Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_pilon, whole genome shotgun sequence
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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 52 of 91
Found at i:11462566 original size:22 final size:21
Alignment explanation
Indices: 11462541--11462586 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 21
11462531 CTTTTGGTGC
*
11462541 AGGCTTCTTGTGCATAGGATGA
1 AGGC-TCTTGTGCATAGGATAA
11462563 AGG--CTTGTGCATAGGATAA
1 AGGCTCTTGTGCATAGGATAA
11462582 AGGCT
1 AGGCT
11462587 GGTCAGGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
19 18 0.86
22 3 0.14
ACGTcount: A:0.26, C:0.13, G:0.33, T:0.28
Consensus pattern (21 bp):
AGGCTCTTGTGCATAGGATAA
Found at i:11462571 original size:19 final size:19
Alignment explanation
Indices: 11462547--11462586 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
11462537 GTGCAGGCTT
*
11462547 CTTGTGCATAGGATGAAGG
1 CTTGTGCATAGGATAAAGG
11462566 CTTGTGCATAGGATAAAGG
1 CTTGTGCATAGGATAAAGG
11462585 CT
1 CT
11462587 GGTCAGGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.12, G:0.33, T:0.28
Consensus pattern (19 bp):
CTTGTGCATAGGATAAAGG
Found at i:11476255 original size:16 final size:16
Alignment explanation
Indices: 11476234--11476265 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11476224 TCTTCCACCA
11476234 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11476250 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11476266 GAGCTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:11479845 original size:16 final size:16
Alignment explanation
Indices: 11479824--11479855 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11479814 TCTTCCACCA
11479824 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11479840 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11479856 GAGCTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:11480379 original size:13 final size:12
Alignment explanation
Indices: 11480357--11480386 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
11480347 ACTAAACACC
11480357 TTTCACATACCT
1 TTTCACATACCT
11480369 TTTCTACATACCT
1 TTTC-ACATACCT
11480382 TTTCA
1 TTTCA
11480387 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (12 bp):
TTTCACATACCT
Found at i:11495635 original size:13 final size:13
Alignment explanation
Indices: 11495617--11495661 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
11495607 TATTGCCATT
*
11495617 TCATCATCATCCA
1 TCATCAACATCCA
*
11495630 TCATCAACATCCT
1 TCATCAACATCCA
*
11495643 TCATCAAGA-CCA
1 TCATCAACATCCA
11495655 TCATCAA
1 TCATCAA
11495662 TTCCATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.27
Consensus pattern (13 bp):
TCATCAACATCCA
Found at i:11495889 original size:2 final size:2
Alignment explanation
Indices: 11495882--11495914 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11495872 GTATTTAAAG
11495882 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11495915 AAGATGTGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11501483 original size:2 final size:2
Alignment explanation
Indices: 11501476--11501504 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11501466 ATCACCAACT
11501476 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11501505 TTTCCACTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11510048 original size:24 final size:23
Alignment explanation
Indices: 11509990--11510049 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
11509980 AAATCCAGCA
*
11509990 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAATGAAAGCACTCAAAAG
*
11510013 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATGAAAGCACTC-AAAAG
*
11510037 AAGAAAAAGAAAG
1 AAGAAAATGAAAG
11510050 AAAGAAAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 16 0.50
24 16 0.50
ACGTcount: A:0.62, C:0.12, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAATGAAAGCACTCAAAAG
Found at i:11511302 original size:24 final size:22
Alignment explanation
Indices: 11511268--11511312 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
11511258 TGCACAAGAT
*
11511268 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGAAATTTCAAAGG
*
11511290 ATGTACCTCTTGAAATTTGAAAG
1 ATGT-CCT-TTGAAATTTCAAAG
11511313 AATATTCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 3 0.16
24 12 0.63
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (22 bp):
ATGTCCTTTGAAATTTCAAAGG
Found at i:11517321 original size:20 final size:21
Alignment explanation
Indices: 11517271--11517321 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
11517261 TTTGAATTTC
11517271 TTTTTCTTTTCTTATTTTCTGA
1 TTTTTC-TTTCTTATTTTCTGA
* * *
11517293 ATTTT-TTTCTTCTTTT-TGT
1 TTTTTCTTTCTTATTTTCTGA
11517312 TTTTTCTTTC
1 TTTTTCTTTC
11517322 CTTTTGCACT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
19 6 0.25
20 14 0.58
22 4 0.17
ACGTcount: A:0.06, C:0.14, G:0.04, T:0.76
Consensus pattern (21 bp):
TTTTTCTTTCTTATTTTCTGA
Found at i:11527254 original size:15 final size:16
Alignment explanation
Indices: 11527203--11527255 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
11527193 AGATAGTGAA
11527203 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
11527220 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
11527237 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
11527252 ATAA
1 ATAA
11527256 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:11529906 original size:10 final size:10
Alignment explanation
Indices: 11529891--11529927 Score: 74
Period size: 10 Copynumber: 3.7 Consensus size: 10
11529881 TTCAACTTTC
11529891 TTTCTTTCCT
1 TTTCTTTCCT
11529901 TTTCTTTCCT
1 TTTCTTTCCT
11529911 TTTCTTTCCT
1 TTTCTTTCCT
11529921 TTTCTTT
1 TTTCTTT
11529928 TTTTGAGTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTCTTTCCT
Found at i:11529907 original size:5 final size:5
Alignment explanation
Indices: 11529887--11529928 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
11529877 GTGCTTCAAC
* * *
11529887 TTTC- TTTCT TTCCT TTTCT TTCCT TTTCT TTCCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
11529929 TTTGAGTGCT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTCT
Found at i:11534820 original size:19 final size:20
Alignment explanation
Indices: 11534782--11534834 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
11534772 AATACCCCTT
*
11534782 TGAAAATACATGATTTTTTTGA
1 TGAAAATACATGA--TTTTTCA
11534804 TGAAAATACATGA-TTTTCA
1 TGAAAATACATGATTTTTCA
* *
11534823 TTAAGATACATG
1 TGAAAATACATG
11534835 CTCTTGGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 15 0.54
22 13 0.46
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.40
Consensus pattern (20 bp):
TGAAAATACATGATTTTTCA
Found at i:11535757 original size:20 final size:20
Alignment explanation
Indices: 11535732--11535770 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
11535722 CCATGATATC
11535732 TAAATG-ATATGAAAACATAA
1 TAAATGAATAT-AAAACATAA
11535752 TAAATGAATATAAAACATA
1 TAAATGAATATAAAACATA
11535771 TTGATACAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.26
Consensus pattern (20 bp):
TAAATGAATATAAAACATAA
Found at i:11537001 original size:8 final size:8
Alignment explanation
Indices: 11536981--11537015 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
11536971 AAGCTAAGTA
11536981 ATATAAA-
1 ATATAAAT
11536988 ATATAAAT
1 ATATAAAT
11536996 ATATAAAT
1 ATATAAAT
11537004 ATATAAAT
1 ATATAAAT
11537012 ATAT
1 ATAT
11537016 GGTTCATAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
ATATAAAT
Found at i:11540340 original size:225 final size:225
Alignment explanation
Indices: 11539944--11540390 Score: 799
Period size: 225 Copynumber: 2.0 Consensus size: 225
11539934 TACCGCTTGT
* *
11539944 TGTAAGGCTAACCAGACTTCTTCAATAATGGAGAAGATGTCAACCTTGTTATTTCCCGATCTAGG
1 TGTAAGGCTAACCAGACCTCTTCAATAATGGAGAAGATGACAACCTTGTTATTTCCCGATCTAGG
* *
11540009 AGAGACACCAAATGTTACACCTTGAATTGAAAGTAATCTGCACAAAAGAAGATTGATTGCTTAAG
66 AGAGACACCAAATGCTACACCTTGAATTGAAAGTAATCTGCACAAAAGAAGAATGATTGCTTAAG
11540074 TAAATGAGTAATTAAGAAAGGAAATGGAAAGAATTGAAATGGATAGAATAGTTATCAAAGAAGGG
131 TAAATGAGTAATTAAGAAAGGAAATGGAAAGAATTGAAATGGATAGAATAGTTATCAAAGAAGGG
11540139 CTGCGGAAGTGTTGTAGAATGATCCTTTGA
196 CTGCGGAAGTGTTGTAGAATGATCCTTTGA
