Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold197
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: 1875808
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 64134 characters in sequence are not A, C, G, or T
File 2 of 6
Found at i:323872 original size:40 final size:40
Alignment explanation
Indices: 323836--324028 Score: 280
Period size: 40 Copynumber: 4.8 Consensus size: 40
323826 TCTCTATTTA
* *
323836 GCGTGTTTCAGTTGGATCAGCTCTTATGAGGTTCTATTTG
1 GCGTGTTTCAGTTGGATCAGCTCTTATGAGCTTCTGTTTG
* * *
323876 GCGTGTTTCGGTTGGATCAACTCTTATGAGCTTCTGTCTG
1 GCGTGTTTCAGTTGGATCAGCTCTTATGAGCTTCTGTTTG
*
323916 GTGTGTTTCAGTTGGATCAGCTCTTATGAGCTTCTGTTTG
1 GCGTGTTTCAGTTGGATCAGCTCTTATGAGCTTCTGTTTG
*
323956 GCGTGTTTC-GATTGGATCAACTCTTATGAGCTTCTGTTTG
1 GCGTGTTTCAG-TTGGATCAGCTCTTATGAGCTTCTGTTTG
* * *
323996 GTGTGTTTCGGTTGGATTAGCTCTTATGAGCTT
1 GCGTGTTTCAGTTGGATCAGCTCTTATGAGCTT
324029 GTCTGGTGTG
Statistics
Matches: 137, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 1 0.01
40 135 0.99
41 1 0.01
ACGTcount: A:0.13, C:0.16, G:0.27, T:0.43
Consensus pattern (40 bp):
GCGTGTTTCAGTTGGATCAGCTCTTATGAGCTTCTGTTTG
Found at i:323929 original size:80 final size:80
Alignment explanation
Indices: 323838--324028 Score: 328
Period size: 80 Copynumber: 2.4 Consensus size: 80
323828 TCTATTTAGC
* *
323838 GTGTTTCAGTTGGATCAGCTCTTATGAGGTTCTATTTGGCGTGTTTCGGTTGGATCAACTCTTAT
1 GTGTTTCAGTTGGATCAGCTCTTATGAGCTTCTATTTGGCGTGTTTCGATTGGATCAACTCTTAT
323903 GAGCTTCTGTCTGGT
66 GAGCTTCTGTCTGGT
*
323918 GTGTTTCAGTTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCGATTGGATCAACTCTTAT
1 GTGTTTCAGTTGGATCAGCTCTTATGAGCTTCTATTTGGCGTGTTTCGATTGGATCAACTCTTAT
*
323983 GAGCTTCTGTTTGGT
66 GAGCTTCTGTCTGGT
* *
323998 GTGTTTCGGTTGGATTAGCTCTTATGAGCTT
1 GTGTTTCAGTTGGATCAGCTCTTATGAGCTT
324029 GTCTGGTGTG
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 105 1.00
ACGTcount: A:0.14, C:0.16, G:0.27, T:0.43
Consensus pattern (80 bp):
GTGTTTCAGTTGGATCAGCTCTTATGAGCTTCTATTTGGCGTGTTTCGATTGGATCAACTCTTAT
GAGCTTCTGTCTGGT
Found at i:330286 original size:29 final size:29
Alignment explanation
Indices: 330253--330336 Score: 69
Period size: 29 Copynumber: 3.2 Consensus size: 29
330243 ATTTTGTGTA
330253 GCTTCAGATGTTGAAATATCACTAGTTGT
1 GCTTCAGATGTTGAAATATCACTAGTTGT
* * *
330282 GCTTC---TCTT---ATAT--TTTG-TGT
1 GCTTCAGATGTTGAAATATCACTAGTTGT
330302 AGCTTCAGATGTTGAAATATCACTAGTTGT
1 -GCTTCAGATGTTGAAATATCACTAGTTGT
330332 GCTTC
1 GCTTC
330337 TCTTATGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 20
0.60 0.09 0.31
Matches are distributed among these distances:
20 3 0.08
21 7 0.18
23 4 0.10
24 3 0.08
26 3 0.08
27 4 0.10
29 12 0.31
30 3 0.08
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (29 bp):
GCTTCAGATGTTGAAATATCACTAGTTGT
Found at i:330302 original size:50 final size:50
Alignment explanation
Indices: 330241--330342 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
330231 TAATTTTTTG
330241 ATATTTTGTGTAGCTTCAGATGTTGAAATATCACTAGTTGTGCTTCTCTT
1 ATATTTTGTGTAGCTTCAGATGTTGAAATATCACTAGTTGTGCTTCTCTT
330291 ATATTTTGTGTAGCTTCAGATGTTGAAATATCACTAGTTGTGCTTCTCTT
1 ATATTTTGTGTAGCTTCAGATGTTGAAATATCACTAGTTGTGCTTCTCTT
330341 AT
1 AT
330343 GATTCTATGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.46
Consensus pattern (50 bp):
ATATTTTGTGTAGCTTCAGATGTTGAAATATCACTAGTTGTGCTTCTCTT
Found at i:330372 original size:50 final size:50
Alignment explanation
Indices: 330249--330356 Score: 146
Period size: 50 Copynumber: 2.2 Consensus size: 50
330239 TGATATTTTG
* * * *
330249 TGTAGCTTCAGATGTTGAAATATCACTAGTTGTGCTTCTCTTATATTTTG
1 TGTAGATTCAGATGTAGAAATATCACTAGTTGTGCTTCTCTTATATTCTA
* *
330299 TGTAGCTTCAGATGTTGAAATATCACTAGTTGTGCTTCTCTTATGATTCTA
1 TGTAGATTCAGATGTAGAAATATCACTAGTTGTGCTTCTCTTAT-ATTCTA
330350 TGT-GATT
1 TGTAGATT
330357 ATCTGTAAGA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 47 0.87
51 7 0.13
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (50 bp):
TGTAGATTCAGATGTAGAAATATCACTAGTTGTGCTTCTCTTATATTCTA
Found at i:333971 original size:42 final size:44
Alignment explanation
Indices: 333916--334032 Score: 152
Period size: 42 Copynumber: 2.8 Consensus size: 44
333906 ATGTGATATA
333916 GTGTAAGACCATGTCT-GGACATTGGCATCGATTATA-GATTAC
1 GTGTAAGACCATGTCTAGGACATTGGCATCGATTATATGATTAC
* * * *
333958 GTGTAAGATCATGTCTGGGACATCGGCATCG--TATATGATTTC
1 GTGTAAGACCATGTCTAGGACATTGGCATCGATTATATGATTAC
* *
334000 GTGTAAGACCCTGTCTAGGACAGTGGCATCGAT
1 GTGTAAGACCATGTCTAGGACATTGGCATCGAT
334033 ATTTGATAAC
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.06
42 46 0.73
43 13 0.21
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (44 bp):
GTGTAAGACCATGTCTAGGACATTGGCATCGATTATATGATTAC
Found at i:336143 original size:21 final size:22
Alignment explanation
Indices: 336108--336149 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
336098 AAGGGACTTT
*
336108 ATGATGATATTTGAC-TATGAG
1 ATGATGATATATGACTTATGAG
*
336129 ATGATGATGTATGACTTATGA
1 ATGATGATATATGACTTATGA
336150 TTGTGAAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (22 bp):
ATGATGATATATGACTTATGAG
Found at i:338008 original size:35 final size:35
Alignment explanation
Indices: 337941--338067 Score: 175
Period size: 35 Copynumber: 3.6 Consensus size: 35
337931 GTACATCGAC
337941 AATCCAACC-AAACCACACCAGATGCTCATAAGAGCT
1 AATCCAACCGAAA-CACACCA-ATGCTCATAAGAGCT
* *
337977 AATCCATCCGAAACACACCAATGCTTATAAGAGCT
1 AATCCAACCGAAACACACCAATGCTCATAAGAGCT
***
338012 AATCCTTTCGAAACACACCAATGCTCATAAGAGCT
1 AATCCAACCGAAACACACCAATGCTCATAAGAGCT
*
338047 AGTCCAACCGAAACACACCAA
1 AATCCAACCGAAACACACCAA
338068 AACAGAGAGT
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
35 63 0.78
36 15 0.19
37 3 0.04
ACGTcount: A:0.41, C:0.31, G:0.11, T:0.17
Consensus pattern (35 bp):
AATCCAACCGAAACACACCAATGCTCATAAGAGCT
Found at i:340266 original size:414 final size:414
Alignment explanation
Indices: 339496--340328 Score: 1666
Period size: 414 Copynumber: 2.0 Consensus size: 414
339486 GTGATCGTTT
339496 TTAAAGAAAACTATCTGATATGAAAACAGAGAAAATTATTAGTAGGAGCATGTAGTTAAGTTAAA
1 TTAAAGAAAACTATCTGATATGAAAACAGAGAAAATTATTAGTAGGAGCATGTAGTTAAGTTAAA
339561 AATCTGGTATCGAGCTCAGGGAATAAATTGAATAAATTGGAAAAGTATATAGACTAAAGTGCAAT
66 AATCTGGTATCGAGCTCAGGGAATAAATTGAATAAATTGGAAAAGTATATAGACTAAAGTGCAAT
339626 TGTCCTATTTTTATTTTGATAGAAATGACTTAATGGCAATTTTACCATTACTTAAAAAAATCAAT
131 TGTCCTATTTTTATTTTGATAGAAATGACTTAATGGCAATTTTACCATTACTTAAAAAAATCAAT
339691 GGTTTCATTATGGCTTTTAAATGATAATTTTATTAAATAATTATTATTTAATATTTTATTTAAAA
196 GGTTTCATTATGGCTTTTAAATGATAATTTTATTAAATAATTATTATTTAATATTTTATTTAAAA
339756 TATTAGTATCTTATTAAGTATTATTATGATATAAATAAAAGAAGAAGAACATATTTCTTTATGTT
261 TATTAGTATCTTATTAAGTATTATTATGATATAAATAAAAGAAGAAGAACATATTTCTTTATGTT
339821 TCTTTCTTATTCACGAAAGTTGGGGAAAGAAGAAGAAAAAAATTATTTCATCATTTTCCTTCAAA
326 TCTTTCTTATTCACGAAAGTTGGGGAAAGAAGAAGAAAAAAATTATTTCATCATTTTCCTTCAAA
339886 TTCAAGCATAAGATATGGTTTTTC
391 TTCAAGCATAAGATATGGTTTTTC
339910 TTAAAGAAAACTATCTGATATGAAAACAGAGAAAATTATTAGTAGGAGCATGTAGTTAAGTTAAA
1 TTAAAGAAAACTATCTGATATGAAAACAGAGAAAATTATTAGTAGGAGCATGTAGTTAAGTTAAA
339975 AATCTGGTATCGAGCTCAGGGAATAAATTGAATAAATTGGAAAAGTATATAGACTAAAGTGCAAT
66 AATCTGGTATCGAGCTCAGGGAATAAATTGAATAAATTGGAAAAGTATATAGACTAAAGTGCAAT
340040 TGTCCTATTTTTATTTTGATAGAAATGACTTAATGGCAATTTTACCATTACTTAAAAAAATCAAT
131 TGTCCTATTTTTATTTTGATAGAAATGACTTAATGGCAATTTTACCATTACTTAAAAAAATCAAT
340105 GGTTTCATTATGGCTTTTAAATGATAATTTTATTAAATAATTATTATTTAATATTTTATTTAAAA
196 GGTTTCATTATGGCTTTTAAATGATAATTTTATTAAATAATTATTATTTAATATTTTATTTAAAA
340170 TATTAGTATCTTATTAAGTATTATTATGATATAAATAAAAGAAGAAGAACATATTTCTTTATGTT
261 TATTAGTATCTTATTAAGTATTATTATGATATAAATAAAAGAAGAAGAACATATTTCTTTATGTT
340235 TCTTTCTTATTCACGAAAGTTGGGGAAAGAAGAAGAAAAAAATTATTTCATCATTTTCCTTCAAA
326 TCTTTCTTATTCACGAAAGTTGGGGAAAGAAGAAGAAAAAAATTATTTCATCATTTTCCTTCAAA
340300 TTCAAGCATAAGATATGGTTTTTC
391 TTCAAGCATAAGATATGGTTTTTC
340324 TTAAA
1 TTAAA
340329 ACTTTTCATA
Statistics
Matches: 419, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
414 419 1.00
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (414 bp):
TTAAAGAAAACTATCTGATATGAAAACAGAGAAAATTATTAGTAGGAGCATGTAGTTAAGTTAAA
AATCTGGTATCGAGCTCAGGGAATAAATTGAATAAATTGGAAAAGTATATAGACTAAAGTGCAAT
TGTCCTATTTTTATTTTGATAGAAATGACTTAATGGCAATTTTACCATTACTTAAAAAAATCAAT
GGTTTCATTATGGCTTTTAAATGATAATTTTATTAAATAATTATTATTTAATATTTTATTTAAAA
TATTAGTATCTTATTAAGTATTATTATGATATAAATAAAAGAAGAAGAACATATTTCTTTATGTT
TCTTTCTTATTCACGAAAGTTGGGGAAAGAAGAAGAAAAAAATTATTTCATCATTTTCCTTCAAA
TTCAAGCATAAGATATGGTTTTTC
Found at i:348077 original size:25 final size:25
Alignment explanation
Indices: 348035--348083 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
348025 CTTTTTTTGA
* *
348035 TAGTATATCCTAAAACTATTATAGG
1 TAGTATATACTAAAACTACTATAGG
* *
348060 TAGTATATACTGAGACTACTATAG
1 TAGTATATACTAAAACTACTATAG
348084 ATAGACTGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (25 bp):
TAGTATATACTAAAACTACTATAGG
Found at i:359063 original size:23 final size:23
Alignment explanation
Indices: 359037--359092 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
359027 GTTCTACAAA
**
359037 GCCTTTGTGGCGTATTCTATGAT
1 GCCTTTGTGGAATATTCTATGAT
* *
359060 GCCTTTATGGAATATTCTGTGAT
1 GCCTTTGTGGAATATTCTATGAT
* *
359083 ACATTTGTGG
1 GCCTTTGTGG
359093 TGAAATTTTT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.18, C:0.14, G:0.25, T:0.43
Consensus pattern (23 bp):
GCCTTTGTGGAATATTCTATGAT
Found at i:360936 original size:56 final size:54
Alignment explanation
Indices: 360874--361023 Score: 205
Period size: 53 Copynumber: 2.7 Consensus size: 54
360864 GGGTGTTAAT
360874 ATATTATTATGGGATATTATCTTTTAGCAATTTGATTCCTAATGAGATATTACAA
1 ATATTATTATGGGATATTAT-TTTTAGCAATTTGATTCCTAATGAGATATTACAA
* * *
360929 A-A-TATTATGGGATATTATTTCTTAGCAATTTGATTCCTAATGGGATATTATAGG
1 ATATTATTATGGGATATTATTT-TTAGCAATTTGATTCCTAATGAGATATTACA-A
* *
360983 ATATTATTATGGGAAATTATATTTTAACAATTTGATTCCTA
1 ATATTATTATGGGATATTAT-TTTTAGCAATTTGATTCCTA
361024 CGTAACTATT
Statistics
Matches: 85, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
52 2 0.02
53 45 0.53
54 2 0.02
55 2 0.02
56 32 0.38
57 2 0.02
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (54 bp):
ATATTATTATGGGATATTATTTTTAGCAATTTGATTCCTAATGAGATATTACAA
Found at i:361050 original size:2 final size:2
Alignment explanation
Indices: 361038--361069 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
361028 ACTATTATTG
*
361038 TA TA GA 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
361070 CCTTTGAGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:369181 original size:32 final size:32
Alignment explanation
Indices: 369105--369166 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
369095 CATTATTTGT
369105 AATACATTAAATAAATATATTACTATCTTACA
1 AATACATTAAATAAATATATTACTATCTTACA
369137 AATACATTAAATAAATATATTACTATCTTA
1 AATACATTAAATAAATATATTACTATCTTA
369167 ATAATCTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (32 bp):
AATACATTAAATAAATATATTACTATCTTACA
Found at i:371933 original size:27 final size:27
Alignment explanation
Indices: 371866--371933 Score: 106
Period size: 25 Copynumber: 2.6 Consensus size: 27
371856 AAAAATAAAA
371866 ATTTACCAAAATAT-TATAACTTTTTTT
1 ATTTACCAAAATATATATAAC-TTTTTT
371893 ATTTACCAAAATATATAT-A-TTTTTT
