Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 14 of 410
Found at i:3602707 original size:29 final size:29
Alignment explanation
Indices: 3602675--3602769 Score: 73
Period size: 29 Copynumber: 3.0 Consensus size: 29
3602665 TATCTCGTAG
3602675 ATAAACATTAAATTAAATTTAATATTAAA
1 ATAAACATTAAATTAAATTTAATATTAAA
* * *
3602704 ATAACCACTTTAATATTAAATTAAAAATAATATTTAG
1 ATAA--ACATTAA-ATTAAATT-----TAATATTAAA
**
3602741 ATAAGTATTAAATTAAATTTAATATTAAA
1 ATAAACATTAAATTAAATTTAATATTAAA
3602770 CTATTAAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 16
0.68 0.11 0.22
Matches are distributed among these distances:
29 12 0.24
31 6 0.12
32 8 0.16
34 8 0.16
35 4 0.08
37 12 0.24
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (29 bp):
ATAAACATTAAATTAAATTTAATATTAAA
Found at i:3605067 original size:64 final size:64
Alignment explanation
Indices: 3604987--3605170 Score: 174
Period size: 67 Copynumber: 2.8 Consensus size: 64
3604977 AGACATTATG
* * *
3604987 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACAATGTATACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTATACAAGAGAGCTACGAGATAA
* * * * * * *
3605051 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTATACAAGAGAGCTACGAGAT
3605116 AA
63 AA
* * * * * *
3605118 ACTG--GCTAGGTCACATGGTTGGTACTAAGTGTTCACCATGTGTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTATACAAGAGAGC
3605171 CGAACTATAT
Statistics
Matches: 94, Mismatches: 22, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
63 19 0.20
64 21 0.22
65 8 0.09
66 15 0.16
67 29 0.31
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTATACAAGAGAGCTACGAGATAA
Found at i:3606951 original size:12 final size:12
Alignment explanation
Indices: 3606923--3606961 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
3606913 AAAGAAATAC
*
3606923 AATAAAATAACAG
1 AATAAAA-AAAAG
3606936 AATAAAAAAAAG
1 AATAAAAAAAAG
3606948 AATAAAAAATAAG
1 AATAAAAAA-AAG
3606961 A
1 A
3606962 TTTTTTACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (12 bp):
AATAAAAAAAAG
Found at i:3607077 original size:18 final size:18
Alignment explanation
Indices: 3607054--3607093 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3607044 GCCGGAGCCC
* *
3607054 CTCCCCTCTCTCTCTTCT
1 CTCCCCGCTCCCTCTTCT
*
3607072 CTCCCCGCTCCCTCTTTT
1 CTCCCCGCTCCCTCTTCT
3607090 CTCC
1 CTCC
3607094 TTCCCTTCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.57, G:0.03, T:0.40
Consensus pattern (18 bp):
CTCCCCGCTCCCTCTTCT
Found at i:3607579 original size:12 final size:12
Alignment explanation
Indices: 3607562--3607601 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
3607552 TTTTTTTACA
3607562 TATTATTAATAT
1 TATTATTAATAT
*
3607574 TATTATTAGTAT
1 TATTATTAATAT
*
3607586 TTTTATTAATA-
1 TATTATTAATAT
3607597 TATTA
1 TATTA
3607602 ATTATTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (12 bp):
TATTATTAATAT
Found at i:3607687 original size:13 final size:14
Alignment explanation
Indices: 3607663--3607693 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
3607653 ATCATTATTA
3607663 ATATTAATATATGT
1 ATATTAATATATGT
3607677 ATATT-ATATATGT
1 ATATTAATATATGT
3607690 ATAT
1 ATAT
3607694 ATTCGTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
ATATTAATATATGT
Found at i:3607960 original size:2 final size:2
Alignment explanation
Indices: 3607953--3607979 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3607943 CTTTTATACT
3607953 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3607980 CTAATATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3613304 original size:131 final size:133
Alignment explanation
Indices: 3613093--3613370 Score: 465
Period size: 131 Copynumber: 2.1 Consensus size: 133
3613083 CATTGGGCCT
* *
3613093 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATT-TGGTAACAGTGGTACT-GGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
3613158 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AA
64 AGCCCCTTATTCAGATAACAGTATGGCCCATAGG-CCATTTC-AAATACATGCAACATCAATAAA
3613222 CATATGC
127 CATATGC
3613229 AAGCCCATTTGGTAACAGTGGTACT-GCCAAAGCCCTTTTCAGATTACAAT-AACT-GGCCTTAG
1 AAGCCCATTTGGTAACAGTGGTACTGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTTAG
*
3613291 CCCCTTATTCAGATAACAGTATGGCCCATAGGCCATTTCAAATACATGCAACATCAGTAAACATA
66 CCCCTTATTCAGATAACAGTATGGCCCATAGGCCATTTCAAATACATGCAACATCAATAAACATA
3613356 TGC
131 TGC
3613359 AAGCCCATTTGG
1 AAGCCCATTTGG
3613371 GGAGATACTC
Statistics
Matches: 138, Mismatches: 3, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
129 18 0.13
130 28 0.20
131 40 0.29
132 4 0.03
133 24 0.17
135 15 0.11
136 9 0.07
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (133 bp):
AAGCCCATTTGGTAACAGTGGTACTGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTTAG
CCCCTTATTCAGATAACAGTATGGCCCATAGGCCATTTCAAATACATGCAACATCAATAAACATA
TGC
Found at i:3613651 original size:25 final size:26
Alignment explanation
Indices: 3613614--3613666 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
3613604 TCAAACATGC
*
3613614 ATTTAGGTCAATTTAACCCTAGGGGT
1 ATTTAGGTCAATTTAACACTAGGGGT
* **
3613640 ATTTCGGT-AATTTTGCACTAGGGGT
1 ATTTAGGTCAATTTAACACTAGGGGT
3613665 AT
1 AT
3613667 AACAGTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.38
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACACTAGGGGT
Found at i:3613674 original size:25 final size:26
Alignment explanation
Indices: 3613632--3613704 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
3613622 CAATTTAACC
* * *
3613632 CTAGGGGTATTTCGGTAATTTTGC-A
1 CTAGGGGTATTACAGTAATTTTCCTA
*
3613657 CTAGGGGTATAACAGTAAATTTTCCTA
1 CTAGGGGTATTACAGT-AATTTTCCTA
*
3613684 CATAGGGGTATTATAGTAATT
1 C-TAGGGGTATTACAGTAATT
3613705 AACTCTTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 13 0.33
26 7 0.18
27 6 0.15
28 13 0.33
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (26 bp):
CTAGGGGTATTACAGTAATTTTCCTA
Found at i:3615173 original size:26 final size:26
Alignment explanation
Indices: 3615137--3615297 Score: 270
Period size: 26 Copynumber: 6.2 Consensus size: 26
3615127 CATGATATTC
3615137 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
3615163 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
3615189 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
3615215 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
3615241 TTATCATGGAACATTTACCTAACACA
1 TTATCATGAAACATTTACCTAACCCA
*
3615267 TTATCATG-AACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
3615292 TTATCA
1 TTATCA
3615298 ATTTGTACCA
Statistics
Matches: 127, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
25 21 0.17
26 106 0.83
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:3623803 original size:71 final size:71
Alignment explanation
Indices: 3623682--3623815 Score: 214
Period size: 71 Copynumber: 1.9 Consensus size: 71
3623672 GTTTTCCAAG
* * *
3623682 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
3623747 GTTTCA
66 GTTTCA
* * *
3623753 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
3623816 CTGCTTTTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
GTTTCA
Found at i:3623893 original size:160 final size:160
Alignment explanation
Indices: 3623629--3624292 Score: 1228
Period size: 160 Copynumber: 4.2 Consensus size: 160
3623619 ACTTCTGTCA
3623629 CAGGGCACGCTGAGGTATTTTCAATTTCTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCA
1 CAGGGCACGCTGAGGTATTTTCAATTTCTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCA
3623694 TATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAAAATC
66 TATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAAAATC
3623759 AACTCATATTGCGAGAAGTGAGTTGAGCCT
131 AACTCATATTGCGAGAAGTGAGTTGAGCCT
3623789 CAGGGCACGCTGAGGTATTTTCAATTTCTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCA
1 CAGGGCACGCTGAGGTATTTTCAATTTCTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCA
3623854 TATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAAAATC
66 TATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAAAATC
3623919 AACTCATATTGCGAGAAGTGAGTTGAGCCT
131 AACTCATATTGCGAGAAGTGAGTTGAGCCT
3623949 CAGGGCACGCTGAGGTATTTTCAATTTCTGCTTTTTAAATTCATGTTTTCCAAGAAAATCAGCTC
1 CAGGGCACGCTGAGGTATTTTCAATTTCTGCTTTTT-AATTCATGTTTTCCAAGAAAATCAGCTC
*
3624014 ATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATG-TTCAAAAAT
65 ATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAAAAT
3624078 CAACTCATATTGCGAGAA-TGAGTTGAGCCT
130 CAACTCATATTGCGAGAAGTGAGTTGAGCCT
*
3624108 CAGGGCACGCTGAGGTATTTTCAATTTCTGCTTCTTAAATTCATGTTTT-CAAGAAAATCAGCTC
1 CAGGGCACGCTGAGGTATTTTCAATTTCTGCTT-TTTAATTCATGTTTTCCAAGAAAATCAGCTC
3624172 ATATTGCGAGAGGTGAGTTGAGCC-CAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAAAAT
65 ATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAAAAT
* *
3624236 CAACTCATATCGCGAGAAGTGAGTTGAACCT
130 CAACTCATATTGCGAGAAGTGAGTTGAGCCT
* *
3624267 CGGGGCACGCTGAGGTAATTTCAATT
1 CAGGGCACGCTGAGGTATTTTCAATT
3624293 CCTATTAATC
Statistics
Matches: 493, Mismatches: 7, Indels: 9
0.97 0.01 0.02
Matches are distributed among these distances:
157 30 0.06
158 64 0.13
159 92 0.19
160 225 0.46
161 82 0.17
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (160 bp):
CAGGGCACGCTGAGGTATTTTCAATTTCTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCA
TATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAAAATC
AACTCATATTGCGAGAAGTGAGTTGAGCCT
Found at i:3623963 original size:71 final size:71
Alignment explanation
Indices: 3623842--3623975 Score: 214
Period size: 71 Copynumber: 1.9 Consensus size: 71
3623832 GTTTTCCAAG
* * *
3623842 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
3623907 GTTTCA
66 GTTTCA
* * *
3623913 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
3623976 CTGCTTTTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
GTTTCA
