Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold12
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: 2382857
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.28
Warning! 280777 characters in sequence are not A, C, G, or T
File 2 of 12
Found at i:168765 original size:35 final size:35
Alignment explanation
Indices: 168708--168774 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 35
168698 CTTTTTTCTT
* * *
168708 TTTTTTCTTTTTGACATTTTTTTGTAATTTTTGAC
1 TTTTTTATTTTTGAAATATTTTTGTAATTTTTGAC
* * *
168743 TTTTTTATTTTTTAAATATTTTTTTATTTTTT
1 TTTTTTATTTTTGAAATATTTTTGTAATTTTT
168775 TGTGTTCAGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 26 1.00
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.75
Consensus pattern (35 bp):
TTTTTTATTTTTGAAATATTTTTGTAATTTTTGAC
Found at i:172707 original size:51 final size:52
Alignment explanation
Indices: 172601--172719 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 52
172591 ATTTGCCCAC
* * * * *
172601 ATGTATCGATACATTTAAGTAAAAAACCCAGAATATATCGATATATTGAACA
1 ATGTATCGATACATTTAAGTAAAAAACCCAAAATATATAGATACAATGAAAA
* ** *
172653 ATGTATCGATACATTT-GGTTCAAAACCTAAAATATATAGATACAATGAAAA
1 ATGTATCGATACATTTAAGTAAAAAACCCAAAATATATAGATACAATGAAAA
172704 ATGTATCGATACATTT
1 ATGTATCGATACATTT
172720 TTATTCCAGA
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
51 42 0.72
52 16 0.28
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.31
Consensus pattern (52 bp):
ATGTATCGATACATTTAAGTAAAAAACCCAAAATATATAGATACAATGAAAA
Found at i:173606 original size:52 final size:52
Alignment explanation
Indices: 173543--173807 Score: 269
Period size: 52 Copynumber: 5.1 Consensus size: 52
173533 GTGATATCAA
* * * *
173543 ACTTAAAGATGAGAAAGGTGCCAATGTACTAATTCAAGGCCAGCAACATTGG
1 ACTTAAAGATGAGAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGG
* * ** * * *
173595 ATTTTAAGATGAGAAAAATGCCAATATGCTGATTCAGGGTTAGCGACATTGG
1 ACTTAAAGATGAGAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGG
* * * *
173647 ACTTAAAAATGATAAAGGTGCTAATGTGCTGATTCAAGGCTAGTGACATTGG
1 ACTTAAAGATGAGAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGG
* * * * * * ***
173699 GCTTAAAAATGATAAAAGTGCCAATATGCTGATTCAAGGCTAGCGATATCAA
1 ACTTAAAGATGAGAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGG
* * * * *
173751 ACTTGAAGATGACAAAGGTGCTAATGTGCTGATTCAAGGCCAGCGACATTAG
1 ACTTAAAGATGAGAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGG
173803 ACTTA
1 ACTTA
173808 GAAAGAGGTG
Statistics
Matches: 170, Mismatches: 43, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
52 170 1.00
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (52 bp):
ACTTAAAGATGAGAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGG
Found at i:173682 original size:104 final size:104
Alignment explanation
Indices: 173526--173807 Score: 339
Period size: 104 Copynumber: 2.7 Consensus size: 104
173516 CCAATATGCT
* * * * * * *
173526 AAGGCTAGTGATATCAAACTTAAAGATGAGAAAGGTGCCAATGTACTAATTCAAGGCCAGCAACA
1 AAGGCTAGCGACATCAAACTTAAAGATGACAAAGGTGCTAATGTGCTGATTCAAGGCCAGCGACA
* * *
173591 TTGGATTTTAAGATGAGAAAAATGCCAATATGCTGATTC
66 TTGGACTTAAAAATGAGAAAAATGCCAATATGCTGATTC
* * *** * * * *
173630 AGGGTTAGCGACATTGGACTTAAAAATGATAAAGGTGCTAATGTGCTGATTCAAGGCTAGTGACA
1 AAGGCTAGCGACATCAAACTTAAAGATGACAAAGGTGCTAATGTGCTGATTCAAGGCCAGCGACA
* * *
173695 TTGGGCTTAAAAATGATAAAAGTGCCAATATGCTGATTC
66 TTGGACTTAAAAATGAGAAAAATGCCAATATGCTGATTC
* *
173734 AAGGCTAGCGATATCAAACTTGAAGATGACAAAGGTGCTAATGTGCTGATTCAAGGCCAGCGACA
1 AAGGCTAGCGACATCAAACTTAAAGATGACAAAGGTGCTAATGTGCTGATTCAAGGCCAGCGACA
*
173799 TTAGACTTA
66 TTGGACTTA
173808 GAAAGAGGTG
Statistics
Matches: 144, Mismatches: 34, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
104 144 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.26
Consensus pattern (104 bp):
AAGGCTAGCGACATCAAACTTAAAGATGACAAAGGTGCTAATGTGCTGATTCAAGGCCAGCGACA
TTGGACTTAAAAATGAGAAAAATGCCAATATGCTGATTC
Found at i:173984 original size:33 final size:33
Alignment explanation
Indices: 173877--174069 Score: 234
Period size: 33 Copynumber: 6.0 Consensus size: 33
173867 GAAAGAGATG
* *
173877 CCACTGACTTGTGTGGGCTTT-GAAAAGGATTT
1 CCACTGACTTGTGTGGGCTTTAGAAAAGGGTTA
* *
173909 CCA-TCGACTTGTGTAGGCTTTA-AAAA-GGTTG
1 CCACT-GACTTGTGTGGGCTTTAGAAAAGGGTTA
*
173940 CCACTGACTTGTGTGGACTTTAGAAAAGGGTTA
1 CCACTGACTTGTGTGGGCTTTAGAAAAGGGTTA
* *
173973 CCATTGACTTGTGTGGGCTTTTGAAAAGGGTTA
1 CCACTGACTTGTGTGGGCTTTAGAAAAGGGTTA
* *
174006 CCACCGACTTGTGTGGGCTTTA-AAAAAGGTTA
1 CCACTGACTTGTGTGGGCTTTAGAAAAGGGTTA
* * *
174038 CCACTAACTTGTGTGGACTTTAGAAAAAGGTT
1 CCACTGACTTGTGTGGGCTTTAGAAAAGGGTT
174070 GTCATGGTCT
Statistics
Matches: 139, Mismatches: 16, Indels: 11
0.84 0.10 0.07
Matches are distributed among these distances:
31 22 0.16
32 55 0.40
33 62 0.45
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (33 bp):
CCACTGACTTGTGTGGGCTTTAGAAAAGGGTTA
Found at i:174060 original size:98 final size:96
Alignment explanation
Indices: 173881--174069 Score: 297
Period size: 98 Copynumber: 1.9 Consensus size: 96
173871 GAGATGCCAC
* * * *
173881 TGACTTGTGTGGGCTTTGAAAAGGATTTCCATCGACTTGTGTAGGCTTTAAAAAGGTTGCCACTG
1 TGACTTGTGTGGGCTTTGAAAAGGATTACCACCGACTTGTGTAGGCTTTAAAAAGGTTACCACTA
*
173946 ACTTGTGTGGACTTTAGAAAAGGGTTACCAT
66 ACTTGTGTGGACTTTAGAAAAAGGTTACCAT
* *
173977 TGACTTGTGTGGGCTTTTGAAAAGGGTTACCACCGACTTGTGTGGGCTTTAAAAAAGGTTACCAC
1 TGACTTGTGTGGGC-TTTGAAAAGGATTACCACCGACTTGTGTAGGCTTT-AAAAAGGTTACCAC
174042 TAACTTGTGTGGACTTTAGAAAAAGGTT
64 TAACTTGTGTGGACTTTAGAAAAAGGTT
174070 GTCATGGTCT
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
96 14 0.17
97 31 0.37
98 39 0.46
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.33
Consensus pattern (96 bp):
TGACTTGTGTGGGCTTTGAAAAGGATTACCACCGACTTGTGTAGGCTTTAAAAAGGTTACCACTA
ACTTGTGTGGACTTTAGAAAAAGGTTACCAT
Found at i:174082 original size:98 final size:96
Alignment explanation
Indices: 173882--174121 Score: 294
Period size: 98 Copynumber: 2.5 Consensus size: 96
173872 AGATGCCACT
* * * * *
173882 GACTTGTGTGGGCTTTGAAAAGGATTTCCATCGACTTGTGTAGGCTTTAAAAAGGTTGCCACTGA
1 GACTTGTGTGGGCTTTGAAAAGGGTTACCACCGACTTGTGTAGGCTTTAAAAAGGTTACCACTAA
* *
173947 CTTGTGTGGACTTTAGAAAAGGGTTACCATT
66 CTTGTGTGGACTTTAGAAAAAGGTTACCATG
*
173978 GACTTGTGTGGGCTTTTGAAAAGGGTTACCACCGACTTGTGTGGGCTTTAAAAAAGGTTACCACT
1 GACTTGTGTGGGC-TTTGAAAAGGGTTACCACCGACTTGTGTAGGCTTT-AAAAAGGTTACCACT
**
174043 AACTTGTGTGGACTTTAGAAAAAGGTTGTCATG
64 AACTTGTGTGGACTTTAGAAAAAGGTTACCATG
* * * *
174076 GTC-T-TGTGGGCTTT-AAAAGGG-TGCCACTGAC--ATGTAGGCTTTAAAA
1 GACTTGTGTGGGCTTTGAAAAGGGTTACCACCGACTTGTGTAGGCTTTAAAA
174122 GTGTGCCACT
Statistics
Matches: 127, Mismatches: 15, Indels: 10
0.84 0.10 0.07
Matches are distributed among these distances:
90 4 0.03
91 9 0.07
93 8 0.06
94 7 0.06
95 3 0.02
96 20 0.16
97 32 0.25
98 44 0.35
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.32
Consensus pattern (96 bp):
GACTTGTGTGGGCTTTGAAAAGGGTTACCACCGACTTGTGTAGGCTTTAAAAAGGTTACCACTAA
CTTGTGTGGACTTTAGAAAAAGGTTACCATG
Found at i:174115 original size:28 final size:28
Alignment explanation
Indices: 173875--174667 Score: 529
Period size: 28 Copynumber: 26.9 Consensus size: 28
173865 TAGAAAGAGA
*
173875 TGCCACTGACTTGTGTGGGCTTTGAAAAGGAT
1 TGCCACTGAC-T-TGTGGGCTTT-AAAAGG-G
* *
173907 TTCCA-TCGACTTGTGTAGGCTTTAAAAAGGT
1 TGCCACT-GACTTGTG--GGCTTT-AAAAGGG
173938 TGCCACTGACTTGTGTGGACTTTAGAAAAGGG
1 TGCCACTGACTTGTG-GG-CTTT--AAAAGGG
* *
173970 TTACCATTGACTTGTGTGGGCTTTTGAAAAGGG
1 -TGCCACTGAC-T-TGTGGGC-TTT-AAAAGGG
* * *
174003 TTACCACCGACTTGTGTGGGCTTTAAAAAAGGT
1 -TGCCACTGAC-T-TGTGGGCTTT--AAAAGGG
* * *
174036 TACCACTAACTTGTGTGGACTTTAGAAAAAGGT
1 TGCCACTGACTTGTG-GG-CTTT---AAAAGGG
* *
174069 TGTCA-TGGTCTTGTGGGCTTTAAAAGGG
1 TGCCACT-GACTTGTGGGCTTTAAAAGGG
* * *
174097 TGCCACTGACATGTAGGCTTTAAAAGTG
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
*
174125 TGCCACTGACTTGTAGGCTTTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
* *
174153 TGCAACTGACTTGAGGGCTTTAAAAGAAGG
1 TGCCACTGACTTGTGGGCTTTAAAAG--GG
* *
174183 TTGCCACTAACTTGTGGGCTTTGAAAAGCG
1 -TGCCACTGACTTGTGGGCTTT-AAAAGGG
*
174213 TGCCACTGACTTGTGGGCTTGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
*
174241 TGCCACTGACTTGTGCGCTTTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
* * *
174269 TTGCCA-TAACTTATGCGAGCTTTAAAAAAAAGGT
1 -TGCCACTGACTTGTG-G-GCTTT----AAAAGGG
* *
174303 TACCATTGACTTGTGGGCTTTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
* * * *
174331 TGCCACTAACATGTCGGTTTTGAAAA-GG
1 TGCCACTGACTTGTGGGCTTT-AAAAGGG
* * *
174359 TGCAACTGACTTGTGGGATTTAAAATGG
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
** ** *
174387 TGCCACCAACTAATGAGCTTTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
* *
174415 TGCCACTAACTTATGGGCTTTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
*** * *
174443 TGCCACTGACTTGCAAGCTCTAGAAAAGG
1 TGCCACTGACTTGTGGGCTTTA-AAAGGG
* * *
174472 TGCCACTAACTTATGAGCTTTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
* * * *
174500 TGTCGCTGATTTGTGGGCTTTAAAAAGG
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
*
174528 TGCCACTAACTTGTGGGCTTTAAAAGGG
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
* * * * *
174556 TGCCACTAACTTATGGGCTTTGAAATGA
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
* *
174584 TGCCACTAACTTGTGGGCTTTAGAAAAAGGT
1 TGCCACTGACTTGTGGGCTTT---AAAAGGG
* *
174615 TGCCACTGACATGTGGGCATTGAAAA--G
1 TGCCACTGACTTGTGGGC-TTTAAAAGGG
* *
174642 TGCCACGGAGTTGTGGAG-TTTAAAAG
1 TGCCACTGACTTGTGG-GCTTTAAAAG
174668 AGATGCTATT
Statistics
Matches: 614, Mismatches: 110, Indels: 79
0.76 0.14 0.10
Matches are distributed among these distances:
26 6 0.01
27 17 0.03
28 311 0.51
29 55 0.09
30 18 0.03
31 64 0.10
32 56 0.09
33 64 0.10
34 19 0.03
35 4 0.01
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTAAAAGGG
Found at i:174701 original size:30 final size:30
Alignment explanation
Indices: 174654--174746 Score: 118
Period size: 30 Copynumber: 3.1 Consensus size: 30
174644 CCACGGAGTT
* *
174654 GTGGAGTTTAA-AAGAGATGCTATTGAGTC
1 GTGGACTTTAAGAAGAGATGCTATTAAGTC
* *
174683 GTGGACTTTAAGAAGAGATGCCACTAAGTC
1 GTGGACTTTAAGAAGAGATGCTATTAAGTC
*
174713 GTGGACTTTGAGAAGAGATG-TCATTAAGTC
1 GTGGACTTTAAGAAGAGATGCT-ATTAAGTC
174743 GTGG
1 GTGG
174747 CGTTTTAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
29 10 0.18
30 45 0.82
ACGTcount: A:0.30, C:0.11, G:0.31, T:0.28
Consensus pattern (30 bp):
GTGGACTTTAAGAAGAGATGCTATTAAGTC
Found at i:175601 original size:26 final size:26
Alignment explanation
Indices: 175571--175622 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
175561 AACTAAATGG
*
175571 CAAATG-TGTAGATATTGTTTGAGGTA
1 CAAATGCT-TAGATATTGTATGAGGTA
175597 CAAATGCTTAGATATTGTATGAGGTA
1 CAAATGCTTAGATATTGTATGAGGTA
175623 TGGAGGGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.37
Consensus pattern (26 bp):
CAAATGCTTAGATATTGTATGAGGTA
Found at i:176219 original size:20 final size:20
Alignment explanation
Indices: 176194--176265 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
176184 TACTCAAATA
176194 TATCGATACATTGTTCAATG
1 TATCGATACATTGTTCAATG
*
176214 TATCGATACA-TGTATGAATG
1 TATCGATACATTGT-TCAATG
176234 TATCGATACATTGTTCAATG
1 TATCGATACATTGTTCAATG
*
