Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 150 of 172
Found at i:49081937 original size:75 final size:76
Alignment explanation
Indices: 49081779--49081939 Score: 193
Period size: 75 Copynumber: 2.1 Consensus size: 76
49081769 TTTCAAAATC
* *
49081779 TATTTTCAATTTCTGTTCATCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGCT
1 TATTTTCAATTTATGTTCATC-AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTGGGCT
* **
49081844 CACACGCTGAGG
65 CACACACCAAGG
* *
49081856 TATTTTCAATTTATGTTCGTC-AAAAATCAACTCATATTGTC-AGAGGTGAGTTGAGTCTCGGGC
1 TATTTTCAATTTATGTTCATCAAAAAATCAACTCATATTG-CAAGAGGTGAGTTGAGCCT-GGGC
*
49081919 -CACATACCAAGG
64 TCACACACCAAGG
*
49081931 TCTTTTCAA
1 TATTTTCAA
49081940 ATTCTGTTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
75 50 0.68
76 4 0.05
77 19 0.26
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (76 bp):
TATTTTCAATTTATGTTCATCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTGGGCTC
ACACACCAAGG
Found at i:49082016 original size:168 final size:168
Alignment explanation
Indices: 49081631--49082565 Score: 778
Period size: 168 Copynumber: 5.6 Consensus size: 168
49081621 TCTGCCTTTC
* * * * *
49081631 AAAAAAATCAACTCATATTACGAGAGGTGAGTTGAG-CTTCAGATTACACACTGAGGTATTTTTT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT-GGCTCACACGCTGAGGTA-TTTTT
* ** * * * *
49081695 CAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGTCACATG
64 CAATTTATGTTCGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGGCCACATG
* * * * * * **
49081760 TCGAGGTATTTTCAAAATCTATTTTCAATTTCTGTTCATC--
127 CCAAGGTCTTTTCAAATTCTATTTTTAATTTCTATTTTTCAA
*
49081800 AAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGGTA-TTTTCA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGGTATTTTTCA
*
49081864 ATTTATGTTCGTCAAAAATCAACTCATATTGTC-AGAGGTGAGTTGAGTCTCGGGCCACATACCA
66 ATTTATGTTCGTCAAAAATCAACTCATATTG-CGAGAGGTGAGTTGAGTCTCGGGCCACATGCCA
*
49081928 AGGTCTTTTCAAATTCTGTTTTTAATTTCTATTTTTCAAA
130 AGGTCTTTTCAAATTCTATTTTTAATTTCTATTTTTC-AA
*
49081968 AAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGGTA-TTTTCA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGGTATTTTTCA
* * *
49082032 ATTTCTGTTCGTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGTCTCGAGCCACATGCCGA
66 ATTTATGTTCGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGGCCACATGCC-A
49082097 A-GTCTTTTCAAATTCTATTTTTAATTTCTATTTTTC-A
130 AGGTCTTTTCAAATTCTATTTTTAATTTCTATTTTTCAA
* * *
49082134 AAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGG-TCACACGCCGAGGTATTTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACACGCTGAGGTATTTTTC
* ** * * * * * * *
49082198 AATTTCTGTTTTTTTTTTAAAAAATTAACTCATATTACGAGAGATGAGTTGAGGCTCGGGTCACG
65 AATTTATG-----TTCGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGGCCACA
* *
49082263 CGCCGAGG-----T---A---T-TTTTTAATTTCTATTTTTC-A
125 TGCCAAGGTCTTTTCAAATTCTATTTTTAATTTCTATTTTTCAA
**** * *
49082294 AAAAAAATCAACTCATATTAG-GAGAGGTGAGTTGAGCCTCAAATCACGCACTGAGGTA-TTTTC
1 AAAAAAATCAACTCATATT-GCGAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGGTATTTTTC
* ** * ** *
49082357 AATTTCTGTTTTTCAAAAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAACCTCGGGTCACA
65 AATTTATGTTCGTC-----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGGCCACA
** * * *
49082422 CACCGAGG-----T---A---T-TTTTCAATTTCTGTTTTTCAA
125 TGCCAAGGTCTTTTCAAATTCTATTTTTAATTTCTATTTTTCAA
* *
49082454 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGG-TCACACGCTGAGGTA-TTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACACGCTGAGGTATTTTTC
* ** *
49082517 AATTTTTTTGGCTTTTTTAAAAATCAACTCATAATT-CGAGAGGTGAGTT
65 AA--TTTAT-G-TTCGTCAAAAATCAACTCAT-ATTGCGAGAGGTGAGTT
49082566 AAACTTCGGG
Statistics
Matches: 669, Mismatches: 67, Indels: 70
0.83 0.08 0.09
Matches are distributed among these distances:
154 5 0.01
159 108 0.16
160 129 0.19
161 2 0.00
162 4 0.01
163 1 0.00
164 6 0.01
165 72 0.11
166 55 0.08
167 33 0.05
168 153 0.23
169 50 0.07
170 3 0.00
171 1 0.00
172 47 0.07
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (168 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGGTATTTTTCA
ATTTATGTTCGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGGCCACATGCCAA
GGTCTTTTCAAATTCTATTTTTAATTTCTATTTTTCAA
Found at i:49082105 original size:75 final size:75
Alignment explanation
Indices: 49081970--49082112 Score: 189
Period size: 75 Copynumber: 1.9 Consensus size: 75
49081960 TTTTCAAAAA
* * * * * *
49081970 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCTCACACGCCGAAGTATTTTCAAAT
49082035 TCTGTTCGTC
66 TCTGTTCGTC
* * *
49082045 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGTCTCGAGC-CACATGCCGAAGTCTTTTCAAA
1 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCG-GCTCACACGCCGAAGTATTTTCAAA
49082109 TTCT
65 TTCT
49082113 ATTTTTAATT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
75 56 0.97
76 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (75 bp):
AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCTCACACGCCGAAGTATTTTCAAAT
TCTGTTCGTC
Found at i:49082220 original size:80 final size:80
Alignment explanation
Indices: 49082112--49082521 Score: 499
Period size: 80 Copynumber: 5.2 Consensus size: 80
49082102 TTTCAAATTC
* * *
49082112 TATTTTT-AATTTCT-ATTTTTCAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCA
1 TATTTTTCAATTTCTGTTTTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
49082175 GGTCACACGCCGAGG
66 GGTCACACGCCGAGG
*** * * * *
49082190 TATTTTTCAATTTCTGTTTTTTTTTTAAAAAATTAACTCATATTACGAGAGATGAGTTGAGGCTC
1 TATTTTTCAATTTCTG-TTTTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
* *
49082255 GGGTCACGCGCCGAGG
65 AGGTCACACGCCGAGG
* * *
49082271 TATTTTTTAATTTCT-ATTTTTCAAAAAAAATCAACTCATATTAG-GAGAGGTGAGTTGAGCCTC
1 TATTTTTCAATTTCTGTTTTTTAAAAAAAAATCAACTCATATT-GCGAGAGGTGAGTTGAGCCTC
** * * *
49082334 AAATCACGCACTGAGG
65 AGGTCACACGCCGAGG
* * *
49082350 TA-TTTTCAATTTCTGTTTTTCAAAAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAACCTC
1 TATTTTTCAATTTCTGTTTTT-TAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
* *
49082414 GGGTCACACACCGAGG
65 AGGTCACACGCCGAGG
* *
49082430 TATTTTTCAATTTCTGTTTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCA
1 TATTTTTCAATTTCTGTTTTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
*
49082495 GGTCACACGCTGAGG
66 GGTCACACGCCGAGG
49082510 TA-TTTTCAATTT
1 TATTTTTCAATTT
49082522 TTTTGGCTTT
Statistics
Matches: 281, Mismatches: 43, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
78 18 0.06
79 74 0.26
80 104 0.37
81 85 0.30
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (80 bp):
TATTTTTCAATTTCTGTTTTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
GGTCACACGCCGAGG
Found at i:49082333 original size:160 final size:158
Alignment explanation
Indices: 49082114--49082576 Score: 619
Period size: 160 Copynumber: 2.9 Consensus size: 158
49082104 TCAAATTCTA
*
49082114 TTTTTAATTTCTATTTTTCAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGTC
1 TTTTTAATTTCTATTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTC
* *
49082179 ACACGCCGAGGTATTTTTCAATTTCTGTTTTTTTTTTAAAAAATTAACTCATATTACGAGAGATG
66 ACACGCTGAGGTA-TTTTCAATTTCTGTTTTTTTTTTAAAAAATCAACTCATATT-CGAGAGATG
** * *
49082244 AGTTGAGGCTCGGGTCACGCGCCGAGGTAT
129 AGTTGAACCTCGGGTCACACACCGAGGTAT
**
49082274 TTTTTAATTTCTATTTTTCAAAAAAAATCAACTCATATTAG-GAGAGGTGAGTTGAGCCTCAAAT
1 TTTTTAATTTCTATTTTTCAAAAAAAATCAACTCATATT-GCGAGAGGTGAGTTGAGCCTCAGGT
* * *****
49082338 CACGCACTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAAAAATCAACTCATATTGCGAGAGATG
65 CACACGCTGAGGTATTTTCAATTTCTGTTTTTTTTTTAAAAAATCAACTCATATT-CGAGAGATG
49082403 AGTTGAACCTCGGGTCACACACCGAGGTAT
129 AGTTGAACCTCGGGTCACACACCGAGGTAT
* * *
49082433 TTTTCAATTTCTGTTTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGT
1 TTTTTAATTTCTATTTTTC-AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
* *
49082498 CACACGCTGAGGTATTTTCAATTT-T-TTTGGCTTTTTT-AAAAATCAACTCATAATTCGAGAGG
65 CACACGCTGAGGTATTTTCAATTTCTGTTT--TTTTTTTAAAAAATCAACTCAT-ATTCGAGAGA
* *
49082560 TGAGTTAAACTTCGGGT
127 TGAGTTGAACCTCGGGT
49082577 AGCATCCCGA
Statistics
Matches: 265, Mismatches: 32, Indels: 13
0.85 0.10 0.04
Matches are distributed among these distances:
158 3 0.01
159 124 0.47
160 137 0.52
161 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (158 bp):
TTTTTAATTTCTATTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTC
ACACGCTGAGGTATTTTCAATTTCTGTTTTTTTTTTAAAAAATCAACTCATATTCGAGAGATGAG
TTGAACCTCGGGTCACACACCGAGGTAT
Found at i:49082539 original size:80 final size:79
Alignment explanation
Indices: 49082134--49082567 Score: 404
Period size: 80 Copynumber: 5.4 Consensus size: 79
49082124 CTATTTTTCA
* *
49082134 AAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTTCA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACGCCGAGGTATTTTTCA
*
49082199 ATTTCTGTTTTTTTTT
66 ATTT-T-TTTGTTTTT
* * * * * * * * *
49082215 TAAAAAATTAACTCATATTACGAGAGATGAGTTGAGGCTCGGGTCACGCGCCGAGGTATTTTTTA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACGCCGAGGTATTTTTCA
* **
49082280 ATTTCTATT-TTTCA
66 ATTT-TTTTGTTTTT
* ** * * *
49082294 AAAAAAATCAACTCATATTAG-GAGAGGTGAGTTGAGCCTCAAATCACGCACTGAGGTA-TTTTC
1 AAAAAAATCAACTCATATT-GCGAGAGGTGAGTTAAGCCTCAGGTCACACGCCGAGGTATTTTTC
*
49082357 AA--TTTCTGTTTTT
65 AATTTTTTTGTTTTT
* * *
49082370 CAAAAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAA-CCTCGGGTCACACACCGAGGTATT
1 ----AAAAAAATCAACTCATATTGCGAGAGGTGAGTT-AAGCCTCAGGTCACACGCCGAGGTATT
*
49082434 TTTCAA--TTTCTGTTTTT
61 TTTCAATTTTTTTGTTTTT
*
49082451 CAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACGCTGAGGTA-TTT
1 ---AAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACGCCGAGGTATTTT
49082515 TCAATTTTTTTGGCTTTTT
63 TCAATTTTTTT-G-TTTTT
*
49082534 -TAAAAATCAACTCATAATT-CGAGAGGTGAGTTAA
1 AAAAAAATCAACTCAT-ATTGCGAGAGGTGAGTTAA
49082568 ACTTCGGGTA
Statistics
Matches: 297, Mismatches: 41, Indels: 32
0.80 0.11 0.09
Matches are distributed among these distances:
75 2 0.01
76 4 0.01
78 6 0.02
79 89 0.30
80 105 0.35
81 85 0.29
82 1 0.00
83 5 0.02
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (79 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACGCCGAGGTATTTTTCA
ATTTTTTTGTTTTT
Found at i:49082539 original size:159 final size:155
Alignment explanation
Indices: 49081946--49082612 Score: 645
Period size: 159 Copynumber: 4.1 Consensus size: 155
49081936 TCAAATTCTG
*
49081946 TTTTT-AATTTCTATTTTTCAAAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCT-TG
1 TTTTTCAATTTCTATTTTTC--AAAAAAAATCAACTCATATTG-GAGAGGTGAGTTGAGCCTCAG
* *
49082009 GCTCACACGCTGAGGTATTTTCAATTTCTG-TTC---GTCAAAAATCAACTCATATTGCGAGAGA
63 G-TCACACGCTGAGGTATTTTCAATTTCTGTTTCTTTTTTAAAAATCAACTCATATT-CGAGAGA
** * * * *
49082070 TGAGTTGAGTCTCGAGCCACATGCCGAAGTCTTTTCAAA
126 TGAGTTGAACCTCGGGTCACA-CCCG-AG----GT---A
*
49082109 TTCTATTTTTAATTTCTATTTTTCAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTC
1 ---T-TTTTCAATTTCTATTTTTCAAAAAAAATCAACTCATATTG-GAGAGGTGAGTTGAGCCTC
* * *
49082174 AGGTCACACGCCGAGGTATTTTTCAATTTCTGTTTTTTTTTTAAAAAATTAACTCATATTACGAG
61 AGGTCACACGCTGAGGTA-TTTTCAATTTCTGTTTCTTTTTT-AAAAATCAACTCATATT-CGAG
** *
49082239 AGATGAGTTGAGGCTCGGGTCACGCGCCGAGGTA
123 AGATGAGTTGAACCTCGGGTCACAC-CCGAGGTA
* **
49082273 TTTTTTAATTTCTATTTTTCAAAAAAAATCAACTCATATTAGGAGAGGTGAGTTGAGCCTCAAAT
1 TTTTTCAATTTCTATTTTTCAAAAAAAATCAACTCATATT-GGAGAGGTGAGTTGAGCCTCAGGT
* * ****
49082338 CACGCACTGAGGTATTTTCAATTTCTGTTT-TTCAAAAAAAAAATCAACTCATATTGCGAGAGAT
65 CACACGCTGAGGTATTTTCAATTTCTGTTTCTT--TTTTAAAAATCAACTCATATT-CGAGAGAT
49082402 GAGTTGAACCTCGGGTCACACACCGAGGTA
127 GAGTTGAACCTCGGGTCACAC-CCGAGGTA
* *
49082432 TTTTTCAATTTCTGTTTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGG
1 TTTTTCAATTTCTATTTTTC-AAAAAAAATCAACTCATATTG-GAGAGGTGAGTTGAGCCTCAGG
*
49082497 TCACACGCTGAGGTATTTTCAATTT-T-TTTGGCTTTTTTAAAAATCAACTCATAATTCGAGAGG
64 TCACACGCTGAGGTATTTTCAATTTCTGTTT--CTTTTTTAAAAATCAACTCAT-ATTCGAGAGA
* * *
49082560 TGAGTTAAACTTCGGGT-AGCATCCCGAGCTA
126 TGAGTTGAACCTCGGGTCA-CA-CCCGAGGTA
*
49082591 -TTTTCAATTTCTTGTTTTTCAA
1 TTTTTCAATTTC-TATTTTTCAA
49082613 TAAAGAATAA
Statistics
Matches: 436, Mismatches: 43, Indels: 52
0.82 0.08 0.10
Matches are distributed among these distances:
158 19 0.04
159 138 0.32
160 137 0.31
161 4 0.01
164 1 0.00
166 55 0.13
167 20 0.05
168 16 0.04
171 3 0.01
172 43 0.10
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (155 bp):
TTTTTCAATTTCTATTTTTCAAAAAAAATCAACTCATATTGGAGAGGTGAGTTGAGCCTCAGGTC
ACACGCTGAGGTATTTTCAATTTCTGTTTCTTTTTTAAAAATCAACTCATATTCGAGAGATGAGT
TGAACCTCGGGTCACACCCGAGGTA
Found at i:49083114 original size:17 final size:17
Alignment explanation
Indices: 49083092--49083137 Score: 76
Period size: 16 Copynumber: 2.8 Consensus size: 17
49083082 GAGAAAAAAG
49083092 AGCAAAAAAAAAATTCC
1 AGCAAAAAAAAAATTCC
*
49083109 AGC-AAAAAAAATTTCC
1 AGCAAAAAAAAAATTCC
49083125 AGCAAAAAAAAAA
1 AGCAAAAAAAAAA
49083138 CTAAAAAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 15 0.58
17 11 0.42
ACGTcount: A:0.67, C:0.15, G:0.07, T:0.11
Consensus pattern (17 bp):
AGCAAAAAAAAAATTCC
Found at i:49091450 original size:25 final size:25
Alignment explanation
Indices: 49091416--49091469 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
49091406 CATAAACATA
*
49091416 TCATACAAAGCAATAATTGCCAAAT
1 TCATACAAAGCAATAATTACCAAAT
49091441 TCATACAAAGCAATAATTACCAAAT
1 TCATACAAAGCAATAATTACCAAAT
49091466 TCAT
1 TCAT
49091470 TCATTCTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.48, C:0.20, G:0.06, T:0.26
Consensus pattern (25 bp):
TCATACAAAGCAATAATTACCAAAT
Found at i:49095027 original size:55 final size:54
Alignment explanation
Indices: 49094966--49095109 Score: 182
Period size: 55 Copynumber: 2.6 Consensus size: 54
49094956 AGGGAATGAA
* **
49094966 GCCAAAGTGAAAACTCACAAAGGGTGCTTTGAGACTT-CTTAAAATAAAAAAAGGG
1 GCCAAAGTGAAAACCCACAAAGGGTGCTTTGAGACTTGAATAAAA-AAAAAAA-GG
* * ***
49095021 GCCAAAGTGAAAACCCACAAAGGGTACTTTGGGACTTGAATAAAAATGGAAAGG
1 GCCAAAGTGAAAACCCACAAAGGGTGCTTTGAGACTTGAATAAAAAAAAAAAGG
*
49095075 GCCAAAGTGAAAACCCACAAAGGGCGCTTTGAGAC
1 GCCAAAGTGAAAACCCACAAAGGGTGCTTTGAGAC
49095110 CCAATAATAA
Statistics
Matches: 77, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
54 34 0.44
55 38 0.49
56 5 0.06
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17
Consensus pattern (54 bp):
GCCAAAGTGAAAACCCACAAAGGGTGCTTTGAGACTTGAATAAAAAAAAAAAGG
Found at i:49096554 original size:180 final size:179
Alignment explanation
Indices: 49096235--49096975 Score: 923
Period size: 180 Copynumber: 4.2 Consensus size: 179
49096225 ACATTGGTAA
* * * * * ***
49096235 AAATTGAAGATCTTATTTCCCTGAAGTTGCAGTGGAGTAGATCTTTGGAGATGGTGAATCTTATC
1 AAATTGAAGATTTTATCTCCCTGAAGTTACAATGGAGCAGATCTTCACAGATGGTGAATCTTATC
* * * * * * *
49096300 TCCATGTATCGGTAATGGAGCAGATTTTACCACCAAGCCTTACCTCTCTAAGGTAGCAAGAGAGT
66 TCCATGTATCGGCAATGGAGCAGATTTAACCACTAAACCTTATCTCTCTGAGGTAGCAAGAGAGC
*
49096365 AGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTG
131 AAGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTG
* *
49096414 AGAATTAAAGATTTTATCTCCCTGAAGTTACAACGGAGCAGATCTTCACAGATGGCT-AATCTTA
1 A-AATTGAAGATTTTATCTCCCTGAAGTTACAATGGAGCAGATCTTCACAGATGG-TGAATCTTA
* *
49096478 TCTCCATGTATCGGCAATGGAGCAGATTTAAGCC-TTAAACCTTATCTCTTTGAGGTAGCAAGAG
64 TCTCCATGTATCGGCAATGGAGCAGATTTAA-CCACTAAACCTTATCTCTCTGAGGTAGCAAGAG
* * *
49096542 AGCAAGTTGAAGATTGAGTCTTATCTTTCTGAGGTAGCAAGAAAGCAGACTG
128 AGCAAGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTG
* * * *
49096594 AAGATTGAAGGTTTTATCTCCCT-AA---ACAGTAGTGGAGCAAATC--GA-AGACGGTGAATCT
1 AA-ATTGAAGATTTTATCTCCCTGAAGTTACA--A-TGGAGCAGATCTTCACAGATGGTGAATCT
* * *
49096652 TATCTCCGTGTATCGGCAATGGAGCAGATTTTACCACT-AACCTCATCTCTCTGAGGTAGCAAGA
62 TATCTCCATGTATCGGCAATGGAGCAGATTTAACCACTAAACCTTATCTCTCTGAGGTAGCAAGA
* *
49096716 GAGCAAGTTGAAGAATGAGTCTTATCTTCTTGAGGTAGCAAGGAAGCAGACCG
127 GAGCAAGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTG
* * **
49096769 AAGATTGAAGATTCTATCTCCCTGAAGTTGCAGGGGAGCAGATCTTCACAGATGGCT-AATCTTA
1 AA-ATTGAAGATTTTATCTCCCTGAAGTTACAATGGAGCAGATCTTCACAGATGG-TGAATCTTA
* * * *
49096833 TCTCTATGTATCGGCAATGGAGCAGATTTAAGCC-TTAAGCCTTATCTCTCTGAAGTAGCAAGAG
64 TCTCCATGTATCGGCAATGGAGCAGATTTAA-CCACTAAACCTTATCTCTCTGAGGTAGCAAGAG
*
49096897 AGCAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTG
128 AGCAAGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTG
49096949 AAAATTGAAGATTTTATCTCCCT-AAGT
1 -AAATTGAAGATTTTATCTCCCTGAAGT
49096976 AGTAGCGGAG
Statistics
Matches: 484, Mismatches: 58, Indels: 40
0.83 0.10 0.07
Matches are distributed among these distances:
175 96 0.20
176 56 0.12
177 1 0.00
178 2 0.00
179 60 0.12
180 264 0.55
181 5 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (179 bp):
AAATTGAAGATTTTATCTCCCTGAAGTTACAATGGAGCAGATCTTCACAGATGGTGAATCTTATC
TCCATGTATCGGCAATGGAGCAGATTTAACCACTAAACCTTATCTCTCTGAGGTAGCAAGAGAGC
AAGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTG
Found at i:49096575 original size:43 final size:43
Alignment explanation
Indices: 49096518--49096601 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
49096508 AGCCTTAAAC
* *
49096518 CTTATCTCTTTGAGGTAGCAAGAGAGCA-AGTTGAAGATTGAGT
1 CTTATCTCTTTGAGGTAGCAAGAAAGCAGA-CTGAAGATTGAGT
49096561 CTTATCT-TTCTGAGGTAGCAAGAAAGCAGACTGAAGATTGA
1 CTTATCTCTT-TGAGGTAGCAAGAAAGCAGACTGAAGATTGA
49096602 AGGTTTTATC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
42 2 0.05
43 34 0.92
44 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (43 bp):
CTTATCTCTTTGAGGTAGCAAGAAAGCAGACTGAAGATTGAGT
Found at i:49096878 original size:355 final size:356
Alignment explanation
Indices: 49096287--49097037 Score: 1130
Period size: 355 Copynumber: 2.1 Consensus size: 356
49096277 CTTTGGAGAT
* *
49096287 GGTGAATCTTATCTCCATGTATCGGTAATGGAGCAGATTTTACCACCAAGCCTTACCTCTCTAAG
1 GGTGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTTACCACCAAGCCTCACCTCTCTAAG
* * *
49096352 GTAGCAAGAGAGTAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAGA
66 GTAGCAAGAGAGCAAGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACCGAGA
*
49096417 ATTAAAGATTTTATCTCCCTGAAGTTACAACGGAGCAGATCTTCACAGATGGCTAATCTTATCTC
131 ATTAAAGATTCTATCTCCCTGAAGTTACAACGGAGCAGATCTTCACAGATGGCTAATCTTATCTC
* *
49096482 CATGTATCGGCAATGGAGCAGATTTAAGCCTTAAACCTTATCTCTTTGAGGTAGCAAGAGAGCAA
196 CATGTATCGGCAATGGAGCAGATTTAAGCCTTAAACCTTATCTCTCTGAAGTAGCAAGAGAGCAA
* * * *
49096547 GTTGAAGATTGAGTCTTATCTTTCTGAGGTAGCAAGAAAGCAGACTGAAGATTGAAGGTTTTATC
261 GTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGAAAGCAGACTGAAAATTGAAGATTTTATC
*
49096612 TCCCTAAACAGTAGTGGAGCAAATCGAAGAC
326 TCCCTAAACAGTAGCGGAGCAAATCGAAGAC
* * * *
49096643 GGTGAATCTTATCTCCGTGTATCGGCAATGGAGCAGATTTTACCACTAA-CCTCATCTCTCTGAG
1 GGTGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTTACCACCAAGCCTCACCTCTCTAAG
*
49096707 GTAGCAAGAGAGCAAGTTGAAGAATGAGTCTTATCTTCTTGAGGTAGCAAGGAAGCAGACCGA-A
66 GTAGCAAGAGAGCAAGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACCGAGA
* * **
49096771 GATTGAAGATTCTATCTCCCTGAAGTTGCAGGGGAGCAGATCTTCACAGATGGCTAATCTTATCT
131 -ATTAAAGATTCTATCTCCCTGAAGTTACAACGGAGCAGATCTTCACAGATGGCTAATCTTATCT
* *
49096836 CTATGTATCGGCAATGGAGCAGATTTAAGCCTTAAGCCTTATCTCTCTGAAGTAGCAAGAGAGCA
195 CCATGTATCGGCAATGGAGCAGATTTAAGCCTTAAACCTTATCTCTCTGAAGTAGCAAGAGAGCA
* *
49096901 GGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAAATTGAAGATTTTAT
260 AGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGAAAGCAGACTGAAAATTGAAGATTTTAT
** * ** *
49096966 CTCCCTAAGTAGTAGCGGAGCAGATCGGGGAT
325 CTCCCTAAACAGTAGCGGAGCAAATCGAAGAC
**** *
49096998 AACAAATCTTATCTTCATGTA-CTGGCAATGGAGCAGATTT
1 GGTGAATCTTATCTCCATGTATC-GGCAATGGAGCAGATTT
49097038 AAGTCACCAG
Statistics
Matches: 355, Mismatches: 38, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
354 2 0.01
355 307 0.86
356 46 0.13
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (356 bp):
GGTGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTTACCACCAAGCCTCACCTCTCTAAG
GTAGCAAGAGAGCAAGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACCGAGA
ATTAAAGATTCTATCTCCCTGAAGTTACAACGGAGCAGATCTTCACAGATGGCTAATCTTATCTC
CATGTATCGGCAATGGAGCAGATTTAAGCCTTAAACCTTATCTCTCTGAAGTAGCAAGAGAGCAA
GTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGAAAGCAGACTGAAAATTGAAGATTTTATC
TCCCTAAACAGTAGCGGAGCAAATCGAAGAC
Found at i:49098090 original size:26 final size:24
Alignment explanation
