Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 11 of 97
Found at i:5321953 original size:24 final size:24
Alignment explanation
Indices: 5321892--5321954 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 24
5321882 TTAAAAAATA
*
5321892 AAAAATAATTGATCATAATAATATTT
1 AAAAAT-ATTAAT-ATAATAATATTT
*
5321918 AAATTAA-A-TAATATATTAATATTT
1 AAA--AATATTAATATAATAATATTT
5321942 AAAAATATTAATA
1 AAAAATATTAATA
5321955 ATCAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
22 2 0.06
23 1 0.03
24 19 0.61
25 3 0.10
26 4 0.13
28 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
AAAAATATTAATATAATAATATTT
Found at i:5322167 original size:193 final size:194
Alignment explanation
Indices: 5321817--5322167 Score: 557
Period size: 193 Copynumber: 1.8 Consensus size: 194
5321807 TCCAACTTTA
*
5321817 AATAAAATATTAATATTTAAATTATCTATTGTTAATATTTTAAATAAATAATCAATTATTAATAT
1 AATAAAATATTAATATTTAAATTATCTATTATTAATATTTTAAATAAATAATCAATTATTAATAT
*
5321882 TTAAAAAATAAAAAATAATTGATCATAATAATATTTAAATTAAATAATATATTAATATTTAAAAA
66 TTAAAAAAT-AAAAATAATTAATCATAATAATATTTAAATTAAATAATATATTAATATTTAAAAA
*
5321947 TATTAATAATCAAATTATAAATAAAATAATAACATTTTTCTATAACTTTTTGAATAGTTATATTC
130 TATTAATAATCAAATTACAAATAAAATAATAACATTTTTCTATAACTTTTTGAATAGTTATATTC
* * *
5322012 AATAAAATATTAATATTTACATTAT-TAATTATTAATATTTTAAATAACTTATCAATTATTAATA
1 AATAAAATATTAATATTTAAATTATCT-ATTATTAATATTTTAAATAAATAATCAATTATTAATA
*
5322076 TTTAAAAAAT-AAAATAATTAATCATAATAATATTTAAATTAAATACAT-TATTAATATTTTAAA
65 TTTAAAAAATAAAAATAATTAATCATAATAATATTTAAATTAAATA-ATATATTAATATTTAAAA
* *
5322139 ATATTGATAATTATAA-TACAAATAAAATA
129 ATATTAATAATCA-AATTACAAATAAAATA
5322168 CTAATACTTA
Statistics
Matches: 144, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
193 71 0.49
194 5 0.03
195 68 0.47
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (194 bp):
AATAAAATATTAATATTTAAATTATCTATTATTAATATTTTAAATAAATAATCAATTATTAATAT
TTAAAAAATAAAAATAATTAATCATAATAATATTTAAATTAAATAATATATTAATATTTAAAAAT
ATTAATAATCAAATTACAAATAAAATAATAACATTTTTCTATAACTTTTTGAATAGTTATATTC
Found at i:5322194 original size:22 final size:22
Alignment explanation
Indices: 5322163--5322204 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5322153 AATACAAATA
5322163 AAATACTAATACTTAAATTACT
1 AAATACTAATACTTAAATTACT
* * *
5322185 AAATATTAATATTTTAATTA
1 AAATACTAATACTTAAATTA
5322205 ATTTATAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATACTAATACTTAAATTACT
Found at i:5322204 original size:53 final size:53
Alignment explanation
Indices: 5322137--5322306 Score: 152
Period size: 53 Copynumber: 3.3 Consensus size: 53
5322127 TAATATTTTA
*
5322137 AAATATTGATAATTATAATACAAATAAAATACTAATACTTAAATTACTAAATAT
1 AAATATT-TTAATTATAATACAAATAAAATACTAATACTTAAATTACTAAATAT
* ** * * * * * * *
5322191 TAATATTTTAA-T-TAAT--TTATAAATTAATGATATTTAAA-AAATCAAATAA
1 AAATATTTTAATTATAATACAAATAAAATACTAATACTTAAATTACT-AAATAT
*** *
5322240 AAATAAAATAATTATAATACACATAAAATACTAATACTTAAATTACTAAATAT
1 AAATATTTTAATTATAATACAAATAAAATACTAATACTTAAATTACTAAATAT
5322293 AAATATTTTAATTA
1 AAATATTTTAATTA
5322307 ATTTATAAAT
Statistics
Matches: 83, Mismatches: 27, Indels: 13
0.67 0.22 0.11
Matches are distributed among these distances:
48 2 0.02
49 28 0.34
50 1 0.01
51 8 0.10
52 1 0.01
53 35 0.42
54 8 0.10
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (53 bp):
AAATATTTTAATTATAATACAAATAAAATACTAATACTTAAATTACTAAATAT
Found at i:5322228 original size:49 final size:49
Alignment explanation
Indices: 5322175--5322330 Score: 143
Period size: 49 Copynumber: 3.1 Consensus size: 49
5322165 ATACTAATAC
*
5322175 TTAAATTACTAAATATTAATATTTTAATTAATTTATAAATTAATGATAT
1 TTAAATTACTAAATATAAATATTTTAATTAATTTATAAATTAATGATAT
* * * *** ** * * * *
5322224 TTAAA-AAATCAAATAAAAATAAAATAATTATAATACACATAAAATACTAATAC
1 TTAAATTACT-AAATATAAATATTTTAA-T-TAAT--TTATAAATTAATGATAT
5322277 TTAAATTACTAAATATAAATATTTTAATTAATTTATAAATTAATGATAT
1 TTAAATTACTAAATATAAATATTTTAATTAATTTATAAATTAATGATAT
5322326 TTAAA
1 TTAAA
5322331 AAATCAAATA
Statistics
Matches: 76, Mismatches: 25, Indels: 12
0.67 0.22 0.11
Matches are distributed among these distances:
48 2 0.03
49 33 0.43
50 1 0.01
51 8 0.11
52 1 0.01
53 29 0.38
54 2 0.03
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (49 bp):
TTAAATTACTAAATATAAATATTTTAATTAATTTATAAATTAATGATAT
Found at i:5322266 original size:102 final size:101
Alignment explanation
Indices: 5322145--5322356 Score: 388
Period size: 102 Copynumber: 2.1 Consensus size: 101
5322135 TAAAATATTG
*
5322145 ATAATTATAATACAAATAAAATACTAATACTTAAATTACTAAATATTAATATTTTAATTAATTTA
1 ATAATTATAATACAAATAAAATACTAATACTTAAATTACTAAATATAAATATTTTAATTAATTTA
5322210 TAAATTAATGATATTTAAAAAATCAAATAAAAATAAA
66 TAAATTAATGATATTTAAAAAATCAAATAAAAAT-AA
*
5322247 ATAATTATAATACACATAAAATACTAATACTTAAATTACTAAATATAAATATTTTAATTAATTTA
1 ATAATTATAATACAAATAAAATACTAATACTTAAATTACTAAATATAAATATTTTAATTAATTTA
5322312 TAAATTAATGATATTTAAAAAATCAAATAAAAATAA
66 TAAATTAATGATATTTAAAAAATCAAATAAAAATAA
*
5322348 ACAATTATA
1 ATAATTATA
5322357 TATATAATAA
Statistics
Matches: 107, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
101 10 0.09
102 97 0.91
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.37
Consensus pattern (101 bp):
ATAATTATAATACAAATAAAATACTAATACTTAAATTACTAAATATAAATATTTTAATTAATTTA
TAAATTAATGATATTTAAAAAATCAAATAAAAATAA
Found at i:5322340 original size:49 final size:49
Alignment explanation
Indices: 5322192--5322346 Score: 150
Period size: 49 Copynumber: 3.1 Consensus size: 49
5322182 ACTAAATATT
5322192 AATATTTTAATTAATTTATAAATTAATGATATTTAAAAAATCAAATAAA
1 AATATTTTAATTAATTTATAAATTAATGATATTTAAAAAATCAAATAAA
*** ** * * * * ** *
5322241 AATAAAATAATTATAATACACATAAAATACTAATACTTAAATTA-CTAAATATA
1 AATATTTTAA-T-TAAT--TTATAAATTAATGATATTTAAAAAATC-AAATAAA
5322294 AATATTTTAATTAATTTATAAATTAATGATATTTAAAAAATCAAATAAA
1 AATATTTTAATTAATTTATAAATTAATGATATTTAAAAAATCAAATAAA
5322343 AATA
1 AATA
5322347 AACAATTATA
Statistics
Matches: 76, Mismatches: 24, Indels: 12
0.68 0.21 0.11
Matches are distributed among these distances:
49 34 0.45
50 2 0.03
51 8 0.11
52 2 0.03
53 30 0.39
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (49 bp):
AATATTTTAATTAATTTATAAATTAATGATATTTAAAAAATCAAATAAA
Found at i:5322348 original size:53 final size:53
Alignment explanation
Indices: 5322192--5322348 Score: 157
Period size: 53 Copynumber: 3.0 Consensus size: 53
5322182 ACTAAATATT
5322192 AATATTTTAATTAATTTATAAATTAATGATATTTAAAAAATCAAATAAAAATAA
1 AATATTTTAATTAATTTATAAATTAATGATATTTAAAAAATCAAATAAAAAT-A
* * * * * * * * *
5322246 AATAATTATAA-TACA--CATAAAATACTAATACTT---AAAT-TACTAAATATA
1 AAT-ATTTTAATTA-ATTTATAAATTAATGATATTTAAAAAATCAAATAAAAATA
5322294 AATATTTTAATTAATTTATAAATTAATGATATTTAAAAAATCAAATAAAAATA
1 AATATTTTAATTAATTTATAAATTAATGATATTTAAAAAATCAAATAAAAATA
5322347 AA
1 AA
5322349 CAATTATATA
Statistics
Matches: 76, Mismatches: 18, Indels: 19
0.67 0.16 0.17
Matches are distributed among these distances:
47 7 0.09
48 6 0.08
49 20 0.26
50 4 0.05
52 4 0.05
53 23 0.30
54 5 0.07
55 7 0.09
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (53 bp):
AATATTTTAATTAATTTATAAATTAATGATATTTAAAAAATCAAATAAAAATA
Found at i:5322363 original size:49 final size:48
Alignment explanation
Indices: 5322199--5322363 Score: 134
Period size: 49 Copynumber: 3.3 Consensus size: 48
5322189 ATTAATATTT
*
5322199 TAATTAATTTATAAATTAATGATATTTAAAAAATCAAATAAAAATAAAA
1 TAATTAATATATAAATTAATGATATTTAAAAAATCAAATAAAAAT-AAA
* * * * * ** * **
5322248 TAATTATAATACACATAAAATACTAATACTTAAATTA-CTAAATATAAATATTT
1 TAA-T-TAAT--ATATAAATTAATGATATTTAAAAAATC-AAATAAAAATA-AA
*
5322301 TAATTAATTTATAAATTAATGATATTTAAAAAATCAAATAAAAATAAA
1 TAATTAATATATAAATTAATGATATTTAAAAAATCAAATAAAAATAAA
*
5322349 CAATTATATATATAA
1 TAATTA-ATATATAA
5322364 TAAAAAACAC
Statistics
Matches: 84, Mismatches: 24, Indels: 16
0.68 0.19 0.13
Matches are distributed among these distances:
48 5 0.06
49 37 0.44
50 2 0.02
51 8 0.10
52 3 0.04
53 29 0.35
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.36
Consensus pattern (48 bp):
TAATTAATATATAAATTAATGATATTTAAAAAATCAAATAAAAATAAA
Found at i:5334126 original size:22 final size:22
Alignment explanation
Indices: 5334098--5334144 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
