Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 147 of 172
Found at i:48281543 original size:11 final size:11
Alignment explanation
Indices: 48281527--48281572 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 11
48281517 TTCTTTATAT
48281527 ATTTTTTTGAA
1 ATTTTTTTGAA
48281538 ATTTTTTTG-A
1 ATTTTTTTGAA
48281548 ATTTTTTAT-AA
1 ATTTTTT-TGAA
*
48281559 A-TATTTTGAA
1 ATTTTTTTGAA
48281569 ATTT
1 ATTT
48281573 AAAAATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
9 1 0.03
10 15 0.52
11 13 0.45
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (11 bp):
ATTTTTTTGAA
Found at i:48282372 original size:17 final size:20
Alignment explanation
Indices: 48282352--48282396 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
48282342 ACTATTTAAT
48282352 TAAATAA-AT-TTA-TTTTA
1 TAAATAATATATTAGTTTTA
*
48282369 TAAAATAATGTATTAGTTTTA
1 T-AAATAATATATTAGTTTTA
48282390 TAAATAA
1 TAAATAA
48282397 GAATTCTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 6 0.26
19 1 0.04
20 9 0.39
21 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (20 bp):
TAAATAATATATTAGTTTTA
Found at i:48284085 original size:18 final size:20
Alignment explanation
Indices: 48284059--48284099 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
48284049 GAAATATTTA
*
48284059 TTTTGATGT-TTTTA-GTAT
1 TTTTGATGTATTATATGTAT
*
48284077 TTTTTATGTATTATATGTAT
1 TTTTGATGTATTATATGTAT
48284097 TTT
1 TTT
48284100 AAAATTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 8 0.42
19 4 0.21
20 7 0.37
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (20 bp):
TTTTGATGTATTATATGTAT
Found at i:48284130 original size:12 final size:12
Alignment explanation
Indices: 48284100--48284132 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
48284090 TATGTATTTT
48284100 AAAATT-ATATA
1 AAAATTAATATA
48284111 AAAA-TAATATA
1 AAAATTAATATA
48284122 AAAATTAATAT
1 AAAATTAATAT
48284133 TGGTAGGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:48298947 original size:310 final size:310
Alignment explanation
Indices: 48298385--48299004 Score: 1231
Period size: 310 Copynumber: 2.0 Consensus size: 310
48298375 TTACTTTAGT
48298385 TTTATATTGGTATAAGTGGATTCCTCCCTTTATTAGGGTTGAAATTCCAACAAGAATAAAAATCA
1 TTTATATTGGTATAAGTGGATTCCTCCCTTTATTAGGGTTGAAATTCCAACAAGAATAAAAATCA
48298450 AAACTATGTTGAACATTGCACTCAATAAAAGAGCTAAAATCATATTTCGATTAAAAGATTTGTCT
66 AAACTATGTTGAACATTGCACTCAATAAAAGAGCTAAAATCATATTTCGATTAAAAGATTTGTCT
48298515 AATATATTGAAACTCTTCCCTAAATTTAAACTTTGCTCCTATCAATTAAGGTTTTGGATAAAAAA
131 AATATATTGAAACTCTTCCCTAAATTTAAACTTTGCTCCTATCAATTAAGGTTTTGGATAAAAAA
48298580 TTATAGAGAATAAATTTGATCTTTAATATAAATAAATTGTATATTTTGAGTAAAATTAGGTTAAT
196 TTATAGAGAATAAATTTGATCTTTAATATAAATAAATTGTATATTTTGAGTAAAATTAGGTTAAT
48298645 ATGGTGTTTATAAAATTAAAAAATATATTATGAAAAATATAATAAATAAA
261 ATGGTGTTTATAAAATTAAAAAATATATTATGAAAAATATAATAAATAAA
*
48298695 TTTATATTGGTATAAGTGGATTCCTCCCTTTCTTAGGGTTGAAATTCCAACAAGAATAAAAATCA
1 TTTATATTGGTATAAGTGGATTCCTCCCTTTATTAGGGTTGAAATTCCAACAAGAATAAAAATCA
48298760 AAACTATGTTGAACATTGCACTCAATAAAAGAGCTAAAATCATATTTCGATTAAAAGATTTGTCT
66 AAACTATGTTGAACATTGCACTCAATAAAAGAGCTAAAATCATATTTCGATTAAAAGATTTGTCT
48298825 AATATATTGAAACTCTTCCCTAAATTTAAACTTTGCTCCTATCAATTAAGGTTTTGGATAAAAAA
131 AATATATTGAAACTCTTCCCTAAATTTAAACTTTGCTCCTATCAATTAAGGTTTTGGATAAAAAA
48298890 TTATAGAGAATAAATTTGATCTTTAATATAAATAAATTGTATATTTTGAGTAAAATTAGGTTAAT
196 TTATAGAGAATAAATTTGATCTTTAATATAAATAAATTGTATATTTTGAGTAAAATTAGGTTAAT
48298955 ATGGTGTTTATAAAATTAAAAAATATATTATGAAAAATATAATAAATAAA
261 ATGGTGTTTATAAAATTAAAAAATATATTATGAAAAATATAATAAATAAA
48299005 GAGAAGGAAA
Statistics
Matches: 309, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
310 309 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (310 bp):
TTTATATTGGTATAAGTGGATTCCTCCCTTTATTAGGGTTGAAATTCCAACAAGAATAAAAATCA
AAACTATGTTGAACATTGCACTCAATAAAAGAGCTAAAATCATATTTCGATTAAAAGATTTGTCT
AATATATTGAAACTCTTCCCTAAATTTAAACTTTGCTCCTATCAATTAAGGTTTTGGATAAAAAA
TTATAGAGAATAAATTTGATCTTTAATATAAATAAATTGTATATTTTGAGTAAAATTAGGTTAAT
ATGGTGTTTATAAAATTAAAAAATATATTATGAAAAATATAATAAATAAA
Found at i:48300335 original size:6 final size:6
Alignment explanation
Indices: 48300314--48300347 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
48300304 AACCCTAATA
*
48300314 ACCTAT A-CTAT GCCTAT ACCTAT ACCTAT ACCTA
1 ACCTAT ACCTAT ACCTAT ACCTAT ACCTAT ACCTA
48300348 ACCCAGTGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.32
Consensus pattern (6 bp):
ACCTAT
Found at i:48302636 original size:22 final size:21
Alignment explanation
Indices: 48302593--48302640 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
48302583 TTAGGGTTTT
48302593 ATAATTTTATAAAAATATTTA
1 ATAATTTTATAAAAATATTTA
* *
48302614 ACTAATTTT-TAGAATTATATTA
1 A-TAATTTTATAAAAATAT-TTA
48302636 ATAAT
1 ATAAT
48302641 AAAATATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
ATAATTTTATAAAAATATTTA
Found at i:48306175 original size:19 final size:18
Alignment explanation
Indices: 48306139--48306178 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
48306129 TTTCCACTCG
*
48306139 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
48306157 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
48306176 TTT
1 TTT
48306179 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:48307259 original size:13 final size:13
Alignment explanation
Indices: 48307241--48307292 Score: 86
Period size: 14 Copynumber: 3.8 Consensus size: 13
48307231 ACTAGCTCTC
48307241 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
48307254 TTTTTTTTTTCACAA
1 -TTTTTTTTTCA-AA
48307269 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
48307282 TTTTTTTTTCA
1 TTTTTTTTTCA
48307293 CAACTTGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
13 13 0.35
14 22 0.59
15 2 0.05
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:48307274 original size:28 final size:27
Alignment explanation
Indices: 48307241--48307295 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
48307231 ACTAGCTCTC
48307241 TTTTTTTTTCAAATTTTTTTTTTCACAA
1 TTTTTTTTTCAAA-TTTTTTTTTCACAA
48307269 TTTTTTTTTCAAATTTTTTTTTCACAA
1 TTTTTTTTTCAAATTTTTTTTTCACAA
48307296 CTTGATATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTTTTTTCAAATTTTTTTTTCACAA
Found at i:48307351 original size:12 final size:12
Alignment explanation
Indices: 48307334--48307377 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
48307324 GGAAACTAGT
48307334 TTTTTTTTCGAA
1 TTTTTTTTCGAA
*
48307346 TTTTTTTTTCAAA
1 -TTTTTTTTCGAA
* *
48307359 TTTTTTTTTGAG
1 TTTTTTTTCGAA
48307371 TTTTTTT
1 TTTTTTT
48307378 CGAGAAACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.75
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:48307351 original size:13 final size:13
Alignment explanation
Indices: 48307333--48307377 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
48307323 TGGAAACTAG
48307333 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
*
48307346 TTTTTTTTTCAAA
1 TTTTTTTTTCGAA
*
48307359 TTTTTTTTT-GAG
1 TTTTTTTTTCGAA
48307371 TTTTTTT
1 TTTTTTT
48307378 CGAGAAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 8 0.28
13 21 0.72
ACGTcount: A:0.13, C:0.04, G:0.07, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:48307961 original size:54 final size:54
Alignment explanation
Indices: 48307897--48308004 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
48307887 AAAAAGTTCT
*
48307897 CTCTCTATGGCTGATTACATCTATTTATAATGCTAAAACAAGGTAACCGAATGG
1 CTCTCTATGGCTGATTACATCTATTTATAATGCTAAAACAAGGTAACCAAATGG
48307951 CTCTCTATGGCTGATTACATCTATTTATAATGCTAAAACAAGGTAACCAAATGG
1 CTCTCTATGGCTGATTACATCTATTTATAATGCTAAAACAAGGTAACCAAATGG
48308005 TCAAAAACAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (54 bp):
CTCTCTATGGCTGATTACATCTATTTATAATGCTAAAACAAGGTAACCAAATGG
Found at i:48315709 original size:34 final size:34
Alignment explanation
Indices: 48315671--48315766 Score: 83
Period size: 34 Copynumber: 2.8 Consensus size: 34
48315661 GAAGATATAC
*
48315671 ATACATAAAATAATATGAAATCAATAATACATAT
1 ATACATAAAATAATATGAAATCAATAATAAATAT
* *
48315705 ATACACATAAA-AA-ATGAAA--AATTAAAGGAAATAT
1 ATACATA-AAATAATATGAAATCAA-T-AA-TAAATAT
* *
48315739 TTACATAAAATAATAGGAAATCAATAAT
1 ATACATAAAATAATATGAAATCAATAAT
48315767 GTATACTTAG
Statistics
Matches: 47, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
31 2 0.04
32 1 0.02
33 11 0.23
34 20 0.43
35 10 0.21
36 1 0.02
37 2 0.04
ACGTcount: A:0.60, C:0.07, G:0.06, T:0.26
Consensus pattern (34 bp):
ATACATAAAATAATATGAAATCAATAATAAATAT
Found at i:48317423 original size:133 final size:133
Alignment explanation
Indices: 48317115--48317412 Score: 434
Period size: 133 Copynumber: 2.2 Consensus size: 133
48317105 GCCACCTTCG
* * * * *
48317115 ATCTGCTCCATAGTCGATACAGGGAAATAAGATCTGTTATTTTCAGTCTGTTTCCTTGCTACCTC
1 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTTATTTTCAGTCTGCTTCCTTACTACCTC
* * * *
48317180 AAGAAGATAAGACTTGCATATTGAGCCTGCTCCACTACAACTTCAGAGAGATAATGCTAGTGGCT
66 AAGAAGATAAGACTTGCATATTGAACCTACTCCACTACAACTTCAGAGAGATAAGGCTAGTGACT
48317245 AAA
131 AAA
* * *
48317248 ATCTGTTCCATAGCCGATACATGAAGATAAGATCTGTTATTTTCAGTCTGCTTCCTTACTACCTT
1 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTTATTTTCAGTCTGCTTCCTTACTACCTC
* * * *
48317313 AGGAAGATAAGACTTGCATATTGAACCTACTCCACTTCAACTTCAGGGAGATAAGGCTGGTGACT
66 AAGAAGATAAGACTTGCATATTGAACCTACTCCACTACAACTTCAGAGAGATAAGGCTAGTGACT
48317378 AAA
131 AAA
* *
48317381 ATTTGCTCTATAGCCGATACATGGAGATAAGA