1 ATTTACCAAAATATATATAACTTTTTT
371918 ATTTACCAAAATATAT
1 ATTTACCAAAATATAT
371934 CAAAAAAACC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
25 22 0.55
27 15 0.38
28 3 0.08
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTTACCAAAATATATATAACTTTTTT
Found at i:372109 original size:18 final size:18
Alignment explanation
Indices: 372080--372143 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 18
372070 GGGGGGGCAG
372080 AAGGAGAGGGAAAGAAAGA
1 AAGGAGA-GGAAAGAAAGA
372099 AAGGAGAGGAAAGAAAGA
1 AAGGAGAGGAAAGAAAGA
*
372117 AA-AAGAAGGAAAGAAAAGGA
1 AAGGAG-AGGAAAG-AAA-GA
372137 AAGGAGA
1 AAGGAGA
372144 AGAATTATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.05
18 20 0.51
19 10 0.26
20 5 0.13
21 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (18 bp):
AAGGAGAGGAAAGAAAGA
Found at i:372128 original size:14 final size:15
Alignment explanation
Indices: 372107--372147 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
372097 GAAAGGAGAG
372107 GAAA-GAAAGAAAAA
1 GAAAGGAAAGAAAAA
*
372121 G-AAGGAAAGAAAAG
1 GAAAGGAAAGAAAAA
372135 GAAAGGAGAAGAA
1 GAAAGGA-AAGAA
372148 TTATATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 2 0.09
14 11 0.48
15 5 0.22
16 5 0.22
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (15 bp):
GAAAGGAAAGAAAAA
Found at i:372332 original size:240 final size:241
Alignment explanation
Indices: 371908--372386 Score: 951
Period size: 240 Copynumber: 2.0 Consensus size: 241
371898 CCAAAATATA
371908 TATATTTTTTATTTACCAAAATATATCAAAAAAACCCAAAAAAAACCTGCAAAAAAAAAATCAGA
1 TATATTTTTTATTTACCAAAATATATCAAAAAAACCCAAAAAAAACCTGCAAAAAAAAAATCAGA
371973 TCGATGTGACGAGTTACTGGTCACGCCAATGGGATTGGCGGCACCAATGGTGCCAATACCATTGG
66 TCGATGTGACGAGTTACTGGTCACGCCAATGGGATTGGCGGCACCAATGGTGCCAATACCATTGG
372038 CGGCACCAGTTAATAATAGGGGGGTCGGTGGTGGGGGGGCAGAAGGAGAGGGAAAGAAAGAAAGG
131 CGGCACCAGTTAATAATAGGGGGGTCGGTGGTGGGGGGGCAGAAGGAGAGGGAAAGAAAGAAAGG
372103 AGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAT
196 AGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAT
372149 TATATTTTTT-TTTACCAAAATATATCAAAAAAACCCAAAAAAAACCTGCAAAAAAAAAATCAGA
1 TATATTTTTTATTTACCAAAATATATCAAAAAAACCCAAAAAAAACCTGCAAAAAAAAAATCAGA
372213 TCGATGTGACGAGTTACTGGTCACGCCAATGGGATTGGCGGCACCAATGGTGCCAATACCATTGG
66 TCGATGTGACGAGTTACTGGTCACGCCAATGGGATTGGCGGCACCAATGGTGCCAATACCATTGG
372278 CGGCACCAGTTAATAATAGGGGGGTCGGTGGTGGGGGGGCAGAAGGAGAGGGAAAGAAAGAAAGG
131 CGGCACCAGTTAATAATAGGGGGGTCGGTGGTGGGGGGGCAGAAGGAGAGGGAAAGAAAGAAAGG
372343 AGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGA
196 AGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGA
372387 GAGAAAAAAA
Statistics
Matches: 238, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
240 228 0.96
241 10 0.04
ACGTcount: A:0.43, C:0.13, G:0.28, T:0.16
Consensus pattern (241 bp):
TATATTTTTTATTTACCAAAATATATCAAAAAAACCCAAAAAAAACCTGCAAAAAAAAAATCAGA
TCGATGTGACGAGTTACTGGTCACGCCAATGGGATTGGCGGCACCAATGGTGCCAATACCATTGG
CGGCACCAGTTAATAATAGGGGGGTCGGTGGTGGGGGGGCAGAAGGAGAGGGAAAGAAAGAAAGG
AGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAT
Found at i:372349 original size:18 final size:18
Alignment explanation
Indices: 372320--372383 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 18
372310 GGGGGGGCAG
372320 AAGGAGAGGGAAAGAAAGA
1 AAGGAGA-GGAAAGAAAGA
372339 AAGGAGAGGAAAGAAAGA
1 AAGGAGAGGAAAGAAAGA
*
372357 AA-AAGAAGGAAAGAAAAGGA
1 AAGGAG-AGGAAAG-AAA-GA
372377 AAGGAGA
1 AAGGAGA
372384 AGAGAGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.05
18 20 0.51
19 10 0.26
20 5 0.13
21 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (18 bp):
AAGGAGAGGAAAGAAAGA
Found at i:375357 original size:3 final size:3
Alignment explanation
Indices: 375349--375554 Score: 412
Period size: 3 Copynumber: 68.7 Consensus size: 3
375339 NNNNNNNNNN
375349 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
375397 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
375445 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
375493 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
375541 AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AA
375555 TAATAATAAT
Statistics
Matches: 203, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 203 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:375559 original size:3 final size:3
Alignment explanation
Indices: 375553--375590 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
375543 CAACAACAAC
*
375553 AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT AACT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT A
375591 CTATTATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:375716 original size:11 final size:11
Alignment explanation
Indices: 375700--375737 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
375690 AAAAATACCT
*
375700 TCTTTTTTTCC
1 TCTTTTTCTCC
375711 TCTTTTTCT-C
1 TCTTTTTCTCC
*
375721 TCTTTTTCTCT
1 TCTTTTTCTCC
375732 TCTTTT
1 TCTTTT
375738 CCGCAGCAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (11 bp):
TCTTTTTCTCC
Found at i:375738 original size:10 final size:10
Alignment explanation
Indices: 375704--375737 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
375694 ATACCTTCTT
375704 TTTTTC-CTC
1 TTTTTCTCTC
375713 TTTTTCTCTC
1 TTTTTCTCTC
375723 TTTTTCTCTTC
1 TTTTTCTC-TC
375734 TTTT
1 TTTT
375738 CCGCAGCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 6 0.26
10 11 0.48
11 6 0.26
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTCTCTC
Found at i:375866 original size:27 final size:27
Alignment explanation
Indices: 375836--375920 Score: 109
Period size: 27 Copynumber: 3.1 Consensus size: 27
375826 CCAATTAGTA
375836 TGGCACCATTGGTGCCGCCAATGGCAT
1 TGGCACCATTGGTGCCGCCAATGGCAT
* **
375863 TGGCACCATTGGAGCCGCCAATGGTTT
1 TGGCACCATTGGTGCCGCCAATGGCAT
**
375890 TGGCA-CATTTGGTGCCGCCAATCCCAT
1 TGGCACCA-TTGGTGCCGCCAATGGCAT
375917 TGGC
1 TGGC
375921 GTGACCAGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 2 0.04
27 47 0.96
ACGTcount: A:0.18, C:0.29, G:0.28, T:0.25
Consensus pattern (27 bp):
TGGCACCATTGGTGCCGCCAATGGCAT
Found at i:376008 original size:23 final size:25
Alignment explanation
Indices: 375978--376044 Score: 102
Period size: 23 Copynumber: 2.7 Consensus size: 25
375968 TTTGTTTTTT
375978 TATATATTTTGGTAAAT-AAAAAA-
1 TATATATTTTGGTAAATAAAAAAAG
376001 TATATATTTTGGTAAATAAAAAAAG
1 TATATATTTTGGTAAATAAAAAAAG
376026 TTATAATATTTTGGTAAAT
1 -TAT-ATATTTTGGTAAAT
376045 TTTTATTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
23 17 0.43
24 6 0.15
26 3 0.08
27 14 0.35
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (25 bp):
TATATATTTTGGTAAATAAAAAAAG
Found at i:377222 original size:21 final size:21
Alignment explanation
Indices: 377196--377251 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
377186 AACAGCGGTG
*
377196 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
377217 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
377238 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
377252 AACAATGGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:378311 original size:11 final size:12
Alignment explanation
Indices: 378282--378314 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
378272 TTCAGCTTGG
*
378282 ATGCTGGTCTGC
1 ATGCTGGTTTGC
378294 ATGCTGGTTTGC
1 ATGCTGGTTTGC
378306 -TGCTGGTTT
1 ATGCTGGTTT
378315 CCTGTTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.06, C:0.18, G:0.33, T:0.42
Consensus pattern (12 bp):
ATGCTGGTTTGC
Found at i:381554 original size:13 final size:13
Alignment explanation
Indices: 381521--381560 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
381511 ATAAAAGGAC
381521 ATAAT-AAATAAT
1 ATAATAAAATAAT
381533 ACGTAATAAAATAAT
1 A--TAATAAAATAAT
381548 ATAATAAAATAAT
1 ATAATAAAATAAT
381561 TATATACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.04
13 12 0.48
14 4 0.16
15 8 0.32
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (13 bp):
ATAATAAAATAAT
Found at i:383661 original size:147 final size:146
Alignment explanation
Indices: 383474--383791 Score: 397
Period size: 147 Copynumber: 2.2 Consensus size: 146
383464 TCAGTCTGCT
* * * *
383474 CCACTGTAACTTTAGGGAGATAAGACTTGTAGCTTCAATAAAGTCTGATGCGACCTGTTCTATTA
1 CCACTGCAACTTCAGGG-GATAAGACTTGTAGCTTCAATAAAGTCTGATGCGACCAGTTCTACTA
*
383539 CAACTTCAAAAAGATAAGATCCATCATTTTGACCCAT-TCCACTGCAACTTCAAGGAAATAAGAC
65 CAACTTCAAAAAGATAAGATCCATCATTTTGACCC-TCTACACTGCAACTTCAAGGAAATAAGAC
383603 TCG-TATCTTCAACTTGCC
129 T-GATATCTTCAACTTGCC
** * * * * * *
383621 CCACTGCAACTTCAGGGGATAAGACTTGTAATTTTTAATAAAGTTTGATGTGATCAGTTTTACTG
1 CCACTGCAACTTCAGGGGATAAGACTTGT-AGCTTCAATAAAGTCTGATGCGACCAGTTCTACTA
* * * * *
383686 CAACTTCAGAGAGATAAGATCCATCATTTTGACCCTCTACACTGCAACTTCAGGGAGATAGGACT
65 CAACTTCAAAAAGATAAGATCCATCATTTTGACCCTCTACACTGCAACTTCAAGGAAATAAGACT
*
383751 GATATCTTTAACTTGCC
130 GATATCTTCAACTTGCC
*
383768 CCACTGCAACTTCATGAGGATAAG
1 CCACTGCAACTTCA-GGGGATAAG
383792 GTTTGCTATT
Statistics
Matches: 147, Mismatches: 20, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
146 14 0.10
147 125 0.85
148 8 0.05
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (146 bp):
CCACTGCAACTTCAGGGGATAAGACTTGTAGCTTCAATAAAGTCTGATGCGACCAGTTCTACTAC
AACTTCAAAAAGATAAGATCCATCATTTTGACCCTCTACACTGCAACTTCAAGGAAATAAGACTG
ATATCTTCAACTTGCC
Found at i:383968 original size:173 final size:173
Alignment explanation
Indices: 383660--384005 Score: 541
Period size: 173 Copynumber: 2.0 Consensus size: 173
383650 AATTTTTAAT
* * * *
383660 AAAGTTTGATGTGATCAGTTTTACTGCAACTTCAGAGAGATAAGATCCATCATTTTGACCCTCTA
1 AAAGATTGATATGATCAGCTTTACTGCAACTTCAGAGAGACAAGATCCATCATTTTGACCCTCTA
*
383725 CACTGCAACTTCAGGGAGATAGGACTGATATCTTTAACTTGCCCCACTGCAACTTCATGAGGATA
66 CACTGCAACTTCAGGGAGATAGGACTGATATCTTCAACTTGCCCCACTGCAACTTCATGAGGATA
** *
383790 AGGTTTGCTATTTCAACATGCTCTGTTGTAACTTCAGAGAGAC
131 AGGTTTGCTATTTCAACATGCTCTACTGCAACTTCAGAGAGAC
* *
383833 AAAGATTGATATGATCTGCTTTACTGCAACTTCAGAGAGACGAGATCCATCATTTTGA-CCTGCT
1 AAAGATTGATATGATCAGCTTTACTGCAACTTCAGAGAGACAAGATCCATCATTTTGACCCT-CT
* * * *
383897 CCACTGCAACTTCAGGGAGATAGGACTTATATCTTCAACTTGCCCCACTGTAACTTCATGGGGAT
65 ACACTGCAACTTCAGGGAGATAGGACTGATATCTTCAACTTGCCCCACTGCAACTTCATGAGGAT
*
383962 AAGGTTTGCTATTTCAACCTGCTCTACTGCAACTTCAGAGAGAC
130 AAGGTTTGCTATTTCAACATGCTCTACTGCAACTTCAGAGAGAC
384006 GAGATCTGTT
Statistics
Matches: 157, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
172 3 0.02
173 154 0.98
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (173 bp):
AAAGATTGATATGATCAGCTTTACTGCAACTTCAGAGAGACAAGATCCATCATTTTGACCCTCTA
CACTGCAACTTCAGGGAGATAGGACTGATATCTTCAACTTGCCCCACTGCAACTTCATGAGGATA
AGGTTTGCTATTTCAACATGCTCTACTGCAACTTCAGAGAGAC
Found at i:384224 original size:43 final size:41
Alignment explanation
Indices: 384134--384367 Score: 157
Period size: 43 Copynumber: 5.4 Consensus size: 41
384124 TCCTACTACA
* *
384134 TTAGGAAGATAAGATTTGCAGTCTTCGACCTGTTCCACTACTGC
1 TTAGGAAGATAAGA-TTGCAGT-TTCAACCT-ATCCACTACTGC
384178 TTAGGAAGATAAGATCTGCAAGTTTCAACCTATCCACTACTGC
1 TTAGGAAGATAAGAT-TGC-AGTTTCAACCTATCCACTACTGC
* * ** * * * *
384221 TTAGGGAGATAGGATTGGTGGCTTAAATCTACTTCCTATTA-T-C
1 TTAGGAAGATAAGATT-GCAGTTTCAACCTA--TCC-ACTACTGC
* ** *
384264 TTAGGAAGATAAGATTCGCCGTCTTTGATCTACTCCACTACTGC