* *
11540169 TGTATGGCTAACCAGGCCTCTTCAATAATGGAGAAGATGACAACCTTGTTATTTCCCGATCTAGG
1 TGTAAGGCTAACCAGACCTCTTCAATAATGGAGAAGATGACAACCTTGTTATTTCCCGATCTAGG
*
11540234 AGAGACACCAAATGCTACACCTTGAATTGAAAAGTAATTTGCAC-AAAGAAGAATGATTAG-TTA
66 AGAGACACCAAATGCTACACCTTGAATTG-AAAGTAATCTGCACAAAAGAAGAATGATT-GCTTA
11540297 AGTAAATGAGTAATTAAGAAAGGAAATGGAAAGAATTGAAATGGATAGAATAGTTATCAAAGAAG
129 AGTAAATGAGTAATTAAGAAAGGAAATGGAAAGAATTGAAATGGATAGAATAGTTATCAAAGAAG
11540362 GGCTGCGGAAGTGTTGTAGAATGATCCTT
194 GGCTGCGGAAGTGTTGTAGAATGATCCTT
11540391 AAAGTGATAA
Statistics
Matches: 213, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
225 199 0.93
226 14 0.07
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (225 bp):
TGTAAGGCTAACCAGACCTCTTCAATAATGGAGAAGATGACAACCTTGTTATTTCCCGATCTAGG
AGAGACACCAAATGCTACACCTTGAATTGAAAGTAATCTGCACAAAAGAAGAATGATTGCTTAAG
TAAATGAGTAATTAAGAAAGGAAATGGAAAGAATTGAAATGGATAGAATAGTTATCAAAGAAGGG
CTGCGGAAGTGTTGTAGAATGATCCTTTGA
Found at i:11543434 original size:10 final size:10
Alignment explanation
Indices: 11543421--11543453 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
11543411 AAAAAACAAA
*
11543421 AAAAAAAGGC
1 AAAAAAAGCC
11543431 AAAAAAAGCC
1 AAAAAAAGCC
11543441 -AAAAAAGCC
1 AAAAAAAGCC
11543450 AAAA
1 AAAA
11543454 TTTCAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.73, C:0.15, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAAGCC
Found at i:11548135 original size:12 final size:12
Alignment explanation
Indices: 11548118--11548160 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
11548108 TATTTGTTTT
11548118 CAAAAAAAAAAA
1 CAAAAAAAAAAA
**
11548130 CAAAAAAAAAGG
1 CAAAAAAAAAAA
11548142 C--AAAAAAAAA
1 CAAAAAAAAAAA
11548152 CAAAAAAAA
1 CAAAAAAAA
11548161 GCCAAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 8 0.32
12 17 0.68
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:11548136 original size:10 final size:10
Alignment explanation
Indices: 11548121--11548160 Score: 62
Period size: 10 Copynumber: 3.8 Consensus size: 10
11548111 TTGTTTTCAA
11548121 AAAAAAAAAC
1 AAAAAAAAAC
11548131 AAAAAAAAAGGC
1 AAAAAAAAA--C
11548143 AAAAAAAAAC
1 AAAAAAAAAC
11548153 AAAAAAAA
1 AAAAAAAA
11548161 GCCAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 18 0.64
12 10 0.36
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:11548161 original size:21 final size:22
Alignment explanation
Indices: 11548121--11548167 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
11548111 TTGTTTTCAA
*
11548121 AAAAAAAAACAAAAAAAAAGGC
1 AAAAAAAAACAAAAAAAAAGCC
11548143 AAAAAAAAAC-AAAAAAAAGCC
1 AAAAAAAAACAAAAAAAAAGCC
11548164 AAAA
1 AAAA
11548168 TTTCAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (22 bp):
AAAAAAAAACAAAAAAAAAGCC
Found at i:11565310 original size:16 final size:16
Alignment explanation
Indices: 11565279--11565325 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
11565269 TGGTAATGAA
11565279 ATAAGAAAAGATGAAA-G
1 ATAA-AAAA-ATGAAATG
*
11565296 AATAAAGAAATGAAATG
1 -ATAAAAAAATGAAATG
11565313 ATAAAAAAATGAA
1 ATAAAAAAATGAA
11565326 GATAACTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 18 0.69
17 4 0.15
18 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (16 bp):
ATAAAAAAATGAAATG
Found at i:11565527 original size:11 final size:11
Alignment explanation
Indices: 11565511--11565542 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
11565501 GTTGTATGAG
11565511 TCTTTTTCTTT
1 TCTTTTTCTTT
11565522 TCTTTTTC-TT
1 TCTTTTTCTTT
11565532 T-TTTTTCTTT
1 TCTTTTTCTTT
11565542 T
1 T
11565543 TTCTTGTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 6 0.30
10 6 0.30
11 8 0.40
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TCTTTTTCTTT
Found at i:11565547 original size:16 final size:16
Alignment explanation
Indices: 11565514--11565543 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11565504 GTATGAGTCT
11565514 TTTTCTTTTCTTTTTC
1 TTTTCTTTTCTTTTTC
11565530 TTTT-TTTTCTTTTT
1 TTTTCTTTTCTTTTT
11565544 TCTTGTTGCT
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:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTCTTTTCTTTTTC
Found at i:11567484 original size:36 final size:36
Alignment explanation
Indices: 11567419--11567526 Score: 173
Period size: 36 Copynumber: 3.0 Consensus size: 36
11567409 GTTGGTTATA
**
11567419 ATATAGGCGTGAT-ATGGTGATAAAATATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGAATATGGTGATG
*
11567454 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGAATATGGTGATG
*
11567490 ATATAGGCGTGATAATGGTGATGGAAGATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGAATATGGTGATG
11567526 A
1 A
11567527 ACAGATTGTA
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
35 13 0.19
36 54 0.81
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.30
Consensus pattern (36 bp):
ATATAGGCGTGATAATGGTGATGGAATATGGTGATG
Found at i:11567943 original size:27 final size:23
Alignment explanation
Indices: 11567880--11567930 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
11567870 CCACATGCAT
11567880 GGCACATGAGTGGCTGTTCATGA
1 GGCACATGAGTGGCTGTTCATGA
*
11567903 GGCACATGTGTGGCTGTTCATGA
1 GGCACATGAGTGGCTGTTCATGA
11567926 GGCAC
1 GGCAC
11567931 TCACATGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.35, T:0.25
Consensus pattern (23 bp):
GGCACATGAGTGGCTGTTCATGA
Found at i:11570816 original size:11 final size:13
Alignment explanation
Indices: 11570784--11570813 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
11570774 TGGCCAAAGA
11570784 TGAAAAGGTATAT
1 TGAAAAGGTATAT
11570797 TGAAAAGGTATA-
1 TGAAAAGGTATAT
11570809 TGAAA
1 TGAAA
11570814 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATAT
Found at i:11571766 original size:21 final size:21
Alignment explanation
Indices: 11571742--11571785 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
11571732 AAGGAGGATT
11571742 AATGAAATG-ATAAAGATAAGG
1 AATGAAATGAATAAAGA-AAGG
11571763 AATGAAATGAAATAAAGAAAGG
1 AATGAAATG-AATAAAGAAAGG
11571785 A
1 A
11571786 TAGAGATGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.43
22 5 0.24
23 7 0.33
ACGTcount: A:0.61, C:0.00, G:0.23, T:0.16
Consensus pattern (21 bp):
AATGAAATGAATAAAGAAAGG
Found at i:11573838 original size:19 final size:20
Alignment explanation
Indices: 11573814--11573864 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
11573804 CGGCCAAGAG
* **
11573814 CATGTATCTTCATTTAAA-T
1 CATGTATTTTCATAAAAAGT
11573833 CATGTATTTTCATAAAAAGT
1 CATGTATTTTCATAAAAAGT
11573853 CATGTATTTTCA
1 CATGTATTTTCA
11573865 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAGT
Found at i:11574254 original size:36 final size:35
Alignment explanation
Indices: 11574203--11574313 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 35
11574193 TAAGATACTA
11574203 CCTA-AACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
* *
11574238 CCTATAACATCACCATCTTCCATTACCATTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * *
11574273 CCTATATCATTACCATCTTCTATCACCATTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
11574308 CCTATA
1 CCTATA
11574314 TAACCACCAA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 46 0.68
36 22 0.32
ACGTcount: A:0.28, C:0.37, G:0.04, T:0.32
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:11578926 original size:2 final size:2
Alignment explanation
Indices: 11578919--11579003 Score: 131
Period size: 2 Copynumber: 43.5 Consensus size: 2
11578909 TAATAATAAG
*
11578919 AT AT AT AT A- AT AT ACT AT AG AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
11578960 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11579001 AT A
1 AT A
11579004 GATGATGATA
Statistics
Matches: 77, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
1 3 0.04
2 72 0.94
3 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11578960 original size:33 final size:33
Alignment explanation
Indices: 11578919--11579006 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 33
11578909 TAATAATAAG
*
11578919 ATATATATA-ATATACTATAGATTATATATATAT
1 ATATATATATATATA-TATAGATAATATATATAT
*
11578952 ATATATATATATATATATATATAATATATATAT
1 ATATATATATATATATATAGATAATATATATAT
11578985 ATATATATATATATATATAGAT
1 ATATATATATATATATATAGAT
11579007 GATGATAACT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