1 ATCTGCTCCATAGCCGATACATGGAGATAAGA
48317413 CTCGCCATTT
Statistics
Matches: 145, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
133 145 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (133 bp):
ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTTATTTTCAGTCTGCTTCCTTACTACCTC
AAGAAGATAAGACTTGCATATTGAACCTACTCCACTACAACTTCAGAGAGATAAGGCTAGTGACT
AAA
Found at i:48317525 original size:177 final size:176
Alignment explanation
Indices: 48317254--48317824 Score: 793
Period size: 177 Copynumber: 3.2 Consensus size: 176
48317244 TAAAATCTGT
* * * *
48317254 TCCATAGCCGATACATGAAGATAAGATCTGTTATTTTCAGTCTGCTTCCTTACTACCTTAGGAAG
1 TCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCC-TACAACTTTAGGAAG
* * * *
48317319 ATAAGACTTGCATATTGAACCTACTCCACTTCAACTTCAGGGAGATAAGGCTGGTGACTAAAATT
65 ATAAGACTTGCATATTGAACCTGCTCCACTTCAACCTCAGGGAGATAAGGCTGGTGGCTAAAATC
* *
48317384 TGCTCTATAGCCGATACATGGAGATAAGACTCGCCATTTTTGATCTA
130 TGCTCCATAGCCGATACATGGAGATAAGACTCACCATTTTTGATCTA
*
48317431 CTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTACTTCCTACAACTTTAGGAAG
1 -TCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTACAACTTTAGGAAG
* * ** *
48317496 ATAAGACTTGCATATTGAGCCTGCTCCACTGCAAGGTCAAGGAGATAAGGCTGGTGGCTAAAATC
65 ATAAGACTTGCATATTGAACCTGCTCCACTTCAACCTCAGGGAGATAAGGCTGGTGGCTAAAATC
* * *
48317561 TACTCCGTAGCCGATACATGGAGATAAGACTCACCATTTTCGATCTGA
130 TGCTCCATAGCCGATACATGGAGATAAGACTCACCATTTTTGATCT-A
* * * *
48317609 TCCATAGCCGATACATAGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAGGAATA
1 TCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTACAACTTTAGGAAGA
* * * * * * *
48317674 TAAGACTTGTATCTTCAACCTGCT-CTCTTGCTACCTCAGAGAGATAAAGCTGGTGGCTAAAATC
66 TAAGACTTGCATATTGAACCTGCTCCACTT-CAACCTCAGGGAGATAAGGCTGGTGGCTAAAATC
*
48317738 TGCTCCATAGCCGATACATGGAGATAAGACTCACCATTTTTGATCTGT
130 TGCTCCATAGCCGATACATGGAGATAAGACTCACCATTTTTGATCT-A
* *
48317786 TCCATAGCCGATACATGGAGATAAGTTCTATAATTTTCA
1 TCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCA
48317825 TCGATATCGC
Statistics
Matches: 349, Mismatches: 42, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
176 3 0.01
177 299 0.86
178 47 0.13
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (176 bp):
TCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTACAACTTTAGGAAGA
TAAGACTTGCATATTGAACCTGCTCCACTTCAACCTCAGGGAGATAAGGCTGGTGGCTAAAATCT
GCTCCATAGCCGATACATGGAGATAAGACTCACCATTTTTGATCTA
Found at i:48322484 original size:21 final size:21
Alignment explanation
Indices: 48322459--48322504 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
48322449 GAAATGCAAG
48322459 AAAAGAAAATTTACTCA-AGAT
1 AAAAGAAAATTTACTCAGA-AT
* *
48322480 AAAAGAATATTTGCTCAGAAT
1 AAAAGAAAATTTACTCAGAAT
48322501 AAAA
1 AAAA
48322505 CATGAAAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.24
Consensus pattern (21 bp):
AAAAGAAAATTTACTCAGAAT
Found at i:48327680 original size:47 final size:47
Alignment explanation
Indices: 48327545--48327715 Score: 166
Period size: 47 Copynumber: 3.6 Consensus size: 47
48327535 ATAGTAAAAC
* * * *
48327545 TATGGTCTTGCACA-TAGTCACATATCACATACCGAGGCCATAGCCCAGC
1 TATGGTCTTACACAGTAG-CACATATCAC--ACCGATGCCATATCCCAGA
* * * *
48327594 CATGGTCTTACAC-GGATCACATATCACACTGATGCCATATCCCAGA
1 TATGGTCTTACACAGTAGCACATATCACACCGATGCCATATCCCAGA
* * *
48327640 TATGGTCTTATACAGTAGCACATATCACACCGATGTCATATCCCGGA
1 TATGGTCTTACACAGTAGCACATATCACACCGATGCCATATCCCAGA
* ** *
48327687 TATGGTCTTATATGGAAGCACATATCACA
1 TATGGTCTTACACAGTAGCACATATCACA
48327716 TTTCTCCGAA
Statistics
Matches: 102, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
46 26 0.25
47 54 0.53
48 10 0.10
49 12 0.12
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (47 bp):
TATGGTCTTACACAGTAGCACATATCACACCGATGCCATATCCCAGA
Found at i:48329844 original size:36 final size:36
Alignment explanation
Indices: 48329790--48329858 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
48329780 TTAAATCTAT
* * *
48329790 GCCACGGCTTCGCTCATGATATGATATCTATCCTGA
1 GCCACAGCTTCACCCATGATATGATATCTATCCTGA
*
48329826 GCCACAGCTTCACCCATGATATGATCTCTATCC
1 GCCACAGCTTCACCCATGATATGATATCTATCC
48329859 CTGACCTGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.29
Consensus pattern (36 bp):
GCCACAGCTTCACCCATGATATGATATCTATCCTGA
Found at i:48331302 original size:22 final size:23
Alignment explanation
Indices: 48331276--48331321 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
48331266 CAACCAAACC
48331276 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
48331298 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
48331321 A
1 A
48331322 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:48331327 original size:23 final size:23
Alignment explanation
Indices: 48331283--48331327 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
48331273 ACCAATTCAA
*
48331283 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
48331306 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
48331328 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:48334464 original size:63 final size:63
Alignment explanation
Indices: 48334360--48334485 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
48334350 TTATTTCTAA
48334360 AAACCGAGTCGTAAATATTTTTATAAATATTTACGAAGTGGCAATAAGATGGTATTAAAGTTT
1 AAACCGAGTCGTAAATATTTTTATAAATATTTACGAAGTGGCAATAAGATGGTATTAAAGTTT
*
48334423 AAACTGAGTCGTAAATATTTTTATAAATATTTACGAAGTGGCAATAAGATGGTATTAAAGTTT
1 AAACCGAGTCGTAAATATTTTTATAAATATTTACGAAGTGGCAATAAGATGGTATTAAAGTTT
48334486 CGTTGAAAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (63 bp):
AAACCGAGTCGTAAATATTTTTATAAATATTTACGAAGTGGCAATAAGATGGTATTAAAGTTT
Found at i:48337774 original size:29 final size:29
Alignment explanation
Indices: 48337731--48337887 Score: 129
Period size: 29 Copynumber: 5.4 Consensus size: 29
48337721 CCGTAACCGA
* *
48337731 GCACTGTGTGGGCGAGATCGGTTGTTGAG
1 GCACTGTGTGTGCGAGATCCGTTGTTGAG
* ** *
48337760 GCACTGTGTGTGCGAGTTCCGTAATCGA-
1 GCACTGTGTGTGCGAGATCCGTTGTTGAG
*
48337788 GCACTGTGTGTGCGAGATCAGTTGTTGAG
1 GCACTGTGTGTGCGAGATCCGTTGTTGAG
* * **** *
48337817 GCACTGTGTGTGTGAGTTCCG-TAACAAA
1 GCACTGTGTGTGCGAGATCCGTTGTTGAG
* * *
48337845 GCACTGTGTGTGCAAGATCGGTTGTTGGG
1 GCACTGTGTGTGCGAGATCCGTTGTTGAG
48337874 GCACTAAGTGTGTG
1 GCACT--GTGTGTG
48337888 AAATGAGATC
Statistics
Matches: 95, Mismatches: 29, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
28 42 0.44
29 46 0.48
31 7 0.07
ACGTcount: A:0.18, C:0.16, G:0.37, T:0.29
Consensus pattern (29 bp):
GCACTGTGTGTGCGAGATCCGTTGTTGAG
Found at i:48337789 original size:57 final size:56
Alignment explanation
Indices: 48337701--48337888 Score: 277
Period size: 57 Copynumber: 3.3 Consensus size: 56
48337691 AAGTGAACAT
*
48337701 AGGCACTGTGTGTGTGAGTTCCGTAACCGAGCACTGTGTGGGCGAGATCGGTTGTTG
1 AGGCACTGTGTGTGTGAGTTCCGTAA-CGAGCACTGTGTGTGCGAGATCGGTTGTTG
* *
48337758 AGGCACTGTGTGTGCGAGTTCCGTAATCGAGCACTGTGTGTGCGAGATCAGTTGTTG
1 AGGCACTGTGTGTGTGAGTTCCGTAA-CGAGCACTGTGTGTGCGAGATCGGTTGTTG
* *
48337815 AGGCACTGTGTGTGTGAGTTCCGTAACAAAGCACTGTGTGTGCAAGATCGGTTGTTG
1 AGGCACTGTGTGTGTGAGTTCCGTAAC-GAGCACTGTGTGTGCGAGATCGGTTGTTG
* **
48337872 GGGCACTAAGTGTGTGA
1 AGGCACTGTGTGTGTGA
48337889 AATGAGATCA
Statistics
Matches: 119, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
56 1 0.01
57 118 0.99
ACGTcount: A:0.19, C:0.16, G:0.36, T:0.29
Consensus pattern (56 bp):
AGGCACTGTGTGTGTGAGTTCCGTAACGAGCACTGTGTGTGCGAGATCGGTTGTTG
Found at i:48337798 original size:28 final size:28
Alignment explanation
Indices: 48337703--48337857 Score: 141
Period size: 28 Copynumber: 5.5 Consensus size: 28
48337693 GTGAACATAG
* *
48337703 GCACTGTGTGTGTGAGTTCCGTAACCGA
1 GCACTGTGTGTGCGAGTTCCGTAATCGA
* * * ** *
48337731 GCACTGTGTGGGCGAGATCGGTTGTTGA
1 GCACTGTGTGTGCGAGTTCCGTAATCGA
48337759 GGCACTGTGTGTGCGAGTTCCGTAATCGA
1 -GCACTGTGTGTGCGAGTTCCGTAATCGA
* * ** *
48337788 GCACTGTGTGTGCGAGATCAGTTGTTGA
1 GCACTGTGTGTGCGAGTTCCGTAATCGA
* *
48337816 GGCACTGTGTGTGTGAGTTCCGTAA-CAAA
1 -GCACTGTGTGTGCGAGTTCCGTAATC-GA
48337845 GCACTGTGTGTGC
1 GCACTGTGTGTGC
48337858 AAGATCGGTT
Statistics
Matches: 97, Mismatches: 27, Indels: 6
0.75 0.21 0.05
Matches are distributed among these distances:
28 55 0.57
29 42 0.43
ACGTcount: A:0.17, C:0.18, G:0.35, T:0.29
Consensus pattern (28 bp):
GCACTGTGTGTGCGAGTTCCGTAATCGA
Found at i:48342870 original size:28 final size:28
Alignment explanation
Indices: 48342830--48342908 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
48342820 GCAATCAAAT
* * *
48342830 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
48342858 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
* *
48342886 ATGACACTTAGTGTGCAAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
48342909 CGAATGATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:48350227 original size:24 final size:25
Alignment explanation
Indices: 48350195--48350241 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
48350185 TGGAATGGAT
48350195 TTTACTTTTTAAA-ATTCTTTTACAA
1 TTTACTTTTTAAATATT-TTTTACAA
48350220 TTTA-TTTTTAAATATTTTTTAC
1 TTTACTTTTTAAATATTTTTTAC
48350242 TAATAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTACTTTTTAAATATTTTTTACAA
Found at i:48350363 original size:14 final size:14
Alignment explanation
Indices: 48350344--48350386 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 14
48350334 TCTATTTATA
48350344 CATTATATGGATTT
1 CATTATATGGATTT
*
48350358 CATTATAATAGATTT
1 CATTAT-ATGGATTT
*
48350373 CATTATCTGGATTT
1 CATTATATGGATTT