5334088 GATGTAATTA
* *
5334098 AAATTTTTTTTATAAATTA-AAT
1 AAATTTTATTAAT-AATTATAAT
5334120 AAATTTTATTAATAATTATAAT
1 AAATTTTATTAATAATTATAAT
5334142 AAA
1 AAA
5334145 AAAATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATTTTATTAATAATTATAAT
Found at i:5346897 original size:16 final size:16
Alignment explanation
Indices: 5346876--5346915 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
5346866 AACCTAGCAC
5346876 ATTAGAAGCTTTTACA
1 ATTAGAAGCTTTTACA
5346892 ATTAGAAGCTTTTACA
1 ATTAGAAGCTTTTACA
5346908 ATTAGAAG
1 ATTAGAAG
5346916 GGGGGGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (16 bp):
ATTAGAAGCTTTTACA
Found at i:5347383 original size:27 final size:26
Alignment explanation
Indices: 5347330--5347379 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
5347320 ACTTTAATAT
5347330 TCAAGGCAATTTTTGTATTGGTGCAA
1 TCAAGGCAATTTTTGTATTGGTGCAA
*
5347356 TCAAGGCAATTTTTTTATTGGTGC
1 TCAAGGCAATTTTTGTATTGGTGC
5347380 CAATAGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (26 bp):
TCAAGGCAATTTTTGTATTGGTGCAA
Found at i:5349438 original size:17 final size:18
Alignment explanation
Indices: 5349410--5349443 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5349400 AGCGTTTGAG
5349410 CTTTTTTATAATATTAAC
1 CTTTTTTATAATATTAAC
*
5349428 CTTTTTT-TAATTTTAA
1 CTTTTTTATAATATTAA
5349444 GATGTGCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (18 bp):
CTTTTTTATAATATTAAC
Found at i:5349930 original size:17 final size:16
Alignment explanation
Indices: 5349907--5349948 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
5349897 AAATAATAAA
5349907 ATTATTAATTCTACTGT
1 ATTATTAATTC-ACTGT
* *
5349924 TTTATTAAGTCACTGT
1 ATTATTAATTCACTGT
5349940 ATTA-TAATT
1 ATTATTAATT
5349949 GATTTTATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 4 0.19
16 8 0.38
17 9 0.43
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (16 bp):
ATTATTAATTCACTGT
Found at i:5349944 original size:16 final size:17
Alignment explanation
Indices: 5349907--5349944 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
5349897 AAATAATAAA
*
5349907 ATTATTAATTCTACTGT
1 ATTATTAAGTCTACTGT
*
5349924 TTTATTAAGTC-ACTGT
1 ATTATTAAGTCTACTGT
5349940 ATTAT
1 ATTAT
5349945 AATTGATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.53
Consensus pattern (17 bp):
ATTATTAAGTCTACTGT
Found at i:5352355 original size:80 final size:80
Alignment explanation
Indices: 5352261--5352408 Score: 215
Period size: 80 Copynumber: 1.9 Consensus size: 80
5352251 GATTTTAAGG
* *
5352261 AAGAAAAGAGCATTAGATTTTCCTTATAAATTATAAGGAAGAGAAGCGAAAGATTTAACTTTCTT
1 AAGAAAAGAGCATTAGATTTTCCTTACAAATTATAAGGAAGAGAAGAGAAAGATTTAACTTTCTT
5352326 TTACAAATTCTAGGA
66 TTACAAATTCTAGGA
* * ** * * *
5352341 AAGAGAAGAGCATTAGTTTTTTGTTACAAATTATAAGGAAGATAAGATAAAGATTTGACTTTCTT
1 AAGAAAAGAGCATTAGATTTTCCTTACAAATTATAAGGAAGAGAAGAGAAAGATTTAACTTTCTT
5352406 TTA
66 TTA
5352409 TTGTAGAACA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 59 1.00
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (80 bp):
AAGAAAAGAGCATTAGATTTTCCTTACAAATTATAAGGAAGAGAAGAGAAAGATTTAACTTTCTT
TTACAAATTCTAGGA
Found at i:5353861 original size:2 final size:2
Alignment explanation
Indices: 5353850--5353928 Score: 94
Period size: 2 Copynumber: 40.5 Consensus size: 2
5353840 CAAAATTTTA
*
5353850 AT AT -T AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5353890 AT AT AT AT AT AA AT AT ANT -T AT -T ACT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT A
5353929 ATAAAGGCAT
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
1 4 0.06
2 60 0.90
3 3 0.04
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5364035 original size:21 final size:19
Alignment explanation
Indices: 5364010--5364065 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
5364000 TGTTTTATCG
5364010 TTTTATATATTTATTAAATA
1 TTTTATATA-TTATTAAATA
* *
5364030 TATTTATATACGTATTTAATA
1 T-TTTATATA-TTATTAAATA
5364051 TTTTA-ATATTATTAA
1 TTTTATATATTATTAA
5364066 TTTATTAGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.17
19 3 0.10
20 5 0.17
21 17 0.57
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTTATATATTATTAAATA
Found at i:5370446 original size:5 final size:5
Alignment explanation
Indices: 5370436--5370528 Score: 68
Period size: 5 Copynumber: 19.2 Consensus size: 5
5370426 ACGTTATAAT
* * * * *
5370436 TAAAA TAAAA TATAT TAAAA TAAAA TAAAA TATAT TAAAA TAAAA T-ATA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
* * * *
5370485 TAATA TAAAA -ATTAA -AAAA TAAAA TAAAA TATAA -AAAT TAAAA T
1 TAAAA TAAAA TA-AAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T
5370529 TTATATAATA
Statistics
Matches: 68, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
4 8 0.12
5 60 0.88
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (5 bp):
TAAAA
Found at i:5370490 original size:20 final size:20
Alignment explanation
Indices: 5370436--5370482 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
5370426 ACGTTATAAT
5370436 TAAAATAAAATATATTAAAA
1 TAAAATAAAATATATTAAAA
5370456 TAAAATAAAATATATTAAAA
1 TAAAATAAAATATATTAAAA
5370476 TAAAATA
1 TAAAATA
5370483 TATAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAATAAAATATATTAAAA
Found at i:5370495 original size:20 final size:20
Alignment explanation
Indices: 5370437--5370538 Score: 86
Period size: 20 Copynumber: 5.0 Consensus size: 20
5370427 CGTTATAATT
5370437 AAAATAAAATATATTAAAAT-
1 AAAATAAAATATA-TAAAATA
5370457 AAAATAAAATATATTAAAATA
1 AAAATAAAATATA-TAAAATA
*
5370478 AAATATATAATATA-AAAATTAA
1 AAA-ATAAAATATATAAAA-T-A
*
5370500 AAAATAAAATA-A-AATATA
1 AAAATAAAATATATAAAATA
* *
5370518 AAAATTAAAATTTATATAATA
1 AAAA-TAAAATATATAAAATA
5370539 TAGGTAAAAG
Statistics
Matches: 69, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
18 5 0.07
19 7 0.10
20 29 0.42
21 15 0.22
22 13 0.19
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATAAAATATATAAAATA
Found at i:5376461 original size:120 final size:120
Alignment explanation
Indices: 5376255--5376495 Score: 405
Period size: 120 Copynumber: 2.0 Consensus size: 120
5376245 TGGAATGCGA
*
5376255 AGTTAGTACTAAATATCCTCTCACATACATTCACCCTAGTCCTTACCTCAGTTAACCAACCAAAT
1 AGTTAGTACTAAATATCCTCTCACATACATTCACCCTAATCCTTACCTCAGTTAACCAACCAAAT
* *
5376320 TTAGTAAAAAAGTTTTAAATCAACCG-ACATGCAGTGCGTAAAACTATAAATGCTG
66 TTAGTAAAAAAGTTTTAAATCAA-CGAACATACAGTGCATAAAACTATAAATGCTG
*
5376375 AGTTAGTAGTAAAT-TCTCTCTCACATACATTCACCCTAATCCTTACCTCAGTTAACCAACCAAA
1 AGTTAGTACTAAATATC-CTCTCACATACATTCACCCTAATCCTTACCTCAGTTAACCAACCAAA
*
5376439 TTTAGTAAAAAAGTTTTAAATCAACGAACATACAGTGCATAAAACTATAACTGCTG
65 TTTAGTAAAAAAGTTTTAAATCAACGAACATACAGTGCATAAAACTATAAATGCTG
5376495 A
1 A
5376496 AATAGGGAAT
Statistics
Matches: 114, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
119 4 0.04
120 110 0.96
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (120 bp):
AGTTAGTACTAAATATCCTCTCACATACATTCACCCTAATCCTTACCTCAGTTAACCAACCAAAT
TTAGTAAAAAAGTTTTAAATCAACGAACATACAGTGCATAAAACTATAAATGCTG
Found at i:5376553 original size:48 final size:48
Alignment explanation
Indices: 5376501--5376596 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
5376491 GCTGAAATAG
*
5376501 GGAATGCACGCCTCTTTCTATGAACTCATTAAAAAAAATATTTATATA
1 GGAATGCACGCCTCTTTCTATGAACTCATCAAAAAAAATATTTATATA
* *
5376549 GGAATGCATGCCTCTTTCTATGAACTTATCAAAAAAAATATTTATATA
1 GGAATGCACGCCTCTTTCTATGAACTCATCAAAAAAAATATTTATATA
5376597 AGTCAAGACT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (48 bp):
GGAATGCACGCCTCTTTCTATGAACTCATCAAAAAAAATATTTATATA
Found at i:5384735 original size:18 final size:18
Alignment explanation
Indices: 5384712--5384748 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5384702 ATTAAGTATA
*
5384712 ACTTAATAACTTAATAAT
1 ACTTAATAAATTAATAAT
5384730 ACTTAATAAATTAATAAT
1 ACTTAATAAATTAATAAT
5384748 A
1 A
5384749 AAAAAAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (18 bp):
ACTTAATAAATTAATAAT
Found at i:5386239 original size:21 final size:22
Alignment explanation
Indices: 5386204--5386260 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
5386194 TAATCACCGT
*
5386204 GTGACTAGTTTTTAGTCATTAC
1 GTGACTAGTTTTTAGGCATTAC
*
5386226 GTGATTAG-TTTTAGGCATTAC
1 GTGACTAGTTTTTAGGCATTAC
5386247 GT-AGCTAGTTTTTA
