Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008709.1 Hibiscus syriacus cultivar Beakdansim tig00111758_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3030657
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 15
Found at i:357804 original size:43 final size:43
Alignment explanation
Indices: 357746--357865 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 43
357736 TGTCATCCAT
* *
357746 CGACCAGACCTCCTCATCATGTAGGAGCCGTGTCAACCTTAGA
1 CGACCAGAACTCCTCATCACGTAGGAGCCGTGTCAACCTTAGA
* * * * *
357789 TGACCAGATCTCCTCATTACATAGGAGCCGTGTCACCCTTAGA
1 CGACCAGAACTCCTCATCACGTAGGAGCCGTGTCAACCTTAGA
* * *
357832 CGACCAGAACTCTTCATCACGTATGAGCAGTGTC
1 CGACCAGAACTCCTCATCACGTAGGAGCCGTGTC
357866 GTCCCCAACA
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (43 bp):
CGACCAGAACTCCTCATCACGTAGGAGCCGTGTCAACCTTAGA
Found at i:366900 original size:6 final size:6
Alignment explanation
Indices: 366889--366924 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
366879 AATTCATTTT
*
366889 TCCATA TCCATA TCCATA TCCATA TCCATA TACATA
1 TCCATA TCCATA TCCATA TCCATA TCCATA TCCATA
366925 CGCATACAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (6 bp):
TCCATA
Found at i:368345 original size:2 final size:2
Alignment explanation
Indices: 368340--368378 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
368330 TTTTTTCTAA
368340 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
368379 ATTAGTTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:368799 original size:31 final size:30
Alignment explanation
Indices: 368763--368820 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
368753 ATAAAATCAT
* *
368763 TTAATATTTGATAAATACAATAATAAATGTA
1 TTAATATTAGACAAA-ACAATAATAAATGTA
*
368794 TTAATATTAGACAAAGCAATAATAAAT
1 TTAATATTAGACAAAACAATAATAAAT
368821 ACATTAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.34
Consensus pattern (30 bp):
TTAATATTAGACAAAACAATAATAAATGTA
Found at i:370923 original size:26 final size:26
Alignment explanation
Indices: 370876--370938 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 26
370866 AAAATGAAAT
** *
370876 AAAAATTAAACGTTATATATAATTAAA
1 AAAAATTAAAAATTATAAATAA-TAAA
370903 AAAAATTAAAAATT-TAAATAATAAA
1 AAAAATTAAAAATTATAAATAATAAA
*
370928 ACAAA-TAAAAA
1 AAAAATTAAAAA
370939 CTGATATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.25
26 6 0.19
27 12 0.38
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (26 bp):
AAAAATTAAAAATTATAAATAATAAA
Found at i:382364 original size:19 final size:19
Alignment explanation
Indices: 382342--382380 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
382332 ATACTTATAT
* *
382342 CTTACTGTCAGATTCATAG
1 CTTACTCTCAAATTCATAG
*
382361 CTTATTCTCAAATTCATAG
1 CTTACTCTCAAATTCATAG
382380 C
1 C
382381 CCAATGCATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.38
Consensus pattern (19 bp):
CTTACTCTCAAATTCATAG
Found at i:384864 original size:29 final size:29
Alignment explanation
Indices: 384812--384872 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
384802 AAAATTTATC
* *
384812 TAGTGACTAAATGTAAATTTTG-AAAGTT
1 TAGTGACTAAATATAAAATTTGAAAAGTT
*
384840 TAGTGGCTAAAGTATAAAATTTGAAAAGTT
1 TAGTGACTAAA-TATAAAATTTGAAAAGTT
384870 TAG
1 TAG
384873 GGATCGAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 10 0.36
29 9 0.32
30 9 0.32
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.36
Consensus pattern (29 bp):
TAGTGACTAAATATAAAATTTGAAAAGTT
Found at i:387084 original size:14 final size:14
Alignment explanation
Indices: 387055--387098 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
387045 CTACACAAGT
387055 ATGGTATTT-TTATG
1 ATGG-ATTTATTATG
*
387069 ATGGATTTATTCTG
1 ATGGATTTATTATG
387083 ATGGATTTATTATG
1 ATGGATTTATTATG
387097 AT
1 AT
387099 ACATCATCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 4 0.15
14 23 0.85
ACGTcount: A:0.25, C:0.02, G:0.20, T:0.52
Consensus pattern (14 bp):
ATGGATTTATTATG
Found at i:387217 original size:36 final size:35
Alignment explanation
Indices: 387170--387266 Score: 133
Period size: 36 Copynumber: 2.7 Consensus size: 35
387160 GTATTATAAG
387170 CTTTGATACATTCTTGTATCAATGTTATCATATCAA
1 CTTTGATACATT-TTGTATCAATGTTATCATATCAA
* *
387206 CTTTGGTACA-TTTGTATTTCAATGTTATCATATCAG
1 CTTTGATACATTTTGTA--TCAATGTTATCATATCAA
387242 CTTTGATACATTTGTGTATCAATGT
1 CTTTGATACATTT-TGTATCAATGT
387267 CTAACACCCC
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
34 5 0.09
35 1 0.02
36 42 0.78
37 2 0.04
38 4 0.07
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.46
Consensus pattern (35 bp):
CTTTGATACATTTTGTATCAATGTTATCATATCAA
Found at i:390074 original size:94 final size:95
Alignment explanation
Indices: 389944--390135 Score: 287
Period size: 94 Copynumber: 2.0 Consensus size: 95
389934 ATATTATATG
* * *
389944 TATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACACCCTGACATTATGGAGAAG
1 TATACAATAAAGCCTGAGCTATCCCTCTAAAGCAATTGGTTAAACACCCCGACATTATGGAGAAG
390009 ATTCAGCTAGCCTGATAAAGGTGATTATAA
66 ATTCAGCTAGCCTGATAAAGGTGATTATAA
* * ** * * *
390039 TATACAATAAAGCCTGAGTTAT-CCTCTAGAGCAATTGGTTAAATGCCCCGACTTTATGGATAAT
1 TATACAATAAAGCCTGAGCTATCCCTCTAAAGCAATTGGTTAAACACCCCGACATTATGGAGAAG
390103 ATTCAGCTAGCCTGATAAAGGTGATTATAA
66 ATTCAGCTAGCCTGATAAAGGTGATTATAA
390133 TAT
1 TAT
390136 CTATAGAATG
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
94 68 0.78
95 19 0.22
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (95 bp):
TATACAATAAAGCCTGAGCTATCCCTCTAAAGCAATTGGTTAAACACCCCGACATTATGGAGAAG
ATTCAGCTAGCCTGATAAAGGTGATTATAA
Found at i:390653 original size:19 final size:18
Alignment explanation
Indices: 390619--390654 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
390609 TCGAATAAGT
*
390619 TTGTTTTTTGTGTTTGTG
1 TTGTTTTTTATGTTTGTG
390637 TTGTTTGTTTATGTTTGT
1 TTGTTT-TTTATGTTTGT
390655 TTATTGTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.03, C:0.00, G:0.25, T:0.72
Consensus pattern (18 bp):
TTGTTTTTTATGTTTGTG
Found at i:392172 original size:83 final size:83
Alignment explanation
Indices: 392023--392808 Score: 963
Period size: 83 Copynumber: 9.5 Consensus size: 83
392013 GAACTATTGA
* * * *
392023 CAGCATAACTCAAGGCAAGAAGGGTTATCTATTAACAAAGACCTTCGAGTTCAATTACACTCAGC
1 CAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGC
*
392088 TCAAAGGCACATCATCTG
66 TCAAAGGCACATCATTTG
* * * * *
392106 CAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAGACCTTTGAGTTCGATTATACTTAGC
1 CAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGC
*
392171 TCAAAGACACATCATTTG
66 TCAAAGGCACATCATTTG
* * *
392189 CAGCATAGCTCAAGGCAAGAAGGGATATCTG-C--CAAAGAACTTCGAGTTCGATTACACTCAAC
1 CAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGC
*
392251 TTAAAGGCACATCATTTG
66 TCAAAGGCACATCATTTG
* * *
392269 CAGCATAGCTCAAGGCAAGAAGGGTTATCTG-C--CAAAGACCTTTGAGTTCGATTACATTCAAC
1 CAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGC
*
392331 TCAAAGGCACATCATTTA
66 TCAAAGGCACATCATTTG
* * * *
392349 CAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTTGATTCCACTCAGC
1 CAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGC
*
392414 TCAAAGGCACATCATTTA
66 TCAAAGGCACATCATTTG
* * ** * *
392432 CAGTATAACTCAAGGTTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTTGATTACACTTAGC
1 CAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGC
392497 TCAAAGGCACATCATTTG
66 TCAAAGGCACATCATTTG
* * * *
392515 TAGCATAGCTCAAGGCAAGAAGGGTTATCAGCCAACGAAAGACCTTCGAGTTCAATTACACTCAG
1 CAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAG
392580 CTCAAAGGCACATCATTTG
65 CTCAAAGGCACATCATTTG
* * * * * *
392599 CAGCATATCTTAAGGCTAGAAGGGCTATCTGCCAAAAAATGACCTTCGAGTTCGATTACACTCAG
1 CAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAACAAA-GACCTTCGAGTTCGATTACACTCAG
*
392664 CTCAAAGGCACATCCAATTTA
65 CTCAAAGGCACAT-C-ATTTG
* * * * * * * *
392685 CAACATAACTCAAGGCGAGAAGGGTTATCTATCATCAAAGACCTTCGAATTCAATTACATTCAGC
1 CAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGC
* * **
392750 TCAGAGGCAAATCAAATTAA
66 TCAAAGGCACATC--ATTTG
* * * *
392770 CAGGATAGCTCAAGGCAAAAAGGGCTAACTGTCAACAAA
1 CAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAACAAA
392809 ATTGTCGAGT
Statistics
Matches: 615, Mismatches: 80, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
80 144 0.23
81 1 0.00
82 1 0.00
83 255 0.41
84 111 0.18
85 69 0.11
86 34 0.06
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (83 bp):
CAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGC
TCAAAGGCACATCATTTG
Found at i:392259 original size:163 final size:164
Alignment explanation
Indices: 392022--392808 Score: 954
Period size: 163 Copynumber: 4.7 Consensus size: 164
392012 AGAACTATTG
**
392022 ACAGCATAACTCAAGGCAAGAAGGGTTATCTATTAACAAAGACCTTCGAGTTCAATTACACTCAG
1 ACAGCATAACTCAAGGCAAGAAGGGTTATC--TGCACAAAGACCTTCGAGTTCAATTACACTCAG
* *
392087 CTCAAAGGCACATCATCTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAGACCTTT
64 CTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAGACCTTC
* *
392152 GAGTTCGATTATACTTAGCTCAAAGACACATCATTT
129 GAGTTCGATTACACTTAGCTCAAAGGCACATCATTT
* * * * * *
392188 GCAGCATAGCTCAAGGCAAGAAGGGATATCTGC-CAAAGAACTTCGAGTTCGATTACACTCAACT
1 ACAGCATAACTCAAGGCAAGAAGGGTTATCTGCACAAAGACCTTCGAGTTCAATTACACTCAGCT
* * *
392252 TAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTG-C--CAAAGACCTTTGA
66 CAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAGACCTTCGA
*
392314 GTTCGATTACA-TTCAACTCAAAGGCACATCATTT
131 GTTCGATTACACTT-AGCTCAAAGGCACATCATTT
* ** *
392348 ACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTTGATTCCACTCAG
1 ACAGCATAACTCAAGGCAAGAAGGGTTATCTG-C-ACAAAGACCTTCGAGTTCAATTACACTCAG
* * * ** * *
392413 CTCAAAGGCACATCATTTACAGTATAACTCAAGGTTAGAAGGGTTATCTGTCAACAAAGACCTTC
64 CTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAGACCTTC
*
392478 GAGTTTGATTACACTTAGCTCAAAGGCACATCATTT
129 GAGTTCGATTACACTTAGCTCAAAGGCACATCATTT
** * *
392514 GTAGCATAGCTCAAGGCAAGAAGGGTTATCAGCCAACGAAAGACCTTCGAGTTCAATTACACTCA
1 ACAGCATAACTCAAGGCAAGAAGGGTTATCTG-C-AC-AAAGACCTTCGAGTTCAATTACACTCA
* * * *
392579 GCTCAAAGGCACATCATTTGCAGCATATCTTAAGGCTAGAAGGGCTATCTGCCAAAAAATGACCT
63 GCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAA-GACCT
*
392644 TCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTT
127 TCGAGTTCGATTACACTTAGCTCAAAGGCACAT-C-ATTT
* * * * *
392684 ACAACATAACTCAAGGCGAGAAGGGTTATCTATCATCAAAGACCTTCGAATTCAATTACATTCAG
1 ACAGCATAACTCAAGGCAAGAAGGGTTATCT-GCA-CAAAGACCTTCGAGTTCAATTACACTCAG
* * ** * * * *
392749 CTCAGAGGCAAATCAAATTAACAGGATAGCTCAAGGCAAAAAGGGCTAACTGTCAACAAA
64 CTCAAAGGCACATC--ATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAA
392809 ATTGTCGAGT
Statistics
Matches: 534, Mismatches: 71, Indels: 27
0.84 0.11 0.04
Matches are distributed among these distances:
159 2 0.00
160 69 0.13
161 1 0.00
162 1 0.00
163 142 0.27
164 2 0.00
166 99 0.19
167 77 0.14
168 36 0.07
169 40 0.07
170 31 0.06
171 34 0.06
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (164 bp):
ACAGCATAACTCAAGGCAAGAAGGGTTATCTGCACAAAGACCTTCGAGTTCAATTACACTCAGCT
CAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAGACCTTCGA
GTTCGATTACACTTAGCTCAAAGGCACATCATTT
Found at i:394557 original size:2 final size:2
Alignment explanation
Indices: 394552--394653 Score: 123
Period size: 2 Copynumber: 55.5 Consensus size: 2
394542 TATATGTTAT
*
394552 TA TA TA TA TA TA TA TA T- TA T- TA -A TG T- TA T- TA T- TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
394587 TA T- TA T- TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
394627 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
394654 CTTTATTAAA
Statistics
Matches: 89, Mismatches: 2, Indels: 18
0.82 0.02 0.17
Matches are distributed among these distances:
1 9 0.10
2 80 0.90
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (2 bp):
TA
Found at i:394932 original size:37 final size:36
Alignment explanation
Indices: 394886--394969 Score: 93
Period size: 37 Copynumber: 2.4 Consensus size: 36
394876 TTGGTGTATG
394886 TTTT-TTCTTTTTTAATTTTACTATGTTTT-TTATTT
1 TTTTATTCTTTTTTAATTTTACTAT-TTTTATTATTT
* ** *
394921 TATTTATTCTTTGTTCTTTTTATTATTTTTATTATTT
1 T-TTTATTCTTTTTTAATTTTACTATTTTTATTATTT
394958 TTTTATT-TTTTT
1 TTTTATTCTTTTT
394970 CGATTGACTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
35 5 0.12
36 13 0.32
37 23 0.56
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (36 bp):
TTTTATTCTTTTTTAATTTTACTATTTTTATTATTT
Found at i:394968 original size:9 final size:9
Alignment explanation
Indices: 394911--394969 Score: 57
Period size: 9 Copynumber: 6.6 Consensus size: 9
394901 TTTTACTATG
394911 TTTTTTATT
1 TTTTTTATT
*
394920 TTATTTATT
1 TTTTTTATT
* *
394929 CTTTGTTCTT
1 -TTTTTTATT
*
394939 TTTATTATT
1 TTTTTTATT
*
394948 TTTATTA-T
1 TTTTTTATT
394956 TTTTTTATT
1 TTTTTTATT
394965 TTTTT
1 TTTTT
394970 CGATTGACTT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
8 7 0.17
9 28 0.68
10 6 0.15
ACGTcount: A:0.14, C:0.03, G:0.02, T:0.81
Consensus pattern (9 bp):
TTTTTTATT
Found at i:394992 original size:35 final size:36
Alignment explanation
Indices: 394943--395021 Score: 101
Period size: 35 Copynumber: 2.2 Consensus size: 36
394933 GTTCTTTTTA
* *
394943 TTATTTTTATTATTTTTTTA-TT-TTTTTCGATTGACT
1 TTATTTTTAATATTTATTTATTTATTTTTC-ATT-ACT
394979 TT-TTTTTAATATTTATTTATTTATTTTTCATTACT
1 TTATTTTTAATATTTATTTATTTATTTTTCATTACT
395014 TTATTTTT
1 TTATTTTT
395022 TTATGTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
35 20 0.53
36 12 0.32
37 6 0.16
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (36 bp):
TTATTTTTAATATTTATTTATTTATTTTTCATTACT
Found at i:394995 original size:4 final size:4
Alignment explanation
Indices: 394988--395058 Score: 51
Period size: 4 Copynumber: 18.0 Consensus size: 4
394978 TTTTTTTTAA
* * *
394988 TATT TATT TATT TATT T-TT CA-T TACTT TATT TTTT TATGT T-TT TCTT
1 TATT TATT TATT TATT TATT TATT TA-TT TATT TATT TAT-T TATT TATT
*
395035 TAATT TATT TA-A TATT TATT TATT
1 T-ATT TATT TATT TATT TATT TATT
395059 ATTATTATCG
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
3 8 0.15
4 37 0.70
5 8 0.15
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (4 bp):
TATT
Found at i:395003 original size:59 final size:58
Alignment explanation
Indices: 394939--395064 Score: 143
Period size: 59 Copynumber: 2.2 Consensus size: 58
394929 CTTTGTTCTT
* * *
394939 TTTATTATTT-TTA-TTATTTTTTTATTTTTTTCGATTGACTTTTTTTTAATATTTATTTA
1 TTTATTATTTATTACTTATTTTTTTATGTTTTTC--TTGA-ATTTATTTAATATTTATTTA
*
394998 TTTATT-TTTCATTACTTTATTTTTTTATGTTTTTCTTTAATTTATTTAATATTTATTTA
1 TTTATTATTT-ATTAC-TTATTTTTTTATGTTTTTCTTGAATTTATTTAATATTTATTTA
395057 -TTATTATT
1 TTTATTATT
395065 ATCGTTGTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
58 8 0.14
59 26 0.45
60 6 0.10
62 18 0.31
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.72
Consensus pattern (58 bp):
TTTATTATTTATTACTTATTTTTTTATGTTTTTCTTGAATTTATTTAATATTTATTTA
Found at i:398380 original size:11 final size:10
Alignment explanation
Indices: 398337--398382 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
398327 GACCCTACCT
398337 GTTGACCGCC
1 GTTGACCGCC
**
398347 GTTGAATG-C
1 GTTGACCGCC
398356 GTTGACCGCC
1 GTTGACCGCC
398366 GTTGACCGACC
1 GTTGACCG-CC
398377 GTTGAC
1 GTTGAC
398383 TTTTTCCGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 7 0.23
10 15 0.50
11 8 0.27
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (10 bp):
GTTGACCGCC
Found at i:398703 original size:2 final size:2
Alignment explanation
Indices: 398696--398721 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
398686 AAATGCATGG
398696 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
398722 GATTGGTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:403120 original size:16 final size:17
Alignment explanation
Indices: 403099--403133 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
403089 GACATTTATT
*
403099 ATTATTTAATATA-AAA
1 ATTATTTAAAATATAAA
403115 ATTATTTAAAATATAAA
1 ATTATTTAAAATATAAA
403132 AT
1 AT
403134 AAAAACAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTATTTAAAATATAAA
Found at i:403536 original size:17 final size:18
Alignment explanation
Indices: 403506--403542 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
403496 AATATTATTT
403506 TATTATTTATTTTAA-AG
1 TATTATTTATTTTAATAG
403523 TATT-TTTATATTTAATAG
1 TATTATTTAT-TTTAATAG
403541 TA
1 TA
403543 ATAATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 9 0.50
18 4 0.22
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
TATTATTTATTTTAATAG
Found at i:403536 original size:51 final size:51
Alignment explanation
Indices: 403462--403571 Score: 159
Period size: 51 Copynumber: 2.2 Consensus size: 51
403452 TTGGCGGAGA
* *
403462 TTATTTT-AAGTCTTTTTAAATTTAATAATAATAAAATATTATTTTATTAT
1 TTATTTTAAAGTATTTTTAAATTTAATAATAATAAAATATTACTTTATTAT
* * *
403512 TTATTTTAAAGTATTTTTATATTTAATAGTAATAATATATTACTTTATTAT
1 TTATTTTAAAGTATTTTTAAATTTAATAATAATAAAATATTACTTTATTAT
403563 TTATGTTTA
1 TTAT-TTTA
403572 TATTTTATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
50 7 0.13
51 42 0.79
52 4 0.08
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (51 bp):
TTATTTTAAAGTATTTTTAAATTTAATAATAATAAAATATTACTTTATTAT
Found at i:404550 original size:62 final size:62
Alignment explanation
Indices: 404484--404610 Score: 150
Period size: 62 Copynumber: 2.0 Consensus size: 62
404474 AATTTATCTT
* * * *
404484 AAAAATAAATACCGTTCGGC-ATTTAT-GTGGTAACTATACAAATTACCATATTTGTCACCATA
1 AAAAACAAATACC-TTCAGCGATTTATAG-GGTAACTACACAAATTACCATATTCGTCACCATA
* * * *
404546 AAAAACAAATACCTTCAGCGGTTTATAGGGTAATTACATAAATTATCATATTCGTCACCATA
1 AAAAACAAATACCTTCAGCGATTTATAGGGTAACTACACAAATTACCATATTCGTCACCATA
404608 AAA
1 AAA
404611 GACTACTATC
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
61 5 0.09
62 49 0.89
63 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (62 bp):
AAAAACAAATACCTTCAGCGATTTATAGGGTAACTACACAAATTACCATATTCGTCACCATA
Found at i:404960 original size:26 final size:26
Alignment explanation
Indices: 404930--404985 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
404920 ATATTTTCAA
*
404930 ATTAAA-AATTATATATTTTAATTTAT
1 ATTAAATAATTATATATTCT-ATTTAT
* *
404956 ATTAAATAATTTTGTATTCTATTTAT
1 ATTAAATAATTATATATTCTATTTAT
404982 ATTA
1 ATTA
404986 GCTCAACCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (26 bp):
ATTAAATAATTATATATTCTATTTAT
Found at i:414037 original size:46 final size:46
Alignment explanation
Indices: 413985--414122 Score: 125
Period size: 46 Copynumber: 3.2 Consensus size: 46
413975 GTCTCCACAA
413985 AAGAGTAGTGGAACAGATTTTTCAGCAAAGTATGAAATCTTCACGG
1 AAGAGTAGTGGAACAGATTTTTCAGCAAAGTATGAAATCTTCACGG
*** * * *
414031 AAGAGTAGT-G-A-AG---TAAAAGC-AA--AT-AAGTCTCCACGA
1 AAGAGTAGTGGAACAGATTTTTCAGCAAAGTATGAAATCTTCACGG
* **
414067 AAGAGTAGTGGAACGGATTTTTCAATAAAGTATGAAATCTTCACGG
1 AAGAGTAGTGGAACAGATTTTTCAGCAAAGTATGAAATCTTCACGG
414113 AAGAGTAGTG
1 AAGAGTAGTG
414123 AAGTAAAAGT
Statistics
Matches: 67, Mismatches: 15, Indels: 20
0.66 0.15 0.20
Matches are distributed among these distances:
36 18 0.27
37 3 0.04
38 1 0.01
39 3 0.04
40 4 0.06
42 2 0.03
43 4 0.06