48350387 TATATAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (14 bp):
CATTATATGGATTT
Found at i:48351209 original size:10 final size:10
Alignment explanation
Indices: 48351180--48351239 Score: 70
Period size: 10 Copynumber: 6.0 Consensus size: 10
48351170 TAATTTTAGG
48351180 ATTTAT-TTT
1 ATTTATCTTT
*
48351189 CATTCATCTTT
1 -ATTTATCTTT
48351200 ATTTATCTTT
1 ATTTATCTTT
*
48351210 AATTATCTTT
1 ATTTATCTTT
48351220 ATTTAT-TTGT
1 ATTTATCTT-T
48351230 ATTTATCTTT
1 ATTTATCTTT
48351240 TAGAATTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
9 2 0.05
10 36 0.84
11 5 0.12
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.67
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:48355142 original size:12 final size:13
Alignment explanation
Indices: 48355114--48355146 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
48355104 TTATTTCTTT
48355114 TTCTCCATCTACC
1 TTCTCCATCTACC
*
48355127 TTCTCC-TCTTCC
1 TTCTCCATCTACC
48355139 TTCTCCAT
1 TTCTCCAT
48355147 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:48355803 original size:28 final size:28
Alignment explanation
Indices: 48355763--48355827 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
48355753 ATGTACTAGA
*
48355763 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
48355791 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
48355819 ATACCCCTA
1 ATACCCCTA
48355828 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:48355991 original size:27 final size:27
Alignment explanation
Indices: 48355933--48356022 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 27
48355923 AGGAAGCGTC
48355933 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
48355961 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
48355988 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
48356017 CTGGTG
1 CTGGTG
48356023 ACTCTGTCAT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:48356041 original size:55 final size:56
Alignment explanation
Indices: 48355933--48356047 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
48355923 AGGAAGCGTC
* *
48355933 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * * *
48355988 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCATAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
48356044 CTGG
1 CTGG
48356048 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.59
56 20 0.39
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:48359678 original size:5 final size:5
Alignment explanation
Indices: 48359663--48359715 Score: 67
Period size: 5 Copynumber: 10.8 Consensus size: 5
48359653 TAACCCAATT
48359663 TTTTA -TTTA TTTTA TTTTA TTTTA TTTTA CTATTTA --TTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -T-TTTA TTTTA TTTTA TTTTA
48359712 TTTT
1 TTTT
48359716 TTTGGATGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
3 3 0.07
4 4 0.09
5 31 0.72
6 1 0.02
7 4 0.09
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:48361300 original size:10 final size:10
Alignment explanation
Indices: 48361285--48361334 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
48361275 TAATCTTAGG
48361285 ATTTAT-TTT
1 ATTTATCTTT
48361294 CATTTATCTTT
1 -ATTTATCTTT
*
48361305 AATTATCTTT
1 ATTTATCTTT
48361315 ATTTAT-TTGT
1 ATTTATCTT-T
48361325 ATTTATCTTT
1 ATTTATCTTT
48361335 TAAAATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:48369249 original size:42 final size:41
Alignment explanation
Indices: 48369163--48369300 Score: 161
Period size: 42 Copynumber: 3.3 Consensus size: 41
48369153 CATGTAGTAT
* * *
48369163 AATTCGTATTCTATTTTGATTTTTT-TTGAAATAATAGTTC
1 AATTAGTATTATATTTTGATTTTTTATTGAAATAATAGTTA
48369203 AATTAGTATTATATTTTGATTCTTTTATTGAAATAATAGTTA
1 AATTAGTATTATATTTTGATT-TTTTATTGAAATAATAGTTA
* *
48369245 AATTAGTATTGTATTTTTATTTTTATTTTATTGAAATAATAGTTA
1 AATTAGTATTATATTTTGA---TT-TTTTATTGAAATAATAGTTA
* *
48369290 TATAAGTATTA
1 AATTAGTATTA
48369301 AATGAAAAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
40 19 0.23
41 4 0.05
42 31 0.37
45 30 0.36
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.54
Consensus pattern (41 bp):
AATTAGTATTATATTTTGATTTTTTATTGAAATAATAGTTA
Found at i:48370185 original size:20 final size:20
Alignment explanation
Indices: 48370160--48370197 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48370150 TAAAATAAAG
* *
48370160 ATATTTCAAAATTTATATAA
1 ATATTTAAAAATATATATAA
48370180 ATATTTAAAAATATATAT
1 ATATTTAAAAATATATAT
48370198 TCTTATGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATTTAAAAATATATATAA
Found at i:48372494 original size:25 final size:26
Alignment explanation
Indices: 48372465--48372523 Score: 102
Period size: 25 Copynumber: 2.3 Consensus size: 26
48372455 TTTTTGAATT
48372465 TATATTATAAGATGTAAGATCACT-A
1 TATATTATAAGATGTAAGATCACTGA
48372490 TATATTATAAGATGTAAGATCACTGA
1 TATATTATAAGATGTAAGATCACTGA
*
48372516 TTTATTAT
1 TATATTAT
48372524 GTGTATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 24 0.75
26 8 0.25
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.41
Consensus pattern (26 bp):
TATATTATAAGATGTAAGATCACTGA
Found at i:48372979 original size:18 final size:18
Alignment explanation
Indices: 48372956--48373017 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
48372946 TGTATTAAAT
48372956 AAATATTATAATAAGTAA
1 AAATATTATAATAAGTAA
* *
48372974 AAATATGTAATGTATTAA-TAT
1 AAATAT-T-A--TAATAAGTAA
*
48372995 AAATATTATTATAAGTAA
1 AAATATTATAATAAGTAA
48373013 AAATA
1 AAATA
48373018 AGAGTGGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
17 4 0.12
18 13 0.38
19 2 0.06
20 2 0.06
21 8 0.24
22 5 0.15
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.37
Consensus pattern (18 bp):
AAATATTATAATAAGTAA
Found at i:48373475 original size:13 final size:13
Alignment explanation
Indices: 48373459--48373485 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
48373449 TAAATTTTAT
48373459 AAAAATAATATAA
1 AAAAATAATATAA
48373472 AAAAATAATATAA
1 AAAAATAATATAA
48373485 A
1 A
48373486 GTACTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAAATAATATAA
Found at i:48386040 original size:21 final size:21
Alignment explanation
Indices: 48386014--48386054 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
48386004 AGACGAGCAA
* *
48386014 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
48386035 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
48386055 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:48388953 original size:96 final size:96
Alignment explanation
Indices: 48388789--48388980 Score: 375
Period size: 96 Copynumber: 2.0 Consensus size: 96
48388779 TCTGAAAGCA
*
48388789 TTGATCATCCTATTAATTCATTTCGCCTTTGCAAAGCCATTTAGTTCGGGTGCCCTCTCTCATGA
1 TTGATCACCCTATTAATTCATTTCGCCTTTGCAAAGCCATTTAGTTCGGGTGCCCTCTCTCATGA
48388854 GAATTGATCAACCTGGGATAAGATCCACCAT
66 GAATTGATCAACCTGGGATAAGATCCACCAT
48388885 TTGATCACCCTATTAATTCATTTCGCCTTTGCAAAGCCATTTAGTTCGGGTGCCCTCTCTCATGA
1 TTGATCACCCTATTAATTCATTTCGCCTTTGCAAAGCCATTTAGTTCGGGTGCCCTCTCTCATGA
48388950 GAATTGATCAACCTGGGATAAGATCCACCAT
66 GAATTGATCAACCTGGGATAAGATCCACCAT
48388981 AGATAGCAGA
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.33
Consensus pattern (96 bp):
TTGATCACCCTATTAATTCATTTCGCCTTTGCAAAGCCATTTAGTTCGGGTGCCCTCTCTCATGA
GAATTGATCAACCTGGGATAAGATCCACCAT
Found at i:48394419 original size:42 final size:42
Alignment explanation
Indices: 48394360--48394482 Score: 165
Period size: 42 Copynumber: 2.9 Consensus size: 42
48394350 ATTCTTGAAC
* * * *
48394360 ATTAGCTTGCTCACAAACGGGTAGCAAGGAAACATGAAAAAT
1 ATTAGCTTGCTAACAAACGTGCAGCAAGGAAGCATGAAAAAT
* *
48394402 ATTAGCTTGCTAACAAACGTGCAACAAAGAAGCATGAAAAAT
1 ATTAGCTTGCTAACAAACGTGCAGCAAGGAAGCATGAAAAAT
* * *
48394444 ATCAGCTTACTGACAAACGTGCAGCAAGGAAGCATGAAA
1 ATTAGCTTGCTAACAAACGTGCAGCAAGGAAGCATGAAA
48394483 CAATCTGCTC
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (42 bp):
ATTAGCTTGCTAACAAACGTGCAGCAAGGAAGCATGAAAAAT
Found at i:48397064 original size:2 final size:2
Alignment explanation
Indices: 48397057--48397083 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48397047 TTCATTTTAT
48397057 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
48397084 TATATATATC
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:48403990 original size:26 final size:26
Alignment explanation
Indices: 48403950--48404012 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
48403940 AAGATGATAT
48403950 GAAAAAGTAAATTTTT-TATTAATTAAA
1 GAAAAA-T-AATTTTTGTATTAATTAAA
*
48403977 GAAAAATAATTTTTGTATTATTTAAA
1 GAAAAATAATTTTTGTATTAATTAAA
48404003 -ATAAAATAAT
1 GA-AAAATAAT
48404013 GATTATTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 8 0.24
26 19 0.58
27 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.41
Consensus pattern (26 bp):
GAAAAATAATTTTTGTATTAATTAAA
Found at i:48404166 original size:31 final size:31
Alignment explanation
Indices: 48404131--48404194 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
48404121 CAGCATGATA
48404131 GGTTTTTTACTAAAATAACGTTAACCATATT
1 GGTTTTTTACTAAAATAACGTTAACCATATT
*
48404162 GGTTTTTTACTAAAATAACGTTAATCATATT
1 GGTTTTTTACTAAAATAACGTTAACCATATT
48404193 GG
1 GG
48404195 ATTCTTGGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.42
Consensus pattern (31 bp):
GGTTTTTTACTAAAATAACGTTAACCATATT
Found at i:48405263 original size:30 final size:30
Alignment explanation
Indices: 48405217--48405310 Score: 152
Period size: 30 Copynumber: 3.1 Consensus size: 30
48405207 TTTTATTATG
