Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 191 of 213
Found at i:57473319 original size:18 final size:18
Alignment explanation
Indices: 57473266--57473319 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
57473256 TAAAATTAAA
* *
57473266 TAAAATTTATTAAATTAT
1 TAAAATTTATAAAAATAT
57473284 TAAAATTTAATAAAAAATAT
1 TAAAATTT-AT-AAAAATAT
*
57473304 TAAAAATTATAAAAAT
1 TAAAATTTATAAAAAT
57473320 CGTAAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 14 0.45
19 4 0.13
20 13 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTATAAAAATAT
Found at i:57473338 original size:30 final size:29
Alignment explanation
Indices: 57473240--57473366 Score: 88
Period size: 30 Copynumber: 4.4 Consensus size: 29
57473230 GACATGTCGC
*
57473240 AAAAAATGATAAAAA--AT-AAAAT-TAA
1 AAAAAATTATAAAAATTATAAAAATATAA
* * * *
57473265 ATAAAATT-TATTAAATTATTAAAATTTAA
1 AAAAAATTATA-AAAATTATAAAAATATAA
*
57473294 TAAAAAA-TATTAAAAATTATAAAAATCGTAA
1 -AAAAAATTA-TAAAAATTATAAAAAT-ATAA
* *
57473325 AAAAAATTAT-AAAATATATAGAAATATAG
1 AAAAAATTATAAAAAT-TATAAAAATATAA
57473354 AAAAAATTATAAA
1 AAAAAATTATAAA
57473367 GTTTTATAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 19
0.73 0.09 0.17
Matches are distributed among these distances:
24 2 0.03
25 9 0.11
27 2 0.03
28 5 0.06
29 21 0.26
30 34 0.43
31 7 0.09
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (29 bp):
AAAAAATTATAAAAATTATAAAAATATAA
Found at i:57473638 original size:19 final size:19
Alignment explanation
Indices: 57473606--57473643 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
57473596 TTAAAGTGTC
*
57473606 TTTTTGATGCATTTTATAA
1 TTTTTGATGAATTTTATAA
*
57473625 TTTTTTATGAATTTTATAA
1 TTTTTGATGAATTTTATAA
57473644 AATTTTACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.61
Consensus pattern (19 bp):
TTTTTGATGAATTTTATAA
Found at i:57473723 original size:19 final size:19
Alignment explanation
Indices: 57473689--57473735 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
57473679 TATTTCTTTT
57473689 ATTTTTATTAAATTTTAATA
1 ATTTTTA-TAAATTTTAATA
* * *
57473709 ATTTTTATAACTTTTATTG
1 ATTTTTATAAATTTTAATA
57473728 ATTTTTAT
1 ATTTTTAT
57473736 TTTTATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTTATAAATTTTAATA
Found at i:57473735 original size:10 final size:10
Alignment explanation
Indices: 57473689--57473736 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
57473679 TATTTCTTTT
57473689 ATTTTTATTA
1 ATTTTTATTA
* *
57473699 AATTTTAATA
1 ATTTTTATTA
57473709 ATTTTTA-TA
1 ATTTTTATTA
* *
57473718 ACTTTTATTG
1 ATTTTTATTA
57473728 ATTTTTATT
1 ATTTTTATT
57473737 TTTATAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
9 8 0.26
10 23 0.74
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (10 bp):
ATTTTTATTA
Found at i:57474698 original size:53 final size:50
Alignment explanation
Indices: 57474640--57474770 Score: 138
Period size: 49 Copynumber: 2.5 Consensus size: 50
57474630 ATAAGTTTTG
*
57474640 AAATAAAAAGATAAATTAGTTTAAATTCAAAAATAAATCTAATTACCTAAGAT
1 AAATAAAAAGATAAAATAGTTTAAATT--AAAA-AAATCTAATTACCTAAGAT
* * * **
57474693 AAATAAAAA-ATAAAAAATTTTAAATTAAAAAAATCTATTTATTTAAGAT
1 AAATAAAAAGATAAAATAGTTTAAATTAAAAAAATCTAATTACCTAAGAT
57474742 AAATTAAAAAAGAATAAAACTAGTTTAAA
1 AAA-T-AAAAAG-ATAAAA-TAGTTTAAA
57474771 AAAAATCTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
49 19 0.29
50 5 0.08
51 5 0.08
52 14 0.22
53 15 0.23
54 7 0.11
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (50 bp):
AAATAAAAAGATAAAATAGTTTAAATTAAAAAAATCTAATTACCTAAGAT
Found at i:57475249 original size:49 final size:51
Alignment explanation
Indices: 57475149--57475261 Score: 131
Period size: 49 Copynumber: 2.2 Consensus size: 51
57475139 ATAAGTTTTG
**
57475149 AAATAAAAAGATAAATTAGTTTAAATTCAAAAATAAATCTAATTACCTAAGAT
1 AAATAAAAA-ATAAAAAAGTTTAAATT-AAAAATAAATCTAATTACCTAAGAT
* * **
57475202 AAATAAAAAATAAAAAATTTTAAATT-AAAA-AAATCTATTTATTTAAGAT
1 AAATAAAAAATAAAAAAGTTTAAATTAAAAATAAATCTAATTACCTAAGAT
57475251 AAATTAAAAAA
1 AAA-TAAAAAA
57475262 GAATAAAACT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
49 19 0.36
50 11 0.21
52 14 0.26
53 9 0.17
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (51 bp):
AAATAAAAAATAAAAAAGTTTAAATTAAAAATAAATCTAATTACCTAAGAT
Found at i:57475552 original size:508 final size:508
Alignment explanation
Indices: 57474596--57476120 Score: 3034
Period size: 508 Copynumber: 3.0 Consensus size: 508
57474586 TAAACATACG
57474596 AGAAAATATTACTCAACAACTTCATTGATTAATTATAAGTTTTGAAATAAAAAGATAAATTAGTT
1 AGAAAATATTACTCAACAACTTCATTGATTAATTATAAGTTTTGAAATAAAAAGATAAATTAGTT
57474661 TAAATTCAAAAATAAATCTAATTACCTAAGATAAATAAAAAATAAAAAATTTTAAATTAAAAAAA
66 TAAATTCAAAAATAAATCTAATTACCTAAGATAAATAAAAAATAAAAAATTTTAAATTAAAAAAA
57474726 TCTATTTATTTAAGATAAATTAAAAAAGAATAAAACTAGTTTAAAAAAAATCTTATTTCTCTAAT
131 TCTATTTATTTAAGATAAATTAAAAAAGAATAAAACTAGTTT-AAAAAAATCTTATTTCTCTAAT
57474791 ATACATAAAAATAATATTTATTACAAACAACAAAAGATATTTATCTATGATACGAGTATATAATA
195 ATACATAAAAATAATATTTATTACAAACAACAAAAGATATTTATCTATGATACGAGTATATAATA
57474856 ATTATTACAAATACAAAAAAAAATGTATATAATAGCCAATAGGGGTTGATTTTCGAGAAATTATT
260 ATTATTACAAATACAAAAAAAAATGTATATAATAGCCAATAGGGGTTGATTTTCGAGAAATTATT
57474921 TTGTAGTTTCTTTTCACCGAGAAATTATTTTATAGAATCTTTTTATTATATCATTCATGATTTTT
325 TTGTAGTTTCTTTTCACCGAGAAATTATTTTATAGAATCTTTTTATTATATCATTCATGATTTTT
57474986 TTCTAATTATTTAACGATATTTCAATAATTTTTTTAATACTATTAACACATTTTTTATAATTTTT
390 TTCTAATTATTTAACGATATTTCAATAATTTTTTTAATACTATTAACACATTTTTTATAATTTTT
57475051 TTATCTTAACCCCGAATCTCGAACCCTGAACCCAAGTTCAAGATTTAAGATTCA
455 TTATCTTAACCCCGAATCTCGAACCCTGAACCCAAGTTCAAGATTTAAGATTCA
57475105 AGAAAATATTACTCAACAACTTCATTGATTAATTATAAGTTTTGAAATAAAAAGATAAATTAGTT
1 AGAAAATATTACTCAACAACTTCATTGATTAATTATAAGTTTTGAAATAAAAAGATAAATTAGTT
57475170 TAAATTCAAAAATAAATCTAATTACCTAAGATAAATAAAAAATAAAAAATTTTAAATTAAAAAAA
66 TAAATTCAAAAATAAATCTAATTACCTAAGATAAATAAAAAATAAAAAATTTTAAATTAAAAAAA
57475235 TCTATTTATTTAAGATAAATTAAAAAAGAATAAAACTAGTTTAAAAAAATCTTATTTCTCTAATA
131 TCTATTTATTTAAGATAAATTAAAAAAGAATAAAACTAGTTTAAAAAAATCTTATTTCTCTAATA
57475300 TACATAAAAATAATATTTATTACAAACAACAAAAGATATTTATCTATGATACGAGTATATAATAA
196 TACATAAAAATAATATTTATTACAAACAACAAAAGATATTTATCTATGATACGAGTATATAATAA
57475365 TTATTACAAATACAAAAAAAAATGTATATAATAGCCAATAGGGGTTGATTTTCGAGAAATTATTT
261 TTATTACAAATACAAAAAAAAATGTATATAATAGCCAATAGGGGTTGATTTTCGAGAAATTATTT
57475430 TGTAGTTTCTTTTCACCGAGAAATTATTTTATAGAATCTTTTTATTATATCATTCATGATTTTTT
326 TGTAGTTTCTTTTCACCGAGAAATTATTTTATAGAATCTTTTTATTATATCATTCATGATTTTTT
57475495 TCTAATTATTTAACGATATTTCAATAATTTTTTTAATACTATTAACACATTTTTTATAATTTTTT
391 TCTAATTATTTAACGATATTTCAATAATTTTTTTAATACTATTAACACATTTTTTATAATTTTTT
57475560 TATCTTAACCCCGAATCTCGAACCCTGAACCCAAGTTCAAGATTTAAGATTCA
456 TATCTTAACCCCGAATCTCGAACCCTGAACCCAAGTTCAAGATTTAAGATTCA
57475613 AGAAAATATTACTCAACAACTTCATTGATTAATTATAAGTTTTGAAATAAAAAGATAAATTAGTT
1 AGAAAATATTACTCAACAACTTCATTGATTAATTATAAGTTTTGAAATAAAAAGATAAATTAGTT
57475678 TAAATTCAAAAATAAATCTAATTACCTAAGATAAATAAAAAATAAAAAATTTTAAATTAAAAAAA
66 TAAATTCAAAAATAAATCTAATTACCTAAGATAAATAAAAAATAAAAAATTTTAAATTAAAAAAA
57475743 TCTATTTATTTAAGATAAATTAAAAAAGAATAAAACTAGTTTAAAAAAATCTTATTTCTCTAATA
131 TCTATTTATTTAAGATAAATTAAAAAAGAATAAAACTAGTTTAAAAAAATCTTATTTCTCTAATA
57475808 TACATAAAAATAATATTTATTACAAACAACAAAAGATATTTATCTATGATACGAGTATATAATAA
196 TACATAAAAATAATATTTATTACAAACAACAAAAGATATTTATCTATGATACGAGTATATAATAA
57475873 TTATTACAAATAC-AAAAAAAATGTATATAATAGCCAATAGGGGTTGATTTTCGAGAAATTATTT
261 TTATTACAAATACAAAAAAAAATGTATATAATAGCCAATAGGGGTTGATTTTCGAGAAATTATTT
57475937 TGTAGTTTCTTTTCACCGAGAAATTATTTTATAGAATCTTTTTATTATATCATTCATGATTTTTT
326 TGTAGTTTCTTTTCACCGAGAAATTATTTTATAGAATCTTTTTATTATATCATTCATGATTTTTT
57476002 TCTAATTATTTAACGATATTTCAATAATTTTTTTAATACTATTAACACATTTTTTATAATTTTTT
391 TCTAATTATTTAACGATATTTCAATAATTTTTTTAATACTATTAACACATTTTTTATAATTTTTT
57476067 TATCTTAACCCCGAATCTCGAACCCTGAACCCAAGTTCAAGATTTAAGATTCA
456 TATCTTAACCCCGAATCTCGAACCCTGAACCCAAGTTCAAGATTTAAGATTCA
57476120 A
1 A
57476121 AGTTCGGAGT
Statistics
Matches: 1016, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
507 235 0.23
508 609 0.60
509 172 0.17
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.38
Consensus pattern (508 bp):
AGAAAATATTACTCAACAACTTCATTGATTAATTATAAGTTTTGAAATAAAAAGATAAATTAGTT
TAAATTCAAAAATAAATCTAATTACCTAAGATAAATAAAAAATAAAAAATTTTAAATTAAAAAAA
TCTATTTATTTAAGATAAATTAAAAAAGAATAAAACTAGTTTAAAAAAATCTTATTTCTCTAATA
TACATAAAAATAATATTTATTACAAACAACAAAAGATATTTATCTATGATACGAGTATATAATAA
TTATTACAAATACAAAAAAAAATGTATATAATAGCCAATAGGGGTTGATTTTCGAGAAATTATTT
TGTAGTTTCTTTTCACCGAGAAATTATTTTATAGAATCTTTTTATTATATCATTCATGATTTTTT
TCTAATTATTTAACGATATTTCAATAATTTTTTTAATACTATTAACACATTTTTTATAATTTTTT
TATCTTAACCCCGAATCTCGAACCCTGAACCCAAGTTCAAGATTTAAGATTCA
Found at i:57475757 original size:49 final size:51
Alignment explanation
Indices: 57475657--57475769 Score: 131
Period size: 49 Copynumber: 2.2 Consensus size: 51
57475647 ATAAGTTTTG
**
57475657 AAATAAAAAGATAAATTAGTTTAAATTCAAAAATAAATCTAATTACCTAAGAT
1 AAATAAAAA-ATAAAAAAGTTTAAATT-AAAAATAAATCTAATTACCTAAGAT
* * **
57475710 AAATAAAAAATAAAAAATTTTAAATT-AAAA-AAATCTATTTATTTAAGAT
1 AAATAAAAAATAAAAAAGTTTAAATTAAAAATAAATCTAATTACCTAAGAT
57475759 AAATTAAAAAA
1 AAA-TAAAAAA
57475770 GAATAAAACT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
49 19 0.36
50 11 0.21
52 14 0.26
53 9 0.17
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (51 bp):
AAATAAAAAATAAAAAAGTTTAAATTAAAAATAAATCTAATTACCTAAGAT
Found at i:57480460 original size:4 final size:4
Alignment explanation
Indices: 57480444--57480473 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
57480434 AGATTTCCAA
*
57480444 TATG TAAG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TA
57480474 ACTCGAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:57481361 original size:20 final size:22
Alignment explanation
Indices: 57481319--57481368 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
57481309 ATTTTAGATC
* *
57481319 TTTAAGTTTAATTATTAATATT
1 TTTAAGTTTAATTAATAACATT
57481341 TTTAA-TTT-ATTAATAACATT
1 TTTAAGTTTAATTAATAACATT
*
57481361 TTAAAGTT
1 TTTAAGTT
57481369 AAAAAATACA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 14 0.58
21 5 0.21
22 5 0.21
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTAAGTTTAATTAATAACATT
Found at i:57498711 original size:14 final size:13
Alignment explanation
Indices: 57498686--57498727 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
57498676 ACCACGTAAT
*
57498686 AAGAAAACAAAGA
1 AAGAAAAAAAAGA
57498699 AAGTAAAAAAAAGA
1 AAG-AAAAAAAAGA
*
57498713 AAGAAAGAAAAGA
