Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold165.1
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: 1724686
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 30232 characters in sequence are not A, C, G, or T
File 2 of 8
Found at i:126368 original size:29 final size:29
Alignment explanation
Indices: 126307--126385 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 29
126297 AGTTCTTGTA
* * **
126307 CTATTTGTATATTT-GAAATTTAATCTTT
1 CTATTTTTATTTTTAGAAATTTAATCCCT
*
126335 ATATTTTTATTTTTAGAAATTTAATCCCT
1 CTATTTTTATTTTTAGAAATTTAATCCCT
*
126364 CTATTTTTAAATTTTA-AAATTT
1 CTATTTTT-ATTTTTAGAAATTT
126386 CAAATGTGAT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 11 0.26
29 25 0.60
30 6 0.14
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.57
Consensus pattern (29 bp):
CTATTTTTATTTTTAGAAATTTAATCCCT
Found at i:127555 original size:13 final size:13
Alignment explanation
Indices: 127539--127580 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
127529 AATAAATATA
127539 TATTTTTTATTTT
1 TATTTTTTATTTT
127552 TATTTTTTAATTTT
1 TATTTTTT-ATTTT
* *
127566 TAATTTTTAATTT
1 TATTTTTTATTTT
127579 TA
1 TA
127581 AAATACTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:127581 original size:6 final size:7
Alignment explanation
Indices: 127540--127579 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
127530 ATAAATATAT
*
127540 ATTTTTT
1 ATTTTTA
127547 ATTTTTA
1 ATTTTTA
*
127554 TTTTTTA
1 ATTTTTA
127561 ATTTTTA
1 ATTTTTA
127568 ATTTTTA
1 ATTTTTA
127575 ATTTT
1 ATTTT
127580 AAAATACTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (7 bp):
ATTTTTA
Found at i:127933 original size:31 final size:32
Alignment explanation
Indices: 127879--127948 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
127869 AAAAAAATAT
* * *
127879 TTTAACTCTCTTTCAAAAGATTAATAATTAAA
1 TTTAATTCTCTTTCAAAAGATTAAGAACTAAA
* *
127911 TTTAATTCT-TTTTAAAATATTAAGAACTAAA
1 TTTAATTCTCTTTCAAAAGATTAAGAACTAAA
127942 TTTAATT
1 TTTAATT
127949 TTAAAAAAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
31 25 0.76
32 8 0.24
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.46
Consensus pattern (32 bp):
TTTAATTCTCTTTCAAAAGATTAAGAACTAAA
Found at i:130454 original size:21 final size:21
Alignment explanation
Indices: 130428--130469 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
130418 TAATAAACAC
* *
130428 AAAAAAATTATTTTAAAAATA
1 AAAAAAAGTATTATAAAAATA
*
130449 AAAAAAAGTATTATAGAAATA
1 AAAAAAAGTATTATAAAAATA
130470 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (21 bp):
AAAAAAAGTATTATAAAAATA
Found at i:131005 original size:280 final size:280
Alignment explanation
Indices: 130504--131048 Score: 1090
Period size: 280 Copynumber: 1.9 Consensus size: 280
130494 AATTTATTAT
130504 ATTCGGGTCGGGACGAGCTCAGGCCAAAAAAACAGGCCTCTTTTTTTGCCCAAACTCATATTTCG
1 ATTCGGGTCGGGACGAGCTCAGGCCAAAAAAACAGGCCTCTTTTTTTGCCCAAACTCATATTTCG
130569 GACCTATATTTTTACCCAAACCCTCCCATATTTTGGGCGGACCGTCGAGCTAGGATAAATGTAAT
66 GACCTATATTTTTACCCAAACCCTCCCATATTTTGGGCGGACCGTCGAGCTAGGATAAATGTAAT
130634 AGTCAGAATTAAGGTACAAAAGATAAAAGTGAACAACTCAGTCATATCTTAAATTAATACCACAT
131 AGTCAGAATTAAGGTACAAAAGATAAAAGTGAACAACTCAGTCATATCTTAAATTAATACCACAT
130699 CATTTAATTAATTCCACCTCATAAAACTAACTGTTTTTTTTTCCTTCAATTGTTATATAAATGAT
196 CATTTAATTAATTCCACCTCATAAAACTAACTGTTTTTTTTTCCTTCAATTGTTATATAAATGAT
130764 CATTTAATTAATTCCACATC
261 CATTTAATTAATTCCACATC
130784 ATTCGGGTCGGGACGAGCTCAGGCCAAAAAAACAGGCCTCTTTTTTTGCCCAAACTCATATTTCG
1 ATTCGGGTCGGGACGAGCTCAGGCCAAAAAAACAGGCCTCTTTTTTTGCCCAAACTCATATTTCG
130849 GACCTATATTTTTACCCAAACCCTCCCATATTTTGGGCGGACCGTCGAGCTAGGATAAATGTAAT
66 GACCTATATTTTTACCCAAACCCTCCCATATTTTGGGCGGACCGTCGAGCTAGGATAAATGTAAT
130914 AGTCAGAATTAAGGTACAAAAGATAAAAGTGAACAACTCAGTCATATCTTAAATTAATACCACAT
131 AGTCAGAATTAAGGTACAAAAGATAAAAGTGAACAACTCAGTCATATCTTAAATTAATACCACAT
130979 CATTTAATTAATTCCACCTCATAAAACTAACTGTTTTTTTTTCCTTCAATTGTTATATAAATGAT
196 CATTTAATTAATTCCACCTCATAAAACTAACTGTTTTTTTTTCCTTCAATTGTTATATAAATGAT
131044 CATTT
261 CATTT
131049 TGCGTGTATT
Statistics
Matches: 265, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
280 265 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (280 bp):
ATTCGGGTCGGGACGAGCTCAGGCCAAAAAAACAGGCCTCTTTTTTTGCCCAAACTCATATTTCG
GACCTATATTTTTACCCAAACCCTCCCATATTTTGGGCGGACCGTCGAGCTAGGATAAATGTAAT
AGTCAGAATTAAGGTACAAAAGATAAAAGTGAACAACTCAGTCATATCTTAAATTAATACCACAT
CATTTAATTAATTCCACCTCATAAAACTAACTGTTTTTTTTTCCTTCAATTGTTATATAAATGAT
CATTTAATTAATTCCACATC
Found at i:134798 original size:20 final size:20
Alignment explanation
Indices: 134769--134823 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
134759 TCTTTATATA
*
134769 TTATATATATTTTGAAATTT
1 TTATAAATATTTTGAAATTT
**
134789 TTATAAATATTTAAAAATTT
1 TTATAAATATTTTGAAATTT
*
134809 TGA-AAATTATTTTGA
1 TTATAAA-TATTTTGA
134824 TTTATTTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
TTATAAATATTTTGAAATTT
Found at i:137206 original size:195 final size:188
Alignment explanation
Indices: 136866--137230 Score: 478
Period size: 195 Copynumber: 1.9 Consensus size: 188
136856 AGCTACTTTA
* * * *
136866 GAGGTTACGATCTTAAACCGGTTAGCCTTTATAATATTAGCTAGGAACGTAGGTCCGTGAGCTGT
1 GAGGTTACGATCTTAAACCAGTGAGCCTTTATAATATTAGCTAGGAACATAGGTCCGTGAACTGT
* *
136931 TTTGGAGGCTTAAACCAGCGAGCCTTTATAATATCAATTGGGAACGTAGGTCCGCGAGTTGTTTT
66 TTTGGAGGCTTAAACCAGCGAGCCTTTATAATATCAATTGGGAACGTAAGTCCGCGAGCTGTTTT
* * *
136996 GGAGGCTGCGATCTTAGACCGGCGAGTCTTTATAATATCAACTAGGAGTGTTGTTTTG
131 GAAGGCTGCGATCTTAAACCGGCGAGCCTTTATAATATCAACTAGGAGTGTTGTTTTG
* * * *
137054 GAGGTTGCGATCTTAAACCAGTGAGCTTTTATAATATTAGCTGGGAGCATAGGTCCGTGAACTGT
1 GAGGTTACGATCTTAAACCAGTGAGCCTTTATAATATTAGCTAGGAACATAGGTCCGTGAACTGT
** * * * **
137119 TTTGGAGGCTGTGATCTTAAACTGGTGAGCCTTTATAATATCAGTTGGGAATGTAAGTTTGCGAG
66 TTTGGA----G-G--CTTAAACCAGCGAGCCTTTATAATATCAATTGGGAACGTAAGTCCGCGAG
*
137184 CTGTTTTGAAGGCTGCGATCTTAAACCGGTGAGCCTTTATAATATCA
124 CTGTTTTGAAGGCTGCGATCTTAAACCGGCGAGCCTTTATAATATCA
137231 GTTGGGAGCG
Statistics
Matches: 149, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
188 63 0.42
192 1 0.01
193 1 0.01
195 84 0.56
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.33
Consensus pattern (188 bp):
GAGGTTACGATCTTAAACCAGTGAGCCTTTATAATATTAGCTAGGAACATAGGTCCGTGAACTGT
TTTGGAGGCTTAAACCAGCGAGCCTTTATAATATCAATTGGGAACGTAAGTCCGCGAGCTGTTTT
GAAGGCTGCGATCTTAAACCGGCGAGCCTTTATAATATCAACTAGGAGTGTTGTTTTG
Found at i:137253 original size:69 final size:69
Alignment explanation
Indices: 137047--137263 Score: 263
Period size: 69 Copynumber: 3.1 Consensus size: 69
137037 CTAGGAGTGT
* * * * * * * *
137047 TGTTTTGGAGGTTGCGATCTTAAACCAGTGAGCTTTTATAATATTAGCTGGGAGCATAGGTCCGT
1 TGTTTTGAAGGCTGCGATCTTAAACCGGTGAGCCTTTATAATATCAGTTGGGAGCGTAGGTCCGC
*
137112 GAAC
66 GAGC
* * * ** * **
137116 TGTTTTGGAGGCTGTGATCTTAAACTGGTGAGCCTTTATAATATCAGTTGGGAATGTAAGTTTGC
1 TGTTTTGAAGGCTGCGATCTTAAACCGGTGAGCCTTTATAATATCAGTTGGGAGCGTAGGTCCGC
137181 GAGC
66 GAGC
*
137185 TGTTTTGAAGGCTGCGATCTTAAACCGGTGAGCCTTTATAATATCAGTTGGGAGCGTAGGTCCAC
1 TGTTTTGAAGGCTGCGATCTTAAACCGGTGAGCCTTTATAATATCAGTTGGGAGCGTAGGTCCGC
137250 GAGC
66 GAGC
*
137254 TATTTTGAAG
1 TGTTTTGAAG
137264 TTGCAAGCTT
Statistics
Matches: 123, Mismatches: 25, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
69 123 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (69 bp):
TGTTTTGAAGGCTGCGATCTTAAACCGGTGAGCCTTTATAATATCAGTTGGGAGCGTAGGTCCGC
GAGC
Found at i:141002 original size:13 final size:14
Alignment explanation
Indices: 140980--141025 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
140970 AAAATATTGT
140980 TTTTTAATTTATTA
1 TTTTTAATTTATTA
140994 TTTTT-ATTTATT-
1 TTTTTAATTTATTA
141006 TTTATTAAATTT-TTA
1 TTT-TT-AATTTATTA
141021 TTTTT
1 TTTTT
141026 TATAGGTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 3 0.11
13 9 0.32
14 9 0.32
15 7 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTAATTTATTA
Found at i:149357 original size:684 final size:684
Alignment explanation
Indices: 148050--149415 Score: 2588
Period size: 684 Copynumber: 2.0 Consensus size: 684
148040 AAAATTTCAG
148050 ATGTTGCCTTCATCCTTGTATCTTTTGATTCCATTAACTTATCCTGAAACTTCTGCAACATTTTC
1 ATGTTGCCTTCATCCTTGTATCTTTTGATTCCATTAACTTATCCTGAAACTTCTGCAACATTTTC
* * *
148115 CCTAAAGGTATATTTGCCAACATAACAAGTACAGTTGCAATGAAAGTGACAATGGATCCTAGCCT
66 CCCAAAGGTATATTTGCCAACATAACAAGTACAGTAGCAATGAAAGTGACAATGGATCCTAGCCC
* *
148180 CAAGGTCTTATACAAGATCAACAAGGCCAAAGCAACTTGCAAAACTACCTTCCATGGATCATGCA
131 CAAGGTCTTATACAAGATCAACAAGGCCAAACCAACTTGCAAAACTACCATCCATGGATCATGCA
148245 TGTACCAACTAAAGTCACCCACCCTTTCTGCATCAACAGTCATGAAATTGATGATCTCCCCACTG
196 TGTACCAACTAAAGTCACCCACCCTTTCTGCATCAACAGTCATGAAATTGATGATCTCCCCACTG
*
148310 GTATGGCTCTGCTTCGACTGGCATGAAAGGGTTAACCCCTTGTTATATATCATTGCTACCAATAC
261 GTATGGCTCTGCTTCGACTGGCACGAAAGGGTTAACCCCTTGTTATATATCATTGCTACCAATAC
*
148375 AGCCCTCTGCCTAAGTCCAACTTGTTGCAACTTAAAGAACCAGCGCCTCTGAGACAAGCACTCCA
326 AGCCCTCTGCCTAAGTCCAACTTGTTGCAACTTAAAGAACCAGCGCCTCTCAGACAAGCACTCCA
148440 CTAGCTTGGCAACAAAGAAAGCAGCAACTAGAAGATACCCCTCAGCCTTAAATTCCCTTTGCCCA
391 CTAGCTTGGCAACAAAGAAAGCAGCAACTAGAAGATACCCCTCAGCCTTAAATTCCCTTTGCCCA
*
148505 TTCAGATACTGAACAAAAGTGTCGATGAGGTATGGGCCAACATATGAAGCCACCGTGTAAGTAAA
456 TTCAGATACTGAACAAAAGTGTCGATGAGGAATGGGCCAACATATGAAGCCACCGTGTAAGTAAA