Indices: 49098059--49098108 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
49098049 AAATAAAAAA
*
49098059 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
49098085 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
49098109 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:49098128 original size:21 final size:21
Alignment explanation
Indices: 49098079--49098137 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
49098069 ATAATAAATC
*
49098079 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
49098099 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
49098121 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
49098138 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:49100735 original size:14 final size:14
Alignment explanation
Indices: 49100716--49100780 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
49100706 TGATTTTGGG
*
49100716 TTTTTTATTTGTGTTT
1 TTTTTTATTTCTG--T
49100732 TTTTTTATTTCTGT
1 TTTTTTATTTCTGT
* *
49100746 TTTATT-TTT-GGT
1 TTTTTTATTTCTGT
* *
49100758 TTTTTAATTTCTAT
1 TTTTTTATTTCTGT
49100772 TTTTTTATT
1 TTTTTTATT
49100781 CTAATGGGCC
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
12 6 0.15
13 6 0.15
14 15 0.38
16 12 0.31
ACGTcount: A:0.11, C:0.03, G:0.08, T:0.78
Consensus pattern (14 bp):
TTTTTTATTTCTGT
Found at i:49100737 original size:16 final size:16
Alignment explanation
Indices: 49100716--49100754 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
49100706 TGATTTTGGG
*
49100716 TTTTTTATTTGTGTTT
1 TTTTTTATTTCTGTTT
49100732 TTTTTTATTTCTGTTT
1 TTTTTTATTTCTGTTT
49100748 TATTTTT
1 T-TTTTT
49100755 GGTTTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.08, C:0.03, G:0.08, T:0.82
Consensus pattern (16 bp):
TTTTTTATTTCTGTTT
Found at i:49100775 original size:27 final size:27
Alignment explanation
Indices: 49100716--49100775 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
49100706 TGATTTTGGG
* *
49100716 TTTTTTATTTGTGTTTTTTTTTATTTC
1 TTTTTTATTTGTGTGTTTTTTAATTTC
* *
49100743 TGTTTTATTTTTG-GTTTTTTAATTTC
1 TTTTTTATTTGTGTGTTTTTTAATTTC
49100769 TATTTTT
1 T-TTTTT
49100776 TTATTCTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.10, C:0.03, G:0.08, T:0.78
Consensus pattern (27 bp):
TTTTTTATTTGTGTGTTTTTTAATTTC
Found at i:49104792 original size:25 final size:26
Alignment explanation
Indices: 49104764--49104820 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
49104754 ATTTTGGGTT
*
49104764 TTTTATTTGT-GTGTTTTT-ATTTCTG
1 TTTTATTTGTGGT-TTTTTAATTTCTA
*
49104789 TTTTATTTTTGGTTTTTTAATTTCTA
1 TTTTATTTGTGGTTTTTTAATTTCTA
49104815 TTTTAT
1 TTTTAT
49104821 ATTCTAATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 14 0.50
26 14 0.50
ACGTcount: A:0.12, C:0.04, G:0.11, T:0.74
Consensus pattern (26 bp):
TTTTATTTGTGGTTTTTTAATTTCTA
Found at i:49105486 original size:2 final size:2
Alignment explanation
Indices: 49105479--49105503 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49105469 TGTAACAAAC
49105479 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
49105504 AAGGTTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49108440 original size:57 final size:57
Alignment explanation
Indices: 49108352--49108466 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
49108342 TGTATTGGCT
49108352 GCCAATACACCCCTAATCAGTAGGGCCCCACTTAATCCCCTTTAATCCTTTGTTTTG
1 GCCAATACACCCCTAATCAGTAGGGCCCCACTTAATCCCCTTTAATCCTTTGTTTTG
*
49108409 GCCAATACACCCCTAATCAGTAGGGCCCCACTTAATCCCTTTTAATCCTTTGTTTTG
1 GCCAATACACCCCTAATCAGTAGGGCCCCACTTAATCCCCTTTAATCCTTTGTTTTG
49108466 G
1 G
49108467 TTTAGGGTAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.23, C:0.32, G:0.13, T:0.32
Consensus pattern (57 bp):
GCCAATACACCCCTAATCAGTAGGGCCCCACTTAATCCCCTTTAATCCTTTGTTTTG
Found at i:49111494 original size:16 final size:16
Alignment explanation
Indices: 49111473--49111540 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
49111463 GATTTGCTAT
49111473 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
49111489 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
49111505 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
49111521 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
49111537 TACA
1 TACA
49111541 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:49114250 original size:68 final size:70
Alignment explanation
Indices: 49114162--49114295 Score: 184
Period size: 68 Copynumber: 1.9 Consensus size: 70
49114152 TAATAAATTT
* * * * *
49114162 AATATTAAATTTAATTTAATACTTATCTTA-AT-AGTATTTTATT-AATTTAATATTAAAGTGAT
1 AATATTAAATTTAATATAATACTTATC-AAGATAAATATTATATTAAATTTAATATTAAAGCGAT
49114224 TATCTC
65 TATCTC
*
49114230 AATATTAAATTTAATATAATATTTATCAAGATAAATATTATATTAAATTTAATATTAAAGCGATT
1 AATATTAAATTTAATATAATACTTATCAAGATAAATATTATATTAAATTTAATATTAAAGCGATT
49114295 A
66 A
49114296 AGTTTAATTA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
67 1 0.02
68 27 0.47
69 9 0.16
70 20 0.35
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (70 bp):
AATATTAAATTTAATATAATACTTATCAAGATAAATATTATATTAAATTTAATATTAAAGCGATT
ATCTC
Found at i:49122611 original size:23 final size:22
Alignment explanation
Indices: 49122559--49122612 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
49122549 ACACAACCGT
49122559 GAATTTTTTGGACTTTTTAACA
1 GAATTTTTTGGACTTTTTAACA
* * *
49122581 GAAATTTTTGTACCTTTTTTACTA
1 GAATTTTTTGGA-CTTTTTAAC-A
49122605 -AATTTTTT
1 GAATTTTTT
49122613 CAAAGTTGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 10 0.38
23 15 0.58
24 1 0.04
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.56
Consensus pattern (22 bp):
GAATTTTTTGGACTTTTTAACA
Found at i:49134137 original size:122 final size:122
Alignment explanation
Indices: 49133907--49134163 Score: 342
Period size: 122 Copynumber: 2.1 Consensus size: 122
49133897 TACCTAACTG
* *
49133907 AATTTTAATACGACATTCTAATAACCTTATAAATATTAAATAAATAATATTTACTAATTCACTGG
1 AATTTTAATACGACACTCTAATAACCTTATAAATATTAAATAAATAATATTTACTAACTCACTGG
** * *
49133972 TCAGAATTGTGGTCCCAAAACCACTTTTTCTGACATCATTGAAAAT-GAGTTATTACA
66 TCAGAATTGTGGTCCCAAAACCACGATTTCCGACATCACTGAAAATAG-GTTATTACA
* * *
49134029 AATTTTGATATGACACTCTAATAACCTTATAAATATTAAATAAATAATATTTACTAACTCATTGG
1 AATTTTAATACGACACTCTAATAACCTTATAAATATTAAATAAATAATATTTACTAACTCACTGG
** *
49134094 TCTA-AATTGTGG-CCACAAAATTACGATTTCCGACA-CTACTGAAAATAGGTTGTTACA
66 TC-AGAATTGTGGTCC-CAAAACCACGATTTCCGACATC-ACTGAAAATAGGTTATTACA
49134151 AATTTTAATACGA
1 AATTTTAATACGA
49134164 AATTGTAGTC
Statistics
Matches: 117, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
121 3 0.03
122 112 0.96
123 2 0.02
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (122 bp):
AATTTTAATACGACACTCTAATAACCTTATAAATATTAAATAAATAATATTTACTAACTCACTGG
TCAGAATTGTGGTCCCAAAACCACGATTTCCGACATCACTGAAAATAGGTTATTACA
Found at i:49137013 original size:15 final size:15
Alignment explanation
Indices: 49136995--49137025 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
49136985 AAAATAAGGT
49136995 TTTTTAAAATATTTA
1 TTTTTAAAATATTTA
*
49137010 TTTTTATAATATTTA
1 TTTTTAAAATATTTA
49137025 T
1 T
49137026 CTAAAATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTTAAAATATTTA
Found at i:49142831 original size:36 final size:36
Alignment explanation
Indices: 49142784--49142856 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
49142774 AATTAATTAG
49142784 TGAGTATTGTTACAATTGAATTTGCCACGTTTATTC
1 TGAGTATTGTTACAATTGAATTTGCCACGTTTATTC
49142820 TGAGTATTGTTACAATTGAATTTGCCACGTTTATTC
1 TGAGTATTGTTACAATTGAATTTGCCACGTTTATTC
49142856 T
1 T
49142857 TTCTTTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (36 bp):
TGAGTATTGTTACAATTGAATTTGCCACGTTTATTC
Found at i:49143469 original size:68 final size:68
Alignment explanation
Indices: 49143355--49143497 Score: 268
Period size: 68 Copynumber: 2.1 Consensus size: 68
49143345 CACTCACTTG
*
49143355 TGGTAGAAACATCTGAGAAGCCAAGTAAGCTTGAGTGTCCCAAGTTTGATGGTAGTGATTTTCGA
1 TGGTGGAAACATCTGAGAAGCCAAGTAAGCTTGAGTGTCCCAAGTTTGATGGTAGTGATTTTCGA
49143420 GGA
66 GGA
*
49143423 TGGTGGAAACATCTGAGAAGGCAAGTAAGCTTGAGTGTCCCAAGTTTGATGGTAGTGATTTTCGA
1 TGGTGGAAACATCTGAGAAGCCAAGTAAGCTTGAGTGTCCCAAGTTTGATGGTAGTGATTTTCGA
49143488 GGA
66 GGA
49143491 TGGTGGA
1 TGGTGGA
49143498 CTAAGCTTGA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 73 1.00
ACGTcount: A:0.28, C:0.12, G:0.32, T:0.28
Consensus pattern (68 bp):
TGGTGGAAACATCTGAGAAGCCAAGTAAGCTTGAGTGTCCCAAGTTTGATGGTAGTGATTTTCGA
GGA
Found at i:49144080 original size:16 final size:18
Alignment explanation
Indices: 49144049--49144092 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
49144039 GTATTTAAGT
49144049 ATTAAAAGATATTTATTA
1 ATTAAAAGATATTTATTA
*
49144067 ATTAAAAAATTTATTTATTA
1 ATTAAAAGA--TATTTATTA
49144087 ATTAAA
1 ATTAAA
49144093 TAATTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAAAAGATATTTATTA
Found at i:49144081 original size:20 final size:21
Alignment explanation
Indices: 49144057--49144102 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
49144047 GTATTAAAAG
49144057 ATATTTATTAATTAAAAAATT
1 ATATTTATTAATTAAAAAATT
*
49144078 -TATTTATTAATTAAATAATT
1 ATATTTATTAATTAAAAAATT
49144098 ATATT
1 ATATT
49144103 ATAAGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATATTTATTAATTAAAAAATT
Found at i:49144333 original size:20 final size:18
Alignment explanation
Indices: 49144304--49144348 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
49144294 AACGAAAAGC
49144304 AGGG-AAAGAAAGAAAGAA
1 AGGGAAAAGAAAG-AAGAA
49144322 AGGAGAAAAGAAAGAAGAA
1 AGG-GAAAAGAAAGAAGAA
49144341 AGGGAAAA
1 AGGGAAAA
49144349 TTCAAGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 9 0.36
20 8 0.32
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AGGGAAAAGAAAGAAGAA
Found at i:49146020 original size:21 final size:21
Alignment explanation
Indices: 49145992--49146184 Score: 278
Period size: 21 Copynumber: 9.1 Consensus size: 21
49145982 CCTGATCAGT
* * *
49145992 ATACGACACATAAAGTGCCTA
1 ATACGACACATGAGGTGCCTG
* *
49146013 AAACGACACACGAGGTGCCTG
1 ATACGACACATGAGGTGCCTG
49146034 ATACGACACATGAGGTGCCTG
1 ATACGACACATGAGGTGCCTG
*
49146055 ATACGACACACGAGGTGCCTG
1 ATACGACACATGAGGTGCCTG
49146076 ATACGACACATGAGGTGCCTG
1 ATACGACACATGAGGTGCCTG
