Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 139 of 172
Found at i:40003608 original size:26 final size:26
Alignment explanation
Indices: 40003579--40003642 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
40003569 AGTTCTTCAT
*
40003579 TGCTTTTAAAAAGTACTTTTGAGAAG
1 TGCTTTTGAAAAGTACTTTTGAGAAG
* * *
40003605 TGCTGTGGAAAAGTGCTTTTGAGAAG
1 TGCTTTTGAAAAGTACTTTTGAGAAG
*
40003631 TGTTTTTGAAAA
1 TGCTTTTGAAAA
40003643 TTTTGAGTGT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (26 bp):
TGCTTTTGAAAAGTACTTTTGAGAAG
Found at i:40008105 original size:2 final size:2
Alignment explanation
Indices: 40008098--40008144 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
40008088 GAGGTTTAGA
40008098 AG AG AG AG AG AG 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
40008140 AG AG A
1 AG AG A
40008145 AGCAAAGTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40008447 original size:16 final size:16
Alignment explanation
Indices: 40008408--40008450 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
40008398 GTATTGGATC
* * *
40008408 AGAGGTGCATTGAATT
1 AGAGGTGTAATGAAAT
40008424 AGAGGTGTAATGAAAT
1 AGAGGTGTAATGAAAT
40008440 AGAGGTGTAAT
1 AGAGGTGTAAT
40008451 AGCAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.33, T:0.28
Consensus pattern (16 bp):
AGAGGTGTAATGAAAT
Found at i:40008705 original size:18 final size:17
Alignment explanation
Indices: 40008684--40008718 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40008674 TTATTATTAA
*
40008684 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
40008702 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
40008719 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:40008772 original size:157 final size:157
Alignment explanation
Indices: 40008571--40008887 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
40008561 TAGAATACCC
* *
40008571 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* *
40008636 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
40008701 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
*
40008728 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
40008793 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
40008858 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
40008885 TTA
1 TTA
40008888 ATATTCTTAT
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TTAGCAGAAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:40008858 original size:16 final size:16
Alignment explanation
Indices: 40008821--40008862 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
40008811 TTAATCATAT
*
40008821 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
40008837 TT-AAATATATTATAA
1 TTAAAATATATTATAA
40008852 TTAAAATATAT
1 TTAAAATATAT
40008863 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:40008869 original size:14 final size:15
Alignment explanation
Indices: 40008830--40008871 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40008820 TTTAAACATA
*
40008830 ATTATTATTAAATAT
1 ATTATAATTAAATAT
40008845 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
40008859 A-TATAATTTAATA
1 ATTATAATTAAATA
40008872 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:40008960 original size:120 final size:120
Alignment explanation
Indices: 40008827--40009055 Score: 449
Period size: 120 Copynumber: 1.9 Consensus size: 120
40008817 ATATTTAAAC
40008827 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
*
40008892 TCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAAT
66 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATTAAT
40008947 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
40009012 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAA
66 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAA
40009056 GAAAATTTGA
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 108 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATTAAT
Found at i:40008965 original size:16 final size:17
Alignment explanation
Indices: 40008944--40008981 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
40008934 AATATAAATT
*
40008944 AATATAATTATTATT-A
1 AATATAATTATAATTAA
40008960 AATAT-ATTATAATTAA
1 AATATAATTATAATTAA
40008976 AATATA
1 AATATA
40008982 TAATTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATATAATTATAATTAA
Found at i:40008989 original size:14 final size:15
Alignment explanation
Indices: 40008940--40008991 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40008930 GTAAAATATA
40008940 AATT-AATATAATTAT
1 AATTAAATAT-ATTAT
*
40008955 TATTAAATATATTAT
1 AATTAAATATATTAT
40008970 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
40008983 AATTTAATA
1 AATTAAATA
40008992 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 4 0.12
15 14 0.44
16 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:40018352 original size:15 final size:15
Alignment explanation
Indices: 40018317--40018368 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40018307 TTAAGAATTT
*
40018317 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40018331 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40018345 TATTTAATAATAAT-
1 TATTTAATTATAATA
40018359 TATATTAATT
1 TAT-TTAATT
40018369 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40018393 original size:120 final size:120
Alignment explanation
Indices: 40018253--40018481 Score: 449
Period size: 120 Copynumber: 1.9 Consensus size: 120
40018243 TCAAATTTTC
*
40018253 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTT
1 TTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTT
40018318 ATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATATTAATTTATA
66 ATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATATTAATTTATA
40018373 TTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTT
1 TTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTT
40018438 ATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT
66 ATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT
40018482 GTTTAAATAT
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 108 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
TTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTT
ATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATATTAATTTATA
Found at i:40018467 original size:16 final size:16
Alignment explanation
Indices: 40018446--40018487 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
40018436 TTATTAAATT
*
40018446 ATATATTTTAATTATA
1 ATATATTTTAATAATA
40018462 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
40018477 AT-TATGTTTAA
1 ATATAT-TTTAA
40018488 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:40018472 original size:15 final size:15
Alignment explanation
Indices: 40018437--40018478 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40018427 TTAAGAATTT
*
40018437 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40018451 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40018465 TATTTAATAATAAT
1 TATTTAATTATAAT
40018479 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40018596 original size:157 final size:157
Alignment explanation
Indices: 40018421--40018737 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
40018411 ATAAGAATAT
*
40018421 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
40018486 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
* *
40018551 TAATAATTTACCAAAATAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
40018578 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
40018643 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
40018708 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
40018735 TAA
1 TAA
40018738 GAGTATTCTA
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:40018618 original size:18 final size:17
Alignment explanation
Indices: 40018590--40018624 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40018580 ATTATTAAGA
*
40018590 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
40018607 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
40018625 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:40018658 original size:75 final size:75
Alignment explanation
Indices: 40018422--40018660 Score: 200
Period size: 75 Copynumber: 3.1 Consensus size: 75
40018412 TAAGAATATT
*
40018422 AATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
40018487 AATATGATTA
66 AATATGATTA
* ** * * * * *
40018497 AATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATA-A--CAATAATAATT
1 AATTATTAAGAATT-TTATT-A-AA--TTA-TATATTTTAATTAA-AATATATTTAATAATAATT
**** * *
40018559 -TACCAAAATAAAT-TTCTGCT
59 ATGTTTAAAT--ATGAT-T--A
40018579 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
40018644 AATATGATTA
66 AATATGATTA
40018654 AATTATT
1 AATTATT
40018661 TATTATTGAT
Statistics
Matches: 118, Mismatches: 29, Indels: 34
0.65 0.16 0.19
Matches are distributed among these distances:
75 22 0.19
76 16 0.14
77 7 0.06
78 18 0.15
79 18 0.15
80 7 0.06
81 15 0.13
82 15 0.13
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (75 bp):
AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
AATATGATTA
Found at i:40018879 original size:16 final size:16
Alignment explanation
Indices: 40018860--40018911 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
40018850 AATTTGCTAT
*
40018860 TACACCTCTATTCCAT
1 TACACCTCTATTCCAA
40018876 TACACCTCTAATT-CAA
1 TACACCTCT-ATTCCAA
*
40018892 TACACCTCTAATCCAA
1 TACACCTCTATTCCAA
40018908 TACA
1 TACA
40018912 GCGAACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 2 0.06
16 27 0.84
17 3 0.09
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (16 bp):
TACACCTCTATTCCAA
Found at i:40019171 original size:2 final size:2
Alignment explanation
Indices: 40019164--40019200 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
40019154 TCACTTTGCT
40019164 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
40019201 TTTTCTTCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:40023684 original size:13 final size:13
Alignment explanation
Indices: 40023666--40023726 Score: 59
Period size: 13 Copynumber: 4.7 Consensus size: 13
40023656 CTCAAAATTT
*
40023666 TCAAAAACACTTC
1 TCAAAAGCACTTC
*
40023679 TCAAAAGCACTTT
1 TCAAAAGCACTTC
* *
40023692 TCCACAGCACTTC
1 TCAAAAGCACTTC
* *
40023705 TCAAAAGTACTTT
1 TCAAAAGCACTTC
*
40023718 TTAAAAGCA
1 TCAAAAGCA
40023727 ATGAAGAACT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.28
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:40023726 original size:26 final size:26
Alignment explanation
Indices: 40023663--40023726 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
40023653 ACACTCAAAA
*
40023663 TTTTCAAAAACACTTCTCAAAAGCAC
1 TTTTCAAAAGCACTTCTCAAAAGCAC
* * *
40023689 TTTTCCACAGCACTTCTCAAAAGTAC
1 TTTTCAAAAGCACTTCTCAAAAGCAC
*
40023715 TTTTTAAAAGCA
1 TTTTCAAAAGCA
40023727 ATGAAGAACT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (26 bp):
TTTTCAAAAGCACTTCTCAAAAGCAC
Found at i:40030619 original size:35 final size:34
Alignment explanation
Indices: 40030563--40030630 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 34
40030553 TATATATACT
*
40030563 TATAAAAATAAAAATATGTATATGTATAGATATA
1 TATAAAAATAAAAATATGTATACGTATAGATATA
* *
40030597 TATAAAAA-AGAAATATGAGTATACGTATATATAT
1 TATAAAAATAAAAATAT--GTATACGTATAGATAT
40030631 TAAACAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 7 0.24
34 8 0.28
35 14 0.48
ACGTcount: A:0.54, C:0.01, G:0.10, T:0.34
Consensus pattern (34 bp):
TATAAAAATAAAAATATGTATACGTATAGATATA
Found at i:40030771 original size:3 final size:3
Alignment explanation
Indices: 40030760--40030802 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
40030750 CAATAATACC
*