Found at i:3624130 original size:69 final size:70
Alignment explanation
Indices: 3624003--3624134 Score: 212
Period size: 69 Copynumber: 1.9 Consensus size: 70
3623993 GTTTTCCAAG
* *
3624003 AAAATCAGCTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
3624068 GTTCA
66 GTTCA
* * *
3624073 AAAATCAACTCATATTGCGAGAA-TGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
3624135 CTGCTTCTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
69 35 0.61
70 22 0.39
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.30
Consensus pattern (70 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
GTTCA
Found at i:3624319 original size:74 final size:71
Alignment explanation
Indices: 3624161--3624369 Score: 242
Period size: 74 Copynumber: 2.9 Consensus size: 71
3624151 TGTTTTCAAG
* * * * *
3624161 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCC-CAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTCAATTTAT
*
3624225 GTTTCA
66 GTATCA
* * *
3624231 AAAATCAACTCATATCGCGAGAAGTGAGTTGAACCTCGGGGCACGCTGAGGTAATTTCAATTCCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTCAATT--T
3624296 AT-TAATCTA
64 ATGT-ATC-A
* * * * *
3624305 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGCGGCACGCTAAGGTATTTTCAAATTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTCAATTTAT
3624370 ATTCATATTG
Statistics
Matches: 118, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
70 31 0.26
71 22 0.19
72 4 0.03
73 5 0.04
74 56 0.47
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTCAATTTAT
GTATCA
Found at i:3624617 original size:68 final size:68
Alignment explanation
Indices: 3624445--3624685 Score: 412
Period size: 68 Copynumber: 3.5 Consensus size: 68
3624435 TTCAAAGATC
* * *
3624445 AACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTTCTTTTTTCAAAATCTACTTTTCAAA-G
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTTCGTTTCTCAAAATCTACTTTTCAAATT
*
3624509 ATC
66 ATT
3624512 AACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTTCGTTTCTCAAAATCTACTTTTCAAATT
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTTCGTTTCTCAAAATCTACTTTTCAAATT
3624577 ATT
66 ATT
*
3624580 AACTCATGTTGCGAGAGGTGAGTTGAGCCTTTAATTTTCGTTTCTCAAAATCTACTTTTCAAATT
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTTCGTTTCTCAAAATCTACTTTTCAAATT
3624645 ATT
66 ATT
*
3624648 AACTCATGTTGCGAGAGGTGAGTTGAGCCTTTTAATTT
1 AACTCATATTGCGAGAGGTGAGTTGAGCC-TTTAATTT
3624686 CTGCTTTAAA
Statistics
Matches: 167, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
67 61 0.37
68 98 0.59
69 8 0.05
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (68 bp):
AACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTTCGTTTCTCAAAATCTACTTTTCAAATT
ATT
Found at i:3626420 original size:12 final size:12
Alignment explanation
Indices: 3626403--3626442 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
3626393 TTTTTTTACA
3626403 TATTATTAATAT
1 TATTATTAATAT
*
3626415 TATTATTAGTAT
1 TATTATTAATAT
*
3626427 TTTTATTAATA-
1 TATTATTAATAT
3626438 TATTA
1 TATTA
3626443 ATTATTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (12 bp):
TATTATTAATAT
Found at i:3626528 original size:13 final size:14
Alignment explanation
Indices: 3626504--3626534 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
3626494 ATCATTATTA
3626504 ATATTAATATATGT
1 ATATTAATATATGT
3626518 ATATT-ATATATGT
1 ATATTAATATATGT
3626531 ATAT
1 ATAT
3626535 ATTCGTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
ATATTAATATATGT
Found at i:3626800 original size:2 final size:2
Alignment explanation
Indices: 3626793--3626821 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3626783 TTTATACTAT
3626793 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3626822 CTAATATTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3629353 original size:22 final size:22
Alignment explanation
Indices: 3629328--3629381 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
3629318 TTTTCAAATT
* *
3629328 TATTTTAATTTAAATCTC-ATAA
1 TATTCTAATTTAAAT-TCAAAAA
*
3629350 TATTCTGATTTAAATTCAAAAA
1 TATTCTAATTTAAATTCAAAAA
3629372 TATTCTAATT
1 TATTCTAATT
3629382 ATTTATCTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (22 bp):
TATTCTAATTTAAATTCAAAAA
Found at i:3630046 original size:9 final size:9
Alignment explanation
Indices: 3630001--3630050 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
3629991 TAATTTTTTT
3630001 TAAAAATTA
1 TAAAAATTA
3630010 TATAAAATT-
1 TA-AAAATTA
*
3630019 T-AAAATTC
1 TAAAAATTA
3630027 T-AAAATATA
1 TAAAAAT-TA
3630036 TAAAAATTA
1 TAAAAATTA
3630045 TAAAAA
1 TAAAAA
3630051 AAATTGTCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
7 6 0.17
8 6 0.17
9 13 0.36
10 11 0.31
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (9 bp):
TAAAAATTA
Found at i:3630865 original size:7 final size:7
Alignment explanation
Indices: 3630850--3630886 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
3630840 TTGTTGGGTC
*
3630850 ATTTCAT
1 ATTTAAT
3630857 ATTTAAT
1 ATTTAAT
3630864 ATTTAAT
1 ATTTAAT
3630871 ATTTAAT
1 ATTTAAT
3630878 ATTTAAT
1 ATTTAAT
3630885 AT
1 AT
3630887 ATGCTTCTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTTAAT
Found at i:3631623 original size:16 final size:16
Alignment explanation
Indices: 3631604--3631654 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
3631594 TATAAATAAA
*
3631604 TATATTATAAAATTTT
1 TATATAATAAAATTTT
3631620 TATA-ACATAAATTATTTT
1 TATATA-ATAAA--ATTTT
3631638 T-TATAATAAAATTTT
1 TATATAATAAAATTTT
3631653 TA
1 TA
3631655 CCATAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
15 6 0.21
16 9 0.31
17 7 0.24
18 7 0.24
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATAATAAAATTTT
Found at i:3633082 original size:3 final size:3
Alignment explanation
Indices: 3633074--3633103 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3633064 ATTCGTTGGC
3633074 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3633104 AAACATGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3634314 original size:15 final size:16
Alignment explanation
Indices: 3634295--3634335 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
3634285 GGGCTAAAAC
*
3634295 AAACCCAACTAAAGCT
1 AAACCCAACTAAACCT
*
3634311 -AACCCAAAT-AACCT
1 AAACCCAACTAAACCT
3634325 AAACCCAACTA
1 AAACCCAACTA
3634336 TCCAAACTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 4
0.74 0.11 0.15
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.51, C:0.34, G:0.02, T:0.12
Consensus pattern (16 bp):
AAACCCAACTAAACCT
Found at i:3635474 original size:3 final size:3
Alignment explanation
Indices: 3635466--3635880 Score: 212
Period size: 3 Copynumber: 139.3 Consensus size: 3
3635456 ATTTAATATA
* * * *
3635466 TAT TAT TAT TAC TAT CAT TAT T-T TAC TAT TAT T-T AGAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
* * * *
3635510 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAC TGT TAC T-T TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
3635556 T-T AAT ATAT TAT TAT TACCT TTT TAT TAT TAT TAC TAC TAT T-G TAT
1 TAT TAT -TAT TAT TAT TA--T TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
3635602 TAT TAC TAT TAT TA- TAT T-T TCAT CTA- TATT TAT T-T TCT TAT TATT
1 TAT TAT TAT TAT TAT TAT TAT T-AT -TAT TA-T TAT TAT TAT TAT TA-T
* *
3635647 TAT CTAGT TTT TATT TAT CTAT T-T ATAT T-T TGT TAT TAT TA- TAT
1 TAT -TA-T TAT TA-T TAT -TAT TAT -TAT TAT TAT TAT TAT TAT TAT
* * *
3635691 T-T TAGG TAT TA- TAT CT-T TAT T-T ATATT TAT GTAT TAA TAT CAT
1 TAT TA-T TAT TAT TAT -TAT TAT TAT -TA-T TAT -TAT TAT TAT TAT
* ** *
3635734 TAT T-T TAC TAT TGC TA- TAT T-T T-T TA- TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
3635777 TAC TAT TA- TACT T-T TAT TAC TAC TAC TACGG TAT TAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TA--T TAT TAT TAT TAT TAT
3635823 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3635871 TAT TAT TAT T
1 TAT TAT TAT T
3635881 TACTTGTTTT
Statistics
Matches: 320, Mismatches: 48, Indels: 88
0.70 0.11 0.19
Matches are distributed among these distances:
2 41 0.13
3 243 0.76
4 29 0.09
5 7 0.02
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3635587 original size:20 final size:20
Alignment explanation
Indices: 3635466--3635612 Score: 78
Period size: 20 Copynumber: 7.5 Consensus size: 20
3635456 ATTTAATATA
*
3635466 TATTATTATTACTA-T-CAT
1 TATTATTATTACTATTGTAT
* *
3635484 TATT-TTACTATTATT-TA-
1 TATTATTATTACTATTGTAT
* *
3635501 GATTATTATTATTA-T-TAT
1 TATTATTATTACTATTGTAT
* *
3635519 TATTATTATTATTATTATAT
1 TATTATTATTACTATTGTAT
* *
3635539 TACTGTTACTTTACTATT-TAAT
1 TATTATTA--TTACTATTGT-AT
*
3635561 ATATTATTATTACCT-TTTTAT
1 -TATTATTATTA-CTATTGTAT
*
3635582 TATTATTACTACTATTGTAT
1 TATTATTATTACTATTGTAT
*
3635602 TATTACTATTA
1 TATTATTATTA
3635613 TTATATTTTC
Statistics
Matches: 102, Mismatches: 15, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
17 13 0.13
18 27 0.26
19 3 0.03
20 33 0.32
21 8 0.08
22 12 0.12
23 6 0.06
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.59
Consensus pattern (20 bp):
TATTATTATTACTATTGTAT
Found at i:3635602 original size:17 final size:17
Alignment explanation
Indices: 3635582--3635619 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3635572 ACCTTTTTAT
*
3635582 TATTATTACTACTATTG
1 TATTATTACTACTATTA
*
3635599 TATTATTACTATTATTA
1 TATTATTACTACTATTA
3635616 TATT
1 TATT
3635620 TTCATCTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.58
Consensus pattern (17 bp):
TATTATTACTACTATTA
Found at i:3635700 original size:17 final size:16
Alignment explanation
Indices: 3635669--3635702 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3635659 ATTTATCTAT
*
3635669 TTATATTTTGTTATTA
1 TTATATTTTGGTATTA
3635685 TTATATTTTAGGTATTA
1 TTATATTTT-GGTATTA
3635702 T
1 T
3635703 ATCTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (16 bp):
TTATATTTTGGTATTA
