Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 6 of 185
Found at i:1789033 original size:15 final size:15
Alignment explanation
Indices: 1789015--1789046 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1789005 GAAATTGTTC
*
1789015 TAGATGAATTATATA
1 TAGATGAATTACATA
1789030 TAGATGAATTACATA
1 TAGATGAATTACATA
1789045 TA
1 TA
1789047 ATATCTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (15 bp):
TAGATGAATTACATA
Found at i:1789937 original size:17 final size:16
Alignment explanation
Indices: 1789897--1789929 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1789887 AACATTTAGC
1789897 AAAAAGAGA-AAACCAA
1 AAAAAGA-ATAAACCAA
1789913 AAAAAGAATAAACCAA
1 AAAAAGAATAAACCAA
1789929 A
1 A
1789930 TTAAAGAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 15 0.94
ACGTcount: A:0.76, C:0.12, G:0.09, T:0.03
Consensus pattern (16 bp):
AAAAAGAATAAACCAA
Found at i:1791779 original size:19 final size:19
Alignment explanation
Indices: 1791752--1791794 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1791742 ATATGTGTTT
* *
1791752 TAATTATAATAAAATAAAG
1 TAATAATAATAAAAGAAAG
1791771 TAATAATAATAAAAGAAAG
1 TAATAATAATAAAAGAAAG
1791790 -AATAA
1 TAATAA
1791795 AGAAAAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (19 bp):
TAATAATAATAAAAGAAAG
Found at i:1797888 original size:23 final size:23
Alignment explanation
Indices: 1797861--1797904 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1797851 TTTGCTTATT
*
1797861 TATTTTTCTTAATATAAAAAAAC
1 TATTTTTATTAATATAAAAAAAC
1797884 TATTTTTATTAATATAAAAAA
1 TATTTTTATTAATATAAAAAA
1797905 CCAATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTTTTATTAATATAAAAAAAC
Found at i:1797911 original size:23 final size:23
Alignment explanation
Indices: 1797862--1797911 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1797852 TTGCTTATTT
* *
1797862 ATTTTTCTTAATATAAAAAAACT
1 ATTTTTATTAATATAAAAAAACA
*
1797885 ATTTTTATTAATATAAAAAACCA
1 ATTTTTATTAATATAAAAAAACA
1797908 ATTT
1 ATTT
1797912 AAAAAATTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTTTTATTAATATAAAAAAACA
Found at i:1798955 original size:13 final size:13
Alignment explanation
Indices: 1798923--1798956 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1798913 TTGTAATGAA
1798923 TTGAAATATTTTT
1 TTGAAATATTTTT
**
1798936 TAAAAATATTTTT
1 TTGAAATATTTTT
1798949 TTGAAATA
1 TTGAAATA
1798957 ATGAAAGAAT
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (13 bp):
TTGAAATATTTTT
Found at i:1809465 original size:3 final size:3
Alignment explanation
Indices: 1809445--1809510 Score: 55
Period size: 3 Copynumber: 22.3 Consensus size: 3
1809435 TTATGTAAAT
* * * * *
1809445 TAA TAA -AA AAA TAA -AA TAA TAA TGA TAA TGA TAA CAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1809491 TAA TAC TAA TAA TAAA TAA T
1 TAA TAA TAA TAA T-AA TAA T
1809511 CTAGAGTTTG
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
2 4 0.08
3 42 0.86
4 3 0.06
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:1816632 original size:3 final size:3
Alignment explanation
Indices: 1816624--1816683 Score: 95
Period size: 3 Copynumber: 20.3 Consensus size: 3
1816614 TAACAATGAT
*
1816624 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1816672 ACA ATA A-A ATA A
1 ATA ATA ATA ATA A
1816684 AATTGCTAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1818334 original size:44 final size:44
Alignment explanation
Indices: 1818281--1818601 Score: 237
Period size: 44 Copynumber: 7.3 Consensus size: 44
1818271 AATTGCAACT
* *
1818281 TCAGAGAGATAGGATTACTATCTTCAATCTACTCCGCTGTAATC
1 TCAGGGAGATAAGATTACTATCTTCAATCTACTCCGCTGTAATC
*
1818325 TCAGGGAGATAAGATTACTATCTTCAATCTGCTCCGCTGTAATC
1 TCAGGGAGATAAGATTACTATCTTCAATCTACTCCGCTGTAATC
* * ** * ** *
1818369 TCAGAGAGATAAGATTTCTGGCTTCAATCTGCTCTACTGTAACC
1 TCAGGGAGATAAGATTACTATCTTCAATCTACTCCGCTGTAATC
* ** * *
1818413 TCAGGGAGATAAGATCTGA-AATTCTTCGGTCTACTCCACTGTAACC
1 TCAGGGAGATAAGAT-T-ACTA-TCTTCAATCTACTCCGCTGTAATC
* * * * *
1818459 TCAGGGTGATAAGA--CCTGA--TGCGATCTACTCTGCTGTAA-C
1 TCAGGGAGATAAGATTACT-ATCTTCAATCTACTCCGCTGTAATC
* * * ** *
1818499 TTCAGAGAGATAAGATCCT-TTAT-TTTAATCCGC-CCACTGTAATC
1 -TCAGGGAGATAAGAT--TACTATCTTCAATCTACTCCGCTGTAATC
* * * *
1818543 TCAGGGAGATAGGATTACTAGCTTCAATCTACTTCGTTGTAATC
1 TCAGGGAGATAAGATTACTATCTTCAATCTACTCCGCTGTAATC
1818587 TCAGGGAGATAAGAT
1 TCAGGGAGATAAGAT
1818602 CTGAAATTCT
Statistics
Matches: 215, Mismatches: 47, Indels: 30
0.74 0.16 0.10
Matches are distributed among these distances:
40 1 0.00
41 29 0.13
42 2 0.01
43 28 0.13
44 122 0.57
45 1 0.00
46 32 0.15
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (44 bp):
TCAGGGAGATAAGATTACTATCTTCAATCTACTCCGCTGTAATC
Found at i:1818338 original size:88 final size:87
Alignment explanation
Indices: 1818219--1818646 Score: 307
Period size: 88 Copynumber: 4.9 Consensus size: 87
1818209 ACTGGATGCG
* * * * *
1818219 ATCTACTCTGCTGCAAAT-TCAGAGAGATAAGATCTGTGATTTTAATCCGCTCAATTGCAA-CTT
1 ATCTACTCTGCTG-TAATCTCAGGGAGATAAGATCTGT-ATTTTAATCCGCTCCACTGTAATC-T
* *
1818282 CAGAGAGATAGGATTACTATCTTCA
63 CAGAGAGATAAGATTACTAGCTTCA
* * * * *
1818307 ATCTACTCCGCTGTAATCTCAGGGAGATAAGAT-TACTATCTTCAATCTGCTCCGCTGTAATCTC
1 ATCTACTCTGCTGTAATCTCAGGGAGATAAGATCT-GTAT-TTTAATCCGCTCCACTGTAATCTC
* *
1818371 AGAGAGATAAGATTTCTGGCTTCA
64 AGAGAGATAAGATTACTAGCTTCA
* * * * ** ** *
1818395 ATCTGCTCTACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCT
1 ATCTACTCTGCTGTAATCTCAGGGAGATAAGATCTG-TATT-TT-AATCCGCTCCACTGTAATCT
* * * * * *
1818460 CAGGGTGATAAGA--CCT-GATGCG
63 CAGAGAGATAAGATTACTAGCTTCA
* *
1818482 ATCTACTCTGCTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGC-CCACTGTAATCTC
1 ATCTACTCTGCTGTAATC-TCAGGGAGATAAGAT-CTGTATTTTAATCCGCTCCACTGTAATCTC
* *
1818545 AGGGAGATAGGATTACTAGCTTCA
64 AGAGAGATAAGATTACTAGCTTCA
* * ** * *
1818569 ATCTACT-TCGTTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTGTAATC
1 ATCTACTCT-GCTGTAATCTCAGGGAGATAAGATCTG-TA-T-TTTAATCCGCTCCACTGTAATC
*
1818633 TCAGGGAGATAAGA
62 TCAGAGAGATAAGA
1818647 CCTGTATAAT
Statistics
Matches: 264, Mismatches: 57, Indels: 36
0.74 0.16 0.10
Matches are distributed among these distances:
84 22 0.08
85 3 0.01
86 8 0.03
87 71 0.27
88 99 0.38
89 11 0.04
90 50 0.19
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (87 bp):
ATCTACTCTGCTGTAATCTCAGGGAGATAAGATCTGTATTTTAATCCGCTCCACTGTAATCTCAG
AGAGATAAGATTACTAGCTTCA
Found at i:1818460 original size:46 final size:45
Alignment explanation
Indices: 1818301--1818646 Score: 171
Period size: 44 Copynumber: 7.8 Consensus size: 45
1818291 AGGATTACTA
* * * *
1818301 TCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGAT-T-ACT
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGATCTGAAT
* * * * *
1818344 ATCTTCAATCTGCTCCGCTGTAATCTCAGAGAGATAAGATTTCTG---
1 -TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGA--TCTGAAT
* * * *
1818389 GCTTCAATCTGCTCTACTGTAACCTCAGGGAGATAAGATCTGAAAT
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGATCTG-AAT
* * *
1818435 TCTTCGGTCTACTCCACTGTAACCTCAGGGTGATAAGACCTG-A-
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGATCTGAAT
* ** * * **
1818478 --TGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTAT
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGAT-CTGAAT
* ** * * *
1818522 T-TT-AATCCGC-CCACTGTAATCTCAGGGAGATAGGAT-T-ACT
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGATCTGAAT
* * * ** *
1818562 AGCTTCAATCTACTTCGTTGTAATCTCAGGGAGATAAGATCTGAAAT
1 -TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGATCTG-AAT
* * ** *
1818609 TCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGA
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGA
1818647 CCTGTATAAT
Statistics
Matches: 231, Mismatches: 52, Indels: 36
0.72 0.16 0.11
Matches are distributed among these distances:
40 1 0.00
41 30 0.13
42 8 0.03
43 26 0.11
44 96 0.42
45 2 0.01
46 65 0.28
47 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (45 bp):
TCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGATCTGAAT
Found at i:1831084 original size:3 final size:3
Alignment explanation
Indices: 1831076--1831118 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
1831066 TAACAATGAT
* *
1831076 ATA ATA ATAA ATA ATA ATA ATA ATA ATA GTA ACA ATA A-A ATA A
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1831119 AATTGCTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:1832661 original size:30 final size:28
Alignment explanation
Indices: 1832627--1832682 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
1832617 AGGTGGGATG
1832627 GGAAGAGAATAAAAGTTTTAGGGGAAAAGT
1 GGAAGAGAATAAAA-TTTT-GGGGAAAAGT
* *
1832657 GGAAGGGAGTAAAATTTTGGGGAAAA
1 GGAAGAGAATAAAATTTTGGGGAAAA
1832683 ATAAAAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.33
29 4 0.17
30 12 0.50
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.20
Consensus pattern (28 bp):
GGAAGAGAATAAAATTTTGGGGAAAAGT
Found at i:1832915 original size:9 final size:9
Alignment explanation
Indices: 1832901--1832937 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1832891 TATAGTTTGA
1832901 TATTCGAAT
1 TATTCGAAT
1832910 TATTCGAAT
1 TATTCGAAT
*
1832919 TATTCGAGT
1 TATTCGAAT
1832928 TATTCGAAT
1 TATTCGAAT
1832937 T
1 T
1832938 CGAAAGCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:1833007 original size:9 final size:9
Alignment explanation
Indices: 1832990--1833020 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1832980 TCGAGTTGAT
1832990 TCGAATAAC
1 TCGAATAAC
*
1832999 TCGATTAAC
1 TCGAATAAC
1833008 TCGAATAAC
1 TCGAATAAC
1833017 TCGA
1 TCGA
1833021 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:1837552 original size:10 final size:8
