Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007973.1 Hibiscus syriacus cultivar Beakdansim tig00110410_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: 1299094
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:201811 original size:36 final size:36
Alignment explanation
Indices: 201770--201888 Score: 105
Period size: 36 Copynumber: 3.2 Consensus size: 36
201760 TTACATTTCA
*
201770 ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAAAAAGCACAAATAAGAATTATTTACAC
* *** * *
201806 ATCAATTAAACAAATCAACTTTTACA-AATCAACTTTTACAA
1 ATCAATTAAA-AAAGC-ACAAATA-AGAAT-TA--TTTACAC
*
201847 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAAAAAGCACAAATAAGAATTATTTACAC
201883 ATCAAT
1 ATCAAT
201889 ATTAAACAAA
Statistics
Matches: 62, Mismatches: 14, Indels: 14
0.69 0.16 0.16
Matches are distributed among these distances:
36 22 0.35
37 3 0.05
38 9 0.15
39 9 0.15
40 3 0.05
41 16 0.26
ACGTcount: A:0.51, C:0.17, G:0.03, T:0.29
Consensus pattern (36 bp):
ATCAATTAAAAAAGCACAAATAAGAATTATTTACAC
Found at i:201834 original size:14 final size:14
Alignment explanation
Indices: 201815--201851 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
201805 CATCAATTAA
201815 ACAAATCAACTTTT
1 ACAAATCAACTTTT
201829 ACAAATCAACTTTT
1 ACAAATCAACTTTT
201843 ACAAATCAA
1 ACAAATCAA
201852 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:201868 original size:77 final size:79
Alignment explanation
Indices: 201748--201941 Score: 320
Period size: 79 Copynumber: 2.4 Consensus size: 79
201738 ATTGAAATCA
*
201748 ACAAATCAACTTTTACATTTCAATCAATTAAATAAGCACAAATAAGAATTATTTACACATC-A-A
1 ACAAATCAACTTTTACA----AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATA
201811 TTAAACAAATCAACTTTT
62 TTAAACAAATCAACTTTT
201829 ACAAATCAACTTTTACAAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATATTAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATATTAA
201894 ACAAATCAACTTTT
66 ACAAATCAACTTTT
*
201908 ACAAATCAATTTTTACAAATCAATTAAACAAGCA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCA
201942 AAAAATGCTA
Statistics
Matches: 109, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
77 39 0.36
78 1 0.01
79 52 0.48
81 17 0.16
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.30
Consensus pattern (79 bp):
ACAAATCAACTTTTACAAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATATTAA
ACAAATCAACTTTT
Found at i:201910 original size:29 final size:28
Alignment explanation
Indices: 201876--201930 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
201866 ATAAGAATTA
*
201876 TTTACACATCAATATTAAACAAATCAACT
1 TTTACAAATCAAT-TTAAACAAATCAACT
**
201905 TTTACAAATCAATTTTTACAAATCAA
1 TTTACAAATCAATTTAAACAAATCAA
201931 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (28 bp):
TTTACAAATCAATTTAAACAAATCAACT
Found at i:201931 original size:14 final size:14
Alignment explanation
Indices: 201871--201932 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
201861 CACAAATAAG
*
201871 AATTATTTACACATC
1 AATT-TTTACAAATC
**
201886 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
201901 AACTTTTACAAATC
1 AATTTTTACAAATC
201915 AATTTTTACAAATC
1 AATTTTTACAAATC
201929 AATT
1 AATT
201933 AAACAAGCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 26 0.67
15 12 0.31
16 1 0.03
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:203375 original size:42 final size:42
Alignment explanation
Indices: 203316--203436 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 42
203306 ATGAATCGGG
* *
203316 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAAGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAAGGGC
* ** * *
203358 CTCTTAAACGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACCTCTTGAACGATGACAAGGGC
* *
203400 CTCTTGAACGATAGGAGAGG-CCTCTTGAACGATGACA
1 CTCTTGAACGGTGGGAG-GGACCTCTTGAACGATGACA
203437 GGTGAGTCGG
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
41 1 0.02
42 58 0.92
43 4 0.06
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAAGGGC
Found at i:203949 original size:20 final size:20
Alignment explanation
Indices: 203924--203987 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
203914 AACTTAATTT
203924 GCAACGCGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
*
203944 GCAACGCGGAAATGACTATC
1 GCAACGCGAAAATGACTATC
* ** *
203964 GCAACACGAATTTAACTATC
1 GCAACGCGAAAATGACTATC
203984 GCAA
1 GCAA
203988 TGGGATAATC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATC
Found at i:204070 original size:19 final size:19
Alignment explanation
Indices: 204025--204061 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
204015 TCGCAACGAG
204025 AAAATCGCAACACGAAACC
1 AAAATCGCAACACGAAACC
*
204044 AAAATCGCAACGCGAAAC
1 AAAATCGCAACACGAAAC
204062 TAAATTCGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.30, G:0.14, T:0.05
Consensus pattern (19 bp):
AAAATCGCAACACGAAACC
Found at i:204181 original size:20 final size:20
Alignment explanation
Indices: 204137--204185 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
204127 GCGATTATCC
204137 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* ** *
204157 TGTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCAAATTCG
204177 CGTTGCGAT
1 CGTTGCGAT
204186 TTTTAAGTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:206182 original size:59 final size:60
Alignment explanation
Indices: 206092--206214 Score: 203
Period size: 59 Copynumber: 2.1 Consensus size: 60
206082 GAAAATGAAA
**
206092 ATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAAAGCGAATTTGACT
1 ATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAAAGCGAATTAAACT
* *
206152 ATCGCAACGCG-AAATGAAAATCGCAACACGAAAATGACTATCGCAATGCGAATTAAACT
1 ATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAAAGCGAATTAAACT
206211 ATCG
1 ATCG
206215 TTGCAATTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
59 49 0.83
60 10 0.17
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (60 bp):
ATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAAAGCGAATTAAACT
Found at i:206203 original size:20 final size:20
Alignment explanation
Indices: 206069--206188 Score: 154
Period size: 20 Copynumber: 6.0 Consensus size: 20
206059 TCTGAAACTT
206069 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
206089 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
206109 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** **
206129 ACTATCGCAA-AGCGAATTTG
1 AAAATCGCAACA-CGAAAATG
** *
206149 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
206168 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
206188 A
1 A
206189 CTATCGCAAT
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 15 0.17
20 72 0.83
ACGTcount: A:0.49, C:0.21, G:0.17, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:206607 original size:20 final size:21
Alignment explanation
Indices: 206582--206646 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
206572 TCTGAGAGAT
206582 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
206602 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
* * *
206624 AGAGATGGGGACGGATGTCGCC
1 GGAGAT-GAGACGGATTTCGCC
206646 G
1 G
206647 TAGAGAGTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 6 0.16
22 31 0.84
ACGTcount: A:0.22, C:0.17, G:0.43, T:0.18
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:206616 original size:22 final size:22
Alignment explanation
Indices: 206589--206646 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
206579 GATGGAGATA
206589 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
206611 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
206633 GACGGATGTCGCCG
1 GACGGATTTCGCCG
206647 TAGAGAGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.43, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:206814 original size:21 final size:21
Alignment explanation
Indices: 206790--206879 Score: 85
Period size: 21 Copynumber: 4.3 Consensus size: 21
206780 GAAAATCGCA
* *
206790 TTGCGATTTTGTATTATTGCG
1 TTGCGATTATGTATTATAGCG
206811 TTGCGATTATGTATTATAGCG
1 TTGCGATTATGTATTATAGCG
* ** *
206832 TTGC-AATA-GTCAGAATCGCG
1 TTGCGATTATGT-ATTATAGCG
* *
206852 TTGCGATTATGCATTATCGCG
1 TTGCGATTATGTATTATAGCG
206873 TTGCGAT
1 TTGCGAT
206880 AGTCAGAATC
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.04
20 13 0.23
21 40 0.71
22 1 0.02
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.40
Consensus pattern (21 bp):
TTGCGATTATGTATTATAGCG
Found at i:206868 original size:41 final size:41
Alignment explanation
Indices: 206808--206900 Score: 159
Period size: 41 Copynumber: 2.3 Consensus size: 41
206798 TTGTATTATT
*
206808 GCGTTGCGATTATGTATTATAGCGTTGCAATAGTCAGAATC
1 GCGTTGCGATTATGCATTATAGCGTTGCAATAGTCAGAATC
* *
