Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 103 of 190
Found at i:31314147 original size:33 final size:33
Alignment explanation
Indices: 31314048--31314179 Score: 129
Period size: 34 Copynumber: 3.9 Consensus size: 33
31314038 TTGATTTATG
* *** *
31314048 ATAAGCATATTAATTGCAATTGTATTGACCTGTT
1 ATAAGCATATTAATTGCTA-CCAATTGATCTGTT
* * **
31314082 ATAAGCATATTAAGTACTACTGTATTGATCTGTT
1 ATAAGCATATTAATTGCTAC-CAATTGATCTGTT
31314116 ATAAGCATATTAATTGCTACCAATTGATCTGTT
1 ATAAGCATATTAATTGCTACCAATTGATCTGTT
* * *
31314149 ATAAGCACATTAAATGCTATCACATTGATCT
1 ATAAGCATATTAATTGCTACCA-ATTGATCT
31314180 AAGCATGCCA
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
33 30 0.36
34 54 0.64
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (33 bp):
ATAAGCATATTAATTGCTACCAATTGATCTGTT
Found at i:31314431 original size:45 final size:45
Alignment explanation
Indices: 31314257--31314418 Score: 182
Period size: 45 Copynumber: 3.6 Consensus size: 45
31314247 AAATTTGCTA
* * *
31314257 TGTATCCATAGCTAGAGGCAGATTCTATCTGTGAGATATTTGTTG
1 TGTATCCACAGCTAGAGGCAGATTCTATCTGTAAGATTTTTGTTG
* * * *
31314302 TGCATCCACAGCTAGAGGTAGATTCTAACTGTAGGA-TTTTGTTG
1 TGTATCCACAGCTAGAGGCAGATTCTATCTGTAAGATTTTTGTTG
* * * * * *
31314346 TGTTTTCACAGCTAGAAGCAGATTGTGTCTGCAAGATTTTTGTTG
1 TGTATCCACAGCTAGAGGCAGATTCTATCTGTAAGATTTTTGTTG
* *
31314391 TGTATCCACAGCCAGAGGCAAATTCTAT
1 TGTATCCACAGCTAGAGGCAGATTCTAT
31314419 TTGTGGGATT
Statistics
Matches: 92, Mismatches: 24, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
44 33 0.36
45 59 0.64
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (45 bp):
TGTATCCACAGCTAGAGGCAGATTCTATCTGTAAGATTTTTGTTG
Found at i:31314486 original size:22 final size:22
Alignment explanation
Indices: 31314446--31314488 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
31314436 GTGTCCACAT
* *
31314446 CCATTGGTAGTTTATCTACAAA
1 CCATTGGTAGTTAAACTACAAA
*
31314468 CCATTGGTGGTTAAACTACAA
1 CCATTGGTAGTTAAACTACAA
31314489 CTCGATGTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (22 bp):
CCATTGGTAGTTAAACTACAAA
Found at i:31319119 original size:32 final size:32
Alignment explanation
Indices: 31319080--31319163 Score: 107
Period size: 32 Copynumber: 2.6 Consensus size: 32
31319070 TATTGAATTT
*
31319080 AGTTTGTTGGATTTTGAAATTATTATGTCTTGA
1 AGTTTGTTGGATATTGAAATTATTATGT-TTGA
* * *
31319113 A-TTTGTTAGATATTGAATTTATTATGTTTTA
1 AGTTTGTTGGATATTGAAATTATTATGTTTGA
*
31319144 AGCTTGTTGGATATTGAAAT
1 AGTTTGTTGGATATTGAAAT
31319164 GATTGACAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
31 4 0.09
32 38 0.88
33 1 0.02
ACGTcount: A:0.27, C:0.02, G:0.19, T:0.51
Consensus pattern (32 bp):
AGTTTGTTGGATATTGAAATTATTATGTTTGA
Found at i:31320614 original size:18 final size:19
Alignment explanation
Indices: 31320569--31320606 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
31320559 CATCCAAACA
*
31320569 CCAGAAAAATAAATCATTT
1 CCAGAAAAACAAATCATTT
31320588 CCAGAAAAACAAATCATTT
1 CCAGAAAAACAAATCATTT
31320607 TTAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.18, G:0.05, T:0.24
Consensus pattern (19 bp):
CCAGAAAAACAAATCATTT
Found at i:31321296 original size:27 final size:28
Alignment explanation
Indices: 31321266--31321319 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
31321256 TTTTTAAAAA
*
31321266 AAATTATAAAAAC-ATTAAAAGTTATAC
1 AAATTATAAAAACAATAAAAAGTTATAC
31321293 AAATTATAAAAACAATAAAAAGTTATA
1 AAATTATAAAAACAATAAAAAGTTATA
31321320 GAAAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.28
Consensus pattern (28 bp):
AAATTATAAAAACAATAAAAAGTTATAC
Found at i:31321812 original size:19 final size:18
Alignment explanation
Indices: 31321790--31321832 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
31321780 TATTCTTTAG
31321790 ATTTTTATAAAAATATATA
1 ATTTTTATAAAAATATA-A
* *
31321809 ATTTTTTTTAAAATATAA
1 ATTTTTATAAAAATATAA
31321827 ATTTTT
1 ATTTTT
31321833 TTATTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTTATAAAAATATAA
Found at i:31321843 original size:18 final size:18
Alignment explanation
Indices: 31321822--31321859 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
31321812 TTTTTTAAAA
* *
31321822 TATAAATTTTTTTATTTT
1 TATAAATATTTTTAATTT
31321840 TATAAATATTTTTAATTT
1 TATAAATATTTTTAATTT
31321858 TA
1 TA
31321860 ATTTTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATAAATATTTTTAATTT
Found at i:31321851 original size:19 final size:18
Alignment explanation
Indices: 31321822--31321858 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
31321812 TTTTTTAAAA
*
31321822 TATAAATTTTTTTATTTT
1 TATAAATTTTTTAATTTT
31321840 TATAAATATTTTTAATTTT
1 TATAAAT-TTTTTAATTTT
31321859 AATTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TATAAATTTTTTAATTTT
Found at i:31321879 original size:10 final size:10
Alignment explanation
Indices: 31321824--31321884 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
31321814 TTTTAAAATA
31321824 TAAATTTTTT
1 TAAATTTTTT
*
31321834 T--ATTTTTA
1 TAAATTTTTT
*
31321842 TAAATATTTT
1 TAAATTTTTT
*
31321852 TAATTTTAATTT
1 TAAATTT--TTT
31321864 TAAATTTTTT
1 TAAATTTTTT
*
31321874 TGAATTTTTT
1 TAAATTTTTT
31321884 T
1 T
31321885 TTGTAATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
8 7 0.17
10 24 0.60
12 9 0.22
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (10 bp):
TAAATTTTTT
Found at i:31322155 original size:14 final size:14
Alignment explanation
Indices: 31322136--31322162 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31322126 AGATTGGTCT
31322136 TGTGTGGGGTGCCG
1 TGTGTGGGGTGCCG
31322150 TGTGTGGGGTGCC
1 TGTGTGGGGTGCC
31322163 AACTGAGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.56, T:0.30
Consensus pattern (14 bp):
TGTGTGGGGTGCCG
Found at i:31326137 original size:34 final size:34
Alignment explanation
Indices: 31326099--31326208 Score: 157
Period size: 34 Copynumber: 3.2 Consensus size: 34
31326089 ATTAATTCGC
* * *
31326099 TATAAGCATATTAATTACTACCGTATTGATCGGT
1 TATAAGCATATTAATTGCTACCATATTGATCTGT
* * *
31326133 TATAAGCATATTATTTGTTATCATATTGATCTGT
1 TATAAGCATATTAATTGCTACCATATTGATCTGT
*
31326167 TATAAGCATATTAATTGCTACCATATTGATCTTT
1 TATAAGCATATTAATTGCTACCATATTGATCTGT
31326201 TATAAGCA
1 TATAAGCA
31326209 AGCCATATTG
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 66 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.43
Consensus pattern (34 bp):
TATAAGCATATTAATTGCTACCATATTGATCTGT
Found at i:31326178 original size:19 final size:19
Alignment explanation
Indices: 31326122--31326178 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
31326112 ATTACTACCG
*
31326122 TATTGATCGGTTATAAGCA
1 TATTGATCTGTTATAAGCA
*
31326141 TATT-ATTTGTTAT---CA
1 TATTGATCTGTTATAAGCA
31326156 TATTGATCTGTTATAAGCA
1 TATTGATCTGTTATAAGCA
31326175 TATT
1 TATT
31326179 AATTGCTACC
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 6 0.19
16 8 0.26
18 7 0.23
19 10 0.32
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (19 bp):
TATTGATCTGTTATAAGCA
Found at i:31329702 original size:36 final size:36
Alignment explanation
Indices: 31329662--31329744 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 36
31329652 TGATGATTGT
* * *
31329662 TGTGAAAG-AGAATATGTGGGTTTACTGTTCATGCCA
1 TGTGAAAGTA-AATATGTGAGTATACTATTCATGCCA
* **
31329698 TGTGACAGTAAATATGTGAGTATGTTATTCATGCCA
1 TGTGAAAGTAAATATGTGAGTATACTATTCATGCCA
*
31329734 TGTGACAGTAA
1 TGTGAAAGTAA
31329745 TTATAATGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
36 39 0.98
37 1 0.03
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (36 bp):
TGTGAAAGTAAATATGTGAGTATACTATTCATGCCA
Found at i:31335601 original size:35 final size:36
Alignment explanation
Indices: 31335529--31335610 Score: 112
Period size: 35 Copynumber: 2.3 Consensus size: 36
31335519 TGATGATTGT
* * * *
31335529 TGTGAAAGAAAATATGTGGGTATGTTATTCGTTCCA
1 TGTGACAGTAAATATGTGGGTATGTTATTCATGCCA
31335565 TG-GACAGTAAATATGTGGGTATGTTATTCATGCCA
1 TGTGACAGTAAATATGTGGGTATGTTATTCATGCCA
*
31335600 TGTGATAGTAA
1 TGTGACAGTAA
31335611 TTGTAATGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 31 0.77
36 9 0.22
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35
Consensus pattern (36 bp):
TGTGACAGTAAATATGTGGGTATGTTATTCATGCCA
Found at i:31336024 original size:12 final size:12
Alignment explanation
Indices: 31336007--31336032 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31335997 CAAAATAGGC
31336007 TTTTAGCGGCGT
1 TTTTAGCGGCGT
31336019 TTTTAGCGGCGT
1 TTTTAGCGGCGT
31336031 TT
1 TT
31336033 GGACAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:31336066 original size:41 final size:38
Alignment explanation
Indices: 31336021--31336112 Score: 94
Period size: 40 Copynumber: 2.3 Consensus size: 38
31336011 AGCGGCGTTT
*
31336021 TTAGCGGCGTTTGGACAAAAAACGCCTCTAAAAATCGAGCA
1 TTAGCGGCGTTT-GA-AAAAAACGCCGCTAAAAAT-GAGCA
* ** *
31336062 TTAGCGGCGCTTTTATGAAAGCGCCGCTAAAAATGAGCA
1 TTAGCGGCG-TTTGAAAAAAACGCCGCTAAAAATGAGCA
*
31336101 TTAGCGGTGTTT
1 TTAGCGGCGTTT
31336113 TTCGGAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
38 3 0.07
39 13 0.30
40 15 0.34
41 10 0.23
42 3 0.07
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (38 bp):
TTAGCGGCGTTTGAAAAAAACGCCGCTAAAAATGAGCA
Found at i:31336133 original size:39 final size:40
Alignment explanation
Indices: 31336039--31336121 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 40
31336029 GTTTGGACAA
* *
31336039 AAAACGCCTCTAAAAATCGAGCATTAGCGGCGCTTTTATG
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTTAGG
* * * *
31336079 AAAGCGCCGCTAAAAAT-GAGCATTAGCGGTGTTTTTCGG
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTTAGG
31336118 AAAA
1 AAAA
31336122 ACGTCGCAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
39 21 0.58
40 15 0.42
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTTAGG
Found at i:31336134 original size:40 final size:40
Alignment explanation
Indices: 31336039--31336134 Score: 95
Period size: 40 Copynumber: 2.4 Consensus size: 40
31336029 GTTTGGACAA
* * *
31336039 AAAACGCCTCTAAAAATCGAGCATTAGCGGCGCTTTTATG
1 AAAACGCCGCAAAAAATCGAGCATTAGCGGCGCTTTTAGG
* * * * *
31336079 AAAGCGCCGCTAAAAAT-GAGCATTAGCGGTGTTTTTCGG
