Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 25 of 318
Found at i:9447831 original size:19 final size:20
Alignment explanation
Indices: 9447779--9447828 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
9447769 AAATTGAAAC
*
9447779 AGCTTATAAAAATT-ATATA
1 AGCTTATAAAAATTCATACA
**
9447798 AAATTATAAAAATTCATACA
1 AGCTTATAAAAATTCATACA
9447818 AGCTTATAAAA
1 AGCTTATAAAA
9447829 TTCTTAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (20 bp):
AGCTTATAAAAATTCATACA
Found at i:9450325 original size:47 final size:47
Alignment explanation
Indices: 9450273--9450426 Score: 161
Period size: 47 Copynumber: 3.3 Consensus size: 47
9450263 TTTGCTTCCA
*
9450273 TATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTACTG
1 TATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTACTG
** * *
9450320 TATAAGACCATATCTGGGATATGGCATCAATGTGATATGTGATTC-G
1 TATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTACTG
* * *
9450366 TGTAAGACCAT-TGCTGGGCTATGGCCTCGGTATGTGATATGTGACTA-TG
1 TATAAGACCATAT-CTGGGATATGGCATCGG--TGTGATATGTG-CTACTG
**
9450415 TGCAAGACCATA
1 TATAAGACCATA
9450427 GTTTTACTAT
Statistics
Matches: 88, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
45 1 0.01
46 24 0.27
47 40 0.45
48 11 0.12
49 12 0.14
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (47 bp):
TATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTACTG
Found at i:9457457 original size:9 final size:8
Alignment explanation
Indices: 9457431--9457456 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
9457421 CATTTGCTTC
9457431 TTCTTTTT
1 TTCTTTTT
9457439 TTCTTTTT
1 TTCTTTTT
9457447 TTCTTTTT
1 TTCTTTTT
9457455 TT
1 TT
9457457 TAACATGAGA
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTCTTTTT
Found at i:9461036 original size:16 final size:17
Alignment explanation
Indices: 9461015--9461049 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
9461005 TAATGTCTAG
9461015 GAAAATTA-TTAATTGA
1 GAAAATTACTTAATTGA
9461031 GAAAATTATCTTAATTGA
1 GAAAATTA-CTTAATTGA
9461049 G
1 G
9461050 GGGTTAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.37
Consensus pattern (17 bp):
GAAAATTACTTAATTGA
Found at i:9462240 original size:31 final size:31
Alignment explanation
Indices: 9462156--9462247 Score: 139
Period size: 31 Copynumber: 3.0 Consensus size: 31
9462146 CAAGGACAAA
* *
9462156 TGATCAGTGAAAAGTGGTAGCTCCAGCTACC
1 TGATCAGTGAAAAGTGGTAGCTTCGGCTACC
*
9462187 TGATCAGTGAAAAATGGTAGCTTCGGCTACC
1 TGATCAGTGAAAAGTGGTAGCTTCGGCTACC
* *
9462218 TGATCAATGAATAGTGGTAGCTTCGGCTAC
1 TGATCAGTGAAAAGTGGTAGCTTCGGCTAC
9462248 AAGTGACAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (31 bp):
TGATCAGTGAAAAGTGGTAGCTTCGGCTACC
Found at i:9462421 original size:49 final size:47
Alignment explanation
Indices: 9462350--9462488 Score: 164
Period size: 42 Copynumber: 3.0 Consensus size: 47
9462340 TCAGTGAGAT
* *
9462350 ATGTGATT-CGTGTAAGACCATAGCTGGGTTATGGCATCGATATGTGA
1 ATGTGATTATGTGTAAGACCATAGCTGGGCTATGGCATC-ATATGTGA
9462397 CATGTGATTATGTGTAAGACCATAGCTGGGCTATGGCATCA-ATGT--
1 -ATGTGATTATGTGTAAGACCATAGCTGGGCTATGGCATCATATGTGA
* * *
9462442 A--TGAATATGTGTAAGACCATAACTGGGCTATGACATCATTATGTGA
1 ATGTGATTATGTGTAAGACCATAGCTGGGCTATGGCATCA-TATGTGA
9462488 A
1 A
9462489 GTTGTGTAAG
Statistics
Matches: 81, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
42 34 0.42
44 5 0.06
46 1 0.01
47 4 0.05
48 9 0.11
49 28 0.35
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (47 bp):
ATGTGATTATGTGTAAGACCATAGCTGGGCTATGGCATCATATGTGA
Found at i:9462468 original size:42 final size:43
Alignment explanation
Indices: 9462405--9462501 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 43
9462395 GACATGTGAT
* * *
9462405 TATGTGTAAGACCATAGCTGGGCTATGGCATCAATGTATGAA-
1 TATGTGTAAGACCATAACTGGGCTATGACATCAATATATGAAG
* *
9462447 TATGTGTAAGACCATAACTGGGCTATGACATCATTATGTGAAG
1 TATGTGTAAGACCATAACTGGGCTATGACATCAATATATGAAG
9462490 T-TGTGTAAGACC
1 TATGTGTAAGACC
9462502 GTAGTTGAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
42 48 0.98
43 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (43 bp):
TATGTGTAAGACCATAACTGGGCTATGACATCAATATATGAAG
Found at i:9464040 original size:93 final size:93
Alignment explanation
Indices: 9463928--9464099 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
9463918 GCCCATAAGT
* *
9463928 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
9463993 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
9464021 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
9464086 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
9464100 CAAACATCCT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:9464095 original size:46 final size:46
Alignment explanation
Indices: 9463920--9464095 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
9463910 TGTAACCCGC
* * *
9463920 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
* *
9463966 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-ATTTGCAT
* *
9464016 CTC-T---CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
*
9464059 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
9464096 TGCCCAAACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 1 0.01
43 8 0.07
44 1 0.01
46 65 0.59
47 28 0.25
49 1 0.01
50 6 0.05
51 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
Found at i:9466264 original size:29 final size:30
Alignment explanation
Indices: 9466221--9466300 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
9466211 CTTGAGCCAC
* * *
9466221 AATTAGAGTTTCATGTGTATAATTACACA-A
1 AATTAAAG-TTCATGTATAAAATTACACATA
9466251 AATTAAAGTTCATGTATAAAATTACACATTA
1 AATTAAAGTTCATGTATAAAATTACACA-TA
* *
9466282 AATCAAAGTTCACGTATAA
1 AATTAAAGTTCATGTATAA
9466301 TTTTAAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 18 0.42
30 7 0.16
31 18 0.42
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (30 bp):
AATTAAAGTTCATGTATAAAATTACACATA
Found at i:9466302 original size:29 final size:27
Alignment explanation
Indices: 9466237--9466302 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 27
9466227 AGTTTCATGT
* *
9466237 GTATAATTACACAAAATTAAAGTTCAT
1 GTATAATTACACAAAATCAAAGTTCAC
9466264 GTATAAAATTACACATTAAATCAAAGTTCAC
1 GTAT--AATTACACA--AAATCAAAGTTCAC
9466295 GTATAATT
1 GTATAATT
9466303 TTAAAATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 4 0.12
29 13 0.39
31 16 0.48
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (27 bp):
GTATAATTACACAAAATCAAAGTTCAC
Found at i:9468328 original size:12 final size:12
Alignment explanation
Indices: 9468311--9468336 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9468301 CTCCGAAACC
9468311 TTTTTATTTTGG
1 TTTTTATTTTGG
9468323 TTTTTATTTTGG
1 TTTTTATTTTGG
9468335 TT
1 TT
9468337 GCTTTTTTTT
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:0.08, C:0.00, G:0.15, T:0.77
Consensus pattern (12 bp):
TTTTTATTTTGG
Found at i:9470404 original size:2 final size:2
Alignment explanation
Indices: 9470397--9470422 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9470387 TTTGGAATCT
9470397 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
9470423 AGTACTTCTG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:9487145 original size:41 final size:41
Alignment explanation
Indices: 9487088--9487167 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
9487078 CAAAGTTAAT
* *
9487088 TTTTTTTTCCTTTAACCTCGAATGAATGAATCTCAAACTAC
1 TTTTTTTTCCGTTAACCTCAAATGAATGAATCTCAAACTAC
9487129 TTTTTTTTCCGTTAACCTCAAATGAATGAATCTCAAACT
1 TTTTTTTTCCGTTAACCTCAAATGAATGAATCTCAAACT
9487168 TCAAAATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.41
Consensus pattern (41 bp):
TTTTTTTTCCGTTAACCTCAAATGAATGAATCTCAAACTAC
Found at i:9489337 original size:27 final size:27
Alignment explanation
Indices: 9489307--9489361 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
9489297 AAAGCTGGTG
*
9489307 CAGCAGCAGCCACCCCAGGGTTAAACC
1 CAGCAGCAGCAACCCCAGGGTTAAACC
* *
9489334 CAGCAGCAGCAACTCCAGGGTTGAACC
1 CAGCAGCAGCAACCCCAGGGTTAAACC
9489361 C
1 C
9489362 CACTCCCACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.38, G:0.24, T:0.09
Consensus pattern (27 bp):
