Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold63
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: 2211945
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 524 characters in sequence are not A, C, G, or T
File 4 of 16
Found at i:607859 original size:33 final size:32
Alignment explanation
Indices: 607815--607897 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 32
607805 TTATATTTAA
607815 AATAATATATATT-TATAAATATTTTAATATATT
1 AATAATATATATTATATAAA-A-TTTAATATATT
* *
607848 AATAATTTATATTATATAAAATTTATTATATT
1 AATAATATATATTATATAAAATTTAATATATT
* * *
607880 TATATGTACATATTATAT
1 AATA-ATATATATTATAT
607898 TTAATTATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
32 13 0.31
33 23 0.55
34 6 0.14
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (32 bp):
AATAATATATATTATATAAAATTTAATATATT
Found at i:608442 original size:12 final size:12
Alignment explanation
Indices: 608420--608450 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
608410 TAATTTTATG
608420 ATATA-AATAAA
1 ATATATAATAAA
608431 ATATATAATAAA
1 ATATATAATAAA
608443 ATATATAA
1 ATATATAA
608451 AATATGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATATATAATAAA
Found at i:608473 original size:33 final size:31
Alignment explanation
Indices: 608436--608507 Score: 74
Period size: 32 Copynumber: 2.2 Consensus size: 31
608426 ATAAAATATA
* *
608436 TAATA-AAATATATAAAATATGTTAAATTTTATT
1 TAATATAAAT-TAT-AAATATATTAAAATTT-TT
*
608469 TAATATAAATTATTAATATATTAAAATTTTT
1 TAATATAAATTATAAATATATTAAAATTTTT
608500 TAAATATA
1 T-AATATA
608508 TATTTTTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 3 0.09
32 19 0.56
33 8 0.24
34 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (31 bp):
TAATATAAATTATAAATATATTAAAATTTTT
Found at i:608612 original size:11 final size:11
Alignment explanation
Indices: 608596--608658 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
608586 TAATAATTAA
608596 ATATTTATATT
1 ATATTTATATT
608607 ATATTTATA-T
1 ATATTTATATT
608617 ATTATTT-TATT
1 A-TATTTATATT
*
608628 ATAATTAT-TT
1 ATATTTATATT
* ** *
608638 TTAAATATTTT
1 ATATTTATATT
608649 ATATTTATAT
1 ATATTTATAT
608659 AAATTTTAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
10 16 0.39
11 25 0.61
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTTATATT
Found at i:608653 original size:17 final size:17
Alignment explanation
Indices: 608633--608674 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
608623 TTATTATAAT
*
608633 TATTTT-TAAATATTTTA
1 TATTTTATAAAT-TTTAA
608650 TATTTATATAAATTTTAA
1 TATTT-TATAAATTTTAA
608668 TATTTTA
1 TATTTTA
608675 ATAATTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 10 0.45
19 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTTTATAAATTTTAA
Found at i:608656 original size:27 final size:26
Alignment explanation
Indices: 608596--608683 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 26
608586 TAATAATTAA
* *
608596 ATATTTATATTATATTTATATATTATT
1 ATATTTATATTATTTTTAAATATT-TT
*
608623 TTA-TTATAATTATTTTTAAATATTTT
1 ATATTTAT-ATTATTTTTAAATATTTT
* *
608649 ATATTTATATAAATTTT-AATATTTT
1 ATATTTATATTATTTTTAAATATTTT
608674 AATAATTTAT
1 -AT-ATTTAT
608684 GGTATAGCAT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
25 8 0.16
26 17 0.33
27 26 0.51
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
ATATTTATATTATTTTTAAATATTTT
Found at i:608777 original size:2 final size:2
Alignment explanation
Indices: 608772--608804 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
608762 TCCAACTCCA
*
608772 CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
608805 AAGCCAAAGC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:617119 original size:18 final size:20
Alignment explanation
Indices: 617096--617144 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
617086 TATATTTGTG
617096 TTATATAATTT-GATT-CAT
1 TTATATAATTTAGATTACAT
* * *
617114 TTATATATTTTATATTATAT
1 TTATATAATTTAGATTACAT
617134 TTATATAATTT
1 TTATATAATTT
617145 TTTTATATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 10 0.40
19 3 0.12
20 12 0.48
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
TTATATAATTTAGATTACAT
Found at i:617138 original size:11 final size:11
Alignment explanation
Indices: 617057--617217 Score: 99
Period size: 11 Copynumber: 15.0 Consensus size: 11
617047 TAATATTCAG
*
617057 TATATTTTTAT
1 TATATTTATAT
*
617068 TATTTTTAATAT
1 TATATTT-ATAT
617080 TATATTTATAT
1 TATATTTATAT
*
617091 T-TGTGTTATA-
1 TATAT-TTATAT
*
617101 TA-ATTT-GAT
1 TATATTTATAT
*
617110 T-CATTTATA-
1 TATATTTATAT
617119 TAT-TTTATAT
1 TATATTTATAT
617129 TATATTTATAT
1 TATATTTATAT
* *
617140 AATTTTTTTATAT
1 --TATATTTATAT
*
617153 CATATTTTATAT
1 TATA-TTTATAT
617165 TATATTT-TAAT
1 TATATTTAT-AT
*
617176 TATTTTTATAT
1 TATATTTATAT
617187 TATATTTATAT
1 TATATTTATAT
* *
617198 CATATTTAAAT
1 TATATTTATAT
617209 T-TA-TTATAT
1 TATATTTATAT
617218 CAATATAAAT
Statistics
Matches: 116, Mismatches: 20, Indels: 30
0.70 0.12 0.18
Matches are distributed among these distances:
8 1 0.01
9 19 0.16
10 11 0.09
11 56 0.48
12 20 0.17
13 9 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (11 bp):
TATATTTATAT
Found at i:617165 original size:36 final size:36
Alignment explanation
Indices: 617118--617205 Score: 121
Period size: 33 Copynumber: 2.5 Consensus size: 36
617108 ATTCATTTAT
617118 ATATTTTATATTATATTTATATAATT-TTTTTATATC
1 ATATTTTATATTATATTTAT-TAATTATTTTTATATC
*
617154 ATATTTTATATTATA-TT-TTAATTATTTTTATATT
1 ATATTTTATATTATATTTATTAATTATTTTTATATC
*
617188 ATA-TTTATATCATATTTA
1 ATATTTTATATTATATTTA
617206 AATTTATTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
33 15 0.32
34 15 0.32
35 2 0.04
36 15 0.32
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (36 bp):
ATATTTTATATTATATTTATTAATTATTTTTATATC
Found at i:620243 original size:14 final size:15
Alignment explanation
Indices: 620224--620257 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
620214 TTGATTTATT
620224 AATTTAT-TTTAAAA
1 AATTTATCTTTAAAA
*
620238 AATTTATCTTTAATA
1 AATTTATCTTTAAAA
620253 AATTT
1 AATTT
620258 GAATTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTTATCTTTAAAA
Found at i:620894 original size:15 final size:16
Alignment explanation
Indices: 620876--620912 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
620866 TTAATTTATT
620876 TTTAATTAAATTT-AA
1 TTTAATTAAATTTAAA
*
620891 TTT-ATAAAATTTAAA
1 TTTAATTAAATTTAAA
620906 TTTAATT
1 TTTAATT
620913 TAAAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
14 8 0.44
15 8 0.44
16 2 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTAATTAAATTTAAA
Found at i:621001 original size:25 final size:27
Alignment explanation
Indices: 620973--621025 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
620963 AGTAAAAAAG
*
620973 TAAACTCGATT-TTTATATT-AAACTT
1 TAAACTCAATTATTTATATTAAAACTT
* *
620998 TAAATTCAATTATTTGTATTAAAACTT
1 TAAACTCAATTATTTATATTAAAACTT
621025 T
1 T
621026 TATTTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 9 0.39
26 7 0.30
27 7 0.30
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (27 bp):
TAAACTCAATTATTTATATTAAAACTT
Found at i:621108 original size:137 final size:138
Alignment explanation
Indices: 620886--621133 Score: 444
Period size: 137 Copynumber: 1.8 Consensus size: 138
620876 TTTAATTAAA
* *
620886 TTTAATTTATAAAATTTAAATTTAATTTAAAATAAAAATTAAATTATTTGATCTCATTTGATTAA
1 TTTAATTTATAAAATTTAAATTTAATTTAAAATAAAAATCAAATTATTTGATCTCATTTAATTAA
*
620951 GCTTATTGACCTAGTAAAAAAGTAAACTCGATTTTTATATTAAACTTTAAATTCAATTATTTGTA
66 GCTTATTGACCTAGTAAAAAAATAAACTCGATTTTTATATTAAACTTTAAATTCAATTATTTGTA
621016 TTAAAACT
131 TTAAAACT
* *
621024 TTTATTTTA-AAAATTTAAATTTGATTTAAAATAAAAATCAAATTATTTGATCTCATTTAATTAA
1 TTTAATTTATAAAATTTAAATTTAATTTAAAATAAAAATCAAATTATTTGATCTCATTTAATTAA
621088 GCTTATTGACCTAGTAAAAAAATAAACTCGATTTTTATATTAAACT
66 GCTTATTGACCTAGTAAAAAAATAAACTCGATTTTTATATTAAACT
621134 CGATTATTTA
Statistics
Matches: 105, Mismatches: 5, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
137 97 0.92
138 8 0.08
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.44
Consensus pattern (138 bp):
TTTAATTTATAAAATTTAAATTTAATTTAAAATAAAAATCAAATTATTTGATCTCATTTAATTAA