1 AAAACGCCGCAAAAAATCGAGCATTAGCGGCGCTTTTAGG
*
31336118 AAAAACGTCGCAAAAAA
1 -AAAACGCCGCAAAAAA
31336135 CCTAAGCCCA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
39 18 0.39
40 28 0.61
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (40 bp):
AAAACGCCGCAAAAAATCGAGCATTAGCGGCGCTTTTAGG
Found at i:31336403 original size:41 final size:41
Alignment explanation
Indices: 31336171--31336405 Score: 317
Period size: 41 Copynumber: 5.7 Consensus size: 41
31336161 CCTTTTGGGG
* *
31336171 CTTTAGCGGCGTTTTTAAAAAAAGCGTCGCTAATGCTCAGAT
1 CTTTAGCGGCGTTTTT-GAAAAAGCGCCGCTAATGCTCAGAT
*
31336213 CTTTAGCGGCGTTTTTGAAAATGCGCCGCTAATGCTCAGAT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
* * * *
31336254 CTTTAACGGCGTTTTTGAAAATGCGCCACTAATACTCAGAT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
*
31336295 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
* * * * **
31336336 CTTTAGCGGCGTTTTTGGAAAGGCACCGCTAATGCTCGGGG
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
* *
31336377 CTTTAGTGGCGTTTTTGAAAAAGCACCGC
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGC
31336406 AAAAACATTT
Statistics
Matches: 174, Mismatches: 19, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
41 158 0.91
42 16 0.09
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
Found at i:31336550 original size:26 final size:26
Alignment explanation
Indices: 31336502--31336552 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
31336492 AAAATGGATA
** * *
31336502 AATTTGAAATAATGACACGTAGAAAT
1 AATTTGAAATAAAAAAACATAGAAAT
31336528 AATTTGAAATAAAAAAACATAGAAA
1 AATTTGAAATAAAAAAACATAGAAA
31336553 AATATTTGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (26 bp):
AATTTGAAATAAAAAAACATAGAAAT
Found at i:31337034 original size:89 final size:90
Alignment explanation
Indices: 31336941--31337111 Score: 281
Period size: 90 Copynumber: 1.9 Consensus size: 90
31336931 TTTAGTGTCA
*
31336941 GGTTAGGGTTTAGGATTTAGATTAATTAGTG-TGTTTTAATTTATATATTAAACAATGTTTAGGG
1 GGTTAGGGTTTAGGATTTAGATTAATTAGTGTTGTTTTAATTTATATATTAAACAAGGTTTAGGG
*
31337005 GTTAGGGGTTAGGGATTCGGGGTCG
66 GTTAGGGGTTAAGGATTCGGGGTCG
* * *
31337030 GGTTAGGGTTTATGATTTAGATTAATTAGTGTTTTTTTAATTTATATATTAAATAAGGTTTAGGG
1 GGTTAGGGTTTAGGATTTAGATTAATTAGTGTTGTTTTAATTTATATATTAAACAAGGTTTAGGG
*
31337095 GTTAGTGGTTAAGGATT
66 GTTAGGGGTTAAGGATT
31337112 TGGAGTTTGG
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
89 30 0.40
90 45 0.60
ACGTcount: A:0.26, C:0.02, G:0.28, T:0.44
Consensus pattern (90 bp):
GGTTAGGGTTTAGGATTTAGATTAATTAGTGTTGTTTTAATTTATATATTAAACAAGGTTTAGGG
GTTAGGGGTTAAGGATTCGGGGTCG
Found at i:31342438 original size:43 final size:43
Alignment explanation
Indices: 31342336--31342558 Score: 286
Period size: 43 Copynumber: 5.2 Consensus size: 43
31342326 AGATTATGTT
* * * *
31342336 TTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCTTGGTC
*
31342378 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCTTGGTC
* *
31342421 TATAGCGGCGTTTGTGATAAAAGCGTCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCTTGGTC
* * ** * *
31342464 TTTAGCAGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCATGGTT
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCTTGGTC
* * **
31342507 TTTAGTGGCATTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCTTGGTC
31342550 TTTAGCGGC
1 TTTAGCGGC
31342559 ATTTTTTCCG
Statistics
Matches: 157, Mismatches: 23, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
42 33 0.21
43 124 0.79
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:31344793 original size:68 final size:68
Alignment explanation
Indices: 31344684--31344955 Score: 307
Period size: 68 Copynumber: 4.0 Consensus size: 68
31344674 ATTAGAAATC
* * ** *
31344684 CACCAAGACAAGAAACATCG-GATCATATTGTGTAAGACCATAGTTGGGCTATGGCAACATATGG
1 CACCAGGACAATAAACAT-GAGATCATATCATGTAAGACCATAGCTGGGCTATGGCAACATATGG
31344748 AGTT
65 AGTT
* * * * *
31344752 CACCAGGACAGTAACCATGAGATCATATCATGTAAGACCATAGTTGGGTTATGACAACATATGGA
1 CACCAGGACAATAAACATGAGATCATATCATGTAAGACCATAGCTGGGCTATGGCAACATATGGA
*
31344817 GTC
66 GTT
* * *
31344820 CGCCAAGACAATAAACAT-AGGATCATATCATGTAAGACCATAGCTGGGCTATGGCAAAATATGG
1 CACCAGGACAATAAACATGA-GATCATATCATGTAAGACCATAGCTGGGCTATGGCAACATATGG
31344884 AG-T
65 AGTT
* * * * * * *
31344887 CTTCCAGGACAATAAACATGGGATCATATAATGTAAGACCATAACTGGGTTATGGCAACAAATGA
1 C-ACCAGGACAATAAACATGAGATCATATCATGTAAGACCATAGCTGGGCTATGGCAACATATGG
31344952 AGTT
65 AGTT
31344956 TGCTAGAATG
Statistics
Matches: 172, Mismatches: 27, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
67 3 0.02
68 168 0.98
69 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (68 bp):
CACCAGGACAATAAACATGAGATCATATCATGTAAGACCATAGCTGGGCTATGGCAACATATGGA
GTT
Found at i:31344936 original size:136 final size:136
Alignment explanation
Indices: 31344686--31344946 Score: 380
Period size: 136 Copynumber: 1.9 Consensus size: 136
31344676 TAGAAATCCA
* ** * *
31344686 CCAAGACAAGAAACATCGGATCATATTGTGTAAGACCATAGTTGGGCTATGGCAACATATGGAGT
1 CCAAGACAAGAAACATAGGATCATATCATGTAAGACCATAGCTGGGCTATGGCAAAATATGGAGT
* * * **
31344751 TCACCAGGACAGTAACCATGAGATCATATCATGTAAGACCATAGTTGGGTTATGACAACATATGG
66 TCACCAGGACAATAAACATGAGATCATATAATGTAAGACCATAACTGGGTTATGACAACATATGG
31344816 AGTCCG
131 AGTCCG
*
31344822 CCAAGACAATAAACATAGGATCATATCATGTAAGACCATAGCTGGGCTATGGCAAAATATGGAG-
1 CCAAGACAAGAAACATAGGATCATATCATGTAAGACCATAGCTGGGCTATGGCAAAATATGGAGT
* * *
31344886 TCTTCCAGGACAATAAACATGGGATCATATAATGTAAGACCATAACTGGGTTATGGCAACA
66 TC-ACCAGGACAATAAACATGAGATCATATAATGTAAGACCATAACTGGGTTATGACAACA
31344947 AATGAAGTTT
Statistics
Matches: 110, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
135 2 0.02
136 108 0.98
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (136 bp):
CCAAGACAAGAAACATAGGATCATATCATGTAAGACCATAGCTGGGCTATGGCAAAATATGGAGT
TCACCAGGACAATAAACATGAGATCATATAATGTAAGACCATAACTGGGTTATGACAACATATGG
AGTCCG
Found at i:31359214 original size:33 final size:33
Alignment explanation
Indices: 31359174--31359240 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
31359164 ATGATCGACT
31359174 AAGGCACAAACATGTTAAACATGAATAAAATAG
1 AAGGCACAAACATGTTAAACATGAATAAAATAG
31359207 AAGGCACAAACATGTTAAACATGAATAAAATAG
1 AAGGCACAAACATGTTAAACATGAATAAAATAG
31359240 A
1 A
31359241 TCTTATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.55, C:0.12, G:0.15, T:0.18
Consensus pattern (33 bp):
AAGGCACAAACATGTTAAACATGAATAAAATAG
Found at i:31361468 original size:26 final size:26
Alignment explanation
Indices: 31361426--31361475 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
31361416 TCTTGTACAT
*
31361426 GTATGCTCATACGAGCTATGAATCGG
1 GTATGCTCATACAAGCTATGAATCGG
31361452 GTATGCTC-TCACAAGCTATGAATC
1 GTATGCTCAT-ACAAGCTATGAATC
31361476 AATATACTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (26 bp):
GTATGCTCATACAAGCTATGAATCGG
Found at i:31361493 original size:25 final size:26
Alignment explanation
Indices: 31361436--31361493 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
31361426 GTATGCTCAT
** *
31361436 ACGAGCTATGAATCGGGTATGCTCTC
1 ACGAGCTATGAATCGAATATACTCTC
*
31361462 ACAAGCTATGAATC-AATATACTCTC
1 ACGAGCTATGAATCGAATATACTCTC
31361487 ACGAGCT
1 ACGAGCT
31361494 GTAAATCGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (26 bp):
ACGAGCTATGAATCGAATATACTCTC
Found at i:31361528 original size:24 final size:24
Alignment explanation
Indices: 31361487--31361561 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
31361477 ATATACTCTC
*
31361487 ACGAGCTGTAAATCGGTAAGCTCAT
1 ACGAGCTG-AAATTGGTAAGCTCAT
31361512 ACGAGCTGAAATTGGTAAGCTC-T
1 ACGAGCTGAAATTGGTAAGCTCAT
*
31361535 CACGAGCTAAAATTGGTAAGCTCAT
1 -ACGAGCTGAAATTGGTAAGCTCAT
31361560 AC
1 AC
31361562 AAGTTGTGGT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.02
24 36 0.78
25 9 0.20
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (24 bp):
ACGAGCTGAAATTGGTAAGCTCAT
Found at i:31366095 original size:50 final size:50
Alignment explanation
Indices: 31366020--31366119 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
31366010 TTTCAAGTTG
31366020 GAACCTTTTTCCAACATCATAAGTTGATTCTTCAAGATGGAATCAAACCT
1 GAACCTTTTTCCAACATCATAAGTTGATTCTTCAAGATGGAATCAAACCT
31366070 GAACCTTTTTCCAACATCATAAGTTGATTCTTCAAGATGGAATCAAACCT
1 GAACCTTTTTCCAACATCATAAGTTGATTCTTCAAGATGGAATCAAACCT
31366120 TTCTTTCACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (50 bp):
GAACCTTTTTCCAACATCATAAGTTGATTCTTCAAGATGGAATCAAACCT
Found at i:31377805 original size:56 final size:56
Alignment explanation
Indices: 31377742--31377854 Score: 190
Period size: 56 Copynumber: 2.0 Consensus size: 56
31377732 TCTCATGGTC
31377742 CTGCATTTCACAACAGGACAATTGTTTCAAGTTCCAGTTCAATTGTCAATTAGTGT
1 CTGCATTTCACAACAGGACAATTGTTTCAAGTTCCAGTTCAATTGTCAATTAGTGT
* * * *
31377798 CTGCATTTCACAATATGACAATTGTTTCATGTTCCAGTTCAATTGTCAGTTAGTGT
1 CTGCATTTCACAACAGGACAATTGTTTCAAGTTCCAGTTCAATTGTCAATTAGTGT
31377854 C
1 C
31377855 CACAATGTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (56 bp):
CTGCATTTCACAACAGGACAATTGTTTCAAGTTCCAGTTCAATTGTCAATTAGTGT
Found at i:31379885 original size:18 final size:18
Alignment explanation
Indices: 31379851--31379884 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31379841 ATCAATATCG
*
31379851 ATTTAACATGATTAAAAT
1 ATTTAACATGATAAAAAT
31379869 ATTTAACA-GATAAAAA
1 ATTTAACATGATAAAAA
31379885 AAACTCAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (18 bp):
ATTTAACATGATAAAAAT
Found at i:31379990 original size:2 final size:2
Alignment explanation
Indices: 31379983--31380020 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
31379973 ACATTAAATC
31379983 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31380021 TATTTGGGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31393401 original size:16 final size:16
Alignment explanation
Indices: 31393350--31393394 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 16
31393340 GGGTGAGAAG
31393350 TAAAAGTTTTGGAGGAAAA
1 TAAAAGTTTTGG-GG--AA
31393369 TAAAAAGTTTTGGGGAA
1 T-AAAAGTTTTGGGGAA
31393386 TAAAAGTTT
1 TAAAAGTTT
31393395 GAGGGAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.32
17 3 0.12
19 3 0.12
20 11 0.44