33 46 0.90
34 5 0.10
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (33 bp):
ATATATATATATATATATAGATAATATATATAT
Found at i:11587043 original size:72 final size:71
Alignment explanation
Indices: 11586925--11587061 Score: 170
Period size: 72 Copynumber: 1.9 Consensus size: 71
11586915 AATACATCCT
* * * * * *
11586925 TTGGCTGAATTCATCCCACCTTGTGTGAACTTGTTGATTTGTCTTCTATGGATGAATGTTCATGA
1 TTGGCTGAATTCATCCCACCTTGTGTGAACATGCTGATTTGGCTTCT-TGCATGAATATGCATGA
11586990 ATGTATC
65 ATGTATC
*
11586997 TTGGCTGAAATTCTTCCC-CCTTGTGTGAACATGACT-ATTTGGCTTCTTGCATGAATATGCATG
1 TTGGCTG-AATTCATCCCACCTTGTGTGAACATG-CTGATTTGGCTTCTTGCATGAATATGCATG
11587060 AA
64 AA
11587062 CGGATAAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
71 15 0.27
72 31 0.55
73 10 0.18
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (71 bp):
TTGGCTGAATTCATCCCACCTTGTGTGAACATGCTGATTTGGCTTCTTGCATGAATATGCATGAA
TGTATC
Found at i:11596644 original size:5 final size:5
Alignment explanation
Indices: 11596634--11596659 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
11596624 CTCCAACTTC
11596634 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
11596660 CTTTTTGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:11596682 original size:28 final size:28
Alignment explanation
Indices: 11596648--11596714 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
11596638 TTTTCTTTTC
* *
11596648 TTTTCTTTTCTTCTTTTTGAGTGCTGGA
1 TTTTCTTTTCTTCTTTTGGAGTGCTGCA
*
11596676 TTTTC-TTTCTTTCTTTTGGAGTGCTTCA
1 TTTTCTTTTC-TTCTTTTGGAGTGCTGCA
*
11596704 ATTTCTTTTCT
1 TTTTCTTTTCT
11596715 GATTTTCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 4 0.12
28 25 0.76
29 4 0.12
ACGTcount: A:0.07, C:0.16, G:0.13, T:0.63
Consensus pattern (28 bp):
TTTTCTTTTCTTCTTTTGGAGTGCTGCA
Found at i:11598763 original size:27 final size:26
Alignment explanation
Indices: 11598725--11598784 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
11598715 GCTTGCTTTC
11598725 TCTTTT-TGAA-TTTCGTTTCTTTTTT-
1 TCTTTTCTGAATTTTC--TTCTTTTTTG
11598750 TCTTTTCTGAAATTTTCTTCTTTTTTG
1 TCTTTTCTG-AATTTTCTTCTTTTTTG
11598777 TCTTTTCT
1 TCTTTTCT
11598785 TTTCTTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
25 6 0.19
26 11 0.35
27 10 0.32
28 4 0.13
ACGTcount: A:0.08, C:0.15, G:0.07, T:0.70
Consensus pattern (26 bp):
TCTTTTCTGAATTTTCTTCTTTTTTG
Found at i:11604270 original size:12 final size:12
Alignment explanation
Indices: 11604253--11604277 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11604243 GCCCTTGACT
11604253 TACTTTGCAATG
1 TACTTTGCAATG
11604265 TACTTTGCAATG
1 TACTTTGCAATG
11604277 T
1 T
11604278 TAGAACACTT
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:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (12 bp):
TACTTTGCAATG
Found at i:11604330 original size:12 final size:13
Alignment explanation
Indices: 11604315--11604344 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
11604305 TCTTTTTGAA
11604315 TTTCTTTTCTT-T
1 TTTCTTTTCTTCT
11604327 TTTCTTTTCTTCT
1 TTTCTTTTCTTCT
11604340 TTTCT
1 TTTCT
11604345 GAATTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTCTTTTCTTCT
Found at i:11604715 original size:22 final size:21
Alignment explanation
Indices: 11604689--11604729 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
11604679 GCTGTGGAAT
*
11604689 TGATGGTTTTGATGGATGAAGA
1 TGATGGTGTTGAT-GATGAAGA
11604711 TGATGGTGTTGATGATGAA
1 TGATGGTGTTGATGATGAA
11604730 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.00, G:0.37, T:0.37
Consensus pattern (21 bp):
TGATGGTGTTGATGATGAAGA
Found at i:11613565 original size:35 final size:36
Alignment explanation
Indices: 11613499--11613566 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 36
11613489 ATACAATCTG
*
11613499 TCCATCACCATTACCACGCCTATATCATCACCATAT
1 TCCATCACCATTACCACGCATATATCATCACCATAT
* * *
11613535 TCCATCACCA-TATCATGCATATATTATCACCA
1 TCCATCACCATTACCACGCATATATCATCACCA
11613567 ACTTCTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 18 0.64
36 10 0.36
ACGTcount: A:0.32, C:0.35, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTACCACGCATATATCATCACCATAT
Found at i:11613983 original size:19 final size:22
Alignment explanation
Indices: 11613939--11613984 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
11613929 GTGCTACAAT
*
11613939 AAAAAAACAACAAGAAAGAAGA
1 AAAAAAACAAAAAGAAAGAAGA
11613961 AAAAAAACAAAAAG-AA-AAGA
1 AAAAAAACAAAAAGAAAGAAGA
11613981 AAAA
1 AAAA
11613985 GACTCTTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.35
21 2 0.09
22 13 0.57
ACGTcount: A:0.83, C:0.07, G:0.11, T:0.00
Consensus pattern (22 bp):
AAAAAAACAAAAAGAAAGAAGA
Found at i:11613984 original size:18 final size:19
Alignment explanation
Indices: 11613940--11613976 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
11613930 TGCTACAATA
11613940 AAAAAACAACAAGAAAGAAG
1 AAAAAA-AACAAGAAAGAAG
11613960 AAAAAAAACAA-AAAGAA
1 AAAAAAAACAAGAAAGAA
11613977 AAGAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 5 0.29
20 6 0.35
ACGTcount: A:0.81, C:0.08, G:0.11, T:0.00
Consensus pattern (19 bp):
AAAAAAAACAAGAAAGAAG
Found at i:11614070 original size:24 final size:24
Alignment explanation
Indices: 11614015--11614063 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
11614005 AGTGCAAAAG
* *
11614015 AAAGAAAAGAAAAAGAAGAATCAA
1 AAAGCAAAGAAAAAGAAGAAGCAA
*
11614039 AAAGCAAAGAAAAAG-TGAAGCAA
1 AAAGCAAAGAAAAAGAAGAAGCAA
11614062 AA
1 AA
11614064 TTGCAAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.71, C:0.06, G:0.18, T:0.04
Consensus pattern (24 bp):
AAAGCAAAGAAAAAGAAGAAGCAA
Found at i:11626704 original size:2 final size:2
Alignment explanation
Indices: 11626687--11626754 Score: 120
Period size: 2 Copynumber: 34.5 Consensus size: 2
11626677 TCATAATAAC
*
11626687 TA TA GA TA TA -A 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
11626728 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
11626755 GATGATAACT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:11628020 original size:24 final size:21
Alignment explanation
Indices: 11627986--11628028 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
11627976 TCCACAAGAC
*
11627986 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AGTTCAAAGG
11628008 ATGTACCTCTTGAAGTTCAAA
1 ATGT-CCT-TTGAAGTTCAAA
11628029 AGAATGTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAGTTCAAAGG
Found at i:11652351 original size:22 final size:21
Alignment explanation
Indices: 11652312--11652353 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
11652302 CCATCTCCAT
* *
11652312 TTCATCATCACTATCATCAAC
1 TTCATCATCAATACCATCAAC
11652333 TTCATCCATCAATACCATCAA
1 TTCAT-CATCAATACCATCAA
11652354 TTCTACAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (21 bp):
TTCATCATCAATACCATCAAC
Found at i:11656304 original size:19 final size:20
Alignment explanation
Indices: 11656280--11656361 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
11656270 TGATAGTGTC
11656280 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATTATGTATT
* *
11656299 TTCATTAAAAATTATTTATC
1 TTCATTAAAAATTATGTATT
11656319 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATTATGTATT
* *
11656338 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATTATGTATT
11656358 TTCA
1 TTCA
11656362 AAGGGGTTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
19 23 0.42
20 32 0.58
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.50
Consensus pattern (20 bp):
TTCATTAAAAATTATGTATT
Found at i:11662968 original size:19 final size:20
Alignment explanation
Indices: 11662940--11662979 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
11662930 GGATAATAAT
11662940 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
* *
11662960 ATAAG-AATGATATGAAATA
1 ATAAGTAATGAAAAGAAATA
11662979 A
1 A
11662980 AGAAAGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:11672318 original size:6 final size:6
Alignment explanation
Indices: 11672307--11672350 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
11672297 GATATAGGAG
*
11672307 TCTTTT TC-TTT TCTTTT TGTTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
11672351 TACTGCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:11672330 original size:12 final size:12
