Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 9 of 75
Found at i:2408034 original size:15 final size:16
Alignment explanation
Indices: 2407982--2408044 Score: 76
Period size: 15 Copynumber: 3.9 Consensus size: 16
2407972 AAGGAGGAGG
2407982 AAGAAAGAAGAAA-AA
1 AAGAAAGAAGAAAGAA
2407997 AAGAAAGAAGAAAGAA
1 AAGAAAGAAGAAAGAA
*
2408013 AAGAAGAAAAAGAAAGAA
1 AAG-A-AAGAAGAAAGAA
*
2408031 AAGATA-AAGAAAGA
1 AAGAAAGAAGAAAGA
2408045 GAGAAGAGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
15 21 0.49
16 6 0.14
17 2 0.05
18 14 0.33
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (16 bp):
AAGAAAGAAGAAAGAA
Found at i:2408170 original size:20 final size:17
Alignment explanation
Indices: 2408147--2408185 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 17
2408137 AAAGAGGAAG
2408147 AAGAAAGGGAGAAGAAGAAA
1 AAGAAA-GGA-AAGAA-AAA
2408167 AAGAAAGGAAAGAAAAA
1 AAGAAAGGAAAGAAAAA
2408184 AA
1 AA
2408186 AAGAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 3 0.16
20 6 0.32
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (17 bp):
AAGAAAGGAAAGAAAAA
Found at i:2408181 original size:15 final size:16
Alignment explanation
Indices: 2408161--2408198 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
2408151 AAGGGAGAAG
*
2408161 AAGAAAAAGAAAG-GA
1 AAGAAAAAAAAAGAGA
2408176 AAGAAAAAAAAAGAGA
1 AAGAAAAAAAAAGAGA
2408192 AA-AAAAA
1 AAGAAAAA
2408199 CTACATTCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAAAGAGA
Found at i:2408986 original size:19 final size:19
Alignment explanation
Indices: 2408958--2409013 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 19
2408948 TTTATCAAAT
*
2408958 ATTTCTTGTTTTCAAAAAA
1 ATTTCGTGTTTTCAAAAAA
2408977 ATTTCGTG-TTTC--AAAA
1 ATTTCGTGTTTTCAAAAAA
*
2408993 ATTTCCGTTTTTTCAAAAAA
1 ATTT-CGTGTTTTCAAAAAA
2409013 A
1 A
2409014 ATGATGTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
16 8 0.26
17 3 0.10
18 8 0.26
19 7 0.23
20 5 0.16
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (19 bp):
ATTTCGTGTTTTCAAAAAA
Found at i:2408992 original size:17 final size:19
Alignment explanation
Indices: 2408967--2409012 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
2408957 TATTTCTTGT
2408967 TTTCAAAAAAATTT-CG-TG
1 TTTC-AAAAAATTTCCGTTG
*
2408985 TTTC-AAAAATTTCCGTTT
1 TTTCAAAAAATTTCCGTTG
2409003 TTTCAAAAAA
1 TTTCAAAAAA
2409013 AATGATGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 8 0.33
17 2 0.08
18 9 0.38
19 5 0.21
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (19 bp):
TTTCAAAAAATTTCCGTTG
Found at i:2408994 original size:16 final size:18
Alignment explanation
Indices: 2408973--2409011 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2408963 TTGTTTTCAA
2408973 AAAAATTT-CG-TGTTTC
1 AAAAATTTCCGTTGTTTC
*
2408989 AAAAATTTCCGTTTTTTC
1 AAAAATTTCCGTTGTTTC
2409007 AAAAA
1 AAAAA
2409012 AAATGATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (18 bp):
AAAAATTTCCGTTGTTTC
Found at i:2409898 original size:13 final size:15
Alignment explanation
Indices: 2409866--2409903 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
2409856 AGAGAGGAAA
*
2409866 AGAGAAGAATTTTGG
1 AGAGAAAAATTTTGG
2409881 AGAGAAAAATTTTGG
1 AGAGAAAAATTTTGG
2409896 AGAGAAAA
1 AGAGAAAA
2409904 TAATCTCTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (15 bp):
AGAGAAAAATTTTGG
Found at i:2422451 original size:7 final size:7
Alignment explanation
Indices: 2422439--2422469 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
2422429 TAAAACAATT
2422439 AAATATA
1 AAATATA
2422446 AAATATA
1 AAATATA
2422453 AAATATA
1 AAATATA
2422460 AAATATA
1 AAATATA
2422467 AAA
1 AAA
2422470 ACTTATTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATATA
Found at i:2422607 original size:6 final size:6
Alignment explanation
Indices: 2422596--2422636 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
2422586 AAAAATTATA
* *
2422596 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAC AAAAAC AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
2422637 ATATAGATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (6 bp):
AAAAAT
Found at i:2422617 original size:19 final size:19
Alignment explanation
Indices: 2422593--2422639 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
2422583 TTAAAAAATT
*
2422593 ATAAAAAATAAAAATAAAA
1 ATAAAAAATAAAAACAAAA
2422612 AT-AAAAATAAAAACAAAA
1 ATAAAAAATAAAAACAAAA
*
2422630 ACAAAAAATA
1 ATAAAAAATA
2422640 TAGATAACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.83, C:0.04, G:0.00, T:0.13
Consensus pattern (19 bp):
ATAAAAAATAAAAACAAAA
Found at i:2426572 original size:14 final size:14
Alignment explanation
Indices: 2426549--2426579 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2426539 TGTCGCGTTC
*
2426549 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
2426563 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
2426577 TTA
1 TTA
2426580 AAACAATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:2429129 original size:18 final size:17
Alignment explanation
Indices: 2429106--2429139 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2429096 TTAATACATA
2429106 TTATTTTGAGTATTTTTT
1 TTATTTT-AGTATTTTTT
*
2429124 TTATTTTTGTATTTTT
1 TTATTTTAGTATTTTT
2429140 ATAAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (17 bp):
TTATTTTAGTATTTTTT
Found at i:2430180 original size:24 final size:24
Alignment explanation
Indices: 2430159--2430207 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
2430149 TTTTAAAAGA
*
2430159 AAAAAATTAAATTTATAAAAAATG
1 AAAAAATTAAAATTATAAAAAATG
*
2430183 AAAAAATTAAAATTATAAACAATG
1 AAAAAATTAAAATTATAAAAAATG
2430207 A
1 A
2430208 TGACATATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (24 bp):
AAAAAATTAAAATTATAAAAAATG
Found at i:2430185 original size:25 final size:25
Alignment explanation
Indices: 2430153--2430207 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
2430143 AGAAAATTTT
*
2430153 AAAA-GAAAAAAATTAAATTTATAA
1 AAAATGAAAAAAATTAAAATTATAA
2430177 AAAATG-AAAAAATTAAAATTATAA
1 AAAATGAAAAAAATTAAAATTATAA
*
2430201 ACAATGA
1 AAAATGA
2430208 TGACATATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (25 bp):
AAAATGAAAAAAATTAAAATTATAA
Found at i:2439466 original size:81 final size:82
Alignment explanation
Indices: 2439351--2439515 Score: 323
Period size: 81 Copynumber: 2.0 Consensus size: 82
2439341 GAAAGTGAAT
2439351 AACTATTTTTTAAAAGTAAAAAAATTAAAAAACCATATCCCCAGAAAATTACAAGATCATTATTT
1 AACTATTTTTTAAAAGTAAAAAAATTAAAAAACCATATCCCCAGAAAATTACAAGATCATTATTT
2439416 AACGTGTAATAATTTTA
66 AACGTGTAATAATTTTA
2439433 AACTATTTTTT-AAAGTAAAAAAATTAAAAAACCATATCCCCAGAAAATTACAAGATCATTATTT
1 AACTATTTTTTAAAAGTAAAAAAATTAAAAAACCATATCCCCAGAAAATTACAAGATCATTATTT
2439497 AACGTGTAATAATTTTA
66 AACGTGTAATAATTTTA
2439514 AA
1 AA
2439516 ACCAACATAA
Statistics
Matches: 83, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 72 0.87
82 11 0.13
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (82 bp):
AACTATTTTTTAAAAGTAAAAAAATTAAAAAACCATATCCCCAGAAAATTACAAGATCATTATTT
AACGTGTAATAATTTTA
Found at i:2444627 original size:29 final size:29
Alignment explanation
Indices: 2444585--2444657 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
2444575 CACTACTGAT
* ***
2444585 GCCACATGGGCGTGTGGTGAGCTGTGTGG
1 GCCACACGGGCGTGTGCCAAGCTGTGTGG
2444614 GCCACACGGGCGTGTGCCAAGCTGTGTGG
1 GCCACACGGGCGTGTGCCAAGCTGTGTGG
*
2444643 ACCACACGGGCGTGT
1 GCCACACGGGCGTGT
2444658 AAGTCCATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.14, C:0.25, G:0.42, T:0.19
Consensus pattern (29 bp):
GCCACACGGGCGTGTGCCAAGCTGTGTGG
Found at i:2445338 original size:23 final size:23
Alignment explanation
Indices: 2445306--2445349 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2445296 TGGGTAGGAA
2445306 GTTTTCTGAAACAT-CTGCATTAT
1 GTTTTCTGAAA-ATACTGCATTAT
*
2445329 GTTTTTTGAAAATACTGCATT
1 GTTTTCTGAAAATACTGCATT
2445350 GACATAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (23 bp):
GTTTTCTGAAAATACTGCATTAT
Found at i:2447536 original size:36 final size:37
Alignment explanation
Indices: 2447460--2447536 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
2447450 ACTACAATTT
* * *
2447460 TTTTTAAAAAAATTAAACATTTTTAATTATCTTTGAA
1 TTTTAAAAAAAATTAAACATTTTTAATTAACTTCGAA
*
2447497 TTTTAAAAAAAATTAAAC-TTTTTAAATTAAC-TCGTA
1 TTTTAAAAAAAATTAAACATTTTT-AATTAACTTCGAA
2447533 TTTT
1 TTTT
2447537 TGTTAAAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 12 0.34
37 23 0.66
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (37 bp):
TTTTAAAAAAAATTAAACATTTTTAATTAACTTCGAA
Found at i:2447828 original size:16 final size:16
Alignment explanation
Indices: 2447790--2447833 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
2447780 ATAAAAATAT
*
2447790 TTAAAATTAACATTAAG
1 TTAAAATTAA-ATTAAA
*
2447807 TAAAAATTAAATTAAA
1 TTAAAATTAAATTAAA
*
2447823 TTAAAAATAAA
1 TTAAAATTAAA
2447834 AAAATTGATC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (16 bp):
TTAAAATTAAATTAAA
Found at i:2453200 original size:3 final size:3
Alignment explanation
Indices: 2453192--2453222 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
2453182 AATTAAAAGC
2453192 TAA TAA TAA TTAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
2453223 ATCGAGAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2454880 original size:1 final size:1
Alignment explanation
Indices: 2454874--2454912 Score: 78
Period size: 1 Copynumber: 39.0 Consensus size: 1
2454864 CCCTAAATTT
2454874 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2454913 GAGGGGAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2454960 original size:2 final size:2
Alignment explanation