Alignment explanation
Indices: 1837520--1837566 Score: 53
Period size: 8 Copynumber: 5.8 Consensus size: 8
1837510 AAAAACCTTA
1837520 AAAATAATT
1 AAAA-AATT
1837529 -AAAAA-T
1 AAAAAATT
1837535 AAAAAATT
1 AAAAAATT
1837543 ACAAAGAATT
1 A-AAA-AATT
1837553 AAAAAATT
1 AAAAAATT
1837561 AAAAAA
1 AAAAAA
1837567 ATAATATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
6 1 0.03
7 7 0.21
8 15 0.44
9 6 0.18
10 5 0.15
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (8 bp):
AAAAAATT
Found at i:1837819 original size:26 final size:26
Alignment explanation
Indices: 1837785--1837836 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1837775 ATTATTTAAA
*
1837785 TAATGAAAATAATATTATTTATTATT
1 TAATGAAAATAACATTATTTATTATT
* *
1837811 TAATTAAAATAACATTATTTTTTATT
1 TAATGAAAATAACATTATTTATTATT
1837837 ATTTAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
TAATGAAAATAACATTATTTATTATT
Found at i:1839796 original size:15 final size:17
Alignment explanation
Indices: 1839760--1839796 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
1839750 ATAATAAAAA
1839760 TATAATTTCATCATCTT
1 TATAATTTCATCATCTT
*
1839777 AATAATTT-AT-ATCTT
1 TATAATTTCATCATCTT
1839792 TATAA
1 TATAA
1839797 ATTTTAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
15 9 0.50
16 2 0.11
17 7 0.39
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (17 bp):
TATAATTTCATCATCTT
Found at i:1843609 original size:13 final size:14
Alignment explanation
Indices: 1843586--1843614 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1843576 TTTTAAGTTT
1843586 ATTTAAGAATTTGG
1 ATTTAAGAATTTGG
1843600 ATTT-AGAATTTGG
1 ATTTAAGAATTTGG
1843613 AT
1 AT
1843615 ATAAATGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (14 bp):
ATTTAAGAATTTGG
Found at i:1857629 original size:3 final size:3
Alignment explanation
Indices: 1857621--1857665 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
1857611 TAACAATGAT
* *
1857621 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ACA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1857666 AATTGCTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1859230 original size:30 final size:29
Alignment explanation
Indices: 1859196--1859252 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
1859186 AGGTGGGATG
*
1859196 GGAAGAGAATAAAAGTTTTAGGGGAAAAGT
1 GGAAGAGAATAAAAATTTT-GGGGAAAAGT
* *
1859226 GGAAGGGAGTAAAAATTTTGGGGAAAA
1 GGAAGAGAATAAAAATTTTGGGGAAAA
1859253 ATAAAAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.46, C:0.00, G:0.35, T:0.19
Consensus pattern (29 bp):
GGAAGAGAATAAAAATTTTGGGGAAAAGT
Found at i:1859486 original size:9 final size:9
Alignment explanation
Indices: 1859472--1859508 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1859462 TATAGTTTGA
1859472 TATTCGAAT
1 TATTCGAAT
1859481 TATTCGAAT
1 TATTCGAAT
*
1859490 TATTCGAGT
1 TATTCGAAT
1859499 TATTCGAAT
1 TATTCGAAT
1859508 T
1 T
1859509 CGAAAGCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:1859578 original size:9 final size:9
Alignment explanation
Indices: 1859561--1859591 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1859551 TCGAGTTGAT
1859561 TCGAATAAC
1 TCGAATAAC
*
1859570 TCGATTAAC
1 TCGAATAAC
1859579 TCGAATAAC
1 TCGAATAAC
1859588 TCGA
1 TCGA
1859592 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:1864127 original size:10 final size:8
Alignment explanation
Indices: 1864095--1864141 Score: 53
Period size: 8 Copynumber: 5.8 Consensus size: 8
1864085 AAAAACCTTA
1864095 AAAATAATT
1 AAAA-AATT
1864104 -AAAAA-T
1 AAAAAATT
1864110 AAAAAATT
1 AAAAAATT
1864118 ACAAAGAATT
1 A-AAA-AATT
1864128 AAAAAATT
1 AAAAAATT
1864136 AAAAAA
1 AAAAAA
1864142 ATAATATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
6 1 0.03
7 7 0.21
8 15 0.44
9 6 0.18
10 5 0.15
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (8 bp):
AAAAAATT
Found at i:1864395 original size:26 final size:26
Alignment explanation
Indices: 1864361--1864412 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1864351 ATTATTTAAA
*
1864361 TAATGAAAATAATATTATTTATTATT
1 TAATGAAAATAACATTATTTATTATT
* *
1864387 TAATTAAAATAACATTATTTTTTATT
1 TAATGAAAATAACATTATTTATTATT
1864413 ATTTAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
TAATGAAAATAACATTATTTATTATT
Found at i:1866372 original size:15 final size:17
Alignment explanation
Indices: 1866336--1866372 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
1866326 ATAATAAAAA
1866336 TATAATTTCATCATCTT
1 TATAATTTCATCATCTT
*
1866353 AATAATTT-AT-ATCTT
1 TATAATTTCATCATCTT
1866368 TATAA
1 TATAA
1866373 ATTTTAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
15 9 0.50
16 2 0.11
17 7 0.39
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (17 bp):
TATAATTTCATCATCTT
Found at i:1872774 original size:22 final size:23
Alignment explanation
Indices: 1872717--1872776 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
1872707 TTAATAATTT
*
1872717 TTATCTTTAGATTATAGTAAAAA
1 TTATATTTAGATTATAGTAAAAA
* *
1872740 TTATCTTTAGATTATAGT-AATA
1 TTATATTTAGATTATAGTAAAAA
1872762 TTAATATTT-GATTAT
1 TT-ATATTTAGATTAT
1872777 TTATGAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 11 0.32
23 23 0.68
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.50
Consensus pattern (23 bp):
TTATATTTAGATTATAGTAAAAA
Found at i:1875019 original size:42 final size:42
Alignment explanation
Indices: 1874960--1875044 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
1874950 GTTCCCTACA
*
1874960 TTACTTCGATTTGAGTGTTAGTGTCTGATACAGAAATGTGTC
1 TTACTTCCATTTGAGTGTTAGTGTCTGATACAGAAATGTGTC
*
1875002 TTACTTCCATTTGAGTGTTAGTGTCTGGTACAGAAATGTGTC
1 TTACTTCCATTTGAGTGTTAGTGTCTGATACAGAAATGTGTC
1875044 T
1 T
1875045 GAGACAGGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.22, C:0.13, G:0.24, T:0.41
Consensus pattern (42 bp):
TTACTTCCATTTGAGTGTTAGTGTCTGATACAGAAATGTGTC
Found at i:1879777 original size:3 final size:3
Alignment explanation
Indices: 1879763--1879813 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
1879753 AAACATAAAC
* *
1879763 TAA TACA TAA TAA TAT TAA TAA TAA TAA -AA TTAA TAA T-A TAA AAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
1879808 TAA TAA
1 TAA TAA
1879814 GAGTATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.10
3 31 0.77
4 5 0.12
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1879795 original size:15 final size:15
Alignment explanation
Indices: 1879763--1879813 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
1879753 AAACATAAAC
*
1879763 TAATACATAATAATAT
1 TAATA-ATAATAAAAT
1879779 TAATAATAATAAAAT
1 TAATAATAATAAAAT
*
1879794 TAATAAT-ATAAAAA
1 TAATAATAATAAAAT
1879808 TAATAA
1 TAATAA
1879814 GAGTATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.36
15 16 0.48
16 5 0.15
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
TAATAATAATAAAAT
Found at i:1880291 original size:6 final size:6
Alignment explanation
Indices: 1880282--1880309 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1880272 GAAAAAAGAA
1880282 AGGGAG AGGGAG AGGGAG AGGGAG AGGG
1 AGGGAG AGGGAG AGGGAG AGGGAG AGGG
1880310 CGATTTCCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
AGGGAG
Found at i:1881311 original size:21 final size:21
Alignment explanation
Indices: 1881286--1881326 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1881276 GCGATGGCAC
*
1881286 CACCTCCACGGTATGCTGCTG
1 CACCTCCACAGTATGCTGCTG
*
1881307 CACCTCCACATTATGCTGCT
1 CACCTCCACAGTATGCTGCT
1881327 CCTTACCCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.39, G:0.17, T:0.27
Consensus pattern (21 bp):
CACCTCCACAGTATGCTGCTG
Found at i:1881377 original size:78 final size:78
Alignment explanation
Indices: 1881249--1881392 Score: 243
Period size: 78 Copynumber: 1.8 Consensus size: 78
1881239 TTGTCCTTAC
* *
1881249 CCTTACCCTCCTCAAGGTTATCCCCCAGCGATGGCACCACCTCCACGGTATGCTGCTGCACCTCC
1 CCTTACCCTCCTCAACGTTATCCCCCAGCGATGGCACCACCTCCACGGTATGCTGCTCCACCTCC
1881314 ACATTATGCTGCT
66 ACATTATGCTGCT
* * *
1881327 CCTTACCCTGCTCAACGTTGTCCCCCAGTGATGGCACCACCTCCACGGTATGCTGCTCCACCTCC
1 CCTTACCCTCCTCAACGTTATCCCCCAGCGATGGCACCACCTCCACGGTATGCTGCTCCACCTCC
1881392 A
66 A
1881393 AGGCCTGGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 61 1.00
ACGTcount: A:0.17, C:0.42, G:0.17, T:0.24
Consensus pattern (78 bp):
CCTTACCCTCCTCAACGTTATCCCCCAGCGATGGCACCACCTCCACGGTATGCTGCTCCACCTCC
ACATTATGCTGCT
Found at i:1882125 original size:13 final size:13
Alignment explanation
Indices: 1882107--1882148 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
1882097 TAACTCTTCA
1882107 ATATTACATCAAT
1 ATATTACATCAAT
**
1882120 ATATTA-ATGTA-
1 ATATTACATCAAT
1882131 ATATTACATCAAT
1 ATATTACATCAAT
1882144 ATATT
1 ATATT
1882149 CAAACATAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
11 6 0.26
12 6 0.26
13 11 0.48
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (13 bp):
ATATTACATCAAT
Found at i:1882361 original size:67 final size:66
Alignment explanation
Indices: 1882254--1882387 Score: 223
Period size: 67 Copynumber: 2.0 Consensus size: 66
1882244 TTACTTTAAT
* *
1882254 ATATTGATGTAATATTGAAGAGTTAATTGATTAAAAAAATAAATGCAACAAGTACAAAACAGATT
1 ATATTAATGTAATATTGAAGAGTTAATTGATTAAAAAAATAAATGCAAC-AGTACAAAAAAGATT
1882319 CA
65 CA
* *
1882321 ATATTAATGTCATATTGAAGAGTTAATTGATTAAAAAAATAAATGCAACAGTACAAAAAATATTC
1 ATATTAATGTAATATTGAAGAGTTAATTGATTAAAAAAATAAATGCAACAGTACAAAAAAGATTC
1882386 A
66 A
1882387 A
1 A
1882388 AATTGTTACC
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
66 16 0.25
67 47 0.75
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.29
Consensus pattern (66 bp):
ATATTAATGTAATATTGAAGAGTTAATTGATTAAAAAAATAAATGCAACAGTACAAAAAAGATTC
A
