Score: 314
Period size: 59 Copynumber: 5.2 Consensus size: 59
5395864 AGTTTGGAAT
* *
5395874 TTTTGAAAAGTTT-AGGGATTAAAATGTGA-TTTTGGGAAGTTT-GGGGTCAAAATGTGA
1 TTTTGAAAAGTTTAAGGG-TTAAAATGTGATTTTTGGAAAGTTTAGGTGTCAAAATGTGA
* * * *
5395931 TTTTAAGAAAGTTTAAGGGTTAAAATATGATTTTTGAAAAGTTTAGGTGCCAAAATGTGA
1 TTTTGA-AAAGTTTAAGGGTTAAAATGTGATTTTTGGAAAGTTTAGGTGTCAAAATGTGA
* * * *
5395991 TTTTGAAAAGTTTGAGGGTTAAAATTTGATTTTTGGAAAGATTAAG-GTCAAAATGTGA
1 TTTTGAAAAGTTTAAGGGTTAAAATGTGATTTTTGGAAAGTTTAGGTGTCAAAATGTGA
* * * *
5396049 TTTTAGAAAAGTTTAAGGGTTAAAATGGGATTTTGGGAAAGTTCGAGG-GTCAAAATATGA
1 TTTT-GAAAAGTTTAAGGGTTAAAATGTGATTTTTGGAAAGTT-TAGGTGTCAAAATGTGA
* * * * * *
5396109 TTTTTGAAAAGTTTAGGGGTCAAAATGTGA-TTTT-GAAAGAGTTGGGAGTCAAAATATGA
1 -TTTTGAAAAGTTTAAGGGTTAAAATGTGATTTTTGGAAAG-TTTAGGTGTCAAAATGTGA
*
5396168 TTTTTAAAA
1 TTTTGAAAA
5396177 AGTTCGAAAG
Statistics
Matches: 208, Mismatches: 29, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
57 5 0.02
58 47 0.23
59 99 0.48
60 53 0.25
61 4 0.02
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (59 bp):
TTTTGAAAAGTTTAAGGGTTAAAATGTGATTTTTGGAAAGTTTAGGTGTCAAAATGTGA
Found at i:5401491 original size:26 final size:25
Alignment explanation
Indices: 5401437--5401498 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 25
5401427 TTCTTGTACG
5401437 TATTTAATTGAAATAGTTTTTTTGAA
1 TATTTAATTGAAATAGTTTTTTT-AA
5401463 TATTTAATTGAAATAGTTATTATTT-A
1 TATTTAATTGAAATAGTT-TT-TTTAA
5401489 TA-TTAATTGA
1 TATTTAATTGA
5401499 TGATCTTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
25 8 0.24
26 21 0.62
27 2 0.06
28 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (25 bp):
TATTTAATTGAAATAGTTTTTTTAA
Found at i:5401969 original size:44 final size:44
Alignment explanation
Indices: 5401879--5401968 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
5401869 TTGAATTTAA
** *
5401879 TTTAATTTTTTTATTTTTTATTTTGAAGTAAATAAGATTATATT
1 TTTAATTGATTTATTTTTTATTTTGAAGTAAATAAAATTATATT
5401923 TTTAATTGATTTATTTTTTATTTTGAA-TGAAATAAAATTA-ATT
1 TTTAATTGATTTATTTTTTATTTTGAAGT-AAATAAAATTATATT
5401966 TTT
1 TTT
5401969 TTTAGTTAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 7 0.17
44 35 0.83
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (44 bp):
TTTAATTGATTTATTTTTTATTTTGAAGTAAATAAAATTATATT
Found at i:5412146 original size:6 final size:6
Alignment explanation
Indices: 5412137--5412189 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
5412127 GTAGAAGATG
* * * * *
5412137 ATGATA ATGATG ATGTTG ATGATA ATGATA ATGATA ATGATG ATGACA
1 ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA
5412185 ATGAT
1 ATGAT
5412190 GAGGGCAACC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.34
Consensus pattern (6 bp):
ATGATA
Found at i:5412148 original size:9 final size:9
Alignment explanation
Indices: 5412134--5412191 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
5412124 GAAGTAGAAG
5412134 ATGATGATA
1 ATGATGATA
*
5412143 ATGATGATG
1 ATGATGATA
*
5412152 TTGATGAT-
1 ATGATGATA
5412160 A--ATGATA
1 ATGATGATA
* *
5412167 ATGATAATG
1 ATGATGATA
*
5412176 ATGATGACA
1 ATGATGATA
5412185 ATGATGA
1 ATGATGA
5412192 GGGCAACCAT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
6 5 0.13
7 1 0.03
9 32 0.84
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (9 bp):
ATGATGATA
Found at i:5412191 original size:3 final size:3
Alignment explanation
Indices: 5412133--5412182 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
5412123 TGAAGTAGAA
* * * * *
5412133 GAT GAT GAT AAT GAT GAT GTT GAT GAT AAT GAT AAT GAT AAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
5412181 GA
1 GA
5412183 CAATGATGAG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.40, C:0.00, G:0.26, T:0.34
Consensus pattern (3 bp):
GAT
Found at i:5413152 original size:13 final size:13
Alignment explanation
Indices: 5413134--5413158 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5413124 ACAATTTAAG
5413134 AAAAATAAAATTA
1 AAAAATAAAATTA
5413147 AAAAATAAAATT
1 AAAAATAAAATT
5413159 CTCTAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATAAAATTA
Found at i:5413631 original size:25 final size:25
Alignment explanation
Indices: 5413581--5413648 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 25
5413571 TTTTTTTAAA
*
5413581 TTTTAAAGATTTTGTAATTGGAAAAATG
1 TTTT-AAGATTTT-T-ATTGGAAAAAAG
5413609 TTTTAAGATTTTTATTGGAAAAAAG
1 TTTTAAGATTTTTATTGGAAAAAAG
*
5413634 TTATAA-ACTTTTTAT
1 TTTTAAGA-TTTTTAT
5413649 CTATTAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
24 1 0.03
25 23 0.62
26 1 0.03
27 8 0.22
28 4 0.11
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.47
Consensus pattern (25 bp):
TTTTAAGATTTTTATTGGAAAAAAG
Found at i:5414874 original size:6 final size:6
Alignment explanation
Indices: 5414863--5414907 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