Alignment explanation
Indices: 11672307--11672350 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
11672297 GATATAGGAG
11672307 TCTTTTTC-TTT
1 TCTTTTTCTTTT
*
11672318 TCTTTTTGTTTT
1 TCTTTTTCTTTT
11672330 TCTTCTTTCTTTT
1 TCTT-TTTCTTTT
11672343 TCTCTTTT
1 TCT-TTTT
11672351 TACTGCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 7 0.25
12 7 0.25
13 13 0.46
14 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:11679389 original size:13 final size:12
Alignment explanation
Indices: 11679367--11679396 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
11679357 ACTAAACACC
11679367 TTTCACATACCT
1 TTTCACATACCT
11679379 TTTCGACATACCT
1 TTTC-ACATACCT
11679392 TTTCA
1 TTTCA
11679397 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.23, C:0.30, G:0.03, T:0.43
Consensus pattern (12 bp):
TTTCACATACCT
Found at i:11682151 original size:14 final size:14
Alignment explanation
Indices: 11682131--11682166 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
11682121 AGTGCTTCAA
11682131 CTTCTTTTCTTTTT
1 CTTCTTTTCTTTTT
* *
11682145 TTTCTTTGCTTTTT
1 CTTCTTTTCTTTTT
11682159 CTTCTTTT
1 CTTCTTTT
11682167 AAGTGATGGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (14 bp):
CTTCTTTTCTTTTT
Found at i:11682700 original size:198 final size:198
Alignment explanation
Indices: 11682309--11682700 Score: 488
Period size: 198 Copynumber: 2.0 Consensus size: 198
11682299 TGATTACCGC
* * * *
11682309 TTGATGTAAGGCACTTGTACCTTGTCGATTGATTATGGATATAGGAAGGAAGCAAAACAACCTGC
1 TTGATGTAAGGCAATTCTACCTTCTCGATTGATTATGGATATAGGAAGGAAGCAAAACAACATGC
* * * *
11682374 ATAAGTGAATGACTAAAAACATATGGTTAAGGGTGGTAAATGTATGGTGAATAGCTAGGCTATTT
66 ACAAGTGAATGACTAAAAACAAATGGATAAGGGTGGTAAACGTATGGTGAATAGCTAGGCTATTT
* * * *
11682439 AAATAATGAGTGATGGAAGTGAAAGATGGTTGATATGGCTATGGTTTATGGTTGATAAAACAAAG
131 AAATAATGAGTGATGGAAGCGAAAGATGATTGAAATGGCTATGGTTTATGGTCGATAAAACAAAG
11682504 GGA
196 GGA
* * *
11682507 TTGATGTAAGGTAATTCTACCTTCTC-ATTTGATTGTGGATCTAGGAAGGAAGCAAAACAACATG
1 TTGATGTAAGGCAATTCTACCTTCTCGA-TTGATTATGGATATAGGAAGGAAGCAAAACAACATG
* * * * *
11682571 CACAAGTGAATGGCTCAAAACAGAATGGATAAGGGTGGTAAACGTATGGTTTAATTGGTAGGCTA
65 CACAAGTGAATGACTAAAAACA-AATGGATAAGGGTGGTAAACGTATGG-TGAATAGCTAGGCTA
* * * *
11682636 TTT-AATAAATGAGAT-ATGGAAGCGGAATATGATTGAAATGGTTATGG-TTATGG-CGATGAAA
128 TTTAAAT-AATGAG-TGATGGAAGCGAAAGATGATTGAAATGGCTATGGTTTATGGTCGATAAAA
11682697 CAAA
191 CAAA
11682701 AAAAGATGGT
Statistics
Matches: 165, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
197 1 0.01
198 84 0.51
199 32 0.19
200 47 0.28
201 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.29
Consensus pattern (198 bp):
TTGATGTAAGGCAATTCTACCTTCTCGATTGATTATGGATATAGGAAGGAAGCAAAACAACATGC
ACAAGTGAATGACTAAAAACAAATGGATAAGGGTGGTAAACGTATGGTGAATAGCTAGGCTATTT
AAATAATGAGTGATGGAAGCGAAAGATGATTGAAATGGCTATGGTTTATGGTCGATAAAACAAAG
GGA
Found at i:11685120 original size:24 final size:21
Alignment explanation
Indices: 11685085--11685127 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
11685075 GGCACATTCT
*
11685085 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
11685108 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
11685128 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:11686419 original size:15 final size:15
Alignment explanation
Indices: 11686384--11686412 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11686374 GTGCTTCAAC
11686384 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
11686398 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
11686413 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:11696739 original size:15 final size:16
Alignment explanation
Indices: 11696719--11696764 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
11696709 GTTCTAAGTT
*
11696719 GAAAAATAAGAAAAA-
1 GAAAAAGAAGAAAAAG
11696734 GAAAAAGAAGAAAAAG
1 GAAAAAGAAGAAAAAG
*
11696750 GAAAAGGAA-AAAAAG
1 GAAAAAGAAGAAAAAG
11696765 AATAAAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 20 0.71
16 8 0.29
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (16 bp):
GAAAAAGAAGAAAAAG
Found at i:11696781 original size:21 final size:20
Alignment explanation
Indices: 11696723--11696781 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
11696713 TAAGTTGAAA
*
11696723 AATAAGAAAAAGAAAAAGAAG
1 AATAA-AAAAAGAAAAAAAAG
*
11696744 AA-AAAGGAAAAGGAAAAAAAG
1 AATAAA--AAAAGAAAAAAAAG
11696765 AATAAAAAAGAGAAAAA
1 AATAAAAAA-AGAAAAA
11696782 CGTTTAGGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 1 0.03
20 5 0.16
21 22 0.71
22 3 0.10
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (20 bp):
AATAAAAAAAGAAAAAAAAG
Found at i:11696848 original size:7 final size:7
Alignment explanation
Indices: 11696822--11696855 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
11696812 TAAATTGAAA
11696822 AAAAAAG
1 AAAAAAG
11696829 -AAAAAG
1 AAAAAAG
11696835 AACAAAAG
1 AA-AAAAG
11696843 AAAAAAG
1 AAAAAAG
11696850 AAAAAA
1 AAAAAA
11696856 TAAGGTGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.24
7 12 0.48
8 7 0.28
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:11697791 original size:90 final size:89
Alignment explanation
Indices: 11697637--11697812 Score: 298
Period size: 90 Copynumber: 2.0 Consensus size: 89
11697627 CTAACACACT
*
11697637 CTTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAAACTATAT
1 CTTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTATCATTTCAAATTAATTAAAACTATAT
* *
11697702 TTAATTAATTGGAATTTAATAATC
66 TTAATTAATTGAAATTAAATAATC
* *
11697726 CTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATCATTTCAAATTAATTAAATCTATA
1 CTTTTATAGCCAAGTTACCCTAATCATATTA-GGATTTTATCATTTCAAATTAATTAAAACTATA
11697791 TTTAATTAATTGAAATTAAATA
65 TTTAATTAATTGAAATTAAATA
11697813 TTCGGGATTA
Statistics
Matches: 81, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 30 0.37
90 51 0.63
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (89 bp):
CTTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTATCATTTCAAATTAATTAAAACTATAT
TTAATTAATTGAAATTAAATAATC
Found at i:11704573 original size:90 final size:89
Alignment explanation
Indices: 11704416--11704592 Score: 300
Period size: 90 Copynumber: 2.0 Consensus size: 89
11704406 CCTAACACAC
* *
11704416 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTTAAATTAATTAAATCTATA
1 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCAATA
* *
11704481 TTTAATTAATTGAAATTTAATAAT
66 TTTAATTAATTAAAATTAAATAAT
*
11704505 CCTTTTATATCCAAGTTACCCTAATCATATTTGGGATTTTATTATTTCAAATTAATTAAATCAAT
1 CCTTTTATATCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCAAT
11704570 ATTTAATTAATTAAAATTAAATA
65 ATTTAATTAATTAAAATTAAATA
11704593 TTCAGAATTA
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 34 0.41
90 48 0.59
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (89 bp):
CCTTTTATATCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCAATA
TTTAATTAATTAAAATTAAATAAT
Found at i:11704914 original size:18 final size:18
Alignment explanation
Indices: 11704866--11704908 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
11704856 CCTTTATATC
11704866 TAGAATAGGCACAAGTCT
1 TAGAATAGGCACAAGTCT
11704884 TAGAATAGGCACAAGTCT
1 TAGAATAGGCACAAGTCT
*
11704902 TGGAATA
1 TAGAATA
11704909 TTCACACTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (18 bp):
TAGAATAGGCACAAGTCT
Found at i:11706154 original size:43 final size:42
Alignment explanation
Indices: 11706101--11706221 Score: 143
Period size: 43 Copynumber: 2.8 Consensus size: 42
11706091 CGAAGGGGCC
*
11706101 ATCCACGATTTCAATTCTAAGACGGAGGATATCGTACCCATAA
1 ATCCACGATTTCAATTC-ACGACGGAGGATATCGTACCCATAA
* * * * *
11706144 ATCCATGATTTCAACTCCACGATGGAGGATATCGTACTCATAT
1 ATCCACGATTTCAA-TTCACGACGGAGGATATCGTACCCATAA
* *
11706187 ATCCGCGATTTCAACTTCACGACGAAGGATATCGT
1 ATCCACGATTTCAA-TTCACGACGGAGGATATCGT
11706222 GCCAACTCTA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
43 64 0.97
44 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.27
Consensus pattern (42 bp):
ATCCACGATTTCAATTCACGACGGAGGATATCGTACCCATAA
Found at i:11708401 original size:14 final size:15
Alignment explanation
Indices: 11708384--11708422 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
11708374 TTTTTTACTC