GCTTATTGACCTAGTAAAAAAATAAACTCGATTTTTATATTAAACTTTAAATTCAATTATTTGTA
TTAAAACT
Found at i:621133 original size:18 final size:19
Alignment explanation
Indices: 621110--621150 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
621100 AGTAAAAAAA
621110 TAAACTCGATT-TTTATAT
1 TAAACTCGATTATTTATAT
621128 TAAACTCGATTATTTATAT
1 TAAACTCGATTATTTATAT
621147 TAAA
1 TAAA
621151 ATTTGAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (19 bp):
TAAACTCGATTATTTATAT
Found at i:621193 original size:137 final size:131
Alignment explanation
Indices: 620890--621163 Score: 372
Period size: 137 Copynumber: 2.1 Consensus size: 131
620880 ATTAAATTTA
* * * *
620890 ATTTATAAAATTTAAATTTAATTTAAAATAAAAATTAAATTATTTGATCTCATTTGATTAAGCTT
1 ATTTAAAAAATTTAAATTTAATTAAAAATAAAAATCAAATTATTTGATCTCATTTAATTAAGCTT
* *
620955 ATTGACCTAGTAAAAAAGTAAACTCGATTTTTATATTAAACTTTAAATTCAATTATTTGTATTAA
66 ATTGACCTAGTAAAAAAATAAACTCGATTTTTATATTAAAC------TTCAATTATTTATATTAA
*
621020 AACTTTT
125 AACTTTG
* * *
621027 ATTTTAAAAATTTAAATTTGATTTAAAATAAAAATCAAATTATTTGATCTCATTTAATTAAGCTT
1 ATTTAAAAAATTTAAATTTAATTAAAAATAAAAATCAAATTATTTGATCTCATTTAATTAAGCTT
*
621092 ATTGACCTAGTAAAAAAATAAACTCGATTTTTATATTAAAC-TCGATTATTTATATTAAAA-TTT
66 ATTGACCTAGTAAAAAAATAAACTCGATTTTTATATTAAACTTCAATTATTTATATTAAAACTTT
621155 G
131 G
621156 AGTTTAAA
1 A-TTTAAA
621164 TTAAGATTTT
Statistics
Matches: 126, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
129 4 0.03
130 22 0.17
137 100 0.79
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.43
Consensus pattern (131 bp):
ATTTAAAAAATTTAAATTTAATTAAAAATAAAAATCAAATTATTTGATCTCATTTAATTAAGCTT
ATTGACCTAGTAAAAAAATAAACTCGATTTTTATATTAAACTTCAATTATTTATATTAAAACTTT
G
Found at i:622479 original size:3 final size:3
Alignment explanation
Indices: 622466--622498 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
622456 ACTGCCGTTA
*
622466 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
622499 TTGAGTAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:627655 original size:2 final size:2
Alignment explanation
Indices: 627648--627681 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
627638 TTTAAACATG
627648 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
627682 TGTGGAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:627882 original size:22 final size:21
Alignment explanation
Indices: 627857--627905 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
627847 TGTATCATCT
627857 TTTATATATAATATTTAATATA
1 TTTATATATAAT-TTTAATATA
* * *
627879 TTTAAAATTTAATTTTAATATT
1 TTT-ATATATAATTTTAATATA
627901 TTTAT
1 TTTAT
627906 CTTATATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
21 1 0.05
22 14 0.64
23 7 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTATATATAATTTTAATATA
Found at i:635648 original size:28 final size:27
Alignment explanation
Indices: 635629--635699 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
635619 TTAAATATTT
635629 TTATATATTTATAATTATTTTTAAAATA
1 TTATATATTTATAATTA-TTTTAAAATA
* *
635657 TTATATATTTAT-ATAAATTTTAATATA
1 TTATATATTTATAAT-TATTTTAAAATA
*
635684 TAATAT-TTTAT-ATTAT
1 TTATATATTTATAATTAT
635700 ATAAATTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
25 2 0.05
26 7 0.18
27 16 0.42
28 13 0.34
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TTATATATTTATAATTATTTTAAAATA
Found at i:635649 original size:20 final size:18
Alignment explanation
Indices: 635616--635682 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
635606 CGCGGTCTCG
635616 TATTTAAATATTTTTATA
1 TATTTAAATATTTTTATA
635634 TATTTATAATTATTTTTA-A
1 TATTTA-AA-TATTTTTATA
* * *
635653 AATATTATATATTTATATA
1 TAT-TTAAATATTTTTATA
* *
635672 AATTTTAATAT
1 TATTTAAATAT
635683 ATAATATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
18 19 0.47
19 10 0.25
20 11 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTTAAATATTTTTATA
Found at i:635683 original size:20 final size:20
Alignment explanation
Indices: 635618--635684 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
635608 CGGTCTCGTA
*
635618 TTTAA-ATATTTTTATATAT
1 TTTAATATATTTTTATAAAT
635637 TTATAAT-TATTTTTA-AAAT
1 TT-TAATATATTTTTATAAAT
* *
635656 ATT-ATATATTTATATAAAT
1 TTTAATATATTTTTATAAAT
635675 TTTAATATAT
1 TTTAATATAT
635685 AATATTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 2 0.05
18 8 0.21
19 12 0.31
20 17 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAATATATTTTTATAAAT
Found at i:635710 original size:16 final size:16
Alignment explanation
Indices: 635660--635715 Score: 80
Period size: 16 Copynumber: 3.5 Consensus size: 16
635650 TAAAATATTA
635660 TATATTTATATAAATTT
1 TATA-TTATATAAATTT
635677 TA-A-TATATAATATTT
1 TATATTATATAA-ATTT
635692 TATATTATATAAATTT
1 TATATTATATAAATTT
635708 TATATTAT
1 TATATTAT
635716 TTTTATATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 7 0.19
15 6 0.17
16 14 0.39
17 9 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATTATATAAATTT
Found at i:635735 original size:28 final size:28
Alignment explanation
Indices: 635654--635744 Score: 103
Period size: 28 Copynumber: 3.1 Consensus size: 28
635644 TATTTTTAAA
*
635654 ATATTATATATTTATATAAATTTTAATATAT
1 ATATTTTATA-TTATATAAATTTT-ATAT-T
635685 AATATTTTATATTATATAAATTTTATATT
1 -ATATTTTATATTATATAAATTTTATATT
* *
635714 AT-TTTTATATTATAATATATTTTTTATT
1 ATATTTTATATTAT-ATAAATTTTATATT
635742 ATA
1 ATA
635745 ATTATTTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
27 11 0.20
28 16 0.30
29 1 0.02
30 4 0.07
31 13 0.24
32 9 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
ATATTTTATATTATATAAATTTTATATT
Found at i:635736 original size:18 final size:17
Alignment explanation
Indices: 635707--635763 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
635697 TATATAAATT
635707 TTAT-ATTATTTTTATA
1 TTATAATTATTTTTATA
635723 TTATAATATATTTTT-TA
1 TTATAAT-TATTTTTATA
*
635740 TTATAATTATTTTTTATT
1 TTATAATTA-TTTTTATA
635758 TTATAA
1 TTATAA
635764 CATGCTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
16 6 0.17
17 16 0.44
18 14 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATAATTATTTTTATA
Found at i:635741 original size:17 final size:16
Alignment explanation
Indices: 635707--635757 Score: 77
Period size: 16 Copynumber: 3.1 Consensus size: 16
635697 TATATAAATT
635707 TTAT-ATTATTTTTATA
1 TTATAATTATTTTT-TA
635723 TTATAATATATTTTTTA
1 TTATAAT-TATTTTTTA
635740 TTATAATTATTTTTTA
1 TTATAATTATTTTTTA
635756 TT
1 TT
635758 TTATAACATG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.45
17 11 0.33
18 7 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATAATTATTTTTTA
Found at i:635745 original size:42 final size:42
Alignment explanation
Indices: 635655--635745 Score: 100
Period size: 41 Copynumber: 2.2 Consensus size: 42
635645 ATTTTTAAAA
*
635655 TATTATATATTTATATAAATTTTAATATATAATATTTTATAT
1 TATTATAAATTTATATAAATTTTAATATATAATATTTTATAT
* *
635697 TA-TATAAATTT-TATATTATTTTTATATTATAATATATTT-T-T
1 TATTATAAATTTATATA-AATTTTAATA-TATAATAT-TTTATAT
635738 TATTATAA
1 TATTATAA
635746 TTATTTTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
40 4 0.10
41 19 0.45
42 16 0.38
43 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (42 bp):
TATTATAAATTTATATAAATTTTAATATATAATATTTTATAT
Found at i:636826 original size:2 final size:2
Alignment explanation
Indices: 636819--636845 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
636809 ATTTATTTGC
636819 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 A
636846 CTTATTTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:640916 original size:14 final size:15
Alignment explanation
Indices: 640886--640923 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
640876 CGAATCTTGA
*
640886 TAATACTTTTTATTT
1 TAATATTTTTTATTT
640901 TAATATTTTTTA-TT
1 TAATATTTTTTATTT
640915 TAA-ATTTTT
1 TAATATTTTT
640924 ATTACCTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.27
14 5 0.23
15 11 0.50
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TAATATTTTTTATTT
Found at i:645901 original size:47 final size:47
Alignment explanation
Indices: 645832--645925 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
645822 AATTGGTAGG
* *