5414853 TCACATGTAA
*
5414863 GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT AAGAGT GAGAGT GAG
1 GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAG
5414908 TCATTGTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.36, C:0.00, G:0.49, T:0.16
Consensus pattern (6 bp):
GAGAGT
Found at i:5419731 original size:19 final size:18
Alignment explanation
Indices: 5419695--5419732 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5419685 TGGTTTTCTC
*
5419695 AAAATGAAAATGGAAATG
1 AAAATGAAAACGGAAATG
5419713 AAAATGAAAACGAGAAATG
1 AAAATGAAAACG-GAAATG
5419732 A
1 A
5419733 TTCACTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.63, C:0.03, G:0.21, T:0.13
Consensus pattern (18 bp):
AAAATGAAAACGGAAATG
Found at i:5424638 original size:25 final size:25
Alignment explanation
Indices: 5424604--5424662 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
5424594 AGATTGTGTC
5424604 CAAACCTGACCCGAATTATAGAAAT
1 CAAACCTGACCCGAATTATAGAAAT
5424629 CAAACCTGACCCGAATTATAGAAAT
1 CAAACCTGACCCGAATTATAGAAAT
5424654 CAAACCTGA
1 CAAACCTGA
5424663 ACATTTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.44, C:0.25, G:0.12, T:0.19
Consensus pattern (25 bp):
CAAACCTGACCCGAATTATAGAAAT
Found at i:5424703 original size:17 final size:17
Alignment explanation
Indices: 5424669--5424711 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
5424659 CTGAACATTT
*
5424669 AAAAACATTAAAACTAC
1 AAAAAAATTAAAACTAC
5424686 AAAAAAATTGAAAA-TAC
1 AAAAAAATT-AAAACTAC
*
5424703 ATAAAAATT
1 AAAAAAATT
5424712 TCTTTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.67, C:0.09, G:0.02, T:0.21
Consensus pattern (17 bp):
AAAAAAATTAAAACTAC
Found at i:5435837 original size:28 final size:30
Alignment explanation
Indices: 5435798--5435860 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 30
5435788 ATGGGGTCAA
*
5435798 AAAATGAAATTTAGGAGAA-TTCGA-GGTC
1 AAAATGAAATTTAGGAAAAGTTCGAGGGTC
* **
5435826 AAAATGAGATTTTTGAAAAGTTCGAGGGTC
1 AAAATGAAATTTAGGAAAAGTTCGAGGGTC
5435856 AAAAT
1 AAAAT
5435861 ATGATTTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 15 0.52
29 5 0.17
30 9 0.31
ACGTcount: A:0.43, C:0.06, G:0.24, T:0.27
Consensus pattern (30 bp):
AAAATGAAATTTAGGAAAAGTTCGAGGGTC
Found at i:5435856 original size:30 final size:30
Alignment explanation
Indices: 5435791--5435906 Score: 114
Period size: 30 Copynumber: 3.9 Consensus size: 30
5435781 TAAAAAAATG
* * *
5435791 GGGTCAAAAAATGAAATTTAGGAGAA-TTCGA
1 GGGTCAAAATATG--ATTTTGGAAAAGTTCGA
*
5435822 -GGTCAAAATGA-GATTTTTGAAAAGTTCGA
1 GGGTCAAAAT-ATGATTTTGGAAAAGTTCGA
* *
5435851 GGGTCAAAATATGATTTTGGGAAAGTTTG-
1 GGGTCAAAATATGATTTTGGAAAAGTTCGA
*
5435880 GGGTTAAAATATGATTTTGGAAAAGTT
1 GGGTCAAAATATGATTTTGGAAAAGTT
5435907 TGGAATTTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
28 8 0.11
29 31 0.43
30 32 0.44
31 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (30 bp):
GGGTCAAAATATGATTTTGGAAAAGTTCGA
Found at i:5435896 original size:59 final size:57
Alignment explanation
Indices: 5435826--5436131 Score: 213
Period size: 59 Copynumber: 5.4 Consensus size: 57
5435816 ATTCGAGGTC
*
5435826 AAAATGAGATTTTTGAAAAGTTCGAGGGTCAAAATATGATTTTGGGAAAGTTTGGGGTT
1 AAAATGTGATTTTTGAAAAGTT-GAGGGTCAAAATATGATTTT-GGAAAGTTTGGGGTT
* * * * * **
5435885 AAAATATGATTTTGGAAAAGTT--TGG-----A-AT--TTTTGAAAAATTTAAAGGTT
1 AAAATGTGATTTTTGAAAAGTTGAGGGTCAAAATATGATTTTGGAAAGTTT-GGGGTT
* * * * **
5435933 AAAATGTGATTTTTG-GAAGTTTAGGGTTAAAATGTGATTTAAAGAAAGTTTGAGGGTT
1 AAAATGTGATTTTTGAAAAGTTGAGGGTCAAAATATGATTT-TGGAAAGTTTG-GGGTT
* * *
5435991 AAAATATGATTTTTGAAAAGTTTAAGGGTCAAAATA-GAATTTTGGGAAAGTTTGAGGGTC
1 AAAATGTGATTTTTGAAAAG-TTGAGGGTCAAAATATG-ATTTT-GGAAAGTTTG-GGGTT
* * * * * *
5436051 AAAATGTGATTTTTGAAAAGTTTAGGGTTAAAATATAATTTTGGAAGGGTTTAGGAGTC
1 AAAATGTGATTTTTGAAAAGTTGAGGGTCAAAATATGATTTTGGAA-AGTTT-GGGGTT
*
5436110 AAAATGTGATTTTTAAAAAGTT
1 AAAATGTGATTTTTGAAAAGTT
5436132 CGGGAGATTA
Statistics
Matches: 193, Mismatches: 34, Indels: 40
0.72 0.13 0.15
Matches are distributed among these distances:
47 12 0.06
48 21 0.11
49 2 0.01
50 2 0.01
51 1 0.01
54 1 0.01
55 1 0.01
56 2 0.01
57 3 0.02
58 28 0.15
59 70 0.36
60 50 0.26
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (57 bp):
AAAATGTGATTTTTGAAAAGTTGAGGGTCAAAATATGATTTTGGAAAGTTTGGGGTT
Found at i:5435907 original size:29 final size:29
Alignment explanation
Indices: 5435822--5435909 Score: 115
Period size: 29 Copynumber: 3.0 Consensus size: 29
5435812 GAGAATTCGA
* *
5435822 GGTCAAAATGA-GATTTTTGAAAAGTTCGAG
1 GGTCAAAAT-ATGATTTTGGAAAAGTTTG-G
*
5435852 GGTCAAAATATGATTTTGGGAAAGTTTGG
1 GGTCAAAATATGATTTTGGAAAAGTTTGG
*
5435881 GGTTAAAATATGATTTTGGAAAAGTTTGG
1 GGTCAAAATATGATTTTGGAAAAGTTTGG
5435910 AATTTTTGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
29 29 0.56
30 23 0.44
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.34
