Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007912.1 Hibiscus syriacus cultivar Beakdansim tig00110313_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: 1361188
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 4 of 6
Found at i:800321 original size:3 final size:3
Alignment explanation
Indices: 800313--800421 Score: 150
Period size: 3 Copynumber: 36.7 Consensus size: 3
800303 GTAATATTTG
800313 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
* **
800359 TAA TAA TAA TAA TAA TAA TAA T-A TGA TAA TAA TAA TTG TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
800405 TAA AAA TAA AAA TAA TA
1 TAA TAA TAA TAA TAA TA
800422 TATTCTCGGA
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
2 4 0.04
3 87 0.93
4 3 0.03
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:813941 original size:10 final size:10
Alignment explanation
Indices: 813926--813951 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
813916 TGTTGTTGTG
813926 GCCGTTTCAA
1 GCCGTTTCAA
813936 GCCGTTTCAA
1 GCCGTTTCAA
813946 GCCGTT
1 GCCGTT
813952 GGAGGTTGTT
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:0.15, C:0.31, G:0.23, T:0.31
Consensus pattern (10 bp):
GCCGTTTCAA
Found at i:822616 original size:2 final size:2
Alignment explanation
Indices: 822609--822643 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
822599 TCGAATGAGT
822609 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
822644 TCTATCTAAA
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:829008 original size:22 final size:22
Alignment explanation
Indices: 828982--829028 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
828972 TTAGGCGTAG
828982 TTTTTACTATGCACTATCAATT
1 TTTTTACTATGCACTATCAATT
* * *
829004 TTTTTTCTATGTACTATTAATT
1 TTTTTACTATGCACTATCAATT
829026 TTT
1 TTT
829029 CCTTCATTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.04, T:0.60
Consensus pattern (22 bp):
TTTTTACTATGCACTATCAATT
Found at i:836213 original size:58 final size:59
Alignment explanation
Indices: 836107--836217 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 59
836097 GGAGGGTTGG
* * * * *
836107 TTAGATCCGTATTATCGAGTTTTCCTTTTCATTGTGACTAGGAGGGTTCGATAAGAGAA
1 TTAGAGCCATATTATCGAGTTTTCCCTTTCATTGCGACTAGGACGGTTCGATAAGAGAA
836166 TTAGAGCCATATTATCGAG-TTTCCCTTTCATTGCGACTAGGACGGTTCGATA
1 TTAGAGCCATATTATCGAGTTTTCCCTTTCATTGCGACTAGGACGGTTCGATA
836218 GGACACTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
58 30 0.64
59 17 0.36
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (59 bp):
TTAGAGCCATATTATCGAGTTTTCCCTTTCATTGCGACTAGGACGGTTCGATAAGAGAA
Found at i:845112 original size:15 final size:15
Alignment explanation
Indices: 845092--845121 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
845082 AACCACGTCC
845092 CTGGCTTTAGTAATG
1 CTGGCTTTAGTAATG
845107 CTGGCTTTAGTAATG
1 CTGGCTTTAGTAATG
845122 TCACAACAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (15 bp):
CTGGCTTTAGTAATG
Found at i:845277 original size:16 final size:17
Alignment explanation
Indices: 845232--845277 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
845222 GTCTTAAAAC
845232 ATTATT-TCAATTAAAT
1 ATTATTATCAATTAAAT
*
845248 ATTATATATC-ATTATA-
1 ATTAT-TATCAATTAAAT
845264 ATTATTATCAATTA
1 ATTATTATCAATTA
845278 CAAGTTTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.15
16 14 0.54
17 6 0.23
18 2 0.08
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTATTATCAATTAAAT
Found at i:846016 original size:21 final size:21
Alignment explanation
Indices: 845960--846008 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
845950 TAGCACTATA
** *
845960 AATTATCACGTTAATATTTTG
1 AATTATCATATTAATATTGTG
845981 AATTATCATATTAATATTGT-
1 AATTATCATATTAATATTGTG
846001 AATTATCA
1 AATTATCA
846009 ATGATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (21 bp):
AATTATCATATTAATATTGTG
Found at i:846661 original size:21 final size:22
Alignment explanation
Indices: 846637--846677 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
846627 TTCTGAGTAA
846637 ATTAATTTT-TTTGTAAAATAT
1 ATTAATTTTATTTGTAAAATAT
* *
846658 ATTATTTTTATTTTTAAAAT
1 ATTAATTTTATTTGTAAAAT
846678 TAAAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
ATTAATTTTATTTGTAAAATAT
Found at i:847042 original size:13 final size:13
Alignment explanation
Indices: 847024--847050 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
847014 ACAGTCAAAT
847024 AATATTTTTTTTA
1 AATATTTTTTTTA
847037 AATATTTTTTTTA
1 AATATTTTTTTTA
847050 A
1 A
847051 TTTATCAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
AATATTTTTTTTA
Found at i:848146 original size:18 final size:17
Alignment explanation
Indices: 848118--848191 Score: 76
Period size: 18 Copynumber: 3.9 Consensus size: 17
848108 AAAATGTTAT
848118 TTATTATTTGTTTTGTA
1 TTATTATTTGTTTTGTA
*
848135 CTATTCATTTGTTTTATGTTA
1 TTATT-ATTTG-TTT-TG-TA
848156 TTTATTATTTGTTTTGTA
1 -TTATTATTTGTTTTGTA
848174 TTATTCATTTGTATTTGT
1 TTATT-ATTTGT-TTTGT
848192 TTTAACATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
17 9 0.19
18 13 0.27
19 10 0.21
20 5 0.10
21 7 0.15
22 4 0.08
ACGTcount: A:0.18, C:0.04, G:0.11, T:0.68
Consensus pattern (17 bp):
TTATTATTTGTTTTGTA
Found at i:848161 original size:39 final size:40
Alignment explanation
Indices: 848096--848185 Score: 146
Period size: 39 Copynumber: 2.3 Consensus size: 40
848086 TTTGTATCAT
848096 TATTCATTTGTTAAAATGTTATTTATTATTTGTTTTGTAC
1 TATTCATTTGTTAAAATGTTATTTATTATTTGTTTTGTAC
** *
848136 TATTCATTTGTT-TTATGTTATTTATTATTTGTTTTGTAT
1 TATTCATTTGTTAAAATGTTATTTATTATTTGTTTTGTAC
848175 TATTCATTTGT
1 TATTCATTTGT
848186 ATTTGTTTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.74
40 12 0.26
ACGTcount: A:0.21, C:0.04, G:0.10, T:0.64
Consensus pattern (40 bp):
TATTCATTTGTTAAAATGTTATTTATTATTTGTTTTGTAC
Found at i:848167 original size:21 final size:21
Alignment explanation
Indices: 848111--848170 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
848101 ATTTGTTAAA
848111 ATGTTATTTATTATTTG-TTT
1 ATGTTATTTATTATTTGTTTT
*
848131 -TG-TA-CTATTCATTTGTTTT
1 ATGTTATTTATT-ATTTGTTTT
848150 ATGTTATTTATTATTTGTTTT
1 ATGTTATTTATTATTTGTTTT
848171 GTATTATTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
17 4 0.12
18 7 0.21
19 5 0.15
20 2 0.06
21 11 0.33
22 4 0.12
ACGTcount: A:0.18, C:0.03, G:0.10, T:0.68
Consensus pattern (21 bp):
ATGTTATTTATTATTTGTTTT
Found at i:848177 original size:21 final size:21
Alignment explanation
Indices: 848114--848178 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
848104 TGTTAAAATG
848114 TTATTTATTATTTGTTTTGTA
1 TTATTTATTATTTGTTTTGTA
* * * *
848135 CTA--T-TCATTTGTTTTATG
1 TTATTTATTATTTGTTTTGTA
848153 TTATTTATTATTTGTTTTGTA
1 TTATTTATTATTTGTTTTGTA
848174 TTATT
1 TTATT
848179 CATTTGTATT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 13 0.39
19 1 0.03
20 1 0.03
21 18 0.55
ACGTcount: A:0.18, C:0.03, G:0.09, T:0.69
Consensus pattern (21 bp):
TTATTTATTATTTGTTTTGTA
Found at i:848412 original size:18 final size:17
Alignment explanation
Indices: 848391--848429 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
848381 TCTTTTCTGG
848391 TATTCATTTTATTTGTTT
1 TATTCATTTTATTT-TTT
**
848409 TATTTGTTTTATTTTTT
1 TATTCATTTTATTTTTT
848426 TATT
1 TATT
848430 TTTAAGGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (17 bp):
TATTCATTTTATTTTTT
Found at i:848432 original size:9 final size:9
Alignment explanation
Indices: 848397--848430 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
848387 CTGGTATTCA
848397 TTTTATTTG
1 TTTTATTTG
848406 TTTTATTTG
1 TTTTATTTG
848415 TTTTATTT-
1 TTTTATTTG
848423 TTTTATTT
1 TTTTATTT
848431 TTAAGGGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (9 bp):
TTTTATTTG
Found at i:848542 original size:3 final size:3
Alignment explanation
Indices: 848534--848558 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
848524 AAACCAATGT
848534 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
848559 GCTAATTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:848594 original size:17 final size:17
Alignment explanation
Indices: 848574--848621 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
848564 TTGTTTTATG
*
848574 TTTTTATATGTTTTTTA
1 TTTTTATATGTTTTTAA
848591 TTTTCTAT-T-TTTTTAA
1 TTTT-TATATGTTTTTAA
*
848607 ATTTTATATGTTTTT
1 TTTTTATATGTTTTT
848622 GGTTTTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 3 0.12
16 10 0.38
17 10 0.38
18 3 0.12
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.75
Consensus pattern (17 bp):
TTTTTATATGTTTTTAA
Found at i:848674 original size:17 final size:17
Alignment explanation
Indices: 848654--848778 Score: 55
Period size: 18 Copynumber: 7.0 Consensus size: 17
848644 TTTTTATACA
848654 TTATATGTTTTTATTTT
1 TTATATGTTTTTATTTT
* *
848671 TTATTTTCTGTTTTTATATT
1 TTA---TATGTTTTTATTTT
*
848691 TTATTTGTTTTTCCTATTTAT
1 TTATATG-TTTT--TATTT-T
*
848712 TTATTTGTTTTT-TGTTT
1 TTATATGTTTTTAT-TTT
*
848729 TTAT-T-TATTTT-TTGT
1 TTATATGT-TTTTATTTT
848744 TT-TATGTTATTTATTTGT
1 TTATATGTT-TTTATTT-T
848762 TT-TATGTTATTTATTTT
1 TTATATGTT-TTTATTTT
848779 CTATTCTAAC
Statistics
Matches: 88, Mismatches: 6, Indels: 28
0.72 0.05 0.23
Matches are distributed among these distances:
14 1 0.01
15 7 0.08
16 10 0.11
17 15 0.17
18 24 0.27
20 23 0.26
21 8 0.09
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.76
Consensus pattern (17 bp):
TTATATGTTTTTATTTT
Found at i:848682 original size:20 final size:20
Alignment explanation
Indices: 848659--848696 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
848649 ATACATTATA
*
848659 TGTTTTTATTTTTTATTTTC
1 TGTTTTTATATTTTATTTTC
848679 TGTTTTTATATTTTATTT
1 TGTTTTTATATTTTATTT
848697 GTTTTTCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.05, T:0.79