*
48405217 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
48405248 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* *
48405278 CCATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
48405308 CCA
1 CCA
48405311 TAAATATGGA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
30 53 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:48405272 original size:15 final size:15
Alignment explanation
Indices: 48405227--48405304 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
48405217 CCAATATCTC
48405227 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
48405242 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
48405257 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
48405272 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
48405287 GATACCCATATCTTT
1 GATACCCATATCTTT
48405302 GAT
1 GAT
48405305 TTTCCATAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.19
15 29 0.62
16 9 0.19
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:48409930 original size:30 final size:30
Alignment explanation
Indices: 48409880--48410003 Score: 185
Period size: 30 Copynumber: 4.1 Consensus size: 30
48409870 TTTTATTATG
*
48409880 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
*
48409911 CCAATATTTGATACTCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
48409941 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * * *
48409971 CTATTATTTGATACCCATATATTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
48410001 CCA
1 CCA
48410004 TAAATATGGA
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
30 78 0.92
31 7 0.08
ACGTcount: A:0.27, C:0.23, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:48409993 original size:15 final size:15
Alignment explanation
Indices: 48409890--48409997 Score: 69
Period size: 15 Copynumber: 7.2 Consensus size: 15
48409880 CCAATATCTC
*
48409890 GATACCCATATCTTT
1 GATACCCATATATTT
**
48409905 GACTTTCCA-ATATTT
1 GA-TACCCATATATTT
* *
48409920 GATACTCATATCTTT
1 GATACCCATATATTT
**
48409935 GACTTTCCA-ATATTT
1 GA-TACCCATATATTT
*
48409950 GATACCCATATCTTT
1 GATACCCATATATTT
** *
48409965 GACTTTCTAT-TATTT
1 GA-TACCCATATATTT
48409980 GATACCCATATATTT
1 GATACCCATATATTT
48409995 GAT
1 GAT
48409998 TTTCCATAAA
Statistics
Matches: 66, Mismatches: 21, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
14 11 0.17
15 44 0.67
16 11 0.17
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.45
Consensus pattern (15 bp):
GATACCCATATATTT
Found at i:48412717 original size:83 final size:83
Alignment explanation
Indices: 48412590--48412839 Score: 491
Period size: 83 Copynumber: 3.0 Consensus size: 83
48412580 TTTCTTTCAT
48412590 ATGAAAAATAGACTCAATAAGCTTCAATTTCATATTTTATTCATCATCTAGTTCTGTCTCTACTA
1 ATGAAAAATAGACTCAATAAGCTTCAATTTCATATTTTATTCATCATCTAGTTCTGTCTCTACTA
48412655 TTTTTAGTGATTTTTTAA
66 TTTTTAGTGATTTTTTAA
48412673 ATGAAAAATAGACTCAATAAGCTTCAATTTCATATTTTATTCATCATCTAGTTCTGTCTCTACTA
1 ATGAAAAATAGACTCAATAAGCTTCAATTTCATATTTTATTCATCATCTAGTTCTGTCTCTACTA
48412738 TTTTTAGTGATTTTTTAA
66 TTTTTAGTGATTTTTTAA
*
48412756 ATGAAAAATAGACTCAATAAGCTTCAATTTCATATTTTATTCATCATCTAGTTCTGTCTTTACTA
1 ATGAAAAATAGACTCAATAAGCTTCAATTTCATATTTTATTCATCATCTAGTTCTGTCTCTACTA
48412821 TTTTTAGTGATTTTTTAA
66 TTTTTAGTGATTTTTTAA
48412839 A
1 A
48412840 CTCACGTCAT
Statistics
Matches: 166, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 166 1.00
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (83 bp):
ATGAAAAATAGACTCAATAAGCTTCAATTTCATATTTTATTCATCATCTAGTTCTGTCTCTACTA
TTTTTAGTGATTTTTTAA
Found at i:48415088 original size:29 final size:29
Alignment explanation
Indices: 48415055--48415118 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
48415045 TGTGTCATGG
48415055 CCGTGTGTCTCACACGGCCAACAGACAGT
1 CCGTGTGTCTCACACGGCCAACAGACAGT
48415084 CCGTGTGTCTCACACGGCCAACAGACAGT
1 CCGTGTGTCTCACACGGCCAACAGACAGT
48415113 CCGTGT
1 CCGTGT
48415119 CACAGGCCGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.22, C:0.34, G:0.25, T:0.19
Consensus pattern (29 bp):
CCGTGTGTCTCACACGGCCAACAGACAGT
Found at i:48415121 original size:25 final size:27
Alignment explanation
Indices: 48415063--48415126 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 27
48415053 GGCCGTGTGT
48415063 CTCACACGGCCAACAGACAGTCCGTGTG
1 CTCACACGGCCAACAGACAGTCCG-GTG
48415091 TCTCACACGGCCAACAGACAGTCC-GTG
1 -CTCACACGGCCAACAGACAGTCCGGTG
48415118 -TCACA-GGCC
1 CTCACACGGCC
48415127 GTGTGGACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.11
25 5 0.14
27 3 0.09
29 23 0.66
ACGTcount: A:0.25, C:0.38, G:0.23, T:0.14
Consensus pattern (27 bp):
CTCACACGGCCAACAGACAGTCCGGTG
Found at i:48416110 original size:53 final size:53
Alignment explanation
Indices: 48416052--48416162 Score: 188
Period size: 53 Copynumber: 2.1 Consensus size: 53
48416042 AACATAGAAA
48416052 ATTAAACAAAGTAAGCTATATAGCTTAGTAAGCT-AGTATAAATTATACTTAAT
1 ATTAAACAAAGTAAGCTATATAGCTTAGTAAGCTCA-TATAAATTATACTTAAT
*
48416105 ATTAAACAAAGTAAGCTATATAGCTTAGTAAGCTCATATGAATTATACTTAAT
1 ATTAAACAAAGTAAGCTATATAGCTTAGTAAGCTCATATAAATTATACTTAAT
*
48416158 CTTAA
1 ATTAA
48416163 CATAGATATA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
53 54 0.98
54 1 0.02
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (53 bp):
ATTAAACAAAGTAAGCTATATAGCTTAGTAAGCTCATATAAATTATACTTAAT
Found at i:48439599 original size:38 final size:40
Alignment explanation
Indices: 48439557--48439649 Score: 97
Period size: 38 Copynumber: 2.4 Consensus size: 40
48439547 AAAAAAACAG
*
48439557 TATATTCTTATTTTGTT-AA-AATA-ATATG-TACAAATATA
1 TATATTCTTATTTTGTTAAACAAAACATATGTTA-AAATA-A
*
48439595 TATATATC-AATTTTGTTAAACAAAACTATATGTTAAAATAA
1 TATAT-TCTTATTTTGTTAAACAAAAC-ATATGTTAAAATAA
48439636 TATATTCTTATTTT
1 TATATTCTTATTTT
48439650 ATAGTAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
38 13 0.29
39 4 0.09
40 5 0.11
41 11 0.24
42 10 0.22
43 2 0.04
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (40 bp):
TATATTCTTATTTTGTTAAACAAAACATATGTTAAAATAA
Found at i:48440106 original size:16 final size:16
Alignment explanation
Indices: 48440084--48440152 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
48440074 TTTGGTTCGC
48440084 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
48440100 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
48440116 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
48440133 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
48440149 TGTA
1 TGTA
48440153 ATAGCTAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:48440130 original size:33 final size:32
Alignment explanation
Indices: 48440084--48440152 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
48440074 TTTGGTTCGC
48440084 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
*
48440116 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCGTATTGGATTAGAGG
48440149 TGTA
1 TGTA
48440153 ATAGCTAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCGTATTGGATTAGAGG
Found at i:48440409 original size:18 final size:17
Alignment explanation
Indices: 48440388--48440422 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48440378 TTATTATTAA
*
48440388 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
48440406 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
48440423 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:48440529 original size:18 final size:17
Alignment explanation
Indices: 48440508--48440542 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48440498 TTATTATTAA
*
48440508 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
48440526 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
48440543 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:48440584 original size:120 final size:120
Alignment explanation
Indices: 48440371--48440633 Score: 526
Period size: 120 Copynumber: 2.2 Consensus size: 120
48440361 ATCATATTTA
48440371 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
48440436 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
48440491 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
48440556 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
48440611 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
48440634 AACTTGAAAA
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 143 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:48453819 original size:32 final size:32
Alignment explanation
Indices: 48453783--48453851 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
48453773 GATATAGAGA
*
48453783 TTTTAATTATGTGGACCAACTTCTGTTTTTAG
1 TTTTAATTATGTGGACCAACCTCTGTTTTTAG
48453815 TTTTAATTATGTGGACCAACCTCTGTTTTTAG
1 TTTTAATTATGTGGACCAACCTCTGTTTTTAG
48453847 TTTTA
1 TTTTA
48453852 GTATGCCTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.22, C:0.13, G:0.14, T:0.51
Consensus pattern (32 bp):
TTTTAATTATGTGGACCAACCTCTGTTTTTAG
Found at i:48455047 original size:18 final size:18
Alignment explanation
Indices: 48455007--48455049 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
48454997 CAAAATTCCT
*
48455007 TTAAAATATAAAAATTCA
1 TTAAAATATAAAAAATCA
48455025 TTAAAATATAAAAAAATCA
1 TTAAAATAT-AAAAAATCA
48455044 -TAAAAT
1 TTAAAAT
48455050 TAGTAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (18 bp):
TTAAAATATAAAAAATCA
Found at i:48459913 original size:2 final size:2
Alignment explanation
Indices: 48459906--48459941 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
48459896 AATACCTATG