206849 GCGTTGCGATTATGCATTATCGCGTTGCGATAGTCAGAATC
1 GCGTTGCGATTATGCATTATAGCGTTGCAATAGTCAGAATC
206890 GCGTTGCGATT
1 GCGTTGCGATT
206901 TATATATTCG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (41 bp):
GCGTTGCGATTATGCATTATAGCGTTGCAATAGTCAGAATC
Found at i:206897 original size:20 final size:20
Alignment explanation
Indices: 206829--206899 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
206819 ATGTATTATA
*
206829 GCGTTGCAATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
**
206849 GCGTTGCGATTA-TGCATTATC
1 GCGTTGCGA-TAGT-CAGAATC
206870 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
206890 GCGTTGCGAT
1 GCGTTGCGAT
206900 TTATATATTC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
20 26 0.60
21 17 0.40
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAATC
Found at i:207018 original size:20 final size:19
Alignment explanation
Indices: 206995--207040 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
206985 GGAAACTGAT
*
206995 TTGCGATACTGGAGATCGCA
1 TTGCGAT-CTAGAGATCGCA
*
207015 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
207034 TTGCGAT
1 TTGCGAT
207041 TTTGTTGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:207030 original size:19 final size:19
Alignment explanation
Indices: 207006--207042 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
206996 TGCGATACTG
207006 GAGATCGCATTGCGATTTA
1 GAGATCGCATTGCGATTTA
207025 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
207043 TGTTGGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:210306 original size:16 final size:16
Alignment explanation
Indices: 210285--210315 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
210275 AATAAATAGA
210285 CGAACATAAACGAACG
1 CGAACATAAACGAACG
*
210301 CGAACATAAATGAAC
1 CGAACATAAACGAAC
210316 AAAATTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.23, G:0.16, T:0.10
Consensus pattern (16 bp):
CGAACATAAACGAACG
Found at i:210408 original size:16 final size:16
Alignment explanation
Indices: 210387--210451 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
210377 TAATACATAA
210387 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
210403 ACGAACATAAACCAAC
1 ACGAACATAAACGAAC
*
210419 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
210435 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
210451 A
1 A
210452 TAAACGTTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.58, C:0.25, G:0.09, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:211222 original size:14 final size:14
Alignment explanation
Indices: 211205--211260 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
211195 AATGAACATA
*
211205 AACGAACATAATCG
1 AACGAACATAACCG
211219 AACGAACAT-A---
1 AACGAACATAACCG
211229 AACGAACATAACCG
1 AACGAACATAACCG
211243 AACGAACATAACCG
1 AACGAACATAACCG
211257 AACG
1 AACG
211261 TTCATGAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.52, C:0.25, G:0.14, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:211225 original size:24 final size:24
Alignment explanation
Indices: 211185--211259 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
211175 GATTGGGTTA
*
211185 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
211209 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* *
211233 AACATAACCGAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
211257 AAC
1 AAC
211260 GTTCATGAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 3 0.06
24 44 0.94
ACGTcount: A:0.55, C:0.21, G:0.12, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:211259 original size:10 final size:10
Alignment explanation
Indices: 211198--211245 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
211188 ATAAATGAAT
211198 GAACATAAAC
1 GAACATAAAC
211208 GAACATAATCGAAC
1 GAACAT-A---AAC
211222 GAACATAAAC
1 GAACATAAAC
*
211232 GAACATAACC
1 GAACATAAAC
211242 GAAC
1 GAAC
211246 GAACATAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:211924 original size:14 final size:14
Alignment explanation
Indices: 211909--211957 Score: 73
Period size: 14 Copynumber: 3.5 Consensus size: 14
211899 TACCCCAAAT
211909 CACTAAACCTAAAT-
1 CACTAAACCT-AATC
*
211923 CACTAAACCTACTC
1 CACTAAACCTAATC
211937 CACTAAACCTAATC
1 CACTAAACCTAATC
211951 CACTAAA
1 CACTAAA
211958 ACCCAACTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
13 2 0.06
14 30 0.94
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.20
Consensus pattern (14 bp):
CACTAAACCTAATC
Found at i:214630 original size:30 final size:31
Alignment explanation
Indices: 214596--214665 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
214586 TTTGTTATTA
* *
214596 TTATTATTTTTTCCTTCATTTTA-TTTCGTT
1 TTATTATTTTTTACTTCATTTTATTTTAGTT
* * * *
214626 TTATTATTATTTATTTTATTTTATTTTATTT
1 TTATTATTTTTTACTTCATTTTATTTTAGTT
214657 TTATTATTT
1 TTATTATTT
214666 ATTATTTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (31 bp):
TTATTATTTTTTACTTCATTTTATTTTAGTT
Found at i:214634 original size:3 final size:3
Alignment explanation
Indices: 214626--214688 Score: 53
Period size: 3 Copynumber: 21.7 Consensus size: 3
214616 TTATTTCGTT
*
214626 TTA TTA TTA TTTA TT- TTA TT- TTA TT- TTA TTT TTA TTA TTTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
* *
214670 TTT TTA TT- TTC TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
214689 TTTCCTTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
2 8 0.16
3 35 0.71
4 6 0.12
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (3 bp):
TTA
Found at i:214638 original size:10 final size:10
Alignment explanation
Indices: 214625--214677 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
214615 TTTATTTCGT
214625 TTTATTATTA
1 TTTATTATTA
214635 TTTATT-TTA
1 TTTATTATTA
214644 TTTTATT-TTA
1 -TTTATTATTA
214654 TTT-TTATTA
1 TTTATTATTA
214663 TTTATTATT-
1 TTTATTATTA
214672 TTTATT
1 TTTATT
214678 TTCTTATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.05
9 18 0.45
10 20 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTATTATTA
Found at i:214642 original size:25 final size:24
Alignment explanation
Indices: 214613--214688 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 24
214603 TTTTTCCTTC
*
214613 ATTTTATTTCGTTTTATTATTATTT
1 ATTTTATTTCATTTTATTATTA-TT
* *
214638 ATTTTATTTTATTTTATTTTTATT
1 ATTTTATTTCATTTTATTATTATT
* *
214662 ATTTATTATTTTTATTTTCTTATTATT
1 A-TT-TTA-TTTCATTTTATTATTATT
214689 TTTCCTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
24 3 0.07
25 21 0.49
26 3 0.07
27 16 0.37
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (24 bp):
ATTTTATTTCATTTTATTATTATT
Found at i:214646 original size:9 final size:9
Alignment explanation
Indices: 214625--214731 Score: 71
Period size: 9 Copynumber: 11.6 Consensus size: 9
214615 TTTATTTCGT
214625 TTTATTATTA
1 TTTATT-TTA
214635 TTTATTTTA
1 TTTATTTTA
214644 TTTTATTTTA
1 -TTTATTTTA
214654 TTT-TTATTA
1 TTTATT-TTA
214663 TTTATTATT-
1 TTTATT-TTA
214672 TTTATTTT-
1 TTTATTTTA
*
214680 CTTATTATT-
1 TTTATT-TTA
*
214689 TTTCCTTTTTA
1 TTT--ATTTTA
**
214700 CTCAATTTTA
1 -TTTATTTTA
214710 TTTATTTTA
1 TTTATTTTA
214719 TTTATTTT-
1 TTTATTTTA
214727 TTTAT
1 TTTAT
214732 ATTAATATTT
Statistics
Matches: 81, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
8 14 0.17
9 37 0.46
10 27 0.33
11 2 0.02
12 1 0.01
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTATTTTA
Found at i:214684 original size:17 final size:16
Alignment explanation
Indices: 214639--214731 Score: 75
Period size: 17 Copynumber: 5.8 Consensus size: 16
214629 TTATTATTTA
214639 TTTTATTTTATT-TTAT
1 TTTTATTTT-TTATTAT
*
214655 TTTTATTATTTATTAT
1 TTTTATTTTTTATTAT
214671 TTTTATTTTCTTATTAT
1 TTTTATTTT-TTATTAT
** * *
214688 TTTTCCTTTTTACTCAA
1 TTTTATTTTTTA-TTAT
*
214705 TTTTATTTATT-TTAT
1 TTTTATTTTTTATTAT
*
214720 TTAT-TTTTTTAT
1 TTTTATTTTTTAT
214732 ATTAATATTT
Statistics
Matches: 60, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
14 5 0.08
15 8 0.13
16 23 0.38
17 24 0.40
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTATTTTTTATTAT
Found at i:214699 original size:24 final size:22
Alignment explanation
Indices: 214629--214691 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
214619 TTTCGTTTTA
*
214629 TTATTATTTATTTTATTTTA-TT
1 TTATTATTTATTAT-TTTTATTT
214651 TTATT-TTTATTATTTATTATTT
1 TTATTATTTATTATTT-TTATTT
*
214673 TTATTTTCTTATTATTTTT
1 TTATTAT-TTATTATTTTT
214692 CCTTTTTACT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 2 0.06
21 10 0.28
22 12 0.33
23 3 0.08
24 9 0.25
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.78
Consensus pattern (22 bp):
TTATTATTTATTATTTTTATTT
Found at i:214727 original size:10 final size:10
Alignment explanation
Indices: 214614--214727 Score: 53
Period size: 10 Copynumber: 11.4 Consensus size: 10
