Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold79
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: 4189514
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 5041 characters in sequence are not A, C, G, or T
File 4 of 26
Found at i:454293 original size:38 final size:38
Alignment explanation
Indices: 454237--454313 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 38
454227 AAAGTCAATC
* * *
454237 ATTTAAATTTATTCAAATCAAATTTAAAAA-TAATTTAA
1 ATTTAAAATAATTCAAATC-AATTAAAAAATTAATTTAA
*
454275 ATTTAAAATAATTTAAATCAATTAAAAAATTAATTTAA
1 ATTTAAAATAATTCAAATCAATTAAAAAATTAATTTAA
454313 A
1 A
454314 ATTATCTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 9 0.26
38 25 0.74
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (38 bp):
ATTTAAAATAATTCAAATCAATTAAAAAATTAATTTAA
Found at i:454747 original size:14 final size:14
Alignment explanation
Indices: 454711--454740 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
454701 CTTTTAATGT
454711 TTTAAAAAATTAAA
1 TTTAAAAAATTAAA
454725 TTTAAAAAA-TAAA
1 TTTAAAAAATTAAA
454738 TTT
1 TTT
454741 GATAAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TTTAAAAAATTAAA
Found at i:458335 original size:49 final size:48
Alignment explanation
Indices: 458269--458640 Score: 529
Period size: 49 Copynumber: 7.7 Consensus size: 48
458259 GCTACTTTCA
* *
458269 CGTTTCTTTTTCCTTTTTT-TTCTCCCCCTTTGCCGTGAGCTGCTT-T
1 CGTTCCTTTTTCTTTTTTTCTTCTCCCCCTTTGCCGTGAGCTGCTTAT
458315 CACGTTCCTTTTTTCTTTTTTTCTTCTCCCCCTTTGCCGTGAGCTGCTTAT
1 --CGTTCC-TTTTTCTTTTTTTCTTCTCCCCCTTTGCCGTGAGCTGCTTAT
*
458366 CATTCCTTTTTTCTTTTTTTCTTCTCCCCCTTTGCCGTGAGCTGCTTAT
1 CGTTCC-TTTTTCTTTTTTTCTTCTCCCCCTTTGCCGTGAGCTGCTTAT
458415 CGTTCCTTTTTTCTTTTTTTTTTCTTCTCCCCCTTTGCCGTGAGCTGCTTAT
1 CGTTCC-TTTTTC---TTTTTTTCTTCTCCCCCTTTGCCGTGAGCTGCTTAT
* * * **
458467 TGTTCCTTTTTCTTTTTTTCTTCTCCCCCTTTGTCATGAGCTATTTAT
1 CGTTCCTTTTTCTTTTTTTCTTCTCCCCCTTTGCCGTGAGCTGCTTAT
458515 CGTTCC--TTT-TTTTTTTCTTCTCCCCCTTTGCCGTGAGCTGCTTAT
1 CGTTCCTTTTTCTTTTTTTCTTCTCCCCCTTTGCCGTGAGCTGCTTAT
* * *
458560 CGTTCCTTTTTTCTTTTTCTCTTCTCCCCCTTTGCCGCGAGTTGCTTAT
1 CGTTCC-TTTTTCTTTTTTTCTTCTCCCCCTTTGCCGTGAGCTGCTTAT
458609 CGTTCCTTTTTCTTTTTTTCTTCTCCCCCTTT
1 CGTTCCTTTTTCTTTTTTTCTTCTCCCCCTTT
458641 ATTTGCAAGC
Statistics
Matches: 296, Mismatches: 18, Indels: 20
0.89 0.05 0.06
Matches are distributed among these distances:
45 38 0.13
46 3 0.01
48 70 0.24
49 111 0.38
50 26 0.09
51 7 0.02
52 41 0.14
ACGTcount: A:0.05, C:0.30, G:0.11, T:0.54
Consensus pattern (48 bp):
CGTTCCTTTTTCTTTTTTTCTTCTCCCCCTTTGCCGTGAGCTGCTTAT
Found at i:458557 original size:194 final size:192
Alignment explanation
Indices: 458274--458640 Score: 562
Period size: 194 Copynumber: 1.9 Consensus size: 192
458264 TTTCACGTTT
* *
458274 CTTTTTCCTTTTTTTTCTCCCCCTTTGCCGTGAGCTGCTTTCACGTTCCTTTTTTCTTTTTTTCT
1 CTTTTTCCTTTTTTTTCTCCCCCTTTGCCATGAGCTGATTTCACGTTCC--TTTTCTTTTTTTCT
* *
458339 TCTCCCCCTTTGCCGTGAGCTGCTTATCATTCCTTTTTTCTTTTTTTCTTCTCCCCCTTTGCCGT
64 TCTCCCCCTTTGCCGTGAGCTGCTTATCATTCCTTTTTTCTTTTTCTCTTCTCCCCCTTTGCCGC
458404 GAGCTGCTTATCGTTCCTTTTTTCTTTTTTTTTTCTTCTCCCCCTTTGCCGTGAGCTGCTTATTG
129 GAGCTGCTTATCGTTCC-TTTTTC---TTTTTTTCTTCTCCCCCTTTGCCGTGAGCTGCTTATTG
458469 TTC
190 TTC
* *
458472 CTTTTTCTTTTTTTCTTCTCCCCCTTTGTCATGAGCT-ATTT-ATCGTTCC-TTT-TTTTTTTCT
1 CTTTTTCCTTTTTT-TTCTCCCCCTTTGCCATGAGCTGATTTCA-CGTTCCTTTTCTTTTTTTCT
*
458533 TCTCCCCCTTTGCCGTGAGCTGCTTATCGTTCCTTTTTTCTTTTTCTCTTCTCCCCCTTTGCCGC
64 TCTCCCCCTTTGCCGTGAGCTGCTTATCATTCCTTTTTTCTTTTTCTCTTCTCCCCCTTTGCCGC
*
458598 GAGTTGCTTATCGTTCCTTTTTCTTTTTTTCTTCTCCCCCTTT
129 GAGCTGCTTATCGTTCCTTTTTCTTTTTTTCTTCTCCCCCTTT
458641 ATTTGCAAGC
Statistics
Matches: 159, Mismatches: 8, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
190 20 0.13
193 6 0.04
194 87 0.55
195 3 0.02
197 1 0.01
198 22 0.14
199 20 0.13
ACGTcount: A:0.05, C:0.31, G:0.11, T:0.54
Consensus pattern (192 bp):
CTTTTTCCTTTTTTTTCTCCCCCTTTGCCATGAGCTGATTTCACGTTCCTTTTCTTTTTTTCTTC
TCCCCCTTTGCCGTGAGCTGCTTATCATTCCTTTTTTCTTTTTCTCTTCTCCCCCTTTGCCGCGA
GCTGCTTATCGTTCCTTTTTCTTTTTTTCTTCTCCCCCTTTGCCGTGAGCTGCTTATTGTTC
Found at i:459231 original size:12 final size:13
Alignment explanation
Indices: 459211--459239 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
459201 TTTATTATTT
459211 TTTTGAATTTTAA
1 TTTTGAATTTTAA
459224 TTTT-AATTTTAA
1 TTTTGAATTTTAA
459236 TTTT
1 TTTT
459240 TGATTTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTTGAATTTTAA
Found at i:460060 original size:214 final size:213
Alignment explanation
Indices: 459692--460108 Score: 807
Period size: 214 Copynumber: 2.0 Consensus size: 213
459682 AAAGATTGGG
459692 AAAAAATTTCAACTTAAAAAAATTACTTTAATTTTAAAAATATTAACAAGAATAATAAATCAAAA
1 AAAAAATTTCAACTTAAAAAAATTACTTTAATTTTAAAAATATTAACAAGAATAATAAATCAAAA
459757 TATTTTTAAATGTATCTCATAACTTACTTCAGATAATTAAAAAATAATTAAATGATAATTATAAT
66 TATTTTTAAATGTATCTCATAACTTACTTCAGATAATTAAAAAATAATTAAATGATAATTATAAT
*
459822 CAAATTTAAATTCAATCATGATTCAAAGTAAAAAATTTTGGTAAAAATCTGGTAAAATCCAATAT
131 CAAATTTAAATTCAATCATGATTCAAAGTAAAAAATTTTGGTAAAAATCCGGTAAAATCCAATAT
459887 ATATATATTTTTTAATTT
196 ATATATATTTTTTAATTT
*
459905 AAAAAATTTCAACTTAAAAAAATTACTTTAATTTTAAAAAATATTAACAAGAATAATAAATCGAA
1 AAAAAATTTCAACTTAAAAAAATTACTTTAATTTT-AAAAATATTAACAAGAATAATAAATCAAA
459970 ATATTTTTAAATGTATCTCATAACTTACTTCAGATAATTAAAAAATAATTAAATGATAATTATAA
65 ATATTTTTAAATGTATCTCATAACTTACTTCAGATAATTAAAAAATAATTAAATGATAATTATAA
460035 TCAAATTTAAATTCAATCATGATTCAAAGTAAAAAATTTTGGTAAAAATCCGGTAAAATCCAATA
130 TCAAATTTAAATTCAATCATGATTCAAAGTAAAAAATTTTGGTAAAAATCCGGTAAAATCCAATA
460100 TATATATAT
195 TATATATAT
460109 ATATATATAT
Statistics
Matches: 201, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
213 35 0.17
214 166 0.83
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.36
Consensus pattern (213 bp):
AAAAAATTTCAACTTAAAAAAATTACTTTAATTTTAAAAATATTAACAAGAATAATAAATCAAAA
TATTTTTAAATGTATCTCATAACTTACTTCAGATAATTAAAAAATAATTAAATGATAATTATAAT
CAAATTTAAATTCAATCATGATTCAAAGTAAAAAATTTTGGTAAAAATCCGGTAAAATCCAATAT
ATATATATTTTTTAATTT
Found at i:460104 original size:2 final size:2
Alignment explanation
Indices: 460097--460131 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
460087 GTAAAATCCA
460097 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
460132 ACTAACCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:460424 original size:2 final size:2
Alignment explanation
Indices: 460417--460444 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
460407 ATCAATCACT
460417 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
460445 TGGGTGGTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:467761 original size:16 final size:16
Alignment explanation
Indices: 467709--467753 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
467699 ATTGATTAAC
467709 TTGAACTTGAAATAAT
1 TTGAACTTGAAATAAT
*
467725 TTGAA-TCTCAAATAAT
1 TTGAACT-TGAAATAAT
467741 TTGAACTTGAAAT
1 TTGAACTTGAAAT
467754 GAGTTGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 1 0.04
16 23 0.92
17 1 0.04
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (16 bp):
TTGAACTTGAAATAAT
Found at i:467779 original size:16 final size:17
Alignment explanation
Indices: 467749--467797 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
467739 ATTTGAACTT
* *
467749 GAAATGAGTTGAATTCA
1 GAAATGACTTAAATTCA
*
467766 G-AATGACTTAAATT-T
1 GAAATGACTTAAATTCA
467781 GAAATGACTTAAATTCA
1 GAAATGACTTAAATTCA
467798 TATAACTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 1 0.04
16 24 0.92
17 1 0.04
