Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 66 of 187
Found at i:19222664 original size:24 final size:21
Alignment explanation
Indices: 19222626--19222674 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 21
19222616 TTTAAAATAT
*
19222626 GGTTGACAAAAAAAAATAAAA
1 GGTTGACAAAAAAAAAAAAAA
19222647 GGTTGACATAGAATAAAAAAAAAA
1 GGTTGACA-A-AA-AAAAAAAAAA
19222671 GGTT
1 GGTT
19222675 ATGTAAGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 8 0.33
22 1 0.04
23 2 0.08
24 13 0.54
ACGTcount: A:0.59, C:0.04, G:0.18, T:0.18
Consensus pattern (21 bp):
GGTTGACAAAAAAAAAAAAAA
Found at i:19224293 original size:22 final size:22
Alignment explanation
Indices: 19224265--19224308 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
19224255 GGCTGGATGG
19224265 AGTTGTCCGTGGGGTGAAACGT
1 AGTTGTCCGTGGGGTGAAACGT
19224287 AGTTGTCCGTGGGGTGAAACGT
1 AGTTGTCCGTGGGGTGAAACGT
19224309 TGTGGTGTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.41, T:0.27
Consensus pattern (22 bp):
AGTTGTCCGTGGGGTGAAACGT
Found at i:19228999 original size:42 final size:41
Alignment explanation
Indices: 19228949--19229054 Score: 149
Period size: 42 Copynumber: 2.5 Consensus size: 41
19228939 CTACGGGTCA
*
19228949 CACCACAACACCACCTACCAATCTTCCTACTCCTATGGAACC
1 CACCACAACACCACC-ACCAATCTTCCCACTCCTATGGAACC
* * *
19228991 CATCACAACACTACCCACCAATCTTCCCACTCCTATGGATCC
1 CACCACAACACCA-CCACCAATCTTCCCACTCCTATGGAACC
19229033 CACCACAACACCATCCACCAAT
1 CACCACAACACCA-CCACCAAT
19229055 TTAACGTCTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 54 0.96
43 2 0.04
ACGTcount: A:0.32, C:0.46, G:0.04, T:0.18
Consensus pattern (41 bp):
CACCACAACACCACCACCAATCTTCCCACTCCTATGGAACC
Found at i:19231950 original size:147 final size:151
Alignment explanation
Indices: 19231767--19232086 Score: 387
Period size: 153 Copynumber: 2.1 Consensus size: 151
19231757 CCCAAGACCT
* * *
19231767 CAACACAAACAAAATTTTTTACAAACAAAAATATAATCTTAAACATTAAATTTAAATATT-AA-A
1 CAACACAAAC-AAATTTTTTACAAACAAAAATATAATATTAAACATTAAATCTAAAGATTAAATA
* * * *
19231830 AA-TAAAAAATAGACATATAATATAAAAATTATTATTACAA-ACTAAAAAAAAACCTTAAACCTA
65 AATTAAAAAATAAACATATAATATAAAAATTATTATTACAACAATAAAAAAAAACATTAAAACTA
* *
19231893 TCATAAACTATCTCTAAAACTC
130 TCACAAACTATCCCTAAAACTC
* * * *
19231915 CAACACAAACAGATTTTTTATAAACAAAAATATAATATTAAATATTTAATCTAAAGATTAACAAT
1 CAACACAAACAAATTTTTTACAAACAAAAATATAATATTAAACATTAAATCTAAAGATT-A-AAT
* * * *
19231980 AAATTAAAATATAAACATATAATATACAAATTATTATTACAACAATAAAAACACACATTAAAACT
64 AAATTAAAAAATAAACATATAATATAAAAATTATTATTACAACAATAAAAAAAAACATTAAAACT
* ** * *
19232045 TTCACAATTTCTCCCTAAAATTC
129 ATCACAAACTATCCCTAAAACTC
19232068 CAACACAAACAAATTTTTT
1 CAACACAAACAAATTTTTT
19232087 TCCTCCCAAA
Statistics
Matches: 143, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
147 42 0.29
148 10 0.07
150 2 0.01
151 3 0.02
152 35 0.24
153 51 0.36
ACGTcount: A:0.54, C:0.15, G:0.01, T:0.30
Consensus pattern (151 bp):
CAACACAAACAAATTTTTTACAAACAAAAATATAATATTAAACATTAAATCTAAAGATTAAATAA
ATTAAAAAATAAACATATAATATAAAAATTATTATTACAACAATAAAAAAAAACATTAAAACTAT
CACAAACTATCCCTAAAACTC
Found at i:19243690 original size:19 final size:17
Alignment explanation
Indices: 19243657--19243708 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 17
19243647 TGGTAAAAAA
*
19243657 ATAAAAATCAATAAAAGTT
1 ATAAAAATTAAT-AAA-TT
*
19243676 ATAAAAATTATTAAATT
1 ATAAAAATTAATAAATT
19243693 A-AAAAATTAA-AAATT
1 ATAAAAATTAATAAATT
19243708 A
1 A
19243709 GAATTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 6 0.20
16 8 0.27
17 3 0.10
18 3 0.10
19 10 0.33
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (17 bp):
ATAAAAATTAATAAATT
Found at i:19244080 original size:9 final size:9
Alignment explanation
Indices: 19244068--19244092 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
19244058 TTTTTTTGTA
19244068 ATTTTTAAT
1 ATTTTTAAT
19244077 ATTTTTAAT
1 ATTTTTAAT
19244086 ATTTTTA
1 ATTTTTA
19244093 TTAAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:19244101 original size:30 final size:29
Alignment explanation
Indices: 19244012--19244102 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
19244002 TTCAATATAT
*
19244012 TTTATAATTCTTTTACA-ATTTTTA-TAAAA
1 TTTACAATT-TTTTA-ATATTTTTATTAAAA
* * **
19244041 TTTACAATTTTTTTATGTTTTT-TTGTAA
1 TTTACAATTTTTTAATATTTTTATTAAAA
**
19244069 TTTTTAATATTTTTAATATTTTTATTAAAA
1 TTTACAAT-TTTTTAATATTTTTATTAAAA
19244099 TTTA
1 TTTA
19244103 ATAATTTGTA
Statistics
Matches: 46, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
27 1 0.02
28 18 0.39
29 20 0.43
30 7 0.15
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (29 bp):
TTTACAATTTTTTAATATTTTTATTAAAA
Found at i:19246031 original size:2 final size:2
Alignment explanation
Indices: 19246024--19246049 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19246014 GTATGGCTAT
19246024 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
19246050 CAGCATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19246455 original size:2 final size:2
Alignment explanation
Indices: 19246450--19246474 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19246440 CATAATCATT
19246450 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
19246475 CAAATGCATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19246556 original size:41 final size:41
Alignment explanation
Indices: 19246506--19246691 Score: 284
Period size: 41 Copynumber: 4.5 Consensus size: 41
19246496 TTTAACATAT
* * * ** *
19246506 TCACTGGCACTTAGCATGTTAGACTTATAGCCTGATTCCA-A
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT-CAGA
*
19246547 TCACCGGCACTTAGCCTGCCAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
19246588 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAAA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
19246629 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
19246670 TCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
19246692 ACTTAAAGTC
Statistics
Matches: 134, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 2 0.01
41 132 0.99
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:19248424 original size:7 final size:6
Alignment explanation
Indices: 19248398--19248422 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19248388 GAATAATAAA
19248398 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
19248423 TAACTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:19248443 original size:11 final size:11
Alignment explanation
Indices: 19248427--19248451 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19248417 ATTTTTTAAC
19248427 TTTAAAATACT
1 TTTAAAATACT
19248438 TTTAAAATACT
1 TTTAAAATACT
19248449 TTT
1 TTT
19248452 TTTTAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTAAAATACT
Found at i:19248475 original size:16 final size:16
Alignment explanation
Indices: 19248451--19248482 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19248441 AAAATACTTT
*
19248451 TTTTTAATTTTTTTAA
1 TTTTAAATTTTTTTAA
19248467 TTTTAAATTTTTTTAA
1 TTTTAAATTTTTTTAA
19248483 AAATACTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTAAATTTTTTTAA
Found at i:19248493 original size:39 final size:39
Alignment explanation
Indices: 19248418--19248541 Score: 169
Period size: 40 Copynumber: 3.1 Consensus size: 39
19248408 TTTATTTTTA
* **
19248418 TTTTTTAACTTTAAAATACTTTTAAAATACTTTTTTTTAAT
1 TTTTTTAA-TTTTAAATTTTTTTAAAATAC-TTTTTTTAAT
*
19248459 TTTTTTAATTTTAAATTTTTTTAAAAATAC-TTTTTTAAA
1 TTTTTTAATTTTAAATTTTTTT-AAAATACTTTTTTTAAT
19248498 TTTTTTAATTTTAAAATTTTTTTAAAATACTTTTTTTAAT
1 TTTTTTAATTTT-AAATTTTTTTAAAATACTTTTTTTAAT
19248538 TTTT
1 TTTT
19248542 ATTTTAATTT
Statistics
Matches: 75, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
39 27 0.36
40 33 0.44
41 15 0.20
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (39 bp):
TTTTTTAATTTTAAATTTTTTTAAAATACTTTTTTTAAT
Found at i:19249528 original size:19 final size:21
Alignment explanation
Indices: 19249486--19249529 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
19249476 AAGTATATTT
*
19249486 TATATAAAATAAATATGCGTA
1 TATATAAAATAAATATGCGCA
*
19249507 TATAT-AAA-AAATATGTGCA
1 TATATAAAATAAATATGCGCA
19249526 TATA
1 TATA
19249530 GGTGTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.62
20 3 0.14
21 5 0.24
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (21 bp):
TATATAAAATAAATATGCGCA
Found at i:19249529 original size:21 final size:21
Alignment explanation
Indices: 19249486--19249529 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
19249476 AAGTATATTT
*
19249486 TATATAAAATAAATATGCGTA
1 TATATAAAATAAATATGCATA
*
19249507 TATATAAAA-AATATGTGCATA
1 TATATAAAATAA-ATATGCATA
19249528 TA
1 TA
19249530 GGTGTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (21 bp):
TATATAAAATAAATATGCATA
Found at i:19249658 original size:2 final size:2
Alignment explanation
Indices: 19249651--19249681 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19249641 AAACTAATAA
*