CAGCAGCAGCAACCCCAGGGTTAAACC
Found at i:9490344 original size:6 final size:6
Alignment explanation
Indices: 9490335--9490416 Score: 76
Period size: 6 Copynumber: 13.7 Consensus size: 6
9490325 CTCCTCTTCC
** * *
9490335 TCCTCT TCCTCT TCCTCT TCCTCT TCCAGT TCCACT TCCTCT TCTTCT
1 TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT
** * *
9490383 TCAACC TCCTCT T-CTACT TCCTCT TCCACT TCCT
1 TCCTCT TCCTCT TCCT-CT TCCTCT TCCTCT TCCT
9490417 GTAGTTTCTG
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
5 2 0.03
6 57 0.93
7 2 0.03
ACGTcount: A:0.07, C:0.46, G:0.01, T:0.45
Consensus pattern (6 bp):
TCCTCT
Found at i:9510644 original size:22 final size:22
Alignment explanation
Indices: 9510615--9510682 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
9510605 TGCACAAACG
9510615 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* *
9510637 TACAGAGAGCAC-AGATGTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
*
9510659 AACAGAGAGCACTTAACGTGCTA
1 AACAGAGAGCAC-TAAAGTGCTA
9510682 A
1 A
9510683 TAATAGAATG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.74
23 8 0.21
24 1 0.03
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:9514142 original size:7 final size:7
Alignment explanation
Indices: 9514124--9514187 Score: 51
Period size: 7 Copynumber: 8.4 Consensus size: 7
9514114 GGCTGTTACA
9514124 ATAATAAT
1 ATAAT-AT
9514132 ATAATAT
1 ATAATAT
9514139 ATAATAT
1 ATAATAT
9514146 ATTAATACT
1 A-TAATA-T
9514155 -TAA-AT
1 ATAATAT
9514160 ATTAAGTTAAT
1 A-TAA--T-AT
9514171 ATAATAT
1 ATAATAT
9514178 ATAATAT
1 ATAATAT
9514185 ATA
1 ATA
9514188 TTTTGATATC
Statistics
Matches: 48, Mismatches: 0, Indels: 17
0.74 0.00 0.26
Matches are distributed among these distances:
5 1 0.02
6 1 0.02
7 28 0.58
8 11 0.23
9 1 0.02
10 3 0.06
11 3 0.06
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (7 bp):
ATAATAT
Found at i:9515207 original size:15 final size:14
Alignment explanation
Indices: 9515139--9515267 Score: 70
Period size: 15 Copynumber: 8.9 Consensus size: 14
9515129 TTATTCCTAT
9515139 TATTTTTATGTT-TC
1 TATTTTTAT-TTATC
*
9515153 TATTTATATTTAT-
1 TATTTTTATTTATC
*
9515166 T-TTGTTATTCTAATAC
1 TATTTTTATT-T-AT-C
*
9515182 TATTATTATTTATC
1 TATTTTTATTTATC
9515196 TAATTTTTATTTATC
1 T-ATTTTTATTTATC
* *
9515211 TATTTATATTTCTAC
1 TATTTTTATTTAT-C
*
9515226 TATTATTATATT-TC
1 TATTTTTAT-TTATC
*
9515240 TATTTATTATATT-TT
1 TATTT-TTAT-TTATC
*
9515255 TATTTCTATTTAT
1 TATTTTTATTTAT
9515268 ATACTAATAT
Statistics
Matches: 92, Mismatches: 12, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
12 6 0.07
13 6 0.07
14 32 0.35
15 37 0.40
16 4 0.04
17 7 0.08
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.66
Consensus pattern (14 bp):
TATTTTTATTTATC
Found at i:9515220 original size:29 final size:28
Alignment explanation
Indices: 9515139--9515246 Score: 78
Period size: 29 Copynumber: 3.8 Consensus size: 28
9515129 TTATTCCTAT
*
9515139 TATTTTTATGTTTCTATTTATATTTAT-
1 TATTTTTATATTTCTATTTATATTTATC
* * * *
9515166 TTTGTTATTCTAATACTA-TTATTATTTATC
1 TAT-TT-TTATATTTCTATTTA-TATTTATC
*
9515196 TAATTTTTAT-TTATCTATTTATATTTCTAC
1 T-ATTTTTATATT-TCTATTTATATTTAT-C
*
9515226 TATTATTATATTTCTATTTAT
1 TATTTTTATATTTCTATTTAT
9515247 TATATTTTTA
Statistics
Matches: 61, Mismatches: 11, Indels: 16
0.69 0.12 0.18
Matches are distributed among these distances:
27 2 0.03
28 6 0.10
29 42 0.69
30 10 0.16
31 1 0.02
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (28 bp):
TATTTTTATATTTCTATTTATATTTATC
Found at i:9515252 original size:23 final size:24
Alignment explanation
Indices: 9515179--9515293 Score: 83
Period size: 21 Copynumber: 5.2 Consensus size: 24
9515169 GTTATTCTAA
9515179 TACTATTATTAT-TTATCTAATTT-T
1 TACTATTATTATATT-TCT-ATTTAT
* * *
9515203 TA-T-TTA-TCTATTTATATTT-C
1 TACTATTATTATATTTCTATTTAT
9515223 TACTATTATTATATTTCTATTTAT
1 TACTATTATTATATTTCTATTTAT
9515247 TA-TATT-TT-TATTTCTATTTAT
1 TACTATTATTATATTTCTATTTAT
*
9515268 ATACTAATATTAT-TTTC-A-TTAT
1 -TACTATTATTATATTTCTATTTAT
9515290 TACT
1 TACT
9515294 TTTTTCTTAT
Statistics
Matches: 75, Mismatches: 7, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
20 6 0.08
21 22 0.29
22 16 0.21
23 20 0.27
24 10 0.13
25 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.63
Consensus pattern (24 bp):
TACTATTATTATATTTCTATTTAT
Found at i:9515343 original size:4 final size:4
Alignment explanation
Indices: 9515334--9515358 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
9515324 TTTAACATTC
9515334 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
9515359 TACATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:9516617 original size:31 final size:32
Alignment explanation
Indices: 9516572--9516637 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
9516562 TTTTTTAGCT
*
9516572 AAATTTACTCATTAA-CTTCTT-AAAAAGAGTC
1 AAATTTACTCATTAATCTT-TTGAAAAAGAGCC
9516603 AAATTTGACT-ATTAATCTTTTGAAAAAGAGCC
1 AAATTT-ACTCATTAATCTTTTGAAAAAGAGCC
9516635 AAA
1 AAA
9516638 ATGATAATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (32 bp):
AAATTTACTCATTAATCTTTTGAAAAAGAGCC
Found at i:9516760 original size:22 final size:20
Alignment explanation
Indices: 9516735--9516791 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 20
9516725 AATTATGAAC
9516735 TTTTTATATATTTTTATTTTAA
1 TTTTTATATATTTTT-TTTT-A
*
9516757 TTTTGAT-TAATTTGTTTTTTA
1 TTTTTATAT-ATTT-TTTTTTA
9516778 TTTTTATA-ATTTTT
1 TTTTTATATATTTTT
9516792 GAATAATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
19 2 0.07
20 4 0.13
21 8 0.27
22 14 0.47
23 2 0.07
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.74
Consensus pattern (20 bp):
TTTTTATATATTTTTTTTTA
Found at i:9533682 original size:2 final size:2
Alignment explanation
Indices: 9533675--9533723 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
9533665 TAAGTGGAAA
9533675 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
9533717 AG AG AG A
1 AG AG AG A
9533724 AAACAAGTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9543252 original size:11 final size:11
Alignment explanation
Indices: 9543238--9543277 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
9543228 GTTTTCTCCA
*
9543238 TATTTTGCTAC
1 TATTTTGCTAT
*
9543249 TATTTTACTAT
1 TATTTTGCTAT
*
9543260 TATATTGCTAT
1 TATTTTGCTAT
9543271 TATTTTG
1 TATTTTG
9543278 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (11 bp):
TATTTTGCTAT
Found at i:9543364 original size:29 final size:31
Alignment explanation
Indices: 9543314--9543375 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
9543304 ATTTATTTTC
9543314 TTGTTAATTTTTTTATTTA-TTTAAAGGCAT
1 TTGTTAATTTTTTTATTTATTTTAAAGGCAT
*
9543344 TTGTTAATTTTTTTA-TTATTTTAGAGGCAT
1 TTGTTAATTTTTTTATTTATTTTAAAGGCAT
9543374 TT
1 TT
9543376 ACTTGTTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 3 0.10
30 27 0.90
ACGTcount: A:0.24, C:0.03, G:0.11, T:0.61
Consensus pattern (31 bp):
TTGTTAATTTTTTTATTTATTTTAAAGGCAT
Found at i:9554039 original size:21 final size:21
Alignment explanation
Indices: 9553977--9554040 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
9553967 GAATTCAAGT
*
9553977 TTTTATGTTATATAATAAAATA
1 TTTTATGTTAT-TAATAAAAAA
* ** *
9553999 TTTT-TATTACTGGATTAAAAA
1 TTTTATGTTA-TTAATAAAAAA
9554020 TTTTATGTTATTAATAAAAAA
1 TTTTATGTTATTAATAAAAAA
9554041 CATTAGTTAA
Statistics
Matches: 31, Mismatches: 9, Indels: 5
0.69 0.20 0.11
Matches are distributed among these distances:
21 22 0.71
22 9 0.29
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (21 bp):
TTTTATGTTATTAATAAAAAA
Found at i:9554771 original size:18 final size:19
Alignment explanation
Indices: 9554734--9554772 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
9554724 TTAATAATAT
*
9554734 AATAACGAAACAATAGTAA
1 AATAACGAAACAAAAGTAA
*
9554753 AATAATGAAA-AAAAGTAA
1 AATAACGAAACAAAAGTAA
9554771 AA
1 AA
9554773 AAAACAGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (19 bp):
AATAACGAAACAAAAGTAA
Found at i:9560049 original size:13 final size:14
Alignment explanation
Indices: 9560031--9560059 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
9560021 TCTTCTACTC
