Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 51 of 135
Found at i:18128519 original size:21 final size:22
Alignment explanation
Indices: 18128469--18128519 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
18128459 GAAATAATAT
* *
18128469 TTTAG-TTAAACTATTTATTTG
1 TTTAGATTAAACTATTGATTAG
18128490 TTTCA-ATTAAACT-TTGATTAG
1 TTT-AGATTAAACTATTGATTAG
18128511 TTTAGATTA
1 TTTAGATTA
18128520 TTTTATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 1 0.04
21 16 0.64
22 8 0.32
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.53
Consensus pattern (22 bp):
TTTAGATTAAACTATTGATTAG
Found at i:18132221 original size:26 final size:27
Alignment explanation
Indices: 18132164--18132226 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
18132154 TGTTTTCTCC
* *
18132164 AAAATAATAT-AAAAATTTTAATTATT
1 AAAATAATATGAAAAATATTAATTACT
18132190 AAAATAATATGAAAAA-ATTAATTACT
1 AAAATAATATGAAAAATATTAATTACT
**
18132216 GGAATAATATG
1 AAAATAATATG
18132227 GATTACCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 27 0.84
27 5 0.16
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (27 bp):
AAAATAATATGAAAAATATTAATTACT
Found at i:18138562 original size:26 final size:25
Alignment explanation
Indices: 18138505--18138567 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
18138495 CCATGCACAA
* *
18138505 TTCATATTATTTTGGTAAATTTTCT
1 TTCATATTATTCTGATAAATTTTCT
* *
18138530 TTCATATTATTCTGATAATTTTTTT
1 TTCATATTATTCTGATAAATTTTCT
18138555 TTCAATATTATTC
1 TTC-ATATTATTC
18138568 CTGAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
25 24 0.73
26 9 0.27
ACGTcount: A:0.25, C:0.10, G:0.05, T:0.60
Consensus pattern (25 bp):
TTCATATTATTCTGATAAATTTTCT
Found at i:18140017 original size:24 final size:23
Alignment explanation
Indices: 18139966--18140023 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
18139956 AATCTCATAT
**
18139966 ATATTACTAAAATATTAATATTTT
1 ATATTA-TAAAATATTAATATTGA
18139990 ATATTATAAAATATTAATTATTGA
1 ATATTATAAAATATTAA-TATTGA
18140014 ATATTTATAA
1 ATA-TTATAA
18140024 TTTGCAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 11 0.37
24 13 0.43
25 6 0.20
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATTATAAAATATTAATATTGA
Found at i:18140055 original size:23 final size:22
Alignment explanation
Indices: 18140029--18140094 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 22
18140019 TATAATTTGC
18140029 AATATATTTATTAAAAGTATTAA
1 AATATATTTATTAAAA-TATTAA
*
18140052 AATATATTTAATAAAATATTAA
1 AATATATTTATTAAAATATTAA
18140074 AA-ATA-TTATTTAAAA-ATTAA
1 AATATATTTA-TTAAAATATTAA
18140094 A
1 A
18140095 TTACTGCTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.22
21 8 0.20
22 8 0.20
23 15 0.38
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
AATATATTTATTAAAATATTAA
Found at i:18140181 original size:25 final size:23
Alignment explanation
Indices: 18140137--18140196 Score: 61
Period size: 25 Copynumber: 2.6 Consensus size: 23
18140127 ATATTAAATG
18140137 ATTTTATT-A-AAATAATATATT
1 ATTTTATTAATAAATAATATATT
*
18140158 AATTTTATTAATAAATTATCATATT
1 -ATTTTATTAATAAATAAT-ATATT
*
18140183 ATTTTGTTTAATAA
1 ATTTT-ATTAATAA
18140197 TTTTGTTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 8 0.25
23 1 0.03
24 11 0.34
25 12 0.38
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTTTATTAATAAATAATATATT
Found at i:18146659 original size:47 final size:47
Alignment explanation
Indices: 18146588--18146677 Score: 144
Period size: 47 Copynumber: 1.9 Consensus size: 47
18146578 TTAACGACTG
*
18146588 AGCCGAAGGAATTCATGCTCATACTCCATGATAGACATTCTACACTA
1 AGCCGAAGGAATTCACGCTCATACTCCATGATAGACATTCTACACTA
* * *
18146635 AGCCGAAGGAATTCGCGCTTATACTCTATGATAGACATTCTAC
1 AGCCGAAGGAATTCACGCTCATACTCCATGATAGACATTCTAC
18146678 CTTGTTTTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (47 bp):
AGCCGAAGGAATTCACGCTCATACTCCATGATAGACATTCTACACTA
Found at i:18152817 original size:22 final size:21
Alignment explanation
Indices: 18152787--18152827 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
18152777 CCCTCATTTT
18152787 TAGGTAGATCCTTCTAGTGTA
1 TAGGTAGATCCTTCTAGTGTA
18152808 TAGGTTAGATCCTTCTAGTG
1 TAGG-TAGATCCTTCTAGTG
18152828 CTTCATACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (21 bp):
TAGGTAGATCCTTCTAGTGTA
Found at i:18154694 original size:17 final size:17
Alignment explanation
Indices: 18154670--18154708 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
18154660 GTGACCCTTG
*
18154670 TTTCCCCAATTTTCATGT
1 TTTCCCAAATTTT-ATGT
18154688 TTTCCCAAAATTTTATGT
1 TTTCCC-AAATTTTATGT
18154706 TTT
1 TTT
18154709 ATTTCAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.54
Consensus pattern (17 bp):
TTTCCCAAATTTTATGT
Found at i:18159549 original size:17 final size:17
Alignment explanation
Indices: 18159527--18159565 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
18159517 AGGTGGAGAA
* *
18159527 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
18159544 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
18159561 CTTGT
1 CTTGT
18159566 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:18161495 original size:10 final size:9
Alignment explanation
Indices: 18161467--18161623 Score: 86
Period size: 10 Copynumber: 16.4 Consensus size: 9
18161457 CATATGATAA
18161467 AAAAATTAT
1 AAAAATTAT
18161476 AAAAA-T-T
1 AAAAATTAT
18161483 AAAAATTAAT
1 AAAAATT-AT
*
18161493 AAAAGTTAT
1 AAAAATTAT
*
18161502 -TAAATTATT
1 AAAAATTA-T
**
18161511 AAATTTTAAT
1 AAAAATT-AT
*
18161521 AAAAATATTT
1 AAAAAT-TAT
*
18161531 AAAATTTAT
1 AAAAATTAT
* *
18161540 TAAAATTAGAA
1 AAAAATT--AT
18161551 AAATAATTAT
1 AAA-AATTAT
*
18161561 AAAAATCAT
1 AAAAATTAT
18161570 AAATAAATTAT
1 -AA-AAATTAT
18161581 AAAACATTAT
1 AAAA-ATTAT
*
18161591 AAAATTTTAT
1 AAAA-ATTAT
*
18161601 AAAAATCAT
1 AAAAATTAT
18161610 AAAAACTTAT
1 AAAAA-TTAT
18161620 AAAA
1 AAAA
18161624 TGCAGCAAAA
Statistics
Matches: 111, Mismatches: 23, Indels: 27
0.69 0.14 0.17
Matches are distributed among these distances:
7 6 0.05
8 7 0.06
9 30 0.27
10 53 0.48
11 11 0.10
12 4 0.04
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (9 bp):
AAAAATTAT
Found at i:18161532 original size:28 final size:30
Alignment explanation
Indices: 18161488--18161543 Score: 73
Period size: 28 Copynumber: 1.9 Consensus size: 30
18161478 AAATTAAAAA
*
18161488 TTAATAAAAGTTATT-AAA-TTATTAAATT
1 TTAATAAAAATTATTAAAATTTATTAAATT
18161516 TTAATAAAAA-TATTTAAAATTTATTAAA
1 TTAATAAAAATTA-TTAAAATTTATTAAA
18161544 ATTAGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 2 0.08
28 11 0.46
29 3 0.12
30 8 0.33
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (30 bp):
TTAATAAAAATTATTAAAATTTATTAAATT
Found at i:18161829 original size:21 final size:20
Alignment explanation
Indices: 18161807--18161880 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 20
18161797 GTATGAAAAT
18161807 TTTTATAAATTTTTTACGAA
1 TTTTATAAATTTTTTACGAA
*
18161827 TTTTAT--ATTTCTTTAC-ATT
1 TTTTATAAATTT-TTTACGA-A
*
18161846 TTTTTTATAATTTTCTTACG-A
1 TTTTATA-AATTTT-TTACGAA
18161867 TTTTATAAAATTTT
1 TTTTAT-AAATTTT
18161881 ATTCTATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 15
0.69 0.07 0.25
Matches are distributed among these distances:
18 5 0.12
19 10 0.24
20 6 0.14
21 12 0.29
22 9 0.21
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTATAAATTTTTTACGAA
Found at i:18161864 original size:22 final size:22
Alignment explanation
Indices: 18161827--18161870 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
18161817 TTTTTACGAA
18161827 TTTTATATTTCTTTAC-ATTTT
1 TTTTATATTTCTTTACGATTTT
18161848 TTTTATAATTT-TCTTACGATTTT
1 TTTTAT-ATTTCT-TTACGATTTT
18161871 ATAAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 7 0.35
22 8 0.40
23 5 0.25
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTTATATTTCTTTACGATTTT
Found at i:18161931 original size:21 final size:21
Alignment explanation
Indices: 18161900--18161967 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 21
18161890 TTCTATATAG
18161900 TTTAT-AAATTTTTTACGATT
1 TTTATAAAATTTTTTACGATT
*
18161920 TTTATAAAA--TTTTACAATT
1 TTTATAAAATTTTTTACGATT
* * *
18161939 TTTTTATAATTCTTTTTATGATT
1 TTTATA-AAAT-TTTTTACGATT
18161962 TTTATA
1 TTTATA
18161968 TTTTTTTCTA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
19 14 0.38
20 7 0.19
21 3 0.08
23 13 0.35
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (21 bp):
TTTATAAAATTTTTTACGATT
Found at i:18161956 original size:12 final size:11
Alignment explanation
Indices: 18161929--18161983 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
18161919 TTTTATAAAA
*
18161929 TTTTACAATTT
1 TTTTATAATTT
18161940 TTTTATAATTCT
1 TTTTATAATT-T
*
18161952 TTTTATGA--T
1 TTTTATAATTT
18161961 TTTTAT-ATTT
1 TTTTATAATTT
*
18161971 TTTTCTAATTT
1 TTTTATAATTT
18161982 TT
1 TT
18161984 AATATTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
8 1 0.03
9 7 0.19
10 6 0.16
11 15 0.41
12 8 0.22
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:18161963 original size:52 final size:51
Alignment explanation
Indices: 18161847--18161964 Score: 123
Period size: 52 Copynumber: 2.3 Consensus size: 51
18161837 CTTTACATTT
* *
18161847 TTTTTATAATTTTCTTACGATTTTATAAAATTTTATTCTATATTTCTATATAG
1 TTTTTATAATTTT-TTACGATTTTATAAAATTTTA-TCAATATTTCTATATAC
* * * *
18161900 TTTATA-AATTTTTTACGATTTTTATAAAATTTTA-CAATTTTTTTATAATTC
1 TTTTTATAATTTTTTACGA-TTTTATAAAATTTTATCAATATTTCTAT-ATAC
*
18161951 TTTTTATGATTTTT
1 TTTTTATAATTTTT
18161965 ATATTTTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
50 9 0.17
51 13 0.24
52 27 0.50
53 5 0.09
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (51 bp):
TTTTTATAATTTTTTACGATTTTATAAAATTTTATCAATATTTCTATATAC
Found at i:18161981 original size:19 final size:19
Alignment explanation
Indices: 18161939--18162023 Score: 68
Period size: 19 Copynumber: 4.4 Consensus size: 19
18161929 TTTTACAATT
*
18161939 TTTTTATAATTCTTTTTATGA
1 TTTTTAT-ATT-TTTTTATAA
*
18161960 TTTTTATATTTTTTTCTAA
1 TTTTTATATTTTTTTATAA
18161979 TTTTTAATATTTTTATTA-AA
1 TTTTT-ATATTTTT-TTATAA
* *
18161999 -ATTTA-ATTAATTTTATAA
1 TTTTTATATT-TTTTTATAA
18162017 TTTTTAT
1 TTTTTAT
18162024 TGATTTATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
17 6 0.12
18 5 0.10
19 19 0.37
20 13 0.25
21 9 0.17
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.67
Consensus pattern (19 bp):
TTTTTATATTTTTTTATAA
Found at i:18162002 original size:92 final size:91
Alignment explanation
Indices: 18161805--18161994 Score: 226
Period size: 92 Copynumber: 2.1 Consensus size: 91
18161795 TGGTATGAAA
** *
18161805 ATTTTTATAAATTTTTTACGAATTTTATATTTCTTTACATTTTTTTTATAATTTTCTTACGATTT
1 ATTTTTATAAATTTTTTACGAATTTTATAAATCTTTACAATTTTTTTATAATTTTCTTACGATTT
18161870 TATAAAATTTTATTCTATATTTCTAT
66 TATAAAATTTTATTCTATATTTCTAT
* * * *
18161896 ATAGTTTATAAATTTTTTACGATTTTTATAAAAT-TTTACAATTTTTTTATAATTCTTTTTATGA
1 AT-TTTTATAAATTTTTTACGAATTTTAT-AAATCTTTACAATTTTTTTATAATT-TTCTTACGA
* * *
18161960 TTTT-T-ATATTTTTTTCTA-ATTTTTAAT
63 TTTTATAAAATTTTATTCTATATTTCT-AT
18161987 ATTTTTAT
1 ATTTTTAT
18161995 TAAAATTTAA
Statistics
Matches: 84, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
90 10 0.12
91 17 0.20
92 44 0.52
93 13 0.15
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (91 bp):
ATTTTTATAAATTTTTTACGAATTTTATAAATCTTTACAATTTTTTTATAATTTTCTTACGATTT
TATAAAATTTTATTCTATATTTCTAT
Found at i:18172949 original size:21 final size:19
Alignment explanation
Indices: 18172920--18172974 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
18172910 GGAGTTTTTG
*
18172920 GTATTGGTAGATGCATGACTT
1 GTATCGGTAGAT-CAT-ACTT
18172941 GTATCGGTAGAAATCATACTT
1 GTATCGGTAG--ATCATACTT
*
18172962 GTATCAGTAGATC
1 GTATCGGTAGATC
18172975 TAGCACAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 3 0.10
21 22 0.73
22 3 0.10
23 2 0.07
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.35
Consensus pattern (19 bp):
GTATCGGTAGATCATACTT
Found at i:18175296 original size:16 final size:16
Alignment explanation
Indices: 18175272--18175332 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
18175262 GTTTTTTTCC
18175272 TCTTGTTTTTCCTTTA
1 TCTTGTTTTTCCTTTA
* *
18175288 TCTTCTTTTTTTCCCTTTT
1 TC-T-TGTTTTT-CCTTTA
