Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold374
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: 633698
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 28962 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:259376 original size:19 final size:19
Alignment explanation
Indices: 259352--259388 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
259342 GTAAATATTT
*
259352 TTATCATTTTGACTTTTAA
1 TTATCATTTTAACTTTTAA
259371 TTATCATTTTAACTTTTA
1 TTATCATTTTAACTTTTA
259389 TCATTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.11, G:0.03, T:0.59
Consensus pattern (19 bp):
TTATCATTTTAACTTTTAA
Found at i:259647 original size:45 final size:43
Alignment explanation
Indices: 259586--259795 Score: 224
Period size: 43 Copynumber: 4.8 Consensus size: 43
259576 ACGTTTTTTA
* ** *
259586 AAAAAGCGCCACTAAAGGTCATTGTCATTAGCGGCGTTTGTGG
1 AAAAAGCGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGTGG
* *
259629 AAAAAAAGCGCCGCTAAAGGTCAGGGTCTTTAACGGCGCTTGTGG
1 --AAAAAGCGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGTGG
* ** * *
259674 AAATAGCGTTGTTAAAGGTCAGGGTCTTTAGCGGCGATTGTAGG
1 AAAAAGCGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGT-GG
* * *
259718 -AAAAGCGCCGCTAAAGATCAGGGTCTTTAGCAGCGTTTGTCG
1 AAAAAGCGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGTGG
* * * *
259760 AACAAGCGCCACTAAAGGTCATGGTCTTTAGTGGCG
1 AAAAAGCGCCGCTAAAGGTCAGGGTCTTTAGCGGCG
259796 CAATCCCAAA
Statistics
Matches: 137, Mismatches: 26, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
42 1 0.01
43 97 0.71
44 2 0.01
45 37 0.27
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (43 bp):
AAAAAGCGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGTGG
Found at i:270742 original size:17 final size:18
Alignment explanation
Indices: 270709--270747 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
270699 TTTTTAACTT
270709 TTTTTTAATATTCTTTAA
1 TTTTTTAATATTCTTTAA
270727 TTTTTTAGA-ATT-TTTAA
1 TTTTTTA-ATATTCTTTAA
270744 TTTT
1 TTTT
270748 AAAAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 10 0.50
19 1 0.05
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTTTAATATTCTTTAA
Found at i:270809 original size:19 final size:19
Alignment explanation
Indices: 270753--270816 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 19
270743 ATTTTAAAAA
*
270753 AATTTTAAAATATAAATTTTGG
1 AATTTTAAAA-AT-TATTTT-G
*
270775 AATTTTTATAAA-TATTTTG
1 AA-TTTTAAAAATTATTTTG
*
270794 AATTTTAAAAATTATTTTA
1 AATTTTAAAAATTATTTTG
270813 AATT
1 AATT
270817 ATTTTGTAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
18 8 0.22
19 13 0.36
20 5 0.14
22 3 0.08
23 7 0.19
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (19 bp):
AATTTTAAAAATTATTTTG
Found at i:270916 original size:18 final size:18
Alignment explanation
Indices: 270893--270931 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
270883 ATACTAATTC
*
270893 ATTATTTGAGTTATTCAA
1 ATTATTTGACTTATTCAA
*
270911 ATTATTTGACTTATTCTA
1 ATTATTTGACTTATTCAA
270929 ATT
1 ATT
270932 GTAAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (18 bp):
ATTATTTGACTTATTCAA
Found at i:273938 original size:40 final size:40
Alignment explanation
Indices: 273863--274181 Score: 347
Period size: 40 Copynumber: 8.0 Consensus size: 40
273853 TATTATATAT
* * *
273863 TGAAATGTATGCGCTTTCAAGCCTTACCTACTGAATCTAC
1 TGAAATGTATGCGCTTTCGAGCCATACCTATTGAATCTAC
* * *
273903 TGAAATGTATGTGTTTTCGAGCCATACATATTGAATCTAC
1 TGAAATGTATGCGCTTTCGAGCCATACCTATTGAATCTAC
* * * *
273943 TAAAATGTATGTGCTTTCGAGCCATACCTAATAAATCTAC
1 TGAAATGTATGCGCTTTCGAGCCATACCTATTGAATCTAC
* * *
273983 AGAAATGTACGCGCTTTTGAGCCATACCTATTGAATCTAC
1 TGAAATGTATGCGCTTTCGAGCCATACCTATTGAATCTAC
* * * *
274023 TGAAATGTATACGCTTTCTAGCCATACCTACTGAATCCA-
1 TGAAATGTATGCGCTTTCGAGCCATACCTATTGAATCTAC
* * * *
274062 TCGAAATATATGCACTTTCGAGCCATACGTATTAAATCTAC
1 T-GAAATGTATGCGCTTTCGAGCCATACCTATTGAATCTAC
* * * *
274103 CGAAATGTATGCGCTTTTGAGCCATACCTATCGATTCTAC
1 TGAAATGTATGCGCTTTCGAGCCATACCTATTGAATCTAC
* * *
274143 TGAAA-GTATGCCCTATT-GAGCCATACCTACTGATTCTAC
1 TGAAATGTATGCGCT-TTCGAGCCATACCTATTGAATCTAC
274182 AAAAAGCTGC
Statistics
Matches: 231, Mismatches: 45, Indels: 7
0.82 0.16 0.02
Matches are distributed among these distances:
39 29 0.13
40 202 0.87
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (40 bp):
TGAAATGTATGCGCTTTCGAGCCATACCTATTGAATCTAC
Found at i:274080 original size:120 final size:120
Alignment explanation
Indices: 273864--274175 Score: 387
Period size: 120 Copynumber: 2.6 Consensus size: 120
273854 ATTATATATT
** * * * *
273864 GAAATGTATGCGCTTTCAAGCCTTACCTACTGAATCTACTGAAATGTATGTGTTTTCGAGCCATA
1 GAAATGTATGCGCTTTTGAGCCATACCTATTGAATCTACTGAAATGTATGCGCTTTCGAGCCATA
* * * * **
273929 CATATTGAATCTACTAAAATGTATGTGCTTTCGAGCCATACCTAATAAATCTACA
66 CCTACTGAATCCACTAAAATATATGCACTTTCGAGCCATACCTAATAAATCTACA
* * *
273984 GAAATGTACGCGCTTTTGAGCCATACCTATTGAATCTACTGAAATGTATACGCTTTCTAGCCATA
1 GAAATGTATGCGCTTTTGAGCCATACCTATTGAATCTACTGAAATGTATGCGCTTTCGAGCCATA
* * * *
274049 CCTACTGAATCCA-TCGAAATATATGCACTTTCGAGCCATACGTATTAAATCTACC
66 CCTACTGAATCCACT-AAAATATATGCACTTTCGAGCCATACCTAATAAATCTACA
* * *
274104 GAAATGTATGCGCTTTTGAGCCATACCTATCGATTCTACTGAAA-GTATGCCCTATT-GAGCCAT
1 GAAATGTATGCGCTTTTGAGCCATACCTATTGAATCTACTGAAATGTATGCGCT-TTCGAGCCAT
274167 ACCTACTGA
65 ACCTACTGA
274176 TTCTACAAAA
Statistics
Matches: 165, Mismatches: 25, Indels: 5
0.85 0.13 0.03
Matches are distributed among these distances:
119 23 0.14
120 142 0.86
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.32
Consensus pattern (120 bp):
GAAATGTATGCGCTTTTGAGCCATACCTATTGAATCTACTGAAATGTATGCGCTTTCGAGCCATA
CCTACTGAATCCACTAAAATATATGCACTTTCGAGCCATACCTAATAAATCTACA
Found at i:283192 original size:27 final size:27
Alignment explanation
Indices: 283154--283240 Score: 111
Period size: 27 Copynumber: 3.2 Consensus size: 27
283144 GAAAGTGTGG
*
283154 TCGCCAATCTGTTTGGCAAGCTGGGGT
1 TCGCCAATCTGTTTGGCGAGCTGGGGT
* *
283181 TCGCCAATCTGTTCGACGAGCTGGGGT
1 TCGCCAATCTGTTTGGCGAGCTGGGGT
* * * *
283208 TCGCTAGTGTGTTTAGCGAGCTGGGGT
1 TCGCCAATCTGTTTGGCGAGCTGGGGT
283235 TCGCCA
1 TCGCCA
283241 GTTGAGTTGT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (27 bp):
TCGCCAATCTGTTTGGCGAGCTGGGGT
Found at i:283265 original size:25 final size:25
Alignment explanation
Indices: 283231--283283 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
283221 TAGCGAGCTG
*
283231 GGGTTCGCCAGTTGAGTTGTGAACT
1 GGGTTCGCCAGTTGAGTTGCGAACT
*
283256 GGGTTTGCCAGTTGAGTTGCGAACT
1 GGGTTCGCCAGTTGAGTTGCGAACT
283281 GGG
1 GGG
283284 GGTTCGCATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.15, C:0.15, G:0.40, T:0.30
Consensus pattern (25 bp):
GGGTTCGCCAGTTGAGTTGCGAACT
Found at i:283421 original size:19 final size:18
Alignment explanation
Indices: 283379--283421 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
283369 TTCTAAACTG
283379 ACTAGGGTTCCTAAGTCT
1 ACTAGGGTTCCTAAGTCT
*
283397 AGTAGGGTATCCTAAGATC-
1 ACTAGGGT-TCCTAAG-TCT
283416 ACTAGG
1 ACTAGG
283422 TCACTTAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 7 0.33
19 12 0.57
20 2 0.10
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (18 bp):
ACTAGGGTTCCTAAGTCT
Found at i:284199 original size:18 final size:18
Alignment explanation
Indices: 284170--284213 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
284160 TATTTTTTGT
*
284170 AACCCTTGTATG-ATTGCG
1 AACCCTTATATGCA-TGCG
*
284188 ACCCCTTATATGCATGCG
1 AACCCTTATATGCATGCG
284206 AACCCTTA
1 AACCCTTA
284214 GGAGCGATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.30
Consensus pattern (18 bp):
AACCCTTATATGCATGCG
Found at i:284474 original size:68 final size:68
Alignment explanation
Indices: 284379--284591 Score: 282
Period size: 68 Copynumber: 3.1 Consensus size: 68
284369 ATTCATGTTT
* * * * *
284379 TTGTGTGAATTCATGCTTATTGTTGTTATGCGAACTCATGTGTTACTTCGATATGCGAACTTATG
1 TTGTGTGAATTCATGCTTATTGTTGTTATGAGAACTCATGTGTAACTTAGATATGCGAACCTACG
284444 TTG
66 TTG
** ** * *
284447 TTGTGCAAATTCATGCTTATTACTGTTATGTGAACTCATGTGTGACTTAGATATGCGAACCTACG
1 TTGTGTGAATTCATGCTTATTGTTGTTATGAGAACTCATGTGTAACTTAGATATGCGAACCTACG
284512 TTG
66 TTG
* * * * *
284515 TTGTGTGAATTCATGTTTATTGTTGTTATGAAAAATAATGTGAAACTTAGATATGCGAACCTACG
1 TTGTGTGAATTCATGCTTATTGTTGTTATGAGAACTCATGTGTAACTTAGATATGCGAACCTACG
284580 TTG
66 TTG
284583 TTGTGTGAA
1 TTGTGTGAA
284592 CCTTAATAAT
Statistics
Matches: 125, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 125 1.00
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (68 bp):
TTGTGTGAATTCATGCTTATTGTTGTTATGAGAACTCATGTGTAACTTAGATATGCGAACCTACG
TTG
Found at i:286238 original size:37 final size:37
Alignment explanation
Indices: 286168--286301 Score: 173
Period size: 37 Copynumber: 3.6 Consensus size: 37
286158 AGTACCAAGA
* **
286168 AATCCAACCGA-AACACGCC-GATCGCTTGTAAGAGCT
1 AATCCAACCGATAACACGCCAAAT-GCTCATAAGAGCT
* * *
286204 AATCCATCCGATAAAATGCCAAATGCTCATAAGAGCT
1 AATCCAACCGATAACACGCCAAATGCTCATAAGAGCT
* *
286241 AATCCACCCGATAACACGCCAATTGCTCATAAGAGCT
1 AATCCAACCGATAACACGCCAAATGCTCATAAGAGCT
286278 AATCCAACCGATAACACGCCAAAT
1 AATCCAACCGATAACACGCCAAAT
286302 CAGGGAGTAT
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
36 10 0.12
37 72 0.86
38 2 0.02
ACGTcount: A:0.38, C:0.30, G:0.14, T:0.18
Consensus pattern (37 bp):
AATCCAACCGATAACACGCCAAATGCTCATAAGAGCT
Found at i:296209 original size:21 final size:21
Alignment explanation
Indices: 296185--296247 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
296175 CATGCTTATA
296185 ATGTTTGTGCCTCAATCGATC
1 ATGTTTGTGCCTCAATCGATC
* *
296206 ATG-TT-T---TCAAT-TATA
1 ATGTTTGTGCCTCAATCGATC
296221 ATGTTTGTGCCTCAATCGATC
1 ATGTTTGTGCCTCAATCGATC
296242 ATGTTT
1 ATGTTT
296248 TCAATTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
15 5 0.16
16 7 0.22
17 1 0.03
19 1 0.03
20 7 0.22
21 11 0.34
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.44
Consensus pattern (21 bp):
ATGTTTGTGCCTCAATCGATC
Found at i:296227 original size:36 final size:36
Alignment explanation
Indices: 296180--296254 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
296170 TGATTCATGC
296180 TTATAATGTTTGTGCCTCAATCGATCATGTTTTCAA
1 TTATAATGTTTGTGCCTCAATCGATCATGTTTTCAA
296216 TTATAATGTTTGTGCCTCAATCGATCATGTTTTCAA
1 TTATAATGTTTGTGCCTCAATCGATCATGTTTTCAA
296252 TTA
1 TTA
296255 AAATCAAGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.45
Consensus pattern (36 bp):
TTATAATGTTTGTGCCTCAATCGATCATGTTTTCAA
Found at i:297161 original size:45 final size:45
Alignment explanation
Indices: 297068--297172 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 45
297058 CCTAAACAGT
* * * * *
297068 AATCAGTAATAGTAACAGTAACAGTATTCAACATAGACAGTGCTG
1 AATCGGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTG
* * * *
297113 AATCTGTACCAGTAACAGTAATAGTATTTAACACACAAAGTG-TCG
1 AATCGGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCT-G
297158 AATCGGTAACAGTAA
1 AATCGGTAACAGTAA
297173 TAGTTGTCGG
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
44 1 0.02
45 48 0.98
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (45 bp):
AATCGGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTG
Found at i:297475 original size:40 final size:40
Alignment explanation
Indices: 297377--297484 Score: 121
Period size: 40 Copynumber: 2.7 Consensus size: 40
297367 AATTCATTAC
* * * * *
297377 TTCAATAATTTCACAGTTCAATGCAGTACACATAACAATA
1 TTCAGTAACTTCACAATTCAATTCAGTACACAAAACAATA
*
297417 TTCAGTAACTTCACAATTCAATTCAGTACTCAAAAACAATA
1 TTCAGTAACTTCACAATTCAATTCAGTACAC-AAAACAATA
*
297458 TTCAGT-A-TTCCATAATTCAATTCAGTA
1 TTCAGTAACTT-CACAATTCAATTCAGTA
297485 TCAGTCTCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 2 0.03
40 43 0.73
41 14 0.24
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.32
Consensus pattern (40 bp):
TTCAGTAACTTCACAATTCAATTCAGTACACAAAACAATA
Found at i:298198 original size:16 final size:16
Alignment explanation
Indices: 298165--298222 Score: 71
Period size: 17 Copynumber: 3.5 Consensus size: 16
298155 AAACCCTAAT
* *
298165 TTTCCCTTTCTTCTTTC
1 TTTCCTTTTTTTC-TTC
298182 TTTCCTTTTTTTCTTC
1 TTTCCTTTTTTTCTTC
298198 TTTCCTTTTTTTTCTTC
1 TTTCC-TTTTTTTCTTC
*
298215 TCTCCTTT
1 TTTCCTTT
298223 CTCTGTTTCG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.30
17 26 0.70
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTCCTTTTTTTCTTC
Found at i:298588 original size:25 final size:23
Alignment explanation
Indices: 298544--298604 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
298534 ATTTTGATTT
*
298544 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
298568 ATTTAATTATCATAA-ATTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
*
298592 ATATAAATTATAT
1 AT-TTAATTATAT
298605 TTAAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Found at i:298607 original size:35 final size:35
Alignment explanation
Indices: 298552--298631 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
298542 TTATTTAATA
* *
298552 ATATAATAT-CATTATAATTTAATTATCATAAATT
1 ATATAATATAAATTATAATTTAAATATCATAAATT
*
298586 CATATAATATAAATTAT-ATTTAAATATCATTAATT
1 -ATATAATATAAATTATAATTTAAATATCATAAATT
298621 ATATAAT-TAAA
1 ATATAATATAAA
298632 ACAAATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
33 4 0.10
34 7 0.17
35 25 0.61
36 5 0.12
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (35 bp):
ATATAATATAAATTATAATTTAAATATCATAAATT
Found at i:304684 original size:39 final size:39
Alignment explanation
Indices: 304639--304735 Score: 104
Period size: 45 Copynumber: 2.3 Consensus size: 39
304629 AAGTAACAGC
* * *
304639 AACAGTAATAGTATTCAACACACAAAGTGTTGAATCTGT
1 AACAGTAATAGTATTCAACACACAAAGTGTAGAACCGGT
*
304678 AACAGTAATGGTAACATTATTCAACACACAAAGTGTAGAACCGGT
1 AACAGTAA---T---AGTATTCAACACACAAAGTGTAGAACCGGT
304723 AACAGTAATAGTA
1 AACAGTAATAGTA
304736 GCCAGCATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
39 11 0.23
42 2 0.04
45 34 0.72
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.25
Consensus pattern (39 bp):
AACAGTAATAGTATTCAACACACAAAGTGTAGAACCGGT
Found at i:305350 original size:25 final size:23
Alignment explanation
Indices: 305306--305366 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
305296 ATTTTGATTT
*
305306 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
305330 ATTTAATTATCATAA-ATTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
*
305354 ATATAAATTATAT
1 AT-TTAATTATAT
305367 TTAAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Found at i:305369 original size:35 final size:35
Alignment explanation
Indices: 305314--305393 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
305304 TTATTTAATA
* *
305314 ATATAATAT-CATTATAATTTAATTATCATAAATT
1 ATATAATATAAATTATAATTTAAATATCATAAATT
*
305348 CATATAATATAAATTAT-ATTTAAATATCATTAATT
1 -ATATAATATAAATTATAATTTAAATATCATAAATT
305383 ATATAAT-TAAA
1 ATATAATATAAA
305394 ACAAATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
33 4 0.10
34 7 0.17
35 25 0.61
36 5 0.12
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (35 bp):
ATATAATATAAATTATAATTTAAATATCATAAATT
Found at i:305635 original size:145 final size:147
Alignment explanation
Indices: 305469--305750 Score: 460
Period size: 145 Copynumber: 1.9 Consensus size: 147
305459 ATTTTAGTCC
305469 TTTTTACTTTCTTTTAATCTATAATTAGACTTTCACTCTTTATTCAATTTGATCATTTTTCCTAA
1 TTTTTACTTTCTTTTAATCTATAATTAGACTTTCACTCTTTATTCAATTTGATCATTTTTCCTAA
* *
305534 TTACTTTAAATTAAACTAACTTCAC-AAAAAAA-AATTAAACACACTATCAGACTCATAATTTTA
66 TTACTTTAAATTAAAATAAATTCACAAAAAAAATAATTAAACACACTATCAGACTCATAATTTTA
305597 AATTGCCATTTGAGCCA
131 AATTGCCATTTGAGCCA
*
305614 TTTTTACTTTCTTTTAATCTATAATTAGACTTTCACTCTTTATTCAATTTGATCCTTTTTCCTAA
1 TTTTTACTTTCTTTTAATCTATAATTAGACTTTCACTCTTTATTCAATTTGATCATTTTTCCTAA
305679 TTACTTTAAATTAAAATAAATTCACTAAATAAAAAAATCTAATTAAACACACTATCAGACTCATA
66 TTACTTTAAATTAAAATAAATTCAC---A-AAAAAAA--TAATTAAACACACTATCAGACTCATA
*
305744 TTTTTAA
125 ATTTTAA
305751 TTACTCCTAA
Statistics
Matches: 125, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
145 87 0.70
150 7 0.06
153 31 0.25
ACGTcount: A:0.37, C:0.17, G:0.03, T:0.43
Consensus pattern (147 bp):
TTTTTACTTTCTTTTAATCTATAATTAGACTTTCACTCTTTATTCAATTTGATCATTTTTCCTAA
TTACTTTAAATTAAAATAAATTCACAAAAAAAATAATTAAACACACTATCAGACTCATAATTTTA
AATTGCCATTTGAGCCA
Found at i:312877 original size:17 final size:16
Alignment explanation
Indices: 312852--312887 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
312842 CATAATTTAA
312852 TTCACTTTAATTCAATT
1 TTCACTTTAATTC-ATT
*
312869 TTCATTTTAATTCATT
1 TTCACTTTAATTCATT
312885 TTC
1 TTC
312888 CAATCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.25, C:0.17, G:0.00, T:0.58
Consensus pattern (16 bp):
TTCACTTTAATTCATT
Found at i:317415 original size:14 final size:14
Alignment explanation
Indices: 317396--317423 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
317386 TAAAGTTATA
317396 TTAAATAATTCATT
1 TTAAATAATTCATT
317410 TTAAATAATTCATT
1 TTAAATAATTCATT
317424 AATAAATTGG
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:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAAATAATTCATT
Found at i:318640 original size:21 final size:22
Alignment explanation
Indices: 318611--318651 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
318601 AGTTTATTTA
318611 TGTTATAATTGTTAC-AAAATTG
1 TGTTATAATT-TTACTAAAATTG
318633 TGTT-TAATTTTACTAAAAT
1 TGTTATAATTTTACTAAAAT
318652 GTATTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.49
Consensus pattern (22 bp):
TGTTATAATTTTACTAAAATTG
Found at i:328445 original size:52 final size:50
Alignment explanation
Indices: 328330--328447 Score: 157
Period size: 50 Copynumber: 2.3 Consensus size: 50
328320 TAATAAAGTT
*
328330 ATGCATTATGTAACTTCCATGCTAGTTAAGTATGCATCATAAATAATGAC
1 ATGCATTATGTAACTCCCATGCTAGTTAAGTATGCATCATAAATAATGAC
* *
328380 ATGCATTATGTAACTCCCATGCTAGTTTAAGTCTGCATCATTAAATTAA-GTC
1 ATGCATTATGTAACTCCCATGCTAG-TTAAGTATGCATCA-TAAA-TAATGAC
* *
328432 TTGCATTAAGTAACTC
1 ATGCATTATGTAACTC
328448 ATTTGTTCAT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
50 24 0.40
51 13 0.22
52 20 0.33
53 3 0.05
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.36
Consensus pattern (50 bp):
ATGCATTATGTAACTCCCATGCTAGTTAAGTATGCATCATAAATAATGAC
Found at i:330811 original size:12 final size:12
Alignment explanation
Indices: 330791--330834 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
330781 AGTTTTAATA
*
330791 AAATCGAAAAAG
1 AAATAGAAAAAG
330803 AAATAGAAAAAG
1 AAATAGAAAAAG
**
330815 AAAGGGAAAAAG
1 AAATAGAAAAAG
330827 AAA-AGAAA
1 AAATAGAAA
330835 TCAAAAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 4 0.14
12 24 0.86
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (12 bp):
AAATAGAAAAAG
Found at i:334247 original size:20 final size:19
Alignment explanation
Indices: 334222--334284 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
334212 CTTGTATAGA
334222 TTTGCACTTTGGTGCCTCTG
1 TTTGCACTTT-GTGCCTCTG
*
334242 TTTGCACTTCAGTGCCTCTG
1 TTTGCACTT-TGTGCCTCTG
* *
334262 ATCGCACATTTGTGCCTCTG
1 TTTGCAC-TTTGTGCCTCTG
334282 TTT
1 TTT
334285 CGCATATATG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 33 0.94
21 2 0.06
ACGTcount: A:0.10, C:0.27, G:0.21, T:0.43
Consensus pattern (19 bp):
TTTGCACTTTGTGCCTCTG
Found at i:341101 original size:25 final size:25
Alignment explanation
Indices: 341062--341143 Score: 110
Period size: 25 Copynumber: 3.3 Consensus size: 25
341052 GAGATTCATG
341062 AACTCACGCCTACAAGCATCAACAT
1 AACTCACGCCTACAAGCATCAACAT
* * *
341087 AGCTCACGCCCACAAGAATCAACAT
1 AACTCACGCCTACAAGCATCAACAT
* * *
341112 AACGCACACCTACGAGCATCAACAT
1 AACTCACGCCTACAAGCATCAACAT
341137 AACTCAC
1 AACTCAC
341144 ACCTTAGAAG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.40, C:0.37, G:0.10, T:0.13
Consensus pattern (25 bp):
AACTCACGCCTACAAGCATCAACAT
Found at i:359034 original size:12 final size:13
Alignment explanation
Indices: 359013--359045 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
359003 AATGGACATG
359013 TAAATAAAT-AAA
1 TAAATAAATAAAA
*
359025 TAAATGAATAAAA
1 TAAATAAATAAAA
359038 TAAATAAA
1 TAAATAAA
359046 AGATACACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:360168 original size:16 final size:17
Alignment explanation
Indices: 360147--360181 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
360137 TCTTATGCAG
360147 AAGATAAAATAAAA-AA
1 AAGATAAAATAAAATAA
360163 AAGATAAAATAAAATAA
1 AAGATAAAATAAAATAA
360180 AA
1 AA
360182 CAAGCAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (17 bp):
AAGATAAAATAAAATAA
Found at i:361167 original size:40 final size:41
Alignment explanation
Indices: 361067--361776 Score: 246
Period size: 44 Copynumber: 16.7 Consensus size: 41
361057 CTTCTGTCTA
* * * *
361067 CTCCACTACTGCTTAGGGAGATAGGA-TTGGTTTC-TTCTG
1 CTCCACTACTGCTTAGGGAGATAAGACTTGATTGCAATCTG
* * *
361106 TCTGGTCCACTACTACCTAGGGAGATAAGACTTGA-TGCGATCTG
1 -C---TCCACTACTGCTTAGGGAGATAAGACTTGATTGCAATCTG
* * ** * * *
361150 CTCCACTATTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAA-GACT-TGAT-TGCAATCTG
* * * * * ***
361194 TTCCACTGCTGCTCAAGGAGATAGGA-TTGATT-TTGTCTG
1 CTCCACTACTGCTTAGGGAGATAAGACTTGATTGCAATCTG
*
361233 CTCCACTACTACTTAGGGAGATAAGACTTGA-TGCAATCTG
1 CTCCACTACTGCTTAGGGAGATAAGACTTGATTGCAATCTG
* * * *
361273 CTCTACTACTGCTTAGGGAGATAAGA-TTGGTTTCTTCTATCTG
1 CTCCACTACTGCTTAGGGAGATAAGACTT-G-AT-TGCAATCTG
* * ** * * *
361316 CTTCACTACTGCTTAGGAAGATAAGATCTACAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGA-CT-TGAT-TGCAATCTG
* * * * *
361360 CTCCACTACTGCTCAAGGAGATAGGACTGGTGGCTT-AAATCTG
1 CTCCACTACTGCTTAGGGAGATAAGACT--T-GATTGCAATCTG
* * * * *
361403 CTTCACTACTGCTTAGGAAGATAAGA-TTCACCGTCTTCGATCTG
1 CTCCACTACTGCTTAGGGAGATAAGACTTGA---T-TGCAATCTG
* *** *
361447 CTCCGCTACTGCTTAGGGAGATAAGATCTACT-ATCTTTGACCTG
1 CTCCACTACTGCTTAGGGAGATAAGA-CT--TGAT-TGCAATCTG
* ** * *
361491 CTCCACTACTGCTTAGGGAGATAGGACTACCATCTTCGA-CTTG
1 CTCCACTACTGCTTAGGGAGATAAGACT-TGAT-TGCAATC-TG
* * *
361534 CTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTT-AAATCTG
1 CTCCACTACTGCTTAGGGAGATAAGACT--T-GATTGCAATCTG
* * * * * *
361577 TTTCACTACTGCTTAGGAAGATAAGA-TTCGCCGTCTTCGATCTG
1 CTCCACTACTGCTTAGGGAGATAAGACTT-G--AT-TGCAATCTG
* * ** ** *
