Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 33 of 199
Found at i:9350365 original size:9 final size:9
Alignment explanation
Indices: 9350340--9350380 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
9350330 AATTTTTAAA
9350340 TTATATAAC
1 TTATATAAC
* *
9350349 TTACATAAA
1 TTATATAAC
9350358 TTATATAAC
1 TTATATAAC
*
9350367 TTACATAAC
1 TTATATAAC
9350376 TTATA
1 TTATA
9350381 AATATTTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (9 bp):
TTATATAAC
Found at i:9350422 original size:17 final size:18
Alignment explanation
Indices: 9350402--9350435 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
9350392 ACATTTTTAA
9350402 TATATATTTTT-AAAATC
1 TATATATTTTTCAAAATC
*
9350419 TATATTTTTTTCAAAAT
1 TATATATTTTTCAAAAT
9350436 TTATCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATTTTTCAAAATC
Found at i:9350544 original size:9 final size:9
Alignment explanation
Indices: 9350532--9350836 Score: 279
Period size: 9 Copynumber: 34.6 Consensus size: 9
9350522 TAACATACAA
9350532 TACATAACT
1 TACATAACT
*
9350541 TACATAAAT
1 TACATAACT
*
9350550 TAAATAACT
1 TACATAACT
9350559 TACATAACT
1 TACATAACT
9350568 TACATAACT
1 TACATAACT
*
9350577 TACATAAAT
1 TACATAACT
*
9350586 TAAATAACT
1 TACATAACT
9350595 TACATAACT
1 TACATAACT
9350604 TACATAACT
1 TACATAACT
*
9350613 TAAATAACT
1 TACATAACT
*
9350622 TATATAACT
1 TACATAACT
9350631 TACATAACT
1 TACATAACT
*
9350640 TAAATAACT
1 TACATAACT
9350649 TACATAA--
1 TACATAACT
9350656 TACATAACT
1 TACATAACT
* *
9350665 TTCCTAACT
1 TACATAACT
* *
9350674 TACATTATT
1 TACATAACT
9350683 TACATAA--
1 TACATAACT
9350690 TACATAACTT
1 TACATAAC-T
9350700 AGTACATAACT
1 --TACATAACT
9350711 TACAT-A-T
1 TACATAACT
*** **
9350718 TTTTTTTC-
1 TACATAACT
* **
9350726 TAAATTGCT
1 TACATAACT
*
9350735 TACATAAAT
1 TACATAACT
*
9350744 TAAATAACT
1 TACATAACT
9350753 TACATAACT
1 TACATAACT
*
9350762 TAAATAACT
1 TACATAACT
9350771 TACATAACT
1 TACATAACT
*
9350780 TACATATCT
1 TACATAACT
9350789 TACATAACT
1 TACATAACT
*
9350798 TACATAAAT
1 TACATAACT
9350807 TACATAA--
1 TACATAACT
9350814 TACATAACCT
1 TACATAA-CT
*
9350824 T-CCTAACT
1 TACATAACT
9350832 TACAT
1 TACAT
9350837 TATTGTTCAA
Statistics
Matches: 240, Mismatches: 42, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
7 24 0.10
8 8 0.03
9 198 0.82
10 1 0.00
11 1 0.00
12 8 0.03
ACGTcount: A:0.45, C:0.18, G:0.01, T:0.37
Consensus pattern (9 bp):
TACATAACT
Found at i:9350737 original size:158 final size:157
Alignment explanation
Indices: 9350575--9350873 Score: 492
Period size: 158 Copynumber: 1.9 Consensus size: 157
9350565 ACTTACATAA
* *
9350575 CTTACATAAATTAAATAACTTACATAACTTACATAACTTAAATAACTTATATAACTTACATAACT
1 CTTACATAAATTAAATAACTTACATAACTTAAATAACTTAAATAACTTACATAACTTACATAACT
* * *
9350640 TAAATAACTTACATAATACATAACTTTCCTAACTTACATTATT-TACATAATACATAACTTAGTA
66 TAAATAAATTACATAATACATAACCTTCCTAACTTACATTATTGTAC--AATACACAACTTAGTA
9350704 CATAACTTACATATTTTTTTTCTAAATTG
129 CATAACTTACATATTTTTTTTCTAAATTG
* *
9350733 CTTACATAAATTAAATAACTTACATAACTTAAATAACTTACATAACTTACATATCTTACATAACT
1 CTTACATAAATTAAATAACTTACATAACTTAAATAACTTAAATAACTTACATAACTTACATAACT
* *
9350798 TACATAAATTACATAATACATAACCTTCCTAACTTACATTATTGTTCAATACACAACTTAGTACA
66 TAAATAAATTACATAATACATAACCTTCCTAACTTACATTATTGTACAATACACAACTTAGTACA
9350863 TAACTTACATA
131 TAACTTACATA
9350874 ACTCATTTAT
Statistics
Matches: 131, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
157 28 0.21
158 101 0.77
159 2 0.02
ACGTcount: A:0.43, C:0.18, G:0.01, T:0.37
Consensus pattern (157 bp):
CTTACATAAATTAAATAACTTACATAACTTAAATAACTTAAATAACTTACATAACTTACATAACT
TAAATAAATTACATAATACATAACCTTCCTAACTTACATTATTGTACAATACACAACTTAGTACA
TAACTTACATATTTTTTTTCTAAATTG
Found at i:9356345 original size:21 final size:20
Alignment explanation
Indices: 9356321--9356386 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 20
9356311 GGAAATATGA
*
9356321 AGGCGGCAGCGAGGGAAGCAG
1 AGGC-GCAGCGAGAGAAGCAG
*
9356342 AGGCTGCAGCGAGAAAAGCAG
1 AGGC-GCAGCGAGAGAAGCAG
9356363 AGGACGCAGCGAGAGAAGCAG
1 AGG-CGCAGCGAGAGAAGCAG
9356384 AGG
1 AGG
9356387 TTCAAAAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 39 0.98
22 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.45, T:0.02
Consensus pattern (20 bp):
AGGCGCAGCGAGAGAAGCAG
Found at i:9356857 original size:43 final size:43
Alignment explanation
Indices: 9356810--9356891 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
9356800 TATAGTGGCG
9356810 TTTGTGAAAT-AAGCGCCGCGAAAGAACACTACTTTTAGCAGCA
1 TTTGT-AAATGAAGCGCCGCGAAAGAACACTACTTTTAGCAGCA
* * *
9356853 TTTGTAGATGAAGCGCCGCTAAAGAACATTACTTTTAGC
1 TTTGTAAATGAAGCGCCGCGAAAGAACACTACTTTTAGC
9356892 GGCGCTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 3 0.09
43 32 0.91
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (43 bp):
TTTGTAAATGAAGCGCCGCGAAAGAACACTACTTTTAGCAGCA
Found at i:9357041 original size:43 final size:43
Alignment explanation
Indices: 9356863--9357174 Score: 418
Period size: 42 Copynumber: 7.3 Consensus size: 43
9356853 TTTGTAGATG
* * * *
9356863 AAGCGCCGCTAAAGAACATTA-CTTTTAGCGGCGCTTTTTACC-
1 AAGCGCCGCTAAAGAACATGATC-ATTAGCGGCGTTTTTTTCCT
*
9356905 AAGCGCCGCTAAAGAACATGATCATTAGCGGTG-TTTTTTCCT
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCT
9356947 AAGCGCCGCTAAAGAACATGATCATTAGCGGCG-TTTTTTCCT
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCT
9356989 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCT
* * * * * * *
9357032 AAACGCCGCTAAAGATCATGTTCTTTAGTGGC-ATTTTTTCCC
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCT
9357074 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCT
* * * *
9357117 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCATTTTTTTCTGT
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTC-CT
*
9357161 AAGCGCCGCAAAAG
1 AAGCGCCGCTAAAG
9357175 TTAGCGACGT
Statistics
Matches: 241, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
41 7 0.03
42 137 0.57
43 83 0.34
44 14 0.06
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (43 bp):
AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCT
Found at i:9357155 original size:85 final size:85
Alignment explanation
Indices: 9356863--9357155 Score: 444
Period size: 85 Copynumber: 3.5 Consensus size: 85
9356853 TTTGTAGATG
* * ** *
9356863 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGCTTTTTACCAAGCGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCATTTTTTCCCAAGCGCCGCTAAAGAACATGATC
*
9356928 ATTAGCGGTG-TTTTTTCCT
66 ATTAGCGGCGTTTTTTTCCT
* * * *
9356947 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCATTTTTTCCCAAGCGCCGCTAAAGAACATGATC
9357012 ATTAGCGGCGTTTTTTTCCT
66 ATTAGCGGCGTTTTTTTCCT
* * ** *
9357032 AAACGCCGCTAAAGATCATGTTCTTTAGTGGCATTTTTTCCCAAGCGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCATTTTTTCCCAAGCGCCGCTAAAGAACATGATC
9357097 ATTAGCGGCGTTTTTTTCCT
66 ATTAGCGGCGTTTTTTTCCT
9357117 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCATTTTTT
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCATTTTTT
9357156 TCTGTAAGCG
Statistics
Matches: 188, Mismatches: 20, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
84 67 0.36
85 121 0.64
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (85 bp):
AAGCGCCGCTAAAGAACATGACCTTTAGCGGCATTTTTTCCCAAGCGCCGCTAAAGAACATGATC
ATTAGCGGCGTTTTTTTCCT
Found at i:9358281 original size:17 final size:16
Alignment explanation
Indices: 9358240--9358288 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
9358230 GAATATTTTT
9358240 ATAGATTATTAATTTG
1 ATAGATTATTAATTTG
* *
9358256 AGAAAATTAGTTAATTTG
1 A-TAGATTA-TTAATTTG
9358274 ATAGATTAATTAATT
1 ATAGATT-ATTAATT
9358289 AAGGGATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
16 1 0.04
17 15 0.58
18 10 0.38
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (16 bp):
ATAGATTATTAATTTG
Found at i:9360713 original size:104 final size:104
Alignment explanation
Indices: 9360424--9361058 Score: 752
Period size: 104 Copynumber: 6.1 Consensus size: 104
9360414 AATAGCTCAT
* * * *
9360424 TGATTTAATATCGC-AGCTAACGATTATTTGAGTTAGTTGATTTAATATCGCAACTCCAAACAGC
1 TGATTTAAGATCGCAACCTAA-GTTTATTTGAGTTAGTTGATTTAATATCGCAACTCCGAACAGC
9360488 TCGCTGACCTACGTTCACAGCTGATATTATTAAGGTTAGC
65 TCGCTGACCTACGTTCACAGCTGATATTATTAAGGTTAGC
* * * * * * * *
9360528 TAATTTAAGATAGAAAACCTAAGTTTATTTTAGTTAGTTGATTTAAGATCACAACTCTGAACAGA
1 TGATTTAAGATCG-CAACCTAAGTTTATTTGAGTTAGTTGATTTAATATCGCAACTCCGAACAGC
* *
9360593 TCACTGACCTACGTTCACAGCCGATATTATTAAGGTTAGC
65 TCGCTGACCTACGTTCACAGCTGATATTATTAAGGTTAGC
* *
9360633 TGATTTAAGATCGCAACCTAAGTTTATTTGAGTTAGTTGATTTAATATCGTAACTCCGAATAGCT
1 TGATTTAAGATCGCAACCTAAGTTTATTTGAGTTAGTTGATTTAATATCGCAACTCCGAACAGCT
* * * *
9360698 CACTAACCTTCGTTCACAGTTGATATTATTAAGGTTAGC
66 CGCTGACCTACGTTCACAGCTGATATTATTAAGGTTAGC
* ** * * * *
9360737 TTATTTAAGATTTCAACCTAAGTTTATTTGAGTTAGCTAATTTAATATCGCAAATCCTAACAGCT
1 TGATTTAAGATCGCAACCTAAGTTTATTTGAGTTAGTTGATTTAATATCGCAACTCCGAACAGCT
*
9360802 CGTTGACCTACGTTCACAGCTGATATTATTAAGGTTAGC
66 CGCTGACCTACGTTCACAGCTGATATTATTAAGGTTAGC
* * * * *
9360841 TAATTTAAGATCGGAACCTAAGTTTATTTGAGTTTGTTGATTTAAGATTC-CAACTCCTAACAGC
1 TGATTTAAGATCGCAACCTAAGTTTATTTGAGTTAGTTGATTTAATA-TCGCAACTCCGAACAGC
* * * *
9360905 TCGCTGACCTATGTTCACAGTTGATATTATTCAGTTTAGC
65 TCGCTGACCTACGTTCACAGCTGATATTATTAAGGTTAGC
* * * * * * * *
9360945 TGATTTAATATCGCAACCTAAGTTTATTTGAGTTCGCTAATTTAAGATCACAACTCCTAACAGTT
1 TGATTTAAGATCGCAACCTAAGTTTATTTGAGTTAGTTGATTTAATATCGCAACTCCGAACAGCT
* * * * * * *
9361010 CGTTGATCTACGATCACAACTGATATTTTTAAAGTTCGC
66 CGCTGACCTACGTTCACAGCTGATATTATTAAGGTTAGC
9361049 TCGATTTAAG
1 T-GATTTAAG
9361059 TTCACGATTT
Statistics
Matches: 451, Mismatches: 75, Indels: 9
0.84 0.14 0.02
Matches are distributed among these distances:
103 2 0.00
104 350 0.78
105 94 0.21
106 5 0.01
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (104 bp):
TGATTTAAGATCGCAACCTAAGTTTATTTGAGTTAGTTGATTTAATATCGCAACTCCGAACAGCT
CGCTGACCTACGTTCACAGCTGATATTATTAAGGTTAGC
Found at i:9361036 original size:312 final size:313
Alignment explanation
Indices: 9360447--9361041 Score: 836
Period size: 312 Copynumber: 1.9 Consensus size: 313
9360437 CAGCTAACGA
* * *
9360447 TTATTTGAGTTAGTTGATTTAATATCGCAACTCCAAACAGCTCGCTGACCTACGTTCACAGCTGA
1 TTATTTGAGTTAGCTAATTTAATATCGCAAATCCAAACAGCTCGCTGACCTACGTTCACAGCTGA
*
9360512 TATTATTAAGGTTAGCTAATTTAAGATAGAAAACCTAAGTTTATTTTAGTTAGTTGATTTAAGAT
66 TATTATTAAGGTTAGCTAATTTAAGATAGAAAACCTAAGTTTATTTGAGTTAGTTGATTTAAGAT
9360577 CACAACTCTGAACAGATCACTGACCTACGTTCACAGCCGATATTATTAAGGTTAGCTGATTTAAG
131 CACAACTCTGAACAGATCACTGACCTACGTTCACAGCCGATATTATTAAGGTTAGCTGATTTAAG
* * * ** *
9360642 ATCGCAACCTAAGTTTATTTGAGTTAGTTGATTTAATATCGTAACTCCGAATAGCTCACTAACCT
196 ATCGCAACCTAAGTTTATTTGAGTTAGCTAATTTAAGATCACAACTCCGAACAGCTCACTAACCT
* * **
9360707 TCGTTCACAGTTGATATTATTAAGGTTAGCTTATTTAAGATTTCAACCTAAGT
261 ACGATCACAACTGATATTATTAAGGTTAGCTTATTTAAGATTTCAACCTAAGT
* *
9360760 TTATTTGAGTTAGCTAATTTAATATCGCAAATCCTAACAGCTCGTTGACCTACGTTCACAGCTGA
1 TTATTTGAGTTAGCTAATTTAATATCGCAAATCCAAACAGCTCGCTGACCTACGTTCACAGCTGA
* * *
9360825 TATTATTAAGGTTAGCTAATTTAAGATCG-GAACCTAAGTTTATTTGAGTTTGTTGATTTAAGAT
66 TATTATTAAGGTTAGCTAATTTAAGATAGAAAACCTAAGTTTATTTGAGTTAGTTGATTTAAGA-
* * * ** * *
9360889 TC-CAACTCCT-AACAGCTCGCTGACCTATGTTCACAGTTGATATTATTCAGTTTAGCTGATTTA
130 TCACAACT-CTGAACAGATCACTGACCTACGTTCACAGCCGATATTATTAAGGTTAGCTGATTTA
* * * * ** * *
