Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 91 of 131
Found at i:30519036 original size:131 final size:132
Alignment explanation
Indices: 30518795--30519055 Score: 391
Period size: 131 Copynumber: 2.0 Consensus size: 132
30518785 AAACCATAAG
* * * *
30518795 TCCTGTCTCCCTATGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGAAGTA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGACGAATCTTATCTTCCCAAGGAAGTA
* *
30518860 GGAAAACAGATTTAAGCCACTAGTACTATCTCCCTGAGCAACAGTGGAGTA-GTTGAAGATTGTA
66 GGAAAACAGATTTAAGCCACCAGTACTATCTCCCTAAGCAACAGTGGAGTAGGTTGAAGATTGTA
30518924 GA
131 GA
* * *
30518926 TCCTATCTCCCTAAGCAGTAGTGGAGCAAATCTAAGACGACGAATCTTATCTTCTCAAGGTAGTA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGACGAATCTTATCTTCCCAAGGAAGTA
* * *
30518991 -GAGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGT
66 GGA-AAACAGATTTAAGCCACCAGTACTATCTCCCTAAGCAACAGTGGAGTAGGTTGAAGATTGT
30519055 A
130 A
30519056 AATCATGTCT
Statistics
Matches: 116, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
130 2 0.02
131 101 0.87
132 13 0.11
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (132 bp):
TCCTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGACGAATCTTATCTTCCCAAGGAAGTA
GGAAAACAGATTTAAGCCACCAGTACTATCTCCCTAAGCAACAGTGGAGTAGGTTGAAGATTGTA
GA
Found at i:30520596 original size:15 final size:15
Alignment explanation
Indices: 30520573--30520607 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
30520563 CGCCCTTCAA
30520573 TTTTATTTTATTTTC
1 TTTTATTTTATTTTC
* *
30520588 TTTTTTTTTATTTTG
1 TTTTATTTTATTTTC
30520603 TTTTA
1 TTTTA
30520608 AAACCATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.11, C:0.03, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTATTTTATTTTC
Found at i:30520800 original size:27 final size:25
Alignment explanation
Indices: 30520763--30520847 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 25
30520753 ATTAATATTG
30520763 TTTAAATTTATCGCATATTATTATTAT
1 TTTAAATTTAT--CATATTATTATTAT
*
30520790 TTTAAATTTATCATA-TATAATTAT
1 TTTAAATTTATCATATTATTATTAT
* *
30520814 TTTAAGTTT-TCAT-TCATTATTAT
1 TTTAAATTTATCATATTATTATTAT
*
30520837 TTCAAATTTAT
1 TTTAAATTTAT
30520848 TATGTATTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
23 18 0.36
24 17 0.34
25 4 0.08
27 11 0.22
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (25 bp):
TTTAAATTTATCATATTATTATTAT
Found at i:30520835 original size:23 final size:24
Alignment explanation
Indices: 30520763--30520858 Score: 97
Period size: 24 Copynumber: 3.9 Consensus size: 24
30520753 ATTAATATTG
30520763 TTTAAATTTATCGCATATTATTATTAT
1 TTTAAATTTAT--CATA-TATTATTAT
*
30520790 TTTAAATTTATCATATATAATTAT
1 TTTAAATTTATCATATATTATTAT
*
30520814 TTTAAGTTT-TCAT-TCATTATTAT
1 TTTAAATTTATCATAT-ATTATTAT
* * *
30520837 TTCAAATTTATTATGTATTATT
1 TTTAAATTTATCATATATTATT
30520859 TTATATATCT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
22 1 0.02
23 18 0.30
24 25 0.42
25 5 0.08
27 11 0.18
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.57
Consensus pattern (24 bp):
TTTAAATTTATCATATATTATTAT
Found at i:30525787 original size:17 final size:17
Alignment explanation
Indices: 30525767--30525799 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
30525757 TTTAACTGTC
30525767 AAATTAAATTAATTCAA
1 AAATTAAATTAATTCAA
*
30525784 AAATTAATTTAATTCA
1 AAATTAAATTAATTCA
30525800 TTTGACAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATTAAATTAATTCAA
Found at i:30532771 original size:23 final size:24
Alignment explanation
Indices: 30532729--30532775 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
30532719 CAGTGAAAGG
30532729 CATCAATTTATCACGCAGGATTTTAT
1 CATCAATTTATCA--CAGGATTTTAT
30532755 CATCAATTTATCA-AGGATTTT
1 CATCAATTTATCACAGGATTTT
30532776 TCCAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.38
26 13 0.62
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (24 bp):
CATCAATTTATCACAGGATTTTAT
Found at i:30537730 original size:14 final size:14
Alignment explanation
Indices: 30537711--30537755 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
30537701 GTTTAGGTAG
30537711 GAAGCAAGAAAAGA
1 GAAGCAAGAAAAGA
30537725 GAAGCAAGAAAAGA
1 GAAGCAAGAAAAGA
* *
30537739 GAAGTAGGAAAAGA
1 GAAGCAAGAAAAGA
30537753 GAA
1 GAA
30537756 TAAAGGATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.62, C:0.04, G:0.31, T:0.02
Consensus pattern (14 bp):
GAAGCAAGAAAAGA
Found at i:30541576 original size:12 final size:12
Alignment explanation
Indices: 30541559--30541585 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
30541549 TTATCAATTA
30541559 TAACATGATATT
1 TAACATGATATT
30541571 TAACATGATATT
1 TAACATGATATT
30541583 TAA
1 TAA
30541586 AATTTTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (12 bp):
TAACATGATATT
Found at i:30543182 original size:50 final size:50
Alignment explanation
Indices: 30543065--30543309 Score: 257
Period size: 50 Copynumber: 4.9 Consensus size: 50
30543055 GATAATAACA
* * * ** * * ***
30543065 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCCT-TTAT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** *
30543114 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
30543164 TGGCC-ATGCCATGTCCCAGACATGGTCTTAC--GGGACACCTCTCATCA-CGG
1 T-GCCAATGCCATGTCCCAGACATGGTCTTACATGGG--ACCTCTCAT-ATCGG
* *
30543214 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
*
30543264 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
30543310 ACCTCAATGA
Statistics
Matches: 166, Mismatches: 21, Indels: 17
0.81 0.10 0.08
Matches are distributed among these distances:
48 3 0.02
49 39 0.23
50 117 0.70
51 4 0.02
52 3 0.02
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:30543325 original size:56 final size:49
Alignment explanation
Indices: 30543064--30543361 Score: 201
Period size: 50 Copynumber: 5.9 Consensus size: 49
30543054 TGATAATAAC
* * ** * **
30543064 ATGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTC--CTTT
1 ATGCCAAAGCCATGT-CCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * * ** * *
30543112 ATTGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATTG
1 A-TGCCAAAGCCATGT-CCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * *
30543163 GTGGCC-ATGCCATGTCCCAGACATGGTCTTAC--GGGACACCTCTCATCACG
1 AT-GCCAAAGCCATGT-CCAGACATGGTCTTACATGGG--ACCTCTCATCTCG
* *
30543213 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
1 ATGCCAAAGCCATGT-CCAGACATGGTCTTACATGGGACCTCTCATCTCG
* *
30543263 GTGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAACCTCAATG
1 ATGCCAAAGCCATGTCC-AGACATGGTCTTACATGGGACCTCTCAT---CTC---G
* * *
30543319 ATGCCAAAGCCATGAACCAGACTTGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATG-TCCAGACATGGTCTTACATGGGACCTCT
30543362 TTACCAAAAA
Statistics
Matches: 207, Mismatches: 26, Indels: 26
0.80 0.10 0.10
Matches are distributed among these distances:
48 4 0.02
49 40 0.19
50 114 0.55
51 5 0.02
52 3 0.01
53 3 0.01
56 36 0.17
57 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (49 bp):
ATGCCAAAGCCATGTCCAGACATGGTCTTACATGGGACCTCTCATCTCG
Found at i:30549117 original size:50 final size:50
Alignment explanation
Indices: 30549050--30549296 Score: 287
Period size: 50 Copynumber: 4.8 Consensus size: 50
30549040 TTCCTTTACG
* * **
30549050 GCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGT
* * ** *
30549100 GCCCATGCCATGTCCCAGACAGGGTCTTACGGGGGACCTCTCATCTCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGT
* * * *
30549150 GCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTTTTATCTCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGT
* *
30549200 GCCAATGCCATGTCCCAGACGTGGTCTTACATGGGACCTCTCATAACCTCAATGAT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGT
* *
30549256 GCCAATGCCATGTCCCAGAGATGGTCTTACATGGGATCTCT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
30549297 TTAACGAAAT
Statistics
Matches: 166, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
50 124 0.75
53 2 0.01
56 40 0.24
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGT
Found at i:30556343 original size:50 final size:50
Alignment explanation
Indices: 30556264--30556450 Score: 236
Period size: 50 Copynumber: 3.7 Consensus size: 50
30556254 TTTCTTGTAC
* * * *
30556264 TGCCAATTCCATA-TCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCA-AGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
* *
30556314 TGTCC-ATGCCAAGTCCCAGACACGGTCTTACAGGGGACCTT-TCATCTCGG
1 TG-CCAATGCCAAGTCCCAGACATGGTCTTACATGGGA-CTTCTCATCTCGG
*
30556364 TGCCAATGCCAAGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCAAGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
* * *
30556414 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGA
1 TGCCAATGCCAAGTCCCAGACATGGTCTTACATGGGA
30556451 TCTCATTCCT
Statistics
Matches: 120, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
49 5 0.04
50 111 0.93
51 4 0.03
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCAAGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
Found at i:30563097 original size:50 final size:50
Alignment explanation
Indices: 30562976--30563207 Score: 213
Period size: 50 Copynumber: 4.5 Consensus size: 50
30562966 ACATGTCAAA
* * *
30562976 GCCATGTCCCAGACATGGTCTTACATGGGATG-TTTCTTGTAC--TGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-GCTCTCATAT-CGGTGCCAAT
* * * * * *
30563025 GGCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGTGCCAAT
* * *
30563075 GCCATGTCCCAAACATGGTCTTAC--GGGAGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGAG--CTCTCATATCGGTGCCAAT
* *
30563125 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCAT-A--TC---GGTGCCAAT
30563181 GCCATGTCCCAGACATGGTCTTACATG
1 GCCATGTCCCAGACATGGTCTTACATG
30563208 AGATTTCATT
Statistics
Matches: 150, Mismatches: 20, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
48 7 0.05
49 31 0.21
50 72 0.48
52 4 0.03
53 2 0.01
56 34 0.23
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGTGCCAAT
Found at i:30567047 original size:19 final size:18
Alignment explanation
Indices: 30567006--30567051 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
30566996 TTTTTACTAT
* *
30567006 ATTTTTATTTTTTGGGTG
1 ATTTTTAATTTTTGCGTG
*
30567024 ATTTTTAATTTTTGCGTT
1 ATTTTTAATTTTTGCGTG
*
30567042 AGTTTTAATT
1 ATTTTTAATT
30567052 AGTTGGGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.65
Consensus pattern (18 bp):
ATTTTTAATTTTTGCGTG
Found at i:30567455 original size:127 final size:127
Alignment explanation
Indices: 30567315--30567612 Score: 325
Period size: 127 Copynumber: 2.3 Consensus size: 127
30567305 TAGCGTTTAC
* * **
30567315 AGAAAAAAAACGCCGTTAAAGGTCATGTTCTTTAACGGCGC-TACAAAAAAAACGTTGCT-AAAG
1 AGAAAAAAAACGCCGCTAAAGATCATGTTCTTTAACGGCGCTTA-AAAAAAAACGCCGCTAAAAG
* * * *
30567378 ATCATGTCCTTTAGCTGCGCTT-AAAAAAAGACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
65 -TAATGTCCTATAGCGGCGCTTGAAAAAAA-ACGCCACTAAAGATCATGTTCTTTAGCGGCGCTT
* * *
30567442 AGAAAAAATACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAACAAAAACGCCGCTAAAAGT
1 AGAAAAAAAACGCCGCTAAAGATCATGTTCTTTAACGGCGCTTAAAAAAAAACGCCGCTAAAAGT
* ** *
30567507 AATGTTCTATAGCGGCGCTTGGCAAAAAACGCCACTACAGATCATGTTCTTTAGCGGCGCTT
66 AATGTCCTATAGCGGCGCTTGAAAAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTT
** ** * * * *
30567569 TCACTACAAACGCCGCTAAA-AGTAATGTTCTTTAGCGACGCTTA
1 AGAAAAAAAACGCCGCTAAAGA-TCATGTTCTTTAACGGCGCTTA
30567613 CTTCACAAAC
Statistics
Matches: 144, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
126 1 0.01
127 132 0.92
128 11 0.08
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (127 bp):