1 AAGAAAAAAAAGA
57498726 AA
1 AA
57498728 TAAGCATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (13 bp):
AAGAAAAAAAAGA
Found at i:57498715 original size:18 final size:17
Alignment explanation
Indices: 57498689--57498723 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
57498679 ACGTAATAAG
57498689 AAAACAAAGAAAGTAAAA
1 AAAACAAAGAAAG-AAAA
*
57498707 AAAAGAAAGAAAGAAAA
1 AAAACAAAGAAAGAAAA
57498724 GAAATAAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.80, C:0.03, G:0.14, T:0.03
Consensus pattern (17 bp):
AAAACAAAGAAAGAAAA
Found at i:57508849 original size:17 final size:17
Alignment explanation
Indices: 57508817--57508850 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
57508807 ATTTTTTGAC
57508817 ATTTTTAAATATATATA
1 ATTTTTAAATATATATA
57508834 ATTTATTAAATA-ATATA
1 ATTT-TTAAATATATATA
57508851 CTGGTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTTAAATATATATA
Found at i:57522527 original size:91 final size:91
Alignment explanation
Indices: 57522358--57522539 Score: 240
Period size: 91 Copynumber: 2.0 Consensus size: 91
57522348 GATTAAATTA
* ** **
57522358 TTGAATGATATAATGTTTAAATGTTTCTAATTGTACGGTAATGCTCTGTAACCCCAATCTGGCGA
1 TTGAATGATATAATGTTTAAATGTTTCTAATTGTACGATAACACTCTGTAACCCCAATCCAGCGA
*
57522423 CGGAGACAAGTTAGGGGTGTTACATG
66 CGAAGACAAGTTAGGGGTGTTACATG
* * *
57522449 TTGAATGATATAATGTTTAAATGTTT-TCGATTGTACGATAACACTCTGTAACCCTAATCCAGTG
1 TTGAATGATATAATGTTTAAATGTTTCT-AATTGTACGATAACACTCTGTAACCCCAATCCAGCG
***
57522513 ACGAAGATGGGTTAGGGGTGTTACATG
65 ACGAAGACAAGTTAGGGGTGTTACATG
57522540 GAAAATGAAG
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
90 1 0.01
91 77 0.99
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.34
Consensus pattern (91 bp):
TTGAATGATATAATGTTTAAATGTTTCTAATTGTACGATAACACTCTGTAACCCCAATCCAGCGA
CGAAGACAAGTTAGGGGTGTTACATG
Found at i:57523410 original size:28 final size:26
Alignment explanation
Indices: 57523357--57523415 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 26
57523347 TTTTTGACAA
*
57523357 AAATATCAAATAGAGATTAAATTGTG
1 AAATATCAAATAGAGATTAAAATGTG
* *
57523383 AAATATGCAAATTGAGTGTTAAAATGTG
1 AAATAT-CAAATAGAG-ATTAAAATGTG
57523411 AAATA
1 AAATA
57523416 AATGAAAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 6 0.21
27 8 0.29
28 14 0.50
ACGTcount: A:0.49, C:0.03, G:0.17, T:0.31
Consensus pattern (26 bp):
AAATATCAAATAGAGATTAAAATGTG
Found at i:57523791 original size:34 final size:33
Alignment explanation
Indices: 57523741--57523829 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 33
57523731 AATGTTTTTA
* * *
57523741 AATTTATTTGTGTATGTATACATATATATTGCCG
1 AATTAATTTGTATATGTATA-ATATATATTACCG
57523775 AATTAATTTGTATATG--T-ATATATATTACCG
1 AATTAATTTGTATATGTATAATATATATTACCG
*
57523805 AATTGATTTGTATATGTAT-ATATAT
1 AATTAATTTGTATATGTATAATATAT
57523830 TGTTGAATTG
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 27 0.55
32 8 0.16
34 14 0.29
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (33 bp):
AATTAATTTGTATATGTATAATATATATTACCG
Found at i:57523838 original size:30 final size:30
Alignment explanation
Indices: 57523762--57523844 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
57523752 GTATGTATAC
*
57523762 ATATATATTGCCGAATTAATTTGTATATGT
1 ATATATATTGCCGAATTGATTTGTATATGT
*
57523792 ATATATATTACCGAATTGATTTGTATATGT
1 ATATATATTGCCGAATTGATTTGTATATGT
**
57523822 ATATATATTGTTGAATTGATTTG
1 ATATATATTGCCGAATTGATTTG
57523845 AGCATTGGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (30 bp):
ATATATATTGCCGAATTGATTTGTATATGT
Found at i:57527940 original size:13 final size:13
Alignment explanation
Indices: 57527923--57527981 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
57527913 CATTGCTGTG
57527923 GAAAAGTGCTTTT
1 GAAAAGTGCTTTT
* * * *
57527936 TAAAAGTACTGTG
1 GAAAAGTGCTTTT
57527949 GAAAAGTGCTTTT
1 GAAAAGTGCTTTT
* *
57527962 GAGAAGTGTTTTT
1 GAAAAGTGCTTTT
57527975 GAAAAGT
1 GAAAAGT
57527982 TTGGTTTAAA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (13 bp):
GAAAAGTGCTTTT
Found at i:57527968 original size:26 final size:26
Alignment explanation
Indices: 57527918--57527968 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
57527908 TTCTTCATTG
*
57527918 CTGTGGAAAAGTGCTTTTTAAAAGTA
1 CTGTGGAAAAGTGCTTTTGAAAAGTA
*
57527944 CTGTGGAAAAGTGCTTTTGAGAAGT
1 CTGTGGAAAAGTGCTTTTGAAAAGT
57527969 GTTTTTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.33
Consensus pattern (26 bp):
CTGTGGAAAAGTGCTTTTGAAAAGTA
Found at i:57528209 original size:24 final size:24
Alignment explanation
Indices: 57528175--57528220 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
57528165 TATATGAAAT
* *
57528175 ATAAATTTTAAATATTTTTAAACA
1 ATAAATATTAAATATTTATAAACA
*
57528199 ATAAATATTAATTATTTATAAA
1 ATAAATATTAAATATTTATAAA
57528221 ATTTAATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAACA
Found at i:57531478 original size:34 final size:33
Alignment explanation
Indices: 57531435--57531523 Score: 114
Period size: 30 Copynumber: 2.8 Consensus size: 33
57531425 AATGTTTTTA
*
57531435 AATTTATTTGTATATGTATACATATATATTCCCG
1 AATTTATTTGTATATGTATA-ATATATATGCCCG
*
57531469 AATTTATTTGTATATG--T-ATATATATGGCCG
1 AATTTATTTGTATATGTATAATATATATGCCCG
*
57531499 AATTGATTTGTATATGTAT-ATATAT
1 AATTTATTTGTATATGTATAATATAT
57531524 TGTCGAATTG
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
30 26 0.52
32 8 0.16
34 16 0.32
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (33 bp):
AATTTATTTGTATATGTATAATATATATGCCCG
Found at i:57531492 original size:30 final size:30
Alignment explanation
Indices: 57531456--57531538 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
57531446 ATATGTATAC
* *
57531456 ATATATATTCCCGAATTTATTTGTATATGT
1 ATATATATTGCCGAATTGATTTGTATATGT
*
57531486 ATATATATGGCCGAATTGATTTGTATATGT
1 ATATATATTGCCGAATTGATTTGTATATGT
*
57531516 ATATATATTGTCGAATTGATTTG
1 ATATATATTGCCGAATTGATTTG
57531539 AGCATTGGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (30 bp):
ATATATATTGCCGAATTGATTTGTATATGT
Found at i:57535440 original size:41 final size:41
Alignment explanation
Indices: 57535395--57535531 Score: 150
Period size: 41 Copynumber: 3.3 Consensus size: 41
57535385 GACTCAGTAC
* * **
57535395 CTAGCAGGCTT-GTTGCCAGTGAAACCATTCAGACTTTACGT
1 CTAGCAGGCTTAATT-CCAGTAAAAAAATTCAGACTTTACGT
*
57535436 CTAGCAGGCTTAATTCTAGTAAAAAAATTCAGACTTTACGT
1 CTAGCAGGCTTAATTCCAGTAAAAAAATTCAGACTTTACGT
* * * * *
57535477 CTAGCAGGCTTAATGCCGGTAAAATAAATTCGGACTATAAGT
1 CTAGCAGGCTTAATTCCAGTAAAA-AAATTCAGACTTTACGT
*
57535519 CTAGCGGGCTTAA
1 CTAGCAGGCTTAA
57535532 AGCTGGTGTA
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
41 54 0.66
42 28 0.34
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (41 bp):
CTAGCAGGCTTAATTCCAGTAAAAAAATTCAGACTTTACGT
Found at i:57544212 original size:23 final size:22
Alignment explanation
Indices: 57544169--57544212 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
57544159 AAAAAAAGGA
* * *
57544169 TAAAAATAGTTTAAATTGTAAG
1 TAAAAAGAATTTAAATGGTAAG
57544191 TAAAAAGAATTTAAATAGGTAA
1 TAAAAAGAATTTAAAT-GGTAA
57544213 ATACATCAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.32
Consensus pattern (22 bp):
TAAAAAGAATTTAAATGGTAAG
Found at i:57547169 original size:13 final size:13
Alignment explanation
Indices: 57547151--57547176 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57547141 GCCCAAACGT
57547151 CAAAATTTTCATA
1 CAAAATTTTCATA
57547164 CAAAATTTTCATA
1 CAAAATTTTCATA
57547177 GAATAATTCT
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:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
CAAAATTTTCATA
Found at i:57551111 original size:43 final size:43
Alignment explanation
Indices: 57551064--57551186 Score: 158
Period size: 43 Copynumber: 2.9 Consensus size: 43
57551054 GAAATCTTGT
*
57551064 ATCGATGCCAATAGCCCAGCTACGGTCTTATACGAAATCTCAA
1 ATCGATGCCAATAGCCCAGCTACGGTCTTACACGAAATCTCAA
* **
57551107 ATCGATGCCAATAGCCTAGCTATTGTCTTACACGAAATCTCAA
1 ATCGATGCCAATAGCCCAGCTACGGTCTTACACGAAATCTCAA
* * * *
57551150 ATTGATGTCAATAGCCCAGAC-ATGGTCTTACATGAAA
1 ATCGATGCCAATAGCCCAG-CTACGGTCTTACACGAAA
57551187 CCACACCTCG
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
43 69 0.99
44 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.26
Consensus pattern (43 bp):
ATCGATGCCAATAGCCCAGCTACGGTCTTACACGAAATCTCAA
Found at i:57551367 original size:31 final size:31
Alignment explanation
Indices: 57551306--57551400 Score: 129
Period size: 31 Copynumber: 3.1 Consensus size: 31
57551296 ATCCAATGCT
* *
57551306 CAAATC-AATTCGGCAATATATATCCATATA
1 CAAATCAAATTCGGCAATGTATAACCATATA
* *
57551336 CAAATCAAATTAGCCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATAACCATATA
*
57551367 CAAATCAAATTCGGCAATGTATAAAACATATA
1 CAAATCAAATTCGGCAATGTAT-AACCATATA
57551399 CA
1 CA
57551401 TTTAAATTCA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
30 6 0.11
31 40 0.71
32 10 0.18
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.26
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATAACCATATA
Found at i:57553935 original size:6 final size:6
Alignment explanation
Indices: 57553918--57553947 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
57553908 CAATAATATG
57553918 AAAATAT AAAATT AAAATT AAAATT AAAAT
1 AAAAT-T AAAATT AAAATT AAAATT AAAAT
57553948 GAAGTTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:57567918 original size:18 final size:18
Alignment explanation
Indices: 57567895--57567930 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
57567885 AAATTACATA
57567895 AAATTATGA-AAATATAAT
1 AAATTAT-ACAAATATAAT
57567913 AAATTATACAAATATAAT
1 AAATTATACAAATATAAT
57567931 GATCAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 16 0.94
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (18 bp):
AAATTATACAAATATAAT
Found at i:57568961 original size:27 final size:28
Alignment explanation
Indices: 57568857--57568963 Score: 80
Period size: 27 Copynumber: 3.8 Consensus size: 28
57568847 AAATAGGGTT
* * *
57568857 TTTTTTATAATTTTATAA-TATGATATA
1 TTTTTAATAATTTTATAATTTTTATATA
*
57568884 TTTTTCATAATTTTATATATACTTTCTATA-A
1 TTTTTAATAATTTTATA-AT--TTT-TATATA
*
57568915 TTTTCTATTAATTTT-T-ATTTTTATATA
1 TTTT-TAATAATTTTATAATTTTTATATA
*
57568942 TTTTT-GTAATTTTATAATTTTT
1 TTTTTAATAATTTTATAATTTTT
57568964 TAAACATTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
25 7 0.11
26 6 0.09
27 30 0.46
28 1 0.02
29 2 0.03
31 8 0.12
32 11 0.17
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (28 bp):
TTTTTAATAATTTTATAATTTTTATATA
Found at i:57591535 original size:25 final size:25