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.31
Consensus pattern (16 bp):
TAAAAGTTTTGGGGAA
Found at i:31393779 original size:9 final size:9
Alignment explanation
Indices: 31393765--31393801 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
31393755 TATAGTTTGA
31393765 TATTCGAAT
1 TATTCGAAT
31393774 TATTCGAAT
1 TATTCGAAT
*
31393783 TATTCGAGT
1 TATTCGAAT
31393792 TATTCGAAT
1 TATTCGAAT
31393801 T
1 T
31393802 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:31393871 original size:9 final size:9
Alignment explanation
Indices: 31393854--31393884 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
31393844 TCGAGTTGAT
31393854 TCGAATAAC
1 TCGAATAAC
*
31393863 TCGATTAAC
1 TCGAATAAC
31393872 TCGAATAAC
1 TCGAATAAC
31393881 TCGA
1 TCGA
31393885 TTCGTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:31397667 original size:8 final size:8
Alignment explanation
Indices: 31397633--31397684 Score: 59
Period size: 8 Copynumber: 6.0 Consensus size: 8
31397623 TTTTTTTGTG
31397633 AAATTTTA
1 AAATTTTA
31397641 TAAATTTATA
1 -AAATTT-TA
*
31397651 TACATTTTTA
1 -A-AATTTTA
31397661 AAATTTTA
1 AAATTTTA
31397669 AAATTTTA
1 AAATTTTA
31397677 AAATTTTA
1 AAATTTTA
31397685 GATGTTGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
8 22 0.56
9 7 0.18
10 6 0.15
11 4 0.10
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (8 bp):
AAATTTTA
Found at i:31398626 original size:28 final size:29
Alignment explanation
Indices: 31398577--31398648 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 29
31398567 TAAAAAAATA
**
31398577 AAAATTATGAAAATAAATAAAA-ACTATTT
1 AAAATTAAAAAAATAAATAAAATA-TATTT
*
31398606 AAAATTAAAAAAATAAA-AAAATATTTTT
1 AAAATTAAAAAAATAAATAAAATATATTT
31398634 AAAATATAAATAAAA
1 AAAAT-TAAA-AAAA
31398649 ATTCCAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 13 0.35
29 20 0.54
30 4 0.11
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (29 bp):
AAAATTAAAAAAATAAATAAAATATATTT
Found at i:31398643 original size:29 final size:30
Alignment explanation
Indices: 31398586--31398648 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 30
31398576 AAAAATTATG
31398586 AAAATAAATAAAAACTATTTAAAATTAAA-
1 AAAATAAATAAAAACTATTTAAAATTAAAT
*
31398615 AAAATAAA-AAAATA-TTTTTAAAATATAAAT
1 AAAATAAATAAAA-ACTATTTAAAAT-TAAAT
31398645 AAAA
1 AAAA
31398649 ATTCCAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 13 0.43
29 13 0.43
30 4 0.13
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (30 bp):
AAAATAAATAAAAACTATTTAAAATTAAAT
Found at i:31398914 original size:6 final size:6
Alignment explanation
Indices: 31398905--31398945 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
31398895 CAAAAATAAA
*
31398905 AATATT AATATT AATATA AATATT AATATT AATATT AATAT
1 AATATT AATATT AATATT AATATT AATATT AATATT AATAT
31398946 ATATAAATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AATATT
Found at i:31398925 original size:18 final size:18
Alignment explanation
Indices: 31398899--31398945 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
31398889 AAAAAACAAA
*
31398899 AATAAAAATATTAATATT
1 AATATAAATATTAATATT
31398917 AATATAAATATTAATATT
1 AATATAAATATTAATATT
*
31398935 AATATTAATAT
1 AATATAAATAT
31398946 ATATAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATATAAATATTAATATT
Found at i:31400227 original size:7 final size:7
Alignment explanation
Indices: 31400215--31400247 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
31400205 TGCCACATTA
31400215 TAAAAAT
1 TAAAAAT
31400222 TAAAAAT
1 TAAAAAT
31400229 TAAAAAT
1 TAAAAAT
31400236 TAAAAAT
1 TAAAAAT
31400243 TAAAA
1 TAAAA
31400248 GAAATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAAAAT
Found at i:31401267 original size:11 final size:10
Alignment explanation
Indices: 31401253--31401314 Score: 52
Period size: 11 Copynumber: 5.8 Consensus size: 10
31401243 AAATAACAAC
31401253 AAAACAATGA
1 AAAACAATGA
*
31401263 TAAAACAATAGG
1 -AAAACAAT-GA
**
31401275 AAAACAACAA
1 AAAACAATGA
31401285 CAAAACAATGA
1 -AAAACAATGA
*
31401296 AAAACAATAGC
1 AAAACAAT-GA
31401307 AAAACAAT
1 AAAACAAT
31401315 AGTTTTTTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
10 8 0.20
11 32 0.78
12 1 0.02
ACGTcount: A:0.68, C:0.15, G:0.08, T:0.10
Consensus pattern (10 bp):
AAAACAATGA
Found at i:31401301 original size:21 final size:22
Alignment explanation
Indices: 31401264--31401316 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
31401254 AAACAATGAT
*
31401264 AAAACAATAGGAAAACAACAAC
1 AAAACAATAGAAAAACAACAAC
* *
31401286 AAAACAAT-GAAAAACAATAGC
1 AAAACAATAGAAAAACAACAAC
31401307 AAAACAATAG
1 AAAACAATAG
31401317 TTTTTTTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.68, C:0.15, G:0.09, T:0.08
Consensus pattern (22 bp):
AAAACAATAGAAAAACAACAAC
Found at i:31401305 original size:32 final size:33
Alignment explanation
Indices: 31401247--31401313 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 33
31401237 ATAGTGAAAT
*
31401247 AACAACAAAACAATGATAAAACAATAGGAAAAC
1 AACAACAAAACAATGATAAAACAATAGCAAAAC
31401280 AACAACAAAACAATGA-AAAACAATAGCAAAAC
1 AACAACAAAACAATGATAAAACAATAGCAAAAC
31401312 AA
1 AA
31401314 TAGTTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.52
33 16 0.48
ACGTcount: A:0.69, C:0.16, G:0.07, T:0.07
Consensus pattern (33 bp):
AACAACAAAACAATGATAAAACAATAGCAAAAC
Found at i:31401315 original size:11 final size:11
Alignment explanation
Indices: 31401264--31401316 Score: 63
Period size: 11 Copynumber: 4.9 Consensus size: 11
31401254 AAACAATGAT
*
31401264 AAAACAATAGG
1 AAAACAATAGC
* *
31401275 AAAACAACAAC
1 AAAACAATAGC
*
31401286 AAAACAAT-GA
1 AAAACAATAGC
31401296 AAAACAATAGC
1 AAAACAATAGC
31401307 AAAACAATAG
1 AAAACAATAG
31401317 TTTTTTTCTT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
10 8 0.24
11 26 0.76
ACGTcount: A:0.68, C:0.15, G:0.09, T:0.08
Consensus pattern (11 bp):
AAAACAATAGC
Found at i:31402032 original size:21 final size:21
Alignment explanation
Indices: 31402008--31402050 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
31401998 TTATTTACAA
*
31402008 ATTTAT-AATTTTTAACAAAAT
1 ATTTATAAAATTTTAA-AAAAT
*
31402029 ATTTTTAAAATTTTAAAAAAT
1 ATTTATAAAATTTTAAAAAAT
31402050 A
1 A
31402051 AGTTTTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTATAAAATTTTAAAAAAT
Found at i:31402056 original size:22 final size:22
Alignment explanation
Indices: 31402017--31402061 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
31402007 AATTTATAAT
*
31402017 TTTTAACAAAATATTTTTAAAA
1 TTTTAACAAAATAGTTTTAAAA
*
31402039 TTTTAA-AAAATAAGTTTTGAAA
1 TTTTAACAAAAT-AGTTTTAAAA
31402061 T
1 T
31402062 AAATGAACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (22 bp):
TTTTAACAAAATAGTTTTAAAA
Found at i:31405724 original size:58 final size:58
Alignment explanation
Indices: 31405655--31405776 Score: 208
Period size: 58 Copynumber: 2.1 Consensus size: 58
31405645 ATAAAGAAAT
* *
31405655 AATCATACCAATGTTGATTGAAACGCAGAGTAGTAAATCTCTCTATTGGGATAACGAG
1 AATCATACCAATGTTGATTGAAACGCAGAGTAGTAAATCTCCCGATTGGGATAACGAG
* *
31405713 AATCATACCAATGTTGATTGAAACGTAGAGTAGTAAATCTCCCGATTTGGATAACGAG
1 AATCATACCAATGTTGATTGAAACGCAGAGTAGTAAATCTCCCGATTGGGATAACGAG
31405771 AATCAT
1 AATCAT
31405777 TGCTTGCAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.28
Consensus pattern (58 bp):
AATCATACCAATGTTGATTGAAACGCAGAGTAGTAAATCTCCCGATTGGGATAACGAG
Found at i:31409298 original size:12 final size:12
Alignment explanation
Indices: 31409256--31409303 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 12
31409246 AGAGCTCGAA
31409256 AAAACATAGCTTAT
1 AAAACATA-CTT-T
*
31409270 AAAACTGTACTTTT
1 AAAAC-ATAC-TTT
31409284 AAAACATACTTT
1 AAAACATACTTT
31409296 AAAACATA
1 AAAACATA
31409304 AGCTTGCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 11 0.37
13 3 0.10
14 12 0.40
15 4 0.13
ACGTcount: A:0.50, C:0.15, G:0.04, T:0.31
Consensus pattern (12 bp):
AAAACATACTTT
Found at i:31409456 original size:16 final size:16
Alignment explanation
Indices: 31409437--31409471 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
31409427 TTCTTGGAAA
31409437 ACATAACAGTTTGCAC
1 ACATAACAGTTTGCAC
31409453 ACATAACAGTTTGCAC
1 ACATAACAGTTTGCAC
31409469 ACA
1 ACA
31409472 AGTTATGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (16 bp):
ACATAACAGTTTGCAC
Found at i:31411743 original size:72 final size:73
Alignment explanation
Indices: 31411615--31411753 Score: 262
Period size: 72 Copynumber: 1.9 Consensus size: 73
31411605 AAACATGGTC
*
31411615 AAAATATACCTATACCAACAAGGCACTCGTCATTTATGCTACATTTACATTCCAAACTTATATAA
1 AAAATATACCTATACCAACAAGGCACTCGTCATTTATGCTACATTTACATTCCAAACTTACATAA
31411680 TTCTAGTT
66 TTCTAGTT
31411688 AAAATATACCTATACCAACAAGGCACTC-TCATTTATGCTACATTTACATTCCAAACTTACATAA
1 AAAATATACCTATACCAACAAGGCACTCGTCATTTATGCTACATTTACATTCCAAACTTACATAA
31411752 TT
66 TT
31411754 GTAGCATATC
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
72 37 0.57
73 28 0.43
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (73 bp):
AAAATATACCTATACCAACAAGGCACTCGTCATTTATGCTACATTTACATTCCAAACTTACATAA
TTCTAGTT
Found at i:31412886 original size:12 final size:12
Alignment explanation
Indices: 31412869--31412893 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31412859 TATAATAATT
31412869 AATTTATAAATA
1 AATTTATAAATA
31412881 AATTTATAAATA
1 AATTTATAAATA
31412893 A
1 A
31412894 GTAATCAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AATTTATAAATA
Found at i:31414792 original size:23 final size:22
Alignment explanation
Indices: 31414766--31414941 Score: 167
Period size: 23 Copynumber: 7.8 Consensus size: 22
31414756 TTATCACCCA
31414766 CCAAACACAACCAATCATAGCCT
1 CCAAACACAACCAAT-ATAGCCT
* *
31414789 CCAACCACAACCAATTTAGCCT
1 CCAAACACAACCAATATAGCCT
* * *
31414811 CCAAACGCAATCAATTATAGTCT
1 CCAAACACAACCAA-TATAGCCT
* *
31414834 CTAAACACAACCAATTTA-CCTT
1 CCAAACACAACCAATATAGCC-T
31414856 CCAAACACAACCAATCATAGCCT
1 CCAAACACAACCAAT-ATAGCCT
*
31414879 CCAAACACAACCAAT-TTGCCCT
1 CCAAACACAACCAATATAG-CCT
* * * *
31414901 TCGAACACAACCAAGTGTACCCT
1 CCAAACACAACCAA-TATAGCCT
*
31414924 CCAAAGACAACCAATATA
1 CCAAACACAACCAATATA
31414942 CCTTTCAACA