Found at i:3635730 original size:26 final size:26
Alignment explanation
Indices: 3635681--3635738 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
3635671 ATATTTTGTT
3635681 ATTA-TTATATTTTAGGTATTATATC
1 ATTATTTATATTTTAGGTATTATATC
* *
3635706 TTTATTTATA-TTTATGTATTAATATC
1 ATTATTTATATTTTAGGTATT-ATATC
3635732 ATTATTT
1 ATTATTT
3635739 TACTATTGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 12 0.43
26 16 0.57
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.60
Consensus pattern (26 bp):
ATTATTTATATTTTAGGTATTATATC
Found at i:3635927 original size:25 final size:26
Alignment explanation
Indices: 3635829--3635953 Score: 71
Period size: 25 Copynumber: 4.8 Consensus size: 26
3635819 TTATTATTAT
* * *
3635829 TATTATTATTATTA-TTATTATTATTAT
1 TATTTTTATTTTTATTTATT-TTATT-C
* *
3635856 TATTATTATTATTA-TTATTATTATT-
1 TATTTTTATTTTTATTTATT-TTATTC
* *
3635881 TACTTGTT-TTTTTGTTTATTTTATTC
1 TA-TTTTTATTTTTATTTATTTTATTC
*
3635907 TATTTTTATTTTTATTT-TTTTCTTC
1 TATTTTTATTTTTATTTATTTTATTC
* * *
3635932 TCTTTTTCTTTCTTATTGATTT
1 TATTTTTATTT-TTATTTATTT
3635954 GTTTAAAGTT
Statistics
Matches: 83, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
25 31 0.37
26 24 0.29
27 28 0.34
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (26 bp):
TATTTTTATTTTTATTTATTTTATTC
Found at i:3635942 original size:6 final size:6
Alignment explanation
Indices: 3635810--3635925 Score: 67
Period size: 6 Copynumber: 19.3 Consensus size: 6
3635800 TACTACGGTA
* * * * * * * *
3635810 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
* * * *
3635858 TTATTA TTATTA TTATTA TTATTT ACTTGTTT TT-TTGT TTA-TT TTA-TT
1 TTATTT TTATTT TTATTT TTATTT --TTATTT TTATT-T TTATTT TTATTT
*
3635906 CTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TT
3635926 TTCTTCTCTT
Statistics
Matches: 101, Mismatches: 4, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
5 10 0.10
6 86 0.85
8 5 0.05
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (6 bp):
TTATTT
Found at i:3645046 original size:30 final size:30
Alignment explanation
Indices: 3644945--3645061 Score: 96
Period size: 30 Copynumber: 3.9 Consensus size: 30
3644935 AAGTAATGAG
*
3644945 AATTTTCAAAAATTTTGAA-AGTTTAACTAA
1 AATTTTCAAAAA-TTTGAAGAGTTTAAGTAA
* * * ** *
3644975 TA-TTTCAAAACTTTTGTAGAACTTAACTAA
1 AATTTTCAAAA-ATTTGAAGAGTTTAAGTAA
* *
3645005 AATTTTTAAAAAATTT-AAGGGTTTAAGTAA
1 AA-TTTTCAAAAATTTGAAGAGTTTAAGTAA
*
3645035 CATTTTCAAAAATTTGAAGAGTTTAAG
1 AATTTTCAAAAATTTGAAGAGTTTAAG
3645062 CCCCAAGCAT
Statistics
Matches: 66, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
29 25 0.38
30 31 0.47
31 3 0.05
32 7 0.11
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (30 bp):
AATTTTCAAAAATTTGAAGAGTTTAAGTAA
Found at i:3645423 original size:2 final size:2
Alignment explanation
Indices: 3645411--3645452 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
3645401 GTAGACTTTG
* * *
3645411 TA TA AA TA TA TA TA TA TA TA TA TG TA TA AA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3645453 CTTATAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:3659770 original size:35 final size:33
Alignment explanation
Indices: 3659706--3659783 Score: 81
Period size: 34 Copynumber: 2.4 Consensus size: 33
3659696 ACAATAATAA
* *
3659706 ATATTTTATAAAATAATTTGATATTAATATTTAT
1 ATATTTTATAAAATAATTTAATATAAATA-TTAT
*
3659740 ATATTTTATAAATTAAATTTAA-ATAAAATATTAT
1 ATATTTTATAAAAT-AATTTAATAT-AAATATTAT
3659774 -TATTTT-TAAA
1 ATATTTTATAAA
3659784 CAATAGTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
32 4 0.10
33 6 0.15
34 19 0.49
35 10 0.26
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (33 bp):
ATATTTTATAAAATAATTTAATATAAATATTAT
Found at i:3667227 original size:2 final size:2
Alignment explanation
Indices: 3667220--3667244 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3667210 GAAAACAAGA
3667220 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
3667245 AAAGATAGCC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3672056 original size:92 final size:93
Alignment explanation
Indices: 3671890--3672157 Score: 251
Period size: 92 Copynumber: 2.8 Consensus size: 93
3671880 ATTTGTGTGC
* *
3671890 TAGTGTAAGACATGTCTGGGACATGTATCAGCCACATTATGAGAGCCAGTATAAGACCATGTCTG
1 TAGTGTAAGACATGTCTGAGACATGCATCAGCCACA-TATGAGAGCCAGTATAAGACCATGTCTG
*
3671955 GGACATGGCATTGGCATTGAGACGAGAGT
65 GGACATGGCATCGGCATTGAGACGAGAGT
* * * * *
3671984 TAGTGTAAGACATGTCTGAGACATGCATCGGCTACA-A-GATGTGTCAGTGTAAGACCATGTCTG
1 TAGTGTAAGACATGTCTGAGACATGCATCAGCCACATATGA-GAGCCAGTATAAGACCATGTCTG
*
3672047 GGACATGGCATCGGCACGTAT-AGA-G-GTGT
65 GGACATGGCATCGGCA--T-TGAGACGAGAGT
* * * * * *
3672076 CAGTGTAAGACCATGTCT-AGGACATGGCATCGGCACGGAGATGTGAGAGCCAGTGTAAGACTAT
1 TAGTGTAAGA-CATGTCTGA-GACAT-GCATCAGC-C--ACATATGAGAGCCAGTATAAGACCAT
*
3672140 GTCTGAGACATGGCATCG
60 GTCTGGGACATGGCATCG
3672158 ACCTCGATTT
Statistics
Matches: 145, Mismatches: 17, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
91 2 0.01
92 49 0.34
93 13 0.09
94 44 0.30
95 1 0.01
97 2 0.01
98 32 0.22
99 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (93 bp):
TAGTGTAAGACATGTCTGAGACATGCATCAGCCACATATGAGAGCCAGTATAAGACCATGTCTGG
GACATGGCATCGGCATTGAGACGAGAGT
Found at i:3672085 original size:48 final size:48
Alignment explanation
Indices: 3671936--3672206 Score: 211
Period size: 48 Copynumber: 5.7 Consensus size: 48
3671926 TTATGAGAGC
* * *
3671936 CAGTATAAGACCATGTCTGGGACATGGCATTGGCA--T-TGAGACGAGAGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTAT-AGA-G-GTGT
* * *
3671984 TAGTGTAAGA-CATGTCTGAGACAT-GCATCGGCTAC--A-AGATGTGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACGTATAGAGGTGT
3672028 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGT
* * * * * *
3672076 CAGTGTAAGACCATGTCTAGGACATGGCATCGGCACGGAGATGTGAGAGC
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATA-GAG-GTGT
* * * * * *
3672126 CAGTGTAAGACTATGTCTGAGACATGGCATCGACCTCGATTTTGA--TAGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCG-GCACG-TATAGAGGT-GT
* *
3672175 CAGTGCAAGACCATGTCTGGGACATGACATCG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCG
3672207 ACTTGATGGA
Statistics
Matches: 179, Mismatches: 31, Indels: 25
0.76 0.13 0.11
Matches are distributed among these distances:
44 12 0.07
45 15 0.08
46 18 0.10
47 15 0.08
48 53 0.30
49 31 0.17
50 31 0.17
51 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (48 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGT
Found at i:3672251 original size:96 final size:99
Alignment explanation
Indices: 3672074--3672255 Score: 255
Period size: 96 Copynumber: 1.9 Consensus size: 99
3672064 GTATAGAGGT
* * * *
3672074 GTCAGTGTAAGACCATGTCTAGGACATGGCATCGGCACGGAGATGTGAGAGCCAGTGTAAGACTA
1 GTCAGTGCAAGACCATGTCTAGGACATGACATCGGCACGGAGATGTGAGAGCCAGCGTAAGACCA
*
3672139 TGTCTGAGACATGGCATCGACCTCGATTTTGATA
66 TGTCTAAGACATGGCATCGACCTCGATTTTGATA
* **
3672173 GTCAGTGCAAGACCATGTCTGGGACATGACATC-G-AC-TTGATG-GATGAGCCAGCGTAAGACC
1 GTCAGTGCAAGACCATGTCTAGGACATGACATCGGCACGGAGATGTGA-GAGCCAGCGTAAGACC
3672234 ATGTCTAAGACATGGCATCGAC
65 ATGTCTAAGACATGGCATCGAC
3672256 ATTACACCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
95 2 0.03
96 39 0.53
97 2 0.03
98 1 0.01
99 30 0.41
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (99 bp):
GTCAGTGCAAGACCATGTCTAGGACATGACATCGGCACGGAGATGTGAGAGCCAGCGTAAGACCA
TGTCTAAGACATGGCATCGACCTCGATTTTGATA
Found at i:3679485 original size:2 final size:2
Alignment explanation
Indices: 3679478--3679510 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3679468 TTTTGCTTAC
3679478 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3679511 AATTTTTGTC
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3684774 original size:6 final size:6
Alignment explanation
Indices: 3684763--3684792 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3684753 CCAGAACAAC
3684763 AAGAAA AAGAAA AAGAAA AAGAAA AA-AAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA A
3684793 CACTGTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:3703494 original size:25 final size:25
Alignment explanation
Indices: 3703460--3703507 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
3703450 CGGGGACTTA
* *
3703460 AATTGTTCACACGAGCTGTGAATGT
1 AATTGCTCACACGAGCTATGAATGT
3703485 AATTGCTCACACGAGCTATGAAT
1 AATTGCTCACACGAGCTATGAAT
3703508 TGGGACTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (25 bp):
AATTGCTCACACGAGCTATGAATGT
Found at i:3709291 original size:46 final size:46
Alignment explanation
Indices: 3709224--3709395 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
3709214 AACCCGCCCC
* *
3709224 TAAGTGAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
3709270 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATCCA
* * * *
3709318 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
3709363 TAGGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
3709396 ATGCTCAACC
Statistics
Matches: 106, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 1 0.01
46 59 0.56
47 28 0.26
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
Found at i:3709337 original size:93 final size:93
Alignment explanation
Indices: 3709229--3709399 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
3709219 GCCCCTAAGT
* *
3709229 GAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
3709294 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
3709322 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
3709387 CGAGTTCGGATGC
66 CGAGTTCGGATGC
3709400 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:3709856 original size:30 final size:30
Alignment explanation
Indices: 3709822--3709881 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
3709812 ATTTAATACG
3709822 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
3709852 AACTTTTGCAGAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