*
49146097 ATACGACACACGAGGTGCCTG
1 ATACGACACATGAGGTGCCTG
49146118 ATACGACACATGAGGTGCCTG
1 ATACGACACATGAGGTGCCTG
*
49146139 ATACGACACACGAGGTGCCTG
1 ATACGACACATGAGGTGCCTG
* *
49146160 AAATACGACACATAAAGTGCCTG
1 --ATACGACACATGAGGTGCCTG
49146183 AT
1 AT
49146185 CGATAAAGCC
Statistics
Matches: 155, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
21 137 0.88
23 18 0.12
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (21 bp):
ATACGACACATGAGGTGCCTG
Found at i:49146052 original size:42 final size:42
Alignment explanation
Indices: 49145992--49146184 Score: 314
Period size: 42 Copynumber: 4.5 Consensus size: 42
49145982 CCTGATCAGT
* * * *
49145992 ATACGACACATAAAGTGCCTAAAACGACACACGAGGTGCCTG
1 ATACGACACATGAGGTGCCTGATACGACACACGAGGTGCCTG
49146034 ATACGACACATGAGGTGCCTGATACGACACACGAGGTGCCTG
1 ATACGACACATGAGGTGCCTGATACGACACACGAGGTGCCTG
49146076 ATACGACACATGAGGTGCCTGATACGACACACGAGGTGCCTG
1 ATACGACACATGAGGTGCCTGATACGACACACGAGGTGCCTG
49146118 ATACGACACATGAGGTGCCTGATACGACACACGAGGTGCCTG
1 ATACGACACATGAGGTGCCTGATACGACACACGAGGTGCCTG
* *
49146160 AAATACGACACATAAAGTGCCTGAT
1 --ATACGACACATGAGGTGCCTGAT
49146185 CGATAAAGCC
Statistics
Matches: 143, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
42 122 0.85
44 21 0.15
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (42 bp):
ATACGACACATGAGGTGCCTGATACGACACACGAGGTGCCTG
Found at i:49146580 original size:15 final size:15
Alignment explanation
Indices: 49146555--49146612 Score: 80
Period size: 15 Copynumber: 3.8 Consensus size: 15
49146545 TCATATATAT
*
49146555 TATATAATTCAAACAA
1 TATA-AATTCAATCAA
49146571 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
49146586 AATAATTTCAATCAA
1 TATAAATTCAATCAA
49146601 TATAAATTCAAT
1 TATAAATTCAAT
49146613 AAATTCATCG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 33 0.89
16 4 0.11
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:49146897 original size:24 final size:22
Alignment explanation
Indices: 49146848--49146897 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
49146838 AATTTTCCAT
* *
49146848 TTTCTCCCCTTCTTTCTTTCTT
1 TTTCTCCCCTTCTCTCTTTCTA
*
49146870 TTTCTCCCCTGCTCTCTGTTTCTA
1 TTTCTCCCCT--TCTCTCTTTCTA
49146894 TTTC
1 TTTC
49146898 CTTTCATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 10 0.43
24 13 0.57
ACGTcount: A:0.02, C:0.36, G:0.04, T:0.58
Consensus pattern (22 bp):
TTTCTCCCCTTCTCTCTTTCTA
Found at i:49146932 original size:5 final size:5
Alignment explanation
Indices: 49146919--49146950 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
49146909 TTCTTTAGTT
49146919 TATATA TATAA TATAA TATAA TATAA TATAA T
1 TATA-A TATAA TATAA TATAA TATAA TATAA T
49146951 TAAAACATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TATAA
Found at i:49146986 original size:8 final size:8
Alignment explanation
Indices: 49146973--49147001 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
49146963 TATCTTTATT
49146973 ATATAATA
1 ATATAATA
49146981 ATATAATA
1 ATATAATA
49146989 ATATAATA
1 ATATAATA
49146997 ATATA
1 ATATA
49147002 CTAAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:49150553 original size:20 final size:20
Alignment explanation
Indices: 49150520--49150565 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
49150510 AAATTTCATT
49150520 GAAGG-ATTGCCGAACTCAA
1 GAAGGAATTGCCGAACTCAA
* *
49150539 GAAGGAATTGTCGAACTTAA
1 GAAGGAATTGCCGAACTCAA
49150559 GAAGGAA
1 GAAGGAA
49150566 GAATTCCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.41, C:0.13, G:0.28, T:0.17
Consensus pattern (20 bp):
GAAGGAATTGCCGAACTCAA
Found at i:49152349 original size:273 final size:273
Alignment explanation
Indices: 49151862--49152407 Score: 1029
Period size: 273 Copynumber: 2.0 Consensus size: 273
49151852 TTTCCTGACC
*
49151862 CTAAGGATGAAATCGTCATTAATTAAAAGTTTAGGGGCAAAATGGTAATTTTTCCTAGAGCATTA
1 CTAAGGATGAAATCGTCATTAATTAAAAGTTTAGGGGCAAAATGGTAATTTTGCCTAGAGCATTA
49151927 ATTAAATGCATTAGAATATGAAATGAATGAAAATGATGATCAAATTTATTTATAAAGATCCGGAC
66 ATTAAATGCATTAGAATATGAAATGAATGAAAATGATGATCAAATTTATTTATAAAGATCCGGAC
49151992 GACTCAAATACGAGACTTGATCGAGGAAAAGAAAAGATATCAGATTAATGAAATTATAAACACAA
131 GACTCAAATACGAGACTTGATCGAGGAAAAGAAAAGATATCAGATTAATGAAATTATAAACACAA
49152057 ACAAGCAATGAAGTAAGTTTGTGTAACTTGAATTGTATTTTTAAATACTTGAAATATGTGGTTAT
196 ACAAGCAATGAAGTAAGTTTGTGTAACTTGAATTGTATTTTTAAATACTTGAAATATGTGGTTAT
49152122 GTGATAAAAATAT
261 GTGATAAAAATAT
49152135 CTAAGGATGAAATCGTCATTAATTAAAAGTTTAGGGGCAAAATGGTAATTTTGCCTAGAGCATTA
1 CTAAGGATGAAATCGTCATTAATTAAAAGTTTAGGGGCAAAATGGTAATTTTGCCTAGAGCATTA
49152200 ATTAAATGCATTAGAATATGAAATGAATGAAAATGATGATCAAATTTATTTATAAAGATCCGGAC
66 ATTAAATGCATTAGAATATGAAATGAATGAAAATGATGATCAAATTTATTTATAAAGATCCGGAC
* * *
49152265 GACTCAAATATGAGACTTGATCGTGGAAAAGAAAAGATATCGGATTAATGAAATTATAAACACAA
131 GACTCAAATACGAGACTTGATCGAGGAAAAGAAAAGATATCAGATTAATGAAATTATAAACACAA
* *
49152330 ACAAGCAATGAGGTAAGTTTGTGTAACTTGAATTGTATTTTTAAATGCTTGAAATATGTGGTTAT
196 ACAAGCAATGAAGTAAGTTTGTGTAACTTGAATTGTATTTTTAAATACTTGAAATATGTGGTTAT
*
49152395 GTGATGAAAATAT
261 GTGATAAAAATAT
49152408 GATTTGAATT
Statistics
Matches: 266, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
273 266 1.00
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (273 bp):
CTAAGGATGAAATCGTCATTAATTAAAAGTTTAGGGGCAAAATGGTAATTTTGCCTAGAGCATTA
ATTAAATGCATTAGAATATGAAATGAATGAAAATGATGATCAAATTTATTTATAAAGATCCGGAC
GACTCAAATACGAGACTTGATCGAGGAAAAGAAAAGATATCAGATTAATGAAATTATAAACACAA
ACAAGCAATGAAGTAAGTTTGTGTAACTTGAATTGTATTTTTAAATACTTGAAATATGTGGTTAT
GTGATAAAAATAT
Found at i:49152858 original size:46 final size:46
Alignment explanation
Indices: 49152806--49153538 Score: 1002
Period size: 46 Copynumber: 16.0 Consensus size: 46
49152796 GCTTTCTGAA
* **
49152806 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGGC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** * *
49152852 ATGAAATGAATAAGACCATGGTTGAAAGACACCATGGAAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
49152898 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
49152944 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
49152990 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * *
49153036 ATAAAATGTGTAAGACCATGGTTAAAAGACACCATGGCAACACGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
49153082 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
49153128 ATAAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
49153174 ATGAAATGTGTAAAACCATGGTTGAAAGATACCAAGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
49153220 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * * *
49153266 ATAAAATGTCTAAGACCACGGTTGACAGACACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
49153312 ATGAAATGTGTAAAACCATGGTTGAAAGATACCAAGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
49153358 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGA-
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** * ** * ** * *
49153403 CGGGAATGAATAAGACCATGGTTGAAAGATAACATGGCAATGTAAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*** * * *
49153449 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGAAACCTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * * *
49153495 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
49153539 TCAAAGATAA
Statistics
Matches: 611, Mismatches: 74, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
45 36 0.06
46 575 0.94
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:49164110 original size:5 final size:5
Alignment explanation
Indices: 49164100--49164132 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
49164090 ATTTGTGTGT
49164100 TTTTA TTTTA TTTTA -TTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
49164133 TTCACAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:49164118 original size:14 final size:14
Alignment explanation
Indices: 49164101--49164131 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
49164091 TTTGTGTGTT
49164101 TTTATTTTATTTTA
1 TTTATTTTATTTTA
49164115 TTTATTTTATTTTA
1 TTTATTTTATTTTA
49164129 TTT
1 TTT
49164132 TTTCACAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:49168700 original size:39 final size:39
Alignment explanation
Indices: 49168646--49168725 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
49168636 CTTAAATTAT
49168646 CAAAAACATCACGGTCAGTCATATTAAGATTATCAAGCC
1 CAAAAACATCACGGTCAGTCATATTAAGATTATCAAGCC
49168685 CAAAAACATCACGGTCAGTCATATTAAGATTATCAAGCC
1 CAAAAACATCACGGTCAGTCATATTAAGATTATCAAGCC
49168724 CA
1 CA
49168726 CCGGATTCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.23
Consensus pattern (39 bp):
CAAAAACATCACGGTCAGTCATATTAAGATTATCAAGCC
Found at i:49176528 original size:12 final size:12
Alignment explanation
Indices: 49176511--49176544 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
49176501 CGGCCCACCC
49176511 ATATTAATTTTT
1 ATATTAATTTTT
*
49176523 ATATTATTTTTT
1 ATATTAATTTTT
49176535 ATA-TAATTTT
1 ATATTAATTTT
49176545 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:49176711 original size:30 final size:30
Alignment explanation
Indices: 49176668--49176729 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
49176658 CTTAACAAGA
49176668 AAATGCCTATAAAATAATAACAAAATTAAC
1 AAATGCCTATAAAATAATAACAAAATTAAC
* *
49176698 AAATGTCTTTAAAATAATAACAAAATTAAC
1 AAATGCCTATAAAATAATAACAAAATTAAC
49176728 AA
1 AA
49176730 TAAATAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.60, C:0.11, G:0.03, T:0.26
Consensus pattern (30 bp):
AAATGCCTATAAAATAATAACAAAATTAAC
Found at i:49177537 original size:18 final size:17
Alignment explanation
Indices: 49177497--49177552 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
49177487 AATTAAACTC
49177497 AATTCAAATAATTAATTT
1 AATT-AAATAATTAATTT
49177515 AATTATAA-AATTAATTT
1 AATTA-AATAATTAATTT
*
49177532 ATATTAAATAAATAATTT
1 A-ATTAAATAATTAATTT
49177550 AAT
1 AAT
49177553 AAAAAAATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
17 15 0.44
18 19 0.56
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTAAATAATTAATTT
Found at i:49179536 original size:112 final size:112
Alignment explanation
Indices: 49179392--49179632 Score: 428
Period size: 112 Copynumber: 2.1 Consensus size: 112
49179382 AAAATTGTAC
*