214604 TTTTCCTTCA
**
214614 TTTTATTTCG
1 TTTTATTTAT
214624 TTTTA-TTAT
1 TTTTATTTAT
214633 TATTTATTT-T
1 T-TTTATTTAT
214643 ATTTTATTTTAT
1 -TTTTA-TTTAT
214655 TTTTA-TTAT
1 TTTTATTTAT
214664 TTATTATTT-T
1 TT-TTATTTAT
214674 TATTT-TCTTAT
1 T-TTTAT-TTAT
**
214685 TATTT-TTCCT
1 T-TTTATTTAT
* * *
214695 TTTTACTCAA
1 TTTTATTTAT
214705 TTTTATTTA-
1 TTTTATTTAT
214714 TTTTATTTAT
1 TTTTATTTAT
214724 TTTT
1 TTTT
214728 TTATATTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 24
0.72 0.08 0.21
Matches are distributed among these distances:
9 22 0.27
10 39 0.47
11 21 0.25
12 1 0.01
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.75
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:214750 original size:52 final size:54
Alignment explanation
Indices: 214648--214750 Score: 131
Period size: 56 Copynumber: 1.9 Consensus size: 54
214638 ATTTTATTTT
* *
214648 ATTTTATTTTTATTATTTATTATTTTTATTTTCTTATTATTTTTCCTTTTTACTCA
1 ATTTTATTTTTATTATTTATTATTTTTA--TTATTAATATTTTTCCTTTTTACTCA
*
214704 ATTTTATTTATT-TTATTTATT-TTTTTA-TATTAATATTTTTCTTTTTT
1 ATTTTATTT-TTATTATTTATTATTTTTATTATTAATATTTTTCCTTTTT
214751 TCATATTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
52 17 0.40
55 6 0.14
56 18 0.42
57 2 0.05
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (54 bp):
ATTTTATTTTTATTATTTATTATTTTTATTATTAATATTTTTCCTTTTTACTCA
Found at i:216631 original size:21 final size:19
Alignment explanation
Indices: 216570--216619 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 19
216560 ATGCCTCGAA
216570 CATTTTATGCATTCTTGCATTCT
1 CATTTT-TGCA-TCTT-CATT-T
216593 ACATTTTTGCATCTTCATTT
1 -CATTTTTGCATCTTCATTT
216613 CATTTTT
1 CATTTTT
216620 AAGCATTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 7 0.27
20 1 0.04
21 4 0.15
22 4 0.15
23 4 0.15
24 6 0.23
ACGTcount: A:0.18, C:0.20, G:0.06, T:0.56
Consensus pattern (19 bp):
CATTTTTGCATCTTCATTT
Found at i:217845 original size:8 final size:8
Alignment explanation
Indices: 217834--217896 Score: 65
Period size: 8 Copynumber: 7.8 Consensus size: 8
217824 ACAAAAAGGG
217834 AAAAAAGA
1 AAAAAAGA
217842 AAAAAAGA
1 AAAAAAGA
* *
217850 AAATAAGC
1 AAAAAAGA
*
217858 AAAAAAGG
1 AAAAAAGA
*
217866 AAAAAACA
1 AAAAAAGA
217874 AAAGAAA-A
1 AAA-AAAGA
217882 AAAAAAGA
1 AAAAAAGA
217890 ACAAAAA
1 A-AAAAA
217897 TCAAAAGGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
7 3 0.07
8 35 0.76
9 8 0.17
ACGTcount: A:0.83, C:0.05, G:0.11, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:217861 original size:16 final size:16
Alignment explanation
Indices: 217821--217896 Score: 66
Period size: 16 Copynumber: 4.6 Consensus size: 16
217811 AGATTCAATC
217821 AGAACAAAAAGGGAAAAA
1 AGAA-AAAAA-GGAAAAA
217839 AGAAAAAAA-GAAAATA
1 AGAAAAAAAGGAAAA-A
*
217855 AGCAAAAAAGGAAAAA
1 AGAAAAAAAGGAAAAA
* *
217871 ACAAAAGAAA-AAAAAA
1 AGAAAA-AAAGGAAAAA
217887 AGAACAAAAA
1 AGAA-AAAAA
217897 TCAAAAGGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
15 5 0.10
16 25 0.51
17 15 0.31
18 4 0.08
ACGTcount: A:0.79, C:0.05, G:0.14, T:0.01
Consensus pattern (16 bp):
AGAAAAAAAGGAAAAA
Found at i:217881 original size:11 final size:11
Alignment explanation
Indices: 217834--217896 Score: 56
Period size: 12 Copynumber: 5.3 Consensus size: 11
217824 ACAAAAAGGG
217834 AAAAAAGAAAA
1 AAAAAAGAAAA
217845 AAAGAAA-ATAAGCA
1 AAA-AAAGA-AA--A
*
217859 AAAAAGGAAAA
1 AAAAAAGAAAA
217870 AACAAAAGAAAA
1 AA-AAAAGAAAA
217882 AAAAAAGAACAA
1 AAAAAAGAA-AA
217894 AAA
1 AAA
217897 TCAAAAGGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
11 14 0.33
12 20 0.47
13 4 0.09
14 5 0.12
ACGTcount: A:0.83, C:0.05, G:0.11, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:217885 original size:24 final size:24
Alignment explanation
Indices: 217834--217909 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
217824 ACAAAAAGGG
* * **
217834 AAAAAAGAAAAAAAGAAAATAAGC
1 AAAAAAGAAAAAAACAAAAGAAAA
*
217858 AAAAAAGGAAAAAACAAAAGAAAA
1 AAAAAAGAAAAAAACAAAAGAAAA
*
217882 AAAAAAGAACAAAAATCAAAAGGAAA
1 AAAAAAGAA-AAAAA-CAAAAGAAAA
217908 AA
1 AA
217910 GGGACAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 27 0.63
25 5 0.12
26 11 0.26
ACGTcount: A:0.80, C:0.05, G:0.12, T:0.03
Consensus pattern (24 bp):
AAAAAAGAAAAAAACAAAAGAAAA
Found at i:218949 original size:18 final size:18
Alignment explanation
Indices: 218926--218961 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
218916 TCAACATCAA
*
218926 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
218944 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
218962 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:219422 original size:72 final size:76
Alignment explanation
Indices: 219316--219472 Score: 189
Period size: 72 Copynumber: 2.1 Consensus size: 76
219306 CTCACTTGAG
* * *
219316 ATTGCTTTTCTTAAAACAGACTTTGTCTAACTTGAGACTGTTTT-ACTCGAAAGAA-G-ATTT-A
1 ATTGTTTTTCTTAAAACAGACTTTGTCTAACTTGAGACCGTTTTCACTAGAAAGAAGGCATTTCA
*
219377 TTTCATTCAAA
66 TTTCACTCAAA
* **
219388 ATTGTTTTTCTTAAAACAAGA-TTTTTCTTGCTTGAGACCGTTTTCACTAGAAAGAAGGCATTTC
1 ATTGTTTTTCTTAAAAC-AGACTTTGTCTAACTTGAGACCGTTTTCACTAGAAAGAAGGCATTTC
*
219452 ATTTCACTCAAG
65 ATTTCACTCAAA
*
219464 ACTGTTTTT
1 ATTGTTTTT
219473 AAAGAAGATT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
72 35 0.49
73 13 0.18
74 1 0.01
75 4 0.06
76 18 0.25
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.41
Consensus pattern (76 bp):
ATTGTTTTTCTTAAAACAGACTTTGTCTAACTTGAGACCGTTTTCACTAGAAAGAAGGCATTTCA
TTTCACTCAAA
Found at i:219481 original size:72 final size:72
Alignment explanation
Indices: 219321--219497 Score: 175
Period size: 72 Copynumber: 2.5 Consensus size: 72
219311 TTGAGATTGC
* * ** * * *
219321 TTTTCTTAAAAC-AGACTTTGTCTAACTTGAGACTGTTTTACTCGAAAGAAGATTTATTTCATTC
1 TTTTCTTAAAACAAGATTTTATCTCGCTTGAGACCGTTTTACTAGAAAGAAGATTTATTTCACTC
*
219385 AAAATTG
66 AAAACTG
*
219392 TTTTTCTTAAAACAAGATTTT-TCTTGCTTGAGACCGTTTTCACTAGAAAGAAGGCATTTCATTT
1 -TTTTCTTAAAACAAGATTTTATCTCGCTTGAGACCGTTTT-ACTAGAAAGAA-G-ATTT-ATTT
*
219456 CACTCAAGACTG
61 CACTCAAAACTG
*
219468 -TTT-TT-AAAGAAGATTTTATCTCGCTTGAGA
1 TTTTCTTAAAACAAGATTTTATCTCGCTTGAGA
219498 TAGTTTCCCT
Statistics
Matches: 89, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
72 39 0.44
73 29 0.33
74 4 0.04
75 4 0.04
76 13 0.15
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (72 bp):
TTTTCTTAAAACAAGATTTTATCTCGCTTGAGACCGTTTTACTAGAAAGAAGATTTATTTCACTC
AAAACTG
Found at i:219531 original size:36 final size:36
Alignment explanation
Indices: 219480--219550 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
219470 TTTAAAGAAG
* *
219480 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAA
* *
219516 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA
219551 TAAACTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (36 bp):
ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAA
Found at i:220003 original size:106 final size:106
Alignment explanation
Indices: 219882--220098 Score: 362
Period size: 106 Copynumber: 2.0 Consensus size: 106
219872 ATATCATGCC
219882 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAATAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAATAATTTCCC
* * *
219947 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
66 AATTCCAGAACCAATTTCAACTTCACAGCGAAGGATATTAG
219988 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAATAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAATAATTTCCC
** * * *
220053 GGTTCCAGAACCAATTTCAACTTCACGGCGGAGGATATTGG
66 AATTCCAGAACCAATTTCAACTTCACAGCGAAGGATATTAG
220094 ACTCG
1 ACTCG
220099 GAATAATACA
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 103 1.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.22
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAATAATTTCCC
AATTCCAGAACCAATTTCAACTTCACAGCGAAGGATATTAG
Found at i:222218 original size:3 final size:3
Alignment explanation
Indices: 222210--222275 Score: 82
Period size: 3 Copynumber: 21.7 Consensus size: 3
222200 TCGTTTTTAT
222210 TTA TTA TTA TTA TTTA TT- TTA TTTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA
*
222257 TTA TTA TT- TTC TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
222276 TTTCTTTTTT
Statistics
Matches: 57, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
2 4 0.07
3 44 0.77
4 9 0.16
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:222238 original size:29 final size:28
Alignment explanation
Indices: 222206--222275 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 28
222196 TATTTCGTTT
222206 TTATTTATTATTATTATTTATT-TTATTTA
1 TTATTTATTATTATTA-TTATTATTA-TTA
222235 TTATTTATTATTATTATTATTATTATTA
1 TTATTTATTATTATTATTATTATTATTA
*
222263 TTTTCTTATTATT
1 TTAT-TTATTATT
