Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold421
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: 278460
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 8749 characters in sequence are not A, C, G, or T
Found at i:4307 original size:50 final size:50
Alignment explanation
Indices: 4218--4341 Score: 153
Period size: 50 Copynumber: 2.5 Consensus size: 50
4208 TATCCCAAAT
* * *
4218 ATGGTCTTACATGGGG--TTCTCATATCGGTGCCCATGCCATGTCCCAGAC
1 ATGGTCTTACA-GGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGAC
* * * *
4267 ATGGTCTTACGGGGGACCTCTCATCTCGGTGCGAACGCCATGTCCTAGAC
1 ATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGAC
*
4317 ATGGTCTTACATGGGACCTCTCATA
1 ATGGTCTTACAGGGGACCTCTCATA
4342 ACCTCAATTA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
48 4 0.06
49 10 0.16
50 49 0.78
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.27
Consensus pattern (50 bp):
ATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGAC
Found at i:7997 original size:37 final size:36
Alignment explanation
Indices: 7946--8091 Score: 159
Period size: 37 Copynumber: 4.0 Consensus size: 36
7936 ACATAAGTAG
* *
7946 TCCAACCGA-AACACGCCAAATGCTCATAAGAGCTAT
1 TCCAACTGATAACACGCCAAATGCTCA-AAGAGCTAA
* *
7982 TCCAACTAATAACACGCCAAGTGCTCCAAAGAGCTAA
1 TCCAACTGATAACACGCCAAATGCT-CAAAGAGCTAA
* *
8019 TCCAACTGATAACACACCAAATGCTCCGAAGAGCTAA
1 TCCAACTGATAACACGCCAAATGCT-CAAAGAGCTAA
* * * *
8056 TCGAACCGATAACACGCCAAATACTTCGAAGAGCTA
1 TCCAACTGATAACACGCCAAATGC-TCAAAGAGCTA
8092 TATATTTGCC
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
36 7 0.07
37 85 0.89
38 3 0.03
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.16
Consensus pattern (36 bp):
TCCAACTGATAACACGCCAAATGCTCAAAGAGCTAA
Found at i:8088 original size:74 final size:73
Alignment explanation
Indices: 7946--8091 Score: 175
Period size: 74 Copynumber: 2.0 Consensus size: 73
7936 ACATAAGTAG
* * * * * *
7946 TCCAACCGAAACACGCCAAATGCTCATAAGAGCTATTCCAACTAATAACACGCCAAGTGCTCCAA
1 TCCAACCGAAACACACCAAATGCTCAGAAGAGCTAATCCAACCAATAACACGCCAAATACTCCAA
8011 AGAGCTAA
66 AGAGCTAA
* * * * * *
8019 TCCAACTGATAACACACCAAATGCTCCGAAGAGCTAATCGAACCGATAACACGCCAAATACTTCG
1 TCCAACCGA-AACACACCAAATGCTCAGAAGAGCTAATCCAACCAATAACACGCCAAATACTCCA
8084 AAGAGCTA
65 AAGAGCTA
8092 TATATTTGCC
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
73 8 0.13
74 52 0.87
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.16
Consensus pattern (73 bp):
TCCAACCGAAACACACCAAATGCTCAGAAGAGCTAATCCAACCAATAACACGCCAAATACTCCAA
AGAGCTAA
Found at i:20081 original size:20 final size:20
Alignment explanation
Indices: 20057--20110 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
20047 TAATTTTTCT
20057 TGTCTTAATTAAATTAAATGA
1 TGTCTTAATTAAATTAAAT-A
* **
20078 -GTCTTGATTTTATTAAATA
1 TGTCTTAATTAAATTAAATA
20097 TGTCTTAAATTAAA
1 TGTCTT-AATTAAA
20111 ACATGAATTA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
19 1 0.04
20 20 0.80
21 4 0.16
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (20 bp):
TGTCTTAATTAAATTAAATA
Found at i:40324 original size:13 final size:13
Alignment explanation
Indices: 40306--40330 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40296 TTAAAACTAA
40306 AATTAACTAAATT
1 AATTAACTAAATT
40319 AATTAACTAAAT
1 AATTAACTAAAT
40331 AACACGACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAACTAAATT
Found at i:45914 original size:60 final size:59
Alignment explanation
Indices: 45849--45961 Score: 172
Period size: 59 Copynumber: 1.9 Consensus size: 59
45839 AATAAATAGA
*
45849 AAATTAAATCTATTTTAAAACATTTTTAAAATTGGGATTTAAATATTTTATATAAGTTTT
1 AAATT-AATCTAATTTAAAACATTTTTAAAATTGGGATTTAAATATTTTATATAAGTTTT
* * * *
45909 AAATTAATTTAATTTAATATATTTTTAAAATTTGGATTTAAATATTTTATATA
1 AAATTAATCTAATTTAAAACATTTTTAAAATTGGGATTTAAATATTTTATATA
45962 GATTTCAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 43 0.90
60 5 0.10
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.50
Consensus pattern (59 bp):
AAATTAATCTAATTTAAAACATTTTTAAAATTGGGATTTAAATATTTTATATAAGTTTT
Found at i:46410 original size:71 final size:70
Alignment explanation
Indices: 46276--46459 Score: 192
Period size: 71 Copynumber: 2.6 Consensus size: 70
46266 GGGTGTTACA
* * ** * *
46276 AGGATATTAAATGAATGA-AGTATCAGTGTTGTGGCAGGATGTTAAATGAATAAGATGTTGGTGT
1 AGGATATTAAATGAATGAGA-TATCGGTGTTGTGGCGGGATGTTAAACAAATAAGATATCGGTGT
**
46340 TGTGGCGG
65 T-AAG-GG
* * *
46348 AGG-TATTAAATGAATGAGATATCGGTATTATGGCGGGATGTTAAACAAATGAGATATCGGTGTT
1 AGGATATTAAATGAATGAGATATCGGTGTTGTGGCGGGATGTTAAACAAATAAGATATCGGTGTT
*
46412 AAGGT
66 AAGGG
* * *
46417 AGGATGTTAAACGATTGAGATATCGGTGTTGTGGCGGGATGTT
1 AGGATATTAAATGAATGAGATATCGGTGTTGTGGCGGGATGTT
46460 GAAGGTATTG
Statistics
Matches: 93, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
69 4 0.04
70 35 0.38
71 50 0.54
72 4 0.04
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.32
Consensus pattern (70 bp):
AGGATATTAAATGAATGAGATATCGGTGTTGTGGCGGGATGTTAAACAAATAAGATATCGGTGTT
AAGGG
Found at i:46457 original size:35 final size:35
Alignment explanation
Indices: 46277--46459 Score: 170
Period size: 35 Copynumber: 5.2 Consensus size: 35
46267 GGTGTTACAA
* * * *
46277 GGATATTAAATGAATGA-AGTATCAGTGTTGTGGCA
1 GGATGTTAAACGAATGAGA-TATCGGTGTTGTGGCG
* * * *
46312 GGATGTTAAATGAATAAGATGTTGGTGTTGTGGCG
1 GGATGTTAAACGAATGAGATATCGGTGTTGTGGCG
* * * * *
46347 GAGGTATTAAATGAATGAGATATCGGTATTATGGCG
1 G-GATGTTAAACGAATGAGATATCGGTGTTGTGGCG
* ** **
46383 GGATGTTAAACAAATGAGATATCGGTGTTAAGGTA
1 GGATGTTAAACGAATGAGATATCGGTGTTGTGGCG
*
46418 GGATGTTAAACGATTGAGATATCGGTGTTGTGGCG
1 GGATGTTAAACGAATGAGATATCGGTGTTGTGGCG
46453 GGATGTT
1 GGATGTT
46460 GAAGGTATTG
Statistics
Matches: 119, Mismatches: 27, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
35 90 0.76
36 29 0.24
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.32
Consensus pattern (35 bp):
GGATGTTAAACGAATGAGATATCGGTGTTGTGGCG
Found at i:64149 original size:22 final size:22
Alignment explanation
Indices: 64124--64167 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
64114 ATAAAATAAA
* *
64124 GAAAAATGTCATAAAGTGAATT
1 GAAAAATATCATAAAGTAAATT
*
64146 GAAATATATCATAAAGTAAATT
1 GAAAAATATCATAAAGTAAATT
64168 ATTTTTTGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.30
Consensus pattern (22 bp):
GAAAAATATCATAAAGTAAATT
Found at i:84359 original size:272 final size:272
Alignment explanation
Indices: 83873--84419 Score: 824
Period size: 272 Copynumber: 2.0 Consensus size: 272
83863 TCTTGGGTTC
*
83873 GATCCTTGGAATACTCTAGTGTTCCATTGTAACACTACAAATATTACAACTGACATGTCACACTT
1 GATCCTTGGAATACTCCAGTGTTCCATTGTAACACTACAAATATTACAACTGACATGTCACACTT
* * * *
83938 GCAGTAAAGCTGCGATATTTATATTCGTTTTAATCCCAGTGTTGATTCTTTTTCTCTCTTTGTTC
66 ACAGTAAAGCCGCGATATTTATACTCGTTTTAATCCCAGTGTTGATTCTTTTTCTCTCTTCGTTC
* * * **
84003 AAGAGGACGGAGATAGGAGCGATCAGTAATAAACGAATATGTTCAATATTCTTTCACGGATAACA
131 AAGAGGACAGAGATAGGAGCGATCAGTAATAAACAAATATGTTCAATATTCTTTAACAAATAACA
* * *
84068 AGCCACAGAGTTTGGCAGACCTCTATAAGAGGGCTCATAGGTTTGCGGAGGCAGAGGAGGTAAAG
196 AGCCACAGAGTTTGGCAGACCTCTATAAGAGGGCTCACAGGTTCGCGAAGGCAGAGGAGGTAAAG
84133 AGGACAACTCAT
261 AGGACAACTCAT
* *
84145 GATCCTTGGAATACTCCAGTGTTCCATTGTAACACTACAAATATTACAACTGACCTGTTACACTT
1 GATCCTTGGAATACTCCAGTGTTCCATTGTAACACTACAAATATTACAACTGACATGTCACACTT
* * *
84210 ACAGTAAAGCCGTGATATTTATACTCGTTTTAATCCTAGTGTTGATTCTTTTTCTCTCTTCGTTT
66 ACAGTAAAGCCGCGATATTTATACTCGTTTTAATCCCAGTGTTGATTCTTTTTCTCTCTTCGTTC
* * * * * *
84275 GAGAGGACAGAGATAGGAGTGGTCAGTAATAAACAAATATGTTCGATATTCTTTAACAAATGATA
131 AAGAGGACAGAGATAGGAGCGATCAGTAATAAACAAATATGTTCAATATTCTTTAACAAATAACA
* * * * * *
84340 GGCCACAGAGTTTGGCAGACTTTTATGAGAGTGCTCACAGGTTCGCGAAGGTAGAGGAGGTAAAG
196 AGCCACAGAGTTTGGCAGACCTCTATAAGAGGGCTCACAGGTTCGCGAAGGCAGAGGAGGTAAAG
84405 AGGACAACTCAT
261 AGGACAACTCAT
84417 GAT
1 GAT
84420 GTTTTGTATA
Statistics
Matches: 245, Mismatches: 30, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
272 245 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (272 bp):
GATCCTTGGAATACTCCAGTGTTCCATTGTAACACTACAAATATTACAACTGACATGTCACACTT
ACAGTAAAGCCGCGATATTTATACTCGTTTTAATCCCAGTGTTGATTCTTTTTCTCTCTTCGTTC
AAGAGGACAGAGATAGGAGCGATCAGTAATAAACAAATATGTTCAATATTCTTTAACAAATAACA
AGCCACAGAGTTTGGCAGACCTCTATAAGAGGGCTCACAGGTTCGCGAAGGCAGAGGAGGTAAAG
AGGACAACTCAT
Found at i:88325 original size:12 final size:12
Alignment explanation
Indices: 88308--88332 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
88298 TTCTAAACTC
88308 TCATTAAAAGTT
1 TCATTAAAAGTT
88320 TCATTAAAAGTT
1 TCATTAAAAGTT
88332 T
1 T
88333 TCAAGGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TCATTAAAAGTT