3709882 GGCTCGAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:3713254 original size:29 final size:30
Alignment explanation
Indices: 3713212--3713272 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
3713202 CTTAGCAAGT
* *
3713212 AAATGCCTCTAAAATAATAA-AAATTTAAC
1 AAATACCTCTAAAATAATAACAAAATTAAC
*
3713241 AAATACCTTTAAAATAATAACAAAATTAAC
1 AAATACCTCTAAAATAATAACAAAATTAAC
3713271 AA
1 AA
3713273 GAAAATAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.59, C:0.13, G:0.02, T:0.26
Consensus pattern (30 bp):
AAATACCTCTAAAATAATAACAAAATTAAC
Found at i:3713327 original size:22 final size:22
Alignment explanation
Indices: 3713302--3713344 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3713292 TATCCAAACA
3713302 ATAACAATAAAATAGTAGTAAC
1 ATAACAATAAAATAGTAGTAAC
* *
3713324 ATAATAATAAAATGGTAGTAA
1 ATAACAATAAAATAGTAGTAA
3713345 AATAGGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.05, G:0.12, T:0.26
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGTAAC
Found at i:3723568 original size:20 final size:20
Alignment explanation
Indices: 3723522--3723568 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
3723512 TATTTAAATT
*
3723522 AAATTTAATGTAAATTATCA
1 AAATTTAATGAAAATTATCA
* *
3723542 TATTTTAATGAAATATTA-CA
1 AAATTTAATGAAA-ATTATCA
3723562 AAATTTA
1 AAATTTA
3723569 TGACAAAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (20 bp):
AAATTTAATGAAAATTATCA
Found at i:3738072 original size:12 final size:12
Alignment explanation
Indices: 3738057--3738083 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3738047 TTATTTGTTT
3738057 TTTGTTTTAATA
1 TTTGTTTTAATA
3738069 TTTGTTTTAATA
1 TTTGTTTTAATA
3738081 TTT
1 TTT
3738084 TTAGATGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTGTTTTAATA
Found at i:3738101 original size:24 final size:24
Alignment explanation
Indices: 3738067--3738127 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
3738057 TTTGTTTTAA
* *
3738067 TATTTGTTTTAATAT-TTTTAGAT
1 TATTTGATTTAATATATTTTAAAT
*
3738090 GTATTTGATTTATTATATTTTAAAT
1 -TATTTGATTTAATATATTTTAAAT
*
3738115 T-TTTTATTTAATA
1 TATTTGATTTAATA
3738128 AAAAAAGCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 10 0.32
24 14 0.45
25 7 0.23
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (24 bp):
TATTTGATTTAATATATTTTAAAT
Found at i:3749639 original size:3 final size:3
Alignment explanation
Indices: 3749633--3749657 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3749623 CCAAAATTGT
3749633 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
3749658 AAACTTGATT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3750629 original size:20 final size:22
Alignment explanation
Indices: 3750604--3750646 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3750594 ATTGTCCAAA
*
3750604 TTAATTT-TTTA-TGTATAATT
1 TTAATTTGTTTATTGAATAATT
3750624 TTAATTTGTTTATTGAATAATT
1 TTAATTTGTTTATTGAATAATT
3750646 T
1 T
3750647 CATTATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 4 0.20
22 9 0.45
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (22 bp):
TTAATTTGTTTATTGAATAATT
Found at i:3751598 original size:12 final size:12
Alignment explanation
Indices: 3751562--3751603 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
3751552 AGAGAGAGAG
*
3751562 AGAAAGAGAAAT
1 AGAAAGAGCAAT
* *
3751574 ATAAATA-CAAT
1 AGAAAGAGCAAT
3751585 AGAAAGAGCAAT
1 AGAAAGAGCAAT
3751597 AGAAAGA
1 AGAAAGA
3751604 AAGAGGAAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.64, C:0.05, G:0.19, T:0.12
Consensus pattern (12 bp):
AGAAAGAGCAAT
Found at i:3761001 original size:13 final size:12
Alignment explanation
Indices: 3760978--3761002 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3760968 GTTTAAATTG
3760978 TCACTAAAAAAA
1 TCACTAAAAAAA
3760990 TCACTAAAAAAA
1 TCACTAAAAAAA
3761002 T
1 T
3761003 GGGTTTTTTC
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:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (12 bp):
TCACTAAAAAAA
Found at i:3762394 original size:19 final size:19
Alignment explanation
Indices: 3762359--3762416 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 19
3762349 TATTTTAAAA
*
3762359 TATAAAT-TTTGGAATTTT
1 TATAAATATTTTGAATTTT
3762377 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
3762396 TGA-AAATTATTTTGAATTTT
1 T-ATAAA-TATTTTGAATTTT
3762416 T
1 T
3762417 TTATAATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
18 7 0.19
19 14 0.39
20 15 0.42
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:3762427 original size:19 final size:19
Alignment explanation
Indices: 3762364--3762428 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
3762354 TAAAATATAA
*
3762364 ATTTTGGAATTTTTATAAAT
1 ATTTT-GAATTTTTTTAAAT
**
3762384 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTTTAAA-T
3762404 ATTTTGAATTTTTTTATAAT
1 ATTTTGAATTTTTTTA-AAT
3762424 -TTTTG
1 ATTTTG
3762429 TTGAGAGGCT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
19 16 0.41
20 21 0.54
21 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (19 bp):
ATTTTGAATTTTTTTAAAT
Found at i:3763280 original size:18 final size:18
Alignment explanation
Indices: 3763254--3763289 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3763244 AAAATTGTAA
3763254 TAAAAATATTTATAAAAT
1 TAAAAATATTTATAAAAT
*
3763272 TAAATATATTTATAAAAT
1 TAAAAATATTTATAAAAT
3763290 CTTATAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAAATATTTATAAAAT
Found at i:3763486 original size:44 final size:43
Alignment explanation
Indices: 3763431--3763523 Score: 159
Period size: 44 Copynumber: 2.1 Consensus size: 43
3763421 GGAAAACCTC
*
3763431 AAAAATTAAATCAAATTATTACCGATGATTTAAATGATTTAAA
1 AAAAATTAAATCAAATTATTACCGATAATTTAAATGATTTAAA
*
3763474 AAAAAGTTAAATCAAATTATTACCGATAATTTAAATGATTTTAA
1 AAAAA-TTAAATCAAATTATTACCGATAATTTAAATGATTTAAA
3763518 AAAAAT
1 AAAAAT
3763524 GATTGTCTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 6 0.13
44 41 0.87
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (43 bp):
AAAAATTAAATCAAATTATTACCGATAATTTAAATGATTTAAA
Found at i:3765105 original size:26 final size:26
Alignment explanation
Indices: 3765076--3765129 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
3765066 TTGATTGCAG
* * *
3765076 TAGTTGATTTGATTAATTGATTCTAT
1 TAGTTGATTTGATGAACTAATTCTAT
*
3765102 TAGTTTATTTGATGAACTAATTCTAT
1 TAGTTGATTTGATGAACTAATTCTAT
3765128 TA
1 TA
3765130 ATTGTTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.52
Consensus pattern (26 bp):
TAGTTGATTTGATGAACTAATTCTAT
Found at i:3774468 original size:22 final size:22
Alignment explanation
Indices: 3774409--3774470 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
3774399 GGGTAAGATA
* *
3774409 TGATATGATATGATATGAAATG
1 TGATATGATAAGATATGAAATC
* *
3774431 TGCTACAAGAT-A-ATATGAAATC
1 TG--ATATGATAAGATATGAAATC
3774453 TGATATGATAAGATATGA
1 TGATATGATAAGATATGA
3774471 TAAAAGATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
20 5 0.17
21 1 0.03
22 19 0.63
24 5 0.17
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (22 bp):
TGATATGATAAGATATGAAATC
Found at i:3774706 original size:9 final size:9
Alignment explanation
Indices: 3774692--3774719 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3774682 TTTGTTTATA
3774692 TGGACATTT
1 TGGACATTT
3774701 TGGACATTT
1 TGGACATTT
3774710 TGGACATTT
1 TGGACATTT
3774719 T
1 T
3774720 AAATTGTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.46
Consensus pattern (9 bp):
TGGACATTT
Found at i:3781576 original size:31 final size:31
Alignment explanation
Indices: 3781540--3781602 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
3781530 TAAATTTTGG
* **
3781540 ATTAATT-GAAATAAATTATTTTATTTTTTTA
1 ATTAATTCG-AATAAATAATTAAATTTTTTTA
3781571 ATTAATTCGAATAAATAATTAAATTTTTTTA
1 ATTAATTCGAATAAATAATTAAATTTTTTTA
3781602 A
1 A
3781603 GGTGAGTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (31 bp):
ATTAATTCGAATAAATAATTAAATTTTTTTA
Found at i:3784430 original size:179 final size:177
Alignment explanation
Indices: 3784120--3784448 Score: 455
Period size: 179 Copynumber: 1.8 Consensus size: 177
3784110 ACATGACCAT
* * * * *
3784120 CAGGAACAGTGAGCGGCAGCAACGGAAAGTTCACATCAAAGATAAATGTAATCCATATACGGTAA
1 CAGGAACAGTGAGCGGCAGCAACGGAAAGTTAAAATCAAAGAAAAATGAAATCCATATACGCTAA
** *
3784185 GTATAATCATAATTAAAAATGAAATCCAAATATGCTTTTTCAAATGACCAAACCTTAATAAAAGG
66 GTATAATCATAATTAAAAATGAAATCCAAATACACTTTTTCAAATGACCAAACCTCAATAAAAGG
*
3784250 GAAAAAGATTTAATC-TAAATCCAATTAATCTTAAATTGGAAGTGCAA
131 GAAAAA-AGTTAATCTTAAATCCAATTAATCTTAAATTGGAAGTGCAA
*
3784297 CAGGAACAGTGAGAGCGGCAGCAACAGG-AAGTTAAAATCAAAGAAAAATGAAATCCATATATGC
1 CAGGAACAGT--GAGCGGCAGCAAC-GGAAAGTTAAAATCAAAGAAAAATGAAATCCATATACGC
* * ** ** *
3784361 TGAGTATAATCATAATTAAAACTGAAATCCGTATACACTTTTTTGAATGACCAAACCTCACTAAA
63 TAAGTATAATCATAATTAAAAATGAAATCCAAATACACTTTTTCAAATGACCAAACCTCAATAAA
3784426 AGGGAAAAAAGTTAATCTTAAAT
128 AGGGAAAAAAGTTAATCTTAAAT
3784449 TAAGATGTAG
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
177 10 0.08
178 7 0.05
179 112 0.85
180 2 0.02
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (177 bp):
CAGGAACAGTGAGCGGCAGCAACGGAAAGTTAAAATCAAAGAAAAATGAAATCCATATACGCTAA
GTATAATCATAATTAAAAATGAAATCCAAATACACTTTTTCAAATGACCAAACCTCAATAAAAGG
GAAAAAAGTTAATCTTAAATCCAATTAATCTTAAATTGGAAGTGCAA
Found at i:3786045 original size:144 final size:143
Alignment explanation
Indices: 3785779--3786049 Score: 326
Period size: 144 Copynumber: 1.9 Consensus size: 143
3785769 CTCGGATGTA
* ** * * *
3785779 GTTCTTCATCTTAGTTTCCTTGAGTAAATCTTTATCTTTGATTAAACCACGCACCAAATTAGTAT
1 GTTCTTCATCTCAACTTCCTTGAGTAAATCTTTATCTTTAATTAAACCACACACCAAATTAGCAT
* * * *** * * * **
3785844 TACAGTCTCCTTTTTGGCACTTGTGATGGCGGATAACAATCATTCACACGGTATTAGAAGGTATT
66 CAAAGCCTCCTTTCCAGCACCTATGATGGCAGATAACAATCATTCACACGACATTAGAAGGTATT
3785909 ACTCTGAATTGTT