18175307 TCTTGTTTTTCCTTTA
1 TCTTGTTTTTCCTTTA
18175323 T-TT-TTTTTCC
1 TCTTGTTTTTCC
18175333 GGTTTGTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 7 0.18
15 2 0.05
16 8 0.21
17 7 0.18
18 7 0.18
19 7 0.18
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.72
Consensus pattern (16 bp):
TCTTGTTTTTCCTTTA
Found at i:18175299 original size:19 final size:18
Alignment explanation
Indices: 18175272--18175325 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
18175262 GTTTTTTTCC
18175272 TCTTGTTTTTCCTTTATCT
1 TCTTGTTTTTCCTTTAT-T
*
18175291 TCTT-TTTTTCCCTT-TT
1 TCTTGTTTTTCCTTTATT
18175307 TCTTGTTTTTCCTTTATT
1 TCTTGTTTTTCCTTTATT
18175325 T
1 T
18175326 TTTTTCCGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 5 0.16
17 10 0.32
18 12 0.39
19 4 0.13
ACGTcount: A:0.04, C:0.20, G:0.04, T:0.72
Consensus pattern (18 bp):
TCTTGTTTTTCCTTTATT
Found at i:18175326 original size:19 final size:19
Alignment explanation
Indices: 18175272--18175326 Score: 71
Period size: 17 Copynumber: 3.1 Consensus size: 19
18175262 GTTTTTTTCC
*
18175272 TCTTGTTTTTCCTTTATCT
1 TCTTGTTTTTCCTTTATTT
*
18175291 TCTT-TTTTTCC-CT-TTT
1 TCTTGTTTTTCCTTTATTT
18175307 TCTTGTTTTTCCTTTATTT
1 TCTTGTTTTTCCTTTATTT
18175326 T
1 T
18175327 TTTTCCGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 6 0.20
17 8 0.27
18 8 0.27
19 8 0.27
ACGTcount: A:0.04, C:0.20, G:0.04, T:0.73
Consensus pattern (19 bp):
TCTTGTTTTTCCTTTATTT
Found at i:18177882 original size:17 final size:16
Alignment explanation
Indices: 18177862--18177901 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
18177852 ATGCCACGTC
*
18177862 AAAAAAATTTAAATTTA
1 AAAAAAAATTAAA-TTA
18177879 AAAAATAAATTAAATTA
1 AAAAA-AAATTAAATTA
18177896 AAAAAA
1 AAAAAA
18177902 TAAAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 13 0.62
18 7 0.33
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAAAAATTAAATTA
Found at i:18177891 original size:18 final size:18
Alignment explanation
Indices: 18177870--18177905 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
18177860 TCAAAAAAAT
*
18177870 TTAAATTTAAAAAATAAA
1 TTAAATTAAAAAAATAAA
18177888 TTAAATTAAAAAAATAAA
1 TTAAATTAAAAAAATAAA
18177906 ATATTTACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAATTAAAAAAATAAA
Found at i:18179134 original size:62 final size:63
Alignment explanation
Indices: 18179028--18179192 Score: 196
Period size: 62 Copynumber: 2.6 Consensus size: 63
18179018 GAAACCTAAG
* * * *
18179028 TCTCGAAAATCCGCAAATTTTTATACTTAAACCAAA-ATCTCCAAACCCAACAA-CCTGAAAAA
1 TCTCGAAAATCCCCAAATTTTTAAACCTAAACCAAATTTCTCCAAACCCAACAACCCT-AAAAA
18179090 TCTCG-AAATCCCCAAATTTCTTAAACCTAAACCAAATTTC-CCAAACCCAACAACCCTAAAAA
1 TCTCGAAAATCCCCAAATTT-TTAAACCTAAACCAAATTTCTCCAAACCCAACAACCCTAAAAA
*
18179152 TC-CTGAAAATCCCGAAATTTTTAAAACCTAAATCCCAAATT
1 TCTC-GAAAATCCCCAAATTTTT-AAACCTAAA--CCAAATT
18179193 CTCAAAAATT
Statistics
Matches: 90, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
61 14 0.16
62 42 0.47
63 27 0.30
65 7 0.08
ACGTcount: A:0.44, C:0.29, G:0.04, T:0.24
Consensus pattern (63 bp):
TCTCGAAAATCCCCAAATTTTTAAACCTAAACCAAATTTCTCCAAACCCAACAACCCTAAAAA
Found at i:18179939 original size:41 final size:40
Alignment explanation
Indices: 18179893--18179981 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
18179883 GCACTTTTAA
* *
18179893 CGGCGTTTGGATA-AAAAACGCAGCAAAATGTGAAGCAATAG
1 CGGCGTTT--ATACAAAAACGCAGCAAAAGGTAAAGCAATAG
* * * *
18179934 TGGCGTTTTTACATAAACGCCGCAAAAGGTAAAGCAATAG
1 CGGCGTTTATACAAAAACGCAGCAAAAGGTAAAGCAATAG
18179974 CGGCGTTT
1 CGGCGTTT
18179982 TTCCATAAGT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
39 2 0.05
40 31 0.77
41 7 0.17
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (40 bp):
CGGCGTTTATACAAAAACGCAGCAAAAGGTAAAGCAATAG
Found at i:18179959 original size:40 final size:40
Alignment explanation
Indices: 18179908--18180022 Score: 122
Period size: 40 Copynumber: 2.9 Consensus size: 40
18179898 TTTGGATAAA
* * *
18179908 AAACGCAGCAAAATGTGAAGCAATAGTGGCGTTTTTACAT
1 AAACGCAGCAAAAGGTAAAGCAATAGCGGCGTTTTTACAT
* *
18179948 AAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTTTCCAT
1 AAACGCAGCAAAAGGTAAAGCAATAGCGGCGTTTTTACAT
** * * * *
18179988 AAGTGCCGCTAAAGGTCAGAGCATTAGCGGCGTTT
1 AAACGCAGCAAAAGGT-AAAGCAATAGCGGCGTTT
18180023 ATGGGAAAGC
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
40 48 0.75
41 16 0.25
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (40 bp):
AAACGCAGCAAAAGGTAAAGCAATAGCGGCGTTTTTACAT
Found at i:18180143 original size:123 final size:123
Alignment explanation
Indices: 18179994--18180255 Score: 346
Period size: 123 Copynumber: 2.1 Consensus size: 123
18179984 CCATAAGTGC
* *
18179994 CGCTAAAGGTCAGAGCATTAGCGGCGTTTATGGGAAAGCGTCGCTAAAGATCAGAGTAATAGCGA
1 CGCTAAAGGTCAGAGCAATAGCGGCGTTTATGGGAAAGCGCCGCTAAAGATCAGAGTAATAGCGA
* * * * * *
18180059 CGTTTATTGA-AAAGCGCTGCTAAAAGTCAAAGTAATAGTGGCGTTTATGTGAAAGCGT
66 CGTTT-TTGAGAAAACGCCGCTAAAAGTCAAAGTAATAGCGGCATTTATGAGAAAACGT
* * * * * *
18180117 CGCTAAAGGTTAGAGTAATAGTGGCGTTTATGTGAAAGTGCCGCTAAAGGTCAGAGTAATAGCGA
1 CGCTAAAGGTCAGAGCAATAGCGGCGTTTATGGGAAAGCGCCGCTAAAGATCAGAGTAATAGCGA
* * *
18180182 CGTTTTTGAGAAAACGCCGCTTAAGGTCAGAGTAATAGCGGCATTTATGAGAAAACGT
66 CGTTTTTGAGAAAACGCCGCTAAAAGTCAAAGTAATAGCGGCATTTATGAGAAAACGT
*
18180240 CGCTAAATGTCAGAGC
1 CGCTAAAGGTCAGAGC
18180256 TTTAGCGGTG
Statistics
Matches: 118, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
122 4 0.03
123 114 0.97
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.24
Consensus pattern (123 bp):
CGCTAAAGGTCAGAGCAATAGCGGCGTTTATGGGAAAGCGCCGCTAAAGATCAGAGTAATAGCGA
CGTTTTTGAGAAAACGCCGCTAAAAGTCAAAGTAATAGCGGCATTTATGAGAAAACGT
Found at i:18180263 original size:41 final size:41
Alignment explanation
Indices: 18179994--18180254 Score: 292
Period size: 41 Copynumber: 6.4 Consensus size: 41
18179984 CCATAAGTGC
* * *
18179994 CGCTAAAGGTCAGAGCATTAGCGGCGTTTATGGGAAAGCGT
1 CGCTAAAGGTCAGAGTAATAGCGGCGTTTATGAGAAAGCGT
* *
18180035 CGCTAAAGATCAGAGTAATAGCGACGTTTATTGA-AAAGCG-
1 CGCTAAAGGTCAGAGTAATAGCGGCGTTTA-TGAGAAAGCGT
* * * *
18180075 CTGCTAAAAGTCAAAGTAATAGTGGCGTTTATGTGAAAGCGT
1 C-GCTAAAGGTCAGAGTAATAGCGGCGTTTATGAGAAAGCGT
* * * * *
18180117 CGCTAAAGGTTAGAGTAATAGTGGCGTTTATGTGAAAGTGC
1 CGCTAAAGGTCAGAGTAATAGCGGCGTTTATGAGAAAGCGT
* * * *
18180158 CGCTAAAGGTCAGAGTAATAGCGACGTTTTTGAGAAAACGC
1 CGCTAAAGGTCAGAGTAATAGCGGCGTTTATGAGAAAGCGT
* * *
18180199 CGCTTAAGGTCAGAGTAATAGCGGCATTTATGAGAAAACGT
1 CGCTAAAGGTCAGAGTAATAGCGGCGTTTATGAGAAAGCGT
*
18180240 CGCTAAATGTCAGAG
1 CGCTAAAGGTCAGAG
18180255 CTTTAGCGGT
Statistics
Matches: 186, Mismatches: 30, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
40 3 0.02
41 180 0.97
42 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.25
Consensus pattern (41 bp):
CGCTAAAGGTCAGAGTAATAGCGGCGTTTATGAGAAAGCGT
Found at i:18185072 original size:16 final size:17
Alignment explanation
Indices: 18185051--18185093 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
18185041 TCAAAATCAT
18185051 TATTTAATTATTT-AAA
1 TATTTAATTATTTGAAA
* *
18185067 TATTTAAATATTTGTAA
1 TATTTAATTATTTGAAA
18185084 TATTATAATT
1 TATT-TAATT
18185094 TAAATCTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 12 0.55
17 6 0.27
18 4 0.18
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TATTTAATTATTTGAAA
Found at i:18194181 original size:18 final size:20
Alignment explanation
Indices: 18194144--18194186 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
18194134 TGATATATAA
18194144 AATTTAAATTTTATTAAATC
1 AATTTAAATTTTATTAAATC
18194164 AATTTAAA-TTTA-TAAATC
1 AATTTAAATTTTATTAAATC
*
18194182 TATTT
1 AATTT
18194187 TAATATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
19 4 0.18
20 8 0.36
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTTAAATTTTATTAAATC
Found at i:18207479 original size:6 final size:6
Alignment explanation
Indices: 18207470--18207530 Score: 65
Period size: 6 Copynumber: 10.3 Consensus size: 6
18207460 TTTTAATTTT
* *
18207470 ATTTAA ATTTAA ATTT-- ATTTAA ATTTAA TTATTTAA ATTT-A CTTTGA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA ATTTAA
18207517 ATTTAA ATTTAA AT
1 ATTTAA ATTTAA AT
18207531 AAAAATTAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
4 4 0.09
5 4 0.09
6 33 0.70
8 6 0.13
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:18207503 original size:24 final size:23
Alignment explanation
Indices: 18207470--18207530 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 23
18207460 TTTTAATTTT
18207470 ATTTAAATTTAAATTTA-TTTAA
1 ATTTAAATTTAAATTTACTTTAA
*
18207492 ATTTAATTATTTAAATTTACTTTGA
1 ATTTAA--ATTTAAATTTACTTTAA
18207517 ATTTAAATTTAAAT
1 ATTTAAATTTAAAT
18207531 AAAAATTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
22 6 0.17
23 8 0.23
24 11 0.31
25 10 0.29
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
ATTTAAATTTAAATTTACTTTAA
Found at i:18207504 original size:30 final size:30
Alignment explanation
Indices: 18207468--18207528 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
18207458 ATTTTTAATT
18207468 TTATTTAAATTTAAATTT-ATTTAAATTTAA
1 TTATTTAAATTT-AATTTAATTTAAATTTAA
*
18207498 TTATTTAAATTTACTTTGAATTTAAATTTAA
1 TTATTTAAATTTAATTT-AATTTAAATTTAA
18207529 ATAAAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 4 0.14
30 12 0.43
31 12 0.43
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (30 bp):
TTATTTAAATTTAATTTAATTTAAATTTAA
Found at i:18207550 original size:20 final size:20
Alignment explanation
Indices: 18207525--18207569 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
18207515 GAATTTAAAT
18207525 TTAAA-TAAAAATTAAAAACA
1 TTAAATTAAAAATTAAAAA-A
* *
18207545 TTAAATTTAACATTAAAAAA
1 TTAAATTAAAAATTAAAAAA
18207565 TTAAA
1 TTAAA
18207570 AGTTCAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
TTAAATTAAAAATTAAAAAA
Found at i:18209372 original size:58 final size:57
Alignment explanation
Indices: 18209269--18209520 Score: 353
Period size: 58 Copynumber: 4.4 Consensus size: 57
18209259 AAACAGTCTA
* **
18209269 AAAATTACCATTTTACCCCTGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACC
1 AAAATTACCATTTTACCCCCGAA-CTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * *
18209327 GGAAATTACCAATTTACCCCCGAACTTCCAAAATTCCATTTTTAACCCCAATTTCACC
1 -AAAATTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCCCGATTTCACC
*
18209385 AAAAATTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACACCGATTTCACC
1 -AAAATTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * *
18209443 AAAAGTTACCATTTTACCCTCGAACTTTCCAAAATTCCA-TTTAAACCCCGTTTTCACC
1 AAAA-TTACCATTTTACCCCCGAAC-TTCCAAAATTCCATTTTTAACCCCGATTTCACC
*
18209501 AAAATTACCATTTTGCCCCC
1 AAAATTACCATTTTACCCCC
18209521 AGGTATCCAC
Statistics
Matches: 174, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
57 18 0.10
58 123 0.71
59 33 0.19
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.33
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:18209374 original size:29 final size:28
Alignment explanation
Indices: 18209269--18209484 Score: 131
Period size: 30 Copynumber: 7.4 Consensus size: 28
18209259 AAACAGTCTA
* **
18209269 AAAATTACCA-TTTTACCCCTGAATCTTTT
1 AAAATT-CCATTTTTACCCCCGAA-CTTCC
* *
18209298 AAAATTCCATTTTTAACCCCG-ATTTCACC
1 AAAATTCCATTTTTACCCCCGAACTT--CC
* *
18209327 GGAAATTACCA-ATTTACCCCCGAACTTCC
1 -AAAATT-CCATTTTTACCCCCGAACTTCC
* *
18209356 AAAATTCCATTTTTAACCCC-AATTTCACC
1 AAAATTCCATTTTTACCCCCGAACTT--CC
18209385 AAAAATTACCA-TTTTACCCCCGAACTTCC
1 -AAAATT-CCATTTTTACCCCCGAACTTCC
* * *
18209414 AAAATTCCATTTTTAACACCG-ATTTCACC
1 AAAATTCCATTTTTACCCCCGAACTT--CC
*
18209443 AAAAGTTACCA-TTTTACCCTCGAACTTTCC
1 AAAA-TT-CCATTTTTACCCCCGAAC-TTCC
18209473 AAAATTCCATTT
1 AAAATTCCATTT
18209485 AAACCCCGTT
Statistics
Matches: 145, Mismatches: 22, Indels: 40
0.70 0.11 0.19
Matches are distributed among these distances:
27 15 0.10
28 35 0.24
29 31 0.21
30 45 0.31
31 17 0.12
32 2 0.01
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCCCGAACTTCC
Found at i:18209502 original size:28 final size:29
Alignment explanation
Indices: 18209298--18209514 Score: 168
Period size: 28 Copynumber: 7.5 Consensus size: 29
18209288 TGAATCTTTT
18209298 AAAATT-CCATTTTTAACCCCGATTTCACC