AGAAAAAAAACGCCGCTAAAGATCATGTTCTTTAACGGCGCTTAAAAAAAAACGCCGCTAAAAGT
AATGTCCTATAGCGGCGCTTGAAAAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTT
Found at i:30567476 original size:85 final size:83
Alignment explanation
Indices: 30567317--30567612 Score: 344
Period size: 85 Copynumber: 3.5 Consensus size: 83
30567307 GCGTTTACAG
* * * * * **
30567317 AAAAAAAACGCCGTTAAAGGTCATGTTCTTTAACGGCGC-TACAAAAAAAACGTTGCTAAAGATC
1 AAAAAAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTA-GAAAAAAACGCCGCTAAAGATC
* *
30567381 ATGTCCTTTAGCTGCGCTT
65 ATGTTCTTTAGCGGCGCTT
*
30567400 AAAAAAAGACGCCGCT-AAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAATACGCCGCTAAAGA
1 AAAAAAA-ACGCCGCTAAAAG-TAATGTTCTTTAGCGGCGCTTAGAAAAAA-ACGCCGCTAAAGA
30567464 TCATGTTCTTTAGCGGCGCTT
63 TCATGTTCTTTAGCGGCGCTT
* * * * *
30567485 AAACAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTGGCAAAAAACGCCACTACAGATC
1 AAA-AAAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATC
30567550 ATGTTCTTTAGCGGCGCTTT
65 ATGTTCTTTAGCGGCGC-TT
** * *
30567570 CACTACAAACGCCGCTAAAAGTAATGTTCTTTAGCGACGCTTA
1 -AAAAAAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTA
30567613 CTTCACAAAC
Statistics
Matches: 185, Mismatches: 20, Indels: 14
0.84 0.09 0.06
Matches are distributed among these distances:
83 10 0.05
84 61 0.33
85 105 0.57
86 9 0.05
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (83 bp):
AAAAAAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCA
TGTTCTTTAGCGGCGCTT
Found at i:30567621 original size:43 final size:42
Alignment explanation
Indices: 30567318--30567654 Score: 319
Period size: 42 Copynumber: 8.0 Consensus size: 42
30567308 CGTTTACAGA
* * *
30567318 AAAAAAACGCCGTTAAAGGTCATGTTCTTTAACGGCGC-TAC
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAC
** * *
30567359 AAAAAAAACGTTGCTAAAGATCATGTCCTTTAGCTGCGCTTA-
1 -AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAC
*
30567401 AAAAAAGACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
1 AAAAAA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAC
30567444 AAAAAATACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA-
1 AAAAAA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAC
* * *
30567486 AACAAAAACGCCGCTAAA-AGTAATGTTCTATAGCGGCGCTTGGC
1 AA-AAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTT-AC
* * *
30567530 -AAAAAACGCCACTACAGATCATGTTCTTTAGCGGCGCTTTC
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAC
* * * *
30567571 ACTACAAACGCCGCTAAA-AGTAATGTTCTTTAGCGACGCTTAC
1 A-AAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTAC
** * * * *
30567614 TTCACAAACGCCGCTATAGAACATGAAT-TTTAGCGGCGCTT
1 -AAAAAAACGCCGCTAAAGATCATG-TTCTTTAGCGGCGCTT
30567655 TTATAAAAAA
Statistics
Matches: 247, Mismatches: 34, Indels: 27
0.80 0.11 0.09
Matches are distributed among these distances:
41 8 0.03
42 127 0.51
43 110 0.45
44 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAC
Found at i:30568087 original size:21 final size:21
Alignment explanation
Indices: 30568059--30568148 Score: 99
Period size: 21 Copynumber: 4.3 Consensus size: 21
30568049 GCTTTTCTCG
*
30568059 CTGCTTCTCTCGTTGCAGCCT
1 CTGCTTCCCTCGTTGCAGCCT
* * * *
30568080 CTGTTTCTCTCATTGTAGCCT
1 CTGCTTCCCTCGTTGCAGCCT
* *
30568101 CTGCTTCCCTAGCTGCAGCCT
1 CTGCTTCCCTCGTTGCAGCCT
* *
30568122 CTGCTTCCCTCGATGCCGCCT
1 CTGCTTCCCTCGTTGCAGCCT
30568143 CTGCTT
1 CTGCTT
30568149 TAAGTTGTAG
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.07, C:0.39, G:0.18, T:0.37
Consensus pattern (21 bp):
CTGCTTCCCTCGTTGCAGCCT
Found at i:30572768 original size:25 final size:25
Alignment explanation
Indices: 30572737--30573090 Score: 154
Period size: 25 Copynumber: 13.6 Consensus size: 25
30572727 TGATATATAA
*
30572737 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
30572762 TTATGTACGTGT-A-TAAGTTATGTAAG
1 TTATGTA--T-TAAGTAAGTTATGTAAG
*
30572788 TTATGTATTAAGTAAGCTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
* *
30572813 TTGTGTATTATGTAAGTTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
** * *
30572838 TTATCAAAGTAATGTATGTTATGTAAG
1 TTAT-GTATTAA-GTAAGTTATGTAAG
30572865 -T-TGTAAGTTATATGT-A-TTATTGTAAG
1 TTATGT-A-TTA-A-GTAAGTTA-TGTAAG
*
30572891 TTATGTAAGTTATGTAAGTTAAATGT-A-
1 TTATGT-A-TTAAGTAAGTT--ATGTAAG
* *
30572918 TTATGTAGGTTATGTAAGTTGTGTAAG
1 TTATGTA--TTAAGTAAGTTATGTAAG
* * * *
30572945 ATATTTAAGTTATGTAAGTTTTGT-A-
1 TTATGT-A-TTAAGTAAGTTATGTAAG
* *
30572970 TTATGTAAGTTATGTAAGTAATGTAAG
1 TTATGT-A-TTAAGTAAGTTATGTAAG
* * *
30572997 TTAAATGTATTATGTAGGTTATGCAAG
1 TT--ATGTATTAAGTAAGTTATGTAAG
* **
30573024 -TAGTGTAAGATATTTAAGTTATGTAAG
1 TTA-TGT-A-TTAAGTAAGTTATGTAAG
* * *
30573051 TTTTGTATTATGTAAGTTATGTATG
1 TTATGTATTAAGTAAGTTATGTAAG
* *
30573076 CTATGTATTATGTAA
1 TTATGTATTAAGTAA
30573091 TTTGTTATGT
Statistics
Matches: 263, Mismatches: 37, Indels: 58
0.73 0.10 0.16
Matches are distributed among these distances:
23 1 0.00
24 3 0.01
25 103 0.39
26 40 0.15
27 92 0.35
28 16 0.06
29 7 0.03
30 1 0.00
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (25 bp):
TTATGTATTAAGTAAGTTATGTAAG
Found at i:30572787 original size:9 final size:9
Alignment explanation
Indices: 30572748--30573122 Score: 263
Period size: 9 Copynumber: 42.8 Consensus size: 9
30572738 TATGTATTAA
*
30572748 GTAAATTAT
1 GTAAGTTAT
30572757 GTAAGTTAT
1 GTAAGTTAT
*
30572766 GTACGTGTA-
1 GTAAGT-TAT
30572775 -TAAGTTAT
1 GTAAGTTAT
30572783 GTAAGTTAT
1 GTAAGTTAT
*
30572792 GT-A-TTAA
1 GTAAGTTAT
*
30572799 GTAAGCTAT
1 GTAAGTTAT
*
30572808 GTAAGTTGT
1 GTAAGTTAT
30572817 GT-A-TTAT
1 GTAAGTTAT
30572824 GTAAGTTAT
1 GTAAGTTAT
30572833 GTAAGTTAT
1 GTAAGTTAT
** *
30572842 CAAAGTAAT
1 GTAAGTTAT
*
30572851 GTATGTTAT
1 GTAAGTTAT
30572860 GTAAG-T-T
1 GTAAGTTAT
30572867 GTAAGTTATAT
1 GTAAG-T-TAT
30572878 GT-A-TTATT
1 GTAAGTTA-T
30572886 GTAAGTTAT
1 GTAAGTTAT
30572895 GTAAGTTAT
1 GTAAGTTAT
30572904 GTAAGTTAAAT
1 GTAAGTT--AT
30572915 GT-A-TTAT
1 GTAAGTTAT
*
30572922 GTAGGTTAT
1 GTAAGTTAT
*
30572931 GTAAGTTGT
1 GTAAGTTAT
*
30572940 GTAAGATAT
1 GTAAGTTAT
*
30572949 TTAAGTTAT
1 GTAAGTTAT
*
30572958 GTAAGTTTT
1 GTAAGTTAT
30572967 GT-A-TTAT
1 GTAAGTTAT
30572974 GTAAGTTAT
1 GTAAGTTAT
*
30572983 GTAAGTAAT
1 GTAAGTTAT
30572992 GTAAGTTAAAT
1 GTAAGTT--AT
30573003 GT-A-TTAT
1 GTAAGTTAT
*
30573010 GTAGGTTAT
1 GTAAGTTAT
*
30573019 GCAAG-TAGT
1 GTAAGTTA-T
*
30573028 GTAAGATAT
1 GTAAGTTAT
*
30573037 TTAAGTTAT
1 GTAAGTTAT
*
30573046 GTAAGTTTT
1 GTAAGTTAT
30573055 GT-A-TTAT
1 GTAAGTTAT
30573062 GTAAGTTAT
1 GTAAGTTAT
* *
30573071 GTATGCTAT
1 GTAAGTTAT
30573080 GT-A-TTAT
1 GTAAGTTAT
30573087 GTAATTTGTTAT
1 GTAA---GTTAT
* *
30573099 GTTA-TTAC
1 GTAAGTTAT
30573107 GTAAGTTAT
1 GTAAGTTAT
*
30573116 GCAAGTT
1 GTAAGTT
30573123 TATATATAAG
Statistics
Matches: 285, Mismatches: 47, Indels: 68
0.71 0.12 0.17
Matches are distributed among these distances:
7 43 0.15
8 26 0.09
9 187 0.66
10 11 0.04
11 11 0.04
12 7 0.02
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:30572999 original size:88 final size:88
Alignment explanation
Indices: 30572739--30573082 Score: 378
Period size: 88 Copynumber: 3.9 Consensus size: 88
30572729 ATATATAATT
* * * * * * * *
30572739 ATGTATTAAGTAAATTATGTAAGTTATGTACG-TGTATAAGTTATGTAAGTTATGTATTAAGTAA
1 ATGTATTATGTAAGTTATGTAAGTAATGTAAGATATTTAAGTTATGTAAGTTTTGTATTATGTAA
* *
30572803 GCTATGTAAGTTGTGT-A-TT--
66 GTTATGTAAGTTATGTAAGTTAA
** * * *
30572822 ATGTAAGTTATGTAAGTTATCAAAGTAATGTATGTTATGTAAG-T-TGTAAGTTATATGTATTAT
1 ATGT-A-TTATGTAAGTTATGTAAGTAATGTAAGATATTTAAGTTATGTAAGTT-T-TGTATTA-
30572885 TGTAAGTTATGTAAGTTATGTAAGTTAA
61 TGTAAGTTATGTAAGTTATGTAAGTTAA
* **
30572913 ATGTATTATGTAGGTTATGTAAGTTGTGTAAGATATTTAAGTTATGTAAGTTTTGTATTATGTAA
1 ATGTATTATGTAAGTTATGTAAGTAATGTAAGATATTTAAGTTATGTAAGTTTTGTATTATGTAA
*
30572978 GTTATGTAAGTAATGTAAGTTAA
66 GTTATGTAAGTTATGTAAGTTAA
* * *
30573001 ATGTATTATGTAGGTTATGCAAGTAGTGTAAGATATTTAAGTTATGTAAGTTTTGTATTATGTAA
1 ATGTATTATGTAAGTTATGTAAGTAATGTAAGATATTTAAGTTATGTAAGTTTTGTATTATGTAA
* *
30573066 GTTATGTATGCTATGTA
66 GTTATGTAAGTTATGTA
30573083 TTATGTAATT
Statistics
Matches: 223, Mismatches: 26, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
83 4 0.02
84 9 0.04
85 22 0.10
86 13 0.06
87 18 0.08
88 105 0.47
89 37 0.17
90 3 0.01
91 12 0.05
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.44
Consensus pattern (88 bp):
ATGTATTATGTAAGTTATGTAAGTAATGTAAGATATTTAAGTTATGTAAGTTTTGTATTATGTAA
GTTATGTAAGTTATGTAAGTTAA
Found at i:30574865 original size:6 final size:6
Alignment explanation
Indices: 30574854--30574891 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
30574844 AGCAGAGAGC
* *
30574854 GACGGT GACGGT GACGGT GACAGT GACAGT GACGGT GA
1 GACGGT GACGGT GACGGT GACGGT GACGGT GACGGT GA
30574892 TGCAGTAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.24, C:0.16, G:0.45, T:0.16
Consensus pattern (6 bp):
GACGGT
Found at i:30575794 original size:65 final size:65
Alignment explanation
Indices: 30575690--30575819 Score: 251
Period size: 65 Copynumber: 2.0 Consensus size: 65
30575680 TTTTCCTGAT
*
30575690 AATTAGGATAATTTTGCGGCGTTGTTTTGTAAAACGCCACTAAGAACATGGAAATTTTGAAAAAA
1 AATTAGGATAATTTTGCGGCGGTGTTTTGTAAAACGCCACTAAGAACATGGAAATTTTGAAAAAA
30575755 AATTAGGATAATTTTGCGGCGGTGTTTTGTAAAACGCCACTAAGAACATGGAAATTTTGAAAAAA
1 AATTAGGATAATTTTGCGGCGGTGTTTTGTAAAACGCCACTAAGAACATGGAAATTTTGAAAAAA
30575820 TTAAGTTAAA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (65 bp):
AATTAGGATAATTTTGCGGCGGTGTTTTGTAAAACGCCACTAAGAACATGGAAATTTTGAAAAAA
Found at i:30576306 original size:7 final size:7
Alignment explanation
Indices: 30576294--30576343 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
30576284 GACAAAGCGG
30576294 CCTAAAC
1 CCTAAAC
*
30576301 CCTAAAT
1 CCTAAAC
*
30576308 CCTAAAT
1 CCTAAAC
*
30576315 CTTAAAC
1 CCTAAAC
30576322 CCTAAAC
1 CCTAAAC
*
30576329 TTCTAAAC
1 -CCTAAAC
30576337 CCTAAAC
1 CCTAAAC
30576344 TCAAAACACC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
7 30 0.83
8 6 0.17
ACGTcount: A:0.42, C:0.34, G:0.00, T:0.24
Consensus pattern (7 bp):
CCTAAAC
Found at i:30576405 original size:35 final size:35
Alignment explanation
Indices: 30576332--30576411 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 35
30576322 CCTAAACTTC
**
30576332 TAAACCCTAAACTCAAAACACCAAAACCTACATCA
1 TAAACCCTAAACTCAAAACACCAAAACCTACAAAA
* * * **
30576367 TAAACCCTAAACTCAAAACTCTAATATTTACAAAA
1 TAAACCCTAAACTCAAAACACCAAAACCTACAAAA
30576402 TAAA-CCTAAA
1 TAAACCCTAAA
30576412 ACCCTAAACT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 6 0.16
35 32 0.84
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.20
Consensus pattern (35 bp):
TAAACCCTAAACTCAAAACACCAAAACCTACAAAA
Found at i:30576618 original size:16 final size:17
Alignment explanation
Indices: 30576599--30576633 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30576589 CAAATATGAC
30576599 AAACTA-AATATATAAT
1 AAACTACAATATATAAT
*
30576615 AAACTACATTATATAAT
1 AAACTACAATATATAAT
30576632 AA
1 AA
30576634 CCTAGCGGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (17 bp):
AAACTACAATATATAAT
Found at i:30576901 original size:114 final size:114
Alignment explanation
Indices: 30576653--30577443 Score: 895
Period size: 114 Copynumber: 6.9 Consensus size: 114
30576643 GCTTCCCAAA
* * * * * * * * * *
30576653 ACGCGCCGCTAATAATATGTTTTCGTGGTGTTTTCCCGTAAGCGCCACTACTGCTAGTATACATC
1 ACGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTC
* * * * *
30576718 AAGACCAAATCGCTGCGTTTTTGTTAATATATTTTGCGGCGCTTTCCACC
66 AAGACCAAA-CTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTCACG
* * *