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (17 bp):
GAAATGACTTAAATTCA
Found at i:468081 original size:16 final size:17
Alignment explanation
Indices: 468046--468082 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
468036 GAAATAAAAT
*
468046 TAAAATAAATTATTTTA
1 TAAAATAAATTATTTAA
468063 TAAAATAAA-TATTTAA
1 TAAAATAAATTATTTAA
468079 TAAA
1 TAAA
468083 TCAAACGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAATAAATTATTTAA
Found at i:469162 original size:8 final size:8
Alignment explanation
Indices: 469149--469173 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
469139 GATGGTTGAA
469149 GGGCAAAG
1 GGGCAAAG
469157 GGGCAAAG
1 GGGCAAAG
469165 GGGCAAAG
1 GGGCAAAG
469173 G
1 G
469174 ATGACCCTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.52, T:0.00
Consensus pattern (8 bp):
GGGCAAAG
Found at i:473373 original size:2 final size:2
Alignment explanation
Indices: 473366--473394 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
473356 ATTTCTCGTG
473366 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
473395 GTATGTATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:478676 original size:16 final size:16
Alignment explanation
Indices: 478651--478685 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
478641 AAATAATATG
478651 AATAAATTAAATAAAA
1 AATAAATTAAATAAAA
*
478667 AATAACTTAAATAAAA
1 AATAAATTAAATAAAA
478683 AAT
1 AAT
478686 TTAAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAAATTAAATAAAA
Found at i:480588 original size:2 final size:2
Alignment explanation
Indices: 480581--480609 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
480571 TTTATCCATT
480581 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
480610 CACATAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:482248 original size:33 final size:33
Alignment explanation
Indices: 482188--482251 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
482178 TGTATTATAC
*
482188 ATTAACAATATTAAAAGTTTTATAATATAAATT
1 ATTAACAATATTAAAAGTTTAATAATATAAATT
482221 ATTAA-AATATTAAAA-TTTAAATAAATATAAA
1 ATTAACAATATTAAAAGTTT-AAT-AATATAAA
482252 ATAATTTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 3 0.11
32 12 0.43
33 13 0.46
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (33 bp):
ATTAACAATATTAAAAGTTTAATAATATAAATT
Found at i:482294 original size:18 final size:18
Alignment explanation
Indices: 482271--482308 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
482261 CTATAATTAT
482271 AATATAATAAAATATATA
1 AATATAATAAAATATATA
* *
482289 AATATAATTAAATATTTA
1 AATATAATAAAATATATA
482307 AA
1 AA
482309 ACTATCGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATATAATAAAATATATA
Found at i:482684 original size:21 final size:22
Alignment explanation
Indices: 482660--482748 Score: 80
Period size: 22 Copynumber: 4.0 Consensus size: 22
482650 ATTTTATTTT
482660 TTTAAAATATT-AATTTTAATA
1 TTTAAAATATTAAATTTTAATA
*
482681 TTTAAATTATTAAATTATT--TA
1 TTTAAAATATTAAATT-TTAATA
*
482702 TTAAAGTAATATTAAATTTTAATA
1 TTTAA--AATATTAAATTTTAATA
482726 TCATT-AAATA-TAAATTTTAATA
1 T--TTAAAATATTAAATTTTAATA
482748 T
1 T
482749 AGTATTGATA
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
21 16 0.29
22 19 0.34
23 16 0.29
24 3 0.05
25 1 0.02
26 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (22 bp):
TTTAAAATATTAAATTTTAATA
Found at i:483046 original size:21 final size:20
Alignment explanation
Indices: 483016--483060 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
483006 ATTACTTTCC
* *
483016 AAAAAATTTATAATATCTTA
1 AAAAAATTTAAAAAATCTTA
*
483036 AAAAAATTTTAAAAAATTTTA
1 AAAAAA-TTTAAAAAATCTTA
483057 AAAA
1 AAAA
483061 TTAATAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAAATTTAAAAAATCTTA
Found at i:483062 original size:9 final size:10
Alignment explanation
Indices: 483036--483060 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
483026 TAATATCTTA
483036 AAAAAATTTT
1 AAAAAATTTT
483046 AAAAAATTTT
1 AAAAAATTTT
483056 AAAAA
1 AAAAA
483061 TTAATAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:483520 original size:17 final size:17
Alignment explanation
Indices: 483499--483533 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
483489 AAGTCAAGAA
*
483499 AAAAATAATTTTTATTTT
1 AAAAA-AATATTTATTTT
483517 AAAAAAATATTTATTTT
1 AAAAAAATATTTATTTT
483534 TTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AAAAAAATATTTATTTT
Found at i:483528 original size:19 final size:20
Alignment explanation
Indices: 483497--483538 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
483487 GAAAGTCAAG
483497 AAAAAAATAATTT-TTATTTT
1 AAAAAAATAATTTATT-TTTT
483517 AAAAAAAT-ATTTATTTTTT
1 AAAAAAATAATTTATTTTTT
483536 AAA
1 AAA
483539 TTAAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AAAAAAATAATTTATTTTTT
Found at i:484020 original size:39 final size:38
Alignment explanation
Indices: 483933--484024 Score: 98
Period size: 42 Copynumber: 2.3 Consensus size: 38
483923 GATTTAATAA
* *
483933 ATTTAAACATGAAAAAAATTATAATATAAGCATGATAT
1 ATTTAAATATGAAAAAAATTATAATATAAGCATGACAT
483971 ATTTAATAAATAT-AAAAAAATATAATAAATATAA-CATGACAT
1 A-TT--TAAATATGAAAAAAAT-T-AT-AATATAAGCATGACAT
484013 ATTTAAATATGA
1 ATTTAAATATGA
484025 TTGACATGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
38 1 0.02
39 9 0.20
40 9 0.20
41 9 0.20
42 10 0.22
43 7 0.16
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (38 bp):
ATTTAAATATGAAAAAAATTATAATATAAGCATGACAT
Found at i:485157 original size:17 final size:19
Alignment explanation
Indices: 485124--485159 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
485114 ATGTTATTGG
485124 GTTAGAAATATATTTTAAA
1 GTTAGAAATATATTTTAAA
485143 GTTA-AAATA-ATTTTAAA
1 GTTAGAAATATATTTTAAA
485160 ACAAAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 5 0.29
19 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (19 bp):
GTTAGAAATATATTTTAAA
Found at i:485238 original size:29 final size:29
Alignment explanation
Indices: 485206--485302 Score: 99
Period size: 29 Copynumber: 3.3 Consensus size: 29
485196 TTTATTACAT
485206 CTAAATAAAT-TTTAATATTTAATTTATAA
1 CTAAATAAATATTTAATATTTAATTTAT-A
* * *
485235 CTAAATAAATCTTTAATATTTCATTTTTA
1 CTAAATAAATATTTAATATTTAATTTATA
* * *
485264 CCAATTAAATATTTAACT-TATAATTTATA
1 CTAAATAAATATTTAA-TATTTAATTTATA
485293 CATAAATAAA
1 C-TAAATAAA
485303 CTTCTTTCAT
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
29 33 0.60
30 22 0.40
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.45
Consensus pattern (29 bp):
CTAAATAAATATTTAATATTTAATTTATA
Found at i:485382 original size:28 final size:27
Alignment explanation
Indices: 485324--485415 Score: 73
Period size: 28 Copynumber: 3.4 Consensus size: 27
485314 TTTTTTCATT
*
485324 TAAAATAAAATTTATTTAAATATAAAT
1 TAAAATAAAATTTATTTAAATATAAAG
* * * *
485351 TAAAATATTAATTTATTTAATTGTAACG
1 TAAAATA-AAATTTATTTAAATATAAAG
* *
485379 TAAATATAAAAATTTACTTCAA-ATAAA-
1 TAAA-AT-AAAATTTATTTAAATATAAAG
485406 T-AAATAAAAT
1 TAAAATAAAAT
485416 ACTCCAAAGA
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
24 5 0.10
25 2 0.04
26 2 0.04
27 8 0.16
28 22 0.43
29 11 0.22
30 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.39
Consensus pattern (27 bp):
TAAAATAAAATTTATTTAAATATAAAG
Found at i:490360 original size:19 final size:19
Alignment explanation
Indices: 490336--490373 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
490326 AACCGAGCCG
490336 TTACAAAAGTTCTAGTTCA
1 TTACAAAAGTTCTAGTTCA
490355 TTACAAAAGTTCTAGTTCA
1 TTACAAAAGTTCTAGTTCA
490374 GTGGTCCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