Alignment explanation
Indices: 57591477--57591535 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
57591467 TGTAAATAGA
* * * *
57591477 AAGCTCCTCCGAGCTGAATAACGGG
1 AAGCTCATGCGAGCTAAATAACAGG
*
57591502 AAGCTCATGCGAGCTAAATATCAGG
1 AAGCTCATGCGAGCTAAATAACAGG
57591527 AAGCTCATG
1 AAGCTCATG
57591536 AAAGTTGTGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (25 bp):
AAGCTCATGCGAGCTAAATAACAGG
Found at i:57595009 original size:10 final size:10
Alignment explanation
Indices: 57594996--57595062 Score: 64
Period size: 10 Copynumber: 6.4 Consensus size: 10
57594986 AAAAACAAAT
57594996 AAAGAAAGAA
1 AAAGAAAGAA
57595006 AAAGAAATAGAA
1 AAAG-AA-AGAA
*
57595018 ACAACAAACGAA
1 A-AAGAAA-GAA
57595030 AAAGAAAGAA
1 AAAGAAAGAA
* *
57595040 ACAGAAAG-G
1 AAAGAAAGAA
57595049 AAAGAAAGAA
1 AAAGAAAGAA
57595059 AAAG
1 AAAG
57595063 GGAAGGAAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
9 7 0.15
10 18 0.39
11 8 0.17
12 11 0.24
13 2 0.04
ACGTcount: A:0.73, C:0.06, G:0.19, T:0.01
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:57595070 original size:20 final size:19
Alignment explanation
Indices: 57595030--57595076 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
57595020 AACAAACGAA
*
57595030 AAAGAAAGAAACAGAAAGG
1 AAAGAAAGAAAAAGAAAGG
*
57595049 AAAGAAAGAAAAAGGGAAGG
1 AAAGAAAGAAAAA-GAAAGG
57595069 AAAGAAAG
1 AAAGAAAG
57595077 GAGAAAGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAGAAAGAAAAAGAAAGG
Found at i:57597454 original size:9 final size:9
Alignment explanation
Indices: 57597437--57597473 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
57597427 TGAGTTTTCG
57597437 AATTCGAAT
1 AATTCGAAT
*
57597446 AACTCGAAT
1 AATTCGAAT
57597455 AATTCGAAT
1 AATTCGAAT
57597464 AATTCGAAT
1 AATTCGAAT
57597473 A
1 A
57597474 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:57600147 original size:40 final size:40
Alignment explanation
Indices: 57600102--57600236 Score: 107
Period size: 40 Copynumber: 3.4 Consensus size: 40
57600092 GTTTGGAACA
*
57600102 AAAGCGCCACAAAAAATCGAGCATTAGCGGCGATTTATCC
1 AAAGCGCCACAAAAAATAGAGCATTAGCGGCGATTTATCC
* * **
57600142 AAAGCGCCGCTAAAGGTAGAGC-TTCAGCGGCGA-TTATCC
1 AAAGCGCCACAAAAAATAGAGCATT-AGCGGCGATTTATCC
* * * * * *
57600181 GGAAGCGCCGCTAAAAATAG-GAATTAGCGGCGTTTTA-CAT
1 -AAAGCGCCACAAAAAATAGAGCATTAGCGGCGATTTATC-C
*
57600221 AAAACGCCACAAAAAA
1 AAAGCGCCACAAAAAA
57600237 CCTAAGACCA
Statistics
Matches: 75, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
39 29 0.39
40 46 0.61
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (40 bp):
AAAGCGCCACAAAAAATAGAGCATTAGCGGCGATTTATCC
Found at i:57600210 original size:39 final size:39
Alignment explanation
Indices: 57600102--57600217 Score: 110
Period size: 40 Copynumber: 2.9 Consensus size: 39
57600092 GTTTGGAACA
* * *
57600102 AAAGCGCCACAAAAAATCGAGCATTAGCGGCGATTTATCC
1 AAAGCGCCGCTAAAAATAGAG-ATTAGCGGCGATTTATCC
** *
57600142 AAAGCGCCGCTAAAGGTAGAGCTTCAGCGGCGA-TTATCC
1 AAAGCGCCGCTAAAAATAGAGATT-AGCGGCGATTTATCC
* *
57600181 GGAAGCGCCGCTAAAAATAG-GAATTAGCGGCGTTTTA
1 -AAAGCGCCGCTAAAAATAGAG-ATTAGCGGCGATTTA
57600218 CATAAAACGC
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
39 16 0.26
40 45 0.74
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (39 bp):
AAAGCGCCGCTAAAAATAGAGATTAGCGGCGATTTATCC
Found at i:57600332 original size:41 final size:41
Alignment explanation
Indices: 57600275--57600454 Score: 272
Period size: 41 Copynumber: 4.4 Consensus size: 41
57600265 TTTTTTAAAC
*
57600275 CTTTAGCGGCGTTTTTGTGTAAGCGCCGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTGTGTAGGCGCCGCTAATGCTCGGAT
*
57600316 CTTTAGCGGCGTTTTTGTGTAGGCGTCGCTAATGCTC-GAGT
1 CTTTAGCGGCGTTTTTGTGTAGGCGCCGCTAATGCTCGGA-T
* *
57600357 CTTTAGCGGCGTTTTCGTGTAGGCGCCTCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTGTGTAGGCGCCGCTAATGCTCGGAT
* * *
57600398 CTTTAGCGGCGTTTTTGTCTATGCGCCGCTAATGCTTGGAT
1 CTTTAGCGGCGTTTTTGTGTAGGCGCCGCTAATGCTCGGAT
*
57600439 CTTTATCGGCGTTTTT
1 CTTTAGCGGCGTTTTT
57600455 AACTGAGCGC
Statistics
Matches: 126, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
40 2 0.02
41 122 0.97
42 2 0.02
ACGTcount: A:0.12, C:0.22, G:0.28, T:0.38
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGTGTAGGCGCCGCTAATGCTCGGAT
Found at i:57600465 original size:82 final size:81
Alignment explanation
Indices: 57600275--57600513 Score: 252
Period size: 82 Copynumber: 2.9 Consensus size: 81
57600265 TTTTTTAAAC
* * * *
57600275 CTTTAGCGGCGTTTTTGTGTAAGCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTTGTGTAGGC
1 CTTTAGCGGCGTTTTCGTGT-AGCGCCACTAATGCTCGGATCTTTAGCGGCGTTTTTGTCTAAGC
*
57600340 GTCGCTAATGCTCGAGT
65 GCCGCTAATGCTCGAGT
* *
57600357 CTTTAGCGGCGTTTTCGTGTAGGCGCCTCTAATGCTCGGATCTTTAGCGGCGTTTTTGTCTATGC
1 CTTTAGCGGCGTTTTCGTGTA-GCGCCACTAATGCTCGGATCTTTAGCGGCGTTTTTGTCTAAGC
*
57600422 GCCGCTAATGCTTG-GAT
65 GCCGCTAATGCTCGAG-T
* * * * * * *
57600439 CTTTATCGGCGTTTTTAAC-TG-AGCGCCACTAATTCTCTTG-TCTTCAGCGGTGTTTGTATCTA
1 CTTTAGCGGCG-TTTT--CGTGTAGCGCCACTAATGCTC-GGATCTTTAGCGGCGTTTTTGTCTA
57600501 AGCGCCGCTAATG
62 AGCGCCGCTAATG
57600514 TATTTACCTT
Statistics
Matches: 136, Mismatches: 15, Indels: 12
0.83 0.09 0.07
Matches are distributed among these distances:
81 2 0.01
82 125 0.92
83 6 0.04
84 2 0.01
85 1 0.01
ACGTcount: A:0.14, C:0.23, G:0.27, T:0.36
Consensus pattern (81 bp):
CTTTAGCGGCGTTTTCGTGTAGCGCCACTAATGCTCGGATCTTTAGCGGCGTTTTTGTCTAAGCG
CCGCTAATGCTCGAGT
Found at i:57600506 original size:123 final size:123
Alignment explanation
Indices: 57600275--57600553 Score: 287
Period size: 123 Copynumber: 2.3 Consensus size: 123
57600265 TTTTTTAAAC
* *
57600275 CTTTAGCGGCGTTTTTGTGTAAGCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTTGTGTAGGC
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTTCTGTAGGC
* * * * * * *
57600340 GTCGCTAATGCTCGAGTCTTTAGCGGCGTTTTCGTGTAGGCGCCTCTAATGCTCGGAT
66 GCCACTAATGCTCGAGTCTTCAGCGGCGTTTTCATCTAAGCGCCGCTAATGCTCGGAT
* * *
57600398 CTTTAGCGGCGTTTTTGTCTATGCGCCGCTAATGCTTGGATCTTTATCGGCGTTTTTAACTG-A-
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTT--CTGTAG
* ** * *** *
57600461 GCGCCACTAATTCTCTTGTCTTCAGCGGTGTTTGT-ATCTAAGCGCCGCTAATG-TATTTAC
64 GCGCCACTAATGCTCGAGTCTTCAGCGGCGTTT-TCATCTAAGCGCCGCTAATGCT-CGGAT
** *
57600521 CTTTAGCGGCGTTTTTACCGAAGCGCCGCTAAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAAT
57600554 AGTAACAAAA
Statistics
Matches: 128, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
122 1 0.01
123 123 0.96
124 2 0.02
125 2 0.02
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (123 bp):
CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTTCTGTAGGC
GCCACTAATGCTCGAGTCTTCAGCGGCGTTTTCATCTAAGCGCCGCTAATGCTCGGAT
Found at i:57600987 original size:16 final size:17
Alignment explanation
Indices: 57600966--57600997 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
57600956 TACGGGGTAT
57600966 AGATTTAAGG-TAATTG
1 AGATTTAAGGTTAATTG
57600982 AGATTTAAGGTTAATT
1 AGATTTAAGGTTAATT
57600998 TAGGGGTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.41
Consensus pattern (17 bp):
AGATTTAAGGTTAATTG
Found at i:57605389 original size:23 final size:23
Alignment explanation
Indices: 57605356--57605402 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
57605346 AATATTATAC
57605356 ATAACTGACAACTTACATAACTT
1 ATAACTGACAACTTACATAACTT
*
57605379 ATAACTTACAACTTACATAACTT
1 ATAACTGACAACTTACATAACTT
57605402 A
1 A
57605403 CATTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.32
Consensus pattern (23 bp):
ATAACTGACAACTTACATAACTT
Found at i:57605398 original size:16 final size:16
Alignment explanation
Indices: 57605353--57605405 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
57605343 ATTAATATTA
*
57605353 TACATAACTGACAACT
1 TACATAACTTACAACT
*
57605369 TACATAACTTATAACT
1 TACATAACTTACAACT
57605385 TAC--AACTTACATAACT
1 TACATAACTTAC--AACT
57605401 TACAT
1 TACAT
57605406 TTTTTAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 6 0.20
16 24 0.80
ACGTcount: A:0.43, C:0.23, G:0.02, T:0.32
Consensus pattern (16 bp):
TACATAACTTACAACT
Found at i:57605487 original size:65 final size:63
Alignment explanation
Indices: 57605325--57605942 Score: 371
Period size: 65 Copynumber: 9.6 Consensus size: 63
57605315 ACCCATCTCT
* * * *
57605325 AATTACATAACTTAGTTAATTAATATTATACATAACTGAC--AACTTACA-TAA-CTTATAACTT
1 AATTACATAACTTA-TTAATTAATATTATACATAAATTACATAACTTA-ATTAATATTAT-ACAT
57605386 A
63 A
* * * *
57605387 CAACTTACATAACTTACATT-TTTTA-ATTATTCATAAATTACATAACATACATTAATATTATAC
1 -AA-TTACATAACTT--ATTAATTAATATTATACATAAATTACATAACTTA-ATTAATATTATAC
57605450 ATA
61 ATA
*
57605453 AATTACATAACTTAGTTAATTAATATTATACATAAATTACATAACTTAATT-TTATGT-T-C-T-
1 AATTACATAACTTA-TTAATTAATATTATACATAAATTACATAACTTAATTAATAT-TATACATA
* * *
57605513 TA-TACATAACTTA--CATTAATATTATACATAAATTACATAACTTAATT-TTATGT-T--AT-
1 AATTACATAACTTATTAATTAATATTATACATAAATTACATAACTTAATTAATAT-TATACATA
* * *
57605569 TA-TACATAACTTA--CATTAATATTATACATAAATTACATAACTTAATTAATTAATATACATA
1 AATTACATAACTTATTAATTAATATTATACATAAATTACATAACTTAATTAA-TATTATACATA
* * *
57605630 AGTTACATAACTTA--CATTAATATGATACATAAATTACATAACTTAGTTAATTAATATTATACA
1 AATTACATAACTTATTAATTAATATTATACATAAATTACATAAC----TTAATTAATATTATACA
57605693 TA
62 TA
** *
57605695 TGTTACATAACTTA-T-ATTAATATGATACATAAATTACATAACTTAGTTAATTAATATTATACA
1 AATTACATAACTTATTAATTAATATTATACATAAATTACATAAC----TTAATTAATATTATACA
57605758 TA
62 TA
* * * **
57605760 ACTTAC--AACTTACATAACTTACA-ACTTACAACTTACATAACTTACATAACTTACATTTTTTT
1 AATTACATAACTTA-TTAA-TTA-ATA-TT---A--TACATAAATTACATAACTTA-A--TTAAT
*
57605822 AATTATTCATA
54 -ATTATACATA
* *
57605833 AATTACATAACTTAATTAGTTAATATACATAAATTACATAACTTA-ATTAA-TTAATTAATATTA
1 AATTACATAACTT-ATTAATTAATAT---T--A-TACATAAATTACA-TAACTTAATTAATATTA
57605896 TACATA
58 TACATA
*
57605902 AATTACATAACTTAGTTAATTAATATTATACATAATTTACA
1 AATTACATAACTTA-TTAATTAATATTATACATAAATTACA
57605943 ACTTACATAA
Statistics
Matches: 468, Mismatches: 38, Indels: 97
0.78 0.06 0.16
Matches are distributed among these distances:
56 88 0.19
57 1 0.00
58 3 0.01
59 11 0.02
60 3 0.01
61 1 0.00
62 40 0.09
63 37 0.08
64 34 0.07
65 111 0.24
66 18 0.04
67 8 0.02
68 3 0.01
69 35 0.07
70 4 0.01
71 1 0.00
72 4 0.01
73 36 0.08
74 19 0.04
75 9 0.02
76 2 0.00
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (63 bp):
AATTACATAACTTATTAATTAATATTATACATAAATTACATAACTTAATTAATATTATACATA
Found at i:57605531 original size:56 final size:59
Alignment explanation
Indices: 57605471--57605766 Score: 342
Period size: 56 Copynumber: 5.0 Consensus size: 59
57605461 AACTTAGTTA