9560031 TACTCACATG-ATT
1 TACTCACATGTATT
9560044 TACTCACATGTATT
1 TACTCACATGTATT
9560058 TA
1 TA
9560060 AGATTTCCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (14 bp):
TACTCACATGTATT
Found at i:9562219 original size:54 final size:54
Alignment explanation
Indices: 9562135--9562244 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
9562125 TCACCGCCAC
*
9562135 AAATTCCTAACTCATCTAATCTCTTTTGTGACATCATTATCTAATGAGCTAATT
1 AAATTCCTAACTCATCTAATCTCTTATGTGACATCATTATCTAATGAGCTAATT
9562189 AAATTCCTAACTCATCTAATCTCTTATGTGACATCATTATCTAATGAGCTAATT
1 AAATTCCTAACTCATCTAATCTCTTATGTGACATCATTATCTAATGAGCTAATT
9562243 AA
1 AA
9562245 TTCTTTTGGG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (54 bp):
AAATTCCTAACTCATCTAATCTCTTATGTGACATCATTATCTAATGAGCTAATT
Found at i:9568911 original size:24 final size:24
Alignment explanation
Indices: 9568879--9568928 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
9568869 CTTGAGGCAG
9568879 AAAACACCTTATGCACAATGCTGC
1 AAAACACCTTATGCACAATGCTGC
9568903 AAAACACCTTATGCACAATGCTGC
1 AAAACACCTTATGCACAATGCTGC
9568927 AA
1 AA
9568929 TTGTAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.28, G:0.12, T:0.20
Consensus pattern (24 bp):
AAAACACCTTATGCACAATGCTGC
Found at i:9571189 original size:195 final size:196
Alignment explanation
Indices: 9570829--9571219 Score: 660
Period size: 195 Copynumber: 2.0 Consensus size: 196
9570819 ATGGAGAAAC
*
9570829 AAATTATGTTTAAAGTTAGATTTCACTCAATTTAAAATTTAATTGAAGTTTAATGTTATTATTGT
1 AAATTATGTTTAAAGTTAGATTTCACTCAATTTAAAATTTAATTGAAGTTTAATGTCATTATTGT
9570894 ATACCAAAAGGCTTTTAAAAAAATCTAATAATATAGTAACGAGTGACAAATTTTTTTAAGGGAAC
66 ATACCAAAAGGCTTTTAAAAAAATCTAATAATATAGTAACGAGTGACAAATTTTTTTAAGGGAAC
* * * *
9570959 AAATAATATTTAAGGTAGAGTTTTGTTATAGTGAAATTCTGTA-GAAT-TTTTTAGATCAATTAT
131 AAATAAAATTTAAGGTAGAGTTTTATTAGAGTGAAATTCTATAGGAATCTTTTTAGATCAATTAT
9571022 T
196 T
* *
9571023 AAATTATGTTTAGAGTTAAGATTTCACTCAATTTAGAATTTAATTGAAGTTTAATGTCATTATTG
1 AAATTATGTTTAAAGTT-AGATTTCACTCAATTTAAAATTTAATTGAAGTTTAATGTCATTATTG
* * *
9571088 TATACTAAAAGGCTTTTAAAACAATCTAATAATATAGTAATGAGTGACAAATTTTTTTAAGGGAA
65 TATACCAAAAGGCTTTTAAAAAAATCTAATAATATAGTAACGAGTGACAAATTTTTTTAAGGGAA
*
9571153 CAAATAAAATTTAAGGTGGAGTTTTATTAGAGTGAAATTCTATAGGAATCTTTTTAGATCAATTA
130 CAAATAAAATTTAAGGTAGAGTTTTATTAGAGTGAAATTCTATAGGAATCTTTTTAGATCAATTA
9571218 TT
195 TT
9571220 GTAGTTAAGA
Statistics
Matches: 183, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
194 16 0.09
195 146 0.80
196 4 0.02
197 17 0.09
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.40
Consensus pattern (196 bp):
AAATTATGTTTAAAGTTAGATTTCACTCAATTTAAAATTTAATTGAAGTTTAATGTCATTATTGT
ATACCAAAAGGCTTTTAAAAAAATCTAATAATATAGTAACGAGTGACAAATTTTTTTAAGGGAAC
AAATAAAATTTAAGGTAGAGTTTTATTAGAGTGAAATTCTATAGGAATCTTTTTAGATCAATTAT
T
Found at i:9572414 original size:20 final size:20
Alignment explanation
Indices: 9572389--9572438 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
9572379 TGGCTTAAAA
9572389 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
9572409 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
9572426 GTGGTAGTGGATT
1 TTGGTAGTGGATT
9572439 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:9577053 original size:20 final size:20
Alignment explanation
Indices: 9577028--9577077 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
9577018 TGGCTTAAAA
9577028 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
9577048 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
9577065 GTGGTAGTGGATT
1 TTGGTAGTGGATT
9577078 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:9590119 original size:14 final size:14
Alignment explanation
Indices: 9590100--9590139 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
9590090 TGAATTACTA
9590100 TAAAATAAATAATT
1 TAAAATAAATAATT
* *
9590114 TAAAATTAATACTT
1 TAAAATAAATAATT
*
9590128 AAAAATAAATAA
1 TAAAATAAATAA
9590140 CTTGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAAATAAATAATT
Found at i:9592617 original size:2 final size:2
Alignment explanation
Indices: 9592612--9592638 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9592602 AATTAAAAAA
9592612 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
9592639 AAGTGGGGTT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9593120 original size:30 final size:31
Alignment explanation
Indices: 9593079--9593149 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 31
9593069 ATATCTAAAC
* *
9593079 AATAACAACAAAATAGTGAAAAA-AATAAGA
1 AATAACAACAAAATAGTAAAAAATAACAAGA
*
9593109 AATAGCAACAAAATAGTAAAAAATAACAAGA
1 AATAACAACAAAATAGTAAAAAATAACAAGA
*
9593140 AA-AAAAACAA
1 AATAACAACAA
9593150 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 27 0.77
31 8 0.23
ACGTcount: A:0.72, C:0.08, G:0.08, T:0.11
Consensus pattern (31 bp):
AATAACAACAAAATAGTAAAAAATAACAAGA
Found at i:9593890 original size:37 final size:35
Alignment explanation
Indices: 9593841--9593961 Score: 97
Period size: 37 Copynumber: 3.4 Consensus size: 35
9593831 AATTTAATAC
*
9593841 TATTTTATATTATATTGATTTTAGGGTATTAGAGGT
1 TATTTTTTATTATATTGATTTTAGGGTATTA-AGGT
* * * ***
9593877 TATTTTCTTATTATACATCA-TTTA--AT-TTAATAC
1 TATTTT-TTATTATA-TTGATTTTAGGGTATTAAGGT
9593910 TATTTTTATATTATATTGATTTTAGGGTATTACAGGT
1 TATTTTT-TATTATATTGATTTTAGGGTATTA-AGGT
9593947 TATTTTTTTATTATA
1 TA-TTTTTTATTATA
9593962 GTTTTTTTTT
Statistics
Matches: 63, Mismatches: 13, Indels: 17
0.68 0.14 0.18
Matches are distributed among these distances:
32 3 0.05
33 18 0.29
34 3 0.05
35 2 0.03
36 9 0.14
37 21 0.33
38 7 0.11
ACGTcount: A:0.29, C:0.04, G:0.11, T:0.56
Consensus pattern (35 bp):
TATTTTTTATTATATTGATTTTAGGGTATTAAGGT
Found at i:9593890 original size:69 final size:70
Alignment explanation
Indices: 9593817--9593961 Score: 256
Period size: 70 Copynumber: 2.1 Consensus size: 70
9593807 AGAAAAATCA
*
9593817 ATTATACATCATTCAATTTAATACTA-TTTTATATTATATTGATTTTAGGGTATTAGAGGTTATT
1 ATTATACATCATTCAATTTAATACTATTTTTATATTATATTGATTTTAGGGTATTACAGGTTATT
9593881 TTCTT
66 TTCTT
*
9593886 ATTATACATCATTTAATTTAATACTATTTTTATATTATATTGATTTTAGGGTATTACAGGTTATT
1 ATTATACATCATTCAATTTAATACTATTTTTATATTATATTGATTTTAGGGTATTACAGGTTATT
*
9593951 TTTTT
66 TTCTT
9593956 ATTATA
1 ATTATA
9593962 GTTTTTTTTT
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
69 25 0.35
70 47 0.65
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.54
Consensus pattern (70 bp):
ATTATACATCATTCAATTTAATACTATTTTTATATTATATTGATTTTAGGGTATTACAGGTTATT
TTCTT
Found at i:9597870 original size:20 final size:21
Alignment explanation
Indices: 9597819--9597870 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 21
9597809 GATAATTTTT
*
9597819 TAAAGTTAAATAATCAAAACG
1 TAAACTTAAATAATCAAAACG
* **
9597840 TGAACTT-AATAAT-AAATTG
1 TAAACTTAAATAATCAAAACG
9597859 TAAACTTAAATA
1 TAAACTTAAATA
9597871 TAATTTACTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 10 0.40
20 10 0.40
21 5 0.20
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (21 bp):
TAAACTTAAATAATCAAAACG
Found at i:9612949 original size:15 final size:15
Alignment explanation
Indices: 9612931--9612981 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
9612921 TCACATTAAA
9612931 TATTTTTATATTATT
1 TATTTTTATATTATT
* *
9612946 TATTTTTA-ACATAAT
1 TATTTTTATA-TTATT
9612961 TATTTTTATAATTATT
1 TATTTTTAT-ATTATT
9612977 T-TTTT
1 TATTTT
9612982 ATTAGCTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 23 0.79
16 4 0.14
17 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTTATATTATT
Found at i:9614690 original size:25 final size:25
Alignment explanation
Indices: 9614656--9614706 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
9614646 CTTCAAGTAT
9614656 GTCATTTTCATAAAATCAGGAACTA
1 GTCATTTTCATAAAATCAGGAACTA
9614681 GTCATTTTCATAAAATCAGGAACTA
1 GTCATTTTCATAAAATCAGGAACTA
9614706 G
1 G
9614707 ACTTCTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (25 bp):
GTCATTTTCATAAAATCAGGAACTA
Found at i:9621166 original size:10 final size:10
Alignment explanation
Indices: 9621151--9621183 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
9621141 TTAGCAAACA
9621151 AAAAAAAAAG
