Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007943.1 Hibiscus syriacus cultivar Beakdansim tig00110365_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: 1187827
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:639229 original size:200 final size:200
Alignment explanation
Indices: 638886--639336 Score: 681
Period size: 200 Copynumber: 2.3 Consensus size: 200
638876 TGTAATAGGT
* * *
638886 AATATACCGGTTTTATGAGAGAATAGGTCTATAACATGTATCGACACTATATAAATTTGTGACGA
1 AATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAAATTTGTGACGA
* * * * *
638951 TACTTTTTGTCCATAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCGATACATTTTCAAAGA
66 TACTTTATGTCCAGAATGGATGCCAAAAAGGATGAACGCACAAAGTGCCAATACATTTTCAAAAA
*
639016 GTGTCGATCCCAAAAATATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACCA
131 GTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACCA
639081 GTATA
196 GTATA
* *
639086 AATATACCGGTTTTATGAGAGAATAGGTCTACAACATATATCGACACTTTTT-AATATTGTGTCG
1 AATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAAAT-TTGTGACG
* * *
639150 ATACTTTATGTCTAGAATGGATGCCAAAAAGGGTGAACGCACAAAGTGCCAATATATTTTCAAAA
65 ATACTTTATGTCCAGAATGGATGCCAAAAAGGATGAACGCACAAAGTGCCAATACATTTTCAAAA
* * *
639215 AGTGTCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATATGTAATTTTTTAATATAACC
130 AGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACC
*
639280 GGTATA
195 AGTATA
* * * *
639286 AATATACC-GTTTTATAAGAGAATAGATTTACAACATGTAGCGACACTTTTT
1 AATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTT
639337 TATTTTGATT
Statistics
Matches: 227, Mismatches: 23, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
199 41 0.18
200 186 0.82
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (200 bp):
AATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAAATTTGTGACGA
TACTTTATGTCCAGAATGGATGCCAAAAAGGATGAACGCACAAAGTGCCAATACATTTTCAAAAA
GTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACCA
GTATA
Found at i:642213 original size:199 final size:196
Alignment explanation
Indices: 641722--642422 Score: 707
Period size: 200 Copynumber: 3.5 Consensus size: 196
641712 ACCTAAATAT
* * * * *
641722 GTGTTGATACATTTAT-ACAAGTATCGACCCAAAAAACATCAAAACTAATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATA
* * * * *
641786 GGTAAATTAACAATGTAACCGGTATAAATATATCGGTTAATTAGAAAATA-TGTCAACATAATGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGTTTTATGAGAAAATAGT-TC-ACATAATGT
* * *
641850 ATCGACACTTGTGGAATTTGTGTCGATACTTATTGTCCAGGATGAATG-CACAAACGAGGTGC-A
129 ATCGACACTTGT-AAATTTGTGTCGATACTT-TTGTCCAGAATGAATGCCA-AAAAG-GGTGCAA
641913 CGCATAAA
190 C-CATAAA
* * * * * * *
641921 ATGTCGATACATTTATTAAAAGTATCGATCCTAAAAATATCGAAATCGATAATTATAATGTATTA
1 GTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATA
* * *
641986 GGTAAATTTACAATGTAACCGATATAAATATACCGATTTTATGATAAAATAGTTCAGCATAAAGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCG-TTTTATGAGAAAATAGTTCA-CATAATGT
* *
642051 ATTGACACTTGCTAAATTTATGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACC
129 ATCGACACTTG-TAAATTTGTGTCGATACTTTT-GTCCAGAATGAATGCCAAAAAGGGTGCAACC
642116 ATAAA
192 ATAAA
** * *
642121 GTGTCGATACATTTATAAAAAGTATCGATCC-GGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATA
* * * * *
642185 TGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTAAATAATGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACC-GTTTTATGAGAAAATAGTTC-ACATAATGT
* * * * **
642250 ATCGACACTTTGTTAGTTTGTGTCGATATTTTTTTCCAGAATGAAATATGAATGCCCAACCA-GG
129 ATCGACAC-TTGTAAATTTGTGTCGATACTTTTGTCC---A-G--A-ATGAATG-CCAAAAAGGG
* *
642314 TACAAGCATAAA
185 TGCAACCATAAA
* * *
642326 GTGTCGATACATTTA-AAATTA-TATCGATCTAAAAAACATCGAAACCAATAATAATAATGTAAT
1 GTGTCGATACATTTATAAA-AAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAAT
** *
642389 AGGTAAATTTGTAATGTTACCGGTATAAATATAC
65 AGGTAAATTTACAATGTAACCGGTATAAATATAC
642423 TGGTTTACTT
Statistics
Matches: 419, Mismatches: 62, Indels: 36
0.81 0.12 0.07
Matches are distributed among these distances:
198 3 0.01
199 117 0.28
200 119 0.28
201 66 0.16
202 5 0.01
204 12 0.03
205 92 0.22
206 5 0.01
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (196 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGGTATAAATATACCGTTTTATGAGAAAATAGTTCACATAATGTAT
CGACACTTGTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAA
A
Found at i:642397 original size:205 final size:199
Alignment explanation
Indices: 641722--642428 Score: 725
Period size: 199 Copynumber: 3.5 Consensus size: 199
641712 ACCTAAATAT
* * * * * *
641722 GTGTTGATACATTTATACAAGTATCGACCCAAAAAACATCAAAACTAATAATTATAATGTAATAG
1 GTGTCGATACATTTATAAAAGTATCGATCTAAAAAACATCGAAACCAATAATTATAATGTAATAG
* * * * *
641787 GTAAATTAACAATGTAACCGGTATAAATATATCGG-TTAATTAGAAAATATGTCAACATAATGTA
66 GTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAA-ATAATGTA
* * * * *
641851 TCGACACTTGTGGAATTTGTGTCGATACTTATTGTCCAG-G-ATGAATGCACAAACGAGGTGCAC
130 TCGACACTTGT-AAATTTGTGTCGATACTTTTTGTCCAGAGAATGAATGC-CCAACAAGGTGCAA
641914 GCATAAA
193 GCATAAA
* * * * *
641921 ATGTCGATACATTTATTAAAAGTATCGATCCT-AAAAATATCGAAATCGATAATTATAATGTATT
1 GTGTCGATACATTTA-TAAAAGTATCGAT-CTAAAAAACATCGAAACCAATAATTATAATGTAAT
* * * * * *
641985 AGGTAAATTTACAATGTAACCGATATAAATATACCGATTTTATGATAAAATAGTTCAGCATAAAG
64 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCA-AATAATG
* * * *
642050 TATTGACACTTGCTAAATTTATGTCGATACTTTTGGTCC--AGAATGAATG-CCAAAAAGGGTGC
128 TATCGACACTTG-TAAATTTGTGTCGATACTTTTTGTCCAGAGAATGAATGCCCAACAA-GGTGC
*
642112 AACCATAAA
191 AAGCATAAA
*** * *
642121 GTGTCGATACATTTATAAAAAGTATCGATC-CGGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATACATTTAT-AAAAGTATCGATCTAAAAAACATCGAAACCAATAATTATAATGTAATA
* * *
642185 TGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTAAATAATGT
65 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTC-AAATAATGT
* * * *
642250 ATCGACACTTTGTTAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAATATGAATGCCCAACCAGG
129 ATCGACAC-TTGTAAATTTGTGTCGATACTTTTTGTCCAG-A-G--A-ATGAATGCCCAACAAGG
*
642314 TACAAGCATAAA
188 TGCAAGCATAAA
*
642326 GTGTCGATACATTTA-AAATTA-TATCGATCTAAAAAACATCGAAACCAATAATAATAATGTAAT
1 GTGTCGATACATTTATAAA--AGTATCGATCTAAAAAACATCGAAACCAATAATTATAATGTAAT
** * *
642389 AGGTAAATTTGTAATGTTACCGGTATAAATATACTGGTTT
64 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTT
642429 ACTTCGAAAA
Statistics
Matches: 415, Mismatches: 70, Indels: 40
0.79 0.13 0.08
Matches are distributed among these distances:
198 7 0.02
199 119 0.29
200 113 0.27
201 60 0.14
202 2 0.00
203 3 0.01
204 9 0.02
205 97 0.23
206 5 0.01
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (199 bp):
GTGTCGATACATTTATAAAAGTATCGATCTAAAAAACATCGAAACCAATAATTATAATGTAATAG
GTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAAATAATGTAT
CGACACTTGTAAATTTGTGTCGATACTTTTTGTCCAGAGAATGAATGCCCAACAAGGTGCAAGCA
TAAA
Found at i:642580 original size:23 final size:23
Alignment explanation
Indices: 642530--642574 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
642520 TGCTTATTTT
*
642530 ATTATATAAGCGTTACCTATTAC
1 ATTATATAAGCGTTACCTAATAC
642553 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGTTACCTAATA
642575 TGTTATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGTTACCTAATAC
Found at i:642605 original size:87 final size:87
Alignment explanation
Indices: 642446--642608 Score: 265
Period size: 87 Copynumber: 1.9 Consensus size: 87
642436 AAATAAGTCA
*
642446 ATATAAGCGCTATCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
*
642511 CTGGTTAAATGCTTATTTTATT
66 CTAGTTAAATGCTTATTTTATT
* * *
642533 ATATAAGCGTTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
642598 AC-AGTTAAATG
66 -CTAGTTAAATG
642609 ATATAACATT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
87 69 0.99
88 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.43
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
CTAGTTAAATGCTTATTTTATT
Found at i:643096 original size:2 final size:2
Alignment explanation
Indices: 643089--643134 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
643079 TAGTGACCAT
643089 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
643131 TA TA
1 TA TA
643135 ACGGGTAAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:647586 original size:14 final size:14
Alignment explanation
Indices: 647567--647619 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
647557 CGAGCTGAAT
*
647567 ATAAACGAATAAAC
1 ATAAACGAACAAAC
*
647581 ATAAACTAACAAAC
1 ATAAACGAACAAAC
* *
647595 ATAAACAAACAACC
1 ATAAACGAACAAAC
*
647609 ATAAATGAACA
1 ATAAACGAACA
647620 TATTACTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.64, C:0.19, G:0.04, T:0.13
Consensus pattern (14 bp):
ATAAACGAACAAAC
Found at i:649004 original size:17 final size:18
Alignment explanation
Indices: 648982--649015 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
648972 AATGTTTTAT
*
648982 TTAG-TTATTTTTTAATA
1 TTAGTTTATATTTTAATA
648999 TTAGTTTATATTTTAAT
1 TTAGTTTATATTTTAAT
649016 TTGTATACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
TTAGTTTATATTTTAATA
Found at i:651307 original size:21 final size:21
Alignment explanation
Indices: 651281--651337 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
651271 TAATTAGGTG
*
651281 TTATATAAGCTTAAAGAAAGC
1 TTATATAAGCTTAAAGAAAAC
651302 TTATATAAGCTTAAAGAAAAC
1 TTATATAAGCTTAAAGAAAAC
651323 TTATATAAGCTTAAA
1 TTATATAAGCTTAAA
651338 ATACCAAGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.32
Consensus pattern (21 bp):
TTATATAAGCTTAAAGAAAAC
Found at i:652729 original size:18 final size:18
Alignment explanation
Indices: 652660--652721 Score: 106
Period size: 18 Copynumber: 3.4 Consensus size: 18
652650 GAGGGTCTAT
652660 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
652678 GTGGTCATTCGGGACACA
1 GTGGTCCTTCGGGACATA
652696 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
652714 GTGGTCCT
1 GTGGTCCT
652722 ACTGGACAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.16, C:0.23, G:0.34, T:0.27
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:652729 original size:36 final size:36
Alignment explanation
Indices: 652660--652729 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
652650 GAGGGTCTAT
*
652660 GTGGTCCTTCGGGACATAGTGGTCATTCGGGACACA
1 GTGGTCCTTCGGGACATAGTGGTCATACGGGACACA
* *
652696 GTGGTCCTTCGGGACATAGTGGTCCTACTGGACA
1 GTGGTCCTTCGGGACATAGTGGTCATACGGGACA
652730 AATTCTACGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.19, C:0.23, G:0.33, T:0.26
Consensus pattern (36 bp):
GTGGTCCTTCGGGACATAGTGGTCATACGGGACACA
Found at i:656376 original size:2 final size:2
Alignment explanation
Indices: 656369--656412 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
656359 CCTAATAAAA
656369 AT AT AT AT 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
656411 AT
1 AT
656413 CGAATCGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:656888 original size:18 final size:16
Alignment explanation
Indices: 656854--656897 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
656844 TTTTAAAATT
*
656854 TTATAATTTAATAAAA
1 TTATAATTTAAAAAAA
656870 TTATAATTTAAAAGTAAA
1 TTATAATTTAAAA--AAA
*
656888 TAATAATTTA
1 TTATAATTTA
656898 TATATATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 12 0.50
18 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
TTATAATTTAAAAAAA
Found at i:656890 original size:62 final size:60
Alignment explanation
Indices: 656824--656975 Score: 162
