Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 132 of 163
Found at i:42697054 original size:28 final size:29
Alignment explanation
Indices: 42697023--42697078 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
42697013 ATAACTTTTT
*
42697023 ATTATTTATGAAAAT-ATCCATTTTAAAA
1 ATTATGTATGAAAATGATCCATTTTAAAA
* *
42697051 ATTATGTATGTAAATGATTCATTTTAAA
1 ATTATGTATGAAAATGATCCATTTTAAA
42697079 CAGTAAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (29 bp):
ATTATGTATGAAAATGATCCATTTTAAAA
Found at i:42697345 original size:26 final size:27
Alignment explanation
Indices: 42697306--42697357 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
42697296 ATTAAATTGA
*
42697306 AATAACCTTTAAAAAATAT-TAAAAAC
1 AATAACCTTAAAAAAATATATAAAAAC
*
42697332 AATAATCTTAAAAAAATATATAAAAA
1 AATAACCTTAAAAAAATATATAAAAA
42697358 TCTTATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (27 bp):
AATAACCTTAAAAAAATATATAAAAAC
Found at i:42697827 original size:136 final size:136
Alignment explanation
Indices: 42697583--42697842 Score: 439
Period size: 136 Copynumber: 1.9 Consensus size: 136
42697573 AGTTTGTATG
** * * *
42697583 AGGTTCACAAAATTTGGGATGAGGATGCATAGTCCCTTCTCGTCCAGTGATTATGCAAAACCAAG
1 AGGTTCACAAAAACTGGGATCAGGATGCATAGTCCCTTCTCGTCCAGTGATTATGCAAAAACAAA
* *
42697648 TTTGACTGTTAGATAATATCCTATCTCAATTTTCTCTTCATAGGCCTAAAATTAATAATAGCTGA
66 TTTGACTGTTAGATAATATCCTACCTCAATTTTCTCCTCATAGGCCTAAAATTAATAATAGCTGA
42697713 AATTTT
131 AATTTT
* *
42697719 AGGTTCATAAAAACTGGGATCATGATGCATAGTCCCTTCTCGTCCAGTGATTATGCAAAAACAAA
1 AGGTTCACAAAAACTGGGATCAGGATGCATAGTCCCTTCTCGTCCAGTGATTATGCAAAAACAAA
42697784 TTTGACTGTTAGATAATATCCTACCTCAATTTTCTCCTCATAGGCCTAAAATTAATAAT
66 TTTGACTGTTAGATAATATCCTACCTCAATTTTCTCCTCATAGGCCTAAAATTAATAAT
42697843 TAGATCTTTA
Statistics
Matches: 115, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
136 115 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (136 bp):
AGGTTCACAAAAACTGGGATCAGGATGCATAGTCCCTTCTCGTCCAGTGATTATGCAAAAACAAA
TTTGACTGTTAGATAATATCCTACCTCAATTTTCTCCTCATAGGCCTAAAATTAATAATAGCTGA
AATTTT
Found at i:42698456 original size:5 final size:6
Alignment explanation
Indices: 42698440--42698465 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
42698430 TTTAAAATTT
42698440 TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA
42698466 CATATAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:42700249 original size:6 final size:6
Alignment explanation
Indices: 42700238--42700265 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
42700228 AGTGGAATAA
42700238 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
42700266 TTTTTAACCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:42702268 original size:20 final size:20
Alignment explanation
Indices: 42702243--42702289 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
42702233 TCTTTCTCGT
42702243 TTAGTTTTCATAAACTTCAA
1 TTAGTTTTCATAAACTTCAA
42702263 TTAGTTTTCATAAACTTCAA
1 TTAGTTTTCATAAACTTCAA
42702283 TTAGTTT
1 TTAGTTT
42702290 AGCCAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.49
Consensus pattern (20 bp):
TTAGTTTTCATAAACTTCAA
Found at i:42705216 original size:10 final size:10
Alignment explanation
Indices: 42705198--42705278 Score: 60
Period size: 10 Copynumber: 8.1 Consensus size: 10
42705188 TATTTAATAT
*
42705198 TATAGAATTA
1 TATAAAATTA
*
42705208 TAGAAAATTA
1 TATAAAATTA
*
42705218 TATAAATATAA
1 TATAAA-ATTA
*
42705229 T-TAAAATGA
1 TATAAAATTA
*
42705238 TA-AAAATTC
1 TATAAAATTA
42705247 TATAAAATTAA
1 TATAAAATT-A
*
42705258 TAAAAAATTA
1 TATAAAATTA
42705268 TA-AAAACTTA
1 TATAAAA-TTA
42705278 T
1 T
42705279 TGAAAGTATA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
9 15 0.26
10 30 0.53
11 12 0.21
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (10 bp):
TATAAAATTA
Found at i:42705243 original size:29 final size:30
Alignment explanation
Indices: 42705211--42705278 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
42705201 AGAATTATAG
*
42705211 AAAATTATAT-AAATATAAT-TAAAATGATA
1 AAAATTATATAAAAT-TAATAAAAAATGATA
* *
42705240 AAAATTCTATAAAATTAATAAAAAATTATA
1 AAAATTATATAAAATTAATAAAAAATGATA
42705270 AAAACTTAT
1 AAAA-TTAT
42705279 TGAAAGTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 13 0.41
30 16 0.50
31 3 0.09
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (30 bp):
AAAATTATATAAAATTAATAAAAAATGATA
Found at i:42711220 original size:22 final size:21
Alignment explanation
Indices: 42711179--42711223 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
42711169 TCCAACTTAA
*
42711179 TTTAAATATAATAAATTAATT
1 TTTAAATATAATAAAATAATT
42711200 TTTAAATTATAA-ACAAATAATT
1 TTTAAA-TATAATA-AAATAATT
42711222 TT
1 TT
42711224 ATTCTTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTAAATATAATAAAATAATT
Found at i:42715581 original size:107 final size:108
Alignment explanation
Indices: 42715424--42715638 Score: 423
Period size: 107 Copynumber: 2.0 Consensus size: 108
42715414 TCCATATTCA
42715424 TTCAAAATGATTTTTTTAAATTATATAAAGTTTAAAAAAATATTAAAAATTATTTTTCTTTAAAA
1 TTCAAAATGATTTTTTTAAATTATATAAAGTTTAAAAAAATATTAAAAATTATTTTTCTTTAAAA
42715489 ACTGATATGTGTATAAATTTTTAATTTTATTGGTACCTTTTAG
66 ACTGATATGTGTATAAATTTTTAATTTTATTGGTACCTTTTAG
42715532 TTCAAAATGA-TTTTTTAAATTATATAAAGTTTAAAAAAATATTAAAAATTATTTTTCTTTAAAA
1 TTCAAAATGATTTTTTTAAATTATATAAAGTTTAAAAAAATATTAAAAATTATTTTTCTTTAAAA
42715596 ACTGATATGTGTATAAATTTTTAATTTTATTGGTACCTTTTAG
66 ACTGATATGTGTATAAATTTTTAATTTTATTGGTACCTTTTAG
42715639 AATGTATAAA
Statistics
Matches: 107, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
107 97 0.91
108 10 0.09
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (108 bp):
TTCAAAATGATTTTTTTAAATTATATAAAGTTTAAAAAAATATTAAAAATTATTTTTCTTTAAAA
ACTGATATGTGTATAAATTTTTAATTTTATTGGTACCTTTTAG
Found at i:42725917 original size:31 final size:31
Alignment explanation
Indices: 42725881--42725942 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
42725871 AACGGATTCA
42725881 GAATTAATTATAATTGGGTCAAGTCTAATGT
1 GAATTAATTATAATTGGGTCAAGTCTAATGT
*
42725912 GAATTAATTATACTTGGGTCAAGTCTAATGT
1 GAATTAATTATAATTGGGTCAAGTCTAATGT
42725943 ATCATTCTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (31 bp):
GAATTAATTATAATTGGGTCAAGTCTAATGT
Found at i:42730535 original size:27 final size:28
Alignment explanation
Indices: 42730505--42730571 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
42730495 ACAACTATTG
42730505 AAAAAT-AAAATAAATATAATTTTTTTA
1 AAAAATAAAAATAAATATAATTTTTTTA
* * *
42730532 AAAATTAAAAATTAATATATTTTTTTTA
1 AAAAATAAAAATAAATATAATTTTTTTA
*
42730560 AAATAACAAAAA
1 AAA-AATAAAAA
42730572 GAATTTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
27 5 0.15
28 22 0.67
29 6 0.18
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (28 bp):
AAAAATAAAAATAAATATAATTTTTTTA
Found at i:42730570 original size:28 final size:28
Alignment explanation
Indices: 42730511--42730570 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
42730501 ATTGAAAAAT
*
42730511 AAAATAAATATAATTTTTTTAAAAATTA
1 AAAATAAATATAATTTTTTTAAAAATAA
* *
42730539 AAAATTAATAT-ATTTTTTTTAAAATAA
1 AAAATAAATATAATTTTTTTAAAAATAA
42730566 CAAAA
1 -AAAA
42730571 AGAATTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
AAAATAAATATAATTTTTTTAAAAATAA
Found at i:42734093 original size:18 final size:18
Alignment explanation
Indices: 42734072--42734108 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
42734062 TTTTTGTTAA
42734072 TTTATATATTTTTAATTT
1 TTTATATATTTTTAATTT
42734090 TTTATATATTTTTAATTT
1 TTTATATATTTTTAATTT
42734108 T
1 T
42734109 AAAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTATATATTTTTAATTT
Found at i:42734101 original size:10 final size:10
Alignment explanation
Indices: 42734072--42734103 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
42734062 TTTTTGTTAA
42734072 TTTATATATT
1 TTTATATATT
42734082 TTTA-AT-TT
1 TTTATATATT
42734090 TTTATATATT
1 TTTATATATT
42734100 TTTA
1 TTTA
42734104 ATTTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 6 0.30
9 4 0.20
10 10 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTATATATT
Found at i:42734108 original size:16 final size:16
Alignment explanation
Indices: 42734068--42734109 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
42734058 TTTCTTTTTG
42734068 TTAA-TTTATATATTT
1 TTAATTTTATATATTT
42734083 TTAATTTTTTATATATTT
1 TTAA--TTTTATATATTT
42734101 TTAATTTTA
1 TTAATTTTA
42734110 AAATAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.17
16 5 0.21
18 15 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTAATTTTATATATTT
Found at i:42735498 original size:18 final size:17
Alignment explanation
Indices: 42735457--42735503 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 17
42735447 ATTCTTGTAG
*
42735457 AGATTAATAAGGTATAT
1 AGATTAATAAGGTAAAT
*
42735474 AGA--AATAATGTGAAAT
1 AGATTAATAAGGT-AAAT
42735490 AGATTAATAAGGTA
1 AGATTAATAAGGTA
42735504 TATGGAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
15 7 0.29
16 6 0.25
17 4 0.17
18 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (17 bp):
AGATTAATAAGGTAAAT
Found at i:42736327 original size:9 final size:9
Alignment explanation
Indices: 42736313--42736343 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
42736303 GTTAAACGAA
42736313 TCGAGTTAT
1 TCGAGTTAT
*
42736322 TCGAGTTAA
1 TCGAGTTAT
42736331 TCGAGTTAT
1 TCGAGTTAT
42736340 TCGA
1 TCGA
42736344 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:42739440 original size:45 final size:46
Alignment explanation
Indices: 42739373--42739460 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
42739363 ATGATGTTAC
* * * *
42739373 GTATTTAATATATTGTT-GAAAAATGGAATGTTGTTAAATTATTAT
1 GTATTTAACATATTGTTAAAAAAATGAAATATTGTTAAATTATTAT
*
42739418 GTATTTAGCATATTGTTAAAAAAATGAAATATTGTTAAATTAT
1 GTATTTAACATATTGTTAAAAAAATGAAATATTGTTAAATTAT
42739461 GAATTGAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 15 0.41
46 22 0.59
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.44
Consensus pattern (46 bp):
GTATTTAACATATTGTTAAAAAAATGAAATATTGTTAAATTATTAT
Found at i:42739546 original size:24 final size:24
Alignment explanation
Indices: 42739519--42739566 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
42739509 TCGTTTTGTG
*
42739519 GCAAAGGATCAATTGA-AGACAAAT
1 GCAAAGGATAAATTGACAG-CAAAT
42739543 GCAAAGGATAAATTGACAGCAAAT
1 GCAAAGGATAAATTGACAGCAAAT
42739567 TACCCAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.17
Consensus pattern (24 bp):
GCAAAGGATAAATTGACAGCAAAT
Found at i:42739680 original size:21 final size:21
Alignment explanation
Indices: 42739656--42739722 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
42739646 ACTCATATGA
42739656 GTTTCAGTTTAACCCTTATAG
1 GTTTCAGTTTAACCCTTATAG
* * * * *
42739677 GTTTCTGTTCATCTCTTTTTA-
1 GTTTCAGTTTAAC-CCTTATAG
* *
42739698 GCTTCAGTTTAACCCTTATGG
1 GTTTCAGTTTAACCCTTATAG
42739719 GTTT
1 GTTT
42739723 TTGTTCAGCT
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 4 0.13
21 22 0.71
22 5 0.16
ACGTcount: A:0.16, C:0.19, G:0.15, T:0.49
Consensus pattern (21 bp):
GTTTCAGTTTAACCCTTATAG
Found at i:42739706 original size:42 final size:42
Alignment explanation
Indices: 42739658--42739765 Score: 144
Period size: 42 Copynumber: 2.6 Consensus size: 42
42739648 TCATATGAGT
* * ***
42739658 TTCAGTTTAACCCTTATAGGTTTCTGTTCATCTCTTTTTAGC
1 TTCAGTTTAACCCTTATGGGTTTCTGTTCAGCTCTTACGAGC
*
42739700 TTCAGTTTAACCCTTATGGGTTTTTGTTCAGCTCTTACGAGC
1 TTCAGTTTAACCCTTATGGGTTTCTGTTCAGCTCTTACGAGC
* *
42739742 TTCAGTTCAAACCTTATGGGTTTC
1 TTCAGTTTAACCCTTATGGGTTTC
42739766 ACTTATGTGC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.45
Consensus pattern (42 bp):
TTCAGTTTAACCCTTATGGGTTTCTGTTCAGCTCTTACGAGC
Found at i:42743569 original size:44 final size:42
Alignment explanation
Indices: 42743506--42743645 Score: 126
Period size: 42 Copynumber: 3.3 Consensus size: 42
42743496 AATGTGTTAT
*
42743506 CGTGTAAGACCAC-GTCTGGGACATTGGCATGGATT-TGA-GATTTA
1 CGTGTAAGACC-CTATCTGGGACATTGGCAT--ATTAT-ATGA-TTA
* *
42743550 CGTGTAAGACCCTATCTGGGACATTAGCATCTTATATGATTA
1 CGTGTAAGACCCTATCTGGGACATTGGCATATTATATGATTA
* * *
42743592 CGTGTAAGACCCTATCTGGGATAGTGGCAT-TGATATTTGATTA
1 CGTGTAAGACCCTATCTGGGACATTGGCATAT--TATATGATTA
*
42743635 CTTGTAAGACC
1 CGTGTAAGACC
42743646 ACGTTTGGGA
Statistics
Matches: 83, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
41 1 0.01
42 33 0.40
43 23 0.28
44 26 0.31
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32
Consensus pattern (42 bp):
CGTGTAAGACCCTATCTGGGACATTGGCATATTATATGATTA
Found at i:42759426 original size:14 final size:15
Alignment explanation
Indices: 42759400--42759435 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
42759390 TAGATGAAAC
42759400 TAAATAGTTAAAAAT
1 TAAATAGTTAAAAAT
*
42759415 TGAATA-TTAAAAAT
1 TAAATAGTTAAAAAT
42759429 TAAATAG
1 TAAATAG
42759436 AGCTGAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (15 bp):
TAAATAGTTAAAAAT
Found at i:42762280 original size:12 final size:12
Alignment explanation
Indices: 42762245--42762283 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 12
42762235 AAACTGAAAA
42762245 AATGGAAAATTG
1 AATGGAAAATTG
42762257 AATGGTGAAAAATTG
1 AAT-G-G-AAAATTG
42762272 AATGGAAAATTG
1 AATGGAAAATTG
42762284 CATTTGATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 10 0.42
13 2 0.08
14 2 0.08
15 10 0.42
ACGTcount: A:0.49, C:0.00, G:0.26, T:0.26
Consensus pattern (12 bp):
AATGGAAAATTG
Found at i:42763305 original size:9 final size:10
Alignment explanation
Indices: 42763267--42763307 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
42763257 AGATAAATAT
*
42763267 TTAAAAATTA
1 TTAAGAATTA
42763277 TTAAGAATTA
1 TTAAGAATTA
42763287 -TAAGAGATTA
1 TTAAGA-ATTA
42763297 TTAA-AATTA
1 TTAAGAATTA
42763306 TT
1 TT
42763308 TTAAATTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 11 0.39
10 14 0.50
11 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (10 bp):
TTAAGAATTA
Found at i:42766861 original size:29 final size:30
Alignment explanation
Indices: 42766798--42766861 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
42766788 AATTTACAAT
* *
42766798 AATTAGATCAAATGAAAATTTCGTATATAA
1 AATTAGATAAAATGAAAATTTCATATATAA
* * *
42766828 AATTATATAAAATTAAAA-TTCATATATAC
1 AATTAGATAAAATGAAAATTTCATATATAA
42766857 AATTA
1 AATTA
42766862 CACATTAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.53, C:0.06, G:0.05, T:0.36
Consensus pattern (30 bp):
AATTAGATAAAATGAAAATTTCATATATAA
Found at i:42780229 original size:31 final size:31
Alignment explanation
Indices: 42780191--42780252 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
42780181 AAGAAAAAAA
42780191 ATTGAGTTATTCAATATTTTAATATTTTATG
1 ATTGAGTTATTCAATATTTTAATATTTTATG
42780222 ATTGAGTTATTCAATATTTTAATATTTTATG
1 ATTGAGTTATTCAATATTTTAATATTTTATG
42780253 TATTTTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.55
Consensus pattern (31 bp):
ATTGAGTTATTCAATATTTTAATATTTTATG
Found at i:42780912 original size:348 final size:349
Alignment explanation
Indices: 42780487--42781184 Score: 1380
Period size: 348 Copynumber: 2.0 Consensus size: 349
42780477 AATTGGAAGT
42780487 TAATAATTTAAAATAAAATTATTATTTTATTAGAAAACATGAAAAGATAAAAACACTGTTGTATT
1 TAATAATTT-AAATAAAATTATTATTTTATTAGAAAACATGAAAAGATAAAAACACTGTTGTATT