176254 TATTGATACATT
1 TATCGATACATT
176266 CTATTTTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
19 3 0.06
20 41 0.87
21 3 0.06
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.40
Consensus pattern (20 bp):
TATCGATACATTGTTCAATG
Found at i:183100 original size:13 final size:13
Alignment explanation
Indices: 183082--183107 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
183072 AATTTTTTTG
183082 TGTATCGATACAT
1 TGTATCGATACAT
183095 TGTATCGATACAT
1 TGTATCGATACAT
183108 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:183885 original size:20 final size:20
Alignment explanation
Indices: 183850--183899 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
183840 GGTAATTTAC
183850 ACACATATCAAAAATTTATTT
1 ACACATA-CAAAAATTTATTT
*
183871 ACACATACGAAAATTTATTT
1 ACACATACAAAAATTTATTT
*
183891 GCACATACA
1 ACACATACA
183900 TCTATTCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.46, C:0.18, G:0.04, T:0.32
Consensus pattern (20 bp):
ACACATACAAAAATTTATTT
Found at i:185687 original size:13 final size:13
Alignment explanation
Indices: 185669--185707 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
185659 ATAATCCCCC
*
185669 TGTATCGATACAG
1 TGTATCGATACAA
*
185682 TGTATCGACACAA
1 TGTATCGATACAA
185695 TGTATCGATACAA
1 TGTATCGATACAA
185708 AGAAAAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:187807 original size:15 final size:15
Alignment explanation
Indices: 187787--187817 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
187777 ATTTCGTTTG
*
187787 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
187802 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
187817 G
1 G
187818 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:189551 original size:32 final size:30
Alignment explanation
Indices: 189515--189573 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
189505 GAAATCAAAT
189515 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
189547 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
189574 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:189862 original size:13 final size:13
Alignment explanation
Indices: 189844--189869 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
189834 CAATTTTTTG
189844 TGTATCGATACAT
1 TGTATCGATACAT
189857 TGTATCGATACAT
1 TGTATCGATACAT
189870 ATTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:192452 original size:13 final size:13
Alignment explanation
Indices: 192434--192458 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
192424 ATAATCCCCC
192434 TGTATCGATACAT
1 TGTATCGATACAT
192447 TGTATCGATACA
1 TGTATCGATACA
192459 AAGAAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:194560 original size:15 final size:15
Alignment explanation
Indices: 194540--194570 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
194530 ATTTCGTTTG
*
194540 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
194555 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
194570 G
1 G
194571 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:198343 original size:32 final size:30
Alignment explanation
Indices: 198307--198365 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
198297 GAAATCAAAT
198307 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
198339 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
198366 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:198664 original size:13 final size:13
Alignment explanation
Indices: 198646--198671 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
198636 CAATTTTTTA
198646 TGTATCGATACAT
1 TGTATCGATACAT
198659 TGTATCGATACAT
1 TGTATCGATACAT
198672 ATTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:198687 original size:32 final size:33
Alignment explanation
Indices: 198626--198689 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
198616 TCCAAGCCAA
* *
198626 TGTATCGATACAATTTTTTATGTATCGATACAT
1 TGTATCGATACAATATTTGATGTATCGATACAT
*
198659 TGTATCGATAC-ATATTTGGTGTATCGATACA
1 TGTATCGATACAATATTTGATGTATCGATACA
198690 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATATTTGATGTATCGATACAT
Found at i:198766 original size:20 final size:21
Alignment explanation
Indices: 198719--198773 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
198709 ATTCCCAATG
* *
198719 ACATGTATCGATACATCTTTT
1 ACATGTATCGATACATCTGTA
*
198740 TCATGTATCGATACAT-TGTA
1 ACATGTATCGATACATCTGTA
198760 ACATGTATCGATAC
1 ACATGTATCGATAC
198774 TTTGAATTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (21 bp):
ACATGTATCGATACATCTGTA
Found at i:201847 original size:13 final size:13
Alignment explanation
Indices: 201829--201854 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
201819 AATTTTTTTG
201829 TGTATCGATACAT
1 TGTATCGATACAT
201842 TGTATCGATACAT
1 TGTATCGATACAT
201855 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:204279 original size:20 final size:21
Alignment explanation
Indices: 204250--204291 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
204240 TGGGGGCTGC
*
204250 CCGGTTGCGACCTGG-GAGTG
1 CCGGTCGCGACCTGGTGAGTG
204270 CCGGTCGCGACCTGGTGAGTG
1 CCGGTCGCGACCTGGTGAGTG
204291 C
1 C
204292 TGCCTAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.10, C:0.29, G:0.43, T:0.19
Consensus pattern (21 bp):
CCGGTCGCGACCTGGTGAGTG
Found at i:210927 original size:13 final size:13
Alignment explanation
Indices: 210909--210934 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
210899 ACATTTGGTC
210909 ATGTATCGATACA
1 ATGTATCGATACA
210922 ATGTATCGATACA
1 ATGTATCGATACA
210935 TCTTGTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:210929 original size:33 final size:32
Alignment explanation
Indices: 210887--210954 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
210877 CGTTACAAGC
210887 CAATGTATCGATACAT-TTGGTCATGTATCGATA
1 CAATGTATCGATACATCTT-GT-ATGTATCGATA
210920 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
210952 CAA
1 CAA
210955 ACAGTTAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 18 0.53
34 2 0.06
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:211053 original size:13 final size:13
Alignment explanation
Indices: 211035--211092 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
211025 ATATTTGGTC
211035 ATGTATCGATACA
1 ATGTATCGATACA
*
211048 ATGTATCGATACT
1 ATGTATCGATACA
*
211061 ATG---C-A-A-T
1 ATGTATCGATACA
211068 ATGTATCGATACA
1 ATGTATCGATACA
211081 ATGTATCGATAC
1 ATGTATCGATAC
211093 TATGCAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
7 4 0.11
8 1 0.03
9 1 0.03
10 2 0.05
11 1 0.03
12 1 0.03
13 27 0.73
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:211072 original size:33 final size:33
Alignment explanation
Indices: 211035--211113 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
211025 ATATTTGGTC
211035 ATGTATCGATACAATGTATCGATACTATGCAAT
1 ATGTATCGATACAATGTATCGATACTATGCAAT
211068 ATGTATCGATACAATGTATCGATACTATGCAAT
1 ATGTATCGATACAATGTATCGATACTATGCAAT
211101 ATGTATCGATACA
1 ATGTATCGATACA
211114 TCTGAAGGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (33 bp):
ATGTATCGATACAATGTATCGATACTATGCAAT
Found at i:211073 original size:20 final size:20
Alignment explanation
Indices: 211048--211112 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
211038 TATCGATACA
211048 ATGTATCGATACTATGCAAT
1 ATGTATCGATACTATGCAAT
211068 ATGTATCG--A-TA--C-A-
1 ATGTATCGATACTATGCAAT
211081 ATGTATCGATACTATGCAAT
1 ATGTATCGATACTATGCAAT
211101 ATGTATCGATAC
1 ATGTATCGATAC
211113 ATCTGAAGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 8 0.21
14 1 0.03
15 2 0.05
16 2 0.05
17 2 0.05
18 2 0.05
19 1 0.03
20 20 0.53
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACTATGCAAT
Found at i:211613 original size:33 final size:32
Alignment explanation
Indices: 211567--211630 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
211557 CGTTACATGC
211567 CAATGTATCGATACAT-TTGGTCATGTATCGATA
1 CAATGTATCGATACATCTT-GT-ATGTATCGATA
*
211600 CAATGTATTGATACATCTTGTATGTATCGAT
1 CAATGTATCGATACATCTTGTATGTATCGAT
211631 GCAAACAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 10 0.34
33 17 0.59
34 2 0.07
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:214208 original size:13 final size:13
Alignment explanation
Indices: 214190--214226 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
214180 AAACCTTTTG
*
214190 TATCGATACACTA
1 TATCGATACAATA
*
214203 TATCGATACAATG
1 TATCGATACAATA
214216 TATCGATACAA
1 TATCGATACAA
214227 AGAGTGTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.30
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:225007 original size:30 final size:30
Alignment explanation
Indices: 224945--225114 Score: 119
Period size: 29 Copynumber: 5.6 Consensus size: 30
224935 TTTTCAAAAC
* * * *
224945 TCCACAACTCTGTGGCATCCTTCTT-AAAG
1 TCCACAACTCAGTGGCATCTTTTTTCCAAG
*
224974 TCCACAACTCAGTGACATCTTTTTTCCAAG
1 TCCACAACTCAGTGGCATCTTTTTTCCAAG
* *
225004 TCCACGACTTAGTGGCATCCTTTTTCTTCCAAAAG
1 TCCACAACTCAGTGGCAT-C-TTTT-TTCC--AAG
* * * * * *
225039 CCCACGACTCTGTGGCACCCTTTTT-AAAG
1 TCCACAACTCAGTGGCATCTTTTTTCCAAG
* * *
225068 TCCACAACTCAGTAGCATCTCTTCTCCAAG
1 TCCACAACTCAGTGGCATCTTTTTTCCAAG
* *
225098 TCCACGACTCAATGGCA
1 TCCACAACTCAGTGGCA
225115 GCTCTTCTTT
Statistics
Matches: 108, Mismatches: 26, Indels: 13
0.73 0.18 0.09
Matches are distributed among these distances:
29 41 0.38
30 35 0.32
31 1 0.01
32 6 0.06
33 7 0.06
34 1 0.01
35 17 0.16
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.29
Consensus pattern (30 bp):
TCCACAACTCAGTGGCATCTTTTTTCCAAG
Found at i:225120 original size:30 final size:30
Alignment explanation
Indices: 225065--225132 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
225055 ACCCTTTTTA
* *
225065 AAGTCCACAACTCAGTAGCATCTCTTCTCC
1 AAGTCCACAACTCAATAGCAGCTCTTCTCC
* * **
225095 AAGTCCACGACTCAATGGCAGCTCTTCTTT
1 AAGTCCACAACTCAATAGCAGCTCTTCTCC
225125 AAGTCCAC
1 AAGTCCAC
225133 CCTTTTTCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.34, G:0.13, T:0.26
Consensus pattern (30 bp):
AAGTCCACAACTCAATAGCAGCTCTTCTCC
Found at i:225268 original size:61 final size:60
Alignment explanation
Indices: 225173--225681 Score: 240
Period size: 61 Copynumber: 8.1 Consensus size: 60
225163 GCACCTTTTT
* * * * *
225173 ACCCTTTTAAGCCCGCAACTCCATGGCA-CCTTTTTCTTTTCAAAG-CCTTTAACTTCGTGGC
1 ACCCTTTTAAGTCCACAACTCTATGGCATCCTTTTTCTTTT--AAGTCC-ATAACTCCGTGGC
*
225234 ACCCTTTTACGTCCACAACTCTATGGCA-CCTTTTT-TTTTAAGTCCATAACTCCGTGGC
1 ACCCTTTTAAGTCCACAACTCTATGGCATCCTTTTTCTTTTAAGTCCATAACTCCGTGGC
* * *
225292 ACTTTTTTCCTTTTCAAAGTCTACAACTCTATGGCATCCTTTTTGTTTTCAAAG-CCTACAACTC
1 AC------CCTTTT--AAGTCCACAACTCTATGGCATCCTTTTTCTTTT--AAGTCC-ATAACTC
**
225356 CGTGAT
55 CGTGGC
* * * *
225362 ACCCTTTTAAGCCCACAA-TTTCGTGGCATCCTTTTTCCTTTTAAGTCCGTAACTCCGTGGC
1 ACCCTTTTAAGTCCACAACTCT-ATGGCATCCTTTTT-CTTTTAAGTCCATAACTCCGTGGC
* ** * * ** *
225423 ACCCTTTTAGGTCCACAACTCCGTGGCAT-C-----CTTTTAAGCCCACAACTTGGTGAC
1 ACCCTTTTAAGTCCACAACTCTATGGCATCCTTTTTCTTTTAAGTCCATAACTCCGTGGC
* * *
225477 ACCCTTTTTCCTTTTAAGCCCACAACTTTGTGGCA-CCTTTTTCTTTTCAAAG-CC-TACTACTC
1 A--C-----CCTTTTAAGTCCACAACTCTATGGCATCCTTTTTCTTTT--AAGTCCATA--ACTC
*
225539 TGTGGC
55 CGTGGC
* * * * *
225545 ACCCTTTTAAGTCCACAACTCTATGG-AACCTTTTTTCTTTTACGTCCACAACTCTGTGGA