19249651 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19249682 CAAATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19251521 original size:97 final size:97
Alignment explanation
Indices: 19251354--19251780 Score: 710
Period size: 97 Copynumber: 4.4 Consensus size: 97
19251344 GCGTCGCCTG
* *
19251354 GAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCGCC
1 GAAGTAAGATTCGCCGCTGTGGCTTCGATCTTTTAAA-TGCAATGTCGGGGAAGTGAGATTCGCT
* *
19251419 ATTGTAGTTTCAATCTGTTCCACTGCATCGCCA
65 ATTGTAGCTTCAATCTGCTCCACTGCATCGCCA
* * * *
19251452 AAAATAAGATTCACCGCTGTGGCTTCGATCTTTTAAATGCAATGTCGGGGAAGTGAGATTCGCTG
1 GAAGTAAGATTCGCCGCTGTGGCTTCGATCTTTTAAATGCAATGTCGGGGAAGTGAGATTCGCTA
19251517 TTGTAGCTTCAATCTGCTCCACTGCATCGCCA
66 TTGTAGCTTCAATCTGCTCCACTGCATCGCCA
19251549 GAAGTAAGATTCGCCGCTGTGGCTTCGATCTTTTAAATGCAATGTCGGGGAAGTGAGATTCGCTA
1 GAAGTAAGATTCGCCGCTGTGGCTTCGATCTTTTAAATGCAATGTCGGGGAAGTGAGATTCGCTA
*
19251614 TTGTAGCTTCAATCTGCTCCACTGCATCGCAA
66 TTGTAGCTTCAATCTGCTCCACTGCATCGCCA
* * * *
19251646 GAAGTAAGATTCGCCGCTGTGGCTTCGATCTTTTAAATGCAATGTCAGGGAAGTAAGATCCGCTG
1 GAAGTAAGATTCGCCGCTGTGGCTTCGATCTTTTAAATGCAATGTCGGGGAAGTGAGATTCGCTA
*
19251711 TTGTAGCTTCAATCTGCTCCACTGTATCGCCA
66 TTGTAGCTTCAATCTGCTCCACTGCATCGCCA
*
19251743 GAAGTAAGATTTGCCGCTGTGGCTTCGATCTTTTAAAT
1 GAAGTAAGATTCGCCGCTGTGGCTTCGATCTTTTAAAT
19251781 TGCAGACTGT
Statistics
Matches: 309, Mismatches: 20, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
97 276 0.89
98 33 0.11
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (97 bp):
GAAGTAAGATTCGCCGCTGTGGCTTCGATCTTTTAAATGCAATGTCGGGGAAGTGAGATTCGCTA
TTGTAGCTTCAATCTGCTCCACTGCATCGCCA
Found at i:19251560 original size:48 final size:48
Alignment explanation
Indices: 19251501--19251753 Score: 199
Period size: 48 Copynumber: 5.2 Consensus size: 48
19251491 CAATGTCGGG
*
19251501 GAAGTGAGATTCGCTGTTGTAGCTTCAATCTGCTCCACTGCATCGCCA
1 GAAGTAAGATTCGCTGTTGTAGCTTCAATCTGCTCCACTGCATCGCCA
* * * * * ** * **
19251549 GAAGTAAGATTCGCCGCTGTGGCTTCGATCT-TTTAAATGCAAT-GTCGGG
1 GAAGTAAGATTCGCTGTTGTAGCTTCAATCTGCTCCACTGC-ATCG-C-CA
* * *
19251598 GAAGTGAGATTCGCTATTGTAGCTTCAATCTGCTCCACTGCATCGCAA
1 GAAGTAAGATTCGCTGTTGTAGCTTCAATCTGCTCCACTGCATCGCCA
* * * * * ** * *
19251646 GAAGTAAGATTCGCCGCTGTGGCTTCGATCT-TTTAAATGCAAT-GTCA
1 GAAGTAAGATTCGCTGTTGTAGCTTCAATCTGCTCCACTGC-ATCGCCA
* *
19251693 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGCTCCACTGTATCGCCA
1 --GAAGTAAGATTCGCTGTTGTAGCTTCAATCTGCTCCACTGCATCGCCA
19251743 GAAGTAAGATT
1 GAAGTAAGATT
19251754 TGCCGCTGTG
Statistics
Matches: 148, Mismatches: 47, Indels: 20
0.69 0.22 0.09
Matches are distributed among these distances:
47 13 0.09
48 66 0.45
49 56 0.38
50 13 0.09
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (48 bp):
GAAGTAAGATTCGCTGTTGTAGCTTCAATCTGCTCCACTGCATCGCCA
Found at i:19251768 original size:48 final size:48
Alignment explanation
Indices: 19251404--19251773 Score: 176
Period size: 48 Copynumber: 7.6 Consensus size: 48
19251394 CAATGTCGGG
* ** * * * *
19251404 GAAGTGAGATTCGCCATTGTAGTTTCAATCTGTTCCACTGCATCGCCA
1 GAAGTAAGATTCGCCGCTGTGGCTTCAATCTGCTCCACTGAATCGCCA
* * * * * ** * **
19251452 AAAATAAGATTCACCGCTGTGGCTTCGATCT-TTTAAATGCAAT-GTCGGG
1 GAAGTAAGATTCGCCGCTGTGGCTTCAATCTGCTCCACTG-AATCG-C-CA
* * * * *
19251501 GAAGTGAGATTCGCTGTTGTAGCTTCAATCTGCTCCACTGCATCGCCA
1 GAAGTAAGATTCGCCGCTGTGGCTTCAATCTGCTCCACTGAATCGCCA
* * ** * **
19251549 GAAGTAAGATTCGCCGCTGTGGCTTCGATCT-TTTAAATGCAAT-GTCGGG
1 GAAGTAAGATTCGCCGCTGTGGCTTCAATCTGCTCCACTG-AATCG-C-CA
* *** * * *
19251598 GAAGTGAGATTCGCTATTGTAGCTTCAATCTGCTCCACTGCATCGCAA
1 GAAGTAAGATTCGCCGCTGTGGCTTCAATCTGCTCCACTGAATCGCCA
* * ** * *
19251646 GAAGTAAGATTCGCCGCTGTGGCTTCGATCT-TTTAAATGCAAT-GTCA
1 GAAGTAAGATTCGCCGCTGTGGCTTCAATCTGCTCCACTG-AATCGCCA
* * * * *
19251693 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGCTCCACTGTATCGCCA
1 --GAAGTAAGATTCGCCGCTGTGGCTTCAATCTGCTCCACTGAATCGCCA
* *
19251743 GAAGTAAGATTTGCCGCTGTGGCTTCGATCT
1 GAAGTAAGATTCGCCGCTGTGGCTTCAATCT
19251774 TTTAAATTGC
Statistics
Matches: 222, Mismatches: 85, Indels: 30
0.66 0.25 0.09
Matches are distributed among these distances:
47 17 0.08
48 106 0.48
49 82 0.37
50 17 0.08
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (48 bp):
GAAGTAAGATTCGCCGCTGTGGCTTCAATCTGCTCCACTGAATCGCCA
Found at i:19265481 original size:6 final size:5
Alignment explanation
Indices: 19265456--19265491 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
19265446 AAACAAACAA
19265456 AAAAT AAAAT AAAAT AAAAT AGAAAT -AAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT A
19265492 GCAATGTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 21 0.72
6 4 0.14
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:19274400 original size:43 final size:43
Alignment explanation
Indices: 19274280--19274466 Score: 189
Period size: 43 Copynumber: 4.3 Consensus size: 43
19274270 TCGCCGCAAA
* * * *
19274280 CTTTAGCGGCGCTTTTACCACAAACGTCGCTATAGATCAGGAC
1 CTTTAGCGGCGCTTTTACAACAAACGCCACTATAGCTCAGGAC
* * * * ** *
19274323 CTATAGCGGCGCTTCTAC-ACAAACGCCGCAATAGCTTGGGAT
1 CTTTAGCGGCGCTTTTACAACAAACGCCACTATAGCTCAGGAC
*
19274365 CTTTAGCGGCGCTTTT-CTAACAAACGCCACTATAGCTCAAGAC
1 CTTTAGCGGCGCTTTTAC-AACAAACGCCACTATAGCTCAGGAC
* * * *
19274408 CTTTAACGGCGCTTTTACCACAAACGCCACTATAGATCAAAGAC
1 CTTTAGCGGCGCTTTTACAACAAACGCCACTATAGCTC-AGGAC
*
19274452 CTTTAGCGACGCTTT
1 CTTTAGCGGCGCTTT
19274467 GATTACAAAC
Statistics
Matches: 119, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.01
42 32 0.27
43 67 0.56
44 19 0.16
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTACAACAAACGCCACTATAGCTCAGGAC
Found at i:19279207 original size:47 final size:47
Alignment explanation
Indices: 19279108--19279208 Score: 159
Period size: 47 Copynumber: 2.1 Consensus size: 47
19279098 ATACATAGGT
* *
19279108 TTTTTTAAGTTATATTTATAAAAATTAGATAAAATTAAAAAATTTAG
1 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAAATTTAA
*
19279155 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATT-AAAAGTTTAA
1 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAAATTTAA
19279201 TGTTTTTA
1 T-TTTTTA
19279209 NNNNNNNNNN
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
46 9 0.18
47 41 0.82
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (47 bp):
TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAAATTTAA
Found at i:19279746 original size:15 final size:15
Alignment explanation
Indices: 19279711--19279748 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
19279701 GTCCCTTAAT
19279711 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
19279725 T-AATCCATAATCCC
1 TAAATCCATAATCCC
19279739 TAAATCCATA
1 TAAATCCATA
19279749 TATATAGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 12 0.55
15 8 0.36
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:19280050 original size:17 final size:17
Alignment explanation
Indices: 19280024--19280067 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
19280014 CCAACCCTTA
*
19280024 ATTAAACCATAATCCCT
1 ATTAATCCATAATCCCT
19280041 ATTAATCCATAATCCCT
1 ATTAATCCATAATCCCT
19280058 A--AATCCATAA
1 ATTAATCCATAA
19280068 ATACTCCCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 9 0.35
17 17 0.65
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (17 bp):
ATTAATCCATAATCCCT
Found at i:19294219 original size:2 final size:2
Alignment explanation
Indices: 19294212--19294239 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19294202 AATAAAAGGA
19294212 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19294240 GTGAAAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19299443 original size:13 final size:14
Alignment explanation
Indices: 19299424--19299461 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
19299414 TAATGACATA
19299424 GAAATAATATAAAC
1 GAAATAATATAAAC
19299438 -AAATAA-ATAAAC
1 GAAATAATATAAAC
19299450 GAAATAAATATA
1 GAAAT-AATATA
19299462 TATAAAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 2 0.10
15 3 0.14
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (14 bp):
GAAATAATATAAAC
Found at i:19314888 original size:13 final size:14
Alignment explanation
Indices: 19314869--19314906 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
19314859 CAATGACATA
19314869 GAAATAATATAAAC
1 GAAATAATATAAAC
19314883 -AAATAA-ATAAAC
1 GAAATAATATAAAC
19314895 GAAATGAATATA
1 GAAAT-AATATA
19314907 TATAAAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 2 0.10
15 3 0.14
ACGTcount: A:0.66, C:0.05, G:0.08, T:0.21
Consensus pattern (14 bp):
GAAATAATATAAAC
Found at i:19321825 original size:108 final size:109
Alignment explanation
Indices: 19321614--19321905 Score: 417
Period size: 108 Copynumber: 2.6 Consensus size: 109
19321604 TTATTAATTA
* * *
19321614 TTATAAATTGTTTGTGTTTAGTTTAGTATTTTGTAATTTTTTATGAATGTAAATTTTTTGTTTTT
1 TTATAAATTGTTTGTGTTTAGTTTAGTGTTTTGTGATTTTTTATGAATGT-AA-TTTTT-TTTGT
* * * *
19321679 TGTTTTTAAATTATTTTATAGTTATTTTGTTAGTAATTTATTATTAGG
63 T-TTTTTAAATTATTTTAAAGTCATTTTGTCAGTAATTTATGATTAGG
* * *
19321727 TTATATATTGTTTGTGTTTA-CTTAGTGTTTTGTGAGTTTTTATGAATGTAATTTTTTTTGTTTT