1 TTAGGAAGATAAGATT-GCAGT-TTCAACCTA-TCCACTACTGC
* * *
384308 TTAGGGAGATAAGATTTGTAAGTTTCAACCTATCCACTACGGC
1 TTAGGAAGATAAGA-TTG-CAGTTTCAACCTATCCACTACTGC
* *
384351 TTAGGGAGATAGGATTG
1 TTAGGAAGATAAGATTG
384368 GTGGCTTAAA
Statistics
Matches: 151, Mismatches: 28, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
42 15 0.10
43 70 0.46
44 56 0.37
45 10 0.07
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (41 bp):
TTAGGAAGATAAGATTGCAGTTTCAACCTATCCACTACTGC
Found at i:384331 original size:130 final size:129
Alignment explanation
Indices: 384093--384459 Score: 581
Period size: 130 Copynumber: 2.8 Consensus size: 129
384083 CTGCAACTTC
* *
384093 AGGGAGATAGGATTGGTGGCTTAAATCTGCTTCCTACTACATTAGGAAGATAAGATTTGCAGTCT
1 AGGGAGATAGGATTGGTGGCTTAAATCTGCTTCCTACTAC-TTAGGAAGATAAGATTCGCCGTCT
* * ** * *
384158 TCGACCTGTTCCACTACTGCTTAGGAAGATAAGATCTGCAAGTTTCAACCTATCCACTACTGCTT
65 TTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGCAAGTTTCAACCTATCCACTACGGCTT
* *
384223 AGGGAGATAGGATTGGTGGCTTAAATCTACTTCCTATTATCTTAGGAAGATAAGATTCGCCGTCT
1 AGGGAGATAGGATTGGTGGCTTAAATCTGCTTCCTACTA-CTTAGGAAGATAAGATTCGCCGTCT
* *
384288 TTGATCTACTCCACTACTGCTTAGGGAGATAAGATTTGTAAGTTTCAACCTATCCACTACGGCTT
65 TTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGCAAGTTTCAACCTATCCACTACGGCTT
* *
384353 AGGGAGATAGGATTGGTGGCTTAAATATGCTTCCTACTACCTTAGGAAGATAAGATTCGTCGTCT
1 AGGGAGATAGGATTGGTGGCTTAAATCTGCTTCCTACTA-CTTAGGAAGATAAGATTCGCCGTCT
384418 TTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGCAAG
65 TTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGCAAG
384460 CTTCGATCTA
Statistics
Matches: 217, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
130 216 1.00
131 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (129 bp):
AGGGAGATAGGATTGGTGGCTTAAATCTGCTTCCTACTACTTAGGAAGATAAGATTCGCCGTCTT
TGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGCAAGTTTCAACCTATCCACTACGGCTT
Found at i:384468 original size:44 final size:42
Alignment explanation
Indices: 384134--384476 Score: 178
Period size: 44 Copynumber: 7.9 Consensus size: 42
384124 TCCTACTACA
* * **
384134 TTAGGAAGATAAGATTTGCAGTCTTCGACCTGTTCCACTACTGC
1 TTAGGAAGATAAGA-TTGCAG-CTTCAATCTACTCCACTACTGC
* *
384178 TTAGGAAGATAAGATCTGCAAGTTTCAACCTA-TCCACTACTGC
1 TTAGGAAGATAAGAT-TGC-AGCTTCAATCTACTCCACTACTGC
* * ** * *
384221 TTAGGGAGATAGGATTGGTGGCTTAAATCTACTTCCTATTA-T-C
1 TTAGGAAGATAAGATT-GCAGCTTCAATCTAC-TCC-ACTACTGC
* **
384264 TTAGGAAGATAAGATTCGCCGTCTTTGATCTACTCCACTACTGC
1 TTAGGAAGATAAGATT-GCAG-CTTCAATCTACTCCACTACTGC
* * * * *
384308 TTAGGGAGATAAGATTTGTAAGTTTCAACCTA-TCCACTACGGC
1 TTAGGAAGATAAGA-TTG-CAGCTTCAATCTACTCCACTACTGC
* * ** * * *
384351 TTAGGGAGATAGGATTGGTGGCTTAAATATGCTTCCTACTAC--C
1 TTAGGAAGATAAGATT-GCAGCTTCAATCTAC-TCC-ACTACTGC
**
384394 TTAGGAAGATAAGATTCGTC-GTCTTTGATCTACTCCACTACTGC
1 TTAGGAAGATAAGATT-G-CAG-CTTCAATCTACTCCACTACTGC
* * *
384438 TTAGGGAGATAAGATCTGCAAGCTTCGATCTACTTCACT
1 TTAGGAAGATAAGAT-TGC-AGCTTCAATCTACTCCACT
384477 GCCAATACAA
Statistics
Matches: 231, Mismatches: 46, Indels: 44
0.72 0.14 0.14
Matches are distributed among these distances:
42 25 0.11
43 92 0.40
44 99 0.43
45 15 0.06
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (42 bp):
TTAGGAAGATAAGATTGCAGCTTCAATCTACTCCACTACTGC
Found at i:384500 original size:45 final size:45
Alignment explanation
Indices: 384448--384544 Score: 167
Period size: 45 Copynumber: 2.2 Consensus size: 45
384438 TTAGGGAGAT
384448 AAGATCTGCAAGCTTCGATCTACTTCACTGCCAATACAAGAAGAC
1 AAGATCTGCAAGCTTCGATCTACTTCACTGCCAATACAAGAAGAC
* * *
384493 AAGATCTGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGAC
1 AAGATCTGCAAGCTTCGATCTACTTCACTGCCAATACAAGAAGAC
384538 AAGATCT
1 AAGATCT
384545 ACTACTTCTA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (45 bp):
AAGATCTGCAAGCTTCGATCTACTTCACTGCCAATACAAGAAGAC
Found at i:385956 original size:5 final size:5
Alignment explanation
Indices: 385946--386003 Score: 75
Period size: 5 Copynumber: 11.8 Consensus size: 5
385936 CATTTTTCAT
*
385946 TTTTC TTTTC TTTT- TCTTC TTTTC TTTTC TTTTC TTTTC TTTTC TCTTT-
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T-TTTC
*
385995 TCTTC TTTT
1 TTTTC TTTT
386004 TTTGTTTGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
4 5 0.11
5 38 0.83
6 3 0.07
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:385960 original size:19 final size:19
Alignment explanation
Indices: 385938--386003 Score: 70
Period size: 15 Copynumber: 3.7 Consensus size: 19
385928 TGGCCTCTCA
385938 TTTTTCAT-TTTTCTTTTC
1 TTTTTCATCTTTTCTTTTC
*
385956 TTTTTCTTCTTTTCTTTTC
1 TTTTTCATCTTTTCTTTTC
385975 --TTT--TCTTTTCTTTTC
1 TTTTTCATCTTTTCTTTTC
*
385990 TCTTTTCTTCTTTT
1 T-TTTTCATCTTTT
386004 TTTGTTTGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
15 12 0.29
17 3 0.07
18 10 0.24
19 10 0.24
20 6 0.15
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTCATCTTTTCTTTTC
Found at i:388358 original size:12 final size:12
Alignment explanation
Indices: 388327--388360 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
388317 CTTTTCTAGT
388327 TGTTCTTGCATC
1 TGTTCTTGCATC
**
388339 TGAACTTGCATC
1 TGTTCTTGCATC
388351 TGTTCTTGCA
1 TGTTCTTGCA
388361 ATTACTCTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (12 bp):
TGTTCTTGCATC
Found at i:390597 original size:12 final size:12
Alignment explanation
Indices: 390582--390613 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
390572 TAATGAAAAT
390582 ATAAATAAAGAA
1 ATAAATAAAGAA
390594 ATAAATAAAGAA
1 ATAAATAAAGAA
*
390606 ATTAATAA
1 ATAAATAA
390614 GATTATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (12 bp):
ATAAATAAAGAA
Found at i:390641 original size:19 final size:22
Alignment explanation
Indices: 390598--390643 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
390588 AAAGAAATAA
*
390598 ATAAAGAAATTAATAAGATTAT
1 ATAAAGAAAGTAATAAGATTAT
390620 ATAAA-AAAGTAA-AAGATATAT
1 ATAAAGAAAGTAATAAGAT-TAT
390641 ATA
1 ATA
390644 TATATATGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 12 0.55
22 5 0.23
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (22 bp):
ATAAAGAAAGTAATAAGATTAT
Found at i:391034 original size:13 final size:13
Alignment explanation
Indices: 391001--391040 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
390991 ATAAAAGGAC
391001 ATAAT-AAATAAT
1 ATAATAAAATAAT
391013 ACGTAATAAAATAAT
1 A--TAATAAAATAAT
391028 ATAATAAAATAAT
1 ATAATAAAATAAT
391041 TATATACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.04
13 12 0.48
14 4 0.16
15 8 0.32
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (13 bp):
ATAATAAAATAAT
Found at i:392830 original size:24 final size:24
Alignment explanation
Indices: 392787--392833 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
392777 TTTGCAACCC
392787 AAGGGGAAGGGGAAAGAGAAGGGG
1 AAGGGGAAGGGGAAAGAGAAGGGG
*
392811 AAGGGGAAAGGGGAGA-AGAAGGG
1 AAGGGG-AAGGGGAAAGAGAAGGG
392834 TAACCAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (24 bp):
AAGGGGAAGGGGAAAGAGAAGGGG
Found at i:397341 original size:24 final size:24
Alignment explanation
Indices: 397305--397510 Score: 144
Period size: 24 Copynumber: 8.7 Consensus size: 24
397295 AATCATACGC
** *
397305 GATAAATCCAAAATAATAGTATAT
1 GATAAATTTAAAATAATAATATAT
*
397329 AATAAATTTAAAAT-AT--TA-AT
1 GATAAATTTAAAATAATAATATAT
*
397349 GATAAATTGTAAAATAA-ATATACAT
1 GATAAATT-TAAAATAATA-ATATAT
* *
397374 GATAAATTTAAAATAAT-GT-TAC
1 GATAAATTTAAAATAATAATATAT
397396 GATAAATTTAAAATAATAATAT-T
1 GATAAATTTAAAATAATAATATAT
* **
397419 GATAAA-TTACAAATAATAAAACGT
1 GATAAATTTA-AAATAATAATATAT
* *
397443 GATAAATCTAAAATAATAATATAC
1 GATAAATTTAAAATAATAATATAT
* **
397467 AATAAA-TTAACTTAGATAATATTAAT
1 GATAAATTTAAAATA-ATAATA-T-AT
397493 GATAAATTTAATAATAAT
1 GATAAATTTAA-AATAAT
397511 TACTTTAAAC
Statistics
Matches: 141, Mismatches: 24, Indels: 31
0.72 0.12 0.16
Matches are distributed among these distances:
20 9 0.06
21 8 0.06
22 22 0.16
23 25 0.18
24 50 0.35
25 13 0.09
26 6 0.04
27 6 0.04
28 2 0.01
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (24 bp):
GATAAATTTAAAATAATAATATAT
Found at i:397363 original size:45 final size:47
Alignment explanation
Indices: 397305--397510 Score: 165
Period size: 45 Copynumber: 4.4 Consensus size: 47
397295 AATCATACGC
** *
397305 GATAAATCCAAAATAATAGTATATAATAAATTTA-AAAT-AT-TAAT
1 GATAAATTTAAAATAATAATATATAATAAATTTACAAATAATATAAT
* * * * *
397349 GATAAATTGTAAAATAA-ATATACATGATAAATTTA-AAATAATGTTAC
1 GATAAATT-TAAAATAATA-ATATATAATAAATTTACAAATAATATAAT
* *
397396 GATAAATTTAAAATAATAATAT-TGATAAA-TTACAAATAATAAAACGT
1 GATAAATTTAAAATAATAATATATAATAAATTTACAAATAATATAA--T
* * * *
397443 GATAAATCTAAAATAATAATATACAATAAATTAACTTAGATAATATTAAT
1 GATAAATTTAAAATAATAATATATAATAAATTTAC--AAATAATA-TAAT
397493 GATAAATTTAATAATAAT
1 GATAAATTTAA-AATAAT
397511 TACTTTAAAC
Statistics
Matches: 129, Mismatches: 19, Indels: 21
0.76 0.11 0.12
Matches are distributed among these distances:
44 11 0.09
45 39 0.30
46 13 0.10
47 32 0.25
48 5 0.04
49 3 0.02
50 11 0.09
51 13 0.10
52 2 0.02
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (47 bp):
GATAAATTTAAAATAATAATATATAATAAATTTACAAATAATATAAT
Found at i:397375 original size:25 final size:24
Alignment explanation
Indices: 397339--397434 Score: 94
Period size: 22 Copynumber: 4.1 Consensus size: 24
397329 AATAAATTTA
397339 AAATATTAATGATAAATTGTAAAAT
1 AAATATTAATGATAAATT-TAAAAT
397364 AAATA-TACATGATAAATTTAAAAT
1 AAATATTA-ATGATAAATTTAAAAT
* *
397388 -AATGTT-ACGATAAATTTAAAAT
1 AAATATTAATGATAAATTTAAAAT
* *
397410 -AATAATATTGATAAA-TTACAAAT
1 AAATATTAATGATAAATTTA-AAAT
397433 AA
1 AA
397435 TAAAACGTGA
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
22 22 0.37
23 13 0.22
24 10 0.17
25 15 0.25
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.34
Consensus pattern (24 bp):
AAATATTAATGATAAATTTAAAAT
Found at i:397402 original size:22 final size:21
Alignment explanation
Indices: 397330--397412 Score: 87
Period size: 22 Copynumber: 3.8 Consensus size: 21
397320 ATAGTATATA
* *
397330 ATAAATTTAAAAT-ATTAATG
1 ATAAATTTAAAATAATTTACG
*
397350 ATAAATTGTAAAATAAATATACATG
1 ATAAATT-TAAAAT-AATTTAC--G
397375 ATAAATTTAAAATAATGTTACG
1 ATAAATTTAAAATAAT-TTACG
397397 ATAAATTTAAAATAAT
1 ATAAATTTAAAATAAT
397413 AATATTGATA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
20 7 0.13
21 6 0.11
22 17 0.32
23 6 0.11
24 9 0.17
25 8 0.15
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.36
Consensus pattern (21 bp):
ATAAATTTAAAATAATTTACG
Found at i:398894 original size:15 final size:16
Alignment explanation
Indices: 398867--398896 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
398857 TCAAAAATGA
398867 ACTTTTAATTTTTTTT
1 ACTTTTAATTTTTTTT
398883 ACTTTT-ATTTTTTT
1 ACTTTTAATTTTTTT
398897 AAGAGTCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.77
Consensus pattern (16 bp):
ACTTTTAATTTTTTTT
Found at i:405088 original size:28 final size:28
Alignment explanation
Indices: 405048--405104 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
405038 TAAATACGAC
*
405048 AACAAATCTATCTAGATATGATTGAAGT
1 AACAAATCTATCTAGATATGACTGAAGT
405076 AACAAATCTATCTAGATATGACTGAAGT
1 AACAAATCTATCTAGATATGACTGAAGT
405104 A
1 A
405105 TTCGGTTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (28 bp):
AACAAATCTATCTAGATATGACTGAAGT