44 1 0.01
45 3 0.04
46 28 0.42
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.24
Consensus pattern (46 bp):
AAGAGTAGTGGAACAGATTTTTCAGCAAAGTATGAAATCTTCACGG
Found at i:414176 original size:165 final size:166
Alignment explanation
Indices: 413858--414211 Score: 473
Period size: 165 Copynumber: 2.1 Consensus size: 166
413848 CCAAATCAAA
* * * * *
413858 CTTCACGGAAGAGTAGTGAAG-CAAAGTAAAATTCGAGCTCTACGGAAGAGTAGTGGAATGGATT
1 CTTCACGGAAGAGTAGTGAAGTAAAAGTAAAATTCAAGCTCCACGAAAGAGTAGTGGAACGGATT
* *
413922 TTTCAGCAAAGTATGAAATCTTCAAGGAAGAGTAGTAAAGTAAAAGCAAATCAGTCTCCACAAAA
66 TTTCAACAAAGTATGAAATCTTCAAGGAAGAGTAGTAAAGTAAAAGCAAATCAGACTCCACAAAA
*
413987 GAGTAGTGGAACAGATTTTTCAGCAAAGTATGAAAT
131 GAGTAGTGAAACAGATTTTTCAGCAAAGTATGAAAT
*
414023 CTTCACGGAAGAGTAGTGAAGTAAAAG-CAAA-T-AAGTCTCCACGAAAGAGTAGTGGAACGGAT
1 CTTCACGGAAGAGTAGTGAAGTAAAAGTAAAATTCAAG-CTCCACGAAAGAGTAGTGGAACGGAT
* * * * ** * *
414085 TTTTCAATAAAGTATGAAATCTTCACGGAAGAGTAGTGAAGTAAAAGTAAATTTGAACTCCGCGA
65 TTTTCAACAAAGTATGAAATCTTCAAGGAAGAGTAGTAAAGTAAAAGCAAATCAG-ACTCCACAA
**
414150 AAGAGTAGTGAAATGGATTTTTCAGCAAAGTATGAAAT
129 AAGAGTAGTGAAACAGATTTTTCAGCAAAGTATGAAAT
**
414188 CTTCACATAAGAGTAGTGAAGTAA
1 CTTCACGGAAGAGTAGTGAAGTAA
414212 TCCAAGTTTG
Statistics
Matches: 165, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
163 2 0.01
164 72 0.44
165 87 0.53
166 4 0.02
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.24
Consensus pattern (166 bp):
CTTCACGGAAGAGTAGTGAAGTAAAAGTAAAATTCAAGCTCCACGAAAGAGTAGTGGAACGGATT
TTTCAACAAAGTATGAAATCTTCAAGGAAGAGTAGTAAAGTAAAAGCAAATCAGACTCCACAAAA
GAGTAGTGAAACAGATTTTTCAGCAAAGTATGAAAT
Found at i:414209 original size:83 final size:82
Alignment explanation
Indices: 413858--414211 Score: 444
Period size: 82 Copynumber: 4.3 Consensus size: 82
413848 CCAAATCAAA
* * * * * *
413858 CTTCACGGAAGAGTAGTGAAG-CAAAGTAAAATTCGAG-CTCTACGGAAGAGTAGTGGAATGGAT
1 CTTCACAGAAGAGTAGTGAAGTAAAAG-CAAATT--AGTCTCCACGAAAGAGTAGTGGAACGGAT
413921 TTTTCAGCAAAGTATGAAAT
63 TTTTCAGCAAAGTATGAAAT
* * * *
413941 CTTCA-AGGAAGAGTAGTAAAGTAAAAGCAAATCAGTCTCCACAAAAGAGTAGTGGAACAGATTT
1 CTTCACA-GAAGAGTAGTGAAGTAAAAGCAAATTAGTCTCCACGAAAGAGTAGTGGAACGGATTT
414005 TTCAGCAAAGTATGAAAT
65 TTCAGCAAAGTATGAAAT
* *
414023 CTTCACGGAAGAGTAGTGAAGTAAAAGCAAATAAGTCTCCACGAAAGAGTAGTGGAACGGATTTT
1 CTTCACAGAAGAGTAGTGAAGTAAAAGCAAATTAGTCTCCACGAAAGAGTAGTGGAACGGATTTT
**
414088 TCAATAAAGTATGAAAT
66 TCAGCAAAGTATGAAAT
* * * * * * *
414105 CTTCACGGAAGAGTAGTGAAGTAAAAGTAAATTTGAACTCCGCGAAAGAGTAGTGAAATGGATTT
1 CTTCACAGAAGAGTAGTGAAGTAAAAGCAAATTAG-TCTCCACGAAAGAGTAGTGGAACGGATTT
414170 TTCAGCAAAGTATGAAAT
65 TTCAGCAAAGTATGAAAT
*
414188 CTTCACATAAGAGTAGTGAAGTAA
1 CTTCACAGAAGAGTAGTGAAGTAA
414212 TCCAAGTTTG
Statistics
Matches: 238, Mismatches: 28, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
81 2 0.01
82 147 0.62
83 85 0.36
84 4 0.02
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.24
Consensus pattern (82 bp):
CTTCACAGAAGAGTAGTGAAGTAAAAGCAAATTAGTCTCCACGAAAGAGTAGTGGAACGGATTTT
TCAGCAAAGTATGAAAT
Found at i:414732 original size:10 final size:10
Alignment explanation
Indices: 414719--414744 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
414709 ATATGTTATT
414719 ATATATAATA
1 ATATATAATA
414729 ATATATAATA
1 ATATATAATA
414739 ATATAT
1 ATATAT
414745 TATTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
ATATATAATA
Found at i:417099 original size:24 final size:24
Alignment explanation
Indices: 417066--417112 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
417056 TTTATTAGTT
*
417066 TAATTTAATATATAAAATTATTAA
1 TAATTAAATATATAAAATTATTAA
* *
417090 TAATTAAATATGTAATATTATTA
1 TAATTAAATATATAAAATTATTA
417113 TATATACAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TAATTAAATATATAAAATTATTAA
Found at i:426791 original size:2 final size:2
Alignment explanation
Indices: 426784--426812 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
426774 ATTGAAATGA
426784 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
426813 AAAGAAACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:437306 original size:13 final size:13
Alignment explanation
Indices: 437279--437315 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
437269 AAGGATATAC
437279 AATCAAGGTGAGAA
1 AATCAAGG-GAGAA
*
437293 AGTCAAGGGAGAA
1 AATCAAGGGAGAA
437306 AATCAAGGGA
1 AATCAAGGGA
437316 TTTTCACGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.49, C:0.08, G:0.32, T:0.11
Consensus pattern (13 bp):
AATCAAGGGAGAA
Found at i:444751 original size:15 final size:15
Alignment explanation
Indices: 444731--444767 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
444721 CTATAAAAAA
*
444731 TTATTATTATTTTAT
1 TTATTATTATTATAT
444746 TTATTATTATTATAT
1 TTATTATTATTATAT
444761 TT-TTATT
1 TTATTATT
444768 TAAATCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTATTATTATTATAT
Found at i:444756 original size:21 final size:21
Alignment explanation
Indices: 444730--444769 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
444720 TCTATAAAAA
444730 ATTATTAT-TATTTTATTTATT
1 ATTATTATAT-TTTTATTTATT
444751 ATTATTATATTTTTATTTA
1 ATTATTATATTTTTATTTA
444770 AATCATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTATTATATTTTTATTTATT
Found at i:445087 original size:17 final size:17
Alignment explanation
Indices: 445061--445110 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
445051 CATCAGTCAC
445061 CAACACCAGCTCAGCCA
1 CAACACCAGCTCAGCCA
*
445078 CAATACCAGCTCAGCCA
1 CAACACCAGCTCAGCCA
* *
445095 TAACACTAGCTCAGCC
1 CAACACCAGCTCAGCC
445111 GCCGTCACTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.34, C:0.42, G:0.12, T:0.12
Consensus pattern (17 bp):
CAACACCAGCTCAGCCA
Found at i:449101 original size:2 final size:2
Alignment explanation
Indices: 449096--449132 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
449086 CAGAATATAT
449096 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
449133 ATAAGCTGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:450535 original size:36 final size:36
Alignment explanation
Indices: 450495--450640 Score: 152
Period size: 36 Copynumber: 4.0 Consensus size: 36
450485 TATTTAAAAA
* * *
450495 AAAAACAAAGTGTCGTCTTGCTAGAGACAATTT-TCT
1 AAAAACAAA-TTTCGTCTCGCTTGAGACAATTTCTCT
* * *
450531 AAAAATAAATTTTGCCTCGCTTGAGACAACTTTCTCT
1 AAAAACAAATTTCGTCTCGCTTGAGACAA-TTTCTCT
*
450568 AAAAACAAAATTT-GTCTCGCTTGAGATAATTTCTCT
1 AAAAAC-AAATTTCGTCTCGCTTGAGACAATTTCTCT
* * *
450604 CAAAATAAATTTCGTCTCGCTTGAGACATTTTTCTCT
1 AAAAACAAATTTCGTCTCGCTTGAGACA-ATTTCTCT
450641 GAGATACAAA
Statistics
Matches: 92, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
35 21 0.23
36 36 0.39
37 29 0.32
38 6 0.07
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (36 bp):
AAAAACAAATTTCGTCTCGCTTGAGACAATTTCTCT
Found at i:450569 original size:37 final size:36
Alignment explanation
Indices: 450509--450640 Score: 158
Period size: 37 Copynumber: 3.6 Consensus size: 36
450499 ACAAAGTGTC
* *
450509 GTCTTGCTAGAGACAATTT-TCTAAAAATAAATTTT
1 GTCTCGCTTGAGACAATTTCTCTAAAAATAAATTTT
* * *
450544 GCCTCGCTTGAGACAACTTTCTCTAAAAACAAAATTT
1 GTCTCGCTTGAGACAA-TTTCTCTAAAAATAAATTTT
* * *
450581 GTCTCGCTTGAGATAATTTCTCTCAAAATAAATTTC
1 GTCTCGCTTGAGACAATTTCTCTAAAAATAAATTTT
*
450617 GTCTCGCTTGAGACATTTTTCTCT
1 GTCTCGCTTGAGACA-ATTTCTCT
450641 GAGATACAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
35 13 0.16
36 33 0.41
37 35 0.43
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (36 bp):
GTCTCGCTTGAGACAATTTCTCTAAAAATAAATTTT
Found at i:450609 original size:73 final size:73
Alignment explanation
Indices: 450495--450640 Score: 186
Period size: 73 Copynumber: 2.0 Consensus size: 73
450485 TATTTAAAAA
* * *
450495 AAAAACAAAGTGTCGTCTTGCTAGAGACAATTTTCTAAAAATAAATTTTGCCTCGCTTGAGACAA
1 AAAAACAAAATGTCGTCTCGCTAGAGACAATTTTCTAAAAATAAATTTCGCCTCGCTTGAGACAA
450560 CTTTCTCT
66 CTTTCTCT
* * * * *
450568 AAAAACAAAAT-TTGTCTCGCTTGAGATAATTTCTCTCAAAATAAATTTCGTCTCGCTTGAGACA
1 AAAAACAAAATGTCGTCTCGCTAGAGACAATTT-TCTAAAAATAAATTTCGCCTCGCTTGAGACA
**
450632 TTTTTCTCT
65 ACTTTCTCT
450641 GAGATACAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
72 17 0.27
73 45 0.73
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (73 bp):
AAAAACAAAATGTCGTCTCGCTAGAGACAATTTTCTAAAAATAAATTTCGCCTCGCTTGAGACAA
CTTTCTCT
Found at i:450923 original size:69 final size:69
Alignment explanation
Indices: 450755--450944 Score: 188
Period size: 69 Copynumber: 2.8 Consensus size: 69
450745 TTCTGAAATT
* * * * * *
450755 GTTTCACTGGAAACAAATTTTATAATC-CTTGAAACCGTTTCTCATGAAACAACAACCCTCTTTG
1 GTTTCCCTTGAAACAAATCTTAT-CTCTCTTGAGACCGTTTCTCATGAAACAACAACCATCTTTG
450819 AGATC
65 AGATC
* * * * * *
450824 GTTTCTCTTGAAGCAAATCTTATTTTTCTTGAGACCTTTTCTCATGAAACAACAAATCATCTTTG
1 GTTTCCCTTGAAACAAATCTTATCTCTCTTGAGACCGTTTCTCATGAAACAAC-AACCATCTTTG
450889 AG-TC
65 AGATC
* * * *
450893 GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCT-ATTGAAACAA
1 GTTTCCCTTGAAACAAATCTTATCTCTCTTGAGACCGTTTCTCA-TGAAACAA
450945 TCATCTTTGA
Statistics
Matches: 99, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
68 2 0.02
69 86 0.87
70 11 0.11
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (69 bp):
GTTTCCCTTGAAACAAATCTTATCTCTCTTGAGACCGTTTCTCATGAAACAACAACCATCTTTGA
GATC
Found at i:451053 original size:38 final size:39
Alignment explanation
Indices: 451006--451079 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 39
450996 TTCTTGTGAA
*
451006 AAAACCTTTGCA-TCTGTTTCCCTTGAAA-AAAAACAAAC
1 AAAACCTTTG-AGTCTGTTACCCTTGAAACAAAAACAAAC
* *
451044 AAAATCTTTGAGTCTGTTACTCTTGAAACAAAAACA
