Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 74 of 210
Found at i:22275106 original size:37 final size:37
Alignment explanation
Indices: 22275056--22275127 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
22275046 CTGAGGATCG
*
22275056 TTACTGTTCATCTCCATTTTTTATTTGCAGAGAATTT
1 TTACTGTTCATCTCCATTTTTTATTTGCAAAGAATTT
* ** *
22275093 TTACTGTTTATCTCTGTTTTTTCTTTGCAAAGAAT
1 TTACTGTTCATCTCCATTTTTTATTTGCAAAGAAT
22275128 CACTCATGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.21, C:0.15, G:0.11, T:0.53
Consensus pattern (37 bp):
TTACTGTTCATCTCCATTTTTTATTTGCAAAGAATTT
Found at i:22275143 original size:37 final size:37
Alignment explanation
Indices: 22275102--22275269 Score: 97
Period size: 37 Copynumber: 4.5 Consensus size: 37
22275092 TTTACTGTTT
* *
22275102 ATCTCTGTTTTTTCTTTGCAAAGAATCACTCATGCTC
1 ATCTCAGTCTTTTCTTTGCAAAGAATCACTCATGCTC
* * * * *
22275139 ATCTCAGTCTTTTCTTTGTAGAGAATCTCTCTTGTTC
1 ATCTCAGTCTTTTCTTTGCAAAGAATCACTCATGCTC
* ** ** * *
22275176 ATCTTTA-TCTTTTCTTTATAGGGAATCACTCCTGTTC
1 ATC-TCAGTCTTTTCTTTGCAAAGAATCACTCATGCTC
* * * * ** * *
22275213 ATATCTGTCTTTGCTTTGTAGGGAATCACTCTTGCTT
1 ATCTCAGTCTTTTCTTTGCAAAGAATCACTCATGCTC
*
22275250 ATCTTCA-TCTTTACTTTGCA
1 ATC-TCAGTCTTTTCTTTGCA
22275270 GGGAATATTT
Statistics
Matches: 104, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
36 1 0.01
37 99 0.95
38 4 0.04
ACGTcount: A:0.18, C:0.22, G:0.12, T:0.47
Consensus pattern (37 bp):
ATCTCAGTCTTTTCTTTGCAAAGAATCACTCATGCTC
Found at i:22275273 original size:37 final size:37
Alignment explanation
Indices: 22275124--22275275 Score: 148
Period size: 37 Copynumber: 4.1 Consensus size: 37
22275114 TCTTTGCAAA
* * *
22275124 GAATCACTCATGCTCATC-TCAGTCTTTTCTTTGTAGA
1 GAATCACTCTTGTTCATCTTCA-TCTTTTCTTTGTAGG
* * *
22275161 GAATCTCTCTTGTTCATCTTTATCTTTTCTTTATAGG
1 GAATCACTCTTGTTCATCTTCATCTTTTCTTTGTAGG
* * * *
22275198 GAATCACTCCTGTTCAT-ATCTGTCTTTGCTTTGTAGG
1 GAATCACTCTTGTTCATCTTC-ATCTTTTCTTTGTAGG
* *
22275235 GAATCACTCTTGCTT-ATCTTCATCTTTACTTTGCAGG
1 GAATCACTCTTG-TTCATCTTCATCTTTTCTTTGTAGG
22275272 GAAT
1 GAAT
22275276 ATTTGAAGGT
Statistics
Matches: 93, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
36 1 0.01
37 86 0.92
38 6 0.06
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.45
Consensus pattern (37 bp):
GAATCACTCTTGTTCATCTTCATCTTTTCTTTGTAGG
Found at i:22275273 original size:74 final size:74
Alignment explanation
Indices: 22275115--22275275 Score: 189
Period size: 74 Copynumber: 2.2 Consensus size: 74
22275105 TCTGTTTTTT
** * * *
22275115 CTTTGCAAAGAATCACTCATGCTCATCTCAGTCTTTTCTTTGTAGAGAATCTCTCTTGTTCATCT
1 CTTTGCAGGGAATCACTCATGCTCATATCAGTCTTTGCTTTGTAGAGAATCACTCTTGTTCATCT
* *
22275180 TTATCTTTT
66 TCATCTTTA
** * * * *
22275189 CTTTATAGGGAATCACTCCTGTTCATATCTGTCTTTGCTTTGTAGGGAATCACTCTTGCTT-ATC
1 CTTTGCAGGGAATCACTCATGCTCATATCAGTCTTTGCTTTGTAGAGAATCACTCTTG-TTCATC
22275253 TTCATCTTTA
65 TTCATCTTTA
22275263 CTTTGCAGGGAAT
1 CTTTGCAGGGAAT
22275276 ATTTGAAGGT
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
74 69 0.97
75 2 0.03
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (74 bp):
CTTTGCAGGGAATCACTCATGCTCATATCAGTCTTTGCTTTGTAGAGAATCACTCTTGTTCATCT
TCATCTTTA
Found at i:22278101 original size:5 final size:5
Alignment explanation
Indices: 22278093--22278178 Score: 93
Period size: 5 Copynumber: 17.2 Consensus size: 5
22278083 TAATTTATTA
* * *
22278093 CATAT CATAT CATAT CATAT TAGAT CATAT CATAT CTTAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
* * **
22278143 CGTAT CATAT CA-AGT TATAT TGTAT CATAT CATAT C
1 CATAT CATAT CATA-T CATAT CATAT CATAT CATAT C
22278179 CTACCCCCAT
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
4 1 0.01
5 65 0.97
6 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.42
Consensus pattern (5 bp):
CATAT
Found at i:22279059 original size:6 final size:6
Alignment explanation
Indices: 22279048--22279751 Score: 816
Period size: 6 Copynumber: 116.5 Consensus size: 6
22279038 GAAAGGTATG
22279048 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * *
22279096 GTAATA ATAATA ATAATA ATAATA ATAATA ATAATA ACAATA ACAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
*
22279144 ATAATA ATAATA ATAACA ATAATA ATAATA ATAATA ATAATA ATAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * * * *
22279192 ACAATA ACAATA ACAATA ACAAACA ATAATA ATAATA ATAATA ATAATA
1 ATAATA ATAATA ATAATA A-TAATA ATAATA ATAATA ATAATA ATAATA
* * *
22279241 ATAATA ATAATA ATAATA ATAACA ATAATA A-AACA ATAATA ATAACA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * * * * *
22279288 ATAATA ATAACA ATAATA ATAACA ATAATA ACAACA ATAACA ACAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * *
22279336 ATAACA ATAATA ATAATA ATAATA ACAATA ATAATA ACAATA ATAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * * * * * *
22279384 ACAATA ATAATA ACAATA ACAATA ACAATA ATAACA ATAACA ATAACA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * * * * *
22279432 ATAATA ATAACA ATAACA ATAACA ATAATA ACAATA ACAATA ACAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * * * * * * *
22279480 ACAATA ACAACTA ACAATA ACGAACTTA ACGAATA ACAATA ACAATA ACAATA
1 ATAATA ATAA-TA ATAATA A-TAA--TA A-TAATA ATAATA ATAATA ATAATA
* * * * * * * *
22279533 ACAATA ACAATA ACAATA ACAATA ACAATA ACAATA ACAATA ACAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* *
22279581 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ACAACA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * *
22279629 ATAATA ATAATA ATAATA ACAATA ATAATA ACAATA ACAATA ATAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * *
22279677 ATAATA ATAATA ATAATA ATAACA ATAATA ATAACA ATAATA ATAACA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
*
22279725 ATAATA ATAACA ATAATA ATAATA ATA
1 ATAATA ATAATA ATAATA ATAATA ATA
22279752 GTGGATCATG
Statistics
Matches: 631, Mismatches: 61, Indels: 12
0.90 0.09 0.02
Matches are distributed among these distances:
5 4 0.01
6 605 0.96
7 15 0.02
9 7 0.01
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (6 bp):
ATAATA
Found at i:22279794 original size:13 final size:13
Alignment explanation
Indices: 22279772--22279805 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
22279762 CAAATTAAAC
22279772 AAAGAAAAGAAAAG
1 AAAGAAAAG-AAAG
22279786 AAA-AAAAGAAAG
1 AAAGAAAAGAAAG
22279798 AAAGAAAA
1 AAAGAAAA
22279806 TGAGAAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.37
13 9 0.47
14 3 0.16
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAGAAAAGAAAG
Found at i:22286734 original size:21 final size:20
Alignment explanation
Indices: 22286687--22286741 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
22286677 ATCATTGTTT
* *
22286687 CTAATCTCACTGCTACAGTA
1 CTAATCTCACCGCTACAATA
*
22286707 TTCAATCTCACCGCTACAATAA
1 CT-AATCTCACCGCTACAAT-A
22286729 CTAATCTCACCGC
1 CTAATCTCACCGC
22286742 CATCGCTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 1 0.03
21 26 0.90
22 2 0.07
ACGTcount: A:0.31, C:0.35, G:0.07, T:0.27
Consensus pattern (20 bp):
CTAATCTCACCGCTACAATA
Found at i:22290904 original size:41 final size:41
Alignment explanation
Indices: 22290825--22290906 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
22290815 AGACCAATTT
* *
22290825 AATTGGATCAATCATTGTACGATTAATCATACAGTTTATTC
1 AATTAGATCAATCATTGTACGATTAATCATACAATTTATTC
** *
22290866 AATTAGATCAATGGTTGTACGATTAAT-GTCACAATTTATTC
1 AATTAGATCAATCATTGTACGATTAATCAT-ACAATTTATTC
22290907 GATCATGCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 1 0.03
41 34 0.97
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (41 bp):
AATTAGATCAATCATTGTACGATTAATCATACAATTTATTC
Found at i:22291387 original size:41 final size:41
Alignment explanation
Indices: 22291325--22291414 Score: 137
Period size: 41 Copynumber: 2.2 Consensus size: 41
22291315 ACATGGACTG
* *
22291325 ATTCAATTGGATCAATGATTGTACAGTTAAT-TATACAATTT
1 ATTCAATTGGATCAATGATTGTACAATTAATGT-CACAATTT
*
22291366 ATTCAATTGGATCAATTATTGTACAATTAATGTCACAATTT
1 ATTCAATTGGATCAATGATTGTACAATTAATGTCACAATTT
22291407 ATTCAATT
1 ATTCAATT
22291415 ATGCTAGTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 44 0.98
42 1 0.02
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (41 bp):
ATTCAATTGGATCAATGATTGTACAATTAATGTCACAATTT
Found at i:22291775 original size:501 final size:500
Alignment explanation
Indices: 22290614--22292207 Score: 2056
Period size: 501 Copynumber: 3.2 Consensus size: 500
22290604 TACTCTTCAA
* * *
22290614 GTTAGTACATTCGTACATAGATCCGATTCAATTGGTTCAATGTCATAAGCATTCAATTACATTTG
1 GTTAGTACATTCGTATATAGACCCGATTCAATTGGTTCAATGTCATAAGCATTCAATTACATTAG
* * ** * *
22290679 TAGTTAG-GG--TGCATAATTGATAAATACTCTTAAATGGATGACAA-ACGTAAAATTAAACATT
66 TAGTTAGAGGAATGCATAATTGATAAATACTCTTAAATTGATCA-AATATTTGAAATTAAACATA
* * * * *
22290740 GATGGTCCAAAATTTTGATATATTTCACTATATGATAATGAATTCCAAA-ATGTATGCTCAATGT
130 GGTGGTCCAAAGTTTTGATATATTTCACTATATGATATTGAATTCTAAACATGTATACTCAATGT
* * * * * *
22290804 TGTGTTTACATAGACCAATTTAATTGGATCAATCATTGTACGATTAATCATACAGTTTATTCAAT
195 AGTGTTTACATGGACCAATTCAATTGGATCAATGATTGTACGATTAATTATACAATTTATTCAAT
* * * * *
22290869 TAGATCAATGGTTGTACGATTAATGTCACAATTTATTCGATCATGCTAACTAATAATTAGAGGAA
260 TGGATCAATGATTGTACAATTAATGTCACAATTTATTCGATTATG----CTAGTAATTAGAGGAA
* ** ** **
22290934 TATACAATTGATCAATACTCTTAAAAATACCTATACACTACAATGACATTATTTTCATACATAGA
321 TATACAATTGATCAATACTTTTAAAAATATTTATACACTACAATGTTATTACCTTCATACATAGA
* * * * * *
22290999 TTCATTCAATTAAATCAATGATTGTACAATTATTGTCATAACTCATTCAACTACATTGGA-AATT
386 TTAATTCAATTAAATCAATGATTGTACAATTAATGACATAACTCATTCAATTACGTT-AATAATT
* * * * *
22291063 AGAGAAATGAAAAAGTGATC-ATGACTTTTCAAATTACTCATACACCACAAT
450 AGAGAAATGTACAATTGATCAAT-ACTTTTTAAATTACTCGTACACCACAAT
* * * * * * *
22291114 GCTAGTACATTTGTATATAGACCTGATTCAATTAGTTCAATGTCATTATCATTCAATTACATAAG
1 GTTAGTACATTCGTATATAGACCCGATTCAATTGGTTCAATGTCATAAGCATTCAATTACATTAG
* *
22291179 TAGTTAGAGGAATGCATAAGTGATAAATACTCTTAAATTGATCAAATATTTGAAATTAAACATCG
66 TAGTTAGAGGAATGCATAATTGATAAATACTCTTAAATTGATCAAATATTTGAAATTAAACATAG
* * * *
22291244 GTAGTCCAAAGTTTTGATATATTTCACTATATGATATTGCATTCTAAACATGTATAATCAAAGTA
131 GTGGTCCAAAGTTTTGATATATTTCACTATATGATATTGAATTCTAAACATGTATACTCAATGTA
**
22291309 GTGTTTACATGGACTGATTCAATTGGATCAATGATTGTAC-AGTTAATTATACAATTTATTCAAT
196 GTGTTTACATGGACCAATTCAATTGGATCAATGATTGTACGA-TTAATTATACAATTTATTCAAT
* *