49179392 TTTCGCCCCCTTAAAAATAATAAAAATTTGATTTAATCCATTAAAAATTATAAAAATATAGGCTA
1 TTTCGCCCCC-TAAAAATAATAAAAATTTGATTTAATCCATTAAAAATTATAAAAATATAAGCTA
*
49179457 TTCAAATGGTGAAATTGCATTTTTACTATAGTAAAAATTACAATTTAA
65 TTCAAATGGTGAAATTACATTTTTACTATAGTAAAAATTACAATTTAA
*
49179505 TTTCGCCCCCTAAAAATAATAAAAATTTGATTTAATCCATTAAAAATTATAAGAATATAAGCTAT
1 TTTCGCCCCCTAAAAATAATAAAAATTTGATTTAATCCATTAAAAATTATAAAAATATAAGCTAT
* *
49179570 TCAAATGGTGAAATTACATTTTTACTGTCGTAAAAATTACAATTTAA
66 TCAAATGGTGAAATTACATTTTTACTATAGTAAAAATTACAATTTAA
49179617 TTTCGCCCCCTAAAAA
1 TTTCGCCCCCTAAAAA
49179633 AATTTCTAGC
Statistics
Matches: 123, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
112 113 0.92
113 10 0.08
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (112 bp):
TTTCGCCCCCTAAAAATAATAAAAATTTGATTTAATCCATTAAAAATTATAAAAATATAAGCTAT
TCAAATGGTGAAATTACATTTTTACTATAGTAAAAATTACAATTTAA
Found at i:49188706 original size:35 final size:35
Alignment explanation
Indices: 49188654--49188736 Score: 109
Period size: 35 Copynumber: 2.4 Consensus size: 35
49188644 CCCCAAATCT
*
49188654 TTAAACCA-TGAATCCCAAACTCATAACACGTAAA-C
1 TTAAACCATTGAA-CCCAAACCCATAACAC-TAAACC
*
49188689 TTGAACCATTGAACCCAAACCCATAACACTAAACC
1 TTAAACCATTGAACCCAAACCCATAACACTAAACC
49188724 TTAAACC-TTGAAC
1 TTAAACCATTGAAC
49188737 ACTAAATTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
34 10 0.23
35 29 0.67
36 4 0.09
ACGTcount: A:0.43, C:0.30, G:0.06, T:0.20
Consensus pattern (35 bp):
TTAAACCATTGAACCCAAACCCATAACACTAAACC
Found at i:49188750 original size:21 final size:21
Alignment explanation
Indices: 49188705--49188762 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
49188695 CATTGAACCC
49188705 AAACCCAT-AACACTAAACCTT
1 AAACCC-TGAACACTAAACCTT
* *
49188726 AAACCTTGAACACTAAA-TTT
1 AAACCCTGAACACTAAACCTT
*
49188746 CAAACCCTGAACCCTAA
1 -AAACCCTGAACACTAA
49188763 GCCTCGAGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 3 0.10
21 28 0.90
ACGTcount: A:0.45, C:0.31, G:0.03, T:0.21
Consensus pattern (21 bp):
AAACCCTGAACACTAAACCTT
Found at i:49189276 original size:10 final size:10
Alignment explanation
Indices: 49189240--49189292 Score: 70
Period size: 10 Copynumber: 5.1 Consensus size: 10
49189230 TCTAAATTTT
49189240 ATTTTTTAAA
1 ATTTTTTAAA
49189250 ATATTTTTAGAA
1 AT-TTTTTA-AA
*
49189262 CTTTTTTAAA
1 ATTTTTTAAA
*
49189272 ATTTTTTATA
1 ATTTTTTAAA
49189282 ATTTTTTAAA
1 ATTTTTTAAA
49189292 A
1 A
49189293 ATATAAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
10 22 0.59
11 12 0.32
12 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:49189435 original size:17 final size:18
Alignment explanation
Indices: 49189415--49189448 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
49189405 AATTTTTTAT
49189415 TTTAA-TTATTCGAATTA
1 TTTAAGTTATTCGAATTA
49189432 TTTAAGTTATTCGAATT
1 TTTAAGTTATTCGAATT
49189449 GTAAAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (18 bp):
TTTAAGTTATTCGAATTA
Found at i:49205581 original size:51 final size:51
Alignment explanation
Indices: 49205510--49205670 Score: 259
Period size: 51 Copynumber: 3.2 Consensus size: 51
49205500 CTGATCACAT
49205510 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
49205561 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
* * * * * *
49205612 TTGTCACTTGTCATTGATCAGGTAAGTGTGGCTGAGGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
*
49205663 TTGTCACT
1 TTATCACT
49205671 GATCAGAAGT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 104 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
Found at i:49212668 original size:51 final size:51
Alignment explanation
Indices: 49212592--49212701 Score: 175
Period size: 51 Copynumber: 2.2 Consensus size: 51
49212582 CTGATCACAT
* *
49212592 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAAATAAGTGTAGCTAAAACTACCACTTATAAC
* *
49212643 TTATCACTTGTCATTGATCAAATAAGTGTAGCTAAAGCTACCACTTATAAC
1 TTATCACTTGTCACTGATCAAATAAGTGTAGCTAAAACTACCACTTATAAC
*
49212694 TTGTCACT
1 TTATCACT
49212702 GATCAGAAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAAATAAGTGTAGCTAAAACTACCACTTATAAC
Found at i:49213813 original size:23 final size:23
Alignment explanation
Indices: 49213785--49213830 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
49213775 CACTGTTCCG
*
49213785 ACACCATTGAAAATTTAGGCTAT
1 ACACCACTGAAAATTTAGGCTAT
49213808 ACACCACTGAAAATTTAGGCTAT
1 ACACCACTGAAAATTTAGGCTAT
49213831 TACAGGGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (23 bp):
ACACCACTGAAAATTTAGGCTAT
Found at i:49214535 original size:60 final size:59
Alignment explanation
Indices: 49214469--49214623 Score: 170
Period size: 60 Copynumber: 2.6 Consensus size: 59
49214459 TAATAAGATT
* * *
49214469 ATTATTAAATATAATTTAATAAAAATATTA-ATAAGTAATTAATTATATT-TTAACATAATT
1 ATTATTAAATATAATTTAATAAAAATAATATATAA-T--TTAATAATATTCTTAACATAATA
* * * *
49214529 TTTATTAAATACAATTTTATAAAAATAATATATAATTTAATAATATTCTTAATATAATA
1 ATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAATATTCTTAACATAATA
* *
49214588 ATTATTAAAATATAAATTAATAAAAATTATAATATA
1 ATTATT-AAATATAATTTAATAAAAATAAT-ATATA
49214624 TAATATTAGA
Statistics
Matches: 79, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
58 10 0.13
59 14 0.18
60 46 0.58
61 9 0.11
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.44
Consensus pattern (59 bp):
ATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAATATTCTTAACATAATA
Found at i:49216578 original size:2 final size:2
Alignment explanation
Indices: 49216571--49216596 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
49216561 GAAAGGGGAT
49216571 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
49216597 TAGAGACTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:49221781 original size:19 final size:20
Alignment explanation
Indices: 49221759--49221803 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
49221749 ACAAAATATT
49221759 TATAAACATAAAT-AAAATA
1 TATAAACATAAATAAAAATA
*
49221778 TATAAATATAAATAAAAATA
1 TATAAACATAAATAAAAATA
49221798 TATAAA
1 TATAAA
49221804 AGAACTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
TATAAACATAAATAAAAATA
Found at i:49221812 original size:29 final size:29
Alignment explanation
Indices: 49221736--49221812 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 29
49221726 TATAATTTAT
* * **
49221736 AATATATAAATTAACAAAATATTTATAAA
1 AATATATAAAATAACTAAATATAAATAAA
* *
49221765 CATAAATAAAATATA-TAAATATAAATAAA
1 AATATATAAAATA-ACTAAATATAAATAAA
*
49221794 AATATATAAAAGAACTAAA
1 AATATATAAAATAACTAAA
49221813 AAGCATATCT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
28 1 0.03
29 35 0.95
30 1 0.03
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.29
Consensus pattern (29 bp):
AATATATAAAATAACTAAATATAAATAAA
Found at i:49221814 original size:20 final size:20
Alignment explanation
Indices: 49221768--49221814 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
49221758 TTATAAACAT
*
49221768 AAAT-AAAATATATAAATAT
1 AAATAAAAATATATAAATAG
49221787 AAATAAAAATATATAAA-AG
1 AAATAAAAATATATAAATAG
*
49221806 AACTAAAAA
1 AAATAAAAA
49221815 GCATATCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (20 bp):
AAATAAAAATATATAAATAG
Found at i:49222398 original size:40 final size:40
Alignment explanation
Indices: 49222340--49222418 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
49222330 AAGAATAAAC
49222340 TACATATTATGCTATGTTTGGATAAACAATAATTGAAAGT
1 TACATATTATGCTATGTTTGGATAAACAATAATTGAAAGT
*
49222380 TACATATTATGCTTTGTTTGGATAAACAATAATTGAAAG
1 TACATATTATGCTATGTTTGGATAAACAATAATTGAAAG
49222419 AATGTTGTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (40 bp):
TACATATTATGCTATGTTTGGATAAACAATAATTGAAAGT
Found at i:49226043 original size:27 final size:28
Alignment explanation
Indices: 49225967--49226043 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 28
49225957 GAGATATTTT
* *
49225967 GATATTTTATAATTATT-TAATTAGATAA
1 GATATTTTATTATTATTAT-TTTAGATAA
* *
49225995 -ATATTATT-TTATTAATACTTTA-ATAA
1 GATATT-TTATTATTATTATTTTAGATAA
49226021 GATATTTTATTATTATTATTTTA
1 GATATTTTATTATTATTATTTTA
49226044 TTAGTATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
26 6 0.15
27 31 0.79
28 2 0.05
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (28 bp):
GATATTTTATTATTATTATTTTAGATAA
Found at i:49234902 original size:12 final size:12
Alignment explanation
Indices: 49234885--49234911 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
49234875 ATATGGTTTA
49234885 TTCAAGGATTTG
1 TTCAAGGATTTG
49234897 TTCAAGGATTTG
1 TTCAAGGATTTG
49234909 TTC
1 TTC
49234912 CACAGTGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.44
Consensus pattern (12 bp):
TTCAAGGATTTG
Found at i:49236535 original size:26 final size:26
Alignment explanation
Indices: 49236505--49236558 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
49236495 TTATTGTAGG
49236505 ACACTTTCAACACATAATTTTATTTT
1 ACACTTTCAACACATAATTTTATTTT
49236531 ACACTTTCAACACATAATTTTATTTT
1 ACACTTTCAACACATAATTTTATTTT
49236557 AC
1 AC
49236559 TTTTCTTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.44
Consensus pattern (26 bp):
ACACTTTCAACACATAATTTTATTTT
Found at i:49238108 original size:12 final size:12
Alignment explanation
Indices: 49238091--49238115 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49238081 GATTGAAAAC
49238091 TAACGACTTAGA
1 TAACGACTTAGA
49238103 TAACGACTTAGA
1 TAACGACTTAGA
49238115 T
1 T
49238116 GACTCTGTCT
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:0.16, G:0.16, T:0.28
Consensus pattern (12 bp):
TAACGACTTAGA
Found at i:49239309 original size:27 final size:26
Alignment explanation
Indices: 49239256--49239331 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 26
49239246 CTCTCTCAAC
49239256 AAAAATTACAAAAAAATTCAAAATATTTAT
1 AAAAATT--AAAAAAATT-AAAATA-TTAT
* *
49239286 AAAAATTAAAAAAATTATATTATTAT
1 AAAAATTAAAAAAATTAAAATATTAT
49239312 AAAAATTTAAAAAAATTAAA
1 AAAAA-TTAAAAAAATTAAA
49239332 GGATATATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 9 0.21
27 17 0.40
28 9 0.21
30 7 0.17
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (26 bp):
AAAAATTAAAAAAATTAAAATATTAT
Found at i:49239338 original size:26 final size:26
Alignment explanation