40030760 AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40030803 GCAAAAGTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:40031843 original size:16 final size:17
Alignment explanation
Indices: 40031824--40031857 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40031814 ATTAATGTTT
40031824 TGGGCT-ATTTGGGCTG
1 TGGGCTAATTTGGGCTG
*
40031840 TGGGTTAATTTGGGCTG
1 TGGGCTAATTTGGGCTG
40031857 T
1 T
40031858 TAATTTGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.09, C:0.09, G:0.41, T:0.41
Consensus pattern (17 bp):
TGGGCTAATTTGGGCTG
Found at i:40032224 original size:41 final size:41
Alignment explanation
Indices: 40032178--40032367 Score: 166
Period size: 44 Copynumber: 4.5 Consensus size: 41
40032168 CTTCTTTGCA
* *
40032178 GCAACTTCAGGGAAATAAGACTTGATGCGATCTGCTCTACT
1 GCAACTTCAGAGAGATAAGACTTGATGCGATCTGCTCTACT
*** *
40032219 GCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCTACT
1 GCAACTTCAGAGAGATAAGA-CT-TGA-TGCGATCTGCTCTACT
* * * * *
40032263 GCAACTTCAGAGAGATAGGA-TTGGTTTCTTCTATCTGCTCCACT
1 GCAACTTCAGAGAGATAAGACTT-G---ATGCGATCTGCTCTACT
* * *
40032307 GCAACTTCAGGGAGATAAGACTTGATGCGATCTACTCTGCT
1 GCAACTTCAGAGAGATAAGACTTGATGCGATCTGCTCTACT
* *
40032348 GTAACCTCAGAGAGATAAGA
1 GCAACTTCAGAGAGATAAGA
40032368 TCCTTTATTT
Statistics
Matches: 118, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
41 47 0.40
42 4 0.03
43 3 0.03
44 62 0.53
45 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GCAACTTCAGAGAGATAAGACTTGATGCGATCTGCTCTACT
Found at i:40032269 original size:44 final size:43
Alignment explanation
Indices: 40032211--40032408 Score: 168
Period size: 44 Copynumber: 4.6 Consensus size: 43
40032201 GATGCGATCT
40032211 GCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCC
1 GCTCTACTGCAACTTCAGAGAGATAAGATCT-TGATTTTAATCC
* * * * *
40032255 GCTCTACTGCAACTTCAGAGAGATAGGAT-TGGTTTCTTCTATCT
1 GCTCTACTGCAACTTCAGAGAGATAAGATCTTGATT-TT-AATCC
* * *** *
40032299 GCTCCACTGCAACTTCAGGGAGATAAGA-CTTGA-TGCGATCT
1 GCTCTACTGCAACTTCAGAGAGATAAGATCTTGATTTTAATCC
* * * * *
40032340 ACTCTGCTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCC
1 GCTCTACTGCAACTTCAGAGAGATAAGAT-CTTGATTTTAATCC
* * *
40032384 GCTCCACTGTAACTTCAGGGAGATA
1 GCTCTACTGCAACTTCAGAGAGATA
40032409 GGATAGTGTC
Statistics
Matches: 119, Mismatches: 29, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
41 26 0.22
42 3 0.03
43 8 0.07
44 82 0.69
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (43 bp):
GCTCTACTGCAACTTCAGAGAGATAAGATCTTGATTTTAATCC
Found at i:40032368 original size:129 final size:128
Alignment explanation
Indices: 40032178--40032502 Score: 411
Period size: 129 Copynumber: 2.5 Consensus size: 128
40032168 CTTCTTTGCA
* * *
40032178 GCAACTTCAGGGAAATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTG
1 GCAACTTCAGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACCTCAGAGAGATAAGATCTG
* * * *
40032243 TGATTTTAATCCGCTCTACTGCAACTTCAGAGAGATAGGATTGGTTTCTTCTATCTGCTCCACT
66 TGATTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGA-TAGTGTCTTCGATCTGCTCCACT
* *
40032307 GCAACTTCAGGGAGATAAGACTTGATGCGATCTACTCTGCTGTAACCTCAGAGAGATAAGATCCT
1 GCAACTTCAGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACCTCAGAGAGATAAGAT-CT
* * * *
40032372 -TTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCT
65 GTGATTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATAGTGTCTTCGATCTGCTCCACT
* * * * * *
40032435 GTAA-TCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGA
1 GCAACT-TCAGGGAGATAAGA-CT-T-GATGCGATCTGCTCTACTGTAACCTCAGAGAGATAAGA
40032499 TCTG
62 TCTG
40032503 AAATTCTCCG
Statistics
Matches: 169, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
127 1 0.01
128 36 0.21
129 95 0.56
130 5 0.03
131 32 0.19
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (128 bp):
GCAACTTCAGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACCTCAGAGAGATAAGATCTG
TGATTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATAGTGTCTTCGATCTGCTCCACT
Found at i:40032445 original size:43 final size:42
Alignment explanation
Indices: 40032289--40032889 Score: 291
Period size: 44 Copynumber: 14.0 Consensus size: 42
40032279 AGGATTGGTT
* *
40032289 TCTTCTATCTGCTCCACTGCAA-CTTCAGGGAGATAAGA-CT-
1 TCTTCGATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTG
* * * ** * * *
40032329 TGATGCGATCTACTCTGCTGTAACCTCAGAGAGATAAGATCCTT
1 T-CTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-CTG
* ** * * *
40032373 TATTTTAATCCGCTCCACTGTAA-CTTCAGGGAGATAGGATAGTG
1 T-CTTCGATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT-CTG
*
40032417 TCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTG
1 TCTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGA--TCTG
* * *
40032461 GCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTG
1 TCTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG
* * * * *
40032503 AAATTCTCCGGTCTACTCCACTGTAATCCTCAGAGAGATAAGACCTG
1 ----TCTTCGATCTGCTCCACTGTAAT-CTCAGGGAGATAAGATCTG
* * * * ** *
40032550 -ATGCGGTCTACTCTGCTGTAA-CTTCAGAGAGATAAGATCT-
1 TCTTCGATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTG
* * * * *
40032590 T-TT-AATCCGCTCCATTGTAAAT-TCAGGGAGATAGGATAGTG
1 TCTTCGATCTGCTCCACTGT-AATCTCAGGGAGATAAGAT-CTG
* *
40032631 TCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCCG
1 TCTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG
* ** *
40032673 AAATTCTT-TAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTG
1 ----TCTTCGA-TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG
* * *
40032719 AT-GT-GATCTTCTCTACTGTAA-CTTCAGGGAGATAAGATC--
1 -TCTTCGATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTG
** * * * * *
40032758 -CTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTA
1 TCTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGA-T-CTG
* *
40032801 TCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTG
1 TCTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG
* * * *
40032843 AAATTCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTG
1 ----TCTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG
40032889 T
1 T
40032890 ATAATAAACC
Statistics
Matches: 424, Mismatches: 96, Indels: 80
0.71 0.16 0.13
Matches are distributed among these distances:
38 1 0.00
39 45 0.11
40 9 0.02
41 72 0.17
42 33 0.08
43 59 0.14
44 97 0.23
45 2 0.00
46 89 0.21
47 17 0.04
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (42 bp):
TCTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG
Found at i:40032451 original size:87 final size:85
Alignment explanation
Indices: 40032290--40032498 Score: 224
Period size: 87 Copynumber: 2.4 Consensus size: 85
40032280 GGATTGGTTT
* * * *
40032290 CTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGATGCGATCTACTCTGCTGTAACCT
1 CTTCAATCCGCTCCACTGTAACTTCAGGGAGATAAGACTTGATGCGATCTACTCCGCTGTAACCT
*
40032355 CAGAGAGATAAGATC-CTTTA
66 CAGAGAGATAAGATCTC-TGA
* * * * * *
40032375 TTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGA-TAGTGTCTTCGATCTGCTCCGCTGTAA
1 CTTCAATCCGCTCCACTGTAACTTCAGGGAGATAAGACT--TG-ATGCGATCTACTCCGCTGTAA
* * *
40032439 TCTCAGGGAGATAAGATCTCTGG
63 CCTCAGAGAGATAAGATCTCTGA
* *
40032462 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGA
1 CTTCAATCCGCTCCACTGTAACTTCAGGGAGATAAGA
40032499 TCTGAAATTC
Statistics
Matches: 101, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
84 1 0.01
85 31 0.31
86 2 0.02
87 66 0.65
88 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (85 bp):
CTTCAATCCGCTCCACTGTAACTTCAGGGAGATAAGACTTGATGCGATCTACTCCGCTGTAACCT
CAGAGAGATAAGATCTCTGA
Found at i:40032545 original size:47 final size:41
Alignment explanation
Indices: 40032472--40032589 Score: 128
Period size: 47 Copynumber: 2.7 Consensus size: 41
40032462 CTTCAATCTG
*
40032472 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTCCGGTCTA
1 CTCCACTGTAACCTCAGAGAGATAAGATCTG--A---TCCGGTCTA
* *
40032518 CTCCACTGTAATCCTCAGAGAGATAAGACCTGATGCGGTCTA
1 CTCCACTGTAA-CCTCAGAGAGATAAGATCTGATCCGGTCTA
** *
40032560 CTCTGCTGTAACTTCAGAGAGATAAGATCT
1 CTCCACTGTAACCTCAGAGAGATAAGATCT
40032590 TTTAATCCGC
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
41 17 0.27
42 17 0.27
45 1 0.02
46 11 0.17
47 18 0.28
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (41 bp):
CTCCACTGTAACCTCAGAGAGATAAGATCTGATCCGGTCTA
Found at i:40032714 original size:46 final size:45
Alignment explanation
Indices: 40032638--40032884 Score: 157
Period size: 46 Copynumber: 5.7 Consensus size: 45
40032628 GTGTCTTCGA
* *
40032638 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCCGAAATTCTTTAG
1 TCTGTTCCACTGTAATCTCAGGGAGATAAGATCCG-AATTCTTTAG
* * *
40032684 TCTATTCCACTGTAATCTCAGGGAGATAAGA-CCTG-A-T-GTGA-
1 TCTGTTCCACTGTAATCTCAGGGAGATAAGATCC-GAATTCTTTAG
* *
40032725 TCT-TCTCTACTGTAA-CTTCAGGGAGATAAGAT-C-----CTTTAA
1 TCTGT-TCCACTGTAATC-TCAGGGAGATAAGATCCGAATTCTTTAG
* * * * * * *
40032764 TCCGCTCCATTGTAATCTCAAGGAGATAGGAT--TACTATCTTT-G
1 TCTGTTCCACTGTAATCTCAGGGAGATAAGATCCGAAT-TCTTTAG
* * * *
40032807 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGG
1 -TCTGTTCCACTGTAATCTCAGGGAGATAAGATCCG-AATTCTTTAG
40032854 TCTGTTCCACTGTAATCTCAGGGAGATAAGA
1 TCTGTTCCACTGTAATCTCAGGGAGATAAGA
40032885 CCTGTATAAT
Statistics
Matches: 158, Mismatches: 24, Indels: 38
0.72 0.11 0.17
Matches are distributed among these distances:
38 2 0.01
39 23 0.15
40 3 0.02
41 27 0.17
42 2 0.01
43 1 0.01
44 32 0.20
45 2 0.01
46 63 0.40
47 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (45 bp):
TCTGTTCCACTGTAATCTCAGGGAGATAAGATCCGAATTCTTTAG
Found at i:40032765 original size:169 final size:170
Alignment explanation
Indices: 40032434--40032888 Score: 646
Period size: 170 Copynumber: 2.7 Consensus size: 170
40032424 TCTGCTCCGC
* * ** * * *
40032434 TGTAATCTCAGGGAGATAAGATCT-CTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAG
1 TGTAATCTCAAGGAGATAGGAT-TACTATCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
** * * *
40032498 ATCTGAAATTCTCCGGTCTACTCCACTGTAATCCTCAGAGAGATAAGACCTGATGCGGTCTACTC
65 ATCTGAAATTCTTTGGTCTATTCCACTGTAAT-CTCAGGGAGATAAGACCTGATGCGATCTACTC
* *
40032563 TGCTGTAACTTCAGAGAGATAAGATCTTTTAATCCGCTCCAT
129 TACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCAT
* * *
40032605 TGTAAAT-TCAGGGAGATAGGA-TAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
1 TGT-AATCTCAAGGAGATAGGATTACTATCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
* * * *
40032668 ATCCGAAATTCTTTAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCT
65 ATCTGAAATTCTTTGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCT
*
40032733 ACTGTAACTTCAGGGAGATAAGATCCTTTAATCCGCTCCAT
130 ACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCAT
*
40032774 TGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
1 TGTAATCTCAAGGAGATAGGATTACTATCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
*
40032839 TCTGAAATTCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTG
66 TCTGAAATTCTTTGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTG
40032889 TATAATAAAC
Statistics
Matches: 255, Mismatches: 25, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
168 3 0.01
169 84 0.33
170 149 0.58
171 16 0.06
172 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (170 bp):
TGTAATCTCAAGGAGATAGGATTACTATCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
TCTGAAATTCTTTGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTA
CTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCAT
Found at i:40045498 original size:35 final size:34
Alignment explanation
Indices: 40045442--40045509 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 34
40045432 TATATATACT
*
40045442 TATAAAAATAAAAATATGTATATGTATAGATATA
1 TATAAAAATAAAAATATGTATACGTATAGATATA
* *
40045476 TATAAAAA-AGAAATATGAGTATACGTATATATAT
1 TATAAAAATAAAAATAT--GTATACGTATAGATAT