Consensus pattern (20 bp):
TGTTTTTATATTTTATTTTC
Found at i:848716 original size:21 final size:20
Alignment explanation
Indices: 848690--848764 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 20
848680 GTTTTTATAT
848690 TTTATTTGTTTTTCCTATTTA
1 TTTATTTGTTTTT-CTATTTA
* *
848711 TTTATTTGTTTTTTGTTTTTA
1 TTTATTTG-TTTTTCTATTTA
*
848732 TTTATTT-TTTGTTTTATGTTA
1 TTTATTTGTTT-TTCTAT-TTA
848753 TTTATTTGTTTT
1 TTTATTTGTTTT
848765 ATGTTATTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.07
20 4 0.09
21 31 0.67
22 8 0.17
ACGTcount: A:0.12, C:0.03, G:0.08, T:0.77
Consensus pattern (20 bp):
TTTATTTGTTTTTCTATTTA
Found at i:848756 original size:25 final size:24
Alignment explanation
Indices: 848705--848769 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 24
848695 TTGTTTTTCC
*
848705 TATTTATTTATTTGTTTTTTGTTTT
1 TATTTATTT-TTTGTTTTATGTTTT
848730 TATTTATTTTTTGTTTTATGTTATT
1 TATTTATTTTTTGTTTTATGTT-TT
* *
848755 TATTTGTTTTATGTT
1 TATTTATTTTTTGTT
848770 ATTTATTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 12 0.33
25 24 0.67
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (24 bp):
TATTTATTTTTTGTTTTATGTTTT
Found at i:848760 original size:18 final size:18
Alignment explanation
Indices: 848722--848777 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
848712 TTATTTGTTT
848722 TTTGTTTTTAT-TTATTT-
1 TTTG-TTTTATGTTATTTA
848739 TTTGTTTTATGTTATTTA
1 TTTGTTTTATGTTATTTA
848757 TTTGTTTTATGTTATTTA
1 TTTGTTTTATGTTATTTA
848775 TTT
1 TTT
848778 TCTATTCTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
16 6 0.16
17 10 0.27
18 21 0.57
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (18 bp):
TTTGTTTTATGTTATTTA
Found at i:851034 original size:56 final size:58
Alignment explanation
Indices: 850973--851087 Score: 162
Period size: 58 Copynumber: 2.0 Consensus size: 58
850963 TATTGTAGGG
*
850973 TGCTACTACTTTTACATTTA-TTGTTT-TTCATTAATTTTCATGAATTTCAACAAGCA
1 TGCTACTACTTTTACATTTACTTGTTTATTCATTAATTTTCATAAATTTCAACAAGCA
* * * * *
851029 TGCTACTGCTTTTACATTTACTTTTTTATTTATTAATTTTCATAAATTTTAGCAAGCA
1 TGCTACTACTTTTACATTTACTTGTTTATTCATTAATTTTCATAAATTTCAACAAGCA
851087 T
1 T
851088 ATAAATGAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
56 19 0.37
57 5 0.10
58 27 0.53
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (58 bp):
TGCTACTACTTTTACATTTACTTGTTTATTCATTAATTTTCATAAATTTCAACAAGCA
Found at i:851244 original size:22 final size:22
Alignment explanation
Indices: 851219--851279 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
851209 ATTGGACTTA
* *
851219 GTCTTAATGCTGATTGGAAACT
1 GTCTTAATGCTAATTAGAAACT
* *
851241 GTCTGAATGCTAATTAGAAATT
1 GTCTTAATGCTAATTAGAAACT
*
851263 GT-TTGAATGCTTATTAG
1 GTCTT-AATGCTAATTAG
851280 TTTTGGTCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 1 0.03
22 31 0.97
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (22 bp):
GTCTTAATGCTAATTAGAAACT
Found at i:855903 original size:21 final size:21
Alignment explanation
Indices: 855861--855904 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
855851 ACTCCGGGAG
* *
855861 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
855882 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
855903 CT
1 CT
855905 CCTCCGACTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:860985 original size:23 final size:21
Alignment explanation
Indices: 860931--860992 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
860921 TTTTGGTGCA
860931 GAGGGAATCGATACCCCC-AT
1 GAGGGAATCGATACCCCCTAT
* * *
860951 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATACCCCCTAT
860972 GAAGGGGAATCGATACCCCCT
1 G-A-GGGAATCGATACCCCCT
860993 GGGGTTCTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 16 0.47
21 2 0.06
22 1 0.03
23 15 0.44
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAATCGATACCCCCTAT
Found at i:865096 original size:17 final size:19
Alignment explanation
Indices: 865069--865117 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
865059 TATTTTGAAA
865069 CATCGAATGCACT-TGA-TG
1 CATC-AATGCACTCTGAGTG
*
865087 CATCAATGCACTCTTAGTG
1 CATCAATGCACTCTGAGTG
*
865106 CACCAATGCACT
1 CATCAATGCACT
865118 AAGGGTCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 8 0.30
18 6 0.22
19 13 0.48
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (19 bp):
CATCAATGCACTCTGAGTG
Found at i:869262 original size:49 final size:48
Alignment explanation
Indices: 869179--869375 Score: 270
Period size: 49 Copynumber: 4.0 Consensus size: 48
869169 ATACCATGAG
*
869179 TGGCACCTTTTATACCGAAAATGCACCGTTATGCATTTGAA-TTTCATTA
1 TGGCACCTTTTATGCC-AAAATGCACCGTTATGCATTT-AACTTTCATTA
* *
869228 TTGGCATCTTTTATGCCAAAATACACCGTTATGCATTTAACTTTCATTA
1 -TGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTTTCATTA
* *
869277 CTGGCACCTTTAATGCCAAAATGCACGGTTATGCATTTAACTTTCATTA
1 -TGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTTTCATTA
* * *
869326 CGAGCACCTTTTATGCCAAAATGCACCGTTATGCATGTAACTTTCTTTA
1 TG-GCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTTTCATTA
869375 T
1 T
869376 TCATTTTAGA
Statistics
Matches: 131, Mismatches: 14, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
48 3 0.02
49 114 0.87
50 14 0.11
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (48 bp):
TGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTTTCATTA
Found at i:887405 original size:20 final size:20
Alignment explanation
Indices: 887380--887421 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
887370 GAAAGTCTCA
887380 TTACTTTTCTTTTCCATATT
1 TTACTTTTCTTTTCCATATT
887400 TTACTTTTCTTTTCCATATT
1 TTACTTTTCTTTTCCATATT
887420 TT
1 TT
887422 GAAGAGTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (20 bp):
TTACTTTTCTTTTCCATATT
Found at i:895792 original size:14 final size:16
Alignment explanation
Indices: 895773--895809 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
895763 CATTATGGAT
895773 ATCCAT-CAATCA-AC
1 ATCCATACAATCACAC
895787 ATCCATACAATCACAC
1 ATCCATACAATCACAC
*
895803 ATGCATA
1 ATCCATA
895810 AAACGGTGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 6 0.30
15 6 0.30
16 8 0.40
ACGTcount: A:0.43, C:0.32, G:0.03, T:0.22
Consensus pattern (16 bp):
ATCCATACAATCACAC
Found at i:905270 original size:15 final size:15
Alignment explanation
Indices: 905244--905291 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
905234 TTCAAACATC
*
905244 CAAACAAATCCAAAGT
1 CAAAC-AATCCAAAAT
*
905260 CTAACAATCCACAAAAT
1 CAAACAAT-C-CAAAAT
905277 CAAACAATCCAAAAT
1 CAAACAATCCAAAAT
905292 ATTCAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 9 0.33
16 6 0.22
17 12 0.44
ACGTcount: A:0.56, C:0.27, G:0.02, T:0.15
Consensus pattern (15 bp):
CAAACAATCCAAAAT
Found at i:907272 original size:21 final size:21
Alignment explanation
Indices: 907246--907285 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
907236 CAGAACCCCA
*
907246 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
907267 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
907286 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:923258 original size:45 final size:45
Alignment explanation
Indices: 923209--923296 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
923199 AAAATAGCCA
* * *
923209 GAGTGCATCGATGCATGGTTTATGCATCGATGCATCAAATGCAAT
1 GAGTGCATCGATGCATGGTATATGCATAGATGCATAAAATGCAAT
* * *
923254 GAGTGTATCGATGCATGGTATGTGCATAGATTCATAAAATGCA
1 GAGTGCATCGATGCATGGTATATGCATAGATGCATAAAATGCA
923297 TTTGATGTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30
Consensus pattern (45 bp):
GAGTGCATCGATGCATGGTATATGCATAGATGCATAAAATGCAAT
Found at i:925743 original size:29 final size:29
Alignment explanation
Indices: 925676--925743 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
925666 TTTTGGGCTC
*
925676 AACCCTAAACCAAAACCTTAAATAAAATA
1 AACCTTAAACCAAAACCTTAAATAAAATA
* * *
925705 AATCTCAAACC-AAAGCTTAAAATAAAATA
1 AACCTTAAACCAAAACCTT-AAATAAAATA
*
925734 TACCTTAAAC
1 AACCTTAAAC
925744 TAAACCCCAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
28 6 0.19
29 25 0.81
ACGTcount: A:0.56, C:0.22, G:0.01, T:0.21
Consensus pattern (29 bp):
AACCTTAAACCAAAACCTTAAATAAAATA
Found at i:926164 original size:9 final size:8
Alignment explanation
Indices: 926152--926185 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
926142 TTTTTTATAG
926152 AAAATAACA
1 AAAATAA-A
926161 AAAATAAA
1 AAAATAAA
926169 AAAATAAA
1 AAAATAAA
926177 AAATATAAA
1 AAA-ATAAA
926186 TGGCTTAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 12 0.50
9 12 0.50
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (8 bp):
AAAATAAA
Found at i:926174 original size:17 final size:17
Alignment explanation
Indices: 926152--926185 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
926142 TTTTTTATAG
926152 AAAATAACAAAA-ATAAA
1 AAAATAA-AAAATATAAA
926169 AAAATAAAAAATATAAA
1 AAAATAAAAAATATAAA
926186 TGGCTTAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAATAAAAAATATAAA
Found at i:927243 original size:22 final size:22
Alignment explanation
Indices: 927201--927243 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
927191 CAAACTTAGA
* *
927201 AATTAGGACGACAATCTAGTTT
1 AATTAGGAAGACAATCGAGTTT
927223 AATTAGGAAG-CAATTCGAGTT
1 AATTAGGAAGACAA-TCGAGTT
927244 GAGTTTTCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (22 bp):
AATTAGGAAGACAATCGAGTTT
Found at i:931757 original size:23 final size:23
Alignment explanation
Indices: 931731--931796 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
931721 CACCACAGCT
*
931731 CGTATAATTGCACCGAAGTGCCA
1 CGTAAAATTGCACCGAAGTGCCA
* *
931754 CGTAGAATTGCACCGTAA-TGCCG
1 CGTAAAATTGCACCG-AAGTGCCA
* *
931777 CATAAAAATGCACCGAAGTG
1 CGTAAAATTGCACCGAAGTG
931797 TCGTATAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 2 0.06