Indices: 49239282--49239342 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
49239272 TTCAAAATAT
* **
49239282 TTATAAAAATTAAAAAAATTATATTA
1 TTATAAAAATTAAAAAAATTAAAGGA
49239308 TTATAAAAATTTAAAAAAATTAAAGGA
1 TTATAAAAA-TTAAAAAAATTAAAGGA
49239335 TATATAAA
1 T-TATAAA
49239343 GAAAGTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 9 0.30
27 15 0.50
28 6 0.20
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (26 bp):
TTATAAAAATTAAAAAAATTAAAGGA
Found at i:49241033 original size:20 final size:20
Alignment explanation
Indices: 49240996--49241033 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
49240986 TGATGGGGAG
*
49240996 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
49241016 CAAGAA-ATCGAAGCTGGA
1 CAAGAATATC-AAGCTGGA
49241034 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:49242985 original size:46 final size:46
Alignment explanation
Indices: 49242933--49243206 Score: 487
Period size: 46 Copynumber: 6.0 Consensus size: 46
49242923 AGTGTGCTCT
49242933 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
49242979 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
49243025 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
49243071 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
49243117 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
49243163 CTGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
49243207 TCATGTCAAA
Statistics
Matches: 222, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
45 1 0.00
46 221 1.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:49245087 original size:14 final size:14
Alignment explanation
Indices: 49245068--49245097 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
49245058 ACCAACTACT
49245068 TATCAGTAGCATTC
1 TATCAGTAGCATTC
49245082 TATCAGTAGCATTC
1 TATCAGTAGCATTC
49245096 TA
1 TA
49245098 CCTTAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (14 bp):
TATCAGTAGCATTC
Found at i:49249386 original size:14 final size:14
Alignment explanation
Indices: 49249367--49249411 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
49249357 AATAAATTTT
49249367 TTAAAAATAAGAAA
1 TTAAAAATAAGAAA
*
49249381 TTAAAAATAAAAATTA
1 TTAAAAATAAGAA--A
49249397 TTAAAAATAGAGAAA
1 TTAAAAATA-AGAAA
49249412 ACCAATTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 12 0.46
15 1 0.04
16 10 0.38
17 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (14 bp):
TTAAAAATAAGAAA
Found at i:49250420 original size:18 final size:19
Alignment explanation
Indices: 49250397--49250434 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
49250387 TTCTTTGAAT
*
49250397 TATTTCTACTATTGT-TTA
1 TATTTCAACTATTGTATTA
*
49250415 TATTTCAATTATTGTATTA
1 TATTTCAACTATTGTATTA
49250434 T
1 T
49250435 CTTTTTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.61
Consensus pattern (19 bp):
TATTTCAACTATTGTATTA
Found at i:49250600 original size:19 final size:21
Alignment explanation
Indices: 49250564--49250605 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
49250554 AAAGTTATTG
* *
49250564 TTTGATTTAAGT-TTTTAATA
1 TTTGATTTAAGTAATTAAATA
49250584 TTTGA-TTAAGTAATTAAATA
1 TTTGATTTAAGTAATTAAATA
49250604 TT
1 TT
49250606 AAAAAGTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.55
Consensus pattern (21 bp):
TTTGATTTAAGTAATTAAATA
Found at i:49256328 original size:13 final size:13
Alignment explanation
Indices: 49256310--49256341 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
49256300 GGGTCTTTTT
49256310 TTCGAGTTTCGAG
1 TTCGAGTTTCGAG
49256323 TTCGAG-TTCGAG
1 TTCGAGTTTCGAG
49256335 TT-GAGTT
1 TTCGAGTT
49256342 GAATTTCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 9 0.50
13 6 0.33
ACGTcount: A:0.16, C:0.12, G:0.31, T:0.41
Consensus pattern (13 bp):
TTCGAGTTTCGAG
Found at i:49262103 original size:80 final size:81
Alignment explanation
Indices: 49261950--49262103 Score: 186
Period size: 80 Copynumber: 1.9 Consensus size: 81
49261940 ATAATATACC
* * * * *
49261950 TATTTACAATCTAAGAAAAAAAATAAAAAAATTTGCGTTATTGTATTCTATTGTATTTCATATCA
1 TATTTACAATCTAACAAAAAAAATAAAAAAATTTGCGTTATTGTATTCTACTATATTTCACATAA
*
49262015 ATAGTATATACTTATT
66 ATAATATATACTTATT
* * ** *
49262031 TATTTACAATCT-ACAAAAACAAT-AAAAATTTTGTTTATATTGTATTCTACTATATTTTACATA
1 TATTTACAATCTAACAAAAAAAATAAAAAAATTTGCGT-TATTGTATTCTACTATATTTCACATA
49262094 AATAATATAT
65 AATAATATAT
49262104 CAATATTTAC
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
79 10 0.16
80 39 0.64
81 12 0.20
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (81 bp):
TATTTACAATCTAACAAAAAAAATAAAAAAATTTGCGTTATTGTATTCTACTATATTTCACATAA
ATAATATATACTTATT
Found at i:49262111 original size:80 final size:81
Alignment explanation
Indices: 49261950--49262127 Score: 179
Period size: 80 Copynumber: 2.3 Consensus size: 81
49261940 ATAATATACC
* * * * *
49261950 TATTTACAATCTAAGAAAAAAAATAAAAAAATTTGCGTTATTGTATTCTATTGTATTTCATATCA
1 TATTTACAATCTAACAAAAAAAATAAAAAAATTTGCGTTATTGTATTCTACTATATTTCACATAA
* *
49262015 ATAGTATATACTTATT
66 ATAATATATACATATT
* * ** *
49262031 TATTTACAATCT-ACAAAAACAAT-AAAAATTTTGTTTATATTGTATTCTACTATATTTTACATA
1 TATTTACAATCTAACAAAAAAAATAAAAAAATTTGCGT-TATTGTATTCTACTATATTTCACATA
49262094 AATAATATAT-CA-A--
65 AATAATATATACATATT
* *
49262107 TATTTACAATTTACCAAAAAA
1 TATTTACAATCTAACAAAAAA
49262128 TGAAAAGCAA
Statistics
Matches: 80, Mismatches: 15, Indels: 8
0.78 0.15 0.08
Matches are distributed among these distances:
76 11 0.14
77 6 0.08
78 1 0.01
79 11 0.14
80 39 0.49
81 12 0.15
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.41
Consensus pattern (81 bp):
TATTTACAATCTAACAAAAAAAATAAAAAAATTTGCGTTATTGTATTCTACTATATTTCACATAA
ATAATATATACATATT
Found at i:49263475 original size:23 final size:22
Alignment explanation
Indices: 49263398--49263484 Score: 56
Period size: 23 Copynumber: 3.8 Consensus size: 22
49263388 GTCACAACTG
49263398 TTATTAA-TGAA-TTTGAAAATA
1 TTATTAATTGAATTTTGAAAA-A
* **
49263419 TTATTAAGTTGATATAATTGATTAA
1 TTATTAA-TTGA-AT-TTTGAAAAA
49263444 TT-TTGAATTGAATTCTTGAAAAA
1 TTATT-AATTGAATT-TTGAAAAA
49263467 TTATTAATT-AATATTTGA
1 TTATTAATTGAAT-TTTGA
49263485 TGAACTGATT
Statistics
Matches: 51, Mismatches: 6, Indels: 17
0.69 0.08 0.23
Matches are distributed among these distances:
21 7 0.14
22 7 0.14
23 18 0.35
24 9 0.18
25 5 0.10
26 5 0.10
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.47
Consensus pattern (22 bp):
TTATTAATTGAATTTTGAAAAA
Found at i:49265727 original size:14 final size:13
Alignment explanation
Indices: 49265709--49265744 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 13
49265699 TTGAAAAAAA
49265709 AAATTAAAAATAT
1 AAATTAAAAATAT
49265722 AGAATTAAAAAATAT
1 A-AATT-AAAAATAT
49265737 AAATTAAA
1 AAATTAAA
49265745 TCTACAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.19
14 8 0.38
15 9 0.43
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (13 bp):
AAATTAAAAATAT
Found at i:49265734 original size:15 final size:14
Alignment explanation
Indices: 49265709--49265744 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
49265699 TTGAAAAAAA
49265709 AAATT-AAAAATAT
1 AAATTAAAAAATAT
49265722 AGAATTAAAAAATAT
1 A-AATTAAAAAATAT
49265737 AAATTAAA
1 AAATTAAA
49265745 TCTACAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 11 0.52
15 9 0.43
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (14 bp):
AAATTAAAAAATAT
Found at i:49266273 original size:13 final size:13
Alignment explanation
Indices: 49266217--49266270 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
49266207 GGTTAGTTTG
*
49266217 ATTAATTAATTCT
1 ATTAATTAATTTT
* *
49266230 ATTAATTGATTTA
1 ATTAATTAATTTT
*
49266243 ATCAATTAATTTT
1 ATTAATTAATTTT
49266256 ATTAATT-ATTTT
1 ATTAATTAATTTT
49266268 ATT
1 ATT
49266271 TAAAAGTGTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
12 8 0.24
13 26 0.76
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (13 bp):
ATTAATTAATTTT
Found at i:49272592 original size:51 final size:51
Alignment explanation
Indices: 49272507--49272654 Score: 190
Period size: 51 Copynumber: 2.9 Consensus size: 51
49272497 CGGATACACG
* * *
49272507 GTGGCCTGCACATAGTACCAC-CGTTGTAGCCAAAGCTATTTTATTTACAAA
1 GTGGCCTTCACATAGTACCACAC-TTGTATCCAAAGCTATTTTATTCACAAA
* * * *
49272558 GTGGGCTTTACATAGTACCACACTTGTTTCCAAAGCTATTATATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTATCCAAAGCTATTTTATTCACAAA
* * *
49272609 GTGGCCTTCACATAGCACTACACTTGTGTCCAAAGCTATTTTATTC
1 GTGGCCTTCACATAGTACCACACTTGTATCCAAAGCTATTTTATTC
49272655 TTAAGGTTTA
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
51 82 0.99
52 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTATCCAAAGCTATTTTATTCACAAA
Found at i:49272710 original size:28 final size:28
Alignment explanation
Indices: 49272678--49272794 Score: 151
Period size: 24 Copynumber: 4.5 Consensus size: 28
49272668 GGGAAATTTC
*
49272678 TCACTTAGCACAATGCTATGGACTTATT
1 TCACTTAGCACAATGCCATGGACTTATT
49272706 TCACTTAG----ATGCCATGGACTTATT
1 TCACTTAGCACAATGCCATGGACTTATT
*
49272730 TCACTTAGCACACTGCCATGGACTTATT
1 TCACTTAGCACAATGCCATGGACTTATT
*
49272758 TCACTTAG----ATGCCATGGTCTTATT
1 TCACTTAGCACAATGCCATGGACTTATT
49272782 TCACTTAGCACAA
1 TCACTTAGCACAA
49272795 CGTCATATCC
Statistics
Matches: 77, Mismatches: 4, Indels: 16
0.79 0.04 0.16
Matches are distributed among these distances:
24 45 0.58
28 32 0.42
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (28 bp):
TCACTTAGCACAATGCCATGGACTTATT
Found at i:49272734 original size:52 final size:52
Alignment explanation
Indices: 49272678--49272794 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
49272668 GGGAAATTTC
*
49272678 TCACTTAGCACAATGCTATGGACTTATTTCACTTAGATGCCATGGACTTATT
1 TCACTTAGCACAATGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
* *
49272730 TCACTTAGCACACTGCCATGGACTTATTTCACTTAGATGCCATGGTCTTATT
1 TCACTTAGCACAATGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
49272782 TCACTTAGCACAA
1 TCACTTAGCACAA
49272795 CGTCATATCC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (52 bp):
TCACTTAGCACAATGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
Found at i:49274300 original size:13 final size:13
Alignment explanation
Indices: 49274284--49274321 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