Period size: 62 Copynumber: 2.5 Consensus size: 60
656814 TCTTTTTATC
* * * *
656824 AATAAAAATTTATA-ATTTTTTTTTAAAATTTTATAATTTAATAAAATTATAATTTAAAAGT
1 AATAAAAATTTATATATTTTTTTTTAAAA--TTAAAATTCAAAAAAAATATAATTTAAAAGT
* * *
656885 AAATAATAATTTATATATATATTTTTTAAAATTAAAATTCAAAAAAAATATAATTTAAACGT
1 -AATAAAAATTTATATAT-TTTTTTTTAAAATTAAAATTCAAAAAAAATATAATTTAAAAGT
*** *
656947 AAGCGAAATTTATATATTTTTTTTAAAAA
1 AATAAAAATTTATATATTTTTTTTTAAAA
656976 AATCATAATT
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
60 10 0.13
61 13 0.17
62 39 0.52
63 2 0.03
64 11 0.15
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.45
Consensus pattern (60 bp):
AATAAAAATTTATATATTTTTTTTTAAAATTAAAATTCAAAAAAAATATAATTTAAAAGT
Found at i:667843 original size:77 final size:77
Alignment explanation
Indices: 667746--667900 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
667736 TACTTCATGC
667746 AAGCATATGTGTGCTATAAATGATTGGGGAACAAATTTTTGCACGCATCAAAACATAGTGGGTTG
1 AAGCATATGTGTGCTATAAATGATTGGGGAACAAATTTTTGCACGCATCAAAACATAGTGGGTTG
667811 AAAGAATAACTT
66 AAAGAATAACTT
667823 AAGCATATGTGTGCTATAAATGATTGGGGAACAAATTTTTGCACGCATCAAAACATAGTGGGTTG
1 AAGCATATGTGTGCTATAAATGATTGGGGAACAAATTTTTGCACGCATCAAAACATAGTGGGTTG
667888 AAAGAATAACTT
66 AAAGAATAACTT
667900 A
1 A
667901 CATGGTATGA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (77 bp):
AAGCATATGTGTGCTATAAATGATTGGGGAACAAATTTTTGCACGCATCAAAACATAGTGGGTTG
AAAGAATAACTT
Found at i:670894 original size:7 final size:7
Alignment explanation
Indices: 670890--670937 Score: 78
Period size: 7 Copynumber: 6.9 Consensus size: 7
670880 TCCCCCTTTC
670890 CCCTTCA
1 CCCTTCA
670897 CCCTTCA
1 CCCTTCA
670904 CCCTTCA
1 CCCTTCA
*
670911 CCCTTCC
1 CCCTTCA
670918 CCCTTCA
1 CCCTTCA
*
670925 CCCTTCC
1 CCCTTCA
670932 CCCTTC
1 CCCTTC
670938 TCATAGCAGC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.08, C:0.62, G:0.00, T:0.29
Consensus pattern (7 bp):
CCCTTCA
Found at i:670900 original size:14 final size:14
Alignment explanation
Indices: 670878--670937 Score: 93
Period size: 14 Copynumber: 4.3 Consensus size: 14
670868 TGCTTCCTCT
* *
670878 CTTCCCCCTTTCCC
1 CTTCACCCTTCCCC
*
670892 CTTCACCCTTCACC
1 CTTCACCCTTCCCC
670906 CTTCACCCTTCCCC
1 CTTCACCCTTCCCC
670920 CTTCACCCTTCCCC
1 CTTCACCCTTCCCC
670934 CTTC
1 CTTC
670938 TCATAGCAGC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 42 1.00
ACGTcount: A:0.07, C:0.62, G:0.00, T:0.32
Consensus pattern (14 bp):
CTTCACCCTTCCCC
Found at i:670902 original size:21 final size:21
Alignment explanation
Indices: 670878--670937 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
670868 TGCTTCCTCT
*
670878 CTTCCCCCTTTCCCCTTCACC
1 CTTCACCCTTTCCCCTTCACC
*
670899 CTTCACCC-TTCACCCTTCCCC
1 CTTCACCCTTTC-CCCTTCACC
*
670920 CTTCACCCTTCCCCCTTC
1 CTTCACCCTTTCCCCTTC
670938 TCATAGCAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.09
21 29 0.85
22 2 0.06
ACGTcount: A:0.07, C:0.62, G:0.00, T:0.32
Consensus pattern (21 bp):
CTTCACCCTTTCCCCTTCACC
Found at i:675410 original size:23 final size:23
Alignment explanation
Indices: 675380--675425 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
675370 CTTTAATATC
675380 ACCGATTACCATTGATATAGAAA
1 ACCGATTACCATTGATATAGAAA
675403 ACCGATTACCATTGATATAGAAA
1 ACCGATTACCATTGATATAGAAA
675426 CTAATCCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (23 bp):
ACCGATTACCATTGATATAGAAA
Found at i:675436 original size:20 final size:23
Alignment explanation
Indices: 675380--675440 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
675370 CTTTAATATC
*
675380 ACCGATTACCATTGATATAGAAA
1 ACCGAATACCATTGATATAGAAA
*
675403 ACCGATTACCATTGATATAG-AA
1 ACCGAATACCATTGATATAGAAA
*
675425 A-CTAAT-CCATTGATAT
1 ACCGAATACCATTGATAT
675441 CGAACAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 10 0.28
21 3 0.08
22 3 0.08
23 20 0.56
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (23 bp):
ACCGAATACCATTGATATAGAAA
Found at i:684348 original size:43 final size:42
Alignment explanation
Indices: 684296--684381 Score: 102
Period size: 41 Copynumber: 2.0 Consensus size: 42
684286 CGACATTTTT
*
684296 TTCCTAAAAACGTCGCTAAATGTTCTGACATATAGCGGCGTTTG
1 TTCCTAAAAACGCCGCTAAATG-T-TGACATATAGCGGCGTTTG
* * * *
684340 TTCC-AAAAATGCCTCTAAATGTTGTCATATAGTGGCGTTTG
1 TTCCTAAAAACGCCGCTAAATGTTGACATATAGCGGCGTTTG
684381 T
1 T
684382 GAATGTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
41 18 0.49
42 1 0.03
43 14 0.38
44 4 0.11
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (42 bp):
TTCCTAAAAACGCCGCTAAATGTTGACATATAGCGGCGTTTG
Found at i:693870 original size:51 final size:51
Alignment explanation
Indices: 693794--693896 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
693784 TCCAGAAGAA
693794 GTCGAGGGGATAAGCCTAGTATCAAGGAGCTTCAAGATCCCGTTACAGATG
1 GTCGAGGGGATAAGCCTAGTATCAAGGAGCTTCAAGATCCCGTTACAGATG
693845 GTCGAGGGGATAAGCCTAGTATCAAGGAGCTTCAAGATCCCGTTACAGATG
1 GTCGAGGGGATAAGCCTAGTATCAAGGAGCTTCAAGATCCCGTTACAGATG
693896 G
1 G
693897 AAGTAAGGTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.21
Consensus pattern (51 bp):
GTCGAGGGGATAAGCCTAGTATCAAGGAGCTTCAAGATCCCGTTACAGATG
Found at i:694443 original size:40 final size:40
Alignment explanation
Indices: 694398--694710 Score: 178
Period size: 40 Copynumber: 7.7 Consensus size: 40
694388 CTAAAGAATG
* * * **
694398 AGTATTTAGCGTCATTTGTATACAAACGTCACTAAACTAT
1 AGTATTTAGCGGCATTTATATAAAAACACCACTAAACTAT
*
694438 AGTATTTAGCGGCATTTATATAAAAACACCACTAAAGTAT
1 AGTATTTAGCGGCATTTATATAAAAACACCACTAAACTAT
* * * *** * *
694478 AGTTTTTAGCGGCGTTTATCTAAAAGTGCCACTACAGTAT
1 AGTATTTAGCGGCATTTATATAAAAACACCACTAAACTAT
* * * * * * ** * *
694518 GAGTATTTAACGACGTTTGTGCTTAAAATGCCACTAAAGTACG
1 -AGTATTTAGCGGCATTTAT-ATAAAAACACCACTAAACTA-T
* * ** *
694561 AGTATTTAGTGGCATTTGTATAAAAACACCACTAAAGAACA
1 AGTATTTAGCGGCATTTATATAAAAACACCACTAAACTA-T
* * * * *
694602 AGTATTTAGCGGCATTTGTACTTAAAACGCCACTAAAGTAAG
1 AGTATTTAGCGGCATTTATA-TAAAAACACCACTAAACT-AT
* ** * ** *
694644 AGTCTTTAGCGGTGTTTGTATAAAAATGCCACTGAACTAT
1 AGTATTTAGCGGCATTTATATAAAAACACCACTAAACTAT
*
694684 AGTATTTAGCGGCGTTTAT-TCAAAAAC
1 AGTATTTAGCGGCATTTATAT-AAAAAC
694711 CGCCGCTAAA
Statistics
Matches: 219, Mismatches: 48, Indels: 12
0.78 0.17 0.04
Matches are distributed among these distances:
39 1 0.00
40 89 0.41
41 64 0.29
42 64 0.29
43 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (40 bp):
AGTATTTAGCGGCATTTATATAAAAACACCACTAAACTAT
Found at i:694579 original size:42 final size:41
Alignment explanation
Indices: 694387--694696 Score: 207
Period size: 41 Copynumber: 7.6 Consensus size: 41
694377 AAAAGTAAAG
* * * * *
694387 ACTAAAGAATGAGTATTTAGCGTCATTTGT-ATACAAACGTC
1 ACTAAAGTACGAGTATTTAGCGGCATTTGTCTTA-AAACGCC
* * * * * *
694428 ACTAAACTA-TAGTATTTAGCGGCATTTATATAAAAACACC
1 ACTAAAGTACGAGTATTTAGCGGCATTTGTCTTAAAACGCC
* * * * *
694468 ACTAAAGTA-TAGTTTTTAGCGGCGTTTATC-TAAAAGTGCC
1 ACTAAAGTACGAGTATTTAGCGGCATTTGTCTTAAAA-CGCC
* * * * * *
694508 ACTACAGTATGAGTATTTAACGACGTTTGTGCTTAAAATGCC
1 ACTAAAGTACGAGTATTTAGCGGCATTTGT-CTTAAAACGCC
* * * *
694550 ACTAAAGTACGAGTATTTAGTGGCATTTGTATAAAAACACC
1 ACTAAAGTACGAGTATTTAGCGGCATTTGTCTTAAAACGCC
* *
694591 ACTAAAGAACAAGTATTTAGCGGCATTTGTACTTAAAACGCC
1 ACTAAAGTACGAGTATTTAGCGGCATTTGT-CTTAAAACGCC
* * ** * * *
694633 ACTAAAGTAAGAGTCTTTAGCGGTGTTTGTATAAAAATGCC
1 ACTAAAGTACGAGTATTTAGCGGCATTTGTCTTAAAACGCC
* * *
694674 ACTGAACTA-TAGTATTTAGCGGC
1 ACTAAAGTACGAGTATTTAGCGGC
694697 GTTTATTCAA
Statistics
Matches: 211, Mismatches: 52, Indels: 13
0.76 0.19 0.05
Matches are distributed among these distances:
39 4 0.02
40 69 0.33
41 72 0.34
42 61 0.29
43 5 0.02
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (41 bp):
ACTAAAGTACGAGTATTTAGCGGCATTTGTCTTAAAACGCC
Found at i:694585 original size:83 final size:82
Alignment explanation
Indices: 694387--694676 Score: 233
Period size: 83 Copynumber: 3.5 Consensus size: 82
694377 AAAAGTAAAG
* * * * * * ** * * *
694387 ACTAAAGAATGAGTATTTAGCGTCATTTGTATACAAACGTCACTAAACTA-TAGTATTTAGCGGC
1 ACTAAAGTA-GAGTATTTAGCGGCGTTTGTATAAAAATGCCACTAAAGAACAAGTATTTAACGAC
* * *
694451 ATTTATA-TAAAAACACC
65 ATTTGTACTTAAAACGCC
* * * * * * * ** *
694468 ACTAAAGTATAGTTTTTAGCGGCGTTTATCTAAAAGTGCCACTACAGTATGAGTATTTAACGACG
1 ACTAAAGTAGAGTATTTAGCGGCGTTTGTATAAAAATGCCACTAAAGAACAAGTATTTAACGACA
* *
694533 TTTGTGCTTAAAATGCC
66 TTTGTACTTAAAACGCC
* * ** * *
694550 ACTAAAGTACGAGTATTTAGTGGCATTTGTATAAAAACACCACTAAAGAACAAGTATTTAGCGGC
1 ACTAAAGTA-GAGTATTTAGCGGCGTTTGTATAAAAATGCCACTAAAGAACAAGTATTTAACGAC
694615 ATTTGTACTTAAAACGCC
65 ATTTGTACTTAAAACGCC
* *
694633 ACTAAAGTAAGAGTCTTTAGCGGTGTTTGTATAAAAATGCCACT
1 ACTAAAGT-AGAGTATTTAGCGGCGTTTGTATAAAAATGCCACT
694677 GAACTATAGT
Statistics
Matches: 159, Mismatches: 46, Indels: 6
0.75 0.22 0.03
Matches are distributed among these distances:
80 28 0.18
81 23 0.14
82 16 0.10
83 91 0.57
84 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (82 bp):
ACTAAAGTAGAGTATTTAGCGGCGTTTGTATAAAAATGCCACTAAAGAACAAGTATTTAACGACA
TTTGTACTTAAAACGCC
Found at i:705098 original size:2 final size:2
Alignment explanation
Indices: 705091--705142 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
705081 TGTGTATTAT
705091 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
705132 TA TA TA TA TA T
1 TA TA TA TA TA T
705143 GTTTATTGGT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:706330 original size:11 final size:11
Alignment explanation
Indices: 706314--706339 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
706304 AATCTTGTTT
706314 AAAATAATATC
1 AAAATAATATC
706325 AAAATAATATC
1 AAAATAATATC
706336 AAAA
1 AAAA
706340 ACCATGTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATAATATC
Found at i:709125 original size:2 final size:2
Alignment explanation
Indices: 709062--709107 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
709052 GTATTTGCGG
709062 AT AT AT AT 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
709104 AT AT
1 AT AT
709108 GAATAAGGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:709668 original size:23 final size:23
Alignment explanation
Indices: 709608--709668 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
709598 ATATGCATTT
709608 CAGTGCATTTCTACGCGGCACTA
1 CAGTGCATTTCTACGCGGCACTA
* * *
709631 CAGTGCAATTCTACGGGGCACTT
1 CAGTGCATTTCTACGCGGCACTA
* *
709654 CGGTGCATTTATACG
1 CAGTGCATTTCTACG
709669 AGCTGTGGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (23 bp):
CAGTGCATTTCTACGCGGCACTA
Found at i:715682 original size:2 final size:2
Alignment explanation
Indices: 715677--715706 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
715667 AAATACACAC
715677 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
715707 TAGGTAAAAC
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:716864 original size:14 final size:13
Alignment explanation
Indices: 716834--716867 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
716824 AAATATGTAA
*
716834 ATTATATATATAT
1 ATTATATATATAC
716847 ATTATATAATATAC
1 ATTATAT-ATATAC
716861 ATTATAT
1 ATTATAT
716868 GGACAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTATATATATAC
Found at i:717397 original size:15 final size:15
Alignment explanation
Indices: 717374--717405 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
717364 TTTTTGTGTT
*
717374 TCAAGAGAAACTGTC
1 TCAAAAGAAACTGTC
717389 TCAAAAGAAACTGTC
1 TCAAAAGAAACTGTC
717404 TC
1 TC
717406 GAGTGAGACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.22