Found at i:1888463 original size:26 final size:27
Alignment explanation
Indices: 1888434--1888497 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
1888424 CCTATCTCAA
*
1888434 AGGCGCCAATGGTGGTGCCAT-CTGGG
1 AGGCGCCAATGGTGGTGCCATACTGAG
* **
1888460 AGGCGCCATTATTGGTGCCATACTGAG
1 AGGCGCCAATGGTGGTGCCATACTGAG
1888487 AGGCGCCAATG
1 AGGCGCCAATG
1888498 CTCTGATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
26 18 0.58
27 13 0.42
ACGTcount: A:0.20, C:0.23, G:0.36, T:0.20
Consensus pattern (27 bp):
AGGCGCCAATGGTGGTGCCATACTGAG
Found at i:1888608 original size:22 final size:23
Alignment explanation
Indices: 1888555--1888608 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
1888545 TAGAGAAACG
*
1888555 GAAGAAATAAGAAGGAAGGAAGCA
1 GAAGAAA-AAGAAGGAAGGAAGAA
1888579 GAAG-AAAAGAAGGAAGGAA-AA
1 GAAGAAAAAGAAGGAAGGAAGAA
1888600 GAAGAAAAA
1 GAAGAAAAA
1888609 AATAAGGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.18
22 17 0.61
23 2 0.07
24 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.31, T:0.02
Consensus pattern (23 bp):
GAAGAAAAAGAAGGAAGGAAGAA
Found at i:1888610 original size:24 final size:22
Alignment explanation
Indices: 1888555--1888615 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 22
1888545 TAGAGAAACG
*
1888555 GAAG-AAATAAGAAGGAAGGAA
1 GAAGAAAAAAAGAAGGAAGGAA
* *
1888576 GCAGAAGAAAAGAAGGAAGGAAAA
1 GAAGAAAAAAAGAAGGAAGG--AA
*
1888600 GAAGAAAAAAATAAGG
1 GAAGAAAAAAAGAAGG
1888616 TATTTTGGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 3 0.10
22 13 0.42
24 15 0.48
ACGTcount: A:0.64, C:0.02, G:0.31, T:0.03
Consensus pattern (22 bp):
GAAGAAAAAAAGAAGGAAGGAA
Found at i:1888919 original size:16 final size:15
Alignment explanation
Indices: 1888888--1888931 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
1888878 ACAAAATCAA
1888888 ATAAAATTAAATTAT
1 ATAAAATTAAATTAT
*
1888903 ATAAAAGTTACATTAT
1 ATAAAA-TTAAATTAT
1888919 ATAAAAATTAAAT
1 AT-AAAATTAAAT
1888932 GAGTTAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.24
16 15 0.60
17 4 0.16
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
ATAAAATTAAATTAT
Found at i:1889009 original size:38 final size:38
Alignment explanation
Indices: 1888966--1889047 Score: 137
Period size: 38 Copynumber: 2.2 Consensus size: 38
1888956 AAAAAGTCAG
*
1888966 TTATAATTAAACTTTTAGTAAAATGATTTTTAATTCTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTCTT
* *
1889004 TTATAATTAAACTTTTAATGAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTCTT
1889042 TTATAA
1 TTATAA
1889048 ACTTTATATG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.54
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTCTT
Found at i:1889157 original size:60 final size:60
Alignment explanation
Indices: 1889081--1889202 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
1889071 ATACTAAACT
* * * * * *
1889081 AAACACAACAACTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCCAAATTACTAACAAATT-AATTATAAAATAATTAC
*
1889141 AAACACAAAAATTTATAACATAATCCCAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCCAAATTACTAACAAATTAATTATAAAATAATTAC
1889201 AA
1 AA
1889203 TATTCATACA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 4 0.07
60 50 0.93
ACGTcount: A:0.54, C:0.15, G:0.01, T:0.30
Consensus pattern (60 bp):
AAACACAAAAACTTATAACATAATCCCAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:1889215 original size:22 final size:22
Alignment explanation
Indices: 1889190--1889352 Score: 129
Period size: 22 Copynumber: 7.2 Consensus size: 22
1889180 AATTAATTAT
1889190 AAAATAATTACAATATTCATAC
1 AAAATAATTACAATATTCATAC
*
1889212 -AAA-AATTACAATATTACAATAT
1 AAAATAATTACAATATT-C-ATAC
****
1889234 ATCCCGACATTACAATATTCATAC
1 A-AAATA-ATTACAATATTCATAC
1889258 AAAATTACAAAATTACAATATTCATAC
1 AAAA-T----AATTACAATATTCATAC
* *
1889285 AAAAAAATTGCAATATTCATAC
1 AAAATAATTACAATATTCATAC
*
1889307 --AA-AATTATAATATTCATAC
1 AAAATAATTACAATATTCATAC
*
1889326 AAAAAAATTACAATATTCATAC
1 AAAATAATTACAATATTCATAC
1889348 AAAAT
1 AAAAT
1889353 TACAATATTA
Statistics
Matches: 112, Mismatches: 15, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
19 15 0.13
20 14 0.12
21 6 0.05
22 39 0.35
24 4 0.04
25 2 0.02
26 11 0.10
27 20 0.18
28 1 0.01
ACGTcount: A:0.54, C:0.15, G:0.01, T:0.30
Consensus pattern (22 bp):
AAAATAATTACAATATTCATAC
Found at i:1889312 original size:49 final size:49
Alignment explanation
Indices: 1889190--1889422 Score: 257
Period size: 49 Copynumber: 5.1 Consensus size: 49
1889180 AATTAATTAT
* *
1889190 AAAATAATTACAATATTCATACAAAAATTACAATATTACAATA-T-AT-C
1 AAAAAAATTACAATATTCATAC-AAAATTACAAAATTACAATATTCATAC
*** *
1889237 -CCGACATTACAATATTCATACAAAATTACAAAATTACAATATTCATAC
1 AAAAAAATTACAATATTCATACAAAATTACAAAATTACAATATTCATAC
*
1889285 AAAAAAATTGCAATATTCATACAAAATT-----A-T--AATATTCATAC
1 AAAAAAATTACAATATTCATACAAAATTACAAAATTACAATATTCATAC
*
1889326 AAAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
1 AAAAAAATTACAATATTCATACAAAATTACAAAATTACAATATTCATAC
*
1889375 AAAAAAATTGCAATATTCATAC--AA--A-AAAATTACAATATTCATAC
1 AAAAAAATTACAATATTCATACAAAATTACAAAATTACAATATTCATAC
1889419 AAAA
1 AAAA
1889423 TACTAATCCA
Statistics
Matches: 160, Mismatches: 14, Indels: 27
0.80 0.07 0.13
Matches are distributed among these distances:
41 38 0.24
43 1 0.01
44 23 0.14
45 20 0.12
46 18 0.11
47 5 0.03
48 1 0.01
49 54 0.34
ACGTcount: A:0.55, C:0.15, G:0.01, T:0.30
Consensus pattern (49 bp):
AAAAAAATTACAATATTCATACAAAATTACAAAATTACAATATTCATAC
Found at i:1889313 original size:41 final size:41
Alignment explanation
Indices: 1889263--1889544 Score: 229
Period size: 41 Copynumber: 6.6 Consensus size: 41
1889253 CATACAAAAT
*
1889263 TACAAAATTACAATATTCATACAAAAAAATTGCAATATTCA
1 TACAAAATTACAATATTCATACAAAAAAATTACAATATTCA
*
1889304 TACAAAATTATAATATTCATACAAAAAAATTACAATATTCA
1 TACAAAATTACAATATTCATACAAAAAAATTACAATATTCA
*
1889345 TACAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCA
1 TAC------A-AA-ATTACAATATTCATACAAAAAAATTACAATATTCA
* * *
1889394 TACAAAAAAATTACAATATTCATACAAAATACTAA-TCCAAAACT-A
1 TAC---AAAATTACAATATTCATACAAAA-A--AATTACAATATTCA
* * * *
1889439 TA-AATA-TA-AAT-TTAATTATAAAATAATTACAATATTCA
1 TACAAAATTACAATATTCA-TACAAAAAAATTACAATATTCA
*
1889477 TACAACATTACAATATTCAT--AAAAAAATTACAATATTCATA
1 TACAAAATTACAATATTCATACAAAAAAATTACAATATTC--A
* *
1889518 TAAAAAAATTAGAATATTCATACAAAA
1 T-ACAAAATTACAATATTCATACAAAA
1889545 TTCTAATCTA
Statistics
Matches: 196, Mismatches: 22, Indels: 43
0.75 0.08 0.16
Matches are distributed among these distances:
36 2 0.01
37 6 0.03
38 6 0.03
39 29 0.15
40 4 0.02
41 51 0.26
42 19 0.10
44 24 0.12
45 6 0.03
46 8 0.04
47 3 0.02
48 2 0.01
49 36 0.18
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.30
Consensus pattern (41 bp):
TACAAAATTACAATATTCATACAAAAAAATTACAATATTCA
Found at i:1889347 original size:90 final size:90
Alignment explanation
Indices: 1889242--1889546 Score: 328
Period size: 90 Copynumber: 3.2 Consensus size: 90
1889232 ATATCCCGAC
1889242 ATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATAC
1 ATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATAC
*
1889307 AAAATTATAATATTCATACAAAAAA
66 AAAATTACAATATTCATACAAAAAA
*
1889332 ATTACAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATAC
1 ATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATAC
1889397 AAAAAAATTACAATATTCATACAAAATACTA
66 ---AAAATTACAATATTCATACAAAA-A--A
* * ** * * * *
1889428 ATCCAAAACTATAAATATAAATTTAATTATAAAATAATTACAATATTCATAC---AACATTACAA
1 AT-TACAA-TATTCATA-CAA---AA-T-TACAA-AATTACAATATTCATACAAAAAAATTGCAA
* *
1889490 TATTCATAAAAAAATTACAATATTCATATAAAAAA
57 TATTCAT-ACAAAATTACAATATTCATACAAAAAA
*
1889525 ATTAGAATATTCATACAAAATT
1 ATTACAATATTCATACAAAATT
1889547 CTAATCTAAA
Statistics
Matches: 181, Mismatches: 18, Indels: 33
0.78 0.08 0.14
Matches are distributed among these distances:
89 1 0.01
90 65 0.36
91 2 0.01
93 22 0.12
94 3 0.02
95 6 0.03
96 6 0.03
97 6 0.03
98 6 0.03
99 3 0.02
100 22 0.12
102 17 0.09
103 2 0.01
104 4 0.02
105 16 0.09
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (90 bp):
ATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATAC
AAAATTACAATATTCATACAAAAAA
Found at i:1889389 original size:22 final size:22
Alignment explanation
Indices: 1889242--1889544 Score: 205
Period size: 22 Copynumber: 13.9 Consensus size: 22
1889232 ATATCCCGAC
1889242 ATTACAATATTCATACAAAATTACAAA
1 ATTACAATATTCATAC--AA--A-AAA
1889269 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
*
1889291 ATTGCAATATTCATAC---AAA
1 ATTACAATATTCATACAAAAAA
*
1889310 ATTATAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
1889332 ATTACAATATTCATAC---AAA
1 ATTACAATATTCATACAAAAAA
1889351 ATTACAATATTACAATATTCATACAAAAAA
1 ATTACAATATT-C-ATA--C--A-AAAA-A
*
1889381 ATTGCAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
1889403 ATTACAATATTCATAC---AAA
1 ATTACAATATTCATACAAAAAA
* * *
1889422 A-TACTA-ATCCA-A-AACTATAA
1 ATTACAATATTCATACAA--AAAA
* * *
1889442 ATATA-AAT-TTAATTATAAAATA
1 AT-TACAATATTCA-TACAAAAAA
*
1889464 ATTACAATATTCATAC---AAC
1 ATTACAATATTCATACAAAAAA
1889483 ATTACAATATTCAT--AAAAAA
1 ATTACAATATTCATACAAAAAA
*
1889503 ATTACAATATTCATATAAAAAA
1 ATTACAATATTCATACAAAAAA
*
1889525 ATTAGAATATTCATACAAAA
1 ATTACAATATTCATACAAAA
1889545 TTCTAATCTA
Statistics
Matches: 223, Mismatches: 21, Indels: 69
0.71 0.07 0.22
Matches are distributed among these distances:
16 1 0.00
17 4 0.02
18 4 0.02
19 50 0.22
20 20 0.09
21 8 0.04
22 87 0.39
23 10 0.04
24 3 0.01
25 2 0.01
26 1 0.00
27 16 0.07
28 3 0.01
29 3 0.01
30 11 0.05
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (22 bp):
ATTACAATATTCATACAAAAAA
Found at i:1889467 original size:61 final size:60
Alignment explanation