Consensus pattern (29 bp):
GGTCAAAATATGATTTTGGAAAAGTTTGG
Found at i:5435947 original size:30 final size:29
Alignment explanation
Indices: 5435911--5436131 Score: 196
Period size: 30 Copynumber: 7.5 Consensus size: 29
5435901 AAAGTTTGGA
* *
5435911 ATTTTTGAAAAATTTAAAGGTTAAAATGTG
1 ATTTTTGAAAAGTTT-AGGGTTAAAATGTG
*
5435941 ATTTTTG-GAAGTTTAGGGTTAAAATGTG
1 ATTTTTGAAAAGTTTAGGGTTAAAATGTG
** *
5435969 A-TTTAAAGAAAGTTTGAGGGTTAAAATATG
1 ATTTTTGA-AAAGTTT-AGGGTTAAAATGTG
* *
5435999 ATTTTTGAAAAGTTTAAGGGTCAAAATAG-A
1 ATTTTTGAAAAGTTT-AGGGTTAAAAT-GTG
* * *
5436029 ATTTTGGGAAAGTTTGAGGGTCAAAATGTG
1 ATTTTTGAAAAGTTT-AGGGTTAAAATGTG
* *
5436059 ATTTTTGAAAAGTTTAGGGTTAAAATATA
1 ATTTTTGAAAAGTTTAGGGTTAAAATGTG
* ** *
5436088 ATTTTGGAAGGGTTTAGGAGTCAAAATGTG
1 ATTTTTGAAAAGTTTAGG-GTTAAAATGTG
*
5436118 ATTTTTAAAAAGTT
1 ATTTTTGAAAAGTT
5436132 CGGGAGATTA
Statistics
Matches: 152, Mismatches: 32, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
27 3 0.02
28 14 0.09
29 38 0.25
30 93 0.61
31 4 0.03
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.38
Consensus pattern (29 bp):
ATTTTTGAAAAGTTTAGGGTTAAAATGTG
Found at i:5436043 original size:60 final size:58
Alignment explanation
Indices: 5435933--5436131 Score: 233
Period size: 59 Copynumber: 3.4 Consensus size: 58
5435923 TTTAAAGGTT
* * ** *
5435933 AAAATGTGATTTTTG-GAAGTTTAGGGTTAAAAT-GTGATTTAAAGAAAGTTTGAGGGTT
1 AAAATGTGATTTTTGAAAAGTTTAGGGTTAAAATAG-AATTT-TGGAAAGTTTGAGGGTC
* *
5435991 AAAATATGATTTTTGAAAAGTTTAAGGGTCAAAATAGAATTTTGGGAAAGTTTGAGGGTC
1 AAAATGTGATTTTTGAAAAGTTT-AGGGTTAAAATAGAATTTT-GGAAAGTTTGAGGGTC
* *
5436051 AAAATGTGATTTTTGAAAAGTTTAGGGTTAAAATATAATTTTGGAAGGGTTT-AGGAGTC
1 AAAATGTGATTTTTGAAAAGTTTAGGGTTAAAATAGAATTTTGGAA-AGTTTGAGG-GTC
*
5436110 AAAATGTGATTTTTAAAAAGTT
1 AAAATGTGATTTTTGAAAAGTT
5436132 CGGGAGATTA
Statistics
Matches: 123, Mismatches: 12, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
58 21 0.17
59 51 0.41
60 50 0.41
61 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (58 bp):
AAAATGTGATTTTTGAAAAGTTTAGGGTTAAAATAGAATTTTGGAAAGTTTGAGGGTC
Found at i:5437832 original size:23 final size:23
Alignment explanation
Indices: 5437805--5437861 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
5437795 GCTAGCGTGT
*
5437805 TTTGGGTTTAGGTCTGTTTAGGA
1 TTTGGGTTTAGATCTGTTTAGGA
5437828 TTTGGGTTTAGATCTGTTTAGGA
1 TTTGGGTTTAGATCTGTTTAGGA
5437851 TTTGGGTTTAG
1 TTTGGGTTTAG
5437862 TGGTATTGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.14, C:0.04, G:0.33, T:0.49
Consensus pattern (23 bp):
TTTGGGTTTAGATCTGTTTAGGA
Found at i:5437838 original size:13 final size:13
Alignment explanation
Indices: 5437820--5437861 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
5437810 GTTTAGGTCT
5437820 GTTTAGGATTTGG
1 GTTTAGGATTTGG
*
5437833 GTTTA-GATCT--
1 GTTTAGGATTTGG
5437843 GTTTAGGATTTGG
1 GTTTAGGATTTGG
5437856 GTTTAG
1 GTTTAG
5437862 TGGTATTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 5 0.21
11 4 0.17
12 4 0.17
13 11 0.46
ACGTcount: A:0.17, C:0.02, G:0.33, T:0.48
Consensus pattern (13 bp):
GTTTAGGATTTGG
Found at i:5438706 original size:73 final size:73
Alignment explanation
Indices: 5438585--5438724 Score: 271
Period size: 73 Copynumber: 1.9 Consensus size: 73
5438575 GATGATTGAA
*
5438585 TCATGATTAGAAAAATAGAGCGTAATGCCACCGATTGATCAGATAGCACTGACGAGTACTGTAGC
1 TCATGATTAGAAAAATAGAGCGTAATGCCACCGATTGATCAGACAGCACTGACGAGTACTGTAGC
5438650 ATACGATG
66 ATACGATG
5438658 TCATGATTAGAAAAATAGAGCGTAATGCCACCGATTGATCAGACAGCACTGACGAGTACTGTAGC
1 TCATGATTAGAAAAATAGAGCGTAATGCCACCGATTGATCAGACAGCACTGACGAGTACTGTAGC
5438723 AT
66 AT
5438725 TAGATTAATT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (73 bp):
TCATGATTAGAAAAATAGAGCGTAATGCCACCGATTGATCAGACAGCACTGACGAGTACTGTAGC
ATACGATG
Found at i:5439117 original size:19 final size:19
Alignment explanation
Indices: 5439093--5439130 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5439083 CCACTGTCAC
*
5439093 CTATCGTAATCAAATTTGT
1 CTATCGTAATCAAAATTGT
5439112 CTATCGTAATCAAAATTGT
1 CTATCGTAATCAAAATTGT
5439131 TATTAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (19 bp):
CTATCGTAATCAAAATTGT
Found at i:5441389 original size:31 final size:31
Alignment explanation
Indices: 5441300--5441392 Score: 93
Period size: 31 Copynumber: 3.0 Consensus size: 31
5441290 ATTTTTTAAA
* * *
5441300 ATATGTATAATTAAATCAAAATTAAAATTT-T
1 ATATATATAATTATATC-AAATCAAAATTTAT
*
5441331 ATATATAT-ATTATAACCATAATC-AAATTTAT
1 ATATATATAATTAT-ATCA-AATCAAAATTTAT
*
5441362 ATATATATAATTGTATCAAATCAAAATTTAT
1 ATATATATAATTATATCAAATCAAAATTTAT
5441393 CAAACCGTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
30 15 0.29
31 32 0.63
32 4 0.08
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (31 bp):
ATATATATAATTATATCAAATCAAAATTTAT
Found at i:5441579 original size:13 final size:13
