Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 139 of 202
Found at i:43198652 original size:5 final size:5
Alignment explanation
Indices: 43198642--43198668 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
43198632 ATATCCTAAG
43198642 AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AA
43198669 GATCCCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:43200467 original size:50 final size:50
Alignment explanation
Indices: 43200395--43200649 Score: 221
Period size: 50 Copynumber: 5.1 Consensus size: 50
43200385 AAAGTGAAAG
*
43200395 TGAT-GGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACTGGAA
1 TGATAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAA
* * * * ** *
43200444 TGATAGGTCGCATGTGTAGTACTATGTGCAGGCTATTATGCATACCGGAA
1 TGATAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAA
* * * * * * *
43200494 AGCTTCGATCATGTGTGTAGTACTATGTGCAGGCTACCACGTGTATTGGATA
1 TG-ATAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGA-A
* * * * *
43200546 TTA-ATGGTCATGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGAAA
1 TGATA-GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAA
* * * * *
43200596 AGTTTGAG-CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA-TCGAA
1 TGATAG-GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAA
43200645 TGATA
1 TGATA
43200650 ATAGTTAAAT
Statistics
Matches: 155, Mismatches: 45, Indels: 12
0.73 0.21 0.06
Matches are distributed among these distances:
49 8 0.05
50 73 0.47
51 73 0.47
52 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.31
Consensus pattern (50 bp):
TGATAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAA
Found at i:43200516 original size:101 final size:99
Alignment explanation
Indices: 43200402--43200676 Score: 295
Period size: 101 Copynumber: 2.7 Consensus size: 99
43200392 AAGTGATGGT
* *
43200402 CACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACTGGAATGATA-GGTCGCATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA-TGGAATGATATGGTCACATGTGTAGTAC
* * *
43200466 TATGTGCAGGCTATTA-TGCATACCGGAAAGCTTCGAT
65 TATGTGCAGGCTACTACTG-A-ACCGAAAAG-TTCGAG
* * * * **
43200503 CATGTGTGTAGTACTATGTGCAGGCTACCACGTGTATTGGATATTA-ATGGTCATGTGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA-TGGA-ATGATATGGTCACATGTGTAGTA
*
43200567 CTATGTGCAGGCTACTACGTGAACCGAAAAGTTTGAG
64 CTATGTGCAGGCTACTAC-TGAACCGAAAAGTTCGAG
* * * * * *
43200604 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAATGATAATAGTTAAATGAGTGGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATGGAATGAT-ATGGTCACATGTGTAGTAC
43200669 TATGTGCA
65 TATGTGCA
43200677 AACCACCGAA
Statistics
Matches: 145, Mismatches: 23, Indels: 12
0.81 0.13 0.07
Matches are distributed among these distances:
99 3 0.02
100 3 0.02
101 96 0.66
102 40 0.28
103 1 0.01
104 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (99 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATGGAATGATATGGTCACATGTGTAGTACT
ATGTGCAGGCTACTACTGAACCGAAAAGTTCGAG
Found at i:43204310 original size:40 final size:40
Alignment explanation
Indices: 43204252--43204374 Score: 151
Period size: 40 Copynumber: 3.1 Consensus size: 40
43204242 CACCAGACAG
* *
43204252 AAGCTCATAAGAGTTGGTCCACCCGAAATATGCCAAAAAA
1 AAGCTCATAAGAGCTGGTCCACCCGAAACATGCCAAAAAA
* * *
43204292 AAGCTCATAAGAGCTGGTCCACCCGAAACATTCC-AATAG
1 AAGCTCATAAGAGCTGGTCCACCCGAAACATGCCAAAAAA
* *
43204331 AAGCTCAT-AGTTGCTGATCCACCCGAAACATGCCAAAAAGA
1 AAGCTCATAAG-AGCTGGTCCACCCGAAACATGCCAAAAA-A
43204372 AAG
1 AAG
43204375 TATAACGCGA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
38 2 0.03
39 31 0.44
40 34 0.49
41 3 0.04
ACGTcount: A:0.40, C:0.25, G:0.18, T:0.17
Consensus pattern (40 bp):
AAGCTCATAAGAGCTGGTCCACCCGAAACATGCCAAAAAA
Found at i:43204352 original size:39 final size:39
Alignment explanation
Indices: 43204252--43204369 Score: 139
Period size: 39 Copynumber: 3.0 Consensus size: 39
43204242 CACCAGACAG
* * *
43204252 AAGCTCATAAGAGTTGGTCCACCCGAAATATGCCAAAAAA
1 AAGCTCATAAGAGCTGATCCACCCGAAACATGCC-AAAAA
* * * *
43204292 AAGCTCATAAGAGCTGGTCCACCCGAAACATTCCAATAG
1 AAGCTCATAAGAGCTGATCCACCCGAAACATGCCAAAAA
*
43204331 AAGCTCAT-AGTTGCTGATCCACCCGAAACATGCCAAAAA
1 AAGCTCATAAG-AGCTGATCCACCCGAAACATGCCAAAAA
43204370 GAAAGTATAA
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
38 2 0.03
39 34 0.51
40 31 0.46
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.18
Consensus pattern (39 bp):
AAGCTCATAAGAGCTGATCCACCCGAAACATGCCAAAAA
Found at i:43205318 original size:10 final size:10
Alignment explanation
Indices: 43205303--43205327 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
43205293 TTTTTCATTC
43205303 TTTAATTTTG
1 TTTAATTTTG
43205313 TTTAATTTTG
1 TTTAATTTTG
43205323 TTTAA
1 TTTAA
43205328 ACTTTCATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (10 bp):
TTTAATTTTG
Found at i:43218609 original size:16 final size:16
Alignment explanation
Indices: 43218588--43218619 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
43218578 TCGTAGTCGA
43218588 AGTAAACCTGAACTCT
1 AGTAAACCTGAACTCT
43218604 AGTAAACCTGAACTCT
1 AGTAAACCTGAACTCT
43218620 GCCTATCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (16 bp):
AGTAAACCTGAACTCT
Found at i:43222941 original size:18 final size:19
Alignment explanation
Indices: 43222905--43222941 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
43222895 GAATGCAAAA
*
43222905 TTGGTATTGATATAAATTT
1 TTGGTATCGATATAAATTT
43222924 TTGGTATCGATA-AAATTT
1 TTGGTATCGATATAAATTT
43222942 AATAAGTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGGTATCGATATAAATTT
Found at i:43222970 original size:20 final size:20
Alignment explanation
Indices: 43222926--43222975 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
43222916 ATAAATTTTT
43222926 GGTATCGATAAAATTTAATAA
1 GGTATCGATAAAATTT-ATAA
*
43222947 -GTATCGATATAATTT-TCAA
1 GGTATCGATAAAATTTAT-AA
*
43222966 GGTATTGATA
1 GGTATCGATA
43222976 CTTATTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 1 0.04
19 2 0.08
20 22 0.88
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (20 bp):
GGTATCGATAAAATTTATAA
Found at i:43223606 original size:30 final size:30
Alignment explanation
Indices: 43223572--43223631 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
43223562 TTTTATGTAA
43223572 AATTTGACACATTTATGTACATGAGTCATG
1 AATTTGACACATTTATGTACATGAGTCATG
43223602 AATTTGACACATTTATGTACATGAGTCATG
1 AATTTGACACATTTATGTACATGAGTCATG
43223632 TTCTTATTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (30 bp):
AATTTGACACATTTATGTACATGAGTCATG
Found at i:43224655 original size:21 final size:22
Alignment explanation
Indices: 43224601--43224653 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
43224591 CTTTCTAAGT
43224601 TAATTTTTTTATGTAAAAGACA
1 TAATTTTTTTATGTAAAAGACA
43224623 TAATTTTTTTATGTAAAAGACA
1 TAATTTTTTTATGTAAAAGACA
43224645 TAATTTTTT
1 TAATTTTTT
43224654 ATTAGATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.51
Consensus pattern (22 bp):
TAATTTTTTTATGTAAAAGACA
Found at i:43232266 original size:14 final size:15
Alignment explanation
Indices: 43232243--43232271 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43232233 CTTTATTTTG
43232243 CTTTTAACTTTTTCA
1 CTTTTAACTTTTTCA
43232258 CTTTT-ACTTTTTCA
1 CTTTTAACTTTTTCA
43232272 TCTCAAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (15 bp):
CTTTTAACTTTTTCA
Found at i:43233571 original size:12 final size:12
Alignment explanation
Indices: 43233537--43233573 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
43233527 GTAAAGGAAA
43233537 TAAA-AATA-TT
1 TAAATAATATTT
43233547 TAAATAATGATTT
1 TAAATAAT-ATTT
43233560 TAAATAATATTT
1 TAAATAATATTT
43233572 TA
1 TA
43233574 TTAAGAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.17
11 3 0.12
12 7 0.29
13 10 0.42
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (12 bp):
TAAATAATATTT
Found at i:43237993 original size:16 final size:16
Alignment explanation
Indices: 43237968--43237998 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43237958 TCAAAAAAGT
43237968 TTTCAAATATATATAG
1 TTTCAAATATATATAG
*
43237984 TTTCACATATATATA
1 TTTCAAATATATATA
43237999 CATATATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (16 bp):
TTTCAAATATATATAG
Found at i:43238983 original size:23 final size:21
Alignment explanation
Indices: 43238953--43238995 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
43238943 TTCTTTAAAT
43238953 AAATTAAAAATATAGAAAAAAA
1 AAATTAAAAATATA-AAAAAAA
*
43238975 AAATGTAAAATTATAAAAAAA
1 AAAT-TAAAAATATAAAAAAA
43238996 TCCTAAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (21 bp):
AAATTAAAAATATAAAAAAAA
Found at i:43239218 original size:19 final size:20
Alignment explanation
Indices: 43239193--43239237 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
43239183 GAACAAAAAT
43239193 GAAAAAAGAAAA-AAAATCA
1 GAAAAAAGAAAAGAAAATCA
*
43239212 TAAAAAAGAAAAGAAAATCA
1 GAAAAAAGAAAAGAAAATCA
43239232 GAAAAA
1 GAAAAA
43239238 TAGTCATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.78, C:0.04, G:0.11, T:0.07
Consensus pattern (20 bp):
GAAAAAAGAAAAGAAAATCA
Found at i:43247853 original size:26 final size:26
Alignment explanation
Indices: 43247816--43247874 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
43247806 CTGTCATCAG
43247816 ACCATCGTCGTCACTACCGTAGCACT
1 ACCATCGTCGTCACTACCGTAGCACT
* *
43247842 GCCATCGTCGTCGCTACCGTAGCACT
1 ACCATCGTCGTCACTACCGTAGCACT
43247868 ACCATCG
1 ACCATCG
43247875 ATGATTGTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.20, C:0.39, G:0.19, T:0.22
Consensus pattern (26 bp):
ACCATCGTCGTCACTACCGTAGCACT
Found at i:43248842 original size:19 final size:19
Alignment explanation
Indices: 43248818--43248854 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
43248808 CTTACATGCC
*
43248818 AAAGTGAAAAATTGATTTG
1 AAAGTGAAAAAGTGATTTG
43248837 AAAGTGAAAAAGTGATTT
1 AAAGTGAAAAAGTGATTT
43248855 TTATGGCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.30
Consensus pattern (19 bp):
AAAGTGAAAAAGTGATTTG
Found at i:43250002 original size:15 final size:15
Alignment explanation
Indices: 43249982--43250014 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
43249972 TATTTATACT
*
43249982 TGAAACTTTAGATTA
1 TGAAACCTTAGATTA
43249997 TGAAACCTTAGATTA
1 TGAAACCTTAGATTA
43250012 TGA
1 TGA