222276 TTTCTTTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
28 11 0.29
29 27 0.71
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.71
Consensus pattern (28 bp):
TTATTTATTATTATTATTATTATTATTA
Found at i:222242 original size:26 final size:27
Alignment explanation
Indices: 222205--222276 Score: 89
Period size: 26 Copynumber: 2.7 Consensus size: 27
222195 TTATTTCGTT
222205 TTTATT-TATTATTATTATTTATT-TTA
1 TTTATTAT-TTATTATTATTTATTATTA
222231 TTTATTATTTATTATTA-TTATTATTA
1 TTTATTATTTATTATTATTTATTATTA
*
222257 -TTATTATTTTCTTATTATTT
1 TTTATTA-TTTATTATTATTT
222277 TTCTTTTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
25 11 0.27
26 27 0.66
27 3 0.07
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTATTATTTATTATTATTTATTATTA
Found at i:226187 original size:21 final size:21
Alignment explanation
Indices: 226162--226201 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
226152 GGTCATCGGC
226162 GGAGAAAGTGACGGAGACGGA
1 GGAGAAAGTGACGGAGACGGA
**
226183 GGAGACGGTGACGGAGACG
1 GGAGAAAGTGACGGAGACG
226202 AATCCATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.50, T:0.05
Consensus pattern (21 bp):
GGAGAAAGTGACGGAGACGGA
Found at i:227044 original size:17 final size:18
Alignment explanation
Indices: 227008--227048 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
226998 ATATTATGTA
*
227008 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
227026 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
227043 TTTACT
1 TTTACT
227049 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:232408 original size:20 final size:21
Alignment explanation
Indices: 232351--232419 Score: 77
Period size: 22 Copynumber: 3.3 Consensus size: 21
232341 CTCTATATAT
* *
232351 TATTTTTTTCAATTAAATTAA
1 TATTTTTTTCAATAAAAATAA
*
232372 TATTTTTATTGAATAAAAATAA
1 TATTTTT-TTCAATAAAAATAA
* *
232394 TATTTTTTT-AATAAATATAT
1 TATTTTTTTCAATAAAAATAA
232414 TATTTT
1 TATTTT
232420 GGGTCTGATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
20 15 0.36
21 9 0.21
22 18 0.43
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (21 bp):
TATTTTTTTCAATAAAAATAA
Found at i:233224 original size:44 final size:44
Alignment explanation
Indices: 233174--233262 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
233164 ACATCATTAA
233174 AACTAGTGAGACCATGACCCCTTAAAATATTGGAACAATAATAT
1 AACTAGTGAGACCATGACCCCTTAAAATATTGGAACAATAATAT
233218 AACTAGTGAGACCATGACCCCTTAAAATATTGGAACAATAATAT
1 AACTAGTGAGACCATGACCCCTTAAAATATTGGAACAATAATAT
233262 A
1 A
233263 TATATATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (44 bp):
AACTAGTGAGACCATGACCCCTTAAAATATTGGAACAATAATAT
Found at i:233265 original size:2 final size:2
Alignment explanation
Indices: 233258--233287 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
233248 TGGAACAATA
233258 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
233288 GAAATTATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:237841 original size:2 final size:2
Alignment explanation
Indices: 237834--237859 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
237824 TTTATTTTAA
237834 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
237860 GAAAAATATT
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:246844 original size:6 final size:6
Alignment explanation
Indices: 246833--246858 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
246823 TAATAGTAGT
246833 TTTCTC TTTCTC TTTCTC TTTCTC TT
1 TTTCTC TTTCTC TTTCTC TTTCTC TT
246859 GGCCTCTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTCTC
Found at i:247013 original size:6 final size:6
Alignment explanation
Indices: 247004--247029 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
246994 TAATAGTAAT
247004 TTTCTC TTTCTC TTTCTC TTTCTC TT
1 TTTCTC TTTCTC TTTCTC TTTCTC TT
247030 GGCCTCTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTCTC
Found at i:247079 original size:171 final size:174
Alignment explanation
Indices: 246794--247139 Score: 662
Period size: 171 Copynumber: 2.0 Consensus size: 174
246784 ATATGTGCTT
*
246794 ACACTCAAGAATATTTCTGAATCAGTGGCTAATAGTAGTTTTCTCTTTCTCTTTCTCTTTCTCTT
1 ACACTCAAGAATATTTCTGAATCAGTGGCTAATAGTAATTTTCTCTTTCTCTTTCTCTTTCTCTT
246859 GGCCTCTAATTTATCAGAGTATTGAATGGTAAAGCTTGACGGTGCTAAAAACCAGG-TTCGGAAA
66 GGCCTCTAATTTATCAGAGTATTGAATGGTAAAGCTTGACGGTGCTAAAAACCAGGTTTCGGAAA
246923 CAGGGCTG-CTGGCTGCCTACCTGG-TTTTCCCTTTTTCTTCAA
131 CAGGGCTGTCTGGCTGCCTACCTGGTTTTTCCCTTTTTCTTCAA
246965 ACACTCAAGAATATTTCTGAATCAGTGGCTAATAGTAATTTTCTCTTTCTCTTTCTCTTTCTCTT
1 ACACTCAAGAATATTTCTGAATCAGTGGCTAATAGTAATTTTCTCTTTCTCTTTCTCTTTCTCTT
247030 GGCCTCTAATTTATCAGAGTATTGAATGGTAAAGCTTGACGGTGCTAAAAACCAGGTTTCGGAAA
66 GGCCTCTAATTTATCAGAGTATTGAATGGTAAAGCTTGACGGTGCTAAAAACCAGGTTTCGGAAA
247095 CAGGGCTGTCTGGCTGCCTACCTGGTTTTTCCCTTTTTCTTCAA
131 CAGGGCTGTCTGGCTGCCTACCTGGTTTTTCCCTTTTTCTTCAA
247139 A
1 A
247140 TTTAAATTAT
Statistics
Matches: 171, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
171 120 0.70
172 16 0.09
173 16 0.09
174 19 0.11
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.37
Consensus pattern (174 bp):
ACACTCAAGAATATTTCTGAATCAGTGGCTAATAGTAATTTTCTCTTTCTCTTTCTCTTTCTCTT
GGCCTCTAATTTATCAGAGTATTGAATGGTAAAGCTTGACGGTGCTAAAAACCAGGTTTCGGAAA
CAGGGCTGTCTGGCTGCCTACCTGGTTTTTCCCTTTTTCTTCAA
Found at i:263456 original size:16 final size:16
Alignment explanation
Indices: 263435--263472 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
263425 CTTCTGGCAC
263435 GTTCATTCAGAGTTCT
1 GTTCATTCAGAGTTCT
263451 GTTCATTCAGAGTTCT
1 GTTCATTCAGAGTTCT
263467 GTTCAT
1 GTTCAT
263473 ACGCTCTGTT
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:0.18, G:0.18, T:0.45
Consensus pattern (16 bp):
GTTCATTCAGAGTTCT
Found at i:270950 original size:185 final size:184
Alignment explanation
Indices: 270710--271097 Score: 629
Period size: 185 Copynumber: 2.1 Consensus size: 184
270700 TTTTCTAATT
* * * *
270710 TATATAA-AAATTAAATA-TTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
*
270773 TATAAAAT-AAAAATTCCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTAT
66 TATAAAATAAAAAATT-CACATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTAT
* *
270837 TGGATCTTAAATTATTAATTGAGTTTTAAATTGTTTGGGCTTAGCCCAAATGTTA
130 TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTA
270892 TATATAATATATTTAATATTTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTAAAAAAA-AGTTTACAATTAATTTAAATAATATATAA
* * *
270957 TTATAAAATAAAAAATTTACATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
65 TTATAAAATAAAAAATTCACATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTAT
* *
271022 TGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
130 TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTA
271077 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
271098 AAAATTTAAT
Statistics
Matches: 190, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
182 7 0.04
183 8 0.04
184 15 0.08
185 153 0.81
186 7 0.04
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAAATTCACATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATT
GGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTA
Found at i:271122 original size:9 final size:9
Alignment explanation
Indices: 271103--271136 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
271093 TATTTAAAAT
271103 TTAATTTCGG
1 TTAA-TTCGG
271113 TTAATTCGG
1 TTAATTCGG
*
271122 TTAATTCAG
1 TTAATTCGG
271131 TTAATT
1 TTAATT
271137 AACCGAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (9 bp):
TTAATTCGG
Found at i:271642 original size:28 final size:29
Alignment explanation
Indices: 271598--271666 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
271588 TACGTGGATA
* *
271598 GTTTG-GGGGTATATTTTCAATTAATG-TT
1 GTTTGAGGGTTAT-TTTTCAATAAATGATT
271626 GTTTGAGGGTTACTTTTTCAATAAATGAATT
1 GTTTGAGGGTTA-TTTTTCAATAAATG-ATT
271657 -TTTGAGGGTT
1 GTTTGAGGGTT
271667 TTTAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 5 0.14
29 17 0.49
30 11 0.31
31 2 0.06
ACGTcount: A:0.23, C:0.04, G:0.25, T:0.48
Consensus pattern (29 bp):
GTTTGAGGGTTATTTTTCAATAAATGATT
Found at i:280738 original size:14 final size:14
Alignment explanation
Indices: 280721--280758 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
280711 TTAAAAGTAA
280721 TATTATTTTTATAT
1 TATTATTTTTATAT
*
280735 TATTATTTTTTGTAT
1 TATTA-TTTTTATAT
280750 TA-TATTTTT
1 TATTATTTTT
280759 CTTTTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 7 0.32
15 10 0.45
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (14 bp):
TATTATTTTTATAT
Found at i:280750 original size:15 final size:15
Alignment explanation
Indices: 280721--280758 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
280711 TTAAAAGTAA
280721 TATTA-TTTTTATAT
1 TATTATTTTTTATAT
*
280735 TATTATTTTTTGTAT