*
11708384 TTTTATTATTAT-TT
1 TTTTATTATTATCAT
11708398 TTTTATTATTATCAT
1 TTTTATTATTATCAT
11708413 TTTTATTATT
1 TTTTATTATT
11708423 TTATTTAGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTATTATTATCAT
Found at i:11708408 original size:17 final size:18
Alignment explanation
Indices: 11708386--11708427 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
11708376 TTTTACTCTT
11708386 TTATTATTATTTTT-TTA
1 TTATTATTATTTTTATTA
*
11708403 TTATTATCATTTTTATTA
1 TTATTATTATTTTTATTA
11708421 TT-TTATT
1 TTATTATT
11708428 TAGTCTTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTATTATTTTTATTA
Found at i:11708424 original size:26 final size:25
Alignment explanation
Indices: 11708389--11708457 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 25
11708379 TACTCTTTTA
*
11708389 TTATTATTTTTTTATTATTATCATTT
1 TTATTATTTTTTTATTATTA-CATAT
* *
11708415 TTATTATTTTATTTAGTCTTACATAT
1 TTATTATTTT-TTTATTATTACATAT
*
11708441 TTATTTTTTATTTTATT
1 TTATTATTT-TTTTATT
11708458 TATTTATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 27 0.75
27 9 0.25
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.71
Consensus pattern (25 bp):
TTATTATTTTTTTATTATTACATAT
Found at i:11708459 original size:16 final size:16
Alignment explanation
Indices: 11708438--11708485 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
11708428 TAGTCTTACA
11708438 TATTTATTTTTTATTT
1 TATTTATTTTTTATTT
11708454 TATTTATTTATTT-TTT
1 TATTTATTT-TTTATTT
* *
11708470 TCTTT-TCTTTTATTT
1 TATTTATTTTTTATTT
11708485 T
1 T
11708486 TATCCTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 3 0.11
15 6 0.21
16 16 0.57
17 3 0.11
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (16 bp):
TATTTATTTTTTATTT
Found at i:11708486 original size:6 final size:6
Alignment explanation
Indices: 11708440--11708555 Score: 51
Period size: 6 Copynumber: 18.3 Consensus size: 6
11708430 GTCTTACATA
*
11708440 TTTATT TTT-TAT TTTATTT ATTTATT TTT-TT CTTT-TCT TTTATT TTTATCC
1 TTTATT TTTAT-T TTTA-TT -TTTATT TTTATT -TTTAT-T TTTATT TTTAT-T
* ** * * *
11708491 TTTATC TTTATT TTT-TAT TTTCCT TATATT GGTTCTATT TATATT TATATT
1 TTTATT TTTATT TTTAT-T TTTATT TTTATT --TT-TATT TTTATT TTTATT
11708542 TTTATT TTTATT TT
1 TTTATT TTTATT TT
11708556 CCTCTCTTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 26
0.72 0.07 0.21
Matches are distributed among these distances:
5 4 0.05
6 63 0.72
7 11 0.12
8 6 0.07
9 4 0.05
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (6 bp):
TTTATT
Found at i:11708486 original size:19 final size:19
Alignment explanation
Indices: 11708460--11708506 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
11708450 ATTTTATTTA
11708460 TTTATTTTTTT-CTTT-TC
1 TTTATTTTTTTCCTTTATC
*
11708477 TTTTATTTTTATCCTTTATC
1 -TTTATTTTTTTCCTTTATC
11708497 TTTATTTTTT
1 TTTATTTTTT
11708507 ATTTTCCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 10 0.40
19 13 0.52
20 2 0.08
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTATTTTTTTCCTTTATC
Found at i:11708635 original size:8 final size:8
Alignment explanation
Indices: 11708598--11708647 Score: 55
Period size: 8 Copynumber: 5.9 Consensus size: 8
11708588 ATAATTATTA
11708598 TTATTTTCC
1 TTATTTT-C
*
11708607 TTTATTTTA
1 -TTATTTTC
*
11708616 TTCTTATTC
1 TTATT-TTC
11708625 TTATTTTC
1 TTATTTTC
11708633 TTATTTTC
1 TTATTTTC
11708641 TTATTTT
1 TTATTTT
11708648 TGATTATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
8 22 0.63
9 6 0.17
10 7 0.20
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (8 bp):
TTATTTTC
Found at i:11708657 original size:9 final size:9
Alignment explanation
Indices: 11708651--11708803 Score: 77
Period size: 9 Copynumber: 16.4 Consensus size: 9
11708641 TTATTTTTGA
11708651 TTATTTTAT
1 TTATTTTAT
11708660 TTATTTT-T
1 TTATTTTAT
11708668 CTTCA--TT-T
1 -TT-ATTTTAT
11708676 TTATTTTAT
1 TTATTTTAT
11708685 TTCATTTTTAT
1 TT-A-TTTTAT
*
11708696 GTATTTTATT
1 TTATTTTA-T
11708706 TTATTTTAT
1 TTATTTTAT
* *
11708715 TT-TTATCT
1 TTATTTTAT
11708723 TTATTTTAT
1 TTATTTTAT
11708732 TT-TTATGTAT
1 TTATT-T-TAT
11708742 TT-TCTTTAT
1 TTAT-TTTAT
*
11708751 CTTATTTTCT
1 -TTATTTTAT
* *
11708761 TTGTTTACAT
1 TTATTT-TAT
*
11708771 TTCTTTTATT
1 TTATTTTA-T
*
11708781 TTATTTTTCT
1 TTA-TTTTAT
11708791 TTATTTTAT
1 TTATTTTAT
11708800 TTAT
1 TTAT
11708804 CTTCATTGCT
Statistics
Matches: 112, Mismatches: 15, Indels: 34
0.70 0.09 0.21
Matches are distributed among these distances:
6 1 0.01
7 2 0.02
8 14 0.12
9 45 0.40
10 37 0.33
11 13 0.12
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.75
Consensus pattern (9 bp):
TTATTTTAT
Found at i:11708667 original size:10 final size:10
Alignment explanation
Indices: 11708641--11708744 Score: 53
Period size: 11 Copynumber: 10.7 Consensus size: 10
11708631 TCTTATTTTC
11708641 TTATTTTTGA-
1 TTATTTTT-AT
11708651 TTA-TTTTAT
1 TTATTTTTAT
*
11708660 TTATTTTTCT
1 TTATTTTTAT
*
11708670 TCA--TTT--
1 TTATTTTTAT
11708676 TTAT-TTTAT
1 TTATTTTTAT
11708685 TTCATTTTTAT
1 TT-ATTTTTAT
*
11708696 GTA-TTTTATT
1 TTATTTTTA-T
*
11708706 TTATTTTATTT
1 TTATTTT-TAT
*
11708717 TTATCTTTATT
1 TTATTTTTA-T
11708728 TTATTTTTAT
1 TTATTTTTAT
*
11708738 GTATTTT
1 TTATTTT
11708745 CTTTATCTTA
Statistics
Matches: 73, Mismatches: 10, Indels: 22
0.70 0.10 0.21
Matches are distributed among these distances:
6 2 0.03
7 3 0.04
8 4 0.05
9 14 0.19
10 24 0.33
11 25 0.34
12 1 0.01
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.75
Consensus pattern (10 bp):
TTATTTTTAT
Found at i:11708675 original size:19 final size:18
Alignment explanation
Indices: 11708628--11708733 Score: 69
Period size: 19 Copynumber: 5.9 Consensus size: 18
11708618 CTTATTCTTA
*
11708628 TTTTCTTATTTT-CTTAT
1 TTTTCTTATTTTATTTAT
*
11708645 TTTTGATTATTTTATTTAT
1 TTTT-CTTATTTTATTTAT
11708664 TTTTCTTCATTTTTATTT-T
1 TTTTCTT-A-TTTTATTTAT
* * *
11708683 ATTTCAT-TTTTATGTAT
1 TTTTCTTATTTTATTTAT
*
11708700 TTTATTTTATTTTA-TT-T
1 TTT-TCTTATTTTATTTAT
*
11708717 TTATCTTTATTTTATTT
1 TTTTC-TTATTTTATTT
11708734 TTATGTATTT
Statistics
Matches: 68, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
16 8 0.12
17 18 0.26
18 14 0.21
19 20 0.29
20 8 0.12
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTTCTTATTTTATTTAT
Found at i:11708753 original size:6 final size:5
Alignment explanation
Indices: 11708592--11708801 Score: 98
Period size: 5 Copynumber: 41.2 Consensus size: 5
11708582 GTACATATAA
** *
11708592 TTATT ATTATT TTCCT TTATT TTATT CTTATT CTTATT TTCTT ATT-TT
1 TTATT -TTATT TTATT TTATT TTATT -TTATT -TTATT TTATT -TTATT
* *
11708640 CTTATT TT-TGA TTATT TTA-T TTATT TT-TCT TCATTT TTATT TTATT
1 -TTATT TTAT-T TTATT TTATT TTATT TTAT-T TTA-TT TTATT TTATT
* *
11708686 TCATT TT-TAT GTATT TTATT TTATT TTATTT TTATCT TTATT TTATT
1 TTATT TTAT-T TTATT TTATT TTATT TTA-TT TTAT-T TTATT TTATT
* * * * * * *
11708733 TT-TAT GTATT TT-CT TTATC TTATT TT-CT TT-GT TTACAT TTCTT TTATT
1 TTAT-T TTATT TTATT TTATT TTATT TTATT TTATT TTA-TT TTATT TTATT
11708781 TTATT TT-TCT TTATT TTATT T
1 TTATT TTAT-T TTATT TTATT T
11708802 ATCTTCATTG
Statistics
Matches: 158, Mismatches: 26, Indels: 41
0.70 0.12 0.18
Matches are distributed among these distances:
4 18 0.11
5 99 0.63
6 40 0.25
7 1 0.01
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.74
Consensus pattern (5 bp):
TTATT
Found at i:11708795 original size:15 final size:15
Alignment explanation
Indices: 11708655--11708806 Score: 84
Period size: 16 Copynumber: 10.1 Consensus size: 15
11708645 TTTTGATTAT
11708655 TTTA-TTTATTTTTC
1 TTTATTTTATTTTTC
*
11708669 TTCATTTTTATTTTAT-
1 TTTA-TTTTATTTT-TC
* * *
11708685 TTCATTTTTATGTAT-
1 TTTA-TTTTATTTTTC
*
11708700 TTTATTTTATTTTATT
1 TTTATTTTATTTT-TC
*
11708716 TTTATCTTTATTTTATT
1 TTTAT-TTTATTTT-TC
*
11708733 TTTA-TGTA-TTTTC
1 TTTATTTTATTTTTC
*
11708746 TTTATCTTA-TTTTC
1 TTTATTTTATTTTTC
* **
11708760 TTT-GTTTACATTTC
1 TTTATTTTATTTTTC
11708774 TTTTATTTTATTTTTC
1 -TTTATTTTATTTTTC
*
11708790 TTTATTTTATTTATC
1 TTTATTTTATTTTTC
11708805 TT
1 TT
11708807 CATTGCTTTT
Statistics
Matches: 111, Mismatches: 17, Indels: 19
0.76 0.12 0.13
Matches are distributed among these distances:
13 8 0.07
14 27 0.24
15 27 0.24
16 33 0.30
17 16 0.14
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTATTTTATTTTTC
Found at i:11719613 original size:16 final size:16
Alignment explanation
Indices: 11719605--11719636 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11719595 AAAAAAAGGC
*
11719605 AAAAAAAAAGGCAAAA
1 AAAAAAAAAGCCAAAA
11719621 AAAAAAAAAGCCAAAA
1 AAAAAAAAAGCCAAAA
11719637 TTTCTAAAAA
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:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGCCAAAA
Found at i:11719636 original size:13 final size:12
Alignment explanation
Indices: 11719594--11719625 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
11719584 TCAAAAAAAC
11719594 AAAAAAAAGGCA
1 AAAAAAAAGGCA
11719606 AAAAAAAAGGCA
1 AAAAAAAAGGCA
11719618 AAAAAAAA
1 AAAAAAAA
11719626 AAAAGCCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGGCA
Found at i:11724361 original size:24 final size:24
Alignment explanation
Indices: 11724334--11724380 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
11724324 CCTCAAAGAC
*
11724334 CACAACTTGTGGTACTTCAAGTGA
1 CACAACTTGTGGAACTTCAAGTGA
* * *
11724358 CACATCTTTTTGAACTTCAAGTG
1 CACAACTTGTGGAACTTCAAGTG
11724381 GCATAACTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CACAACTTGTGGAACTTCAAGTGA
Found at i:11725676 original size:23 final size:23
Alignment explanation
Indices: 11725649--11725693 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
11725639 CCTTCCTTTC
*
11725649 TTTTTTCTTTTTTTAAGTGCTTGA
1 TTTTTT-TTCTTTTAAGTGCTTGA
*
11725673 TTTTTTTTCTTTTGAGTGCTT
1 TTTTTTTTCTTTTAAGTGCTT
11725694 CACTTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.09, C:0.09, G:0.13, T:0.69
Consensus pattern (23 bp):
TTTTTTTTCTTTTAAGTGCTTGA
Found at i:11732552 original size:2 final size:2
Alignment explanation
Indices: 11732541--11732570 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
11732531 TCATTATAGC
11732541 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11732571 GAATATAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11752973 original size:21 final size:22
Alignment explanation
Indices: 11752949--11752990 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
11752939 ATCCTCCCCA
11752949 TGAA-GGAACCAATTCCCCCTT
1 TGAAGGGAACCAATTCCCCCTT
*
11752970 TGAATGGGAACCGATTCCCCC
1 TGAA-GGGAACCAATTCCCCC
11752991 CCACAGGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
23 14 0.78
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.21
Consensus pattern (22 bp):
TGAAGGGAACCAATTCCCCCTT
Found at i:11753731 original size:12 final size:12
Alignment explanation
Indices: 11753698--11753723 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11753688 TAGTCGTCAA
11753698 CCAAATCCTCCT
1 CCAAATCCTCCT
11753710 CCAAATCCTCCT
1 CCAAATCCTCCT
11753722 CC
1 CC
11753724 TATTCCTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.54, G:0.00, T:0.23
Consensus pattern (12 bp):
CCAAATCCTCCT
Found at i:11755321 original size:45 final size:45
Alignment explanation
Indices: 11755266--11755355 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
11755256 GTGTGTGTTT
11755266 TAAGTGTGTTTTAAAATGATAAATGGGAGAAGTGTTAAAGTAAGG
1 TAAGTGTGTTTTAAAATGATAAATGGGAGAAGTGTTAAAGTAAGG
*
11755311 TAAGTGTGTTTTCAAATGATAAATGGGAGAAGTGTTAAAGTAAGG
1 TAAGTGTGTTTTAAAATGATAAATGGGAGAAGTGTTAAAGTAAGG
11755356 GGGAGTAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.39, C:0.01, G:0.29, T:0.31
Consensus pattern (45 bp):
TAAGTGTGTTTTAAAATGATAAATGGGAGAAGTGTTAAAGTAAGG
Found at i:11755700 original size:14 final size:14
Alignment explanation
Indices: 11755681--11755718 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
11755671 CTCATAGGGA
11755681 ACCGATTCCCGGGT
1 ACCGATTCCCGGGT
11755695 ACCGATTCCCGGGT
1 ACCGATTCCCGGGT
11755709 ACCGATTCCC
1 ACCGATTCCC
11755719 CCTGAATGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.16, C:0.39, G:0.24, T:0.21
Consensus pattern (14 bp):
ACCGATTCCCGGGT
Found at i:11761206 original size:46 final size:46
Alignment explanation
Indices: 11761137--11761413 Score: 378
Period size: 46 Copynumber: 6.0 Consensus size: 46
11761127 AAAACCATGA
* * *
11761137 GTGGCA-CCTTTTATGTCGTTAATGCACCGTTATGCATTTTTATTT
1 GTGGCATCCTTTCATGTCGATAATGCACCGTTATGCATTTTCATTT
* *
11761182 GTGGCATTCTTTCATGTCGATAATGCACTGTTATGCATTTTCATTT
1 GTGGCATCCTTTCATGTCGATAATGCACCGTTATGCATTTTCATTT
*
11761228 GTGGCATCCTTTCATG-CTGATAATGCACCATTATGCATTTTCATTT
1 GTGGCATCCTTTCATGTC-GATAATGCACCGTTATGCATTTTCATTT
* *
11761274 GTGGCATCCTTTCATGCCGATAATGTACCGTTATGCATTTTCATTT
1 GTGGCATCCTTTCATGTCGATAATGCACCGTTATGCATTTTCATTT
** * * * * *
11761320 GTGAAATCCTTTCATGCCAATAATGTACCATTATTCATTTTCATTT
1 GTGGCATCCTTTCATGTCGATAATGCACCGTTATGCATTTTCATTT
* *
11761366 GTGACATCCTTTCATGTCGATAATGTACCGTTATGCATTTTCATTT
1 GTGGCATCCTTTCATGTCGATAATGCACCGTTATGCATTTTCATTT
11761412 GT
1 GT
11761414 TCATTCATTT
Statistics
Matches: 209, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
45 7 0.03
46 201 0.96
47 1 0.00
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (46 bp):
GTGGCATCCTTTCATGTCGATAATGCACCGTTATGCATTTTCATTT
Found at i:11773428 original size:22 final size:22
Alignment explanation
Indices: 11773401--11773451 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
11773391 ACAACATAAT
*
11773401 ATAAATAAAATCATTTTTGTCC
1 ATAAATAAAATCATTTTTATCC
11773423 ATAAATAAAATCATTTTTATCC
1 ATAAATAAAATCATTTTTATCC
11773445 ATAAATA
1 ATAAATA
11773452 TTGCCCACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (22 bp):
ATAAATAAAATCATTTTTATCC
Found at i:11773850 original size:24 final size:24
Alignment explanation
Indices: 11773818--11773863 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
11773808 TCTTCCAGAT
11773818 GATGTATAAAACATATATGTACAG
1 GATGTATAAAACATATATGTACAG
*
11773842 GATGTATAAAACATCTATGTAC
1 GATGTATAAAACATATATGTAC
11773864 CATATCATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (24 bp):
GATGTATAAAACATATATGTACAG
Found at i:11776766 original size:49 final size:49
Alignment explanation
Indices: 11776709--11776877 Score: 205
Period size: 49 Copynumber: 3.4 Consensus size: 49
11776699 CATGAGTGTC
* * *
11776709 ACCTTTTATGCCGAAATGCACCGCTATGCATTTAACTTTCGTTTGTGGT
1 ACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTTATGGT
* * * * *
11776758 ACCTTTTATGTCAAAATGCAACGTTATACATTTAACTTTCATTTATGGA
1 ACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTTATGGT
* * * *
11776807 ATCTTTTATGCCGAATTACACCGTTATGCATTTAACTTACATTTAT-GT
1 ACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTTATGGT
*
11776855 CACCTTTTATACCGAAATGCACC
1 -ACCTTTTATGCCGAAATGCACC
11776878 TATGACTCTC
Statistics
Matches: 98, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
48 1 0.01
49 97 0.99
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.39
Consensus pattern (49 bp):
ACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTTATGGT
Found at i:11780579 original size:24 final size:24
Alignment explanation
Indices: 11780547--11780596 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
11780537 AGAGTGAGAC
11780547 TAGAAATGCATGGCCATGCTCGAA
1 TAGAAATGCATGGCCATGCTCGAA
11780571 TAGAAATGCATGGCCATGCTCGAA
1 TAGAAATGCATGGCCATGCTCGAA
11780595 TA
1 TA
11780597 AGTTGATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (24 bp):
TAGAAATGCATGGCCATGCTCGAA
Found at i:11792017 original size:17 final size:17
Alignment explanation
Indices: 11791978--11792049 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 17
11791968 ATTCATGTAT
11791978 CTAGTTCATTTAA-TAAA
1 CTAGTTCA-TTAATTAAA
*
11791995 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
11792013 CTAG-TCTATTCATCAAA
1 CTAGTTC-ATTAATTAAA
*
11792030 CTAGTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
11792047 CTA
1 CTA
11792050 ACTATTAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
16 2 0.04
17 30 0.67
18 13 0.29
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.42
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:11794985 original size:17 final size:17
Alignment explanation
Indices: 11794941--11795012 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 17
11794931 ATTCATGCAT
11794941 CTAGTTCATTTAAT-AAA
1 CTAGTTCA-TTAATCAAA
* * *
11794958 GATAGTTCATTATTTAAA
1 -CTAGTTCATTAATCAAA
*
11794976 CTAGTCCATTAATCAAA
1 CTAGTTCATTAATCAAA
11794993 CTAGTTCATTTAAT-AAA
1 CTAGTTCA-TTAATCAAA
