Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 169 of 226
Found at i:54028223 original size:18 final size:17
Alignment explanation
Indices: 54028181--54028220 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
54028171 TTTTATTAAC
* *
54028181 ATTTTATATATTTTTTTA
1 ATTTTAAATA-TTTTATA
54028199 ATTTTAAATATTTTATA
1 ATTTTAAATATTTTATA
54028216 ATTTT
1 ATTTT
54028221 TAATTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTAAATATTTTATA
Found at i:54028809 original size:9 final size:9
Alignment explanation
Indices: 54028795--54029185 Score: 82
Period size: 9 Copynumber: 41.0 Consensus size: 9
54028785 TGAAATAAAC
54028795 TTATAAAAA
1 TTATAAAAA
54028804 TTATAAAAA
1 TTATAAAAA
*
54028813 TAATATAAAAT
1 T--TATAAAAA
54028824 TTATAAAAA
1 TTATAAAAA
54028833 -TATAATAAA
1 TTATAA-AAA
54028842 -TATAATAAA
1 TTATAA-AAA
*
54028851 TTCTAACAAA
1 TTATAA-AAA
*
54028861 GTATAAAAA
1 TTATAAAAA
*
54028870 TTATAAAAG
1 TTATAAAAA
*
54028879 TAATAAAGCACAA
1 TTAT-AA--A-AA
* **
54028892 TTA-GAATT
1 TTATAAAAA
*
54028900 TTACAAAAA
1 TTATAAAAA
54028909 TGTATAAAAA
1 T-TATAAAAA
* *
54028919 TTCTTAAAAC
1 TT-ATAAAAA
* * *
54028929 CTATAATAT
1 TTATAAAAA
*
54028938 TTCACAAAAA
1 TT-ATAAAAA
54028948 -TATAAATAA
1 TTATAAA-AA
* *
54028957 TCATAAATA
1 TTATAAAAA
*
54028966 TTAT-TAAA
1 TTATAAAAA
54028974 -TATTAAAAA
1 TTA-TAAAAA
** *
54028983 TATATTGAGA
1 T-TATAAAAA
* *
54028993 TTGATGTAAAC
1 TT-AT-AAAAA
*
54029004 TTATAACAA
1 TTATAAAAA
54029013 TTAT-AAAA
1 TTATAAAAA
*
54029021 TAATAATAAA
1 TTATAA-AAA
*
54029031 TAATAAAAA
1 TTATAAAAA
* *
54029040 TTTATGAATA
1 -TTATAAAAA
54029050 TTATAAAAA
1 TTATAAAAA
*
54029059 -TATAAGATA
1 TTATAA-AAA
54029068 TTATAAAATA
1 TTATAAAA-A
*
54029078 TT-TATAAAG
1 TTATA-AAAA
54029087 TTAATAAAACA
1 TT-ATAAAA-A
* *
54029098 TATTTAAAATT
1 T-TATAAAA-A
54029109 TTATAAAAAA
1 TTAT-AAAAA
54029119 CTTATAAAAAA
1 -TTAT-AAAAA
*
54029130 TCATAAAAA
1 TTATAAAAA
* * *
54029139 CCTAGATATAA
1 -TTATA-AAAA
54029150 -TATAAAAA
1 TTATAAAAA
*
54029158 TTCTAATAAA
1 TTATAA-AAA
*
54029168 TTATAAAAT
1 TTATAAAAA
54029177 TTATAAAAA
1 TTATAAAAA
54029186 AAATCATTTA
Statistics
Matches: 274, Mismatches: 71, Indels: 74
0.65 0.17 0.18
Matches are distributed among these distances:
7 2 0.01
8 29 0.11
9 109 0.40
10 88 0.32
11 41 0.15
12 2 0.01
13 3 0.01
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (9 bp):
TTATAAAAA
Found at i:54028841 original size:20 final size:20
Alignment explanation
Indices: 54028796--54028834 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
54028786 GAAATAAACT
54028796 TATAAAAATTATAAAAATAA
1 TATAAAAATTATAAAAATAA
*
54028816 TATAAAATTTATAAAAATA
1 TATAAAAATTATAAAAATA
54028835 TAATAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TATAAAAATTATAAAAATAA
Found at i:54029055 original size:19 final size:18
Alignment explanation
Indices: 54029033--54029082 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
54029023 ATAATAAATA
54029033 ATAAAAATTTATGAATATT
1 ATAAAAATTTATG-ATATT
* *
54029052 ATAAAAATATAAGATATT
1 ATAAAAATTTATGATATT
54029070 ATAAAATATTTAT
1 ATAAAA-ATTTAT
54029083 AAAGTTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
ATAAAAATTTATGATATT
Found at i:54029078 original size:10 final size:10
Alignment explanation
Indices: 54029012--54029137 Score: 61
Period size: 10 Copynumber: 12.9 Consensus size: 10
54029002 ACTTATAACA
54029012 ATTATAAAAT
1 ATTATAAAAT
*
54029022 AATA-ATAAAT
1 ATTATA-AAAT
*
54029032 AATA-AAAAT
1 ATTATAAAAT
*
54029041 -TTAT-GAAT
1 ATTATAAAAT
54029049 ATTATAAAA-
1 ATTATAAAAT
*
54029058 A-TATAAGAT
1 ATTATAAAAT
54029067 ATTATAAAAT
1 ATTATAAAAT
*
54029077 ATTTATAAAGT
1 A-TTATAAAAT
*
54029088 -TAATAAAACAT
1 ATTAT-AAA-AT
54029099 ATT-TAAAAT
1 ATTATAAAAT
* *
54029108 TTTATAAAAA
1 ATTATAAAAT
*
54029118 ACTTATAAAAA
1 A-TTATAAAAT
*
54029129 ATCATAAAA
1 ATTATAAAA
54029138 ACCTAGATAT
Statistics
Matches: 90, Mismatches: 14, Indels: 24
0.70 0.11 0.19
Matches are distributed among these distances:
8 11 0.12
9 18 0.20
10 40 0.44
11 20 0.22
12 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (10 bp):
ATTATAAAAT
Found at i:54029095 original size:20 final size:20
Alignment explanation
Indices: 54029070--54029126 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
54029060 ATAAGATATT
54029070 ATAAAATATTTATAAAGTTA
1 ATAAAATATTTATAAAGTTA
* *
54029090 ATAAAACATATTTA-AAATTTT
1 AT-AAA-ATATTTATAAAGTTA
* *
54029111 ATAAAAAACTTATAAA
1 ATAAAATATTTATAAA
54029127 AAATCATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
19 5 0.17
20 8 0.27
21 10 0.33
22 7 0.23
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (20 bp):
ATAAAATATTTATAAAGTTA
Found at i:54029117 original size:22 final size:22
Alignment explanation
Indices: 54029075--54029116 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
54029065 ATATTATAAA
54029075 ATATTTATAAAGTTAATAAAAC
1 ATATTTATAAAGTTAATAAAAC
* *
54029097 ATATTTA-AAATTTTATAAAA
1 ATATTTATAAAGTTAATAAAA
54029117 AACTTATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
ATATTTATAAAGTTAATAAAAC
Found at i:54029128 original size:11 final size:10
Alignment explanation
Indices: 54029017--54029186 Score: 50
Period size: 10 Copynumber: 17.4 Consensus size: 10
54029007 TAACAATTAT
*
54029017 AAAATAATAA
1 AAAATTATAA
* *
54029027 TAAATAATAA
1 AAAATTATAA
* *
54029037 AAATTTAT-G
1 AAAATTATAA
*
54029046 AATATTAT-A
1 AAAATTATAA
54029055 AAAA-TATAA
1 AAAATTATAA
* *
54029064 GATATTATAA
1 AAAATTATAA
* *
54029074 AATATT-TAT
1 AAAATTATAA
*
54029083 AAAGTTAATAA
1 AAAATT-ATAA
54029094 AACATATT-TAA
1 AA-A-ATTATAA
**
54029105 AATTTTATAA
1 AAAATTATAA
54029115 AAAACTTATAA
1 AAAA-TTATAA
*
54029126 AAAATCATAA
1 AAAATTATAA
** * *
54029136 AAACCTAGAT
1 AAAATTATAA
*
54029146 ATAA-TAT-A
1 AAAATTATAA
*
54029154 AAAATTCTAA
1 AAAATTATAA
*
54029164 TAAATTAT-A
1 AAAATTATAA
*
54029173 AAATTTATAA
1 AAAATTATAA
54029183 AAAA
1 AAAA
54029187 AATCATTTAA
Statistics
Matches: 111, Mismatches: 38, Indels: 22
0.65 0.22 0.13
Matches are distributed among these distances:
8 6 0.05
9 31 0.28
10 52 0.47
11 19 0.17
12 1 0.01
13 2 0.02
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.34
Consensus pattern (10 bp):
AAAATTATAA
Found at i:54029775 original size:9 final size:9
Alignment explanation
Indices: 54029754--54030042 Score: 101
Period size: 9 Copynumber: 31.7 Consensus size: 9
54029744 GTTCAAGTTT
54029754 ATTTTT-TA
1 ATTTTTATA
*
54029762 TTTTTTATA
1 ATTTTTATA
54029771 ATTTTTATA
1 ATTTTTATA
*
54029780 CTTTTATATTA
1 ATTTT-TA-TA
*
54029791 TTTTTTATA
1 ATTTTTATA
*
54029800 ATTTATTA-G
1 ATTT-TTATA
54029809 ATTTATTAT-
1 ATTT-TTATA
54029818 ATGTTTTATA
1 AT-TTTTATA
*
54029828 ATATTTATA
1 ATTTTTATA
*
54029837 AGTTTTTATT
1 A-TTTTTATA
54029847 ATTTTT-T-
1 ATTTTTATA
54029854 A---TTATA
1 ATTTTTATA
54029860 ATTTTTTATA
1 A-TTTTTATA
*
54029870 AGTTTATATTA
1 A-TTTTTA-TA
54029881 A-TTTT-TA
1 ATTTTTATA
54029888 ATTTTT-TA
1 ATTTTTATA
*
54029896 ATTTTAATA
1 ATTTTTATA
54029905 A-TTTTATGA
1 ATTTTTAT-A
*
54029914 GTTTTTAATA
1 ATTTTT-ATA
**
54029924 ATTTTCCT-
1 ATTTTTATA
54029932 ATTTTTA-A
1 ATTTTTATA
**
54029940 TATTTTT-CC
1 -ATTTTTATA
54029949 ATTTTTATGA
1 ATTTTTAT-A
*
54029959 TTTTTTATA
1 ATTTTTATA
54029968 ATTTTTTTATA
1 A--TTTTTATA
54029979 ATTTTATATAA
1 ATTTT-TAT-A
54029990 TATTTTTTTATA
1 -A--TTTTTATA
*
54030002 ATTTATTA-G
1 ATTT-TTATA
*
54030011 ATTTATTA-G
1 ATTT-TTATA
54030020 ATTTTTATA
1 ATTTTTATA
*
54030029 ATATTTAT-
1 ATTTTTATA
54030037 ATTTTT
1 ATTTTT
54030043 TTATTACTTT
Statistics
Matches: 218, Mismatches: 29, Indels: 68
0.69 0.09 0.22
Matches are distributed among these distances:
4 2 0.01
5 1 0.00
6 1 0.00
7 4 0.02
8 41 0.19
9 87 0.40
10 51 0.23
11 22 0.10
12 2 0.01
13 3 0.01
14 4 0.02
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (9 bp):
ATTTTTATA
Found at i:54029776 original size:10 final size:10
Alignment explanation
Indices: 54029761--54030086 Score: 86
Period size: 9 Copynumber: 33.6 Consensus size: 10
54029751 TTTATTTTTT
54029761 ATTTTTTATA
1 ATTTTTTATA
54029771 A-TTTTTATA
1 ATTTTTTATA
* * *
54029780 CTTTTATATT
1 ATTTTTTATA
54029790 ATTTTTTATA
1 ATTTTTTATA
* *
54029800 ATTTATTA-G
1 ATTTTTTATA
*
54029809 ATTTATTAT-
1 ATTTTTTATA
*
54029818 ATGTTTTATA
1 ATTTTTTATA
*
54029828 A-TATTTATA
1 ATTTTTTATA
*
54029837 AGTTTTTATTA
1 ATTTTTTA-TA
*
54029848 TTTTTTATTATA
1 -ATTTT-TTATA
54029860 ATTTTTTATA
1 ATTTTTTATA
* *
54029870 AGTTTATATTA
1 ATTTTTTA-TA
54029881 A--TTTT-TA
1 ATTTTTTATA
54029888 A-TTTTT-TA
1 ATTTTTTATA
*
54029896 A-TTTTAATA
1 ATTTTTTATA
54029905 A--TTTTATGA
1 ATTTTTTAT-A
* *
54029914 GTTTTTAATA
1 ATTTTTTATA
**
54029924 A-TTTTCCT-
1 ATTTTTTATA
*
54029932 ATTTTTAAT-
1 ATTTTTTATA
**
54029941 A-TTTTT-CC
1 ATTTTTTATA
*
54029949 A-TTTTTATG
1 ATTTTTTATA
54029958 ATTTTTTATA
1 ATTTTTTATA
54029968 ATTTTTTTATA
1 A-TTTTTTATA
54029979 ATTTTATATAATA
1 ATTTT-T-T-ATA
*
54029992 TTTTTTTATA
1 ATTTTTTATA
* *
54030002 ATTTATTA-G
1 ATTTTTTATA
* *
54030011 ATTTATTA-G
1 ATTTTTTATA
54030020 A-TTTTTATA
1 ATTTTTTATA
*
54030029 A-TATTTATA
1 ATTTTTTATA
*
54030038 TTTTTTTATTA
1 ATTTTTTA-TA
*
54030049 CTTTTTAGTATA
1 ATTTTT--TATA
*
54030061 A-TATTTATA
1 ATTTTTTATA
* *
54030070 AGTTTATATTA
1 ATTTTTTA-TA
54030081 ATTTTT
1 ATTTTT
54030087 GTTATGAATA
Statistics
Matches: 239, Mismatches: 49, Indels: 55
0.70 0.14 0.16
Matches are distributed among these distances:
7 3 0.01
8 32 0.13
9 72 0.30
10 69 0.29
11 42 0.18
12 9 0.04
13 12 0.05
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.64
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:54029871 original size:33 final size:32
Alignment explanation
Indices: 54029810--54029887 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
54029800 ATTTATTAGA
* *
54029810 TTTATTATATGTT-TTATAATATTTATAAGTT
1 TTTATTATTTTTTATTATAATATTTATAAGTT
*
54029841 TTTATTATTTTTTATTATAATTTTTTATAAGTT
1 TTTATTATTTTTTATTATAA-TATTTATAAGTT
* *
54029874 TATATTAATTTTTA
1 TTTATTATTTTTTA
54029888 ATTTTTTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 11 0.28