23 32 0.89
24 2 0.06
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (23 bp):
CGTAAAATTGCACCGAAGTGCCA
Found at i:934227 original size:13 final size:13
Alignment explanation
Indices: 934203--934237 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
934193 TATAGAAATT
934203 TATTTTATTTT-C
1 TATTTTATTTTCC
934215 TATTTTCATTTTCC
1 TATTTT-ATTTTCC
934229 TATTTTATT
1 TATTTTATT
934238 AATTTAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.29
13 8 0.38
14 7 0.33
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTTTATTTTCC
Found at i:934403 original size:20 final size:20
Alignment explanation
Indices: 934378--934440 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
934368 TAAATAATGA
934378 TTCAAAATTATTAAATTAAT
1 TTCAAAATTATTAAATTAAT
*
934398 TTCAAAATCATTCAAATTAA-
1 TTCAAAATTATT-AAATTAAT
* * *
934418 ATCATAATTTATTAATTTAAT
1 TTCA-AAATTATTAAATTAAT
934439 TT
1 TT
934441 TCTATTTTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
20 20 0.59
21 14 0.41
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (20 bp):
TTCAAAATTATTAAATTAAT
Found at i:934580 original size:22 final size:23
Alignment explanation
Indices: 934554--934612 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 23
934544 TATAAAATAT
934554 TTATTTAAAT-TTTATAAATAAAA
1 TTATTTAAATATTTA-AAATAAAA
*
934577 -TATTTAAACTATTTAAACTAAAA
1 TTATTTAAA-TATTTAAAATAAAA
934600 TTCATTTAAATAT
1 TT-ATTTAAATAT
934613 AATTAATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 8 0.26
23 8 0.26
24 8 0.26
25 7 0.23
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
TTATTTAAATATTTAAAATAAAA
Found at i:935449 original size:21 final size:21
Alignment explanation
Indices: 935423--935469 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
935413 AAGACGCTTC
935423 TATGTGTAAGCGCCGTTGACT
1 TATGTGTAAGCGCCGTTGACT
935444 TATGTGTAAGCGCCGTTGACT
1 TATGTGTAAGCGCCGTTGACT
935465 TATGT
1 TATGT
935470 AAGACAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.36
Consensus pattern (21 bp):
TATGTGTAAGCGCCGTTGACT
Found at i:939590 original size:26 final size:26
Alignment explanation
Indices: 939561--939613 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
939551 ACTTTACTCA
939561 AAACCGTATCAAGTAAATTTTACTTG
1 AAACCGTATCAAGTAAATTTTACTTG
939587 AAACCGTATCAAGTAAATTTTACTTG
1 AAACCGTATCAAGTAAATTTTACTTG
939613 A
1 A
939614 TGTGCGCCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (26 bp):
AAACCGTATCAAGTAAATTTTACTTG
Found at i:942586 original size:11 final size:11
Alignment explanation
Indices: 942570--942605 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
942560 TTAGTAATAA
942570 TTATTATTATT
1 TTATTATTATT
*
942581 TTATTATTAAT
1 TTATTATTATT
942592 TTATATATTATT
1 TTAT-TATTATT
942604 TT
1 TT
942606 TTGTAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTATTATT
Found at i:942591 original size:24 final size:24
Alignment explanation
Indices: 942557--942623 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 24
942547 TTAATTTAAA
*
942557 TTATTAGTAATAATTATTATTATT
1 TTATTATTAATAATTATTATTATT
* *
942581 TTATTATTAATTTATATATTATTTTT
1 TTATTATTAA-TAAT-TATTATTATT
942607 TGTAATTATTAATAATT
1 T-T-ATTATTAATAATT
942624 TTAGGAGAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 9 0.26
25 3 0.09
26 11 0.31
27 4 0.11
28 8 0.23
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (24 bp):
TTATTATTAATAATTATTATTATT
Found at i:948457 original size:30 final size:30
Alignment explanation
Indices: 948421--948514 Score: 118
Period size: 30 Copynumber: 3.1 Consensus size: 30
948411 ACCAAAGATA
948421 AGAGGATTGTTAG-GTGATGTTTACGGGTTG
1 AGAGGATTGTT-GTGTGATGTTTACGGGTTG
*
948451 AGAGGATTGTTGTGTGATGTTTACGAGTTG
1 AGAGGATTGTTGTGTGATGTTTACGGGTTG
* ** * *
948481 ATAGGATTACTGTGTGATGTTTACAGGTCG
1 AGAGGATTGTTGTGTGATGTTTACGGGTTG
948511 AGAG
1 AGAG
948515 TGTATTATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 1 0.02
30 54 0.98
ACGTcount: A:0.22, C:0.05, G:0.36, T:0.36
Consensus pattern (30 bp):
AGAGGATTGTTGTGTGATGTTTACGGGTTG
Found at i:954143 original size:58 final size:57
Alignment explanation
Indices: 954081--954201 Score: 136
Period size: 60 Copynumber: 2.1 Consensus size: 57
954071 ATTTGAACGA
* * * ** *
954081 AATTTA-GATGAAATTGGAAGATTCAAAAATTTGGGGACTAATTTAAAATTAGAGTCAT
1 AATTTAGGATAAAAATGGAAGATTAAAAAATTTAAGGACAAATTTAAAA-T-GAGTCAT
* *
954139 AATTTAGGGATAAAAATGGAATATTAAAAAATTTAAGGACAAATTTAAAATGAGTTAT
1 AATTTA-GGATAAAAATGGAAGATTAAAAAATTTAAGGACAAATTTAAAATGAGTCAT
954197 AATTT
1 AATTT
954202 GGAGACATGT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
58 17 0.32
59 1 0.02
60 35 0.66
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (57 bp):
AATTTAGGATAAAAATGGAAGATTAAAAAATTTAAGGACAAATTTAAAATGAGTCAT
Found at i:955323 original size:56 final size:59
Alignment explanation
Indices: 955184--955329 Score: 190
Period size: 56 Copynumber: 2.5 Consensus size: 59
955174 GATCATTTTG
* * **
955184 TAACTTTCAATAGTCGAGAGACTCAACAAAGCAACTCTCTATAGTTGGACGACCACTTTA
1 TAACTTTTAATAGTCGAGAGACTCAACAAAGCAACACTCTATAGGAGGA-GACCACTTTA
*
955244 TAACTTTTAATAGTCGAGTGACTCAACAAAGCAACACTCT-T-GGAGG-GACCACTTTA
1 TAACTTTTAATAGTCGAGAGACTCAACAAAGCAACACTCTATAGGAGGAGACCACTTTA
** *
955300 TAACTTTTAATAGTTAAGGGACTCAACAAA
1 TAACTTTTAATAGTCGAGAGACTCAACAAA
955330 ATAGTATCCT
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
56 37 0.47
58 3 0.04
59 1 0.01
60 37 0.47
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (59 bp):
TAACTTTTAATAGTCGAGAGACTCAACAAAGCAACACTCTATAGGAGGAGACCACTTTA
Found at i:955624 original size:32 final size:32
Alignment explanation
Indices: 955588--955673 Score: 120
Period size: 31 Copynumber: 2.7 Consensus size: 32
955578 ATAGTGATTG
* * *
955588 AATTTTATTAAATTATTATAAAGTGGTCATAA
1 AATTTTATAAAATTGTTATAAAATGGTCATAA
*
955620 AA-TTTATAAAATTGTTATAAAATGGTCATTA
1 AATTTTATAAAATTGTTATAAAATGGTCATAA
*
955651 AATTTTATCAAATTGTTATAAAA
1 AATTTTATAAAATTGTTATAAAA
955674 ATAGTCTTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 27 0.56
32 21 0.44
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.43
Consensus pattern (32 bp):
AATTTTATAAAATTGTTATAAAATGGTCATAA
Found at i:955637 original size:11 final size:11
Alignment explanation
Indices: 955588--955673 Score: 63
Period size: 11 Copynumber: 8.2 Consensus size: 11
955578 ATAGTGATTG
*
955588 AATT-TTATTA
1 AATTGTTATAA
*
955598 AATTATTATAA
1 AATTGTTATAA
* * *
955609 AGTGGTCATAA
1 AATTGTTATAA
955620 AA-T-TTATAA
1 AATTGTTATAA
955629 AATTGTTATAA
1 AATTGTTATAA
* * *
955640 AATGGTCATTA
1 AATTGTTATAA
*
955651 AATT-TTATCA
1 AATTGTTATAA
955661 AATTGTTATAA
1 AATTGTTATAA
955672 AA
1 AA
955674 ATAGTCTTCA
Statistics
Matches: 57, Mismatches: 15, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
9 7 0.12
10 13 0.23
11 37 0.65
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.43
Consensus pattern (11 bp):
AATTGTTATAA
Found at i:955959 original size:95 final size:94
Alignment explanation
Indices: 955851--956044 Score: 289
Period size: 95 Copynumber: 2.1 Consensus size: 94
955841 TTAGATTACA
** *
955851 ATAATTTATGTTATGTTTTTTTAAACAAGATAAAGCAATATTTAATACTTGAATTTCATAAACTT
1 ATAATTTATGTTATGCATTTTTAAACAAGATAAAACAATATTTAATACTTGAATTTCAT-AACTT
* *
955916 TTAAATTTTAATTTAATTTCTTTTGACGTG
65 TTAAAATTTAATTTAATTTCTTATGACGTG
** * *
955946 ATAATTTATGTTATGCATTTTTAAATGAGATAAAACAATATTTAATACTTGAATTTGATAATTTT
1 ATAATTTATGTTATGCATTTTTAAACAAGATAAAACAATATTTAATACTTGAATTTCATAACTTT
*
956011 TAAAATTTAATTTAATTTCTTATGTCGTG
66 TAAAATTTAATTTAATTTCTTATGACGTG
956040 ATAAT
1 ATAAT
956045 ATATAAATGT
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
94 36 0.40
95 53 0.60
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (94 bp):
ATAATTTATGTTATGCATTTTTAAACAAGATAAAACAATATTTAATACTTGAATTTCATAACTTT
TAAAATTTAATTTAATTTCTTATGACGTG
Found at i:958242 original size:34 final size:34
Alignment explanation
Indices: 958197--958303 Score: 160
Period size: 34 Copynumber: 3.1 Consensus size: 34
958187 TAAGTTGAAA
* *
958197 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
958231 TTTAATTTTAAATTTCGAATAATATTATTTTTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
958265 TTTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
958299 TTTAA
1 TTTAA
958304 AAACATTTAT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 65 1.00
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:958855 original size:21 final size:21
Alignment explanation
Indices: 958824--958957 Score: 191
Period size: 21 Copynumber: 6.4 Consensus size: 21
958814 TATGGTATAA
* *
958824 AACCCTACGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
958845 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
958866 AACCCTGCGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGT
958887 AACCCTGCGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGT
* *
958908 AACCCTGCAGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
958929 AACCTTGCGGGCTCA-GAATGT
1 AACCCTGCGGGCT-AGGAATGT
958950 AACCCTGC
1 AACCCTGC
958958 AGAGATGGCA
Statistics
Matches: 102, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
20 3 0.03
21 96 0.94
22 3 0.03
ACGTcount: A:0.24, C:0.26, G:0.31, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:958983 original size:42 final size:42
Alignment explanation
Indices: 958848--958983 Score: 109
Period size: 42 Copynumber: 3.2 Consensus size: 42
958838 GGCATGTAAC
* * * * *
958848 CTGGCGGGCT-AGGAATGTAACCCTGCGGGCTAGGAATGTAACC
1 CTGGCGGGCTCA-GAATGTAACCCTGCAGGATCGGAATATAA-A
* * *
958891 CT-GCGGGCT-AGGAATGTAACCCTGCAGGCTCGGAATGTAAC
1 CTGGCGGGCTCA-GAATGTAACCCTGCAGGATCGGAATATAAA
* *
958932 CTTGCGGGCTCAGAATGTAACCCTGCAGAGAT-GGCATATAAA
1 CTGGCGGGCTCAGAATGTAACCCTGCAG-GATCGGAATATAAA
*
958974 CTGGTGGGCT
1 CTGGCGGGCT