11795010 CTA
1 CTA
11795013 ACTCTTAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
17 30 0.67
18 15 0.33
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (17 bp):
CTAGTTCATTAATCAAA
Found at i:11797154 original size:20 final size:20
Alignment explanation
Indices: 11797129--11797168 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
11797119 TGTCACGTTT
11797129 ATTAAAAATATTATTTATAG
1 ATTAAAAATATTATTTATAG
11797149 ATTAAAAATATTATTTATAG
1 ATTAAAAATATTATTTATAG
11797169 TTTTTAAAAT
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:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTAAAAATATTATTTATAG
Found at i:11798004 original size:49 final size:49
Alignment explanation
Indices: 11797951--11798048 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 49
11797941 TTATCGAAGA
*
11797951 ACACTTGTTGTATTCATTTATAATTCTTTTTTCAGTATTCTATTTGTTC
1 ACACTTGTTGTACTCATTTATAATTCTTTTTTCAGTATTCTATTTGTTC
* * *
11798000 ACACTTGTTTTACTCGTTTATAATTCTTTTTTCAGTGTTCTATTTGTTC
1 ACACTTGTTGTACTCATTTATAATTCTTTTTTCAGTATTCTATTTGTTC
11798049 TTAAATTATG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.18, C:0.15, G:0.09, T:0.57
Consensus pattern (49 bp):
ACACTTGTTGTACTCATTTATAATTCTTTTTTCAGTATTCTATTTGTTC
Found at i:11798521 original size:21 final size:21
Alignment explanation
Indices: 11798497--11798536 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11798487 CTTTCCCTGG
*
11798497 TCATCATCTTAAACCCCTAAT
1 TCATCATCTGAAACCCCTAAT
* *
11798518 TCATCGTCTGAAATCCCTA
1 TCATCATCTGAAACCCCTA
11798537 GCTCATCTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.33, G:0.05, T:0.33
Consensus pattern (21 bp):
TCATCATCTGAAACCCCTAAT
Found at i:11801699 original size:2 final size:2
Alignment explanation
Indices: 11801694--11801729 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
11801684 AAAGTCCATG
11801694 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
11801730 CATACATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11802112 original size:54 final size:57
Alignment explanation
Indices: 11802006--11802115 Score: 220
Period size: 57 Copynumber: 1.9 Consensus size: 57
11801996 CCCAGTTGAA
11802006 GATGATGATGAAGGAGAGTTCTTTGGACCAAAGAGATGATCCAAAGATGATGAAGAT
1 GATGATGATGAAGGAGAGTTCTTTGGACCAAAGAGATGATCCAAAGATGATGAAGAT
11802063 GATGATGATGAAGGAGAGTTCTTTGGACCAAAGAGATGATCCAAAGATGATGA
1 GATGATGATGAAGGAGAGTTCTTTGGACCAAAGAGATGATCCAAAGATGATGA
11802116 TTGTTATGTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.38, C:0.09, G:0.30, T:0.23
Consensus pattern (57 bp):
GATGATGATGAAGGAGAGTTCTTTGGACCAAAGAGATGATCCAAAGATGATGAAGAT
Found at i:11803609 original size:20 final size:20
Alignment explanation
Indices: 11803584--11803623 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
11803574 TGTCACGTTT
11803584 ATTAAAAATATTATTTATAG
1 ATTAAAAATATTATTTATAG
11803604 ATTAAAAATATTATTTATAG
1 ATTAAAAATATTATTTATAG
11803624 TTTTTAAAAT
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:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTAAAAATATTATTTATAG
Found at i:11805339 original size:20 final size:21
Alignment explanation
Indices: 11805292--11805339 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
11805282 GTAGCAAGAT
11805292 ATCGAT-CTATTTTGGAAGGA
1 ATCGATCCTATTTTGGAAGGA
* *
11805312 ATCAATCCT-TTTTGGAAGGG
1 ATCGATCCTATTTTGGAAGGA
11805332 ATCGATCC
1 ATCGATCC
11805340 ATTGCACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (21 bp):
ATCGATCCTATTTTGGAAGGA
Found at i:11806999 original size:34 final size:34
Alignment explanation
Indices: 11806956--11807021 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
11806946 CTAAGACATC
*
11806956 ACCAAATCATCCTAAATAGAGTAAAAACTCTTCT
1 ACCAAATCATCCAAAATAGAGTAAAAACTCTTCT
11806990 ACCAAATCATCCAAAATAGAGTAAAAACTCTT
1 ACCAAATCATCCAAAATAGAGTAAAAACTCTT
11807022 ATCTCTAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.47, C:0.23, G:0.06, T:0.24
Consensus pattern (34 bp):
ACCAAATCATCCAAAATAGAGTAAAAACTCTTCT
Found at i:11829551 original size:35 final size:35
Alignment explanation
Indices: 11829506--11829606 Score: 157
Period size: 35 Copynumber: 2.9 Consensus size: 35
11829496 TGGTAAGGGA
*
11829506 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGCATGAAATGGTGATAGAAG
* *
11829541 ATGGTGATGATATAGGCATGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGCATGAAATGGTGATAGAAG
*
11829576 ATGGTGATGATATAGTCATGAAAATGGTGAT
1 ATGGTGATGATATAGGCATG-AAATGGTGAT
11829607 GATATAGGCG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
35 51 0.85
36 9 0.15
ACGTcount: A:0.34, C:0.04, G:0.35, T:0.28
Consensus pattern (35 bp):
ATGGTGATGATATAGGCATGAAATGGTGATAGAAG
Found at i:11829606 original size:23 final size:23
Alignment explanation
Indices: 11829576--11829630 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
11829566 GTGATGGAAG
*
11829576 ATGGTGATGATATAGTCATGAAA
1 ATGGTGATGATATAGGCATGAAA
*
11829599 ATGGTGATGATATAGGCGTGAAA
1 ATGGTGATGATATAGGCATGAAA
11829622 ATGGTGATG
1 ATGGTGATG
11829631 GAAGATGGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.35, C:0.04, G:0.33, T:0.29
Consensus pattern (23 bp):
ATGGTGATGATATAGGCATGAAA
Found at i:11830024 original size:19 final size:20
Alignment explanation
Indices: 11829986--11830028 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
11829976 GAAACCCCTT
*
11829986 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
11830006 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
11830025 TGAA
1 TGAA
11830029 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:11836298 original size:16 final size:17
Alignment explanation
Indices: 11836262--11836298 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
11836252 TTTTTTTGAA
11836262 ATTTTGGCTTTTTGTTT
1 ATTTTGGCTTTTTGTTT
11836279 -TTTTGGCTTTTT-TTT
1 ATTTTGGCTTTTTGTTT
11836294 ATTTT
1 ATTTT
11836299 TTTGCTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.05, C:0.05, G:0.14, T:0.76
Consensus pattern (17 bp):
ATTTTGGCTTTTTGTTT
Found at i:11837326 original size:20 final size:20
Alignment explanation
Indices: 11837301--11837355 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
11837291 AATCTCTTTC
11837301 AAAATACATGATTTTTAATG
1 AAAATACATGATTTTTAATG
11837321 AAAATACATGA-TTTTAATG
1 AAAATACATGATTTTTAATG
* *
11837340 AAAGTACATGCTTTTT
1 AAAATACATGATTTTT
11837356 CGCCGAATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (20 bp):
AAAATACATGATTTTTAATG
Found at i:11845733 original size:2 final size:2
Alignment explanation
Indices: 11845716--11845757 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
11845706 TCATAATAAC
* *
11845716 TA TA GA TA TA -A TA TA TA TG 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
11845757 T
1 T
11845758 GAAAATAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:11851169 original size:25 final size:23
Alignment explanation
Indices: 11851141--11851188 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
11851131 TCTTTAATGT
11851141 ATATTTAATTTGAATTAATTAAAAA
1 ATATTTAATTT--ATTAATTAAAAA
* *
11851166 ATATTTTATTTATTAATTCAAAA
1 ATATTTAATTTATTAATTAAAAA
11851189 TAACTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 11 0.52
25 10 0.48
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATTTAATTTATTAATTAAAAA
Found at i:11871324 original size:43 final size:46
Alignment explanation
Indices: 11871223--11871328 Score: 130
Period size: 50 Copynumber: 2.3 Consensus size: 46
11871213 AAGATTAGAT
11871223 TTATTATTTTATTAGGAATTAAGGATGAGTTAAAACATTATTTTTAGTTA
1 TTATTATTTTATTAGGAATT-A--ATGAGTTAAAACATTA-TTTTAGTTA
*
11871273 TTATTATTTTATTAGGAATT-A-GAGTTAAGACA-TA-TTTAGTTTA
1 TTATTATTTTATTAGGAATTAATGAGTTAAAACATTATTTTAG-TTA
11871316 TTATTATTTTATT
1 TTATTATTTTATT
11871329 CATTATTTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
42 5 0.09
43 16 0.30
44 2 0.04
45 10 0.19
46 1 0.02
50 20 0.37
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (46 bp):
TTATTATTTTATTAGGAATTAATGAGTTAAAACATTATTTTAGTTA
Found at i:11881721 original size:50 final size:50
Alignment explanation
Indices: 11881646--11881759 Score: 185
Period size: 50 Copynumber: 2.3 Consensus size: 50
11881636 TGAATTAACC
*
11881646 CCCTTGG-TCGAATGGTGGTGAACTTGTTCATCATGGTTCCAAAGACATCT