43250015 GATGATATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (15 bp):
TGAAACCTTAGATTA
Found at i:43254069 original size:28 final size:28
Alignment explanation
Indices: 43254007--43254062 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
43253997 GTTTGAAATG
43254007 GTGAAATAGAGGTATAAGAAGATGAAAA
1 GTGAAATAGAGGTATAAGAAGATGAAAA
43254035 GTGAAATAGAGGTATAAGAAGATGAAAA
1 GTGAAATAGAGGTATAAGAAGATGAAAA
43254063 AGGAAATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.18
Consensus pattern (28 bp):
GTGAAATAGAGGTATAAGAAGATGAAAA
Found at i:43254834 original size:29 final size:30
Alignment explanation
Indices: 43254802--43254878 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 30
43254792 TTTATGGTCC
**
43254802 AAGTGTAAATATTTAAAATGT-AAGGGTTA
1 AAGTGTAAATATTTAAAATGTAAAGGGCCA
* ** *
43254831 AAGTATAAATATGAAAAATTTAAAGGGCCA
1 AAGTGTAAATATTTAAAATGTAAAGGGCCA
43254861 ATAGTGTAAATATCTTAA
1 A-AGTGTAAATAT-TTAA
43254879 GGATGGAAGG
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
29 17 0.47
30 7 0.19
31 10 0.28
32 2 0.06
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.31
Consensus pattern (30 bp):
AAGTGTAAATATTTAAAATGTAAAGGGCCA
Found at i:43258396 original size:42 final size:43
Alignment explanation
Indices: 43258350--43258435 Score: 102
Period size: 46 Copynumber: 2.0 Consensus size: 43
43258340 AGCTTATGTA
*
43258350 GTTCAACC-CAAATGACGATGCTCCTAAGCACGAGTTTAAATT
1 GTTCAACCACAAATGACGATGCTCCTAAGCACGAGCTTAAATT
* * *
43258392 GTTCATCCAAAATAAATGATGATGCTCCTAAGCACGAGCTTAAA
1 GTTCAACC---ACAAATGACGATGCTCCTAAGCACGAGCTTAAA
43258436 CTATTCACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
42 7 0.19
46 29 0.81
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (43 bp):
GTTCAACCACAAATGACGATGCTCCTAAGCACGAGCTTAAATT
Found at i:43264469 original size:42 final size:42
Alignment explanation
Indices: 43264417--43264512 Score: 174
Period size: 42 Copynumber: 2.3 Consensus size: 42
43264407 ATTAAAATCC
*
43264417 AAAAGTTAGAACTCAAGTTGTCGTAAATATTAAAGTAAAAAT
1 AAAAATTAGAACTCAAGTTGTCGTAAATATTAAAGTAAAAAT
43264459 AAAAATTAGAACTCAAGTTGTCGTAAATATTAAAGTAAAAAT
1 AAAAATTAGAACTCAAGTTGTCGTAAATATTAAAGTAAAAAT
43264501 AAAAATTTAGAA
1 AAAAA-TTAGAA
43264513 TTAAAACTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 46 0.88
43 6 0.12
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.28
Consensus pattern (42 bp):
AAAAATTAGAACTCAAGTTGTCGTAAATATTAAAGTAAAAAT
Found at i:43264529 original size:43 final size:42
Alignment explanation
Indices: 43264440--43264530 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
43264430 CAAGTTGTCG
* ** ****
43264440 TAAATATTAAAGTAAAAATAAAAATTAGAACTCAAGTTGTCG
1 TAAATATTAAAGTAAAAATAAAAATTAGAACTAAAACTAAAA
*
43264482 TAAATATTAAAGTAAAAATAAAAATTTAGAATTAAAACTAAAA
1 TAAATATTAAAGTAAAAATAAAAA-TTAGAACTAAAACTAAAA
43264525 TAAATA
1 TAAATA
43264531 ATACATATGA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 24 0.60
43 16 0.40
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (42 bp):
TAAATATTAAAGTAAAAATAAAAATTAGAACTAAAACTAAAA
Found at i:43266769 original size:17 final size:17
Alignment explanation
Indices: 43266747--43266780 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
43266737 TAAAAGAACA
43266747 TTCTACATACCAGTCAG
1 TTCTACATACCAGTCAG
43266764 TTCTACATACCAGTCAG
1 TTCTACATACCAGTCAG
43266781 CAAAATCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (17 bp):
TTCTACATACCAGTCAG
Found at i:43268112 original size:24 final size:24
Alignment explanation
Indices: 43268080--43268129 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
43268070 GTGGATACAC
43268080 TGGCATTGGGATAAACAACATTTT
1 TGGCATTGGGATAAACAACATTTT
43268104 TGGCATTGGGATAAACAACATTTT
1 TGGCATTGGGATAAACAACATTTT
43268128 TG
1 TG
43268130 AACAGTAGAA
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:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (24 bp):
TGGCATTGGGATAAACAACATTTT
Found at i:43268641 original size:7 final size:7
Alignment explanation
Indices: 43268622--43268667 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
43268612 AGGAACGAGA
43268622 GAAA-GG
1 GAAAGGG
*
43268628 GATAGGG
1 GAAAGGG
43268635 GAAAGGG
1 GAAAGGG
43268642 GAAAGGG
1 GAAAGGG
*
43268649 CAAAGGG
1 GAAAGGG
*
43268656 CAAAGGG
1 GAAAGGG
43268663 GAAAG
1 GAAAG
43268668 CGTAATAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
6 3 0.09
7 32 0.91
ACGTcount: A:0.43, C:0.04, G:0.50, T:0.02
Consensus pattern (7 bp):
GAAAGGG
Found at i:43268655 original size:21 final size:20
Alignment explanation
Indices: 43268622--43268667 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
43268612 AGGAACGAGA
* *
43268622 GAAAGGGATAGGGGAAAGGG
1 GAAAGGGAAAGGGCAAAGGG
43268642 GAAAGGGCAAAGGGCAAAGGG
1 GAAAGGG-AAAGGGCAAAGGG
43268663 GAAAG
1 GAAAG
43268668 CGTAATAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.43, C:0.04, G:0.50, T:0.02
Consensus pattern (20 bp):
GAAAGGGAAAGGGCAAAGGG
Found at i:43269495 original size:134 final size:135
Alignment explanation
Indices: 43269204--43269594 Score: 346
Period size: 134 Copynumber: 2.9 Consensus size: 135
43269194 ATAAGAAATT
*
43269204 ATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCTCTAACTCC--TA---TA
1 ATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACC-CTAAC-CCGATACCGAA
* * * * * * ** ***
43269264 TC-ATAAACCCTAAATCATAAAATATAAACC-CTAAACCCCTAACCCCT---CTTTTACAATTAT
64 TCTATAAACCCTAAATCCTTAACTCTTAACCTCT-AACCCCTAACCCCTAACCCTAAACCCCTA-
43269324 A-TA-TGAAC
127 ACTACT-AAC
* * * *
43269332 TTAATTAATATATAAATTAAAAAATACTAATTAATCTAAACCTTAAACCCTAACCCGA-CCCTGA
1 --ATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCTAACCCGATACC-GA
* * * * *
43269396 ATCTCTAAACCTTAAGTCAC-TCACTCTTAACCTCTAACCTCTAA-CCCTAAACCCTAAACCCCT
63 ATCTATAAACCCTAAATC-CTTAACTCTTAACCTCTAACCCCTAACCCCT-AACCCTAAACCCCT
43269459 AACTACTAAC
126 AACTACTAAC
* **
43269469 ATTTAATATATAAATT-AAAAACACTAATTAATCTAAACCCTAAACTCTAACTTGATACCGAATC
1 ATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCTAACCCGATACCGAATC
* *
43269533 TATAAACCCTAAATCCTTAACTCTTAATCTCTAACCCCTAACCCCTAACCCTTAACCCCTAA
66 TATAAACCCTAAATCCTTAACTCTTAACCTCTAACCCCTAACCCCTAACCCTAAACCCCTAA
43269595 ATCACAACCC
Statistics
Matches: 208, Mismatches: 35, Indels: 32
0.76 0.13 0.12
Matches are distributed among these distances:
128 2 0.01
129 5 0.02
130 44 0.21
133 8 0.04
134 113 0.54
135 23 0.11
136 1 0.00
137 11 0.05
138 1 0.00
ACGTcount: A:0.42, C:0.28, G:0.02, T:0.29
Consensus pattern (135 bp):
ATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCTAACCCGATACCGAATC
TATAAACCCTAAATCCTTAACTCTTAACCTCTAACCCCTAACCCCTAACCCTAAACCCCTAACTA
CTAAC
Found at i:43269573 original size:7 final size:7
Alignment explanation
Indices: 43269563--43269594 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
43269553 CTCTTAATCT
43269563 CTAACCC
1 CTAACCC
43269570 CTAACCC
1 CTAACCC
43269577 CTAACCC
1 CTAACCC
*
43269584 TTAACCC
1 CTAACCC
43269591 CTAA
1 CTAA
43269595 ATCACAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.31, C:0.50, G:0.00, T:0.19
Consensus pattern (7 bp):
CTAACCC
Found at i:43269633 original size:14 final size:15
Alignment explanation
Indices: 43269614--43269646 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
43269604 CTTAAACCAG
43269614 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
43269628 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
43269643 AATC
1 AATC
43269647 TTTAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:43277769 original size:35 final size:36
Alignment explanation
Indices: 43277694--43277775 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 36
43277684 TCAATGAGAT
*
43277694 TGAAGTTTAT-TAATTTGAATACATTTGATTCTGAA
1 TGAAGTTTATATAATTTGAATACATTTGATTCTCAA
* * *
43277729 GGAAGTTTATAT-GTTTGAATAGATTTGATT-TCCAA
1 TGAAGTTTATATAATTTGAATACATTTGATTCT-CAA
43277764 TGAAGTTTATAT
1 TGAAGTTTATAT
43277776 CGATAAGATT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 1 0.03
35 38 0.95
36 1 0.03
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (36 bp):
TGAAGTTTATATAATTTGAATACATTTGATTCTCAA
Found at i:43279679 original size:10 final size:10
Alignment explanation
Indices: 43279666--43279699 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
43279656 GAAAAACTGC
43279666 AAAGAAAACT
1 AAAGAAAACT
43279676 AAAGAAAACCT
1 AAAGAAAA-CT
*
43279687 AGAGAAAACT
1 AAAGAAAACT
43279697 AAA
1 AAA
43279700 CCTAAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.68, C:0.12, G:0.12, T:0.09
Consensus pattern (10 bp):
AAAGAAAACT
Found at i:43279973 original size:20 final size:20
Alignment explanation
Indices: 43279948--43280002 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
43279938 CTTGGGAGAT
43279948 GGATATCGCGATACCCAAGG
1 GGATATCGCGATACCCAAGG
43279968 GGATATCGCGATACCCAAGG
1 GGATATCGCGATACCCAAGG
*
43279988 GGATATCGCAATACC
1 GGATATCGCGATACC
43280003 AATGAAGAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.16
Consensus pattern (20 bp):
GGATATCGCGATACCCAAGG
Found at i:43286913 original size:13 final size:13
Alignment explanation
Indices: 43286895--43286920 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43286885 CCCCTTTTTA
43286895 GTTACAAACCATT
1 GTTACAAACCATT
43286908 GTTACAAACCATT
1 GTTACAAACCATT
43286921 CTTCTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
GTTACAAACCATT
Found at i:43294211 original size:16 final size:16
Alignment explanation
Indices: 43294190--43294243 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
43294180 TTTGGTTCGC
43294190 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
43294206 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGG
*
43294222 TGTAATGAAATAGAGG
1 TGTAATGGAATAGAGG
*
43294238 CGTAAT
1 TGTAAT
43294244 AGTAATGCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.39, C:0.04, G:0.31, T:0.26
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:43294273 original size:45 final size:44
Alignment explanation
Indices: 43294222--43294318 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 44
43294212 GGAATAGAGC
43294222 TGTAATGAAATAGAGGCGTAATAGTAATGCAAT-TGTTTGGTTGAA
1 TGTAATGAAATAGAGGCGTAATAGT-ATGC-ATGTGTTTGGTTGAA
* * * *
43294267 TGTAATGGAATAGATGCGTAATAGTATTCTTGTGTTTGGTTGAA
1 TGTAATGAAATAGAGGCGTAATAGTATGCATGTGTTTGGTTGAA
*
43294311 TGAAATGA
1 TGTAATGA
43294319 TGTTGTAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.47