Found at i:405358 original size:16 final size:16
Alignment explanation
Indices: 405337--405369 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
405327 GTAATCGATA
405337 CATAGTCTCAAACTCT
1 CATAGTCTCAAACTCT
405353 CATAGTCTCAAACTCT
1 CATAGTCTCAAACTCT
405369 C
1 C
405370 GTTCTTTCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.06, T:0.30
Consensus pattern (16 bp):
CATAGTCTCAAACTCT
Found at i:412276 original size:14 final size:14
Alignment explanation
Indices: 412240--412278 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
412230 GCATGCCTAG
*
412240 ATGTGTGAACCCTT
1 ATGTGTGAACCCAT
* *
412254 AGGTTTGAACCCAT
1 ATGTGTGAACCCAT
412268 ATGTGTGAACC
1 ATGTGTGAACC
412279 TTAAATCCAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (14 bp):
ATGTGTGAACCCAT
Found at i:447496 original size:18 final size:18
Alignment explanation
Indices: 447470--447508 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
447460 CTCAAGAAAC
* *
447470 TTTATATCCTTCCGGGAT
1 TTTAAATCCTTCAGGGAT
447488 TTTAAATCCTTCAGGGAT
1 TTTAAATCCTTCAGGGAT
447506 TTT
1 TTT
447509 TATATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.46
Consensus pattern (18 bp):
TTTAAATCCTTCAGGGAT
Found at i:449065 original size:36 final size:31
Alignment explanation
Indices: 448994--449055 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
448984 TGGAAATGTC
448994 TAAATGAATGTGAAGTCCATAATTACACTAA
1 TAAATGAATGTGAAGTCCATAATTACACTAA
*
449025 TAAATGAATGTGAAGTCCATAATTCCACTAA
1 TAAATGAATGTGAAGTCCATAATTACACTAA
449056 GTTAATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.29
Consensus pattern (31 bp):
TAAATGAATGTGAAGTCCATAATTACACTAA
Found at i:452043 original size:16 final size:16
Alignment explanation
Indices: 452004--452043 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
451994 TTGACGGAAT
*
452004 GCAAAATAACCTAAAA
1 GCAAAATTACCTAAAA
*
452020 ACAAAATTACCTAAAA
1 GCAAAATTACCTAAAA
452036 GCAAAATT
1 GCAAAATT
452044 TACTATATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.60, C:0.17, G:0.05, T:0.17
Consensus pattern (16 bp):
GCAAAATTACCTAAAA
Found at i:457180 original size:14 final size:15
Alignment explanation
Indices: 457161--457189 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
457151 TATGGTTGAA
457161 AATTTT-GTGTAAGT
1 AATTTTAGTGTAAGT
457175 AATTTTAGTGTAAGT
1 AATTTTAGTGTAAGT
457190 TTTTATTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (15 bp):
AATTTTAGTGTAAGT
Found at i:457912 original size:20 final size:20
Alignment explanation
Indices: 457865--457913 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
457855 CATTTTGCAC
*
457865 ATATGACCAAGGCATCATAA
1 ATATGACCAAAGCATCATAA
*
457885 ACAT-ACCAAAGCATTCAT-A
1 ATATGACCAAAGCA-TCATAA
457904 ATATGACCAA
1 ATATGACCAA
457914 TTCAAATGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.47, C:0.22, G:0.10, T:0.20
Consensus pattern (20 bp):
ATATGACCAAAGCATCATAA
Found at i:464260 original size:17 final size:17
Alignment explanation
Indices: 464238--464270 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
464228 CCATTATTTT
464238 ATCTATCATTTGTTGTC
1 ATCTATCATTTGTTGTC
*
464255 ATCTATCATTTTTTGT
1 ATCTATCATTTGTTGT
464271 TGAATCTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.15, G:0.09, T:0.58
Consensus pattern (17 bp):
ATCTATCATTTGTTGTC
Found at i:478108 original size:32 final size:32
Alignment explanation
Indices: 478073--478135 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
478063 GTTCAAATCT
* * *
478073 TTTTTTTTAT-CAACTTTTAAGGAACTTAAAA
1 TTTTTTTTCTCCAACGTTTAAAGAACTTAAAA
478104 TTTTTTTTCTCCAACGTTTAAAGAACTTAAAA
1 TTTTTTTTCTCCAACGTTTAAAGAACTTAAAA
478136 CCCTATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 9 0.32
32 19 0.68
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (32 bp):
TTTTTTTTCTCCAACGTTTAAAGAACTTAAAA
Found at i:480895 original size:25 final size:25
Alignment explanation
Indices: 480861--480911 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
480851 ATTTTGGAGT
480861 AATGAATGTCATGACAACAAACACC
1 AATGAATGTCATGACAACAAACACC
480886 AATGAATGTCATGACAACAAACACC
1 AATGAATGTCATGACAACAAACACC
480911 A
1 A
480912 CATCCTTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.24, G:0.12, T:0.16
Consensus pattern (25 bp):
AATGAATGTCATGACAACAAACACC
Found at i:482855 original size:51 final size:51
Alignment explanation
Indices: 482795--482896 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
482785 TGCTAAATTA
*
482795 GTCTAAAAATATTAAATTATTTTTAAAAATGGTAGTTATGCTCACTAGTTT
1 GTCTAAAAATATTAAACTATTTTTAAAAATGGTAGTTATGCTCACTAGTTT
**
482846 GTCTAAAAATATTAAACTATTTTTAAAAATGGTAGTTATGCTTGCTAGTTT
1 GTCTAAAAATATTAAACTATTTTTAAAAATGGTAGTTATGCTCACTAGTTT
482897 TGGCATGGCC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (51 bp):
GTCTAAAAATATTAAACTATTTTTAAAAATGGTAGTTATGCTCACTAGTTT
Found at i:491140 original size:3 final size:3
Alignment explanation
Indices: 491125--491154 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
491115 AGCAATAACT
*
491125 ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
491155 GTATAACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:491483 original size:3 final size:3
Alignment explanation
Indices: 491468--491497 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
491458 AGCAATAACT
*
491468 ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
491498 GTATAACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:491504 original size:343 final size:344
Alignment explanation
Indices: 491082--491772 Score: 1312
Period size: 343 Copynumber: 2.0 Consensus size: 344
491072 TATATAAAAA
491082 AAACTATGCGTATATATATATAGTAATGGTAATAGCAATAACTATAATAATGATAATAATAATAA
1 AAACTATGCG-ATATATATATAGTAATGGTAATAGCAATAACTATAATAATGATAATAATAATAA
491147 TAATAATAGTATAACATGATTTTTTTTTAAAAATGAATAAAATAAAAAAAAAGGTTAAATTGAAC
65 TAATAATAGTATAACATGATTTTTTTTTAAAAATGAATAAAATAAAAAAAAAGGTTAAATTGAAC
491212 TAAAAAAGGAAAAAAAAAACTAAATTTGAAATAAATCTGAGAACAGGACCACATTGAATGCGCGC
130 TAAAAAAGGAAAAAAAAAACTAAATTTGAAATAAATCTGAGAACAGGACCACATTGAATGCGCGC
491277 GCAAGTAAGGAGGACCAAAAAGGCAATATGCCCATTGATCCCACGGTGCCGTTTCAATGCAATCT
195 GCAAGTAAGGAGGACCAAAAAGGCAATATGCCCATTGATCCCACGGTGCCGTTTCAATGCAATCT
***
491342 GCAGTCCTGGTTGATGGACCAAATTGAAACAGGCGTGAAATTTTGTGGCAAAATTGCAAACATGC
260 GCAGTCCTGGTTGATGGACCAAATTGAAACAGGCACCAAATTTTGTGGCAAAATTGCAAACATGC
491407 GAAATACTGCATTTAAAATC
325 GAAATACTGCATTTAAAATC
491427 AAACTATGCG-TATATATATAGTAATGGTAATAGCAATAACTATAATAATGATAATAATAATAAT
1 AAACTATGCGATATATATATAGTAATGGTAATAGCAATAACTATAATAATGATAATAATAATAAT
491491 AATAATAGTATAACATGATTTTTTTTTAAAAATGAATAAAATAAAAAAAAAGGTTAAATTGAACT
66 AATAATAGTATAACATGATTTTTTTTTAAAAATGAATAAAATAAAAAAAAAGGTTAAATTGAACT
491556 AAAAAAGGAAAAAAAAAACTAAATTTGAAATAAATCTGAGAACAGGACCACATTGAATGCGCGCG
131 AAAAAAGGAAAAAAAAAACTAAATTTGAAATAAATCTGAGAACAGGACCACATTGAATGCGCGCG
491621 CAAGTAAGGAGGACCAAAAAGGCAATATGCCCATTGATCCCACGGTGCCGTTTCAATGCAATCTG
196 CAAGTAAGGAGGACCAAAAAGGCAATATGCCCATTGATCCCACGGTGCCGTTTCAATGCAATCTG
*
491686 CAGTCCTGGTTGATGGACCAAATTGAAACAGGCACCAAATTTTGTGGCAAAATTGCAAACGTGCG
261 CAGTCCTGGTTGATGGACCAAATTGAAACAGGCACCAAATTTTGTGGCAAAATTGCAAACATGCG
* *
491751 GATTACTGCATTTAAAATC
326 AAATACTGCATTTAAAATC
491770 AAA
1 AAA
491773 ATAAAAAAAG
Statistics
Matches: 340, Mismatches: 6, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
343 330 0.97
345 10 0.03
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (344 bp):
AAACTATGCGATATATATATAGTAATGGTAATAGCAATAACTATAATAATGATAATAATAATAAT
AATAATAGTATAACATGATTTTTTTTTAAAAATGAATAAAATAAAAAAAAAGGTTAAATTGAACT
AAAAAAGGAAAAAAAAAACTAAATTTGAAATAAATCTGAGAACAGGACCACATTGAATGCGCGCG
CAAGTAAGGAGGACCAAAAAGGCAATATGCCCATTGATCCCACGGTGCCGTTTCAATGCAATCTG
CAGTCCTGGTTGATGGACCAAATTGAAACAGGCACCAAATTTTGTGGCAAAATTGCAAACATGCG
AAATACTGCATTTAAAATC
Found at i:492942 original size:18 final size:18
Alignment explanation
Indices: 492911--492945 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
492901 GAACTTAAAG
**
492911 CCTAAAAACTTAAAATAT
1 CCTAAAAAAATAAAATAT
492929 CCTAAAAAAATAAAATA
1 CCTAAAAAAATAAAATA
492946 AAGTAAGGAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.23
Consensus pattern (18 bp):
CCTAAAAAAATAAAATAT
Found at i:500609 original size:44 final size:43
Alignment explanation
Indices: 500556--501257 Score: 570
Period size: 44 Copynumber: 15.9 Consensus size: 43
500546 GGATTTGCCG
* * *
500556 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCT
1 TCTTCGATCTACTTCACACCAATATAGGAAGACAAGATCTGCT
* * * * *
500599 TTTTCCGATCTACTTCACCACCAGTATGGGAAGACAAAATCTGCA
1 TCTT-CGATCTACTTCA-CACCAATATAGGAAGACAAGATCTGCT
* * *
500644 TCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGCT
1 TCTTCGATCTACTTCAC-ACCAATATAGGAAGACAAGATCTGCT
* * * *
500688 ATATTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
1 -TCTTCGATCTACTTCACACCAATATAGGAAGACAAGATCTGC-T
* * * * * *
500733 TTTTCGATTTACTTCGCCACCAGTATGGGAAAACAAGATCTG-T
1 TCTTCGATCTACTTC-ACACCAATATAGGAAGACAAGATCTGCT
* *
500776 ATCTTCGATCCACTTCGCTACCAATATAGGAAGAC-AGAATCTGCT
1 -TCTTCGATCTACTTCAC-ACCAATATAGGAAGACAAG-ATCTGCT
* * * *
500821 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGAACTGCTT
1 -TCTTCGATCTACTTCACACCAATATAGGAAGACAAGATCTGC-T
* * * * *
500866 TCTTCAATCTTCTTCGCCACCAATATGGGAAGACAAGATCTGCA
1 TCTTCGATCTACTTC-ACACCAATATAGGAAGACAAGATCTGCT
* * * * *
500910 TCTTCAATCCACTTC-CTACCAATATAGGAAGATAGGACCTGCT
1 TCTTCGATCTACTTCAC-ACCAATATAGGAAGACAAGATCTGCT
* * * *
500953 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCCGCT
1 -TCTTCGATCTACTTCACACCAATATAGGAAGACAAGATCTGCT
* * ** *
500997 TTTTCGATCTACTTTGC-CACCAGTATTCGAAGACAAGATCTGCA
1 TCTTCGATCTAC-TT-CACACCAATATAGGAAGACAAGATCTGCT
* * * *
501041 TCTTCAATCCACTTCGCTACCAATATAGGAAGA-AAGGATCTGTT
1 TCTTCGATCTACTTCAC-ACCAATATAGGAAGACAA-GATCTGCT
* * * *
501085 ATCTTCGATCTCCTTCACGCCAATACATGAAGACAAGATCTGCTT
1 -TCTTCGATCTACTTCACACCAATATAGGAAGACAAGATCTGC-T
* * * *
501130 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCA
1 TCTTCGATCTACTTC-ACACCAATATAGGAAGACAAGATCTGCT
* * * *
501174 TCTTCGATCCATTTC-CTACCAATATAGGAAGATAGGATCTGCT
1 TCTTCGATCTACTTCAC-ACCAATATAGGAAGACAAGATCTGCT
* * *
501217 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
1 -TCTTCGATCTACTTCACACCAATATAGGAAGACAAGATCT
501258 ACTGCTTTTT
Statistics
Matches: 515, Mismatches: 116, Indels: 55
0.75 0.17 0.08
Matches are distributed among these distances:
42 3 0.01
43 66 0.13
44 308 0.60
45 138 0.27
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (43 bp):
TCTTCGATCTACTTCACACCAATATAGGAAGACAAGATCTGCT
Found at i:500709 original size:133 final size:132
Alignment explanation
Indices: 500523--501257 Score: 1159
Period size: 133 Copynumber: 5.6 Consensus size: 132
500513 TTTGATCTAT
* * * **
500523 TTCGCTACCGATATAGGCAGATAGGATTTGCCGTCTTCGATCTACTTCACGCCAATACATGAAGA
1 TTCGCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
* *
500588 CAAGATCTGCTTTTTCCGATCTACTTCACCACCAGTATGGGAAGACAAAATCTGCATCTTCGATC
66 CAAGATCTGCTTTTT-CGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATC
500653 CAC
130 CAC
* *
500656 TTCGCTACCAATATAGGAAGACAGGATCTGCTATATTCGATCTACTTCACGCCAATACATGAAGA
1 TTCGCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
* * *
500721 CAAGATCTGCTTTTTTCGATTTACTTCGCCACCAGTATGGGAAAACAAGATCTGTATCTTCGATC