32 6 0.15
33 23 0.57
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (32 bp):
TTTATTATTTTTTATTATAATATTTATAAGTT
Found at i:54029879 original size:23 final size:23
Alignment explanation
Indices: 54029832--54029880 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
54029822 TTTATAATAT
* * *
54029832 TTATAAGTTTTTATTATTTTTTA
1 TTATAAGTTTTTATAAGTTTATA
*
54029855 TTATAATTTTTTATAAGTTTATA
1 TTATAAGTTTTTATAAGTTTATA
54029878 TTA
1 TTA
54029881 ATTTTTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (23 bp):
TTATAAGTTTTTATAAGTTTATA
Found at i:54029976 original size:21 final size:22
Alignment explanation
Indices: 54029950--54030005 Score: 78
Period size: 21 Copynumber: 2.5 Consensus size: 22
54029940 TATTTTTCCA
* *
54029950 TTTTTATGATTTTTTATAAT-T
1 TTTTTATAATTTTATATAATAT
54029971 TTTTTATAATTTTATATAATATT
1 TTTTTATAATTTTATATAATA-T
54029994 TTTTTATAATTT
1 TTTTTATAATTT
54030006 ATTAGATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 18 0.58
23 13 0.42
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTTTATAATTTTATATAATAT
Found at i:54030048 original size:30 final size:29
Alignment explanation
Indices: 54030012--54030086 Score: 78
Period size: 32 Copynumber: 2.4 Consensus size: 29
54030002 ATTTATTAGA
**
54030012 TTTATTAGATTTTTATAATATTTATATTTT
1 TTTATTA-ATTTTTATAATATTTATAAGTT
*
54030042 TTTATTACTTTTTAGTATAATATTTATAAGTT
1 TTTATTA-ATTTT--TATAATATTTATAAGTT
*
54030074 TATATTAATTTTT
1 TTTATTAATTTTT
54030087 GTTATGAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
29 1 0.03
30 11 0.30
31 4 0.11
32 21 0.57
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (29 bp):
TTTATTAATTTTTATAATATTTATAAGTT
Found at i:54030080 original size:32 final size:32
Alignment explanation
Indices: 54030025--54030086 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
54030015 ATTAGATTTT
** * *
54030025 TATAATATTTATATTTTTTTATTACTTTTTAG
1 TATAATATTTATAAGTTTATATTAATTTTTAG
54030057 TATAATATTTATAAGTTTATATTAATTTTT
1 TATAATATTTATAAGTTTATATTAATTTTT
54030087 GTTATGAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (32 bp):
TATAATATTTATAAGTTTATATTAATTTTTAG
Found at i:54031547 original size:20 final size:20
Alignment explanation
Indices: 54031522--54031561 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
54031512 ACTTACTATG
54031522 GAGCTTGAAAGCTTGAAAAC
1 GAGCTTGAAAGCTTGAAAAC
*
54031542 GAGCTTGGAAGCTTGAAAAC
1 GAGCTTGAAAGCTTGAAAAC
54031562 CCTAACTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.20
Consensus pattern (20 bp):
GAGCTTGAAAGCTTGAAAAC
Found at i:54044798 original size:23 final size:23
Alignment explanation
Indices: 54044772--54044962 Score: 364
Period size: 23 Copynumber: 8.3 Consensus size: 23
54044762 ATAAGTGCCA
*
54044772 CACTGATATGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
54044795 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
54044818 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
*
54044841 CACTGATATGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
54044864 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
54044887 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
54044910 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
54044933 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
54044956 CACTGAT
1 CACTGAT
54044963 CAATAACACT
Statistics
Matches: 165, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 165 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.19
Consensus pattern (23 bp):
CACTGATACGTAGCCGAAGCTAC
Found at i:54047276 original size:12 final size:12
Alignment explanation
Indices: 54047259--54047289 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
54047249 ATAGAGGAAC
54047259 TCCCAAATACTT
1 TCCCAAATACTT
54047271 TCCCAAATACTT
1 TCCCAAATACTT
54047283 TCCCAAA
1 TCCCAAA
54047290 CTCTTAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (12 bp):
TCCCAAATACTT
Found at i:54050173 original size:57 final size:57
Alignment explanation
Indices: 54050064--54050173 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 57
54050054 TTCAGTGAAA
* * * * *
54050064 TGGGAGCCACGATAGTGTTGTCTCCAATTTGAATTGAATGTCCATCCATCAGTAATG
1 TGGGAGCCACCATAGTGTTGTCTCCAAATTGAATTAAAAGGCCATCCATCAGTAATG
* *
54050121 TGGGAGCCACCATTGTGTTGTCTCCAAATTGGATTAAAAGGCCA-CCATTCAGT
1 TGGGAGCCACCATAGTGTTGTCTCCAAATTGAATTAAAAGGCCATCCA-TCAGT
54050174 TTTGTACAGG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
56 3 0.07
57 42 0.93
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (57 bp):
TGGGAGCCACCATAGTGTTGTCTCCAAATTGAATTAAAAGGCCATCCATCAGTAATG
Found at i:54055931 original size:11 final size:11
Alignment explanation
Indices: 54055917--54055955 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
54055907 GTTTTCTTTT
*
54055917 TATTTTGCTAC
1 TATTTTACTAC
*
54055928 TATTTTACTAT
1 TATTTTACTAC
*
54055939 TATGTTACTAC
1 TATTTTACTAC
54055950 TATTTT
1 TATTTT
54055956 GTTGTTATTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.23, C:0.13, G:0.05, T:0.59
Consensus pattern (11 bp):
TATTTTACTAC
Found at i:54055933 original size:22 final size:22
Alignment explanation
Indices: 54055908--54055964 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 22
54055898 TTTCTTGTTG
* *
54055908 TTTTCTTTTTATTTTGCTACTA
1 TTTTCTTATTATTTTACTACTA
*
54055930 TTTTAC-TATTATGTTACTACTA
1 TTTT-CTTATTATTTTACTACTA
* *
54055952 TTTTGTTGTTATT
1 TTTTCTTATTATT
54055965 GTTTGGATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.18, C:0.11, G:0.07, T:0.65
Consensus pattern (22 bp):
TTTTCTTATTATTTTACTACTA
Found at i:54056153 original size:24 final size:24
Alignment explanation
Indices: 54056124--54056173 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
54056114 TTTCAATTTG
54056124 TTGGGAAATATTTATGTTGATGTT
1 TTGGGAAATATTTATGTTGATGTT
54056148 TTGGGAAATATTTATGTTGATGTT
1 TTGGGAAATATTTATGTTGATGTT
54056172 TT
1 TT
54056174 TAGTATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (24 bp):
TTGGGAAATATTTATGTTGATGTT
Found at i:54056217 original size:11 final size:11
Alignment explanation
Indices: 54056201--54056231 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
54056191 TATACATATT
54056201 TAAAAATTATA
1 TAAAAATTATA
*
54056212 TAAAAATAATA
1 TAAAAATTATA
54056223 TAAAAATTA
1 TAAAAATTA
54056232 ATACAGGCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:54057871 original size:16 final size:18
Alignment explanation
Indices: 54057850--54057883 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
54057840 TTAATTACAT
54057850 AATATAT-AC-CATTCAA
1 AATATATGACACATTCAA
54057866 AATATATGACACATTCAA
1 AATATATGACACATTCAA
54057884 GATCCAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (18 bp):
AATATATGACACATTCAA
Found at i:54061139 original size:38 final size:38
Alignment explanation
Indices: 54061096--54061173 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
54061086 GATACACTAG
54061096 ATCCAACATTAAATCCATAAACTATTTATACATAATAT
1 ATCCAACATTAAATCCATAAACTATTTATACATAATAT
*
54061134 ATCCAACATTAAATCCATAAACTATTTATTCATAATAT
1 ATCCAACATTAAATCCATAAACTATTTATACATAATAT
54061172 AT
1 AT
54061174 GCAGTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (38 bp):
ATCCAACATTAAATCCATAAACTATTTATACATAATAT
Found at i:54072048 original size:17 final size:16
Alignment explanation
Indices: 54072009--54072045 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
54071999 ATGCTAAGTT
54072009 ATTTTAATAATATAAA
1 ATTTTAATAATATAAA
54072025 ATTTTAATTAA-ATAAA
1 ATTTTAA-TAATATAAA
54072041 ATTTT
1 ATTTT
54072046 TAACAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTTAATAATATAAA
Found at i:54077692 original size:137 final size:137
Alignment explanation
Indices: 54077445--54077706 Score: 341
Period size: 137 Copynumber: 1.9 Consensus size: 137
54077435 GTTTACTCAT
* *
54077445 ACAAGCTGTCAGTCGAAATGTAAGCTACACGATGCTGTTCACACAAGCTGTCAAGTATCCGCAAC
1 ACAAGCTGTCAGTCGAAATGT-AGCTACACGATGCTGCTCACACAAGCTGTCAAGTAACCGCAAC
* * * *
54077510 TAATGTCAGACCTCAGCCATCGGTAGGACATTCAAGACCAACACCCAAAACA-TGGTAACCTAGA
65 TAATGCCAAAACTCAGCCACCGGTAGGACATTCAAGACCAACACCCAAAACACT-GTAACCTAGA
54077574 TATGCTTAC
129 TATGCTTAC
* * * * * * *
54077583 ACAAGCTTTCGGTCGAAATGT-GCTAGATGGTGCTGCTCACACAAGCTGTTAAGTAACCGTAAC-
1 ACAAGCTGTCAGTCGAAATGTAGCTACACGATGCTGCTCACACAAGCTGTCAAGTAACCGCAACT
*
54077646 ACATGCCGAAAACTCAGCCACCGGTAGGACGTTCAAGACCAACACCCAAAACACTGTAACC
66 A-ATGCC-AAAACTCAGCCACCGGTAGGACATTCAAGACCAACACCCAAAACACTGTAACC
54077707 CTAATGACAT
Statistics
Matches: 107, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
135 1 0.01
136 39 0.36
137 47 0.44
138 20 0.19
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (137 bp):
ACAAGCTGTCAGTCGAAATGTAGCTACACGATGCTGCTCACACAAGCTGTCAAGTAACCGCAACT
AATGCCAAAACTCAGCCACCGGTAGGACATTCAAGACCAACACCCAAAACACTGTAACCTAGATA
TGCTTAC
Found at i:54080554 original size:27 final size:27
Alignment explanation
Indices: 54080405--54080554 Score: 115
Period size: 27 Copynumber: 5.6 Consensus size: 27
54080395 GCATTGATAG
* * * * *
54080405 CCTTCGTGGCGTACCTTGAATGAATCA
1 CCTTTGTGGCATACTTTGTATGGATCA
* *
54080432 CTTTTGTGGCATACTTTGTATAGAT-A
1 CCTTTGTGGCATACTTTGTATGGATCA
** * * * *
54080458 GCCTTCATGGCGTACCTTGAATGAATCA
1 -CCTTTGTGGCATACTTTGTATGGATCA
* *
54080486 CCTTTGTGGCATACTCTGTATAGAT-A
1 CCTTTGTGGCATACTTTGTATGGATCA
*
54080512 GCCTTTGTGGCATACTTTGTATGGGTCA
1 -CCTTTGTGGCATACTTTGTATGGATCA
*
54080540 CCTTTGTGGCGTACT
1 CCTTTGTGGCATACT
54080555 CTGATTAGAT
Statistics
Matches: 92, Mismatches: 27, Indels: 8
0.72 0.21 0.06
Matches are distributed among these distances:
26 2 0.02
27 88 0.96
28 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.37
Consensus pattern (27 bp):
CCTTTGTGGCATACTTTGTATGGATCA
Found at i:54080564 original size:54 final size:54
Alignment explanation
Indices: 54080389--54080557 Score: 230
Period size: 54 Copynumber: 3.1 Consensus size: 54
54080379 CTTTGTGCTG
* * *
54080389 TACTCTGCATTGATAGCCTTCGTGGCGTACCTTGAATGAATCACTTTTGTGGCA
1 TACTCTGTATAGATAGCCTTCGTGGCGTACCTTGAATGAATCACCTTTGTGGCA