1 AAAATTACCA-TTTTAACCCCGATTTCACC
* * * *
18209327 GGAAATTACCAATTTACCCCCGAACTT--CC
1 -AAAATTACCATTTTAACCCCG-ATTTCACC
*
18209356 AAAATT-CCATTTTTAACCCCAATTTCACC
1 AAAATTACCA-TTTTAACCCCGATTTCACC
* *
18209385 AAAAATTACCATTTTACCCCCGAACTT--CC
1 -AAAATTACCATTTTAACCCCG-ATTTCACC
*
18209414 AAAATT-CCATTTTTAACACCGATTTCACC
1 AAAATTACCA-TTTTAACCCCGATTTCACC
18209443 AAAAGTTACCATTTT-ACCCTCGAACTTT--CC
1 AAAA-TTACCATTTTAACCC-CG-A-TTTCACC
* *
18209473 AAAATT-CCATTTAAACCCCGTTTTCACC
1 AAAATTACCATTTTAACCCCGATTTCACC
18209501 AAAATTACCATTTT
1 AAAATTACCATTTT
18209515 GCCCCCAGGT
Statistics
Matches: 148, Mismatches: 19, Indels: 41
0.71 0.09 0.20
Matches are distributed among these distances:
26 3 0.02
27 12 0.08
28 44 0.30
29 27 0.18
30 43 0.29
31 16 0.11
32 3 0.02
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.32
Consensus pattern (29 bp):
AAAATTACCATTTTAACCCCGATTTCACC
Found at i:18209519 original size:28 final size:29
Alignment explanation
Indices: 18209269--18209519 Score: 126
Period size: 28 Copynumber: 8.7 Consensus size: 29
18209259 AAACAGTCTA
*
18209269 AAAATTACCATTTTACCCCTGAATCTTT---T
1 AAAATTACCATTTTACCCC-G-A-CTTTCACC
18209298 AAAATT-CCATTTTTAACCCCGA-TTTCACC
1 AAAATTACCA-TTTT-ACCCCGACTTTCACC
* *
18209327 GGAAATTACCAATTTACCCCCGAAC-TT--CC
1 -AAAATTACCATTTTA-CCCCG-ACTTTCACC
*
18209356 AAAATT-CCATTTTTAACCCC-AATTTCACC
1 AAAATTACCA-TTTT-ACCCCGACTTTCACC
18209385 AAAAATTACCATTTTACCCCCGAAC-TT--CC
1 -AAAATTACCATTTTA-CCCCG-ACTTTCACC
*
18209414 AAAATT-CCATTTTTAACACCGA-TTTCACC
1 AAAATTACCA-TTTT-ACCCCGACTTTCACC
18209443 AAAAGTTACCATTTTACCCTCGAACTTT--CC
1 AAAA-TTACCATTTTACCC-CG-ACTTTCACC
* *
18209473 AAAATT-CCATTTAAACCCCG-TTTTCACC
1 AAAATTACCATTT-TACCCCGACTTTCACC
*
18209501 AAAATTACCATTTTGCCCC
1 AAAATTACCATTTTACCCC
18209520 CAGGTATCCA
Statistics
Matches: 175, Mismatches: 13, Indels: 69
0.68 0.05 0.27
Matches are distributed among these distances:
26 7 0.04
27 11 0.06
28 50 0.29
29 42 0.24
30 46 0.26
31 15 0.09
32 4 0.02
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCGACTTTCACC
Found at i:18219535 original size:137 final size:137
Alignment explanation
Indices: 18219342--18219961 Score: 981
Period size: 137 Copynumber: 4.5 Consensus size: 137
18219332 ATCGTTTCCT
* * *
18219342 ATCCGCTTGAAATTGAAGTAGAG-TGGATATCACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
18219406 TGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAG
66 TGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAG
18219471 CAACGTC
131 CAACGTC
*
18219478 ATCCTCTTGAAATTGAAGTAGAGTTGGCTATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
18219543 TGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAG
66 TGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAG
18219608 CAACGTC
131 CAACGTC
18219615 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
**
18219680 TGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTACATCTCTGAAATTGAAGTAAGAG
66 TGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAG
18219745 CAACGTC
131 CAACGTC
* * * *
18219752 ATCCCCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGTAA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAG-CA
* * * * *
18219817 CATCGTTTCCTATCCTCTTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTCTGAAATTGA
65 -AT-G--T-C-ATCCCCTTGAAATTGAAGT-AGAGTGGATAACACGTCTTTATCTCTGAAATTGA
*
18219882 AGTAAGAGAAACGTC
123 AGTAAGAGCAACGTC
* * * *
18219897 ATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGCCTTTATCCCTGAAATTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
18219962 GATTATTTCC
Statistics
Matches: 450, Mismatches: 25, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
136 22 0.05
137 303 0.67
138 1 0.00
139 2 0.00
140 1 0.00
142 1 0.00
143 2 0.00
144 19 0.04
145 99 0.22
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (137 bp):
ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
TGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAG
CAACGTC
Found at i:18219541 original size:69 final size:68
Alignment explanation
Indices: 18219342--18219961 Score: 889
Period size: 69 Copynumber: 8.9 Consensus size: 68
18219332 ATCGTTTCCT
* * * *
18219342 ATCCGCTTGAAATTGAAGTAGAGTGGATATCACGTCTTCATCTCTGAAATTGAAGTAAGAGCAAT
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
18219407 GTC
66 GTC
18219410 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
18219475 GTC
66 GTC
* * * *
18219478 ATCCTCTTGAAATTGAAGTAGAGTTGGCTATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCCCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
*
18219543 TGTC
65 CGTC
18219547 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
18219612 GTC
66 GTC
* * *
18219615 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCCCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
*
18219680 TGTC
65 CGTC
**
18219684 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTACATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
18219749 GTC
66 GTC
* *
18219752 ATCCCCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGTAA
1 ATCCCCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAG---
*
18219817 CATCGTTTCC
62 CAACG--T-C
* * * * * *
18219827 TATCCTCTTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGAA
1 -ATCCCCTTGAAATTGAAGT-AGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
18219892 ACGTC
64 ACGTC
* * *
18219897 ATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGCCTTTATCCCTGAAATTGAAGTAAGAGCAA
1 ATCCCCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
18219962 GATTATTTCC
Statistics
Matches: 499, Mismatches: 41, Indels: 23
0.89 0.07 0.04
Matches are distributed among these distances:
68 214 0.43
69 218 0.44
70 1 0.00
71 1 0.00
72 4 0.01
73 3 0.01
74 1 0.00
75 1 0.00
76 54 0.11
77 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (68 bp):
ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
GTC
Found at i:18219803 original size:38 final size:36
Alignment explanation
Indices: 18219349--18219956 Score: 281
Period size: 31 Copynumber: 17.4 Consensus size: 36
18219339 CCTATCCGCT
* *
18219349 TGAAATTGAAGTAGAGTGGATATCACGTCTTCATCTC
1 TGAAATTGAAGTA-AGTGGATAACAAGTCTTCATCTC
* * **
18219386 TGAAATTGAAGTAA---G--AGCAATGTCATCCCCT-
1 TGAAATTGAAGTAAGTGGATAACAA-GTCTTCATCTC
* *
18219417 TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
1 TGAAATTGAAGTA-AGTGGATAACAAGTCTTCATCTC
* * * *
18219454 TGAAATTGAAGTAAG-AG-CAAC--GTCATCCTCT-
1 TGAAATTGAAGTAAGTGGATAACAAGTCTTCATCTC
* * *
18219485 TGAAATTGAAGTAGAGTTGGCTATCAAGTCTTTATCTC
1 TGAAATTGAAGTA-AG-TGGATAACAAGTCTTCATCTC
* * **
18219523 TGAAATTGAAGTAA---G--AGCAATGTCATCCCCT-
1 TGAAATTGAAGTAAGTGGATAACAA-GTCTTCATCTC
* *
18219554 TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
1 TGAAATTGAAGTA-AGTGGATAACAAGTCTTCATCTC
* * * *
18219591 TGAAATTGAAGTAAG-AG-CAAC--GTCATCCTCT-
1 TGAAATTGAAGTAAGTGGATAACAAGTCTTCATCTC
* *
18219622 TGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTC
1 TGAAATTGAAGTA-AG-TGGATAACAAGTCTTCATCTC
* * **
18219660 TGAAATTGAAGTAA---G--AGCAATGTCATCCCCT-
1 TGAAATTGAAGTAAGTGGATAACAA-GTCTTCATCTC
* *
18219691 TGAAATTGAAGTAGAGTGGATAACACGTCTACATCTC
1 TGAAATTGAAGTA-AGTGGATAACAAGTCTTCATCTC
* * * **
18219728 TGAAATTGAAGTAAG-AG-CAAC--GTCATCCCCT-
1 TGAAATTGAAGTAAGTGGATAACAAGTCTTCATCTC
18219759 TGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTC
1 TGAAATTGAAGTA-AG-TGGATAACAAGTCTTCATCTC
* *
18219797 TGAAATTGAAGTAAG-AG-TAACATCGT-TTCCTATCCTC
1 TGAAATTGAAGTAAGTGGATAACA-AGTCTT-C-AT-CTC
* * *
18219834 TTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTC
1 -TGAAATTGAAGT--AAGTGGATAACAAGTCTTCATCTC
* * *
18219873 TGAAATTGAAGTAAG-AGA-AAC--GTCATCCTCT-
1 TGAAATTGAAGTAAGTGGATAACAAGTCTTCATCTC
* * * *
18219904 TGAAATTGAAGTAGAGTTGGATAACACGCCTTTATCCC
1 TGAAATTGAAGTA-AG-TGGATAACAAGTCTTCATCTC
18219942 TGAAATTGAAGTAAG
1 TGAAATTGAAGTAAG
18219957 AGCAAGATTA
Statistics
Matches: 424, Mismatches: 85, Indels: 124
0.67 0.13 0.20
Matches are distributed among these distances:
31 102 0.24
32 57 0.13
33 3 0.01
34 23 0.05
35 22 0.05
36 29 0.07
37 96 0.23
38 76 0.18
39 3 0.01
40 4 0.01
41 3 0.01
42 6 0.01
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (36 bp):
TGAAATTGAAGTAAGTGGATAACAAGTCTTCATCTC
Found at i:18220335 original size:6 final size:6
Alignment explanation
Indices: 18220326--18220386 Score: 56
Period size: 6 Copynumber: 10.3 Consensus size: 6
18220316 TTTTAATTTT
* * *
18220326 ATTTAA ATTTAA ATTT-- ATCTAA ATTTAA TTATTTAA ATTT-A CTTTGA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA ATTTAA
18220373 ATTTAA ATTTAA AT
1 ATTTAA ATTTAA AT
18220387 AAAAATTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
4 3 0.07
5 4 0.09
6 32 0.71
8 6 0.13
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:18220336 original size:16 final size:16
Alignment explanation
Indices: 18220317--18220384 Score: 77
Period size: 16 Copynumber: 4.3 Consensus size: 16
18220307 TAAATTGATT
18220317 TTTAATTTTATTTAAA
1 TTTAATTTTATTTAAA
* *
18220333 TTTAAATTTATCTAAA
1 TTTAATTTTATTTAAA
18220349 TTTAA--TTATTTAAA
1 TTTAATTTTATTTAAA
* *
18220363 TTTACTTTGAATTTAAA
1 TTTAATTT-TATTTAAA
18220380 TTTAA
1 TTTAA
18220385 ATAAAAATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
14 12 0.28
16 20 0.47
17 11 0.26
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (16 bp):
TTTAATTTTATTTAAA
Found at i:18220406 original size:20 final size:20
Alignment explanation
Indices: 18220381--18220425 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
18220371 GAATTTAAAT
18220381 TTAAA-TAAAAATTAAAAACA
1 TTAAATTAAAAATTAAAAA-A
* *
18220401 TTAAATTTAACATTAAAAAA
1 TTAAATTAAAAATTAAAAAA
18220421 TTAAA
1 TTAAA
18220426 AGTTCAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
TTAAATTAAAAATTAAAAAA
Found at i:18222084 original size:164 final size:161
Alignment explanation
Indices: 18221898--18222264 Score: 531
Period size: 162 Copynumber: 2.3 Consensus size: 161
18221888 TTCAATTTAA
* *
18221898 TCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGGCTTATTTATGCATTT
1 TCCTTTGACTG-TTGGCTGCACCAGAGGCTGCCACGTGTCACTTTTT-GACTTATTTATGCATTT
* *
18221963 AGTCCCTGATATTTTTTAATTTGTTTTAATTTAATCCCTAAATAGAGTTTTACTTAATTACAAAA
64 AGTCCCTGACA-TTTTTAATTTGTTTTAATTTAATCCCTAAATAGACTTTTACTTAATTACAAAA
* *
18222028 TTGGCCCAACAATTTTTCAAGATTTATAAATTAG
128 TTAGCCCAACAATTTTTCAAGATTTACAAATTAG
18222062 TCCTTTGACTGTGTGGCTGCACCAG-GGACTGCCACGTGTCACTTTTTGACTTATTTATGCATTT
1 TCCTTTGACTGT-TGGCTGCACCAGAGG-CTGCCACGTGTCACTTTTTGACTTATTTATGCATTT
*
18222126 AGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATTGACTTTTACTTAATTACAAAAT
64 AGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATAGACTTTTACTTAATTACAAAAT
* * *
18222191 TAGCCCAAGAATTTTTCAAGATTTACAATTTGG
129 TAGCCCAACAATTTTTCAAGATTTACAAATTAG
* * * **
18222224 TCCCTTAACTGTTGGATGC-CTGTGAGGCTGCCACGTGTCAC
1 TCCTTTGACTGTTGGCTGCAC-CAGAGGCTGCCACGTGTCAC
18222265 CCACTCTTTG
Statistics
Matches: 184, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
160 1 0.01
161 21 0.11
162 92 0.50
163 29 0.16
164 41 0.22
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (161 bp):
TCCTTTGACTGTTGGCTGCACCAGAGGCTGCCACGTGTCACTTTTTGACTTATTTATGCATTTAG
TCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATAGACTTTTACTTAATTACAAAATTA
GCCCAACAATTTTTCAAGATTTACAAATTAG
Found at i:18222181 original size:162 final size:164
Alignment explanation
Indices: 18221898--18222215 Score: 534
Period size: 162 Copynumber: 2.0 Consensus size: 164
18221888 TTCAATTTAA
* *
18221898 TCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGGCTTATTTATGCATTT
1 TCCTTTGACTGTGTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGACTTATTTATGCATTT
* *
18221963 AGTCCCTGATATTTTTTAATTTGTTTTAATTTAATCCCTAAATAGAGTTTTACTTAATTACAAAA
66 AGTCCCTGACATTTTTTAATTTGTTTTAATTTAATCCCTAAATAGACTTTTACTTAATTACAAAA
*
18222028 TTGGCCCAACAATTTTTCAAGATTTATAAATTAG
131 TTAGCCCAACAATTTTTCAAGATTTATAAATTAG
*
18222062 TCCTTTGACTGTGTGGCTGCACCAG-GGACTGCCACGTGTCACTTTTT-GACTTATTTATGCATT
1 TCCTTTGACTGTGTGACTGCACCAGAGG-CTGCCACGTGTCACTTTTTGGACTTATTTATGCATT
*
18222125 TAGTCCCTGACA-TTTTTAATTTGTTTTAATTTAATCCCTAAATTGACTTTTACTTAATTACAAA
65 TAGTCCCTGACATTTTTTAATTTGTTTTAATTTAATCCCTAAATAGACTTTTACTTAATTACAAA