148570 TGCAAACAAAGCTGTCCAAAGAATATCTTTCCAAGCTGAAAAGAACAGTGCCTTCACCAGCTTAA
521 TGCAAACAAAGCTGTCCAAAGAATATCTTTCCAAGCTGAAAAGAACAGTGCCTTCACCAGCTTAA
148635 GTGAGGTAACAACATTCCCCTCACTATCAGCTGATTCAAGCCTGTTTTTAGATTTTGGAAAAGCC
586 GTGAGGTAACAACATTCCCCTCACTATCAGCTGATTCAAGCCTGTTTTTAGATTTTGGAAAAGCC
148700 CCAATAACACTATCATGGCTATCTAGCTGAGGGA
651 CCAATAACACTATCATGGCTATCTAGCTGAGGGA
*
148734 ATGTTGCCTTCATCCTTGTATCTTTTGATTCCATTAACTTATCCTGAAACTTCTGCAGCATTTTC
1 ATGTTGCCTTCATCCTTGTATCTTTTGATTCCATTAACTTATCCTGAAACTTCTGCAACATTTTC
*
148799 CCCAAAGGTATATTTGCCAACATAACAAGTACAGTAGCAATGAAAGTGACAATGGATGCTAGCCC
66 CCCAAAGGTATATTTGCCAACATAACAAGTACAGTAGCAATGAAAGTGACAATGGATCCTAGCCC
*
148864 CAGGGTCTTATACAAGATCAACAAGGCCAAACCAACTTGCAAAACTACCATCCATGGATCATGCA
131 CAAGGTCTTATACAAGATCAACAAGGCCAAACCAACTTGCAAAACTACCATCCATGGATCATGCA
148929 TGTACCAACTAAAGTCACCCACCCTTTCTGCATCAACAGTCATGAAATTGATGATCTCCCCACTG
196 TGTACCAACTAAAGTCACCCACCCTTTCTGCATCAACAGTCATGAAATTGATGATCTCCCCACTG
*
148994 GTATGGCTCTGCTTCGAGTGGCACGAAAGGGTTAACCCCTTGTTATATATCATTGCTACCAATAC
261 GTATGGCTCTGCTTCGACTGGCACGAAAGGGTTAACCCCTTGTTATATATCATTGCTACCAATAC
149059 AGCCCTCTGCCTAAGTCCAACTTGTTGCAACTTAAAGAACCAGCGCCTCTCAGACAAGCACTCCA
326 AGCCCTCTGCCTAAGTCCAACTTGTTGCAACTTAAAGAACCAGCGCCTCTCAGACAAGCACTCCA
*
149124 CTAGCTTGGCAACAAAGAAAGCAGCAACTAGAAGATACCCCTCAGCCTTAAATTCCCTTTTCCCA
391 CTAGCTTGGCAACAAAGAAAGCAGCAACTAGAAGATACCCCTCAGCCTTAAATTCCCTTTGCCCA
* *
149189 TTCAGATACTGAACGAAAGTGTCGATGAGGAATGGGCCAACATATGAAGCCACCGTGTACGTAAA
456 TTCAGATACTGAACAAAAGTGTCGATGAGGAATGGGCCAACATATGAAGCCACCGTGTAAGTAAA
149254 TGCAAACAAAGCTGTCCAAAGAATATCTTTCCAAGCTGAAAAGAACAGTGCCTTCACCAGCTTAA
521 TGCAAACAAAGCTGTCCAAAGAATATCTTTCCAAGCTGAAAAGAACAGTGCCTTCACCAGCTTAA
*
149319 GTGAGGTAACACCATTCCCCTCACTATCAGCTGATTCAAGCCTGTTTTTAGATTTTGGAAAAGCC
586 GTGAGGTAACAACATTCCCCTCACTATCAGCTGATTCAAGCCTGTTTTTAGATTTTGGAAAAGCC
149384 CCAATAACACTATCATGGCTATCTAGCTGAGG
651 CCAATAACACTATCATGGCTATCTAGCTGAGG
149416 AACATCCTCA
Statistics
Matches: 666, Mismatches: 16, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
684 666 1.00
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.26
Consensus pattern (684 bp):
ATGTTGCCTTCATCCTTGTATCTTTTGATTCCATTAACTTATCCTGAAACTTCTGCAACATTTTC
CCCAAAGGTATATTTGCCAACATAACAAGTACAGTAGCAATGAAAGTGACAATGGATCCTAGCCC
CAAGGTCTTATACAAGATCAACAAGGCCAAACCAACTTGCAAAACTACCATCCATGGATCATGCA
TGTACCAACTAAAGTCACCCACCCTTTCTGCATCAACAGTCATGAAATTGATGATCTCCCCACTG
GTATGGCTCTGCTTCGACTGGCACGAAAGGGTTAACCCCTTGTTATATATCATTGCTACCAATAC
AGCCCTCTGCCTAAGTCCAACTTGTTGCAACTTAAAGAACCAGCGCCTCTCAGACAAGCACTCCA
CTAGCTTGGCAACAAAGAAAGCAGCAACTAGAAGATACCCCTCAGCCTTAAATTCCCTTTGCCCA
TTCAGATACTGAACAAAAGTGTCGATGAGGAATGGGCCAACATATGAAGCCACCGTGTAAGTAAA
TGCAAACAAAGCTGTCCAAAGAATATCTTTCCAAGCTGAAAAGAACAGTGCCTTCACCAGCTTAA
GTGAGGTAACAACATTCCCCTCACTATCAGCTGATTCAAGCCTGTTTTTAGATTTTGGAAAAGCC
CCAATAACACTATCATGGCTATCTAGCTGAGGGA
Found at i:161338 original size:14 final size:14
Alignment explanation
Indices: 161317--161347 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
161307 TTCTTGTTCG
161317 ATTTTTTTCTCTTTT
1 ATTTTTTTC-CTTTT
161332 ATTTTTTTCCTTTT
1 ATTTTTTTCCTTTT
161346 AT
1 AT
161348 ACTAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (14 bp):
ATTTTTTTCCTTTT
Found at i:162145 original size:26 final size:26
Alignment explanation
Indices: 162107--162200 Score: 68
Period size: 26 Copynumber: 3.6 Consensus size: 26
162097 AAACTGTTTG
**
162107 ATATTATCAATTTTAAATTG-TTTCAT
1 ATATTATTTATTTTAAATTGCTTTC-T
**
162133 ATATTATTTATTTCGAATTGCTTTC-
1 ATATTATTTATTTTAAATTGCTTTCT
* * *
162158 -TATTATTTTATCTTAAACTGTTTTACGT
1 ATATTA-TTTATTTTAAATTGCTTT-C-T
162186 ATATTATTTATTTTA
1 ATATTATTTATTTTA
162201 GATTTTTACG
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
24 5 0.10
25 13 0.25
26 17 0.33
27 4 0.08
28 8 0.15
29 5 0.10
ACGTcount: A:0.29, C:0.09, G:0.05, T:0.57
Consensus pattern (26 bp):
ATATTATTTATTTTAAATTGCTTTCT
Found at i:166535 original size:21 final size:21
Alignment explanation
Indices: 166509--166548 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
166499 CCACTAACTA
*
166509 CATCTCGTAATGAACCAATGT
1 CATCTCGCAATGAACCAATGT
*
166530 CATCTCGCAATGACCCAAT
1 CATCTCGCAATGAACCAAT
166549 TGCATTGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.25
Consensus pattern (21 bp):
CATCTCGCAATGAACCAATGT
Found at i:168691 original size:23 final size:24
Alignment explanation
Indices: 168639--168692 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
168629 TCAAATTCGA
* *
168639 AACTCGAATTACTTATTCAATTTG
1 AACTCGAATAACTGATTCAATTTG
168663 AA-TCGAATAACTCGATTCAA-TT-
1 AACTCGAATAACT-GATTCAATTTG
168685 AACTCGAA
1 AACTCGAA
168693 ATTCAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 2 0.08
23 16 0.62
24 8 0.31
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (24 bp):
AACTCGAATAACTGATTCAATTTG
Found at i:171833 original size:37 final size:37
Alignment explanation
Indices: 171783--171857 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
171773 TAATAATAAG
171783 AAACCCCACTTTTTGCATCATGTTCATCATCTTCTAA
1 AAACCCCACTTTTTGCATCATGTTCATCATCTTCTAA
* *
171820 AAACCCCACTTTTTGCATCCTTTTCATCATCTTCTAA
1 AAACCCCACTTTTTGCATCATGTTCATCATCTTCTAA
171857 A
1 A
171858 CCCCCTAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.27, C:0.31, G:0.04, T:0.39
Consensus pattern (37 bp):
AAACCCCACTTTTTGCATCATGTTCATCATCTTCTAA
Found at i:172228 original size:82 final size:82
Alignment explanation
Indices: 172111--172269 Score: 205
Period size: 82 Copynumber: 1.9 Consensus size: 82
172101 TTTCTGGAGT
* *
172111 AGCGCCGCTAATGCTGTGGGTTTTAAAGGCGTTTTTA-AAATAGCGCCGCCAATGCTCAGGGTTT
1 AGCGCCGCTAATGCTGTGGGTTTTAAAGGCATTTTTAGAAA-AGCGCCGCCAAAGCTCAGGGTTT
172175 TAGCAGCGTTTTTTATTA
65 TAGCAGCGTTTTTTATTA
* ** * * *
172193 AGCGCCGCTAATGTTCG-GGGTTTTAGCGGCATTTTTAGAAAGGCGCCGCTAAAGCTCGGGGTTT
1 AGCGCCGCTAATGCT-GTGGGTTTTAAAGGCATTTTTAGAAAAGCGCCGCCAAAGCTCAGGGTTT
*
172257 TAGCTGCGTTTTT
65 TAGCAGCGTTTTT
172270 GTGAAAGTGC
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
82 62 0.94
83 4 0.06
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.33
Consensus pattern (82 bp):
AGCGCCGCTAATGCTGTGGGTTTTAAAGGCATTTTTAGAAAAGCGCCGCCAAAGCTCAGGGTTTT
AGCAGCGTTTTTTATTA
Found at i:172259 original size:41 final size:39
Alignment explanation
Indices: 172111--172269 Score: 158
Period size: 41 Copynumber: 3.9 Consensus size: 39
172101 TTTCTGGAGT
**
172111 AGCGCCGCTAATGCT-GTGGGTTTTAAAGGCGTTTTTAAAA
1 AGCGCCGCTAATGCTCG-GGGTTTTAGCGGCGTTTTT-AAA
* * * *
172151 TAGCGCCGCCAATGCTCAGGGTTTTAGCAGCGTTTTTTATTA
1 -AGCGCCGCTAATGCTCGGGGTTTTAGCGGCG-TTTTTA-AA
* *
172193 AGCGCCGCTAATGTTCGGGGTTTTAGCGGCATTTTTAGAA
1 AGCGCCGCTAATGCTCGGGGTTTTAGCGGCGTTTTTA-AA
* *
172233 AGGCGCCGCTAAAGCTCGGGGTTTTAGCTGCGTTTTT
1 A-GCGCCGCTAATGCTCGGGGTTTTAGCGGCGTTTTT
172270 GTGAAAGTGC
Statistics
Matches: 97, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
40 8 0.08
41 83 0.86
42 6 0.06
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.33
Consensus pattern (39 bp):
AGCGCCGCTAATGCTCGGGGTTTTAGCGGCGTTTTTAAA
Found at i:174194 original size:87 final size:87
Alignment explanation
Indices: 173999--174187 Score: 306
Period size: 87 Copynumber: 2.2 Consensus size: 87
173989 TACTCAACTT
* *
173999 AAAGCAGAGGCAGCATCGAGAGAAGCTAAGGTTCAAAGAAAATATGAAGAACTCCAGCTACAACT
1 AAAGCAGAGGCAGCATCGAGAGAAGCTGAGGTTCAAAGAAAATATAAAGAACTCCAGCTACAACT
* * *
174064 TAGAGCAAATGCAGCGGTGAGG
66 TAAAGCAAATGCAGCAGCGAGG
*
174086 GAAGCAGAGGCAGCATCGAGAGAAGCTGAGGTTCAAAGAAAATATAAAGAACTCCAGCTACAACT
1 AAAGCAGAGGCAGCATCGAGAGAAGCTGAGGTTCAAAGAAAATATAAAGAACTCCAGCTACAACT
**
174151 TAAAGCTGATGCAGCAGCGAGG
66 TAAAGCAAATGCAGCAGCGAGG
174173 AAAGCAGAGGCAGCA
1 AAAGCAGAGGCAGCA
174188 ATGAGAGCAG
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 93 1.00
ACGTcount: A:0.41, C:0.18, G:0.28, T:0.13
Consensus pattern (87 bp):
AAAGCAGAGGCAGCATCGAGAGAAGCTGAGGTTCAAAGAAAATATAAAGAACTCCAGCTACAACT
TAAAGCAAATGCAGCAGCGAGG
Found at i:174199 original size:21 final size:21
Alignment explanation
Indices: 174174--174223 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
174164 GCAGCGAGGA
174174 AAGCAGAGGCAGCAATGAGAG
1 AAGCAGAGGCAGCAATGAGAG
* * * *
174195 CAGCAGAGGCTGCAGTGAGGG
1 AAGCAGAGGCAGCAATGAGAG
174216 AAGCAGAG
1 AAGCAGAG
174224 CAGAGAAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.42, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCAGCAATGAGAG
Found at i:176320 original size:16 final size:16
Alignment explanation
Indices: 176298--176366 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
176288 TTTGGTTCGC
176298 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
176314 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
176330 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
176347 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
176363 TGTA
1 TGTA
176367 ATAGCTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:176344 original size:33 final size:32
Alignment explanation
Indices: 176298--176366 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
176288 TTTGGTTCGC
176298 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
*
176330 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCGTATTGGATTAGAGG
176363 TGTA
1 TGTA
176367 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCGTATTGGATTAGAGG
Found at i:176431 original size:44 final size:45
Alignment explanation
Indices: 176347--176437 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
176337 GGATTAGAGG
* * *
176347 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
176392 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
176436 TG
1 TG
176438 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:176622 original size:18 final size:17
Alignment explanation
Indices: 176601--176635 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
176591 TTATTATTAA
*
176601 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
176619 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
176636 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:176742 original size:18 final size:17
Alignment explanation
Indices: 176721--176755 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
176711 TTATTATTAA
*
176721 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
176739 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
176756 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:176797 original size:120 final size:120
Alignment explanation
Indices: 176584--177206 Score: 1131
Period size: 120 Copynumber: 5.2 Consensus size: 120
176574 ATCATATTTA
176584 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
176649 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
176704 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
176769 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
176824 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
176889 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
* * *
176944 AACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAGTAAAATTCTTAAT-ATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATT-A
* * * * * *
177008 ATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAATTT
65 ATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
* *
177064 AACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
177129 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
177184 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
177207 NNNNNNNNNN
Statistics
Matches: 484, Mismatches: 17, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
119 3 0.01
120 478 0.99
121 3 0.01
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:176862 original size:18 final size:17
Alignment explanation
Indices: 176841--176875 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
176831 TTATTATTAA
*
176841 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
176859 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
176876 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:184164 original size:7 final size:7
Alignment explanation
Indices: 184152--184189 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
184142 TTTAATCCTC
184152 TTTTAAA
1 TTTTAAA
184159 TTTTAAA
1 TTTTAAA
184166 TTTTAAA
1 TTTTAAA
*
184173 TTTT-TA
1 TTTTAAA
*
184179 TTTTATA
1 TTTTAAA
184186 TTTT
1 TTTT
184190 CGTATTATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 5 0.17
7 24 0.83
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TTTTAAA
Found at i:184183 original size:13 final size:14
Alignment explanation
Indices: 184152--184189 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
184142 TTTAATCCTC
184152 TTTTAAATTTTAAA
1 TTTTAAATTTTAAA
*
184166 TTTTAAATTTT-TA
1 TTTTAAATTTTAAA
*
184179 TTTTATATTTT
1 TTTTAAATTTT
184190 CGTATTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTAAATTTTAAA
Found at i:185201 original size:26 final size:26
Alignment explanation
Indices: 185165--185218 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
185155 CATGGCCTAG
*
185165 ACTTTATGGTCGTATTTGACGATGTC
1 ACTTTATGGTCCTATTTGACGATGTC
185191 ACTTTATGGTCCTATTTGACGATGTC
1 ACTTTATGGTCCTATTTGACGATGTC
185217 AC
1 AC
185219 ATGAAAGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (26 bp):
ACTTTATGGTCCTATTTGACGATGTC
Found at i:190971 original size:21 final size:21
Alignment explanation
Indices: 190929--190986 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
190919 CTTAAACCTA
**
190929 ACACATCTCTCATACTTTGAT
1 ACACATCTCTCATACTCCGAT
*
190950 ATACATCTCTCATACTCCGAT
1 ACACATCTCTCATACTCCGAT
* *
190971 ACATATCTCTTATACT
1 ACACATCTCTCATACT
190987 TCGACACCAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.29, G:0.03, T:0.38
Consensus pattern (21 bp):
ACACATCTCTCATACTCCGAT
Found at i:191905 original size:14 final size:15
Alignment explanation
Indices: 191877--191907 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
191867 GAATGTTTAA
191877 AATTCTTTGAAAACC
1 AATTCTTTGAAAACC
191892 AATTCTTT-AAAACC
1 AATTCTTTGAAAACC
191906 AA
1 AA
191908 ATTTTGGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.32
Consensus pattern (15 bp):
AATTCTTTGAAAACC
Found at i:191910 original size:15 final size:16
Alignment explanation
Indices: 191876--191910 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
191866 AGAATGTTTA
191876 AAATTCTTTGAAAACC
1 AAATTCTTTGAAAACC
191892 -AATTCTTT-AAAACC
1 AAATTCTTTGAAAACC
191906 AAATT
1 AAATT
191911 TTGGAACCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (16 bp):
AAATTCTTTGAAAACC
Found at i:201367 original size:3 final size:3
Alignment explanation
Indices: 201352--201385 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
201342 TGTATTCATT
*
201352 TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
201386 CTCTAATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:208478 original size:10 final size:10
Alignment explanation
Indices: 208460--208493 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
208450 TTGTATAGAT
208460 TACACTACAA
1 TACACTACAA
*
208470 TAGACTACAA
1 TACACTACAA
*
208480 TACAATACAA
1 TACACTACAA
208490 TACA
1 TACA
208494 AACCATACCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.53, C:0.24, G:0.03, T:0.21
Consensus pattern (10 bp):
TACACTACAA
Found at i:211687 original size:23 final size:23
Alignment explanation
Indices: 211657--211702 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
211647 AAATAAAACC
211657 ATCAGTCCTTCTAAACAAGGTAA
1 ATCAGTCCTTCTAAACAAGGTAA
211680 ATCAGTCCTTCTAAACAAGGTAA
1 ATCAGTCCTTCTAAACAAGGTAA
211703 TGTTAAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (23 bp):
ATCAGTCCTTCTAAACAAGGTAA
Found at i:212717 original size:5 final size:5
Alignment explanation
Indices: 212679--212716 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
212669 TATAGGAAGC
*
212679 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAGT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
212717 GGTTAATGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:221636 original size:274 final size:274
Alignment explanation
Indices: 221147--221694 Score: 1069
Period size: 274 Copynumber: 2.0 Consensus size: 274
221137 ATTCGAATTA
221147 ATTACAAGAGAAATAGACTATGTCTATTTATAGGCTTGTAAAACATTATTCTAATAGGAGTAAAA
1 ATTACAAGAGAAATAGACTATGTCTATTTATAGGCTTGTAAAACATTATTCTAATAGGAGTAAAA
*
221212 CTCCTTATTCTAATCAATATCAAATAGATGGAGTTTAATAAGGTTTAAAAAAACCTTATTTTCAA
66 CTCCTTATTCTAATCAATATCAAATAGATGGAGTTTAATAAGGTTTAAAAAAACCTTATTTTAAA
*
221277 ATAAAACAAAAGACCTATAATTCTATAGCGATTTTACTTTTATTTTATTTTACCACTGTATTTGA
131 ATAAAACAAAAGAACTATAATTCTATAGCGATTTTACTTTTATTTTATTTTACCACTGTATTTGA
221342 TTTAAATAAGGATTCGAGTCACTTAATTCTAACAATTTCCACATTGACACGAATTCTTAATGAAC
196 TTTAAATAAGGATTCGAGTCACTTAATTCTAACAATTTCCACATTGACACGAATTCTTAATGAAC
221407 AAGTTCTTCATCTT
261 AAGTTCTTCATCTT
221421 ATTACAAGAGAAATAGACTATGTCTATTTATAGGCTTGTAAAACATTATTCTAATAGGAGTAAAA
1 ATTACAAGAGAAATAGACTATGTCTATTTATAGGCTTGTAAAACATTATTCTAATAGGAGTAAAA
221486 CTCCTTATTCTAATCAATATCAAATAGATGGAGTTTAATAAGGTTTAAAAAAACCTTATTTTAAA
66 CTCCTTATTCTAATCAATATCAAATAGATGGAGTTTAATAAGGTTTAAAAAAACCTTATTTTAAA
*
221551 ATAAAATAAAAGAACTATAATTCTATAGCGATTTTACTTTTATTTTATTTTACCACTGTATTTGA
131 ATAAAACAAAAGAACTATAATTCTATAGCGATTTTACTTTTATTTTATTTTACCACTGTATTTGA
221616 TTTAAATAAGGATTCGAGTCACTTAATTCTAACAATTTCCACATTGACACGAATTCTTAATGAAC
196 TTTAAATAAGGATTCGAGTCACTTAATTCTAACAATTTCCACATTGACACGAATTCTTAATGAAC
221681 AAGTTCTTCATCTT
261 AAGTTCTTCATCTT
221695 GAACTCTCAA
Statistics
Matches: 271, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
274 271 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (274 bp):
ATTACAAGAGAAATAGACTATGTCTATTTATAGGCTTGTAAAACATTATTCTAATAGGAGTAAAA
CTCCTTATTCTAATCAATATCAAATAGATGGAGTTTAATAAGGTTTAAAAAAACCTTATTTTAAA
ATAAAACAAAAGAACTATAATTCTATAGCGATTTTACTTTTATTTTATTTTACCACTGTATTTGA
TTTAAATAAGGATTCGAGTCACTTAATTCTAACAATTTCCACATTGACACGAATTCTTAATGAAC
AAGTTCTTCATCTT
Found at i:224816 original size:9 final size:9
Alignment explanation
Indices: 224802--224832 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
224792 GTTAAACGAA
224802 TCGAGTTAT
1 TCGAGTTAT
*
224811 TCGAGTTAA
1 TCGAGTTAT
224820 TCGAGTTAT
1 TCGAGTTAT
224829 TCGA
1 TCGA
224833 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:224903 original size:9 final size:9
Alignment explanation
Indices: 224886--224922 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
224876 TGAGTTTTCA
224886 AATTCGAAT
1 AATTCGAAT
*
224895 AACTCGAAT
1 AATTCGAAT
224904 AATTCGAAT
1 AATTCGAAT
224913 AATTCGAAT
1 AATTCGAAT
224922 A
1 A