Indices: 2454953--2454977 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2454943 AAACAGAAAA
2454953 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
2454978 AAAGCAGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2459110 original size:330 final size:330
Alignment explanation
Indices: 2458509--2459174 Score: 1332
Period size: 330 Copynumber: 2.0 Consensus size: 330
2458499 TTTTGATTAA
2458509 AAAAAAACAATATCATATTGTTTAATGCTTATTATAATGACTGTAAGTGGGAATAAGGTGGAGTA
1 AAAAAAACAATATCATATTGTTTAATGCTTATTATAATGACTGTAAGTGGGAATAAGGTGGAGTA
2458574 AGAAAAATTGAAAATAGATTCAAATCGAGATGTCTAGACGATTTATTGAATGTAAATTTAAAAAC
66 AGAAAAATTGAAAATAGATTCAAATCGAGATGTCTAGACGATTTATTGAATGTAAATTTAAAAAC
2458639 TATAATTATTTGAAACCGAATCGAATTTAATTTTTTATTTAATTTATAATTAATTTTAATTTTTA
131 TATAATTATTTGAAACCGAATCGAATTTAATTTTTTATTTAATTTATAATTAATTTTAATTTTTA
2458704 TATTTAAAATAGTAAAAATAATTTAAAAATTCTTAAAAATTTATTGTATTTTAAAAATATTTATG
196 TATTTAAAATAGTAAAAATAATTTAAAAATTCTTAAAAATTTATTGTATTTTAAAAATATTTATG
2458769 AAAAAAAGCTAAAAACTAATATAAAAATCGTTAATCAAGTCGAACCGAATCAAATAATAAAGGAC
261 AAAAAAAGCTAAAAACTAATATAAAAATCGTTAATCAAGTCGAACCGAATCAAATAATAAAGGAC
2458834 TGTTC
326 TGTTC
2458839 AAAAAAACAATATCATATTGTTTAATGCTTATTATAATGACTGTAAGTGGGAATAAGGTGGAGTA
1 AAAAAAACAATATCATATTGTTTAATGCTTATTATAATGACTGTAAGTGGGAATAAGGTGGAGTA
2458904 AGAAAAATTGAAAATAGATTCAAATCGAGATGTCTAGACGATTTATTGAATGTAAATTTAAAAAC
66 AGAAAAATTGAAAATAGATTCAAATCGAGATGTCTAGACGATTTATTGAATGTAAATTTAAAAAC
2458969 TATAATTATTTGAAACCGAATCGAATTTAATTTTTTATTTAATTTATAATTAATTTTAATTTTTA
131 TATAATTATTTGAAACCGAATCGAATTTAATTTTTTATTTAATTTATAATTAATTTTAATTTTTA
2459034 TATTTAAAATAGTAAAAATAATTTAAAAATTCTTAAAAATTTATTGTATTTTAAAAATATTTATG
196 TATTTAAAATAGTAAAAATAATTTAAAAATTCTTAAAAATTTATTGTATTTTAAAAATATTTATG
2459099 AAAAAAAGCTAAAAACTAATATAAAAATCGTTAATCAAGTCGAACCGAATCAAATAATAAAGGAC
261 AAAAAAAGCTAAAAACTAATATAAAAATCGTTAATCAAGTCGAACCGAATCAAATAATAAAGGAC
2459164 TGTTC
326 TGTTC
2459169 AAAAAA
1 AAAAAA
2459175 TTCGATTTAA
Statistics
Matches: 336, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
330 336 1.00
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (330 bp):
AAAAAAACAATATCATATTGTTTAATGCTTATTATAATGACTGTAAGTGGGAATAAGGTGGAGTA
AGAAAAATTGAAAATAGATTCAAATCGAGATGTCTAGACGATTTATTGAATGTAAATTTAAAAAC
TATAATTATTTGAAACCGAATCGAATTTAATTTTTTATTTAATTTATAATTAATTTTAATTTTTA
TATTTAAAATAGTAAAAATAATTTAAAAATTCTTAAAAATTTATTGTATTTTAAAAATATTTATG
AAAAAAAGCTAAAAACTAATATAAAAATCGTTAATCAAGTCGAACCGAATCAAATAATAAAGGAC
TGTTC
Found at i:2467107 original size:15 final size:15
Alignment explanation
Indices: 2467087--2467116 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2467077 TAATCCTTAA
2467087 TAATTATCTCAATAT
1 TAATTATCTCAATAT
*
2467102 TAATTATCTTAATAT
1 TAATTATCTCAATAT
2467117 AATAGAGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCTCAATAT
Found at i:2472049 original size:1 final size:1
Alignment explanation
Indices: 2472043--2472070 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
2472033 CCTCAAAAGC
2472043 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
2472071 GTCGATTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2478827 original size:12 final size:12
Alignment explanation
Indices: 2478810--2478845 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2478800 TGAAACTGCC
2478810 TTTTATGATGCA
1 TTTTATGATGCA
*
2478822 TTTTATGATGCC
1 TTTTATGATGCA
2478834 TTTTATGATGCA
1 TTTTATGATGCA
2478846 CTCGTAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (12 bp):
TTTTATGATGCA
Found at i:2484258 original size:15 final size:15
Alignment explanation
Indices: 2484238--2484288 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
2484228 TATTCCTTAA
2484238 CCTAAAAATATAAAC
1 CCTAAAAATATAAAC
**
2484253 CCTAAACCCT-TAAA-
1 CCTAAA-AATATAAAC
2484267 CCTAAAAACTATAAAC
1 CCTAAAAA-TATAAAC
2484283 CCTAAA
1 CCTAAA
2484289 CTCTTAAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
14 7 0.25
15 14 0.50
16 7 0.25
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (15 bp):
CCTAAAAATATAAAC
Found at i:2484282 original size:30 final size:29
Alignment explanation
Indices: 2484232--2484296 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 29
2484222 TAGTTTTATT
2484232 CCTT-AACCTAAAAATATAAACCCTAAAC
1 CCTTAAACCTAAAAATATAAACCCTAAAC
2484260 CCTTAAACCTAAAAACTATAAACCCTAAAC
1 CCTTAAACCTAAAAA-TATAAACCCTAAAC
*
2484290 TCTTAAA
1 CCTTAAA
2484297 ACCCTAACCC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 4 0.12
29 10 0.29
30 20 0.59
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (29 bp):
CCTTAAACCTAAAAATATAAACCCTAAAC
Found at i:2484298 original size:16 final size:16
Alignment explanation
Indices: 2484249--2484303 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
2484239 CTAAAAATAT
*
2484249 AAACCCTAAACCCTT-
1 AAACCCTAAACACTTA
*
2484264 AAA-CCTAAAAAC-TA
1 AAACCCTAAACACTTA
*
2484278 TAAACCCTAAACTCTTA
1 -AAACCCTAAACACTTA
2484295 AAACCCTAA
1 AAACCCTAA
2484304 CCCTTAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
13 1 0.03
14 7 0.22
15 6 0.19
16 16 0.50
17 2 0.06
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (16 bp):
AAACCCTAAACACTTA
Found at i:2484309 original size:15 final size:16
Alignment explanation
Indices: 2484249--2484311 Score: 62
Period size: 15 Copynumber: 4.1 Consensus size: 16
2484239 CTAAAAATAT
2484249 AAACCCTAAACCCTT-
1 AAACCCTAAACCCTTA
**
2484264 AAA-CCTAAAAAC-TA
1 AAACCCTAAACCCTTA
*
2484278 TAAACCCTAAACTCTTA
1 -AAACCCTAAACCCTTA
2484295 AAACCCT-AACCCTTA
1 AAACCCTAAACCCTTA
2484310 AA
1 AA
2484312 TTAAAAACAC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
13 1 0.03
14 7 0.18
15 15 0.38
16 14 0.36
17 2 0.05
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.21
Consensus pattern (16 bp):
AAACCCTAAACCCTTA
Found at i:2484420 original size:44 final size:44
Alignment explanation
Indices: 2484360--2484715 Score: 167
Period size: 44 Copynumber: 7.8 Consensus size: 44
2484350 AACTTTTAAC
* * *
2484360 TAAAAAAACCGAAACTCTTAACTTAAAAATCTTAAACCATAAAT
1 TAAAAAACCCTAAACTCTTAACTTAAAAATCTTAAACCTTAAAT
* *
2484404 TAAAAAACCCTAAACTCTTAACCTAAAACTATAAACCCTAAACCTTAAACT
1 TAAAAAACCCTAAACTCTTAACTTAAAA--AT----CTTAAACCTTAAA-T
* * * * **
2484455 T-AAAAACCATAAAAC-CTTAACCTAAAAACCTTAAATTCTTAACC
1 TAAAAAACCCT-AAACTCTTAACTTAAAAATCTTAAA-CCTTAAAT
* * * * * *
2484499 T-AAAAACCCTAAAGC-ATAAACTAAAAAACCTTAACCTCTTAACCT
1 TAAAAAACCCTAAA-CTCTTAACTTAAAAATCTTAAAC-CTTAA-AT
* * * * * *
2484544 AAAAACCTAAATCCTAAAAC-CTTAAACCTAAAAATCATAAACCTTTAAC
1 -TAAA---AAACCCT-AAACTCTT-AACTTAAAAATCTTAAACCTTAAAT
* *
2484593 TAAAAAACCCTAAA-TCTTAAACCTTTAAAATCCT-AACCTTTAAAT
1 TAAAAAACCCTAAACTCTT-AA-CTTAAAAATCTTAAACC-TTAAAT
* * * *
2484638 T-AAAAACACT-AACCCTAAACTT-AAAATCTTTAACCCTT-AAT
1 TAAAAAACCCTAAACTCTTAACTTAAAAATC-TTAAACCTTAAAT
*
2484679 TAAAAAACCCTAAACTCTTAACTTAAAAACCTTAAAC
1 TAAAAAACCCTAAACTCTTAACTTAAAAATCTTAAAC
2484716 TTTTAACTTG
Statistics
Matches: 236, Mismatches: 48, Indels: 57
0.69 0.14 0.17
Matches are distributed among these distances:
41 10 0.04
42 14 0.06
43 25 0.11
44 88 0.37
45 26 0.11
46 2 0.01
47 2 0.01
48 4 0.02
50 43 0.18
51 22 0.09
ACGTcount: A:0.50, C:0.24, G:0.01, T:0.25
Consensus pattern (44 bp):
TAAAAAACCCTAAACTCTTAACTTAAAAATCTTAAACCTTAAAT
Found at i:2484561 original size:15 final size:15
Alignment explanation
Indices: 2484539--2484587 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
2484529 TTAACCTCTT
2484539 AACCTAAAAACC-TA
1 AACCTAAAAACCTTA
2484553 AATCCT-AAAACCTTA
1 AA-CCTAAAAACCTTA
* *
2484568 AACCTAAAAATCATA
1 AACCTAAAAACCTTA
2484583 AACCT
1 AACCT
2484588 TTAACTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (15 bp):
AACCTAAAAACCTTA
Found at i:2484562 original size:14 final size:14
Alignment explanation
Indices: 2484539--2484576 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
2484529 TTAACCTCTT
2484539 AACCTAAAAACC-TA
1 AACCT-AAAACCTTA
2484553 AATCCTAAAACCTTA
1 AA-CCTAAAACCTTA
2484568 AACCTAAAA
1 AACCTAAAA
2484577 ATCATAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.18
Consensus pattern (14 bp):
AACCTAAAACCTTA
Found at i:2484565 original size:66 final size:67
Alignment explanation
Indices: 2484425--2484565 Score: 173
Period size: 66 Copynumber: 2.1 Consensus size: 67
2484415 AAACTCTTAA
* * *
2484425 CCTAAAA-CTATAAACCCTAAACCTTAAACTTAAAAACCATAAAACCTTAACCTAAAAACCTTAA
1 CCTAAAACCTAAAAACCCTAAACCATAAACTAAAAAACCATAAAACCTTAACCTAAAAACCTTAA
2484489 AT
66 AT
* * * * *
2484491 TCT-TAACCTAAAAACCCTAAAGCATAAACTAAAAAACC-TTAACCTCTTAACCTAAAAACC-TA
1 CCTAAAACCTAAAAACCCTAAACCATAAACTAAAAAACCATAAAAC-CTTAACCTAAAAACCTTA
2484553 AAT
65 AAT
2484556 CCTAAAACCT
1 CCTAAAACCT
2484566 TAAACCTAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
65 13 0.21
66 49 0.79
ACGTcount: A:0.50, C:0.27, G:0.01, T:0.23
Consensus pattern (67 bp):
CCTAAAACCTAAAAACCCTAAACCATAAACTAAAAAACCATAAAACCTTAACCTAAAAACCTTAA
AT
Found at i:2484649 original size:21 final size:20
Alignment explanation
Indices: 2484617--2484797 Score: 62
Period size: 21 Copynumber: 8.5 Consensus size: 20
2484607 TCTTAAACCT
*
2484617 TTAAAATCCTAACCTTTAAA
1 TTAAAAACCTAACCTTTAAA
*
2484637 TTAAAAACACTAACC-CTAAA
1 TTAAAAAC-CTAACCTTTAAA
* * *
2484657 CTTAAAATCTTTAACCCTT-AA
1 -TTAAAAAC-CTAACCTTTAAA
* *
2484678 TTAAAAAACCCTAAACTCTTAAC
1 TT-AAAAA-CCTAACCT-TTAAA
* *
2484701 TTAAAAACCTTAAACTTTTAAC
1 TTAAAAACC-T-AACCTTTAAA
* * *
2484723 TT-GAAACCATAAACTCTAAA
1 TTAAAAACC-TAACCTTTAAA
* * *
2484743 CCCTAAAACCCTAAACTTTAAA
1 --TTAAAAACCTAACCTTTAAA
*
2484765 CTTAAAAACCATAAACCTTTAAC
1 -TTAAAAACC-T-AACCTTTAAA
*
2484788 TAAAAAACCT
1 TTAAAAACCT
2484798 TAAATCCTAA
Statistics
Matches: 119, Mismatches: 28, Indels: 27
0.68 0.16 0.16
Matches are distributed among these distances:
20 19 0.16