TTACAAAAGTTCTAGTTCA
Found at i:493812 original size:17 final size:17
Alignment explanation
Indices: 493790--493823 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
493780 GATGCTTTGC
*
493790 TACTGTTTTCTGTAGTA
1 TACTGTTTTCTGCAGTA
493807 TACTGTTTTCTGCAGTA
1 TACTGTTTTCTGCAGTA
493824 AAGTTATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.50
Consensus pattern (17 bp):
TACTGTTTTCTGCAGTA
Found at i:498742 original size:2 final size:2
Alignment explanation
Indices: 498735--498776 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
498725 AGTAATAGAG
498735 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
498777 GTAAGTAGGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:502983 original size:3 final size:3
Alignment explanation
Indices: 502975--503004 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
502965 GAGGCATCAC
502975 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
503005 TTGCATCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:503204 original size:2 final size:2
Alignment explanation
Indices: 503197--503232 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
503187 CAAAGAACAG
503197 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
503233 TTAAAAGGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:506868 original size:10 final size:11
Alignment explanation
Indices: 506851--506881 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
506841 CACGAATGCT
506851 TAAAAAAATTA
1 TAAAAAAATTA
506862 TAAAAAAATTA
1 TAAAAAAATTA
*
506873 TAACAAAAT
1 TAAAAAAAT
506882 CCGGATAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (11 bp):
TAAAAAAATTA
Found at i:507930 original size:7 final size:7
Alignment explanation
Indices: 507899--507948 Score: 57
Period size: 7 Copynumber: 6.9 Consensus size: 7
507889 AGAATGGAAG
*
507899 GGTCTTG
1 GGTCTTT
507906 GGT-TTT
1 GGTCTTT
507912 CGGTCGTTT
1 -GGTC-TTT
507921 GGTCTTT
1 GGTCTTT
507928 GGTCTTT
1 GGTCTTT
507935 GGTCTTT
1 GGTCTTT
507942 GGGTCTT
1 -GGTCTT
507949 AATTTCTTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
6 2 0.05
7 23 0.61
8 10 0.26
9 3 0.08
ACGTcount: A:0.00, C:0.14, G:0.34, T:0.52
Consensus pattern (7 bp):
GGTCTTT
Found at i:507938 original size:22 final size:22
Alignment explanation
Indices: 507898--507948 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
507888 AAGAATGGAA
507898 GGGTCTTGGGTTTTCGGTCGTTT
1 GGGTCTTGGGTTTTCGGTC-TTT
*
507921 -GGTCTTTGGTCTTT-GGTCTTT
1 GGGTCTTGGGT-TTTCGGTCTTT
507942 GGGTCTT
1 GGGTCTT
507949 AATTTCTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 3 0.12
22 19 0.76
23 3 0.12
ACGTcount: A:0.00, C:0.14, G:0.35, T:0.51
Consensus pattern (22 bp):
GGGTCTTGGGTTTTCGGTCTTT
Found at i:507946 original size:15 final size:15
Alignment explanation
Indices: 507898--507948 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
507888 AAGAATGGAA
*
507898 GGGTCTTGGGT-TTT
1 GGGTCTTTGGTCTTT
*
507912 CGGTCGTTTGGTCTTT
1 GGGTC-TTTGGTCTTT
507928 -GGTCTTTGGTCTTT
1 GGGTCTTTGGTCTTT
507942 GGGTCTT
1 GGGTCTT
507949 AATTTCTTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 14 0.44
15 15 0.47
16 3 0.09
ACGTcount: A:0.00, C:0.14, G:0.35, T:0.51
Consensus pattern (15 bp):
GGGTCTTTGGTCTTT
Found at i:508076 original size:2 final size:2
Alignment explanation
Indices: 508071--508105 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
508061 AGAAATGGAA
*
508071 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
508106 CTGCGGACGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:508086 original size:12 final size:12
Alignment explanation
Indices: 508051--508101 Score: 57
Period size: 12 Copynumber: 4.0 Consensus size: 12
508041 GTTGAAGAAG
508051 AAGAGAGAAGAGA
1 AAGAGAG-AGAGA
*
508064 AATGGAAAGAGAGA
1 AA--GAGAGAGAGA
508078 AAGAGAGAGAGA
1 AAGAGAGAGAGA
*
508090 GAGAGAGAGAGA
1 AAGAGAGAGAGA
508102 GAGACTGCGG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 20 0.61
13 2 0.06
14 7 0.21
15 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.41, T:0.02
Consensus pattern (12 bp):
AAGAGAGAGAGA
Found at i:508663 original size:27 final size:27
Alignment explanation
Indices: 508611--508668 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
508601 GAAGAAATTA
* *
508611 TAAAAATTTAATTTTTAATTATTAAAAT
1 TAAAAATTTAATTTTTAATCAAT-AAAT
508639 TAAAAA-TTAATATTTT-ATCAATAAAT
1 TAAAAATTTAAT-TTTTAATCAATAAAT
508665 TAAA
1 TAAA
508669 TAATGATCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 8 0.30
27 9 0.33
28 10 0.37
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
TAAAAATTTAATTTTTAATCAATAAAT
Found at i:509496 original size:2 final size:2
Alignment explanation
Indices: 509489--509518 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
509479 TGATAAATAA
509489 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
509519 TATGCGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:513668 original size:34 final size:34
Alignment explanation
Indices: 513590--513669 Score: 81
Period size: 34 Copynumber: 2.3 Consensus size: 34
513580 GTATGTGTAT
*
513590 ATGATAAATAATTAAAAATATATTTTTATTAAATA
1 ATGAT-AATAAATAAAAATATATTTTTATTAAATA
* * * **
513625 ATAAAAATAAATAAAATTATATTTATT-TTTTATA
1 ATGATAATAAATAAAAATATATTT-TTATTAAATA
513659 ATGATAATAAA
1 ATGATAATAAA
513670 AATTATTAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
34 31 0.86
35 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (34 bp):
ATGATAATAAATAAAAATATATTTTTATTAAATA
Found at i:513705 original size:30 final size:32
Alignment explanation
Indices: 513664--513733 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 32
513654 TTATAATGAT
* *
513664 AATAA-AAATTATTAAA-TTCTATTTATATTA
1 AATAATAAATTATTAAAGTTATATTTATATCA
513694 AA-AATAAATTATTAAAGTTATATTTATATCA
1 AATAATAAATTATTAAAGTTATATTTATATCA
513725 AATAATAAA
1 AATAATAAA
513734 ATATATGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 2 0.06
30 13 0.37
31 14 0.40
32 6 0.17
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (32 bp):
AATAATAAATTATTAAAGTTATATTTATATCA
Found at i:514643 original size:2 final size:2
Alignment explanation
Indices: 514636--514661 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
514626 TATTATCTTT
514636 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
514662 AATTAATTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:514885 original size:2 final size:2
Alignment explanation
Indices: 514878--514907 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
514868 ACAATGACAA
514878 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
514908 GTTAATTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:515326 original size:21 final size:21
Alignment explanation
Indices: 515302--515345 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
515292 ATTTTTTATT
515302 TAAAT-TTAAGTATAAAATATA
1 TAAATATTAA-TATAAAATATA
515323 TAAATATTAATATAAAATATA
1 TAAATATTAATATAAAATATA
515344 TA
1 TA
515346 TTTTTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:515883 original size:29 final size:29
Alignment explanation
Indices: 515848--515937 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 29
515838 TAAAAATTAT
515848 TAAAAGTATATTTATATTAAATAATAAAA
1 TAAAAGTATATTTATATTAAATAATAAAA
* *
515877 TATAAGTTATAATATT-TATTCAAAATAATAAAT
1 TAAAAG-TAT-AT-TTATATT--AAATAATAAAA
* *
515910 TAAAATTATATTTATATTAAAAAATAAA
1 TAAAAGTATATTTATATTAAATAATAAA
515938 TGAATAATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
29 14 0.28
30 5 0.10
31 12 0.24
32 5 0.10
33 14 0.28
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (29 bp):