224923 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:228393 original size:17 final size:17
Alignment explanation
Indices: 228369--228421 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 17
228359 ACTTTCCTTC
228369 AAACTTTTATT-TCCCA
1 AAACTTTTATTCTCCCA
*
228385 AAACTTTTTATTCTCCCCCT
1 AAAC-TTTTATTCT--CCCA
228405 AAACTTTTACTTCTCCC
1 AAACTTTTA-TTCTCCC
228422 CCTTTACTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
16 4 0.13
17 7 0.23
18 4 0.13
19 5 0.16
20 11 0.35
ACGTcount: A:0.25, C:0.32, G:0.00, T:0.43
Consensus pattern (17 bp):
AAACTTTTATTCTCCCA
Found at i:228410 original size:20 final size:20
Alignment explanation
Indices: 228385--228424 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
228375 TTATTTCCCA
228385 AAACTTTTTA-TTCTCCCCCT
1 AAAC-TTTTACTTCTCCCCCT
228405 AAACTTTTACTTCTCCCCCT
1 AAACTTTTACTTCTCCCCCT
228425 TTACTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (20 bp):
AAACTTTTACTTCTCCCCCT
Found at i:231853 original size:23 final size:23
Alignment explanation
Indices: 231827--231882 Score: 87
Period size: 23 Copynumber: 2.4 Consensus size: 23
231817 ATTCAAAAAA
231827 TTAAA-TATAAAGATAAAATAAAT
1 TTAAACTA-AAAGATAAAATAAAT
*
231850 TTAAACTAAAAGATAAAATGAAT
1 TTAAACTAAAAGATAAAATAAAT
231873 TTAAACTAAA
1 TTAAACTAAA
231883 CTGATACAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 29 0.94
24 2 0.06
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (23 bp):
TTAAACTAAAAGATAAAATAAAT
Found at i:232779 original size:14 final size:13
Alignment explanation
Indices: 232751--232798 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
232741 AATGTTATTT
232751 TTTTCAAT--AAA
1 TTTTCAATAAAAA
232762 -TTTCAAATAAAAA
1 TTTTC-AATAAAAA
*
232775 TTTTCAACAAAAA
1 TTTTCAATAAAAA
232788 TTTTCAATAAA
1 TTTTCAATAAA
232799 TTTGATTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
10 4 0.13
11 3 0.10
13 20 0.65
14 4 0.13
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTTCAATAAAAA
Found at i:258373 original size:18 final size:16
Alignment explanation
Indices: 258350--258389 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 16
258340 AGAATAATAC
258350 AAAAATAATAATTATATT
1 AAAAATAA-AATTATA-T
258368 AAAAAT-AAATTATAT
1 AAAAATAAAATTATAT
258383 AAAAATA
1 AAAAATA
258390 TTACACATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 7 0.33
17 1 0.05
18 6 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAATAAAATTATAT
Found at i:261787 original size:13 final size:13
Alignment explanation
Indices: 261769--261820 Score: 52
Period size: 13 Copynumber: 3.7 Consensus size: 13
261759 ATCGTTCAAT
261769 TTAAATTATATTA
1 TTAAATTATATTA
261782 TTAAATTATATTCAA
1 TTAAATTATATT--A
261797 TTTTAAATTATATT-
1 --TTAAATTATATTA
261811 TTAAAATTAT
1 TT-AAATTAT
261821 CTATCGGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 2 0.06
13 19 0.56
15 1 0.03
17 12 0.35
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (13 bp):
TTAAATTATATTA
Found at i:261802 original size:30 final size:29
Alignment explanation
Indices: 261763--261820 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
261753 ATTATTATCG
261763 TTCAATTTAAATTATATTATT-AAATTATA
1 TTCAATTTAAATTATATT-TTAAAATTATA
261792 TTCAATTTTAAATTATATTTTAAAATTAT
1 TTCAA-TTTAAATTATATTTTAAAATTAT
261821 CTATCGGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (29 bp):
TTCAATTTAAATTATATTTTAAAATTATA
Found at i:261804 original size:17 final size:16
Alignment explanation
Indices: 261763--261810 Score: 66
Period size: 13 Copynumber: 3.1 Consensus size: 16
261753 ATTATTATCG
261763 TTCAATTTAAATTATA
1 TTCAATTTAAATTATA
261779 TT--A-TTAAATTATA
1 TTCAATTTAAATTATA
261792 TTCAATTTTAAATTATA
1 TTCAA-TTTAAATTATA
261809 TT
1 TT
261811 TTAAAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 12 0.43
14 1 0.04
15 1 0.04
16 2 0.07
17 12 0.43
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (16 bp):
TTCAATTTAAATTATA
Found at i:271033 original size:22 final size:21
Alignment explanation
Indices: 271004--271047 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
270994 TTTTAATAAA
*
271004 TAAATAAAATATTAAAAATAT
1 TAAATAAAATAATAAAAATAT
*
271025 TAAATTAAAATAATATAAATAT
1 TAAA-TAAAATAATAAAAATAT
271047 T
1 T
271048 CTTCAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATAAAATAATAAAAATAT
Found at i:278599 original size:63 final size:63
Alignment explanation
Indices: 278407--278600 Score: 210
Period size: 63 Copynumber: 3.1 Consensus size: 63
278397 AATACAAGAC
* * * * * * *
278407 GGAAGAACCTGATCATAGTGAACCCAAAGCTATA-GATATGACTACCGAACAGCTTCCCGTGGA
1 GGAAGAACCTGATCATACTGAAGCCAAAGCTA-AGGATTTGAGTACCGGACCGCTTCTCGTGGA
* * * * * * * *
278470 GGAAGTACCTGATCCTACTGAAGCCAAAGGTGAGGATTTGAGTACCAGACCGCTTGTTGCGGA
1 GGAAGAACCTGATCATACTGAAGCCAAAGCTAAGGATTTGAGTACCGGACCGCTTCTCGTGGA
* * *
278533 GGAAGAACCTGAGCATACTGAAGCCAAAGCTAAGGATTTGAGTACCGGACCGCTTCTCATGAA
1 GGAAGAACCTGATCATACTGAAGCCAAAGCTAAGGATTTGAGTACCGGACCGCTTCTCGTGGA
278596 GGAAG
1 GGAAG
278601 GAAGCACCGT
Statistics
Matches: 104, Mismatches: 26, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
62 1 0.01
63 103 0.99
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (63 bp):
GGAAGAACCTGATCATACTGAAGCCAAAGCTAAGGATTTGAGTACCGGACCGCTTCTCGTGGA
Found at i:286454 original size:32 final size:32
Alignment explanation
Indices: 286411--286476 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
286401 ATTAAACAAA
*
286411 ATGAGTAACCCATTGATTCATCTTAAGGCCAT
1 ATGAGTAACCCATTGATTCACCTTAAGGCCAT
*
286443 ATGAGTGACCCATTGATTCACCTTAAGGCCAT
1 ATGAGTAACCCATTGATTCACCTTAAGGCCAT
286475 AT
1 AT
286477 CTACACTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (32 bp):
ATGAGTAACCCATTGATTCACCTTAAGGCCAT
Found at i:294935 original size:35 final size:35
Alignment explanation
Indices: 294889--294959 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
294879 CTCGGGCTCG
**
294889 AGAAGTCGCCTTGTTAAAGAGTCTACTAGTTTGCC
1 AGAAGTCGCCTTGGGAAAGAGTCTACTAGTTTGCC
294924 AGAAGTCGCCTTGGGAAAGAGTCTACTAGTTTGCC
1 AGAAGTCGCCTTGGGAAAGAGTCTACTAGTTTGCC
294959 A
1 A
294960 AGACGAGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (35 bp):
AGAAGTCGCCTTGGGAAAGAGTCTACTAGTTTGCC
Found at i:304357 original size:174 final size:170
Alignment explanation
Indices: 304050--304382 Score: 440
Period size: 174 Copynumber: 1.9 Consensus size: 170
304040 TTGAAGCCAG
* * *
304050 AGATCTTATATCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATATCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATT
* *
304115 ACAATGGAGCGGATTAAAGGATCCTATCTCTCTGAAGTTACAGTAGAAAAGATCACATCAGGTCT
66 ACAATGGAGCGGATTAAAGGATCCTATCTCTCTGAAGTTACAGCAGAAAAGATCACATCAAGTCT
*
304180 TA-TTCCTCT-GAGATTACAGTGGAACAGACCAAAGAATTTC
131 TATTTCC-CTAAAGA-TACAGTGGAACAGACCAAAGAATTTC
* *
304220 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCTGA-AGT
1 AGATCTTATATCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGA-T
* * ** *
304283 TACAATGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATC
65 TACAATGGAGCGGA-T----TAAAGGATCCTATCTCTCTGAAGTTACAGCAGAAAAGATCACATC
*
304348 AAGTCTTATTTCCCTAAAGATGCAGTGGAACAGAC
125 AAGTCTTATTTCCCTAAAGATACAGTGGAACAGAC
304383 TGAAAACAAT
Statistics
Matches: 141, Mismatches: 14, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
168 1 0.01
169 29 0.21
170 42 0.30
174 62 0.44
175 7 0.05
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (170 bp):
AGATCTTATATCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATT
ACAATGGAGCGGATTAAAGGATCCTATCTCTCTGAAGTTACAGCAGAAAAGATCACATCAAGTCT
TATTTCCCTAAAGATACAGTGGAACAGACCAAAGAATTTC
Found at i:306054 original size:53 final size:53
Alignment explanation
Indices: 305996--306101 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
305986 GAGGATCCGC
305996 GTGTTTTCTTTGCGAAGGGGCTAATTGCTCGTTTAACCCCTCCGCAATTTTAA
1 GTGTTTTCTTTGCGAAGGGGCTAATTGCTCGTTTAACCCCTCCGCAATTTTAA
* *
306049 GTGTTTTCTTTGCGAAGGGGCTAATTGCTCGTTTAGCCCCTCCGCAGTTTTAA
1 GTGTTTTCTTTGCGAAGGGGCTAATTGCTCGTTTAACCCCTCCGCAATTTTAA
306102 TTATTTTTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (53 bp):
GTGTTTTCTTTGCGAAGGGGCTAATTGCTCGTTTAACCCCTCCGCAATTTTAA
Found at i:306556 original size:19 final size:21
Alignment explanation
Indices: 306532--306573 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
306522 TCCTGCTTTT
*
306532 TATTTATTTA-ATAT-CTATA
1 TATTTATATACATATACTATA
306551 TATTTATATACATATACTATA
1 TATTTATATACATATACTATA
306572 TA
1 TA
306574 ATATTTATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 4 0.20
21 7 0.35
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTTATATACATATACTATA
Found at i:309934 original size:36 final size:36
Alignment explanation
Indices: 309887--309958 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
309877 CGCCTTGTTA
309887 AAGAGTCTACTAGTTTGCCAAGACGAGAAGACGGAG
1 AAGAGTCTACTAGTTTGCCAAGACGAGAAGACGGAG
309923 AAGAGTCTACTAGTTTGCCAAGACGAGAAGACGGAG
1 AAGAGTCTACTAGTTTGCCAAGACGAGAAGACGGAG
309959 TTGAAGATCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.17, G:0.31, T:0.17
Consensus pattern (36 bp):
AAGAGTCTACTAGTTTGCCAAGACGAGAAGACGGAG
Found at i:319340 original size:174 final size:170
Alignment explanation
Indices: 319033--319365 Score: 440
Period size: 174 Copynumber: 1.9 Consensus size: 170
319023 TTGAAGCCAG
* * *