1 AAAAAAAAAG
9621161 AAAAAAAAAG
1 AAAAAAAAAG
9621171 AAAAAAAAAG
1 AAAAAAAAAG
9621181 AAA
1 AAA
9621184 TGATAATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:9638462 original size:9 final size:8
Alignment explanation
Indices: 9638448--9638472 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
9638438 TTCTTTAAGC
9638448 AAAAAAAG
1 AAAAAAAG
9638456 AAAAAAAG
1 AAAAAAAG
9638464 AAAAAAAG
1 AAAAAAAG
9638472 A
1 A
9638473 GTTATTCGTA
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:9649581 original size:15 final size:15
Alignment explanation
Indices: 9649561--9649590 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
9649551 AATATTCATG
9649561 GTGAAATTAAGTAAT
1 GTGAAATTAAGTAAT
9649576 GTGAAATTAAGTAAT
1 GTGAAATTAAGTAAT
9649591 CAAGTGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (15 bp):
GTGAAATTAAGTAAT
Found at i:9653812 original size:29 final size:29
Alignment explanation
Indices: 9653757--9653812 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
9653747 AATCTACCCA
* * *
9653757 AAAATCTTGATTTTTAAGTTATCCTCACT
1 AAAATCTTGATCTTCAAGCTATCCTCACT
* *
9653786 AAAATCTTTATCTTCAAGCTATTCTCA
1 AAAATCTTGATCTTCAAGCTATCCTCA
9653813 AATGATTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (29 bp):
AAAATCTTGATCTTCAAGCTATCCTCACT
Found at i:9657694 original size:4 final size:4
Alignment explanation
Indices: 9657685--9657709 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
9657675 ATACCTACAA
9657685 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
9657710 TTTATCAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:9659416 original size:21 final size:22
Alignment explanation
Indices: 9659385--9659425 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
9659375 CTTACCATTT
9659385 TTAAAGTTAAAA-ATCAAAATCA
1 TTAAAGTTAAAACA-CAAAATCA
9659407 TTAAA-TTAAAACACAAAAT
1 TTAAAGTTAAAACACAAAAT
9659426 TACGTCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (22 bp):
TTAAAGTTAAAACACAAAATCA
Found at i:9660746 original size:13 final size:14
Alignment explanation
Indices: 9660728--9660757 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
9660718 TTACAATTAC
9660728 AATCATTT-TATAA
1 AATCATTTATATAA
9660741 AATCATTTATATAA
1 AATCATTTATATAA
9660755 AAT
1 AAT
9660758 TTGAAATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATCATTTATATAA
Found at i:9664654 original size:10 final size:11
Alignment explanation
Indices: 9664639--9664667 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
9664629 ACAATACATG
9664639 AAAACAGAG-C
1 AAAACAGAGCC
9664649 AAAACAGAGCC
1 AAAACAGAGCC
9664660 AAAACAGA
1 AAAACAGA
9664668 ATAAGGACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.62, C:0.21, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAACAGAGCC
Found at i:9670711 original size:12 final size:12
Alignment explanation
Indices: 9670694--9670719 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9670684 CTCTGTCACA
9670694 ATTAATATTATT
1 ATTAATATTATT
9670706 ATTAATATTATT
1 ATTAATATTATT
9670718 AT
1 AT
9670720 ATTTTATAAC
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTAATATTATT
Found at i:9674568 original size:11 final size:10
Alignment explanation
Indices: 9674551--9674580 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
9674541 GCCCTACAAA
9674551 TCCCCCCCCC
1 TCCCCCCCCC
9674561 TCCCCCCCCC
1 TCCCCCCCCC
9674571 TCCCCCCCCC
1 TCCCCCCCCC
9674581 AAAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.90, G:0.00, T:0.10
Consensus pattern (10 bp):
TCCCCCCCCC
Found at i:9675106 original size:15 final size:15
Alignment explanation
Indices: 9675081--9675117 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
9675071 AAGATATAAT
9675081 TTTATTATTTTAATAG
1 TTTATTATTTT-ATAG
9675097 TTTA-TATTTTATAG
1 TTTATTATTTTATAG
9675111 TTT-TTAT
1 TTTATTAT
9675118 AATATTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 10 0.50
15 6 0.30
16 4 0.20
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (15 bp):
TTTATTATTTTATAG
Found at i:9675144 original size:29 final size:29
Alignment explanation
Indices: 9675102--9675176 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
9675092 AATAGTTTAT
*
9675102 ATTTTA-TAGTTTTTATAATATTAAATTAAA
1 ATTTTATTA-TTTTTA-AAAATTAAATTAAA
*
9675132 ATTTTATTATTTTTAAAAATTAAATTATA
1 ATTTTATTATTTTTAAAAATTAAATTAAA
*
9675161 ATTTTATTATTATTAA
1 ATTTTATTATTTTTAA
9675177 TTTAAAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
29 27 0.66
30 12 0.29
31 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (29 bp):
ATTTTATTATTTTTAAAAATTAAATTAAA
Found at i:9675147 original size:22 final size:22
Alignment explanation
Indices: 9675112--9675189 Score: 59
Period size: 29 Copynumber: 3.3 Consensus size: 22
9675102 ATTTTATAGT
*
9675112 TTTTA-TAATATTAAATTAAAA
1 TTTTATTATTATTAAATTAAAA
*
9675133 TTTTATTATTTTTAAAAATTAAATTATAA
1 TTTTATTATTATT--AAATT--A--A-AA
*
9675162 TTTTATTATTATTAATTTAAAA
1 TTTTATTATTATTAAATTAAAA
9675184 TTTTAT
1 TTTTAT
9675190 AAATTATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 15
0.70 0.06 0.23
Matches are distributed among these distances:
21 5 0.11
22 13 0.29
23 1 0.02
24 5 0.11
25 1 0.02
26 1 0.02
27 4 0.09
28 1 0.02
29 14 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTATTATTATTAAATTAAAA
Found at i:9677174 original size:19 final size:21
Alignment explanation
Indices: 9677132--9677187 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
9677122 TATATTAACG
9677132 TTTAATTAATTTTTAAAAATAT
1 TTTAA-TAATTTTTAAAAATAT
* *
9677154 TTTCAT-ATTTTTAAATA-AT
1 TTTAATAATTTTTAAAAATAT
9677173 TTTAATAATTTTTAA
1 TTTAATAATTTTTAA
9677188 TTTTTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 7 0.23
20 18 0.60
21 1 0.03
22 4 0.13
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTAATAATTTTTAAAAATAT
Found at i:9677185 original size:10 final size:10
Alignment explanation
Indices: 9677132--9677188 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
9677122 TATATTAACG
9677132 TTTAATTAATT
1 TTTAA-TAATT
*
9677143 TTTAAAAATAT
1 TTTAATAAT-T
*
9677154 TTTCAT-ATT
1 TTTAATAATT
9677163 TTTAAATAA-T
1 TTT-AATAATT
9677173 TTTAATAATT
1 TTTAATAATT
9677183 TTTAAT
1 TTTAAT
9677189 TTTTTTGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
9 9 0.24
10 18 0.47
11 11 0.29
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTAATAATT
Found at i:9686993 original size:28 final size:28
Alignment explanation
Indices: 9686953--9687008 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
9686943 TCACCCCTAC
* *
9686953 CCTCAACATTTACAAAATTTGTCAATTT
1 CCTCAACATTTACAAAATCTATCAATTT
9686981 CCTCAACATTTACAAAATCTATCAATTT
1 CCTCAACATTTACAAAATCTATCAATTT
9687009 ACTCCTAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.38
Consensus pattern (28 bp):
CCTCAACATTTACAAAATCTATCAATTT
Found at i:9692700 original size:22 final size:22
Alignment explanation
Indices: 9692650--9692691 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
9692640 ATAATATGAC
*
9692650 AATAAAATAGTAGCAACATAAT
1 AATAAAATAGTAGCAAAATAAT
*
9692672 AATAAAATAGTAGTAAAATA
1 AATAAAATAGTAGCAAAATA
9692692 GTGAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (22 bp):
AATAAAATAGTAGCAAAATAAT
Found at i:9693597 original size:25 final size:25
Alignment explanation
Indices: 9693563--9693612 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
9693553 GTAGATGTAG
9693563 AACAAAATTTAAGAAAAATTAATAT
1 AACAAAATTTAAGAAAAATTAATAT
9693588 AACAAAATTTAAGAAAAATTAATAT
1 AACAAAATTTAAGAAAAATTAATAT
9693613 GATAATCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (25 bp):
AACAAAATTTAAGAAAAATTAATAT
Found at i:9696654 original size:23 final size:23
Alignment explanation
Indices: 9696628--9696695 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 23
9696618 GATGGATTAT
9696628 ATTATTCTGGTGTGTTTGGGAGG
1 ATTATTCTGGTGTGTTTGGGAGG
*
9696651 ATTATATGATACTGGTGTGTTTTGGAGG
1 A-T-TAT--T-CTGGTGTGTTTGGGAGG
*
9696679 ATTATACTGGTGTGTTT
1 ATTATTCTGGTGTGTTT
9696696 TGGTTGGACA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
23 12 0.32
24 1 0.03
25 3 0.08
26 3 0.08
27 2 0.05
28 17 0.45
ACGTcount: A:0.18, C:0.04, G:0.32, T:0.46