42780552 AAATTTTTTTATTTTACAAAAATAAAATATAAGTATAAATAAGGTAAGCATATTACGTTAAGAGA
65 AAATTTTTTTATTTTACAAAAATAAAATATAAGTATAAATAAGGTAAGCATATTACGTTAAGAGA
42780617 TAAGAACCAGAGAGACAAAGAATCTTAAGCCAATTGAATTATTTTTGGTATGAACAACAAAAGCA
130 TAAGAACCAGAGAGACAAAGAATCTTAAGCCAATTGAATTATTTTTGGTATGAACAACAAAAGCA
42780682 ACACATCCGATGCTGCCAAAGCCAATATTTCGGATCTTGTATGGCATATAACTGCATAGAATATG
195 ACACATCCGATGCTGCCAAAGCCAATATTTCGGATCTTGTATGGCATATAACTGCATAGAATATG
42780747 TTCCAAAGTAACAGTGTGTTTTTCCTTCTTGTTTTTGGGTTACGTAACCCGCATAATATACTCTA
260 TTCCAAAGTAACAGTGTGTTTTTCCTTCTTGTTTTTGGGTTACGTAACCCGCATAATATACTCTA
42780812 AATCTCTGTATTTTATTATATTTAG
325 AATCTCTGTATTTTATTATATTTAG
42780837 TAATAATTT-AATAAAATTATTATTTTATTAGAAAACATGAAAAGATAAAAACACTGTTGTATTA
1 TAATAATTTAAATAAAATTATTATTTTATTAGAAAACATGAAAAGATAAAAACACTGTTGTATTA
42780901 AATTTTTTTATTTTACAAAAATAAAATATAAGTATAAATAAGGTAAGCATATTACGTTAAGAGAT
66 AATTTTTTTATTTTACAAAAATAAAATATAAGTATAAATAAGGTAAGCATATTACGTTAAGAGAT
42780966 AAGAACCAGAGAGACAAAGAATCTTAAGCCAATTGAATTATTTTTGGTATGAACAACAAAAGCAA
131 AAGAACCAGAGAGACAAAGAATCTTAAGCCAATTGAATTATTTTTGGTATGAACAACAAAAGCAA
42781031 CACATCCGATGCTGCCAAAGCCAATATTTCGGATCTTGTATGGCATATAACTGCATAGAATATGT
196 CACATCCGATGCTGCCAAAGCCAATATTTCGGATCTTGTATGGCATATAACTGCATAGAATATGT
42781096 TCCAAAGTAACAGTGTGTTTTTCCTTCTTGTTTTTGGGTTACGTAACCCGCATAATATACTCTAA
261 TCCAAAGTAACAGTGTGTTTTTCCTTCTTGTTTTTGGGTTACGTAACCCGCATAATATACTCTAA
42781161 ATCTCTGTATTTTATTATATTTAG
326 ATCTCTGTATTTTATTATATTTAG
42781185 AATTTAGACT
Statistics
Matches: 348, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
348 339 0.97
350 9 0.03
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (349 bp):
TAATAATTTAAATAAAATTATTATTTTATTAGAAAACATGAAAAGATAAAAACACTGTTGTATTA
AATTTTTTTATTTTACAAAAATAAAATATAAGTATAAATAAGGTAAGCATATTACGTTAAGAGAT
AAGAACCAGAGAGACAAAGAATCTTAAGCCAATTGAATTATTTTTGGTATGAACAACAAAAGCAA
CACATCCGATGCTGCCAAAGCCAATATTTCGGATCTTGTATGGCATATAACTGCATAGAATATGT
TCCAAAGTAACAGTGTGTTTTTCCTTCTTGTTTTTGGGTTACGTAACCCGCATAATATACTCTAA
ATCTCTGTATTTTATTATATTTAG
Found at i:42798122 original size:31 final size:31
Alignment explanation
Indices: 42798084--42798146 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
42798074 TACCACAAAT
42798084 AGAACTCTGGGTATGGTAATGGGAGAGAATC
1 AGAACTCTGGGTATGGTAATGGGAGAGAATC
42798115 AGAACTCTGGGTATGGTAATGGGAGAGAATC
1 AGAACTCTGGGTATGGTAATGGGAGAGAATC
42798146 A
1 A
42798147 TTTTTGGTTA
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:0.33, C:0.10, G:0.35, T:0.22
Consensus pattern (31 bp):
AGAACTCTGGGTATGGTAATGGGAGAGAATC
Found at i:42801372 original size:25 final size:25
Alignment explanation
Indices: 42801338--42801385 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
42801328 CTGCATTTCT
42801338 GTTGAAAAACAACAATTTAACTTCC
1 GTTGAAAAACAACAATTTAACTTCC
42801363 GTTGAAAAACAACAATTTAACTT
1 GTTGAAAAACAACAATTTAACTT
42801386 TATTTGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (25 bp):
GTTGAAAAACAACAATTTAACTTCC
Found at i:42801392 original size:25 final size:25
Alignment explanation
Indices: 42801338--42801394 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
42801328 CTGCATTTCT
*
42801338 GTTGAAAAACAACAATTTAACTTCC
1 GTTGAAAAACAACAATTTAACTTCA
*
42801363 GTTGAAAAACAACAATTTAACTTTA
1 GTTGAAAAACAACAATTTAACTTCA
*
42801388 TTTGAAA
1 GTTGAAA
42801395 TGATGAATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.32
Consensus pattern (25 bp):
GTTGAAAAACAACAATTTAACTTCA
Found at i:42801791 original size:27 final size:26
Alignment explanation
Indices: 42801740--42801792 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
42801730 AAGTTTTTAA
42801740 TTTTTAAAAAATTTAAAAAGTTATAAC
1 TTTTTAAAAAATTTAAAAAG-TATAAC
42801767 TTTTTAAAAAAATTTAAGAAA-TATAA
1 TTTTT-AAAAAATTTAA-AAAGTATAA
42801793 AAATTATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 10 0.42
28 11 0.46
29 3 0.12
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (26 bp):
TTTTTAAAAAATTTAAAAAGTATAAC
Found at i:42805877 original size:2 final size:2
Alignment explanation
Indices: 42805872--42805904 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
42805862 AGCGTGTGTT
42805872 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
42805905 AGTAAAAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:42815312 original size:1 final size:1
Alignment explanation
Indices: 42815306--42815343 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
42815296 CACAAGGAAA
42815306 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
42815344 GAGTTGATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:42840372 original size:18 final size:18
Alignment explanation
Indices: 42840338--42840373 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42840328 GAGACGGTGA
*
42840338 CCTTTAGTTTCTGCCTCT
1 CCTTTAGTTCCTGCCTCT
*
42840356 CCTTTAGTTCCTTCCTCT
1 CCTTTAGTTCCTGCCTCT
42840374 TTTTTGCATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.36, G:0.08, T:0.50
Consensus pattern (18 bp):
CCTTTAGTTCCTGCCTCT
Found at i:42844402 original size:10 final size:11
Alignment explanation
Indices: 42844379--42844403 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42844369 CTCTCTTTTC
42844379 TTTTTCTTATT
1 TTTTTCTTATT
42844390 TTTTTCTTATT
1 TTTTTCTTATT
42844401 TTT
1 TTT
42844404 CCATTTCCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTCTTATT
Found at i:42846089 original size:23 final size:22
Alignment explanation
Indices: 42846063--42846106 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42846053 AATCTAATTT
42846063 TTAAAATCTAAAAAATAAAAAAA
1 TTAAAATCT-AAAAATAAAAAAA
* *
42846086 TTAAATTCTGAAAATAAAAAA
1 TTAAAATCTAAAAATAAAAAA
42846107 CAGTGATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (22 bp):
TTAAAATCTAAAAATAAAAAAA
Found at i:42849985 original size:45 final size:45
Alignment explanation
Indices: 42849918--42850005 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
42849908 AGCTTTTAAC
* * *
42849918 TCTCGCTAACTGTTTGGTGGACAACTGAGAGCTTTTAACTCTCGT
1 TCTCGCTAACTGTTTAGAGGACAACTGAGAGCTCTTAACTCTCGT
**
42849963 TCTCGCTATTTGTTTAGAGGACAACTGAGAGCTCTTAACTCTC
1 TCTCGCTAACTGTTTAGAGGACAACTGAGAGCTCTTAACTCTC
42850006 TTTAACTGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (45 bp):
TCTCGCTAACTGTTTAGAGGACAACTGAGAGCTCTTAACTCTCGT
Found at i:42865729 original size:65 final size:65
Alignment explanation
Indices: 42865618--42865740 Score: 165
Period size: 65 Copynumber: 1.9 Consensus size: 65
42865608 CAAAATAACA
* * * * * *
42865618 TATAAATTGTTAAGAAATTAAAAATTATATTAGAAATATGTTTGTGAGAAATATTTAAGTACATC
1 TATAAATTGTTAAGAAACTAAAAATTAAATAAGAAATATATATGTGAAAAATATTTAAGTACATC
* * *
42865683 TATAATTTGTTAAGAAACTAAAATTTAAATAATAAATATATATGTGAAAAATATTTAA
1 TATAAATTGTTAAGAAACTAAAAATTAAATAAGAAATATATATGTGAAAAATATTTAA
42865741 AAATATGAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
65 49 1.00
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (65 bp):
TATAAATTGTTAAGAAACTAAAAATTAAATAAGAAATATATATGTGAAAAATATTTAAGTACATC
Found at i:42871403 original size:25 final size:25
Alignment explanation
Indices: 42871368--42871439 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
42871358 CTCTCTCTCA
42871368 AGCCATATAACGGGAAGCTCATGT-G
1 AGCCATATAACGGGAAGCTCAT-TCG
* *
42871393 AGCCATGTAACGGGAAGCTTATTCG
1 AGCCATATAACGGGAAGCTCATTCG
**
42871418 AGCTGTATAACGGGAAGCTCAT
1 AGCCATATAACGGGAAGCTCAT
42871440 AATAGTCATA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
24 1 0.03
25 39 0.98
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (25 bp):
AGCCATATAACGGGAAGCTCATTCG
Found at i:42874502 original size:28 final size:28
Alignment explanation