1 AAAACCTTTGAGTCTGTTACCCTTGAAACAAAAACA
451080 TCTTTAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 1 0.03
38 23 0.74
39 7 0.23
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.28
Consensus pattern (39 bp):
AAAACCTTTGAGTCTGTTACCCTTGAAACAAAAACAAAC
Found at i:451102 original size:32 final size:33
Alignment explanation
Indices: 451036--451105 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 33
451026 CCTTGAAAAA
*
451036 AAACAAACAAAATCTTTGAGTCTGTTACTCTTG
1 AAACAAACAAAATCTTTAAGTCTGTTACTCTTG
* * * *
451069 AAACAAA-AACATCTTTAAGTTTGTTTCTTTTG
1 AAACAAACAAAATCTTTAAGTCTGTTACTCTTG
451101 AAACA
1 AAACA
451106 CTTAACTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 25 0.78
33 7 0.22
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.36
Consensus pattern (33 bp):
AAACAAACAAAATCTTTAAGTCTGTTACTCTTG
Found at i:451284 original size:41 final size:40
Alignment explanation
Indices: 451227--451369 Score: 142
Period size: 40 Copynumber: 3.5 Consensus size: 40
451217 TGACTTGTCG
* * *
451227 TCCTCATCGCATAGGAATCGTGTCATCCCCCCGACCAGACC
1 TCCTCATCACGTAGGAACCGTGTCAT-CCCCCGACCAGACC
* *
451268 TCCTCATCACGTAGGAACCGTGTCATCCCCTGGCCAGACC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACC
* * * ** * *
451308 TCCTCATCAAGTAGGAGCCGTGTCAACCCTAGATAACCAGTCG
1 TCCTCATCACGTAGGAACCGTGTCATCCCCCG---ACCAGACC
451351 TCCTCATCACGTAGGAACC
1 TCCTCATCACGTAGGAACC
451370 ATGTTATCAC
Statistics
Matches: 84, Mismatches: 15, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
40 39 0.46
41 23 0.27
43 22 0.26
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.20
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACC
Found at i:451669 original size:3 final size:3
Alignment explanation
Indices: 451661--451696 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
451651 CTACCAAAAA
451661 TAT TAT TAT TAT T-T TATT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
451697 GTTTTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:451718 original size:27 final size:28
Alignment explanation
Indices: 451660--451719 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
451650 TCTACCAAAA
* *
451660 ATATTATTATTATTTTATTTATTATTAT
1 ATATTATTATTATTTTATTTATAATCAT
451688 -TATTATTATGT-TTTTATTTA-AATCAT
1 ATATTATTAT-TATTTTATTTATAATCAT
451714 ATATTA
1 ATATTA
451720 CATTTTGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 4 0.14
27 23 0.82
28 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (28 bp):
ATATTATTATTATTTTATTTATAATCAT
Found at i:460680 original size:13 final size:13
Alignment explanation
Indices: 460662--460687 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
460652 AAATTACACG
460662 CATATATATATAT
1 CATATATATATAT
460675 CATATATATATAT
1 CATATATATATAT
460688 TAATATTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
CATATATATATAT
Found at i:469421 original size:20 final size:20
Alignment explanation
Indices: 469392--469429 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
469382 TTTCCACCAC
*
469392 ATGCAACTATATGCTCCTCA
1 ATGCAACTATATGATCCTCA
*
469412 ATGCATCTATATGATCCT
1 ATGCAACTATATGATCCT
469430 ATATGAGCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (20 bp):
ATGCAACTATATGATCCTCA
Found at i:471556 original size:18 final size:18
Alignment explanation
Indices: 471535--471569 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
471525 ATTCCTGACG
*
471535 TGGTAGAGATTTCTAATA
1 TGGTAGAGATTCCTAATA
471553 TGGTAGAGATTCCTAAT
1 TGGTAGAGATTCCTAAT
471570 GTGGAAGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.37
Consensus pattern (18 bp):
TGGTAGAGATTCCTAATA
Found at i:474404 original size:31 final size:31
Alignment explanation
Indices: 474366--474424 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
474356 AGAGTCGAGG
*
474366 GTTACCTATGTCCTTCGGGACATATGGACAA
1 GTTACCTATGTCCTTCGAGACATATGGACAA
*
474397 GTTACCTATGTTCTTCGAGACATATGGA
1 GTTACCTATGTCCTTCGAGACATATGGA
474425 TAGGTCCTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (31 bp):
GTTACCTATGTCCTTCGAGACATATGGACAA
Found at i:479146 original size:27 final size:27
Alignment explanation
Indices: 479108--479166 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
479098 ATATGAGAAT
*
479108 GTTATAGGAATTAATTAATAATAATAA
1 GTTATAGGAATTAAGTAATAATAATAA
479135 GTTATAGGAATTAAGTAATAATAATAA
1 GTTATAGGAATTAAGTAATAATAATAA
479162 GTTAT
1 GTTAT
479167 CATAATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (27 bp):
GTTATAGGAATTAAGTAATAATAATAA
Found at i:479515 original size:17 final size:16
Alignment explanation
Indices: 479490--479537 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
479480 TTATTCAAGT
*
479490 ATAACTTAAACAAATTA
1 ATAATTTAAA-AAATTA
*
479507 ATAATTTAAAATTGATTA
1 ATAATTTAAAA--AATTA
479525 ATAATTTAAAAAA
1 ATAATTTAAAAAA
479538 ATAAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 2 0.08
17 9 0.35
18 15 0.58
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (16 bp):
ATAATTTAAAAAATTA
Found at i:482058 original size:17 final size:17
Alignment explanation
Indices: 482036--482073 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
482026 TAGCTATGGT
*
482036 TTTCCTTC-TTACTTCTC
1 TTTCCTTCATT-CTTCTA
482053 TTTCCTTCATTCTTCTA
1 TTTCCTTCATTCTTCTA
482070 TTTC
1 TTTC
482074 ATTTCTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.08, C:0.32, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTCCTTCATTCTTCTA
Found at i:482660 original size:21 final size:21
Alignment explanation
Indices: 482627--482704 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
482617 TCTCTGTTTA
** *
482627 AAAGGATCAATCCCTCGGGAG
1 AAAGGATTGATCCCTCGAGAG
*
482648 AAAGGATTGATCCCT-TAGAG
1 AAAGGATTGATCCCTCGAGAG
* *
482668 AAAATGATTGATCCCTCGAAAG
1 -AAAGGATTGATCCCTCGAGAG
**
482690 AAATTATTGATCCCT
1 AAAGGATTGATCCCT
482705 TCTTTGTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
20 3 0.06
21 41 0.87
22 3 0.06
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (21 bp):
AAAGGATTGATCCCTCGAGAG
Found at i:485527 original size:64 final size:64
Alignment explanation
Indices: 485411--485615 Score: 179
Period size: 64 Copynumber: 3.2 Consensus size: 64
485401 ATTCAAGGTG
* * * * * *
485411 ATGCACCGATGCATCAAACCATGCATCGATGCACCTATGAT-TTAATT-GAACATCGAATGCATT
1 ATGCACCGATGC-GCAAGCAATGCATCGATGCACC-AGGATATT-TTTCAAACATCGAATGCATT
485474 TC
63 TC
**
485476 ATGCACCGA-G-GCACTCTAAATGCATCGATGCACTC-GGA-ATATTTTCAAACATCGAATGCAT
1 ATGCACCGATGCGCAAGC--AATGCATCGATGCAC-CAGGATAT-TTTTCAAACATCGAATGCAT
*
485537 TTG
62 TTC
* * * *
485540 AAGCATCGATGCGCAAGCAATGCATCGATGCACCAGGCTATTTTTCAAACATCGAATGCATTTT
1 ATGCACCGATGCGCAAGCAATGCATCGATGCACCAGGATATTTTTCAAACATCGAATGCATTTC
*
485604 ATGCATCGATGC
1 ATGCACCGATGC
485616 ATCCTTAGTG
Statistics
Matches: 115, Mismatches: 15, Indels: 21
0.76 0.10 0.14
Matches are distributed among these distances:
62 3 0.03
63 6 0.05
64 89 0.77
65 13 0.11
66 4 0.03
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (64 bp):
ATGCACCGATGCGCAAGCAATGCATCGATGCACCAGGATATTTTTCAAACATCGAATGCATTTC
Found at i:493017 original size:21 final size:21
Alignment explanation
Indices: 492975--493018 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
492965 ACCCCGGGAG
*
492975 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
492996 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
493017 CT
1 CT
493019 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:493675 original size:31 final size:31
Alignment explanation
Indices: 493604--493683 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
493594 ATTTAACAAA
* * **
493604 AAGGGGGAGAAAATTTAAGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
493635 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
*
493666 AAGGGGGAGTAAGATTTT
1 AAGGGGGAGTAAGTTTTT
493684 CAAAATCAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.33, C:0.03, G:0.35, T:0.30
Consensus pattern (31 bp):
AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
Found at i:494224 original size:64 final size:65
Alignment explanation
Indices: 494047--494204 Score: 205
Period size: 64 Copynumber: 2.5 Consensus size: 65
494037 GATTTAATTG
* * * *
494047 AACATCGAATGCATTTCATGCACCGATGCACTCTCAATGCATCGATGCA-CTCGGAATATTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTAAATGCATCGATGCACCTCGCAATATTTTCA
* ** *
494111 AACATCGAATGCATTTGATGCATCGATGCACAAGAAATGCATCGATGCACCAT-GCTAT-TTTTC
1 AACATCGAATGCATTTCATGCATCGATGCACACTAAATGCATCGATGCACC-TCGCAATATTTTC
494174 A
65 A
*
494175 AACATCGAATGCATTTTATGCATCGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCA
494205 TCCTTAGTGC
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
64 78 0.94
65 4 0.05
66 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTAAATGCATCGATGCACCTCGCAATATTTTCA
Found at i:498973 original size:45 final size:45
Alignment explanation
Indices: 498913--499022 Score: 114
Period size: 45 Copynumber: 2.5 Consensus size: 45
498903 ACGGACCTAG
* * * *
498913 CCTAAGGTA-TTGGGAGATGTCAATGCTATATGATCCAAACCTCG
1 CCTAAGATACTTGGGAGATGTCAATGCTATATAACCCAAACCTCA
* * * * * * *
498957 CCTGATATACTTGGGAGGTGTCGATGTTATGTAACCCATACCTCA
1 CCTAAGATACTTGGGAGATGTCAATGCTATATAACCCAAACCTCA
499002 CCTAAGATACTTGGGAGATGT
1 CCTAAGATACTTGGGAGATGT
499023 TGATGATGTG
Statistics
Matches: 51, Mismatches: 14, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
44 6 0.12
45 45 0.88
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (45 bp):
CCTAAGATACTTGGGAGATGTCAATGCTATATAACCCAAACCTCA
Found at i:501462 original size:23 final size:22
Alignment explanation