645832 ATAAGAGTAGGTTAGATACCATGCAAAATATCACAAAACTAGATTTT
1 ATAAGAATAGGTAAGATACCATGCAAAATATCACAAAACTAGATTTT
645879 ATAAGAATAGGTAAGATACCATGCAAAATATCACAAAACTAGATTTT
1 ATAAGAATAGGTAAGATACCATGCAAAATATCACAAAACTAGATTTT
645926 TGAATAATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.27
Consensus pattern (47 bp):
ATAAGAATAGGTAAGATACCATGCAAAATATCACAAAACTAGATTTT
Found at i:647397 original size:21 final size:21
Alignment explanation
Indices: 647371--647434 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
647361 TAAATAATTA
647371 TTTATTAATTAAAATATTATT
1 TTTATTAATTAAAATATTATT
* * *
647392 TTTATTTATAAAAATA-TATA
1 TTTATTAATTAAAATATTATT
**
647412 AATATTAATTAAAAATATT-TT
1 TTTATTAATT-AAAATATTATT
647433 TT
1 TT
647435 AATATTTTAT
Statistics
Matches: 31, Mismatches: 10, Indels: 4
0.69 0.22 0.09
Matches are distributed among these distances:
20 9 0.29
21 21 0.68
22 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTATTAATTAAAATATTATT
Found at i:647473 original size:57 final size:57
Alignment explanation
Indices: 647385--647510 Score: 193
Period size: 57 Copynumber: 2.2 Consensus size: 57
647375 TTAATTAAAA
* * *
647385 TATTAT-TTTTATTTATAAAAATATATAAATATTAATTAAAAATATTTTTTAATATTT
1 TATTATATTTTAATCATAAAAATATATAAATATTAATTAAAAA-ATTTTATAATATTT
647442 TATTATATTTTAATCAT-AAAATATATAAATATTAATTAAAAAATTTTATAATATTT
1 TATTATATTTTAATCATAAAAATATATAAATATTAATTAAAAAATTTTATAATATTT
*
647498 TATGATATTTTAA
1 TATTATATTTTAA
647511 ACAATAATTT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
56 25 0.39
57 31 0.48
58 8 0.12
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.52
Consensus pattern (57 bp):
TATTATATTTTAATCATAAAAATATATAAATATTAATTAAAAAATTTTATAATATTT
Found at i:647510 original size:56 final size:57
Alignment explanation
Indices: 647402--647510 Score: 193
Period size: 56 Copynumber: 1.9 Consensus size: 57
647392 TTTATTTATA
* *
647402 AAAATATATAAATATTAATTAAAAATATTTTTTAATATTTTATTATATTTTAATCAT
1 AAAATATATAAATATTAATTAAAAATATTTTATAATATTTTATGATATTTTAATCAT
647459 AAAATATATAAATATTAATTAAAAA-ATTTTATAATATTTTATGATATTTTAA
1 AAAATATATAAATATTAATTAAAAATATTTTATAATATTTTATGATATTTTAA
647511 ACAATAATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
56 25 0.50
57 25 0.50
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (57 bp):
AAAATATATAAATATTAATTAAAAATATTTTATAATATTTTATGATATTTTAATCAT
Found at i:649670 original size:16 final size:16
Alignment explanation
Indices: 649651--649693 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
649641 TCTTATAATT
*
649651 TTAATATTTT-TTATTA
1 TTAAT-TTTTATTATAA
649667 TTAATTTTTATTATAA
1 TTAATTTTTATTATAA
649683 TTAATTTTTAT
1 TTAATTTTTAT
649694 AATATTTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTAATTTTTATTATAA
Found at i:651258 original size:13 final size:14
Alignment explanation
Indices: 651240--651271 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
651230 GAATTTTATT
651240 TTATTTATT-TTTA
1 TTATTTATTATTTA
651253 TTATTTATTATTTA
1 TTATTTATTATTTA
651267 -TATTT
1 TTATTT
651272 TAATAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTATTTATTATTTA
Found at i:651273 original size:7 final size:7
Alignment explanation
Indices: 651240--651271 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
651230 GAATTTTATT
651240 TTATTTA
1 TTATTTA
651247 TT-TTTA
1 TTATTTA
651253 TTATTTA
1 TTATTTA
651260 TTATTTA
1 TTATTTA
651267 -TATTT
1 TTATTT
651272 TAATAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 11 0.46
7 13 0.54
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
TTATTTA
Found at i:651384 original size:11 final size:11
Alignment explanation
Indices: 651368--651396 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
651358 TAACTAAGAC
651368 TATAATATAAA
1 TATAATATAAA
651379 TATAATATAAA
1 TATAATATAAA
651390 TATAATA
1 TATAATA
651397 CAAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TATAATATAAA
Found at i:652040 original size:22 final size:22
Alignment explanation
Indices: 652005--652051 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
651995 TTTTTTTCAT
652005 TTTATGTTCATGTTATGTCATAA
1 TTTATGTTCATGTTATGT-ATAA
* *
652028 TTTAT-TTTATGTTTTGTATAA
1 TTTATGTTCATGTTATGTATAA
652049 TTT
1 TTT
652052 TTTCAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 10 0.45
23 5 0.23
ACGTcount: A:0.23, C:0.04, G:0.11, T:0.62
Consensus pattern (22 bp):
TTTATGTTCATGTTATGTATAA
Found at i:653276 original size:19 final size:18
Alignment explanation
Indices: 653252--653299 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
653242 ATGTAAATTA
653252 AAATATAATATAAATTATT
1 AAATATAATATAAATT-TT
*
653271 AAATATATTA-AAATTTT
1 AAATATAATATAAATTTT
653288 AAATATTAATAT
1 AAATA-TAATAT
653300 GATATTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 7 0.28
18 9 0.36
19 9 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATATAATATAAATTTT
Found at i:654332 original size:22 final size:24
Alignment explanation
Indices: 654288--654342 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
654278 ATCTTTATAC
654288 TAAT-ATTTATTATTATATTTAAA
1 TAATAATTTATTATTATATTTAAA
*
654311 TAA-AATTTTTTATTA-ATTTAAA
1 TAATAATTTATTATTATATTTAAA
654333 TAATAATTTA
1 TAATAATTTA
654343 AGTCAAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TAATAATTTATTATTATATTTAAA
Found at i:654460 original size:14 final size:14
Alignment explanation
Indices: 654441--654490 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 14
654431 TTTTATATTC
654441 ATATAAATTTTAAA
1 ATATAAATTTTAAA
654455 ATATAAATAATTTAAA
1 ATATAAAT--TTTAAA
*
654471 TTATATAAAATTTAAA
1 --ATATAAATTTTAAA
654487 ATAT
1 ATAT
654491 TTATATTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
14 12 0.39
16 12 0.39
18 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATAAATTTTAAA
Found at i:654470 original size:16 final size:16
Alignment explanation
Indices: 654441--654490 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
654431 TTTTATATTC
654441 ATATAAAT--TTTAAA
1 ATATAAATAATTTAAA
654455 ATATAAATAATTTAAA
1 ATATAAATAATTTAAA
*
654471 TTATATAA-AATTTAAA
1 ATATA-AATAATTTAAA
654487 ATAT
1 ATAT
654491 TTATATTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 8 0.26
16 21 0.68
17 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAAATAATTTAAA
Found at i:654498 original size:25 final size:25
Alignment explanation
Indices: 654444--654501 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
654434 TATATTCATA
654444 TAAATT-T-TAAAATATAAATAATT
1 TAAATTATATAAAATATAAATAATT
*
654467 TAAATTATATAAAATTTAAA-ATATT
1 TAAATTATATAAAATATAAATA-ATT
*
654492 TATATTATAT
1 TAAATTATAT
654502 TCTTATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 6 0.20
24 2 0.07
25 22 0.73
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TAAATTATATAAAATATAAATAATT
Found at i:654512 original size:16 final size:15
Alignment explanation
Indices: 654490--654534 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
654480 ATTTAAAATA
*
654490 TTTATATTATATTCT
1 TTTATATTATATTAT
*
654505 TATTATATTTTATATAT
1 T-TTATATTATAT-TAT
654522 TTTATATTATATT
1 TTTATATTATATT
654535 TTAATTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 2 0.08
16 20 0.80
17 3 0.12
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTATATTATATTAT
Found at i:654522 original size:9 final size:10
Alignment explanation
Indices: 654487--654550 Score: 67
Period size: 11 Copynumber: 6.0 Consensus size: 10
654477 AAAATTTAAA
654487 ATATTTATATT
1 ATATTT-TATT
654498 ATATTCTTATT
1 ATATT-TTATT
654509 ATATTTTA-T
1 ATATTTTATT
654518 ATATTTTATATT
1 ATA-TTT-TATT
654530 ATATTTTAATT
1 ATATTTT-ATT
*
654541 ATTTTTTATT
1 ATATTTTATT
654551 CAAATTTAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
9 4 0.09
10 10 0.21
11 28 0.60
12 5 0.11
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
ATATTTTATT
Found at i:654542 original size:16 final size:15
Alignment explanation
Indices: 654491--654542 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
654481 TTTAAAATAT
654491 TTATATTATATTCTTA
1 TTATATTATATT-TTA
*
654507 TTATATTTTATATATT-
1 TTATA--TTATATTTTA
654523 TTATATTATATTTTAA
1 TTATATTATATTTT-A
654539 TTAT
1 TTAT
654543 TTTTTATTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 8 0.27
