Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 113 of 150
Found at i:34975278 original size:19 final size:19
Alignment explanation
Indices: 34975164--34975265 Score: 168
Period size: 19 Copynumber: 5.3 Consensus size: 19
34975154 AATTTTTGAG
*
34975164 GATATGCAATCTTAGATAT
1 GATATGCAATCCTAGATAT
34975183 GATATGCAATCCTAGATAT
1 GATATGCAATCCTAGATAT
34975202 GATATGCAATCCTAGATAT
1 GATATGCAATCCTAGATAT
*
34975221 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCCTAGATAT
34975242 GATATGCAATCCTAGATAT
1 GATATGCAATCCTAGATAT
34975261 GATAT
1 GATAT
34975266 ATAATCTTAG
Statistics
Matches: 78, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
19 60 0.77
21 18 0.23
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (19 bp):
GATATGCAATCCTAGATAT
Found at i:34975971 original size:25 final size:25
Alignment explanation
Indices: 34975908--34975974 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
34975898 TTTTTTGTAG
*
34975908 TATA-ATATAATTATTTTTTATTTA
1 TATATATATAATTATTTTTTATCTA
* *
34975932 TTTATATGTAATTATTTTTTATCTA
1 TATATATATAATTATTTTTTATCTA
* *
34975957 TATGTATATATTTATTTT
1 TATATATATAATTATTTT
34975975 AGTATACATA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
24 3 0.09
25 32 0.91
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (25 bp):
TATATATATAATTATTTTTTATCTA
Found at i:34976044 original size:25 final size:24
Alignment explanation
Indices: 34976016--34976072 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
34976006 TTTTAACTAA
* *
34976016 TTTTTATATATATGAACATAT-TT
1 TTTTTATATAAATGAAAATATATT
*
34976039 ATTTTT-TTTAAATGAAAATATATT
1 -TTTTTATATAAATGAAAATATATT
34976063 TTTTTATATA
1 TTTTTATATA
34976073 CTTTATAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (24 bp):
TTTTTATATAAATGAAAATATATT
Found at i:34983470 original size:44 final size:44
Alignment explanation
Indices: 34983381--34983932 Score: 409
Period size: 44 Copynumber: 12.5 Consensus size: 44
34983371 GCAGATCAGT
* * * * *
34983381 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
* *
34983425 GAAGATGCAGATCTTGTCTTCCCATATTAGTGGCGGAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
* * *** * *
34983469 GAAGAAAGCAGATCTTGTTTTCATGTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
* * * * *
34983513 GAAGATAGCAAATCCTGTCTTCCTATATTGGTAGCGAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
* * *
34983558 GAAGATGTAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
* * * *** ** *
34983602 GAAGAAAGCAAATATTGTCTTCATGTATT-GACGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
* * * * *
34983646 AAAGATAGCATG-TCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCA-GATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
* *
34983690 GAAGATGCAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
* *** * *
34983734 GAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
* * * * * *
34983778 GAAAATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
* *
34983822 GACGATGCAAATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
* *** * *
34983866 GAAGAAAGCAGATCTTGTCTTCATTTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
* * *
34983910 GAAAATAGCAGGTCTTGGCTTCC
1 GAAGAT-GCAGATCTTGTCTTCC
34983933 TGCACCAACA
Statistics
Matches: 395, Mismatches: 97, Indels: 32
0.75 0.19 0.06
Matches are distributed among these distances:
42 1 0.00
43 68 0.17
44 230 0.58
45 96 0.24
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (44 bp):
GAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
Found at i:34983752 original size:132 final size:133
Alignment explanation
Indices: 34983382--34983933 Score: 896
Period size: 132 Copynumber: 4.2 Consensus size: 133
34983372 CAGATCAGTG
34983382 AAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
1 AAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
* * * *
34983447 CATATTAGTGGCGGAGTAGATCGAAGAAAGCAGATCTTGTTTTCATGTATTGGCGTGAAGTAGAT
66 CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
34983512 CG-
131 CGA
** *
34983514 AAGATAGCAAATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGTAGATCTTGTCTTC
1 AAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTTC
* * * *
34983579 CCATACTGGTGGTGAAGTAGATCGAAGAAAGCAAATATTGTCTTCATGTATTGACGTGAAGTAGA
65 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
34983644 TC-A
130 TCGA
* *
34983647 AAGATAGCATGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTATCTTCC
1 AAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
34983712 CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
66 CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
34983777 CGA
131 CGA
* *
34983780 AA-ATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAAATCTTGTCTTCC
1 AAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
* *
34983844 CATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATTTATTGGCGTGAAGTAGAT
66 CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
34983909 CGA
131 CGA
* *
34983912 AA-ATAGCAGGTCTTGGCTTCCT
1 AAGATAGCAGGTCCTGTCTTCCT
34983934 GCACCAACAG
Statistics
Matches: 390, Mismatches: 27, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
132 267 0.68
133 123 0.32
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (133 bp):
AAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
CGA
Found at i:34983957 original size:265 final size:265
Alignment explanation
Indices: 34983421--34983959 Score: 785
Period size: 265 Copynumber: 2.0 Consensus size: 265
34983411 GTAGGAAGTG
* * *
34983421 GATCGAAGATGCAGATCTTGTCTTCCCATATTAGTGGCGGAGTAGATCGAAGAAAGCAGATCTTG
1 GATCGAAGATGCAGATCTTATCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAGCAGATCTTG
* *
34983486 TTTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAAATCCTGTCTTCCTATATTGGTAGCGAA
66 TCTTCATGTATTGGCGTGAAGTAGATCGAAAATAGCAAATCCTGTCTTCCTATATTGGTAGCGAA
* * *
34983551 GTGGATCGAAGATGTAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAAATA
131 GTGGATCGAAGATGCAAATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAAATA
* * * *****
34983616 TTGTCTTCATGTATTGACGTGAAGTAGATCAAAGATAGCATGTCCTGTCTTCCTATATTGGTAGG
196 TTGTCTTCATGTATTGACGTGAAGTAGATCAAAGATAGCAGGTCCTGGCTTCCTACACCAACAGG
**
34983681 AAGTG
261 AAGCA
*
34983686 GATCGAAGATGCAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTG
1 GATCGAAGATGCAGATCTTATCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAGCAGATCTTG
**
34983751 TCTTCATGTATTGGCGTGAAGTAGATCGAAAATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAA
66 TCTTCATGTATTGGCGTGAAGTAGATCGAAAATAGCAAATCCTGTCTTCCTATATTGGTAGCGAA
* * * *
34983815 GTGGATCGACGATGCAAATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATC
131 GTGGATCGAAGATGCAAATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAAATA
* * * *
34983880 TTGTCTTCATTTATTGGCGTGAAGTAGATCGAAA-ATAGCAGGTCTTGGCTTCCTGCACCAACAG
196 TTGTCTTCATGTATTGACGTGAAGTAGATC-AAAGATAGCAGGTCCTGGCTTCCTACACCAACAG
34983944 TGAAGCA
260 -GAAGCA
34983951 GATCGAAGA
1 GATCGAAGA
34983960 CGTCAGTCCT
Statistics
Matches: 243, Mismatches: 29, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
264 109 0.45
265 134 0.55
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (265 bp):
GATCGAAGATGCAGATCTTATCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAGCAGATCTTG
TCTTCATGTATTGGCGTGAAGTAGATCGAAAATAGCAAATCCTGTCTTCCTATATTGGTAGCGAA
GTGGATCGAAGATGCAAATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAAATA
TTGTCTTCATGTATTGACGTGAAGTAGATCAAAGATAGCAGGTCCTGGCTTCCTACACCAACAGG
AAGCA
Found at i:34984477 original size:19 final size:19
Alignment explanation
Indices: 34984453--34984585 Score: 185
Period size: 19 Copynumber: 6.8 Consensus size: 19
34984443 AATTTTTGAG
34984453 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
34984472 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
34984491 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
34984510 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
34984531 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
**
34984550 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* *
34984569 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
34984586 GATTTAATTT
Statistics
Matches: 103, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
19 72 0.70
20 12 0.12
21 19 0.18
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:34984520 original size:59 final size:59
Alignment explanation
Indices: 34984454--34984585 Score: 221
Period size: 59 Copynumber: 2.3 Consensus size: 59
34984444 ATTTTTGAGG
*
34984454 ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATATGAT
*
34984513 ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATATAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATATGAT
* *
34984572 -TTTGTAATCTTAGA
1 ATATGCAATCTTAGA
34984586 GATTTAATTT
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
58 12 0.17
59 57 0.83
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (59 bp):
ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATATGAT
Found at i:34993497 original size:130 final size:132
Alignment explanation
Indices: 34993249--34993531 Score: 480
Period size: 130 Copynumber: 2.2 Consensus size: 132
34993239 ACCGGTGAAA
*
34993249 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGCAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGCAGATCTTATCTCCCTAA
* * *
34993314 GCAATAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAATGGGAAGCAGATTTGA
66 GCAATAGTGGAACAGATCGAAGACGGCGAATCTCATCTTTCCAAGATAATGGGAAGCAGATTTAA
34993379 GC
131 GC
*
34993381 CACCAAG-CTTG-CTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGCAGATCTTATCTCCCTAA
* * *
34993444 GCAGTAGTGGAACAGATCGAAGACGGCGAATCTCATCTTTTCAAGATAGTGGGAAGCAGATTTAA
66 GCAATAGTGGAACAGATCGAAGACGGCGAATCTCATCTTTCCAAGATAATGGGAAGCAGATTTAA
34993509 GC
131 GC
34993511 CACCAAGCCTTGTCTCCCTGA
1 CACCAAGCCTTGTCTCCCTGA
34993532 AGTGGCAGGG
Statistics
Matches: 141, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
130 118 0.84
131 8 0.06
132 15 0.11
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (132 bp):
CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGCAGATCTTATCTCCCTAA
GCAATAGTGGAACAGATCGAAGACGGCGAATCTCATCTTTCCAAGATAATGGGAAGCAGATTTAA
GC
Found at i:34998752 original size:13 final size:13
Alignment explanation
Indices: 34998733--34998798 Score: 72
Period size: 13 Copynumber: 5.5 Consensus size: 13
34998723 TAGATTTTTC