1 TATTATTTTTTATAT
280750 TA-TATTTTT
1 TATTATTTTT
280759 CTTTTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (15 bp):
TATTATTTTTTATAT
Found at i:293334 original size:24 final size:24
Alignment explanation
Indices: 293302--293351 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
293292 AAAATCCAAC
*
293302 TAAATATAAACGAATATAAACAAA
1 TAAAAATAAACGAATATAAACAAA
*
293326 TAAAAATAAACTAATATAAACAAA
1 TAAAAATAAACGAATATAAACAAA
293350 TA
1 TA
293352 TATTAATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.68, C:0.08, G:0.02, T:0.22
Consensus pattern (24 bp):
TAAAAATAAACGAATATAAACAAA
Found at i:297306 original size:39 final size:39
Alignment explanation
Indices: 297252--297330 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
297242 AACCAACAGA
*
297252 TACATTATTGCAATCATCATCACTTGAAACAAGCATAGT
1 TACATCATTGCAATCATCATCACTTGAAACAAGCATAGT
*
297291 TACATCATTGCAATCATCATCACTTGAAAGAAGCATAGT
1 TACATCATTGCAATCATCATCACTTGAAACAAGCATAGT
297330 T
1 T
297331 CCCTCTTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.30
Consensus pattern (39 bp):
TACATCATTGCAATCATCATCACTTGAAACAAGCATAGT
Found at i:303611 original size:11 final size:11
Alignment explanation
Indices: 303590--303646 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
303580 ACTTTTTTTT
303590 AAAAT-CAATA
1 AAAATGCAATA
303600 AAAATGCAATA
1 AAAATGCAATA
*
303611 AAAAAG-AATTA
1 AAAATGCAA-TA
*
303622 AAAGTG-AAT-
1 AAAATGCAATA
*
303631 AAAATTCAATA
1 AAAATGCAATA
303642 AAAAT
1 AAAAT
303647 AGAATATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
9 4 0.11
10 11 0.29
11 23 0.61
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (11 bp):
AAAATGCAATA
Found at i:303651 original size:21 final size:19
Alignment explanation
Indices: 303589--303652 Score: 56
Period size: 21 Copynumber: 3.1 Consensus size: 19
303579 CACTTTTTTT
303589 TAAAATCAATAAAAATGCAA
1 TAAAATCAATAAAAATG-AA
** *
303609 TAAAAAAGAATTAAAAGTGAA
1 T-AAAATCAA-TAAAAATGAA
303630 TAAAATTCAATAAAAATAGAA
1 TAAAA-TCAATAAAAAT-GAA
303651 TA
1 TA
303653 TAAACCTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 11 0.32
21 16 0.47
22 7 0.21
ACGTcount: A:0.66, C:0.05, G:0.08, T:0.22
Consensus pattern (19 bp):
TAAAATCAATAAAAATGAA
Found at i:303652 original size:11 final size:10
Alignment explanation
Indices: 303590--303652 Score: 54
Period size: 10 Copynumber: 6.0 Consensus size: 10
303580 ACTTTTTTTT
*
303590 AAAATCAATA
1 AAAATGAATA
303600 AAAATGCAATA
1 AAAATG-AATA
*
303611 AAAAAGAATTA
1 AAAATGAA-TA
*
303622 AAAGTGAATA
1 AAAATGAATA
* *
303632 AAATTCAATA
1 AAAATGAATA
303642 AAAATAGAATA
1 AAAAT-GAATA
303653 TAAACCTAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
10 21 0.50
11 21 0.50
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.21
Consensus pattern (10 bp):
AAAATGAATA
Found at i:303667 original size:32 final size:31
Alignment explanation
Indices: 303599--303667 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
303589 TAAAATCAAT
*
303599 AAAAATGCAATAAAAAAGAATTAAAAGTGAA
1 AAAAATGCAATAAAAAAGAATTAAAACTGAA
* * *
303630 TAAAATTCAATAAAAATAGAATATAAACCT-AA
1 AAAAATGCAATAAAAA-AGAAT-TAAAACTGAA
303662 AAAAAT
1 AAAAAT
303668 AGAATGTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
31 14 0.45
32 12 0.39
33 5 0.16
ACGTcount: A:0.67, C:0.06, G:0.07, T:0.20
Consensus pattern (31 bp):
AAAAATGCAATAAAAAAGAATTAAAACTGAA
Found at i:303688 original size:20 final size:21
Alignment explanation
Indices: 303641--303686 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
303631 AAAATTCAAT
303641 AAAAATAGAATATAAACCTAA
1 AAAAATAGAATATAAACCTAA
* *
303662 AAAAATAGAATGTAAAGCTAA
1 AAAAATAGAATATAAACCTAA
303683 AAAA
1 AAAA
303687 TACCACCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.67, C:0.07, G:0.09, T:0.17
Consensus pattern (21 bp):
AAAAATAGAATATAAACCTAA
Found at i:307057 original size:36 final size:36
Alignment explanation
Indices: 306978--307060 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
306968 TATGAATCTT
*
306978 AAGACTTCTAGGAACTTCGAAGACCATGGACCTTCA
1 AAGACTTCAAGGAACTTCGAAGACCATGGACCTTCA
* * * *
307014 AAAACTTCAAGGAACTT-GAGATATCATGGACCTTCG
1 AAGACTTCAAGGAACTTCGA-AGACCATGGACCTTCA
*
307050 TAGACTTCAAG
1 AAGACTTCAAG
307061 AAAGTCCGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 2 0.05
36 37 0.95
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (36 bp):
AAGACTTCAAGGAACTTCGAAGACCATGGACCTTCA
Found at i:309128 original size:19 final size:19
Alignment explanation
Indices: 309104--309155 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
309094 AATGCATTGA
309104 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
309123 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
309142 GTGCATCGATGCAT
1 GTGCATCGATGCAT
309156 AAAATGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:309211 original size:20 final size:20
Alignment explanation
Indices: 309183--309220 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
309173 TGAAAAATTA
309183 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
309203 ATTGGTGCATCGGTGCAT
1 ATTGATGCATCGATGCAT
309221 CACTTTGAAA
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:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:314720 original size:2 final size:2
Alignment explanation
Indices: 314713--314770 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
314703 TGCATGTGAT
314713 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
314755 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
314771 GATAAATATG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:318370 original size:21 final size:21
Alignment explanation
Indices: 318352--318442 Score: 130
Period size: 21 Copynumber: 4.3 Consensus size: 21
318342 ACCAAGGACA
*
318352 AGAAGACCATTCACAAGGACG
1 AGAAGACCATTCACAAAGACG
*
318373 AGAAGACCATTCATAAAGACG
1 AGAAGACCATTCACAAAGACG
*
318394 AGAAGACCATTCATAAAGACG
1 AGAAGACCATTCACAAAGACG
*
318415 ATAAGACCATTCACAAAGAC-
1 AGAAGACCATTCACAAAGACG
318435 ATGAAGAC
1 A-GAAGAC
318443 TACTTTGCAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 1 0.02
21 63 0.98
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (21 bp):
AGAAGACCATTCACAAAGACG
Found at i:322817 original size:36 final size:36
Alignment explanation
Indices: 322776--322952 Score: 250
Period size: 36 Copynumber: 4.9 Consensus size: 36
322766 GGCAAAGTCA
*
322776 ATCTTAAGCCTTCACCTGAGAGTAGTGAAGCAATCC
1 ATCTTAAGCCTTCACCTGAGAGTAGTGAAGCAAACC
*
322812 ATCTTAAGCCTTCACCTGAGAGTAGTGAAGCAATCC
1 ATCTTAAGCCTTCACCTGAGAGTAGTGAAGCAAACC
* * *
322848 ATCTTAAGCTTTCACCGGAGAGCAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCTGAGAGTAGTGAAGCAAACC
* *
322884 ATTTTAAGCCTTCA-TTGGAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCT-GAGAGTAGTGAAGCAAACC
322920 ATCTTAAGCCTTCACC-GAAGAAGTAGTGAAGCA
1 ATCTTAAGCCTTCACCTG-AG-AGTAGTGAAGCA
322953 GAAGAAGATG
Statistics
Matches: 126, Mismatches: 11, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
35 1 0.01
36 113 0.90
37 12 0.10
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.24
Consensus pattern (36 bp):
ATCTTAAGCCTTCACCTGAGAGTAGTGAAGCAAACC
Found at i:323022 original size:54 final size:55
Alignment explanation
Indices: 322952--323169 Score: 248
Period size: 56 Copynumber: 4.0 Consensus size: 55
322942 GTAGTGAAGC
* * * * *
322952 AGAAGAAGA-TGTTCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGTGAACCCATA
1 AGAAGAAGATTATTCGAGTTCCATACT-CCTGAAAGAAAGAGGGAGAGAACCCGTT
*
323006 AGAAGAAGA-TATTCGAGTTCCATACTCCTGAAAGAAAGAGGGAGAGAACTCGTT
1 AGAAGAAGATTATTCGAGTTCCATACTCCTGAAAGAAAGAGGGAGAGAACCCGTT
* * *
323060 TGTAGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCA-AACCCGTT
1 AGAAGAAGATTATTCGAGTTCCATAC-TCCTGAAAGAAAGAGGGAG-AGAACCCGTT
* * *
323116 TGCAGAAGATTATTCGAGTTCTATACTGCCTGAAAGAAAGAGGGAGCA-AACCCG
1 AGAAGAAGATTATTCGAGTTCCATACT-CCTGAAAGAAAGAGGGAG-AGAACCCG
323170 ATTGTTGAAG
Statistics
Matches: 148, Mismatches: 11, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
53 3 0.02
54 51 0.34
55 16 0.11
56 77 0.52
57 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (55 bp):
AGAAGAAGATTATTCGAGTTCCATACTCCTGAAAGAAAGAGGGAGAGAACCCGTT
Found at i:323290 original size:55 final size:55
Alignment explanation
Indices: 323027--323932 Score: 784
Period size: 55 Copynumber: 16.4 Consensus size: 55
323017 TTCGAGTTCC
* * * * *
323027 ATACTC-CTGAAAGAAAGAGGGAG-AGAACTCGTTTGTAGAAGATTATTCGAGT-TCT
1 ATACTCTCTG-AAGAAATAGGGAGCAG-ACACGATTGTTGAAGATTGTTCGAGTCT-T
* * * * ** *
323082 ATACT-TCCTGAAAGAAAGAGGGAGCAAACCCGTTTGCAGAAGATTATTCGAGT-TCT
1 ATACTCT-CTG-AAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCT-T
* * *
323138 ATACTGC-CTGAAAGAAAGAGGGAGCAAACCCGATTGTTGAAGATTGTTCGAGTCTT