1 TTATAAATTGTTTGTGTTTAGTTTAGTGTTTTGTGATTTTTTATGAATGTAATTTTTTTTGTTTT
*
19321791 TTTAAATTATTTTAAAGTCATTTTGTCAGTAATTTATGGTTAGG
66 TTTAAATTATTTTAAAGTCATTTTGTCAGTAATTTATGATTAGG
19321835 TTATAAATTGTTTGTGTTTAGTTTAGTGTTTATTGTGATTTTTTATGAATGTAA-TTTTTTTGTT
1 TTATAAATTGTTTGTGTTTAGTTTAGTG-TT-TTGTGATTTTTTATGAATGTAATTTTTTTTGTT
19321899 TTTTTAA
64 TTTTTAA
19321906 GGGTAAACTA
Statistics
Matches: 162, Mismatches: 14, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
108 60 0.37
109 11 0.07
110 24 0.15
111 23 0.14
112 25 0.15
113 19 0.12
ACGTcount: A:0.23, C:0.01, G:0.15, T:0.61
Consensus pattern (109 bp):
TTATAAATTGTTTGTGTTTAGTTTAGTGTTTTGTGATTTTTTATGAATGTAATTTTTTTTGTTTT
TTTAAATTATTTTAAAGTCATTTTGTCAGTAATTTATGATTAGG
Found at i:19322797 original size:112 final size:110
Alignment explanation
Indices: 19322655--19322918 Score: 365
Period size: 112 Copynumber: 2.4 Consensus size: 110
19322645 ATTATAAATT
*
19322655 GTTT-GTGTTTATTGTGATTTTTTATGAATGTAAATTTTCTTTTGT-TTTTTTAA-TTATTTTAA
1 GTTTAGTGTTTATTGTGATTTGTTAT-AATGTAAATTTT-TTTTGTGTTTTTTAATTTATTTTAA
*
19322717 AGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTTA
64 AGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATT-ATT-TGTTTA
* * *
19322766 GTTTAGTGTTTATTGTGACTTGTTATAAATGTATA-TTTTTTTGTGTTTTTTAATTTTTTTTAAA
1 GTTTAGTGTTTATTGTGATTTGTTAT-AATGTAAATTTTTTTTGTGTTTTTTAATTTATTTTAAA
19322830 GTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTATTTGTTTA
65 GTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTATTTGTTTA
* * * *
19322876 GTTTAATGTGTCTTGTGATTTGTTATAATGTAATTTTATTTTT
1 GTTTAGTGTTTATTGTGATTTGTTATAATGTAAATTT-TTTTT
19322919 TTGATTTATT
Statistics
Matches: 136, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
109 6 0.04
110 36 0.26
111 22 0.16
112 72 0.53
ACGTcount: A:0.23, C:0.01, G:0.15, T:0.60
Consensus pattern (110 bp):
GTTTAGTGTTTATTGTGATTTGTTATAATGTAAATTTTTTTTGTGTTTTTTAATTTATTTTAAAG
TTATTTTGTTAGTAATTTATGATTAGGTTATAAATTATTTGTTTA
Found at i:19322805 original size:100 final size:99
Alignment explanation
Indices: 19322602--19322912 Score: 269
Period size: 100 Copynumber: 3.0 Consensus size: 99
19322592 TAGTTTACCC
* *
19322602 TTTTTAATTA-TTTGAAGTTATTTTGTTAGTAATTTATGATTAGATTATAAATTGTTTGTGTTTA
1 TTTTTAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTTA
* * * * **
19322666 -TTGTGATTTTTTATGAATGTAAATT-TTCTTTTGT-T-
66 GTT-T-AATGTTTAT---TGTGAATTGTTATAATGTATA
19322701 TTTTTAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTTA
1 TTTTTAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTTA
* *
19322766 GTTTAGTGTTTATTGTGACTTGTTATAAATGTATA
66 GTTTAATGTTTATTGTGAATTGTTAT-AATGTATA
*
19322801 TTTTTTTGTGTTTTTTAATTTTTTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAAT
1 -----------TTTTTAA-TTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAAT
* * * *
19322866 T-ATT-TGTTTAGTTTAATGTGTCTTGTGATTTGTTATAATGTA-A
54 TGTTTGTGTTTAGTTTAATGTTTATTGTGAATTGTTATAATGTATA
19322909 TTTT
1 TTTT
19322913 ATTTTTTTGA
Statistics
Matches: 179, Mismatches: 15, Indels: 38
0.77 0.06 0.16
Matches are distributed among these distances:
96 6 0.03
97 7 0.04
98 3 0.02
99 18 0.10
100 53 0.30
101 2 0.01
108 1 0.01
109 6 0.03
110 28 0.16
111 9 0.05
112 46 0.26
ACGTcount: A:0.25, C:0.01, G:0.15, T:0.59
Consensus pattern (99 bp):
TTTTTAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTTA
GTTTAATGTTTATTGTGAATTGTTATAATGTATA
Found at i:19322937 original size:21 final size:21
Alignment explanation
Indices: 19322913--19322954 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
19322903 ATGTAATTTT
19322913 ATTTTT-TTGATTTATTTGACA
1 ATTTTTATTGATTTA-TTGACA
19322934 ATTTTTATTGATTTATTGACA
1 ATTTTTATTGATTTATTGACA
19322955 TGTCGATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.60
Consensus pattern (21 bp):
ATTTTTATTGATTTATTGACA
Found at i:19325065 original size:33 final size:33
Alignment explanation
Indices: 19325023--19325085 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
19325013 CCAATGCCAT
* *
19325023 CGCAGTACTCGACTTC-TCCTGGCTCGTATCCAC
1 CGCAGTACTCCACTTCTTCC-GGCCCGTATCCAC
19325056 CGCAGTACTCCACTTCTTCCGGCCCGTATC
1 CGCAGTACTCCACTTCTTCCGGCCCGTATC
19325086 TTTGCCGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 24 0.89
34 3 0.11
ACGTcount: A:0.14, C:0.41, G:0.17, T:0.27
Consensus pattern (33 bp):
CGCAGTACTCCACTTCTTCCGGCCCGTATCCAC
Found at i:19327244 original size:26 final size:25
Alignment explanation
Indices: 19327201--19327249 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
19327191 ATAAACATTA
*
19327201 AACTAAAAAATTAATTTATAATAGT
1 AACTAAAAAATTAATTTAAAATAGT
19327226 AACTAACAAAA-TAACTTTAAAATA
1 AACTAA-AAAATTAA-TTTAAAATA
19327250 AAAAAACAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (25 bp):
AACTAAAAAATTAATTTAAAATAGT
Found at i:19327369 original size:16 final size:17
Alignment explanation
Indices: 19327348--19327383 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
19327338 AATAAAAATA
19327348 TCTTATCC-TTCTTTTT
1 TCTTATCCTTTCTTTTT
19327364 TCTTATCCTTTCTTTTT
1 TCTTATCCTTTCTTTTT
19327381 TCT
1 TCT
19327384 CCTTCTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (17 bp):
TCTTATCCTTTCTTTTT
Found at i:19327704 original size:2 final size:2
Alignment explanation
Indices: 19327697--19327721 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19327687 TTTTGGTATT
19327697 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
19327722 TTTAGAATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19329695 original size:20 final size:20
Alignment explanation
Indices: 19329670--19329708 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
19329660 GTTTTTACAT
19329670 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
19329690 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
19329709 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:19332537 original size:26 final size:26
Alignment explanation
Indices: 19332505--19332557 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
19332495 ACAAATTATG
19332505 AACATCAACGAGTAAACAAACGGTTT
1 AACATCAACGAGTAAACAAACGGTTT
19332531 AACATCAACGAGTAAACAAACGGTTT
1 AACATCAACGAGTAAACAAACGGTTT
19332557 A
1 A
19332558 CCTTAAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.19
Consensus pattern (26 bp):
AACATCAACGAGTAAACAAACGGTTT
Found at i:19338632 original size:24 final size:24
Alignment explanation
Indices: 19338604--19338655 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
19338594 TTTTATTATA
19338604 TATAGTATATTTTTAGAATGTAAC
1 TATAGTATATTTTTAGAATGTAAC
19338628 TATAGTATATTTTTAGAATGTAAC
1 TATAGTATATTTTTAGAATGTAAC
19338652 TATA
1 TATA
19338656 AGAATTGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (24 bp):
TATAGTATATTTTTAGAATGTAAC
Found at i:19340245 original size:29 final size:29
Alignment explanation
Indices: 19340187--19340247 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
19340177 TTAATCCCAA
**
19340187 TTATCATCCCCCATCTGCAAGTATAAATC
1 TTATCATCCCCCATCTGCAACCATAAATC
* *
19340216 TTATCATCTCTCATCTGCAACCA-AATATC
1 TTATCATCCCCCATCTGCAACCATAA-ATC
19340245 TTA
1 TTA
19340248 GGCTTACTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 2 0.07
29 25 0.93
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (29 bp):
TTATCATCCCCCATCTGCAACCATAAATC
Found at i:19341747 original size:22 final size:22
Alignment explanation
Indices: 19341722--19341764 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
19341712 ATATCAAATC
*
19341722 TAAA-TCTATTATTCATAACAAT
1 TAAAGTCTATTATCCA-AACAAT
19341744 TAAAGTCTATTATCCAAACAA
1 TAAAGTCTATTATCCAAACAA
19341765 CCATTACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (22 bp):
TAAAGTCTATTATCCAAACAAT
Found at i:19347240 original size:115 final size:115
Alignment explanation
Indices: 19347022--19347240 Score: 260
Period size: 115 Copynumber: 1.9 Consensus size: 115
19347012 ACCAATTCGT
* * * * *
19347022 GTGTAAATTCATCACAGGAACGCTCAACAACTAGTCCTTATCGAATGAACAACCACGAAACAAGC
1 GTGTAAATTAATCACAGGAACGCTCAAAAACTAATCCTTACCGAACGAACAACCACGAAACAAGC
* * * * *
19347087 ATCCACAATTTAGCTTTCTAGTAGCCTTGCGGATTAGAAGAGTCCAACTC
66 ATCCACAATTTAGCTCTCTAGTAACCTTACGAACTAGAAGAGTCCAACTC
* * * * *
19347137 GTGTAAATTAATCACAGGAATGCTGAAAAACTAATTCTTACCGAACGAACAACCACGAAACACGT
1 GTGTAAATTAATCACAGGAACGCTCAAAAACTAATCCTTACCGAACGAACAACCACGAAACAAGC
* * *
19347202 GTCCATAGTTTAGCTCTCT-GATAACCTTACGAACTAGAA
66 ATCCACAATTTAGCTCTCTAG-TAACCTTACGAACTAGAA
19347241 TAATCCAATT
Statistics
Matches: 85, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
114 1 0.01
115 84 0.99
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.24
Consensus pattern (115 bp):
GTGTAAATTAATCACAGGAACGCTCAAAAACTAATCCTTACCGAACGAACAACCACGAAACAAGC
ATCCACAATTTAGCTCTCTAGTAACCTTACGAACTAGAAGAGTCCAACTC
Found at i:19359373 original size:20 final size:20
Alignment explanation
Indices: 19359348--19359387 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
19359338 CTGACAAACT
19359348 CTCTTTCATACTCAACTATG
1 CTCTTTCATACTCAACTATG
19359368 CTCTTTCATACTCAACTATG
1 CTCTTTCATACTCAACTATG