57605471 ATTAATATTATACATAAATTACATAACTTAATT-TT-ATGTTC-TTATACATAACTTAC
1 ATTAATATTATACATAAATTACATAACTTAATTATTAATGTTCATTATACATAACTTAC
57605527 ATTAATATTATACATAAATTACATAACTTAATT-TT-ATGTT-ATTATACATAACTTAC
1 ATTAATATTATACATAAATTACATAACTTAATTATTAATGTTCATTATACATAACTTAC
* * *
57605583 ATTAATATTATACATAAATTACATAACTTAATTAATTAATATACATAAGTTACATAACTTAC
1 ATTAATATTATACATAAATTACATAACTTAATT-ATTAATGTTCATTA--TACATAACTTAC
* * * * *
57605645 ATTAATATGATACATAAATTACATAACTTAGTTAATTAATATTATACATATGTTACATAACTTAT
1 ATTAATATTATACATAAATTACATAACTTAATT-ATTAAT-GT-T-CAT-T-ATACATAACTTAC
* *
57605710 ATTAATATGATACATAAATTACATAACTTAGTTAATTAA---T-ATTATACATAACTTAC
1 ATTAATATTATACATAAATTACATAACTTAATT-ATTAATGTTCATTATACATAACTTAC
57605766 A
1 A
57605767 ACTTACATAA
Statistics
Matches: 216, Mismatches: 12, Indels: 24
0.86 0.05 0.10
Matches are distributed among these distances:
56 100 0.46
57 1 0.00
58 4 0.02
59 3 0.01
60 4 0.02
62 50 0.23
63 1 0.00
65 53 0.25
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.42
Consensus pattern (59 bp):
ATTAATATTATACATAAATTACATAACTTAATTATTAATGTTCATTATACATAACTTAC
Found at i:57605532 original size:30 final size:30
Alignment explanation
Indices: 57605498--57605593 Score: 85
Period size: 30 Copynumber: 3.3 Consensus size: 30
57605488 ATTACATAAC
*
57605498 TTAATTTTATGTTCTTATACATAACTTACA
1 TTAATATTATGTTCTTATACATAACTTACA
* * * *
57605528 TTAATATTA--TAC--ATAAATTACATA-A
1 TTAATATTATGTTCTTATACATAACTTACA
* *
57605553 CTTAATTTTATGTTATTATACATAACTTACA
1 -TTAATATTATGTTCTTATACATAACTTACA
57605584 TTAATATTAT
1 TTAATATTAT
57605594 ACATAAATTA
Statistics
Matches: 48, Mismatches: 12, Indels: 12
0.67 0.17 0.17
Matches are distributed among these distances:
25 1 0.02
26 17 0.35
28 3 0.06
30 26 0.54
31 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (30 bp):
TTAATATTATGTTCTTATACATAACTTACA
Found at i:57605593 original size:25 final size:25
Alignment explanation
Indices: 57605490--57605593 Score: 77
Period size: 25 Copynumber: 3.9 Consensus size: 25
57605480 ATACATAAAT
* * *
57605490 TACATAACTTAATTTTATGTTCTTA
1 TACATAACTTAATTTAATATTATTA
57605515 TACATAACTTACA-TTAATATTATACATAAA
1 TACATAACTTA-ATTTAATATTAT---T--A
* *
57605545 TTACATAACTTAATTTTATGTTATTA
1 -TACATAACTTAATTTAATATTATTA
57605571 TACATAACTTACA-TTAATATTAT
1 TACATAACTTA-ATTTAATATTAT
57605594 ACATAAATTA
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
25 37 0.59
26 3 0.05
28 2 0.03
30 2 0.03
31 19 0.30
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.46
Consensus pattern (25 bp):
TACATAACTTAATTTAATATTATTA
Found at i:57605594 original size:22 final size:22
Alignment explanation
Indices: 57605566--57605668 Score: 76
Period size: 22 Copynumber: 4.9 Consensus size: 22
57605556 AATTTTATGT
*
57605566 TATTATACATAACTTACATTAA
1 TATTATACATAAATTACATTAA
57605588 TATTATACATAAATTACA-T-A
1 TATTATACATAAATTACATTAA
* *
57605608 -ACT-TA-ATTAATTA-ATATACA
1 TATTATACATAAATTACAT-TA-A
* *
57605628 TAAGT-TACATAACTTACATTAA
1 T-ATTATACATAAATTACATTAA
*
57605650 TATGATACATAAATTACAT
1 TATTATACATAAATTACAT
57605669 AACTTAGTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
16 1 0.02
17 7 0.11
18 3 0.05
19 2 0.03
20 2 0.03
21 2 0.03
22 36 0.57
23 8 0.13
24 2 0.03
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.39
Consensus pattern (22 bp):
TATTATACATAAATTACATTAA
Found at i:57605771 original size:7 final size:7
Alignment explanation
Indices: 57605759--57605796 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
57605749 TATTATACAT
57605759 AACTTAC
1 AACTTAC
57605766 AACTTAC
1 AACTTAC
57605773 ATAACTTAC
1 --AACTTAC
57605782 AACTTAC
1 AACTTAC
57605789 AACTTAC
1 AACTTAC
57605796 A
1 A
57605797 TAACTTACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 22 0.76
9 7 0.24
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (7 bp):
AACTTAC
Found at i:57605775 original size:16 final size:16
Alignment explanation
Indices: 57605754--57605814 Score: 90
Period size: 16 Copynumber: 3.8 Consensus size: 16
57605744 ATTAATATTA
57605754 TACATAACTTACAACT
1 TACATAACTTACAACT
57605770 TACATAACTTACAACT
1 TACATAACTTACAACT
57605786 TAC--AACTTACATAACT
1 TACATAACTTAC--AACT
57605802 TACATAACTTACA
1 TACATAACTTACA
57605815 TTTTTTTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 7 0.17
16 27 0.66
18 7 0.17
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (16 bp):
TACATAACTTACAACT
Found at i:57605778 original size:9 final size:9
Alignment explanation
Indices: 57605720--57606130 Score: 95
Period size: 9 Copynumber: 48.3 Consensus size: 9
57605710 ATTAATATGA
*
57605720 TACATAAAT
1 TACATAACT
57605729 TACATAACT
1 TACATAACT
**
57605738 TAGTTAA-T
1 TACATAACT
*
57605746 TA-AT-ATT
1 TACATAACT
57605753 ATACATAACT
1 -TACATAACT
57605763 TAC--AACT
1 TACATAACT
57605770 TACATAACT
1 TACATAACT
57605779 TAC--AACT
1 TACATAACT
57605786 TAC--AACT
1 TACATAACT
57605793 TACATAACT
1 TACATAACT
57605802 TACATAACT
1 TACATAACT
***
57605811 TACATTTTTT
1 TACA-TAACT
*
57605821 TA-ATTA-T
1 TACATAACT
*
57605828 T-CATAAAT
1 TACATAACT
57605836 TACATAACT
1 TACATAACT
* *
57605845 TA-ATTAGT
1 TACATAACT
57605853 TA-AT-A--
1 TACATAACT
*
57605858 TACATAAAT
1 TACATAACT
57605867 TACATAACT
1 TACATAACT
57605876 TA-ATTAA-T
1 TACA-TAACT
*
57605884 TA-ATTAATATT
1 TACA-T-A-ACT
*
57605895 ATACATAAAT
1 -TACATAACT
57605905 TACATAACT
1 TACATAACT
**
57605914 TAGTTAA-T
1 TACATAACT
*
57605922 TA-AT-ATT
1 TACATAACT
*
57605929 ATACATAATT
1 -TACATAACT
57605939 TAC--AACT
1 TACATAACT
57605946 TACATAACT
1 TACATAACT
***
57605955 TACAATTTTT
1 TAC-ATAACT
*
57605965 TA-ATTA-T
1 TACATAACT
* *
57605972 T-CGTAAAT
1 TACATAACT
57605980 TACATAACT
1 TACATAACT
* *
57605989 TACTTAATT
1 TACATAACT
*
57605998 TTCATAA--
1 TACATAACT
*
57606005 TAAATAACT
1 TACATAACT
57606014 TACATAACT
1 TACATAACT
57606023 TAC--AACT
1 TACATAACT
57606030 TACATAACT
1 TACATAACT
* ** *
57606039 TATACGACA
1 TACATAACT
57606048 TACATAACT
1 TACATAACT
* *
57606057 TACATAGCA
1 TACATAACT
*
57606066 TA-ATTTGACT
1 TACA--TAACT
*
57606076 AATACACAACT
1 --TACATAACT
*
57606087 TACATAATT
1 TACATAACT
*
57606096 TTCATAA--
1 TACATAACT
*
57606103 TAAATAACT
1 TACATAACT
57606112 TACATAA--
1 TACATAACT
57606119 TACATAACT
1 TACATAACT
57606128 TAC
1 TAC
57606131 GTAGCTTAGT
Statistics
Matches: 301, Mismatches: 56, Indels: 90
0.67 0.13 0.20
Matches are distributed among these distances:
5 2 0.01
6 4 0.01
7 66 0.22
8 35 0.12
9 163 0.54
10 19 0.06
11 5 0.02
12 5 0.02
13 2 0.01
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.39
Consensus pattern (9 bp):
TACATAACT
Found at i:57605789 original size:23 final size:24
Alignment explanation
Indices: 57605754--57605814 Score: 97
Period size: 23 Copynumber: 2.5 Consensus size: 24
57605744 ATTAATATTA
57605754 TACATAACTTACAACTTACATAACT
1 TACA-AACTTACAACTTACATAACT
57605779 TAC-AACTTACAACTTACATAACT
1 TACAAACTTACAACTTACATAACT
57605802 TACATAACTTACA
1 TACA-AACTTACA
57605815 TTTTTTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 23 0.68
25 11 0.32
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (24 bp):
TACAAACTTACAACTTACATAACT
Found at i:57606029 original size:16 final size:16
Alignment explanation
Indices: 57606010--57606060 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
57606000 CATAATAAAT
57606010 AACTTACATAACTTAC
1 AACTTACATAACTTAC
57606026 AACTTACATAACTTATAC
1 AACTTACATAAC-T-TAC
* *
57606044 GACATACATAACTTAC
1 AACTTACATAACTTAC
57606060 A
1 A
57606061 TAGCATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 15 0.50
17 2 0.07
18 13 0.43
ACGTcount: A:0.45, C:0.24, G:0.02, T:0.29
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:57606109 original size:16 final size:16
Alignment explanation
Indices: 57606098--57606130 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
57606088 ACATAATTTT
57606098 CATAATAAATAACTTA
1 CATAATAAATAACTTA
*
57606114 CATAATACATAACTTA
1 CATAATAAATAACTTA
57606130 C
1 C
57606131 GTAGCTTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (16 bp):
CATAATAAATAACTTA
Found at i:57611667 original size:66 final size:65
Alignment explanation
Indices: 57611560--57611730 Score: 209
Period size: 66 Copynumber: 2.6 Consensus size: 65
57611550 GAACAAATTA
* * * *
57611560 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
57611624 G
65 G
* *
57611625 CTACAACTGAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
57611690 G
65 G
* * * * *
57611691 CAGCAGCTTAAAGTAGATGCGGCAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
57611731 CGGCAGCGAG
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 2 0.02
66 85 0.93
67 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.28, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:57611752 original size:21 final size:21
Alignment explanation
Indices: 57611709--57611752 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
57611699 TAAAGTAGAT
*
57611709 GCGGCAGCAAGAGAAGCAGAG
1 GCGGCAGCAAGAGAAGCACAG
* *
57611730 GCGGCAGCGAGAGAAGTACAG
1 GCGGCAGCAAGAGAAGCACAG
57611751 GC
1 GC
57611753 TAAAGCGAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.43, T:0.02
Consensus pattern (21 bp):
GCGGCAGCAAGAGAAGCACAG
Found at i:57611773 original size:21 final size:21
Alignment explanation
Indices: 57611721--57611792 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
57611711 GGCAGCAAGA
* * *
57611721 GAAGCAGAGGCGGCAGCGAGA
1 GAAGCAGAGGCTGAAGCGAGG
* * *
57611742 GAAGTACAGGCTAAAGCGAGG
1 GAAGCAGAGGCTGAAGCGAGG
*
57611763 GAAGCAGAGGCTGTAGCGAGG
1 GAAGCAGAGGCTGAAGCGAGG
57611784 GAAGCAGAG
1 GAAGCAGAG
57611793 CAGCGTCAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.35, C:0.15, G:0.44, T:0.06
Consensus pattern (21 bp):
GAAGCAGAGGCTGAAGCGAGG
Found at i:57612197 original size:43 final size:42
Alignment explanation
Indices: 57612150--57612454 Score: 177
Period size: 43 Copynumber: 7.1 Consensus size: 42
57612140 GGCCTTTAGT
* * *
57612150 GGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGGCTTTGGC
1 GGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGTCTTT-GC
** * ** *
57612193 GGCGTTTGTGGAAAAAGCGCCACTAAAGATCATAGTCTTTAAC
1 GGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGTCTTT-GC
*
57612236 GGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGTCTATTGC
1 GGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGTCT-TTGC
* ** * ** * *
57612279 GGCGTTTGAGGGGAAAGCGCCGCTAAAGACCCTGATCTTTAGT
1 GGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGTCTTT-GC
* * * * *
57612322 GGCGTTTTTGG-GAGAAGTGCCGCTAAAGATAAGGATCTTTAGC
1 GGCGTTTGTGGTCA-AAGCGCCGCTAAAGATCAGGGTCTTT-GC