16 14 0.47
17 2 0.07
18 6 0.20
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATATTATATTTTA
Found at i:654550 original size:21 final size:21
Alignment explanation
Indices: 654490--654550 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 21
654480 ATTTAAAATA
*
654490 TTTATATTATATTCTTATTATAT
1 TTTA-ATTAT-TTTTTATTATAT
*
654513 TTT-ATATATTTTATATTATAT
1 TTTAAT-TATTTTTTATTATAT
654534 TTTAATTATTTTTTATT
1 TTTAATTATTTTTTATT
654551 CAAATTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 25 0.76
22 5 0.15
23 3 0.09
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTAATTATTTTTTATTATAT
Found at i:655064 original size:15 final size:16
Alignment explanation
Indices: 655041--655075 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
655031 TCTTTCTATC
655041 ACTTCTCTTATATAAA
1 ACTTCTCTTATATAAA
655057 ACTT-TCTTATATAAA
1 ACTTCTCTTATATAAA
655072 ACTT
1 ACTT
655076 GGTCGTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (16 bp):
ACTTCTCTTATATAAA
Found at i:658025 original size:14 final size:14
Alignment explanation
Indices: 658002--658031 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
657992 ATGAATATCG
658002 AATAAATTAAAAAT
1 AATAAATTAAAAAT
*
658016 AATAATTTAAAAAT
1 AATAAATTAAAAAT
658030 AA
1 AA
658032 AAAAATATTA
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAAATTAAAAAT
Found at i:660332 original size:2 final size:2
Alignment explanation
Indices: 660327--660364 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
660317 ATAATTCTCC
*
660327 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
660365 TCTAATCTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:661987 original size:2 final size:2
Alignment explanation
Indices: 661980--662016 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
661970 CTTGAAGAAG
661980 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
662017 TTGCCACCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:662615 original size:21 final size:21
Alignment explanation
Indices: 662569--662630 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
662559 TTAATTTAAA
662569 TTTAAT-TATAAAATATAAAAT
1 TTTAATATATAAAA-ATAAAAT
* **
662590 ATTAATATATAAAAATATTAT
1 TTTAATATATAAAAATAAAAT
662611 TTTAATAATATAATAAATAA
1 TTTAAT-ATATAA-AAATAA
662631 TAAAATATAC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
21 15 0.45
22 13 0.39
23 5 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTAATATATAAAAATAAAAT
Found at i:681155 original size:2 final size:2
Alignment explanation
Indices: 681150--681175 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
681140 GAGAAACCCT
681150 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
681176 AGATTCTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:681362 original size:2 final size:2
Alignment explanation
Indices: 681355--681394 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
681345 AGCGTTGAAG
*
681355 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
681395 TTAAGAACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:683528 original size:18 final size:17
Alignment explanation
Indices: 683505--683538 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
683495 TATATTTTTT
683505 ATATTTAAATATATTTAA
1 ATATTTAAATA-ATTTAA
*
683523 ATATTTTAATAATTTA
1 ATATTTAAATAATTTA
683539 TATTATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTTAAATAATTTAA
Found at i:683549 original size:27 final size:28
Alignment explanation
Indices: 683475--683547 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 28
683465 TTATTAATTC
* *
683475 AATAATTTATGTTATATTTATATATTTT
1 AATAATTTATATTATATTTAAATATTTT
* *
683503 -TTATATTTA-AATATATTTAAATATTTT
1 AATA-ATTTATATTATATTTAAATATTTT
683530 AATAATTTATATTATATT
1 AATAATTTATATTATATT
683548 AATTTTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (28 bp):
AATAATTTATATTATATTTAAATATTTT
Found at i:684703 original size:54 final size:54
Alignment explanation
Indices: 684640--684865 Score: 301
Period size: 54 Copynumber: 4.2 Consensus size: 54
684630 CATTTCCGGC
* * * *
684640 TGCTTGCTAGCAAAAAGAGAAAGAATCATCACGACAACAAAAATC-ATTCCCAGT
1 TGCTTGCTAGCAAAAAGGGAAAGTACCATCACGACAACAAAAAACAATT-CCAGT
* * *
684694 TGCTAGCTAGCGAAAAGGGAAAGTACCATCACCACAACAAAAAACAATTCCAGT
1 TGCTTGCTAGCAAAAAGGGAAAGTACCATCACGACAACAAAAAACAATTCCAGT
* * *
684748 TGCTTGCTAGCAAAAAGGGAAAGTACCATCACGACAACACAAAACAATTCCGGC
1 TGCTTGCTAGCAAAAAGGGAAAGTACCATCACGACAACAAAAAACAATTCCAGT
** * * *
684802 TGCTCACTAGCGAAAAGGGAAAGTACCATCGCGACATCAAAAAACAATTCCAGT
1 TGCTTGCTAGCAAAAAGGGAAAGTACCATCACGACAACAAAAAACAATTCCAGT
684856 TGCTTGCTAG
1 TGCTTGCTAG
684866 TTAAAGGAAA
Statistics
Matches: 148, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
54 145 0.98
55 3 0.02
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.17
Consensus pattern (54 bp):
TGCTTGCTAGCAAAAAGGGAAAGTACCATCACGACAACAAAAAACAATTCCAGT
Found at i:684829 original size:108 final size:108
Alignment explanation
Indices: 684640--684865 Score: 332
Period size: 108 Copynumber: 2.1 Consensus size: 108
684630 CATTTCCGGC
* *
684640 TGCTTGCTAGCAAAAAGAGAAAGAATCATCACGACAACAAAAATCATTCCCAGTTGCTAGCTAGC
1 TGCTTGCTAGCAAAAAGAGAAAGAACCATCACGACAACAAAAATCATTCCCAGCTGCTAGCTAGC
684705 GAAAAGGGAAAGTACCATCACCACAACAAAAAACAATTCCAGT
66 GAAAAGGGAAAGTACCATCACCACAACAAAAAACAATTCCAGT
* * *
684748 TGCTTGCTAGCAAAAAGGGAAAGTACCATCACGACAACACAAAA-CAATT-CCGGCTGCTCA-CT
1 TGCTTGCTAGCAAAAAGAGAAAGAACCATCACGACAACA-AAAATC-ATTCCCAGCTGCT-AGCT
* * *
684810 AGCGAAAAGGGAAAGTACCATCGCGACATCAAAAAACAATTCCAGT
63 AGCGAAAAGGGAAAGTACCATCACCACAACAAAAAACAATTCCAGT
684856 TGCTTGCTAG
1 TGCTTGCTAG
684866 TTAAAGGAAA
Statistics
Matches: 107, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
108 99 0.93
109 8 0.07
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.17
Consensus pattern (108 bp):
TGCTTGCTAGCAAAAAGAGAAAGAACCATCACGACAACAAAAATCATTCCCAGCTGCTAGCTAGC
GAAAAGGGAAAGTACCATCACCACAACAAAAAACAATTCCAGT
Found at i:694043 original size:18 final size:20
Alignment explanation
Indices: 694012--694049 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
694002 CAAAGATTTT
694012 AAAATATTGAAAA-TTCAAA
1 AAAATATTGAAAATTTCAAA
*
694031 AAAAT-TTGCAAATTTCAAA
1 AAAATATTGAAAATTTCAAA
694050 GAACACATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAATATTGAAAATTTCAAA
Found at i:694519 original size:10 final size:11
Alignment explanation
Indices: 694504--694532 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
694494 ATTATTAATA
694504 TATTTAAA-TT
1 TATTTAAATTT
694514 TATTTAAATTT
1 TATTTAAATTT
694525 TATTTAAA
1 TATTTAAA
694533 ATATAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TATTTAAATTT
Found at i:694842 original size:41 final size:43
Alignment explanation
Indices: 694790--694879 Score: 112
Period size: 41 Copynumber: 2.1 Consensus size: 43
694780 TAATAATAAT
***
694790 TAATAATTAAAATATAATATA-ATTACTTTTTTATTT-AAAAA
1 TAATAATTAAAATATAATATATATTACTTTAAAATTTAAAAAA
* * *
694831 TAATATTTAAAATTTAATATATTTTACTTTAAAATTTAAAAAA
1 TAATAATTAAAATATAATATATATTACTTTAAAATTTAAAAAA
694874 TAATAA
1 TAATAA
694880 ATGTTCTACA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 19 0.47
42 11 0.28
43 10 0.25
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (43 bp):
TAATAATTAAAATATAATATATATTACTTTAAAATTTAAAAAA
Found at i:694877 original size:29 final size:28
Alignment explanation
Indices: 694835--694914 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
694825 TAAAAATAAT
**
694835 ATTTAAAATTTAATATATTTTACTTTA-AA
1 ATTTAAAAAATAATATATTTTAC--TACAA
* *
694864 ATTTAAAAAATAATAAATGTT-CTACAA
1 ATTTAAAAAATAATATATTTTACTACAA
694891 ATATTAAAAAATAAATATATTTTA
1 AT-TTAAAAAAT-AATATATTTTA
694915 TAATAATCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.05
27 4 0.10
28 10 0.24
29 25 0.61
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (28 bp):
ATTTAAAAAATAATATATTTTACTACAA
Found at i:700902 original size:22 final size:23
Alignment explanation
Indices: 700877--700934 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
700867 TTATATTATA
700877 TTATAATTATATTTAAAATA-TT
1 TTATAATTATATTTAAAATATTT
*
700899 TTAT-ATATAAATTTTAAAATATTT