22291373 TGGATCAATTATTGTACAATTAATGTCACAATTTATTCAATTATGCTAGTAATTAGAGGAATATA
260 TGGATCAATGATTGTACAATTAATGTCACAATTTATTCGATTATGCTAGTAATTAGAGGAATATA
*
22291438 CAATTGATCAATACTTTTAAAAATATTTATACACTACAACGTTATTACCTTCATACATAGATTAA
325 CAATTGATCAATACTTTTAAAAATATTTATACACTACAATGTTATTACCTTCATACATAGATTAA
* *
22291503 TTCGATTAAATCAATAATTGTACAATTAATGACATAACTCATTCAATTACGTTAATAATTAGAGA
390 TTCAATTAAATCAATGATTGTACAATTAATGACATAACTCATTCAATTACGTTAATAATTAGAGA
* * * * *
22291568 AACGTGCAATTCATCAATACTTTTTTAAATTACTTGTATACCACAAT
455 AATGTACAATTGATCAATAC-TTTTTAAATTACTCGTACACCACAAT
* * * * * * *
22291615 GTTAGTATATTCGTATATAAACCCAATCCAATTGGCTCAATGTCATAATCACTCAATTACATTAG
1 GTTAGTACATTCGTATATAGACCCGATTCAATTGGTTCAATGTCATAAGCATTCAATTACATTAG
* * * *
22291680 TATTTAGAGGAATGCATAATTGATAAATACCCTTAAATTGATCAAATATTTGAAGTTAAATATAG
66 TAGTTAGAGGAATGCATAATTGATAAATACTCTTAAATTGATCAAATATTTGAAATTAAACATAG
*
22291745 GTGGTCCAATGTTTTGATATATTTCACTATATGATATTGAATTCTAAACATGTATACTCAATGTT
131 GTGGTCCAAAGTTTTGATATATTTCACTATATGATATTGAATTCTAAACATGTATACTCAATG-T
** *
22291810 A-TGTTTACATGGACCAATTCAATTACATCAATGATTGTATGATTAATTATACAATTTATTCAAT
195 AGTGTTTACATGGACCAATTCAATTGGATCAATGATTGTACGATTAATTATACAATTTATTCAAT
* * ** * *
22291874 TGGATCTATGATTGTACAATTAATGTCACAATTTATTTGATTACACTAGTAATTAGTGGAATAGA
260 TGGATCAATGATTGTACAATTAATGTCACAATTTATTCGATTATGCTAGTAATTAGAGGAATATA
* * * *
22291939 CAATTGATCAATACTTTTAAAAGTATTTATGCACTACAATGTTATTACCTTTATACATAGATTTA
325 CAATTGATCAATACTTTTAAAAATATTTATACACTACAATGTTATTACCTTCATACATAGATTAA
* * * *
22292004 TTCAATTAGATCAAGGATTGTACAATTAAT-ATCATAACTCATGCAATTATGTTAATAATTAGAG
390 TTCAATTAAATCAATGATTGTACAATTAATGA-CATAACTCATTCAATTACGTTAATAATTAGAG
* * * *
22292068 AAATGTACAATTGGTTAATACTTTTTGAATTACTCGTACACCATAAT
454 AAATGTACAATTGATCAATACTTTTTAAATTACTCGTACACCACAAT
* * * * * *
22292115 GTTAGTACATTCATATATAGATCCGATTTAATTGGTTCAATGCCATAAGCATTCAATTACGTTTG
1 GTTAGTACATTCGTATATAGACCCGATTCAATTGGTTCAATGTCATAAGCATTCAATTACATTAG
22292180 TAGTTAGAGGAATGCATAATTGATAAAT
66 TAGTTAGAGGAATGCATAATTGATAAAT
22292208 TGTGACGCCC
Statistics
Matches: 945, Mismatches: 137, Indels: 24
0.85 0.12 0.02
Matches are distributed among these distances:
499 1 0.00
500 306 0.32
501 441 0.47
502 5 0.01
503 86 0.09
504 106 0.11
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (500 bp):
GTTAGTACATTCGTATATAGACCCGATTCAATTGGTTCAATGTCATAAGCATTCAATTACATTAG
TAGTTAGAGGAATGCATAATTGATAAATACTCTTAAATTGATCAAATATTTGAAATTAAACATAG
GTGGTCCAAAGTTTTGATATATTTCACTATATGATATTGAATTCTAAACATGTATACTCAATGTA
GTGTTTACATGGACCAATTCAATTGGATCAATGATTGTACGATTAATTATACAATTTATTCAATT
GGATCAATGATTGTACAATTAATGTCACAATTTATTCGATTATGCTAGTAATTAGAGGAATATAC
AATTGATCAATACTTTTAAAAATATTTATACACTACAATGTTATTACCTTCATACATAGATTAAT
TCAATTAAATCAATGATTGTACAATTAATGACATAACTCATTCAATTACGTTAATAATTAGAGAA
ATGTACAATTGATCAATACTTTTTAAATTACTCGTACACCACAAT
Found at i:22291896 original size:41 final size:41
Alignment explanation
Indices: 22291826--22291910 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 41
22291816 ACATGGACCA
** *
22291826 ATTCAATTACATCAATGATTGTATGATTAAT-TATACAATTT
1 ATTCAATTACATCAATGATTGTACAATTAATGT-CACAATTT
** *
22291867 ATTCAATTGGATCTATGATTGTACAATTAATGTCACAATTT
1 ATTCAATTACATCAATGATTGTACAATTAATGTCACAATTT
22291908 ATT
1 ATT
22291911 TGATTACACT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
41 36 0.97
42 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (41 bp):
ATTCAATTACATCAATGATTGTACAATTAATGTCACAATTT
Found at i:22295170 original size:42 final size:42
Alignment explanation
Indices: 22295113--22295212 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
22295103 TACATTAATG
** * * *
22295113 CTCACACGTGCTGTGGGTC-AGAATATAAGCTACACGATGTTG
1 CTCACACAAGCTGTGGGTCGA-AATATAAGCTACACAATGCTA
*
22295155 CTCAGACAAGCTGTGGGTCGAAATATAAGCTACACAATGCTA
1 CTCACACAAGCTGTGGGTCGAAATATAAGCTACACAATGCTA
*
22295197 CTTACACAAGCTGTGG
1 CTCACACAAGCTGTGG
22295213 TGAATAGTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 48 0.98
43 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (42 bp):
CTCACACAAGCTGTGGGTCGAAATATAAGCTACACAATGCTA
Found at i:22295701 original size:13 final size:13
Alignment explanation
Indices: 22295680--22295723 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
22295670 CACGGGCGTA
* *
22295680 TGGCTTGGCCGTG
1 TGGCATGGCCATG
22295693 TGGCATGGCCATG
1 TGGCATGGCCATG
22295706 TGGCATGGCCATG
1 TGGCATGGCCATG
22295719 TGGCA
1 TGGCA
22295724 CAAGTCAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.11, C:0.23, G:0.41, T:0.25
Consensus pattern (13 bp):
TGGCATGGCCATG
Found at i:22297995 original size:41 final size:41
Alignment explanation
Indices: 22297881--22298030 Score: 169
Period size: 41 Copynumber: 3.7 Consensus size: 41
22297871 CATAATTTAA
* *
22297881 CATATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CATA-TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
* *
22297923 CATATCACTGGCACGTAGCCTGCTAGGTTTATAACCTGATT
1 CATATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
* ** **
22297964 CCA-ATCACCGGCACTTAGCCTGCTAGATTTATAGTCTGAAA
1 -CATATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
* *
22298005 AAT-TCACCGGCATTTAGCCTGCTAGG
1 CATATCACCGGCACTTAGCCTGCTAGG
22298031 CGCTTAGCCT
Statistics
Matches: 92, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
40 22 0.24
41 64 0.70
42 6 0.07
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (41 bp):
CATATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
Found at i:22298043 original size:40 final size:40
Alignment explanation
Indices: 22297884--22298050 Score: 117
Period size: 41 Copynumber: 4.1 Consensus size: 40
22297874 AATTTAACAT
***
22297884 ATTCACCGGCACTTAGCCTGCTAG-GCTTATAGCCTGATTC
1 ATTCACCGGCACTTAGCCTGCTAGAGC-TATAGCCTGAAAA
* * * * **
22297924 ATATCACTGGCACGTAGCCTGCTAG-GTTTATAACCTGATTCCA
1 AT-TCACCGGCACTTAGCCTGCTAGAG-CTATAGCCTGA--AAA
** *
22297967 A-TCACCGGCACTTAGCCTGCTAGATTTATAGTCTGAAAA
1 ATTCACCGGCACTTAGCCTGCTAGAGCTATAGCCTGAAAA
* *
22298006 ATTCACCGGCATTTAGCCTGCTAGGCGCT-TAGCCTGAAAA
1 ATTCACCGGCACTTAGCCTGCTA-GAGCTATAGCCTGAAAA
*
22298046 TTTCA
1 ATTCA
22298051 ATTTCACAGA
Statistics
Matches: 100, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
39 2 0.02
40 36 0.36
41 61 0.61
43 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.29
Consensus pattern (40 bp):
ATTCACCGGCACTTAGCCTGCTAGAGCTATAGCCTGAAAA
Found at i:22302071 original size:13 final size:15
Alignment explanation
Indices: 22302044--22302075 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
22302034 CTTTATTATG
22302044 TTTTTCTTATCAATT
1 TTTTTCTTATCAATT
22302059 TTTTTCTT-T-AATT
1 TTTTTCTTATCAATT
22302072 TTTT
1 TTTT
22302076 GCCCTATGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 1 0.06
15 8 0.47
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTCTTATCAATT
Found at i:22303621 original size:16 final size:17
Alignment explanation
Indices: 22303600--22303635 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
22303590 GACTTTTATT
*
22303600 TATTTATTATAT-TTAA
1 TATTTAATATATATTAA
22303616 TATTTAATATATATTAA
1 TATTTAATATATATTAA
22303633 TAT
1 TAT
22303636 ACTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTAATATATATTAA
Found at i:22304180 original size:49 final size:49
Alignment explanation
Indices: 22304108--22304201 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
22304098 TGCTATGCAA
* * *
22304108 TGCTAAACTTGGTCTTCCACTGTCTACACTCTTATCAGTATTTATACAT
1 TGCTAAAATTAGTCTTCCACTGTCTACACTCTTATCACTATTTATACAT
*
22304157 TGCTAAAATTAGTCTTCTACTGTCTACACTCTTATCACTATTTAT
1 TGCTAAAATTAGTCTTCCACTGTCTACACTCTTATCACTATTTAT
22304202 CCCTTCTTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.43
Consensus pattern (49 bp):
TGCTAAAATTAGTCTTCCACTGTCTACACTCTTATCACTATTTATACAT
Found at i:22305620 original size:44 final size:44
Alignment explanation
Indices: 22305569--22305655 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
22305559 TCATATTTCA
*
22305569 TTTCTCATCTCATAATCATTTCTTATATTTGCCATTTCAATATT
1 TTTCTCATCTCATAATCATTTCTCATATTTGCCATTTCAATATT
* * * *
22305613 TTTCTCATCTCATATTTATTTCTCATCTTTTCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTTGCCATTTCAATAT
22305656 CAATTATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.23, C:0.22, G:0.01, T:0.54
Consensus pattern (44 bp):
TTTCTCATCTCATAATCATTTCTCATATTTGCCATTTCAATATT
Found at i:22318434 original size:25 final size:25
Alignment explanation
Indices: 22318406--22318489 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 25
22318396 TGAGCCCTTT
22318406 TCCAATTGGTTTTCGTCATTTCTAG
1 TCCAATTGGTTTTCGTCATTTCTAG
** * *
22318431 TCCAATTAATTTTCGCCA--TCGAG
1 TCCAATTGGTTTTCGTCATTTCTAG
* **
22318454 T-TAA-TGGTTTTTTTCATTTCTAG
1 TCCAATTGGTTTTCGTCATTTCTAG
22318477 TCCAATTGGTTTT
1 TCCAATTGGTTTT
22318490 TTTTTTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
21 7 0.16
22 2 0.05
23 10 0.23
24 2 0.05
25 22 0.51
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.49
Consensus pattern (25 bp):
TCCAATTGGTTTTCGTCATTTCTAG
Found at i:22320751 original size:22 final size:22
Alignment explanation
Indices: 22320725--22320778 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
22320715 AATAAAATTT
22320725 AACTTACCTCTGTAAGTTATCA
1 AACTTACCTCTGTAAGTTATCA
22320747 AACTTACCTCTGTAAGTTATCA
1 AACTTACCTCTGTAAGTTATCA
22320769 AACTTACCTC
1 AACTTACCTC
22320779 AACACATTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.35
Consensus pattern (22 bp):
AACTTACCTCTGTAAGTTATCA
Found at i:22322855 original size:16 final size:16
Alignment explanation
Indices: 22322834--22322867 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
22322824 TAAGTATAAC
22322834 TTAAAAAT-TTTTTGAT
1 TTAAAAATATTTTT-AT
22322850 TTAAAAATATTTTTAT
1 TTAAAAATATTTTTAT
22322866 TT
1 TT
22322868 GATATTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTAAAAATATTTTTAT
Found at i:22340078 original size:29 final size:30
Alignment explanation
Indices: 22340035--22340093 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
22340025 GAATTGGATC
* * *
22340035 AAATCAAAATTTTATGTATAAAATTGCACA
1 AAATCAAAAGTTTATATATAAAATTACACA
*
22340065 AAATC-AAAGTTTATATATACAATTACACA
1 AAATCAAAAGTTTATATATAAAATTACACA
22340094 TTAAAACATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (30 bp):
AAATCAAAAGTTTATATATAAAATTACACA
Found at i:22343077 original size:242 final size:242
Alignment explanation
Indices: 22342651--22343108 Score: 643