9360952 ATATCGCAACCTAAGTTTATTTGAGTTCGCTAATTTAAGATCACAACTCCTAACAGTTCGTTGAT
194 AGATCGCAACCTAAGTTTATTTGAGTTAGCTAATTTAAGATCACAACTCCGAACAGCTCACTAAC
*
9361017 CTACGATCACAACTGATATTTTTAA
259 CTACGATCACAACTGATATTATTAA
9361042 AGTTCGCTCG
Statistics
Matches: 245, Mismatches: 35, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
312 153 0.62
313 92 0.38
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (313 bp):
TTATTTGAGTTAGCTAATTTAATATCGCAAATCCAAACAGCTCGCTGACCTACGTTCACAGCTGA
TATTATTAAGGTTAGCTAATTTAAGATAGAAAACCTAAGTTTATTTGAGTTAGTTGATTTAAGAT
CACAACTCTGAACAGATCACTGACCTACGTTCACAGCCGATATTATTAAGGTTAGCTGATTTAAG
ATCGCAACCTAAGTTTATTTGAGTTAGCTAATTTAAGATCACAACTCCGAACAGCTCACTAACCT
ACGATCACAACTGATATTATTAAGGTTAGCTTATTTAAGATTTCAACCTAAGT
Found at i:9361304 original size:52 final size:52
Alignment explanation
Indices: 9361247--9361353 Score: 214
Period size: 52 Copynumber: 2.1 Consensus size: 52
9361237 CACCATCGAA
9361247 CAACAGAACCTACTTATTAAAGTTTCGTATGAAAACTTAAGTAGTAAGCCCC
1 CAACAGAACCTACTTATTAAAGTTTCGTATGAAAACTTAAGTAGTAAGCCCC
9361299 CAACAGAACCTACTTATTAAAGTTTCGTATGAAAACTTAAGTAGTAAGCCCC
1 CAACAGAACCTACTTATTAAAGTTTCGTATGAAAACTTAAGTAGTAAGCCCC
9361351 CAA
1 CAA
9361354 TTACATGTTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.26
Consensus pattern (52 bp):
CAACAGAACCTACTTATTAAAGTTTCGTATGAAAACTTAAGTAGTAAGCCCC
Found at i:9367291 original size:16 final size:18
Alignment explanation
Indices: 9367252--9367295 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
9367242 TTGAATTTTA
*
9367252 AATATTTTTCATAAATAT
1 AATATTTTTCAAAAATAT
9367270 CAATATTTTT-AAAAATAT
1 -AATATTTTTCAAAAATAT
9367288 -ATATTTTT
1 AATATTTTT
9367296 TATGCAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 8 0.33
18 7 0.29
19 9 0.38
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (18 bp):
AATATTTTTCAAAAATAT
Found at i:9372635 original size:20 final size:20
Alignment explanation
Indices: 9372610--9372649 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9372600 AATATTTTCC
*
9372610 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
9372630 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
9372650 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:9372655 original size:34 final size:35
Alignment explanation
Indices: 9372598--9372664 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
9372588 CAAACACTAG
*
9372598 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
9372633 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
9372665 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:9373512 original size:21 final size:21
Alignment explanation
Indices: 9373452--9373505 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
9373442 GAGTGAAAAT
9373452 ACCTTCGATGTCGCGACACTA
1 ACCTTCGATGTCGCGACACTA
9373473 ACCTTCGATGTCGCGACACTA
1 ACCTTCGATGTCGCGACACTA
9373494 ACCTTCGATGTC
1 ACCTTCGATGTC
9373506 ACAACACCGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.26
Consensus pattern (21 bp):
ACCTTCGATGTCGCGACACTA
Found at i:9375683 original size:46 final size:46
Alignment explanation
Indices: 9375616--9375823 Score: 332
Period size: 46 Copynumber: 4.6 Consensus size: 46
9375606 TTTGAGTACT
*
9375616 TCTGATCAAGTGACAAAGTGATAAGTGGTAACTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
9375662 TCTGATCAAGTGACATAGTGATAAGTGGTAGCTTTAACTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
9375708 TCTGATCAAGTAACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
9375754 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
9375799 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
9375824 ATCATATATA
Statistics
Matches: 151, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
43 12 0.08
44 5 0.03
45 19 0.13
46 115 0.76
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:9378384 original size:29 final size:28
Alignment explanation
Indices: 9378322--9378486 Score: 179
Period size: 29 Copynumber: 5.8 Consensus size: 28
9378312 ATAAATAAGA
* *
9378322 CTTTGTGGCTATCTTTGTTAAAGGAAGA
1 CTTTGTGGCTATCTCTGTTAAAGGAAGC
*
9378350 CTTTGTGGCGATCTCTGTTATAAGGAAGC
1 CTTTGTGGCTATCTCTGTTA-AAGGAAGC
* *
9378379 CTTTGTGGCGATCTATGTTATAAGGAAGC
1 CTTTGTGGCTATCTCTGTTA-AAGGAAGC
* **
9378408 CTTAGTGGCTATCTCTGTTAAAAAAATGC
1 CTTTGTGGCTATCTCTGTTAAAGGAA-GC
* * *
9378437 ATTTGTGGCTATCTCAGTTAAATGGATG-
1 CTTTGTGGCTATCTCTGTTAAA-GGAAGC
*
9378465 CTTTGTGGCTATCTTTGTTAAA
1 CTTTGTGGCTATCTCTGTTAAA
9378487 ATGATGCTTA
Statistics
Matches: 116, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 41 0.35
29 74 0.64
30 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (28 bp):
CTTTGTGGCTATCTCTGTTAAAGGAAGC
Found at i:9378469 original size:86 final size:86
Alignment explanation
Indices: 9378326--9378484 Score: 198
Period size: 86 Copynumber: 1.8 Consensus size: 86
9378316 ATAAGACTTT
* ** *
9378326 GTGGCTATCTTTGTTAAAGGAAGACTTTGTGGCGATCTCTGTTATAAGGAAGCCTTTGTGGCGAT
1 GTGGCTATCTCTGTTAAAAAAAGACTTTGTGGCGATCTCAGTTATAAGGAAGCCTTTGTGGCGAT
9378391 CTATGTTATAAGGAAGCCTTA
66 CTATGTTATAAGGAAGCCTTA
* *
9378412 GTGGCTATCTCTGTTAAAAAAATG-CATTTGTGGCTATCTCAGTTA-AATGGATG-CTTTGTGGC
1 GTGGCTATCTCTGTTAAAAAAA-GAC-TTTGTGGCGATCTCAGTTATAA-GGAAGCCTTTGTGGC
* *
9378474 TATCTTTGTTA
63 GATCTATGTTA
9378485 AAATGATGCT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
86 40 0.65
87 22 0.35
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.38
Consensus pattern (86 bp):
GTGGCTATCTCTGTTAAAAAAAGACTTTGTGGCGATCTCAGTTATAAGGAAGCCTTTGTGGCGAT
CTATGTTATAAGGAAGCCTTA
Found at i:9385896 original size:22 final size:22
Alignment explanation
Indices: 9385871--9385914 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
9385861 ATTATGTAAA
9385871 ACTAATATATAAAAAATAAATC
1 ACTAATATATAAAAAATAAATC
9385893 ACTAATATATAAAAAATAAATC
1 ACTAATATATAAAAAATAAATC
9385915 TCAAATATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (22 bp):
ACTAATATATAAAAAATAAATC
Found at i:9385921 original size:22 final size:22
Alignment explanation
Indices: 9385874--9385922 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
9385864 ATGTAAAACT
*
9385874 AATATATAAAAAATAAATCACT
1 AATATATAAAAAATAAATCACA
*
9385896 AATATATAAAAAATAAATCTCA
1 AATATATAAAAAATAAATCACA
9385918 AATAT
1 AATAT
9385923 GAATATGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (22 bp):
AATATATAAAAAATAAATCACA
Found at i:9396874 original size:6 final size:6
Alignment explanation
Indices: 9396865--9396901 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
9396855 ATTATAAATG
* *
9396865 TTTTTG TTTTTG TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T
9396902 ATTTCTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.11, C:0.00, G:0.05, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:9397657 original size:18 final size:18
Alignment explanation
Indices: 9397634--9397669 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9397624 TTACTATTTT
*
9397634 ATATTTTTCATGAATTAA
1 ATATTTATCATGAATTAA
*
9397652 ATATTTATGATGAATTAA
1 ATATTTATCATGAATTAA
9397670 CTTAATTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (18 bp):
ATATTTATCATGAATTAA
Found at i:9398727 original size:29 final size:29
Alignment explanation
Indices: 9398694--9398751 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
9398684 TGAAAAATAA
9398694 TGTCATTTGCAAGAAAATAATCTTGGTTT
1 TGTCATTTGCAAGAAAATAATCTTGGTTT
9398723 TGTCATTTGCAAGAAAATAATCTTGGTTT
1 TGTCATTTGCAAGAAAATAATCTTGGTTT
9398752 CGTCTCATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41
Consensus pattern (29 bp):
TGTCATTTGCAAGAAAATAATCTTGGTTT
Found at i:9400676 original size:50 final size:50
Alignment explanation
Indices: 9400548--9400838 Score: 343
Period size: 50 Copynumber: 5.8 Consensus size: 50
9400538 GATAATAACA
* * ** * * *
9400548 TGCCAAAGCTATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * ** * *
9400597 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * **
9400647 TGCCCATGCCATGTCTCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
9400697 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
9400747 TGTCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
9400797 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
9400839 TTACCCAAAT
Statistics
Matches: 207, Mismatches: 33, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
49 38 0.18
50 169 0.82
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:9407433 original size:68 final size:68
Alignment explanation
Indices: 9407196--9407494 Score: 305
Period size: 68 Copynumber: 4.4 Consensus size: 68
9407186 TGAAATTTAA
* * * * * * * *
9407196 TGTGTATGACCATAGCTTGGCTATAGTAACAAAAGGAGTCTACCAGGATGTTAAACATGAGTTCC
1 TGTGTAAGACCATAGCTCGGCTATGGCAACAAAGGGAGTCTATCAGAATGTTAAACATGGGTTCC
9407261 TAC
66 TAC
* * * * * *
9407264 TGTGTAAGACCATAGCTTGGCAATGGCAGCAAATGGAGTCTGCTAAGACA--TTAAACATGGGTT
1 TGTGTAAGACCATAGCTCGGCTATGGCAACAAAGGGAGTCT-ATCAGA-ATGTTAAACATGGGTT
9407327 CCTAC
64 CCTAC
* * *
9407332 TGTGTAAAACCATAGCTCGGCTATGGCAACAAAGGGAGTCTATTAGAATGTTAAACATAGGTTCC
1 TGTGTAAGACCATAGCTCGGCTATGGCAACAAAGGGAGTCTATCAGAATGTTAAACATGGGTTCC
*
9407397 TAT
66 TAC
* * * * * * *
9407400 TGTGTAAGACCATAACTCGACTATGGCAACAAAGAGAGTTTGTCAGGATGTTAAACATGGGTTCA
1 TGTGTAAGACCATAGCTCGGCTATGGCAACAAAGGGAGTCTATCAGAATGTTAAACATGGGTTCC
9407465 TAC
66 TAC
* * * *
9407468 TATATAAGAACATAGCTCGGATATGGC
1 TGTGTAAGACCATAGCTCGGCTATGGC
9407495 GTCAGGTAAA
Statistics
Matches: 190, Mismatches: 37, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
66 1 0.01
67 4 0.02
68 182 0.96
69 2 0.01
70 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (68 bp):
TGTGTAAGACCATAGCTCGGCTATGGCAACAAAGGGAGTCTATCAGAATGTTAAACATGGGTTCC
TAC
Found at i:9418420 original size:19 final size:20
Alignment explanation
Indices: 9418396--9418436 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
9418386 ATATTAGTAA
*
9418396 TAATAATAGACAA-TAATAG
1 TAATAATAAACAAGTAATAG
9418415 TAATAATAAACAAGTAATAG
1 TAATAATAAACAAGTAATAG
9418435 TA
1 TA
9418437 CCATAAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.59, C:0.05, G:0.10, T:0.27
Consensus pattern (20 bp):
TAATAATAAACAAGTAATAG
Found at i:9420613 original size:45 final size:45
Alignment explanation
Indices: 9420564--9420879 Score: 136
Period size: 45 Copynumber: 7.1 Consensus size: 45
9420554 TGTCTATGCA
9420564 GGAAGGCAAGATCTGCTATCTTCAATCTATTCCGCTGCTACCCAG
1 GGAAGGCAAGATCTGCTATCTTCAATCTATTCCGCTGCTACCCAG
* * ** * * * *
9420609 GGAA-G-TAGAAT-TACTGGCTTCAATATACTCCACTG-TAACCACG
1 GGAAGGCAAG-ATCTGCTATCTTCAATCTATTCCGCTGCTACCCA-G
* * * * * * **
9420652 GGGAGGTAAAATCTGCCATCTTCGATCTGCTT-CGCTGTCTATGCA-
1 GGAAGGCAAGATCTGCTATCTTCAATCT-ATTCCGCTG-CTACCCAG
*
9420697 GGAAGGCAAGATCTGCTATCTTCAATCTATTCCGCTGCTGCCCAG
1 GGAAGGCAAGATCTGCTATCTTCAATCTATTCCGCTGCTACCCAG
* * ** * * * *
9420742 GGAA-G-TAGAAT-TACTGGCTTCAATGTACTCCACTG-TAACCACG
1 GGAAGGCAAG-ATCTGCTATCTTCAATCTATTCCGCTGCTACCCA-G
* * * * * * * ***
9420785 AGG-AGGTAAAATCCGCCATCTTCGATATGCTT-CGCTGTCTATGTA-
1 -GGAAGGCAAGATCTGCTATCTTCAATCT-ATTCCGCTG-CTACCCAG
*
9420830 GGAAGGCAAGATCTGCTATCTTCAATCTATTCCGCTGCTGCCCAG
1 GGAAGGCAAGATCTGCTATCTTCAATCTATTCCGCTGCTACCCAG
9420875 GGAAG
1 GGAAG
9420880 TAGAATTATT
Statistics
Matches: 183, Mismatches: 66, Indels: 44
0.62 0.23 0.15
Matches are distributed among these distances:
42 9 0.05
43 46 0.25
44 27 0.15
45 92 0.50
46 2 0.01
47 7 0.04
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (45 bp):
GGAAGGCAAGATCTGCTATCTTCAATCTATTCCGCTGCTACCCAG