Consensus pattern (23 bp):
ATTATTCTGGTGTGTTTGGGAGG
Found at i:9696654 original size:28 final size:28
Alignment explanation
Indices: 9696601--9696684 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
9696591 CACTTTGTGC
*
9696601 TATTTTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
*
9696630 TATTCTGGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* *
9696658 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
9696685 CTGGTGTGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 33 0.66
29 17 0.34
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.48
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:9696919 original size:23 final size:23
Alignment explanation
Indices: 9696889--9696975 Score: 94
Period size: 21 Copynumber: 4.0 Consensus size: 23
9696879 GCTTTACTGA
*
9696889 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTTATGTGTCGTATT
* *
9696912 TCAGGCACCTTGTGTGTCGCA--
1 TCAGGCACCTTATGTGTCGTATT
* *
9696933 GCAGGCACCTCATGTGTCG--TT
1 TCAGGCACCTTATGTGTCGTATT
9696954 TCAGGCA-CTTATGTGTCGTATT
1 TCAGGCACCTTATGTGTCGTATT
9696976 CTGATCAGGT
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
20 10 0.19
21 22 0.42
22 2 0.04
23 18 0.35
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.36
Consensus pattern (23 bp):
TCAGGCACCTTATGTGTCGTATT
Found at i:9698831 original size:28 final size:28
Alignment explanation
Indices: 9698771--9698833 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
9698761 ATGGCACGAA
* *
9698771 ATATTGAGAATGGCACTTAATGTGCGAG
1 ATATTGAGAATGACACTTAATGTGCAAG
*
9698799 ATATTGAGAATGACACTTAGTGTGCAA-
1 ATATTGAGAATGACACTTAATGTGCAAG
9698826 AGTATTGA
1 A-TATTGA
9698834 ATGATTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 1 0.03
28 30 0.97
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (28 bp):
ATATTGAGAATGACACTTAATGTGCAAG
Found at i:9698949 original size:39 final size:39
Alignment explanation
Indices: 9698906--9699117 Score: 329
Period size: 39 Copynumber: 5.5 Consensus size: 39
9698896 GACTTTATAA
*
9698906 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGT
1 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGC
* *
9698945 TGGTGTTATATCCGAGCTAAGTCCTGAAGGCATTCATGC
1 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGC
*
9698984 TGGT-TTATATTCGGGCTAAGT-CTCGAAGGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCT-GAAGGCATTCGTGC
* *
9699022 TGGTGTTATATCCGGGCTAAGTCCCGAAAGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGC
* *
9699061 TGGTGTTATATCCGGGCTAAGCCCCGAAGGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGC
9699100 TGGTGTTATATCCGGGCT
1 TGGTGTTATATCCGGGCT
9699118 TAAAGTCCCG
Statistics
Matches: 159, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
37 2 0.01
38 32 0.20
39 124 0.78
40 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (39 bp):
TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGC
Found at i:9699005 original size:77 final size:78
Alignment explanation
Indices: 9698906--9699127 Score: 322
Period size: 77 Copynumber: 2.8 Consensus size: 78
9698896 GACTTTATAA
* *
9698906 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGTTGGTGTTATATCCGAGCTAAGTCCTG
1 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCGAGCTAAGTCCCG
*
9698971 AAGGCATTCATGC
66 AAAGCATTCATGC
* *
9698984 TGGT-TTATATTCGGGCTAAGT-CTCGAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCC
1 TGGTGTTATATCCGGGCTAAGTCCT-GAAGGCATTCGTGCTGGTGTTATATCCGAGCTAAGTCCC
*
9699047 GAAAGCATTCGTGC
65 GAAAGCATTCATGC
* * *
9699061 TGGTGTTATATCCGGGCTAAGCCCCGAAGGCATTCGTGCTGGTGTTATATCCGGGCTTAAAGTCC
1 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCGAGC-T-AAGTCC
9699126 CG
64 CG
9699128 CATGCTTTGT
Statistics
Matches: 130, Mismatches: 9, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
76 2 0.02
77 68 0.52
78 50 0.38
79 2 0.02
80 8 0.06
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (78 bp):
TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCGAGCTAAGTCCCG
AAAGCATTCATGC
Found at i:9715539 original size:18 final size:18
Alignment explanation
Indices: 9715516--9715551 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
9715506 TGGCTTCACC
9715516 TTAAATACAATCACAGCA
1 TTAAATACAATCACAGCA
9715534 TTAAATACAATCACAGCA
1 TTAAATACAATCACAGCA
9715552 GAGTAATTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22
Consensus pattern (18 bp):
TTAAATACAATCACAGCA
Found at i:9715684 original size:24 final size:24
Alignment explanation
Indices: 9715656--9715703 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
9715646 TTGTTATCAG
9715656 TAAGATGTTAAATTAAGTAAAAAT
1 TAAGATGTTAAATTAAGTAAAAAT
9715680 TAAGATGTTAAATTAAGTAAAAAT
1 TAAGATGTTAAATTAAGTAAAAAT
9715704 GGTGTACCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.33
Consensus pattern (24 bp):
TAAGATGTTAAATTAAGTAAAAAT
Found at i:9715694 original size:13 final size:13
Alignment explanation
Indices: 9715656--9715696 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
9715646 TTGTTATCAG
9715656 TAAGATGTTAAAT
1 TAAGATGTTAAAT
**
9715669 TAAG-T-AAAAAT
1 TAAGATGTTAAAT
9715680 TAAGATGTTAAAT
1 TAAGATGTTAAAT
9715693 TAAG
1 TAAG
9715697 TAAAAATGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
11 8 0.36
12 2 0.09
13 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (13 bp):
TAAGATGTTAAAT
Found at i:9718521 original size:16 final size:16
Alignment explanation
Indices: 9718500--9718540 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
9718490 TAATGCCAAA
9718500 ATAAAATTAT-TAAGAT
1 ATAAAATTATATAA-AT
9718516 ATAAAATTCATATAAAT
1 ATAAAATT-ATATAAAT
9718533 -TAAAATTA
1 ATAAAATTA
9718541 CTTTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 15 0.65
17 4 0.17
18 3 0.13
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (16 bp):
ATAAAATTATATAAAT
Found at i:9727769 original size:42 final size:42
Alignment explanation
Indices: 9727710--9727794 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
9727700 TGTGACACTA
*
9727710 ACTTAATTAGGGGCTTAAATAATAGTATAGTATAAATAATAT
1 ACTTAATTAGGGACTTAAATAATAGTATAGTATAAATAATAT
9727752 ACTTAATTAGGGACTTAAATAATAGTATAGTATAAATAATAT
1 ACTTAATTAGGGACTTAAATAATAGTATAGTATAAATAATAT
9727794 A
1 A
9727795 TATGATATCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.35
Consensus pattern (42 bp):
ACTTAATTAGGGACTTAAATAATAGTATAGTATAAATAATAT
Found at i:9728251 original size:20 final size:20
Alignment explanation
Indices: 9728206--9728251 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
9728196 TAATTCCAAT
9728206 ATCTTTTATAATATTGTATA
1 ATCTTTTATAATATTGTATA
*
9728226 AT-TTTTAATAAT-TTTTATA
1 ATCTTTT-ATAATATTGTATA
*
9728245 TTCTTTT
1 ATCTTTT
9728252 TTATAAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (20 bp):
ATCTTTTATAATATTGTATA
Found at i:9728991 original size:24 final size:24
Alignment explanation
Indices: 9728940--9728991 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
9728930 AGATTTAGAA
*
9728940 TTTTTGTTTACTCTTGTAGCACGG
1 TTTTTGTCTACTCTTGTAGCACGG
*
9728964 TTTTTGTCTAC-CTTGTAGCACGT
1 TTTTTGTCTACTCTTGTAGCACGG
9728987 TTTTT
1 TTTTT
9728992 AGTTTGATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.54
Consensus pattern (24 bp):
TTTTTGTCTACTCTTGTAGCACGG
Found at i:9729315 original size:13 final size:13
Alignment explanation
Indices: 9729297--9729333 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
9729287 TTTTTTTCTA
9729297 CAATTGTATGATT
1 CAATTGTATGATT
9729310 CAATTGTATGATT
1 CAATTGTATGATT
*
9729323 CAATTGAATGA
1 CAATTGTATGA
9729334 ATTAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (13 bp):
CAATTGTATGATT
Found at i:9731212 original size:90 final size:90
Alignment explanation
Indices: 9730506--9731200 Score: 1039
Period size: 90 Copynumber: 7.7 Consensus size: 90
9730496 GTGGACCCAT
* * * * *
9730506 GGTTTGCGCATTGACTAGAGCAGGAGAAACAGTTTGCATGCTAGTAGCTGAGCCAGTTGAAGGGA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGA
* *
9730571 TCCCTGAAGCAGTGGAAGGCTGCAA
66 TCCCTGAAGCAGTAGAACGCTGCAA
*
9730596 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGGAGGGA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGA
* *
9730661 TCCCTGAAGCAGTGGAAGGCTGCAA
66 TCCCTGAAGCAGTAGAACGCTGCAA
* * * * * * * *
9730686 GGTTTGTGCATTGGCTGCAGCAAGTGAAACAGTTTGCACAGTAGAAGTTGAGCTAGTTGAAGGTA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGA
*
9730751 TCCCTGAAGTAGTAGAACGCTGCAA
66 TCCCTGAAGCAGTAGAACGCTGCAA
* * * *
9730776 AGTTTGTGCATTGACTACAACAGGTGAAACAGTTTGCACAGTAGAAGCTGAGCCAGTTGAAGGGA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGA
*
9730841 TCCCTGAAGTAGTAGAACGCTGCAA
66 TCCCTGAAGCAGTAGAACGCTGCAA
** *
9730866 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATGGTAGAAGCTGAGCCAGTTGAAGGAA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGA
9730931 TCCCTGAAGCAGTAGAACGCTGCAA
66 TCCCTGAAGCAGTAGAACGCTGCAA
* *
9730956 TGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAGTAGAAGCTGAGCCAGTTGAAGGGA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGA
9731021 TCCCTGAAGCAGTAGAACGCTGCAA
66 TCCCTGAAGCAGTAGAACGCTGCAA
** * * *
9731046 TATTTGTGCATTAACTACAGCGGGTGAAACAGTTCGCATACTAGAAGCTGAGCCAGTTGAAGGGA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGA
9731111 TCCCTGAAGCAGTAGAACGCTGCAA
66 TCCCTGAAGCAGTAGAACGCTGCAA
** * * *
9731136 TATTTGTGCATTAACTACAGCGGGTGAAACAGTTCGCATACTAGAAGCTGAGCCAGTTGAAGGGA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGA
9731201 GACCAGAAGC
Statistics
Matches: 565, Mismatches: 40, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 565 1.00
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.23
Consensus pattern (90 bp):
GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGA
TCCCTGAAGCAGTAGAACGCTGCAA
Found at i:9732550 original size:47 final size:48
Alignment explanation
Indices: 9732481--9732574 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
9732471 GTATTGAAAG
9732481 TATAATCTCTCCAAATCTC-AAAATAGTCTCCTTACCACAAGTATAGA
1 TATAATCTCTCCAAATCTCAAAAATAGTCTCCTTACCACAAGTATAGA
9732528 TATAATCTCTCCAAATCTCAAAAATAGTCTCCTTACCACAAGTATAG
1 TATAATCTCTCCAAATCTCAAAAATAGTCTCCTTACCACAAGTATAG
9732575 GTTAAATAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 19 0.41
48 27 0.59
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (48 bp):
TATAATCTCTCCAAATCTCAAAAATAGTCTCCTTACCACAAGTATAGA
Found at i:9747042 original size:42 final size:42
Alignment explanation
Indices: 9746794--9747034 Score: 349
Period size: 42 Copynumber: 5.7 Consensus size: 42
9746784 TTAAATCATT
*
9746794 ATCTCCATCATCCTTAGCTTTCCTACTAGAAGATCTAGTACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
* * *
9746836 ATCTCCATCATCCTTAGCCTTCCTACTAGATGATCTGGTACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
* * *
9746878 ATCTCCATCATTCTTAGCTTTCCTACTAGAGGATCTGGTACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
* * * *
9746920 ACCTCCATCATCCTCAGCTTTCCTACTAGGCGATCTAATACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
* *
9746962 ATCTTCGTCATCCTTAGCTTTCCTA-TCAGACGATCTAGTACC
1 ATCTCCATCATCCTTAGCTTTCCTACT-AGACGATCTAGTACC
9747004 ATCTCCATCATCCTTAGCTTTCCTACTAGAC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGAC
9747035 AACCTAGTGC
Statistics
Matches: 176, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
41 1 0.01
42 174 0.99
43 1 0.01
ACGTcount: A:0.23, C:0.33, G:0.11, T:0.34
Consensus pattern (42 bp):
ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
Found at i:9747979 original size:24 final size:24
Alignment explanation
Indices: 9747935--9747980 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
9747925 CTATTTTATT
* *
9747935 ATTTATTTTTATTAATATTAAATA
1 ATTTATTTTAATAAATATTAAATA
*
9747959 ATTTATTTTAATAAATTTTAAA
1 ATTTATTTTAATAAATATTAAA
9747981 AATAATATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTATTTTAATAAATATTAAATA
Found at i:9750561 original size:24 final size:24
Alignment explanation
Indices: 9750534--9750605 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
9750524 ATTTAATTTG
9750534 ATTAAGGTTTATTGGGTTTTAGTT
1 ATTAAGGTTTATTGGGTTTTAGTT
* * * *
9750558 ATTAAAG-TGATT-TGATTT-G--
1 ATTAAGGTTTATTGGGTTTTAGTT
9750577 ATTAAGGTTTATTGGGTTTTAGTT
1 ATTAAGGTTTATTGGGTTTTAGTT
9750601 ATTAA
1 ATTAA
9750606 ATAAAGTATA
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
19 6 0.17
20 4 0.11
21 5 0.14
22 5 0.14
23 4 0.11
24 11 0.31
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.51
Consensus pattern (24 bp):
ATTAAGGTTTATTGGGTTTTAGTT
Found at i:9750576 original size:43 final size:43
Alignment explanation
Indices: 9750514--9750606 Score: 168
Period size: 43 Copynumber: 2.1 Consensus size: 43
9750504 ATTAACCTAA
9750514 ATTAAGAGTGATTTAATTTGATTAAGGTTTATTGGGTTTTAGTT
1 ATTAA-AGTGATTTAATTTGATTAAGGTTTATTGGGTTTTAGTT
*
9750558 ATTAAAGTGATTTGATTTGATTAAGGTTTATTGGGTTTTAGTT
1 ATTAAAGTGATTTAATTTGATTAAGGTTTATTGGGTTTTAGTT
9750601 ATTAAA
1 ATTAAA
9750607 TAAAGTATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 43 0.90
44 5 0.10
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (43 bp):
ATTAAAGTGATTTAATTTGATTAAGGTTTATTGGGTTTTAGTT
Found at i:9751811 original size:13 final size:15
Alignment explanation
Indices: 9751781--9751812 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
9751771 TCATTTCATG
9751781 CATTTCATCAATAAT
1 CATTTCATCAATAAT
9751796 CATTTCAT-AA-AAT
1 CATTTCATCAATAAT
9751809 CATT
1 CATT
9751813 ATTTCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (15 bp):
CATTTCATCAATAAT
Found at i:9753543 original size:7 final size:7
Alignment explanation
Indices: 9753526--9753612 Score: 61
Period size: 7 Copynumber: 11.9 Consensus size: 7
9753516 TTTACTTTAC
9753526 TATAT-A
1 TATATAA
*
9753532 TATAAAA
1 TATATAA
9753539 TATAATAA
1 TAT-ATAA
9753547 TAATATAA
1 T-ATATAA
9753555 TATATAA
1 TATATAA
9753562 TATATAA
1 TATATAA
9753569 TA-ATACA
1 TATATA-A
*
9753576 TAATAAACA
1 T-ATATA-A
* *
9753585 TATTTAT
1 TATATAA
*
9753592 TATTTAA
1 TATATAA
9753599 TAATATAA
1 T-ATATAA
9753607 TATATA
1 TATATA
9753613 TTAAATTTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
6 7 0.11
7 33 0.50
8 19 0.29
9 7 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (7 bp):
TATATAA
Found at i:9753548 original size:3 final size:3
Alignment explanation
Indices: 9753540--9753581 Score: 50
Period size: 3 Copynumber: 13.3 Consensus size: 3
9753530 TATATAAAAT
9753540 ATA ATA ATA AT- ATA ATA TATA ATA TATA ATA ATA CATA ATA A
1 ATA ATA ATA ATA ATA ATA -ATA ATA -ATA ATA ATA -ATA ATA A
9753582 ACATATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 2 0.06
3 24 0.69
4 9 0.26
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:9754022 original size:14 final size:14
Alignment explanation
Indices: 9753998--9754034 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
9753988 CACTATTTTA
*
9753998 ATTTATTTAATAAT
1 ATTTATATAATAAT
*
9754012 ATTTTTATAATAAT
1 ATTTATATAATAAT
9754026 ATTTATATA
1 ATTTATATA
9754035 TCTAAGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTATATAATAAT
Found at i:9760565 original size:18 final size:18
Alignment explanation
Indices: 9760544--9760606 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 18
9760534 AAAAAGTTAT
9760544 AAAAATATTTTAAAATAA
1 AAAAATATTTTAAAATAA
*
9760562 AAAAA-A--TTAAAATTA
1 AAAAATATTTTAAAATAA
* * *
9760577 TAAAATAGTTATAAATTATA
1 AAAAATA-TTTTAAAATA-A
9760597 AAAAATATTT
1 AAAAATATTT
9760607 CTTTAACATT
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
15 12 0.36
16 1 0.03
17 1 0.03
18 5 0.15
19 7 0.21
20 7 0.21
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
AAAAATATTTTAAAATAA
Found at i:9760768 original size:24 final size:26
Alignment explanation
Indices: 9760717--9760768 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 26
9760707 TCTATTTTAA
* *
9760717 AATAATATAACAACAAATACAAATTT
1 AATAATATAACAACAAATAAAAAATT
*
9760743 AATAAT-TAA-AATAAATAAAAAATT
1 AATAATATAACAACAAATAAAAAATT
9760767 AA
1 AA
9760769 ATAAAATACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 14 0.61
25 3 0.13
26 6 0.26
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (26 bp):
AATAATATAACAACAAATAAAAAATT
Found at i:9762908 original size:18 final size:19
Alignment explanation
Indices: 9762876--9762911 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