1 ACCCTTTTAAGTCCACAACTCTATGGCATCC-TTTTTCTTTTAAGTCCATAACTCCGTGGC
** * *
225605 ACCTTTTTTCTTTTCAAAGTCCACAACTCCGTGGCATCCTTTTTCTTTTCAAAGCCCACAACTCC
1 ACC------CTTTT--AAGTCCACAACTCTATGGCATCCTTTTTCTTTT--AAGTCCATAACTCC
225670 GTGGC
56 GTGGC
225675 ACCCTTT
1 ACCCTTT
225682 GTCGTAACGT
Statistics
Matches: 347, Mismatches: 51, Indels: 97
0.70 0.10 0.20
Matches are distributed among these distances:
54 19 0.05
56 1 0.00
58 16 0.05
59 2 0.01
60 20 0.06
61 116 0.33
62 35 0.10
63 4 0.01
64 16 0.05
66 30 0.09
67 9 0.03
68 41 0.12
69 5 0.01
70 33 0.10
ACGTcount: A:0.20, C:0.31, G:0.12, T:0.36
Consensus pattern (60 bp):
ACCCTTTTAAGTCCACAACTCTATGGCATCCTTTTTCTTTTAAGTCCATAACTCCGTGGC
Found at i:225368 original size:128 final size:129
Alignment explanation
Indices: 225188--225424 Score: 318
Period size: 128 Copynumber: 1.8 Consensus size: 129
225178 TTTAAGCCCG
** * * * *
225188 CAACTCCATGGCACCTTTTTCTTTTCAAAGCCTTTAACTTCGTGGCACCCTTTTACGTCCACAA-
1 CAACTCCATGGCACCTTTTTCTTTTCAAAGCCTACAACTCCGTGACACCCTTTTAAGCCCACAAT
225252 CTCTATGGCA-CCTTTTT-TTTTAAGTCCATAACTCCGTGGCACTTTTTTCCTTTTCAAAGTCTA
66 CTC-ATGGCATCCTTTTTCTTTTAAGTCCATAACTCCGTGGCACTTTTTTCCTTTTCAAAGTCTA
* * *
225315 CAACTCTATGGCATCCTTTTTGTTTTCAAAGCCTACAACTCCGTGATACCCTTTTAAGCCCACAA
1 CAACTCCATGGCA-CCTTTTTCTTTTCAAAGCCTACAACTCCGTGACACCCTTTTAAGCCCACAA
* * *
225380 TTTCGTGGCATCCTTTTTCCTTTTAAGTCCGTAACTCCGTGGCAC
65 TCTCATGGCATCCTTTTT-CTTTTAAGTCCATAACTCCGTGGCAC
225425 CCTTTTAGGT
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
127 12 0.13
128 48 0.52
129 9 0.10
131 24 0.26
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.38
Consensus pattern (129 bp):
CAACTCCATGGCACCTTTTTCTTTTCAAAGCCTACAACTCCGTGACACCCTTTTAAGCCCACAAT
CTCATGGCATCCTTTTTCTTTTAAGTCCATAACTCCGTGGCACTTTTTTCCTTTTCAAAGTCTA
Found at i:225379 original size:27 final size:27
Alignment explanation
Indices: 225343--225484 Score: 86
Period size: 27 Copynumber: 5.0 Consensus size: 27
225333 TTTGTTTTCA
* *
225343 AAGCCTACAACTCCGTGATACCCTTTT
1 AAGCCCACAACTCCGTGACACCCTTTT
* * *
225370 AAGCCCACAATTTCGTGGCATCCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGACA--C-----CCTTTT
* ** *
225404 AAGTCCGTAACTCCGTGGCACCCTTTT
1 AAGCCCACAACTCCGTGACACCCTTTT
* * * *
225431 AGGTCCACAACTCCGTGGCATCCTTTT
1 AAGCCCACAACTCCGTGACACCCTTTT
**
225458 AAGCCCACAACTTGGTGACACCCTTTT
1 AAGCCCACAACTCCGTGACACCCTTTT
225485 TCCTTTTAAG
Statistics
Matches: 88, Mismatches: 20, Indels: 14
0.72 0.16 0.11
Matches are distributed among these distances:
27 65 0.74
29 1 0.01
32 1 0.01
34 21 0.24
ACGTcount: A:0.21, C:0.32, G:0.15, T:0.32
Consensus pattern (27 bp):
AAGCCCACAACTCCGTGACACCCTTTT
Found at i:225494 original size:34 final size:33
Alignment explanation
Indices: 225451--225523 Score: 112
Period size: 34 Copynumber: 2.2 Consensus size: 33
225441 CTCCGTGGCA
225451 TCCTTTTAAGCCCACAACTTGGTGACACCCTTTT
1 TCCTTTTAAGCCCACAACTTGGTGACA-CCTTTT
* *
225485 TCCTTTTAAGCCCACAACTTTGTGGCACCTTTT
1 TCCTTTTAAGCCCACAACTTGGTGACACCTTTT
225518 T-CTTTT
1 TCCTTTT
225524 CAAAGCCTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 5 0.14
33 7 0.19
34 25 0.68
ACGTcount: A:0.18, C:0.30, G:0.11, T:0.41
Consensus pattern (33 bp):
TCCTTTTAAGCCCACAACTTGGTGACACCTTTT
Found at i:225510 original size:88 final size:88
Alignment explanation
Indices: 225349--225518 Score: 223
Period size: 88 Copynumber: 1.9 Consensus size: 88
225339 TTCAAAGCCT
* * * * * **
225349 ACAACTCCGTGATACCCTTTTAAGCCCACAATTTCGTGGCATCCTTTTTCCTTTTAAGTCCGTAA
1 ACAACTCCGTGACACCCTTTTAAGCCCACAACTTCGTGACACCCTTTTTCCTTTTAAGCCCACAA
225414 CTCCGTGGCACCCTTTTAGGTCC
66 CTCCGTGGCACCCTTTTAGGTCC
* * *
225437 ACAACTCCGTGGCATCCTTTTAAGCCCACAACTTGGTGACACCCTTTTTCCTTTTAAGCCCACAA
1 ACAACTCCGTGACACCCTTTTAAGCCCACAACTTCGTGACACCCTTTTTCCTTTTAAGCCCACAA
** *
225502 CTTTGTGGCACCTTTTT
66 CTCCGTGGCACCCTTTT
225519 CTTTTCAAAG
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
88 69 1.00
ACGTcount: A:0.20, C:0.32, G:0.14, T:0.34
Consensus pattern (88 bp):
ACAACTCCGTGACACCCTTTTAAGCCCACAACTTCGTGACACCCTTTTTCCTTTTAAGCCCACAA
CTCCGTGGCACCCTTTTAGGTCC
Found at i:225674 original size:35 final size:32
Alignment explanation
Indices: 225237--225677 Score: 199
Period size: 35 Copynumber: 13.8 Consensus size: 32
225227 TCGTGGCACC
* * *
225237 CTTTTACGTCCACAACTCTATGGCACCTTTTT
1 CTTTTAAGCCCACAACTCTGTGGCACCTTTTT
* * * *
225269 -TTTTAAGTCCATAACTCCGTGGCACTTTTTT
1 CTTTTAAGCCCACAACTCTGTGGCACCTTTTT
* * *
225300 CCTTTTCAAAGTCTACAACTCTATGGCATCCTTTTT
1 -CTTTT--AAGCCCACAACTCTGTGGCA-CCTTTTT
* * * **
225336 GTTTTCAAAGCCTACAACTCCGTGATACC-----
1 CTTTT--AAGCCCACAACTCTGTGGCACCTTTTT
*
225365 CTTTTAAGCCCACAA-TTTCGTGGCATCCTTTTT
1 CTTTTAAGCCCACAACTCT-GTGGCA-CCTTTTT
* ** *
225398 CCTTTTAAGTCCGTAACTCCGTGGCACC-----
1 -CTTTTAAGCCCACAACTCTGTGGCACCTTTTT
* * * *
225426 CTTTTAGGTCCACAACTCCGTGGCA-----TC
1 CTTTTAAGCCCACAACTCTGTGGCACCTTTTT
*
225453 CTTTTAAGCCCACAACT-TGGTGACACCCTTTTT
1 CTTTTAAGCCCACAACTCT-GTGGCA-CCTTTTT
*
225486 CCTTTTAAGCCCACAACTTTGTGGCACCTTTTT
1 -CTTTTAAGCCCACAACTCTGTGGCACCTTTTT
* *
225519 CTTTTCAAAGCCTACTACTCTGTGGCACC-----
1 CTTTT--AAGCCCACAACTCTGTGGCACCTTTTT
* * *
225548 CTTTTAAGTCCACAACTCTATGGAACCTTTTTT
1 CTTTTAAGCCCACAACTCTGTGGCACC-TTTTT
* * *
225581 CTTTTACGTCCACAACTCTGTGGAACCTTTTTT
1 CTTTTAAGCCCACAACTCTGTGGCACC-TTTTT
* *
225614 CTTTTCAAAGTCCACAACTCCGTGGCATCCTTTTT
1 CTTTT--AAGCCCACAACTCTGTGGCA-CCTTTTT
*
225649 CTTTTCAAAGCCCACAACTCCGTGGCACC
1 CTTTT--AAGCCCACAACTCTGTGGCACC
225678 CTTTGTCGTA
Statistics
Matches: 323, Mismatches: 50, Indels: 70
0.73 0.11 0.16
Matches are distributed among these distances:
26 1 0.00
27 72 0.22
28 2 0.01
29 9 0.03
31 26 0.08
32 5 0.02
33 50 0.15
34 63 0.20
35 87 0.27
36 8 0.02
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.37
Consensus pattern (32 bp):
CTTTTAAGCCCACAACTCTGTGGCACCTTTTT
Found at i:228914 original size:13 final size:13
Alignment explanation
Indices: 228892--228949 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
228882 AGCAGTAGCT
*
228892 TTGTAGCGATACA
1 TTGTATCGATACA
228905 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
228921 CTTATGTATCGATACA
1 --T-TGTATCGATACA
228937 TTGTATCGATACA
1 TTGTATCGATACA
228950 AATTGTTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:229809 original size:49 final size:49
Alignment explanation
Indices: 229687--230204 Score: 481
Period size: 49 Copynumber: 10.7 Consensus size: 49
229677 TGAAGAAGAA
** *
229687 TGCCAATATGCTGAGACAAGGCCAGCGACATTGGGCTTTAAAGATGACGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC-TTAAAGAT-A--AAGG
** *
229740 CACCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGG
* *
229789 TGCCAATGTGCTGAGTCAAGGCCAGCGACATTGGACTTAAAGA-AGAA--
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATA-AAGG
* * * * **
229836 TGCCAATGTGTTGATTCAAGGCCAACAACATTGGGTTTTAAAGATGACGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGAT-A--AAGG
* * * * *
229889 CGCTAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGG
* * * * *
229938 TGCCAATGTGCTGAGTCAAGGCCAACGACATTGGTCTTAAAGATAAAGC
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGG
* * * *
229987 TACCAATATGCTGATTCAAGGCCAACAATATTGGAC-T-----TAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGG
* * * *
230030 TGCCAATTTACTAATTCAAGGCCAGAGACATTGGACTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGG
* * *
230079 TGCCAAAATGCTAATTCAAGGCCAGCGATATTGGAC-T-----TAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGG
* * *
230122 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGG
* * *
230171 TGCCAATATGCTGAATCAAGGTCAGCGATATTGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGG
230205 GCTTGGAAGG
Statistics
Matches: 380, Mismatches: 66, Indels: 42
0.78 0.14 0.09
Matches are distributed among these distances:
43 70 0.18
44 2 0.01
47 28 0.07
48 12 0.03
49 189 0.50
50 1 0.00
51 4 0.01
52 18 0.05
53 56 0.15
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGG
Found at i:229876 original size:149 final size:145
Alignment explanation
Indices: 229668--230204 Score: 565
Period size: 149 Copynumber: 3.7 Consensus size: 145
229658 TGGTCAGCAT
* * ** * * *
229668 CATTAGACTTGAAGAAGAATGCCAATATGCTGAGACAAGGCCAGCGACATTGGGCTTTAAAGATG
1 CATTGGACTTAAAGAAGAATGCCAATATGCTGATTCAAGGCCAACAACATTGGTC-TT-AA-A-G
*
229733 ACGAAGGCACCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTGCCAATGT
62 ACGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTGCCAATGT
229798 GCTGAGTCAAGGCCAGCGA
127 GCTGAGTCAAGGCCAGCGA
* * *
229817 CATTGGACTTAAAGAAGAATGCCAATGTGTTGATTCAAGGCCAACAACATTGGGTTTTAAAGATG
1 CATTGGACTTAAAGAAGAATGCCAATATGCTGATTCAAGGCCAACAACATT-GGTCTT-AA-A-G
* * *
229882 ACGAAGGCGCTAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGGTGCCAATGT
62 ACGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTGCCAATGT
*
229947 GCTGAGTCAAGGCCAACGA
127 GCTGAGTCAAGGCCAGCGA
* * * *
229966 CATTGGTCTTAAAGATA-AAGCTACCAATATGCTGATTCAAGGCCAACAATATTGGACTT----A
1 CATTGGACTTAAAGA-AGAA--TGCCAATATGCTGATTCAAGGCCAACAACATTGGTCTTAAAGA
* * * * * * **
230026 --AAGGTGCCAATTTACTAATTCAAGGCCAGAGACATTGGACTTAAAGATAAAGGTGCCAAAATG
63 CGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTGCCAATGTG
* *
230089 CTAATTCAAGGCCAGCGA
128 CTGAGTCAAGGCCAGCGA
* * * * *
230107 TATTGGACTTAAAG--G--TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAA
1 CATTGGACTTAAAGAAGAATGCCAATATGCTGATTCAAGGCCAACAACATTGGTCTTAAAGACGA
* * *
230168 AGGTGCCAATATGCTGAATCAAGGTCAGCGATATTGG
66 AGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGG
230205 GCTTGGAAGG
Statistics
Matches: 326, Mismatches: 51, Indels: 30
0.80 0.13 0.07
Matches are distributed among these distances:
135 32 0.10
139 1 0.00
141 110 0.34
143 1 0.00
149 147 0.45
150 7 0.02
151 28 0.09
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (145 bp):
CATTGGACTTAAAGAAGAATGCCAATATGCTGATTCAAGGCCAACAACATTGGTCTTAAAGACGA
AGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTG
AGTCAAGGCCAGCGA
Found at i:230047 original size:43 final size:43
Alignment explanation
Indices: 229934--230163 Score: 183
Period size: 43 Copynumber: 5.1 Consensus size: 43
229924 CTTAAAGATG
* * * *
229934 AAGGTGCCAATGTGCTGAGTCAAGGCCAACGACATTGGTCTTA
1 AAGGTGCCAATATGCTAATTCAAGGCCAACGACATTGGACTTA
* * * *
229977 AAGATAAAGCTACCAATATGCTGATTCAAGGCCAACAATATTGGACTTA
1 AAG-----G-TGCCAATATGCTAATTCAAGGCCAACGACATTGGACTTA
* *
230026 AAGGTGCCAATTTACTAATTCAAGGCCAGA-GACATTGGACTTAAAGATA
1 AAGGTGCCAATATGCTAATTCAAGGCCA-ACGACATTGGAC-T-----TA
* * *
230075 AAGGTGCCAAAATGCTAATTCAAGGCCAGCGATATTGGACTTA
1 AAGGTGCCAATATGCTAATTCAAGGCCAACGACATTGGACTTA
* * * *
230118 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA
1 AAGGTGCCAATATGCTAATTCAAGGCCAACGACATTGGACTTA
230161 AAG
1 AAG
230164 ACAAAGGTGC
Statistics
Matches: 151, Mismatches: 22, Indels: 28
0.75 0.11 0.14
Matches are distributed among these distances:
43 74 0.49
44 3 0.02
48 2 0.01
49 72 0.48
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (43 bp):
AAGGTGCCAATATGCTAATTCAAGGCCAACGACATTGGACTTA
Found at i:230073 original size:92 final size:92
Alignment explanation
Indices: 229742--230204 Score: 507
Period size: 92 Copynumber: 4.9 Consensus size: 92
229732 GACGAAGGCA
* * * * * *