361621 CTCCACTACTGCTGAGGGAGATAAAATCTACCATCTTTAACCTG
1 CTCCACTACTGCTTAGGGAGATAAGA-CT-TGAT-TGCAATCTG
* *
361665 CTCCACTACTGCTTAGGGAGATAGGACTTGATGTG--ATCTA
1 CTCCACTACTGCTTAGGGAGATAAGACTTGAT-TGCAATCTG
* * * *
361705 CTCTACTACTGCTTAGGGAGATAAGATCTGTAATCTTTC-GTCTG
1 CTCCACTACTGCTTAGGGAGATAAGA-CT-TGA--TTGCAATCTG
361749 CTCCACTACTGCTTAGGGAGATAAGACT
1 CTCCACTACTGCTTAGGGAGATAAGACT
361777 GTAATCTTCA
Statistics
Matches: 499, Mismatches: 125, Indels: 89
0.70 0.18 0.12
Matches are distributed among these distances:
39 25 0.05
40 85 0.17
41 7 0.01
42 12 0.02
43 154 0.31
44 209 0.42
45 3 0.01
46 2 0.00
47 1 0.00
48 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (41 bp):
CTCCACTACTGCTTAGGGAGATAAGACTTGATTGCAATCTG
Found at i:361260 original size:123 final size:127
Alignment explanation
Indices: 361068--361297 Score: 351
Period size: 123 Copynumber: 1.8 Consensus size: 127
361058 TTCTGTCTAC
* * * *
361068 TCCACTACTGCTTAGGGAGATAGGATTGGTTTCTTCTGTCTGGTCCACTACTACCTAGGGAGATA
1 TCCACTACTGCTCAAGGAGATAGGATTGGTATCTTCTGTCTGCTCCACTACTACCTAGGGAGATA
* *
361133 AGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTAT
66 AGACTTGATGCAATCTGCTCCACTACTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTAT
* *
361195 TCCACTGCTGCTCAAGGAGATAGGATT-G-AT-TT-TGTCTGCTCCACTACTACTTAGGGAGATA
1 TCCACTACTGCTCAAGGAGATAGGATTGGTATCTTCTGTCTGCTCCACTACTACCTAGGGAGATA
*
361256 AGACTTGATGCAATCTGCTCTACTACTGCTTAGGGAGATAAG
66 AGACTTGATGCAATCTGCTCCACTACTGCTTAGGGAGATAAG
361298 ATTGGTTTCT
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
123 66 0.70
124 2 0.02
125 1 0.01
126 1 0.01
127 24 0.26
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (127 bp):
TCCACTACTGCTCAAGGAGATAGGATTGGTATCTTCTGTCTGCTCCACTACTACCTAGGGAGATA
AGACTTGATGCAATCTGCTCCACTACTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTAT
Found at i:361367 original size:44 final size:44
Alignment explanation
Indices: 361145--361774 Score: 393
Period size: 44 Copynumber: 14.7 Consensus size: 44
361135 ACTTGATGCG
* * *
361145 ATCTGCTCCACTATTGCTTAGGGAGATAAGGTCTACAATCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCA
* ** * * * * * *
361189 ACCTATTCCACTGCTGCTCAAGGAGATAGGAT-T--GAT-TT-T
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCA
* * ** *
361228 GTCTGCTCCACTACTACTTAGGGAGATAAGA-CT-TGA--TGCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCA
* **** *
361268 ATCTGCTCTACTACTGCTTAGGGAGATAAGAT-TGGTTTCTTCT
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCA
* * *
361311 ATCTGCTTCACTACTGCTTAGGAAGATAAGATCTACAATCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCA
* * * * * ***** *
361355 ACCTACTCCACTACTGCTCAAGGAGATAGGA-CTGGTGGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCA
* * * *
361398 ATCTGCTTCACTACTGCTTAGGAAGATAAGAT-TCACCGTCTTCG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-ACCATCTTCA
* * **
361442 ATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTACTATCTTTG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCA
* * *
361486 ACCTGCTCCACTACTGCTTAGGGAGATAGGA-CTACCATCTTCG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCA
* ***** *
361529 A-CTTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAA
1 ATC-TGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCA
* * * * * *
361572 ATCTGTTTCACTACTGCTTAGGAAGATAAGAT-TCGCCGTCTTCG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-ACCATCTTCA
* * *
361616 ATCTGCTCCACTACTGCTGAGGGAGATAAAATCTACCATCTTTA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCA
* * ** * *
361660 ACCTGCTCCACTACTGCTTAGGGAGATAGGA-CT-TGAT-GT-G
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCA
* * ***
361700 ATCTACTCTACTACTGCTTAGGGAGATAAGATCTGTAATCTTTC-
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATC-TTCA
*
361744 GTCTGCTCCACTACTGCTTAGGGAGATAAGA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGA
361775 CTGTAATCTT
Statistics
Matches: 448, Mismatches: 117, Indels: 42
0.74 0.19 0.07
Matches are distributed among these distances:
39 24 0.05
40 60 0.13
41 5 0.01
42 6 0.01
43 135 0.30
44 216 0.48
45 2 0.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (44 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCA
Found at i:361402 original size:87 final size:87
Alignment explanation
Indices: 361145--361643 Score: 390
Period size: 87 Copynumber: 5.8 Consensus size: 87
361135 ACTTGATGCG
* * * ** * * *
361145 ATCTGCTCCACTATTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTATTCCACTGCTGCTCAA
1 ATCTGCTCCACTACTGCTTAGGAAGATAAGATCTACAATCTTCAACCTGCTCCACTACTGCTTAG
* **
361210 GGAGATAGGA-T--T-GATTTT
66 GGAGATAGGACTGGTGGCTTAA
* * * ** * * *
361228 GTCTGCTCCACTACTACTTAGGGAGATAAGA-CT-TGA--TGCAATCTGCTCTACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGAAGATAAGATCTACAATCTTCAACCTGCTCCACTACTGCTTAG
* * ** **
361289 GGAGATAAGATTGGTTTCTTCT
66 GGAGATAGGACTGGTGGCTTAA
* * * *
361311 ATCTGCTTCACTACTGCTTAGGAAGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAA
1 ATCTGCTCCACTACTGCTTAGGAAGATAAGATCTACAATCTTCAACCTGCTCCACTACTGCTTAG
361376 GGAGATAGGACTGGTGGCTTAA
66 GGAGATAGGACTGGTGGCTTAA
* ** * * *
361398 ATCTGCTTCACTACTGCTTAGGAAGATAAGAT-TCACCGTCTTCGATCTGCTCCGCTACTGCTTA
1 ATCTGCTCCACTACTGCTTAGGAAGATAAGATCT-ACAATCTTCAACCTGCTCCACTACTGCTTA
* ** ** **
361462 GGGAGATAAGATCTACTATCTTTG
65 GGGAGATAGGA-CTGGTGGCTTAA
* * * * * *
361486 ACCTGCTCCACTACTGCTTAGGGAGATAGGA-CTACCATCTTCGACTTGCTCCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGAAGATAAGATCTACAATCTTCAACCTGCTCCACTACTGCTTAG
361550 GGAGATAGGACTGGTGGCTTAA
66 GGAGATAGGACTGGTGGCTTAA
* * * ** * * *
361572 ATCTGTTTCACTACTGCTTAGGAAGATAAGAT-TCGCCGTCTTCGATCTGCTCCACTACTGCTGA
1 ATCTGCTCCACTACTGCTTAGGAAGATAAGATCT-ACAATCTTCAACCTGCTCCACTACTGCTTA
361636 GGGAGATA
65 GGGAGATA
361644 AAATCTACCA
Statistics
Matches: 327, Mismatches: 76, Indels: 22
0.77 0.18 0.05
Matches are distributed among these distances:
79 26 0.08
80 1 0.00
81 1 0.00
82 3 0.01
83 57 0.17
84 2 0.01
85 1 0.00
86 34 0.10
87 168 0.51
88 34 0.10
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (87 bp):
ATCTGCTCCACTACTGCTTAGGAAGATAAGATCTACAATCTTCAACCTGCTCCACTACTGCTTAG
GGAGATAGGACTGGTGGCTTAA
Found at i:361471 original size:131 final size:130
Alignment explanation
Indices: 361267--361518 Score: 344
Period size: 131 Copynumber: 1.9 Consensus size: 130
361257 GACTTGATGC
* **** * *
361267 AATCTGCTCTACTACTGCTTAGGGAGATAAGATTGGTTTCTTCTATCTGCTTCACTACTGCTTAG
1 AATCTGCTCTACTACTGCTTAGGAAGATAAGATTACCGTCTTCGATCTGCTCCACTACTGCTTAG
361332 GAAGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAAGGAGATAGGACTGGTGGCTTA
66 GAAGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAAGGAGATAGGACTGGTGGCTTA
*
361397 AATCTGCT-TCACTACTGCTTAGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCTT
1 AATCTGCTCT-ACTACTGCTTAGGAAGATAAGATT-ACCGTCTTCGATCTGCTCCACTACTGCTT
* * ** * * *
361461 AGGGAGATAAGATCTACTATCTTTGACCTGCTCCACTACTGCTTAGGGAGATAGGACT
64 AGGAAGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAAGGAGATAGGACT
361519 ACCATCTTCG
Statistics
Matches: 105, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
129 1 0.01
130 31 0.30
131 73 0.70
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (130 bp):
AATCTGCTCTACTACTGCTTAGGAAGATAAGATTACCGTCTTCGATCTGCTCCACTACTGCTTAG
GAAGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAAGGAGATAGGACTGGTGGCTTA
Found at i:361540 original size:174 final size:173
Alignment explanation
Indices: 361147--361692 Score: 662
Period size: 174 Copynumber: 3.2 Consensus size: 173
361137 TTGATGCGAT
* * * *
361147 CTGCTCCACTATTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTATTCCACTGCTGCTCAAGG
1 CTGCTCCACTACTGCTTAGGGAGAT-AGGACTACAATCTTCAACCTACTCCACTACTGCTCAAGG
* *** * * * * * *
361212 AGATAGGA-T--T-GATTTTGTCTGCTCCACTACTACTTAGGGAGATAAGACTT----G-ATGCA
65 AGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGA-TTCACCGTCTTCG
* ** * *
361268 ATCTGCTCTACTACTGCTTAGGGAGATAAGAT-TGGTTTCTTCTAT
129 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACTATCTT-TAC
* * *
361313 CTGCTTCACTACTGCTTAGGAAGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAAGG
1 CTGCTCCACTACTGCTTAGGGAGATAGGA-CTACAATCTTCAACCTACTCCACTACTGCTCAAGG
361378 AGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCACCGTCTTCGA
65 AGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCACCGTCTTCGA
*
361443 TCTGCTCCGCTACTGCTTAGGGAGATAAGATCTACTATCTTTGAC
130 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTACTATCTTT-AC
* * * * * *
361488 CTGCTCCACTACTGCTTAGGGAGATAGGACTACCATCTTCGACTTGCTCCACTACTGCTTAGGGA
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTACAATCTTCAACCTACTCCACTACTGCTCAAGGA
* *
361553 GATAGGACTGGTGGCTTAAATCTGTTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTCGAT
66 GATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCACCGTCTTCGAT
* * *
361618 CTGCTCCACTACTGCTGAGGGAGATAAAATCTACCATCTTTAAC
131 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACTATCTTT-AC
361662 CTGCTCCACTACTGCTTAGGGAGATAGGACT
1 CTGCTCCACTACTGCTTAGGGAGATAGGACT
361693 TGATGTGATC
Statistics
Matches: 329, Mismatches: 39, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
165 2 0.01
166 63 0.19
167 1 0.00
169 3 0.01
170 30 0.09
173 1 0.00
174 196 0.60
175 33 0.10
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (173 bp):
CTGCTCCACTACTGCTTAGGGAGATAGGACTACAATCTTCAACCTACTCCACTACTGCTCAAGGA
GATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCACCGTCTTCGAT
CTGCTCCACTACTGCTTAGGGAGATAAGATCTACTATCTTTAC
Found at i:362995 original size:7 final size:7
Alignment explanation
Indices: 362985--363017 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
362975 CACTTTTACT
362985 TTTTTCA
1 TTTTTCA
362992 TTTTTCA
1 TTTTTCA
*
362999 TTTTTTA
1 TTTTTCA
363006 TTTTTCA
1 TTTTTCA
363013 TTTTT
1 TTTTT
363018 TTTCTTACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTCA
Found at i:363018 original size:14 final size:15
Alignment explanation
Indices: 362984--363018 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
362974 CCACTTTTAC
362984 TTTTTTCATTTTTCA
1 TTTTTTCATTTTTCA
362999 TTTTTT-ATTTTTCA
1 TTTTTTCATTTTTCA
363013 TTTTTT
1 TTTTTT
363019 TTCTTACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTCATTTTTCA
Found at i:364020 original size:23 final size:26
Alignment explanation
Indices: 363994--364050 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 26
363984 TTCTTTCTTC
363994 TTTTTGTTTTTTT-TTT-ATTTTGAT
1 TTTTTGTTTTTTTATTTGATTTTGAT
364018 TTTTTGATATTTTTTACTTTGATTTTGAT
1 TTTTTG-T-TTTTTTA-TTTGATTTTGAT
364047 TTTT
1 TTTT
364051 CTTTTTCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.21
25 1 0.04
26 6 0.21
28 3 0.11
29 12 0.43
ACGTcount: A:0.12, C:0.02, G:0.09, T:0.77
Consensus pattern (26 bp):
TTTTTGTTTTTTTATTTGATTTTGAT
Found at i:364055 original size:23 final size:23
Alignment explanation
Indices: 363994--364070 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
363984 TTCTTTCTTC
* *
363994 TTTTTGTTTTTTTTTTATTTTGA
1 TTTTTGATTTTTTTTTACTTTGA
*
364017 TTTTTTGA-TATTTTTTACTTTGA
1 -TTTTTGATTTTTTTTTACTTTGA
* **
364040 -TTTTGATTTTTCTTTTTCTTCCA