9762866 AATGTTTATT
*
9762876 TACTTAATTTTTTAATTTA
1 TACTTAATTTATTAATTTA
9762895 TACTT-ATTTATTAATTT
1 TACTTAATTTATTAATTT
9762912 TTTAAAATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
TACTTAATTTATTAATTTA
Found at i:9764576 original size:46 final size:46
Alignment explanation
Indices: 9764508--9764595 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 46
9764498 AAAATTAAAT
* * *
9764508 TTTATATTTTTATGATAGTTAAAATA-TAATTTTATTTTTTTAGTAG
1 TTTATATTTTTATAATAGTTAAAAAATTAA-ATTATTTTTTTAGTAG
9764554 TTTATATTTTTATAATTA-TTAAAAAATTAAATTATTTTTTTA
1 TTTATATTTTTATAA-TAGTTAAAAAATTAAATTATTTTTTTA
9764596 TATTTTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
46 32 0.86
47 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (46 bp):
TTTATATTTTTATAATAGTTAAAAAATTAAATTATTTTTTTAGTAG
Found at i:9764607 original size:29 final size:30
Alignment explanation
Indices: 9764555--9764634 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 30
9764545 TTTTAGTAGT
* *
9764555 TTATATTTTTATAATTATTAAAAAATTAAA
1 TTATTTTTTTATAATTATTAAAAAATAAAA
* * *
9764585 TTATTTTTTTAT-ATTTTTTAAAAGTAAAA
1 TTATTTTTTTATAATTATTAAAAAATAAAA
* * *
9764614 ATATTATTTTATCATTATTAA
1 TTATTTTTTTATAATTATTAA
9764635 GCCCCTACTG
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 23 0.57
30 17 0.43
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (30 bp):
TTATTTTTTTATAATTATTAAAAAATAAAA
Found at i:9772566 original size:53 final size:53
Alignment explanation
Indices: 9772495--9772623 Score: 161
Period size: 53 Copynumber: 2.4 Consensus size: 53
9772485 TCATACCAAA
* * * *
9772495 GCCATATCCCAGAC-ATGGTTTTATACGGAATCACATTATCACATTATATCGAT
1 GCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTATCACATTACACCGAT
* * *
9772548 GCCATAGCGCAGCTATGGTCTTATACGGAGTCACATTATCACATTGCACCGAT
1 GCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATTACACCGAT
* *
9772601 GCTATAGCCCAGCTACGGTCTTA
1 GCCATAGCCCAGCTATGGTCTTA
9772624 AATGGGCACA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
52 1 0.02
53 64 0.98
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (53 bp):
GCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATTACACCGAT
Found at i:9803585 original size:5 final size:5
Alignment explanation
Indices: 9803575--9803604 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
9803565 AATAATTAAG
9803575 TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT
9803605 AAAAGAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:9806054 original size:5 final size:5
Alignment explanation
Indices: 9806044--9806083 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
9806034 TGTTTCTTTT
9806044 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
9806084 CTTAATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:9808115 original size:46 final size:46
Alignment explanation
Indices: 9808048--9808217 Score: 215
Period size: 46 Copynumber: 3.7 Consensus size: 46
9808038 TGTAACCCGC
*
9808048 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCACAT
9808094 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C-A-TTCACAT
* **
9808144 -C-TCAA--GAACTCGGACTCAACTCAACGAGTTCGAACATTCACAT
1 CCAT-AAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCACAT
9808187 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
9808218 TTCAGATGCT
Statistics
Matches: 109, Mismatches: 4, Indels: 22
0.81 0.03 0.16
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
44 4 0.04
45 1 0.01
46 59 0.54
47 26 0.24
48 2 0.02
49 4 0.04
50 4 0.04
51 2 0.02
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCACAT
Found at i:9808168 original size:93 final size:93
Alignment explanation
Indices: 9808056--9808226 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
9808046 GCCCATAAGT
** *
9808056 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
*
9808121 CGAGCTCGGATGCCTAGTTACATCTCAA
66 CGAGCTCAGATGCCTAGTTACATCTCAA
*
9808149 GAACTCGGACTCAACTCAACGAGTTCGAACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
*
9808214 CGAGTTCAGATGC
66 CGAGCTCAGATGC
9808227 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCAGATGCCTAGTTACATCTCAA
Found at i:9812449 original size:17 final size:16
Alignment explanation
Indices: 9812410--9812471 Score: 54
Period size: 18 Copynumber: 3.7 Consensus size: 16
9812400 TTTTTTTTTC
*
9812410 AAAATATATCTTATC-T
1 AAAA-ATATTTTATCTT
*
9812426 AATAATACTTTTATCTT
1 AAAAATA-TTTTATCTT
*
9812443 AAAAATATTTTTTATCTC
1 AAAAATA--TTTTATCTT
9812461 AAAAATATTTT
1 AAAAATATTTT
9812472 TTAGAAGCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 3 0.08
16 13 0.34
17 7 0.18
18 15 0.39
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
AAAAATATTTTATCTT
Found at i:9812457 original size:18 final size:18
Alignment explanation
Indices: 9812434--9812474 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
9812424 CTAATAATAC
*
9812434 TTTTATCTTAAAAATATT
1 TTTTATCTCAAAAATATT
9812452 TTTTATCTCAAAAATATT
1 TTTTATCTCAAAAATATT
9812470 TTTTA
1 TTTTA
9812475 GAAGCAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTATCTCAAAAATATT
Found at i:9812472 original size:17 final size:16
Alignment explanation
Indices: 9812410--9812472 Score: 63
Period size: 17 Copynumber: 3.7 Consensus size: 16
9812400 TTTTTTTTTC
*
9812410 AAAATATATCTTATCTA
1 AAAATAT-TTTTATCTA
* *
9812427 ATAATACTTTTATCTTA
1 AAAATATTTTTATC-TA
9812444 AAAATATTTTTTATCTCA
1 AAAATA-TTTTTATCT-A
9812462 AAAATATTTTT
1 AAAATATTTTT
9812473 TAGAAGCAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 6 0.16
17 18 0.47
18 14 0.37
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAATATTTTTATCTA
Found at i:9815242 original size:18 final size:20
Alignment explanation
Indices: 9815221--9815265 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
9815211 TATCAAGTTA
9815221 ATAATT-TGATATAA-ATAT
1 ATAATTATGATATAATATAT
* *
9815239 ATAATTATTATTTAATATAT
1 ATAATTATGATATAATATAT
9815259 ATAATTA
1 ATAATTA
9815266 ATATAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 6 0.26
19 6 0.26
20 11 0.48
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATAATTATGATATAATATAT
Found at i:9815272 original size:18 final size:19
Alignment explanation
Indices: 9815229--9815272 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
9815219 TAATAATTTG
9815229 ATATAA-ATATATAATTATT
1 ATATAATATATATAATTA-T
*
9815248 ATTTAATATATATAATTA-
1 ATATAATATATATAATTAT
9815266 ATATAAT
1 ATATAAT
9815273 TATGTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 6 0.27
19 5 0.23
20 11 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATAATATATATAATTAT
Found at i:9821732 original size:15 final size:17
Alignment explanation
Indices: 9821696--9821734 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
9821686 TTGATAAAAC
9821696 TAAAATATAACATTACT
1 TAAAATATAACATTACT
*
9821713 TAAAATTTAA-ATTA-T
1 TAAAATATAACATTACT
9821728 TAAAATA
1 TAAAATA
9821735 ATTTGTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 7 0.35
16 4 0.20
17 9 0.45
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAATATAACATTACT
Found at i:9833198 original size:20 final size:20
Alignment explanation
Indices: 9833159--9833198 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
9833149 AATTGTATAT
* *
9833159 TTTTTTAAAATAAATTCAAA
1 TTTTTAAAAATAAATACAAA
*
9833179 TTTTTAAAAATATATACAAA
1 TTTTTAAAAATAAATACAAA
9833199 CTTAAAAGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTTTAAAAATAAATACAAA
Found at i:9833205 original size:18 final size:18
Alignment explanation
Indices: 9833182--9833216 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
9833172 ATTCAAATTT
9833182 TTAAAA-ATATATACAAAC
1 TTAAAAGAT-TATACAAAC
9833200 TTAAAAGATTATACAAA
1 TTAAAAGATTATACAAA
9833217 ATTATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.60, C:0.09, G:0.03, T:0.29
Consensus pattern (18 bp):
TTAAAAGATTATACAAAC
Found at i:9837224 original size:13 final size:13
Alignment explanation
Indices: 9837208--9837258 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
9837198 TAAACCAAAT
9837208 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
9837221 TTTTTC-ACAGCAC
1 -TTTTCAAAAGCAC
*