1 GTGA-CTAGTTTTTA
5386261 TAGATTGCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 1 0.03
21 17 0.57
22 12 0.40
ACGTcount: A:0.23, C:0.11, G:0.21, T:0.46
Consensus pattern (22 bp):
GTGACTAGTTTTTAGGCATTAC
Found at i:5386327 original size:23 final size:23
Alignment explanation
Indices: 5386294--5386498 Score: 132
Period size: 26 Copynumber: 8.7 Consensus size: 23
5386284 GCAATGCCTA
*
5386294 AGTCACACAATGCCTTACAAACT
1 AGTCACGCAATGCCTTACAAACT
** * *
5386317 AGTCACGCAATATCTTACTAACA
1 AGTCACGCAATGCCTTACAAACT
* * *
5386340 AGTCACGTAATGCCTTACTAACA
1 AGTCACGCAATGCCTTACAAACT
*
5386363 AGTCACGCAATACC-TATC-AACT
1 AGTCACGCAATGCCTTA-CAAACT
* *
5386385 AATCATGCAATGCCTTATCAGAAACT
1 AGTCACGCAATGCCTTA-C--AAACT
*
5386411 AGTCACGCAATGTCTTATCAGAAACT
1 AGTCACGCAATGCCTTA-C--AAACT
* * *
5386437 AGTCACGCAATACCTTATTAAAAATT
1 AGTCACGCAATGCC---TTACAAACT
*
5386463 AGTCACGCAATGCC---CAAAGT
1 AGTCACGCAATGCCTTACAAACT
5386483 CAGTCACGCAATGCCT
1 -AGTCACGCAATGCCT
5386499 ATTTACAAGT
Statistics
Matches: 148, Mismatches: 24, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
20 4 0.03
21 14 0.09
22 16 0.11
23 55 0.37
26 56 0.38
29 3 0.02
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (23 bp):
AGTCACGCAATGCCTTACAAACT
Found at i:5386607 original size:95 final size:95
Alignment explanation
Indices: 5386406--5386607 Score: 235
Period size: 95 Copynumber: 2.1 Consensus size: 95
5386396 GCCTTATCAG
* * ** * * *
5386406 AAACTAGTCACGCAATGTCTTATCAGAAACTAGTCACGCAATACCTTATTAAAAATTAGTCACGC
1 AAACTAATCACACAATACCTTATCAGAAACTAGTAACGCAATACCTTATAAAAAATCAGTCACGC
* *
5386471 AATGCCCAAAGTCAGTCACGCAATGCCTAT
66 AATGCCCAAAGTCAGTCACACAATGCCTAA
** *
5386501 TTAC-AAGTCACACAATACCTTATCAGAAACTAGTAACGCAATATCTTATAAAAAATCAGTCACG
1 AAACTAA-TCACACAATACCTTATCAGAAACTAGTAACGCAATACCTTATAAAAAATCAGTCACG
* * * **
5386565 TAATGTCCAAAGTCAGTTACACAATGTTTAA
65 CAATGCCCAAAGTCAGTCACACAATGCCTAA
5386596 AAACTAATCACA
1 AAACTAATCACA
5386608 TAATTCTCAA
Statistics
Matches: 86, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
94 1 0.01
95 83 0.97
96 2 0.02
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (95 bp):
AAACTAATCACACAATACCTTATCAGAAACTAGTAACGCAATACCTTATAAAAAATCAGTCACGC
AATGCCCAAAGTCAGTCACACAATGCCTAA
Found at i:5393841 original size:26 final size:26
Alignment explanation
Indices: 5393805--5393859 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
5393795 TTTATATTAA
* *
5393805 ATTTTATTATATTTGATATTATTATT
1 ATTTTATTATAATTGATATTATAATT
* * *
5393831 ATTTTGTTATAATTGTTTTTATAATT
1 ATTTTATTATAATTGATATTATAATT
5393857 ATT
1 ATT
5393860 AATTTTAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.65
Consensus pattern (26 bp):
ATTTTATTATAATTGATATTATAATT
Found at i:5395472 original size:28 final size:28
Alignment explanation
Indices: 5395414--5395467 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
5395404 AAAATATTAC
5395414 AAATAAATAAATCACATCAAATATAAAT
1 AAATAAATAAATCACATCAAATATAAAT
*
5395442 AAATAAATAAATTACAT-AAATA-AAAT
1 AAATAAATAAATCACATCAAATATAAAT
5395468 TTAAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.16
27 5 0.20
28 16 0.64
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (28 bp):
AAATAAATAAATCACATCAAATATAAAT
Found at i:5395484 original size:18 final size:19
Alignment explanation
Indices: 5395458--5395497 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
5395448 ATAAATTACA
5395458 TAAATAAAATTTAAAATTT
1 TAAATAAAATTTAAAATTT
5395477 TAAA-AAAATTTAAAATTT
1 TAAATAAAATTTAAAATTT
5395495 TAA
1 TAA
5395498 CACAAACTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATAAAATTTAAAATTT
Found at i:5400568 original size:33 final size:33
Alignment explanation
Indices: 5400526--5400591 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
5400516 TTTACCTGTA
5400526 ACTTATATGTTTATGCAGTATAATCAATAATTT
1 ACTTATATGTTTATGCAGTATAATCAATAATTT
5400559 ACTTATATGTTTATGCAGTATAATCAATAATTT
1 ACTTATATGTTTATGCAGTATAATCAATAATTT
5400592 TTCTTTCCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (33 bp):
ACTTATATGTTTATGCAGTATAATCAATAATTT
Found at i:5405084 original size:42 final size:42
Alignment explanation
Indices: 5405019--5405103 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
5405009 TATCTGATCC
* **
5405019 ATATTCATCATTTTTAACGTATGCAGAGGAAGCCGTTTCAAG
1 ATATTCATCATTTTTAACATATGCAGAAAAAGCCGTTTCAAG
*
5405061 ATATTCATCATTTTCT-ACATATGCAGAAAAAGTCGTTTCAAG
1 ATATTCATCATTTT-TAACATATGCAGAAAAAGCCGTTTCAAG
5405103 A
1 A
5405104 AAATTATACA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 37 0.97
43 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (42 bp):
ATATTCATCATTTTTAACATATGCAGAAAAAGCCGTTTCAAG
Found at i:5411221 original size:29 final size:30
Alignment explanation
Indices: 5411165--5411228 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
5411155 AATATCAAAA
5411165 TAAAAATATAATAATTTAATTTAAATTTTT
1 TAAAAATATAATAATTTAATTTAAATTTTT
5411195 TAAAAA-ATAA-AATTT-ATTTAATTATTTTT
1 TAAAAATATAATAATTTAATTTAA--ATTTTT
5411224 TAAAA
1 TAAAA
5411229 CCTTTTACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
27 6 0.19
28 5 0.16
29 15 0.47
30 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TAAAAATATAATAATTTAATTTAAATTTTT
Found at i:5421496 original size:2 final size:2
Alignment explanation
Indices: 5421489--5421521 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5421479 GAATTCTTTT
*
5421489 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5421522 TTTGTGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5432156 original size:3 final size:3
Alignment explanation
Indices: 5432150--5432184 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
5432140 AACTATACAC
* *
5432150 AAG AAG AAG AAG AAG AAG AAG AAT TAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
5432185 CCCATTGTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.06
Consensus pattern (3 bp):
AAG
Found at i:5435629 original size:2 final size:2
Alignment explanation
Indices: 5435622--5435647 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5435612 ACCCCCAATA
5435622 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5435648 TAGTGTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5438789 original size:25 final size:29
Alignment explanation
Indices: 5438755--5438811 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 29
5438745 ATCAGAGAAG
5438755 AAATCCAGCAGCAT-A-A-AAAAAAAA-A
1 AAATCCAGCAGCATCACATAAAAAAAAGA
5438780 AAATCCAGCAGCATCACATAAAAAAAAGA
1 AAATCCAGCAGCATCACATAAAAAAAAGA
5438809 AAA
1 AAA
5438812 AGAAAAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 14 0.50
26 1 0.04
27 1 0.04
28 8 0.29
29 4 0.14
ACGTcount: A:0.65, C:0.18, G:0.09, T:0.09
Consensus pattern (29 bp):
AAATCCAGCAGCATCACATAAAAAAAAGA
Found at i:5446058 original size:12 final size:12
Alignment explanation
Indices: 5446041--5446066 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5446031 GACAAAATTT
5446041 AAGCTTCTAATC
1 AAGCTTCTAATC
5446053 AAGCTTCTAATC
1 AAGCTTCTAATC
5446065 AA
1 AA
5446067 ATTAAAGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (12 bp):
AAGCTTCTAATC
Found at i:5446812 original size:18 final size:18
Alignment explanation
Indices: 5446789--5446825 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5446779 TGTCCAACAA
5446789 TGAAGAAGAGAGGCTCAG
1 TGAAGAAGAGAGGCTCAG
5446807 TGAAGAAGAGAGGCTCAG
1 TGAAGAAGAGAGGCTCAG
5446825 T
1 T
5446826 TCTGCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.38, T:0.14
Consensus pattern (18 bp):
TGAAGAAGAGAGGCTCAG
Found at i:5456555 original size:21 final size:20
Alignment explanation
Indices: 5456526--5456565 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5456516 AGTAGATTAT
5456526 AAAAGCAAGAAACAAAGAAG
1 AAAAGCAAGAAACAAAGAAG
* *
5456546 AAAAGGCAAGCAACCAAGAA
1 AAAA-GCAAGAAACAAAGAA
5456566 ACAATAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.65, C:0.15, G:0.20, T:0.00
Consensus pattern (20 bp):
AAAAGCAAGAAACAAAGAAG
Found at i:5480290 original size:14 final size:15
Alignment explanation
Indices: 5480273--5480303 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5480263 TTATTTTTAT
5480273 AATTTTA-ATTAATA
1 AATTTTATATTAATA
5480287 AATTTTATATTAATA
1 AATTTTATATTAATA
5480302 AA
1 AA