Indices: 42874462--42874547 Score: 109
Period size: 28 Copynumber: 3.1 Consensus size: 28
42874452 TCAGCGAGAT
*
42874462 TATCTTTCAAGTAAGAGTTCGCATGAAC
1 TATCTTTCAAGTAAGAGTCCGCATGAAC
* *
42874490 TATCTTTCAAGTAGGAGTCCGCATGGAC
1 TATCTTTCAAGTAAGAGTCCGCATGAAC
* * * *
42874518 TATCTTTCAAATAAGAATCCCCAAGAAC
1 TATCTTTCAAGTAAGAGTCCGCATGAAC
42874546 TA
1 TA
42874548 ATTGATGAGT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (28 bp):
TATCTTTCAAGTAAGAGTCCGCATGAAC
Found at i:42876644 original size:39 final size:38
Alignment explanation
Indices: 42876602--42876676 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 38
42876592 GACATTTTAA
42876602 AAAAAGTCAA-ATAGATTTTTTTAATAAAAATATTGACT
1 AAAAAGTCAATATA-ATTTTTTTAATAAAAATATTGACT
* *
42876640 AAAAAGTCAATTTTAATTTTTTTAATGAAAATATTGA
1 AAAAAGTCAA-TATAATTTTTTTAATAAAAATATTGA
42876677 TTTTCAATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 10 0.30
39 21 0.64
40 2 0.06
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (38 bp):
AAAAAGTCAATATAATTTTTTTAATAAAAATATTGACT
Found at i:42878134 original size:15 final size:15
Alignment explanation
Indices: 42878099--42878131 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
42878089 TGATATAAAA
42878099 TAAATATTTCATATT
1 TAAATATTTCATATT
*
42878114 TAAATATTT-TTATT
1 TAAATATTTCATATT
42878128 TAAA
1 TAAA
42878132 ATAGGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAATATTTCATATT
Found at i:42880840 original size:32 final size:32
Alignment explanation
Indices: 42880780--42880842 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
42880770 GACTGTCATT
* *
42880780 ATAATTATTTTTTATCCAACAAGTTAAGGTTC
1 ATAATTAATTTTTATCCAACAAGATAAGGTTC
42880812 ATAATTAATTTTTATCCAA-ACAGATAAGGTT
1 ATAATTAATTTTTATCCAACA-AGATAAGGTT
42880843 AGGTTAAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (32 bp):
ATAATTAATTTTTATCCAACAAGATAAGGTTC
Found at i:42894985 original size:6 final size:6
Alignment explanation
Indices: 42894974--42894999 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
42894964 TAAATAAAGA
42894974 AGGGAG AGGGAG AGGGAG AGGGAG AG
1 AGGGAG AGGGAG AGGGAG AGGGAG AG
42895000 TAGGTGTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
AGGGAG
Found at i:42905038 original size:6 final size:7
Alignment explanation
Indices: 42905020--42905050 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
42905010 CTTCCATTTA
42905020 ATTTTTT
1 ATTTTTT
42905027 ATTTTTT
1 ATTTTTT
42905034 ATTTTTT
1 ATTTTTT
42905041 ATTTTTT
1 ATTTTTT
42905048 ATT
1 ATT
42905051 AAATGAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
ATTTTTT
Found at i:42905082 original size:21 final size:20
Alignment explanation
Indices: 42905038--42905082 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
42905028 TTTTTTATTT
* * *
42905038 TTTATTTTTTATTAAATGAG
1 TTTATTTTTTATCAAATCAC
42905058 TTTATATTTTTATCAAATCAC
1 TTTAT-TTTTTATCAAATCAC
42905079 TTTA
1 TTTA
42905083 AATTAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTATTTTTTATCAAATCAC
Found at i:42911865 original size:24 final size:23
Alignment explanation
Indices: 42911838--42911892 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
42911828 TTAAAATTTA
42911838 TAAAATATAAGTTATTA-TAATTGT
1 TAAAATATAA-TTATTACT-ATTGT
* *
42911862 TAAATTAT-ATTTTTACTATTGT
1 TAAAATATAATTATTACTATTGT
42911884 TAAAATATA
1 TAAAATATA
42911893 CAACTTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 17 0.65
23 2 0.08
24 7 0.27
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (23 bp):
TAAAATATAATTATTACTATTGT
Found at i:42913736 original size:100 final size:100
Alignment explanation
Indices: 42913623--42913814 Score: 321
Period size: 100 Copynumber: 1.9 Consensus size: 100
42913613 ATTGAAAATT
* * *
42913623 TTTATATAGTCATCTTAATATTATTTTAATATTTACATTAGAGTAGTATTATATATTTAGTATAA
1 TTTATATACTCATCTTAACAATATTTTAATATTTACATTAGAGTAGTATTATATATTTAGTATAA
42913688 GTTTACTTTTTTAATGTATTCTAAAATAAAATTTC
66 GTTTACTTTTTTAATGTATTCTAAAATAAAATTTC
* * *
42913723 TTTATATACTCATCTTAACAATATTTTAATGTTTACATTAGAGTTGTATTATATATTTAGTATAG
1 TTTATATACTCATCTTAACAATATTTTAATATTTACATTAGAGTAGTATTATATATTTAGTATAA
*
42913788 GTTTATTTTTTTAATGTATTCTAAAAT
66 GTTTACTTTTTTAATGTATTCTAAAAT
42913815 GCCTAATATA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 85 1.00
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52
Consensus pattern (100 bp):
TTTATATACTCATCTTAACAATATTTTAATATTTACATTAGAGTAGTATTATATATTTAGTATAA
GTTTACTTTTTTAATGTATTCTAAAATAAAATTTC
Found at i:42931993 original size:15 final size:16
Alignment explanation
Indices: 42931973--42932005 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42931963 AAATTTATTC
*
42931973 TAATTT-ATTGATTTT
1 TAATTTGATTGAATTT
42931988 TAATTTGATTGAATTT
1 TAATTTGATTGAATTT
42932004 TA
1 TA
42932006 TAAAGATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (16 bp):
TAATTTGATTGAATTT
Found at i:42932558 original size:130 final size:130
Alignment explanation
Indices: 42932321--42932983 Score: 593
Period size: 130 Copynumber: 5.1 Consensus size: 130
42932311 AAAAGAATTT
* * * **
42932321 AAATTTGATTGCATAAGTTTGAGGCAACCTGAATCGAGTAATTGATGAATTTACTAAATGAGTGA
1 AAATTTGATTGCGTAAGTTTGAGGCAACCTGAATCGAGTGATTGATAAATTTACTAAAAAAGTGA
* * ** * *
42932386 TTACGCGTTCATACCAAAT-TCTAAGATAATTTGAATACTTTTTCAATTAAAGTAACCTAAAGTT
66 CTACGTGTTCATATTAAATCT-TAAGAGAATTTGAATATTTTTTCAATTAAAGTAACCTAAAGTT
42932450 A
130 A
* * ** *
42932451 TAATTTGATTGTGTAAGTTTGAGGCAACCCCAAACGAGTGATTGATAAATTTACTAAAAAAGTGA
1 AAATTTGATTGCGTAAGTTTGAGGCAACCTGAATCGAGTGATTGATAAATTTACTAAAAAAGTGA
* * * **
42932516 CTACGTGTTTATATTAAGTCTTAAGAGAATTTGAATATTTTTTCAATTAGAGTAA-CTTGAGATT
66 CTACGTGTTCATATTAAATCTTAAGAGAATTTGAATATTTTTTCAATTAAAGTAACCTAAAG-TT
42932580 A
130 A
* * * *
42932581 AAATTTGGTTGCGTAAGTTTGAGACAACCTGAATCGAGTGATGATAGATAAATTTACTAAAAGAC
1 AAATTTGATTGCGTAAGTTTGAGGCAACCTGAATCGAGTGAT--T-GATAAATTTACTAAAAAAG
* * * * * * * **
42932646 TGACTATGTGTTCATATTAAATCCTAAGAGGATTTAAATACTTTTTT-AGTTAGAGTAATCTATC
63 TGACTACGTGTTCATATTAAATCTTAAGAGAATTTGAATA-TTTTTTCAATTAAAGTAACCTAAA
42932710 GTTA
127 GTTA
** * * * * **
42932714 AAATTTGATTGCGTAAGTTTGAGATAACCTGAATTGAGGGATCGATAAATTTATTAAAAAAAAAG
1 AAATTTGATTGCGTAAGTTTGAGGCAACCTGAATCGAGTGATTGATAAATTTACT-AAAAAAGTG
* * * * *
42932779 ACTACGTGTTCATATTAAATCCTAAGAGAATTTGAATATTTTTTCAATTGAAGTGACATAAGGTT
65 ACTACGTGTTCATATTAAATCTTAAGAGAATTTGAATATTTTTTCAATTAAAGTAACCTAAAGTT
42932844 A
130 A
* * * * * * * *
42932845 AAACTAGGTTGTGTAAATTTGAGGCAACCTGAATC-ATGGGATTGATAAAATTACT-AAAAGGTG
1 AAATTTGATTGCGTAAGTTTGAGGCAACCTGAATCGA-GTGATTGATAAATTTACTAAAAAAGTG
* * ** * ** * * * * *
42932908 ACTACAT-TT-ATATCAAGCCTTATGAGAATCCGAATAATTTTCCATTTAAAATAACTTAAAAGT
65 ACTACGTGTTCATATTAAATCTTAAGAGAATTTGAATATTTTTTCAATTAAAGTAACCT-AAAGT
42932971 TA
129 TA
42932973 AAATTTGATTG
1 AAATTTGATTG
42932984 TGAAATAACT
Statistics
Matches: 429, Mismatches: 93, Indels: 24
0.79 0.17 0.04
Matches are distributed among these distances:
127 34 0.08
128 16 0.04
129 15 0.03
130 155 0.36
131 97 0.23
132 1 0.00
133 102 0.24
134 9 0.02
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (130 bp):
AAATTTGATTGCGTAAGTTTGAGGCAACCTGAATCGAGTGATTGATAAATTTACTAAAAAAGTGA
CTACGTGTTCATATTAAATCTTAAGAGAATTTGAATATTTTTTCAATTAAAGTAACCTAAAGTTA
Found at i:42940371 original size:34 final size:34
Alignment explanation
Indices: 42940330--42940396 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
42940320 TAATAATCAC
* *
42940330 TTATCATACTGCTGTTTGTAATGATGTTATTTCG
1 TTATCATACTGCTATATGTAATGATGTTATTTCG
*
42940364 TTATCATACTGCTATATGTAATGGTGTTATTTC
1 TTATCATACTGCTATATGTAATGATGTTATTTC
42940397 ATTGGCTGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.49