9837234 TTTTTAAAAGCAC
1 TTTTCAAAAGCAC
*
9837247 TTTGCAAAAGCA
1 TTTTCAAAAGCA
9837259 TTGCCAAACT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 4 0.13
13 22 0.71
14 5 0.16
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:9838432 original size:7 final size:7
Alignment explanation
Indices: 9838420--9838444 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
9838410 AAAAATACTT
9838420 TATATAA
1 TATATAA
9838427 TATATAA
1 TATATAA
9838434 TATATAA
1 TATATAA
9838441 TATA
1 TATA
9838445 ATATCTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TATATAA
Found at i:9838888 original size:30 final size:29
Alignment explanation
Indices: 9838819--9838888 Score: 70
Period size: 30 Copynumber: 2.3 Consensus size: 29
9838809 TTAAATAATT
* *
9838819 TATAATTTATAATTTTTAAAGGATTAAAT
1 TATAATTTATAATTTTAAAAGGATTAAAG
* *
9838848 TA-AATTTTTATAATTTTAAAAGAGGTTAAGG
1 TATAA--TTTATAATTTTAAAAG-GATTAAAG
9838879 TATAATTTAT
1 TATAATTTAT
9838889 TTTTATTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
28 2 0.06
29 2 0.06
30 20 0.61
31 7 0.21
32 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (29 bp):
TATAATTTATAATTTTAAAAGGATTAAAG
Found at i:9852806 original size:38 final size:38
Alignment explanation
Indices: 9852755--9852830 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
9852745 TAATTGATTT
9852755 GCCATGGAAAAGATGGAATCATAGAGAAATCATACATA
1 GCCATGGAAAAGATGGAATCATAGAGAAATCATACATA
*
9852793 GCCATGGAAAAGATGGAGTCATAGAGAAATCATACATA
1 GCCATGGAAAAGATGGAATCATAGAGAAATCATACATA
9852831 AGTGAGTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.46, C:0.13, G:0.22, T:0.18
Consensus pattern (38 bp):
GCCATGGAAAAGATGGAATCATAGAGAAATCATACATA
Found at i:9856328 original size:21 final size:21
Alignment explanation
Indices: 9856302--9856342 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9856292 AGACGAGCAA
* *
9856302 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
9856323 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
9856343 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:9862978 original size:20 final size:21
Alignment explanation
Indices: 9862955--9863009 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
9862945 AAGGATATAA
9862955 ATTTTGAAATTTTT-ATAAA-T
1 ATTTTGAAATTTTTGA-AAATT
*
9862975 ATTTTGAATTTTTTGAAAATT
1 ATTTTGAAATTTTTGAAAATT
9862996 ATTTTGAAATTTTT
1 ATTTTGAAATTTTT
9863010 TTTGTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTTTGAAATTTTTGAAAATT
Found at i:9862995 original size:11 final size:10
Alignment explanation
Indices: 9862956--9863010 Score: 60
Period size: 10 Copynumber: 5.4 Consensus size: 10
9862946 AGGATATAAA
9862956 TTTTGAAATT
1 TTTTGAAATT
*
9862966 TTTAT-AAATA
1 TTT-TGAAATT
9862976 TTTTG-AATT
1 TTTTGAAATT
9862985 TTTTGAAAATT
1 TTTTG-AAATT
9862996 ATTTTGAAATT
1 -TTTTGAAATT
9863007 TTTT
1 TTTT
9863011 TTGTAAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 9 0.24
10 14 0.37
11 10 0.26
12 5 0.13
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (10 bp):
TTTTGAAATT
Found at i:9863028 original size:23 final size:24
Alignment explanation
Indices: 9862983--9863029 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
9862973 ATATTTTGAA
**
9862983 TTTTTTGAAAATTATTTTGAAATT
1 TTTTTTGAAAATTATTTCAAAATT
*
9863007 TTTTTTGTAAA-TATTTCAAAATT
1 TTTTTTGAAAATTATTTCAAAATT
9863030 GACACCGACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.57
Consensus pattern (24 bp):
TTTTTTGAAAATTATTTCAAAATT
Found at i:9863085 original size:18 final size:18
Alignment explanation
Indices: 9863062--9863100 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
9863052 ACACCAAACT
*
9863062 ATTATTCAAGTTATTTGA
1 ATTATTCAAGTTATTTAA
9863080 ATTATTCAAGTTATTTAA
1 ATTATTCAAGTTATTTAA
9863098 ATT
1 ATT
9863101 GTAAAATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (18 bp):
ATTATTCAAGTTATTTAA
Found at i:9865835 original size:2 final size:2
Alignment explanation
Indices: 9865828--9865852 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9865818 TTCTTTTCAT
9865828 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 A
9865853 TATATATACT
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:9865921 original size:23 final size:23
Alignment explanation
Indices: 9865862--9865921 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
9865852 ATATATATAC
9865862 TAAAT-AA-AATAA-TAAAATAA
1 TAAATAAATAATAATTAAAATAA
* * *
9865882 T-AATAAATATCTTATTAAAATAT
1 TAAATAAATA-ATAATTAAAATAA
9865905 TAAATAAATAATAATTA
1 TAAATAAATAATAATTA
9865922 TCTAATTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.10
20 3 0.10
21 1 0.03
22 2 0.07
23 13 0.43
24 8 0.27
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAATAAATAATAATTAAAATAA
Found at i:9865944 original size:34 final size:31
Alignment explanation
Indices: 9865856--9865932 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
9865846 ACACACATAT
*
9865856 ATATACTAAATAAAATAATAAAAT-AATAATAA
1 ATAT-CTAATTAAAAT-ATAAAATAAATAATAA
* *
9865888 ATATCTTATTAAAATATTAAATAAATAATAA
1 ATATCTAATTAAAATATAAAATAAATAATAA
*
9865919 TTATCTAATTAAAA
1 ATATCTAATTAAAA
9865933 AACTATAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 6 0.15
31 29 0.74
32 4 0.10
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (31 bp):
ATATCTAATTAAAATATAAAATAAATAATAA
Found at i:9868679 original size:14 final size:13
Alignment explanation
Indices: 9868658--9868687 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
9868648 GTAAAATATT
9868658 TTTCGGAAAATGA
1 TTTCGGAAAATGA
9868671 TTTCTGGAAAATGA
1 TTTC-GGAAAATGA
9868685 TTT
1 TTT
9868688 ACTTTTCTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (13 bp):
TTTCGGAAAATGA
Found at i:9868703 original size:19 final size:20
Alignment explanation
Indices: 9868671--9868714 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
9868661 CGGAAAATGA
9868671 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
*
9868691 TTTCTGG-AAATGATTTATT
1 TTTCTGGAAAATGATTTACT
9868710 TTTCT
1 TTTCT
9868715 AGTTTTTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.25, C:0.09, G:0.14, T:0.52
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:9870804 original size:24 final size:24
Alignment explanation
Indices: 9870669--9870830 Score: 98
Period size: 24 Copynumber: 6.8 Consensus size: 24
9870659 ATCAACCGAT
* **
9870669 TTCGCACACATAGTGCTAAACAAA
1 TTCGCACACATAGTGCCATTCAAA
* * *
9870693 TTCACACACATAGTGCCATGCTACA
1 TTCGCACACATAGTGCCATTC-AAA
* * *
9870718 CT-GCACACATAATGCC-TTGAAGA
1 TTCGCACACATAGTGCCATTCAA-A
* * ** * * *
9870741 TTCACTCATGTATTGACATCCAAA
1 TTCGCACACATAGTGCCATTCAAA
9870765 -TCAGCACACATAGTGCCATTC-AA
1 TTC-GCACACATAGTGCCATTCAAA
*
9870788 TTCCGCATACATAGTGCCATTCAAA
1 TT-CGCACACATAGTGCCATTCAAA
*
9870813 TTCGCACACTTAGTGCCA
1 TTCGCACACATAGTGCCA
9870831 ATGTTGACCC
Statistics
Matches: 100, Mismatches: 30, Indels: 16
0.68 0.21 0.11
Matches are distributed among these distances:
22 1 0.01
23 7 0.07
24 81 0.81
25 11 0.11
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.25
Consensus pattern (24 bp):
TTCGCACACATAGTGCCATTCAAA
Found at i:9873107 original size:32 final size:32
Alignment explanation
Indices: 9873066--9873143 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
9873056 TCAATCATTG
*
9873066 CAATATCCAACAAGCTT-AAAACATAACAAATT
1 CAATATCCAACAA-ATTCAAAACATAACAAATT
* * *
9873098 CAATATCCAACAAATTCAAGACATAATAATTT
1 CAATATCCAACAAATTCAAAACATAACAAATT
*
9873130 CAAAATCCAACAAA
1 CAATATCCAACAAA
9873144 CTAGAATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 2 0.05
32 38 0.95
ACGTcount: A:0.54, C:0.22, G:0.03, T:0.22
Consensus pattern (32 bp):
CAATATCCAACAAATTCAAAACATAACAAATT
Found at i:9878190 original size:25 final size:25
Alignment explanation
Indices: 9878143--9878190 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
9878133 CGACTAGAAG
*
9878143 ATGAAGAAAGGAAGAAGGAAAAGGA
1 ATGAAGAAAGGAAGAAGAAAAAGGA
*
9878168 ATGAAGAACGGAA-AAGAAGAAAG
1 ATGAAGAAAGGAAGAAGAA-AAAG
9878191 ACTTAACTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.60, C:0.02, G:0.33, T:0.04
Consensus pattern (25 bp):
ATGAAGAAAGGAAGAAGAAAAAGGA
Done.