958984 TGGCATATGA
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
41 3 0.04
42 74 0.90
43 5 0.06
ACGTcount: A:0.24, C:0.23, G:0.32, T:0.21
Consensus pattern (42 bp):
CTGGCGGGCTCAGAATGTAACCCTGCAGGATCGGAATATAAA
Found at i:958989 original size:21 final size:21
Alignment explanation
Indices: 958963--959010 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
958953 CCTGCAGAGA
*
958963 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
958984 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
959005 GGGCAT
1 TGGCAT
959011 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:960801 original size:30 final size:32
Alignment explanation
Indices: 960737--960815 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 32
960727 TTAATAATTC
*
960737 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAATAATAATTACATAAATATTA-TTTAA
*
960771 TAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAATAATAATTACATAAATATTATTTAA
960801 TATAAAATATAATAA
1 TA-AAAA-ATAATAA
960816 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 6 0.15
31 4 0.10
32 8 0.20
33 18 0.45
34 4 0.10
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
TAAAAAATAATAATTACATAAATATTATTTAA
Found at i:961047 original size:16 final size:16
Alignment explanation
Indices: 961026--961056 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
961016 TGGAAGGCGC
961026 GTCCCTGGGGATGCGT
1 GTCCCTGGGGATGCGT
961042 GTCCCTGGGGATGCG
1 GTCCCTGGGGATGCG
961057 CTTTCCACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.26, G:0.45, T:0.23
Consensus pattern (16 bp):
GTCCCTGGGGATGCGT
Found at i:961166 original size:52 final size:51
Alignment explanation
Indices: 961038--961175 Score: 222
Period size: 51 Copynumber: 2.7 Consensus size: 51
961028 CCCTGGGGAT
*
961038 GCGTGTCCCTGGGGATGCGCTTTCCACACGTGGCAGTCGAGCTGGCGAAAG
1 GCGTGTCCCCGGGGATGCGCTTTCCACACGTGGCAGTCGAGCTGGCGAAAG
* * *
961089 GCGCGTCCCCGTGGATGCGCTTTCCACACGTGGCAGTCTAGCTGGCGAAAAG
1 GCGTGTCCCCGGGGATGCGCTTTCCACACGTGGCAGTCGAGCTGGCG-AAAG
*
961141 GCGTGTCCCCGGGGATGCGCCTTCCACACGTGGCA
1 GCGTGTCCCCGGGGATGCGCTTTCCACACGTGGCA
961176 TCCAACTCAG
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
51 43 0.54
52 36 0.46
ACGTcount: A:0.15, C:0.31, G:0.35, T:0.19
Consensus pattern (51 bp):
GCGTGTCCCCGGGGATGCGCTTTCCACACGTGGCAGTCGAGCTGGCGAAAG
Found at i:965741 original size:44 final size:44
Alignment explanation
Indices: 965669--965775 Score: 162
Period size: 44 Copynumber: 2.4 Consensus size: 44
965659 TATAAAATTT
*
965669 CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTACCAATATA
1 CTTACCATTTAT-CCATAAGCTCATAAGCTTATTTTACCAATACA
*
965714 CTTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATACA
1 CTTACCATTTATCCATAAGCTCATAAGCTTATTTTACCAATACA
*
965758 CTTGCCA-TTATTCCATAA
1 CTTACCATTTA-TCCATAA
965776 CCATATACCA
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
43 3 0.05
44 43 0.74
45 12 0.21
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (44 bp):
CTTACCATTTATCCATAAGCTCATAAGCTTATTTTACCAATACA
Found at i:970171 original size:30 final size:31
Alignment explanation
Indices: 970113--970172 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
970103 AAGTTACCAA
**
970113 TTTACCCTTAAAATTTCATAATCCTTACTAT
1 TTTACCCTTAAAATTTCATAATAATTACTAT
* *
970144 TTTACCCTT-GAATTTCATGATAATTACTA
1 TTTACCCTTAAAATTTCATAATAATTACTA
970173 AATTATCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.45
Consensus pattern (31 bp):
TTTACCCTTAAAATTTCATAATAATTACTAT
Found at i:976336 original size:19 final size:19
Alignment explanation
Indices: 976292--976342 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
976282 GTTAACGGGC
976292 CAGGTCAAAGTCAATGAGT
1 CAGGTCAAAGTCAATGAGT
**
976311 TGGGTCAAAGTCAATGAGT
1 CAGGTCAAAGTCAATGAGT
*
976330 CATGTCAAAGTCA
1 CAGGTCAAAGTCA
976343 TTGCCAGCGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (19 bp):
CAGGTCAAAGTCAATGAGT
Found at i:977136 original size:29 final size:29
Alignment explanation
Indices: 977102--977166 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
977092 ACTGAGCTAC
977102 AAACTTTTAAAAATTTGTAATTTGGTCCT
1 AAACTTTTAAAAATTTGTAATTTGGTCCT
977131 AAACTTTTAAAAATTTGTAATTTGGTCCT
1 AAACTTTTAAAAATTTGTAATTTGGTCCT
*
977160 CAACTTT
1 AAACTTT
977167 CATTTAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (29 bp):
AAACTTTTAAAAATTTGTAATTTGGTCCT
Found at i:981112 original size:22 final size:22
Alignment explanation
Indices: 981087--981148 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
981077 ACTTTTTTAA
981087 TCAAAGTCAACGGTCATAGCGG
1 TCAAAGTCAACGGTCATAGCGG
981109 TCAAAGTCAACGGTCATAGCGG
1 TCAAAGTCAACGGTCATAGCGG
*
981131 TCGAAGTCAACGGTCATA
1 TCAAAGTCAACGGTCATA
981149 CTGGTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (22 bp):
TCAAAGTCAACGGTCATAGCGG
Found at i:981182 original size:19 final size:19
Alignment explanation
Indices: 981158--981213 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
981148 ACTGGTTAAC
*
981158 AGTCAATGGGTCAGGTCCA
1 AGTCAATGGGTCAGGTCAA
*** **
981177 AGTCAACAAGTTGGGTCAA
1 AGTCAATGGGTCAGGTCAA
981196 AGTCAATGGGTCAGGTCA
1 AGTCAATGGGTCAGGTCA
981214 GGTTGACTCA
Statistics
Matches: 26, Mismatches: 11, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.21
Consensus pattern (19 bp):
AGTCAATGGGTCAGGTCAA
Found at i:984020 original size:24 final size:25
Alignment explanation
Indices: 983974--984021 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
983964 TTAAATATAT
*
983974 TTGCACTCGAAAGTGCCTTGTAGAA
1 TTGCACTCGAAAGTGCCTCGTAGAA
983999 TTGCACTCGAAA-TGCCTCGTAGA
1 TTGCACTCGAAAGTGCCTCGTAGA
984022 TTTGTACCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (25 bp):
TTGCACTCGAAAGTGCCTCGTAGAA
Found at i:1005029 original size:1 final size:1
Alignment explanation
Indices: 1005025--1005076 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
1005015 CTTTTTTGGC
* *** * *
1005025 TTTTTTTTTGTTTTTTTTTTTTTGCCTTTTTTTGTTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1005077 AAATAGCAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.88
Consensus pattern (1 bp):
T
Found at i:1005038 original size:9 final size:9
Alignment explanation
Indices: 1005025--1005075 Score: 61
Period size: 9 Copynumber: 5.8 Consensus size: 9
1005015 CTTTTTTGGC
1005025 TTTTTTT-T
1 TTTTTTTGT
*
1005033 TGTTTTT-T
1 TTTTTTTGT
*
1005041 TTTTTTTGCC
1 TTTTTTTG-T
1005051 TTTTTTTGT
1 TTTTTTTGT
1005060 TTTTTTTGT
1 TTTTTTTGT
1005069 TTTTTTT
1 TTTTTTT
1005076 TAAATAGCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
8 13 0.35
9 16 0.43
10 8 0.22
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.88
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:1005043 original size:24 final size:24
Alignment explanation
Indices: 1005016--1005071 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 24
1005006 AAATTTTGGC
*
1005016 TTTTTTGGCTTTTTTTTTGTTTTTT
1 TTTTTTGGC-CTTTTTTTGTTTTTT
*
1005041 TTTTTTTGCCTTTTTTTGTTTTTT
1 TTTTTTGGCCTTTTTTTGTTTTTT
1005065 TTGTTTT
1 TT-TTTT
1005072 TTTTTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 16 0.57
25 12 0.43
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.84
Consensus pattern (24 bp):
TTTTTTGGCCTTTTTTTGTTTTTT
Found at i:1006424 original size:24 final size:24
Alignment explanation
Indices: 1006390--1006445 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1006380 CGGAGATATC
1006390 AGAAATCAGAGCAAAAATCAGAAA
1 AGAAATCAGAGCAAAAATCAGAAA
* * *
1006414 AGAAATTAGAGCAGAAATCAGAAC
1 AGAAATCAGAGCAAAAATCAGAAA
1006438 AGAAATCA
1 AGAAATCA
1006446 AAGAAAACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.59, C:0.12, G:0.18, T:0.11
Consensus pattern (24 bp):
AGAAATCAGAGCAAAAATCAGAAA
Found at i:1013904 original size:24 final size:24
Alignment explanation
Indices: 1013872--1013923 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
1013862 GTCAGAATTT
*
1013872 CTCGAATAAGTACCTCTCACATTA
1 CTCGAATAAGTAACTCTCACATTA
*
1013896 CTCGGATAAGTAACTCTCACATTA
1 CTCGAATAAGTAACTCTCACATTA
1013920 CTCG
1 CTCG
1013924 TGAGGTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (24 bp):
CTCGAATAAGTAACTCTCACATTA
Found at i:1026637 original size:28 final size:28
Alignment explanation
Indices: 1026605--1026660 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1026595 ATAAAGATTG
1026605 TTATTGAATATATCTCGATATATGTAGT
1 TTATTGAATATATCTCGATATATGTAGT
1026633 TTATTGAATATATCTCGATATATGTAGT
1 TTATTGAATATATCTCGATATATGTAGT
1026661 GGGTTGTGTA
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:0.07, G:0.14, T:0.46
Consensus pattern (28 bp):
TTATTGAATATATCTCGATATATGTAGT
Found at i:1029756 original size:20 final size:20
Alignment explanation
Indices: 1029731--1029810 Score: 79
Period size: 20 Copynumber: 3.7 Consensus size: 20
1029721 TTAAATTATG
*
1029731 GCATCCTATCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
1029751 GCATCCTTCCATGCGTTTTAGTTAT
1 GCATCCTTTCATGC--CTTA---AT
1029776 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
1029797 GCATCCTTTCATGC
1 GCATCCTTTCATGC
1029811 ATTTTTTGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 26 0.53
21 2 0.04
22 3 0.06
24 3 0.06
25 2 0.04
26 13 0.27
ACGTcount: A:0.19, C:0.29, G:0.14, T:0.39
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:1029835 original size:27 final size:27
Alignment explanation
Indices: 1029797--1029992 Score: 146
Period size: 27 Copynumber: 8.0 Consensus size: 27
1029787 ATGCCTTAAT
*
1029797 GCATCCTTTCATGCATTTTTTGTTATG
1 GCATCCTTTCATGCATTTTTAGTTATG
*
1029824 GCATCCTTTCATG---TCTTA---AT-
1 GCATCCTTTCATGCATTTTTAGTTATG
*
1029844 GCATACTTTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCATTTTTAGTTATG
*
1029871 GCATCATTTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCATTTTTAGTTATG
* * *
1029898 GCATCATTTCATGC---CTTA---CT-
1 GCATCCTTTCATGCATTTTTAGTTATG
1029918 GCATCCTTTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCATTTTTAGTTATG
* * *
1029945 GAATCCTTTTATGC---CTTA---AT-
1 GCATCCTTTCATGCATTTTTAGTTATG
*
1029965 GCATCCTTTCATGCATTTTTAATTATG
1 GCATCCTTTCATGCATTTTTAGTTATG
1029992 G
1 G
1029993 TTTAAAACTC
Statistics
Matches: 131, Mismatches: 17, Indels: 42
0.69 0.09 0.22
Matches are distributed among these distances:
20 37 0.28
21 5 0.04
23 10 0.08
24 9 0.07
26 5 0.04
27 65 0.50
ACGTcount: A:0.20, C:0.19, G:0.13, T:0.47
Consensus pattern (27 bp):
GCATCCTTTCATGCATTTTTAGTTATG
Found at i:1029842 original size:47 final size:47
Alignment explanation
Indices: 1029726--1029884 Score: 248
Period size: 47 Copynumber: 3.4 Consensus size: 47
1029716 TACATTTAAA
* * *
1029726 TTATGGCATCCTATCATGCCTTAATGCATCCTTCCATGC-GTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
*
1029772 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTTG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
* *
1029819 TTATGGCATCCTTTCATGTCTTAATGCATACTTTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
*
1029866 TTATGGCATCATTTCATGC
1 TTATGGCATCCTTTCATGC
1029885 ATTTTTAGTT
Statistics
Matches: 103, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
46 37 0.36
47 66 0.64
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44
Consensus pattern (47 bp):
TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
Found at i:1029889 original size:74 final size:74
Alignment explanation
Indices: 1029797--1029945 Score: 244
Period size: 74 Copynumber: 2.0 Consensus size: 74
1029787 ATGCCTTAAT
* * * *
1029797 GCATCCTTTCATGCATTTTTTGTTATGGCATCCTTTCATGTCTTAATGCATACTTTCATGCATTT
1 GCATCATTTCATGCATTTTTAGTTATGGCATCATTTCATGCCTTAATGCATACTTTCATGCATTT
1029862 TTAGTTATG
66 TTAGTTATG
* *
1029871 GCATCATTTCATGCATTTTTAGTTATGGCATCATTTCATGCCTTACTGCATCCTTTCATGCATTT
1 GCATCATTTCATGCATTTTTAGTTATGGCATCATTTCATGCCTTAATGCATACTTTCATGCATTT
1029936 TTAGTTATG
66 TTAGTTATG
1029945 G
1 G
1029946 AATCCTTTTA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.47
Consensus pattern (74 bp):
GCATCATTTCATGCATTTTTAGTTATGGCATCATTTCATGCCTTAATGCATACTTTCATGCATTT
TTAGTTATG
Found at i:1029909 original size:121 final size:121
Alignment explanation
Indices: 1029766--1029992 Score: 382
Period size: 121 Copynumber: 1.9 Consensus size: 121
1029756 CTTCCATGCG
* * *
1029766 TTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTTGTTATGGCATCCT
1 TTTTAGTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGAATCCT
* *
1029831 TTCATGTCTTAATGCATACTTTCATGCATTTTTAGTTATGGCATCATTTCATGCAT
66 TTCATGCCTTAATGCATACTTTCATGCATTTTTAATTATGGCATCATTTCATGCAT
*
1029887 TTTTAGTTATGGCATCATTTCATGCCTTACTGCATCCTTTCATGCATTTTTAGTTATGGAATCCT
1 TTTTAGTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGAATCCT
* *
1029952 TTTATGCCTTAATGCATCCTTTCATGCATTTTTAATTATGG
66 TTCATGCCTTAATGCATACTTTCATGCATTTTTAATTATGG
1029993 TTTAAAACTC
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 98 1.00
ACGTcount: A:0.20, C:0.19, G:0.13, T:0.47
Consensus pattern (121 bp):
TTTTAGTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGAATCCT
TTCATGCCTTAATGCATACTTTCATGCATTTTTAATTATGGCATCATTTCATGCAT
Found at i:1029922 original size:47 final size:47
Alignment explanation
Indices: 1029871--1029992 Score: 190
Period size: 47 Copynumber: 2.6 Consensus size: 47
1029861 TTTAGTTATG
* * *
1029871 GCATCATTTCATGCATTTTTAGTTATGGCATCATTTCATGCCTTACT
1 GCATCCTTTCATGCATTTTTAGTTATGGAATCATTTCATGCCTTAAT
* *
1029918 GCATCCTTTCATGCATTTTTAGTTATGGAATCCTTTTATGCCTTAAT
1 GCATCCTTTCATGCATTTTTAGTTATGGAATCATTTCATGCCTTAAT
*
1029965 GCATCCTTTCATGCATTTTTAATTATGG
1 GCATCCTTTCATGCATTTTTAGTTATGG
1029993 TTTAAAACTC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 69 1.00
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.46
Consensus pattern (47 bp):
GCATCCTTTCATGCATTTTTAGTTATGGAATCATTTCATGCCTTAAT
Found at i:1030499 original size:95 final size:96
Alignment explanation
Indices: 1030389--1030580 Score: 264
Period size: 95 Copynumber: 2.0 Consensus size: 96
1030379 TACCGATCTT
* * * * *
1030389 CTATACTATGGTACTGATACCCCCTTCCGGTATCAATACCGAAATTAGCTTCGATG-TTTCCTAG
1 CTATACTATGGTACTGATACCCCCTTACGATATCAATACCAAAATTAGATTCAATGTTTTCCTAG
*
1030453 TATTGATATCC-TTACCAA-GGTATCGATACTA
66 TATCGATA-CCTTTA-CAATGGTATCGATACTA
* * *
1030484 CTATACTATGGTACTGATACCCCCTTACGATATCAATACCAAAATTATATTCAATGTTTTCTTGG
1 CTATACTATGGTACTGATACCCCCTTACGATATCAATACCAAAATTAGATTCAATGTTTTCCTAG
1030549 TATCGATACCTTTACAATGGTATCGATACTA
66 TATCGATACCTTTACAATGGTATCGATACTA
1030580 C
1 C
1030581 CTCAACGGTA
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
95 55 0.65
96 30 0.35
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (96 bp):
CTATACTATGGTACTGATACCCCCTTACGATATCAATACCAAAATTAGATTCAATGTTTTCCTAG
TATCGATACCTTTACAATGGTATCGATACTA
Found at i:1036725 original size:20 final size:20
Alignment explanation
Indices: 1036700--1036827 Score: 76
Period size: 20 Copynumber: 5.7 Consensus size: 20
1036690 TTTATTTATC
1036700 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
1036720 GCATCCTTTCATGCATATTTACTTAT
1 GCATCCTTTCATGC---CTTA---AT
* *
1036746 GGAATCCTTTAATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* * *
1036767 GCGTCCTTTCTTGCATTTTTAGTTAT
1 GCATCCTTTCATGC---CTTA---AT
1036793 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
1036814 GCATCCTTTCATGC
1 GCATCCTTTCATGC
1036828 ATTTTTAGTT
Statistics
Matches: 82, Mismatches: 12, Indels: 28
0.67 0.10 0.23
Matches are distributed among these distances:
20 38 0.46
21 4 0.05
23 6 0.07
24 6 0.07
26 4 0.05
27 24 0.29
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.43
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:1036774 original size:47 final size:47
Alignment explanation
Indices: 1036657--1036854 Score: 290
Period size: 47 Copynumber: 4.2 Consensus size: 47
1036647 AATTATGGTG
* * * * *
1036657 TCCTATCATGCCTTAATGCATTCTTCCATGCA-TTTTATTTATCGCA
1 TCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCA
* * *
1036703 TCCTTTCATGCCTTAATGCATCCTTTCATGCATATTTACTTATGGAA
1 TCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCA
* * *
1036750 TCCTTTAATGCCTTAATGCGTCCTTTCTTGCATTTTTAGTTATGGCA
1 TCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCA
1036797 TCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCA
1 TCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCA
1036844 TCCTTTCATGC
1 TCCTTTCATGC
1036855 ATTTTTAGTT
Statistics
Matches: 135, Mismatches: 16, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
46 29 0.21
47 106 0.79
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.44
Consensus pattern (47 bp):
TCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCA
Found at i:1036852 original size:27 final size:27
Alignment explanation
Indices: 1036814--1037008 Score: 119
Period size: 27 Copynumber: 8.0 Consensus size: 27
1036804 ATGCCTTAAT
1036814 GCATCCTTTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCATTTTTAGTTATG
1036841 GCATCCTTTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCATTTTTAGTTATG
* * *
1036868 ACATCATTTCATGC-------CTTAT-
1 GCATCCTTTCATGCATTTTTAGTTATG
* *
1036887 GAATCCTTTCATGCGTTTTTAGTTATG
1 GCATCCTTTCATGCATTTTTAGTTATG
* * *
1036914 GCATCATTTCATGC----CT-G-AAT-
1 GCATCCTTTCATGCATTTTTAGTTATG
* *
1036934 GAATCATTTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCATTTTTAGTTATG
* *
1036961 ACATCCTTTCATGC---CTTA---AT-
1 GCATCCTTTCATGCATTTTTAGTTATG
*
1036981 GCATCCTTTCATGTATTTTTAGTTATG
1 GCATCCTTTCATGCATTTTTAGTTATG
1037008 G
1 G
1037009 TATAAAACTC
Statistics
Matches: 125, Mismatches: 21, Indels: 44
0.66 0.11 0.23
Matches are distributed among these distances:
19 11 0.09
20 29 0.23
21 4 0.03
22 1 0.01
23 4 0.03
24 4 0.03
25 1 0.01
26 8 0.06
27 63 0.50
ACGTcount: A:0.22, C:0.19, G:0.14, T:0.46
Consensus pattern (27 bp):
GCATCCTTTCATGCATTTTTAGTTATG
Found at i:1036887 original size:94 final size:93
Alignment explanation
Indices: 1036683--1036900 Score: 219
Period size: 94 Copynumber: 2.3 Consensus size: 93
1036673 TGCATTCTTC
*
1036683 CATGCATTT-TATTTATCGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATATTTACTTATG
1 CATGCATTTATAGTTAT-GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATATTTACTTATG
* * * **
1036747 GAATCCTTTAATGCCTTAATGCGTCCTTT
65 GAATCCTTTAATGCATTAATGAGTCATGA
* * * *
1036776 CTTGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
1 CATGCATTTATAGTTAT-GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATATTTACTTATG
* * * * *
1036841 GCATCCTTTCATGCATT-TTTAGTTATGA
65 GAATCCTTTAATGCATTAATGAGTCATGA
*
1036869 CAT-CATTTCAT-GCCTTATGAATCCTTTCATGC
1 CATGCATTT-ATAG--TTATGCATCCTTTCATGC
1036901 GTTTTTAGTT
Statistics
Matches: 103, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
92 6 0.06
93 28 0.27
94 69 0.67
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.45
Consensus pattern (93 bp):
CATGCATTTATAGTTATGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATATTTACTTATGG
AATCCTTTAATGCATTAATGAGTCATGA
Found at i:1036898 original size:19 final size:20
Alignment explanation
Indices: 1036863--1036900 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1036853 GCATTTTTAG
1036863 TTATGACATCATTTCATGCC
1 TTATGACATCATTTCATGCC
*
1036883 TTATGA-ATCCTTTCATGC
1 TTATGACATCATTTCATGC
1036901 GTTTTTAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.42
Consensus pattern (20 bp):
TTATGACATCATTTCATGCC
Found at i:1036906 original size:46 final size:46
Alignment explanation
Indices: 1036843--1037007 Score: 249
Period size: 47 Copynumber: 3.5 Consensus size: 46
1036833 TAGTTATGGC
1036843 ATCCTTTCATGCATTTTTAGTTATGACATCATTTCATGCCTTATGA
1 ATCCTTTCATGCATTTTTAGTTATGACATCATTTCATGCCTTATGA
