Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008150.1 Hibiscus syriacus cultivar Beakdansim tig00110716_pilon, whole genome shotgun sequence
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: 3012591
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 14
Found at i:6912 original size:19 final size:20
Alignment explanation
Indices: 6866--6919 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
6856 TAAGCTGCTG
* *
6866 GAAAACGGTTTGACCAGTTT
1 GAAACCGGTTTGACCAGTCT
*
6886 GAAACCGGTTTGACCGGTCT
1 GAAACCGGTTTGACCAGTCT
*
6906 G-AACCGGGTTGACC
1 GAAACCGGTTTGACC
6920 CGACCCGACT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (20 bp):
GAAACCGGTTTGACCAGTCT
Found at i:6935 original size:17 final size:17
Alignment explanation
Indices: 6913--6970 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
6903 TCTGAACCGG
*
6913 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
*
6930 GTTGACCCGACCAGACC
1 GTTGACCCGACCCGACC
6947 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
6964 GTTGACC
1 GTTGACC
6971 GTTGACCGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.19, C:0.41, G:0.24, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:6970 original size:7 final size:7
Alignment explanation
Indices: 6960--6996 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
6950 GACCCGACCC
6960 GACCGTT
1 GACCGTT
6967 GACCGTT
1 GACCGTT
6974 GACCG-T
1 GACCGTT
6980 GACCGTT
1 GACCGTT
6987 GACCGTT
1 GACCGTT
6994 GAC
1 GAC
6997 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:6984 original size:13 final size:13
Alignment explanation
Indices: 6960--6992 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
6950 GACCCGACCC
6960 GACCGTTGACCGTT
1 GACCG-TGACCGTT
6974 GACCGTGACCGTT
1 GACCGTGACCGTT
6987 GACCGT
1 GACCGT
6993 TGACTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:11791 original size:17 final size:17
Alignment explanation
Indices: 11769--11809 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
11759 CTAAACTTCA
11769 TATGTTTCAAAATTATT
1 TATGTTTCAAAATTATT
11786 TATGTTTCAAAATTATT
1 TATGTTTCAAAATTATT
11803 TATGTTT
1 TATGTTT
11810 TATTTTGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (17 bp):
TATGTTTCAAAATTATT
Found at i:12861 original size:20 final size:20
Alignment explanation
Indices: 12795--13003 Score: 123
Period size: 20 Copynumber: 10.5 Consensus size: 20
12785 AATGACCAAG
*
12795 AAATCCGCAACGCG-A-TCTC
1 AAATTCGCAACGCGAATTC-C
*
12814 AAATTCGCAACGTG-A-TCTC
1 AAATTCGCAACGCGAATTC-C
12833 AAATTCGCAACGCGAATTCC
1 AAATTCGCAACGCGAATTCC
* * *
12853 AATTTCGCAACTC-AGTTTCC
1 AAATTCGCAACGCGA-ATTCC
*
12873 AAATTCGCAACGCGATTTTCC
1 AAATTCGCAACGCGA-ATTCC
* *
12894 AAATTCGCAATGCGAAAGT-C
1 AAATTCGCAACGCG-AATTCC
* *
12914 AAATTCGCAATGCGAAAGT-C
1 AAATTCGCAACGCG-AATTCC
**
12934 AAATTCGCAACGCGAATTTGT
1 AAATTCGCAACGCGAA-TTCC
* * *
12955 AAA-TCGCAACACATAAGT-C
1 AAATTCGCAACGC-GAATTCC
*
12974 AAATTCGCAACGCGATAGT-C
1 AAATTCGCAACGCGA-ATTCC
12994 AAATTCGCAA
1 AAATTCGCAA
13004 ATCGAAAGTC
Statistics
Matches: 159, Mismatches: 21, Indels: 19
0.80 0.11 0.10
Matches are distributed among these distances:
19 37 0.23
20 94 0.59
21 27 0.17
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (20 bp):
AAATTCGCAACGCGAATTCC
Found at i:12949 original size:40 final size:39
Alignment explanation
Indices: 12893--13017 Score: 139
Period size: 40 Copynumber: 3.1 Consensus size: 39
12883 CGCGATTTTC
*
12893 CAAATTCGCAATGCGAAAGTCAAATTCGCAATGCGAAAGT
1 CAAATTCGCAACGCGAAAGTCAAATTCGCAAT-CGAAAGT
* *
12933 CAAATTCGCAACGCGAATTTGT-AAA-TCGCAA-CACATAAGT
1 CAAATTCGCAACGCGAA--AGTCAAATTCGCAATC-GA-AAGT
*
12973 CAAATTCGCAACGCGATAGTCAAATTCGCAAATCGAAAGT
1 CAAATTCGCAACGCGAAAGTCAAATTCGC-AATCGAAAGT
13013 CAAAT
1 CAAAT
13018 GTTTTTACGC
Statistics
Matches: 71, Mismatches: 6, Indels: 16
0.76 0.06 0.17
Matches are distributed among these distances:
38 3 0.04
39 4 0.06
40 55 0.77
41 6 0.08
42 3 0.04
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.21
Consensus pattern (39 bp):
CAAATTCGCAACGCGAAAGTCAAATTCGCAATCGAAAGT
Found at i:12994 original size:60 final size:61
Alignment explanation
Indices: 12872--13003 Score: 178
Period size: 60 Copynumber: 2.2 Consensus size: 61
12862 ACTCAGTTTC
* ** *
12872 CAAATTCGCAACGCGATTTTCCAAATTCGCAATGCGAAAGTCAAATTCGCAATGCGAAAGT
1 CAAATTCGCAACGCGAATTTCCAAATTCGCAACACGAAAGTCAAATTCGCAACGCGAAAGT
** *
12933 CAAATTCGCAACGCGAATTTGTAAA-TCGCAACAC-ATAAGTCAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAATTTCCAAATTCGCAACACGA-AAGTCAAATTCGCAACGCGAAAGT
12993 CAAATTCGCAA
1 CAAATTCGCAA
13004 ATCGAAAGTC
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
59 1 0.02
60 40 0.63
61 22 0.35
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (61 bp):
CAAATTCGCAACGCGAATTTCCAAATTCGCAACACGAAAGTCAAATTCGCAACGCGAAAGT
Found at i:13013 original size:20 final size:20
Alignment explanation
Indices: 12893--13017 Score: 100
Period size: 20 Copynumber: 6.2 Consensus size: 20
12883 CGCGATTTTC
12893 CAAATTCGC-AATGCGAAAGT
1 CAAATTCGCAAAT-CGAAAGT
12913 CAAATTCGC-AATGCGAAAGT
1 CAAATTCGCAAAT-CGAAAGT
** *
12933 CAAATTCGCAACGCGAATTTGT
1 CAAATTCGCAAATCGAA--AGT
12955 -AAA-TCGCAACA-C-ATAAGT
1 CAAATTCGCAA-ATCGA-AAGT
** *
12973 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAAATCGAAAGT
12993 CAAATTCGCAAATCGAAAGT
1 CAAATTCGCAAATCGAAAGT
13013 CAAAT
1 CAAAT
13018 GTTTTTACGC
Statistics
Matches: 86, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
18 2 0.02
19 4 0.05
20 73 0.85
21 5 0.06
22 2 0.02
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAAATCGAAAGT
Found at i:13176 original size:22 final size:22
Alignment explanation
Indices: 13151--13193 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
13141 CGACACCCGT
13151 CCCCATCTCCGACGAAATCCGA
1 CCCCATCTCCGACGAAATCCGA
*
13173 CCCCATTTCCGACGAAATCCG
1 CCCCATCTCCGACGAAATCCG
13194 TCTATCTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.44, G:0.14, T:0.16
Consensus pattern (22 bp):
CCCCATCTCCGACGAAATCCGA
Found at i:13490 original size:19 final size:20
Alignment explanation
Indices: 13452--13492 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
13442 CACCAAATTT
13452 GCAACGCGAAAATGAAAATC
1 GCAACGCGAAAATGAAAATC
*
13472 GCAACGCGAAACT-AAAATC
1 GCAACGCGAAAATGAAAATC
13491 GC
1 GC
13493 GTTGCGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (20 bp):
GCAACGCGAAAATGAAAATC
Found at i:15677 original size:21 final size:21
Alignment explanation
Indices: 15651--15725 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
15641 GATGCACCTA
*
15651 TCATCATTCAAGAGGCCCCTC
1 TCATCATTCAAGAAGCCCCTC
*
15672 TCATCATTGAAGAAGCCCCTC
1 TCATCATTCAAGAAGCCCCTC
* * * *
15693 CCACCATTCAAGATGCCCCTG
1 TCATCATTCAAGAAGCCCCTC
*
15714 TCATCGTTCAAG
1 TCATCATTCAAG
15726 TGGTCTCGCC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.25, C:0.36, G:0.15, T:0.24
Consensus pattern (21 bp):
TCATCATTCAAGAAGCCCCTC
Found at i:17177 original size:14 final size:14
Alignment explanation
Indices: 17141--17194 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
17131 TTTTGATTAA
17141 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
17155 ATGAATTGTAAAAG
1 TTGATTTGTAAAAG
** *
17169 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
17183 TTGATTTGTAAA
1 TTGATTTGTAAA
17195 TAAGAATTTT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:17328 original size:20 final size:20
Alignment explanation
Indices: 17302--17357 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
17292 GTTGAAGGTA
17302 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
17322 TAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
17342 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
17358 TTTTCGGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:17669 original size:39 final size:39
Alignment explanation
Indices: 17613--17699 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
17603 TCAAGTTGTA
*
17613 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGAACCATATGAGATTTG
* *
17652 GATTTTGATTTCGTTTTGCTTGGAACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGAACCATATGAGATTTG
17691 GATTTTGAT
1 GATTTTGAT
17700 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.18, C:0.13, G:0.22, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGAACCATATGAGATTTG
Found at i:18031 original size:18 final size:18
Alignment explanation
Indices: 18008--18044 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17998 TGAAATTTAT
18008 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
18026 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
18044 A
1 A
18045 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:18465 original size:25 final size:25
Alignment explanation
Indices: 18431--18480 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
18421 ATTATTTTTC
*
18431 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
18456 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
18481 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:18569 original size:20 final size:20
Alignment explanation
Indices: 18546--18612 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
18536 TGTTAAAGGT
* *
18546 AAATTTGCAACACGAAAGTC
1 AAATTCGCAACGCGAAAGTC
* *
18566 AAATTCGCTACGCGATAGTC
1 AAATTCGCAACGCGAAAGTC
18586 AAATTCGCAACGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
18606 AAATTCG
1 AAATTCG