* *
54080443 TACTTTGTATAGATAGCCTTCATGGCGTACCTTGAATGAATCACCTTTGTGGCA
1 TACTCTGTATAGATAGCCTTCGTGGCGTACCTTGAATGAATCACCTTTGTGGCA
* * * * ** *
54080497 TACTCTGTATAGATAGCCTTTGTGGCATACTTTGTATGGGTCACCTTTGTGGCG
1 TACTCTGTATAGATAGCCTTCGTGGCGTACCTTGAATGAATCACCTTTGTGGCA
54080551 TACTCTG
1 TACTCTG
54080558 ATTAGATTGA
Statistics
Matches: 101, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 101 1.00
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (54 bp):
TACTCTGTATAGATAGCCTTCGTGGCGTACCTTGAATGAATCACCTTTGTGGCA
Found at i:54089536 original size:25 final size:25
Alignment explanation
Indices: 54089487--54089536 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
54089477 AAAGCGTAAT
* *
54089487 TTATTGTCCGGTAAGCCTGCGCGAG
1 TTATTGTCCGGTAAGCCTCCCCGAG
54089512 TTATTGTCCGGTAAGCCTCCCCGAG
1 TTATTGTCCGGTAAGCCTCCCCGAG
54089537 GGAGGTATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (25 bp):
TTATTGTCCGGTAAGCCTCCCCGAG
Found at i:54089679 original size:31 final size:31
Alignment explanation
Indices: 54089644--54089706 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
54089634 TCTAGCTTTC
54089644 CTTAAGCTAGATTGTCAAGGATCTATATTTT
1 CTTAAGCTAGATTGTCAAGGATCTATATTTT
54089675 CTTAAGCTAGATTGTCAAGGATCTATATTTT
1 CTTAAGCTAGATTGTCAAGGATCTATATTTT
54089706 C
1 C
54089707 AAGGAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (31 bp):
CTTAAGCTAGATTGTCAAGGATCTATATTTT
Found at i:54089710 original size:16 final size:16
Alignment explanation
Indices: 54089658--54089711 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
54089648 AGCTAGATTG
54089658 TCAAGGATCTATATTT
1 TCAAGGATCTATATTT
* *
54089674 TCTTAA-G--CTAGATTG
1 TC--AAGGATCTATATTT
54089689 TCAAGGATCTATATTT
1 TCAAGGATCTATATTT
54089705 TCAAGGA
1 TCAAGGA
54089712 AAATATAGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
13 2 0.07
14 1 0.03
15 8 0.28
16 15 0.52
17 1 0.03
18 2 0.07
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (16 bp):
TCAAGGATCTATATTT
Found at i:54098554 original size:40 final size:40
Alignment explanation
Indices: 54098496--54098693 Score: 245
Period size: 40 Copynumber: 5.0 Consensus size: 40
54098486 TAATTATTTT
* *
54098496 CTGAATGCACATATGTGCCCTTATTTGTACTTCAGTACCC
1 CTGAATGCACATACGTGCCCTTATTTGTACTTCGGTACCC
*
54098536 CTGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCC
1 CTGAATGCACATACGTGCCCTTATTTGTACTTCGGTACCC
* ** * * *
54098576 CTAAATGCACATGTGTGCCCCTGTTTGTACTTTGGTACCC
1 CTGAATGCACATACGTGCCCTTATTTGTACTTCGGTACCC
* * *
54098616 ATGAATGCACATACATGCCCCTT-TTTGTACTTCGATACCC
1 CTGAATGCACATACGTG-CCCTTATTTGTACTTCGGTACCC
* * *
54098656 CTGAATCCACATACGTGCCCTTATTAGTACTTTGGTAC
1 CTGAATGCACATACGTGCCCTTATTTGTACTTCGGTAC
54098694 TCTTGAAGGC
Statistics
Matches: 134, Mismatches: 22, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
39 5 0.04
40 125 0.93
41 4 0.03
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (40 bp):
CTGAATGCACATACGTGCCCTTATTTGTACTTCGGTACCC
Found at i:54098635 original size:80 final size:80
Alignment explanation
Indices: 54098499--54098693 Score: 273
Period size: 80 Copynumber: 2.4 Consensus size: 80
54098489 TTATTTTCTG
** * *
54098499 AATGCACATATGTGCCCTTATTTGTACTTCAGTACCCCTGAATGCACATACGTGCCCCTATTTGT
1 AATGCACATATGTGCCCTTATTTGTACTTTGGTACCCATGAATGCACATACATGCCCCTATTTGT
*
54098564 ACTTCGGTACCCCTA
66 ACTTCGATACCCCTA
* * * *
54098579 AATGCACATGTGTGCCCCTGTTTGTACTTTGGTACCCATGAATGCACATACATGCCCCTTTTTGT
1 AATGCACATATGTGCCCTTATTTGTACTTTGGTACCCATGAATGCACATACATGCCCCTATTTGT
*
54098644 ACTTCGATACCCCTG
66 ACTTCGATACCCCTA
* * *
54098659 AATCCACATACGTGCCCTTATTAGTACTTTGGTAC
1 AATGCACATATGTGCCCTTATTTGTACTTTGGTAC
54098694 TCTTGAAGGC
Statistics
Matches: 99, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 99 1.00
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (80 bp):
AATGCACATATGTGCCCTTATTTGTACTTTGGTACCCATGAATGCACATACATGCCCCTATTTGT
ACTTCGATACCCCTA
Found at i:54103517 original size:14 final size:14
Alignment explanation
Indices: 54103483--54103521 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
54103473 CCAGAAAAGT
54103483 AAGTCATTTTCCAG
1 AAGTCATTTTCCAG
* *
54103497 AAATCATTTTCCGG
1 AAGTCATTTTCCAG
*
54103511 GAGTCATTTTC
1 AAGTCATTTTC
54103522 AGTGAAACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (14 bp):
AAGTCATTTTCCAG
Found at i:54124518 original size:182 final size:181
Alignment explanation
Indices: 54124199--54124539 Score: 472
Period size: 182 Copynumber: 1.9 Consensus size: 181
54124189 TAAGTTGTTC
* * * *
54124199 AAGGAAAGGAGCAGACTCCGGCATAATGCAAAGATTTAGAAACGAGAATTTTTTCCAAGAAAAAA
1 AAGGAAAGGAGCAAACTCCGACATAATGCAAAGATTCAGAAACGACAATTTTTTCCAAGAAAAAA
* *
54124264 AGTTCTGTTATTTAACTCAAGATTAAAATTATTCCCTGGCAAGCTAAAATCAAGATGGACTAGCG
66 AGTTATGTTATTTAACTCAAGATTAAAATTATTCCATGGCAAGCTAAAATCAAGATGGACTAGCG
54124329 CATACACTATAAACCAGGTGACACCTTACAGGGTGATAAAACTCATTAGAA
131 CATACACTATAAACCAGGTGACACCTTACAGGGTGATAAAACTCATTAGAA
* ** * *
54124380 AAGGGAAGGAGCAAACTCCGACATAATGCAAAGAGATTCAGAAACGACAA-TTTTTCTTAGACAC
1 AAGGAAAGGAGCAAACTCCGACATAATGC-AA-AGATTCAGAAACGACAATTTTTTCCAAGAAAA
** * *
54124444 AAAGTTATGTTATTTAACTTGAGATTAAAATTATTCCATGGCAAGTTGAAATCAAGATGGACT-G
64 AAAGTTATGTTATTTAACTCAAGATTAAAATTATTCCATGGCAAGCTAAAATCAAGATGGACTAG
* *
54124508 -GTCTATACACTATCAACCAGGTGACATCTTAC
129 CG-C-ATACACTATAAACCAGGTGACACCTTAC
54124540 GGGGAGGTAC
Statistics
Matches: 139, Mismatches: 17, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
180 1 0.01
181 28 0.20
182 95 0.68
183 15 0.11
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (181 bp):
AAGGAAAGGAGCAAACTCCGACATAATGCAAAGATTCAGAAACGACAATTTTTTCCAAGAAAAAA
AGTTATGTTATTTAACTCAAGATTAAAATTATTCCATGGCAAGCTAAAATCAAGATGGACTAGCG
CATACACTATAAACCAGGTGACACCTTACAGGGTGATAAAACTCATTAGAA
Found at i:54126009 original size:17 final size:17
Alignment explanation
Indices: 54125989--54126022 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
54125979 CTCCAAAAGG
54125989 AAGATGAATA-ATACATT
1 AAGAT-AATATATACATT
54126006 AAGATAATATATACATT
1 AAGATAATATATACATT
54126023 TAGTAGGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (17 bp):
AAGATAATATATACATT
Found at i:54126821 original size:21 final size:21
Alignment explanation
Indices: 54126797--54126836 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54126787 CCAATATATG
*
54126797 CAAAAAGAAAAAATAAAAATT
1 CAAAAACAAAAAATAAAAATT
*
54126818 CAAAAACTAAAAATAAAAA
1 CAAAAACAAAAAATAAAAA
54126837 AGAGCAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.78, C:0.07, G:0.03, T:0.12
Consensus pattern (21 bp):
CAAAAACAAAAAATAAAAATT
Found at i:54127114 original size:17 final size:18
Alignment explanation
Indices: 54127083--54127116 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54127073 ACGACGTGCC
54127083 AAACTATTTTCATGCTTG
1 AAACTATTTTCATGCTTG
*
54127101 AAACT-TTTTGATGCTT
1 AAACTATTTTCATGCTT
54127117 ACTGTTCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.47
Consensus pattern (18 bp):
AAACTATTTTCATGCTTG
Found at i:54132655 original size:14 final size:14
Alignment explanation
Indices: 54132617--54132661 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
54132607 AAGTAGATTT
54132617 GTAAAAAAAAGA-TC
1 GTAAAAAAAA-ATTC
*
54132631 GTTAAAAAAAATTC
1 GTAAAAAAAAATTC
54132645 GTAAAAAAAAATT-
1 GTAAAAAAAAATTC
54132658 GTAA
1 GTAA
54132662 TTATTTTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 5 0.18
14 23 0.82
ACGTcount: A:0.62, C:0.04, G:0.11, T:0.22
Consensus pattern (14 bp):
GTAAAAAAAAATTC
Found at i:54135167 original size:20 final size:21
Alignment explanation
Indices: 54135115--54135169 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
54135105 GCAAAGGAGC
54135115 AAAAAG-AAAAGAT-AGAAAAT
1 AAAAAGAAAAAG-TGAGAAAAT
* *
54135135 GAAAA-AAAGAGTGAGAAAA-
1 AAAAAGAAAAAGTGAGAAAAT
54135154 AAAAAGAAAAAGTGAG
1 AAAAAGAAAAAGTGAG
54135170 TTAAAATCGA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.07
Consensus pattern (21 bp):
AAAAAGAAAAAGTGAGAAAAT
Found at i:54138384 original size:28 final size:28
Alignment explanation
Indices: 54138352--54138407 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
54138342 TTAAATGTTT
* *
54138352 TTTTATTATATGTTATTAATG-TGTCTAA
1 TTTTATTACATGCT-TTAATGATGTCTAA
54138380 TTTTATTACATGCTTTAATGATGTCTAA
1 TTTTATTACATGCTTTAATGATGTCTAA
54138408 GTCAAGTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.54
Consensus pattern (28 bp):
TTTTATTACATGCTTTAATGATGTCTAA
Found at i:54141572 original size:35 final size:34
Alignment explanation
Indices: 54141526--54141598 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
54141516 AATGATGTTA
* **
54141526 AATTGAATGTATTTATTATGTACATAGCCGAATTG
1 AATTGAATGTATGTA-TAACTACATAGCCGAATTG
* *
54141561 AATTGTATGTATGTATAACTACATTGCCGAATTG
1 AATTGAATGTATGTATAACTACATAGCCGAATTG
54141595 AATT
1 AATT
54141599 TAGCATGGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
34 20 0.61
35 13 0.39
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (34 bp):
AATTGAATGTATGTATAACTACATAGCCGAATTG
Found at i:54142976 original size:42 final size:42
Alignment explanation
Indices: 54142869--54142976 Score: 171
Period size: 42 Copynumber: 2.6 Consensus size: 42
54142859 TACACCGACT
* * * *
54142869 TTAAGCCTACTAGACTTATAGTCCGAATTTATTTCACCGGCA
1 TTAAGCCTACTAGACGTAAAGTCTGAATTTATTTCACCAGCA
54142911 TTAAGCCTACTAGACGTAAAGTCTGAATTTATTTCACCAGCA
1 TTAAGCCTACTAGACGTAAAGTCTGAATTTATTTCACCAGCA
*
54142953 TTAAGCCTGCTAGACGTAAAGTCT
1 TTAAGCCTACTAGACGTAAAGTCT
54142977 AAATGGTTTC
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (42 bp):
TTAAGCCTACTAGACGTAAAGTCTGAATTTATTTCACCAGCA
Found at i:54155577 original size:27 final size:27
Alignment explanation
Indices: 54155546--54155604 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
54155536 TTTGAGGCTT
* *
54155546 ATCTAGATCCGTACAAGGTTTATCTAG
1 ATCTAGATCCATACAAGGCTTATCTAG
*
54155573 ATCTAGATCCATACGAGGCTTATCTAG
1 ATCTAGATCCATACAAGGCTTATCTAG
54155600 ATCTA
1 ATCTA