* * *
1036889 ATCCTTTCATGCGTTTTTAGTTATGGCATCATTTCATGCCTGAATGA
1 ATCCTTTCATGCATTTTTAGTTATGACATCATTTCATGCCT-TATGA
* * *
1036936 ATCATTTCATGCATTTTTAGTTATGACATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTTAGTTATGACATCATTTCATGCCTT-ATGA
*
1036983 ATCCTTTCATGTATTTTTAGTTATG
1 ATCCTTTCATGCATTTTTAGTTATG
1037008 GTATAAAACT
Statistics
Matches: 106, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
46 39 0.37
47 67 0.63
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.46
Consensus pattern (46 bp):
ATCCTTTCATGCATTTTTAGTTATGACATCATTTCATGCCTTATGA
Found at i:1036918 original size:120 final size:121
Alignment explanation
Indices: 1036720--1036974 Score: 370
Period size: 120 Copynumber: 2.1 Consensus size: 121
1036710 ATGCCTTAAT
* ** *
1036720 GCATCCTTTCATGCATATTTACTTATGGAATCCTTTAATGCCTTAATGCGTCCTTTCTTGCATTT
1 GCATCCTTTCATGCATATTTACTTATGGAATCATTTAATGCCTTAATGAATCCTTTCATGCATTT
* * * *
1036785 TTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
66 TTAGTTATGGCATCATTTCATGCCTGAATGAATCATTTCATGCATTTTTAGTTATG
* * * *
1036841 GCATCCTTTCATGCATTTTTAGTTAT-GACATCATTTCATGCCTT-ATGAATCCTTTCATGCGTT
1 GCATCCTTTCATGCATATTTACTTATGGA-ATCATTTAATGCCTTAATGAATCCTTTCATGCATT
1036904 TTTAGTTATGGCATCATTTCATGCCTGAATGAATCATTTCATGCATTTTTAGTTATG
65 TTTAGTTATGGCATCATTTCATGCCTGAATGAATCATTTCATGCATTTTTAGTTATG
*
1036961 ACATCCTTTCATGC
1 GCATCCTTTCATGC
1036975 CTTAATGCAT
Statistics
Matches: 120, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
120 83 0.69
121 37 0.31
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (121 bp):
GCATCCTTTCATGCATATTTACTTATGGAATCATTTAATGCCTTAATGAATCCTTTCATGCATTT
TTAGTTATGGCATCATTTCATGCCTGAATGAATCATTTCATGCATTTTTAGTTATG
Found at i:1036924 original size:73 final size:74
Alignment explanation
Indices: 1036773--1036927 Score: 249
Period size: 73 Copynumber: 2.1 Consensus size: 74
1036763 TAATGCGTCC
* * * *
1036773 TTTCTTGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTT
1 TTTCATGCATTTTTAGTTATGACATCATTTCATGCCTTAATGAATCCTTTCATGCATTTTTAGTT
*
1036838 ATGGCATCC
66 ATGGCATCA
*
1036847 TTTCATGCATTTTTAGTTATGACATCATTTCATGCCTT-ATGAATCCTTTCATGCGTTTTTAGTT
1 TTTCATGCATTTTTAGTTATGACATCATTTCATGCCTTAATGAATCCTTTCATGCATTTTTAGTT
1036911 ATGGCATCA
66 ATGGCATCA
1036920 TTTCATGC
1 TTTCATGC
1036928 CTGAATGAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
73 40 0.53
74 35 0.47
ACGTcount: A:0.19, C:0.20, G:0.14, T:0.47
Consensus pattern (74 bp):
TTTCATGCATTTTTAGTTATGACATCATTTCATGCCTTAATGAATCCTTTCATGCATTTTTAGTT
ATGGCATCA
Found at i:1036959 original size:167 final size:167
Alignment explanation
Indices: 1036674--1037008 Score: 476
Period size: 167 Copynumber: 2.0 Consensus size: 167
1036664 ATGCCTTAAT
* * * *
1036674 GCATTCTTCCATGCATTTTATTTATCGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATATT
1 GCATCCTTCCATGCATTTTAGTTATCGCATCATTTCATGCCTTAATGAATCCTTTCATGCATATT
* * ** * * *
1036739 TACTTATGGAATCCTTTAATGCCTTAATGCGTCCTTTCTTGCATTTTTAGTTATGGCATCCTTTC
66 TACTTATGGAATCATTTAATGCCTGAATGAATCATTTCATGCATTTTTAGTTATGACATCCTTTC
1036804 ATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
131 ATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
* * *
1036841 GCATCCTTTCATGCATTTTTAGTTAT-GACATCATTTCATGCCTT-ATGAATCCTTTCATGCGTT
1 GCATCCTTCCATGCA-TTTTAGTTATCG-CATCATTTCATGCCTTAATGAATCCTTTCATGCATA
* * *
1036904 TTTAGTTATGGCATCATTTCATGCCTGAATGAATCATTTCATGCATTTTTAGTTATGACATCCTT
64 TTTACTTATGGAATCATTTAATGCCTGAATGAATCATTTCATGCATTTTTAGTTATGACATCCTT
*
1036969 TCATGCCTTAATGCATCCTTTCATGTATTTTTAGTTATG
129 TCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
1037008 G
1 G
1037009 TATAAAACTC
Statistics
Matches: 148, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
167 124 0.84
168 24 0.16
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (167 bp):
GCATCCTTCCATGCATTTTAGTTATCGCATCATTTCATGCCTTAATGAATCCTTTCATGCATATT
TACTTATGGAATCATTTAATGCCTGAATGAATCATTTCATGCATTTTTAGTTATGACATCCTTTC
ATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
Found at i:1037555 original size:96 final size:98
Alignment explanation
Indices: 1037406--1037590 Score: 257
Period size: 97 Copynumber: 1.9 Consensus size: 98
1037396 ACCGATACTT
*** * *
1037406 CTATACTATGGTATTGATACCCCCTTCCGATATCGATACCAAAATTAGCTTCGATG-TTGCCTAG
1 CTATACTATGGTACCAATACCCCCTTACGATATCGATACCAAAATTAGATTCGATGTTTGCCTAG
*
1037470 TATCGATACCCTTACCATGGTATCATCTCACTA
66 TATCGATACCCTTACAATGGTATCATCTCACTA
* * * *
1037503 CTATACTATGGTACCAATA-CCCCTTACGGTATCGATACCAAAATTATATTCGATGTTTGCTTGG
1 CTATACTATGGTACCAATACCCCCTTACGATATCGATACCAAAATTAGATTCGATGTTTGCCTAG
*
1037567 TATCGATACCCTTATAATGGTATC
66 TATCGATACCCTTACAATGGTATC
1037591 GATACTGCCT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
96 32 0.42
97 44 0.58
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (98 bp):
CTATACTATGGTACCAATACCCCCTTACGATATCGATACCAAAATTAGATTCGATGTTTGCCTAG
TATCGATACCCTTACAATGGTATCATCTCACTA
Found at i:1040030 original size:45 final size:45
Alignment explanation
Indices: 1039981--1040246 Score: 352
Period size: 45 Copynumber: 5.9 Consensus size: 45
1039971 TCTATAATAT
* * **
1039981 CTTTTCTGTTGATAATGCACCCATATGTATTTCTACTATAATATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGCATA
* * * *
1040026 CTTTTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGCATA
* * * *
1040071 CTTTTCTGTTGATAATGTACCCATATACATTTCAGCTCTAGCATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGCATA
* *
1040116 CTCTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGCATA
* *
1040161 CATTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGCATA
* * * *
1040206 CTCTTCTGTTGATAATGTACCCATATACATTTCAACCATAG
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAG
1040247 TACACCTTTT
Statistics
Matches: 199, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 199 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.39
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGCATA
Found at i:1040103 original size:90 final size:89
Alignment explanation
Indices: 1039981--1040248 Score: 394
Period size: 90 Copynumber: 3.0 Consensus size: 89
1039971 TCTATAATAT
* * ** *
1039981 CTTTTCTGTTGATAATGCACCCATATGTATTTCTACTATAATATACTTTTCTGTTGATAATGTAC
1 CTTTTCTGTTGATAATGCACCCATATGCATTTC-ACTCTAGCATACTCTTCTGTTGATAATGTAC
1040046 CCATATACATTTCAACCATAGTATA
65 CCATATACATTTCAACCATAGTATA
* * *
1040071 CTTTTCTGTTGATAATGTACCCATATACATTTCAGCTCTAGCATACTCTTCTGTTGATAATGCAC
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCA-CTCTAGCATACTCTTCTGTTGATAATGTAC
* *
1040136 CCATATGCATTTCAACTC-TAGCATA
65 CCATATACATTTCAAC-CATAGTATA
*
1040161 CATTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTCTTCTGTTGATAATGTAC
1 CTTTTCTGTTGATAATGCACCCATATGCATTTC-ACTCTAGCATACTCTTCTGTTGATAATGTAC
1040226 CCATATACATTTCAACCATAGTA
65 CCATATACATTTCAACCATAGTA
1040249 CACCTTTTTC
Statistics
Matches: 158, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
89 2 0.01
90 154 0.97
91 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (89 bp):
CTTTTCTGTTGATAATGCACCCATATGCATTTCACTCTAGCATACTCTTCTGTTGATAATGTACC
CATATACATTTCAACCATAGTATA
Found at i:1040173 original size:135 final size:135
Alignment explanation
Indices: 1039984--1040239 Score: 406
Period size: 135 Copynumber: 1.9 Consensus size: 135
1039974 ATAATATCTT
* * * * *
1039984 TTCTGTTGATAATGCACCCATATGTATTTCTACTATAATATACTTTTCTGTTGATAATGTACCCA
1 TTCTGTTGATAATGCACCCATATGCATTTCAACTATAACATACATTTCTGTTGATAATGCACCCA
* *
1040049 TATACATTTCAAC-CATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTCAGCTCTAGC
66 TATACATTTCAACTC-TAGCATACTCTTCTGTTGATAATGTACCCATATACATTTCAGCTCTAGC
1040113 ATACTC
130 ATACTC
* *
1040119 TTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACATTTCTGTTGATAATGCACCCA
1 TTCTGTTGATAATGCACCCATATGCATTTCAACTATAACATACATTTCTGTTGATAATGCACCCA
*
1040184 TATGCATTTCAACTCTAGCATACTCTTCTGTTGATAATGTACCCATATACATTTCA
66 TATACATTTCAACTCTAGCATACTCTTCTGTTGATAATGTACCCATATACATTTCA
1040240 ACCATAGTAC
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
135 109 0.99
136 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (135 bp):
TTCTGTTGATAATGCACCCATATGCATTTCAACTATAACATACATTTCTGTTGATAATGCACCCA
TATACATTTCAACTCTAGCATACTCTTCTGTTGATAATGTACCCATATACATTTCAGCTCTAGCA
TACTC
Found at i:1054916 original size:45 final size:45
Alignment explanation
Indices: 1054867--1055173 Score: 346
Period size: 45 Copynumber: 6.8 Consensus size: 45
1054857 CTATAACATT
* * *
1054867 TTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATAC
* * * *
1054912 TTTTCTGTTGATAATGTACTCATATACATTTCAACCATAGTATAT
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATAC
* * *
1054957 TTTTCTATTGATAATGTACCCATATACATTTCAACTCTAGCATGC
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATAC
* * * *
1055002 TCTTT-TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATGC
1 T-TTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATAC
* * ** * * *
1055047 ATTTCTATTGATAATACACCCATATGCATTTCAACTCTAGCATAT
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATAC
* ** *
1055092 TTTTCTGTTGATAATGTACCCATATACATTTCAACCATAATACAC
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATAC
* * *
1055137 CTTTATATTGATAATGTACCCATATACATTTCAACTA
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACTA
1055174 GGCATCCTTT
Statistics
Matches: 225, Mismatches: 35, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
44 3 0.01
45 219 0.97
46 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.40
Consensus pattern (45 bp):
TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATAC
Found at i:1054962 original size:90 final size:90
Alignment explanation
Indices: 1054867--1055173 Score: 384
Period size: 90 Copynumber: 3.4 Consensus size: 90
1054857 CTATAACATT
* * * *