18613 GTTTGCGATT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAGTC
Found at i:18959 original size:18 final size:18
Alignment explanation
Indices: 18936--18971 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
18926 AAGCCGGTTG
*
18936 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
18954 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
18972 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:21251 original size:24 final size:24
Alignment explanation
Indices: 21224--21277 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
21214 TTCCATCACC
*
21224 ATCAAAATCCGTGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
* *
21248 ATCAAAGTCCGGGTATTGGCCAAG
1 ATCAAAATCCGGGTATTGACCAAG
21272 ATCAAA
1 ATCAAA
21278 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:21424 original size:12 final size:12
Alignment explanation
Indices: 21403--21436 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
21393 GGTTGTGGGT
*
21403 TTTGAGATTGTG
1 TTTGATATTGTG
21415 TTTGATATTGTG
1 TTTGATATTGTG
*
21427 TTTGGTATTG
1 TTTGATATTG
21437 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:22048 original size:22 final size:22
Alignment explanation
Indices: 22022--22064 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
22012 TGTAAAAAAA
*
22022 TAGATATGGGGAA-GGATGTCGT
1 TAGATAT-AGGAACGGATGTCGT
22044 TAGATATAGGAACGGATGTCG
1 TAGATATAGGAACGGATGTCG
22065 CCGGAGAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.30, C:0.07, G:0.37, T:0.26
Consensus pattern (22 bp):
TAGATATAGGAACGGATGTCGT
Found at i:22220 original size:20 final size:20
Alignment explanation
Indices: 22195--22250 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
22185 GAAATTAAAT
22195 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
* * *
22215 TCGCGTTACAAATTTGACTT
1 TCGCGTTGCGAATTTGACTA
22235 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
22251 TTGGTCATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:25622 original size:26 final size:26
Alignment explanation
Indices: 25586--25662 Score: 129
Period size: 26 Copynumber: 3.0 Consensus size: 26
25576 ATTTTGATGA
25586 ATCATTA-TGCCAACTAATGCACTTT
1 ATCATTACTGCCAACTAATGCACTTT
*
25611 ATCATTGCTGCCAACTAATGCACTTT
1 ATCATTACTGCCAACTAATGCACTTT
*
25637 ATCATTACTGTCAACTAATGCACTTT
1 ATCATTACTGCCAACTAATGCACTTT
25663 CGGTGCATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
25 6 0.12
26 42 0.88
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (26 bp):
ATCATTACTGCCAACTAATGCACTTT
Found at i:32644 original size:33 final size:34
Alignment explanation
Indices: 32598--32672 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 34
32588 AATATTATCA
* *
32598 TTTCTAATATTATTTAT-GTTCAATCTTTTAAAC
1 TTTCTAATTTTATTTATAATTCAATCTTTTAAAC
* *
32631 TTTCTAATTTTATTTATAATTCGATTTTTTAAAC
1 TTTCTAATTTTATTTATAATTCAATCTTTTAAAC
32665 TTTC-AATT
1 TTTCTAATT
32673 CCAAATTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
33 20 0.54
34 17 0.46
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.57
Consensus pattern (34 bp):
TTTCTAATTTTATTTATAATTCAATCTTTTAAAC
Found at i:35011 original size:19 final size:19
Alignment explanation
Indices: 34989--35026 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
34979 TTCTTTACCA
34989 CAAAATGATATATTTATAG
1 CAAAATGATATATTTATAG
35008 CAAAATGATATATTTATAG
1 CAAAATGATATATTTATAG
35027 GGACAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (19 bp):
CAAAATGATATATTTATAG
Found at i:37071 original size:58 final size:58
Alignment explanation
Indices: 36963--37072 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
36953 AAATAATGAC
* *
36963 CAAAATAAAATAAATTAAAAGTATAGAATTAAATTGAAAAATATATAAAATTCATGGT
1 CAAAATAAAATAAATTAAAAGTATAGAATTAAAATGAAAAATATACAAAATTCATGGT
*
37021 CAAAATGAAAAT-AATTAAAA-TATCAGAGATTAAAATGTAAAATAT-CAAAATT
1 CAAAAT-AAAATAAATTAAAAGTAT-AGA-ATTAAAATGAAAAATATACAAAATT
37073 AAAGGCTCTA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
57 3 0.07
58 23 0.50
59 20 0.43
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (58 bp):
CAAAATAAAATAAATTAAAAGTATAGAATTAAAATGAAAAATATACAAAATTCATGGT
Found at i:37792 original size:22 final size:24
Alignment explanation
Indices: 37767--37814 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
37757 CTGTTTTTGT
37767 TTGGT-GTTGTT-GTGCTTTTCTC
1 TTGGTGGTTGTTCGTGCTTTTCTC
*
37789 TTGGTGGTTGTTCGTGTTTTTCTC
1 TTGGTGGTTGTTCGTGCTTTTCTC
37813 TT
1 TT
37815 TCGCAGGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.22
23 6 0.26
24 12 0.52
ACGTcount: A:0.00, C:0.12, G:0.27, T:0.60
Consensus pattern (24 bp):
TTGGTGGTTGTTCGTGCTTTTCTC
Found at i:37814 original size:24 final size:22
Alignment explanation
Indices: 37758--37814 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 22
37748 TTTCTTGCTC
*
37758 TGTTTTTGT-TTGGTGTTGTTG
1 TGTTTTTCTCTTGGTGTTGTTG
*
37779 TGCTTTTCTCTTGGTGGTTGTTCG
1 TGTTTTTCTCTTGGT-GTTGTT-G
37803 TGTTTTTCTCTT
1 TGTTTTTCTCTT
37815 TCGCAGGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.23
22 5 0.17
23 6 0.20
24 12 0.40
ACGTcount: A:0.00, C:0.11, G:0.26, T:0.63
Consensus pattern (22 bp):
TGTTTTTCTCTTGGTGTTGTTG
Found at i:38244 original size:3 final size:3
Alignment explanation
Indices: 38238--38272 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
38228 AATAATAATA
38238 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
38273 ATTTATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:38283 original size:3 final size:3
Alignment explanation
Indices: 38277--38309 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
38267 TATTATATTT
38277 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
38310 ATGGGCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:40481 original size:12 final size:13
Alignment explanation
Indices: 40464--40494 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40454 ACATAATCTG
40464 AAAATT-ATTTTT
1 AAAATTCATTTTT
40476 AAAATTCATTTTT
1 AAAATTCATTTTT
40489 AAAATT
1 AAAATT
40495 TATAAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (13 bp):
AAAATTCATTTTT
Found at i:41159 original size:2 final size:2
Alignment explanation
Indices: 41152--41179 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41142 ACAAACAAGA
41152 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41180 TTTATTCGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44128 original size:22 final size:21
Alignment explanation
Indices: 44085--44326 Score: 168
Period size: 22 Copynumber: 10.7 Consensus size: 21
44075 TATTATACAG
44085 TTTTAAAAACATATAATATATAGT
1 TTTTAAAAAC--AT-ATATATAGT
* *
44109 TTTTGAAAATATATAGTATAGT
1 TTTTAAAAACATATA-TATAGT
44131 TTTTAAAAAAACATATAATATAGT
1 TTTT--AAAAACATAT-ATATAGT
*
44155 TTTTGAAAACATATTATATAGT
1 TTTTAAAAACATA-TATATAGT
* *
44177 TTTAAAAAAAATATATATAG-
1 TTTTAAAAACATATATATAGT
* *
44197 TTTT-AAAATATATAGTGTAG-
1 TTTTAAAAACATATA-TATAGT
44217 TTTTAAAAACATATAGTATAGT
1 TTTTAAAAACATATA-TATAGT
*
44239 TTTTGAAAACATAT-TATAGT
1 TTTTAAAAACATATATATAGT
44259 TTTATAAATATACATATTGTTATATAGT
1 TTT-TAAA-A-ACATA----TATATAGT
* *
44287 TTTGAAAACATATAATATATATAGT
1 TTT-TAAA-A-A-CATATATATAGT
44312 TTTTGAAAAACATAT
1 TTTT-AAAAACATAT
44327 GTAATATATA
Statistics
Matches: 179, Mismatches: 21, Indels: 38
0.75 0.09 0.16
Matches are distributed among these distances:
19 9 0.05
20 20 0.11
21 27 0.15
22 55 0.31
23 7 0.04
24 27 0.15
25 15 0.08
27 1 0.01
28 15 0.08
29 3 0.02
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (21 bp):
TTTTAAAAACATATATATAGT
Found at i:44304 original size:21 final size:21
Alignment explanation
Indices: 44074--44305 Score: 157
Period size: 21 Copynumber: 10.5 Consensus size: 21
44064 ATGATAATAT
* *
44074 ATATTATACAGTTTTAAAAAC
1 ATATAATATAGTTTTAAAAAC
* *
44095 ATATAATATATAGTTTTTGAAAAT
1 ATAT-A-ATATAG-TTTTAAAAAC
*
44119 ATATAGTATAGTTTTTAAAAAAAC
1 ATATAATATAG-TTTT--AAAAAC
*
44143 ATATAATATAGTTTTTGAAAAC
1 ATATAATATAG-TTTTAAAAAC
*
44165 ATATTATATAGTTTTAAAAA-
1 ATATAATATAGTTTTAAAAAC
* *
44185 AAATATATATAGTTTT-AAAAT
1 ATATA-ATATAGTTTTAAAAAC
* *
44206 ATATAGTGTAGTTTTAAAAAC
1 ATATAATATAGTTTTAAAAAC
* *
44227 ATATAGTATAGTTTTTGAAAAC
1 ATATAATATAG-TTTTAAAAAC
44249 ATAT--TATAGTTTTATAAATATAC
1 ATATAATATAG-TTT-TAAA-A-AC
* *
44272 ATATTGTTATATAGTTTTGAAAAC
1 ATA---TAATATAGTTTTAAAAAC
44296 ATATAATATA
1 ATATAATATA
44306 TATAGTTTTT
Statistics
Matches: 172, Mismatches: 22, Indels: 34
0.75 0.10 0.15
Matches are distributed among these distances:
20 24 0.14
21 49 0.28
22 39 0.23
23 11 0.06
24 36 0.21
25 1 0.01
26 4 0.02
27 3 0.02
28 5 0.03
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.42
Consensus pattern (21 bp):
ATATAATATAGTTTTAAAAAC
Found at i:44312 original size:25 final size:28
Alignment explanation
Indices: 44279--44338 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 28
44269 TACATATTGT
44279 TATATAG-TTTTG-AAAACATA-TAATA
1 TATATAGTTTTTGAAAAACATAGTAATA
44304 TATATAGTTTTTGAAAAACATATGTAATA
1 TATATAGTTTTTGAAAAACATA-GTAATA
44333 TATATA
1 TATATA
44339 TATATAACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
25 7 0.23
26 5 0.16
27 8 0.26
29 11 0.35
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (28 bp):
TATATAGTTTTTGAAAAACATAGTAATA
Found at i:46217 original size:60 final size:61
Alignment explanation
Indices: 46144--46290 Score: 174
Period size: 60 Copynumber: 2.4 Consensus size: 61
46134 AATTTAAAGT
* * * *
46144 CTAATTTAGAATGACAGTCATATTTTGGGGAGGAAATTGAAA-TCTTTAAAAGTTTGAGG-A