34998733 CTAAATATTATCA
1 CTAAATATTATCA
*
34998746 ATAAATA--ATC-
1 CTAAATATTATCA
34998756 CTAAATATTATCA
1 CTAAATATTATCA
*
34998769 CTAAATA--AT-T
1 CTAAATATTATCA
34998779 CTAAATATTATCA
1 CTAAATATTATCA
34998792 CTAAATA
1 CTAAATA
34998799 ATTAAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 13 0.30
11 5 0.12
12 5 0.12
13 20 0.47
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:34998759 original size:23 final size:23
Alignment explanation
Indices: 34998731--34998800 Score: 122
Period size: 23 Copynumber: 3.0 Consensus size: 23
34998721 GCTAGATTTT
*
34998731 TCCTAAATATTATCAATAAATAA
1 TCCTAAATATTATCACTAAATAA
34998754 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
*
34998777 TTCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
34998800 T
1 T
34998801 TAAAAATTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (23 bp):
TCCTAAATATTATCACTAAATAA
Found at i:34998954 original size:18 final size:18
Alignment explanation
Indices: 34998931--34998968 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
34998921 AATCTTTATC
*
34998931 CAGTCATCTTTTAGTCTT
1 CAGTCATCTTTGAGTCTT
34998949 CAGTCATCTTTGAGTCTT
1 CAGTCATCTTTGAGTCTT
34998967 CA
1 CA
34998969 TTCTTTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.24, G:0.13, T:0.45
Consensus pattern (18 bp):
CAGTCATCTTTGAGTCTT
Found at i:35004308 original size:26 final size:26
Alignment explanation
Indices: 35004272--35004323 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
35004262 TTTTTGTGCT
35004272 TCAAAACAATCCAAAAACATAAACTC
1 TCAAAACAATCCAAAAACATAAACTC
35004298 TCAAAACAATCCAAAAACATAAACTC
1 TCAAAACAATCCAAAAACATAAACTC
35004324 ATTCTTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.58, C:0.27, G:0.00, T:0.15
Consensus pattern (26 bp):
TCAAAACAATCCAAAAACATAAACTC
Found at i:35011478 original size:29 final size:29
Alignment explanation
Indices: 35011436--35011507 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
35011426 AATGGCAAAA
35011436 TTTTGAAATTATAAAAGTTTCAAGTATGG
1 TTTTGAAATTATAAAAGTTTCAAGTATGG
35011465 TTTTGAAATTATAAAAGTTTCAAGTATGG
1 TTTTGAAATTATAAAAGTTTCAAGTATGG
*
35011494 TCTTGAAATTATAA
1 TTTTGAAATTATAA
35011508 TTTTTTTATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.39, C:0.04, G:0.15, T:0.42
Consensus pattern (29 bp):
TTTTGAAATTATAAAAGTTTCAAGTATGG
Found at i:35035634 original size:12 final size:12
Alignment explanation
Indices: 35035609--35035647 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
35035599 ACTCGCTTCT
* *
35035609 TTACTTACTCAC
1 TTACTTGCTTAC
*
35035621 TTACTTGTTTAC
1 TTACTTGCTTAC
35035633 TTACTTGCTTAC
1 TTACTTGCTTAC
35035645 TTA
1 TTA
35035648 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:35035989 original size:50 final size:50
Alignment explanation
Indices: 35035896--35036037 Score: 169
Period size: 50 Copynumber: 2.8 Consensus size: 50
35035886 TTTTCTGTAC
* * * * * **
35035896 TGCCAATGTCATATCCTAGATATGGTCTTACATGGGAGTTCTCATAC-CGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCAT-CTCGG
* *
35035946 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
35035996 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
35036038 TTACCCAAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
49 1 0.01
50 77 0.99
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:35044846 original size:27 final size:28
Alignment explanation
Indices: 35044828--35044880 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 28
35044818 GCAGCACCAG
* * *
35044828 TGGTGCCAGTGGCAGAGGCAGCACC-GA
1 TGGTGCCACTGCCACAGGCAGCACCAGA
*
35044855 TGGTGCCACTGCCACAGGCTGCACCA
1 TGGTGCCACTGCCACAGGCAGCACCA
35044881 CTCACCTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.21, C:0.32, G:0.34, T:0.13
Consensus pattern (28 bp):
TGGTGCCACTGCCACAGGCAGCACCAGA
Found at i:35044954 original size:4 final size:4
Alignment explanation
Indices: 35044945--35045003 Score: 50
Period size: 4 Copynumber: 14.0 Consensus size: 4
35044935 GAAAGGAGAG
35044945 GAAA GAAA GAAA G-AA -AAA GAAA GAAA GAAAA GGAAA GGAAA GGAGAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA -GAAA -GA-AA
*
35044992 GAAA AAAA GAAA
1 GAAA GAAA GAAA
35045004 AAGAAAGGAG
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
3 4 0.08
4 25 0.52
5 16 0.33
6 3 0.06
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:35044963 original size:14 final size:14
Alignment explanation
Indices: 35044946--35045010 Score: 85
Period size: 14 Copynumber: 4.6 Consensus size: 14
35044936 AAAGGAGAGG
35044946 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
35044960 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
* *
35044974 AAGGAAAGGAAAGGA
1 AAAGAAA-GAAAGAA
* *
35044989 GAAGAAAAAAAGAA
1 AAAGAAAGAAAGAA
35045003 AAAGAAAG
1 AAAGAAAG
35045011 GAGAAGAAGA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
14 31 0.74
15 11 0.26
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAAAGAA
Found at i:35044981 original size:5 final size:5
Alignment explanation
Indices: 35044934--35044988 Score: 53
Period size: 5 Copynumber: 11.6 Consensus size: 5
35044924 AAATGGAGAG
* * * *
35044934 GGAAA GGAGA GGAAA -GAAA -GAAA GAAAA AGAAA -GAAA GAAAA GGAAA
1 GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA
35044981 GGAAA GGA
1 GGAAA GGA
35044989 GAAGAAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
4 12 0.29
5 29 0.71
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (5 bp):
GGAAA
Found at i:35044995 original size:29 final size:30
Alignment explanation
Indices: 35044946--35045023 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
35044936 AAAGGAGAGG
* *
35044946 AAAGAAA-GA-AAGAAAAAGAAAGAAAGAA
1 AAAGAAAGGAGAAGAAGAAGAAAAAAAGAA
* *
35044974 AAGGAAAGGA-AAGGAGAAGAAAAAAAGAA
1 AAAGAAAGGAGAAGAAGAAGAAAAAAAGAA
35045003 AAAGAAAGGAGAAGAAGAAGA
1 AAAGAAAGGAGAAGAAGAAGA
35045024 GGGAAGGAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 6 0.14
29 27 0.64
30 9 0.21
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (30 bp):
AAAGAAAGGAGAAGAAGAAGAAAAAAAGAA
Found at i:35044999 original size:24 final size:24
Alignment explanation
Indices: 35044934--35045032 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
35044924 AAATGGAGAG
* *
35044934 GGAAAGGAGAGGAAAGAAA-GAAA
1 GGAAAGGAGAAGAAAAAAAGGAAA
* *
35044957 GAAAAAGA-AAGAAAGAAAAGGAAA
1 GGAAAGGAGAAGAAA-AAAAGGAAA
*
35044981 GGAAAGGAGAAGAAAAAAAGAAAA
1 GGAAAGGAGAAGAAAAAAAGGAAA
* * * *
35045005 AGAAAGGAGAAGAAGAAGAGGGAA
1 GGAAAGGAGAAGAAAAAAAGGAAA
35045029 GGAA
1 GGAA
35045033 GGAAAACGAA
Statistics
Matches: 60, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
22 5 0.08
23 9 0.15
24 40 0.67
25 6 0.10
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (24 bp):
GGAAAGGAGAAGAAAAAAAGGAAA
Found at i:35045018 original size:53 final size:53
Alignment explanation
Indices: 35044950--35045052 Score: 120
Period size: 53 Copynumber: 1.9 Consensus size: 53
35044940 GAGAGGAAAG
* *
35044950 AAAGAAAGAAAAAGAAAGAA-AGAAAAGGAAAGG-AAAGGAGAAGAAAAAAAGAA
1 AAAGAAAGAAAAAG-AAGAAGAGAAAAGG-AAGGAAAACGAAAAGAAAAAAAGAA
* * **
35045003 AAAGAAAGGAGAAGAAGAAGAGGGAAGGAAGGAAAACGAAAAGAAAAAAA
1 AAAGAAAGAAAAAGAAGAAGAGAAAAGGAAGGAAAACGAAAAGAAAAAAA
35045053 AGAACTAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
52 9 0.21
53 33 0.79
ACGTcount: A:0.70, C:0.01, G:0.29, T:0.00
Consensus pattern (53 bp):
AAAGAAAGAAAAAGAAGAAGAGAAAAGGAAGGAAAACGAAAAGAAAAAAAGAA
Found at i:35045029 original size:13 final size:13
Alignment explanation
Indices: 35044935--35045021 Score: 50
Period size: 10 Copynumber: 7.2 Consensus size: 13
35044925 AATGGAGAGG
*
35044935 GAAAGGAGAGGAAA
1 GAAAGGAGAAG-AA
35044949 GAAA-GA-AAGAA
1 GAAAGGAGAAGAA
35044960 -AAA-GA-AAGAAA
1 GAAAGGAGAAG-AA
35044971 GAAAAGGA-AAG--
1 G-AAAGGAGAAGAA
35044982 GAAAGGAGAAGAA
1 GAAAGGAGAAGAA
* *
35044995 -AAA-AAGAAAAA
1 GAAAGGAGAAGAA
35045006 GAAAGGAGAAGAA
1 GAAAGGAGAAGAA
35045019 GAA
1 GAA
35045022 GAGGGAAGGA
Statistics
Matches: 59, Mismatches: 5, Indels: 19
0.71 0.06 0.23
Matches are distributed among these distances:
10 14 0.24
11 14 0.24
12 8 0.14
13 14 0.24
14 9 0.15
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
GAAAGGAGAAGAA
Found at i:35045752 original size:156 final size:155
Alignment explanation
Indices: 35045390--35046229 Score: 790
Period size: 156 Copynumber: 5.6 Consensus size: 155
35045380 AAAAATTATA
35045390 TATTT-AAAAACACACTAAA-TTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAAT
1 TATTTAAAAAACACACTAAATTTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAAT
* * *
35045453 AAAATTCAAAAAT-ATGATA-TTTT-TT-AAAGTAATAAAATGCAGAGAAAAAAATACGAACAAA
66 AAAATACGAAAATAAT-ATATTTTTATTGAAAGTAATAAAAT--AG-GGAAAAAATACGAACAAA
* *
35045514 TGGCCGAAGTAAAGGTTTTTTACTAAATT
127 GGGCCGAAATAAAGGTTTTTTACTAAATT
* * * * *
35045543 TA---AAAAAA-ATA-GAAATAATTAATACATTTAAAACATAATGTACTAAAATAATGTAAAAAA
1 TATTTAAAAAACACACTAAAT--TTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATA
* *
35045603 ATAAAATACGAAAATAATATATTTTTATTGAAAGTAGTAAAAATAGGGAAAAAATACGAGCAAAG
64 ATAAAATACGAAAATAATATATTTTTATTGAAAGTAAT-AAAATAGGGAAAAAATACGAACAAAG
* * * *
35045668 GGTCGAAATGAGGGTTTTTT-TTAAATT
128 GGCCGAAATAAAGGTTTTTTACTAAATT
* *
35045695 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATATACTAAAATAATGTAAAATAA
1 TATTTAAAAAACACACTAAATTTA-ATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
* * *
35045760 TAAAATTA-GAAAATAGTATA-TTTT-TTAAAAGTAATAAAATTCGGGAAAAAATACGAACAAAG
65 TAAAA-TACGAAAATAATATATTTTTATTGAAAGTAATAAAA-TAGGGAAAAAATACGAACAAAG
*
35045822 GGCCGAAATAAGGGTTTTTTACTAAA-T
128 GGCCGAAATAAAGGTTTTTTACTAAATT
* * * * * * * *
35045849 T-TTAAAAAAATAGAATTAA-TTAATAAATTTCTAACATAATGTACTAAGATAAAGTAAAATAAT
1 TATTTAAAAAACACACTAAATTTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAAT
** *
35045912 AAAATACG-AAATAATATATTTTTATTGAAAGTAATAAAATTCGGAAAAATATAACGAGCAAAGG
66 AAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAATAGGGAAAAA-AT-ACGAACAAAGG
*
35045976 GTCGAAATAAAGGTTTTTT--TAAAATT
129 GCCGAAATAAAGGTTTTTTACT-AAATT
*
35046002 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
1 TATTTAAAAAACACACTAAATTTA-ATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
* * *
35046067 TAAAATTA-GAAAAT-ATGATA--TTT-TT-AAAGTAAT-AAA-AGGCGGAGAAA-A--AA-ATA
65 TAAAA-TACGAAAATAAT-ATATTTTTATTGAAAGTAATAAAATAGG-GAAAAAATACGAACAAA
* *
35046120 ----CG-AATAAAAGTTTTTTAGT-AATT