*
18222189 ATTAGCCCAAGAATTTTTCAAGATTTA
130 ATTAGCCCAACAATTTTTCAAGATTTA
18222216 CAATTTGGTC
Statistics
Matches: 145, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
162 75 0.52
163 28 0.19
164 42 0.29
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (164 bp):
TCCTTTGACTGTGTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGACTTATTTATGCATTT
AGTCCCTGACATTTTTTAATTTGTTTTAATTTAATCCCTAAATAGACTTTTACTTAATTACAAAA
TTAGCCCAACAATTTTTCAAGATTTATAAATTAG
Found at i:18222339 original size:29 final size:28
Alignment explanation
Indices: 18222307--18222522 Score: 140
Period size: 29 Copynumber: 7.5 Consensus size: 28
18222297 AAACAGTCCA
*
18222307 AAAATTACCATTTTACCCCCAAATCTTTT
1 AAAATTACCATTTTACCCCCAAA-CTTTC
* * *
18222336 AAAATT-CCATTTTTAACCCC-GATTTCATC
1 AAAATTACCA-TTTTACCCCCAAACTT--TC
* *
18222365 GAAAATTACCATTTTACCCTCGAACTTTCC
1 -AAAATTACCATTTTACCCCCAAACTTT-C
* *
18222395 AAAATTA-TATTTTGACCCCAAAACTTTC
1 AAAATTACCATTTT-ACCCCCAAACTTTC
* *
18222423 AAAAATTACCATTTTACCCCCGAACTTCC
1 -AAAATTACCATTTTACCCCCAAACTTTC
* *
18222452 AAAATT-CCATTTTTAACCCC-GA-TTTCACC
1 AAAATTACCA-TTTTACCCCCAAACTTT---C
* *
18222481 AAAAATTACCATTTTACCCCCGAACTTCC
1 -AAAATTACCATTTTACCCCCAAACTTTC
18222510 AAAATT-CCATTTT
1 AAAATTACCATTTT
18222523 TAACACCGAT
Statistics
Matches: 147, Mismatches: 22, Indels: 38
0.71 0.11 0.18
Matches are distributed among these distances:
26 2 0.01
27 13 0.09
28 31 0.21
29 54 0.37
30 35 0.24
31 10 0.07
32 2 0.01
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCCAAACTTTC
Found at i:18222441 original size:58 final size:55
Alignment explanation
Indices: 18222303--18222610 Score: 309
Period size: 58 Copynumber: 5.3 Consensus size: 55
18222293 CCCCAAACAG
* **
18222303 TCCAAAAATTACCATTTTACCCCCAAATCTTTTAAAATTCCATTTTTAACCCCGATT
1 TCCAAAAATTACCATTTTACCCCCGAA-CTTCCAAAATT-CATTTTTAACCCCGATT
* * * *
18222360 TCATCGAAAATTACCATTTTACCCTCGAACTTTCCAAAATT-ATATTTTGACCCCAAAACTT
1 TC--CAAAAATTACCATTTTACCCCCGAAC-TTCCAAAATTCAT-TTTTAACCCC--GA-TT
18222421 T-CAAAAATTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCCCGATT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAATT-CATTTTTAACCCCGATT
*
18222476 TCACCAAAAATTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACACCGATT
1 T--CCAAAAATTACCATTTTACCCCCGAACTTCCAAAATT-CATTTTTAACCCCGATT
* * *
18222534 TCACCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCA--TTTAAACCCTATTT
1 T--CCAAAAATTACCATTTTACCCCCGAAC-TTCCAAAATT-CATTTTTAACCCCGA-TT
*
18222592 TCACCAAAATTACCATTTT
1 TC-CAAAAATTACCATTTT
18222611 GCCTCCGGGT
Statistics
Matches: 219, Mismatches: 17, Indels: 30
0.82 0.06 0.11
Matches are distributed among these distances:
55 3 0.01
56 2 0.01
57 37 0.17
58 128 0.58
59 45 0.21
60 1 0.00
61 3 0.01
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (55 bp):
TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAATTCATTTTTAACCCCGATT
Found at i:18222498 original size:116 final size:112
Alignment explanation
Indices: 18222303--18222610 Score: 372
Period size: 116 Copynumber: 2.7 Consensus size: 112
18222293 CCCCAAACAG
* ** *
18222303 TCCAAAAATTACCATTTTACCCCCAAATCTTTTAAAATTCCATTTTTAACCCCGATTTCATCGAA
1 TCCAAAAATTACCATTTTACCCCCGAA-CTTCCAAAATTCCATTTTTAACCCCGATTTCA-CCAA
* * *
18222368 AATTACCATTTTACCCTCGAACTTTCCAAAATT-ATATTTTGACCCCAAAACTT
64 AATTACCATTTTACCCCCGAAC-TTCCAAAATTCAT-TTTTAACACC--AA-TT
18222421 T-CAAAAATTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCCCGATTTCACC-AAA
*
18222485 ATTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACACCGATT
65 ATTACCATTTTACCCCCGAACTTCCAAAATT-CATTTTTAACACCAATT
* * *
18222534 TCACCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCA--TTTAAACCCTATTTTCACC
1 T--CCAAAAATTACCATTTTACCCCCGAAC-TTCCAAAATTCCATTTTTAACCCCGA-TTTCACC
18222597 AAAATTACCATTTT
62 AAAATTACCATTTT
18222611 GCCTCCGGGT
Statistics
Matches: 171, Mismatches: 11, Indels: 19
0.85 0.05 0.09
Matches are distributed among these distances:
113 3 0.02
114 1 0.01
115 34 0.20
116 93 0.54
117 39 0.23
118 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (112 bp):
TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
TTACCATTTTACCCCCGAACTTCCAAAATTCATTTTTAACACCAATT
Found at i:18222540 original size:29 final size:29
Alignment explanation
Indices: 18222336--18222610 Score: 163
Period size: 30 Copynumber: 9.5 Consensus size: 29
18222326 CAAATCTTTT
*
18222336 AAAATT-CCATTTTTAACCCCGATTTCATCG
1 AAAATTACCA-TTTTAACCCCGATTTCA-CC
18222366 AAAATTACCATTTT-ACCCTCGAACTTT--CC
1 AAAATTACCATTTTAACCC-CG-A-TTTCACC
* * *
18222395 AAAATTA-TATTTTGACCCCAAAACTTTCA--
1 AAAATTACCATTTTAACCCC--GA-TTTCACC
* *
18222424 AAAATTACCATTTTACCCCCGAACTT--CC
1 AAAATTACCATTTTAACCCCG-ATTTCACC
18222452 AAAATT-CCATTTTTAACCCCGATTTCACC
1 AAAATTACCA-TTTTAACCCCGATTTCACC
* *
18222481 AAAAATTACCATTTTACCCCCGAACTT--CC
1 -AAAATTACCATTTTAACCCCG-ATTTCACC
*
18222510 AAAATT-CCATTTTTAACACCGATTTCACC
1 AAAATTACCA-TTTTAACCCCGATTTCACC
18222539 AAAAATTACCATTTT-ACCCTCGAACTTT--CC
1 -AAAATTACCATTTTAACCC-CG-A-TTTCACC
* *
18222569 AAAATT-CCA-TTTAAACCCTATTTTCACC
1 AAAATTACCATTTTAACCCCGA-TTTCACC
18222597 AAAATTACCATTTT
1 AAAATTACCATTTT
18222611 GCCTCCGGGT
Statistics
Matches: 194, Mismatches: 19, Indels: 64
0.70 0.07 0.23
Matches are distributed among these distances:
26 4 0.02
27 16 0.08
28 53 0.27
29 47 0.24
30 54 0.28
31 14 0.07
32 6 0.03
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATTACCATTTTAACCCCGATTTCACC
Found at i:18232889 original size:59 final size:58
Alignment explanation
Indices: 18232794--18232943 Score: 157
Period size: 56 Copynumber: 2.6 Consensus size: 58
18232784 GGAATCTAAC
* * *
18232794 TTTGATAC-TTTTTTTTAATTTGGTACATAAACTTTTTCTAG-CCCGATTTGGTACTTAAA
1 TTTGACACTTTTTTTTTAATTTGGTACATAAA-TTTTT-TAGACCCAATTTGGTAC-CAAA
* * * *
18232853 TTTGACACTTTTTTTTTAATTTAGTATC-TAAATTTTTTTGACCTAATTTGGTACCGAA
1 TTTGACACTTTTTTTTTAATTTGGTA-CATAAATTTTTTAGACCCAATTTGGTACCAAA
*
18232911 TTTG-CA-TTTTTTTTTAATTTGGTACTTAAATTT
1 TTTGACACTTTTTTTTTAATTTGGTACATAAATTT
18232944 ATTAAATATT
Statistics
Matches: 79, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
55 1 0.01
56 24 0.30
57 2 0.03
58 8 0.10
59 23 0.29
60 20 0.25
61 1 0.01
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.53
Consensus pattern (58 bp):
TTTGACACTTTTTTTTTAATTTGGTACATAAATTTTTTAGACCCAATTTGGTACCAAA
Found at i:18233128 original size:31 final size:31
Alignment explanation
Indices: 18233085--18233148 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
18233075 ATTAAAAAAA
18233085 TTAACTATCAAATT-AGAAAAAAGTGTCAAGT
1 TTAACTATCAAATTAAGAAAAAA-TGTCAAGT
*
18233116 TTAAGTATCAAATTAAGAAAAAATGTCAAGT
1 TTAACTATCAAATTAAGAAAAAATGTCAAGT
18233147 TT
1 TT
18233149 GAGTGCCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 23 0.74
32 8 0.26
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.31
Consensus pattern (31 bp):
TTAACTATCAAATTAAGAAAAAATGTCAAGT
Found at i:18233159 original size:31 final size:32
Alignment explanation
Indices: 18233093--18233162 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 32
18233083 AATTAACTAT
*
18233093 CAAATT-AGAAAAAAGTGTCAAGTTTAAGTAT
1 CAAATTAAGAAAAAAGTGTCAAGTTTAAGTAC
* *
18233124 CAAATTAAGAAAAAA-TGTCAAGTTTGAGTGC
1 CAAATTAAGAAAAAAGTGTCAAGTTTAAGTAC
18233155 CAAATTAA
1 CAAATTAA
18233163 ACAAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 27 0.77
32 8 0.23
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.27
Consensus pattern (32 bp):
CAAATTAAGAAAAAAGTGTCAAGTTTAAGTAC
Found at i:18233169 original size:32 final size:31
Alignment explanation
Indices: 18233093--18233170 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
18233083 AATTAACTAT
* * *
18233093 CAAATTAGAAAAAAGTGTCAAGTTTAAGTAT
1 CAAATTAAAAAAAAATGTCAAGTTTAAGTAC
* * *
18233124 CAAATTAAGAAAAAATGTCAAGTTTGAGTGC
1 CAAATTAAAAAAAAATGTCAAGTTTAAGTAC
18233155 CAAATTAAACAAAAAA
1 CAAATTAAA-AAAAAA
18233171 AAATTAAGTA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 33 0.85
32 6 0.15
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.24
Consensus pattern (31 bp):
CAAATTAAAAAAAAATGTCAAGTTTAAGTAC
Found at i:18234500 original size:19 final size:19
Alignment explanation
Indices: 18234473--18234513 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
18234463 GTGCATGGCA
*
18234473 CATCCTGGCACACAAAGTG
1 CATCATGGCACACAAAGTG
*
18234492 CATCATGGCGCACAAAGTG
1 CATCATGGCACACAAAGTG
18234511 CAT
1 CAT
18234514 ATCTAGCACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.32, C:0.29, G:0.22, T:0.17
Consensus pattern (19 bp):
CATCATGGCACACAAAGTG
Found at i:18235118 original size:30 final size:29
Alignment explanation
Indices: 18235061--18235118 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
18235051 CTTTTTTACT
* *
18235061 TTTCCCCTAAAACTTTTACTCCTTCCCAC
1 TTTCCCCCAAAACTTTTACTCCCTCCCAC
18235090 TTTCCCCCAAAACTTTTACTCTCCTCCCA
1 TTTCCCCCAAAACTTTTACTC-CCTCCCA
18235119 TCCCACCCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.21, C:0.43, G:0.00, T:0.36
Consensus pattern (29 bp):
TTTCCCCCAAAACTTTTACTCCCTCCCAC
Found at i:18235872 original size:19 final size:19
Alignment explanation
Indices: 18235848--18235885 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
18235838 AAAGTTAATA
* *
18235848 ACAAATTTGATTATGGTGG
1 ACAAATTTAATTATAGTGG
18235867 ACAAATTTAATTATAGTGG
1 ACAAATTTAATTATAGTGG
18235886 GTGACGGTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (19 bp):
ACAAATTTAATTATAGTGG
Found at i:18237599 original size:2 final size:2
Alignment explanation
Indices: 18237594--18237621 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18237584 GGTGCAGTAA
18237594 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
18237622 TAAGATTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18238992 original size:18 final size:18
Alignment explanation
Indices: 18238944--18238983 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
18238934 CTAGCAAAAA
*
18238944 TAAA-AAATTATTATTTT
1 TAAATAAATTATAATTTT
*
18238961 TAAATAAATAATAATTTT
1 TAAATAAATTATAATTTT
18238979 TAAAT
1 TAAAT
18238984 TATTTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATAAATTATAATTTT
Found at i:18239048 original size:10 final size:10
Alignment explanation
Indices: 18239010--18239051 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
18239000 AAAAGTTATT
*
18239010 AAAAAATATA
1 AAAAAATTTA
*
18239020 AAAATA-TTA
1 AAAAAATTTA
18239029 AAAAAATTTA
1 AAAAAATTTA
*
18239039 AAAAAGTTTA
1 AAAAAATTTA
18239049 AAA
1 AAA
18239052 TTAATAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.26
10 20 0.74
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (10 bp):
AAAAAATTTA
Found at i:18239051 original size:9 final size:9
Alignment explanation
Indices: 18239008--18239051 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
18238998 TAAAAAGTTA
18239008 TTAAAAAAT
1 TTAAAAAAT
*
18239017 ATAAAAATAT
1 TTAAAAA-AT
*
18239027 TAAAAAAAT
1 TTAAAAAAT
18239036 TTAAAAAAGT
1 TTAAAAAA-T
18239046 TTAAAA
1 TTAAAA
18239052 TTAATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 15 0.52
10 14 0.48
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
TTAAAAAAT
Found at i:18239051 original size:19 final size:19
Alignment explanation
Indices: 18239008--18239051 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
18238998 TAAAAAGTTA
18239008 TTAAAAAATATAAAAATAT
1 TTAAAAAATATAAAAATAT
* *
18239027 TAAAAAAATTTAAAAA-AGT
1 TTAAAAAATATAAAAATA-T
18239046 TTAAAA
1 TTAAAA
18239052 TTAATAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
TTAAAAAATATAAAAATAT
Found at i:18244321 original size:3 final size:3
Alignment explanation
Indices: 18244313--18244359 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
18244303 CAAAACGTAG
* *
18244313 AGA AGA AGA AGA AGA AGA AGA AGT AGA AGA AAA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
18244360 TAAATGCACC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:18244855 original size:15 final size:17
Alignment explanation
Indices: 18244821--18244861 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
18244811 ATTTTCCTTT
18244821 AATTAATTTAGAAAATTC
1 AATTAA-TTAGAAAATTC
18244839 AATTAATTA-AAAA-TC
1 AATTAATTAGAAAATTC