1 ATACT-CTCTG-AAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTT
* * * *
323194 ATACTCTCTCTGAAGAAATAGGGAGTAGACATGACTATTGAAGATTGTTCGAGTCTT
1 ATA--CTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTT
* *
323251 ATACTCTCTGAAGAAATAGGGAGCAGACATGATCGTTGAAGATTGTTCGAGTCTT
1 ATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTT
* * *
323306 ATACTCTCTGAAGGAATAGGGAGCGGACACGATTGTTGAAGATTGTTGGAGTCTT
1 ATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTT
* * *
323361 ATACTCTCTGAATG-AATAGAGAGCATACACGATTGTTGAAGATTGTTTGAGTCTT
1 ATACTCTCTGAA-GAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTT
*
323416 ATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTT
1 ATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTT
* * *
323471 ATACTCTCTGAAGGAATAGGGATCAGACACGATTGTTGAA-AATGTTCGAGT-TCT
1 ATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCT-T
* * * * *
323525 ATACTCCCTAAAGAAAGAGGGAGC-GAACCCGATT-TCAGAAGATT-TTCGAGT-TCT
1 ATACTCTCTGAAGAAATAGGGAGCAG-ACACGATTGT-TGAAGATTGTTCGAGTCT-T
* * * * * *
323579 ATACTCCCTGAACAAAGAGGGAGC-GA-AC--CTGTAAGAAGAAGATGTTCGAGT-TCT
1 ATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT-TGAAG-A-TTGTTCGAGTCT-T
* * ** * *
323633 ATACT-TCCTGAAAGAAAGAGGGAGC-GA-ACTCATTTGCAGAGGATTGTTCGAGT-TCC
1 ATACTCT-CTG-AAGAAATAGGGAGCAGACAC-GA-TTGTTGAAGATTGTTCGAGTCT-T
* * * * * * * ** **
323689 ATACTCCCTAAATAAAGAGGGA-CCGAACCCGTTTGAAGAAGA-TGTTTAAGTCTT
1 ATACTCTCTGAAGAAATAGGGAGCAG-ACACGATTGTTGAAGATTGTTCGAGTCTT
*
323743 ATACTCTTTGAA-AGAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTT
1 ATACTCTCTGAAGA-AATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTT
* *
323798 ATACTCTCTGAAGGAATAGGGAGCAGACATGATTGTTGAAGATTGTTCGAGTCTT
1 ATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTT
* *
323853 ATTCTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGT-TCT
1 ATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCT-T
* *
323908 ATACTCCCTGAAAGAAAGAGGGAGC
1 ATACTCTCTG-AAGAAATAGGGAGC
323933 GAACCCGTTG
Statistics
Matches: 731, Mismatches: 84, Indels: 71
0.83 0.09 0.08
Matches are distributed among these distances:
50 1 0.00
51 6 0.01
52 2 0.00
53 6 0.01
54 129 0.18
55 403 0.55
56 127 0.17
57 46 0.06
58 9 0.01
59 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (55 bp):
ATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTT
Found at i:327414 original size:117 final size:117
Alignment explanation
Indices: 327195--327415 Score: 275
Period size: 117 Copynumber: 1.9 Consensus size: 117
327185 TTTCAAATTA
* * *
327195 AAATTTTCTTTTTCAATATTTTCAAATTTCATTTTTGAAAGTTCTAAATCCTTCTTCAAGAGTTC
1 AAATTTTCTTTTTCAATATTTTCAAATTTCAGTTTTGAAAGCTCTAAATCCTTCTTCAACAGTTC
* *
327260 ATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTTG
66 ATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
* * * * *
327312 AAATTTTCTTTTTCAA-AGTTTTCAGATTTTAGTTTTGAAAGCTCTAACTCCTTTTTCAACATTT
1 AAATTTTCTTTTTCAATA-TTTTCAAATTTCAGTTTTGAAAGCTCTAAATCCTTCTTCAACAGTT
* * * **
327376 CATTTTGTTTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
65 CATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
327416 ATTATTTTTA
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
116 1 0.01
117 82 0.94
118 4 0.05
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (117 bp):
AAATTTTCTTTTTCAATATTTTCAAATTTCAGTTTTGAAAGCTCTAAATCCTTCTTCAACAGTTC
ATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
Found at i:328839 original size:26 final size:26
Alignment explanation
Indices: 328808--328870 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
328798 GCAGGGTATT
*
328808 GTGCATCGATGCATCAGATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
328834 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
328860 GTGCATCGATG
1 GTGCATCGATG
328871 AATGGTATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (26 bp):
GTGCATCGATGCATCAAATGCACTGA
Found at i:331030 original size:24 final size:24
Alignment explanation
Indices: 330984--331030 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
330974 CATTGTATAT
*
330984 TATATATGATGTTTATCATGAATA
1 TATATATGATGTTTATCACGAATA
* *
331008 TATATATGATGTTTGTTACGAAT
1 TATATATGATGTTTATCACGAAT
331031 GTTATTTCAT
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:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
TATATATGATGTTTATCACGAATA
Found at i:331268 original size:58 final size:59
Alignment explanation
Indices: 331170--331365 Score: 272
Period size: 59 Copynumber: 3.3 Consensus size: 59
331160 CTAGCAGGCT
*
331170 TCATATTCGGGATTGCACTAAAGTATAACTAGTGCATATGGTGGGCACTATCTTATGTG
1 TCATATTCGGGATTGCACTAAAGTATAACTAGTGCATATGGTGGGCACTACCTTATGTG
* * ** *
331229 TCATATTCGGGATTTCACT-AAGTATAACTAGTGTATATGGTGAACACAACCTTATGTG
1 TCATATTCGGGATTGCACTAAAGTATAACTAGTGCATATGGTGGGCACTACCTTATGTG
* *
331287 TCATATTCGGGACTGCACTAAAGTATAACTAGTGCAGATGGTGGGCA-TAACCTTATGTG
1 TCATATTCGGGATTGCACTAAAGTATAACTAGTGCATATGGTGGGCACT-ACCTTATGTG
*
331346 TCATACTCGGG-TTAGCACTA
1 TCATATTCGGGATT-GCACTA
331366 CAGTGCATAT
Statistics
Matches: 119, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
58 52 0.44
59 67 0.56
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (59 bp):
TCATATTCGGGATTGCACTAAAGTATAACTAGTGCATATGGTGGGCACTACCTTATGTG
Found at i:337210 original size:29 final size:29
Alignment explanation
Indices: 337168--337226 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
337158 ATTTTCAGCT
337168 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
337197 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
337226 A
1 A
337227 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:341901 original size:29 final size:29
Alignment explanation
Indices: 341859--341917 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
341849 ATTTTCACCT
*
341859 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGAAATGACATCAA
341888 AACTAAATTGATGTAAGAAATGACATCAA
1 AACTAAATTGATGTAAGAAATGACATCAA
341917 A
1 A
341918 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGAAATGACATCAA
Found at i:343574 original size:16 final size:16
Alignment explanation
Indices: 343526--343586 Score: 86
Period size: 16 Copynumber: 3.8 Consensus size: 16
343516 TTGATTAAGT
*
343526 GCTGAATGATTCAAAT
1 GCTGAATGATTCAAAC
* *
343542 ACTAAATGATTCAAAC
1 GCTGAATGATTCAAAC
343558 GCTGAATGATTCAAAC
1 GCTGAATGATTCAAAC
*
343574 GTTGAATGATTCA
1 GCTGAATGATTCA
343587 GAGGCTCTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (16 bp):
GCTGAATGATTCAAAC
Found at i:347275 original size:14 final size:14
Alignment explanation
Indices: 347256--347290 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
347246 CATTTAAATG
347256 ATAAACGAACACAA
1 ATAAACGAACACAA
*
347270 ATAAACGAACATAA
1 ATAAACGAACACAA
*
347284 ACAAACG
1 ATAAACG
347291 GATGTAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.20, G:0.09, T:0.09
Consensus pattern (14 bp):
ATAAACGAACACAA
Found at i:347317 original size:20 final size:20
Alignment explanation
Indices: 347284--347334 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
347274 ACGAACATAA
* * *
347284 ACAAACGGATGTAAATGAAT
1 ACAAACGAACGTAAATGAAC
*
347304 ATAAACGAACGTAAATGAAC
1 ACAAACGAACGTAAATGAAC
347324 ACAAACGAACG
1 ACAAACGAACG
347335 AACGTAAACG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.53, C:0.16, G:0.18, T:0.14
Consensus pattern (20 bp):
ACAAACGAACGTAAATGAAC
Found at i:347593 original size:28 final size:28
Alignment explanation
Indices: 347560--347614 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
347550 GATTTGGCTA
*
347560 AACATAAATGAACACATATAAACAAACG
1 AACATAAATGAACACACATAAACAAACG
347588 AACATAAATGAACACACATAAACAAAC
1 AACATAAATGAACACACATAAACAAAC
347615 ATATTACTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.62, C:0.20, G:0.05, T:0.13
Consensus pattern (28 bp):
AACATAAATGAACACACATAAACAAACG
Found at i:347831 original size:16 final size:16
Alignment explanation
Indices: 347819--347849 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
347809 AAATTGGTTG
347819 TTCGAATTTTTGGATA
1 TTCGAATTTTTGGATA
*
347835 TTCGGATTTTTGGAT
1 TTCGAATTTTTGGAT
347850 CAAATATTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.23, T:0.52
Consensus pattern (16 bp):
TTCGAATTTTTGGATA
Found at i:348970 original size:12 final size:12
Alignment explanation
Indices: 348928--348972 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
348918 AAAATATTAA
348928 TTATTATAATAT
1 TTATTATAATAT
**
348940 TTAAAAT-ATAT
1 TTATTATAATAT
348951 TTA-T-TAATAT
1 TTATTATAATAT
348961 TTATTATAATAT
1 TTATTATAATAT
348973 AATATTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
9 1 0.04
10 7 0.26
11 8 0.30
12 11 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTATTATAATAT
Found at i:349051 original size:22 final size:22