127 GGGCCGAAATAAAGGTTTTTTACTAAATT
** * * * * * * *
35046143 T-TAAAAAAAAAAGAATTAA-TTAATACATTTCAAACATAATGTACTAAGATAAAGTAAAATAAT
1 TATTTAAAAAACACACTAAATTTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAAT
35046206 AAAATACGAAAATAATATTATTTT
66 AAAATACGAAAATAATA-TATTTT
35046230 CAGGAAAAAA
Statistics
Matches: 574, Mismatches: 74, Indels: 90
0.78 0.10 0.12
Matches are distributed among these distances:
137 2 0.00
138 48 0.08
139 7 0.01
140 12 0.02
141 20 0.03
142 2 0.00
143 1 0.00
146 2 0.00
147 1 0.00
149 4 0.01
150 13 0.02
151 61 0.11
152 92 0.16
153 94 0.16
154 68 0.12
155 30 0.05
156 102 0.18
157 15 0.03
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.31
Consensus pattern (155 bp):
TATTTAAAAAACACACTAAATTTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAAT
AAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAATAGGGAAAAAATACGAACAAAGGGC
CGAAATAAAGGTTTTTTACTAAATT
Found at i:35045971 original size:307 final size:305
Alignment explanation
Indices: 35045390--35046229 Score: 1214
Period size: 307 Copynumber: 2.8 Consensus size: 305
35045380 AAAAATTATA
*
35045390 TATTT-AAAAACACACTAAA-TTA-ATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
1 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
*
35045452 TAAAATTCA-AAAATATGATATTTTTTAAAGTAATAAAATGCAGAGAAAAAAATACGAACAAATG
66 TAAAATT-AGAAAATATGATATTTTTTAAAGTAATAAAATGC-G-GGAAAAAATACGAACAAA-G
* * * *
35045516 GCCGAAGTAAAGGTTTTTTACTAAATTTAAAAAAAATAGAAATAATTAATACATTTAAAACATAA
127 GCCGAAATAAAGGTTTTTTACTAAATTTTAAAAAAATAGAATTAATTAATACATTTCAAACATAA
* * * *
35045581 TGTACTAAAATAATGTAAAAAAATAAAATACGAAAATAATATATTTTTATTGAAAGTAGTAAAAA
192 TGTACTAAGATAAAGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAAA
* * * *
35045646 TAGGGAAAAAATACGAGCAAAGGGTCGAAATGAGGGTTTTTTTTAAATT
257 TACGGAAAAAATACGAGCAAAGGGTCGAAATAAAGGTTTTTTTAAAATT
*
35045695 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATATACTAAAATAATGTAAAATAA
1 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
*
35045760 TAAAATTAGAAAATA-GTATATTTTTTAAAAGTAATAAAATTCGGGAAAAAATACGAACAAAGGG
66 TAAAATTAGAAAATATG-ATATTTTTT-AAAGTAATAAAATGCGGGAAAAAATACGAACAAA-GG
* * *
35045824 CCGAAATAAGGGTTTTTTACTAAATTTTAAAAAAATAGAATTAATTAATAAATTTCTAACATAAT
128 CCGAAATAAAGGTTTTTTACTAAATTTTAAAAAAATAGAATTAATTAATACATTTCAAACATAAT
35045889 GTACTAAGATAAAGTAAAATAATAAAATACG-AAATAATATATTTTTATTGAAAGTAAT-AAAAT
193 GTACTAAGATAAAGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAAAT
*
35045952 TCGGAAAAATATAACGAGCAAAGGGTCGAAATAAAGGTTTTTTTAAAATT
258 ACGGAAAAA-AT-ACGAGCAAAGGGTCGAAATAAAGGTTTTTTTAAAATT
35046002 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
1 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
* * *
35046067 TAAAATTAGAAAATATGATA-TTTTTAAAGTAATAAAAGGC-GG-AGAAA-A--AA-ATA---CG
66 TAAAATTAGAAAATATGATATTTTTTAAAGTAATAAAATGCGGGAAAAAATACGAACAAAGGCCG
* * *
35046122 -AATAAAAGTTTTTTAGT-AATTTTAAAAAAAAAAGAATTAATTAATACATTTCAAACATAATGT
131 AAATAAAGGTTTTTTACTAAATTTT-AAAAAAATAGAATTAATTAATACATTTCAAACATAATGT
35046185 ACTAAGATAAAGTAAAATAATAAAATACGAAAATAATATTATTTT
195 ACTAAGATAAAGTAAAATAATAAAATACGAAAATAATA-TATTTT
35046230 CAGGAAAAAA
Statistics
Matches: 491, Mismatches: 32, Indels: 33
0.88 0.06 0.06
Matches are distributed among these distances:
293 6 0.01
294 79 0.16
295 10 0.02
296 6 0.01
299 2 0.00
300 2 0.00
302 1 0.00
303 4 0.01
304 2 0.00
305 30 0.06
306 47 0.10
307 226 0.46
308 62 0.13
309 14 0.03
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.31
Consensus pattern (305 bp):
TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
TAAAATTAGAAAATATGATATTTTTTAAAGTAATAAAATGCGGGAAAAAATACGAACAAAGGCCG
AAATAAAGGTTTTTTACTAAATTTTAAAAAAATAGAATTAATTAATACATTTCAAACATAATGTA
CTAAGATAAAGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAAATACG
GAAAAAATACGAGCAAAGGGTCGAAATAAAGGTTTTTTTAAAATT
Found at i:35046289 original size:26 final size:28
Alignment explanation
Indices: 35046235--35046292 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
35046225 ATTTTCAGGA
* *
35046235 AAAAATATATTTTTATTTAAATTTCAAT
1 AAAAATATATTTTTATTGAAATGTCAAT
35046263 AAAAATATATTTTTATTGAAA-GT-AAT
1 AAAAATATATTTTTATTGAAATGTCAAT
35046289 AAAA
1 AAAA
35046293 TTCGGGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 7 0.25
27 1 0.04
28 20 0.71
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (28 bp):
AAAAATATATTTTTATTGAAATGTCAAT
Found at i:35048144 original size:12 final size:12
Alignment explanation
Indices: 35048123--35048169 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
35048113 AGATCATGAT
*
35048123 CCCGAACCAGAG
1 CCCGAGCCAGAG
*
35048135 CCCGAGCCAGAA
1 CCCGAGCCAGAG
*
35048147 CCCGAGTCAGAG
1 CCCGAGCCAGAG
35048159 CCCGAGCCAGA
1 CCCGAGCCAGA
35048170 TCCTGAGCAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.30, C:0.40, G:0.28, T:0.02
Consensus pattern (12 bp):
CCCGAGCCAGAG
Found at i:35048755 original size:77 final size:77
Alignment explanation
Indices: 35048669--35049244 Score: 999
Period size: 77 Copynumber: 7.4 Consensus size: 77
35048659 TTTTTATATC
*
35048669 ATTTTAATTATTCCAAATGAATTTTACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
1 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
*
35048734 ATAAGCTAAATA
66 ATAAGCTGAATA
35048746 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
1 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
*
35048811 ATAAACTGAATA
66 ATAAGCTGAATA
*
35048823 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAAC
1 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
*
35048888 ATAAGCTAAATA
66 ATAAGCTGAATA
* * *
35048900 GTTTTAATTTTTCCAAATGAATTATATTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
1 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
*
35048965 ATAAACTGAATA
66 ATAAGCTGAATA
35048977 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
1 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
35049042 ATAAGCTGAATA
66 ATAAGCTGAATA
*
35049054 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGT
1 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
*
35049119 ATAAACTGAATA
66 ATAAGCTGAATA
* *
35049131 ATTTTAATTATTCCAAATGAATTATATTTTTTATAACTTACTTAATTTGAATACAATTTAAGCAT
1 ATTTTAATTATTCCAAATGAATTATACTTTTTAT-A---ACTTAATTTGGATACAATTTAAGCAT
35049196 AAGCATAAGCTGAATA
62 AAGCATAAGCTGAATA
35049212 ATTTTAATTATTCCAAATGAATTATACTTTTTA
1 ATTTTAATTATTCCAAATGAATTATACTTTTTA
35049245 CAACATTACA
Statistics
Matches: 472, Mismatches: 23, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
77 400 0.85
78 1 0.00
81 71 0.15
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.42
Consensus pattern (77 bp):
ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
ATAAGCTGAATA
Found at i:35052189 original size:39 final size:41
Alignment explanation
Indices: 35052140--35052351 Score: 126
Period size: 40 Copynumber: 5.4 Consensus size: 41
35052130 ACTAACACAA
* *
35052140 TAACAATAATAA-TA-GTTTTATACTCAAAATAAT-ACTAAC
1 TAACAATAATAATTAGGGTTT-TACTAAAAATAATAACTAAC
*
35052179 TAACCATAATAATTAGGGTTTTACTAAAAATAATAACTAAC
1 TAACAATAATAATTAGGGTTTTACTAAAAATAATAACTAAC
* *** * *
35052220 -AATAAT-ATAA-T---GTAAAAACTAACAATCAT-ACTAAC
1 TAACAATAATAATTAGGGT-TTTACTAAAAATAATAACTAAC
***
35052255 TAA-AATAATAATTAGGGTTTTTACTAATCCTAATAACTAACC
1 TAACAATAATAATTAGGG-TTTTACTAAAAATAATAACTAA-C
* ** * *
35052297 ATAATAATAAT-ATTAGTTTTTTACTAACAATAAT-ACTAAG
1 -TAACAATAATAATTAGGGTTTTACTAAAAATAATAACTAAC
*
35052337 TAACAATAATTATTA
1 TAACAATAATAATTA
35052352 ATAACTAAAC
Statistics
Matches: 133, Mismatches: 24, Indels: 31
0.71 0.13 0.16
Matches are distributed among these distances:
35 11 0.08
36 16 0.12
37 1 0.01
38 1 0.01
39 24 0.18
40 31 0.23
41 21 0.16
42 14 0.11
43 8 0.06
44 6 0.05
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.34
Consensus pattern (41 bp):
TAACAATAATAATTAGGGTTTTACTAAAAATAATAACTAAC
Found at i:35052258 original size:23 final size:23
Alignment explanation
Indices: 35052213--35052259 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
35052203 TAAAAATAAT
*
35052213 AACTAACAATAATATAATGTAAA
1 AACTAACAATAATATAATCTAAA
*
35052236 AACTAACAATCATACTAA-CTAAA
1 AACTAACAATAATA-TAATCTAAA
35052259 A
1 A
35052260 TAATAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.60, C:0.15, G:0.02, T:0.23
Consensus pattern (23 bp):
AACTAACAATAATATAATCTAAA
Found at i:35052591 original size:3 final size:3
Alignment explanation
Indices: 35052585--35052630 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
35052575 CCTCCTCCTC
35052585 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT -TT -TT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
35052631 TTCCTTCAGC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
CTT
Found at i:35053574 original size:31 final size:30
Alignment explanation
Indices: 35053508--35053577 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 30
35053498 TAATTTTTTA
*
35053508 AAAAAATTATAAAAATTATTTTTAAAAATTT
1 AAAAAATTATAAAAAATATTTTT-AAAATTT
35053539 -AAAAATTATAAAAAACATATTTTT-AAATTT
1 AAAAAATTAT-AAAAA-ATATTTTTAAAATTT
35053569 AAAAAATTA
1 AAAAAATTA
35053578 ATTAATTTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
30 15 0.43
31 13 0.37
32 7 0.20
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (30 bp):
AAAAAATTATAAAAAATATTTTTAAAATTT
Found at i:35054244 original size:20 final size:22
Alignment explanation
Indices: 35054221--35054272 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 22
35054211 GCCCAAACTT
35054221 AATATATTATATA-TAAAC-CC
1 AATATATTATATACTAAACTCC
35054241 AATATGTATTATATATCTAAACTCC
1 AATA--TATTATATA-CTAAACTCC
35054266 AATATAT
1 AATATAT
35054273 ATAAACTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 4 0.15
22 9 0.33
23 3 0.11
24 5 0.19
25 6 0.22
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.38
Consensus pattern (22 bp):
AATATATTATATACTAAACTCC
Found at i:35054253 original size:22 final size:24
Alignment explanation
Indices: 35054225--35054270 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
35054215 AAACTTAATA
35054225 TATTATATA-TAAAC-CCAATATG
1 TATTATATACTAAACTCCAATATG
35054247 TATTATATATCTAAACTCCAATAT
1 TATTATATA-CTAAACTCCAATAT
35054271 ATATAAACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.43
24 5 0.24
25 7 0.33
ACGTcount: A:0.43, C:0.15, G:0.02, T:0.39
Consensus pattern (24 bp):
TATTATATACTAAACTCCAATATG