Found at i:9420619 original size:133 final size:132
Alignment explanation
Indices: 9420041--9421119 Score: 1308
Period size: 133 Copynumber: 8.1 Consensus size: 132
9420031 CTTAGAGAGA
* * * *
9420041 CAAGATCTGAAATCTTCAATCTATTCTACTGCTGCTCAAGG-AGATAGAATTACTGGCTTCAATA
1 CAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATG
* * * **
9420105 TACTCCACTGTAACCAC-AGGGAGGTAAAATTCACCATCTTTGATCTGC--CC-CACTACTGCTT
65 TACTCCACTGTAACCACGA-GGAGGTAAAATCCGCCATCTTCGATCTGCTTCCTGTCTA-TGC--
* *
9420166 AGGGAGA
126 AGGAAGG
* *
9420173 CAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCATGGAAGTAAAATTACTGGCTTCAATGT
1 CAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGT
* * * * **
9420238 ACTCCACTGTATCCAC-AGGGAGGTAAAATTCACCATCTTTGATCTGC--CC-CACTACTGCTTA
66 ACTCCACTGTAACCACGA-GGAGGTAAAATCCGCCATCTTCGATCTGCTTCCTGTCTA-TGC--A
* *
9420299 GGGAGA
127 GGAAGG
*
9420305 CAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGTTTCAATGT
1 CAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGT
* * * **
9420370 ACTCCACTGTAACCAC-AGGGAGGTAAAATTCACCATCTTTGATCTGC--CC-CACTACTGCTTA
66 ACTCCACTGTAACCACGA-GGAGGTAAAATCCGCCATCTTCGATCTGCTTCCTGTCTA-TGC--A
* *
9420431 GGGAGA
127 GGAAGG
* * *
9420437 CAAGATTTGAAATCTTCAATCTATTCCACTGCTGTCCAGGGAAGTAGAATTGCTGGCTTCAATGT
1 CAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGT
*
9420502 ACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGATTTGCTTCGCTGTCTATGCAGGA
66 ACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGATCTGCTTC-CTGTCTATGCAGGA
9420567 AGG
130 AGG
** * * *
9420570 CAAGATCTGCTATCTTCAATCTATTCCGCTGCTACCCAGGGAAGTAGAATTACTGGCTTCAATAT
1 CAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGT
* *
9420635 ACTCCACTGTAACCACGGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGTCTATGCAGGA
66 ACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGATCTGCTTC-CTGTCTATGCAGGA
9420700 AGG
130 AGG
** *
9420703 CAAGATCTGCTATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGT
1 CAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGT
* *
9420768 ACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGATATGCTTCGCTGTCTATGTAGGA
66 ACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGATCTGCTTC-CTGTCTATGCAGGA
9420833 AGG
130 AGG
** * *
9420836 CAAGATCTGCTATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTATTGGCTTCAATGT
1 CAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGT
* *
9420901 ACTCCACTGTAACCACGAGGAGGTAAAATTCGCCATCTTCGATCTGCTTCACTGTCTATGTAGGA
66 ACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGATCTGCTTC-CTGTCTATGCAGGA
9420966 AGG
130 AGG
*** * *
9420969 CAAGATCTGCTCTCTTCAATCTATTCCGCTGCTGCCCAGGAAAGTAGAATTACTGGCTTCAATGT
1 CAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGT
* * * *
9421034 ACTCCACTGTAACCACGAGGAGGTAAAATCCGCAATTTTTGATCTGC-TCC--ACTACTGCTTAG
66 ACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGATCTGCTTCCTGTCTA-TGC--AG
* *
9421096 GGAGA
128 GAAGG
9421101 CAAGATCTGAAATCTTCAA
1 CAAGATCTGAAATCTTCAA
9421120 CCTGCTCCAT
Statistics
Matches: 881, Mismatches: 57, Indels: 18
0.92 0.06 0.02
Matches are distributed among these distances:
129 3 0.00
130 2 0.00
131 1 0.00
132 376 0.43
133 491 0.56
134 1 0.00
135 4 0.00
136 3 0.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (132 bp):
CAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGT
ACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGATCTGCTTCCTGTCTATGCAGGAA
GG
Found at i:9422441 original size:8 final size:8
Alignment explanation
Indices: 9422430--9422459 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
9422420 CCATTTTTAC
9422430 TTTTTCA-
1 TTTTTCAT
9422437 TTTTTCAT
1 TTTTTCAT
9422445 TTTTTCAT
1 TTTTTCAT
9422453 TTTTTCA
1 TTTTTCA
9422460 CATCACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTTCAT
Found at i:9422448 original size:15 final size:14
Alignment explanation
Indices: 9422421--9422456 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
9422411 TTAGCCTCTC
9422421 CATTTTTACTTTTT
1 CATTTTTACTTTTT
*
9422435 CATTTTTCATTTTTT
1 CATTTTT-ACTTTTT
9422450 CATTTTT
1 CATTTTT
9422457 TCACATCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (14 bp):
CATTTTTACTTTTT
Found at i:9427456 original size:5 final size:5
Alignment explanation
Indices: 9427446--9427479 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
9427436 TAAAAGAGAG
9427446 AAATA AAATA AAATA AAATA AAA-A GAAATA AAAT
1 AAATA AAATA AAATA AAATA AAATA -AAATA AAAT
9427480 GTATGCGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 1 0.04
5 25 0.93
6 1 0.04
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:9427675 original size:19 final size:20
Alignment explanation
Indices: 9427651--9427691 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
9427641 ATATTAGTAA
*
9427651 TAATAATAGACAA-TAATAG
1 TAATAATAAACAAGTAATAG
9427670 TAATAATAAACAAGTAATAG
1 TAATAATAAACAAGTAATAG
9427690 TA
1 TA
9427692 CCATAAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.59, C:0.05, G:0.10, T:0.27
Consensus pattern (20 bp):
TAATAATAAACAAGTAATAG
Found at i:9431633 original size:21 final size:21
Alignment explanation
Indices: 9431597--9431638 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
9431587 TAGGTTTTAA
*
9431597 GGCTCAACACAGGTTG-ATGT
1 GGCTCAACAAAGGTTGCATGT
9431617 GGCTCAACATAAGGTTGCATGT
1 GGCTCAACA-AAGGTTGCATGT
9431639 TGTAACACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 6 0.32
22 4 0.21
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (21 bp):
GGCTCAACAAAGGTTGCATGT
Found at i:9439686 original size:26 final size:26
Alignment explanation
Indices: 9439650--9439702 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
9439640 AAGGTAGAAC
9439650 TGCAGGAAGCTTTTGCCACTCTAGCT
1 TGCAGGAAGCTTTTGCCACTCTAGCT
9439676 TGCAGGAAGCTTTTGCCACTCTAGCT
1 TGCAGGAAGCTTTTGCCACTCTAGCT
9439702 T
1 T
9439703 TCACTTCGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (26 bp):
TGCAGGAAGCTTTTGCCACTCTAGCT
Found at i:9444033 original size:33 final size:33
Alignment explanation
Indices: 9443986--9444051 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
9443976 CAGATATTTC
* *
9443986 ACAATGCATGATTATCACCCAGCATTATCTATG
1 ACAAAGCATGATTATCACCCAACATTATCTATG
9444019 ACAAAGCATGATTATCACCCAACATTATCTATG
1 ACAAAGCATGATTATCACCCAACATTATCTATG
9444052 TACCAAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (33 bp):
ACAAAGCATGATTATCACCCAACATTATCTATG
Found at i:9445847 original size:70 final size:66
Alignment explanation
Indices: 9445745--9445873 Score: 168
Period size: 70 Copynumber: 1.9 Consensus size: 66
9445735 TCTGAATAAG
* * ** *
9445745 AAAAGGTAAAATATGTCGTTTTGATAAATGTTTACCTTTTCTAAAGTTAAAAGTCAAAACCATTA
1 AAAAGGTAAAATACGTCGCTTTGATAAATGTTTA-CTCAT-TAAA-TTAAAAGACAAAACCATTA
9445810 AGTT
63 AGTT
*
9445814 AAAAGGTAAAACTACGTTGCTTTGATAAATGTTTACTCATTAAATTAAAAGACAAAACCA
1 AAAAGGTAAAA-TACGTCGCTTTGATAAATGTTTACTCATTAAATTAAAAGACAAAACCA
9445874 CTATATTGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
67 15 0.28
68 4 0.08
69 14 0.26
70 20 0.38
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (66 bp):
AAAAGGTAAAATACGTCGCTTTGATAAATGTTTACTCATTAAATTAAAAGACAAAACCATTAAGT
T
Found at i:9448415 original size:23 final size:23
Alignment explanation
Indices: 9448325--9448406 Score: 110
Period size: 23 Copynumber: 3.6 Consensus size: 23
9448315 ATAGAACTTC
* *
9448325 CCACAAAGACATTGTAGGATACA
1 CCACAAAGACATTGCAGAATACA
* *
9448348 CCACAAAGGCATTGCAGAATACG
1 CCACAAAGACATTGCAGAATACA
* *
9448371 CCACATAGGCATTGCAGAATACA
1 CCACAAAGACATTGCAGAATACA
9448394 CCACAAAGACATT
1 CCACAAAGACATT
9448407 ATAGTATACG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (23 bp):
CCACAAAGACATTGCAGAATACA
Found at i:9448416 original size:46 final size:46
Alignment explanation
Indices: 9448325--9448426 Score: 123
Period size: 46 Copynumber: 2.2 Consensus size: 46
9448315 ATAGAACTTC
* * * * *
9448325 CCACAAAGACATTGTAGGATACACCACAAAGGCATTGCAGAATACG
1 CCACAAAGGCATTGCAGAATACACCACAAAGACATTACAGAATACG
* * *
9448371 CCACATAGGCATTGCAGAATACACCACAAAGACATTATAGTATACG
1 CCACAAAGGCATTGCAGAATACACCACAAAGACATTACAGAATACG
*
9448417 TCACAAAGGC
1 CCACAAAGGC
9448427 TCCATCGAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.41, C:0.25, G:0.18, T:0.17
Consensus pattern (46 bp):
CCACAAAGGCATTGCAGAATACACCACAAAGACATTACAGAATACG
Found at i:9448470 original size:23 final size:23
Alignment explanation
Indices: 9448444--9448519 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
9448434 AATATGTCGT
* *
9448444 AAAGGCTTCATATATTATGCTAC
1 AAAGGCTTCATAGATTAAGCTAC
* * * *
9448467 AAAGGCTCCAAAGAATACA-CTAT
1 AAAGGCTTCATAGATTA-AGCTAC
*
9448490 AAAGGCTTCATAGATTAAGCCAC
1 AAAGGCTTCATAGATTAAGCTAC
9448513 AAAGGCT
1 AAAGGCT
9448520 CCACAAAATA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
22 1 0.03
23 39 0.98
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.24
Consensus pattern (23 bp):
AAAGGCTTCATAGATTAAGCTAC
Found at i:9448554 original size:92 final size:92
Alignment explanation
Indices: 9448443--9448688 Score: 264
Period size: 92 Copynumber: 2.7 Consensus size: 92
9448433 GAATATGTCG
* * * *
9448443 TAAAGGCTTCATATATTATGCTACAAAGGCTCCAAAGAATACACTATAAAGGCTTCATAGATTAA
1 TAAAGGCTTAATATATTATGCCACAAAGGCTCCAAAGAATACACCATAAAGGCATCATAGATTAA
*
9448508 GCCACAAAGGCTCCACAAAATACACTA
66 GCCAAAAAGGCTCCACAAAATACACTA
* *
9448535 TAAAGGCTTAATAGT-TTATGCCACAAAGGCTCCACAGAATACGCCATAAAGGCATCATAGATTA
1 TAAAGGCTTAATA-TATTATGCCACAAAGGCTCCAAAGAATACACCATAAAGGCATCATAGATTA
* * ** *
9448599 TGCCAAAAAGGCTCCACAGAATATGCCA
65 AGCCAAAAAGGCTCCACAAAATACACTA
* * * * *** *
9448627 TAAAGGCATCATAAAATT-TTCCACAAAGGCTCCATAA-AATGTGCCATAAAGACATCATAGAT
1 TAAAGGCTTAAT-ATATTATGCCACAAAGGCTCCA-AAGAATACACCATAAAGGCATCATAGAT
9448689 AACCTATAAC
Statistics
Matches: 130, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
92 125 0.96
93 5 0.04
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (92 bp):
TAAAGGCTTAATATATTATGCCACAAAGGCTCCAAAGAATACACCATAAAGGCATCATAGATTAA
GCCAAAAAGGCTCCACAAAATACACTA
Found at i:9448580 original size:23 final size:23
Alignment explanation
Indices: 9448467--9448633 Score: 111
Period size: 23 Copynumber: 7.3 Consensus size: 23
9448457 ATTATGCTAC
* * *
9448467 AAAGGCTCCAAAGAATACACTAT
1 AAAGGCTCCACAGAATACGCCAT
* * * * *
9448490 AAAGGCTTCATAGATTAAGCCAC
1 AAAGGCTCCACAGAATACGCCAT
* * *
9448513 AAAGGCTCCACAAAATACACTAT
1 AAAGGCTCCACAGAATACGCCAT
** * ** * *
9448536 AAAGGCTTAATAGTTTATGCCAC
1 AAAGGCTCCACAGAATACGCCAT
9448559 AAAGGCTCCACAGAATACGCCAT
1 AAAGGCTCCACAGAATACGCCAT
* * * *
9448582 AAAGGCAT-CATAGATTATGCCAA
1 AAAGGC-TCCACAGAATACGCCAT
*
9448605 AAAGGCTCCACAGAATATGCCAT
1 AAAGGCTCCACAGAATACGCCAT
9448628 AAAGGC
1 AAAGGC
9448634 ATCATAAAAT
Statistics
Matches: 103, Mismatches: 39, Indels: 4
0.71 0.27 0.03
Matches are distributed among these distances:
22 1 0.01
23 101 0.98
24 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (23 bp):
AAAGGCTCCACAGAATACGCCAT
Found at i:9448654 original size:23 final size:23
Alignment explanation
Indices: 9448577--9448685 Score: 69
Period size: 23 Copynumber: 4.7 Consensus size: 23
9448567 CACAGAATAC
* * * *
9448577 GCCATAAAGGCATCATAGATTAT
1 GCCACAAAGGCATCATAAAATGT
* * * *
9448600 GCCAAAAAGGC-TCCACAGAATAT
1 GCCACAAAGGCAT-CATAAAATGT
* *
9448623 GCCATAAAGGCATCATAAAATTT
1 GCCACAAAGGCATCATAAAATGT
*
9448646 TCCACAAAGGC-TCCATAAAATGT
1 GCCACAAAGGCAT-CATAAAATGT