66 CAAGATCTGC-TTTTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATC
500786 CAC
130 CAC
* *
500789 TTCGCTACCAATATAGGAAGACAGAATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
1 TTCGCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
* * * * *
500854 CAAGAACTGCTTTCTTCAATCTTCTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCAATC
66 CAAGATCTGCTTT-TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATC
500919 CAC
130 CAC
*
500922 TTC-CTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
1 TTCGCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
* * ** *
500986 CAAGATCCGCTTTTTCGATCTACTTTGCCACCAGTATTCGAAGACAAGATCTGCATCTTCAATCC
66 CAAGATCTGCTTTTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCC
501051 AC
131 AC
* * *
501053 TTCGCTACCAATATAGGAAGAAAGGATCTGTTATCTTCGATCTCCTTCACGCCAATACATGAAGA
1 TTCGCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
501118 CAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATC
66 CAAGATCTGCTTT-TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATC
*
501183 CAT
130 CAC
501186 TTC-CTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
1 TTCGCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
501250 CAAGATCT
66 CAAGATCT
501258 ACTGCTTTTT
Statistics
Matches: 552, Mismatches: 46, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
131 51 0.09
132 207 0.38
133 289 0.52
134 5 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (132 bp):
TTCGCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
CAAGATCTGCTTTTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCC
AC
Found at i:501105 original size:264 final size:265
Alignment explanation
Indices: 500523--501256 Score: 1175
Period size: 264 Copynumber: 2.8 Consensus size: 265
500513 TTTGATCTAT
* * * * **
500523 TTCGCTACCGATATAGGCAGATAGGATTTGCCGTCTTCGATCTACTTCACGCCAATACATGAAGA
1 TTCGCTACCAATATAGGAAGAAAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
* *
500588 CAAGATCTGCTTT-TTCCGATCTACTTCACCACCAGTATGGGAAGACAAAATCTGCATCTTCGAT
66 CAAGATCTGCTTTCTT-CGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGAT
* *
500652 CCACTTCGCTACCAATATAGGAAGACAGGATCTGCTATATTCGATCTACTTCACGCCAATACATG
130 CCACTTC-CTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
* * * *
500717 AAGACAAGATCTGCTTTTTTCGATTTACTTCGCCACCAGTATGGGAAAACAAGATCTGTATCTTC
194 AAGACAAGATCCGCTTTTTTCGATCTACTTCGCCACCAGTATGCGAAAACAAGATCTGCATCTTC
*
500782 GATCCAC
259 AATCCAC
* *
500789 TTCGCTACCAATATAGGAAGACAGAATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
1 TTCGCTACCAATATAGGAAGAAAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
* * * * *
500854 CAAGAACTGCTTTCTTCAATCTTCTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCAATC
66 CAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATC
*
500919 CACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAA
131 CACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAA
* * *
500984 GACAAGATCCGC-TTTTTCGATCTACTTTGCCACCAGTATTCGAAGACAAGATCTGCATCTTCAA
196 GACAAGATCCGCTTTTTTCGATCTACTTCGCCACCAGTATGCGAAAACAAGATCTGCATCTTCAA
501048 TCCAC
261 TCCAC
* *
501053 TTCGCTACCAATATAGGAAGAAAGGATCTGTTATCTTCGATCTCCTTCACGCCAATACATGAAGA
1 TTCGCTACCAATATAGGAAGAAAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
501118 CAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATC
66 CAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATC
*
501183 CATTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAA
131 CACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAA
501248 GACAAGATC
196 GACAAGATC
501257 TACTGCTTTT
Statistics
Matches: 431, Mismatches: 36, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
264 243 0.56
265 67 0.16
266 119 0.28
267 2 0.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (265 bp):
TTCGCTACCAATATAGGAAGAAAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
CAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATC
CACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAA
GACAAGATCCGCTTTTTTCGATCTACTTCGCCACCAGTATGCGAAAACAAGATCTGCATCTTCAA
TCCAC
Found at i:504129 original size:33 final size:33
Alignment explanation
Indices: 504092--504159 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
504082 ATTTACTAGT
504092 GAAAGGATGATAATCTCCATTTGGAGATACCAG
1 GAAAGGATGATAATCTCCATTTGGAGATACCAG
504125 GAAAGGATGATAATCTCCATTTGGAGATACCAG
1 GAAAGGATGATAATCTCCATTTGGAGATACCAG
504158 GA
1 GA
504160 CTGCCCCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.24
Consensus pattern (33 bp):
GAAAGGATGATAATCTCCATTTGGAGATACCAG
Found at i:508545 original size:159 final size:158
Alignment explanation
Indices: 508255--508579 Score: 438
Period size: 159 Copynumber: 2.0 Consensus size: 158
508245 ACCAGAAACA
* * * * *
508255 ATTTATCACTTTCAATAGGAAATTAATTCTCTTAATAGATATCAGTCGAATTGTTATTCACAGAA
1 ATTTATCACTTTCAATAGGAAAATAATTCTCTTAATAGAAACCAGTAGAA-T-TTAATCACAGAA
* **
508320 AATAGAATTTATACTTAGAAAATAAATTATCACTATTTTTGGGAAAAATAAAAATATTGAAAACT
64 AATAAAATTTATACTTAGAAAATAAATTATCACTATTTTTCAGAAAAATAAAAATATTGAAAACT
* *
508385 GTTGTATGTATAGCCCTACCAGTACCATAT
129 GTTGTATGTATAGCCCTACCAATACCAAAT
* * *
508415 ATTTATCACTTTTAGTAGGAAAATAATTCTCTCTCAATAGAAACCAGTAGAA-TTAATCTCAGAA
1 ATTTATCACTTTCAATAGGAAAATAATTCTCT-T-AATAGAAACCAGTAGAATTTAATCACAGAA
** *
508479 AATAAAATTTATACTTAGAAAATAAATTATCACTA-TTTTCAGACTGAATAACAATATTGAAAAC
64 AATAAAATTTATACTTAGAAAATAAATTATCACTATTTTTCAGA-AAAATAAAAATATTGAAAAC
*
508543 TGTTGTATGTATAGCTCTACCAATACCAAAT
128 TGTTGTATGTATAGCCCTACCAATACCAAAT
508574 ATTTAT
1 ATTTAT
508580 AGGAAGATAT
Statistics
Matches: 145, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
158 6 0.04
159 95 0.66
160 29 0.20
161 1 0.01
162 14 0.10
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (158 bp):
ATTTATCACTTTCAATAGGAAAATAATTCTCTTAATAGAAACCAGTAGAATTTAATCACAGAAAA
TAAAATTTATACTTAGAAAATAAATTATCACTATTTTTCAGAAAAATAAAAATATTGAAAACTGT
TGTATGTATAGCCCTACCAATACCAAAT
Found at i:511920 original size:27 final size:27
Alignment explanation
Indices: 511886--511959 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
511876 TTAATAGTGC
511886 GCCACAAAGGCATTCCTTAT-AGAGTTT
1 GCCACAAAGGCATTCCTT-TCAGAGTTT
* * * *
511913 GCCACAAAGGCTTTTCTTTCATATTTT
1 GCCACAAAGGCATTCCTTTCAGAGTTT
511940 GCCACAAAGGC-TTCTCTTTC
1 GCCACAAAGGCATTC-CTTTC
511960 CTTACGTGCT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 3 0.08
27 37 0.93
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (27 bp):
GCCACAAAGGCATTCCTTTCAGAGTTT
Found at i:514230 original size:19 final size:19
Alignment explanation
Indices: 514202--514261 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
514192 TTCTAGGTTT
* *
514202 TTTTAT-TTTCCCAGTAGA
1 TTTTATATTTCCTAGTAAA
*
514220 TTTTATATTTCCTAATAAA
1 TTTTATATTTCCTAGTAAA
*
514239 TTTTATATTTCCTAGTAAC
1 TTTTATATTTCCTAGTAAA
514258 TTTT
1 TTTT
514262 CTTCTTGTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
18 6 0.17
19 30 0.83
ACGTcount: A:0.27, C:0.13, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTTATATTTCCTAGTAAA
Found at i:520702 original size:27 final size:27
Alignment explanation
Indices: 520668--520762 Score: 118
Period size: 27 Copynumber: 3.5 Consensus size: 27
520658 CACGCCAGAA
*
520668 AAATGGAAGCCTTTGTGACAATCTATG
1 AAATGGAAGCCTTTGTGACAATATATG
* *
520695 AAATGGAAGCCTTTGTGGCGATATATG
1 AAATGGAAGCCTTTGTGACAATATATG
* * *
520722 AAATGGAAGCCTTTGTGGCGATATAAG
1 AAATGGAAGCCTTTGTGACAATATATG
*
520749 AAAAGGAAAGCCTT
1 AAATGG-AAGCCTT
520763 AGTGGCAAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
27 55 0.89
28 7 0.11
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (27 bp):
AAATGGAAGCCTTTGTGACAATATATG
Found at i:522065 original size:13 final size:14
Alignment explanation
Indices: 522047--522081 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
522037 ATTTTGGTTG
522047 TTTTGTGT-TTTGT
1 TTTTGTGTGTTTGT
522060 TTTTGTGTGTTTGT
1 TTTTGTGTGTTTGT
522074 TTTATGTG
1 TTT-TGTG
522082 CAATGGGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.40
14 8 0.40
15 4 0.20
ACGTcount: A:0.03, C:0.00, G:0.26, T:0.71
Consensus pattern (14 bp):
TTTTGTGTGTTTGT
Found at i:522070 original size:15 final size:15
Alignment explanation
Indices: 522050--522081 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
522040 TTGGTTGTTT
522050 TGTGT-TTTGTTTT-
1 TGTGTGTTTGTTTTA
522063 TGTGTGTTTGTTTTA
1 TGTGTGTTTGTTTTA
522078 TGTG
1 TGTG
522082 CAATGGGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.29
14 8 0.47
15 4 0.24
ACGTcount: A:0.03, C:0.00, G:0.28, T:0.69
Consensus pattern (15 bp):
TGTGTGTTTGTTTTA
Found at i:530287 original size:27 final size:26
Alignment explanation
Indices: 530257--530357 Score: 80
Period size: 27 Copynumber: 3.8 Consensus size: 26
530247 TGTCCCGATG
530257 GACTACCTCGCGTTTAATGTCCTAGCA
1 GACTACCTCGCGTTTAATGTCCT-GCA
** *
530284 GACTACC-CTATGTTTATTGTCCTGACA
1 GACTACCTC-GCGTTTAATGTCCTG-CA
* * *
530311 GACTACCT-GGGTTTAATGTCTTGGTA
1 GACTACCTCGCGTTTAATGTCCT-GCA
* *
530337 GACTACCCCGCATTTAATGTC
1 GACTACCTCGCGTTTAATGTC
530358 TTGATGGACT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
26 20 0.34
27 38 0.66
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.34
Consensus pattern (26 bp):
GACTACCTCGCGTTTAATGTCCTGCA
Found at i:530379 original size:27 final size:27
Alignment explanation
Indices: 530283--530381 Score: 92
Period size: 27 Copynumber: 3.7 Consensus size: 27
530273 ATGTCCTAGC
* * * *
530283 AGACTACCCTATGTTTATTGTCCTGAC
1 AGACTACCCTACGTTTAATGTCTTGAT
** *
530310 AGACTA-CCTGGGTTTAATGTCTTGGT
1 AGACTACCCTACGTTTAATGTCTTGAT
** *
530336 AGACTACCCCGCATTTAATGTCTTGAT
1 AGACTACCCTACGTTTAATGTCTTGAT
*
530363 GGACTACCCTACGTTTAAT
1 AGACTACCCTACGTTTAAT
530382 AACTTGGAAT
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
26 20 0.35
27 37 0.65
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.35
Consensus pattern (27 bp):
AGACTACCCTACGTTTAATGTCTTGAT
Found at i:530473 original size:27 final size:27
Alignment explanation
Indices: 530443--530543 Score: 103
Period size: 27 Copynumber: 3.7 Consensus size: 27
530433 GTTCCAGCAA
* *
530443 ACTACCTCATATTTATTGTCCCAACGG
1 ACTACCCCACATTTATTGTCCCAACGG
* * * *
530470 ACTACCCCACGTTTAATGTCCCAGCAG
1 ACTACCCCACATTTATTGTCCCAACGG
* * *
530497 ACTACTCCACAATTATTGTCCCGACGG
1 ACTACCCCACATTTATTGTCCCAACGG
**
530524 ACTACCCCATGTTTATTGTC
1 ACTACCCCACATTTATTGTC
530544 TCGGAAGATT
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.25, C:0.33, G:0.13, T:0.30
Consensus pattern (27 bp):
ACTACCCCACATTTATTGTCCCAACGG
Found at i:530494 original size:54 final size:54
Alignment explanation
Indices: 530427--530543 Score: 155
Period size: 54 Copynumber: 2.2 Consensus size: 54
530417 CTATTCTACA
* * *
530427 TTTAATGTTCCAGCAAACTAC-CTCATATTTATTGTCCCAACGGACTACCCCACG
1 TTTAATGTCCCAGCAAACTACTC-CACAATTATTGTCCCAACGGACTACCCCACG
* * *
530481 TTTAATGTCCCAGCAGACTACTCCACAATTATTGTCCCGACGGACTACCCCATG
1 TTTAATGTCCCAGCAAACTACTCCACAATTATTGTCCCAACGGACTACCCCACG
*
530535 TTTATTGTC
1 TTTAATGTC
530544 TCGGAAGATT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 54 0.98
55 1 0.02
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.31
Consensus pattern (54 bp):
TTTAATGTCCCAGCAAACTACTCCACAATTATTGTCCCAACGGACTACCCCACG
Found at i:530659 original size:27 final size:27