45 23 0.51
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (44 bp):
TGTAATGAAATAGAGGCGTAATAGTATGCATGTGTTTGGTTGAA
Found at i:43294615 original size:18 final size:18
Alignment explanation
Indices: 43294592--43294638 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
43294582 TTATTATTAA
43294592 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
*
43294610 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAAAT
43294628 AT-TAATATTAA
1 ATATAAT-TTAA
43294639 ATATTCTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:43294727 original size:120 final size:120
Alignment explanation
Indices: 43294453--43295086 Score: 1017
Period size: 120 Copynumber: 5.3 Consensus size: 120
43294443 TTAATCATAT
*
43294453 TTTAACATAATTATTATTAAATATAATTTAATAAAAACATATAATTTAATAAAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
* * *
43294518 AAATATTCTTATATGACTTTTCT-AAATTATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
43294572 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTATTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
* * *
43294637 AAATATTCTTATATGAATTTTCTAGAATCAAAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
43294692 TTTAACATAATTATTATTGAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
* * *
43294757 AAATATTCTTATATGAATTTAATAAAATCATAATATATAATATTATATAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* *
43294812 TTTAAAATAATTATTATTAAATATAAATTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
* * *
43294877 AAATATTCTTAAATGCATTTACTAAAATCATAATATATAATACTACAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* **
43294932 TTTAAAATAATTATTATTAAAAATATAATTTTGTAAAAATATATAATTTAATAAAATTCTTAATA
1 TTTAACATAATTATTATT--AAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATA
43294997 TTAAATATTC-T-TA-GAATTTACTAAAATCATAATATATAATACTATAAAATATAA
64 TTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
43295051 TTTAA-ATTAATTATTTTTAAATATAATTTAATAAAA
1 TTTAACA-TAATTATTATTAAATATAATTTAATAAAA
43295087 TTCTTAATAT
Statistics
Matches: 479, Mismatches: 32, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
117 16 0.03
118 1 0.00
119 139 0.29
120 270 0.56
121 1 0.00
122 52 0.11
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:43294834 original size:26 final size:25
Alignment explanation
Indices: 43294793--43294851 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
43294783 ATCATAATAT
*
43294793 ATAATATTATATAATATAATTTAAA
1 ATAATATTATATAATATAAATTAAA
43294818 ATAATTATTAT-TAAATATAAATTAATA
1 ATAA-TATTATAT-AATATAAATTAA-A
*
43294845 AAAATAT
1 ATAATAT
43294852 ATAATTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 5 0.17
26 20 0.69
27 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATAATATTATATAATATAAATTAAA
Found at i:43294878 original size:18 final size:19
Alignment explanation
Indices: 43294712--43294878 Score: 62
Period size: 18 Copynumber: 8.6 Consensus size: 19
43294702 TTATTATTGA
43294712 ATATAAT-TTAATAAAAAT
1 ATATAATATTAATAAAAAT
*
43294730 ATATAAT-TTAATAAAATT
1 ATATAATATTAATAAAAAT
* ****
43294748 CT-TAATATTAAATATTCTT
1 ATATAATATT-AATAAAAAT
43294767 ATATGAAT-TTAATAAAATCATAAT
1 ATAT-AATATTAAT--AA--A-AAT
43294791 ATATAATATTATATAATATAAT
1 ATATAATATTA-ATAA-A-AAT
* * * **
43294813 TTAAAATAATTATTATTAA-
1 ATATAAT-ATTAATAAAAAT
43294832 ATATAA-ATTAATAAAAAT
1 ATATAATATTAATAAAAAT
*
43294850 ATATAAT-TTAATAAAATT
1 ATATAATATTAATAAAAAT
*
43294868 CT-TAATATTAA
1 ATATAATATTAA
43294879 ATATTCTTAA
Statistics
Matches: 111, Mismatches: 23, Indels: 30
0.68 0.14 0.18
Matches are distributed among these distances:
17 16 0.14
18 41 0.37
19 14 0.13
20 5 0.05
21 4 0.04
22 12 0.11
23 9 0.08
24 8 0.07
25 2 0.02
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (19 bp):
ATATAATATTAATAAAAAT
Found at i:43295164 original size:15 final size:17
Alignment explanation
Indices: 43295130--43295174 Score: 76
Period size: 15 Copynumber: 2.8 Consensus size: 17
43295120 TAAAATCATG
43295130 ATATATAATACTATTAA
1 ATATATAATACTATTAA
43295147 ATATATAATACTA-T-A
1 ATATATAATACTATTAA
43295162 ATATATAATACTA
1 ATATATAATACTA
43295175 GAAAGATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 14 0.50
16 1 0.04
17 13 0.46
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATATAATACTATTAA
Found at i:43298086 original size:17 final size:18
Alignment explanation
Indices: 43298046--43298093 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
43298036 TCCAGATTTG
*
43298046 AGCACAAGCAAAAGCAAA
1 AGCAAAAGCAAAAGCAAA
43298064 AGCAAAAGCAAAA-CAAA
1 AGCAAAAGCAAAAGCAAA
* *
43298081 ATCAAAATCAAAA
1 AGCAAAAGCAAAA
43298094 TTGATTTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.67, C:0.19, G:0.10, T:0.04
Consensus pattern (18 bp):
AGCAAAAGCAAAAGCAAA
Found at i:43298094 original size:6 final size:6
Alignment explanation
Indices: 43298046--43298093 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
43298036 TCCAGATTTG
* * *
43298046 AGCACA AGCAAA AGCAAA AGCAAA AGCAAA A-CAAA ATCAAA ATCAAA
1 AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA
43298093 A
1 A
43298094 TTGATTTTAC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
5 5 0.12
6 35 0.88
ACGTcount: A:0.67, C:0.19, G:0.10, T:0.04
Consensus pattern (6 bp):
AGCAAA
Found at i:43305123 original size:16 final size:16
Alignment explanation
Indices: 43305074--43305115 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
43305064 AAAATAAACC
43305074 TAAAACCTAAGAAGAAA
1 TAAAA-CTAAGAAGAAA
43305091 TAAAACTAAGAAGAAA
1 TAAAACTAAGAAGAAA
43305107 TAAAACTAA
1 TAAAACTAA
43305116 ACTGAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.14
Consensus pattern (16 bp):
TAAAACTAAGAAGAAA
Found at i:43305666 original size:30 final size:30
Alignment explanation
Indices: 43305624--43305696 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
43305614 TTAATTAAAT
* *
43305624 AATATATTTGCTTTCAAGCTCCTAAATATTT
1 AATATAATTGCTTTCAAGCTCCTAAA-ATTA
43305655 AAT-TAATTGCTTTCAAGCTCCTAAAATTA
1 AATATAATTGCTTTCAAGCTCCTAAAATTA
*
43305684 AATATATTTGCTT
1 AATATAATTGCTT
43305697 AAAGATTCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 6 0.16
30 29 0.76
31 3 0.08
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (30 bp):
AATATAATTGCTTTCAAGCTCCTAAAATTA
Found at i:43305776 original size:16 final size:17
Alignment explanation
Indices: 43305749--43305783 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
43305739 TAGACTTGGG
*
43305749 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
43305766 TTGAG-AAATTAATTAA
1 TTGAGAAAATTAATTAA
43305782 TT
1 TT
43305784 TAAATTAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:43309020 original size:50 final size:50
Alignment explanation
Indices: 43308899--43309289 Score: 494
Period size: 50 Copynumber: 7.8 Consensus size: 50
43308889 TAATAACATC
* ** *
43308899 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTG
* * * * ** *
43308950 CCCATGCCAAGTCCTAGACATGGTCTTACGGGGGACCTTTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
43309000 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* ** *
43309050 CCAACGCCATGTCCCAGACATGGTCTTTCATGGGAATTCTCATTTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * * ** *
43309100 CCAACGCCATGTCCTAGACTTTGTCTTACATAAGACATCTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * * * * *
43309150 CCAATGTCATGTCCTAAACATGATCTTACATAGGACCTCTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * *
43309200 CCAACGCCATGTCCCAGACTTGGTCTTTCATGGGACCTCTCAACTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
*
43309250 CCAACGCCATGTCTCAGACATGGTCTTACATGGGACCTCT
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
43309290 TTACCCAAAT
Statistics
Matches: 290, Mismatches: 50, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
50 261 0.90
51 29 0.10
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.27
Consensus pattern (50 bp):
CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
Found at i:43312672 original size:318 final size:318
Alignment explanation
Indices: 43312095--43312731 Score: 1040
Period size: 318 Copynumber: 2.0 Consensus size: 318
43312085 TACTCGGATG
*
43312095 ATAATCAATAACCAATTCATAATCTTTTATCAATTCTAGCCATCTGCGTTGTCTCAAATTCAAAT
1 ATAATCAATAACCAATTCATAATCTTTTATCAATTCTAGCCATCTACGTTGTCTCAAATTCAAAT
43312160 CTTTCTGTGTCATCAAATACTTCAAGATTTTATGATCAGTATAAATATGACACTTTTCAACATAA
66 CTTTCTGTGTCATCAAATACTTCAAGATTTTATGATCAGTATAAATATGACACTTTTCAACATAA
* * * * * *
43312225 AAATGATGCCTCCATATTTTCAATGCAAATACAGTAGCAACTAATTTAAGATCATGTACCGGGCA
131 AAATAATGCCGCCATATTTTCAATGCAAACACAATAGCAACTAATTCAAGATCATGTACCGCGCA
*
43312290 GTTTCTTTCATGTGGCTTAAGTTGTCTTGAAGCATAGCCTATTACTTTATCTTCTTGCATCAAGA
196 GCTTCTTTCATGTGGCTTAAGTTGTCTTGAAGCATAGCCTATTACTTTATCTTCTTGCATCAAGA
* *
43312355 CACAACCCAAACCATTTAATGATGCATTACTATAAATAATAAATTCCTTACCAGATTC
261 CACAACCCAAACCATTTAATAATGCATCACTATAAATAATAAATTCCTTACCAGATTC
* *
43312413 ATAATCAATAACGAATTCATAATCTTTTATGAATTCTAGCCATCTACGTTGTCTCAAATTCAAAT
1 ATAATCAATAACCAATTCATAATCTTTTATCAATTCTAGCCATCTACGTTGTCTCAAATTCAAAT
* * *
43312478 CTTTCTGTGTCATCAAATACTTCAAGCTTTTATGATCAGTATAAATATGACACTTTTCACCATAC
66 CTTTCTGTGTCATCAAATACTTCAAGATTTTATGATCAGTATAAATATGACACTTTTCAACATAA
* * * *
43312543 AAATAATGCCGCCATATTTTCAATGCAAACATAATAGCAGCTAATTCAAGATCATGTACTGCGTA
131 AAATAATGCCGCCATATTTTCAATGCAAACACAATAGCAACTAATTCAAGATCATGTACCGCGCA
* * *
43312608 GCTTCTTTCATGTTGCTTAAGTTGTCTTGAAGCATAGCCTATTACTTTGTCTTCTTGTATCAAGA
196 GCTTCTTTCATGTGGCTTAAGTTGTCTTGAAGCATAGCCTATTACTTTATCTTCTTGCATCAAGA
* * * *
43312673 CACAACCCAAACCATTTAATAATGCATCAGTATAAATAATAATTTTCTTACCCGATTC
261 CACAACCCAAACCATTTAATAATGCATCACTATAAATAATAAATTCCTTACCAGATTC
43312731 A
1 A
43312732 GGCTGTACCA
Statistics
Matches: 293, Mismatches: 26, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
318 293 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (318 bp):
ATAATCAATAACCAATTCATAATCTTTTATCAATTCTAGCCATCTACGTTGTCTCAAATTCAAAT
CTTTCTGTGTCATCAAATACTTCAAGATTTTATGATCAGTATAAATATGACACTTTTCAACATAA
AAATAATGCCGCCATATTTTCAATGCAAACACAATAGCAACTAATTCAAGATCATGTACCGCGCA
GCTTCTTTCATGTGGCTTAAGTTGTCTTGAAGCATAGCCTATTACTTTATCTTCTTGCATCAAGA
CACAACCCAAACCATTTAATAATGCATCACTATAAATAATAAATTCCTTACCAGATTC
Found at i:43316892 original size:50 final size:50
Alignment explanation
Indices: 43316785--43316968 Score: 197
Period size: 50 Copynumber: 3.7 Consensus size: 50