Consensus pattern (15 bp):
TCAAAAGAAACTGTC
Found at i:717586 original size:15 final size:15
Alignment explanation
Indices: 717563--717594 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
717553 TTTTTGTGTT
*
717563 TCAAGAGAAACTGTC
1 TCAAAAGAAACTGTC
717578 TCAAAAGAAACTGTC
1 TCAAAAGAAACTGTC
717593 TC
1 TC
717595 GAGTGAGACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.22
Consensus pattern (15 bp):
TCAAAAGAAACTGTC
Found at i:717593 original size:189 final size:191
Alignment explanation
Indices: 717271--717650 Score: 730
Period size: 189 Copynumber: 2.0 Consensus size: 191
717261 TAGCTTTTCT
717271 CGACTTAAGCTATGCTGTAAATTATGTGCCTTTGAGCTGAGGCGAAACTGAAACTCGAAGGTTTG
1 CGACTTAAGCTATGCTGTAAATTATGTGCCTTTGAGCTGAGGCGAAACTGAAACTCGAAGGTTTG
717336 GTGTTTCAAGAGAAACATTTTCAAAGATTTTTTGTGTTTCAAGAGAAACTGTCTCAAAAGAAACT
66 GTGTTTCAAGAGAAACATTTTCAAAGATTTTTTGTGTTTCAAGAGAAACTGTCTCAAAAGAAACT
717401 GTCTCGAGTGAGACGAAATTTGTTTAATGGAAAATAGATTCAAAAGA-TTTGTTTTCAAGGG
131 GTCTCGAGTGAGACGAAATTTGTTTAATGGAAAATAGATTCAAAAGATTTTG-TTTCAAGGG
717462 CGACTTAAGCTATGCTGTAAATTATGTGCCTTTGAGCTGA-GCGAAACTG-AACTCGAAGGTTTG
1 CGACTTAAGCTATGCTGTAAATTATGTGCCTTTGAGCTGAGGCGAAACTGAAACTCGAAGGTTTG
717525 GTGTTTCAAGAGAAACATTTTCAAAGATTTTTTGTGTTTCAAGAGAAACTGTCTCAAAAGAAACT
66 GTGTTTCAAGAGAAACATTTTCAAAGATTTTTTGTGTTTCAAGAGAAACTGTCTCAAAAGAAACT
717590 GTCTCGAGTGAGACGAAATTTGTTTAATGGAAAATAGATTCAAAAGATTTTGTTTCAAGGG
131 GTCTCGAGTGAGACGAAATTTGTTTAATGGAAAATAGATTCAAAAGATTTTGTTTCAAGGG
717651 AAATGTCTCA
Statistics
Matches: 188, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
189 135 0.72
190 13 0.07
191 40 0.21
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (191 bp):
CGACTTAAGCTATGCTGTAAATTATGTGCCTTTGAGCTGAGGCGAAACTGAAACTCGAAGGTTTG
GTGTTTCAAGAGAAACATTTTCAAAGATTTTTTGTGTTTCAAGAGAAACTGTCTCAAAAGAAACT
GTCTCGAGTGAGACGAAATTTGTTTAATGGAAAATAGATTCAAAAGATTTTGTTTCAAGGG
Found at i:717694 original size:102 final size:101
Alignment explanation
Indices: 717580--717828 Score: 347
Period size: 102 Copynumber: 2.4 Consensus size: 101
717570 AAACTGTCTC
* * * *
717580 AAAAGAAACTGTCTCGAGTGAGACGAAATTTGTTTAATGGAAAATAGATTCAAAAGATTTTGTTT
1 AAAAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTC-AAAGATTTTGTTT
717645 CAAGGGAAA-TGTCTCAAGAGAGACAAAATTTAGTTCT
65 CAAGGGAAACTGTCTCAAGAGAGACAAAATTT-GTTCT
* *
717682 AAAAGAAACTGTCTCAAGAGAGATGAAATTTGTTTAAAGGAAAACAGATTCAGAGATTTTGTTTC
1 AAAAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAAAGATTTTGTTTC
*
717747 AAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTT
66 AAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTCT
** * * *
717783 ACGAGAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAAA
1 AAAAGAAACTGTCTCAAGAGAGACGAAATTT-GTT-TAAAGGAAAA
717829 TGTCTCAAGA
Statistics
Matches: 131, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
101 51 0.39
102 71 0.54
103 9 0.07
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.27
Consensus pattern (101 bp):
AAAAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAAAGATTTTGTTTC
AAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTCT
Found at i:717695 original size:37 final size:37
Alignment explanation
Indices: 717650--717884 Score: 228
Period size: 37 Copynumber: 6.6 Consensus size: 37
717640 TGTTTCAAGG
717650 GAAA-TGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
1 GAAACTGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
** *
717686 GAAACTGTCTCAAGAGAGATGAAATTT-GTT-TAAAG
1 GAAACTGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
* * **
717721 GAAAACAGAT-TC---AGAG-----ATTTTGTT-TCAAGG
1 G-AAACTG-TCTCAAGAGAGACAAAATTTAGTTCT-AAAA
* **
717751 GAAACTGTCTCAAGAGAGACAAAATTT-GTTTTACGA
1 GAAACTGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
*
717787 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
1 GAAACTGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
*
717824 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
1 GAAACTGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
*
717861 GAAACTGTTTCAAGAGAGACAAAA
1 GAAACTGTCTCAAGAGAGACAAAA
717885 CTTTGTTTCA
Statistics
Matches: 169, Mismatches: 14, Indels: 31
0.79 0.07 0.14
Matches are distributed among these distances:
28 5 0.03
29 11 0.07
30 4 0.02
32 4 0.02
33 4 0.02
35 5 0.03
36 45 0.27
37 91 0.54
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (37 bp):
GAAACTGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
Found at i:717779 original size:36 final size:36
Alignment explanation
Indices: 717739--718041 Score: 246
Period size: 36 Copynumber: 8.4 Consensus size: 36
717729 ATTCAGAGAT
*
717739 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
717775 TTTGTTTTACGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
717811 TTTAG-TTCTAAAAGAAAATGTCTCAAGAGAGACAAAA
1 TTT-GTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAA
* *
717848 TTTAG-TTCTAAAAGAAACTGTTTCAAGAGAGACAAAA
1 TTT-GTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAA
** *******
717885 CTTTGTTTCAAG-GAAAACAAAT-TCAA-AG-TTTTTTT
1 -TTTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
* **
717920 TTTGTTTCAAGGGAAACCATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
717956 TTTGTTTTAAGAGAAAATGTCTCAAGAGATACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
717992 TTTGTTT-TA-AGAAATTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
718026 CTTTGTTTCAAG-GAAA
1 -TTTGTTTCAAGAGAAA
718042 ACAAATTCGA
Statistics
Matches: 217, Mismatches: 37, Indels: 26
0.77 0.13 0.09
Matches are distributed among these distances:
33 2 0.01
34 42 0.19
35 11 0.05
36 82 0.38
37 73 0.34
38 7 0.03
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:717974 original size:181 final size:172
Alignment explanation
Indices: 717651--718025 Score: 552
Period size: 181 Copynumber: 2.1 Consensus size: 172
717641 GTTTCAAGGG
**
717651 AAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGATGAAATTTGTT
1 AAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTT
* * **
717716 TAAAGGAAAACAGATTCAGAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
66 TAAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACCATCTCAAGAGAGACAAAATTTGTT
*
717781 TTACGAGAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGA
131 TTAAGAGAAAATGTCTCAAGAGAGACAAAATTT-GTT-T-AAAGA
*
717826 AAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTTTCAAGAGAGACAAAACTTTGT
1 AAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACAAAA-TTTGT
* *
717891 TTCAAGGAAAACAAATTCAAAGTTTTTTTTTTGTTTCAAGGGAAACCATCTCAAGAGAGACAAAA
65 TTAAAGGAAAACAAATTCAAAG-----ATTTTGTTTCAAGGGAAACCATCTCAAGAGAGACAAAA
* *
717956 TTTGTTTTAAGAGAAAATGTCTCAAGAGATACAAAATTTGTTTTAAGA
125 TTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTAAAGA
*
718004 AATTGTCTCAAGAGAGACAAAA
1 AAATGTCTCAAGAGAGACAAAA
718026 CTTTGTTTCA
Statistics
Matches: 181, Mismatches: 13, Indels: 9
0.89 0.06 0.04
Matches are distributed among these distances:
175 56 0.31
176 24 0.13
178 25 0.14
179 1 0.01
180 3 0.02
181 72 0.40
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (172 bp):
AAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTT
TAAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACCATCTCAAGAGAGACAAAATTTGTT
TTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTAAAGA
Found at i:718031 original size:141 final size:140
Alignment explanation
Indices: 717794--718104 Score: 484
Period size: 141 Copynumber: 2.2 Consensus size: 140
717784 CGAGAAAATG
* *
717794 TCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAA
1 TCTCAAGAGAGACAAAATTT-GTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAA
*
717859 AAGAAACTGTTTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACAAATTCAAAGTTTTTTTTTTG
65 AAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACAAATTCAAAG----TTTTTTG
717924 TTTCAAGGGAAACCA
126 TTTCAAGGGAAACCA
* *
717939 TCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGATACAAAATTT-GTT-T-TA
1 TCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAA
* *
718001 AGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACAAATTCGAAGTTTTTTGTTTCA
66 AGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACAAATTCAAAGTTTTTTGTTTCA
718066 AGGGAAACCA
131 AGGGAAACCA
*
718076 TCGCAAGAGAGACAAAATTTGTTTTAAGA
1 TCTCAAGAGAGACAAAATTTGTTTTAAGA
718105 AACTGTAATC
Statistics
Matches: 158, Mismatches: 8, Indels: 8
0.91 0.05 0.05
Matches are distributed among these distances:
137 50 0.32
141 51 0.32
142 1 0.01
143 3 0.02
144 33 0.21
145 20 0.13
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (140 bp):
TCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAA
AGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACAAATTCAAAGTTTTTTGTTTCA
AGGGAAACCA
Found at i:719421 original size:95 final size:95
Alignment explanation
Indices: 719258--719440 Score: 287
Period size: 95 Copynumber: 1.9 Consensus size: 95
719248 AATATGTAAA
* * *
719258 TACCTTTATCAGATTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGG
1 TACCTTTATCAGACTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTGCCTTAGAGG
* *
719323 GACAACTCAAGCTTTATTGTATAGCATAAT
66 GACAACTCAAGATTTATTATATAGCATAAT
* *
719353 TACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGTGTTTAACCAATTG-CTCTAGAG
1 TACCTTTATCAGACTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTGCCT-TAGAG
719417 GGACAACTCAAGATTTATTATATA
65 GGACAACTCAAGATTTATTATATA
719441 TATATATATA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
94 2 0.03
95 78 0.98
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (95 bp):
TACCTTTATCAGACTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTGCCTTAGAGG
GACAACTCAAGATTTATTATATAGCATAAT
Found at i:721153 original size:10 final size:10
Alignment explanation
Indices: 721140--721182 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
721130 TATAGTATTT
721140 AAAAAAAATA
1 AAAAAAAATA
*
721150 AAAAGAAATA
1 AAAAAAAATA
*
721160 AAAAATAATA
1 AAAAAAAATA
*
721170 AAAAATAATA
1 AAAAAAAATA
721180 AAA
1 AAA
721183 TACATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.84, C:0.00, G:0.02, T:0.14
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:721164 original size:17 final size:17
Alignment explanation
Indices: 721142--721184 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
721132 TAGTATTTAA
721142 AAAAAATAA-AAAGAAAT
1 AAAAAATAATAAA-AAAT
721159 AAAAAATAATAAAAAAT
1 AAAAAATAATAAAAAAT
721176 AATAAAATA
1 AA-AAAATA
721185 CATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.16
Consensus pattern (17 bp):
AAAAAATAATAAAAAAT
Found at i:723748 original size:15 final size:13
Alignment explanation
Indices: 723719--723746 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
723709 TTATAAGGTA
723719 ATTTTTTTATAAT
1 ATTTTTTTATAAT
723732 ATTTTTTTATAAT
1 ATTTTTTTATAAT
723745 AT
1 AT
723747 ATGATTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTTTTTATAAT
Found at i:723896 original size:22 final size:22
Alignment explanation
Indices: 723866--723912 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
723856 ATATAAAATT
*
723866 AAATTATTTACGTTTATGTGTA
1 AAATGATTTACGTTTATGTGTA
723888 AAATGATTTACGTTTATGTGTA
1 AAATGATTTACGTTTATGTGTA
723910 AAA
1 AAA
723913 ATTTTATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (22 bp):
AAATGATTTACGTTTATGTGTA
Found at i:727316 original size:34 final size:32
Alignment explanation
Indices: 727278--727369 Score: 112
Period size: 34 Copynumber: 2.8 Consensus size: 32