229742 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAGTCA
1 CCAATGTGCTGATTCAAGGCCAGAGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATTCA
* *
229807 AGGCCAGCGACATTGGACTTAAAGAAGAATG
66 AGGCCAGCAATATTGGACTTAAAG--G--TG
* * * * *
229838 CCAATGTGTTGATTCAAGGCCA-ACAACATTGGGTTTTAAAGATGACGAAGGCGCTAATATGCTG
1 CCAATGTGCTGATTCAAGGCCAGA-GACATT-GGTCTTAAAGAT-A--AAGGTGCCAATATGCTG
229902 ATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGGTG
61 ATTCAAGGCCAGCAATATTGGACTT----A--AAGGTG
* * *
229940 CCAATGTGCTGAGTCAAGGCCA-ACGACATTGGTCTTAAAGATAAAGCTACCAATATGCTGATTC
1 CCAATGTGCTGATTCAAGGCCAGA-GACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATTC
*
230004 AAGGCCAACAATATTGGACTTAAAGGTG
65 AAGGCCAGCAATATTGGACTTAAAGGTG
* * * * * *
230032 CCAATTTACTAATTCAAGGCCAGAGACATTGGACTTAAAGATAAAGGTGCCAAAATGCTAATTCA
1 CCAATGTGCTGATTCAAGGCCAGAGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATTCA
*
230097 AGGCCAGCGATATTGGACTTAAAGGTG
66 AGGCCAGCAATATTGGACTTAAAGGTG
* * *
230124 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGAATCA
1 CCAATGTGCTGATTCAAGGCCAGAGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATTCA
* *
230189 AGGTCAGCGATATTGG
66 AGGCCAGCAATATTGG
230205 GCTTGGAAGG
Statistics
Matches: 312, Mismatches: 43, Indels: 28
0.81 0.11 0.07
Matches are distributed among these distances:
92 156 0.50
93 1 0.00
94 1 0.00
96 24 0.08
97 10 0.03
98 38 0.12
100 37 0.12
101 11 0.04
102 29 0.09
104 2 0.01
106 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (92 bp):
CCAATGTGCTGATTCAAGGCCAGAGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATTCA
AGGCCAGCAATATTGGACTTAAAGGTG
Found at i:230353 original size:34 final size:32
Alignment explanation
Indices: 230280--230527 Score: 272
Period size: 34 Copynumber: 7.6 Consensus size: 32
230270 TTTAGAAGGG
* *
230280 GGTGCCACGGGGTTGTGGACTTAAAAGGAAAA
1 GGTGCCACGGAGTTGTGGACTTAAAAGAAAAA
230312 GGATGCCACGGAGTTGTGGACTTTAACAAGAAAAA
1 GG-TGCCACGGAGTTGTGGAC-TTAA-AAGAAAAA
*
230347 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAA
1 GGTGCCACGGAGTTGTGGACTTA-AAAGAAAAA
* *
230380 GAGTACCACGGAGTTGTGGGCTTTAAAAAGAAAAA
1 G-GTGCCACGGAGTTGTGGAC-TT-AAAAGAAAAA
* * *
230415 TGTGCCACGGAGTTGTGAACTTAGAATGAAAAA
1 GGTGCCACGGAGTTGTGGACTTA-AAAGAAAAA
*
230448 GAGTGCCACGGAGTTGTGGGCTT-----AAAAA
1 G-GTGCCACGGAGTTGTGGACTTAAAAGAAAAA
230476 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
1 GGTGCCACGGAGTTGTGGACTTAAAA-GAAAAA
*
230509 GAGTGCCATGGAGTTGTGG
1 G-GTGCCACGGAGTTGTGG
230528 GCTTCTAGAA
Statistics
Matches: 184, Mismatches: 16, Indels: 30
0.80 0.07 0.13
Matches are distributed among these distances:
27 20 0.11
28 6 0.03
32 3 0.02
33 44 0.24
34 91 0.49
35 19 0.10
36 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.21
Consensus pattern (32 bp):
GGTGCCACGGAGTTGTGGACTTAAAAGAAAAA
Found at i:230411 original size:68 final size:68
Alignment explanation
Indices: 230280--230700 Score: 376
Period size: 80 Copynumber: 6.0 Consensus size: 68
230270 TTTAGAAGGG
* * * *
230280 GGTGCCACGGGGTTGTGGACTTAAAAGGAAAAGGA-TGCCACGGAGTTGTGGACTTTAACAAGAA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
230344 AAA
66 AAA
* *
230347 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTACCACGGAGTTGTGGGCTTTAAAAAGAA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
230412 AAA
66 AAA
* * * *
230415 TGTGCCACGGAGTTGTGAACTTAGAATGAAAAAGAGTGCCACGGAGTTGTGGGC-TT------AA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
230473 AAA
66 AAA
*
230476 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTCTAGAAAAA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT-T-----AA
230541 GATGCACAGGAAAAA
60 -A---A-A-GAAAAA
* * * *
230556 AGTGCCACGGAGTTGTGGACTTAAAGGGAAAAAGAGTGCCATGGAGTTATGGGCTTCTGGAAAAA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT-T-----AA
230621 GATGCACAGGAAAAA
60 -A---A-A-GAAAAA
* * * *
230636 AGTGCCATGGAGTTGTGGACTTAACAGG-AAAACAGTGCCACGGAGTTGTGGGC-TTAAAGAAGA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AAGA
230699 AA
65 AA
230701 TGCCACTGAG
Statistics
Matches: 308, Mismatches: 26, Indels: 40
0.82 0.07 0.11
Matches are distributed among these distances:
61 54 0.18
62 1 0.00
63 1 0.00
67 38 0.12
68 80 0.26
69 1 0.00
71 1 0.00
72 2 0.01
77 1 0.00
78 1 0.00
79 22 0.07
80 106 0.34
ACGTcount: A:0.35, C:0.13, G:0.32, T:0.20
Consensus pattern (68 bp):
GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
AAA
Found at i:230474 original size:27 final size:28
Alignment explanation
Indices: 230444--230502 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 28
230434 CTTAGAATGA
*
230444 AAAAGA-GTGCCACGGAGTTGTGGGCTT
1 AAAAGAGGTGCCACGGAGTTGTGGACTT
230471 AAAA-AGGTGCCACGGAGTTGTGGACTT
1 AAAAGAGGTGCCACGGAGTTGTGGACTT
230498 AAAAG
1 AAAAG
230503 GAAAAAGAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 1 0.03
27 28 0.97
ACGTcount: A:0.32, C:0.14, G:0.34, T:0.20
Consensus pattern (28 bp):
AAAAGAGGTGCCACGGAGTTGTGGACTT
Found at i:230673 original size:33 final size:33
Alignment explanation
Indices: 230626--230692 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
230616 AAAAAGATGC
*
230626 ACAGGAAAAAAGTGCCATGGAGTTGTGGACTTA
1 ACAGGAAAAAAGTGCCACGGAGTTGTGGACTTA
* *
230659 ACAGGAAAACAGTGCCACGGAGTTGTGGGCTTA
1 ACAGGAAAAAAGTGCCACGGAGTTGTGGACTTA
230692 A
1 A
230693 AGAAGAAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.15, G:0.31, T:0.19
Consensus pattern (33 bp):
ACAGGAAAAAAGTGCCACGGAGTTGTGGACTTA
Found at i:230744 original size:33 final size:33
Alignment explanation
Indices: 230700--230942 Score: 200
Period size: 33 Copynumber: 7.6 Consensus size: 33
230690 TAAAGAAGAA
230700 ATGCCACTGAGTCATGGACTTTGAAGAAAAAAG
1 ATGCCACTGAGTCATGGACTTTGAAGAAAAAAG
* * * * * *
230733 AAGCCATTGAGTCGTAGACTTTG--G-GAAGAG
1 ATGCCACTGAGTCATGGACTTTGAAGAAAAAAG
230763 ATTGCCACTGAGTCATGGACTTTGAAGAAAAAAG
1 A-TGCCACTGAGTCATGGACTTTGAAGAAAAAAG
** * * *
230797 ATGCCACTGAGTTGTGGACTTGGATGAAAACAG
1 ATGCCACTGAGTCATGGACTTTGAAGAAAAAAG
* * * * *
230830 ATGCCATTGAGTCGTGGACTTGGATG-AAAAGG
1 ATGCCACTGAGTCATGGACTTTGAAGAAAAAAG
* *
230862 ATGCCACTGAGTTATGGAC-TT--AGAAAAGAG
1 ATGCCACTGAGTCATGGACTTTGAAGAAAAAAG
** *
230892 ATGCCACTGAGTTGTGGAC-TT--AGAAAAGAG
1 ATGCCACTGAGTCATGGACTTTGAAGAAAAAAG
**
230922 ATGCCACTGAGTTGTGGACTT
1 ATGCCACTGAGTCATGGACTT
230943 CGAGAAGAGA
Statistics
Matches: 175, Mismatches: 29, Indels: 14
0.80 0.13 0.06
Matches are distributed among these distances:
29 1 0.01
30 57 0.33
31 21 0.12
32 20 0.11
33 71 0.41
34 5 0.03
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (33 bp):
ATGCCACTGAGTCATGGACTTTGAAGAAAAAAG
Found at i:230897 original size:30 final size:30
Alignment explanation
Indices: 230645--230953 Score: 228
Period size: 30 Copynumber: 9.8 Consensus size: 30
230635 AAGTGCCATG
* *
230645 GAGTTGTGGACTTAACAGGAAAACAG-TGCCACG
1 GAGTTGTGGACTT---A-GAAAAGAGATGCCACT
* *
230678 GAGTTGTGGGCTTA-AAGAAGAAATGCCACT
1 GAGTTGTGGACTTAGAA-AAGAGATGCCACT
** * * *
230708 GAGTCATGGACTTTGAAGAAAAAAGAAGCCATT
1 GAGTTGTGGAC-TT--AGAAAAGAGATGCCACT
* * * **
230741 GAGTCGTAGACTTTGGGAAGAGATTGCCACT
1 GAGTTGTGGACTTAGAAAAGAGA-TGCCACT
** *
230772 GAGTCATGGACTTTGAAGAAAAAAGATGCCACT
1 GAGTTGTGGAC-TT--AGAAAAGAGATGCCACT
* *
230805 GAGTTGTGGACTTGGATGAAAACAGATGCCATT
1 GAGTTGTGGACTT--A-GAAAAGAGATGCCACT
*
230838 GAGTCGTGGACTTGGATGAAAAG-GATGCCACT
1 GAGTTGTGGACTT--A-GAAAAGAGATGCCACT
*
230870 GAGTTATGGACTTAGAAAAGAGATGCCACT
1 GAGTTGTGGACTTAGAAAAGAGATGCCACT
230900 GAGTTGTGGACTTAGAAAAGAGATGCCACT
1 GAGTTGTGGACTTAGAAAAGAGATGCCACT
* *
230930 GAGTTGTGGACTTCGAGAAGAGAT
1 GAGTTGTGGACTTAGAAAAGAGAT
230954 TTGAAGAATT
Statistics
Matches: 226, Mismatches: 38, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
28 2 0.01
29 9 0.04
30 82 0.36
31 16 0.07
32 27 0.12
33 82 0.36
34 8 0.04
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (30 bp):
GAGTTGTGGACTTAGAAAAGAGATGCCACT
Found at i:231491 original size:60 final size:60
Alignment explanation
Indices: 231308--231518 Score: 195
Period size: 60 Copynumber: 3.6 Consensus size: 60
231298 GAGGTGTCTA
* * * * * * *
231308 CACCCTTTTAAGCCCACAAATCTGCGGCACCCATTTTCTTTTTAAGTCCATAACTCCGTGG
1 CACCCTTTTAAGTCCACAACTCTGCGGCACCC-TTTTCCTTTTAAGCCCACAACTCTGTAG
* *** *
231369 CACCCTTTTAAGTCCATAACTCCATGGCA------TCCTTTTAAGCCCACAACTCTGTGG
1 CACCCTTTTAAGTCCACAACTCTGCGGCACCCTTTTCCTTTTAAGCCCACAACTCTGTAG
* * *
231423 CACCCTTTTATG-CTCACAACTCTGCGGCACCTTTTTCCTTTTAAGTCCACAACT-TCGTAG
1 CACCCTTTTAAGTC-CACAACTCTGCGGCACCCTTTTCCTTTTAAGCCCACAACTCT-GTAG
*
231483 CACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTT
1 CACCCTTTTAAGTCCACAACTCTGCGGCACCCTTTT
231519 AAGTCCACAA
Statistics
Matches: 121, Mismatches: 20, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
53 1 0.01
54 43 0.36
59 1 0.01
60 52 0.43
61 24 0.20
ACGTcount: A:0.22, C:0.34, G:0.12, T:0.32
Consensus pattern (60 bp):
CACCCTTTTAAGTCCACAACTCTGCGGCACCCTTTTCCTTTTAAGCCCACAACTCTGTAG
Found at i:231500 original size:87 final size:88
Alignment explanation
Indices: 231372--231574 Score: 257
Period size: 87 Copynumber: 2.3 Consensus size: 88
231362 TCCGTGGCAC
* * * * * *
231372 CCTTTTAAGTCCATAACTCCATGGCATCCTTTTAAGCCCACAACTCTGTGGCACCCTTTTATG-C
1 CCTTTTAAGTCCACAACTTCGTAGCACCCTTTTAAGCCCACAACTCTGTGGCACCCTTTTAAGTC
* *
231436 TCACAACTCTGCGGCA-CCTTTTT
66 -CACAACTCCGCGGCATACTTTTT
*
231459 CCTTTTAAGTCCACAACTTCGTAGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTC
1 CCTTTTAAGTCCACAACTTCGTAGCACCCTTTTAAGCCCACAACTCTGTGGCACCCTTTTAAGTC
* *
231524 CACAACTCCGTGGCATATTTTTT
66 CACAACTCCGCGGCATACTTTTT
* * *
231547 CCTTTTAAGCCCACAACGTCGTCGCACC
1 CCTTTTAAGTCCACAACTTCGTAGCACC
231575 TTTCTCTTCT
Statistics
Matches: 100, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
87 69 0.69
88 31 0.31
ACGTcount: A:0.22, C:0.33, G:0.13, T:0.32
Consensus pattern (88 bp):
CCTTTTAAGTCCACAACTTCGTAGCACCCTTTTAAGCCCACAACTCTGTGGCACCCTTTTAAGTC
CACAACTCCGCGGCATACTTTTT
Found at i:231511 original size:114 final size:115
Alignment explanation
Indices: 231308--231538 Score: 329
Period size: 114 Copynumber: 2.0 Consensus size: 115
231298 GAGGTGTCTA
* * *
231308 CACCCTTTTAAGCCCACAAATCTGCGGCACCCATTTTCTTTTTAAGTCCATAACTCCGTGGCACC
1 CACCCTTTTAAGCCCACAAATCTGCGGCACCCATTTTCCTTTTAAGTCCACAACTCCGTAGCACC
* * *
231373 CTTTTAAGTCCATAACTCCATGGCATCCTTTTAAGCCCACAACTCTGTGG
66 CTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGCCCACAACTCCGTGG
* * * * *
231423 CACCCTTTTATGCTCACAACTCTGCGGCA-CCTTTTTCCTTTTAAGTCCACAACTTCGTAGCACC
1 CACCCTTTTAAGCCCACAAATCTGCGGCACCCATTTTCCTTTTAAGTCCACAACTCCGTAGCACC
** *
231487 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGG
66 CTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGCCCACAACTCCGTGG
231537 CA
1 CA
231539 TATTTTTTCC
Statistics
Matches: 102, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
114 76 0.75
115 26 0.25
ACGTcount: A:0.23, C:0.34, G:0.13, T:0.31
Consensus pattern (115 bp):
CACCCTTTTAAGCCCACAAATCTGCGGCACCCATTTTCCTTTTAAGTCCACAACTCCGTAGCACC
CTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGCCCACAACTCCGTGG
Found at i:231545 original size:27 final size:27
Alignment explanation
Indices: 231347--231538 Score: 206
Period size: 27 Copynumber: 6.9 Consensus size: 27
231337 CCCATTTTCT
*