18244854 AATTAATT
1 AATTAATT
18244862 TACTTGGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.43
16 4 0.17
17 3 0.13
18 6 0.26
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (17 bp):
AATTAATTAGAAAATTC
Found at i:18245192 original size:186 final size:187
Alignment explanation
Indices: 18244868--18245214 Score: 534
Period size: 186 Copynumber: 1.9 Consensus size: 187
18244858 AATTTACTTG
* * * * *
18244868 GTTGAACGTTCACGTTGGCATTTAAAACTCATTTTAACTGCCACACCGGATTGTCTTTTGGGAGG
1 GTTGAACATTCACGTTGGCATTTAAAACTCATTTTAACTACCACACCAGACTGTCATTTGGGAGG
* * * * *
18244933 TAACAGATCTTAACGGCAGAGTGATAATTTCGTAACAAAACGATAACGTAAGTAACTAAAACGTA
66 TAACAGATCTTAACGACAGAGTGATAACTTCGTAACAAAACGACAACGTAAATAACTAAAACATA
18244998 ACATTTCAAACATAAGTAACT-AAATGTAATTTGAGACAAATAAAAGTGACAATTTT
131 ACATTTCAAACATAAGTAACTAAAATGTAATTTGAGACAAATAAAAGTGACAATTTT
* **
18245054 GTTGAACATTCACGTTGGCATTTAAAACTCATTTTAACTATCACGTCAGACTGTCATTTGGGAGG
1 GTTGAACATTCACGTTGGCATTTAAAACTCATTTTAACTACCACACCAGACTGTCATTTGGGAGG
* * *
18245119 TAACAGATCTTAACGACAGAGTGATTACTTCGTAACATAATGACAACGTAAATAACTAAAACATA
66 TAACAGATCTTAACGACAGAGTGATAACTTCGTAACAAAACGACAACGTAAATAACTAAAACATA
*
18245184 ATATTTCAAACATAAGTAACTAAAATGTAAT
131 ACATTTCAAACATAAGTAACTAAAATGTAAT
18245215 CGGAATCATA
Statistics
Matches: 143, Mismatches: 17, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
186 134 0.94
187 9 0.06
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (187 bp):
GTTGAACATTCACGTTGGCATTTAAAACTCATTTTAACTACCACACCAGACTGTCATTTGGGAGG
TAACAGATCTTAACGACAGAGTGATAACTTCGTAACAAAACGACAACGTAAATAACTAAAACATA
ACATTTCAAACATAAGTAACTAAAATGTAATTTGAGACAAATAAAAGTGACAATTTT
Found at i:18250248 original size:24 final size:24
Alignment explanation
Indices: 18250215--18250261 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
18250205 GAAAAAAATC
* *
18250215 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
18250239 TTTCAATTAAACTCTATTTATTT
1 TTTCAATTAAACTCTATTTATTT
18250262 ATTTGAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.13, G:0.06, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:18250274 original size:24 final size:24
Alignment explanation
Indices: 18250223--18250277 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
18250213 TCTTTCAGTT
* * *
18250223 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTATTTATTTATTTCAATC
* *
18250247 AAACTCTATTTATTTATTTGAGTC
1 AAACTCTATTTATTTATTTCAATC
18250271 AAACTCT
1 AAACTCT
18250278 TATTACTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (24 bp):
AAACTCTATTTATTTATTTCAATC
Found at i:18252236 original size:24 final size:24
Alignment explanation
Indices: 18252208--18252269 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
18252198 AGAAATAATC
18252208 TTTCAGTTAAACTCCGTTTATTTG
1 TTTCAGTTAAACTCCGTTTATTTG
* *
18252232 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCCGTTTATTTG
* *
18252256 TTTGAGTCAAACTC
1 TTTCAGTTAAACTC
18252270 TTATTGCTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.48
Consensus pattern (24 bp):
TTTCAGTTAAACTCCGTTTATTTG
Found at i:18257046 original size:61 final size:61
Alignment explanation
Indices: 18256973--18257102 Score: 237
Period size: 61 Copynumber: 2.2 Consensus size: 61
18256963 ACAAGCGAAT
18256973 ATTAAA-A-CTATAAAATATTGAAACCACCGACCCAACCCTACTACATTTCCAATGCCCTC
1 ATTAAATATCTATAAAATATTGAAACCACCGACCCAACCCTACTACATTTCCAATGCCCTC
*
18257032 ATTAAATATCTATAAAATATTGAAACCACCGGCCCAACCCTACTACATTTCCAATGCCCTC
1 ATTAAATATCTATAAAATATTGAAACCACCGACCCAACCCTACTACATTTCCAATGCCCTC
18257093 ATTAAATATC
1 ATTAAATATC
18257103 CGTCCCAGAA
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
59 6 0.09
60 1 0.01
61 61 0.90
ACGTcount: A:0.38, C:0.30, G:0.05, T:0.26
Consensus pattern (61 bp):
ATTAAATATCTATAAAATATTGAAACCACCGACCCAACCCTACTACATTTCCAATGCCCTC
Found at i:18261665 original size:2 final size:2
Alignment explanation
Indices: 18261658--18261684 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18261648 ATAAATGAAA
18261658 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
18261685 AATAATGAAG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18268028 original size:19 final size:19
Alignment explanation
Indices: 18268004--18268041 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
18267994 ACGACCTGCT
18268004 TAAACTTGACCTTATACTC
1 TAAACTTGACCTTATACTC
18268023 TAAACTTGACCTTATACTC
1 TAAACTTGACCTTATACTC
18268042 GAATCTTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (19 bp):
TAAACTTGACCTTATACTC
Found at i:18268049 original size:19 final size:19
Alignment explanation
Indices: 18268005--18268049 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
18267995 CGACCTGCTT
*
18268005 AAACTTGACCTTATACTCT
1 AAACTTGACCTTATACTCG
18268024 AAACTTGACCTTATACTCG
1 AAACTTGACCTTATACTCG
*
18268043 AATCTTG
1 AAACTTG
18268050 CTATGTCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (19 bp):
AAACTTGACCTTATACTCG
Found at i:18268825 original size:19 final size:18
Alignment explanation
Indices: 18268801--18268843 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
18268791 AGTCAAATTA
18268801 AATAACACACA-CATATTT
1 AATAACACA-AGCATATTT
*
18268819 AACTAACTCAAGCATATTT
1 AA-TAACACAAGCATATTT
18268838 AATAAC
1 AATAAC
18268844 TAAGATGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.49, C:0.21, G:0.02, T:0.28
Consensus pattern (18 bp):
AATAACACAAGCATATTT
Found at i:18272394 original size:400 final size:400
Alignment explanation
Indices: 18271654--18272458 Score: 1504
Period size: 400 Copynumber: 2.0 Consensus size: 400
18271644 ATATTTGTTT
*
18271654 TATTTATGTCAACAAGAGACTTACTATCATTCAGAACCTCAAGGCAATAATCTCCAACCTCATCC
1 TATTTATGTCAACAAGAGACTTACCATCATTCAGAACCTCAAGGCAATAATCTCCAACCTCATCC
18271719 CATTATATGCCAGCAATTTTGATAGAACAGAGTTGGCAAACCATCCGATCCCAACACTTTAGTTG
66 CATTATATGCCAGCAATTTTGATAGAACAGAGTTGGCAAACCATCCGATCCCAACACTTTAGTTG
* *
18271784 ACGCCATAACTTTCAAAGTAATAAGAACTTCATTCCTCTCATATCTAGCATTTAGGCACACATTC
131 ACGCCATAACTTTCAAAGAAATAAGAACTTCATTCCTCTCATATCTAGCAGTTAGGCACACATTC
18271849 ATTTCTTTAGTAATGCAAGGTTCCACCCCCTCTAAAATATGATCAGCATTCCTCTCTTTTTGCAA
196 ATTTCTTTAGTAATGCAAGGTTCCACCCCCTCTAAAATATGATCAGCATTCCTCTCTTTTTGCAA
*
18271914 TATAAATAACTACACGAAATAATCATTTTCAATGTCAAACAAACCATCCTTGTCCGAAACAAATT
261 AATAAATAACTACACGAAATAATCATTTTCAATGTCAAACAAACCATCCTTGTCCGAAACAAATT
18271979 GCCCACCTCATCCCATTAAACCTTTAATTCTATTCATTCTCCGCCTCTATAACACAAATCAATGA
326 GCCCACCTCATCCCATTAAACCTTTAATTCTATTCATTCTCCGCCTCTATAACACAAATCAATGA
18272044 GGAAACCCAG
391 GGAAACCCAG
18272054 TATTTATGTCAACAAGAGACTTACCATCATTCAGAACCTCAAGGCAATAATCTCCAACCTCATCC
1 TATTTATGTCAACAAGAGACTTACCATCATTCAGAACCTCAAGGCAATAATCTCCAACCTCATCC
**
18272119 CATTATATGCCAGCAATTTTGATAGAACAGAGTTGGCAAACCATCC-AGTCCCAATGCTTTAGTT
66 CATTATATGCCAGCAATTTTGATAGAACAGAGTTGGCAAACCATCCGA-TCCCAACACTTTAGTT
*
18272183 GACGCCATAGCTTTCAAAGAAATAAGAACTTCATTCCTCTCATATCTAGCAGTTAGGCACACATT
130 GACGCCATAACTTTCAAAGAAATAAGAACTTCATTCCTCTCATATCTAGCAGTTAGGCACACATT
18272248 CATTTCTTTAGTAATGCAAGGTTCCACCCCCTCTAAAATATGATCAGCATTCCTCTCTTTTTGCA
195 CATTTCTTTAGTAATGCAAGGTTCCACCCCCTCTAAAATATGATCAGCATTCCTCTCTTTTTGCA
18272313 AAATAAATAACTACACGAAATAATCATTTTCAATGTCAAACAAACCATCCTTGTCCGAAACAAAT
260 AAATAAATAACTACACGAAATAATCATTTTCAATGTCAAACAAACCATCCTTGTCCGAAACAAAT
* *
18272378 TGCCCACCTCATCCCATTAAGCCTTTAATTCTATTCATTCTCCGCCTCTATAACACAAATTAATG
325 TGCCCACCTCATCCCATTAAACCTTTAATTCTATTCATTCTCCGCCTCTATAACACAAATCAATG
*
18272443 AGGAAACCTAG
390 AGGAAACCCAG
18272454 TATTT
1 TATTT
18272459 CAATCCTCCC
Statistics
Matches: 394, Mismatches: 10, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
399 1 0.00
400 393 1.00
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.30
Consensus pattern (400 bp):
TATTTATGTCAACAAGAGACTTACCATCATTCAGAACCTCAAGGCAATAATCTCCAACCTCATCC
CATTATATGCCAGCAATTTTGATAGAACAGAGTTGGCAAACCATCCGATCCCAACACTTTAGTTG
ACGCCATAACTTTCAAAGAAATAAGAACTTCATTCCTCTCATATCTAGCAGTTAGGCACACATTC
ATTTCTTTAGTAATGCAAGGTTCCACCCCCTCTAAAATATGATCAGCATTCCTCTCTTTTTGCAA
AATAAATAACTACACGAAATAATCATTTTCAATGTCAAACAAACCATCCTTGTCCGAAACAAATT
GCCCACCTCATCCCATTAAACCTTTAATTCTATTCATTCTCCGCCTCTATAACACAAATCAATGA
GGAAACCCAG
Found at i:18276696 original size:9 final size:9
Alignment explanation
Indices: 18276682--18276876 Score: 83
Period size: 10 Copynumber: 20.1 Consensus size: 9
18276672 TTATATTTTT
18276682 TTATAAAAA
1 TTATAAAAA
18276691 TTAT-AAAA
1 TTATAAAAA
18276699 TTATTAAAAA
1 TTA-TAAAAA
*
18276709 TATATAAACA
1 T-TATAAAAA
*
18276719 -TCTAAAAA
1 TTATAAAAA
18276727 TTATAAAATA
1 TTATAAAA-A
*
18276737 TTATACTAAA
1 TTATA-AAAA
18276747 TTATAAAAA
1 TTATAAAAA
*
18276756 ATAT-AAAA
1 TTATAAAAA
18276764 TTAATAAAATA
1 TT-ATAAAA-A
* *
18276775 TATTTAAAATT
1 T-TATAAAA-A
*
18276786 TTATAAAAC
1 TTATAAAAA
**
18276795 TTATAAGGA
1 TTATAAAAA
18276804 TTCATAAAAAAA
1 TT-AT--AAAAA
18276816 CTTA-AAAATA
1 -TTATAAAA-A
* *
18276826 ATATAAAAG
1 TTATAAAAA
*
18276835 TTTTAGAAAA
1 TTATA-AAAA
*
18276845 GTTCTAATAAA
1 -TTATAA-AAA
18276856 TTATAAAAA
1 TTATAAAAA
18276865 TTTATTAAAAA
1 -TTA-TAAAAA
18276876 T
1 T
18276877 ATTTTAGAAA
Statistics
Matches: 141, Mismatches: 24, Indels: 41
0.68 0.12 0.20
Matches are distributed among these distances:
8 18 0.13
9 39 0.28
10 51 0.36
11 26 0.18
12 5 0.04
13 2 0.01
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:18276716 original size:10 final size:10
Alignment explanation
Indices: 18276683--18276793 Score: 60
Period size: 9 Copynumber: 11.7 Consensus size: 10
18276673 TATATTTTTT
18276683 TATAAAAAT-
1 TATAAAAATA
*
18276692 TATAAAATTA
1 TATAAAAATA
18276702 T-TAAAAATA
1 TATAAAAATA
*
18276711 TAT--AAACA
1 TATAAAAATA
*
18276719 TCTAAAAAT-
1 TATAAAAATA
18276728 TAT-AAAATA
1 TATAAAAATA
*
18276737 TTATACTAAAT-
1 -TATA-AAAATA
18276748 TATAAAAA-A
1 TATAAAAATA
*
18276757 TATAAAATTA
1 TATAAAAATA
18276767 -ATAAAATATA
1 TATAAAA-ATA
* * *
18276777 TTTAAAATTT
1 TATAAAAATA
18276787 TATAAAA
1 TATAAAA
18276794 CTTATAAGGA
Statistics
Matches: 76, Mismatches: 14, Indels: 23
0.67 0.12 0.20
Matches are distributed among these distances:
8 11 0.14
9 34 0.45
10 22 0.29
11 5 0.07
12 4 0.05
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (10 bp):
TATAAAAATA
Found at i:18276763 original size:38 final size:35
Alignment explanation
Indices: 18276683--18276775 Score: 100
Period size: 36 Copynumber: 2.5 Consensus size: 35
18276673 TATATTTTTT
*
18276683 TATAAAAATTATAAAATTATTAAAAATATATAAACA
1 TATAAAAATTATAAAA-TATTAAAAATATATAAAAA
*
18276719 TCTAAAAATTATAAAATATTATACTAAAT-TATAAAAA
1 TATAAAAATTATAAAATATTA-A--AAATATATAAAAA
18276756 -ATATAAAATTAATAAAATAT
1 TATA-AAAATT-ATAAAATAT
18276776 ATTTAAAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
35 5 0.10
36 18 0.37
37 13 0.27
38 13 0.27
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (35 bp):
TATAAAAATTATAAAATATTAAAAATATATAAAAA
Found at i:18276913 original size:17 final size:17
Alignment explanation
Indices: 18276881--18276913 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18276871 AAAAATATTT
*
18276881 TAGAAATTATACAAAAC
1 TAGAAATTATAAAAAAC
18276898 TAGAAATTATAAAAAA
1 TAGAAATTATAAAAAA
18276914 AAAAGTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
TAGAAATTATAAAAAAC
Found at i:18277482 original size:56 final size:55
Alignment explanation
Indices: 18277383--18277503 Score: 140
Period size: 56 Copynumber: 2.2 Consensus size: 55
18277373 GATCCGTTCT
* * * *
18277383 TTAAAAGTTGGTAAAAAAAATTTGGGTCCTTAAAAGTTAAATTTTTTTGGGGA-CCC
1 TTAAAAATTGGTAAAAAAAATTTGGGACCTTAAAAATTAAATTTTTTT--GAACCCC
*
18277439 TTAAAAATTGGTAAAAAAAAATTT-TGACCTTTAAAAATT-AATTTTTTTGAACCCC
1 TTAAAAATTGGT-AAAAAAAATTTGGGACC-TTAAAAATTAAATTTTTTTGAACCCC
18277494 TTAAAAATTG
1 TTAAAAATTG
18277504 AAAAACAATA
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
54 2 0.04
55 13 0.23
56 23 0.40
57 19 0.33
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (55 bp):
TTAAAAATTGGTAAAAAAAATTTGGGACCTTAAAAATTAAATTTTTTTGAACCCC
Found at i:18277945 original size:2 final size:2
Alignment explanation
Indices: 18277940--18277974 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
18277930 ATATATATGT
18277940 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