5480304 ATTATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTTTATATTAATA
Found at i:5480420 original size:22 final size:22
Alignment explanation
Indices: 5480387--5480461 Score: 80
Period size: 22 Copynumber: 3.2 Consensus size: 22
5480377 AAAATAAATA
5480387 AATTATTAATAATTAAATTATT
1 AATTATTAATAATTAAATTATT
*
5480409 AATT-TTATATAATTAAATATATAA
1 AATTATTA-ATAATTAAAT-TAT-T
5480433 AATTATTAAATTAATTAAAATTATT
1 AATTATT-AA-TAATT-AAATTATT
5480458 AATT
1 AATT
5480462 TTTTTAATTC
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
21 3 0.07
22 14 0.32
23 3 0.07
24 4 0.09
25 7 0.16
26 9 0.20
27 4 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATTATTAATAATTAAATTATT
Found at i:5480443 original size:8 final size:8
Alignment explanation
Indices: 5480385--5480459 Score: 66
Period size: 8 Copynumber: 9.4 Consensus size: 8
5480375 ATAAAATAAA
5480385 TAAATTAT
1 TAAATTAT
*
5480393 T-AATAAT
1 TAAATTAT
5480400 TAAATTAT
1 TAAATTAT
5480408 T-AATT-T
1 TAAATTAT
* *
5480414 TATATAAT
1 TAAATTAT
5480422 TAAATATAT
1 TAAAT-TAT
*
5480431 AAAATTAT
1 TAAATTAT
5480439 TAAATTAAT
1 TAAATT-AT
5480448 TAAAATTAT
1 T-AAATTAT
5480457 TAA
1 TAA
5480460 TTTTTTTAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
6 2 0.04
7 12 0.23
8 22 0.42
9 12 0.23
10 5 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TAAATTAT
Found at i:5494013 original size:15 final size:16
Alignment explanation
Indices: 5493984--5494026 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
5493974 CGTTGCGAAC
5493984 AAAAA-AGGGAGAAAA
1 AAAAAGAGGGAGAAAA
5493999 AAAAAGAGGGA-AAAA
1 AAAAAGAGGGAGAAAA
* *
5494014 GAAAAGAGAGAGA
1 AAAAAGAGGGAGA
5494027 GAGGCAACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (16 bp):
AAAAAGAGGGAGAAAA
Found at i:5510704 original size:51 final size:49
Alignment explanation
Indices: 5510594--5510707 Score: 124
Period size: 51 Copynumber: 2.2 Consensus size: 49
5510584 AATTTTTCAT
*
5510594 TAAAAATAATTTTTAATTTAATAATATTATAAATATAAATAATAATAAAAA
1 TAAAAATAA-TTTTAATTTAAAAATATTATAAATATAAATAATAAT-AAAA
*
5510645 TAATAAATAATTTTAATTTAAAAAATGTTAT-AATAATAGCAATAATAAT-AAA
1 TAA-AAATAATTTTAATTT-AAAAATATTATAAAT-ATA--AATAATAATAAAA
*
5510697 TTAAAATAATT
1 TAAAAATAATT
5510708 ATTTTACAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
51 23 0.42
52 23 0.42
54 9 0.16
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (49 bp):
TAAAAATAATTTTAATTTAAAAATATTATAAATATAAATAATAATAAAA
Found at i:5511927 original size:16 final size:19
Alignment explanation
Indices: 5511884--5511928 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
5511874 GTTTTTATTC
5511884 AATATTATTAAAATTAAAA
1 AATATTATTAAAATTAAAA
*
5511903 AATATTATTAAGATTAAAA
1 AATATTATTAAAATTAAAA
5511922 AATATTA
1 AATATTA
5511929 CAGTTGAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AATATTATTAAAATTAAAA
Found at i:5515638 original size:41 final size:41
Alignment explanation
Indices: 5515593--5515679 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
5515583 TAACATATTG
* *
5515593 GGTTATTAGATTGAACAATTGAGATATAATATGTTATGATA
1 GGTTATTAGATTGAACAATTAAGATATAATATGTTATAATA
* * **
5515634 GGTTATTAGGTTGGACTGTTAAGATATAATATGTTATAATA
1 GGTTATTAGATTGAACAATTAAGATATAATATGTTATAATA
*
5515675 AGTTA
1 GGTTA
5515680 AACTTTATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.40
Consensus pattern (41 bp):
GGTTATTAGATTGAACAATTAAGATATAATATGTTATAATA
Found at i:5516293 original size:21 final size:22
Alignment explanation
Indices: 5516228--5516293 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
5516218 CAAGAAAATC
* *
5516228 TATAGAGATTTAAAAAATATAAG
1 TATATAGAATTAAAAAA-ATAAG
*
5516251 TATATAGAATAAAAATAAATAA-
1 TATATAGAATTAAAA-AAATAAG
5516273 TAATATA-AATTAAAAAAATAA
1 T-ATATAGAATTAAAAAAATAA
5516294 AAAACTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
21 6 0.16
22 8 0.22
23 21 0.57
24 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (22 bp):
TATATAGAATTAAAAAAATAAG
Found at i:5518128 original size:19 final size:19
Alignment explanation
Indices: 5518106--5518147 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
5518096 TTATAGGGAT
*
5518106 AAAATTATAAA-ATTTTAAA
1 AAAATTA-AAATATGTTAAA
5518125 AAAATTAAAATATGTTAAA
1 AAAATTAAAATATGTTAAA
5518144 AAAA
1 AAAA
5518148 AAATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTAAAATATGTTAAA
Found at i:5533269 original size:2 final size:2
Alignment explanation
Indices: 5533262--5533328 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
5533252 TTTACTAGCC
5533262 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5533304 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5533329 CACATAGATT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5548520 original size:12 final size:13
Alignment explanation
Indices: 5548503--5548534 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5548493 AGGGAAGAAT
5548503 GAATGAGAAT-GA
1 GAATGAGAATGGA
5548515 GAATGAGAATGGA
1 GAATGAGAATGGA
5548528 GAA-GAGA
1 GAATGAGA
5548535 GGGGCAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.38, T:0.12
Consensus pattern (13 bp):
GAATGAGAATGGA
Found at i:5550243 original size:12 final size:12
Alignment explanation
Indices: 5550226--5550259 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5550216 ATTAATATTT
*
5550226 TATATATATTAA
1 TATATATAATAA
*
5550238 TATATATAATAT
1 TATATATAATAA
5550250 TATATATAAT
1 TATATATAAT
5550260 TTTTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATATAATAA
Found at i:5550245 original size:14 final size:14
Alignment explanation
Indices: 5550218--5550257 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
5550208 AGGATCAAAT
5550218 TAATATT-T-TATA
1 TAATATTATATATA
5550230 T-ATATTAATATATA
1 TAATATT-ATATATA
5550244 TAATATTATATATA
1 TAATATTATATATA
5550258 ATTTTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 5 0.21
12 1 0.04
13 1 0.04
14 12 0.50
15 5 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATATTATATATA
Found at i:5550249 original size:17 final size:17
Alignment explanation
Indices: 5550216--5550256 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
5550206 AAAGGATCAA
*
5550216 ATTAATATTTTATATAT
1 ATTAATATTATATATAT
5550233 ATTAATA-TATATA-AT
1 ATTAATATTATATATAT
5550248 ATTATATAT
1 ATTA-ATAT
5550257 AATTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.29
16 8 0.38
17 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTAATATTATATATAT
Found at i:5552288 original size:109 final size:113
Alignment explanation
Indices: 5552073--5552288 Score: 241
Period size: 109 Copynumber: 1.9 Consensus size: 113
5552063 TTATATTTTT
* *
5552073 ATTAAAATTTTAAATATTAATTAATTTATCATTAAATTATTAATATAATTTTTATTTCAATTTCT
1 ATTAAAATTTTAAACATTAATTAATTTATCATTAAATTATTAATATAATTTTTATTT-AATCTCT
* * ** *
5552138 TTTTATTTTTTAGTTGTATTTTTATTTTTTAATCTTTTAATTCTATTTC
65 TTTTATTTTTTAGTTGTATTTTTACTTTGTAAGATTGTAATTCTATTTC
5552187 ATTAAAA-TTTAAACATTAA-TAATTTAGT-ATTAAATTATTAATATAAATTTTTAATTT-A-CT
1 ATTAAAATTTTAAACATTAATTAATTTA-TCATTAAATTATTAATAT-AATTTTT-ATTTAATCT
* * *
5552247 -TTTTTA-TTTTTATTTTTATTTTCT-CTTTGTAGGATTGTAATT
63 CTTTTTATTTTTTAGTTGTATTTT-TACTTTGTAAGATTGTAATT
5552289 ATTTTTAATA
Statistics
Matches: 88, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
109 26 0.30
110 7 0.08
111 1 0.01
112 24 0.27
113 19 0.22
114 11 0.12
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (113 bp):
ATTAAAATTTTAAACATTAATTAATTTATCATTAAATTATTAATATAATTTTTATTTAATCTCTT
TTTATTTTTTAGTTGTATTTTTACTTTGTAAGATTGTAATTCTATTTC
Found at i:5552912 original size:30 final size:30
Alignment explanation
Indices: 5552871--5552932 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
5552861 AACTTAAAAT
*
5552871 AAAAATAAAAGAGTTTGATTAAACATAATAA
1 AAAAATAAAAGA-CTTGATTAAACATAATAA
* *
5552902 AAAAAT-AAAGACTTGATTGAATATAATAA
1 AAAAATAAAAGACTTGATTAAACATAATAA
5552931 AA
1 AA
5552933 TATTAAAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 17 0.61
30 5 0.18
31 6 0.21
ACGTcount: A:0.61, C:0.03, G:0.10, T:0.26
Consensus pattern (30 bp):
AAAAATAAAAGACTTGATTAAACATAATAA
Found at i:5552939 original size:29 final size:29
Alignment explanation
Indices: 5552868--5552939 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
5552858 TTTAACTTAA
* *