231347 TTTTAAGTCCATAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* * *
231374 TTTTAAGTCCATAACTCCATGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* *
231401 TTTTAAGCCCACAACTCTGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* * *
231428 TTTTATG-CTCACAACTCTGCGGCACCTTTTTCC
1 TTTTAAGTC-CACAACTCCGTGGCA-C-----CC
* *
231461 TTTTAAGTCCACAACTTCGTAGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
231488 TTTTAAGTCCACAACTCTGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
231515 TTTTAAGTCCACAACTCCGTGGCA
1 TTTTAAGTCCACAACTCCGTGGCA
231539 TATTTTTTCC
Statistics
Matches: 139, Mismatches: 18, Indels: 16
0.80 0.10 0.09
Matches are distributed among these distances:
26 1 0.01
27 116 0.83
28 1 0.01
32 1 0.01
33 19 0.14
34 1 0.01
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.31
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCGTGGCACCC
Found at i:231629 original size:34 final size:33
Alignment explanation
Indices: 231515--231647 Score: 99
Period size: 34 Copynumber: 3.9 Consensus size: 33
231505 TGTGGCACCC
* ** *
231515 TTTTAAGTCCACAACTCCGTGGCATATTTTTTCC
1 TTTTAAGCCCACAACTCCGT-GCACCTTTTTTCT
*
231549 TTTTAAGCCCACAACGT-CGTCGCACC-TTTCTCT
1 TTTTAAGCCCACAAC-TCCGT-GCACCTTTTTTCT
** *
231582 TCTCAAAGCCCACAACTCCGTGAAACCTTTTTTCT
1 T-TTTAAGCCCACAACTCCGTG-CACCTTTTTTCT
* * *
231617 TTTTAAGTCCACAACTCTGTGGCACCCTTTT
1 TTTTAAGCCCACAACTCCGT-GCACCTTTTT
231648 AAGTCCACCA
Statistics
Matches: 77, Mismatches: 16, Indels: 12
0.73 0.15 0.11
Matches are distributed among these distances:
33 8 0.10
34 60 0.78
35 9 0.12
ACGTcount: A:0.21, C:0.32, G:0.11, T:0.36
Consensus pattern (33 bp):
TTTTAAGCCCACAACTCCGTGCACCTTTTTTCT
Found at i:231669 original size:27 final size:26
Alignment explanation
Indices: 231617--231673 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
231607 CCTTTTTTCT
** *
231617 TTTTAAGTCCACAACTCTGTGGCACCC
1 TTTTAAGTCCACAACTCCATGACA-CC
*
231644 TTTTAAGTCCACCACTCCATGACACC
1 TTTTAAGTCCACAACTCCATGACACC
231670 TTTT
1 TTTT
231674 CCCTCTAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.23, C:0.33, G:0.11, T:0.33
Consensus pattern (26 bp):
TTTTAAGTCCACAACTCCATGACACC
Found at i:231715 original size:31 final size:31
Alignment explanation
Indices: 231677--231765 Score: 124
Period size: 32 Copynumber: 2.8 Consensus size: 31
231667 ACCTTTTCCC
*
231677 TCTAAAGCCCACACAAGTTGGTGGCACCCCT
1 TCTAAAGCCCACACAAGTTGGTGGCACCACT
* * *
231708 TCTAAAGCCCACACATGTTAGTGGCAACCATT
1 TCTAAAGCCCACACAAGTTGGTGGC-ACCACT
*
231740 TCAAAAGCCCACACAAGTTGGTGGCA
1 TCTAAAGCCCACACAAGTTGGTGGCA
231766 TCTCTTTCTA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 24 0.48
32 26 0.52
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.20
Consensus pattern (31 bp):
TCTAAAGCCCACACAAGTTGGTGGCACCACT
Found at i:232152 original size:61 final size:56
Alignment explanation
Indices: 232118--232223 Score: 130
Period size: 52 Copynumber: 2.0 Consensus size: 56
232108 CTTCAAATCC
* * * * *
232118 AATAACGCTGGCCTTGAATCAACACATTGGCACCTTTGTCA-TCTT-TAAGC--CA
1 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTTCTAATCTTCA
*
232170 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTTCTCATCTT
1 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTTCTAATCTT
232224 TAAGCCCAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
52 37 0.84
53 4 0.09
54 3 0.07
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.34
Consensus pattern (56 bp):
AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTTCTAATCTTCA
Found at i:232215 original size:113 final size:111
Alignment explanation
Indices: 231985--232223 Score: 284
Period size: 111 Copynumber: 2.1 Consensus size: 111
231975 AGCATATTGG
* ** ** * * * *
231985 CATTCTTCTCATCTTCAAGTGTAATGTCACTGGTCATGAATCAACACATTGGCAATCTTCGCATC
1 CATTCTTCTCATCTTCAAATCCAATAACGCTGGCCTTGAATCAACACATTGGCAACCTTCGCATC
*
232050 TTTACCCAACATTGTTGGCCTTGAATCAGCATATCGACACCTTTAT
66 TTTACCCAACATTGCTGGCCTTGAATCAGCATATCGACACCTTTAT
* * *
232096 TATTCTTCTTATCTTCAAATCCAATAACGCTGGCCTTGAATCAACACATTGGC-ACCTTTGTCAT
1 CATTCTTCTCATCTTCAAATCCAATAACGCTGGCCTTGAATCAACACATTGGCAACCTTCG-CAT
* * *
232160 CTTTAAGCCAA-ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
65 CTTT-ACCCAACAT-T-GCTGGCCTTGAATCAGCATATCGACACCTTTAT
232209 CATTCTTCTCATCTT
1 CATTCTTCTCATCTT
232224 TAAGCCCAAT
Statistics
Matches: 106, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
110 5 0.05
111 52 0.49
112 6 0.06
113 43 0.41
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.36
Consensus pattern (111 bp):
CATTCTTCTCATCTTCAAATCCAATAACGCTGGCCTTGAATCAACACATTGGCAACCTTCGCATC
TTTACCCAACATTGCTGGCCTTGAATCAGCATATCGACACCTTTAT
Found at i:232233 original size:113 final size:111
Alignment explanation
Indices: 232021--232234 Score: 279
Period size: 113 Copynumber: 1.9 Consensus size: 111
232011 TCACTGGTCA
* *
232021 TGAATCAACACATTGGCAATCTTCGCATCTTTACCCAACATTGTTGGCCTTGAATCAGCATATCG
1 TGAATCAACACATTGGCAACCTTCGCATCTTTACCCAACATTGCTGGCCTTGAATCAGCATATCG
* * *
232086 ACACCTTTATTATTCTTCTTATCTTCAAATCCAATAACGCTGGCCT
66 ACACCTTTATCATTCTTCTCATCTTCAAACCCAATAACGCTGGCCT
* *
232132 TGAATCAACACATTGGC-ACCTTTGTCATCTTTAAGCCAA-ATATCGCTGGCCTTGAATCAGCAT
1 TGAATCAACACATTGGCAACCTTCG-CATCTTT-ACCCAACAT-T-GCTGGCCTTGAATCAGCAT
* * * *
232195 ATTGGCACCTTTATCATTCTTCTCATCTTTAAGCCCAATA
62 ATCGACACCTTTATCATTCTTCTCATCTTCAAACCCAATA
232235 TCGTTAGGCG
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
110 5 0.06
111 26 0.30
112 6 0.07
113 51 0.58
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (111 bp):
TGAATCAACACATTGGCAACCTTCGCATCTTTACCCAACATTGCTGGCCTTGAATCAGCATATCG
ACACCTTTATCATTCTTCTCATCTTCAAACCCAATAACGCTGGCCT
Found at i:232255 original size:61 final size:61
Alignment explanation
Indices: 232156--232282 Score: 177
Period size: 61 Copynumber: 2.1 Consensus size: 61
232146 GGCACCTTTG
*
232156 TCATCTTTAAGCCAAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTTC
1 TCATCTTTAAGCCAAATATCGCTGGCCGTGAATCAGCATATTGGCACCTTTATCATTCTTC
* * * *
232217 TCATCTTTAAGCCCAATATCGTTAGG-CGTGAAAT-AGCATATTGGCACCTTTATCATTTTTT
1 TCATCTTTAAGCCAAATATCGCT-GGCCGTG-AATCAGCATATTGGCACCTTTATCATTCTTC
232278 TCATC
1 TCATC
232283 CTTATCATCT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
61 54 0.92
62 5 0.08
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (61 bp):
TCATCTTTAAGCCAAATATCGCTGGCCGTGAATCAGCATATTGGCACCTTTATCATTCTTC
Found at i:232263 original size:113 final size:113
Alignment explanation
Indices: 232065--232272 Score: 267
Period size: 113 Copynumber: 1.8 Consensus size: 113
232055 CCAACATTGT
* * *
232065 TGGCCTTGAATCAGCATATCGACACCTTTATTATTCTTCTTATCTTCAAATCCAATAACGCTGGC
1 TGGCCTTGAATCAGCATATCGACACCTTTATCATTCTTCTCATCTTCAAACCCAATAACGCTGGC
* *
232130 CTTGAATCAACACATTGGCACCTTTGTCATCTTTAAGCCAAATATCGC
66 CGTGAATCAACACATTGGCACCTTTATCATCTTTAAGCCAAATATCGC
* * * * * *
232178 TGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTTCTCATCTTTAAGCCCAATATCGTTAGG
1 TGGCCTTGAATCAGCATATCGACACCTTTATCATTCTTCTCATCTTCAAACCCAATAACGCT-GG
* *
232243 -CGTGAAAT-AGCATATTGGCACCTTTATCAT
65 CCGTG-AATCAACACATTGGCACCTTTATCAT
232273 TTTTTTCATC
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
113 75 0.94
114 5 0.06
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (113 bp):
TGGCCTTGAATCAGCATATCGACACCTTTATCATTCTTCTCATCTTCAAACCCAATAACGCTGGC
CGTGAATCAACACATTGGCACCTTTATCATCTTTAAGCCAAATATCGC
Found at i:234958 original size:20 final size:20
Alignment explanation
Indices: 234933--234970 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
234923 AAACCAATTT
234933 GAAATAAATTCAAAATGCCC
1 GAAATAAATTCAAAATGCCC
234953 GAAATAAATTCAAAATGC
1 GAAATAAATTCAAAATGC
234971 GGGATAACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.16, G:0.11, T:0.21
Consensus pattern (20 bp):
GAAATAAATTCAAAATGCCC
Found at i:235353 original size:97 final size:97
Alignment explanation
Indices: 235194--235429 Score: 346
Period size: 97 Copynumber: 2.4 Consensus size: 97
235184 ATTTTATTTA
* * * *
235194 TCGGGGATACTCCAACCCTATTCCTTCGAGGGGATACTCTAACCCTGCTTTTGAAACATATCAAT
1 TCGGGGACACTCCAACCCTATTCCTTCGAGAGGATACTCCAACCCTGCTTTTAAAACATATCAAT
**
235259 ATTCAAATCTTATTTTGATTAAATTAGGGTCG
66 ATTCAAATCTTATTTTGATTAAATTAGCATCG
* *
235291 TCGGGGACACTCCAACCCTATTCCTTCGAGTGGATACTCCAACCCTGCTTTTAAAACTTATCAAT
1 TCGGGGACACTCCAACCCTATTCCTTCGAGAGGATACTCCAACCCTGCTTTTAAAACATATCAAT
*
235356 ATTCAAATCTTATTTTGCTTAAATTAGCATCG
66 ATTCAAATCTTATTTTGATTAAATTAGCATCG
* * * *
235388 CCGGGGACACTCCAACCCCAATTCCTCCGAAAGGATACTCCA
1 TCGGGGACACTCCAA-CCCTATTCCTTCGAGAGGATACTCCA
235430 GCCCCATTTT
Statistics
Matches: 125, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
97 103 0.82
98 22 0.18
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (97 bp):
TCGGGGACACTCCAACCCTATTCCTTCGAGAGGATACTCCAACCCTGCTTTTAAAACATATCAAT
ATTCAAATCTTATTTTGATTAAATTAGCATCG
Found at i:238117 original size:16 final size:16
Alignment explanation
Indices: 238096--238127 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
238086 AGGTACCGAT
238096 TTGTGCGTGATGAATC
1 TTGTGCGTGATGAATC
238112 TTGTGCGTGATGAATC
1 TTGTGCGTGATGAATC
238128 ATGAGGAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.31, T:0.38
Consensus pattern (16 bp):
TTGTGCGTGATGAATC
Found at i:241112 original size:21 final size:21
Alignment explanation
Indices: 241079--241119 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
241069 CTAAGTAAAA
241079 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
241100 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
241120 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:241184 original size:20 final size:19
Alignment explanation
Indices: 241159--241229 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
241149 ACCCTGAAAA
241159 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
241179 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
**
241198 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
241219 GTATCGATACA
1 GTATCGATACA
241230 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:241282 original size:53 final size:53
Alignment explanation
Indices: 241199--241335 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
241189 AGATTGCATA
*
241199 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
*
241253 GTATCGATACACACAATATGTATCGATACAGGTCACTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
* *
241306 GTATCGATATACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
241336 AGTGAATTAG
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 65 0.82
54 14 0.18
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
Found at i:244625 original size:21 final size:21
Alignment explanation
Indices: 244592--244632 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
244582 CTAAGTAAAA
244592 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
244613 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
244633 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:244697 original size:20 final size:19
Alignment explanation
Indices: 244672--244742 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
244662 ACCCTGAAAA
244672 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
244692 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