Found at i:35054275 original size:22 final size:21
Alignment explanation
Indices: 35054221--35054275 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 21
35054211 GCCCAAACTT
35054221 AATATAT-TATATATAAACCC
1 AATATATATATATATAAACCC
*
35054241 AATATGTATTATATATCTAAACTCC
1 AATA--TA-TATATATATAAAC-CC
35054266 AATATATATA
1 AATATATATA
35054276 AACTGAATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
20 4 0.14
22 6 0.21
23 3 0.10
24 10 0.34
25 6 0.21
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.38
Consensus pattern (21 bp):
AATATATATATATATAAACCC
Found at i:35056941 original size:22 final size:23
Alignment explanation
Indices: 35056898--35056942 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
35056888 AAGTTGAATT
*
35056898 TAAAGTTATGAATTATATATATA
1 TAAAGTTATGAATTATAGATATA
35056921 TAAAGTT-TGAATGTAT-GATATA
1 TAAAGTTATGAAT-TATAGATATA
35056943 AGTTCTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (23 bp):
TAAAGTTATGAATTATAGATATA
Found at i:35057047 original size:65 final size:66
Alignment explanation
Indices: 35056977--35057192 Score: 216
Period size: 64 Copynumber: 3.4 Consensus size: 66
35056967 TATGAATTAT
* * * * * * *
35056977 ATATATATGCACATATGGTTCGAATATATATATT-TAAAGTTCTTGAGCTGTATTTAATGTATGA
1 ATATATATACATATGTGGTTCGAATATATAGATTACAAAGTTCTTGAGCGGAATTTAATGTATGA
35057041 A
66 A
* *
35057042 ATATATATACATATGTGGTTC-AA-ATATAGGTTACAAAGTTTTTGAGCGGAATTTAATGTATGA
1 ATATATATACATATGTGGTTCGAATATATAGATTACAAAGTTCTTGAGCGGAATTTAATGTATGA
35057105 A
66 A
* * * * *
35057106 TTTTACATACATATGTGGTTCG-A-ATATAGGTTACAAA-TTCTTTGAGCTGAAATTTAATGT-T
1 ATATATATACATATGTGGTTCGAATATATAGATTACAAAGTTC-TTGAGC-GGAATTTAATGTAT
*
35057167 GTA
64 GAA
35057170 A-AT-TATACATATGTGGTTCGAAT
1 ATATATATACATATGTGGTTCGAAT
35057193 GTTTGTTTGA
Statistics
Matches: 127, Mismatches: 18, Indels: 13
0.80 0.11 0.08
Matches are distributed among these distances:
62 16 0.13
63 11 0.09
64 71 0.56
65 29 0.23
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (66 bp):
ATATATATACATATGTGGTTCGAATATATAGATTACAAAGTTCTTGAGCGGAATTTAATGTATGA
A
Found at i:35057099 original size:64 final size:64
Alignment explanation
Indices: 35057012--35057188 Score: 227
Period size: 64 Copynumber: 2.8 Consensus size: 64
35057002 ATATATATTT
* * *
35057012 AAAGTTCTTGAGCTGTATTTAATGTATGAAATATATATACATATGTGGTTCAAATATAGGTTAC
1 AAAGTTTTTGAGCGGAATTTAATGTATGAAATATATATACATATGTGGTTCAAATATAGGTTAC
* * * *
35057076 AAAGTTTTTGAGCGGAATTTAATGTATGAATTTTACATACATATGTGGTTCGAATATAGGTTAC
1 AAAGTTTTTGAGCGGAATTTAATGTATGAAATATATATACATATGTGGTTCAAATATAGGTTAC
* *
35057140 AAA-TTCTTTGAGCTGAAATTTAATGT-TGTAA-AT-TATACATATGTGGTTC
1 AAAGTT-TTTGAGC-GGAATTTAATGTATGAAATATATATACATATGTGGTTC
35057189 GAATGTTTGT
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
62 15 0.15
63 3 0.03
64 70 0.71
65 11 0.11
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (64 bp):
AAAGTTTTTGAGCGGAATTTAATGTATGAAATATATATACATATGTGGTTCAAATATAGGTTAC
Found at i:35057411 original size:41 final size:41
Alignment explanation
Indices: 35057308--35057414 Score: 160
Period size: 41 Copynumber: 2.6 Consensus size: 41
35057298 ATCTGAGATT
* * * *
35057308 TTCAGGCTTAATGCCTAGCAGACTTGATGTCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGGCTTGATGTCGGTGAATTAC
* *
35057349 TTCAGACTTTATGTCTAGCAGGCTTGATGTCGTTGAATTTC
1 TTCAGACTTTATGTCTAGCAGGCTTGATGTCGGTGAATTAC
35057390 TTCAGACTTTATGTCTAGCAGGCTT
1 TTCAGACTTTATGTCTAGCAGGCTT
35057415 TGTGCCGATG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (41 bp):
TTCAGACTTTATGTCTAGCAGGCTTGATGTCGGTGAATTAC
Found at i:35064512 original size:22 final size:22
Alignment explanation
Indices: 35064486--35064529 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
35064476 TTACAATTCT
*
35064486 TGAATATATCTTAATAATCAAC
1 TGAATATATCTTAACAATCAAC
*
35064508 TGAATATATTTTAACAATCAAC
1 TGAATATATCTTAACAATCAAC
35064530 AGATCATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (22 bp):
TGAATATATCTTAACAATCAAC
Found at i:35081507 original size:54 final size:54
Alignment explanation
Indices: 35081448--35081615 Score: 207
Period size: 54 Copynumber: 3.1 Consensus size: 54
35081438 AATCATGAGT
* *
35081448 AAATGA-CTGAATTACCCTCGAAGGGTAAAATGATTGAATTACCCTTAAAGGGTA
1 AAATGATC-GAATTACCCCCGAAGGGTAAAATGATTGAATTACCCTCAAAGGGTA
* * *
35081502 AAATGATCGAATTACCCCCGAAGGGAAAAATGATCGAATTACCCCCGAAA-GGTA
1 AAATGATCGAATTACCCCCGAAGGGTAAAATGATTGAATTACCCTC-AAAGGGTA
* * * *
35081556 AAATGATCAAATTACCCCCGAAGGGTAAAATGACAT-AAATACCCTCATAGGGTA
1 AAATGATCGAATTACCCCCGAAGGGTAAAATGA-TTGAATTACCCTCAAAGGGTA
35081610 AAATGA
1 AAATGA
35081616 CTGTTATACC
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
53 2 0.02
54 92 0.94
55 4 0.04
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (54 bp):
AAATGATCGAATTACCCCCGAAGGGTAAAATGATTGAATTACCCTCAAAGGGTA
Found at i:35081599 original size:27 final size:27
Alignment explanation
Indices: 35081448--35081588 Score: 194
Period size: 27 Copynumber: 5.2 Consensus size: 27
35081438 AATCATGAGT
*
35081448 AAATGA-CTGAATTACCCTCGAAGGGTA
1 AAATGATC-GAATTACCCCCGAAGGGTA
* ***
35081475 AAATGATTGAATTACCCTTAAAGGGTA
1 AAATGATCGAATTACCCCCGAAGGGTA
*
35081502 AAATGATCGAATTACCCCCGAAGGGAA
1 AAATGATCGAATTACCCCCGAAGGGTA
*
35081529 AAATGATCGAATTACCCCCGAAAGGTA
1 AAATGATCGAATTACCCCCGAAGGGTA
*
35081556 AAATGATCAAATTACCCCCGAAGGGTA
1 AAATGATCGAATTACCCCCGAAGGGTA
35081583 AAATGA
1 AAATGA
35081589 CATAAATACC
Statistics
Matches: 101, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
27 101 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (27 bp):
AAATGATCGAATTACCCCCGAAGGGTA
Found at i:35081599 original size:81 final size:81
Alignment explanation
Indices: 35081448--35081618 Score: 195
Period size: 81 Copynumber: 2.1 Consensus size: 81
35081438 AATCATGAGT
* * ** **
35081448 AAATGACTGAATTACCCTCGAAGGGTAAAATGATTGAATTACCCTTAAAGGGTAAAATGATCGAA
1 AAATGACTGAATTACCCCCGAAAGGTAAAATGATCAAATTACCCCCAAAGGGTAAAATGATCGAA
*
35081513 TTACCCCCGAAGGGAA
66 ATACCCCCGAAGGGAA
* *
35081529 AAATGA-TCGAATTACCCCCGAAAGGTAAAATGATCAAATTACCCCCGAAGGGTAAAATGA-CAT
1 AAATGACT-GAATTACCCCCGAAAGGTAAAATGATCAAATTACCCCCAAAGGGTAAAATGATC-G
* *
35081592 AAATACCCTC-ATAGGGTA
64 AAATACCCCCGA-AGGGAA
35081610 AAATGACTG
1 AAATGACTG
35081619 TTATACCCCT
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
80 3 0.04
81 71 0.95
82 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (81 bp):
AAATGACTGAATTACCCCCGAAAGGTAAAATGATCAAATTACCCCCAAAGGGTAAAATGATCGAA
ATACCCCCGAAGGGAA
Found at i:35081607 original size:27 final size:26
Alignment explanation
Indices: 35081495--35081616 Score: 120
Period size: 27 Copynumber: 4.5 Consensus size: 26
35081485 ATTACCCTTA
* *
35081495 AAGGGTAAAATGATCGAATTACCCCCG
1 AAGGGTAAAATGA-CAAAATACCCCCG
* * *
35081522 AAGGGAAAAATGATCGAATTACCCCCG
1 AAGGGTAAAATGA-CAAAATACCCCCG
* *
35081549 AAAGGTAAAATGATCAAATTACCCCCG
1 AAGGGTAAAATGA-CAAAATACCCCCG
*
35081576 AAGGGTAAAATGACATAAATACCCTC-
1 AAGGGTAAAATGACA-AAATACCCCCG
35081602 ATAGGGTAAAATGAC
1 A-AGGGTAAAATGAC
35081617 TGTTATACCC
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
26 3 0.03
27 83 0.97
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.18
Consensus pattern (26 bp):
AAGGGTAAAATGACAAAATACCCCCG
Found at i:35081791 original size:27 final size:26
Alignment explanation
Indices: 35081769--35081826 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
35081759 TGTACTGGTG
35081769 GCTTTACCACATATACTGTTACTGGCA
1 GCTTTACCACAT-TACTGTTACTGGCA
* * *
35081796 GCTTTGCTACATTACTGTTAATGGCA
1 GCTTTACCACATTACTGTTACTGGCA
35081822 GCTTT
1 GCTTT
35081827 GTTGCATCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 18 0.64
27 10 0.36
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.38
Consensus pattern (26 bp):
GCTTTACCACATTACTGTTACTGGCA
Found at i:35081820 original size:26 final size:26
Alignment explanation
Indices: 35081777--35081855 Score: 95
Period size: 26 Copynumber: 3.0 Consensus size: 26
35081767 TGGCTTTACC
35081777 ACATATACTGTTACTGGCAGCTTTGCT
1 ACAT-TACTGTTACTGGCAGCTTTGCT
* *
35081804 ACATTACTGTTAATGGCAGCTTTGTT
1 ACATTACTGTTACTGGCAGCTTTGCT
* * * *
35081830 GCATCACTATTACTAGCAGCTTTGCT
1 ACATTACTGTTACTGGCAGCTTTGCT
35081856 GCAATATTGG
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 40 0.91
27 4 0.09
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.38
Consensus pattern (26 bp):
ACATTACTGTTACTGGCAGCTTTGCT
Found at i:35082466 original size:28 final size:28
Alignment explanation
Indices: 35082424--35082478 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
35082414 ATTGTATTGA
*
35082424 TTACTGTATTAGGCTAAGGCCCACACTG
1 TTACTGTAATAGGCTAAGGCCCACACTG
*
35082452 TTACTGTAATGGGCTAAGGCCCACACT
1 TTACTGTAATAGGCTAAGGCCCACACT
35082479 ATACTGATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (28 bp):
TTACTGTAATAGGCTAAGGCCCACACTG
Found at i:35084319 original size:26 final size:25
Alignment explanation
Indices: 35084277--35084352 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 25
35084267 AATATTTTCT
*
35084277 CAAAATTTTACCAGGGGTAAAATCAC
1 CAAAATTTTA-CGGGGGTAAAATCAC
*
35084303 CAAATATTTTACGGGGGTAAAATCAT
1 CAAA-ATTTTACGGGGGTAAAATCAC
*
35084329 CAAAACTTTACTGGGGGGTAAAAT
1 CAAAATTTTAC--GGGGGTAAAAT
35084353 AGGGATGAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
25 6 0.14
26 21 0.48
27 17 0.39
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.26
Consensus pattern (25 bp):
CAAAATTTTACGGGGGTAAAATCAC
Found at i:35086014 original size:19 final size:20
Alignment explanation
Indices: 35085990--35086035 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
35085980 GTTGAAAAAG
35085990 TTTCAAT-TGTGTTAAACAT
1 TTTCAATGTGTGTTAAACAT
* *
35086009 TTTCAAATGTGTTTTAACCAT
1 TTTC-AATGTGTGTTAAACAT
35086030 TTTCAA
1 TTTCAA
35086036 ATAAGTCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.17
20 5 0.22
21 14 0.61
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.48
Consensus pattern (20 bp):
TTTCAATGTGTGTTAAACAT
Found at i:35086122 original size:22 final size:22
Alignment explanation
Indices: 35086063--35086111 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
35086053 CAGAACAAAA
* *
35086063 AAGTACCGATACTTTTTTCTCT
1 AAGTATCGATATTTTTTTCTCT
*
35086085 AAGTATCGATATTTTTTTGTCT
1 AAGTATCGATATTTTTTTCTCT
35086107 AAGTA
1 AAGTA
35086112 ATTATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (22 bp):
AAGTATCGATATTTTTTTCTCT