727268 AATGGTAATA
* *
727278 AACAAAATTATCAAAATCAATTAACAAAAAGTCC
1 AACAAAATTAACAAAATAAATTAA-AAAAA-TCC
*
727312 AACAAAATAAACAAAATAAATTTTAAAAAAATCC
1 AACAAAATTAACAAAATAAA--TTAAAAAAATCC
*
727346 AACCAAATTAACAAAATAAATTAA
1 AACAAAATTAACAAAATAAATTAA
727370 TTATTAAATG
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
32 4 0.08
34 38 0.75
35 5 0.10
36 4 0.08
ACGTcount: A:0.64, C:0.14, G:0.01, T:0.21
Consensus pattern (32 bp):
AACAAAATTAACAAAATAAATTAAAAAAATCC
Found at i:729670 original size:16 final size:16
Alignment explanation
Indices: 729646--729694 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
729636 ATATCTTCAA
* *
729646 AAAAAATTAAGTAAAT
1 AAAATATTAAATAAAT
*
729662 AAAATATTAAATAATT
1 AAAATATTAAATAAAT
*
729678 TAAATAGTTAAATAAAT
1 AAAATA-TTAAATAAAT
729695 TACTAACAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (16 bp):
AAAATATTAAATAAAT
Found at i:735221 original size:24 final size:20
Alignment explanation
Indices: 735194--735251 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 20
735184 GCATAAGGAG
*
735194 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCAC-TG-T-A-GAA
* *
735218 TGCAACGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
735238 TGCATCGATGCACT
1 TGCATCGATGCACT
735252 TCAAGGGGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 14 0.48
21 1 0.03
22 1 0.03
23 2 0.07
24 11 0.38
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:736805 original size:23 final size:23
Alignment explanation
Indices: 736769--736838 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
736759 TCTTAGGGAT
* *
736769 AATTTTATATGGCACTTCGGTGC
1 AATTCTATACGGCACTTCGGTGC
* *
736792 AATTCTATGCGGCACTTCGATGC
1 AATTCTATACGGCACTTCGGTGC
*
736815 AATTCTATACAGCACTTCGGTGC
1 AATTCTATACGGCACTTCGGTGC
736838 A
1 A
736839 TTTATATGAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (23 bp):
AATTCTATACGGCACTTCGGTGC
Found at i:743355 original size:20 final size:19
Alignment explanation
Indices: 743332--743369 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
743322 AAAGATAACA
*
743332 TAAATAATAATATAAAAATT
1 TAAAAAATAAT-TAAAAATT
743352 TAAAAAATAATTAAAAAT
1 TAAAAAATAATTAAAAAT
743370 ACCACATCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAAATAATTAAAAATT
Found at i:745823 original size:7 final size:7
Alignment explanation
Indices: 745811--745912 Score: 129
Period size: 7 Copynumber: 14.7 Consensus size: 7
745801 ATGCCACGTC
745811 AGAAGGA
1 AGAAGGA
745818 AGAAGGA
1 AGAAGGA
745825 AGGAAGGA
1 A-GAAGGA
745833 AGAAGGA
1 AGAAGGA
745840 AGAAGGA
1 AGAAGGA
745847 AGAAGGA
1 AGAAGGA
745854 AGAAGGA
1 AGAAGGA
*
745861 AGAATGA
1 AGAAGGA
*
745868 AGAATGA
1 AGAAGGA
745875 AGAAGG-
1 AGAAGGA
745881 AGAA-GA
1 AGAAGGA
*
745887 AGAA-AA
1 AGAAGGA
*
745893 AGTAGGA
1 AGAAGGA
745900 AGAAAGGA
1 AG-AAGGA
745908 AGAAG
1 AGAAG
745913 AAAAAGAAAT
Statistics
Matches: 85, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
5 1 0.01
6 12 0.14
7 59 0.69
8 13 0.15
ACGTcount: A:0.58, C:0.00, G:0.39, T:0.03
Consensus pattern (7 bp):
AGAAGGA
Found at i:745826 original size:4 final size:4
Alignment explanation
Indices: 745812--745862 Score: 67
Period size: 4 Copynumber: 14.0 Consensus size: 4
745802 TGCCACGTCA
745812 GAAG GAA- GAAG GAAG GAAG GAA- GAAG GAA- GAAG GAA- GAAG GAA-
1 GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG
745855 GAAG GAAG
1 GAAG GAAG
745863 AATGAAGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
3 15 0.36
4 27 0.64
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (4 bp):
GAAG
Found at i:750571 original size:21 final size:20
Alignment explanation
Indices: 750547--750585 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
750537 ACCATTTAAT
*
750547 TATTAACTCTTTTATTTTTAC
1 TATTAA-TCTTTTAGTTTTAC
750568 TATTAATCTTTTAGTTTT
1 TATTAATCTTTTAGTTTT
750586 GTCAATCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.64
Consensus pattern (20 bp):
TATTAATCTTTTAGTTTTAC
Found at i:751014 original size:58 final size:57
Alignment explanation
Indices: 750944--751174 Score: 204
Period size: 58 Copynumber: 4.0 Consensus size: 57
750934 TTAAATTTAC
* * *
750944 ATTTACATTTTAACATTAAAAATATATTTTA-TTTTATCTTAGA-TTAGTATATATTTTT
1 ATTTTCATTTTAAC-TTAAAAATATATTTTACTCTTATTTTA-ACTTA-TATATATTTTT
* * *
751002 ATTTTCATTTTAACTTAAAAAATATATTTTAGTCTTATTTTAACTTAAAAATATATTTT
1 ATTTTCATTTTAACTT-AAAAATATATTTTACTCTTATTTTAACTTATATATAT-TTTT
* * * * *
751061 AGTCTT-ATTTTAGCTTAAAAATATATTTTAATCTTATTTTAGCTTAT-T-T-TTTTA
1 A-TTTTCATTTTAACTTAAAAATATATTTTACTCTTATTTTAACTTATATATATTTTT
* * * * *
751115 ATTTTTATCTTAACTTATGAAATATATTTTACTTTTATTTTAATTTAATATATATTTTT
1 ATTTTCATTTTAACTTA-AAAATATATTTTACTCTTATTTTAACTT-ATATATATTTTT
751174 A
1 A
751175 AAAGTAAATA
Statistics
Matches: 141, Mismatches: 21, Indels: 21
0.77 0.11 0.11
Matches are distributed among these distances:
53 3 0.02
54 13 0.09
55 24 0.17
56 3 0.02
57 3 0.02
58 62 0.44
59 30 0.21
60 3 0.02
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (57 bp):
ATTTTCATTTTAACTTAAAAATATATTTTACTCTTATTTTAACTTATATATATTTTT
Found at i:751052 original size:29 final size:28
Alignment explanation
Indices: 750950--751106 Score: 165
Period size: 29 Copynumber: 5.4 Consensus size: 28
750940 TTACATTTAC
*
750950 ATTTTAACATTAAAAATATATTTTATTTT
1 ATTTTAAC-TTAAAAATATATTTTATCTT
* ** *
750979 ATCTTAGA-TT-AGTATATATTTTTATTTT
1 ATTTTA-ACTTAAAAATATA-TTTTATCTT
751007 CATTTTAACTTAAAAAATATATTTTAGTCTT
1 -ATTTTAACTT-AAAAATATATTTTA-TCTT
751038 ATTTTAACTTAAAAATATATTTTAGTCTT
1 ATTTTAACTTAAAAATATATTTTA-TCTT
*
751067 ATTTTAGCTTAAAAATATATTTTAATCTT
1 ATTTTAACTTAAAAATATATTTT-ATCTT
*
751096 ATTTTAGCTTA
1 ATTTTAACTTA
751107 TTTTTTTAAT
Statistics
Matches: 112, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
27 6 0.05
28 12 0.11
29 68 0.61
30 17 0.15
31 9 0.08
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (28 bp):
ATTTTAACTTAAAAATATATTTTATCTT
Found at i:751131 original size:25 final size:24
Alignment explanation
Indices: 751086--751132 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
751076 TAAAAATATA
* *
751086 TTTTAATCTTATTTTAGCTTATTT
1 TTTTAATCTTATCTTAACTTATTT
*
751110 TTTTAATTTTTATCTTAACTTAT
1 TTTTAA-TCTTATCTTAACTTAT
751133 GAAATATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 6 0.32
25 13 0.68
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTTAATCTTATCTTAACTTATTT
Found at i:751151 original size:30 final size:28
Alignment explanation
Indices: 751117--751172 Score: 51
Period size: 28 Copynumber: 2.0 Consensus size: 28
751107 TTTTTTTAAT
* *
751117 TTTTATCTTAACTTATGAAATATATTTTA
1 TTTTATTTTAACTTA-AAAATATATTTTA
* *
751146 CTTTTATTTTAA-TTTAATATATATTTT
1 -TTTTATTTTAACTTAAAAATATATTTT
751173 TAAAAGTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
28 10 0.45
29 2 0.09
30 10 0.45
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTTATTTTAACTTAAAAATATATTTTA
Found at i:757087 original size:23 final size:23
Alignment explanation
Indices: 757006--757087 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
756996 ACACTAGTTA
*
757006 GTGCATCGATGCA-TCCCTTGAAT
1 GTGCATCGATGCACT-CATTGAAT
* *
757029 GTGCATCGATTCAC-CA-TGAAG
1 GTGCATCGATGCACTCATTGAAT
757050 GTGCATCGATGCACTCATTGAAT
1 GTGCATCGATGCACTCATTGAAT
*
757073 GTGCATCAATGCACT
1 GTGCATCGATGCACT
757088 TTGCTGTGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
21 17 0.34
22 3 0.06
23 30 0.60
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (23 bp):
GTGCATCGATGCACTCATTGAAT
Found at i:759354 original size:21 final size:21
Alignment explanation
Indices: 759329--759371 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
759319 AAAGGGGGGA
759329 GAAGATGTGTTATAATAAGGG
1 GAAGATGTGTTATAATAAGGG
*
759350 GAAGATGTGTTATAGTAAGGG
1 GAAGATGTGTTATAATAAGGG
759371 G
1 G
759372 GTAATTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (21 bp):
GAAGATGTGTTATAATAAGGG
Found at i:759406 original size:13 final size:14
Alignment explanation
Indices: 759375--759406 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
759365 TAAGGGGGTA
759375 ATTTTCAAAAATTG
1 ATTTTCAAAAATTG
759389 A-TTTCAAAAA-TG
1 ATTTTCAAAAATTG
759401 ATTTTC
1 ATTTTC
759407 TTGAAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 13 0.76
14 1 0.06
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (14 bp):
ATTTTCAAAAATTG
Found at i:759881 original size:64 final size:65
Alignment explanation
Indices: 759760--759912 Score: 179
Period size: 64 Copynumber: 2.4 Consensus size: 65
759750 TTACATTTCA
* * **
759760 AATGCATTTTTTATACCGATGCACAAGGTATGCATCGATGCACTCCTGAATATTTTG-AACATCG
1 AATGCATTTTATGTACCGATGCACAAGCCATGCATCGATGCACTCCTGAATATTTTGAAACATCG
*
759824 AATGCATTTTATGTACCGATGCACATA-CCATGCATCGATGCACTCCATG-CTCA-TTTGAAACA
1 AATGCATTTTATGTACCGATGCACA-AGCCATGCATCGATGCACTCC-TGAAT-ATTTTGAAACA
759886 TCG
63 TCG
* * *
759889 AATGTATTTTATGCATCGATGCAC
1 AATGCATTTTATGTACCGATGCAC
759913 CACTAGTGTA
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
64 45 0.58
65 32 0.42
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.32
Consensus pattern (65 bp):
AATGCATTTTATGTACCGATGCACAAGCCATGCATCGATGCACTCCTGAATATTTTGAAACATCG
Found at i:759912 original size:65 final size:64
Alignment explanation
Indices: 759789--759912 Score: 171
Period size: 65 Copynumber: 1.9 Consensus size: 64
759779 TGCACAAGGT
*
759789 ATGCATCGATGCACTCCTGAATATTTTGAACATCGAATGCATTTTATGTACCGATGCACATACC
1 ATGCATCGATGCACTCCTGAATATTTTGAACATCGAATGCATTTTATGCACCGATGCACATACC
* * *
759853 ATGCATCGATGCACTCCATG-CTCA-TTTGAAACATCGAATGTATTTTATGCATCGATGCAC
1 ATGCATCGATGCACTCC-TGAAT-ATTTTG-AACATCGAATGCATTTTATGCACCGATGCAC
759913 CACTAGTGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
64 22 0.42
65 31 0.58
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (64 bp):
ATGCATCGATGCACTCCTGAATATTTTGAACATCGAATGCATTTTATGCACCGATGCACATACC
Found at i:767669 original size:21 final size:21
Alignment explanation
Indices: 767644--767686 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
767634 AAAGGGGGGA
*
767644 GAAGATGTGTTATATTAAGGG
1 GAAGATGTGTTATAGTAAGGG
767665 GAAGATGTGTTATAGTAAGGG
1 GAAGATGTGTTATAGTAAGGG
767686 G
1 G
767687 GAGTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (21 bp):
GAAGATGTGTTATAGTAAGGG
Found at i:768806 original size:16 final size:16
Alignment explanation
Indices: 768787--768823 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
768777 ATCCTTAGTA
768787 TGGATAGCTAAGGTAG
1 TGGATAGCTAAGGTAG
768803 TGGATAGCTAAGGTAG
1 TGGATAGCTAAGGTAG
768819 TGGAT
1 TGGAT
768824 GTAGACTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.05, G:0.38, T:0.27
Consensus pattern (16 bp):
TGGATAGCTAAGGTAG
Found at i:769025 original size:30 final size:29
Alignment explanation
Indices: 768960--769029 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
768950 GATTAACTCA
* * *
768960 ATAATATATTTTTAAGTTGAAATAAGATT
1 ATAATATATTTTTAACTTAAAACAAGATT
*
768989 AAAATATATATTTTAACTTAAAACAA-ATAT
1 ATAATATAT-TTTTAACTTAAAACAAGAT-T
769019 ATAATATATTT
1 ATAATATATTT
769030 AATAAGTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
29 12 0.35
30 22 0.65
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (29 bp):
ATAATATATTTTTAACTTAAAACAAGATT
Found at i:769084 original size:19 final size:20
Alignment explanation
Indices: 769060--769106 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
769050 AAATAGATTT
769060 TTTAATATTAAG-ATGTGAA
1 TTTAATATTAAGTATGTGAA
*