Period size: 242 Copynumber: 1.9 Consensus size: 242
22342641 ATGTTGGTAG
* * * *
22342651 AAAGAAAATCAAGGTGAAAATCGAGGGATGATAGGAGATTTGGTATCGAAATTCAAGGGGTTGGA
1 AAAGAAAATAAAGGCGAAAATCGAGGGATGATAAGAGATTTGGTATCGAAATTCAAGGGGTTGAA
* * ** * * *
22342716 TCTTCTGGATCCCGTTTCAATATCTTGGCTAATGGAAATAAGGGAAGGAATGATACTGTGGGGAT
66 TCTTCTAGATCCCATTTCAATATCTTGGCTAATAAAAATAAAGAAAGGAATGATAATGTGGGGAT
* *
22342781 TGGGGAAATCGATAAAGGGCAGTCGAAGGGAGTTCTAAATGGTAATAAAAGTGAAGCTATTAATT
131 TGGGGAAATCGAGAAAGGGCAGTCGAAGGGACTTCTAAATGGTAATAAAAGTGAAGCTATTAATT
*
22342846 TTAGTAAAAATTCAGGATTGGGTGAGAGGGCAATAGTTGTTTCCAAC
196 TGAGTAAAAATTCAGGATTGGGTGAGAGGGCAATAGTTGTTTCCAAC
* *
22342893 AAAGAAAATAAAGGCGGAAATCGAGGGATGATAA-AGGATTTGG-AGTTGAAATTCAAGGGGTTG
1 AAAGAAAATAAAGGCGAAAATCGAGGGATGATAAGA-GATTTGGTA-TCGAAATTCAAGGGGTTG
* * *
22342956 AATCTTTTAGATCTCATTTCAATATCTTGGCTGATAAAAATAAAGAAAGGAATGATAATGTGGGG
64 AATCTTCTAGATCCCATTTCAATATCTTGGCTAATAAAAATAAAGAAAGGAATGATAATGTGGGG
* * * * *
22343021 ATTGGGGAAAT-TAGGAAGGAGCAGTTGAAGGGACTTTTAAATGGTAATAGAAGTGAAGCTATTA
129 ATTGGGGAAATCGAGAAAGG-GCAGTCGAAGGGACTTCTAAATGGTAATAAAAGTGAAGCTATTA
*
22343085 ATTTGAGTAAAAATTCAGGGTTGG
193 ATTTGAGTAAAAATTCAGGATTGG
22343109 ATAAGATGGT
Statistics
Matches: 188, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
241 7 0.04
242 181 0.96
ACGTcount: A:0.36, C:0.08, G:0.29, T:0.27
Consensus pattern (242 bp):
AAAGAAAATAAAGGCGAAAATCGAGGGATGATAAGAGATTTGGTATCGAAATTCAAGGGGTTGAA
TCTTCTAGATCCCATTTCAATATCTTGGCTAATAAAAATAAAGAAAGGAATGATAATGTGGGGAT
TGGGGAAATCGAGAAAGGGCAGTCGAAGGGACTTCTAAATGGTAATAAAAGTGAAGCTATTAATT
TGAGTAAAAATTCAGGATTGGGTGAGAGGGCAATAGTTGTTTCCAAC
Found at i:22346735 original size:5 final size:5
Alignment explanation
Indices: 22346725--22346776 Score: 61
Period size: 5 Copynumber: 10.2 Consensus size: 5
22346715 CATTTTCCTA
* *
22346725 TTTAT TTTA- TTTAT TATTAT TTTAT TATTAA TTCAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT T-TTAT TTTAT T-TTAT TTTAT TTTAT TTTAT TTTAT
22346776 T
1 T
22346777 CCTTTACTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 4 0.10
5 27 0.68
6 9 0.22
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:22348444 original size:12 final size:12
Alignment explanation
Indices: 22348411--22348444 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
22348401 ATTTTATTTG
22348411 TTTTCTTTTTAA
1 TTTTCTTTTTAA
**
22348423 TTTTAATTTTAA
1 TTTTCTTTTTAA
22348435 TTTTCTTTTT
1 TTTTCTTTTT
22348445 TTATGTTTAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTTAA
Found at i:22354653 original size:9 final size:9
Alignment explanation
Indices: 22354604--22354660 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
22354594 TTTGGTTAAA
22354604 AATTAACCG
1 AATTAACCG
*
22354613 AA-TAACTG
1 AATTAACCG
*
22354621 AATTACCCG
1 AATTAACCG
* *
22354630 AATTACCCT
1 AATTAACCG
22354639 AATTAACCG
1 AATTAACCG
*
22354648 AATTAACCA
1 AATTAACCG
22354657 AATT
1 AATT
22354661 GAATCACTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
8 7 0.17
9 33 0.82
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:22354786 original size:18 final size:18
Alignment explanation
Indices: 22354763--22354811 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
22354753 AATTTTTATG
*
22354763 ATTGGGTTGGGATGGATA
1 ATTGGGTTGGGATGAATA
*
22354781 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGATGAATA
* *
22354799 CTTGGGTTTGGAT
1 ATTGGGTTGGGAT
22354812 TGGGTTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.02, G:0.41, T:0.39
Consensus pattern (18 bp):
ATTGGGTTGGGATGAATA
Found at i:22364191 original size:14 final size:13
Alignment explanation
Indices: 22364167--22364204 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
22364157 CAAAATGTAC
22364167 AATATAATTAAAT
1 AATATAATTAAAT
22364180 AATATAAATTAAAT
1 AATAT-AATTAAAT
*
22364194 AATTTAATTAA
1 AATATAATTAA
22364205 CTATTTACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AATATAATTAAAT
Found at i:22367250 original size:24 final size:24
Alignment explanation
Indices: 22367222--22367273 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
22367212 CCGATTCATA
* *
22367222 TTTTTGTATTGCTTTTGGATTACT
1 TTTTTCTATTGATTTTGGATTACT
* *
22367246 TTTTTCTGTTGATTTTGGATTGCT
1 TTTTTCTATTGATTTTGGATTACT
22367270 TTTT
1 TTTT
22367274 CTTTTTTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.10, C:0.08, G:0.17, T:0.65
Consensus pattern (24 bp):
TTTTTCTATTGATTTTGGATTACT
Found at i:22367591 original size:125 final size:126
Alignment explanation
Indices: 22367369--22367623 Score: 368
Period size: 125 Copynumber: 2.0 Consensus size: 126
22367359 GGAGTTGGAT
* * * **
22367369 TTTTTTAATTTTACTGTAAGAGAACAATAACGGGAATAGCTGCCCATCATTGCCACAATTGGTCG
1 TTTTTTAATTTTACTGTAACAAAACAATAACAGGAATAGAGGCCCATCATTGCCACAATTGGTCG
*
22367434 TTACCTGTAAAATTGCAACCGCGATCCACCGCTATTGGTGTGGTTCCGCTTC-CATCGCTA
66 TTACCCGTAAAATTGCAACCGCGATCCACCGCTATTGGTGTGGTTCCGCTTCACATCGCTA
** * ***
22367494 TTTTTTAATTTTACTGTAACAAAACAATAACAGGAATAGAGGCCTGTTATTGCTGTAATTGGTCG
1 TTTTTTAATTTTACTGTAACAAAACAATAACAGGAATAGAGGCCCATCATTGCCACAATTGGTCG
* * *
22367559 TTACCCGTTAAATTGCGACCGCGATCCACCGCTATTGGTGTGGTTCTGCTTCACATCGCTA
66 TTACCCGTAAAATTGCAACCGCGATCCACCGCTATTGGTGTGGTTCCGCTTCACATCGCTA
22367620 TTTT
1 TTTT
22367624 CAGCAATAAC
Statistics
Matches: 114, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
125 102 0.89
126 12 0.11
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (126 bp):
TTTTTTAATTTTACTGTAACAAAACAATAACAGGAATAGAGGCCCATCATTGCCACAATTGGTCG
TTACCCGTAAAATTGCAACCGCGATCCACCGCTATTGGTGTGGTTCCGCTTCACATCGCTA
Found at i:22368869 original size:47 final size:47
Alignment explanation
Indices: 22368793--22369118 Score: 496
Period size: 47 Copynumber: 7.0 Consensus size: 47
22368783 ATTTTCACAC
* * * *
22368793 CAAAATTTGGACAGCATAT--ATACAAAATTGGACTGCATTTGTACAT
1 CAAAAATT-GACAGCATATACATATATAATTGGACTGCATTTATACAT
* * *
22368839 CAAAAATTGACAGCATATAAATATATAATTGGACTGTATTTGTACAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
22368886 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
22368933 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATA-AGT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACA-T
* *
22368980 TAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACGT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* * *
22369027 CAAAAATTGACAGCATATACATATGTATTTGGACTGCATTTGTACAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
*
22369074 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATAC
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATAC
22369119 GTNNNNNNNN
Statistics
Matches: 258, Mismatches: 18, Indels: 7
0.91 0.06 0.02
Matches are distributed among these distances:
45 10 0.04
46 8 0.03
47 240 0.93
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (47 bp):
CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
Found at i:22370036 original size:14 final size:15
Alignment explanation
Indices: 22370010--22370044 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
22370000 NNNNNNCATT
22370010 ACCATATAAATACTA
1 ACCATATAAATACTA
22370025 ACCATA-AAATACTA
1 ACCATATAAATACTA
22370039 ATCCAT
1 A-CCAT
22370045 GATTAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:22372643 original size:30 final size:30
Alignment explanation
Indices: 22372598--22372719 Score: 167
Period size: 30 Copynumber: 4.1 Consensus size: 30
22372588 ATAGAAACTA
*
22372598 ATATCAGTTAACTGATTCTTAGGAAATTAGG
1 ATATCAATT-ACTGATTCTTAGGAAATTAGG
*
22372629 ATATCAATTACTGATTCTTAGGAAAACTA--
1 ATATCAATTACTGATTCTTAGG-AAATTAGG
*
22372658 ATATCAGTTACTGATTCTTAGGAAATTAGG
1 ATATCAATTACTGATTCTTAGGAAATTAGG
* *
22372688 ATATCGATTATTGATTCTTAGGAAATTAGG
1 ATATCAATTACTGATTCTTAGGAAATTAGG
22372718 AT
1 AT
22372720 TTATTTCCTT
Statistics
Matches: 81, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
28 5 0.06
29 21 0.26
30 42 0.52
31 13 0.16
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (30 bp):
ATATCAATTACTGATTCTTAGGAAATTAGG
Found at i:22372685 original size:59 final size:60
Alignment explanation
Indices: 22372592--22372712 Score: 217
Period size: 59 Copynumber: 2.0 Consensus size: 60
22372582 TTGTAAATAG
22372592 AAACTAATATCAGTTAACTGATTCTTAGGAAATTAGGATATCAATTACTGATTCTTAGGA
1 AAACTAATATCAGTTAACTGATTCTTAGGAAATTAGGATATCAATTACTGATTCTTAGGA
* *
22372652 AAACTAATATCAGTT-ACTGATTCTTAGGAAATTAGGATATCGATTATTGATTCTTAGGA
1 AAACTAATATCAGTTAACTGATTCTTAGGAAATTAGGATATCAATTACTGATTCTTAGGA
22372711 AA
1 AA
22372713 TTAGGATTTA
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
59 44 0.75
60 15 0.25
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (60 bp):
AAACTAATATCAGTTAACTGATTCTTAGGAAATTAGGATATCAATTACTGATTCTTAGGA
Found at i:22377357 original size:30 final size:30
Alignment explanation
Indices: 22377312--22377433 Score: 185
Period size: 30 Copynumber: 4.1 Consensus size: 30
22377302 ATAGAAACTA
*
22377312 ATATCAGTTAACTGATTCTTAGGAAATTAGG
1 ATATCAATT-ACTGATTCTTAGGAAATTAGG
*
22377343 ATATCAATTACTGATTCTTAGGAAAACTA--
1 ATATCAATTACTGATTCTTAGG-AAATTAGG
*
22377372 ATATCAGTTACTGATTCTTAGGAAATTAGG
1 ATATCAATTACTGATTCTTAGGAAATTAGG
22377402 ATATCAATTACTGATTCTTAGGAAATTAGG
1 ATATCAATTACTGATTCTTAGGAAATTAGG
22377432 AT
1 AT
22377434 TTATTTCCTT
Statistics
Matches: 83, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
28 5 0.06
29 21 0.25
30 44 0.53
31 13 0.16
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (30 bp):
ATATCAATTACTGATTCTTAGGAAATTAGG
Found at i:22377399 original size:59 final size:60
Alignment explanation
Indices: 22377306--22377426 Score: 235
Period size: 59 Copynumber: 2.0 Consensus size: 60
22377296 TTGTAAATAG
22377306 AAACTAATATCAGTTAACTGATTCTTAGGAAATTAGGATATCAATTACTGATTCTTAGGA
1 AAACTAATATCAGTTAACTGATTCTTAGGAAATTAGGATATCAATTACTGATTCTTAGGA
22377366 AAACTAATATCAGTT-ACTGATTCTTAGGAAATTAGGATATCAATTACTGATTCTTAGGA
1 AAACTAATATCAGTTAACTGATTCTTAGGAAATTAGGATATCAATTACTGATTCTTAGGA
22377425 AA
1 AA
22377427 TTAGGATTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
59 46 0.75
60 15 0.25
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (60 bp):
AAACTAATATCAGTTAACTGATTCTTAGGAAATTAGGATATCAATTACTGATTCTTAGGA
Found at i:22378573 original size:24 final size:24
Alignment explanation
Indices: 22378499--22378610 Score: 122
Period size: 24 Copynumber: 4.6 Consensus size: 24
22378489 GTACATGTAT
*
22378499 GCTCATACGAGCT-ATGAATCGGTAT