43316775 ATGCCAAAGC
** * * * * *
43316785 CATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCATGT
1 CATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGATACCAACGT
* * ** *
43316836 CATGTCCTAGACATGGTCTAACGGGGGACCTCTCATCTTGATACCAACGT
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATACCAACGT
* * * * *
43316886 CATGTCCCAGACTTGGTCTTTCATGGGACCTCTCATCTCGGTGCCAACGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATACCAACGT
*
43316936 CATGCCCCAGACATGGTCTTACATGGGACCTCT
1 CATGTCCCAGACATGGTCTTACATGGGACCTCT
43316969 TTACCCAAAT
Statistics
Matches: 108, Mismatches: 25, Indels: 1
0.81 0.19 0.01
Matches are distributed among these distances:
50 84 0.78
51 24 0.22
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.28
Consensus pattern (50 bp):
CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATACCAACGT
Found at i:43316964 original size:100 final size:101
Alignment explanation
Indices: 43316785--43316968 Score: 244
Period size: 100 Copynumber: 1.8 Consensus size: 101
43316775 ATGCCAAAGC
** * * * * *
43316785 CATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCATGTCATGTCCTAGACAT
1 CATGTCCCAGACATGGTCTTACATGGGATCCTCTCATATCGGTGCCAACGCCATGCCCCAGACAT
*
43316850 GGTCTAACGGGGGACCTCTCATCTTGATACCAACGT
66 GGTCTAACAGGGGACCTCTCATCTTGATACCAACGT
* * *
43316886 CATGTCCCAGACTTGGTCTTTCATGGGA-CCTCTCATCTCGGTGCCAACGCCATGCCCCAGACAT
1 CATGTCCCAGACATGGTCTTACATGGGATCCTCTCATATCGGTGCCAACGCCATGCCCCAGACAT
* *
43316950 GGTCTTACATGGGACCTCT
66 GGTCTAACAGGGGACCTCT
43316969 TTACCCAAAT
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
100 44 0.63
101 26 0.37
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.28
Consensus pattern (101 bp):
CATGTCCCAGACATGGTCTTACATGGGATCCTCTCATATCGGTGCCAACGCCATGCCCCAGACAT
GGTCTAACAGGGGACCTCTCATCTTGATACCAACGT
Found at i:43321495 original size:48 final size:48
Alignment explanation
Indices: 43321407--43321602 Score: 196
Period size: 48 Copynumber: 4.1 Consensus size: 48
43321397 TAGATTTCTC
* * * * * * *
43321407 GGTGGCCTGCACACAGTCCGTACCACCTTTGTGTAATAACAG-ATACTC
1 GGTGGTCTGCACACAGTCCGTGCCACCCTTATATCATAACAGAATA-TT
* * * * * **
43321455 AGTGGTCTACACATAGTCTGTGCCACCCTTATATCTTAACAGTTTATT
1 GGTGGTCTGCACACAGTCCGTGCCACCCTTATATCATAACAGAATATT
* * *
43321503 GGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAATAGAATATT
1 GGTGGTCTGCACACAGTCCGTGCCACCCTTATATCATAACAGAATATT
* * *
43321551 GGTGGTCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGAATATC
1 GGTGGTCTGCACACAGTCCGTGCCACCCTTATATCATAACAGAATATT
43321599 GGTG
1 GGTG
43321603 CGCATAGTAG
Statistics
Matches: 120, Mismatches: 27, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
48 118 0.98
49 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.29
Consensus pattern (48 bp):
GGTGGTCTGCACACAGTCCGTGCCACCCTTATATCATAACAGAATATT
Found at i:43321574 original size:96 final size:96
Alignment explanation
Indices: 43321407--43321580 Score: 242
Period size: 96 Copynumber: 1.8 Consensus size: 96
43321397 TAGATTTCTC
* * *
43321407 GGTGGCCTGCACACAGTCCGTACCACCTTTGTGTAATAACAGATACTCAGTGGTCTACACATAGT
1 GGTGGCCTGCACACAGTCCGTACCACCCTTGTATAATAACAGATACTCAGTGGTCTACACACAGT
*
43321472 CTGTGCCACCCTTATATCTTAACAGTTTATT
66 CCGTGCCACCCTTATATCTTAACAGTTTATT
* * * ** *
43321503 GGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAATAGAATA-TTGGTGGTCTGCACACAG
1 GGTGGCCTGCACACAGTCCGTACCACCCTTGTATAATAACAG-ATACTCAGTGGTCTACACACAG
43321567 TCCGTGCCACCCTT
65 TCCGTGCCACCCTT
43321581 GTGTCATAAC
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
96 64 0.96
97 3 0.04
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (96 bp):
GGTGGCCTGCACACAGTCCGTACCACCCTTGTATAATAACAGATACTCAGTGGTCTACACACAGT
CCGTGCCACCCTTATATCTTAACAGTTTATT
Found at i:43324516 original size:48 final size:48
Alignment explanation
Indices: 43324457--43324654 Score: 202
Period size: 48 Copynumber: 4.1 Consensus size: 48
43324447 AATAGATTTC
* * *
43324457 TCGGTGGCCTGCACACAGTCCGTAG-CACCTTTGTGTAATAACAGATTC
1 TCGGTGGCCTGCACACAGTCCGT-GCCACCCTTGTATAATAACAGATTA
* * * * * *
43324505 TCGGTGGCCTGCACATACTCTGTGCCACCATTGTATATTAACAGTTTA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATAATAACAGATTA
* * *
43324553 TTGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAACAGAATA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATAATAACAGATTA
* * * * * *
43324601 GT-GGTGGCTTACACACAGTCCATGCCACCCTTGTGTCATAACAGAATA
1 -TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATAATAACAGATTA
43324649 TCGGTG
1 TCGGTG
43324655 CGCATAGTAG
Statistics
Matches: 126, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
47 2 0.02
48 123 0.98
49 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.28
Consensus pattern (48 bp):
TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATAATAACAGATTA
Found at i:43325925 original size:21 final size:21
Alignment explanation
Indices: 43325873--43325926 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
43325863 ACAACGTATA
*
43325873 TGCAATTCAGGGGTACTAATG
1 TGCAATTCAGGGGCACTAATG
* *
43325894 TACAAAT-AGGGGCAC-ATATG
1 TGCAATTCAGGGGCACTA-ATG
43325914 TGCAATTCAGGGG
1 TGCAATTCAGGGG
43325927 TAACGAAGTA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 15 0.58
21 10 0.38
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (21 bp):
TGCAATTCAGGGGCACTAATG
Found at i:43325925 original size:41 final size:41
Alignment explanation
Indices: 43325873--43326045 Score: 197
Period size: 41 Copynumber: 4.2 Consensus size: 41
43325863 ACAACGTATA
* *
43325873 TGCAATTCAGGGGTACTAATGTACAAATAGGGGCACATATG
1 TGCAATTCAGGGGTACTAAAGTACAAACAGGGGCACATATG
* ** *
43325914 TGCAATTCAGGGGTAAC-GAAGTACAAACAGGGGCATGTGTG
1 TGCAATTCAGGGGT-ACTAAAGTACAAACAGGGGCACATATG
* * *
43325955 TGCAATTTAGGGGTA-TCAAAGTACAAACAGGGGCACGTAAG
1 TGCAATTCAGGGGTACT-AAAGTACAAACAGGGGCACATATG
* * * *
43325996 TGCAATTCAGTGGTACCAAAGTACAAATAGGGGCACATTTG
1 TGCAATTCAGGGGTACTAAAGTACAAACAGGGGCACATATG
43326037 TGCAATTCA
1 TGCAATTCA
43326046 ACAATATTCT
Statistics
Matches: 110, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
40 1 0.01
41 107 0.97
42 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.23
Consensus pattern (41 bp):
TGCAATTCAGGGGTACTAAAGTACAAACAGGGGCACATATG
Found at i:43326018 original size:82 final size:82
Alignment explanation
Indices: 43325873--43326045 Score: 222
Period size: 82 Copynumber: 2.1 Consensus size: 82
43325863 ACAACGTATA
* * * *
43325873 TGCAATTCAGGGGTACTAATGTACAAATAGGGGCACATATGTGCAATTCAGGGGTAACGAAGTAC
1 TGCAATTCAGGGGTACTAAAGTACAAACAGGGGCACATAAGTGCAATTCAGGGGTAACAAAGTAC
43325938 AAACAGGGGCATGTGTG
66 AAACAGGGGCATGTGTG
* * * *
43325955 TGCAATTTAGGGGTA-TCAAAGTACAAACAGGGGCACGTAAGTGCAATTCAGTGGTACCAAAGTA
1 TGCAATTCAGGGGTACT-AAAGTACAAACAGGGGCACATAAGTGCAATTCAGGGGTAACAAAGTA
* ** *
43326019 CAAATAGGGGCACATTTG
65 CAAACAGGGGCATGTGTG
43326037 TGCAATTCA
1 TGCAATTCA
43326046 ACAATATTCT
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
81 1 0.01
82 76 0.99
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.23
Consensus pattern (82 bp):
TGCAATTCAGGGGTACTAAAGTACAAACAGGGGCACATAAGTGCAATTCAGGGGTAACAAAGTAC
AAACAGGGGCATGTGTG
Found at i:43334613 original size:42 final size:43
Alignment explanation
Indices: 43334476--43334625 Score: 155
Period size: 42 Copynumber: 3.6 Consensus size: 43
43334466 AACCGTAACT
* * *
43334476 CGGTGGAATCAGCACTTAGCAACCACC-TTATATTCAGTGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTACAATCAATGATA
* * * * *
43334518 CGG-GGAATCAACACATAACAACCA-CTTTCACAATTAAGGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTT-ACAATCAATGATA
* * * *
43334560 CGGTGGAATCAGCACTTAGCAACCACCTTTAGAAGCAATAATT
1 CGGTGGAATCAGCACTTAGCAACCACCTTTACAATCAATGATA
43334603 CGG-GGAATCAGCACTTAGCAACC
1 CGGTGGAATCAGCACTTAGCAACC
43334626 CCTCGAGGAA
Statistics
Matches: 87, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
40 1 0.01
41 20 0.23
42 34 0.39
43 28 0.32
44 4 0.05
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (43 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTACAATCAATGATA
Found at i:43334689 original size:41 final size:41
Alignment explanation
Indices: 43334632--43334819 Score: 277
Period size: 41 Copynumber: 4.6 Consensus size: 41
43334622 AACCCCTCGA
* *
43334632 GGAATTTGCACTTAGCAACCCCTTTTTGATCAGAGTTTCAG
1 GGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGATTCAG
*
43334673 GGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGTTTCAG
1 GGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGATTCAG
* * * * *
43334714 TGAATCTGTACTTGGCAACCCCTTTTTGATCAGTGATTCGG
1 GGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGATTCAG
* *
43334755 GGAATCTGCACTTAGCAACCCCTTTTTGATCAGTGATTCGG
1 GGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGATTCAG
*
43334796 GGAATCTGCACTAAGCAACCCCTT
1 GGAATCTGCACTTAGCAACCCCTT
43334820 ACATTCAATG
Statistics
Matches: 136, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 136 1.00
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.32
Consensus pattern (41 bp):
GGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGATTCAG
Found at i:43342313 original size:41 final size:41
Alignment explanation
Indices: 43342268--43342459 Score: 244
Period size: 41 Copynumber: 4.7 Consensus size: 41
43342258 TAACAACCCC
*
43342268 TCGGGGAATCTGCACTTAGCAACCTCTTTTTGATAAGAGTT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATAAGAGTT
* *
43342309 TCGGGGAATCTGCACTTACCAACCCCTTTTTGATCAGAGTT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATAAGAGTT
* * * * *
43342350 TCAGGGAATCTGCACTTGGCAACCTCTTTTTGATTAGTGATT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATAAGAG-TT
* *
43342392 T-GGGGAATCTGCACTTAGCAACCCCTTTTTGA-ACAGTGAT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATA-AGAGTT
* *
43342432 TCAGGGAATCTGCACTAAGCAACCCCTT
1 TCGGGGAATCTGCACTTAGCAACCCCTT
43342460 ACATTTAATG
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
40 2 0.02
41 127 0.96
42 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (41 bp):
TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATAAGAGTT
Found at i:43342408 original size:82 final size:82
Alignment explanation
Indices: 43342271--43342455 Score: 282
Period size: 82 Copynumber: 2.3 Consensus size: 82
43342261 CAACCCCTCG
43342271 GGGAATCTGCACTTAGCAACCTCTTTTTGATAAGAGTTTCGGGGAATCTGCACTTACCAACCCCT