TAAAAGTATATTTATATTAAATAATAAAA
Found at i:515938 original size:29 final size:29
Alignment explanation
Indices: 515846--515938 Score: 98
Period size: 31 Copynumber: 3.1 Consensus size: 29
515836 ATTAAAAATT
* *
515846 ATTAAAAGTATATTTATATTAAATAATAA
1 ATTAAAATTATATTTATATTAAAAAATAA
* *
515875 AATATAAGTTATAATATT-TATTCAAAATAATAA
1 ATTA-AAATTAT-AT-TTATATT-AAAA-AATAA
515908 ATTAAAATTATATTTATATTAAAAAATAA
1 ATTAAAATTATATTTATATTAAAAAATAA
515937 AT
1 AT
515939 GAATAATATA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
29 10 0.19
30 11 0.21
31 12 0.23
32 11 0.21
33 8 0.15
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (29 bp):
ATTAAAATTATATTTATATTAAAAAATAA
Found at i:515948 original size:29 final size:29
Alignment explanation
Indices: 515846--515948 Score: 86
Period size: 29 Copynumber: 3.4 Consensus size: 29
515836 ATTAAAAATT
*
515846 ATTAA-AAGTATATTTATATTAAATAATAAA
1 ATTAATAA-TATATTTATATTAAAAAAT-AA
* *
515876 ATATAAGTTATAATATTTAT-TCAAAATAATAA
1 AT-TAA-TAAT-ATATTTATATTAAAA-AATAA
515908 ATTAA-AATTATATTTATATTAAAAAATAA
1 ATTAATAA-TATATTTATATTAAAAAATAA
*
515937 ATGAATAATATA
1 ATTAATAATATA
515949 AGTAAAAAAG
Statistics
Matches: 59, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
29 22 0.37
30 10 0.17
31 6 0.10
32 9 0.15
33 12 0.20
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (29 bp):
ATTAATAATATATTTATATTAAAAAATAA
Found at i:522098 original size:3 final size:3
Alignment explanation
Indices: 522092--522122 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
522082 ATAAACTATC
522092 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
522123 ATAAAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:522274 original size:32 final size:31
Alignment explanation
Indices: 522236--522306 Score: 97
Period size: 32 Copynumber: 2.3 Consensus size: 31
522226 AAAAATTAAA
* * *
522236 AAAATAATGATGATCTAAAAAATTAAAATTTT
1 AAAATAATAATAATCTAAAAAATTAAAA-TAT
*
522268 AAAATAATAATAATCTAAAAAATTTAAATAT
1 AAAATAATAATAATCTAAAAAATTAAAATAT
522299 AAAATAAT
1 AAAATAAT
522307 TTTAAATCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
31 10 0.29
32 25 0.71
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (31 bp):
AAAATAATAATAATCTAAAAAATTAAAATAT
Found at i:522781 original size:19 final size:19
Alignment explanation
Indices: 522743--522781 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
522733 TAAACATATT
*
522743 TTTTATATTTTAATTTTAA
1 TTTTATATTTTAATTCTAA
522762 TTTTATTATTTT-ATTCTAA
1 TTTTA-TATTTTAATTCTAA
522781 T
1 T
522782 ATTAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTATATTTTAATTCTAA
Found at i:523590 original size:20 final size:21
Alignment explanation
Indices: 523567--523608 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
523557 TAATTTAATA
* *
523567 AATTATTAATAAATT-ATTTT
1 AATTAATAAAAAATTAATTTT
523587 AATTAATAAAAAATTAATTTT
1 AATTAATAAAAAATTAATTTT
523608 A
1 A
523609 TTTTAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATTAATAAAAAATTAATTTT
Found at i:523602 original size:28 final size:26
Alignment explanation
Indices: 523561--523616 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 26
523551 AATTAATAAT
**
523561 TTAATAAATTATTAATAAATTATTTTAA
1 TTAATAAAAAATTAAT--ATTATTTTAA
*
523589 TTAATAAAAAATTAATTTTATTTTAA
1 TTAATAAAAAATTAATATTATTTTAA
523615 TT
1 TT
523617 TTTTTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.44
28 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTAATAAAAAATTAATATTATTTTAA
Found at i:525656 original size:2 final size:2
Alignment explanation
Indices: 525649--525673 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
525639 TTAGAAACAT
525649 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
525674 TTTAAAATAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:527475 original size:52 final size:52
Alignment explanation
Indices: 527414--527517 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
527404 GATTGGAAGG
527414 AGCCTTTTATAGGCAAGATTGTGGAGCCAAAAATGGAGATATTTGGGATATT
1 AGCCTTTTATAGGCAAGATTGTGGAGCCAAAAATGGAGATATTTGGGATATT
527466 AGCCTTTTATAGGCAAGATTGTGGAGCCAAAAATGGAGATATTTGGGATATT
1 AGCCTTTTATAGGCAAGATTGTGGAGCCAAAAATGGAGATATTTGGGATATT
527518 TTCTTTCTTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.31
Consensus pattern (52 bp):
AGCCTTTTATAGGCAAGATTGTGGAGCCAAAAATGGAGATATTTGGGATATT
Found at i:527932 original size:20 final size:20
Alignment explanation
Indices: 527904--527960 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
527894 CAAAAACCCA
*
527904 AAATATATCGATACAATGAG
1 AAATGTATCGATACAATGAG
* * *
527924 AAATGTATCGATATAATTAT
1 AAATGTATCGATACAATGAG
527944 AAGCATGTATCGATACA
1 AA--ATGTATCGATACA
527961 TTAACTAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 18 0.60
22 12 0.40
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.30
Consensus pattern (20 bp):
AAATGTATCGATACAATGAG
Found at i:528072 original size:21 final size:20
Alignment explanation
Indices: 528025--528078 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
528015 CATTTTAGGC
* * *
528025 ATGTATCAATACATTCATTT
1 ATGTATCGATACATTCACTA
528045 ATGTATCGATACATTCACTA
1 ATGTATCGATACATTCACTA
528065 ATTGTATCGATACA
1 A-TGTATCGATACA
528079 AATCATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCACTA
Found at i:528665 original size:14 final size:14
Alignment explanation
Indices: 528646--528672 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
528636 ATATGTAGTT
528646 ATAAAATATTTTAC
1 ATAAAATATTTTAC
528660 ATAAAATATTTTA
1 ATAAAATATTTTA
528673 TAGTTGCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAAAATATTTTAC
Found at i:531673 original size:51 final size:50
Alignment explanation
Indices: 531616--531782 Score: 183
Period size: 51 Copynumber: 3.3 Consensus size: 50
531606 TTTTCATCTC
* * *
531616 GGGGATACTTCAA-TCTCGGTTTCATTTTTGAAACATCAATTTTTCTTAATT
1 GGGGATACTTCAACTC-CGATTTTATTTTT-AAACATCAATTTTTCATAATT
* * * ** * *
531667 GGGGATACTCCAACTCCGATTTTATTTCTAAAGCATCGATTTACCACAATC
1 GGGGATACTTCAACTCCGATTTTATTTTTAAA-CATCAATTTTTCATAATT
*
531718 GGGGATACTTCAACTCCGATTTTATTTTTAAAACACCAATTTTTCATAATT
1 GGGGATACTTCAACTCCGATTTTATTTTT-AAACATCAATTTTTCATAATT
*
531769 GGGGATACTCCAAC
1 GGGGATACTTCAAC
531783 CCCGTTATTT
Statistics
Matches: 94, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
50 3 0.03
51 86 0.91
52 5 0.05
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (50 bp):
GGGGATACTTCAACTCCGATTTTATTTTTAAACATCAATTTTTCATAATT
Found at i:531838 original size:28 final size:28
Alignment explanation
Indices: 531769--531842 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
531759 TTTCATAATT
**
531769 GGGGATACTCCAACCCCGTTATTTCATC
1 GGGGATACTCCAACCCCGTTATTTCAGA
* * * * *
531797 GGAGAAACTTCAACCCTGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATTTCAGA
531825 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
531843 GCTTTATATC
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCAGA
Found at i:531996 original size:51 final size:51
Alignment explanation
Indices: 531937--532050 Score: 176
Period size: 51 Copynumber: 2.2 Consensus size: 51
531927 ATTTCCAAGA
* *
531937 GGATACTCCAACTCCGATTTTATTTTTAAAATACCAATTT-TCCACAATCGG
1 GGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTCT-CACAATCGG
*
531988 GGATACTCCAACTTCGATTTTATTTTCAAAACACCAATTTCTCACAATCGG
1 GGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTCTCACAATCGG
*
532039 AGATACTCCAAC
1 GGATACTCCAAC
532051 CTCGTTATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
51 57 0.98