* *
9448669 GCCATAAAGACATCATA
1 GCCACAAAGGCATCATA
9448686 GATAACCTAT
Statistics
Matches: 69, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
22 2 0.03
23 65 0.94
24 2 0.03
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.21
Consensus pattern (23 bp):
GCCACAAAGGCATCATAAAATGT
Found at i:9448672 original size:46 final size:47
Alignment explanation
Indices: 9448418--9448685 Score: 233
Period size: 46 Copynumber: 5.8 Consensus size: 47
9448408 TAGTATACGT
* * * *
9448418 CACAAAGGCTCCATC-GAATATGTCGTAAAGGCTTCAT-ATATTATGC
1 CACAAAGGCTCCA-CAGAATATGCCATAAAGGCATCATAAAATTATGC
* * ** * * * *
9448464 TACAAAGGCTCCAAAGAATACACTATAAAGGCTTCAT-AGATTAAGC
1 CACAAAGGCTCCACAGAATATGCCATAAAGGCATCATAAAATTATGC
* ** * * * **
9448510 CACAAAGGCTCCACAAAATACACTATAAAGGCTTAAT-AGTTTATGC
1 CACAAAGGCTCCACAGAATATGCCATAAAGGCATCATAAAATTATGC
* *
9448556 CACAAAGGCTCCACAGAATACGCCATAAAGGCATCAT-AGATTATGC
1 CACAAAGGCTCCACAGAATATGCCATAAAGGCATCATAAAATTATGC
* *
9448602 CAAAAAGGCTCCACAGAATATGCCATAAAGGCATCATAAAATT-TTC
1 CACAAAGGCTCCACAGAATATGCCATAAAGGCATCATAAAATTATGC
* * * *
9448648 CACAAAGGCTCCATAAAATGTGCCATAAAGACATCATA
1 CACAAAGGCTCCACAGAATATGCCATAAAGGCATCATA
9448686 GATAACCTAT
Statistics
Matches: 190, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
46 186 0.98
47 4 0.02
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (47 bp):
CACAAAGGCTCCACAGAATATGCCATAAAGGCATCATAAAATTATGC
Found at i:9450142 original size:87 final size:87
Alignment explanation
Indices: 9449989--9450172 Score: 246
Period size: 87 Copynumber: 2.1 Consensus size: 87
9449979 ACGACGTATC
* * * * *
9449989 GACGCCCATCGAATATGAAAAGGGATAGTTTCGATTATCAACTGTGAAAAGGGATGATGACGACC
1 GACGACCATCAAATATGAAAAGGGATAGTTTCGACTATCAACTATGAAAAGGGATGATGACAACC
9450054 ATC-AACTATGAAAAGGGATGGT
66 ATCGAA-TATGAAAAGGGATGGT
* *
9450076 GACGACCATCAAATATGAAAAGAGG-TAGTTTCGACTATCGACTATGAAAAGGGATGGTGACAAC
1 GACGACCATCAAATATGAAAAG-GGATAGTTTCGACTATCAACTATGAAAAGGGATGATGACAAC
*
9450140 CATCGAATATGAAAATGGATGGT
65 CATCGAATATGAAAAGGGATGGT
**
9450163 TTCGACCATC
1 GACGACCATC
9450173 GATTAAAGAA
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
87 81 0.95
88 4 0.05
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (87 bp):
GACGACCATCAAATATGAAAAGGGATAGTTTCGACTATCAACTATGAAAAGGGATGATGACAACC
ATCGAATATGAAAAGGGATGGT
Found at i:9450161 original size:29 final size:29
Alignment explanation
Indices: 9449989--9450192 Score: 162
Period size: 29 Copynumber: 7.0 Consensus size: 29
9449979 ACGACGTATC
* *
9449989 GACGCCCATCGAATATGAAAAGGGATAGT
1 GACGACCATCGAATATGAAAAGGGATGGT
** ** * *
9450018 TTCGATTATC-AACTGTGAAAAGGGATGAT
1 GACGACCATCGAA-TATGAAAAGGGATGGT
9450047 GACGACCATC-AACTATGAAAAGGGATGGT
1 GACGACCATCGAA-TATGAAAAGGGATGGT
* *
9450076 GACGACCATCAAATATGAAAAGAGG-TAGT
1 GACGACCATCGAATATGAAAAG-GGATGGT
** * *
9450105 TTCGACTATCGACTATGAAAAGGGATGGT
1 GACGACCATCGAATATGAAAAGGGATGGT
* *
9450134 GACAACCATCGAATATGAAAATGGATGGT
1 GACGACCATCGAATATGAAAAGGGATGGT
** * * *
9450163 TTCGACCATCGATTAAAGAAAATGGATGGT
1 GACGACCATCGAAT-ATGAAAAGGGATGGT
9450193 TTCGATCATC
Statistics
Matches: 138, Mismatches: 32, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
28 4 0.03
29 116 0.84
30 18 0.13
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (29 bp):
GACGACCATCGAATATGAAAAGGGATGGT
Found at i:9450165 original size:58 final size:58
Alignment explanation
Indices: 9450049--9450192 Score: 182
Period size: 58 Copynumber: 2.5 Consensus size: 58
9450039 GGGATGATGA
* * *
9450049 CGACCATCAACTATGAAAAGGGATGGTGACGACCATCAAATATGAAAAGAGGTAGTTT
1 CGACCATCGACTATGAAAAGGGATGGTGACAACCATCAAATATGAAAAGAGATAGTTT
* * *
9450107 CGACTATCGACTATGAAAAGGGATGGTGACAACCATCGAATATGAAAATG-GATGGTTT
1 CGACCATCGACTATGAAAAGGGATGGTGACAACCATCAAATATGAAAA-GAGATAGTTT
* * *
9450165 CGACCATCGATTAAAGAAAATGGATGGT
1 CGACCATCGACT-ATGAAAAGGGATGGT
9450193 TTCGATCATC
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
58 60 0.81
59 14 0.19
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (58 bp):
CGACCATCGACTATGAAAAGGGATGGTGACAACCATCAAATATGAAAAGAGATAGTTT
Found at i:9456103 original size:18 final size:18
Alignment explanation
Indices: 9456084--9456122 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
9456074 TTCTTTCTGG
*
9456084 TTTCTACCCTATCTCAGGT
1 TTTC-ACCCCATCTCAGGT
*
9456103 TTTCGCCCCATCTCAGGT
1 TTTCACCCCATCTCAGGT
9456121 TT
1 TT
9456123 GGTGATCTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.13, C:0.33, G:0.13, T:0.41
Consensus pattern (18 bp):
TTTCACCCCATCTCAGGT
Found at i:9461681 original size:34 final size:35
Alignment explanation
Indices: 9461637--9461703 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
9461627 CAGTAAAATA
*
9461637 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
9461671 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
9461704 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:9465233 original size:24 final size:24
Alignment explanation
Indices: 9465201--9465252 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
9465191 TTAGTTTCGC
9465201 AAAC-ACATGGAAACACATCAATT
1 AAACAACATGGAAACACATCAATT
*
9465224 AAACAACATGGACACACATCAATT
1 AAACAACATGGAAACACATCAATT
9465248 AAACA
1 AAACA
9465253 TGAATTTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.54, C:0.23, G:0.08, T:0.15
Consensus pattern (24 bp):
AAACAACATGGAAACACATCAATT
Found at i:9467249 original size:19 final size:18
Alignment explanation
Indices: 9467204--9467250 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
9467194 AATAGCAAAA
* *
9467204 GAGAAGGAAGAGGAGAGG
1 GAGAAGAAAGAAGAGAGG
9467222 GAGAAGAAAGAAGAGAGG
1 GAGAAGAAAGAAGAGAGG
9467240 GAGAAAGAAAG
1 GAG-AAGAAAG
9467251 GAAAAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (18 bp):
GAGAAGAAAGAAGAGAGG
Found at i:9470397 original size:31 final size:33
Alignment explanation
Indices: 9470350--9470413 Score: 114
Period size: 31 Copynumber: 2.0 Consensus size: 33
9470340 AGCGTACAAG
9470350 TTAGAGCCACACATTTTCCAACAAAGAATGACT
1 TTAGAGCCACACATTTTCCAACAAAGAATGACT
9470383 TTAGAG-C-CACATTTTCCAACAAAGAATGACT
1 TTAGAGCCACACATTTTCCAACAAAGAATGACT
9470414 CGACTTGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 24 0.77
32 1 0.03
33 6 0.19
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.25
Consensus pattern (33 bp):
TTAGAGCCACACATTTTCCAACAAAGAATGACT
Found at i:9471667 original size:33 final size:33
Alignment explanation
Indices: 9471604--9471689 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 33
9471594 CGATGAACTT
* * ***
9471604 GAGCTGAAAGAAGTGGAGTACTGCGGTGGATAC
1 GAGCCGAAAGGAGTGGAGTACTGAAATGGATAC
* * **
9471637 GGGCTGGGAGGAGTGGAGTACTGAAATGGATAC
1 GAGCCGAAAGGAGTGGAGTACTGAAATGGATAC
9471670 GAGCCGAAAGGAGTGGAGTA
1 GAGCCGAAAGGAGTGGAGTA
9471690 TTGTAGTGGT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.30, C:0.10, G:0.43, T:0.16
Consensus pattern (33 bp):
GAGCCGAAAGGAGTGGAGTACTGAAATGGATAC
Found at i:9473517 original size:11 final size:12
Alignment explanation
Indices: 9473490--9473519 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
9473480 CGTGAGTAAC
*
9473490 AAAAAACACAGT
1 AAAAAACACAAT
9473502 AAAAAACACAAT
1 AAAAAACACAAT
9473514 AAAAAA
1 AAAAAA
9473520 TATCTCAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.77, C:0.13, G:0.03, T:0.07
Consensus pattern (12 bp):
AAAAAACACAAT
Found at i:9473885 original size:110 final size:111
Alignment explanation
Indices: 9473751--9474571 Score: 1002
Period size: 110 Copynumber: 7.6 Consensus size: 111
9473741 ATAAATAAAT
* * * * * *
9473751 AAAAACAAAATAAAATTACATT-ATAACATATCACATTACACATTAAACT-AA-ACAAATAATTT
1 AAAAACAAAA-AAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTT
9473813 ATAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTAA
65 ATAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTAA
* * * * *
9473860 AAAACACAAAAAAAATTATATTTATAACAAGTCACAATAAATACTAAACTAAACACAAACAATTT
1 AAAA-ACAAAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTT
*
9473925 ATAACCTAATCATAAATTACTAACAAAATAACTTTCAAATAATTTAA
65 ATAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTAA
*
9473972 AAGAAC-AAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTA
1 AAAAACAAAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTA
* *
9474036 TAACTTAATCATAAATTACTAACAAAATAACTTTCAAATAA-TTAA
66 TAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTAA
* *
9474081 AAATAA-AATAAAAAATTTTACATCCATAAAAAATCACAATAAACATTAAACTAAACACAAACAA
1 AAA-AACAA-AAAAAA--TTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAA
* *
9474145 TTTA-AACCTAACCATAAATTACTAACAAAATTACTTTAAAATAATTTAA
62 TTTATAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTAA
*
9474194 AAATACAAAAAAAATTACATTCATAAAAAATCAC-A-AAACACTAAACTAAACACAAACAATTTA
1 AAAAACAAAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTA
* *
9474257 TAACCTAATCATAAATTACTAA-AAGAATAACTATAAAATAATTTTA
66 TAACCTAATCATAAATTACTAACAA-AATAACTTTAAAATAATTTAA
* *
9474303 AAAAA-TAAAAAATTTACATTCATAAAAAATCAC-A-AAACACTAAACTAAACACAAACAATTTA
1 AAAAACAAAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTA
* *
9474365 TAACCTAATCATAAATTATTAACAAAATAACTATAAAATAATTT--
66 TAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTAA
**** * * * * *
9474409 ---TTTTAAAAAAATTACATTAATAAAAATTTAC-A-AAACACTAAATTAAACACAGACAATTTA
1 AAAAACAAAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTA
* *
9474469 TAACCTAATCATAAATTACTAACCAAATAATTTTAAAATAA-TT--
66 TAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTAA
* * *
9474512 ------AAAAAAATTTACGTTCATAACAAATCAC-A-AAACACTAAACTAAACACAAACAATTTA
1 AAAAACAAAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTA
9474569 TAA
66 TAA
9474572 TAATTAATAA
Statistics
Matches: 642, Mismatches: 55, Indels: 39
0.87 0.07 0.05
Matches are distributed among these distances:
100 51 0.08
103 2 0.00
104 88 0.14
108 124 0.19
109 65 0.10
110 142 0.22
111 10 0.02
112 102 0.16
113 58 0.09
ACGTcount: A:0.58, C:0.15, G:0.01, T:0.27
Consensus pattern (111 bp):
AAAAACAAAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTA
TAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTAA
Found at i:9474155 original size:222 final size:218
Alignment explanation
Indices: 9473751--9474571 Score: 1024
Period size: 222 Copynumber: 3.8 Consensus size: 218
9473741 ATAAATAAAT
* * * * *
9473751 AAAAACAAAATAAAATTACATT-ATAACATATCACATTACACATTAAACT-AA-ACAAATAATTT
1 AAAAAC-AAA-AAAATTACATTCATAAAAAATCACA--AAACACTAAACTAAACACAAACAATTT
9473813 ATAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTAAAAAACACAA-AAAAAA-T
62 ATAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAA-TTAAAAAA-A-AATAAAAAATT
* * * * *
9473876 TATATTTATAACAAGTCACAATAAATACTAAACTAAACACAAACAATTTATAACCTAATCATAAA
124 TACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAA
*
9473941 TTACTAACAAAATAACTTTCAAATAATTTA
189 TTACTAACAAAATAACTTTAAAATAATTTA
9473971 AAAGAACAAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTA
1 AAA-AACAAAAAAATTACATTCATAAAAAATCAC-A-AAACACTAAACTAAACACAAACAATTTA
* *
9474036 TAACTTAATCATAAATTACTAACAAAATAACTTTCAAATAATTAAAAATAAAATAAAAAATTTTA
63 TAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTAAAAA-AAAATAAAAAA-TTTA
* * *
9474101 CATCCATAAAAAATCACAATAAACATTAAACTAAACACAAACAATTTA-AACCTAACCATAAATT
126 CATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATT
*
9474165 ACTAACAAAATTACTTTAAAATAATTTA
191 ACTAACAAAATAACTTTAAAATAATTTA