1 TTTTTGATTTTT-TTTTACTTTGA
364063 TTTTTGAT
1 TTTTTGAT
364071 CTGAGCCTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
21 6 0.14
22 3 0.07
23 21 0.49
24 13 0.30
ACGTcount: A:0.12, C:0.06, G:0.08, T:0.74
Consensus pattern (23 bp):
TTTTTGATTTTTTTTTACTTTGA
Found at i:369104 original size:14 final size:14
Alignment explanation
Indices: 369085--369114 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
369075 TTTCTTATGC
*
369085 AAAAGATAAAATAA
1 AAAAGATAAAAGAA
369099 AAAAGATAAAAGAA
1 AAAAGATAAAAGAA
369113 AA
1 AA
369115 GAAAACAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (14 bp):
AAAAGATAAAAGAA
Found at i:373919 original size:19 final size:19
Alignment explanation
Indices: 373892--373930 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
373882 CTCTGTTTTA
373892 CCCTCTGCCTCTTCTGTTC
1 CCCTCTGCCTCTTCTGTTC
*
373911 CCCTTTGCCTCTTCTGTTC
1 CCCTCTGCCTCTTCTGTTC
373930 C
1 C
373931 TCCCTTCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.00, C:0.46, G:0.10, T:0.44
Consensus pattern (19 bp):
CCCTCTGCCTCTTCTGTTC
Found at i:379333 original size:16 final size:16
Alignment explanation
Indices: 379312--379365 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
379302 TTGATTTGCT
*
379312 ATTACACTTCTATTCC
1 ATTACACCTCTATTCC
379328 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
* *
379344 ATTACATCTCTAATCC
1 ATTACACCTCTATTCC
*
379360 AATACA
1 ATTACA
379366 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:382619 original size:101 final size:101
Alignment explanation
Indices: 382499--382683 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 101
382489 AAAGTGATGG
*
382499 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAAT-G-ATGGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG-ATGGAAT-GGTCACATGTGTAGT
382562 ACTATGTGCAGGCTACTATGCGTACCAAATAGCTTCGA
64 ACTATGTGCAGGCTACTATGCGTACCAAATAGCTTCGA
*
382600 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGCTGGAAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGG-AATGGTCACATGTGTAGTA
382665 CTATGTGCAGGCTACTATG
65 CTATGTGCAGGCTACTATG
382684 TGAACCGGGT
Statistics
Matches: 79, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
100 1 0.01
101 42 0.53
102 34 0.43
103 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGAATGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGTACCAAATAGCTTCGA
Found at i:382630 original size:51 final size:50
Alignment explanation
Indices: 382499--382681 Score: 169
Period size: 51 Copynumber: 3.6 Consensus size: 50
382489 AAAGTGATGG
* ** * *
382499 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGATGGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATCCAAATGATCGA
* * * *
382549 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTA-CCAAATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATCCAAAT-G-ATCGA
*
382600 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGCTGGAAATG---G-
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATC--C---AAATGATCGA
*
382651 TCACATGTGTAGTACTATGTGCAGGCTACTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTA
382682 TGTGAACCGG
Statistics
Matches: 111, Mismatches: 14, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
49 4 0.04
50 34 0.31
51 65 0.59
52 2 0.02
54 1 0.01
56 1 0.01
57 4 0.04
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATCCAAATGATCGA
Found at i:388068 original size:11 final size:12
Alignment explanation
Indices: 388036--388069 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
388026 AGTATCCAAA
388036 ATCTTTACTTAT
1 ATCTTTACTTAT
388048 ATCTTTACTTAT
1 ATCTTTACTTAT
388060 ATC-TTACTTA
1 ATCTTTACTTA
388070 CTTATATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.56
Consensus pattern (12 bp):
ATCTTTACTTAT
Found at i:388072 original size:15 final size:13
Alignment explanation
Indices: 388039--388079 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 13
388029 ATCCAAAATC
388039 TTTACTTATATC-
1 TTTACTTATATCT
388051 TTTACTTATATCT
1 TTTACTTATATCT
388064 TACTTACTTATATCT
1 T--TTACTTATATCT
388079 T
1 T
388080 GTTAGAATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.46
13 1 0.04
15 13 0.50
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTACTTATATCT
Found at i:390079 original size:27 final size:27
Alignment explanation
Indices: 390017--390081 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
390007 TTCTCTCAAT
* * * *
390017 GTTCACCATACGCACTATTTCTTTAGA
1 GTTCACCATATGCAATATTCCTTCAGA
** *
390044 GTTTTCCATATGTAATATTCCTTCAGA
1 GTTCACCATATGCAATATTCCTTCAGA
390071 GTTCACCATAT
1 GTTCACCATAT
390082 CTATCATTCT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (27 bp):
GTTCACCATATGCAATATTCCTTCAGA
Found at i:390197 original size:28 final size:27
Alignment explanation
Indices: 390165--390218 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
390155 AATGCACCAA
*
390165 AAAAGCGTT-CATTTCCATAGATTGCCAT
1 AAAAGC-TTCCATTT-CAAAGATTGCCAT
390193 AAAAGCTTCCATTTCAAAGATTGCCA
1 AAAAGCTTCCATTTCAAAGATTGCCA
390219 CAAAGAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (27 bp):
AAAAGCTTCCATTTCAAAGATTGCCAT
Found at i:396498 original size:14 final size:14
Alignment explanation
Indices: 396481--396527 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
396471 GTTCAGACTC
396481 AAAAAAAATAACAAA
1 AAAAAAAATAAC-AA
*
396496 AAAACAAAAAAACAA
1 AAAA-AAAATAACAA
396511 AAACAAAAATAA-AA
1 AAA-AAAAATAACAA
396525 AAA
1 AAA
396528 TCGAAGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 5 0.18
15 15 0.54
16 8 0.29
ACGTcount: A:0.87, C:0.09, G:0.00, T:0.04
Consensus pattern (14 bp):
AAAAAAAATAACAA
Found at i:396501 original size:8 final size:8
Alignment explanation
Indices: 396484--396513 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
396474 CAGACTCAAA
396484 AAAAATAAC
1 AAAAA-AAC
396493 AAAAAAAC
1 AAAAAAAC
396501 AAAAAAAC
1 AAAAAAAC
396509 AAAAA
1 AAAAA
396514 CAAAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.87, C:0.10, G:0.00, T:0.03
Consensus pattern (8 bp):
AAAAAAAC
Found at i:396557 original size:24 final size:23
Alignment explanation
Indices: 396495--396573 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 23
396485 AAAATAACAA
* *
396495 AAAAACAAAAAAAC--A-AAAAC
1 AAAAAGAAAAAAACGAAGAAAAG
*
396515 AAAAATAAAAAAATCGAAGTCAAAA-
1 AAAAAGAAAAAAA-CGAAG--AAAAG
396540 AAAAGAGAAAAAAA-GAAGAAAAG
1 AAAA-AGAAAAAAACGAAGAAAAG
396563 AAAAAGAAAAA
1 AAAAAGAAAAA
396574 GGAGAGGTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
20 12 0.24
21 1 0.02
22 11 0.22
23 5 0.10
24 4 0.08
25 4 0.08
26 12 0.24
ACGTcount: A:0.80, C:0.06, G:0.10, T:0.04
Consensus pattern (23 bp):
AAAAAGAAAAAAACGAAGAAAAG
Found at i:407429 original size:30 final size:30
Alignment explanation
Indices: 407393--407456 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
407383 TATGAGGACG
407393 TTCAGGAACTTAAGAAGAC-CAAATATCTCA
1 TTCAGGAACTTAAGAAGACTC-AATATCTCA
* ** *
407423 TTCAGGAGCTTGGGAGGACTCAATATCTCA
1 TTCAGGAACTTAAGAAGACTCAATATCTCA
407453 TTCA
1 TTCA
407457 AGATCTTAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (30 bp):
TTCAGGAACTTAAGAAGACTCAATATCTCA
Found at i:407569 original size:36 final size:35
Alignment explanation
Indices: 407405--407567 Score: 93
Period size: 30 Copynumber: 4.9 Consensus size: 35
407395 CAGGAACTTA
* *
407405 AGAAGACCAAATATCTCATTCAGGAGCTTGG---G
1 AGAAGACCTAATATCTCATTCAGGATCTTGGATTG
*
407437 AG--GA-CTCAATATCTCATTCAAGATCTTAGGATTG
1 AGAAGACCT-AATATCTCATTCAGGATCTT-GGATTG
* * *
407471 AGAAGACATGATATCTCATTTAGGA-----GATTCG
1 AGAAGACCTAATATCTCATTCAGGATCTTGGATT-G
* * *
407502 A-AAGA-CTCGATATCGCATTCAAGAGT-TTGGGATTG
1 AGAAGACCT-AATATCTCATTCAGGA-TCTT-GGATTG
407537 AGAAGACCTAATATCTCATTCAGGATCTTGG
1 AGAAGACCTAATATCTCATTCAGGATCTTGG
407568 GAAGATACGA
Statistics
Matches: 98, Mismatches: 14, Indels: 35
0.67 0.10 0.24
Matches are distributed among these distances:
29 2 0.02
30 41 0.42
31 4 0.04
32 2 0.02
34 3 0.03
35 5 0.05
36 38 0.39
37 3 0.03
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (35 bp):
AGAAGACCTAATATCTCATTCAGGATCTTGGATTG
Found at i:407579 original size:66 final size:66
Alignment explanation
Indices: 407405--407580 Score: 212
Period size: 66 Copynumber: 2.7 Consensus size: 66
407395 CAGGAACTTA
* * * *
407405 AGAAGACCAAATATCTCATTCAGGAGCTTGGGAGGACTCAATATCTCATTCAAGATCTTAGGATT
1 AGAAGACCTAATATCTCATTCAGGAGCTTGGGAAGACTCGATATCGCATTCAAGATCTTAGGATT
407470 G
66 G
* * * * * * *
407471 AGAAGACATGATATCTCATTTAGGAGATTCGAAAGACTCGATATCGCATTCAAGAGT-TTGGGAT
1 AGAAGACCTAATATCTCATTCAGGAGCTTGGGAAGACTCGATATCGCATTCAAGA-TCTTAGGAT
407535 TG
65 TG
*
407537 AGAAGACCTAATATCTCATTCAGGATCTTGGGAAGA-TACGATAT
1 AGAAGACCTAATATCTCATTCAGGAGCTTGGGAAGACT-CGATAT
407581 TTATTCTTTT
Statistics
Matches: 90, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
65 1 0.01
66 88 0.98
67 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (66 bp):
AGAAGACCTAATATCTCATTCAGGAGCTTGGGAAGACTCGATATCGCATTCAAGATCTTAGGATT
G
Found at i:409250 original size:133 final size:133
Alignment explanation
Indices: 409064--409330 Score: 525
Period size: 133 Copynumber: 2.0 Consensus size: 133
409054 TTATATTATG
*
409064 TATATTAATTAATTTTTAAAAAGGATTACAAAATAAAAATATTTTAAAACGTATACTCATGCCCA
1 TATATTAATTAATTTTAAAAAAGGATTACAAAATAAAAATATTTTAAAACGTATACTCATGCCCA
409129 CGTGATACCGAAAACTAATTATCCCAACTATAATACCACTAATGGAAATAATAAAATGAAATGGA
66 CGTGATACCGAAAACTAATTATCCCAACTATAATACCACTAATGGAAATAATAAAATGAAATGGA
409194 TTT
131 TTT
409197 TATATTAATTAATTTTAAAAAAGGATTACAAAATAAAAATATTTTAAAACGTATACTCATGCCCA
1 TATATTAATTAATTTTAAAAAAGGATTACAAAATAAAAATATTTTAAAACGTATACTCATGCCCA
409262 CGTGATACCGAAAACTAATTATCCCAACTATAATACCACTAATGGAAATAATAAAATGAAATGGA
66 CGTGATACCGAAAACTAATTATCCCAACTATAATACCACTAATGGAAATAATAAAATGAAATGGA
409327 TTT
131 TTT
409330 T
1 T
409331 GATTTAGCCC
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 133 1.00
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.31
Consensus pattern (133 bp):
TATATTAATTAATTTTAAAAAAGGATTACAAAATAAAAATATTTTAAAACGTATACTCATGCCCA
CGTGATACCGAAAACTAATTATCCCAACTATAATACCACTAATGGAAATAATAAAATGAAATGGA
TTT
Found at i:437398 original size:27 final size:27
Alignment explanation
Indices: 437358--437454 Score: 158
Period size: 27 Copynumber: 3.6 Consensus size: 27
437348 AGGTCAATAT
*
437358 ATGATTGAAATACCCCTATAGGGTAAA
1 ATGATCGAAATACCCCTATAGGGTAAA
* *
437385 ATGATCGAAGTACCCCTGTAGGGTAAA
1 ATGATCGAAATACCCCTATAGGGTAAA
437412 ATGATCGAAATACCCCTATAGGGTAAA
1 ATGATCGAAATACCCCTATAGGGTAAA
*
437439 ATGACCGAAATACCCC
1 ATGATCGAAATACCCC
437455 CATATACCCT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (27 bp):
ATGATCGAAATACCCCTATAGGGTAAA
Found at i:437440 original size:54 final size:55
Alignment explanation
Indices: 437358--437695 Score: 355
Period size: 54 Copynumber: 6.1 Consensus size: 55
437348 AGGTCAATAT
* * * * *
437358 ATGATTGAAATACCCCTATAGGGTAAAATGATCGAAGTACCCCT-GTAGGGTAAA
1 ATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTCATAGGGTAAA
*
437412 ATGATCGAAATACCCCTATAGGGTAAAATGACCGAAATACCCCCATATACCCTCATAGGGTAAA
1 ATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATA----C-----CCCTCATAGGGTAAA