48459906 TC TC TC TC TC 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 TC TC TC TC TC
48459942 CACTTGCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:48464235 original size:3 final size:3
Alignment explanation
Indices: 48464227--48464254 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
48464217 AAAATGTTGC
48464227 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
48464255 TGGATTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:48466174 original size:20 final size:19
Alignment explanation
Indices: 48466146--48466232 Score: 67
Period size: 19 Copynumber: 4.7 Consensus size: 19
48466136 ATTGATTAGA
*
48466146 TAAAAATTGTTAAAATTAT
1 TAAAAATTGTAAAAATTAT
48466165 TAAAATATTGTAAAAATTA-
1 TAAAA-ATTGTAAAAATTAT
* *
48466184 T--AAATTGTTTAAAA-CAT
1 TAAAAATTG-TAAAAATTAT
*
48466201 TAAAAATTTGTAAAAAATA-
1 TAAAAA-TTGTAAAAATTAT
*
48466220 GAAAAATTGTAAA
1 TAAAAATTGTAAA
48466233 TTTTTTAAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
16 5 0.09
17 8 0.15
18 7 0.13
19 19 0.35
20 16 0.29
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.36
Consensus pattern (19 bp):
TAAAAATTGTAAAAATTAT
Found at i:48466187 original size:19 final size:19
Alignment explanation
Indices: 48466145--48466232 Score: 78
Period size: 18 Copynumber: 4.8 Consensus size: 19
48466135 CATTGATTAG
*
48466145 ATAAAA-ATTGTTAAAATT
1 ATAAAATATTGTAAAAATT
48466163 ATTAAAATATTGTAAAAATT
1 A-TAAAATATTGTAAAAATT
* *
48466183 ATAAATTGTT-TAAAACATT
1 ATAAAATATTGTAAAA-ATT
*
48466202 A-AAAAT-TTGTAAAAAAT
1 ATAAAATATTGTAAAAATT
*
48466219 AGAAAA-ATTGTAAA
1 ATAAAATATTGTAAA
48466233 TTTTTTAAAG
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
17 5 0.08
18 26 0.44
19 16 0.27
20 12 0.20
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.35
Consensus pattern (19 bp):
ATAAAATATTGTAAAAATT
Found at i:48468500 original size:15 final size:15
Alignment explanation
Indices: 48468468--48468503 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
48468458 AGTACTTTAG
*
48468468 TTTTCAATACTTAAT
1 TTTTCAACACTTAAT
*
48468483 TTTTCAACACTTATT
1 TTTTCAACACTTAAT
48468498 TTTTCA
1 TTTTCA
48468504 GTTTATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTTCAACACTTAAT
Found at i:48468710 original size:16 final size:15
Alignment explanation
Indices: 48468687--48468716 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
48468677 ATAAATTTAC
48468687 AAAAAAATGATGTTA
1 AAAAAAATGATGTTA
48468702 AAAATAAATGATGTT
1 AAAA-AAATGATGTT
48468717 TTGGTAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (15 bp):
AAAAAAATGATGTTA
Found at i:48477358 original size:28 final size:28
Alignment explanation
Indices: 48477318--48477376 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
48477308 AAGTGAGCCT
48477318 TAAGCGTTTTACCTTTTCCTTTAAAAAC
1 TAAGCGTTTTACCTTTTCCTTTAAAAAC
48477346 TAAGCGTTTTACCTTTTCCTTTAAAAAC
1 TAAGCGTTTTACCTTTTCCTTTAAAAAC
48477374 TAA
1 TAA
48477377 CTTGATTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (28 bp):
TAAGCGTTTTACCTTTTCCTTTAAAAAC
Found at i:48486378 original size:16 final size:17
Alignment explanation
Indices: 48486342--48486378 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
48486332 AATTTTATTT
*
48486342 TAATAATAATTTTTAAA
1 TAATAATAATATTTAAA
48486359 -AATAATAA-ATTTAAA
1 TAATAATAATATTTAAA
48486374 TAATA
1 TAATA
48486379 TTCTTCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATAATAATATTTAAA
Found at i:48486403 original size:7 final size:7
Alignment explanation
Indices: 48486391--48486417 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
48486381 CTTCATTTAA
48486391 AATATTC
1 AATATTC
48486398 AATATTC
1 AATATTC
48486405 AATATTC
1 AATATTC
48486412 AATATT
1 AATATT
48486418 TTAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (7 bp):
AATATTC
Found at i:48491004 original size:42 final size:43
Alignment explanation
Indices: 48490860--48491038 Score: 245
Period size: 43 Copynumber: 4.2 Consensus size: 43
48490850 ATATGTAACA
* * *
48490860 CCGCTAAAGACCAGGACTTTTAGCGGCGGTTGTATAAAAAATG
1 CCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTATAAAAAACG
*
48490903 CCGCTAAAGACCAGGACTTTTAGCGGCGCTTATATAAAAAACG
1 CCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTATAAAAAACG
*
48490946 CTGCTAAAGACCAGGACTTTTAGCGGCGCTTTTATAAAAAA-G
1 CCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTATAAAAAACG
* * * * *
48490988 CCACTATAGAACAGGACTTTTAACGGCG-TTTTTTAAAAAAGCG
1 CCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTATAAAAAA-CG
48491031 CCGCTAAA
1 CCGCTAAA
48491039 TGTCCTGGTC
Statistics
Matches: 121, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
41 11 0.09
42 24 0.20
43 86 0.71
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (43 bp):
CCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTATAAAAAACG
Found at i:48495344 original size:15 final size:16
Alignment explanation
Indices: 48495314--48495346 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
48495304 AAATATTTAT
48495314 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
48495331 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
48495346 A
1 A
48495347 AAATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:48504268 original size:9 final size:9
Alignment explanation
Indices: 48504254--48504420 Score: 163
Period size: 9 Copynumber: 17.6 Consensus size: 9
48504244 ATGTATTTGT
48504254 TAAGTTATG
1 TAAGTTATG
48504263 TAAGTTGTTATG
1 TAA---GTTATG
*
48504275 TACGTTATG
1 TAAGTTATG
*
48504284 TGAGTTATG
1 TAAGTTATG
*
48504293 TAAATTATG
1 TAAGTTATG
48504302 TAAGTTATG
1 TAAGTTATG
*
48504311 TGAGTTATG
1 TAAGTTATG
48504320 TAAGTTGTTATG
1 TAA---GTTATG
*
48504332 TAAATTATG
1 TAAGTTATG
48504341 TAAGTTATG
1 TAAGTTATG
*
48504350 TGAGTTATG
1 TAAGTTATG
48504359 TAAGTTGGTATG
1 TAAG-T--TATG
*
48504371 TAAATTATG
1 TAAGTTATG
*
48504380 TAAGTTATA
1 TAAGTTATG
48504389 TAAGTTATG
1 TAAGTTATG
48504398 TAAGTTATG
1 TAAGTTATG
* *
48504407 TAATTTATT
1 TAAGTTATG
48504416 TAAGT
1 TAAGT
48504421 AATGATCAAA
Statistics
Matches: 130, Mismatches: 19, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
9 104 0.80
10 1 0.01
11 1 0.01
12 24 0.18
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:48504330 original size:39 final size:39
Alignment explanation
Indices: 48504287--48504403 Score: 207
Period size: 39 Copynumber: 3.0 Consensus size: 39
48504277 CGTTATGTGA
48504287 GTTATGTAAATTATGTAAGTTATGTGAGTTATGTAAGTT
1 GTTATGTAAATTATGTAAGTTATGTGAGTTATGTAAGTT
48504326 GTTATGTAAATTATGTAAGTTATGTGAGTTATGTAAGTT
1 GTTATGTAAATTATGTAAGTTATGTGAGTTATGTAAGTT
* * *
48504365 GGTATGTAAATTATGTAAGTTATATAAGTTATGTAAGTT
1 GTTATGTAAATTATGTAAGTTATGTGAGTTATGTAAGTT
48504404 ATGTAATTTA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.45
Consensus pattern (39 bp):
GTTATGTAAATTATGTAAGTTATGTGAGTTATGTAAGTT
Found at i:48504330 original size:48 final size:43
Alignment explanation
Indices: 48504269--48504408 Score: 170
Period size: 39 Copynumber: 3.4 Consensus size: 43
48504259 TATGTAAGTT
*
48504269 GTTATGTACGTTATGTGAGTTATGTAAATTATGTAAGTTATGTGA
1 GTTATGTAAG-TATGT-AGTTATGTAAATTATGTAAGTTATGTGA
48504314 GTTATGTAAG--T-T-GTTATGTAAATTATGTAAGTTATGTGA
1 GTTATGTAAGTATGTAGTTATGTAAATTATGTAAGTTATGTGA
* *
48504353 GTTATGTAAGT-TG--G-TATGTAAATTATGTAAGTTATATAA
1 GTTATGTAAGTATGTAGTTATGTAAATTATGTAAGTTATGTGA
48504392 GTTATGTAAGTTATGTA
1 GTTATGTAAG-TATGTA
48504409 ATTTATTTAA
Statistics
Matches: 86, Mismatches: 3, Indels: 14
0.83 0.03 0.14
Matches are distributed among these distances:
39 70 0.81
40 3 0.03
41 3 0.03
42 1 0.01
45 9 0.10
ACGTcount: A:0.31, C:0.01, G:0.23, T:0.45
Consensus pattern (43 bp):
GTTATGTAAGTATGTAGTTATGTAAATTATGTAAGTTATGTGA
Found at i:48504347 original size:57 final size:58
Alignment explanation
Indices: 48504254--48504420 Score: 198
Period size: 57 Copynumber: 2.9 Consensus size: 58
48504244 ATGTATTTGT
* *
48504254 TAAGTTATGTAAGTTGTTATGTACGTTATGTGAGTTATGTAAATTATGTAAGT-TATG
1 TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAATTATGTAAGTGTATG
* * * *
48504311 TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATGTGAGTTATGTAAGTTGGTATG
1 TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAATTATGTAAG-T-GTATG
* * * *
48504371 TAAATTATGTAA---GTTATATAAGTTATGTAAGTTATGTAATTTATTTAAGT
1 TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAATTATGTAAGT
48504421 AATGATCAAA
Statistics
Matches: 94, Mismatches: 13, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
56 1 0.01
57 78 0.83
58 1 0.01
60 14 0.15
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.46
Consensus pattern (58 bp):
TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAATTATGTAAGTGTATG
Found at i:48504409 original size:48 final size:48
Alignment explanation
Indices: 48504254--48504409 Score: 188
Period size: 48 Copynumber: 3.2 Consensus size: 48
48504244 ATGTATTTGT
* * * *
48504254 TAAGTTATGTAAGTTGTTATGTACGTTATGTGAGTTATGTAAATTATG
1 TAAGTTATGTAAGTTGGTATGTAAGTTATGTAAGTTATGTAAGTTATG
* * * * *
48504302 TAAGTTATGTGAGTTATGTAAGT-TGTTATGTAAATTATGTAAGTTATG
1 TAAGTTATGTAAGTT-GGTATGTAAGTTATGTAAGTTATGTAAGTTATG
* * *
48504350 TGAGTTATGTAAGTTGGTATGTAAATTATGTAAGTTATATAAGTTATG
1 TAAGTTATGTAAGTTGGTATGTAAGTTATGTAAGTTATGTAAGTTATG
48504398 TAAGTTATGTAA
1 TAAGTTATGTAA
48504410 TTTATTTAAG
Statistics
Matches: 89, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
47 5 0.06
48 80 0.90
49 4 0.04
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.45
Consensus pattern (48 bp):
TAAGTTATGTAAGTTGGTATGTAAGTTATGTAAGTTATGTAAGTTATG