54155605 AATAAGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (27 bp):
ATCTAGATCCATACAAGGCTTATCTAG
Found at i:54157019 original size:26 final size:27
Alignment explanation
Indices: 54156974--54157045 Score: 137
Period size: 26 Copynumber: 2.7 Consensus size: 27
54156964 CATTATGCCA
54156974 TTACTCAAATTGGACTATGATAACTCC
1 TTACTCAAATTGGACTATGATAACTCC
54157001 TTACTCAAA-TGGACTATGATAACTCC
1 TTACTCAAATTGGACTATGATAACTCC
54157027 TTACTCAAATTGGACTATG
1 TTACTCAAATTGGACTATG
54157046 TTTTCATATA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
26 26 0.59
27 18 0.41
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (27 bp):
TTACTCAAATTGGACTATGATAACTCC
Found at i:54166797 original size:548 final size:542
Alignment explanation
Indices: 54165693--54167217 Score: 2419
Period size: 548 Copynumber: 2.8 Consensus size: 542
54165683 CATATTTTAT
*** *
54165693 AAATATATAGAAAAATCCTATATAATTCCAAGTTTACACCTATCCATGAACAACTTAACCCCAAA
1 AAATATATAGAAAAATCCTATATAATTTTGAGTTTACACCTATCCATGAACAACTTAACCCCGAA
** * *
54165758 CTAGTCTGGACTGTGAGGTCGAGAGATAAAGAGTTCTTCCTGACTCGTTATTCTAATGGAAGATC
66 CCGGTCTGGACTGTGAGGTCGAGAGATAAATAGTTCTTCCTGACTCGTTATTCTAGTGGAAGATC
* * * * * *
54165823 GAAAGGTCCAGCTGGGGTATTGGCTAGTTGATTGAAAAAAAAAACCCGAATCGATAGTTGGTTAT
131 GAAAGATCCAGCTGGGGTATCGACTAGTTGATTGAACAAGAAAACCCGAAGCGATAGTTGGTTAT
* *
54165888 GATTACCGAAGCGAGCTAATCACCAATGCTCGGATTTGACAGGTTCTGCTATTTGATTTCTTGTT
196 GATTACCGAAGCGAGCTAATCACCCATGCTAGGATTTGACAGGTTCTGCTATTTGATTTCTTGTT
* **
54165953 GTTTATTTATTTCTTTTATTTTTACTATTATTATTACAAATCCCAAAAACCTTTCTATATATTTT
261 GTTTATTTATTTCTTTTCTTTTTACTATTATTATTACAAATCCCAAAAACCTTTCTATATATTCC
* * * *
54166018 ACCATAATATAATCTATCTAAAGTACTAATTAGATATATATTTGCTTAGGTTAG-TTTAACTTAG
326 ATCATAATATAATCTATCTAAAGTACTAATTAGATCTATTTTTGCTTAGGTTAGAGTTAA--TAG
* *
54166082 TGCTCGTGTCCCTTGTGTACAATCCTCGGAGTACTCATCTACTCCTAATTTCACATATTTTGTAA
389 TGCTCGCGTCCCTTGTGTACAATCCTCGGAGTACTCACCTACTCCTAATTTCACATATTTTGTAA
54166147 ATTCATGTCCAATATTATTAATTAAGTAAAATTCACTTATTTTAATAATAATTACTCATTAACAT
454 ATTCATGTCCAATATTATTAATTAAGTAAAATTCACTTATTTTAATAATAATTACTCATTAACAT
54166212 ATTTATTATGTCAAAAGGTGGTAA
519 ATTTATTATGTCAAAAGGTGGTAA
* *
54166236 ATATATATAGAAAAATCCTAAATAATTTTGAGTTTACACCTATCCATGAACAACTTAACCCCGAA
1 AAATATATAGAAAAATCCTATATAATTTTGAGTTTACACCTATCCATGAACAACTTAACCCCGAA
* * *
54166301 CCGGTCTGGACAGTGAGGTCGAGAGATAAATAGTTCTTCCTGACCCCTTATTCTAGTGGAAGATC
66 CCGGTCTGGACTGTGAGGTCGAGAGATAAATAGTTCTTCCTGACTCGTTATTCTAGTGGAAGATC
*
54166366 GAAAGATCCAGCTGGGGTATCGACTAGTTGATTGAACAAGAAAACCTGAAGCGATAGTTGGTTAT
131 GAAAGATCCAGCTGGGGTATCGACTAGTTGATTGAACAAGAAAACCCGAAGCGATAGTTGGTTAT
* * * *
54166431 GATTACCGAAGCGATAGTTGGTTATGATCACCCATGCTTGGATTTGACAGGTTCTTCTATTTTAT
196 GATTACCGAAGCG--A----GCTA--ATCACCCATGCTAGGATTTGACAGGTTCTGCTATTTGAT
*
54166496 TTCTTGTAGTTTATTTATTTCTTTTCTTTTTACTATTATTATTACAAATCCCAAAAACCTTTCTA
253 TTCTTGTTGTTTATTTATTTCTTTTCTTTTTACTATTATTATTACAAATCCCAAAAACCTTTCTA
*
54166561 TATATTCCATCATAATATAATCTATCTAAAGTACTAATTAGATCTATTTTTGCTTAGTTTAGAGT
318 TATATTCCATCATAATATAATCTATCTAAAGTACTAATTAGATCTATTTTTGCTTAGGTTAGAGT
* *
54166626 T-A-AGTGTTCGCGTCCCTTGTGTACAATCCTCAGAGTACTCACCTACTCCTAATTTCACATATT
383 TAATAGTGCTCGCGTCCCTTGTGTACAATCCTCGGAGTACTCACCTACTCCTAATTTCACATATT
54166689 TTGTAAATTCATGTCCAATATTATTAATTAAGTAAAATTCACTTATTTTAATAATAATTACTCAT
448 TTGTAAATTCATGTCCAATATTATTAATTAAGTAAAATTCACTTATTTTAATAATAATTACTCAT
54166754 TAACATATTTATTATGTCAAAAGGTGGTAA
513 TAACATATTTATTATGTCAAAAGGTGGTAA
** *
54166784 AAATATATAGAAAAATCCTATATAATTTTGAGTTTACACCTATCCATGAACTTCTTAATCCCGAA
1 AAATATATAGAAAAATCCTATATAATTTTGAGTTTACACCTATCCATGAACAACTTAACCCCGAA
* * *
54166849 CCGGTCTGGATTGTGAGGTCGAGAGATAAATAGCTCTTCTTGACTCGTTATTCTAGTGGAAGATC
66 CCGGTCTGGACTGTGAGGTCGAGAGATAAATAGTTCTTCCTGACTCGTTATTCTAGTGGAAGATC
* * * *
54166914 GAAAGATCCAGCTAGAGTATCGACTAGTTAATTGAACAAGAAAACCCGAAGCGATGGTTGGTTAT
131 GAAAGATCCAGCTGGGGTATCGACTAGTTGATTGAACAAGAAAACCCGAAGCGATAGTTGGTTAT
54166979 GATTACCGAAGCGAGCTAATCACCCATGCTAGGATTTGACAGGTTCTGCTATTTGATTTCTTGTT
196 GATTACCGAAGCGAGCTAATCACCCATGCTAGGATTTGACAGGTTCTGCTATTTGATTTCTTGTT
54167044 GTTTATTTATTTCTTTTCTTTTTACTATTATTATTACAAATCCCAAAAACCTTTCTATATA-TCT
261 GTTTATTTATTTCTTTTCTTTTTACTATTATTATTACAAATCCCAAAAACCTTTCTATATATTC-
*
54167108 CATCATAATATAATCTATCTAAAGTACTAATTAGATCTATTTATGCTTAGGTTAGAGTTAACTTA
325 CATCATAATATAATCTATCTAAAGTACTAATTAGATCTATTTTTGCTTAGGTTAGAGTTAA--TA
* * * *
54167173 GTGCTCACATCCCTTGGGTACAATCCTCGGAGTATTCACCTACTC
388 GTGCTCGCGTCCCTTGTGTACAATCCTCGGAGTACTCACCTACTC
54167218 TGTCATAACT
Statistics
Matches: 901, Mismatches: 67, Indels: 27
0.91 0.07 0.03
Matches are distributed among these distances:
539 2 0.00
540 161 0.18
541 1 0.00
542 3 0.00
543 188 0.21
544 40 0.04
545 1 0.00
546 1 0.00
548 344 0.38
549 3 0.00
551 155 0.17
552 2 0.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (542 bp):
AAATATATAGAAAAATCCTATATAATTTTGAGTTTACACCTATCCATGAACAACTTAACCCCGAA
CCGGTCTGGACTGTGAGGTCGAGAGATAAATAGTTCTTCCTGACTCGTTATTCTAGTGGAAGATC
GAAAGATCCAGCTGGGGTATCGACTAGTTGATTGAACAAGAAAACCCGAAGCGATAGTTGGTTAT
GATTACCGAAGCGAGCTAATCACCCATGCTAGGATTTGACAGGTTCTGCTATTTGATTTCTTGTT
GTTTATTTATTTCTTTTCTTTTTACTATTATTATTACAAATCCCAAAAACCTTTCTATATATTCC
ATCATAATATAATCTATCTAAAGTACTAATTAGATCTATTTTTGCTTAGGTTAGAGTTAATAGTG
CTCGCGTCCCTTGTGTACAATCCTCGGAGTACTCACCTACTCCTAATTTCACATATTTTGTAAAT
TCATGTCCAATATTATTAATTAAGTAAAATTCACTTATTTTAATAATAATTACTCATTAACATAT
TTATTATGTCAAAAGGTGGTAA
Found at i:54172663 original size:56 final size:50
Alignment explanation
Indices: 54172566--54172864 Score: 292
Period size: 50 Copynumber: 5.9 Consensus size: 50
54172556 CATTTGGGTA
* * **
54172566 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGATT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGC---ACCGAGA-T
54172620 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 A--AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* * * * * *
54172672 GAGAGGTTCGATGTAAGATCATGCCTGGGACACGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* * * * *
54172722 AAGAGGTCCCATGTAAGATCATGTCTGGGACATGACGCTCGCACTGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
** * * * *
54172772 AAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* ** * * * *
54172822 GAGAACTCTCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
54172865 GTACAAGAAA
Statistics
Matches: 204, Mismatches: 39, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
50 158 0.77
52 1 0.00
53 5 0.02
54 1 0.00
56 39 0.19
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
Found at i:54172898 original size:49 final size:50
Alignment explanation
Indices: 54172572--54172913 Score: 154
Period size: 50 Copynumber: 6.7 Consensus size: 50
54172562 GGTAAAGAGA
* ** * **
54172572 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCA--CCT-ACA--A-GAGAAC
* * * * * **
54172628 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCTACAAGAGAAC
* * * * * * * * * **
54172678 TTCGATGTAAGATCATGCCTGGGACACGGCGTTGGCACCGAGATA-AGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCTACA-AGAGAAC
* * * ** * * **
54172728 TCCCATGTAAGATCATGTCTGGGACATGACGCTCGCA-CTGAGATA-AGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCT-ACA-AGAGAAC
** * * * *
54172778 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCTACAAGAGAAC
* * *
54172828 TCTCATGTAAGACCATATCTGGGATATGGCATTGGCA-GTACAAGA-AAC
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCTACAAGAGAAC
* * *
54172876 ATCCCATGTAAGACTATGTCTGGGATATAGCTTTGGCA
1 -TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCA
54172914 TGTTATATTT
Statistics
Matches: 236, Mismatches: 45, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
48 3 0.01
49 38 0.16
50 154 0.65
51 2 0.01
53 3 0.01
56 36 0.15
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCTACAAGAGAAC
Found at i:54176361 original size:24 final size:24
Alignment explanation
Indices: 54176333--54176384 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
54176323 TTAGTAAGTC
* *
54176333 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
54176357 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
54176381 AAAT
1 AAAT
54176385 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:54182597 original size:18 final size:17
Alignment explanation
Indices: 54182556--54182606 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 17
54182546 TTTTTTGACT
54182556 ACTCTC-TTCTTTTTC-
1 ACTCTCTTTCTTTTTCA
*
54182571 ACTC-GTTTCTTTTTCA
1 ACTCTCTTTCTTTTTCA
54182587 ATCTCTCTTTCTTTTTCA
1 A-CTCTCTTTCTTTTTCA
54182605 AC
1 AC
54182607 AACAACACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 13 0.43
16 1 0.03
17 4 0.13
18 12 0.40
ACGTcount: A:0.12, C:0.29, G:0.02, T:0.57
Consensus pattern (17 bp):
ACTCTCTTTCTTTTTCA
Found at i:54189467 original size:19 final size:19
Alignment explanation
Indices: 54189443--54189483 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
54189433 CGGGTAGCCG
54189443 ATTCGGGTCTAGGAATTAA
1 ATTCGGGTCTAGGAATTAA
54189462 ATTCGGGTCTAGGAATTAA
1 ATTCGGGTCTAGGAATTAA
54189481 ATT
1 ATT
54189484 TGGGAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (19 bp):
ATTCGGGTCTAGGAATTAA
Found at i:54193150 original size:21 final size:21
Alignment explanation
Indices: 54193126--54193197 Score: 60
Period size: 24 Copynumber: 3.3 Consensus size: 21
54193116 CACTACATAA
54193126 TATATATTATGTTTTTGTTTT
1 TATATATTATGTTTTTGTTTT
*
54193147 TATAATGCATTATATTTTTG--TT
1 TAT-AT--ATTATGTTTTTGTTTT
54193169 T-TATATTATGTTATTTGTGTTT
1 TATATATTATGTT-TTTGT-TTT
*
54193191 TTTATAT
1 TATATAT
54193198 GTTTACGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
18 7 0.17
19 4 0.10
20 2 0.05
21 4 0.10
22 8 0.20
23 5 0.12
24 11 0.27
ACGTcount: A:0.22, C:0.01, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATATTATGTTTTTGTTTT
Found at i:54193200 original size:20 final size:21
Alignment explanation
Indices: 54193128--54193200 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
54193118 CTACATAATA
54193128 TATATTATGTT-TTTGT-TTT
1 TATATTATGTTATTTGTGTTT
* *