1 GGGAATCTGCACTTAGCAACCTCTTTTTGATAAGAGTTTCGGGGAATCTGCACTTACCAACCCCT
* *
43342336 TTTTGATCAGAGTTTCA
66 TTTTGAACAGAGATTCA
* * * *
43342353 GGGAATCTGCACTTGGCAACCTCTTTTTGATTAGTGATTT-GGGGAATCTGCACTTAGCAACCCC
1 GGGAATCTGCACTTAGCAACCTCTTTTTGATAAGAG-TTTCGGGGAATCTGCACTTACCAACCCC
*
43342417 TTTTTGAACAGTGATTCA
65 TTTTTGAACAGAGATTCA
*
43342435 GGGAATCTGCACTAAGCAACC
1 GGGAATCTGCACTTAGCAACC
43342456 CCTTACATTT
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
82 90 0.97
83 3 0.03
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (82 bp):
GGGAATCTGCACTTAGCAACCTCTTTTTGATAAGAGTTTCGGGGAATCTGCACTTACCAACCCCT
TTTTGAACAGAGATTCA
Found at i:43349375 original size:27 final size:27
Alignment explanation
Indices: 43349337--43349392 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
43349327 CGAGATCCCC
*
43349337 GATACCTGTATTTATTTCTCCAGACTA
1 GATACATGTATTTATTTCTCCAGACTA
43349364 GATACATGTATTTATTTCTCCAGACTA
1 GATACATGTATTTATTTCTCCAGACTA
43349391 GA
1 GA
43349393 GATACTCAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (27 bp):
GATACATGTATTTATTTCTCCAGACTA
Found at i:43363975 original size:20 final size:19
Alignment explanation
Indices: 43363947--43364005 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
43363937 ATAGTATTTT
43363947 ATTAACTTAATATTAAAGTA
1 ATTAACTTAATATTAAA-TA
*
43363967 ATTATCTTAATATTAAATTAA
1 ATTAACTTAATATTAAA-T-A
*
43363988 ATTAAATTAA-ATTAAATA
1 ATTAACTTAATATTAAATA
43364006 TTTATCTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 23 0.68
21 9 0.26
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTAACTTAATATTAAATA
Found at i:43363988 original size:5 final size:5
Alignment explanation
Indices: 43363973--43364004 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
43363963 AGTAATTATC
43363973 TTAATA TTAAA TTAAA TTAAA TTAAA TTAAA T
1 TTAA-A TTAAA TTAAA TTAAA TTAAA TTAAA T
43364005 ATTTATCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:43377138 original size:25 final size:26
Alignment explanation
Indices: 43377065--43377139 Score: 91
Period size: 26 Copynumber: 2.9 Consensus size: 26
43377055 TCTCATCTGT
*
43377065 ATTTTACCCCTA-TCAAAATTTTGACG
1 ATTTTATCCCTAGT-AAAATTTTGACG
* *
43377091 ATTTTATCCCTTGTAAAAATTTGACG
1 ATTTTATCCCTAGTAAAATTTTGACG
*
43377117 ATTTT-TTCCTAGTAAAATTTTGA
1 ATTTTATCCCTAGTAAAATTTTGA
43377140 AAAAATATGT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
25 15 0.36
26 26 0.62
27 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (26 bp):
ATTTTATCCCTAGTAAAATTTTGACG
Found at i:43377307 original size:18 final size:18
Alignment explanation
Indices: 43377284--43377320 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
43377274 TGCAAATGGA
*
43377284 TCATTTCCATTTTAATTT
1 TCATTTCCATTTCAATTT
43377302 TCATTTCCATTTCAATTT
1 TCATTTCCATTTCAATTT
43377320 T
1 T
43377321 TGGAAACCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (18 bp):
TCATTTCCATTTCAATTT
Found at i:43378112 original size:26 final size:26
Alignment explanation
Indices: 43378082--43378138 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
43378072 TCTCATCCTT
43378082 ATTTTAACCCTAACAAAATTTTAACG
1 ATTTTAACCCTAACAAAATTTTAACG
* *** *
43378108 ATTTTACCCCTTGTAAAATTTTGACG
1 ATTTTAACCCTAACAAAATTTTAACG
43378134 ATTTT
1 ATTTT
43378139 TCCCTGGTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (26 bp):
ATTTTAACCCTAACAAAATTTTAACG
Found at i:43378149 original size:25 final size:26
Alignment explanation
Indices: 43378096--43378156 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 26
43378086 TAACCCTAAC
* *
43378096 AAAATTTTAACGATTTTACCCCTTGT
1 AAAATTTTGACGATTTTACCCCTGGT
*
43378122 AAAATTTTGACGATTTT-TCCCTGGT
1 AAAATTTTGACGATTTTACCCCTGGT
43378147 AAAATTTTGA
1 AAAATTTTGA
43378157 GAAAATATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 16 0.50
26 16 0.50
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (26 bp):
AAAATTTTGACGATTTTACCCCTGGT
Found at i:43389644 original size:22 final size:22
Alignment explanation
Indices: 43389616--43389664 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
43389606 ACTGGTGTCG
*
43389616 TGACACCCTAGTGTTTATGTAA
1 TGACACCCTAGTGTCTATGTAA
* *
43389638 TGACACCCTATTGTCTATGTCA
1 TGACACCCTAGTGTCTATGTAA
43389660 TGACA
1 TGACA
43389665 TTGAAGGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (22 bp):
TGACACCCTAGTGTCTATGTAA
Found at i:43390401 original size:14 final size:14
Alignment explanation
Indices: 43390382--43390412 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
43390372 AAGATTGGAC
43390382 TATACAAGTGTGAA
1 TATACAAGTGTGAA
43390396 TATACAAGTGTGAA
1 TATACAAGTGTGAA
43390410 TAT
1 TAT
43390413 TTCATAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (14 bp):
TATACAAGTGTGAA
Found at i:43394410 original size:119 final size:119
Alignment explanation
Indices: 43394196--43394435 Score: 453
Period size: 119 Copynumber: 2.0 Consensus size: 119
43394186 TCACTTGGCG
*
43394196 TTAGATATATGATTGATTGGTCTTAGTGTTAGTGGGATATTGTTAGAGTATGCCTAAAGATTAAT
1 TTAGATATATGATTGATTGGTCTTAGTGTTAGTGGGATATTGTTAGAGTATGCCTAAAGACTAAT
*
43394261 CATGAGATGATTGTAATCACATACTTGTTTTACCCTATTTGCTAATATAAGGCA
66 CATGAGATGATTGTAATCACATACTCGTTTTACCCTATTTGCTAATATAAGGCA
43394315 TTAGATATATGATTGATTGGTCTTAGTGTTAGTGGGATATTGTTAGAGTATGCCTAAAGACTAAT
1 TTAGATATATGATTGATTGGTCTTAGTGTTAGTGGGATATTGTTAGAGTATGCCTAAAGACTAAT
*
43394380 CATGAGATTATTGTAATCACATACTCGTTTTACCCTATTTGCTAATATAAGGCA
66 CATGAGATGATTGTAATCACATACTCGTTTTACCCTATTTGCTAATATAAGGCA
43394434 TT
1 TT
43394436 GTCATTTTTA
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
119 118 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.40
Consensus pattern (119 bp):
TTAGATATATGATTGATTGGTCTTAGTGTTAGTGGGATATTGTTAGAGTATGCCTAAAGACTAAT
CATGAGATGATTGTAATCACATACTCGTTTTACCCTATTTGCTAATATAAGGCA
Found at i:43396744 original size:59 final size:59
Alignment explanation
Indices: 43396658--43396805 Score: 154
Period size: 59 Copynumber: 2.5 Consensus size: 59
43396648 AAACTATAAT
* * ** **
43396658 ATTCTAAAAATCTTGTAACCAGGGTAAAC-AGTTGTGATTGTAAATCAACGAATTGCAAG
1 ATTCTAAAAATATTGTAAGCAAAGTAAACGA-TTGTGATTGTAAATCAACGAACCGCAAG
* * * * ** **
43396717 ATTCTGAAAATCTTGTATGCGAAGTAAACGATTGTTTTTGTAAATCAGTGAACCGCAAG
1 ATTCTAAAAATATTGTAAGCAAAGTAAACGATTGTGATTGTAAATCAACGAACCGCAAG
43396776 ATTCTAAAAATATTGTAAGCAAAGTAAACG
1 ATTCTAAAAATATTGTAAGCAAAGTAAACG
43396806 TTTATGATCA
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
59 71 0.99
60 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (59 bp):
ATTCTAAAAATATTGTAAGCAAAGTAAACGATTGTGATTGTAAATCAACGAACCGCAAG
Found at i:43396820 original size:59 final size:59
Alignment explanation
Indices: 43396712--43396827 Score: 142
Period size: 59 Copynumber: 2.0 Consensus size: 59
43396702 TCAACGAATT
* * * * * ** **
43396712 GCAAGATTCTGAAAATCTTGTATGCGAAGTAAACGATTGTTTTTGTAAATCAGTGAACC
1 GCAAGATTCTAAAAATATTGTAAGCAAAGTAAACGATTATGATCATAAATCAGTGAACC
*
43396771 GCAAGATTCTAAAAATATTGTAAGCAAAGTAAACGTTTATGATCATAAATCAGTGAA
1 GCAAGATTCTAAAAATATTGTAAGCAAAGTAAACGATTATGATCATAAATCAGTGAA
43396828 ACTTAAGTTT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
59 47 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (59 bp):
GCAAGATTCTAAAAATATTGTAAGCAAAGTAAACGATTATGATCATAAATCAGTGAACC
Found at i:43401417 original size:28 final size:28
Alignment explanation
Indices: 43401379--43401435 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
43401369 CGTTTACCTT
43401379 AATTAAATAAAAAATGTTTAATTAATTA
1 AATTAAATAAAAAATGTTTAATTAATTA
* * * * *
43401407 AATTAATTAAACATTTTTTATTTAATTA
1 AATTAAATAAAAAATGTTTAATTAATTA
43401435 A
1 A
43401436 GGTAAACGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (28 bp):
AATTAAATAAAAAATGTTTAATTAATTA
Found at i:43402816 original size:115 final size:110
Alignment explanation
Indices: 43402319--43402872 Score: 402
Period size: 114 Copynumber: 4.9 Consensus size: 110
43402309 TAAGTTACAG
* * * * * * * *
43402319 TTAGTGGCGCTTAAGGAAAAACGCCGCTAAAGGATAATATTAGCGGCG-TTTGACAAGCGCCACA
1 TTAGTGGCGC-CAAGG-AAATCGCCGCTAAAGCATACTATTAGCGGAGCTTTTAGAAGCGCCGCA
43402383 AAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAA
64 AAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAA
* * * **
43402430 TTAGTGGCGCAAAGCGAACA-CGCCACTAAGGCATACTATTAGCGGCA-CTTTGGGCTAAGCGCC
1 TTAGTGGCGCCAAG-GAA-ATCGCCGCTAAAGCATACTATTAGCGG-AGCTTTTAG--AAGCGCC
* * * * * * * *
43402493 GTAAAATTTCTTAACGAAAACGTAGCGTTTCTGTCTTGATGTATACTATAA
61 GCAAAATATCTTAACCAAAACGCAGAGTTT-GGTCTTGAGGTATACTAGAA
* ** * * * * *
43402544 TTAGTGGCG-CATACTGGAAAACGCCGCTAACTC-CAGTATTAGCGGTGCTTTTAATAAAACGCC
1 TTAGTGGCGCCA-A--GGAAATCGCCGCTAAAGCATACTATTAGCGGAGCTTTT-A-GAAGCGCC
* * ** *
43402607 GCAAAATATAC-TCACCAAAACGCAGAGTTTTGTCTTGAGGTATGTTAGTA
61 GCAAAATAT-CTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAA
* * * * *
43402657 TTAGTGGCGCTTATGGGAGCAT-ACCGCTAAAGAATACTATTAGCGGAGCGTTCTTAGAAGCGCC
1 TTAGTGGCGC-CA-AGGA-AATCGCCGCTAAAGCATACTATTAGCGGAGC-TT-TTAGAAGCGCC
* * * * *
43402721 GCAAAATATATTAACCAAAACGCAGCGTTTAGGTCTTGATGTATAGTGGAA
61 GCAAAATATCTTAACCAAAACGCAGAGTTT-GGTCTTGAGGTATACTAGAA
* * *
43402772 TTAGTGGCGTCCAAGAGAAATCGCCTCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAAGCGCCG
1 TTAGTGGCG-CCAAG-GAAATCGCCGCTAAAGCATACTATTAGCGGAGC-TTTT-AGAAGCGCCG
*
43402837 GAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTT
62 CAAAATATCTTAACCAAAACGCAGAG-TTTGGTCTT
43402873 AACCATGCAT
Statistics
Matches: 342, Mismatches: 73, Indels: 52
0.73 0.16 0.11
Matches are distributed among these distances:
110 26 0.08
111 16 0.05
113 66 0.19
114 120 0.35
115 107 0.31
116 7 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (110 bp):
TTAGTGGCGCCAAGGAAATCGCCGCTAAAGCATACTATTAGCGGAGCTTTTAGAAGCGCCGCAAA
ATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAA
Found at i:43405292 original size:8 final size:8
Alignment explanation
Indices: 43405279--43405305 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
43405269 TACCAGTTTG
43405279 TTTGGGAA
1 TTTGGGAA
43405287 TTTGGGAA
1 TTTGGGAA
43405295 TTTGGGAA
1 TTTGGGAA
43405303 TTT
1 TTT
43405306 TTGTATGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.44
Consensus pattern (8 bp):
TTTGGGAA
Found at i:43406554 original size:7 final size:6
Alignment explanation
Indices: 43406528--43406552 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43406518 GAGAGAGAAG