131 ACTCTGAATTGTT
* * *
3785922 GTTCTTCATCTCAACTTCCTTGAGTAATTTCTTTATCTTTAATTAAACCGCACACCAAATTGGCA
1 GTTCTTCATCTCAACTTCCTTGAGTAA-ATCTTTATCTTTAATTAAACCACACACCAAATTAGCA
* * *
3785987 TCAAAGCCTCCTTTCCAGCACCTATGATGGCAGATAACAATCCTTCACATGACCTTAGAAGGT
65 TCAAAGCCTCCTTTCCAGCACCTATGATGGCAGATAACAATCATTCACACGACATTAGAAGGT
3786050 TGGAAGAGTT
Statistics
Matches: 104, Mismatches: 23, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
143 24 0.23
144 80 0.77
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (143 bp):
GTTCTTCATCTCAACTTCCTTGAGTAAATCTTTATCTTTAATTAAACCACACACCAAATTAGCAT
CAAAGCCTCCTTTCCAGCACCTATGATGGCAGATAACAATCATTCACACGACATTAGAAGGTATT
ACTCTGAATTGTT
Found at i:3797211 original size:26 final size:26
Alignment explanation
Indices: 3797175--3797230 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
3797165 TTATAAAACA
3797175 GGCCGGGCCTCGGGTAAGAGTTTTTT
1 GGCCGGGCCTCGGGTAAGAGTTTTTT
3797201 GGCCGGGCCTCGGGTAAGAGTTTTTT
1 GGCCGGGCCTCGGGTAAGAGTTTTTT
3797227 GGCC
1 GGCC
3797231 CGAACTCGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.11, C:0.21, G:0.39, T:0.29
Consensus pattern (26 bp):
GGCCGGGCCTCGGGTAAGAGTTTTTT
Found at i:3797238 original size:26 final size:26
Alignment explanation
Indices: 3797183--3797239 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
3797173 CAGGCCGGGC
* **
3797183 CTCGGGTAAGAGTTTTTTGGCCGGGC
1 CTCGGGTAAGAGTTTTTTGGCCCGAA
3797209 CTCGGGTAAGAGTTTTTTGGCCCGAA
1 CTCGGGTAAGAGTTTTTTGGCCCGAA
3797235 CTCGG
1 CTCGG
3797240 CCCGAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.14, C:0.21, G:0.35, T:0.30
Consensus pattern (26 bp):
CTCGGGTAAGAGTTTTTTGGCCCGAA
Found at i:3797371 original size:21 final size:22
Alignment explanation
Indices: 3797345--3797403 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
3797335 GTTTTAAGAA
*
3797345 TTGTTTTAGTA-TCATTTTTAT
1 TTGTTTTAATATTCATTTTTAT
*
3797366 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTCATTTTTAT
* *
3797388 GT-TTTTAA-ATTTATTT
1 TTGTTTTAATATTCATTT
3797404 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.24
21 16 0.47
22 10 0.29
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTCATTTTTAT
Found at i:3797420 original size:26 final size:25
Alignment explanation
Indices: 3797375--3797434 Score: 86
Period size: 26 Copynumber: 2.4 Consensus size: 25
3797365 TTTGTTTTAA
*
3797375 TATTTATTT-TTATGTTTTTAAATT
1 TATTTATTTATTATATTTTTAAATT
3797399 TATTTGATTTATTATATTTTTAAATT
1 TATTT-ATTTATTATATTTTTAAATT
*
3797425 TTTTTATTTA
1 TATTTATTTA
3797435 ATGAAATAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 5 0.16
25 9 0.28
26 18 0.56
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (25 bp):
TATTTATTTATTATATTTTTAAATT
Found at i:3799458 original size:17 final size:18
Alignment explanation
Indices: 3799417--3799464 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
3799407 GCTTAATAGA
*
3799417 AGAGTCCGCC-AATTCTC
1 AGAGTCCGCCAAATCCTC
*
3799434 AGAATCCGCCAAATCCT-
1 AGAGTCCGCCAAATCCTC
*
3799451 AGAGTCCGTCAAAT
1 AGAGTCCGCCAAAT
3799465 GACAAATCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 21 0.81
18 5 0.19
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (18 bp):
AGAGTCCGCCAAATCCTC
Found at i:3799517 original size:18 final size:18
Alignment explanation
Indices: 3799494--3799528 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3799484 CCACCTAGTC
3799494 AAAAACGAATATTTCACA
1 AAAAACGAATATTTCACA
3799512 AAAAACGAATATTTCAC
1 AAAAACGAATATTTCAC
3799529 TAACTTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.17, G:0.06, T:0.23
Consensus pattern (18 bp):
AAAAACGAATATTTCACA
Found at i:3809511 original size:8 final size:8
Alignment explanation
Indices: 3809498--3809523 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3809488 TCATAATTTT
3809498 ATTTAATA
1 ATTTAATA
3809506 ATTTAATA
1 ATTTAATA
3809514 ATTTAATA
1 ATTTAATA
3809522 AT
1 AT
3809524 ATTATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATTTAATA
Found at i:3812958 original size:19 final size:17
Alignment explanation
Indices: 3812934--3812968 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
3812924 TATTATATGA
3812934 TGAATTGATGAATTGATGT
1 TGAATTGA-GAA-TGATGT
3812953 TGAATTGAGAATGATG
1 TGAATTGAGAATGATG
3812969 GAATGTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (17 bp):
TGAATTGAGAATGATGT
Found at i:3814312 original size:29 final size:29
Alignment explanation
Indices: 3814246--3814302 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
3814236 GATTCAAAGA
*
3814246 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
3814275 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
3814303 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:3816751 original size:30 final size:28
Alignment explanation
Indices: 3816698--3816753 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
3816688 TTCTTCCACG
* *
3816698 CTTTCTTTTTGCTCACTCTCTTTTTCAA
1 CTTTCTTTTTGCACACACTCTTTTTCAA
3816726 CTTTACTTTCTTGCACACACTCTTTTTC
1 CTTT-CTTT-TTGCACACACTCTTTTTC
3816754 TTTTTCGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.12, C:0.30, G:0.04, T:0.54
Consensus pattern (28 bp):
CTTTCTTTTTGCACACACTCTTTTTCAA
Found at i:3817808 original size:13 final size:13
Alignment explanation
Indices: 3817783--3817823 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
3817773 TATGTTCAAA
3817783 TTTTCAG-ATTTT
1 TTTTCAGAATTTT
3817795 TTTTCAGAATTTT
1 TTTTCAGAATTTT
3817808 TTATT--GAATTTT
1 TT-TTCAGAATTTT
3817820 TTTT
1 TTTT
3817824 TCGTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.07
12 16 0.59
13 7 0.26
14 2 0.07
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (13 bp):
TTTTCAGAATTTT
Found at i:3817873 original size:15 final size:15
Alignment explanation
Indices: 3817849--3817879 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3817839 TTTTGGTATC
3817849 AGAGTATCCCCTTTA
1 AGAGTATCCCCTTTA
*
3817864 AGAGTGTCCCCTTTA
1 AGAGTATCCCCTTTA
3817879 A
1 A
3817880 TCCTCTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (15 bp):
AGAGTATCCCCTTTA
Found at i:3824640 original size:2 final size:2
Alignment explanation
Indices: 3824633--3824672 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3824623 TTGATTCTCA
3824633 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
3824673 GTGTGGTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3826284 original size:19 final size:20
Alignment explanation
Indices: 3826245--3826289 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
3826235 ATTAATGTAG
**
3826245 TTTAAAAATATCTAATTAAA
1 TTTAAAAATATCTAAAAAAA
3826265 TTTAAAAATAT-TAAAAAAA
1 TTTAAAAATATCTAAAAAAA
*
3826284 TGTAAA
1 TTTAAA
3826290 TTTATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
TTTAAAAATATCTAAAAAAA
Found at i:3828410 original size:3 final size:3
Alignment explanation
Indices: 3828402--3828443 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
3828392 CCGTCATGGA
* * *
3828402 GAT GAT GAT GGT GAT AAT GAT GAT GTT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
3828444 TGGTTCAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (3 bp):
GAT
Found at i:3833283 original size:20 final size:20
Alignment explanation
Indices: 3833258--3833304 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3833248 ACCCTGATTT
3833258 TTTTTTACTTTTTTTTAAAC
1 TTTTTTACTTTTTTTTAAAC
* **
3833278 TTTTTTCCTTTTTTTTTTAC
1 TTTTTTACTTTTTTTTAAAC
3833298 TTTTTTA
1 TTTTTTA
3833305 AGTTTTGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTTACTTTTTTTTAAAC
Found at i:3833425 original size:12 final size:12
Alignment explanation
Indices: 3833398--3833504 Score: 75
Period size: 13 Copynumber: 9.0 Consensus size: 12
3833388 ATTTTTTAAA
*
3833398 ATTTTTAATATAT
1 ATTTTTAAAAT-T
*
3833411 ATTTTTGAAATT
1 ATTTTTAAAATT
3833423 ATTTTTTAAAA--
1 A-TTTTTAAAATT
3833434 A-TTTTAAATATT
1 ATTTTTAAA-ATT
*
3833446 ATTTTTGAAATT
1 ATTTTTAAAATT
*
3833458 ATTTTTTAAA--
1 ATTTTTAAAATT
3833468 A-TTTTAAATATT
1 ATTTTTAAA-ATT
3833480 AATTTTT-AAATT
1 -ATTTTTAAAATT
3833492 ATTTTTTAAAATT
1 A-TTTTTAAAATT
3833505 TTAAATATAT
Statistics
Matches: 76, Mismatches: 6, Indels: 24
0.72 0.06 0.23
Matches are distributed among these distances:
9 13 0.17
10 3 0.04
11 2 0.03
12 23 0.30
13 31 0.41
14 4 0.05
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
ATTTTTAAAATT
Found at i:3833466 original size:70 final size:67
Alignment explanation
Indices: 3833387--3833518 Score: 212
Period size: 70 Copynumber: 1.9 Consensus size: 67
3833377 TTATAATATA
*
3833387 TATTTTTTAAAATTTTTAATA-TATATTTTTGAAATTATTTTTTAAAAATTTTAAATATTATTTT
1 TATTTTTTAAAATTTTAAATATTA-ATTTTT-AAATTATTTTTT-AAAATTTTAAATA-TATTTT
3833451 TGAAAT
62 TGAAAT
3833457 TATTTTTTAAAATTTTAAATATTAATTTTTAAATTATTTTTTAAAATTTTAAATATATTTTT
1 TATTTTTTAAAATTTTAAATATTAATTTTTAAATTATTTTTTAAAATTTTAAATATATTTTT
3833519 TAAAATTTAT
Statistics
Matches: 60, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
67 7 0.12
68 13 0.22
69 12 0.20
70 26 0.43
71 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (67 bp):
TATTTTTTAAAATTTTAAATATTAATTTTTAAATTATTTTTTAAAATTTTAAATATATTTTTGAA
AT
Found at i:3833504 original size:21 final size:21
Alignment explanation
Indices: 3833411--3833526 Score: 85
Period size: 22 Copynumber: 5.2 Consensus size: 21
3833401 TTTAATATAT
3833411 ATTTTTGAAATTATTTTTTAAAA
1 ATTTTT-AAATTATTTTTT-AAA
* *
3833434 ATTTTAAATATTATTTTTGAAA
1 ATTTTTAA-ATTATTTTTTAAA
* *
3833456 TTATTTTTTAAA--ATTTTAAATATTA
1 --A-TTTTTAAATTATTTT--TTA-AA
3833481 ATTTTTAAATTATTTTTTAAA
1 ATTTTTAAATTATTTTTTAAA
3833502 A-TTTTAAATATATTTTTTAAA
1 ATTTTTAAAT-TATTTTTTAAA
3833523 ATTT
1 ATTT
3833527 ATATACTTAA
Statistics
Matches: 74, Mismatches: 8, Indels: 23
0.70 0.08 0.22
Matches are distributed among these distances:
20 8 0.11
21 14 0.19
22 22 0.30
23 15 0.20
24 8 0.11