Alignment explanation
Indices: 530602--530676 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
530592 CTACCCCATC
* * *
530602 TTTATTATCCCGGTGGACTATTCCGCA
1 TTTATTGTCCCGGTAGACTACTCCGCA
* *
530629 TTTATTGTCCCGGTAGACTACTCCTCG
1 TTTATTGTCCCGGTAGACTACTCCGCA
* *
530656 TTTAATGTCCCAGTAGACTAC
1 TTTATTGTCCCGGTAGACTAC
530677 CTCGCGTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (27 bp):
TTTATTGTCCCGGTAGACTACTCCGCA
Found at i:530684 original size:27 final size:27
Alignment explanation
Indices: 530617--530692 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
530607 TATCCCGGTG
* * * *
530617 GACTATTCCGCATTTATTGTCCCGGTA
1 GACTACTCCGCGTTTAATGTCCCAGTA
*
530644 GACTACTCCTCGTTTAATGTCCCAGTA
1 GACTACTCCGCGTTTAATGTCCCAGTA
530671 GACTAC-CTCGCGTTTAATGTCC
1 GACTACTC-CGCGTTTAATGTCC
530693 TAAAGGACTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 1 0.02
27 41 0.98
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (27 bp):
GACTACTCCGCGTTTAATGTCCCAGTA
Found at i:534933 original size:14 final size:15
Alignment explanation
Indices: 534914--534950 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
534904 TCATTGATAG
534914 ATTATACAAAATAA-
1 ATTATACAAAATAAT
534928 ATTATA-AAAATAAT
1 ATTATACAAAATAAT
*
534942 ATGATACAA
1 ATTATACAA
534951 TACGAATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 7 0.35
14 11 0.55
15 2 0.10
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (15 bp):
ATTATACAAAATAAT
Found at i:535968 original size:126 final size:127
Alignment explanation
Indices: 535721--536054 Score: 544
Period size: 127 Copynumber: 2.6 Consensus size: 127
535711 AACTTCAGGG
* * * * *
535721 AGATAAGATTTGCCATCTTCAATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAA-TTCCC
*
535786 ACCTATTCCACTGTTGACCAGGGACATAGGACTTGTGGCCTAAATCTGCTTCCTTACACTTGA
65 ACCTATTCCACTGCTGACCAGGGACATAGGACTTGTGGCCTAAATCTGCTTCCTTACACTTGA
*
535849 AGAT-AGATTCGCTGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTCCCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTCCCA
* * *
535913 CCTATTCCACTGCTGACTAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
66 CCTATTCCACTGCTGACCAGGGACATAGGACTTGTGGCCTAAATCTGCTTCCTTACACTTGA
* *
535975 AGATAAGATTCGCCGTCTTTGATCTACTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTCCCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTCCCA
536040 CCTATTCCACTGCTG
66 CCTATTCCACTGCTG
536055 GTCAGGGAGC
Statistics
Matches: 192, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
126 67 0.35
127 121 0.63
128 4 0.02
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.31
Consensus pattern (127 bp):
AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTCCCA
CCTATTCCACTGCTGACCAGGGACATAGGACTTGTGGCCTAAATCTGCTTCCTTACACTTGA
Found at i:537389 original size:8 final size:7
Alignment explanation
Indices: 537350--537388 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
537340 AGCCTCTCTA
537350 TTTTCAT
1 TTTTCAT
537357 TTTTCAT
1 TTTTCAT
537364 TTTTCA-
1 TTTTCAT
537370 TTTTCATT
1 TTTTCA-T
537378 TTTTCAT
1 TTTTCAT
537385 TTTT
1 TTTT
537389 TACACATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 6 0.20
7 18 0.60
8 6 0.20
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTCAT
Found at i:538877 original size:16 final size:16
Alignment explanation
Indices: 538856--538894 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
538846 CAAGATCTGT
538856 CTATCCTATCGTGCTA
1 CTATCCTATCGTGCTA
*
538872 CTATCCTCTCGTGCTA
1 CTATCCTATCGTGCTA
*
538888 CCATCCT
1 CTATCCT
538895 CAACAAGTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.15, C:0.38, G:0.10, T:0.36
Consensus pattern (16 bp):
CTATCCTATCGTGCTA
Found at i:543353 original size:14 final size:15
Alignment explanation
Indices: 543334--543370 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
543324 TCATTGATAG
543334 ATTATACAAAATAA-
1 ATTATACAAAATAAT
543348 ATTATA-AAAATAAT
1 ATTATACAAAATAAT
*
543362 ATGATACAA
1 ATTATACAA
543371 TACGAATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 7 0.35
14 11 0.55
15 2 0.10
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (15 bp):
ATTATACAAAATAAT
Found at i:547264 original size:70 final size:70
Alignment explanation
Indices: 547150--547493 Score: 225
Period size: 70 Copynumber: 4.9 Consensus size: 70
547140 TTCTCACCAA
* * * * * *
547150 GTTGATGTTGCAAAGTTC-GAAATGAGCCCTCTTCTC-TCCGTGTTGAAGTTGTAAGTGCTCTTC
1 GTTGATGCTGCAAAGTTCAG-AATGGGCCCTCCTCTCAT-CATGTTGAAGTTGTAAGGGTTCTTC
547213 CCGCCAT
64 CCGCCAT
547220 GTTGATGCTGCAAAGTTCAGAATGGGCCCTCCTCTCATCATGTTGAAGTTGTAAGGGTTCTTCCC
1 GTTGATGCTGCAAAGTTCAGAATGGGCCCTCCTCTCATCATGTTGAAGTTGTAAGGGTTCTTCCC
* *
547285 ACCCT
66 GCCAT
** * * * * * * * * * *** *
547290 ACTGATGTTGTAAAGTCCAAAATGGGTCCTCC-CATCACCATGTTGAGGGTGCAAAACTTATGT-
1 GTTGATGCTGCAAAGTTCAGAATGGGCCCTCCTC-TCATCATGTTGAAGTTGTAAGGGTTCT-TC
*
547353 CTGCCAT
64 CCGCCAT
* * * * * ** * * *
547360 GTTAATGATGCATAGTTCA-ATTAGGGCCCTCCTATCGCCATATTGAAGTTGAAAGGGTTCTTCT
1 GTTGATGCTGCAAAGTTCAGAAT-GGGCCCTCCTCTCATCATGTTGAAGTTGTAAGGGTTCTTCC
*
547424 CGTCAT
65 CGCCAT
* * * **
547430 GTTCATGCTGCAAAGTT-TGAAATTGGTTCTCCTCTCATCATGTTGAAGTTGTAA-GGTTCTTCC
1 GTTGATGCTGCAAAGTTCAG-AATGGGCCCTCCTCTCATCATGTTGAAGTTGTAAGGGTTCTTCC
547493 C
65 C
547494 ATTATGTTGA
Statistics
Matches: 203, Mismatches: 62, Indels: 19
0.71 0.22 0.07
Matches are distributed among these distances:
69 13 0.06
70 185 0.91
71 5 0.02
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (70 bp):
GTTGATGCTGCAAAGTTCAGAATGGGCCCTCCTCTCATCATGTTGAAGTTGTAAGGGTTCTTCCC
GCCAT
Found at i:547529 original size:29 final size:28
Alignment explanation
Indices: 547465--547532 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
547455 GTTCTCCTCT
*
547465 CATCATGTTGAAGTTGTAAGGTTCTTCC
1 CATCATGTTGAAGTTGCAAGGTTCTTCC
*
547493 CATTATGTTGAAGTTGCAAGGGTTCTTCC
1 CATCATGTTGAAGTTGCAA-GGTTCTTCC
**
547522 TGTCATGTTGA
1 CATCATGTTGA
547533 TTTTGCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 17 0.50
29 17 0.50
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.40
Consensus pattern (28 bp):
CATCATGTTGAAGTTGCAAGGTTCTTCC
Found at i:551195 original size:14 final size:15
Alignment explanation
Indices: 551165--551195 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
551155 AATACTCTTA
551165 TACAATATTTAATTT
1 TACAATATTTAATTT
551180 TACAATATTT-ATTT
1 TACAATATTTAATTT
551194 TA
1 TA
551196 AACCTTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (15 bp):
TACAATATTTAATTT
Found at i:551593 original size:9 final size:9
Alignment explanation
Indices: 551581--551615 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
551571 GAAAATCTCA
551581 AAAAATTTT
1 AAAAATTTT
551590 AAAAATATTCT
1 AAAAAT-TT-T
551601 AAAAATTTT
1 AAAAATTTT
551610 AAAAAT
1 AAAAAT
551616 ATATATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 13 0.54
10 4 0.17
11 7 0.29
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (9 bp):
AAAAATTTT
Found at i:553136 original size:30 final size:30
Alignment explanation
Indices: 553098--553164 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
553088 GACATATATC
*
553098 TTGATTTTATTTAATTCTAATCAATTTGAT
1 TTGATTTTATTTAATTCTAATCAAATTGAT
* *
553128 TTTATTTTATTTTATTCTAATCAAATTGAT
1 TTGATTTTATTTAATTCTAATCAAATTGAT
553158 TTGATTT
1 TTGATTT
553165 AAATCAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (30 bp):
TTGATTTTATTTAATTCTAATCAAATTGAT
Found at i:557702 original size:18 final size:17
Alignment explanation
Indices: 557678--557722 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
557668 AAAGCTAAAG
557678 TTATATTTTTGGATTTT
1 TTATATTTTTGGATTTT
* *
557695 TATATATTTCTTTGCTTTT
1 T-TATATTT-TTGGATTTT
557714 TTATATTTT
1 TTATATTTT
557723 AAAATTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 2 0.08
18 14 0.58
19 8 0.33
ACGTcount: A:0.18, C:0.04, G:0.07, T:0.71
Consensus pattern (17 bp):
TTATATTTTTGGATTTT
Found at i:565517 original size:21 final size:21
Alignment explanation
Indices: 565492--565534 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
565482 TATTAGAATA
*
565492 GAAAT-AAAATTATAAGATTTT
1 GAAATCAAAATTA-AAAATTTT
*
565513 GAAATCAAAGTTAAAAATTTT
1 GAAATCAAAATTAAAAATTTT
565534 G
1 G
565535 TGTTAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.35
Consensus pattern (21 bp):
GAAATCAAAATTAAAAATTTT
Found at i:566463 original size:51 final size:51
Alignment explanation
Indices: 566395--566496 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
566385 TACAAGATGG
566395 AGAAATTCAAAACAAGAAATTTAAAACAAACCCTAACCCTAAATACAAAGC
1 AGAAATTCAAAACAAGAAATTTAAAACAAACCCTAACCCTAAATACAAAGC
566446 AGAAATTCAAAACAAGAAATTTAAAACAAACCCTAACCCTAAATACAAAGC
1 AGAAATTCAAAACAAGAAATTTAAAACAAACCCTAACCCTAAATACAAAGC
566497 TCTCTGGCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.57, C:0.22, G:0.06, T:0.16
Consensus pattern (51 bp):
AGAAATTCAAAACAAGAAATTTAAAACAAACCCTAACCCTAAATACAAAGC
Found at i:568110 original size:29 final size:28
Alignment explanation
Indices: 568070--568134 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 28
568060 AAAATTAGAA
568070 ATAAG-TGGGGTTAAATTGAAAGAAGCC
1 ATAAGTTGGGGTTAAATTGAAAGAAGCC
* *
568097 ATAAGTTGGTGGTTAAATTGATAGAAGTC
1 ATAAGTTGG-GGTTAAATTGAAAGAAGCC
568126 ATAAGTTGG
1 ATAAGTTGG
568135 CGGTCTCTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 5 0.15
28 3 0.09
29 26 0.76
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.29
Consensus pattern (28 bp):
ATAAGTTGGGGTTAAATTGAAAGAAGCC
Found at i:575716 original size:19 final size:19
Alignment explanation
Indices: 575666--575718 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
575656 ATAAAGAAAT
*
575666 TTTTTTAATTTATTTTCAA
1 TTTTTTAATATATTTTCAA
* * *
575685 TTTGTTGAGATATTTT-AA
1 TTTTTTAATATATTTTCAA
575703 TATTTTTAATATATTT
1 T-TTTTTAATATATTT
575719 GGTGTATTAT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
18 3 0.12
19 23 0.88
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (19 bp):
TTTTTTAATATATTTTCAA
Found at i:576984 original size:115 final size:113
Alignment explanation
Indices: 576811--577124 Score: 441
Period size: 114 Copynumber: 2.8 Consensus size: 113
576801 AAAATAAGCA
* * * *
576811 TTAGCGGCGTTTTTGCTAAAGCGCCGCAAAATAA-CTAAGCCCAATGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
*
576875 TCGGGGGATTTAGCGACGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCT
66 TC-GGGGATTTAGCG-CGTTTTTAAGGAAGCGCCGCTAATGCCCAGGGCT
* *
576925 TTAGTGGCGTTTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGTTT
1 TTAGCGGCGTTTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* **
576990 TCGGGGATTTAGCGGGTTTTTTGGGGAAGCGCCGCTAATGCCCAGGGCT
66 TCGGGGATTTAGCGCG-TTTTTAAGGAAGCGCCGCTAATGCCCAGGGCT
* * * * * *
577039 TTAACGACGATTTTGCGAAAGTGCCACAAAAAAACCTAAGCCCAACGATGCTGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
577104 TCGGGGATTTAGCGGCGTTTT
66 TCGGGGATTTAGC-GCGTTTT
577125 GATAAAGCGC
Statistics
Matches: 178, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
113 1 0.01
114 145 0.81
115 32 0.18
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (113 bp):
TTAGCGGCGTTTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGCGCGTTTTTAAGGAAGCGCCGCTAATGCCCAGGGCT
Found at i:577018 original size:114 final size:114
Alignment explanation
Indices: 576811--577657 Score: 469