43406528 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
43406553 TACGAATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:43407501 original size:9 final size:9
Alignment explanation
Indices: 43407487--43407825 Score: 303
Period size: 9 Copynumber: 39.4 Consensus size: 9
43407477 TAGTAACCAA
43407487 ATAACTTAC
1 ATAACTTAC
43407496 ATAACTTAC
1 ATAACTTAC
43407505 ATAACTTAC
1 ATAACTTAC
* * *
43407514 AAAAATTAA
1 ATAACTTAC
43407523 ATAACTTAC
1 ATAACTTAC
43407532 ATAACTTAC
1 ATAACTTAC
* *
43407541 ATAAATTAA
1 ATAACTTAC
43407550 ATAACTTAC
1 ATAACTTAC
43407559 ATAACTTAC
1 ATAACTTAC
43407568 ATAACTTAC
1 ATAACTTAC
* *
43407577 ATAAATTAA
1 ATAACTTAC
43407586 ATAACTTAC
1 ATAACTTAC
43407595 ATTAA-TTAC
1 A-TAACTTAC
43407604 ATAACTTAC
1 ATAACTTAC
* *
43407613 ATAAATTAA
1 ATAACTTAC
43407622 ATAACTTAC
1 ATAACTTAC
43407631 ATTAA-TTAC
1 A-TAACTTAC
43407640 ATAACTTAC
1 ATAACTTAC
43407649 AT---TGTAC
1 ATAACT-TAC
* *
43407656 ACAACTCAC
1 ATAACTTAC
43407665 ATAA-TTA-
1 ATAACTTAC
*
43407672 AT-ATTATAC
1 ATAACT-TAC
*
43407681 ACAACTTAC
1 ATAACTTAC
43407690 ATAA--TAC
1 ATAACTTAC
*
43407697 ATTACTTAC
1 ATAACTTAC
43407706 ATAACTTAC
1 ATAACTTAC
43407715 AGT-ACTTAC
1 A-TAACTTAC
43407724 ATAA--TAC
1 ATAACTTAC
43407731 ATAA--TAC
1 ATAACTTAC
*
43407738 ATTACTTAC
1 ATAACTTAC
43407747 ATAACTTAC
1 ATAACTTAC
43407756 AGT-ACTTAC
1 A-TAACTTAC
43407765 ATAA--TAC
1 ATAACTTAC
43407772 ATAACTTAC
1 ATAACTTAC
43407781 AGT-ACTTAC
1 A-TAACTTAC
43407790 AGT-ACTTAC
1 A-TAACTTAC
43407799 ATAA--TAC
1 ATAACTTAC
43407806 ATAA--TAC
1 ATAACTTAC
43407813 ATAACTTAC
1 ATAACTTAC
43407822 ATAA
1 ATAA
43407826 TACAAATTTC
Statistics
Matches: 275, Mismatches: 29, Indels: 52
0.77 0.08 0.15
Matches are distributed among these distances:
6 2 0.01
7 47 0.17
8 13 0.05
9 201 0.73
10 12 0.04
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.33
Consensus pattern (9 bp):
ATAACTTAC
Found at i:43407666 original size:25 final size:25
Alignment explanation
Indices: 43407638--43407694 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
43407628 TACATTAATT
*
43407638 ACATAACTT-ACATTGTACACAACTC
1 ACATAA-TTAACATTATACACAACTC
* *
43407663 ACATAATTAATATTATACACAACTT
1 ACATAATTAACATTATACACAACTC
43407688 ACATAAT
1 ACATAAT
43407695 ACATTACTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 2 0.07
25 26 0.93
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.32
Consensus pattern (25 bp):
ACATAATTAACATTATACACAACTC
Found at i:43407708 original size:41 final size:41
Alignment explanation
Indices: 43407678--43407825 Score: 184
Period size: 41 Copynumber: 3.7 Consensus size: 41
43407668 ATTAATATTA
43407678 TACACAACTTACATAATACATTACTTACATAACTTACAGTACT
1 TACACAA--TACATAATACATTACTTACATAACTTACAGTACT
*
43407721 TACATAATACATAATACATTACTTACATAACTTACAGTACT
1 TACACAATACATAATACATTACTTACATAACTTACAGTACT
* *
43407762 TACATAATACAT-A-AC-TTAC--A-GT-ACTTACAGTACT
1 TACACAATACATAATACATTACTTACATAACTTACAGTACT
* *
43407796 TACATAATACATAATACATAACTTACATAA
1 TACACAATACATAATACATTACTTACATAA
43407826 TACAAATTTC
Statistics
Matches: 94, Mismatches: 4, Indels: 16
0.82 0.04 0.14
Matches are distributed among these distances:
34 24 0.26
35 2 0.02
36 3 0.03
37 3 0.03
38 4 0.04
39 3 0.03
40 2 0.02
41 47 0.50
43 6 0.06
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (41 bp):
TACACAATACATAATACATTACTTACATAACTTACAGTACT
Found at i:43407722 original size:75 final size:76
Alignment explanation
Indices: 43407678--43407825 Score: 212
Period size: 75 Copynumber: 2.0 Consensus size: 76
43407668 ATTAATATTA
* *
43407678 TACACAACTTACATAATACATTACTTACA-TAACTTACAGTACTTACATAATACATAATACATTA
1 TACACAACTTACATAATACATAACTTACAGTAACTTACAGTACTTACATAATACACAATACATTA
*
43407742 CTTACATAACT
66 ATTACATAACT
** *
43407753 TACAGTACTTACATAATACATAACTTACAGT-ACTTACAGTACTTACATAATACATAATACA-TA
1 TACACAACTTACATAATACATAACTTACAGTAACTTACAGTACTTACATAATACACAATACATTA
43407816 ACTTACATAA
66 A-TTACATAA
43407826 TACAAATTTC
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
74 2 0.03
75 64 0.96
76 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (76 bp):
TACACAACTTACATAATACATAACTTACAGTAACTTACAGTACTTACATAATACACAATACATTA
ATTACATAACT
Found at i:43413305 original size:21 final size:21
Alignment explanation
Indices: 43413279--43413348 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
43413269 CAACTTAAAA
* *
43413279 CAGAGGTGGCAGCGAGGGAAG
1 CAGAGGTCGCAGCGAGAGAAG
*
43413300 CAGAGGTTGCAGCGAGAGAAG
1 CAGAGGTCGCAGCGAGAGAAG
*
43413321 CAGAGGCCGCAGCGAGAGAAG
1 CAGAGGTCGCAGCGAGAGAAG
43413342 CAGAGGT
1 CAGAGGT
43413349 TCAAAAGAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.31, C:0.17, G:0.46, T:0.06
Consensus pattern (21 bp):
CAGAGGTCGCAGCGAGAGAAG
Found at i:43413785 original size:43 final size:42
Alignment explanation
Indices: 43413719--43413858 Score: 165
Period size: 43 Copynumber: 3.3 Consensus size: 42
43413709 AATCCCAAAA
* * *
43413719 TTAGTGGCGTTTGTGAAATAAGCGCCGCGAAAGAACACTACTT
1 TTAGCGGCGTTTGT-AAATAAGCGCCGCTAAAGAACATTACTT
*
43413762 TTAGCGGCGTTTGTAGATGAAGCGCCGCTAAAGAACATTACTT
1 TTAGCGGCGTTTGTAAAT-AAGCGCCGCTAAAGAACATTACTT
* ** * *
43413805 TTAGCGGCGTTT-TCTACCAAGCGCCACTATAGAACATTACTT
1 TTAGCGGCGTTTGT-AAATAAGCGCCGCTAAAGAACATTACTT
43413847 TTAGCGGCGTTT
1 TTAGCGGCGTTT
43413859 TTTTCCTAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
42 38 0.45
43 47 0.55
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (42 bp):
TTAGCGGCGTTTGTAAATAAGCGCCGCTAAAGAACATTACTT
Found at i:43413840 original size:42 final size:42
Alignment explanation
Indices: 43413738--43413990 Score: 240
Period size: 43 Copynumber: 5.9 Consensus size: 42
43413728 TTTGTGAAAT
* * ** **
43413738 AAGCGCCGCGAAAGAACACTACTTTTAGCGGCGTTTGTAGATG
1 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTT-TTTACC
*
43413781 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTCTACC
1 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACC
* * *
43413823 AAGCGCCACTATAGAACATTACTTTTAGCGGCGTTTTTTTCC
1 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACC
* * * * * *
43413865 TAAACTCCGCTAAGGATCATGTTC-TTTAGCGGCGTTTTTTCCC
1 -AAGCGCCGCTAAAGAACAT-TACTTTTAGCGGCGTTTTTTACC
* * *
43413908 AAGCGCCGCTAAAGAACATGA-TCATTAGCGGCGTTTTTTTTCC
1 AAGCGCCGCTAAAGAACATTACT-TTTAGCGGCG-TTTTTTACC
* * *
43413951 TAAGCGCCGCTAAAGAAAATGACCTTTAGCGGCGTTTTTT
1 -AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTT
43413991 TGTAAGCGCC
Statistics
Matches: 174, Mismatches: 29, Indels: 14
0.80 0.13 0.06
Matches are distributed among these distances:
42 64 0.37
43 79 0.45
44 31 0.18
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACC
Found at i:43413947 original size:44 final size:42
Alignment explanation
Indices: 43413781--43413991 Score: 219
Period size: 42 Copynumber: 4.9 Consensus size: 42
43413771 TTTGTAGATG
* * *
43413781 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCG-TTTTCTACC
1 AAGCGCCGCTAAAGAACATGAC-TTTAGCGGCGTTTTTTTCCC
* * * *
43413823 AAGCGCCACTATAGAACATTACTTTTAGCGGCGTTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGAC-TTTAGCGGCGTTTTTTTCCC
* * * * *
43413866 AAACTCCGCTAAGGATCATGTTCTTTAGCGGCG-TTTTTTCCC
1 AAGCGCCGCTAAAGAACATG-ACTTTAGCGGCGTTTTTTTCCC
* *
43413908 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGA-CTTTAGCGGCG-TTTTTTTCCC
*
43413952 AAGCGCCGCTAAAGAAAATGACCTTTAGCGGCGTTTTTTT
1 AAGCGCCGCTAAAGAACATGA-CTTTAGCGGCGTTTTTTT
43413992 GTAAGCGCCG
Statistics
Matches: 140, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
42 65 0.46
43 36 0.26
44 39 0.28
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGACTTTAGCGGCGTTTTTTTCCC
Found at i:43414001 original size:86 final size:85
Alignment explanation
Indices: 43413738--43413990 Score: 260
Period size: 85 Copynumber: 3.0 Consensus size: 85
43413728 TTTGTGAAAT
* * * *** *
43413738 AAGCGCCGCGAAAGAACACT-ACTTTTAGCGGCG-TTTGTAGATGAAGCGCCGCTAAAGAACATT
1 AAGCGCCGCTAAAGAACA-TGACTATTAGCGGCGTTTTTTTCCT-AAGCGCCGCTAAAGAACATG
* *
43413801 ACTTTTAGCGGCGTTTTCTACC
64 ACCTTTAGCGGCGTTTTTTACC
* * * * * * * * **
43413823 AAGCGCCACTATAGAACATTACTTTTAGCGGCGTTTTTTTCCTAAACTCCGCTAAGGATCATGTT
1 AAGCGCCGCTAAAGAACATGACTATTAGCGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGAC
*
43413888 CTTTAGCGGCGTTTTTTCCC
66 CTTTAGCGGCGTTTTTTACC
*
43413908 AAGCGCCGCTAAAGAACATGA-TCATTAGCGGCGTTTTTTTTCCTAAGCGCCGCTAAAGAAAATG
1 AAGCGCCGCTAAAGAACATGACT-ATTAGCGGCG-TTTTTTTCCTAAGCGCCGCTAAAGAACATG
43413972 ACCTTTAGCGGCGTTTTTT
64 ACCTTTAGCGGCGTTTTTT
43413991 TGTAAGCGCC
Statistics
Matches: 136, Mismatches: 28, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
84 2 0.01
85 87 0.64
86 47 0.35
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (85 bp):
AAGCGCCGCTAAAGAACATGACTATTAGCGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGAC
CTTTAGCGGCGTTTTTTACC
Found at i:43414752 original size:30 final size:30
Alignment explanation
Indices: 43414718--43414777 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
43414708 TATTTTATTA
43414718 TTAATTTTGTTATTATTTTAAAGACATTTG
1 TTAATTTTGTTATTATTTTAAAGACATTTG
* *
43414748 TTAATTTTGTTATTATTTTAGAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGACATTTG
43414778 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGACATTTG
Found at i:43427748 original size:23 final size:22
Alignment explanation
Indices: 43427711--43427753 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
43427701 GTGAAATAAA
43427711 AACTAAAAAATTAAATAAGTACT
1 AACTAAAAAATTAAA-AAGTACT
43427734 AACTAAGAAAA-TAAAAAGTA
1 AACTAA-AAAATTAAAAAGTA
43427754 AAATTCCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 10 0.53
24 4 0.21
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.21
Consensus pattern (22 bp):
AACTAAAAAATTAAAAAGTACT
Found at i:43428947 original size:21 final size:22
Alignment explanation
Indices: 43428916--43428966 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
43428906 TTAGTTTTAA
43428916 ATGTTATTTAGTCC-TTAAAAC-C
1 ATGTT-TTTAG-CCATTAAAACAC
*
43428938 ATGTTTTTAGCCATTAAATCAC
1 ATGTTTTTAGCCATTAAAACAC
43428960 ATGTTTT
1 ATGTTTT
43428967 AAATAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 11 0.42
22 13 0.50
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (22 bp):
ATGTTTTTAGCCATTAAAACAC
Found at i:43429693 original size:190 final size:190
Alignment explanation