18277975 GAGACACTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:18288803 original size:2 final size:2
Alignment explanation
Indices: 18288798--18288822 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18288788 ACTTGAAAAA
18288798 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 A
18288823 CCTATGGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18290234 original size:15 final size:16
Alignment explanation
Indices: 18290203--18290235 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18290193 ATTAAGTTAA
18290203 TTTAAATAAATTAATT
1 TTTAAATAAATTAATT
*
18290219 TTTAATTAAA-TAATT
1 TTTAAATAAATTAATT
18290234 TT
1 TT
18290236 CTCAACCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTAAATAAATTAATT
Found at i:18291829 original size:13 final size:12
Alignment explanation
Indices: 18291799--18291834 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 12
18291789 TTTGTGCTTT
18291799 AATGAAAAAATC
1 AATGAAAAAATC
18291811 AATGAAAAAATC
1 AATGAAAAAATC
18291823 AAGTGAAGAAAA
1 AA-TGAA-AAAA
18291835 GCTTTATGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 14 0.64
13 4 0.18
14 4 0.18
ACGTcount: A:0.67, C:0.06, G:0.14, T:0.14
Consensus pattern (12 bp):
AATGAAAAAATC
Found at i:18294839 original size:29 final size:29
Alignment explanation
Indices: 18294809--18295056 Score: 166
Period size: 30 Copynumber: 8.4 Consensus size: 29
18294799 CCAATTCCAT
* *
18294809 AAAATTTTAAGGTAAAAAT-TCAATTTTATA
1 AAAATTTTAGGGTAAAAATGT-AATTTTA-G
** *
18294839 AAAATTTGGGGGTCAAAATGTAATTTT-G
1 AAAATTTTAGGGTAAAAATGTAATTTTAG
* *
18294867 AAAAAGTTTT-GGGTAAAAATTTAATTTTGG
1 -AAAA-TTTTAGGGTAAAAATGTAATTTTAG
***
18294897 AAAAGTTCGGGGGTAAAAAT-TCAATTTTAG
1 AAAA-TTTTAGGGTAAAAATGT-AATTTTAG
* * *
18294927 AAAAGTTTAAGGTCAAAATGTAATTTTAG
1 AAAATTTTAGGGTAAAAATGTAATTTTAG
*
18294956 AAAATTTTAGGGTCAAAATGTAATTTTA-
1 AAAATTTTAGGGTAAAAATGTAATTTTAG
* * *
18294984 AAAAGTTTTAAAGGTTAAAATGTAATTTTGG
1 AAAA-TTTT-AGGGTAAAAATGTAATTTTAG
* * * *
18295015 AAAAGTTTGAGGGTCAAAATATGATTTCTA-
1 AAAA-TTTTAGGGTAAAAATGTAATTT-TAG
*
18295045 AAAAATTTAGGG
1 AAAATTTTAGGG
18295057 ACCTTTTAGG
Statistics
Matches: 177, Mismatches: 30, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
28 4 0.02
29 81 0.46
30 82 0.46
31 10 0.06
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (29 bp):
AAAATTTTAGGGTAAAAATGTAATTTTAG
Found at i:18294845 original size:30 final size:29
Alignment explanation
Indices: 18294809--18295056 Score: 162
Period size: 29 Copynumber: 8.4 Consensus size: 29
18294799 CCAATTCCAT
*
18294809 AAAATTTTAAGGTAAAAAT-TCAATTTTATA
1 AAAATTTTAGGGTAAAAATGT-AATTTTA-A
** *
18294839 AAAATTTGGGGGTCAAAATGTAATTTTGAA
1 AAAATTTTAGGGTAAAAATGTAATTTT-AA
* * *
18294869 AAAGTTTT-GGGTAAAAATTTAATTTTGGA
1 AAAATTTTAGGGTAAAAATGTAATTTT-AA
* *** *
18294898 AAAGTTCGGGGGTAAAAAT-TCAATTTTAG
1 AAAATTTTAGGGTAAAAATGT-AATTTTAA
* * * *
18294927 AAAAGTTTAAGGTCAAAATGTAATTTTAG
1 AAAATTTTAGGGTAAAAATGTAATTTTAA
*
18294956 AAAATTTTAGGGTCAAAATGTAATTTTAA
1 AAAATTTTAGGGTAAAAATGTAATTTTAA
* * * *
18294985 AAAGTTTTAAAGGTTAAAATGTAATTTTGGA
1 AAAATTTT-AGGGTAAAAATGTAATTTT-AA
* * * * *
18295016 AAAGTTTGAGGGTCAAAATATGATTTCTAA
1 AAAATTTTAGGGTAAAAATGTAATTT-TAA
18295046 AAAA-TTTAGGG
1 AAAATTTTAGGG
18295057 ACCTTTTAGG
Statistics
Matches: 175, Mismatches: 35, Indels: 17
0.77 0.15 0.07
Matches are distributed among these distances:
29 84 0.48
30 80 0.46
31 11 0.06
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (29 bp):
AAAATTTTAGGGTAAAAATGTAATTTTAA
Found at i:18294882 original size:59 final size:56
Alignment explanation
Indices: 18294809--18295048 Score: 196
Period size: 59 Copynumber: 4.1 Consensus size: 56
18294799 CCAATTCCAT
18294809 AAAA-TTTTAAGGTAAAAATTCAATTTTATAAAAATTTGGGGGTCAAAATGTAATTTTGA
1 AAAAGTTTT-AGGTAAAAATT-AATTTTA-AAAAATTTGGGGGTCAAAATGTAATTTT-A
* * * * *
18294868 AAAAGTTTTGGGTAAAAATTTAATTTTGGAAAAGTTCGGGGGTAAAAAT-TCAATTTTA
1 AAAAGTTTTAGGTAAAAA-TTAATTTT-AAAAAATTTGGGGGTCAAAATGT-AATTTTA
* * * **
18294926 GAAAAGTTTAAGGTCAAAATGTAATTTTAGAAAATTTTAGGGTCAAAATGTAATTTTA
1 -AAAAGTTTTAGGTAAAAAT-TAATTTTAAAAAATTTGGGGGTCAAAATGTAATTTTA
* * * * * *
18294984 AAAAGTTTTAAAGGTTAAAATGTAATTTTGGAAAAGTTTGAGGGTCAAAATATGATTTCTA
1 AAAAGTTTT--AGGTAAAAAT-TAATTTT-AAAAAATTTGGGGGTCAAAATGTAATTT-TA
18295045 AAAA
1 AAAA
18295049 ATTTAGGGAC
Statistics
Matches: 147, Mismatches: 23, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
57 8 0.05
58 24 0.16
59 81 0.55
60 28 0.19
61 6 0.04
ACGTcount: A:0.43, C:0.03, G:0.18, T:0.36
Consensus pattern (56 bp):
AAAAGTTTTAGGTAAAAATTAATTTTAAAAAATTTGGGGGTCAAAATGTAATTTTA
Found at i:18297187 original size:39 final size:39
Alignment explanation
Indices: 18297062--18297918 Score: 311
Period size: 39 Copynumber: 22.6 Consensus size: 39
18297052 ATGATGTCTT
* * *
18297062 CAATCTGCCCCATGATCGGGGTAAAAGATTGAATGGTTG
1 CAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
* * * * *
18297101 TAATCTG-CCCTAGGTCGAGGTAAAAGATTGGCTAATGG-TG
1 CAATCTGCCCCAAGCTCGGGGTAAAAGA-T--CGAATGGTTG
* *
18297141 --ATTTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTA
1 CAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
* *
18297178 CAATCTGCCCCAAGCT--AGG-----GCT-G-ATGG-TG
1 CAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
*
18297207 --ATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTA
1 CAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
* ** *
18297244 CAATTTGAGCCAAGCTC-GGG-----GCT-G-ATGG-TG
1 CAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
* ** * * ***
18297274 --ATCTGCCTCAAGCTCAAGATAAAAGATCGGATAACTG
1 CAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
* * *
18297311 CAATCTGCCCTAGGCTCGGGGTAAGAGATTAGCTG-ATGGTT-
1 CAATCTGCCCCAAGCTCGGGGTAAAAGA-T--C-GAATGGTTG
* * * *
18297352 --ATCTGCTCCAAGCTCGGAGTAAAAGATCGGATGGTTA
1 CAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
* * * ** * *
18297389 CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGG
1 CAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
** * *
18297428 TGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTG
1 CAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
* * * * *
18297467 CAATCTGCCCCAAGTTCAGGGTAAAAGATTGAATGGCTA
1 CAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
* * * * * * *
18297506 CAATCTGCCCCAGGCTCGGGATAAGAGATTGATTGATGG
1 CAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
** * * *
18297545 TGATTTG-CCCAATGCTCGGGGTAAAAGATCGGATAGTTG
1 CAATCTGCCCCAA-GCTCGGGGTAAAAGATCGAATGGTTG
* * * * ** * *
18297584 CAATCTACCCTAGGCTCGGGGTAAAAGATTGGCTGATGG
1 CAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
** ** * *
18297623 TGATCTGCCATAGGCTCGGGGTAAAAGATCGAATGGCTG
1 CAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
* * * * *
18297662 CAATCTACCCTAAGCTCGGGGTAAGAGATTAGTTGATGG-TG
1 CAATCTGCCCCAAGCTCGGGGTAAAAGA-TCG--AATGGTTG
* * **
18297703 --ATCTGCCCCTAA-CTCGAGGTAAGAGATCGAATGACTG
1 CAATCTGCCCC-AAGCTCGGGGTAAAAGATCGAATGGTTG
* * * * ** * *
18297740 CAATCTG-CCCAGGCTCGAGGTAAGAGATTGGCTGATGG
1 CAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
** * * *
18297778 TGATCTGCCCCAAGCTCGGGGTAAAAAATTGAATGGCTG
1 CAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
* * * * * * *
18297817 TAATCTGTCCTAGGCTCGGGGTAAGAGATTGGCTAATAG-TG
1 CAATCTGCCCCAAGCTCGGGGTAAAAGA-T--CGAATGGTTG
* * * * *
18297858 --ATCTGCCGC-AGACTCGGGGTAAGAGATTGAATGGCTA
1 CAATCTGCCCCAAG-CTCGGGGTAAAAGATCGAATGGTTG
18297895 CAATCTGCCCCAAGCTCGGGGTAA
1 CAATCTGCCCCAAGCTCGGGGTAA
18297919 GAAATCAAAA
Statistics
Matches: 595, Mismatches: 166, Indels: 114
0.68 0.19 0.13
Matches are distributed among these distances:
27 14 0.02
28 11 0.02
29 4 0.01
30 5 0.01
31 5 0.01
32 3 0.01
33 2 0.00
34 4 0.01
35 3 0.01
36 26 0.04
37 10 0.02
38 61 0.10
39 412 0.69
40 13 0.02
41 9 0.02
42 12 0.02
43 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (39 bp):
CAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
Found at i:18297328 original size:67 final size:66
Alignment explanation
Indices: 18297130--18297331 Score: 181
Period size: 66 Copynumber: 3.0 Consensus size: 66
18297120 GTAAAAGATT
* * ** * ***
18297130 GGCTAATGGTGATTTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTACAATCTGCCCCAAGCT-
1 GGCTGATGGTGATCTGCCCCAAGCTCAAGATAAAAGATCGAATAACTACAATCTG-CCCAAGCTC
*
18297194 AG
65 GG
** * *** * *
18297196 GGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTACAATTTGAGCCAAGCTC
1 GGCTGATGGTGATCTGCCCCAAGCTCAAGATAAAAGATCGAATAACTACAATCTG-CCCAAGCTC
18297261 GG
65 GG
* * * *
18297263 GGCTGATGGTGATCTGCCTCAAGCTCAAGATAAAAGATCGGATAACTGCAATCTGCCCTAGGCTC
1 GGCTGATGGTGATCTGCCCCAAGCTCAAGATAAAAGATCGAATAACTACAATCTGCCC-AAGCTC
18297328 GG
65 GG
18297330 GG
1 GG
18297332 TAAGAGATTA
Statistics
Matches: 116, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
66 61 0.53
67 55 0.47
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.22
Consensus pattern (66 bp):
GGCTGATGGTGATCTGCCCCAAGCTCAAGATAAAAGATCGAATAACTACAATCTGCCCAAGCTCG
G
Found at i:18297480 original size:117 final size:117
Alignment explanation
Indices: 18297352--18297823 Score: 412
Period size: 117 Copynumber: 4.0 Consensus size: 117
18297342 GCTGATGGTT
* * **
18297352 ATCTGCTCCAAGCTCGGAGTAAAAGATCGGATGGTTACAATCTGCCCCAGGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGAGTAAAAGATCGAATGACTACAATCTGCCCCAGGCTCGGGGTAAGAGA
18297417 TTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCA
66 TTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCA
* * * *
18297469 ATCTGCCCCAAGTTCAGG-GTAAAAGATTGAATGGCTACAATCTGCCCCAGGCTCGGGATAAGAG
1 ATCTGCCCCAAGCTC-GGAGTAAAAGATCGAATGACTACAATCTGCCCCAGGCTCGGGGTAAGAG
** * * *
18297533 ATTGATTGATGGTGATTTG-CCCAATGCTCGGGGTAAAAGATCGGATAGTTGCA
65 ATTGGCTGATGGTGATCTGCCCCAA-GCTCGGGGTAAAAGATCGGATGGCTGCA
* * * * * ** *** ** *
18297586 ATCTACCCTAGGCTCGGGGTAAAAGATTGGCTGA-TGGTGATCTGCCATAGGCTCGGGGTAAAAG
1 ATCTGCCCCAAGCTCGGAGTAAAAGATCGAATGACT-ACAATCTGCCCCAGGCTCGGGGTAAGAG
* * * *
18297650 A-T--C-GAATGGCTGCAATCTACCCTAAGCTCGGGGTAAGAGATTAGTTGATGG-TG--
65 ATTGGCTG-ATGG-TG--ATCTGCCCCAAGCTCGGGGTAAAAGA-TCG--GATGGCTGCA
* * *
18297703 ATCTGCCCCTAA-CTC-GAGGTAAGAGATCGAATGACTGCAATCTG-CCCAGGCTCGAGGTAAGA
1 ATCTGCCCC-AAGCTCGGA-GTAAAAGATCGAATGACTACAATCTGCCCCAGGCTCGGGGTAAGA
* * * *
18297765 GATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAAATTGAATGGCTGTA
64 GATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCA
18297819 ATCTG
1 ATCTG
18297824 TCCTAGGCTC
Statistics
Matches: 281, Mismatches: 52, Indels: 45
0.74 0.14 0.12
Matches are distributed among these distances:
113 5 0.02
114 6 0.02
115 4 0.01
116 53 0.19
117 189 0.67
118 12 0.04
119 7 0.02
120 5 0.02
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (117 bp):
ATCTGCCCCAAGCTCGGAGTAAAAGATCGAATGACTACAATCTGCCCCAGGCTCGGGGTAAGAGA
TTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCA
Found at i:18297512 original size:78 final size:75
Alignment explanation
Indices: 18297352--18297920 Score: 414
Period size: 78 Copynumber: 7.3 Consensus size: 75
18297342 GCTGATGGTT
* * * * * *
18297352 ATCTGCTCCAAGCTCGGAGTAAAAGATCGGATGGTTACAATCTGCCCCAGGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATCGGATGG-T--GATCTGCCCCAAGCTCGGGGTAAAAGA
*
18297417 TTGGCTGATGG-TG--
63 TT-G--AATGGCTGCA
* * *
18297430 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGTTCAGGGTAAAAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATCGGATGG-TG--ATCTGCCCCAAGCTCGGGGTAAAAGA
*
18297495 TTGAATGGCTACA
63 TTGAATGGCTGCA
* * * *
18297508 ATCTGCCCCAGGCTCGGGATAAGAGATTGATTGATGGTGATTTG-CCCAATGCTCGGGGTAAAAG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATCG---GATGGTGATCTGCCCCAA-GCTCGGGGTAAAAG
* * * *
18297572 ATCGGATAGTTGCA
62 ATTGAATGGCTGCA
* * * * * ** *
18297586 ATCTACCCTAGGCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCATAGGCTCGGGGTAAAAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGA-T--CGGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
*
18297651 TCGAATGGCTGCA
63 TTGAATGGCTGCA
* * * * *
18297664 ATCTACCCTAAGCTCGGGGTAAGAGATTAGTTGATGGTGATCTGCCCCTAA-CTCGAGGTAAGAG
1 ATCTGCCCCAAGCTCGGGGTAAGAGA-TCG--GATGGTGATCTGCCCC-AAGCTCGGGGTAAAAG
* *
18297728 ATCGAATGACTGCA
62 ATTGAATGGCTGCA
* * * *
18297742 ATCTG-CCCAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAAA
1 ATCTGCCCCAAGCTCGGGGTAAGAGA-T--CGGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
*
18297806 TTGAATGGCTGTA
63 TTGAATGGCTGCA
* * * * * * *
18297819 ATCTGTCCTAGGCTCGGGGTAAGAGATTGGCTAATAGTGATCTGCCGC-AGACTCGGGGTAAGAG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATCGG---ATGGTGATCTGCCCCAAG-CTCGGGGTAAAAG
*
18297883 ATTGAATGGCTACA
62 ATTGAATGGCTGCA
18297897 ATCTGCCCCAAGCTCGGGGTAAGA
1 ATCTGCCCCAAGCTCGGGGTAAGA
18297921 AATCAAAATC
Statistics
Matches: 397, Mismatches: 70, Indels: 48
0.77 0.14 0.09
Matches are distributed among these distances:
75 5 0.01
76 3 0.01
77 70 0.18
78 308 0.78
79 4 0.01
80 2 0.01
81 5 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.23
Consensus pattern (75 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATCGGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATTG
AATGGCTGCA
Found at i:18297848 original size:233 final size:234
Alignment explanation
Indices: 18297486--18297920 Score: 597
Period size: 233 Copynumber: 1.9 Consensus size: 234
18297476 CCAAGTTCAG
* * * *
18297486 GGTAAAAGATTGAATGGCTACAATCTGCCCCAGGCTCGGGATAAGAGATTGATTGATGGTGATTT
1 GGTAAAAGATCGAATGACTACAATCTGCCCCAGGCTCGGGATAAGAGATTGACTGATGGTGATCT
* * *
18297551 GCCCAATGCTCGGGGTAAAAGATCGGATAGTTGCAATCTACCCTAGGCTCGGGGTAAAAGATTGG
66 GCCCAATGCTCGGGGTAAAAAATCGAATAGCTGCAATCTACCCTAGGCTCGGGGTAAAAGATTGG
* * * * * *
18297616 CTGATGGTGATCTGCCATAGGCTCGGGGTAAAAGATCGAATGGCTGCAATCTACCCTAAGCTCGG
131 CTAATAGTGATCTGCCACAGACTCGGGGTAAAAGATCGAATGGCTACAATCTACCCCAAGCTCGG
18297681 GGTAAGAGATTAGTTGATGGTGATCTGCCCCTAACTCGA
196 GGTAAGAGATTAGTTGATGGTGATCTGCCCCTAACTCGA
* * *
18297720 GGTAAGAGATCGAATGACTGCAATCTG-CCCAGGCTCGAGG-TAAGAGATTGGCTGATGGTGATC
1 GGTAAAAGATCGAATGACTACAATCTGCCCCAGGCTCG-GGATAAGAGATTGACTGATGGTGATC
* * * ** *
18297783 TGCCCCAA-GCTCGGGGTAAAAAATTGAATGGCTGTAATCTGTCCTAGGCTCGGGGTAAGAGATT
65 TG-CCCAATGCTCGGGGTAAAAAATCGAATAGCTGCAATCTACCCTAGGCTCGGGGTAAAAGATT
* * * *
18297847 GGCTAATAGTGATCTGCCGCAGACTCGGGGTAAGAGATTGAATGGCTACAATCTGCCCCAAGCTC
129 GGCTAATAGTGATCTGCCACAGACTCGGGGTAAAAGATCGAATGGCTACAATCTACCCCAAGCTC
18297912 GGGGTAAGA
194 GGGGTAAGA
18297921 AATCAAAATC
Statistics
Matches: 173, Mismatches: 26, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
233 143 0.83
234 30 0.17
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (234 bp):
GGTAAAAGATCGAATGACTACAATCTGCCCCAGGCTCGGGATAAGAGATTGACTGATGGTGATCT
GCCCAATGCTCGGGGTAAAAAATCGAATAGCTGCAATCTACCCTAGGCTCGGGGTAAAAGATTGG
CTAATAGTGATCTGCCACAGACTCGGGGTAAAAGATCGAATGGCTACAATCTACCCCAAGCTCGG
GGTAAGAGATTAGTTGATGGTGATCTGCCCCTAACTCGA
Found at i:18297939 original size:155 final size:154
Alignment explanation
Indices: 18297636--18297927 Score: 338
Period size: 155 Copynumber: 1.9 Consensus size: 154
18297626 TCTGCCATAG
* * * *
18297636 GCTCGGGGTAAAAGATCGAATGGCTGCAATCTACCCTAAGCTCGGGGTAAGAGATTAGTTGATGG
1 GCTCGGGGTAAAAAATCGAATGGCTGCAATCTACCCTAAGCTCGGGGTAAGAGATTAGCTAATAG
* *
18297701 TGATCTGCCCCTAACTCGAGGTAAGAGATCGAATGACTGCAATCTGCCCAGGCTCGAGGTAAGAG
66 TGATCTGCCCCTAACTCGAGGTAAGAGATCGAATGACTACAATCTGCCCAAGCTCGAGGTAAGAG
* ** * *
18297766 ATTGGCTGATGGTGATCTGCCCCAA
131 AAT-GCAAATCGTAATCTGCCCCAA
* * ** * *
18297791 GCTCGGGGTAAAAAATTGAATGGCTGTAATCTGTCCTAGGCTCGGGGTAAGAGATTGGCTAATAG
1 GCTCGGGGTAAAAAATCGAATGGCTGCAATCTACCCTAAGCTCGGGGTAAGAGATTAGCTAATAG
* * * * *
18297856 TGATCTGCCGC-AGACTCGGGGTAAGAGATTGAATGGCTACAATCTGCCCCAAGCTCGGGGTAAG
66 TGATCTGCCCCTA-ACTCGAGGTAAGAGATCGAATGACTACAATCTG-CCCAAGCTCGAGGTAAG
18297920 A-AAT-CAAA
129 AGAATGCAAA
18297928 ATCTTCAATC
Statistics
Matches: 115, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
153 2 0.02
154 1 0.01
155 96 0.83
156 16 0.14
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (154 bp):
GCTCGGGGTAAAAAATCGAATGGCTGCAATCTACCCTAAGCTCGGGGTAAGAGATTAGCTAATAG
TGATCTGCCCCTAACTCGAGGTAAGAGATCGAATGACTACAATCTGCCCAAGCTCGAGGTAAGAG
AATGCAAATCGTAATCTGCCCCAA
Found at i:18298318 original size:49 final size:49
Alignment explanation
Indices: 18298169--18298447 Score: 197
Period size: 49 Copynumber: 5.7 Consensus size: 49
18298159 AGACTCACTG
* * * * *
18298169 TTGCGGCCTCAACCTTTCTCATCATAT-TTCATGGTATCGATTTCGTCG
1 TTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTATCGAGTTCGCCA
* * * * * *
18298217 TTGCGGCCTCAATCC-CTCTCATCACATCTTTTAAGGTGTCGAGTTCACCA
1 TTGCGGCCTCAA-CCTTTCCCATCACATC-TTCATGGTATCGAGTTCGCCA
* * * *
18298267 TTGTGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATCGAGTTTGCCA
1 TTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTATCGAGTTCGCCA
** ** * * * * *
18298316 TTGCGGTTTCAAATTTTCCAATCGCATCTTCATGGTACCG-GATTTGTCA
1 TTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTATCGAG-TTCGCCA
* * * * *
18298365 TTGCTGCCTCAATCC-TTCCCATCACATCTTCTAAGGTATCGGGTTCGTCG
1 TTGCGGCCTCAA-CCTTTCCCATCACATCTTC-ATGGTATCGAGTTCGCCA
* * *
18298415 TTGCGGCCTCAACTTTTCCCTTCATATCTTCAT
1 TTGCGGCCTCAACCTTTCCCATCACATCTTCAT
18298448 ATTTCCTCGG
Statistics
Matches: 176, Mismatches: 46, Indels: 17
0.74 0.19 0.07
Matches are distributed among these distances:
48 23 0.13
49 81 0.46
50 71 0.40
51 1 0.01
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.37
Consensus pattern (49 bp):
TTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTATCGAGTTCGCCA
Found at i:18301664 original size:88 final size:88
Alignment explanation
Indices: 18301554--18301723 Score: 232
Period size: 88 Copynumber: 1.9 Consensus size: 88
18301544 TTAGACATTT
* * * *
18301554 GGGAGCAAAAATGTAATTTTTGGACAGTCGAGGGCAAAGTAGTAATTTTTGAATGTTCGGGGGTA
1 GGGAGCAAAAATGTAATTTTTGGACAGTCAAGGGCAAAATAGTAATTTTTGAATATTCAGGGGTA
18301619 AAACGATAATTTTTGGAAAGTTC
66 AAACGATAATTTTTGGAAAGTTC
* * * * * * *
18301642 GGGATCAAAAATGTAATTTTTGGATATTTAAGGGTAAAATGGTAATTTTTGGATATTCAGGGGTA
1 GGGAGCAAAAATGTAATTTTTGGACAGTCAAGGGCAAAATAGTAATTTTTGAATATTCAGGGGTA
*
18301707 AAACGGTAATTTTTGGA
66 AAACGATAATTTTTGGA
18301724 CATACAATGA
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
88 70 1.00
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.34
Consensus pattern (88 bp):
GGGAGCAAAAATGTAATTTTTGGACAGTCAAGGGCAAAATAGTAATTTTTGAATATTCAGGGGTA
AAACGATAATTTTTGGAAAGTTC
Found at i:18301888 original size:60 final size:58
Alignment explanation
Indices: 18301774--18301956 Score: 199
Period size: 59 Copynumber: 3.1 Consensus size: 58
18301764 TAAAAATGCG
* *
18301774 ATTTTTGAAAAGTTTAGGGCAAAATGGTAATTTTTA-AAAGTTCGAGAGTAAAAATGA-A
1 ATTTTTAAAAAGTTTAGGGTAAAAT-GTAATTTTTATAAAGTTCGAGAGTAAAAAT-ATA
* * * *
18301832 ATTTTTAAAAAGTTTGAGGGTAAAAATGTAAGTTTTATGAAGTTCGAGGGTTAAAATATA
1 ATTTTTAAAAAGTTT-AGGGT-AAAATGTAATTTTTATAAAGTTCGAGAGTAAAAATATA
* * *** *
18301892 ATTTTTAGAAAGTTTAGGGGTAAAATGTAATTTTTGTAAAGTTCGATCTTCAAAATATA
1 ATTTTTAAAAAGTTTA-GGGTAAAATGTAATTTTTATAAAGTTCGAGAGTAAAAATATA
18301951 ATTTTT
1 ATTTTT
18301957 GGAAAGTTCG
Statistics
Matches: 106, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
58 14 0.13
59 52 0.49
60 40 0.38
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.38
Consensus pattern (58 bp):
ATTTTTAAAAAGTTTAGGGTAAAATGTAATTTTTATAAAGTTCGAGAGTAAAAATATA
Found at i:18301915 original size:29 final size:29
Alignment explanation
Indices: 18301738--18301934 Score: 113
Period size: 30 Copynumber: 6.7 Consensus size: 29
18301728 CAATGACAAG
* * *
18301738 AATGTGATTTTTTGGAAG-TTAGGGGGTAAA
1 AATGTAATTTTTAGAAAGTTTA-GGGGT-AA
** *
18301768 AATGCGATTTTT-GAAAAGTTTA-GGGCAA
1 AATGTAATTTTTAG-AAAGTTTAGGGGTAA
* *
18301796 AATGGTAATTTTTA-AAAG-TTCGAGAGTAAA
1 AAT-GTAATTTTTAGAAAGTTTAG-GGGT-AA
* *
18301826 AATGAAATTTTTAAAAAGTTT-GAGGGTAAA
1 AATGTAATTTTTAGAAAGTTTAG-GGGT-AA
* * *
18301856 AATGTAAGTTTTATG-AAGTTCGAGGGTTAA
1 AATGTAATTTTTA-GAAAGTT-TAGGGGTAA
*
18301886 AATATAATTTTTAGAAAGTTTAGGGGTAA
1 AATGTAATTTTTAGAAAGTTTAGGGGTAA
18301915 AATGTAATTTTT-GTAAAGTT
1 AATGTAATTTTTAG-AAAGTT
18301935 CGATCTTCAA
Statistics
Matches: 133, Mismatches: 20, Indels: 29
0.73 0.11 0.16
Matches are distributed among these distances:
27 2 0.02
28 10 0.08
29 47 0.35
30 65 0.49
31 8 0.06
32 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (29 bp):
AATGTAATTTTTAGAAAGTTTAGGGGTAA
Found at i:18301975 original size:30 final size:30
Alignment explanation
Indices: 18301503--18301995 Score: 226
Period size: 29 Copynumber: 16.7 Consensus size: 30
18301493 AATGGAGTAA
* *
18301503 AAAATGTAATTTTTGG-ACGCTCGAGGG-C
1 AAAATGTAATTTTTGGAAAGTTCGAGGGTC
* * *
18301531 AAAATGGTAATTTTTAGACA-TTTG-GGAG-C
1 AAAAT-GTAATTTTTGGAAAGTTCGAGG-GTC
*
18301560 AAAAATGTAATTTTTGGACAG-TCGAGGG-C
1 -AAAATGTAATTTTTGGAAAGTTCGAGGGTC
* * *
18301589 AAAGTAGTAATTTTT-GAATGTTCGGGGGT-
1 AAAAT-GTAATTTTTGGAAAGTTCGAGGGTC
* *
18301618 AAAACGATAATTTTTGGAAAGTTCG-GGATC
1 AAAATG-TAATTTTTGGAAAGTTCGAGGGTC
* **
18301648 AAAAATGTAATTTTTGGATA-TTTAAGGGT-
1 -AAAATGTAATTTTTGGAAAGTTCGAGGGTC
*
18301677 AAAATGGTAATTTTTGGATA-TTC-AGGGGT-
1 AAAAT-GTAATTTTTGGAAAGTTCGA-GGGTC
* * * ** *
18301706 AAAACGGTAATTTTTGGACA-TAC-AATGAC
1 AAAA-TGTAATTTTTGGAAAGTTCGAGGGTC
* * * *
18301735 AAGAATGTGATTTTTTGG-AAGTTAGGGGGTA
1 AA-AATGT-AATTTTTGGAAAGTTCGAGGGTC
** * *
18301766 AAAATGCGATTTTTGAAAAGTT-TAGGG-C
1 AAAATGTAATTTTTGGAAAGTTCGAGGGTC
* * *
18301794 AAAATGGTAATTTTT-AAAAGTTCGAGAGTA
1 AAAAT-GTAATTTTTGGAAAGTTCGAGGGTC
* ** * *
18301824 AAAATGAAATTTTTAAAAAGTTTGAGGGTA
1 AAAATGTAATTTTTGGAAAGTTCGAGGGTC
*
18301854 AAAATGTAAGTTTTAT-G-AAGTTCGAGGGTT
1 AAAATGTAA-TTTT-TGGAAAGTTCGAGGGTC
* * *
18301884 AAAATATAATTTTTAGAAAGTT-TAGGGGT-
1 AAAATGTAATTTTTGGAAAGTTCGA-GGGTC
* ***
18301913 AAAATGTAATTTTTGTAAAGTTCGATCTTC
1 AAAATGTAATTTTTGGAAAGTTCGAGGGTC
*
18301943 AAAATATAATTTTTGGAAAGTTCGAGGGTC
1 AAAATGTAATTTTTGGAAAGTTCGAGGGTC
* * *
18301973 AAAACGTGATTTTTTGAACAGTT
1 AAAATGTAATTTTTGGAA-AGTT
18301996 TAAGGACCTT
Statistics
Matches: 356, Mismatches: 74, Indels: 67
0.72 0.15 0.13
Matches are distributed among these distances:
28 35 0.10
29 160 0.45
30 144 0.40
31 16 0.04
32 1 0.00
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAGTTCGAGGGTC
Found at i:18303141 original size:13 final size:13
Alignment explanation
Indices: 18303110--18303175 Score: 55
Period size: 13 Copynumber: 5.2 Consensus size: 13
18303100 TTTTCCTTTT
*
18303110 TTATTT-TTATTA
1 TTATTTATTAATA
* *
18303122 ATATTTATTAATG
1 TTATTTATTAATA
*
18303135 TTATTTATTACTA
1 TTATTTATTAATA
*
18303148 TTATTTATTATTA
1 TTATTTATTAATA
* *
18303161 TT-GTTATTATTA
1 TTATTTATTAATA
18303173 TTA
1 TTA
18303176 ATCGTTTTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
12 16 0.36
13 28 0.64
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (13 bp):
TTATTTATTAATA
Found at i:18303158 original size:3 final size:3
Alignment explanation
Indices: 18303110--18303175 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
18303100 TTTTCCTTTT
* * * * *
18303110 TTA TTT TTA TTA ATA TTTA TTA ATG TTA TTTA TTA CTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA
*
18303158 TTA TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
18303176 ATCGTTTTTA
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
3 40 0.83
4 8 0.17
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:18303862 original size:17 final size:18
Alignment explanation
Indices: 18303821--18303862 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
18303811 TAAATTTGAT
*
18303821 AATAAATTTAAACTTAAA
1 AATAAATTCAAACTTAAA
*
18303839 AACAAATTCAAACTT-AA
1 AATAAATTCAAACTTAAA
18303856 AATAAAT
1 AATAAAT
18303863 CTAAAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.29
Consensus pattern (18 bp):
AATAAATTCAAACTTAAA
Found at i:18303869 original size:18 final size:18
Alignment explanation
Indices: 18303821--18303869 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
18303811 TAAATTTGAT
*
18303821 AATAAATTTAAACTTAAA
1 AATAAATTAAAACTTAAA
* *
18303839 AACAAATTCAAACTT-AA
1 AATAAATTAAAACTTAAA
18303856 AATAAATCTAAAAC
1 AATAAAT-TAAAAC
18303870 AAAATAGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (18 bp):
AATAAATTAAAACTTAAA
Found at i:18309438 original size:11 final size:11
Alignment explanation
Indices: 18309422--18309449 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
18309412 ACACGGAAGT
18309422 GAAAACTTCAC
1 GAAAACTTCAC
18309433 GAAAACTTCAC
1 GAAAACTTCAC
18309444 GAAAAC
1 GAAAAC