Found at i:95934 original size:175 final size:174
Alignment explanation
Indices: 95656--96122 Score: 528
Period size: 175 Copynumber: 2.7 Consensus size: 174
95646 ATTACAACAC
* * *
95656 TCAAACTTTAAAGA-TATTCAAAATCTTAGAGCTAGCAATTTAAGATTGCGACTCTCCTTTAAGG
1 TCAAACTTCAAAGACT-TTCAAAATCTTAGAGCTAGC-GTTTAAGATCGCGACTC-CCTTTAAGG
*** * **
95720 TTTTGCGATTTCAA-ATCGCAACCTTCAAACTTCAAAGATTTTCAGAATCTTAAAGCTAGTGATT
63 TTCACCGATTT-AAGATCGCAACCTTCAAACTTTAAAGATTTTCAGAATCTTAAAGCTAGCCATT
* * * *
95784 TAAGATCGTGACATC-CTTTTAAGGTTTGT-TGATTTAAGATTGCAACCT
127 TAAGACCGTGAC-TCTCCTTTAAGGTTT-TCTAATTTAAGATCGCAACCT
* * *
95832 TCAAACTTCAAATACTTTCATAATCTTAGAACTAGCGTTTAAGATCGCGACTCCCTTTTAAGGTT
1 TCAAACTTCAAAGACTTTCAAAATCTTAGAGCTAGCGTTTAAGATCGCGACTCCC-TTTAAGGTT
* * * *
95897 CACCTATTTAAGATTGCAACCTTCAAACTTTAAAGATTTTAAGAATCTTAGAGCTAGCCATTTAA
65 CACCGATTTAAGATCGCAACCTTCAAACTTTAAAGATTTTCAGAATCTTAAAGCTAGCCATTTAA
* * *
95962 GACCGTGGCTCTCCTTTATGGTTTTCTAATTTAATATCGCAACCT
130 GACCGTGACTCTCCTTTAAGGTTTTCTAATTTAAGATCGCAACCT
* * * * * ** *
96007 TCAAACTTCAAAGATTTTCAAAACCATAGAGTTAGCGATTTAAGATGGTAACTCCCCTTTAAAGT
1 TCAAACTTCAAAGACTTTCAAAATCTTAGAGCTAGCG-TTTAAGATCGCGACT-CCCTTTAAGGT
* *
96072 TCGCCGATTTAAGATCACAACCTTCAAACTTTAAAGATTTTCAGAATCTTA
64 TCACCGATTTAAGATCGCAACCTTCAAACTTTAAAGATTTTCAGAATCTTA
96123 GTGTTAGTAA
Statistics
Matches: 245, Mismatches: 39, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
174 7 0.03
175 139 0.57
176 95 0.39
177 4 0.02
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (174 bp):
TCAAACTTCAAAGACTTTCAAAATCTTAGAGCTAGCGTTTAAGATCGCGACTCCCTTTAAGGTTC
ACCGATTTAAGATCGCAACCTTCAAACTTTAAAGATTTTCAGAATCTTAAAGCTAGCCATTTAAG
ACCGTGACTCTCCTTTAAGGTTTTCTAATTTAAGATCGCAACCT
Found at i:96083 original size:263 final size:264
Alignment explanation
Indices: 95587--96123 Score: 672
Period size: 263 Copynumber: 2.0 Consensus size: 264
95577 AAAAATTTTT
* * * *
95587 AGAATCTTATAGCTAGCGATTTAAAATCGCGACTCCCCTTTAAGGTTCACCGATTTCATATTACA
1 AGAATCTTAGAACTAGCGATTTAAAATCGCGACTCCCCTTTAAGGTTCACCGATTTAAGATTACA
**
95652 ACACTCAAACTTTAAAGATATTCAAAATCTTAGAGCTAGCAATTTAAGATTGCGACTCTCCTTTA
66 ACACTCAAACTTTAAAGATATTCAAAATCTTAGAGCTAGCAATTTAAGACCGCGACTCTCCTTTA
* * * * *
95717 AGGTTTTGCGATTTCAAATCGCAACCTTCAAACTTCAAAGATTTTCAGAATCTTAAAGCTAGTGA
131 AGGTTTTGCAATTTCAAATCGCAACCTTCAAACTTCAAAGATTTTCAAAACCATAAAGCTAGCGA
* * * * ** ** *
95782 TTTAAGATCGTGACATCCTTTTAAGGTTTGTTGATTTAAGATTGCAACCTTCAAACTTCAAATAC
196 TTTAAGATCGTAACATCCCTTTAAAGTTCGCCGATTTAAGATCACAACCTTCAAACTTCAAAGAC
95847 TTTC
261 TTTC
* * * * *
95851 ATAATCTTAGAACTAGCG-TTTAAGATCGCGACTCCCTTTTAAGGTTCACCTATTTAAGATTGCA
1 AGAATCTTAGAACTAGCGATTTAAAATCGCGACTCCCCTTTAAGGTTCACCGATTTAAGATTACA
* * * *
95915 AC-CTTCAAACTTTAAAGAT-TTTAAGAATCTTAGAGCTAGCCATTTAAGACCGTGGCTCTCCTT
66 ACAC-TCAAACTTTAAAGATATTCAA-AATCTTAGAGCTAGCAATTTAAGACCGCGACTCTCCTT
* * *
95978 TATGGTTTT-CTAATTT-AATATCGCAACCTTCAAACTTCAAAGATTTTCAAAACCATAGAGTTA
129 TAAGGTTTTGC-AATTTCAA-ATCGCAACCTTCAAACTTCAAAGATTTTCAAAACCATAAAGCTA
* *
96041 GCGATTTAAGATGGTAAC-TCCCCTTTAAAGTTCGCCGATTTAAGATCACAACCTTCAAACTTTA
192 GCGATTTAAGATCGTAACAT-CCCTTTAAAGTTCGCCGATTTAAGATCACAACCTTCAAACTTCA
*
96105 AAGATTTTC
256 AAGACTTTC
96114 AGAATCTTAG
1 AGAATCTTAG
96124 TGTTAGTAAT
Statistics
Matches: 232, Mismatches: 36, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
262 9 0.04
263 208 0.90
264 15 0.06
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.34
Consensus pattern (264 bp):
AGAATCTTAGAACTAGCGATTTAAAATCGCGACTCCCCTTTAAGGTTCACCGATTTAAGATTACA
ACACTCAAACTTTAAAGATATTCAAAATCTTAGAGCTAGCAATTTAAGACCGCGACTCTCCTTTA
AGGTTTTGCAATTTCAAATCGCAACCTTCAAACTTCAAAGATTTTCAAAACCATAAAGCTAGCGA
TTTAAGATCGTAACATCCCTTTAAAGTTCGCCGATTTAAGATCACAACCTTCAAACTTCAAAGAC
TTTC
Found at i:96129 original size:88 final size:88
Alignment explanation
Indices: 95574--96123 Score: 534
Period size: 88 Copynumber: 6.3 Consensus size: 88
95564 ACTTTCGAAT
* * * * *
95574 TTCAAAAATTTTTAGAATCTTATAGCTAGCGATTTAAAATCGCGACTCCCCTTTAAGGTTCACCG
1 TTCAAAGATTTTCAGAATCTTAGAGCTAGCGATTTAAGATCGCGACTCCCCTTTAAGGTTCGCCG
* * **
95639 ATTTCATATTACAACAC-TCAAAC
66 ATTTAAGATCGCAAC-CTTCAAAC
* * * * * * *
95662 TTTAAAGATATTCAAAATCTTAGAGCTAGCAATTTAAGATTGCGACTCTCCTTTAAGGTTTTG-C
1 TTCAAAGATTTTCAGAATCTTAGAGCTAGCGATTTAAGATCGCGACTCCCCTTTAAGG-TTCGCC
95726 GATTTCAA-ATCGCAACCTTCAAAC
65 GATTT-AAGATCGCAACCTTCAAAC
* * * * * **
95750 TTCAAAGATTTTCAGAATCTTAAAGCTAGTGATTTAAGATCGTGACAT-CCTTTTAAGGTTTGTT
1 TTCAAAGATTTTCAGAATCTTAGAGCTAGCGATTTAAGATCGCGAC-TCCCCTTTAAGGTTCGCC
*
95814 GATTTAAGATTGCAACCTTCAAAC
65 GATTTAAGATCGCAACCTTCAAAC
* * * * * * *
95838 TTCAAATACTTTCATAATCTTAGAACTAGCG-TTTAAGATCGCGACTCCCTTTTAAGGTTCACCT
1 TTCAAAGATTTTCAGAATCTTAGAGCTAGCGATTTAAGATCGCGACTCCCCTTTAAGGTTCGCCG
*
95902 ATTTAAGATTGCAACCTTCAAAC
66 ATTTAAGATCGCAACCTTCAAAC
* * * * * * * * ** **
95925 TTTAAAGATTTTAAGAATCTTAGAGCTAGCCATTTAAGACCGTGGCTCTCCTTTATGGTTTTCTA
1 TTCAAAGATTTTCAGAATCTTAGAGCTAGCGATTTAAGATCGCGACTCCCCTTTAAGGTTCGCCG
*
95990 ATTTAATATCGCAACCTTCAAAC
66 ATTTAAGATCGCAACCTTCAAAC
* * * * * ** *
96013 TTCAAAGATTTTCAAAACCATAGAGTTAGCGATTTAAGATGGTAACTCCCCTTTAAAGTTCGCCG
1 TTCAAAGATTTTCAGAATCTTAGAGCTAGCGATTTAAGATCGCGACTCCCCTTTAAGGTTCGCCG
*
96078 ATTTAAGATCACAACCTTCAAAC
66 ATTTAAGATCGCAACCTTCAAAC
*
96101 TTTAAAGATTTTCAGAATCTTAG
1 TTCAAAGATTTTCAGAATCTTAG
96124 TGTTAGTAAT
Statistics
Matches: 372, Mismatches: 82, Indels: 16
0.79 0.17 0.03
Matches are distributed among these distances:
86 1 0.00
87 79 0.21
88 288 0.77
89 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (88 bp):
TTCAAAGATTTTCAGAATCTTAGAGCTAGCGATTTAAGATCGCGACTCCCCTTTAAGGTTCGCCG
ATTTAAGATCGCAACCTTCAAAC
Found at i:98809 original size:93 final size:93
Alignment explanation
Indices: 98494--99185 Score: 821
Period size: 93 Copynumber: 7.4 Consensus size: 93
98484 CCTTAAAAGA
* ** * * * *
98494 GGTTACATGTGTAAGACCATAGTTTGAATATTGCAACATGGGGAGTCCG-CCAGGATAGTAAACA
1 GGTTACATGTGTAAGACCATAGCTTGGCTATGGCAACATGGGGAGTCTGTCGA-GATCGTAAACA
* *
98558 TGGGGTAGTCTACCAGAACATTAAACATG
65 TGGGGTAGTCCACCAGGACATTAAACATG
* * * * *** * *
98587 GTGTTACATGTGTATGACCATAGCTCGGCAATGGCAACATGAGGAGTCCACCGGGATAGTAAACA
1 G-GTTACATGTGTAAGACCATAGCTTGGCTATGGCAACATGGGGAGTCTGTCGAGATCGTAAACA
* * * * *
98652 AGAGTTAGTCCGCCAGGCCA-TAAACATG
65 TGGGGTAGTCCACCAGGACATTAAACATG
* * *
98680 GGTTACATGTGTAAGACCATAGCTTGACTATGGCAACATGAGGAGTCTGTCAAGATCGTAAACAT
1 GGTTACATGTGTAAGACCATAGCTTGGCTATGGCAACATGGGGAGTCTGTCGAGATCGTAAACAT
* *
98745 GGGTTAGTCCGCCAGGACATTAAACATG
66 GGGGTAGTCCACCAGGACATTAAACATG
* * * * *
98773 GGTTATATGTGTAAGACCATAGCTTAGCTGTGGCAACATGGGGAGTCTGTTGAGATTGTAAACAT
1 GGTTACATGTGTAAGACCATAGCTTGGCTATGGCAACATGGGGAGTCTGTCGAGATCGTAAACAT
* ** * *
98838 GGGGTAGTTCGTCAGGATATTAAATATG
66 GGGGTAGTCCACCAGGACATTAAACATG
* *
98866 GGTTACATCTGTAAGACCATAGCTTGGCTATGGCAACATGGGGAGTCTGTCGAGACCGTAAACAT
1 GGTTACATGTGTAAGACCATAGCTTGGCTATGGCAACATGGGGAGTCTGTCGAGATCGTAAACAT
*
98931 GGGGTAGTCCACCAGGACATTAAACGTG
66 GGGGTAGTCCACCAGGACATTAAACATG
* *
98959 GGTTACATGTGTAAGACCATAGCTTGGCTATGGAAACATGGGGAGTCTGTCGAGACCGTAAACAT
1 GGTTACATGTGTAAGACCATAGCTTGGCTATGGCAACATGGGGAGTCTGTCGAGATCGTAAACAT
*
99024 GGGGTAGTCCACCAGGACATTAAACGTG
66 GGGGTAGTCCACCAGGACATTAAACATG
* *
99052 GGTTACATGTGTAAGACCATAGCTTGGCTATGGAAACATGGGGAGTCTGTCGAGACCGTAAACAT
1 GGTTACATGTGTAAGACCATAGCTTGGCTATGGCAACATGGGGAGTCTGTCGAGATCGTAAACAT
* * * * * *
99117 GGGGTAGTCCTCTATGAAAATAAACATAC
66 GGGGTAGTCCACCAGGACATTAAACAT-G
* * * * * *
99146 AGTTACATGTGGAAGACTATAGCTCGACTATGGCAGCATG
1 GGTTACATGTGTAAGACCATAGCTTGGCTATGGCAACATG
99186 TGAAGTCTAC
Statistics
Matches: 522, Mismatches: 73, Indels: 7
0.87 0.12 0.01
Matches are distributed among these distances:
92 70 0.13
93 355 0.68
94 96 0.18
95 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.24
Consensus pattern (93 bp):
GGTTACATGTGTAAGACCATAGCTTGGCTATGGCAACATGGGGAGTCTGTCGAGATCGTAAACAT
GGGGTAGTCCACCAGGACATTAAACATG
Found at i:102904 original size:21 final size:21
Alignment explanation
Indices: 102862--102906 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
102852 AGAACATACA
*
102862 AATATGTGGACAAGCCACCAG
1 AATATGTGGACAAGCCAACAG
*
102883 AATATGTGGATATA-CCAACAG
1 AATATGTGGACA-AGCCAACAG
102904 AAT
1 AAT
102907 GTGTCGATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (21 bp):
AATATGTGGACAAGCCAACAG
Found at i:104436 original size:32 final size:32
Alignment explanation
Indices: 104389--104455 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
104379 AGCTCAGCTC
*
104389 AGCTCGCCACACCACTCAGCTCACCACCGTCT
1 AGCTCGACACACCACTCAGCTCACCACCGTCT
* * *