Indices: 501426--501494 Score: 86
Period size: 22 Copynumber: 3.0 Consensus size: 22
501416 AGAATTCGTC
501426 AAAAAATTACAATAATATAAACTA
1 AAAAAATTA-AATAATATAAA-TA
*
501450 AAAAAATTAAATATTATAAATA
1 AAAAAATTAAATAATATAAATA
*
501472 AATAAATTAAAATAA-ATAAATA
1 AAAAAATT-AAATAATATAAATA
501494 A
1 A
501495 GCATAGAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
22 17 0.41
23 15 0.37
24 9 0.22
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAAAATTAAATAATATAAATA
Found at i:501473 original size:22 final size:23
Alignment explanation
Indices: 501426--501491 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
501416 AGAATTCGTC
501426 AAAAAATTACAATAATATAAACTA
1 AAAAAATTA-AATAATATAAACTA
*
501450 AAAAAATTAAATATTATAAA-TA
1 AAAAAATTAAATAATATAAACTA
*
501472 AATAAATTAAAATAA-ATAAA
1 AAAAAATT-AAATAATATAAA
501492 TAAGCATAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 14 0.37
23 15 0.39
24 9 0.24
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAAAATTAAATAATATAAACTA
Found at i:501474 original size:18 final size:17
Alignment explanation
Indices: 501457--501493 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
501447 CTAAAAAAAT
501457 TAAATATTATAAATAAA
1 TAAATATTATAAATAAA
501474 T-AA-ATTA-AAATAAA
1 TAAATATTATAAATAAA
501488 TAAATA
1 TAAATA
501494 AGCATAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 5
0.78 0.00 0.22
Matches are distributed among these distances:
14 8 0.44
15 6 0.33
16 3 0.17
17 1 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAATATTATAAATAAA
Found at i:501492 original size:22 final size:22
Alignment explanation
Indices: 501429--501508 Score: 72
Period size: 22 Copynumber: 3.4 Consensus size: 22
501419 ATTCGTCAAA
* *
501429 AAATTACAATAATATAAACTAAAA
1 AAATTAAAATAA-ATAAA-TAAAT
*
501453 AAATT-AAATATTATAAATAAAT
1 AAATTAAAATA-AATAAATAAAT
501475 AAATTAAAATAAATAAATAAGCAT
1 AAATTAAAATAAATAAATAA--AT
501499 AGAATTAAAA
1 A-AATTAAAA
501509 AATTACATGT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
22 17 0.36
23 14 0.30
24 8 0.17
25 8 0.17
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.28
Consensus pattern (22 bp):
AAATTAAAATAAATAAATAAAT
Found at i:501944 original size:4 final size:4
Alignment explanation
Indices: 501935--502031 Score: 54
Period size: 4 Copynumber: 24.0 Consensus size: 4
501925 ATATCCCTTC
* ** * *
501935 AAAT AAAT AAAT AAAT AATT TCA- AAAT AAAT AAAT AAAT AATTTT GAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA--AT AAAT
* * * ** *
501984 AAAG AACT AAAT AAAT GAAAT AAGT TCA- AAAT AAAT AAAT CAAT AAAT
1 AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
502032 CAAAATTATT
Statistics
Matches: 66, Mismatches: 22, Indels: 10
0.67 0.22 0.10
Matches are distributed among these distances:
3 2 0.03
4 58 0.88
5 4 0.06
6 2 0.03
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:501963 original size:23 final size:23
Alignment explanation
Indices: 501935--501978 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
501925 ATATCCCTTC
501935 AAATAAATAAATAAATAATTTCA
1 AAATAAATAAATAAATAATTTCA
501958 AAATAAATAAATAAATAATTT
1 AAATAAATAAATAAATAATTT
501979 TGAATAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATAAATAAATAAATAATTTCA
Found at i:502045 original size:58 final size:53
Alignment explanation
Indices: 501937--502057 Score: 129
Period size: 58 Copynumber: 2.2 Consensus size: 53
501927 ATCCCTTCAA
* **
501937 ATAAATAAATAAATAATTTCAAAATAAATAAATAAATAATTTTGAATAAAGA-
1 ATAAATAAATAAATAAGTTCAAAATAAATAAATAAATAAAATTGAATAAAGAG
*
501989 ACTAAATAAATGAAATAAGTTCAAAATAAATAAATCAATAAATCAAAATT-ATTAAAGAG
1 A-TAAATAAAT-AAATAAGTTCAAAATAAAT--A--AATAAAT-AAAATTGAATAAAGAG
502048 ATAAATAAAT
1 ATAAATAAAT
502058 TAATCAAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
52 1 0.02
53 9 0.16
54 18 0.32
56 1 0.02
58 23 0.40
59 5 0.09
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (53 bp):
ATAAATAAATAAATAAGTTCAAAATAAATAAATAAATAAAATTGAATAAAGAG
Found at i:502063 original size:30 final size:30
Alignment explanation
Indices: 502018--502074 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
502008 TTCAAAATAA
* *
502018 ATAAATCAATAAATCAAAATTATTAAAGAG
1 ATAAATAAATAAATCAAAATAATTAAAGAG
*
502048 ATAAATAAATTAATCAAAATAATTAAA
1 ATAAATAAATAAATCAAAATAATTAAA
502075 AATTTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (30 bp):
ATAAATAAATAAATCAAAATAATTAAAGAG
Found at i:502520 original size:34 final size:37
Alignment explanation
Indices: 502476--502576 Score: 158
Period size: 34 Copynumber: 2.8 Consensus size: 37
502466 TTTCGTCCTA
502476 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
502511 -TAGGATTCAAACTCCT-AAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
502545 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
502577 GTTCTACTAT
Statistics
Matches: 60, Mismatches: 0, Indels: 9
0.87 0.00 0.13
Matches are distributed among these distances:
32 1 0.02
33 12 0.20
34 19 0.32
36 16 0.27
37 11 0.18
38 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:503177 original size:16 final size:18
Alignment explanation
Indices: 503156--503190 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
503146 TTTACTCATT
503156 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
503172 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
503190 T
1 T
503191 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:503186 original size:27 final size:27
Alignment explanation
Indices: 503139--503201 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
503129 TTTACTTTTT
* *
503139 TTTTTAT-TTTACTCATTTATTTATCTA
1 TTTTTATATTTACTCATATATTT-TATA
* *
503166 TTTTTATATTTA-TCCTATATTTTATG
1 TTTTTATATTTACTCATATATTTTATA
503192 TTTTTATATT
1 TTTTTATATT
503202 CTTTTACTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 12 0.39
27 15 0.48
28 4 0.13
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (27 bp):
TTTTTATATTTACTCATATATTTTATA
Found at i:504481 original size:19 final size:20
Alignment explanation
Indices: 504445--504482 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
504435 ACCTTGCTAA
*
504445 CTCTTTTCATTTTTTTTCCT
1 CTCTTTTCATTTTATTTCCT
504465 CTCTTTT-ATTTTATTTCC
1 CTCTTTTCATTTTATTTCC
504483 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (20 bp):
CTCTTTTCATTTTATTTCCT
Found at i:507890 original size:16 final size:16
Alignment explanation
Indices: 507864--507945 Score: 66
Period size: 16 Copynumber: 5.1 Consensus size: 16
507854 AGATCCAATC
507864 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
507879 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
*
507896 AA-AA-AAACAAAGAAA
1 AAGAACAAA-AAAGCAA
507911 AAGAGA-AACAAGAA-CAA
1 AAGA-ACAA-AA-AAGCAA
*
507928 AAGAAAAAAAAAGCAA
1 AAGAACAAAAAAGCAA
507944 AA
1 AA
507946 ATCAAAAAGA
Statistics
Matches: 56, Mismatches: 2, Indels: 17
0.75 0.03 0.23
Matches are distributed among these distances:
14 3 0.05
15 15 0.27
16 19 0.34
17 16 0.29
18 3 0.05
ACGTcount: A:0.78, C:0.09, G:0.13, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:507911 original size:22 final size:22
Alignment explanation
Indices: 507870--507936 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 22
507860 AATCAAGAAC
507870 AAAAAAGAAA-AGAAGCAAAAAAG
1 AAAAAAGAAACA-AAG-AAAAAAG
507893 CAAAAAA-AAACAAAGAAAAAGAG
1 -AAAAAAGAAACAAAGAAAAA-AG
*
507916 AAACAAG-AACAAAAGAAAAAA
1 AAAAAAGAAAC-AAAGAAAAAA
507937 AAAGCAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
22 14 0.37
23 17 0.45
24 7 0.18
ACGTcount: A:0.79, C:0.07, G:0.13, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAACAAAGAAAAAAG
Found at i:507930 original size:38 final size:37
Alignment explanation
Indices: 507871--507944 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
507861 ATCAAGAACA
*
507871 AAAAAGAAAAGAAGCAAAAAAGCAAAAAAAAA-CAAAG
1 AAAAAGAAAACAAGCAAAAAAG-AAAAAAAAAGCAAAG
507908 AAAAAGAGAAACAAG-AACAAAAGAAAAAAAAAGCAAA
1 AAAAAGA-AAACAAGCAA-AAAAGAAAAAAAAAGCAAA
507945 AATCAAAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
37 18 0.55
38 15 0.45
ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00
Consensus pattern (37 bp):
AAAAAGAAAACAAGCAAAAAAGAAAAAAAAAGCAAAG
Found at i:507937 original size:8 final size:8
Alignment explanation
Indices: 507870--507937 Score: 59
Period size: 8 Copynumber: 8.8 Consensus size: 8
507860 AATCAAGAAC
507870 AAAAAAGA
1 AAAAAAGA
* *
507878 AAAGAAGC
1 AAAAAAGA
*
507886 AAAAAAGC
1 AAAAAAGA
507894 AAAAAA-A
1 AAAAAAGA
*
507901 AACAAAGA
1 AAAAAAGA
*
507909 AAAAGAG-
1 AAAAAAGA
*
507916 AAACAAGA
1 AAAAAAGA
*
507924 ACAAAAGA
1 AAAAAAGA
507932 AAAAAA
1 AAAAAA
507938 AAGCAAAAAT
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
7 10 0.22
8 36 0.78
ACGTcount: A:0.79, C:0.07, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:509034 original size:18 final size:18
Alignment explanation
Indices: 509011--509046 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
509001 TCAACATCAA
* *
509011 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
509029 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
509047 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:509514 original size:36 final size:35
Alignment explanation
Indices: 509474--509795 Score: 221
Period size: 36 Copynumber: 9.1 Consensus size: 35
509464 ACTCATGATT
* * *
509474 GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACC
1 GTTTCTCTTAAAACAA-ATTTGTCTCTCTTGAGACA
* * * **
509510 GTTT-TCACTAGAAGAGTTTTGTCTCTCTTGAGACA
1 GTTTCTC-TTAAAACAAATTTGTCTCTCTTGAGACA
* *
509545 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAA-TTTGTCTCTCTTGAGACA