** * * **
57612365 GGCGTTTAAGAG--AGAAGCGTCGCTAAAGACCATTGTCTTTAGC
1 GGCGTTTGTG-GTCA-AAGCGCCGCTAAAGATCAGGGTCTTT-GC
* * ** *
57612408 GGCGCTTCT-CCCAAAAACGCCGCTAAAGATCAGGGTCTTTAGC
1 GGCGTTTGTGGTC-AAAGCGCCGCTAAAGATCAGGGTCTTT-GC
57612451 GGCG
1 GGCG
57612455 CTTCCACTAA
Statistics
Matches: 203, Mismatches: 52, Indels: 14
0.75 0.19 0.05
Matches are distributed among these distances:
42 4 0.02
43 195 0.96
44 4 0.02
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (42 bp):
GGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGTCTTTGC
Found at i:57612263 original size:86 final size:85
Alignment explanation
Indices: 57612150--57612454 Score: 278
Period size: 86 Copynumber: 3.5 Consensus size: 85
57612140 GGCCTTTAGT
* *
57612150 GGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGGCTTTGGCGGCGTTTGTGGAAAAAGCGCCA
1 GGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTT-GCGGCGTTTGAGGAAAAAGCGCCA
*
57612215 CTAAAGATCAT-AGTCTTTAAC
65 CTAAAGACCATGA-TCTTTAAC
* ** *
57612236 GGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGTCTATTGCGGCGTTTGAGGGGAAAGCGCCG
1 GGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCT-TTGCGGCGTTTGAGGAAAAAGCGCCA
* **
57612301 CTAAAGACCCTGATCTTTAGT
65 CTAAAGACCATGATCTTTAAC
* * * * * *
57612322 GGCGTTTTTGG-GAGAAGTGCCGCTAAAGATAAGGATCTTTAGCGGCGTTT-AAGAGAGAAGCGT
1 GGCGTTTTTGGTCA-AAGCGCCGCTAAAGATAAGGGTCTTT-GCGGCGTTTGAGGA-AAAAGCGC
* *
57612385 CGCTAAAGACCATTG-TCTTTAGC
63 CACTAAAGACCA-TGATCTTTAAC
* * ** * *
57612408 GGCGCTTCT-CCCAAAAACGCCGCTAAAGATCAGGGTCTTTAGCGGCG
1 GGCGTTTTTGGTC-AAAGCGCCGCTAAAGATAAGGGTCTTT-GCGGCG
57612455 CTTCCACTAA
Statistics
Matches: 182, Mismatches: 29, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
85 5 0.03
86 171 0.94
87 6 0.03
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (85 bp):
GGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTGCGGCGTTTGAGGAAAAAGCGCCAC
TAAAGACCATGATCTTTAAC
Found at i:57612455 original size:43 final size:42
Alignment explanation
Indices: 57612385--57612477 Score: 123
Period size: 43 Copynumber: 2.2 Consensus size: 42
57612375 AGAGAAGCGT
** *
57612385 CGCTAAAGACCATTGTCTTTAGCGGCGCTTCTCCCAAAAACGC
1 CGCTAAAGACCAGGGTCTTTAGCGGCGCTTC-CACAAAAACGC
* * *
57612428 CGCTAAAGATCAGGGTCTTTAGCGGCGCTTCCACTAAAGCGC
1 CGCTAAAGACCAGGGTCTTTAGCGGCGCTTCCACAAAAACGC
57612470 CGCTAAAG
1 CGCTAAAG
57612478 GTCTTAGTCT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 16 0.36
43 28 0.64
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.22
Consensus pattern (42 bp):
CGCTAAAGACCAGGGTCTTTAGCGGCGCTTCCACAAAAACGC
Found at i:57612488 original size:42 final size:43
Alignment explanation
Indices: 57612385--57612496 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 43
57612375 AGAGAAGCGT
* ** *
57612385 CGCTAAAGACCATTGTCTTTAGCGGCGCTTCTCCCAAAAACGC
1 CGCTAAAGATCAGAGTCTTTAGCGGCGCTTCTCACAAAAACGC
* * *
57612428 CGCTAAAGATCAGGGTCTTTAGCGGCGCTTC-CACTAAAGCGC
1 CGCTAAAGATCAGAGTCTTTAGCGGCGCTTCTCACAAAAACGC
* ** *
57612470 CGCTAAAGGTCTTAGTCTTCAGCGGCG
1 CGCTAAAGATCAGAGTCTTTAGCGGCG
57612497 TTTGTGCAAG
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
42 30 0.52
43 28 0.48
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.23
Consensus pattern (43 bp):
CGCTAAAGATCAGAGTCTTTAGCGGCGCTTCTCACAAAAACGC
Found at i:57612620 original size:22 final size:22
Alignment explanation
Indices: 57612592--57612634 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
57612582 CTGCGGCGCT
*
57612592 AAAAAGCACCGCTAAAGGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
*
57612614 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCACCGCTAAAAGCCT
57612635 GTTTTAGTGT
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:57624295 original size:19 final size:17
Alignment explanation
Indices: 57624265--57624318 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 17
57624255 GTTTTAGGGT
*
57624265 TTTTAATTTTTTAAATAG
1 TTTTAAATTTTTAAA-AG
57624283 TTTTAAATATTTTATAAAG
1 TTTTAAAT-TTTTA-AAAG
*
57624302 TATATAAATTTTTAAAA
1 T-TTTAAATTTTTAAAA
57624319 CATGTTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 10 0.32
19 13 0.42
20 8 0.26
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTTAAATTTTTAAAAG
Found at i:57626854 original size:108 final size:109
Alignment explanation
Indices: 57626658--57626880 Score: 349
Period size: 108 Copynumber: 2.1 Consensus size: 109
57626648 TGGGAACATG
* *
57626658 TTTTTTTATACACATGGAATCAAACTAATCTCTAAATATAAGTAAAGAATTATATTTAAATGCTT
1 TTTTTTTATACACATGGAATCAAACCAATCTCTAAATACAAGTAAAGAATTATATTTAAATGCTT
*
57626723 TTATATCAAAATTCGACA-CTTTTTCCTAATTTCGCATCTAAAT
66 TTATACCAAAATTCGACATCTTTTTCCTAATTTCGCATCTAAAT
*
57626766 TTTTTTTATACACATGGAATCAAACCAATCTTTAAATACAAGTAAAGAATTATATTTAAATGCTT
1 TTTTTTTATACACATGGAATCAAACCAATCTCTAAATACAAGTAAAGAATTATATTTAAATGCTT
** * * * *
57626831 TTATACCTGAATTCGATATTTTTTTCTTAATTTCGTATCTAAAT
66 TTATACCAAAATTCGACATCTTTTTCCTAATTTCGCATCTAAAT
57626875 TTTTTT
1 TTTTTT
57626881 GGGTCTAATT
Statistics
Matches: 104, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
108 76 0.73
109 28 0.27
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (109 bp):
TTTTTTTATACACATGGAATCAAACCAATCTCTAAATACAAGTAAAGAATTATATTTAAATGCTT
TTATACCAAAATTCGACATCTTTTTCCTAATTTCGCATCTAAAT
Found at i:57627479 original size:3 final size:3
Alignment explanation
Indices: 57627471--57627507 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
57627461 AAGGGCCTTA
57627471 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
57627508 TAGATAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:57628075 original size:26 final size:26
Alignment explanation
Indices: 57628019--57628075 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
57628009 TTTGAATTTG
* *
57628019 AATAGTATTTAATAAAAAATATTATT
1 AATAGTATTTAATAAAAAAAATTATA
*
57628045 GATAGTATTTAATAAAAATAAATTA-A
1 AATAGTATTTAATAAAAA-AAATTATA
57628071 AATAG
1 AATAG
57628076 ATAGTTGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (26 bp):
AATAGTATTTAATAAAAAAAATTATA
Found at i:57628399 original size:17 final size:16
Alignment explanation
Indices: 57628342--57628382 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
57628332 TAAAAGTCCA
57628342 AAAAATATATATTTAAT
1 AAAAATATAT-TTTAAT
*
57628359 AAAAAGTATATTTTATT
1 AAAAA-TATATTTTAAT
57628376 AAAAATA
1 AAAAATA
57628383 AAAATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 15 0.68
18 5 0.23
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAAATATATTTTAAT
Found at i:57629504 original size:108 final size:107
Alignment explanation
Indices: 57629278--57629606 Score: 448
Period size: 108 Copynumber: 3.1 Consensus size: 107
57629268 GGCATGGATT
* * *
57629278 AAAATTCAAGAGGATATTTGGCTATTTGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGGC
1 AAAATTTAAAAGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGC
* * * *
57629341 ACG-TTCCTCGAATTTCTAAACGCAAAACATTGCCTTATTTTGA
66 ACGTTTTCTCGAA-TTCCAAACGCAAAATATTGCCTTACTTT-A
** * *
57629384 AATTTTTGAAAGGATATTTGGCTATTTGGTTGAATGAGAAAAATCGAAACCCAGCACATTAGGGC
1 AAAATTTAAAAGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGC
* *
57629449 ACGTTTTCTCAAATCTCCAAACGCAAAATATTACCTTACTTTA
66 ACGTTTTCTCGAAT-TCCAAACGCAAAATATTGCCTTACTTTA
** * *
57629492 AAAATTTAAAAGGATATTTAACTATTTGGTTGAACGAGAAAAATCGAAACCCAGCAGATTAGAGC
1 AAAATTTAAAAGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGC
57629557 ACGTTTTCTCGAATTCCCAAACGCAAAATATTGCCTTACTTTA
66 ACGTTTTCTCGAATT-CCAAACGCAAAATATTGCCTTACTTTA
57629600 AAAATTT
1 AAAATTT
57629607 TTCCTTTTTG
Statistics
Matches: 195, Mismatches: 23, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
106 31 0.16
107 1 0.01
108 133 0.68
109 30 0.15
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (107 bp):
AAAATTTAAAAGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGC
ACGTTTTCTCGAATTCCAAACGCAAAATATTGCCTTACTTTA
Found at i:57629747 original size:4 final size:4
Alignment explanation
Indices: 57629738--57629814 Score: 59
Period size: 4 Copynumber: 18.8 Consensus size: 4
57629728 ATACAATAAC
* ** * *
57629738 AAAT AAAT AAAT AAAT AAACT AAA- ACAT AAA- AAAT GGAC ATAT AAAT
1 AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAAT
57629785 AAAT AAAT AAAT AAAT GAACAT AAAGT AAA
1 AAAT AAAT AAAT AAAT -AA-AT AAA-T AAA
57629815 ATAATAATAA
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
3 5 0.09
4 39 0.67
5 12 0.21
6 2 0.03
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:57629853 original size:23 final size:21
Alignment explanation
Indices: 57629802--57629854 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
57629792 TAAATAAATG
* *
57629802 AACATAAAGTAAAATAATAAT
1 AACATAAAGGAAAATAATAAA
57629823 AACAATAAAGGAAAATAGATAAA
1 AAC-ATAAAGGAAAATA-ATAAA
57629846 AATCATAAA
1 AA-CATAAA
57629855 ATATGAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 3 0.11
22 12 0.44
23 11 0.41
24 1 0.04
ACGTcount: A:0.68, C:0.06, G:0.08, T:0.19
Consensus pattern (21 bp):
AACATAAAGGAAAATAATAAA
Found at i:57629957 original size:16 final size:16
Alignment explanation
Indices: 57629920--57629958 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
57629910 AATTATAAAA
57629920 ATATATAAAAACATGT
1 ATATATAAAAACATGT
* **
57629936 ACATATAAAAGTATGT
1 ATATATAAAAACATGT
57629952 ATATATA
1 ATATATA
57629959 TGTATACTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (16 bp):
ATATATAAAAACATGT
Found at i:57630214 original size:15 final size:16
Alignment explanation
Indices: 57630189--57630219 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
57630179 ATATCCTAAA
57630189 ATATGAAAATACATAT
1 ATATGAAAATACATAT
57630205 ATAT-AAAATACATAT
1 ATATGAAAATACATAT
57630220 TTTAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (16 bp):
ATATGAAAATACATAT
Found at i:57630289 original size:41 final size:42
Alignment explanation
Indices: 57630244--57630334 Score: 98
Period size: 41 Copynumber: 2.2 Consensus size: 42
57630234 GAATATGTAA
* * *
57630244 GTATATATATATTTATGAAA-ATAA-AATAATTATATAGACAC
1 GTATATATAAAATTATGAAATATAAGAA-AAATATATAGACAC
* **
57630285 GTATA-AAAAAATTATGAAATATAAGAAAAATATATAGGTAC
1 GTATATATAAAATTATGAAATATAAGAAAAATATATAGACAC
57630326 GTATATATA
1 GTATATATA
57630335 CATATGTAGA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
40 11 0.28
41 25 0.62
42 4 0.10
ACGTcount: A:0.54, C:0.03, G:0.10, T:0.33
Consensus pattern (42 bp):
GTATATATAAAATTATGAAATATAAGAAAAATATATAGACAC
Found at i:57631928 original size:44 final size:44
Alignment explanation
Indices: 57631877--57632309 Score: 403