Statistics
Matches: 123, Mismatches: 23, Indels: 15
0.76 0.14 0.09
Matches are distributed among these distances:
21 3 0.02
22 53 0.43
23 64 0.52
24 3 0.02
ACGTcount: A:0.41, C:0.35, G:0.06, T:0.18
Consensus pattern (22 bp):
CCAAACACAACCAATATAGCCT
Found at i:31414816 original size:45 final size:45
Alignment explanation
Indices: 31414766--31414938 Score: 199
Period size: 45 Copynumber: 3.8 Consensus size: 45
31414756 TTATCACCCA
*
31414766 CCAAACACAACCAATCATAGCCTCCAACCACAACCAATTTAGCCT
1 CCAAACACAACCAATCATAGCCTCCAAACACAACCAATTTAGCCT
* * * * *
31414811 CCAAACGCAATCAATTATAGTCTCTAAACACAACCAATTTA-CCTT
1 CCAAACACAACCAATCATAGCCTCCAAACACAACCAATTTAGCC-T
31414856 CCAAACACAACCAATCATAGCCTCCAAACACAACCAATTT-GCCCT
1 CCAAACACAACCAATCATAGCCTCCAAACACAACCAATTTAG-CCT
* * * * *
31414901 TCGAACACAACCAAGT-GTACCCTCCAAAGACAACCAAT
1 CCAAACACAACCAA-TCATAGCCTCCAAACACAACCAAT
31414939 ATACCTTTCA
Statistics
Matches: 108, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
44 2 0.02
45 103 0.95
46 3 0.03
ACGTcount: A:0.40, C:0.36, G:0.06, T:0.18
Consensus pattern (45 bp):
CCAAACACAACCAATCATAGCCTCCAAACACAACCAATTTAGCCT
Found at i:31414934 original size:90 final size:90
Alignment explanation
Indices: 31414766--31414945 Score: 236
Period size: 90 Copynumber: 2.0 Consensus size: 90
31414756 TTATCACCCA
* * * * *
31414766 CCAAACACAACCAATCATAGCCTCCAACCACAACCAATTTAGCCTCCAAACGCAATCAATTATAG
1 CCAAACACAACCAATCATAGCCTCCAAACACAACCAATTTAGCCTCCAAACACAACCAAGTATAC
* * *
31414831 TCTCTAAACACAACCAATTTACCTT
66 CCTCCAAACACAACCAATATACCTT
* * *
31414856 CCAAACACAACCAATCATAGCCTCCAAACACAACCAATTT-GCCCTTCGAACACAACCAAGTGTA
1 CCAAACACAACCAATCATAGCCTCCAAACACAACCAATTTAG-CCTCCAAACACAACCAAGTATA
*
31414920 CCCTCCAAAGACAACCAATATACCTT
65 CCCTCCAAACACAACCAATATACCTT
31414946 TCAACATATC
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
89 1 0.01
90 76 0.99
ACGTcount: A:0.40, C:0.36, G:0.06, T:0.19
Consensus pattern (90 bp):
CCAAACACAACCAATCATAGCCTCCAAACACAACCAATTTAGCCTCCAAACACAACCAAGTATAC
CCTCCAAACACAACCAATATACCTT
Found at i:31419467 original size:22 final size:22
Alignment explanation
Indices: 31419269--31419494 Score: 119
Period size: 22 Copynumber: 10.4 Consensus size: 22
31419259 GGATTTATAA
*
31419269 GGACAAACAAA-TTAAATTACAG
1 GGACAAA-AAATTTGAATTACAG
* *
31419291 GGACAAAAAAGTTGAATTACAA
1 GGACAAAAAATTTGAATTACAG
*
31419313 GGACAAAAAATGTTGAATTAAAG
1 GGACAAAAAAT-TTGAATTACAG
* * *
31419336 GG-GAAAAAATTCGACTTAC-G
1 GGACAAAAAATTTGAATTACAG
* * *
31419356 GG-GAAAAAA--T-AACTACAT
1 GGACAAAAAATTTGAATTACAG
* * *
31419374 GAACTAAAAAATTTTAATTATAG
1 GGAC-AAAAAATTTGAATTACAG
* *
31419397 GGACAAAAAA-TTCAATTTACAAA
1 GGACAAAAAATTTGAA-TTAC-AG
* * *
31419420 GGCCAAAAAAGTTGAATTACAA
1 GGACAAAAAATTTGAATTACAG
* *
31419442 GGAGAAAAAATTTGACTTACAG
1 GGACAAAAAATTTGAATTACAG
* ** *
31419464 GGAGGAAAAAA-ACGAACTACAG
1 GGA-CAAAAAATTTGAATTACAG
31419486 GGACAAAAA
1 GGACAAAAA
31419495 TATTAAAATT
Statistics
Matches: 158, Mismatches: 34, Indels: 25
0.73 0.16 0.12
Matches are distributed among these distances:
17 4 0.03
18 1 0.01
20 16 0.10
21 18 0.11
22 75 0.47
23 40 0.25
24 4 0.03
ACGTcount: A:0.52, C:0.11, G:0.18, T:0.19
Consensus pattern (22 bp):
GGACAAAAAATTTGAATTACAG
Found at i:31421419 original size:2 final size:2
Alignment explanation
Indices: 31421412--31421440 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31421402 TGGGTTAATT
31421412 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31421441 GCCCAATAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31424504 original size:6 final size:6
Alignment explanation
Indices: 31424493--31424535 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
31424483 TAATTTAGCC
* * * *
31424493 ATTTTT ATTTTT ATTATA ATTTTT ATTTTT AGTTTA ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
31424536 CAGTCTAATT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (6 bp):
ATTTTT
Found at i:31424514 original size:18 final size:18
Alignment explanation
Indices: 31424493--31424535 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
31424483 TAATTTAGCC
31424493 ATTTTTATTTTTA-TTATA
1 ATTTTTATTTTTAGTT-TA
31424511 ATTTTTATTTTTAGTTTA
1 ATTTTTATTTTTAGTTTA
31424529 ATTTTTA
1 ATTTTTA
31424536 CAGTCTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (18 bp):
ATTTTTATTTTTAGTTTA
Found at i:31433179 original size:6 final size:6
Alignment explanation
Indices: 31433168--31433210 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
31433158 CAATTTAGCC
* * * *
31433168 ATTTTT ATTTTT ATTATA ATTTTT ATTTTT AGTTTA ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
31433211 CATTCTAAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (6 bp):
ATTTTT
Found at i:31433189 original size:18 final size:18
Alignment explanation
Indices: 31433168--31433210 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
31433158 CAATTTAGCC
31433168 ATTTTTATTTTTA-TTATA
1 ATTTTTATTTTTAGTT-TA
31433186 ATTTTTATTTTTAGTTTA
1 ATTTTTATTTTTAGTTTA
31433204 ATTTTTA
1 ATTTTTA
31433211 CATTCTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (18 bp):
ATTTTTATTTTTAGTTTA
Found at i:31437407 original size:27 final size:27
Alignment explanation
Indices: 31437377--31437429 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
31437367 ATAAAAGAGT
31437377 TGTTAATTAA-AAAAATTGAAAAAAATA
1 TGTTAATTAATAAAAATT-AAAAAAATA
*
31437404 TGTTTATTAATTAAAAATTAAAAAAA
1 TGTTAATTAA-TAAAAATTAAAAAAA
31437430 GCTTGAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 9 0.39
28 7 0.30
29 7 0.30
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (27 bp):
TGTTAATTAATAAAAATTAAAAAAATA
Found at i:31444505 original size:50 final size:50
Alignment explanation
Indices: 31444405--31444693 Score: 269
Period size: 50 Copynumber: 5.7 Consensus size: 50
31444395 AATGAGATCT
* *
31444405 CATGTAAGACCATGTTTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTCC
*
31444461 CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
* * * *
31444511 CATGTAAGACCATTTCTGGGACATTGCGTTGGCACCGGGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
** * * * **
31444561 CCCGTAAGACCATGTCTTGGACATGGCATGGGCACCGATATGAGAACTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
* * * * * * *
31444611 CATGTAAGACCATATTTGGGATATGGCATTGGTA--GTACA-GAAAGCATCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAG-GTCC
* * *
31444660 CATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
31444694 TGTATTATCA
Statistics
Matches: 195, Mismatches: 36, Indels: 11
0.81 0.15 0.05
Matches are distributed among these distances:
48 4 0.02
49 32 0.16
50 123 0.63
53 3 0.02
55 1 0.01
56 32 0.16
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
Found at i:31444924 original size:16 final size:15
Alignment explanation
Indices: 31444903--31444938 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
31444893 TAAGTAAGCA
31444903 AGTAAGTAAACAAGT
1 AGTAAGTAAACAAGT
*
31444918 GAGTAAGTAAAGAAGT
1 -AGTAAGTAAACAAGT
31444934 AGTAA
1 AGTAA
31444939 AGATTCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.53, C:0.03, G:0.25, T:0.19
Consensus pattern (15 bp):
AGTAAGTAAACAAGT
Found at i:31446809 original size:16 final size:16
Alignment explanation
Indices: 31446788--31446826 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
31446778 TATTATGATC
*
31446788 TTTACTTTCTTCTTTA
1 TTTACTTTCTTATTTA
* *
31446804 TTTACTCTCTTATTTG
1 TTTACTTTCTTATTTA
31446820 TTTACTT
1 TTTACTT
31446827 ACTTGCTTAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.13, C:0.18, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTACTTTCTTATTTA
Found at i:31447183 original size:50 final size:50
Alignment explanation
Indices: 31447129--31447235 Score: 160
Period size: 50 Copynumber: 2.1 Consensus size: 50
31447119 ACATGAGAGT
* * *
31447129 TCTCATATCGGTGCCCATGCCATGTCCTAGACATGGTCTTATGGGGGACC
1 TCTCATATCGGTGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACC
* * *
31447179 TCTCATCTTGGTGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACC
1 TCTCATATCGGTGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACC
31447229 TCTCATA
1 TCTCATA
31447236 ACCTCAATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.29
Consensus pattern (50 bp):
TCTCATATCGGTGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACC
Found at i:31447252 original size:56 final size:50
Alignment explanation
Indices: 31447140--31447282 Score: 160
Period size: 50 Copynumber: 2.7 Consensus size: 50
31447130 CTCATATCGG
* * * **
31447140 TGCCCATGCCATGTCCTAGACATGGTCTTATGGGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACGTGGGACCTCTCATCTTAA
*
31447190 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCTAGACATGGTCTTACGTGGGACCTCTCAT---CT---TAA
* *
31447246 TGCCAATGCCATGTCATAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCTAGACATGGTCTTACGTGGGA
31447283 TCTCATTCCC
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
50 41 0.53
53 2 0.03
56 35 0.45
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCTAGACATGGTCTTACGTGGGACCTCTCATCTTAA
Found at i:31453506 original size:42 final size:42
Alignment explanation
Indices: 31453454--31453566 Score: 145
Period size: 42 Copynumber: 2.7 Consensus size: 42
31453444 ATTTTTTGTC
* **
31453454 CACACGGCCAGAAACATGGGCGTGTGTCTCAGCCGTGTGTGA
1 CACATGGCCAGAAACATGGGCGTGTGTCTCAGCCGTGCATGA
* *
31453496 CACATGGCCAGAGACATAGGCGTGTGTCTCAGCCGTGCATGA
1 CACATGGCCAGAAACATGGGCGTGTGTCTCAGCCGTGCATGA
* * *
31453538 CACATGGCCAAGCAACATGGCCATGTGTC
1 CACATGGCC-AGAAACATGGGCGTGTGTC
31453567 CTTGTTAGCT
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 46 0.77
43 14 0.23
ACGTcount: A:0.24, C:0.27, G:0.30, T:0.19
Consensus pattern (42 bp):
CACATGGCCAGAAACATGGGCGTGTGTCTCAGCCGTGCATGA
Found at i:31465021 original size:28 final size:26
Alignment explanation
Indices: 31464977--31465028 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
31464967 ATATTATTAA
31464977 TATAATATATAAATGTTATAATAAGG
1 TATAATATATAAATGTTATAATAAGG
*
31465003 TATAATATATTATTATGTTATAATAA
1 TATAATATA-TA-AATGTTATAATAA
31465029 ACATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 9 0.39
27 2 0.09
28 12 0.52