1 GCTCATACGAGCTGA--AATCGGTAA
22378524 GCTC-TAACGAGCTGTAAATCGGTAA
1 GCTCAT-ACGAGCTG-AAATCGGTAA
* *
22378549 GCTCATACGAGCTGAAATTGATAA
1 GCTCATACGAGCTGAAATCGGTAA
22378573 GCTC-TCACGAGCTGAAATCGGTAA
1 GCTCAT-ACGAGCTGAAATCGGTAA
*
22378597 GCTCATACAAGCTG
1 GCTCATACGAGCTG
22378611 TGGTGTGTCC
Statistics
Matches: 75, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
23 1 0.01
24 40 0.53
25 32 0.43
26 1 0.01
27 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (24 bp):
GCTCATACGAGCTGAAATCGGTAA
Found at i:22388280 original size:34 final size:35
Alignment explanation
Indices: 22388230--22388327 Score: 146
Period size: 34 Copynumber: 2.9 Consensus size: 35
22388220 GTGTAGAGTT
* *
22388230 TTTTAAAAAAACTAATTAAATTAGGTTTTAAGGG-
1 TTTTAAATAAATTAATTAAATTAGGTTTTAAGGGA
*
22388264 TTTTAAATAAATTAATTAAATTAAGTTTT-AGGGA
1 TTTTAAATAAATTAATTAAATTAGGTTTTAAGGGA
*
22388298 TTTTAAATAAATTAATTAAATTAGGGTTTA
1 TTTTAAATAAATTAATTAAATTAGGTTTTA
22388328 GTTTTTTTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
33 4 0.07
34 53 0.93
ACGTcount: A:0.44, C:0.01, G:0.12, T:0.43
Consensus pattern (35 bp):
TTTTAAATAAATTAATTAAATTAGGTTTTAAGGGA
Found at i:22388336 original size:34 final size:34
Alignment explanation
Indices: 22388211--22388338 Score: 141
Period size: 34 Copynumber: 3.7 Consensus size: 34
22388201 TTTTAGAAAA
* * * *
22388211 TAAATTAGGGTGTAGAGTTTTTTAAAAAAACTAAT
1 TAAATTAGGGTTTAG-GGTTTTTAAATAAATTAAT
*
22388246 TAAATTAGGTTTTAAGGG-TTTTAAATAAATTAAT
1 TAAATTAGGGTTT-AGGGTTTTTAAATAAATTAAT
* * *
22388280 TAAATTAAGTTTTAGGGATTTTAAATAAATTAAT
1 TAAATTAGGGTTTAGGGTTTTTAAATAAATTAAT
**
22388314 TAAATTAGGGTTTAGTTTTTTTAAA
1 TAAATTAGGGTTTAGGGTTTTTAAA
22388339 ATAATTTTTG
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
33 4 0.05
34 62 0.77
35 12 0.15
36 2 0.03
ACGTcount: A:0.41, C:0.01, G:0.15, T:0.44
Consensus pattern (34 bp):
TAAATTAGGGTTTAGGGTTTTTAAATAAATTAAT
Found at i:22391932 original size:18 final size:18
Alignment explanation
Indices: 22391906--22391948 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
22391896 GACTGAGAAA
* *
22391906 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
22391924 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
22391942 AGGATAC
1 AGGATAC
22391949 TCACCTGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:22393724 original size:17 final size:17
Alignment explanation
Indices: 22393702--22393762 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
22393692 ATTGAATCAC
22393702 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
22393719 TACATAAGACTTTGAATCAC
1 TACAT-A-A-TTAAAAACAT
22393739 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
22393756 TACATAA
1 TACATAA
22393763 GTCTTGAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 18 0.55
18 2 0.06
19 2 0.06
20 11 0.33
ACGTcount: A:0.52, C:0.15, G:0.03, T:0.30
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:22393740 original size:37 final size:37
Alignment explanation
Indices: 22393693--22393763 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
22393683 ATTACCCGAA
22393693 TTGAATCACTACATAATTAAAAACATTACATAAGACT
1 TTGAATCACTACATAATTAAAAACATTACATAAGACT
22393730 TTGAATCACTACATAATTAAAAACATTACATAAG
1 TTGAATCACTACATAATTAAAAACATTACATAAG
22393764 TCTTGAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGACT
Found at i:22393781 original size:37 final size:37
Alignment explanation
Indices: 22393693--22393784 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 37
22393683 ATTACCCGAA
*
22393693 TTGAATCACTACATAATTAAAAACATTACATAAGACT
1 TTGAATAACTACATAATTAAAAACATTACATAAGACT
* *
22393730 TTGAATCACTACATAATTAAAAACATTACATAAGTC-
1 TTGAATAACTACATAATTAAAAACATTACATAAGACT
22393766 TTGAAATTAAC-ACATAATT
1 TTG-AA-TAACTACATAATT
22393785 GAAATGTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
36 3 0.06
37 45 0.88
38 3 0.06
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.32
Consensus pattern (37 bp):
TTGAATAACTACATAATTAAAAACATTACATAAGACT
Found at i:22393939 original size:38 final size:39
Alignment explanation
Indices: 22393895--22394011 Score: 191
Period size: 39 Copynumber: 3.0 Consensus size: 39
22393885 GACTTAGAGT
*
22393895 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTAGGTAATTGGG
* *
22393933 TAGACTTTAGTTTTAGTTTTATTGGGTTAAGTAATTTGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTAGGTAATTGGG
*
22393972 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTAGGTAATTGGG
22394011 T
1 T
22394012 TGGGTTGGAT
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
38 27 0.38
39 45 0.62
ACGTcount: A:0.20, C:0.03, G:0.26, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTAGGTAATTGGG
Found at i:22394010 original size:13 final size:13
Alignment explanation
Indices: 22393992--22394016 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22393982 TTTTAGTTTT
22393992 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
22394005 ATTGGGTTGGGT
1 ATTGGGTTGGGT
22394017 TGGATAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:22395384 original size:2 final size:2
Alignment explanation
Indices: 22395379--22395435 Score: 105
Period size: 2 Copynumber: 28.0 Consensus size: 2
22395369 TAGTAGTGTG
22395379 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
22395421 TA TA TA TA TCA TA TA
1 TA TA TA TA T-A TA TA
22395436 ACAAGTATTA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 52 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:22395842 original size:23 final size:20
Alignment explanation
Indices: 22395798--22395847 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 20
22395788 ATTTAATAAT
22395798 ATAAAA-ATATATAAATTTA
1 ATAAAATATATATAAATTTA
22395817 ATAAAATATATAATTAATATTTA
1 ATAAAATATAT-A-TAA-ATTTA
22395840 ATAAAATA
1 ATAAAATA
22395848 ATTATATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.22
20 4 0.15
21 1 0.04
22 3 0.11
23 13 0.48
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAAAATATATATAAATTTA
Found at i:22395862 original size:16 final size:18
Alignment explanation
Indices: 22395826--22395863 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
22395816 AATAAAATAT
22395826 ATAATTAATATTTAATAAA
1 ATAATTAATATTT-ATAAA
22395845 ATAATT-ATATTT-TAAA
1 ATAATTAATATTTATAAA
22395861 ATA
1 ATA
22395864 TGGATAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
18 6 0.32
19 6 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTAATATTTATAAA
Found at i:22396327 original size:2 final size:2
Alignment explanation
Indices: 22396320--22396351 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
22396310 CAAGAAGTAA
22396320 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22396352 TAATAGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22401061 original size:179 final size:179
Alignment explanation
Indices: 22400704--22401221 Score: 550
Period size: 179 Copynumber: 2.9 Consensus size: 179
22400694 ATGAACCAAT
* * * * * * *
22400704 ATCGATGATAAGGAATCAAATGCCTCAACTACAACCATCCC-CACCCACTTCCTCTTTTCCAATT
1 ATCGATAATAAGCAATCGAATGTCTCAACTACAATCA-CCCTCCCCCACTTCCTCTTTTCCATTT
* **
22400768 TGGAGATATTGCTAGACATAATATTCGGGTAAAACACAGTCGACACCC-T-AGTAAAGGTTAAAA
65 TGGAGATATTGCTAGACATAATGTTCGGGTAAAACACAGTCGACACCCTTGAAAAAAGG-TAAAA
* *
22400831 CAGTAAGAC-TTAGAGCCACCACTTAGATGATACAAATCACATAACTAACAAAC
129 CAGTAAGACATT-GAGCCACCACTCAGATAATACAAATCAC--AACTAACAAAC
* * * * * * *
22400884 AT-TATCAATGAGGAATTGAATGTCTCAACTATAATCATCCT-GCCCACTTCCTCTTTTCCATTT
1 ATCGAT-AATAAGCAATCGAATGTCTCAACTACAATCACCCTCCCCCACTTCCTCTTTTCCATTT
* *
22400947 TGGAGGTATTGCTAGACATAATGTT-TGGTAAAACAACAGTCGACACCCTTGCAAAAAAAAGGTA
65 TGGAGATATTGCTAGACATAATGTTCGGGTAAAAC-ACAGTCGACACCCTTG---AAAAAAGGTA
* * *
22401011 AAACGGTAAGGCATTGAGCCACCGCTCAGATAATACAAATCAC-A-TAACAAAC
126 AAACAGTAAGACATTGAGCCACCACTCAGATAATACAAATCACAACTAACAAAC
* * * *
22401063 ATCGATGATAAGCAGTCGAATGTCTCACCTACAATCACCCTCCCCCACTTCCTCCTTTTTCATTT
1 ATCGATAATAAGCAATCGAATGTCTCAACTACAATCACCCTCCCCCACTTCCT-CTTTTCCATTT
* * * *
22401128 TGGAGATATTGCTATACATAATGTTCGGGTAAAACACAGTCAGACGCTCTTGTAAAAAAGTTAAA
65 TGGAGATATTGCTAGACATAATGTTCGGGTAAAACACAGTC-GACACCCTTG-AAAAAAGGTAAA
* *
22401193 ACAGTAAGACATAGAGCCACCATTCAGAT
128 ACAGTAAGACATTGAGCCACCACTCAGAT
22401222 TTCAGATGAT
Statistics
Matches: 280, Mismatches: 44, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
178 8 0.03
179 97 0.35
180 75 0.27
181 39 0.14
182 16 0.06
183 37 0.13
184 8 0.03
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.26
Consensus pattern (179 bp):
ATCGATAATAAGCAATCGAATGTCTCAACTACAATCACCCTCCCCCACTTCCTCTTTTCCATTTT
GGAGATATTGCTAGACATAATGTTCGGGTAAAACACAGTCGACACCCTTGAAAAAAGGTAAAACA
GTAAGACATTGAGCCACCACTCAGATAATACAAATCACAACTAACAAAC
Found at i:22403538 original size:23 final size:22
Alignment explanation
Indices: 22403512--22403554 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
22403502 TTTTAAATAT
*
22403512 TTTATCTTATTCTAAAATTTTCA
1 TTTAT-TTATTATAAAATTTTCA
*
22403535 TTTATTTCTTATAAAATTTT
1 TTTATTTATTATAAAATTTT
22403555 AAATTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTATTTATTATAAAATTTTCA
Found at i:22403624 original size:20 final size:20
Alignment explanation
Indices: 22403599--22403647 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
22403589 CTAAAAATAA
22403599 TAAAAATTTGATTTAATCCT
1 TAAAAATTTGATTTAATCCT
* *
22403619 TAAAAAATTGATTTAATCTT
1 TAAAAATTTGATTTAATCCT
*
22403639 TTAAAATTT
1 TAAAAATTT
22403648 ATTGTACTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (20 bp):
TAAAAATTTGATTTAATCCT
Found at i:22405034 original size:12 final size:12
Alignment explanation
Indices: 22405013--22405050 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
22405003 TATTATTATC
22405013 ATATTTAATTTT
1 ATATTTAATTTT
22405025 AT-TATTAATTATT
1 ATAT-TTAATT-TT
22405038 ATATTTAATTTT
1 ATATTTAATTTT
22405050 A
1 A
22405051 GAAAAATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 1 0.04
12 11 0.48
13 10 0.43
14 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATATTTAATTTT
Found at i:22405041 original size:25 final size:24
Alignment explanation
Indices: 22404997--22405050 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
22404987 GTTGAAGATG
22404997 ATTTT-TTATTATTATCATATTTA
1 ATTTTATTATTATTATCATATTTA
*
22405020 ATTTTATTATTAATTATTATATTTA
1 ATTTTATTATT-ATTATCATATTTA
22405045 ATTTTA
1 ATTTTA