52 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.32
Consensus pattern (51 bp):
GGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTCTCACAATCGG
Found at i:532012 original size:110 final size:105
Alignment explanation
Indices: 531720--531999 Score: 276
Period size: 110 Copynumber: 2.6 Consensus size: 105
531710 CCACAATCGG
* *
531720 GGATACTTCAACTCCGATTTTATTTTTAAAACACCAATTTTTCATAATTGGGGATACTCCAACCC
1 GGATACTCCAACTCCGATTTTATTTTTAAAATACCAATTTTTCATAA-TGGGGATACTCCAA--C
* * *
531785 CG-TTATTTCATCGGAGAAACTTCAACCCTGTTATTTCCGAGG
63 CGTTTATTTCATCGGAGAAACTCCAACCCTGTTATTTCCAAGA
* ** * * ** * *
531827 GGATACTCCAACCCCGGCTTTATATCTACAAATATTGATTTCTTTCATAATTGGGAGTACTCCAA
1 GGATACTCCAACTCCGATTTTATTTTTA-AAATA-CCAATT-TTTCATAATGGGGA-TACTCCAA
* * * *
531892 CCCTATTATTTCATTGGGGATACTCCAATCCC-GTTATTTCCAAGA
62 CCGT-TTATTTCATCGGAGAAACTCCAA-CCCTGTTATTTCCAAGA
* *
531937 GGATACTCCAACTCCGATTTTATTTTTAAAATACCAATTTTCCACAATCGGGGATACTCCAAC
1 GGATACTCCAACTCCGATTTTATTTTTAAAATACCAATTTTTCATAAT-GGGGATACTCCAAC
532000 TTCGATTTTA
Statistics
Matches: 136, Mismatches: 29, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
107 38 0.28
108 13 0.10
109 13 0.10
110 69 0.51
111 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (105 bp):
GGATACTCCAACTCCGATTTTATTTTTAAAATACCAATTTTTCATAATGGGGATACTCCAACCGT
TTATTTCATCGGAGAAACTCCAACCCTGTTATTTCCAAGA
Found at i:532202 original size:82 final size:79
Alignment explanation
Indices: 531990--532207 Score: 224
Period size: 79 Copynumber: 2.7 Consensus size: 79
531980 ACAATCGGGG
** * * * * *
531990 ATACTCCAACTTCGATTTTATTT-TCAAAACACCAATTTCTCACAATCGGAGATACTCCAACCTC
1 ATACTCCAACCCCGATTTTATTTCT-AAAACACCGATTTTTCATAATCGGGGATACTCCAACCCC
* * *
532054 GTTATTTCTGAGGGG
65 ATTATTTCTGAAGGA
* * * ** *
532069 ATACTCTAACCCCGACTTTATTTCTAAAATATTGATTTTTCATAATTGGGGATACTCCAACCCCA
1 ATACTCCAACCCCGATTTTATTTCTAAAACACCGATTTTTCATAATCGGGGATACTCCAACCCCA
532134 TTATTT-TCGAAGGA
66 TTATTTCT-GAAGGA
*
532148 ATACTCCAACCCCTATTTTTTTATTTCTAAAACACCGATTTTTCATAATCGGGGATACTC
1 ATACTCCAACCCCGA---TTTTATTTCTAAAACACCGATTTTTCATAATCGGGGATACTC
532208 TAGCTCCGTT
Statistics
Matches: 111, Mismatches: 23, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
78 1 0.01
79 72 0.65
80 1 0.01
82 37 0.33
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (79 bp):
ATACTCCAACCCCGATTTTATTTCTAAAACACCGATTTTTCATAATCGGGGATACTCCAACCCCA
TTATTTCTGAAGGA
Found at i:537050 original size:15 final size:15
Alignment explanation
Indices: 537034--537070 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
537024 CTAAAAATTA
537034 AAAATAGT-TAAAGT
1 AAAATAGTATAAAGT
537048 AAAATAGTATAAA-T
1 AAAATAGTATAAAGT
*
537062 AATATAGTA
1 AAAATAGTA
537071 AATATTCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (15 bp):
AAAATAGTATAAAGT
Found at i:538719 original size:13 final size:14
Alignment explanation
Indices: 538695--538728 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
538685 GTAACGGCCA
538695 CCGACGAGTGGTGG
1 CCGACGAGTGGTGG
*
538709 CCGAC-AGTGGTTG
1 CCGACGAGTGGTGG
538722 CCGACGA
1 CCGACGA
538729 CCGATGTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.18, C:0.26, G:0.41, T:0.15
Consensus pattern (14 bp):
CCGACGAGTGGTGG
Found at i:543864 original size:20 final size:19
Alignment explanation
Indices: 543841--543936 Score: 61
Period size: 21 Copynumber: 4.7 Consensus size: 19
543831 TCTATTTTCA
543841 TTTTAGTATAATTATTATTC
1 TTTTAG-ATAATTATTATTC
* *
543861 TTTTTAAATATATAATTA-TC
1 -TTTTAGATA-ATTATTATTC
543881 TCTTTAGGATAAGTT-TTATTC
1 T-TTTA-GATAA-TTATTATTC
*
543902 TTTTAAGATAAGTAATTATTAC
1 TTTT-AGATAA-TTATTATT-C
*
543924 TTTAAGATAATTA
1 TTTTAGATAATTA
543937 CTATAGTTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
19 1 0.02
20 25 0.42
21 30 0.50
22 4 0.07
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.52
Consensus pattern (19 bp):
TTTTAGATAATTATTATTC
Found at i:543918 original size:41 final size:41
Alignment explanation
Indices: 543842--543936 Score: 108
Period size: 41 Copynumber: 2.3 Consensus size: 41
543832 CTATTTTCAT
*
543842 TTTAGTATAATTATTATTCTTTTTAAATATATAATTATCT-C
1 TTTAGGATAATTATTATTCTTTTTAAATATATAATTAT-TAC
543883 TTTAGGATAAGTT-TTATTC-TTTTAAGATA-AGTAATTATTAC
1 TTTAGGATAA-TTATTATTCTTTTTAA-ATATA-TAATTATTAC
*
543924 TTTAAGATAATTA
1 TTTAGGATAATTA
543937 CTATAGTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
40 10 0.21
41 35 0.74
42 2 0.04
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (41 bp):
TTTAGGATAATTATTATTCTTTTTAAATATATAATTATTAC
Found at i:543927 original size:21 final size:20
Alignment explanation
Indices: 543873--543933 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
543863 TTTAAATATA
*
543873 TAATTATCTCTTTAGGATAAG
1 TAATTAT-TCTTTAAGATAAG
*
543894 T-TTTATTCTTTTAAGATAAG
1 TAATTATTC-TTTAAGATAAG
543914 TAATTATTACTTTAAGATAA
1 TAATTATT-CTTTAAGATAA
543934 TTACTATAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 2 0.06
20 15 0.44
21 16 0.47
22 1 0.03
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.48
Consensus pattern (20 bp):
TAATTATTCTTTAAGATAAG
Found at i:543936 original size:17 final size:19
Alignment explanation
Indices: 543910--543951 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
543900 TCTTTTAAGA
543910 TAAG-TAATTA-T-TACTT
1 TAAGATAATTACTATACTT
*
543926 TAAGATAATTACTATAGTT
1 TAAGATAATTACTATACTT
543945 TAAGATA
1 TAAGATA
543952 TATATTAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 6 0.27
18 1 0.05
19 11 0.50
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.43
Consensus pattern (19 bp):
TAAGATAATTACTATACTT
Found at i:545652 original size:4 final size:4
Alignment explanation
Indices: 545643--545669 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
545633 TTATTGATAA
545643 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
545670 CTTTTGGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:546210 original size:22 final size:20
Alignment explanation
Indices: 546171--546230 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 20
546161 CAGTATCTAT
* *
546171 ATATTTTTATATATTATAATC
1 ATATTTTAATATATTAT-ATA
546192 ATA-TTTAATATATTATATA
1 ATATTTTAATATATTATATA
*
546211 A-ATTTTAATATGTTAT-TA
1 ATATTTTAATATATTATATA
546229 AT
1 AT
546231 TTATGTTCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.12
19 15 0.44
20 12 0.35
21 3 0.09
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
ATATTTTAATATATTATATA
Found at i:546428 original size:2 final size:2
Alignment explanation
Indices: 546415--546449 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
546405 AGACATGCAG
*
546415 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
546450 AATAACACAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:554332 original size:25 final size:27
Alignment explanation
Indices: 554304--554361 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
554294 ATCGATTATC
554304 AATTTCTCAACAAAATT-AA-TA-AAAA
1 AATTT-TCAACAAAATTAAATTATAAAA
* *
554329 AATTTTTAACTAAATTAAATTATAAAA
1 AATTTTCAACAAAATTAAATTATAAAA
554356 AATTTT
1 AATTTT
554362 AAAATCACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 9 0.32
25 7 0.25
26 2 0.07
27 10 0.36
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (27 bp):
AATTTTCAACAAAATTAAATTATAAAA
Found at i:556656 original size:74 final size:74
Alignment explanation
Indices: 556564--556754 Score: 197
Period size: 74 Copynumber: 2.6 Consensus size: 74
556554 TTAATCTCAT
* * * * *
556564 AAATAAAAATAAATTATACCTTAAAAAAATTTGATCTCCTATAATT-AACTCAAAAAATAAATTT
1 AAATAAAAATAAACTATACCAT-AAAAAATTTAAACTCCTATAATTAAACTAAAAAAATAAATTT