1054867 TTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCTGTTGATAATGTACT
1 TTTTCTATTGATAATGCACCCATATACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACC
*
1054932 CATATACATTTCAACCATAGTATAT
66 CATATACATTTCAACCATAGTATAC
* * * *
1054957 TTTTCTATTGATAATGTACCCATATACATTTCAACTCTAGCATGCTCTTT-TGTTGATAATGCAC
1 TTTTCTATTGATAATGCACCCATATACATTTCAACTATAGCATACT-TTTCTGTTGATAATGTAC
* * *
1055021 CCATATGCATTTCAACTC-TAGCATGC
65 CCATATACATTTCAAC-CATAGTATAC
* * * * *
1055047 ATTTCTATTGATAATACACCCATATGCATTTCAACTCTAGCATATTTTTCTGTTGATAATGTACC
1 TTTTCTATTGATAATGCACCCATATACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACC
* *
1055112 CATATACATTTCAACCATAATACAC
66 CATATACATTTCAACCATAGTATAC
* * *
1055137 CTTTATATTGATAATGTACCCATATACATTTCAACTA
1 TTTTCTATTGATAATGCACCCATATACATTTCAACTA
1055174 GGCATCCTTT
Statistics
Matches: 183, Mismatches: 30, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
89 4 0.02
90 175 0.96
91 4 0.02
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.40
Consensus pattern (90 bp):
TTTTCTATTGATAATGCACCCATATACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACC
CATATACATTTCAACCATAGTATAC
Found at i:1055052 original size:135 final size:135
Alignment explanation
Indices: 1054872--1055173 Score: 396
Period size: 135 Copynumber: 2.2 Consensus size: 135
1054862 ACATTTTTTC
* * * ** *
1054872 TGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCTGTTGATAATGTACTCATAT
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACATTTCTATTGATAATACACCCATAT
*
1054937 ACATTTCAAC-CATAGTATATTTTTCTATTGATAATGTACCCATATACATTTCAACTCTAGCATG
66 ACATTTCAACTC-TAGCATATTTTTCTATTGATAATGTACCCATATACATTTCAACTCTAGCATG
1055001 CTCTTT
130 CTCTTT
* *
1055007 TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATGCATTTCTATTGATAATACACCCATAT
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACATTTCTATTGATAATACACCCATAT
* * *
1055072 GCATTTCAACTCTAGCATATTTTTCTGTTGATAATGTACCCATATACATTTCAAC-CATA--ATA
66 ACATTTCAACTCTAGCATATTTTTCTATTGATAATGTACCCATATACATTTCAACTC-TAGCATG
*
1055134 CACCTTT
130 C-TCTTT
* * *
1055141 ATATTGATAATGTACCCATATACATTTCAACTA
1 -TGTTGATAATGCACCCATATGCATTTCAACTA
1055174 GGCATCCTTT
Statistics
Matches: 146, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
133 3 0.02
134 5 0.03
135 137 0.94
136 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (135 bp):
TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACATTTCTATTGATAATACACCCATAT
ACATTTCAACTCTAGCATATTTTTCTATTGATAATGTACCCATATACATTTCAACTCTAGCATGC
TCTTT
Found at i:1057461 original size:2 final size:2
Alignment explanation
Indices: 1057454--1057507 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1057444 TGCATTCTAC
1057454 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
1057496 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1057508 CCATTTGTTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1058689 original size:21 final size:20
Alignment explanation
Indices: 1058603--1058760 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1058593 AAATGACCAA
**
1058603 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1058622 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1058642 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1058662 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1058683 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1058704 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1058724 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1058745 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1058761 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1058776 original size:40 final size:40
Alignment explanation
Indices: 1058727--1058881 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
1058717 CGATTTTCCA
* ** *
1058727 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
1058767 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
1058807 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
1058847 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1058882 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:1058789 original size:20 final size:20
Alignment explanation
Indices: 1058727--1058880 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
1058717 CGATTTTCCA
* ** *
1058727 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1058747 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1058767 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1058787 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1058807 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1058827 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1058847 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1058868 AAATCGCAACGCG
1 AAATCGCAACGCG
1058881 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1059302 original size:33 final size:33
Alignment explanation
Indices: 1059263--1059333 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1059253 TTCACTTAGA
*
1059263 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1059296 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1059329 TTTCA
1 TTTCA
1059334 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1059470 original size:41 final size:41
Alignment explanation
Indices: 1059412--1059489 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1059402 TTGCAGAAGA
*
1059412 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
1059453 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1059490 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:1059486 original size:21 final size:21
Alignment explanation
Indices: 1059413--1059488 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1059403 TGCAGAAGAG
*
1059413 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
1059434 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
1059454 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
1059475 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1059489 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:1059492 original size:14 final size:14
Alignment explanation
Indices: 1059473--1059529 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1059463 GAGAAATGAA
1059473 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1059487 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1059506 AATCGCAACAAGAG
1 AATCGCAACGAGAG
1059520 AATCGCAACG
1 AATCGCAACG
1059530 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1059505 original size:33 final size:33
Alignment explanation
Indices: 1059465--1059545 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
1059455 CGCAACGAGA
*
1059465 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACAAGAGAATCGCAACGC
1059498 GAAATGAAAATCGCAACAAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACAAGAGAATCGCAACGC
**
1059531 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1059546 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.48, C:0.22, G:0.21, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACAAGAGAATCGCAACGC
Found at i:1059563 original size:19 final size:19
Alignment explanation
Indices: 1059541--1059638 Score: 99
Period size: 19 Copynumber: 5.7 Consensus size: 19
1059531 GAAACCAAAA
*
1059541 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1059560 TCGCGTTGCGATTTTC---
1 TCGCGTTGCGATTTTCATT
1059576 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1059593 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
**
1059607 TCTAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1059626 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1059639 CTCTCGTTGC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 22 0.34
16 4 0.06
17 4 0.06
19 34 0.53
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1059580 original size:14 final size:14
Alignment explanation
Indices: 1059558--1059655 Score: 70
Period size: 14 Copynumber: 6.3 Consensus size: 14
1059548 GCGATTTTCA
*
1059558 TTTCGCGTTGCGAT
1 TTTCTCGTTGCGAT
1059572 TTTCTCGTTGCGAT
1 TTTCTCGTTGCGAT
1059586 TTTCATTTCGCGTTGCGAT
1 TTTC---T--CGTTGCGAT
* *
1059605 TCTCTAGTTGCGAT
1 TTTCTCGTTGCGAT
1059619 TTTCATTTCGCGTTGCGAT
1 TTTC---T--CGTTGCGAT
*
1059638 TCTCTCGTTGCGAT
1 TTTCTCGTTGCGAT
1059652 TTTC
1 TTTC
1059656 ATTTCAACCA
Statistics
Matches: 67, Mismatches: 7, Indels: 20
0.71 0.07 0.21
Matches are distributed among these distances:
14 40 0.60
16 2 0.03
17 2 0.03
19 23 0.34
ACGTcount: A:0.09, C:0.22, G:0.21, T:0.47
Consensus pattern (14 bp):
TTTCTCGTTGCGAT
Found at i:1059588 original size:33 final size:33
Alignment explanation
Indices: 1059546--1059660 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1059536 CAAAATCGCA
*
1059546 TTGCGATTTTCATTTCGCGTTGCGATTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1059579 TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1059612 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1059645 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1059661 AACCAAACGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.10, C:0.22, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1061517 original size:93 final size:93
Alignment explanation
Indices: 1061358--1061826 Score: 922
Period size: 93 Copynumber: 5.1 Consensus size: 93
1061348 TAGATTGCTT
*
1061358 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1061423 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1061451 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1061516 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1061544 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1061609 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1061637 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1061702 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1061730 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1061795 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1061822 AGTAA