769079 TTTAAT-TT-AGTTTGTGAA
1 TTTAATATTAAGTATGTGAA
769097 TTTAA-ATTAA
1 TTTAATATTAA
769107 ATTGTGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 2 0.08
18 15 0.62
19 7 0.29
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (20 bp):
TTTAATATTAAGTATGTGAA
Found at i:769111 original size:18 final size:18
Alignment explanation
Indices: 769060--769112 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
769050 AAATAGATTT
769060 TTTAATATTAAGA-TGTGAA
1 TTTAA-ATTAA-ATTGTGAA
* **
769079 TTTAATTTAGTTTGTGAA
1 TTTAAATTAAATTGTGAA
769097 TTTAAATTAAATTGTG
1 TTTAAATTAAATTGTG
769113 TAAATTTATG
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (18 bp):
TTTAAATTAAATTGTGAA
Found at i:770674 original size:14 final size:14
Alignment explanation
Indices: 770655--770690 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
770645 AATTTTCATT
770655 GCACATATAGATAA
1 GCACATATAGATAA
770669 GCACATATAGATAA
1 GCACATATAGATAA
*
770683 GAACATAT
1 GCACATAT
770691 CTTCTGATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.22
Consensus pattern (14 bp):
GCACATATAGATAA
Found at i:773597 original size:9 final size:9
Alignment explanation
Indices: 773583--773636 Score: 81
Period size: 9 Copynumber: 5.7 Consensus size: 9
773573 TGAAGTAAGG
773583 AAGAAGGAA
1 AAGAAGGAA
773592 AAGAAGGAA
1 AAGAAGGAA
773601 AAGAAGGAA
1 AAGAAGGAA
773610 AAGAAGGAAGA
1 AAGAAGG-A-A
773621 AAGAAGGAA
1 AAGAAGGAA
773630 GAAGAAG
1 -AAGAAG
773637 AATAAATTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
9 26 0.62
10 8 0.19
11 8 0.19
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (9 bp):
AAGAAGGAA
Found at i:773604 original size:18 final size:20
Alignment explanation
Indices: 773562--773636 Score: 91
Period size: 18 Copynumber: 3.7 Consensus size: 20
773552 ATACCACGTC
* *
773562 AGAAGGAAGAATGAAGTAAGGA
1 AGAAGGAA-AA-GAAGGAAGAA
773584 AGAAGGAAAAGAAGG-A-AA
1 AGAAGGAAAAGAAGGAAGAA
773602 AGAAGGAAAAGAAGGAAGAA
1 AGAAGGAAAAGAAGGAAGAA
773622 AGAAGGAAGAAGAAG
1 AGAAGGAA-AAGAAG
773637 AATAAATTGT
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
18 16 0.33
19 2 0.04
20 14 0.29
21 8 0.17
22 8 0.17
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.03
Consensus pattern (20 bp):
AGAAGGAAAAGAAGGAAGAA
Found at i:774354 original size:22 final size:21
Alignment explanation
Indices: 774320--774376 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
774310 ATTTAAATTT
774320 ATATTTATATTTTAACATTAAAA
1 ATATTT-TATTTTAAC-TTAAAA
* * *
774343 ATATTTTATTTTTATCTTATAT
1 ATATTTTA-TTTTAACTTAAAA
774365 ATATTTTATTTT
1 ATATTTTATTTT
774377 CATTTTAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 4 0.13
22 14 0.47
23 12 0.40
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTTTATTTTAACTTAAAA
Found at i:774397 original size:30 final size:28
Alignment explanation
Indices: 774363--774524 Score: 122
Period size: 29 Copynumber: 5.8 Consensus size: 28
774353 TTTATCTTAT
774363 ATATATTTTATTTTCATTTTAACTTAAAA
1 ATATATTTTATTTT-ATTTTAACTTAAAA
* *
774392 TATATATTTTATTTTTATTTTTATTTAAAA
1 -ATATATTTTA-TTTTATTTTAACTTAAAA
* * *
774422 ATATATTTTAGTCTTATTTTAGCTTCAAA
1 ATATATTTTA-TTTTATTTTAACTTAAAA
* *
774451 ATATATTTTAATATTATTTTAGC-T----
1 ATATATTTT-ATTTTATTTTAACTTAAAA
* *
774475 AT-T-TTTTATTTTTATCTTAACTTATGAA
1 ATATATTTTA-TTTTATTTTAACTTA-AAA
774503 ATATATTTTACTTTTATTTTAA
1 ATATATTTTA-TTTTATTTTAA
774525 TTTTATATAT
Statistics
Matches: 107, Mismatches: 14, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
21 1 0.01
22 13 0.12
23 2 0.02
24 2 0.02
28 3 0.03
29 44 0.41
30 38 0.36
31 4 0.04
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (28 bp):
ATATATTTTATTTTATTTTAACTTAAAA
Found at i:774438 original size:29 final size:28
Alignment explanation
Indices: 774344--774470 Score: 116
Period size: 29 Copynumber: 4.4 Consensus size: 28
774334 ACATTAAAAA
*
774344 TATTTTATTTTTATCTT--ATATATATTT
1 TATTTTATTTTTA-CTTAAAAATATATTT
*
774371 TATTTTCATTTTAACTTAAAATATATATTT
1 TATTTT-ATTTTTACTTAAAA-ATATATTT
*
774401 TATTTTTATTTTTATTTAAAAATATATTT
1 TA-TTTTATTTTTACTTAAAAATATATTT
* *
774430 TAGTCTTA-TTTTAGCTTCAAAATATATTT
1 TA-TTTTATTTTTA-CTTAAAAATATATTT
*
774459 TAATATTATTTT
1 T-ATTTTATTTT
774471 AGCTATTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
27 9 0.11
28 11 0.13
29 33 0.40
30 26 0.31
31 4 0.05
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (28 bp):
TATTTTATTTTTACTTAAAAATATATTT
Found at i:774455 original size:58 final size:58
Alignment explanation
Indices: 774345--774470 Score: 150
Period size: 58 Copynumber: 2.2 Consensus size: 58
774335 CATTAAAAAT
* *
774345 ATTTTATTTTTATCTTATATATATTTTATTTTCATTTTAACTTAAAATATATATTTTA
1 ATTTTATTTTTATCTTAAATATATTTTATCTTCATTTTAACTTAAAATATATATTTTA
* * *
774403 TTTTTATTTTTAT-TTAAAAATATATTTTAGTCTT-ATTTTAGCTTCAAA-ATATATTTTA
1 ATTTTATTTTTATCTT--AAATATATTTTA-TCTTCATTTTAACTTAAAATATATATTTTA
*
774461 ATATTATTTT
1 ATTTTATTTT
774471 AGCTATTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
57 2 0.03
58 30 0.52
59 23 0.40
60 3 0.05
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (58 bp):
ATTTTATTTTTATCTTAAATATATTTTATCTTCATTTTAACTTAAAATATATATTTTA
Found at i:774580 original size:31 final size:28
Alignment explanation
Indices: 774529--774665 Score: 121
Period size: 30 Copynumber: 4.6 Consensus size: 28
774519 TTTTAATTTT
** *
774529 ATATATTTTTAAAACTAAATATAAGAATAAT
1 ATATATTTTT-AAGTTAAA-ATAA-AATAAA
*
774560 ATATATTTTTAAGTTAAAATAAGATTAAA
1 ATATATTTTTAAGTTAAAATAA-AATAAA
* * *
774589 GTATATTTTTTAATTTAAAAAAAATATAAA
1 ATATA-TTTTTAAGTTAAAATAAA-ATAAA
* *
774619 ATATATTTAATAAGTTAAGATAAAATAAA
1 ATATATTT-TTAAGTTAAAATAAAATAAA
774648 ATATATTTTTAATGTTAA
1 ATATATTTTTAA-GTTAA
774666 GATGTGAATT
Statistics
Matches: 88, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
28 3 0.03
29 35 0.40
30 40 0.45
31 10 0.11
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.42
Consensus pattern (28 bp):
ATATATTTTTAAGTTAAAATAAAATAAA
Found at i:774668 original size:29 final size:29
Alignment explanation
Indices: 774529--774665 Score: 125
Period size: 29 Copynumber: 4.6 Consensus size: 29
774519 TTTTAATTTT
** *
774529 ATATATTTTTAAAACTAAATATAAGAATAAT
1 ATATATTTTT-AAGTTAAA-ATAAGAATAAA
*
774560 ATATATTTTTAAGTTAAAATAAGATTAAA
1 ATATATTTTTAAGTTAAAATAAGAATAAA
* * *
774589 GTATATTTTTTAATTTAAAA-AAAATATAAA
1 ATATA-TTTTTAAGTTAAAATAAGA-ATAAA
* *
774619 ATATATTTAATAAGTTAAGATAA-AATAAA
1 ATATATTT-TTAAGTTAAAATAAGAATAAA
774648 ATATATTTTTAATGTTAA
1 ATATATTTTTAA-GTTAA
774666 GATGTGAATT
Statistics
Matches: 88, Mismatches: 13, Indels: 12
0.78 0.12 0.11
Matches are distributed among these distances:
28 3 0.03
29 37 0.42
30 36 0.41
31 12 0.14
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.42
Consensus pattern (29 bp):
ATATATTTTTAAGTTAAAATAAGAATAAA
Found at i:777983 original size:23 final size:23
Alignment explanation
Indices: 777920--778001 Score: 83
Period size: 23 Copynumber: 3.5 Consensus size: 23
777910 ACGGAATTTG
*
777920 TCCCGAAGGACCACGTAAAATTTA
1 TCCCGAAGGACCACATAAAA-TTA
* * * * *
777944 TCCCCAAGGATCGCATAGATTTA
1 TCCCGAAGGACCACATAAAATTA
* *
777967 TCCTGAATGACCACATAAAATTA
1 TCCCGAAGGACCACATAAAATTA
777990 TCCCGAAGGACC
1 TCCCGAAGGACC
778002 GCGTAGAACC
Statistics
Matches: 43, Mismatches: 15, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
23 29 0.67
24 14 0.33
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (23 bp):
TCCCGAAGGACCACATAAAATTA
Found at i:778853 original size:20 final size:20
Alignment explanation
Indices: 778807--778919 Score: 140
Period size: 20 Copynumber: 5.6 Consensus size: 20
778797 TATTTCAATT
*
778807 TCAGTATCGAGACCTTC-CTA
1 TCAGTATCGATACCTTCAC-A
**
778827 TTGGTATCGATACCTTCACA
1 TCAGTATCGATACCTTCACA
*
778847 TCAGTATTGATACCTTCACA
1 TCAGTATCGATACCTTCACA
778867 TCAGTATCGATACCTTCACA
1 TCAGTATCGATACCTTCACA
778887 TCAGTATCGATACTACTTCA-A
1 TCAGTATCGATAC--CTTCACA
*
778908 TCAGTATAGATA
1 TCAGTATCGATA
778920 TTGTTCATCG
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
20 64 0.78
21 13 0.16
22 5 0.06
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (20 bp):
TCAGTATCGATACCTTCACA
Found at i:780172 original size:34 final size:34
Alignment explanation
Indices: 780129--780193 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
780119 AACTCCTTAG
* *
780129 TTTTTCACGGGATAAACTAGAACCTTTCCCTAGC
1 TTTTACACGGGATAAACTAGAACATTTCCCTAGC
* *
780163 TTTTACACGGGCTAAGCTAGAACATTTCCCT
1 TTTTACACGGGATAAACTAGAACATTTCCCT
780194 TTTACAAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (34 bp):
TTTTACACGGGATAAACTAGAACATTTCCCTAGC
Found at i:784220 original size:22 final size:20
Alignment explanation
Indices: 784179--784221 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
784169 ATACTCTTAT
*
784179 TATATACATGCCTATTACCA
1 TATATACATGCCTATCACCA
*
784199 TATATAGATGCCTTCATCACCA
1 TATATACATGCC-T-ATCACCA
784221 T
1 T
784222 TTCACCGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 1 0.05
22 7 0.37
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.35
Consensus pattern (20 bp):
TATATACATGCCTATCACCA
Found at i:787749 original size:34 final size:34
Alignment explanation
Indices: 787652--787750 Score: 180
Period size: 34 Copynumber: 2.9 Consensus size: 34
787642 ATACACACAT
*
787652 ACGTATGATCTTAAATTTATGTATAAAACATTAA
1 ACGTATGATCTTAAATTTATGTATAAAACTTTAA
787686 ACGTATGATCTTAAATTTATGTATAAAACTTTAA
1 ACGTATGATCTTAAATTTATGTATAAAACTTTAA
*
787720 ACGTATGATCTTAAATTTATGTATTAAACTT
1 ACGTATGATCTTAAATTTATGTATAAAACTT
787751 GAAATTTGAT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.41
Consensus pattern (34 bp):
ACGTATGATCTTAAATTTATGTATAAAACTTTAA
Found at i:789280 original size:20 final size:19
Alignment explanation
Indices: 789251--789291 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
789241 TCGAACAAGG
*
789251 GTATCAATACTTTTCTTACA
1 GTATCAATACTATTCTT-CA
*
789271 GTATCGATACTATTCTTCA
1 GTATCAATACTATTCTTCA
789290 GT
1 GT
789292 TAAGGCTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.44
Consensus pattern (19 bp):
GTATCAATACTATTCTTCA
Found at i:803687 original size:2 final size:2
Alignment explanation
Indices: 803680--803710 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
803670 GCATCATTCT
803680 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
803711 TTTCCACCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:805130 original size:54 final size:54
Alignment explanation
Indices: 805064--805245 Score: 283
Period size: 54 Copynumber: 3.4 Consensus size: 54
805054 TTCTTTGAGA
* * * *
805064 TGCACACGTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCCGTGGGT
* * * *
805118 TGCACACTTAGTGGCTATACGATCGTTCATTAACATATGATGAATTACGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCCGTGGGT
*
805172 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCCGTGGGT
805226 TGCACACTTAGTGCCTATAC
1 TGCACACTTAGTGCCTATAC
805246 TGTAACACTC
Statistics
Matches: 117, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 117 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (54 bp):
TGCACACTTAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCCGTGGGT
Found at i:806317 original size:2 final size:2
Alignment explanation
Indices: 806310--806336 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
806300 CTTATTCATG
806310 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
806337 CCGCAAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:810596 original size:211 final size:208
Alignment explanation