30576768 AAGCACCGCTAATACTATGCATTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTC
1 ACGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTC
* * *
30576833 AAGACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTGATG
66 AAGACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTCACG
* * * * * **
30576882 ACGCGCCGCTAATATTATGCATTAACGACATTTTCGAATAAGCGCCACTAATTCTAATATACCTC
1 ACGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTC
* *
30576947 AAGACCAAACTCTGCGTTTTGGTTAAGATATGTTGCGGCGCTTTTTACG
66 AAGACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTCACG
*
30576996 ACGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCCAATAAGCGCCACTAATTCTAATATACCTC
1 ACGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTC
* * * * *
30577061 AAGACCAAACTTTGCGTTTTGGTTAAGATATGTTGCAGCGCTTTTTACA
66 AAGACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTCACG
* * ** * **
30577110 ACACGCCACTAATACTAAACGTTAGATGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTC
1 ACGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTC
* * * *
30577175 AAGACCAAAATCTGCATTTTGGTTAATATATTTTGCGGCGCTTTTCACA
66 AAGACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTCACG
** ** * * *
30577224 AATCGCCGCTAATACT-TGCTTTAGCGGCGTTTTTTCATATGCGCCACTAATTCTAATATACATA
1 ACGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTC
* * * **
30577288 AAGACCAAACTCTGCATTTTGGTTAAGATATGTTGCGGCGCGTTTGGCG
66 AAGACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTCACG
* * * * * * * *
30577337 A-TCGCTGCTAATACT-TTCTTTGGCGGCGTTTTCCTATAATCGCCACTAATTCTAGTATACATC
1 ACGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTC
* * * * *
30577400 TAGACCAAAACGCTGTGTTTTGGTTAAGAGATTTTGCAGCGCTT
66 AAGACC-AAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTT
30577444 GATAGTAAAC
Statistics
Matches: 580, Mismatches: 95, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
112 57 0.10
113 111 0.19
114 351 0.61
115 61 0.11
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (114 bp):
ACGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCCCATAAGCGCCACTAATTCTAATATACCTC
AAGACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTCACG
Found at i:30579129 original size:15 final size:15
Alignment explanation
Indices: 30579109--30579139 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30579099 AAAACAACAT
*
30579109 AACTCTTGGCCTTTC
1 AACTCTTGACCTTTC
30579124 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
30579139 A
1 A
30579140 CTTACATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.32, G:0.10, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:30583433 original size:15 final size:15
Alignment explanation
Indices: 30583410--30583440 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30583400 AAAACAACAT
30583410 AACTATTGACCTTTC
1 AACTATTGACCTTTC
*
30583425 AACTCTTGACCTTTC
1 AACTATTGACCTTTC
30583440 A
1 A
30583441 CTTACATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTATTGACCTTTC
Found at i:30584313 original size:14 final size:14
Alignment explanation
Indices: 30584294--30584334 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
30584284 TTCCTGATTG
30584294 GTTTATTTTTTTTT
1 GTTTATTTTTTTTT
*
30584308 GTTTATTTGTTTTT
1 GTTTATTTTTTTTT
*
30584322 ATTTATTTCTTTT
1 GTTTATTT-TTTT
30584335 CATTGTTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 20 0.87
15 3 0.13
ACGTcount: A:0.10, C:0.02, G:0.07, T:0.80
Consensus pattern (14 bp):
GTTTATTTTTTTTT
Found at i:30584352 original size:31 final size:28
Alignment explanation
Indices: 30584295--30584354 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 28
30584285 TCCTGATTGG
*
30584295 TTTATTTTTTTTTGTTTATTTGTTTTTA
1 TTTATTTTTTTTTGTTTATTTATTTTTA
*
30584323 TTTATTTCTTTTCATTGTTTGTTTATTTTTA
1 TTTATTT-TTTT--TTGTTTATTTATTTTTA
30584354 T
1 T
30584355 CTTTTCAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 7 0.26
29 4 0.15
31 16 0.59
ACGTcount: A:0.12, C:0.03, G:0.07, T:0.78
Consensus pattern (28 bp):
TTTATTTTTTTTTGTTTATTTATTTTTA
Found at i:30589005 original size:18 final size:18
Alignment explanation
Indices: 30588982--30589017 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
30588972 TGGAAGCTGC
30588982 TTTTAGACTATCCCGAAT
1 TTTTAGACTATCCCGAAT
30589000 TTTTAGACTATCCCGAAT
1 TTTTAGACTATCCCGAAT
30589018 CAGCCTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (18 bp):
TTTTAGACTATCCCGAAT
Found at i:30589269 original size:27 final size:27
Alignment explanation
Indices: 30589239--30589292 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
30589229 CATCGGAGTA
*
30589239 TATCTTCCAATACCTGAATTACACACT
1 TATCTTCCAATACCTAAATTACACACT
30589266 TATCTTCCAATACCTAAATTACACACT
1 TATCTTCCAATACCTAAATTACACACT
30589293 CAGATTGACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (27 bp):
TATCTTCCAATACCTAAATTACACACT
Found at i:30594406 original size:50 final size:50
Alignment explanation
Indices: 30594289--30594424 Score: 173
Period size: 50 Copynumber: 2.7 Consensus size: 50
30594279 ACATGTCAAA
** * *
30594289 GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGATGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATATCGATGCCAAC
* * ** * *
30594340 GCCATGTTCCAAACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGATGCCAAC
30594390 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
30594425 TTACCCAAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 45 0.63
51 26 0.37
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGATGCCAAC
Found at i:30597408 original size:16 final size:16
Alignment explanation
Indices: 30597387--30597418 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30597377 GTTTTGTCGC
*
30597387 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
30597403 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
30597419 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:30597707 original size:51 final size:51
Alignment explanation
Indices: 30597643--30597776 Score: 182
Period size: 51 Copynumber: 2.6 Consensus size: 51
30597633 GATACCAGTT
30597643 CACATAGTAGCCTGCACATAGTACTACACATGTGA-CCATCA-CTATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGATCCA--AGCTATCCGATA
* * * * *
30597694 CACGTCGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGATCCAAGCTATCCGATA
*
30597745 CGCATAGTAGCCTGCACATAGTACTACACATG
1 CACATAGTAGCCTGCACATAGTACTACACATG
30597777 NNNNNNNNNN
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
50 1 0.01
51 69 0.96
52 2 0.03
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACATGTGATCCAAGCTATCCGATA
Found at i:30599507 original size:24 final size:23
Alignment explanation
Indices: 30599440--30599507 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 23
30599430 AAGCTGCTCT
30599440 TTGTGGTCAAACCACTCAAATATGA
1 TTGTGG-CAAACCACTC-AATATGA
30599465 -TGTGGCAAAGCCACTCAATA-GCA
1 TTGTGGCAAA-CCACTCAATATG-A
30599488 TTGTGGACAAACCACTCAAT
1 TTGTGG-CAAACCACTCAAT
30599508 TTTTTCAGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
22 1 0.03
23 9 0.23
24 25 0.64
25 4 0.10
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (23 bp):
TTGTGGCAAACCACTCAATATGA
Found at i:30601843 original size:27 final size:28
Alignment explanation
Indices: 30601807--30601860 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
30601797 TTGAAATTCA
*
30601807 CACTTTAATTA-TAAAATAATTAATTTG
1 CACTTCAATTATTAAAATAATTAATTTG
* *
30601834 CACTTCAATTATTAACATATTTAATTT
1 CACTTCAATTATTAAAATAATTAATTT
30601861 TAATTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.46
Consensus pattern (28 bp):
CACTTCAATTATTAAAATAATTAATTTG
Found at i:30607753 original size:28 final size:28
Alignment explanation
Indices: 30607714--30607832 Score: 150
Period size: 28 Copynumber: 4.3 Consensus size: 28
30607704 CTATTCAGTA
**
30607714 ACAGT-ACAGTGTGGGCCTTAGCCTGAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
**
30607741 ACAGTAACAGTGTGGTTCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* * * * *
30607769 ATAGTAATAGTGTAGGACTTAGCCAAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
30607797 ACAGTAACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
30607825 ACAGTAAC
1 ACAGTAAC
30607833 CAGTACAGTG
Statistics
Matches: 76, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
27 5 0.07
28 71 0.93
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
ACAGTAACAGTGTGGGCCTTAGCCCAAT
Found at i:30607966 original size:26 final size:26
Alignment explanation
Indices: 30607937--30607991 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
30607927 AACACACCAA
* *
30607937 TATCGCAGCAAAGCTTCCAATAATAG
1 TATCGCAGCAAAGCTGCCAATAACAG
* *
30607963 TATCGCAGCGAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAATAACAG
30607989 TAT
1 TAT
30607992 ATGTGGCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAATAACAG
Found at i:30608214 original size:27 final size:27
Alignment explanation
Indices: 30608184--30608586 Score: 405
Period size: 27 Copynumber: 15.0 Consensus size: 27
30608174 GGTATAACAA
30608184 TCATTTTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* ** *
30608211 TCATTCTA-CCTATAAGGGTATTTCAG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * * *
30608237 TTATTTTACCTTACGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
** *
30608264 TCATTTTACCCTACAGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
*
30608291 TCATTTTACCCTATGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* *** *
30608318 CCATTTTACCCTACAAGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGG
* * **
30608345 TCATTTTACCTTACGGGGGTATTTTAG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
30608372 TCATTTTATCCTATGGGGCTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGG
* *
30608399 TCAGTTTACCCTATGAGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
30608426 TCATTTTACTCTACGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* *
30608453 CCATTTTACCCTATGGGGGTATTTCAG
1 TCATTTTACCCTATGGGGGTATTTCGG
** * *
30608480 TCATTTTACCCTATAAGGGTATTTTGA
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
30608507 TTATTTTACCCTATAGAGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
*** *
30608534 TCATTTTACCCTACAAGGGTATTTCAG
1 TCATTTTACCCTATGGGGGTATTTCGG
*
30608561 TCATTTTACCTTAT-GGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
30608587 GGTCTCGGTG
Statistics
Matches: 303, Mismatches: 72, Indels: 3
0.80 0.19 0.01
Matches are distributed among these distances:
26 31 0.10
27 272 0.90
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGG
Found at i:30608309 original size:54 final size:54
Alignment explanation
Indices: 30608184--30608586 Score: 452
Period size: 54 Copynumber: 7.5 Consensus size: 54
30608174 GGTATAACAA
* * *
30608184 TCATTTTACCCTATGGGGGTATTTCGGTCATTCTA-CCTATAAGGGTATTTCAG
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTACAAGGGTATTTCGG
* * * * * *
30608237 TTATTTTACCTTACGGGGGTATTTTGGTCATTTTACCCTACAGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTACAAGGGTATTTCGG
* * *
30608291 TCATTTTACCCTATGGGGGTATTTTGGCCATTTTACCCTACAAGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTACAAGGGTATTTCGG
* * ** * ** *
30608345 TCATTTTACCTTACGGGGGTATTTTAGTCATTTTATCCTA-TGGGGCTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTACAAGGG-TATTTCGG
* * * ** *
30608399 TCAGTTTACCCTATGAGGGTATTTCGGTCATTTTACTCTACGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTACAAGGGTATTTCGG
* * * * *
30608453 CCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTATAAGGGTATTTTGA
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTACAAGGGTATTTCGG
* * * *