1 TTATAAT-TATA-TTTAAAATATTT
*
700923 TTATATTTATAT
1 TTATAATTATAT
700935 ATTATTCTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
21 2 0.07
22 7 0.24
23 10 0.34
24 9 0.31
25 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTATAATTATATTTAAAATATTT
Found at i:700979 original size:20 final size:21
Alignment explanation
Indices: 700956--700994 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
700946 TAACTTTTTT
700956 TATTAT-ATCATTTTTTTTAA
1 TATTATAATCATTTTTTTTAA
* *
700976 TATTTTAATTATTTTTTTT
1 TATTATAATCATTTTTTTT
700995 TGGTTTAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (21 bp):
TATTATAATCATTTTTTTTAA
Found at i:700981 original size:27 final size:31
Alignment explanation
Indices: 700916--700981 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 31
700906 TAAATTTTAA
700916 AATATTTTTATATTTATATATTATTCTTGTT
1 AATATTTTTATATTTATATATTATTCTTGTT
700947 AACT-TTTTT-TA-TTATATCATT-TT-TT-TT
1 AA-TATTTTTATATTTATAT-ATTATTCTTGTT
700974 AATATTTT
1 AATATTTT
700982 AATTATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
26 1 0.03
27 8 0.25
28 2 0.06
29 8 0.25
30 5 0.16
31 7 0.22
32 1 0.03
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (31 bp):
AATATTTTTATATTTATATATTATTCTTGTT
Found at i:701452 original size:50 final size:50
Alignment explanation
Indices: 701393--701637 Score: 366
Period size: 50 Copynumber: 4.9 Consensus size: 50
701383 TATACTTAGA
*
701393 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
701443 GTCAACAATTATGGCCACCTC-CTTTTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTC-TCTATTGTCAAAGGTTGGTGAAGAATC
* * *
701493 GTCAACAATTATGGTCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* ** *
701543 GTCAACAATTATAGTAACCTCTTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
701593 GTCAACAATTATGGCTACTTCTCTCTATTGTCAAAGGTTGATGAA
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAA
701638 TGATAATCAA
Statistics
Matches: 177, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
49 1 0.01
50 175 0.99
51 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:705526 original size:14 final size:14
Alignment explanation
Indices: 705507--705540 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
705497 ATATTCATCC
705507 AATATTTTATTATT
1 AATATTTTATTATT
*
705521 AATATTTTTTTATT
1 AATATTTTATTATT
705535 -ATATTT
1 AATATTT
705541 ATAATTTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
AATATTTTATTATT
Found at i:707798 original size:106 final size:107
Alignment explanation
Indices: 707605--707799 Score: 266
Period size: 106 Copynumber: 1.8 Consensus size: 107
707595 TTTACATATC
* * *
707605 CATCGTGTGTTGAATAAAGTTTTTACTACGGTTGAATTATCTATATGCCTCAAAAAACTTTACAT
1 CATCATGTGTTGAATAAAGTTTTTACTA--GTTAAATTATCTATATGCCTCAAAAAACTTGACAT
* * *
707670 GAATAGATTAGATTTTAAATAATTATGATTTGAATTTAATTATG
64 AAATAAATTAAATTTTAAATAATTATGATTTGAATTTAATTATG
* * ** *
707714 CATCATGTGTTGAATAAAGTTTTTACT-GTTAAATTATTTATCTGGTTCAAAAGACTTGACATAA
1 CATCATGTGTTGAATAAAGTTTTTACTAGTTAAATTATCTATATGCCTCAAAAAACTTGACATAA
707778 ATAAATTAAATTTTAAATAATT
66 ATAAATTAAATTTTAAATAATT
707800 TTTTTACAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
106 49 0.65
109 26 0.35
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (107 bp):
CATCATGTGTTGAATAAAGTTTTTACTAGTTAAATTATCTATATGCCTCAAAAAACTTGACATAA
ATAAATTAAATTTTAAATAATTATGATTTGAATTTAATTATG
Found at i:707918 original size:127 final size:127
Alignment explanation
Indices: 707684--707962 Score: 463
Period size: 127 Copynumber: 2.2 Consensus size: 127
707674 AGATTAGATT
*
707684 TTAAATAATTATGATTTGAATTTAATTATGCATCATGTGTTGAATAAAGTTTTTACTGTTAAATT
1 TTAAATAATTATGATTTGAATTTAATTATGCACCATGTGTTGAATAAAGTTTTTACTGTTAAATT
*
707749 ATTTATCTGGTTCAAAAGACTTGACATAAATAAATTAAATTTTAAATA-ATTTTTTTACAAAA
66 ATTTATCTGATTCAAAAGACTTGACATAAATAAATTAAATTTTAAATATA-TTTTTTACAAAA
707811 TTAAATAATTATGATTTGAATTTAATTATGCACCATGTGTTGAATAAAGTTTTTA-TGATTAAAT
1 TTAAATAATTATGATTTGAATTTAATTATGCACCATGTGTTGAATAAAGTTTTTACTG-TTAAAT
* * * *
707875 TATTTATCTGATTCAAAAGGCTTGACATAAATAGATTAGATTTTAAATATATTTTTTATAAAA
65 TATTTATCTGATTCAAAAGACTTGACATAAATAAATTAAATTTTAAATATATTTTTTACAAAA
*
707938 TTAAATAAGTATGATTTGAATTTAA
1 TTAAATAATTATGATTTGAATTTAA
707963 ATAATTAATT
Statistics
Matches: 143, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
126 2 0.01
127 140 0.98
128 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.44
Consensus pattern (127 bp):
TTAAATAATTATGATTTGAATTTAATTATGCACCATGTGTTGAATAAAGTTTTTACTGTTAAATT
ATTTATCTGATTCAAAAGACTTGACATAAATAAATTAAATTTTAAATATATTTTTTACAAAA
Found at i:708408 original size:22 final size:23
Alignment explanation
Indices: 708318--708405 Score: 60
Period size: 22 Copynumber: 3.8 Consensus size: 23
708308 ACATGTAAGA
* * *
708318 TAATTTATGTATTTATATAATGTTA
1 TAATTTAT-AATTTATA-AATATTT
708343 TAA-TTAT-ATTTA-AAATATTT
1 TAATTTATAATTTATAAATATTT
*
708363 TATATGTA-AATTTTGATAAAT-TTT
1 TA-ATTTATAA-TTT-ATAAATATTT
708387 TAATTTATAATTTATAAAT
1 TAATTTATAATTTATAAAT
708406 TTTAAAATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 17
0.71 0.05 0.23
Matches are distributed among these distances:
20 7 0.13
21 2 0.04
22 14 0.27
23 10 0.19
24 12 0.23
25 7 0.13
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (23 bp):
TAATTTATAATTTATAAATATTT
Found at i:713921 original size:21 final size:21
Alignment explanation
Indices: 713894--713940 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 21
713884 CTCCTCAGCT
*
713894 TTCTCTTCTTCTTCCTTCTCGTC
1 TTCT-TTC-TCTTCCTTCTCATC
713917 TTCTTTCTCTTCCTTCTCATC
1 TTCTTTCTCTTCCTTCTCATC
713938 TTC
1 TTC
713941 CTCCATAGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.70
22 3 0.13
23 4 0.17
ACGTcount: A:0.02, C:0.38, G:0.02, T:0.57
Consensus pattern (21 bp):
TTCTTTCTCTTCCTTCTCATC
Found at i:713924 original size:12 final size:12
Alignment explanation
Indices: 713903--713942 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
713893 TTTCTCTTCT
713903 TCTTCCTTCTCG
1 TCTTCCTTCTCG
713915 TCTT-CTT-TC-
1 TCTTCCTTCTCG
*
713924 TCTTCCTTCTCA
1 TCTTCCTTCTCG
713936 TCTTCCT
1 TCTTCCT
713943 CCATAGTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 4 0.16
10 5 0.20
11 5 0.20
12 11 0.44
ACGTcount: A:0.03, C:0.40, G:0.03, T:0.55
Consensus pattern (12 bp):
TCTTCCTTCTCG
Found at i:713993 original size:66 final size:67
Alignment explanation
Indices: 713854--714006 Score: 199
Period size: 66 Copynumber: 2.3 Consensus size: 67
713844 TTTTAGTCCC
*
713854 CTCCTC-TCCATTTTCATCTTCCTCCATAGCCTCCTCAGCTTTCTCTTCTTCTTCCTTCTCGTCT
1 CTCCTCTTCC-TTCTCATCTTCCTCCATAGCCTCCTCAGCTTTCTCTTCTTCTTCCTTCTC-TCT
713918 TCTT
64 TCTT
* *
713922 -T-CTCTTCCTTCTCATCTTCCTCCATAGTCTCCTCAGCTTTTTCTTCTTCTT-CTTCT-TCTTC
1 CTCCTCTTCCTTCTCATCTTCCTCCATAGCCTCCTCAGCTTTCTCTTCTTCTTCCTTCTCTCTTC
713983 TAT
66 T-T
* *
713986 CTCCTCTTCTTTCTCAACTTC
1 CTCCTCTTCCTTCTCATCTTC
714007 TTCGTCTTTA
Statistics
Matches: 76, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
63 6 0.08
64 1 0.01
65 6 0.08
66 59 0.78
67 4 0.05
ACGTcount: A:0.08, C:0.39, G:0.03, T:0.50
Consensus pattern (67 bp):
CTCCTCTTCCTTCTCATCTTCCTCCATAGCCTCCTCAGCTTTCTCTTCTTCTTCCTTCTCTCTTC
TT
Found at i:717880 original size:21 final size:21
Alignment explanation
Indices: 717850--717898 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
717840 TAAATTTGAG
*
717850 TTTAA-ATTAAATTGAAT-TAT
1 TTTAATATT-AATTAAATATAT
717870 TTTAATATTAATTAAATATAT
1 TTTAATATTAATTAAATATAT
*
717891 TTTGATAT
1 TTTAATAT
717899 ATGTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTAATATTAATTAAATATAT
Found at i:717969 original size:29 final size:29
Alignment explanation
Indices: 717927--717983 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
717917 TAGTTAGCTC
717927 GAAAGTATTAAGATATTCATATTTAATTT
1 GAAAGTATTAAGATATTCATATTTAATTT
*
717956 GAAAGTATTAAGATATTTATATTTAATT
1 GAAAGTATTAAGATATTCATATTTAATT
717984 CGTCAACAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.46
Consensus pattern (29 bp):
GAAAGTATTAAGATATTCATATTTAATTT
Found at i:721478 original size:20 final size:22
Alignment explanation
Indices: 721449--721491 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
721439 ATATATTGTA
*