104421 AGCTCGACACTCCACTCAGGTCACCACTGTCT
1 AGCTCGACACACCACTCAGCTCACCACCGTCT
104453 AGC
1 AGC
104456 CTGCCCACTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.22, C:0.45, G:0.15, T:0.18
Consensus pattern (32 bp):
AGCTCGACACACCACTCAGCTCACCACCGTCT
Found at i:110237 original size:24 final size:24
Alignment explanation
Indices: 110210--110255 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
110200 AGAACAGTCC
* *
110210 CAAAAGGAAATGCAGGAGCAGCTT
1 CAAAAGCAAATGAAGGAGCAGCTT
*
110234 CAAAAGCAAATGAATGAGCAGC
1 CAAAAGCAAATGAAGGAGCAGC
110256 AAAAAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (24 bp):
CAAAAGCAAATGAAGGAGCAGCTT
Found at i:114611 original size:44 final size:43
Alignment explanation
Indices: 114552--114762 Score: 239
Period size: 45 Copynumber: 4.8 Consensus size: 43
114542 GATCGCATTT
* * *
114552 AGTCTTATCCCCCTGAAGTTGCAATGGAGTAGACTAAGCAAGCA
1 AGTCTTATCCTCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
*
114596 AGTCTTGTCCTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATAGCA
1 AGTCTTATCCTCCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCA
*
114641 AATCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCCT-CCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* * *
114685 AGTCTTATCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGATAGCA
1 AGTCTTATCCTCCTGAAGTTGCAGTGGAGCAGACT-AAGA-AGCA
*
114730 AATCTTAT-CTACCTGAAGTTGCAGTGGAGCAGA
1 AGTCTTATCCT-CCTGAAGTTGCAGTGGAGCAGA
114763 TTAGAGCCGA
Statistics
Matches: 144, Mismatches: 13, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
43 2 0.01
44 69 0.48
45 71 0.49
46 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (43 bp):
AGTCTTATCCTCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
Found at i:114658 original size:45 final size:44
Alignment explanation
Indices: 114554--114803 Score: 253
Period size: 44 Copynumber: 5.6 Consensus size: 44
114544 TCGCATTTAG
* * * *
114554 TCTTATCCCCCTGAAGTTGCAATGGAGTAGACTAAGCA-AGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-ATAGCAAA
*
114598 TCTTGTC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATAGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGATAGCAAA
*
114643 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-TAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAT-AGCAAA
* * *
114687 TCTTATCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGATAGCAAA
* *
114732 TCTTATCTACCTGAAGTTGCAGTGGAGCAGA-TTAG--AGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGATAG-C-A-AA
* *
114776 TCCTATCTCCCTGAAGTTGCAGGGGAGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGC
114804 GGATTAAAAC
Statistics
Matches: 178, Mismatches: 16, Indels: 24
0.82 0.07 0.11
Matches are distributed among these distances:
41 2 0.01
42 1 0.01
43 7 0.04
44 92 0.52
45 72 0.40
46 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGATAGCAAA
Found at i:114661 original size:89 final size:89
Alignment explanation
Indices: 114554--114762 Score: 337
Period size: 89 Copynumber: 2.3 Consensus size: 89
114544 TCGCATTTAG
* * * *
114554 TCTTATCCCCCTGAAGTTGCAATGGAGTAGACTAAGCAAGCAAGTCTTGTCCTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCTTATCCTCCTGAAGTTGCA
*
114619 GTGAGGCAGACTGAAGATAGCAAA
66 GTGAAGCAGACTGAAGATAGCAAA
* *
114643 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCTTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCTTATCCTCCTGAAGTTGCA
*
114708 GTGAAGCAGATTGAAGATAGCAAA
66 GTGAAGCAGACTGAAGATAGCAAA
*
114732 TCTTATCTACCTGAAGTTGCAGTGGAGCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
114763 TTAGAGCCGA
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
89 111 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (89 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCTTATCCTCCTGAAGTTGCA
GTGAAGCAGACTGAAGATAGCAAA
Found at i:114783 original size:89 final size:88
Alignment explanation
Indices: 114554--114797 Score: 294
Period size: 89 Copynumber: 2.7 Consensus size: 88
114544 TCGCATTTAG
** * * * * * *
114554 TCTTATCCCCCTGAAGTTGCAATGGAGTAGACTAAGCAAGCAAGTCTTGTCCTCCTGAAGTTGCA
1 TCTTATCTACCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAATCCTATCTTCCTGAAGTTGCA
*
114619 GTGAGGCAGACTGAAGATAGCAAA
65 GTGAAGCAGACTGAAGATAGCAAA
* * *
114643 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCTTCCTGAAGTTGCA
1 TCTTATCTACCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAATCCTATCTTCCTGAAGTTGCA
*
114708 GTGAAGCAGATTGAAGATAGCAAA
65 GTGAAGCAGACTGAAGATAGCAAA
* *
114732 TCTTATCTACCTGAAGTTGCAGTGGAGCAGA-TTAG-AGCCGATAATCCTATCTCCCTGAAGTTG
1 TCTTATCTACCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AATCCTATCTTCCTGAAGTTG
114795 CAG
63 CAG
114798 GGGAGCGGAT
Statistics
Matches: 139, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
86 2 0.01
87 1 0.01
88 4 0.03
89 132 0.95
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (88 bp):
TCTTATCTACCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAATCCTATCTTCCTGAAGTTGCAG
TGAAGCAGACTGAAGATAGCAAA
Found at i:114803 original size:44 final size:42
Alignment explanation
Indices: 114468--114890 Score: 241
Period size: 44 Copynumber: 9.8 Consensus size: 42
114458 GGTAGCCAAT
* ** * * *
114468 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATAAAAATCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAAGCA
* * * ***
114510 AGGATCTTATCTCTCTGAAGTTGCAGAT--AGCAGA-TCGCATTT
1 A--ATCTTATCTCCCTGAAGTTGCAG-TGGAGCAGATTAGAAGCA
* * * * *
114552 AGTCTTATCCCCCTGAAGTTGCAATGGAGTAGACTAAGCAAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAG-AAGCA
* * *
114596 AGTCTTGTC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATAGCA
1 AATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-T-TAGA-AGCA
*
114641 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAG-AAGCA
* * *
114685 AGTCTTATCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT--AGA-AGCA
*
114730 AATCTTATCTACCTGAAGTTGCAGTGGAGCAGATTAG-AGCCGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAAG-C-A
* * * * *
114773 TAATCCTATCTCCCTGAAGTTGCAGGGGAGCGGATTAAAACCTTA
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAAGC--A
* * * * * * * *
114818 GATCTTATCTCTCTGAAGTTGCAG-AGAGCATA-TCGCATCT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAAGCA
* * *
114858 AGTCTTATCTCCTTCAAGTTGCAGTGGAGCAGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
114891 CTAATGGAGT
Statistics
Matches: 299, Mismatches: 58, Indels: 49
0.74 0.14 0.12
Matches are distributed among these distances:
39 1 0.00
40 38 0.13
41 13 0.04
42 8 0.03
43 17 0.06
44 142 0.47
45 77 0.26
46 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (42 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAAGCA
Found at i:120926 original size:21 final size:22
Alignment explanation
Indices: 120900--120945 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
120890 AATCTATATA
120900 TATACATGT-ATATTTATTTTT
1 TATACATGTAATATTTATTTTT
120921 TATACATGTACATATTTATTTTT
1 TATACATGTA-ATATTTATTTTT
120944 TA
1 TA
120946 ACTAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 9 0.39
23 14 0.61
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (22 bp):
TATACATGTAATATTTATTTTT
Found at i:121280 original size:16 final size:16
Alignment explanation
Indices: 121259--121291 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
121249 TTACGCACTC
121259 TCTTTTCTTTT-TTTTT
1 TCTTTT-TTTTATTTTT
121275 TCTTTTTTTTATTTTT
1 TCTTTTTTTTATTTTT
121291 T
1 T
121292 TGTTGATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (16 bp):
TCTTTTTTTTATTTTT
Found at i:121421 original size:19 final size:20
Alignment explanation
Indices: 121380--121421 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
121370 ATTTCTCTGC
* *
121380 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
121400 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
121419 CAT
1 CAT
121422 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:129811 original size:89 final size:90
Alignment explanation
Indices: 129710--129887 Score: 241
Period size: 97 Copynumber: 1.9 Consensus size: 90
129700 AAAAATTTAT
* *
129710 AGAAACTTTATGG-TTACCATTTCTCAATAAAAGCACAATTCACTTGGCTCTTTTCTAGTGGATA
1 AGAAACTTTATGGATTACCATTTCTCAATAAAAGCACAATTCACATGGCTATTTTCTAGTGGATA
*
129774 AAATGGACGGTGGCTGCAAATTGAC
66 AAACGGACGGTGGCTGCAAATTGAC
*
129799 AGAAACTTTATGGTTACCAACTTACCATTTCTCAATAAAAGCACAATTTACATGGCTATTTTCTA
1 AGAAACTTTATGG------A-TTACCATTTCTCAATAAAAGCACAATTCACATGGCTATTTTCTA
*
129864 GTGGTTAAAACGGACGGTGGCTGC
59 GTGGATAAAACGGACGGTGGCTGC
129888 CCCTAATTAA
Statistics
Matches: 76, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