Consensus pattern (34 bp):
TTATCATACTGCTATATGTAATGATGTTATTTCG
Found at i:42952436 original size:111 final size:110
Alignment explanation
Indices: 42952311--42952520 Score: 291
Period size: 111 Copynumber: 1.9 Consensus size: 110
42952301 ACTTATCAAC
* *
42952311 TTTTTATTTATTAGTAAAAAA-ACTTTCTA-TTTAAAAAATTAAATCTTGAAACAAATTCAAAAA
1 TTTTTATTTATTAGTAAAAAACA-TTT-TACTTAAAAAAATTAAATCATGAAACAAATTCAAAAA
* *
42952374 TTAAAATTGGTCTCAAAATCTATTAAAAACAAATAGAATAAAAAGTTGA
64 TTAAAATTAGACTCAAAATCTATTAAAAA-AAA-AGAATAAAAAGTTGA
* * **
42952423 TTTTT-TTTATTAGTAAAATACATTTTACTTAAAAAAATTAAATCATGAAACAAGTTGGAAAATT
1 TTTTTATTTATTAGTAAAAAACATTTTACTTAAAAAAATTAAATCATGAAACAAATTCAAAAATT
42952487 AAAATTAGACTCAAAATCTATTAAAAAAAAAGAA
66 AAAATTAGACTCAAAATCTATTAAAAAAAAAGAA
42952521 ACTTTATCGT
Statistics
Matches: 88, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
109 4 0.05
110 5 0.06
111 73 0.83
112 6 0.07
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (110 bp):
TTTTTATTTATTAGTAAAAAACATTTTACTTAAAAAAATTAAATCATGAAACAAATTCAAAAATT
AAAATTAGACTCAAAATCTATTAAAAAAAAAGAATAAAAAGTTGA
Found at i:42956548 original size:9 final size:9
Alignment explanation
Indices: 42956519--42956555 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
42956509 TGAGTTTTCG
42956519 AATTCGAAT
1 AATTCGAAT
*
42956528 AACTCGAAT
1 AATTCGAAT
42956537 AATTCGAAT
1 AATTCGAAT
*
42956546 AATTTGAAT
1 AATTCGAAT
42956555 A
1 A
42956556 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:42956974 original size:19 final size:19
Alignment explanation
Indices: 42956925--42956985 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
42956915 TATTTACTTT
42956925 CCCTCAAACTTTTA--TT-C
1 CCCT-AAACTTTTATTTTCC
*
42956942 CCCAAAACTTTTTATTTTCC
1 CCCTAAAC-TTTTATTTTCC
*
42956962 CCCTAAACTTTTACTTTTCA
1 CCCTAAACTTTTA-TTTTCC
42956982 CCCT
1 CCCT
42956986 CTACTCTCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
16 4 0.11
17 8 0.22
19 7 0.19
20 17 0.47
ACGTcount: A:0.23, C:0.34, G:0.00, T:0.43
Consensus pattern (19 bp):
CCCTAAACTTTTATTTTCC
Found at i:42957663 original size:53 final size:53
Alignment explanation
Indices: 42957583--42957691 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
42957573 TCAAACCAAT
42957583 CATCAACATGTTTACAAATTATCCATCATTCAACCATACTATCACACATTAAA
1 CATCAACATGTTTACAAATTATCCATCATTCAACCATACTATCACACATTAAA
42957636 CATCAACATGTTTACAAATTATCCATCATTCAACCATACTATCACACATTAAA
1 CATCAACATGTTTACAAATTATCCATCATTCAACCATACTATCACACATTAAA
42957689 CAT
1 CAT
42957692 GATAAGACCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.41, C:0.27, G:0.02, T:0.30
Consensus pattern (53 bp):
CATCAACATGTTTACAAATTATCCATCATTCAACCATACTATCACACATTAAA
Found at i:42959047 original size:50 final size:50
Alignment explanation
Indices: 42958933--42959343 Score: 419
Period size: 50 Copynumber: 7.8 Consensus size: 50
42958923 GATAATAACA
* * * ** *
42958933 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
42958984 TGCCCATGCCATGTCCCAAACATGGTCTTAC-GGGGGCACTCTCATCTCGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACAGGGGAC-CTCTCATCTCGG
* *
42959034 TGCCAATGCCATGTCCCAGACATGGTCTTACAGAGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACAGGGGACCTCTC---ATCTC--GG
* * *
42959089 ATGTCAATGCCATGTCCTAAACATGGTCTTACATGGGACCTCTCATCTCGG
1 -TGCCAATGCCATGTCCCAAACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
42959140 TGCCAATGCCATGTCCCAGACATGGTCTTACAGAGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACAGGGGACCTCTC---ATCTC--GG
* * *
42959195 ATGTCAATGCCATGTCCTAAACATGGTCTTACATGGGACCTCTCATCTCGG
1 -TGCCAATGCCATGTCCCAAACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
42959246 TGCCAATGCCATGTCTCAGACATGGTCTTACAGAGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACAGGGGACCTCTC---ATCTC--GG
* * *
42959301 ATGTCAATGCCATGTCCTAAACATGGTCTTACATGGGACCTCT
1 -TGCCAATGCCATGTCCCAAACATGGTCTTACAGGGGACCTCT
42959344 TTATCCAAAT
Statistics
Matches: 301, Mismatches: 39, Indels: 35
0.80 0.10 0.09
Matches are distributed among these distances:
50 122 0.41
51 36 0.12
53 25 0.08
55 6 0.02
56 112 0.37
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAAACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:42959097 original size:56 final size:49
Alignment explanation
Indices: 42959093--42959343 Score: 277
Period size: 56 Copynumber: 4.8 Consensus size: 49
42959083 TCAAGGATGT
*
42959093 CAATGCCATGTCCTAAACATGGTCTTACATGGGACCTCTCATCTCGGTGC
1 CAATGCCATGTCCCAAACATGGTCTTACA-GGGACCTCTCATCTCGGTGC
* *
42959143 CAATGCCATGTCCCAGACATGGTCTTACAGAGGACCTCTCATGATCTCAAGGATGT
1 CAATGCCATGTCCCAAACATGGTCTTACAG-GGACCTCTC---ATCTC--GG-TGC
*
42959199 CAATGCCATGTCCTAAACATGGTCTTACATGGGACCTCTCATCTCGGTGC
1 CAATGCCATGTCCCAAACATGGTCTTACA-GGGACCTCTCATCTCGGTGC
* * *
42959249 CAATGCCATGTCTCAGACATGGTCTTACAGAGGACCTCTCATGATCTCAAGGATGT
1 CAATGCCATGTCCCAAACATGGTCTTACAG-GGACCTCTC---ATCTC--GG-TGC
*
42959305 CAATGCCATGTCCTAAACATGGTCTTACATGGGACCTCT
1 CAATGCCATGTCCCAAACATGGTCTTACA-GGGACCTCT
42959344 TTATCCAAAT
Statistics
Matches: 172, Mismatches: 13, Indels: 26
0.82 0.06 0.12
Matches are distributed among these distances:
49 2 0.01
50 73 0.42
51 2 0.01
53 15 0.09
55 4 0.02
56 74 0.43
57 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (49 bp):
CAATGCCATGTCCCAAACATGGTCTTACAGGGACCTCTCATCTCGGTGC
Found at i:42959133 original size:106 final size:106
Alignment explanation
Indices: 42958989--42959343 Score: 658
Period size: 106 Copynumber: 3.3 Consensus size: 106
42958979 GTCGGTGCCC
* * *
42958989 ATGCCATGTCCCAAACATGGTCTTAC-GGGGGCACTCTCATCTCGGTGCCAATGCCATGTCCCAG
1 ATGCCATGTCCTAAACATGGTCTTACATGGGAC-CTCTCATCTCGGTGCCAATGCCATGTCCCAG
42959053 ACATGGTCTTACAGAGGACCTCTCATGATCTCAAGGATGTCA
65 ACATGGTCTTACAGAGGACCTCTCATGATCTCAAGGATGTCA
42959095 ATGCCATGTCCTAAACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAGA
1 ATGCCATGTCCTAAACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAGA
42959160 CATGGTCTTACAGAGGACCTCTCATGATCTCAAGGATGTCA
66 CATGGTCTTACAGAGGACCTCTCATGATCTCAAGGATGTCA
*
42959201 ATGCCATGTCCTAAACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCTCAGA
1 ATGCCATGTCCTAAACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAGA
42959266 CATGGTCTTACAGAGGACCTCTCATGATCTCAAGGATGTCA
66 CATGGTCTTACAGAGGACCTCTCATGATCTCAAGGATGTCA
42959307 ATGCCATGTCCTAAACATGGTCTTACATGGGACCTCT
1 ATGCCATGTCCTAAACATGGTCTTACATGGGACCTCT
42959344 TTATCCAAAT
Statistics
Matches: 244, Mismatches: 4, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
106 240 0.98
107 4 0.02
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.26
Consensus pattern (106 bp):
ATGCCATGTCCTAAACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAGA
CATGGTCTTACAGAGGACCTCTCATGATCTCAAGGATGTCA
Found at i:42959302 original size:212 final size:207
Alignment explanation
Indices: 42958933--42959343 Score: 648
Period size: 212 Copynumber: 2.0 Consensus size: 207
42958923 GATAATAACA
** *
42958933 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCGGTGCCCATGCCATGT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATGTCGGTGCCAATGCCATGT
*
42958998 CCCAAACATGGTCTTACGGGGGCACTCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTT
66 CCCAAACATGGTCTTACGGGGACACTCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTT
42959063 ACAGAGGACCTCTCATGATCTCAAGGATGTCAATGCCATGTCCTAAACATGGTCTTACATGGGAC
131 ACAGAGGACCTCTCATGATCTCAAGGATGTCAATGCCATGTCCTAAACATGGTCTTACATGGGAC
42959128 CTCTCATCTCGG
196 CTCTCATCTCGG
* *
42959140 TGCCAATGCCATGTCCCAGACATGGTCTTACA-GAGGA-CCTCTCATGATCTCAAGGATGTCAAT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATG-GGATCCTCTCATG---TC--GG-TGCCAAT