54193147 TATAATGCAT-TATATTTTTGTTT
1 TAT-AT-TATGT-TATTTGTGTTT
54193170 TATATTATGTTATTTGTGTTT
1 TATATTATGTTATTTGTGTTT
*
54193191 TTTA-TATGTT
1 TATATTATGTT
54193201 TACGTTTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
19 3 0.07
20 9 0.21
21 18 0.42
22 7 0.16
23 6 0.14
ACGTcount: A:0.21, C:0.01, G:0.11, T:0.67
Consensus pattern (21 bp):
TATATTATGTTATTTGTGTTT
Found at i:54193450 original size:21 final size:21
Alignment explanation
Indices: 54193425--54193478 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
54193415 CTATTTTTAA
54193425 TCTCATTGCTACCATATCCAC
1 TCTCATTGCTACCATATCCAC
*
54193446 TCTCATTGCTACCATATTCAC
1 TCTCATTGCTACCATATCCAC
*
54193467 TCTCACTGCTAC
1 TCTCATTGCTAC
54193479 AATAACTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.37, G:0.06, T:0.35
Consensus pattern (21 bp):
TCTCATTGCTACCATATCCAC
Found at i:54201258 original size:2 final size:2
Alignment explanation
Indices: 54201251--54201278 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
54201241 GGTTCACTTT
54201251 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
54201279 GTTTGAGACA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:54209186 original size:9 final size:8
Alignment explanation
Indices: 54209165--54209216 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
54209155 TCATACTAAT
54209165 TTTTTTAA
1 TTTTTTAA
54209173 CTTTTTATAA
1 -TTTTT-TAA
*
54209183 TTTTTTTA
1 TTTTTTAA
54209191 -TTTTTAA
1 TTTTTTAA
54209198 TTTTTTTAA
1 -TTTTTTAA
*
54209207 TTTTTAAA
1 TTTTTTAA
54209215 TT
1 TT
54209217 ATTTGTTGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
7 6 0.16
8 11 0.30
9 17 0.46
10 3 0.08
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTTTAA
Found at i:54209211 original size:16 final size:16
Alignment explanation
Indices: 54209161--54209213 Score: 72
Period size: 16 Copynumber: 3.2 Consensus size: 16
54209151 TACTTCATAC
54209161 TAATTTTTTTAACTTTTT
1 TAATTTTTTTAA--TTTT
54209179 ATAATTTTTTT-ATTTT
1 -TAATTTTTTTAATTTT
54209195 TAATTTTTTTAATTTT
1 TAATTTTTTTAATTTT
54209211 TAA
1 TAA
54209214 ATTATTTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
15 10 0.30
16 12 0.36
18 1 0.03
19 10 0.30
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (16 bp):
TAATTTTTTTAATTTT
Found at i:54209415 original size:25 final size:26
Alignment explanation
Indices: 54209356--54209416 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 26
54209346 ACTCTTTTTT
* * *
54209356 AAATGTTAATAACCAAATTTAGCTAAA
1 AAATG-TAAAAACCAAATTGAGCAAAA
*
54209383 AAGT-TAAAAACCAAATTGA-CAAAA
1 AAATGTAAAAACCAAATTGAGCAAAA
54209407 AAATGTAAAA
1 AAATGTAAAA
54209417 GTTGAGGACT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
24 7 0.25
25 18 0.64
27 3 0.11
ACGTcount: A:0.59, C:0.10, G:0.08, T:0.23
Consensus pattern (26 bp):
AAATGTAAAAACCAAATTGAGCAAAA
Found at i:54210265 original size:15 final size:17
Alignment explanation
Indices: 54210240--54210271 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
54210230 ATCGATAGAG
54210240 TTTAGAGTTTT-TCTTT
1 TTTAGAGTTTTGTCTTT
54210256 TTTA-AGTTTTGTCTTT
1 TTTAGAGTTTTGTCTTT
54210272 ATTGGGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.12, C:0.06, G:0.12, T:0.69
Consensus pattern (17 bp):
TTTAGAGTTTTGTCTTT
Found at i:54211750 original size:25 final size:25
Alignment explanation
Indices: 54211722--54211781 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
54211712 TGGTAAGCTC
54211722 ATACGAGCTGCAAATCGGGAAACTT
1 ATACGAGCTGCAAATCGGGAAACTT
* * *
54211747 ATACAAGCTGCAAATTGGGAAGCTT
1 ATACGAGCTGCAAATCGGGAAACTT
54211772 ATACGAGCTG
1 ATACGAGCTG
54211782 TGGTGTGTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (25 bp):
ATACGAGCTGCAAATCGGGAAACTT
Found at i:54213997 original size:21 final size:20
Alignment explanation
Indices: 54213966--54214022 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
54213956 TTCTCAATCC
54213966 AATATACATTTCAATTGCACAAT
1 AATAT-CATTTCAATT-CA-AAT
54213989 AAT-TCATTT-AATTCAAAT
1 AATATCATTTCAATTCAAAT
*
54214007 CATATCATTTGCAATT
1 AATATCATTT-CAATT
54214023 TCCATTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 5 0.17
19 8 0.27
20 4 0.13
21 9 0.30
22 1 0.03
23 3 0.10
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (20 bp):
AATATCATTTCAATTCAAAT
Found at i:54215679 original size:51 final size:50
Alignment explanation
Indices: 54215616--54215802 Score: 216
Period size: 51 Copynumber: 3.7 Consensus size: 50
54215606 TCGGTTTGCA
* *
54215616 TAGTAGCATGCACATAGTACTACACATGTGACCATTACCATCC-GATACCCG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATCCAG-TACACG
* * * * * * *
54215667 TAGTATCCTGCACATAGTACTACACACGTGATCGAAACTATCCAGTACGCA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCATCCAGTACACG
* *
54215718 TAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCAGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TCCAGTACACG
*
54215768 TAGTAGCCTGCACATAGTACTACACAAGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAT
54215803 CACTTTCACT
Statistics
Matches: 113, Mismatches: 19, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
49 2 0.02
50 41 0.36
51 67 0.59
52 3 0.03
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATACCATCCAGTACACG
Found at i:54215834 original size:101 final size:100
Alignment explanation
Indices: 54215615--54215798 Score: 237
Period size: 101 Copynumber: 1.8 Consensus size: 100
54215605 TTCGGTTTGC
* * * * *
54215615 ATAGTAGCATGCACATAGTACTACACATGTGACCATTACCATCCGATACCCGTAGTATCCTGCAC
1 ATAGTAGCCTACACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTGCAC
* *
54215680 ATAGTACTACACACGTGATCGAAACTATCCAGTACG
65 ATAGTACTACACAAGTGATCCAAACTATCCAGTACG
* *
54215716 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCC-AGTACACGTAGTAGCCTGC
1 -ATAGTAGCCTACACATAGTACTACACATGCGACCATACCA-TCCGA-TACACGTAGTAGCCTGC
54215779 ACATAGTACTACACAAGTGA
63 ACATAGTACTACACAAGTGA
54215799 CCATCACTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
100 5 0.07
101 37 0.50
102 32 0.43
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (100 bp):
ATAGTAGCCTACACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTGCACA
TAGTACTACACAAGTGATCCAAACTATCCAGTACG
Found at i:54218366 original size:16 final size:18
Alignment explanation
Indices: 54218340--54218372 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54218330 TAACATTGTG
54218340 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
54218357 TTGA-AAAATTAATTTA
1 TTGAGAAAATTAATTTA
54218373 TCTTATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:54222433 original size:14 final size:14
Alignment explanation
Indices: 54222414--54222452 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
54222404 TCAGGAAAGT
54222414 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
54222428 AAATCATTTTCCGG
1 AAATCATTTTCCAG
*
54222442 AAACCATTTTC
1 AAATCATTTTC
54222453 AATGAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:54224267 original size:20 final size:20
Alignment explanation
Indices: 54224220--54224267 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
54224210 TGAATCGAGT
* *
54224220 TAAGTTTACATTTCATTTTA
1 TAAGATTACATTTCAATTTA
* * *
54224240 AAATATTACATTTGAATTTA
1 TAAGATTACATTTCAATTTA
54224260 TAAGATTA
1 TAAGATTA
54224268 ATTGATATCT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (20 bp):
TAAGATTACATTTCAATTTA
Found at i:54228526 original size:24 final size:24
Alignment explanation
Indices: 54228489--54228578 Score: 92
Period size: 24 Copynumber: 3.8 Consensus size: 24
54228479 TCTATAAGGC
*
54228489 CCTTT-TGGCTTATTCTGTAAGTG
1 CCTTTGTGGCATATTCTGTAAGTG
* * *
54228512 CCTTTGTGGCGTATTTTGAAAGTG
1 CCTTTGTGGCATATTCTGTAAGTG
* * * *
54228536 CCTTTATGGCATATTATATAAATG
1 CCTTTGTGGCATATTCTGTAAGTG
*
54228560 CCTTTGTAGCATATTCTGT
1 CCTTTGTGGCATATTCTGT
54228579 GTTGTGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
23 5 0.09
24 48 0.91
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.44
Consensus pattern (24 bp):
CCTTTGTGGCATATTCTGTAAGTG
Found at i:54239726 original size:24 final size:24
Alignment explanation
Indices: 54239672--54239751 Score: 115
Period size: 24 Copynumber: 3.3 Consensus size: 24
54239662 TCATGTAAAT
54239672 GTATGCTCACACGAGCTGTAAATCA
1 GTATGCTCACACGAGCTGT-AATCA
** *
54239697 ACATGCTCACACGAGCTGTAATCG
1 GTATGCTCACACGAGCTGTAATCA
*
54239721 GTATGCTCTCACGAGCTGTAATCA
1 GTATGCTCACACGAGCTGTAATCA
54239745 GTATGCT
1 GTATGCT
54239752 TTCATGAGCT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
24 31 0.65
25 17 0.35
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (24 bp):
GTATGCTCACACGAGCTGTAATCA
Found at i:54239760 original size:24 final size:24
Alignment explanation
Indices: 54239672--54239763 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
54239662 TCATGTAAAT
*
54239672 GTATGCTCACACGAGCTGTAAATCA
1 GTATGCTCTCACGAGCTGT-AATCA
** * *
54239697 ACATGCTCACACGAGCTGTAATCG
1 GTATGCTCTCACGAGCTGTAATCA
54239721 GTATGCTCTCACGAGCTGTAATCA
1 GTATGCTCTCACGAGCTGTAATCA
* *
54239745 GTATGCTTTCATGAGCTGT
1 GTATGCTCTCACGAGCTGT
54239764 GGGTTAGAAC
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
24 41 0.71
25 17 0.29
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (24 bp):
GTATGCTCTCACGAGCTGTAATCA
Found at i:54248718 original size:24 final size:24
Alignment explanation
Indices: 54248650--54248719 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
54248640 TGTAAATCAA
* *
54248650 TATACTCACAC-GAGCTGTAATTGG
1 TATACTCTCACAG-GCTGTAATCGG
* * * *
54248674 TATGCTCTCACAAGTTATAATCGG
1 TATACTCTCACAGGCTGTAATCGG
54248698 TATACTCTCACAGGCTGTAATC
1 TATACTCTCACAGGCTGTAATC
54248720 TACATGCTTT
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (24 bp):
TATACTCTCACAGGCTGTAATCGG
Found at i:54248750 original size:24 final size:24
Alignment explanation
Indices: 54248658--54248763 Score: 106
Period size: 24 Copynumber: 4.4 Consensus size: 24
54248648 AATATACTCA
*
54248658 CACGAGCTGTAATTGGTATGCTCT
1 CACGAGCTGTAATCGGTATGCTCT
* * * *