Indices: 43429357--43429738 Score: 629
Period size: 190 Copynumber: 2.0 Consensus size: 190
43429347 TAATGAATCC
* * * * *
43429357 TTGGCTAATTTTTGGATGTATTGTTGTGTGAATTTATTATTTTGAAGTTCTAGATTTGATAGAAT
1 TTGGATAATTTTTGGATGTATTGTTGTGTGAATTTATTATGTTGAAGTTCCAGATTCGATAGAAC
* *
43429422 CTTCTACGAGTAGAGATAAAGGCAAGGAAAAGCTAGTTTGAGCATTCGGCTTTTAAGCAAAAGCG
66 CTTCTACGAGTAGAGATAAAGGCAAGGAAAAGCTAGTTTGAGCATTCAGCTTTTAAGCAAAAGCA
* *
43429487 TAATTGGTGACTGTATGGAATAATTGCTTGTGGACATGCTTCAATGCATTATTTGGGAAT
131 TAATTAGTGACTGTATGGAATAATTACTTGTGGACATGCTTCAATGCATTATTTGGGAAT
*
43429547 TTGGATAATTTTTGGATGTATTGTTGTGTGAATTTATTGTGTTGAAGTTCCAGATTCGATAGAAC
1 TTGGATAATTTTTGGATGTATTGTTGTGTGAATTTATTATGTTGAAGTTCCAGATTCGATAGAAC
* * *
43429612 CTTCTATGAGTAGAGATAAAGGCAAGGAAAAGCTAGTTTGAGCTTTCAGCTTTTAGGCAAAAGCA
66 CTTCTACGAGTAGAGATAAAGGCAAGGAAAAGCTAGTTTGAGCATTCAGCTTTTAAGCAAAAGCA
* *
43429677 TAATTAGTGGCTGTATGGAATAATTACTTGTGGACATGCTTCAATGCGTTATTTGGGAAT
131 TAATTAGTGACTGTATGGAATAATTACTTGTGGACATGCTTCAATGCATTATTTGGGAAT
43429737 TT
1 TT
43429739 AGTAGTAGCC
Statistics
Matches: 177, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
190 177 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (190 bp):
TTGGATAATTTTTGGATGTATTGTTGTGTGAATTTATTATGTTGAAGTTCCAGATTCGATAGAAC
CTTCTACGAGTAGAGATAAAGGCAAGGAAAAGCTAGTTTGAGCATTCAGCTTTTAAGCAAAAGCA
TAATTAGTGACTGTATGGAATAATTACTTGTGGACATGCTTCAATGCATTATTTGGGAAT
Found at i:43435443 original size:17 final size:15
Alignment explanation
Indices: 43435405--43435447 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
43435395 AATGAATTCA
43435405 TTTTTTTCTCTCTTC
1 TTTTTTTCTCTCTTC
* *
43435420 ATCTTTTCTCTCTTCCC
1 TTTTTTTCTCTCTT--C
43435437 TTTTTTTCTCT
1 TTTTTTTCTCT
43435448 ACTCCTCCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.55
17 10 0.45
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTTTCTCTCTTC
Found at i:43437703 original size:48 final size:48
Alignment explanation
Indices: 43437632--43437733 Score: 186
Period size: 48 Copynumber: 2.1 Consensus size: 48
43437622 AACTACCCTA
*
43437632 CATCCCCAATCCCCACATTCAACCTAACTAGACGAGTAGGAGAAATCT
1 CATCCCCAATCCCCACATTCAACCTAACTAGACGAGTAGGAAAAATCT
*
43437680 CATCCCCAATCCCCATATTCAACCTAACTAGACGAGTAGGAAAAATCT
1 CATCCCCAATCCCCACATTCAACCTAACTAGACGAGTAGGAAAAATCT
43437728 CATCCC
1 CATCCC
43437734 TTATTGGTCT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.35, C:0.34, G:0.11, T:0.20
Consensus pattern (48 bp):
CATCCCCAATCCCCACATTCAACCTAACTAGACGAGTAGGAAAAATCT
Found at i:43439905 original size:23 final size:22
Alignment explanation
Indices: 43439877--43439928 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
43439867 CCTTTGTGGC
*
43439877 GCATTCTAAATTTGGCGTTTATG
1 GCATTCT-AATTTGGCCTTTATG
** *
43439900 GCATTCTGGTTTGGCCTTTGTG
1 GCATTCTAATTTGGCCTTTATG
43439922 GCATTCT
1 GCATTCT
43439929 GTTAGCCCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.44
Consensus pattern (22 bp):
GCATTCTAATTTGGCCTTTATG
Found at i:43439923 original size:22 final size:22
Alignment explanation
Indices: 43439887--43439929 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
43439877 GCATTCTAAA
*
43439887 TTTGGCGTTTATGGCATTCTGG
1 TTTGGCCTTTATGGCATTCTGG
*
43439909 TTTGGCCTTTGTGGCATTCTG
1 TTTGGCCTTTATGGCATTCTG
43439930 TTAGCCCTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.07, C:0.16, G:0.30, T:0.47
Consensus pattern (22 bp):
TTTGGCCTTTATGGCATTCTGG
Found at i:43439942 original size:20 final size:20
Alignment explanation
Indices: 43439852--43439963 Score: 80
Period size: 20 Copynumber: 5.2 Consensus size: 20
43439842 AGGTGCTTGG
*
43439852 GTGGCATTTTGTTAGCCTTT
1 GTGGCATTCTGTTAGCCTTT
* * *
43439872 GTGGCGCATTCTAAATTTGGCGTTT
1 GT-G-GCATTCT---GTTAGCCTTT
* *
43439897 ATGGCATTCTGGTTTGGCCTTT
1 GTGGCATTCT-G-TTAGCCTTT
*
43439919 GTGGCATTCTGTTAGCCCTT
1 GTGGCATTCTGTTAGCCTTT
* *
43439939 GTGGCAATCTGTTAACCTTT
1 GTGGCATTCTGTTAGCCTTT
43439959 GTGGC
1 GTGGC
43439964 GTATTCTATA
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
20 31 0.43
21 2 0.03
22 23 0.32
23 7 0.10
24 1 0.01
25 8 0.11
ACGTcount: A:0.12, C:0.19, G:0.27, T:0.42
Consensus pattern (20 bp):
GTGGCATTCTGTTAGCCTTT
Found at i:43458293 original size:3 final size:3
Alignment explanation
Indices: 43458285--43458333 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
43458275 TTCTTTTTAT
43458285 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43458333 T
1 T
43458334 CACATACGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:43458788 original size:23 final size:23
Alignment explanation
Indices: 43458748--43458794 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
43458738 AGAATTTAGG
* *
43458748 TTTTTTATATTAAGTTTTGTTTT
1 TTTTTTAGATTAAGTTTTGATTT
43458771 TTTTTTAGATTATA-TTTTGATTT
1 TTTTTTAGATTA-AGTTTTGATTT
43458794 T
1 T
43458795 GAAATCTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (23 bp):
TTTTTTAGATTAAGTTTTGATTT
Found at i:43460261 original size:15 final size:15
Alignment explanation
Indices: 43460241--43460270 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
43460231 TTAAGATTAA
43460241 TTAAAAGAACATGAG
1 TTAAAAGAACATGAG
43460256 TTAAAAGAACATGAG
1 TTAAAAGAACATGAG
43460271 AACTCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (15 bp):
TTAAAAGAACATGAG
Found at i:43463452 original size:6 final size:6
Alignment explanation
Indices: 43463419--43463451 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
43463409 AATTAGTTTA
*
43463419 ATTGAC ATTGAC ATTGAC ATTGAC ATTAAC ATT
1 ATTGAC ATTGAC ATTGAC ATTGAC ATTGAC ATT
43463452 ATTATCAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (6 bp):
ATTGAC
Found at i:43464590 original size:21 final size:22
Alignment explanation
Indices: 43464566--43464613 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
43464556 TATAAAAGAG
43464566 TTTGAATAAC-TTATATAAAAT
1 TTTGAATAACTTTATATAAAAT
* * * *
43464587 TTTGGATTACTTTTTATATAAT
1 TTTGAATAACTTTATATAAAAT
43464609 TTTGA
1 TTTGA
43464614 GCTGAAACTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.52
Consensus pattern (22 bp):
TTTGAATAACTTTATATAAAAT
Found at i:43466409 original size:17 final size:18
Alignment explanation
Indices: 43466371--43466412 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
43466361 TGCTTCTAAG
43466371 AAGCACTTTTAGGACAAA
1 AAGCACTTTTAGGACAAA
*
43466389 AAGCACTTTTGGGAC-AA
1 AAGCACTTTTAGGACAAA
43466406 AAGCACT
1 AAGCACT
43466413 CTTAAACAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (18 bp):
AAGCACTTTTAGGACAAA
Found at i:43469115 original size:50 final size:49
Alignment explanation
Indices: 43469056--43469335 Score: 341
Period size: 50 Copynumber: 5.7 Consensus size: 49
43469046 GGCAGTGAGT
*
43469056 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATCGAGGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGA-CGAGGA
** *
43469106 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCAACACGGACAGAGGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAC-GAGGA
* * * * *
43469156 GAG-TCAGTGTAAGACCATGTTTGGGACATGACATCGGCTC-GA-GATGA
1 GTGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACGAGGA
* *
43469203 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATCGAGTA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGA-CGAGGA
*
43469253 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGACAGAGGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAC-GAGGA
* * * * *
43469303 GAGTTAGTGTAAGATCACGTTTGGGACATGGCA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCA
43469336 AAGGCACCGA
Statistics
Matches: 197, Mismatches: 26, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
47 38 0.19
48 2 0.01
49 5 0.03
50 152 0.77
ACGTcount: A:0.27, C:0.19, G:0.33, T:0.20
Consensus pattern (49 bp):
GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACGAGGA
Found at i:43469236 original size:97 final size:98
Alignment explanation
Indices: 43469060--43469335 Score: 333
Period size: 97 Copynumber: 2.8 Consensus size: 98
43469050 GTGAGTGTGC
*
43469060 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATCGAGGAGTGCTAGTGTAAGACCATG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGA-CGAGGAGTGCCAGTGTAAGACCATG
*
43469125 TCTGGGACATGGCATCAACACGGA-CAGAGGAGAG
65 TCTGGGACATGGCATCAACACAGATC-GAGGAGAG
* * * *
43469159 TCAGTGTAAGACCATGTTTGGGACATGACATCGGCTC-GA-GATGAGTGCCAGTGTAAGACCATG
1 -CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACGAGGAGTGCCAGTGTAAGACCATG
** * *
43469222 TCTGGGACATGGCATCGGCACAGATCGAGTAGTG
65 TCTGGGACATGGCATCAACACAGATCGAGGAGAG
* * ** * *
43469256 CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGACAGAGGAGAGTTAGTGTAAGATCAC
1 C-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAC-GAGGAGTGCCAGTGTAAGACCAT
*
43469321 GTTTGGGACATGGCA
64 GTCTGGGACATGGCA
43469336 AAGGCACCGA
Statistics
Matches: 151, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
96 1 0.01
97 81 0.54
98 3 0.02
99 2 0.01
100 64 0.42
ACGTcount: A:0.28, C:0.19, G:0.33, T:0.20
Consensus pattern (98 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACGAGGAGTGCCAGTGTAAGACCATGT
CTGGGACATGGCATCAACACAGATCGAGGAGAG
Found at i:43469325 original size:147 final size:147
Alignment explanation
Indices: 43469056--43469332 Score: 500
Period size: 147 Copynumber: 1.9 Consensus size: 147
43469046 GGCAGTGAGT
43469056 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATCGAGGAGTGCTAGTGTAAGAC
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATCGAGGAGTGCTAGTGTAAGAC
*
43469121 CATGTCTGGGACATGGCATCAACACGGACAGAGGAGAGTCAGTGTAAGACCATGTTTGGGACATG
66 CATGTCTGGGACATGGCATCAACACGGACAGAGGAGAGTCAGTGTAAGACCACGTTTGGGACATG
43469186 ACATCGGCTCGAGATGA
131 ACATCGGCTCGAGATGA
*
43469203 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATCGAGTAGTGCTAGTGTAAGAC
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATCGAGGAGTGCTAGTGTAAGAC
** * *
43469268 CATGTCTGGGACATGGCATCGGCACGGACAGAGGAGAGTTAGTGTAAGATCACGTTTGGGACATG
66 CATGTCTGGGACATGGCATCAACACGGACAGAGGAGAGTCAGTGTAAGACCACGTTTGGGACATG
43469333 GCAAAGGCAC
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
147 124 1.00
ACGTcount: A:0.27, C:0.19, G:0.33, T:0.21
Consensus pattern (147 bp):
GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATCGAGGAGTGCTAGTGTAAGAC
CATGTCTGGGACATGGCATCAACACGGACAGAGGAGAGTCAGTGTAAGACCACGTTTGGGACATG
ACATCGGCTCGAGATGA