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (26 bp):
TATAATATATAAATGTTATAATAAGG
Found at i:31465974 original size:41 final size:41
Alignment explanation
Indices: 31465928--31466042 Score: 194
Period size: 41 Copynumber: 2.8 Consensus size: 41
31465918 CAGTGATATT
31465928 CAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATAA
1 CAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATAA
** *
31465969 CAGGCTTTATGCCTAGCAGGCTTTATGCTAGTGAATTATAT
1 CAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATAA
*
31466010 CAGGCTTTATGCCTAGCAGGCTTTGTGCCGGTG
1 CAGGCTTTATGCCTAGCAGGCTTTATGCCGGTG
31466043 TATCATATTT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (41 bp):
CAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATAA
Found at i:31468377 original size:15 final size:15
Alignment explanation
Indices: 31468357--31468388 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31468347 CATTTCACTA
*
31468357 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
31468372 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
31468387 TT
1 TT
31468389 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:31473948 original size:27 final size:27
Alignment explanation
Indices: 31473895--31473966 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
31473885 TTGGTTTGGC
** *
31473895 GAACTAGGG-TTCGTCAGTCGAGTTGT
1 GAACTAGGGATTCACCAGTCGAGCTGT
*
31473921 GAACTAGGGATTCACCAGTTGAGCTGT
1 GAACTAGGGATTCACCAGTCGAGCTGT
*
31473948 GAACTAGGGA-TCTCCAGTC
1 GAACTAGGGATTCACCAGTC
31473967 AAAAGTCGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 16 0.41
27 23 0.59
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (27 bp):
GAACTAGGGATTCACCAGTCGAGCTGT
Found at i:31474453 original size:14 final size:14
Alignment explanation
Indices: 31474431--31474461 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31474421 ATAAACTCTG
*
31474431 TTTTCAAGTTATGT
1 TTTTAAAGTTATGT
31474445 TTTTAAAGTTATGT
1 TTTTAAAGTTATGT
31474459 TTT
1 TTT
31474462 ATGTGTGCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.13, T:0.61
Consensus pattern (14 bp):
TTTTAAAGTTATGT
Found at i:31475567 original size:30 final size:30
Alignment explanation
Indices: 31475531--31475592 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
31475521 TATGTGTTAA
31475531 TACCATATGCGAGCCAGTTTTATGGCATAG
1 TACCATATGCGAGCCAGTTTTATGGCATAG
31475561 TACCATATGCGAGCCAGTTTTATGGCATAG
1 TACCATATGCGAGCCAGTTTTATGGCATAG
31475591 TA
1 TA
31475593 TTATTTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (30 bp):
TACCATATGCGAGCCAGTTTTATGGCATAG
Found at i:31476800 original size:68 final size:68
Alignment explanation
Indices: 31476551--31476786 Score: 296
Period size: 68 Copynumber: 3.5 Consensus size: 68
31476541 CATAAGTTGA
* * * *
31476551 CATAGCCGAGCTATGGTCATACA-CTTGTAACCCCATGTTTAATGTCTTGAC-AGACTATATTGG
1 CATAGCCGAGCTATGGTCTTACACCTTGTAACCCCATGTTTAATGTCATGGCGA-ACTCTATTGG
*
31476614 TTGC
65 TTTC
* * * * *
31476618 CATAGTCGAGATTTGGTCTTACACCTTGTAACCCCATGTTTAATGTCATGGCGGACTCTATAGGT
1 CATAGCCGAGCTATGGTCTTACACCTTGTAACCCCATGTTTAATGTCATGGCGAACTCTATTGGT
31476683 TTC
66 TTC
* * * * * *
31476686 CATAGCCTAGTTATGGTATTTCACCTTGTAACCTCATGTTTAATGTCCTGGCGAACTCTATTGGT
1 CATAGCCGAGCTATGGTCTTACACCTTGTAACCCCATGTTTAATGTCATGGCGAACTCTATTGGT
31476751 TTC
66 TTC
*
31476754 CATAGCCGAGCTATGGTCTTACACATTGTAACC
1 CATAGCCGAGCTATGGTCTTACACCTTGTAACC
31476787 TCTTTTGAGA
Statistics
Matches: 142, Mismatches: 25, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
67 19 0.13
68 123 0.87
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (68 bp):
CATAGCCGAGCTATGGTCTTACACCTTGTAACCCCATGTTTAATGTCATGGCGAACTCTATTGGT
TTC
Found at i:31479386 original size:23 final size:23
Alignment explanation
Indices: 31479358--31479529 Score: 165
Period size: 23 Copynumber: 7.4 Consensus size: 23
31479348 TACTTGTAAC
*
31479358 GCCTTTGTGGCGTATCCTGAAAT
1 GCCTTTGTGGCGTATTCTGAAAT
* *
31479381 GCCTTTGTGGCGAATTCTGTAAT
1 GCCTTTGTGGCGTATTCTGAAAT
31479404 GCCTTTGTGGCGTATTC-GATAAT
1 GCCTTTGTGGCGTATTCTGA-AAT
* *
31479427 GCCTTTGTGGCATATTCTGTAAT
1 GCCTTTGTGGCGTATTCTGAAAT
* *
31479450 GACTTTTGTGGCATATTCT-AAA-
1 G-CCTTTGTGGCGTATTCTGAAAT
*
31479472 GCACCTTTGTGGCATATTCT-ATAAT
1 G--CCTTTGTGGCGTATTCTGA-AAT
* *
31479497 GCCTTTGTGGTGTATTAT-ACAAT
1 GCCTTTGTGGCGTATTCTGA-AAT
31479520 GCCTTTGTGG
1 GCCTTTGTGG
31479530 TAAGTTCTAT
Statistics
Matches: 129, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
22 2 0.02
23 107 0.83
24 19 0.15
25 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.40
Consensus pattern (23 bp):
GCCTTTGTGGCGTATTCTGAAAT
Found at i:31479408 original size:46 final size:46
Alignment explanation
Indices: 31479352--31479529 Score: 202
Period size: 46 Copynumber: 3.8 Consensus size: 46
31479342 GCAAGTTACT
* *
31479352 TGTAACGCCTTTGTGGCGTATCCTGA-AATGCCTTTGTGGCGA-ATTC
1 TGTAATGCCTTTGTGGCGTATTCT-ACAATGCCTTTGTGGC-ATATTC
* *
31479398 TGTAATGCCTTTGTGGCGTATTCGATAATGCCTTTGTGGCATATTC
1 TGTAATGCCTTTGTGGCGTATTCTACAATGCCTTTGTGGCATATTC
* *
31479444 TGTAATGACTTTTGTGGCATATTCTA-AA-GCACCTTTGTGGCATATTC
1 TGTAATG-CCTTTGTGGCGTATTCTACAATG--CCTTTGTGGCATATTC
* * *
31479491 TATAATGCCTTTGTGGTGTATTATACAATGCCTTTGTGG
1 TGTAATGCCTTTGTGGCGTATTCTACAATGCCTTTGTGG
31479530 TAAGTTCTAT
Statistics
Matches: 114, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
45 3 0.03
46 71 0.62
47 39 0.34
48 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (46 bp):
TGTAATGCCTTTGTGGCGTATTCTACAATGCCTTTGTGGCATATTC
Found at i:31479468 original size:70 final size:68
Alignment explanation
Indices: 31479358--31479506 Score: 176
Period size: 70 Copynumber: 2.1 Consensus size: 68
31479348 TACTTGTAAC
* * *
31479358 GCCTTTGTGGCGTATCCTGAAATGCCTTTGTGGCGAATTCTGTAATG-CCTTTGTGGCGTATTCG
1 GCCTTTGTGGCATATCCTGAAATGCCTTTGTGGCGAATTC--TAAAGACCTTTGTGGCATATTCG
31479422 ATAAT
64 ATAAT
* * *
31479427 GCCTTTGTGGCATATTCTGTAATGACTTTTGTGGC-ATATTCTAAAGCACCTTTGTGGCATATTC
1 GCCTTTGTGGCATATCCTGAAATG-CCTTTGTGGCGA-ATTCTAAAG-ACCTTTGTGGCATATTC
*
31479491 TATAAT
63 GATAAT
31479497 GCCTTTGTGG
1 GCCTTTGTGG
31479507 TGTATTATAC
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
68 4 0.06
69 22 0.32
70 43 0.62
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (68 bp):
GCCTTTGTGGCATATCCTGAAATGCCTTTGTGGCGAATTCTAAAGACCTTTGTGGCATATTCGAT
AAT
Found at i:31484035 original size:91 final size:90
Alignment explanation
Indices: 31483908--31484095 Score: 241
Period size: 91 Copynumber: 2.1 Consensus size: 90
31483898 GTAACCATTT
* * * *
31483908 GATAACACACCAGATGTAATAGTGTAAAGCCTATAGGCTAAGTATTCTCCCCCAATAACACAACA
1 GATAACACACCAGATGCAATAGTGCAAAGCCCATAGGCTAAATATTCTCCCCCAATAACACAACA
*
31483973 ATTTTCTCATAAGAGCTTTCCAACA
66 ATTTTCTCATAAGAACTTTCCAACA
* ** ***
31483998 GATAACACACCATATGCACATAGTGCAAAGCCCATAGGCTAAATATTCTCCCCTGATAACATGCC
1 GATAACACACCAGATGCA-ATAGTGCAAAGCCCATAGGCTAAATATTCTCCCCCAATAACACAAC
* * *
31484063 AGTTTTCTCGTAAGAACTTTCCAACC
65 AATTTTCTCATAAGAACTTTCCAACA
31484089 GATAACA
1 GATAACA
31484096 TGCTAGAATC
Statistics
Matches: 83, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
90 16 0.19
91 67 0.81
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (90 bp):
GATAACACACCAGATGCAATAGTGCAAAGCCCATAGGCTAAATATTCTCCCCCAATAACACAACA
ATTTTCTCATAAGAACTTTCCAACA
Found at i:31487389 original size:21 final size:21
Alignment explanation
Indices: 31487365--31487417 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
31487355 TTTAAAACCC
31487365 AATGAGTATCGATACTTTTTA
1 AATGAGTATCGATACTTTTTA
*
31487386 AATGAGTATCGATATTTTTTA
1 AATGAGTATCGATACTTTTTA
*
31487407 AA-AAGTATCGA
1 AATGAGTATCGA
31487418 AAAAACAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 8 0.27
21 22 0.73
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.40
Consensus pattern (21 bp):
AATGAGTATCGATACTTTTTA
Found at i:31497735 original size:28 final size:28
Alignment explanation
Indices: 31497656--31497737 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 28
31497646 GTGACACTTA
31497656 CTTGAAAGATAGTCCATGCAGACTCTTG
1 CTTGAAAGATAGTCCATGCAGACTCTTG
* **
31497684 -TTGGATAGATAGTCCATGTGGACTCTTG
1 CTT-GAAAGATAGTCCATGCAGACTCTTG
* *
31497712 CTTGAAAAAGAGTCCATGCAGACTCT
1 CTTGAAAGATAGTCCATGCAGACTCT
31497738 CATATGGTGG
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
27 2 0.05
28 40 0.91
29 2 0.05
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (28 bp):
CTTGAAAGATAGTCCATGCAGACTCTTG
Found at i:31499800 original size:27 final size:27
Alignment explanation
Indices: 31499770--31500030 Score: 174
Period size: 27 Copynumber: 9.7 Consensus size: 27
31499760 AAACCAACAG
* *
31499770 AGTCTACTAGGACAGTAAACACAGGGT
1 AGTCCACTGGGACAGTAAACACAGGGT
* *
31499797 AGTCCACTGGGATAGTAAACACGGGGT
1 AGTCCACTGGGACAGTAAACACAGGGT
* * * * **
31499824 AATCC-GTCAGGACAATAAACATGGGGT
1 AGTCCACT-GGGACAGTAAACACAGGGT
* * * * * *
31499851 AGTCTACCGAGATAATAAACACGGGGT
1 AGTCCACTGGGACAGTAAACACAGGGT
* * * *
31499878 AATCCACCGGGACATTAAAGAC-GAGGT
1 AGTCCACTGGGACAGTAAACACAG-GGT
**
31499905 AGTCTGTCT-GGACAGTAAACACAGGGT
1 AGTC-CACTGGGACAGTAAACACAGGGT
* *
31499932 AGTCCACTAGGACTG-AAACACAGGGT
1 AGTCCACTGGGACAGTAAACACAGGGT
* *
31499958 AGTCCA-TCGGGACATTAAACACAAGGT
1 AGTCCACT-GGGACAGTAAACACAGGGT
*
31499985 AGTCCACTGGGAC-GTTAAACACGGGGT
1 AGTCCACTGGGACAG-TAAACACAGGGT
* *
31500012 AGTCCGCTGGGACAATAAA
1 AGTCCACTGGGACAGTAAA
31500031 AATGGGGAAG
Statistics
Matches: 181, Mismatches: 42, Indels: 22
0.74 0.17 0.09
Matches are distributed among these distances:
25 1 0.01
26 25 0.14
27 152 0.84
28 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.18
Consensus pattern (27 bp):
AGTCCACTGGGACAGTAAACACAGGGT
Found at i:31499918 original size:81 final size:79
Alignment explanation
Indices: 31499785--31499989 Score: 212
Period size: 81 Copynumber: 2.6 Consensus size: 79
31499775 ACTAGGACAG
* * * * * **
31499785 TAAACACAGGGTAGTCCACTGGGATAGTAAACACGGGGTAATCCGTCAGGACAATAAACATGGGG
1 TAAACACAGGGTAGTCCACCGGGACATTAAACACGAGGTAGTCCGTCAGGACAATAAACACAGGG
* *
31499850 TAGTCTACCGAGATAA
66 TAGTCCA-CGAG-GAA
* * * * * *
31499866 TAAACACGGGGTAATCCACCGGGACATTAAAGACGAGGTAGTCTGTCTGGACAGTAAACACAGGG