9474193 AAAATACAAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTAT
1 AAAA-AC-AAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTAT
* **
9474258 AACCTAATCATAAATTACTAA-AAGAATAACTATAAAATAATT-TTAAAAAATAAAAAATTTACA
64 AACCTAATCATAAATTACTAACAA-AATAACTTTAAAATAATTAAAAAAAAATAAAAAATTTACA
*
9474321 TTCATAAAAAATCAC-A-AAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTAT
128 TTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTAC
*
9474384 TAACAAAATAACTATAAAATAATTT-
193 TAACAAAATAACTTTAAAATAATTTA
**** * * * * *
9474409 --TTTTAAAAAAATTACATTAATAAAAATTTACAAAACACTAAATTAAACACAGACAATTTATAA
1 AAAAACAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAA
* * *
9474472 CCTAATCATAAATTACTAACCAAATAATTTTAAAATAATT--------A-AAAAAATTTACGTTC
66 CCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTAAAAAAAAATAAAAAATTTACATTC
*
9474528 ATAACAAATCAC-A-AAACACTAAACTAAACACAAACAATTTATAA
131 ATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAA
9474572 TAATTAATAA
Statistics
Matches: 545, Mismatches: 42, Indels: 44
0.86 0.07 0.07
Matches are distributed among these distances:
204 57 0.10
205 1 0.00
212 89 0.16
213 1 0.00
216 27 0.05
217 40 0.07
218 20 0.04
219 22 0.04
220 33 0.06
221 86 0.16
222 98 0.18
223 71 0.13
ACGTcount: A:0.58, C:0.15, G:0.01, T:0.27
Consensus pattern (218 bp):
AAAAACAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAA
CCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTAAAAAAAAATAAAAAATTTACATTC
ATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAA
CAAAATAACTTTAAAATAATTTA
Found at i:9474497 original size:104 final size:104
Alignment explanation
Indices: 9474089--9474571 Score: 600
Period size: 108 Copynumber: 4.6 Consensus size: 104
9474079 AAAAATAAAA
* * *
9474089 TAAAAAATTTTACATCCATAAAAAATCACAATAAACATTAAACTAAACACAAACAATTTA-AACC
1 TAAAAAA-ATTACATTCATAAAAAATCAC-A-AAACACTAAACTAAACACAAACAATTTATAACC
* * * *
9474153 TAACCATAAATTACTAACAAAATTACTTTAAAATAATTTAAAAATAC
63 TAATCATAAATTACTAACAAAATAACTATAAAATAATTT-----TAT
*
9474200 AAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAA
1 TAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAA
*
9474265 TCATAAATTACTAA-AAGAATAACTATAAAATAATTTTAAAAAA
66 TCATAAATTACTAACAA-AATAACTATAAAATAATTTT----AT
*
9474308 TAAAAAATTTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAA
1 TAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAA
* *
9474373 TCATAAATTATTAACAAAATAACTATAAAATAATTTTTT
66 TCATAAATTACTAACAAAATAACTATAAAATAATTTTAT
* * * * *
9474412 TAAAAAAATTACATTAATAAAAATTTACAAAACACTAAATTAAACACAGACAATTTATAACCTAA
1 TAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAA
* * *
9474477 TCATAAATTACTAACCAAATAATTTTAAAATAA--TTA-
66 TCATAAATTACTAACAAAATAACTATAAAATAATTTTAT
* * *
9474513 -AAAAAATTTACGTTCATAACAAATCACAAAACACTAAACTAAACACAAACAATTTATAA
1 TAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAA
9474572 TAATTAATAA
Statistics
Matches: 333, Mismatches: 32, Indels: 25
0.85 0.08 0.06
Matches are distributed among these distances:
100 51 0.15
102 2 0.01
104 89 0.27
108 126 0.38
109 40 0.12
110 19 0.06
111 6 0.02
ACGTcount: A:0.58, C:0.15, G:0.01, T:0.27
Consensus pattern (104 bp):
TAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAA
TCATAAATTACTAACAAAATAACTATAAAATAATTTTAT
Found at i:9475026 original size:24 final size:24
Alignment explanation
Indices: 9474986--9475035 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
9474976 TGACACCACT
9474986 AATAAAATAATAATTTT-TCTAAAA
1 AATAAAATAATAATTTTAT-TAAAA
9475010 AATAAAA-AATAAGTTTTATTAAAA
1 AATAAAATAATAA-TTTTATTAAAA
9475034 AA
1 AA
9475036 AAGTGGTGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 5 0.21
24 18 0.75
25 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (24 bp):
AATAAAATAATAATTTTATTAAAA
Found at i:9475458 original size:2 final size:2
Alignment explanation
Indices: 9475451--9475485 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9475441 ATATGAAAAG
9475451 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9475486 TAGATTATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9476474 original size:38 final size:39
Alignment explanation
Indices: 9476420--9476498 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
9476410 TTTAATGAAT
* *
9476420 TTTTTTAAAATTTTAAAAT-TTTAAAAA-ATATAAAAACTA
1 TTTTTTAAAATATTAAAATCATTAAAAATAT-TAAAAA-TA
9476459 TTTTTTAAAA-ATTAAAATCATTAAAAATATTAAAAATA
1 TTTTTTAAAATATTAAAATCATTAAAAATATTAAAAATA
9476497 TT
1 TT
9476499 AAAAATATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
38 11 0.31
39 23 0.64
40 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (39 bp):
TTTTTTAAAATATTAAAATCATTAAAAATATTAAAAATA
Found at i:9476483 original size:9 final size:9
Alignment explanation
Indices: 9476472--9476517 Score: 65
Period size: 9 Copynumber: 4.8 Consensus size: 9
9476462 TTTAAAAATT
9476472 AAAATCATTA
1 AAAAT-ATTA
9476482 AAAATATTA
1 AAAATATTA
9476491 AAAATATTA
1 AAAATATTA
9476500 AAAATATTTTA
1 AAAATA--TTA
9476511 AAAATAT
1 AAAATAT
9476518 CTTAAAAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
9 20 0.59
10 5 0.15
11 9 0.26
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAATATTA
Found at i:9476484 original size:16 final size:16
Alignment explanation
Indices: 9476463--9476504 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
9476453 AAACTATTTT
9476463 TTAAAAATT-AAAATCA
1 TTAAAAATTAAAAAT-A
9476479 TTAAAAATATTAAAAATA
1 TT-AAAA-ATTAAAAATA
9476497 TTAAAAAT
1 TTAAAAAT
9476505 ATTTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.17
17 8 0.35
18 6 0.26
19 5 0.22
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
TTAAAAATTAAAAATA
Found at i:9476513 original size:11 final size:10
Alignment explanation
Indices: 9476479--9476537 Score: 68
Period size: 11 Copynumber: 5.8 Consensus size: 10
9476469 ATTAAAATCA
9476479 TTAAAAATA-
1 TTAAAAATAT
9476488 TTAAAAATA-
1 TTAAAAATAT
9476497 TTAAAAATATT
1 TTAAAAATA-T
9476508 TTAAAAATAT
1 TTAAAAATAT
*
9476518 CTTAAAAACATT
1 -TTAAAAATA-T
9476530 TTAAAAAT
1 TTAAAAAT
9476538 TAATTAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
9 18 0.41
10 1 0.02
11 24 0.55
12 1 0.02
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.37
Consensus pattern (10 bp):
TTAAAAATAT
Found at i:9476525 original size:22 final size:20
Alignment explanation
Indices: 9476472--9476537 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 20
9476462 TTTAAAAATT
9476472 AAAATCATTAAAAATA--TTA
1 AAAAT-ATTAAAAATATTTTA
9476491 AAAATATTAAAAATATTTTA
1 AAAATATTAAAAATATTTTA
*
9476511 AAAATATCTTAAAAACATTTTA
1 AAAATA--TTAAAAATATTTTA
9476533 AAAAT
1 AAAAT
9476538 TAATTAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
18 10 0.24
19 5 0.12
20 9 0.21
22 18 0.43
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATATTAAAAATATTTTA
Found at i:9476544 original size:22 final size:21
Alignment explanation
Indices: 9476472--9476545 Score: 73
Period size: 22 Copynumber: 3.6 Consensus size: 21
9476462 TTTAAAAATT
* *
9476472 AAAATCATT-AAAA-ATATTA
1 AAAATAATTAAAAACATTTTA
*
9476491 AAAAT-ATTAAAAATATTTTA
1 AAAATAATTAAAAACATTTTA
*
9476511 AAAATATCTTAAAAACATTTTA
1 AAAATA-ATTAAAAACATTTTA
9476533 AAAATTAATTAAA
1 AAAA-TAATTAAA
9476546 TTTTGATATG
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
18 3 0.07
19 9 0.20
20 10 0.22
22 22 0.48
23 2 0.04
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATAATTAAAAACATTTTA
Found at i:9476666 original size:5 final size:5
Alignment explanation
Indices: 9476656--9476680 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
9476646 CAAGGCGGCA
9476656 AAACC AAACC AAACC AAACC AAACC
1 AAACC AAACC AAACC AAACC AAACC
9476681 CGAGGGTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACC
Found at i:9483674 original size:12 final size:11
Alignment explanation
Indices: 9483643--9483697 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
9483633 AACATCAATT
*
9483643 TTTTAAAAAAA
1 TTTTAAAAATA
*
9483654 TTTAAAAAAAGTA
1 TTT-TAAAAA-TA
9483667 TTTTAAAAATA
1 TTTTAAAAATA
9483678 TTTT--AAA-A
1 TTTTAAAAATA
9483686 TTTTAAAAATA
1 TTTTAAAAATA
9483697 T
1 T
9483698 AAAAATATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
8 5 0.14
9 3 0.08
10 3 0.08
11 11 0.31
12 10 0.28
13 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:9503517 original size:83 final size:83
Alignment explanation
Indices: 9503390--9503544 Score: 274
Period size: 83 Copynumber: 1.9 Consensus size: 83
9503380 GTAACGCGTA
*
9503390 GGTTTGTGCAAGTGTAAACAGTCGTTATCAAGTAATAAGTAAGTATCGAGTTATCGTCTCCACAA
1 GGTTTGTGCAAGTGTAAACAGTCGTCATCAAGTAATAAGTAAGTATCGAGTTATCGTCTCCACAA
9503455 GGATTGTTGTAATGCTGG
66 GGATTGTTGTAATGCTGG
* * *
9503473 GGTTTGTGCAAGTGTACACAGTCGTCATCAAGTAATAAGTAAGTATTGAGTTATCGTCTCCACAG
1 GGTTTGTGCAAGTGTAAACAGTCGTCATCAAGTAATAAGTAAGTATCGAGTTATCGTCTCCACAA
9503538 GGATTGT
66 GGATTGT
9503545 ATTTGTGCTA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 68 1.00
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.32
Consensus pattern (83 bp):
GGTTTGTGCAAGTGTAAACAGTCGTCATCAAGTAATAAGTAAGTATCGAGTTATCGTCTCCACAA
GGATTGTTGTAATGCTGG
Found at i:9507259 original size:38 final size:38
Alignment explanation
Indices: 9507209--9507304 Score: 165
Period size: 38 Copynumber: 2.5 Consensus size: 38
9507199 TATCCAACAT
9507209 ATAAGCTCGTAGAGGAGCTCACATAGAATACTTATCAC
1 ATAAGCTCGTAGAGGAGCTCACATAGAATACTTATCAC
* *
9507247 ATAAGCTTGTAGAGGAGCTCATATAGAATACTTATCAC
1 ATAAGCTCGTAGAGGAGCTCACATAGAATACTTATCAC
*
9507285 ATAGGCTCGTAGAGGAGCTC
1 ATAAGCTCGTAGAGGAGCTC
9507305 GTACAAAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (38 bp):
ATAAGCTCGTAGAGGAGCTCACATAGAATACTTATCAC
Found at i:9507315 original size:38 final size:37
Alignment explanation
Indices: 9507209--9507319 Score: 143
Period size: 38 Copynumber: 2.9 Consensus size: 37
9507199 TATCCAACAT
9507209 ATAAGCTCGTAGAGGAGCTC-ACATAGAATACTTATCAC
1 ATAAGCTCGTAGAGGAGCTCTACA-A-AATACTTATCAC
* * *
9507247 ATAAGCTTGTAGAGGAGCTCATATAGAATACTTATCAC
1 ATAAGCTCGTAGAGGAGCTC-TACAAAATACTTATCAC
*
9507285 ATAGGCTCGTAGAGGAGCTCGTACAAAATACTTAT
1 ATAAGCTCGTAGAGGAGCTC-TACAAAATACTTAT
9507320 TAGTTTCAGC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
38 61 0.97
40 2 0.03
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (37 bp):
ATAAGCTCGTAGAGGAGCTCTACAAAATACTTATCAC
Found at i:9513507 original size:38 final size:38
Alignment explanation
Indices: 9513464--9513561 Score: 115
Period size: 38 Copynumber: 2.6 Consensus size: 38
9513454 AAATCCTTGG
* *
9513464 TATAATTATTGTAATTATAATTTATGATCGAATATTAT
1 TATAATTATTGTAATTATAATTTATGATCAAACATTAT
* * * * * *
9513502 TATAATTACTATAATTGTAATTTTTGGTTAAACATTAT
1 TATAATTATTGTAATTATAATTTATGATCAAACATTAT
*
9513540 TATAATTATGGTAATTATAATT
1 TATAATTATTGTAATTATAATT
9513562 ATTATATTTG
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (38 bp):
TATAATTATTGTAATTATAATTTATGATCAAACATTAT
Found at i:9518244 original size:9 final size:9
Alignment explanation
Indices: 9518232--9518258 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
9518222 ATAATTAAAC
9518232 AAATTGAAT
1 AAATTGAAT
9518241 AAATTGAAT
1 AAATTGAAT
9518250 AAATTGAAT
1 AAATTGAAT
9518259 TAAACCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (9 bp):
AAATTGAAT
Found at i:9532259 original size:119 final size:119
Alignment explanation
Indices: 9532044--9532267 Score: 256
Period size: 119 Copynumber: 1.9 Consensus size: 119