Indices: 810230--810650 Score: 711
Period size: 211 Copynumber: 2.0 Consensus size: 208
810220 CACTCACACG
* *
810230 CTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAACTTCTTAATCATGCATG
1 CTAAGTCTATGAATTAGTGAGGCATTAAACACATAAAAGTAACTCT-ACTACTTAATCATGCATG
810295 AACATATCATATCATGCTATCACACAAAAATATAGCATTTCATATAATCAAATGTACACATATAC
65 AACATATCATATCATGCTATCACACAAAAATATAGCATTTCATATAATCAAATGTA-ACATATAC
*
810360 ATATCATTCATTCAACATCTTTCCATCATTAACCTTACTTTACTATCAATATGATTAGTATTTAT
129 ACATCATTCATTCAACATCTTTCCATCATTAACCTTACTTTACTATC-A-AT-ATTAGTATTTAT
810425 ATCTTGTAATCATATCCT
191 ATCTTGTAATCATATCCT
810443 CTAAGTCTATGAATTAGTGAGGCATTAAACACATAAAAGTAACTCT-CTACTTAATCATGCATGA
1 CTAAGTCTATGAATTAGTGAGGCATTAAACACATAAAAGTAACTCTACTACTTAATCATGCATGA
* *
810507 ACATATCATATCATGTTATCACACAAAACAATATAGCATTTCATGTAATCAAATGT-ACATATAC
66 ACATATCATATCATGCTATCACAC-AAA-AATATAGCATTTCATATAATCAAATGTAACATATAC
*
810571 ACATCATTCATTCAACATTTTTCCATCATTAACCTTACTTTACTATCAATATTAGTATTTATATC
129 ACATCATTCATTCAACATCTTTCCATCATTAACCTTACTTTACTATCAATATTAGTATTTATATC
810636 TTGTAATCATATCCT
194 TTGTAATCATATCCT
810651 TTCGTACTAA
Statistics
Matches: 200, Mismatches: 6, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
208 30 0.15
209 2 0.01
210 1 0.00
211 93 0.47
212 3 0.01
213 71 0.35
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (208 bp):
CTAAGTCTATGAATTAGTGAGGCATTAAACACATAAAAGTAACTCTACTACTTAATCATGCATGA
ACATATCATATCATGCTATCACACAAAAATATAGCATTTCATATAATCAAATGTAACATATACAC
ATCATTCATTCAACATCTTTCCATCATTAACCTTACTTTACTATCAATATTAGTATTTATATCTT
GTAATCATATCCT
Found at i:814192 original size:536 final size:541
Alignment explanation
Indices: 810443--814201 Score: 6606
Period size: 530 Copynumber: 7.0 Consensus size: 541
810433 ATCATATCCT
*
810443 CTAAGTCTATGAATTAGTGAGGCATTAAACACATAAAAGTAACTCT--CTACTTAATCATGCATG
1 CTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAACTACTTAATCATGCATG
*
810506 AACATATCATATCATGTTATCACACAAAACAATATAGCATTTCATGTAATCAAATGT--ACATAT
66 AACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAATCAAATGTACACATAT
810569 ACACATCATTCATTCAACATT-TTTCCATCATTAACCTTACTTTACTATC-A-AT-ATTAGTATT
131 ACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTATCAATATGATTAGTATT
810630 TATATCTTGTAATCATATCCTTTCGTAC-TAACGTTTTAACCAACATGACTCATTTAACCACGCA
196 TATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGACTCATTTAACCACGCA
*
810694 AT--ACATGTCATCATTAAAATCATATGATACAATTCATCTCACAAAAGCATATACATCACTTGT
261 ATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAGCATATACATCACTTGT
*
810757 -A-ATATCTATTGTATAAAAACGTATAGTTTTACAAATTGATCAGAGCGTATCCAATAC-AATCT
326 AATATATCTATTGTAT-AAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCT
810819 TTTATCTTACATGCCAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATT
390 TTTATCTTACATGCCAACTACATTTCATATGAC-AAATACATATAATTTAAACATATTTCTGATT
*
810884 TGAATTGTGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGATTTCCGGAA
454 TGAATTGTGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAA
*
810949 CCTACGTATGAAACACTCACACG
519 CCTACGTGTGAAACACTCACACG
810972 CTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAACTACTTAATCATGCATG
1 CTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAACTACTTAATCATGCATG
811037 AACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAATCAAATGTACACATAT
66 AACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAATCAAATGTACACATAT
811102 ACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTATCAATATGATTAGTATT
131 ACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTATCAATATGATTAGTATT
*
811167 TATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGACTCATTTAACCATGCA
196 TATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGACTCATTTAACCACGCA
811232 ATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAGCATATACATCACTTGT
261 ATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAGCATATACATCACTTGT
* *
811297 AATATATCTATTGTATAAAACGTATGGTTTTACAAATTGATTAGAGCGTATCCAATACAAATATT
326 AATATATCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTT
811362 TTATCTTACATGCCAACTACATTTCATATGACAAATACATATAATTTAAACATATTTCTGATTTG
391 TTATCTTACATGCCAACTACATTTCATATGACAAATACATATAATTTAAACATATTTCTGATTTG
* *
811427 AATTGTGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTACTTTCCAGAACC
456 AATTGTGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACC
811492 TACGTGTGAAACACTCACACG
521 TACGTGTGAAACACTCACACG
811513 CTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAACTACTTAATCAT-CATG
1 CTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAACTACTTAATCATGCATG
811577 AACATATC--ATCATGCTATCACACAAAACAATATAGCATTTCATGTAATCAAATGTACAC--AT
66 AACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAATCAAATGTACACATAT
*
811638 ACACATCATTCATTCAACATTCTTTCCAT-ATTTAACCTTACTTTATTATCAATATGATTAGTAT
131 ACACATCATTCATTCAACATTCTTTCCATCA-TTAACCTTACTTTACTATCAATATGATTAGTAT
*
811702 TTATATCTTGTAATCATATCCTTTCGTACTTAACATTTTAACCAACATGACTCATTTAACCACGC
195 TTATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGACTCATTTAACCACGC
* *
811767 AATACACATATCATCATTAAAACCATATGATACAATTCATCTCAAAAAAGCATATACATCACTTG
260 AATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAGCATATACATCACTTG
*
811832 TAATATATCTATTGTATAAAAACTTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATC
325 TAATATATCTATTGTAT-AAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATC
*
811897 TTTTATCTTACATGCCAACTACATTTCACATGACAAAATAC--AT-ATTTAAAC-TATTTCTGAT
389 TTTTATCTTACATGCCAACTACATTTCATATGAC-AAATACATATAATTTAAACATATTTCTGAT
* *
811958 TTGAATTGTAGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTTTTGCTTTCCGGA
453 TTGAATTGTGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGA
812023 ACCTAC--GTGAAACACTCACACG
518 ACCTACGTGTGAAACACTCACACG
*
812045 CTAAGTCTATGAATTAGTGAGGCATTAAACACAT-AAAGTAACTCTAACTACTTAATCATGCATG
1 CTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAACTACTTAATCATGCATG
*
812109 AACATATCATATCATGTTATCACACAAAAC-ATATAGCATTTCATGTAATCAAATGTACACATAT
66 AACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAATCAAATGTACACATAT
*
812173 ACACATCATTCATTCAACATTCTTTTCATCATTAACCTTACTTTACTATCAATATGATTAGTATT
131 ACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTATCAATATGATTAGTATT
812238 TATATCTTGTAATCATATCCTTTCGTAC-TAA-GTTTTAACCAACATGACTCATTTAACCA-GCA
196 TATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGACTCATTTAACCACGCA
*
812300 ATACACATGTCATCATT-AAATCATATGATACAATTCATCTCACAAAAGCATATACATCACTTGT
261 ATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAGCATATACATCACTTGT
812364 -A-ATATCTATTGTAT-AAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATC-T
326 AATATATCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTT
812425 TTATCTTACATGCCAACTACATTTCATATGACAAA-ACATATAATTT-AACATATTTCTGATTTG
391 TTATCTTACATGCCAACTACATTTCATATGACAAATACATATAATTTAAACATATTTCTGATTTG
812488 AATTGTGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACC
456 AATTGTGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACC
* *
812553 TACGTATGAAACACTCACATG
521 TACGTGTGAAACACTCACACG
812574 CTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAACTACTTAATCATGCATG
1 CTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAACTACTTAATCATGCATG
812639 AA-ATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAATCAAATGTACACATAT
66 AACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAATCAAATGTACACATAT
* * *
812703 ACACATCATTCATTCAACATTGTTTCCATCATTAACCTTACTTTACTGTCATTATGATTAGTATT
131 ACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTATCAATATGATTAGTATT
* *
812768 TATATCTTGTAATCATATCCTTTCATACTTAACGTTTTAACCAACATGACTCATTTAACCATGCA
196 TATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGACTCATTTAACCACGCA
812833 ATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAGCATATACATCACTTGT
261 ATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAGCATATACATCACTTGT
* *
812898 AATATATCTATTATATAAAACGTATGGTTTTACAAATTGATTAGAGCGTATCCAATACAAATCTT
326 AATATATCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTT
*
812963 TTATCTTACATGCCAACTACATTTCATATGACAAATACATATAATTTAAACATATTTCTGATTTA
391 TTATCTTACATGCCAACTACATTTCATATGACAAATACATATAATTTAAACATATTTCTGATTTG
* *
813028 AATTGTGAAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCCCTTCTTGCTTTCCGGAACC
456 AATTGTGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACC
*
813093 TACGTGTGAAACACTCTCACG
521 TACGTGTGAAACACTCACACG
813114 CTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAACTACTTAATCATGCATG
1 CTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAACTACTTAATCATGCATG
813179 AACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAATCAAATGTACACATAT
66 AACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAATCAAATGTACACATAT
813244 ACACATCATTCATTCAACATTCTTTCCATCATTAACCTTAC-TT--TATCAATATG---AGTATT
131 ACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTATCAATATGATTAGTATT
* *
813303 TATAACTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGACTCATTTAACCACACA
196 TATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGACTCATTTAACCACGCA
813368 ATACAC--ATCATCATTAAAATCATATGATACAATTCATCTCACAAAAGCATATACATCACTTGT
261 ATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAGCATATACATCACTTGT
*
813431 -A-ATATCTATTGTATAAAACGTATGGTTTTACAAATTGATCAAAGCGTATCCAATACAAATC-T
326 AATATATCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTT
813493 TTATCTTACATGCCAACT-CATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTT
391 TTATCTTACATGCCAACTACATTTCATATGAC-AAATACATATAATTTAAACATATTTCTGATTT
*
813557 GAATTGTGGAAAGGTGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAAC
455 GAATTGTGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAAC
813622 CTACGTGTGAAACACTCACACG
520 CTACGTGTGAAACACTCACACG
*
813644 CTAAGTCTATGACTTACTGAGGCATTAAACACATAAAAGTAACTCTAACTACTTAATCATGCATG
1 CTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAACTACTTAATCATGCATG
*
813709 AACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTTATCAAATGTACACATAT
66 AACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAATCAAATGTACACATAT
* *
813774 ACACATCATTCATTCAACATTCGTTCCATCATTAACCTTACTTTACTATCATTATGATTAGTATT
131 ACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTATCAATATGATTAGTATT
813839 TAT-TCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGACTCATTTAACCACGCA
196 TATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGACTCATTTAACCACGCA
*
813903 ATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAGCATATAC-TCAATTGT
261 ATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAGCATATACATCACTTGT
*
813967 AATATATCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATATT
326 AATATATCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTT
* *
814032 TTATCTTACATGCCAACTACATTTCATATGATAAAATATATATAATTTAAACATATTTCTGATTT
391 TTATCTTACATGCCAACTACATTTCATATGA-CAAATACATATAATTTAAACATATTTCTGATTT
*
814097 GAATTGTGGAAA-G-GAATCTGACCTATCTTGC-CCT-TAAACTTCTCTTCTTGCTTTCCGGAAC
455 GAATTGTGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAAC
*
814158 CTACGTGTGAAACACTCACACT
520 CTACGTGTGAAACACTCACACG
814180 CTAAGTCTATGACTTAGTGAGG
1 CTAAGTCTATGACTTAGTGAGG
814202 TTGTGCACTA
Statistics
Matches: 3091, Mismatches: 83, Indels: 105
0.94 0.03 0.03
Matches are distributed among these distances:
524 2 0.00
525 3 0.00
526 37 0.01
527 128 0.04
529 144 0.05
530 456 0.15
531 205 0.07
532 109 0.04
533 169 0.05
534 174 0.06
535 240 0.08
536 308 0.10
537 211 0.07