40045510 TAAACAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 7 0.24
34 8 0.28
35 14 0.48
ACGTcount: A:0.54, C:0.01, G:0.10, T:0.34
Consensus pattern (34 bp):
TATAAAAATAAAAATATGTATACGTATAGATATA
Found at i:40045652 original size:3 final size:3
Alignment explanation
Indices: 40045641--40045680 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
40045631 CAATAATACC
*
40045641 AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40045681 GCAAAAGTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:40046722 original size:16 final size:17
Alignment explanation
Indices: 40046703--40046736 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40046693 ATTAATGTTT
40046703 TGGGCT-ATTTGGGCTG
1 TGGGCTAATTTGGGCTG
*
40046719 TGGGTTAATTTGGGCTG
1 TGGGCTAATTTGGGCTG
40046736 T
1 T
40046737 TAATTTGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.09, C:0.09, G:0.41, T:0.41
Consensus pattern (17 bp):
TGGGCTAATTTGGGCTG
Found at i:40058298 original size:26 final size:25
Alignment explanation
Indices: 40058237--40058334 Score: 85
Period size: 26 Copynumber: 3.9 Consensus size: 25
40058227 CATATAATGG
*
40058237 TTTAAAATGAATCATATATAAAAAA
1 TTTAAAATAAATCATATATAAAAAA
*
40058262 TTT-AAATAAAT-AGTATGTAAAACAA
1 TTTAAAATAAATCA-TATATAAAA-AA
* *
40058287 TTTAAAATAAATGATAAATAAAAAAA
1 TTTAAAATAAATCATATAT-AAAAAA
* * *
40058313 ATTAAAACAAATAATA-ATAAAA
1 TTTAAAATAAATCATATATAAAA
40058335 GAGTTTTTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
23 1 0.02
24 19 0.31
25 10 0.16
26 26 0.43
27 5 0.08
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (25 bp):
TTTAAAATAAATCATATATAAAAAA
Found at i:40060034 original size:28 final size:28
Alignment explanation
Indices: 40059994--40060092 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
40059984 TGACTTTCGA
40059994 CACTAAGTGTGCGAATTTAATTATAAAG
1 CACTAAGTGTGCGAATTTAATTATAAAG
* ***
40060022 CACTAAGTGTGCGAGTTTAATGGCAAAG
1 CACTAAGTGTGCGAATTTAATTATAAAG
* * *
40060050 CACTAAGTGTGCGAGTTTGATTATTGAA-
1 CACTAAGTGTGCGAATTTAATTA-TAAAG
40060078 CACTAAGTGTGCGAA
1 CACTAAGTGTGCGAA
40060093 CTTATTAAAC
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
28 58 0.97
29 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (28 bp):
CACTAAGTGTGCGAATTTAATTATAAAG
Found at i:40060849 original size:23 final size:23
Alignment explanation
Indices: 40060788--40061181 Score: 324
Period size: 23 Copynumber: 17.0 Consensus size: 23
40060778 TCTAAAATTG
*
40060788 GTATATATATGCTG-CCTAATTTT
1 GTATATACATGCTGTCC-AATTTT
*
40060811 GGTGA-ATAAATGCTGTCCAATTTT
1 -GT-ATATACATGCTGTCCAATTTT
*
40060835 GTATATACATGCTGTCAAATTTT
1 GTATATACATGCTGTCCAATTTT
* *
40060858 GTGTATA-AGTGCTGTCCAA-ATT
1 GTATATACA-TGCTGTCCAATTTT
* * *
40060880 GCTACATATATGCTGCCCAATTTT
1 G-TATATACATGCTGTCCAATTTT
* *
40060904 GGTAAATAAATGCTGTCCAATTTT
1 -GTATATACATGCTGTCCAATTTT
*
40060928 GTATATACATGCTGTCAAATTTT
1 GTATATACATGCTGTCCAATTTT
* *
40060951 GTGTATA-AGTGCTGTCCAA-ATT
1 GTATATACA-TGCTGTCCAATTTT
* * *
40060973 GCTACATATATGCTGCCCAATTTT
1 G-TATATACATGCTGTCCAATTTT
*
40060997 GGTGA-ATAAATGCTGTCCAATTTT
1 -GT-ATATACATGCTGTCCAATTTT
*
40061021 GTATATACATGCTGTACAATTTT
1 GTATATACATGCTGTCCAATTTT
* * *
40061044 GTGTATA-AGTGCTGTCCAAATTG
1 GTATATACA-TGCTGTCCAATTTT
* *
40061067 GTATATATATGCTGCCCAATTTT
1 GTATATACATGCTGTCCAATTTT
*
40061090 GGTGA-ATAAATGCTGTCCAATTTT
1 -GT-ATATACATGCTGTCCAATTTT
*
40061114 GTATATACATGCTGTCAAATTTT
1 GTATATACATGCTGTCCAATTTT
* * *
40061137 GTGTATA-AGTGCTGTCCAAATTG
1 GTATATACA-TGCTGTCCAATTTT
40061160 GTATATACATGCTG-CTCAATTT
1 GTATATACATGCTGTC-CAATTT
40061182 CTGATGTATA
Statistics
Matches: 302, Mismatches: 45, Indels: 47
0.77 0.11 0.12
Matches are distributed among these distances:
22 14 0.05
23 200 0.66
24 81 0.27
25 7 0.02
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (23 bp):
GTATATACATGCTGTCCAATTTT
Found at i:40060941 original size:93 final size:93
Alignment explanation
Indices: 40060782--40061203 Score: 713
Period size: 93 Copynumber: 4.5 Consensus size: 93
40060772 TAATGGTCTA
*
40060782 AAATTGGTATATATATGCTGCCTAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
40060847 TGTCAAATTTTGTGTATAAGTGCTGTCC
66 TGTCAAATTTTGTGTATAAGTGCTGTCC
* * *
40060875 AAATTGCTACATATATGCTGCCCAATTTTGGTAAATAAATGCTGTCCAATTTTGTATATACATGC
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
40060940 TGTCAAATTTTGTGTATAAGTGCTGTCC
66 TGTCAAATTTTGTGTATAAGTGCTGTCC
* *
40060968 AAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
40061033 TGT-ACAATTTTGTGTATAAGTGCTGTCC
66 TGTCA-AATTTTGTGTATAAGTGCTGTCC
40061061 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
40061126 TGTCAAATTTTGTGTATAAGTGCTGTCC
66 TGTCAAATTTTGTGTATAAGTGCTGTCC
* * * *
40061154 AAATTGGTATATACATGCTGCTCAATTTCTGATGTATAAGA-GCTGTCCAA
1 AAATTGGTATATATATGCTGCCCAATTT-TGGTGAATAA-ATGCTGTCCAA
40061204 ACAGGATAGA
Statistics
Matches: 314, Mismatches: 11, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
92 1 0.00
93 294 0.94
94 18 0.06
95 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.39
Consensus pattern (93 bp):
AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
TGTCAAATTTTGTGTATAAGTGCTGTCC
Found at i:40062305 original size:23 final size:23
Alignment explanation
Indices: 40062280--40062322 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
40062270 TGGACTATTT
*
40062280 TTTTTATTT-TTTTTGGGTTTTA
1 TTTTTGTTTATTTTTGGGTTTTA
40062302 TTTTTGTTTATTTTTGGGTTT
1 TTTTTGTTTATTTTTGGGTTT
40062323 GGGCCCGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.07, C:0.00, G:0.16, T:0.77
Consensus pattern (23 bp):
TTTTTGTTTATTTTTGGGTTTTA
Found at i:40064378 original size:19 final size:20
Alignment explanation
Indices: 40064337--40064378 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
40064327 GTTTCTATGT
* *
40064337 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
40064357 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
40064376 CAT
1 CAT
40064379 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:40072121 original size:27 final size:27
Alignment explanation
Indices: 40072079--40072138 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
40072069 CGCGCCACAC
* *
40072079 CCCAAAATTTCTACTGCTCCATTTATG
1 CCCAATATTTCCACTGCTCCATTTATG
*
40072106 CCCAATATTTCCACTGCTTCATTTATG
1 CCCAATATTTCCACTGCTCCATTTATG
40072133 CCCAAT
1 CCCAAT
40072139 TGAAAATTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.25, C:0.32, G:0.07, T:0.37
Consensus pattern (27 bp):
CCCAATATTTCCACTGCTCCATTTATG
Found at i:40085182 original size:14 final size:14
Alignment explanation
Indices: 40085163--40085190 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40085153 TTGCCTTTAA
40085163 AAATAAGTTAATTC
1 AAATAAGTTAATTC
40085177 AAATAAGTTAATTC
1 AAATAAGTTAATTC
40085191 TTTTTAAAGA
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:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
AAATAAGTTAATTC
Found at i:40088802 original size:42 final size:42
Alignment explanation
Indices: 40088731--40089037 Score: 372
Period size: 42 Copynumber: 7.2 Consensus size: 42
40088721 GCAAACATTT
* * *
40088731 GCGGCGCTTACAGAAAAAAATGCCACTAAAGATCATGTTCTTTA
1 GCGGCGCTT--AGAAATAAACGCCGCTAAAGATCATGTTCTTTA
*
40088775 GCGGCGCTTAGAAAGAAACGCCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTTAGAAATAAACGCCGCTAAAGATCATGTTCTTTA
* * *
40088817 GCGGCGCTAAAAAATAAACGCCACTAAAGA-CAATGTTCTTTA
1 GCGGCGCTTAGAAATAAACGCCGCTAAAGATC-ATGTTCTTTA
* * *
40088859 GCGGCGCTCAGAAATAAACGCCACTAAAGAGCATGTTCTTTA
1 GCGGCGCTTAGAAATAAACGCCGCTAAAGATCATGTTCTTTA
40088901 GCGGCGCTTAGAAATAAACGCCAG-TAAAGATCATGTTCTTTA
1 GCGGCGCTTAGAAATAAACGCC-GCTAAAGATCATGTTCTTTA
* *
40088943 GCGGCGCTAAGGAAATAAATGCCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTTA-GAAATAAACGCCGCTAAAGATCATGTTCTTTA
* *
40088986 GCGGCGCTTAGGATAA-AAACACCGCTAAA-AGT-ACTGTTCTATA
1 GCGGCGCTTA-GA-AATAAACGCCGCTAAAGA-TCA-TGTTCTTTA
40089029 GCGGCGCTT
1 GCGGCGCTT
40089038 GTTTAAAAAC
Statistics
Matches: 237, Mismatches: 18, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
41 1 0.00
42 154 0.65
43 71 0.30
44 11 0.05
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (42 bp):
GCGGCGCTTAGAAATAAACGCCGCTAAAGATCATGTTCTTTA
Found at i:40088885 original size:126 final size:128
Alignment explanation
Indices: 40088731--40089037 Score: 410
Period size: 126 Copynumber: 2.4 Consensus size: 128
40088721 GCAAACATTT
* *
40088731 GCGGCGCTTACAGAAAAAAATGCCACTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAGAAACGC
1 GCGGCGC-TACAGAAAAAAACGCCACTAAAGAGCATGTTCTTTAGCGGCGCTTAGAAAGAAACGC
40088796 C-GCTAAAGATCATGTTCTTTAGCGGCGCTAA-AAAATAAACGCCACTAAAGA-CAATGTTCTTT
65 CAG-TAAAGATCATGTTCTTTAGCGGCGCTAAGAAAATAAACGCCACTAAAGATC-ATGTTCTTT
40088858 A
128 A
* *
40088859 GCGGCGCT-CAGAAATAAACGCCACTAAAGAGCATGTTCTTTAGCGGCGCTTAGAAATAAACGCC
1 GCGGCGCTACAGAAAAAAACGCCACTAAAGAGCATGTTCTTTAGCGGCGCTTAGAAAGAAACGCC
* * *
40088923 AGTAAAGATCATGTTCTTTAGCGGCGCTAAGGAAATAAATGCCGCTAAAGATCATGTTCTTTA
66 AGTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAATAAACGCCACTAAAGATCATGTTCTTTA
* * * * * *
40088986 GCGGCGCTTA-GGATAAAAACACCGCTAAA-AGTACTGTTCTATAGCGGCGCTT
1 GCGGCGC-TACAGAAAAAAACGCCACTAAAGAGCA-TGTTCTTTAGCGGCGCTT
40089038 GTTTAAAAAC
Statistics
Matches: 159, Mismatches: 14, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
126 80 0.50
127 39 0.25
128 40 0.25
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (128 bp):
GCGGCGCTACAGAAAAAAACGCCACTAAAGAGCATGTTCTTTAGCGGCGCTTAGAAAGAAACGCC
AGTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAATAAACGCCACTAAAGATCATGTTCTTTA
Found at i:40089058 original size:42 final size:43
Alignment explanation
Indices: 40088934--40089060 Score: 127
Period size: 43 Copynumber: 3.0 Consensus size: 43
40088924 GTAAAGATCA
* * **
40088934 TGTTCTTTAGCGGCGCTAAGGA-AATAAATGCCGCT-AAAG-ATC
1 TGTTCTATAGCGGCGCTTAGGATAA-AAACACCGCTAAAAGTA-C
*
40088976 ATGTTCTTTAGCGGCGCTTAGGATAAAAACACCGCTAAAAGTAC
1 -TGTTCTATAGCGGCGCTTAGGATAAAAACACCGCTAAAAGTAC
** *
40089020 TGTTCTATAGCGGCGCTT-GTTTAAAAACGCCGCTAAAAGTA
1 TGTTCTATAGCGGCGCTTAGGATAAAAACACCGCTAAAAGTA
40089061 GTATTCTTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
42 20 0.27
43 46 0.62
44 7 0.09
45 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (43 bp):
TGTTCTATAGCGGCGCTTAGGATAAAAACACCGCTAAAAGTAC
Found at i:40089526 original size:12 final size:12
Alignment explanation
Indices: 40089505--40089541 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
40089495 TGAACATCTA
*
40089505 CTTCTATCGCTG
1 CTTCTCTCGCTG
40089517 CTTCTCTCGCTG
1 CTTCTCTCGCTG
*
40089529 CTTCTCTCACTG
1 CTTCTCTCGCTG
40089541 C
1 C
40089542 AGCCTTTGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.05, C:0.41, G:0.14, T:0.41
Consensus pattern (12 bp):
CTTCTCTCGCTG
Found at i:40089579 original size:21 final size:21
Alignment explanation
Indices: 40089526--40089594 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
40089516 GCTTCTCTCG
*
40089526 CTGCTTCTCTCACTGCAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
40089547 TTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* * *
40089568 CTGCTTCTCTCGTTACTGCCT
1 CTGCTTCTCTCGCTGCAGCCT
40089589 CTGCTT
1 CTGCTT
40089595 TAAGTTTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.04, C:0.39, G:0.17, T:0.39
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:40093039 original size:90 final size:92
Alignment explanation
Indices: 40092854--40093234 Score: 725
Period size: 91 Copynumber: 4.2 Consensus size: 92
40092844 TATGTGTTAT
40092854 GTAAATGAATATATGTATAATATTAAAAAAATAGTAATACTTATTTAAGTTATAAATTTATTATT
1 GTAAATGAATATATGTATAATATTAAAAAAATAGTAATACTTATTTAAGTTATAAATTTATTATT
40092919 AAT-AAATTTAAATATAGCTTACATAC
66 AATAAAATTTAAATATAGCTTACATAC