* * *
509581 ATTTCTCTTTAAACAAATTTCGTCTATCTTGAGACA
1 GTTTCTCTTAAAACAAATTT-GTCTCTCTTGAGACA
* * *
509617 GTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAA-TTTGTCTCTCTTGAGACA
* * * * *
509653 GTTTCCCTTGAAACAAA-----ATAT-TTGA-ATA
1 GTTTCTCTTAAAACAAATTTGTCTCTCTTGAGACA
* *
509681 TGTTT-TCTTTGAAACAAATTTCGTCTCCCTTGAGACA
1 -GTTTCTC-TTAAAACAAATTT-GTCTCTCTTGAGACA
* ** *
509718 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAAC-AA-ATTTGTCTCTCTTGAGACA
* *
509755 ATTTCTCTTAAAACAAATTTCGTCTATCTTGAGACA
1 GTTTCTCTTAAAACAAATTT-GTCTCTCTTGAGACA
509791 GTTTC
1 GTTTC
509796 CCTTGAAAGA
Statistics
Matches: 224, Mismatches: 43, Indels: 38
0.73 0.14 0.12
Matches are distributed among these distances:
28 3 0.01
29 18 0.08
30 2 0.01
35 33 0.15
36 133 0.59
37 32 0.14
38 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (35 bp):
GTTTCTCTTAAAACAAATTTGTCTCTCTTGAGACA
Found at i:509581 original size:21 final size:21
Alignment explanation
Indices: 509551--509648 Score: 58
Period size: 21 Copynumber: 5.2 Consensus size: 21
509541 GACAGTTTCC
509551 CTTGAAACAAATTTTGTCTCT
1 CTTGAAACAAATTTTGTCTCT
*
509572 CTTGAGAC-AA--TT-TCTCT
1 CTTGAAACAAATTTTGTCTCT
* *
509589 -TT-AAACAAATTTCGTCTAT
1 CTTGAAACAAATTTTGTCTCT
* *
509608 CTTGAGAC--A-GTT-TC-C-
1 CTTGAAACAAATTTTGTCTCT
*
509623 CTTGAAATAAATTTTGTCTCT
1 CTTGAAACAAATTTTGTCTCT
509644 CTTGA
1 CTTGA
509649 GACAGTTTCC
Statistics
Matches: 54, Mismatches: 11, Indels: 24
0.61 0.12 0.27
Matches are distributed among these distances:
15 9 0.17
16 4 0.07
17 8 0.15
18 6 0.11
19 7 0.13
20 5 0.09
21 15 0.28
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (21 bp):
CTTGAAACAAATTTTGTCTCT
Found at i:509628 original size:72 final size:71
Alignment explanation
Indices: 509527--509795 Score: 266
Period size: 72 Copynumber: 3.8 Consensus size: 71
509517 CTAGAAGAGT
* * *
509527 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTTA
1 TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTTA
509592 AACAAA
66 AACAAA
* * * *
509598 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTT
509663 AAACAAA
65 AAACAAA
* * * * *
509670 -----ATAT-TTGA-ATATGTTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCT-TTT
1 TTTGTCTATCTTGAGACA-GTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTT
* *
509727 GGAACTAAGT
65 -AAAC-AA-A
* * * * *
509737 TTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTCGTCTATCTTGAGACAGTTTC
1 TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTC
509796 CCTTGAAAGA
Statistics
Matches: 160, Mismatches: 26, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
64 4 0.03
65 43 0.27
66 5 0.03
71 3 0.02
72 65 0.41
73 38 0.24
74 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.41
Consensus pattern (71 bp):
TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTTA
AACAAA
Found at i:509799 original size:138 final size:137
Alignment explanation
Indices: 509546--509870 Score: 418
Period size: 138 Copynumber: 2.4 Consensus size: 137
509536 CTTGAGACAG
* *
509546 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTTAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTTAAACAAATTTCGTCTATCTT
* * * * *
509611 GAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAATTTCCCTTAAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTT
*
509676 GAATATG
131 GAATATA
* * * * * * *
509683 TTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCT-TTTGGAACTAAGTTTTGTCTCTC
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTT-AAAC-AAATTTCGTCTATC
* * *
509747 TTGAGACAATTTCTCTTAAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAAGAAAATCT
64 TTGAGACAATTTCCCTTAAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATAT
*
509812 TTGAATTTA
129 TTGAATATA
* * * *
509821 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTTAAACA
509871 CAAAATCTTC
Statistics
Matches: 158, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
136 3 0.02
137 40 0.25
138 113 0.72
139 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.40
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTTAAACAAATTTCGTCTATCTT
GAGACAATTTCCCTTAAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTT
GAATATA
Found at i:509866 original size:65 final size:67
Alignment explanation
Indices: 509763--509921 Score: 205
Period size: 65 Copynumber: 2.4 Consensus size: 67
509753 CAATTTCTCT
* ** * * **
509763 TAAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-AGAAAATCTTTGAATTTATTTCC
1 TAAAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACACAAAATCTTCAAATTTATTTCC
509826 CC
66 CC
*
509828 TAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCC
1 TAAAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACACAAAATCTTCAAATTTATTTCC
*
509893 CT
66 CC
*
509895 TAAAACATAATTTTGTTTCCCTTGAGA
1 TAAAACA-AATTTTGTCTCCCTTGAGA
509922 TCGTTTCTCA
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
65 33 0.41
66 2 0.02
67 28 0.35
68 18 0.22
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.37
Consensus pattern (67 bp):
TAAAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACACAAAATCTTCAAATTTATTTCC
CC
Found at i:509870 original size:174 final size:168
Alignment explanation
Indices: 509530--509836 Score: 397
Period size: 174 Copynumber: 1.8 Consensus size: 168
509520 GAAGAGTTTT
* *
509530 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTTAAAC
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTAAAAC
* *
509595 AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCC
66 AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAAGAAA-----TATCTCTTGAGACAGTTTCCC
* * * *
509660 TTGAAACAAAATATTTGAATATGTTTTCTTTGAAACAAATTTC
126 CTAAAACAAAATATTTGAACATGTTCTCTTTGAAACAAATTTC
** * *
509703 GTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAATTTCTCTTAAAA
1 GTCTCCCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAATTTCTCTTAAAA
*
509768 CAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAAGAAA-ATCT-TTGA-ATTTA-TTTCCCCT
65 CAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAAGAAATATCTCTTGAGA--CAGTTTCCCCT
509829 AAAACAAA
128 AAAACAAA
509837 TTTTGTCTCC
Statistics
Matches: 120, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
166 1 0.01
167 18 0.15
168 4 0.03
173 25 0.21
174 72 0.60
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (168 bp):
GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTAAAAC
AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAAGAAATATCTCTTGAGACAGTTTCCCCTAAA
ACAAAATATTTGAACATGTTCTCTTTGAAACAAATTTC
Found at i:510775 original size:105 final size:105
Alignment explanation
Indices: 510543--511203 Score: 963
Period size: 105 Copynumber: 6.3 Consensus size: 105
510533 ACCATCCGCG
* * * * * *
510543 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * * *
510608 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCTA
63 GGGACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
510652 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
510717 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
510757 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
510822 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCGGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
510862 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
510927 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
510967 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
511032 ACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* ** *
511067 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAATACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * ** *
511132 ACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* *
511173 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
511204 TGGAACAATG
Statistics
Matches: 512, Mismatches: 34, Indels: 15
0.91 0.06 0.03
Matches are distributed among these distances:
100 82 0.16
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 308 0.60
106 84 0.16
107 3 0.01
109 22 0.04
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
Found at i:511795 original size:34 final size:37
Alignment explanation
Indices: 511751--511852 Score: 167
Period size: 34 Copynumber: 2.8 Consensus size: 37
511741 TTTCATCCTA
511751 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
511786 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
511821 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
511853 GTTCTACTAT
Statistics
Matches: 62, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
33 1 0.02
34 29 0.47
35 3 0.05
37 28 0.45
38 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:512450 original size:16 final size:18
Alignment explanation
Indices: 512429--512463 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
512419 TTTACTCATT
512429 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
512445 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
512463 T
1 T
512464 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:517367 original size:12 final size:12
Alignment explanation
Indices: 517350--517376 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
517340 GCGACTTTAA
517350 TGCTATATCTTG
1 TGCTATATCTTG
517362 TGCTATATCTTG
1 TGCTATATCTTG
517374 TGC
1 TGC
517377 GGGTGATCGT
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:0.15, C:0.19, G:0.19, T:0.48
Consensus pattern (12 bp):
TGCTATATCTTG
Found at i:534309 original size:16 final size:16
Alignment explanation
Indices: 534288--534325 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