21 45 0.38
22 37 0.31
23 18 0.15
ACGTcount: A:0.48, C:0.24, G:0.01, T:0.28
Consensus pattern (20 bp):
TTAAAAACCTAACCTTTAAA
Found at i:2484686 original size:42 final size:42
Alignment explanation
Indices: 2484617--2484706 Score: 103
Period size: 42 Copynumber: 2.1 Consensus size: 42
2484607 TCTTAAACCT
*
2484617 TTAAAATCCTAACCTTTAAATTAAAAACACT-AACCCTAAAC
1 TTAAAATCCTAACCCTTAAATTAAAAACACTAAACCCTAAAC
* * * *
2484658 TTAAAATCTTTAACCCTT-AATTAAAAAACCCTAAACTCTTAAC
1 TTAAAATC-CTAACCCTTAAATT-AAAAACACTAAACCCTAAAC
2484701 TTAAAA
1 TTAAAA
2484707 ACCTTAAACT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 12 0.29
42 15 0.37
43 14 0.34
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (42 bp):
TTAAAATCCTAACCCTTAAATTAAAAACACTAAACCCTAAAC
Found at i:2484706 original size:22 final size:22
Alignment explanation
Indices: 2484340--2485014 Score: 145
Period size: 22 Copynumber: 30.2 Consensus size: 22
2484330 ACCCTAAACC
* *
2484340 TAAAACCCCT-AACTTTTAACT
1 TAAAAACCCTAAACTCTTAACT
* * *
2484361 AAAAAAACCGAAACTCTTAACT
1 TAAAAACCCTAAACTCTTAACT
* * * *
2484383 TAAAAATCTTAAAC-CATAAAT
1 TAAAAACCCTAAACTCTTAACT
2484404 TAAAAAACCCTAAACTCTTAACCT
1 T-AAAAACCCTAAACTCTTAA-CT
*
2484428 AAAACTATAAACCCTAAAC-CTTAAACT
1 -----TAAAAACCCTAAACTCTT-AACT
* *
2484455 TAAAAACCATAAAAC-CTTAACC
1 TAAAAACCCT-AAACTCTTAACT
* * *
2484477 TAAAAACCTTAAATTCTTAACC
1 TAAAAACCCTAAACTCTTAACT
* *
2484499 TAAAAACCCTAAAGC-ATAAACT
1 TAAAAACCCTAAA-CTCTTAACT
* * * *
2484521 AAAAAACCTTAACCTCTTAACC
1 TAAAAACCCTAAACTCTTAACT
*
2484543 TAAAAA-CCTAAA-TCCTAAAACCT
1 TAAAAACCCTAAACT-CT-TAA-CT
* *
2484566 T--AAA-CCTAAAAATCATAAACCTT
1 TAAAAACCCT-AAACTC-TTAA-C-T
2484589 TAACTAAAAAACCCTAAA-TCTTAAACCT
1 T-----AAAAACCCTAAACTCTT-AA-CT
* * * *
2484617 TTAAAATCCTAACCT-TTAAAT
1 TAAAAACCCTAAACTCTTAACT
* * *
2484638 TAAAAACACT-AACCCTAAACT
1 TAAAAACCCTAAACTCTTAACT
* * * *
2484659 T-AAAATCTTTAACCCTTAA-T
1 TAAAAACCCTAAACTCTTAACT
2484679 TAAAAAACCCTAAACTCTTAACT
1 T-AAAAACCCTAAACTCTTAACT
* *
2484702 TAAAAACCTTAAACTTTTAACT
1 TAAAAACCCTAAACTCTTAACT
* * * *
2484724 T-GAAACCATAAACTCTAAACCC
1 TAAAAACCCTAAACTCTTAA-CT
2484746 T-AAAACCCTAAACT-TTAAACT
1 TAAAAACCCTAAACTCTT-AACT
*
2484767 TAAAAACCATAAAC-CTTTAACT
1 TAAAAACCCTAAACTC-TTAACT
* * *
2484789 AAAAAACCTTAAA-TCCTAAACTT
1 TAAAAACCCTAAACT-CTTAAC-T
** * ** *
2484812 TTGAAACCATAGCCT-TTAAAT
1 TAAAAACCCTAAACTCTTAACT
* * * *
2484833 TAAAAACACT-AACCCTAAACC
1 TAAAAACCCTAAACTCTTAACT
* *
2484854 TAAAAACCC-AAACCCTAAATCT
1 TAAAAACCCTAAACTCTTAA-CT
2484876 T--AAACCCTAAACT-TTAAACCCTTAACT
1 TAAAAACCCTAAACTCTT--A-----A-CT
*
2484903 TAAAAACCCTAAA-TCATAAACT
1 TAAAAACCCTAAACTC-TTAACT
* *
2484925 AAAAAACCCT-AAC-CTTAAACC
1 TAAAAACCCTAAACTCTT-AACT
2484946 T-AAAACTCCTAAAC-CTTTAACT
1 TAAAAAC-CCTAAACTC-TTAACT
* * * * *
2484968 AAAAAATCCTAAACCCTAAACC
1 TAAAAACCCTAAACTCTTAACT
*
2484990 TAAAAACCCT-AACCCTTAACT
1 TAAAAACCCTAAACTCTTAACT
2485011 TAAA
1 TAAA
2485015 TATAATTTGA
Statistics
Matches: 478, Mismatches: 109, Indels: 134
0.66 0.15 0.19
Matches are distributed among these distances:
20 24 0.05
21 119 0.25
22 228 0.48
23 49 0.10
24 3 0.01
27 9 0.02
28 19 0.04
29 17 0.04
30 7 0.01
31 3 0.01
ACGTcount: A:0.49, C:0.26, G:0.01, T:0.25
Consensus pattern (22 bp):
TAAAAACCCTAAACTCTTAACT
Found at i:2484724 original size:65 final size:65
Alignment explanation
Indices: 2484560--2484809 Score: 175
Period size: 65 Copynumber: 3.8 Consensus size: 65
2484550 CTAAATCCTA
* * * * * * * ** *
2484560 AAACCTTAAACCTAAAAATCATAAACCTTTAACTAAAAAACCCTAAATCTTAAACCTTTAAAATC
1 AAACTTTAAACTTAAAAACCATAAACCTTTAACT-TAAAACCATAAACCCTAAACC-AAAAAACC
2484625 CT
64 CT
* * * * * * * **
2484627 AACCTTTAAA-TTAAAAA-CACT-AACCCTAAACTTAAAATCTTTAACCCTTAATTAAAAAACCC
1 AAACTTTAAACTTAAAAACCA-TAAACCTTTAACTTAAAACCATAAACCCTAAACCAAAAAACCC
2484689 T
65 T
* * * * **
2484690 AAACTCTT-AACTTAAAAACCTTAAACTTTTAACTTGAAACCATAAACTCTAAACCCTAAAACCC
1 AAACT-TTAAACTTAAAAACCATAAACCTTTAACTTAAAACCATAAACCCTAAACCAAAAAACCC
2484754 T
65 T
* * *
2484755 AAACTTTAAACTTAAAAACCATAAACCTTTAACTAAAAAACCTTAAATCCTAAAC
1 AAACTTTAAACTTAAAAACCATAAACCTTTAACT-TAAAACCATAAACCCTAAAC
2484810 TTTTGAAACC
Statistics
Matches: 137, Mismatches: 39, Indels: 15
0.72 0.20 0.08
Matches are distributed among these distances:
63 13 0.09
64 24 0.18
65 70 0.51
66 22 0.16
67 8 0.06
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.27
Consensus pattern (65 bp):
AAACTTTAAACTTAAAAACCATAAACCTTTAACTTAAAACCATAAACCCTAAACCAAAAAACCCT
Found at i:2484730 original size:43 final size:44
Alignment explanation
Indices: 2484572--2484801 Score: 140
Period size: 43 Copynumber: 5.3 Consensus size: 44
2484562 ACCTTAAACC
* * * *
2484572 TAAAAATCATAAACCTTT-AACTAAAAAACCCTAAA-TCTTAAACCTT
1 TAAAAACCTTAAA-CTTTAAACTTAAAAACCATAAACTCTT-AA-C-T
* * * *
2484618 TAAAATCC-TAACCTTTAAA-TTAAAAA-CACT-AACCCTAAACT
1 TAAAAACCTTAAACTTTAAACTTAAAAACCA-TAAACTCTTAACT
* * * * *
2484659 TAAAATCTTTAACCCTT-AA-TTAAAAAACCCTAAACTCTTAACT
1 TAAAAACCTTAAACTTTAAACTT-AAAAACCATAAACTCTTAACT
* * * *
2484702 TAAAAACCTTAAACTTTTAACTT-GAAACCATAAACTCTAAACCC
1 TAAAAACCTTAAACTTTAAACTTAAAAACCATAAACTCTTAA-CT
*
2484746 T-AAAACCCTAAACTTTAAACTTAAAAACCATAAAC-CTTTAACT
1 TAAAAACCTTAAACTTTAAACTTAAAAACCATAAACTC-TTAACT
*
2484789 AAAAAACCTTAAA
1 TAAAAACCTTAAA
2484802 TCCTAAACTT
Statistics
Matches: 144, Mismatches: 27, Indels: 28
0.72 0.14 0.14
Matches are distributed among these distances:
41 12 0.08
42 14 0.10
43 64 0.44
44 41 0.28
45 7 0.05
46 6 0.04
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (44 bp):
TAAAAACCTTAAACTTTAAACTTAAAAACCATAAACTCTTAACT
Found at i:2484879 original size:43 final size:44
Alignment explanation
Indices: 2484828--2485014 Score: 138
Period size: 43 Copynumber: 4.2 Consensus size: 44
2484818 CCATAGCCTT
2484828 TAAA-TTAAAAACACT-AACCCTAAACCTAAAAACCC-AAACCC
1 TAAACTTAAAAACACTAAACCCTAAACCTAAAAACCCTAAACCC
* * * *
2484869 TAAATCTTAAACCCTAA-ACTTTAAACCCTTAACTTAAAAACCCTAAATCA
1 TAAA-CTTAAA----AACAC--TAAACCCTAAACCTAAAAACCCTAAACCC
* * * *
2484919 TAAACTAAAAAACCCT-AACCTTAAACCT-AAAACTCCTAAACCT
1 TAAACTTAAAAACACTAAACCCTAAACCTAAAAAC-CCTAAACCC
* *
2484962 TTAACTAAAAAATC-CTAAACCCTAAACCTAAAAACCCT-AACCC
1 TAAACTTAAAAA-CACTAAACCCTAAACCTAAAAACCCTAAACCC
*
2485005 TTAACTTAAA
1 TAAACTTAAA
2485015 TATAATTTGA
Statistics
Matches: 116, Mismatches: 15, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
41 4 0.03
42 5 0.04
43 47 0.41
44 16 0.14
45 7 0.06
46 3 0.03
47 2 0.02
48 1 0.01
49 23 0.20
50 8 0.07
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (44 bp):
TAAACTTAAAAACACTAAACCCTAAACCTAAAAACCCTAAACCC
Found at i:2484887 original size:21 final size:21
Alignment explanation
Indices: 2484833--2485014 Score: 73
Period size: 21 Copynumber: 8.2 Consensus size: 21
2484823 GCCTTTAAAT
* *
2484833 TAAAAACACTAACCCTAAACC
1 TAAAAACCCAAACCCTAAACC
*
2484854 TAAAAACCCAAACCCTAAATCT
1 TAAAAACCCAAACCCTAAA-CC
** * *
2484876 TAAACCCTAAACTTTAAACCCTTAACT
1 T-AA----AAAC-CCAAACCCTAAACC
* *
2484903 TAAAAACCCTAAATCATAAA-C
1 TAAAAACCC-AAACCCTAAACC
* *
2484924 TAAAAAACCCTAACCTTAAACC
1 T-AAAAACCCAAACCCTAAACC
* *
2484946 T-AAAACTCCTAAACCTTTAA-C
1 TAAAAAC-CC-AAACCCTAAACC
*
2484967 TAAAAAATCCTAAACCCTAAACC
1 T-AAAAA-CCCAAACCCTAAACC
* * *
2484990 TAAAAACCCTAACCCTTAACT
1 TAAAAACCCAAACCCTAAACC
2485011 TAAA
1 TAAA
2485015 TATAATTTGA
Statistics
Matches: 121, Mismatches: 24, Indels: 32
0.68 0.14 0.18
Matches are distributed among these distances:
20 5 0.04
21 44 0.36
22 44 0.36
23 9 0.07
24 1 0.01
26 2 0.02
27 7 0.06
28 9 0.07
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (21 bp):
TAAAAACCCAAACCCTAAACC
Found at i:2484911 original size:15 final size:14
Alignment explanation
Indices: 2484863--2484915 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
2484853 CTAAAAACCC
2484863 AAACCCTAAATCTT-
1 AAACCCTAAA-CTTA
*
2484877 AAACCCTAAACTTT
1 AAACCCTAAACTTA
*
2484891 AAACCCTTAACTTAA
1 AAACCCTAAACTT-A
2484906 AAACCCTAAA
1 AAACCCTAAA
2484916 TCATAAACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 3 0.09
14 22 0.65
15 9 0.26
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (14 bp):
AAACCCTAAACTTA
Found at i:2484973 original size:65 final size:64
Alignment explanation
Indices: 2484863--2485008 Score: 170
Period size: 65 Copynumber: 2.2 Consensus size: 64
2484853 CTAAAAACCC
* * * *
2484863 AAACCCTAAATCTTAAACCCTAAACTTTAAACCCTTAACTTAAAAACCCTAAATCATAAA-CTAA
1 AAACCCT-AACCTTAAACCCTAAACTCTAAACCCTTAACTAAAAAACCCTAAACCATAAACCT-A
2484927 A
64 A
* * *
2484928 AAACCCTAACCTTAAA-CCTAAAACTCCTAAACCTTTAACTAAAAAATCCTAAACCCTAAACCTA
1 AAACCCTAACCTTAAACCCT-AAACT-CTAAACCCTTAACTAAAAAACCCTAAACCATAAACCTA
2484992 A
64 A
2484993 AAACCCTAACCCTTAA
1 AAACCCTAA-CCTTAA
2485009 CTTAAATATA
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
63 3 0.04
64 13 0.19
65 46 0.66
66 8 0.11
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (64 bp):
AAACCCTAACCTTAAACCCTAAACTCTAAACCCTTAACTAAAAAACCCTAAACCATAAACCTAA
Found at i:2486207 original size:53 final size:53
Alignment explanation
Indices: 2485111--2486185 Score: 1830
Period size: 53 Copynumber: 20.3 Consensus size: 53
2485101 TGACCGGTAC
*
2485111 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAATATTAATACAAT
1 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAACATTAATACAAT
*
2485164 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAATATTAATACAAT
1 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAACATTAATACAAT
*
2485217 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAATATTAATACAAT
1 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAACATTAATACAAT
*
2485270 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAATATTAATACAAT
1 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAACATTAATACAAT
*
2485323 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAATATTAATACAAT
1 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAACATTAATACAAT
*
2485376 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAATATTAATACAAT
1 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAACATTAATACAAT
*
2485429 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAATATTAATACAAT
1 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAACATTAATACAAT
*
2485482 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAATATTAATACAAT
1 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAACATTAATACAAT
*
2485535 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAATATTAATACAAT
1 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAACATTAATACAAT
*
2485588 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAATATTAATACAAT
1 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAACATTAATACAAT
* *
2485641 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAACCATTACTACAAT
1 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAACATTAATACAAT
* *
2485694 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAACCATTACTACAAT
1 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAACATTAATACAAT
* *
2485747 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAACCATTACTACAAT
1 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAACATTAATACAAT
* *
2485800 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAACCATTACTACAAT
1 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAACATTAATACAAT
* *
2485853 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAACCATTACTACAAT
1 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAACATTAATACAAT
* *
2485906 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAACCATTACTACAAT
1 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAACATTAATACAAT
*
2485959 TATCAATTAATAATTTGATATAATTTG-TAAATTTTACTAACCATTAATACAAT
1 TATCAATTAATAATTTGATATAATTTGAT-AATTTTACTAAACATTAATACAAT
* * * *
2486012 TATCAATTAATAATTAGATATAATTTGATGATTTTACTAACCATTACTACAAT
1 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAACATTAATACAAT
* *
2486065 GATCAATTAATAATTTGATATAATTT-ATAAATTTTACTAACCATTAATACAAT
1 TATCAATTAATAATTTGATATAATTTGAT-AATTTTACTAAACATTAATACAAT
* * *
2486118 TATCAATTAATAATTAGATATAATTTGATAATTTTACTAACCATCAATACAAT
1 TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAACATTAATACAAT
2486171 TATCAATTAATAATT
1 TATCAATTAATAATT
2486186 GAAAAAAATA
Statistics
Matches: 1004, Mismatches: 14, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
52 3 0.00
53 998 0.99
54 3 0.00
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (53 bp):
TATCAATTAATAATTTGATATAATTTGATAATTTTACTAAACATTAATACAAT
Found at i:2489470 original size:126 final size:126
Alignment explanation
Indices: 2489187--2489641 Score: 698
Period size: 126 Copynumber: 3.6 Consensus size: 126
2489177 CCCGAACATG
* *
2489187 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTTTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACATGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * **
2489252 -AGGAAGCGTTTTTTTTATACTATTTGCTCAGAAATGTCAACTCGGCATTATTTTTTCCAGGAC
66 TA-GAAGCG--TTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCCAGGAC
* * *
2489315 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAACGCATCCTGG
1 CTACTGTAGCAAAAGCGCGTCCACATGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
*
2489380 TAGAAGCGTTTTTTATACTATTCGCTCAGAAACATCAACTCGAAATTATTTTTTCCAGGAC
66 TAGAAGCGTTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCCAGGAC
* *
2489441 CTACTGTAGCAAAAGCGCGTCCACATGGGCGCGATTTCACAAATTCTTCTTATAACGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACATGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
2489506 TAGAAGCGTTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCCAGGAC
66 TAGAAGCGTTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCCAGGAC
* * * * * *
2489567 CAACTATAGCAAAAGCACGTCCACGA-GGGCGCAATTTCACAAATTCTTCTCATAAAACATCATG
1 CTACTGTAGCAAAAGCGCGTCCAC-ATGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTG
2489631 CTAGAAGCGTT
65 CTAGAAGCGTT
2489642 ATCTTAAAAA
Statistics
Matches: 305, Mismatches: 20, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
126 235 0.77
127 1 0.00
128 68 0.22
129 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCACATGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TAGAAGCGTTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCCAGGAC
Found at i:2490034 original size:29 final size:29
Alignment explanation
Indices: 2489974--2490032 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
2489964 AGGGAAAAAC
*
2489974 GGCCCATTCCGGTAAATAATAAAATATAG
1 GGCCCATTCCGGTAAATAATAAAATAAAG
*
2490003 GGCCCATTTCGGTAAATTAA-AAAA-AAAG
1 GGCCCATTCCGGTAAA-TAATAAAATAAAG
2490031 GG
1 GG
2490033 GCTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 5 0.19
29 19 0.70
30 3 0.11
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.22
Consensus pattern (29 bp):
GGCCCATTCCGGTAAATAATAAAATAAAG
Found at i:2492492 original size:15 final size:16
Alignment explanation
Indices: 2492472--2492502 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2492462 AATTAAAATA
2492472 TAATTTTATC-ATTAT
1 TAATTTTATCAATTAT
2492487 TAATTTTATCAATTAT
1 TAATTTTATCAATTAT
2492503 AAAGGATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATTTTATCAATTAT
Found at i:2509743 original size:44 final size:44
Alignment explanation
Indices: 2509657--2509743 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
2509647 GCGTTCTTGG
* *
2509657 AAAAAATAAAAAAATAACAGAATTAAAGGTTTGGATCTGAAAAC
1 AAAAAATAAAAAAATAACAGAATTAAAGATTTGAATCTGAAAAC
2509701 AAAAAATAAAATAAA-AACAGAATT-AAGAATATTGAATC-GAAAA
1 AAAAAATAAAA-AAATAACAGAATTAAAG-AT-TTGAATCTGAAAA
2509744 TTCGAGAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
43 3 0.08
44 26 0.68
45 9 0.24
ACGTcount: A:0.63, C:0.06, G:0.11, T:0.20
Consensus pattern (44 bp):
AAAAAATAAAAAAATAACAGAATTAAAGATTTGAATCTGAAAAC
Found at i:2512626 original size:24 final size:24
Alignment explanation
Indices: 2512551--2512626 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 24
2512541 CCAGGCAATA
* *
2512551 TAATGGGAAGCTCACAAAGAGC-CT
1 TAATGGGTAGCTC-CGAAGAGCACT
* * *
2512575 ATAATGGGTAACTCCGAAGAGTAAT
1 -TAATGGGTAGCTCCGAAGAGCACT
2512600 TAATGGGTAGCTCCGAAGAGCACT
1 TAATGGGTAGCTCCGAAGAGCACT
2512624 TAA
1 TAA
2512627 CAGGAAGCAC
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
24 30 0.71
25 12 0.29
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (24 bp):
TAATGGGTAGCTCCGAAGAGCACT
Found at i:2514820 original size:28 final size:28
Alignment explanation
Indices: 2514788--2514859 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
2514778 TAATGAGATT
*
2514788 AGCACTAAGTGTGCGAGTTTAATGGTAA
1 AGCACTAAGTGTGCGAGTTTAATGATAA
* * *
2514816 AGCACTAAGTGTGCGAGTTTGATTATTA
1 AGCACTAAGTGTGCGAGTTTAATGATAA
*
2514844 AGCACTAAATGTGCGA
1 AGCACTAAGTGTGCGA
2514860 ACTTATTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTAATGATAA
Found at i:2518428 original size:3 final size:3
Alignment explanation
Indices: 2518420--2518454 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2518410 ATTCGATTCT
2518420 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2518455 TAAAGATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2519892 original size:24 final size:23
Alignment explanation
Indices: 2519846--2519894 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2519836 GAAATAGTTG
* *
2519846 AAAAAGATTAAAACTTTTTTTTA
1 AAAAAAATTAAAACTTTTCTTTA
*
2519869 AAAAAAATTTAAACTTTTCCTTTA
1 AAAAAAATTAAAACTTTT-CTTTA
2519893 AA
1 AA
2519895 TGACTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (23 bp):
AAAAAAATTAAAACTTTTCTTTA
Found at i:2520089 original size:146 final size:146
Alignment explanation
Indices: 2519810--2520088 Score: 397
Period size: 145 Copynumber: 1.9 Consensus size: 146
2519800 AAATCACTAC
* *
2519810 TTTCTTAAAAATAAAAATTTTATTTAGAAATAGTTGAAAAAGATTAAAACTTTTTTTTAAAAAAA
1 TTTCTTAAAAATAAAAATTTTATTTAGAAATAGTTGAAAAAAATCAAAACTTTTTTTT--AAAAA
2519875 ATTTAAACTTTTCCTTTAAATGACTAAAAAATAGATTTTTATTTTAAAAATCTAAACTTTCTCTT
64 ATTTAAACTTTTCCTTTAAATGACTAAAAAATAGATTTTTATTTTAAAAATCTAAACTTTCTCTT
2519940 TTTTAAAAAACCACCATT
129 TTTTAAAAAACCACCATT
* ** *
2519958 TTTCTTAAAGATCAAAGCTTTTATTTTGAAATAGTTGAAAAAAATCAAAA-TTTTGTTTT-AAAA
1 TTTCTTAAAAAT-AAAAATTTTATTTAGAAATAGTTGAAAAAAATCAAAACTTTT-TTTTAAAAA
* *
2520021 ATTTAAAC-TTTCCTTTAAAATGATTAAAAAAT-TATTTTTAGTTTT-AAAATCTAAACTTTCTC
64 ATTTAAACTTTTCCTTT-AAATGACTAAAAAATAGATTTTTA-TTTTAAAAATCTAAACTTTCTC
2520083 TTTTTT
127 TTTTTT
2520089 TTTAAATAAA
Statistics
Matches: 119, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
145 38 0.32
146 30 0.25
148 15 0.13
149 36 0.30
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (146 bp):
TTTCTTAAAAATAAAAATTTTATTTAGAAATAGTTGAAAAAAATCAAAACTTTTTTTTAAAAAAT
TTAAACTTTTCCTTTAAATGACTAAAAAATAGATTTTTATTTTAAAAATCTAAACTTTCTCTTTT
TTAAAAAACCACCATT
Found at i:2520522 original size:2 final size:2
Alignment explanation
Indices: 2520515--2520546 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2520505 CTTTCTCTTG
2520515 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2520547 AATTTTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2520584 original size:23 final size:24
Alignment explanation
Indices: 2520549--2520600 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 24
2520539 CTCTCTCTAA
2520549 TTTTTCTTCTTTT-TT-TTTGGTTTC
1 TTTTTCTTCTTTTGTTGTTT--TTTC
*
2520573 TTTTTC-TGTTTTGTTGTTTTTTC
1 TTTTTCTTCTTTTGTTGTTTTTTC
2520596 TTTTT
1 TTTTT
2520601 TATTCTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 14 0.56