40092945 GTAAATGAATATATGTATAATATTAAAAAAATAGTAATACTTATTTAAGTTATAAA-TT-TTATT
1 GTAAATGAATATATGTATAATATTAAAAAAATAGTAATACTTATTTAAGTTATAAATTTATTATT
40093008 AATAAAATTTAAATATAGCTTACATAC
66 AATAAAATTTAAATATAGCTTACATAC
40093035 GTAAATGAATATATGTATAATATTAAAAAAATAGTAATACTTATTTAAGTTATAAATTTATTATT
1 GTAAATGAATATATGTATAATATTAAAAAAATAGTAATACTTATTTAAGTTATAAATTTATTATT
40093100 AATAAAATTTAAATATAGCTTACATAC
66 AATAAAATTTAAATATAGCTTACATAC
*
40093127 GTAAATGAATATATGTACAATATT-AAAAAATAGTAATACTTATTTAAGTTATAAATTTATTATT
1 GTAAATGAATATATGTATAATATTAAAAAAATAGTAATACTTATTTAAGTTATAAATTTATTATT
40093191 AATAAAATTTAAATATAGCTTACATAC
66 AATAAAATTTAAATATAGCTTACATAC
40093218 GTAAATGAATATATGTA
1 GTAAATGAATATATGTA
40093235 AGTTATGTAA
Statistics
Matches: 286, Mismatches: 1, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
89 8 0.03
90 81 0.28
91 142 0.50
92 55 0.19
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (92 bp):
GTAAATGAATATATGTATAATATTAAAAAAATAGTAATACTTATTTAAGTTATAAATTTATTATT
AATAAAATTTAAATATAGCTTACATAC
Found at i:40093158 original size:181 final size:183
Alignment explanation
Indices: 40092854--40093234 Score: 723
Period size: 181 Copynumber: 2.1 Consensus size: 183
40092844 TATGTGTTAT
40092854 GTAAATGAATATATGTATAATATTAAAAAAATAGTAATACTTATTTAAGTTATAAATTTATTATT
1 GTAAATGAATATATGTATAATATTAAAAAAATAGTAATACTTATTTAAGTTATAAATTTATTATT
*
40092919 AATAAATTTAAATATAGCTTACATACGTAAATGAATATATGTATAATATTAAAAAAATAGTAATA
66 AATAAATTTAAATATAGCTTACATACGTAAATGAATATATGTACAATATTAAAAAAATAGTAATA
40092984 CTTATTTAAGTTATAAA-TT-TTATTAATAAAATTTAAATATAGCTTACATAC
131 CTTATTTAAGTTATAAATTTATTATTAATAAAATTTAAATATAGCTTACATAC
40093035 GTAAATGAATATATGTATAATATTAAAAAAATAGTAATACTTATTTAAGTTATAAATTTATTATT
1 GTAAATGAATATATGTATAATATTAAAAAAATAGTAATACTTATTTAAGTTATAAATTTATTATT
40093100 AATAAAATTTAAATATAGCTTACATACGTAAATGAATATATGTACAATATT-AAAAAATAGTAAT
66 AAT-AAATTTAAATATAGCTTACATACGTAAATGAATATATGTACAATATTAAAAAAATAGTAAT
40093164 ACTTATTTAAGTTATAAATTTATTATTAATAAAATTTAAATATAGCTTACATAC
130 ACTTATTTAAGTTATAAATTTATTATTAATAAAATTTAAATATAGCTTACATAC
40093218 GTAAATGAATATATGTA
1 GTAAATGAATATATGTA
40093235 AGTTATGTAA
Statistics
Matches: 196, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
181 99 0.51
182 48 0.24
183 49 0.25
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (183 bp):
GTAAATGAATATATGTATAATATTAAAAAAATAGTAATACTTATTTAAGTTATAAATTTATTATT
AATAAATTTAAATATAGCTTACATACGTAAATGAATATATGTACAATATTAAAAAAATAGTAATA
CTTATTTAAGTTATAAATTTATTATTAATAAAATTTAAATATAGCTTACATAC
Found at i:40093254 original size:12 final size:12
Alignment explanation
Indices: 40093237--40093261 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40093227 TATATGTAAG
40093237 TTATGTAAGTTA
1 TTATGTAAGTTA
40093249 TTATGTAAGTTA
1 TTATGTAAGTTA
40093261 T
1 T
40093262 GCAAGATTAT
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:0.16, T:0.52
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:40093279 original size:22 final size:21
Alignment explanation
Indices: 40093233--40093284 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
40093223 TGAATATATG
* * *
40093233 TAAGTTATGTAAGTTATTATG
1 TAAGTTATGCAAGTTATAATA
40093254 TAAGTTATGCAAGATTATAATA
1 TAAGTTATGCAAG-TTATAATA
40093276 TAAGTTATG
1 TAAGTTATG
40093285 TATTATGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.42
Consensus pattern (21 bp):
TAAGTTATGCAAGTTATAATA
Found at i:40093298 original size:8 final size:7
Alignment explanation
Indices: 40093280--40093317 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
40093270 ATAATATAAG
40093280 TTATGTA
1 TTATGTA
40093287 TTATGTTA
1 TTATG-TA
40093295 TTATGTA
1 TTATGTA
40093302 TTATGTA
1 TTATGTA
40093309 --ATGTA
1 TTATGTA
40093314 TTAT
1 TTAT
40093318 CAGATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.18
7 16 0.57
8 7 0.25
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (7 bp):
TTATGTA
Found at i:40093374 original size:21 final size:19
Alignment explanation
Indices: 40093322--40093378 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
40093312 TATTATCAGA
*
40093322 TTATATATAAGTTACGAAAG
1 TTATATATAAGTTA-TAAAG
*
40093342 TTATTATGTAAGTTATACAAG
1 TTA-TATATAAGTTATA-AAG
40093363 CTTATATATAAGTTAT
1 -TTATATATAAGTTAT
40093379 GTATTATGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 4 0.13
21 24 0.77
22 3 0.10
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.42
Consensus pattern (19 bp):
TTATATATAAGTTATAAAG
Found at i:40093403 original size:95 final size:96
Alignment explanation
Indices: 40093227--40093404 Score: 304
Period size: 96 Copynumber: 1.9 Consensus size: 96
40093217 CGTAAATGAA
* * * *
40093227 TATATGTAAGTTATGTAAGTTATTATGTAAGTTATGCAAGATTATAATATAAGTTATGTATTATG
1 TATATATAAGTTACGAAAGTTATTATGTAAGTTATACAAGATTATAATATAAGTTATGTATTATG
40093292 TTATTATGTATTATGTAATGTATTATCAGAT
66 TTATTATGTATTATGTAATGTATTATCAGAT
*
40093323 TATATATAAGTTACGAAAGTTATTATGTAAGTTATACAAGCTTAT-ATATAAGTTATGTATTATG
1 TATATATAAGTTACGAAAGTTATTATGTAAGTTATACAAGATTATAATATAAGTTATGTATTATG
40093387 TTATTATGTATTATGTAA
66 TTATTATGTATTATGTAA
40093405 GTTATGCAAG
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
95 37 0.48
96 40 0.52
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.46
Consensus pattern (96 bp):
TATATATAAGTTACGAAAGTTATTATGTAAGTTATACAAGATTATAATATAAGTTATGTATTATG
TTATTATGTATTATGTAATGTATTATCAGAT
Found at i:40093421 original size:52 final size:52
Alignment explanation
Indices: 40093343--40093451 Score: 175
Period size: 52 Copynumber: 2.1 Consensus size: 52
40093333 TTACGAAAGT
*
40093343 TATTATGTAAGTTATACAAGCTTATATA-TAAGTTATGTATTATGTTATTATG
1 TATTATGTAAGTTATACAAGCTTATATACCAA-TTATGTATTATGTTATTATG
* *
40093395 TATTATGTAAGTTATGCAAGCTTATATACCAATTATGTATTGTGTTATTATG
1 TATTATGTAAGTTATACAAGCTTATATACCAATTATGTATTATGTTATTATG
40093447 TATTA
1 TATTA
40093452 AGTTATATAC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
52 51 0.96
53 2 0.04
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.48
Consensus pattern (52 bp):
TATTATGTAAGTTATACAAGCTTATATACCAATTATGTATTATGTTATTATG
Found at i:40094713 original size:52 final size:52
Alignment explanation
Indices: 40094652--40094750 Score: 180
Period size: 52 Copynumber: 1.9 Consensus size: 52
40094642 GGTTATGTAA
*
40094652 ATTATTACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAATTTACCGT
1 ATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAATTTACCGT
*
40094704 ATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAGTTTGAATTT
1 ATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAATTT
40094751 TCTTATTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.31, C:0.18, G:0.06, T:0.44
Consensus pattern (52 bp):
ATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAATTTACCGT
Found at i:40094735 original size:27 final size:27
Alignment explanation
Indices: 40094657--40094735 Score: 65
Period size: 25 Copynumber: 3.0 Consensus size: 27
40094647 TGTAAATTAT
40094657 TACCTAAAAATGTTCTTACTTTCTTAA
1 TACCTAAAAATGTTCTTACTTTCTTAA
* ** * ** *
40094684 -CCCT-AATTTGAAT-TTACCGTATTAA
1 TACCTAAAAATG-TTCTTACTTTCTTAA
40094709 TACCTAAAAATGTTCTTACTTTCTTAA
1 TACCTAAAAATGTTCTTACTTTCTTAA
40094736 CCCTAGTTTG
Statistics
Matches: 34, Mismatches: 14, Indels: 8
0.61 0.25 0.14
Matches are distributed among these distances:
25 13 0.38
26 8 0.24
27 13 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (27 bp):
TACCTAAAAATGTTCTTACTTTCTTAA
Found at i:40096713 original size:28 final size:28
Alignment explanation
Indices: 40096658--40096715 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
40096648 ACTCTTAAAT
* *
40096658 CTTAAACCATAAACTTTAAAGCATAACC
1 CTTAAACCATAAACTTAAAACCATAACC
*
40096686 CTTAAACCCTAAACTGTAAAACCA-AACC
1 CTTAAACCATAAACT-TAAAACCATAACC
40096714 CT
1 CT
40096716 AAATATATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.45, C:0.29, G:0.03, T:0.22
Consensus pattern (28 bp):
CTTAAACCATAAACTTAAAACCATAACC
Found at i:40098829 original size:52 final size:49
Alignment explanation
Indices: 40098732--40099098 Score: 431
Period size: 46 Copynumber: 7.6 Consensus size: 49
40098722 TTTGAGTACT
* * **
40098732 TCTGATCAAGTG---ATAAAGTGATAAGTGGTAACTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
* *
40098778 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
40098830 TCTGATCAAGTG---ATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
40098876 TCTGATCAAGTGAC---AAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
40098922 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
* *
40098974 TCTGATCAAGTGATAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
* **
40099026 TCTGATCAAGAGAC---AAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
40099072 TCTGATCAAGTGAC---AAAGTGATAAGTG
1 TCTGATCAAGTGACAATAAAGTGATAAGTG
40099099 GCTACACTTA
Statistics
Matches: 288, Mismatches: 19, Indels: 28
0.86 0.06 0.08
Matches are distributed among these distances:
46 154 0.53
48 1 0.00
49 2 0.01
50 1 0.00
52 130 0.45
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (49 bp):
TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
Found at i:40098852 original size:98 final size:97
Alignment explanation
Indices: 40098732--40099098 Score: 492
Period size: 98 Copynumber: 3.7 Consensus size: 97
40098722 TTTGAGTACT
* * *
40098732 TCTGATCAAGTGATAAAGTGATAAGTGGTAACTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-
*
40098797 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
* *
40098830 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
40098890 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
66 AAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
40098922 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGTG---A-T--AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
*
40098987 TAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
60 CAAGTG-AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* * *
40099026 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-AAGT
40099091 GATAAGTG
65 GA-AAGTG
40099099 GCTACACTTA
Statistics
Matches: 238, Mismatches: 17, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
92 41 0.17
95 1 0.00
96 1 0.00
98 143 0.60
99 10 0.04
101 1 0.00
104 41 0.17
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (97 bp):
TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:40098993 original size:7 final size:7
Alignment explanation
Indices: 40098976--40099009 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
40098966 TACACTTATC
40098976 TGATCAAG
1 TGAT-AAG
40098984 TGATAAG
1 TGATAAG
*
40098991 TGAAAAG
1 TGATAAG
40098998 TGATAAG
1 TGATAAG
40099005 TGATA
1 TGATA
40099010 GCTTCGGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.44, C:0.03, G:0.26, T:0.26
Consensus pattern (7 bp):
TGATAAG
Found at i:40099080 original size:196 final size:196
Alignment explanation
Indices: 40098746--40099098 Score: 598
Period size: 196 Copynumber: 1.8 Consensus size: 196
40098736 ATCAAGTGAT
* * *
40098746 AAAGTGATAAGTGGTAACTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTA
1 AAAGTGATAAGTGATAACTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
* * * *
40098811 ATAGCTTCGGCTATACTTATCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
40098876 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
131 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
40098941 G
196 G
* * * *
40098942 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGATAAGTGAAAAGTGATAAGTG
1 AAAGTGATAAGTGATAACTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
*
40099007 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
40099072 TCTGATCAAGTGACAAAGTGATAAGTG
131 TCTGATCAAGTGACAAAGTGATAAGTG
40099099 GCTACACTTA
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