**
244711 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
244732 GTATCGATACA
1 GTATCGATACA
244743 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:244795 original size:53 final size:53
Alignment explanation
Indices: 244712--244848 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
244702 AGATTGCATA
*
244712 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
*
244766 GTATCGATACACACAATATGTATCGATACAGGTCACTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
* *
244819 GTATCGATATACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
244849 TTGGTAGTAG
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 65 0.82
54 14 0.18
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
Found at i:244895 original size:14 final size:14
Alignment explanation
Indices: 244872--244901 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
244862 AATCTCATTT
*
244872 TCACTGTTCATGTA
1 TCACTATTCATGTA
244886 TCACTATTCATGTA
1 TCACTATTCATGTA
244900 TC
1 TC
244902 GTAAAAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.43
Consensus pattern (14 bp):
TCACTATTCATGTA
Found at i:244952 original size:13 final size:13
Alignment explanation
Indices: 244930--244968 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
244920 TCACTATTCA
*
244930 TGTATTGATACAT
1 TGTATCGATACAT
*
244943 TGTATCGATACAG
1 TGTATCGATACAT
244956 TGTATCGATACAT
1 TGTATCGATACAT
244969 CATAAATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:246329 original size:53 final size:52
Alignment explanation
Indices: 246244--246383 Score: 169
Period size: 52 Copynumber: 2.7 Consensus size: 52
246234 ATTTGTCTAC
* *
246244 ATGTATCGATAC-ATTGAAGAATGTATCGATACATTTGGCTCAAGAA-CTCAGA
1 ATGTATCGATACAATTGAAAAATGTATCAATACATTTGGCTCAA-AACCT-AGA
* *
246296 ATGTATCGATACAATTGAAAAATGTATTAATACATTTGGGTCAAAACCTAGA
1 ATGTATCGATACAATTGAAAAATGTATCAATACATTTGGCTCAAAACCTAGA
* * * *
246348 ATGCATCGATACAA-TGAAATATGCATCGATACATTT
1 ATGTATCGATACAATTGAAAAATGTATCAATACATTT
246384 TCATTCTAGA
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
51 18 0.23
52 30 0.39
53 29 0.38
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (52 bp):
ATGTATCGATACAATTGAAAAATGTATCAATACATTTGGCTCAAAACCTAGA
Found at i:248285 original size:156 final size:155
Alignment explanation
Indices: 248000--248676 Score: 622
Period size: 156 Copynumber: 4.4 Consensus size: 155
247990 CTAAGTTTAA
* * *
248000 GAAAAATTATGAAAATGCCCCTAGAAGATACCTTCGACGTAGAAGTA-CCCGATACCCCTAAAGG
1 GAAAAATTATGAAAATGCCCTTAGAGGATACCTTCGACGTAAAAGTATCCCGATACCCCTAAAGG
* * * *
248064 ACTT-AAAAGAGACTATAAGAGGGATGAACCTATCCTGAATACCCACCTTCGACATATAAGCGAA
66 ACTTAAAAAGA-ACTATAAAAAGGATGAACCTATCCTAAATACCCACCTTCGACATAAAAG-GAA
* * *
248128 CCTGATTATAACTTAGAACTCAATTTT
129 CCTGATTATAACTTAGGACTCAGTTAT
** * *
248155 GAAAAATTATGAAAACACCCTTAGAGGATACTTTCGACATAAAAGTATCCC-AGTACCCCTAAAG
1 GAAAAATTATGAAAATGCCCTTAGAGGATACCTTCGACGTAAAAGTATCCCGA-TACCCCTAAAG
*
248219 GACTTAAAAAGAACTATAAAAAGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGTGAA
65 GACTTAAAAAGAACTATAAAAAGGATGAACCTATCCTAAATACCCACCTTCGACATAAAAG-GAA
* * *
248284 CCT-AGTTTTAACCTAGGACTCAGTTCT
129 CCTGA-TTATAACTTAGGACTCAGTTAT
* * * * * *
248311 GAAAAATTATGAAAATGCTCC-TCGA-GATACCTTCGACGTGAAAGTATCTCGGTACTCTTAAAG
1 GAAAAATTATGAAAATGC-CCTTAGAGGATACCTTCGACGTAAAAGTATCCCGATACCCCTAAAG
* * * * * * *
248374 GACTTAAAAAGGACTATAAAAAGGATAAACCAATCCTAAATATCTACCTTCGACATAAAAGCAAA
65 GACTTAAAAAGAACTATAAAAAGGATGAACCTATCCTAAATACCCACCTTCGACATAAAAGGAAC
* * * **
248439 CTCGATGATGA-TGTAGGAGTTGGTTAT
130 CT-GATTATAACT-TAGGACTCAGTTAT
* * * * **
248466 -AGAAAATTA-CAAAAGTTCCCTTAAAGGATACCTTTGACGTAAAAGTATCTTGATACCCCTAAA
1 GA-AAAATTATGAAAA-TGCCCTTAGAGGATACCTTCGACGTAAAAGTATCCCGATACCCCTAAA
* * * * *
248529 GGACTTAAAAAGGACTATAAAAGGGATGAACCTATCCTAAGTACCTACCTTCGACATAAAAGCAA
64 GGACTTAAAAAGAACTATAAAAAGGATGAACCTATCCTAAATACCCACCTTCGACATAAAAG-GA
* ** * * ** *
248594 ACCCGACGATGA-TGTAGGAGTTGGTTCT
128 ACCTGATTATAACT-TAGGACTCAGTTAT
* ** *
248622 AAAAAATTACAAAAATGCCCTTAG-GAGATACCTTCGACGTAAAAGTA-CTCGATAC
1 GAAAAATTATGAAAATGCCCTTAGAG-GATACCTTCGACGTAAAAGTATCCCGATAC
248677 TCTTAGGGGA
Statistics
Matches: 436, Mismatches: 69, Indels: 34
0.81 0.13 0.06
Matches are distributed among these distances:
154 11 0.03
155 159 0.36
156 250 0.57
157 16 0.04
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (155 bp):
GAAAAATTATGAAAATGCCCTTAGAGGATACCTTCGACGTAAAAGTATCCCGATACCCCTAAAGG
ACTTAAAAAGAACTATAAAAAGGATGAACCTATCCTAAATACCCACCTTCGACATAAAAGGAACC
TGATTATAACTTAGGACTCAGTTAT
Found at i:248386 original size:11 final size:12
Alignment explanation
Indices: 248370--248398 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
248360 CGGTACTCTT
248370 AAAGGACT-TAA
1 AAAGGACTATAA
248381 AAAGGACTATAA
1 AAAGGACTATAA
248393 AAAGGA
1 AAAGGA
248399 TAAACCAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.59, C:0.07, G:0.21, T:0.14
Consensus pattern (12 bp):
AAAGGACTATAA
Found at i:249422 original size:341 final size:340
Alignment explanation
Indices: 248818--249573 Score: 1152
Period size: 341 Copynumber: 2.2 Consensus size: 340
248808 GAAAACCAAT
* * * *
248818 GGATACGAAAAGTTTTGAAAATATTCATACCCCTACGGAAAACCATAAGAATATTAGAAATCTTA
1 GGATACGAAAAGTTTTGAAAATTTTTATACCTCTATGGAAAACCATAAGAATATTAGAAATCTTA
* *
248883 AATAAA--ATGATTAACTTTATTTTAAAATGGTTGAAATGATTTCATTTCAATTATTATTTATTT
66 AA-AAACTAAGATTAACTTTATTTGAAAATGGTTGAAATGATTTCATTTCAATTATTATTTATTT
* * * *
248946 AGTTCTTAAAAAAATCATTTCGTACTCAATGAAAAATCAAGGGATACGAAATTTTTGAAAATTTC
130 AATTCTTAAAAAAATCATTTCATACCCAATGAAAAATCAAGGGATACGAAAGTTTTGAAAATTTC
*
249011 TATACCCTTACGGAAACCATAGGGAATATTAGAAATATTAAAAAACTAAGATTAACCTTATTTTA
195 TATACCCTTACGAAAACCATAGGGAATATTAGAAATATTAAAAAACTAAGATTAACCTTATTTTA
* *
249076 AAATGGTTGAAATGATTTCATTTCAATTATTATTTATTTCATTCTTAAAAAAAATCATTTCGTA-
260 AAATGGTTGAAATGATTTCATTTCAATTATTATTTATTTAATTCTTAAAAAAAATCAATTCGTAT
249140 GTCGACA-AAAAATCAGG
325 GT-GA-AGAAAAATCAGG
* * * *
249157 GGATACGAAAAGTTTTGAAAATTTTTATACCTCTATGGAAAACTATAGGAATTTTAAAAATCTTA
1 GGATACGAAAAGTTTTGAAAATTTTTATACCTCTATGGAAAACCATAAGAATATTAGAAATCTTA
*
249222 AAAAACTAAGATTAACTTTATTTGAAAATGGTTGAAATGATTTCATTTCAATTATTTTTTATTTA
66 AAAAACTAAGATTAACTTTATTTGAAAATGGTTGAAATGATTTCATTTCAATTATTATTTATTTA
* *
249287 ATTCTTAAAAAAAATCATTTTATACCCGATGAAAAATCAAGGGATACGAAAAGTTTTGAAAATTT
131 ATTCTT-AAAAAAATCATTTCATACCCAATGAAAAATCAAGGGATACG-AAAGTTTTGAAAATTT
* *
249352 CTATA-CCTCTACGAAAAACCATA-GGAATATTAGAAATCTT-AAAAACTAAGATTAACTTTATT
194 CTATACCCT-TACG-AAAACCATAGGGAATATTAGAAATATTAAAAAACTAAGATTAACCTTATT
*
249414 TTAAAATGGTTGAAATGATTTCATTTCAATTGTTATTTATTTAATTCTTAAAAAAAATCAATTCG
257 TTAAAATGGTTGAAATGATTTCATTTCAATTATTATTTATTTAATTCTTAAAAAAAATCAATTCG
249479 TATGTGAAGAAAAATCAGG
322 TATGTGAAGAAAAATCAGG
* *
249498 GTATA-GAAAAAGTTTTG-AAATTTCTATACCTCTATGGAAAACCATAAGAATATTAGAAATCTT
1 GGATACG-AAAAGTTTTGAAAATTTTTATACCTCTATGGAAAACCATAAGAATATTAGAAATCTT
249561 AAAAAACTAAGAT
65 AAAAAACTAAGAT
249574 ATTAATTTTT
Statistics
Matches: 379, Mismatches: 29, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
338 3 0.01
339 59 0.16
340 116 0.31
341 151 0.40
342 42 0.11
343 8 0.02
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (340 bp):
GGATACGAAAAGTTTTGAAAATTTTTATACCTCTATGGAAAACCATAAGAATATTAGAAATCTTA
AAAAACTAAGATTAACTTTATTTGAAAATGGTTGAAATGATTTCATTTCAATTATTATTTATTTA
ATTCTTAAAAAAATCATTTCATACCCAATGAAAAATCAAGGGATACGAAAGTTTTGAAAATTTCT
ATACCCTTACGAAAACCATAGGGAATATTAGAAATATTAAAAAACTAAGATTAACCTTATTTTAA
AATGGTTGAAATGATTTCATTTCAATTATTATTTATTTAATTCTTAAAAAAAATCAATTCGTATG
TGAAGAAAAATCAGG
Found at i:249431 original size:170 final size:171
Alignment explanation
Indices: 248792--249573 Score: 1095
Period size: 171 Copynumber: 4.6 Consensus size: 171
248782 TTTGAAGTTA
* * * * *
248792 CATTTCGTAC-CAGACGGAAAACCAATGGATACGAAAAGTTTTGAAAATATTC-ATACCCCTACG
1 CATTTCGTACTC-GATGAAAAATCAAGGGATACGAAAAGTTTTGAAAAT-TTCTATACCTCTACG
* *
248855 GAAAACCATAAGAATATTAGAAATCTTAAATAAA--ATGATTAACTTTATTTTAAAATGGTTGAA
64 GAAAACCATAGGAATATTAGAAATCTTAAA-AAACTAAGATTAACTTTATTTTAAAATGGTTGAA
*
248918 ATGATTTCATTTCAATTATTATTTATTTAGTTCTT-AAAAAAAT
128 ATGATTTCATTTCAATTATTATTTATTTAATTCTTAAAAAAAAT
* *
248961 CATTTCGTACTCAATGAAAAATCAAGGGATACG-AAATTTTTGAAAATTTCTATACC-CTTACGG
1 CATTTCGTACTCGATGAAAAATCAAGGGATACGAAAAGTTTTGAAAATTTCTATACCTC-TACGG
* *
249024 -AAACCATAGGGAATATTAGAAATATTAAAAAACTAAGATTAACCTTATTTTAAAATGGTTGAAA
65 AAAACCATA-GGAATATTAGAAATCTTAAAAAACTAAGATTAACTTTATTTTAAAATGGTTGAAA
*
249088 TGATTTCATTTCAATTATTATTTATTTCATTCTTAAAAAAAAT
129 TGATTTCATTTCAATTATTATTTATTTAATTCTTAAAAAAAAT
* ** * * *
249131 CATTTCGTAGTCGACAAAAAATCAGGGGATACGAAAAGTTTTGAAAATTTTTATACCTCTATGGA
1 CATTTCGTACTCGATGAAAAATCAAGGGATACGAAAAGTTTTGAAAATTTCTATACCTCTACGGA
* * * *
249196 AAACTATAGGAATTTTAAAAATCTTAAAAAACTAAGATTAACTTTATTTGAAAATGGTTGAAATG
66 AAACCATAGGAATATTAGAAATCTTAAAAAACTAAGATTAACTTTATTTTAAAATGGTTGAAATG
*
249261 ATTTCATTTCAATTATTTTTTATTTAATTCTTAAAAAAAAT
131 ATTTCATTTCAATTATTATTTATTTAATTCTTAAAAAAAAT
** * *
249302 CATTTTATACCCGATGAAAAATCAAGGGATACGAAAAGTTTTGAAAATTTCTATACCTCTACGAA
1 CATTTCGTACTCGATGAAAAATCAAGGGATACGAAAAGTTTTGAAAATTTCTATACCTCTACGGA
249367 AAACCATAGGAATATTAGAAATCTT-AAAAACTAAGATTAACTTTATTTTAAAATGGTTGAAATG
66 AAACCATAGGAATATTAGAAATCTTAAAAAACTAAGATTAACTTTATTTTAAAATGGTTGAAATG
*
249431 ATTTCATTTCAATTGTTATTTATTTAATTCTTAAAAAAAAT
131 ATTTCATTTCAATTATTATTTATTTAATTCTTAAAAAAAAT
* * * *
249472 CAATTCGTA-TGTGAAGAAAAATC-AGGGTATA-GAAAAAGTTTTG-AAATTTCTATACCTCTAT
1 CATTTCGTACT-CGATGAAAAATCAAGGG-ATACG-AAAAGTTTTGAAAATTTCTATACCTCTAC
*
249533 GGAAAACCATAAGAATATTAGAAATCTTAAAAAACTAAGAT
63 GGAAAACCATAGGAATATTAGAAATCTTAAAAAACTAAGAT
249574 ATTAATTTTT
Statistics
Matches: 546, Mismatches: 53, Indels: 27
0.87 0.08 0.04
Matches are distributed among these distances:
167 15 0.03
168 41 0.08
169 134 0.25
170 155 0.28
171 193 0.35
172 8 0.01
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (171 bp):
CATTTCGTACTCGATGAAAAATCAAGGGATACGAAAAGTTTTGAAAATTTCTATACCTCTACGGA
AAACCATAGGAATATTAGAAATCTTAAAAAACTAAGATTAACTTTATTTTAAAATGGTTGAAATG
ATTTCATTTCAATTATTATTTATTTAATTCTTAAAAAAAAT
Found at i:250980 original size:55 final size:55
Alignment explanation
Indices: 250921--251030 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
250911 GTTGGTTACT
250921 TTTACTTGTTGCTGGTGTTGTTTCTGCCATTGCTGGTATTTGCTGTGTCGTGCTG
1 TTTACTTGTTGCTGGTGTTGTTTCTGCCATTGCTGGTATTTGCTGTGTCGTGCTG
250976 TTTACTTGTTGCTGGTGTTGTTTCTGCCATTGCTGGTATTTGCTGTGTCGTGCTG
1 TTTACTTGTTGCTGGTGTTGTTTCTGCCATTGCTGGTATTTGCTGTGTCGTGCTG
251031 CTGTTTACTG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.05, C:0.16, G:0.29, T:0.49
Consensus pattern (55 bp):
TTTACTTGTTGCTGGTGTTGTTTCTGCCATTGCTGGTATTTGCTGTGTCGTGCTG
Found at i:251081 original size:14 final size:14
Alignment explanation
Indices: 251057--251097 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
251047 ATTGCTGGTG
251057 GTTGT-TCGTTGCT
1 GTTGTGTCGTTGCT
251070 GTTGTGTCGTTGCT
1 GTTGTGTCGTTGCT
* *
251084 ATTGTGTTGTTGCT
1 GTTGTGTCGTTGCT
251098 CCATCAGCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 5 0.20
14 20 0.80
ACGTcount: A:0.02, C:0.12, G:0.32, T:0.54
Consensus pattern (14 bp):
GTTGTGTCGTTGCT
Found at i:251202 original size:20 final size:20