1 TAAACACAGGGTAGTCCACCGGGACATTAAACACGAGGTAGTCCGTCAGGACAATAAACACAGGG
* *
31499931 TAGTCCACTAGGAC
66 TAGTCCACGAGGAA
* *
31499945 TGAAACACAGGGTAGTCCATCGGGACATTAAACACAAGGTAGTCC
1 T-AAACACAGGGTAGTCCACCGGGACATTAAACACGAGGTAGTCC
31499990 ACTGGGACGT
Statistics
Matches: 100, Mismatches: 23, Indels: 3
0.79 0.18 0.02
Matches are distributed among these distances:
79 2 0.02
80 40 0.40
81 58 0.58
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (79 bp):
TAAACACAGGGTAGTCCACCGGGACATTAAACACGAGGTAGTCCGTCAGGACAATAAACACAGGG
TAGTCCACGAGGAA
Found at i:31499977 original size:53 final size:54
Alignment explanation
Indices: 31499914--31500016 Score: 154
Period size: 53 Copynumber: 1.9 Consensus size: 54
31499904 TAGTCTGTCT
*
31499914 GGACAGTAAACACAGGGTAGTCCACTAGGAC-TGAAACACAGGGTAGTCCATCG
1 GGACAGTAAACACAAGGTAGTCCACTAGGACGTGAAACACAGGGTAGTCCATCG
* * * *
31499967 GGACATTAAACACAAGGTAGTCCACTGGGACGTTAAACACGGGGTAGTCC
1 GGACAGTAAACACAAGGTAGTCCACTAGGACGTGAAACACAGGGTAGTCC
31500017 GCTGGGACAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 28 0.64
54 16 0.36
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (54 bp):
GGACAGTAAACACAAGGTAGTCCACTAGGACGTGAAACACAGGGTAGTCCATCG
Found at i:31500004 original size:80 final size:80
Alignment explanation
Indices: 31499867--31500016 Score: 196
Period size: 80 Copynumber: 1.9 Consensus size: 80
31499857 CCGAGATAAT
* * * **
31499867 AAACACGGGGTAATCCACCGGGACATTAAAGACGAGGTAGTCTGTCTGGACAGTAAACACAGGGT
1 AAACACAGGGTAATCCACCGGGACATTAAACACAAGGTAGTCTCACTGGACAGTAAACACAGGGT
31499932 AGTCCACTAGGACTG
66 AGTCCACTAGGACTG
* * *
31499947 AAACACAGGGTAGTCCATCGGGACATTAAACACAAGGTAGTC-CACTGGGAC-GTTAAACACGGG
1 AAACACAGGGTAATCCACCGGGACATTAAACACAAGGTAGTCTCACT-GGACAG-TAAACACAGG
31500010 GTAGTCC
64 GTAGTCC
31500017 GCTGGGACAA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
79 3 0.05
80 57 0.95
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (80 bp):
AAACACAGGGTAATCCACCGGGACATTAAACACAAGGTAGTCTCACTGGACAGTAAACACAGGGT
AGTCCACTAGGACTG
Found at i:31509491 original size:2 final size:2
Alignment explanation
Indices: 31509484--31509508 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31509474 ATAGAAGCTA
31509484 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
31509509 TTACCTATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31523518 original size:22 final size:22
Alignment explanation
Indices: 31523490--31523533 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31523480 TTCCCAAATA
*
31523490 TTCCCCTAGCGTAATGGATTTC
1 TTCCCCTAGCGTAATAGATTTC
31523512 TTCCCCTAGCGTAATAGATTTC
1 TTCCCCTAGCGTAATAGATTTC
31523534 CTGAACACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.36
Consensus pattern (22 bp):
TTCCCCTAGCGTAATAGATTTC
Found at i:31534098 original size:116 final size:116
Alignment explanation
Indices: 31533894--31534151 Score: 363
Period size: 116 Copynumber: 2.2 Consensus size: 116
31533884 TGAACAAGCC
* * * * ** * *
31533894 ACACACGGCCGTATGCCAGGCCGTGTAACTCTTTAAGTTGCCACACACGGTTGTGTGCCAGGCCG
1 ACACACGGCCGTGTGCCAGGCTGTGTAACTCTCTAAGTTGCCACAAACGGTCATGAGCCAGGCCA
* *
31533959 TGTACTAAGCCGTGTAACACACTGGCTTGAAATATCAAAATTTTGCAAATG
66 TGTACTAAGCCGTGAAACACACTGACTTGAAATATCAAAATTTTGCAAATG
*
31534010 ACACATGGCCGTGTGCCAGGCTGTGTAACTCTCTAAGTTGCCACAAACGGTCATGAGCCAGGCCA
1 ACACACGGCCGTGTGCCAGGCTGTGTAACTCTCTAAGTTGCCACAAACGGTCATGAGCCAGGCCA
* * *
31534075 TGTACTAAGCTGTGAAACACACTGACTTGAAATATTAAAATTTTTCAAATG
66 TGTACTAAGCCGTGAAACACACTGACTTGAAATATCAAAATTTTGCAAATG
* * *
31534126 ACACACGACCGTGTGACAGCCTGTGT
1 ACACACGGCCGTGTGCCAGGCTGTGT
31534152 CCCAGGCTGT
Statistics
Matches: 124, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
116 124 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.25
Consensus pattern (116 bp):
ACACACGGCCGTGTGCCAGGCTGTGTAACTCTCTAAGTTGCCACAAACGGTCATGAGCCAGGCCA
TGTACTAAGCCGTGAAACACACTGACTTGAAATATCAAAATTTTGCAAATG
Found at i:31536115 original size:20 final size:20
Alignment explanation
Indices: 31536078--31536116 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31536068 TCATCTTTTC
*
31536078 TTACTTAATTTTCTTTTTAG
1 TTACTTAATTTTCATTTTAG
31536098 TTAC-TAATTTATCATTTTA
1 TTACTTAATTT-TCATTTTA
31536117 CCCTTATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.10, G:0.03, T:0.62
Consensus pattern (20 bp):
TTACTTAATTTTCATTTTAG
Found at i:31546197 original size:94 final size:94
Alignment explanation
Indices: 31546090--31546264 Score: 244
Period size: 94 Copynumber: 1.9 Consensus size: 94
31546080 GATAAAAAGG
* * * * *
31546090 GGATTTGATATATTCCTAATTAGATACA-TAAATAGAATTTAATTATTATTTAAAAGAGTTCTAT
1 GGATTTGATATATTCCTAATCAAATA-AGGAAATAGAATTTAATTATAATTTAAAAGAGTTCTAG
*
31546154 AGAAGTAATAATTAAAATTCAAAATCAAAA
65 AGAAATAATAATTAAAATTCAAAATCAAAA
* * *
31546184 GGATTTGGTATATTCCTTATCAAATAAGGAAATAGAATTTAATTATAATTTAAAAGAGTTTTAGA
1 GGATTTGATATATTCCTAATCAAATAAGGAAATAGAATTTAATTATAATTTAAAAGAGTTCTAGA
*
31546249 TAAATAATAATTAAAA
66 GAAATAATAATTAAAA
31546265 CATAATTTAA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
93 1 0.01
94 69 0.99
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (94 bp):
GGATTTGATATATTCCTAATCAAATAAGGAAATAGAATTTAATTATAATTTAAAAGAGTTCTAGA
GAAATAATAATTAAAATTCAAAATCAAAA
Found at i:31548029 original size:50 final size:50
Alignment explanation
Indices: 31547963--31548070 Score: 162
Period size: 50 Copynumber: 2.2 Consensus size: 50
31547953 AACGGGCATG
* *
31547963 AAAAAAGAAAAGAAAGGTATGTGTTCAAATAAACTATGTCATGAAATTAT
1 AAAAAGGAAAAGAAAGGTATGTATTCAAATAAACTATGTCATGAAATTAT
* * *
31548013 AAAAAGGAAAGGAAAGGTATGTATTCGAATGAACTATGTCATGAAATTAT
1 AAAAAGGAAAAGAAAGGTATGTATTCAAATAAACTATGTCATGAAATTAT
*
31548063 GAAAAGGA
1 AAAAAGGA
31548071 TTAAAACAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.50, C:0.06, G:0.20, T:0.24
Consensus pattern (50 bp):
AAAAAGGAAAAGAAAGGTATGTATTCAAATAAACTATGTCATGAAATTAT
Found at i:31551953 original size:46 final size:44
Alignment explanation
Indices: 31551882--31551977 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 44
31551872 TATGTGAACC
*
31551882 GATATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCCCACCG
1 GATATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-CCACCG
* *
31551926 GATATCATTGATTACAAAGGGTGGTTGCTGTGTGCTGAATCCACCG
1 GATATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCCACCG
*
31551972 TATATC
1 GATATC
31551978 TGTTATTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
44 13 0.29
45 2 0.04
46 28 0.62
47 2 0.04
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (44 bp):
GATATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCCACCG
Found at i:31552147 original size:37 final size:38
Alignment explanation
Indices: 31552078--31552150 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 38
31552068 ATGTGTGGAA
* **
31552078 TTGAATTGAATATTGACGTGAAAATGGCAAAGTGAATT
1 TTGAATTGAATAGTGACGTGAAAATGAAAAAGTGAATT
* *
31552116 TTGAATTGAATAGTGA-TTGAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGACGTGAAAATGAAAAAGTGAA
31552151 ATTATGAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 15 0.50
38 15 0.50
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.30
Consensus pattern (38 bp):
TTGAATTGAATAGTGACGTGAAAATGAAAAAGTGAATT
Found at i:31555559 original size:32 final size:32
Alignment explanation
Indices: 31555518--31555584 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
31555508 TCCCTTTCAA
*
31555518 TGAAACTAGAAGGGACAACAATATAGGGGGTT
1 TGAAACTAGAAGGGACAAAAATATAGGGGGTT
31555550 TGAAACTAGAAGGGACAAAAATATAGGGGGTT
1 TGAAACTAGAAGGGACAAAAATATAGGGGGTT
31555582 TGA
1 TGA
31555585 CCAAAATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.42, C:0.07, G:0.31, T:0.19
Consensus pattern (32 bp):
TGAAACTAGAAGGGACAAAAATATAGGGGGTT
Found at i:31560425 original size:26 final size:26
Alignment explanation
Indices: 31560382--31560454 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 26
31560372 TCTCATTCCT
* * *
31560382 ATTTTACCTCTAGAAAAATTTTGACA
1 ATTTTACCCCTGGTAAAATTTTGACA
* * *
31560408 ATTTTACCCCTGTTAAAATTTTGGCG
1 ATTTTACCCCTGGTAAAATTTTGACA
* *
31560434 ATTTTGCCCTTGGTAAAATTT
1 ATTTTACCCCTGGTAAAATTT
31560455 CGAGAAAATA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.42
Consensus pattern (26 bp):
ATTTTACCCCTGGTAAAATTTTGACA
Found at i:31561559 original size:33 final size:33
Alignment explanation
Indices: 31561516--31561578 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
31561506 TTTTATTAAA
* *
31561516 CTTATTTTAGTTAATTAATTGCTGGAATAAATG
1 CTTATATTAGTTAATTAATTGCTAGAATAAATG
*
31561549 CTTATATTAGTTTATTAATTGCTAGAATAA
1 CTTATATTAGTTAATTAATTGCTAGAATAA
31561579 CTTATTGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (33 bp):
CTTATATTAGTTAATTAATTGCTAGAATAAATG
Found at i:31564316 original size:25 final size:25
Alignment explanation
Indices: 31564275--31564332 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
31564265 TAGGCCCATT
*
31564275 TCACAGCTCATGTGAGCATTTACAG
1 TCACAGCTCATGAGAGCATTTACAG
* *
31564300 TCACAGCTCGTGAGAGCATTTACCG
1 TCACAGCTCATGAGAGCATTTACAG
*
31564325 TCATAGCT
1 TCACAGCT
31564333 TGTGTGAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (25 bp):
TCACAGCTCATGAGAGCATTTACAG
Found at i:31564419 original size:27 final size:27
Alignment explanation
Indices: 31564389--31564446 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
31564379 CATCGGGTGA
*
31564389 GAAATGAGTAAATGGAAATGGATATAT
1 GAAATGAGTAAATGGAAATAGATATAT
** *
31564416 GAAATGTTTATATGGAAATAGATATAT
1 GAAATGAGTAAATGGAAATAGATATAT
31564443 GAAA
1 GAAA
31564447 AGGTCAGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.22, T:0.29
Consensus pattern (27 bp):
GAAATGAGTAAATGGAAATAGATATAT
Found at i:31564421 original size:13 final size:13
Alignment explanation
Indices: 31564403--31564446 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
31564393 TGAGTAAATG
31564403 GAAATGGATATAT
1 GAAATGGATATAT
**
31564416 GAAATGTTTATAT
1 GAAATGGATATAT
*
31564429 GGAAATAGATATAT
1 -GAAATGGATATAT
31564443 GAAA
1 GAAA
31564447 AGGTCAGATG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (13 bp):
GAAATGGATATAT
Found at i:31581848 original size:45 final size:45