19359388 GTCAGACGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.05, T:0.40
Consensus pattern (20 bp):
CTCTTTCATACTCAACTATG
Found at i:19360320 original size:18 final size:17
Alignment explanation
Indices: 19360287--19360325 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
19360277 TTGTATAAAT
19360287 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
19360305 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
19360322 TGTG
1 TGTG
19360326 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:19360443 original size:8 final size:8
Alignment explanation
Indices: 19360430--19360458 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
19360420 CACTAGAGAC
19360430 CAGTGTTA
1 CAGTGTTA
19360438 CAGTGTTA
1 CAGTGTTA
19360446 CAGTGTTA
1 CAGTGTTA
19360454 CAGTG
1 CAGTG
19360459 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:19360572 original size:23 final size:23
Alignment explanation
Indices: 19360545--19360620 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
19360535 AGTGTTATTG
19360545 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
19360568 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
19360591 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
19360614 ATCAGTG
1 ATCAGTG
19360621 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:19375430 original size:24 final size:24
Alignment explanation
Indices: 19375380--19375430 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
19375370 TTCTATTATA
* *
19375380 GCACTTTGGTGCAACTCTGTTATG
1 GCACTTTGATGCAACTCTGTTAAG
* *
19375404 GCACTTTGATGCGACTTTGTTAAG
1 GCACTTTGATGCAACTCTGTTAAG
19375428 GCA
1 GCA
19375431 ATTCAATACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (24 bp):
GCACTTTGATGCAACTCTGTTAAG
Found at i:19379705 original size:2 final size:2
Alignment explanation
Indices: 19379698--19379723 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19379688 ATCCCAATTT
19379698 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
19379724 TACATATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:19390071 original size:46 final size:52
Alignment explanation
Indices: 19390000--19390150 Score: 188
Period size: 53 Copynumber: 3.0 Consensus size: 52
19389990 TGGTCCTTCC
*
19390000 CATATGATGTCATAACCCACCAGTTACGGTCTTACAC-A-CT-TC-T-TTTT
1 CATATGATGTCATAACCCACTAGTTACGGTCTTACACGATCTGTCTTCTTTT
* *
19390047 -ATATGATGTCATAACTCACTAGTTACGGCCTTACACGATCTGGTCTTCTTTT
1 CATATGATGTCATAACCCACTAGTTACGGTCTTACACGATCT-GTCTTCTTTT
* * *
19390099 CATAGGATGTCATAACCCACTAGTTATGGTCTTACACGATATGATCTTCTTT
1 CATATGATGTCATAACCCACTAGTTACGGTCTTACACGATCTG-TCTTCTTT
19390151 AGTGACATTG
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
46 33 0.38
47 1 0.01
48 2 0.02
50 2 0.02
51 1 0.01
52 5 0.06
53 44 0.50
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (52 bp):
CATATGATGTCATAACCCACTAGTTACGGTCTTACACGATCTGTCTTCTTTT
Found at i:19400592 original size:32 final size:31
Alignment explanation
Indices: 19400532--19400602 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
19400522 ATCTACAAGT
*
19400532 TAAGTATATTAAATTAATAAAACATATTAAGA
1 TAAGTAT-TTAAATTAATAAAACATATTAAAA
*
19400564 TAAGTATTTAATTTAATATTAAAC-TATTAAAA
1 TAAGTATTTAAATTAATA--AAACATATTAAAA
19400596 TAA-TATT
1 TAAGTATT
19400603 ATTTTTGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 14 0.40
32 17 0.49
33 4 0.11
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (31 bp):
TAAGTATTTAAATTAATAAAACATATTAAAA
Found at i:19409631 original size:16 final size:16
Alignment explanation
Indices: 19409610--19409641 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19409600 TACAAGAATT
19409610 TACAACGAAATTGAAA
1 TACAACGAAATTGAAA
*
19409626 TACAACGAGATTGAAA
1 TACAACGAAATTGAAA
19409642 ATGGAAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.12, G:0.16, T:0.19
Consensus pattern (16 bp):
TACAACGAAATTGAAA
Found at i:19409834 original size:22 final size:22
Alignment explanation
Indices: 19409791--19409835 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
19409781 GCAATTTGAA
* *
19409791 TATTTGATATTTTTTCTCTTGG
1 TATTTGAGATTTTTTCTATTGG
19409813 TATTTGAGATTGTTTT-TATTGG
1 TATTTGAGATT-TTTTCTATTGG
19409835 T
1 T
19409836 TGACGAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.16, C:0.04, G:0.18, T:0.62
Consensus pattern (22 bp):
TATTTGAGATTTTTTCTATTGG
Found at i:19411922 original size:16 final size:16
Alignment explanation
Indices: 19411903--19411944 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
19411893 TTTTTAAAAA
19411903 TATAATTTTGGAATTT
1 TATAATTTTGGAATTT
*
19411919 TATAAATATTTTGAATTT
1 TAT-AAT-TTTGGAATTT
19411937 TA-AATTTT
1 TATAATTTT
19411945 TTTTTGTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 3 0.13
16 6 0.26
17 3 0.13
18 11 0.48
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (16 bp):
TATAATTTTGGAATTT
Found at i:19416473 original size:21 final size:22
Alignment explanation
Indices: 19416426--19416473 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
19416416 ATATAATAAT
* * *
19416426 AAAATTATATTTTAACTTCGTA
1 AAAATTATAATTTAAATCCGTA
19416448 AAAATTATAATTTAAATCCG-A
1 AAAATTATAATTTAAATCCGTA
19416469 AAAAT
1 AAAAT
19416474 AAAAGTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (22 bp):
AAAATTATAATTTAAATCCGTA
Found at i:19418169 original size:15 final size:15
Alignment explanation
Indices: 19418146--19418180 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
19418136 GTTTTCCTTT
*
19418146 CAACTGTAACTTTTC
1 CAACGGTAACTTTTC
19418161 CAACGGTAACTTTTC
1 CAACGGTAACTTTTC
19418176 CAACG
1 CAACG
19418181 ACTAGTAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.31
Consensus pattern (15 bp):
CAACGGTAACTTTTC
Found at i:19418323 original size:7 final size:7
Alignment explanation
Indices: 19418313--19418365 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
19418303 TCAATCCCAT
19418313 TTTTCAA
1 TTTTCAA
19418320 TTTT-ATA
1 TTTTCA-A
19418327 TTTTCAA
1 TTTTCAA
*
19418334 TCTTCAAA
1 TTTTC-AA
19418342 TTTT-AA
1 TTTTCAA
19418348 TTTTCAA
1 TTTTCAA
*
19418355 TTTTTAA
1 TTTTCAA
19418362 TTTT
1 TTTT
19418366 TAATCCTCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 7 0.18
7 26 0.67
8 6 0.15
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTTCAA
Found at i:19418350 original size:21 final size:21
Alignment explanation
Indices: 19418318--19418369 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
19418308 CCCATTTTTC
19418318 AATTTTATATTTTCAATCTTCA
1 AATTTTA-ATTTTCAATCTTCA
* *
19418340 AATTTTAATTTTCAATTTTTA
1 AATTTTAATTTTCAATCTTCA
*
19418361 ATTTTTAAT
1 AATTTTAAT
19418370 CCTCAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.60
Consensus pattern (21 bp):
AATTTTAATTTTCAATCTTCA
Found at i:19422341 original size:27 final size:28
Alignment explanation
Indices: 19422311--19422369 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
19422301 ACACACCCGG
**
19422311 AATAATAT-AAATCCTCCTTAACACACC
1 AATAATATCAAATCCTCCCAAACACACC
*
19422338 AAT-ATATCATATCCTCCCAAACACACC
1 AATAATATCAAATCCTCCCAAACACACC
19422365 AATAA
1 AATAA
19422370 GGCATTAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 4 0.15
27 22 0.81
28 1 0.04
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.24
Consensus pattern (28 bp):
AATAATATCAAATCCTCCCAAACACACC
Found at i:19422935 original size:22 final size:24
Alignment explanation
Indices: 19422893--19422936 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
19422883 TAACTAAGCT
19422893 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
19422917 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
19422937 TCTTGCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:19423527 original size:5 final size:5
Alignment explanation
Indices: 19423508--19423578 Score: 69
Period size: 5 Copynumber: 14.6 Consensus size: 5
19423498 TTAGTTTATT
* *
19423508 TAATA T-ATAA TAATA TAATA AAATA TAAT- TAATA TAATA TAATA TATTA
1 TAATA TAAT-A TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
*
19423557 T-ATGA TAAAA TAATA T-ATA TAA
1 TAAT-A TAATA TAATA TAATA TAA
19423579 AACATAAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
4 11 0.20
5 40 0.74
6 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (5 bp):
TAATA
Found at i:19423564 original size:29 final size:29
Alignment explanation
Indices: 19423507--19423578 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 29
19423497 TTTAGTTTAT
19423507 TTAATATATAATAATATAATAAAATAT-AA
1 TTAATATAT-ATAATATAATAAAATATAAA
* *
19423536 TTAATATAATATAATAT-ATTATATGATAAA
1 TTAATAT-ATATAATATAATAAAAT-ATAAA
*
19423566 ATAATATATATAA
1 TTAATATATATAA
19423579 AACATAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 5 0.14
29 22 0.59
30 10 0.27
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (29 bp):
TTAATATATATAATATAATAAAATATAAA
Found at i:19428040 original size:19 final size:19
Alignment explanation
Indices: 19428016--19428053 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
19428006 CTCAAGCATA
19428016 GATAAAAATAAATCTACAG
1 GATAAAAATAAATCTACAG