556628 AAACTCCTAC
65 AAACTCCTAC
* * **
556638 AAATAAAAGTAAACTATACCATAAAAATTTTAAACTTGTATAATTAAACTAAAAAAATAAATTTA
1 AAATAAAAATAAACTATACCATAAAAAATTTAAACTCCTATAATTAAACTAAAAAAATAAATTTA
* *
556703 AACTCTTAA
66 AACTCCTAC
* * * * * *
556712 AAATTAAAATATA-TCATATCTTACAAAATTTAAACTCATATAA
1 AAATAAAAATAAACT-ATACCATAAAAAATTTAAACTCCTATAA
556755 AAAATCATAC
Statistics
Matches: 95, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
73 19 0.20
74 76 0.80
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (74 bp):
AAATAAAAATAAACTATACCATAAAAAATTTAAACTCCTATAATTAAACTAAAAAAATAAATTTA
AACTCCTAC
Found at i:557203 original size:19 final size:19
Alignment explanation
Indices: 557155--557204 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
557145 ATTATTTTAA
557155 TTTAATTAAATTTAAAAATTT
1 TTTAATTAAA--TAAAAATTT
* *
557176 ATT-ATTAAATAACAATTT
1 TTTAATTAAATAAAAATTT
557194 TTTAATTAAAT
1 TTTAATTAAAT
557205 GATGAAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 10 0.40
19 7 0.28
20 6 0.24
21 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAATTAAATAAAAATTT
Found at i:557521 original size:2 final size:2
Alignment explanation
Indices: 557516--557555 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
557506 ACACTCATTC
*
557516 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CC CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
557556 TATTTTTTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:559127 original size:2 final size:2
Alignment explanation
Indices: 559120--559183 Score: 92
Period size: 2 Copynumber: 32.0 Consensus size: 2
559110 TGCTTTCATT
* *
559120 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
559162 TG TC TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
559184 CACACGCATA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:559802 original size:31 final size:30
Alignment explanation
Indices: 559766--559828 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
559756 AATATTATGA
559766 TTATAT-TTAAAAAAAGTATATGTATATAAAT
1 TTATATATT-AAAAAAGTATAT-TATATAAAT
* **
559797 TTATATATTAATAATTTATATTATATAAAT
1 TTATATATTAAAAAAGTATATTATATAAAT
559827 TT
1 TT
559829 TAAAATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 11 0.39
31 15 0.54
32 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (30 bp):
TTATATATTAAAAAAGTATATTATATAAAT
Found at i:559849 original size:29 final size:30
Alignment explanation
Indices: 559782--559852 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
559772 TTAAAAAAAG
* *
559782 TATATGTATATAAATTTATATATTAATAATT
1 TATAT-TATATAAATTTATAAAATAATAATT
559813 TATATTATATAAATTT-TAAAAT-ATATATT
1 TATATTATATAAATTTATAAAATAATA-ATT
559842 TATATTATATA
1 TATATTATATA
559853 TTAATTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 3 0.08
29 18 0.49
30 11 0.30
31 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (30 bp):
TATATTATATAAATTTATAAAATAATAATT
Found at i:560584 original size:14 final size:15
Alignment explanation
Indices: 560564--560601 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
560554 TATATGATAT
*
560564 TTAAAAAATTTTAAA
1 TTAAAAAATATTAAA
560579 -T-AAAAATATTAAA
1 TTAAAAAATATTAAA
560592 TTAAAAAATA
1 TTAAAAAATA
560602 AATTTAGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
13 11 0.55
14 2 0.10
15 7 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAAAAAATATTAAA
Found at i:560615 original size:17 final size:17
Alignment explanation
Indices: 560593--560639 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
560583 AATATTAAAT
560593 TAAAAAATAAATTTAGA
1 TAAAAAATAAATTTAGA
**
560610 T-AAAAATAAAATTTATT
1 TAAAAAAT-AAATTTAGA
560627 TAAATAAATAAAT
1 TAAA-AAATAAAT
560640 CGAGTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 6 0.24
17 9 0.36
18 6 0.24
19 4 0.16
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
TAAAAAATAAATTTAGA
Found at i:561049 original size:23 final size:23
Alignment explanation
Indices: 561023--561067 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
561013 GACATTTGGA
* *
561023 TAAATTTTTAATTATAAGATATT
1 TAAATTTTCAATGATAAGATATT
561046 TAAATTTTCAATGATAAGATAT
1 TAAATTTTCAATGATAAGATAT
561068 GAAAATGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (23 bp):
TAAATTTTCAATGATAAGATATT
Found at i:561073 original size:23 final size:23
Alignment explanation
Indices: 561024--561073 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
561014 ACATTTGGAT
* * **
561024 AAATTTTTAATTATAAGATATTT
1 AAATTTTCAATGATAAGATATGA
561047 AAATTTTCAATGATAAGATATGA
1 AAATTTTCAATGATAAGATATGA
561070 AAAT
1 AAAT
561074 GAATTCAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (23 bp):
AAATTTTCAATGATAAGATATGA
Found at i:562300 original size:26 final size:22
Alignment explanation
Indices: 562253--562294 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
562243 TATATATAAA
562253 TATATATGTATGATTACTTTGT
1 TATATATGTATGATTACTTTGT
562275 TATATATGTATGATTACTTT
1 TATATATGTATGATTACTTT
562295 CTTTGTCCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.55
Consensus pattern (22 bp):
TATATATGTATGATTACTTTGT
Found at i:563510 original size:28 final size:28
Alignment explanation
Indices: 563457--563511 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
563447 ACTCGAATTC
*
563457 TAAAAAATATTTAATATATCTATTTAAA
1 TAAAAAATATTTAATATATATATTTAAA
563485 TAAAAATATAATTTAAT-TATAT-TTTAA
1 TAAAAA-AT-ATTTAATATATATATTTAA
563512 CTTGATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 11 0.46
29 6 0.25
30 7 0.29
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (28 bp):
TAAAAAATATTTAATATATATATTTAAA
Found at i:563549 original size:19 final size:17
Alignment explanation
Indices: 563525--563567 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
563515 GATAAAAATT
*
563525 AAAAATAATTTTGTAGTTA
1 AAAAATAATTTT-TA-ATA
563544 AAAAAT-ATTTTTAATA
1 AAAAATAATTTTTAATA
563560 AAAAATAA
1 AAAAATAA
563568 AAATAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 8 0.36
17 3 0.14
18 5 0.23
19 6 0.27
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (17 bp):
AAAAATAATTTTTAATA
Found at i:563832 original size:29 final size:29
Alignment explanation
Indices: 563799--563863 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
563789 TTTACATTTT
*
563799 AATATATATAATT-TATGTAAAAAAT-ATAA
1 AATATA-ATAATTAAAT-TAAAAAATAATAA
*
563828 AATATAATTATTAAATTAAAAAATAATAA
1 AATATAATAATTAAATTAAAAAATAATAA
563857 AA-ATAAT
1 AATATAAT
563864 TTAAGTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (29 bp):
AATATAATAATTAAATTAAAAAATAATAA
Found at i:564120 original size:9 final size:9
Alignment explanation
Indices: 564106--564130 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
564096 GTAATGAAAA
564106 TTTATTAAT
1 TTTATTAAT
564115 TTTATTAAT
1 TTTATTAAT
564124 TTTATTA
1 TTTATTA
564131 TTAAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTATTAAT
Found at i:564133 original size:21 final size:20
Alignment explanation
Indices: 564106--564152 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
564096 GTAATGAAAA
* *
564106 TTTATTAATTTTATTAATTT
1 TTTATTAAATTAATTAATTT
564126 TATTATTAAATTAATTAATTT
1 T-TTATTAAATTAATTAATTT
564147 TTTATT
1 TTTATT
564153 TTTTAATCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTATTAAATTAATTAATTT
Found at i:565948 original size:2 final size:2
Alignment explanation
Indices: 565936--565968 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
565926 GCAAGAAAAC
*
565936 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