Alignment explanation
Indices: 349007--349087 Score: 67
Period size: 22 Copynumber: 3.6 Consensus size: 22
348997 TATACTCAAT
*
349007 TATATTATAATAATATAAGATATTA
1 TATATT-TATTAATA-AA-ATATTA
* * *
349032 TATATTTTTTAATAATATATAA
1 TATATTTATTAATAAAATATTA
*
349054 TA-AATTATTAATAAAAT-TTA
1 TATATTTATTAATAAAATATTA
349074 TATTATTTATTAAT
1 TA-TATTTATTAAT
349088 TTCATAAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
20 4 0.09
21 12 0.27
22 16 0.36
23 1 0.02
24 6 0.13
25 6 0.13
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (22 bp):
TATATTTATTAATAAAATATTA
Found at i:349116 original size:27 final size:26
Alignment explanation
Indices: 349054--349134 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 26
349044 TAATATATAA
* *
349054 TAAATTATTAATAAAATTTATATTAT
1 TAAATTATTTATAAAAATTATATTAT
*
349080 T-TATTAATTTCATAAAAATTATATTAT
1 TAAATT-ATTT-ATAAAAATTATATTAT
* *
349107 TAAATTATTTATAATGAATAATATTAT
1 TAAATTATTTATAA-AAATTATATTAT
349134 T
1 T
349135 TATGTATTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
25 3 0.07
26 8 0.18
27 31 0.69
28 3 0.07
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (26 bp):
TAAATTATTTATAAAAATTATATTAT
Found at i:349142 original size:27 final size:25
Alignment explanation
Indices: 349057--349144 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 25
349047 TATATAATAA
* * *
349057 ATTATTAATAAAATTTATATTATTT
1 ATTATTTATAAAAATAATATTATTT
* *
349082 ATTAATTTCATAAAAATTATATTATTAA
1 ATT-ATTT-ATAAAAATAATATTATT-T
*
349110 ATTATTTATAATGAATAATATTATTT
1 ATTATTTATAA-AAATAATATTATTT
349136 ATGTATTTA
1 AT-TATTTA
349145 ATTTTAATAC
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
25 3 0.06
26 9 0.17
27 37 0.71
28 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (25 bp):
ATTATTTATAAAAATAATATTATTT
Found at i:349236 original size:23 final size:23
Alignment explanation
Indices: 349206--349250 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
349196 TTTTAAAATA
349206 TAATATAATATTAT-TATTTTAAT
1 TAATATAAT-TTATATATTTTAAT
349229 TAATATAATTTATAATATTTTA
1 TAATATAATTTAT-ATATTTTA
349251 TTTTAATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 9 0.45
24 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TAATATAATTTATATATTTTAAT
Found at i:349245 original size:30 final size:27
Alignment explanation
Indices: 349202--349257 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 27
349192 CACTTTTTAA
349202 AATATAATATAATATTATTATTTTAATT
1 AATATAATATAATATT-TTATTTTAATT
349230 AATATAATTTATAATATTTTATTTTAAT
1 AATATAA--TATAATATTTTATTTTAAT
349258 AGACTGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 7 0.27
29 10 0.38
30 9 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
AATATAATATAATATTTTATTTTAATT
Found at i:351596 original size:32 final size:32
Alignment explanation
Indices: 351545--351632 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 32
351535 ATTATCTTGG
* * * *
351545 GGGCCTGATAGCCTTCCCAATGG-AGTACCTTA
1 GGGCCTAAGAGCCTACCCAA-GGAAGTAACTTA
* *
351577 GGGCCTAAGAGCTTACCCAAGGAAGTAACTTG
1 GGGCCTAAGAGCCTACCCAAGGAAGTAACTTA
*
351609 GGGCCTTAGAGCCTACCCAAGGAA
1 GGGCCTAAGAGCCTACCCAAGGAA
351633 ATGTCTTGGG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 2 0.04
32 45 0.96
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.19
Consensus pattern (32 bp):
GGGCCTAAGAGCCTACCCAAGGAAGTAACTTA
Found at i:351641 original size:32 final size:32
Alignment explanation
Indices: 351577--351662 Score: 118
Period size: 32 Copynumber: 2.7 Consensus size: 32
351567 GAGTACCTTA
* *
351577 GGGCCTAAGAGCTTACCCAAGGAAGTAACTTG
1 GGGCCTTAGAGCTTACCCAAGGAAATAACTTG
* **
351609 GGGCCTTAGAGCCTACCCAAGGAAATGTCTTG
1 GGGCCTTAGAGCTTACCCAAGGAAATAACTTG
*
351641 GGGCCTTAAAGCTTACCCAAGG
1 GGGCCTTAGAGCTTACCCAAGG
351663 TCACCTTAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.20
Consensus pattern (32 bp):
GGGCCTTAGAGCTTACCCAAGGAAATAACTTG
Found at i:352798 original size:28 final size:27
Alignment explanation
Indices: 352740--352812 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
352730 ACAGGGCTTG
* *
352740 GGGGTACTTTAGGTTATTTTACACTTCA
1 GGGGTA-TTTAGGTCATTTTACAATTCA
* *
352768 GGGGTATTTTGGTCATTTTATAATTCA
1 GGGGTATTTAGGTCATTTTACAATTCA
*
352795 AGGGTATTTCA-GTCATTT
1 GGGGTATTT-AGGTCATTT
352813 CCTTCCGTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 32 0.84
28 6 0.16
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.45
Consensus pattern (27 bp):
GGGGTATTTAGGTCATTTTACAATTCA
Found at i:352847 original size:18 final size:18
Alignment explanation
Indices: 352826--352872 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
352816 TCCGTTCAGC
352826 CTTTTCATTTAATTTAAA
1 CTTTTCATTTAATTTAAA
352844 CTTTTCATTTAATTTAAA
1 CTTTTCATTTAATTTAAA
*
352862 CTTGTCATTTA
1 CTTTTCATTTA
352873 TTTCATTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.30, C:0.13, G:0.02, T:0.55
Consensus pattern (18 bp):
CTTTTCATTTAATTTAAA
Found at i:353721 original size:22 final size:22
Alignment explanation
Indices: 353680--353723 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
353670 GTTTGACTTT
*
353680 TTGGTCAAAGTCAACGGTCAAA
1 TTGGTCAAAGTCAACAGTCAAA
353702 TTGGTCAAAGGTCAA-AGTCAAA
1 TTGGTCAAA-GTCAACAGTCAAA
353724 GCCAAGGGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (22 bp):
TTGGTCAAAGTCAACAGTCAAA
Found at i:353723 original size:13 final size:13
Alignment explanation
Indices: 353682--353724 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
353672 TTGACTTTTT
*
353682 GGTCAAAGTCAAC
1 GGTCAAAGTCAAA
353695 GGTCAAATTGGTCAAA
1 GGTCAAA---GTCAAA
353711 GGTCAAAGTCAAA
1 GGTCAAAGTCAAA
353724 G
1 G
353725 CCAAGGGGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 14 0.54
16 12 0.46
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.19
Consensus pattern (13 bp):
GGTCAAAGTCAAA
Found at i:358548 original size:12 final size:12
Alignment explanation
Indices: 358531--358575 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
358521 TTCAAAGAGG
358531 TTTTATATTTAA
1 TTTTATATTTAA
358543 TTTTATA-TTATA
1 TTTTATATTTA-A
358555 TTTTAT-TTTAA
1 TTTTATATTTAA
358566 TTTTAATATT
1 TTTT-ATATT
358576 ATTTTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 8 0.28
12 19 0.66
13 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:358558 original size:24 final size:24
Alignment explanation
Indices: 358531--358583 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
358521 TTCAAAGAGG
358531 TTTTATATTTAATTTT-ATATTATA
1 TTTTAT-TTTAATTTTAATATTATA
*
358555 TTTTATTTTAATTTTAATATTATT
1 TTTTATTTTAATTTTAATATTATA
358579 TTTTA
1 TTTTA
358584 AATAAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTATTTTAATTTTAATATTATA
Found at i:358584 original size:13 final size:13
Alignment explanation
Indices: 358566--358656 Score: 57
Period size: 13 Copynumber: 7.2 Consensus size: 13
358556 TTTATTTTAA
358566 TTTTAATATTATT
1 TTTTAATATTATT
*
358579 TTTTAA-A-TA-A
1 TTTTAATATTATT
* * *
358589 ATTAAATATTAAT
1 TTTTAATATTATT
*
358602 TTTTAATATTATA
1 TTTTAATATTATT
* *
358615 TTATAGATATTA-A
1 TTTTA-ATATTATT
358628 TTTTAATATTAATT
1 TTTTAATATT-ATT
358642 TTTTAA-ATTTATT
1 TTTTAATA-TTATT
358655 TT
1 TT
358657 ATATCATATA
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 4 0.07
11 3 0.05
12 8 0.13
13 31 0.52
14 14 0.23
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (13 bp):
TTTTAATATTATT
Found at i:358591 original size:24 final size:24
Alignment explanation
Indices: 358541--358607 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 24
358531 TTTTATATTT
* ** *
358541 AATTTT-ATATTATATTTTATTTT
1 AATTTTAATATTATTTTTTAAATA
358564 AATTTTAATATTATTTTTTAAATA
1 AATTTTAATATTATTTTTTAAATA
* *
358588 AA-TTAAATATTAATTTTTAA
1 AATTTTAATATTATTTTTTAA
358608 TATTATATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
23 22 0.59
24 15 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
AATTTTAATATTATTTTTTAAATA
Found at i:358628 original size:27 final size:25
Alignment explanation
Indices: 358570--358639 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 25
358560 TTTTAATTTT
*
358570 AATATTATTTTTTAA-A-TAAATTA
1 AATATTAATTTTTAATATTAAATTA
*
358593 AATATTAATTTTTAATATTATATTA
1 AATATTAATTTTTAATATTAAATTA
358618 TAGATATTAA-TTTTAATATTAA
1 -A-ATATTAATTTTTAATATTAA
358640 TTTTTTAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
23 14 0.35
24 1 0.03
25 6 0.15
26 12 0.30
27 7 0.17
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (25 bp):
AATATTAATTTTTAATATTAAATTA
Found at i:358638 original size:12 final size:12
Alignment explanation
Indices: 358539--358643 Score: 92
Period size: 12 Copynumber: 8.7 Consensus size: 12
358529 GGTTTTATAT
358539 TTAATTTT-ATA
1 TTAATTTTAATA
*