9532034 TCAAAGTCGT
* * * * * * *
9532044 AATTTAAAAAGGATATTTTGCTATTTAGGTTTAACGAGGAAATCGTAACCCCGTAAGTTAGGGTA
1 AATTTAAAAAGGATATTCTGCTATTTAGATCTAACGAGAAAACCGAAACCCAGTAAGTTAGGGTA
* * *
9532109 CGATATCTCGAATCACCGAAACGCGAAAATATTA-CCTTATGAGATTTTATTTGA
66 CAATATCTAGAATCACCAAAACGCGAAAATA-TAGCCTTATGAGATTTTATTTGA
* * *
9532163 AATTTTAAAAGGATATTCTGCTATTTAGATCTAGCGAGAAAACCGAAACCCAGTAAGTTATGGTA
1 AATTTAAAAAGGATATTCTGCTATTTAGATCTAACGAGAAAACCGAAACCCAGTAAGTTAGGGTA
* * *
9532228 CAATTTCTAGAATTTC-CCAAAATGC-ATAATATAGCCTTAT
66 CAATATCTAGAA--TCACCAAAACGCGAAAATATAGCCTTAT
9532268 TTTTAAAGAA
Statistics
Matches: 86, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
118 2 0.02
119 75 0.87
120 7 0.08
121 2 0.02
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (119 bp):
AATTTAAAAAGGATATTCTGCTATTTAGATCTAACGAGAAAACCGAAACCCAGTAAGTTAGGGTA
CAATATCTAGAATCACCAAAACGCGAAAATATAGCCTTATGAGATTTTATTTGA
Found at i:9533880 original size:15 final size:16
Alignment explanation
Indices: 9533848--9533881 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9533838 TGGGCTAGAC
*
9533848 TTTGGGTTTTGGTCTA
1 TTTGGGTTTGGGTCTA
9533864 TTTGGGTTTGGGT-TA
1 TTTGGGTTTGGGTCTA
9533879 TTT
1 TTT
9533882 TATTTGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.06, C:0.03, G:0.32, T:0.59
Consensus pattern (16 bp):
TTTGGGTTTGGGTCTA
Found at i:9534328 original size:44 final size:44
Alignment explanation
Indices: 9534253--9534349 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
9534243 TTGCAGTTTT
* * *
9534253 AGGGAGATAGGATTAATAGCTTCAATATGCTCCGCTGCAACTTC
1 AGGGAGATAGGATTAATAGCTTCAACATGCTCCACTGCAACTCC
** * * *
9534297 AGGGAGATAGGATTGGTATCTTTAACCTGCTCCACTGCAACTCC
1 AGGGAGATAGGATTAATAGCTTCAACATGCTCCACTGCAACTCC
*
9534341 AGTGAGATA
1 AGGGAGATA
9534350 AGGCTTGATG
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.27
Consensus pattern (44 bp):
AGGGAGATAGGATTAATAGCTTCAACATGCTCCACTGCAACTCC
Found at i:9534426 original size:129 final size:129
Alignment explanation
Indices: 9534281--9534523 Score: 355
Period size: 129 Copynumber: 1.9 Consensus size: 129
9534271 GCTTCAATAT
* *
9534281 GCTCCGCTGCAACTTCAGGGAGATAGGATTGGTATCTT-TAACCTGCTCCACTGCAAC-TCCAGT
1 GCTCCACTGCAACTTCAGGGAGATAGGATTGGTATCTTCT-ACCTGCTCCACTGCAACTTCAAG-
* * * *
9534344 GAGATAAGGCTTGATGCGATTTGCTCTACTGCAACTTTAGAGAGATAAGATTCATGGTTTTAATC
64 GAGATAAGACTGGATGCGATCTGCTCTACTACAACTTTAGAGAGATAAGATTCATGGTTTTAATC
9534409 C
129 C
* * **
9534410 GCTCCACTGCAACTTCATGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCAACTTCAAGGA
1 GCTCCACTGCAACTTCAGGGAGATAGGATTGGTATCTTCTACCTGCTCCACTGCAACTTCAAGGA
*
9534475 GATAAGACTGGATGTGATCTGCTCTACTACAACTTTAGAGAGATAAGAT
66 GATAAGACTGGATGCGATCTGCTCTACTACAACTTTAGAGAGATAAGAT
9534524 CTGTGATTTT
Statistics
Matches: 101, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
129 96 0.95
130 5 0.05
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (129 bp):
GCTCCACTGCAACTTCAGGGAGATAGGATTGGTATCTTCTACCTGCTCCACTGCAACTTCAAGGA
GATAAGACTGGATGCGATCTGCTCTACTACAACTTTAGAGAGATAAGATTCATGGTTTTAATCC
Found at i:9534434 original size:44 final size:43
Alignment explanation
Indices: 9534366--9534481 Score: 103
Period size: 44 Copynumber: 2.6 Consensus size: 43
9534356 GATGCGATTT
* *
9534366 GCTCTACTGCAACTTTAGAGAGATAAGATTCATGG-TT-TT-AATCC
1 GCTCCACTGCAACTTCAG-GAGATAAGA-T--TGGTTTCTTCAATCC
* ** *
9534410 GCTCCACTGCAACTTCATGGAGATAGGATTGGTTTCTTCTGTCT
1 GCTCCACTGCAACTTCA-GGAGATAAGATTGGTTTCTTCAATCC
9534454 GCTCCACTGCAACTTCAAGGAGATAAGA
1 GCTCCACTGCAACTTC-AGGAGATAAGA
9534482 CTGGATGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
41 3 0.05
42 2 0.03
43 3 0.05
44 50 0.83
45 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (43 bp):
GCTCCACTGCAACTTCAGGAGATAAGATTGGTTTCTTCAATCC
Found at i:9534819 original size:89 final size:89
Alignment explanation
Indices: 9534669--9534948 Score: 334
Period size: 89 Copynumber: 3.1 Consensus size: 89
9534659 AATCTTTAAC
* * * * * * *
9534669 CTACTCCACTGCAAACTCAGAGAGGCGAGGCTGATGTTTTCGATCCGCTTCACTACCAATACAGG
1 CTACTCCATTGCAAACTCAGAGAGGCGAGGCTGGTGTCTTCGATCTGCTTCGCTGCAAATACAGG
*
9534734 AAGACAAGACCTGCTATCTTCAGT
66 AAGACAAGATCTGCTATCTTCAGT
* * * *
9534758 CTACTCCATTGCAAACTCA-AGGAGGCAAGGCTGGTGTCTTCAATCTACTTCGCTGCTAATACAG
1 CTACTCCATTGCAAACTCAGA-GAGGCGAGGCTGGTGTCTTCGATCTGCTTCGCTGCAAATACAG
*
9534822 GAAGACAAGATCTACTATCTTCAGT
65 GAAGACAAGATCTGCTATCTTCAGT
** *
9534847 CTGTTCC-TGCTACAAACTCAGAGAGGCGAGGCTGGTGTCTTCGATCTGCTTCGCTGCAAACT-C
1 CTACTCCAT--TGCAAACTCAGAGAGGCGAGGCTGGTGTCTTCGATCTGCTTCGCTGCAAA-TAC
9534910 AGGAAGACAAGATCTGCTATCTTC-GAT
63 AGGAAGACAAGATCTGCTATCTTCAG-T
*
9534937 CTACTTCATTGC
1 CTACTCCATTGC
9534949 CAATAGAGGA
Statistics
Matches: 160, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
88 2 0.01
89 83 0.52
90 72 0.45
91 3 0.02
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (89 bp):
CTACTCCATTGCAAACTCAGAGAGGCGAGGCTGGTGTCTTCGATCTGCTTCGCTGCAAATACAGG
AAGACAAGATCTGCTATCTTCAGT
Found at i:9534937 original size:45 final size:44
Alignment explanation
Indices: 9534730--9534943 Score: 134
Period size: 45 Copynumber: 4.8 Consensus size: 44
9534720 ACTACCAATA
* * **
9534730 CAGGAAGACAAGACCTGCTATCTTCAGTCTACTCCATTGCAAACT
1 CAGGAAGACAAGAGCTGCTATCTTCA-TCTACTTCGCTGCAAACT
* * * *
9534775 CAAGG-AGGCAAG-GCTGGTGTCTTCAATCTACTTCGCTGCTAA-T
1 C-AGGAAGACAAGAGCTGCTATCTTC-ATCTACTTCGCTGCAAACT
* * * *
9534818 ACAGGAAGACAAGATCTACTATCTTCAGTCT-GTTCCTGCTACAAACT
1 -CAGGAAGACAAGAGCTGCTATCTTCA-TCTACTT-C-GCTGCAAACT
* * * * *
9534865 CA-GAGAGGCGAG-GCTGGTGTCTTCGATCTGCTTCGCTGCAAACT
1 CAGGA-AGACAAGAGCTGCTATCTTC-ATCTACTTCGCTGCAAACT
*
9534909 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTC
1 CAGGAAGACAAGAGCTGCTATCTTC-ATCTACTTC
9534944 ATTGCCAATA
Statistics
Matches: 125, Mismatches: 30, Indels: 28
0.68 0.16 0.15
Matches are distributed among these distances:
43 4 0.03
44 47 0.38
45 54 0.43
46 19 0.15
47 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (44 bp):
CAGGAAGACAAGAGCTGCTATCTTCATCTACTTCGCTGCAAACT
Found at i:9542920 original size:27 final size:27
Alignment explanation
Indices: 9542882--9542934 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
9542872 AACTATGTCG
9542882 TTGTATACTATTGTCTTAATTTTTTCA
1 TTGTATACTATTGTCTTAATTTTTTCA
*
9542909 TTGTATACTATTGTCTTATTTTTTTC
1 TTGTATACTATTGTCTTAATTTTTTC
9542935 TTTCATCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.11, G:0.08, T:0.62
Consensus pattern (27 bp):
TTGTATACTATTGTCTTAATTTTTTCA
Found at i:9543052 original size:8 final size:8
Alignment explanation
Indices: 9543039--9543063 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
9543029 CCTATATTGT
9543039 TAATTAAA
1 TAATTAAA
9543047 TAATTAAA
1 TAATTAAA
9543055 TAATTAAA
1 TAATTAAA
9543063 T
1 T
9543064 GCGAACATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TAATTAAA
Found at i:9543291 original size:17 final size:17
Alignment explanation
Indices: 9543269--9543304 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
9543259 AATTCAGTCG
9543269 TATAAGATTATTTTTCA
1 TATAAGATTATTTTTCA
9543286 TATAAGATTATTTTTCA
1 TATAAGATTATTTTTCA
9543303 TA
1 TA
9543305 CCTTAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.53
Consensus pattern (17 bp):
TATAAGATTATTTTTCA
Found at i:9546050 original size:24 final size:24
Alignment explanation
Indices: 9545995--9546053 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
9545985 GGTTTAATGC
* *
9545995 AAATGGAGATATTTTGGAGAGATG
1 AAATGGATATATTTTGGAAAGATG
9546019 AAATGGATATATTTTGGAAAGATG
1 AAATGGATATATTTTGGAAAGATG
9546043 AAATGGATATA
1 AAATGGATATA
9546054 AATGGAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (24 bp):
AAATGGATATATTTTGGAAAGATG
Found at i:9546125 original size:17 final size:17
Alignment explanation
Indices: 9546103--9546200 Score: 61
Period size: 17 Copynumber: 5.4 Consensus size: 17
9546093 AATTCAAGAC
9546103 TTATGTAATATTTTTAA
1 TTATGTAATATTTTTAA
* ***
9546120 TTATGTAGTGATTCAAAGA
1 TTATGTAAT-ATTTTTA-A
9546139 CTTATGTAATATTTTTAA
1 -TTATGTAATATTTTTAA
* ** *
9546157 TTATGTAGTGATTCAAATAT
1 TTATGTAAT-ATT--TTTAA
*
9546177 TTATGTAATGTTTTTAA
1 TTATGTAATATTTTTAA
9546194 TTATGTA
1 TTATGTA
9546201 GTGATTTAAT
Statistics
Matches: 58, Mismatches: 17, Indels: 12
0.67 0.20 0.14
Matches are distributed among these distances:
17 25 0.43
18 8 0.14
19 7 0.12
20 18 0.31
ACGTcount: A:0.34, C:0.03, G:0.12, T:0.51
Consensus pattern (17 bp):
TTATGTAATATTTTTAA
Found at i:9546148 original size:37 final size:37
Alignment explanation
Indices: 9546094--9546206 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
9546084 TTATGTGTTA
9546094 ATTC-AAGACTTATGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
9546130 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
* * *
9546167 ATTCAAATATTTATGTAATGTTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
9546204 ATT
1 ATT
9546207 TAATTCGGGT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 4 0.05
37 69 0.95
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (37 bp):
ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
Found at i:9546221 original size:9 final size:9
Alignment explanation
Indices: 9546207--9546321 Score: 160
Period size: 9 Copynumber: 12.6 Consensus size: 9
9546197 TGTAGTGATT
9546207 TAATTCGGG
1 TAATTCGGG
9546216 TAATTCGGG
1 TAATTCGGG
*
9546225 TAATTTGGG
1 TAATTCGGG
9546234 TAATTTTCGGG
1 TAA--TTCGGG
*
9546245 TAATTTGGG
1 TAATTCGGG
9546254 TAATTCGGG
1 TAATTCGGG
9546263 TAATTCGGG
1 TAATTCGGG
9546272 TAATTCGGG
1 TAATTCGGG
*
9546281 TAAGTCGGG
1 TAATTCGGG
9546290 TAATTCGGG
1 TAATTCGGG
*
9546299 TAAGTCGGG
1 TAATTCGGG
9546308 TAAGTT-GGG
1 TAA-TTCGGG
9546317 TAATT
1 TAATT
9546322 TTTAACCAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
8 2 0.02
9 84 0.88
10 1 0.01
11 8 0.08
ACGTcount: A:0.23, C:0.08, G:0.34, T:0.36
Consensus pattern (9 bp):
TAATTCGGG
Found at i:9552744 original size:15 final size:16
Alignment explanation
Indices: 9552713--9552745 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9552703 GGGCTAGACG
*
9552713 TTGGGTTTTGGTCTAT
1 TTGGGTTTGGGTCTAT
9552729 TTGGGTTTGGGT-TAT
1 TTGGGTTTGGGTCTAT
9552744 TT
1 TT
9552746 TATTTGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.06, C:0.03, G:0.33, T:0.58
Consensus pattern (16 bp):
TTGGGTTTGGGTCTAT
Found at i:9553882 original size:17 final size:17
Alignment explanation
Indices: 9553862--9553956 Score: 54
Period size: 17 Copynumber: 5.6 Consensus size: 17
9553852 TTTTAGTAGT
9553862 TTTAATATTAAATATAA
1 TTTAATATTAAATATAA
* *
9553879 TTTAATATT-TATCTTAA
1 TTTAATATTAAAT-ATAA
* **
9553896 --TAGTATTTTAT-TAA
1 TTTAATATTAAATATAA
* *
9553910 TTTAATATTAAGGTGATTA
1 TTTAATATTAA-AT-ATAA
*
9553929 TCTTAATATTAAATTTAA
1 T-TTAATATTAAATATAA
9553947 TTTAATATTA
1 TTTAATATTA
9553957 TCTTGTAGAT
Statistics
Matches: 59, Mismatches: 11, Indels: 16
0.69 0.13 0.19
Matches are distributed among these distances:
14 3 0.05
15 6 0.10
16 11 0.19
17 22 0.37
18 3 0.05
19 4 0.07
20 10 0.17
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (17 bp):
TTTAATATTAAATATAA
Found at i:9553995 original size:60 final size:58
Alignment explanation
Indices: 9553931--9554045 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 58
9553921 GGTGATTATC
* * *
9553931 TTAATATTAAATTTAATTTAATA-TTATCTTGTAGATAAGTATTCTATTAATTTAATAGAT
1 TTAATATTAAATTTAATCTAATATTTAT-AT-T-GATAAGTATTATATTAATTTAATAGAT
*