Alignment explanation
Indices: 31581779--31581869 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
31581769 AGATATTGAA
* *
31581779 TGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCCGG
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGG
*
31581824 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTTCGG
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGG
31581869 T
1 T
31581870 TCACATAGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (45 bp):
TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGG
Found at i:31581934 original size:51 final size:49
Alignment explanation
Indices: 31581875--31582061 Score: 171
Period size: 51 Copynumber: 3.7 Consensus size: 49
31581865 TCGGTTCACA
** *
31581875 TAGTAGCCTGTACATAGTACTACAAATGTGACCATTACGATCCGATACACG
1 TAGTAGCCTACACATAGTACTACACATGTGACCA-TAC-ATCCGATACACG
* * * * *
31581926 TAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATCC-AGTACGCA
1 TAGTAGCCTACACATAGTACTACACATGTGA-CCATAC-ATCCGA-TACACG
* * *
31581977 TAGTAGCCTACACATAGTACTACACATGCGACC-TATCATTTCGGTACACG
1 TAGTAGCCTACACATAGTACTACACATGTGACCATA-CA-TCCGATACACG
* * *
31582027 TAGTAGCCTGCACATAGTACTACTCACGTGACCAT
1 TAGTAGCCTACACATAGTACTACACATGTGACCAT
31582062 CAGTCTCACT
Statistics
Matches: 109, Mismatches: 21, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
49 2 0.02
50 38 0.35
51 67 0.61
52 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTACACATAGTACTACACATGTGACCATACATCCGATACACG
Found at i:31583274 original size:45 final size:45
Alignment explanation
Indices: 31583174--31583300 Score: 130
Period size: 45 Copynumber: 2.8 Consensus size: 45
31583164 ACCATGATAC
* * *
31583174 CATAGCTTCTTTCAACCATGGCCTTACTCA-CTTATATCATGACAT
1 CATAGCATCTTTCAACCATGGTCTTACTCATCTT-TAGCATGACAT
* * * **
31583219 CCTAGTATCTTTCAACTATGGTCTTACTCATCTTTAGCATGATGT
1 CATAGCATCTTTCAACCATGGTCTTACTCATCTTTAGCATGACAT
* * * *
31583264 CATGGCATCTTTCAGCCATGATCTTACTAATCTTTAG
1 CATAGCATCTTTCAACCATGGTCTTACTCATCTTTAG
31583301 GCGTGTAGCC
Statistics
Matches: 66, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
45 63 0.95
46 3 0.05
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (45 bp):
CATAGCATCTTTCAACCATGGTCTTACTCATCTTTAGCATGACAT
Found at i:31586973 original size:22 final size:22
Alignment explanation
Indices: 31586894--31586965 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
31586884 ATTGTTCAAA
* **
31586894 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
31586916 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
31586938 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
31586960 CATGAG
1 CATGAG
31586966 GGTTTAGTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:31589837 original size:10 final size:10
Alignment explanation
Indices: 31589806--31589830 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
31589796 CCCTTTTATA
31589806 TTTTTGAATT
1 TTTTTGAATT
31589816 TTTTTGAATT
1 TTTTTGAATT
31589826 TTTTT
1 TTTTT
31589831 TATTTTTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (10 bp):
TTTTTGAATT
Found at i:31593417 original size:45 final size:45
Alignment explanation
Indices: 31593368--31593534 Score: 192
Period size: 45 Copynumber: 3.7 Consensus size: 45
31593358 AACGAGTAAT
*
31593368 ACCATAGCTGAAAGACGTTATGGCATCACGATTTTATTGAATAAG
1 ACCATAGCTGAAAGACGTTATGGCATCACGATTTTATAGAATAAG
* * * * *
31593413 ACCATAGCTAAAAGATGTTATGGCATCACGATTCTATCGAGTAAG
1 ACCATAGCTGAAAGACGTTATGGCATCACGATTTTATAGAATAAG
* * * *
31593458 ACCATAGCTGAAAGATGATATGGCATCACGA-ATTAAAGAAGTAAG
1 ACCATAGCTGAAAGACGTTATGGCATCACGATTTTATAGAA-TAAG
* ** *
31593503 ACCATAGTTGAAAGACACTATGGCAACACGAT
1 ACCATAGCTGAAAGACGTTATGGCATCACGAT
31593535 GGAAAATGAA
Statistics
Matches: 103, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
44 4 0.04
45 99 0.96
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (45 bp):
ACCATAGCTGAAAGACGTTATGGCATCACGATTTTATAGAATAAG
Found at i:31593525 original size:90 final size:92
Alignment explanation
Indices: 31593319--31593534 Score: 237
Period size: 90 Copynumber: 2.4 Consensus size: 92
31593309 AGGAAATGAT
* *
31593319 TAAGACCATAGTTGAAAGACACTATTGCAC-C-ATACCATAAACGAGTAATACCATAGCTGAAAG
1 TAAGACCATAGTTGAAAGACACTATGGCACACGATACCATAAACGAGTAAGACCATAGCTGAAAG
* * **
31593382 ACGTTATGGCATCACGATTTTATTGAA
66 ACGATATGGCATCACGATATTAAAGAA
* * *** * *
31593409 TAAGACCATAGCTAAAAGATGTTATGGCATCACGAT-TC-T-ATCGAGTAAGACCATAGCTGAAA
1 TAAGACCATAGTTGAAAGACACTATGGCA-CACGATACCATAAACGAGTAAGACCATAGCTGAAA
*
31593471 GATGATATGGCATCACGA-ATTAAAGAA
65 GACGATATGGCATCACGATATTAAAGAA
31593498 GTAAGACCATAGTTGAAAGACACTATGGCAACACGAT
1 -TAAGACCATAGTTGAAAGACACTATGGC-ACACGAT
31593535 GGAAAATGAA
Statistics
Matches: 102, Mismatches: 19, Indels: 10
0.78 0.15 0.08
Matches are distributed among these distances:
89 6 0.06
90 89 0.87
91 3 0.03
92 2 0.02
93 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.24
Consensus pattern (92 bp):
TAAGACCATAGTTGAAAGACACTATGGCACACGATACCATAAACGAGTAAGACCATAGCTGAAAG
ACGATATGGCATCACGATATTAAAGAA
Found at i:31593558 original size:45 final size:45
Alignment explanation
Indices: 31593499--31593617 Score: 134
Period size: 45 Copynumber: 2.6 Consensus size: 45
31593489 ATTAAAGAAG
* * * *
31593499 TAAGACCATAGTTGAAAGACACTATGGCAACACGATGGAAAATGAA
1 TAAGACCATGGTTGAAAGACACTATGGCAACAAGA-CGAAAATAAA
* * *
31593545 TAAGA-CATGGTTGAAAGACACTATGCCATCAAGACGAGAATAAA
1 TAAGACCATGGTTGAAAGACACTATGGCAACAAGACGAAAATAAA
*
31593589 TAAGACCAGGGTTGAAAGACA-TCATGGCA
1 TAAGACCATGGTTGAAAGACACT-ATGGCA
31593618 CTCTTCGATC
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
44 13 0.21
45 44 0.71
46 5 0.08
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.18
Consensus pattern (45 bp):
TAAGACCATGGTTGAAAGACACTATGGCAACAAGACGAAAATAAA
Found at i:31595203 original size:12 final size:12
Alignment explanation
Indices: 31595186--31595214 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
31595176 TGTAGTTCCC
31595186 ACACGGGTTGAG
1 ACACGGGTTGAG
31595198 ACACGGGTTGAG
1 ACACGGGTTGAG
31595210 ACACG
1 ACACG
31595215 ACCGTGTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.21, G:0.38, T:0.14
Consensus pattern (12 bp):
ACACGGGTTGAG
Found at i:31598784 original size:109 final size:109
Alignment explanation
Indices: 31598588--31598909 Score: 461
Period size: 109 Copynumber: 3.0 Consensus size: 109
31598578 AAGGAAAATT
* *
31598588 TTTCAAAGTAAGGCAATATTTTGTGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATATTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
*
31598653 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCAAAATATCCTTTTAAAAA
* * *
31598697 TTTCAAAATAAGGCAATGTTTTGCGTTTGTAAATTCGAGAAAACGTGCCCTAATGTGCTAGGTTT
1 TTTCAAAATAAGGCAATATTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* *
31598762 CGATTTTTCTCGTTCGATCAAATAGCAAAATATCCTTTT-AAAA
66 CGATTTTTCTCGTTCAACCAAATAGCAAAATATCCTTTTAAAAA
** * * * * *
31598805 TTTTGAAATAAGACAATATTTTACGTTTGGAAATTCGAGGAAATGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATATTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* * *
31598870 CGA--TTTCTCGTTTAACCAAATAGCCAAATATCCTCTTAAA
66 CGATTTTTCTCGTTCAACCAAATAGCAAAATATCCTTTTAAA
31598910 TTTTAATCCA
Statistics
Matches: 190, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
106 29 0.15
107 2 0.01
108 63 0.33
109 96 0.51
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Consensus pattern (109 bp):
TTTCAAAATAAGGCAATATTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
CGATTTTTCTCGTTCAACCAAATAGCAAAATATCCTTTTAAAAA
Found at i:31602157 original size:28 final size:27
Alignment explanation
Indices: 31602125--31602187 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
31602115 GTATGGGGTG
*
31602125 CAAAAAAAAATA-AAACAAAACAAAAAA
1 CAAAAAAAAATATAAA-AAAAAAAAAAA
**
31602152 CAAAAAACAAATATAAAAATTAAAAAAA
1 CAAAAAA-AAATATAAAAAAAAAAAAAA
31602180 CAAAAAAA
1 CAAAAAAA
31602188 TCTCTGCAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 8 0.26
28 20 0.65
29 3 0.10
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.08
Consensus pattern (27 bp):
CAAAAAAAAATATAAAAAAAAAAAAAA
Found at i:31602583 original size:6 final size:6
Alignment explanation
Indices: 31602561--31602596 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
31602551 AAAATATTTT
*
31602561 GAAAAA GAAGAA G-AAAA GAAAAA GAAAAA GAAAAA G
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA G
31602597 GAGCGGCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:31602583 original size:17 final size:17
Alignment explanation
Indices: 31602561--31602594 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
31602551 AAAATATTTT
*
31602561 GAAAAAGAAGAAGAAAA
1 GAAAAAGAAAAAGAAAA
31602578 GAAAAAGAAAAAGAAAA
1 GAAAAAGAAAAAGAAAA
31602595 AGGAGCGGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
GAAAAAGAAAAAGAAAA
Found at i:31603565 original size:24 final size:24
Alignment explanation
Indices: 31603531--31603584 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
31603521 ATGTCCCAAA
*
31603531 ATTACAGTGGACTT-AACCTTGAAG
1 ATTACAATGGA-TTGAACCTTGAAG
**
31603555 ATTACAATGGATTGAAGTTTGAAG
1 ATTACAATGGATTGAACCTTGAAG
31603579 ATTACA
1 ATTACA
31603585 GTGGGGGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 2 0.08
24 24 0.92
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (24 bp):
ATTACAATGGATTGAACCTTGAAG
Found at i:31603885 original size:46 final size:46
Alignment explanation
Indices: 31603818--31605373 Score: 1220
Period size: 46 Copynumber: 34.2 Consensus size: 46
31603808 CCCAGAGAAC
* *
31603818 AGATCGAAGATAGTAGATCTTGTCTTTCTGTATTTGGCAGCGGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
31603864 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
* * * *
31603910 AGATCGAAGATAGCAGATCTTGTCTTCCTATACTTGGTAGCAGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
* * *
31603956 AGATCGAAGAAAGCAGATCTTGTCTTCCTGTATTTTGCAACGGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
* * * **
31604002 AGATCGAAGATAGAAGATCTTGTTTTCCTGTGTTTGGCAGTAGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
* * * ** *