24 8 0.32
25 3 0.12
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.81
Consensus pattern (24 bp):
TTTTTCTTCTTTTGTTGTTTTTTC
Found at i:2520675 original size:13 final size:13
Alignment explanation
Indices: 2520657--2520722 Score: 62
Period size: 13 Copynumber: 5.1 Consensus size: 13
2520647 AGTTTAGCAT
*
2520657 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
2520670 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
*
2520683 TG-TTATGGAAAAG
1 TGCTT-TTGAAAAG
* *
2520696 TGATTTTGAGAAG
1 TGCTTTTGAAAAG
*
2520709 TACTTTTGAAAAG
1 TGCTTTTGAAAAG
2520722 T
1 T
2520723 TTGGTTTAAG
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
12 2 0.05
13 38 0.90
14 2 0.05
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:2528646 original size:61 final size:61
Alignment explanation
Indices: 2528518--2528647 Score: 138
Period size: 61 Copynumber: 2.1 Consensus size: 61
2528508 AATATATTTT
* * * * * *
2528518 AATTTTTAGAGTTAAGAATAAATTGAAAAATTTTGTAAATATTAAGGGTCAAATTTATTGA
1 AATTTTTAGAGATAAGAATAAAATGAAAAATTTTGTAAACATTAAGGATCAAATTCATTAA
* * * *
2528579 ATTTTTTAGA-ATGAGAACTAAAATGATAAATTTTGTAAACATTAAAGGAT-AAATTCGTTAA
1 AATTTTTAGAGATAAGAA-TAAAATGAAAAATTTTGTAAACATT-AAGGATCAAATTCATTAA
2528640 AATTTTTA
1 AATTTTTA
2528648 ACATAATTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
60 5 0.09
61 46 0.82
62 5 0.09
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.39
Consensus pattern (61 bp):
AATTTTTAGAGATAAGAATAAAATGAAAAATTTTGTAAACATTAAGGATCAAATTCATTAA
Found at i:2541517 original size:21 final size:21
Alignment explanation
Indices: 2541482--2541535 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
2541472 AAATACTAAT
* * *
2541482 AACAATATTATTATTATCAAC
1 AACAATAATAATATTACCAAC
*
2541503 AACAGTAATAATATTACCAAC
1 AACAATAATAATATTACCAAC
*
2541524 AATAATAATAAT
1 AACAATAATAAT
2541536 TTTGAGTTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.31
Consensus pattern (21 bp):
AACAATAATAATATTACCAAC
Found at i:2555110 original size:40 final size:41
Alignment explanation
Indices: 2555038--2555114 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
2555028 CATTTAATTA
* *
2555038 ATTTTTAAATTTAAAAAATTTAAAAGAGTATATAAAAAACC
1 ATTTTAAAAATTAAAAAATTTAAAAGAGTATATAAAAAACC
*
2555079 ATTTTAAAAATTAAAATTATTTAAAA-A-TATATAAAA
1 ATTTTAAAAATTAAAA-AATTTAAAAGAGTATATAAAA
2555115 TTTATAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
40 9 0.28
41 15 0.47
42 8 0.25
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (41 bp):
ATTTTAAAAATTAAAAAATTTAAAAGAGTATATAAAAAACC
Found at i:2557252 original size:15 final size:15
Alignment explanation
Indices: 2557228--2557261 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2557218 CATATGCCTC
*
2557228 TCATCATCTTTGTCA
1 TCATCATCTTTATCA
*
2557243 TCATCGTCTTTATCA
1 TCATCATCTTTATCA
2557258 TCAT
1 TCAT
2557262 GGCTATCTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.26, G:0.06, T:0.47
Consensus pattern (15 bp):
TCATCATCTTTATCA
Found at i:2559065 original size:22 final size:24
Alignment explanation
Indices: 2559017--2559066 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
2559007 TGTCAAGCCT
*
2559017 AAAAT-CATTTTATAAACAACATC
1 AAAATACACTTTATAAACAACATC
2559040 -AAATACACTTTA-AAACAAC-TC
1 AAAATACACTTTATAAACAACATC
2559061 AAAATA
1 AAAATA
2559067 TGTCAATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 2 0.08
22 16 0.67
23 6 0.25
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (24 bp):
AAAATACACTTTATAAACAACATC
Found at i:2560006 original size:71 final size:71
Alignment explanation
Indices: 2559890--2560071 Score: 258
Period size: 71 Copynumber: 2.6 Consensus size: 71
2559880 GTGCTCAGTG
* * * *
2559890 CTAGTCGGGTAAACCGGCAGTAGATGTGCCTTGCACTAGTTAAATAAATCGATAAAAATTTGCGC
1 CTAGTCAGGTAAACCGACAGTAGATGTGCCCTGCACTAGTCAAATAAATCGATAAAAATTTGCGC
2559955 CCAGCA
66 CCAGCA
* * *
2559961 CTAGTTAGGTAAACCGACAGTAGATGTGCCCTGCACTAGTCAAATAAATCGATAAATATTTGTGC
1 CTAGTCAGGTAAACCGACAGTAGATGTGCCCTGCACTAGTCAAATAAATCGATAAAAATTTGCGC
* *
2560026 CTAGCG
66 CCAGCA
*
2560032 CTAGTCGGGTAAACCGACAGTAGATGT-CTCCTGCACTAGT
1 CTAGTCAGGTAAACCGACAGTAGATGTGC-CCTGCACTAGT
2560072 GTAATAGCCT
Statistics
Matches: 99, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
70 1 0.01
71 98 0.99
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (71 bp):
CTAGTCAGGTAAACCGACAGTAGATGTGCCCTGCACTAGTCAAATAAATCGATAAAAATTTGCGC
CCAGCA
Found at i:2562641 original size:36 final size:36
Alignment explanation
Indices: 2562592--2562825 Score: 159
Period size: 36 Copynumber: 6.4 Consensus size: 36
2562582 GGGTGTTACA
* *
2562592 ACTAGTCGAATAAATCGACAAAGATTTGCGCCCAAC
1 ACTAGTCGGATAAATCGACAAAGATTTGCGCCCAGC
* * * * * *
2562628 GCTAGTCGGATAAACCGATGATATTAAATGTGTGCCCAGC
1 ACTAGTCGGATAAATCGA-CA-A--AGATTTGCGCCCAGC
*
2562668 ACTAGTCGGATTAA-CAGACAAAGATTTGCGCCCAGC
1 ACTAGTCGGATAAATC-GACAAAGATTTGCGCCCAGC
* * * * *
2562704 GCTAATCGGATAAATCGATAGTAGATTTGCTCCCAGC
1 ACTAGTCGGATAAATCGACA-AAGATTTGCGCCCAGC
* * * * ** * *
2562741 GCTAGTTGGATAAA-CTA-ACAGTAAATGTGCCCTGC
1 ACTAGTCGGATAAATCGACAAAG-ATTTGCGCCCAGC
* *
2562776 ACTAGTCGAATAAATCGACAAAGATTTACGCCCAGC
1 ACTAGTCGGATAAATCGACAAAGATTTGCGCCCAGC
*
2562812 ACTAGTCAGATAAA
1 ACTAGTCGGATAAA
2562826 CTGACGATAT
Statistics
Matches: 147, Mismatches: 41, Indels: 20
0.71 0.20 0.10
Matches are distributed among these distances:
34 2 0.01
35 20 0.14
36 65 0.44
37 31 0.21
38 2 0.01
39 2 0.01
40 25 0.17
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.23
Consensus pattern (36 bp):
ACTAGTCGGATAAATCGACAAAGATTTGCGCCCAGC
Found at i:2563104 original size:2 final size:2
Alignment explanation
Indices: 2563097--2563548 Score: 904
Period size: 2 Copynumber: 226.0 Consensus size: 2
2563087 TAACTACATC
2563097 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2563139 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2563181 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2563223 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2563265 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2563307 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2563349 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2563391 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2563433 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2563475 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2563517 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2563549 ATTCCACAAC
Statistics
Matches: 450, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 450 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2565468 original size:16 final size:18
Alignment explanation
Indices: 2565432--2565469 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
2565422 ATATCTTTCC
2565432 AAATAAAAATAAATATTA
1 AAATAAAAATAAATATTA
*
2565450 AAAT-AAAAT-AATCTTA
1 AAATAAAAATAAATATTA
2565466 AAAT
1 AAAT
2565470 CTAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 5 0.26
18 4 0.21
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAAAAATAAATATTA
Found at i:2567588 original size:38 final size:38
Alignment explanation
Indices: 2567546--2567660 Score: 95
Period size: 38 Copynumber: 3.2 Consensus size: 38
2567536 ACTTCTAGTG
2567546 TTGTAGAAACTATTGAGACAATTTCAAACTACTTACTT
1 TTGTAGAAACTATTGAGACAATTTCAAACTACTTACTT
* * * *
2567584 TTGTAGTAAAAACTCATT---A-TA-TT---ACTTC-TAGTG
1 TTGTAG---AAACT-ATTGAGACAATTTCAAACTACTTACTT
2567617 TTGTAGAAACTATTGAGACAATTTCAAACTACTTACTT
1 TTGTAGAAACTATTGAGACAATTTCAAACTACTTACTT
2567655 TTGTAG
1 TTGTAG
2567661 TAAAAACTCA
Statistics
Matches: 56, Mismatches: 8, Indels: 26
0.62 0.09 0.29
Matches are distributed among these distances:
29 3 0.05
30 5 0.09
32 1 0.02
33 10 0.18
34 6 0.11
37 6 0.11
38 16 0.29
39 1 0.02
41 5 0.09
42 3 0.05
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (38 bp):
TTGTAGAAACTATTGAGACAATTTCAAACTACTTACTT
Found at i:2567617 original size:71 final size:71
Alignment explanation
Indices: 2567501--2567715 Score: 412
Period size: 71 Copynumber: 3.0 Consensus size: 71
2567491 TCAAGGAAAC
* *
2567501 AACTACATACTTTTGTAGTAAAAACTCATTTTATTACTTCTAGTGTTGTAGAAACTATTGAGACA
1 AACTACTTACTTTTGTAGTAAAAACTCATTATATTACTTCTAGTGTTGTAGAAACTATTGAGACA
2567566 ATTTCA
66 ATTTCA
2567572 AACTACTTACTTTTGTAGTAAAAACTCATTATATTACTTCTAGTGTTGTAGAAACTATTGAGACA
1 AACTACTTACTTTTGTAGTAAAAACTCATTATATTACTTCTAGTGTTGTAGAAACTATTGAGACA
2567637 ATTTCA
66 ATTTCA
2567643 AACTACTTACTTTTGTAGTAAAAACTCATTATATTACTTCTAGTGTTGTAGAAACTATTGAGACA
1 AACTACTTACTTTTGTAGTAAAAACTCATTATATTACTTCTAGTGTTGTAGAAACTATTGAGACA
2567708 ATTTCA
66 ATTTCA
2567714 AA
1 AA
2567716 AGAGGATAGT
Statistics
Matches: 142, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 142 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (71 bp):
AACTACTTACTTTTGTAGTAAAAACTCATTATATTACTTCTAGTGTTGTAGAAACTATTGAGACA
ATTTCA
Found at i:2568207 original size:15 final size:15
Alignment explanation
Indices: 2568187--2568218 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2568177 TTAGTGTTAG
2568187 GATGATTAATGATTT
1 GATGATTAATGATTT
*
2568202 GATGATTGATGATTT
1 GATGATTAATGATTT
2568217 GA
1 GA
2568219 AAATAAGTAA
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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GATGATTAATGATTT
Found at i:2574718 original size:91 final size:92
Alignment explanation
Indices: 2574607--2574790 Score: 361
Period size: 91 Copynumber: 2.0 Consensus size: 92
2574597 TTTTACATTA
2574607 GTAATAATATATTATCTTATTATAAATTAATGATATATTAATTCATATTTTATGGGCCCCTAAAG
1 GTAATAATATATTATCTTATTATAAATTAATGATATATTAATTCATATTTTATGGGCCCCTAAAG
2574672 TGAAAAAATTTTCAAAAAAATAAATTT
66 TGAAAAAATTTTCAAAAAAATAAATTT