Found at i:48505023 original size:241 final size:241
Alignment explanation
Indices: 48504600--48505086 Score: 875
Period size: 241 Copynumber: 2.0 Consensus size: 241
48504590 TTAAGGTTAT
*
48504600 ATAAATATTCCATAGTAAATGAGCTCGATAGAACATTTTCCAAGTCTTTTTGAATTTTTTAAGAT
1 ATAAATATTCAATAGTAAATGAGCTCGATAGAACATTTTCCAAGTCTTTTTGAATTTTTTAAGAT
* **
48504665 TCATCATACGTGGCGTTGTTGCACCTAAGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
66 TCATCATACATGGCGTTGTAACACCTAAGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
48504730 ACCCGTCAGGTTTCCAACCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
131 ACCCGTCAGGTTTCCAACCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
48504795 GGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTA
196 GGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTA
* * * *
48504841 ATAAATATTCAATAGTAAATGAGCTCGATAGAACTTTTTTCAAGTCTTTTTTAATTTTTTATGAT
1 ATAAATATTCAATAGTAAATGAGCTCGATAGAACATTTTCCAAGTCTTTTTGAATTTTTTAAGAT
*
48504906 TCATCATACATGGCGTTGTAACACCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
66 TCATCATACATGGCGTTGTAACACCTAAGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
*
48504971 ACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
131 ACCCGTCAGGTTTCCAACCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
*
48505036 GGTCAGGTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTA
196 GGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTA
48505082 ATAAA
1 ATAAA
48505087 ATTAATTCAT
Statistics
Matches: 235, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
241 235 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (241 bp):
ATAAATATTCAATAGTAAATGAGCTCGATAGAACATTTTCCAAGTCTTTTTGAATTTTTTAAGAT
TCATCATACATGGCGTTGTAACACCTAAGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
ACCCGTCAGGTTTCCAACCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
GGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTA
Found at i:48508707 original size:37 final size:37
Alignment explanation
Indices: 48508626--48508741 Score: 128
Period size: 37 Copynumber: 3.1 Consensus size: 37
48508616 TGCACGGGGC
*
48508626 GAAGGCGATGGAGGCCGAGATGGGTTGCGATGA-AC-GGTGC
1 GAAGGCGATGGAGG--G-GATGGGTTGCGAT-ACACAGG-GA
*
48508666 GAAGGCGATGGAGGGGATGGTTTGCGATACACAGGGA
1 GAAGGCGATGGAGGGGATGGGTTGCGATACACAGGGA
* * *
48508703 GAAGGCGATGGAGGAGATGGGTTGCAATGCACAGGGA
1 GAAGGCGATGGAGGGGATGGGTTGCGATACACAGGGA
48508740 GA
1 GA
48508742 TTTGGGGGAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
36 1 0.01
37 50 0.74
38 3 0.04
40 14 0.21
ACGTcount: A:0.27, C:0.12, G:0.47, T:0.15
Consensus pattern (37 bp):
GAAGGCGATGGAGGGGATGGGTTGCGATACACAGGGA
Found at i:48510141 original size:21 final size:21
Alignment explanation
Indices: 48510117--48510167 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
48510107 GCCTAACCTC
48510117 TAAAACCATGAACATTAGTAT
1 TAAAACCATGAACATTAGTAT
*
48510138 TAAAACCATGAACATTTGTAT
1 TAAAACCATGAACATTAGTAT
48510159 TAAAACCAT
1 TAAAACCAT
48510168 AAACCCTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (21 bp):
TAAAACCATGAACATTAGTAT
Found at i:48510198 original size:14 final size:14
Alignment explanation
Indices: 48510159--48510201 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
48510149 ACATTTGTAT
48510159 TAAAACCATAAACCC
1 TAAAA-CATAAACCC
** *
48510174 TAAAATTTAAACTC
1 TAAAACATAAACCC
48510188 TAAAACATAAACCC
1 TAAAACATAAACCC
48510202 AACCCCCAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAAACATAAACCC
Found at i:48510699 original size:40 final size:38
Alignment explanation
Indices: 48510635--48510738 Score: 104
Period size: 40 Copynumber: 2.6 Consensus size: 38
48510625 CTGAACACTG
*
48510635 TTGCGGCGTTTTCTTAAAAACGCCGCT-AATGTTTGAT-TAT
1 TTGCGGCGTTTT-TTAAAAACGCCGCTAAAAG-TT-ATCT-T
* *
48510675 TTGCGGCGTTTTTTCATAAGCGCCGCTAAAAGTTATCTT
1 TTGCGGCGTTTTTT-AAAAACGCCGCTAAAAGTTATCTT
48510714 TTGCGGCGTTTTTTTAACAAACGCC
1 TTGCGGCG-TTTTTTAA-AAACGCC
48510739 ACTATATCTC
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
39 14 0.26
40 37 0.69
41 3 0.06
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (38 bp):
TTGCGGCGTTTTTTAAAAACGCCGCTAAAAGTTATCTT
Found at i:48511310 original size:25 final size:25
Alignment explanation
Indices: 48511276--48511326 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
48511266 AATGAAGGTG
48511276 ATAGATACATGATATATATAAAGTA
1 ATAGATACATGATATATATAAAGTA
48511301 ATAGATACATGATATATATAAAGTA
1 ATAGATACATGATATATATAAAGTA
48511326 A
1 A
48511327 GCATAATGTA
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:0.53, C:0.04, G:0.12, T:0.31
Consensus pattern (25 bp):
ATAGATACATGATATATATAAAGTA
Found at i:48522528 original size:15 final size:15
Alignment explanation
Indices: 48522510--48522561 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
48522500 ATTTAATATT
*
48522510 AATATATTGATAATA
1 AATATATTAATAATA
*
48522525 AATATTTATTACAATTATA
1 AATA--TATT--AATAATA
48522544 AATATATTAATAATA
1 AATATATTAATAATA
48522559 AAT
1 AAT
48522562 GTTATAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 13 0.43
17 8 0.27
19 9 0.30
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
AATATATTAATAATA
Found at i:48522957 original size:26 final size:24
Alignment explanation
Indices: 48522920--48522973 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 24
48522910 TACAAGGACT
48522920 TATGACATATTTTAACTTAGTATAAAA
1 TATGACATATTTTAA-TTA-TAT-AAA
48522947 TATGA-ATATTTTAATTATATAAA
1 TATGACATATTTTAATTATATAAA
48522970 TATG
1 TATG
48522974 CAGTATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.26
24 3 0.11
25 3 0.11
26 9 0.33
27 5 0.19
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (24 bp):
TATGACATATTTTAATTATATAAA
Found at i:48522988 original size:37 final size:37
Alignment explanation
Indices: 48522938--48523010 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
48522928 ATTTTAACTT
48522938 AGTATAAAATATGAATATTTTAATTATATAAATATGC
1 AGTATAAAATATGAATATTTTAATTATATAAATATGC
48522975 AGTATAAAATATGAATATTTTAATTATATAAATATG
1 AGTATAAAATATGAATATTTTAATTATATAAATATG
48523011 TATATTTGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.49, C:0.01, G:0.08, T:0.41
Consensus pattern (37 bp):
AGTATAAAATATGAATATTTTAATTATATAAATATGC
Found at i:48540212 original size:105 final size:104
Alignment explanation
Indices: 48540026--48540234 Score: 382
Period size: 105 Copynumber: 2.0 Consensus size: 104
48540016 AGATGAGTAT
* *
48540026 AAATCTATGCAAGACAATAAAGTTTGGGAACTTGTCTCATTACCTGAAGGTGTAAAACCAATTGG
1 AAATCTATGCAAGACAATAAAGTTTGGGAACTTGTCCCATTACCTGAAGGTGCAAAACCAATTGG
48540091 TTGTAAATGGATATTTAAAACCAAGAGGGATGCAAATGG
66 TTGTAAATGGATATTTAAAACCAAGAGGGATGCAAATGG
48540130 AAATACTATGCAAGACAATAAAGTTTGGGAACTTGTCCCATTACCTGAAGGTGCAAAACCAATTG
1 AAAT-CTATGCAAGACAATAAAGTTTGGGAACTTGTCCCATTACCTGAAGGTGCAAAACCAATTG
*
48540195 GTTGTAAATGGTTATTTAAAACCAAGAGGGATGCAAATGG
65 GTTGTAAATGGATATTTAAAACCAAGAGGGATGCAAATGG
48540235 TAATGTGGAA
Statistics
Matches: 101, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
104 4 0.04
105 97 0.96
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.26
Consensus pattern (104 bp):
AAATCTATGCAAGACAATAAAGTTTGGGAACTTGTCCCATTACCTGAAGGTGCAAAACCAATTGG
TTGTAAATGGATATTTAAAACCAAGAGGGATGCAAATGG
Found at i:48547606 original size:18 final size:17
Alignment explanation
Indices: 48547580--48547613 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
48547570 TTTAAAATTT
48547580 GTAAATAAAAAGTTATAA
1 GTAAAT-AAAAGTTATAA
*
48547598 GTAATTAAAAGTTATA
1 GTAAATAAAAGTTATA
48547614 TCACTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (17 bp):
GTAAATAAAAGTTATAA
Found at i:48551674 original size:31 final size:30
Alignment explanation
Indices: 48551617--48551674 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
48551607 TAGCAAAATT
* *
48551617 AACAATAAAACAAAAGTTATATAATATTCA
1 AACAATAAAACAAAAGTGATACAATATTCA
48551647 AACAATAACAACAAAA-TGATAGCAATAT
1 AACAATAA-AACAAAAGTGATA-CAATAT
48551675 AATAGCGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.60, C:0.12, G:0.05, T:0.22
Consensus pattern (30 bp):
AACAATAAAACAAAAGTGATACAATATTCA
Found at i:48560868 original size:25 final size:25
Alignment explanation
Indices: 48560816--48560869 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
48560806 AAATATTTTC
* ** *
48560816 TAAAATTAAATATTTTAATTAATGA
1 TAAAATTAAAAATAATAATTAATAA
*
48560841 TAAAATTAAAAATAATAATTACTAA
1 TAAAATTAAAAATAATAATTAATAA
48560866 TAAA
1 TAAA
48560870 TGTAATAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
TAAAATTAAAAATAATAATTAATAA
Found at i:48562780 original size:14 final size:15
Alignment explanation
Indices: 48562760--48562794 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
48562750 AAAGTGTTGT
48562760 AAAATA-TTAAAAAA
1 AAAATATTTAAAAAA
*
48562774 TAAATATTTAAAAAA
1 AAAATATTTAAAAAA
48562789 AAAATA
1 AAAATA
48562795 CTTGTCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATATTTAAAAAA
Found at i:48562910 original size:17 final size:16
Alignment explanation
Indices: 48562862--48562917 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
48562852 TACCAAATAC
*
48562862 TAATCCATTTAAATTT
1 TAATACATTTAAATTT
*
48562878 ATAATAAATCTTAAATTT
1 -TAATACAT-TTAAATTT
*
48562896 TAATACATTTCAAATTA
1 TAATACATTT-AAATTT
48562913 TAATA
1 TAATA
48562918 TGGGTTTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 2 0.06
17 23 0.70
18 8 0.24
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATACATTTAAATTT
Found at i:48563922 original size:55 final size:54
Alignment explanation
Indices: 48563851--48563958 Score: 198
Period size: 55 Copynumber: 2.0 Consensus size: 54
48563841 TTTTGGAAGA
*
48563851 TAGCTAAGCTTCCTTGTCTCTTTGTCTTAATATCATGTAATAGAAAGGAGATTAT
1 TAGCTAAGCTTACTTGTCTCTTTGTCTTAATAT-ATGTAATAGAAAGGAGATTAT
48563906 TAGCTAAGCTTACTTGTCTCTTTGTCTTAATATATGTAATAGAAAGGAGATTA
1 TAGCTAAGCTTACTTGTCTCTTTGTCTTAATATATGTAATAGAAAGGAGATTA
48563959 GTTAATACAA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
54 20 0.38
55 32 0.62
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.40
Consensus pattern (54 bp):
TAGCTAAGCTTACTTGTCTCTTTGTCTTAATATATGTAATAGAAAGGAGATTAT
Found at i:48573642 original size:83 final size:81
Alignment explanation
Indices: 48573499--48573676 Score: 248
Period size: 83 Copynumber: 2.2 Consensus size: 81
48573489 CCTTGGCCTA
* ** * * *
48573499 CAAAAATAAAAATTTGTTATTTCAGTCCCCTCATAAATAATAAAATTGTAAATTAATATATGGTG
1 CAAAAATAAAAAATTACTATTTCAGACCCCTCATAAATAATAAAATTATAAATTAATATATAGTG
48573564 AAATTGCACTTTGACC
66 AAATTGCACTTTGACC
* * *
48573580 ATCAAAAATAAAAAATTACTATTTTAGACCCCTCATAAATAATGAAATTATAAATTACTATATAG
1 --CAAAAATAAAAAATTACTATTTCAGACCCCTCATAAATAATAAAATTATAAATTAATATATAG
48573645 TGAAATTGCACTTTGACC
64 TGAAATTGCACTTTGACC
*
48573663 CTAAAATAAAAAAT
1 CAAAAATAAAAAAT
48573677 CTTTTTAGTC
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 13 0.15
83 72 0.85
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (81 bp):
CAAAAATAAAAAATTACTATTTCAGACCCCTCATAAATAATAAAATTATAAATTAATATATAGTG
AAATTGCACTTTGACC
Found at i:48573728 original size:77 final size:82
Alignment explanation
Indices: 48573498--48573728 Score: 213
Period size: 83 Copynumber: 2.9 Consensus size: 82
48573488 GCCTTGGCCT
* ** * * * * * * * *
48573498 ACAAAAATAAAAATTTGTTATTTCAGTCCCCTCATAAATAATAAAATTGTAAATTAATATATGGT
1 ACAAAAATAAAAAATTACTATTTTAGACCCCTAAAAAAGAATGAAATTATAAATTAATATATGAT
48573563 GAAATTGCACTTTGACC
66 GAAATTGCACTTTGACC
* * * *
48573580 ATCAAAAATAAAAAATTACTATTTTAGACCCCTCATAAATAATGAAATTATAAATTACTATAT-A
1 A-CAAAAATAAAAAATTACTATTTTAGACCCCTAAAAAAGAATGAAATTATAAATTAATATATGA
48573644 GTGAAATTGCACTTTGACC
65 -TGAAATTGCACTTTGACC
* * * * *
48573663 -CTAAAATAAAAAA-T-CT-TTTTAG-TCCCTAAAAAAGGATGAAATTATAAATGAATAAATGAT
1 ACAAAAATAAAAAATTACTATTTTAGACCCCTAAAAAAGAATGAAATTATAAATTAATATATGAT
*
48573723 AAAATT
66 GAAATT
48573729 ATGTTTTGAC
Statistics
Matches: 127, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
77 33 0.26
78 7 0.06
79 2 0.02
80 1 0.01
81 12 0.09
82 1 0.01
83 71 0.56
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (82 bp):
ACAAAAATAAAAAATTACTATTTTAGACCCCTAAAAAAGAATGAAATTATAAATTAATATATGAT
GAAATTGCACTTTGACC
Found at i:48576201 original size:29 final size:30
Alignment explanation
Indices: 48576138--48576203 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 30
48576128 TACACTACTA
48576138 GTCACCCAATTATCAGCAAATTTCTTTTTTG
1 GTCACCCAATTAT-AGCAAATTTCTTTTTTG
*
48576169 GTCACCCAATTAT-TC-AATTGTCTTTTTTG
1 GTCACCCAATTATAGCAAATT-TCTTTTTTG
48576198 GTCACC
1 GTCACC
48576204 AAAGGGCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
28 4 0.12
29 16 0.48
31 13 0.39
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (30 bp):
GTCACCCAATTATAGCAAATTTCTTTTTTG
Found at i:48583655 original size:30 final size:30
Alignment explanation
Indices: 48583621--48583679 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
48583611 AAAGACGAAT
*
48583621 TCCACACAGGCTGAG-CACACGCCCGTGTGA
1 TCCACACAGGCTG-GCCACACGCCCATGTGA
48583651 TCCACACAGGCTGGCCACACGCCCATGTG
1 TCCACACAGGCTGGCCACACGCCCATGTG
48583680 GCATCCCGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.22, C:0.39, G:0.25, T:0.14
Consensus pattern (30 bp):
TCCACACAGGCTGGCCACACGCCCATGTGA
Found at i:48608280 original size:171 final size:171
Alignment explanation
Indices: 48607994--48608333 Score: 635
Period size: 171 Copynumber: 2.0 Consensus size: 171
48607984 AAGTTGGTTT
48607994 AAAATACAACTCCAATTCTGTATTTAGATTAAGAACTCAGCTACTTCATATGAGCCAATTCAAAG
1 AAAATACAACTCCAATTCTGTATTTAGATTAAGAACTCAGCTACTTCATATGAGCCAATTCAAAG
* * *
48608059 ATGAAAGAGAAAAAACGTAAAAGATCAAAGATGACGCCAGGGTTTTGCTGGCCAAAGGGAGAATG
66 ATAAAAGAGAAAAAACGTAAAAGATCAAAGATGACGCCAGGGTATTGCTGGCCAAAGGAAGAATG
48608124 TTATAAAACCAAGAATCTTTGGATCTAAGAAATCCTAACTA
131 TTATAAAACCAAGAATCTTTGGATCTAAGAAATCCTAACTA
*
48608165 AAAATACAACTCCAATTCTGTATTTAGATTAAGAACTGAGCTACTTCATATGAGCCAATTCAAAG
1 AAAATACAACTCCAATTCTGTATTTAGATTAAGAACTCAGCTACTTCATATGAGCCAATTCAAAG
*
48608230 ATAAAAGAGAAAAAACGTAAAAGATCAGAGATGACGCCAGGGTATTGCTGGCCAAAGGAAGAATG
66 ATAAAAGAGAAAAAACGTAAAAGATCAAAGATGACGCCAGGGTATTGCTGGCCAAAGGAAGAATG
48608295 TTATAAAACCAAGAATCTTTGGATCTAAGAAATCCTAAC
131 TTATAAAACCAAGAATCTTTGGATCTAAGAAATCCTAAC
48608334 CATGAATTAA
Statistics
Matches: 164, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
171 164 1.00
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.24
Consensus pattern (171 bp):
AAAATACAACTCCAATTCTGTATTTAGATTAAGAACTCAGCTACTTCATATGAGCCAATTCAAAG
ATAAAAGAGAAAAAACGTAAAAGATCAAAGATGACGCCAGGGTATTGCTGGCCAAAGGAAGAATG
TTATAAAACCAAGAATCTTTGGATCTAAGAAATCCTAACTA
Found at i:48609968 original size:13 final size:13
Alignment explanation
Indices: 48609950--48610010 Score: 70
Period size: 13 Copynumber: 4.8 Consensus size: 13
48609940 TCTGTTTGGT
48609950 AATGCTTTTGAAA
1 AATGCTTTTGAAA
48609963 AATGCTTTTGAAA
1 AATGCTTTTGAAA
* *
48609976 AGTG-TTGTGAAA
1 AATGCTTTTGAAA
* *
48609988 AATACTTTTGAGA
1 AATGCTTTTGAAA
*
48610001 AGTGCTTTTG
1 AATGCTTTTG
48610011 TAAATTTAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
12 9 0.23
13 30 0.77
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.39
Consensus pattern (13 bp):
AATGCTTTTGAAA
Found at i:48610015 original size:25 final size:26
Alignment explanation
Indices: 48609952--48610010 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 26
48609942 TGTTTGGTAA
*
48609952 TGCTTTTGAAAAATGCTTTTGAAAAG
1 TGCTTTTGAAAAATACTTTTGAAAAG
* *
48609978 TG-TTGTGAAAAATACTTTTGAGAAG
1 TGCTTTTGAAAAATACTTTTGAAAAG
48610003 TGCTTTTG
1 TGCTTTTG
48610011 TAAATTTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 22 0.79
26 6 0.21
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.41
Consensus pattern (26 bp):
TGCTTTTGAAAAATACTTTTGAAAAG
Found at i:48619840 original size:196 final size:196
Alignment explanation
Indices: 48619499--48619949 Score: 426
Period size: 196 Copynumber: 2.3 Consensus size: 196
48619489 AAATCGAAGC
*
48619499 ACACAAAATGTTTTAATTTTTCTCTTCTTTAACATAATTTGTCATAAACTCTTACTAATCAATTT
1 ACACAAAATGTTATAATTTTTCTCTTCTTTAACATAATTTGTCATAAACTCTTACTAATCAATTT
* * ** * * * ** * *
48619564 GACCTTTAATTCATTTGCTTACAAATCGAGGTCTACCCCAATGGTTAAGGGTGTTTATTACCCCA
66 AACCTTTAATTCATTTACTTACAAATCGAACTCTACCCCAATAGTCAAAGGCATTCACTACCCCA
** * *
48619629 GGTGTAGTCTGAGTTCAAGTCACACTAGTCGCATTGGTTATTCAGGCTTTGCCCTATTATTGCAA
131 AATATACTCTGAGTTCAAGTCACACTAGTCGCATTGGTTATTCAGGCTTTGCCCTATTATTGCAA
48619694 A
196 A
* * *
48619695 ACACAAAATGTTATAATTTTTCTCTTCTTTTACATAATTTTTCTTAAACTCTTACTAATCAATTT
1 ACACAAAATGTTATAATTTTTCTCTTCTTTAACATAATTTGTCATAAACTCTTACTAATCAATTT
* * * * * * *
48619760 AACCTTTAATTTATTTACTTATAAGAT-TAACTTTACCTCGATAGTCAAAGGCATTCACTGCCCC
66 AACCTTTAATTCATTTACTTACAA-ATCGAACTCTACCCCAATAGTCAAAGGCATTCACTACCCC
* * * * * ** **
48619824 AAATATGACT-TGAGTTCGAGTCGCACTAAT--C-TTAGTTGTTCAAACTTTGTCATGTTATTGT
130 AAATAT-ACTCTGAGTTCAAGTCACACTAGTCGCATTGGTTATTCAGGCTTTG-C--CCTA-T-T
*
48619885 AATTCACAAA
189 -ATT-GCAAA
* * * *
48619895 ACACAAAATGTTTTAATTTTTCACTTCTTTTACATAAATTGTCATAAACTCTTAC
1 ACACAAAATGTTATAATTTTTCTCTTCTTTAACATAATTTGTCATAAACTCTTAC
48619950 CTTTAATTTA
Statistics
Matches: 205, Mismatches: 41, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
193 14 0.07
194 2 0.01
196 126 0.61
197 5 0.02
198 1 0.00
199 3 0.01
200 54 0.26
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (196 bp):
ACACAAAATGTTATAATTTTTCTCTTCTTTAACATAATTTGTCATAAACTCTTACTAATCAATTT
AACCTTTAATTCATTTACTTACAAATCGAACTCTACCCCAATAGTCAAAGGCATTCACTACCCCA
AATATACTCTGAGTTCAAGTCACACTAGTCGCATTGGTTATTCAGGCTTTGCCCTATTATTGCAA
A
Found at i:48620001 original size:35 final size:35
Alignment explanation
Indices: 48619951--48620026 Score: 145
Period size: 35 Copynumber: 2.2 Consensus size: 35
48619941 AACTCTTACC
48619951 TTTA-ATTTATTTGCTTACGAATCAGATTATAACA
1 TTTACATTTATTTGCTTACGAATCAGATTATAACA
48619985 TTTACATTTATTTGCTTACGAATCAGATTATAACA
1 TTTACATTTATTTGCTTACGAATCAGATTATAACA
48620020 TTTACAT
1 TTTACAT
48620027 AAAAGAGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 4 0.10
35 37 0.90
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (35 bp):
TTTACATTTATTTGCTTACGAATCAGATTATAACA
Found at i:48626095 original size:2 final size:2
Alignment explanation
Indices: 48626088--48626125 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
48626078 GAAAATGAGT
* *
48626088 GA GA GA GA GA GA GA GG GA GA GG GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
48626126 AAGTGATTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
GA
Found at i:48627009 original size:19 final size:21
Alignment explanation
Indices: 48626987--48627032 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
48626977 AAAATATAAA
*
48626987 AAAATTCTTAAT-T-TTTTTG
1 AAAATTCGTAATCTATTTTTG
*
48627006 AAAATTCGTAATCTATTTTTT
1 AAAATTCGTAATCTATTTTTG
48627027 AAAATT
1 AAAATT
48627033 ATATAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 11 0.48
20 1 0.04
21 11 0.48