Period size: 44 Copynumber: 9.8 Consensus size: 44
57631867 GGTGTCTTTT
** * * * *
57631877 GATCTGCTTCATTGCCAGTACAGGAAGGCAAGGCTGGTGTCCTC
1 GATCTGCTTCGCTGTCAGTACAGGAAGGCAAGACTGGTATCTTC
* ** **
57631921 GATCTGCTTCTCTACCAGTACAGGAAGGCAAGATCTACTATCTTC
1 GATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA-CTGGTATCTTC
* * * *
57631966 -AGTCTGCTCCGCCGTCAGTACAGGAAGGCAAGGCTGGTGTCTTC
1 GA-TCTGCTTCGCTGTCAGTACAGGAAGGCAAGACTGGTATCTTC
**
57632010 GATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTC
1 GATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA-CTGGTATCTTC
* *
57632055 -AGTCTGC-TCTGCTGTCAGTACAGTG-AGGCAAGACTAGTGTCTTC
1 GA-TCTGCTTC-GCTGTCAGTACAG-GAAGGCAAGACTGGTATCTTC
* * * *
57632099 GATCTGCTTCGCTGCCAGTACAGGAAGGTATGACTGGTTTCTTC
1 GATCTGCTTCGCTGTCAGTACAGGAAGGCAAGACTGGTATCTTC
* *
57632143 GATCTGCTTCGCCGTCAGTACAGGAAGG-AATGATCTGCTATCTT-
1 GATCTGCTTCGCTGTCAGTACAGGAAGGCAA-GA-CTGGTATCTTC
* *
57632187 TAGTCTGCTTCGCTGTCAGTACAGGAAGGCAAGACTGGTTTCTTC
1 GA-TCTGCTTCGCTGTCAGTACAGGAAGGCAAGACTGGTATCTTC
* * * * * *
57632232 GATTTGCTTCACCGTCAGTACAGGAAGGCATGATTTGCTATCTT-
1 GATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA-CTGGTATCTTC
* *
57632276 TAGTCTGCTCCGCTGTCAGTACAGGAAGGCAAGA
1 GA-TCTGCTTCGCTGTCAGTACAGGAAGGCAAGA
57632310 TCTACTATCT
Statistics
Matches: 319, Mismatches: 53, Indels: 33
0.79 0.13 0.08
Matches are distributed among these distances:
43 2 0.01
44 175 0.55
45 139 0.44
46 3 0.01
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (44 bp):
GATCTGCTTCGCTGTCAGTACAGGAAGGCAAGACTGGTATCTTC
Found at i:57631994 original size:89 final size:89
Alignment explanation
Indices: 57631892--57632322 Score: 437
Period size: 89 Copynumber: 4.8 Consensus size: 89
57631882 GCTTCATTGC
* * *
57631892 CAGTACAGGAAGGCAAGGCTGGTGTCCTCGATCTGCTTCTCTACCAGTACAGGAAGGCAAGATCT
1 CAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCT
57631957 ACTATCTTCAGTCTGCTCCGCCGT
66 ACTATCTTCAGTCTGCTCCGCCGT
*
57631981 CAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCT
1 CAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCT
* *
57632046 ACTATCTTCAGTCTGCTCTGCTGT
66 ACTATCTTCAGTCTGCTCCGCCGT
* * * *
57632070 CAGTACAGTG-AGGCAAGACTAGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGTATGA-C
1 CAGTACAG-GAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATC
** * *
57632133 TGGTTTCTTC-GATCTGCTTCGCCGT
65 TACTATCTTCAG-TCTGCTCCGCCGT
* * * * *
57632158 CAGTACAGGAAGG-AATGATCTGCTATCTT-TAGTCTGCTTCGCTGTCAGTACAGGAAGGCAAGA
1 CAGTACAGGAAGGCAA-G-GCTGGTGTCTTCGA-TCTGCTTCGCTGCCAGTACAGGAAGGCAAGA
** * * * *
57632221 -CTGGTTTCTTC-GATTTGCTTCACCGT
63 TCTACTATCTTCAG-TCTGCTCCGCCGT
* ** * * * * *
57632247 CAGTACAGGAAGGCATGATTTGCTATCTT-TAGTCTGCTCCGCTGTCAGTACAGGAAGGCAAGAT
1 CAGTACAGGAAGGCAAG-GCTGGTGTCTTCGA-TCTGCTTCGCTGCCAGTACAGGAAGGCAAGAT
57632311 CTACTATCTTCA
64 CTACTATCTTCA
57632323 TTGATCTGTT
Statistics
Matches: 300, Mismatches: 33, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
87 4 0.01
88 31 0.10
89 255 0.85
90 10 0.03
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (89 bp):
CAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCT
ACTATCTTCAGTCTGCTCCGCCGT
Found at i:57632105 original size:133 final size:133
Alignment explanation
Indices: 57631936--57632322 Score: 487
Period size: 133 Copynumber: 2.9 Consensus size: 133
57631926 GCTTCTCTAC
* * * *
57631936 CAGTACAGGAAGGCAAGATCTACTATCTTC-AGTCTGCTCCGCCGTCAGTACAGGAAGGCAAGGC
1 CAGTACAGGAAGGCAAGA-CTAGTATCTTCGA-TCTGCTTCGCCGTCAGTACAGGAAGGCATGAC
*
57632000 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGC-TC
64 TGGTATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTTC
57632064 TGCTGT
129 -GCTGT
* * * *
57632070 CAGTACAGTG-AGGCAAGACTAGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGTATGACT
1 CAGTACAG-GAAGGCAAGACTAGTATCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCATGACT
* * * *
57632134 GGTTTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGG-AATGATCTGCTATCTTTAGTCTGCTTC
65 GGTATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAA-GATCTACTATCTTCAGTCTGCTTC
57632198 GCTGT
129 GCTGT
* * * * *
57632203 CAGTACAGGAAGGCAAGACTGGTTTCTTCGATTTGCTTCACCGTCAGTACAGGAAGGCATGATTT
1 CAGTACAGGAAGGCAAGACTAGTATCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCATGA-CT
* * *
57632268 GCTATCTT-TAGTCTGCTCCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTCA
65 GGTATCTTCGA-TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTCA
57632323 TTGATCTGTT
Statistics
Matches: 218, Mismatches: 27, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
132 3 0.01
133 149 0.68
134 63 0.29
135 3 0.01
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (133 bp):
CAGTACAGGAAGGCAAGACTAGTATCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCATGACTG
GTATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTTCGC
TGT
Found at i:57632275 original size:222 final size:223
Alignment explanation
Indices: 57631868--57632309 Score: 611
Period size: 222 Copynumber: 2.0 Consensus size: 223
57631858 GCAAACTATG
* * * *
57631868 GTGTCTTTTGATCTGCTTCATTGCCAGTACAGGAAGGCAAGGCTGGTGTCCTCGATCTGCTTCTC
1 GTGTCTTTCGATCTGCTTCACTGCCAGTACAGGAAGGCAAGACTGGTGTCCTCGATCTGCTTCGC
*
57631933 TACCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTCCGCCGTCAGTACAGGAAGGCAAG
66 CACCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTCCGCCGTCAGTACAGGAAGGCAAG
* * *
57631998 GCTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCT
131 ACTGGTGTCTTCGATCTGCTTCACCGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCT
*
57632063 CTGCTGTCAGTACAGTG-AGGCAAGACTA
196 CCGCTGTCAGTACAG-GAAGGCAAGACTA
* * * * *
57632091 GTGTC-TTCGATCTGCTTCGCTGCCAGTACAGGAAGGTATGACTGGTTTCTTCGATCTGCTTCGC
1 GTGTCTTTCGATCTGCTTCACTGCCAGTACAGGAAGGCAAGACTGGTGTCCTCGATCTGCTTCGC
** * * * *
57632155 CGTCAGTACAGGAAGG-AATGATCTGCTATCTTTAGTCTGCTTCGCTGTCAGTACAGGAAGGCAA
66 CACCAGTACAGGAAGGCAA-GATCTACTATCTTCAGTCTGCTCCGCCGTCAGTACAGGAAGGCAA
* * * * * *
57632219 GACTGGTTTCTTCGATTTGCTTCACCGTCAGTACAGGAAGGCATGATTTGCTATCTTTAGTCTGC
130 GACTGGTGTCTTCGATCTGCTTCACCGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGC
57632284 TCCGCTGTCAGTACAGGAAGGCAAGA
195 TCCGCTGTCAGTACAGGAAGGCAAGA
57632310 TCTACTATCT
Statistics
Matches: 191, Mismatches: 26, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
221 3 0.02
222 183 0.96
223 5 0.03
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (223 bp):
GTGTCTTTCGATCTGCTTCACTGCCAGTACAGGAAGGCAAGACTGGTGTCCTCGATCTGCTTCGC
CACCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTCCGCCGTCAGTACAGGAAGGCAAG
ACTGGTGTCTTCGATCTGCTTCACCGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCT
CCGCTGTCAGTACAGGAAGGCAAGACTA
Found at i:57633546 original size:22 final size:23
Alignment explanation
Indices: 57633514--57633558 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
57633504 TTGGCCTCTC
*
57633514 CTTTTCTCCTTTTCTTCTTTTTT
1 CTTTTCTCCTTCTCTTCTTTTTT
*
57633537 CTTTT-TCCTTCTCTTTTTTTTT
1 CTTTTCTCCTTCTCTTCTTTTTT
57633559 TGAAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (23 bp):
CTTTTCTCCTTCTCTTCTTTTTT
Found at i:57635506 original size:9 final size:9
Alignment explanation
Indices: 57635463--57635570 Score: 69
Period size: 10 Copynumber: 11.4 Consensus size: 9
57635453 ACATGTGGCA
57635463 AAAAATTAT
1 AAAAATTAT
57635472 AAAAA--AT
1 AAAAATTAT
*
57635479 AAAAATGAAT
1 AAAAAT-TAT
* *
57635489 AAGATTTAT
1 AAAAATTAT
57635498 AAAAATTATT
1 AAAAATTA-T
*
57635508 AAACATTAAT
1 AAAAATT-AT
*
57635518 AAAAAAATATT
1 -AAAAATTA-T
*
57635529 AAAAATTAGG
1 AAAAATTA-T
57635539 AAAAA-TAT
1 AAAAATTAT
57635547 AAAAATTAT
1 AAAAATTAT
57635556 AAAAAATTTAT
1 -AAAAA-TTAT
57635567 AAAA
1 AAAA
57635571 TGCATCAAAA
Statistics
Matches: 77, Mismatches: 12, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
7 7 0.09
8 5 0.06
9 18 0.23
10 36 0.47
11 11 0.14
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:57635542 original size:21 final size:20
Alignment explanation
Indices: 57635498--57635571 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 20
57635488 TAAGATTTAT
* * *
57635498 AAAAATTATTAAACATTAATA
1 AAAAAATATTAAAAATTAA-G
57635519 AAAAAATATTAAAAATT-AG
1 AAAAAATATTAAAAATTAAG
* *
57635538 GAAAAATA-TAAAAATT-AT
1 AAAAAATATTAAAAATTAAG
57635556 AAAAAAT-TTATAAAAT
1 AAAAAATATTA-AAAAT
57635572 GCATCAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
18 17 0.38
19 12 0.27
20 1 0.02
21 15 0.33
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (20 bp):
AAAAAATATTAAAAATTAAG
Found at i:57639522 original size:23 final size:20
Alignment explanation
Indices: 57639496--57639539 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 20
57639486 AAATATATTT
57639496 ATATAATCTTATAAAATTACGAA
1 ATATAAT-TT-TAAAATTA-GAA
*
57639519 ATATAGTTTTAAAATTAGAA
1 ATATAATTTTAAAATTAGAA
57639539 A
1 A
57639540 AAAAAAGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 8 0.40
22 2 0.10
23 6 0.30
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (20 bp):
ATATAATTTTAAAATTAGAA
Found at i:57640566 original size:19 final size:19
Alignment explanation
Indices: 57640542--57640578 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
57640532 TAATAACAAA
57640542 TTTGATTACT-GTGGGTAAT
1 TTTGATTA-TGGTGGGTAAT
57640561 TTTGATTATGGTGGGTAA
1 TTTGATTATGGTGGGTAA
57640579 CAGTGGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.22, C:0.03, G:0.30, T:0.46
Consensus pattern (19 bp):
TTTGATTATGGTGGGTAAT
Found at i:57653784 original size:12 final size:12
Alignment explanation
Indices: 57653767--57653800 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
57653757 GTTTCCTTAC
57653767 TTACTTAATTAA
1 TTACTTAATTAA
57653779 TTACTTAATTAA
1 TTACTTAATTAA
57653791 TTAACTTAAT
1 TT-ACTTAAT
57653801 GTTTGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (12 bp):
TTACTTAATTAA
Found at i:57657498 original size:18 final size:18
Alignment explanation
Indices: 57657475--57657509 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
57657465 AATTTTCTCA
*
57657475 TTTTTTGGTAATTTGTAT
1 TTTTTTGATAATTTGTAT
*
57657493 TTTTTTGATATTTTGTA
1 TTTTTTGATAATTTGTA
57657510 ATAATATTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (18 bp):
TTTTTTGATAATTTGTAT
Found at i:57662244 original size:23 final size:23
Alignment explanation
Indices: 57662218--57662272 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
57662208 GAATTATAAA
57662218 ATATATAAAATATGTACATATAT
1 ATATATAAAATATGTACATATAT
* *
57662241 ATATGTAAAATATGTATATATAT
1 ATATATAAAATATGTACATATAT
*
57662264 ATTTATAAA
1 ATATATAAA