2574699 GTAATAATAT-TTATCTTATTATAAATTAATGATATATTAATTCATATTTTATGGGCCCCTAAAG
1 GTAATAATATATTATCTTATTATAAATTAATGATATATTAATTCATATTTTATGGGCCCCTAAAG
2574763 TGAAAAAATTTTCAAAAAAATAAATTT
66 TGAAAAAATTTTCAAAAAAATAAATTT
2574790 G
1 G
2574791 AAATTAGATT
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
91 82 0.89
92 10 0.11
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (92 bp):
GTAATAATATATTATCTTATTATAAATTAATGATATATTAATTCATATTTTATGGGCCCCTAAAG
TGAAAAAATTTTCAAAAAAATAAATTT
Found at i:2578053 original size:207 final size:208
Alignment explanation
Indices: 2577687--2578102 Score: 825
Period size: 207 Copynumber: 2.0 Consensus size: 208
2577677 TTTAAAAAAT
2577687 ATTTTTACTGATTCATTTATTAGTTTGTGTAAATTTTAATTAAAGTTTAGCGTTAGCCTGGATTG
1 ATTTTTACTGATTCATTTATTAGTTTGTGTAAATTTTAATTAAAGTTTAGCGTTAGCCTGGATTG
2577752 TTGCAGCACAATTTTTGTTGTTAAACATCATGCGTTCTCGGATATTTAAATCCGCAATCCAAACT
66 TTGCAGCACAATTTTTGTTGTTAAACATCATGCGTTCTCGGATATTTAAATCCGCAATCCAAACT
2577817 GTCATCCTTAAATGTTATAGTAGAACCACATAATATACTAACAAAGGAATTACAATTCGTACATA
131 GTCATCCTTAAATGTTATAGTAGAACCACATAATATACTAACAAAGGAATTACAATTCGTACATA
2577882 TTTTATGATCTTC
196 TTTTATGATCTTC
2577895 ATTTTTACTG-TTCATTTATTAGTTTGTGTAAATTTTAATTAAAGTTTAGCGTTAGCCTGGATTG
1 ATTTTTACTGATTCATTTATTAGTTTGTGTAAATTTTAATTAAAGTTTAGCGTTAGCCTGGATTG
2577959 TTGCAGCACAATTTTTGTTGTTAAACATCATGCGTTCTCGGATATTTAAATCCGCAATCCAAACT
66 TTGCAGCACAATTTTTGTTGTTAAACATCATGCGTTCTCGGATATTTAAATCCGCAATCCAAACT
2578024 GTCATCCTTAAATGTTATAGTAGAACCACATAATATACTAACAAAGGAATTACAATTCGTACATA
131 GTCATCCTTAAATGTTATAGTAGAACCACATAATATACTAACAAAGGAATTACAATTCGTACATA
2578089 TTTTATGATCTTC
196 TTTTATGATCTTC
2578102 A
1 A
2578103 CATATAATGA
Statistics
Matches: 208, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
207 198 0.95
208 10 0.05
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (208 bp):
ATTTTTACTGATTCATTTATTAGTTTGTGTAAATTTTAATTAAAGTTTAGCGTTAGCCTGGATTG
TTGCAGCACAATTTTTGTTGTTAAACATCATGCGTTCTCGGATATTTAAATCCGCAATCCAAACT
GTCATCCTTAAATGTTATAGTAGAACCACATAATATACTAACAAAGGAATTACAATTCGTACATA
TTTTATGATCTTC
Found at i:2578937 original size:31 final size:31
Alignment explanation
Indices: 2578897--2578965 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
2578887 TTACAATTTG
*
2578897 ATCACTGAACTATT-AAAAAGTTTTTATTTAA
1 ATCACTGAACTATTCAAAAA-CTTTTATTTAA
* *
2578928 ATCATTGAACTATTCAAAAACTTTTATTTTA
1 ATCACTGAACTATTCAAAAACTTTTATTTAA
*
2578959 GTCACTG
1 ATCACTG
2578966 GGCTATTAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 27 0.84
32 5 0.16
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (31 bp):
ATCACTGAACTATTCAAAAACTTTTATTTAA
Found at i:2583779 original size:19 final size:20
Alignment explanation
Indices: 2583741--2583780 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2583731 ATACATGAAA
* *
2583741 TTAAAAAAATAACTCTTAAT
1 TTAAAAAAATAACACGTAAT
2583761 TTAAAAAAATAA-ACGTAAT
1 TTAAAAAAATAACACGTAAT
2583780 T
1 T
2583781 ATCTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (20 bp):
TTAAAAAAATAACACGTAAT
Found at i:2594770 original size:28 final size:29
Alignment explanation
Indices: 2594708--2594776 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 29
2594698 CTAATGACAA
*
2594708 AAGTTCCAACTT-GGGGGAAAAAATAGTTT
1 AAGTACCAACTTAGGGGG-AAAAATAGTTT
*
2594737 AGGTACCAACTTAGGGGG-AAAATAGTTT
1 AAGTACCAACTTAGGGGGAAAAATAGTTT
2594765 AAGTACC-ACTTA
1 AAGTACCAACTTA
2594777 TGATAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 5 0.14
28 16 0.44
29 10 0.28
30 5 0.14
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (29 bp):
AAGTACCAACTTAGGGGGAAAAATAGTTT
Found at i:2594785 original size:27 final size:28
Alignment explanation
Indices: 2594708--2594785 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 28
2594698 CTAATGACAA
* * *
2594708 AAGTTCCAACTTGGGGGAAAAAATAGTTT
1 AAGTACCAACTTAGGAG-AAAAATAGTTT
* * *
2594737 AGGTACCAACTTAGGGGGAAAATAGTTT
1 AAGTACCAACTTAGGAGAAAAATAGTTT
* *
2594765 AAGTACC-ACTTATGATAAAAA
1 AAGTACCAACTTAGGAGAAAAA
2594786 AAATGTTTTG
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 10 0.25
28 16 0.40
29 14 0.35
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.26
Consensus pattern (28 bp):
AAGTACCAACTTAGGAGAAAAATAGTTT
Found at i:2601089 original size:2 final size:2
Alignment explanation
Indices: 2601084--2601144 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
2601074 TATATATACA
2601084 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2601126 TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG T
2601145 ACTACATCGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:2604969 original size:108 final size:108
Alignment explanation
Indices: 2604840--2605492 Score: 1081
Period size: 108 Copynumber: 6.0 Consensus size: 108
2604830 CAATATTTAG
* * *
2604840 TTATATACAAAGAGGTTGGATGGGTTAGGGAATAGGGTTGTGTTTAGTTTAAATCGATTTAGGGT
1 TTAT-TACAAAGAGGTTGGATGGGATAGGGAATAGGGTTGTGTTGAGTTTAGATCGATTTAGGGT
* *
2604905 TTACGTCATTTTCGTTATGCTAATTAATAACAAAAGGTTGAGAT
65 TTACGTCATTTTTGTTATGCTAGTTAATAACAAAAGGTTGAGAT
* *
2604949 TTATTACAAAAAGGTTGGATGGGATAGGGAATAAGGTTGTGTTGAGTTTAGATCGATTTAGGGTT
1 TTATTACAAAGAGGTTGGATGGGATAGGGAATAGGGTTGTGTTGAGTTTAGATCGATTTAGGGTT
** *
2605014 TACGTCATTTTTGTTATGCTAGTTAATAACAAAATATTGGGAT
66 TACGTCATTTTTGTTATGCTAGTTAATAACAAAAGGTTGAGAT
*
2605057 TTATTACAAAGAGGTTGGATGGGATAGGGAATAGGGTTGTGTTGAGTTTAGATCAATTTAGGGTT
1 TTATTACAAAGAGGTTGGATGGGATAGGGAATAGGGTTGTGTTGAGTTTAGATCGATTTAGGGTT
* * *
2605122 TATGTTATTTTTGTTATGCTAGTTAATAACAAAAGGTTGGGAT
66 TACGTCATTTTTGTTATGCTAGTTAATAACAAAAGGTTGAGAT
*
2605165 TTATTACAAAGAGGTTGGATGGGATAGGAAATAGGGTTGTGTTGAGTTTAGATCGATTTAGGGTT
1 TTATTACAAAGAGGTTGGATGGGATAGGGAATAGGGTTGTGTTGAGTTTAGATCGATTTAGGGTT
* * *
2605230 TACGCCGTTTTTGTTATGATAGTTAATAACAAAAGGTTGAGAT
66 TACGTCATTTTTGTTATGCTAGTTAATAACAAAAGGTTGAGAT
*
2605273 TTATTACAAAGAGGTTCGATGGGATAGGGAATAGGGTTGTGTTGAGTTTAGATCGATTTAGGGTT
1 TTATTACAAAGAGGTTGGATGGGATAGGGAATAGGGTTGTGTTGAGTTTAGATCGATTTAGGGTT
*
2605338 TACGTCATTTTTGTTATGATAGTTAATAACAAAAGGTTGAGAT
66 TACGTCATTTTTGTTATGCTAGTTAATAACAAAAGGTTGAGAT
* *
2605381 TTATTACAAAGAGGTTCGATGGGATAGGGAATAGGGTTGTGTTGAGTTTAGATCGATTTAGGGCT
1 TTATTACAAAGAGGTTGGATGGGATAGGGAATAGGGTTGTGTTGAGTTTAGATCGATTTAGGGTT
* *
2605446 TACGCCATTTTTGTTATGCTAGTTAATAACAAAAAGTTGAGAT
66 TACGTCATTTTTGTTATGCTAGTTAATAACAAAAGGTTGAGAT
2605489 TTAT
1 TTAT
2605493 ATAGTTATAT
Statistics
Matches: 511, Mismatches: 33, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
108 507 0.99
109 4 0.01
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (108 bp):
TTATTACAAAGAGGTTGGATGGGATAGGGAATAGGGTTGTGTTGAGTTTAGATCGATTTAGGGTT
TACGTCATTTTTGTTATGCTAGTTAATAACAAAAGGTTGAGAT
Found at i:2608828 original size:29 final size:29
Alignment explanation
Indices: 2608771--2608828 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
2608761 TTTAGATTAA
*
2608771 TGTGCAATATGATACATAAACTTTTATTT
1 TGTGCAATATGATACATAAACTTTGATTT
2608800 TGTGCAAT-TGTATACATAATA-TTTGATTT
1 TGTGCAATATG-ATACATAA-ACTTTGATTT
2608829 GATTCAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 2 0.08
29 23 0.88
30 1 0.04
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.47
Consensus pattern (29 bp):
TGTGCAATATGATACATAAACTTTGATTT
Found at i:2611207 original size:4 final size:4
Alignment explanation
Indices: 2611198--2611222 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2611188 GTTTTCACAT
2611198 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
2611223 TATTAGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:2613714 original size:40 final size:41
Alignment explanation
Indices: 2613637--2613733 Score: 151
Period size: 40 Copynumber: 2.3 Consensus size: 41
2613627 ACCAAAACTT
2613637 TATTTTAAAAATTAAAATAAAAATAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAATAAAAATAAAAAAAGTATTTTAAAAA
*
2613680 TATTTTAAAATTAAA-AAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAATAAAAATAAAAAAAGTATTTTAAAAA
*
2613720 AATTTTAAAATTAA
1 TATTTTAAAATTAA
2613734 TCGGGCCGGG
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
40 37 0.71
41 3 0.06
42 6 0.12
43 6 0.12
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (41 bp):
TATTTTAAAATTAAATAAAAATAAAAAAAGTATTTTAAAAA
Found at i:2615411 original size:9 final size:9
Alignment explanation
Indices: 2615397--2615427 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2615387 TTCTTTTCTT
2615397 TTTTTATAA
1 TTTTTATAA
2615406 TTTTTATAA
1 TTTTTATAA
*
2615415 TTTTTGTAA
1 TTTTTATAA
2615424 TTTT
1 TTTT
2615428 AAATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (9 bp):
TTTTTATAA
Found at i:2615447 original size:12 final size:13
Alignment explanation
Indices: 2615424--2615452 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2615414 ATTTTTGTAA
2615424 TTTTAAATTTATT
1 TTTTAAATTTATT
2615437 TTTTAAA-TTATT
1 TTTTAAATTTATT
2615449 TTTT
1 TTTT
2615453 GATGTAGCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTAAATTTATT
Found at i:2618988 original size:24 final size:25
Alignment explanation
Indices: 2618941--2618989 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
2618931 AATATACAAG
*
2618941 TTAATTATTATGAGATTTTTTAAATTT
1 TTAATTATTATGAGA--TTATAAATTT
2618968 TTAATTATTATGAGA-TATAAAT
1 TTAATTATTATGAGATTATAAAT
2618990 AAGTATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
27 15 0.71
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (25 bp):
TTAATTATTATGAGATTATAAATTT
Found at i:2624144 original size:28 final size:30
Alignment explanation
Indices: 2624084--2624144 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 30
2624074 TTTGATTAAA
* *
2624084 ATTTTTGAATTATATTTATAAATTTAATTT
1 ATTTTTGAATTATATTCATAAATTTAATCT
2624114 ATTTTT-AA-TATATTCAT-AATTTATATCT
1 ATTTTTGAATTATATTCATAAATTTA-ATCT