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (21 bp):
AAAATTCGTAATCTATTTTTG
Found at i:48627064 original size:23 final size:23
Alignment explanation
Indices: 48626997--48627065 Score: 56
Period size: 22 Copynumber: 3.1 Consensus size: 23
48626987 AAAATTCTTA
* *
48626997 ATTTTTTTGAAAATTCGTAAT-CT
1 ATTTTTTTG-AAATTTGTAATAAT
* *
48627020 A-TTTTTT-AAAATTAT-ATAAAT
1 ATTTTTTTGAAATTTGTAAT-AAT
48627041 ATTTTTTTGAAATTTGTAATAAT
1 ATTTTTTTGAAATTTGTAATAAT
48627064 AT
1 AT
48627066 GAAAAATACT
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 2 0.06
22 12 0.34
23 12 0.34
24 2 0.06
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.54
Consensus pattern (23 bp):
ATTTTTTTGAAATTTGTAATAAT
Found at i:48634352 original size:22 final size:22
Alignment explanation
Indices: 48634326--48634369 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
48634316 TAAACATTTA
*
48634326 TTTA-TTTTAGTAGAAAACTTAC
1 TTTATTTTTAG-AAAAAACTTAC
48634348 TTTATTTTTAGAAAAAACTTAC
1 TTTATTTTTAGAAAAAACTTAC
48634370 GAGTTATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (22 bp):
TTTATTTTTAGAAAAAACTTAC
Found at i:48634427 original size:52 final size:53
Alignment explanation
Indices: 48634348--48634451 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 53
48634338 GAAAACTTAC
48634348 TTTATTTTTAGAAAAAACTTACGAGTTATCAAAACCGACTTAGATTAACTAAG
1 TTTATTTTTAGAAAAAACTTACGAGTTATCAAAACCGACTTAGATTAACTAAG
48634401 TTTATTTTTAG-AAAAACTTACGAGTTATCAAAACCGACTTAGATTAACTAA
1 TTTATTTTTAGAAAAAACTTACGAGTTATCAAAACCGACTTAGATTAACTAA
48634452 CCTATGTAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 40 0.78
53 11 0.22
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (53 bp):
TTTATTTTTAGAAAAAACTTACGAGTTATCAAAACCGACTTAGATTAACTAAG
Found at i:48640893 original size:23 final size:21
Alignment explanation
Indices: 48640846--48640981 Score: 83
Period size: 23 Copynumber: 5.9 Consensus size: 21
48640836 GATATGTTGA
*
48640846 AGGGTATATTGGTTGTGTTTTG
1 AGGGTATATTGGTTGTG-TTAG
48640868 AGGGTATACTTGGTTGTGTTAGG
1 AGGGTATA-TTGGTTGTGTTA-G
* *
48640891 AGGTTATATGCATGGTTATGATTAG
1 AGGGTATAT---TGGTTGTG-TTAG
* ** *
48640916 AGGGTAGATTTGGTTGCATTCGG
1 AGGGTATA-TTGGTTGTGTT-AG
*
48640939 AGGGTACATATGGTTGTGTTTAG
1 AGGGTATAT-TGGTTGTG-TTAG
*
48640962 AGGCTATGATTGGTTGTGTT
1 AGGGTAT-ATTGGTTGTGTT
48640982 TGGTGGGTGA
Statistics
Matches: 88, Mismatches: 15, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
22 16 0.18
23 50 0.57
24 4 0.05
25 14 0.16
26 4 0.05
ACGTcount: A:0.19, C:0.04, G:0.35, T:0.41
Consensus pattern (21 bp):
AGGGTATATTGGTTGTGTTAG
Found at i:48649219 original size:2 final size:2
Alignment explanation
Indices: 48649202--48649237 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
48649192 TAACTCAACA
* *
48649202 AT AT AC AT AA 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
48649238 GTCATATCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:48649753 original size:29 final size:29
Alignment explanation
Indices: 48649721--48649785 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
48649711 AAATTAGTCT
*
48649721 TCAAACTTTAAAATATTCTAATTACATCC
1 TCAAACTTTAAAACATTCTAATTACATCC
48649750 TCAAACTTTAAAACATTCTAATTACATCC
1 TCAAACTTTAAAACATTCTAATTACATCC
48649779 TCAAACT
1 TCAAACT
48649786 ATCAATGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (29 bp):
TCAAACTTTAAAACATTCTAATTACATCC
Found at i:48650026 original size:56 final size:56
Alignment explanation
Indices: 48649960--48650073 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
48649950 GTTTTTTTTT
48649960 ATAGAAATTATCGTTTACTCTCTCTTTTTTCATTTTTACTTATTTTTGGTTTTAAA
1 ATAGAAATTATCGTTTACTCTCTCTTTTTTCATTTTTACTTATTTTTGGTTTTAAA
*
48650016 ATAGAAATTATCGTTTACTCTCTCTTTTTTTATTTTTACTTATTTTTGGTTTTAAA
1 ATAGAAATTATCGTTTACTCTCTCTTTTTTCATTTTTACTTATTTTTGGTTTTAAA
48650072 AT
1 AT
48650074 TTAAAAGTTA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.58
Consensus pattern (56 bp):
ATAGAAATTATCGTTTACTCTCTCTTTTTTCATTTTTACTTATTTTTGGTTTTAAA
Found at i:48655847 original size:85 final size:85
Alignment explanation
Indices: 48655699--48655874 Score: 316
Period size: 85 Copynumber: 2.1 Consensus size: 85
48655689 ATATCCTAGA
*
48655699 TGAGATCGTTATTCTACTTAATAAATGATACAGATAGGTCATAATTCAAACTGATAACATTGAAT
1 TGAGATCGTTATTCTACTTAATAAATGATACAGATAAGTCATAATTCAAACTGATAACATTGAAT
48655764 TAGTCCAAACCTTTGACTGT
66 TAGTCCAAACCTTTGACTGT
* *
48655784 TGAGATCTTTATTCTACTTAATAAATGATACAGATAAGTCATAATTCAAACTGATAACTTTGAAT
1 TGAGATCGTTATTCTACTTAATAAATGATACAGATAAGTCATAATTCAAACTGATAACATTGAAT
*
48655849 TAGTCCAAACCTTTGATTGT
66 TAGTCCAAACCTTTGACTGT
48655869 TGAGAT
1 TGAGAT
48655875 TGGAGGATCT
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 87 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (85 bp):
TGAGATCGTTATTCTACTTAATAAATGATACAGATAAGTCATAATTCAAACTGATAACATTGAAT
TAGTCCAAACCTTTGACTGT
Found at i:48656419 original size:89 final size:89
Alignment explanation
Indices: 48656219--48656419 Score: 249
Period size: 89 Copynumber: 2.2 Consensus size: 89
48656209 TTTTAAAAGG
** * * *
48656219 AGCAATTAAGCCGTTGTCTTTTTTTTTCCACTCATTTGGATACTTGAATTTTCAAAATGCATCAA
1 AGCAATTAAGCCCATG-C-TTTTTTTTCCACTCAATTGGATACTTAAACTTTCAAAATGCATCAA
* **
48656284 AAAGGCCCTGGAACCTTTAAAAAAAA
64 AAAGACCCTCAAACCTTTAAAAAAAA
* * *
48656310 AGCAATTAAGCCCCTACTTTTTTTTCCACTCAATTGGGTACTTAAACTTTCAAAATGCATCAAAA
1 AGCAATTAAGCCCATGCTTTTTTTTCCACTCAATTGGATACTTAAACTTTCAAAATGCATCAAAA
* * **
48656375 AGATCCTCAAACTTTTTCAAAAAA
66 AGACCCTCAAACCTTTAAAAAAAA
48656399 AGCAATTAAGCCCATGCTTTT
1 AGCAATTAAGCCCATGCTTTT
48656420 ATTAAAAATT
Statistics
Matches: 94, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
89 80 0.85
90 1 0.01
91 13 0.14
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (89 bp):
AGCAATTAAGCCCATGCTTTTTTTTCCACTCAATTGGATACTTAAACTTTCAAAATGCATCAAAA
AGACCCTCAAACCTTTAAAAAAAA
Found at i:48656540 original size:19 final size:19
Alignment explanation
Indices: 48656516--48656576 Score: 88
Period size: 19 Copynumber: 3.2 Consensus size: 19
48656506 AAATTTTATT
48656516 AAAAA-TGAGAAAAAATATA
1 AAAAATTGA-AAAAAATATA
*
48656535 AAAAATTGTAAAAAATATA
1 AAAAATTGAAAAAAATATA
48656554 AAAAATTGTAAAAAAATATA
1 AAAAATTG-AAAAAAATATA
48656574 AAA
1 AAA
48656577 TATATAGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 23 0.61
20 15 0.39
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (19 bp):
AAAAATTGAAAAAAATATA
Found at i:48656575 original size:10 final size:10
Alignment explanation
Indices: 48656525--48656576 Score: 61
Period size: 10 Copynumber: 5.3 Consensus size: 10
48656515 TAAAAATGAG
48656525 AAAAAATATA
1 AAAAAATATA
* *
48656535 AAAAATTGT-
1 AAAAAATATA
48656544 AAAAAATATA
1 AAAAAATATA
* *
48656554 AAAAATTGTA
1 AAAAAATATA
48656564 AAAAAATATA
1 AAAAAATATA
48656574 AAA
1 AAA
48656577 TATATAGAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
9 7 0.21
10 26 0.79
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (10 bp):
AAAAAATATA
Found at i:48656581 original size:29 final size:29
Alignment explanation
Indices: 48656525--48656601 Score: 50
Period size: 29 Copynumber: 2.7 Consensus size: 29
48656515 TAAAAATGAG
*
48656525 AAAAAATATAAAAAATTGTA-AAAAATATA
1 AAAAAATATAAAAAA-TATAGAAAAATATA
* * *
48656554 AAAAATTGTAAAAAAATATA-AAATATATA
1 AAAAAATAT-AAAAAATATAGAAAAATATA
* * * *
48656583 GAAATATTTAAAAATTATA
1 AAAAAATATAAAAAATATA
48656602 ATTTGTTATA
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
28 9 0.24
29 23 0.61
30 6 0.16
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.29
Consensus pattern (29 bp):
AAAAAATATAAAAAATATAGAAAAATATA
Found at i:48656597 original size:10 final size:9
Alignment explanation
Indices: 48656525--48656602 Score: 66
Period size: 9 Copynumber: 8.2 Consensus size: 9
48656515 TAAAAATGAG
48656525 AAAAAATAT
1 AAAAAATAT
*
48656534 AAAAAATTGT
1 AAAAAA-TAT
48656544 AAAAAATAT
1 AAAAAATAT
*
48656553 AAAAAATTGT
1 AAAAAA-TAT
48656563 AAAAAAATAT
1 -AAAAAATAT
*
48656573 AAAATATAT
1 AAAAAATAT
* *
48656582 AGAAATATTT
1 A-AAAAATAT
*
48656592 AAAAATTAT
1 AAAAAATAT
48656601 AA
1 AA
48656603 TTTGTTATAA
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
9 30 0.54
10 20 0.36
11 6 0.11
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (9 bp):
AAAAAATAT
Found at i:48656939 original size:57 final size:56
Alignment explanation
Indices: 48656860--48656966 Score: 128
Period size: 57 Copynumber: 1.9 Consensus size: 56
48656850 TTTTGATGCA
*
48656860 TTTTATAATTTTGTTATGATTTTT-ATAGAAGTTTACAATTTTT-TATTTTTTACGAT
1 TTTTATAATTTTGTTATAATTTTTAATA-AAGTTTA-AATTTTTATATTTTTTACGAT
* * * *
48656916 TTTTATAAATTTTTTTCTAATTTTTAATAAATTTTAACTTTTTATATTTTT
1 TTTTAT-AATTTTGTTATAATTTTTAATAAAGTTTAAATTTTTATATTTTT
48656967 ATTAAAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
56 12 0.28
57 28 0.65
58 3 0.07
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.64
Consensus pattern (56 bp):
TTTTATAATTTTGTTATAATTTTTAATAAAGTTTAAATTTTTATATTTTTTACGAT
Found at i:48656977 original size:18 final size:18
Alignment explanation
Indices: 48656956--48657004 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
48656946 ATTTTAACTT
48656956 TTTATATTTTTATTAAAA
1 TTTATATTTTTATTAAAA
* *
48656974 TTTAATAATTTTACTAAAA
1 TTT-ATATTTTTATTAAAA
48656993 TTTAT-TTTTTAT
1 TTTATATTTTTAT
48657005 AATTTTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 5 0.19
18 5 0.19
19 16 0.62
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTATATTTTTATTAAAA
Done.