Found at i:35086236 original size:20 final size:20
Alignment explanation
Indices: 35086213--35086251 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35086203 TATCAATACT
*
35086213 TTTCTTAAAGTATCGATATA
1 TTTCCTAAAGTATCGATATA
*
35086233 TTTCCTAAGGTATCGATAT
1 TTTCCTAAAGTATCGATAT
35086252 TCTTGATCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (20 bp):
TTTCCTAAAGTATCGATATA
Found at i:35087485 original size:35 final size:35
Alignment explanation
Indices: 35087423--35087508 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
35087413 ATTTTATTTG
*
35087423 TTTA-ATTATATAATTAATGATATTTAAA-TATAA
1 TTTATATTATATAATTAATGATAATTAAATTATAA
*
35087456 TTTATATTATATGAATTTATGATAATTAAATTATAA
1 TTTATATTATAT-AATTAATGATAATTAAATTATAA
* *
35087492 -TGATATTATATTATTAA
1 TTTATATTATATAATTAA
35087509 ATAAATCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 4 0.09
34 11 0.24
35 25 0.56
36 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (35 bp):
TTTATATTATATAATTAATGATAATTAAATTATAA
Found at i:35087494 original size:25 final size:23
Alignment explanation
Indices: 35087450--35087510 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
35087440 TGATATTTAA
*
35087450 ATATAATTTATATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
35087474 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
35087499 ATATTATTAAAT
1 ATATAATTAAAT
35087511 AAATCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:35088833 original size:3 final size:3
Alignment explanation
Indices: 35088813--35088889 Score: 136
Period size: 3 Copynumber: 25.7 Consensus size: 3
35088803 GTGAGGTAAG
* *
35088813 TAT TAA TAT TAG 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
35088861 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
35088890 ATATGAGTAG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:35089077 original size:24 final size:27
Alignment explanation
Indices: 35089040--35089103 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
35089030 AATTGCGGAT
*
35089040 TAATTATTG-ATTGAAAG-GTG-GAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
35089064 -AATGATTGAATTGAAAGTGTGAGAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
**
35089090 TTGTGATTGAATTG
1 TAATGATTGAATTG
35089104 GGATTATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 3 0.09
26 4 0.12
27 11 0.33
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (27 bp):
TAATGATTGAATTGAAAGTGTGAGAAA
Found at i:35089337 original size:39 final size:37
Alignment explanation
Indices: 35089248--35089343 Score: 104
Period size: 39 Copynumber: 2.5 Consensus size: 37
35089238 CAGATAGATT
* * *
35089248 CGATGAGGTACTGGGTACCAACTTTCTTCAACTTTGC
1 CGATGAGGCACTGGGTGCCAACTTTCTTCAACTATGC
* * *
35089285 TGATGAGACACTGGGTGTCAACTATTGCTTCGAACTAT-C
1 CGATGAGGCACTGGGTGCCAACT-TT-CTTC-AACTATGC
35089324 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
35089344 TTCTGGTGTG
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
37 18 0.38
38 2 0.04
39 22 0.47
40 5 0.11
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (37 bp):
CGATGAGGCACTGGGTGCCAACTTTCTTCAACTATGC
Found at i:35093093 original size:11 final size:12
Alignment explanation
Indices: 35093077--35093106 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
35093067 AAATTGTTTA
35093077 TAAACTA-TAAT
1 TAAACTATTAAT
35093088 TAAACTATTAAT
1 TAAACTATTAAT
35093100 TAAACTA
1 TAAACTA
35093107 ACTAAGCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (12 bp):
TAAACTATTAAT
Found at i:35095465 original size:27 final size:27
Alignment explanation
Indices: 35095427--35095549 Score: 124
Period size: 27 Copynumber: 4.6 Consensus size: 27
35095417 TCCAAAATTT
**
35095427 GTAAAATGACCGTAATGCCTTTGTAGA
1 GTAAAATGACCGTAATGCCCATGTAGA
*
35095454 GTAAAATGACCGTAATGCCCATGTAGG
1 GTAAAATGACCGTAATGCCCATGTAGA
* * *
35095481 GTAAAATGACTGTAATGCCCCTGCA-A
1 GTAAAATGACCGTAATGCCCATGTAGA
* * *
35095507 GGTAAAATGACTGTGATGCCCCTGTAG-
1 -GTAAAATGACCGTAATGCCCATGTAGA
* *
35095534 GTAAAATAACTGTAAT
1 GTAAAATGACCGTAAT
35095550 ACCCCTGTCA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
26 14 0.17
27 69 0.83
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (27 bp):
GTAAAATGACCGTAATGCCCATGTAGA
Found at i:35095496 original size:54 final size:53
Alignment explanation
Indices: 35095427--35095556 Score: 154
Period size: 54 Copynumber: 2.4 Consensus size: 53
35095417 TCCAAAATTT
* ** *
35095427 GTAAAATGACCGTAATGCCTTTG-TAGAGTAAAATGACCGTAATGCCCATGTAGG
1 GTAAAATGACTGTAATGCCCCTGCAAG-GTAAAATGACCGTAATGCCCATGTA-G
* * *
35095481 GTAAAATGACTGTAATGCCCCTGCAAGGTAAAATGACTGTGATGCCCCTGTAG
1 GTAAAATGACTGTAATGCCCCTGCAAGGTAAAATGACCGTAATGCCCATGTAG
* *
35095534 GTAAAATAACTGTAATACCCCTG
1 GTAAAATGACTGTAATGCCCCTG
35095557 TCAGGTGAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
53 22 0.33
54 42 0.64
55 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (53 bp):
GTAAAATGACTGTAATGCCCCTGCAAGGTAAAATGACCGTAATGCCCATGTAG
Found at i:35095705 original size:24 final size:24
Alignment explanation
Indices: 35095616--35095707 Score: 96
Period size: 24 Copynumber: 3.8 Consensus size: 24
35095606 CCCTCGAGGT
** *
35095616 TAAATGATTGATTCATCTGTGATG
1 TAAATGATTGATTTGTCTGTAATG
* *
35095640 TAAGTGATTGATTTGTCCG-AGATG
1 TAAATGATTGATTTGTCTGTA-ATG
* * *
35095664 TAAATGACTAATTTGTCTGTAATT
1 TAAATGATTGATTTGTCTGTAATG
35095688 TAAATGATTGATTTGTCTGT
1 TAAATGATTGATTTGTCTGT
35095708 GATTGGTATA
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
24 53 0.98
25 1 0.02
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (24 bp):
TAAATGATTGATTTGTCTGTAATG
Found at i:35097729 original size:15 final size:14
Alignment explanation
Indices: 35097706--35097753 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
35097696 TTTTCAAGTT
35097706 AAAAAAATATTATA
1 AAAAAAATATTATA
35097720 AAAAAGAATATTATTA
1 AAAAA-AATATTA-TA
* *
35097736 TAAATAAATAATATA
1 -AAAAAAATATTATA
35097751 AAA
1 AAA
35097754 TTGCAATATG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 8 0.28
15 9 0.31
16 8 0.28
17 4 0.14
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (14 bp):
AAAAAAATATTATA
Found at i:35097736 original size:18 final size:19
Alignment explanation
Indices: 35097713--35097749 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
35097703 GTTAAAAAAA
35097713 TATTATAAA-AAAGAATAT
1 TATTATAAATAAAGAATAT
*
35097731 TATTATAAATAAATAATAT
1 TATTATAAATAAAGAATAT
35097750 AAAATTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TATTATAAATAAAGAATAT
Found at i:35103033 original size:17 final size:16
Alignment explanation
Indices: 35103013--35103047 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
35103003 GTTTAATATA
35103013 TAATTTTATATAAATTT
1 TAATTTTATAT-AATTT
*
35103030 TAATTTTATGTAATTT
1 TAATTTTATATAATTT
35103046 TA
1 TA
35103048 TATATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
TAATTTTATATAATTT
Found at i:35106621 original size:103 final size:103
Alignment explanation
Indices: 35106490--35106696 Score: 414
Period size: 103 Copynumber: 2.0 Consensus size: 103
35106480 AGATCACCTA
35106490 AGGTTTCCCTCATATCCTCTTGTAGCTCCTCTAAGCTCATCTCGAGACTCCATCATTGTTGAACT
1 AGGTTTCCCTCATATCCTCTTGTAGCTCCTCTAAGCTCATCTCGAGACTCCATCATTGTTGAACT
35106555 TGATCTCCTTAAGAGAATCCTCGGTATCCTCCACCCAC
66 TGATCTCCTTAAGAGAATCCTCGGTATCCTCCACCCAC
35106593 AGGTTTCCCTCATATCCTCTTGTAGCTCCTCTAAGCTCATCTCGAGACTCCATCATTGTTGAACT
1 AGGTTTCCCTCATATCCTCTTGTAGCTCCTCTAAGCTCATCTCGAGACTCCATCATTGTTGAACT
35106658 TGATCTCCTTAAGAGAATCCTCGGTATCCTCCACCCAC
66 TGATCTCCTTAAGAGAATCCTCGGTATCCTCCACCCAC
35106696 A
1 A
35106697 TAAGGACATC
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.32
Consensus pattern (103 bp):
AGGTTTCCCTCATATCCTCTTGTAGCTCCTCTAAGCTCATCTCGAGACTCCATCATTGTTGAACT
TGATCTCCTTAAGAGAATCCTCGGTATCCTCCACCCAC
Found at i:35116947 original size:26 final size:25
Alignment explanation
Indices: 35116859--35116949 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 25
35116849 TTAATATGTA
* *
35116859 TTTTTTTATTTTAGGGTGTTTCAAG
1 TTTTTTTATTTTAAGGTGTTTCAAT
*
35116884 TTTTTTTATTTTAAGTGATGTTTATAAT
1 TTTTTTTATTTTAAG-G-TGTTT-CAAT
*
35116912 TATGTATTTTAATTTTACGGTGTTTCAAT
1 T-T-T-TTTT-ATTTTAAGGTGTTTCAAT
35116941 TTGTTTTTA
1 TT-TTTTTA
35116950 ATTACACCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
25 14 0.26
26 2 0.04
27 9 0.17
28 6 0.11
29 5 0.09
30 6 0.11
31 5 0.09
32 7 0.13
ACGTcount: A:0.21, C:0.03, G:0.14, T:0.62
Consensus pattern (25 bp):
TTTTTTTATTTTAAGGTGTTTCAAT
Found at i:35117391 original size:17 final size:17
Alignment explanation
Indices: 35117369--35117402 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
35117359 ATACTTAATG
*
35117369 TATACATCACTTGGGTA
1 TATACATCACTTAGGTA
35117386 TATACATCACTTAGGTA
1 TATACATCACTTAGGTA
35117403 CATGCCACGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (17 bp):
TATACATCACTTAGGTA
Found at i:35118841 original size:18 final size:17
Alignment explanation
Indices: 35118815--35118848 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
35118805 TATTTATTAT
35118815 AAAAAATGTGTATTTTG
1 AAAAAATGTGTATTTTG
35118832 AAAAACATGTGTATTTT
1 AAAAA-ATGTGTATTTT
35118849 AAGACGTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (17 bp):
AAAAAATGTGTATTTTG
Found at i:35119024 original size:2 final size:2
Alignment explanation
Indices: 35119019--35119065 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
35119009 GTGAAAAAAA
*
35119019 AT AT AT TT AT 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 AT AT AT AT AT
35119061 AT AT A
1 AT AT A
35119066 AACGTATACT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:35121096 original size:45 final size:46
Alignment explanation
Indices: 35121001--35121106 Score: 160
Period size: 45 Copynumber: 2.3 Consensus size: 46
35120991 AGCAGTGACA
* * *
35121001 GTAACAGTAACATTAACAGTATTTCAACACACAAAGTGCTGAATCT
1 GTAACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATCG
* *
35121047 GTAACAGTAACGGTAACAGTA-TTCGACACACAAAGTGCCGAATCG
1 GTAACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATCG
35121092 GTAACAGTAACAGTA
1 GTAACAGTAACAGTA
35121107 GTCGGCACAT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
45 35 0.65
46 19 0.35
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (46 bp):
GTAACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATCG
Found at i:35122325 original size:25 final size:25