49274274 AAGCAGCTAT
49274284 TAAAATTTTATAA
1 TAAAATTTTATAA
* *
49274297 TAAAA-TTCAAAA
1 TAAAATTTTATAA
49274309 TAAAATTTTATAA
1 TAAAATTTTATAA
49274322 GAATGAACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (13 bp):
TAAAATTTTATAA
Found at i:49275751 original size:17 final size:18
Alignment explanation
Indices: 49275729--49275762 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
49275719 CTTAATGAAA
49275729 AAATAAAATAC-AAAAAG
1 AAATAAAATACGAAAAAG
49275746 AAATAAAATACGAAAAA
1 AAATAAAATACGAAAAA
49275763 ATAACTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (18 bp):
AAATAAAATACGAAAAAG
Found at i:49275761 original size:32 final size:32
Alignment explanation
Indices: 49275694--49275766 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
49275684 AAAATAGTAT
* **
49275694 AAAAAATAAAATACTAAAAGAATATCTTAATG
1 AAAAAATAAAATACAAAAAGAATATCAAAATG
49275726 AAAAAATAAAATACAAAAAGAA-AT-AAAATACG
1 AAAAAATAAAATACAAAAAGAATATCAAAAT--G
49275758 AAAAAATAA
1 AAAAAATAA
49275767 CTTTTTTGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 3 0.08
31 2 0.06
32 31 0.86
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.18
Consensus pattern (32 bp):
AAAAAATAAAATACAAAAAGAATATCAAAATG
Found at i:49275824 original size:13 final size:13
Alignment explanation
Indices: 49275806--49275835 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
49275796 TTTTTACTAA
49275806 ATATGAAAATAAT
1 ATATGAAAATAAT
49275819 ATATGAAAATAAT
1 ATATGAAAATAAT
49275832 ATAT
1 ATAT
49275836 TTTAGAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (13 bp):
ATATGAAAATAAT
Found at i:49276502 original size:41 final size:41
Alignment explanation
Indices: 49276457--49276539 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
49276447 TTAAAATTAA
49276457 TAACCGAAATTTATTTTGAAATTACAGGCATCGCAATGGCT
1 TAACCGAAATTTATTTTGAAATTACAGGCATCGCAATGGCT
49276498 TAACCGAAATTTATTTTGAAATTACAGGCATCGCAATGGCT
1 TAACCGAAATTTATTTTGAAATTACAGGCATCGCAATGGCT
49276539 T
1 T
49276540 CATTGATTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Consensus pattern (41 bp):
TAACCGAAATTTATTTTGAAATTACAGGCATCGCAATGGCT
Found at i:49277921 original size:7 final size:7
Alignment explanation
Indices: 49277905--49278010 Score: 167
Period size: 7 Copynumber: 15.1 Consensus size: 7
49277895 TTATCTAATC
*
49277905 AGTGACA
1 AGTGATA
49277912 AGTGATA
1 AGTGATA
49277919 AGTGATA
1 AGTGATA
49277926 AGTGATA
1 AGTGATA
*
49277933 AGTGACA
1 AGTGATA
49277940 AGTGATA
1 AGTGATA
49277947 AGTGATA
1 AGTGATA
49277954 AGTGATA
1 AGTGATA
49277961 AGTGATA
1 AGTGATA
49277968 AGTGATA
1 AGTGATA
49277975 AGTGATA
1 AGTGATA
49277982 AGTGATA
1 AGTGATA
*
49277989 AGTGACA
1 AGTGATA
* *
49277996 AATGACA
1 AGTGATA
49278003 AGTGATA
1 AGTGATA
49278010 A
1 A
49278011 ATGTGATCCG
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 92 1.00
ACGTcount: A:0.44, C:0.04, G:0.27, T:0.25
Consensus pattern (7 bp):
AGTGATA
Found at i:49280473 original size:19 final size:20
Alignment explanation
Indices: 49280446--49280483 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
49280436 TGATTTTGGT
49280446 TTTTATTTGTGTTT-TTTTTA
1 TTTTATTTGT-TTTATTTTTA
49280466 TTTT-TTTGTTTTATTTTT
1 TTTTATTTGTTTTATTTTT
49280484 GGTTTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.18
19 10 0.59
20 4 0.24
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (20 bp):
TTTTATTTGTTTTATTTTTA
Found at i:49280505 original size:28 final size:27
Alignment explanation
Indices: 49280445--49280508 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
49280435 CTGATTTTGG
* * *
49280445 TTTTTATTTGTGTTTTTTTTATTTTTT
1 TTTTTATTTGTGGTTTTTTAATTTTAT
*
49280472 TGTTTTATTTTTGGTTTTTTAATTTCTAT
1 T-TTTTATTTGTGGTTTTTTAATTT-TAT
49280501 TTTTTATT
1 TTTTTATT
49280509 CCAATGGGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 1 0.03
28 27 0.87
29 3 0.10
ACGTcount: A:0.11, C:0.02, G:0.08, T:0.80
Consensus pattern (27 bp):
TTTTTATTTGTGGTTTTTTAATTTTAT
Found at i:49281859 original size:20 final size:20
Alignment explanation
Indices: 49281821--49281868 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
49281811 TAAATTCTAA
* **
49281821 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
49281841 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
49281861 AAA-ATAAA
1 AAAGATAAA
49281869 ATCCTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:49282692 original size:14 final size:14
Alignment explanation
Indices: 49282673--49282708 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
49282663 TCTTTATAAT
49282673 GATACTATTCTAAC
1 GATACTATTCTAAC
49282687 GATACTATTCTAAC
1 GATACTATTCTAAC
49282701 GATACTAT
1 GATACTAT
49282709 ATTTACTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.36
Consensus pattern (14 bp):
GATACTATTCTAAC
Found at i:49283607 original size:33 final size:33
Alignment explanation
Indices: 49283543--49283619 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
49283533 ATTGGGTCGA
* *** * *
49283543 ATCCACCGCAGTACAGTACTTTTCTCGGCCCGT
1 ATCCACCGCAGTACAGCACTACCCCCAGCCCGT
49283576 ATCCACCGCAGTACAGCACTACCCCCAGCCCGT
1 ATCCACCGCAGTACAGCACTACCCCCAGCCCGT
*
49283609 ATGCACCGCAG
1 ATCCACCGCAG
49283620 CATGGCACTC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.22, C:0.42, G:0.18, T:0.18
Consensus pattern (33 bp):
ATCCACCGCAGTACAGCACTACCCCCAGCCCGT
Found at i:49287574 original size:12 final size:12
Alignment explanation
Indices: 49287532--49287581 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
49287522 ACACATAATT
49287532 AATCTAAATACA
1 AATCTAAATACA
*
49287544 AAACTAAA-ACA
1 AATCTAAATACA
*
49287555 CATACTAAATACA
1 AAT-CTAAATACA
49287568 AATCTAAATACA
1 AATCTAAATACA
49287580 AA
1 AA
49287582 ATTAAATTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 4 0.12
12 23 0.72
13 5 0.16
ACGTcount: A:0.62, C:0.18, G:0.00, T:0.20
Consensus pattern (12 bp):
AATCTAAATACA
Found at i:49287587 original size:12 final size:12
Alignment explanation
Indices: 49287535--49287588 Score: 65
Period size: 12 Copynumber: 4.5 Consensus size: 12
49287525 CATAATTAAT
49287535 CTAAATACAAAA
1 CTAAATACAAAA
*
49287547 CTAAA-ACACATA
1 CTAAATACA-AAA
*
49287559 CTAAATACAAAT
1 CTAAATACAAAA
49287571 CTAAATACAAAA
1 CTAAATACAAAA
*
49287583 TTAAAT
1 CTAAAT
49287589 TAGTAAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 3 0.09
12 29 0.83
13 3 0.09
ACGTcount: A:0.61, C:0.17, G:0.00, T:0.22
Consensus pattern (12 bp):
CTAAATACAAAA
Found at i:49287915 original size:13 final size:13
Alignment explanation
Indices: 49287876--49287918 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
49287866 TTCTCCTTCC
49287876 TTCTTTCTCTCTATT
1 TTCTTTCT-TCT-TT
*
49287891 CTCTTT-TTCTTT
1 TTCTTTCTTCTTT
49287903 TTCTTTCTTCTTT
1 TTCTTTCTTCTTT
49287916 TTC
1 TTC
49287919 CCTCACCAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 7 0.28
13 12 0.48
14 1 0.04
15 5 0.20
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (13 bp):
TTCTTTCTTCTTT
Found at i:49287963 original size:11 final size:11
Alignment explanation
Indices: 49287938--49287984 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
49287928 TGTTGCCCTC
* *
49287938 TCTTCTCATTC
1 TCTTCTCTTTT
49287949 TCTTCTCTTTT
1 TCTTCTCTTTT
49287960 TCTT-TCTTTT
1 TCTTCTCTTTT
* *
49287970 TCTTTTCTTCT
1 TCTTCTCTTTT
49287981 TCTT
1 TCTT
49287985 GCTTCTTGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
10 10 0.31
11 22 0.69
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (11 bp):
TCTTCTCTTTT
Found at i:49288811 original size:13 final size:15
Alignment explanation
Indices: 49288778--49288814 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
49288768 TATTCTATGA
49288778 AAATTTAATAGAATAT
1 AAATTT-ATAGAATAT
49288794 AAATTTATAG-AT-T
1 AAATTTATAGAATAT
49288807 AAATTTAT
1 AAATTTAT
49288815 TAAATAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.43
14 2 0.10
15 4 0.19
16 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (15 bp):
AAATTTATAGAATAT
Found at i:49288827 original size:20 final size:20
Alignment explanation
Indices: 49288802--49288839 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
49288792 ATAAATTTAT
*
49288802 AGATTAAATTTATTAAATAA
1 AGATTAAATTTATAAAATAA
49288822 AGATTAAATTTATAAAAT
1 AGATTAAATTTATAAAAT
49288840 TTATAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (20 bp):
AGATTAAATTTATAAAATAA
Found at i:49295796 original size:18 final size:18
Alignment explanation
Indices: 49295773--49295831 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
49295763 AACTCTTTTG
49295773 CTTTTAGATTCAAAAGCA
1 CTTTTAGATTCAAAAGCA
* *
49295791 CTTTTA-ACTCCAAAAGTTA
1 CTTTTAGA-TTCAAAAG-CA
*
49295810 TTTGTTAGATTCAAAAGCA
1 CTT-TTAGATTCAAAAGCA
49295829 CTT
1 CTT
49295832 CTTATTTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
17 1 0.03
18 13 0.42
19 6 0.19
20 10 0.32
21 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (18 bp):
CTTTTAGATTCAAAAGCA
Found at i:49296421 original size:24 final size:24
Alignment explanation
Indices: 49296373--49296423 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
49296363 TTAATTTTAG
*
49296373 AAAAAGAAAAATATAAAATATAAA
1 AAAAAGAAAAAAATAAAATATAAA
*
49296397 AAAAAGAAAAACAATGAAATA-AAA
1 AAAAAGAAAAA-AATAAAATATAAA
49296421 AAA
1 AAA
49296424 TATAACTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.80, C:0.02, G:0.06, T:0.12
Consensus pattern (24 bp):
AAAAAGAAAAAAATAAAATATAAA
Found at i:49301103 original size:18 final size:18
Alignment explanation
Indices: 49301021--49301115 Score: 82
Period size: 18 Copynumber: 5.3 Consensus size: 18
49301011 GGTTTCATTT
* *
49301021 AGTAACATTCAATTATTC
1 AGTAACAATCAGTTATTC
* * *
49301039 AGTAGCAGTTAGTTATTC
1 AGTAACAATCAGTTATTC
* **
49301057 AGTAACAATCATTTGCTC
1 AGTAACAATCAGTTATTC
* *
49301075 AATAGCAATCAGTTATTC
1 AGTAACAATCAGTTATTC
* *
49301093 AGTAACGATCAATTATTC
1 AGTAACAATCAGTTATTC
49301111 AGTAA
1 AGTAA
49301116 TAGTTAGTCA
Statistics
Matches: 58, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 58 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (18 bp):
AGTAACAATCAGTTATTC
Found at i:49301129 original size:36 final size:35
Alignment explanation
Indices: 49301015--49301132 Score: 110