30608507 TTATTTTACCCTATAGAGGTATTTCGGTCATTTTACCCTACAAGGGTATTTCAG
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTACAAGGGTATTTCGG
*
30608561 TCATTTTACCTTAT-GGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
30608587 GGTCTCGGTG
Statistics
Matches: 292, Mismatches: 55, Indels: 6
0.83 0.16 0.02
Matches are distributed among these distances:
53 44 0.15
54 244 0.84
55 4 0.01
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.42
Consensus pattern (54 bp):
TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTACAAGGGTATTTCGG
Found at i:30611658 original size:21 final size:21
Alignment explanation
Indices: 30611633--30611710 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 21
30611623 ATCTTCAAGG
30611633 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
30611654 ATATGCAATCTTGGATATG--
1 ATATGCAATCTTAGATATGAT
30611673 ATATGCAATCTTGGAAGATATGAT
1 ATATGCAATCTT---AGATATGAT
* *
30611697 -TTTGTAATCTTAGA
1 ATATGCAATCTTAGA
30611711 GATTTAATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
19 12 0.25
20 3 0.06
21 18 0.38
22 6 0.12
23 9 0.19
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:30611694 original size:17 final size:19
Alignment explanation
Indices: 30611632--30611687 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
30611622 AATCTTCAAG
*
30611632 GATATGCAATCTTAGATAT
1 GATATGCAATCTTGGATAT
30611651 GATATATGCAATCTTGGATAT
1 G--ATATGCAATCTTGGATAT
30611672 GATATGCAATCTTGGA
1 GATATGCAATCTTGGA
30611688 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 16 0.47
21 18 0.53
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTGGATAT
Found at i:30612576 original size:14 final size:15
Alignment explanation
Indices: 30612550--30612582 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
30612540 TCCCAAGCTG
30612550 GGAAGGACCTTATGT
1 GGAAGGACCTTATGT
*
30612565 GGAAGG-CCTTATTT
1 GGAAGGACCTTATGT
30612579 GGAA
1 GGAA
30612583 AAGCATCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.27
Consensus pattern (15 bp):
GGAAGGACCTTATGT
Found at i:30612861 original size:42 final size:42
Alignment explanation
Indices: 30612781--30612861 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
30612771 CCTGAAAAGG
* *
30612781 GCAGCTCAAATATCGATCAGAATGGGGCATAAGGTGATCAGA
1 GCAGCTCAAATATAGATCAGAATGGGGCATAAGATGATCAGA
* * * *
30612823 GCAGTTCAAATTTAGATCAGATTGGGGCATATGATGATC
1 GCAGCTCAAATATAGATCAGAATGGGGCATAAGATGATC
30612862 TTGAATCAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (42 bp):
GCAGCTCAAATATAGATCAGAATGGGGCATAAGATGATCAGA
Found at i:30614060 original size:44 final size:44
Alignment explanation
Indices: 30613924--30614067 Score: 139
Period size: 44 Copynumber: 3.3 Consensus size: 44
30613914 GATAATAGAT
*
30613924 CTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAAC
1 CTTGCCTCCCTGCACCGATAGCGAAGCAGATCGAAGACACCAAC
** * ** * * * *
30613968 CTTGCCTCCCTG-AGTTG-TAGCGAAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGCA-CCGATAGCGAAGCAGATCGAAGACACCA-AC
* * *
30614012 CTTGCCTTCCTGCACCGACAGCGAAGAAGATCGAAGACACCAAC
1 CTTGCCTCCCTGCACCGATAGCGAAGCAGATCGAAGACACCAAC
30614056 CTTGCCTCCCTG
1 CTTGCCTCCCTG
30614068 GGTTGCAGCG
Statistics
Matches: 73, Mismatches: 23, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
43 19 0.26
44 37 0.51
45 17 0.23
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (44 bp):
CTTGCCTCCCTGCACCGATAGCGAAGCAGATCGAAGACACCAAC
Found at i:30614085 original size:88 final size:88
Alignment explanation
Indices: 30613920--30614867 Score: 1110
Period size: 88 Copynumber: 10.8 Consensus size: 88
30613910 TGAAGATAAT
* * * * * * *
30613920 AGATCTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGAGTTG
1 AGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTGGGTTG
* *
30613985 TAGCGAAGCAGGTTAAAAATAGC
66 CAGCGGAGCAGGTTAAAAATAGC
* * * * * *
30614008 AGATCTTGCCTTCCTGCACCGACAGCGAAGAAGATCGAAGACACCAACCTTGCCTCCCTGGGTTG
1 AGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTGGGTTG
* *
30614073 CAGCGGAACAGGTTGAAAATAGC
66 CAGCGGAGCAGGTTAAAAATAGC
* ** * *
30614096 AGATCTTGCCTTCCTATACTAACAATGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTGGGTTG
1 AGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTGGGTTG
* *
30614161 CAGCGGAGCACGTTAAAAATTGC
66 CAGCGGAGCAGGTTAAAAATAGC
* * ** *
30614184 AGATCTTACCTTCCTGTACCGGCAGTGAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGGGTTG
1 AGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTGGGTTG
** *
30614249 CAGTAGAGCAGGTTGAAAATTA-C
66 CAGCGGAGCAGGTT-AAAAATAGC
** * * * * * * * *
30614272 AGATCTTATCTCCCT-AAGC-AGTAGTGGAGTAGATTGAAGACACTAGCCTTGCCTCCCTCGGTA
1 AGATCTTGCCTTCCTGTACCGA-CAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTGGGTT
* *
30614335 GCAGCGGAGCAGGTTAAAGATAAC
65 GCAGCGGAGCAGGTTAAAAATAGC
* * * * *
30614359 AGATATTGCCTTCCTGTACTGACAGTGAAGCAGATTGAAGACACTTGCCTTGCCTCCCTCGGTGG
1 AGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTGGGTTG
* * *
30614424 CAGCGAAGCAGGTTAAAGATAAC
66 CAGCGGAGCAGGTTAAAAATAGC
* * * ** *
30614447 AGATATTGCCTTCCTGTACTGACAATGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTCAGTGG
1 AGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTGGGTTG
* *
30614512 CAGCGGAGCAGCTTAAAGATAGC
66 CAGCGGAGCAGGTTAAAAATAGC
* ** * *
30614535 ATATCTTGCCTTCCTGTACTAACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTCGGTGG
1 AGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTGGGTTG
* *
30614600 CAGCGGAGCAGGTTAAAGATAGT
66 CAGCGGAGCAGGTTAAAAATAGC
* * * *
30614623 AGATCTTGCCTTCCTATACTGACAGTGAAGCAAATTGAAGACACTAGCCTTGCCTCCCTAGGTTG
1 AGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTGGGTTG
30614688 CAGCGGAGCAGGTTAAAAATAGC
66 CAGCGGAGCAGGTTAAAAATAGC
* * * *
30614711 AGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCATGGGTTG
1 AGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTGGGTTG
30614776 CAGCGGAGCAGGTTAAAAATAGC
66 CAGCGGAGCAGGTTAAAAATAGC
* * *** * * *
30614799 AGATCTTGCCTTCCTGCACCGATAACAAAGCAGATTGAAGACACAAGTCTTGCCTCCCTGAGTTG
1 AGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTGGGTTG
30614864 CAGC
66 CAGC
30614868 AGATCAAGTT
Statistics
Matches: 754, Mismatches: 101, Indels: 10
0.87 0.12 0.01
Matches are distributed among these distances:
86 5 0.01
87 61 0.08
88 682 0.90
89 6 0.01
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (88 bp):
AGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTGGGTTG
CAGCGGAGCAGGTTAAAAATAGC
Found at i:30614369 original size:44 final size:44
Alignment explanation
Indices: 30614320--30614457 Score: 122
Period size: 44 Copynumber: 3.1 Consensus size: 44
30614310 GACACTAGCC
*
30614320 TTGCCTCCCTCGGTAGCAGCGGAGCAGGTTAAAGATAACAGATA
1 TTGCCTCCCTCGGTAGCAGCGAAGCAGGTTAAAGATAACAGATA
* * * * * * **
30614364 TTGCCTTCCT--GTACTGACAGTGAAGCAGATTGAAGA-CACTTG-CC
1 TTGCCTCCCTCGGTA--G-CAGCGAAGCAGGTTAAAGATAAC-AGATA
*
30614408 TTGCCTCCCTCGGTGGCAGCGAAGCAGGTTAAAGATAACAGATA
1 TTGCCTCCCTCGGTAGCAGCGAAGCAGGTTAAAGATAACAGATA
30614452 TTGCCT
1 TTGCCT
30614458 TCCTGTACTG
Statistics
Matches: 68, Mismatches: 18, Indels: 16
0.67 0.18 0.16
Matches are distributed among these distances:
42 3 0.04
43 17 0.25
44 30 0.44
45 16 0.24
46 2 0.03
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (44 bp):
TTGCCTCCCTCGGTAGCAGCGAAGCAGGTTAAAGATAACAGATA
Found at i:30614719 original size:44 final size:44
Alignment explanation
Indices: 30614583--30614809 Score: 120
Period size: 44 Copynumber: 5.2 Consensus size: 44
30614573 AGACACTAGC
* * *
30614583 CTTGCCTCCCTCGGTGGCAGCGGAGCAGGTTAAAGATAGTAGAT
1 CTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAGATAGCAGAT
* *** * * ** * * *
30614627 CTTGCCTTCCTATACTGACAGTGAAGCAAATTGAAGACA-CTAG-C
1 CTTGCCTCCCTAGGTTG-CAGCGGAGCAGGTTAAAGATAGC-AGAT
*
30614671 CTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAGATAGCAGAT
* *** * * * ** * * *
30614715 CTTGCCTTCCT-GCACCGACAGTGAAGCAGATCGAAGACACCAG-C
1 CTTGCCTCCCTAG-GTTG-CAGCGGAGCAGGTTAAAGATAGCAGAT
* * *
30614759 CTTGCCTCCATGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAGATAGCAGAT
30614803 CTTGCCT
1 CTTGCCT
30614810 TCCTGCACCG
Statistics
Matches: 122, Mismatches: 53, Indels: 16
0.64 0.28 0.08
Matches are distributed among these distances:
43 34 0.28
44 53 0.43
45 35 0.29
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (44 bp):
CTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAGATAGCAGAT
Found at i:30615301 original size:19 final size:19
Alignment explanation
Indices: 30615228--30615298 Score: 115
Period size: 19 Copynumber: 3.6 Consensus size: 19
30615218 ATCTTCAAGT
30615228 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
30615247 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
*
30615266 ATATATGCAATCTTGGATATG
1 --ATATGCAATCTTAGATATG
30615287 ATATGCAATCTT
1 ATATGCAATCTT
30615299 GGAAGATATG
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
19 31 0.63
21 18 0.37
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.38
Consensus pattern (19 bp):
ATATGCAATCTTAGATATG
Found at i:30642229 original size:9 final size:9
Alignment explanation
Indices: 30642211--30642252 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
30642201 GGTTTCCATT
30642211 AAAA-AAAG
1 AAAATAAAG
30642219 AAAATAAAG
1 AAAATAAAG
*
30642228 AAGATAAAG
1 AAAATAAAG
*
30642237 AAAA-AAGG
1 AAAATAAAG
30642245 AAAATAAA
1 AAAATAAA
30642253 TTTATGAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
8 11 0.39
9 17 0.61
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (9 bp):
AAAATAAAG
Found at i:30642690 original size:21 final size:22
Alignment explanation
Indices: 30642666--30642710 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
30642656 TTGCTTGTAC
30642666 TTAAGTACACTTT-GTT-GCATT
1 TTAAG-ACACTTTAGTTAGCATT
*
30642687 TTAAGACATTTTAGTTAGCATT
1 TTAAGACACTTTAGTTAGCATT
30642709 TT
1 TT
30642711 TGCATTAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 8 0.38
22 7 0.33
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.49
Consensus pattern (22 bp):
TTAAGACACTTTAGTTAGCATT
Found at i:30649230 original size:30 final size:29
Alignment explanation
Indices: 30649172--30649232 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
30649162 TGCTTTCTGA
* *
30649172 AATATTTACAAAAAAAGCATCTAATTTTT
1 AATATTTACAAAAAAAGCACCAAATTTTT
*
30649201 AATATTTACAAAAAGAGCAACCAAATTTTT
1 AATATTTACAAAAAAAGC-ACCAAATTTTT
30649231 AA
1 AA
30649233 AAATAATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.33
Consensus pattern (29 bp):
AATATTTACAAAAAAAGCACCAAATTTTT
Found at i:30657927 original size:27 final size:27
Alignment explanation
Indices: 30657897--30657958 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
30657887 CTGTCAGGAA
* * *
30657897 AGTAAACACGGGATAGTCCTCCA-AGAC
1 AGTAAACAAGGGATAATCCACCAGA-AC
30657924 AGTAAACAAGGGATAATCCACCAGAAC
1 AGTAAACAAGGGATAATCCACCAGAAC
30657951 AGTAAACA
1 AGTAAACA
30657959 TGGGGTACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.13
Consensus pattern (27 bp):
AGTAAACAAGGGATAATCCACCAGAAC
Found at i:30669477 original size:41 final size:41
Alignment explanation
Indices: 30669420--30669572 Score: 198
Period size: 41 Copynumber: 3.7 Consensus size: 41
30669410 TTCTATAAGT
*
30669420 TCAGGCTTTATGCCTAGCAGGCTTTATGCCCGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCCAGTGAATTATA
* *
30669461 TCAGGCTTTATGCCTAGCAGGCTCTGTGCCAGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCCAGTGAATTATA
** * * * *
30669502 TCAAACTTTATGTCTAGCAGGCTTTGTGCCAGTGAAATGTA
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCCAGTGAATTATA
* * *