319033 AGATCTTATATCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATATCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATT
* *
319098 ACAATGGAGCGGATTAAAGGATCCTATCTCTCTGAAGTTACAGTAGAAAAGATCACATCAGGTCT
66 ACAATGGAGCGGATTAAAGGATCCTATCTCTCTGAAGTTACAGCAGAAAAGATCACATCAAGTCT
*
319163 TA-TTCCTCT-GAGATTACAGTGGAACAGACCAAAGAATTTC
131 TATTTCC-CTAAAGA-TACAGTGGAACAGACCAAAGAATTTC
* *
319203 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCTGA-AGT
1 AGATCTTATATCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGA-T
* * ** *
319266 TACAATGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATC
65 TACAATGGAGCGGA-T----TAAAGGATCCTATCTCTCTGAAGTTACAGCAGAAAAGATCACATC
*
319331 AAGTCTTATTTCCCTAAAGATGCAGTGGAACAGAC
125 AAGTCTTATTTCCCTAAAGATACAGTGGAACAGAC
319366 TGAAAACAAT
Statistics
Matches: 141, Mismatches: 14, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
168 1 0.01
169 29 0.21
170 42 0.30
174 62 0.44
175 7 0.05
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (170 bp):
AGATCTTATATCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATT
ACAATGGAGCGGATTAAAGGATCCTATCTCTCTGAAGTTACAGCAGAAAAGATCACATCAAGTCT
TATTTCCCTAAAGATACAGTGGAACAGACCAAAGAATTTC
Found at i:324320 original size:43 final size:43
Alignment explanation
Indices: 324272--324359 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
324262 TGAATCTTAC
* *
324272 ATTGAGATAATCTTATATTCCATTATAATCTTATATTTAGGTA
1 ATTGAGATAATCTTACATTCCACTATAATCTTATATTTAGGTA
*
324315 ATTGAGATAATCTTACATTCCACTATAATCTTATATTTCGGTA
1 ATTGAGATAATCTTACATTCCACTATAATCTTATATTTAGGTA
324358 AT
1 AT
324360 CTTATTACGA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.44
Consensus pattern (43 bp):
ATTGAGATAATCTTACATTCCACTATAATCTTATATTTAGGTA
Found at i:325300 original size:16 final size:18
Alignment explanation
Indices: 325274--325314 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
325264 AAATTAAGTC
*
325274 AAAATAATATAAAATTTAA
1 AAAAT-ATATAACATTTAA
*
325293 AAAATATATAACCTTTAA
1 AAAATATATAACATTTAA
325311 AAAA
1 AAAA
325315 CAAGGTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATATATAACATTTAA
Found at i:326195 original size:21 final size:21
Alignment explanation
Indices: 326152--326209 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
326142 TTAAATCTCA
*
326152 AACCTCAAA-ATTGAATCA-TG
1 AACCTCAAACATT-AAACACTG
*
326172 AACTTCAAACATTAAACACTG
1 AACCTCAAACATTAAACACTG
* *
326193 AACCTCGAACCTTAAAC
1 AACCTCAAACATTAAAC
326210 GGGTTCGGGG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 12 0.39
21 19 0.61
ACGTcount: A:0.45, C:0.26, G:0.07, T:0.22
Consensus pattern (21 bp):
AACCTCAAACATTAAACACTG
Found at i:332356 original size:10 final size:10
Alignment explanation
Indices: 332321--332368 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
332311 TTTTTGCATA
332321 TCTTTCCTTCT
1 TCTTTCC-TCT
*
332332 TCTTT-CTCA
1 TCTTTCCTCT
332341 TCTTTCCTCT
1 TCTTTCCTCT
332351 TCTTTCCCTCT
1 TCTTT-CCTCT
*
332362 TTTTTCC
1 TCTTTCC
332369 CTAATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 7 0.22
10 11 0.34
11 14 0.44
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (10 bp):
TCTTTCCTCT
Found at i:333504 original size:12 final size:12
Alignment explanation
Indices: 333464--333504 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
333454 CTGAAGCAGT
333464 GGCTCCAGCTCC
1 GGCTCCAGCTCC
* *
333476 GGATCCGGCTCC
1 GGCTCCAGCTCC
333488 GGCTCCAGCTCC
1 GGCTCCAGCTCC
*
333500 AGCTC
1 GGCTC
333505 TGGTTCTGGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.10, C:0.46, G:0.27, T:0.17
Consensus pattern (12 bp):
GGCTCCAGCTCC
Found at i:337558 original size:12 final size:12
Alignment explanation
Indices: 337518--337558 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
337508 CTGAAGCAGT
337518 GGCTCCAGCTCC
1 GGCTCCAGCTCC
* *
337530 GGATCCGGCTCC
1 GGCTCCAGCTCC
337542 GGCTCCAGCTCC
1 GGCTCCAGCTCC
*
337554 AGCTC
1 GGCTC
337559 TGGTTCTGGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.10, C:0.46, G:0.27, T:0.17
Consensus pattern (12 bp):
GGCTCCAGCTCC
Found at i:340432 original size:24 final size:24
Alignment explanation
Indices: 340402--340448 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
340392 TTTTGCCGAG
340402 ATCATTTATTTAAATACAACATTC
1 ATCATTTATTTAAATACAACATTC
*
340426 ATCATTTATTTACATACAACATT
1 ATCATTTATTTAAATACAACATT
340449 TTTTTTTGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (24 bp):
ATCATTTATTTAAATACAACATTC
Found at i:344870 original size:18 final size:17
Alignment explanation
Indices: 344848--344891 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
344838 AAATCAAAGT
344848 AATTTTTAAAATTCAAA
1 AATTTTTAAAATTCAAA
* *
344865 ATATTTATAAAAATTCTAA
1 A-ATTT-TTAAAATTCAAA
344884 AATTTTTA
1 AATTTTTA
344892 TTTTAAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
17 3 0.14
18 8 0.36
19 11 0.50
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTTTAAAATTCAAA
Found at i:344877 original size:19 final size:20
Alignment explanation
Indices: 344855--344892 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
344845 AGTAATTTTT
344855 AAAATTC-AAAATATTTATA
1 AAAATTCTAAAATATTTATA
*
344874 AAAATTCTAAAATTTTTAT
1 AAAATTCTAAAATATTTAT
344893 TTTAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATTCTAAAATATTTATA
Found at i:344954 original size:18 final size:17
Alignment explanation
Indices: 344900--344957 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
344890 TATTTTAAAC
344900 AAAAATTATAAATTTA-A
1 AAAAATTA-AAATTTATA
*
344917 AAAAACTCTAAAAATATATA
1 AAAAA-T-T-AAAATTTATA
344937 AAAAATTAAAATTTTATA
1 AAAAATTAAAA-TTTATA
344955 AAA
1 AAA
344958 TAATAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 9 0.26
18 10 0.29
19 8 0.24
20 7 0.21
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAATTAAAATTTATA
Found at i:347485 original size:17 final size:16
Alignment explanation
Indices: 347450--347488 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
347440 GGTGAGAAGT
347450 AAAAGTTTAGGGAAAA
1 AAAAGTTTAGGGAAAA
* * *
347466 AAAAGTTTTGGGGAAT
1 AAAAGTTTAGGGAAAA
347482 AAAAGTT
1 AAAAGTT
347489 AGAGGGAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.26, T:0.26
Consensus pattern (16 bp):
AAAAGTTTAGGGAAAA
Found at i:347620 original size:30 final size:31
Alignment explanation
Indices: 347581--347640 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
347571 AGAGGTGGGA
*
347581 TGGGAAGAGAACAAAAGTTTTAGGGGAAAAG
1 TGGGAAGAGAACAAAAATTTTAGGGGAAAAG
** *
347612 TGGG-AGAGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGAGAACAAAAATTTTAGGGGAAAA
347641 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.43, C:0.02, G:0.37, T:0.18
Consensus pattern (31 bp):
TGGGAAGAGAACAAAAATTTTAGGGGAAAAG
Found at i:360253 original size:25 final size:25
Alignment explanation
Indices: 360218--360277 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
360208 TTCATATTCA
360218 AGAATGCTCATATGAGCATGTA-AACG
1 AGAA-GCTCATATGAGC-TGTATAACG
*
360244 AGAAGCTCATGTGAGCTGTATAACG
1 AGAAGCTCATATGAGCTGTATAACG
360269 AGAAGCTCA
1 AGAAGCTCA
360278 ACCGAGTTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 4 0.12
25 24 0.75
26 4 0.12
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.22
Consensus pattern (25 bp):
AGAAGCTCATATGAGCTGTATAACG
Found at i:360288 original size:25 final size:24
Alignment explanation
Indices: 360231--360288 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
360221 ATGCTCATAT
***
360231 GAGCATGTAAACGAGAAGCTCATGT
1 GAGC-TGTAAACGAGAAGCTCAACC
360256 GAGCTGTATAACGAGAAGCTCAACC
1 GAGCTGTA-AACGAGAAGCTCAACC
*
360281 GAGTTGTA
1 GAGCTGTA
360289 CATCAGGAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 4 0.14
25 24 0.86
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (24 bp):
GAGCTGTAAACGAGAAGCTCAACC
Found at i:360357 original size:25 final size:25
Alignment explanation
Indices: 360294--360359 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
360284 TTGTACATCA
*
360294 GGAAGCTCATGTGAGCCATAAATCG
1 GGAAGCTCATGAGAGCCATAAATCG
* * *
360319 GGAAGCTCAAGAGAGCCATTAATTG
1 GGAAGCTCATGAGAGCCATAAATCG
*
360344 GGAAGCTCGTGAGAGC
1 GGAAGCTCATGAGAGC
360360 TAAATATCAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.18
Consensus pattern (25 bp):
GGAAGCTCATGAGAGCCATAAATCG
Found at i:361603 original size:25 final size:25
Alignment explanation
Indices: 361573--361630 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
361563 AACCCATATT
361573 AAATATATATTTTATTAAAAATAAA
1 AAATATATATTTTATTAAAAATAAA
361598 AAATATATATTTTATTAAAAATAAA
1 AAATATATATTTTATTAAAAATAAA
*
361623 ATATATAT
1 AAATATAT
361631 TTAATATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AAATATATATTTTATTAAAAATAAA
Found at i:361902 original size:13 final size:13
Alignment explanation
Indices: 361884--361919 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
361874 GTAAACGGTA
361884 AAATTTCTTA-ACG
1 AAATTT-TTATACG
361897 AAATTTTTATACG
1 AAATTTTTATACG
361910 AAATTTTTAT
1 AAATTTTTAT
361920 CATACTGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 3 0.14
13 19 0.86
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (13 bp):
AAATTTTTATACG
Found at i:367272 original size:5 final size:6
Alignment explanation
Indices: 367255--367282 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
367245 ATAATTTTAC