54248682 CACAAGTTATAATCGGTATACTCT
1 CACGAGCTGTAATCGGTATGCTCT
*** *
54248706 CAC-AGGCTGTAATCTACATGCTTT
1 CACGA-GCTGTAATCGGTATGCTCT
*
54248730 CACGAGCTGTAATCGGTATGCTAT
1 CACGAGCTGTAATCGGTATGCTCT
54248754 CACGAGCTGT
1 CACGAGCTGT
54248764 GGGTCGAAAC
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
23 1 0.02
24 62 0.97
25 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (24 bp):
CACGAGCTGTAATCGGTATGCTCT
Found at i:54253037 original size:27 final size:27
Alignment explanation
Indices: 54253005--54253388 Score: 524
Period size: 27 Copynumber: 14.2 Consensus size: 27
54252995 TATAACAGAT
* *
54253005 ATTTTACCCTTC-AGGGGCATTTTGATC
1 ATTTTACCCTTCGA-GGGTATTTCGATC
* *
54253032 AATTTACCTTTCGAGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGATC
* * *
54253059 ATTTTACCCTTCAAGGGTATTTTGGTC
1 ATTTTACCCTTCGAGGGTATTTCGATC
*
54253086 ATTTTACCCTTTGAGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGATC
54253113 ATTTTACCCTTCGAGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGATC
* *
54253140 GTTTTACCCTTCGAGGGTATTTTGATC
1 ATTTTACCCTTCGAGGGTATTTCGATC
54253167 ATTTTACCCTTCGAGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGATC
*
54253194 ATTTTACCCATCGAGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGATC
* *
54253221 ATTTTACCCTTCGAGGGTATTTCAATT
1 ATTTTACCCTTCGAGGGTATTTCGATC
* *
54253248 ATTTTACCCTTCGAGGGTATTTCAATT
1 ATTTTACCCTTCGAGGGTATTTCGATC
*
54253275 ATTTTACCCTTCGAGGGTGTTTC-AGTC
1 ATTTTACCCTTCGAGGGTATTTCGA-TC
*
54253302 ATTTTATCCTTCGAGGGTATTTC-AGTC
1 ATTTTACCCTTCGAGGGTATTTCGA-TC
*
54253329 ATTTTACCCTTTGAGGGTATTTCAGA-C
1 ATTTTACCCTTCGAGGGTATTTC-GATC
* *
54253356 ATTTTACCTTTCAAGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGATC
54253383 ATTTTA
1 ATTTTA
54253389 GGCCCATTAC
Statistics
Matches: 321, Mismatches: 31, Indels: 10
0.89 0.09 0.03
Matches are distributed among these distances:
26 3 0.01
27 316 0.98
28 1 0.00
29 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGATC
Found at i:54264224 original size:24 final size:24
Alignment explanation
Indices: 54264188--54264236 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
54264178 TGCTTAGTTC
*
54264188 TTTACAGGGTGATTTTGGTCATTA
1 TTTACAGGATGATTTTGGTCATTA
54264212 TTTACAGGATGATTTTGGTCATTA
1 TTTACAGGATGATTTTGGTCATTA
54264236 T
1 T
54264237 AGCCATACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.47
Consensus pattern (24 bp):
TTTACAGGATGATTTTGGTCATTA
Found at i:54264343 original size:3 final size:3
Alignment explanation
Indices: 54264335--54264393 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
54264325 TACACCTTAA
54264335 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
54264383 AAT AAT AAT AA
1 AAT AAT AAT AA
54264394 ACAATTATGC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:54266136 original size:31 final size:31
Alignment explanation
Indices: 54266098--54266160 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
54266088 GAGAAAAAAA
*
54266098 TCACATGAAGTAAACAAATGCTCTAGGGCCT
1 TCACATGAAGCAAACAAATGCTCTAGGGCCT
54266129 TCACATGAAGCAAACAAATGCTCTAGGGCCT
1 TCACATGAAGCAAACAAATGCTCTAGGGCCT
54266160 T
1 T
54266161 TTAAGCACCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (31 bp):
TCACATGAAGCAAACAAATGCTCTAGGGCCT
Found at i:54269482 original size:27 final size:27
Alignment explanation
Indices: 54269436--54269487 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
54269426 CACCGCCTCG
*
54269436 TCCTCCGCGTCCTCCGCCGCCGCCGCC
1 TCCTCCGCGTCCACCGCCGCCGCCGCC
* * *
54269463 TCCTCGGCGTCCACCTCCGCGGCCG
1 TCCTCCGCGTCCACCGCCGCCGCCG
54269488 GAGTTGGGAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.02, C:0.58, G:0.25, T:0.15
Consensus pattern (27 bp):
TCCTCCGCGTCCACCGCCGCCGCCGCC
Found at i:54269930 original size:27 final size:27
Alignment explanation
Indices: 54269890--54269965 Score: 95
Period size: 27 Copynumber: 2.8 Consensus size: 27
54269880 CACTCTGGTC
54269890 GTGCCAAGATGATTGGCGGCACCAAAT-
1 GTGCCAAGATGATTGGCGGCACC-AATG
54269917 GTGCCAAGGA-GATTGGCGGCACCAATG
1 GTGCCAA-GATGATTGGCGGCACCAATG
*
54269944 GTGCCATA-CTGATTGGCGGCAC
1 GTGCCA-AGATGATTGGCGGCAC
54269966 TACTCGTGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
26 3 0.07
27 38 0.86
28 3 0.07
ACGTcount: A:0.25, C:0.24, G:0.33, T:0.18
Consensus pattern (27 bp):
GTGCCAAGATGATTGGCGGCACCAATG
Found at i:54270204 original size:3 final size:3
Alignment explanation
Indices: 54270196--54270251 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
54270186 TTTTAGTTAG
54270196 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
54270244 TAT TAT TA
1 TAT TAT TA
54270252 NNNNNNNNNN
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:54271054 original size:18 final size:18
Alignment explanation
Indices: 54271027--54271064 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
54271017 GGTTGGTAGT
54271027 GAAGAAGAAGGTGCTGGC
1 GAAGAAGAAGGTGCTGGC
* *
54271045 GAAGAGGAAGGTGGTGGC
1 GAAGAAGAAGGTGCTGGC
54271063 GA
1 GA
54271065 TCATTGGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.50, T:0.11
Consensus pattern (18 bp):
GAAGAAGAAGGTGCTGGC
Found at i:54278339 original size:45 final size:44
Alignment explanation
Indices: 54278284--54278422 Score: 131
Period size: 45 Copynumber: 3.1 Consensus size: 44
54278274 AACACCACCC
* *
54278284 TTATAATCAATAGTACTCAGTGAAATCAGCACATAGCAACTACCT
1 TTATACTCAATGGTACTCAGTGAAATCAGCACATAGCAA-TACCT
*** * *
54278329 TTATACTCAATGGTACAGGGTGAATTCAACACATAGCAAT-CACT
1 TTATACTCAATGGTACTCAGTGAAATCAGCACATAGCAATAC-CT
*
54278373 TATATAAC-CATTGGTA-TCCAGTGAAATCAGCACATAGCAATCACCT
1 T-TAT-ACTCAATGGTACT-CAGTGAAATCAGCACATAGCAAT-ACCT
54278419 TTAT
1 TTAT
54278423 TTTCATTAAT
Statistics
Matches: 75, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
43 1 0.01
44 4 0.05
45 64 0.85
46 5 0.07
47 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (44 bp):
TTATACTCAATGGTACTCAGTGAAATCAGCACATAGCAATACCT
Found at i:54278436 original size:45 final size:45
Alignment explanation
Indices: 54278301--54278463 Score: 138
Period size: 45 Copynumber: 3.6 Consensus size: 45
54278291 CAATAGTACT
* *
54278301 CAGTGAAATCAGCACATAGCAA-CTACCTTTATACTCAATGGTA--
1 CAGTGAAATCAGCACATAGCAATC-ACCTTTATATTCATTGGTATC
* * **
54278344 CAGGGTGAATTCAACACATAGCAATCA-CTTATATAACCATTGGTATC
1 CA--GTGAAATCAGCACATAGCAATCACCTT-TATATTCATTGGTATC
* **
54278391 CAGTGAAATCAGCACATAGCAATCACCTTTATTTTCATTAATATC
1 CAGTGAAATCAGCACATAGCAATCACCTTTATATTCATTGGTATC
* * *
54278436 CGGTGGAATCAGCGA-ATAGCATTCACCT
1 CAGTGAAATCAGC-ACATAGCAATCACCT
54278464 ATATTTCCAA
Statistics
Matches: 97, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
43 2 0.02
44 3 0.03
45 85 0.88
46 5 0.05
47 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (45 bp):
CAGTGAAATCAGCACATAGCAATCACCTTTATATTCATTGGTATC
Found at i:54279024 original size:50 final size:48
Alignment explanation
Indices: 54278858--54279084 Score: 228
Period size: 50 Copynumber: 4.7 Consensus size: 48
54278848 TAGGACGCCA
* * * * * * *
54278858 ATGCCATATCCCAGATATGGTCTTACATGGGATC-ACATATCGATACCG
1 ATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCCATGTCG-TGCCG
* * *
54278906 ATGCCATGTCCCAGACATGGTCTTAC-TCTGGCCCT-CATCTCGAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACAT-TGGCTCTCCATGTCGTGCCG
54278953 ATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCCTATGTCCGTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCC-ATGT-CGTGCCG
* * * * *
54279003 ATGCCATATCCCAGACATGGTCTTACACTAGCACTCC-TCGGTCTGTGCTG
1 ATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCCAT--GTC-GTGCCG
54279053 ATGCCATGTCCCAGACATGGTCTTACATTGGC
1 ATGCCATGTCCCAGACATGGTCTTACATTGGC
54279085 ACACTCACTG
Statistics
Matches: 151, Mismatches: 19, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
47 36 0.24
48 36 0.24
49 4 0.03
50 75 0.50
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.28
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCCATGTCGTGCCG
Found at i:54279079 original size:100 final size:97
Alignment explanation
Indices: 54278903--54279084 Score: 274
Period size: 97 Copynumber: 1.8 Consensus size: 97
54278893 CATATCGATA
* * * *
54278903 CCGATGCCATGTCCCAGACATGGTCTTACTCTGGCCCTCATCTCGAGCCGATGCCATGTCCCAGA
1 CCGATGCCATATCCCAGACATGGTCTTACACTAGCACTCATCTCGAGCCGATGCCATGTCCCAGA
54278968 CATGGTCTTACATTGGCTCTCCTATGTCCGTG
66 CATGGTCTTACATTGGCTCTCCTATGTCCGTG
* * *
54279000 CCGATGCCATATCCCAGACATGGTCTTACACTAGCACTCCTCGGTCTGTGCTGATGCCATGTCCC
1 CCGATGCCATATCCCAGACATGGTCTTACACTAGCACTCATC--TC-GAGCCGATGCCATGTCCC
54279065 AGACATGGTCTTACATTGGC
63 AGACATGGTCTTACATTGGC
54279085 ACACTCACTG
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
97 37 0.49
99 2 0.03
100 36 0.48
ACGTcount: A:0.18, C:0.33, G:0.21, T:0.27
Consensus pattern (97 bp):
CCGATGCCATATCCCAGACATGGTCTTACACTAGCACTCATCTCGAGCCGATGCCATGTCCCAGA
CATGGTCTTACATTGGCTCTCCTATGTCCGTG
Found at i:54280619 original size:3 final size:3
Alignment explanation
Indices: 54280613--54280706 Score: 51
Period size: 3 Copynumber: 33.3 Consensus size: 3
54280603 CTTCCTTCCC
* * *
54280613 TCT TCT TCT TCT TCT T-T TTT TC- TCT TC- TCT TCT CCT T-T CCT T-T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * *
54280656 TCT T-T CCT TCT TTT TCTT TCT T-T T-T TCT TCT CCTT TCC TCT TCT
1 TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TC-T TCT TCT TCT
54280700 TCT TCT T
1 TCT TCT T
54280707 TCTTTTTTTT
Statistics
Matches: 69, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
2 14 0.20
3 50 0.72
4 5 0.07
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:54280675 original size:4 final size:4
Alignment explanation
Indices: 54280654--54280811 Score: 123
Period size: 4 Copynumber: 38.0 Consensus size: 4
54280644 CTCCTTTCCT
*
54280654 TTTC TTTC CTTC -TT- TTTC TTTC TTT- TTTC TTCTCC TTTCC TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C T-TTC
*
54280699 -TTC -TTC TTTC TTT- TTT- TTCTC TTCTCC TTTCC TTTTC TTTC CTTC
1 TTTC TTTC TTTC TTTC TTTC TT-TC TT-T-C TTT-C -TTTC TTTC TTTC
*