565969 GTACCAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:566237 original size:25 final size:25
Alignment explanation
Indices: 566203--566252 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
566193 CACATCCTGT
566203 GGTTTTGGCATTTATTATTGCCAGC
1 GGTTTTGGCATTTATTATTGCCAGC
566228 GGTTTTGGCATTTATTATTGCCAGC
1 GGTTTTGGCATTTATTATTGCCAGC
566253 CAACCCCCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (25 bp):
GGTTTTGGCATTTATTATTGCCAGC
Found at i:567115 original size:69 final size:70
Alignment explanation
Indices: 567004--567138 Score: 227
Period size: 69 Copynumber: 1.9 Consensus size: 70
566994 AGATTATGCT
* *
567004 TATAACAGACTACGGACTTTCATCCTATAACAGGTATAACAACTAGCCCAAGTACT-TCTTTCTT
1 TATAACAGACTACAGACTTTCATCCTAGAACAGGTATAACAACTAGCCCAAGTACTATCTTTCTT
567068 CATCC
66 CATCC
*
567073 TATAACAGACTACAGACTTTCATCCTGGAACAGGTATAACAACTAGCCCAAGTACTCATCTTTCT
1 TATAACAGACTACAGACTTTCATCCTAGAACAGGTATAACAACTAGCCCAAGTACT-ATCTTTCT
567138 T
65 T
567139 TCTTTTTTGC
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
69 53 0.87
71 8 0.13
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.30
Consensus pattern (70 bp):
TATAACAGACTACAGACTTTCATCCTAGAACAGGTATAACAACTAGCCCAAGTACTATCTTTCTT
CATCC
Found at i:570151 original size:3 final size:3
Alignment explanation
Indices: 570143--570168 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
570133 GGTCAGTCAA
570143 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
570169 GAAAAAGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:577570 original size:7 final size:7
Alignment explanation
Indices: 577508--577576 Score: 53
Period size: 6 Copynumber: 10.7 Consensus size: 7
577498 GTGACAATTA
577508 ATATATT
1 ATATATT
577515 -TATATT
1 ATATATT
577521 AT-T-TT
1 ATATATT
*
577526 TTATATT
1 ATATATT
577533 ATA-ATT
1 ATATATT
577539 ATA-ATT
1 ATATATT
577545 -TA-ATT
1 ATATATT
*
577550 ATAAATTT
1 ATATA-TT
*
577558 AAATATT
1 ATATATT
577565 ATATATT
1 ATATATT
577572 ATATA
1 ATATA
577577 AAATTTGAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
5 8 0.16
6 19 0.37
7 19 0.37
8 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATATATT
Found at i:577779 original size:6 final size:6
Alignment explanation
Indices: 577749--577796 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
577739 CTGATGCGTC
* * * *
577749 TATTCT TATTCT TATTAT TATTTTT TATTTT TATTTT TATATT TATTT
1 TATTTT TATTTT TATTTT TA-TTTT TATTTT TATTTT TATTTT TATTT
577797 ATTTCAATTC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
6 32 0.86
7 5 0.14
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (6 bp):
TATTTT
Found at i:577783 original size:25 final size:25
Alignment explanation
Indices: 577749--577796 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
577739 CTGATGCGTC
577749 TATTCTTATTCTTAT-TATTATTTTT
1 TATTCTTATTCTTATAT-TTATTTTT
* *
577774 TATTTTTATTTTTATATTTATTT
1 TATTCTTATTCTTATATTTATTT
577797 ATTTCAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 19 0.95
26 1 0.05
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (25 bp):
TATTCTTATTCTTATATTTATTTTT
Found at i:577866 original size:24 final size:24
Alignment explanation
Indices: 577834--577881 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
577824 TCGGACGGCT
577834 TTTCTATCTGGTGTCTGAGGAGAA
1 TTTCTATCTGGTGTCTGAGGAGAA
577858 TTTCTATCTGGTGTCTGAGGAGAA
1 TTTCTATCTGGTGTCTGAGGAGAA
577882 AGATAAGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.29, T:0.38
Consensus pattern (24 bp):
TTTCTATCTGGTGTCTGAGGAGAA
Found at i:578746 original size:54 final size:54
Alignment explanation
Indices: 578683--578790 Score: 182
Period size: 54 Copynumber: 2.0 Consensus size: 54
578673 CTTTGCATCA
*
578683 TTAGTGTTCAAATTAGTTTGAT-GCATATAATCTTTGTTTAATAGTTTATACTCT
1 TTAGTGTTCAAATTAGTTTGATAG-ACATAATCTTTGTTTAATAGTTTATACTCT
*
578737 TTAGTGTTCAAATTAGTTTGATAGACATAATCTTTGTTTAATAGTTTATGCTCT
1 TTAGTGTTCAAATTAGTTTGATAGACATAATCTTTGTTTAATAGTTTATACTCT
578791 AATCACAGCC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
54 50 0.98
55 1 0.02
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49
Consensus pattern (54 bp):
TTAGTGTTCAAATTAGTTTGATAGACATAATCTTTGTTTAATAGTTTATACTCT
Found at i:585600 original size:2 final size:2
Alignment explanation
Indices: 585593--585628 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
585583 TAATTATAAT
585593 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
585629 GATATTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:592772 original size:5 final size:5
Alignment explanation
Indices: 592764--592799 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
592754 TTAATTTATA
592764 CAAAC CAAAC C-AAC CAAAC CAAAC CAAAC CAAAC CA
1 CAAAC CAAAC CAAAC CAAAC CAAAC CAAAC CAAAC CA
592800 TTCATATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.58, C:0.42, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAC
Found at i:592780 original size:9 final size:9
Alignment explanation
Indices: 592766--592795 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
592756 AATTTATACA
592766 AACCAAACC
1 AACCAAACC
592775 AACCAAACC
1 AACCAAACC
592784 AAACCAAACC
1 -AACCAAACC
592794 AA
1 AA
592796 ACCATTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (9 bp):
AACCAAACC
Found at i:593136 original size:20 final size:21
Alignment explanation
Indices: 593095--593152 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 21
593085 TTAAATTAAA
*
593095 TATATATTTTAAATTTATTATT
1 TATATA-TTTAAAATTATTATT
*
593117 TATTTAATATTAAAATTATTATT
1 TATAT-AT-TTAAAATTATTATT
593140 TATATATTTAAAA
1 TATATATTTAAAA
593153 ATAATTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 6 0.19
22 7 0.23
23 18 0.58
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATATATTTAAAATTATTATT
Found at i:597702 original size:2 final size:2
Alignment explanation
Indices: 597689--597740 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
597679 ATTTAATTCA
*
597689 TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
597731 TC TC TC TC TC
1 TC TC TC TC TC
597741 ACATATGTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:599357 original size:2 final size:2
Alignment explanation
Indices: 599350--599390 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
599340 GTATAGTAGG
599350 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
599391 GTAGTATAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:607975 original size:2 final size:2
Alignment explanation
Indices: 607923--607961 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
607913 TCATTTCTTG
* *
607923 AT AT AT AT AT AT AT AT A- AT AA AT TT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
607962 TGTTAAAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:608425 original size:13 final size:13
Alignment explanation
Indices: 608392--608424 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
608382 GAATTTGATA
*
608392 TTTATTATATATT
1 TTTATTTTATATT
608405 TTTATTTTATA-T
1 TTTATTTTATATT
608417 TTTATTTT
1 TTTATTTT
608425 TTAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATATT
Found at i:608988 original size:8 final size:9
Alignment explanation
Indices: 608957--608983 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
608947 GTTGTTACTT
608957 AAATTTTAA
1 AAATTTTAA
608966 AAATTTTAA
1 AAATTTTAA
608975 AAATTTTAA
1 AAATTTTAA
608984 GATTTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AAATTTTAA
Found at i:609120 original size:20 final size:20
Alignment explanation
Indices: 609097--609150 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