25 7 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTTTTAAATTATTTTTTAAA
Found at i:3833525 original size:34 final size:35
Alignment explanation
Indices: 3833387--3833525 Score: 214
Period size: 34 Copynumber: 4.0 Consensus size: 35
3833377 TTATAATATA
*
3833387 TATTTTTTAAAATTTTTAATATATATTTTTGAAAT
1 TATTTTTTAAAATTTTAAATATATATTTTTGAAAT
3833422 TATTTTTTAAAAATTTTAAATAT-TATTTTTGAAAT
1 TATTTTTT-AAAATTTTAAATATATATTTTTGAAAT
3833457 TATTTTTTAAAATTTTAAATAT-TAATTTTT-AAAT
1 TATTTTTTAAAATTTTAAATATAT-ATTTTTGAAAT
*
3833491 TATTTTTTAAAATTTTAAATATAT-TTTTTAAAAT
1 TATTTTTTAAAATTTTAAATATATATTTTTGAAAT
3833525 T
1 T
3833526 TATATACTTA
Statistics
Matches: 99, Mismatches: 1, Indels: 9
0.91 0.01 0.08
Matches are distributed among these distances:
33 5 0.05
34 46 0.46
35 35 0.35
36 13 0.13
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (35 bp):
TATTTTTTAAAATTTTAAATATATATTTTTGAAAT
Found at i:3833527 original size:20 final size:20
Alignment explanation
Indices: 3833413--3833526 Score: 90
Period size: 20 Copynumber: 6.2 Consensus size: 20
3833403 TAATATATAT
3833413 TTTTGAAATTATTTTTTAAAAA
1 TTTT-AAATTATTTTTT-AAAA
*
3833435 TTTTAAA-TA-TTATT----
1 TTTTAAATTATTTTTTAAAA
*
3833449 TTTGAAATTATTTTTTAAAA
1 TTTTAAATTATTTTTTAAAA
*
3833469 TTTTAAA-TA----TT-AAT
1 TTTTAAATTATTTTTTAAAA
3833483 TTTTAAATTATTTTTTAAAA
1 TTTTAAATTATTTTTTAAAA
3833503 TTTTAAATATATTTTTTAAAA
1 TTTTAAAT-TATTTTTTAAAA
3833524 TTT
1 TTT
3833527 ATATACTTAA
Statistics
Matches: 73, Mismatches: 6, Indels: 27
0.69 0.06 0.25
Matches are distributed among these distances:
14 15 0.21
15 6 0.08
16 4 0.05
19 8 0.11
20 18 0.25
21 18 0.25
22 4 0.05
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTAAATTATTTTTTAAAA
Found at i:3833718 original size:12 final size:11
Alignment explanation
Indices: 3833650--3833719 Score: 55
Period size: 9 Copynumber: 6.7 Consensus size: 11
3833640 AATTTTAAAA
3833650 TTTTAATATA-
1 TTTTAATATAT
3833660 -TTTAATATAT
1 TTTTAATATAT
*
3833670 TTTTAAAAATAT
1 TTTT-AATATAT
3833682 ATTTTAA-A-A-
1 -TTTTAATATAT
3833691 TTTTAATATA-
1 TTTTAATATAT
3833701 -TTTAATATATT
1 TTTTAATATA-T
3833712 TTTTAATA
1 TTTTAATA
3833720 GGAAAAGAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
8 6 0.12
9 19 0.38
10 2 0.04
11 4 0.08
12 15 0.30
13 4 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAATATAT
Found at i:3833793 original size:16 final size:17
Alignment explanation
Indices: 3833739--3833808 Score: 70
Period size: 17 Copynumber: 4.0 Consensus size: 17
3833729 AAAAAATAAT
*
3833739 TTTTTAATATATTTAAAA
1 TTTTAAATATA-TTAAAA
*
3833757 TTTTAAA-AAACTTAAAAA
1 TTTTAAATATA-TT-AAAA
*
3833775 ATTTAAATATATTAAAA
1 TTTTAAATATATTAAAA
*
3833792 TTTTAAATATGTTAAAA
1 TTTTAAATATATTAAAA
3833809 GAAAATATTG
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
17 23 0.53
18 18 0.42
19 2 0.05
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (17 bp):
TTTTAAATATATTAAAA
Found at i:3834313 original size:13 final size:13
Alignment explanation
Indices: 3834295--3834320 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3834285 AAATTTAAAA
3834295 ATATTTAAAATAT
1 ATATTTAAAATAT
3834308 ATATTTAAAATAT
1 ATATTTAAAATAT
3834321 TATAAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATTTAAAATAT
Found at i:3834396 original size:24 final size:24
Alignment explanation
Indices: 3834355--3834410 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
3834345 AGGTCATATC
*
3834355 TTTAAAAATAATATATTTTAAATAA
1 TTTAAAAATAATATATTTCAAAT-A
*
3834380 TTTAAAAATCATA-ATTTCAAATA
1 TTTAAAAATAATATATTTCAAATA
3834403 TTATAAAA
1 TT-TAAAA
3834411 CAAATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 3 0.11
24 13 0.46
25 12 0.43
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (24 bp):
TTTAAAAATAATATATTTCAAATA
Found at i:3834530 original size:21 final size:21
Alignment explanation
Indices: 3834503--3834568 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
3834493 ACAATATTTA
*
3834503 AATATTTTATATTATTAAAAAT
1 AATATTTAATATT-TTAAAAAT
*
3834525 -ATATTTAATATTTAAAAAAT
1 AATATTTAATATTTTAAAAAT
*
3834545 AATATTTAAAATTTTAAAAA-
1 AATATTTAATATTTTAAAAAT
3834565 AATA
1 AATA
3834569 ATTTCAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.28
21 28 0.72
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATATTTAATATTTTAAAAAT
Found at i:3834607 original size:21 final size:20
Alignment explanation
Indices: 3834519--3834608 Score: 80
Period size: 21 Copynumber: 4.5 Consensus size: 20
3834509 TTATATTATT
*
3834519 AAAAATATATTTAATATTTA
1 AAAAATATATTTAAAATTTA
3834539 AAAAATAATATTTAAAATTTTA
1 AAAAAT-ATATTTAAAA-TTTA
*
3834561 AAAAA-ATAATTTCAAA--T-
1 AAAAATAT-ATTTAAAATTTA
* *
3834578 ATATATATATTTAAAATTTTA
1 AAAAATATATTTAAAA-TTTA
3834599 AAAAATATAT
1 AAAAATATAT
3834609 ATTATAAAAC
Statistics
Matches: 55, Mismatches: 7, Indels: 15
0.71 0.09 0.19
Matches are distributed among these distances:
17 10 0.18
18 3 0.05
20 9 0.16
21 24 0.44
22 9 0.16
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAATATATTTAAAATTTA
Found at i:3834688 original size:9 final size:9
Alignment explanation
Indices: 3834674--3834719 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
3834664 GGATAAAGAC
3834674 AAAAAGTAA
1 AAAAAGTAA
3834683 AAAAAGTAA
1 AAAAAGTAA
**
3834692 AAAACTTAA
1 AAAAAGTAA
3834701 AAAAAGTAA
1 AAAAAGTAA
3834710 AAAAAG-AA
1 AAAAAGTAA
3834718 AA
1 AA
3834720 GAAAAAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
8 4 0.12
9 29 0.88
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.11
Consensus pattern (9 bp):
AAAAAGTAA
Found at i:3834725 original size:14 final size:14
Alignment explanation
Indices: 3834702--3834731 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3834692 AAAACTTAAA
*
3834702 AAAAGTAAAAAAAG
1 AAAAGAAAAAAAAG
3834716 AAAAGAAAAAAAAG
1 AAAAGAAAAAAAAG
3834730 AA
1 AA
3834732 GGATAAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAAAAAG
Found at i:3834728 original size:34 final size:33
Alignment explanation
Indices: 3834699--3834763 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
3834689 TAAAAAACTT
3834699 AAAAAAAG-TAAAAAAAGAAAAGAAAAAAAAGAAG
1 AAAAAAAGTTAAAAAAA-AAAAGAAAAAAAA-AAG
* *
3834733 GATAAAAGTTAAAAAAAAAAAGAAAAAAAAA
1 AAAAAAAGTTAAAAAAAAAAAGAAAAAAAAA
3834764 GTAACAAGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 1 0.04
34 19 0.68
35 8 0.29
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (33 bp):
AAAAAAAGTTAAAAAAAAAAAGAAAAAAAAAAG
Found at i:3840339 original size:129 final size:126
Alignment explanation
Indices: 3840123--3840592 Score: 520
Period size: 127 Copynumber: 3.7 Consensus size: 126
3840113 TATCGAATTT
* * * * * *
3840123 CCAAATACGAAACATTGCCTCATTTTAA-TTTGAGAAAACATGGATGAAACTTCAAAAGGATATT
1 CCAAATACGAAATATTGCCTCATTTTAATTTTAAAAAAACATGGACGAAATTTCTAAAGGATATT
** * * * *
3840187 TTGTATTTT-AGTCGGATGGAAAATTGAAGCCCAGTACGATTGGGCACGACTCCCCAAACTC
66 CCGTATTTTAACT-GAATGAAAAATTGAAGCCCAGCACGATTGGGCACGACTCCCCAAACTC
3840248 CTCAAATACGAAATATTGCCTCATTTTAATTTTAAAAAAAAACATGGACGAAATTTCTAAAGGAT
1 C-CAAATACGAAATATTGCCTCATTTTAATTTT--AAAAAAACATGGACGAAATTTCTAAAGGAT
* * *
3840313 ATTCCGTATTTTAACTAAATGAAAAATTGAAGCCCAGCACGATTGGGCACGACTCTCTAAACTCC
63 ATTCCGTATTTTAACTGAATGAAAAATTGAAGCCCAGCACGATTGGGCACGACTCCCCAAACT-C
* * * * * *
3840378 CCAAATACGAAATATTACCTCATTTTAATTTTTAAAAAACATAGACGAAGTTTCCAAAAGATATT
1 CCAAATACGAAATATTGCCTCATTTTAATTTTAAAAAAACATGGACGAAATTTCTAAAGGATATT
* * * * *
3840443 CCGTATTTTAGCCGAAT-AGAAAATTGAAGCCCAGCACGATTGGGCATGAC-CCCCAACCTT
66 CCGTATTTTAACTGAATGA-AAAATTGAAGCCCAGCACGATTGGGCACGACTCCCCAAACTC
* * *
3840503 CCAAACACGAAATATTGCCTCGTTTTAATTTTTTAAAAAAA-ATTGGACAAAATTT-TCAAAGGA
1 CCAAATACGAAATATTGCCTCATTTTAA--TTTTAAAAAAACA-TGGACGAAATTTCT-AAAGGA
* * *
3840566 TATTTCGTATCTTAACTGAACGAAAAA
62 TATTCCGTATTTTAACTGAATGAAAAA
3840593 AAATCAAAAC
Statistics
Matches: 290, Mismatches: 43, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
125 26 0.09
126 34 0.12
127 119 0.41
128 1 0.00
129 106 0.37
130 4 0.01
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (126 bp):
CCAAATACGAAATATTGCCTCATTTTAATTTTAAAAAAACATGGACGAAATTTCTAAAGGATATT
CCGTATTTTAACTGAATGAAAAATTGAAGCCCAGCACGATTGGGCACGACTCCCCAAACTC
Found at i:3840539 original size:256 final size:253
Alignment explanation
Indices: 3840123--3840592 Score: 624
Period size: 256 Copynumber: 1.8 Consensus size: 253
3840113 TATCGAATTT
* * * * *
3840123 CCAAATACGAAACATTGCCTCATTTTAATTTGAGAAAACATGGATGAAACTTCAAAAGGATATTT
1 CCAAATACGAAACATTACCTCATTTTAATTTGAAAAAACATAGACGAAACTTCAAAAGGATATTC
* * * * *
3840188 TGTATTTTAGTCGGATGGAAAATTGAAGCCCAGTACGATTGGGCACGACTCCCCAAACTCCTCAA
66 CGTATTTTAGCCGAATAGAAAATTGAAGCCCAGCACGATTGGGCACGACTCCCCAAACTCCTCAA
* *
3840253 ATACGAAATATTGCCTCATTTTAATTTTAAAAAAAAACATGGACGAAA-TTTCTAAAGGATATTC
131 ACACGAAATATTGCCTCATTTTAATTTT-AAAAAAAA-ATGGACAAAATTTTC-AAAGGATATTC
* *
3840317 CGTATTTTAACTAAATGAAAAATTGAAGCCCAGCACGATTGGGCACGACTCTCTAAACTCC
193 CGTATCTTAACTAAACGAAAAATTGAAGCCCAGCACGATTGGGCACGACTCTCTAAACTCC
* * **
3840378 CCAAATACGAAATATTACCTCATTTTAATTTTTAAAAAACATAGACGAAGTTTCCAAAA-GATAT
1 CCAAATACGAAACATTACCTCATTTTAA-TTTGAAAAAACATAGACGAAACTT-CAAAAGGATAT
* * *
3840442 TCCGTATTTTAGCCGAATAGAAAATTGAAGCCCAGCACGATTGGGCATGAC-CCCCAACCTTC-C
64 TCCGTATTTTAGCCGAATAGAAAATTGAAGCCCAGCACGATTGGGCACGACTCCCCAAACTCCTC
* *
3840505 AAACACGAAATATTGCCTCGTTTTAATTTTTTAAAAAAAATTGGACAAAATTTTCAAAGGATATT
129 AAACACGAAATATTGCCTCATTTTAA--TTTTAAAAAAAAATGGACAAAATTTTCAAAGGATATT
* *
3840570 TCGTATCTTAACTGAACGAAAAA
192 CCGTATCTTAACTAAACGAAAAA
3840593 AAATCAAAAC
Statistics
Matches: 185, Mismatches: 25, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
254 62 0.34
255 47 0.25
256 71 0.38
257 5 0.03
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (253 bp):
CCAAATACGAAACATTACCTCATTTTAATTTGAAAAAACATAGACGAAACTTCAAAAGGATATTC
CGTATTTTAGCCGAATAGAAAATTGAAGCCCAGCACGATTGGGCACGACTCCCCAAACTCCTCAA