Period size: 36 Copynumber: 3.3 Consensus size: 35
49301005 TTTATCGGTT
*
49301015 TCATTTAGTAACATTCAATTATTCAGTAGCAGTTAG
1 TCATTCAGTAACA-TCAATTATTCAGTAGCAGTTAG
* * ** * * *
49301051 TTATTCAGTAACAATCATTTGCTCAATAGCAATCAG
1 TCATTCAGTAAC-ATCAATTATTCAGTAGCAGTTAG
* **
49301087 TTATTCAGTAACGATCAATTATTCAGTAATAGTTAG
1 TCATTCAGTAAC-ATCAATTATTCAGTAGCAGTTAG
49301123 TCATTCAGTA
1 TCATTCAGTA
49301133 CTTTTATTTA
Statistics
Matches: 63, Mismatches: 18, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
36 62 0.98
37 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (35 bp):
TCATTCAGTAACATCAATTATTCAGTAGCAGTTAG
Found at i:49302598 original size:13 final size:13
Alignment explanation
Indices: 49302559--49302600 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
49302549 TTTATTTTAT
49302559 ATATATTATAATA
1 ATATATTATAATA
49302572 ATATAATT-TAATA
1 ATAT-ATTATAATA
49302585 ATATACTTAT-ATA
1 ATATA-TTATAATA
49302598 ATA
1 ATA
49302601 AGTAAACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.04
13 21 0.81
14 4 0.15
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (13 bp):
ATATATTATAATA
Found at i:49304746 original size:13 final size:14
Alignment explanation
Indices: 49304722--49304750 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
49304712 GTGTATATGG
49304722 AAAATTCATTTTAA
1 AAAATTCATTTTAA
49304736 AAAATTC-TTTTAA
1 AAAATTCATTTTAA
49304749 AA
1 AA
49304751 TGGTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAATTCATTTTAA
Found at i:49314944 original size:53 final size:54
Alignment explanation
Indices: 49314881--49314987 Score: 173
Period size: 53 Copynumber: 2.0 Consensus size: 54
49314871 CTTAAATATA
* *
49314881 TAATTAAATTAACTAT-GATAATGGCAATCACATGCA-TTTTTTCATGCATGGCC
1 TAATTAAATTAACTATAG-TAATGACAACCACATGCATTTTTTTCATGCATGGCC
49314934 TAATTAAATTAACTATAGTAATGACAACCACATGCATTTTTTTCATGCATGGCC
1 TAATTAAATTAACTATAGTAATGACAACCACATGCATTTTTTTCATGCATGGCC
49314988 CTAAAGAGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
53 32 0.64
54 18 0.36
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.36
Consensus pattern (54 bp):
TAATTAAATTAACTATAGTAATGACAACCACATGCATTTTTTTCATGCATGGCC
Found at i:49317662 original size:2 final size:2
Alignment explanation
Indices: 49317655--49317690 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
49317645 AAGGGGACTT
49317655 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
49317691 TAAAGATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:49335751 original size:133 final size:134
Alignment explanation
Indices: 49335431--49335830 Score: 508
Period size: 133 Copynumber: 3.0 Consensus size: 134
49335421 TTTAGAGAGT
* * * * * *
49335431 ATGAGTGAAATTCTAAAGGAATC-TTCGATCATTTTGAACAAAC-AGGAGATCGCAACCCAGCAC
1 ATGAATGAAATTCTAAAGGGA-CATTCGATTATTTTGAGCAAACGA-GAAATTGCAACCCAGCAC
* * * * * **
49335494 GATAGGGCACGATT-TCCCGAATTGCTAAACATCGAACATTGCCTTCGTTTTGGAGAATTTTTAA
64 GTTAGGGCACGATTCT-GCGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAAGAATTTTTAA
* *
49335558 ACG---C
128 AAGAATA
* * *
49335562 ATGAATGAAATTCTAAAGGGACATTCAATTATTTTGAGTAAACGAGAAATTGCAACCCAACACGT
1 ATGAATGAAATTCTAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGT
*
49335627 TAGGGCACGATTCTGTGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAAGAA-TTTTAAAAG
66 TAGGGCACGATTCTGCGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAAGAATTTTTAAAAG
49335691 AATA
131 AATA
49335695 ATGAATGAAATTCTAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGT
1 ATGAATGAAATTCTAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGT
* * * * *
49335760 TAGGGCACGATTCCGGGAATTGCCAAATATCGAACACCGCCTTCATTTTAAAGAATTTTTAAATG
66 TAGGGCACGATTCTGCGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAAGAATTTTTAAAAG
49335825 AATA
131 AATA
49335829 AT
1 AT
49335831 TGCAAAAATA
Statistics
Matches: 235, Mismatches: 27, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
130 9 0.04
131 97 0.41
132 2 0.01
133 113 0.48
134 14 0.06
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (134 bp):
ATGAATGAAATTCTAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGT
TAGGGCACGATTCTGCGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAAGAATTTTTAAAAG
AATA
Found at i:49344210 original size:19 final size:18
Alignment explanation
Indices: 49344188--49344227 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
49344178 TGAATAAAAC
*
49344188 TTATTTACCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
*
49344207 TTATCTAGCTAAATAAAT
1 TTATCTACCTAAATAAAT
49344225 TTA
1 TTA
49344228 AAATATATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:49353476 original size:42 final size:42
Alignment explanation
Indices: 49353425--49353522 Score: 144
Period size: 42 Copynumber: 2.3 Consensus size: 42
49353415 ACTTAAATAG
49353425 AGAAAATAGTTCTTTTATTCTAATAAACTACTAAAACATAAA
1 AGAAAATAGTTCTTTTATTCTAATAAACTACTAAAACATAAA
** *
49353467 AGAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAA
1 AGAAAATAGTTCTTTTATTCTAATAAACTACTAAAACATAAA
*
49353509 ATAAAAATA-TTCTT
1 A-GAAAATAGTTCTT
49353523 AGAATATGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
42 43 0.88
43 6 0.12
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (42 bp):
AGAAAATAGTTCTTTTATTCTAATAAACTACTAAAACATAAA
Found at i:49353561 original size:19 final size:18
Alignment explanation
Indices: 49353539--49353578 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
49353529 TGAATAAAAC
*
49353539 TTATCTATCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
49353558 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
49353576 TTA
1 TTA
49353579 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:49369285 original size:121 final size:121
Alignment explanation
Indices: 49369122--49369363 Score: 441
Period size: 121 Copynumber: 2.0 Consensus size: 121
49369112 ACAAGTGGAT
* *
49369122 GTTTAGGTTCAGATGAATGTGGACAATTAAACTTAGACATTCATTTGTTCAAATTTATTTTGGAA
1 GTTTAGATTCAGATGAATGTGGACAATTAAACTTAGACATTCATTTGTTCAAATTTATTTCGGAA
*
49369187 GTGAAATATTTTTTTATTAATTTATATATATTTTTAAAAAAATTAAAGATTATATA
66 GTGAAATAATTTTTTATTAATTTATATATATTTTTAAAAAAATTAAAGATTATATA
49369243 GTTTAGATTCAGATGAATGTGGACAATTAAACTTA-AGCATTCATTTGTTCAAATTTATTTCGGA
1 GTTTAGATTCAGATGAATGTGGACAATTAAACTTAGA-CATTCATTTGTTCAAATTTATTTCGGA
49369307 AGTGAAATAATTTTTTATTAATTTATATATATTTTTAAAAAAATTAAAGATTATATA
65 AGTGAAATAATTTTTTATTAATTTATATATATTTTTAAAAAAATTAAAGATTATATA
49369364 ATTTCTTTTT
Statistics
Matches: 117, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
120 1 0.01
121 116 0.99
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (121 bp):
GTTTAGATTCAGATGAATGTGGACAATTAAACTTAGACATTCATTTGTTCAAATTTATTTCGGAA
GTGAAATAATTTTTTATTAATTTATATATATTTTTAAAAAAATTAAAGATTATATA
Found at i:49369859 original size:3 final size:3
Alignment explanation
Indices: 49369851--49369898 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
49369841 CGTCTGCCAT
49369851 GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC
1 GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC
49369899 TTCCTTGCCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
GTC
Found at i:49371433 original size:15 final size:16
Alignment explanation
Indices: 49371399--49371433 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
49371389 TCTTGATGCC
*
49371399 AAAATCTACCTTGAGA
1 AAAACCTACCTTGAGA
49371415 AAAACCTACCTTGAGA
1 AAAACCTACCTTGAGA
49371431 AAA
1 AAA
49371434 TTAATATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.20, G:0.11, T:0.20
Consensus pattern (16 bp):
AAAACCTACCTTGAGA
Found at i:49377888 original size:23 final size:22
Alignment explanation
Indices: 49377836--49377888 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
49377826 TCCACGTCTT
*
49377836 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
49377858 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
49377881 TTTCTTTT
1 TTTCTTTT
49377889 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:49384676 original size:20 final size:20
Alignment explanation
Indices: 49384643--49384682 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
49384633 AAAAGAAGGA
*
49384643 AAAGAGGGTAGTGAAAAAGT
1 AAAGAAGGTAGTGAAAAAGT
*
49384663 AAAGAAGGTCGTGAAAAAGT
1 AAAGAAGGTAGTGAAAAAGT
49384683 TTTACCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.33, T:0.15
Consensus pattern (20 bp):
AAAGAAGGTAGTGAAAAAGT
Found at i:49409445 original size:12 final size:12
Alignment explanation
Indices: 49409428--49409475 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
49409418 TAAAATAAAA
49409428 TAATATATCAAC
1 TAATATATCAAC
49409440 TAATATATCAAC
1 TAATATATCAAC
*
49409452 TAAT-T-T-TA-
1 TAATATATCAAC
49409460 TAATATATCAAC
1 TAATATATCAAC
49409472 TAAT
1 TAAT
49409476 TTTCTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
8 4 0.13
9 2 0.07
10 2 0.07
11 2 0.07
12 20 0.67
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (12 bp):
TAATATATCAAC
Found at i:49409483 original size:24 final size:20
Alignment explanation
Indices: 49409440--49409478 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
49409430 ATATATCAAC
49409440 TAATATATCAACTAATTTTA
1 TAATATATCAACTAATTTTA
49409460 TAATATATCAACTAATTTT
1 TAATATATCAACTAATTTT
49409479 CTTTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATATATCAACTAATTTTA
Found at i:49411154 original size:29 final size:29
Alignment explanation
Indices: 49411122--49411197 Score: 152
Period size: 29 Copynumber: 2.6 Consensus size: 29
49411112 CTCATATTAT
49411122 ATTTTAGTCACTTATGTTTGAAATGTTAC
1 ATTTTAGTCACTTATGTTTGAAATGTTAC
49411151 ATTTTAGTCACTTATGTTTGAAATGTTAC
1 ATTTTAGTCACTTATGTTTGAAATGTTAC
49411180 ATTTTAGTCACTTATGTT
1 ATTTTAGTCACTTATGTT
49411198 ATATGTTATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (29 bp):
ATTTTAGTCACTTATGTTTGAAATGTTAC
Found at i:49421345 original size:16 final size:17
Alignment explanation
Indices: 49421324--49421361 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
49421314 TTATATTTAA
49421324 TAATATAA-TGAATTAT
1 TAATATAACTGAATTAT
* *
49421340 TAATATAACTTAATTTT
1 TAATATAACTGAATTAT
49421357 TAATA
1 TAATA
49421362 AATTATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TAATATAACTGAATTAT
Done.