Alignment explanation
Indices: 251150--251203 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
251140 GTTCATGCTT
251150 GCTGTC-GTGTTGCTGCTATA
1 GCTGTCTGT-TTGCTGCTATA
*
251170 GCT-TGCTGGTTGCTGCTATA
1 GCTGT-CTGTTTGCTGCTATA
251190 GCTGTCTGTTTGCT
1 GCTGTCTGTTTGCT
251204 TGCTGTGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 1 0.03
20 26 0.90
21 2 0.07
ACGTcount: A:0.07, C:0.20, G:0.30, T:0.43
Consensus pattern (20 bp):
GCTGTCTGTTTGCTGCTATA
Found at i:251784 original size:13 final size:12
Alignment explanation
Indices: 251762--251791 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
251752 GTGTTTTGCC
251762 TTTTTTTTTCTT
1 TTTTTTTTTCTT
251774 TTTTCTTTTTCTT
1 TTTT-TTTTTCTT
251787 TTTTT
1 TTTTT
251792 ATTGATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:253364 original size:15 final size:15
Alignment explanation
Indices: 253327--253356 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
253317 GGCAATAGGC
253327 GAAATAATGTTGTAT
1 GAAATAATGTTGTAT
253342 GAAATAATGTTGTAT
1 GAAATAATGTTGTAT
253357 AAAGTAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (15 bp):
GAAATAATGTTGTAT
Found at i:255441 original size:19 final size:18
Alignment explanation
Indices: 255395--255448 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
255385 TTTTTATAAT
255395 TTGTATCGATACAAAGAG
1 TTGTATCGATACAAAGAG
*
255413 TAAATGTATCGATACATAAGTG
1 T---TGTATCGATACA-AAGAG
255435 TTGTATCGATACAA
1 TTGTATCGATACAA
255449 TGTATCGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 2 0.06
19 12 0.39
21 12 0.39
22 5 0.16
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (18 bp):
TTGTATCGATACAAAGAG
Found at i:255454 original size:13 final size:13
Alignment explanation
Indices: 255436--255461 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
255426 ACATAAGTGT
255436 TGTATCGATACAA
1 TGTATCGATACAA
255449 TGTATCGATACAA
1 TGTATCGATACAA
255462 AGTTGCCCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:259868 original size:62 final size:61
Alignment explanation
Indices: 259824--260001 Score: 169
Period size: 68 Copynumber: 2.8 Consensus size: 61
259814 TGACATTGGA
* *
259824 CTTAAAGATGCA-AAGAAATGATAAAGGTGCCAATATGCTGATTCATGGCTAACGATATCAAG
1 CTTAAAGATG-AGAAG-AATGATAAAGGTGCCAATATGCTGATTCAAGGCTAACGACATCAAG
* * * *
259886 CTTGAATATGAGAAGAATGATAAAGGTGCCAATATGCTGATTCAAGATTCATGGCTAGCGATATC
1 CTTAAAGATGAGAAGAATGATAAAGGTGCCAATATGCTGATTC---A---A-GGCTAACGACATC
**
259951 GGG
59 AAG
* * *
259954 CTTGAATATGAGAAGAATGATAAAGGTGCTAATATGCTGATTCAAGGC
1 CTTAAAGATGAGAAGAATGATAAAGGTGCCAATATGCTGATTCAAGGC
260002 CAGCGATAGT
Statistics
Matches: 101, Mismatches: 7, Indels: 17
0.81 0.06 0.14
Matches are distributed among these distances:
61 32 0.32
62 12 0.12
64 1 0.01
65 1 0.01
68 55 0.54
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (61 bp):
CTTAAAGATGAGAAGAATGATAAAGGTGCCAATATGCTGATTCAAGGCTAACGACATCAAG
Found at i:259918 original size:61 final size:61
Alignment explanation
Indices: 259840--259997 Score: 217
Period size: 68 Copynumber: 2.5 Consensus size: 61
259830 GATGCAAAGA
259840 AATGATAAAGGTGCCAATATGCTGATTCATGGCTAACGATATCAAGCTTGAATATGAGAAG
1 AATGATAAAGGTGCCAATATGCTGATTCATGGCTAACGATATCAAGCTTGAATATGAGAAG
* **
259901 AATGATAAAGGTGCCAATATGCTGATTCAAGATTCATGGCTAGCGATATCGGGCTTGAATATGAG
1 AATGATAAAGGTGCCAATATGC----T---GATTCATGGCTAACGATATCAAGCTTGAATATGAG
259966 AAG
59 AAG
*
259969 AATGATAAAGGTGCTAATATGCTGATTCA
1 AATGATAAAGGTGCCAATATGCTGATTCA
259998 AGGCCAGCGA
Statistics
Matches: 86, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
61 28 0.33
64 1 0.01
65 1 0.01
68 56 0.65
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (61 bp):
AATGATAAAGGTGCCAATATGCTGATTCATGGCTAACGATATCAAGCTTGAATATGAGAAG
Found at i:259972 original size:68 final size:68
Alignment explanation
Indices: 259863--259999 Score: 238
Period size: 68 Copynumber: 2.0 Consensus size: 68
259853 CCAATATGCT
259863 GATTCATGGCTAACGATATCAAGCTTGAATATGAGAAGAATGATAAAGGTGCCAATATGCTGATT
1 GATTCATGGCTAACGATATCAAGCTTGAATATGAGAAGAATGATAAAGGTGCCAATATGCTGATT
259928 CAA
66 CAA
* ** *
259931 GATTCATGGCTAGCGATATCGGGCTTGAATATGAGAAGAATGATAAAGGTGCTAATATGCTGATT
1 GATTCATGGCTAACGATATCAAGCTTGAATATGAGAAGAATGATAAAGGTGCCAATATGCTGATT
259996 CAA
66 CAA
259999 G
1 G
260000 GCCAGCGATA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (68 bp):
GATTCATGGCTAACGATATCAAGCTTGAATATGAGAAGAATGATAAAGGTGCCAATATGCTGATT
CAA
Found at i:262230 original size:79 final size:78
Alignment explanation
Indices: 262122--262732 Score: 522
Period size: 79 Copynumber: 7.8 Consensus size: 78
262112 ATTAGGATTA
* ** * *
262122 GAGTATCCCCTCGAAGATGGT-GGGATTGGAGTATCCCCGAGATGAAAATTTTAATATTTTGGTA
1 GAGTATCCCCTCGAAAATAATAGGG-TTAGAGTATCCCCGAGATGAAAA-TTTAATATTTTGGAA
*
262186 GTAAAAACGAGGTTG
64 ATAAAAACGAGGTTG
* * * * * * *
262201 GAGTATCCCCTC-AGAAATGATGGGGTTGGAATATCCTCGATTG-TGAAAAATTGATATTTTGGA
1 GAGTATCCCCTCGA-AAATAATAGGGTTAGAGTATCCCCGA--GATGAAAATTTAATATTTTGGA
* *
262264 AATAAGAACGGGGTTG
63 AATAAAAACGAGGTTG
* * * * *
262280 GAGTATCCCTTCAAAAATAACAGGTTTAGAGTATCCCCGAGATAAAAATTTTAATATTTTGGAAA
1 GAGTATCCCCTCGAAAATAATAGGGTTAGAGTATCCCCGAGATGAAAA-TTTAATATTTTGGAAA
* *
262345 TAAAAATGGGGTTG
65 TAAAAACGAGGTTG
* * ** * * ** *
262359 GAGTAT-TCCTCGAAAATAATGGGGTTAGAGTATTACCAATGGTGAAAA-TCGATGTTTTGGAAA
1 GAGTATCCCCTCGAAAATAATAGGGTTAGAGTATCCCCGA-GATGAAAATTTAATATTTTGGAAA
262422 TAAAAACGAGGTTG
65 TAAAAACGAGGTTG
* *
262436 GAGTATCCCCT-GAAAAATAAT-GAGGTTAGAGTATCCCTGAGATGCAAATTTAATATTTTGGAA
1 GAGTATCCCCTCG-AAAATAATAG-GGTTAGAGTATCCCCGAGATGAAAATTTAATATTTTGGAA
262499 ATAAAAAC-AGGATTG
64 ATAAAAACGAGG-TTG
* * * ** * * * *
262514 GAGTATCCTCTCGAAAATAACAGGGATAGAGTATCCTTGATGGTCAAAAATTGATATTTTGGAAA
1 GAGTATCCCCTCGAAAATAATAGGGTTAGAGTATCCCCGA-GATGAAAATTTAATATTTTGGAAA
* *
262579 TAAAAATG-GAGTTT
65 TAAAAACGAG-GTTG
* * *
262593 GAGTATCCCCTCGAAAATAATAGGGTTGGAGTATCCCCAAAATGAAAATTTTAATATTTT-GAAA
1 GAGTATCCCCTCGAAAATAATAGGGTTAGAGTATCCCCGAGATGAAAA-TTTAATATTTTGGAAA
* *
262657 GTAAAAATGGGGTTG
65 -TAAAAACGAGGTTG
* * * * *
262672 GAGTGTCCCCTCGAAAATAATAGGGTTGGAGCATCCCCGATAGTGAAAAATTTGATATTTT
1 GAGTATCCCCTCGAAAATAATAGGGTTAGAGTATCCCCGAGA-TG-AAAATTTAATATTTT
262733 AGAAGTGAGA
Statistics
Matches: 431, Mismatches: 78, Indels: 45
0.78 0.14 0.08
Matches are distributed among these distances:
77 42 0.10
78 117 0.27
79 243 0.56
80 24 0.06
81 5 0.01
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (78 bp):
GAGTATCCCCTCGAAAATAATAGGGTTAGAGTATCCCCGAGATGAAAATTTAATATTTTGGAAAT
AAAAACGAGGTTG
Found at i:265231 original size:33 final size:33
Alignment explanation
Indices: 265194--265260 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
265184 TTCAACGATT
265194 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
265227 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
265260 T
1 T
265261 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:265232 original size:13 final size:13
Alignment explanation
Indices: 265214--265238 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
265204 CATAAAATGT
265214 TGTATCGATACAA
1 TGTATCGATACAA
265227 TGTATCGATACA
1 TGTATCGATACA
265239 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:266598 original size:51 final size:51
Alignment explanation
Indices: 266538--266675 Score: 190
Period size: 51 Copynumber: 2.7 Consensus size: 51
266528 AATAGCTTGC
* *
266538 ATGTATCGATA-AATTGAAGAATGTATCAATACATTT-GCGTTAAAACCCAAA
1 ATGTATCGATATAA-TGAAAAATGTATCAATACATTTAG-GCTAAAACCCAAA
*
266589 ATGTATCGATATAATGAAAAATGTATCAATACATTTAGGCTAAAACCCAGA
1 ATGTATCGATATAATGAAAAATGTATCAATACATTTAGGCTAAAACCCAAA
* * *
266640 ATGTATCGATATAATAAAAAATGAATCGATACATTT
1 ATGTATCGATATAATGAAAAATGTATCAATACATTT
266676 TCTTTCCAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 76 0.96
52 3 0.04
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (51 bp):
ATGTATCGATATAATGAAAAATGTATCAATACATTTAGGCTAAAACCCAAA
Found at i:266755 original size:20 final size:21
Alignment explanation
Indices: 266732--266785 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
266722 CATTTCAGAC
266732 ATGTATCAATACATTCACT-T
1 ATGTATCAATACATTCACTAT
266752 ATGTATCAATACATTCACTAT
1 ATGTATCAATACATTCACTAT
* *
266773 TTGTATCGATACA
1 ATGTATCAATACA
266786 AACTGTAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (21 bp):
ATGTATCAATACATTCACTAT
Found at i:274800 original size:233 final size:232
Alignment explanation
Indices: 274393--274862 Score: 888
Period size: 233 Copynumber: 2.0 Consensus size: 232
274383 TGGTGATTTT
274393 TTGACCATGCTTTGACAATCTTGAATCACTCAAGGGTAGTGACGGTTTGTTGCTCCATGACTAAT
1 TTGACCATGCTTTGACAATCTTGAATCACTCAAGGGTAGTGACGGTTTGTTGCTCCATGACTAAT
*
274458 GCCCCTTGCTGAACACTAAACCATGAACCAATTTTCCCGCGATGATGATGATCATGATGGAATGC
66 GCCCCTTGCTGAACACTAAACCATGAACCAATTTTCCCGCGATAATGATGATCATGATGGAATGC
274523 ATGCATGTATCAAACAAAAACAAATAGGAATTTAGTTAGTGACTGTACAAAAATAATAGAAATGA
131 ATGCATGTATCAAACAAAAACAAATAGGAATTTAGTTAGTGACTGTACAAAAATAATAGAAATGA
274588 ATAACAAGAATAAAAGAATAAACATCAATCAAAATGAG
196 ATAA-AAGAATAAAAGAATAAACATCAATCAAAATGAG
* * *
274626 TTGACCATGCTTTGACATTCTTGAATGATTCAAGGGTAGTGACGGTTTGTTGCTCCATGACTAAT
1 TTGACCATGCTTTGACAATCTTGAATCACTCAAGGGTAGTGACGGTTTGTTGCTCCATGACTAAT
274691 GCCCCTTGCTGAACACTAAACCATGAACCAATTTTCCCGCGATAATGATGATCATGATGGAATGC
66 GCCCCTTGCTGAACACTAAACCATGAACCAATTTTCCCGCGATAATGATGATCATGATGGAATGC
274756 ATGCATGTATCAAACAAAAACAAATAGGAATTTAGTTAGTGACTGTACAAAAATAATAGAAATGA
131 ATGCATGTATCAAACAAAAACAAATAGGAATTTAGTTAGTGACTGTACAAAAATAATAGAAATGA
274821 ATAAAAGAATAAAAGAATAAACATCAATCAAAATGAG
196 ATAAAAGAATAAAAGAATAAACATCAATCAAAATGAG
274858 -TGACC
1 TTGACC
274863 CTTTATTAGG
Statistics
Matches: 233, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
231 5 0.02
232 33 0.14
233 195 0.84
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (232 bp):
TTGACCATGCTTTGACAATCTTGAATCACTCAAGGGTAGTGACGGTTTGTTGCTCCATGACTAAT
GCCCCTTGCTGAACACTAAACCATGAACCAATTTTCCCGCGATAATGATGATCATGATGGAATGC
ATGCATGTATCAAACAAAAACAAATAGGAATTTAGTTAGTGACTGTACAAAAATAATAGAAATGA
ATAAAAGAATAAAAGAATAAACATCAATCAAAATGAG
Found at i:274840 original size:16 final size:18
Alignment explanation
Indices: 274805--274841 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
274795 TGACTGTACA
*
274805 AAAATAATAGAAATGAAT
1 AAAAGAATAGAAATGAAT
274823 AAAAGAATA-AAA-GAAT
1 AAAAGAATAGAAATGAAT
274839 AAA
1 AAA
274842 CATCAATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (18 bp):
AAAAGAATAGAAATGAAT
Found at i:276803 original size:9 final size:9
Alignment explanation
Indices: 276789--276814 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
276779 GTAGTTTTAG
276789 GATGATTTT
1 GATGATTTT
276798 GATGATTTT
1 GATGATTTT
276807 GATGATTT
1 GATGATTT
276815 GAAATCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (9 bp):
GATGATTTT
Found at i:276899 original size:125 final size:125
Alignment explanation
Indices: 276747--277005 Score: 484
Period size: 125 Copynumber: 2.1 Consensus size: 125
276737 ACCCTCTTAG
276747 GATCAT-CATGCATGATTGTGGCTTTGGATGTGGTAGTTTTAGGATGATTTTGATGATTTTGATG
1 GATCATGCATGCATGATTGTGGCTTTGGATGTGGTAGTTTTAGGATGATTTTGATGATTTTGATG
276811 ATTTGAAATCATTTGTGTGCCTAACATGCCATATCCATCTCCATCATTTTGATAAACCTT
66 ATTTGAAATCATTTGTGTGCCTAACATGCCATATCCATCTCCATCATTTTGATAAACCTT