Period size: 115 Copynumber: 7.1 Consensus size: 114
576801 AAAATAAGCA
* * * *
576811 TTAGCGGCGTTTTTGCTAAAGCGCCGCAAAATAA-CTAAGCCCAATGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
576875 TCGGGGGATTTAGCGACG-TTTTTAAGGAAGCGCCGCTAATGCTCAGGGCT
66 TC-GGGGATTTAGCG-GGTTTTTTAAGGAAGCGCCGCTAATGCCCAGGGCT
* *
576925 TTAGTGGCGTTTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGTTT
1 TTAGCGGCGTTTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
**
576990 TCGGGGATTTAGCGGGTTTTTTGGGGAAGCGCCGCTAATGCCCAGGGCT
66 TCGGGGATTTAGCGGGTTTTTTAAGGAAGCGCCGCTAATGCCCAGGGCT
* * * * * *
577039 TTAACGACGATTTTGCGAAAGTGCCACAAAAAAACCTAAGCCCAACGATGCTGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *** *
577104 TCGGGGATTTAGCGGCGTTTTGATAAAGCGCCACAGAAAAAC-CTAAT-CCCAACGACGTCGT
66 TCGGGGATTTAGCGG-GTTTT--TTAAG-G--A-AG--CGCCGCTAATGCCC-A-G--GGC-T
*** ** * * * * *** **** * *
577165 TTTTTGAGC-TTTCGGGGATTTAGCGGCGTTTTTACTAAAGCGCC-ACAAAAAAACCTAAGCC--
1 TTAGCG-GCGTTTTTGCGA--AAGC-GC-----CACAAAAAAACCTA-AGCCCAA-CGACGCCGT
*** *** * * * ** * *
577226 CAAC-GACGCCGTTT-TCTGAGCTT-TCGGGGATTTTGCGGCGTTTTTAATTAAGCGCCACTATT
55 TTTCTGA-G-C-TTTCGGGGA-TTTAGC-GGGTTTTT----------TAAGGAAGCGCCGCTAAT
*
577288 GCTCAGGGGCT
105 GCCCAGG-GCT
* * *
577299 TTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACGACACCATTTTCTGAGCTT
1 TTAGCGGCGTTTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * * *
577364 TCGGGGATTTAGCGGCGTTTTTTAAGTAAGTGCCACTAATGCTCAGGGCT
66 TCGGGGATTTAGCGG-GTTTTTTAAGGAAGCGCCGCTAATGCCCAGGGCT
* **
577414 TTAGCGGCATTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * *
577479 TCGGGGATGTAGCGGCGTTTTTTAAGTAAGCGCCGCTAATGCTCA-GGCTT
66 TCGGGGATTTAGCGG-GTTTTTTAAGGAAGCGCCGCTAATGCCCAGGGC-T
* * * * *
577529 TTAGCGGCGTTTTTGGGAAGGCGCCGCAAAGAAACCTAAGCCCAACGACGCCGTTTTCTTAGCTT
1 TTAGCGGCGTTTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *** ** * *
577594 TCGTGGATTTAGTAACG-TTTTTAATAAAGCGCCGCTAATGCTCAGTGCT
66 TCGGGGATTTAG-CGGGTTTTTTAAGGAAGCGCCGCTAATGCCCAGGGCT
577643 TTAGCGGCGTTTTTG
1 TTAGCGGCGTTTTTG
577658 AGGATGCGCC
Statistics
Matches: 558, Mismatches: 119, Indels: 112
0.71 0.15 0.14
Matches are distributed among these distances:
113 1 0.00
114 187 0.34
115 213 0.38
116 22 0.04
117 2 0.00
118 1 0.00
120 1 0.00
121 5 0.01
122 6 0.01
123 2 0.00
125 13 0.02
126 28 0.05
127 4 0.01
128 4 0.01
129 2 0.00
131 2 0.00
132 6 0.01
133 5 0.01
134 28 0.05
135 12 0.02
136 2 0.00
137 5 0.01
138 4 0.01
139 1 0.00
142 2 0.00
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGCGGGTTTTTTAAGGAAGCGCCGCTAATGCCCAGGGCT
Found at i:577239 original size:73 final size:72
Alignment explanation
Indices: 577056--577283 Score: 348
Period size: 73 Copynumber: 3.1 Consensus size: 72
577046 CGATTTTGCG
* * *
577056 AAAGTGCCACAAAAAAACCTAAGCCCAACGATGCTGTTTTCTGAGCTTTCGGGGATTTAGCGGCG
1 AAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCG
*
577121 TTTTGAT
66 TTTTTAT
* * * *
577128 AAAGCGCCACAGAAAAACCTAATCCCAACGACGTCGTTTTTTGAGCTTTCGGGGATTTAGCGGCG
1 AAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCG
577193 TTTTTACT
66 TTTTTA-T
*
577201 AAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTTGCGGCG
1 AAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCG
577266 TTTTTAAT
66 TTTTT-AT
*
577274 TAAGCGCCAC
1 AAAGCGCCAC
577284 TATTGCTCAG
Statistics
Matches: 140, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
72 63 0.45
73 76 0.54
74 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (72 bp):
AAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCG
TTTTTAT
Found at i:577332 original size:115 final size:115
Alignment explanation
Indices: 577183--577657 Score: 688
Period size: 115 Copynumber: 4.1 Consensus size: 115
577173 CTTTCGGGGA
*
577183 TTTAGCGGCGTTTTTACTAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * *
577248 TTCGGGGATTTTGCGGCG-TTTTTAATTAAGCGCCACTATTGCTCAGGGGC
66 TTCGGGGATTTAGCGGCGTTTTTTAAGTAAGCGCCACTAATGCTCA-GGGC
* *
577298 TTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACGACACCATTTTCTGAGCT
1 TTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
*
577363 TTCGGGGATTTAGCGGCGTTTTTTAAGTAAGTGCCACTAATGCTCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTTAAGTAAGCGCCACTAATGCTCAGGGC
* *
577413 TTTAGCGGCATTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* *
577478 TTCGGGGATGTAGCGGCGTTTTTTAAGTAAGCGCCGCTAATGCTCA-GGC
66 TTCGGGGATTTAGCGGCGTTTTTTAAGTAAGCGCCACTAATGCTCAGGGC
** * * * *
577527 TTTTAGCGGCGTTTTTGGGAAGGCGCCGCAAAGAAACCTAAGCCCAACGACGCCGTTTTCTTAGC
1 -TTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGC
* *** * *
577592 TTTCGTGGATTTAGTAACG-TTTTTAA-TAAAGCGCCGCTAATGCTCAGTGC
65 TTTCGGGGATTTAGCGGCGTTTTTTAAGT-AAGCGCCACTAATGCTCAGGGC
577642 TTTAGCGGCGTTTTTG
1 TTTAGCGGCGTTTTTG
577658 AGGATGCGCC
Statistics
Matches: 329, Mismatches: 27, Indels: 9
0.90 0.07 0.02
Matches are distributed among these distances:
113 1 0.00
114 44 0.13
115 260 0.79
116 24 0.07
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (115 bp):
TTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
TTCGGGGATTTAGCGGCGTTTTTTAAGTAAGCGCCACTAATGCTCAGGGC
Found at i:578033 original size:7 final size:7
Alignment explanation
Indices: 578021--578060 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
578011 TTTAAAATTT
*
578021 GGGTTAA
1 GGGTTAG
578028 GGGTTAG
1 GGGTTAG
578035 GGGTTAG
1 GGGTTAG
578042 GGGTTA-
1 GGGTTAG
578048 -GGTTAG
1 GGGTTAG
578054 GGGTTAG
1 GGGTTAG
578061 ATGTTAAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 5 0.17
7 25 0.83
ACGTcount: A:0.17, C:0.00, G:0.53, T:0.30
Consensus pattern (7 bp):
GGGTTAG
Found at i:578066 original size:14 final size:12
Alignment explanation
Indices: 578022--578060 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
578012 TTAAAATTTG
*
578022 GGTTAAGGGTTA
1 GGTTAGGGGTTA
578034 GGGGTTAGGGGTTA
1 --GGTTAGGGGTTA
578048 GGTTAGGGGTTA
1 GGTTAGGGGTTA
578060 G
1 G
578061 ATGTTAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 13 0.54
14 11 0.46
ACGTcount: A:0.18, C:0.00, G:0.51, T:0.31
Consensus pattern (12 bp):
GGTTAGGGGTTA
Found at i:578066 original size:19 final size:19
Alignment explanation
Indices: 578029--578066 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
578019 TTGGGTTAAG
*
578029 GGTTAGGGGTTAGGGGTTA
1 GGTTAGGGGTTAGAGGTTA
*
578048 GGTTAGGGGTTAGATGTTA
1 GGTTAGGGGTTAGAGGTTA
578067 AGAGCTAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.47, T:0.34
Consensus pattern (19 bp):
GGTTAGGGGTTAGAGGTTA
Found at i:578221 original size:27 final size:29
Alignment explanation
Indices: 578171--578242 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 29
578161 TAGGGGTTAT
* * *
578171 GGATTAGGAGTTAAGGGTTAGGGA-TTCA
1 GGATTGGGATTTAGGGGTTAGGGATTTCA
*
578199 GGATTGGG-TTTAGGGGTTAGGGATTTGA
1 GGATTGGGATTTAGGGGTTAGGGATTTCA
*
578227 GGTTTGGGATTTAGGG
1 GGATTGGGATTTAGGG
578243 TTTCAACGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 13 0.35
28 17 0.46
29 7 0.19
ACGTcount: A:0.21, C:0.01, G:0.44, T:0.33
Consensus pattern (29 bp):
GGATTGGGATTTAGGGGTTAGGGATTTCA
Found at i:578650 original size:24 final size:24
Alignment explanation
Indices: 578623--578703 Score: 99
Period size: 24 Copynumber: 3.2 Consensus size: 24
578613 AATAAACAAA
578623 TAAATAAATAGGTAATTAATTATT
1 TAAATAAATAGGTAATTAATTATT
* *
578647 TAAATTAATTTTTAGGTAATTAATTGTT
1 TAAA-TAA---ATAGGTAATTAATTATT
*
578675 TAAATAGATAGGTAATTAATTATT
1 TAAATAAATAGGTAATTAATTATT
578699 TAAAT
1 TAAAT
578704 GAATGATACA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
24 24 0.50
25 3 0.06
27 2 0.04
28 19 0.40
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (24 bp):
TAAATAAATAGGTAATTAATTATT
Found at i:578651 original size:28 final size:28
Alignment explanation
Indices: 578620--578703 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 28
578610 ATAAATAAAC
578620 AAATAAATAAATAGGTAATTAATTATTT
1 AAATAAATAAATAGGTAATTAATTATTT
* *** *
578648 AAATTAATTTTTAGGTAATTAATT-GTT
1 AAATAAATAAATAGGTAATTAATTATTT
*
578675 ---TAAATAGATAGGTAATTAATTATTT
1 AAATAAATAAATAGGTAATTAATTATTT
578700 AAAT
1 AAAT
578704 GAATGATACA
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
24 17 0.40
25 2 0.05
27 2 0.05
28 21 0.50
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (28 bp):
AAATAAATAAATAGGTAATTAATTATTT
Found at i:579433 original size:365 final size:366
Alignment explanation
Indices: 578750--579462 Score: 1198
Period size: 365 Copynumber: 2.0 Consensus size: 366
578740 TAAGATTTTG
*
578750 CGGCGTTTTGATAAAAAAACGCCACAAAAATTTATTGCATTTACCGATACGGCTTCGTTTCGGCT
1 CGGCGTTTTGATAAAAAAACGCCACAAAAATTTATTGCATTTACCGATACAGCTTCGTTTCGGCT
** * * * *
578815 TAGGGAATAAGTTTTAGTTGTGGCATTTTTCCGAAAAGCGCCTTAAATAATATTTAAACTTTGCC
66 TAGGGAATAAAATTTAGTTGTGGCATGTTCCCGAAAAGCGCCGTAAATAATATTTAAACTTTGCA
* * *
578880 GAAACGGCGCCGTTTCAGTTGAAGGATGGAATATTTTAGTGGCGTTTTATTATAAATGCCGCAAG
131 AAAACGGCGCCGTTTCAGTTGAAGGATGGAATATTTTAGTGGCGTTTTATTAAAAACGCCGCAAG
* * * *
578945 GATGTATAAAATTTTCTGAAAATGACGCCGGTTCGATAATATATTAATTGTGGCATTTTTGGGAG
196 GATGTATAAAATTTACTGAAAACGACGCCGGTTCGATAATATATTAATTGTGGCATGTTTGGGAA
* *
579010 AACGCTAGAATGTTTCCTTATATTTTTATAAAATGGCGCTGTTTCTTTCTGTACTTGAAATTTTA
261 AACGCCAGAATGTTTCCTTATATTTTTATAAAACGGCGCTGTTTCTTTCTGTACTTGAAATTTTA
579075 GTGGCGTTTTTAATTAAAACGCCACAAAAGGTAGACATTAC
326 GTGGCGTTTTTAATTAAAACGCCACAAAAGGTAGACATTAC
*
579116 CGGCGTTTTGAT-AAAAAACGCCACAAATATTTATTGCATTTACCGATACAGCGTT-GTTTCGGC
1 CGGCGTTTTGATAAAAAAACGCCACAAAAATTTATTGCATTTACCGATACAGC-TTCGTTTCGGC
* *
579179 TTAGGGAATAAAATTTAGTTGTGGCATGTTCCCTAAAAGCGCCGTAAATAATATTTGAACTTTGC
65 TTAGGGAATAAAATTTAGTTGTGGCATGTTCCCGAAAAGCGCCGTAAATAATATTTAAACTTTGC
*
579244 AAAAACGGCGCCGTTTCAGTTGAAGGATGGAATCTTTTAGTGGCGTTTTATTAAAAACGCCGCAA
130 AAAAACGGCGCCGTTTCAGTTGAAGGATGGAATATTTTAGTGGCGTTTTATTAAAAACGCCGCAA
*
579309 GGATGTATAAAATTTACTGAAAACGACGCCGGTTCGATAATATATTAATTGTGGCGTGTTTGGGA
195 GGATGTATAAAATTTACTGAAAACGACGCCGGTTCGATAATATATTAATTGTGGCATGTTTGGGA
579374 AAACGCCAGAATGTTTCCTTATATTTTTATAAAACGGCGAC-GTTTCTTTCTGTACTTGAAATTT
260 AAACGCCAGAATGTTTCCTTATATTTTTATAAAACGGCG-CTGTTTCTTTCTGTACTTGAAATTT
579438 TAGTGGCGTTTTTAATTAAAACGCC
324 TAGTGGCGTTTTTAATTAAAACGCC
579463 GTAAATGTCG
Statistics
Matches: 324, Mismatches: 21, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
365 309 0.95
366 15 0.05
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34
Consensus pattern (366 bp):
CGGCGTTTTGATAAAAAAACGCCACAAAAATTTATTGCATTTACCGATACAGCTTCGTTTCGGCT
TAGGGAATAAAATTTAGTTGTGGCATGTTCCCGAAAAGCGCCGTAAATAATATTTAAACTTTGCA
AAAACGGCGCCGTTTCAGTTGAAGGATGGAATATTTTAGTGGCGTTTTATTAAAAACGCCGCAAG
GATGTATAAAATTTACTGAAAACGACGCCGGTTCGATAATATATTAATTGTGGCATGTTTGGGAA
AACGCCAGAATGTTTCCTTATATTTTTATAAAACGGCGCTGTTTCTTTCTGTACTTGAAATTTTA
GTGGCGTTTTTAATTAAAACGCCACAAAAGGTAGACATTAC
Found at i:581020 original size:132 final size:132
Alignment explanation
Indices: 580779--581022 Score: 332
Period size: 132 Copynumber: 1.8 Consensus size: 132
580769 TAGACAGCGA
* * *
580779 AGCAGATCGAAGATGGCTGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGACAGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * *
580844 TCTATCTCCCTGGGCGACAGTGGAATAGAGTGAAGATTATAGATCTTATCTCCCTAAGTAGTAGT
66 TCTATCCCCCCGGGCGACAGTGGAATAGAGTGAAGATAACAGATCTTATCTCCCTAAGTAGTAGT
580909 GG