ACACGAAATATTGCCTCATTTTAATTTTAAAAAAAAATGGACAAAATTTTCAAAGGATATTCCGT
ATCTTAACTAAACGAAAAATTGAAGCCCAGCACGATTGGGCACGACTCTCTAAACTCC
Found at i:3841187 original size:2 final size:2
Alignment explanation
Indices: 3841175--3841212 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3841165 TGGAAACCTA
3841175 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3841213 AACTATTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3841396 original size:18 final size:20
Alignment explanation
Indices: 3841360--3841402 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
3841350 CAATTAATGT
3841360 AAAAAAATAAGAAAAATAA-
1 AAAAAAATAAGAAAAATAAC
* *
3841379 AAAAAAATCA-AAAGATAAC
1 AAAAAAATAAGAAAAATAAC
3841398 AAAAA
1 AAAAA
3841403 CTTAACAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.81, C:0.05, G:0.05, T:0.09
Consensus pattern (20 bp):
AAAAAAATAAGAAAAATAAC
Found at i:3843312 original size:3 final size:3
Alignment explanation
Indices: 3843304--3843599 Score: 150
Period size: 3 Copynumber: 98.3 Consensus size: 3
3843294 AGGGAGAGTG
*
3843304 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * ** *
3843352 TTT TTT TTA -TA TTG TTC TTA TTA TTA GCA -CA TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
* *
3843396 TTAA TGTA TCA TTG TTA TT- TT- TTA TT- TTA TTA TTA CTT- TTA TTA
1 TT-A T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
* *
3843440 CTA TTG TT- TCTA TTA TTA TTA TT- TTCA TTA CTTCCA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TT-A TTA -TT--A TTA TTA TTA
* * * * *
3843485 TCA TTA TT- TTCAA TTA TCA TTA ATA -TG TTG TT- TGT- TTA TTA TTA
1 TTA TTA TTA TT--A TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
* ** * * *
3843529 TTA TTA TTA TTT TTA ACA CTA TTA TCA TCA TTA -TA TTTA CTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA
* *
3843575 TTA TTA TTA CTA TTA TTT TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
3843600 CCGTCTTATT
Statistics
Matches: 234, Mismatches: 35, Indels: 48
0.74 0.11 0.15
Matches are distributed among these distances:
2 22 0.09
3 188 0.80
4 18 0.08
5 5 0.02
6 1 0.00
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3852128 original size:14 final size:14
Alignment explanation
Indices: 3852109--3852139 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3852099 AATGAATGAT
3852109 TAACATGTGTGCTC
1 TAACATGTGTGCTC
3852123 TAACATGTGTGCTC
1 TAACATGTGTGCTC
3852137 TAA
1 TAA
3852140 TAAAATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (14 bp):
TAACATGTGTGCTC
Found at i:3852476 original size:19 final size:19
Alignment explanation
Indices: 3852452--3852520 Score: 97
Period size: 19 Copynumber: 3.6 Consensus size: 19
3852442 CATAAATTTA
3852452 TAATTTAATATTTATACGT
1 TAATTTAATATTTATACGT
3852471 TAATTTAATATAGTT-TA-GT
1 TAATTTAATAT--TTATACGT
3852490 TAAATTTAATATTTATACGT
1 T-AATTTAATATTTATACGT
3852510 TAATTTAATAT
1 TAATTTAATAT
3852521 AATTTAGTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.04
19 26 0.58
20 15 0.33
21 2 0.04
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (19 bp):
TAATTTAATATTTATACGT
Found at i:3852497 original size:20 final size:18
Alignment explanation
Indices: 3852452--3852529 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 18
3852442 CATAAATTTA
3852452 TAATTTAATAT-TTATACGT
1 TAATTTAATATATT-TA-GT
3852471 TAATTTAATATAGTTTAGT
1 TAATTTAATATA-TTTAGT
3852490 TAAATTTAATAT-TTATACGT
1 T-AATTTAATATATT-TA-GT
3852510 TAATTTAATATAATTTAGT
1 TAATTTAATAT-ATTTAGT
3852529 T
1 T
3852530 TTTTATTATT
Statistics
Matches: 52, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
18 2 0.04
19 29 0.56
20 17 0.33
21 4 0.08
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (18 bp):
TAATTTAATATATTTAGT
Found at i:3852507 original size:39 final size:39
Alignment explanation
Indices: 3852453--3852529 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
3852443 ATAAATTTAT
*
3852453 AATTTAATATTTATACGTTAATTTAATATAGTTTAGTTA
1 AATTTAATATTTATACGTTAATTTAATATAATTTAGTTA
3852492 AATTTAATATTTATACGTTAATTTAATATAATTTAGTT
1 AATTTAATATTTATACGTTAATTTAATATAATTTAGTT
3852530 TTTTATTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (39 bp):
AATTTAATATTTATACGTTAATTTAATATAATTTAGTTA
Found at i:3853051 original size:29 final size:29
Alignment explanation
Indices: 3852991--3853053 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
3852981 AATTTTTAAT
* * *
3852991 ATTTTCTAAAATTTTAAATTATTTTTTGA
1 ATTTTCTAAAATTTTAAAATATTATATGA
3853020 ATTTTCTAAAATTTTAAAAATATTATAT-A
1 ATTTTCTAAAATTTT-AAAATATTATATGA
3853049 ATTTT
1 ATTTT
3853054 AGGAATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (29 bp):
ATTTTCTAAAATTTTAAAATATTATATGA
Found at i:3853313 original size:22 final size:23
Alignment explanation
Indices: 3853265--3853314 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
3853255 TAAGATAATT
*
3853265 AAATTTGAAAAGATTTGACTTTC
1 AAATTTGAAAAGATTTGACTTTA
*
3853288 AAATTT-AAATGATTTGAAC-TTA
1 AAATTTGAAAAGATTTG-ACTTTA
3853310 AAATT
1 AAATT
3853315 ATTACAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (23 bp):
AAATTTGAAAAGATTTGACTTTA
Found at i:3855856 original size:21 final size:21
Alignment explanation
Indices: 3855838--3856296 Score: 420
Period size: 21 Copynumber: 21.4 Consensus size: 21
3855828 ACCACCACTA
*
3855838 CCACCGGTCCACTCCCCACCC
1 CCACCAGTCCACTCCCCACCC
* *
3855859 CCACCAGTGCACTCACCACCC
1 CCACCAGTCCACTCCCCACCC
* *
3855880 CCACCAGTGCACTCACCA-CC
1 CCACCAGTCCACTCCCCACCC
* * *
3855900 CCACCAGTCTTCTCACCACCACCA
1 CCACCAGTC--CACTCC-CCACCC
*
3855924 CCACCAGTCCACTCTCCACCC
1 CCACCAGTCCACTCCCCACCC
* *
3855945 CCACCCGTTCACTCCCCACCC
1 CCACCAGTCCACTCCCCACCC
* *
3855966 CCACCCGTTCACTCCCCACCC
1 CCACCAGTCCACTCCCCACCC
* *
3855987 CCACCAGTGCACTCACCACCC
1 CCACCAGTCCACTCCCCACCC
*
3856008 CCACCCGTCCACTCACCACCACCC
1 CCACCAGTCCACT--CC-CCACCC
* *
3856032 CCACCCGTCCACTCACCACCC
1 CCACCAGTCCACTCCCCACCC
* * *
3856053 CCACCAGTCTTCTCACCACCACCA
1 CCACCAGTC--CACTCC-CCACCC
3856077 CCACCAGTCCACTCCCCACCC
1 CCACCAGTCCACTCCCCACCC
* *
3856098 CCACCCGTCCACTCCCCACCA
1 CCACCAGTCCACTCCCCACCC
*
3856119 CCACCAGTCCACTCGCCACCC
1 CCACCAGTCCACTCCCCACCC
* *
3856140 CCACCCA-TCCACTCACCACCA
1 CCA-CCAGTCCACTCCCCACCC
* * *
3856161 CCACCCGTCTACTCACCACCACCA
1 CCACCAGTCCACT--CC-CCACCC
* *
3856185 CCACCAGTCCGCTCCCCACCT
1 CCACCAGTCCACTCCCCACCC
*
3856206 CCACCCGTCCACT-CCCACCC
1 CCACCAGTCCACTCCCCACCC
* * *
3856226 CCACCCGTCCACTCACCACCA
1 CCACCAGTCCACTCCCCACCC
* * * *
3856247 CCACCCGTCTACTCACCACCA
1 CCACCAGTCCACTCCCCACCC
*
3856268 CCACCAGTCTACTCCCCACCC
1 CCACCAGTCCACTCCCCACCC
3856289 CCACCAGT
1 CCACCAGT
3856297 ACAATCTCTA
Statistics
Matches: 369, Mismatches: 53, Indels: 32
0.81 0.12 0.07
Matches are distributed among these distances:
20 31 0.08
21 255 0.69
22 16 0.04
23 8 0.02
24 59 0.16
ACGTcount: A:0.21, C:0.62, G:0.06, T:0.12
Consensus pattern (21 bp):
CCACCAGTCCACTCCCCACCC
Found at i:3856086 original size:153 final size:153
Alignment explanation
Indices: 3855838--3856296 Score: 580
Period size: 153 Copynumber: 3.1 Consensus size: 153
3855828 ACCACCACTA
* * * * *
3855838 CCACCGGTCCACTCCCCACCCCCACCAGTGCACT---CACCACCCCCACCAGTGCACTCACCA-C
1 CCACCAGTCCACTCACCACCCCCACCCGTCCACTCACCACCACCCCCACCAGTCCACTCACCACC
*
3855899 CCCACCAGTCTTCTCACCACCACCACCACCAGTCCACTCTCCACCCCCACCCGTTCACTCCCCAC
66 CCCACCAGTCTTCTCACCACCACCACCACCAGTCCACTCACCACCCCCACCCGTTCACTCCCCAC
* *
3855964 CCCCACCCGTTCACTCCCCACCC
131 CACCACCAGTTCACTCCCCACCC
* *
3855987 CCACCAGTGCACTCACCACCCCCACCCGTCCACTCACCACCACCCCCACCCGTCCACTCACCACC
1 CCACCAGTCCACTCACCACCCCCACCCGTCCACTCACCACCACCCCCACCAGTCCACTCACCACC
* *
3856052 CCCACCAGTCTTCTCACCACCACCACCACCAGTCCACTCCCCACCCCCACCCGTCCACTCCCCAC
66 CCCACCAGTCTTCTCACCACCACCACCACCAGTCCACTCACCACCCCCACCCGTTCACTCCCCAC
* *
3856117 CACCACCAGTCCACTCGCCACCC
131 CACCACCAGTTCACTCCCCACCC
* * * * *
3856140 CCACCCA-TCCACTCACCACCACCACCCGTCTACTCACCACCACCACCACCAGTCCGCTCCCCAC
1 CCA-CCAGTCCACTCACCACCCCCACCCGTCCACTCACCACCACCCCCACCAGTCCACTCACCAC
* * ** * * *
3856204 CTCCACCCGTCCACTC-CCA-C-CC-CCACCCGTCCACTCACCACCACCACCCG-TCTACTCACC
65 CCCCACCAGTCTTCTCACCACCACCACCACCAGTCCACTCACCACCCCCACCCGTTC-ACTCCCC
3856264 ACCACCACCAG-TCTACTCCCCACCC
129 ACCACCACCAGTTC-ACTCCCCACCC
3856289 CCACCAGT
1 CCACCAGT
3856297 ACAATCTCTA
Statistics
Matches: 271, Mismatches: 31, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
148 5 0.02
149 85 0.31
150 2 0.01
151 1 0.00
152 27 0.10
153 148 0.55
154 3 0.01
ACGTcount: A:0.21, C:0.62, G:0.06, T:0.12
Consensus pattern (153 bp):
CCACCAGTCCACTCACCACCCCCACCCGTCCACTCACCACCACCCCCACCAGTCCACTCACCACC
CCCACCAGTCTTCTCACCACCACCACCACCAGTCCACTCACCACCCCCACCCGTTCACTCCCCAC
CACCACCAGTTCACTCCCCACCC
Found at i:3857523 original size:19 final size:19
Alignment explanation
Indices: 3857499--3857543 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3857489 TCCTAAACTT
3857499 TTTTACTTTCCCT-AAAAA
1 TTTTACTTTCCCTCAAAAA
*
3857517 TTATTACTTTTCCTCAAAAA
1 TT-TTACTTTCCCTCAAAAA
3857537 TTTTACT
1 TTTTACT
3857544 CCTCCCTGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 2 0.08
19 15 0.62
20 7 0.29
ACGTcount: A:0.31, C:0.20, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTTACTTTCCCTCAAAAA
Found at i:3860232 original size:21 final size:21
Alignment explanation
Indices: 3860228--3860283 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
3860218 ATCCAATCTC
3860228 CACCACCACCACCAATGCACT
1 CACCACCACCACCAATGCACT
* ** * *
3860249 CACCACCACCGCCCGTCCATT
1 CACCACCACCACCAATGCACT
3860270 CACCACCACCACCA
1 CACCACCACCACCA
3860284 TCGGTTCCTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.57, G:0.05, T:0.09
Consensus pattern (21 bp):
CACCACCACCACCAATGCACT
Found at i:3860456 original size:62 final size:63
Alignment explanation
Indices: 3860273--3860661 Score: 638
Period size: 63 Copynumber: 6.2 Consensus size: 63
3860263 GTCCATTCAC