5552868 AATAAAAATAAAAGAGTTTGATTAAACAT
1 AATAAAAATTAAAGAGCTTGATTAAACAT
* * *
5552897 AATAAAAAAATAAAGA-CTTGATTGAATAT
1 AAT-AAAAATTAAAGAGCTTGATTAAACAT
5552926 AATAAAATATTAAA
1 AATAAAA-ATTAAA
5552940 ACTCATTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 4 0.11
29 21 0.60
30 10 0.29
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (29 bp):
AATAAAAATTAAAGAGCTTGATTAAACAT
Found at i:5560282 original size:2 final size:2
Alignment explanation
Indices: 5560277--5560309 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5560267 AATAACAATA
5560277 AC AC AC AC AC AC 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 A
5560310 AAACAGAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5560678 original size:2 final size:2
Alignment explanation
Indices: 5560673--5560700 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5560663 AAAAAAAAGC
5560673 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5560701 AACCGCACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5561169 original size:31 final size:31
Alignment explanation
Indices: 5561131--5561232 Score: 195
Period size: 31 Copynumber: 3.3 Consensus size: 31
5561121 GGACATGAAT
*
5561131 AATAGCTTAATATGTGAAAGCTCATTTTAGC
1 AATAGCTTAATATGTGAAAGCTCTTTTTAGC
5561162 AATAGCTTAATATGTGAAAGCTCTTTTTAGC
1 AATAGCTTAATATGTGAAAGCTCTTTTTAGC
5561193 AATAGCTTAATATGTGAAAGCTCTTTTTAGC
1 AATAGCTTAATATGTGAAAGCTCTTTTTAGC
5561224 AATAGCTTA
1 AATAGCTTA
5561233 GAACATTGTT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
31 70 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (31 bp):
AATAGCTTAATATGTGAAAGCTCTTTTTAGC
Found at i:5585657 original size:15 final size:16
Alignment explanation
Indices: 5585637--5585674 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5585627 ACATTAAAGG
*
5585637 TTTAAAATTTTA-TTT
1 TTTAAAATTATACTTT
5585652 TTTAAAATTATACTTT
1 TTTAAAATTATACTTT
*
5585668 TATAAAA
1 TTTAAAA
5585675 ATAATAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTAAAATTATACTTT
Found at i:5586766 original size:2 final size:2
Alignment explanation
Indices: 5586759--5586802 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
5586749 GCTAGATGGC
5586759 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5586800 TA T
1 TA T
5586803 GATCAATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5610667 original size:16 final size:16
Alignment explanation
Indices: 5610611--5610669 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
5610601 TAATCAATTT
5610611 AAATTAAAAATATTAAAA
1 AAATTAAAAATA--AAAA
* *
5610629 AGATT-AAATTAAAATA
1 AAATTAAAAATAAAA-A
*
5610645 AATTTAAAAATAAAAA
1 AAATTAAAAATAAAAA
5610661 AAATTAAAA
1 AAATTAAAA
5610670 TATTACAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
15 3 0.09
16 13 0.39
17 13 0.39
18 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (16 bp):
AAATTAAAAATAAAAA
Found at i:5611326 original size:13 final size:14
Alignment explanation
Indices: 5611302--5611337 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5611292 ACATTATAAC
* *
5611302 TTATAAAAAAAAAT
1 TTATTAAAAAAATT
5611316 TTATTAAAAAAATT
1 TTATTAAAAAAATT
5611330 TTATTAAA
1 TTATTAAA
5611338 TAACTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TTATTAAAAAAATT
Found at i:5624611 original size:2 final size:2
Alignment explanation
Indices: 5624604--5624636 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5624594 TCTAGATGAA
5624604 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5624637 GAGAGTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5629692 original size:15 final size:15
Alignment explanation
Indices: 5629674--5629706 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
5629664 GTTTTTCTTG
5629674 AAATTTT-TTTTTTCA
1 AAATTTTATTTTTT-A
5629689 AAATTTTATTTTTTA
1 AAATTTTATTTTTTA
5629704 AAA
1 AAA
5629707 AAAAATTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
AAATTTTATTTTTTA
Found at i:5629707 original size:16 final size:15
Alignment explanation
Indices: 5629674--5629707 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
5629664 GTTTTTCTTG
*
5629674 AAATTTTTTTTTTCA
1 AAATTTTTTTTTTAA
5629689 AAATTTTATTTTTTAA
1 AAATTTT-TTTTTTAA
5629705 AAA
1 AAA
5629708 AAAATTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
AAATTTTTTTTTTAA
Found at i:5629952 original size:17 final size:16
Alignment explanation
Indices: 5629891--5629952 Score: 56
Period size: 17 Copynumber: 3.9 Consensus size: 16
5629881 AATTATCTAA
*
5629891 ATTATTTAAATAAAGTT
1 ATTATTTAATTAAA-TT
* *
5629908 ATTATATAA-T-ATTT
1 ATTATTTAATTAAATT
*
5629922 ATTATTTTATTAAATT
1 ATTATTTAATTAAATT
5629938 ATTATATTAATTAAA
1 ATTAT-TTAATTAAA
5629953 ATTGTATTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
14 9 0.25
15 2 0.06
16 9 0.25
17 16 0.44
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTATTTAATTAAATT
Found at i:5633746 original size:28 final size:29
Alignment explanation
Indices: 5633710--5633766 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5633700 TATTTGACCC
*
5633710 CCAAAAAAAG-AATAGAGCTTGA-TTGAAT
1 CCAAAAAAAGAAAAAGAGCTT-ATTTGAAT
*
5633738 CCAATAAAAGAAAAAGAGCTTATTTGAAT
1 CCAAAAAAAGAAAAAGAGCTTATTTGAAT
5633767 TTTCTTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.23
Consensus pattern (29 bp):
CCAAAAAAAGAAAAAGAGCTTATTTGAAT
Found at i:5638942 original size:15 final size:16
Alignment explanation
Indices: 5638915--5638948 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5638905 AACAATTTTT
5638915 ATTAATAAATTTATAA
1 ATTAATAAATTTATAA
*
5638931 ATTAAT-AATTTATTA
1 ATTAATAAATTTATAA
5638946 ATT
1 ATT
5638949 TATTGATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAATAAATTTATAA
Found at i:5641166 original size:15 final size:15
Alignment explanation
Indices: 5641146--5641192 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
5641136 TGACATTAAA
5641146 AAAATTA-TAACTTAT
1 AAAATTATTAA-TTAT
5641161 AAAATTATTAATTAT
1 AAAATTATTAATTAT
*
5641176 AATATATATATAATTAT
1 AAAAT-TAT-TAATTAT
5641193 TTATATAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 15 0.54
16 6 0.21
17 7 0.25
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATTATTAATTAT
Found at i:5641173 original size:22 final size:22
Alignment explanation
Indices: 5641148--5641211 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 22
5641138 ACATTAAAAA
5641148 AATTATAACTTATAAAATTATT
1 AATTATAACTTATAAAATTATT
5641170 AATTATAA-TATATATATAATTATT
1 AATTATAACT-TATA-A-AATTATT
*
5641194 TA-TATAAACTTATAAAAT
1 AATTAT-AACTTATAAAAT
5641212 ATACACTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
21 1 0.03
22 15 0.42
23 5 0.14
24 14 0.39
25 1 0.03
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTATAACTTATAAAATTATT
Found at i:5646735 original size:20 final size:20
Alignment explanation
Indices: 5646697--5646735 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5646687 GGCAAACTTT
* * *
5646697 ATTTTATTGGTCATTTGGAC
1 ATTTCATTGGCCATATGGAC
5646717 ATTTCATTGGCCATATGGA
1 ATTTCATTGGCCATATGGA
5646736 TTCCGACATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.44
Consensus pattern (20 bp):
ATTTCATTGGCCATATGGAC
Found at i:5652355 original size:27 final size:27
Alignment explanation
Indices: 5652325--5652377 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
5652315 ATATTTCCTT
5652325 CTGTACTAATTGCAGAAATAAGAGGAA
1 CTGTACTAATTGCAGAAATAAGAGGAA
*
5652352 CTGTACTAATTGCAGAAATAGGAGGA
1 CTGTACTAATTGCAGAAATAAGAGGA
5652378 CTATGCCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.23
Consensus pattern (27 bp):
CTGTACTAATTGCAGAAATAAGAGGAA
Found at i:5660481 original size:20 final size:20
Alignment explanation
Indices: 5660444--5660486 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
5660434 TGGAACCGGC
*
5660444 AATCTTTTTATTTAAGGTCT
1 AATCTTTTTATTTAAGGTAT
*
5660464 AATCTGTTTTA-TTCAGGTAT
1 AATCT-TTTTATTTAAGGTAT
5660484 AAT
1 AAT
5660487 TACTTCCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.51
Consensus pattern (20 bp):
AATCTTTTTATTTAAGGTAT
Found at i:5668146 original size:4 final size:4
Alignment explanation
Indices: 5668137--5668169 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
5668127 CTGTACCCGG
5668137 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