54280744 TGTTGC TTTC TTTCC TCTCC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 T-TT-C TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
54280792 TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC
54280812 CCTCTCCTTC
Statistics
Matches: 134, Mismatches: 5, Indels: 30
0.79 0.03 0.18
Matches are distributed among these distances:
3 18 0.13
4 80 0.60
5 22 0.16
6 14 0.10
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:54280728 original size:21 final size:22
Alignment explanation
Indices: 54280630--54280744 Score: 92
Period size: 21 Copynumber: 5.7 Consensus size: 22
54280620 CTTCTTCTTT
54280630 TTTTCTCTTCTCTTCTCCTTTCC
1 TTTTCT-TTCTCTTCTCCTTTCC
*
54280653 TTTTCTTTC-CTTCT--TTTTC
1 TTTTCTTTCTCTTCTCCTTTCC
*
54280672 -TTTCTTTTTTCTTCTCCTTTCC
1 TTTTC-TTTCTCTTCTCCTTTCC
*
54280694 ---TC--T-TCTTCTTCTTT-C
1 TTTTCTTTCTCTTCTCCTTTCC
*
54280709 TTTTTTTTCTCTTCTCCTTTCC
1 TTTTCTTTCTCTTCTCCTTTCC
54280731 TTTTCTTTC-CTTCT
1 TTTTCTTTCTCTTCT
54280745 GTTGCTTTCT
Statistics
Matches: 74, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
15 1 0.01
16 10 0.14
17 1 0.01
18 5 0.07
19 7 0.09
20 8 0.11
21 20 0.27
22 16 0.22
23 6 0.08
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTCTTTCTCTTCTCCTTTCC
Found at i:54280737 original size:78 final size:80
Alignment explanation
Indices: 54280587--54280756 Score: 258
Period size: 78 Copynumber: 2.2 Consensus size: 80
54280577 ATTACCTTTT
*
54280587 TTTTTCTTT-TTTTTTCCTTCCTTCCCTCTTCTTCTTCTTCTTTTTTTCTCTTCTCTTCTCCTTT
1 TTTTTCTTTCTTTTTTCCTTCCTTCCCTCTTCTTCTTCTTCTCTTTTTCTCTTCTCTTCTCCTTT
54280651 CCTTTTCTTTCCTTC
66 CCTTTTCTTTCCTTC
* *
54280666 TTTTTCTTTCTTTTTTCTTCTCCTTTCCTCTTCTTCTTCTT-TCTTTTT-T-TTCTCTTCTCCTT
1 TTTTTCTTTCTTTTTTCCT-TCCTTCCCTCTTCTTCTTCTTCTCTTTTTCTCTTCTCTTCTCCTT
54280728 TCCTTTTCTTTCCTTC
65 TCCTTTTCTTTCCTTC
* *
54280744 TGTTGCTTTCTTT
1 TTTTTCTTTCTTT
54280757 CCTCTCCTTT
Statistics
Matches: 84, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
78 40 0.48
79 10 0.12
80 14 0.17
81 20 0.24
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.68
Consensus pattern (80 bp):
TTTTTCTTTCTTTTTTCCTTCCTTCCCTCTTCTTCTTCTTCTCTTTTTCTCTTCTCTTCTCCTTT
CCTTTTCTTTCCTTC
Found at i:54280807 original size:78 final size:69
Alignment explanation
Indices: 54280654--54280810 Score: 162
Period size: 74 Copynumber: 2.2 Consensus size: 69
54280644 CTCCTTTCCT
*
54280654 TTTCTTTCCTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTCTTCTTCTTCTTTCTTTTTTTTCT
1 TTTCTTTCCTTCTTTTTCTTTCTTTTTTCCTCTCCTTTCCTCTTCTTCTTCTTTCTTTTTTTTCT
54280719 CTTC
66 CTTC
*
54280723 -TCCTTTCCTTTTCTTTCCTTCTGTTGCTTTCTTTCCTCTCCTTT-CT-TTCTTTCTTTCTTTC-
1 TTTCTTTCC--TTCTTT--TTCT-TT-CTTT-TTTCCTCTCCTTTCCTCTTC-TTC-TTCTTTCT
*
54280784 TTTCTTTCT-TTC
57 TTTTTTTCTCTTC
*
54280796 TTTCTTTCTTTCTTT
1 TTTCTTTCCTTCTTT
54280811 CCCTCTCCTT
Statistics
Matches: 73, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
68 7 0.10
70 6 0.08
72 10 0.14
73 8 0.11
74 23 0.32
75 19 0.26
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.69
Consensus pattern (69 bp):
TTTCTTTCCTTCTTTTTCTTTCTTTTTTCCTCTCCTTTCCTCTTCTTCTTCTTTCTTTTTTTTCT
CTTC
Found at i:54280891 original size:27 final size:27
Alignment explanation
Indices: 54280853--54280904 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
54280843 TATTATAACA
*
54280853 TTGGTGCCGCCAATGACTTTGGCACCT
1 TTGGTGCCGCCAATCACTTTGGCACCT
54280880 TTGGTGCCGCCAATCACTTTGGCAC
1 TTGGTGCCGCCAATCACTTTGGCAC
54280905 GACCAGGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.15, C:0.31, G:0.25, T:0.29
Consensus pattern (27 bp):
TTGGTGCCGCCAATCACTTTGGCACCT
Found at i:54281275 original size:27 final size:26
Alignment explanation
Indices: 54281224--54281275 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
54281214 TTGATTGTAT
**
54281224 AATTTTATTAAATATTAATTTAATTC
1 AATTTTATTAAATATTAATACAATTC
54281250 AATTTTCA-TAAATTATTAATACAATT
1 AATTTT-ATTAAA-TATTAATACAATT
54281276 ATCGATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (26 bp):
AATTTTATTAAATATTAATACAATTC
Found at i:54282477 original size:33 final size:33
Alignment explanation
Indices: 54282427--54282501 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 33
54282417 AAACTAATCC
* *
54282427 TCTCTCAAATTTCCTCTC-AATTTCTTCTAAATT
1 TCTCTC-AATTTCCTCTCAAATTCCTTCAAAATT
*
54282460 TCCTCTCAATTTGCTCTCAAATTCCTTCAAAATT
1 T-CTCTCAATTTCCTCTCAAATTCCTTCAAAATT
54282494 TCTCTCAA
1 TCTCTCAA
54282502 ATCCATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 18 0.49
34 19 0.51
ACGTcount: A:0.25, C:0.29, G:0.01, T:0.44
Consensus pattern (33 bp):
TCTCTCAATTTCCTCTCAAATTCCTTCAAAATT
Found at i:54282484 original size:22 final size:22
Alignment explanation
Indices: 54282427--54282503 Score: 97
Period size: 22 Copynumber: 3.5 Consensus size: 22
54282417 AAACTAATCC
54282427 TCTCTCAAATTTCCTCTCAATT
1 TCTCTCAAATTTCCTCTCAATT
54282449 TCT-TCTAAATTTCCTCTCAATT
1 TCTCTC-AAATTTCCTCTCAATT
54282471 TGCTCTCAAA-TTCCT-TCAAAATT
1 T-CTCTCAAATTTCCTCTC--AATT
54282494 TCTCTCAAAT
1 TCTCTCAAAT
54282504 CCATATTTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.08
22 33 0.67
23 10 0.20
24 2 0.04
ACGTcount: A:0.26, C:0.29, G:0.01, T:0.44
Consensus pattern (22 bp):
TCTCTCAAATTTCCTCTCAATT
Found at i:54282503 original size:11 final size:11
Alignment explanation
Indices: 54282427--54282503 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
54282417 AAACTAATCC
54282427 TCTCTCAAATT
1 TCTCTCAAATT
54282438 TCCTCTC-AATT
1 T-CTCTCAAATT
54282449 TCT-TCTAAATT
1 TCTCTC-AAATT
54282460 TCCTCTC-AATT
1 T-CTCTCAAATT
54282471 TGCTCTCAAATT
1 T-CTCTCAAATT
*
54282483 CCT-TCAAAATT
1 TCTCTC-AAATT
54282494 TCTCTCAAAT
1 TCTCTCAAAT
54282504 CCATATTTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
9 2 0.04
10 4 0.07
11 34 0.62
12 13 0.24
13 2 0.04
ACGTcount: A:0.26, C:0.29, G:0.01, T:0.44
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:54282527 original size:51 final size:51
Alignment explanation
Indices: 54282465--54282562 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
54282455 AAATTTCCTC
54282465 TCAATTTGCTCTCAAATTCCT-TCAAAATTTCTCTCAAATCCATATTTATTT
1 TCAATTTGCTCTCAAATTCCTCT-AAAATTTCTCTCAAATCCATATTTATTT
* * * *
54282516 TCAATTTGCTCTCAAGTTCCTCTTAAATTTCTCTTAAATCCTTATTT
1 TCAATTTGCTCTCAAATTCCTCTAAAATTTCTCTCAAATCCATATTT
54282563 TTAAATAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 41 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.03, T:0.47
Consensus pattern (51 bp):
TCAATTTGCTCTCAAATTCCTCTAAAATTTCTCTCAAATCCATATTTATTT
Found at i:54282597 original size:14 final size:14
Alignment explanation
Indices: 54282565--54282597 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
54282555 CCTTATTTTT
*
54282565 AAATAATTTAAAAA
1 AAATTATTTAAAAA
54282579 AAATTATTTAAAAA
1 AAATTATTTAAAAA
54282593 AAATT
1 AAATT
54282598 TAAACCGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATTATTTAAAAA
Found at i:54288637 original size:53 final size:54
Alignment explanation
Indices: 54288556--54288659 Score: 138
Period size: 53 Copynumber: 1.9 Consensus size: 54
54288546 AACATTTGAA
* *
54288556 TTAGACCTTCATTGTCTAGATGCCTTGCTTTCAACA-TAGTCACACTTGATCTC
1 TTAGACCTTCAGTGTCTAGATGACTTGCTTTCAACATTAGTCACACTTGATCTC
* * * * *
54288609 TTAGACCTTCCGTGTCTATATGAGTTGCTTTTAACATTAGTTACACTTGAT
1 TTAGACCTTCAGTGTCTAGATGACTTGCTTTCAACATTAGTCACACTTGAT
54288660 TTCTCCAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 30 0.70
54 13 0.30
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.40
Consensus pattern (54 bp):
TTAGACCTTCAGTGTCTAGATGACTTGCTTTCAACATTAGTCACACTTGATCTC
Found at i:54300566 original size:14 final size:14
Alignment explanation
Indices: 54300547--54300573 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54300537 ATTTATAATC
54300547 TAATATATTTTATG
1 TAATATATTTTATG
54300561 TAATATATTTTAT
1 TAATATATTTTAT
54300574 ATTGGGTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (14 bp):
TAATATATTTTATG
Found at i:54308861 original size:22 final size:22
Alignment explanation
Indices: 54308836--54308898 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 22
54308826 AGCACATGTG
*
54308836 AAAGAGAAACAATCAGGCAGCT
1 AAAGAGAAACAATCAGACAGCT
54308858 AAAGAGAAACAAACAATCAGACAGCT
1 AAAGAG----AAACAATCAGACAGCT
54308884 AAAGAGAAACAATCA
1 AAAGAGAAACAATCA
54308899 TGCATATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
22 15 0.42
26 21 0.58
ACGTcount: A:0.57, C:0.17, G:0.17, T:0.08
Consensus pattern (22 bp):
AAAGAGAAACAATCAGACAGCT
Found at i:54308871 original size:26 final size:26
Alignment explanation
Indices: 54308842--54308895 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
54308832 TGTGAAAGAG
*
54308842 AAACAATCAGGCAGCTAAAGAGAAAC
1 AAACAATCAGACAGCTAAAGAGAAAC
54308868 AAACAATCAGACAGCTAAAGAGAAAC
1 AAACAATCAGACAGCTAAAGAGAAAC
54308894 AA
1 AA
54308896 TCATGCATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.57, C:0.19, G:0.17, T:0.07
Consensus pattern (26 bp):
AAACAATCAGACAGCTAAAGAGAAAC
Found at i:54310199 original size:23 final size:23
Alignment explanation
Indices: 54310169--54310220 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 23
54310159 TGGAGGTGTT
*
54310169 ATTG-GTTCATCAAGTGGTGGTTG
1 ATTGTGTTC-TCAAGTGGTGGATG
54310192 A-TGTG-T-TCAAGTGGTGGATG
1 ATTGTGTTCTCAAGTGGTGGATG
54310212 ATTGTGTTC
1 ATTGTGTTC
54310221 GACGCTCAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
20 14 0.58
21 4 0.17
22 4 0.17
23 2 0.08
ACGTcount: A:0.17, C:0.08, G:0.35, T:0.40
Consensus pattern (23 bp):
ATTGTGTTCTCAAGTGGTGGATG
Found at i:54310203 original size:20 final size:21
Alignment explanation
Indices: 54310178--54310220 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
54310168 TATTGGTTCA
*
54310178 TCAAGTGGTGGTTGA-TGTGT
1 TCAAGTGGTGGATGATTGTGT
54310198 TCAAGTGGTGGATGATTGTGT
1 TCAAGTGGTGGATGATTGTGT
54310219 TC
1 TC
54310221 GACGCTCAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.16, C:0.07, G:0.37, T:0.40
Consensus pattern (21 bp):