19428035 GATAAAAATAAATCTACAG
1 GATAAAAATAAATCTACAG
19428054 ACTTCTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.21
Consensus pattern (19 bp):
GATAAAAATAAATCTACAG
Found at i:19431881 original size:11 final size:11
Alignment explanation
Indices: 19431865--19431889 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19431855 CGGAGATGAC
19431865 TTGGAACAAAA
1 TTGGAACAAAA
19431876 TTGGAACAAAA
1 TTGGAACAAAA
19431887 TTG
1 TTG
19431890 TTTATAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (11 bp):
TTGGAACAAAA
Found at i:19432188 original size:42 final size:43
Alignment explanation
Indices: 19432091--19432226 Score: 206
Period size: 43 Copynumber: 3.2 Consensus size: 43
19432081 GAGGGTCTCG
19432091 AGGTGCCGATG-GTGCTCGAGGCTCCCGCACAT-CTGAGCCACCA
1 AGGTGCCGATGCG-GCTCGAGGCTCCCGCACATCCT-AGCCACCA
* *
19432134 AGGTGCTGATGCGGCTCGAGGCTCTCGCACATCCTAG-CACCA
1 AGGTGCCGATGCGGCTCGAGGCTCCCGCACATCCTAGCCACCA
*
19432176 AGGTGCCGATGCGGCTCGAGGCTCCCGCACATCCGAGCCACCA
1 AGGTGCCGATGCGGCTCGAGGCTCCCGCACATCCTAGCCACCA
19432219 AGGTGCCG
1 AGGTGCCG
19432227 GCCACCAGTT
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
42 39 0.46
43 43 0.51
44 3 0.04
ACGTcount: A:0.18, C:0.35, G:0.31, T:0.15
Consensus pattern (43 bp):
AGGTGCCGATGCGGCTCGAGGCTCCCGCACATCCTAGCCACCA
Found at i:19432987 original size:2 final size:2
Alignment explanation
Indices: 19432980--19433005 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19432970 TTAACAAATA
19432980 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
19433006 TAATTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19436223 original size:17 final size:18
Alignment explanation
Indices: 19436192--19436226 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19436182 ATTTAATTAT
19436192 CAATTTATACAAATTTTG
1 CAATTTATACAAATTTTG
*
19436210 CAATTTATTC-AATTTTG
1 CAATTTATACAAATTTTG
19436227 TCCCTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (18 bp):
CAATTTATACAAATTTTG
Found at i:19448261 original size:20 final size:21
Alignment explanation
Indices: 19448236--19448280 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
19448226 GAATTTATGG
19448236 TTTAAGGTTT-ATATTAAATT
1 TTTAAGGTTTAATATTAAATT
* *
19448256 TTTAAGTTTTAGATTTTAAATT
1 TTTAAGGTTTA-ATATTAAATT
19448278 TTT
1 TTT
19448281 GATTTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
22 12 0.57
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (21 bp):
TTTAAGGTTTAATATTAAATT
Found at i:19448274 original size:14 final size:14
Alignment explanation
Indices: 19448255--19448292 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
19448245 TATATTAAAT
*
19448255 TTTTAAGTTTTAGA
1 TTTTAAATTTTAGA
*
19448269 TTTTAAATTTTTGA
1 TTTTAAATTTTAGA
19448283 TTTTAAATTT
1 TTTTAAATTT
19448293 ATGTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (14 bp):
TTTTAAATTTTAGA
Found at i:19448836 original size:30 final size:29
Alignment explanation
Indices: 19448802--19448878 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 29
19448792 ATAAAAGTAG
* *
19448802 AAAATTATAAAAATTATAGAATAACTATAA
1 AAAATTATAAAAATTATACAA-AACTACAA
*
19448832 AAAATTATAAAAATATTATACAAAATTACAA
1 AAAATTAT-AAAA-ATTATACAAAACTACAA
19448863 AAAA-TATAAAAATTAT
1 AAAATTATAAAAATTAT
19448879 TAATATATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.12
29 4 0.10
30 11 0.26
31 14 0.33
32 8 0.19
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.30
Consensus pattern (29 bp):
AAAATTATAAAAATTATACAAAACTACAA
Found at i:19448851 original size:21 final size:21
Alignment explanation
Indices: 19448805--19448914 Score: 88
Period size: 21 Copynumber: 5.5 Consensus size: 21
19448795 AAAGTAGAAA
*
19448805 ATTAT-AAAAATTAT-AGAAT
1 ATTATAAAAAATTATAAAAAT
*
19448824 AACTATAAAAAATTATAAAAAT
1 -ATTATAAAAAATTATAAAAAT
* *
19448846 ATTATACAAAATTACAAAAA-
1 ATTATAAAAAATTATAAAAAT
* *
19448866 A-TAT-AAAAATTATTAATAT
1 ATTATAAAAAATTATAAAAAT
* **
19448885 ATTATGAAAAA-TATGCAAAT
1 ATTATAAAAAATTATAAAAAT
19448905 ATTATAAAAA
1 ATTATAAAAA
19448915 CTAGAATTAT
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
18 10 0.14
19 4 0.06
20 23 0.32
21 31 0.43
22 4 0.06
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.32
Consensus pattern (21 bp):
ATTATAAAAAATTATAAAAAT
Found at i:19448895 original size:30 final size:28
Alignment explanation
Indices: 19448802--19448898 Score: 79
Period size: 29 Copynumber: 3.3 Consensus size: 28
19448792 ATAAAAGTAG
* * *
19448802 AAAATTATAAAAATTATAGAATAACTATA
1 AAAAATATAAAAATTAT-TAATAATTATA
* *
19448831 AAAAATTATAAAAA-TATTATACAAAATTACA
1 AAAAA-TATAAAAATTA-T-TA-ATAATTATA
*
19448862 AAAAATATAAAAATTATTAATATATTATG
1 AAAAATATAAAAATTATTAATA-ATTATA
19448891 AAAAATAT
1 AAAAATAT
19448899 GCAAATATTA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
28 2 0.04
29 20 0.36
30 20 0.36
31 13 0.24
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (28 bp):
AAAAATATAAAAATTATTAATAATTATA
Found at i:19448896 original size:39 final size:38
Alignment explanation
Indices: 19448805--19448914 Score: 103
Period size: 39 Copynumber: 2.7 Consensus size: 38
19448795 AAAGTAGAAA
* *
19448805 ATTATAAAAATTATAGAATAACTATAAAAAATTATAAAAAT
1 ATTATAAAAATTACA-AA-AAATAT-AAAAATTATAAAAAT
* *
19448846 ATTATACAAAATTACAAAAAATATAAAAATTATTAATAT
1 ATTATA-AAAATTACAAAAAATATAAAAATTATAAAAAT
* * *
19448885 ATTATGAAAAATATGCAAATATTATAAAAA
1 ATTAT-AAAAAT-TACAAAAAATATAAAAA
19448915 CTAGAATTAT
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
39 23 0.39
40 20 0.34
41 8 0.14
42 8 0.14
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.32
Consensus pattern (38 bp):
ATTATAAAAATTACAAAAAATATAAAAATTATAAAAAT
Found at i:19449424 original size:11 final size:11
Alignment explanation
Indices: 19449385--19449430 Score: 62
Period size: 10 Copynumber: 4.5 Consensus size: 11
19449375 TGCTTTTATG
19449385 ATTTTAATA-A
1 ATTTTAATATA
19449395 ATTTTAA-ATA
1 ATTTTAATATA
*
19449405 ATTTT-ATATC
1 ATTTTAATATA
19449415 ATTTTAATATA
1 ATTTTAATATA
19449426 ATTTT
1 ATTTT
19449431 CTATGACTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 2 0.06
10 20 0.65
11 9 0.29
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTTAATATA
Found at i:19450018 original size:4 final size:4
Alignment explanation
Indices: 19450009--19450045 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
19449999 ATCTAACCTC
*
19450009 GTAT GTAT GTAT GTAT GTAT GTAT GCAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
19450046 AGTTTAGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.24, C:0.03, G:0.27, T:0.46
Consensus pattern (4 bp):
GTAT
Found at i:19456866 original size:6 final size:6
Alignment explanation
Indices: 19456855--19456880 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
19456845 AGAATCATGC
19456855 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
19456881 CTTTTGGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:19459668 original size:15 final size:15
Alignment explanation
Indices: 19459648--19459680 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
19459638 TTCCAAATGT
19459648 TAGTTGTTCTCAACA
1 TAGTTGTTCTCAACA
*
19459663 TAGTTGTTCTCAATA
1 TAGTTGTTCTCAACA
19459678 TAG
1 TAG
19459681 AGATTGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (15 bp):
TAGTTGTTCTCAACA
Found at i:19459786 original size:16 final size:16
Alignment explanation
Indices: 19459765--19459824 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
19459755 GGAAAAAAAA
19459765 TTGTTCTAAATACA-AG
1 TTGTTCTAAA-ACATAG
*
19459781 TTGTTCCAAAACATAG
1 TTGTTCTAAAACATAG
19459797 TTGTTCT-AAACATAG
1 TTGTTCTAAAACATAG
*
19459812 TTATTCCTAAAAC
1 TTGTT-CTAAAAC
19459825 GTCATTATTC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
15 15 0.39
16 19 0.50
17 4 0.11
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (16 bp):
TTGTTCTAAAACATAG
Found at i:19459809 original size:15 final size:15
Alignment explanation
Indices: 19459765--19459813 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
19459755 GGAAAAAAAA
19459765 TTGTTCTAAATACA-AG
1 TTGTTCT-AA-ACATAG
*
19459781 TTGTTCCAAAACATAG
1 TTGTT-CTAAACATAG
19459797 TTGTTCTAAACATAG
1 TTGTTCTAAACATAG
19459812 TT
1 TT
19459814 ATTCCTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 14 0.48
16 14 0.48
17 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (15 bp):
TTGTTCTAAACATAG
Found at i:19468408 original size:23 final size:22
Alignment explanation
Indices: 19468366--19468408 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
19468356 ATGAGACCAA
*
19468366 AAAAAATTCAAGTATCAATTTG
1 AAAAAATTCAAGTATAAATTTG
19468388 AAAAAATT-AAGGTACTAAATT
1 AAAAAATTCAA-GTA-TAAATT
19468409 AAATATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 2 0.11
22 11 0.61
23 5 0.28
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.30
Consensus pattern (22 bp):
AAAAAATTCAAGTATAAATTTG
Found at i:19478542 original size:25 final size:25
Alignment explanation
Indices: 19478508--19478620 Score: 124
Period size: 25 Copynumber: 4.5 Consensus size: 25
19478498 GACACACTAT