Alignment explanation
Indices: 5441539--5441585 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
5441529 TTCTTGTAGG
5441539 TATTTAATTGAAA
1 TATTTAATTGAAA
**
5441552 TAGTTTTTTTG-AA
1 TA-TTTAATTGAAA
5441565 TATTTAATTGAAA
1 TATTTAATTGAAA
*
5441578 TAGTTAAT
1 TATTTAAT
5441586 ATTTATATTC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
12 6 0.22
13 15 0.56
14 6 0.22
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (13 bp):
TATTTAATTGAAA
Found at i:5442060 original size:44 final size:44
Alignment explanation
Indices: 5441970--5442059 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
5441960 TCGAATTTAA
** *
5441970 TTTAATTTTTTTATTTTTTATTTTAAAGTAAATAAGATTATATT
1 TTTAATTGATTTATTTTTTATTTTAAAGTAAATAAAATTATATT
5442014 TTTAATTGATTTATTTTTTATTTTAAA-TGAAATAAAATTA-ATT
1 TTTAATTGATTTATTTTTTATTTTAAAGT-AAATAAAATTATATT
5442057 TTT
1 TTT
5442060 TTTAGTTTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 7 0.17
44 35 0.83
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (44 bp):
TTTAATTGATTTATTTTTTATTTTAAAGTAAATAAAATTATATT
Found at i:5444298 original size:155 final size:156
Alignment explanation
Indices: 5443994--5444311 Score: 613
Period size: 155 Copynumber: 2.0 Consensus size: 156
5443984 AAACAAGGTA
5443994 TAAAATACTCTCCATAATTACCACAAAACTCTCACTAAAACTCATATGCAGTTACATCTTGCCGT
1 TAAAATACTCTCCATAATTACCACAAAACTCTCACTAAAACTCATATGCAGTTACATCTTGCCGT
5444059 CCCAAAAAAAAAAACCCTTTTTCTGATTGGCATCTCAAAAGAGAGATACAAGGTCCCTTAAAATA
66 CCCAAAAAAAAAAACCCTTTTTCTGATTGGCATCTCAAAAGAGAGATACAAGGTCCCTTAAAATA
5444124 AGCTAAGATTAGAGTTCTAATTATAG
131 AGCTAAGATTAGAGTTCTAATTATAG
5444150 TAAAATACTCTCCATAATTACCACAAAACTCTCACTAAAACTCATATGCAGTTACATCTTGCCGT
1 TAAAATACTCTCCATAATTACCACAAAACTCTCACTAAAACTCATATGCAGTTACATCTTGCCGT
5444215 CCC-AAAAAAAAAACCCTTTTTCTGATTGGCATCTCAAAAGAGAGATACAAGGT-CCTTGAAAAT
66 CCCAAAAAAAAAAACCCTTTTTCTGATTGGCATCTCAAAAGAGAGATACAAGGTCCCTT-AAAAT
5444278 AAGCTAAGATTAGAGTTCTAATTATAG
130 AAGCTAAGATTAGAGTTCTAATTATAG
5444305 TAAAATA
1 TAAAATA
5444312 TCTTGTCGAA
Statistics
Matches: 161, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
154 4 0.02
155 89 0.55
156 68 0.42
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (156 bp):
TAAAATACTCTCCATAATTACCACAAAACTCTCACTAAAACTCATATGCAGTTACATCTTGCCGT
CCCAAAAAAAAAAACCCTTTTTCTGATTGGCATCTCAAAAGAGAGATACAAGGTCCCTTAAAATA
AGCTAAGATTAGAGTTCTAATTATAG
Found at i:5445459 original size:29 final size:29
Alignment explanation
Indices: 5445427--5445617 Score: 95
Period size: 29 Copynumber: 6.5 Consensus size: 29
5445417 AACCGACATC
5445427 AAAAATGGAATTTTTGAACATTCAGGGGT
1 AAAAATGGAATTTTTGAACATTCAGGGGT
* * * *
5445456 -AAAATGGTAATATTTAGAAGAATC-GGGAT
1 AAAAATGG-AAT-TTTTGAACATTCAGGGGT
* * * *
5445485 CAAAAATAGAATTTTTTG-ACATACGGGGGC
1 -AAAAATGGAA-TTTTTGAACATTCAGGGGT
* * **
5445515 AAAAATGTAATTTTTGGAA-GTTCGAGGGCA
1 AAAAATGGAATTTTT-GAACATTC-AGGGGT
* **
5445545 AAAAATGAAATTTTTGGAAGTTTCA-GGGT
1 AAAAATGGAATTTTT-GAACATTCAGGGGT
* * * * *
5445574 CAAATTGGAATTTTTGAAAATTTAGGGGC
1 AAAAATGGAATTTTTGAACATTCAGGGGT
*
5445603 AAAAATGTAATTTTT
1 AAAAATGGAATTTTT
5445618 AAAAGTTTCA
Statistics
Matches: 119, Mismatches: 32, Indels: 22
0.69 0.18 0.13
Matches are distributed among these distances:
28 18 0.15
29 50 0.42
30 41 0.34
31 10 0.08
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (29 bp):
AAAAATGGAATTTTTGAACATTCAGGGGT
Found at i:5445460 original size:59 final size:59
Alignment explanation
Indices: 5445248--5445534 Score: 249
Period size: 59 Copynumber: 4.8 Consensus size: 59
5445238 TTTTGGGGTT
* * * * * * * * * *
5445248 AAAAAT-GAAATTTTAGAAATTCGAGGGCAAAATGGTGATTTTTAAAAAAAATCAAGATAA
1 AAAAATAGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTT-AGAAGAATCGAGAT-C
* * *
5445308 AAAAATAGAATTTTTGGACA-TCTGGGGGTAAAACGGTAATTTTTAGAAAAAAATCAAGATC
1 AAAAATAGAATTTTTGGACATTC-GGGGGTAAAATGGTAATTTTTAG--AAGAATCGAGATC
* * * * *
5445369 -AAAATGGAATTTTTGGATATTTGGGGGTAAAATGGTAATTTTTAGAAGAACCGACATC
1 AAAAATAGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTAGAAGAATCGAGATC
* * * * *
5445427 AAAAATGGAATTTTTGAACATTCAGGGGTAAAATGGTAATATTTAGAAGAATCGGGATC
1 AAAAATAGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTAGAAGAATCGAGATC
* * * *
5445486 AAAAATAGAATTTTTTGACATACGGGGGCAAAAAT-GTAATTTTTGGAAG
1 AAAAATAGAATTTTTGGACATTCGGGGG-TAAAATGGTAATTTTTAGAAG
5445535 TTCGAGGGCA
Statistics
Matches: 187, Mismatches: 33, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
58 9 0.05
59 85 0.45
60 53 0.28
61 28 0.15
62 12 0.06
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (59 bp):
AAAAATAGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTAGAAGAATCGAGATC
Found at i:5445520 original size:119 final size:117
Alignment explanation
Indices: 5445308--5445534 Score: 260
Period size: 119 Copynumber: 1.9 Consensus size: 117
5445298 ATCAAGATAA