538 213 0.07
539 31 0.01
540 293 0.09
541 318 0.10
542 50 0.02
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.34
Consensus pattern (541 bp):
CTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAACTACTTAATCATGCATG
AACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAATCAAATGTACACATAT
ACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTATCAATATGATTAGTATT
TATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGACTCATTTAACCACGCA
ATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAGCATATACATCACTTGT
AATATATCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTT
TTATCTTACATGCCAACTACATTTCATATGACAAATACATATAATTTAAACATATTTCTGATTTG
AATTGTGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACC
TACGTGTGAAACACTCACACG
Found at i:814601 original size:3 final size:3
Alignment explanation
Indices: 814584--814657 Score: 82
Period size: 3 Copynumber: 25.0 Consensus size: 3
814574 CATATGATTT
* *
814584 TTA TTA -TA TTT TTA TTA TTA TT- TTT TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
814630 TCA TTA TTA TTA TT- TATA TTA TATA TTA
1 TTA TTA TTA TTA TTA T-TA TTA T-TA TTA
814658 ATACATATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
2 5 0.08
3 52 0.85
4 4 0.07
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:815934 original size:21 final size:21
Alignment explanation
Indices: 815895--815934 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
815885 TTAATTTTAC
* *
815895 TTATTATATATTTAAATATTT
1 TTATTATATAGTCAAATATTT
*
815916 TTATTATATAGTCATATAT
1 TTATTATATAGTCAAATAT
815935 ATATAATATA
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:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (21 bp):
TTATTATATAGTCAAATATTT
Found at i:815981 original size:13 final size:13
Alignment explanation
Indices: 815943--815986 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
815933 ATATATAATA
*
815943 TAATATTTATTTC
1 TAATATTTATTTT
* *
815956 AAATAATTA-TTT
1 TAATATTTATTTT
815968 TAATATTTATTTT
1 TAATATTTATTTT
815981 TAATAT
1 TAATAT
815987 CGAAGAAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (13 bp):
TAATATTTATTTT
Found at i:819827 original size:15 final size:15
Alignment explanation
Indices: 819804--819835 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
819794 TTTGGGATCA
*
819804 ATACCTTTTGCATAC
1 ATACATTTTGCATAC
819819 ATACATTTTGCATAC
1 ATACATTTTGCATAC
819834 AT
1 AT
819836 CATCATTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (15 bp):
ATACATTTTGCATAC
Found at i:827387 original size:16 final size:18
Alignment explanation
Indices: 827368--827413 Score: 69
Period size: 16 Copynumber: 2.6 Consensus size: 18
827358 CTATTTCAAG
827368 TTCAATTTATTT-GAAA-
1 TTCAATTTATTTCGAAAT
827384 TTCAATTTATTTTCGAAAT
1 TTCAATTTA-TTTCGAAAT
827403 TTCAATTTATT
1 TTCAATTTATT
827414 CTTCTATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.33
17 3 0.11
18 6 0.22
19 9 0.33
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (18 bp):
TTCAATTTATTTCGAAAT
Found at i:827408 original size:19 final size:17
Alignment explanation
Indices: 827368--827413 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 17
827358 CTATTTCAAG
827368 TTCAATTTA-TTTGAAA
1 TTCAATTTATTTTGAAA
827384 TTCAATTTATTTTCGAAA
1 TTCAATTTATTTT-GAAA
827402 TTTCAATTTATT
1 -TTCAATTTATT
827414 CTTCTATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.33
17 3 0.11
18 4 0.15
19 11 0.41
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (17 bp):
TTCAATTTATTTTGAAA
Found at i:828370 original size:83 final size:83
Alignment explanation
Indices: 828168--828440 Score: 397
Period size: 83 Copynumber: 3.3 Consensus size: 83
828158 TCCAAACCTT
* * *
828168 ATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTAATTTGGTTT
1 ATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
** *
828233 GGTA-AACCAATTATTGA
66 GACAGAACCAATCATTGA
* **
828250 ATTTAGAAGATGAAT-TTATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 ATTTGGAAGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
828314 TGACAGAACCAATCATTGA
65 TGACAGAACCAATCATTGA
* *
828333 ATTTGGAGGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTG
1 ATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
*
828398 GACAGAACCAATCATTAA
66 GACAGAACCAATCATTGA
* *
828416 ATTTGGAAGATAAATTTGCTCATAG
1 ATTTGGAAGATGAATGTGCTCATAG
828441 TAGAAATAAG
Statistics
Matches: 170, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
81 3 0.02
82 57 0.34
83 107 0.63
84 3 0.02
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.37
Consensus pattern (83 bp):
ATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
GACAGAACCAATCATTGA
Found at i:829481 original size:113 final size:113
Alignment explanation
Indices: 829238--829894 Score: 729
Period size: 113 Copynumber: 5.9 Consensus size: 113
829228 GAGTCCATAA
*
829238 TGATGGATCAGCTTTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1 TGATGGATCAGCTTTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAA
* ** *
829303 GTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTGAATTCATCAT-T
66 ATTCATAATGAGAAGAACTTGTTCAACCTTTT-GCTCAAATCCATC-TCT
* * ***
829351 CGAT-GAGTCA-ATATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAG
1 TGATGGA-TCAGCT-TTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAG
*
829414 AAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCTCT
64 AAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCTCT
* *
829464 TGATGGATCAGCTTTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAA-AA
1 TGATGGATCAGCTTTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAA
*
829528 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACT
66 A-TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCTCT
* * * *
829577 TGATGGATCAGCTTTTCCAGAAAAAGTTCATCATAAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1 TGATGGATCAGCTTTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAA
* * *
829642 ATTCATAATGAGAAGAATTTATTCAACCTTTT-TTC--AT-CA--T-T
66 ATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCTCT
* * * * ** *
829683 TGAGGGATCAACATTGCCAGGTAGAGTTCATAATAAGAAGAACTCATCATCTGAAGAAA-GAAGA
1 TGATGGATCAGCTTTTCCAGAAAGAGTTCATAATGAGAAGAA--C-TCATCTGAA-AAAGGAAGA
* * * * ** *
829747 AGAAGTTTATAATAAGAAGAACTTGTTCAA-CTTTTCGCTCGAATTTATCACT
62 AGAAATTCATAATGAGAAGAACTTGTTCAACCTTTT-GCTCAAATCCATCTCT
* * * *
829799 CGATGGATCAACTTTTCCAGAGAGAGTTCATCATGAGAAGAACTCATCTGAAGAAA-GAAGAAG-
1 TGATGGATCAGCTTTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAA-AAAGGAAGAAGA
*
829862 --TTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
65 AATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
829895 ATGATTCTAT
Statistics
Matches: 467, Mismatches: 56, Indels: 45
0.82 0.10 0.08
Matches are distributed among these distances:
106 35 0.07
108 6 0.01
109 41 0.09
110 30 0.06
111 5 0.01
112 11 0.02
113 292 0.63
114 12 0.03
116 35 0.07
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (113 bp):
TGATGGATCAGCTTTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAA
ATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCTCT
Found at i:829636 original size:226 final size:219
Alignment explanation
Indices: 829238--829894 Score: 844
Period size: 226 Copynumber: 3.0 Consensus size: 219
829228 GAGTCCATAA
*
829238 TGATGGATCAGCTTTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1 TGATGGATCAGCTTTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAA
* *
829303 GTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCA-TTCGAT-GAGTCAATATT
66 GTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTCGAATTCATCACTT-GATGGA-TCACT-TT
*** * *
829366 TCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAATTCATAATGAGAAG
128 TCCAGAAAGAGTTCATCATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAG
829431 AATTTGTTCAACCTTTTGCTCAAATCCATCTCT
193 AATTTGTTCAACCTTTTGCTC--AT-CA--T-T
*
829464 TGATGGATCAGCTTTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAAAA
1 TGATGGATCAGCTTTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAA
* *
829529 GTTCATAATGAGAAGAACTTGTTCAACCTTTT-GCTCAAATCCATCACTTGATGGATCAGCTTTT
66 GTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTCGAATTCATCACTTGATGGATCA-CTTTT
* *
829593 CCAGAAAAAGTTCATCATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGA
129 CCAGAAAGAGTTCATCATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGA
* *
829658 ATTTATTCAACCTTTT-TTCATCATT
194 ATTTGTTCAACCTTTTGCTCATCATT
* * * * ** *
829683 TGAGGGATCAACATTGCCAGGTAGAGTTCATAATAAGAAGAACTCATCATCTGAAGAA-AGAAGA
1 TGATGGATCAGCTTTTCCAGAAAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGA-AAGA
* * * *
829747 AGAAGTTTATAATAAGAAGAACTTGTTCAACTTTTCGCTCGAATTTATCACTCGATGGATCAACT
62 AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTCGAATTCATCACTTGATGGATC-ACT
* *
829812 TTTCCAGAGAGAGTTCATCATGAGAAGAACTCATCTGAAG-A--AAGAAGAAGTTCATAATGAGA
126 TTTCCAGAAAGAGTTCATCATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGA
**
829874 AGAGCTTGTTCAACCTTTTGC
191 AGAATTTGTTCAACCTTTTGC
829895 ATGATTCTAT
Statistics
Matches: 383, Mismatches: 37, Indels: 28
0.85 0.08 0.06
Matches are distributed among these distances:
219 72 0.19
220 1 0.00
221 8 0.02
222 105 0.27
223 3 0.01
225 2 0.01
226 182 0.48
227 10 0.03
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (219 bp):
TGATGGATCAGCTTTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAA
GTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTCGAATTCATCACTTGATGGATCACTTTTCC
AGAAAGAGTTCATCATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
TTGTTCAACCTTTTGCTCATCATT
Found at i:830087 original size:114 final size:115
Alignment explanation
Indices: 829815--830088 Score: 333
Period size: 120 Copynumber: 2.3 Consensus size: 115
829805 ATCAACTTTT
* * *
829815 CCAG-AGAGAGTTCATCATGAGAAGAACTCATCTGAAGAAAGAAGAAGTTCATAATGAGAAGAGC
1 CCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AAGAAGAAGTTCACAATGAGAAGAGC
* * *
829879 TTGTTCAACCTTTTGCATGATTCTATCATAGAAAGAGATATATCATCATCA
65 TTGTGCAACCTTTTGCATGATTCTATCACAGAAAGAGATAAATCATCATCA
* *
829930 GCATTTCTAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAA
1 CCA--GC-AGAA--AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAA
* **
829995 GAGCTTGTGCAACC-TTTGC-TAGATTAC-ATCACAGAATGAGATAAATTGTCATTC-
61 GAGCTTGTGCAACCTTTTGCAT-GATT-CTATCACAGAAAGAGATAAATCATCA-TCA
830049 CCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
1 CCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
830089 AGAGAAGAAT
Statistics
Matches: 137, Mismatches: 13, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
114 31 0.23
115 2 0.01
116 4 0.03
117 1 0.01
118 1 0.01
119 33 0.24
120 37 0.27
121 28 0.20
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (115 bp):
CCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAGCT
TGTGCAACCTTTTGCATGATTCTATCACAGAAAGAGATAAATCATCATCA
Found at i:830246 original size:3 final size:3
Alignment explanation
Indices: 830238--830301 Score: 110
Period size: 3 Copynumber: 21.0 Consensus size: 3
830228 CCATATTGAT
*
830238 TTA TTA TTA TTA TTT TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
830284 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
830302 AATATATTAA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 55 0.95
4 3 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:830448 original size:15 final size:16
Alignment explanation
Indices: 830428--830469 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