1 CTAATTTAGAATGACAGTCATATTTTAGAGAGAAAATTGAAACT-TTTAAAAGTTTAAGGAA
* * * *
46204 CTAATTTAGAATGATATTCATAATTTAGAGATAAAATTGAAACTTTTAAAAGTTTAAGGAA
1 CTAATTTAGAATGACAGTCATATTTTAGAGAGAAAATTGAAACTTTTAAAAGTTTAAGGAA
* *
46265 C-AATTTAAAATGAGAGTCATATTTTA
1 CTAATTTAGAATGACAGTCATATTTTA
46291 AAGATATGTG
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
60 70 0.96
61 3 0.04
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.35
Consensus pattern (61 bp):
CTAATTTAGAATGACAGTCATATTTTAGAGAGAAAATTGAAACTTTTAAAAGTTTAAGGAA
Found at i:47975 original size:28 final size:28
Alignment explanation
Indices: 47935--47990 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
47925 TATTTAACAA
47935 AAGTAAACTACCTCAAGGGCCCTTTTAG
1 AAGTAAACTACCTCAAGGGCCCTTTTAG
47963 AAGTAAACTACCTCAAGGGCCCTTTTAG
1 AAGTAAACTACCTCAAGGGCCCTTTTAG
47991 TAGTTTAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (28 bp):
AAGTAAACTACCTCAAGGGCCCTTTTAG
Found at i:52033 original size:16 final size:16
Alignment explanation
Indices: 52008--52038 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51998 TTCGTTATAA
52008 ACGAACATAAACGAAT
1 ACGAACATAAACGAAT
*
52024 ACGAATATAAACGAA
1 ACGAACATAAACGAA
52039 CACGGTCATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.16, G:0.13, T:0.13
Consensus pattern (16 bp):
ACGAACATAAACGAAT
Found at i:53085 original size:14 final size:14
Alignment explanation
Indices: 53066--53106 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
53056 GATTGAGTTA
*
53066 AACATAAATGAACG
1 AACATAAACGAACG
*
53080 AACATAACCGAACG
1 AACATAAACGAACG
53094 AACATAAACGAAC
1 AACATAAACGAAC
53107 ATAACCGAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.56, C:0.22, G:0.12, T:0.10
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:53117 original size:14 final size:14
Alignment explanation
Indices: 53075--53117 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
53065 AAACATAAAT
53075 GAACGAACATAACC
1 GAACGAACATAACC
53089 GAACGAACAT-A--
1 GAACGAACATAACC
53100 -AACGAACATAACC
1 GAACGAACATAACC
53113 GAACG
1 GAACG
53118 TTCTCAAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 9 0.36
11 1 0.04
13 1 0.04
14 14 0.56
ACGTcount: A:0.51, C:0.26, G:0.16, T:0.07
Consensus pattern (14 bp):
GAACGAACATAACC
Found at i:55326 original size:24 final size:24
Alignment explanation
Indices: 55296--55351 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
55286 TAGAAGTTCG
*
55296 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCAAAAATTTGAGCTCA
55320 ATTGAAGCCAAAAATTTGAGCTCA
1 ATTGAAGCCAAAAATTTGAGCTCA
55344 ATTGAAGC
1 ATTGAAGC
55352 GAAAGAATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (24 bp):
ATTGAAGCCAAAAATTTGAGCTCA
Found at i:55870 original size:13 final size:13
Alignment explanation
Indices: 55852--55877 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55842 ATATAAAATT
55852 CGGTTCAACCGCG
1 CGGTTCAACCGCG
55865 CGGTTCAACCGCG
1 CGGTTCAACCGCG
55878 GTTGAACCCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.31, T:0.15
Consensus pattern (13 bp):
CGGTTCAACCGCG
Found at i:55891 original size:10 final size:11
Alignment explanation
Indices: 55863--55895 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
55853 GGTTCAACCG
*
55863 CGCGGTTCAAC
1 CGCGGTTGAAC
55874 CGCGGTTGAAC
1 CGCGGTTGAAC
55885 C-CGGTTGAAC
1 CGCGGTTGAAC
55895 C
1 C
55896 AGTGAACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.18, C:0.33, G:0.30, T:0.18
Consensus pattern (11 bp):
CGCGGTTGAAC
Found at i:56239 original size:13 final size:13
Alignment explanation
Indices: 56229--56285 Score: 60
Period size: 13 Copynumber: 4.4 Consensus size: 13
56219 TCTATGACGT
56229 GCATTTATGACAC
1 GCATTTATGACAC
56242 GCATTTATGACAC
1 GCATTTATGACAC
** * *
56255 ATATTTATAACGC
1 GCATTTATGACAC
* *
56268 TCATTTATGACGC
1 GCATTTATGACAC
56281 GCATT
1 GCATT
56286 GAGCGTCATT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (13 bp):
GCATTTATGACAC
Found at i:60017 original size:105 final size:105
Alignment explanation
Indices: 59889--60098 Score: 330
Period size: 105 Copynumber: 2.0 Consensus size: 105
59879 TTCACTATGC
* * *
59889 TTGTGAAGAGAGAAAATATAGAAGAAGAGAGGAGAATGCAGAAATGAGTAAGTTAAAAATGAAGG
1 TTGTGAAGAGAGAAAACACAGAAGAAGAGAGGAGAATGAAGAAATGAGTAAGTTAAAAATGAAGG
* *
59954 AGAGAGCCTCCTTTTATAGTTAAAAATTAAGGGTACTTAG
66 AGAGAACCTCCTTTTATAGCTAAAAATTAAGGGTACTTAG
* * *
59994 TTGTGAAGATAGAAAACACAGAAGAAGAGAGGAGAATGAAGAAATGAGTGAGTTGAAAATGAAGG
1 TTGTGAAGAGAGAAAACACAGAAGAAGAGAGGAGAATGAAGAAATGAGTAAGTTAAAAATGAAGG
* *
60059 AGATAACCTCCTTTTATAGCTAAAAATTAAGTGTACTTAG
66 AGAGAACCTCCTTTTATAGCTAAAAATTAAGGGTACTTAG
60099 GTAAAAATGT
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
105 95 1.00
ACGTcount: A:0.45, C:0.07, G:0.26, T:0.23
Consensus pattern (105 bp):
TTGTGAAGAGAGAAAACACAGAAGAAGAGAGGAGAATGAAGAAATGAGTAAGTTAAAAATGAAGG
AGAGAACCTCCTTTTATAGCTAAAAATTAAGGGTACTTAG
Found at i:64381 original size:17 final size:17
Alignment explanation
Indices: 64340--64381 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
64330 TTTATTACTT
64340 TTATTATTTTATTGATA
1 TTATTATTTTATTGATA
*
64357 TT-TGTATTTTATTTATA
1 TTAT-TATTTTATTGATA
64374 TTATTATT
1 TTATTATT
64382 ATTAATAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 20 0.91
18 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (17 bp):
TTATTATTTTATTGATA
Found at i:69023 original size:12 final size:12
Alignment explanation
Indices: 69002--69044 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
68992 TTGATCAGAG
*
69002 TTGACTGTTGAC
1 TTGACCGTTGAC
69014 TTGACCGTTGAC
1 TTGACCGTTGAC
* *
69026 ATGATCGTTGAC
1 TTGACCGTTGAC
69038 TTTGACC
1 -TTGACC
69045 AGAATTGTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 21 0.84
13 4 0.16
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (12 bp):
TTGACCGTTGAC
Found at i:70552 original size:21 final size:21
Alignment explanation
Indices: 70526--70612 Score: 72
Period size: 21 Copynumber: 4.1 Consensus size: 21
70516 TTGAGGGTTC
*
70526 TATGTGGTTCTTCGGGACAAT
1 TATGTGGTACTTCGGGACAAT
* *
70547 TATGTGGCACTTCGGTG-CAAACC
1 TATGTGGTACTTCGG-GAC-AA-T
70570 TATGT-GT-CATTCGGGACAAT
1 TATGTGGTAC-TTCGGGACAAT
* *
70590 TATGTGGTACTTCGTGAAAAT
1 TATGTGGTACTTCGGGACAAT
70611 TA
1 TA
70613 CGAGCTGTGG
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
20 5 0.10
21 31 0.60
22 11 0.21
23 5 0.10
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.34
Consensus pattern (21 bp):
TATGTGGTACTTCGGGACAAT
Found at i:78276 original size:17 final size:17
Alignment explanation
Indices: 78256--78296 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
78246 TTATTACTGT
78256 TATTATTTTATTGATAC
1 TATTATTTTATTGATAC
* *
78273 TATTATTTTATTTATAT
1 TATTATTTTATTGATAC
78290 TATTATT
1 TATTATT
78297 AATAGAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (17 bp):
TATTATTTTATTGATAC
Found at i:86115 original size:193 final size:193
Alignment explanation
Indices: 85874--86275 Score: 540
Period size: 193 Copynumber: 2.1 Consensus size: 193
85864 ACATTTATAT
* * **
85874 ATAACATCACTATATAATTAATATTCAATGACAACTAATTATGTCACTAAATTATGTAAAATTTC
1 ATAACGTCACTATATAATTAATATTCAATGACAACTAATTACGTCACTAAATTAAATAAAATTTC
* ** * *
85939 GTTATTGAT-GATTTATATCGTCATGAATAATACATTAAAATCAACATATATGTGACGAAAGAGA
66 GTTATTGATAG-CTTATATCGTCACAAATAATACATTAAAATCAACATATATATGACGAAAAAGA
* *
86003 TATTGTCAAATTTTTAGTGACATAATATAAAT-GTTACCTAATAATATTATGAATGATGTTTA-G
130 TACTGTCAAATTTTTAGTGACATAATAT--ATCGTTACCTAATAATATTATGAATGATGATTATG
86066 C
193 C
* * * ** ** *
86067 ATAACGTCACTTTATAATTTATATTCTATGACAGTTGGTTACGTCACTAAATTAAATAAGATTTC
1 ATAACGTCACTATATAATTAATATTCAATGACAACTAATTACGTCACTAAATTAAATAAAATTTC
* * *
86132 GTTATTGATAGCTTATATTGTCACAAATAATGCATTAAAATCAACTTATATATGACGAAAAAGAT
66 GTTATTGATAGCTTATATCGTCACAAATAATACATTAAAATCAACATATATATGACGAAAAAGAT
*
86197 ACTGTCACATTTTTAGTGACATAATATATCGTTACCTAATAATATTATGAATGATGATTATGC
131 ACTGTCAAATTTTTAGTGACATAATATATCGTTACCTAATAATATTATGAATGATGATTATGC
*
86260 ATAACGTCACCATATA
1 ATAACGTCACTATATA
86276 GAATGTCACC
Statistics
Matches: 181, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
191 2 0.01
192 29 0.16
193 149 0.82
194 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (193 bp):
ATAACGTCACTATATAATTAATATTCAATGACAACTAATTACGTCACTAAATTAAATAAAATTTC
GTTATTGATAGCTTATATCGTCACAAATAATACATTAAAATCAACATATATATGACGAAAAAGAT
ACTGTCAAATTTTTAGTGACATAATATATCGTTACCTAATAATATTATGAATGATGATTATGC
Found at i:87208 original size:18 final size:19
Alignment explanation
Indices: 87166--87210 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
87156 ATGATTTCAA
*
87166 AAAATAAAAATTAGACTCT
1 AAAATAAAAATTAAACTCT
*
87185 AAAATAAAAA-TAAACTTT
1 AAAATAAAAATTAAACTCT
*
87203 ATAATAAA
1 AAAATAAA
87211 TATCAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAATAAAAATTAAACTCT
Found at i:89181 original size:2 final size:2
Alignment explanation
Indices: 89176--89217 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
89166 ATTTTTTAAG
89176 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
89217 T
1 T
89218 GTAAGTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:94159 original size:28 final size:27
Alignment explanation
Indices: 94086--94159 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
94076 AAATATTAAG
* * *
94086 AAATAAAATGATAGACATA-TAATATAT
1 AAATAAAAT-ATAAACATATTAAGAAAT
* *
94113 AAATAAAATAAAAAAATATTAAGAAAT