* * *
42959203 GCCATGTCCTAAACATGGTCTTACATGGGAC-CTCTCATCTCGGTGCCAATGCCATGTCTCAGAC
59 GCCATGTCCCAAACATGGTCTTAC-GGGGACACTCTCATCTCGGTGCCAATGCCATGTCCCAGAC
42959267 ATGGTCTTACAGAGGACCTCTCATGATCTCAAGGATGTCAATGCCATGTCCTAAACATGGTCTTA
123 ATGGTCTTACAGAGGACCTCTCATGATCTCAAGGATGTCAATGCCATGTCCTAAACATGGTCTTA
42959332 CATGGGACCTCT
188 CATGGGACCTCT
42959344 TTATCCAAAT
Statistics
Matches: 187, Mismatches: 9, Indels: 11
0.90 0.04 0.05
Matches are distributed among these distances:
206 8 0.04
207 34 0.18
209 2 0.01
211 2 0.01
212 137 0.73
213 4 0.02
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.27
Consensus pattern (207 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATGTCGGTGCCAATGCCATGT
CCCAAACATGGTCTTACGGGGACACTCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTT
ACAGAGGACCTCTCATGATCTCAAGGATGTCAATGCCATGTCCTAAACATGGTCTTACATGGGAC
CTCTCATCTCGG
Found at i:42960627 original size:26 final size:26
Alignment explanation
Indices: 42960591--42960645 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
42960581 ATAAAACAGA
42960591 GTAAGCATTTAATGCTTAGTAAGTTC
1 GTAAGCATTTAATGCTTAGTAAGTTC
42960617 GTAAGCATTTAATGCTTAGTAAGTTC
1 GTAAGCATTTAATGCTTAGTAAGTTC
42960643 GTA
1 GTA
42960646 TAACATGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (26 bp):
GTAAGCATTTAATGCTTAGTAAGTTC
Found at i:42962041 original size:16 final size:17
Alignment explanation
Indices: 42962014--42962045 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
42962004 ATATGAATTT
42962014 ATGATAATTAAATTATA
1 ATGATAATTAAATTATA
42962031 ATGAT-ATTAAATTAT
1 ATGATAATTAAATTAT
42962046 TAAATAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATGATAATTAAATTATA
Found at i:42965107 original size:9 final size:9
Alignment explanation
Indices: 42965093--42965117 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
42965083 ATGAGGTAAC
42965093 ATATTATAT
1 ATATTATAT
42965102 ATATTATAT
1 ATATTATAT
42965111 ATATTAT
1 ATATTAT
42965118 GTGTAATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATATTATAT
Found at i:42965331 original size:235 final size:232
Alignment explanation
Indices: 42964916--42965380 Score: 716
Period size: 235 Copynumber: 2.0 Consensus size: 232
42964906 GATATAAATG
42964916 CTTAACAAATACATTCAAATAGTCATTTGAAAATATGATATTCAACATTGAATACGTAGAATATG
1 CTTAACAAATACATTCAAATAGTCATTTGAAAATATGATATTCAACATTGAATACGTAGAATATG
* * * * * * *
42964981 AGAAAGTATGTGATGTTTTTATGAGGGGGAGTAAATATGTGTTGTATTCTTTTTCCCTTAACTGA
66 AGAAAGTATGTGATGTTTTCATAAGGGGGAGTAAATATGCGCTATACTCTTTTTCCCTTAACCGA
* * * *
42965046 TGTTTTGTTCTATTAAATTTTCTTGGTAAGATTTTTAATGAGGTAACATATTATATATATTATAT
131 TGTTTTGTTCCATTAAATTTTCTTGATAAGATTTTTAATGAAGCAACATATTATATATA-T-TAT
* *
42965111 ATATTATGTGTAATCTTTTTCCTTCACTAGGATTTTTTCC
194 AGA-TATGCGTAATCTTTTTCCTTCACTAGGATTTTTTCC
* *
42965151 CTTAACAAATACATTCAAATAGTCATTTGAAAATCT-AGTATTCAAGATTGAATACGTAGAATAT
1 CTTAACAAATACATTCAAATAGTCATTTGAAAATATGA-TATTCAACATTGAATACGTAGAATAT
*
42965215 GAGAAAGTATGTGATGTTTTCATAAGGGGGAGTAAATATGCGCTATGCTCTTTTTCCCTTAACCG
65 GAGAAAGTATGTGATGTTTTCATAAGGGGGAGTAAATATGCGCTATACTCTTTTTCCCTTAACCG
* *
42965280 ATGTTTTTTTCCATTAAGTTTTCTTGATAAGATTTTTAATGAAGCAACATATTATATATATTATA
130 ATGTTTTGTTCCATTAAATTTTCTTGATAAGATTTTTAATGAAGCAACATATTATATATATTATA
*
42965345 GATATGCGTACTCTTTTTCCTTCACTAGGATTTTTT
195 GATATGCGTAATCTTTTTCCTTCACTAGGATTTTTT
42965381 TTCCCACATG
Statistics
Matches: 210, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
232 32 0.15
233 5 0.02
234 2 0.01
235 171 0.81
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (232 bp):
CTTAACAAATACATTCAAATAGTCATTTGAAAATATGATATTCAACATTGAATACGTAGAATATG
AGAAAGTATGTGATGTTTTCATAAGGGGGAGTAAATATGCGCTATACTCTTTTTCCCTTAACCGA
TGTTTTGTTCCATTAAATTTTCTTGATAAGATTTTTAATGAAGCAACATATTATATATATTATAG
ATATGCGTAATCTTTTTCCTTCACTAGGATTTTTTCC
Found at i:42971004 original size:21 final size:22
Alignment explanation
Indices: 42970962--42971005 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
42970952 ATCTTCAAAG
*
42970962 TAATATATATTTATATAAATTT
1 TAATATATATTTACATAAATTT
* *
42970984 TAATAT-TTTTTACATAGATTT
1 TAATATATATTTACATAAATTT
42971005 T
1 T
42971006 CACTTCTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TAATATATATTTACATAAATTT
Found at i:42971633 original size:15 final size:15
Alignment explanation
Indices: 42971613--42971642 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
42971603 CAATAAATAA
42971613 TCATAATTTTGAAAT
1 TCATAATTTTGAAAT
42971628 TCATAATTTTGAAAT
1 TCATAATTTTGAAAT
42971643 ATAAAATCTT
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:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (15 bp):
TCATAATTTTGAAAT
Found at i:42972112 original size:20 final size:20
Alignment explanation
Indices: 42972083--42972123 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
42972073 ACCCCAAACC
42972083 CTTTAATTTATACTAGTTGG
1 CTTTAATTTATACTAGTTGG
* *
42972103 CTTTAGTTTATACTGGTTGG
1 CTTTAATTTATACTAGTTGG
42972123 C
1 C
42972124 ATGATGGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.49
Consensus pattern (20 bp):
CTTTAATTTATACTAGTTGG
Found at i:42972310 original size:20 final size:20
Alignment explanation
Indices: 42972285--42972323 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
42972275 CAGTAAAATA
*
42972285 TTTTTTGGAAAATGATTTAT
1 TTTTTTGAAAAATGATTTAT
42972305 TTTTTTGAAAAATGATTTA
1 TTTTTTGAAAAATGATTTA
42972324 CTAGAAAATA
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:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (20 bp):
TTTTTTGAAAAATGATTTAT
Found at i:42974685 original size:20 final size:17
Alignment explanation
Indices: 42974645--42974687 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
42974635 TTTAATCAGT
*
42974645 TTAATATTAAATTTAAT
1 TTAATATTAAATTTAAA
42974662 TTAATATTAAATCTATTAAA
1 TTAATATTAAA--T-TTAAA
42974682 TTAATA
1 TTAATA
42974688 GAATAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 11 0.50
19 1 0.05
20 10 0.45
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAATATTAAATTTAAA
Found at i:42982648 original size:6 final size:6
Alignment explanation
Indices: 42982637--42982665 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
42982627 TCTGAGGGGA
42982637 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
42982666 AACACTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:43010539 original size:22 final size:23
Alignment explanation
Indices: 43010513--43010571 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
43010503 TCTTTTGCAA
43010513 ATTTTATTTTTATAATT-TATAT
1 ATTTTATTTTTATAATTATATAT
* * * *
43010535 GTTTTCTTTCTA-GATTATATAT
1 ATTTTATTTTTATAATTATATAT
43010557 ATTTTGATTTTTATA
1 ATTTT-ATTTTTATA
43010572 TGATTTTTAA
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
21 3 0.12
22 18 0.69
23 5 0.19
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.64
Consensus pattern (23 bp):
ATTTTATTTTTATAATTATATAT
Found at i:43013079 original size:1 final size:1
Alignment explanation
Indices: 43013033--43013071 Score: 69
Period size: 1 Copynumber: 39.0 Consensus size: 1
43013023 TTCTAGTTAG
*
43013033 TTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
43013072 ACCTTTTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:43020456 original size:23 final size:23
Alignment explanation
Indices: 43020424--43020490 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
43020414 TACATATACT
*
43020424 TATAAAATATAAATAAAAATAAG
1 TATAATATATAAATAAAAATAAG
* * *
43020447 TATAATATATTAATAAAGTATGAG
1 TATAATATATAAATAAA-AATAAG
* *
43020471 TATATATATGTATATAAAAA
1 TATA-ATATATAAATAAAAA
43020491 AATATGAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