2624142 ATT
1 ATT
2624145 AAAAATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 6 0.21
28 14 0.50
29 2 0.07
30 6 0.21
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (30 bp):
ATTTTTGAATTATATTCATAAATTTAATCT
Found at i:2624360 original size:118 final size:119
Alignment explanation
Indices: 2624167--2624404 Score: 469
Period size: 118 Copynumber: 2.0 Consensus size: 119
2624157 AAAAACCAAA
2624167 TGAAATTTTGATTAAGAAAATCATGATATTTTTTACTATGCAAGGATTTTTACCCATTTTATATA
1 TGAAATTTTGATTAAGAAAATCATGATATTTTTTACTATGCAAGGATTTTTACCCATTTTATATA
2624232 TATAAAAAAAGTATGATTTTCGAATAACTCATTAAACTAATTTAATAAAAGGTT
66 TATAAAAAAAGTATGATTTTCGAATAACTCATTAAACTAATTTAATAAAAGGTT
2624286 TGAAATTTTGA-TAAGAAAATCATGATATTTTTTACTATGCAAGGATTTTTACCCATTTTATATA
1 TGAAATTTTGATTAAGAAAATCATGATATTTTTTACTATGCAAGGATTTTTACCCATTTTATATA
2624350 TATAAAAAAAGTATGATTTTCGAATAACTCATTAAACTAATTTAATAAAAGGTT
66 TATAAAAAAAGTATGATTTTCGAATAACTCATTAAACTAATTTAATAAAAGGTT
2624404 T
1 T
2624405 TAAGTATAGT
Statistics
Matches: 119, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
118 108 0.91
119 11 0.09
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.40
Consensus pattern (119 bp):
TGAAATTTTGATTAAGAAAATCATGATATTTTTTACTATGCAAGGATTTTTACCCATTTTATATA
TATAAAAAAAGTATGATTTTCGAATAACTCATTAAACTAATTTAATAAAAGGTT
Found at i:2624921 original size:14 final size:14
Alignment explanation
Indices: 2624902--2624930 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2624892 AAGCACCCTT
2624902 AAATAATGGGCTGA
1 AAATAATGGGCTGA
2624916 AAATAATGGGCTGA
1 AAATAATGGGCTGA
2624930 A
1 A
2624931 TCTCATCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.28, T:0.21
Consensus pattern (14 bp):
AAATAATGGGCTGA
Found at i:2630543 original size:21 final size:20
Alignment explanation
Indices: 2630519--2630557 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2630509 TAAAATTTTT
*
2630519 TTTTATTGTTGTTTGTTGCCG
1 TTTTACTGTTGTTT-TTGCCG
*
2630540 TTTTGCTGTTGTTTTTGC
1 TTTTACTGTTGTTTTTGC
2630558 TATTATATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.03, C:0.10, G:0.23, T:0.64
Consensus pattern (20 bp):
TTTTACTGTTGTTTTTGCCG
Found at i:2635698 original size:13 final size:13
Alignment explanation
Indices: 2635680--2635707 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2635670 GCTTTTTTAT
2635680 TATTTTTAATTAA
1 TATTTTTAATTAA
2635693 TATTTTTAATTAA
1 TATTTTTAATTAA
2635706 TA
1 TA
2635708 AATATATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTTTTAATTAA
Found at i:2636424 original size:29 final size:31
Alignment explanation
Indices: 2636379--2636444 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
2636369 AAATTGTAAA
*
2636379 TTTAGTCTCTATAC-TTTT-ATTTGATCAAT
1 TTTAGTCTCTATACTTTTTGAATTGATCAAT
* * *
2636408 TTTAGTCTTTATGCTTTTTGAATTGATCACT
1 TTTAGTCTCTATACTTTTTGAATTGATCAAT
2636439 TTTAGT
1 TTTAGT
2636445 TGCTGTACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 12 0.39
30 4 0.13
31 15 0.48
ACGTcount: A:0.21, C:0.12, G:0.11, T:0.56
Consensus pattern (31 bp):
TTTAGTCTCTATACTTTTTGAATTGATCAAT
Found at i:2643473 original size:10 final size:10
Alignment explanation
Indices: 2643455--2643484 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2643445 TAATATATTT
2643455 AAAATTTAAA
1 AAAATTTAAA
*
2643465 AAAACTTAAA
1 AAAATTTAAA
2643475 AAAATTTAAA
1 AAAATTTAAA
2643485 TATATTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:2643502 original size:19 final size:18
Alignment explanation
Indices: 2643473--2643512 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
2643463 AAAAAACTTA
*
2643473 AAAAAATTTAAATATATT
1 AAAAAATTTAAATATAAT
*
2643491 AAAAAATGTTAAGTATAAT
1 AAAAAAT-TTAAATATAAT
2643510 AAA
1 AAA
2643513 TTTTAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
AAAAAATTTAAATATAAT
Found at i:2643579 original size:17 final size:17
Alignment explanation
Indices: 2643559--2643677 Score: 62
Period size: 17 Copynumber: 6.4 Consensus size: 17
2643549 AAAAAATATT
2643559 TTTTAATATATTTAAAA
1 TTTTAATATATTTAAAA
* *
2643576 TTTTAA-AAACTTAAAGAA
1 TTTTAATATA-TTTAA-AA
2643594 TTTTAA-ATATATTAAAA
1 TTTTAATATAT-TTAAAA
* *
2643611 TTTTAAGTATGTTGAAAAAA
1 TTTTAA-TATATT--TAAAA
*
2643631 TGTTAAATATAATCAATTTTAAAA
1 T-TT-TA-AT-AT--A-TTTAAAA
2643655 TTTTAATATATTTAAAA
1 TTTTAATATATTTAAAA
2643672 TTTTAA
1 TTTTAA
2643678 AAAAACTTTA
Statistics
Matches: 78, Mismatches: 10, Indels: 28
0.67 0.09 0.24
Matches are distributed among these distances:
16 2 0.03
17 32 0.41
18 15 0.19
19 3 0.04
20 7 0.09
21 4 0.05
22 3 0.04
23 5 0.06
24 5 0.06
26 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (17 bp):
TTTTAATATATTTAAAA
Found at i:2643583 original size:36 final size:34
Alignment explanation
Indices: 2643543--2643616 Score: 78
Period size: 36 Copynumber: 2.1 Consensus size: 34
2643533 TTTTAATACG
*
2643543 TAAAA-TAAAAAATATTTTTTAATATATTTAAAATTT
1 TAAAACTAAAAAA-A-TTTTAAATATA-TTAAAATTT
* *
2643579 TAAAAACTTAAAGAATTTTAAATATATTAAAATTT
1 T-AAAACTAAAAAAATTTTAAATATATTAAAATTT
2643614 TAA
1 TAA
2643617 GTATGTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
34 2 0.06
35 10 0.30
36 11 0.33
37 5 0.15
38 5 0.15
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (34 bp):
TAAAACTAAAAAAATTTTAAATATATTAAAATTT
Found at i:2643658 original size:8 final size:8
Alignment explanation
Indices: 2643645--2643679 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
2643635 AAATATAATC
2643645 AATTTTAA
1 AATTTTAA
2643653 AATTTTAA
1 AATTTTAA
*
2643661 TATATTTAA
1 AAT-TTTAA
2643670 AATTTTAA
1 AATTTTAA
2643678 AA
1 AA
2643680 AAACTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
AATTTTAA
Found at i:2644397 original size:15 final size:16
Alignment explanation
Indices: 2644375--2644412 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2644365 CATCACCCTG
*
2644375 CTTTTTTTTATTTGTT
1 CTTTTTTTTATTTGTC
*
2644391 CTTTTTTTTGTTTGTC
1 CTTTTTTTTATTTGTC
2644407 CTTTTT
1 CTTTTT
2644413 CATTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.03, C:0.11, G:0.08, T:0.79
Consensus pattern (16 bp):
CTTTTTTTTATTTGTC
Found at i:2644443 original size:24 final size:24
Alignment explanation
Indices: 2644391--2644444 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
2644381 TTTATTTGTT
2644391 CTTTTTTTTGTTTGTCCTTTTTCA
1 CTTTTTTTTGTTTGTCCTTTTTCA
*
2644415 TTTTTTTTTGTTT-TACCTTATTT-A
1 CTTTTTTTTGTTTGT-CCTT-TTTCA
2644439 CTTTTT
1 CTTTTT
2644445 CAGTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 1 0.04
24 22 0.85
25 3 0.12
ACGTcount: A:0.07, C:0.13, G:0.06, T:0.74
Consensus pattern (24 bp):
CTTTTTTTTGTTTGTCCTTTTTCA
Found at i:2644468 original size:32 final size:32
Alignment explanation
Indices: 2644407--2644470 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
2644397 TTTGTTTGTC
* *
2644407 CTTTTTCATTTTTTTTTGTTTTACCTTATTTA
1 CTTTTTCATTTTTTTATGTTGTACCTTATTTA
2644439 CTTTTTCAGTTTTTTTAT-TTGT-CCTTTATTTA
1 CTTTTTCA-TTTTTTTATGTTGTACC-TTATTTA
2644471 TTATTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 2 0.07
32 18 0.64
33 8 0.29
ACGTcount: A:0.12, C:0.12, G:0.05, T:0.70
Consensus pattern (32 bp):
CTTTTTCATTTTTTTATGTTGTACCTTATTTA
Found at i:2644472 original size:4 final size:4
Alignment explanation
Indices: 2644463--2644526 Score: 55
Period size: 4 Copynumber: 16.8 Consensus size: 4
2644453 TTATTTGTCC
* * *
2644463 TTTA TTTA -TTA TTTA TTTA TTCTG TTTA TTTA TTTG TTTG TTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA
*
2644510 TTTG TTT- TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTT
2644527 GTCTTATAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
3 12 0.24
4 36 0.71
5 3 0.06
ACGTcount: A:0.16, C:0.02, G:0.06, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2644492 original size:13 final size:12
Alignment explanation
Indices: 2644463--2644501 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
2644453 TTATTTGTCC
*
2644463 TTTATTTA-TTA
1 TTTATTTATTTG
2644474 TTTATTTATTCTG
1 TTTATTTATT-TG
2644487 TTTATTTATTTG
1 TTTATTTATTTG
2644499 TTT
1 TTT
2644502 GTTTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 8 0.32
12 6 0.24
13 11 0.44
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (12 bp):
TTTATTTATTTG
Found at i:2644493 original size:17 final size:16
Alignment explanation
Indices: 2644471--2644526 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 16
2644461 CCTTTATTTA
2644471 TTATTTATTTATTCTGT
1 TTATTTATTTATT-TGT
*
2644488 TTATTTATTTGTTTGT
1 TTATTTATTTATTTGT
*
2644504 TT-TTTATTTGTTT-T
1 TTATTTATTTATTTGT
2644518 TTA-TTATTT
1 TTATTTATTT
2644527 GTCTTATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
14 9 0.24
15 11 0.30
16 5 0.14
17 12 0.32
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.77
Consensus pattern (16 bp):
TTATTTATTTATTTGT
Found at i:2654879 original size:8 final size:7
Alignment explanation
Indices: 2654851--2654878 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
2654841 AGCTAAAATA
2654851 AAATTTT
1 AAATTTT
2654858 AAATTTT
1 AAATTTT
2654865 AAATTTT
1 AAATTTT
2654872 AAATTTT
1 AAATTTT
2654879 TATATTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AAATTTT
Found at i:2654984 original size:23 final size:23
Alignment explanation
Indices: 2654966--2655009 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2654956 TAAAATATTG
* *
2654966 TTTTTTTAAAATTTTAAATATAA
1 TTTTTTAAAAAGTTTAAATATAA
*
2654989 TTTTTTAAAAAGTTTGAATAT
1 TTTTTTAAAAAGTTTAAATAT
2655010 CTTTAAAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (23 bp):
TTTTTTAAAAAGTTTAAATATAA
Found at i:2655039 original size:25 final size:25
Alignment explanation
Indices: 2655011--2655058 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