Found at i:43474604 original size:8 final size:8
Alignment explanation
Indices: 43474591--43474615 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
43474581 GAGGATCAAT
43474591 TTGTTAAA
1 TTGTTAAA
43474599 TTGTTAAA
1 TTGTTAAA
43474607 TTGTTAAA
1 TTGTTAAA
43474615 T
1 T
43474616 GTTTAAAATT
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:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (8 bp):
TTGTTAAA
Found at i:43475484 original size:20 final size:19
Alignment explanation
Indices: 43475461--43475515 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
43475451 GGTGCCTTTG
43475461 TTTGCACTTCGATGCCCCTA
1 TTTGCACTTCG-TGCCCCTA
* *
43475481 TTTGTACATTTGTGCCCCTA
1 TTTGCAC-TTCGTGCCCCTA
*
43475501 TCTGCACTTCAGTGC
1 TTTGCACTTC-GTGC
43475516 TCTTGTTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 2 0.07
20 23 0.82
21 3 0.11
ACGTcount: A:0.15, C:0.31, G:0.16, T:0.38
Consensus pattern (19 bp):
TTTGCACTTCGTGCCCCTA
Found at i:43476327 original size:20 final size:20
Alignment explanation
Indices: 43476287--43476328 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
43476277 ATAATGGTAT
* * *
43476287 GTATAGGATGTTTTGTTATG
1 GTATAGGATGATATGTAATG
43476307 GTATAGGATGATATGTAATG
1 GTATAGGATGATATGTAATG
43476327 GT
1 GT
43476329 GATTTGGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (20 bp):
GTATAGGATGATATGTAATG
Found at i:43481298 original size:13 final size:13
Alignment explanation
Indices: 43481280--43481304 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43481270 TCGTAACATT
43481280 CTTGTTTTATTTA
1 CTTGTTTTATTTA
43481293 CTTGTTTTATTT
1 CTTGTTTTATTT
43481305 TGCACATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.08, G:0.08, T:0.72
Consensus pattern (13 bp):
CTTGTTTTATTTA
Found at i:43485452 original size:24 final size:24
Alignment explanation
Indices: 43485425--43485476 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
43485415 TTAGTAAGTC
*
43485425 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* * *
43485449 AAATATATTGTACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
43485473 AAAT
1 AAAT
43485477 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:43485649 original size:18 final size:18
Alignment explanation
Indices: 43485626--43485663 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
43485616 GTATGTGTAA
*
43485626 GGTTTGGAAAGCTATGTT
1 GGTTTGAAAAGCTATGTT
*
43485644 GGTTTGAAAAGCTTTGTT
1 GGTTTGAAAAGCTATGTT
43485662 GG
1 GG
43485664 AAAGCTATGC
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:0.21, C:0.05, G:0.34, T:0.39
Consensus pattern (18 bp):
GGTTTGAAAAGCTATGTT
Found at i:43493463 original size:51 final size:50
Alignment explanation
Indices: 43493336--43493520 Score: 171
Period size: 51 Copynumber: 3.7 Consensus size: 50
43493326 AAAGTGATGG
* * * * *
43493336 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGG
1 TCACATGTGTAGTACTATGAGCAGGCTACTATGCGTACCGGATAGT-AT-GA
*
43493386 TCGCATGTGTAGTACTAT-ATGCAGGCTACTATGCGTACCGGATAGCT-TCGA
1 TCACATGTGTAGTACTATGA-GCAGGCTACTATGCGTACCGGATAG-TAT-GA
* * * * * *
43493437 TCACGTGTGTAGTACTATGAGTAGGCTACTACGTGTATCGGATAGTGATGG
1 TCACATGTGTAGTACTATGAGCAGGCTACTATGCGTACCGGATAGT-ATGA
*
43493488 TCACATGTGTAGTACTATGTGCAGGCTACTATG
1 TCACATGTGTAGTACTATGAGCAGGCTACTATG
43493521 TGAGCCGATA
Statistics
Matches: 110, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
50 37 0.34
51 70 0.64
52 2 0.02
53 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGAGCAGGCTACTATGCGTACCGGATAGTATGA
Found at i:43493463 original size:101 final size:102
Alignment explanation
Indices: 43493336--43493520 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 102
43493326 AAAGTGATGG
* *
43493336 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACATGTGTAGTACTATGAGCAGGCTACTACGTGTACCAGATAGTGAT-GGTCACATGTGTAGT
43493399 ACTATATGCAGGCTACTATGCGTACCGGATAGCTTCGA
65 ACTATATGCAGGCTACTATGCGTACCGGATAGCTTCGA
* * * *
43493437 TCACGTGTGTAGTACTATGAGTAGGCTACTACGTGTATCGGATAGTGATGGTCACATGTGTAGTA
1 TCACATGTGTAGTACTATGAGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
*
43493502 CTATGTGCAGGCTACTATG
66 CTATATGCAGGCTACTATG
43493521 TGAGCCGATA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
101 37 0.49
102 34 0.45
103 4 0.05
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (102 bp):
TCACATGTGTAGTACTATGAGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
CTATATGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:43493590 original size:33 final size:33
Alignment explanation
Indices: 43493548--43493886 Score: 182
Period size: 33 Copynumber: 9.8 Consensus size: 33
43493538 ACATAAAAGG
43493548 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
43493581 GGTTGCTAAGTGCTGATTCCACTGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---GGT
* *
43493623 GGTTGCTAGGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
43493650 GGTTGCTAAGTGCTGATTCTCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
43493683 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---GGT
* *
43493725 GGTTGCTAAGTGCTGACTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
43493752 GGTTGCTAAGTGCTGATTCTCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
43493785 GGTTGCTAAGTGTTGATTCCACCG-TATCATTGAATGT
1 GGTTGCTAAGTGCTGATTCC-CCGAT-TCATTG---GT
* *
43493822 GAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 ------GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
43493861 GGTTGCTAAGTGCTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCC-CCGAT
43493887 AACGGATAAC
Statistics
Matches: 237, Mismatches: 26, Indels: 85
0.68 0.07 0.24
Matches are distributed among these distances:
27 40 0.17
28 4 0.02
31 4 0.02
32 4 0.02
33 79 0.33
34 18 0.08
35 2 0.01
37 6 0.03
38 4 0.02
39 4 0.02
41 3 0.01
42 50 0.21
43 19 0.08
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:43493720 original size:102 final size:102
Alignment explanation
Indices: 43493544--43493849 Score: 531
Period size: 102 Copynumber: 3.0 Consensus size: 102
43493534 TTGAACATAA
* *
43493544 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACTGTATT
1 AAGGGGTTGCTAAGTGCTGATTCTCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
*
43493609 TTAAATGTGAAGGGGGTTGCTAGGTGCTGATTCCCCC
66 TTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
43493646 AAGGGGTTGCTAAGTGCTGATTCTCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCTCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
*
43493711 TTAAATGTGAAGGGGGTTGCTAAGTGCTGACTCCCCC
66 TTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
*
43493748 AAGGGGTTGCTAAGTGCTGATTCTCCGATTCATTGGTGGTTGCTAAGTGTTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCTCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAT-
* * *
43493813 ATTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
65 TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCC
43493850 GAATCACTGG
Statistics
Matches: 194, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
102 161 0.83
103 33 0.17
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.33
Consensus pattern (102 bp):
AAGGGGTTGCTAAGTGCTGATTCTCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
TTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:43494737 original size:49 final size:49
Alignment explanation
Indices: 43494653--43494753 Score: 123
Period size: 49 Copynumber: 2.1 Consensus size: 49
43494643 ACGAGTACTT
* * * * *
43494653 TCGGTAAGTGATATGTGATTCCGTATAGGAGCATAGCTGGGCTATGGCA
1 TCGGTAAGTGATATGTGATTACATATAAGACCATAGCTGGACTATGGCA
* *
43494702 TCGGTATA-TGATATGTGATTACATGTAAGACCATAGTTGGACTATGGCA
1 TCGGTA-AGTGATATGTGATTACATATAAGACCATAGCTGGACTATGGCA
43494751 TCG
1 TCG
43494754 AGAAAACGAG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
49 43 0.98
50 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (49 bp):
TCGGTAAGTGATATGTGATTACATATAAGACCATAGCTGGACTATGGCA
Found at i:43496181 original size:8 final size:8
Alignment explanation
Indices: 43496168--43496195 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
43496158 GATTTTTAAA
43496168 TATTATTT
1 TATTATTT
43496176 TATTATTT
1 TATTATTT
43496184 TATTATTT
1 TATTATTT
43496192 TATT
1 TATT
43496196 GTTTAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TATTATTT
Found at i:43500207 original size:30 final size:30
Alignment explanation
Indices: 43500171--43500227 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
43500161 AAGACACGAC
*
43500171 CATGTGTCCTTAGTTCGAAGGTTACACAGT
1 CATGTGTCCCTAGTTCGAAGGTTACACAGT
* *
43500201 CATGTGTCCCTAGTTTGAATGTTACAC
1 CATGTGTCCCTAGTTCGAAGGTTACAC
43500228 GACTGTGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (30 bp):
CATGTGTCCCTAGTTCGAAGGTTACACAGT
Found at i:43505668 original size:18 final size:17
Alignment explanation
Indices: 43505636--43505675 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
43505626 ATAAAAAACA
43505636 ATTAAAATCATATTTAT
1 ATTAAAATCATATTTAT
*
43505653 ATTAAATATTATATTTAT
1 ATTAAA-ATCATATTTAT
43505671 ATTAA
1 ATTAA
43505676 TGTTAAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTAAAATCATATTTAT
Found at i:43507764 original size:34 final size:35
Alignment explanation
Indices: 43507710--43507776 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
43507700 CAAACACCAG
*
43507710 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
43507745 AAAACATTTTCTAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
43507777 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:43509315 original size:89 final size:88
Alignment explanation
Indices: 43509204--43509370 Score: 244
Period size: 89 Copynumber: 1.9 Consensus size: 88
43509194 TAGTGAAAAA
* * *
43509204 AATTGTATGGTCGCAATAATAATTAATAATAGTGACATGATATGTTATCACTATTACATCAGTTC
1 AATTGTATGGCCACAATAATAATTAATAATAGTGACATGATATGATATCACTATTACATCAGTTC
43509269 TCAAGAAAAAAAAACTTGAAGGC
66 TCAAGAAAAAAAAACTTGAAGGC
* * * *
43509292 AATTCGTATGGCCACAATAATAATTAATAATAGTGACTTTATATGATGTCACTATTACATCATTT
1 AATT-GTATGGCCACAATAATAATTAATAATAGTGACATGATATGATATCACTATTACATCAGTT
* *
43509357 CTCGAGGAAAAAAA
65 CTCAAGAAAAAAAA
43509371 GAATTTGGAG
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
88 4 0.06
89 65 0.94
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (88 bp):
AATTGTATGGCCACAATAATAATTAATAATAGTGACATGATATGATATCACTATTACATCAGTTC
TCAAGAAAAAAAAACTTGAAGGC
Done.