367255 ATAAAA ATAAAA ATAAAA ATAAAA ATAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAA
367283 TATAGACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:367494 original size:28 final size:28
Alignment explanation
Indices: 367445--367499 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
367435 CTACACTACT
* * *
367445 TTATGTATTATTTCATGCCACTGCAATC
1 TTATGCATTATTACATGCCACTACAATC
* *
367473 TTATGCATTATTAGATGTCACTACAAT
1 TTATGCATTATTACATGCCACTACAAT
367500 GCAATAAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (28 bp):
TTATGCATTATTACATGCCACTACAATC
Found at i:367826 original size:48 final size:48
Alignment explanation
Indices: 367755--367851 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
367745 CTCATTTGGT
367755 CATAGTTTAGGAATGTTTCTCAAAAGTGCTTTTGGAAAAAAAAAAACA
1 CATAGTTTAGGAATGTTTCTCAAAAGTGCTTTTGGAAAAAAAAAAACA
367803 CATAGTTTAGGAATGTTTCTCAAAAGTGCTTTTGGAAAAAAAAAAACA
1 CATAGTTTAGGAATGTTTCTCAAAAGTGCTTTTGGAAAAAAAAAAACA
367851 C
1 C
367852 TTTTAGGAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.29
Consensus pattern (48 bp):
CATAGTTTAGGAATGTTTCTCAAAAGTGCTTTTGGAAAAAAAAAAACA
Found at i:382635 original size:36 final size:36
Alignment explanation
Indices: 382595--382666 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
382585 CATGACTTGT
**
382595 TAAAAGCATTGTTCTACTATTAACCTATGAAAATGA
1 TAAAAGCATTGTTCTACTATTAACCTACAAAAATGA
382631 TAAAAGCATTGTTCTACTATTAACCTACAAAAATGA
1 TAAAAGCATTGTTCTACTATTAACCTACAAAAATGA
382667 GTATAGTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (36 bp):
TAAAAGCATTGTTCTACTATTAACCTACAAAAATGA
Found at i:384029 original size:39 final size:41
Alignment explanation
Indices: 383949--384029 Score: 103
Period size: 39 Copynumber: 2.0 Consensus size: 41
383939 AAAATAAACA
*
383949 TTAAAAATATTTTTAAAATAAAAAAAATAAAAAAATTTATT
1 TTAAAAATATTTTTAAAATAAAAAAAATAAAAAAATATATT
* * * *
383990 TTAAAAGTA-TTTTAAAAT-TAAAAATTAAAAATATATATT
1 TTAAAAATATTTTTAAAATAAAAAAAATAAAAAAATATATT
384029 T
1 T
384030 ATTATATTCG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.51
40 9 0.26
41 8 0.23
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (41 bp):
TTAAAAATATTTTTAAAATAAAAAAAATAAAAAAATATATT
Found at i:387887 original size:6 final size:6
Alignment explanation
Indices: 387878--387903 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
387868 CAACAACAAC
387878 GCCGAG GCCGAG GCCGAG GCCGAG GC
1 GCCGAG GCCGAG GCCGAG GCCGAG GC
387904 TTTTTATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.35, G:0.50, T:0.00
Consensus pattern (6 bp):
GCCGAG
Found at i:393180 original size:3 final size:3
Alignment explanation
Indices: 393172--393196 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
393162 TTAAAATTTG
393172 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
393197 TCTGCATAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:394195 original size:24 final size:25
Alignment explanation
Indices: 394161--394222 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
394151 TATATTAAAT
394161 ATATATATTTTTA-TTTTTAATCAA
1 ATATATATTTTTATTTTTTAATCAA
*
394185 ATATATTTTTTTATTTTTTAATCAA
1 ATATATATTTTTATTTTTTAATCAA
*
394210 ATATATATATTTA
1 ATATATATTTTTA
394223 ACATGGGTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 12 0.35
25 22 0.65
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (25 bp):
ATATATATTTTTATTTTTTAATCAA
Found at i:395402 original size:35 final size:35
Alignment explanation
Indices: 395356--395544 Score: 117
Period size: 35 Copynumber: 5.4 Consensus size: 35
395346 TATAAGTTAT
*
395356 AACAGTATATTACAAATTTTATAATAGTATATTAA
1 AACAGTATATTACAAATTTTATAACAGTATATTAA
** *** *
395391 AACAGTATATTATATCAAAAATTA-AGGTGTAGTATTTAT
1 AACAGTATA-T-TA-CAAATTTTATAACAGTA-TA-TTAA
* * * *
395430 AACAATATATTAAAACAGTATATTAAAACATTATATTAA
1 AACAGTATATTACAA-A-T-T-TTATAACAGTATATTAA
395469 AACA--ATA-T----A-TTTATAACAGTATATTAA
1 AACAGTATATTACAAATTTTATAACAGTATATTAA
**
395496 AACAAAATATTACAAATTTTATAACAGTATATTAA
1 AACAGTATATTACAAATTTTATAACAGTATATTAA
395531 AACAGTATATTACA
1 AACAGTATATTACA
395545 TTAAAAATTA
Statistics
Matches: 117, Mismatches: 19, Indels: 36
0.68 0.11 0.21
Matches are distributed among these distances:
27 19 0.16
28 1 0.01
29 3 0.03
30 1 0.01
31 1 0.01
34 1 0.01
35 39 0.33
36 4 0.03
37 12 0.10
38 10 0.09
39 18 0.15
40 5 0.04
41 3 0.03
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.36
Consensus pattern (35 bp):
AACAGTATATTACAAATTTTATAACAGTATATTAA
Found at i:395414 original size:81 final size:81
Alignment explanation
Indices: 395271--395431 Score: 261
Period size: 81 Copynumber: 2.0 Consensus size: 81
395261 AATATTATAT
* *
395271 TTATAACATTATATTACAAATTTTATAACAATATATTAAAACAGTATATTACAATAATAATTAAG
1 TTATAACAGTATATTACAAATTTTATAACAATATATTAAAACAGTATATTACAATAAAAATTAAG
395336 GTGTAGTATTTATAAG
66 GTGTAGTATTTATAAG
* * *
395352 TTATAACAGTATATTACAAATTTTATAATAGTATATTAAAACAGTATATTA-TATCAAAAATTAA
1 TTATAACAGTATATTACAAATTTTATAACAATATATTAAAACAGTATATTACAAT-AAAAATTAA
395416 GGTGTAGTATTTATAA
65 GGTGTAGTATTTATAA
395432 CAATATATTA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
80 2 0.03
81 72 0.97
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (81 bp):
TTATAACAGTATATTACAAATTTTATAACAATATATTAAAACAGTATATTACAATAAAAATTAAG
GTGTAGTATTTATAAG
Found at i:395451 original size:13 final size:13
Alignment explanation
Indices: 395421--395542 Score: 119
Period size: 13 Copynumber: 9.7 Consensus size: 13
395411 ATTAAGGTGT
*
395421 AGTAT-TTATAAC
1 AGTATATTAAAAC
*
395433 AATATATTAAAAC
1 AGTATATTAAAAC
395446 AGTATATTAAAAC
1 AGTATATTAAAAC
*
395459 ATTATATTAAAAC
1 AGTATATTAAAAC
* *
395472 AATATATTTATAAC
1 AGTATA-TTAAAAC
395486 AGTATATTAAAAC
1 AGTATATTAAAAC
** *
395499 AAAATATTACAA-
1 AGTATATTAAAAC
*
395511 A-T-T-TTATAAC
1 AGTATATTAAAAC
395521 AGTATATTAAAAC
1 AGTATATTAAAAC
395534 AGTATATTA
1 AGTATATTA
395543 CATTAAAAAT
Statistics
Matches: 90, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
9 5 0.06
10 2 0.02
11 1 0.01
12 6 0.07
13 65 0.72
14 11 0.12
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.36
Consensus pattern (13 bp):
AGTATATTAAAAC
Found at i:396356 original size:23 final size:25
Alignment explanation
Indices: 396302--396351 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
396292 ATTATACATG
396302 TACATATATACATATTCGAAACTAA
1 TACATATATACATATTCGAAACTAA
396327 TACATATATACATATTCGAAACTAA
1 TACATATATACATATTCGAAACTAA
396352 CATATACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (25 bp):
TACATATATACATATTCGAAACTAA
Found at i:396360 original size:29 final size:28
Alignment explanation
Indices: 396296--396364 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 28
396286 CAAGAAATTA
*
396296 TACATGTACATATATACATATTCGAAAC
1 TACATATACATATATACATATTCGAAAC
396324 T--A-ATACATATATACATATTCGAAAC
1 TACATATACATATATACATATTCGAAAC
396349 TAACATATACATATAT
1 T-ACATATACATATAT
396365 CAATTCATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
25 23 0.64
26 1 0.03
28 2 0.06
29 10 0.28
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.33
Consensus pattern (28 bp):
TACATATACATATATACATATTCGAAAC
Found at i:397635 original size:7 final size:7
Alignment explanation
Indices: 397623--397671 Score: 64
Period size: 7 Copynumber: 7.1 Consensus size: 7
397613 ACACGGGGTC
397623 GGGAAAT
1 GGGAAAT
397630 GGGAAAT
1 GGGAAAT
397637 GGGAAAT
1 GGGAAAT
397644 GGGAAAT
1 GGGAAAT
* *
397651 GGG-GAG
1 GGGAAAT
*
397657 GGGAATT
1 GGGAAAT
397664 GGGAAAT
1 GGGAAAT
397671 G
1 G
397672 TAAATGTAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
6 4 0.11
7 31 0.89
ACGTcount: A:0.37, C:0.00, G:0.49, T:0.14
Consensus pattern (7 bp):
GGGAAAT
Found at i:397666 original size:20 final size:21
Alignment explanation
Indices: 397623--397671 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
397613 ACACGGGGTC
*
397623 GGGAAATGGGAAATGGGAAAT
1 GGGAAATGGGAAAGGGGAAAT
* *
397644 GGGAAATGGG-GAGGGGAATT
1 GGGAAATGGGAAAGGGGAAAT
397664 GGGAAATG
1 GGGAAATG
397672 TAAATGTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.37, C:0.00, G:0.49, T:0.14
Consensus pattern (21 bp):
GGGAAATGGGAAAGGGGAAAT
Found at i:397730 original size:5 final size:5
Alignment explanation
Indices: 397720--397746 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
397710 TTAATTAGAT
397720 CCGGG CCGGG CCGGG CCGGG CCGGG CC
1 CCGGG CCGGG CCGGG CCGGG CCGGG CC
397747 CGGGACAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.44, G:0.56, T:0.00
Consensus pattern (5 bp):
CCGGG
Found at i:398549 original size:72 final size:75
Alignment explanation
Indices: 398467--398628 Score: 195
Period size: 80 Copynumber: 2.1 Consensus size: 75
398457 ATTTAATTAT
*
398467 CCTTTTTATTTAATTAGGT-TC-GAA-CTTTTAGTTTGTGTTTTCCTAAAAGAGAACTCCTTTTA
1 CCTTTCTATTTAATTAGGTCTCAGAATCTTTTAGTTTGTGTTTTCCTAAAAGAGAACTCCTTTTA
398529 TTAATATCAA
66 TTAATATCAA
* * *
398539 CCTTTCTATTTAATTAGGTCGTCAATAGGAATTTTTTAGTTTGTGTTTTTCTAAAAGGGAACTCC
1 CCTTTCTATTTAATTAGGTC-TC---A-GAATCTTTTAGTTTGTGTTTTCCTAAAAGAGAACTCC
*
398604 TTTTATTAATGTCAA
61 TTTTATTAATATCAA
**
398619 ATTTTCTATT
1 CCTTTCTATT
398629 AATGTTGAAG
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
72 18 0.24
74 2 0.03
79 3 0.04
80 52 0.69
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (75 bp):