22405051 GAAAAATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 5 0.18
24 5 0.18
25 18 0.64
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
ATTTTATTATTATTATCATATTTA
Found at i:22405045 original size:13 final size:13
Alignment explanation
Indices: 22405007--22405047 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
22404997 ATTTTTTATT
*
22405007 ATTATCATATTTA
1 ATTATTATATTTA
22405020 ATT-TTAT-TATTA
1 ATTATTATAT-TTA
22405032 ATTATTATATTTA
1 ATTATTATATTTA
22405045 ATT
1 ATT
22405048 TTAGAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
11 1 0.04
12 9 0.38
13 13 0.54
14 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTATTATATTTA
Found at i:22405516 original size:19 final size:19
Alignment explanation
Indices: 22405494--22405536 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
22405484 TATATATATA
22405494 TATATATATTCTTTATAAT
1 TATATATATTCTTTATAAT
22405513 TATATATATTCTTTATAAT
1 TATATATATTCTTTATAAT
22405532 TATAT
1 TATAT
22405537 TCTAAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATATATTCTTTATAAT
Found at i:22405539 original size:15 final size:18
Alignment explanation
Indices: 22405488--22405536 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
22405478 GATATATATA
22405488 TATATATATATATATTCTT
1 TATA-ATATATATATTCTT
22405507 TATAATTATATATATTCTT
1 TATAA-TATATATATTCTT
22405526 TATAAT-TATAT
1 TATAATATATAT
22405537 TCTAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.17
18 2 0.07
19 22 0.76
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (18 bp):
TATAATATATATATTCTT
Found at i:22409387 original size:19 final size:18
Alignment explanation
Indices: 22409363--22409427 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 18
22409353 TGGAAAGTAA
22409363 ATTGAATTGAAATGTGATT
1 ATTGAATTGAAAT-TGATT
*
22409382 ATTGAATAGAAATTGA--
1 ATTGAATTGAAATTGATT
* **
22409398 AATGGTTTGAAATTGAATT
1 ATTGAATTGAAATTG-ATT
22409417 ATTGAATTGAA
1 ATTGAATTGAA
22409428 CTGGAATATT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
16 11 0.31
17 1 0.03
18 3 0.09
19 20 0.57
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (18 bp):
ATTGAATTGAAATTGATT
Found at i:22409840 original size:45 final size:45
Alignment explanation
Indices: 22409775--22409879 Score: 158
Period size: 45 Copynumber: 2.3 Consensus size: 45
22409765 ATGTGCCGAC
* * *
22409775 TACTGTTACTGTTACTGATTC-GATACTTTGTGTGTCGAATATTGT
1 TACTGTTACTGTTACAGATTCAG-CACTTTGTGTGTCGAATACTGT
*
22409820 TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATACTGT
22409865 TACTGTTACTGTTAC
1 TACTGTTACTGTTAC
22409880 TGCTACCGTT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
45 54 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATACTGT
Found at i:22409870 original size:6 final size:6
Alignment explanation
Indices: 22409859--22409900 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
22409849 GTGTGTTGAA
* *
22409859 TACTGT TACTGT TACTGT TACTGC TACCGT TACTGTT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTG
22409901 ATCAGGTACT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (6 bp):
TACTGT
Found at i:22415606 original size:27 final size:27
Alignment explanation
Indices: 22415573--22415628 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
22415563 GATTATGTGT
*
22415573 TAGGCTTTGGGCCAAATGGATTTAATC
1 TAGGCTTTGGGCCAAATAGATTTAATC
22415600 TAGGCTTTGGGCCAAATAGATTTAATC
1 TAGGCTTTGGGCCAAATAGATTTAATC
22415627 TA
1 TA
22415629 TGTCTTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (27 bp):
TAGGCTTTGGGCCAAATAGATTTAATC
Found at i:22420561 original size:56 final size:56
Alignment explanation
Indices: 22420484--22420595 Score: 163
Period size: 56 Copynumber: 2.0 Consensus size: 56
22420474 TACTGGTGTG
* *
22420484 GAAAAAGATACAAGGGATTGATTTGATCAGACCA-ACTGAAGAGAAAGTGAAAGTGA
1 GAAAAAAATACAAGGGATTGATTTGATCAGA-CAGACTGAAGAAAAAGTGAAAGTGA
* * *
22420540 GAAAAAAATACACGGGGTTGATTTGATCAGAGAGACTGAAGAAAAAGTGAAAGTGA
1 GAAAAAAATACAAGGGATTGATTTGATCAGACAGACTGAAGAAAAAGTGAAAGTGA
22420596 TTCGTGACAG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
55 1 0.02
56 49 0.98
ACGTcount: A:0.46, C:0.08, G:0.28, T:0.18
Consensus pattern (56 bp):
GAAAAAAATACAAGGGATTGATTTGATCAGACAGACTGAAGAAAAAGTGAAAGTGA
Found at i:22421850 original size:28 final size:30
Alignment explanation
Indices: 22421819--22421876 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 30
22421809 GAAAATATAG
*
22421819 ATTAGGGGTTAAAT-TGAGAAAT-GTGAAA
1 ATTAGGGGTCAAATGTGAGAAATGGTGAAA
* *
22421847 ATTATGGGTCAAATGTGGGAAATGGTGAAA
1 ATTAGGGGTCAAATGTGAGAAATGGTGAAA
22421877 TATATGGGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 12 0.48
29 7 0.28
30 6 0.24
ACGTcount: A:0.40, C:0.02, G:0.31, T:0.28
Consensus pattern (30 bp):
ATTAGGGGTCAAATGTGAGAAATGGTGAAA
Found at i:22425184 original size:23 final size:25
Alignment explanation
Indices: 22425123--22425189 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 25
22425113 TTTCTTTGTT
* *
22425123 TTTAAGTTTTTATTTATTT-ACTTTA
1 TTTAAG-TTTTATTTATTTGTCCTTA
22425148 TTTAAGTTTT-TTTATTTGTCCTTA
1 TTTAAGTTTTATTTATTTGTCCTTA
22425172 TTT-A-TTTTATTTATTTGT
1 TTTAAGTTTTATTTATTTGT
22425190 TTATTATTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.11
23 17 0.45
24 11 0.29
25 6 0.16
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.70
Consensus pattern (25 bp):
TTTAAGTTTTATTTATTTGTCCTTA
Found at i:22425269 original size:21 final size:22
Alignment explanation
Indices: 22425233--22425326 Score: 104
Period size: 21 Copynumber: 4.3 Consensus size: 22
22425223 TTTGAAATTT
*
22425233 TTTATAATAT-TATTTTTTAAAA
1 TTTAAAATATATA-TTTTTAAAA
22425255 TTTAAAATATAT-TTTTTAAAA
1 TTTAAAATATATATTTTTAAAA
* *
22425276 TTTTAAATAT-TATTTGTAAAA
1 TTTAAAATATATATTTTTAAAA
*
22425297 TTTTAAATATATATTTTTAATAA
1 TTTAAAATATATATTTTTAA-AA
*
22425320 TATAAAA
1 TTTAAAA
22425327 CATTTAAATA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
20 1 0.02
21 36 0.58
22 17 0.27
23 8 0.13
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (22 bp):
TTTAAAATATATATTTTTAAAA
Found at i:22425285 original size:43 final size:44
Alignment explanation
Indices: 22425206--22425316 Score: 129
Period size: 45 Copynumber: 2.5 Consensus size: 44
22425196 TTGGTTTTAA
* * * * *
22425206 AAAATTTGAAATGTATA-TTTGAAATTTTTTATAATATTATTTTTT
1 AAAATTTAAAATATATATTTTTAAA-ATTTTATAATATTA-TTTGT
22425251 AAAATTTAAAATATAT-TTTTTAAAATTTTA-AATATTATTTGT
1 AAAATTTAAAATATATATTTTTAAAATTTTATAATATTATTTGT
*
22425293 AAAATTTTAAATATATATTTTTAA
1 AAAATTTAAAATATATATTTTTAA
22425317 TAATATAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
42 19 0.33
43 14 0.24
44 5 0.09
45 20 0.34
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (44 bp):
AAAATTTAAAATATATATTTTTAAAATTTTATAATATTATTTGT
Found at i:22425325 original size:22 final size:22
Alignment explanation
Indices: 22425232--22425314 Score: 116
Period size: 21 Copynumber: 3.8 Consensus size: 22
22425222 ATTTGAAATT
22425232 TTTTATAATATTATTTTTTAAAA
1 TTTTA-AATATTATTTTTTAAAA
*
22425255 TTTAAAATA-TATTTTTTAAAA
1 TTTTAAATATTATTTTTTAAAA
*
22425276 TTTTAAATATTA-TTTGTAAAA
1 TTTTAAATATTATTTTTTAAAA
22425297 TTTTAAATATATATTTTT
1 TTTTAAATAT-TATTTTT
22425315 AATAATATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
21 38 0.72
22 8 0.15
23 7 0.13
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (22 bp):
TTTTAAATATTATTTTTTAAAA
Found at i:22425568 original size:18 final size:17
Alignment explanation
Indices: 22425542--22425583 Score: 75
Period size: 18 Copynumber: 2.4 Consensus size: 17
22425532 GAGAAAAAAT
22425542 AAAAAATTTATTTGTTA
1 AAAAAATTTATTTGTTA
22425559 AAAAAGATTTATTTGTTA
1 AAAAA-ATTTATTTGTTA
22425577 AAAAAAT
1 AAAAAAT
22425584 ATGACTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (17 bp):
AAAAAATTTATTTGTTA
Found at i:22425652 original size:21 final size:21
Alignment explanation
Indices: 22425594--22425652 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
22425584 ATGACTTTAT
22425594 TTAAAATATATATATTAAAAAA
1 TTAAAA-ATATATATTAAAAAA
* * * *
22425616 GTAAAAATTTAAATTAGAAAA
1 TTAAAAATATATATTAAAAAA
22425637 TTAAAAATATATATTA
1 TTAAAAATATATATTA
22425653 TAACTGGTCA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (21 bp):
TTAAAAATATATATTAAAAAA
Found at i:22429525 original size:43 final size:43
Alignment explanation
Indices: 22429370--22429526 Score: 140
Period size: 43 Copynumber: 3.7 Consensus size: 43
22429360 TGAGTTATCT
* * * *
22429370 TGTAAGACCACATCTGGGACGTTGGCGTCGAT-TTGAGATTTACG
1 TGTAAGACCACGTCTGGGACATTGGCATCGATATT-AGA-TTACA
* * * * *
22429414 TGTAGGACCATGTCTAGGACATCGGCATCG-TA-TACGATTTCA
1 TGTAAGACCACGTCTGGGACATTGGCATCGATATTA-GATTACA
** * *
22429456 TGTAAGACCTTGTCTGGGACAATGGCATCGATATTTGATTACA
1 TGTAAGACCACGTCTGGGACATTGGCATCGATATTAGATTACA
*
22429499 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACATTGGCAT
22429527 TCTAAGAGCT
Statistics
Matches: 89, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
42 29 0.33
43 36 0.40
44 24 0.27
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGATATTAGATTACA
Found at i:22432025 original size:30 final size:29
Alignment explanation
Indices: 22431916--22432052 Score: 132
Period size: 30 Copynumber: 4.6 Consensus size: 29
22431906 GTCACAGAGC
* *
22431916 AGTTCATATCACTC-GTACATGGGCGGCTTG
1 AGTTCATATCACCCAG-ACATGGGC-GATTG
22431946 AGTTCATATCACCCAGACATGGGCGACTTG
1 AGTTCATATCACCCAGACATGGGCGA-TTG
***
22431976 AGTTCATATCACTTGGACATGGGCGATTCG
1 AGTTCATATCACCCAGACATGGGCGATT-G
* ** *
22432006 AGTTCACATCACCCAGACATAAGCGGTTCG
1 AGTTCATATCACCCAGACATGGGCGATT-G
*
22432036 AGTTCATTTCACCCAGA
1 AGTTCATATCACCCAGA
22432053 GCAACCACCG
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
29 3 0.03
30 86 0.96
31 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (29 bp):
AGTTCATATCACCCAGACATGGGCGATTG
Found at i:22432039 original size:60 final size:60
Alignment explanation
Indices: 22431916--22432047 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
22431906 GTCACAGAGC
* * * **
22431916 AGTTCATATCACTCGTACATGGGCGGCTTGAGTTCATATCACCCAGACATGGGCGACTTG
1 AGTTCATATCACTCGGACATGGGCGGATTGAGTTCACATCACCCAGACATAAGCGACTTG
* *
22431976 AGTTCATATCACTTGGACATGGGC-GATTCGAGTTCACATCACCCAGACATAAGCG-GTTCG
1 AGTTCATATCACTCGGACATGGGCGGATT-GAGTTCACATCACCCAGACATAAGCGACTT-G
*
22432036 AGTTCATTTCAC
1 AGTTCATATCAC
22432048 CCAGAGCAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 5 0.08