131 GG
* *
580911 AGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTGCAGTGGAGT-CTATTGAAGCCAGTAA
1 AGCAGATCAAAGATGACAGATTTTACCTCCCTGAAGTTACAGTGGAGTAC-ATTGAAGCCAGTAA
* * *
580975 TTCTATCCCCCCGGTCGGCAGTGGAATCGA-TCGAAGA-AAGCAGATCTT
65 TTCTATCCCCCCGGGCGACAGTGGAATAGAGT-GAAGATAA-CAGATCTT
581023 GTCTTCATGT
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
131 3 0.03
132 94 0.97
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (132 bp):
AGCAGATCAAAGATGACAGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTATCCCCCCGGGCGACAGTGGAATAGAGTGAAGATAACAGATCTTATCTCCCTAAGTAGTAGT
GG
Found at i:581063 original size:132 final size:132
Alignment explanation
Indices: 580777--581063 Score: 298
Period size: 132 Copynumber: 2.2 Consensus size: 132
580767 CATAGACAGC
** *
580777 GAAGCAGATCGAAGATGGCTGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGCCAGTA
1 GAAGCAGATCGAAGAAAGCAGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGCCAGTA
* * * *
580842 ATTCTATCTCCCTGGGCGACAGTGGAATAGAGTGAAGATTATAGATCTTATCTCCCTAAGTAGTA
66 ATTCTATCCCCCCGGGCGACAGTGGAATAGAGTGAAGATAACAGATCTTATCTCCCTAAGTAGTA
580907 GT
131 GT
* * * * *
580909 GGAGCAGATCAAAG-ATGACAGATTTTACCTCCCTGAGGTTGCAGTGGAGT-CTATTGAAGCCAG
1 GAAGCAGATCGAAGAAAG-CAGATTTTACCTCCCTGAAGTTACAGTGGAGTAC-ATTGAAGCCAG
* * * * * *
580972 TAATTCTATCCCCCCGGTCGGCAGTGGAATCGA-TCGAAGA-AAGCAGATCTTGTCT-TC-ATGT
64 TAATTCTATCCCCCCGGGCGACAGTGGAATAGAGT-GAAGATAA-CAGATCTTATCTCCCTAAGT
*
581033 ATTGACGT
127 AGT-A-GT
*
581041 GAAGTAGATCGAAGAAAGCAGAT
1 GAAGCAGATCGAAGAAAGCAGAT
581064 CTTGTCTTCC
Statistics
Matches: 126, Mismatches: 22, Indels: 14
0.78 0.14 0.09
Matches are distributed among these distances:
130 5 0.04
131 6 0.05
132 113 0.90
133 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (132 bp):
GAAGCAGATCGAAGAAAGCAGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGCCAGTA
ATTCTATCCCCCCGGGCGACAGTGGAATAGAGTGAAGATAACAGATCTTATCTCCCTAAGTAGTA
GT
Found at i:584487 original size:11 final size:11
Alignment explanation
Indices: 584467--584502 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
584457 TTTAATAATT
*
584467 TTTTTTTAAAA
1 TTTTTATAAAA
584478 TTTTTATAAAA
1 TTTTTATAAAA
584489 -TTTTATAAAA
1 TTTTTATAAAA
584499 TTTT
1 TTTT
584503 AAATATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTTATAAAA
Found at i:584492 original size:10 final size:10
Alignment explanation
Indices: 584468--584503 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
584458 TTAATAATTT
*
584468 TTTTTTAAAA
1 TTTTATAAAA
584478 TTTTTATAAAA
1 -TTTTATAAAA
584489 TTTTATAAAA
1 TTTTATAAAA
584499 TTTTA
1 TTTTA
584504 AATATTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTTATAAAA
Found at i:585046 original size:2 final size:2
Alignment explanation
Indices: 585039--585069 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
585029 AGTGAAGCAA
*
585039 AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
585070 GATACTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:585566 original size:73 final size:73
Alignment explanation
Indices: 585447--585597 Score: 268
Period size: 73 Copynumber: 2.1 Consensus size: 73
585437 TTTAATGACA
*
585447 TTTTTGACAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTTTGAGCTTTCGGGGATT
1 TTTTTGACAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATT
585512 TAGCAGCG
66 TAGCAGCG
585520 TTTTTG-CTAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGAT
1 TTTTTGAC-AAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGAT
*
585584 TTAGCGGCG
65 TTAGCAGCG
585593 TTTTT
1 TTTTT
585598 TAAGTAAGCG
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
72 1 0.01
73 74 0.99
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (73 bp):
TTTTTGACAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATT
TAGCAGCG
Found at i:585667 original size:188 final size:185
Alignment explanation
Indices: 585326--585712 Score: 560
Period size: 188 Copynumber: 2.1 Consensus size: 185
585316 AAAATAAGCA
* * * * *
585326 TTAGCGGCGTTTTAGCGAAAGCGCCGCAAAATACCTAATCCCAACGACGTCGTTTTCTGAGCTTT
1 TTAGCGGCGTTTTTGCGAAAGCGCCACAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
* * *
585391 CGGGGAATTAGCGGCGTTTTTGGGAAGCGACGCTAATACCCAGGGCTTTAATGACATTTTTGACA
66 CGGGGAATTAGCGGCGTTTTTAGGAAGCGACGCTAATACCCAGGGCTTTAACGACATTCTTGACA
* *
585456 AAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTTTGAGCTTTCGGGGAT
131 AAGCGCCACAAAAAAACCTAAGCCCAACAACGCCGTTTTCTGAGCTTTCGGGGAT
* *
585511 TTAGCAGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGCGAAAGCGCCAC-AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * * * * *
585576 TCGGGGATTTAGCGGCGTTTTTTAAGTAAGCGCCGCTAATACCCAGGGCTTTAGCGGCGTTCTTG
65 TCGGGGAATTAGCGGCG-TTTTT-AGGAAGCGACGCTAATACCCAGGGCTTTAACGACATTCTTG
*
585641 -CTAAAGCGCCACAAAAAAACCTAAGCCCAACAATGCCGTTTTCTGAGCTTTCGGGGAT
128 AC-AAAGCGCCACAAAAAAACCTAAGCCCAACAACGCCGTTTTCTGAGCTTTCGGGGAT
585699 TTAGCGGCGTTTTT
1 TTAGCGGCGTTTTT
585713 TAAGTAAGCG
Statistics
Matches: 178, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
185 23 0.13
186 50 0.28
187 6 0.03
188 99 0.56
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (185 bp):
TTAGCGGCGTTTTTGCGAAAGCGCCACAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
CGGGGAATTAGCGGCGTTTTTAGGAAGCGACGCTAATACCCAGGGCTTTAACGACATTCTTGACA
AAGCGCCACAAAAAAACCTAAGCCCAACAACGCCGTTTTCTGAGCTTTCGGGGAT
Found at i:585712 original size:115 final size:115
Alignment explanation
Indices: 585510--585792 Score: 478
Period size: 115 Copynumber: 2.5 Consensus size: 115
585500 CTTTCGGGGA
* *
585510 TTTAGCAGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACAACGCCGTTTTCTGAGCT
585575 TTCGGGGATTTAGCGGCGTTTTTTAAGTAAGCGCCGCTAATACCCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTTAAGTAAGCGCCGCTAATACCCAGGGC
* *
585625 TTTAGCGGCGTTCTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACAATGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACAACGCCGTTTTCTGAGCT
* *
585690 TTCGGGGATTTAGCGGCGTTTTTTAAGTAAGCGCCGCTAATGCTCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTTAAGTAAGCGCCGCTAATACCCAGGGC
* * *
585740 TTTAGCGGCGTTTTTGATAAAGCGCCAC-AAAAAATCTAAGCCCAACGACGCCG
1 TTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACAACGCCG
585793 GCGTTTTTTA
Statistics
Matches: 157, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
114 22 0.14
115 135 0.86
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.25
Consensus pattern (115 bp):
TTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACAACGCCGTTTTCTGAGCT
TTCGGGGATTTAGCGGCGTTTTTTAAGTAAGCGCCGCTAATACCCAGGGC
Found at i:586084 original size:114 final size:114
Alignment explanation
Indices: 585882--586141 Score: 414
Period size: 114 Copynumber: 2.3 Consensus size: 114
585872 ACGATTATTA
* * * *
585882 TGGCGTTTTTATGTAAGCGCCGCTACTGGTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGCCGCA
1 TGGCGTTTTTATGTAAGCGCCGCTAATGCTCAAGTCTTTAGCGGCGTTTTTGGGAAAGCACCGCA
*
585947 AAAATACTTCAGCCCAACAACGCCGTTTTCTGAGC-TGAGAAGGATTTAG
66 AAAATACTTCAACCCAACAACGCCGTTTTCTGAGCTTGAG-AGGATTTAG
585996 TGGCGTTTTTATGTAAGCGCCGCTAATGCTCAAGTCTTTAGCGGCGTTTTTGGGAAAGCACCGCA
1 TGGCGTTTTTATGTAAGCGCCGCTAATGCTCAAGTCTTTAGCGGCGTTTTTGGGAAAGCACCGCA
* **
586061 AAAATACTTCAACCCAACGACGCCGTTTTCTGAGCTTTCGAGGATTTAG
66 AAAATACTTCAACCCAACAACGCCGTTTTCTGAGCTTGAGAGGATTTAG
* *
586110 TGGTGTTTTTATGTAAGCGCCGCTAATACTCA
1 TGGCGTTTTTATGTAAGCGCCGCTAATGCTCA
586142 GGGATTTAAA
Statistics
Matches: 135, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
114 133 0.99
115 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (114 bp):
TGGCGTTTTTATGTAAGCGCCGCTAATGCTCAAGTCTTTAGCGGCGTTTTTGGGAAAGCACCGCA
AAAATACTTCAACCCAACAACGCCGTTTTCTGAGCTTGAGAGGATTTAG
Found at i:586399 original size:15 final size:14
Alignment explanation
Indices: 586379--586422 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
586369 AAGTTTTATA
586379 GATTATGGAATTAAG
1 GATTATGG-ATTAAG
*
586394 GATTATGGATTAGG
1 GATTATGGATTAAG
* *
586408 GATTCTGGTTTAAG
1 GATTATGGATTAAG
586422 G
1 G
586423 GTTAATATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.36
Consensus pattern (14 bp):
GATTATGGATTAAG
Found at i:586451 original size:14 final size:14
Alignment explanation
Indices: 586434--586500 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 14
586424 TTAATATGAT
* *
586434 TTAAGGTTTATGGG
1 TTAAGGGTTAGGGG
586448 TTAAGGGTTAGGGG
1 TTAAGGGTTAGGGG
*
586462 TTAGGGGTTA--GG
1 TTAAGGGTTAGGGG
* **
586474 TTAGGGGTTAGATG
1 TTAAGGGTTAGGGG
*
586488 TTAAGAGTTAGGG
1 TTAAGGGTTAGGG
586501 ATCTGGGGTT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
12 12 0.28
14 31 0.72
ACGTcount: A:0.22, C:0.00, G:0.43, T:0.34
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:586477 original size:12 final size:12
Alignment explanation
Indices: 586446--586484 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
586436 AAGGTTTATG
*
586446 GGTTAAGGGTTA
1 GGTTAGGGGTTA
586458 GGGGTTAGGGGTTA
1 --GGTTAGGGGTTA
586472 GGTTAGGGGTTA
1 GGTTAGGGGTTA
586484 G
1 G
586485 ATGTTAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 13 0.54
14 11 0.46
ACGTcount: A:0.18, C:0.00, G:0.51, T:0.31
Consensus pattern (12 bp):
GGTTAGGGGTTA
Found at i:586484 original size:7 final size:7
Alignment explanation
Indices: 586445--586484 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
586435 TAAGGTTTAT
*
586445 GGGTTAA
1 GGGTTAG
586452 GGGTTAG
1 GGGTTAG
586459 GGGTTAG
1 GGGTTAG
586466 GGGTTA-
1 GGGTTAG
586472 -GGTTAG
1 GGGTTAG
586478 GGGTTAG
1 GGGTTAG
586485 ATGTTAAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 5 0.17
7 25 0.83
ACGTcount: A:0.17, C:0.00, G:0.53, T:0.30
Consensus pattern (7 bp):
GGGTTAG
Found at i:586490 original size:19 final size:20
Alignment explanation
Indices: 586446--586500 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 20
586436 AAGGTTTATG
*
586446 GGTTAAGGGTTAGGGGTTAGG
1 GGTTAA-GGTTAGGGGTTAGA
586467 GGTT-AGGTTAGGGGTTAGA
1 GGTTAAGGTTAGGGGTTAGA
*
586486 TGTTAAGAGTTAGGG
1 GGTTAAG-GTTAGGG
586501 ATCTGGGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 16 0.53
20 3 0.10
21 11 0.37
ACGTcount: A:0.22, C:0.00, G:0.47, T:0.31
Consensus pattern (20 bp):
GGTTAAGGTTAGGGGTTAGA
Found at i:586490 original size:26 final size:26
Alignment explanation
Indices: 586446--586499 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
586436 AAGGTTTATG
* * *
586446 GGTTAAGGGTTAGGGGTTAGGGGTTA
1 GGTTAAGGGTTAGAGGTTAAGAGTTA
* *
586472 GGTTAGGGGTTAGATGTTAAGAGTTA
1 GGTTAAGGGTTAGAGGTTAAGAGTTA
586498 GG
1 GG
586500 GATCTGGGGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.46, T:0.31
Consensus pattern (26 bp):
GGTTAAGGGTTAGAGGTTAAGAGTTA
Found at i:587110 original size:24 final size:24
Alignment explanation
Indices: 587083--587163 Score: 99
Period size: 24 Copynumber: 3.2 Consensus size: 24
587073 AACAAACAAA
587083 TAAATAAATAGGTAATTAATTATT
1 TAAATAAATAGGTAATTAATTATT
* *
587107 TAAATTAATTTTTAGGTAATTAATTGTT
1 TAAA-TAA---ATAGGTAATTAATTATT
*
587135 TAAATAGATAGGTAATTAATTATT
1 TAAATAAATAGGTAATTAATTATT
587159 TAAAT
1 TAAAT
587164 GAATGATACA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
24 24 0.50
25 3 0.06
27 2 0.04
28 19 0.40
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (24 bp):
TAAATAAATAGGTAATTAATTATT
Done.