* * *
5445308 AAAAATAGAATTTTTGGACATCTGGGGGTAAAACGGTAATTTTTAGAAAAAAATCAAGATCAAAA
1 AAAAATAGAATTTTTGAACATCTAGGGGTAAAACGGTAATATTTAG-AAAAAATCAAGATCAAAA
* * ** *
5445373 TGGAATTTTTGGATATTTGGGGGTAAAATGGTAATTTTTAGAAGAACCGACATC
65 TAGAATTTTTGGACATACGGGGGAAAAAT-GTAATTTTTAGAAGAACCGACATC
* * * **
5445427 AAAAATGGAATTTTTGAACAT-TCAGGGGTAAAATGGTAATATTTAG-AAGAATCGGGATCAAAA
1 AAAAATAGAATTTTTGAACATCT-AGGGGTAAAACGGTAATATTTAGAAAAAATCAAGATC-AAA
* *
5445490 ATAGAATTTTTTGACATACGGGGGCAAAAATGTAATTTTTGGAAG
64 ATAGAATTTTTGGACATACGGGGG-AAAAATGTAATTTTTAGAAG
5445535 TTCGAGGGCA
Statistics
Matches: 90, Mismatches: 15, Indels: 7
0.80 0.13 0.06
Matches are distributed among these distances:
117 10 0.11
118 36 0.40
119 44 0.49
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (117 bp):
AAAAATAGAATTTTTGAACATCTAGGGGTAAAACGGTAATATTTAGAAAAAATCAAGATCAAAAT
AGAATTTTTGGACATACGGGGGAAAAATGTAATTTTTAGAAGAACCGACATC
Found at i:5445551 original size:30 final size:29
Alignment explanation
Indices: 5445511--5445659 Score: 115
Period size: 30 Copynumber: 5.0 Consensus size: 29
5445501 TGACATACGG
5445511 GGGCAAAAATGTAATTTTTGGAAGTTCGA
1 GGGCAAAAATGTAATTTTTGGAAGTTCGA
*
5445540 GGGCAAAAAATGAAATTTTTGGAAGTTTC-A
1 GGGC-AAAAATGTAATTTTTGGAAG-TTCGA
* * * * *
5445570 GGGTC-AAATTGGAATTTTTGAAAATT-TA
1 GGG-CAAAAATGTAATTTTTGGAAGTTCGA
** *
5445598 GGGGCAAAAATGTAATTTTTAAAAGTTTCAA
1 -GGGCAAAAATGTAATTTTTGGAAG-TTCGA
* * *
5445629 GGTCAAAAATGTAGTTTTAGAGAAGTTCGA
1 GGGCAAAAATGTAATTTTTG-GAAGTTCGA
5445659 G
1 G
5445660 AGTCAAAATA
Statistics
Matches: 95, Mismatches: 16, Indels: 17
0.74 0.12 0.13
Matches are distributed among these distances:
28 4 0.04
29 37 0.39
30 46 0.48
31 8 0.08
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (29 bp):
GGGCAAAAATGTAATTTTTGGAAGTTCGA
Found at i:5445675 original size:88 final size:87
Alignment explanation
Indices: 5445510--5445677 Score: 189
Period size: 88 Copynumber: 1.9 Consensus size: 87
5445500 TTGACATACG
** * * *
5445510 GGGGCAAAAATGTAATTTTTGGAAGTTCGAGGGCAAAAAATGAAATTTTTGGAAGTTTCAGGGTC
1 GGGGCAAAAATGTAATTTTTAAAAGTTCAAGGGCAAAAAATGAAATTTTAGGAAGTTTCAGAGTC
*
5445575 AAATTGGAATTTTTGAAAATTTA
66 AAAAT-GAATTTTTGAAAATTTA
* * *
5445598 GGGGCAAAAATGTAATTTTTAAAAGTTTCAAGGTC-AAAAATGTAGTTTTAGAGAAG-TTCGAGA
1 GGGGCAAAAATGTAATTTTTAAAAG-TTCAAGGGCAAAAAATGAAATTTTAG-GAAGTTTC-AGA
5445661 GTCAAAAT-ACATTTTTG
63 GTCAAAATGA-ATTTTTG
5445678 GATAGTTTAG
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
87 1 0.01
88 46 0.69
89 20 0.30
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.33
Consensus pattern (87 bp):
GGGGCAAAAATGTAATTTTTAAAAGTTCAAGGGCAAAAAATGAAATTTTAGGAAGTTTCAGAGTC
AAAATGAATTTTTGAAAATTTA
Found at i:5446209 original size:16 final size:15
Alignment explanation
Indices: 5446188--5446217 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5446178 TTAAGTTAAA
5446188 ATTTCATTTCTTTTTC
1 ATTTCATTT-TTTTTC
5446204 ATTTCATTTTTTTT
1 ATTTCATTTTTTTT
5446218 AAAAACCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTCATTTTTTTTC
Found at i:5447134 original size:25 final size:26
Alignment explanation
Indices: 5447083--5447136 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
5447073 CTGATTTTTG
* *
5447083 TATTGATTCTCAGAAAAGAGTTTGTA
1 TATTGATTCTCAAAAAAGAGTTCGTA
*
5447109 TATTGATTTTCAAAAAAG-GTTCGTA
1 TATTGATTCTCAAAAAAGAGTTCGTA
5447134 TAT
1 TAT
5447137 ATTTTTCAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41
Consensus pattern (26 bp):
TATTGATTCTCAAAAAAGAGTTCGTA
Found at i:5447550 original size:6 final size:6
Alignment explanation
Indices: 5447541--5447602 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
5447531 AATTTAAAGC
** *
5447541 AAATTT AAATTT AAAAAGAT AAATTT AAATTT AAA-AT AAATTT AAATTT
1 AAATTT AAATTT --AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
**
5447590 AAAAAT AAATTT A
1 AAATTT AAATTT A
5447603 GATCAATTTA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
5 4 0.09
6 35 0.81
8 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (6 bp):
AAATTT
Found at i:5447550 original size:17 final size:17
Alignment explanation
Indices: 5447525--5447602 Score: 84
Period size: 17 Copynumber: 4.4 Consensus size: 17
5447515 GTTTTAAATT
* *
5447525 AATTCAAATTTAAAGCA
1 AATTTAAATTTAAAGTA
5447542 AATTTAAATTTAAAAAGATA
1 AATTTAAATTT--AAAG-TA
*
5447562 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAGTA
*
5447579 AATTTAAATTTAAAAATA
1 AATTTAAATTT-AAAGTA
5447597 AATTTA
1 AATTTA
5447603 GATCAATTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
17 23 0.43
18 15 0.28
19 4 0.07
20 12 0.22
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (17 bp):
AATTTAAATTTAAAGTA
Found at i:5447572 original size:37 final size:35
Alignment explanation
Indices: 5447520--5447602 Score: 112
Period size: 37 Copynumber: 2.3 Consensus size: 35
5447510 ATTAAGTTTT