196 145 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (196 bp):
AAAGTGATAAGTGATAACTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
G
Found at i:40099106 original size:37 final size:37
Alignment explanation
Indices: 40099062--40099207 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
40099052 GATAGCTTTA
**
40099062 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
40099099 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
40099136 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
40099173 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
40099208 ATCATACGTA
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 88 0.85
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:40099135 original size:150 final size:150
Alignment explanation
Indices: 40098732--40099087 Score: 478
Period size: 150 Copynumber: 2.4 Consensus size: 150
40098722 TTTGAGTACT
* * * * *
40098732 TCTGATCAAGTGATAAAGTGATAAGTGGTAACTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* * * *
40098797 GAAAGTGATAAGTAATAGCTTC-G---GCTATACTTATC---TGATCAAGTGATAAAGTGATAAG
66 GAAAGTGATAACT-ATAGCTTCAGCAAACTAAACTGATCAAGTGATCAAGTGATAAAGTGATAAG
40098855 TGATAGCTTCGGCTATACTTA
130 TGATAGCTTCGGCTATACTTA
*
40098876 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* * * * *
40098941 GAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAT-AAGTGA-AAAGTGATAA
66 GAAAGTGATAACT-ATAGCTTCAGC-AAACTAAACTGATCAAGTGATCAAGTGATAAAGTGATAA
40099004 GTGATAGCTTCGGCTATACTTA
129 GTGATAGCTTCGGCTATACTTA
*
40099026 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAA
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAA
40099088 AGTGATAAGT
Statistics
Matches: 192, Mismatches: 12, Indels: 10
0.90 0.06 0.05
Matches are distributed among these distances:
144 82 0.43
145 1 0.01
149 7 0.04
150 92 0.48
151 6 0.03
152 4 0.02
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (150 bp):
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
GAAAGTGATAACTATAGCTTCAGCAAACTAAACTGATCAAGTGATCAAGTGATAAAGTGATAAGT
GATAGCTTCGGCTATACTTA
Found at i:40099874 original size:31 final size:32
Alignment explanation
Indices: 40099812--40099874 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
40099802 TGTTACATAT
*
40099812 ATCCCCACAACCCCTTAAAGCATAACCCCTAA
1 ATCCCCACAACCCCTTAAAGCATAACACCTAA
*
40099844 ATCCCC-CTAACCCC-TAAATCATAACACCTAA
1 ATCCCCAC-AACCCCTTAAAGCATAACACCTAA
40099875 CCCTTAAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.38, C:0.43, G:0.02, T:0.17
Consensus pattern (32 bp):
ATCCCCACAACCCCTTAAAGCATAACACCTAA
Found at i:40099893 original size:21 final size:21
Alignment explanation
Indices: 40099849--40099893 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
40099839 CCTAAATCCC
* * *
40099849 CCTAACCCCTAAATCATAACA
1 CCTAACCCCTAAACCACAAAA
*
40099870 CCTAACCCTTAAACCACAAAA
1 CCTAACCCCTAAACCACAAAA
40099891 CCT
1 CCT
40099894 TGAACCTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.40, G:0.00, T:0.18
Consensus pattern (21 bp):
CCTAACCCCTAAACCACAAAA
Found at i:40100415 original size:111 final size:112
Alignment explanation
Indices: 40100105--40100416 Score: 430
Period size: 113 Copynumber: 2.8 Consensus size: 112
40100095 TAAATCCCTG
* *
40100105 AGCATTAGCGGCGCTTTATTAAAAATGCCGCTAAACCCCTGAAAGCTAAGAAAACGGTGTCGTTG
1 AGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAACCCCCGAAAGCTAAGAAAACGGTGTCGTTG
* *
40100170 GGTTTAATTTTTTTTGCGGCGCTTTCATAAAAGCGCCGCTAAAAACCC
66 GGTTTAA-TTTTTTTGCGGCGCTTCCATAAAAACGCCGCTAAAAACCC
* * * *
40100218 AGCATTAGCGACGCTTTACTAAAAACGCCGCTAAACCCCCGAAAGCAAAGAAAACGATGTCGTTG
1 AGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAACCCCCGAAAGCTAAGAAAACGGTGTCGTTG
*
40100283 GGTTTAATTTTTTTGCGGCGCTTCCATAAAAACGCCGCT-AAAGCCC
66 GGTTTAATTTTTTTGCGGCGCTTCCATAAAAACGCCGCTAAAAACCC
* * * * **
40100329 TGCATTAGCGGCGCATTATTAAAAACGCCGCTAAACCCCCCGGAAGCTTAGAAAACGGCATCGTT
1 AGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAA-CCCCCGAAAGCTAAGAAAACGGTGTCGTT
* * *
40100394 GTGCTT-AGTTTTTTGCGGCGCTT
65 GGGTTTAATTTTTTTGCGGCGCTT
40100417 TAGCAAAAGC
Statistics
Matches: 176, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
111 53 0.30
112 57 0.32
113 66 0.38
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (112 bp):
AGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAACCCCCGAAAGCTAAGAAAACGGTGTCGTTG
GGTTTAATTTTTTTGCGGCGCTTCCATAAAAACGCCGCTAAAAACCC
Found at i:40100430 original size:111 final size:110
Alignment explanation
Indices: 40100105--40100434 Score: 428
Period size: 111 Copynumber: 3.0 Consensus size: 110
40100095 TAAATCCCTG
* *
40100105 AGCATTAGCGGCGCTTTATTAAAAATGCCGCTAAACCCCTGAAAGCTAAGAAAACGGTGTCGTTG
1 AGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAACCCCCGAAAGCTAAGAAAACGGTGTCGTTG
40100170 GGTTTAATTTTTTTTGCGGCGCTTTCATAAAAGCGCCGCTAAAAACCC
66 GGTTTAA-TTTTTTTGCGGCGCTTT-ATAAAAGCGCCGCT-AAAACCC
* * * *
40100218 AGCATTAGCGACGCTTTACTAAAAACGCCGCTAAACCCCCGAAAGCAAAGAAAACGATGTCGTTG
1 AGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAACCCCCGAAAGCTAAGAAAACGGTGTCGTTG
* * *
40100283 GGTTTAATTTTTTTGCGGCGCTTCCATAAAAACGCCGCTAAAGCCC
66 GGTTTAATTTTTTTGCGGCGCTT-TATAAAAGCGCCGCTAAAACCC
* * * * **
40100329 TGCATTAGCGGCGCATTATTAAAAACGCCGCTAAACCCCCCGGAAGCTTAGAAAACGGCATCGTT
1 AGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAA-CCCCCGAAAGCTAAGAAAACGGTGTCGTT
* * * *
40100394 GTGCTT-AGTTTTTTGCGGCGCTTTAGCAAAAGCGCCGCTAA
65 GGGTTTAATTTTTTTGCGGCGCTTTA-TAAAAGCGCCGCTAA
40100435 TCTTATTTTC
Statistics
Matches: 189, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
110 1 0.01
111 66 0.35
112 56 0.30
113 66 0.35
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (110 bp):
AGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAACCCCCGAAAGCTAAGAAAACGGTGTCGTTG
GGTTTAATTTTTTTGCGGCGCTTTATAAAAGCGCCGCTAAAACCC
Found at i:40101292 original size:14 final size:14
Alignment explanation
Indices: 40101269--40101308 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
40101259 ACAGAAAAGT
*
40101269 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
40101283 AAATCATTTTACGG
1 AAAACATTTTACAG
40101297 AAAACATTTTAC
1 AAAACATTTTAC
40101309 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:40101294 original size:34 final size:35
Alignment explanation
Indices: 40101234--40101300 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
40101224 CAAACACCAG
* *
40101234 AAAATATTTTCCAGTAAGTCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
40101269 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
40101301 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:40103842 original size:13 final size:13
Alignment explanation
Indices: 40103824--40103848 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40103814 TTTTTTTATA
40103824 TTTTTAATTAATC
1 TTTTTAATTAATC
40103837 TTTTTAATTAAT
1 TTTTTAATTAAT
40103849 AACTCTTTTA
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:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATC
Found at i:40106942 original size:18 final size:17
Alignment explanation
Indices: 40106921--40106974 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
40106911 GAAAAAACAA
40106921 ATATATTTGAAATATATT
1 ATATATTTGAAATA-ATT
** *
40106939 ATATA-TAAAAATAATA
1 ATATATTTGAAATAATT
40106955 ATGATATTTGAAATAATT
1 AT-ATATTTGAAATAATT
40106973 AT
1 AT
40106975 TTGATTTTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
16 4 0.14
17 9 0.32
18 15 0.54
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.43
Consensus pattern (17 bp):
ATATATTTGAAATAATT
Found at i:40113461 original size:15 final size:16
Alignment explanation
Indices: 40113441--40113478 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
40113431 AAATTATTAT
*
40113441 TTTTTAATTTT-CATA
1 TTTTTAATTTTAAATA
*
40113456 TTTTTATTTTTAAATA
1 TTTTTAATTTTAAATA
40113472 TTTTTAA
1 TTTTTAA
40113479 AACAGAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTAATTTTAAATA
Found at i:40116954 original size:25 final size:24
Alignment explanation
Indices: 40116922--40116970 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
40116912 ATATCTATAA
*
40116922 ATATTTTTATATACATTAATTAAAT
1 ATATTTTTAAATACATTAA-TAAAT
*
40116947 ATATTTTTAAATATATTAATAAAT
1 ATATTTTTAAATACATTAATAAAT
40116971 CCAAAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
ATATTTTTAAATACATTAATAAAT
Found at i:40127661 original size:22 final size:22
Alignment explanation
Indices: 40127602--40127655 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
40127592 TGTTGTTTTG
*
40127602 TTACTATTTTACTATTATATTG
1 TTACTATTTTACTATTATATTA
* *
40127624 CTACTATTTCACTATTATATTA
1 TTACTATTTTACTATTATATTA
40127646 TTACTATTTT
1 TTACTATTTT
40127656 GTTATTTTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.28, C:0.13, G:0.02, T:0.57
Consensus pattern (22 bp):
TTACTATTTTACTATTATATTA
Found at i:40128438 original size:21 final size:22
Alignment explanation
Indices: 40128403--40128444 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
40128393 TAAAACATGA
*
40128403 AAAATAAATGAACTAAATTCTT
1 AAAAGAAATGAACTAAATTCTT
40128425 AAAAGAAA-GAACTAAATTCT
1 AAAAGAAATGAACTAAATTCT
40128445 AAATATACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (22 bp):
AAAAGAAATGAACTAAATTCTT
Found at i:40137756 original size:20 final size:20
Alignment explanation
Indices: 40137731--40137771 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40137721 TTGGTGAAAT
* *
40137731 ATCCTAGAATTTAAATTTGC
1 ATCCTAAAAATTAAATTTGC
*
40137751 ATCCTAAAAATTATATTTGC
1 ATCCTAAAAATTAAATTTGC
40137771 A
1 A
40137772 ATGTGGATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (20 bp):
ATCCTAAAAATTAAATTTGC
Found at i:40159402 original size:22 final size:20
Alignment explanation
Indices: 40159375--40159415 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
40159365 AATAACTTCC
40159375 AAAAAATAGATTGATTTTCTAA
1 AAAAAATAGA-T-ATTTTCTAA
*
40159397 AAAAAATTGATATTTTCTA
1 AAAAAATAGATATTTTCTA
40159416 GTGTTTGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (20 bp):
AAAAAATAGATATTTTCTAA
Found at i:40159878 original size:22 final size:19
Alignment explanation
Indices: 40159833--40159878 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 19
40159823 TAAATAATAT
*
40159833 ATTTAAAATATTATTTGAA
1 ATTTAAAATATTATTTAAA
40159852 ATTTAAAATTATTACTGTTAAA
1 ATTTAAAA-TATTA-T-TTAAA
40159874 ATTTA
1 ATTTA
40159879 TTATTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 5 0.22
21 1 0.04
22 9 0.39
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (19 bp):
ATTTAAAATATTATTTAAA
Found at i:40159902 original size:19 final size:18
Alignment explanation
Indices: 40159870--40159909 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
40159860 TTATTACTGT
*
40159870 TAAAATTTATTATTAAAA
1 TAAAATTTAATATTAAAA
*
40159888 TAAAATTGTAATATTTAAA
1 TAAAATT-TAATATTAAAA
40159907 TAA
1 TAA
40159910 TTTATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:40159906 original size:33 final size:33
Alignment explanation
Indices: 40159869--40159958 Score: 78
Period size: 35 Copynumber: 2.6 Consensus size: 33
40159859 ATTATTACTG
*
40159869 TTAAAATTTATTATTAAAATAA-AATTGTAATA
1 TTAAAATTTATTATTAAAATAATAATTATAATA
*
40159901 TTTAAATAATTTATTA--AAAATAATTAATTATATTA
1 -TT-AA-AATTTATTATTAAAATAA-TAATTATAATA
*
40159936 TTAAATATTTATTTTTAATAATA
1 TTAAA-ATTTATTATTAA-AATA
40159959 TTAAAAATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
32 1 0.02
33 18 0.39
34 4 0.09
35 19 0.41
36 4 0.09
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (33 bp):
TTAAAATTTATTATTAAAATAATAATTATAATA
Found at i:40164192 original size:23 final size:23
Alignment explanation
Indices: 40164164--40164218 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