CCTTTCTATTTAATTAGGTCTCAGAATCTTTTAGTTTGTGTTTTCCTAAAAGAGAACTCCTTTTA
TTAATATCAA
Found at i:403948 original size:17 final size:17
Alignment explanation
Indices: 403926--403959 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
403916 GATTTAACCC
403926 TTTAAAAATTTAATAAT
1 TTTAAAAATTTAATAAT
403943 TTTAAAAATTTAATAAT
1 TTTAAAAATTTAATAAT
403960 AAAATTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAAAATTTAATAAT
Found at i:405470 original size:40 final size:41
Alignment explanation
Indices: 405426--405516 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 41
405416 TCCTTGAGAG
** *
405426 CGCGATTTCCTTCCACGTTAGCAT-C-TCGCGCTGACGTGGA
1 CGCGATTTCCTGACACG-TACCATACATCGCGCTGACGTGGA
*
405466 CGCGATTTCCTGACACGTACCCTGACATCGCGCTGACGTGGA
1 CGCGATTTCCTGACACGTACCAT-ACATCGCGCTGACGTGGA
405508 CGCGATTTC
1 CGCGATTTC
405517 GGGAAAAATG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
39 4 0.09
40 15 0.34
41 1 0.02
42 24 0.55
ACGTcount: A:0.16, C:0.33, G:0.25, T:0.25
Consensus pattern (41 bp):
CGCGATTTCCTGACACGTACCATACATCGCGCTGACGTGGA
Found at i:406420 original size:16 final size:16
Alignment explanation
Indices: 406381--406426 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
406371 AAATTCATAA
*
406381 TTAAATCATTTTAAGAT
1 TTAAATTATTTT-AGAT
* *
406398 TTTAATTATTTTATAT
1 TTAAATTATTTTAGAT
406414 TTAAATTATTTTA
1 TTAAATTATTTTA
406427 ACTATTTACC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (16 bp):
TTAAATTATTTTAGAT
Found at i:412226 original size:13 final size:11
Alignment explanation
Indices: 412198--412222 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
412188 ATTATTTTTA
412198 ATTATATAATT
1 ATTATATAATT
412209 ATTATATAATT
1 ATTATATAATT
412220 ATT
1 ATT
412223 TTATTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTATATAATT
Found at i:413267 original size:6 final size:6
Alignment explanation
Indices: 413256--413304 Score: 89
Period size: 6 Copynumber: 8.2 Consensus size: 6
413246 TACAGGATAG
*
413256 ATACAT ATACAT ATACAT ATACAT ATACAT ATGCAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
413304 A
1 A
413305 AATAAATAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:418244 original size:18 final size:19
Alignment explanation
Indices: 418221--418258 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
418211 TAATATTTTA
418221 TATTTTGTTTATTTT-AAT
1 TATTTTGTTTATTTTGAAT
*
418239 TATTTTTTTTATTTTGAAT
1 TATTTTGTTTATTTTGAAT
418258 T
1 T
418259 TTTCTTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (19 bp):
TATTTTGTTTATTTTGAAT
Found at i:419958 original size:121 final size:122
Alignment explanation
Indices: 419733--419960 Score: 341
Period size: 121 Copynumber: 1.9 Consensus size: 122
419723 TGAAAAAAGA
* * ** * *
419733 AAATCTTTTTTAGTATATGTGTATGTATATGCAAGTGCTTAAGAATGTACACATAGTTAGGCCCT
1 AAATATTTTTTAGCATATGCATATGTATATGCAAGTGCTTAAGAA-GTACACACAATTAGGCCCT
*
419798 TTGACAGGTCTCAAAGATCAGAGGCTCAAATGGATTTATTTGAAATTGTATCAACAAG
65 ATGACAGGTCTCAAAGATCAGAGGCTCAAATGGATTTATTTGAAATTGTATCAACAAG
419856 AAATATTTTTTAGCATATGCATATGTATATGCAAGTGCTTAAGAA-TACACACAATTAGGCCCTA
1 AAATATTTTTTAGCATATGCATATGTATATGCAAGTGCTTAAGAAGTACACACAATTAGGCCCTA
* * * *
419920 TGATAGGTCTCAAAGATCTGAGGTTCAAATGGGTTTATTTG
66 TGACAGGTCTCAAAGATCAGAGGCTCAAATGGATTTATTTG
419961 CTTGCGATTG
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
121 53 0.56
123 41 0.44
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.34
Consensus pattern (122 bp):
AAATATTTTTTAGCATATGCATATGTATATGCAAGTGCTTAAGAAGTACACACAATTAGGCCCTA
TGACAGGTCTCAAAGATCAGAGGCTCAAATGGATTTATTTGAAATTGTATCAACAAG
Found at i:430003 original size:17 final size:18
Alignment explanation
Indices: 429981--430016 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
429971 TTCTTCTTAT
429981 TCTTCAAAAAA-AGTTCC
1 TCTTCAAAAAAGAGTTCC
429998 TCTTCAAAAAAGAGTTCC
1 TCTTCAAAAAAGAGTTCC
430016 T
1 T
430017 GGTAAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (18 bp):
TCTTCAAAAAAGAGTTCC
Found at i:430254 original size:19 final size:19
Alignment explanation
Indices: 430232--430287 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
430222 ATATTTTAAT
430232 TTTATTTTAATAATAAATG
1 TTTATTTTAATAATAAATG
* *
430251 TTTATTATAATTATAAATG
1 TTTATTTTAATAATAAATG
430270 --TA--TTAATAATAAATG
1 TTTATTTTAATAATAAATG
430285 TTT
1 TTT
430288 TGTAGTATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 11 0.35
17 3 0.10
19 17 0.55
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (19 bp):
TTTATTTTAATAATAAATG
Found at i:434977 original size:149 final size:147
Alignment explanation
Indices: 434709--435004 Score: 565
Period size: 149 Copynumber: 2.0 Consensus size: 147
434699 GCAGTGACCC
434709 GAAAAATACGCAAGTACCTTGCCCTTATCATGAAAACTCTCTCTCTATACACACACACATATATA
1 GAAAAATACGCAAGTACCTTGCCCTTATCATGAAAACTCTCTCTCTATACACACACACATATATA
*
434774 CATGTATTTCCTCGTAGTATAATCTTCTAAGACTAGTGTGCTTAATGAATTGTGCAGGCCATGGT
66 CATGTATTTCCGCGTAGTATAATCTTCTAAGACTAGTGTGCTTAATGAATTGTGCAGGCCATGGT
434839 CCTATCATAACGGCGGA
131 CCTATCATAACGGCGGA
434856 GAAAAATACGCAAGTACCTTGCCCTTATCATGAAAACTCTCTCTCTATACACACACACATATATA
1 GAAAAATACGCAAGTACCTTGCCCTTATCATGAAAACTCTCTCTCTATACACACACAC--ATATA
434921 TACATGTATTTCCGCGTAGTATAATCTTCTAAGACTAGTGTGCTTAATGAATTGTGCAGGCCATG
64 TACATGTATTTCCGCGTAGTATAATCTTCTAAGACTAGTGTGCTTAATGAATTGTGCAGGCCATG
434986 GTCCTATCATAACGGCGGA
129 GTCCTATCATAACGGCGGA
435005 TCTTGGCCAA
Statistics
Matches: 146, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
147 58 0.40
149 88 0.60
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (147 bp):
GAAAAATACGCAAGTACCTTGCCCTTATCATGAAAACTCTCTCTCTATACACACACACATATATA
CATGTATTTCCGCGTAGTATAATCTTCTAAGACTAGTGTGCTTAATGAATTGTGCAGGCCATGGT
CCTATCATAACGGCGGA
Found at i:436026 original size:42 final size:42
Alignment explanation
Indices: 435899--436068 Score: 241
Period size: 42 Copynumber: 4.0 Consensus size: 42
435889 AAATTGATTC
* * * *
435899 GGTGAGATTAAATGAAAAACTAAAAACATAAATCCTCCTAATTTA
1 GGTGGGATTAAATGAAAAAATAAAAAGATAAA---TCCTAATTGA
435944 GGTGGGATTAAATGAAAAAAATAAAAAGATAAATCCTAATTGA
1 GGTGGGATTAAATG-AAAAAATAAAAAGATAAATCCTAATTGA
** *
435987 GGTGGGATTAAATGAAAAGCTAAAAAGATAAATCTTAATTGA
1 GGTGGGATTAAATGAAAAAATAAAAAGATAAATCCTAATTGA
436029 GGTGGGATTAAATGAAAAAATAAAAAGATAAATCCTAATT
1 GGTGGGATTAAATGAAAAAATAAAAAGATAAATCCTAATT
436069 CGGGTGACAT
Statistics
Matches: 114, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
42 62 0.54
43 23 0.20
45 13 0.11
46 16 0.14
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (42 bp):
GGTGGGATTAAATGAAAAAATAAAAAGATAAATCCTAATTGA
Found at i:436081 original size:84 final size:87
Alignment explanation
Indices: 435895--436081 Score: 276
Period size: 84 Copynumber: 2.2 Consensus size: 87
435885 ATGTAAATTG
*
435895 ATTC-GGTGAGATTAAATGAAAAACTAAAAACATAAATCCTCCTAATTTAGGTGGGATTAAATGA
1 ATTCGGGTGAGATTAAATGAAAAACTAAAAACATAAATCCT-CTAATTGAGGTGGGATTAAATGA
435959 AAAAAATAAAAAGATAAATCCTA
65 AAAAAATAAAAAGATAAATCCTA
* * *
435982 ATT-GAGGTGGGATTAAATGAAAAGCTAAAAAGATAAAT-CT-TAATTGAGGTGGGATTAAATG-
1 ATTCG-GGTGAGATTAAATGAAAAACTAAAAACATAAATCCTCTAATTGAGGTGGGATTAAATGA
436043 AAAAAATAAAAAGATAAATCCTA
65 AAAAAATAAAAAGATAAATCCTA
*
436066 ATTCGGGTGACATTAA
1 ATTCGGGTGAGATTAA
436082 CTGTGGGGCT
Statistics
Matches: 91, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
84 35 0.38
85 21 0.23
87 5 0.05
88 30 0.33
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.26
Consensus pattern (87 bp):
ATTCGGGTGAGATTAAATGAAAAACTAAAAACATAAATCCTCTAATTGAGGTGGGATTAAATGAA
AAAAATAAAAAGATAAATCCTA
Found at i:438022 original size:24 final size:24
Alignment explanation
Indices: 437995--438046 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
437985 TTAGTAAGTC
*
437995 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
438019 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
438043 AAAT
1 AAAT
438047 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:441705 original size:90 final size:84
Alignment explanation
Indices: 441546--441917 Score: 383
Period size: 94 Copynumber: 4.3 Consensus size: 84
441536 GAACAGAAGT
* * *
441546 ATCCTAATTCAGGCGGGATTAAATGAAAAACTAAAAACATAAGTCCTCCTAATTGAGGTGGGATT
1 ATCCTAATTGAGGTGGGATTAAATGAAAAACTAAAAACATAAATCCT-C-AATT-AGGTGGGATT
* *
441611 AAAAGAAAAACTAAAAACATAA
63 AAATGAAAAGCTAAAAACATAA
*
441633 ATCCTCCTAATTGAGGTGGGATTAAATGAAAAGCTAAAAACATAAATCCTCAA-T-GGTGGGATT
1 A---TCCTAATTGAGGTGGGATTAAATGAAAAACTAAAAACATAAATCCTCAATTAGGTGGGATT
441696 AAATGAAAAGCTAAAAACATAA
63 AAATGAAAAGCTAAAAACATAA
* ** *
441718 ATCCTAATTGAGTTGGGATTAAATGAAAAACTAAAAAGGTAAATCCT-AATTGAGGTGAGATTAA
1 ATCCTAATTGAGGTGGGATTAAATGAAAAACTAAAAACATAAATCCTCAATT-AGGTGGGATTAA
**
441782 ATGAAAATTTAAAAAGATATGCTTATATAA
65 ATGAAAAGCT--AAA-A-A--C----ATAA
* * * ** *
441812 ATCCTAATGGAGGTGGGATTAAAAGAAAAGCTAAAATGATAAATCCT-AATTGAGGTAGGATTAA
1 ATCCTAATTGAGGTGGGATTAAATGAAAAACTAAAAACATAAATCCTCAATT-AGGTGGGATTAA
*
441876 ATGAAAAGCTAAAAAGATAA
65 ATGAAAAGCTAAAAACATAA
441896 ATCCTAATTGAGGTGGGATTAA
1 ATCCTAATTGAGGTGGGATTAA
441918 CTGTGGGGCT
Statistics
Matches: 244, Mismatches: 25, Indels: 35
0.80 0.08 0.12
Matches are distributed among these distances:
81 2 0.01
82 43 0.18
84 43 0.18
85 30 0.12
86 3 0.01
87 3 0.01
88 3 0.01
89 1 0.00
90 44 0.18
91 1 0.00
92 3 0.01
94 68 0.28
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.25