* * *
5447520 AAATTAATTCAAATTTAAAGCAAATTTAAATTTAAA
1 AAATAAATTTAAATTTAAAACAAATTTAAATTT-AA
*
5447556 AAGATAAATTTAAATTTAAAATAAATTTAAATTTAA
1 AA-ATAAATTTAAATTTAAAACAAATTTAAATTTAA
5447592 AAATAAATTTA
1 AAATAAATTTA
5447603 GATCAATTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
35 9 0.21
36 6 0.14
37 27 0.64
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (35 bp):
AAATAAATTTAAATTTAAAACAAATTTAAATTTAA
Found at i:5448046 original size:92 final size:92
Alignment explanation
Indices: 5447887--5448667 Score: 1332
Period size: 92 Copynumber: 8.5 Consensus size: 92
5447877 TGATGTCGAG
* *
5447887 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGAGATAAAGACTTGTTATCCAACTTTACTGCAA
1 GCTTCATCTTGCTCTTACTACAACTTC--AGAGAGATAAAGACTTGCTATCCAACTTTACTACAA
*
5447952 CTTCAAGAGGATAAGAATTGATGTTTGT-A
64 CTTCAAGAGGATAGGAATTGATGTTT-TAA
5447981 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
5448046 TCAAGAGGATAGGAATTGATGTTTTAA
66 TCAAGAGGATAGGAATTGATGTTTTAA
*
5448073 GCTTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
5448138 TCAAGAGGATAGGAATTGATGTTTTAA
66 TCAAGAGGATAGGAATTGATGTTTTAA
* * *
5448165 GATTCATCTTGCTCTTACTACAACTTCAGATAGATAAAGACTTGCTATCCAATTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
5448230 TCAAGAGGATAGGAATTGATGTTTTAA
66 TCAAGAGGATAGGAATTGATGTTTTAA
*
5448257 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTATTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
* * *
5448322 TCAAGAGGATAGGGATTAATGTTTGAA
66 TCAAGAGGATAGGAATTGATGTTTTAA
*
5448349 ACTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
*
5448414 TCAAGAGGATAGGAATTGATGTTTGAA
66 TCAAGAGGATAGGAATTGATGTTTTAA
* *
5448441 ACTTAATC-TGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
5448505 TCAAGAGGATAGGAATTGATGTTTTAA
66 TCAAGAGGATAGGAATTGATGTTTTAA
* *
5448532 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGGTATCCAACTTTACTATAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
* * * *
5448597 TCAAGAGAATAGGGATTAATGTTTGAA
66 TCAAGAGGATAGGAATTGATGTTTTAA
5448624 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTG
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTG
5448668 TTATTTTGAT
Statistics
Matches: 656, Mismatches: 29, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
91 89 0.14
92 540 0.82
94 27 0.04
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (92 bp):
GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
TCAAGAGGATAGGAATTGATGTTTTAA
Found at i:5454054 original size:41 final size:41
Alignment explanation
Indices: 5453959--5454057 Score: 98
Period size: 38 Copynumber: 2.5 Consensus size: 41
5453949 AGCAATAAAG
* * **
5453959 TGACACCCAGTGTCTCATCG-GCCTAGCCGAAGTAAAGTGG
1 TGACACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAATAA
** * *
5453999 TG---CCCAGTACCTCATCGAATCTATCCGAAGTAAAATAA
1 TGACACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAATAA
5454037 TGACACCCAGTGTCTCATCGA
1 TGACACCCAGTGTCTCATCGA
5454058 CTCGAGGTCG
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
37 13 0.29
38 16 0.36
40 2 0.04
41 14 0.31
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (41 bp):
TGACACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAATAA
Found at i:5454978 original size:13 final size:12
Alignment explanation
Indices: 5454908--5454989 Score: 60
Period size: 13 Copynumber: 6.6 Consensus size: 12
5454898 TTCATATACA
*
5454908 TATATATATTAGT
1 TATA-ATATTAAT
*
5454921 TAATAATAATAA-
1 T-ATAATATTAAT
*
5454933 TATAATACTAAT
1 TATAATATTAAT
*
5454945 TA-AATAATAATT
1 TATAATATTAA-T
*
5454957 TATATTATTATAT
1 TATAATATTA-AT
5454970 TATAATATTAAT
1 TATAATATTAAT
5454982 TAATAATA
1 T-ATAATA
5454990 AAAAAATCAA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
11 16 0.29
12 9 0.16
13 27 0.48
14 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (12 bp):
TATAATATTAAT
Found at i:5462876 original size:29 final size:31
Alignment explanation
Indices: 5462823--5462890 Score: 104
Period size: 30 Copynumber: 2.2 Consensus size: 31
5462813 GTAAAACAGT
5462823 AATTTTTAGAAAAAAATCGGGATC-AAAATGG
1 AATTTTTAG-AAAAAATCGGGATCAAAAATGG
*
5462854 AATTTTTAG-AAGAATCGGGATCAAAAATGG
1 AATTTTTAGAAAAAATCGGGATCAAAAATGG
5462884 AATTTTT
1 AATTTTT
5462891 GAACATTCGG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
29 12 0.34
30 14 0.40
31 9 0.26
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (31 bp):
AATTTTTAGAAAAAATCGGGATCAAAAATGG
Found at i:5462883 original size:30 final size:30
Alignment explanation
Indices: 5462823--5462924 Score: 109
Period size: 29 Copynumber: 3.4 Consensus size: 30
5462813 GTAAAACAGT
*
5462823 AATTTTTAGAAAAAAATCGGGATC-AAAATGG
1 AATTTTTAG--AAGAATCGGGATCAAAAATGG
5462854 AATTTTTAGAAGAATCGGGATCAAAAATGG
1 AATTTTTAGAAGAATCGGGATCAAAAATGG
* * ** *
5462884 AATTTTT-GAACATTCGGGGGCAAAAATGT
1 AATTTTTAGAAGAATCGGGATCAAAAATGG