89 13 0.17
97 63 0.83
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (90 bp):
AGAAACTTTATGGATTACCATTTCTCAATAAAAGCACAATTCACATGGCTATTTTCTAGTGGATA
AAACGGACGGTGGCTGCAAATTGAC
Found at i:132451 original size:24 final size:23
Alignment explanation
Indices: 132398--132451 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 23
132388 AGTAAATCAC
* *
132398 TAAATTGTTAAAAATTTTCTTAA
1 TAAATTATTAAAAAATTTCTTAA
* *
132421 AACAATTATTAAAAAATTTCTTTAT
1 TA-AATTATTAAAAAATTTC-TTAA
132446 TAAATT
1 TAAATT
132452 TAAATATATA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
23 1 0.04
24 19 0.79
25 4 0.17
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (23 bp):
TAAATTATTAAAAAATTTCTTAA
Found at i:137275 original size:49 final size:47
Alignment explanation
Indices: 137212--137313 Score: 116
Period size: 49 Copynumber: 2.1 Consensus size: 47
137202 ACGAATAAAT
* * *
137212 ATAAATATAAATATTTATATTAAATACA-AGATCTGAACAAATAATATAA
1 ATAAATATAAATATTTAT-GTAAAAACACAGATCT-AAAAAATAAT-TAA
**
137261 ATAAATATTTATATTTATGTAAAAACATCAGATCTAAAAAATAATTAA
1 ATAAATATAAATATTTATGTAAAAACA-CAGATCTAAAAAATAATTAA
137309 ATAAA
1 ATAAA
137314 CAAGATCTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
48 15 0.33
49 25 0.54
50 6 0.13
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (47 bp):
ATAAATATAAATATTTATGTAAAAACACAGATCTAAAAAATAATTAA
Found at i:138504 original size:21 final size:21
Alignment explanation
Indices: 138472--138517 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
138462 TATAAAATTC
138472 TTATTTTTAAT-A-TTATAAT
1 TTATTTTTAATAACTTATAAT
138491 ATTATTTTTAAATAACTTATAAT
1 -TTATTTTT-AATAACTTATAAT
138514 TTAT
1 TTAT
138518 AATATTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.35
21 3 0.13
22 5 0.22
23 7 0.30
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTTTAATAACTTATAAT
Found at i:138909 original size:13 final size:13
Alignment explanation
Indices: 138891--138918 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
138881 ATTATTATTT
138891 AAACTTTCTTTTA
1 AAACTTTCTTTTA
138904 AAACTTTCTTTTA
1 AAACTTTCTTTTA
138917 AA
1 AA
138919 TTAACTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (13 bp):
AAACTTTCTTTTA
Found at i:143603 original size:9 final size:9
Alignment explanation
Indices: 143589--143614 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
143579 CAATTTCAAG
143589 AATCAAGAA
1 AATCAAGAA
143598 AATCAAGAA
1 AATCAAGAA
143607 AATCAAGA
1 AATCAAGA
143615 TTGCAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.12, G:0.12, T:0.12
Consensus pattern (9 bp):
AATCAAGAA
Found at i:146268 original size:31 final size:32
Alignment explanation
Indices: 146233--146310 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 32
146223 TAAACATCAA
* *
146233 TACATAGTAAC-TGATATAATATGGTCACTGG
1 TACATAGTAACTTGATATAATATAGTCACCGG
*
146264 TACATAGT-ACTTGATATAATATAGTCACCGT
1 TACATAGTAACTTGATATAATATAGTCACCGG
146295 TACATAGT-ACTTGATA
1 TACATAGTAACTTGATA
146311 CTTCAAAACC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 2 0.05
31 41 0.95
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (32 bp):
TACATAGTAACTTGATATAATATAGTCACCGG
Found at i:149615 original size:42 final size:42
Alignment explanation
Indices: 149566--149703 Score: 161
Period size: 42 Copynumber: 3.3 Consensus size: 42
149556 CTGGCATCGT
*
149566 AGTGCATCATCGGATAAATTGAAGGAAATATACTGGCA-ATTA
1 AGTGCATCATCGGATAAATTGAAGCAAATATACTGGCACA-TA
* * * * *
149608 GGTGCATCATCGGACAAGTTGAAGCAATTATATTGGCACATA
1 AGTGCATCATCGGATAAATTGAAGCAAATATACTGGCACATA
* ** * *
149650 AGTGCATCATCGGATGAACCGAACCAAATATACTTGCACATA
1 AGTGCATCATCGGATAAATTGAAGCAAATATACTGGCACATA
149692 AGTGCATCATCG
1 AGTGCATCATCG
149704 ACCAAACCAA
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
42 78 0.99
43 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (42 bp):
AGTGCATCATCGGATAAATTGAAGCAAATATACTGGCACATA
Found at i:149721 original size:42 final size:41
Alignment explanation
Indices: 149636--149759 Score: 142
Period size: 42 Copynumber: 3.0 Consensus size: 41
149626 TTGAAGCAAT
* * **
149636 TATATTGGCACATAAGTGCATCATCGGA-TGAACCGAACCAAA
1 TATATT-GCACATAAGTGCATCATC-GACTAAACCAAAGTAAA
*
149678 TATACTTGCACATAAGTGCATCATCGACCAAACCAAAGTAAA
1 TATA-TTGCACATAAGTGCATCATCGACTAAACCAAAGTAAA
* *
149720 TATATTGACACATAATTGCATCATCGACTAAACTAAAGTA
1 TATATTG-CACATAAGTGCATCATCGACTAAACCAAAGTA
149760 TAGACCCATA
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
41 5 0.07
42 64 0.90
43 2 0.03
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (41 bp):
TATATTGCACATAAGTGCATCATCGACTAAACCAAAGTAAA
Found at i:170209 original size:18 final size:20
Alignment explanation
Indices: 170173--170210 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
170163 CTTTGTTAAA
170173 TTTTATTTTATTAAATCTTG
1 TTTTATTTTATTAAATCTTG
170193 TTTTATTTT-TT-AATCTTG
1 TTTTATTTTATTAAATCTTG
170211 GGGGTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
20 9 0.50
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTATTTTATTAAATCTTG
Found at i:171108 original size:53 final size:53
Alignment explanation
Indices: 171025--171233 Score: 267
Period size: 53 Copynumber: 3.9 Consensus size: 53
171015 GGCACTAAAG
* * * *
171025 GACCATATCGTGCAAGATCGTATCTGGTGGGTTATGACATCATAT-GAGAAGAA
1 GACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGGA-AAGAA
* * *
171078 GACCATATTGTGTAAGACCGTAACTGGTGGGTTGTGGCATCATATGGAAAAAA
1 GACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGGAAAGAA
* *
171131 GACCATATCGTGTAAGAACGTAACTGCTGGGTTATGGCATCATATGGAAAGAA
1 GACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGGAAAGAA
* * * * * *
171184 TACCACATCATGTAAGACCATAACTGGTGGGTCATGTCATCATATGGAAA
1 GACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGGAAA
171234 AATTTAGGAA
Statistics
Matches: 135, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
53 133 0.99
54 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (53 bp):
GACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGGAAAGAA
Found at i:182016 original size:1 final size:1
Alignment explanation
Indices: 181937--182006 Score: 95
Period size: 1 Copynumber: 70.0 Consensus size: 1
181927 CTTTCTTCTG
*****
181937 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAAAATTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
182002 TTTTT
1 TTTTT
182007 GTCTATTTTT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:192902 original size:20 final size:20
Alignment explanation
Indices: 192865--192912 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
192855 TAAATTTTTA
*
192865 TATTTT-ACCTTTATTATTT
1 TATTTTGACCTTTAATATTT
*
192884 TATTTTGACTTTTAATATTT
1 TATTTTGACCTTTAATATTT
192904 TATTGTTGA
1 TATT-TTGA
192913 TGTAGCACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.24
20 15 0.60
21 4 0.16
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (20 bp):
TATTTTGACCTTTAATATTT
Found at i:196686 original size:15 final size:15
Alignment explanation
Indices: 196666--196695 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
196656 CTCTTTCTTC
196666 AGAATGAGATGCCAA
1 AGAATGAGATGCCAA
*
196681 AGAATGATATGCCAA
1 AGAATGAGATGCCAA
196696 TATTCTTCTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.13, G:0.23, T:0.17
Consensus pattern (15 bp):
AGAATGAGATGCCAA
Found at i:197634 original size:43 final size:43
Alignment explanation
Indices: 197568--197827 Score: 378
Period size: 43 Copynumber: 6.1 Consensus size: 43
197558 TTTTATAAAT
** *
197568 GCCGCTAAAGGTCATGACTTTTAGCGGCGCTTCTACCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAAC
* *
197611 GCCGCTAAAGATCATGACCTTTAGCGGCGCTTC-CCCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAAC
* ** *
197653 GCCGCTAAAGAACAAGACCTTTAGTTGCGCTTCTACCACAAAT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAAC
* * *
197696 GCCACGAAAGAACATGACCTTTAGCGGCGATTCTACCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAAC
*
197739 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCATAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAAC
* *
197782 GCCGCTAAAGATCATGACCTTTAGCGGCGCTTATACCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAAC
197825 GCC
1 GCC
197828 ACTATAAGGA
Statistics
Matches: 193, Mismatches: 23, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
42 37 0.19
43 156 0.81
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (43 bp):
GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAAC
Found at i:197771 original size:86 final size:86
Alignment explanation
Indices: 197568--197882 Score: 372
Period size: 86 Copynumber: 3.7 Consensus size: 86