31604048 AGATCGAATATAGCAGATCTT-CCCTGATGGTATTCGGCAGCGGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCT-GTATTTGGCAGCGGAGT
* * * *
31604094 AGATCGAAGATAGCAGATCTTCTCTTCCAGTATTTGGTAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
* * * *
31604140 AGATCGAAGAAAGTAGATCTTGTCTTCTTATATTTGGCAGCGGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
*
31604186 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTTGGCAGCGGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
* * *
31604232 AGATCGAAGAAAGCAGATCTTGTCTTCCTGTATTTCGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
*
31604278 AGATCGAAGATAGCAGATCTTGTCTTCCTGTGTTTGGCAGCGGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
** * *
31604324 AGATCGAAGATAGCAGATCTTGTC-TAATGGTATTCGGCAGTGGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCT-GTATTTGGCAGCGGAGT
* * *
31604370 AGATCGAAGATAGCAGATCTTCTCTTCCTGTATTTGGTAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
* **** * *
31604416 AGATCGAAGATTA-CAGAT-TCTGTC-TCC-CTAAGCAGTAGTGGAGT
1 AGATCGAAGA-TAGCAGATCT-TGTCTTCCTGTATTTGGCAGCGGAGT
* * * * *
31604460 AGATCGAAGATGGC-GAATCTTATCTTCCCAAG-ATAATGG-A--GAAGT
1 AGATCGAAGATAGCAG-ATCTTGTCTT-CC-TGTAT-TTGGCAGCGGAGT
** ** ** * * * ** * * *
31604505 AGATTTAAGCCATTAG-TCCTATC-TCC-CTAAGTAGTAGTGGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
* * ** **** * * *
31604548 AGGTTC-AAGATGGCAGAT-TCTGTC--CCCCTAAGCAGTAGTGGAGA
1 A-GATCGAAGATAGCAGATCT-TGTCTTCCTGTATTTGGCAGCGGAGT
* * * * * * *
31604592 AGATCGAACATGGC-GAATCGTATCTTCCCAAG-ATAGTGG-A--GAAGT
1 AGATCGAAGATAGCAG-ATCTTGTCTT-CC-TGTAT-TTGGCAGCGGAGT
* ** ** ** * ** ** * * *
31604637 AAATTTAAGCCATTAG-TCTTATC-TCC-CCAAGTAGTAGTGGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
* * * * ** *
31604680 AGGTTGAAGATTGCAGATTTTGTC--CCCCTA---GGCA-CTAGTTGAGC
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC--G--GAGT
* * * * * * * *
31604724 AGATCAAAGATGGCAAATCTTATCTTCCCCAG-ATAGTGG--G-GAAGC
1 AGATCGAAGATAGCAGATCTTGTCTT--CCTGTAT-TTGGCAGCGGAGT
** ** * * * * **** * *
31604769 AGATTTAAG-CCGTTAG-TCCTATC-TCC-CTAAGCAGTAGTGGAGT
1 AGATCGAAGATAG-CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
* * * *
31604812 AGGTTGAAGATACCAGATCTTGTCTTCCTGTATTTAGCAGCGGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
*
31604858 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGTAGCGGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
*
31604904 AGATCTAAGATAGCAGATCTTGTCTTCCTGTATTTTGG-AGCGGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTA-TTTGGCAGCGGAGT
* *
31604950 AGATCGAAGATAGCGGAACTTGTCTTCCTGTATTTGGCAGCGGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
* *
31604996 AGATCGAAGATAACAGATCTTGACTTCCTGTATTTGGCAGCGGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
31605042 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
**
31605088 AGACTTCG-ATCTAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
1 AGA--TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
* *
31605135 AGATCGAATATAGCAGATCTTGTCTTCCTGTATTTGGTAGCGGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
* * * *
31605181 ACATCGAAGAAAGAAGATCTTGTCTTCCTGTATTTGGCAGCAGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
*
31605227 AGATCAAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
* *
31605273 AGATCGAAGATAACATATCTTGTCTTCCTGTATTTGGCAGCGGAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
* *
31605319 AGATCGAAGATAGCAGATCTTGTC-T-CTGTATTTGGTAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
31605363 AGATCGAAGAT
1 AGATCGAAGAT
31605374 TACAGATTCT
Statistics
Matches: 1219, Mismatches: 226, Indels: 132
0.77 0.14 0.08
Matches are distributed among these distances:
40 7 0.01
41 9 0.01
42 6 0.00
43 47 0.04
44 139 0.11
45 52 0.04
46 890 0.73
47 59 0.05
48 8 0.01
51 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (46 bp):
AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGT
Found at i:31604566 original size:132 final size:132
Alignment explanation
Indices: 31604429--31604822 Score: 590
Period size: 132 Copynumber: 3.0 Consensus size: 132
31604419 TCGAAGATTA
* *
31604429 CAGATTCTGTCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGCGAATCTTATCTTCCCAAGAT
1 CAGATTCTGTCCCCCTAAGCAGTAGTGGAGAAGATCGAAGATGGCGAATCTTATCTTCCCAAGAT
* *
31604494 AATGGAGAAGTAGATTTAAGCCATTAGTCCTATCTCCCTAAGTAGTAGTGGAGTAGGTTCAAGAT
66 AGTGGAGAAGTAGATTTAAGCCATTAGTCCTATCTCCCTAAGTAGTAGTGGAGTAGGTTGAAGAT
31604559 GG
131 GG
* *
31604561 CAGATTCTGTCCCCCTAAGCAGTAGTGGAGAAGATCGAACATGGCGAATCGTATCTTCCCAAGAT
1 CAGATTCTGTCCCCCTAAGCAGTAGTGGAGAAGATCGAAGATGGCGAATCTTATCTTCCCAAGAT
* * *
31604626 AGTGGAGAAGTAAATTTAAGCCATTAGTCTTATCTCCCCAAGTAGTAGTGGAGTAGGTTGAAGAT
66 AGTGGAGAAGTAGATTTAAGCCATTAGTCCTATCTCCCTAAGTAGTAGTGGAGTAGGTTGAAGAT
*
31604691 TG
131 GG
* * * * * * * *
31604693 CAGATTTTGTCCCCCTAGGCACTAGTTGAGCAGATCAAAGATGGCAAATCTTATCTTCCCCAGAT
1 CAGATTCTGTCCCCCTAAGCAGTAGTGGAGAAGATCGAAGATGGCGAATCTTATCTTCCCAAGAT
* * * *
31604758 AGTGGGGAAGCAGATTTAAGCCGTTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGAT
66 AGTGGAGAAGTAGATTTAAGCCATTAGTCCTATCTCCCTAAGTAGTAGTGGAGTAGGTTGAAGAT
31604823 ACCAGATCTT
Statistics
Matches: 235, Mismatches: 27, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
132 235 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (132 bp):
CAGATTCTGTCCCCCTAAGCAGTAGTGGAGAAGATCGAAGATGGCGAATCTTATCTTCCCAAGAT
AGTGGAGAAGTAGATTTAAGCCATTAGTCCTATCTCCCTAAGTAGTAGTGGAGTAGGTTGAAGAT
GG
Found at i:31605524 original size:132 final size:132
Alignment explanation
Indices: 31605368--31606067 Score: 974
Period size: 132 Copynumber: 5.3 Consensus size: 132
31605358 GAAGTAGATC
* * *
31605368 GAAGATTACAGATTCTGTCTCCCTAAGTAGTAGTGGCGCAGATCGAAGATGGTGAATCTTATCTT
1 GAAGATTGCAGATTCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTT
* *
31605433 CCCAAGATAATAGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTAAGAAGTAGTGGAGTAGG
66 CCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTAAGAAGTAGTGGAGTAGG
31605498 TT
131 TT
* * * * *
31605500 GAAGATGGAAGATTCTGTCCCCCTAAGCAGTAGTGGAGAAGATCGAAGATGGCGAATCTTATCTT
1 GAAGATTGCAGATTCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTT
* *
31605565 CCCAAGATAGTGGAGAAGCAGATTTAAACCATTAGTCTTATCTCCCTAAGTAA-TAGTGGAGTAG
66 CCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTAAG-AAGTAGTGGAGTAG
31605629 GTT
130 GTT
* * *
31605632 GAAGATTGCAGATTCTGTCCCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGAATCTTATCTT
1 GAAGATTGCAGATTCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTT
* *
31605697 CCCAAGATAGTGGAGAAGCAGATTTAAGTCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGG
66 CCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTAAGAAGTAGTGGAGTAGG
31605762 TT
131 TT
*
31605764 GTAGATTGCAGATTCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTT
1 GAAGATTGCAGATTCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTT
* * * * * *
31605829 CCCAGGATAGTGAAGAAGCAGATTTAATCCATTAGTCCTATCTTCCTAAGCAGTAGCGGAGTAGG
66 CCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTAAGAAGTAGTGGAGTAGG
*
31605894 TC
131 TT
* * * * ** * * *
31605896 AAAGATTGTAGATTCTGTATCCCTAAGCAATAGTGGAGCAGATAAAAAACGATGAATCTTATCTT
1 GAAGATTGCAGATTCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTT
* * *
31605961 CCCAAGATAGTGGAGAAGCTGATTTAAGCCATTAGTCCTATCCCCCTAAGCAA-CAGTGGAGTAG
66 CCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTAAG-AAGTAGTGGAGTAG
31606025 GTT
130 GTT
* * * * *
31606028 AAAGATTG-TGAATCTTGTCTCTCTAAGCAGTAGTAGAGCA
1 GAAGATTGCAGATTC-TGTCTCCCTAAGCAGTAGTGGAGCA
31606068 AATCAACAAC
Statistics
Matches: 507, Mismatches: 57, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
131 5 0.01
132 499 0.98
133 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (132 bp):
GAAGATTGCAGATTCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTT
CCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTAAGAAGTAGTGGAGTAGG
TT
Found at i:31605666 original size:44 final size:44
Alignment explanation
Indices: 31605470--31605801 Score: 172
Period size: 44 Copynumber: 7.5 Consensus size: 44
31605460 GCCATTAGTC
* * * *
31605470 CTATCTCCCTAAGAAGTAGTGGAGTAGGTTGAAGATGGAAGATT
1 CTATCTCCCTAAGCAGTAGTGGAGAAGGTTGAAGATTGCAGATT
* * * * * *
31605514 CTGTCCCCCTAAGCAGTAGTGGAGAAGATCGAAGATGGC-GAAT
1 CTATCTCCCTAAGCAGTAGTGGAGAAGGTTGAAGATTGCAGATT
* *
31605557 CTTATCTTCCC-AAG-A-TAGTGGAGAAGCAGATTTAAACCATT--AG--T
1 C-TATC-TCCCTAAGCAGTAGTGGAGAAG--G--TTGAA-GATTGCAGATT
* * *
31605601 CTTATCTCCCTAAGTAATAGTGGAGTAGGTTGAAGATTGCAGATT
1 C-TATCTCCCTAAGCAGTAGTGGAGAAGGTTGAAGATTGCAGATT
* * * * ** * *
31605646 CTGTCCCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC-GAAT
1 CTATCTCCCTAAGCAGTAGTGGAGAAGGTTGAAGATTGCAGATT
* *
31605689 CTTATCTTCCC-AAG-A-TAGTGGAGAAGCAGATTTAAGTCATT--AG-TC
1 C-TATC-TCCCTAAGCAGTAGTGGAGAAG--G-TTGAAG--ATTGCAGATT
* *
31605734 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGTAGATTGCAGATT
1 CTATCTCCCTAAGCAGTAGTGGAGAAGGTTGAAGATTGCAGATT
*
31605778 CTGTCTCCCTAAGCAGTAGTGGAG
1 CTATCTCCCTAAGCAGTAGTGGAG
31605802 CAGATCGAAG
Statistics
Matches: 217, Mismatches: 42, Indels: 58
0.68 0.13 0.18
Matches are distributed among these distances:
41 6 0.03
42 25 0.12
43 26 0.12
44 116 0.53
45 15 0.07
46 25 0.12
47 4 0.02
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.27
Consensus pattern (44 bp):
CTATCTCCCTAAGCAGTAGTGGAGAAGGTTGAAGATTGCAGATT
Found at i:31607495 original size:12 final size:12
Alignment explanation
Indices: 31607480--31607515 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
31607470 AATAAATCTA
31607480 TTATGATTATTT
1 TTATGATTATTT
31607492 TTATGATTATTT
1 TTATGATTATTT
31607504 TTAT--TTATTT
1 TTATGATTATTT
31607514 TT
1 TT
31607516 TTCCTCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.33
12 16 0.67
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (12 bp):
TTATGATTATTT
Found at i:31607530 original size:2 final size:2
Alignment explanation
Indices: 31607525--31607550 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31607515 TTTCCTCATT
31607525 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
31607551 CTTATATTTC
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):
TA
Done.