* * * **
437476 ATGACCAAAATACCCCCCATAGGATAAAATGATTGAAATA-CCCTCATAGGGTAAA
1 ATGATCGAAATA-CCCCCATAGGGTAAAATGACCGAAATACCCCTCATAGGGTAAA
* * **
437531 ATGATCGAAATA-CCACAGAGGGTAAAATGACTAAAATA-CCCTCATAGGGTAAA
1 ATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTCATAGGGTAAA
437584 ATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCC-CATAGGGTAAA
1 ATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTCATAGGGTAAA
* * ** * *
437638 ATTATCGAAATACCCCCATAGAGTAGTATGACCAAAATACCAC-CATAGGGTAAA
1 ATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTCATAGGGTAAA
437692 ATGA
1 ATGA
437696 CTGTTATACC
Statistics
Matches: 243, Mismatches: 28, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
53 48 0.20
54 120 0.49
55 28 0.12
58 1 0.00
63 4 0.02
64 19 0.08
65 23 0.09
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.20
Consensus pattern (55 bp):
ATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTCATAGGGTAAA
Found at i:437488 original size:27 final size:27
Alignment explanation
Indices: 437458--437696 Score: 282
Period size: 27 Copynumber: 8.9 Consensus size: 27
437448 ATACCCCCAT
* *
437458 ATACCCTCATAGGGTAAAATGACCAAA
1 ATACCCCCATAGGGTAAAATGACCGAA
* **
437485 ATACCCCCCATAGGATAAAATGATTGAA
1 ATA-CCCCCATAGGGTAAAATGACCGAA
* *
437513 ATACCCTCATAGGGTAAAATGATCGAA
1 ATACCCCCATAGGGTAAAATGACCGAA
* * **
437540 ATA-CCACAGAGGGTAAAATGACTAAA
1 ATACCCCCATAGGGTAAAATGACCGAA
* *
437566 ATACCCTCATAGGGTAAAATGATCGAA
1 ATACCCCCATAGGGTAAAATGACCGAA
437593 ATACCCCCATAGGGTAAAATGACCGAA
1 ATACCCCCATAGGGTAAAATGACCGAA
* *
437620 ATACCCCCATAGGGTAAAATTATCGAA
1 ATACCCCCATAGGGTAAAATGACCGAA
* ** *
437647 ATACCCCCATAGAGTAGTATGACCAAA
1 ATACCCCCATAGGGTAAAATGACCGAA
*
437674 ATACCACCATAGGGTAAAATGAC
1 ATACCCCCATAGGGTAAAATGAC
437697 TGTTATACCC
Statistics
Matches: 178, Mismatches: 32, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
26 21 0.12
27 135 0.76
28 22 0.12
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (27 bp):
ATACCCCCATAGGGTAAAATGACCGAA
Found at i:438669 original size:28 final size:28
Alignment explanation
Indices: 438629--438683 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
438619 GTATCGGTAT
438629 AGTGTGGGCCTTAGCCC-ATTACAGTAAC
1 AGTGTGGGCCTTAGCCCAATT-CAGTAAC
438657 AGTGTGGGCCTTAGCCCAATTCAGTAA
1 AGTGTGGGCCTTAGCCCAATTCAGTAA
438684 TACAATCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (28 bp):
AGTGTGGGCCTTAGCCCAATTCAGTAAC
Found at i:438809 original size:26 final size:26
Alignment explanation
Indices: 438780--438850 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
438770 CCAATATTGT
**
438780 AGCAAAGCTGCCAGTAATAATGACAC
1 AGCAAAGCTGCCAGTAATAACAACAC
* * **
438806 AGCAAAGCTGCCAGTAACAGCAACGT
1 AGCAAAGCTGCCAGTAATAACAACAC
438832 AGCAAAGCTGCCAGTAATA
1 AGCAAAGCTGCCAGTAATA
438851 GTATATGTGG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.41, C:0.24, G:0.21, T:0.14
Consensus pattern (26 bp):
AGCAAAGCTGCCAGTAATAACAACAC
Found at i:439049 original size:27 final size:25
Alignment explanation
Indices: 439019--439278 Score: 117
Period size: 27 Copynumber: 9.7 Consensus size: 25
439009 TCAACTCCTA
439019 GGGGTATAATAGTCATTTTACCCTATG
1 GGGGTAT-ATAGTCATTTTACCC-ATG
* *
439046 GGGGTATTTTGGTCATTTTACCCATCG
1 GGGGTA-TATAGTCATTTTACCCAT-G
* *
439073 GGGGTATGTCAGTTATTTTACCCAATG
1 GGGGTATAT-AGTCATTTTACCC-ATG
* * *
439100 GGGGTATTTCGATAATTTTACCCATCG
1 GGGGTATATAG-TCATTTTACCCAT-G
* * * *
439127 AGGGTATTTTGGTCATTTTACCCATCA
1 GGGGTA-TATAGTCATTTTACCCAT-G
** * *
439154 AAGGTATTTCAGTCATTTTACCCATC
1 GGGGTATAT-AGTCATTTTACCCATG
* * *
439180 AGGGTATTTCGATCATTTTACCCATCG
1 GGGGTATATAG-TCATTTTACCCAT-G
** * *
439207 ATGATATTTCAGTCATTTTACCCA-G
1 GGGGTATAT-AGTCATTTTACCCATG
* *
439232 CGAGGGTATTTCGATCATTTTACCCATTG
1 -G-GGGTATATAG-TCATTTTACCCA-TG
*
439261 GGGGTATGTCAGTCATTT
1 GGGGTATAT-AGTCATTT
439279 GCCTATGAAT
Statistics
Matches: 189, Mismatches: 27, Indels: 34
0.76 0.11 0.14
Matches are distributed among these distances:
25 2 0.01
26 32 0.17
27 144 0.76
28 10 0.05
29 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.38
Consensus pattern (25 bp):
GGGGTATATAGTCATTTTACCCATG
Found at i:439145 original size:54 final size:53
Alignment explanation
Indices: 439030--439278 Score: 268
Period size: 54 Copynumber: 4.6 Consensus size: 53
439020 GGGTATAATA
** * * *
439030 GTCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCATCGGGGGTATGTCA
1 GTCATTTTACCC-ATGGGGGTATTTCAGTCATTTTACCCATCGAGGGTATTTCG
* * *
439084 GTTATTTTACCCAATGGGGGTATTTC-GATAATTTTACCCATCGAGGGTATTTTG
1 GTCATTTTACCC-ATGGGGGTATTTCAG-TCATTTTACCCATCGAGGGTATTTCG
***
439138 GTCATTTTACCCATCAAAGGTATTTCAGTCATTTTACCCATC-AGGGTATTTCG
1 GTCATTTTACCCAT-GGGGGTATTTCAGTCATTTTACCCATCGAGGGTATTTCG
* ** * *
439191 ATCATTTTACCCATCGATGATATTTCAGTCATTTTACCCAGCGAGGGTATTTCG
1 GTCATTTTACCCAT-GGGGGTATTTCAGTCATTTTACCCATCGAGGGTATTTCG
* *
439245 ATCATTTTACCCATTGGGGGTATGTCAGTCATTT
1 GTCATTTTACCCA-TGGGGGTATTTCAGTCATTT
439279 GCCTATGAAT
Statistics
Matches: 167, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
53 50 0.30
54 115 0.69
55 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (53 bp):
GTCATTTTACCCATGGGGGTATTTCAGTCATTTTACCCATCGAGGGTATTTCG
Found at i:439204 original size:53 final size:54
Alignment explanation
Indices: 439114--439258 Score: 229
Period size: 53 Copynumber: 2.7 Consensus size: 54
439104 TATTTCGATA
* * *
439114 ATTTTACCCATCGAGGGTATTTTGGTCATTTTACCCATCAAAGGTATTTCAGTC
1 ATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCAAAGATATTTCAGTC
* *
439168 ATTTTACCCATC-AGGGTATTTCGATCATTTTACCCATCGATGATATTTCAGTC
1 ATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCAAAGATATTTCAGTC
*
439221 ATTTTACCCAGCGAGGGTATTTCGATCATTTTACCCAT
1 ATTTTACCCATCGAGGGTATTTCGATCATTTTACCCAT
439259 TGGGGGTATG
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 47 0.56
54 37 0.44
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (54 bp):
ATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCAAAGATATTTCAGTC
Found at i:439240 original size:80 final size:80
Alignment explanation
Indices: 439057--439258 Score: 262
Period size: 80 Copynumber: 2.5 Consensus size: 80
439047 GGGTATTTTG
* * * **
439057 GTCATTTTACCCATCGGGGGTATGTCAGTTATTTTACCCAATGGGGGTATTTCGATAATTTTACC
1 GTCATTTTACCCATCGAGGGTATTTCAGTCATTTTACCC-ATCAGGGTATTTCGATAATTTTACC
* **
439122 CATCGAGGGTATTTTG
65 CATCGAGGATATTTCA
* * *
439138 GTCATTTTACCCATCAAAGGTATTTCAGTCATTTTACCCATCAGGGTATTTCGATCATTTTACCC
1 GTCATTTTACCCATCGAGGGTATTTCAGTCATTTTACCCATCAGGGTATTTCGATAATTTTACCC
*
439203 ATCGATGATATTTCA
66 ATCGAGGATATTTCA
*
439218 GTCATTTTACCCAGCGAGGGTATTTC-GATCATTTTACCCAT
1 GTCATTTTACCCATCGAGGGTATTTCAG-TCATTTTACCCAT
439259 TGGGGGTATG
Statistics
Matches: 105, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
79 1 0.01
80 70 0.67
81 34 0.32
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (80 bp):
GTCATTTTACCCATCGAGGGTATTTCAGTCATTTTACCCATCAGGGTATTTCGATAATTTTACCC
ATCGAGGATATTTCA
Found at i:441303 original size:43 final size:43
Alignment explanation
Indices: 441245--441331 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
441235 AGAAACCAAC
441245 TCTGGCCCCAGAACTCGCCGCTCGCCCAACTCAGTCCAACAGG
1 TCTGGCCCCAGAACTCGCCGCTCGCCCAACTCAGTCCAACAGG
* *
441288 TCTGGCCCCATAACTCGCCGCTCGCCCAACTCAGTGCAACAGG
1 TCTGGCCCCAGAACTCGCCGCTCGCCCAACTCAGTCCAACAGG
441331 T
1 T
441332 GGGAGTACAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.21, C:0.43, G:0.21, T:0.16
Consensus pattern (43 bp):
TCTGGCCCCAGAACTCGCCGCTCGCCCAACTCAGTCCAACAGG
Found at i:445497 original size:28 final size:28
Alignment explanation
Indices: 445456--445511 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
445446 GTATCGGTAC
*
445456 AGTGTGGGCTTTAGCCCATTACAGTAAT
1 AGTGTGGGCTTTAGCCCAATACAGTAAT
445484 AGTGTGGG-TCTTAGCCCAATACAGTAAT
1 AGTGTGGGCT-TTAGCCCAATACAGTAAT
445512 TAATGCAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (28 bp):
AGTGTGGGCTTTAGCCCAATACAGTAAT
Found at i:445697 original size:26 final size:26
Alignment explanation
Indices: 445627--445697 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
445617 ATATTACAGG
* * *
445627 AAAGCTTCCAGTAATAATGACGCAGC
1 AAAGCTGCCAGTAATAGTAACGCAGC
* * *
445653 AAAGCTGTCAGTAACAGTAACGTAGC
1 AAAGCTGCCAGTAATAGTAACGCAGC
*
445679 AAAGCTGCCATTAATAGTA
1 AAAGCTGCCAGTAATAGTA
445698 TATGTGGCAA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (26 bp):
AAAGCTGCCAGTAATAGTAACGCAGC
Found at i:445919 original size:27 final size:27
Alignment explanation
Indices: 445874--446209 Score: 340
Period size: 27 Copynumber: 12.5 Consensus size: 27
445864 GGGTATAACA
* *
445874 GTCATTTTACCTTAT-GGGGGTACTTT-G
1 GTCATTTTACC-CATCGAGGGTA-TTTCG
* *
445901 GTCATTTTACCCATCGGGGGTGTTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
* *
445928 ATTATTTTACCCATC-AGTGGTATTTCG
1 GTCATTTTACCCATCGAG-GGTATTTCG
* * *
445955 GTCATTTTACCCATCAAGAGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTCG
*
445982 GTCATTTTACCCATCGAGGGTATTTCT
1 GTCATTTTACCCATCGAGGGTATTTCG
* * **
446009 ATCATTTTACCCATCAAGGGTATTTTT
1 GTCATTTTACCCATCGAGGGTATTTCG
* * * *
446036 GTTATTTTACCCATCAATGGTATTTTG
1 GTCATTTTACCCATCGAGGGTATTTCG
*
446063 GTTATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
* * *
446090 ATCATTTTATCCATCGAAGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
* *
446117 ATCATTTTACCCATCGAGGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTCG
* *
446144 ATCATTTTACCCATCGAGGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTCG
* * *
446171 ATCATTTTACCCAT-TAGGGGTATTTCA
1 GTCATTTTACCCATCGA-GGGTATTTCG
446198 GTCA-TTTACCCA
1 GTCATTTTACCCA
446210 CGAAATCCAG
Statistics
Matches: 272, Mismatches: 32, Indels: 11
0.86 0.10 0.03
Matches are distributed among these distances:
26 15 0.06
27 255 0.94
28 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCATCGAGGGTATTTCG
Found at i:446016 original size:81 final size:79
Alignment explanation
Indices: 445901--446209 Score: 386
Period size: 81 Copynumber: 3.8 Consensus size: 79
445891 GGGTACTTTG
* * *
445901 GTCATTTTACCCATCGGGGGTGTTTCGATTATTTTACCCATCAGTGGTATTTCGGTCATTTTACC
1 GTCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCAG-GGTATTTCGGTCATTTTACC
445966 CATCAAGAGTATTTCA
65 CATCAAG-GTATTTCA
* ** *
445982 GTCATTTTACCCATCGAGGGTATTTCTATCATTTTACCCATCAAGGGTATTTTTGTTATTTTACC
1 GTCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATC-AGGGTATTTCGGTCATTTTACC
**
446047 CATCAATGGTATTTTG
65 CATCAA-GGTATTTCA
* * * *
446063 GTTATTTTACCCATCGAGGGTATTTCGATCATTTTATCCATCGAAGGTATTTCGATCATTTTACC
1 GTCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATC-AGGGTATTTCGGTCATTTTACC
*
446128 CATCGAGGGTATTTCA
65 CATC-AAGGTATTTCA
* * * *
446144 ATCATTTTACCCATCGAGGGTATTTCAATCATTTTACCCATTAGGGGTATTTCAGTCA-TTTACC
1 GTCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCA-GGGTATTTCGGTCATTTTACC
446208 CA
65 CA
446210 CGAAATCCAG
Statistics
Matches: 195, Mismatches: 29, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
80 9 0.05
81 182 0.93
82 4 0.02
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.40
Consensus pattern (79 bp):
GTCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCAGGGTATTTCGGTCATTTTACCC
ATCAAGGTATTTCA
Found at i:459444 original size:20 final size:19
Alignment explanation
Indices: 459405--459447 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
459395 CAACACAATG
*
459405 AAAATAAAATAAAATAAAC
1 AAAATAAAATAAAAGAAAC
*
459424 AAAATAACAATAAAAGCAAC
1 AAAATAA-AATAAAAGAAAC
459444 AAAA
1 AAAA
459448 CTTAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.77, C:0.09, G:0.02, T:0.12
Consensus pattern (19 bp):
AAAATAAAATAAAAGAAAC
Found at i:467846 original size:25 final size:27
Alignment explanation
Indices: 467782--467858 Score: 88
Period size: 25 Copynumber: 2.9 Consensus size: 27
467772 CATCCCGACC
**
467782 CACAGCTCGTGTGAGCAGACCCA-ATTT
1 CACAGCTCGTGTGAGCA-ACTTATATTT
*
467809 CACAGCTCATGTGAGCAA-TTATATTT
1 CACAGCTCGTGTGAGCAACTTATATTT
*
467835 -ACAGCTCGTGTGAGCAATTTATAT
1 CACAGCTCGTGTGAGCAACTTATAT
467859 CTGGTGTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
25 17 0.39
26 11 0.25
27 16 0.36
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (27 bp):
CACAGCTCGTGTGAGCAACTTATATTT
Found at i:470955 original size:22 final size:22
Alignment explanation
Indices: 470927--470969 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
470917 AAAAAAGATG
470927 AAAGTTAGGATTTTTAATCTAA
1 AAAGTTAGGATTTTTAATCTAA
470949 AAAGTTAGGATTTTTAATCTA
1 AAAGTTAGGATTTTTAATCTA
470970 GGAAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42
Consensus pattern (22 bp):
AAAGTTAGGATTTTTAATCTAA
Found at i:486724 original size:39 final size:39
Alignment explanation
Indices: 486595--486727 Score: 167
Period size: 39 Copynumber: 3.4 Consensus size: 39
486585 TAGTAGATAA
* *
486595 CTGTTGTACTTCGGTACCCGTGTTTGCACATACGTGCCC
1 CTGTTGTTCTTCGGTACCCCTGTTTGCACATACGTGCCC
* * * * * *
486634 CTATTGTTCTTAGATACCCTTGTTTGTACATATGTGCCC
1 CTGTTGTTCTTCGGTACCCCTGTTTGCACATACGTGCCC
* *
486673 CTGTTGTTCTTCGGTACCCCTATTCGCACATACGTGCCC
1 CTGTTGTTCTTCGGTACCCCTGTTTGCACATACGTGCCC
*
486712 CTGTTGTGCTTCGGTA
1 CTGTTGTTCTTCGGTA
486728 ACATTTATTA
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.14, C:0.29, G:0.20, T:0.38
Consensus pattern (39 bp):
CTGTTGTTCTTCGGTACCCCTGTTTGCACATACGTGCCC
Found at i:492117 original size:54 final size:54
Alignment explanation
Indices: 492030--492146 Score: 171
Period size: 54 Copynumber: 2.2 Consensus size: 54
492020 TATGACATGG
* * * *
492030 CCGTGTGACCCAATTCAGTGAGTTACATAGGCAGAGACACGGGCTGGGACACGA
1 CCGTGTGTCTCAAGTCAGTGAGTTACATAGGCAGAGACACGGGATGGGACACGA
** *
492084 TTGTGTGTCTCAAGTCAGTGAGTTACATGGGCAGAGACACGGGATGGGACACGA
1 CCGTGTGTCTCAAGTCAGTGAGTTACATAGGCAGAGACACGGGATGGGACACGA
492138 CCGTGTGTC
1 CCGTGTGTC
492147 CCCTATTCTA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.25, C:0.21, G:0.33, T:0.21
Consensus pattern (54 bp):
CCGTGTGTCTCAAGTCAGTGAGTTACATAGGCAGAGACACGGGATGGGACACGA
Found at i:497701 original size:45 final size:44
Alignment explanation
Indices: 497651--497743 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
497641 GGTTCGCTAT
**
497651 AATGGAATAGAGGTGTAAAAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAAAAGT-ATTC-ATGTGTTTGGTTGAATGG
* *
497696 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAAAAGTATTCATGTGTTTGGTTGAATGG
497740 AATG
1 AATG
497744 ATGTTGTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.53
45 19 0.44
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAACTGTAAAAGTATTCATGTGTTTGGTTGAATGG
Found at i:505008 original size:41 final size:41
Alignment explanation
Indices: 504959--505051 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 41
504949 TGTTTTTCTT
* * *
504959 ATAAACGCCACAAAAGGTAAAGTAATAGCGGCGTTTCTCCC
1 ATAAACGCCACAAAAGATAAAGCAATAGAGGCGTTTCTCCC
*
505000 ATAAACGCCACAAAAGATAAAGCAATAGAGGCGTTTTTCCC
1 ATAAACGCCACAAAAGATAAAGCAATAGAGGCGTTTCTCCC
*
505041 ATAAACACCAC
1 ATAAACGCCAC
505052 GAATTTTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.18
Consensus pattern (41 bp):
ATAAACGCCACAAAAGATAAAGCAATAGAGGCGTTTCTCCC
Found at i:510153 original size:8 final size:8
Alignment explanation
Indices: 510140--510188 Score: 54
Period size: 7 Copynumber: 6.8 Consensus size: 8
510130 TTCTATGAAC
510140 TTTTTATA
1 TTTTTATA
510148 -TTTT-TA
1 TTTTTATA
510154 TTTTTAT-
1 TTTTTATA
510161 TTTTTA-A
1 TTTTTATA
510168 TTTTTA-A
1 TTTTTATA
510175 TTTTTATA
1 TTTTTATA
*
510183 ATTTTA
1 TTTTTA
510189 AAATTTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
6 2 0.06
7 27 0.75
8 7 0.19
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTATA
Found at i:510159 original size:14 final size:14
Alignment explanation
Indices: 510140--510181 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
510130 TTCTATGAAC
510140 TTTTTATATTTTTA
1 TTTTTATATTTTTA
510154 TTTTTAT-TTTTTAA
1 TTTTTATATTTTT-A
510168 TTTTTA-ATTTTTA
1 TTTTTATATTTTTA
510181 T
1 T
510182 AATTTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.27
14 19 0.73
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTATATTTTTA
Found at i:510164 original size:21 final size:21
Alignment explanation
Indices: 510140--510181 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
510130 TTCTATGAAC
510140 TTTTTATATTTTT-ATTTTTAT
1 TTTTTA-ATTTTTAATTTTTAT
510161 TTTTTAATTTTTAATTTTTAT
1 TTTTTAATTTTTAATTTTTAT
510182 AATTTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTTAATTTTTAATTTTTAT
Found at i:510691 original size:13 final size:13
Alignment explanation
Indices: 510673--510712 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
510663 GTTGACAATC
510673 TATTTGTAACTAA
1 TATTTGTAACTAA
510686 TATTTGTAACTAA
1 TATTTGTAACTAA
*
510699 CT-TTTGTAATTAA
1 -TATTTGTAACTAA
510712 T
1 T
510713 TAGGCCGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 1 0.04
13 23 0.92
14 1 0.04
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.50
Consensus pattern (13 bp):
TATTTGTAACTAA
Found at i:513936 original size:220 final size:220
Alignment explanation
Indices: 513516--514390 Score: 1625
Period size: 220 Copynumber: 4.0 Consensus size: 220
513506 TGAACTATCC
* *
513516 AATATAATGAAAGTTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
1 AATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
*
513581 AGCCGTCTTGACTTTATGCAACTTAGAGAAGATC-TTTCACCTTCGTTCTTCACTATTATGTTGC
66 AGCCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACCTTCGTTCTTCACTATTATGTTGC
513645 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
131 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
513710 CTTATAGAGAGGTGCTAATTTATTT
196 CTTATAGAGAGGTGCTAATTTATTT
513735 AATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
1 AATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
*
513800 AGCCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTTACCTTCGTTCTTCACTATTATGTTGC
66 AGCCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACCTTCGTTCTTCACTATTATGTTGC
513865 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
131 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
513930 CTTATAGAGAGGTGCTAATTTATTT
196 CTTATAGAGAGGTGCTAATTTATTT
*
513955 AATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGATAAAGTACAAGATCA
1 AATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
*
514020 AGTCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACCTTCGTTCTTCACTATTATGTTGC
66 AGCCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACCTTCGTTCTTCACTATTATGTTGC
514085 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
131 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
*
514150 CTTATAGAGAGGTCCT-A---ATTT
196 CTTATAGAGAGGTGCTAATTTATTT
514171 AATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
1 AATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
*
514236 AGCTGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACCTTCGTTCTTCACTATTATGTTGC
66 AGCCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACCTTCGTTCTTCACTATTATGTTGC
* *
514301 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTAGACCAGTTTTCTATCGGTGGCTGTAT
131 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
514366 CTTATAGAGAGGTGCTAATTTATTT
196 CTTATAGAGAGGTGCTAATTTATTT
514391 GCCAAGTTAT
Statistics
Matches: 637, Mismatches: 14, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
216 209 0.33
217 1 0.00
219 97 0.15
220 330 0.52
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (220 bp):
AATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
AGCCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACCTTCGTTCTTCACTATTATGTTGC
ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
CTTATAGAGAGGTGCTAATTTATTT
Found at i:514331 original size:436 final size:437
Alignment explanation
Indices: 513516--514390 Score: 1619
Period size: 436 Copynumber: 2.0 Consensus size: 437
513506 TGAACTATCC
*
513516 AATATAATGAAAGTTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
1 AATATAATGAAAGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
513581 AGCCGTCTTGACTTTATGCAACTTAGAGAAGATCTTTCACCTTCGTTCTTCACTATTATGTTGCA
66 AGCCGTCTTGACTTTATGCAACTTAGAGAAGATCTTTCACCTTCGTTCTTCACTATTATGTTGCA
513646 CTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTATC
131 CTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTATC
*
513711 TTATAGAGAGGTGCTAATTTATTTAATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGA
196 TTATAGAGAGGTCCTAA--TATTTAATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGA
*
513776 AGAACTTGAGAAAGTACAAGATCAAGCCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTTAC
259 AGAACTTGAGAAAGTACAAGATCAAGCCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCAC
*
513841 CTTCGTTCTTCACTATTATGTTGCACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGA
324 CTTCGTTCTTCACTATTATGTTGCACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTAGA
513906 CCAGTTTTCTATCGGTGGATGTATCTTATAGAGAGGTGCTAATTTATTT
389 CCAGTTTTCTATCGGTGGATGTATCTTATAGAGAGGTGCTAATTTATTT
* *
513955 AATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGATAAAGTACAAGATCA
1 AATATAATGAAAGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
* *
514020 AGTCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACCTTCGTTCTTCACTATTATGTTGC
66 AGCCGTCTTGACTTTATGCAACTTAGAGAAGATC-TTTCACCTTCGTTCTTCACTATTATGTTGC
514085 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
130 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
514150 CTTATAGAGAGGTCCT-A-ATTTAATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAA
195 CTTATAGAGAGGTCCTAATATTTAATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAA
*
514213 GAACTTGAGAAAGTACAAGATCAAGCTGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACC
260 GAACTTGAGAAAGTACAAGATCAAGCCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACC
514278 TTCGTTCTTCACTATTATGTTGCACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTAGAC
325 TTCGTTCTTCACTATTATGTTGCACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTAGAC
*
514343 CAGTTTTCTATCGGTGGCTGTATCTTATAGAGAGGTGCTAATTTATTT
390 CAGTTTTCTATCGGTGGATGTATCTTATAGAGAGGTGCTAATTTATTT
514391 GCCAAGTTAT
Statistics
Matches: 425, Mismatches: 10, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