57662273 GGTTAGAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (23 bp):
ATATATAAAATATGTACATATAT
Found at i:57664274 original size:87 final size:85
Alignment explanation
Indices: 57664158--57664445 Score: 247
Period size: 87 Copynumber: 3.4 Consensus size: 85
57664148 AGACTTGATG
* * *
57664158 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA-CT
1 CGATCTGCTCCGCTGTAATCTCAGAGAGATAAGATCC--TATTTTAATCCGCTCCACTGTAATC-
*
57664222 TCAGGGAGATAGGATAGTGTCTT
63 TCAGGGAGATAGGATACTGTCTT
* ** * *
57664245 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-CTGAATTCTTGGTCTGTTCCACTGTAATC
1 CGATCTGCTCCGCTGTAATCTCAGAGAGATAAGATCCT--ATT-TTAATCCGCTCCACTGTAATC
* * *
57664309 TCAGGGA-ATAAGA-CCTGAT-GT
63 TCAGGGAGATAGGATACTG-TCTT
* ** *
57664330 -GATCTTCTCTACTGTAA-CTTCAGAGAGATAAGATCC---TTTAATCCGCTCCATTGTAATCTC
1 CGATCTGCTCCGCTGTAATC-TCAGAGAGATAAGATCCTATTTTAATCCGCTCCACTGTAATCTC
* *
57664390 AAGGAGATAGGATACTATCTT
65 AGGGAGATAGGATACTGTCTT
* *
57664411 TGATCTGC-CCGCTGTAATCTCAGGGAGATAAGATC
1 CGATCTGCTCCGCTGTAATCTCAGAGAGATAAGATC
57664446 TCTGGCTTCA
Statistics
Matches: 159, Mismatches: 30, Indels: 30
0.73 0.14 0.14
Matches are distributed among these distances:
79 22 0.14
80 7 0.04
81 25 0.16
82 7 0.04
83 1 0.01
84 29 0.18
85 4 0.03
86 10 0.06
87 53 0.33
88 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (85 bp):
CGATCTGCTCCGCTGTAATCTCAGAGAGATAAGATCCTATTTTAATCCGCTCCACTGTAATCTCA
GGGAGATAGGATACTGTCTT
Found at i:57664362 original size:171 final size:166
Alignment explanation
Indices: 57664119--57664446 Score: 464
Period size: 166 Copynumber: 1.9 Consensus size: 166
57664109 CTTGTTTTCA
* * *
57664119 GTCTGTTCCACTGCATCTTCAGGGAAATAAGACTTGATGCGATCTACTCTGCTGTAACCTCAGAG
1 GTCTGTTCCACTGAATCTTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGAG
* * *
57664184 AGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA-CTTCAGGGAGATAGGATAGTGTCTTCGA
66 AGATAAGATCC-----TTTAATCCGCTCCACTGTAATC-TCAAGGAGATAGGATACTATCTTCGA
57664248 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAATTCTTG
125 TCTGC-CCGCTGTAATCTCAGGGAGATAAGATCTGAATTCTTG
* * *
57664291 GTCTGTTCCACTGTAATC-TCAGGG-AATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGA
1 GTCTGTTCCACTG-AATCTTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGA
* *
57664354 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATACTATCTTTGATCTGC
65 GAGATAAGATCCTTTAATCCGCTCCACTGTAATCTCAAGGAGATAGGATACTATCTTCGATCTGC
57664419 CCGCTGTAATCTCAGGGAGATAAGATCT
130 CCGCTGTAATCTCAGGGAGATAAGATCT
57664447 CTGGCTTCAA
Statistics
Matches: 143, Mismatches: 11, Indels: 11
0.87 0.07 0.07
Matches are distributed among these distances:
165 28 0.20
166 46 0.32
167 1 0.01
171 46 0.32
172 19 0.13
173 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (166 bp):
GTCTGTTCCACTGAATCTTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGAG
AGATAAGATCCTTTAATCCGCTCCACTGTAATCTCAAGGAGATAGGATACTATCTTCGATCTGCC
CGCTGTAATCTCAGGGAGATAAGATCTGAATTCTTG
Found at i:57676978 original size:24 final size:25
Alignment explanation
Indices: 57676951--57677002 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
57676941 ATGTATGAAT
57676951 TATAAAATATAT-AAAATATGTACA
1 TATAAAATATATAAAAATATGTACA
* * *
57676975 TAT-ATATATGTAAAAATATGTATA
1 TATAAAATATATAAAAATATGTACA
57676999 TATA
1 TATA
57677003 TATTTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (25 bp):
TATAAAATATATAAAAATATGTACA
Found at i:57677012 original size:24 final size:24
Alignment explanation
Indices: 57676957--57677012 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
57676947 GAATTATAAA
57676957 ATATAT-AAAATATGTACATATAT
1 ATATATAAAAATATGTACATATAT
* *
57676980 ATATGTAAAAATATGTATATATAT
1 ATATATAAAAATATGTACATATAT
*
57677004 ATTTATAAA
1 ATATATAAA
57677013 GGTTAGAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (24 bp):
ATATATAAAAATATGTACATATAT
Found at i:57677175 original size:3 final size:3
Alignment explanation
Indices: 57677167--57677205 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
57677157 CTATAAAAGC
*
57677167 AAT AAT AAT AAT AAT AAT AAT GCAAT AAC AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT --AAT AAT AAT AAT AAT A
57677206 TAAAATTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 29 0.91
5 3 0.09
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:57679482 original size:30 final size:30
Alignment explanation
Indices: 57679448--57679510 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
57679438 AACTTATTTA
57679448 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
* *
57679478 TTGTTGATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
57679508 TTG
1 TTG
57679511 CTTGTTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.22, C:0.03, G:0.17, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:57680939 original size:18 final size:18
Alignment explanation
Indices: 57680916--57680953 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
57680906 ATAGTTGGAT
57680916 AACTCAA-TTTCTTGTAAA
1 AACTCAAGTTT-TTGTAAA
*
57680934 AACTCAAGTTTTTTTAAA
1 AACTCAAGTTTTTGTAAA
57680952 AA
1 AA
57680954 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.39
Consensus pattern (18 bp):
AACTCAAGTTTTTGTAAA
Found at i:57699929 original size:98 final size:98
Alignment explanation
Indices: 57699752--57699946 Score: 327
Period size: 98 Copynumber: 2.0 Consensus size: 98
57699742 ACAATAAAAT
*
57699752 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
*
57699817 TCTAGAATCCCAAACTCGGAATATTTCCTTTAC
66 TCTAAAATCCCAAACTCGGAATATTTCCTTTAC
* * *
57699850 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATATGTTATGGCACAATTCT
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
* *
57699915 TTTAAAATCTCAAACTCGGAATATTTCCTTTA
66 TCTAAAATCCCAAACTCGGAATATTTCCTTTA
57699947 TTGTTTTTAG
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
TCTAAAATCCCAAACTCGGAATATTTCCTTTAC
Found at i:57700858 original size:25 final size:22
Alignment explanation
Indices: 57700801--57700850 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
57700791 ATATATAGCT
**
57700801 AAAATAATAATAATTACATATG
1 AAAATAATAATAATTACATAAC
57700823 AAAATAATAATAATTACATTAAC
1 AAAATAATAATAATTACA-TAAC
57700846 AAAAT
1 AAAAT
57700851 TAACTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAATAATAATAATTACATAAC
Found at i:57701429 original size:19 final size:19
Alignment explanation
Indices: 57701405--57701536 Score: 219
Period size: 19 Copynumber: 6.8 Consensus size: 19
57701395 AATCATATAT
57701405 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
57701424 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
57701443 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
57701462 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
57701483 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
57701502 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
57701521 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
57701537 CTCAAAAATT
Statistics
Matches: 105, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
19 86 0.82
21 19 0.18
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:57701489 original size:59 final size:59
Alignment explanation
Indices: 57701398--57701535 Score: 221
Period size: 59 Copynumber: 2.4 Consensus size: 59
57701388 ATTACAAAAT
*
57701398 CATAT-AT-TCTAAGATTGC--ATATCATATCTAAGATTATATATCATATCTAAGATTG
1 CATATCATATCTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTG
* *
57701453 CATATCATATCTAAGATTGCATATATCATATCTAAGATTGCATATCATATCTAGGATTG
1 CATATCATATCTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTG
57701512 CATATCATATCTAAGATTGCATAT
1 CATATCATATCTAAGATTGCATAT
57701536 CCTCAAAAAT
Statistics
Matches: 76, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
55 5 0.07
56 2 0.03
57 11 0.14
59 58 0.76
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.38
Consensus pattern (59 bp):
CATATCATATCTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTG
Found at i:57702897 original size:36 final size:36
Alignment explanation
Indices: 57702850--57702922 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
57702840 ACTCTTTAAG
*
57702850 TGTGGCGTTCAACCTATTGATACCAATTGGTTCCTA
1 TGTGGCGTTCAACCCATTGATACCAATTGGTTCCTA
57702886 TGTGGCGTTCAACCCATTGATACCAATTGGTTCCTA
1 TGTGGCGTTCAACCCATTGATACCAATTGGTTCCTA
57702922 T
1 T
57702923 CTTCCTAGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (36 bp):
TGTGGCGTTCAACCCATTGATACCAATTGGTTCCTA
Found at i:57703983 original size:15 final size:16
Alignment explanation
Indices: 57703950--57703980 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
57703940 TGTTTTCCAC
57703950 TTTCTCCTGAACAAAA
1 TTTCTCCTGAACAAAA
57703966 TTTCTCCTGAACAAA
1 TTTCTCCTGAACAAA
57703981 TTTTTTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (16 bp):
TTTCTCCTGAACAAAA
Found at i:57722515 original size:19 final size:19
Alignment explanation
Indices: 57722464--57722519 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 19
57722454 TCTCTTTTAA
*
57722464 TTTTTAATACTTTCCCAT-AT
1 TTTTTGATAC-TTCCC-TCAT
*
57722484 TTTTTGGTA-TTCCCTCAT
1 TTTTTGATACTTCCCTCAT
57722502 TTTTTGATACTT-CCTCAT
1 TTTTTGATACTTCCCTCAT
57722520 AACTGTTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 1 0.03
18 21 0.68
19 2 0.06
20 7 0.23
ACGTcount: A:0.18, C:0.21, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTTTGATACTTCCCTCAT
Found at i:57722747 original size:57 final size:56
Alignment explanation
Indices: 57722678--57722785 Score: 173
Period size: 57 Copynumber: 1.9 Consensus size: 56
57722668 TTAGGTATTG
57722678 AAAAATTATATTTCATGAT-ACTTTTGTTAAAAATGTGAAAAATTAAATAAAGGACT
1 AAAAATTATATTTCATGATAACTTTT-TTAAAAATGTGAAAAATTAAATAAAGGACT
**
57722734 AAAAAGTTATATTTCATGATAACTTTTTTTTAAATGTGAAAAATTAAATAAA
1 AAAAA-TTATATTTCATGATAACTTTTTTAAAAATGTGAAAAATTAAATAAA
57722786 TGAAAAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
56 5 0.10
57 37 0.77
58 6 0.12
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (56 bp):
AAAAATTATATTTCATGATAACTTTTTTAAAAATGTGAAAAATTAAATAAAGGACT
Found at i:57723403 original size:20 final size:20
Alignment explanation
Indices: 57723340--57723408 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
57723330 CCTTCAAAAA
* *
57723340 TTTTTGGTACTTCCTCGTAAT
1 TTTTTGGTACTTCTTTGT-AT
* *
57723361 TTTTT-GTA-TGCCTTTATACT
1 TTTTTGGTACT-TCTTTGTA-T
57723381 TTTTTGGTACTTCTTTGTA-
1 TTTTTGGTACTTCTTTGTAT
57723400 TTTTTGGTA
1 TTTTTGGTA
57723409 TATTTTCATA
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
19 11 0.29
20 12 0.32
21 14 0.37
22 1 0.03
ACGTcount: A:0.13, C:0.13, G:0.14, T:0.59