197558 TTTTATAAAT
** * * *
197568 GCCGCTAAAGGTCATGACTTTTAGCGGCGCTTCTACCACAAACGCCGCTAAAGATCATGACCTTT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAACGCCACTAAAGAACATGACCTTT
*
197633 AGCGGCGCTTC-CCCACAAAC
66 AGCGGCGCTTCTACCACAAAC
* ** * *
197653 GCCGCTAAAGAACAAGACCTTTAGTTGCGCTTCTACCACAAATGCCACGAAAGAACATGACCTTT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAACGCCACTAAAGAACATGACCTTT
*
197718 AGCGGCGATTCTACCACAAAC
66 AGCGGCGCTTCTACCACAAAC
* * *
197739 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCATAAACGCCGCTAAAGATCATGACCTTT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAACGCCACTAAAGAACATGACCTTT
*
197804 AGCGGCGCTTATACCACAAAC
66 AGCGGCGCTTCTACCACAAAC
* * * * * *
197825 GCCACTATAAG--GATGGCTTTTAGCGGCGCTTTTTA--ACAAATGCCACTAAA-AACATGAC
1 GCCGCTA-AAGAACATGACCTTTAGCGGCGC-TTCTACCACAAACGCCACTAAAGAACATGAC
197883 TTTTTAAAAA
Statistics
Matches: 196, Mismatches: 31, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
83 7 0.04
84 12 0.06
85 80 0.41
86 94 0.48
87 3 0.02
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (86 bp):
GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAACGCCACTAAAGAACATGACCTTT
AGCGGCGCTTCTACCACAAAC
Found at i:197847 original size:128 final size:127
Alignment explanation
Indices: 197580--197852 Score: 386
Period size: 128 Copynumber: 2.1 Consensus size: 127
197570 CGCTAAAGGT
* * *
197580 CATGACTTTTAGCGGCGCTTCTACCACAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTCC
1 CATGACTTTTAGCGGCGATTCTACCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTCA
** * *
197645 CCACAAACGCCGCTAAAGAACAAGACCTTTAGTTGCGCTTCTACCACAAATGCCACGAAAGAA
66 CCACAAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTATACCACAAACGCCACGAAAG-A
*
197708 CATGACCTTTAGCGGCGATTCTACCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTCT
1 CATGACTTTTAGCGGCGATTCTACCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTC-
* * * *
197773 ACCATAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTATACCACAAACGCCACTATAAG-
65 ACCACAAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTATACCACAAACGCCACGA-AAGA
* *
197836 GATGGCTTTTAGCGGCG
1 CATGACTTTTAGCGGCG
197853 CTTTTTAACA
Statistics
Matches: 128, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
128 75 0.59
129 50 0.39
130 3 0.02
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.21
Consensus pattern (127 bp):
CATGACTTTTAGCGGCGATTCTACCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTCA
CCACAAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTATACCACAAACGCCACGAAAGA
Found at i:197888 original size:42 final size:42
Alignment explanation
Indices: 197580--197882 Score: 317
Period size: 43 Copynumber: 7.1 Consensus size: 42
197570 CGCTAAAGGT
* * *
197580 CATGACTTTTAGCGGCGCTTCTACCACAAACGCCGCTAAAGAT
1 CATGACCTTTAGCGGCGCTTCTA-CACAAACGCCACTAAAGAA
** *
197623 CATGACCTTTAGCGGCGCTTCCCCACAAACGCCGCTAAAGAA
1 CATGACCTTTAGCGGCGCTTCTACACAAACGCCACTAAAGAA
* ** * *
197665 CAAGACCTTTAGTTGCGCTTCTACCACAAATGCCACGAAAGAA
1 CATGACCTTTAGCGGCGCTTCTA-CACAAACGCCACTAAAGAA
* *
197708 CATGACCTTTAGCGGCGATTCTACCACAAACGCCGCTAAAGAA
1 CATGACCTTTAGCGGCGCTTCTA-CACAAACGCCACTAAAGAA
* * *
197751 CATGACCTTTAGCGGCGCTTCTACCATAAACGCCGCTAAAGAT
1 CATGACCTTTAGCGGCGCTTCTA-CACAAACGCCACTAAAGAA
*
197794 CATGACCTTTAGCGGCGCTTATACCACAAACGCCACTATAAG--
1 CATGACCTTTAGCGGCGCTTCTA-CACAAACGCCACTA-AAGAA
* * * * *
197836 GATGGCTTTTAGCGGCGCTTTTTA-ACAAATGCCACTAAA-AA
1 CATGACCTTTAGCGGCGC-TTCTACACAAACGCCACTAAAGAA
197877 CATGAC
1 CATGAC
197883 TTTTTAAAAA
Statistics
Matches: 223, Mismatches: 32, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
40 2 0.01
41 16 0.07
42 51 0.23
43 151 0.68
44 3 0.01
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (42 bp):
CATGACCTTTAGCGGCGCTTCTACACAAACGCCACTAAAGAA
Found at i:199056 original size:27 final size:27
Alignment explanation
Indices: 199026--199079 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
199016 AATAACCTGG
199026 GTATATATATAATTTATATTCACATGA
1 GTATATATATAATTTATATTCACATGA
*
199053 GTATATATATAATTTATATTTACATGA
1 GTATATATATAATTTATATTCACATGA
199080 AATTAATCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (27 bp):
GTATATATATAATTTATATTCACATGA
Found at i:200527 original size:15 final size:16
Alignment explanation
Indices: 200507--200536 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
200497 AAAAAAAGAA
200507 AAGC-AATTATAAAAG
1 AAGCAAATTATAAAAG
200522 AAGCAAATTATAAAA
1 AAGCAAATTATAAAA
200537 CCCAGAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.63, C:0.07, G:0.10, T:0.20
Consensus pattern (16 bp):
AAGCAAATTATAAAAG
Found at i:205216 original size:73 final size:72
Alignment explanation
Indices: 205071--205229 Score: 210
Period size: 73 Copynumber: 2.2 Consensus size: 72
205061 ACAATAAGCA
* * * *
205071 TTAGCGGCGTTTTTTAAAAAGCGCCACAAAAAACCTAAGCCCAACGACACCATTTTCTGAGCTTT
1 TTAGCAGCGTTTTTGAAAAAGAGCCACAAAAAACCTAAGCCAAACGACACCATTTTCTGAGCTTT
205136 TGGGGAT
66 TGGGGAT
* * ** * * *
205143 TTAGCTGCGTTTTTGAGAAAGAGCCGTAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCTT
1 TTAGCAGCGTTTTTGAAAAAGAGCCACAAAAAACCTAAGCC-AAACGACACCATTTTCTGAGCTT
205208 TTGGGGAT
65 TTGGGGAT
205216 TTAGCAGCGTTTTT
1 TTAGCAGCGTTTTT
205230 AAGTAAGTGC
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
72 35 0.47
73 40 0.53
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (72 bp):
TTAGCAGCGTTTTTGAAAAAGAGCCACAAAAAACCTAAGCCAAACGACACCATTTTCTGAGCTTT
TGGGGAT
Found at i:205290 original size:114 final size:114
Alignment explanation
Indices: 205142--205648 Score: 780
Period size: 114 Copynumber: 4.4 Consensus size: 114
205132 CTTTTGGGGA
* * * *
205142 TTTAGCTGCGTTTTTGAGAAAGAGCCGTAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATGACGCCGTTTTGTGAGCT
* * * *
205207 TTTGGGGATTTAGCAGCGTTTTTAAGTAAGTGCCGCTAATGCTCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGC
*
205256 TTTAGCGGCGTTTTTGAGAAAGTGCCGCAAAAAACCTAAGCCAAAATGACGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATGACGCCGTTTTGTGAGCT
*
205321 TTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGTTCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGC
* *
205370 TTTTAGTGGCATTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATGACGCCGTTTTGTGAGC
1 -TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATGACGCCGTTTTGTGAGC
*
205435 TTTCGGGGATTTAGCGGCGTTTTTAAGCAAGCGCCGCTAAAGCCGCTAATGCTCAGGGC
65 TTTCGGGGATTTAGCGGCGTTTTTAAGGAA-----GC----GCCGCTAATGCTCAGGGC
*
205494 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATAACGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATGACGCCGTTTTGTGAGCT
*
205559 TTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTTAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGC
*
205608 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGC
205649 GCTTTCGGGG
Statistics
Matches: 363, Mismatches: 20, Indels: 20
0.90 0.05 0.05
Matches are distributed among these distances:
114 162 0.45
115 90 0.25
118 2 0.01
120 2 0.01
123 90 0.25
124 17 0.05
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (114 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATGACGCCGTTTTGTGAGCT
TTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGC
Found at i:205561 original size:238 final size:228
Alignment explanation
Indices: 205142--205648 Score: 791
Period size: 238 Copynumber: 2.2 Consensus size: 228
205132 CTTTTGGGGA
* * * *
205142 TTTAGCTGCGTTTTTGAGAAAGAGCCGTAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
1 TTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
* *
205207 TTTGGGGATTTAGCAGCGTTTTTAAGTAAGTGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
66 TTCGGGGATTTAGCAGCGTTTTTAAGCAAGTGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
* *
205272 AGAAAGTGCCGCAAAAAACCTAAGCCAAAATGACGCCGTTTTGTGAGCTTTCGGGGATTTAGCGG
131 AGAAAGCGCCGCAAAAAACCTAAGCCAAAATAACGCCGTTTTGTGAGCTTTCGGGGATTTAGCGG
205337 CGTTTTTAAGGAAGCGCCGCTAATG-TTCAGGGC
196 CGTTTTTAAGGAAGCGCCGCTAATGCTT-AGGGC
* *
205370 TTTTAGTGGCATTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATGACGCCGTTTTGTGAGC
1 -TTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGC
*
205435 TTTCGGGGATTTAGCGGCGTTTTTAAGCAAGCGCCGCTAAAGCCGCTAATGCTCAGGGCTTTAGC
65 TTTCGGGGATTTAGCAGCGTTTTTAAGCAA-----G-T---GCCGCTAATGCTCAGGGCTTTAGC
205500 GGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATAACGCCGTTTTGTGAGCTTTCGGG
121 GGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATAACGCCGTTTTGTGAGCTTTCGGG
205565 GATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTTAGGGC
186 GATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTTAGGGC
* *
205608 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGC
1 TTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAACCTAAGC
205649 GCTTTCGGGG
Statistics
Matches: 254, Mismatches: 14, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
229 85 0.33
234 1 0.00
235 1 0.00
237 38 0.15
238 127 0.50
239 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (228 bp):
TTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
TTCGGGGATTTAGCAGCGTTTTTAAGCAAGTGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
AGAAAGCGCCGCAAAAAACCTAAGCCAAAATAACGCCGTTTTGTGAGCTTTCGGGGATTTAGCGG
CGTTTTTAAGGAAGCGCCGCTAATGCTTAGGGC
Found at i:206009 original size:29 final size:29
Alignment explanation
Indices: 205975--206056 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
205965 TTTAAAGGCT
205975 GGGTTTAAGG-TTTAGAGG-TTATGAGTTAA
1 GGGTTTAAGGTTTTA-AGGTTTA-GAGTTAA
* *
206004 GGGTTTAGGGTTTTAAGGTTTAGAGTTTA
1 GGGTTTAAGGTTTTAAGGTTTAGAGTTAA
* *
206033 GGGTTTTAAGAGTATTAGGGTTTA
1 GGG-TTTAAG-GTTTTAAGGTTTA
206057 CGTTTTAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
29 21 0.48
30 12 0.27
31 11 0.25
ACGTcount: A:0.24, C:0.00, G:0.34, T:0.41
Consensus pattern (29 bp):
GGGTTTAAGGTTTTAAGGTTTAGAGTTAA
Found at i:206025 original size:15 final size:16
Alignment explanation
Indices: 206000--206056 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 16
205990 AGGTTATGAG
*
206000 TTAAGGGTTTAGGGTT
1 TTAAGGGTTTAGAGTT
206016 TTAA-GGTTTAGAG-T
1 TTAAGGGTTTAGAGTT
*
206030 TT-AGGGTTTTAAGAGTA
1 TTAAGGG-TTT-AGAGTT
206047 TT-AGGGTTTA
1 TTAAGGGTTTA
206057 CGTTTTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 1 0.03
14 5 0.14
15 12 0.34
16 11 0.31
17 6 0.17
ACGTcount: A:0.25, C:0.00, G:0.32, T:0.44
Consensus pattern (16 bp):
TTAAGGGTTTAGAGTT
Found at i:206031 original size:22 final size:24
Alignment explanation
Indices: 206006--206064 Score: 79
Period size: 22 Copynumber: 2.6 Consensus size: 24
205996 TGAGTTAAGG
206006 GTTTAGGGTTTTAAG-GT-TTAGA
1 GTTTAGGGTTTTAAGAGTATTAGA
*
206028 GTTTAGGGTTTTAAGAGTATTAGG
1 GTTTAGGGTTTTAAGAGTATTAGA
*
206052 GTTTA-CGTTTTAA
1 GTTTAGGGTTTTAA
206065 TAAGTACAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 15 0.45
23 9 0.27
24 9 0.27
ACGTcount: A:0.24, C:0.02, G:0.29, T:0.46
Consensus pattern (24 bp):
GTTTAGGGTTTTAAGAGTATTAGA
Found at i:206131 original size:12 final size:12
Alignment explanation
Indices: 206114--206151 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
206104 GATATCCCTT
*
206114 TTTTTAATAAGA
1 TTTTTAATAAAA
206126 TTTTT-ATAAAA
1 TTTTTAATAAAA
*
206137 TTTTTAAAAAAA
1 TTTTTAATAAAA
206149 TTT
1 TTT
206152 CATTTTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (12 bp):
TTTTTAATAAAA
Found at i:208516 original size:54 final size:54
Alignment explanation
Indices: 208458--208567 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
208448 TCAATACAAT
208458 TAGCGGTGGTGCCATTTTTTTCTTACTTGAGTAGCTCCTACACAAAACTGATGC
1 TAGCGGTGGTGCCATTTTTTTCTTACTTGAGTAGCTCCTACACAAAACTGATGC
208512 TAGCGGTGGTGCCATTTTTTTCTTACTTGAGTAGCTCCTACACAAAACTGATGC
1 TAGCGGTGGTGCCATTTTTTTCTTACTTGAGTAGCTCCTACACAAAACTGATGC
208566 TA
1 TA
208568 TGTTGTGTCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (54 bp):
TAGCGGTGGTGCCATTTTTTTCTTACTTGAGTAGCTCCTACACAAAACTGATGC
Found at i:210308 original size:43 final size:43
Alignment explanation
Indices: 210285--210531 Score: 415
Period size: 43 Copynumber: 5.7 Consensus size: 43
210275 TTACCAAAAA
* * *
210285 CGCCGCTAAAGGTCATGTCCTTTAGCGGCGTTTGTAGAG-AAAG
1 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGT-GGGTAAAG
* *
210328 TGCCGCTAAAGATTATGTTCTTTAGCGGCGTTTGTGGGTAAAG
1 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGTAAAG
*
210371 CACCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGTAAAG
1 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGTAAAG
*
210414 CGCCGCTAAAGCTCATGTTCTTTAGCGGCGTTTGTGGGTAAAG
1 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGTAAAG
210457 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGTAAAG
1 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGTAAAG
210500 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTT
1 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTT
210532 GTCAATAGCG
Statistics
Matches: 192, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
42 2 0.01
43 190 0.99
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (43 bp):
CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGTAAAG
Found at i:210783 original size:116 final size:117
Alignment explanation
Indices: 210642--210856 Score: 335
Period size: 117 Copynumber: 1.8 Consensus size: 117
210632 GCGGCGTTTT
* * *
210642 TATTTTATTTGGAATAAAATGACACTATTTTGCTAT-AT-AAAATGGCGCTAATTTTTTAAACTA
1 TATTTCATTTGGAATAAAACGACACTATTTTGCTATGATAAAAATCGCGCT-ATTTTTTAAACTA
210705 AAATTATTTTTGGTGGCGTTTTTTATAAAAACGCCGCTAACGCCGCAAAAAAG
65 AAATTATTTTTGGTGGCGTTTTTTATAAAAACGCCGCTAACGCCGCAAAAAAG
* * * *
210758 TATTTCATTTGGAATAAAACGACACTGTTTTGCTATGCTAAAAATCTCGCTATTTTTTAAAGTAA
1 TATTTCATTTGGAATAAAACGACACTATTTTGCTATGATAAAAATCGCGCTATTTTTTAAACTAA
*
210823 AATTATTTTTTGTGGCGTTTTTTATAAAAACGCC
66 AATTATTTTTGGTGGCGTTTTTTATAAAAACGCC
210857 CAAAAAATTT
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
116 33 0.37
117 47 0.53
118 9 0.10
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (117 bp):
TATTTCATTTGGAATAAAACGACACTATTTTGCTATGATAAAAATCGCGCTATTTTTTAAACTAA
AATTATTTTTGGTGGCGTTTTTTATAAAAACGCCGCTAACGCCGCAAAAAAG
Found at i:211385 original size:14 final size:14
Alignment explanation
Indices: 211305--211388 Score: 55
Period size: 14 Copynumber: 5.9 Consensus size: 14
211295 TAAACCCTAA
211305 CCCAACCCTTAAAT
1 CCCAACCCTTAAAT
*
211319 CCTAAACCC-TAAAT
1 CC-CAACCCTTAAAT
** *
211333 CCCTAACTATT-AAC
1 CCC-AACCCTTAAAT
* *
211347 CCCTAACCCCTAACT
1 CCC-AACCCTTAAAT
* *
211362 CCTAAACCTTAAAT
1 CCCAACCCTTAAAT
211376 CCCAACCCTTAAA
1 CCCAACCCTTAAA
211389 CCATAATCCC
Statistics
Matches: 50, Mismatches: 16, Indels: 8
0.68 0.22 0.11
Matches are distributed among these distances:
14 41 0.82
15 9 0.18
ACGTcount: A:0.37, C:0.40, G:0.00, T:0.23
Consensus pattern (14 bp):
CCCAACCCTTAAAT
Found at i:218672 original size:171 final size:168
Alignment explanation
Indices: 218337--218714 Score: 531
Period size: 171 Copynumber: 2.2 Consensus size: 168
218327 CCAAATCTGC
* * * *
218337 AACCAGCTCTACTGCAACTGATGGAGGCAAGGTTTTATTTTCGATCTGCTTCGCTGTTAACGCAG
1 AACCAGCTCCATTGCAACCGATGGAGGCAAGG--CT-TTTTCGATCTGCTTCGCTGTTAACGCAG
* * *
218402 GAAGGCAAGATCTGTTATCTTTGACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTTTAGATC
63 GAAGGCAAAATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGACGCAAGGCTTTTTAGATC
*
218467 TGCTTCGCTGTTAATACAGGAAGGCAAAATCTGCTATCTTT
128 TGCTTCGCTGTTAACACAGGAAGGCAAAATCTGCTATCTTT
* *
218508 GACCAGCTCCATTGCAACCGATGGAGGCAAGGCTTTTTCGATCTGCTTCGCTGTTAATGCAGGAA
1 AACCAGCTCCATTGCAACCGATGGAGGCAAGGCTTTTTCGATCTGCTTCGCTGTTAACGCAGGAA
* * * *
218573 GGCAAAATCTGCTATCTTTGACTAGCTCCACTGCAACCGATGGACGCAATGCTTTGTTTTCGATT
66 GGCAAAATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGACGCAAGGC--T-TTTTAGATC
* * *
218638 TGCTTTGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTT
128 TGCTTCGCTGTTAACACAGGAAGGCAAAATCTGCTATCTTT
* *
218679 AACCAGCTCCATTACAACCGATAGAGGCAAGGCTTT
1 AACCAGCTCCATTGCAACCGATGGAGGCAAGGCTTT
218715 GTTTTCGATT
Statistics
Matches: 184, Mismatches: 20, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
168 77 0.42
169 1 0.01
170 1 0.01
171 105 0.57
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (168 bp):
AACCAGCTCCATTGCAACCGATGGAGGCAAGGCTTTTTCGATCTGCTTCGCTGTTAACGCAGGAA
GGCAAAATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGACGCAAGGCTTTTTAGATCTGC
TTCGCTGTTAACACAGGAAGGCAAAATCTGCTATCTTT
Found at i:218725 original size:87 final size:86
Alignment explanation
Indices: 218338--218723 Score: 537
Period size: 84 Copynumber: 4.5 Consensus size: 86
218328 CAAATCTGCA
* * *
218338 ACCAGCTCTACTGCAACTGATGGAGGCAAGGTTTTATTTTCGATCTGCTTCGCTGTTAACGCAGG
1 ACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTT-TTTTCGATCTGCTTCGCTGTTAACGCAGG
* *
218403 AAGGCAAGATCTGTTATCTTTG
65 AAGGCAAAATCTGCTATCTTTG
* **
218425 ACCAGCTCCACTGCAACCGATGGAGGCAAGGC--TTTTTAGATCTGCTTCGCTGTTAATACAGGA
1 ACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTTTTTCGATCTGCTTCGCTGTTAACGCAGGA
218488 AGGCAAAATCTGCTATCTTTG
66 AGGCAAAATCTGCTATCTTTG
* *
218509 ACCAGCTCCATTGCAACCGATGGAGGCAAGGC--TTTTTCGATCTGCTTCGCTGTTAATGCAGGA
1 ACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTTTTTCGATCTGCTTCGCTGTTAACGCAGGA