23 15 0.44
24 9 0.26
25 10 0.29
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.34
Consensus pattern (23 bp):
TATAATATATAAATAAAAATAAG
Found at i:43020495 original size:16 final size:16
Alignment explanation
Indices: 43020476--43020519 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
43020466 ATGAGTATAT
43020476 ATATGTATATAAAAAA
1 ATATGTATATAAAAAA
* * *
43020492 ATATGAAAATAAAATA
1 ATATGTATATAAAAAA
43020508 ATAATGTATATA
1 AT-ATGTATATA
43020520 TATATATGTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (16 bp):
ATATGTATATAAAAAA
Found at i:43020634 original size:18 final size:17
Alignment explanation
Indices: 43020594--43020640 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
43020584 CGTGTGAGTG
*
43020594 TATAAAAATAATAATGA
1 TATAAAAATAATAATAA
43020611 TGATAAAAATAATGAATAA
1 T-ATAAAAATAAT-AATAA
*
43020630 TATAATAATAA
1 TATAAAAATAA
43020641 GGATACAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 1 0.04
18 20 0.77
19 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (17 bp):
TATAAAAATAATAATAA
Found at i:43020636 original size:15 final size:15
Alignment explanation
Indices: 43020599--43020653 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
43020589 GAGTGTATAA
43020599 AAATAATAATGATGAT
1 AAATAATAATGA-GAT
43020615 AAA-AATAATGA-AT
1 AAATAATAATGAGAT
*
43020628 AATATAATAATAAGGAT
1 AA-ATAATAATGA-GAT
43020645 ACAATAATA
1 A-AATAATA
43020654 GTATTAACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
13 4 0.12
14 1 0.03
15 15 0.45
16 3 0.09
17 9 0.27
18 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.09, T:0.27
Consensus pattern (15 bp):
AAATAATAATGAGAT
Found at i:43022049 original size:5 final size:6
Alignment explanation
Indices: 43022034--43022058 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43022024 CCTTTTATTA
43022034 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
43022059 TGCATACGAT
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:43032477 original size:35 final size:34
Alignment explanation
Indices: 43032438--43032517 Score: 85
Period size: 35 Copynumber: 2.3 Consensus size: 34
43032428 AATTTAATTT
43032438 ATATTTTATTATTTGATTCA-AATATAATCTGT-AAA
1 ATATTTTATTATTTGATT-AGAATATAAT-T-TAAAA
*
43032473 ATATTTTGA-TATTTTATTATGAATATAATTTAAAA
1 ATATTTT-ATTATTTGATTA-GAATATAATTTAAAA
43032508 ATATTTTATT
1 ATATTTTATT
43032518 GTACATTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
34 3 0.08
35 27 0.69
36 9 0.23
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (34 bp):
ATATTTTATTATTTGATTAGAATATAATTTAAAA
Found at i:43032555 original size:56 final size:56
Alignment explanation
Indices: 43032469--43033285 Score: 1562
Period size: 56 Copynumber: 14.6 Consensus size: 56
43032459 ATATAATCTG
* *
43032469 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTTTATTGTACATT
1 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
* *
43032525 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTTTATTGTACATT
1 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
* *
43032581 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTTTATTGTACATT
1 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
* *
43032637 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTTTATTGTACATT
1 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
43032693 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
1 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
43032749 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
1 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
43032805 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
1 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
43032861 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
1 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
43032917 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
1 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
43032973 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
1 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
43033029 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
1 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
43033085 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
1 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
43033141 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
1 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
43033197 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
1 TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
43033253 TAAAATATTTTGATATTTTATTATGAATATAAT
1 TAAAATATTTTGATATTTTATTATGAATATAAT
43033286 CTGTAAAATA
Statistics
Matches: 759, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 759 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (56 bp):
TAAAATATTTTGATATTTTATTATGAATATAATTTAAAAATATTCTATTGTATATT
Found at i:43033659 original size:103 final size:103
Alignment explanation
Indices: 43033535--43033734 Score: 330
Period size: 103 Copynumber: 1.9 Consensus size: 103
43033525 TTTCTAATCT
*
43033535 CACCGTTACAGTATCCAATCTCA-CTACTACAATAACTAATCTCACAGCCACCGCTGTTTTTAAC
1 CACCGCTACAGTATCCAATCTCACCT-CTACAATAACTAATCTCACAGCCACCGCTGTTTTTAAC
*
43033599 CTCACCGGAGCTAAACACACCGCCCATCCAAACTAAGCC
65 CTCACCGGAACTAAACACACCGCCCATCCAAACTAAGCC
* * *
43033638 CACCGCTACAGTATCCAATCTCACCTCTACAGTACCTAATCTCACCGCCACCGCTGTTTTTAACC
1 CACCGCTACAGTATCCAATCTCACCTCTACAATAACTAATCTCACAGCCACCGCTGTTTTTAACC
*
43033703 TCACCGGAACTAAACACACCGCCTATCCAAAC
66 TCACCGGAACTAAACACACCGCCCATCCAAAC
43033735 CCACCATTCG
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
103 88 0.98
104 2 0.02
ACGTcount: A:0.30, C:0.39, G:0.10, T:0.21
Consensus pattern (103 bp):
CACCGCTACAGTATCCAATCTCACCTCTACAATAACTAATCTCACAGCCACCGCTGTTTTTAACC
TCACCGGAACTAAACACACCGCCCATCCAAACTAAGCC
Found at i:43033667 original size:21 final size:21
Alignment explanation
Indices: 43033638--43033685 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
43033628 AAACTAAGCC
43033638 CACCGCTACAGTATCC-AATCT
1 CACCGCTACAGTA-CCTAATCT
*
43033659 CACCTCTACAGTACCTAATCT
1 CACCGCTACAGTACCTAATCT
43033680 CACCGC
1 CACCGC
43033686 CACCGCTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.27, C:0.42, G:0.08, T:0.23
Consensus pattern (21 bp):
CACCGCTACAGTACCTAATCT
Found at i:43035515 original size:7 final size:7
Alignment explanation
Indices: 43035503--43035531 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
43035493 AAGCACACCG
43035503 ATAAAAA
1 ATAAAAA
43035510 ATAAAAA
1 ATAAAAA
43035517 AT-AAAA
1 ATAAAAA
43035523 ATAAAAA
1 ATAAAAA
43035530 AT
1 AT
43035532 CACATCGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
ATAAAAA
Found at i:43035524 original size:13 final size:13
Alignment explanation
Indices: 43035506--43035531 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43035496 CACACCGATA
43035506 AAAAATAAAAAAT
1 AAAAATAAAAAAT
43035519 AAAAATAAAAAAT
1 AAAAATAAAAAAT
43035532 CACATCGGTG
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:43044466 original size:7 final size:7
Alignment explanation
Indices: 43044454--43044478 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
43044444 CACTATATAT
43044454 AAAAATA
1 AAAAATA
43044461 AAAAATA
1 AAAAATA
43044468 AAAAATA
1 AAAAATA
43044475 AAAA
1 AAAA
43044479 TATGTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:43045884 original size:15 final size:15
Alignment explanation
Indices: 43045861--43045912 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
43045851 AAGTTTGCTT
43045861 GATAGAGAATTAAAG
1 GATAGAGAATTAAAG
*
43045876 GATACAGAATTAAAG