1 AAATAAAATATAAACATATTAAGAAAT
*
94140 AAAGTAAAATATACACATAT
1 AAA-TAAAATATAAACATAT
94160 ATACATAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
26 6 0.16
27 18 0.49
28 13 0.35
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.26
Consensus pattern (27 bp):
AAATAAAATATAAACATATTAAGAAAT
Found at i:94266 original size:2 final size:2
Alignment explanation
Indices: 94261--94306 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
94251 AAAGTTAATG
94261 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
94303 -T AT A
1 AT AT A
94307 ATTAACGTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96312 original size:105 final size:105
Alignment explanation
Indices: 95942--96777 Score: 1127
Period size: 105 Copynumber: 8.0 Consensus size: 105
95932 GTATTGTTCC
* * * * * ** * * * *
95942 GAGTCTAATATCCTCCGCTGTGAAGTTGAATTTGGTTTTGGAACTGGGAAATTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATCGGCTCCGAAATTGGGAAGTTG-TTGTTGACAA
** * * * *
96007 TTAGCCGCCCCTTCG-CTGTGAAGTT-AAGCTTGTGTTGTCTC
65 CCAGCGGTCCCTTCGTC-GTGAAGTTGAA-CTTGCGTTGTCTG
* * * * * **
96048 GAGTCTAATATCCTTCACTGTGAAGTTGAAATTGACTCTG-AA-T--GAAACT-TTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATCGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
* *
96108 CAGCGATCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
96148 GAGTCCAATATCC-T---TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATCGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
*
96209 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
96249 GAGTCCGATATTCTTTGCTGTGAAGTTGAAATCGGCTCCAAAATTGGGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATCGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
*
96314 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
96354 GAGTCCGATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATCGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
96419 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
96459 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATCAGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATCGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
*
96524 CGGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * * *
96564 GAGTCCAATATCATTCTCTGTGAAGTTGAAATCGGCTCTGAAATTGGGAAGCTGTTGCTGAAAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATCGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
*
96629 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
96669 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCCGAAATTGGGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATCGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
96734 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
96774 GAGT
1 GAGT
96778 GATATCCTCC
Statistics
Matches: 658, Mismatches: 61, Indels: 23
0.89 0.08 0.03
Matches are distributed among these distances:
96 21 0.03
97 2 0.00
98 1 0.00
99 1 0.00
100 53 0.08
101 62 0.09
102 6 0.01
104 1 0.00
105 477 0.72
106 34 0.05
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATCGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:108020 original size:14 final size:14
Alignment explanation
Indices: 108001--108033 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
107991 GATAAACTGG
108001 AAATAGAGAA-AGTA
1 AAATAGAGAAGAG-A
108015 AAATAGAGAAGAGA
1 AAATAGAGAAGAGA
108029 AAATA
1 AAATA
108034 AGTAAATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (14 bp):
AAATAGAGAAGAGA
Found at i:110146 original size:23 final size:23
Alignment explanation
Indices: 110119--110168 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
110109 CTACTAATAT
*
110119 AAAACCGCCCATAACATCTAGTA
1 AAAACCACCCATAACATCTAGTA
* **
110142 AAAACCACCCTTAATTTCTAGTA
1 AAAACCACCCATAACATCTAGTA
110165 AAAA
1 AAAA
110169 AAATCATTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.46, C:0.26, G:0.06, T:0.22
Consensus pattern (23 bp):
AAAACCACCCATAACATCTAGTA
Found at i:110443 original size:42 final size:42
Alignment explanation
Indices: 110380--110495 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 42
110370 CTTCACTGTC
* *
110380 ATGGCTGG-GTTTATAACAAAAATGCCACTAAA-TTACATGACT
1 ATGGC-GGCGTTTATAA-AAAAATGCCACTAAAGGTACAAGACT
110422 ATGGCGGCGTTTATATAAAAAATGCCA-TAAAGGTACAAGACT
1 ATGGCGGCGTTTATA-AAAAAATGCCACTAAAGGTACAAGACT
* *
110464 ATTGCGGCGTTTGA-ACAAAAATGCCACTAAAG
1 ATGGCGGCGTTT-ATAAAAAAATGCCACTAAAG
110496 TACGAGTATA
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
41 16 0.25
42 47 0.72
43 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (42 bp):
ATGGCGGCGTTTATAAAAAAATGCCACTAAAGGTACAAGACT
Found at i:110517 original size:41 final size:40
Alignment explanation
Indices: 110437--110574 Score: 111
Period size: 41 Copynumber: 3.4 Consensus size: 40
110427 GGCGTTTATA
* * *
110437 TAAAAAATGCCA-TAAAGGTACAAG-ACTATTGCGGCGTTTG
1 TAAAAAACGCCACTAAA-GTACAAGTA-TATAGCGGTGTTTG
* * *
110477 AACAAAAATGCCACTAAAGTACGAGTATATAGCGGTGTTTG
1 TA-AAAAACGCCACTAAAGTACAAGTATATAGCGGTGTTTG
* * * * *
110518 TATTAAAACGCCACTAAA-AACTAGTCTATAGCGATGTTTG
1 TA-AAAAACGCCACTAAAGTACAAGTATATAGCGGTGTTTG
*
110558 TATAAAACGCCACTAAA
1 TAAAAAACGCCACTAAA
110575 TACCCCTTAA
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
39 15 0.18
40 21 0.25
41 42 0.51
42 5 0.06
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (40 bp):
TAAAAAACGCCACTAAAGTACAAGTATATAGCGGTGTTTG
Found at i:110558 original size:40 final size:40
Alignment explanation
Indices: 110481--110574 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 40
110471 CGTTTGAACA
* * *
110481 AAAATGCCACTAAAGTACGAGTATATAGCGGTGTTTGTATT
1 AAAACGCCACTAAAGAACGAGTATATAGCGATGTTTGTA-T
* *
110522 AAAACGCCACTAAA-AACTAGTCTATAGCGATGTTTGTAT
1 AAAACGCCACTAAAGAACGAGTATATAGCGATGTTTGTAT
110561 AAAACGCCACTAAA
1 AAAACGCCACTAAA
110575 TACCCCTTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 15 0.31
40 20 0.42
41 13 0.27
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (40 bp):
AAAACGCCACTAAAGAACGAGTATATAGCGATGTTTGTAT
Found at i:112878 original size:15 final size:16
Alignment explanation
Indices: 112844--112881 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
112834 TATTTAAGTG
*
112844 ATAAAAGCGATTAATAA
1 ATAAAAGCAATT-ATAA
112861 ATAAAAGCAATT-TAA
1 ATAAAAGCAATTATAA
112876 ATAAAA
1 ATAAAA
112882 ATAAGAGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
17 11 0.55
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.24
Consensus pattern (16 bp):
ATAAAAGCAATTATAA
Found at i:125802 original size:22 final size:23
Alignment explanation
Indices: 125777--125827 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
125767 ATATTATATT
125777 ATATTTTTAAAATTATTAAT-AA
1 ATATTTTTAAAATTATTAATAAA
* * *
125799 ATATATTTTAATATTTTTATTAAA
1 ATAT-TTTTAAAATTATTAATAAA
125823 ATATT
1 ATATT
125828 ATCATATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 4 0.17
23 14 0.58
24 6 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATATTTTTAAAATTATTAATAAA
Found at i:126026 original size:25 final size:24
Alignment explanation
Indices: 125995--126073 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 24
125985 TATGATTGAG
125995 TATATTATTGTAATAATAATATTAT
1 TATATTATTGTAATAATAATATT-T
*
126020 TATATTATAT-TAATAAAAATATTT
1 TATATTAT-TGTAATAATAATATTT
*
126044 TA-AATA-TGTTAATAATTAATATTT
1 TATATTATTG-TAATAA-TAATATTT
126068 T-TATTA
1 TATATTA
126074 AAATGATACT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
21 1 0.02
23 9 0.20
24 14 0.31
25 20 0.44
26 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.52
Consensus pattern (24 bp):
TATATTATTGTAATAATAATATTT
Found at i:127647 original size:4 final size:4
Alignment explanation
Indices: 127638--127666 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
127628 CGCTAACTTG
127638 TTAT TTAT TTAT TTAT TTAT TTA- TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
127667 TATATTCGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:127858 original size:14 final size:14
Alignment explanation
Indices: 127839--127874 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
127829 TTTTTATTTA
*
127839 TTTAATTTCAGTCC
1 TTTAATTTCAGTAC
*
127853 TTTAATTTCATTAC
1 TTTAATTTCAGTAC
127867 TTTAATTT
1 TTTAATTT
127875 TCTATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.14, G:0.03, T:0.58
Consensus pattern (14 bp):
TTTAATTTCAGTAC
Found at i:128035 original size:2 final size:2
Alignment explanation
Indices: 127973--128020 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
127963 AGCCCCATGA
127973 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
128015 AT AT AT
1 AT AT AT
128021 GCATATTTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:129826 original size:3 final size:3
Alignment explanation
Indices: 129818--129843 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
129808 CATTCATTAA
129818 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
129844 GATAAGGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:131484 original size:26 final size:26
Alignment explanation
Indices: 131449--131503 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
131439 ACCTGACCCG
131449 AACCGTTAACTTTGACCCGGCCCGTT
1 AACCGTTAACTTTGACCCGGCCCGTT
* *
131475 AACCGTTAACTTTGACCCGGGCTGTT
1 AACCGTTAACTTTGACCCGGCCCGTT
131501 AAC
1 AAC
131504 TTTGGTCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (26 bp):
AACCGTTAACTTTGACCCGGCCCGTT
Found at i:140728 original size:64 final size:65