218572 AGGCAAAATCTGCTATCTTTG
66 AGGCAAAATCTGCTATCTTTG
* * * * *
218593 ACTAGCTCCACTGCAACCGATGGACGCAATGCTTTGTTTTCGATTTGCTTTGCTGTTAACGCAGG
1 ACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTT-TTTTCGATCTGCTTCGCTGTTAACGCAGG
* *
218658 AAGGCAAGATCTGCTATCTTTA
65 AAGGCAAAATCTGCTATCTTTG
* * *
218680 ACCAGCTCCATTACAACCGATAGAGGCAAGGCTTTGTTTTCGAT
1 ACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTT-TTTTCGAT
218724 TTTCACTGAT
Statistics
Matches: 270, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
84 155 0.57
85 1 0.00
86 1 0.00
87 113 0.42
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (86 bp):
ACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTTTTTCGATCTGCTTCGCTGTTAACGCAGGA
AGGCAAAATCTGCTATCTTTG
Found at i:219949 original size:7 final size:7
Alignment explanation
Indices: 219937--219981 Score: 65
Period size: 7 Copynumber: 6.4 Consensus size: 7
219927 ATTTTTACTC
219937 TTTCATT
1 TTTCATT
219944 TTTCATT
1 TTTCATT
219951 TTTCA-T
1 TTTCATT
*
219957 TTTCACT
1 TTTCATT
219964 TTTCATT
1 TTTCATT
219971 TTTCATCT
1 TTTCAT-T
219979 TTT
1 TTT
219982 TTTTTACATC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
6 6 0.17
7 25 0.71
8 4 0.11
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTCATT
Found at i:219974 original size:14 final size:14
Alignment explanation
Indices: 219926--219981 Score: 71
Period size: 14 Copynumber: 4.0 Consensus size: 14
219916 TTAGCCTCTC
219926 CATTTTT-ACTCTTT
1 CATTTTTCACT-TTT
*
219940 CATTTTTCATTTTT
1 CATTTTTCACTTTT
219954 CA-TTTTCACTTTT
1 CATTTTTCACTTTT
219967 CATTTTTCATCTTTT
1 CATTTTTCA-CTTTT
219982 TTTTTACATC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
13 12 0.32
14 18 0.49
15 7 0.19
ACGTcount: A:0.14, C:0.20, G:0.00, T:0.66
Consensus pattern (14 bp):
CATTTTTCACTTTT
Found at i:219986 original size:14 final size:14
Alignment explanation
Indices: 219935--219992 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 14
219925 CCATTTTTAC
*
219935 TCTTTCATTTTTCA
1 TCTTTTATTTTTCA
219949 T-TTTTCA-TTTTCA
1 TCTTTT-ATTTTTCA
219962 -CTTTTCATTTTTCA
1 TCTTTT-ATTTTTCA
219976 TCTTTT-TTTTTACA
1 TCTTTTATTTTT-CA
219990 TCT
1 TCT
219993 GTTGTCTTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 20 0.53
14 13 0.34
15 5 0.13
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (14 bp):
TCTTTTATTTTTCA
Found at i:219986 original size:20 final size:20
Alignment explanation
Indices: 219937--219976 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
219927 ATTTTTACTC
219937 TTTCATTTTTCATTTTTCAT
1 TTTCATTTTTCATTTTTCAT
*
219957 TTTCACTTTTCATTTTTCAT
1 TTTCATTTTTCATTTTTCAT
219977 CTTTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTCATTTTTCATTTTTCAT
Found at i:229346 original size:21 final size:21
Alignment explanation
Indices: 229317--229378 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
229307 CCTAAAACCC
229317 TAAACCCTT-AACACATAACCTT
1 TAAA-CCTTAAAC-CATAACCTT
* *
229339 TAAACCTTAAACCCTAGCCTT
1 TAAACCTTAAACCATAACCTT
*
229360 TAAACCATAAACCATAACC
1 TAAACCTTAAACCATAACC
229379 CCAAACCTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 27 0.79
22 7 0.21
ACGTcount: A:0.42, C:0.32, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAACCTTAAACCATAACCTT
Found at i:229983 original size:114 final size:114
Alignment explanation
Indices: 229630--230177 Score: 803
Period size: 114 Copynumber: 4.8 Consensus size: 114
229620 ATTTTAAATC
* * *
229630 CCTGAGCATTAGCAGCACTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATC
1 CCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTC
* *
229695 GTTGGGTTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGC
66 GTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
* *** *
229744 CCTGAGCATTAGCGGCGCTTTCTTAAAAACACTATTAAATCCCCGAAAGCTCA-AAAAAGGCGTC
1 CCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTC
* *
229808 ATTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAGGA
66 GTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
* * * *
229857 CCTGAACATTAGCGACGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCGTT
1 CCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTC
*
229922 GTTGGACTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
66 GTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
* * * * * *
229971 CTTGAGCATTAGCGGTGCTTTCTTAAAAACACCGCTAAATCTCCAAAAGTTCAGAAAACGGCGTC
1 CCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTC
* * *
230036 GTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGTCGCTAAAGC
66 GTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
* * * * *
230085 CCTGAGCATTAGCGGCGCTTTTTTAAAAAAGTCGCTAAATCACCGAAATCTCAGAAAACGGCGTC
1 CCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTC
230150 GTTGGGCTTAGG-TTTTTTGCGGCGCTTT
66 GTTGGGCTTAGGTTTTTTTGCGGCGCTTT
230178 TTGAAAAACG
Statistics
Matches: 385, Mismatches: 48, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
113 117 0.30
114 268 0.70
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (114 bp):
CCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTC
GTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
Found at i:230189 original size:227 final size:227
Alignment explanation
Indices: 229624--230177 Score: 822
Period size: 227 Copynumber: 2.4 Consensus size: 227
229614 TAAATTATTT
* * *
229624 TAAATCCCTGAGCATTAGCAGCACTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
* * *
229689 GGCATCGTTGGGTTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATT
66 GGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGACCTGAGCATT
* * *
229754 AGCGGCGCTTTCTTAAAAACACTATTAAATCCCCGAAAGCTCAAAAAAGGCGTCATTGGGCTTAG
131 AGCGGCGCTTTCTTAAAAACACCACTAAATCCCCAAAAGCTCAAAAAAGGCGTCATTGGGCTTAG
229819 GTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
196 GTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * * *
229851 TAAGGACCTGAACATTAGCGACGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
* * * *
229916 AGCGTTGTTGGACTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGACTTGAGCATT
66 GGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGACCTGAGCATT
* * * * * *
229981 AGCGGTGCTTTCTTAAAAACACCGCTAAATCTCCAAAAGTTCAGAAAACGGCGTCGTTGGGCTTA
131 AGCGGCGCTTTCTTAAAAACACCACTAAATCCCCAAAAGCTCA-AAAAAGGCGTCATTGGGCTTA
* *
230046 GGTTTTTTTGCGGCGCTTTCTCAAAAACGTCGC
195 GGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * * * *
230079 TAAAGCCCTGAGCATTAGCGGCGCTTTTTTAAAAAAGTCGCTAAATCACCGAAATCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
230144 GGCGTCGTTGGGCTTAGG-TTTTTTGCGGCGCTTT
66 GGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTT
230178 TTGAAAAACG
Statistics
Matches: 289, Mismatches: 37, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
227 168 0.58
228 121 0.42
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (227 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
GGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGACCTGAGCATT
AGCGGCGCTTTCTTAAAAACACCACTAAATCCCCAAAAGCTCAAAAAAGGCGTCATTGGGCTTAG
GTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
Found at i:237280 original size:28 final size:25
Alignment explanation
Indices: 237248--237305 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 25
237238 GACCCTAAGC
237248 CCAAATATCAAAATCCATACCCATTACA
1 CCAAATAT-AAAAT--ATACCCATTACA
237276 CC-AA-ATAAAATATACCCATTACA
1 CCAAATATAAAATATACCCATTACA
237299 CCAAATA
1 CCAAATA
237306 AAATAACAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
23 14 0.50
24 2 0.07
25 6 0.21
26 2 0.07
27 2 0.07
28 2 0.07
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (25 bp):
CCAAATATAAAATATACCCATTACA
Found at i:237291 original size:23 final size:23
Alignment explanation
Indices: 237264--237310 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
237254 ATCAAAATCC
237264 ATACCCATTACACCAAATAAAAT
1 ATACCCATTACACCAAATAAAAT
237287 ATACCCATTACACCAAATAAAAT
1 ATACCCATTACACCAAATAAAAT
237310 A
1 A
237311 ACAGCCCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (23 bp):
ATACCCATTACACCAAATAAAAT
Found at i:246017 original size:46 final size:45
Alignment explanation
Indices: 245965--246082 Score: 147
Period size: 40 Copynumber: 2.7 Consensus size: 45
245955 CCAACCATTA
*
245965 ATTAACTAAAATGAGTTTAATGAAAATAAAGTCCAACAACTCAATT
1 ATTAACTAAGATGAGTTTAAT-AAAATAAAGTCCAACAACTCAATT
*
246011 ATTAACTAAGATGAGTTTAAT---AT--AGTCCAGCAACTCAATT
1 ATTAACTAAGATGAGTTTAATAAAATAAAGTCCAACAACTCAATT
* *
246051 ATTAACTACGATGAGTTTAATTAAATTAAAGT
1 ATTAACTAAGATGAGTTTAA-TAAAATAAAGT
246083 TCAGCTTGCA
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