60 57 0.92
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (60 bp):
AGTTCATATCACTCGGACATGGGCGGATTGAGTTCACATCACCCAGACATAAGCGACTTG
Found at i:22434926 original size:363 final size:363
Alignment explanation
Indices: 22434261--22434988 Score: 1393
Period size: 363 Copynumber: 2.0 Consensus size: 363
22434251 CAATCGACAA
22434261 CTTTATGATGTATTGTTTGATGGCAGACACACAGTCCACCTTGTTCTCGAACTGTTACCTAACGA
1 CTTTATGATGTATTGTTTGATGGCAGACACACAGTCCACCTTGTTCTCGAACTGTTACCTAACGA
*
22434326 ACAACTCCTCGAACTGCGAATTTGACTCCAATCTATAATTAGGTACTATATCGGTGTACTTAGGG
66 ACAACTCCTCGAACTGCGAATTTGACGCCAATCTATAATTAGGTACTATATCGGTGTACTTAGGG
*
22434391 AACCCGGATGCATGCGTTACATCTGGATCTACGTACAACATGTCGCCCCCAGGTTCATTTCGTAA
131 AACCCGGATGCATGCGCTACATCTGGATCTACGTACAACATGTCGCCCCCAGGTTCATTTCGTAA
* *
22434456 AATAGTGCCATGACTCGGGTTTCTGAATGAAGAGCCGTAAACATCTTCATCCTCCTCCAGGCCTT
196 AATAGTGCCACGACTCGGGTTACTGAATGAAGAGCCGTAAACATCTTCATCCTCCTCCAGGCCTT
*
22434521 CATCATCGATATCGTCCGGAACCTCATCAATATCGGGGTCACTAAAATCTTCAACGTCCTGATCA
261 CATCATCGATATCGTCCGGAACCTCATCAACATCGGGGTCACTAAAATCTTCAACGTCCTGATCA
*
22434586 GAATCTTTACCATTATTGATCATTTCTCTGACATTTGC
326 GAATCTTCACCATTATTGATCATTTCTCTGACATTTGC
22434624 CTTTATGATGTATTGTTTGATGGCAGACACACAGTCCACCTTGTTCTCGAACTGTTACCTAACGA
1 CTTTATGATGTATTGTTTGATGGCAGACACACAGTCCACCTTGTTCTCGAACTGTTACCTAACGA
22434689 ACAACTCCTCGAACTGCGAATTTGACGCCAATCTATAATTAGGTACTATATCGGTGTACTTAGGG
66 ACAACTCCTCGAACTGCGAATTTGACGCCAATCTATAATTAGGTACTATATCGGTGTACTTAGGG
*
22434754 AACTCGGATGCATGCGCTACATCTGGATCTACGTACAACATGTCGCCCCCAGGTTCATTTCGTAA
131 AACCCGGATGCATGCGCTACATCTGGATCTACGTACAACATGTCGCCCCCAGGTTCATTTCGTAA
22434819 AATAGTGCCACGACTCGGGTTACTGAATGAAGAGCCGTAAACATCTTCATCCTCCTCCAGGCCTT
196 AATAGTGCCACGACTCGGGTTACTGAATGAAGAGCCGTAAACATCTTCATCCTCCTCCAGGCCTT
22434884 CATCATCGATATCGTCCGGAACCTCATCAACATCGGGGTCACTAAAATCTTCAACGTCCTGATCA
261 CATCATCGATATCGTCCGGAACCTCATCAACATCGGGGTCACTAAAATCTTCAACGTCCTGATCA
22434949 GAATCTTCACCATTATTGATCATTTCTCTGACATTTGC
326 GAATCTTCACCATTATTGATCATTTCTCTGACATTTGC
22434987 CT
1 CT
22434989 CTGTGCTTAT
Statistics
Matches: 358, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
363 358 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (363 bp):
CTTTATGATGTATTGTTTGATGGCAGACACACAGTCCACCTTGTTCTCGAACTGTTACCTAACGA
ACAACTCCTCGAACTGCGAATTTGACGCCAATCTATAATTAGGTACTATATCGGTGTACTTAGGG
AACCCGGATGCATGCGCTACATCTGGATCTACGTACAACATGTCGCCCCCAGGTTCATTTCGTAA
AATAGTGCCACGACTCGGGTTACTGAATGAAGAGCCGTAAACATCTTCATCCTCCTCCAGGCCTT
CATCATCGATATCGTCCGGAACCTCATCAACATCGGGGTCACTAAAATCTTCAACGTCCTGATCA
GAATCTTCACCATTATTGATCATTTCTCTGACATTTGC
Found at i:22436066 original size:21 final size:21
Alignment explanation
Indices: 22436031--22436087 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
22436021 AAATTTTTTT
*
22436031 AAAA-AATATTTAAATTTAAA
1 AAAATAATATTTAAAATTAAA
*
22436051 AATAT-ATATTTAAAATTAAA
1 AAAATAATATTTAAAATTAAA
22436071 AAAATAATATTATAAAA
1 AAAATAATATT-TAAAA
22436088 CAATTCAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 21 0.68
21 5 0.16
22 5 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATAATATTTAAAATTAAA
Found at i:22437619 original size:39 final size:38
Alignment explanation
Indices: 22437565--22437729 Score: 163
Period size: 40 Copynumber: 4.2 Consensus size: 38
22437555 AAATATATTT
* *
22437565 ATTTTTTAAATTTTAAAATATTTTTTACATACTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTTA-ATATTTTTTAA
* *
22437604 ATTTTTTTAATTTTAAAATATTTTTAAAATAATTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTT-TAAT-ATTTTTTAA
22437644 ATTTTTTTAATTTTAAAATATATTTTTTAAT-TTTTTTAA
1 ATTTTTTTAATTTT-AAA-ATATTTTTTAATATTTTTTAA
** * *
22437683 ATTTTAAAATATTTTTAAAATACTTTTTTTA-ATTTTTTAA
1 ATTTT--TTTAATTTTAAAATA-TTTTTTAATATTTTTTAA
*
22437723 AATTTTT
1 ATTTTTT
22437730 AAAATAAAAA
Statistics
Matches: 105, Mismatches: 13, Indels: 17
0.78 0.10 0.13
Matches are distributed among these distances:
39 41 0.39
40 44 0.42
41 12 0.11
42 8 0.08
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (38 bp):
ATTTTTTTAATTTTAAAATATTTTTTAATATTTTTTAA
Found at i:22437640 original size:12 final size:11
Alignment explanation
Indices: 22437614--22437735 Score: 61
Period size: 12 Copynumber: 11.9 Consensus size: 11
22437604 ATTTTTTTAA
22437614 TTTTAAAATAT
1 TTTTAAAATAT
22437625 TTTTAAAATAAT
1 TTTTAAAAT-AT
**
22437637 TTTTTTAAT-T
1 TTTTAAAATAT
*
22437647 TTTT----TAA
1 TTTTAAAATAT
22437654 TTTTAAAATAT
1 TTTTAAAATAT
**
22437665 ATTTTTTAAT-T
1 -TTTTAAAATAT
*
22437676 TTTT-TAA-A-
1 TTTTAAAATAT
22437684 TTTTAAAATAT
1 TTTTAAAATAT
22437695 TTTTAAAATACT
1 TTTTAAAATA-T
**
22437707 TTTTTTAAT-T
1 TTTTAAAATAT
22437717 TTTT-AAA-AT
1 TTTTAAAATAT
22437726 TTTTAAAATA
1 TTTTAAAATA
22437736 AAAATGGGAC
Statistics
Matches: 86, Mismatches: 10, Indels: 30
0.68 0.08 0.24
Matches are distributed among these distances:
6 1 0.01
7 4 0.05
8 4 0.05
9 12 0.14
10 18 0.21
11 23 0.27
12 24 0.28
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:22437640 original size:70 final size:70
Alignment explanation
Indices: 22437597--22437735 Score: 201
Period size: 70 Copynumber: 2.0 Consensus size: 70
22437587 TTTTACATAC
**
22437597 TTTTTAAATTTTTTT-AATTTTAAAATATTTTTAAAATAATTTTTTTAATTTTTTTAATTTTAAA
1 TTTTTAAATTTTTTTAAATTTTAAAATATTTTTAAAATAATTTTTTTAATTTTAATAATTTTAAA
22437661 ATATA
66 ATATA
* *
22437666 TTTTTTAATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTAA-AATTTTT
1 TTTTTAAATTTTTTTAAATTTTAAAATATTTTTAAAATAATTTTTTTAA--TTTTAATAA-TTTT
22437730 AAAATA
63 AAAATA
22437736 AAAATGGGAC
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
69 14 0.23
70 32 0.52
71 2 0.03
72 14 0.23
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (70 bp):
TTTTTAAATTTTTTTAAATTTTAAAATATTTTTAAAATAATTTTTTTAATTTTAATAATTTTAAA
ATATA
Found at i:22437641 original size:40 final size:39
Alignment explanation
Indices: 22437565--22437735 Score: 173
Period size: 39 Copynumber: 4.5 Consensus size: 39
22437555 AAATATATTT
* * * * *
22437565 ATTTTTTAAATTTTAAAATATTTTTTACATACTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTTA
22437604 ATTTTTTTAATTTTAAAATATTTTTAAAATAATTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAAT-ATTTTTTTA
22437644 ATTTTTTTAATTTT-AAA-A----T---ATA-TTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTTA
22437673 ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTT-AATTTTAAAATATTTTTAAAATA-TTTTTTTA
*
22437714 ATTTTTTAAAATTTTTAAAATA
1 ATTTTTT-TAA-TTTTAAAATA
22437736 AAAATGGGAC
Statistics
Matches: 111, Mismatches: 6, Indels: 27
0.77 0.04 0.19
Matches are distributed among these distances:
29 15 0.14
30 7 0.06
31 5 0.05
32 1 0.01
34 1 0.01
36 1 0.01
38 1 0.01
39 33 0.30
40 21 0.19
41 16 0.14
42 10 0.09
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (39 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTTA
Found at i:22437650 original size:8 final size:9
Alignment explanation
Indices: 22437633--22437687 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
22437623 ATTTTTAAAA
22437633 TAATTTTTT
1 TAATTTTTT
22437642 TAATTTTTT
1 TAATTTTTT
**
22437651 TAATTTTAA
1 TAATTTTTT
*
22437660 AATATATTTTT
1 TA-AT-TTTTT
22437671 TAATTTTTT
1 TAATTTTTT
22437680 TAAATTTT
1 T-AATTTT
22437688 AAAATATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
9 23 0.62
10 10 0.27
11 4 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TAATTTTTT
Found at i:22437657 original size:29 final size:29
Alignment explanation
Indices: 22437625--22437698 Score: 123
Period size: 29 Copynumber: 2.5 Consensus size: 29
22437615 TTTAAAATAT
22437625 TTTTAAAATAATTTTTTTAATTTTTTT-AA
1 TTTTAAAAT-ATTTTTTTAATTTTTTTAAA
22437654 TTTTAAAATATATTTTTTAATTTTTTTAAA
1 TTTTAAAATAT-TTTTTTAATTTTTTTAAA
22437684 TTTTAAAATATTTTT
1 TTTTAAAATATTTTT
22437699 AAAATACTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 2 0.05
29 28 0.65
30 13 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (29 bp):
TTTTAAAATATTTTTTTAATTTTTTTAAA
Found at i:22437711 original size:41 final size:42
Alignment explanation
Indices: 22437654--22437735 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 42
22437644 ATTTTTTTAA
*
22437654 TTTTAAAATATATTTTTTAATTTTTTTAAA-TTTTAAAATAT
1 TTTTAAAATATATTTTTTAATTTTTTAAAATTTTTAAAATAT
22437695 TTTTAAAATACT-TTTTTTAATTTTTTAAAATTTTTAAAATA
1 TTTTAAAATA-TATTTTTTAATTTTTTAAAATTTTTAAAATA
22437736 AAAATGGGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
41 27 0.71
42 11 0.29
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (42 bp):
TTTTAAAATATATTTTTTAATTTTTTAAAATTTTTAAAATAT
Found at i:22437728 original size:31 final size:32
Alignment explanation
Indices: 22437645--22437735 Score: 102
Period size: 32 Copynumber: 3.0 Consensus size: 32
22437635 ATTTTTTTAA
* *
22437645 TTTTTTT-AATTTTAAAATATATTTT---TTAA
1 TTTTTTTAAATTTTAAAATAT-TTTTAAAATAC
22437674 TTTTTTTAAATTTTAAAATATTTTTAAAATAC
1 TTTTTTTAAATTTTAAAATATTTTTAAAATAC
* *
22437706 TTTTTTTAATTTTTTAAA-ATTTTTAAAATA
1 TTTTTTTAAATTTTAAAATATTTTTAAAATA
22437736 AAAATGGGAC
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
29 11 0.20
30 13 0.24
31 12 0.22
32 18 0.33
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (32 bp):
TTTTTTTAAATTTTAAAATATTTTTAAAATAC
Found at i:22438981 original size:27 final size:27
Alignment explanation
Indices: 22438917--22438982 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
22438907 GGTCGAGGGT
22438917 CTGCCACAGGCGGCACCAAAGGTGCCA
1 CTGCCACAGGCGGCACCAAAGGTGCCA
* * *
22438944 GTGGCAGAGGCGGCACCAAAGGTGCCA
1 CTGCCACAGGCGGCACCAAAGGTGCCA
22438971 CTGCCACAGGCG
1 CTGCCACAGGCG
22438983 ACACTTGTGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.24, C:0.33, G:0.35, T:0.08
Consensus pattern (27 bp):
CTGCCACAGGCGGCACCAAAGGTGCCA
Found at i:22439065 original size:3 final size:3
Alignment explanation
Indices: 22439057--22439114 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
22439047 TCAGCTGCAT
* * *
22439057 GAA GAA GAA GAAA GAA -AA GGA -AA GGA GAA GAA AAA GAA GAA GAA
1 GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
22439101 AAA GAA GAA GAA GA
1 GAA GAA GAA GAA GA
22439115 GATCAACATG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
2 3 0.07
3 38 0.86
4 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:22439097 original size:12 final size:12
Alignment explanation
Indices: 22439057--22439112 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
22439047 TCAGCTGCAT