Alignment explanation
Indices: 140640--140798 Score: 275
Period size: 64 Copynumber: 2.4 Consensus size: 65
140630 TATATGATAT
140640 AAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATATTA
1 AAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATATTA
*
140705 AAATT-AATATCTATAATATAATATTAAAATATTAATATTTAATTTATTTAAAAAATTAATATTA
1 AAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATATTA
* *
140769 AAATTAAATATAATATAATATAAAATTAAA
1 AAATTAAATAT-CTATAATATAATATTAAA
140799 TATAAAACCT
Statistics
Matches: 89, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
64 63 0.71
65 10 0.11
66 16 0.18
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (65 bp):
AAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATATTA
Found at i:140747 original size:26 final size:25
Alignment explanation
Indices: 140694--140775 Score: 89
Period size: 25 Copynumber: 3.2 Consensus size: 25
140684 TTATTTAAAA
140694 AATTAATATT-AAAATTAATATCTAT
1 AATTAATATTAAAAATTAATAT-TAT
140719 AATATAATATTAAAATATTAATATT-T
1 AAT-TAATATTAAAA-ATTAATATTAT
* *
140745 AATTTAT-TTAAAAAATTAATATTAA
1 AATTAATATT-AAAAATTAATATTAT
140770 AATTAA
1 AATTAA
140776 ATATAATATA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
24 11 0.22
25 15 0.31
26 11 0.22
27 4 0.08
28 8 0.16
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (25 bp):
AATTAATATTAAAAATTAATATTAT
Found at i:140762 original size:24 final size:27
Alignment explanation
Indices: 140697--140768 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 27
140687 TTTAAAAAAT
140697 TAATATT--AAAATTAATATCTATAATA
1 TAATATTAAAAAATTAATAT-TATAATA
*
140723 TAATATTAAAATATTAATATT-TAAT-
1 TAATATTAAAAAATTAATATTATAATA
*
140748 TTAT-TTAAAAAATTAATATTA
1 TAATATTAAAAAATTAATATTA
140769 AAATTAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 15 0.38
25 3 0.08
26 11 0.28
27 1 0.03
28 10 0.25
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (27 bp):
TAATATTAAAAAATTAATATTATAATA
Found at i:141360 original size:17 final size:18
Alignment explanation
Indices: 141327--141360 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
141317 CCACTATTAG
141327 TGAACCGGTCAGAACCGT
1 TGAACCGGTCAGAACCGT
*
141345 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
141361 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGT
Found at i:141894 original size:23 final size:22
Alignment explanation
Indices: 141868--141910 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
141858 TATAAAAAAT
141868 TATTTTTTATTAAATATTTTTGG
1 TATTTTTTATTAAAT-TTTTTGG
*
141891 TATTTTTTATTTAATTTTTT
1 TATTTTTTATTAAATTTTTT
141911 AAATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (22 bp):
TATTTTTTATTAAATTTTTTGG
Found at i:143060 original size:103 final size:103
Alignment explanation
Indices: 142942--143179 Score: 297
Period size: 104 Copynumber: 2.3 Consensus size: 103
142932 AATTTCAAAT
* * *
142942 TTGTTTTACTTGAAACAATAAATTTTATCTCACTCGAGATTGTTATTTC-GAA-TCAAA-TTTCA
1 TTGTTTCACTCGAAACAA-AAATTTTATCTCACTCGAGATTGTT-TTTCAGAAGACAAACTTT-A
*
143004 TCTCGCTTGAGAT-GGTTTCCTTTGAAATACAAGTTTTGAAA
63 TCTCGCTTGAG-TCAGTTTCCTTTGAAATACAAGTTTTGAAA
* * * *
143045 TTGTTTCACTCGAAACAAAGAATTTTGTCTCACTTGATATTGTTTTTCATAAGACAAACTTTATC
1 TTGTTTCACTCGAAACAAA-AATTTTATCTCACTCGAGATTGTTTTTCAGAAGACAAACTTTATC
*
143110 TCGCTTGAGTCAGTTTCCTTTGAAATGCAAGTTTTGAAA
65 TCGCTTGAGTCAGTTTCCTTTGAAATACAAGTTTTGAAA
* *
143149 TTGTTTCACCCGAAA-TAAAATTTTATCTCAC
1 TTGTTTCACTCGAAACAAAAATTTTATCTCAC
143180 ATAAGATAAC
Statistics
Matches: 118, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
102 17 0.14
103 42 0.36
104 56 0.47
105 3 0.03
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (103 bp):
TTGTTTCACTCGAAACAAAAATTTTATCTCACTCGAGATTGTTTTTCAGAAGACAAACTTTATCT
CGCTTGAGTCAGTTTCCTTTGAAATACAAGTTTTGAAA
Found at i:143758 original size:116 final size:118
Alignment explanation
Indices: 143575--143796 Score: 313
Period size: 117 Copynumber: 1.9 Consensus size: 118
143565 AACAAAAAAA
* * * *
143575 GAGAAGAAGTTCATTATGAGAAGAACTTGTTCAACCTTTTCCCAAATCCATCACAAAAAAAGGTG
1 GAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACATTTTCCCAAATACATCACAAAAAAAGGTG
** * *
143640 GATCGAAATTTTCAATGG-AGAGTTTATAATGAGAAGAACTAGTCCAAAAAGG
66 GATCGAAATTCCCAATGGAAAAGTTCATAATGAGAAGAACTAGTCCAAAAAGG
* * *
143692 GAGAAGAAGTTCGTAATAAGAAGAACTTGTT-AACATTTTCCCAAATACATCACAGAAAGAGGTG
1 GAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACATTTTCCCAAATACATCACAAAAAAAGGTG
* *
143756 GATTGACATTCCCAATGGAAAAGTTCATAATGAGAAGAACT
66 GATCGAAATTCCCAATGGAAAAGTTCATAATGAGAAGAACT
143797 TGTAGCTTAG
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
116 43 0.47
117 48 0.53
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.24
Consensus pattern (118 bp):
GAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACATTTTCCCAAATACATCACAAAAAAAGGTG
GATCGAAATTCCCAATGGAAAAGTTCATAATGAGAAGAACTAGTCCAAAAAGG
Found at i:167510 original size:24 final size:25
Alignment explanation
Indices: 167461--167512 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
167451 TTCATAAGAT
*
167461 AGTTTAATTCATGATGCAAATAAAA
1 AGTTAAATTCATGATGCAAATAAAA
167486 AGTTAAATTCATGATGCAAATAAAA
1 AGTTAAATTCATGATGCAAATAAAA
167511 AG
1 AG
167513 ATACCTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (25 bp):
AGTTAAATTCATGATGCAAATAAAA
Found at i:194568 original size:17 final size:16
Alignment explanation
Indices: 194544--194582 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
194534 TGCCTTCAAA
194544 TTTTTAACATTAA-ATT
1 TTTTTAACA-TAATATT
194560 TTATTTAACATAATATT
1 TT-TTTAACATAATATT
194577 TTTTTA
1 TTTTTA
194583 TTTTAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTTAACATAATATT
Found at i:194905 original size:23 final size:22
Alignment explanation
Indices: 194862--194906 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
194852 TCATATAAAA
* * *
194862 TTAAAAAAAAATTATATATTTT
1 TTAAAAAAAAAATAGAAATTTT
194884 TTAAAAAAGAAAATAGAAATTTT
1 TTAAAAAA-AAAATAGAAATTTT
194907 GAAATAACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
TTAAAAAAAAAATAGAAATTTT
Found at i:196227 original size:15 final size:15
Alignment explanation
Indices: 196207--196235 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
196197 AAAAAAAGTT
196207 TGGTTAATTCGGTTA
1 TGGTTAATTCGGTTA
196222 TGGTTAATTCGGTT
1 TGGTTAATTCGGTT
196236 CGGTCGGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (15 bp):
TGGTTAATTCGGTTA
Found at i:200045 original size:22 final size:22
Alignment explanation
Indices: 199998--200056 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
199988 ACCCTACAGC
* ** *
199998 TGTTTGGTACATGTTCCGCTGT
1 TGTTTGGTACTTGTTCCAATGA
200020 TGTTTGGTACTTGTTCCAATGA
1 TGTTTGGTACTTGTTCCAATGA
*
200042 TG-TTGGTAATTGTTC
1 TGTTTGGTACTTGTTC
200057 GGCCAGCATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 12 0.38
22 20 0.62
ACGTcount: A:0.14, C:0.14, G:0.25, T:0.47
Consensus pattern (22 bp):
TGTTTGGTACTTGTTCCAATGA
Found at i:205661 original size:38 final size:38
Alignment explanation
Indices: 205618--205694 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
205608 CTTGGAAAAT
*
205618 TGACCTCTAAAGATAAAATCTTCTGATCTTCAATAACA
1 TGACCTCTAAAGATAAAATCTTCTAATCTTCAATAACA
** *
205656 TGACCTCTAAAGATGGAATCTTCTAATCTTCAGTAACA
1 TGACCTCTAAAGATAAAATCTTCTAATCTTCAATAACA
205694 T
1 T
205695 TTGGACTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.32
Consensus pattern (38 bp):
TGACCTCTAAAGATAAAATCTTCTAATCTTCAATAACA
Found at i:208457 original size:90 final size:92
Alignment explanation
Indices: 208062--208458 Score: 228
Period size: 93 Copynumber: 4.3 Consensus size: 92
208052 AAGTCGTTGT
* * * * * *
208062 ATTCGAGGTAGGACATGCTACCCAATCACTATGATGAACTAGAAATAAGGCATAACTT-C-ATGA
1 ATTCGAGGTAGGACAGGCTACCCAATCACTATGATGAACCAAAAATATGACGTAACTTACAAT-A
* * *
208125 CGGAAGCATCATCC-C--TACAAAATTCATGGC
65 ---AAG-AT-GTCCACTTTACAAAAGTCATGAC
* * * * * * *
208155 ATTCGAGGTAGGACAGACTACTCAAT-ATTTTTGATGAACCAAAAA-AGTGATGTAACTT-TAAG
1 ATTCGAGGTAGGACAGGCTACCCAATCA-CTATGATGAACCAAAAATA-TGACGTAACTTACAAT
*
208217 ACAAGCA--TCCACTTTACAAAAGAAGTCAT-ATT
64 A-AAG-ATGTCCACTTTAC--AA-AAGTCATGA-C
* * *
208249 ATTCGAGGCAGGACAGGCTACCCAATCACTATGATGAACCATAAATGTGACGTAACTTCACAATA
1 ATTCGAGGTAGGACAGGCTACCCAATCACTATGATGAACCAAAAATATGACGTAACTT-ACAATA
* * * *
208314 AAGATGTCTACTTTATAAAATTCATGGC
65 AAGATGTCCACTTTACAAAAGTCATGAC
* * ** ** *
208342 ATTCGAGGTAAGAC-GGACAACCCAATTGCTATGATGAACCAAAAATATGGTGTAACTT-C-ATG
1 ATTCGAGGTAGGACAGG-CTACCCAATCACTATGATGAACCAAAAATATGACGTAACTTACAATA
** * *
208404 GTGGTGTCCACTTTACAGAAGTCATGAC
65 AAGATGTCCACTTTACAAAAGTCATGAC
*
208432 ATTCGAGGTAGGACATGCTACCCAATC
1 ATTCGAGGTAGGACAGGCTACCCAATC
208459 GTTGTAATAA
Statistics
Matches: 231, Mismatches: 54, Indels: 41
0.71 0.17 0.13
Matches are distributed among these distances:
88 3 0.01
89 1 0.00
90 43 0.19
91 10 0.04
92 4 0.02
93 98 0.42
94 57 0.25
95 4 0.02
96 11 0.05
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (92 bp):
ATTCGAGGTAGGACAGGCTACCCAATCACTATGATGAACCAAAAATATGACGTAACTTACAATAA
AGATGTCCACTTTACAAAAGTCATGAC
Found at i:215665 original size:89 final size:88
Alignment explanation
Indices: 215572--215771 Score: 233
Period size: 88 Copynumber: 2.3 Consensus size: 88
215562 CTAGTTTAGT
* *
215572 AGTGAAGCAAATCAACTCAGATCATGTCTCCCCT-AAATA-GCGACAAAATGGATCATCAACTTA
1 AGTGAAGCAAATCAACTCAGATCATGTCT-CACTAAAAAATG-GA-AAAATGGATCATCAACTTA