* * * * *
3860273 CACCACCACCATCGGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCCCCACCGGTACCCT
1 CACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT
* * *
3860336 CACCACCACCACCAGTTTCTTCACCCCCACCGCCAGTAAAATCTCCACCTCCACCGGTGCCCT
1 CACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT
3860399 CACCACCACCACCAGTTCCTTCA-CCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT
1 CACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT
*
3860461 CACCACCACCACCAGTTCCTTCA-CCCCACCCCCAGTAAAATCCCCACCTCTACCGGTGCCCT
1 CACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT
3860523 CACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT
1 CACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT
* * * *
3860586 CACCACCACCACCAGATCCTTCACCCTCACCACCAGTAAAATCCCTACCTCCACCGGTGCCCT
1 CACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT
*
3860649 CACCACCCCCACC
1 CACCACCACCACC
3860662 TGTGCCATCT
Statistics
Matches: 308, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
62 121 0.39
63 187 0.61
ACGTcount: A:0.23, C:0.54, G:0.08, T:0.15
Consensus pattern (63 bp):
CACCACCACCACCAGTTCCTTCACCCCCACCCCCAGTAAAATCCCCACCTCCACCGGTGCCCT
Found at i:3860763 original size:62 final size:63
Alignment explanation
Indices: 3860627--3860935 Score: 277
Period size: 62 Copynumber: 5.0 Consensus size: 63
3860617 ACCAGTAAAA
* * * * * * *
3860627 TCCCTACCTCCACCGGTGCCCTCACCACCCCCACCTGTGCCA-TCTCCACCCCCACCCGTCCGC
1 TCCCCACCCCCACCTGTGCCCTCTCCACCCCCACCCGT-CCACTCACCACCCCCACCCGTCCAC
* *
3860690 TCCCCACCCCCACCTGTGCCCTCTCCACCCCTACCCGTCCACTC-CCACCCCCACCTGTCCAC
1 TCCCCACCCCCACCTGTGCCCTCTCCACCCCCACCCGTCCACTCACCACCCCCACCCGTCCAC
* ** * * * * *
3860752 TCTCCACCCCCACCTGTGCCCTCTCCACCCCCACCTATCCTCTCTCCA-CCCCACCGGTGCGC
1 TCCCCACCCCCACCTGTGCCCTCTCCACCCCCACCCGTCCACTCACCACCCCCACCCGTCCAC
* * * * * * *
3860814 TCACCA-CCCCACCCGT-CCTTTCTCCACCCCCACCAGTGCGCTCACCACCCCCACCCATCCAC
1 TCCCCACCCCCACCTGTGCC-CTCTCCACCCCCACCCGTCCACTCACCACCCCCACCCGTCCAC
* * ** * * * *
3860876 TCCCCACCCCCACCAGTACATTCACCACCACCACCCGTCTACTCACCACCTCCACCCGTC
1 TCCCCACCCCCACCTGTGCCCTCTCCACCCCCACCCGTCCACTCACCACCCCCACCCGTC
3860936 AAGTCTCCAC
Statistics
Matches: 201, Mismatches: 39, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
60 2 0.01
61 31 0.15
62 89 0.44
63 78 0.39
64 1 0.00
ACGTcount: A:0.15, C:0.61, G:0.08, T:0.16
Consensus pattern (63 bp):
TCCCCACCCCCACCTGTGCCCTCTCCACCCCCACCCGTCCACTCACCACCCCCACCCGTCCAC
Found at i:3860882 original size:21 final size:21
Alignment explanation
Indices: 3860651--3860952 Score: 238
Period size: 21 Copynumber: 14.5 Consensus size: 21
3860641 GGTGCCCTCA
*
3860651 CCACCCCCACCTGTGCCA-TCT
1 CCACCCCCACCCGT-CCACTCT
* *
3860672 CCACCCCCACCCGTCCGCTCC
1 CCACCCCCACCCGTCCACTCT
*
3860693 CCACCCCCACCTGTGCC-CTCT
1 CCACCCCCACCCGT-CCACTCT
*
3860714 CCACCCCTACCCGTCCACTC-
1 CCACCCCCACCCGTCCACTCT
*
3860734 CCACCCCCACCTGTCCACTCT
1 CCACCCCCACCCGTCCACTCT
*
3860755 CCACCCCCACCTGTGCC-CTCT
1 CCACCCCCACCCGT-CCACTCT
** *
3860776 CCACCCCCACCTATCCTCTCT
1 CCACCCCCACCCGTCCACTCT
* * * *
3860797 CCA-CCCCACCGGTGCGCTCA
1 CCACCCCCACCCGTCCACTCT
**
3860817 CCA-CCCCACCCGTCCTTTCT
1 CCACCCCCACCCGTCCACTCT
* * * *
3860837 CCACCCCCACCAGTGCGCTCA
1 CCACCCCCACCCGTCCACTCT
* *
3860858 CCACCCCCACCCATCCACTCC
1 CCACCCCCACCCGTCCACTCT
* * * *
3860879 CCACCCCCACCAGTACATTCA
1 CCACCCCCACCCGTCCACTCT
* * *
3860900 CCACCACCACCCGTCTACTCA
1 CCACCCCCACCCGTCCACTCT
* * *
3860921 CCACCTCCACCCGTCAAGTCT
1 CCACCCCCACCCGTCCACTCT
*
3860942 CCACCACCACC
1 CCACCCCCACC
3860953 AGTAAAATCT
Statistics
Matches: 229, Mismatches: 45, Indels: 14
0.80 0.16 0.05
Matches are distributed among these distances:
20 54 0.24
21 171 0.75
22 4 0.02
ACGTcount: A:0.16, C:0.61, G:0.07, T:0.16
Consensus pattern (21 bp):
CCACCCCCACCCGTCCACTCT
Found at i:3862275 original size:190 final size:191
Alignment explanation
Indices: 3861949--3862396 Score: 570
Period size: 190 Copynumber: 2.4 Consensus size: 191
3861939 AAGTAATAAG
** * *
3861949 TAATGTACTACTATTATATATGTCTATTATTATAATATAGATTATAATAAAAGATATAGTTTTAC
1 TAATGTACTACTATTATATATAACTATTATTATAATATAAATTATAATAAAAGATATAGTATTAC
* * * *
3862014 ATGATATTATTATGTTTAATTATATATAAACTATTAATATATTATATAATATGATATAGCGTTAC
66 ATAATATTATAATGTTTAACTATATATAAACTATTAATATATTATATAATATGATATAACGTTAC
3862079 ATAATATAAT-AGAAGGTTAACTTTCAAATGTACGGAAAATATAAAGACTTGGAGCATATT
131 ATAATATAATAAGAAGGTTAACTTTCAAATGTACGGAAAATATAAAGACTTGGAGCATATT
* * * *
3862139 TAATGTACTACTATTATATATAACTATTATTA-AATTATAAATTATAATAAAGGGTATGGTATTG
1 TAATGTACTACTATTATATATAACTATTATTATAA-TATAAATTATAATAAAAGATATAGTATTA
* *
3862203 CATAATATTATAATGTTTAACTATATATAAACTATTAATATATTATATGATATGATATAACTTTA
65 CATAATATTATAATGTTTAACTATATATAAACTATTAATATATTATATAATATGATATAACGTTA
* * * * *
3862268 TATAATATAGTAAGATGGTTAACTTTCAAA-G---GG---AT-TTAA-A--T----CATATA
130 CATAATATAATAAGAAGGTTAACTTTCAAATGTACGGAAAATATAAAGACTTGGAGCATATT
* *
3862315 TAATGTACTACTATTATATATAACGATTATTATAATATAGATTATAATAAAAGATATAGTATTAC
1 TAATGTACTACTATTATATATAACTATTATTATAATATAAATTATAATAAAAGATATAGTATTAC
*
3862380 ATGATATTATAATGTTT
66 ATAATATTATAATGTTT
3862397 GATCATTGAT
Statistics
Matches: 229, Mismatches: 26, Indels: 20
0.83 0.09 0.07
Matches are distributed among these distances:
176 77 0.34
177 2 0.01
180 1 0.00
182 1 0.00
183 3 0.01
184 2 0.01
187 2 0.01
189 2 0.01
190 122 0.53
191 17 0.07
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (191 bp):
TAATGTACTACTATTATATATAACTATTATTATAATATAAATTATAATAAAAGATATAGTATTAC
ATAATATTATAATGTTTAACTATATATAAACTATTAATATATTATATAATATGATATAACGTTAC
ATAATATAATAAGAAGGTTAACTTTCAAATGTACGGAAAATATAAAGACTTGGAGCATATT
Found at i:3863811 original size:26 final size:26
Alignment explanation
Indices: 3863774--3863828 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
3863764 ACACACCGCA
*
3863774 GCTCTTCGTGAGCTTCCTGA-TATATG
1 GCTCTTCATGAGCTTCCTGATTA-ATG
3863800 GCTCTTCATGAGCTTCCTGATTAATG
1 GCTCTTCATGAGCTTCCTGATTAATG
3863826 GCT
1 GCT
3863829 TTTGGGAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 25 0.93
27 2 0.07
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (26 bp):
GCTCTTCATGAGCTTCCTGATTAATG
Found at i:3863888 original size:24 final size:24
Alignment explanation
Indices: 3863782--3863888 Score: 79
Period size: 24 Copynumber: 4.3 Consensus size: 24
3863772 CAGCTCTTCG
* *
3863782 TGAGCTTCCTGATATATGGCTCTTCA
1 TGAGCTTCCCGATAT-TGGCTCGT-A
* * ** *
3863808 TGAGCTTCCTGATTAATGGCTTTTG
1 TGAGCTTCCCGA-TATTGGCTCGTA
* * *
3863833 GGAGCTTCCCGTTATTGGCTCGCA
1 TGAGCTTCCCGATATTGGCTCGTA
* *
3863857 AGAACTTCCCGATATTGGCTCGTA
1 TGAGCTTCCCGATATTGGCTCGTA
3863881 TGAGCTTC
1 TGAGCTTC
3863889 TCCTTATATG
Statistics
Matches: 63, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
24 33 0.52
25 9 0.14
26 19 0.30
27 2 0.03
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (24 bp):
TGAGCTTCCCGATATTGGCTCGTA
Found at i:3866541 original size:146 final size:145
Alignment explanation
Indices: 3866302--3866595 Score: 471
Period size: 146 Copynumber: 2.0 Consensus size: 145
3866292 TGCCATTAAA
* * * *
3866302 GATCTGAGTGTTTTATCTTGTGTTTTTTCCATCATGTTTTTATCCTATAATGCCCCAAATTTTAA
1 GATCCGAGTGTTTTATCTTGTATTTTTTCCATCATGTTGTTATCCTATAACGCCCCAAATTTTAA
* * * * *
3866367 ACATTTGCTTGTTAAATTTTATCATTAAATGCATGTTTACTTTAGTGGTTTAGTGCTTTAATTGT
66 ACATCTACTTGTTAAATTTTATCATTAAATGCATGTTTACTTTAGTGGTGTAGTACCTTAATTGT
3866432 GTGTTTAAGATTAGG
131 GTGTTTAAGATTAGG
* *
3866447 GATCCGAGTGTTTTATCTTGTATTTTTTCCATCAATGTTGTTATCCTGTAACGCCCCAAATTTTG
1 GATCCGAGTGTTTTATCTTGTATTTTTTCCATC-ATGTTGTTATCCTATAACGCCCCAAATTTTA
*
3866512 AACATCTACTTGTTAAATTTTATCATTAAATTCATGTTTACTTTAGTGGTGTAGTACCTTAATTG
65 AACATCTACTTGTTAAATTTTATCATTAAATGCATGTTTACTTTAGTGGTGTAGTACCTTAATTG
3866577 TGTGTTTAAGATTAGG
130 TGTGTTTAAGATTAGG
3866593 GAT
1 GAT
3866596 TTAAGTCCCA
Statistics
Matches: 136, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
145 31 0.23
146 105 0.77
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (145 bp):
GATCCGAGTGTTTTATCTTGTATTTTTTCCATCATGTTGTTATCCTATAACGCCCCAAATTTTAA
ACATCTACTTGTTAAATTTTATCATTAAATGCATGTTTACTTTAGTGGTGTAGTACCTTAATTGT
GTGTTTAAGATTAGG
Found at i:3870111 original size:19 final size:19
Alignment explanation
Indices: 3870033--3870115 Score: 55
Period size: 19 Copynumber: 4.4 Consensus size: 19
3870023 TTTTAATTAG
* *
3870033 TATTTAAGTTTAGTTTTAA
1 TATTTAATTTTAGCTTTAA
*
3870052 TGTTTAA-TTTAGTACTTTAA
1 TATTTAATTTTAG--CTTTAA
** * *
3870072 -ATTTTTTTCTTA-ATTTTA
1 TATTTAATT-TTAGCTTTAA
3870090 TATTTAATTTTAGCTTTAA
1 TATTTAATTTTAGCTTTAA
3870109 TATTTAA
1 TATTTAA
3870116 ATTGATACTT
Statistics
Matches: 47, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
18 12 0.26
19 26 0.55
20 6 0.13
21 3 0.06
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (19 bp):
TATTTAATTTTAGCTTTAA
Found at i:3872436 original size:27 final size:27
Alignment explanation
Indices: 3872398--3872471 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 27
3872388 TTAGCCCTTA
3872398 TGAGCTTCCCGATTATATGGCTCTTTG
1 TGAGCTTCCCGATTATATGGCTCTTTG
*
3872425 TGAGCTTCCCGATT-TAAGGCTCTTTG
1 TGAGCTTCCCGATTATATGGCTCTTTG
*
3872451 TGAGCTTCTCGA-TA-ATGGCTC
1 TGAGCTTCCCGATTATATGGCTC
3872472 GCTTGAACTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
25 7 0.16
26 22 0.51
27 14 0.33
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (27 bp):
TGAGCTTCCCGATTATATGGCTCTTTG
Found at i:3875343 original size:31 final size:30
Alignment explanation
Indices: 3875286--3875344 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
3875276 GTAAATACTC
* * * *
3875286 AAAATTTGAGGGATTAAAGTGTAAATATGA
1 AAAAGTTGAAGGACTAAAGTGAAAATATGA
3875316 AAAAGTTGAAGGACTAATAGTGAAAATAT
1 AAAAGTTGAAGGACTAA-AGTGAAAATAT
3875345 TTTAAGGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.49, C:0.02, G:0.22, T:0.27
Consensus pattern (30 bp):
AAAAGTTGAAGGACTAAAGTGAAAATATGA
Done.