30669543 TCGGGCTTTGTGCCTAGTAGGCTTTATGCC
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCC
30669573 GGTGTTTTAT
Statistics
Matches: 96, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (41 bp):
TCAGGCTTTATGCCTAGCAGGCTTTATGCCAGTGAATTATA
Found at i:30669596 original size:82 final size:83
Alignment explanation
Indices: 30669422--30669596 Score: 201
Period size: 82 Copynumber: 2.1 Consensus size: 83
30669412 CTATAAGTTC
* * * *
30669422 AGGCTTTATGCCTAGCAGGCTTTATGCCCGTGAATTATATCAGGCTTTATGCCTAGCAGGCTCTG
1 AGGCTTTATGTCTAGCAGGCTTTATGCCAGTGAAATATATCAGGCTTTATGCCTAGCAGGCTCTA
30669487 TGCCAGTGAATTATATCA
66 TGCCAGTGAATTATATCA
* * * * * * *
30669505 A-ACTTTATGTCTAGCAGGCTTTGTGCCAGTGAAATGTATCGGGCTTTGTGCCTAGTAGGCTTTA
1 AGGCTTTATGTCTAGCAGGCTTTATGCCAGTGAAATATATCAGGCTTTATGCCTAGCAGGCTCTA
* **
30669569 TGCCGGTGTTTTATA-CA
66 TGCCAGTGAATTATATCA
*
30669586 AGGCTCTATGT
1 AGGCTTTATGT
30669597 TCTATAAATC
Statistics
Matches: 75, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
81 3 0.04
82 71 0.95
83 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (83 bp):
AGGCTTTATGTCTAGCAGGCTTTATGCCAGTGAAATATATCAGGCTTTATGCCTAGCAGGCTCTA
TGCCAGTGAATTATATCA
Found at i:30670454 original size:22 final size:22
Alignment explanation
Indices: 30670397--30670661 Score: 102
Period size: 23 Copynumber: 11.5 Consensus size: 22
30670387 GCTGTTAAAT
* *
30670397 TTTGGTGTAAAAATGCTGCTCAA
1 TTTGGTGTATATATGCTGC-CAA
*** *
30670420 TTTGGTACGTATATGCTGCCCA
1 TTTGGTGTATATATGCTGCCAA
* **
30670442 TTTGTTGTATATATGCTGTAAAA
1 TTTGGTGTATATATGCTG-CCAA
* *
30670465 TTTTGGTGTAAAAATGCTGCTCAA
1 -TTTGGTGTATATATGCTGC-CAA
* * *
30670489 TTTGGTATGTATATGCTGCCCA
1 TTTGGTGTATATATGCTGCCAA
* **
30670511 TTTGTTGTATATATGCTGTTAAAA
1 TTTGGTGTATATATGCTG--CCAA
* **
30670535 TTTTGGTGTA-AAAGTGCTGTTAAA
1 -TTTGGTGTATATA-TGCTG-CCAA
* * *
30670559 TTTGGTATGTATATGCTGCCCA
1 TTTGGTGTATATATGCTGCCAA
* *
30670581 TTTGTTGT-TATTAAGCTGCCAAA
1 TTTGGTGTATA-TATGCTGCC-AA
* **
30670604 TTTTGGTGTATAAATGCTGTTTAA
1 -TTTGGTGTATATATGCTG-CCAA
* *
30670628 TTTGGTATATAAATGCTGTCCAA
1 TTTGGTGTATATATGCTG-CCAA
* *
30670651 ATTGATGTATA
1 TTTGGTGTATA
30670662 AGAGCTGTCC
Statistics
Matches: 176, Mismatches: 53, Indels: 26
0.69 0.21 0.10
Matches are distributed among these distances:
21 2 0.01
22 48 0.27
23 71 0.40
24 40 0.23
25 15 0.09
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.42
Consensus pattern (22 bp):
TTTGGTGTATATATGCTGCCAA
Found at i:30670566 original size:70 final size:69
Alignment explanation
Indices: 30670385--30670645 Score: 380
Period size: 69 Copynumber: 3.8 Consensus size: 69
30670375 TATTATGTAC
* *
30670385 ATGCTGTTAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTACGTATATGCTGCCCATTTGTTGT
1 ATGCTGTAAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTATGTATATGCTGCCCATTTGTTGT
30670450 ATAT
66 ATAT
30670454 ATGCTGTAAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTATGTATATGCTGCCCATTTGTTGT
1 ATGCTGTAAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTATGTATATGCTGCCCATTTGTTGT
30670519 ATAT
66 ATAT
* * *
30670523 ATGCTGTTAAAATTTTGGTGTAAAAGTGCTGTTAAATTTGGTATGTATATGCTGCCCATTTGTTG
1 ATGCTG-TAAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTATGTATATGCTGCCCATTTGTTG
30670588 T-TATT
65 TATA-T
* ** * * * * *
30670593 AAGCTGCCAAATTTTGGTGTATAAATGCTGTTTAATTTGGTATATAAATGCTG
1 ATGCTGTAAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTATGTATATGCTG
30670646 TCCAAATTGA
Statistics
Matches: 177, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
69 115 0.65
70 62 0.35
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.43
Consensus pattern (69 bp):
ATGCTGTAAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTATGTATATGCTGCCCATTTGTTGT
ATAT
Found at i:30670644 original size:139 final size:138
Alignment explanation
Indices: 30670385--30670645 Score: 389
Period size: 139 Copynumber: 1.9 Consensus size: 138
30670375 TATTATGTAC
*
30670385 ATGCTGTTAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTACGTATATGCTGCCCATTTGTTGT
1 ATGCTGTTAAATTTTGGTGTAAAAATGCTGCTAAATTTGGTACGTATATGCTGCCCATTTGTTGT
* * * *
30670450 ATATATGCTGTAAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTATGTATATGCTGCCCATTTG
66 ATATAAGCTGCAAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTATATAAATGCTGCCCATTTG
30670515 TTGTATAT
131 TTGTATAT
* * *
30670523 ATGCTGTTAAAATTTTGGTGTAAAAGTGCTGTTAAATTTGGTATGTATATGCTGCCCATTTGTTG
1 ATGCTGTT-AAATTTTGGTGTAAAAATGCTGCTAAATTTGGTACGTATATGCTGCCCATTTGTTG
* * * *
30670588 T-TATTAAGCTGCCAAATTTTGGTGTATAAATGCTGTTTAATTTGGTATATAAATGCTG
65 TATA-TAAGCTGCAAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTATATAAATGCTG
30670646 TCCAAATTGA
Statistics
Matches: 109, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
138 10 0.09
139 99 0.91
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.43
Consensus pattern (138 bp):
ATGCTGTTAAATTTTGGTGTAAAAATGCTGCTAAATTTGGTACGTATATGCTGCCCATTTGTTGT
ATATAAGCTGCAAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTATATAAATGCTGCCCATTTG
TTGTATAT
Found at i:30670661 original size:23 final size:23
Alignment explanation
Indices: 30670610--30670674 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
30670600 CAAATTTTGG
** * *
30670610 TGTATAAATGCTGTTTAATTTGG
1 TGTATAAATGCTGTCCAAATTGA
*
30670633 TATATAAATGCTGTCCAAATTGA
1 TGTATAAATGCTGTCCAAATTGA
30670656 TGTATAAGA-GCTGTCCAAA
1 TGTATAA-ATGCTGTCCAAA
30670675 CAAGGTAGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (23 bp):
TGTATAAATGCTGTCCAAATTGA
Found at i:30672783 original size:76 final size:77
Alignment explanation
Indices: 30672657--30672809 Score: 299
Period size: 76 Copynumber: 2.0 Consensus size: 77
30672647 GGTCAAAAAC
30672657 AATTAGGAATATGACAATCAACCTTTGTTTTATTTTACTAATTATTTCTTTATTAAATTACCAA-
1 AATTAGGAATATGACAATCAACCTTTGTTTTATTTTACTAATTATTTCTTTATTAAATTACCAAT
30672721 TTACCCTTCAAT
66 TTACCCTTCAAT
30672733 AATTAGGAATATGACAATCAACCTTTGTTTTATTTTACTAATTATTTCTTTATTAAATTACCAAT
1 AATTAGGAATATGACAATCAACCTTTGTTTTATTTTACTAATTATTTCTTTATTAAATTACCAAT
30672798 TTACCCTTCAAT
66 TTACCCTTCAAT
30672810 TATACATGTA
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 64 0.84
77 12 0.16
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (77 bp):
AATTAGGAATATGACAATCAACCTTTGTTTTATTTTACTAATTATTTCTTTATTAAATTACCAAT
TTACCCTTCAAT
Found at i:30679290 original size:24 final size:25
Alignment explanation
Indices: 30679261--30679332 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 25
30679251 AGTGAAAGAA
30679261 AAAGAAAAATAAGAAAATAGAAAGG
1 AAAGAAAAATAAGAAAATAGAAAGG
* *
30679286 -AAG-AAAATGAGGGAAAATA-ATAGG
1 AAAGAAAAAT-A-AGAAAATAGAAAGG
30679310 AAAGAAAAA-AAGAAAA-AGAAAGG
1 AAAGAAAAATAAGAAAATAGAAAGG
30679333 TACAGTAGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
22 1 0.03
23 14 0.37
24 9 0.24
25 10 0.26
26 4 0.11
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (25 bp):
AAAGAAAAATAAGAAAATAGAAAGG
Found at i:30683667 original size:377 final size:377
Alignment explanation
Indices: 30682973--30683727 Score: 1476
Period size: 377 Copynumber: 2.0 Consensus size: 377
30682963 AAGAGGGATT
*
30682973 TTTTTTTTTTTGGGGGGGGGGGGGGGGGGGGAGACGAAGGTTAAATACCCAAACAAGCTTGAAAT
1 TTTTTTTTTTTGGGGGGGGGGGGGGGGGGAGAGACGAAGGTTAAATACCCAAACAAGCTTGAAAT
30683038 TAAAGGCGTAGACAAAAAGATTCAGCATGATGCATAGGAAGAAATTCTTCAATAAGAAGTGATCA
66 TAAAGGCGTAGACAAAAAGATTCAGCATGATGCATAGGAAGAAATTCTTCAATAAGAAGTGATCA
30683103 ATTTTTGAAAGGGCTATCAGAGACCAGTAAATACAAATATGGCTTGGACCCCTTTGTTTAATGGC
131 ATTTTTGAAAGGGCTATCAGAGACCAGTAAATACAAATATGGCTTGGACCCCTTTGTTTAATGGC
30683168 TAGCTTTTGCTGCAAATTAAAGCATGGAAGCCATTTAAGGAGTCTTCTTTTTCTTTTTTGGGTAC
196 TAGCTTTTGCTGCAAATTAAAGCATGGAAGCCATTTAAGGAGTCTTCTTTTTCTTTTTTGGGTAC
30683233 TTTAAAAAGTCAAATTTTGAGTATGCTGAAGCTCAATGCATTTATTAAAGTACTAAATAACTAAG
261 TTTAAAAAGTCAAATTTTGAGTATGCTGAAGCTCAATGCATTTATTAAAGTACTAAATAACTAAG
30683298 CAATAAAAGTGATTCAGGAATTCAAGAATCCAATTAGAGGCTTTTGAAGCTA
326 CAATAAAAGTGATTCAGGAATTCAAGAATCCAATTAGAGGCTTTTGAAGCTA
*
30683350 TTTTTTTTTTTGGGGGGGGGTGTGGGGGGGAGAGACGAA-GTTAAATACCCAAACAAGCTTGAAA
1 TTTTTTTTTTTGGGGGGGGG-GGGGGGGGGAGAGACGAAGGTTAAATACCCAAACAAGCTTGAAA
30683414 TTAAAGGCGTAGACAAAAAGATTCAGCATGATGCATAGGAAGAAATTCTTCAATAAGAAGTGATC
65 TTAAAGGCGTAGACAAAAAGATTCAGCATGATGCATAGGAAGAAATTCTTCAATAAGAAGTGATC
30683479 AATTTTTGAAAGGGCTATCAGAGACCAGTAAATACAAATATGGCTTGGACCCCTTTGTTTAATGG
130 AATTTTTGAAAGGGCTATCAGAGACCAGTAAATACAAATATGGCTTGGACCCCTTTGTTTAATGG
30683544 CTAGCTTTTGCTGCAAATTAAAGCATGGAAGCCATTTAAGGAGTCTTCTTTTTCTTTTTTGGGTA
195 CTAGCTTTTGCTGCAAATTAAAGCATGGAAGCCATTTAAGGAGTCTTCTTTTTCTTTTTTGGGTA
30683609 CTTTAAAAAGTCAAATTTTGAGTATGCTGAAGCTCAATGCATTTATTAAAGTACTAAATAACTAA
260 CTTTAAAAAGTCAAATTTTGAGTATGCTGAAGCTCAATGCATTTATTAAAGTACTAAATAACTAA
30683674 GCAATAAAAGTGATTCAGGAATTCAAGAATCCAATTAGAGGCTTTTGAAGCTA
325 GCAATAAAAGTGATTCAGGAATTCAAGAATCCAATTAGAGGCTTTTGAAGCTA
30683727 T
1 T
30683728 GTATGACTGT
Statistics
Matches: 375, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
377 359 0.96
378 16 0.04
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (377 bp):
TTTTTTTTTTTGGGGGGGGGGGGGGGGGGAGAGACGAAGGTTAAATACCCAAACAAGCTTGAAAT
TAAAGGCGTAGACAAAAAGATTCAGCATGATGCATAGGAAGAAATTCTTCAATAAGAAGTGATCA
ATTTTTGAAAGGGCTATCAGAGACCAGTAAATACAAATATGGCTTGGACCCCTTTGTTTAATGGC
TAGCTTTTGCTGCAAATTAAAGCATGGAAGCCATTTAAGGAGTCTTCTTTTTCTTTTTTGGGTAC
TTTAAAAAGTCAAATTTTGAGTATGCTGAAGCTCAATGCATTTATTAAAGTACTAAATAACTAAG
CAATAAAAGTGATTCAGGAATTCAAGAATCCAATTAGAGGCTTTTGAAGCTA
Found at i:30689746 original size:220 final size:221
Alignment explanation
Indices: 30689364--30689804 Score: 875
Period size: 220 Copynumber: 2.0 Consensus size: 221
30689354 GTCCAAAATC
30689364 TAGTACAATGTATGGAATGATTCAGTGAGAGTGAAAATGATGGAGTTTTTATTTATTTTATAATA
1 TAGTACAATGTATGGAATGATTCAGTGAGAGTGAAAATGATGGAGTTTTTATTTATTTTATAATA
30689429 TTTTAGATTTTAGATTTTTATTAAGTATTAGATATATCATTGTCAGCCTGGATTATTAGCTAACT
66 TTTTAGATTTTAGATTTTTATTAAGTATTAGATATATCATTGTCAGCCTGGATTATTAGCTAACT
30689494 TTAGGGTTTAAAGGCAAGGAATAAAACTTTATTTGCAAGAAAGCCCAGTAACTTTACTTGAAGGA
131 TTAGGGTTTAAAGGCAAGGAATAAAACTTTATTTGCAAGAAAGCCCAGTAACTTTACTTGAAGGA
30689559 AAAGTCTAGTATAAA-AAGTTGTAAT
196 AAAGTCTAGTATAAATAAGTTGTAAT
30689584 TAGTACAATGTATGGAATGATTCAGTGAGAGTGAAAATGATGGAGTTTTTATTTATTTTATAATA
1 TAGTACAATGTATGGAATGATTCAGTGAGAGTGAAAATGATGGAGTTTTTATTTATTTTATAATA
30689649 TTTTAGATTTTAGATTTTTATTAAGTATTAGATATATCATTGTCAGCCTGGATTATTAGCTAACT
66 TTTTAGATTTTAGATTTTTATTAAGTATTAGATATATCATTGTCAGCCTGGATTATTAGCTAACT
30689714 TTAGGGTTTAAAGGCAAGGAATAAAACTTTATTTGCAAGAAAGCCCAGTAACTTTACTTGAAGGA
131 TTAGGGTTTAAAGGCAAGGAATAAAACTTTATTTGCAAGAAAGCCCAGTAACTTTACTTGAAGGA
30689779 AAAGTCTAGTATAAATAAGTTGTAAT
196 AAAGTCTAGTATAAATAAGTTGTAAT
30689805 GTATGCTTTA
Statistics
Matches: 220, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
220 210 0.95
221 10 0.05
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (221 bp):
TAGTACAATGTATGGAATGATTCAGTGAGAGTGAAAATGATGGAGTTTTTATTTATTTTATAATA
TTTTAGATTTTAGATTTTTATTAAGTATTAGATATATCATTGTCAGCCTGGATTATTAGCTAACT
TTAGGGTTTAAAGGCAAGGAATAAAACTTTATTTGCAAGAAAGCCCAGTAACTTTACTTGAAGGA
AAAGTCTAGTATAAATAAGTTGTAAT
Found at i:30689834 original size:47 final size:47
Alignment explanation
Indices: 30689780--30689872 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
30689770 CTTGAAGGAA
30689780 AAGTCTAGTATAAATAAGTTGTAATGTATGCTTTATAGCCAAAATTG
1 AAGTCTAGTATAAATAAGTTGTAATGTATGCTTTATAGCCAAAATTG
30689827 AAGTCTAGTATAAATAAGTTGTAATGTATGCTTTATAGCCAAAATT
1 AAGTCTAGTATAAATAAGTTGTAATGTATGCTTTATAGCCAAAATT
30689873 ATTATTCTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.37