* * * *
215635 TCCGGATTTGACCTTCCTGAAGTAGC
63 TCCAGATTTAACATTCCTAAAGTAGC
* * * * *
215661 AGTGAAGAAAATCAACTTAGATCATTTCTCACTAAAAAATGGAAAATTTGATCATCAACTTATCC
1 AGTGAAGCAAATCAACTCAGATCATGTCTCACTAAAAAATGGAAAAATGGATCATCAACTTATCC
215726 AGATTTAACATTCCTAAAGTAGC
66 AGATTTAACATTCCTAAAGTAGC
* * *
215749 AGTGAACCAAATCAGCCCAGATC
1 AGTGAAGCAAATCAACTCAGATC
215772 TTATCTATTG
Statistics
Matches: 93, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
88 60 0.65
89 32 0.34
90 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (88 bp):
AGTGAAGCAAATCAACTCAGATCATGTCTCACTAAAAAATGGAAAAATGGATCATCAACTTATCC
AGATTTAACATTCCTAAAGTAGC
Found at i:219955 original size:388 final size:390
Alignment explanation
Indices: 218969--220110 Score: 1515
Period size: 391 Copynumber: 2.9 Consensus size: 390
218959 ATCTTAAAAT
* * *
218969 AATTAATAAGATTTTAAGGTACCTCAAGATGACACCTA-ACAC--ACTGATTTTCAGGAAGAATG
1 AATTAATAGGATTTTAAAGTATCTCAAGATGACACCTAGACACAGACTGATTTTCAGGAAGAATG
* * * * *
219031 GGAATTGCATGGTAGAAATTCTTTTTTATGCTAGTTGGATTAGAGAGTTAACCGACATAAGATCC
66 AGAACTGCATGGTAGAAATTCTTTTTTATGCTAGTTGGACTAGAGAGTTAACCAAAATAAGATCC
* * * * * *
219096 ACGAGTGGTTACTCCTTATCTGTCTGGAGAAACTTGGTTACTTACAGAAGTAAAAAAAAAATTG-
131 ACAAGTGGTTACTGCTCATCTGTCTGGAGAAATTTGGTTACATACAGAAGT-AAGAAAAAATTGT
* * * *
219160 -GTGTCAAGAAGTAGTGTTGAAATAGAATTCCGAGCACTAGTGCGAATTT---AAGGAATGTAGA
195 AGTGTCAAGAAGTAGTGTTGAAGTAGAATTTCGAGCACTAGTACGAATTTAAGAAGGAATGTGGA
* * * * *
219221 TATAAGGAATGTTGGAAAAAA-TAGAAGTGGACTTCAATGGACAGTTCGAGGAAAAAAGCGACAA
260 TACAAGGATTGTT-GAAAAAATTGGAAGTGGACTTCAATGGACAGTTCGAGGTAAAAAGAGACAA
* * * * *
219285 TTAATCTACCATCAACATTACCAAGAATCTTGTCTACCATGATAGAACTAAACAAATGAAAATTA
324 CTAATCTACCATCAACATTGCTAAGAATCTTGTCCACCATGATAGAACTAAACAAATGAAAATCA
219350 AC
389 AC
* *
219352 AATTAATAGGATTTTAAAGTATCTCAAGATGACACCCAGACACAGATTGATTTTCAGGAAGAATG
1 AATTAATAGGATTTTAAAGTATCTCAAGATGACACCTAGACACAGACTGATTTTCAGGAAGAATG
219417 AGAACTGCATGGTAGAAATTCTTTTTTATGCTAGTTGGACTAGAGAGTTAACCAAAATAAGATCC
66 AGAACTGCATGGTAGAAATTCTTTTTTATGCTAGTTGGACTAGAGAGTTAACCAAAATAAGATCC
* ** *
219482 ACAAGTAGTTACTGCTCAGTC-GTCTAAAGAAATTTGGTTACATATAGAAGTAAGAAAAAATTGT
131 ACAAGTGGTTACTGCTCA-TCTGTCTGGAGAAATTTGGTTACATACAGAAGTAAGAAAAAATTGT
* * *
219546 AGTGTCAAGAAGTAGTGTTGAAGTATAATTTCGAGTACTAGTACTAATTTAAGAAGGAATGTGGA
195 AGTGTCAAGAAGTAGTGTTGAAGTAGAATTTCGAGCACTAGTACGAATTTAAGAAGGAATGTGGA
* * * *
219611 TACAAGGATTGTTGAAAAAGATTGGAAGTGGACTTCAATGGACAATACAAAGTAAAAAGAGACAA
260 TACAAGGATTGTTGAAAAA-ATTGGAAGTGGACTTCAATGGACAGTTCGAGGTAAAAAGAGACAA
* * *
219676 CTAATCTACCATCAACATTGCTAAGAATATT-TCCACCATGATAGAACTAAACATATTAAAATCA
324 CTAATCTACCATCAACATTGCTAAGAATCTTGTCCACCATGATAGAACTAAACAAATGAAAATCA
219740 AC
389 AC
219742 AATTAATAGGATTTTAAAGTATCTCAAGATGACACCTAGACACAGACTGATTTTCAGGAA-AAGT
1 AATTAATAGGATTTTAAAGTATCTCAAGATGACACCTAGACACAGACTGATTTTCAGGAAGAA-T
* * * * * *
219806 GAGAACTACAT-GTAGAAATTC-TTTTTATGCTAGTTGGACTAAAGAATTAGCCTAAATATGATC
65 GAGAACTGCATGGTAGAAATTCTTTTTTATGCTAGTTGGACTAGAGAGTTAACCAAAATAAGATC
* *
219869 CACAAGTGGTTACTGCTCATCTGTCTGGAGAAATTTGATTACATACGGAAGTAAGAAAAAATTGT
130 CACAAGTGGTTACTGCTCATCTGTCTGGAGAAATTTGGTTACATACAGAAGTAAGAAAAAATTGT
* * *
219934 AGTGTCAAGAAGTAATGTTGAAGTAGAATTTTGAGCACTGGAGCTTA-GAATTTAAGAAGGAATA
195 AGTGTCAAGAAGTAGTGTTGAAGTAGAATTTCGAGCACT--AG--TACGAATTTAAGAAGGAATG
* ** *
219998 TGGATACAAAGATTGTTGAAAAAAATTGGAAGTGGACTTCAATGGATTGTTCGAGGTAAAAAGAA
256 TGGATACAAGGATTGTTG-AAAAAATTGGAAGTGGACTTCAATGGACAGTTCGAGGTAAAAAGAG
* * *
220063 AAAACCAATCTACCATCGACATTG-TCAAGAATCTTGTCCACCATGATA
320 ACAACTAATCTACCATCAACATTGCT-AAGAATCTTGTCCACCATGATA
220111 AAAATAAATA
Statistics
Matches: 663, Mismatches: 76, Indels: 31
0.86 0.10 0.04
Matches are distributed among these distances:
383 34 0.05
384 4 0.01
385 11 0.02
386 118 0.18
387 47 0.07
388 128 0.19
389 18 0.03
390 126 0.19
391 158 0.24
392 19 0.03
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (390 bp):
AATTAATAGGATTTTAAAGTATCTCAAGATGACACCTAGACACAGACTGATTTTCAGGAAGAATG
AGAACTGCATGGTAGAAATTCTTTTTTATGCTAGTTGGACTAGAGAGTTAACCAAAATAAGATCC
ACAAGTGGTTACTGCTCATCTGTCTGGAGAAATTTGGTTACATACAGAAGTAAGAAAAAATTGTA
GTGTCAAGAAGTAGTGTTGAAGTAGAATTTCGAGCACTAGTACGAATTTAAGAAGGAATGTGGAT
ACAAGGATTGTTGAAAAAATTGGAAGTGGACTTCAATGGACAGTTCGAGGTAAAAAGAGACAACT
AATCTACCATCAACATTGCTAAGAATCTTGTCCACCATGATAGAACTAAACAAATGAAAATCAAC
Found at i:232207 original size:253 final size:245
Alignment explanation
Indices: 231767--232268 Score: 797
Period size: 253 Copynumber: 2.0 Consensus size: 245
231757 AACGTTTTTA
* *
231767 AAATTTTATACATCATTTAAATATGGAAATTAAACATAAAATTTTTATTTATTAATAAAATAAAA
1 AAATTTTATACATCATCTAAATATGGAAATTAAACATAAAATATTTATTTATTAATAAAATAAAA
* *
231832 TAATTTCCAAAAATCCATTTATATATATATATATATATATATTACATAAAAACATATAATCATCG
66 TAATTTCCAAAAATCCATTTATATATATATATATATATATAATACATAAAAACATATAATCATCA
* *
231897 CATATGCAAAATATCAATAATATCATACGTATTTGAAATAATATGTACATACATAATTAGTAGTA
131 CATATACAAAATATCAATAATATCATACGCATTTGAAATAATATGTACATACATAATTAGTAGTA
* * *
231962 AATTTCAATGTCACCAAAATAATGAAGAAACGGGTAAAAGTATTGCAATG
196 AATTTCAATGTCACCAAAATAACGAAGAAACAGATAAAAGTATTGCAATG
232012 AAATTTTATACATCATCTAAATATGGAAATTAAACATAAAATATTTATTTATTAATAAAATAAAA
1 AAATTTTATACATCATCTAAATATGGAAATTAAACATAAAATATTTATTTATTAATAAAATAAAA
* *
232077 TAATTTCCAAAAGTCCATTAAGTCTGTAATATATATATATATATATATAATACATAAAATCATAT
66 TAATTTCCAAAAATCC----A-T-T-T-ATATATATATATATATATATAATACATAAAAACATAT
* *
232142 AATCATCACATGTACAAAATATCAATAATATCATATGCATTTGAAATAATATGTACATACATAAT
123 AATCATCACATATACAAAATATCAATAATATCATACGCATTTGAAATAATATGTACATACATAAT
* *
232207 TAGTAGTAAATTTCAGTGTCACCAAAATAACGAAGAAACAGATAAAAGTGTTGCAATG
188 TAGTAGTAAATTTCAATGTCACCAAAATAACGAAGAAACAGATAAAAGTATTGCAATG
232265 AAAT
1 AAAT
232269 ATAAAAGTAA
Statistics
Matches: 234, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
245 78 0.33
249 1 0.00
250 1 0.00
251 1 0.00
252 1 0.00
253 152 0.65
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (245 bp):
AAATTTTATACATCATCTAAATATGGAAATTAAACATAAAATATTTATTTATTAATAAAATAAAA
TAATTTCCAAAAATCCATTTATATATATATATATATATATAATACATAAAAACATATAATCATCA
CATATACAAAATATCAATAATATCATACGCATTTGAAATAATATGTACATACATAATTAGTAGTA
AATTTCAATGTCACCAAAATAACGAAGAAACAGATAAAAGTATTGCAATG
Found at i:242469 original size:17 final size:17
Alignment explanation
Indices: 242447--242488 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
242437 ACCGAAAATT
242447 AATAATA-ATATAATTAA
1 AATAATACAT-TAATTAA
242464 AATAATTACATTAATTAA
1 AATAA-TACATTAATTAA
*
242482 AAAAATA
1 AATAATA
242489 GGTAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 13 0.59
19 2 0.09
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAATACATTAATTAA
Found at i:242476 original size:14 final size:15
Alignment explanation
Indices: 242443--242506 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 15
242433 AAAGACCGAA
242443 AATTAATAATAATAT
1 AATTAATAATAATAT
242458 AATTAA-AATAAT-T
1 AATTAATAATAATAT
* *
242471 ACATTAATTAAAAAAAT
1 A-ATTAA-TAATAATAT
**
242488 AGGTAATAATAATAAT
1 AATTAATAATAAT-AT
242504 AAT
1 AAT
242507 ACTAAGAAGT
Statistics
Matches: 36, Mismatches: 8, Indels: 9
0.68 0.15 0.17
Matches are distributed among these distances:
13 2 0.06
14 11 0.31
15 11 0.31
16 10 0.28
17 2 0.06
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (15 bp):
AATTAATAATAATAT
Found at i:243722 original size:32 final size:32
Alignment explanation
Indices: 243684--243748 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
243674 TTCAGAAAAT
*
243684 TGTTATGTTCAAATATTTTTTTTAAGTTCAAA
1 TGTTATGTTCAAATATTTTTTTTAAGCTCAAA
*
243716 TGTTATGTTCAAATATTTTTTTTGAGCTCAAA
1 TGTTATGTTCAAATATTTTTTTTAAGCTCAAA
243748 T
1 T
243749 ATTGAATATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.52
Consensus pattern (32 bp):
TGTTATGTTCAAATATTTTTTTTAAGCTCAAA
Found at i:244110 original size:23 final size:22
Alignment explanation
Indices: 244075--244117 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
244065 ATAATTATTT
244075 AAAAAATTAAATAAAAAATATC
1 AAAAAATTAAATAAAAAATATC
*
244097 AAAAATATTTAATAAAAAATA
1 AAAAA-ATTAAATAAAAAATA
244118 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAAAATTAAATAAAAAATATC
Found at i:245453 original size:18 final size:19
Alignment explanation
Indices: 245413--245453 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
245403 TAAGAAAAAT
*
245413 ATATTATATTTTTTATAAG
1 ATATTATATTTTTTAGAAG
245432 ATATT-TATTTATTTAGAA-
1 ATATTATATTT-TTTAGAAG
245450 ATAT
1 ATAT
245454 CAGAAAATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
ATATTATATTTTTTAGAAG
Found at i:247211 original size:15 final size:16
Alignment explanation
Indices: 247185--247214 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
247175 GTCTTGCTGG
247185 GCTATCTGGGCTTCGA
1 GCTATCTGGGCTTCGA
247201 GCTAT-TGGGCTTCG
1 GCTATCTGGGCTTCG
247215 GGTTTGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.10, C:0.23, G:0.33, T:0.33
Consensus pattern (16 bp):
GCTATCTGGGCTTCGA
Found at i:247311 original size:3 final size:3
Alignment explanation
Indices: 247303--247375 Score: 83
Period size: 3 Copynumber: 23.7 Consensus size: 3
247293 ATTTTTTATT
* **
247303 TAA TAA TAA TAA TAA TAA TATA GAA TAA TAA TAA TAA TAA TATA TTT
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA-A TAA
**
247350 TTT TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
247376 GAATAAAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
3 58 0.94