9553991 TTAATATTAAATTTAATCTAATATTTATATTGATAAGTATTATATTATTTTAATA
1 TTAATATTAAATTTAATCTAATATTTATATTGATAAGTATTATATTAATTTAATA
9554046 TTAAAGTGAT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 22 0.44
59 1 0.02
60 23 0.46
61 4 0.08
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (58 bp):
TTAATATTAAATTTAATCTAATATTTATATTGATAAGTATTATATTAATTTAATAGAT
Found at i:9554058 original size:58 final size:59
Alignment explanation
Indices: 9553933--9554065 Score: 148
Period size: 58 Copynumber: 2.3 Consensus size: 59
9553923 TGATTATCTT
* * * *
9553933 AATATTAAATTTAATTTAATATTATCTTGTAGATAAGTATTCTATTAATTTAATAGATTT
1 AATATTAAATTTAATCTAATATTATCATGTAGATAAGTATTATATTAATTTAATA-ATTA
*
9553993 AATATTAAATTTAATCTAATATTTAT-AT-T-GATAAGTATTATATTATTTTAAT-ATTA
1 AATATTAAATTTAATCTAATA-TTATCATGTAGATAAGTATTATATTAATTTAATAATTA
*
9554049 AAGTGATTAAGTTTAAT
1 AA-T-ATTAAATTTAAT
9554066 TATAGTTGAA
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
56 5 0.08
57 1 0.02
58 32 0.50
59 1 0.02
60 21 0.33
61 4 0.06
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (59 bp):
AATATTAAATTTAATCTAATATTATCATGTAGATAAGTATTATATTAATTTAATAATTA
Found at i:9556130 original size:18 final size:17
Alignment explanation
Indices: 9556109--9556147 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
9556099 TGTTTTGAAG
9556109 TTTTAGTTAAACAAAAAA
1 TTTTAGTTAAA-AAAAAA
* *
9556127 TTTTAGTTTAAAACAAA
1 TTTTAGTTAAAAAAAAA
9556144 TTTT
1 TTTT
9556148 TGTTTAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (17 bp):
TTTTAGTTAAAAAAAAA
Found at i:9556146 original size:17 final size:18
Alignment explanation
Indices: 9556109--9556153 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
9556099 TGTTTTGAAG
*
9556109 TTTTAGTTAAACAAAAAA
1 TTTTAGTTTAACAAAAAA
*
9556127 TTTTAGTTTAA-AACAAA
1 TTTTAGTTTAACAAAAAA
*
9556144 TTTTTGTTTA
1 TTTTAGTTTA
9556154 GATTAATTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (18 bp):
TTTTAGTTTAACAAAAAA
Found at i:9559251 original size:10 final size:10
Alignment explanation
Indices: 9559223--9559254 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
9559213 GTTTTAGATT
9559223 TAGTTTTCTC
1 TAGTTTTCTC
9559233 TAGGTTTTCTC
1 TA-GTTTTCTC
9559244 TAGTTTTCTC
1 TAGTTTTCTC
9559254 T
1 T
9559255 GCACTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.09, C:0.19, G:0.12, T:0.59
Consensus pattern (10 bp):
TAGTTTTCTC
Found at i:9564535 original size:43 final size:43
Alignment explanation
Indices: 9564485--9564570 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
9564475 TCATATTTCA
* *
9564485 TTTCTCATCTCATAATCATTTCTCGTATTTTCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTTGCCATTTCAATAT
* *
9564528 TTTCTCATCTCATATTCATTTCTCATCTTTGCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTTGCCATTTCAATAT
9564571 CAATCACACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.22, C:0.24, G:0.02, T:0.51
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTCTCATATTTGCCATTTCAATAT
Found at i:9565729 original size:19 final size:19
Alignment explanation
Indices: 9565693--9565732 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
9565683 TGTCGAGAAC
*
9565693 TTCTTCTTCCTTTCTTTCT
1 TTCTTCTTCCTTTATTTCT
9565712 TTCTT-TTCCTTTTATTTCT
1 TTCTTCTTCC-TTTATTTCT
9565731 TT
1 TT
9565733 TCTAATTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (19 bp):
TTCTTCTTCCTTTATTTCT
Found at i:9574530 original size:16 final size:16
Alignment explanation
Indices: 9574511--9574545 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
9574501 AATTGTGTTG
9574511 TAATTTATTG-TAAACT
1 TAATTT-TTGATAAACT
9574527 TAATTTTTGATAAACT
1 TAATTTTTGATAAACT
9574543 TAA
1 TAA
9574546 ATATTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (16 bp):
TAATTTTTGATAAACT
Found at i:9583471 original size:27 final size:27
Alignment explanation
Indices: 9583440--9583706 Score: 241
Period size: 27 Copynumber: 9.9 Consensus size: 27
9583430 AACCACCTGC
9583440 GCGAGCTTGGCTCGCCAAAACATAT-T
1 GCGAGCTTGGCTCGCCAAAACATATCT
* * * *
9583466 CGCGAGCTTGGCTCACCAAAAGACATTT
1 -GCGAGCTTGGCTCGCCAAAACATATCT
* * * * * *
9583494 GCAAGCATGGCTTGCTAAAACGTATTT
1 GCGAGCTTGGCTCGCCAAAACATATCT
* *
9583521 GTGAGCATGGCTCGCCAAAACATATCT
1 GCGAGCTTGGCTCGCCAAAACATATCT
* * *
9583548 GCAAGCTTGGCTCGCCAAAATATACCT
1 GCGAGCTTGGCTCGCCAAAACATATCT
* * *
9583575 GCGATCTTGGCTAGCCAAAGCATATCT
1 GCGAGCTTGGCTCGCCAAAACATATCT
* * * *
9583602 ACGAGCATAGCTCGTCAAAACATATCT
1 GCGAGCTTGGCTCGCCAAAACATATCT
** * *
9583629 ATGACCTTGGCTCGCCGAAACATATCT
1 GCGAGCTTGGCTCGCCAAAACATATCT
*
9583656 GCGAGCTTGGCTCGCCAAAGCATATCT
1 GCGAGCTTGGCTCGCCAAAACATATCT
* * *
9583683 GTGAGCATGGCTCGTCAAAA-ATAT
1 GCGAGCTTGGCTCGCCAAAACATAT
9583707 TTACCTCTCA
Statistics
Matches: 189, Mismatches: 50, Indels: 3
0.78 0.21 0.01
Matches are distributed among these distances:
26 4 0.02
27 184 0.97
28 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (27 bp):
GCGAGCTTGGCTCGCCAAAACATATCT
Found at i:9583586 original size:81 final size:81
Alignment explanation
Indices: 9583442--9583706 Score: 273
Period size: 81 Copynumber: 3.3 Consensus size: 81
9583432 CCACCTGCGC
* * * * * * *
9583442 GAGCTTGGCTCGCCAAAACATAT-TCGCGAGCTTGGCTCACCAAAAGACATTTGCAAGCATGGCT
1 GAGCATGGCTCGCCAAAACATATCT-GCGAGCTTGGCTCGCCAAAACATATCTGCGAGCTTGGCT
* * * * *
9583506 TGCTAAAACGTATTTGT
65 AGCCAAAGCATATCTGT
* * * *
9583523 GAGCATGGCTCGCCAAAACATATCTGCAAGCTTGGCTCGCCAAAATATACCTGCGATCTTGGCTA
1 GAGCATGGCTCGCCAAAACATATCTGCGAGCTTGGCTCGCCAAAACATATCTGCGAGCTTGGCTA
**
9583588 GCCAAAGCATATCTAC
66 GCCAAAGCATATCTGT
* * ** * * *
9583604 GAGCATAGCTCGTCAAAACATATCTATGACCTTGGCTCGCCGAAACATATCTGCGAGCTTGGCTC
1 GAGCATGGCTCGCCAAAACATATCTGCGAGCTTGGCTCGCCAAAACATATCTGCGAGCTTGGCTA
9583669 GCCAAAGCATATCTGT
66 GCCAAAGCATATCTGT
*
9583685 GAGCATGGCTCGTCAAAA-ATAT
1 GAGCATGGCTCGCCAAAACATAT
9583707 TTACCTCTCA
Statistics
Matches: 152, Mismatches: 31, Indels: 3
0.82 0.17 0.02
Matches are distributed among these distances:
80 4 0.03
81 147 0.97
82 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (81 bp):
GAGCATGGCTCGCCAAAACATATCTGCGAGCTTGGCTCGCCAAAACATATCTGCGAGCTTGGCTA
GCCAAAGCATATCTGT
Found at i:9584314 original size:38 final size:38
Alignment explanation
Indices: 9584263--9584342 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
9584253 GCAGTTCTGT
* *
9584263 GAGCTCATCATAACACAAACACATACCTCGCATATCGC
1 GAGCTCATCATAACACAAACAAACACCTCGCATATCGC
* * * *
9584301 GAGCTTATTATAACACAATCAAACACCTCGCATATTGC
1 GAGCTCATCATAACACAAACAAACACCTCGCATATCGC
9584339 GAGC
1 GAGC
9584343 ATACCTCGCT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.21
Consensus pattern (38 bp):
GAGCTCATCATAACACAAACAAACACCTCGCATATCGC
Found at i:9586255 original size:3 final size:3
Alignment explanation
Indices: 9586247--9586300 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
9586237 ATCTGTAATC
9586247 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9586295 TAT TAT
1 TAT TAT
9586301 AAAATAGCTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:9587042 original size:99 final size:99
Alignment explanation
Indices: 9586934--9587132 Score: 371
Period size: 99 Copynumber: 2.0 Consensus size: 99
9586924 AGGCCTTTAG
*
9586934 CTACCAACATCAATTCAAAATTTAAAACATTCAAAATCCATTCATTATGATTTTTAATTTCAAGT
1 CTACCAACATCAATTCAAAATTTAAAACATTCAAAATCCATTCATTATGATTTTTAATATCAAGT
*
9586999 TCATTTTATATCAAAATCCATTTAACATCTCGTT
66 TCATTTTATATCAAAATCCATTTAAAATCTCGTT
9587033 CTACCAACATCAATTCAAAATTTAAAACATTCAAAATCCATTCATTATGATTTTTAATATCAAGT
1 CTACCAACATCAATTCAAAATTTAAAACATTCAAAATCCATTCATTATGATTTTTAATATCAAGT
*
9587098 TCATTTTATATCAAAATCCTTTTAAAATCTCGTT
66 TCATTTTATATCAAAATCCATTTAAAATCTCGTT
9587132 C
1 C
9587133 GAACCTCTTT
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (99 bp):
CTACCAACATCAATTCAAAATTTAAAACATTCAAAATCCATTCATTATGATTTTTAATATCAAGT
TCATTTTATATCAAAATCCATTTAAAATCTCGTT
Found at i:9591494 original size:2 final size:2
Alignment explanation
Indices: 9591481--9591514 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
9591471 TTTAAGGTTC
*
9591481 AT AT AT AC 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
9591515 GCACAGACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:9604495 original size:27 final size:27
Alignment explanation
Indices: 9604466--9604646 Score: 166
Period size: 27 Copynumber: 6.6 Consensus size: 27
9604456 CTTTATGGTG
* * *
9604466 ATCTAAAAAATGGATGCCGTTGTGGCG
1 ATCTAAGAAATGGAAGCCGTTGTGGCA
* *
9604493 ATCTAAGAAATGGAAGCCTTTGTGACA
1 ATCTAAGAAATGGAAGCCGTTGTGGCA
* *
9604520 ATCTAAGAAATGAAAGCC-TTCATGGCA
1 ATCTAAGAAATGGAAGCCGTT-GTGGCA
* * *
9604547 ATCCAAGAAATAGAAGTCGTTGTGGCA
1 ATCTAAGAAATGGAAGCCGTTGTGGCA
* *
9604574 ATCTAAGAAATGGAAGCCTTTGTGGCG
1 ATCTAAGAAATGGAAGCCGTTGTGGCA
* * * **
9604601 ATCTAAAAAAACTGGAAGCCTTTGTAGTG
1 ATCT-AAGAAA-TGGAAGCCGTTGTGGCA
*
9604630 ATATAAGAAATGGAAGC
1 ATCTAAGAAATGGAAGC
9604647 TTTATGGCAA
Statistics
Matches: 127, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
26 2 0.02
27 95 0.75
28 12 0.09
29 18 0.14
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (27 bp):
ATCTAAGAAATGGAAGCCGTTGTGGCA
Found at i:9604728 original size:26 final size:26
Alignment explanation
Indices: 9604648--9604728 Score: 69
Period size: 27 Copynumber: 3.1 Consensus size: 26
9604638 AATGGAAGCT
* *
9604648 TTATGGCAAATCTTGTAAAGG-ATGCC
1 TTATGGCAAA-CTTCTAAAGGAACGCC
* *
9604674 TTTATGGCACAC-TCTAAA-GAATGGCCC
1 -TTATGGCAAACTTCTAAAGGAA-CG-CC
9604701 TTATGGCAAACTTCTAAAGGAACGCC
1 TTATGGCAAACTTCTAAAGGAACGCC
9604727 TT
1 TT
9604729 TGTGGTAGAC
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
24 1 0.02
25 6 0.14
26 16 0.36
27 18 0.41
28 3 0.07
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (26 bp):
TTATGGCAAACTTCTAAAGGAACGCC
Found at i:9605109 original size:16 final size:16
Alignment explanation
Indices: 9605090--9605121 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
9605080 AGAGATAAAG
9605090 TTTTTAAGAGACATAA
1 TTTTTAAGAGACATAA
9605106 TTTTTAAGAGACATAA
1 TTTTTAAGAGACATAA
9605122 CAAAGTAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (16 bp):
TTTTTAAGAGACATAA
Found at i:9609020 original size:18 final size:17
Alignment explanation
Indices: 9608987--9609025 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
9608977 TTGTATAAAT
9608987 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
9609005 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
9609022 TGTG
1 TGTG
9609026 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:9609143 original size:8 final size:8
Alignment explanation
Indices: 9609130--9609158 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
9609120 CACTAGAGAC
9609130 CAGTGTTA
1 CAGTGTTA
9609138 CAGTGTTA
1 CAGTGTTA
9609146 CAGTGTTA
1 CAGTGTTA
9609154 CAGTG
1 CAGTG
9609159 AGTCTCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:9609271 original size:23 final size:23
Alignment explanation
Indices: 9609245--9609343 Score: 189
Period size: 23 Copynumber: 4.3 Consensus size: 23
9609235 AGTGTTATTG
9609245 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
9609268 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
9609291 ATCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
9609314 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
9609337 ATCAGTG
1 ATCAGTG
9609344 TGGCACTTAT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 74 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.29