* *
19478508 AGCTCTTATGAGCTTATCGATTCTC
1 AGCTCGTATGAGCTTACCGATTCTC
19478533 AGCTCGTATGAGCTTACCGATTCTC
1 AGCTCGTATGAGCTTACCGATTCTC
*
19478558 AACTCGTATGAGCTTACCGATT-TAC
1 AGCTCGTATGAGCTTACCGATTCT-C
* * *
19478583 AACTCATGA-GAGCATACCGATTCAT-
1 AGCTCGT-ATGAGCTTACCGATTC-TC
19478608 AGCTCGTATGAGC
1 AGCTCGTATGAGC
19478621 ATACATGTAT
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
24 2 0.03
25 72 0.95
26 1 0.01
27 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.31
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGATTCTC
Found at i:19486315 original size:51 final size:51
Alignment explanation
Indices: 19486260--19486699 Score: 129
Period size: 50 Copynumber: 8.8 Consensus size: 51
19486250 TGCAATGTCG
* *
19486260 GGGAAACCAGATCTGCCGTTCGTAGCTTCAATCTGTTCCACCACACCGTCA
1 GGGAAACCAGATCTGCCGTTCGTAGCTTCAATCTGTTCCACCACAACATCA
** * * ** *** *
19486311 GGG-AAGTAGGATCTGCCGTT-GTGGCTTCAATCTTTTTAATTGCAATATCA
1 GGGAAACCA-GATCTGCCGTTCGTAGCTTCAATCTGTTCCACCACAACATCA
* * **
19486361 GGGAAACCAAATCCGCCG-TCGTAGCTTCAATCTGTTCCACTGC-AC-TGCTA
1 GGGAAACCAGATCTGCCGTTCGTAGCTTCAATCTGTTCCACCACAACAT-C-A
* *** * * * ** *** *
19486411 AGGAAGTAAGATCCGCCGTT-GTGGCTTCAATCTTTTTAATTGCAATATCA
1 GGGAAACCAGATCTGCCGTTCGTAGCTTCAATCTGTTCCACCACAACATCA
* * **
19486461 GAGAAACCAGATCCGCCG-TCGTAGCTTCAATCTGTTCCACTGC-AC-TGCTA
1 GGGAAACCAGATCTGCCGTTCGTAGCTTCAATCTGTTCCACCACAACAT-C-A
* *** * * ** *** * *
19486511 AGGAAGTAAGATCCGCCGTT-GTGGCTTCAATCT-TTTAATTGCAATATTA
1 GGGAAACCAGATCTGCCGTTCGTAGCTTCAATCTGTTCCACCACAACATCA
* * **
19486560 GGGAAACCAAATCCGCCG-TCGTAGCTTCAATCTGTTCCACTGC-AC-TGCTA
1 GGGAAACCAGATCTGCCGTTCGTAGCTTCAATCTGTTCCACCACAACAT-C-A
* ** * * ** *** *
19486610 AGGAAATAAGATCTGCCGTT-GTGGCTTCAATCTTTTTAATTGCAATATCA
1 GGGAAACCAGATCTGCCGTTCGTAGCTTCAATCTGTTCCACCACAACATCA
* * *
19486660 GGGAAACCAGATCCGCCG-TCGTAGCTTTAATCTATTCCAC
1 GGGAAACCAGATCTGCCGTTCGTAGCTTCAATCTGTTCCAC
19486700 TGCACTGCTA
Statistics
Matches: 280, Mismatches: 87, Indels: 45
0.68 0.21 0.11
Matches are distributed among these distances:
48 4 0.01
49 40 0.14
50 209 0.75
51 25 0.09
52 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (51 bp):
GGGAAACCAGATCTGCCGTTCGTAGCTTCAATCTGTTCCACCACAACATCA
Found at i:19486362 original size:50 final size:49
Alignment explanation
Indices: 19486308--19486747 Score: 251
Period size: 50 Copynumber: 8.8 Consensus size: 49
19486298 CACCACACCG
* *
19486308 TCAGGGAAGTAGGATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCAATA
1 TCAGGGAACTA-GATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATA
* * * * * ** * *
19486358 TCAGGGAAACCAAATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACT-
1 TCAGGG-AACTAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATA
* * *
19486407 GCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATA
1 TC-AGGGAACT-AGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATA
* * * * * ** * *
19486458 TCAGAGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACT-
1 TCAG-GGAACTAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATA
* * *
19486507 GCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATC-TTTTAATTGCAATA
1 TC-AGGGAACT-AGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATA
* * * * * * ** * *
19486557 TTAGGGAAACCAAATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACT-
1 TCAGGG-AACTAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATA
* * * *
19486606 GCTAAGGAAATAAGATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCAATA
1 TC-AGGGAACT-AGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATA
* * * * * ** * *
19486657 TCAGGGAAACCAGATCCGCCGTCGTAGCTTTAATCTATTCCACTGCACT-
1 TCAGGG-AACTAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATA
* ** *
19486706 GCTAATGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTA
1 TC-AGGGAACT-AGATCCGCCGTTGTGGCTTCAATCTTTTTA
19486748 CTTGTCAACC
Statistics
Matches: 276, Mismatches: 98, Indels: 32
0.68 0.24 0.08
Matches are distributed among these distances:
49 44 0.16
50 222 0.80
51 10 0.04
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (49 bp):
TCAGGGAACTAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATA
Found at i:19486429 original size:100 final size:100
Alignment explanation
Indices: 19486234--19486747 Score: 809
Period size: 100 Copynumber: 5.1 Consensus size: 100
19486224 GATCTGTAAT
* * * *
19486234 CTTCAAT-TTGTTCAATTGCAATGTCGGGGAAACCAGATCTGCCGTTCGTAGCTTCAATCTGTTC
1 CTTCAATCTT-TTTAATTGCAATATCAGGGAAACCAGATCCGCCG-TCGTAGCTTCAATCTGTTC
** * * * *
19486298 CACCACACCG-TCAGGGAAGTAGGATCTGCCGTTGTGG
64 CACTGCACTGCT-AAGGAAGTAAGATCCGCCGTTGTGG
*
19486335 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAAATCCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
19486400 CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
66 CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
*
19486435 CTTCAATCTTTTTAATTGCAATATCAGAGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
19486500 CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
66 CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
* *
19486535 CTTCAATC-TTTTAATTGCAATATTAGGGAAACCAAATCCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
* *
19486599 CTGCACTGCTAAGGAAATAAGATCTGCCGTTGTGG
66 CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
* *
19486634 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTTAATCTATTCCA
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
*
19486699 CTGCACTGCTAATGAAGTAAGATCCGCCGTTGTGG
66 CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
19486734 CTTCAATCTTTTTA
1 CTTCAATCTTTTTA
19486748 CTTGTCAACC
Statistics
Matches: 385, Mismatches: 25, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
99 94 0.24
100 252 0.65
101 37 0.10
102 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.30
Consensus pattern (100 bp):
CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
Found at i:19486594 original size:199 final size:199
Alignment explanation
Indices: 19486234--19486745 Score: 821
Period size: 199 Copynumber: 2.6 Consensus size: 199
19486224 GATCTGTAAT
* * * *
19486234 CTTCAAT-TTGTTCAATTGCAATGTCGGGGAAACCAGATCTGCCGTTCGTAGCTTCAATCTGTTC
1 CTTCAATCTT-TTTAATTGCAATATCAGGGAAACCAGATCCGCCG-TCGTAGCTTCAATCTGTTC
** * * * *
19486298 CACCACACCG-TCAGGGAAGTAGGATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCAG
64 CACTGCACTGCT-AAGGAAGTAAGATCCGCCGTTGTGGCTTCAATC-TTTTAATTGCAATATCAG
*
19486362 GGAAACCAAATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGC
127 GGAAACCAAATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAATAAGATCCGC
19486427 CGTTGTGG
192 CGTTGTGG
*
19486435 CTTCAATCTTTTTAATTGCAATATCAGAGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
*
19486500 CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTAATTGCAATATTAGGGAA
66 CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTAATTGCAATATCAGGGAA
*
19486565 ACCAAATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAATAAGATCTGCCGTT
131 ACCAAATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAATAAGATCCGCCGTT
19486630 GTGG
196 GTGG
* *
19486634 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTTAATCTATTCCA
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
*
19486699 CTGCACTGCTAATGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTT
66 CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTT
19486746 TACTTGTCAA
Statistics
Matches: 291, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
199 196 0.67
200 56 0.19
201 37 0.13
202 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.30
Consensus pattern (199 bp):
CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTAATTGCAATATCAGGGAA
ACCAAATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAATAAGATCCGCCGTT
GTGG
Found at i:19492623 original size:92 final size:92
Alignment explanation
Indices: 19492527--19492703 Score: 336
Period size: 92 Copynumber: 1.9 Consensus size: 92
19492517 ATAGAAGTAT
19492527 ATATATATGTATATAAAAGTGATGAAATAAAATAATAAACTATGTATAAAATATGTACAAATATA
1 ATATATATGTATATAAAAGTGATGAAATAAAATAATAAACTATGTATAAAATATGTACAAATATA
*
19492592 CGTGCATTATATACAAAACATATAGAA
66 AGTGCATTATATACAAAACATATAGAA
*
19492619 ATATATATGTATATAAAAGTGATGAAATAAAATAATAAACTATGTATAAAATATGTACCAATATA
1 ATATATATGTATATAAAAGTGATGAAATAAAATAATAAACTATGTATAAAATATGTACAAATATA
19492684 AGTGCATTATATACAAAACA
66 AGTGCATTATATACAAAACA
19492704 ATACATACAT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 83 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.31
Consensus pattern (92 bp):
ATATATATGTATATAAAAGTGATGAAATAAAATAATAAACTATGTATAAAATATGTACAAATATA
AGTGCATTATATACAAAACATATAGAA
Found at i:19492749 original size:92 final size:91
Alignment explanation
Indices: 19492531--19492724 Score: 286
Period size: 92 Copynumber: 2.2 Consensus size: 91
19492521 AAGTATATAT
* * *
19492531 ATATGTATATAAAAGTGATGAAATAAAATAATAAACTATGTATAAAATATGTACAAATATACGTG
1 ATATGTACATAAAAGGGATGAAATAAAATAATAAACTATGTATAAAATATGTACAAATATAAGTG
*
19492596 CATTATATACAAAACATATAGAAATAT