Alignment explanation
Indices: 35122276--35122325 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
35122266 TTTATTTCTT
* *
35122276 GTTTTATTAATATAATAATTTAATA
1 GTTTTATTAATATAATAAGTAAATA
35122301 GTTTTACTTAA-ATAATAAGTAAATA
1 GTTTTA-TTAATATAATAAGTAAATA
35122326 CATAATAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (25 bp):
GTTTTATTAATATAATAAGTAAATA
Found at i:35122422 original size:5 final size:5
Alignment explanation
Indices: 35122414--35122458 Score: 90
Period size: 5 Copynumber: 9.0 Consensus size: 5
35122404 AATTTACCTA
35122414 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
35122459 TTATAACTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:35129089 original size:44 final size:44
Alignment explanation
Indices: 35129036--35129137 Score: 141
Period size: 44 Copynumber: 2.3 Consensus size: 44
35129026 ATTATTCAGT
* * *
35129036 TGTTAGGTTGAATGGAATGGAATAGATATATAATAGTATTCTTG
1 TGTTTGGTTGAATGCAATGGAATAGATATATAATAGTATTATTG
* * *
35129080 TGTTTGGTTGAATGCAATTGAATAGATCTGTAATAGTATTATTG
1 TGTTTGGTTGAATGCAATGGAATAGATATATAATAGTATTATTG
*
35129124 TATTTGGTTGAATG
1 TGTTTGGTTGAATG
35129138 AAATAAATGT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.30, C:0.03, G:0.25, T:0.42
Consensus pattern (44 bp):
TGTTTGGTTGAATGCAATGGAATAGATATATAATAGTATTATTG
Found at i:35129449 original size:13 final size:14
Alignment explanation
Indices: 35129408--35129449 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
35129398 AATCCAAGTC
* *
35129408 AAATAAAACAATTA
1 AAATAAAATAACTA
35129422 AAAT-AAATAACTA
1 AAATAAAATAACTA
35129435 AAATAAAATAA-TA
1 AAATAAAATAACTA
35129448 AA
1 AA
35129450 TCAAAGATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAAATAACTA
Found at i:35129905 original size:25 final size:22
Alignment explanation
Indices: 35129872--35129927 Score: 58
Period size: 25 Copynumber: 2.4 Consensus size: 22
35129862 ATAAAATTCC
*
35129872 TAAATAAATTAAAATACTTAATAA
1 TAAAAAAATTAAAATA--TAATAA
*
35129896 TTAAAAAAATTAGAATATAATAA
1 -TAAAAAAATTAAAATATAATAA
*
35129919 TAATAAAAT
1 TAAAAAAAT
35129928 AATAAGAGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.29
23 6 0.21
25 14 0.50
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (22 bp):
TAAAAAAATTAAAATATAATAA
Found at i:35135792 original size:43 final size:43
Alignment explanation
Indices: 35135739--35135830 Score: 175
Period size: 43 Copynumber: 2.1 Consensus size: 43
35135729 GAAGCGAATA
35135739 AAGAAGATAAATGGAAAGATAGAACGTGGAGTGTGGAAGTCCT
1 AAGAAGATAAATGGAAAGATAGAACGTGGAGTGTGGAAGTCCT
*
35135782 AAGAAGATAAATGGAAAGATAGAACGTGGCGTGTGGAAGTCCT
1 AAGAAGATAAATGGAAAGATAGAACGTGGAGTGTGGAAGTCCT
35135825 AAGAAG
1 AAGAAG
35135831 CCTTGGAAAC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.42, C:0.08, G:0.33, T:0.17
Consensus pattern (43 bp):
AAGAAGATAAATGGAAAGATAGAACGTGGAGTGTGGAAGTCCT
Found at i:35140439 original size:27 final size:27
Alignment explanation
Indices: 35140399--35140688 Score: 269
Period size: 27 Copynumber: 10.7 Consensus size: 27
35140389 GATTCGTGGG
**
35140399 AAAATGACTAAAATACCCCCGAAGGGT
1 AAAATGACCGAAATACCCCCGAAGGGT
*
35140426 AGAATGACCGAAATACCCCCGAAGGGT
1 AAAATGACCGAAATACCCCCGAAGGGT
* **
35140453 AGAATGACTAAAATACCCCCGAAGGGT
1 AAAATGACCGAAATACCCCCGAAGGGT
* * *
35140480 AAAATGATCAAAATACCCTCGAAGGGT
1 AAAATGACCGAAATACCCCCGAAGGGT
** *
35140507 AAAATGATTGAAATACCCTCGAAGGGT
1 AAAATGACCGAAATACCCCCGAAGGGT
** *
35140534 AAAATGATTGAAATACCCTCGAAGGGT
1 AAAATGACCGAAATACCCCCGAAGGGT
** *
35140561 AAAATGACTAAAATACCCCCAAAGGGT
1 AAAATGACCGAAATACCCCCGAAGGGT
* * *
35140588 AAAATAATC-AGAATACCCCTGAAGGGT
1 AAAATGACCGA-AATACCCCCGAAGGGT
** *
35140615 AAAATGACCGAAATACCCCTAAAGTGT
1 AAAATGACCGAAATACCCCCGAAGGGT
*** * *
35140642 AAAATGAAAAAAATA-CCCCTATATGGT
1 AAAATGACCGAAATACCCCCGA-AGGGT
* *
35140669 AAAATAACTGAAATACCCCC
1 AAAATGACCGAAATACCCCC
35140689 ATAGGATAGA
Statistics
Matches: 224, Mismatches: 35, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
26 5 0.02
27 214 0.96
28 5 0.02
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (27 bp):
AAAATGACCGAAATACCCCCGAAGGGT
Found at i:35140486 original size:54 final size:54
Alignment explanation
Indices: 35140399--35140688 Score: 323
Period size: 54 Copynumber: 5.4 Consensus size: 54
35140389 GATTCGTGGG
* *
35140399 AAAATGACTAAAATACCCCCGAAGGGTAGAATGACCGAAATACCCCCGAAGGGT
1 AAAATGACTAAAATACCCCCGAAGGGTAAAATGATCGAAATACCCCCGAAGGGT
* * *
35140453 AGAATGACTAAAATACCCCCGAAGGGTAAAATGATCAAAATACCCTCGAAGGGT
1 AAAATGACTAAAATACCCCCGAAGGGTAAAATGATCGAAATACCCCCGAAGGGT
* * * * *
35140507 AAAATGATTGAAATACCCTCGAAGGGTAAAATGATTGAAATACCCTCGAAGGGT
1 AAAATGACTAAAATACCCCCGAAGGGTAAAATGATCGAAATACCCCCGAAGGGT
* * *
35140561 AAAATGACTAAAATACCCCCAAAGGGTAAAATAATC-AGAATACCCCTGAAGGGT
1 AAAATGACTAAAATACCCCCGAAGGGTAAAATGATCGA-AATACCCCCGAAGGGT
** ** * *** * *
35140615 AAAATGACCGAAATACCCCTAAAGTGTAAAATGAAAAAAATA-CCCCTATATGGT
1 AAAATGACTAAAATACCCCCGAAGGGTAAAATGATCGAAATACCCCCGA-AGGGT
* *
35140669 AAAATAACTGAAATACCCCC
1 AAAATGACTAAAATACCCCC
35140689 ATAGGATAGA
Statistics
Matches: 201, Mismatches: 32, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
53 5 0.02
54 195 0.97
55 1 0.00
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (54 bp):
AAAATGACTAAAATACCCCCGAAGGGTAAAATGATCGAAATACCCCCGAAGGGT
Found at i:35140534 original size:81 final size:80
Alignment explanation
Indices: 35140399--35140705 Score: 323
Period size: 81 Copynumber: 3.8 Consensus size: 80
35140389 GATTCGTGGG
* * * *
35140399 AAAATGACTAAAATACCCCCGAAGGGTAGAATGACCGAAATACCCCCGAAGGGTAGAATGACTAA
1 AAAATGACTAAAATACCCCCGAAGGGTAAAATGACTGAAATA-CCCCGAAGGGTAAAATGACTGA
35140464 AATACCCCCGAAGGGT
65 AATACCCCCGAAGGGT
* * *
35140480 AAAATGA-TCAAAATACCCTCGAAGGGTAAAATGATTGAAATACCCTCGAAGGGTAAAATGATTG
1 AAAATGACT-AAAATACCCCCGAAGGGTAAAATGACTGAAATACCC-CGAAGGGTAAAATGACTG
*
35140544 AAATACCCTCGAAGGGT
64 AAATACCCCCGAAGGGT
* * * *
35140561 AAAATGACTAAAATACCCCCAAAGGGTAAAAT-AATCAGAATACCCCTGAAGGGTAAAATGACCG
1 AAAATGACTAAAATACCCCCGAAGGGTAAAATGACTGA-AATACCCC-GAAGGGTAAAATGACTG
** *
35140625 AAATACCCCTAAAGTGT
64 AAATACCCCCGAAGGGT
** * * * * * *
35140642 AAAATGAAAAAAATA-CCCCTATATGGTAAAATAACTGAAATACCCCCATAGGATAGAATGACTG
1 AAAATGACTAAAATACCCCCGA-AGGGTAAAATGACTGAAATACCCCGA-AGGGTAAAATGACTG
35140706 TTATATCCCA
Statistics
Matches: 190, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
80 14 0.07
81 172 0.91
82 4 0.02
ACGTcount: A:0.44, C:0.20, G:0.19, T:0.18
Consensus pattern (80 bp):
AAAATGACTAAAATACCCCCGAAGGGTAAAATGACTGAAATACCCCGAAGGGTAAAATGACTGAA
ATACCCCCGAAGGGT
Found at i:35140913 original size:26 final size:26
Alignment explanation
Indices: 35140884--35140956 Score: 103
Period size: 26 Copynumber: 2.8 Consensus size: 26
35140874 CATATATTGA
* *
35140884 TACTGGCAGCTTTGCTGTGATACTGT
1 TACTGGCAGCTTTGCTGCGATACTAT
35140910 TACTGGCAG-TTTCGCTGCGATACTAT
1 TACTGGCAGCTTT-GCTGCGATACTAT
*
35140936 TACTAGCAGCTTTGCTGCGAT
1 TACTGGCAGCTTTGCTGCGAT
35140957 GTTGGTGTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
25 3 0.07
26 36 0.86
27 3 0.07
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.36
Consensus pattern (26 bp):
TACTGGCAGCTTTGCTGCGATACTAT
Found at i:35144080 original size:2 final size:2
Alignment explanation
Indices: 35144073--35144100 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35144063 TATCTCCTTA
35144073 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
35144101 TCTATTTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35146395 original size:16 final size:16
Alignment explanation
Indices: 35146374--35146406 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
35146364 ACATTCTTTC
35146374 TGCTTATATTTTATAT
1 TGCTTATATTTTATAT
35146390 TGCTTATATTTTATAT
1 TGCTTATATTTTATAT
35146406 T
1 T
35146407 CTCTAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.64
Consensus pattern (16 bp):
TGCTTATATTTTATAT
Found at i:35148284 original size:15 final size:16
Alignment explanation
Indices: 35148264--35148303 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
35148254 AAAATAATTT
35148264 AAAACTT-AAATTTTG
1 AAAACTTAAAATTTTG
35148279 AAAACTTAAAAATTTTG
1 AAAACTT-AAAATTTTG
35148296 AGAAACTT
1 A-AAACTT
35148304 TGGAACTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.32
17 9 0.41
18 6 0.27
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.35
Consensus pattern (16 bp):
AAAACTTAAAATTTTG
Found at i:35148710 original size:114 final size:114
Alignment explanation
Indices: 35148510--35148716 Score: 326
Period size: 114 Copynumber: 1.8 Consensus size: 114
35148500 ATACAAACTA
* *
35148510 CAGAGAATATTTACTATTCATGCGTCTTTTCTTGCAGGGAATATTTACTGTTTTCACCAGAGAAT
1 CAGAGAATATTTACTATTCATGCATCTTTTCTTGCAGGGAATATTTACTGTTTTCACCAAAGAAT
**
35148575 ATTTCCTGTTCACTTTTCTTTTCTTGCAAGGAATATTTACTTTTTTCGC
66 ATTTCCTGTTCACTCGTCTTTTCTTGCAAGGAATATTTACTTTTTTCGC
* * * *
35148624 CAGAGAATATTTCCTATTCACT-TATCTTTTCTTGCATGGAATATTTACTGTTTTCGCCAAAGAA
1 CAGAGAATATTTACTATTCA-TGCATCTTTTCTTGCAGGGAATATTTACTGTTTTCACCAAAGAA
35148688 TATTTCCTGTTCACTCGTCTTTTCTTGCA
65 TATTTCCTGTTCACTCGTCTTTTCTTGCA
35148717 TCATTTTTTC
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
114 83 0.99
115 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.44
Consensus pattern (114 bp):
CAGAGAATATTTACTATTCATGCATCTTTTCTTGCAGGGAATATTTACTGTTTTCACCAAAGAAT
ATTTCCTGTTCACTCGTCTTTTCTTGCAAGGAATATTTACTTTTTTCGC
Found at i:35148717 original size:57 final size:57
Alignment explanation
Indices: 35148510--35148717 Score: 292
Period size: 57 Copynumber: 3.6 Consensus size: 57
35148500 ATACAAACTA
* * *
35148510 CAGAGAATATTTACTATTCA-TGCGTCTTTTCTTGCAGGGAATATTTACTGTTTTCAC
1 CAGAGAATATTTCCTATTCACT-CGTCTTTTCTTGCATGGAATATTTACTGTTTTCGC
* ** * *
35148567 CAGAGAATATTTCCTGTTCACTTTTCTTTTCTTGCAAGGAATATTTACTTTTTTCGC
1 CAGAGAATATTTCCTATTCACTCGTCTTTTCTTGCATGGAATATTTACTGTTTTCGC
**
35148624 CAGAGAATATTTCCTATTCACTTATCTTTTCTTGCATGGAATATTTACTGTTTTCGC
1 CAGAGAATATTTCCTATTCACTCGTCTTTTCTTGCATGGAATATTTACTGTTTTCGC
* *
35148681 CAAAGAATATTTCCTGTTCACTCGTCTTTTCTTGCAT
1 CAGAGAATATTTCCTATTCACTCGTCTTTTCTTGCAT
35148718 CATTTTTTCT
Statistics
Matches: 135, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
57 134 0.99
58 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.45
Consensus pattern (57 bp):
CAGAGAATATTTCCTATTCACTCGTCTTTTCTTGCATGGAATATTTACTGTTTTCGC
Found at i:35160398 original size:57 final size:56