*
276871 GATCATGCATGCATGATTGTGGCTTTGGATGTGGTAGTTTTAGGATTATTTTGATGATTTTGATG
1 GATCATGCATGCATGATTGTGGCTTTGGATGTGGTAGTTTTAGGATGATTTTGATGATTTTGATG
*
276936 ATTTGAAGTCATTTGTGTGCCTAACATGCCATATCCATCTCCATCATTTTGATAAACCTT
66 ATTTGAAATCATTTGTGTGCCTAACATGCCATATCCATCTCCATCATTTTGATAAACCTT
*
276996 AATCATGCAT
1 GATCATGCAT
277006 TTTTACTATG
Statistics
Matches: 131, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
124 6 0.05
125 125 0.95
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (125 bp):
GATCATGCATGCATGATTGTGGCTTTGGATGTGGTAGTTTTAGGATGATTTTGATGATTTTGATG
ATTTGAAATCATTTGTGTGCCTAACATGCCATATCCATCTCCATCATTTTGATAAACCTT
Found at i:280817 original size:32 final size:33
Alignment explanation
Indices: 280755--280818 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
280745 CACACCCAGA
* *
280755 TGTATCGATACATATTGCTTTGTATCGATACAT
1 TGTATCAATACATATTGCTTCGTATCGATACAT
*
280788 TGTATCAATACATGTT-CTTCGTATCGATACA
1 TGTATCAATACATATTGCTTCGTATCGATACA
280819 CAGTGAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (33 bp):
TGTATCAATACATATTGCTTCGTATCGATACAT
Found at i:282518 original size:12 final size:12
Alignment explanation
Indices: 282503--282533 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
282493 TCAACCATCA
282503 AAGATGATGATG
1 AAGATGATGATG
282515 AAGATGATGATG
1 AAGATGATGATG
*
282527 ATGATGA
1 AAGATGA
282534 AGAAATTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.26
Consensus pattern (12 bp):
AAGATGATGATG
Found at i:290109 original size:13 final size:13
Alignment explanation
Indices: 290091--290129 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
290081 ACATCATTCT
290091 TTGTATCGATACA
1 TTGTATCGATACA
290104 TTGTATCGATACA
1 TTGTATCGATACA
*
290117 CTGTATCGATACA
1 TTGTATCGATACA
290130 GGGGGTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:290292 original size:20 final size:20
Alignment explanation
Indices: 290251--290297 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
290241 AAATCTTTTG
290251 CAAAATACTTGTTTTTCACAT
1 CAAAATACTTGTTTTT-ACAT
*
290272 CAAATTACTTCGTTTTT-CAT
1 CAAAATACTT-GTTTTTACAT
290292 CAAAAT
1 CAAAAT
290298 CAGCTTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 8 0.35
21 9 0.39
22 6 0.26
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTACAT
Found at i:292726 original size:13 final size:13
Alignment explanation
Indices: 292708--292733 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
292698 TACACCAAGT
292708 ATGTATCGATACA
1 ATGTATCGATACA
292721 ATGTATCGATACA
1 ATGTATCGATACA
292734 TCAGAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:298901 original size:20 final size:20
Alignment explanation
Indices: 298876--298945 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
298866 TTTTACCCAT
*
298876 ATGTATCGATACAATTTTCA
1 ATGTATCGATACAATTTTAA
*
298896 ATGTATCGATAC-ATGTATAA
1 ATGTATCGATACAAT-TTTAA
* *
298916 ATGTATCGATACATTTTTTA
1 ATGTATCGATACAATTTTAA
298936 ATGTATCGAT
1 ATGTATCGAT
298946 GCATCTAGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
19 2 0.05
20 40 0.93
21 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACAATTTTAA
Found at i:300026 original size:80 final size:80
Alignment explanation
Indices: 299884--300043 Score: 293
Period size: 80 Copynumber: 2.0 Consensus size: 80
299874 TGTCTGGCAT
299884 CTCATTGAATGTTATTCATCAATTCATTATATGATCATCACATTTTCCATGTAAAGATGCATGCT
1 CTCATTGAATGTTATTCATCAATTCATTATATGATCATCACATTTTCCATGTAAAGATGCATGCT
299949 CGCTTGCATTTGAAA
66 CGCTTGCATTTGAAA
*
299964 CTCATTGAATGTTATTCATCAATTCATTGTATGATCATCACATTTTCCATGTAAAGATGCATGCT
1 CTCATTGAATGTTATTCATCAATTCATTATATGATCATCACATTTTCCATGTAAAGATGCATGCT
* *
300029 TGTTTGCATTTGAAA
66 CGCTTGCATTTGAAA
300044 ATTGATTTTC
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (80 bp):
CTCATTGAATGTTATTCATCAATTCATTATATGATCATCACATTTTCCATGTAAAGATGCATGCT
CGCTTGCATTTGAAA
Found at i:301696 original size:13 final size:13
Alignment explanation
Indices: 301678--301703 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
301668 TACAGCAAGT
301678 ATGTATCGATACA
1 ATGTATCGATACA
301691 ATGTATCGATACA
1 ATGTATCGATACA
301704 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:303955 original size:21 final size:21
Alignment explanation
Indices: 303922--303966 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
303912 TTGCAAGTTG
*
303922 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
303944 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
303964 AAA
1 AAA
303967 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:305791 original size:15 final size:15
Alignment explanation
Indices: 305771--305801 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
305761 TAAAAATGTC
*
305771 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
305786 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
305801 C
1 C
305802 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:307900 original size:13 final size:13
Alignment explanation
Indices: 307882--307917 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
307872 TTTTTCTTTA
307882 TATCGATACATTG
1 TATCGATACATTG
307895 TATCGATACATTG
1 TATCGATACATTG
307908 TATCGATACA
1 TATCGATACA
307918 GGGTGATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:310465 original size:13 final size:13
Alignment explanation
Indices: 310447--310472 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
310437 TACAGCAAGT
310447 ATGTATCGATACA
1 ATGTATCGATACA
310460 ATGTATCGATACA
1 ATGTATCGATACA
310473 CAAAAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:310494 original size:28 final size:31
Alignment explanation
Indices: 310429--310500 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 31
310419 TAGCCAAACT
**
310429 TGTATCGATACAGCAAGTATGTATCGATACAA
1 TGTATCGATACAGCAAAAATGTATCGATA-AA
310461 TGTATCGATACA-CAAAAAT-TATCGAT-AA
1 TGTATCGATACAGCAAAAATGTATCGATAAA
310489 TGTATCGATACA
1 TGTATCGATACA
310501 AATTATCGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 14 0.37
30 7 0.18
31 5 0.13
32 12 0.32
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (31 bp):
TGTATCGATACAGCAAAAATGTATCGATAAA
Found at i:312517 original size:13 final size:13
Alignment explanation
Indices: 312499--312524 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
312489 TACACAAAGT
312499 ATGTATCGATACA
1 ATGTATCGATACA
312512 ATGTATCGATACA
1 ATGTATCGATACA
312525 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:312545 original size:34 final size:32
Alignment explanation
Indices: 312481--312545 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
312471 TAGCCAAACT
** *
312481 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATATATCGATACAA
312513 TGTATCGATACACAAAAAAATTATATCGATACA
1 TGTATCGATACAC-AAAAAA-TATATCGATACA
312546 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 13 0.46
33 4 0.14
34 11 0.39
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATATATCGATACAA
Found at i:315842 original size:80 final size:80
Alignment explanation
Indices: 315647--315843 Score: 218
Period size: 80 Copynumber: 2.5 Consensus size: 80
315637 GCTATCGTGG
** * *
315647 GAGCTACTAAAGGCTACCGTGGAAGCTGCTGGAGTTGTTGGAAGTTGCTATGGGAGCTGTGGGAG
1 GAGCTACTGGAGGCTACCGTGGAAGCTGCTGGAGTTGCTGCAAGTTGCTATGGGAGCTGTGGGAG
315712 CTACTCGGGATTCCT
66 CTACTCGGGATTCCT
* * * * *
315727 GAGCTACTGGAGGCTACCGTGGAAGCTACTAGAGTTGCTGCCAGTTGCTGTGGGAGCTGTGGGGG
1 GAGCTACTGGAGGCTACCGTGGAAGCTGCTGGAGTTGCTGCAAGTTGCTATGGGAGCTGTGGGAG
* *
315792 CTGCTCGTGG-TTGCT
66 CTACTCG-GGATTCCT
** ** *
315807 GAGCTGTTGGAGGCTGTCGT-GAGAGCTGTTGGAGTTG
1 GAGCTACTGGAGGCTACCGTGGA-AGCTGCTGGAGTTG
315844 TTGGAGGCTA
Statistics
Matches: 97, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
79 2 0.02
80 93 0.96
81 2 0.02
ACGTcount: A:0.16, C:0.17, G:0.40, T:0.27
Consensus pattern (80 bp):
GAGCTACTGGAGGCTACCGTGGAAGCTGCTGGAGTTGCTGCAAGTTGCTATGGGAGCTGTGGGAG
CTACTCGGGATTCCT
Found at i:319038 original size:27 final size:27
Alignment explanation
Indices: 319000--319064 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
318990 CATTAGGGAC
319000 ACTCCAACCCCATTCCTTCGAGAGGAT
1 ACTCCAACCCCATTCCTTCGAGAGGAT
319027 ACTCCAACCCCATTCCTTCGAGAGGAT
1 ACTCCAACCCCATTCCTTCGAGAGGAT
319054 ACTCCAACCCC
1 ACTCCAACCCC
319065 GTTTTTTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.26, C:0.42, G:0.12, T:0.20
Consensus pattern (27 bp):
ACTCCAACCCCATTCCTTCGAGAGGAT
Found at i:323033 original size:20 final size:20
Alignment explanation
Indices: 322958--323034 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
322948 TTTTACCCAG
* * *
322958 ATGTATCAATACATTTTTTA
1 ATGTATCGATACATTCTTCA
* * *
322978 ATGGATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
322998 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
*
323018 ATGTGTCGATACATTCT
1 ATGTATCGATACATTCT
323035 GTATTTTTAC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:323058 original size:31 final size:31
Alignment explanation
Indices: 323018--323134 Score: 92
Period size: 31 Copynumber: 3.5 Consensus size: 31
323008 ACATTCTTCA
*
323018 ATGTGTCGATACATTCTGTATTTTTACCCAG
1 ATGTATCGATACATTCTGTATTTTTACCCAG
***
323049 ATGTATCGATACATGTATGACTGTATCGATACAATCTTCA-
1 ATGTATCGATACA--T-T--CTGTATTTTTAC---C--CAG
*
323089 ATGTATCGATACATTCTGTCTTTTTACCCAG
1 ATGTATCGATACATTCTGTATTTTTACCCAG
323120 ATGTATCGATACATT
1 ATGTATCGATACATT
323135 GAATAATATA
Statistics
Matches: 67, Mismatches: 8, Indels: 22
0.69 0.08 0.23
Matches are distributed among these distances:
30 2 0.03
31 27 0.40
32 1 0.01
33 1 0.01
34 1 0.01
35 8 0.12
36 9 0.13
37 1 0.01
38 1 0.01
39 1 0.01
40 13 0.19
41 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (31 bp):
ATGTATCGATACATTCTGTATTTTTACCCAG
Found at i:323152 original size:71 final size:71
Alignment explanation
Indices: 322982--323133 Score: 268
Period size: 71 Copynumber: 2.1 Consensus size: 71
322972 TTTTTAATGG
* *
322982 ATCGATACATGTATGAATGTATCGATACATTCTTCAATGTGTCGATACATTCTGTATTTTTACCC
1 ATCGATACATGTATGAATGTATCGATACAATCTTCAATGTATCGATACATTCTGTATTTTTACCC
323047 AGATGT
66 AGATGT
* *
323053 ATCGATACATGTATGACTGTATCGATACAATCTTCAATGTATCGATACATTCTGTCTTTTTACCC
1 ATCGATACATGTATGAATGTATCGATACAATCTTCAATGTATCGATACATTCTGTATTTTTACCC
323118 AGATGT
66 AGATGT
323124 ATCGATACAT
1 ATCGATACAT
323134 TGAATAATAT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 77 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (71 bp):
ATCGATACATGTATGAATGTATCGATACAATCTTCAATGTATCGATACATTCTGTATTTTTACCC
AGATGT
Found at i:326397 original size:19 final size:19
Alignment explanation
Indices: 326346--326398 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
326336 CTGCCAATCT
* *
326346 CATGTATCGATACAATTGTC
1 CATGTATCGATAC-AGTGAC
* * *
326366 CACGTATCAATACAGTGAG
1 CATGTATCGATACAGTGAC
326385 CATGTATCGATACA
1 CATGTATCGATACA
326399 ATGTATCGAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (19 bp):
CATGTATCGATACAGTGAC
Found at i:326404 original size:13 final size:13
Alignment explanation
Indices: 326386--326412 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
326376 TACAGTGAGC
326386 ATGTATCGATACA
1 ATGTATCGATACA
326399 ATGTATCGATACA
1 ATGTATCGATACA
326412 A
1 A
326413 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Done.