534278 TAAGAATTAA
534288 AGGGTTGCATATTTCT
1 AGGGTTGCATATTTCT
534304 AGGGTTGCATATTTCT
1 AGGGTTGCATATTTCT
534320 AGGGTT
1 AGGGTT
534326 TAGAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.42
Consensus pattern (16 bp):
AGGGTTGCATATTTCT
Found at i:534805 original size:30 final size:30
Alignment explanation
Indices: 534742--534807 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
534732 GTTAACATCG
**
534742 AGTGACCATTTTGAAACAAAAGACAACGTT
1 AGTGACCATTTTGAAACAAAAGACAACACT
* * * *
534772 AGTGATCATTTTGTAACAAACGACAATACT
1 AGTGACCATTTTGAAACAAAAGACAACACT
534802 AGTGAC
1 AGTGAC
534808 AGATTTATGA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.26
Consensus pattern (30 bp):
AGTGACCATTTTGAAACAAAAGACAACACT
Found at i:540159 original size:21 final size:20
Alignment explanation
Indices: 540073--540230 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
540063 AAATGACCAA
**
540073 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
540092 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
540112 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
540132 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
540153 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
540174 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
540194 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
540215 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
540231 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:540221 original size:20 final size:20
Alignment explanation
Indices: 540197--540506 Score: 352
Period size: 20 Copynumber: 15.5 Consensus size: 20
540187 CGATTTTCCA
* ** *
540197 AAATCGCAACGCGAATATGA
1 AAATCGCAACGAGAATCCGT
* *
540217 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGAGAATC-CGT
* *
540237 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* *
540257 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
540277 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
540297 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
540317 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
*
540337 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
540357 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
540377 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
540397 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
540417 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
540437 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
540457 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
540477 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
540497 AAATCACAAC
1 AAATCGCAAC
540507 ACTGAAATTT
Statistics
Matches: 256, Mismatches: 32, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
20 255 1.00
21 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGAGAATCCGT
Found at i:541215 original size:24 final size:24
Alignment explanation
Indices: 541188--541234 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
541178 GAAATTGGTC
541188 TTGGTCAATATC-CGGACTTTGATA
1 TTGGTCAATA-CACGGACTTTGATA
*
541212 TTGGTCAATACACGGATTTTGAT
1 TTGGTCAATACACGGACTTTGAT
541235 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATACACGGACTTTGATA
Found at i:543716 original size:33 final size:33
Alignment explanation
Indices: 543679--543806 Score: 107
Period size: 33 Copynumber: 3.7 Consensus size: 33
543669 GCAACGAGAG
543679 AATCGCAATGCGAAATGAAAATCCCAACATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACATGAA
*
543712 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAA
* * * * *
543751 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACATGAA
*
543784 AATCGCAATGCGAAATTAAAATC
1 AATCGCAATGCGAAATGAAAATC
543807 GCATTGCGAT
Statistics
Matches: 74, Mismatches: 12, Indels: 19
0.70 0.11 0.18
Matches are distributed among these distances:
32 6 0.08
33 27 0.36
34 15 0.20
36 1 0.01
38 2 0.03
39 22 0.30
40 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.16
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAA
Found at i:543742 original size:53 final size:52
Alignment explanation
Indices: 543679--543806 Score: 204
Period size: 53 Copynumber: 2.4 Consensus size: 52
543669 GCAACGAGAG
543679 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACGA-GAAAATCGCAATGC-GAAATGAA
* *
543732 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAAAATCGCAATGCGAAATGAA
*
543784 AATCGCAATGCGAAATTAAAATC
1 AATCGCAATGCGAAATGAAAATC
543807 GCATTGCGAT
Statistics
Matches: 71, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
52 30 0.42
53 40 0.56
54 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.16
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCCCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:543748 original size:19 final size:19
Alignment explanation
Indices: 543679--543815 Score: 159
Period size: 19 Copynumber: 7.7 Consensus size: 19
543669 GCAACGAGAG
543679 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
543698 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
543712 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
543732 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
543751 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
543765 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
543784 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
543803 AATCGCATTGCGA
1 AATCGCAATGCGA
543816 TTCTCCCGTT
Statistics
Matches: 101, Mismatches: 6, Indels: 22
0.78 0.05 0.17
Matches are distributed among these distances:
14 22 0.22
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 55 0.54
20 16 0.16
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:543864 original size:19 final size:19
Alignment explanation
Indices: 543824--543921 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
543814 GATTCTCCCG
543824 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
543844 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
543863 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
543877 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
543896 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
543915 TTGCGAT
1 TTGCGAT
543922 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:543918 original size:52 final size:53
Alignment explanation
Indices: 543805--543921 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
543795 GAAATTAAAA
543805 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
543858 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
543910 TCGCATTGCGAT
1 TCGCATTGCGAT
543922 AGTCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:544047 original size:14 final size:14
Alignment explanation
Indices: 544028--544064 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
544018 CATCAATTAC
544028 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
544042 ACAAATCATCTTTT
1 ACAAATCAACTTTT
544056 ACAAATCAA
1 ACAAATCAA
544065 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:546011 original size:20 final size:20
Alignment explanation
Indices: 545986--546051 Score: 91
Period size: 19 Copynumber: 3.4 Consensus size: 20
545976 TAGTTTACTT
* *
545986 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTCAAAA
546006 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCGAAACTCAAAA
*
546025 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACTCAAAA
546044 TCGCAACG
1 TCGCAACG
546052 ACAGAATCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.45, C:0.27, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:546061 original size:14 final size:14
Alignment explanation
Indices: 546042--546096 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
546032 GCGAAATGAA
*
546042 AATCGCAACGACAG
1 AATCGCAACGAAAG
546056 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
546073 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
546089 AATCGCAA
1 AATCGCAA
546097 TGCGATTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 16 0.46
16 5 0.14
17 6 0.17
19 8 0.23
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:546069 original size:33 final size:33
Alignment explanation
Indices: 546023--546101 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
546013 GCGAAACCAA
* *
546023 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
546056 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
546089 AATCGCAATGCGA
1 AATCGCAATGCGA
546102 TTTTGGTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAG
Found at i:546080 original size:19 final size:17
Alignment explanation
Indices: 546002--546090 Score: 78
Period size: 19 Copynumber: 5.1 Consensus size: 17
545992 CACGAAACTT
*
546002 AAAATCGCAACGCGAAACC
1 AAAATCGCAA-GCGAAA-G
546021 AAAATCGCAACGCGAAATG
1 AAAATCGCAA-GCGAAA-G
*
546040 AAAATCGCAA-CGACAG
1 AAAATCGCAAGCGAAAG
546056 --AATCGCAATGCGAAATG
1 AAAATCGCAA-GCGAAA-G
546073 AAAATCGCAA-CGAAAG
1 AAAATCGCAAGCGAAAG
546089 AA
1 AA
546091 TCGCAATGCG
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
14 8 0.13
16 8 0.13
17 10 0.16
19 35 0.57
ACGTcount: A:0.49, C:0.22, G:0.19, T:0.09
Consensus pattern (17 bp):
AAAATCGCAAGCGAAAG
Found at i:546119 original size:19 final size:19
Alignment explanation
Indices: 546097--546225 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
546087 AGAATCGCAA
546097 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
546116 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
*
546130 TGCGATTTTGGTTTCGTGT
1 TGCGATTTTGGTTTCGCGT
*
546149 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