436 220 0.52
439 95 0.22
440 110 0.26
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (437 bp):
AATATAATGAAAGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
AGCCGTCTTGACTTTATGCAACTTAGAGAAGATCTTTCACCTTCGTTCTTCACTATTATGTTGCA
CTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTATC
TTATAGAGAGGTCCTAATATTTAATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAG
AACTTGAGAAAGTACAAGATCAAGCCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACCT
TCGTTCTTCACTATTATGTTGCACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTAGACC
AGTTTTCTATCGGTGGATGTATCTTATAGAGAGGTGCTAATTTATTT
Found at i:532894 original size:28 final size:28
Alignment explanation
Indices: 532810--532906 Score: 115
Period size: 28 Copynumber: 3.4 Consensus size: 28
532800 TATACAGTAT
* *
532810 CAGT-ACAGTGTAGGCCTTAGCCCATTA
1 CAGTAACAGTGGAGGCCTTAGCCCAATA
* *
532837 CAGTAACAGTGTGTGAGCCTTAGCCTAATA
1 CAGTAACAGTG-GAG-GCCTTAGCCCAATA
532867 CAGTAACAGTGGAGGCCTTAGCCCAATA
1 CAGTAACAGTGGAGGCCTTAGCCCAATA
*
532895 TAGTAATCAGTG
1 CAGTAA-CAGTG
532907 CAATGCAGTA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
27 4 0.07
28 24 0.41
29 8 0.14
30 23 0.39
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25
Consensus pattern (28 bp):
CAGTAACAGTGGAGGCCTTAGCCCAATA
Found at i:533071 original size:26 final size:26
Alignment explanation
Indices: 533011--533087 Score: 91
Period size: 26 Copynumber: 3.0 Consensus size: 26
533001 ACACCAATAT
* *
533011 CGCAGCAAAGCTGCTAGTAATAGTGA
1 CGCAGCAAAGCTGCCAGTAATAGTAA
* *
533037 CACATCAAAGCTGCCAGTAATAGTAA
1 CGCAGCAAAGCTGCCAGTAATAGTAA
* * *
533063 TGCAGCAAAGCTACCAGTAACAGTA
1 CGCAGCAAAGCTGCCAGTAATAGTA
533088 TATGTGGTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.18
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTAATAGTAA
Found at i:533282 original size:27 final size:26
Alignment explanation
Indices: 533262--533707 Score: 235
Period size: 27 Copynumber: 16.7 Consensus size: 26
533252 GGGTATAACA
*
533262 GTCATTTTACCCTATGGGGGTATTTC
1 GTCATTTTACCCTATGAGGGTATTTC
533288 GATCATTTTACCCTATGAGGGTATTTC
1 G-TCATTTTACCCTATGAGGGTATTTC
* *
533315 GGTCATTTTACCCT-TCAGGGGTATTTTG
1 -GTCATTTTACCCTATGA-GGGTA-TTTC
* *
533343 GTTATTTTACCCGTCA--AGGGCA-TTC
1 GTCATTTTACCC-T-ATGAGGGTATTTC
533368 GATCATTTTACCCT-TCGAGGGTATTTC
1 G-TCATTTTACCCTAT-GAGGGTATTTC
* * * *
533395 GATCATTTTACCAT-TCAAAGGTATTCC
1 G-TCATTTTACCCTAT-GAGGGTATTTC
*
533422 AGTCATTTTACCCT-TCAAGGGTATTTC
1 -GTCATTTTACCCTAT-GAGGGTATTTC
* *
533449 GATCATTTTA-CCTTTCGAGGGTATTTTG
1 G-TCATTTTACCCTAT-GAGGGTA-TTTC
*
533477 GTCATTTTACCCT-TCGGGGGTATTTC
1 GTCATTTTACCCTAT-GAGGGTATTTC
* * * *
533503 GATCATTTTACCCTTTAAGGTTATTTTA
1 G-TCATTTTACCCTATGAGGGTA-TTTC
* *
533531 GTCATTTTACCCT-TCAGGGGTATTTTA
1 GTCATTTTACCCTATGA-GGGTA-TTTC
533558 GTTC-TTTTACCCT-TCGAGGGTATTTC
1 G-TCATTTTACCCTAT-GAGGGTATTTC
* * * *
533584 GATTATTTTACCCTTTAAGGGTATTTTG
1 G-TCATTTTACCCTATGAGGGTA-TTTC
* *
533612 GTCATTTTACCCT-TCAGGGGTACTTC
1 GTCATTTTACCCTATGA-GGGTATTTC
533638 GATCATTTTACCCCTCA--AGGGTATTTC
1 G-TCATTTTA-CCCT-ATGAGGGTATTTC
* * *
533665 AGTCATTTTATCCT-TCAAGGCTATTTC
1 -GTCATTTTACCCTAT-GAGGGTATTTC
533692 GGTCA-TTTACCC-ATGA
1 -GTCATTTTACCCTATGA
533708 ATTGCAAGTT
Statistics
Matches: 343, Mismatches: 41, Indels: 73
0.75 0.09 0.16
Matches are distributed among these distances:
25 5 0.01
26 48 0.14
27 257 0.75
28 33 0.10
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (26 bp):
GTCATTTTACCCTATGAGGGTATTTC
Found at i:533336 original size:54 final size:54
Alignment explanation
Indices: 533262--533703 Score: 457
Period size: 54 Copynumber: 8.2 Consensus size: 54
533252 GGGTATAACA
* *
533262 GTCATTTTACCCTAT-GGGGGTATTTCGATCATTTTACCCTAT-GAGGGTATTTCG
1 GTCATTTTACCCT-TCAGGGGTATTTCGATCATTTTACCCT-TCAAGGGTATTTCG
* * * * *
533316 GTCATTTTACCCTTCAGGGGTATTTTGGTTATTTTACCCGTCAAGGGCA-TTCG
1 GTCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCG
* * * * *
533369 ATCATTTTACCCTTC-GAGGGTATTTCGATCATTTTACCATTCAAAGGTATTCCA
1 GTCATTTTACCCTTCAG-GGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCG
* * * *
533423 GTCATTTTACCCTTCAAGGGTATTTCGATCATTTTACCTTTCGAGGGTATTTTG
1 GTCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCG
* * * **
533477 GTCATTTTACCCTTCGGGGGTATTTCGATCATTTTACCCTTTAAGGTTATTTTA
1 GTCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCG
* * *
533531 GTCATTTTACCCTTCAGGGGTATTTTAGTTC-TTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCAGGGGTA-TTTCGATCATTTTACCCTTCAAGGGTATTTCG
* * * * * * * *
533585 ATTATTTTACCCTTTAAGGGTATTTTGGTCATTTTACCCTTCAGGGGTACTTCG
1 GTCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCG
* * * * *
533639 ATCATTTTACCCCTCAAGGGTATTTC-AGTCATTTTATCCTTCAAGGCTATTTCG
1 GTCATTTTACCCTTCAGGGGTATTTCGA-TCATTTTACCCTTCAAGGGTATTTCG
533693 GTCA-TTTACCC
1 GTCATTTTACCC
533704 ATGAATTGCA
Statistics
Matches: 321, Mismatches: 59, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
52 1 0.00
53 58 0.18
54 256 0.80
55 6 0.02
ACGTcount: A:0.19, C:0.21, G:0.18, T:0.42
Consensus pattern (54 bp):
GTCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCG
Found at i:533482 original size:81 final size:81
Alignment explanation
Indices: 533250--533703 Score: 460
Period size: 81 Copynumber: 5.6 Consensus size: 81
533240 TTCAACTCCT
** **
533250 AAGGGTATAACAGTCATTTTACCCTAT-GGGGGTATTTCGATCATTTTACCCTAT-GAGGGTATT
1 AAGGGTATTTCAGTCATTTTACCCT-TCAAGGGTATTTCGATCATTTTACCCT-TCGAGGGTATT
*
533313 TCGGTCATTTTACCCTTC
64 TCGATCATTTTACCCTTC
* ** * * *
533331 AGGGGTATTTTGGTTATTTTACCCGTCAAGGGCA-TTCGATCATTTTACCCTTCGAGGGTATTTC
1 AAGGGTATTTCAGTCATTTTACCCTTCAAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTC
*
533395 GATCATTTTACCATTC
66 GATCATTTTACCCTTC
* * * *
533411 AAAGGTATTCCAGTCATTTTACCCTTCAAGGGTATTTCGATCATTTTACCTTTCGAGGGTATTTT
1 AAGGGTATTTCAGTCATTTTACCCTTCAAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTC
*
533476 GGTCATTTTACCCTTC
66 GATCATTTTACCCTTC
** * * *
533492 GGGGGTATTTC-GATCATTTTACCCTTTAAGGTTATTT-TAGTCATTTTACCCTTC-AGGGGTAT
1 AAGGGTATTTCAG-TCATTTTACCCTTCAAGGGTATTTCGA-TCATTTTACCCTTCGA-GGGTA-
* *
533554 TTTAGTTC-TTTTACCCTTC
62 TTTCGATCATTTTACCCTTC
* * * * * *
533573 GAGGGTATTTC-GATTATTTTACCCTTTAAGGGTATTTTGGTCATTTTACCCTTC-AGGGGTACT
1 AAGGGTATTTCAG-TCATTTTACCCTTCAAGGGTATTTCGATCATTTTACCCTTCGA-GGGTATT
*
533636 TCGATCATTTTACCCCTC
64 TCGATCATTTTACCCTTC
* * *
533654 AAGGGTATTTCAGTCATTTTATCCTTCAAGGCTATTTCGGTCA-TTTACCC
1 AAGGGTATTTCAGTCATTTTACCCTTCAAGGGTATTTCGATCATTTTACCC
533704 ATGAATTGCA
Statistics
Matches: 314, Mismatches: 49, Indels: 21
0.82 0.13 0.05
Matches are distributed among these distances:
79 1 0.00
80 84 0.27
81 222 0.71
82 7 0.02
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (81 bp):
AAGGGTATTTCAGTCATTTTACCCTTCAAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTC
GATCATTTTACCCTTC
Found at i:537044 original size:14 final size:13
Alignment explanation
Indices: 537011--537053 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
537001 TCAAGTCCTT
537011 TACAGATACAGATA
1 TACAGA-ACAGATA
537025 -ACAGAACCAGATA
1 TACAGAA-CAGATA
537038 TACAGAACAGAT-
1 TACAGAACAGATA
537050 TACA
1 TACA
537054 AAATCCCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 5 0.19
13 16 0.59
14 6 0.22
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (13 bp):
TACAGAACAGATA
Found at i:537600 original size:18 final size:17
Alignment explanation
Indices: 537577--537611 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
537567 CGTGTGCAAT
537577 GCCCGTATGGGCCCACAC
1 GCCCGTAT-GGCCCACAC
*
537595 GCCCGTGTGGCCCACAC
1 GCCCGTATGGCCCACAC
537612 TACCAATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.14, C:0.46, G:0.29, T:0.11
Consensus pattern (17 bp):
GCCCGTATGGCCCACAC
Found at i:538702 original size:34 final size:36
Alignment explanation
Indices: 538633--538702 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 36
538623 AAGCTCAAAC
* * * *
538633 AAATCAATACGGTAGCATTTAATTATGCTTTTAACA
1 AAATCAATACGATAGCAATCAATTATGCTTATAACA
538669 AAAT-AATACGATAGCAATCAA-TATGCTTATAACA
1 AAATCAATACGATAGCAATCAATTATGCTTATAACA
538703 GTTCAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 12 0.40
35 14 0.47
36 4 0.13
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.31
Consensus pattern (36 bp):
AAATCAATACGATAGCAATCAATTATGCTTATAACA
Found at i:540027 original size:18 final size:18
Alignment explanation
Indices: 540004--540044 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
539994 CTTTTCCCCC
*
540004 TTCTTTCATTTGTTTATT
1 TTCTTTCATTTATTTATT
*
540022 TTCTTTCGTTTATTTATT
1 TTCTTTCATTTATTTATT
540040 TTCTT
1 TTCTT
540045 ACTTTTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.12, G:0.05, T:0.73
Consensus pattern (18 bp):
TTCTTTCATTTATTTATT
Found at i:541313 original size:28 final size:28
Alignment explanation
Indices: 541278--541340 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
541268 TTTATATGTA
*
541278 TTAATTATTTTACCACTAATATGTATAC
1 TTAATTATTTTACCACTAACATGTATAC
*
541306 TTAATTATTTTACCATTAACATGTATAC
1 TTAATTATTTTACCACTAACATGTATAC
541334 TT-ATTAT
1 TTAATTAT
541341 ATTATCTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
27 5 0.15
28 28 0.85
ACGTcount: A:0.35, C:0.13, G:0.03, T:0.49
Consensus pattern (28 bp):
TTAATTATTTTACCACTAACATGTATAC
Found at i:549477 original size:17 final size:18
Alignment explanation
Indices: 549450--549483 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
549440 TAATTATTTT
549450 ATTAATAATATTAATGAA
1 ATTAATAATATTAATGAA
549468 ATTAAT-ATATTAATGA
1 ATTAATAATATTAATGA
549484 TTACTTACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (18 bp):
ATTAATAATATTAATGAA
Found at i:553529 original size:13 final size:13
Alignment explanation
Indices: 553511--553583 Score: 85
Period size: 13 Copynumber: 5.7 Consensus size: 13
553501 TCTTCATTGT
553511 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
553524 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
* *
553537 TGTGGAAAAGTGC
1 TTTTGAAAAGTGC
* *
553550 TTTTCAGAAGTGC
1 TTTTGAAAAGTGC
* *
553563 TTTTCAGAAGTGC
1 TTTTGAAAAGTGC
553576 TTTT-AAAA
1 TTTTGAAAA
553584 ATTTGGAGTG
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
12 3 0.06
13 50 0.94
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:556781 original size:25 final size:26
Alignment explanation
Indices: 556727--556784 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
556717 AGATATTTAA
*
556727 TTTAAT-TTAATATTAAGATAATCAC
1 TTTAATATTAATATTAAGAAAATCAC
*
556752 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAATATTAATATTAAGAAAATCAC
556776 TATTAATAT
1 T-TTAATAT
556785 ACGTATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 3 0.10
25 22 0.76
26 4 0.14
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (26 bp):
TTTAATATTAATATTAAGAAAATCAC
Found at i:559088 original size:18 final size:16
Alignment explanation
Indices: 559046--559088 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
559036 TAGCATATTT
559046 TTTTTATTCACAATGC
1 TTTTTATTCACAATGC
* *
559062 CTTTAATTCTAACAATGC
1 TTTTTATTC--ACAATGC
559080 TTTTTATTC
1 TTTTTATTC