Indices: 1889379--1889563 Score: 182
Period size: 61 Copynumber: 3.0 Consensus size: 60
1889369 TCATACAAAA
* * *
1889379 AAATTGCAATATTCATACAAAAAAATTACAATATTCATACAAAATACTAATCCAAAACTAT
1 AAATTACAATATTAATATAAAAAAATTACAATATTCATACAAAATACTAAT-CAAAACTAT
* * *
1889440 AAATATA-AAT-TTAATTATAAAATAATTACAATATTCATACAACATTACAATATTCATAAA--A
1 AAAT-TACAATATTAA-TATAAAAAAATTACAATATTCATACAA-AATAC--TAATCA-AAACTA
1889501 -
60 T
* * * *
1889501 AAATTACAATATTCATATAAAAAAATTAGAATATTCATACAAAATTCTAATCTAAACTAT
1 AAATTACAATATTAATATAAAAAAATTACAATATTCATACAAAATACTAATCAAAACTAT
1889561 AAA
1 AAA
1889564 CAGTATATAT
Statistics
Matches: 100, Mismatches: 13, Indels: 23
0.74 0.10 0.17
Matches are distributed among these distances:
57 3 0.03
58 4 0.04
59 1 0.01
60 11 0.11
61 64 0.64
62 9 0.09
63 2 0.02
64 6 0.06
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.31
Consensus pattern (60 bp):
AAATTACAATATTAATATAAAAAAATTACAATATTCATACAAAATACTAATCAAAACTAT
Found at i:1889589 original size:122 final size:123
Alignment explanation
Indices: 1889353--1889580 Score: 325
Period size: 122 Copynumber: 1.8 Consensus size: 123
1889343 CATACAAAAT
* *
1889353 TACAATATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAAAAATTACAATATTCATA
1 TACAACATTACAATATTCATA-AAAAAAATTACAATATTCATACAAAAAAATTACAATATTCATA
* * *
1889418 CAAAATACTAATCCAAAACTATAAATATAAATTTAATTATAAAATAATTACAATATTCA
65 CAAAATACTAATCCAAAACTATAAACATAAATATAATAATAAAATAATTACAATATTCA
* *
1889477 TACAACATTACAATATTCAT-AAAAAAATTACAATATTCATATAAAAAAATTAGAATATTCATAC
1 TACAACATTACAATATTCATAAAAAAAATTACAATATTCATACAAAAAAATTACAATATTCATAC
* * *
1889541 AAAATTCTAAT-CTAAACTATAAACAGTATATATAGATAAT
66 AAAATACTAATCCAAAACTATAAACA-TAAATATA-ATAAT
1889581 TTATAATTAA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
121 12 0.13
122 57 0.62
123 4 0.04
124 19 0.21
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (123 bp):
TACAACATTACAATATTCATAAAAAAAATTACAATATTCATACAAAAAAATTACAATATTCATAC
AAAATACTAATCCAAAACTATAAACATAAATATAATAATAAAATAATTACAATATTCA
Found at i:1889725 original size:14 final size:15
Alignment explanation
Indices: 1889700--1889737 Score: 60
Period size: 14 Copynumber: 2.5 Consensus size: 15
1889690 TTTTTTTTTT
1889700 CTTTCTTCTTCTTCTC
1 CTTTC-TCTTCTTCTC
1889716 C-TTCTCTTCTTCTC
1 CTTTCTCTTCTTCTC
1889730 CTTTCTCT
1 CTTTCTCT
1889738 CTTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 11 0.52
15 9 0.43
16 1 0.05
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (15 bp):
CTTTCTCTTCTTCTC
Found at i:1889885 original size:27 final size:27
Alignment explanation
Indices: 1889855--1889918 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
1889845 AGAAGGCCAC
1889855 CATTGGCGCCTCTCTATGAGGCACCTT
1 CATTGGCGCCTCTCTATGAGGCACCTT
*
1889882 CATTGGTGCCTCTCTATGAGGCACCTT
1 CATTGGCGCCTCTCTATGAGGCACCTT
1889909 CATTGGCGCC
1 CATTGGCGCC
1889919 AACCTGATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.14, C:0.33, G:0.23, T:0.30
Consensus pattern (27 bp):
CATTGGCGCCTCTCTATGAGGCACCTT
Found at i:1890003 original size:10 final size:11
Alignment explanation
Indices: 1889975--1890009 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
1889965 CCGTATTTTT
1889975 TTAAAAAAATTA
1 TTAAAAAAA-TA
1889987 TTAAAAAAATA
1 TTAAAAAAATA
1889998 TT-AAAAAATA
1 TTAAAAAAATA
1890008 TT
1 TT
1890010 TTATTCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.43
11 4 0.17
12 9 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TTAAAAAAATA
Found at i:1890832 original size:45 final size:43
Alignment explanation
Indices: 1890768--1890855 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 43
1890758 ACGCAAATAA
1890768 TTAGTGGGTTTGCTCCCATAGATGCCTTGGGAAAAAAAAAACAAT
1 TTAGTGGGTTTGCTCCCATAGATGCCTT-GG-AAAAAAAAACAAT
1890813 TTAGTGGGTTTGCTCCCATAGATGCCTTGGAAAAAAAAACAAT
1 TTAGTGGGTTTGCTCCCATAGATGCCTTGGAAAAAAAAACAAT
1890856 AGATATAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 13 0.30
44 2 0.05
45 28 0.65
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (43 bp):
TTAGTGGGTTTGCTCCCATAGATGCCTTGGAAAAAAAAACAAT
Found at i:1892976 original size:18 final size:19
Alignment explanation
Indices: 1892955--1892990 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1892945 TCAAAAAAAA
*
1892955 ATTAAAATTTTA-AAAATC
1 ATTAAAATGTTATAAAATC
1892973 ATTAAAATGTTATAAAAT
1 ATTAAAATGTTATAAAAT
1892991 ATATATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (19 bp):
ATTAAAATGTTATAAAATC
Found at i:1896947 original size:19 final size:20
Alignment explanation
Indices: 1896923--1896961 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
1896913 TTATTATTTT
1896923 ATTTTATTAC-ACTTAAAAA
1 ATTTTATTACTACTTAAAAA
1896942 ATTTTATTACTACTTAAAAA
1 ATTTTATTACTACTTAAAAA
1896962 GAAAATTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTTATTACTACTTAAAAA
Found at i:1903541 original size:19 final size:19
Alignment explanation
Indices: 1903517--1903556 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1903507 TTAATTTTGA
1903517 AACCTTGAATTTTTGTCCT
1 AACCTTGAATTTTTGTCCT
1903536 AACCTTGAATTTTTGTCCT
1 AACCTTGAATTTTTGTCCT
1903555 AA
1 AA
1903557 ATAGTAGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (19 bp):
AACCTTGAATTTTTGTCCT
Found at i:1905733 original size:18 final size:17
Alignment explanation
Indices: 1905701--1905867 Score: 119
Period size: 17 Copynumber: 9.5 Consensus size: 17
1905691 CGAGATTTTT
1905701 TTTTGAAAACACGAAAA
1 TTTTGAAAACACGAAAA
* *
1905718 TTTTCAAAACACCGAAAT
1 TTTTGAAAACA-CGAAAA
* * *
1905736 TTTTGAAAACAAGAGGAT
1 TTTTGAAAACACGA-AAA
*
1905754 TTTTG-AAATACGAAAAA
1 TTTTGAAAACACG-AAAA
1905771 TTTTGAAAACACGAAAA
1 TTTTGAAAACACGAAAA
*
1905788 TTTTTG-AAACACGGAAAT
1 -TTTTGAAAACAC-GAAAA
1905806 TTTTG-AAA-ACGAAAA
1 TTTTGAAAACACGAAAA
*
1905821 TTTTTG-AAACACAAAAAA
1 -TTTTGAAAACAC-GAAAA
* *
1905839 TTTTAGAAGACACTAAAAA
1 TTTT-GAAAACAC-GAAAA
1905858 TTTTGGAAAA
1 TTTT-GAAAA
1905868 TGGATTTTTT
Statistics
Matches: 122, Mismatches: 17, Indels: 20
0.77 0.11 0.13
Matches are distributed among these distances:
15 4 0.03
16 10 0.08
17 47 0.39
18 43 0.35
19 18 0.15
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (17 bp):
TTTTGAAAACACGAAAA
Found at i:1905746 original size:35 final size:35
Alignment explanation
Indices: 1905700--1905832 Score: 164
Period size: 35 Copynumber: 3.9 Consensus size: 35
1905690 ACGAGATTTT
**
1905700 TTTTTGAAAACACGAAAATTTTCAAAACACCGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
* ** *
1905735 TTTTTGAAAACAAGAGGATTTTTGAAATA-CGAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCG-AAA
* *
1905770 ATTTTGAAAACACGAAAATTTTTGAAACACGGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
1905805 TTTTTG-AAA-ACGAAAATTTTTGAAACAC
1 TTTTTGAAAACACGAAAATTTTTGAAACAC
1905833 AAAAAATTTT
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
33 19 0.23
34 5 0.06
35 58 0.70
36 1 0.01
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
Found at i:1906078 original size:20 final size:19
Alignment explanation
Indices: 1906040--1906086 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1906030 GAATATATTT
1906040 TTTTTGAAACACGAGAAAAA
1 TTTTTGAAACACG-GAAAAA
*
1906060 TTTTTGAAGGCAC-GAAAAA
1 TTTTTGAA-ACACGGAAAAA
1906079 -TTTTGAAA
1 TTTTTGAAA
1906087 AATAGAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 7 0.29
19 6 0.25
20 8 0.33
21 3 0.12
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.30
Consensus pattern (19 bp):
TTTTTGAAACACGGAAAAA
Found at i:1906109 original size:20 final size:21
Alignment explanation
Indices: 1906086--1906124 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1906076 AAATTTTGAA
*
1906086 AAATA-GAAAGTTTTTTTTGT
1 AAATATGAAACTTTTTTTTGT
*
1906106 AAATATGAGACTTTTTTTT
1 AAATATGAAACTTTTTTTT
1906125 AAATATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (21 bp):
AAATATGAAACTTTTTTTTGT
Found at i:1906459 original size:7 final size:7
Alignment explanation
Indices: 1906447--1906530 Score: 66
Period size: 7 Copynumber: 12.0 Consensus size: 7
1906437 TTGAAACTTT
1906447 TTTTTTC
1 TTTTTTC
1906454 TTTTTTC
1 TTTTTTC
*
1906461 TTCTTT-
1 TTTTTTC
**
1906467 TTTCCT-
1 TTTTTTC
1906473 TTTTTTC
1 TTTTTTC
*
1906480 -TCTTTC
1 TTTTTTC
1906486 TTTTTTTC
1 -TTTTTTC
*
1906494 TTCTTTC
1 TTTTTTC
1906501 TTTTTTTC
1 -TTTTTTC
1906509 TTTTTTC
1 TTTTTTC
*
1906516 TTTCTCTC
1 TTT-TTTC
1906524 TTTTTTC
1 TTTTTTC
1906531 CTGGCCTGCT
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
6 12 0.20
7 31 0.52
8 17 0.28
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:1906459 original size:8 final size:8
Alignment explanation
Indices: 1906446--1906529 Score: 77
Period size: 8 Copynumber: 10.8 Consensus size: 8
1906436 ATTGAAACTT
1906446 TTTTTTTC
1 TTTTTTTC
1906454 TTTTTTCTTC
1 -TTTTT-TTC
*
1906464 TTTTTTCC
1 TTTTTTTC
1906472 TTTTTTTC
1 TTTTTTTC
*
1906480 --TCTTTC
1 TTTTTTTC
1906486 TTTTTTTC
1 TTTTTTTC
*
1906494 -TTCTTTC
1 TTTTTTTC
1906501 TTTTTTTC
1 TTTTTTTC
1906509 -TTTTTTC
1 TTTTTTTC
* *
1906516 TTTCTCTC
1 TTTTTTTC
1906524 TTTTTT
1 TTTTTT
1906530 CCTGGCCTGC
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
6 5 0.08
7 13 0.22
8 29 0.48
9 10 0.17
10 3 0.05
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1906501 original size:40 final size:38
Alignment explanation
Indices: 1906446--1906529 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
1906436 ATTGAAACTT
* *
1906446 TTTTTTTCTTTTTTCTTCTTTTTTCCTTTTTT-TCTCTTTC
1 TTTTTTTCTTCTTTC-T-TTTTTT-CTTTTTTCTCTCTCTC
*
1906486 TTTTTTTCTTCTTTCTTTTTTTCTTTTTTCTTTCTCTC
1 TTTTTTTCTTCTTTCTTTTTTTCTTTTTTCTCTCTCTC
1906524 TTTTTT
1 TTTTTT
1906530 CCTGGCCTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
37 7 0.17
38 18 0.45
39 1 0.03
40 14 0.35