721449 AAAAATTTAAAT-TTGATGAAT
1 AAAAATTTAAATATTGATAAAT
721470 AAAAA-TTAAATATTGATAAAT
1 AAAAATTTAAATATTGATAAAT
721491 A
1 A
721492 TACAAATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (22 bp):
AAAAATTTAAATATTGATAAAT
Found at i:726479 original size:19 final size:19
Alignment explanation
Indices: 726457--726525 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 19
726447 TTTATTATAT
726457 TATTAAAATATTATTTTTA
1 TATTAAAATATTATTTTTA
*
726476 TATTAATAT-TTATATAATTTA
1 TATTAAAATATTAT-T--TTTA
*
726497 TATTTAAAAATATTATTTTAA
1 TA-TT-AAAATATTATTTTTA
726518 TTATTAAA
1 -TATTAAA
726526 TAGTAAATCG
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
18 4 0.10
19 9 0.22
20 3 0.08
21 11 0.28
22 4 0.10
23 5 0.12
24 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTAAAATATTATTTTTA
Found at i:726638 original size:21 final size:21
Alignment explanation
Indices: 726605--726645 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
726595 CTTTAAGAGA
726605 TTAAAAAACTTAACTTGACAT
1 TTAAAAAACTTAACTTGACAT
* * *
726626 TTAAATAATTTAATTTGACA
1 TTAAAAAACTTAACTTGACA
726646 CAAATATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (21 bp):
TTAAAAAACTTAACTTGACAT
Found at i:727787 original size:20 final size:18
Alignment explanation
Indices: 727764--727807 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
727754 AAATTATCCT
727764 ATTATTTTACTTTTAAAATA
1 ATTA-TTTA-TTTTAAAATA
727784 ATTATTTATTTTAAAA-A
1 ATTATTTATTTTAAAATA
727801 A-TATTTA
1 ATTATTTA
727808 CATATTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.25
17 2 0.08
18 8 0.33
19 4 0.17
20 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTATTTATTTTAAAATA
Found at i:728673 original size:39 final size:41
Alignment explanation
Indices: 728629--728726 Score: 111
Period size: 37 Copynumber: 2.5 Consensus size: 41
728619 ATTAAATCTA
*
728629 ATAATATATAAATATATTA-AAAAATAATT-AAA-ATAA-T
1 ATAATATATAAATATATAATAAAAATAATTAAAATATAATT
*
728666 AT-ATAATATAAATATATAATAAAAATTATTAAAATATAATT
1 ATAAT-ATATAAATATATAATAAAAATAATTAAAATATAATT
728707 ATAATATAATAAA-AT-TAATA
1 ATAATAT-ATAAATATATAATA
728727 TTTAAATATA
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
36 2 0.04
37 15 0.29
38 9 0.17
39 3 0.06
40 9 0.17
41 7 0.13
42 7 0.13
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (41 bp):
ATAATATATAAATATATAATAAAAATAATTAAAATATAATT
Found at i:729024 original size:2 final size:2
Alignment explanation
Indices: 729019--729065 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
729009 CTGGTGTGTG
729019 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
729061 TA TA T
1 TA TA T
729066 GTTGTTGTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:730480 original size:2 final size:2
Alignment explanation
Indices: 730473--730507 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
730463 AAAATGATTT
730473 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
730508 CGAAAACCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:730859 original size:8 final size:8
Alignment explanation
Indices: 730841--730873 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
730831 TAAAAGATTT
730841 TAAAA-AA
1 TAAAATAA
730848 TAAAATAA
1 TAAAATAA
730856 TAAAATAA
1 TAAAATAA
*
730864 TAAAAAAA
1 TAAAATAA
730872 TA
1 TA
730874 TTTTTTATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
7 5 0.21
8 19 0.79
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
TAAAATAA
Found at i:730929 original size:17 final size:17
Alignment explanation
Indices: 730878--730931 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
730868 AAAATATTTT
*
730878 TTATCTTAAATTTAATA
1 TTATCTTTAATTTAATA
* * * *
730895 ATAT-TATAAATAAATA
1 TTATCTTTAATTTAATA
730911 TTATCTTTAATTTAATA
1 TTATCTTTAATTTAATA
730928 TTAT
1 TTAT
730932 TAAAAAAATA
Statistics
Matches: 27, Mismatches: 9, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (17 bp):
TTATCTTTAATTTAATA
Found at i:730944 original size:31 final size:33
Alignment explanation
Indices: 730878--730954 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
730868 AAAATATTTT
730878 TTATCTTAAATTTAATAATATTATAAATAAATA
1 TTATCTTAAATTTAATAATATTATAAATAAATA
* *
730911 TTATCTTTAATTTAATATTATTA-AAA-AAATA
1 TTATCTTAAATTTAATAATATTATAAATAAATA
730942 TTATCTTAAATTT
1 TTATCTTAAATTT
730955 TTTTATAAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 17 0.41
32 3 0.07
33 21 0.51
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (33 bp):
TTATCTTAAATTTAATAATATTATAAATAAATA
Found at i:732399 original size:259 final size:260
Alignment explanation
Indices: 731904--732418 Score: 689
Period size: 259 Copynumber: 2.0 Consensus size: 260
731894 AACATCTAAC
731904 GTAAAATTAATTAGTGATAGTTAAAAGAGGTCTAAATTAAATACAAAAATATAAGCAATCTAGTG
1 GTAAAATTAATTAGTGATAGTT--AAGAGGTCTAAATTAAATACAAAAATATAAGCAATCTAGTG
* * * * * **
731969 TTTAATTGATATGGAATAATTCACTTTAACAAGTCAAATCATGCGTATGTAAAGATAAAAAAATT
64 CTTAATAGATATGGAATAATTCAATTTAACAAGTCAAATCATGAGTATGTAAAGACAAAAAAACC
*
732034 TATCAAGTGACAAATTCAAAAAAGATAATAAGTAAAAGTAAATATATAAAATTCTGACATCATAT
129 TATCAAGTGACAAATTCAAAAAAGATAATAAGTAAAAGTAAATAAATAAAATTCTGACATCATAT
* * * * *
732099 TAAACATCTAATTTAAAACTAATTGGATGATAAATAAAAAATTTGATTTGAGTATAAAACCTCCA
194 TAAACATCCAATTTAAAACTAATTAGATGATAAAAAAAAAATTCGATTTGAATATAAAACCTCCA
732164 AT
259 AT
* * *
732166 GTAAAA-TAATTAGTGATAGTT-AGAGGT-TCAAATTAAATATAAGAATATAAGTAATCTAGTGC
1 GTAAAATTAATTAGTGATAGTTAAGAGGTCT-AAATTAAATACAAAAATATAAGCAATCTAGTGC
* * * *
732228 TTAATAGATATGGAATAATCTCAATTTAACAAGTTAGATCATGAGTATGTGAAGACAGAAAAACC
65 TTAATAGATATGGAATAAT-TCAATTTAACAAGTCAAATCATGAGTATGTAAAGACAAAAAAACC
* * * * * * *
732293 TATCACGTGACAAGTTCGAAAGAGATAATAAGTAAAAGT-AATAAAATAAGATTCTGATATCATG
129 TATCAAGTGACAAATTCAAAAAAGATAATAAGTAAAAGTAAAT-AAATAAAATTCTGACATCATA
*
732357 TTAAACATCCAATTTAAAATTAATTAG-TGATAAAGAAAAAAATTCGATTTGAATATAAAACC
193 TTAAACATCCAATTTAAAACTAATTAGATGATAAA-AAAAAAATTCGATTTGAATATAAAACC
732419 ACAAGTAATT
Statistics
Matches: 221, Mismatches: 28, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
257 1 0.00
258 63 0.29
259 136 0.62
261 15 0.07
262 6 0.03
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (260 bp):
GTAAAATTAATTAGTGATAGTTAAGAGGTCTAAATTAAATACAAAAATATAAGCAATCTAGTGCT
TAATAGATATGGAATAATTCAATTTAACAAGTCAAATCATGAGTATGTAAAGACAAAAAAACCTA
TCAAGTGACAAATTCAAAAAAGATAATAAGTAAAAGTAAATAAATAAAATTCTGACATCATATTA
AACATCCAATTTAAAACTAATTAGATGATAAAAAAAAAATTCGATTTGAATATAAAACCTCCAAT
Found at i:732760 original size:24 final size:24
Alignment explanation
Indices: 732733--732795 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
732723 TACATTATAT
*
732733 AATAAAATATATGTTTTA-AAAATA
1 AATAAAATATAT-TTATATAAAATA
*
732757 AATAAAAATACATTTATATAAAATA
1 AAT-AAAATATATTTATATAAAATA
*
732782 AATATAATTATATT
1 AATA-AAATATATT
732796 ATTAAATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
24 8 0.25
25 24 0.75
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
AATAAAATATATTTATATAAAATA
Found at i:732857 original size:98 final size:98
Alignment explanation
Indices: 732738--732932 Score: 320
Period size: 98 Copynumber: 2.0 Consensus size: 98
732728 TATATAATAA
*
732738 AATATATGTTTTAAAAATAAATAAAAATACATTTATA-TAAAATAAATATAATTATATTATTAAA
1 AATATATATTTTAAAAATAAATAAAAATACATTTATAGTAAAATAAATATAATTATATTA-TAAA
*
732802 TTTAAGTTTTATATTATTAAAATATTAATTATCT
65 TTTAAGTTTTAAATTATTAAAATATTAATTATCT
* *
732836 AATATATATTTTAAAAATAAATAAAAATATATTTATATGTAAAATAAATATAATTATATTATAAT
1 AATATATATTTTAAAAATAAATAAAAATACATTTATA-GTAAAATAAATATAATTATATTATAAA
*
732901 TTTAATTTTTAAATTATTAAAATATTAATTAT
65 TTTAAGTTTTAAATTATTAAAATATTAATTAT
732933 ATACCAAATT
Statistics
Matches: 90, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
98 35 0.39
99 33 0.37
100 22 0.24
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.46
Consensus pattern (98 bp):
AATATATATTTTAAAAATAAATAAAAATACATTTATAGTAAAATAAATATAATTATATTATAAAT
TTAAGTTTTAAATTATTAAAATATTAATTATCT
Found at i:732867 original size:27 final size:27
Alignment explanation
Indices: 732837--732905 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
732827 TAATTATCTA
732837 ATATATATTTTAAAAATAAATAAAAAT
1 ATATATATTTTAAAAATAAATAAAAAT
* * * *