Consensus pattern (20 bp):
TTTTTGGTACTTCTTTGTAT
Found at i:57723701 original size:19 final size:20
Alignment explanation
Indices: 57723677--57723785 Score: 77
Period size: 19 Copynumber: 5.5 Consensus size: 20
57723667 ATTTTTTTTA
57723677 CTTATAATTTTTATATTTC-
1 CTTATAATTTTTATATTTCT
*
57723696 CTTATAATTTTTGGTACTTTCT
1 CTTATAATTTTT-ATA-TTTCT
* * **
57723718 CGTGTTTTTTTTATA-TTCT
1 CTTATAATTTTTATATTTCT
*
57723737 CTTATAATTTTTGTA-TTC-
1 CTTATAATTTTTATATTTCT
*
57723755 CTTCCTAATTTTT-TATATTCT
1 CTT-ATAATTTTTATAT-TTCT
57723776 CTTA-AATTTT
1 CTTATAATTTT
57723786 GGTATTCCCT
Statistics
Matches: 70, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
18 5 0.07
19 43 0.61
20 5 0.07
21 9 0.13
22 8 0.11
ACGTcount: A:0.20, C:0.13, G:0.05, T:0.62
Consensus pattern (20 bp):
CTTATAATTTTTATATTTCT
Found at i:57723741 original size:41 final size:40
Alignment explanation
Indices: 57723684--57723793 Score: 122
Period size: 41 Copynumber: 2.8 Consensus size: 40
57723674 TTACTTATAA
* * **
57723684 TTTTTATATT-TCCTTATAATTTTTGGTACTTTC-TCGTGTTT
1 TTTTTATATTCT-CTTATAATTTTTGGTA-TTCCTTCCT-AAT
57723725 TTTTTATATTCTCTTATAATTTTT-GTATTCCTTCCTAAT
1 TTTTTATATTCTCTTATAATTTTTGGTATTCCTTCCTAAT
57723764 TTTTTATATTCTCTTA-AA-TTTTGGTATTCC
1 TTTTTATATTCTCTTATAATTTTTGGTATTCC
57723794 CTTGTTATAC
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
37 4 0.06
38 9 0.15
39 20 0.32
40 6 0.10
41 22 0.35
42 1 0.02
ACGTcount: A:0.18, C:0.14, G:0.06, T:0.62
Consensus pattern (40 bp):
TTTTTATATTCTCTTATAATTTTTGGTATTCCTTCCTAAT
Found at i:57723785 original size:18 final size:18
Alignment explanation
Indices: 57723725--57723785 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 18
57723715 TCTCGTGTTT
57723725 TTTTTATATTCTCTTATAA
1 TTTTTATATTCTCTTA-AA
* * *
57723744 TTTTTGTATTCCTTCCTAAT
1 TTTTTATATT-C-TCTTAAA
57723764 TTTTTATATTCTCTTAAA
1 TTTTTATATTCTCTTAAA
57723782 TTTT
1 TTTT
57723786 GGTATTCCCT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 9 0.26
19 10 0.29
20 11 0.32
21 4 0.12
ACGTcount: A:0.21, C:0.13, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTTATATTCTCTTAAA
Found at i:57723791 original size:18 final size:18
Alignment explanation
Indices: 57723725--57723792 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 18
57723715 TCTCGTGTTT
*
57723725 TTTTTATATTCTCTTATAA
1 TTTTTGTATTCTCTTA-AA
* *
57723744 TTTTTGTATTCCTTCCTAAT
1 TTTTTGTATT-C-TCTTAAA
*
57723764 TTTTTATATTCTCTTAAA
1 TTTTTGTATTCTCTTAAA
*
57723782 TTTTGGTATTC
1 TTTTTGTATTC
57723793 CCTTGTTATA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
18 14 0.36
19 10 0.26
20 11 0.28
21 4 0.10
ACGTcount: A:0.21, C:0.13, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTTTGTATTCTCTTAAA
Found at i:57724504 original size:20 final size:21
Alignment explanation
Indices: 57724468--57724513 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
57724458 CCCTCAAAAA
*
57724468 TTTTGGTACTTTGTCAT-AAT
1 TTTTGGTACCTTGTCATAAAT
57724488 TTTTGGTACACTT-TCATAAAT
1 TTTTGGTAC-CTTGTCATAAAT
57724509 TTTTG
1 TTTTG
57724514 TATGGTCTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.22, C:0.11, G:0.13, T:0.54
Consensus pattern (21 bp):
TTTTGGTACCTTGTCATAAAT
Found at i:57733126 original size:25 final size:25
Alignment explanation
Indices: 57733097--57733148 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
57733087 AAGTTAAGAG
57733097 TAATAAATCAGCTAAAGTACATAAA
1 TAATAAATCAGCTAAAGTACATAAA
57733122 TAATAAATCAGCTAAAGTACATAAA
1 TAATAAATCAGCTAAAGTACATAAA
57733147 TA
1 TA
57733149 TCTTCACAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.25
Consensus pattern (25 bp):
TAATAAATCAGCTAAAGTACATAAA
Found at i:57735740 original size:16 final size:16
Alignment explanation
Indices: 57735719--57735786 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
57735709 TTTGGTTCGC
*
57735719 TGTATTGGATTAGAGG
1 TGTATTGGAATAGAGG
57735735 TGTATTGGAATAGAGG
1 TGTATTGGAATAGAGG
*
57735751 TGTATTGGATTAGAGG
1 TGTATTGGAATAGAGG
57735767 TGTATTGGAATAGAGG
1 TGTATTGGAATAGAGG
57735783 TGTA
1 TGTA
57735787 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGAATAGAGG
Found at i:57735755 original size:32 final size:32
Alignment explanation
Indices: 57735719--57735786 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
57735709 TTTGGTTCGC
57735719 TGTATTGGATTAGAGGTGTATTGGAATAGAGG
1 TGTATTGGATTAGAGGTGTATTGGAATAGAGG
57735751 TGTATTGGATTAGAGGTGTATTGGAATAGAGG
1 TGTATTGGATTAGAGGTGTATTGGAATAGAGG
57735783 TGTA
1 TGTA
57735787 ATAGCAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGAATAGAGG
Found at i:57736050 original size:14 final size:15
Alignment explanation
Indices: 57736011--57736052 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
57736001 TTTTAACATA
*
57736011 ATTATTATTAAATAT
1 ATTATAATTAAATAT
57736026 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
57736040 A-TATAATTTAATA
1 ATTATAATTAAATA
57736053 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:57736361 original size:24 final size:27
Alignment explanation
Indices: 57736310--57736362 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
57736300 TATATGTAAT
*
57736310 ATTATTAAAATAATATTTTTTATTTTA
1 ATTATTAAAATAATATTTTTTATATTA
*
57736337 ATTATTTAAA-AATA-TTTTTA-ATTA
1 ATTATTAAAATAATATTTTTTATATTA
57736361 AT
1 AT
57736363 GCAGTGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.21
25 6 0.25
26 4 0.17
27 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTATTAAAATAATATTTTTTATATTA
Found at i:57744192 original size:5 final size:5
Alignment explanation
Indices: 57744178--57744210 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
57744168 AATTATTAAG
57744178 TATA- TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATA
57744211 ATGATAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:57744241 original size:4 final size:4
Alignment explanation
Indices: 57744234--57744307 Score: 57
Period size: 4 Copynumber: 18.0 Consensus size: 4
57744224 GAATAAATAA
57744234 AAAG AAAG AAAG ATAA- AAACG AAACAG AAAG -AA- AAAG AAAG AAAG
1 AAAG AAAG AAAG A-AAG AAA-G -AA-AG AAAG AAAG AAAG AAAG AAAG
*
57744279 AAAG AAAAG AAAAG AAA- AAGG AAAG AAAG
1 AAAG -AAAG -AAAG AAAG AAAG AAAG AAAG
57744308 GAAGGAGAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 18
0.75 0.03 0.23
Matches are distributed among these distances:
3 8 0.14
4 34 0.58
5 13 0.22
6 3 0.05
7 1 0.02
ACGTcount: A:0.74, C:0.03, G:0.22, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:57744241 original size:17 final size:16
Alignment explanation
Indices: 57744216--57744297 Score: 67
Period size: 17 Copynumber: 4.9 Consensus size: 16
57744206 TTATAATGAT
*
57744216 AAAATAAAGAATAAATA
1 AAAAGAAAGAA-AAATA
*
57744233 AAAAGAAAGAAAGATA
1 AAAAGAAAGAAAAATA
* * *
57744249 AAAACGAAACAGAAAGA
1 AAAA-GAAAGAAAAATA
57744266 AAAAGAAAGAAAGAA-A
1 AAAAGAAAGAAA-AATA
57744282 GAAAAGAAAAGAAAAA
1 -AAAAG-AAAGAAAAA
57744298 GGAAAGAAAG
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
16 15 0.28
17 31 0.58
18 7 0.13
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (16 bp):
AAAAGAAAGAAAAATA
Found at i:57744297 original size:29 final size:29
Alignment explanation
Indices: 57744238--57744307 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
57744228 AAATAAAAAG
57744238 AAAGAAAGATAA-AAACGAAACAGAAAGAA
1 AAAGAAAGA-AAGAAACGAAACAGAAAGAA
57744267 AAAGAAAGAAAGAAA-GAAA-AGAAAAGAA
1 AAAGAAAGAAAGAAACGAAACAG-AAAGAA
57744295 AAAGGAAAGAAAG
1 AAA-GAAAGAAAG
57744308 GAAGGAGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
27 2 0.05
28 15 0.39
29 21 0.55
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.01
Consensus pattern (29 bp):
AAAGAAAGAAAGAAACGAAACAGAAAGAA
Found at i:57744307 original size:33 final size:33
Alignment explanation
Indices: 57744232--57744295 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
57744222 AAGAATAAAT
*
57744232 AAAAAGAAAGAAAGATAAAAACGAAACAGAAAG
1 AAAAAGAAAGAAAGATAAAAAAGAAACAGAAAG
57744265 AAAAAGAAAGAAAGA-AAGAAAAGAAA-AGAAA
1 AAAAAGAAAGAAAGATAA-AAAAGAAACAGAAA
57744296 AAGGAAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 7 0.24
33 22 0.76
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.02
Consensus pattern (33 bp):
AAAAAGAAAGAAAGATAAAAAAGAAACAGAAAG
Found at i:57745300 original size:40 final size:39
Alignment explanation
Indices: 57745162--57745301 Score: 115
Period size: 40 Copynumber: 3.6 Consensus size: 39
57745152 CTTTGAGTCA
* *
57745162 ATGAGACACTGGGTGTCAAATTATTACTTC-AGATTAATTCG
1 ATGAGACACTGGGTGCCAAATTATT-CTTCGA-ATT-ATCCG
* * * ** * *
57745203 GTGAGGCACTGGGTGCCAATTTA-T-TTCGGTTTAGCCA
1 ATGAGACACTGGGTGCCAAATTATTCTTCGAATTATCCG
*
57745240 ATGAGACACTGGGTGTCAAATTATTCCTTCGAATTATCCG
1 ATGAGACACTGGGTGCCAAATTATT-CTTCGAATTATCCG
* *
57745280 ATGAGGCACTGGGTACCAAATT
1 ATGAGACACTGGGTGCCAAATT
57745302 GGTGTGTTTT
Statistics
Matches: 75, Mismatches: 20, Indels: 9
0.72 0.19 0.09
Matches are distributed among these distances:
37 21 0.28
38 6 0.08
40 29 0.39
41 19 0.25
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (39 bp):
ATGAGACACTGGGTGCCAAATTATTCTTCGAATTATCCG
Found at i:57745659 original size:17 final size:18
Alignment explanation
Indices: 57745629--57745662 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
57745619 AATGTGAATT
57745629 TTAAGTATTCAATTGTGC
1 TTAAGTATTCAATTGTGC
*
57745647 TTAA-TATTTAATTGTG
1 TTAAGTATTCAATTGTG
57745663 TCTATTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.06, G:0.15, T:0.50
Consensus pattern (18 bp):
TTAAGTATTCAATTGTGC
Found at i:57764007 original size:19 final size:22
Alignment explanation
Indices: 57763979--57764024 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 22
57763969 CAGCAGCAAA
57763979 AGAA-AAAGGAAG-GAA-GAGG
1 AGAAGAAAGGAAGAGAAGGAGG
57763998 A-AAGAAAGGAAGAGAAGGAGG
1 AGAAGAAAGGAAGAGAAGGAGG
57764019 AGAAGA
1 AGAAGA
57764025 TGGCGGTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.09
19 9 0.39
20 3 0.13
21 5 0.22
22 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (22 bp):
AGAAGAAAGGAAGAGAAGGAGG
Found at i:57764085 original size:3 final size:3
Alignment explanation
Indices: 57764077--57764128 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
57764067 CCTAGGGCTT
57764077 GAA GAA GAA GAA GAA GAA GAA GAA GAAA GAAA GAA -AA -AA GAA -AA
1 GAA GAA GAA GAA GAA GAA GAA GAA G-AA G-AA GAA GAA GAA GAA GAA
57764121 GAA -AA GAA
1 GAA GAA GAA
57764129 AAAGGAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 8 0.18
3 30 0.67
4 7 0.16
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
GAA
Done.