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (38 bp):
TTTTTTTCTTCTTTCTTTTTTTCTTTTTTCTCTCTCTC
Found at i:1906527 original size:15 final size:15
Alignment explanation
Indices: 1906447--1906530 Score: 98
Period size: 15 Copynumber: 5.5 Consensus size: 15
1906437 TTGAAACTTT
1906447 TTTTTTCTTTTTTCTTC
1 TTTTTTC-TTTTT-TTC
1906464 TTTTTTCCTTTTTTTC
1 TTTTTT-CTTTTTTTC
*
1906480 -TCTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
*
1906494 TTCTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
* *
1906509 TTTTTTCTTTCTCTC
1 TTTTTTCTTTTTTTC
1906524 TTTTTTC
1 TTTTTTC
1906531 CTGGCCTGCT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
14 9 0.15
15 37 0.61
16 3 0.05
17 11 0.18
18 1 0.02
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTCTTTTTTTC
Found at i:1906530 original size:22 final size:21
Alignment explanation
Indices: 1906447--1906530 Score: 66
Period size: 22 Copynumber: 4.0 Consensus size: 21
1906437 TTGAAACTTT
*
1906447 TTTTTTCTTTTTTCTTCTTT-
1 TTTTTTCTTTTTTCTTTTTTC
** *
1906467 TTTCCT-TTTTTTC-TCTTTC
1 TTTTTTCTTTTTTCTTTTTTC
*
1906486 TTTTTTTCTTCTTTCTTTTTTTC
1 -TTTTTTCTTTTTTC-TTTTTTC
*
1906509 TTTTTTCTTTCTCTCTTTTTTC
1 TTTTTTCTTT-TTTCTTTTTTC
1906531 CTGGCCTGCT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
18 5 0.10
19 7 0.14
20 8 0.16
21 6 0.12
22 16 0.32
23 8 0.16
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTCTTTTTTCTTTTTTC
Found at i:1906683 original size:16 final size:15
Alignment explanation
Indices: 1906643--1906672 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1906633 GCTGTTTTTT
1906643 CTTTTCTTTTTGGGC
1 CTTTTCTTTTTGGGC
1906658 CTTTTCTTTTTGGGC
1 CTTTTCTTTTTGGGC
1906673 TGCTTTTTTT
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:0.00, C:0.20, G:0.20, T:0.60
Consensus pattern (15 bp):
CTTTTCTTTTTGGGC
Found at i:1906717 original size:21 final size:19
Alignment explanation
Indices: 1906691--1906733 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1906681 TTTGCTTTGG
1906691 TTTTTTTTGGGTTGATTTGTT
1 TTTTTTTTGGGTTG-TTT-TT
*
1906712 TTTTTTTTGTGTTGTTTTT
1 TTTTTTTTGGGTTGTTTTT
1906731 TTT
1 TTT
1906734 AATTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 3 0.14
21 13 0.62
ACGTcount: A:0.02, C:0.00, G:0.19, T:0.79
Consensus pattern (19 bp):
TTTTTTTTGGGTTGTTTTT
Found at i:1906856 original size:3 final size:3
Alignment explanation
Indices: 1906850--1906877 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1906840 TTTTTTTTCT
1906850 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1906878 CCTCCTACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1906978 original size:10 final size:10
Alignment explanation
Indices: 1906943--1906992 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
1906933 ACGCCGGTAC
1906943 TCTT-TCTTT
1 TCTTCTCTTT
* *
1906952 TCTTCTCCTC
1 TCTTCTCTTT
1906962 T-TTCTCTTT
1 TCTTCTCTTT
1906971 TCTTCTCTTT
1 TCTTCTCTTT
*
1906981 TCTTCTTTTT
1 TCTTCTCTTT
1906991 TC
1 TC
1906993 CTTCGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTCTCTTT
Found at i:1906990 original size:19 final size:19
Alignment explanation
Indices: 1906947--1906989 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1906937 CGGTACTCTT
1906947 TCTTTTCTTCTCCTCTTTC
1 TCTTTTCTTCTCCTCTTTC
1906966 TCTTTTCTTCT-CT-TTTC
1 TCTTTTCTTCTCCTCTTTC
1906983 TTCTTTT
1 -TCTTTT
1906990 TTCCTTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTCTCCTCTTTC
Found at i:1907295 original size:30 final size:30
Alignment explanation
Indices: 1907255--1907356 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
1907245 ATTTAGGATT
*
1907255 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
1907285 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* *
1907315 AAAATAAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
1907345 AAAATGCAATTT
1 AAAATGAAATTT
1907357 TTATTTTTTA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 2 0.03
30 58 0.97
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:1907813 original size:54 final size:55
Alignment explanation
Indices: 1907627--1907844 Score: 324
Period size: 54 Copynumber: 4.1 Consensus size: 55
1907617 CACGTGAGCC
* *
1907627 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG-AA
*
1907682 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAG--A---AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAA
* *
1907733 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1907787 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1907842 AAG
1 AAG
1907845 TAGAAATTGA
Statistics
Matches: 150, Mismatches: 6, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
50 14 0.09
51 34 0.23
52 1 0.01
54 52 0.35
55 37 0.25
56 6 0.04
57 6 0.04
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
Found at i:1907842 original size:14 final size:14
Alignment explanation
Indices: 1907823--1907857 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1907813 GAGTTGATTT
1907823 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
**
1907837 TTGAAAAGTAGAAA
1 TTGAAAAACAGAAA
1907851 TTGAAAA
1 TTGAAAA
1907858 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:1908090 original size:85 final size:87
Alignment explanation
Indices: 1907946--1908193 Score: 308
Period size: 85 Copynumber: 2.8 Consensus size: 87
1907936 AACAGAAATT
* * *
1907946 AAAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
1908011 TTGATTTGAAAAG-TAGAATT-AG
65 TTGATTTGAAAAGATAG-ATTGAA
* * * *
1908033 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
1908096 TTGATTTTTGAAAAGCATAGATTGAA
65 TTGA--TTTGAAAAG-ATAGATTGAA
*
1908122 AAAAACATAAATTGAAAATACCTCAGCTTGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
1908186 GTTGATTT
64 GTTGATTT
1908194 TTGAAAAACA
Statistics
Matches: 138, Mismatches: 13, Indels: 18
0.82 0.08 0.11
Matches are distributed among these distances:
84 3 0.02
85 33 0.24
87 32 0.23
88 3 0.02
89 31 0.22
91 33 0.24
93 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (87 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTGAAAAGATAGATTGAA
Found at i:1908139 original size:15 final size:16
Alignment explanation
Indices: 1908106--1908139 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1908096 TTGATTTTTG
* *
1908106 AAAAGCATAGATTGAA
1 AAAAACATAAATTGAA
1908122 AAAAACATAAATTGAA
1 AAAAACATAAATTGAA
1908138 AA
1 AA
1908140 TACCTCAGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (16 bp):
AAAAACATAAATTGAA
Found at i:1908181 original size:91 final size:88
Alignment explanation
Indices: 1907946--1908200 Score: 324
Period size: 91 Copynumber: 2.9 Consensus size: 88
1907936 AACAGAAATT
* * *
1907946 AAAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
1908011 TTGA--TTTGAAAAGTAGAATTAG
65 TTGATTTTTGAAAAGTAGAATTAA
* * * *
1908033 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
1908096 TTGATTTTTGAAAAGCATAG-ATTGAA
65 TTGATTTTTGAAAAG--TAGAATT-AA
*
1908122 AAAAACATAAATTGAAAATACCTCAGCTTGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
1908186 GTTGATTTTTGAAAA
64 GTTGATTTTTGAAAA
1908201 ACAAAAATTA
Statistics
Matches: 145, Mismatches: 13, Indels: 16
0.83 0.07 0.09
Matches are distributed among these distances:
84 3 0.02
85 33 0.23
87 32 0.22
88 3 0.02
89 28 0.19
91 43 0.30
93 3 0.02
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (88 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTTTGAAAAGTAGAATTAA
Found at i:1908629 original size:192 final size:192
Alignment explanation
Indices: 1908158--1908965 Score: 1411
Period size: 192 Copynumber: 4.2 Consensus size: 192
1908148 CTTGTGAGCC
** *
1908158 GAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGGCTTAACT
* *
1908223 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACATCGGCGTGCCCCGAGGCTA
65 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
* * *
1908288 AACTCATTTCTCGCAATATGAGTTGATTTTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
130 AACTCACTTCTCGCAATATGAGTT-A-ATTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTT
1908353 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1908418 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
** *
1908483 ACTCACTTCTCGCAATATGAGTTAATTTTTTTTAAAAATTTAAAAATACGTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTAATTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTT
1908545 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1908610 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
*
1908675 ACTCACTTCTCGCAATATGAGTTGATTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTAATTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTT
1908737 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1908802 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
* * *
1908867 ACTCACTTCTCGCAATATGAGTTGA-TTTTGAAAACAACAATTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTAATTTTTTAAAA-AA-ATTTAAAAATACCTCAACGTGTCTT
* *
1908930 GAGGCTCAACTCATCTCTCGCAATATGAGTTTATTT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTT
1908966 CCCTTGAAAA
Statistics
Matches: 594, Mismatches: 17, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
191 8 0.01
192 380 0.64
193 59 0.10
194 117 0.20
195 30 0.05
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.30
Consensus pattern (192 bp):
GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
ACTCACTTCTCGCAATATGAGTTAATTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTT
Found at i:1908934 original size:71 final size:70
Alignment explanation
Indices: 1908791--1908965 Score: 203
Period size: 71 Copynumber: 2.5 Consensus size: 70
1908781 AAAAATTAAA
* * * **
1908791 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTCATTTTAAAACATAAACTAAAAATACCTCAACGTG