830418 CCTAATCCCT
830428 AGCCGCCTCT-AATCC
1 AGCCGCCTCTGAATCC
**
830443 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGAATCC
830459 AGCCGCCTCTG
1 AGCCGCCTCTG
830470 CCTCCACCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.12, C:0.50, G:0.19, T:0.19
Consensus pattern (16 bp):
AGCCGCCTCTGAATCC
Found at i:830461 original size:16 final size:16
Alignment explanation
Indices: 830440--830479 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
830430 CCGCCTCTAA
830440 TCCAGCCGCCTCTGCC
1 TCCAGCCGCCTCTGCC
830456 TCCAGCCGCCTCTGCC
1 TCCAGCCGCCTCTGCC
830472 TCCA-CCGC
1 TCCAGCCGC
830480 TGCCACGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.07, C:0.57, G:0.17, T:0.17
Consensus pattern (16 bp):
TCCAGCCGCCTCTGCC
Found at i:834390 original size:23 final size:23
Alignment explanation
Indices: 834333--834393 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
834323 CTCATATAAA
* * *
834333 TGCACCGAAATACCACGTAGAAT
1 TGCACCGAAGTGCTACGTAGAAT
834356 TGCACCGAAGTGCTACGTAGAAT
1 TGCACCGAAGTGCTACGTAGAAT
*
834379 TGCACCGTAGTGCTA
1 TGCACCGAAGTGCTA
834394 TATAAAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCTACGTAGAAT
Found at i:845235 original size:72 final size:72
Alignment explanation
Indices: 845112--845314 Score: 167
Period size: 72 Copynumber: 2.8 Consensus size: 72
845102 CGACGTAAAA
* * * * * * * * *
845112 CTAAACCAAGCAACAATGGACCATCTTCATCCAAGACCAAATCGAGTAACAATGCACGATCTACA
1 CTAAACCAAGCAACAATGCACCACCTCCATCCAAGACCAAACCAAGCAACAATCCACCACCTACA
*
845177 CCCAATG
66 CCCAAGG
* * * *
845184 CTGAACCAAGCAACAATGCACCACCTCCATCCAACG-CTAACCCAAGCAACAATCCACCACCTCC
1 CTAAACCAAGCAACAATGCACCACCTCCATCCAA-GACCAAACCAAGCAACAATCCACCACCTAC
*
845248 ACCGAAGG
65 ACCCAAGG
* * * * * * **
845256 TTAAACCAAGC-ACTAGTGCACCACCTCCATCCCAGTCTAGACCAAGCATTAATCCACCA
1 CTAAACCAAGCAAC-AATGCACCACCTCCATCCAAGACCAAACCAAGCAACAATCCACCA
845315 TCTGAAGCTC
Statistics
Matches: 105, Mismatches: 23, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
71 3 0.03
72 101 0.96
73 1 0.01
ACGTcount: A:0.37, C:0.37, G:0.11, T:0.15
Consensus pattern (72 bp):
CTAAACCAAGCAACAATGCACCACCTCCATCCAAGACCAAACCAAGCAACAATCCACCACCTACA
CCCAAGG
Found at i:845282 original size:36 final size:36
Alignment explanation
Indices: 845112--845287 Score: 142
Period size: 36 Copynumber: 4.9 Consensus size: 36
845102 CGACGTAAAA
* * *
845112 CTAAACCAAGCAACAATGGACCATCTTCATCCAA-G
1 CTAAACCAAGCAACAATGCACCACCTCCATCCAACG
* * * * * * * * *
845147 ACCAAATCGAGTAACAATGCACGATCTACACCCAATG
1 -CTAAACCAAGCAACAATGCACCACCTCCATCCAACG
*
845184 CTGAACCAAGCAACAATGCACCACCTCCATCCAACG
1 CTAAACCAAGCAACAATGCACCACCTCCATCCAACG
* * *
845220 CTAACCCAAGCAACAATCCACCACCTCCA-CCGAAGG
1 CTAAACCAAGCAACAATGCACCACCTCCATCC-AACG
* *
845256 TTAAACCAAGC-ACTAGTGCACCACCTCCATCC
1 CTAAACCAAGCAAC-AATGCACCACCTCCATCC
845288 CAGTCTAGAC
Statistics
Matches: 110, Mismatches: 26, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
35 4 0.04
36 103 0.94
37 3 0.03
ACGTcount: A:0.37, C:0.38, G:0.11, T:0.14
Consensus pattern (36 bp):
CTAAACCAAGCAACAATGCACCACCTCCATCCAACG
Found at i:845314 original size:36 final size:36
Alignment explanation
Indices: 845187--845314 Score: 113
Period size: 36 Copynumber: 3.6 Consensus size: 36
845177 CCCAATGCTG
*
845187 AACCAAGCAACAATGCACCACCTCCATCCAACG-CT
1 AACCAAGCAACAATCCACCACCTCCATCCAACGTCT
*
845222 AACCCAAGCAACAATCCACCACCTCCA-CCGAAGGT-T
1 AA-CCAAGCAACAATCCACCACCTCCATCC-AACGTCT
* * *
845258 AAACCAAGC-ACTAGTGCACCACCTCCATCCCA-GTCT
1 -AACCAAGCAAC-AATCCACCACCTCCATCCAACGTCT
**
845294 AGACCAAGCATTAATCCACCA
1 A-ACCAAGCAACAATCCACCA
845315 TCTGAAGCTC
Statistics
Matches: 75, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
35 9 0.12
36 62 0.83
37 4 0.05
ACGTcount: A:0.36, C:0.41, G:0.10, T:0.13
Consensus pattern (36 bp):
AACCAAGCAACAATCCACCACCTCCATCCAACGTCT
Found at i:846715 original size:13 final size:13
Alignment explanation
Indices: 846697--846722 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
846687 GTCTCTATTC
846697 ATAAAAGTCATTG
1 ATAAAAGTCATTG
846710 ATAAAAGTCATTG
1 ATAAAAGTCATTG
846723 TTGCACAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
ATAAAAGTCATTG
Found at i:854587 original size:23 final size:23
Alignment explanation
Indices: 854535--854587 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
854525 TTGTTTACCG
* *
854535 CTTGAACTAACCTCGTTGATACA
1 CTTGAATTAACCCCGTTGATACA
854558 CTTGAATTAACCCCGTTGATACA
1 CTTGAATTAACCCCGTTGATACA
854581 CTTGAAT
1 CTTGAAT
854588 ATGCTTAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (23 bp):
CTTGAATTAACCCCGTTGATACA
Found at i:856844 original size:2 final size:2
Alignment explanation
Indices: 856837--856875 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
856827 CCTGTGACCA
856837 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
856876 GAGAGGGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:862348 original size:23 final size:23
Alignment explanation
Indices: 862322--862382 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
862312 ATTTATATGT
*
862322 CACTTGGGTGCATTTCTACGCTG-
1 CACTTCGGTGCATTTCTACG-TGA
*
862345 CACTTCGGTGCAATTCTACGTGA
1 CACTTCGGTGCATTTCTACGTGA
*
862368 CACATCGGTGCATTT
1 CACTTCGGTGCATTT
862383 ATATGAACTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 2 0.06
23 31 0.94
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGTGA
Found at i:868489 original size:15 final size:15
Alignment explanation
Indices: 868469--868497 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
868459 GAAAGGGGTA
868469 GTATCGATACCATAG
1 GTATCGATACCATAG
868484 GTATCGATACCATA
1 GTATCGATACCATA
868498 AGGCAAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (15 bp):
GTATCGATACCATAG
Found at i:869245 original size:23 final size:23
Alignment explanation
Indices: 869218--869280 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
869208 CATTTTATAT
869218 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * * *
869241 GGCACTTCAGTGCAATTCTTCGT
1 GGCACTTCGGTGCATTTCTACGC
* *
869264 GGCACTTTGATGCATTT
1 GGCACTTCGGTGCATTT
869281 ATATAAGATG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:877478 original size:17 final size:16
Alignment explanation
Indices: 877443--877478 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
877433 AACTTGATCT
*
877443 TATCTAAAAATTTGAA
1 TATCTAAAAATTTCAA
877459 TATCTAAAAATTTCATA
1 TATCTAAAAATTTCA-A
877476 TAT
1 TAT
877479 TGAAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (16 bp):
TATCTAAAAATTTCAA
Found at i:881563 original size:12 final size:12
Alignment explanation
Indices: 881539--881602 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
881529 TTATAATTTG
881539 AATAT-TAACTAT
1 AATATATAA-TAT
881551 AATATATAATAT
1 AATATATAATAT
* * *
881563 ATTTTTTAATAT
1 AATATATAATAT
881575 GAAT-TATAATAT
1 -AATATATAATAT
*
881587 ATATATATATTAT
1 A-ATATATAATAT
881600 AAT
1 AAT
881603 TTGAATATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
11 1 0.02
12 28 0.67
13 13 0.31
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (12 bp):
AATATATAATAT
Found at i:881603 original size:24 final size:23
Alignment explanation
Indices: 881548--881603 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
881538 GAATATTAAC
* *
881548 TATAATATATAATATATTTTTTAA
1 TATAAT-TATAATATATTATATAA
*
881572 TATGAATTATAATATATATATATAT
1 TAT-AATTATAATATAT-TATATAA
881597 TATAATT
1 TATAATT
881604 TGAATATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 17 0.63
25 10 0.37
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TATAATTATAATATATTATATAA
Found at i:881830 original size:23 final size:22
Alignment explanation
Indices: 881804--881854 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
881794 CTCTATAACT
881804 TGTTTTTCTTTATCTTTATGGCA
1 TGTTTTTCTTTATCTTT-TGGCA
* *
881827 TGTTTCTCTTTGTCTTTTGGCA
1 TGTTTTTCTTTATCTTTTGGCA
*
881849 CGTTTT
1 TGTTTT
881855 CGACCGTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.08, C:0.16, G:0.16, T:0.61
Consensus pattern (22 bp):
TGTTTTTCTTTATCTTTTGGCA
Found at i:883137 original size:17 final size:15
Alignment explanation
Indices: 883097--883138 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
883087 TTCCTATGAT
883097 TAATA-ATTATAACA
1 TAATACATTATAACA
883111 TAAT-CATTATGAACA
1 TAATACATTAT-AACA
883126 TGAATACATTATA
1 T-AATACATTATA
883139 GTCTTTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 9 0.38
15 5 0.21
16 4 0.17
17 6 0.25
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (15 bp):
TAATACATTATAACA
Found at i:883264 original size:22 final size:23
Alignment explanation
Indices: 883227--883279 Score: 90
Period size: 22 Copynumber: 2.3 Consensus size: 23
883217 AATTCCTTAT
883227 GTTACATGAATATGAGATTAATG
1 GTTACATGAATATGAGATTAATG
883250 GTTACATG-ATATGAGATTAATG
1 GTTACATGAATATGAGATTAATG
*
883272 GTGACATG
1 GTTACATG
883280 TACATGGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 21 0.72
23 8 0.28
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.34
Consensus pattern (23 bp):
GTTACATGAATATGAGATTAATG
Found at i:883454 original size:21 final size:21
Alignment explanation
Indices: 883428--883488 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
883418 CGAAGGTTTT
883428 ATAGGTCCTTCGGGACAACTC
1 ATAGGTCCTTCGGGACAACTC
* *
883449 ATAGGTCCTTTGGGACATATTC
1 ATAGGTCCTTCGGGACA-ACTC
* *
883471 ACAGGTCATTCGGGACAA
1 ATAGGTCCTTCGGGACAA
883489 ATCTCATATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (21 bp):
ATAGGTCCTTCGGGACAACTC
Found at i:883485 original size:22 final size:21
Alignment explanation
Indices: 883430--883488 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 21
883420 AAGGTTTTAT
*
883430 AGGTCCTTCGGGACAACTCAT
1 AGGTCCTTCGGGACAACTCAC
* *
883451 AGGTCCTTTGGGACATATTCAC
1 AGGTCCTTCGGGACA-ACTCAC
*
883473 AGGTCATTCGGGACAA
1 AGGTCCTTCGGGACAA
883489 ATCTCATATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 15 0.47
22 17 0.53
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (21 bp):
AGGTCCTTCGGGACAACTCAC
Found at i:888775 original size:19 final size:19
Alignment explanation
Indices: 888748--888799 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
888738 AAATTTCATT
*
888748 AGTGTATCGATGCATGAGG
1 AGTGCATCGATGCATGAGG
888767 AGTGCATCGATGCATGAGG
1 AGTGCATCGATGCATGAGG
*
888786 AGCGCATCGATGCA
1 AGTGCATCGATGCA
888800 CCCCCTTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.27, C:0.17, G:0.35, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATGAGG
Found at i:889731 original size:18 final size:18
Alignment explanation
Indices: 889708--889769 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
889698 AAGAGTCTAC
**
889708 GTGGTCCTTCGTTACATA
1 GTGGTCCTTCGGAACATA
* *
889726 GTGGTCCTTCGGGACACA
1 GTGGTCCTTCGGAACATA
889744 GTGGTCCTTCGGAACATA
1 GTGGTCCTTCGGAACATA
889762 GTGGTCCT
1 GTGGTCCT
889770 ACTGGACAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (18 bp):
GTGGTCCTTCGGAACATA
Found at i:889777 original size:36 final size:36
Alignment explanation
Indices: 889708--889777 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
889698 AAGAGTCTAC
** *
889708 GTGGTCCTTCGTTACATAGTGGTCCTTCGGGACACA
1 GTGGTCCTTCGGAACATAGTGGTCCTACGGGACACA
*
889744 GTGGTCCTTCGGAACATAGTGGTCCTACTGGACA
1 GTGGTCCTTCGGAACATAGTGGTCCTACGGGACA
889778 AATTCTACGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.29
Consensus pattern (36 bp):
GTGGTCCTTCGGAACATAGTGGTCCTACGGGACACA
Done.