358550 TTATATTTT-ATT
1 TTA-ATTTTAATA
358562 TTAATTTTAATA
1 TTAATTTTAATA
*
358574 TTATTTTTTAA-A
1 TTA-ATTTTAATA
* *
358586 -TAAATTAAATA
1 TTAATTTTAATA
358597 TTAATTTTTAATA
1 TTAA-TTTTAATA
*
358610 TTATATTATAGATA
1 TTA-ATTTTA-ATA
358624 TTAATTTTAATA
1 TTAATTTTAATA
358636 TTAATTTT
1 TTAATTTT
358644 TTAAATTTAT
Statistics
Matches: 76, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
10 4 0.05
11 11 0.14
12 30 0.39
13 24 0.32
14 7 0.09
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (12 bp):
TTAATTTTAATA
Found at i:358688 original size:20 final size:20
Alignment explanation
Indices: 358644--358713 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 20
358634 TATTAATTTT
358644 TTAAATTTATTTTATATCA-TA
1 TTAAA-TTATTTTATAT-ATTA
358665 -TAAATTATTTTATATATTA
1 TTAAATTATTTTATATATTA
358684 TTAAA--ATTTTATAT-TTA
1 TTAAATTATTTTATATATTA
*
358701 TTTTAATTATTTT
1 -TTAAATTATTTT
358714 GATTTAAGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
17 3 0.07
18 14 0.33
19 13 0.30
20 13 0.30
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAAATTATTTTATATATTA
Found at i:358690 original size:21 final size:21
Alignment explanation
Indices: 358644--358691 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
358634 TATTAATTTT
*
358644 TTAAATTTATTTTATATCATA
1 TTAAAATTATTTTATATCATA
358665 -T-AAATTATTTTATAT-ATTA
1 TTAAAATTATTTTATATCA-TA
358684 TTAAAATT
1 TTAAAATT
358692 TTATATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 1 0.04
19 15 0.65
20 2 0.09
21 5 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAAATTATTTTATATCATA
Found at i:360981 original size:29 final size:29
Alignment explanation
Indices: 360905--360981 Score: 145
Period size: 29 Copynumber: 2.7 Consensus size: 29
360895 CTTCCCAGCA
*
360905 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
360934 TAGGTCGCCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
360963 TAGGTCGCCATGCACTCCT
1 TAGGTCGCCATGCACTCCT
360982 CCTGCTCCTC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCTGGCGACCTTG
Found at i:361074 original size:14 final size:14
Alignment explanation
Indices: 361037--361074 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
361027 GCTCGCTCGA
361037 ATGGCCTCGGTCGG
1 ATGGCCTCGGTCGG
*
361051 ATGCCCTCGGTCGG
1 ATGGCCTCGGTCGG
*
361065 ATGGCTTCGG
1 ATGGCCTCGG
361075 ATGCCCAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.08, C:0.29, G:0.39, T:0.24
Consensus pattern (14 bp):
ATGGCCTCGGTCGG
Found at i:362510 original size:17 final size:17
Alignment explanation
Indices: 362488--362522 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
362478 TAGTTGGTGC
362488 TTTACCTAATACATCAG
1 TTTACCTAATACATCAG
362505 TTTACCTAATACATCAG
1 TTTACCTAATACATCAG
362522 T
1 T
362523 AGATGTCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.37
Consensus pattern (17 bp):
TTTACCTAATACATCAG
Found at i:370312 original size:31 final size:30
Alignment explanation
Indices: 370240--370496 Score: 214
Period size: 30 Copynumber: 8.5 Consensus size: 30
370230 TCATAACATT
* *
370240 AAAAATATATTTTATTTTTATATTAACTTA
1 AAAAATATATTTTATTCTTATCTTAACTTA
** * *
370270 TTAAATATATTTTATTCTTGTCTTAACCTA
1 AAAAATATATTTTATTCTTATCTTAACTTA
*
370300 AAAATATATATTTTAGTCTTTATCTTAACTTA
1 AAAA-ATATATTTTATTC-TTATCTTAACTTA
370332 AAAAATATATTTTATTCTTATCTTAACTTA
1 AAAAATATATTTTATTCTTATCTTAACTTA
** * * * * *
370362 TTACATAAATTATATTCTTAACTTAAATTA
1 AAAAATATATTTTATTCTTATCTTAACTTA
** **
370392 TTAAATAT-TTTATATTCTTATCTTAAAATA
1 AAAAATATATTT-TATTCTTATCTTAACTTA
** * * *
370422 TTAAATATAATTAATTC-TATTTTAACTTA
1 AAAAATATATTTTATTCTTATCTTAACTTA
* * *
370451 AAACATATATTTTATTTTTATCTTAAATT-
1 AAAAATATATTTTATTCTTATCTTAACTTA
*
370480 TAAAATATAATTTTATT
1 AAAAATAT-ATTTTATT
370497 TTAACTAAAA
Statistics
Matches: 182, Mismatches: 39, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
29 28 0.15
30 113 0.62
31 26 0.14
32 15 0.08
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.52
Consensus pattern (30 bp):
AAAAATATATTTTATTCTTATCTTAACTTA
Found at i:370508 original size:24 final size:24
Alignment explanation
Indices: 370481--370532 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
370471 TCTTAAATTT
**
370481 AAAATATAATTTTATTTTAACTA-A
1 AAAAT-TAATTTTACCTTAACTACA
*
370505 AAAATTATTTTTACCTTAACTACA
1 AAAATTAATTTTACCTTAACTACA
370529 AAAA
1 AAAA
370533 ATATTATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (24 bp):
AAAATTAATTTTACCTTAACTACA
Found at i:370516 original size:23 final size:23
Alignment explanation
Indices: 370462--370537 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 23
370452 AACATATATT
* **
370462 TTATTTTTATCTTAAATTTAAAA
1 TTATTTTTATCTTAACTAAAAAA
* *
370485 TATAATTTTATTTTAACTAAAAAA
1 T-TATTTTTATCTTAACTAAAAAA
*
370509 TTATTTTTACCTTAACTACAAAAA
1 TTATTTTTATCTTAACTA-AAAAA
*
370533 ATATT
1 TTATT
370538 ATATTTCTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
23 15 0.36
24 27 0.64
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (23 bp):
TTATTTTTATCTTAACTAAAAAA
Found at i:370605 original size:31 final size:30
Alignment explanation
Indices: 370565--370675 Score: 123
Period size: 30 Copynumber: 3.7 Consensus size: 30
370555 TTAAAATATT
* * * *
370565 ATTATAATAAAATATAAATATTTAAGTTAAA
1 ATTAGAATAAAATAT-ATTTTTTAAATTAAA
* * *
370596 ATTAGAATAAATTATATTTTTTAATTTAAG
1 ATTAGAATAAAATATATTTTTTAAATTAAA
* *
370626 ATGAGATTAAAATATATTTTTTAAATTAAA
1 ATTAGAATAAAATATATTTTTTAAATTAAA
*
370656 ATAAGAATAAAATATATTTT
1 ATTAGAATAAAATATATTTT
370676 GAGGTTACGA
Statistics
Matches: 67, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
30 54 0.81
31 13 0.19
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (30 bp):
ATTAGAATAAAATATATTTTTTAAATTAAA
Found at i:370642 original size:30 final size:30
Alignment explanation
Indices: 370570--370718 Score: 122
Period size: 30 Copynumber: 5.0 Consensus size: 30
370560 ATATTATTAT
* * * *
370570 AATAAAATATAAATATTTAAGTTAAAATTAG
1 AATAAAATAT-ATTTTTTAAATTAAAATAAG
* * * *
370601 AATAAATTATATTTTTTAATTTAAGATGAG
1 AATAAAATATATTTTTTAAATTAAAATAAG
*
370631 ATTAAAATATATTTTTTAAATTAAAATAAG
1 AATAAAATATATTTTTTAAATTAAAATAAG
* ** *
370661 AATAAAATATA-TTTTGAGGTTACGAA-AAG
1 AATAAAATATATTTTTTAAATTA-AAATAAG
** *
370690 AATAAAATATATTTAATAAATTAAGATAA
1 AATAAAATATATTTTTTAAATTAAAATAA
370719 AAAATATTTT
Statistics
Matches: 92, Mismatches: 23, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
29 23 0.25
30 60 0.65
31 9 0.10
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (30 bp):
AATAAAATATATTTTTTAAATTAAAATAAG
Found at i:370746 original size:24 final size:26
Alignment explanation
Indices: 370687--370757 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 26
370677 AGGTTACGAA
370687 AAGA-ATAAAATATATTTAATAAATT
1 AAGATATAAAATATATTTAATAAATT
* * *
370712 AAGATAAAAAATATTTTTAAT-GA-T
1 AAGATATAAAATATATTTAATAAATT
*
370736 AAGATGTAAAAT-TAATTTAATA
1 AAGATATAAAATAT-ATTTAATA
370758 TGTGAATTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
23 1 0.03
24 17 0.46
25 5 0.14
26 14 0.38
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (26 bp):
AAGATATAAAATATATTTAATAAATT
Found at i:371363 original size:16 final size:16
Alignment explanation
Indices: 371342--371372 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
371332 TATAAATTAA
371342 ATTAATGGTGTTCATC
1 ATTAATGGTGTTCATC
371358 ATTAATGGTGTTCAT
1 ATTAATGGTGTTCAT
371373 TGCTTCTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.45
Consensus pattern (16 bp):
ATTAATGGTGTTCATC
Found at i:372518 original size:19 final size:18
Alignment explanation
Indices: 372490--372525 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
372480 ATATTTATTT
372490 ATATAAAATAATAATATA
1 ATATAAAATAATAATATA
372508 ATATGAAAATAATAATAT
1 ATAT-AAAATAATAATAT
372526 TATAATCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
ATATAAAATAATAATATA
Found at i:375008 original size:15 final size:15
Alignment explanation
Indices: 374988--375018 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
374978 AATTTTTTCA
374988 ATAGTACAAGATACG
1 ATAGTACAAGATACG
375003 ATAGTACAAGATACG
1 ATAGTACAAGATACG
375018 A
1 A
375019 AAATAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.19
Consensus pattern (15 bp):
ATAGTACAAGATACG
Found at i:376031 original size:23 final size:23
Alignment explanation
Indices: 376005--376062 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
375995 TAAACTACCA
376005 AAAGGCAGAGAAAAACATGCCAC
1 AAAGGCAGAGAAAAACATGCCAC
* * * * *
376028 AAAGGTAGAGATAAACGTGTCAT
1 AAAGGCAGAGAAAAACATGCCAC
*
376051 AAAGACAGAGAA
1 AAAGGCAGAGAA
376063 CATGTCACAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.52, C:0.14, G:0.24, T:0.10
Consensus pattern (23 bp):
AAAGGCAGAGAAAAACATGCCAC
Done.