2655001 TTTGAATATC
2655011 TTTAAAAGTAATT-TAAAA-AAATACA
1 TTTAAAA-T-ATTATAAAACAAATACA
2655036 TTTAAAATATTATAAAACAAATA
1 TTTAAAATATTATAAAACAAATA
2655059 ATAAATTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 6 0.29
25 12 0.57
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (25 bp):
TTTAAAATATTATAAAACAAATACA
Found at i:2656906 original size:8 final size:7
Alignment explanation
Indices: 2656878--2656905 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
2656868 AGCTAAAATA
2656878 AAATTTT
1 AAATTTT
2656885 AAATTTT
1 AAATTTT
2656892 AAATTTT
1 AAATTTT
2656899 AAATTTT
1 AAATTTT
2656906 TATATTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AAATTTT
Found at i:2657011 original size:23 final size:23
Alignment explanation
Indices: 2656993--2657036 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2656983 TAAAATATTG
* *
2656993 TTTTTTTAAAATTTTAAATATAA
1 TTTTTTAAAAAGTTTAAATATAA
*
2657016 TTTTTTAAAAAGTTTGAATAT
1 TTTTTTAAAAAGTTTAAATAT
2657037 CTTTAAAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (23 bp):
TTTTTTAAAAAGTTTAAATATAA
Found at i:2657066 original size:25 final size:25
Alignment explanation
Indices: 2657038--2657085 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
2657028 TTTGAATATC
2657038 TTTAAAAGTAATT-TAAAA-AAATACA
1 TTTAAAA-T-ATTATAAAACAAATACA
2657063 TTTAAAATATTATAAAACAAATA
1 TTTAAAATATTATAAAACAAATA
2657086 ATAAATTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 6 0.29
25 12 0.57
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (25 bp):
TTTAAAATATTATAAAACAAATACA
Found at i:2657311 original size:17 final size:18
Alignment explanation
Indices: 2657291--2657325 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2657281 GTAAATAGTG
2657291 AAAAAAAAACAAA-AAAA
1 AAAAAAAAACAAATAAAA
*
2657308 AAAAACAAACAAATAAAA
1 AAAAAAAAACAAATAAAA
2657326 GAATCAGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.89, C:0.09, G:0.00, T:0.03
Consensus pattern (18 bp):
AAAAAAAAACAAATAAAA
Found at i:2657325 original size:13 final size:13
Alignment explanation
Indices: 2657291--2657316 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2657281 GTAAATAGTG
2657291 AAAAAAAAACAAA
1 AAAAAAAAACAAA
2657304 AAAAAAAAACAAA
1 AAAAAAAAACAAA
2657317 CAAATAAAAG
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:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAACAAA
Found at i:2659211 original size:14 final size:14
Alignment explanation
Indices: 2659194--2659221 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2659184 CTCACATTTC
2659194 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
2659208 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
2659222 GATTTCTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTCTTTTCTCCA
Found at i:2659212 original size:19 final size:18
Alignment explanation
Indices: 2659174--2659218 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
2659164 TACAGTACGC
2659174 TTCTTTTC-TTCTCACAT
1 TTCTTTTCTTTCTCACAT
2659191 TTCTTTTCTTTTCTC-CATT
1 TTCTTTTC-TTTCTCACA-T
2659210 TTCTTTTCT
1 TTCTTTTCT
2659219 CCAGATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.32
18 3 0.12
19 14 0.56
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (18 bp):
TTCTTTTCTTTCTCACAT
Found at i:2662375 original size:39 final size:43
Alignment explanation
Indices: 2662319--2662426 Score: 116
Period size: 45 Copynumber: 2.6 Consensus size: 43
2662309 TTCCCTTATG
* * *
2662319 CTATTACACCTCCATTCCATT-CAACCAA-ATACAA-GAA-TC
1 CTATTACGCCTCTATTCCATTACAACCAACAAACAATGAATTC
** *
2662358 CTATTACGCCTCTATTCCATTACATTCAATCAAACAATTGAATTG
1 CTATTACGCCTCTATTCCATTACAACCAA-CAAACAA-TGAATTC
2662403 CTATTACGCCTCTATTCCATTACA
1 CTATTACGCCTCTATTCCATTACA
2662427 GCGAACCAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
39 19 0.33
40 5 0.09
42 5 0.09
44 3 0.05
45 25 0.44
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (43 bp):
CTATTACGCCTCTATTCCATTACAACCAACAAACAATGAATTC
Found at i:2663539 original size:126 final size:126
Alignment explanation
Indices: 2663310--2663593 Score: 489
Period size: 126 Copynumber: 2.3 Consensus size: 126
2663300 TTAGGGTTGA
*
2663310 ACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTTCTTAGTAAACAGTG
1 ACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTTCTGAGTAAACAGTG
2663375 TCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAAAAGCTCCCACGTGG
66 TCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAAAAGCTCCCACGTGG
* *
2663436 ACGTGCTTTTGCTATAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTTCTGA-TCAAACAGT
1 ACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTTCTGAGT-AAACAGT
* * *
2663500 GTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGTAGAAGTACTGAAAGAAGCTCCCACGTGG
65 GTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAAAAGCTCCCACGTGG
*
2663562 ATGCGCTTTTGCTACAGTAGCTCCTGAAAAAA
1 ACGCGCTTTTGCTACAGTAGCTCCTGAAAAAA
2663594 GCTCCCATGT
Statistics
Matches: 148, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
125 1 0.01
126 147 0.99
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (126 bp):
ACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTTCTGAGTAAACAGTG
TCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAAAAGCTCCCACGTGG
Found at i:2666737 original size:29 final size:30
Alignment explanation
Indices: 2666670--2666737 Score: 75
Period size: 33 Copynumber: 2.2 Consensus size: 30
2666660 AAATATTTGG
2666670 AATATTGACTTATTTAAAAGAAAATCTATT
1 AATATTGACTTATTTAAAAGAAAATCTATT
* **
2666700 CAACATATTGCCTTATTTAAAAGAATTTCTATT
1 --A-ATATTGACTTATTTAAAAGAAAATCTATT
2666733 -ATATT
1 AATATT
2666738 AAAAATGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 5 0.16
32 1 0.03
33 26 0.81
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (30 bp):
AATATTGACTTATTTAAAAGAAAATCTATT
Found at i:2667264 original size:18 final size:18
Alignment explanation
Indices: 2667238--2667280 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2667228 GACTCGAAAA
* * *
2667238 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
2667256 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
2667274 AGGATAC
1 AGGATAC
2667281 GCACCAGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:2667425 original size:30 final size:30
Alignment explanation
Indices: 2667359--2667428 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
2667349 TGTCGGTGTT
* * * *
2667359 GTTGCTGGGCCTGGTGATTGTATGGGCATT
1 GTTGATGGGCCGGGTGAATGTATGGGCATC
* * *
2667389 GATGATGGGCCGGGTGAATGTCTGGGCCTC
1 GTTGATGGGCCGGGTGAATGTATGGGCATC
2667419 GTTGATGGGC
1 GTTGATGGGC
2667429 TTGCATTGTC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.43, T:0.30
Consensus pattern (30 bp):
GTTGATGGGCCGGGTGAATGTATGGGCATC
Found at i:2669305 original size:22 final size:22
Alignment explanation
Indices: 2669279--2669335 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
2669269 AGGGATTTGG
*
2669279 GAGAAATTTCAGAGCAAAATGA
1 GAGAAAATTCAGAGCAAAATGA
* * *
2669301 GAGAAAATTGAGAGGAAATTGA
1 GAGAAAATTCAGAGCAAAATGA
*
2669323 GAGAATATT-AGAG
1 GAGAAAATTCAGAG
2669336 AAAGGATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.49, C:0.04, G:0.28, T:0.19
Consensus pattern (22 bp):
GAGAAAATTCAGAGCAAAATGA
Found at i:2669715 original size:18 final size:18
Alignment explanation
Indices: 2669694--2669742 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
2669684 TTTTACAATA
2669694 TTTTACATTTTCTAATTT
1 TTTTACATTTTCTAATTT
* * *
2669712 TTTTATATATTTTTTATTT
1 TTTTACAT-TTTCTAATTT
2669731 TTTTACAATTTT
1 TTTTAC-ATTTT
2669743 TAAAAATTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 7 0.28
19 16 0.64
20 2 0.08
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTACATTTTCTAATTT
Found at i:2669743 original size:18 final size:18
Alignment explanation
Indices: 2669680--2669745 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
2669670 GTGTTTTGCC
* *
2669680 CAATTTTTACAATATTTTA
1 CAATTTTTA-ATTTTTTTA
2669699 C-ATTTTCTAATTTTTTTA
1 CAATTTT-TAATTTTTTTA
* *
2669717 TATATTTTTTATTTTTTTA
1 CA-ATTTTTAATTTTTTTA
2669736 CAATTTTTAA
1 CAATTTTTAA
2669746 AAATTCTAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
18 19 0.50
19 14 0.37
20 5 0.13
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.64
Consensus pattern (18 bp):
CAATTTTTAATTTTTTTA
Found at i:2671158 original size:15 final size:15
Alignment explanation
Indices: 2671123--2671160 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2671113 TTACAATACT
*
2671123 TTTTTTTAAATATAG
1 TTTTTTTAAATATAA
2671138 TTTTTTTAAATA-AA
1 TTTTTTTAAATATAA
2671152 TTCTTTTTA
1 TT-TTTTTA
2671161 GCAGAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TTTTTTTAAATATAA
Found at i:2690320 original size:31 final size:29
Alignment explanation
Indices: 2690284--2690360 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
2690274 TTAACAGCTC
* *
2690284 AGTGACTAAAATGTTACACTACATTAACGTA
1 AGTGACTAAAATGTAACACTACA--AACATA
* * *
2690315 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACTACAAACATA
2690344 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
2690361 CCGAGAGAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 21 0.52
31 19 0.47
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACTACAAACATA
Found at i:2694189 original size:15 final size:16
Alignment explanation
Indices: 2694163--2694199 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2694153 AAAATCTTAG
2694163 TTAAAAATTATGTTAAA
1 TTAAAAATTATG-TAAA
2694180 -TAAAAA-TATGTAAA
1 TTAAAAATTATGTAAA
2694194 TTAAAA
1 TTAAAA
2694200 CATAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.21
15 9 0.47
16 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (16 bp):
TTAAAAATTATGTAAA
Done.