Alignment explanation
Indices: 35160310--35160513 Score: 275
Period size: 57 Copynumber: 3.6 Consensus size: 56
35160300 ATACAAACTA
*
35160310 CAGAGAATATTTACTATTCA-TGTGTCTTTTCTTGCAGGGAATATTTACTGTTTTCGC
1 CAGAGAATATTTCCTATTCACT-TGTCTTTTCTTGCAGGGAATATTTACT-TTTTCGC
* * *
35160367 CAGAGAATATTTCCTGTTCACTTATCTTTTCTTGCAGGGAATATTTACTATTTCTGC
1 CAGAGAATATTTCCTATTCACTTGTCTTTTCTTGCAGGGAATATTTACTTTTTC-GC
* * * *
35160424 CAGAGAATATTTCTTGTTCATTTGTCTTTTCTTGCAGAGAATATTTACTATTTTCGC
1 CAGAGAATATTTCCTATTCACTTGTCTTTTCTTGCAGGGAATATTTACT-TTTTCGC
* *
35160481 CAGAGAATATTTCTTATTCACTCGTCTTTTCTT
1 CAGAGAATATTTCCTATTCACTTGTCTTTTCTT
35160514 ACATCATTTT
Statistics
Matches: 132, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
56 4 0.03
57 123 0.93
58 5 0.04
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.46
Consensus pattern (56 bp):
CAGAGAATATTTCCTATTCACTTGTCTTTTCTTGCAGGGAATATTTACTTTTTCGC
Found at i:35164315 original size:20 final size:20
Alignment explanation
Indices: 35164253--35164316 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
35164243 AAAAAACTAA
*
35164253 ATTTTTAACGTAATACAAAT
1 ATTTTTAATGTAATACAAAT
35164273 ATTTTTAATGTAATACCAAAT
1 ATTTTTAATGTAATA-CAAAT
* * *
35164294 -TTTCTAATG-GATACTAAT
1 ATTTTTAATGTAATACAAAT
35164312 ATTTT
1 ATTTT
35164317 AAAGGCAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
18 4 0.11
19 6 0.16
20 22 0.59
21 5 0.14
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (20 bp):
ATTTTTAATGTAATACAAAT
Found at i:35164862 original size:28 final size:29
Alignment explanation
Indices: 35164817--35164873 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
35164807 ACATTACCAT
35164817 AAATATAATAAATGTTTTATTATATTAAA
1 AAATATAATAAATGTTTTATTATATTAAA
*
35164846 AAATAT-ATAATAT-TTTTATTTTATTAAA
1 AAATATAATAA-ATGTTTTATTATATTAAA
35164874 TATAATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
AAATATAATAAATGTTTTATTATATTAAA
Found at i:35166825 original size:17 final size:17
Alignment explanation
Indices: 35166805--35166838 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
35166795 GAGTCGAGGG
35166805 AAAGTGAAAGTCTCGAA
1 AAAGTGAAAGTCTCGAA
35166822 AAAGTGAAAGTCTCGAA
1 AAAGTGAAAGTCTCGAA
35166839 TTAGTTCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.24, T:0.18
Consensus pattern (17 bp):
AAAGTGAAAGTCTCGAA
Found at i:35173273 original size:28 final size:28
Alignment explanation
Indices: 35173217--35173276 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
35173207 ACCACCCTAT
*
35173217 TTTATTTTATATTTGAATTATGTTTGAA
1 TTTATTTTATATTTGAATTATGTTAGAA
*
35173245 TTTA-TTTATATGTTAGAATTGTG-TAGAA
1 TTTATTTTATAT-TT-GAATTATGTTAGAA
35173273 TTTA
1 TTTA
35173277 GTGATTTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.25
28 14 0.50
29 7 0.25
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TTTATTTTATATTTGAATTATGTTAGAA
Found at i:35173639 original size:30 final size:30
Alignment explanation
Indices: 35173605--35173661 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
35173595 GAGTAACATC
* * *
35173605 GATATACTGTTAGCTTGTGTGAGCAACCCT
1 GATATACTGTCAGCTTGTCTGAACAACCCT
*
35173635 GATATATTGTCAGCTTGTCTGAACAAC
1 GATATACTGTCAGCTTGTCTGAACAAC
35173662 TTTTTCCCGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (30 bp):
GATATACTGTCAGCTTGTCTGAACAACCCT
Found at i:35173764 original size:10 final size:11
Alignment explanation
Indices: 35173745--35173773 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
35173735 TAAATGCAAA
35173745 TTTGATATATG
1 TTTGATATATG
35173756 TTT-ATATATG
1 TTTGATATATG
35173766 TTTGATAT
1 TTTGATAT
35173774 TTGATATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (11 bp):
TTTGATATATG
Found at i:35174928 original size:13 final size:11
Alignment explanation
Indices: 35174892--35174922 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
35174882 TCATCCGTAT
35174892 TAATTTTTATA
1 TAATTTTTATA
*
35174903 TTATTTTTATA
1 TAATTTTTATA
35174914 TAATTTTTA
1 TAATTTTTA
35174923 AATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:35175096 original size:30 final size:29
Alignment explanation
Indices: 35175044--35175123 Score: 128
Period size: 30 Copynumber: 2.8 Consensus size: 29
35175034 ACTTAACAAG
*
35175044 CAAATGCCTCTAAAATATAACAAAATTAA
1 CAAATGCCTTTAAAATATAACAAAATTAA
35175073 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTTTAAAAT-ATAACAAAATTAA
35175103 CAAATGCCTTT-AAAT-TAACAA
1 CAAATGCCTTTAAAATATAACAA
35175124 TAAAATAAGT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
27 6 0.12
29 19 0.39
30 24 0.49
ACGTcount: A:0.54, C:0.16, G:0.04, T:0.26
Consensus pattern (29 bp):
CAAATGCCTTTAAAATATAACAAAATTAA
Found at i:35175178 original size:22 final size:22
Alignment explanation
Indices: 35175152--35175200 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
35175142 ATATCCAAAC
35175152 AATAACAATAAAATAGTAGCAA
1 AATAACAATAAAATAGTAGCAA
* * * *
35175174 CATAATAGTAAAATGGTAGCAA
1 AATAACAATAAAATAGTAGCAA
35175196 AATAA
1 AATAA
35175201 GGAGAAAACA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.59, C:0.08, G:0.12, T:0.20
Consensus pattern (22 bp):
AATAACAATAAAATAGTAGCAA
Found at i:35178081 original size:13 final size:13
Alignment explanation
Indices: 35178065--35178097 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
35178055 AAAAACAAAA
35178065 AAATAAATAAGAT
1 AAATAAATAAGAT
*
35178078 AAATAAATAGGAT
1 AAATAAATAAGAT
35178091 -AATAAAT
1 AAATAAAT
35178098 CAAAGATTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (13 bp):
AAATAAATAAGAT
Found at i:35179069 original size:23 final size:23
Alignment explanation
Indices: 35179039--35179097 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
35179029 ACAATAGCAT
35179039 ATCAACATCATCATTTTT-AAAAA
1 ATCAACATCATC-TTTTTAAAAAA
35179062 ATCAACATCATCTTTTTAAAAAA
1 ATCAACATCATCTTTTTAAAAAA
35179085 ATCAACATCATCT
1 ATCAACATCATCT
35179098 CTCCCTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.14
23 30 0.86
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (23 bp):
ATCAACATCATCTTTTTAAAAAA
Found at i:35183653 original size:20 final size:20
Alignment explanation
Indices: 35183630--35183709 Score: 108
Period size: 20 Copynumber: 4.0 Consensus size: 20
35183620 ATTACATATA
*
35183630 TTGGTATCCTGTCAGAAATT
1 TTGGTATCCTGTTAGAAATT
**
35183650 TTGGTATTTTGTTAGAAATT
1 TTGGTATCCTGTTAGAAATT
35183670 TTGGTAT-CTGTTAGAAATT
1 TTGGTATCCTGTTAGAAATT
* *
35183689 TTAGTATCGTGTTAGAAATT
1 TTGGTATCCTGTTAGAAATT
35183709 T
1 T
35183710 AGTACATGCT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
19 17 0.32
20 36 0.68
ACGTcount: A:0.26, C:0.06, G:0.20, T:0.47
Consensus pattern (20 bp):
TTGGTATCCTGTTAGAAATT
Found at i:35183702 original size:39 final size:40
Alignment explanation
Indices: 35183630--35183709 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 40
35183620 ATTACATATA
* **
35183630 TTGGTATCCTGTCAGAAATTTTGGTATTTTGTTAGAAATT
1 TTGGTATCCTGTCAGAAATTTTAGTATCGTGTTAGAAATT
*
35183670 TTGGTAT-CTGTTAGAAATTTTAGTATCGTGTTAGAAATT
1 TTGGTATCCTGTCAGAAATTTTAGTATCGTGTTAGAAATT
35183709 T
1 T
35183710 AGTACATGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.81
40 7 0.19
ACGTcount: A:0.26, C:0.06, G:0.20, T:0.47
Consensus pattern (40 bp):
TTGGTATCCTGTCAGAAATTTTAGTATCGTGTTAGAAATT
Found at i:35183836 original size:19 final size:19
Alignment explanation
Indices: 35183803--35183854 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
35183793 ATTGGCATCA
*
35183803 CATTAAAAATTTTGGTATT
1 CATTAGAAATTTTGGTATT
*
35183822 CCA-TAGAATTTTTGGTATT
1 -CATTAGAAATTTTGGTATT
35183841 CATTAGAAATTTTG
1 CATTAGAAATTTTG
35183855 ATATACTAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 2 0.07
19 24 0.86
20 2 0.07
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (19 bp):
CATTAGAAATTTTGGTATT
Found at i:35184032 original size:20 final size:20
Alignment explanation
Indices: 35183994--35184032 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35183984 TAATGGTTTC
*
35183994 CATTAGAAATATTGTTATTG
1 CATTAGAAATATTGGTATTG
*
35184014 CATTAGAAATTTTGGTATT
1 CATTAGAAATATTGGTATT
35184033 AACTTATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.46
Consensus pattern (20 bp):
CATTAGAAATATTGGTATTG
Found at i:35187600 original size:2 final size:2
Alignment explanation
Indices: 35187593--35187622 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
35187583 CCAAAAATTA
35187593 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
35187623 TANNNNNNNN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35190975 original size:24 final size:24
Alignment explanation
Indices: 35190939--35190986 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
35190929 AGAGCAATCA
* *
35190939 TCCATCCATCCACCCGCCCGCCCG
1 TCCACCCAGCCACCCGCCCGCCCG
*
35190963 TCCACCCAGCCACCCGCCCTCCCG
1 TCCACCCAGCCACCCGCCCGCCCG
35190987 CCAATCAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.12, C:0.65, G:0.12, T:0.10
Consensus pattern (24 bp):
TCCACCCAGCCACCCGCCCGCCCG
Found at i:35215942 original size:50 final size:50
Alignment explanation
Indices: 35215827--35216018 Score: 258
Period size: 50 Copynumber: 3.8 Consensus size: 50
35215817 GATAATAACA
* * * ** *
35215827 TGCCAAAGGCATGTCCTAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
35215878 TGCCCATGTCATGTCTCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
35215928 TGACAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
35215978 TGCCAATGCCATGACCCAGACATGGTCTTACATGGGACCTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTC
35216019 ATTCCCTTAA
Statistics
Matches: 124, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 92 0.74
51 32 0.26
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:35231965 original size:27 final size:25
Alignment explanation
Indices: 35231911--35231965 Score: 58
Period size: 26 Copynumber: 2.1 Consensus size: 25
35231901 AATTCCTCTC
**
35231911 AAAGCTCTTTTTAATTTTTTTCGAA
1 AAAGCTCTTTTTAATTTTTTTAAAA
35231936 AAAGCTCTAATTTT-ATTTTTTTAAATA
1 AAAGCTCT--TTTTAATTTTTTTAAA-A
35231963 AAA
1 AAA
35231966 AAATTGATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 8 0.32
26 9 0.36
27 8 0.32
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.49
Consensus pattern (25 bp):
AAAGCTCTTTTTAATTTTTTTAAAA
Found at i:35233708 original size:18 final size:18
Alignment explanation