4 4 0.06
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:247332 original size:22 final size:22
Alignment explanation
Indices: 247304--247346 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
247294 TTTTTTATTT
247304 AATAATAATAATAATAATATAG
1 AATAATAATAATAATAATATAG
247326 AATAATAATAATAATAATATA
1 AATAATAATAATAATAATATA
247347 TTTTTTTAAT
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:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AATAATAATAATAATAATATAG
Found at i:247623 original size:45 final size:45
Alignment explanation
Indices: 247559--247708 Score: 228
Period size: 45 Copynumber: 3.3 Consensus size: 45
247549 CCCGGAGGCT
* * *
247559 TTTTGAAAACATCCTGCACTGCAGGGCTTACGGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
247604 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* * *
247649 TTTTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAAG
1 -TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
247695 TTTTGAAAATATCA
1 TTTTGAAAACATCA
247709 AAAAGCTCCC
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
45 55 0.57
46 42 0.43
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
Found at i:247761 original size:167 final size:167
Alignment explanation
Indices: 247485--248019 Score: 989
Period size: 167 Copynumber: 3.2 Consensus size: 167
247475 TCTTGAAATG
* *
247485 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTC
1 TTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTC
* *
247550 CCGGAGGCTTTTTGAAAACATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGTTTTGAAAACA
66 CCGAAGGCTTTTTGAAAACATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCA
247615 TCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTT
131 TCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTT
* *
247652 TTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAAGTTTTGAAAATATCAAAAAGCTC
1 TTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTC
247717 CCGAAGGCTTTTTGAAAACATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCA
66 CCGAAGGCTTTTTGAAAACATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCA
*
247782 TCATGCACTGGAGGGCTTACAGATGACCCGAAGGTTT
131 TCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTT
*
247819 TTCAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTC
1 TTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTC
*
247884 CCAAAGGCTTTTTGAAAACATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCA
66 CCGAAGGCTTTTTGAAAACATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCA
247949 TCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTT
131 TCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTT
247986 TTGAAAACATCAAGCACTGAAGGACTTACAGATG
1 TTGAAAACATCAAGCACTGAAGGACTTACAGATG
248020 TGGGAAATAG
Statistics
Matches: 355, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
167 355 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.22
Consensus pattern (167 bp):
TTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTC
CCGAAGGCTTTTTGAAAACATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCA
TCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTT
Found at i:247847 original size:46 final size:46
Alignment explanation
Indices: 247716--247875 Score: 207
Period size: 45 Copynumber: 3.5 Consensus size: 46
247706 TCAAAAAGCT
* * *
247716 CCCGAAGGCTTTTTGAAAACATCCTGCACTGCAGGGCTTACGGATGA
1 CCCGAAGG-TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* *
247763 CCCGAAGG-TTTTGAAAGCATCATGCACTGGAGGGCTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* * *
247808 CCCGAAGGTTTTTCAAAACATCAAGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* *
247854 CCCGAAGG-CTTTGAAAATATCA
1 CCCGAAGGTTTTTGAAAACATCA
247876 AAAAGCTCCC
Statistics
Matches: 100, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
45 52 0.52
46 40 0.40
47 8 0.08
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.23
Consensus pattern (46 bp):
CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:247919 original size:122 final size:122
Alignment explanation
Indices: 247771--247998 Score: 350
Period size: 122 Copynumber: 1.9 Consensus size: 122
247761 GACCCGAAGG
* *
247771 TTTTGAAAGCATCATGCACTGGAGGGCTTACAGATGACCCGAAGGTTTTTCAAAACATCAAGCAC
1 TTTTGAAAACATCATGCACTGCAGGGCTTACAGATGACCCGAAGG-TTTTCAAAACATCAAGCAC
*
247836 TGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAATATCAAAAAGCTCCCAAAGGCT
65 TGAAGGACTTACAGATGACCCGAAGGTCTTTGAAAACATCAAAAAGCTCCCAAAGGCT
* * * * *
247893 TTTTGAAAACATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCATCATGCACT
1 TTTTGAAAACATCATGCACTGCAGGGCTTACAGATGACCCGAAGGTTTTCAAAACATCAAGCACT
* *
247958 GAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAA
66 GAAGGACTTACAGATGACCCGAAGGTCTTTGAAAACATCAA
247999 GCACTGAAGG
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
121 41 0.43
122 54 0.57
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.23
Consensus pattern (122 bp):
TTTTGAAAACATCATGCACTGCAGGGCTTACAGATGACCCGAAGGTTTTCAAAACATCAAGCACT
GAAGGACTTACAGATGACCCGAAGGTCTTTGAAAACATCAAAAAGCTCCCAAAGGCT
Found at i:248005 original size:46 final size:46
Alignment explanation
Indices: 247887--248019 Score: 196
Period size: 45 Copynumber: 2.9 Consensus size: 46
247877 AAAGCTCCCA
* * *
247887 AAGGCTTTTTGAAAACATCCTGCACTGCAGGGCTTACGGATGACCCG
1 AAGG-TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCG
*
247934 AAGG-TTTTGAAAGCATCATGCACTGAAGGGCTTACAGATGACCCG
1 AAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCG
* *
247979 AAGGTTTTTGAAAACATCAAGCACTGAAGGACTTACAGATG
1 AAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
248020 TGGGAAATAG
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
45 41 0.53
46 33 0.42
47 4 0.05
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (46 bp):
AAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCG
Found at i:248706 original size:15 final size:15
Alignment explanation
Indices: 248686--248719 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
248676 TAAAGCTTTC
248686 ATCTTTGAAAAGAGA
1 ATCTTTGAAAAGAGA
248701 ATCTTTGAAAAGAGA
1 ATCTTTGAAAAGAGA
248716 ATCT
1 ATCT
248720 ATCATCTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (15 bp):
ATCTTTGAAAAGAGA
Found at i:248706 original size:22 final size:22
Alignment explanation
Indices: 248701--248753 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
248691 TGAAAAGAGA
*
248701 ATCTTTGAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATATATC
*
248723 ATCTTTAAAAAGAGAATATATC
1 ATCTTTGAAAAGAGAATATATC
248745 ATCTTTGAA
1 ATCTTTGAA
248754 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCTTTGAAAAGAGAATATATC
Found at i:253539 original size:9 final size:9
Alignment explanation
Indices: 253525--253550 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
253515 TTCTTTCTCT
253525 TTTTTTTCC
1 TTTTTTTCC
253534 TTTTTTTCC
1 TTTTTTTCC
253543 TTTTTTTC
1 TTTTTTTC
253551 AAGTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTCC
Found at i:256318 original size:16 final size:15
Alignment explanation
Indices: 256292--256321 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
256282 TAATAAATGT
256292 AATGTAAATGCAAAA
1 AATGTAAATGCAAAA
256307 AATGTGAAATGCAAA
1 AATGT-AAATGCAAA
256322 TGCATGTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.20
Consensus pattern (15 bp):
AATGTAAATGCAAAA
Found at i:257772 original size:27 final size:27
Alignment explanation
Indices: 257741--257802 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
257731 ATCTTGGACA
257741 TTTGCTCTCTTATTTCTCGTATCTCCT
1 TTTGCTCTCTTATTTCTCGTATCTCCT
257768 TTTGCTCTCTTATTTCTCGTATCTCCT
1 TTTGCTCTCTTATTTCTCGTATCTCCT
257795 TTTGCTCT
1 TTTGCTCT
257803 TCAATGGGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.06, C:0.29, G:0.08, T:0.56
Consensus pattern (27 bp):
TTTGCTCTCTTATTTCTCGTATCTCCT
Found at i:258229 original size:11 final size:10
Alignment explanation
Indices: 258203--258228 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
258193 CAGAAAAAAT
258203 AAAAAATTAA
1 AAAAAATTAA
258213 AAAAAATTAA
1 AAAAAATTAA
258223 AAAAAA
1 AAAAAA
258229 AAACAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATTAA
Found at i:258236 original size:18 final size:18
Alignment explanation
Indices: 258196--258237 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
258186 ATTTATTCAG
*
258196 AAAAAATAAAAAATTAAA
1 AAAAAATAAAAAATAAAA
*
258214 AAAAATTAAAAAA-AAAA
1 AAAAAATAAAAAATAAAA
258231 ACAAAAA
1 A-AAAAA
258238 GTTAGAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.86, C:0.02, G:0.00, T:0.12
Consensus pattern (18 bp):
AAAAAATAAAAAATAAAA
Found at i:258726 original size:26 final size:27
Alignment explanation
Indices: 258697--258758 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
258687 TGAAAATAAA
258697 ATAAAAATAT-AAAA-AATAA-TATACAT
1 ATAAAAATATGAAAATAATAAGTAT--AT
*
258723 ATAAATATTATGAAAATAATAAGTATAT
1 ATAAA-AATATGAAAATAATAAGTATAT
258751 ATAAAAAT
1 ATAAAAAT
258759 TTTGAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
26 5 0.17
27 6 0.20
28 11 0.37
29 5 0.17
30 3 0.10
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (27 bp):
ATAAAAATATGAAAATAATAAGTATAT
Found at i:258753 original size:28 final size:26
Alignment explanation
Indices: 258709--258766 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
258699 AAAAATATAA
*
258709 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