Consensus pattern (47 bp):
AAGTCTAGTATAAATAAGTTGTAATGTATGCTTTATAGCCAAAATTG
Found at i:30695424 original size:140 final size:140
Alignment explanation
Indices: 30695167--30695453 Score: 443
Period size: 140 Copynumber: 2.1 Consensus size: 140
30695157 AAATAGAACA
*
30695167 TATTC-TTATTTTGCGATTGAAACCAATGATCCATTCACCATTTTGGTCTCTCAAAACTCCTCCT
1 TATTCATTATTTTGCGATTGAAACCAATGATCCATTCACCATTTTAGTCTCTCAAAACTCCTCCT
* * *
30695231 GCCGAAGCAGAACCTGTGTTGATTTTAACAGCTCCATCAAACCGTATGGTGATAAATTCTCTTCA
66 GCCGAAGCAGAACCTATGTTGATTTTAACAGCTCCATCAAACCGTATAGTGATAAAGTCTCTTCA
*
30695296 AATTTTAAGT
131 AAGTTTAAGT
* * * *
30695306 TATTCATTATTTTGTGATTGAACCCAATGATCTATTCACCATTTTAGTCTCTCAAAACTCCTCTT
1 TATTCATTATTTTGCGATTGAAACCAATGATCCATTCACCATTTTAGTCTCTCAAAACTCCTCCT
* * *
30695371 GCCGAAGCCGAACCTATGTTGATTTTAATAGCTCCA-CTAGACCGTATAGTGATAAAGTCTCTTC
66 GCCGAAGCAGAACCTATGTTGATTTTAACAGCTCCATC-AAACCGTATAGTGATAAAGTCTCTTC
30695435 AAAGTTTAAGT
130 AAAGTTTAAGT
30695446 TATTCATT
1 TATTCATT
30695454 TAGTTTGTAT
Statistics
Matches: 134, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
139 6 0.04
140 128 0.96
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (140 bp):
TATTCATTATTTTGCGATTGAAACCAATGATCCATTCACCATTTTAGTCTCTCAAAACTCCTCCT
GCCGAAGCAGAACCTATGTTGATTTTAACAGCTCCATCAAACCGTATAGTGATAAAGTCTCTTCA
AAGTTTAAGT
Found at i:30697957 original size:26 final size:24
Alignment explanation
Indices: 30697927--30697988 Score: 83
Period size: 23 Copynumber: 2.5 Consensus size: 24
30697917 GAGCTATGAT
30697927 CGGTAAGCTCAT-TCTGAGCTGAAGAA
1 CGGTAAGCTCATATC-GAGCT-AA-AA
30697953 CGGTAAGCTC-TATCGAGCTAAAA
1 CGGTAAGCTCATATCGAGCTAAAA
30697976 CGGTAAGCTCATA
1 CGGTAAGCTCATA
30697989 CAAGCTGTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
23 12 0.35
24 4 0.12
25 6 0.18
26 12 0.35
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (24 bp):
CGGTAAGCTCATATCGAGCTAAAA
Found at i:30697981 original size:23 final size:23
Alignment explanation
Indices: 30697909--30697985 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 23
30697899 ATTATCATTT
* * *
30697909 GCTCTTTCGAGCTATGATCGGTAA
1 GCTCTATCGAGCTA-AAACGGTAA
30697933 GCTC-ATTCTGAGCTGAAGAACGGTAA
1 GCTCTA-TC-GAGCT-AA-AACGGTAA
30697959 GCTCTATCGAGCTAAAACGGTAA
1 GCTCTATCGAGCTAAAACGGTAA
30697982 GCTC
1 GCTC
30697986 ATACAAGCTG
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
23 12 0.27
24 8 0.18
25 10 0.22
26 14 0.31
27 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (23 bp):
GCTCTATCGAGCTAAAACGGTAA
Found at i:30697994 original size:23 final size:25
Alignment explanation
Indices: 30697927--30697995 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 25
30697917 GAGCTATGAT
*
30697927 CGGTAAGCTCATTCTGAGCTGAAGAA
1 CGGTAAGCTCATAC-GAGCTGAAGAA
30697953 CGGTAAGCTC-TATCGAGCT-AA-AA
1 CGGTAAGCTCATA-CGAGCTGAAGAA
*
30697976 CGGTAAGCTCATACAAGCTG
1 CGGTAAGCTCATACGAGCTG
30697996 TGGTGAGTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
23 17 0.45
24 4 0.11
25 6 0.16
26 11 0.29
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (25 bp):
CGGTAAGCTCATACGAGCTGAAGAA
Found at i:30698529 original size:12 final size:12
Alignment explanation
Indices: 30698512--30698536 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30698502 CCACTAACAT
30698512 ATTAATGGTCTA
1 ATTAATGGTCTA
30698524 ATTAATGGTCTA
1 ATTAATGGTCTA
30698536 A
1 A
30698537 GTGTCATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATTAATGGTCTA
Found at i:30700216 original size:197 final size:197
Alignment explanation
Indices: 30699881--30700275 Score: 790
Period size: 197 Copynumber: 2.0 Consensus size: 197
30699871 ATCGTGATTC
30699881 TATCCCATTTCCACTCGGGAATTATAAACGGCTGCAGTAACCTAGACGGTACCTGATGCTCAGCT
1 TATCCCATTTCCACTCGGGAATTATAAACGGCTGCAGTAACCTAGACGGTACCTGATGCTCAGCT
30699946 TTGACTTGTTGATAGATTAAACATTTCGAAACAAATTCTGAAATATCACGTTTCATGCCATGCCA
66 TTGACTTGTTGATAGATTAAACATTTCGAAACAAATTCTGAAATATCACGTTTCATGCCATGCCA
30700011 CCAATAAAGTTGTTTCAAATCATTATACATTTTCGTGCTTCCTGGATGAATAGAGAAACGACTAC
131 CCAATAAAGTTGTTTCAAATCATTATACATTTTCGTGCTTCCTGGATGAATAGAGAAACGACTAC
30700076 TA
196 TA
30700078 TATCCCATTTCCACTCGGGAATTATAAACGGCTGCAGTAACCTAGACGGTACCTGATGCTCAGCT
1 TATCCCATTTCCACTCGGGAATTATAAACGGCTGCAGTAACCTAGACGGTACCTGATGCTCAGCT
30700143 TTGACTTGTTGATAGATTAAACATTTCGAAACAAATTCTGAAATATCACGTTTCATGCCATGCCA
66 TTGACTTGTTGATAGATTAAACATTTCGAAACAAATTCTGAAATATCACGTTTCATGCCATGCCA
30700208 CCAATAAAGTTGTTTCAAATCATTATACATTTTCGTGCTTCCTGGATGAATAGAGAAACGACTAC
131 CCAATAAAGTTGTTTCAAATCATTATACATTTTCGTGCTTCCTGGATGAATAGAGAAACGACTAC
30700273 TA
196 TA
30700275 T
1 T
30700276 GTGCGTCATT
Statistics
Matches: 198, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
197 198 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (197 bp):
TATCCCATTTCCACTCGGGAATTATAAACGGCTGCAGTAACCTAGACGGTACCTGATGCTCAGCT
TTGACTTGTTGATAGATTAAACATTTCGAAACAAATTCTGAAATATCACGTTTCATGCCATGCCA
CCAATAAAGTTGTTTCAAATCATTATACATTTTCGTGCTTCCTGGATGAATAGAGAAACGACTAC
TA
Found at i:30706116 original size:21 final size:22
Alignment explanation
Indices: 30706062--30706116 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 22
30706052 AATTATAGCT
*
30706062 TGATTAATTAA-AACTAACATA
1 TGATTAATTAACCACTAACATA
* *
30706083 TTATT-ATTAAACCACTAATA-A
1 TGATTAATT-AACCACTAACATA
30706104 TGATTAATTAACC
1 TGATTAATTAACC
30706117 TTAATTAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
20 3 0.11
21 15 0.56
22 9 0.33
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (22 bp):
TGATTAATTAACCACTAACATA
Found at i:30708207 original size:25 final size:26
Alignment explanation
Indices: 30708162--30708211 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
30708152 ATGTGAGTTA
*
30708162 ATAATGATAATATGCAAATTGATTAT
1 ATAATGATAATAAGCAAATTGATTAT
30708188 ATAATG-TAATAAG-AACATTGATTA
1 ATAATGATAATAAGCAA-ATTGATTA
30708212 CTGACCTACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 2 0.09
25 14 0.64
26 6 0.27
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.36
Consensus pattern (26 bp):
ATAATGATAATAAGCAAATTGATTAT
Found at i:30708628 original size:22 final size:22
Alignment explanation
Indices: 30708575--30708637 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
30708565 TGCGACACGT
*
30708575 CTCCTATGTTGCA-ACATAGCAA
1 CTCCTGTGTTG-AGACATAGCAA
*
30708597 C-CTTGTGTTGAGACATAGCAA
1 CTCCTGTGTTGAGACATAGCAA
*
30708618 CTCCTGTGTTGAGACGTAGC
1 CTCCTGTGTTGAGACATAGC
30708638 TTGAATGTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 17 0.49
22 17 0.49
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (22 bp):
CTCCTGTGTTGAGACATAGCAA
Found at i:30714315 original size:23 final size:23
Alignment explanation
Indices: 30714272--30714316 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
30714262 GATGACCATG
*
30714272 TTTTCATCATTTTACTTTTATTA
1 TTTTCATCATTTTACTCTTATTA
*
30714295 TTTTCATTATTTTAAC-CTTATT
1 TTTTCATCATTTT-ACTCTTATT
30714317 TTATTATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.22, C:0.13, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTCATCATTTTACTCTTATTA
Found at i:30716699 original size:22 final size:22
Alignment explanation
Indices: 30716674--30716720 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 22
30716664 GGCAATCTAT
30716674 CGGATTATTCGTCCCAATTTGG
1 CGGATTATTCGTCCCAATTTGG
30716696 CGG---ATTCGTCCCAATTTGG
1 CGGATTATTCGTCCCAATTTGG
*
30716715 CAGATT
1 CGGATT
30716721 CTTACCACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
19 18 0.86
22 3 0.14
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (22 bp):
CGGATTATTCGTCCCAATTTGG
Found at i:30716704 original size:19 final size:19
Alignment explanation
Indices: 30716680--30716721 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
30716670 CTATCGGATT
*
30716680 ATTCGTCCCAATTTGGCGG
1 ATTCGTCCCAATTTGGCAG
30716699 ATTCGTCCCAATTTGGCAG
1 ATTCGTCCCAATTTGGCAG
30716718 ATTC
1 ATTC
30716722 TTACCACGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.33
Consensus pattern (19 bp):
ATTCGTCCCAATTTGGCAG
Found at i:30718177 original size:19 final size:19
Alignment explanation
Indices: 30718153--30718214 Score: 106
Period size: 19 Copynumber: 3.3 Consensus size: 19
30718143 AATCTTCAAG
30718153 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* *
30718172 GATATGTAATCTTATATAT
1 GATATGCAATCTTAGATAT
30718191 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
30718210 GATAT
1 GATAT
30718215 TAGATATGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:30718219 original size:12 final size:12
Alignment explanation
Indices: 30718202--30718226 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30718192 ATATGCAATC
30718202 TTAGATATGATA
1 TTAGATATGATA
30718214 TTAGATATGATA
1 TTAGATATGATA
30718226 T
1 T
30718227 GCAATCTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (12 bp):
TTAGATATGATA
Found at i:30718242 original size:22 final size:23
Alignment explanation
Indices: 30718216--30718260 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
30718206 ATATGATATT
30718216 AGATATGA-TATGCAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
* *
30718238 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
30718261 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:30720584 original size:50 final size:50
Alignment explanation
Indices: 30720529--30720700 Score: 191
Period size: 50 Copynumber: 3.3 Consensus size: 50
30720519 TTCTCATGGT
** * *
30720529 ATGGTCTTACATGGGAGTTCTCATATCGGTGCCGATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATATCAGTGCCAATGCCATGTCCCAGAC
** * * *
30720579 ATGGTCTTACGGGGGACCTCTTATCTCAGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATATCAGTGCCAATGCCATGTCCCAGAC
* *
30720629 ATGGTCTTACGTGGGACCTCTCATAACCTCAATAATGCCAATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCAT-A--TC---AGTGCCAATGCCATGTCCCAGAC
30720685 ATGGTCTTACATGGGA
1 ATGGTCTTACATGGGA
30720701 TCTCATTCTC
Statistics
Matches: 101, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
50 63 0.62
53 2 0.02
56 36 0.36
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATATCAGTGCCAATGCCATGTCCCAGAC
Found at i:30721820 original size:47 final size:48
Alignment explanation
Indices: 30721766--30721860 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 48
30721756 AATTGAGTGC
30721766 CCAAACGTCGAAATTTTTGAACAAAATTTTCATGAAAT-ATTCCGTGA
1 CCAAACGTCGAAATTTTTGAACAAAATTTTCATGAAATCATTCCGTGA
30721813 CCAAACGTCGAAATTTTTGAACAAAATTTTCATGAAATCATTCCGTGA
1 CCAAACGTCGAAATTTTTGAACAAAATTTTCATGAAATCATTCCGTGA
30721861 AATTATAGAC
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 38 0.81
48 9 0.19
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.32
Consensus pattern (48 bp):
CCAAACGTCGAAATTTTTGAACAAAATTTTCATGAAATCATTCCGTGA
Found at i:30727962 original size:20 final size:20
Alignment explanation
Indices: 30727926--30727964 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
30727916 TTGCTTTTTC
*
30727926 TTTACTTACTCTTTTACTTG
1 TTTACTTACTCTCTTACTTG
30727946 TTTACTTACT-TGCTTACTT
1 TTTACTTACTCT-CTTACTT
30727965 AAATAACTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.15, C:0.21, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTACTTACTCTCTTACTTG
Found at i:30728284 original size:50 final size:50
Alignment explanation
Indices: 30728221--30728402 Score: 159
Period size: 50 Copynumber: 3.5 Consensus size: 50
30728211 GTACTACCAT
* * * ** *
30728221 TGCCATATCCCAGATATGGTCTTACATGCGAGTTCTCATATCGGTGCCCA
1 TGCCATGTCCCAGACATGGTCTTACAGGCGACCTCTCATATCGGTGCCAA
* * * *
30728271 TGCCATGTCCCAGACATGGTATTACGGGGGACCTCTCATCTCGGTGCCAA