*
5462913 AATTTTTGGAAG
1 AATTTTTAGAAG
5462925 TTCGAGGGTA
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
29 36 0.58
30 17 0.27
31 9 0.15
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (30 bp):
AATTTTTAGAAGAATCGGGATCAAAAATGG
Found at i:5462917 original size:59 final size:60
Alignment explanation
Indices: 5462847--5462979 Score: 144
Period size: 59 Copynumber: 2.2 Consensus size: 60
5462837 AATCGGGATC
* * *
5462847 AAAATGGAATTTTTAGAAGAATCG-GGATCAAAAATGGAATTTTT-GAACATTCGGGGGCA
1 AAAATGTAATTTTTAGAAG-ATCGAGGATAAAAAATGGAATTTTTGGAACATTCGGGGGAA
* * * * ** * *
5462906 AAAATGTAATTTTTGGAAGTTCGAGGGTAAAAAATGTAATTTTTGGAATTTTTGGGGTAA
1 AAAATGTAATTTTTAGAAGATCGAGGATAAAAAATGGAATTTTTGGAACATTCGGGGGAA
5462966 AAAATGTAATTTTT
1 AAAATGTAATTTTT
5462980 GGAAAGTTTG
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
58 3 0.05
59 34 0.56
60 24 0.39
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.35
Consensus pattern (60 bp):
AAAATGTAATTTTTAGAAGATCGAGGATAAAAAATGGAATTTTTGGAACATTCGGGGGAA
Found at i:5462928 original size:29 final size:29
Alignment explanation
Indices: 5462839--5463017 Score: 148
Period size: 30 Copynumber: 6.0 Consensus size: 29
5462829 TAGAAAAAAA
* * * *
5462839 TCGGGATC-AAAATGGAATTTTTAGAAGAA
1 TCGGGGTCAAAAATGTAATTTTTGGAAG-T
* * *
5462868 TCGGGATCAAAAATGGAATTTTT-GAACAT
1 TCGGGGTCAAAAATGTAATTTTTGGAA-GT
*
5462897 TCGGGGGCAAAAATGTAATTTTTGGAAGT
1 TCGGGGTCAAAAATGTAATTTTTGGAAGT
* *
5462926 TCGAGGGTAAAAAATGTAATTTTTGGAATTT
1 TCG-GGGTCAAAAATGTAATTTTTGGAA-GT
* *
5462957 TTGGGGTAAAAAATGTAATTTTTGGAAAGT
1 TCGGGGTCAAAAATGTAATTTTTGG-AAGT
* *
5462987 TTGGGTGTC-AAAATATAATTTTTGGATAGT
1 TCGGG-GTCAAAAATGTAATTTTTGGA-AGT
5463017 T
1 T
5463018 TAGGGACTTT
Statistics
Matches: 129, Mismatches: 13, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
29 36 0.28
30 86 0.67
31 7 0.05
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (29 bp):
TCGGGGTCAAAAATGTAATTTTTGGAAGT
Found at i:5467085 original size:43 final size:43
Alignment explanation
Indices: 5466994--5467147 Score: 193
Period size: 43 Copynumber: 3.6 Consensus size: 43
5466984 CCGCTATAGA
* * * * *
5466994 TCTTTAGCGGCGCTT-TTCCAAAAACACCACTAATGAACATGG
1 TCTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGAACATGG
* * *
5467036 TATTTAGCGGCGCTTATCCCACAGATGCCGCTAAAGAACATGG
1 TCTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGAACATGG
* ** *
5467079 TCTTTAGCGACGCTTATTTCACAAACGCCGCTAAAGAACGTGG
1 TCTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGAACATGG
5467122 TCTTTAGCGGCGCTTATCCCACAAAC
1 TCTTTAGCGGCGCTTATCCCACAAAC
5467148 ACCAATAACA
Statistics
Matches: 93, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
42 14 0.15
43 79 0.85
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (43 bp):
TCTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGAACATGG
Found at i:5470915 original size:23 final size:26
Alignment explanation
Indices: 5470889--5470945 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 26
5470879 TATTTGAAAT
5470889 AAAATTTTATCTGA-A-AACAAAAA-
1 AAAATTTTATCTGATACAACAAAAAC
* *
5470912 AAAAATATATCTGATACAACAAAAAC
1 AAAATTTTATCTGATACAACAAAAAC
*
5470938 ATAATTTT
1 AAAATTTT
5470946 TAAAAAACAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 12 0.46
24 1 0.04
25 8 0.31
26 5 0.19
ACGTcount: A:0.58, C:0.11, G:0.04, T:0.28
Consensus pattern (26 bp):
AAAATTTTATCTGATACAACAAAAAC
Found at i:5472808 original size:41 final size:40
Alignment explanation
Indices: 5472763--5472862 Score: 139
Period size: 41 Copynumber: 2.5 Consensus size: 40
5472753 TCGTAAGCAT
* *
5472763 CGCTATTGCTCTAACTTTTAGCGGCGCTTTCCCATAAA-CGC
1 CGCTATTGCTCT-ACTTTTAACGGCGCTTT-CCAAAAAGCGC
*
5472804 CGCTATTGCTCTGACCTTTAACGGCGCTTTCCAAAAAGCGC
1 CGCTATTGCTCT-ACTTTTAACGGCGCTTTCCAAAAAGCGC
5472845 CGCTATTGCTCTACTTTT
1 CGCTATTGCTCTACTTTT
5472863 TGCGATGTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
40 11 0.21
41 42 0.79
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (40 bp):
CGCTATTGCTCTACTTTTAACGGCGCTTTCCAAAAAGCGC
Found at i:5478108 original size:6 final size:6
Alignment explanation
Indices: 5478099--5478145 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
5478089 GTAGAAGATG
* * * *
5478099 ATGATA ATGATG ATGTTA ATGATA ATGATA ATGATG ATGACA ATGAT
1 ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA ATGAT
5478146 GAGGGCAACC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.34
Consensus pattern (6 bp):
ATGATA
Found at i:5478110 original size:9 final size:9
Alignment explanation
Indices: 5478096--5478147 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
5478086 GAAGTAGAAG
5478096 ATGATGATA
1 ATGATGATA
*
5478105 ATGATGATG
1 ATGATGATA
* *
5478114 TTAATGATA
1 ATGATGATA
* *
5478123 ATGATAATG
1 ATGATGATA
*
5478132 ATGATGACA
1 ATGATGATA
5478141 ATGATGA
1 ATGATGA
5478148 GGGCAACCAT