18309450 ATAGGTACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.25, G:0.11, T:0.14
Consensus pattern (11 bp):
GAAAACTTCAC
Found at i:18311010 original size:30 final size:30
Alignment explanation
Indices: 18310959--18311250 Score: 233
Period size: 30 Copynumber: 9.8 Consensus size: 30
18310949 TTTGAGGTCG
*
18310959 AAAATGTAATTTT-AGAGAAGTTTAGGGGTT
1 AAAATGTAATTTTGA-AAAAGTTTAGGGGTT
** *
18310989 AAAATACAGTTTTGAAAAAGTTTA-GGG-T
1 AAAATGTAATTTTGAAAAAGTTTAGGGGTT
* *
18311017 AAAATTTTAATTTT-AGAAAAGTTT-GGGAGTC
1 AAAA-TGTAATTTTGA-AAAAGTTTAGGG-GTT
* *
18311048 AAAATGTAATTTTGAAAAAATTT-GGGAGTC
1 AAAATGTAATTTTGAAAAAGTTTAGGG-GTT
* *
18311078 AAAATGTAATTTTGGAAACA-TTTAGGGGTA
1 AAAATGTAATTTT-GAAAAAGTTTAGGGGTT
* * * *
18311108 AAAATTTAATTTTGGAAAAGTTTAAGGGTA
1 AAAATGTAATTTTGAAAAAGTTTAGGGGTT
*
18311138 AAAAT-TCAATTTTGGAAAAGTTTAGGGGTT
1 AAAATGT-AATTTTGAAAAAGTTTAGGGGTT
* *
18311168 AAAATGTAATTTTGAAAAAG-TTAAGGGTC
1 AAAATGTAATTTTGAAAAAGTTTAGGGGTT
* * * * *
18311197 AAAATTTAATTTTGGAAAATTTTAGTGGTC
1 AAAATGTAATTTTGAAAAAGTTTAGGGGTT
* * *
18311227 AAAATGTGATTTTTAGAAAGTTTA
1 AAAATGTAATTTTGAAAAAGTTTA
18311251 ATGACCTTCT
Statistics
Matches: 217, Mismatches: 32, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
28 6 0.03
29 48 0.22
30 148 0.68
31 15 0.07
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTGAAAAAGTTTAGGGGTT
Found at i:18311142 original size:90 final size:87
Alignment explanation
Indices: 18310887--18311239 Score: 304
Period size: 89 Copynumber: 3.9 Consensus size: 87
18310877 ATTTTCGAGG
* * * * * *
18310887 AATTTGGGGGTCAAAATTGAAATTTTTTAAAAATTT-GGAATTAAAATTAAAATTTTGGAAAA-T
1 AATTTAGGGGTCAAAA-TGTAA-TTTTGAAAAATTTAGG-GTAAAAATT-TAATTTTGGAAAAGT
*
18310950 TT-GAGGTCGAAAATGTAATTTT-AGAGA
62 TTAG-GGTC-AAAATGTAATTTTGA-AAA
* * ** * * * *
18310977 AGTTTAGGGGTTAAAATACAGTTTTGAAAAAGTTTAGGGTAAAATTTTAATTTTAGAAAAGTTTG
1 AATTTAGGGGTCAAAATGTAATTTTGAAAAA-TTTAGGGTAAAAATTTAATTTTGGAAAAGTTTA
18311042 GGAGTCAAAATGTAATTTTGAAAA
65 GG-GTCAAAATGTAATTTTGAAAA
*
18311066 AATTT-GGGAGTCAAAATGTAATTTTGGAAACATTTAGGGGTAAAAATTTAATTTTGGAAAAGTT
1 AATTTAGGG-GTCAAAATGTAATTTT-GAAAAATTTA-GGGTAAAAATTTAATTTTGGAAAAGTT
* *
18311130 TAAGGGTAAAAAT-TCAATTTTGGAAA
63 T-AGGGTCAAAATGT-AATTTTGAAAA
* * * * *
18311156 AGTTTAGGGGTTAAAATGTAATTTTGAAAAAGTTAAGGGTCAAAATTTAATTTTGGAAAATTTTA
1 AATTTAGGGGTCAAAATGTAATTTTGAAAAA-TTTAGGGTAAAAATTTAATTTTGGAAAAGTTTA
*
18311221 GTGGTCAAAATGTGATTTT
65 G-GGTCAAAATGTAATTTT
18311240 TAGAAAGTTT
Statistics
Matches: 216, Mismatches: 32, Indels: 31
0.77 0.11 0.11
Matches are distributed among these distances:
88 25 0.12
89 95 0.44
90 91 0.42
91 5 0.02
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.37
Consensus pattern (87 bp):
AATTTAGGGGTCAAAATGTAATTTTGAAAAATTTAGGGTAAAAATTTAATTTTGGAAAAGTTTAG
GGTCAAAATGTAATTTTGAAAA
Found at i:18311214 original size:59 final size:59
Alignment explanation
Indices: 18310937--18311248 Score: 299
Period size: 59 Copynumber: 5.3 Consensus size: 59
18310927 TTAAAATTAA
* * * * * * * **
18310937 AATTTTGGAAAATTTGA-GGTCGAAAATGTAATTTTAGAGAAGTTTAGGGGTTAAAATAC
1 AATTTTGAAAAAGTTAAGGGTC-AAAATTTAATTTTGGAAAAGTTTAGGGGTCAAAATGT
* * *
18310996 AGTTTTGAAAAAGTTTAGGGT-AAAATTTTAATTTTAGAAAAGTTT-GGGAGTCAAAATGT
1 AATTTTGAAAAAGTTAAGGGTCAAAA-TTTAATTTTGGAAAAGTTTAGGG-GTCAAAATGT
* ** * * *
18311055 AATTTTGAAAAAATTTGGGAGTCAAAATGTAATTTTGGAAACA-TTTAGGGGTAAAAATTT
1 AATTTTGAAAAAGTTAAGG-GTCAAAATTTAATTTTGGAAA-AGTTTAGGGGTCAAAATGT
* * * *
18311115 AATTTTGGAAAAGTTTAAGGGTAAAAATTCAATTTTGGAAAAGTTTAGGGGTTAAAATGT
1 AATTTTGAAAAAG-TTAAGGGTCAAAATTTAATTTTGGAAAAGTTTAGGGGTCAAAATGT
* *
18311175 AATTTTGAAAAAGTTAAGGGTCAAAATTTAATTTTGGAAAATTTTAGTGGTCAAAATGT
1 AATTTTGAAAAAGTTAAGGGTCAAAATTTAATTTTGGAAAAGTTTAGGGGTCAAAATGT
* * *
18311234 GATTTTTAGAAAGTT
1 AATTTTGAAAAAGTT
18311249 TAATGACCTT
Statistics
Matches: 210, Mismatches: 34, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
58 7 0.03
59 107 0.51
60 84 0.40
61 12 0.06
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (59 bp):
AATTTTGAAAAAGTTAAGGGTCAAAATTTAATTTTGGAAAAGTTTAGGGGTCAAAATGT
Found at i:18312145 original size:49 final size:49
Alignment explanation
Indices: 18312086--18312181 Score: 131
Period size: 49 Copynumber: 2.0 Consensus size: 49
18312076 CATATTGAAA
* * *
18312086 AAAATAAAAAAACTAAATATATAAA-CATGTGTGTATGTATATATATACC
1 AAAATAAAAAAA-TAAATAAATAAATAATGTGTATATGTATATATATACC
* *
18312135 AAAATGAAAAAATAAATAAATAAATAATGTGTATATGTATGTATATA
1 AAAATAAAAAAATAAATAAATAAATAATGTGTATATGTATATATATA
18312182 TATATATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
48 11 0.27
49 30 0.73
ACGTcount: A:0.55, C:0.04, G:0.09, T:0.31
Consensus pattern (49 bp):
AAAATAAAAAAATAAATAAATAAATAATGTGTATATGTATATATATACC
Found at i:18312466 original size:13 final size:13
Alignment explanation
Indices: 18312430--18312459 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
18312420 GTGTCAGATG
18312430 GTGGCAGAGGCAA
1 GTGGCAGAGGCAA
*
18312443 GTGGCAAAGGCAA
1 GTGGCAGAGGCAA
18312456 GTGG
1 GTGG
18312460 GTGAGGCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.47, T:0.10
Consensus pattern (13 bp):
GTGGCAGAGGCAA
Found at i:18315878 original size:15 final size:16
Alignment explanation
Indices: 18315845--18315878 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
18315835 CCTTCTTCTC
*
18315845 ATAAATTTAAAGTTCA
1 ATAAATTTAAAGATCA
18315861 ATAAATTT-AAGATCA
1 ATAAATTTAAAGATCA
18315876 ATA
1 ATA
18315879 TAGTCTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (16 bp):
ATAAATTTAAAGATCA
Found at i:18332085 original size:25 final size:26
Alignment explanation
Indices: 18332048--18332102 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
18332038 TTTCTTATTT
*
18332048 TTTTTACAATTTTTTAATTTT-TGTA
1 TTTTCACAATTTTTTAATTTTATGTA
* *
18332073 TTTTCACACTTTTTTAATTTTATTTA
1 TTTTCACAATTTTTTAATTTTATGTA
18332099 TTTT
1 TTTT
18332103 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (26 bp):
TTTTCACAATTTTTTAATTTTATGTA
Found at i:18333512 original size:17 final size:17
Alignment explanation
Indices: 18333490--18333531 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
18333480 CCCAAAATTT
18333490 TTTTAAATATTTTTTAA
1 TTTTAAATATTTTTTAA
*
18333507 TTTTAATTATTTTTTAA
1 TTTTAAATATTTTTTAA
*
18333524 GTTTAAAT
1 TTTTAAAT
18333532 TCATTTACTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTTAAATATTTTTTAA
Found at i:18333532 original size:18 final size:17
Alignment explanation
Indices: 18333491--18333537 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
18333481 CCAAAATTTT
18333491 TTTAAA-TATTTTTTAA
1 TTTAAATTATTTTTTAA
*
18333507 TTTTAATTATTTTTTAA
1 TTTAAATTATTTTTTAA
18333524 GTTTAAATTCATTT
1 -TTTAAATT-ATTT
18333538 ACTGACGTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 5 0.19
17 10 0.38
18 7 0.27
19 4 0.15
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTAAATTATTTTTTAA
Found at i:18339322 original size:14 final size:14
Alignment explanation
Indices: 18339304--18339336 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
18339294 ATGAGTGAAT
18339304 GGAAGCCAT-TTTG
1 GGAAGCCATGTTTG
18339317 GTGAAGCCATGTTTG
1 G-GAAGCCATGTTTG
18339332 GGAAG
1 GGAAG
18339337 GTCTGATCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 12 0.67
15 5 0.28
ACGTcount: A:0.24, C:0.12, G:0.36, T:0.27
Consensus pattern (14 bp):
GGAAGCCATGTTTG
Found at i:18342098 original size:21 final size:21
Alignment explanation
Indices: 18342073--18342115 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
18342063 TGTAGAATGG
18342073 ATGTGGCAATTTTGAGTTAAA
1 ATGTGGCAATTTTGAGTTAAA
18342094 ATGTGGCAATTTTGAGTTAAA
1 ATGTGGCAATTTTGAGTTAAA
18342115 A
1 A
18342116 CTTATAGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (21 bp):
ATGTGGCAATTTTGAGTTAAA
Found at i:18347676 original size:60 final size:59
Alignment explanation
Indices: 18347579--18347694 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 59
18347569 TACCAAATAA
* * *
18347579 AAAAAAAGATTAGGTACTAAATTAGGAAAAAGAGTCAAGTTTAGGTACCAAATTGGATCCC
1 AAAAAAAGATTAAGTACTAAATTAAGAAAAAGAGTCAAG-TT-CGTACCAAATTGGATCCC
* *
18347640 AAAAAAA-ATTAAGTATTAACTTAAGAAAAA-ATGTCAAGTTCGTACCAAATTGGAT
1 AAAAAAAGATTAAGTACTAAATTAAGAAAAAGA-GTCAAGTTCGTACCAAATTGGAT
18347695 AAAAAAGAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
58 14 0.29
59 3 0.06
60 25 0.51
61 7 0.14
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.25
Consensus pattern (59 bp):
AAAAAAAGATTAAGTACTAAATTAAGAAAAAGAGTCAAGTTCGTACCAAATTGGATCCC
Found at i:18357153 original size:40 final size:40
Alignment explanation
Indices: 18357109--18357226 Score: 173
Period size: 41 Copynumber: 2.9 Consensus size: 40
18357099 TGCTTCAATC
18357109 GAGTCATAAGTCTTCCTTTAAACAATCTTATGCTCTAACT
1 GAGTCATAAGTCTTCCTTTAAACAATCTTATGCTCTAACT
* * *
18357149 GAGTCATAAGTCTTCCTTTAAAACAATCTTATGATATAATT
1 GAGTCATAAGTCTTCCTTT-AAACAATCTTATGCTCTAACT
*
18357190 GAGACATAAGTCTTCCTTTAAACATAATCTTATGCTC
1 GAGTCATAAGTCTTCCTTTAAAC--AATCTTATGCTC
18357227 ATCCCGAGAC
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
40 23 0.33
41 36 0.52
42 10 0.14
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.37
Consensus pattern (40 bp):
GAGTCATAAGTCTTCCTTTAAACAATCTTATGCTCTAACT
Found at i:18357236 original size:42 final size:43
Alignment explanation
Indices: 18357108--18357292 Score: 186
Period size: 42 Copynumber: 4.5 Consensus size: 43
18357098 ATGCTTCAAT
18357108 CGAGTCATAAGTCTTCCTTTAAAC--AATCTTATGCTC-TAAC
1 CGAGTCATAAGTCTTCCTTTAAACATAATCTTATGCTCATAAC
* * * *
18357148 TGAGTCATAAGTCTTCCTTTAAA-ACAATCTTATGAT-ATAAT
1 CGAGTCATAAGTCTTCCTTTAAACATAATCTTATGCTCATAAC
* * *
18357189 TGAGACATAAGTCTTCCTTTAAACATAATCTTATGCTCAT-CC
1 CGAGTCATAAGTCTTCCTTTAAACATAATCTTATGCTCATAAC
* ** * * *
18357231 CGAGACACGAGTCTTCCTTTAAAGATAATCTCATGCTCAT-CC
1 CGAGTCATAAGTCTTCCTTTAAACATAATCTTATGCTCATAAC
**
18357273 CGAGTCACGAGTCTTCCTTT
1 CGAGTCATAAGTCTTCCTTT
18357293 TATACATCAA
Statistics
Matches: 126, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
40 22 0.17
41 35 0.28
42 67 0.53
43 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.35
Consensus pattern (43 bp):
CGAGTCATAAGTCTTCCTTTAAACATAATCTTATGCTCATAAC
Found at i:18360897 original size:52 final size:51
Alignment explanation
Indices: 18360819--18361003 Score: 237
Period size: 52 Copynumber: 3.6 Consensus size: 51
18360809 ATGCAAAAAT
* *
18360819 GTCCGATAACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAG
1 GTCCGATGACTATGTGTCATCGTGAGTATAT-AATCCTTTACGGATTATGAG
* *
18360871 GTCCGCTGACTATGTGTCATCGTGAGTATATTAATCCATTACGGATTATGAG
1 GTCCGATGACTATGTGTCATCGTGAGTATA-TAATCCTTTACGGATTATGAG
* *
18360923 GTCCGATGACTATGTGTCATCGGGAGTATATAGATCCTTTTACGGATT-TAAG
1 GTCCGATGACTATGTGTCATCGTGAGTATATA-ATCC-TTTACGGATTATGAG
* * * *
18360975 GTCCAATGACTTTGTGCCATCATGAGTAT
1 GTCCGATGACTATGTGTCATCGTGAGTAT
18361004 TAAATGGGAA
Statistics
Matches: 117, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
51 2 0.02
52 105 0.90
53 10 0.09
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.35
Consensus pattern (51 bp):
GTCCGATGACTATGTGTCATCGTGAGTATATAATCCTTTACGGATTATGAG
Found at i:18365166 original size:41 final size:41
Alignment explanation
Indices: 18364896--18365158 Score: 357
Period size: 41 Copynumber: 6.4 Consensus size: 41
18364886 TGTATAAATA
** *
18364896 GAAGACTCATGTTTCGAGATGAGCATGAGATTATATTAAAG
1 GAAGACTCATGACTCGAAATGAGCATGAGATTATATTAAAG
* *
18364937 GAAGACTCATGTCTCGAGATGAGCATGAGATTATATTAAAG
1 GAAGACTCATGACTCGAAATGAGCATGAGATTATATTAAAG
18364978 GAAGACTCATGACTCGAAATGAGCATGAGATTATATTAAAG
1 GAAGACTCATGACTCGAAATGAGCATGAGATTATATTAAAG
* * *
18365019 GAAGACTCGTGACTCAAAATGAGCATGAGATTTTATTAAAG
1 GAAGACTCATGACTCGAAATGAGCATGAGATTATATTAAAG
* * *
18365060 GAAGACTCGTGACTCAAAATGAGCATGAGATTTTATTAAAG
1 GAAGACTCATGACTCGAAATGAGCATGAGATTATATTAAAG
* * *
18365101 GAAGACTCGTGACTC-AGGATGAGCACGAGATTATATTTAAAG
1 GAAGACTCATGACTCGA-AATGAGCATGAGATTATA-TTAAAG
* *
18365143 AAAGACTTATGACTCG
1 GAAGACTCATGACTCG
18365159 GTAGAGCATA
Statistics
Matches: 207, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
40 1 0.00
41 188 0.91
42 18 0.09
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (41 bp):
GAAGACTCATGACTCGAAATGAGCATGAGATTATATTAAAG
Done.