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:9611604 original size:137 final size:137
Alignment explanation
Indices: 9611356--9611667 Score: 457
Period size: 137 Copynumber: 2.3 Consensus size: 137
9611346 TCATTGACTT
* * * *
9611356 GAAAAATGAATAAGACCATAGTTGAAATACACTATGACACTATACCGTAAATGAATAAGACCATA
1 GAAAAATGAATAAGACCATAGTTGAAAGACACTATGGCACTATACCGAAAATAAATAAGACCATA
* *
9611421 GTTGAAAGACACTGTGGCACTATACCAAAAAATGAATAAGAACATAGTTGAAAGGCACTATGGC-
66 GTTGAAAGACACTATGGCACTATACCAAAAAATGAATAAGAACATAGTTGAAAGACACTATGGCA
* *
9611485 CCTATATC
131 TC-ATACC
9611493 GAAAAATGAATAAGACCATAGTTGAAAGACACTATGGCACTATACCGAAAATAAATAAGACCATA
1 GAAAAATGAATAAGACCATAGTTGAAAGACACTATGGCACTATACCGAAAATAAATAAGACCATA
* * * *
9611558 GTTGAAAGACACTATGGCCCTATATCAGAAAATGAATAAGACCATAGTTGAAAGACACTATGGCA
66 GTTGAAAGACACTATGGCACTATACCAAAAAATGAATAAGAACATAGTTGAAAGACACTATGGCA
*
9611623 TCATGCC
131 TCATACC
* * *
9611630 G-GAAATAAATAAGACCATAGTTGAAAGAAACTATGGCA
1 GAAAAATGAATAAGACCATAGTTGAAAGACACTATGGCA
9611668 TCATATCGGA
Statistics
Matches: 158, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
136 34 0.22
137 123 0.78
138 1 0.01
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (137 bp):
GAAAAATGAATAAGACCATAGTTGAAAGACACTATGGCACTATACCGAAAATAAATAAGACCATA
GTTGAAAGACACTATGGCACTATACCAAAAAATGAATAAGAACATAGTTGAAAGACACTATGGCA
TCATACC
Found at i:9611674 original size:91 final size:90
Alignment explanation
Indices: 9611358--9611666 Score: 449
Period size: 91 Copynumber: 3.4 Consensus size: 90
9611348 ATTGACTTGA
* * * * * *
9611358 AAAATGAATAAGACCATAGTTGAAATACACTATGACACTATACCGTAAATGAATAAGACCATAGT
1 AAAATAAATAAGACCATAGTTGAAAGACACTATGGCCCTATATCGAAAATGAATAAGACCATAGT
* *
9611423 TGAAAGACACTGTGGCACTATACCAA
66 TGAAAGACACTATGGCACTATACC-G
* * *
9611449 AAAATGAATAAGAACATAGTTGAAAGGCACTATGGCCCTATATCGAAAAATGAATAAGACCATAG
1 AAAATAAATAAGACCATAGTTGAAAGACACTATGGCCCTATATCG-AAAATGAATAAGACCATAG
9611514 TTGAAAGACACTATGGCACTATACCG
65 TTGAAAGACACTATGGCACTATACCG
9611540 AAAATAAATAAGACCATAGTTGAAAGACACTATGGCCCTATATCAGAAAATGAATAAGACCATAG
1 AAAATAAATAAGACCATAGTTGAAAGACACTATGGCCCTATATC-GAAAATGAATAAGACCATAG
*
9611605 TTGAAAGACACTATGGCA-TCATGCCG
65 TTGAAAGACACTATGGCACT-ATACCG
* *
9611631 GAAATAAATAAGACCATAGTTGAAAGAAACTATGGC
1 AAAATAAATAAGACCATAGTTGAAAGACACTATGGC
9611667 ATCATATCGG
Statistics
Matches: 200, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
90 1 0.00
91 156 0.78
92 43 0.22
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (90 bp):
AAAATAAATAAGACCATAGTTGAAAGACACTATGGCCCTATATCGAAAATGAATAAGACCATAGT
TGAAAGACACTATGGCACTATACCG
Found at i:9611690 original size:45 final size:45
Alignment explanation
Indices: 9611358--9611667 Score: 433
Period size: 46 Copynumber: 6.8 Consensus size: 45
9611348 ATTGACTTGA
* *
9611358 AAAATGAATAAGACCATAGTTGAAATACACTATGACACTATACCG
1 AAAATGAATAAGACCATAGTTGAAAGACACTATGGCACTATACCG
* * *
9611403 TAAATGAATAAGACCATAGTTGAAAGACACTGTGGCACTATACCAA
1 AAAATGAATAAGACCATAGTTGAAAGACACTATGGCACTATACC-G
* * * *
9611449 AAAATGAATAAGAACATAGTTGAAAGGCACTATGGCCCTATATCG
1 AAAATGAATAAGACCATAGTTGAAAGACACTATGGCACTATACCG
9611494 AAAAATGAATAAGACCATAGTTGAAAGACACTATGGCACTATACCG
1 -AAAATGAATAAGACCATAGTTGAAAGACACTATGGCACTATACCG
* * *
9611540 AAAATAAATAAGACCATAGTTGAAAGACACTATGGCCCTATATCAG
1 AAAATGAATAAGACCATAGTTGAAAGACACTATGGCACTATA-CCG
*
9611586 AAAATGAATAAGACCATAGTTGAAAGACACTATGGCA-TCATGCCG
1 AAAATGAATAAGACCATAGTTGAAAGACACTATGGCACT-ATACCG
* * *
9611631 GAAATAAATAAGACCATAGTTGAAAGAAACTATGGCA
1 AAAATGAATAAGACCATAGTTGAAAGACACTATGGCA
9611668 TCATATCGGA
Statistics
Matches: 235, Mismatches: 26, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
45 117 0.50
46 118 0.50
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.21
Consensus pattern (45 bp):
AAAATGAATAAGACCATAGTTGAAAGACACTATGGCACTATACCG
Found at i:9611702 original size:45 final size:45
Alignment explanation
Indices: 9611359--9611714 Score: 218
Period size: 45 Copynumber: 7.8 Consensus size: 45
9611349 TTGACTTGAA
* * * * * *
9611359 AAATGAATAAGACCATAGTTGAAATACACTATGACA-CTATACCGT
1 AAATAAATAAGACCATAGCTAAAAGACACTATGGCATC-ATACCGG
* * * * **
9611404 AAATGAATAAGACCATAGTTGAAAGACACTGTGGCA-CTATACCAAA
1 AAATAAATAAGACCATAGCTAAAAGACACTATGGCATC-ATACC-GG
* * * * * * * *
9611450 AAATGAATAAGAACATAGTTGAAAGGCACTATGGC-CCTATATCGAA
1 AAATAAATAAGACCATAGCTAAAAGACACTATGGCATC-ATACCG-G
* * * *
9611496 AAATGAATAAGACCATAGTTGAAAGACACTATGGCA-CTATACCGA
1 AAATAAATAAGACCATAGCTAAAAGACACTATGGCATC-ATACCGG
* * * * *
9611541 AAATAAATAAGACCATAGTTGAAAGACACTATGGC-CCTATATCAGA
1 AAATAAATAAGACCATAGCTAAAAGACACTATGGCATC-ATA-CCGG
* * * *
9611587 AAATGAATAAGACCATAGTTGAAAGACACTATGGCATCATGCCGG
1 AAATAAATAAGACCATAGCTAAAAGACACTATGGCATCATACCGG
* * * *
9611632 AAATAAATAAGACCATAGTTGAAAGAAACTATGGCATCATATCGG
1 AAATAAATAAGACCATAGCTAAAAGACACTATGGCATCATACCGG
* ** * * *
9611677 AAGTGTATAAGACCGTGGCTAAAAGACGCTATGGCATC
1 AAATAAATAAGACCATAGCTAAAAGACACTATGGCATC
9611715 CTTTGTACAG
Statistics
Matches: 271, Mismatches: 33, Indels: 14
0.85 0.10 0.04
Matches are distributed among these distances:
45 152 0.56
46 118 0.44
47 1 0.00
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (45 bp):
AAATAAATAAGACCATAGCTAAAAGACACTATGGCATCATACCGG
Found at i:9612303 original size:31 final size:31
Alignment explanation
Indices: 9612265--9612324 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
9612255 TGAATGAACG
9612265 CATGACCATGATATTGAATTATCTTGTAACT
1 CATGACCATGATATTGAATTATCTTGTAACT
9612296 CATGACCATGATATTGAATTATCTTGTAA
1 CATGACCATGATATTGAATTATCTTGTAA
9612325 AATGTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (31 bp):
CATGACCATGATATTGAATTATCTTGTAACT
Found at i:9613888 original size:61 final size:61
Alignment explanation
Indices: 9613814--9613935 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
9613804 AAAGAACCTG
9613814 ATGTTCGACTTTAACTCATTGGTGAGTCAAACACTTTGAGACATATTCAACAATTTATCTT
1 ATGTTCGACTTTAACTCATTGGTGAGTCAAACACTTTGAGACATATTCAACAATTTATCTT
9613875 ATGTTCGACTTTAACTCATTGGTGAGTCAAACACTTTGAGACATATTCAACAATTTATCTT
1 ATGTTCGACTTTAACTCATTGGTGAGTCAAACACTTTGAGACATATTCAACAATTTATCTT
9613936 TCCATATCCG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (61 bp):
ATGTTCGACTTTAACTCATTGGTGAGTCAAACACTTTGAGACATATTCAACAATTTATCTT
Found at i:9617096 original size:8 final size:8
Alignment explanation
Indices: 9617083--9617116 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
9617073 TGCTTTAACA
9617083 CCCATTTC
1 CCCATTTC
9617091 CCCATTT-
1 CCCATTTC
9617098 CCCATTTC
1 CCCATTTC
9617106 TCCCATTTC
1 -CCCATTTC
9617115 CC
1 CC
9617117 GTTTCCCCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.29
8 9 0.38
9 8 0.33
ACGTcount: A:0.12, C:0.50, G:0.00, T:0.38
Consensus pattern (8 bp):
CCCATTTC
Found at i:9617112 original size:16 final size:15
Alignment explanation
Indices: 9617083--9617124 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
9617073 TGCTTTAACA
9617083 CCCATTTCCCCATTT
1 CCCATTTCCCCATTT
9617098 CCCATTTCTCCCATTT
1 CCCATTTC-CCCATTT
*
9617114 CCCGTTTCCCC
1 CCCATTTCCCC
9617125 TGTTCCACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.10, C:0.50, G:0.02, T:0.38
Consensus pattern (15 bp):
CCCATTTCCCCATTT
Found at i:9617563 original size:25 final size:25
Alignment explanation
Indices: 9617533--9617591 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
9617523 TTTTGGAATA
9617533 TGTATTCTGGATTGTATGCTCAATT
1 TGTATTCTGGATTGTATGCTCAATT
*
9617558 TGTATTCTGGATTGTATGTTCAATT
1 TGTATTCTGGATTGTATGCTCAATT
9617583 TGTATTCTG
1 TGTATTCTG
9617592 CTTAGTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.19, C:0.10, G:0.20, T:0.51
Consensus pattern (25 bp):
TGTATTCTGGATTGTATGCTCAATT
Found at i:9624184 original size:131 final size:131
Alignment explanation
Indices: 9623981--9624370 Score: 575
Period size: 132 Copynumber: 3.0 Consensus size: 131
9623971 CACTGCAATT
* * *
9623981 TCAGGTAGATAAGACTGGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAATATAAGACTTGCCG
1 TCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGA-TTGCCG
* * *
9624046 TCTTTGATCTGCTCCACTACTACTTAGGGAGACATGATATACAATCTTCAACCTACTCCGCTACT
65 TCTTTGATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTACT
*
9624111 GC
130 AC
* *
9624113 TCAGGGAGATAGGACTGGTGGTTTAAATCTGCTT-CCTACTATCTCGGGAAGATAAGATTCGCCG
1 TCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGATT-GCCG
* * * *
9624177 TCTTTGATTTGCTCCACTGCTACTTAGGGAGACAGGATCTACAATTTTCAACCTACTCCACTGCT
65 TCTTTGATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTACT
9624242 AC
130 AC
* * ** *
9624244 TCAAGGAGAAAGGACTGGTGGCTTAAATCTATTTCCCTACTACCTTGGGAAGATAAGATTTGCCG
1 TCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGA-TTGCCG
*
9624309 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACT
65 TCTTTGATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACT
9624371 GCAAACTCAA
Statistics
Matches: 231, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
130 2 0.01
131 113 0.49
132 114 0.49
133 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (131 bp):
TCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGATTGCCGT
CTTTGATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTACTA
C
Found at i:9624371 original size:132 final size:132
Alignment explanation
Indices: 9623959--9624372 Score: 582
Period size: 131 Copynumber: 3.1 Consensus size: 132
9623949 AATTGGTAAT
* * *
9623959 TTCAACCTGCTCCACTGCAATTTC-AGGTAGATAA-GACTGGTGGCTTAAATCTGCTTCCCTACT
1 TTCAACCTACTCCACTGCTA-CTCAAGG-AGA-AAGGACTGGTGGCTTAAATCTGCTTCCCTACT
* * * *
9624022 ACCTCGGGAATATAAGACTTGCCGTCTTTGATCTGCTCCACTACTACTTAGGGAGACATGATATA
63 ACCTCGGGAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTACTTAGGGAGACAGGATCTA
9624087 CAATC
128 CAATC
* * * * * * *
9624092 TTCAACCTACTCCGCTACTGCTCAGGGAGATAGGACTGGTGGTTTAAATCTGCTT-CCTACTATC
1 TTCAACCTACTCCACTGCTACTCAAGGAGAAAGGACTGGTGGCTTAAATCTGCTTCCCTACTACC
* * *
9624156 TCGGGAAGATAAGATTCGCCGTCTTTGATTTGCTCCACTGCTACTTAGGGAGACAGGATCTACAA
66 TCGGGAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAA
*
9624221 TT
131 TC
**
9624223 TTCAACCTACTCCACTGCTACTCAAGGAGAAAGGACTGGTGGCTTAAATCTATTTCCCTACTACC
1 TTCAACCTACTCCACTGCTACTCAAGGAGAAAGGACTGGTGGCTTAAATCTGCTTCCCTACTACC
* *
9624288 TTGGGAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAA
66 TCGGGAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAA
9624353 TC
131 TC
9624355 TTCAACCTACTCCACTGC
1 TTCAACCTACTCCACTGC
9624373 AAACTCAAAG
Statistics
Matches: 245, Mismatches: 33, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
131 115 0.47
132 113 0.46
133 17 0.07
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (132 bp):
TTCAACCTACTCCACTGCTACTCAAGGAGAAAGGACTGGTGGCTTAAATCTGCTTCCCTACTACC
TCGGGAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAA
TC
Found at i:9625862 original size:23 final size:23
Alignment explanation
Indices: 9625836--9625934 Score: 128
Period size: 23 Copynumber: 4.3 Consensus size: 23
9625826 AGTGTTATTG
9625836 ATCAGTGGTAG-TTACGGCTACAT
1 ATCAGTGGTAGCTT-CGGCTACAT
*
9625859 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * * *
9625882 TTTAGTGGTAGCTACGACTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
9625905 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
9625928 ATCAGTG
1 ATCAGTG
9625935 TGGCACTTAT
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
23 61 0.97
24 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Done.