609087 ATTTAATAAG
609097 TAAATATATATTAAAATATT
1 TAAATATATATTAAAATATT
* *
609117 TAAATAAATAATT--ACTATT
1 TAAATATAT-ATTAAAATATT
609136 T-AATATA-ATTAAAAT
1 TAAATATATATTAAAAT
609151 TATATAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
16 3 0.11
18 7 0.26
19 6 0.22
20 8 0.30
21 3 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATATATATTAAAATATT
Found at i:609243 original size:22 final size:21
Alignment explanation
Indices: 609218--609259 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
609208 TAATGTGATT
609218 ATATGATATAAAAATAATAAAA
1 ATATGATATAAAAAT-ATAAAA
* *
609240 ATATTATATAAATATATAAA
1 ATATGATATAAAAATATAAA
609260 CACTTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
ATATGATATAAAAATATAAAA
Found at i:609548 original size:22 final size:20
Alignment explanation
Indices: 609496--609549 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
609486 TTTTTATTCG
609496 AATCATTTTAAATTTAAATC
1 AATCATTTTAAATTTAAATC
* * *
609516 AATTAAGTTTAATATTTAAATT
1 AA-TCATTTTAA-ATTTAAATC
609538 AATCGATTTTAA
1 AATC-ATTTTAA
609550 GTAAACTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
20 2 0.08
21 8 0.31
22 16 0.62
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (20 bp):
AATCATTTTAAATTTAAATC
Found at i:609611 original size:16 final size:16
Alignment explanation
Indices: 609590--609687 Score: 76
Period size: 16 Copynumber: 6.2 Consensus size: 16
609580 AAGTTTAATA
*
609590 ATTTTAGATATAAATT
1 ATTTTAGATTTAAATT
* *
609606 ATTTTA-AGTTCAGATT
1 ATTTTAGA-TTTAAATT
* *
609622 ATTTTAAATTTAAATC
1 ATTTTAGATTTAAATT
*
609638 ATTCTAGATTTAAATT
1 ATTTTAGATTTAAATT
* *
609654 ATTTTAAATTTGAATT
1 ATTTTAGATTTAAATT
*
609670 A-ATTA-ATTTTAAATT
1 ATTTTAGA-TTTAAATT
609685 ATT
1 ATT
609688 AATTTTTTTA
Statistics
Matches: 63, Mismatches: 15, Indels: 8
0.73 0.17 0.09
Matches are distributed among these distances:
14 1 0.02
15 12 0.19
16 49 0.78
17 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (16 bp):
ATTTTAGATTTAAATT
Found at i:609694 original size:15 final size:15
Alignment explanation
Indices: 609646--609693 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
609636 TCATTCTAGA
* *
609646 TTTAAATTATTTTAAA
1 TTTAAATTA-ATTAAT
*
609662 TTTGAATTAATTAAT
1 TTTAAATTAATTAAT
609677 TTTAAATT-ATTAAT
1 TTTAAATTAATTAAT
609691 TTT
1 TTT
609694 TTTATTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 9 0.32
15 11 0.39
16 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
TTTAAATTAATTAAT
Found at i:621388 original size:23 final size:22
Alignment explanation
Indices: 621342--621392 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
621332 TATTATATCA
621342 ATATATAAAATAAAAATTATTT
1 ATATATAAAATAAAAATTATTT
* *
621364 AT-TATATAATAATAAATTTTATT
1 ATATATAAAATAA-AAATTAT-TT
621387 ATATAT
1 ATATAT
621393 TTATTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 9 0.38
22 8 0.33
23 4 0.17
24 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATATAAAATAAAAATTATTT
Found at i:621854 original size:16 final size:18
Alignment explanation
Indices: 621825--621882 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
621815 TTTTATATGT
* *
621825 TTATATATTCATATTTTA
1 TTATATTTTAATATTTTA
*
621843 TT-T-TTTTAATATTATA
1 TTATATTTTAATATTTTA
621859 TTATATTTTAATTATTTT-
1 TTATATTTTAA-TATTTTA
621877 TTATAT
1 TTATAT
621883 CTTGTAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 12 0.36
17 2 0.06
18 14 0.42
19 5 0.15
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATATTTTAATATTTTA
Found at i:621865 original size:21 final size:23
Alignment explanation
Indices: 621824--621867 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
621814 TTTTTATATG
*
621824 TTTATATATTCATATTTTATTTT
1 TTTATATATTCATATTATATTTT
621847 TTTA-ATATT-ATATTATATTTT
1 TTTATATATTCATATTATATTTT
621868 AATTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 5 0.25
23 4 0.20
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTATATATTCATATTATATTTT
Found at i:621869 original size:18 final size:17
Alignment explanation
Indices: 621795--621900 Score: 55
Period size: 16 Copynumber: 6.2 Consensus size: 17
621785 TAATACACTA
621795 ATATTTTATATTATA-T
1 ATATTTTATATTATATT
* *
621811 AAATTTT-TA-TATGTTT
1 ATATTTTATATTAT-ATT
* *
621827 ATATATTCATATTTTATT
1 ATAT-TTTATATTATATT
621845 -T-TTTTAATATTATATT
1 ATATTTT-ATATTATATT
*
621861 ATATTTTA-ATTATTTTTT
1 ATATTTTATATTA--TATT
621879 ATATCTTGTA-ATTATATT
1 ATAT-TT-TATATTATATT
621897 ATAT
1 ATAT
621901 CTAAAATTAT
Statistics
Matches: 68, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
14 3 0.04
15 4 0.06
16 24 0.35
17 5 0.07
18 22 0.32
19 4 0.06
20 6 0.09
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (17 bp):
ATATTTTATATTATATT
Found at i:622528 original size:66 final size:67
Alignment explanation
Indices: 622378--622581 Score: 221
Period size: 66 Copynumber: 3.0 Consensus size: 67
622368 TGCTACAGCC
* * * * * *
622378 TTTCTGCACCATTACTCTGCATGACAAAACTAATGAAAATAAGAGCAGCTCTAAGCATAGCACCT
1 TTTCTACACCACTACTCTGCATGACAGAACCAATGAAAATAAGAGCA--ACTAAGCATAGTACCT
**
622443 TGAG
64 AAAG
* * ** ** *
622447 TTTCTATACCACTACTCTGCATGGCAGAATTAATGAAAAT-AGATTAACTGAGCATAGTACCTAA
1 TTTCTACACCACTACTCTGCATGACAGAACCAATGAAAATAAGAGCAACTAAGCATAGTACCTAA
622511 AG
66 AG
* * *
622513 TTTCTACATCACTACTCTGCATGATAGAACCAATGAAAATAAGAGCAACTAAGTATAGTACCTAA
1 TTTCTACACCACTACTCTGCATGACAGAACCAATGAAAATAAGAGCAACTAAGCATAGTACCTAA
622578 AG
66 AG
622580 TT
1 TT
622582 CTCCCTTTAT
Statistics
Matches: 111, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
66 49 0.44
67 24 0.22
68 4 0.04
69 34 0.31
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (67 bp):
TTTCTACACCACTACTCTGCATGACAGAACCAATGAAAATAAGAGCAACTAAGCATAGTACCTAA
AG
Found at i:627369 original size:14 final size:14
Alignment explanation
Indices: 627330--627372 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
627320 TAAAAGGGAC
*
627330 AAAAGAAAAAGAAA
1 AAAAGAAAAAGGAA
627344 AAAAGAAAAAGGAA
1 AAAAGAAAAAGGAA
*
627358 AAAAGGAAAAGGAA
1 AAAAGAAAAAGGAA
627372 A
1 A
627373 CTTTATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAGGAA
Found at i:628017 original size:48 final size:50
Alignment explanation
Indices: 627919--628019 Score: 118
Period size: 48 Copynumber: 2.1 Consensus size: 50
627909 GTTTCATGAG
* * * * *
627919 AAAATCGAGTCTTTTAAGGCTTAGTTTTGTACTTTTTGTTAAAATTGACC
1 AAAATCAAGTCTTTTAAGGCTTAGTTTTGTACTTTCTATCAAAATAGACC
*
627969 AAAATCAAGTCTTTTATGG-TT-GTTCTT-TACTTTCTATCAAAATAGACC
1 AAAATCAAGTCTTTTAAGGCTTAGTT-TTGTACTTTCTATCAAAATAGACC
628017 AAA
1 AAA
628020 CCGAACCTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
48 23 0.52
49 4 0.09
50 17 0.39
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.42
Consensus pattern (50 bp):
AAAATCAAGTCTTTTAAGGCTTAGTTTTGTACTTTCTATCAAAATAGACC
Found at i:628542 original size:23 final size:24
Alignment explanation
Indices: 628516--628562 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
628506 AATTGACTCA
*
628516 TAAATCCTTTTCATGTAAA-CTTT
1 TAAACCCTTTTCATGTAAATCTTT
628539 TAAACCCTTTTCATGTAAATCTTT
1 TAAACCCTTTTCATGTAAATCTTT
628563 GATTTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.30, C:0.19, G:0.04, T:0.47
Consensus pattern (24 bp):
TAAACCCTTTTCATGTAAATCTTT
Found at i:628805 original size:3 final size:3
Alignment explanation
Indices: 628797--628828 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
628787 ACATTACGAT
628797 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
628829 TAATAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Done.