559089 GTTCGCTTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 7 0.33
18 14 0.67
ACGTcount: A:0.26, C:0.19, G:0.05, T:0.51
Consensus pattern (16 bp):
TTTTTATTCACAATGC
Found at i:561814 original size:14 final size:14
Alignment explanation
Indices: 561775--561825 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
561765 TAATAAATTT
*
561775 ATTATTTAACATAA
1 ATTATTTAATATAA
561789 ATATAAATTTAATATAA
1 AT-T--ATTTAATATAA
*
561806 ATTATTTAATATGA
1 ATTATTTAATATAA
561820 ATTATT
1 ATTATT
561826 ATTAATAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 18 0.56
15 1 0.03
16 1 0.03
17 12 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (14 bp):
ATTATTTAATATAA
Found at i:561826 original size:17 final size:16
Alignment explanation
Indices: 561764--561832 Score: 56
Period size: 17 Copynumber: 4.4 Consensus size: 16
561754 TAATTTTTTA
561764 TTAATA-AATTTATTAT
1 TTAATATAA-TTATTAT
* * *
561780 TTAACATAAATATAAAT
1 TTAATATAATTAT-TAT
561797 TTAATATAA--ATTAT
1 TTAATATAATTATTAT
561811 TTAATATGAATTATTA-
1 TTAATAT-AATTATTAT
561827 TTAATA
1 TTAATA
561833 ATCAATTTGC
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
14 9 0.21
15 4 0.09
16 14 0.33
17 16 0.37
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (16 bp):
TTAATATAATTATTAT
Found at i:563445 original size:14 final size:14
Alignment explanation
Indices: 563406--563456 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
563396 TAATAAATTT
*
563406 ATTATTTAACATAA
1 ATTATTTAATATAA
563420 ATATAAATTTAATATAA
1 AT-T--ATTTAATATAA
*
563437 ATTATTTAATATGA
1 ATTATTTAATATAA
563451 ATTATT
1 ATTATT
563457 ATTAATAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 18 0.56
15 1 0.03
16 1 0.03
17 12 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (14 bp):
ATTATTTAATATAA
Found at i:563457 original size:17 final size:16
Alignment explanation
Indices: 563385--563463 Score: 60
Period size: 16 Copynumber: 5.0 Consensus size: 16
563375 AATCAAAATT
563385 TAATTATT-TATTAATA
1 TAATTATTAT-TTAATA
*
563401 -AATTTATTATTTAACA
1 TAA-TTATTATTTAATA
* *
563417 TAAATATAAATTTAATA
1 TAATTAT-TATTTAATA
563434 TAA--ATTATTTAATA
1 TAATTATTATTTAATA
563448 TGAATTATTA-TTAATA
1 T-AATTATTATTTAATA
563464 ATCAATTTGC
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
14 9 0.18
15 6 0.12
16 19 0.37
17 17 0.33
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (16 bp):
TAATTATTATTTAATA
Found at i:564081 original size:22 final size:20
Alignment explanation
Indices: 564043--564087 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 20
564033 TATATTTTTA
564043 TTTCTATAAAATTTTGAAAT
1 TTTCTATAAAATTTTGAAAT
564063 TTTCTAATAAATATTTTGAAAT
1 TTTCT-ATAAA-ATTTTGAAAT
564085 TTT
1 TTT
564088 GAAGATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 5 0.22
21 5 0.22
22 13 0.57
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (20 bp):
TTTCTATAAAATTTTGAAAT
Found at i:565713 original size:60 final size:60
Alignment explanation
Indices: 565588--565716 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 60
565578 TTAAGTTCTG
* * * * * * * *
565588 TTATTTTCAAAATCTGATGCGCCAAACATATTATCATATGTGTAATGCCCTTTTAGCCTA
1 TTATTTCCAAAACCGGATGCGCCAAACATATTATCATATATGTAATGCCATATCAACCTA
* * *
565648 CTATTTCCAAAACCGGATGCGCCAAACATATTATCATATATGTAATGTCATATCAACTTA
1 TTATTTCCAAAACCGGATGCGCCAAACATATTATCATATATGTAATGCCATATCAACCTA
565708 TTATTTCCA
1 TTATTTCCA
565717 CATATTACTT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (60 bp):
TTATTTCCAAAACCGGATGCGCCAAACATATTATCATATATGTAATGCCATATCAACCTA
Found at i:571193 original size:15 final size:16
Alignment explanation
Indices: 571161--571193 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
571151 CTTCATCTGT
*
571161 TTAATTTATTCTTCCA
1 TTAATTTATTCTTACA
571177 TTAATTT-TTCTTACA
1 TTAATTTATTCTTACA
571192 TT
1 TT
571194 TATAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATTTATTCTTACA
Found at i:582306 original size:7 final size:7
Alignment explanation
Indices: 582294--582326 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
582284 CTTTGGGTCA
582294 AAAAAAG
1 AAAAAAG
582301 AAAAAAG
1 AAAAAAG
*
582308 GAAAAAG
1 AAAAAAG
582315 AAAAAAG
1 AAAAAAG
582322 AAAAA
1 AAAAA
582327 GGAGAGCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:583592 original size:45 final size:45
Alignment explanation
Indices: 583519--583604 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 45
583509 ATTAGAGCCA
583519 CAAGTCCTATCTCCCTGAAATTACAGTGGAACAGACTGAAGATAG
1 CAAGTCCTATCTCCCTGAAATTACAGTGGAACAGACTGAAGATAG
* * * * * * *
583564 CAAGTCTTATTTCCTTGAAGTTGCAGTGGGACAGATTGAAG
1 CAAGTCCTATCTCCCTGAAATTACAGTGGAACAGACTGAAG
583605 CTATAAGCTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 34 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (45 bp):
CAAGTCCTATCTCCCTGAAATTACAGTGGAACAGACTGAAGATAG
Found at i:584690 original size:15 final size:16
Alignment explanation
Indices: 584657--584693 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
584647 TTATTTATTT
*
584657 ATTTATTTATTCTTCC
1 ATTTATTTATTCTTAC
584673 ATTTATTT-TTCTTAC
1 ATTTATTTATTCTTAC
584688 ATTTAT
1 ATTTAT
584694 AATTTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.22, C:0.14, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTATTTATTCTTAC
Found at i:586489 original size:59 final size:62
Alignment explanation
Indices: 586408--586524 Score: 150
Period size: 62 Copynumber: 1.9 Consensus size: 62
586398 ATCACTTTAA
* * * *
586408 TATTAAATTAATATAATATTTATC-A-AA-ATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTATCAATAAGATAAACATTAAATTAAATTTAATATTAAATCT
* * *
586467 TATTAAAATGATAGAATGTTTATCAATAAGATAAACATTAAATTTAATTTAATATTAA
1 TATTAAAATAATAGAATATTTATCAATAAGATAAACATTAAATTAAATTTAATATTAA
586525 GATAATCACT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 20 0.42
60 1 0.02
61 2 0.04
62 25 0.52
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.42
Consensus pattern (62 bp):
TATTAAAATAATAGAATATTTATCAATAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:589116 original size:51 final size:51
Alignment explanation
Indices: 588973--589116 Score: 157
Period size: 51 Copynumber: 2.8 Consensus size: 51
588963 AACGTGATTG
* *
588973 TCACGTGTGTAGTACTATGTGCAGGCTACTAGGTGTACCGGA-ATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATATGATAGA
* * * * ** * *
589023 TCGCATGTGTAGTACAATGTGCAGGCTACTATGCATACCGGATA-GTTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATATG-ATAGA
* *
589074 TCATGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT
589117 GGNNNNNNNN
Statistics
Matches: 75, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
50 37 0.49
51 38 0.51
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATATGATAGA
Found at i:590383 original size:13 final size:13
Alignment explanation
Indices: 590367--590400 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
590357 TATTTGGCAA
590367 GCATGCTTGGTGT
1 GCATGCTTGGTGT
590380 GCATGCTTGGTGT
1 GCATGCTTGGTGT
*
590393 GTATGCTT
1 GCATGCTT
590401 AGGCTTTGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.09, C:0.15, G:0.35, T:0.41
Consensus pattern (13 bp):
GCATGCTTGGTGT
Found at i:591442 original size:25 final size:25
Alignment explanation
Indices: 591413--591493 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
591403 AATTGATTTG
591413 ATTAATTTAATTTTACTTTATCAAA
1 ATTAATTTAATTTTACTTTATCAAA
* * * **
591438 ATTAATTT-TTTGTTAATTGAT--TG
1 ATTAATTTAATT-TTACTTTATCAAA
591461 ATTAATTTAATTTTACTTTATCAAA
1 ATTAATTTAATTTTACTTTATCAAA
591486 ATTAATTT
1 ATTAATTT
591494 TTTTAAAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
23 15 0.36
24 4 0.10
25 23 0.55
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.56
Consensus pattern (25 bp):
ATTAATTTAATTTTACTTTATCAAA
Found at i:591497 original size:49 final size:49
Alignment explanation
Indices: 591399--591496 Score: 189
Period size: 48 Copynumber: 2.0 Consensus size: 49
591389 ATCATATTAA
591399 TGTTAATTGATTTGATTAATTTAATTTTACTTTATCAAAATTAATTTTT
1 TGTTAATTGATTTGATTAATTTAATTTTACTTTATCAAAATTAATTTTT
591448 TGTTAATTGA-TTGATTAATTTAATTTTACTTTATCAAAATTAATTTTT
1 TGTTAATTGATTTGATTAATTTAATTTTACTTTATCAAAATTAATTTTT
591496 T
1 T
591497 TAAAAATCAC
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 39 0.80
49 10 0.20
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (49 bp):
TGTTAATTGATTTGATTAATTTAATTTTACTTTATCAAAATTAATTTTT
Found at i:592915 original size:7 final size:7
Alignment explanation
Indices: 592905--592950 Score: 56
Period size: 7 Copynumber: 6.0 Consensus size: 7
592895 TTTTTAAATT
592905 TTTAAAA
1 TTTAAAA
592912 TTTAAAA
1 TTTAAAA
592919 TTTAAAAA
1 TTT-AAAA
592927 TTTAAAA
1 TTTAAAA
592934 CTCGTTAAAA
1 -T--TTAAAA
592944 TTTAAAA
1 TTTAAAA
592951 AATAAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 20 0.57
8 8 0.23
9 1 0.03
10 6 0.17
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (7 bp):
TTTAAAA
Found at i:592917 original size:15 final size:15
Alignment explanation
Indices: 592897--592933 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
592887 ACATTAAATT
* *
592897 TTTAAATTTTTAAAA
1 TTTAAAATTTAAAAA
592912 TTTAAAATTTAAAAA
1 TTTAAAATTTAAAAA
592927 TTTAAAA
1 TTTAAAA
592934 CTCGTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTAAAATTTAAAAA
Found at i:592974 original size:32 final size:32
Alignment explanation
Indices: 592905--592976 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
592895 TTTTTAAATT
** *
592905 TTTAAAATTTAAAATTTAAAAATTTAAAACTC
1 TTTAAAATTTAAAAAATAAAAATATAAAACTC
* * **
592937 GTTAAAATTTAAAAAATAAAAATATATATTTC
1 TTTAAAATTTAAAAAATAAAAATATAAAACTC
592969 TTTAAAAT
1 TTTAAAAT
592977 ATATTTAAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (32 bp):
TTTAAAATTTAAAAAATAAAAATATAAAACTC
Found at i:594506 original size:60 final size:60
Alignment explanation
Indices: 594407--594520 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
594397 AAATGAGGTG
** * ** *
594407 TTATTCAGGCTTAGTGTTTAGTAGGCTTAGTGCTGGTGTTGTTCAGGCTTAGTGCAAGTA
1 TTATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCAGTGTTATTCAGGCTTAGTGCAAGTA
*
594467 TTATTTAGGCTTAGTGCCTAGCAGGCTTAGTGCCAGTGTTATTCAGGCTTAGTG
1 TTATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCAGTGTTATTCAGGCTTAGTG
594521 TGTAACACCC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.18, C:0.14, G:0.29, T:0.39
Consensus pattern (60 bp):
TTATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCAGTGTTATTCAGGCTTAGTGCAAGTA
Found at i:594513 original size:22 final size:22
Alignment explanation
Indices: 594429--594520 Score: 79
Period size: 22 Copynumber: 4.5 Consensus size: 22
594419 AGTGTTTAGT
** *
594429 AGGCTTAGTGCTGGTGTTGTTC
1 AGGCTTAGTGCCAGTGTTATTC
* * *
594451 AGGCTTAGTGCAAGTATTATTT
1 AGGCTTAGTGCCAGTGTTATTC
*
594473 AGGCTTAGTGCC-----TA-GC
1 AGGCTTAGTGCCAGTGTTATTC
594489 AGGCTTAGTGCCAGTGTTATTC
1 AGGCTTAGTGCCAGTGTTATTC
594511 AGGCTTAGTG
1 AGGCTTAGTG
594521 TGTAACACCC
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
16 12 0.22
17 2 0.04
21 2 0.04
22 39 0.71
ACGTcount: A:0.18, C:0.15, G:0.30, T:0.36
Consensus pattern (22 bp):
AGGCTTAGTGCCAGTGTTATTC
Done.