Indices: 35233685--35233728 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
35233675 ATGCCAGGTG
* *
35233685 TGTATCCTAGCCCTTTTA
1 TGTATCCTAACCCTTATA
35233703 TGTATCCTAACCCTTATA
1 TGTATCCTAACCCTTATA
*
35233721 TGTTTCCT
1 TGTATCCT
35233729 TTTTCTAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.27, G:0.09, T:0.45
Consensus pattern (18 bp):
TGTATCCTAACCCTTATA
Found at i:35237413 original size:126 final size:125
Alignment explanation
Indices: 35237188--35237474 Score: 493
Period size: 126 Copynumber: 2.3 Consensus size: 125
35237178 GCCAAATAGG
*
35237188 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACATTGCATCC
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCC
* *
35237253 TACTTGAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
66 TACTTAAAACGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTT-AGA
35237314 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCC
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCC
* * *
35237379 TGCTTAAAACGTTTTTGACACTATTTGCTCAGAAACGTCTTCTCAAAATTATTTTTTAGG
66 TACTTAAAACGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTAGA
* *
35237439 AACTACTGTAGTAAAATAGCGTCCACGTGGGAGCTT
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTT
35237475 TTTTAAATTA
Statistics
Matches: 153, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
125 36 0.24
126 117 0.76
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (125 bp):
AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCC
TACTTAAAACGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTAGA
Found at i:35237717 original size:95 final size:96
Alignment explanation
Indices: 35237514--35237943 Score: 611
Period size: 95 Copynumber: 4.5 Consensus size: 96
35237504 CTAAACCCCA
* * * *
35237514 AACCCCAAACCTTAATTTATTTGATTTTTCCTTAAAAACCTTAAACACTAAACCCTAATCTAATT
1 AACCCTAAACCCTAATTTATTTGATTTTTTCTTAAAAACCATAAACACTAAACCCTAATCTAA--
35237579 TTTTTTTAAAATTTATAATTAATTTACTCAAGT
64 TTTTTTTAAAATTTATAATTAATTTACTCAAGT
*
35237612 AACTCC-AAACCCTAATTTATTTGATTTTTTCTT-AAAACCCTAAACACTAAACCCTAATCTAAT
1 AAC-CCTAAACCCTAATTTATTTGATTTTTTCTTAAAAACCATAAACACTAAACCCTAATCTAAT
35237675 TTTTTTAAAATTTATAATTAATTTACTCAAGT
65 TTTTTTAAAATTTATAATTAATTTACTCAAGT
* * *
35237707 AACCCTAAACCTTAATTTATTTGATTTTTTTCTTAAAAAACC-TAAACCCTAAACTCTAATCTAA
1 AACCCTAAACCCTAATTTATTTGA-TTTTTTCTT-AAAAACCATAAACACTAAACCCTAATCTAA
35237771 TTTTTTTAAAAATTTATAATTAATTTACTCAAGT
64 TTTTTTT-AAAATTTATAATTAATTTACTCAAGT
* *
35237805 AACCCTAAACACTAATTTATTTGATTTTTTCTTAAAAACTATAAACACTAAACCCTAATCTAA-T
1 AACCCTAAACCCTAATTTATTTGATTTTTTCTTAAAAACCATAAACACTAAACCCTAATCTAATT
* * * * *
35237869 TTTTTAAAATTTATAATTACTTGAATTAAGA
66 TTTTTAAAATTTATAATTAATTTACTCAAGT
*
35237900 AACCCTAAACCCTTATTTATTT-ATTTTTTCCTT-AAAACCATAAA
1 AACCCTAAACCCTAATTTATTTGATTTTTT-CTTAAAAACCATAAA
35237944 ATCTAAAAAC
Statistics
Matches: 305, Mismatches: 19, Indels: 20
0.89 0.06 0.06
Matches are distributed among these distances:
94 19 0.06
95 97 0.32
96 21 0.07
97 84 0.28
98 82 0.27
99 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.41
Consensus pattern (96 bp):
AACCCTAAACCCTAATTTATTTGATTTTTTCTTAAAAACCATAAACACTAAACCCTAATCTAATT
TTTTTAAAATTTATAATTAATTTACTCAAGT
Found at i:35237825 original size:193 final size:195
Alignment explanation
Indices: 35237513--35237936 Score: 648
Period size: 193 Copynumber: 2.2 Consensus size: 195
35237503 CCTAAACCCC
*
35237513 AAACCCCAAACCTTAATTTATTTGA-TTTTTCCTT-AAAAACCTTAAACACTAAACCCTAATCTA
1 AAACCCTAAACCTTAATTTATTTGATTTTTTCCTTAAAAAACCTTAAACACTAAACCCTAATCTA
* *
35237576 ATTTTTTTTTAAAATTTATAATTAATTTACTCAAGTAACTCCAAACCCTAATTTATTTGATTTTT
66 ATTTTTTTTAAAAATTTATAATTAATTTACTCAAGTAACTCCAAACACTAATTTATTTGATTTTT
* * *
35237641 TCTT-AAAACCCTAAACACTAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTCAA
131 TCTTAAAAACCATAAACACTAAACCCTAATCTAA-TTTTTTAAAATTTATAATTAATTGAATCAA
35237705 G
195 G
* * * *
35237706 TAACCCTAAACCTTAATTTATTTGATTTTTTTCTTAAAAAACC-TAAACCCTAAACTCTAATCTA
1 AAACCCTAAACCTTAATTTATTTGATTTTTTCCTTAAAAAACCTTAAACACTAAACCCTAATCTA
35237770 A-TTTTTTTAAAAATTTATAATTAATTTACTCAAGTAAC-CCTAAACACTAATTTATTTGATTTT
66 ATTTTTTTTAAAAATTTATAATTAATTTACTCAAGTAACTCC-AAACACTAATTTATTTGATTTT
* * *
35237833 TTCTTAAAAACTATAAACACTAAACCCTAATCTAATTTTTTAAAATTTATAATTACTTGAATTAA
130 TTCTTAAAAACCATAAACACTAAACCCTAATCTAATTTTTTAAAATTTATAATTAATTGAATCAA
35237898 G
195 G
35237899 AAACCCTAAACCCTT-ATTTATTT-ATTTTTTCCTTAAAA
1 AAACCCTAAA-CCTTAATTTATTTGATTTTTTCCTTAAAA
35237937 CCATAAAATC
Statistics
Matches: 211, Mismatches: 15, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
192 16 0.08
193 129 0.61
194 59 0.28
195 7 0.03
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.42
Consensus pattern (195 bp):
AAACCCTAAACCTTAATTTATTTGATTTTTTCCTTAAAAAACCTTAAACACTAAACCCTAATCTA
ATTTTTTTTAAAAATTTATAATTAATTTACTCAAGTAACTCCAAACACTAATTTATTTGATTTTT
TCTTAAAAACCATAAACACTAAACCCTAATCTAATTTTTTAAAATTTATAATTAATTGAATCAAG
Found at i:35238118 original size:40 final size:41
Alignment explanation
Indices: 35238017--35238118 Score: 129
Period size: 40 Copynumber: 2.5 Consensus size: 41
35238007 CAGGGAAAAT
35238017 GCTTCCTCAAGGAAGCG-TTT-TGTCTACGTGGACACAAAGC
1 GCTTCCTCAAGGAAGCGTTTTCTGTCTACGTGGA-ACAAAGC
** *
35238057 GCACCCTCAAGGACGCGTTTTCTGTCTACGTGG-ACAAAGC
1 GCTTCCTCAAGGAAGCGTTTTCTGTCTACGTGGAACAAAGC
* *
35238097 GCTTCCTTAATGAAGCGTTTTC
1 GCTTCCTCAAGGAAGCGTTTTC
35238119 CTACTTTATC
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
40 38 0.73
41 3 0.06
42 11 0.21
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (41 bp):
GCTTCCTCAAGGAAGCGTTTTCTGTCTACGTGGAACAAAGC
Found at i:35239102 original size:41 final size:42
Alignment explanation
Indices: 35239040--35239131 Score: 161
Period size: 41 Copynumber: 2.2 Consensus size: 42
35239030 TGAATATCAA
*
35239040 TCATGCAGTGAAGGCTTTTTGCTTTAAATTTCTAGGTTGATT
1 TCATGCAGTGAAGGCTGTTTGCTTTAAATTTCTAGGTTGATT
35239082 T-ATGCAGTGAAGGCTGTTTGCTTTAAATTTCTAGGTTGATT
1 TCATGCAGTGAAGGCTGTTTGCTTTAAATTTCTAGGTTGATT
35239123 TCATG-AGTG
1 TCATGCAGTG
35239132 TACATCATGC
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
41 44 0.92
42 4 0.08
ACGTcount: A:0.22, C:0.11, G:0.24, T:0.43
Consensus pattern (42 bp):
TCATGCAGTGAAGGCTGTTTGCTTTAAATTTCTAGGTTGATT
Found at i:35239567 original size:17 final size:17
Alignment explanation
Indices: 35239537--35239569 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
35239527 ATTGTTACCC
35239537 TTGTTGATGATGATGAT
1 TTGTTGATGATGATGAT
35239554 TTGTGTGATG-TGATGA
1 TTGT-TGATGATGATGA
35239570 GGCAACGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (17 bp):
TTGTTGATGATGATGAT
Found at i:35243872 original size:16 final size:16
Alignment explanation
Indices: 35243851--35243890 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
35243841 GCCTACTCCT
35243851 CCCAATTTAAACCCAG
1 CCCAATTTAAACCCAG
* *
35243867 CCCAATTTAAATCTAG
1 CCCAATTTAAACCCAG
35243883 CCCAATTT
1 CCCAATTT
35243891 TCACAACACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.35, C:0.33, G:0.05, T:0.28
Consensus pattern (16 bp):
CCCAATTTAAACCCAG
Found at i:35244606 original size:20 final size:20
Alignment explanation
Indices: 35244581--35244625 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
35244571 AGGCTTAAAT
* *
35244581 ATTTTCGGGTAATTCGGGTC
1 ATTTTCGAGTAATTCGGGTA
35244601 ATTTTCGAGTAATTCGGGTA
1 ATTTTCGAGTAATTCGGGTA
35244621 ATTTT
1 ATTTT
35244626 TAACCAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.11, G:0.24, T:0.44
Consensus pattern (20 bp):
ATTTTCGAGTAATTCGGGTA
Found at i:35246350 original size:5 final size:5
Alignment explanation
Indices: 35246340--35246381 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
35246330 AAACCCAAGT
35246340 ACCCA ACCCA ACCCA ACCCA ACCCA ACCCA ACCCA ACCCA AC
1 ACCCA ACCCA ACCCA ACCCA ACCCA ACCCA ACCCA ACCCA AC
35246382 TACCCAACTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.40, C:0.60, G:0.00, T:0.00
Consensus pattern (5 bp):
ACCCA
Found at i:35246440 original size:6 final size:6
Alignment explanation
Indices: 35246430--35246473 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
35246420 AATAAAAATA
*
35246430 AAAATCT AAATCT AAAACT AAAACT AAAAGTCT AAAACT AAAAC
1 AAAA-CT AAAACT AAAACT AAAACT AAAA--CT AAAACT AAAAC
35246474 ATAGACATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
6 24 0.73
7 3 0.09
8 6 0.18
ACGTcount: A:0.61, C:0.16, G:0.02, T:0.20
Consensus pattern (6 bp):
AAAACT
Found at i:35246445 original size:14 final size:14
Alignment explanation
Indices: 35246422--35246472 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
35246412 ATTTAATAAA
*
35246422 TAAAAATAAAAATC
1 TAAAACTAAAAATC
*
35246436 TAAATCT-AAAA-C
1 TAAAACTAAAAATC
*
35246448 TAAAACTAAAAGTC
1 TAAAACTAAAAATC
35246462 TAAAACTAAAA
1 TAAAACTAAAA
35246473 CATAGACATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 7 0.23
13 7 0.23
14 17 0.55
ACGTcount: A:0.65, C:0.12, G:0.02, T:0.22
Consensus pattern (14 bp):
TAAAACTAAAAATC
Found at i:35246451 original size:20 final size:21
Alignment explanation
Indices: 35246422--35246472 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
35246412 ATTTAATAAA
*
35246422 TAAAAATAAAAATCT-AAA-TC
1 TAAAACTAAAAA-CTAAAAGTC
35246442 TAAAACT-AAAACTAAAAGTC
1 TAAAACTAAAAACTAAAAGTC
35246462 TAAAACTAAAA
1 TAAAACTAAAA
35246473 CATAGACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 2 0.07
19 7 0.26
20 15 0.56
21 3 0.11
ACGTcount: A:0.65, C:0.12, G:0.02, T:0.22
Consensus pattern (21 bp):
TAAAACTAAAAACTAAAAGTC
Found at i:35246451 original size:26 final size:26
Alignment explanation
Indices: 35246422--35246473 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
35246412 ATTTAATAAA
*
35246422 TAAAAATAAAAATCTAAATCTAAAAC
1 TAAAAATAAAAATCTAAAACTAAAAC
* *
35246448 TAAAACTAAAAGTCTAAAACTAAAAC
1 TAAAAATAAAAATCTAAAACTAAAAC
35246474 ATAGACATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.63, C:0.13, G:0.02, T:0.21
Consensus pattern (26 bp):
TAAAAATAAAAATCTAAAACTAAAAC
Found at i:35250412 original size:9 final size:9
Alignment explanation
Indices: 35250398--35250430 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
35250388 ATTCAATGCT
35250398 TTAATTCGG
1 TTAATTCGG
*
35250407 TTAATTTGG
1 TTAATTCGG
35250416 TTAATTCGG
1 TTAATTCGG
35250425 TTAATT
1 TTAATT
35250431 TTTATACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.52
Consensus pattern (9 bp):
TTAATTCGG
Done.