40164154 AGCCCATTTA
40164164 AGCTTCCTGATAGGCTCTTTGTG
1 AGCTTCCTGATAGGCTCTTTGTG
* *
40164187 AGCTTCCCGATATGCTCTTTGTG
1 AGCTTCCTGATAGGCTCTTTGTG
*
40164210 AGTTTCCTG
1 AGCTTCCTG
40164219 TTATATGGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.13, C:0.24, G:0.24, T:0.40
Consensus pattern (23 bp):
AGCTTCCTGATAGGCTCTTTGTG
Found at i:40166347 original size:23 final size:25
Alignment explanation
Indices: 40166321--40166372 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
40166311 TTATAATTAT
40166321 TTAATTA-GATAAATAT-TATTTTA
1 TTAATTATGATAAATATATATTTTA
**
40166344 TTAA-TATTTTAAATATATATTTTA
1 TTAATTATGATAAATATATATTTTA
40166368 TTAAT
1 TTAAT
40166373 ATTTTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 2 0.08
23 11 0.46
24 11 0.46
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTAATTATGATAAATATATATTTTA
Found at i:40166351 original size:11 final size:11
Alignment explanation
Indices: 40166337--40166380 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
40166327 AGATAAATAT
40166337 TATTTTATTAA
1 TATTTTATTAA
*
40166348 TATTTTAAATATA
1 TATTTT-ATTA-A
40166361 TATTTTATTAA
1 TATTTTATTAA
40166372 TATTTTATT
1 TATTTTATT
40166381 TAGTATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:40166364 original size:24 final size:23
Alignment explanation
Indices: 40166330--40166378 Score: 89
Period size: 24 Copynumber: 2.1 Consensus size: 23
40166320 TTTAATTAGA
40166330 TAAATATTATTTTATTAATATTT
1 TAAATATTATTTTATTAATATTT
40166353 TAAATATATATTTTATTAATATTT
1 TAAATAT-TATTTTATTAATATTT
40166377 TA
1 TA
40166379 TTTAGTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TAAATATTATTTTATTAATATTT
Found at i:40167763 original size:207 final size:207
Alignment explanation
Indices: 40167408--40167826 Score: 811
Period size: 207 Copynumber: 2.0 Consensus size: 207
40167398 AAGTAATAGT
*
40167408 GAAATTATAGATAATGTTACATATAAGCATGTTATATACATTAAGGATGTGGAATGGACAGGAGG
1 GAAATTATAGATAATGTTACATATAAGCATGTTATATACATTAAGGATGTGGAATGCACAGGAGG
40167473 AGGAAAATATATATGAATATTCAGCTAGCATGGGTTTACATTAAAAATGGCTAATTTGCATGTTT
66 AGGAAAATATATATGAATATTCAGCTAGCATGGGTTTACATTAAAAATGGCTAATTTGCATGTTT
*
40167538 TAGGCTCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGGGTAATTTTGTAAGAATGTCAAAAA
131 TAGGCTCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGGGTAATTTTGTAAAAATGTCAAAAA
40167603 ACCAAATTGCAA
196 ACCAAATTGCAA
40167615 GAAATTATAGATAATGTTACATATAAGCATGTTATATACATTAAGGATGTGGAATGCACAGGAGG
1 GAAATTATAGATAATGTTACATATAAGCATGTTATATACATTAAGGATGTGGAATGCACAGGAGG
40167680 AGGAAAATATATATGAATATTCAGCTAGCATGGGTTTACATTAAAAATGGCTAATTTGCATGTTT
66 AGGAAAATATATATGAATATTCAGCTAGCATGGGTTTACATTAAAAATGGCTAATTTGCATGTTT
40167745 TAGGCTCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGGGTAATTTTGTAAAAATGTCAAAAA
131 TAGGCTCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGGGTAATTTTGTAAAAATGTCAAAAA
*
40167810 ACCAAATTGCAG
196 ACCAAATTGCAA
40167822 GAAAT
1 GAAAT
40167827 GAATTTTTTT
Statistics
Matches: 209, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
207 209 1.00
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.30
Consensus pattern (207 bp):
GAAATTATAGATAATGTTACATATAAGCATGTTATATACATTAAGGATGTGGAATGCACAGGAGG
AGGAAAATATATATGAATATTCAGCTAGCATGGGTTTACATTAAAAATGGCTAATTTGCATGTTT
TAGGCTCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGGGTAATTTTGTAAAAATGTCAAAAA
ACCAAATTGCAA
Found at i:40170131 original size:105 final size:104
Alignment explanation
Indices: 40169950--40170158 Score: 375
Period size: 105 Copynumber: 2.0 Consensus size: 104
40169940 TGGGTTATTC
40169950 TTGATACGTATAGATTCATATTTGAAATGAATTAATATGATTAAAGTTTATACGAGCTTACTAAG
1 TTGATACGTATAGATTCATATTTGAAATGAATTAATATGATTAAAGTTTATACGAGCTTACTAAG
*
40170015 CATTTGTTGCTTATGTAGTTGTTTT-CTAGTACTTTTCAG
66 CATTTGTTGCTTACGTAGTTGTTTTCCT-GTACTTTTCAG
40170054 TTGATACGTATAGATTTCATATTTGAAATGAATTAATATGATTAAAGTTTATACGAGCTTACTAA
1 TTGATACGTATAGA-TTCATATTTGAAATGAATTAATATGATTAAAGTTTATACGAGCTTACTAA
*
40170119 GCATTTGTTGCTTACGTAGTTGTTTTCCTTTACTTTTCAG
65 GCATTTGTTGCTTACGTAGTTGTTTTCCTGTACTTTTCAG
40170159 ATTATCGAAA
Statistics
Matches: 101, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
104 14 0.14
105 85 0.84
106 2 0.02
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (104 bp):
TTGATACGTATAGATTCATATTTGAAATGAATTAATATGATTAAAGTTTATACGAGCTTACTAAG
CATTTGTTGCTTACGTAGTTGTTTTCCTGTACTTTTCAG
Found at i:40173002 original size:23 final size:23
Alignment explanation
Indices: 40172949--40172992 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
40172939 CTTTCTTACT
*
40172949 GTAGTAATTTTCGGGGTATTAAA
1 GTAGTAATTTTCGGGATATTAAA
40172972 GTAGTAATTTTCGGGATATTA
1 GTAGTAATTTTCGGGATATTA
40172993 CAGTTATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.41
Consensus pattern (23 bp):
GTAGTAATTTTCGGGATATTAAA
Found at i:40175635 original size:12 final size:12
Alignment explanation
Indices: 40175616--40175656 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
40175606 AAAGCCTTAA
40175616 ACACACATACAC
1 ACACACATACAC
*
40175628 AGACACATACAC
1 ACACACATACAC
*
40175640 ACACACACACAC
1 ACACACATACAC
40175652 ACACA
1 ACACA
40175657 TATAAGGCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.51, C:0.41, G:0.02, T:0.05
Consensus pattern (12 bp):
ACACACATACAC
Found at i:40175641 original size:2 final size:2
Alignment explanation
Indices: 40175616--40175656 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
40175606 AAAGCCTTAA
* * *
40175616 AC AC AC AT AC AC AG AC AC AT AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
40175657 TATAAGGCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.41, G:0.02, T:0.05
Consensus pattern (2 bp):
AC
Found at i:40177332 original size:139 final size:138
Alignment explanation
Indices: 40177184--40177460 Score: 511
Period size: 139 Copynumber: 2.0 Consensus size: 138
40177174 TGTGAAATTT
40177184 AATTTAATAATATAAATAGTAGATATAAATAAAATTATTACCATTTATGTTTAGTGATTTTTTTT
1 AATTTAATAATATAAATAGTAGATATAAATAAAATTATTACCATTTATGTTTAGTGATTTTTTTT
*
40177249 GGATAATTTTGATTTTTTTATTTGAGAGTAAAGGGTGATAAGTAAAAGTTTAG-GTGGAAAATAA
66 GGATAATTTTGA-TTTTTTATTTGAGAGTAAAGGGTGAGAAGTAAAAGTTTAGAG-GGAAAATAA
40177313 AAAGTTTTGG
129 AAAGTTTTGG
*
40177323 AATTTAATAATATAAATAGTAGATATAAATAAAATTATTACTATTTATGTTTAGTGATTTTTTTT
1 AATTTAATAATATAAATAGTAGATATAAATAAAATTATTACCATTTATGTTTAGTGATTTTTTTT
40177388 GGATAATTTTGATTTTTTATTTGAGAGTAAAGGGTGAGAAGTAAAAGTTTAGAGGGAAAATAAAA
66 GGATAATTTTGATTTTTTATTTGAGAGTAAAGGGTGAGAAGTAAAAGTTTAGAGGGAAAATAAAA
40177453 AGTTTTGG
131 AGTTTTGG
40177461 GGAATAAAAG
Statistics
Matches: 135, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
138 58 0.43
139 77 0.57
ACGTcount: A:0.39, C:0.01, G:0.18, T:0.42
Consensus pattern (138 bp):
AATTTAATAATATAAATAGTAGATATAAATAAAATTATTACCATTTATGTTTAGTGATTTTTTTT
GGATAATTTTGATTTTTTATTTGAGAGTAAAGGGTGAGAAGTAAAAGTTTAGAGGGAAAATAAAA
AGTTTTGG
Found at i:40177479 original size:16 final size:16
Alignment explanation
Indices: 40177429--40177480 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 16
40177419 GGGTGAGAAG
40177429 TAAAAGTTTAGAGGGAAAA
1 TAAAAGTTT-GAGGG--AA
40177448 TAAAAAGTTTTG-GGGAA
1 T-AAAAG-TTTGAGGGAA
40177465 TAAAAGTTTGAGGGAA
1 TAAAAGTTTGAGGGAA
40177481 AGTAAATAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
15 4 0.13
16 10 0.33
17 3 0.10
19 4 0.13
20 6 0.20
21 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.29, T:0.25
Consensus pattern (16 bp):
TAAAAGTTTGAGGGAA
Found at i:40178174 original size:31 final size:30
Alignment explanation
Indices: 40178133--40178207 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
40178123 TTTTAATTTG
* *
40178133 ATCAAATTTAATCTTAGTATTTTTTGAATTA
1 ATCAATTTTAATCTTA-TACTTTTTGAATTA
*
40178164 ATCAATTTTAATTCTTATACTTTTTGAATTT
1 ATCAATTTTAA-TCTTATACTTTTTGAATTA
* *
40178195 TTAAATTTTAATC
1 ATCAATTTTAATC
40178208 CTAATCTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 2 0.05
31 31 0.82
32 5 0.13
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.55
Consensus pattern (30 bp):
ATCAATTTTAATCTTATACTTTTTGAATTA
Found at i:40186622 original size:42 final size:43
Alignment explanation
Indices: 40186543--40186717 Score: 146
Period size: 42 Copynumber: 4.1 Consensus size: 43
40186533 CTAGTGTATC
* * * *
40186543 TGCTTT-GATTTATTCAATGATGCACTTATGCGTCAGTATAAT
1 TGCTTTCGATATATTCGATGATGCACTTGTGTGTCAGTATAAT
* * *
40186585 TGCTTT-GGTATATTCGATGATGCACTTGTGTGCCAGTATATT
1 TGCTTTCGATATATTCGATGATGCACTTGTGTGTCAGTATAAT
* * * *
40186627 TG-TTTCGATACATCCGATGATGTACTATGTGTGTTAGTATAAT
1 TGCTTTCGATATATTCGATGATGCACT-TGTGTGTCAGTATAAT
* * *
40186670 T-ATTTC-AGT-TCATTCGATAATGCACCTTGTGTGTTAGTATAAT
1 TGCTTTCGA-TAT-ATTCGATGATGCA-CTTGTGTGTCAGTATAAT
40186713 TGCTT
1 TGCTT
40186718 CGACTTGCCC
Statistics
Matches: 107, Mismatches: 19, Indels: 12
0.78 0.14 0.09
Matches are distributed among these distances:
41 3 0.03
42 54 0.50
43 46 0.43
44 4 0.04
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.43
Consensus pattern (43 bp):
TGCTTTCGATATATTCGATGATGCACTTGTGTGTCAGTATAAT
Found at i:40186666 original size:43 final size:43
Alignment explanation
Indices: 40186559--40186720 Score: 143
Period size: 43 Copynumber: 3.8 Consensus size: 43
40186549 GATTTATTCA
* * * * *
40186559 ATGATGCACTTATGCGTCAGTATAATTGCTTT-G-GTATATTCG
1 ATGATGCACTTGTGTGTTAGTATAATTG-TTTCGAGTACATCCG
** *
40186601 ATGATGCACTTGTGTGCCAGTATATTTGTTTCGA-TACATCCG
1 ATGATGCACTTGTGTGTTAGTATAATTGTTTCGAGTACATCCG
* * * *
40186643 ATGATGTACTATGTGTGTTAGTATAATTATTTC-AGTTCATTCG
1 ATGATGCACT-TGTGTGTTAGTATAATTGTTTCGAGTACATCCG
* *
40186686 ATAATGCACCTTGTGTGTTAGTATAATTGCTTCGA
1 ATGATGCA-CTTGTGTGTTAGTATAATTGTTTCGA
40186721 CTTGCCCAAT
Statistics
Matches: 97, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
41 3 0.03
42 41 0.42
43 50 0.52
44 3 0.03
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.41
Consensus pattern (43 bp):
ATGATGCACTTGTGTGTTAGTATAATTGTTTCGAGTACATCCG
Found at i:40191922 original size:5 final size:5
Alignment explanation
Indices: 40191912--40191939 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
40191902 GTGAGATGGA
40191912 AATCG AATCG AATCG AATCG AATCG AAT
1 AATCG AATCG AATCG AATCG AATCG AAT
40191940 ATATTTGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (5 bp):
AATCG
Found at i:40192870 original size:9 final size:9
Alignment explanation
Indices: 40192856--40192892 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
40192846 TATAGTTTGA
40192856 TATTCGAAT
1 TATTCGAAT
40192865 TATTCGAAT
1 TATTCGAAT
*
40192874 TATTCGAGT
1 TATTCGAAT
40192883 TATTCGAAT
1 TATTCGAAT
40192892 T
1 T
40192893 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:40194113 original size:17 final size:18
Alignment explanation
Indices: 40194086--40194138 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
40194076 GTCAGTGAGC
*
40194086 AATTTTGGTATCAATAAA
1 AATTATGGTATCAATAAA
*
40194104 AA-TATGGTATCGATAAA
1 AATTATGGTATCAATAAA
40194121 AATTGTATGGTATCAATA
1 AA-T-TATGGTATCAATA
40194139 CGTTTTGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 15 0.52
18 2 0.07
20 12 0.41
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (18 bp):
AATTATGGTATCAATAAA
Found at i:40194373 original size:23 final size:21
Alignment explanation
Indices: 40194343--40194384 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
40194333 AAAATAAATT
*
40194343 TTATTCAAAAACATTTTATTTG
1 TTATTC-AAAACAATTTATTTG
40194365 TTATATCAAAACAATTTATT
1 TTAT-TCAAAACAATTTATT
40194385 AAATAAAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (21 bp):
TTATTCAAAACAATTTATTTG
Found at i:40197343 original size:28 final size:30
Alignment explanation
Indices: 40197288--40197345 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
40197278 TCATAAATTT