22439057 GAAGAAGAAGAAA
1 GAAGAAGAA-AAA
*
22439070 GAA-AAG-GAAA
1 GAAGAAGAAAAA
*
22439080 GGAGAAGAAAAA
1 GAAGAAGAAAAA
22439092 GAAGAAGAAAAA
1 GAAGAAGAAAAA
22439104 GAAGAAGAA
1 GAAGAAGAA
22439113 GAGATCAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 5 0.14
11 3 0.08
12 26 0.70
13 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:22441050 original size:3 final size:3
Alignment explanation
Indices: 22441042--22441115 Score: 73
Period size: 3 Copynumber: 25.3 Consensus size: 3
22441032 TCAGCTGCAT
* * *
22441042 GAA GAA GAA GAAA GAA -AA GGA -AA GGA GAA GAA AAA GAA GAA GAA
1 GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
22441086 AAA GAA GAA GAA G-A GAA GAA GAA AAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
22441116 GAGGAGGAGA
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
2 5 0.09
3 49 0.86
4 3 0.05
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:22441088 original size:29 final size:27
Alignment explanation
Indices: 22441046--22441127 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 27
22441036 CTGCATGAAG
22441046 AAGAAGAAAGAAAAGGAAAGGAGAAGAAA
1 AAGAAGAAA-AAAAGGAAAGGAGAAG-AA
* *
22441075 AAGAAGAAGAAAAA-G-AAGAAGAAGAG
1 AAGAAGAA-AAAAAGGAAAGGAGAAGAA
*
22441101 AAGAAGAAAAAGAAGGAGGAGGAGAAG
1 AAGAAGAAAAA-AAGGA-AAGGAGAAG
22441128 GAGAGGGCGG
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
25 3 0.07
26 11 0.25
27 9 0.20
28 1 0.02
29 19 0.43
30 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (27 bp):
AAGAAGAAAAAAAGGAAAGGAGAAGAA
Found at i:22441106 original size:23 final size:22
Alignment explanation
Indices: 22441043--22441115 Score: 96
Period size: 23 Copynumber: 3.3 Consensus size: 22
22441033 CAGCTGCATG
22441043 AAGAAGAAGAAAGAA-AAGGAAA
1 AAGAAGAAGAAAGAAGAA-GAAA
*
22441065 GGAGAAGAA-AAAGAAGAAGAAA
1 -AAGAAGAAGAAAGAAGAAGAAA
22441087 AAGAAGAAGAAGAGAAGAAGAAA
1 AAGAAGAAGAA-AGAAGAAGAAA
22441110 AAGAAG
1 AAGAAG
22441116 GAGGAGGAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.16
22 12 0.27
23 26 0.58
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (22 bp):
AAGAAGAAGAAAGAAGAAGAAA
Found at i:22441172 original size:21 final size:20
Alignment explanation
Indices: 22441142--22441189 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
22441132 GGGCGGTGCC
*
22441142 AGAAAAAGAAAAGAAAAAGAG
1 AGAAAGAGAAAAGAAAAAG-G
* *
22441163 AGAAAGAGAATAGAGAAAGG
1 AGAAAGAGAAAAGAAAAAGG
22441183 AGAAAGA
1 AGAAAGA
22441190 AATAGAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (20 bp):
AGAAAGAGAAAAGAAAAAGG
Found at i:22441592 original size:76 final size:76
Alignment explanation
Indices: 22441392--22441610 Score: 228
Period size: 76 Copynumber: 2.8 Consensus size: 76
22441382 GTTATTAACA
* * **
22441392 ATTATTGGTACTTAGTATTATTGTTAGTAAAAAACTAATATTATTATTATGGTTAGTTATTAGGA
1 ATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAC---TATTATTA-T-T-GTTA-TTATTATTA
22441457 TTAGTAAAAACCCTAATT
59 TTAGTAAAAACCCTAATT
* *** * *
22441475 ATTATT-TTAGTTAGTATGATTGTTAGTTTTTACACTA-TATTATTGTTACTTATTATTTTTAGT
1 ATTATTGTTAGTTAGTATTATTGTTAG-TAAAAAACTATTATTATTGTTA-TTATTATTATTAGT
22441538 -AAAACCCTAATT
64 AAAAACCCTAATT
* *
22441550 ATTATTGTTAGTTAGTATTATTTTTAGTAAAAAACTATTATTATTATTATTATTATTATTA
1 ATTATTGTTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATTGTTATTATTATTATTA
22441611 TTATTATTAT
Statistics
Matches: 114, Mismatches: 19, Indels: 14
0.78 0.13 0.10
Matches are distributed among these distances:
75 35 0.31
76 43 0.38
77 1 0.01
78 1 0.01
79 5 0.04
80 2 0.02
82 17 0.15
83 10 0.09
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.50
Consensus pattern (76 bp):
ATTATTGTTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATTGTTATTATTATTATTAGTAA
AAACCCTAATT
Found at i:22441593 original size:3 final size:3
Alignment explanation
Indices: 22441585--22441744 Score: 284
Period size: 3 Copynumber: 53.3 Consensus size: 3
22441575 AGTAAAAAAC
*
22441585 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
22441633 TAT CAT TAT CAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
22441681 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
22441729 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
22441745 GTGTTAGTTA
Statistics
Matches: 149, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 149 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:22444647 original size:8 final size:8
Alignment explanation
Indices: 22444619--22444660 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
22444609 GAGCTTATGC
*
22444619 TGTAAAGT
1 TGTAATGT
*
22444627 TGTTATG-
1 TGTAATGT
22444634 TGTAATGT
1 TGTAATGT
22444642 TGTAATGT
1 TGTAATGT
22444650 TGTAATGT
1 TGTAATGT
22444658 TGT
1 TGT
22444661 TGTAACAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (8 bp):
TGTAATGT
Found at i:22445456 original size:25 final size:26
Alignment explanation
Indices: 22445397--22445456 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
22445387 TAATTAAATT
**
22445397 TATACAAAAAAGTACAAACTTTGTAA
1 TATACAAAAAAGTACAAACTGAGTAA
*
22445423 TATA-AAAAAAATACAAACTAGAGTAA
1 TATACAAAAAAGTACAAACT-GAGTAA
22445449 TAT-CAAAA
1 TATACAAAA
22445457 CCGCAAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 14 0.48
26 15 0.52
ACGTcount: A:0.60, C:0.10, G:0.07, T:0.23
Consensus pattern (26 bp):
TATACAAAAAAGTACAAACTGAGTAA
Found at i:22447807 original size:157 final size:158
Alignment explanation
Indices: 22447461--22447798 Score: 577
Period size: 157 Copynumber: 2.2 Consensus size: 158
22447451 GTCGCGTCAG
22447461 ATTTTATTACTTTCAAAAAATATACTA--TT-TTA--TTA-T--TTTATATTATTTTAGTACATA
1 ATTTTATTACTTTCAAAAAATATACTATTTTCTTATTTTATTAATTTATATTATTTTAGTACATA
22447518 ATGTTTGAAATGTATTATTTTAGTGTGTTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGGC
66 ATGTTTGAAATGTATTATTTTAGTGTGTTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGGC
22447583 CCTTTGTTCGTATTTTTCTTATTTTCGA
131 CCTTTGTTCGTATTTTTCTTATTTTCGA
22447611 ATTTTATTACTTTCAAAAAATATACTATTTTCTTATTTTATTAATTTATATTATTTTAGTACATA
1 ATTTTATTACTTTCAAAAAATATACTATTTTCTTATTTTATTAATTTATATTATTTTAGTACATA
22447676 ATGTTTGAAATGTATTATTTTAGTGTGTTTTTT-TATAAATTTAGTAAAAAACCCTTATTTTGGC
66 ATGTTTGAAATGTATTATTTTAGTGTGTTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGGC
* *
22447740 CCTTTGTTCGTATTTTTCTTTTTTTCGG
131 CCTTTGTTCGTATTTTTCTTATTTTCGA
**
22447768 ATTTTATTACTTTCAGTAAATATACTATTTT
1 ATTTTATTACTTTCAAAAAATATACTATTTT
22447799 TGTTTTTTAA
Statistics
Matches: 176, Mismatches: 4, Indels: 9
0.93 0.02 0.05
Matches are distributed among these distances:
150 27 0.15
152 2 0.01
153 3 0.02
155 3 0.02
156 1 0.01
157 86 0.49
158 54 0.31
ACGTcount: A:0.29, C:0.09, G:0.08, T:0.54
Consensus pattern (158 bp):
ATTTTATTACTTTCAAAAAATATACTATTTTCTTATTTTATTAATTTATATTATTTTAGTACATA
ATGTTTGAAATGTATTATTTTAGTGTGTTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGGC
CCTTTGTTCGTATTTTTCTTATTTTCGA
Found at i:22448000 original size:30 final size:30
Alignment explanation
Indices: 22447955--22448115 Score: 196
Period size: 30 Copynumber: 5.6 Consensus size: 30
22447945 TAACAAATAA
*
22447955 ATAAAATAAAGTAATAAAACATAGAATGTAC
1 ATAACATAAA-TAATAAAACATAGAATGTAC
22447986 ATAACATAAATAATAAAACATA-AA--TA-
1 ATAACATAAATAATAAAACATAGAATGTAC
* *
22448012 AT---A-AAATAATAAGACATAGTATGTAC
1 ATAACATAAATAATAAAACATAGAATGTAC
* *
22448038 ATAACATAAATAATAAGACATAGTATGTAC
1 ATAACATAAATAATAAAACATAGAATGTAC
22448068 ATAACATAAATAATAAAACATAGAATGTAC
1 ATAACATAAATAATAAAACATAGAATGTAC
22448098 ATAACATAAA-AATTAAAA
1 ATAACATAAATAA-TAAAA
22448116 TCAAAACCAA
Statistics
Matches: 116, Mismatches: 5, Indels: 19
0.83 0.04 0.14
Matches are distributed among these distances:
22 14 0.12
23 2 0.02
25 2 0.02
26 4 0.03
27 2 0.02
29 5 0.04
30 78 0.67
31 9 0.08
ACGTcount: A:0.61, C:0.08, G:0.07, T:0.24
Consensus pattern (30 bp):
ATAACATAAATAATAAAACATAGAATGTAC
Found at i:22448007 original size:14 final size:14
Alignment explanation
Indices: 22447960--22448017 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
22447950 AATAAATAAA
22447960 ATAAAGTAATAAAAC
1 ATAAA-TAATAAAAC
*
22447975 ATAGAAT-GTACATAAC
1 ATA-AATAATA-A-AAC
22447991 ATAAATAATAAAAC
1 ATAAATAATAAAAC
22448005 ATAAATAATAAAA
1 ATAAATAATAAAA
22448018 TAATAAGACA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 18 0.49
15 9 0.24
16 10 0.27
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.22
Consensus pattern (14 bp):
ATAAATAATAAAAC
Found at i:22448354 original size:3 final size:3
Alignment explanation
Indices: 22448346--22448454 Score: 55
Period size: 3 Copynumber: 36.3 Consensus size: 3
22448336 CTTCCCTCCC
* * * *
22448346 TCT TCT TCT TCT CCT TC- TCT TTT TCT TTT TCCT TTT TCT TCCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT TCT T-CT TCT
* * * * * * *
22448392 GCG CCT CCT TCC CCT TCT TCA TCT TC- TCT TC- TCT TCT TCT T-T TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
22448437 TCT TCT CTCAT TCT TCT T
1 TCT TCT -TC-T TCT TCT T
22448455 TCCTGTAGCT
Statistics
Matches: 79, Mismatches: 19, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
2 8 0.10
3 61 0.77
4 9 0.11
5 1 0.01
ACGTcount: A:0.02, C:0.37, G:0.02, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:22448432 original size:11 final size:11
Alignment explanation
Indices: 22448405--22448454 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
22448395 CCTCCTTCCC
22448405 CTTCTTCATCTT
1 CTTCTTC-TCTT
22448417 C-TCTTCTCTT
1 CTTCTTCTCTT
*
22448427 CTTCTTTTCTT
1 CTTCTTCTCTT
22448438 CTTC-TCTCATT
1 CTTCTTCTC-TT
22448449 CTTCTT
1 CTTCTT
22448455 TCCTGTAGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 8 0.24
11 23 0.70
12 2 0.06
ACGTcount: A:0.04, C:0.34, G:0.00, T:0.62
Consensus pattern (11 bp):
CTTCTTCTCTT
Found at i:22449005 original size:12 final size:12
Alignment explanation
Indices: 22448990--22449023 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
22448980 TATATATATT
*
22448990 AAAATTATATAA
1 AAAATAATATAA
22449002 AAAATAATATAA
1 AAAATAATATAA
*
22449014 AAATTAATAT
1 AAAATAATAT
22449024 GGACGGGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:22449794 original size:31 final size:29
Alignment explanation
Indices: 22449719--22449795 Score: 91
Period size: 31 Copynumber: 2.6 Consensus size: 29
22449709 GGATTGGATC
22449719 AAAATTTCATGTATAAAATTATACAAAACT
1 AAAA-TTCATGTATAAAATTATACAAAACT
* * * *