1 TGCCATGTCCCAGACATGGTCTTACAGGCGACCTCTCATATCGGTGCCAA
* * ** *
30728321 CGCCATGTCCCAGACATGGTCTTAC-GTGGGACCTCTCATAACCTCAATAATTCCAA
1 TGCCATGTCCCAGACATGGTCTTACAG-GCGACCTCTCAT-A--TC---GGTGCCAA
30728377 TGCCATGTCCCAGACATGGTCTTACA
1 TGCCATGTCCCAGACATGGTCTTACA
30728403 TGGGATCTCA
Statistics
Matches: 107, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
49 1 0.01
50 75 0.70
53 2 0.02
56 29 0.27
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.26
Consensus pattern (50 bp):
TGCCATGTCCCAGACATGGTCTTACAGGCGACCTCTCATATCGGTGCCAA
Found at i:30732127 original size:4 final size:4
Alignment explanation
Indices: 30732118--30732155 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
30732108 TTTCTCCTCT
*
30732118 TTTC TTTC TTTC TGT- TTTC TTTC TTTC TTTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TT
30732156 ATTTAATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 2 0.07
4 24 0.80
5 4 0.13
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:30732137 original size:15 final size:13
Alignment explanation
Indices: 30732115--30732155 Score: 64
Period size: 13 Copynumber: 3.0 Consensus size: 13
30732105 GTCTTTCTCC
30732115 TCTTTTCTTTCTT
1 TCTTTTCTTTCTT
30732128 TCTGTTTTCTTTCTT
1 TC--TTTTCTTTCTT
30732143 TCTTTTCTTTCTT
1 TCTTTTCTTTCTT
30732156 ATTTAATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 13 0.50
15 13 0.50
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (13 bp):
TCTTTTCTTTCTT
Found at i:30738204 original size:17 final size:18
Alignment explanation
Indices: 30738182--30738225 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
30738172 TAAACAAGGT
30738182 AAATAAAAAAATTAA-GA
1 AAATAAAAAAATTAATGA
* *
30738199 AAATAACATAATTAATGA
1 AAATAAAAAAATTAATGA
*
30738217 ATATAAAAA
1 AAATAAAAA
30738226 TTTAGTACGC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAAAATTAATGA
Found at i:30748637 original size:14 final size:14
Alignment explanation
Indices: 30748618--30748645 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30748608 ATCCAATGAT
30748618 TGTGCGAAGCCTAA
1 TGTGCGAAGCCTAA
30748632 TGTGCGAAGCCTAA
1 TGTGCGAAGCCTAA
30748646 AGAAAAGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (14 bp):
TGTGCGAAGCCTAA
Found at i:30752969 original size:26 final size:26
Alignment explanation
Indices: 30752928--30753035 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
30752918 TTTAGAGTTC
* *
30752928 GCCATAAAGGCTTCCATTTCAGATAT
1 GCCAAAAAGGCTTCCATTTTAGATAT
* *
30752954 GCTACAAAGGCTTCCATTTTAGATAT
1 GCCAAAAAGGCTTCCATTTTAGATAT
30752980 GCCAAAAAGGCTTCCATTTTAGATAT
1 GCCAAAAAGGCTTCCATTTTAGATAT
*
30753006 GCCATAAAGGCTTCCATTTTAGATAT
1 GCCAAAAAGGCTTCCATTTTAGATAT
30753032 GCCA
1 GCCA
30753036 CTGATAGGGA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (26 bp):
GCCAAAAAGGCTTCCATTTTAGATAT
Found at i:30754419 original size:46 final size:46
Alignment explanation
Indices: 30754349--30754439 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
30754339 GCGACATTAA
* *
30754349 GATTTCCCTCGGGCTATTCGCCCAACGTAGGACCCGTCAATTTTGG
1 GATTTCCCTCGAGCTATTCACCCAACGTAGGACCCGTCAATTTTGG
*
30754395 GATTTCCTTCGAGCTATTCACCCAACGTAGGACCCGTCAATTTTG
1 GATTTCCCTCGAGCTATTCACCCAACGTAGGACCCGTCAATTTTG
30754440 AGTGTTACAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.30
Consensus pattern (46 bp):
GATTTCCCTCGAGCTATTCACCCAACGTAGGACCCGTCAATTTTGG
Found at i:30759331 original size:38 final size:37
Alignment explanation
Indices: 30759289--30759418 Score: 116
Period size: 38 Copynumber: 3.5 Consensus size: 37
30759279 CTTTGTTCGA
* * * * *
30759289 TTGAGCTTTATTTTAGTATATCTATAGATTTTACTCAT
1 TTGAGCTTCA-TTCAGTATAACAATAGAATTTACTCAT
* *
30759327 TTGAGCTCCATTCAGTATAACAATAGAATTTGCTCAT
1 TTGAGCTTCATTCAGTATAACAATAGAATTTACTCAT
* * * * *
30759364 TTGAGCTTCACATCAGTATAACAGTAAAATTTTCTCGT
1 TTGAGCTTCA-TTCAGTATAACAATAGAATTTACTCAT
* *
30759402 TTGAGCTACTTTCAGTA
1 TTGAGCTTCATTCAGTA
30759419 GAATCATTAG
Statistics
Matches: 75, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
37 37 0.49
38 38 0.51
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (37 bp):
TTGAGCTTCATTCAGTATAACAATAGAATTTACTCAT
Found at i:30759516 original size:40 final size:40
Alignment explanation
Indices: 30759411--30759663 Score: 269
Period size: 40 Copynumber: 6.3 Consensus size: 40
30759401 TTTGAGCTAC
* * *
30759411 TTTCAGTAGAATCATTAGGTATGGCTCGATAA-AACATAC-
1 TTTCAGTAGATTCAGTAGGTATGGCTCGA-AAGCACATACA
* * *
30759450 TTTCAGTAGAATCAGTAGGTAAGGCTCGACAGCACATACA
1 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCACATACA
* * * ** *
30759490 TTTTAGTGAGA-CCAGTAGGTATGGCTCAAAAGTGCATACG
1 TTTCAGT-AGATTCAGTAGGTATGGCTCGAAAGCACATACA
* **
30759530 TTTCAGTAGATTTAGTAGGTATGGCTCGAAAGCACATATG
1 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCACATACA
* * * * * *
30759570 CTTCAGTAGATTCAATAGATATCGCTCAAAAGCACATACC
1 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCACATACA
*
30759610 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCATATACA
1 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCACATACA
30759650 TTTCAGTAGATTCA
1 TTTCAGTAGATTCA
30759664 ATAGATATCT
Statistics
Matches: 176, Mismatches: 34, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
38 1 0.01
39 36 0.20
40 136 0.77
41 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (40 bp):
TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCACATACA
Found at i:30767789 original size:27 final size:27
Alignment explanation
Indices: 30767769--30768141 Score: 404
Period size: 27 Copynumber: 14.0 Consensus size: 27
30767759 GGGTATAACA
*
30767769 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
30767796 GTCATTTTTCCCTATG-GGGATATTTTG
1 GTCATTTTACCCTATGAGGG-TATTTCG
* **
30767823 GTCATTTTACCGTAT-AGGGGTATTTTA
1 GTCATTTTACCCTATGA-GGGTATTTCG
30767850 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
30767877 ATCATTCTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
30767904 GTTATTCTACCCTAT-AGGGGTATTTCA
1 GTCATTTTACCCTATGA-GGGTATTTCG
*
30767931 GTCATTCTACCCTAT-AGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
*
30767957 GTCATTTTACTCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
30767984 ATCATTTTACCCTAT-AGGGGTATTTCA
1 GTCATTTTACCCTATGA-GGGTATTTCG
*
30768011 GTCA-TTTA-CCTATCAGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
30768036 GTCATTTTATCCTATG-GGGTATTGCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
30768062 GTTATTTCACCCTATTGA-GGTAATTCG
1 GTCATTTTACCCTA-TGAGGGTATTTCG
*
30768089 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
30768116 ATCATTCTACCCTATGGGGGTATTTC
1 GTCATTTTACCCTATGAGGGTATTTC
30768142 AATCATAACA
Statistics
Matches: 297, Mismatches: 36, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
25 18 0.06
26 58 0.20
27 217 0.73
28 4 0.01
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTATGAGGGTATTTCG
Found at i:30773909 original size:68 final size:68
Alignment explanation
Indices: 30773783--30773968 Score: 176
Period size: 68 Copynumber: 2.7 Consensus size: 68
30773773 CAGAATCGAG
* * * * * * * *
30773783 AGTCCGCCAAGACATTAAACATGGGACCATATTGTGTCAGATCATCGCTCGACCATGGAAATATA
1 AGTCTGCCAGGACATTAAACATGAGATCATATTGTGTAAGACCATAGCTCGACCATGGAAACATA
**
30773848 TGG
66 TAA
* * * *
30773851 AGTTCT-CTAGGACATTAAACATGAGATCATATTGTGTAAGACCATAGCTTGGCTATGGAAACAT
1 AG-TCTGCCAGGACATTAAACATGAGATCATATTGTGTAAGACCATAGCTCGACCATGGAAACAT
30773915 ATAA
65 ATAA
** * * **
30773919 AGTCTGCCAGGACATTAAACACAAGATCATGTTATGTAAGATAATAGCTC
1 AGTCTGCCAGGACATTAAACATGAGATCATATTGTGTAAGACCATAGCTC
30773969 AGCTATGGCA
Statistics
Matches: 94, Mismatches: 22, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
67 3 0.03
68 89 0.95
69 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.26
Consensus pattern (68 bp):
AGTCTGCCAGGACATTAAACATGAGATCATATTGTGTAAGACCATAGCTCGACCATGGAAACATA
TAA
Found at i:30791988 original size:39 final size:39
Alignment explanation
Indices: 30791934--30792030 Score: 151
Period size: 39 Copynumber: 2.5 Consensus size: 39
30791924 TAAACATGTT
30791934 TTTGAGTATTGTGATATATGCTTGAATGTTATGTGATTA
1 TTTGAGTATTGTGATATATGCTTGAATGTTATGTGATTA
*
30791973 TTTGATTATTGTGATATATGCTTGAATGTTATGTGATTA
1 TTTGAGTATTGTGATATATGCTTGAATGTTATGTGATTA
* *
30792012 TATGTGTGA-TGTGATATAT
1 TTTGAGT-ATTGTGATATAT
30792031 ATTTAAACGT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
39 52 0.98
40 1 0.02
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.49
Consensus pattern (39 bp):
TTTGAGTATTGTGATATATGCTTGAATGTTATGTGATTA
Found at i:30792023 original size:22 final size:22
Alignment explanation
Indices: 30791943--30792015 Score: 86
Period size: 22 Copynumber: 3.5 Consensus size: 22
30791933 TTTTGAGTAT
30791943 TGTGATATATGCTTGAATGTTA
1 TGTGATATATGCTTGAATGTTA
30791965 TGTGAT-TAT--TTG-A--TTA
1 TGTGATATATGCTTGAATGTTA
30791981 TTGTGATATATGCTTGAATGTTA
1 -TGTGATATATGCTTGAATGTTA
30792004 TGTGATTATATG
1 TGTGA-TATATG
30792016 TGTGATGTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
16 3 0.07
17 6 0.14
18 4 0.09
19 3 0.07
20 3 0.07
21 4 0.09
22 11 0.26
23 9 0.21
ACGTcount: A:0.26, C:0.03, G:0.22, T:0.49
Consensus pattern (22 bp):
TGTGATATATGCTTGAATGTTA
Found at i:30797635 original size:15 final size:15
Alignment explanation
Indices: 30797615--30797645 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30797605 GTTATTTAAA
*
30797615 TGAAAGGTCAATAGT
1 TGAAAGGTCAAGAGT
30797630 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
30797645 T
1 T
30797646 ATGTTGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.29, T:0.26
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:30811181 original size:19 final size:18
Alignment explanation
Indices: 30811159--30811195 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
30811149 ATAAAACTTG
*
30811159 TCTACTTAAATAAGATTTA
1 TCTACCTAAATAA-ATTTA
30811178 TCTACCTAAATAAATTTA
1 TCTACCTAAATAAATTTA
30811196 AAATATATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.41
Consensus pattern (18 bp):
TCTACCTAAATAAATTTA
Found at i:30815815 original size:41 final size:42
Alignment explanation
Indices: 30815755--30815834 Score: 135
Period size: 41 Copynumber: 1.9 Consensus size: 42
30815745 CTAATTGGTA
*
30815755 AAATAATTTCCTTATTCTAATAAATTACTAAAACATAAAGGT
1 AAATAATTTCCTTATTCTAATAAACTACTAAAACATAAAGGT
*
30815797 AAATAATTT-CTTATTCTAATAAACTACTAAAAGATAAA
1 AAATAATTTCCTTATTCTAATAAACTACTAAAACATAAA
30815835 ATAAAACATT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 27 0.75
42 9 0.25
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.35
Consensus pattern (42 bp):
AAATAATTTCCTTATTCTAATAAACTACTAAAACATAAAGGT
Found at i:30815902 original size:18 final size:19
Alignment explanation
Indices: 30815856--30815903 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
30815846 CTAGAATATG
*
30815856 AATAAAACTTATCTACCTA
1 AATAAAATTTATCTACCTA
30815875 AATAAAATTTATCTACCTA
1 AATAAAATTTATCTACCTA
30815894 AAT-AAATTTA
1 AATAAAATTTA
30815904 AAATATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (19 bp):
AATAAAATTTATCTACCTA
Found at i:30817134 original size:112 final size:113
Alignment explanation
Indices: 30817012--30817239 Score: 449
Period size: 112 Copynumber: 2.0 Consensus size: 113
30817002 AGTAAACTCC
30817012 TATTCATGTCTTTTTACTTTAAAACCGAAATAAAAGAAAAAGTAATAAACTATTATGCACCTATT
1 TATTCATGTCTTTTTACTTTAAAACCGAAATAAAAGAAAAAGTAATAAACTATTATGCACCTATT
30817077 TATGGGAAAGAGGAGTTTTTTTTTTTTTTTTGAAGATA-TTTATTTTT
66 TATGGGAAAGAGGAGTTTTTTTTTTTTTTTTGAAGATATTTTATTTTT
30817124 TATTCATGTCTTTTTACTTTAAAACCGAAATAAAAGAAAAAGTAATAAACTATTATGCACCTATT