40197288 TTATATTATTTTTTAATATAAAATTTAATCC
1 TTATATTATTTTTT-ATATAAAATTTAATCC
40197319 TTATA-TATTTTTT-TA-AAAATTTTAATC
1 TTATATTATTTTTTATATAAAA-TTTAATC
40197346 TCTATTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 4 0.15
28 9 0.35
30 8 0.31
31 5 0.19
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (30 bp):
TTATATTATTTTTTATATAAAATTTAATCC
Found at i:40200303 original size:14 final size:13
Alignment explanation
Indices: 40200284--40200313 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
40200274 GGATGTCACT
40200284 ACATTGAAGAGCCA
1 ACATTGAAGAG-CA
40200298 ACATTGAAGAGCA
1 ACATTGAAGAGCA
40200311 ACA
1 ACA
40200314 ATCCTCAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (13 bp):
ACATTGAAGAGCA
Found at i:40206794 original size:17 final size:16
Alignment explanation
Indices: 40206770--40206813 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
40206760 CAATAGTCAG
40206770 TCCTTCACCAACCTCC
1 TCCTTCACCAACCTCC
**
40206786 TCACTTCACTCCTCCTCC
1 TC-CTTCAC-CAACCTCC
40206804 TCCTTCACCA
1 TCCTTCACCA
40206814 CCCTATCTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 3 0.13
17 12 0.52
18 8 0.35
ACGTcount: A:0.16, C:0.55, G:0.00, T:0.30
Consensus pattern (16 bp):
TCCTTCACCAACCTCC
Found at i:40222710 original size:21 final size:21
Alignment explanation
Indices: 40222684--40222726 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
40222674 TTGTATGTCT
*
40222684 ACAATTACATTCTCGTTAGGC
1 ACAATTACATTCTCCTTAGGC
*
40222705 ACAATTTCATTCTCCTTAGGC
1 ACAATTACATTCTCCTTAGGC
40222726 A
1 A
40222727 AAATATCAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (21 bp):
ACAATTACATTCTCCTTAGGC
Found at i:40227791 original size:18 final size:18
Alignment explanation
Indices: 40227765--40227809 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
40227755 TTCTTCTTCA
*
40227765 TTTTCTCTTA-TTTATTT
1 TTTTATCTTATTTTATTT
40227782 GTTTTATCTTATTTTATTT
1 -TTTTATCTTATTTTATTT
*
40227801 TTTTTTCTT
1 TTTTATCTT
40227810 TTGCACATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTATCTTATTTTATTT
Found at i:40228616 original size:7 final size:7
Alignment explanation
Indices: 40228598--40228655 Score: 57
Period size: 7 Copynumber: 8.4 Consensus size: 7
40228588 TTTAACCGAA
40228598 TTTTTAT
1 TTTTTAT
40228605 TTTTT-T
1 TTTTTAT
*
40228611 TATTT-T
1 TTTTTAT
*
40228617 TATTTAT
1 TTTTTAT
*
40228624 TGTTTATT
1 TTTTTA-T
40228632 TTTTTAT
1 TTTTTAT
40228639 TTTTTAT
1 TTTTTAT
*
40228646 TTTATAT
1 TTTTTAT
40228653 TTT
1 TTT
40228656 GTGTCCTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
6 11 0.24
7 28 0.62
8 6 0.13
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.83
Consensus pattern (7 bp):
TTTTTAT
Found at i:40228617 original size:15 final size:15
Alignment explanation
Indices: 40228597--40228655 Score: 75
Period size: 15 Copynumber: 3.7 Consensus size: 15
40228587 ATTTAACCGA
40228597 ATTTTTATTTTTTTT
1 ATTTTTATTTTTTTT
40228612 ATTTTTATTTATTGTTT
1 ATTTTTATTT-TT-TTT
40228629 ATTTTT-TTATTTTTT
1 ATTTTTATT-TTTTTT
40228644 ATTTTATATTTT
1 ATTTT-TATTTT
40228656 GTGTCCTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
15 18 0.46
16 9 0.23
17 12 0.31
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (15 bp):
ATTTTTATTTTTTTT
Found at i:40232770 original size:18 final size:18
Alignment explanation
Indices: 40232749--40232797 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
40232739 AATTCACTTG
40232749 AGAAAAAA-ATAAACAAAA
1 AGAAAAAAGA-AAACAAAA
*
40232767 AGAAAAAAGAAAAGAAAA
1 AGAAAAAAGAAAACAAAA
40232785 ACG-AAAAAGAAAA
1 A-GAAAAAAGAAAA
40232798 GAGAAAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 26 0.93
19 2 0.07
ACGTcount: A:0.82, C:0.04, G:0.12, T:0.02
Consensus pattern (18 bp):
AGAAAAAAGAAAACAAAA
Found at i:40232779 original size:12 final size:12
Alignment explanation
Indices: 40232764--40232804 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
40232754 AAAATAAACA
40232764 AAAAGAAAAAAG
1 AAAAGAAAAAAG
*
40232776 AAAAGAAAAACG
1 AAAAGAAAAAAG
*
40232788 AAAAAGAAAAGAG
1 -AAAAGAAAAAAG
40232801 AAAA
1 AAAA
40232805 ATGAGAGGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:40232779 original size:13 final size:13
Alignment explanation
Indices: 40232749--40232805 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
40232739 AATTCACTTG
*
40232749 AGAAAAA-AATAA
1 AGAAAAAGAAAAA
*
40232761 ACAAAAAGAAAAA
1 AGAAAAAGAAAAA
40232774 AG-AAAAGAAAAA
1 AGAAAAAGAAAAA
* *
40232786 CGAAAAAGAAAAG
1 AGAAAAAGAAAAA
40232799 AGAAAAA
1 AGAAAAA
40232806 TGAGAGGCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
12 17 0.46
13 20 0.54
ACGTcount: A:0.81, C:0.04, G:0.14, T:0.02
Consensus pattern (13 bp):
AGAAAAAGAAAAA
Found at i:40232791 original size:25 final size:25
Alignment explanation
Indices: 40232749--40232805 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
40232739 AATTCACTTG
40232749 AGAAAAAAATAAACAAAAAGAAAAA
1 AGAAAAAAATAAACAAAAAGAAAAA
* *
40232774 AGAAAAGAA-AAACGAAAAAGAAAAG
1 AGAAAAAAATAAAC-AAAAAGAAAAA
40232799 AGAAAAA
1 AGAAAAA
40232806 TGAGAGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 4 0.14
25 24 0.86
ACGTcount: A:0.81, C:0.04, G:0.14, T:0.02
Consensus pattern (25 bp):
AGAAAAAAATAAACAAAAAGAAAAA
Found at i:40233328 original size:108 final size:108
Alignment explanation
Indices: 40233139--40233334 Score: 268
Period size: 108 Copynumber: 1.8 Consensus size: 108
40233129 TTTGTATTCT
* **
40233139 AGCAAAATTTGCTATCTTGATTAATTTGTTCATTTAGAGCTTTGCTCTCAACAAATTTCCATCTT
1 AGCAAAATTTGCTATCCTGATTAATTTGTTCATTTAGAGCTTTAATCTCAACAAATTTCCATCTT
40233204 ATCCATTGTGATAATCTTTTTCATCTTATACATCTCGTATCTC
66 ATCCATTGTGATAATCTTTTTCATCTTATACATCTCGTATCTC
* * * ** *
40233247 AGCAAAATTTGCTGTCCTGGTTGATTTGTTTGTTTAGAGCTTTAATCTCAACAAAATTT-CATTT
1 AGCAAAATTTGCTATCCTGATTAATTTGTTCATTTAGAGCTTTAATCTCAAC-AAATTTCCATCT
* * *
40233311 TGTCTATTTTGATAATCTTTTTCA
65 TATCCATTGTGATAATCTTTTTCA
40233335 AGCATTTTTC
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
108 69 0.92
109 6 0.08
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (108 bp):
AGCAAAATTTGCTATCCTGATTAATTTGTTCATTTAGAGCTTTAATCTCAACAAATTTCCATCTT
ATCCATTGTGATAATCTTTTTCATCTTATACATCTCGTATCTC
Found at i:40234083 original size:88 final size:88
Alignment explanation
Indices: 40233791--40234557 Score: 888
Period size: 88 Copynumber: 8.8 Consensus size: 88
40233781 GCCTCCATCA
* *
40233791 GTTGCAGTGGAGCTGGTTAAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGA
1 GTTGTAGTGGAGCTGGTTGAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGA
* *
40233856 AAACA-AAACCTTACCTC-CATCA
66 AGACACAAACCTTACCTCTC-TCG
* ** * *
40233878 GTTGCAGTGGAGCTGGTCAAAGATAGCAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGA
1 GTTGTAGTGGAGCTGGTTGAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGA
* * *
40233943 A-AAAAAAACCTTGCCTCTCTCG
66 AGACACAAACCTTACCTCTCTCG
* ** * *
40233965 GGTGTAGCAGAGCTGGTTGAAGACAGCAGATATTGCCTTTCTGCATTAACAGCGAAGCAGATCGA
1 GTTGTAGTGGAGCTGGTTGAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGA
40234030 AGACACAAACCTTACCTCTCTCG
66 AGACACAAACCTTACCTCTCTCG
* * * * * * *
40234053 GTTTTGGTGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTACACTGACAGCGAAGCAGGTCGA
1 GTTGTAGTGGAGCTGGTTGAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGA
* *
40234118 AGACACAAACCTTGCCTCTTTCG
66 AGACACAAACCTTACCTCTCTCG
* ** *
40234141 GATGTAGCAGAGCTGGTTGAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATTGA
1 GTTGTAGTGGAGCTGGTTGAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGA
* *
40234206 AGACACAAACCTTGCATCTCTCG
66 AGACACAAACCTTACCTCTCTCG
* * * * *
40234229 GTTGTGGTGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTGATAGCGAAGTA-AGTCG
1 GTTGTAGTGGAGCTGGTTGAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGA-TCG
40234293 AAGACACAAACCTTACCTCTCTCG
65 AAGACACAAACCTTACCTCTCTCG
* * * * * *
40234317 GTTGTAGTGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCTTGTATTAACAGCGAAGTAGATCGA
1 GTTGTAGTGGAGCTGGTTGAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGA
*
40234382 AAACA-AAACCTTACCTC-CATCG
66 AGACACAAACCTTACCTCTC-TCG
* * * * * * * *
40234404 GTTGCAGTGGAGCTGGTTAAAAATAGCAGATCTTGCATTCCTGCGTTAACAGTGAAGTAGATCGA
1 GTTGTAGTGGAGCTGGTTGAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGA
* *
40234469 A-A-ACAAATCTTGCCTC-CATCG
66 AGACACAAACCTTACCTCTC-TCG
* * * * *
40234490 GTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTT-CTCTTCCTGTACTGACGGCGAAGCAGATCG
1 GTTGTAGTGGAGCTGGTTGAAGACAGCAGATCTTGC-CTTCCTGCATTAACAGCGAAGCAGATCG
40234554 AAGA
65 AAGA
40234558 AGCCAGTCTT
Statistics
Matches: 583, Mismatches: 88, Indels: 18
0.85 0.13 0.03
Matches are distributed among these distances:
85 2 0.00
86 72 0.12
87 207 0.36
88 301 0.52
89 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.25
Consensus pattern (88 bp):
GTTGTAGTGGAGCTGGTTGAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGA
AGACACAAACCTTACCTCTCTCG
Found at i:40234220 original size:44 final size:44
Alignment explanation
Indices: 40233979--40234220 Score: 120
Period size: 44 Copynumber: 5.5 Consensus size: 44
40233969 TAGCAGAGCT
* ** *
40233979 GGTTGAAGACAGCAGATATTGCCTTTCTGCATTAACAGCGAAGCA
1 GGTTGAAGACA-CAAACCTTGCCTTCCTGCATTAACAGCGAAGCA
* * * * *** * * *
40234024 GATCGAAGACACAAACCTTACC-TCTCT-CGGTT-TTGGTGGAGCT
1 GGTTGAAGACACAAACCTTGCCTTC-CTGC-ATTAACAGCGAAGCA
* * * * *
40234067 GGTTGAAGACAACAGATCTTGCCTTCCTACACTGACAGCGAAGCA
1 GGTTGAAGAC-ACAAACCTTGCCTTCCTGCATTAACAGCGAAGCA
* * * * *
40234112 GGTCGAAGACACAAACCTTGCC-TCTTTCGGATGTAGCA--G-AGCT
1 GGTTGAAGACACAAACCTTGCCTTC-CT-GCAT-TAACAGCGAAGCA
* *
40234155 GGTTGAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCA
1 GGTTGAAGACA-CAAACCTTGCCTTCCTGCATTAACAGCGAAGCA
*
40234200 GATTGAAGACACAAACCTTGC
1 GGTTGAAGACACAAACCTTGC
40234221 ATCTCTCGGT
Statistics
Matches: 136, Mismatches: 47, Indels: 29
0.64 0.22 0.14
Matches are distributed among these distances:
42 4 0.03
43 33 0.24
44 54 0.40
45 42 0.31
46 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (44 bp):
GGTTGAAGACACAAACCTTGCCTTCCTGCATTAACAGCGAAGCA
Found at i:40234815 original size:95 final size:95
Alignment explanation
Indices: 40234635--40234830 Score: 297
Period size: 95 Copynumber: 2.1 Consensus size: 95
40234625 CGACAGCGAG
*
40234635 GCAGATCAAATATGGCAGATTTTACCTCCCTGTGACTACAGTGGAGTACGGTGAAGCCGATAATT
1 GCAGATCAAATATGGCAGATTTTACCTCCCTGTGACTACAGTGGAGTACAGTGAAGCCGATAATT
***
40234700 CTATCTCCCTGGTTGGCAGTGGAATAGATT
66 CTATCTCCCTGGTCAACAGTGGAATAGATT
* *
40234730 GCAGATCAAATATGGCAGATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCC-AGTAGT
1 GCAGATCAAATATGGCAGATTTTACCTCCCTGTGACTACAGTGGAGTACAGTGAAGCCGA-TAAT
40234794 TCTATCTCCCTGAG-CAACAGTGGAATAGATT
65 TCTATCTCCCTG-GTCAACAGTGGAATAGATT
*
40234825 GAAGAT
1 GCAGAT
40234831 TACAGATCTT
Statistics
Matches: 92, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
94 1 0.01
95 90 0.98
96 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (95 bp):
GCAGATCAAATATGGCAGATTTTACCTCCCTGTGACTACAGTGGAGTACAGTGAAGCCGATAATT
CTATCTCCCTGGTCAACAGTGGAATAGATT
Found at i:40235020 original size:124 final size:123
Alignment explanation
Indices: 40234833--40235805 Score: 1236
Period size: 124 Copynumber: 7.8 Consensus size: 123
40234823 TTGAAGATTA
40234833 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
* * * * *
40234898 TAGAGCAGATC-A-CATCAAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAAC
66 TGGAGCAGA-CAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CAAC
*
40234957 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAACAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
*
40235022 TGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATC
66 TGGAGCAGAC--AAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAAC
* *
40235082 AAG-TCTTATCTCCCTAGGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
* * * * * *
40235146 TGGAGTAGATC-A-CATCAAG-TCTTATCTCCCTAAGTAGTAGTGGAGCAGA-CGAAAGAAAC
66 TGGAGCAGA-CAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CAAC
*
40235205 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
*
40235270 TGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATC
66 TGGAGCAGAC--AAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAAC
* * * *
40235330 AAG-TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCACATCAAGTCTTATCTCCCTAAGTATTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
* * * *
40235394 TAGAGCAGACGAAAGAAACCAGATCTTATCTTCCTAAGCAATAGTGGAGCAGATCACATC
66 TGGAGCAGAC--AAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAAC
* *
40235454 AAG-TCTTATATCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
* *
40235518 TGGAGCAGACGAAAGAAACCAGATCTTATATCCCTAAGCAGCAGTGGAGCAGATCACAAC
66 TGGAGCAGAC--AAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAAC
* * * *
40235578 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCAGTCTTATCTCCATAAGCA
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAGTCTTATCTCCCTAAGCA
* * *
40235642 GTAATGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTTGTGGAGCAGA-CGAAGGA
62 GTAGTGGAGCAGAC--AAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC--A--C
40235706 AAC
121 AAC
*
40235709 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
*
40235774 TGGAGCAGACGAAGGAAACCA-ATCCTATCTCC
66 TGGAGCAGAC-AA-GAAACCAGATCTTATCTCC
40235806 TTGAAGTTGC
Statistics
Matches: 756, Mismatches: 64, Indels: 55
0.86 0.07 0.06
Matches are distributed among these distances:
119 1 0.00
120 29 0.04
121 4 0.01
122 2 0.00
123 6 0.01
124 437 0.58
125 38 0.05
126 4 0.01
127 22 0.03
128 172 0.23
129 3 0.00
131 37 0.05
132 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (123 bp):
CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
TGGAGCAGACAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAAC
Found at i:40235275 original size:248 final size:250
Alignment explanation
Indices: 40234837--40235805 Score: 1415
Period size: 248 Copynumber: 3.9 Consensus size: 250
40234827 AGATTACAGA
40234837 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTAGA
* *
40234902 GCAGATC-A-CATCAAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGATCT
66 GCAGA-CAAGAAACAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGATCT
*
40234964 TATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAACAGTAGTGGAGCA
130 TATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
40235029 GACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG
195 GACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG
* *
40235085 TCTTATCTCCCTAGGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTAGA
* * * *
40235150 GTAGATC-A-CATCAAG-TCTTATCTCCCTAAGTAGTAGTGGAGCAGACGAAAGAAACCAGATCT
66 GCAGA-CAAGAAACAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGATCT
*
40235212 TATCTCCCTAAGCAATAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
130 TATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
40235277 GACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG
195 GACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG
* * *
40235333 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCACATCAAGTCTTATCTCCCTAAGTATTAGTAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTAGA
* * * * * *
40235398 GCAGACGAAAGAAACCAGATCTTATCTTCCTAAGCAATAGTGGAGCAGATC---A-CATCAAG-T
66 GCAGAC--AAGAAACAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCAGAT
*
40235458 CTTATATCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAG
128 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAG
* * * *
40235523 CAGACGAAAGAAACCAGATCTTATATCCCTAAGCAGCAGTGGAGCAGATCACAACCAG
193 CAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG
* * * *
40235581 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCAGTCTTATCTCCATAAGCAGTA
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAGTCTTATCTCCCTAAGCAGTA
* * * * *
40235645 ATGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTTGTGGAGCAGACGAAGGAAACC
61 GTAGAGCAGAC--AAGAAACAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
*
40235710 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGT
124 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT
* *
40235775 GGAGCAGACGAAGGAAACCA-ATCCTATCTCC
189 GGAGCAGACGAAAGAAACCAGATCTTATCTCC
40235806 TTGAAGTTGC
Statistics
Matches: 657, Mismatches: 48, Indels: 25
0.90 0.07 0.03
Matches are distributed among these distances:
247 1 0.00
248 425 0.65
249 33 0.05
250 2 0.00
251 6 0.01
252 97 0.15
253 1 0.00
255 13 0.02
256 79 0.12
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (250 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTAGA
GCAGACAAGAAACAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGATCTT
ATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAG
ACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG
Found at i:40235826 original size:44 final size:43
Alignment explanation
Indices: 40234836--40235805 Score: 763
Period size: 40 Copynumber: 23.3 Consensus size: 43
40234826 AAGATTACAG
* *
40234836 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-----ACATCA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCA
* * *
40234875 AGTCTTATCTCCCTAAGCAGTAGTAGAGCAGATC-----ACATCA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCA
40234915 AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCA
* *
40234959 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-----ACATCA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCA
*
40234999 AGTCTTATCTCCCTAAACAGTAGTGGAGCAGACGAAAGAAACCA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCA
* *
40235043 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-----ACATCA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCA
* * *
40235083 AGTCTTATCTCCCTAGGCAGTAGTGGAGCAGATC-----ACATCA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCA
* * *
40235123 AGTCTTATCTCCCTAAGCAGTAGTGGAGTAGATC-----ACATCA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCA
*
40235163 AGTCTTATCTCCCTAAGTAGTAGTGGAGCAGACGAAAGAAACCA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCA
* * *
40235207 GATCTTATCTCCCTAAGCAATAGTGGAGCAGATC-----ACATCA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCA
40235247 AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCA
* *
40235291 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-----ACATCA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCA
* * *
40235331 AGTCTTATCTCCCTAAGCAGTAGTGGAGTAGATC-----ACATCA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCA
* * *
40235371 AGTCTTATCTCCCTAAGTATTAGTAGAGCAGACGAAAGAAACCA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCA
* * * *
40235415 GATCTTATCTTCCTAAGCAATAGTGGAGCAGATC-----ACATCA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCA
* * *
40235455 AGTCTTATATCCCTAAGCAGTAGTGGAGCAGATC-----ACATCA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCA
40235495 AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCA
* * *
40235539 GATCTTATATCCCTAAGCAGCAGTGGAGCAGATC---A-CAACCA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCA
40235580 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCA
* * *
40235624 GTCTTATCTCCATAAGCAGTAATGGAGCAGACGAAAGAAACCA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCA
* *
40235667 GATCTTATCTCCCTAAGCAGTTGTGGAGCAGACGAAGGAAACCA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCA
* *
40235711 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC----G-CATCA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCA
*
40235751 AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAGGAAACCA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCA
*
40235795 ATCCTATCTCC
1 ATCTTATCTCC
40235806 TTGAAGTTGC
Statistics
Matches: 804, Mismatches: 67, Indels: 116
0.81 0.07 0.12
Matches are distributed among these distances:
39 14 0.02
40 416 0.52
41 36 0.04
42 1 0.00
43 51 0.06
44 273 0.34
45 13 0.02
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (43 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCA
Found at i:40235827 original size:84 final size:84
Alignment explanation
Indices: 40234837--40235805 Score: 1257
Period size: 84 Copynumber: 11.6 Consensus size: 84
40234827 AGATTACAGA
* * *
40234837 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTCCCTAAGCAGTA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTCCCTAAGCAGTA
*
40234897 GTAGAGCAGATCACATCAAG
65 GTGGAGCAGATCACATCAAG
40234917 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAG
40234982 TGGAGCAGATCACATCAAG
66 TGGAGCAGATCACATCAAG
*
40235001 TCTTATCTCCCTAAACAGTAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAG
40235066 TGGAGCAGATCACATCAAG
66 TGGAGCAGATCACATCAAG
* * * *
40235085 TCTTATCTCCCTAGGCAGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTCCCTAAGCAGTA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTCCCTAAGCAGTA
*
40235145 GTGGAGTAGATCACATCAAG
65 GTGGAGCAGATCACATCAAG
* *
40235165 TCTTATCTCCCTAAGTAGTAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAATAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAG
40235230 TGGAGCAGATCACATCAAG
66 TGGAGCAGATCACATCAAG
40235249 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAG
40235314 TGGAGCAGATCACATCAAG
66 TGGAGCAGATCACATCAAG
* * * * * *
40235333 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATC---A-CATCAAG-TCTTATCTCCCTAAGTATTA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTCCCTAAGCAGTA
* * * *
40235393 GTAGAGCAGA-CGAAAGAAACCAG
65 GTGGAGCAGATC---A-CATCAAG
* * * * * *
40235416 ATCTTATCTTCCTAAGCAATAGTGGAGCAGATC---A-CATCAAG-TCTTATATCCCTAAGCAGT
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTCCCTAAGCAGT
40235476 AGTGGAGCAGATCACATCAAG
64 AGTGGAGCAGATCACATCAAG
* *
40235497 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGATCTTATATCCCTAAGCAGCAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAG
* *
40235562 TGGAGCAGATCACAACCAG
66 TGGAGCAGATCACATCAAG
*
40235581 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAG-TCTTATCTCCATAAGCAGTA
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTA
* * * *
40235645 ATGGAGCAGA-CGAAAGAAACCAG
65 GTGGAGCAGATC---A-CATCAAG
* *
40235668 ATCTTATCTCCCTAAGCAGTTGTGGAGCAGACGAAGGAAACCAGATCTTATCTCCCTAAGCAGTA
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTA
*
40235733 GTGGAGCAGATCGCATCAAG
65 GTGGAGCAGATCACATCAAG
* *
40235753 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAGGAAACCA-ATCCTATCTCC
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCC
40235806 TTGAAGTTGC
Statistics
Matches: 796, Mismatches: 63, Indels: 57
0.87 0.07 0.06
Matches are distributed among these distances:
79 4 0.01
80 152 0.19
81 12 0.02
82 7 0.01
83 27 0.03
84 466 0.59
85 50 0.06
86 1 0.00
87 48 0.06
88 28 0.04
89 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (84 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAG
TGGAGCAGATCACATCAAG
Found at i:40237303 original size:7 final size:7
Alignment explanation
Indices: 40237285--40237342 Score: 57
Period size: 7 Copynumber: 8.4 Consensus size: 7
40237275 TTTAACCGAA
40237285 TTTTTAT
1 TTTTTAT
40237292 TTTTT-T
1 TTTTTAT
*
40237298 TATTT-T
1 TTTTTAT
*
40237304 TATTTAT
1 TTTTTAT
*
40237311 TGTTTATT
1 TTTTTA-T
40237319 TTTTTAT
1 TTTTTAT
40237326 TTTTTAT
1 TTTTTAT
*
40237333 TTTATAT
1 TTTTTAT
40237340 TTT
1 TTT
40237343 GTGTCCTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
6 11 0.24
7 28 0.62
8 6 0.13
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.83
Consensus pattern (7 bp):
TTTTTAT
Done.