1908855 CCCCG
66 CCCCG
* *
1908860 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACA-ACAATTAAAAATACCTCAACG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTCATTTT-AAAACATA-AACTAAAAATACCTCAACG
* **
1908924 TGTCTTG
64 TGCCCCG
*
1908931 AGGCTCAACTCA-TCTCTCGCAATATGAGTTTATTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTCATTT
1908966 CCCTTGAAAA
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
69 26 0.29
70 7 0.08
71 58 0.64
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTCATTTTAAAACATAAACTAAAAATACCTCAACGTG
CCCCG
Found at i:1917298 original size:12 final size:12
Alignment explanation
Indices: 1917278--1917313 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1917268 TCGGATATGC
*
1917278 AATGTATGAATG
1 AATGCATGAATG
1917290 AATGCATGAATG
1 AATGCATGAATG
1917302 AATGCATGAATG
1 AATGCATGAATG
1917314 TCAAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:1918345 original size:26 final size:26
Alignment explanation
Indices: 1918287--1918339 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1918277 GTAGCGACCT
1918287 AAAAATTGGGCACGGGCGCTAGTCGA
1 AAAAATTGGGCACGGGCGCTAGTCGA
1918313 AAAAATTGGGCACGGGCGCTAGTCGA
1 AAAAATTGGGCACGGGCGCTAGTCGA
1918339 A
1 A
1918340 GTAATTATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.32, C:0.19, G:0.34, T:0.15
Consensus pattern (26 bp):
AAAAATTGGGCACGGGCGCTAGTCGA
Found at i:1918770 original size:17 final size:17
Alignment explanation
Indices: 1918744--1918887 Score: 139
Period size: 17 Copynumber: 8.4 Consensus size: 17
1918734 ACGAGATTTT
1918744 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
*
1918762 TTTTCAAAACACCG-AAA
1 TTTTTAAAACA-CGAAAA
* **
1918779 TTTTTGAAAACAAGAGGA
1 TTTTT-AAAACACGAAAA
* *
1918797 TTTTTGAAATACGAAAAA
1 TTTTTAAAACACG-AAAA
*
1918815 TTTTGAAAACACGAAAA
1 TTTTTAAAACACGAAAA
*
1918832 TTTTTGAAACACGAAAA
1 TTTTTAAAACACGAAAA
*
1918849 TTTTTGAAA-ACGAAAA
1 TTTTTAAAACACGAAAA
* *
1918865 TTTTTGAAACACAAAAA
1 TTTTTAAAACACGAAAA
1918882 TTTTTA
1 TTTTTA
1918888 GAAGACACTA
Statistics
Matches: 104, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
16 16 0.15
17 58 0.56
18 30 0.29
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.31
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:1918772 original size:38 final size:37
Alignment explanation
Indices: 1918656--1918783 Score: 104
Period size: 38 Copynumber: 3.4 Consensus size: 37
1918646 GATCCGATTG
*
1918656 AAACACGAGAATTTCTTGTTTTGAAAACACGAGAATTTTA
1 AAACACGAG-ATTT-TT-TTTTGAAAACACGAAAATTTTA
* * * *
1918696 AGACA-TA-ATATTTTTTTT--AAA-ACTAAAATTTATG
1 AAACACGAGAT-TTTTTTTTGAAAACACGAAAATTT-TA
1918730 AAACACGAGATTTTTTTTTGAAAACACGAAAATTTTCA
1 AAACACGAGATTTTTTTTTGAAAACACGAAAATTTT-A
*
1918768 AAACACCGAAATTTTT
1 AAACA-CGAGATTTTT
1918784 GAAAACAAGA
Statistics
Matches: 69, Mismatches: 10, Indels: 19
0.70 0.10 0.19
Matches are distributed among these distances:
33 8 0.12
34 8 0.12
35 9 0.13
36 6 0.09
37 8 0.12
38 16 0.23
39 10 0.14
40 4 0.06
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (37 bp):
AAACACGAGATTTTTTTTTGAAAACACGAAAATTTTA
Found at i:1918790 original size:35 final size:35
Alignment explanation
Indices: 1918744--1918906 Score: 188
Period size: 35 Copynumber: 4.7 Consensus size: 35
1918734 ACGAGATTTT
**
1918744 TTTTTGAAAACACGAAAATTTTCAAAACACCG-AAA
1 TTTTTGAAAACACGAAAATTTTTGAAACA-CGAAAA
* ** *
1918779 TTTTTGAAAACAAGAGGATTTTTGAAATACGAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACGAAAA
*
1918814 ATTTTGAAAACACGAAAATTTTTGAAACACGAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACGAAAA
*
1918849 TTTTTG-AAA-ACGAAAATTTTTGAAACACAAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACGAAAA
* * *
1918882 TTTTTAGAAGACACTAAAAATTTTG
1 TTTTT-GAAAACACGAAAATTTTTG
1918907 GAAAATGGAA
Statistics
Matches: 108, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
33 28 0.26
34 6 0.06
35 63 0.58
36 11 0.10
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACGAAAA
Found at i:1919122 original size:20 final size:19
Alignment explanation
Indices: 1919084--1919130 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1919074 GAATATATTT
1919084 TTTTTGAAACACGAGAAAAA
1 TTTTTGAAACACG-GAAAAA
*
1919104 TTTTTGAAGGCAC-GAAAAA
1 TTTTTGAA-ACACGGAAAAA
1919123 -TTTTGAAA
1 TTTTTGAAA
1919131 AATAGAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 7 0.29
19 6 0.25
20 8 0.33
21 3 0.12
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.30
Consensus pattern (19 bp):
TTTTTGAAACACGGAAAAA
Found at i:1919503 original size:8 final size:8
Alignment explanation
Indices: 1919490--1919585 Score: 92
Period size: 8 Copynumber: 12.2 Consensus size: 8
1919480 ATTGAAACTC
1919490 TCTTTTTT
1 TCTTTTTT
1919498 TCTTTTTT
1 TCTTTTTT
1919506 TCTTCTTTTT
1 TC-T-TTTTT
*
1919516 TCCTTTTT
1 TCTTTTTT
*
1919524 CCTTTTTT
1 TCTTTTTT
*
1919532 TC-TCTTT
1 TCTTTTTT
1919539 TC-TTTTT
1 TCTTTTTT
*
1919546 TC-TTCTT
1 TCTTTTTT
1919553 TCTTTTTT
1 TCTTTTTT
1919561 TC-TTTTT
1 TCTTTTTT
* *
1919568 TCTTTCTC
1 TCTTTTTT
1919576 TCTTTTTT
1 TCTTTTTT
1919584 TC
1 TC
1919586 CTGGCCTGCT
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
7 25 0.35
8 39 0.54
9 1 0.01
10 7 0.10
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (8 bp):
TCTTTTTT
Found at i:1919505 original size:7 final size:7
Alignment explanation
Indices: 1919490--1919583 Score: 84
Period size: 7 Copynumber: 13.1 Consensus size: 7
1919480 ATTGAAACTC
1919490 TCTTTTT
1 TCTTTTT
*
1919497 T-TCTTT
1 TCTTTTT
*
1919503 T-TTTCT
1 TCTTTTT
1919509 TCTTTTT
1 TCTTTTT
1919516 TCCTTTTT
1 T-CTTTTT
*
1919524 CCTTTTTT
1 TC-TTTTT
*
1919532 TCTCTTT
1 TCTTTTT
1919539 TCTTTTT
1 TCTTTTT
*
1919546 TCTTCTT
1 TCTTTTT
1919553 TCTTTTTT
1 TC-TTTTT
1919561 TCTTTTT
1 TCTTTTT
*
1919568 TCTTTCTC
1 TCTTT-TT
1919576 TCTTTTT
1 TCTTTTT
1919583 T
1 T
1919584 TCCTGGCCTG
Statistics
Matches: 70, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
6 9 0.13
7 37 0.53
8 24 0.34
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
TCTTTTT
Found at i:1919534 original size:23 final size:22
Alignment explanation
Indices: 1919493--1919583 Score: 93
Period size: 22 Copynumber: 4.3 Consensus size: 22
1919483 GAAACTCTCT
1919493 TTTTTTC--TTTT-TTTC-TTC
1 TTTTTTCTTTTTTCTTTCTTTC
* *
1919511 TTTTTTCCTTTTTCCTTTTTTTC
1 TTTTTT-CTTTTTTCTTTCTTTC
*
1919534 TCTTTTCTTTTTTC-TTCTTTC
1 TTTTTTCTTTTTTCTTTCTTTC
*
1919555 TTTTTTTCTTTTTTCTTTCTCTC
1 -TTTTTTCTTTTTTCTTTCTTTC
1919578 TTTTTT
1 TTTTTT
1919584 TCCTGGCCTG
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
18 6 0.10
19 1 0.02
21 9 0.15
22 29 0.49
23 14 0.24
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTTCTTTTTTCTTTCTTTC
Found at i:1919556 original size:44 final size:44
Alignment explanation
Indices: 1919488--1919572 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
1919478 AAATTGAAAC
* *
1919488 TCTCTTTTTTTCTTTTTTTCTTCTTTTTTCCTTTTTCCTTTTTT
1 TCTCTTTTCTTCTTTTCTTCTTCTTTTTTCCTTTTTCCTTTTTT
* *
1919532 TCTCTTTTCTT-TTTTCTTCTTTCTTTTTTTCTTTTTTCTTT
1 TCTCTTTTCTTCTTTTCTTC-TTCTTTTTTCCTTTTTCCTTT
1919573 CTCTCTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 7 0.19
44 29 0.81
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (44 bp):
TCTCTTTTCTTCTTTTCTTCTTCTTTTTTCCTTTTTCCTTTTTT
Found at i:1919570 original size:15 final size:15
Alignment explanation
Indices: 1919490--1919583 Score: 100
Period size: 15 Copynumber: 6.1 Consensus size: 15
1919480 ATTGAAACTC
1919490 TCTTTTTTTCTTTTTT
1 TCTTTTTTTC-TTTTT
1919506 TCTTCTTTTTTCCTTTTT
1 TC-T-TTTTTT-CTTTTT
* *
1919524 CCTTTTTTTCTCTTT
1 TCTTTTTTTCTTTTT
*
1919539 TC-TTTTTTCTTCTT
1 TCTTTTTTTCTTTTT
1919553 TCTTTTTTTCTTTTT
1 TCTTTTTTTCTTTTT
* *
1919568 TCTTTCTCTCTTTTT
1 TCTTTTTTTCTTTTT
1919583 T
1 T
1919584 TCCTGGCCTG
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
14 12 0.18
15 31 0.47
16 8 0.12
17 2 0.03
18 12 0.18
19 1 0.02
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TCTTTTTTTCTTTTT
Found at i:1919715 original size:14 final size:15
Alignment explanation
Indices: 1919698--1919737 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
1919688 GCTGTTTTTT
1919698 CTTTTTTTTTGGGC-
1 CTTTTTTTTTGGGCG
1919712 CTTTTCTTTTTGGGCTG
1 CTTTT-TTTTTGGGC-G
1919729 CTTTTTTTT
1 CTTTTTTTT
1919738 GCTTTGGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 5 0.22
15 9 0.39
16 4 0.17
17 5 0.22
ACGTcount: A:0.00, C:0.15, G:0.17, T:0.68
Consensus pattern (15 bp):
CTTTTTTTTTGGGCG
Found at i:1919753 original size:31 final size:31
Alignment explanation
Indices: 1919713--1919785 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 31
1919703 TTTTTGGGCC
*
1919713 TTTTCTTTTTGGGCTGCTTT-TTTTTGCTTTG-G
1 TTTT-TTTTTGGGCTGATTTGTTTTT--TTTGTG
1919745 TTTTTTTTTGGGCTGATTTGTTTTTTTTGTG
1 TTTTTTTTTGGGCTGATTTGTTTTTTTTGTG
1919776 TTGTTTTTTT
1 TT-TTTTTTT
1919786 TAATTATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
30 4 0.11
31 17 0.46
32 16 0.43
ACGTcount: A:0.01, C:0.07, G:0.21, T:0.71
Consensus pattern (31 bp):
TTTTTTTTTGGGCTGATTTGTTTTTTTTGTG
Found at i:1919910 original size:14 final size:14
Alignment explanation
Indices: 1919888--1919943 Score: 55
Period size: 13 Copynumber: 4.1 Consensus size: 14
1919878 GATTGTTAAA
*
1919888 TTTTT-TTTCTTTT
1 TTTTTCTTTCTTCT
1919901 TTTTTCTTTCTTCT
1 TTTTTCTTTCTTCT
*
1919915 TCTTTC-TTCTTCT
1 TTTTTCTTTCTTCT
1919928 TCTTCTTC-TTCTTCT
1 T-TT-TTCTTTCTTCT
1919943 T
1 T
1919944 CTTCTCCTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 13 0.35
14 13 0.35
15 11 0.30
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTCTTTCTTCT
Found at i:1919914 original size:3 final size:3
Alignment explanation
Indices: 1919908--1919948 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