Consensus pattern (84 bp):
ATCCTAATTGAGGTGGGATTAAATGAAAAACTAAAAACATAAATCCTCAATTAGGTGGGATTAAA
TGAAAAGCTAAAAACATAA
Found at i:441752 original size:42 final size:42
Alignment explanation
Indices: 441546--441917 Score: 399
Period size: 42 Copynumber: 8.5 Consensus size: 42
441536 GAACAGAAGT
* * *
441546 ATCCTAATTCAGGCGGGATTAAATGAAAAACTAAAAACATAA
1 ATCCTAATTGAGGTGGGATTAAATGAAAAGCTAAAAACATAA
* * *
441588 GTCCTCCTAATTGAGGTGGGATTAAAAGAAAAACTAAAAACATAA
1 ---ATCCTAATTGAGGTGGGATTAAATGAAAAGCTAAAAACATAA
441633 ATCCTCCTAATTGAGGTGGGATTAAATGAAAAGCTAAAAACATAA
1 A---TCCTAATTGAGGTGGGATTAAATGAAAAGCTAAAAACATAA
441678 ATCCTCAA-T--GGTGGGATTAAATGAAAAGCTAAAAACATAA
1 ATCCT-AATTGAGGTGGGATTAAATGAAAAGCTAAAAACATAA
* * **
441718 ATCCTAATTGAGTTGGGATTAAATGAAAAACTAAAAAGGTAA
1 ATCCTAATTGAGGTGGGATTAAATGAAAAGCTAAAAACATAA
* **
441760 ATCCTAATTGAGGTGAGATTAAATGAAAATTTAAAAAGATATGCTTATATAA
1 ATCCTAATTGAGGTGGGATTAAATGAAAAGCT--AAA-A-A--C----ATAA
* * **
441812 ATCCTAATGGAGGTGGGATTAAAAGAAAAGCTAAAATGATAA
1 ATCCTAATTGAGGTGGGATTAAATGAAAAGCTAAAAACATAA
* *
441854 ATCCTAATTGAGGTAGGATTAAATGAAAAGCTAAAAAGATAA
1 ATCCTAATTGAGGTGGGATTAAATGAAAAGCTAAAAACATAA
441896 ATCCTAATTGAGGTGGGATTAA
1 ATCCTAATTGAGGTGGGATTAA
441918 CTGTGGGGCT
Statistics
Matches: 281, Mismatches: 29, Indels: 37
0.81 0.08 0.11
Matches are distributed among these distances:
39 2 0.01
40 37 0.13
42 123 0.44
43 2 0.01
44 3 0.01
45 79 0.28
46 1 0.00
49 1 0.00
50 3 0.01
52 30 0.11
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.25
Consensus pattern (42 bp):
ATCCTAATTGAGGTGGGATTAAATGAAAAGCTAAAAACATAA
Found at i:447328 original size:18 final size:18
Alignment explanation
Indices: 447305--447397 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
447295 CCCAACTACT
*
447305 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
447323 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
447341 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
* *
447359 GTATACGTAAATAGTGCC
1 GTATACGTGAATAGTACC
447377 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
447395 GTA
1 GTA
447398 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:447357 original size:36 final size:36
Alignment explanation
Indices: 447305--447397 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
447295 CCCAACTACT
* *
447305 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
447341 GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
447377 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
447398 AACGGTCGTA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
Found at i:451266 original size:139 final size:142
Alignment explanation
Indices: 450940--451312 Score: 422
Period size: 139 Copynumber: 2.6 Consensus size: 142
450930 AGTTGGGATT
* * *
450940 TGAAGAAACTGAAGTGAATTACTGAACATGATCAAATGGGGTTATAGAGTTGCTTATTCTAAATA
1 TGAAGAAACTGAAGTGAATTACTGAAAATGATCAAATGGGGTTGTAGAGTTGCTTATTCTACATA
* * ** *
451005 TGGAAGAAGCTAGGATACATGCCTGGTTTTGATTGTTTGATACATGATCTTGAAGATAGGCCTTC
66 TGGAAGAAACTAGGATAAATGCCTGGTTTTGA-TCATTGATACATGATCTTGAAGATAGGACTTC
*
451070 AAAGGAGAGAAGC
130 AAAGAAGAGAAGC
* * * *
451083 TGAAGAAACTAAAGT-AAGGTACTGAATATGATCAAATGGGGTTGTTA-AGTTGCTTGTTCTACA
1 TGAAGAAACTGAAGTGAA-TTACTGAAAATGATCAAATGGGGTTG-TAGAGTTGCTTATTCTACA
* *
451146 TATGGAAGAAAC-AGGGTAAATGCCTGG-TTT-A-CATTGATACATGATCTTGAA-AGTGGGACT
64 TATGGAAGAAACTAGGATAAATGCCTGGTTTTGATCATTGATACATGATCTTGAAGA-TAGGACT
*
451206 TGAAGAGAAGAGAAGC
128 TCAA-AGAAGAGAAGC
* * *
451222 AT-AAGAAACGGAATTGAATTACTGAAAATGATCAAATGGGGTTGTAGAGTTGCTTATTCCACAT
1 -TGAAGAAACTGAAGTGAATTACTGAAAATGATCAAATGGGGTTGTAGAGTTGCTTATTCTACAT
* ** *
451286 ATGGAGGAGGC-AGGATATATGCCTGGT
65 ATGGAAGAAACTAGGATAAATGCCTGGT
451313 AAAGATGGGA
Statistics
Matches: 195, Mismatches: 27, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
137 1 0.01
138 28 0.14
139 80 0.41
140 4 0.02
141 3 0.02
142 15 0.08
143 62 0.32
144 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (142 bp):
TGAAGAAACTGAAGTGAATTACTGAAAATGATCAAATGGGGTTGTAGAGTTGCTTATTCTACATA
TGGAAGAAACTAGGATAAATGCCTGGTTTTGATCATTGATACATGATCTTGAAGATAGGACTTCA
AAGAAGAGAAGC
Found at i:451401 original size:18 final size:18
Alignment explanation
Indices: 451378--451422 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
451368 TATTGCTTCG
*
451378 AAAAAGCATTTTTGGGAC
1 AAAAAGCATTTTTGAGAC
*
451396 AAAAAGCACTTTTGAGAC
1 AAAAAGCATTTTTGAGAC
451414 -AAAAGCATT
1 AAAAAGCATT
451423 ATAAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.24
Consensus pattern (18 bp):
AAAAAGCATTTTTGAGAC
Found at i:456546 original size:43 final size:42
Alignment explanation
Indices: 456499--456617 Score: 111
Period size: 43 Copynumber: 2.8 Consensus size: 42
456489 GTTCGCATTT
*
456499 AATTAATTTTTTAAAATTTTAAAAATTCTAAAAAAATTATAAA
1 AATTAATTTTTTAAAATTTTAAAAATT-TAAAAAAAGTATAAA
* *
456542 AATT-A-TTTTTGAAATTTATAAGACA-TT-AAAAAAGTATAAA
1 AATTAATTTTTTAAAATTT-TAA-AAATTTAAAAAAAGTATAAA
* * * *
456582 AAGTATATTTTTTAATATTTTTAAAATTTTAAAAAA
1 AATTA-ATTTTTTAAAATTTTAAAAATTTAAAAAAA
456618 TTAATTAAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
40 15 0.25
41 14 0.23
42 10 0.16
43 22 0.36
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (42 bp):
AATTAATTTTTTAAAATTTTAAAAATTTAAAAAAAGTATAAA
Found at i:463946 original size:7 final size:7
Alignment explanation
Indices: 463936--463960 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
463926 ACATTTCGCG
463936 TTTCCCA
1 TTTCCCA
463943 TTTCCCA
1 TTTCCCA
463950 TTTCCCA
1 TTTCCCA
463957 TTTC
1 TTTC
463961 TCGTGTATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.40, G:0.00, T:0.48
Consensus pattern (7 bp):
TTTCCCA
Found at i:465344 original size:26 final size:26
Alignment explanation
Indices: 465308--465358 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
465298 GACCAAGCTT
465308 GTACAACACTGTTTTAAATTCTCTTA
1 GTACAACACTGTTTTAAATTCTCTTA
465334 GTACAACACTGTTTTAAATTCTCTT
1 GTACAACACTGTTTTAAATTCTCTT
465359 GTATGACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (26 bp):
GTACAACACTGTTTTAAATTCTCTTA
Found at i:468180 original size:3 final size:3
Alignment explanation
Indices: 468172--468211 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
468162 CAATGCAAAA
468172 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
468212 GATTTTGGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:486080 original size:41 final size:38
Alignment explanation
Indices: 485982--486083 Score: 98
Period size: 37 Copynumber: 2.6 Consensus size: 38
485972 TCGAAGCAAT
*
485982 AGTTGACACCCAGTGTCTCATCG-GCCAAGCCGAAGTA
1 AGTTGACACCCAGTGTCTCATCGAACCAAGCCGAAGTA
** ** * * *
486019 AGTTGGTACCCAGTACCTCATCGAATCTATCCGAAGTAA
1 AGTTGACACCCAGTGTCTCATCGAACCAAGCCGAAGT-A
486058 CAGTATGACACCCAGTGTCTCATCGA
1 -AGT-TGACACCCAGTGTCTCATCGA
486084 CTCAAGTTCG
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
37 19 0.39
38 9 0.18
39 1 0.02
40 3 0.06
41 17 0.35
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (38 bp):
AGTTGACACCCAGTGTCTCATCGAACCAAGCCGAAGTA
Found at i:487100 original size:27 final size:26
Alignment explanation
Indices: 487062--487118 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
487052 AAATCCCAAA
* *
487062 TTTTCTTTCTTTCCTTCCCT-TTTTCT
1 TTTTCTTTCTTT-CTACCCTATTTTCG
487088 TTTTCTTTCCTTTCTACCCTATTTTCG
1 TTTTCTTT-CTTTCTACCCTATTTTCG
487115 TTTT
1 TTTT
487119 GCTATTCTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.04, C:0.28, G:0.02, T:0.67
Consensus pattern (26 bp):
TTTTCTTTCTTTCTACCCTATTTTCG
Found at i:487247 original size:23 final size:23
Alignment explanation
Indices: 487217--487263 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
487207 AATAAGTATG
487217 TACATATATTAATTACAAATGTA
1 TACATATATTAATTACAAATGTA
* *
487240 TACATATATTTATTACACATGTA
1 TACATATATTAATTACAAATGTA
487263 T
1 T
487264 TTATAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (23 bp):
TACATATATTAATTACAAATGTA
Found at i:492249 original size:30 final size:32
Alignment explanation
Indices: 492210--492269 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
492200 TGTTAATAGT
492210 TGGACCTAAATTTTGAAA-TT-TGAAAAGTAAA
1 TGGACCTAAATTTT-AAATTTATGAAAAGTAAA
492241 TGGA-CTAAATTTTAAATTTATGAAAAGTA
1 TGGACCTAAATTTTAAATTTATGAAAAGTA
492270 TAAAAACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 3 0.11
30 11 0.41
31 13 0.48
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (32 bp):
TGGACCTAAATTTTAAATTTATGAAAAGTAAA
Found at i:492703 original size:22 final size:22
Alignment explanation
Indices: 492678--492720 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
492668 TATCCAAACA
*
492678 AAAACATCAAAATAGTAGCAAT
1 AAAACAGCAAAATAGTAGCAAT
* *
492700 AAAATAGCAAAATGGTAGCAA
1 AAAACAGCAAAATAGTAGCAA
492721 AACAACGGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.14, T:0.16
Consensus pattern (22 bp):
AAAACAGCAAAATAGTAGCAAT
Found at i:496090 original size:15 final size:16
Alignment explanation
Indices: 496072--496104 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
496062 GCAGTGCTGT
*
496072 GCAGTGCAGGGC-AGG
1 GCAGGGCAGGGCAAGG
496087 GCAGGGCAGGGCAAGG
1 GCAGGGCAGGGCAAGG
496103 GC
1 GC
496105 CCGCCTCGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.21, C:0.21, G:0.55, T:0.03
Consensus pattern (16 bp):
GCAGGGCAGGGCAAGG
Done.