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.33
Consensus pattern (9 bp):
ATGATGATA
Found at i:5478112 original size:12 final size:12
Alignment explanation
Indices: 5478095--5478147 Score: 79
Period size: 12 Copynumber: 4.4 Consensus size: 12
5478085 TGAAGTAGAA
5478095 GATGATGATAAT
1 GATGATGATAAT
*
5478107 GATGATGTTAAT
1 GATGATGATAAT
*
5478119 GATAATGATAAT
1 GATGATGATAAT
*
5478131 GATGATGACAAT
1 GATGATGATAAT
5478143 GATGA
1 GATGA
5478148 GGGCAACCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.32
Consensus pattern (12 bp):
GATGATGATAAT
Found at i:5478122 original size:18 final size:18
Alignment explanation
Indices: 5478095--5478145 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
5478085 TGAAGTAGAA
*
5478095 GATGATGATAATGATGAT
1 GATGATGATAATGATAAT
* *
5478113 GTTAATGATAATGATAAT
1 GATGATGATAATGATAAT
*
5478131 GATGATGACAATGAT
1 GATGATGATAATGAT
5478146 GAGGGCAACC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (18 bp):
GATGATGATAATGATAAT
Found at i:5481543 original size:21 final size:20
Alignment explanation
Indices: 5481519--5481568 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
5481509 AAAATGTATG
* *
5481519 AAATTCTCATTAAATCTTCCA
1 AAATTCTAATCAAATC-TCCA
*
5481540 AAATTTTAATCAAATCTCCA
1 AAATTCTAATCAAATCTCCA
5481560 AAATT-TAAT
1 AAATTCTAAT
5481569 GTCAAGATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 4 0.15
20 9 0.35
21 13 0.50
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATTCTAATCAAATCTCCA
Found at i:5481946 original size:19 final size:18
Alignment explanation
Indices: 5481910--5481947 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5481900 TGGTTTTCTC
*
5481910 AAAATGAAAATGGAAATG
1 AAAATGAAAACGGAAATG
5481928 AAAATGAAAACGAGAAATG
1 AAAATGAAAACG-GAAATG
5481947 A
1 A
5481948 TTCATTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.63, C:0.03, G:0.21, T:0.13
Consensus pattern (18 bp):
AAAATGAAAACGGAAATG
Found at i:5482525 original size:24 final size:24
Alignment explanation
Indices: 5482456--5482518 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
5482446 AGAAATAATC
*
5482456 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAGTTG
* *
5482480 TTTCAATTAAATTCTGTTTAGTTG
1 TTTCAGTTAAACTCTGTTTAGTTG
*
5482504 TTTGAGTTAAACTCT
1 TTTCAGTTAAACTCT
5482519 TATTAGTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.52
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAGTTG
Found at i:5484459 original size:24 final size:24
Alignment explanation
Indices: 5484431--5484493 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
5484421 AAAAATAATC
*
5484431 TTTCAGTTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTAGTTG
* * *
5484455 TTTCAATTAAATTCTGTTTAGTTG
1 TTTCAGTTAAACTCTATTTAGTTG
* *
5484479 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
5484494 TATTAGTCTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTAGTTG
Found at i:5489606 original size:18 final size:18
Alignment explanation
Indices: 5489583--5489619 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5489573 ATAGTTTTTT
5489583 ACACCCAAGGTCTTCTTC
1 ACACCCAAGGTCTTCTTC
5489601 ACACCCAAGGTCTTCTTC
1 ACACCCAAGGTCTTCTTC
5489619 A
1 A
5489620 TGTTATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.38, G:0.11, T:0.27
Consensus pattern (18 bp):
ACACCCAAGGTCTTCTTC
Found at i:5491174 original size:23 final size:23
Alignment explanation
Indices: 5491119--5491175 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
5491109 ATATCCAAAT
* *
5491119 AATATGAAAAACGATAGCGAAAC
1 AATATAAAAAACGATAACGAAAC
* * *
5491142 AACATTAAAAACGATAACGAAAG
1 AATATAAAAAACGATAACGAAAC
5491165 AATATAAAAAA
1 AATATAAAAAA
5491176 ATGCACAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.63, C:0.11, G:0.12, T:0.14
Consensus pattern (23 bp):
AATATAAAAAACGATAACGAAAC
Found at i:5498146 original size:2 final size:2
Alignment explanation
Indices: 5498139--5498163 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5498129 AATACTCCAT
5498139 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
5498164 TTTTTTTTTT
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:5499101 original size:17 final size:16
Alignment explanation
Indices: 5499075--5499113 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
5499065 TAAAAACTCA
5499075 TTTTATTTTTAATTTT
1 TTTTATTTTTAATTTT
*
5499091 TTTTCATTTTTAGTTTT
1 TTTT-ATTTTTAATTTT
5499108 TTTTAT
1 TTTTAT
5499114 AAATCTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTATTTTTAATTTT
Found at i:5500629 original size:5 final size:5
Alignment explanation
Indices: 5500619--5500643 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5500609 GTTTTCACAA
5500619 TAATT TAATT TAATT TAATT TAATT
1 TAATT TAATT TAATT TAATT TAATT
5500644 CTTTCTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TAATT
Done.