258735 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
258763 AAAA
1 AAAA
258767 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:259299 original size:18 final size:19
Alignment explanation
Indices: 259259--259299 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
259249 TTAAGAAAAT
*
259259 ATATTATATTTTTTATAAG
1 ATATTATATTTTTTAGAAG
259278 ATATT-TATTTATTTAGAA-
1 ATATTATATTT-TTTAGAAG
259296 ATAT
1 ATAT
259300 CAGAAAAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
ATATTATATTTTTTAGAAG
Found at i:259404 original size:16 final size:18
Alignment explanation
Indices: 259380--259421 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
259370 AACATTTATC
*
259380 TAAAAATAA-TTA-AAAA
1 TAAATATAATTTATAAAA
259396 TAAATATAATTTATAAAA
1 TAAATATAATTTATAAAA
259414 TAAGATAT
1 TAA-ATAT
259422 TTATTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 8 0.36
17 3 0.14
18 7 0.32
19 4 0.18
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
TAAATATAATTTATAAAA
Found at i:259637 original size:2 final size:2
Alignment explanation
Indices: 259596--259628 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
259586 TATTATTTAT
*
259596 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
259629 GGCTATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:261167 original size:3 final size:3
Alignment explanation
Indices: 261159--261236 Score: 93
Period size: 3 Copynumber: 25.0 Consensus size: 3
261149 ATTTTTTATT
*
261159 TAA TAA TAA TAA TAA TAA TATA GAA TAA TAA TAA TAA TAA TAA TATA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TA-A
** *
261206 TTT TATT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
261237 ATAGAATGAA
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
3 59 0.89
4 7 0.11
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:261472 original size:22 final size:22
Alignment explanation
Indices: 261446--261497 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
261436 AAAATCAACA
* *
261446 ATCAATAATCAACA-TTTAATG
1 ATCAACAATCAACAGATTAATG
*
261467 AGTCAACAGTCAACAGATTAATG
1 A-TCAACAATCAACAGATTAATG
261490 ATCAACAA
1 ATCAACAA
261498 GTCGATTCAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 1 0.04
22 17 0.68
23 7 0.28
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.25
Consensus pattern (22 bp):
ATCAACAATCAACAGATTAATG
Found at i:263209 original size:19 final size:19
Alignment explanation
Indices: 263187--263223 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
263177 GCCAATATCT
263187 AAGTATACAATTAATCCCC
1 AAGTATACAATTAATCCCC
*
263206 AAGTATACAATTAGTCCC
1 AAGTATACAATTAATCCC
263224 TTGGCAACAT
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:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (19 bp):
AAGTATACAATTAATCCCC
Found at i:265779 original size:14 final size:14
Alignment explanation
Indices: 265760--265803 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
265750 GCAATAATGT
265760 ATATTATAAAAATA
1 ATATTATAAAAATA
*
265774 ATATTAATCAAAAGT-
1 ATATT-AT-AAAAATA
265789 ATATTATAAAAATA
1 ATATTATAAAAATA
265803 A
1 A
265804 AAGGGACGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 5 0.20
14 8 0.32
15 7 0.28
16 5 0.20
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (14 bp):
ATATTATAAAAATA
Found at i:266415 original size:106 final size:106
Alignment explanation
Indices: 266287--266952 Score: 946
Period size: 106 Copynumber: 6.4 Consensus size: 106
266277 GTATTGTTCC
* * * * * *
266287 GAGTCCAATATCCTCCGATGTGAAGTTGAAATTGGTTCTGGGACTGGAAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGGAAAATTGTTTATTGACAA
* * *
266352 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
266393 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAGAAGTTGTTTACTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGGA-AAATTGTTTATTGACA
* *
266457 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTA
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
266499 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCT-GAATTTGAGAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGGA-AAATTGTTTATTGACA
266563 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
266605 GAGTCCAATATCCTTCGTTGTGAAGTTGAAA-----T-T-G----GG-AAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGGAAAATTGTTTATTGACAA
*
266658 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
266699 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATATTGGGAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGA-ATTGGAAAATTGTTTATTGACA
* * * *
266764 ACCAGTGGTCCCTACGTTGTGAAGTTGAACATGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
266806 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGGAAAATTGTTTATTGACAA
266871 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
266912 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGG
266953 GTAAAACCTG
Statistics
Matches: 507, Mismatches: 38, Indels: 30
0.88 0.07 0.05
Matches are distributed among these distances:
94 86 0.17
96 1 0.00
99 1 0.00
100 3 0.01
101 1 0.00
105 6 0.01
106 316 0.62
107 93 0.18
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGGAAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:266634 original size:43 final size:43
Alignment explanation
Indices: 266573--266728 Score: 125
Period size: 43 Copynumber: 3.4 Consensus size: 43
266563 ACCAGCGGTC
266573 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * * ** ***
266616 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCA-ATAT
*
266666 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
266710 CCTTCG-CTGTGAAGTTGAA
1 CCTTCGTC-GTGAAGTTGAA
266729 ATTGGCTCTG
Statistics
Matches: 83, Mismatches: 21, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
42 1 0.01
43 39 0.47
44 1 0.01
45 3 0.04
46 6 0.07
48 7 0.08
49 3 0.04
50 1 0.01
51 22 0.27
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:266711 original size:94 final size:102
Alignment explanation
Indices: 266631--266943 Score: 446
Period size: 107 Copynumber: 3.0 Consensus size: 102
266621 GTTGTGAAGT
266631 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
266696 CAGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGT--AGTTGAAA-T-GCTC
* * * *
266737 TGAATATTGGGAAATTGTTTATTGACAACCAGTGGTCCCTACGTTGTGAAGTTGAACATGCGTTG
1 TGAA-ATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
* *
266802 TCTGGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTC
65 TCTGGAGTCCAATATCCTTCGCTGT--AGTTGAAA-T-GCTC
*
266844 TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
266909 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
66 CTGGAGTCCAATATCCTTCGCTGT--AGTTGAAAT
266944 TGGCTCTGGG
Statistics
Matches: 193, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
105 1 0.01
106 93 0.48
107 99 0.51
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.34
Consensus pattern (102 bp):
TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGCTGTAGTTGAAATGCTC
Found at i:266870 original size:307 final size:306
Alignment explanation
Indices: 266335--266946 Score: 1026
Period size: 307 Copynumber: 2.0 Consensus size: 306
266325 TGGGACTGGA
* * *
266335 AAATTATTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTATCTGGAGTCCA
1 AAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCAGGAGTCCA
* *
266400 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTACTGACAACCAGCGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTACTGACAACCAGCGG
* * *
266465 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
131 TCCCTACGTCGTGAAGTTGAACATGCGTTGCCTAGAGTCCAATATCATTCGTTGTGAAGTTGAAA
* * *
266530 TTGGTTCTGAATTTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
196 TTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
266595 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGG
261 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGG
* *
266641 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAGGAGTCCA
1 AAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCAGGAGTCCA
* * *
266706 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATATTGGGAAATTGTTTATTGACAACCAGTG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA-ATTGAGAAATTGTTTACTGACAACCAGCG
* * *
266771 GTCCCTACGTTGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCATTCGTTGTGAAGTTGAA
130 GTCCCTACGTCGTGAAGTTGAACATGCGTTGCCTAGAGTCCAATATCATTCGTTGTGAAGTTGAA
* *
266836 ATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
195 ATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
266901 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
260 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
266947 CTCTGGGTAA
Statistics
Matches: 284, Mismatches: 21, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
306 94 0.33
307 190 0.67
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (306 bp):
AAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCAGGAGTCCA
ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTACTGACAACCAGCGG
TCCCTACGTCGTGAAGTTGAACATGCGTTGCCTAGAGTCCAATATCATTCGTTGTGAAGTTGAAA
TTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGG
Found at i:278663 original size:2 final size:2
Alignment explanation
Indices: 278658--278690 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
278648 ATACACACAC
278658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
278691 ACATATAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.