546163 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
546182 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
546201 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
546221 TGCGA
1 TGCGA
546226 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 21 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 47 0.53
20 13 0.15
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:546139 original size:33 final size:33
Alignment explanation
Indices: 546097--546188 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
546087 AGAATCGCAA
546097 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
*
546130 TGCGATTTTGGTTTCGTGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
546163 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
546189 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 52 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:546389 original size:93 final size:93
Alignment explanation
Indices: 546273--546741 Score: 913
Period size: 93 Copynumber: 5.1 Consensus size: 93
546263 ATGGATTGCA
546273 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
546337 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
546365 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
546430 TAGCAGAATTGGTAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
546458 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
546523 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
546551 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
546616 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
546644 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
546709 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
546737 TTACT
1 TTACT
546742 AAGCAATCTA
Statistics
Matches: 373, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 369 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:548466 original size:14 final size:14
Alignment explanation
Indices: 548447--548536 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
548437 TTGAAATGAA
548447 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
548461 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
548480 AATCGCAACTAGAG
1 AATCGCAACGAGAG
*
548494 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
548513 AATCGCAACGAGAG
1 AATCGCAACGAGAG
548527 AATCGCAACG
1 AATCGCAACG
548537 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 30 0.50
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 20 0.33
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:548479 original size:33 final size:33
Alignment explanation
Indices: 548439--548553 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
548429 TCTTTTGGTT
548439 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
548472 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
548505 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
548538 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
548554 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:548485 original size:19 final size:19
Alignment explanation
Indices: 548461--548558 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
548451 GCAACGAGAG
548461 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
548480 AATCGCAA--C--TA-GAG
1 AATCGCAACGCGAAATGAA
548494 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
548513 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
548527 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
548546 AATCGCAATGCGA
1 AATCGCAACGCGA
548559 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 32 0.52
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:548589 original size:14 final size:14
Alignment explanation
Indices: 548570--548626 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
548560 TTTGGTTTCG
548570 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
548584 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
548603 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
548617 CGTTGCGATT
1 CGTTGCGATT
548627 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:548602 original size:33 final size:33
Alignment explanation
Indices: 548554--548634 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
548544 AAAATCGCAA
**
548554 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
548587 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
548620 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
548635 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:548637 original size:21 final size:21
Alignment explanation
Indices: 548611--548686 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
548601 CGCGTTGCGA
548611 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
548632 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
548652 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
548673 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
548687 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:548667 original size:41 final size:41
Alignment explanation
Indices: 548610--548687 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
548600 TCGCGTTGCG
*
548610 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
548651 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
548688 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:548808 original size:33 final size:33
Alignment explanation
Indices: 548766--548836 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
548756 AATACTAACT
*
548766 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
548799 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
548832 TGAAA
1 TGAAA
548837 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:549050 original size:25 final size:25
Alignment explanation
Indices: 549022--549075 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 25
549012 TGTGAGGGAT
549022 TTCGCCGGAGATGGGGACGGAA-ATC
1 TTCGCCGGAGATGGGGAC-GAATATC
*
549047 TT---CGGAGATGGGGACGAATTTC
1 TTCGCCGGAGATGGGGACGAATATC
549069 TTCGCCG
1 TTCGCCG
549076 TAGAGAGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
21 3 0.12
22 17 0.71
25 4 0.17
ACGTcount: A:0.20, C:0.20, G:0.37, T:0.22
Consensus pattern (25 bp):
TTCGCCGGAGATGGGGACGAATATC
Found at i:549244 original size:20 final size:20
Alignment explanation
Indices: 549219--549372 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
549209 CTTTAAATAT
549219 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
549239 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
549261 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
549280 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
549300 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
549320 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
549340 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
549360 CGCGTTGCGATTT
1 CGCGTTGCGATTT
549373 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:549346 original size:40 final size:40
Alignment explanation
Indices: 549218--549372 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
549208 GCTTTAAATA
*
549218 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
549259 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
549299 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
549339 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
549373 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:549389 original size:21 final size:21
Alignment explanation
Indices: 549359--549441 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
549349 ATTTTCATAT
*
549359 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
549380 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
549401 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
549422 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
549442 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:549432 original size:42 final size:43
Alignment explanation
Indices: 549339--549437 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
549329 ATTTATGTGT
* *
549339 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
549380 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
549422 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
549438 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:553163 original size:21 final size:21
Alignment explanation
Indices: 553137--553192 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
553127 TTCTGGATTG
553137 TGTGCATCGATGCATCTTCAA
1 TGTGCATCGATGCATCTTCAA
*
553158 TGTGCATCAATGCATCTTCAA
1 TGTGCATCGATGCATCTTCAA
* *
553179 TGTGTAGCGATGCA
1 TGTGCATCGATGCA
553193 CTCTCAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (21 bp):
TGTGCATCGATGCATCTTCAA
Found at i:554115 original size:18 final size:18
Alignment explanation
Indices: 554092--554126 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
554082 GTTCTTAATG
554092 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
* *
554110 AGTGGTCCTTGGGGACA
1 AGTGGTCATTCGGGACA
554127 AATATATAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.17, G:0.37, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:557299 original size:21 final size:21
Alignment explanation
Indices: 557275--557323 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
557265 TAAAAGATGG
557275 AAAGTTTAGGGACTTAAATGA
1 AAAGTTTAGGGACTTAAATGA
*
557296 AAAGTTTAGGGTCTTAAATGA
1 AAAGTTTAGGGACTTAAATGA
557317 AAAGTTT
1 AAAGTTT
557324 TGATGATGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (21 bp):
AAAGTTTAGGGACTTAAATGA
Done.