5668170 TTGACATGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:5668527 original size:40 final size:40
Alignment explanation
Indices: 5668483--5668565 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
5668473 AAAAGAAATA
5668483 TTTCAGAATAGGAAATAGGGACAATAACTTTCTTATTGCT
1 TTTCAGAATAGGAAATAGGGACAATAACTTTCTTATTGCT
5668523 TTTCAGAATAGGAAATAGGGACAATAACTTTCTTATTGCT
1 TTTCAGAATAGGAAATAGGGACAATAACTTTCTTATTGCT
5668563 TTT
1 TTT
5668566 AAGGTTTGTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (40 bp):
TTTCAGAATAGGAAATAGGGACAATAACTTTCTTATTGCT
Found at i:5676585 original size:20 final size:18
Alignment explanation
Indices: 5676554--5676596 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
5676544 TACACACGAA
*
5676554 TTTTTTTTTTTTTAC-CT
1 TTTTTTTTTTTTTTCTCT
5676571 TTTTTTTTTCATTTTTCTCT
1 TTTTTTTTT--TTTTTCTCT
5676591 TTTTTT
1 TTTTTT
5676597 ATGTATCCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
19 5 0.23
20 8 0.36
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTTTTTTCTCT
Found at i:5677831 original size:2 final size:2
Alignment explanation
Indices: 5677824--5677857 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5677814 GAAAAGAGTA
5677824 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5677858 CAACTTGAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5690787 original size:7 final size:8
Alignment explanation
Indices: 5690770--5690794 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5690760 AGAACTGAGG
5690770 TTTATTTT
1 TTTATTTT
5690778 TTTATTTT
1 TTTATTTT
5690786 TTTATTTT
1 TTTATTTT
5690794 T
1 T
5690795 ACCTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTATTTT
Found at i:5694934 original size:31 final size:31
Alignment explanation
Indices: 5694896--5694958 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
5694886 GTCACCGGTT
5694896 CCTGTTAGAAACAGGTGTGAGATTTATGTTG
1 CCTGTTAGAAACAGGTGTGAGATTTATGTTG
5694927 CCTGTTAGAAACAGGTGTGAGATTTATGTTG
1 CCTGTTAGAAACAGGTGTGAGATTTATGTTG
5694958 C
1 C
5694959 AAGGACATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.35
Consensus pattern (31 bp):
CCTGTTAGAAACAGGTGTGAGATTTATGTTG
Found at i:5718514 original size:20 final size:20
Alignment explanation
Indices: 5718477--5718517 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5718467 AGTTTTTAAA
5718477 ATAATAAAACTTTATAATTT
1 ATAATAAAACTTTATAATTT
* * *
5718497 ATAATTAAAGTTTTTAATTT
1 ATAATAAAACTTTATAATTT
5718517 A
1 A
5718518 ATTTTAAAAT
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:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
ATAATAAAACTTTATAATTT
Found at i:5721404 original size:42 final size:42
Alignment explanation
Indices: 5721344--5721423 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
5721334 GCAGCTTTTT
*
5721344 CCATATAAATGTGCGCAAACCAATATTTGTGGATATAGGCTG
1 CCATATAAATGTGCGCAAACCAATATTTGGGGATATAGGCTG
* * *
5721386 CCATATAAATGTGGGCAAACCAGTATTTGGGGTTATAG
1 CCATATAAATGTGCGCAAACCAATATTTGGGGATATAG
5721424 AATCAACTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29
Consensus pattern (42 bp):
CCATATAAATGTGCGCAAACCAATATTTGGGGATATAGGCTG
Found at i:5731793 original size:38 final size:38
Alignment explanation
Indices: 5731307--5732514 Score: 307
Period size: 38 Copynumber: 32.0 Consensus size: 38
5731297 TTCAATTGGG
* *
5731307 GCCGCATGCTACCTTCTTTGTAGTTCACATCACTTTGT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
***** * * * *
5731345 GTTATGTGTTACCTTCTTTATAACTCACATCACTTTGT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
* * *
5731383 GCTGCATGCTA-C--C-TTGTAGTTCGCATCATTTTGT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
* * ** * * *
5731417 GTCGCGT-CGTATTTTCTTTATAGCTTGCATCAC-GT-T
1 GCCGCATGC-TACCTTCTTTGTAGCTCGCATCACTTTGT
*** * * * *
5731453 GCCATGTGCTACCTTCTTTGTTA-CTTGCATAATTTTCT
1 GCCGCATGCTACCTTCTTTG-TAGCTCGCATCACTTTGT
* * * * *
5731491 ACCACATGCTACCTT-TTTAGTAACGCGCATCATTTTGT
1 GCCGCATGCTACCTTCTTT-GTAGCTCGCATCACTTTGT
** *** * *
5731529 ATCATGTGCTACCTTCTTTATAGCT--CATTGCATTTTGT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCA-T-CACTTTGT
**
5731567 GTTGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
* * * * * *
5731605 GCTGCGTGTTACCTTCTTTGTAACTCGTATCACTTTCT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
* * * * *
5731643 ACTGCGTGTTACCTTCTTTGTAACTCGCATCACTTTGT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
* *
5731681 GCCGCATGTTACCTTCTTTGTAGCTCACATCACTTTGT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
* * * ** * *
5731719 GCCGCATGCTACTTTTTTTATAGCTTACAACACTTTAT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
* * * * *
5731757 GTCACATGCTACCTTCTTTGTATCTTGCATCACTTTAT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
* * * * * * * * * * *
5731795 ACAGCGTGTTATCTTTTTTGTCGCACACTTCACTTAGT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
* * * * * * *
5731833 GACGCGTGCCA-C--CTTTCTAACTTGCGTCACTTTGT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
** * * * * *
5731868 GCTACGTGTTACCTTTTTTGTAGCTCGTC-GCACTTTAT
1 GCCGCATGCTACCTTCTTTGTAGCTCG-CATCACTTTGT
* *** *
5731906 GTCATGTGCTACCCTCTTTGTAGCTCGTC-TCACTTTGT
1 GCCGCATGCTACCTTCTTTGTAGCTCG-CATCACTTTGT
* *** * * *
5731944 GTCATGTGTTACATTCTTTGTAGCTCACCA-CACTTTGT
1 GCCGCATGCTACCTTCTTTGTAGCTC-GCATCACTTTGT
* * * * * *
5731982 GCCGCGTGTTACCTTATTTGTGGCTTAG-AGCACTTTGT
1 GCCGCATGCTACCTTCTTTGTAGC-TCGCATCACTTTGT
* * * * * *
5732020 GCCGCGTGCAACTTTCTTTCTAGCTCGTAACACTTTGT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
***** * * * * *
5732058 GTTATGTGATACCTTATTTGTAGTTCGCTTCATTTTGT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
*** * * * * * * *
5732096 GCCATGTGATACATTTTTTATAGTTTGCATCACTTTAT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
* * * * * *
5732134 GCCACGTGCTACCTTCTTTGTAACACACATCACTTTAT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
* * * * * * *
5732172 GTCGCGTGGTACTTTCTTTGTATCTCGCAACGCTTTGT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
* * * * ** ** *
5732210 GTCGCGTGCTACTTTCTGTGTAGCAAGTGTTACTTTGT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
* * * * * ** * *
5732248 GTCGCGTGTTACTTTTTTTGTAATTCGCATCACCTTGG
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
* * * * * *
5732286 GCCACGTGCTACTTTCTTTGTAACACGCATCACTTTCT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
** ** * * * *
5732324 ATCGTGTGTTACCTTCTTTATAACTCGCATTACTTTGT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
* * * * * * * * *
5732362 ACCCCGTGTTACCTTTTTTATAACCCTGTC-GCACTTTGT
1 GCCGCATGCTACCTTCTTTGTAGCTC-G-CATCACTTTGT
** * * *
5732401 GTTGCATGTTACCTTCTTTGTATCTCACTAT-ACTTTGT
1 GCCGCATGCTACCTTCTTTGTAGCTCGC-ATCACTTTGT
* * * * *
5732439 GCCACATGATACCTTTTTTATAGCTCACATCAC-TTGAT
1 GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTG-T
* * * *
5732477 GTCAGCGTGCTACCTTCTTCGTAGCACGCATCACTTTG
1 G-CCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTG
5732515 ATGCTAAGTG
Statistics
Matches: 864, Mismatches: 273, Indels: 64
0.72 0.23 0.05
Matches are distributed among these distances:
33 1 0.00
34 22 0.03
35 21 0.02
36 24 0.03
37 23 0.03
38 713 0.83
39 54 0.06
40 6 0.01
ACGTcount: A:0.17, C:0.25, G:0.16, T:0.42
Consensus pattern (38 bp):
GCCGCATGCTACCTTCTTTGTAGCTCGCATCACTTTGT
Found at i:5732224 original size:17 final size:17
Alignment explanation
Indices: 5732204--5732262 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 17
5732194 TCTCGCAACG
*
5732204 CTTTGTGTCGCGTGCTA
1 CTTTGTGTCGCGTGTTA
*
5732221 CTTTCTGTGTAGCAAGTGTTA
1 C-TT-TGTGTCGC--GTGTTA
5732242 CTTTGTGTCGCGTGTTA
1 CTTTGTGTCGCGTGTTA
5732259 CTTT
1 CTTT
5732263 TTTTGTAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
17 11 0.31
18 2 0.06
19 14 0.40
20 2 0.06
21 6 0.17
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.46
Consensus pattern (17 bp):
CTTTGTGTCGCGTGTTA
Found at i:5734774 original size:14 final size:15
Alignment explanation
Indices: 5734757--5734789 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5734747 CATATGTGAC
5734757 TTTTAAAACT-TAAT
1 TTTTAAAACTGTAAT
*
5734771 TTTTAAATCTGTAAT
1 TTTTAAAACTGTAAT
5734786 TTTT
1 TTTT
5734790 TTAAAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTTAAAACTGTAAT
Found at i:5748485 original size:45 final size:45
Alignment explanation
Indices: 5748397--5748485 Score: 101
Period size: 45 Copynumber: 2.0 Consensus size: 45
5748387 TTTAACCCCT
* *
5748397 AATAATATTTTCATCAAAAGAAAAAAATAACTAGCATTGTAATTA
1 AATAATATTTTCAACAAAAGAAAAAAATAACTAGCATTATAATTA
* * *
5748442 AATAATATTATT-AACAAAATACAAAAATAACCT-TCATTATAATT
1 AATAATATT-TTCAACAAAAGAAAAAAATAA-CTAGCATTATAATT
5748486 TTGATAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
45 33 0.89
46 4 0.11
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (45 bp):
AATAATATTTTCAACAAAAGAAAAAAATAACTAGCATTATAATTA
Found at i:5748582 original size:46 final size:44
Alignment explanation
Indices: 5748526--5748656 Score: 109
Period size: 46 Copynumber: 2.8 Consensus size: 44
5748516 CCCTTTATTT
* *
5748526 AAACAAAAAATACCTTTTATTATACTTTAATAATATTTTATACTAAC
1 AAAC-AAAAATA-CTTTTATTATA-TTAAATAATATTTTATACTAAA
** * * * * * *
5748573 AAACAAAAATATCACTTATTATAATCAACAGATAATTTGTATTAAA
1 AAACAAAAATA-CTTTTATTATATTAAATA-ATATTTTATACTAAA
5748619 AAACAAAAATACTCTTTATTATAATTAAATAATATTTT
1 AAACAAAAATACT-TTTATTAT-ATTAAATAATATTTT
5748657 TCATGATTTA
Statistics
Matches: 65, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
45 5 0.08
46 51 0.78
47 9 0.14
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.38
Consensus pattern (44 bp):
AAACAAAAATACTTTTATTATATTAAATAATATTTTATACTAAA
Found at i:5749167 original size:26 final size:26
Alignment explanation
Indices: 5749138--5749188 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
5749128 TTTAGATTCC
* * *
5749138 AATAAACTTTCTCACCCATCGAAGTT
1 AATAAACCTTCTCACCAATCCAAGTT
5749164 AATAAACCTTCTCACCAATCCAAGT
1 AATAAACCTTCTCACCAATCCAAGT
5749189 CTGCGGCTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.27
Consensus pattern (26 bp):
AATAAACCTTCTCACCAATCCAAGTT
Found at i:5751199 original size:24 final size:23
Alignment explanation
Indices: 5751154--5751199 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
5751144 ACCAATCCCT
* *
5751154 AACCCTAACCCAAAACAGAACCC
1 AACCCCAACCCAAAACACAACCC
*
5751177 AACCCCAACCCCAAACCACAACC
1 AACCCCAA-CCCAAAACACAACC
5751200 ACCCGTAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.46, C:0.50, G:0.02, T:0.02
Consensus pattern (23 bp):
AACCCCAACCCAAAACACAACCC
Found at i:5760358 original size:2 final size:2
Alignment explanation
Indices: 5760353--5760400 Score: 64
Period size: 2 Copynumber: 24.5 Consensus size: 2
5760343 ACATCCTTTT
*
5760353 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TG TA TA TCA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
5760394 TA TA TA T
1 TA TA TA T
5760401 TAAATGACTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 2 0.05
2 38 0.93
3 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5765609 original size:21 final size:20
Alignment explanation
Indices: 5765584--5765635 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
5765574 GGTGGCTGGA
5765584 GGTGGAGAGGCAGTAGCGGGT
1 GGTGGAGAGGC-GTAGCGGGT
*
5765605 GGTGGAGAGGGCGTGGCGGGT
1 GGTGGAGA-GGCGTAGCGGGT
*
5765626 GGCGGAGAGG
1 GGTGGAGAGG
5765636 GAGTCGTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 23 0.82
22 3 0.11
ACGTcount: A:0.15, C:0.10, G:0.63, T:0.12
Consensus pattern (20 bp):
GGTGGAGAGGCGTAGCGGGT
Found at i:5776282 original size:19 final size:19
Alignment explanation
Indices: 5776245--5776283 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5776235 ACAACATAAT
**
5776245 AATTATTTGAAAATTTATA
1 AATTATTTGAAAAAATATA
*
5776264 AATTATTTTAAAAAATATA
1 AATTATTTGAAAAAATATA
5776283 A
1 A
5776284 TTAAGTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
AATTATTTGAAAAAATATA
Found at i:5776320 original size:30 final size:30
Alignment explanation
Indices: 5776285--5776352 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
5776275 AAAATATAAT
*
5776285 TAAGTTTTTATATTTTTATTTTAAATGAAA
1 TAAGTTTTTATATTTTTATTTTAAATCAAA
*
5776315 TAAGTTTTTATATTTTTATTTTGAATCAAA
1 TAAGTTTTTATATTTTTATTTTAAATCAAA
*
5776345 TAAATTTT
1 TAAGTTTT
5776353 AATAATTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.57
Consensus pattern (30 bp):
TAAGTTTTTATATTTTTATTTTAAATCAAA
Found at i:5776566 original size:24 final size:23
Alignment explanation
Indices: 5776539--5776592 Score: 54
Period size: 24 Copynumber: 2.2 Consensus size: 23
5776529 TGATAAATGG
* *
5776539 TATTTTGATTAATAATAATTAATT
1 TATTTTAATT-ATAAAAATTAATT
*
5776563 TATTATTAATTATAAAAATTTATT
1 TATT-TTAATTATAAAAATTAATT
5776587 TGATTT
1 T-ATTT
5776593 AAAATAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
TATTTTAATTATAAAAATTAATT
Found at i:5776570 original size:21 final size:20
Alignment explanation
Indices: 5776546--5776586 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
5776536 TGGTATTTTG
*
5776546 ATTAATAATAATTAATTTATT
1 ATTAATAATAA-AAATTTATT
*
5776567 ATTAATTATAAAAATTTATT
1 ATTAATAATAAAAATTTATT
5776587 TGATTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTAATAATAAAAATTTATT
Found at i:5778433 original size:19 final size:18
Alignment explanation
Indices: 5778409--5778448 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
5778399 TTTCTCTCCA
5778409 TTTTTTCCTTCCTTCCTTC
1 TTTTTTCCTTCCTT-CTTC
* *
5778428 TTTTTTTCTTTCTTCTTC
1 TTTTTTCCTTCCTTCTTC
5778446 TTT
1 TTT
5778449 CACTTTTCTT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTCCTTCCTTCTTC
Found at i:5796940 original size:2 final size:2
Alignment explanation
Indices: 5796933--5796962 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5796923 AAAACACCCA
5796933 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5796963 GGAAATGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5799261 original size:2 final size:2
Alignment explanation
Indices: 5799254--5799317 Score: 94
Period size: 2 Copynumber: 32.0 Consensus size: 2
5799244 CCTAGAGACA
* *
5799254 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AN CT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5799295 AT ACT AT AT AT AT AT AT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT
5799318 TCAAATTGAT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.02
2 53 0.95
3 2 0.04
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5810466 original size:7 final size:7
Alignment explanation
Indices: 5810450--5810485 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
5810440 AAAATATAAA
5810450 AAAATAAT
1 AAAAT-AT
5810458 AAAATAT
1 AAAATAT
5810465 AAAATAT
1 AAAATAT
5810472 AAAAATAT
1 -AAAATAT
5810480 AAAATA
1 AAAATA
5810486 AAATAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 15 0.56
8 12 0.44
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (7 bp):
AAAATAT
Found at i:5810470 original size:15 final size:16
Alignment explanation
Indices: 5810439--5810486 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 16
5810429 ACCCATTTAA
*
5810439 AAAAATATAAAAAAAT
1 AAAAATATAAAATAAT
5810455 AATAAAATATAAAAT-AT
1 -A-AAAATATAAAATAAT
5810472 AAAAATATAAAATAA
1 AAAAATATAAAATAA
5810487 AATAATGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 12 0.43
16 2 0.07
17 3 0.11
18 11 0.39
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAATATAAAATAAT
Found at i:5810473 original size:25 final size:27
Alignment explanation
Indices: 5810440--5810490 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
5810430 CCCATTTAAA
*
5810440 AAAATATAAAAA-A-ATAATAAAATAT
1 AAAATATAAAAATATAAAATAAAATAT
5810465 AAAATATAAAAATATAAAATAAAATA
1 AAAATATAAAAATATAAAATAAAATA
5810491 ATGAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.52
26 1 0.04
27 10 0.43
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (27 bp):
AAAATATAAAAATATAAAATAAAATAT
Found at i:5811276 original size:13 final size:14
Alignment explanation
Indices: 5811251--5811280 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
5811241 TTAGCCGACT
5811251 AGAGAGAGAAAATA
1 AGAGAGAGAAAATA
5811265 AGAGAG-GAAAATA
1 AGAGAGAGAAAATA
5811278 AGA
1 AGA
5811281 AAAGAGAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.63, C:0.00, G:0.30, T:0.07
Consensus pattern (14 bp):
AGAGAGAGAAAATA
Found at i:5812229 original size:20 final size:20
Alignment explanation
Indices: 5812191--5812229 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5812181 TTTCGTATAA