66 CATTATATACAAAACATATA-AAATAC
* * *
19492623 ATATGTATATAAAAGTGATGAAATAAAATAATAAACTATGTATAAAATATGTACCAATATAAGTG
1 ATATGTACATAAAAGGGATGAAATAAAATAATAAACTATGTATAAAATATGTACAAATATAAGTG
*
19492688 CATTATATACAAAACA-AT-ACATAC
66 CATTATATACAAAACATATAAAATAC
19492712 ATAT-TACATAAAA
1 ATATGTACATAAAA
19492725 ACCGAGGTAT
Statistics
Matches: 97, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
88 8 0.08
89 8 0.08
91 2 0.02
92 79 0.81
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.30
Consensus pattern (91 bp):
ATATGTACATAAAAGGGATGAAATAAAATAATAAACTATGTATAAAATATGTACAAATATAAGTG
CATTATATACAAAACATATAAAATAC
Found at i:19507148 original size:24 final size:24
Alignment explanation
Indices: 19507103--19507148 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
19507093 AATCTGCGTC
* *
19507103 TGCATTTGTATCTAAATTTGAATA
1 TGCATATGTATCTAAATATGAATA
* *
19507127 TGCATATGTATTTGAATATGAA
1 TGCATATGTATCTAAATATGAA
19507149 AATACATCTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (24 bp):
TGCATATGTATCTAAATATGAATA
Found at i:19508164 original size:2 final size:2
Alignment explanation
Indices: 19508157--19508213 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
19508147 CCTTGAATTT
19508157 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19508199 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
19508214 TTCACTTTGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19508652 original size:21 final size:21
Alignment explanation
Indices: 19508608--19508652 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
19508598 TTTGTAGAAA
*
19508608 TTAAAAATATTTGAAATTTCT
1 TTAAAAATATTAGAAATTTCT
*
19508629 TTAAAAACTATTAGAACTTT-T
1 TTAAAAA-TATTAGAAATTTCT
19508650 TTA
1 TTA
19508653 GAACTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (21 bp):
TTAAAAATATTAGAAATTTCT
Found at i:19509284 original size:18 final size:19
Alignment explanation
Indices: 19509249--19509287 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
19509239 TTTAATAACT
**
19509249 TTTTTATATATTTTTAAAA
1 TTTTTATATATTAATAAAA
19509268 TTTTTATA-ATTAATAAAA
1 TTTTTATATATTAATAAAA
19509286 TT
1 TT
19509288 ATCTCTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTTATATATTAATAAAA
Found at i:19509646 original size:9 final size:9
Alignment explanation
Indices: 19509632--19509698 Score: 91
Period size: 9 Copynumber: 7.4 Consensus size: 9
19509622 TTTGGTTAAA
19509632 AATTAACCG
1 AATTAACCG
19509641 AATTAACCG
1 AATTAACCG
*
19509650 AATT-ACTTG
1 AATTAAC-CG
19509659 AATTAACCG
1 AATTAACCG
19509668 AATTAACCG
1 AATTAACCG
* *
19509677 GATTACCCG
1 AATTAACCG
19509686 AATTAACCG
1 AATTAACCG
19509695 AATT
1 AATT
19509699 GAATCACTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
8 2 0.04
9 46 0.92
10 2 0.04
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:19509670 original size:27 final size:27
Alignment explanation
Indices: 19509632--19509698 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
19509622 TTTGGTTAAA
**
19509632 AATTAACCGAATTAACCGAATTACTTG
1 AATTAACCGAATTAACCGAATTACCCG
*
19509659 AATTAACCGAATTAACCGGATTACCCG
1 AATTAACCGAATTAACCGAATTACCCG
19509686 AATTAACCGAATT
1 AATTAACCGAATT
19509699 GAATCACTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (27 bp):
AATTAACCGAATTAACCGAATTACCCG
Found at i:19509749 original size:6 final size:6
Alignment explanation
Indices: 19509718--19509760 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
19509708 CATAATTAAA
*
19509718 TTAGTT TTAGACTT TTAGACT TTAGTT TTAGTT TTAGTT TTAG
1 TTAGTT TTAG--TT TTAG-TT TTAGTT TTAGTT TTAGTT TTAG
19509761 AATTTTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
6 21 0.66
7 5 0.16
8 6 0.19
ACGTcount: A:0.21, C:0.05, G:0.16, T:0.58
Consensus pattern (6 bp):
TTAGTT
Found at i:19509841 original size:18 final size:18
Alignment explanation
Indices: 19509801--19509844 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
19509791 AATTTTTATG
**
19509801 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
19509819 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
19509837 CTTGGGTT
1 ATTGGGTT
19509845 TGGATTGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:19513778 original size:17 final size:17
Alignment explanation
Indices: 19513740--19513788 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
19513730 GGTTGAGAAG
19513740 TAAAAGTTTAGGGGAAAA
1 TAAAAGTTTAGGGG-AAA
*
19513758 TAAAAAGTTTTGGGG-AA
1 T-AAAAGTTTAGGGGAAA
19513775 TAAAAGTTTGAGGG
1 TAAAAGTTT-AGGG
19513789 AAAGTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.30
17 6 0.22
18 1 0.04
19 12 0.44
ACGTcount: A:0.43, C:0.00, G:0.31, T:0.27
Consensus pattern (17 bp):
TAAAAGTTTAGGGGAAA
Found at i:19518836 original size:64 final size:64
Alignment explanation
Indices: 19518756--19518887 Score: 246
Period size: 64 Copynumber: 2.1 Consensus size: 64
19518746 TAATTTTAGG
*
19518756 AACATCCTACAATCAATTCTTTATATACCGCCAATGGGCGGATGCTTTAATGCTAGTATGCGTT
1 AACATCCTACAATCAATTCTTTATATACCGCCAATGGGCGAATGCTTTAATGCTAGTATGCGTT
*
19518820 AACATCCTATAATCAATTCTTTATATACCGCCAATGGGCGAATGCTTTAATGCTAGTATGCGTT
1 AACATCCTACAATCAATTCTTTATATACCGCCAATGGGCGAATGCTTTAATGCTAGTATGCGTT
19518884 AACA
1 AACA
19518888 CTCTAATTTG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (64 bp):
AACATCCTACAATCAATTCTTTATATACCGCCAATGGGCGAATGCTTTAATGCTAGTATGCGTT
Found at i:19535206 original size:11 final size:11
Alignment explanation
Indices: 19535176--19535222 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
19535166 ATATTCAAAC
*
19535176 AATAATAACAA
1 AATAATAGCAA
*
19535187 AATAGTAGCAA
1 AATAATAGCAA
*
19535198 TATAATAGCAA
1 AATAATAGCAA
*
19535209 AATAATAGTAA
1 AATAATAGCAA
19535220 AAT
1 AAT
19535223 GGCAACAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.62, C:0.06, G:0.09, T:0.23
Consensus pattern (11 bp):
AATAATAGCAA
Found at i:19548400 original size:18 final size:17
Alignment explanation
Indices: 19548377--19548410 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
19548367 AATATTTAAT
19548377 ATTAAATTTAAATATTAG
1 ATTAAATTT-AATATTAG
19548395 ATTAAATTTAATATTA
1 ATTAAATTTAATATTA
19548411 AAGTGATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATTAAATTTAATATTAG
Found at i:19558429 original size:37 final size:36
Alignment explanation
Indices: 19558360--19558434 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 36
19558350 AAAGAGTTGT
19558360 ACTCAAAACTTGATGAGTCGTATCTGGAAAGATGTCA
1 ACTCAAAACTTGATGAGTCGTATCTGGAAAGATG-CA
* *
19558397 ACTCAAAACTT-AGTGAGTTGTA-CTTGGGAAGATGCA
1 ACTCAAAACTTGA-TGAGTCGTATC-TGGAAAGATGCA
19558433 AC
1 AC
19558435 CTAAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 6 0.18
37 28 0.82
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.27
Consensus pattern (36 bp):
ACTCAAAACTTGATGAGTCGTATCTGGAAAGATGCA
Found at i:19558746 original size:37 final size:37
Alignment explanation
Indices: 19558667--19558768 Score: 109
Period size: 37 Copynumber: 2.8 Consensus size: 37
19558657 AAGGAGCTAT
* *
19558667 GCTCAAAATTTAGTGAG-TAGACTCTGAGAAGGTATAA
1 GCTCAAAATTTAGTGAGTTATACT-TGAGAAGGTACAA
* *
19558704 ACTCAAAATTTAGTGAGTTATACTTGAGAAGGTACGA
1 GCTCAAAATTTAGTGAGTTATACTTGAGAAGGTACAA
** *
19558741 GCTCAATTTTTAAG-GAGTTGTACTTGAG
1 GCTCAAAATTT-AGTGAGTTATACTTGAG
19558769 GTGTAAACTA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
37 48 0.87
38 7 0.13
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (37 bp):
GCTCAAAATTTAGTGAGTTATACTTGAGAAGGTACAA
Found at i:19558790 original size:71 final size:71
Alignment explanation
Indices: 19558696--19558833 Score: 168
Period size: 71 Copynumber: 1.9 Consensus size: 71
19558686 GACTCTGAGA
* * * * * * *
19558696 AGGTATAAACTCAAAATTTAGTGAGTTATACTTGAGAAGGTACGAGCTCAATTTTTAAGGAGTTG
1 AGGTATAAACTAAAAACTTAGTGAGATATACCTGAAAAGGTACGAGCTCAAATTTTAAGGACTTG
19558761 TACTTG
66 TACTTG
* * ** *
19558767 AGGTGTAAACTAAAAACTTAGTGAGATGTACCTGAAAAGGTGTGAGCTCAAATTTTAGGGACTTG
1 AGGTATAAACTAAAAACTTAGTGAGATATACCTGAAAAGGTACGAGCTCAAATTTTAAGGACTTG
19558832 TA
66 TA
19558834 TTTAGGAAGG
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
71 55 1.00
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (71 bp):
AGGTATAAACTAAAAACTTAGTGAGATATACCTGAAAAGGTACGAGCTCAAATTTTAAGGACTTG
TACTTG
Found at i:19560750 original size:124 final size:124
Alignment explanation
Indices: 19560530--19560777 Score: 487
Period size: 124 Copynumber: 2.0 Consensus size: 124
19560520 TATATATGCG
19560530 TAGCTTTCATAGCTCGCATATATAGCTCGCCACACCATGGAGCCAATATTTATATATGGATTAGA
1 TAGCTTTCATAGCTCGCATATATAGCTCGCCACACCATGGAGCCAATATTTATATATGGATTAGA
19560595 GAATGGCAAGTAGGTATGCCATAAACGAGGAGGAAAAGAAAATAAACGAGAGTGATCTT
66 GAATGGCAAGTAGGTATGCCATAAACGAGGAGGAAAAGAAAATAAACGAGAGTGATCTT
*
19560654 TAGCTTTCATAGCTCGCATATATGGCTCGCCACACCATGGAGCCAATATTTATATATGGATTAGA
1 TAGCTTTCATAGCTCGCATATATAGCTCGCCACACCATGGAGCCAATATTTATATATGGATTAGA
19560719 GAATGGCAAGTAGGTATGCCATAAACGAGGAGGAAAAGAAAATAAACGAGAGTGATCTT
66 GAATGGCAAGTAGGTATGCCATAAACGAGGAGGAAAAGAAAATAAACGAGAGTGATCTT
19560778 AACTTTTGGA