22449749 AAAATTTATATATAAAATTATACTTTAAATT
1 AAAATTCATGTATAAAATTATAC--AAAACT
22449780 AAAATTCATGTATAAA
1 AAAATTCATGTATAAA
22449796 TTTGAGATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 17 0.44
30 4 0.10
31 18 0.46
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAATTCATGTATAAAATTATACAAAACT
Found at i:22451767 original size:7 final size:7
Alignment explanation
Indices: 22451755--22451791 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
22451745 GCTAAGCTAC
22451755 CACTTAT
1 CACTTAT
22451762 CACTTAT
1 CACTTAT
22451769 CACTTAT
1 CACTTAT
*
22451776 CACTTGT
1 CACTTAT
*
22451783 CACTGAT
1 CACTTAT
22451790 CA
1 CA
22451792 AATAAGTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (7 bp):
CACTTAT
Found at i:22451881 original size:51 final size:50
Alignment explanation
Indices: 22451705--22451931 Score: 292
Period size: 51 Copynumber: 4.4 Consensus size: 50
22451695 TACACGGAAT
*
22451705 CACTTATCAATTATCTCTTGTCACTGATCAAATAAGTGTAGCTAAGCTAC
1 CACTTATCAATTATCACTTGTCACTGATCAAATAAGTGTAGCTAAGCTAC
22451755 CACTTATCACTTATCACTTATCACTTGTCACTGATCAAATAAGTGTAGCTAAGCTAC
1 CACTTAT--C--A--A-TTATCACTTGTCACTGATCAAATAAGTGTAGCTAAGCTAC
* *
22451812 CACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAATTATCACTTGTCACTGATCAAATAAGTGTAGCT-AAGCTAC
* * * *
22451863 CACTTATAAATTGTCACTTGTCACTGATCAGATAAGTGCAGCTAAAGCTAC
1 CACTTATCAATTATCACTTGTCACTGATCAAATAAGTGTAGCT-AAGCTAC
* *
22451914 CACTTATCACTTGTCACT
1 CACTTATCAATTATCACT
22451932 GATTAGAAGT
Statistics
Matches: 160, Mismatches: 9, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
50 39 0.24
51 70 0.44
52 1 0.01
53 1 0.01
54 1 0.01
55 1 0.01
56 1 0.01
57 46 0.29
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (50 bp):
CACTTATCAATTATCACTTGTCACTGATCAAATAAGTGTAGCTAAGCTAC
Found at i:22453052 original size:30 final size:30
Alignment explanation
Indices: 22452987--22453074 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
22452977 GGTGCAAGGG
* * *
22452987 TGAGTGCATATTGATAGTAATACATTTTCTA
1 TGAGTGCACATTGATAGTAAAAC-CTTTCTA
** *
22453018 TGAGTGTGCATTGATAGTAAAACCTTTGTA
1 TGAGTGCACATTGATAGTAAAACCTTTCTA
*
22453048 TGAGTGCATATTGATAGTAAAACCTTT
1 TGAGTGCACATTGATAGTAAAACCTTT
22453075 TGTGTTGTGG
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
30 29 0.60
31 19 0.40
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (30 bp):
TGAGTGCACATTGATAGTAAAACCTTTCTA
Found at i:22453238 original size:105 final size:105
Alignment explanation
Indices: 22453048--22453261 Score: 338
Period size: 105 Copynumber: 2.0 Consensus size: 105
22453038 AACCTTTGTA
*
22453048 TGAGTGCATATTGATAGTAAAACCTTTTGTGTTGTGGTTTTACTTGCTAAATTCATAGGAGAGAA
1 TGAGTGCATATTGATAGTAAAACCTTTTGTGTTGTGATTTTACTTGCTAAATTCATAGGAGAGAA
*
22453113 CTTAGTAGTGAGAGTATTAATGATCTTCAAGGTGCAAGGG
66 CTTAGTAGTGAAAGTATTAATGATCTTCAAGGTGCAAGGG
* * * *
22453153 TGAGTGCATATTGATAGTAAAACCTTTTGTGTTGTGATTTTACTTGTTGAATTCATAGGGGTGAA
1 TGAGTGCATATTGATAGTAAAACCTTTTGTGTTGTGATTTTACTTGCTAAATTCATAGGAGAGAA
* * * *
22453218 TTTAGTGGTGAAAGTTTTAATGATTTTCAAGGTGCAAGGG
66 CTTAGTAGTGAAAGTATTAATGATCTTCAAGGTGCAAGGG
22453258 TGAG
1 TGAG
22453262 GAAAATTATC
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 99 1.00
ACGTcount: A:0.28, C:0.08, G:0.27, T:0.37
Consensus pattern (105 bp):
TGAGTGCATATTGATAGTAAAACCTTTTGTGTTGTGATTTTACTTGCTAAATTCATAGGAGAGAA
CTTAGTAGTGAAAGTATTAATGATCTTCAAGGTGCAAGGG
Found at i:22455454 original size:2 final size:2
Alignment explanation
Indices: 22455447--22455479 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
22455437 AATTAGATTT
*
22455447 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22455480 CTTGATGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:22465166 original size:20 final size:20
Alignment explanation
Indices: 22465141--22465195 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
22465131 TGCAGCTTCG
*
22465141 TTGTATCGGTAGAAGGAAAC
1 TTGTATCGGTAAAAGGAAAC
22465161 TTGTATCGGTAAAAGGAAAC
1 TTGTATCGGTAAAAGGAAAC
22465181 TTGTATCGGTAAAAG
1 TTGTATCGGTAAAAG
22465196 TCTTTCTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.27
Consensus pattern (20 bp):
TTGTATCGGTAAAAGGAAAC
Found at i:22467116 original size:21 final size:22
Alignment explanation
Indices: 22467068--22467116 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
22467058 ATAAATAATA
* *
22467068 AATATGTATATACAAAATATGT
1 AATATATATATACAAAATATGG
*
22467090 ACATATATATATA-AAATTATGG
1 A-ATATATATATACAAAATATGG
22467112 AATAT
1 AATAT
22467117 GAAAATAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 4 0.17
22 9 0.39
23 10 0.43
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (22 bp):
AATATATATATACAAAATATGG
Found at i:22467322 original size:3 final size:3
Alignment explanation
Indices: 22467292--22467343 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
22467282 AAATAAAAAC
* ** * *
22467292 ATA ACA ATA ATA ACC ATA ATA TTG ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
22467340 ATA A
1 ATA A
22467344 AAGATGATAA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:22472246 original size:20 final size:19
Alignment explanation
Indices: 22472191--22472243 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 19
22472181 TTAAAATCTT
22472191 TTTTAAAATTTTTAAAAAA
1 TTTTAAAATTTTTAAAAAA
*
22472210 ATTTAAAATCTTTTAAAATTAA
1 TTTTAAAAT-TTTTAAAA--AA
22472232 TTTTAAAATTTT
1 TTTTAAAATTTT
22472244 AAATCACGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 8 0.28
20 8 0.28
21 3 0.10
22 10 0.34
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTAAAATTTTTAAAAAA
Found at i:22473889 original size:41 final size:41
Alignment explanation
Indices: 22473857--22474078 Score: 336
Period size: 41 Copynumber: 5.4 Consensus size: 41
22473847 GCGCTTTACC
22473857 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTG
1 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTG
* * * *
22473898 AAAAAACGCCGCTAGAGGTCTGCACATTAGCGGCGTTTCTTT
1 -AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTG
* * * *
22473940 AAAAACGCCGCTAAAGGTCTGCGCATAAGCGACGCTTATTT
1 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTG
** *
22473981 AAAAACGCCGCTAAAGGTCTGTACATTAGCGGCACTTCTTG
1 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTG
22474022 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTG
1 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTG
22474063 AAAAACGCCGCTAAAG
1 AAAAACGCCGCTAAAG
22474079 ACCTACAAGG
Statistics
Matches: 160, Mismatches: 20, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 123 0.77
42 37 0.23
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTG
Found at i:22474246 original size:40 final size:38
Alignment explanation
Indices: 22474116--22474250 Score: 103
Period size: 40 Copynumber: 3.4 Consensus size: 38
22474106 TGGGCTTAGG
* * *
22474116 TTTTTTGCGGCGTTTCCTCAAAAAACGCCGCTAATGCTCA
1 TTTTTAGCGGCGTTT--TCAGAAAGCGCCGCTAATGCTCA
* * * * * *
22474156 TTTTTAGTGGCGCTTCTCAGAAATCGCCGCGATTGATCGA
1 TTTTTAGCGGCG-TTTTCAGAAAGCGCCGCTAATGCTC-A
22474196 TCTTTT-GCGGCGTTTT-ACGTAAAGCGCCGCTAATGCTCAA
1 T-TTTTAGCGGCGTTTTCA-G-AAAGCGCCGCTAATGCTC-A
22474236 TTTTTAGCGGCGTTT
1 TTTTTAGCGGCGTTT
22474251 GTCTAACAAA
Statistics
Matches: 74, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
38 1 0.01
39 25 0.34
40 42 0.57
41 6 0.08
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (38 bp):
TTTTTAGCGGCGTTTTCAGAAAGCGCCGCTAATGCTCA
Found at i:22495415 original size:41 final size:37
Alignment explanation
Indices: 22495348--22495433 Score: 93
Period size: 40 Copynumber: 2.2 Consensus size: 37
22495338 TTTAATTTAG
22495348 AATTATTAGTTAAAAAATTGATGTAAAATAGAAGTCGTGAT
1 AATTA-TAGTTAAAAAATTGATGTAAAA-A-AA-TCGTGAT
* *
22495389 AATTATATTTAAAAAATT-ATTAGTAAAAAAATTGTGAT
1 AATTATAGTTAAAAAATTGA-T-GTAAAAAAATCGTGAT
22495427 AATTATA
1 AATTATA
22495434 ATTATAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
38 13 0.32
39 3 0.07
40 14 0.34
41 11 0.27
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37
Consensus pattern (37 bp):
AATTATAGTTAAAAAATTGATGTAAAAAAATCGTGAT
Found at i:22495484 original size:15 final size:16
Alignment explanation
Indices: 22495459--22495488 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
22495449 GCAATAATCA
22495459 ATTGTATGTAAAATTT
1 ATTGTATGTAAAATTT
22495475 ATTG-ATGTAAAATT
1 ATTGTATGTAAAATT
22495489 AAGATATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (16 bp):
ATTGTATGTAAAATTT
Found at i:22501980 original size:18 final size:18
Alignment explanation
Indices: 22501957--22501991 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22501947 TTACATATAA
22501957 AAATAATAATTATATTTG
1 AAATAATAATTATATTTG
* *
22501975 AAATAATTATTTTATTT
1 AAATAATAATTATATTT
22501992 TATAATATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AAATAATAATTATATTTG
Found at i:22520124 original size:6 final size:6
Alignment explanation
Indices: 22520115--22520140 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
22520105 ATAGAAGCAA
22520115 ATGAAT ATGAAT ATGAAT ATGAAT AT
1 ATGAAT ATGAAT ATGAAT ATGAAT AT
22520141 TGGAAAAACT
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:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (6 bp):
ATGAAT
Found at i:22525332 original size:2 final size:2
Alignment explanation
Indices: 22525327--22525361 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
22525317 ACACACACAC
22525327 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22525362 ACTCGAGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22527409 original size:38 final size:38
Alignment explanation
Indices: 22527366--22527443 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
22527356 TTCTAGGTAA
22527366 TATCATCATCATCATCGTCAAACCAAAGCCATGGGTTT
1 TATCATCATCATCATCGTCAAACCAAAGCCATGGGTTT
*
22527404 TATCATCATCATCGTCGTCAAACCAAAGCCATGGGTTT
1 TATCATCATCATCATCGTCAAACCAAAGCCATGGGTTT
22527442 TA
1 TA
22527444 GTTTGTTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (38 bp):
TATCATCATCATCATCGTCAAACCAAAGCCATGGGTTT
Found at i:22529194 original size:19 final size:17
Alignment explanation
Indices: 22529162--22529196 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
22529152 TGATTCAATT
22529162 AAATTTTTTTATTTTTA
1 AAATTTTTTTATTTTTA
22529179 AAATTTTTAATTATTTTT
1 AAATTTTT--TTATTTTT
22529197 TAATCAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
AAATTTTTTTATTTTTA
Done.