40 35 0.56
41 1 0.02
42 2 0.03
44 1 0.02
46 23 0.37
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (45 bp):
ATTAACTAAGATGAGTTTAATAAAATAAAGTCCAACAACTCAATT
Found at i:246925 original size:21 final size:21
Alignment explanation
Indices: 246872--246926 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
246862 CCTGCTCCAG
*
246872 GTCTTGAGACAAGAGCCTCTT
1 GTCTTGAGACATGAGCCTCTT
246893 GTCTTGAGACATGAGCCTCTT
1 GTCTTGAGACATGAGCCTCTT
246914 GTCTTGAGACATG
1 GTCTTGAGACATG
246927 CAAACATCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (21 bp):
GTCTTGAGACATGAGCCTCTT
Found at i:252927 original size:46 final size:46
Alignment explanation
Indices: 252811--252995 Score: 183
Period size: 46 Copynumber: 4.0 Consensus size: 46
252801 CAGGGATTAA
* * * * * *
252811 TATTACTGTATTCTCGAGT-TCACAATACATGCAAGAGCTCGAAACC
1 TATTCCTGTATTCTCAAGTCT-GCAACACATGCAGGAGCTCGGAACC
** * * *
252857 TAAACCTGTATTCTCAAGTCTGCAATACATGCATGAGCTTGGAACC
1 TATTCCTGTATTCTCAAGTCTGCAACACATGCAGGAGCTCGGAACC
* * * * *
252903 TATTCCTATATTCTCAAGTTTGCAACATATGTAGGAGCTTGGAACC
1 TATTCCTGTATTCTCAAGTCTGCAACACATGCAGGAGCTCGGAACC
* * *
252949 TATTCTTGTATTCTCGAGTCTGCAACATATGCAGGAGCTCGGAACC
1 TATTCCTGTATTCTCAAGTCTGCAACACATGCAGGAGCTCGGAACC
252995 T
1 T
252996 GGGCAAAACT
Statistics
Matches: 116, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
46 115 0.99
47 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (46 bp):
TATTCCTGTATTCTCAAGTCTGCAACACATGCAGGAGCTCGGAACC
Found at i:265427 original size:50 final size:49
Alignment explanation
Indices: 265361--265543 Score: 213
Period size: 51 Copynumber: 3.6 Consensus size: 49
265351 AAAGTGATGG
* * * * * *
265361 TCACGTGTGTAGTACTATGTACAAGCTACTACGTTTACCGGAAAGATAGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAG-TAGA
* * *
265411 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGCTTAGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAG--TAGA
* *
265462 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGT-A-GA
*
265513 TCACATGTGTAGTACTATGTGTAGGCTACTA
1 TCACATGTGTAGTACTATGTGCAGGCTACTA
265544 TGTGAACCGG
Statistics
Matches: 113, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
49 1 0.01
50 37 0.33
51 75 0.66
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (49 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTAGA
Found at i:265640 original size:46 final size:43
Alignment explanation
Indices: 265549--265647 Score: 110
Period size: 46 Copynumber: 2.2 Consensus size: 43
265539 TACTATGTGA
* *
265549 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTGATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTAATCCC
* *
265592 ACCGGATATCATTGATTACAAAGGGTGGTTGCTGTGTGCTAAAT-CC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCT-AATCCC
265638 ACCGTGTATC
1 ACCG-GTATC
265648 TGTTATTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 5 0.11
44 11 0.23
45 2 0.04
46 26 0.55
47 3 0.06
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTAATCCC
Found at i:267561 original size:3 final size:3
Alignment explanation
Indices: 267553--267578 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
267543 ATGGAGAAAG
267553 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
267579 GTGAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:267971 original size:33 final size:35
Alignment explanation
Indices: 267933--268029 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
267923 ATAGTTGTAT
267933 TTAAATATTTAAAATATATTTTATATATT-C-TAA
1 TTAAATATTTAAAATATATTTTATATATTGCTTAA
* *
267966 TTAAAT-TTTATAAATA-ATTAATATCTATTGCTTAA
1 TTAAATATTTA-AAATATATT-TTATATATTGCTTAA
*
268001 --AAATATTTAAAATTTATATTTCATATATT
1 TTAAATATTTAAAA--TATATTTTATATATT
268030 AAAATATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
32 7 0.14
33 25 0.49
34 5 0.10
35 11 0.22
36 3 0.06
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (35 bp):
TTAAATATTTAAAATATATTTTATATATTGCTTAA
Found at i:269607 original size:111 final size:111
Alignment explanation
Indices: 269413--269746 Score: 625
Period size: 111 Copynumber: 3.0 Consensus size: 111
269403 ACAAATGATG
269413 AAGTATTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTT
1 AAGTATTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTT
269478 CTAAATGTCTGTACATATTAACAAACTTTAATACAACAATACAACT
66 CTAAATGTCTGTACATATTAACAAACTTTAATACAACAATACAACT
* *
269524 AAGTATTGTTGTCTAAAAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTATTTTTT
1 AAGTATTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTT
269589 CTAAATGTCTGTACATATTAACAAACTTTAATACAACAATACAACT
66 CTAAATGTCTGTACATATTAACAAACTTTAATACAACAATACAACT
*
269635 ACA-TGTTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTT
1 A-AGTATTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTT
269699 TCTAAATGTCTGTACATATTAACAAACTTTAATACAACAATACAACT
65 TCTAAATGTCTGTACATATTAACAAACTTTAATACAACAATACAACT
269746 A
1 A
269747 CATGCATGGT
Statistics
Matches: 217, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
111 216 1.00
112 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (111 bp):
AAGTATTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTT
CTAAATGTCTGTACATATTAACAAACTTTAATACAACAATACAACT
Found at i:272471 original size:10 final size:9
Alignment explanation
Indices: 272427--272469 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
272417 TTTTTTTCTA
272427 ATTTTTAAT
1 ATTTTTAAT
*
272436 ATTTTTATT
1 ATTTTTAAT
**
272445 AAAATTTAAT
1 -ATTTTTAAT
272455 ATTTTTAAT
1 ATTTTTAAT
272464 ATTTTT
1 ATTTTT
272470 TATTGATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
9 21 0.78
10 6 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:272471 original size:19 final size:19
Alignment explanation
Indices: 272428--272497 Score: 56
Period size: 19 Copynumber: 3.7 Consensus size: 19
272418 TTTTTTCTAA
* *
272428 TTTTTAATATTTTTATTAA
1 TTTTTAATATTTTTAATAT
**
272447 AATTTAATATTTTTAATAT
1 TTTTTAATATTTTTAATAT
*
272466 TTTTTATTGATTTTT-AT-T
1 TTTTTAAT-ATTTTTAATAT
272484 TTTTATAAT-TTTTT
1 TTTT-TAATATTTTT
272498 GCCACATGTC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
17 5 0.12
18 5 0.12
19 25 0.61
20 6 0.15
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (19 bp):
TTTTTAATATTTTTAATAT
Found at i:272497 original size:17 final size:17
Alignment explanation
Indices: 272463--272496 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
272453 ATATTTTTAA
*
272463 TATTTTTTATTGATTTT
1 TATTTTTTATTAATTTT
272480 TATTTTTTA-TAATTTT
1 TATTTTTTATTAATTTT
272496 T
1 T
272497 TGCCACATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TATTTTTTATTAATTTT
Found at i:272710 original size:92 final size:88
Alignment explanation
Indices: 272602--272834 Score: 229
Period size: 92 Copynumber: 2.6 Consensus size: 88
272592 GCAAATGACT
* * * * *
272602 TTTTTAATGTATTTTAACAGTTCAAGTACTCAATTGAGTAAAAAAAATAAAG-CAGGAGTTTAAT
1 TTTTTGATGCATTTTAA-AGTTAAAGTACTCAATTGAGT-AAAAAAATAAAGTAAGG-GCTTAAT
* * *
272666 TGCTTTTTTTGAAAAAGTTTTGAGGGTC
63 TACTTTTTTGGAAAAAG-TTTGAGAG-C
* *
272694 TTTTTGATGCATTTTAAAAGTTTAAGTACTCAATTGAGTGTAAAAAAA-AAAGTAATGGCTTAAT
1 TTTTTGATGCATTTT-AAAGTTAAAGTACTCAATTGA--GTAAAAAAATAAAGTAAGGGCTTAAT
*
272758 TACTTTTTTGGAAATAGTTTGAGAGC
63 TACTTTTTTGGAAAAAGTTTGAGAGC
* * *
272784 CTTTTGATGCATTTTTAAAGTTAAAGTAAC-CAATTGAATAAGAAAATAAAG
1 TTTTTGATGCA-TTTTAAAGTTAAAGT-ACTCAATTGAGTAAAAAAATAAAG
272835 ACTTAATTAC
Statistics
Matches: 120, Mismatches: 14, Indels: 17
0.79 0.09 0.11
Matches are distributed among these distances:
88 7 0.06
89 4 0.03
90 28 0.23
91 13 0.11
92 55 0.46
93 11 0.09
94 2 0.02
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (88 bp):
TTTTTGATGCATTTTAAAGTTAAAGTACTCAATTGAGTAAAAAAATAAAGTAAGGGCTTAATTAC
TTTTTTGGAAAAAGTTTGAGAGC
Found at i:273416 original size:19 final size:20
Alignment explanation
Indices: 273394--273434 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
273384 TATTTTTTGA
273394 ATTTA-ATATTATTTA-AAAT
1 ATTTATATATT-TTTACAAAT
273413 ATTTATATATTTTTACAAAT
1 ATTTATATATTTTTACAAAT
273433 AT
1 AT
273435 AATGATATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTATATATTTTTACAAAT
Found at i:276467 original size:18 final size:19
Alignment explanation
Indices: 276424--276460 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
276414 TACGGTACGC
276424 TTCTTTTC--TTCTCACAT
1 TTCTTTTCTTTTCTCACAT
276441 TTCTTTTCTTTTCTC-CAT
1 TTCTTTTCTTTTCTCACAT
276459 TT
1 TT
276461 TTATTCTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.44
18 5 0.28
19 5 0.28
ACGTcount: A:0.08, C:0.27, G:0.00, T:0.65
Consensus pattern (19 bp):
TTCTTTTCTTTTCTCACAT
Done.