732864 ATATTTATATGT-AAAATAAATATAATT
1 ATATATAT-TTTAAAAATAAATAAAAAT
732891 ATATTATAATTTTAA
1 ATA-TAT-ATTTTAA
732906 TTTTTAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
27 23 0.72
28 6 0.19
29 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (27 bp):
ATATATATTTTAAAAATAAATAAAAAT
Found at i:733156 original size:22 final size:22
Alignment explanation
Indices: 733104--733191 Score: 66
Period size: 22 Copynumber: 4.3 Consensus size: 22
733094 ATTTTTAAAA
733104 TAATATTTAAAATATTATATATT
1 TAATATTTAAAATATTATATA-T
**
733127 TTTTATTTAAAAT-TTATATAT
1 TAATATTTAAAATATTATATAT
733148 TAATAATTT---ATATTATATA-
1 TAAT-ATTTAAAATATTATATAT
*
733167 -AAT-TTTAATATATT-TATAT
1 TAATATTTAAAATATTATATAT
*
733186 TTATAT
1 TAATAT
733192 GATTTTTATA
Statistics
Matches: 52, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
16 3 0.06
18 7 0.13
19 7 0.13
20 9 0.17
21 4 0.08
22 11 0.21
23 11 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TAATATTTAAAATATTATATAT
Found at i:733196 original size:15 final size:14
Alignment explanation
Indices: 733115--733208 Score: 55
Period size: 15 Copynumber: 6.2 Consensus size: 14
733105 AATATTTAAA
733115 ATATTATATATTT-T
1 ATATT-TATATTTAT
* *
733129 TTATTTAAAATTTAT
1 ATATTT-ATATTTAT
*
733144 ATATTAATAATTTAT
1 ATATTTAT-ATTTAT
* *
733159 ATTATATAAATTTTAAT
1 A-TATTTATA-TTT-AT
733176 ATATTTATATTTAT
1 ATATTTATATTTAT
*
733190 ATGATTTTTATATTAT
1 AT-ATTTATAT-TTAT
733206 ATA
1 ATA
733209 ATCATGATAT
Statistics
Matches: 61, Mismatches: 11, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
13 1 0.02
14 14 0.23
15 24 0.39
16 19 0.31
17 3 0.05
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (14 bp):
ATATTTATATTTAT
Found at i:733940 original size:16 final size:16
Alignment explanation
Indices: 733921--733954 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
733911 TTTCTTAAAT
733921 TTATA-TTAATTATTTA
1 TTATATTTAA-TATTTA
733937 TTATATTTAATATTTA
1 TTATATTTAATATTTA
733953 TT
1 TT
733955 TAATATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATATTTAATATTTA
Found at i:733957 original size:11 final size:12
Alignment explanation
Indices: 733935--733968 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
733925 ATTAATTATT
733935 TATTATATTTAA
1 TATTATATTTAA
733947 TATT-TATTTAA
1 TATTATATTTAA
*
733958 TATTAAATTTA
1 TATTATATTTA
733969 TTTTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTATATTTAA
Found at i:737802 original size:19 final size:19
Alignment explanation
Indices: 737780--737845 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 19
737770 AGCAGATTTC
737780 GAATATATTTTTCGAATAT
1 GAATATATTTTTCGAATAT
*
737799 GAATATATGTTT--AATAT
1 GAATATATTTTTCGAATAT
737816 -AATAATATTAAATTTCGAATAT
1 GAAT-ATATT---TTTCGAATAT
*
737838 GAACATAT
1 GAATATAT
737846 ATGTTTAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
16 3 0.08
17 9 0.24
19 11 0.30
20 3 0.08
22 9 0.24
23 2 0.05
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (19 bp):
GAATATATTTTTCGAATAT
Found at i:737834 original size:39 final size:41
Alignment explanation
Indices: 737789--737865 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
737779 CGAATATATT
737789 TTTCGAATATG-A-ATATATGTTTAATATAATAATATTAAA
1 TTTCGAATATGAACATATATGTTTAATATAATAATATTAAA
737828 TTTCGAATATGAACATATATGTTTAATATAATAATATT
1 TTTCGAATATGAACATATATGTTTAATATAATAATATT
737866 CGATATAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 11 0.31
40 1 0.03
41 24 0.67
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (41 bp):
TTTCGAATATGAACATATATGTTTAATATAATAATATTAAA
Found at i:737864 original size:19 final size:19
Alignment explanation
Indices: 737800--737864 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
737790 TTCGAATATG
737800 AATATATGTTTAATATAAT
1 AATATATGTTTAATATAAT
**
737819 AATATTAAATTTCGAATATGAA-
1 AATA-TATGTTT--AATAT-AAT
*
737841 CATATATGTTTAATATAAT
1 AATATATGTTTAATATAAT
737860 AATAT
1 AATAT
737865 TCGATATAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
18 2 0.06
19 13 0.37
20 5 0.14
21 5 0.14
22 8 0.23
23 2 0.06
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (19 bp):
AATATATGTTTAATATAAT
Found at i:740189 original size:20 final size:20
Alignment explanation
Indices: 740154--740193 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
740144 TAAATTTAAA
740154 TATTTGAATTTAATATATTTT
1 TATTTGAATTTAATAT-TTTT
*
740175 TATTT-AATTTTATATTTTT
1 TATTTGAATTTAATATTTTT
740194 AAAAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 9 0.50
21 5 0.28
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
TATTTGAATTTAATATTTTT
Found at i:740235 original size:17 final size:18
Alignment explanation
Indices: 740198--740254 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
740188 ATTTTTAAAA
*
740198 AAATAATTTAACAAAT-TT
1 AAATAACTTAA-AAATATT
* *
740216 TAATATCTTAAAAATATT
1 AAATAACTTAAAAATATT
740234 AAATAACTTAAATAA-ATT
1 AAATAACTTAAA-AATATT
740252 AAA
1 AAA
740255 ATTTAAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 4 0.12
18 26 0.81
19 2 0.06
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATAACTTAAAAATATT
Found at i:740581 original size:32 final size:37
Alignment explanation
Indices: 740519--740592 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
740509 ATAAAATAAT
740519 TAAAATATAATATATATATATATATTTTAAAATTT-TA
1 TAAAATATAATATATATATATATA-TTTAAAATTTATA
740556 TAAAATATAAT-TAT-TA-ATATA-TTAAAATTTATA
1 TAAAATATAATATATATATATATATTTAAAATTTATA
740589 TAAA
1 TAAA
740593 TATCAAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
32 9 0.25
33 6 0.17
34 5 0.14
35 2 0.06
36 3 0.08
37 11 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (37 bp):
TAAAATATAATATATATATATATATTTAAAATTTATA
Found at i:745002 original size:38 final size:35
Alignment explanation
Indices: 744951--745026 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 35
744941 TTTTAATTAT
744951 TTATTAAATATCAAATTATTAAAACAATTT-ATTTTTAA
1 TTATTAAATATCAAA--A-TAAAA-AATTTAATTTTTAA
* *
744989 TTATTTAATATCAAAATAAAAATTTTAATTTTTAA
1 TTATTAAATATCAAAATAAAAAATTTAATTTTTAA
745024 TTA
1 TTA
745027 AATTATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
34 4 0.11
35 16 0.46
36 1 0.03
38 14 0.40
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (35 bp):
TTATTAAATATCAAAATAAAAAATTTAATTTTTAA
Found at i:745352 original size:10 final size:9
Alignment explanation
Indices: 745337--745412 Score: 55
Period size: 10 Copynumber: 7.7 Consensus size: 9
745327 GATTCGATTA
745337 TTAAATAAGT
1 TTAAATAA-T
745347 TTAAATAAAAAT
1 TTAAAT---AAT
*
745359 TTTAATAAT
1 TTAAATAAT
745368 TTAAATCAAT
1 TTAAAT-AAT
*
745378 TTAATTAAT
1 TTAAATAAT
745387 TTAAATTATTAT
1 TTAAA-TA--AT
745399 TTAAAT-AT
1 TTAAATAAT
745407 TTAAAT
1 TTAAAT
745413 TTTATTTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
8 8 0.15
9 15 0.27
10 16 0.29
11 1 0.02
12 13 0.24
13 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (9 bp):
TTAAATAAT
Found at i:745418 original size:11 final size:11
Alignment explanation
Indices: 745385--745425 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
745375 AATTTAATTA
745385 ATTTAAATTATT
1 ATTTAAATT-TT
745397 ATTTAAA---T
1 ATTTAAATTTT
745405 ATTTAAATTTT
1 ATTTAAATTTT
745416 ATTTAAATTT
1 ATTTAAATTT
745426 AATTATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.31
11 11 0.42
12 7 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTAAATTTT
Found at i:745419 original size:19 final size:20
Alignment explanation
Indices: 745385--745423 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
745375 AATTTAATTA
745385 ATTTAAATTATTATTTAAAT
1 ATTTAAATTATTATTTAAAT
745405 ATTTAAATT-TTATTTAAAT
1 ATTTAAATTATTATTTAAAT
745424 TTAATTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTAAATTATTATTTAAAT
Found at i:746331 original size:18 final size:17
Alignment explanation
Indices: 746290--746342 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
746280 ATATCAAATT
746290 TATATTAATTTTTATAA
1 TATATTAATTTTTATAA
*
746307 TACATTACATTTTTAT-A
1 TATATTA-ATTTTTATAA
**
746324 TCATATTAAAATTTATAA
1 T-ATATTAATTTTTATAA
746342 T
1 T
746343 TTTAAAAGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTAATTTTTATAA
Found at i:746979 original size:22 final size:22
Alignment explanation
Indices: 746924--746986 Score: 53
Period size: 22 Copynumber: 2.9 Consensus size: 22
746914 AATTATTTTT
*
746924 ATATAATTATT-TATAATT-AATA
1 ATAT-ATTATTATAT-ATTAAAAA
*
746946 ATGTATTAATTATATATTAAAAA
1 ATATATT-ATTATATATTAAAAA
746969 ATATATTATTA-A-ATTAAA
1 ATATATTATTATATATTAAA
746987 TATTCATATG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
20 6 0.17
21 4 0.11
22 13 0.37
23 12 0.34
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
ATATATTATTATATATTAAAAA
Found at i:748481 original size:33 final size:37
Alignment explanation
Indices: 748422--748529 Score: 106
Period size: 37 Copynumber: 3.0 Consensus size: 37
748412 AGTATTCGTA
748422 TTATAT-ATTTATATATTAATATTATATTT-ATT-T-TTT
1 TTATATAATTT-T-TATT-ATATTATATTTAATTATATTT
748458 ATTATATAA-TTTT-TTATATTATATTTAAATTATATTT
1 -TTATATAATTTTTATTATATTATATTT-AATTATATTT
*
748495 TTATATAATTTTTATTATATTAT-TAT-ATTATATTT
1 TTATATAATTTTTATTATATTATATTTAATTATATTT
748530 AAAATTATTA
Statistics
Matches: 63, Mismatches: 1, Indels: 16
0.79 0.01 0.20
Matches are distributed among these distances:
33 11 0.17
34 2 0.03
35 13 0.21
36 10 0.16
37 17 0.27
38 10 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (37 bp):
TTATATAATTTTTATTATATTATATTTAATTATATTT
Found at i:748482 original size:22 final size:23
Alignment explanation
Indices: 748420--748528 Score: 88
Period size: 22 Copynumber: 5.0 Consensus size: 23
748410 ATAGTATTCG
* *
748420 TATTATATATTTATA-TAT-TAA
1 TATTATATTTTTATATTATATTA
748441 TATTATATTTATT-T-TT-TATTA
1 TATTATATTT-TTATATTATATTA
*
748462 TATAAT-TTTTTATATTATATTTA
1 TATTATATTTTTATATTATA-TTA
* * *
748485 AATTATATTTTTATATAAT-TTT
1 TATTATATTTTTATATTATATTA
*
748507 TATTATATTATTATATTATATT
1 TATTATATTTTTATATTATATT
748529 TAAAATTATT
Statistics
Matches: 69, Mismatches: 10, Indels: 16
0.73 0.11 0.17
Matches are distributed among these distances:
19 2 0.03
20 5 0.07
21 20 0.29
22 22 0.32
23 9 0.13
24 11 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTATATTTTTATATTATATTA
Found at i:749368 original size:19 final size:19
Alignment explanation
Indices: 749327--749368 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
749317 TAAGATTTAA
*
749327 TTATTATTAAAAAATATTC
1 TTATTATTAAAAAATAATC
*
749346 TTATTAATTAAATAATAAT-
1 TTATT-ATTAAAAAATAATC
749365 TTAT
1 TTAT
749369 GGTTGATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATTATTAAAAAATAATC
Found at i:749923 original size:16 final size:16
Alignment explanation
Indices: 749899--749951 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
749889 AAATTATAGA
*
749899 TTAAATAAACAATTAT
1 TTAAATAAAAAATTAT
* *
749915 TTAACTAAATAAA-AAT
1 TTAAATAAA-AAATTAT
749931 TTAAATAAAAAATTAAT
1 TTAAATAAAAAATT-AT
749948 TTAA
1 TTAA
749952 TTTATTCCTG
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 3 0.10
16 18 0.62
17 8 0.28
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (16 bp):
TTAAATAAAAAATTAT
Found at i:749931 original size:19 final size:18
Alignment explanation
Indices: 749883--749931 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
749873 TTTTATTCAA
*
749883 AAATAAAAATTATAGATT
1 AAATAAAAATTATAGACT
749901 AAATAAACAATTATTTA-ACT
1 AAATAAA-AATTA--TAGACT
749921 AAATAAAAATT
1 AAATAAAAATT
749932 TAAATAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 7 0.26
19 9 0.33
20 9 0.33
21 2 0.07
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (18 bp):
AAATAAAAATTATAGACT
Found at i:750546 original size:20 final size:19
Alignment explanation
Indices: 750521--750599 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 19
750511 TTAAAGTAGT
750521 TTTAATATCATAAATTTATA
1 TTTAATAT-ATAAATTTATA
*
750541 TTTAATTTACTTATAA-TTATA
1 TTTAATATA--TA-AATTTATA
*
750562 TATAATTATATAAATTTATA
1 TTTAA-TATATAAATTTATA
*
750582 TATTATTAT-TAAATTTAT
1 T-TTAATATATAAATTTAT
750600 TATGTTATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
19 12 0.25
20 18 0.38
21 13 0.27
22 5 0.10
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTAATATATAAATTTATA
Found at i:750567 original size:10 final size:10
Alignment explanation
Indices: 750552--750590 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
750542 TTAATTTACT
750552 TATAATTATA
1 TATAATTATA
750562 TATAATTATA
1 TATAATTATA
750572 TA-AATTTATA
1 TATAA-TTATA
*
750582 TATTATTAT
1 TATAATTAT
750591 TAAATTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 23 0.88
11 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TATAATTATA
Found at i:750607 original size:20 final size:19
Alignment explanation
Indices: 750531--750613 Score: 71
Period size: 20 Copynumber: 4.2 Consensus size: 19
750521 TTTAATATCA
750531 TAAATTTATAT-TTAATTTACT
1 TAAATTTATATATT-A-TTA-T
*
750552 TATAA-TTATATATAATTAT
1 TA-AATTTATATATTATTAT
750571 ATAAATTTATATATTATTAT
1 -TAAATTTATATATTATTAT
* *
750591 TAAATTTATTATGTTATTTT
1 TAAATTTA-TATATTATTAT
750611 TAA
1 TAA
750614 TAATTTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
19 11 0.21
20 30 0.57
21 9 0.17
22 3 0.06
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (19 bp):
TAAATTTATATATTATTAT
Found at i:751441 original size:23 final size:23
Alignment explanation
Indices: 751415--751459 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
751405 ATATTTATAT
*
751415 ATTTAATATTTAAA-TTTATTGTA
1 ATTT-ATATTTAAAGATTATTGTA
*
751438 ATTTTTATTTAAAGATTATTGT
1 ATTTATATTTAAAGATTATTGT
751460 TGAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (23 bp):
ATTTATATTTAAAGATTATTGTA
Found at i:751947 original size:2 final size:2
Alignment explanation
Indices: 751942--751968 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
751932 TATAAAATTG
751942 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 A
751969 ATGCCATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:752810 original size:24 final size:23
Alignment explanation
Indices: 752759--752823 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 23
752749 ATCAAATATA
*
752759 AAAATATTTAAATTTAATTTTC-TT
1 AAAATATTTAAATTTAA--TTCGAT
*
752783 AAATTATTTAAATTTAATTCGAT
1 AAAATATTTAAATTTAATTCGAT
*
752806 AAAATA-TTAAATTAAATT
1 AAAATATTTAAATTTAATT
752824 TAATATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.39
23 6 0.17
24 16 0.44
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (23 bp):
AAAATATTTAAATTTAATTCGAT
Found at i:752847 original size:21 final size:23
Alignment explanation
Indices: 752814--752865 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
752804 ATAAAATATT
* * *
752814 AAATTAAATTTAAT-ATTTTTAA
1 AAATAAAATTAAATAATTTATAA
752836 AAATAAAATTAAATAATTTATAA
1 AAATAAAATTAAATAATTTATAA
*
752859 ATATAAA
1 AAATAAA
752866 TATTTTATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATAAAATTAAATAATTTATAA
Found at i:752858 original size:17 final size:17
Alignment explanation
Indices: 752841--752873 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
752831 TTTAAAAATA
752841 AAAT-TAAATAATTTAT
1 AAATATAAATAATTTAT
*
752857 AAATATAAATATTTTAT
1 AAATATAAATAATTTAT
752874 TCACGCTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATATAAATAATTTAT
Found at i:752866 original size:22 final size:21
Alignment explanation
Indices: 752813--752866 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
752803 GATAAAATAT
* *
752813 TAAAT-TAAATTTAATATTTT
1 TAAATATAAATTAAATATTTA
*
752833 TAAAAATAAAATTAAATAATTTA
1 TAAATAT-AAATTAAAT-ATTTA
752856 TAAATATAAAT
1 TAAATATAAAT
752867 ATTTTATTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 4 0.15
21 1 0.04
22 12 0.44
23 10 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATATAAATTAAATATTTA
Found at i:754289 original size:36 final size:36
Alignment explanation
Indices: 754249--754321 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
754239 AAAAACTCAA
*
754249 TGGCATCCCTTGGTGGGTAGGGATAGTATTCATTTT
1 TGGCATCCCTTGGTGGGTAGGAATAGTATTCATTTT
*
754285 TGGCATCCCTTGGTGGGTAGTAATAGTATTCATTTT
1 TGGCATCCCTTGGTGGGTAGGAATAGTATTCATTTT
754321 T
1 T
754322 CTTCTGTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.18, C:0.14, G:0.27, T:0.41
Consensus pattern (36 bp):
TGGCATCCCTTGGTGGGTAGGAATAGTATTCATTTT
Done.