1 TATTCATGTCTTTTTACTTTAAAACCGAAATAAAAGAAAAAGTAATAAACTATTATGCACCTATT
30817189 TATGGGAAAGAGGAGTTTTTTTTTTTTTTTTGAAGATATTTTATTTTT
66 TATGGGAAAGAGGAGTTTTTTTTTTTTTTTTGAAGATATTTTATTTTT
30817237 TAT
1 TAT
30817240 AAAAGTTATT
Statistics
Matches: 115, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
112 103 0.90
113 12 0.10
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (113 bp):
TATTCATGTCTTTTTACTTTAAAACCGAAATAAAAGAAAAAGTAATAAACTATTATGCACCTATT
TATGGGAAAGAGGAGTTTTTTTTTTTTTTTTGAAGATATTTTATTTTT
Found at i:30823963 original size:14 final size:16
Alignment explanation
Indices: 30823935--30823969 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
30823925 TGTGCCTCGT
30823935 TAAAACCTTATTAGGA
1 TAAAACCTTATTAGGA
30823951 -AAAACCTTA-TAGGA
1 TAAAACCTTATTAGGA
30823965 TAAAA
1 TAAAA
30823970 GCCTAATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.26
Consensus pattern (16 bp):
TAAAACCTTATTAGGA
Found at i:30827193 original size:17 final size:17
Alignment explanation
Indices: 30827171--30827219 Score: 89
Period size: 17 Copynumber: 2.8 Consensus size: 17
30827161 TGAGTGTGGC
30827171 CGTGTGGGCCACACAGG
1 CGTGTGGGCCACACAGG
30827188 CGTGTGGGCCACACAGG
1 CGTGTGGGCCACACAGG
30827205 CGTGTGGGCCTACAC
1 CGTGTGGGCC-ACAC
30827220 GCCTACGGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 27 0.87
18 4 0.13
ACGTcount: A:0.16, C:0.31, G:0.39, T:0.14
Consensus pattern (17 bp):
CGTGTGGGCCACACAGG
Found at i:30831956 original size:24 final size:25
Alignment explanation
Indices: 30831929--30831991 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 25
30831919 TAATATATTG
30831929 TTAAT-TGTTAGAATAATTATAAGT
1 TTAATATGTTAGAATAATTATAAGT
* **
30831953 TTAATATGAT-GTTTAATTATAAGT
1 TTAATATGTTAGAATAATTATAAGT
30831977 TT-ATATGTTA-AATAA
1 TTAATATGTTAGAATAA
30831992 ATGTAGAACA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
23 9 0.29
24 19 0.61
25 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (25 bp):
TTAATATGTTAGAATAATTATAAGT
Found at i:30831957 original size:12 final size:12
Alignment explanation
Indices: 30831942--30831979 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
30831932 ATTGTTAGAA
30831942 TAATTATAAGTT
1 TAATTATAAGTT
*
30831954 TAA-TATGATGTT
1 TAATTAT-AAGTT
30831966 TAATTATAAGTT
1 TAATTATAAGTT
30831978 TA
1 TA
30831980 TATGTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.14
12 16 0.73
13 3 0.14
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (12 bp):
TAATTATAAGTT
Found at i:30833841 original size:37 final size:36
Alignment explanation
Indices: 30833747--30833878 Score: 113
Period size: 37 Copynumber: 3.6 Consensus size: 36
30833737 TAATCTTTAC
* * * * *
30833747 TCAGTATAACAGTAGAATTTTCTTGATTAATCATCAT
1 TCAGTATAACGGTA-AATTTGCTAGATTAAGCTTCAT
* *
30833784 TCAGTTTAACGGTAAGATTTGCTTAG-TTAAGCTTTAT
1 TCAGTATAACGGTAA-ATTTGC-TAGATTAAGCTTCAT
* * *
30833821 TCAGTATAACGATATAATTTGCTCGATTGAGCTTCAT
1 TCAGTATAACGGTA-AATTTGCTAGATTAAGCTTCAT
*
30833858 TTAGTATAACGGTAAAATTTG
1 TCAGTATAACGGT-AAATTTG
30833879 GCTCGATTGA
Statistics
Matches: 76, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
36 3 0.04
37 69 0.91
38 4 0.05
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (36 bp):
TCAGTATAACGGTAAATTTGCTAGATTAAGCTTCAT
Found at i:30833868 original size:74 final size:74
Alignment explanation
Indices: 30833736--30833878 Score: 171
Period size: 74 Copynumber: 1.9 Consensus size: 74
30833726 ATCTACTCGT
* * * * * *
30833736 TTAATCTTTACTCAGTATAACAGTAGAATTTTCTTGATTAATCATCATTCAGTTTAACGGTAAGA
1 TTAAGCTTTACTCAGTATAACAGTAGAATTTGCTCGATTAAGCATCATTCAGTATAACGGTAAAA
30833801 TTTGCTTAG
66 TTTGCTTAG
* * * * *
30833810 TTAAGCTTTATTCAGTATAAC-GATATAATTTGCTCGATTGAGCTTCATTTAGTATAACGGTAAA
1 TTAAGCTTTACTCAGTATAACAG-TAGAATTTGCTCGATTAAGCATCATTCAGTATAACGGTAAA
30833874 ATTTG
65 ATTTG
30833879 GCTCGATTGA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
73 1 0.02
74 56 0.98
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (74 bp):
TTAAGCTTTACTCAGTATAACAGTAGAATTTGCTCGATTAAGCATCATTCAGTATAACGGTAAAA
TTTGCTTAG
Found at i:30840835 original size:24 final size:25
Alignment explanation
Indices: 30840807--30840869 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 25
30840797 AGTTATGAAC
30840807 TGGGAAGCTCATACGAGCTGT-AAT
1 TGGGAAGCTCATACGAGCTGTAAAT
* *
30840831 TGGGAAGATTATACGAGCTGTAAAT
1 TGGGAAGCTCATACGAGCTGTAAAT
* *
30840856 CGGAAAGCTCATAC
1 TGGGAAGCTCATAC
30840870 AAACCGTGGT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 19 0.59
25 13 0.41
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (25 bp):
TGGGAAGCTCATACGAGCTGTAAAT
Found at i:30842531 original size:50 final size:50
Alignment explanation
Indices: 30842422--30842606 Score: 187
Period size: 50 Copynumber: 3.7 Consensus size: 50
30842412 GTAAAGAGGG
* * ***
30842422 CCCATGTAAGACCATGTCTGGGACATGGCATTGACACCGAGATGAGAGGT
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATGAGAACA
** * *
30842472 CCCCCGTAAGACCATGTCTGGGACATGGCATAGGCACCGATATGAGAACA
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATGAGAACA
* * * * * *
30842522 CTCATGTAAGACCATATCTAGGATATTGCATTGGCA--GTACAGGA-AACA
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-ACATGAGAACA
*
30842570 TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 -CCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
30842607 TGTTATTATC
Statistics
Matches: 109, Mismatches: 24, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
48 5 0.05
49 34 0.31
50 70 0.64
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (50 bp):
CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATGAGAACA
Found at i:30843587 original size:72 final size:73
Alignment explanation
Indices: 30843450--30843594 Score: 249
Period size: 72 Copynumber: 2.0 Consensus size: 73
30843440 AAAAAATTTG
*
30843450 CCTCACACAAATTTGGAAGAAAACAAAATACTTTCTTTTTTATTCCCCCCCCAATATGTAGAAAG
1 CCTCACACAAATTTGGAAGAAAACAAAATACTCTCTTTTTTATTCCCCCCCCAATATGTAGAAAG
30843515 CAAGCCTA
66 CAAGCCTA
*
30843523 CCTCACACAAATTTGGAAGAAAAC-AAATACTCTC-TTTTTATTCCCTCCCCCAATGTGTAGAAA
1 CCTCACACAAATTTGGAAGAAAACAAAATACTCTCTTTTTTATTCCC-CCCCCAATATGTAGAAA
30843586 GCAAGCCTA
65 GCAAGCCTA
30843595 TTTATAGGCA
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
71 11 0.16
72 34 0.49
73 24 0.35
ACGTcount: A:0.36, C:0.27, G:0.10, T:0.27
Consensus pattern (73 bp):
CCTCACACAAATTTGGAAGAAAACAAAATACTCTCTTTTTTATTCCCCCCCCAATATGTAGAAAG
CAAGCCTA
Found at i:30854081 original size:40 final size:41
Alignment explanation
Indices: 30854029--30854106 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 41
30854019 TTTTGAAAAC
* *
30854029 AAAGTCTTAGAACTTAAAAACAAGGTTTTGTC-AAAAACTT
1 AAAGTCTCAGAACTTAAAAACAAGGTTTTATCGAAAAACTT
*
30854069 AAAGTCTCAGAACTTGAAAACAAGGTTTTATCGAAAAA
1 AAAGTCTCAGAACTTAAAAACAAGGTTTTATCGAAAAA
30854107 TTTCTTTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 29 0.85
41 5 0.15
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (41 bp):
AAAGTCTCAGAACTTAAAAACAAGGTTTTATCGAAAAACTT
Found at i:30857062 original size:22 final size:22
Alignment explanation
Indices: 30857011--30857064 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
30857001 TTTAATTTGA
*
30857011 AGGATTTAGGATTTTAAGGTCT
1 AGGATTTAAGATTTTAAGGTCT
*
30857033 AGTG-TTTAAGATTTT-AGGATTT
1 AG-GATTTAAGATTTTAAGG-TCT
30857055 AGGATTTAAG
1 AGGATTTAAG
30857065 GTCCAGTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 4 0.15
22 22 0.81
23 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.43
Consensus pattern (22 bp):
AGGATTTAAGATTTTAAGGTCT
Found at i:30857094 original size:36 final size:37
Alignment explanation
Indices: 30857005--30857097 Score: 111
Period size: 36 Copynumber: 2.5 Consensus size: 37
30856995 TTAATGTTTA
*
30857005 ATTTGAAGGATTTAGGATTTTAAGGTCTAGTGTTTAAG
1 ATTTGAAGGATTTAGGA-TTTAAGGTCCAGTGTTTAAG
* *
30857043 ATTT-TAGGATTTAGGATTTAAGGTCCAGTGTTTACTG
1 ATTTGAAGGATTTAGGATTTAAGGTCCAGTGTTTA-AG
*
30857080 -TTTGAAGG-TCTAGGATTT
1 ATTTGAAGGATTTAGGATTT
30857098 CAATTGTTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
36 29 0.60
37 15 0.31
38 4 0.08
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.43
Consensus pattern (37 bp):
ATTTGAAGGATTTAGGATTTAAGGTCCAGTGTTTAAG
Found at i:30860895 original size:57 final size:57
Alignment explanation
Indices: 30860826--30860936 Score: 186
Period size: 57 Copynumber: 1.9 Consensus size: 57
30860816 CGTTTTATTT
* *
30860826 AAATTGTTCCCACAGAATCTCAGCCAAGGCTATCACAACCTACATTCAAAAGAACAG
1 AAATTGTTCCCACAGAACCTCAGCCAAGGCCATCACAACCTACATTCAAAAGAACAG
* *
30860883 AAATTGTTCCCACAGAACCTCAGTCAAGGCCATCATAACCTACATTCAAAAGAA
1 AAATTGTTCCCACAGAACCTCAGCCAAGGCCATCACAACCTACATTCAAAAGAA
30860937 TTGAAGTGTG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.20
Consensus pattern (57 bp):
AAATTGTTCCCACAGAACCTCAGCCAAGGCCATCACAACCTACATTCAAAAGAACAG
Found at i:30864728 original size:48 final size:48
Alignment explanation
Indices: 30864663--30864764 Score: 204
Period size: 48 Copynumber: 2.1 Consensus size: 48
30864653 AAGCTACCAC
30864663 TATTATGCTATTCTATGGAGCTTTTTTTTTTTGTTCATTATGCTATTA
1 TATTATGCTATTCTATGGAGCTTTTTTTTTTTGTTCATTATGCTATTA
30864711 TATTATGCTATTCTATGGAGCTTTTTTTTTTTGTTCATTATGCTATTA
1 TATTATGCTATTCTATGGAGCTTTTTTTTTTTGTTCATTATGCTATTA
30864759 TATTAT
1 TATTAT
30864765 CAGTCTTGTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.20, C:0.10, G:0.12, T:0.59
Consensus pattern (48 bp):
TATTATGCTATTCTATGGAGCTTTTTTTTTTTGTTCATTATGCTATTA
Found at i:30866021 original size:16 final size:16
Alignment explanation
Indices: 30865997--30866034 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
30865987 GGAAATTAGA
*
30865997 ATCACTTATTTTAATC
1 ATCAATTATTTTAATC
30866013 ATCAATTATTTTAATC
1 ATCAATTATTTTAATC
30866029 ATCAAT
1 ATCAAT
30866035 GTTTATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (16 bp):
ATCAATTATTTTAATC
Found at i:30866043 original size:16 final size:16
Alignment explanation
Indices: 30865997--30866043 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
30865987 GGAAATTAGA
* *
30865997 ATCACTTATTTTAATC
1 ATCAATTATTATAATC
*
30866013 ATCAATTATTTTAATC
1 ATCAATTATTATAATC
30866029 ATCAATGT-TTATAAT
1 ATCAAT-TATTATAAT
30866044 TTTTGTCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 27 0.96
17 1 0.04
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (16 bp):
ATCAATTATTATAATC
Found at i:30873057 original size:52 final size:54
Alignment explanation
Indices: 30872995--30873115 Score: 126
Period size: 52 Copynumber: 2.3 Consensus size: 54
30872985 TATGAAAGTG
* * * * * *
30872995 ATTATCTTAATATTAAA-TTAA-ATTTAATGTTTATCTTA-TGGATAAGTATTTT
1 ATTATTTTAATATTAAATTTAATATTAAAT-TTAATCTAACTGGATAAATATTAT
*
30873047 ATTATTTTAATA--AAATTTAATATTAAATTTAATCTAACTTGATAAATATTAT
1 ATTATTTTAATATTAAATTTAATATTAAATTTAATCTAACTGGATAAATATTAT
*
30873099 ATTAATTTAATATTAAA
1 ATTATTTTAATATTAAA
30873116 GTGATTAATT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
50 3 0.05
51 11 0.20
52 39 0.70
54 3 0.05
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (54 bp):
ATTATTTTAATATTAAATTTAATATTAAATTTAATCTAACTGGATAAATATTAT
Found at i:30873404 original size:30 final size:30
Alignment explanation
Indices: 30873368--30873428 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
30873358 GCCCACACTC
30873368 GGCAGACGTGAGCTTGAGGATAGCAGATAA
1 GGCAGACGTGAGCTTGAGGATAGCAGATAA
30873398 GGCAGACGTGAGCTTGAGGATAGCAGATAA
1 GGCAGACGTGAGCTTGAGGATAGCAGATAA
30873428 G
1 G
30873429 ACTACTCCGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.38, T:0.16
Consensus pattern (30 bp):
GGCAGACGTGAGCTTGAGGATAGCAGATAA
Done.