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 123 1.00
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (124 bp):
TAGCTTTCATAGCTCGCATATATAGCTCGCCACACCATGGAGCCAATATTTATATATGGATTAGA
GAATGGCAAGTAGGTATGCCATAAACGAGGAGGAAAAGAAAATAAACGAGAGTGATCTT
Found at i:19561861 original size:7 final size:7
Alignment explanation
Indices: 19561851--19561881 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
19561841 AGAGTAGTGA
19561851 GTGGAGG
1 GTGGAGG
19561858 GTGGAGG
1 GTGGAGG
19561865 GTGGAGG
1 GTGGAGG
19561872 GTGGAGG
1 GTGGAGG
19561879 GTG
1 GTG
19561882 ATTTGGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.71, T:0.16
Consensus pattern (7 bp):
GTGGAGG
Found at i:19562759 original size:22 final size:22
Alignment explanation
Indices: 19562738--19562843 Score: 158
Period size: 22 Copynumber: 4.8 Consensus size: 22
19562728 GGGCGTTAGC
**
19562738 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAAA
* * *
19562760 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAAA
19562782 CATGAGAGCTTAGTACGTTAAA
1 CATGAGAGCTTAGTACGTTAAA
*
19562804 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAAA
19562826 CATGAGAGCTTAGTACGT
1 CATGAGAGCTTAGTACGT
19562844 ACTATCAACA
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 75 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.28
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAAA
Found at i:19574326 original size:23 final size:23
Alignment explanation
Indices: 19574299--19574344 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
19574289 AAAAATAAGT
*
19574299 ATAAAAATACGTGGTATTGGATA
1 ATAAAAATACATGGTATTGGATA
19574322 ATAAAAATACATGGTATTGGATA
1 ATAAAAATACATGGTATTGGATA
19574345 TTTACATCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (23 bp):
ATAAAAATACATGGTATTGGATA
Found at i:19578369 original size:12 final size:12
Alignment explanation
Indices: 19578344--19578387 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
19578334 TGCTTCATTA
19578344 CATTCCAT-ATC
1 CATTCCATCATC
19578355 CATGT-CATCATC
1 CAT-TCCATCATC
19578367 CATTCCATCATC
1 CATTCCATCATC
19578379 CATTTCCAT
1 CA-TTCCAT
19578388 ACTCTCATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.24
12 16 0.55
13 6 0.21
ACGTcount: A:0.25, C:0.36, G:0.02, T:0.36
Consensus pattern (12 bp):
CATTCCATCATC
Found at i:19580105 original size:15 final size:15
Alignment explanation
Indices: 19580085--19580135 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
19580075 ATAAAACGAT
19580085 AACGTAAGTGACTAA
1 AACGTAAGTGACTAA
*
19580100 AACGTAA-T-ACTTCA
1 AACGTAAGTGAC-TAA
*
19580114 AACATAAGTGACTAA
1 AACGTAAGTGACTAA
*
19580129 AATGTAA
1 AACGTAA
19580136 ATTGAGACAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 2 0.07
14 9 0.32
15 15 0.54
16 2 0.07
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (15 bp):
AACGTAAGTGACTAA
Found at i:19582794 original size:32 final size:32
Alignment explanation
Indices: 19582751--19582865 Score: 146
Period size: 32 Copynumber: 3.6 Consensus size: 32
19582741 TTTTAAAGGA
*
19582751 ATATTT-TTATCATTTAACAAAATTAAAGTTG
1 ATATTTGTTATCATTTCACAAAATTAAAGTTG
*
19582782 ATATTTGTTATCATTTCACAAAATTGAAGTTG
1 ATATTTGTTATCATTTCACAAAATTAAAGTTG
* * *
19582814 -TAATTTGGTA-CAATTTCACAAAATGAAAGGTG
1 AT-ATTTGTTATC-ATTTCACAAAATTAAAGTTG
19582846 ATATTTGTTATCATTTCACA
1 ATATTTGTTATCATTTCACA
19582866 GAACCATGCA
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
31 8 0.11
32 62 0.86
33 2 0.03
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (32 bp):
ATATTTGTTATCATTTCACAAAATTAAAGTTG
Found at i:19583075 original size:18 final size:20
Alignment explanation
Indices: 19583049--19583090 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 20
19583039 ATACTATATG
19583049 AAATAAAATAGATA-TGTGA
1 AAATAAAATAGATACTGTGA
*
19583068 AAAT-AAATTGATAGCTGTGA
1 AAATAAAATAGATA-CTGTGA
19583088 AAA
1 AAA
19583091 CATATGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 8 0.40
19 4 0.20
20 8 0.40
ACGTcount: A:0.55, C:0.02, G:0.17, T:0.26
Consensus pattern (20 bp):
AAATAAAATAGATACTGTGA
Found at i:19587435 original size:19 final size:20
Alignment explanation
Indices: 19587390--19587436 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
19587380 ATATATCACG
*
19587390 TCAACAAATAATTTAAAAAT
1 TCAAAAAATAATTTAAAAAT
* *
19587410 T-ATAAAAT-ATTTTAAAAT
1 TCAAAAAATAATTTAAAAAT
19587428 TCAAAAAAT
1 TCAAAAAAT
19587437 TATAAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 10 0.45
19 11 0.50
20 1 0.05
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (20 bp):
TCAAAAAATAATTTAAAAAT
Found at i:19587444 original size:18 final size:18
Alignment explanation
Indices: 19587399--19587464 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 18
19587389 GTCAACAAAT
19587399 AATTTAAAAATT-ATAAA
1 AATTTAAAAATTCATAAA
*
19587416 ATATTTTAAAATTCA-AAA
1 A-ATTTAAAAATTCATAAA
*
19587434 AATTATAAAAAAATCATAAA
1 AATT-T-AAAAATTCATAAA
*
19587454 AATTAAAAAAT
1 AATTTAAAAAT
19587465 AAACATACAT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
17 4 0.10
18 20 0.51
19 8 0.21
20 7 0.18
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AATTTAAAAATTCATAAA
Found at i:19587471 original size:20 final size:20
Alignment explanation
Indices: 19587431--19587471 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
19587421 TTAAAATTCA
*
19587431 AAAAATTATAAAAAAATCAT
1 AAAAATTATAAAAAAAACAT
19587451 AAAAATTA-AAAAATAAACAT
1 AAAAATTATAAAAA-AAACAT
19587471 A
1 A
19587472 CATACGTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAAATTATAAAAAAAACAT
Found at i:19589286 original size:45 final size:47
Alignment explanation
Indices: 19589217--19589308 Score: 152
Period size: 45 Copynumber: 2.0 Consensus size: 47
19589207 AGCGTGGCAC
*
19589217 TACTACACTTCTCCTATTGATTAGTTGCAGGCAATAATAAATGCCAA
1 TACTACACTTCTCATATTGATTAGTTGCAGGCAATAATAAATGCCAA
*
19589264 TACTACAC-T-TCATATTGATTAGTTTCAGGCAATAATAAATGCCAA
1 TACTACACTTCTCATATTGATTAGTTGCAGGCAATAATAAATGCCAA
19589309 ATACGAAGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 34 0.79
46 1 0.02
47 8 0.19
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.33
Consensus pattern (47 bp):
TACTACACTTCTCATATTGATTAGTTGCAGGCAATAATAAATGCCAA
Found at i:19600877 original size:5 final size:5
Alignment explanation
Indices: 19600867--19600895 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
19600857 TTATAATTAC
19600867 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
19600896 GCTTTCTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:19603587 original size:10 final size:10
Alignment explanation
Indices: 19603572--19603614 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
19603562 AGTAATATAC
19603572 ATACATACAT
1 ATACATACAT
19603582 ATACATACAT
1 ATACATACAT
* *
19603592 ATATATATAT
1 ATACATACAT
* *
19603602 ATATATATAT
1 ATACATACAT
19603612 ATA
1 ATA
19603615 ATTCAGGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (10 bp):
ATACATACAT
Found at i:19603597 original size:4 final size:4
Alignment explanation
Indices: 19603566--19603614 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
19603556 TTTACAAGTA
* * * * *
19603566 ATAT ACAT ACAT ACAT ATAC ATAC ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
19603614 A
1 A
19603615 ATTCAGGTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (4 bp):
ATAT
Found at i:19603614 original size:14 final size:14
Alignment explanation
Indices: 19603566--19603612 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
19603556 TTTACAAGTA
*
19603566 ATATACATACATAC
1 ATATACATACATAT
19603580 ATATACATACATAT
1 ATATACATACATAT
* *
19603594 ATATATATATATAT
1 ATATACATACATAT
19603608 ATATA
1 ATATA
19603613 TAATTCAGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATACATACATAT
Found at i:19605604 original size:12 final size:12
Alignment explanation
Indices: 19605587--19605611 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19605577 ATGCTTTTCG
19605587 TATCCTAGTCTT
1 TATCCTAGTCTT
19605599 TATCCTAGTCTT
1 TATCCTAGTCTT
19605611 T
1 T
19605612 CGCCTTTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.52
Consensus pattern (12 bp):
TATCCTAGTCTT
Found at i:19605765 original size:23 final size:23
Alignment explanation
Indices: 19605728--19605778 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
19605718 TACTTTTTTT
* **
19605728 GAGTTATCTCAAATAAGTGTTTC
1 GAGTTAACTCAAATAAGTAATTC
*
19605751 GAGTTAACTCGAATAAGTAATTC
1 GAGTTAACTCAAATAAGTAATTC
19605774 GAGTT
1 GAGTT
19605779 TTGAGTTCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (23 bp):
GAGTTAACTCAAATAAGTAATTC
Found at i:19605954 original size:24 final size:24
Alignment explanation
Indices: 19605920--19605965 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
19605910 AATTTATAAT
* *
19605920 ATTTTTAAAAATTTCAAAATTTAC
1 ATTTTTAAAAATATAAAAATTTAC
*
19605944 ATTTTTTAAAATATAAAAATTT
1 ATTTTTAAAAATATAAAAATTT
19605966 TTAAAAAATT
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:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTTTTAAAAATATAAAAATTTAC
Done.