TCAAGTGGTGGATGATTGTGT
Found at i:54313518 original size:17 final size:18
Alignment explanation
Indices: 54313492--54313530 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
54313482 CCTAGGAAGC
54313492 GGGCTAAAATTTTTA-TT
1 GGGCTAAAATTTTTATTT
*
54313509 GGGCTGAAATTTTTATTT
1 GGGCTAAAATTTTTATTT
54313527 GGGC
1 GGGC
54313531 CCAGCCCGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.23, C:0.08, G:0.26, T:0.44
Consensus pattern (18 bp):
GGGCTAAAATTTTTATTT
Found at i:54313854 original size:16 final size:15
Alignment explanation
Indices: 54313836--54313881 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
54313826 TTGGGTTTTT
54313836 TTTTATTTGGGTTGG
1 TTTTATTTGGGTTGG
*
54313851 TTTTA---GGTTTGG
1 TTTTATTTGGGTTGG
54313863 TTTTATTTGGGTTGG
1 TTTTATTTGGGTTGG
54313878 TTTT
1 TTTT
54313882 GGGTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 11 0.42
15 15 0.58
ACGTcount: A:0.07, C:0.00, G:0.30, T:0.63
Consensus pattern (15 bp):
TTTTATTTGGGTTGG
Found at i:54313859 original size:27 final size:27
Alignment explanation
Indices: 54313820--54313887 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
54313810 TTGGGCTGAA
* **
54313820 TTGGATTTGGGTTTTTTTTTATTTGGG
1 TTGGTTTTGGGTTTGGTTTTATTTGGG
*
54313847 TTGGTTTTAGGTTTGGTTTTATTTGGG
1 TTGGTTTTGGGTTTGGTTTTATTTGGG
54313874 TTGGTTTTGGGTTT
1 TTGGTTTTGGGTTT
54313888 ATTTATTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.06, C:0.00, G:0.32, T:0.62
Consensus pattern (27 bp):
TTGGTTTTGGGTTTGGTTTTATTTGGG
Found at i:54314326 original size:19 final size:19
Alignment explanation
Indices: 54314288--54314326 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
54314278 ATATGTTAAT
*
54314288 ATTAAGTAATTGTTATTTA
1 ATTAAGTAATTGTTACTTA
54314307 ATTAAGTGAATT-TTACTTA
1 ATTAAGT-AATTGTTACTTA
54314326 A
1 A
54314327 ATATTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (19 bp):
ATTAAGTAATTGTTACTTA
Found at i:54321867 original size:8 final size:8
Alignment explanation
Indices: 54321856--54321880 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
54321846 CATGTTCATG
54321856 ATTTCACA
1 ATTTCACA
54321864 ATTTCACA
1 ATTTCACA
54321872 ATTTCACA
1 ATTTCACA
54321880 A
1 A
54321881 GCAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (8 bp):
ATTTCACA
Found at i:54336055 original size:50 final size:50
Alignment explanation
Indices: 54335950--54336090 Score: 156
Period size: 50 Copynumber: 2.8 Consensus size: 50
54335940 TTATTGAGGT
* * * * *
54335950 TATGAGAGGTCCCATGTAAGACCATGTCTAGGATATGACGTTGGTACCAA
1 TATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATGGGCACCAA
* ** * *
54336000 GATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
1 TATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATGGGCACCAA
** * *
54336050 TATGAGAACTCTCATGTAAGACCATATCTGGGATATGGCAT
1 TATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCAT
54336091 TTGCAGTAAA
Statistics
Matches: 73, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 73 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
TATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATGGGCACCAA
Found at i:54340398 original size:29 final size:29
Alignment explanation
Indices: 54340356--54340415 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
54340346 TTTCATTTTG
54340356 TGCAATTTGGTCCTTTATCAAATCAAACA
1 TGCAATTTGGTCCTTTATCAAATCAAACA
*
54340385 TGCAATTTGGTCCTTTATCAAATTAAACA
1 TGCAATTTGGTCCTTTATCAAATCAAACA
54340414 TG
1 TG
54340416 TAACCGATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (29 bp):
TGCAATTTGGTCCTTTATCAAATCAAACA
Found at i:54348061 original size:44 final size:42
Alignment explanation
Indices: 54347919--54348091 Score: 161
Period size: 43 Copynumber: 4.0 Consensus size: 42
54347909 AGCTCATTCA
* * *
54347919 ATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAAATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAATCCAA-ATCG
* * * *
54347962 ATGCC-ACTGTCCCCGACAGGGTCTTACACGAACTCC-TATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGAAATCCAAAT-CG
* * *
54348004 ATGTCGATGTCCCAGACATGGTCTTACACGTAAATCGCAAATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACG-AAATC-CAAATCG
* * *
54348048 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAATC-CAAATCG
54348091 A
1 A
54348092 AATCCTATAT
Statistics
Matches: 104, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
41 2 0.02
42 28 0.27
43 43 0.41
44 29 0.28
45 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGAAATCCAAATCG
Found at i:54351629 original size:22 final size:22
Alignment explanation
Indices: 54351604--54351652 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
54351594 TAATTTGGGA
54351604 TTAATAGACAAA-TATTTGAA-AC
1 TTAAT-GACAAATTATTT-AAGAC
*
54351626 TTAATTACAAATTATTTAAGAC
1 TTAATGACAAATTATTTAAGAC
54351648 TTAAT
1 TTAAT
54351653 TATATAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (22 bp):
TTAATGACAAATTATTTAAGAC
Found at i:54351653 original size:22 final size:21
Alignment explanation
Indices: 54351611--54351654 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
54351601 GGATTAATAG
54351611 ACAAATATTTGAAACTTAATT
1 ACAAATATTTGAAACTTAATT
54351632 ACAAATTATTT-AAGACTTAATT
1 ACAAA-TATTTGAA-ACTTAATT
54351654 A
1 A
54351655 TATAAGTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.39
Consensus pattern (21 bp):
ACAAATATTTGAAACTTAATT
Found at i:54355428 original size:29 final size:29
Alignment explanation
Indices: 54355369--54355427 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
54355359 TATAGTTTAA
*
54355369 TGTGTAATTGTATACATGAATTTTAATTT
1 TGTGTAATTGTATACATGAACTTTAATTT
* * *
54355398 TGTGTAATTTTATATATGAAACTTTGATTT
1 TGTGTAATTGTATACATG-AACTTTAATTT
54355428 GATTCAATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.53
Consensus pattern (29 bp):
TGTGTAATTGTATACATGAACTTTAATTT
Found at i:54357855 original size:30 final size:29
Alignment explanation
Indices: 54357814--54357870 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
54357804 TAAAGAAGTA
*
54357814 CAAAAATTAAAAAAAAAACATGAAAAAATT
1 CAAAAAAT-AAAAAAAAACATGAAAAAATT
* *
54357844 CAAAAAATAAAACAAAACATTAAAAAA
1 CAAAAAATAAAAAAAAACATGAAAAAA
54357871 ATGCAACACC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.75, C:0.09, G:0.02, T:0.14
Consensus pattern (29 bp):
CAAAAAATAAAAAAAAACATGAAAAAATT
Found at i:54357871 original size:30 final size:30
Alignment explanation
Indices: 54357814--54357872 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
54357804 TAAAGAAGTA
* *
54357814 CAAAAATTAAAAAAAAAACATGAAAAAATT
1 CAAAAAATAAAAAAAAAACATAAAAAAATT
*
54357844 CAAAAAAT-AAAACAAAACATTAAAAAAAT
1 CAAAAAATAAAAAAAAAACA-TAAAAAAAT
54357873 GCAACACCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (30 bp):
CAAAAAATAAAAAAAAAACATAAAAAAATT
Found at i:54357878 original size:21 final size:21
Alignment explanation
Indices: 54357815--54357872 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
54357805 AAAGAAGTAC
*
54357815 AAAAATTAAAAAAA-AAACATGA
1 AAAAATTAAAAAAATAAA-A-CA
*
54357837 AAAAATTCAAAAAATAAAACA
1 AAAAATTAAAAAAATAAAACA
*
54357858 AAACATTAAAAAAAT
1 AAAAATTAAAAAAAT
54357873 GCAACACCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 14 0.45
22 14 0.45
23 3 0.10
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.16
Consensus pattern (21 bp):
AAAAATTAAAAAAATAAAACA
Found at i:54361108 original size:5 final size:5
Alignment explanation
Indices: 54361098--54361123 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
54361088 GAGATGGAAT
54361098 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
54361124 ATATTTCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:54366026 original size:18 final size:17
Alignment explanation
Indices: 54366004--54366138 Score: 95
Period size: 18 Copynumber: 8.0 Consensus size: 17
54365994 AATACTAAGA
54366004 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
54366021 ATTTTTGTTAAA-T-TAT
1 A-TTTTATTAAATTATAT
* *
54366037 A-TTTAAT-AATAAT-T
1 ATTTTATTAAATTATAT
* *
54366051 ATTTTAAATTATATTTTAT
1 ATTTT--ATTAAATTATAT
* *
54366070 AATATTA-TATATTATA-
1 -ATTTTATTAAATTATAT
*
54366086 ATTTTAGTAAATTCATAT
1 ATTTTATTAAATT-ATAT
54366104 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
54366121 ATTTTTATTAAATTATAT
1 A-TTTTATTAAATTATAT
54366139 TTAATAATAA
Statistics
Matches: 92, Mismatches: 13, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
13 2 0.02
14 6 0.07
15 9 0.10
16 9 0.10
17 20 0.22
18 41 0.45
19 1 0.01
20 4 0.04
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:54366057 original size:26 final size:25
Alignment explanation
Indices: 54366019--54366158 Score: 85
Period size: 26 Copynumber: 5.5 Consensus size: 25
54366009 ATTAAATTAT
*
54366019 ATATTTTTGTTAAATTATATTTAATA
1 ATATTATT-TTAAATTATATTTAATA
*
54366045 ATAATTATTTTAAATTATATTTTATA
1 AT-ATTATTTTAAATTATATTTAATA
* * * *
54366071 ATATTATATATTATAATTTTAGTAAATTC
1 ATATTAT-T-TTA-AATTATATTTAA-TA
*
54366100 ATA-TATTTT--ATTA-AATT-AT-
1 ATATTATTTTAAATTATATTTAATA
*
54366119 ATATTTTTATTAAATTATATTTAATA
1 ATATTATT-TTAAATTATATTTAATA
*
54366145 ATAATTATGTTAAA
1 AT-ATTATTTTAAA
54366159 ATATGATTAA
Statistics
Matches: 87, Mismatches: 14, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
19 3 0.03
20 4 0.05
21 3 0.03
22 2 0.02
23 7 0.08
24 3 0.03
25 7 0.08
26 30 0.34
27 13 0.15
28 11 0.13
29 4 0.05
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (25 bp):
ATATTATTTTAAATTATATTTAATA
Found at i:54366076 original size:15 final size:15
Alignment explanation
Indices: 54366032--54366087 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
54366022 TTTTTGTTAA
*
54366032 ATTATATTTAATAAT
1 ATTATATTTTATAAT
*
54366047 AAT-TA-TTT-TAA-
1 ATTATATTTTATAAT
54366058 ATTATATTTTATAAT
1 ATTATATTTTATAAT
*
54366073 ATTATATATTATAAT
1 ATTATATTTTATAAT
54366088 TTTAGTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
11 2 0.06
12 5 0.15
13 5 0.15
14 5 0.15
15 16 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATATTTTATAAT
Done.