1919898 TTTTTTTTCT
1919908 TTC TTC TTC TTTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1919949 CCTCCTACAC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1920031 original size:10 final size:10
Alignment explanation
Indices: 1919996--1920045 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
1919986 CCGCCGGTAC
1919996 TCTT-TCTTT
1 TCTTCTCTTT
* *
1920005 TCTTCTCCTC
1 TCTTCTCTTT
1920015 T-TTCTCTTT
1 TCTTCTCTTT
1920024 TCTTCTCTTT
1 TCTTCTCTTT
*
1920034 TCTTCTTTTT
1 TCTTCTCTTT
1920044 TC
1 TC
1920046 CTTCGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTCTCTTT
Found at i:1920043 original size:19 final size:19
Alignment explanation
Indices: 1920000--1920042 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1919990 CGGTACTCTT
1920000 TCTTTTCTTCTCCTCTTTC
1 TCTTTTCTTCTCCTCTTTC
1920019 TCTTTTCTTCT-CT-TTTC
1 TCTTTTCTTCTCCTCTTTC
1920036 TTCTTTT
1 -TCTTTT
1920043 TTCCTTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTCTCCTCTTTC
Found at i:1920326 original size:29 final size:29
Alignment explanation
Indices: 1920293--1920409 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
1920283 TGTAATTTTT
*
1920293 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
1920322 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
1920352 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
1920381 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
1920410 TTATTTTTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 14 0.19
30 56 0.78
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:1920348 original size:30 final size:30
Alignment explanation
Indices: 1920308--1920409 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
1920298 ATTTAGGATT
*
1920308 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
1920338 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
1920368 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
1920398 AAAATGCAATTT
1 AAAATGAAATTT
1920410 TTATTTTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 60 0.97
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:1921072 original size:28 final size:29
Alignment explanation
Indices: 1921041--1921102 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
1921031 TAAATAAATA
* ** *
1921041 TATTTTTTA-TTTTAAAATACTTTTTTAT
1 TATTTTATATTTTTAAAATAAATTTTTAG
1921069 TATTTTATATTTTTAAAATAAATTTTTAG
1 TATTTTATATTTTTAAAATAAATTTTTAG
1921098 TATTT
1 TATTT
1921103 ATTAAAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (29 bp):
TATTTTATATTTTTAAAATAAATTTTTAG
Found at i:1923031 original size:17 final size:18
Alignment explanation
Indices: 1922997--1923038 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1922987 AAATTTTAAA
*
1922997 ATTAAAAATATATGAATT
1 ATTAAAAATAAATGAATT
1923015 ATTAAAAATAAAT-AATT
1 ATTAAAAATAAATGAATT
1923032 ATTAAAA
1 ATTAAAA
1923039 TTATTTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
ATTAAAAATAAATGAATT
Found at i:1923100 original size:17 final size:17
Alignment explanation
Indices: 1923078--1923111 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1923068 AAAAGAATAA
1923078 TTTAAAA-TAATTTAATT
1 TTTAAAATTAA-TTAATT
1923095 TTTAAAATTAATTAATT
1 TTTAAAATTAATTAATT
1923112 GCTAGCGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAAATTAATTAATT
Found at i:1929541 original size:40 final size:41
Alignment explanation
Indices: 1929475--1929564 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 41
1929465 AGCGGCACTT
* ** *
1929475 TTAGTGGCGTTTTGTGAAAAAACGCCAGTAAAAATCGGGCA
1 TTAGCGGCGTTTTGTGAAAAAACGCCACAAAAAATAGGGCA
* * * *
1929516 TTAGCGGCG-TTTGTGAGAAAGCGCCACAAAAAATAGGTCT
1 TTAGCGGCGTTTTGTGAAAAAACGCCACAAAAAATAGGGCA
1929556 TTAGCGGCG
1 TTAGCGGCG
1929565 CTTATAAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 33 0.80
41 8 0.20
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (41 bp):
TTAGCGGCGTTTTGTGAAAAAACGCCACAAAAAATAGGGCA
Found at i:1929807 original size:42 final size:42
Alignment explanation
Indices: 1929677--1929811 Score: 141
Period size: 41 Copynumber: 3.3 Consensus size: 42
1929667 TAAACAAACA
* * *
1929677 CCGCTAATGTTATGGTTTTTAGTGGCATTTTTTTCT-GAGCG
1 CCGCTAATGTTAAGGTTTTTAGTGGCATTTTTTTGTAAAGCG
* * * * * *
1929718 CCACTAATTTTAAGGCTTTTAGCGGC--GTTTTTGATAATGCG
1 CCGCTAATGTTAAGGTTTTTAGTGGCATTTTTTTG-TAAAGCG
*
1929759 CCGCTAAAGTTAAGGTTTTTAGTGGCATTTTTTTGTAAAGCG
1 CCGCTAATGTTAAGGTTTTTAGTGGCATTTTTTTGTAAAGCG
*
1929801 TCGCTAATGTT
1 CCGCTAATGTT
1929812 GGAGTTTTAG
Statistics
Matches: 72, Mismatches: 18, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
39 5 0.07
40 1 0.01
41 45 0.62
42 15 0.21
43 6 0.08
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (42 bp):
CCGCTAATGTTAAGGTTTTTAGTGGCATTTTTTTGTAAAGCG
Found at i:1929820 original size:82 final size:81
Alignment explanation
Indices: 1929677--1929830 Score: 202
Period size: 82 Copynumber: 1.9 Consensus size: 81
1929667 TAAACAAACA
* * * *
1929677 CCGCTAATGTTATGGTTTTTAGTGGCATTTTTTTCTGAGCGCCACTAATTTTAAGGCTTTTAGCG
1 CCGCTAAAGTTAAGGTTTTTAGTGGCATTTTTTTCTAAGCGCCACTAATGTT-AGGCTTTTAGCG
1929742 GCGTTTTTGATAATGCG
65 GCGTTTTTGATAATGCG
* * * *
1929759 CCGCTAAAGTTAAGGTTTTTAGTGGCATTTTTTTGTAAAGCGTCGCTAATGTT-GGAGTTTTAGC
1 CCGCTAAAGTTAAGGTTTTTAGTGGCATTTTTTTCT-AAGCGCCACTAATGTTAGG-CTTTTAGC
1929823 GGCGTTTT
64 GGCGTTTT
1929831 GATGGAAACG
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
81 2 0.03
82 48 0.77
83 12 0.19
ACGTcount: A:0.19, C:0.14, G:0.25, T:0.42
Consensus pattern (81 bp):
CCGCTAAAGTTAAGGTTTTTAGTGGCATTTTTTTCTAAGCGCCACTAATGTTAGGCTTTTAGCGG
CGTTTTTGATAATGCG
Found at i:1929843 original size:82 final size:80
Alignment explanation
Indices: 1929672--1929844 Score: 188
Period size: 82 Copynumber: 2.1 Consensus size: 80
1929662 GTTTTTAAAC
* * * * *
1929672 AAACACCGCTAATGTTATGGTTTTTAGTGGCATTTTTTTCTGAGCGCCACTAATTTTAAGGCTTT
1 AAACGCCGCTAAAGTTAAGGTTTTTAGTGGCATTTTTTTCTAAGCGCCACTAATGTT-AGGCTTT
1929737 TAGCGGCGTTTTTGAT
65 TAGCGGCGTTTTTGAT
* * * * *
1929753 AATGCGCCGCTAAAGTTAAGGTTTTTAGTGGCATTTTTTTGTAAAGCGTCGCTAATGTT-GGAGT
1 AA-ACGCCGCTAAAGTTAAGGTTTTTAGTGGCATTTTTTTCT-AAGCGCCACTAATGTTAGG-CT
1929817 TTTAGCGGCG-TTTTGAT
63 TTTAGCGGCGTTTTTGAT
1929834 GGAAACGCCGC
1 --AAACGCCGC
1929845 AAAATACATT
Statistics
Matches: 76, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
81 11 0.14
82 51 0.67
83 14 0.18
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (80 bp):
AAACGCCGCTAAAGTTAAGGTTTTTAGTGGCATTTTTTTCTAAGCGCCACTAATGTTAGGCTTTT
AGCGGCGTTTTTGAT
Found at i:1930459 original size:22 final size:23
Alignment explanation
Indices: 1930433--1930545 Score: 99
Period size: 22 Copynumber: 4.7 Consensus size: 23
1930423 GGAATTAAGG
*
1930433 TTTAGGGGTTAAGGGTTA-GGAA
1 TTTAGGGGTTAAGGGTTAGGGGA
*
1930455 TTTAGGGGTTAGGGGTTAAGGGTTGGTTA
1 TTTAGGGGTTAAGGGTT-A-GG--GG--A
1930484 TTTAGGGGGTT-AGGGTTTAGGTGGA
1 TTTA-GGGGTTAAGGG-TTAGG-GGA
1930509 TTTAGGGGTTAAGGGTTA-GGGA
1 TTTAGGGGTTAAGGGTTAGGGGA
1930531 TTTAGGGGTT-AGGGT
1 TTTAGGGGTTAAGGGT
1930546 GTCAAGGGTA
Statistics
Matches: 78, Mismatches: 3, Indels: 21
0.76 0.03 0.21
Matches are distributed among these distances:
21 5 0.06
22 29 0.37
23 2 0.03
24 9 0.12
25 10 0.13
27 4 0.05
28 2 0.03
29 9 0.12
30 8 0.10
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (23 bp):
TTTAGGGGTTAAGGGTTAGGGGA
Found at i:1930474 original size:29 final size:28
Alignment explanation
Indices: 1930416--1930526 Score: 106
Period size: 29 Copynumber: 4.0 Consensus size: 28
1930406 GGTATGGATT
* *
1930416 AGGGTTTGGAA-TTAAGGTTTAGGGGTTA
1 AGGG-TTGGAATTTAGGGGTTAGGGGTTA
1930444 AGGGTTAGGAATTTAGGGGTTAGGGGTTA
1 AGGGTT-GGAATTTAGGGGTTAGGGGTTA
* *
1930473 AGGGTTGGTTATTTAGGGGGTTA-GGGTTT
1 AGGGTTGG-AATTTA-GGGGTTAGGGGTTA
*
1930502 A-GG-TGG-ATTTAGGGGTTAAGGGTTA
1 AGGGTTGGAATTTAGGGGTTAGGGGTTA
1930527 GGGATTTAGG
Statistics
Matches: 73, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
24 7 0.10
25 10 0.14
27 5 0.07
28 12 0.16
29 32 0.44
30 7 0.10
ACGTcount: A:0.22, C:0.00, G:0.43, T:0.35
Consensus pattern (28 bp):
AGGGTTGGAATTTAGGGGTTAGGGGTTA
Found at i:1930542 original size:7 final size:7
Alignment explanation
Indices: 1930434--1930544 Score: 62
Period size: 7 Copynumber: 14.9 Consensus size: 7
1930424 GAATTAAGGT
1930434 TTAGGGG
1 TTAGGGG
*
1930441 TTAAGGG
1 TTAGGGG
**
1930448 TTAGGAAT
1 TTAGG-GG
1930456 TTAGGGG
1 TTAGGGG
1930463 TTAGGGG
1 TTAGGGG
*
1930470 TTAAGGG
1 TTAGGGG
**
1930477 TT-GGTTAT
1 TTAGG--GG
1930485 TTAGGGGG
1 TTA-GGGG
*
1930493 TTAGGGT
1 TTAGGGG
1930500 TTAGGTGG
1 TTAGG-GG
1930508 ATTTAGGGG
1 --TTAGGGG
*
1930517 TTAAGGG
1 TTAGGGG
*
1930524 TTAGGGAT
1 TTAGGG-G
1930532 TTAGGGG
1 TTAGGGG
1930539 TTAGGG
1 TTAGGG
1930545 TGTCAAGGGT
Statistics
Matches: 77, Mismatches: 18, Indels: 18
0.68 0.16 0.16
Matches are distributed among these distances:
6 1 0.01
7 50 0.65
8 17 0.22
9 2 0.03
10 7 0.09
ACGTcount: A:0.20, C:0.00, G:0.46, T:0.34
Consensus pattern (7 bp):
TTAGGGG
Found at i:1930554 original size:15 final size:15
Alignment explanation
Indices: 1930427--1930554 Score: 63
Period size: 15 Copynumber: 8.5 Consensus size: 15
1930417 GGGTTTGGAA
*
1930427 TTAAGGTTTAGGG-G
1 TTAAGGGTTAGGGTG
*
1930441 TTAAGGGTTAGGAAT-
1 TTAAGGGTTAGG-GTG
*
1930456 TTAGGGGTTAGGG-G
1 TTAAGGGTTAGGGTG
* *
1930470 TTAAGGGTT-GGTTAT
1 TTAAGGGTTAGGGT-G
*
1930485 TTAGGGGGTTAGGGT-
1 TTA-AGGGTTAGGGTG
*
1930500 TTAGGTGGATTTAGGG-G
1 TTAAG-GG--TTAGGGTG
1930517 TTAAGGGTTAGGGAT-
1 TTAAGGGTTAGGG-TG
*
1930532 TTAGGGGTTAGGGTG
1 TTAAGGGTTAGGGTG
*
1930547 TCAAGGGT
1 TTAAGGGT
1930555 ACTCAAGTTA
Statistics
Matches: 87, Mismatches: 13, Indels: 27
0.69 0.10 0.21
Matches are distributed among these distances:
13 2 0.02
14 28 0.32
15 37 0.43
16 7 0.08
17 13 0.15
ACGTcount: A:0.20, C:0.01, G:0.45, T:0.34
Consensus pattern (15 bp):
TTAAGGGTTAGGGTG
Found at i:1932079 original size:24 final size:22
Alignment explanation
Indices: 1932050--1932095 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
1932040 ATCACTTTTC
1932050 TCCCCAAAAATTCCCCCCAAATTT
1 TCCCCAAAAA-T-CCCCCAAATTT
1932074 TCCCCAAAAATCCCCCAAATTT
1 TCCCCAAAAATCCCCCAAATTT
1932096 AGAACCCTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 11 0.50
23 1 0.05
24 10 0.45
ACGTcount: A:0.35, C:0.41, G:0.00, T:0.24
Consensus pattern (22 bp):
TCCCCAAAAATCCCCCAAATTT
Found at i:1936914 original size:45 final size:43
Alignment explanation
Indices: 1936770--1937045 Score: 285
Period size: 43 Copynumber: 6.3 Consensus size: 43
1936760 CTGCCAAAAA
* * * * *
1936770 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAAGCCTTAGTCTT
1 TAGCGGCGTTTGTGTGATAAGCGCCGCT-AAAGGTCTTGGTCTT
* ** * *
1936814 TTGCGGCGTTTGTAAGA-AACGCGCCGCTAAAGATCTTGATCTT
1 TAGCGGCGTTTGTGTGATAA-GCGCCGCTAAAGGTCTTGGTCTT
*
1936857 TAGCGGCGTTTGTCGT-ATAAGCGCCGCTAAAATGGCCATT-GTCTT
1 TAGCGGCGTTTGT-GTGATAAGCGCCGCT-AAA-GGTC-TTGGTCTT
* *
1936902 TAGCGGCATTTGTGTCG-GAAGCGCCGCTAAAGGTCTTGGTCTT
1 TAGCGGCGTTTGTGT-GATAAGCGCCGCTAAAGGTCTTGGTCTT
*
1936945 TAGCGGCGTTTGTGTTG-GAAGCGCCGCTAAAGGTCTTGGTCTT
1 TAGCGGCGTTTGTG-TGATAAGCGCCGCTAAAGGTCTTGGTCTT
*
1936988 TAGCGGCGTTTGTGTGGAT-AGCGCCGCTATAGGTCTTGGTCTT
1 TAGCGGCGTTTGTGT-GATAAGCGCCGCTAAAGGTCTTGGTCTT
*
1937031 TAGCAGCGTTTGTGT
1 TAGCGGCGTTTGTGT
1937046 TGGAAGCGTC
Statistics
Matches: 200, Mismatches: 20, Indels: 25
0.82 0.08 0.10
Matches are distributed among these distances:
42 3 0.01
43 133 0.67
44 34 0.17
45 28 0.14
46 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.31
Consensus pattern (43 bp):
TAGCGGCGTTTGTGTGATAAGCGCCGCTAAAGGTCTTGGTCTT
Found at i:1936932 original size:88 final size:85
Alignment explanation
Indices: 1936770--1937045 Score: 324
Period size: 88 Copynumber: 3.2 Consensus size: 85
1936760 CTGCCAAAAA
* * * * ** *
1936770 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAAGCCTTAGTCTTTTGCGGCGTTTGTAAGAAACG
1 TAGCGGCGTTTGTG-TATAAGCGCCGCTAAAAGGCCTTAGTCTTTAGCGGCGTTTGTGTGGAA-G
* *
1936835 CGCCGCTAAAGATCTTGATCTT
64 CGCCGCTAAAGGTCTTGGTCTT
*
1936857 TAGCGGCGTTTGTCGTATAAGCGCCGCTAAAATGGCCATT-GTCTTTAGCGGCATTTGTGTCGGA
1 TAGCGGCGTTTGT-GTATAAGCGCCGCTAAAA-GGCC-TTAGTCTTTAGCGGCGTTTGTGT-GGA
1936921 AGCGCCGCTAAAGGTCTTGGTCTT
62 AGCGCCGCTAAAGGTCTTGGTCTT
* *
1936945 TAGCGGCGTTTGTGT-TGGAAGCGCCGCT-AAAGGTCTTGGTCTTTAGCGGCGTTTGTGTGGATA
1 TAGCGGCGTTTGTGTAT--AAGCGCCGCTAAAAGGCCTTAGTCTTTAGCGGCGTTTGTGTGGA-A
*
1937008 GCGCCGCTATAGGTCTTGGTCTT
63 GCGCCGCTAAAGGTCTTGGTCTT
*
1937031 TAGCAGCGTTTGTGT
1 TAGCGGCGTTTGTGT
1937046 TGGAAGCGTC
Statistics
Matches: 167, Mismatches: 14, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
85 5 0.03
86 60 0.36
87 33 0.20
88 64 0.38
89 5 0.03
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.31
Consensus pattern (85 bp):
TAGCGGCGTTTGTGTATAAGCGCCGCTAAAAGGCCTTAGTCTTTAGCGGCGTTTGTGTGGAAGCG
CCGCTAAAGGTCTTGGTCTT
Found at i:1937023 original size:86 final size:85
Alignment explanation
Indices: 1936770--1937053 Score: 333
Period size: 86 Copynumber: 3.3 Consensus size: 85
1936760 CTGCCAAAAA
* * * * ** *
1936770 TAGCGGCGTTTGTG-AGAAAAGCGCCGCTAAAAAGCCTTAGTCTTTTGCGGCGTTTGTAAGAAAC
1 TAGCGGCGTTTGTGTTG-GAAGCGCCGCTAAAAGGCCTT-GTCTTTAGCGGCGTTTGTGTGGAA-
* *
1936834 GCGCCGCTAAAGATCTTGATCTT
63 GCGCCGCTAAAGGTCTTGGTCTT
*
1936857 TAGCGGCGTTTGTCGTAT--AAGCGCCGCTAAAATGGCCATTGTCTTTAGCGGCATTTGTGTCGG
1 TAGCGGCGTTTGT-GT-TGGAAGCGCCGCTAAAA-GGCC-TTGTCTTTAGCGGCGTTTGTGT-GG
1936920 AAGCGCCGCTAAAGGTCTTGGTCTT
61 AAGCGCCGCTAAAGGTCTTGGTCTT
*
1936945 TAGCGGCGTTTGTGTTGGAAGCGCCGCT-AAAGGTCTTGGTCTTTAGCGGCGTTTGTGTGGATAG
1 TAGCGGCGTTTGTGTTGGAAGCGCCGCTAAAAGGCCTT-GTCTTTAGCGGCGTTTGTGTGGA-AG
*
1937009 CGCCGCTATAGGTCTTGGTCTT
64 CGCCGCTAAAGGTCTTGGTCTT
*
1937031 TAGCAGCGTTTGTGTTGGAAGCG
1 TAGCGGCGTTTGTGTTGGAAGCG
1937054 TCGTTAAAGT
Statistics
Matches: 174, Mismatches: 13, Indels: 21
0.84 0.06 0.10
Matches are distributed among these distances:
85 5 0.03
86 68 0.39
87 32 0.18
88 64 0.37
89 5 0.03
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.31
Consensus pattern (85 bp):
TAGCGGCGTTTGTGTTGGAAGCGCCGCTAAAAGGCCTTGTCTTTAGCGGCGTTTGTGTGGAAGCG
CCGCTAAAGGTCTTGGTCTT
Found at i:1937147 original size:22 final size:22
Alignment explanation
Indices: 1937119--1937161 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1937109 TGGCGGCGCT
*
1937119 AAAAAGCACCGCTAAAGGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
*
1937141 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCACCGCTAAAAGCCT
1937162 GTTTTGTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAAGCACCGCTAAAAGCCTA
Found at i:1939046 original size:12 final size:12
Alignment explanation
Indices: 1939029--1939054 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1939019 AAGGATGATA
1939029 CCATTAGAGTTC
1 CCATTAGAGTTC
1939041 CCATTAGAGTTC
1 CCATTAGAGTTC
1939053 CC
1 CC
1939055 GAGCTAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (12 bp):
CCATTAGAGTTC
Found at i:1941750 original size:31 final size:31
Alignment explanation
Indices: 1941712--1941781 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
1941702 GTTAGAAGCC
1941712 CTCAAATGTAATCTATATATTGCATCAAATG
1 CTCAAATGTAATCTATATATTGCATCAAATG
1941743 CTCAAATGTAATCTATATATTGCATCAAATG
1 CTCAAATGTAATCTATATATTGCATCAAATG
1941774 CTCAAATG
1 CTCAAATG
1941782 CATCATTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (31 bp):
CTCAAATGTAATCTATATATTGCATCAAATG
Found at i:1944083 original size:62 final size:59
Alignment explanation
Indices: 1944014--1944130 Score: 171
Period size: 62 Copynumber: 1.9 Consensus size: 59
1944004 AGTAATTATC
* * * *
1944014 TTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAATATTCTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTATCTT-T--ATAAATATTATATTAATTTAATAAGAT
1944076 TTAATATTAAATTTAATCTAATATTTATCTTTATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATCTTTATAAATATTATATTAATTTAATA
1944131 TTAAAATGAG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 21 0.41
61 1 0.02
62 29 0.57
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTTTATAAATATTATATTAATTTAATAAGAT
Found at i:1946446 original size:20 final size:20
Alignment explanation
Indices: 1946421--1946466 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1946411 TGAAATATTT
1946421 AAAATATTTAAATTAAA-ATA
1 AAAATA-TTAAATTAAATATA
* *
1946441 AAAATATTAATTTAAATTTA
1 AAAATATTAAATTAAATATA
1946461 AAAATA
1 AAAATA
1946467 CCTTATTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATATTAAATTAAATATA
Found at i:1948047 original size:33 final size:33
Alignment explanation
Indices: 1947995--1948074 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
1947985 TCATCACCCA
* *
1947995 GTAGAAGGTTTTTATACCCTTCTTCTTTCTCCC
1 GTAGAAGGTGTTTAAACCCTTCTTCTTTCTCCC
1948028 GTAGAAGGTGTTTAAACCCTTCTTCTTTCTCCC
1 GTAGAAGGTGTTTAAACCCTTCTTCTTTCTCCC
*
1948061 GAAGAAGGTGTTTA
1 GTAGAAGGTGTTTA
1948075 TTTATACCCT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (33 bp):
GTAGAAGGTGTTTAAACCCTTCTTCTTTCTCCC
Found at i:1953420 original size:24 final size:24
Alignment explanation
Indices: 1953320--1953431 Score: 124
Period size: 24 Copynumber: 4.8 Consensus size: 24
1953310 AATTTGTGTT
1953320 TTATTATTTT-AAGTTCATTATGTA
1 TTATTATTTTAAAGTT-ATTATGTA
* *
1953344 -TGTTGTTTTAAA-TCTATTATGTA
1 TTATTATTTTAAAGT-TATTATGTA
* * *
1953367 TTATTGTTTTAAAATTATTGTGTA
1 TTATTATTTTAAAGTTATTATGTA
*
1953391 TTATTATTTTAAAGTTACTATGTA
1 TTATTATTTTAAAGTTATTATGTA
1953415 TTATTA-TTTAAAGTTAT
1 TTATTATTTTAAAGTTAT
1953432 CTCATATTTA
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
23 26 0.35
24 48 0.64
25 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (24 bp):
TTATTATTTTAAAGTTATTATGTA
Found at i:1953442 original size:24 final size:24
Alignment explanation
Indices: 1953365--1953443 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
1953355 ATCTATTATG
* * * * *
1953365 TATTATTGTTTTAAAATTATTGTG
1 TATTATTATTTTAAAGTTACTATA
*
1953389 TATTATTATTTTAAAGTTACTATG
1 TATTATTATTTTAAAGTTACTATA
1953413 TATTATTA-TTTAAAGTTATCTCATA
1 TATTATTATTTTAAAGTTA-CT-ATA
1953438 T-TTATT
1 TATTATT
1953444 TTATTGTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
23 10 0.21
24 35 0.73
25 3 0.06
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.57
Consensus pattern (24 bp):
TATTATTATTTTAAAGTTACTATA
Found at i:1957221 original size:57 final size:56
Alignment explanation
Indices: 1957125--1957322 Score: 249
Period size: 50 Copynumber: 3.7 Consensus size: 56
1957115 TGAGTACTTC
*
1957125 TGATCAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATTAGTGACAAGTGACAAG
1 TGATAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGA-TAGTGACAAGTGACAAG
1957183 TGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTG--A-T--C-AGTGACAAG
1 TGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATAGTGACAAGTGACAAG
* *
1957233 TGACAAGTGATCAGTGGTAGCTTAGCTACACTTATCTG--A-T--C-AGTGACAAG
1 TGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATAGTGACAAGTGACAAG
* *
1957283 TAACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGAT
1 TGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGAT
1957323 CAGAGATAAT
Statistics
Matches: 133, Mismatches: 5, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
50 93 0.70
51 1 0.01
53 1 0.01
54 1 0.01
57 17 0.13
58 20 0.15
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.30
Consensus pattern (56 bp):
TGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATAGTGACAAGTGACAAG
Done.