* *
5812191 TAAATAAATATCTATATAGT
1 TAAATAAATATCGACATAGT
*
5812211 TAAATATATATCGACATAG
1 TAAATAAATATCGACATAG
5812230 AAATGGTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.36
Consensus pattern (20 bp):
TAAATAAATATCGACATAGT
Found at i:5816978 original size:2 final size:2
Alignment explanation
Indices: 5816971--5816995 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5816961 CTACTGTTTA
5816971 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 T
5816996 TCTTTGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5822277 original size:2 final size:2
Alignment explanation
Indices: 5822270--5822316 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
5822260 TAATACATAC
*
5822270 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5822312 AT AT A
1 AT AT A
5822317 GTAACAAACT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5824324 original size:40 final size:40
Alignment explanation
Indices: 5824238--5824314 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 40
5824228 TTTTGGCCAT
*
5824238 TATTCACCTTAGTGGAGTTTTCTAACCTCATCAAGATTAG
1 TATTCACCTTAGTGGAGTTTTCCAACCTCATCAAGATTAG
* * *
5824278 TATTCACTTTAGTGGAG-TTTCCAACCTCGTCACGATT
1 TATTCACCTTAGTGGAGTTTTCCAACCTCATCAAGATT
5824315 CGTGTTTCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 17 0.52
40 16 0.48
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (40 bp):
TATTCACCTTAGTGGAGTTTTCCAACCTCATCAAGATTAG
Found at i:5829256 original size:40 final size:40
Alignment explanation
Indices: 5829172--5829252 Score: 101
Period size: 39 Copynumber: 2.0 Consensus size: 40
5829162 TTGGTCATTA
* * *
5829172 TTCACCTTAGTGGGGTTTTCTAACCTCATCAAAATTGGTG
1 TTCACCTTAATGGGGATTTCTAACCTCATCAAAATTGATG
* **
5829212 TTCACCTTAAT-GGGATTTCTAACCTCGTCACGATTGATG
1 TTCACCTTAATGGGGATTTCTAACCTCATCAAAATTGATG
5829251 TT
1 TT
5829253 TCACAATGTC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
39 25 0.71
40 10 0.29
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (40 bp):
TTCACCTTAATGGGGATTTCTAACCTCATCAAAATTGATG
Found at i:5829324 original size:33 final size:33
Alignment explanation
Indices: 5829282--5829350 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
5829272 TCACAACGCT
5829282 CCAGTGTCTTCACACTGCTCCAACGTCAACCCC
1 CCAGTGTCTTCACACTGCTCCAACGTCAACCCC
5829315 CCAGTGTCTTCACACTGCTCCAACGTCAACCCC
1 CCAGTGTCTTCACACTGCTCCAACGTCAACCCC
5829348 CCA
1 CCA
5829351 TTGGTCTCGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.22, C:0.46, G:0.12, T:0.20
Consensus pattern (33 bp):
CCAGTGTCTTCACACTGCTCCAACGTCAACCCC
Found at i:5831136 original size:15 final size:15
Alignment explanation
Indices: 5831118--5831161 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
5831108 TGATTAGATT
5831118 TTTAAATATTAATAA
1 TTTAAATATTAATAA
5831133 TTTAAA-ATT--TAA
1 TTTAAATATTAATAA
*
5831145 TTAAAATATTAATAA
1 TTTAAATATTAATAA
5831160 TT
1 TT
5831162 AATAGTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
12 8 0.32
13 3 0.12
14 3 0.12
15 11 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTAAATATTAATAA
Found at i:5833088 original size:12 final size:11
Alignment explanation
Indices: 5833039--5833102 Score: 55
Period size: 11 Copynumber: 5.7 Consensus size: 11
5833029 ACGTATAAAC
5833039 AAATAAAAT-T
1 AAATAAAATAT
5833049 AAATTAAAA-AT
1 AAA-TAAAATAT
5833060 AAATAATAATA-
1 AAATAA-AATAT
5833071 ATAATAATAATAT
1 A-AATAA-AATAT
5833084 AAATAAAA-ATT
1 AAATAAAATA-T
5833095 AAATAAAA
1 AAATAAAA
5833103 ACTTTACTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
10 7 0.15
11 23 0.49
12 16 0.34
13 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAATAAAATAT
Found at i:5833103 original size:12 final size:11
Alignment explanation
Indices: 5833039--5833103 Score: 62
Period size: 12 Copynumber: 5.8 Consensus size: 11
5833029 ACGTATAAAC
5833039 AAAT-AAAATT
1 AAATAAAAATT
5833049 AAATTAAAAA-T
1 AAA-TAAAAATT
* *
5833060 AAATAATAATA
1 AAATAAAAATT
*
5833071 ATAATAATAATAT
1 A-AATAAAAAT-T
5833084 AAATAAAAATT
1 AAATAAAAATT
5833095 AAATAAAAA
1 AAATAAAAA
5833104 CTTTACTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
10 8 0.17
11 16 0.35
12 21 0.46
13 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAATAAAAATT
Found at i:5835206 original size:25 final size:25
Alignment explanation
Indices: 5835156--5835209 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
5835146 GAAGGCAAAT
**
5835156 TACTATAGTATAGTTTATTTAGTAC
1 TACTATAGTATAGTTTAGCTAGTAC
*
5835181 TACTATAGTGTAGTTTAAGCTA-TAC
1 TACTATAGTATAGTTT-AGCTAGTAC
5835206 TACT
1 TACT
5835210 TGTAATCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 22 0.88
26 3 0.12
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.44
Consensus pattern (25 bp):
TACTATAGTATAGTTTAGCTAGTAC
Found at i:5841928 original size:26 final size:27
Alignment explanation
Indices: 5841898--5841956 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
5841888 AATTATGGTG
*
5841898 GATAT-AAACCACTTTTAATGAGTAAA
1 GATATCAAACCACTTCTAATGAGTAAA
* * *
5841924 GATATCCACCCACTTCTAGTGAGTAAA
1 GATATCAAACCACTTCTAATGAGTAAA
*
5841951 GGTATC
1 GATATC
5841957 CATCTACGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (27 bp):
GATATCAAACCACTTCTAATGAGTAAA
Found at i:5841937 original size:27 final size:27
Alignment explanation
Indices: 5841906--5841958 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
5841896 TGGATATAAA
*
5841906 CCACTTTTAATGAGTAAAGATATCCAC
1 CCACTTCTAATGAGTAAAGATATCCAC
* *
5841933 CCACTTCTAGTGAGTAAAGGTATCCA
1 CCACTTCTAATGAGTAAAGATATCCA
5841959 TCTACGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (27 bp):
CCACTTCTAATGAGTAAAGATATCCAC
Found at i:5847628 original size:2 final size:2
Alignment explanation
Indices: 5847621--5847649 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5847611 ACATCAAACC
5847621 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5847650 CAACAAACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5849436 original size:22 final size:21
Alignment explanation
Indices: 5849381--5849492 Score: 84
Period size: 22 Copynumber: 5.1 Consensus size: 21
5849371 TTTTAATATT
5849381 AAATATTATTTAATTATAATAA
1 AAATATTA-TTAATTATAATAA
* *
5849403 AAGGT-TTAATTAACTTCTAATAA
1 AA-ATATT-ATTAA-TTATAATAA
5849426 AAATATTATTAAATTATAATAA
1 AAATATTATT-AATTATAATAA
* * **
5849448 AAATATGT-TTGTATTTTGGTAA
1 AAATAT-TATT-AATTATAATAA
*
5849470 AAATATTATTAATTATAGTAA
1 AAATATTATTAATTATAATAA
5849491 AA
1 AA
5849493 GTTATTTTGA
Statistics
Matches: 71, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
21 11 0.15
22 43 0.61
23 17 0.24
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (21 bp):
AAATATTATTAATTATAATAA
Found at i:5851676 original size:3 final size:3
Alignment explanation
Indices: 5851668--5851692 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5851658 GGAAAATTAA
5851668 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
5851693 TAAAACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5875966 original size:49 final size:49
Alignment explanation
Indices: 5875894--5876006 Score: 226
Period size: 49 Copynumber: 2.3 Consensus size: 49
5875884 GACCAAAAAC
5875894 CTTCAGCTAAAGCAAAAGGATGCGGGCATGCCGCCCGCCCAAGTTGACA
1 CTTCAGCTAAAGCAAAAGGATGCGGGCATGCCGCCCGCCCAAGTTGACA
5875943 CTTCAGCTAAAGCAAAAGGATGCGGGCATGCCGCCCGCCCAAGTTGACA
1 CTTCAGCTAAAGCAAAAGGATGCGGGCATGCCGCCCGCCCAAGTTGACA
5875992 CTTCAGCTAAAGCAA
1 CTTCAGCTAAAGCAA
5876007 GACCAAAAGC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 64 1.00
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.15
Consensus pattern (49 bp):
CTTCAGCTAAAGCAAAAGGATGCGGGCATGCCGCCCGCCCAAGTTGACA
Found at i:5880028 original size:21 final size:20
Alignment explanation
Indices: 5879966--5880037 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
5879956 TTTTATGAAA
* *
5879966 ATTAATGTTTAAGTTAAAAT
1 ATTAATATTTAAATTAAAAT
*
5879986 ATTAATATTTAACTTAAAA-
1 ATTAATATTTAAATTAAAAT
5880005 A-T-AT-TTTAAATTAAAAT
1 ATTAATATTTAAATTAAAAT
5880022 ATTAATATTTAAATTA
1 ATTAATATTTAAATTA
5880038 TTTAATACTA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
16 11 0.24
17 3 0.07
18 2 0.04
19 3 0.07
20 26 0.58
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (20 bp):
ATTAATATTTAAATTAAAAT
Done.