1 CCCTTGGCT-GAATGGTGGTGAACTTGTTCATCATGGTTCCAAAGAAATCT
* *
11881696 CCCTTGGCTGAATGGTGGTGTACTTGTTCATCTTGGTTCCAAAGAAATCT
1 CCCTTGGCTGAATGGTGGTGAACTTGTTCATCATGGTTCCAAAGAAATCT
11881746 CCCTTGGCTGAATG
1 CCCTTGGCTGAATG
11881760 ATGATATGTT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 59 0.98
51 1 0.02
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (50 bp):
CCCTTGGCTGAATGGTGGTGAACTTGTTCATCATGGTTCCAAAGAAATCT
Found at i:11887189 original size:12 final size:12
Alignment explanation
Indices: 11887172--11887198 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
11887162 AAAGAGATGA
11887172 AATTAATAATGG
1 AATTAATAATGG
11887184 AATTAATAATGG
1 AATTAATAATGG
11887196 AAT
1 AAT
11887199 AAGAAATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (12 bp):
AATTAATAATGG
Found at i:11888594 original size:21 final size:22
Alignment explanation
Indices: 11888570--11888615 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
11888560 GGTTATCTTC
*
11888570 CTTTATTTTCAATTTCTTT-AT
1 CTTTATTTTAAATTTCTTTAAT
* *
11888591 CTTTTTTTTAAATTTTTTTAAT
1 CTTTATTTTAAATTTCTTTAAT
11888613 CTT
1 CTT
11888616 GTTTCTTACC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.70
Consensus pattern (22 bp):
CTTTATTTTAAATTTCTTTAAT
Found at i:11901076 original size:16 final size:15
Alignment explanation
Indices: 11901012--11901072 Score: 68
Period size: 16 Copynumber: 3.9 Consensus size: 15
11901002 TAAATAAGTA
*
11901012 AATAATAATATAAAT
1 AATAATAATAAAAAT
*
11901027 AATATATAATAAAACT
1 AATA-ATAATAAAAAT
* *
11901043 ATATTATACTAAAAAT
1 A-ATAATAATAAAAAT
11901059 AATAATAATAAAAA
1 AATAATAATAAAAA
11901073 ATAAAAAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
15 15 0.41
16 20 0.54
17 2 0.05
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (15 bp):
AATAATAATAAAAAT
Found at i:11901102 original size:23 final size:21
Alignment explanation
Indices: 11901076--11901118 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11901066 ATAAAAAATA
11901076 AAAAATATATATTATACATTTTC
1 AAAAAT-T-TATTATACATTTTC
*
11901099 AAAACTTTATTATACATTTT
1 AAAAATTTATTATACATTTT
11901119 TTAAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 1 0.05
23 5 0.26
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAAATTTATTATACATTTTC
Found at i:11901189 original size:36 final size:36
Alignment explanation
Indices: 11901149--11901365 Score: 165
Period size: 36 Copynumber: 5.9 Consensus size: 36
11901139 TCAAAACCTT
*
11901149 TTTTAAAAACTATATAATATACGTTTTCAAAATGCG
1 TTTTAAAAACTATATAATATATGTTTTCAAAATGCG
* * *
11901185 TTTTAAAAATTATATAATATATGTTTTCAAAA-ACTA
1 TTTTAAAAACTATATAATATATGTTTTCAAAATGC-G
* *
11901221 TTTTCCAAAACTATATAATAT-TCGTTTTCAAAAATGTG
1 TTTT-AAAAACTATATAATATAT-GTTTTC-AAAATGCG
* * * *
11901259 TTTTCAAAATTATATAATACATGTTTT-TAAAT-CG
1 TTTTAAAAACTATATAATATATGTTTTCAAAATGCG
* * **
11901293 TATTTTCAAAAAC-ATATTATATATATTTTCAAAACATGATT
1 --TTTT-AAAAACTATATAATATATGTTTTC-AAA-ATG-CG
* *
11901334 TTTTAAAAACTATATGATATATGTTTTTAAAA
1 TTTTAAAAACTATATAATATATGTTTTCAAAA
11901366 ACCATTTTTT
Statistics
Matches: 142, Mismatches: 24, Indels: 29
0.73 0.12 0.15
Matches are distributed among these distances:
34 1 0.01
35 5 0.04
36 52 0.37
37 44 0.31
38 20 0.14
39 20 0.14
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.44
Consensus pattern (36 bp):
TTTTAAAAACTATATAATATATGTTTTCAAAATGCG
Found at i:11901241 original size:37 final size:37
Alignment explanation
Indices: 11901139--11901422 Score: 199
Period size: 37 Copynumber: 7.7 Consensus size: 37
11901129 TTAAAAGCTA
* * *
11901139 TCAAAACCT-TTTTTAAAAACTATATAATATACGTTT
1 TCAAAAACTATTTTCAAAAACTATATAATATATGTTT
* * *
11901175 TCAAAATGC-GTTTT-AAAAATTATATAATATATGTTT
1 TCAAAA-ACTATTTTCAAAAACTATATAATATATGTTT
*
11901211 TCAAAAACTATTTTCCAAAACTATATAATAT-TCGTTT
1 TCAAAAACTATTTTCAAAAACTATATAATATAT-GTTT
* * * *
11901248 TCAAAAATGTGTTTTC-AAAATTATATAATACATGTTT
1 TCAAAAA-CTATTTTCAAAAACTATATAATATATGTTT
* * * *
11901285 T-TAAATCGTATTTTCAAAAAC-ATATTATATATATTT
1 TCAAAAAC-TATTTTCAAAAACTATATAATATATGTTT
* *
11901321 TC-AAAACATGATTTTTTAAAAACTATATGATATATGTTT
1 TCAAAAAC-T-A-TTTTCAAAAACTATATAATATATGTTT
* * * ** *
11901360 TTAAAAACCATTTTTTAAAAACTATATGTTATACGTTTT
1 TCAAAAACTA-TTTTCAAAAACTATATAATATATG-TTT
* *
11901399 TCGAAAA-TATTTTCAAAAAATATA
1 TCAAAAACTATTTTCAAAAACTATA
11901423 CTATATTATT
Statistics
Matches: 200, Mismatches: 33, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
35 1 0.00
36 64 0.32
37 66 0.33
38 42 0.21
39 22 0.11
40 5 0.03
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (37 bp):
TCAAAAACTATTTTCAAAAACTATATAATATATGTTT
Found at i:11901284 original size:74 final size:73
Alignment explanation
Indices: 11901148--11901386 Score: 259
Period size: 74 Copynumber: 3.2 Consensus size: 73
11901138 ATCAAAACCT
* * *
11901148 TTTTTAAAAACTATATAATATACGTTTTC-AAAATGCGTTTTAAAAATTATATAATATATGTTTT
1 TTTTCAAAAACTATATAATATTCGTTTTCAAAAATGTGTTTTAAAAATTATATAATATATGTTTT
11901212 CAAAAACTA
66 -AAAAACTA
* * *
11901221 TTTTCCAAAACTATATAATATTCGTTTTCAAAAATGTGTTTTCAAAATTATATAATACATGTTTT
1 TTTTCAAAAACTATATAATATTCGTTTTCAAAAATGTGTTTTAAAAATTATATAATATATGTTTT
* *
11901286 TAAATCGTA
66 AAAAAC-TA
* * * * *
11901295 TTTTCAAAAAC-ATATTATATAT-ATTTTCAAAACATGATTTTTTAAAAACTATATGATATATGT
1 TTTTCAAAAACTATATAATAT-TCGTTTTCAAAA-ATG-TGTTTTAAAAATTATATAATATATG-
*
11901358 TTTTAAAAACCA
62 TTTTAAAAACTA
*
11901370 TTTTTTAAAAACTATAT
1 -TTTTCAAAAACTATAT
11901387 GTTATACGTT
Statistics
Matches: 138, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
73 47 0.34
74 48 0.35
75 21 0.15
76 18 0.13
77 4 0.03
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (73 bp):
TTTTCAAAAACTATATAATATTCGTTTTCAAAAATGTGTTTTAAAAATTATATAATATATGTTTT
AAAAACTA
Found at i:11903251 original size:11 final size:11
Alignment explanation
Indices: 11903235--11903259 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11903225 TACACAAAAA
11903235 GAAGTGCAAGT
1 GAAGTGCAAGT
11903246 GAAGTGCAAGT
1 GAAGTGCAAGT
11903257 GAA
1 GAA
11903260 AGAAATAAAA
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:0.36, T:0.16
Consensus pattern (11 bp):
GAAGTGCAAGT
Found at i:11903309 original size:23 final size:25
Alignment explanation
Indices: 11903281--11903331 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
11903271 ATTAGCAAAG
*
11903281 AAATTG-ATGCACTCAAAA-GAAGA
1 AAATTGCAAGCACTCAAAAGGAAGA
11903304 AAATTGCAAGCACTCAAAAGGAAGA
1 AAATTGCAAGCACTCAAAAGGAAGA
11903329 AAA
1 AAA
11903332 AAGAAAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 6 0.24
24 11 0.44
25 8 0.32
ACGTcount: A:0.55, C:0.14, G:0.18, T:0.14
Consensus pattern (25 bp):
AAATTGCAAGCACTCAAAAGGAAGA
Found at i:11917026 original size:23 final size:21
Alignment explanation
Indices: 11916989--11917045 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 21
11916979 ACTTTTCTTT
*
11916989 ATTTTCTTTTTGAGTGCTTGA
1 ATTTTCTTTTTGAGTGCTTCA
11917010 ATTTTCTTCTTTTGAGTGCTTCA
1 ATTTTC-T-TTTTGAGTGCTTCA
11917033 A-TTTCTTTGTTGA
1 ATTTTCTTT-TTGA
11917046 TTTTATGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.06
21 11 0.34
22 5 0.16
23 14 0.44
ACGTcount: A:0.14, C:0.12, G:0.16, T:0.58
Consensus pattern (21 bp):
ATTTTCTTTTTGAGTGCTTCA
Found at i:11926345 original size:73 final size:73
Alignment explanation
Indices: 11926226--11926368 Score: 223
Period size: 73 Copynumber: 2.0 Consensus size: 73
11926216 GTGTACATCT
* *
11926226 TGTCGCAACCGTCTTTCGATTGGGCCCCAGAATTGGGCTTCGACTTGAAAAATGTGGATTGGAGA
1 TGTCGCAACCATCTTTCGATTGGGCCCCAGAATTGGGATTCGACTTGAAAAATGTGGATTGGAGA
11926291 CGCCAAGC
66 CGCCAAGC
* * * * *
11926299 TGTCGCAACCATCTTTCGGTTTGGCTCCGGAATTGGGATTCGACTTGAAAAATGTGGATTGGAGT
1 TGTCGCAACCATCTTTCGATTGGGCCCCAGAATTGGGATTCGACTTGAAAAATGTGGATTGGAGA
11926364 CGCCA
66 CGCCA
11926369 CCGATCATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (73 bp):
TGTCGCAACCATCTTTCGATTGGGCCCCAGAATTGGGATTCGACTTGAAAAATGTGGATTGGAGA
CGCCAAGC
Found at i:11926695 original size:4 final size:4
Alignment explanation
Indices: 11926686--11926717 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
11926676 AAATAAAAGG
11926686 ATAA ATAA ATAA ATAA ATAA ATAA ATGAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATA
11926718 TTAATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (4 bp):
ATAA
Done.