1 AGTAA
1061827 TGCAATCCAT
Statistics
Matches: 375, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 6 0.02
93 369 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1061914 original size:19 final size:19
Alignment explanation
Indices: 1061874--1062002 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1061864 TAGTTTACTT
* *
1061874 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1061894 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
* **
1061913 TCGCAACGTGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1061932 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1061946 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1061965 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1061979 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1061998 TCGCA
1 TCGCA
1062003 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 4 0.05
17 3 0.03
18 2 0.02
19 45 0.51
20 13 0.15
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1061953 original size:33 final size:32
Alignment explanation
Indices: 1061910--1062002 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
1061900 CGCGAAACCA
* **
1061910 AAATCGCAACGTGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1061942 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1061975 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1062003 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1062000 original size:52 final size:52
Alignment explanation
Indices: 1061874--1062002 Score: 138
Period size: 52 Copynumber: 2.5 Consensus size: 52
1061864 TAGTTTACTT
** **
1061874 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGTGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGACAAA
* * *
1061926 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGACAAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACGACAA-A
*
1061979 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1062003 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.69
53 2 0.03
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGACAAA
Found at i:1062020 original size:19 final size:18
Alignment explanation
Indices: 1061998--1062116 Score: 110
Period size: 19 Copynumber: 6.8 Consensus size: 18
1061988 GAAACCAAAA
1061998 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGATTTTCATT
1062017 TCGCTTTGCGA--TTC-TT
1 TCGC-TTGCGATTTTCATT
1062033 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
*
1062050 TCGCATTGCGA--TTC-TG
1 TCGC-TTGCGATTTTCATT
1062066 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
**
1062083 TCGCGTTGCGATTTTGGTT
1 TCGC-TTGCGATTTTCATT
1062102 TCGCGTTGCGATTTT
1 TCGC-TTGCGATTTT
1062117 AAGTTTCGTG
Statistics
Matches: 85, Mismatches: 5, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
14 12 0.14
16 15 0.18
17 15 0.18
19 43 0.51
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.48
Consensus pattern (18 bp):
TCGCTTGCGATTTTCATT
Found at i:1062041 original size:14 final size:14
Alignment explanation
Indices: 1062022--1062076 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1062012 TCATTTCGCT
1062022 TTGCGATTCTTTCG
1 TTGCGATTCTTTCG
1062036 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
*
1062053 CATTGCGATTCTGTCG
1 --TTGCGATTCTTTCG
1062069 TTGCGATT
1 TTGCGATT
1062077 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 14 0.40
16 7 0.20
17 8 0.23
19 6 0.17
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:1062045 original size:33 final size:33
Alignment explanation
Indices: 1062003--1062095 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1061993 CAAAATCGCA
* *
1062003 TTGCGATTTTCATTTCGCTTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1062036 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
*
1062069 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
1062096 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
Found at i:1062124 original size:20 final size:19
Alignment explanation
Indices: 1062067--1062132 Score: 89
Period size: 19 Copynumber: 3.4 Consensus size: 19
1062057 GCGATTCTGT
1062067 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTT-AGTTTCG
*
1062086 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
1062105 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-AGTTTCG
*
1062125 TGTTGCGA
1 CGTTGCGA
1062133 AAGTAAACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.11, C:0.17, G:0.27, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:1063714 original size:14 final size:14
Alignment explanation
Indices: 1063695--1063730 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1063685 ATTGTTTAAT
1063695 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1063709 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1063723 TGATTTGT
1 TGATTTGT
1063731 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1063879 original size:19 final size:19
Alignment explanation
Indices: 1063857--1064155 Score: 395
Period size: 19 Copynumber: 16.7 Consensus size: 19
1063847 GAAATAAAAA
*
1063857 TCGCATTGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
1063876 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1063892 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1063909 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1063928 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1063944 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1063961 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1063980 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1063999 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
1064019 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1064038 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1064054 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1064071 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1064090 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1064109 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
1064127 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1064143 TCGCATTGCGATT
1 TCGCATTGCGATT
1064156 CTCTCGTTGC
Statistics
Matches: 249, Mismatches: 9, Indels: 44
0.82 0.03 0.15
Matches are distributed among these distances:
14 29 0.12
16 23 0.09
17 21 0.08
18 1 0.00
19 140 0.56
20 35 0.14
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1063922 original size:52 final size:52
Alignment explanation
Indices: 1063857--1064169 Score: 447
Period size: 52 Copynumber: 5.9 Consensus size: 52
1063847 GAAATAAAAA
*
1063857 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1063909 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
1063961 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATT
1064019 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
1064071 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCA--
1 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATT
*
1064127 T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1064170 GTAATTTCCG
Statistics
Matches: 243, Mismatches: 6, Indels: 29
0.87 0.02 0.10
Matches are distributed among these distances:
47 8 0.03
49 2 0.01
50 2 0.01
51 3 0.01
52 125 0.51
53 24 0.10
54 8 0.03
55 7 0.03
56 8 0.03
58 56 0.23
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1064040 original size:110 final size:110
Alignment explanation
Indices: 1063857--1064169 Score: 522
Period size: 110 Copynumber: 2.9 Consensus size: 110
1063847 GAAATAAAAA
* *
1063857 TCGCATTGCGATTTTAATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATTTCGCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCATT
1063916 GCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
66 GCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1063961 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCATT
1064026 GCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
66 GCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1064071 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCA--T-G--TT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCATT
*
1064131 GGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
66 GCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1064170 GTAATTTCCG
Statistics
Matches: 200, Mismatches: 3, Indels: 11
0.93 0.01 0.05
Matches are distributed among these distances:
104 29 0.14
105 40 0.20
106 3 0.01
107 3 0.01
108 3 0.01
110 122 0.61
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (110 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCATT
GCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1064177 original size:33 final size:33
Alignment explanation
Indices: 1063914--1064169 Score: 298
Period size: 33 Copynumber: 7.2 Consensus size: 33
1063904 TCATTTCGCA
1063914 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1063947 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
1063983 CATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
1 --TTGCGATTTTCATTT-CGCATTGCGA--TTC-TCTCG
1064022 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1064057 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
1064093 CATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
1064129 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1064162 TTGCGATT
1 TTGCGATT
1064170 GTAATTTCCG
Statistics
Matches: 201, Mismatches: 8, Indels: 28
0.85 0.03 0.12
Matches are distributed among these distances:
32 1 0.00
33 72 0.36
34 14 0.07
35 10 0.05
36 13 0.06
37 3 0.01
38 40 0.20
39 48 0.24
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Done.