1 GATAGAGAATTAAAG
* *
43045891 GGTAGAAAATTAAAAG
1 GATAGAGAATT-AAAG
43045907 GATAGA
1 GATAGA
43045913 AAATAATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
15 22 0.71
16 9 0.29
ACGTcount: A:0.54, C:0.02, G:0.25, T:0.19
Consensus pattern (15 bp):
GATAGAGAATTAAAG
Found at i:43049528 original size:9 final size:9
Alignment explanation
Indices: 43049514--43049544 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
43049504 GTTAAACGAA
43049514 TCGAGTTAT
1 TCGAGTTAT
*
43049523 TCGAGTTAA
1 TCGAGTTAT
43049532 TCGAGTTAT
1 TCGAGTTAT
43049541 TCGA
1 TCGA
43049545 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:43049613 original size:9 final size:9
Alignment explanation
Indices: 43049596--43049632 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
43049586 TGAGTTTTCG
43049596 AATTCGAAT
1 AATTCGAAT
*
43049605 AACTCGAAT
1 AATTCGAAT
43049614 AATTCGAAT
1 AATTCGAAT
43049623 AATTCGAAT
1 AATTCGAAT
43049632 A
1 A
43049633 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:43049900 original size:30 final size:31
Alignment explanation
Indices: 43049846--43049905 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
43049836 AAACCTTTTA
*
43049846 TTTTCCCCCAAAATTTTTTCTCCC-TCCCAC
1 TTTTCCCCCAAAATTTTATCTCCCTTCCCAC
*
43049876 TTTTCCCCTAAAACTTTTAT-TCCCTTCCCA
1 TTTTCCCCCAAAA-TTTTATCTCCCTTCCCA
43049906 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.18, C:0.40, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCCAAAATTTTATCTCCCTTCCCAC
Found at i:43058221 original size:42 final size:42
Alignment explanation
Indices: 43058164--43058276 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
43058154 TCAACTCATA
* * * *
43058164 TGAGTTTCAGATTAACCCTTCTGGGTTTTAGTTTAGCTCTTT-
1 TGAGCTTCAGATTAACCCTTATGGGTTTCAATTTAGCT-TTTC
* **
43058206 TGAGCTTCAGTTTAACCCGAATGGGTTTCAATTTAGCTTTTC
1 TGAGCTTCAGATTAACCCTTATGGGTTTCAATTTAGCTTTTC
* *
43058248 TGAGCTTTAGATTAACCCTTATGAGTTTC
1 TGAGCTTCAGATTAACCCTTATGGGTTTC
43058277 CGTTCAGCTC
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
41 3 0.05
42 55 0.95
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.43
Consensus pattern (42 bp):
TGAGCTTCAGATTAACCCTTATGGGTTTCAATTTAGCTTTTC
Found at i:43058291 original size:21 final size:21
Alignment explanation
Indices: 43058267--43058324 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
43058257 GATTAACCCT
43058267 TATGAGTTTCCGTTCAGCTCC
1 TATGAGTTTCCGTTCAGCTCC
* *
43058288 TATGGGTTTCTGTTCAGCTCC
1 TATGAGTTTCCGTTCAGCTCC
43058309 TATGAGCTTT-CGTTCA
1 TATGAG-TTTCCGTTCA
43058325 ACATTTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 29 0.91
22 3 0.09
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.41
Consensus pattern (21 bp):
TATGAGTTTCCGTTCAGCTCC
Found at i:43075996 original size:18 final size:18
Alignment explanation
Indices: 43075973--43076007 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
43075963 CCATAGCCAC
43075973 CTTCAC-CAATCACATTCT
1 CTTCACACAATC-CATTCT
43075991 CTTCACACAATCCATTC
1 CTTCACACAATCCATTC
43076008 GTAGCTAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.29, C:0.40, G:0.00, T:0.31
Consensus pattern (18 bp):
CTTCACACAATCCATTCT
Found at i:43078684 original size:5 final size:5
Alignment explanation
Indices: 43078676--43078712 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
43078666 TGAGATGGTA
43078676 AGGTG AGGTG AGGTG AGGTG AGGTG AGGTG AGGTG AG
1 AGGTG AGGTG AGGTG AGGTG AGGTG AGGTG AGGTG AG
43078713 AGAGGTGGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.22, C:0.00, G:0.59, T:0.19
Consensus pattern (5 bp):
AGGTG
Found at i:43086405 original size:14 final size:11
Alignment explanation
Indices: 43086367--43086403 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
43086357 GTATTTTACA
43086367 AAAATAATA-C
1 AAAATAATATC
43086377 AAAATAATATC
1 AAAATAATATC
43086388 AAAATAATATAC
1 AAAATAATAT-C
43086400 AAAA
1 AAAA
43086404 AAGTTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 9 0.36
11 11 0.44
12 5 0.20
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.22
Consensus pattern (11 bp):
AAAATAATATC
Found at i:43086716 original size:151 final size:152
Alignment explanation
Indices: 43086531--43086860 Score: 497
Period size: 151 Copynumber: 2.2 Consensus size: 152
43086521 TCTTTATTCA
* * *
43086531 TATTTTTTTCTCGAATTTTATTACTTTTAAAAAATATACTATTTTGTAATTTTATTATTTTACAT
1 TATTTTTTCCT-GGATTTTATTACTTTTAAAAAATATACTATTTTCTAATTTTATTATTTTACAT
* *
43086596 TATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAA-TT-AAAAAAA
65 TATTTTAGTACAGTATGTTTGAAATGTATTAATTTAGTGTGTTTTGTAAATAAATTTAAAAAAAA
43086659 CTC-TTATTTCAGCCATTTGTTCG
130 C-CATTATTTCAGCCATTTGTTCG
*
43086682 TATTTTTTCCTAGGATTTTATTATTTTTAAAAAATATACTATTTTCTAATTTTATTATTTTACAT
1 TATTTTTTCCT-GGATTTTATTACTTTTAAAAAATATACTATTTTCTAATTTTATTATTTTACAT
* *
43086747 TTTTTTAGTACAGTATGTTTGAAATGTATTCATTTAGTGTGTTTTGTAAATAAATTTAAAAAAAA
65 TATTTTAGTACAGTATGTTTGAAATGTATTAATTTAGTGTGTTTTGTAAATAAATTTAAAAAAAA
** *
43086812 CCATTATTTTGGCCATTTGTTTG
130 CCATTATTTCAGCCATTTGTTCG
43086835 TATTTTTTTCC-GGATTTTATTACTTT
1 TA-TTTTTTCCTGGATTTTATTACTTT
43086861 CAATAAAAAC
Statistics
Matches: 162, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
151 110 0.68
152 17 0.10
153 27 0.17
154 8 0.05
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.53
Consensus pattern (152 bp):
TATTTTTTCCTGGATTTTATTACTTTTAAAAAATATACTATTTTCTAATTTTATTATTTTACATT
ATTTTAGTACAGTATGTTTGAAATGTATTAATTTAGTGTGTTTTGTAAATAAATTTAAAAAAAAC
CATTATTTCAGCCATTTGTTCG
Found at i:43086986 original size:244 final size:247
Alignment explanation
Indices: 43086662--43087150 Score: 776
Period size: 244 Copynumber: 2.0 Consensus size: 247
43086652 AAAAAAACTC
* * *
43086662 TTATTTCAGCCATTTGTTCGTATTTTTTCCTAGGATTTTATTATTTTTAAAAAATATACTATTTT
1 TTATTTCAGCCATTTATTCATATTTTTTCCTAGGATTTTATTATTTTTAAAAAATATAATATTTT
* *
43086727 CTAATTTTATTATTTTACATTTTTTTAGTACAGTATGTTTGAAATGTATTCATTTAGTGTGTTTT
66 CTAATTTTATTATTTTACATTATTTTAGTACAGTATGTGTGAAATGTATTCATTTAGTGTGTTTT
*
43086792 GTAAATAAATTT-AAAAAAAAC-CATTATTT-TGGCCATTTGTTTGTATTTTTTT-CCGGATTTT
131 GTAAATAAATTTAAAAAAAAACTC-TTATTTCT-GCCATTTGTTCGTATTTTTTTACCGGATTTT
*
43086853 ATTACTTTCAAT-AAAAACACACTAAATTAATACATTTCAAACATAATGTACCT
194 ATTACTTTCAATAAAAAACACACTAAATGAATACATTTCAAACATAATGTACCT
* * *
43086906 TTATTTCGGCCCTTTATTCATATTTTTTTCC-A-GATTTTATTATTTTTTAAAAATATAATATTT
1 TTATTTCAGCCATTTATTCATA-TTTTTTCCTAGGATTTTATTATTTTTAAAAAATATAATATTT
*
43086969 TCTAAATTTTATTATTTTACATTATTTTAGTACATTATGTGTGAAATGTATTCATTTAGTGTGTT
65 TCT-AATTTTATTATTTTACATTATTTTAGTACAGTATGTGTGAAATGTATTCATTTAGTGTGTT
* *
43087034 TTTTAAATAAATTTAAAAAAAAACTCTTATTTCTGCCCTTTGTTCGTATTTTTTTACCGGATTTT
129 TTGTAAATAAATTTAAAAAAAAACTCTTATTTCTGCCATTTGTTCGTATTTTTTTACCGGATTTT
43087099 ATTACTTTCAATAAAAAACACACTAAATGAATACATTTCAAACATAATGTAC
194 ATTACTTTCAATAAAAAACACACTAAATGAATACATTTCAAACATAATGTAC
43087151 TAAAATGATG
Statistics
Matches: 225, Mismatches: 13, Indels: 11
0.90 0.05 0.04
Matches are distributed among these distances:
243 32 0.14
244 90 0.40
245 42 0.19
246 23 0.10
247 38 0.17
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.48
Consensus pattern (247 bp):
TTATTTCAGCCATTTATTCATATTTTTTCCTAGGATTTTATTATTTTTAAAAAATATAATATTTT
CTAATTTTATTATTTTACATTATTTTAGTACAGTATGTGTGAAATGTATTCATTTAGTGTGTTTT
GTAAATAAATTTAAAAAAAAACTCTTATTTCTGCCATTTGTTCGTATTTTTTTACCGGATTTTAT
TACTTTCAATAAAAAACACACTAAATGAATACATTTCAAACATAATGTACCT
Found at i:43087509 original size:41 final size:41
Alignment explanation
Indices: 43087447--43087598 Score: 193
Period size: 41 Copynumber: 3.7 Consensus size: 41
43087437 CCTTTCAGGG
*
43087447 CTTTAGCGGCGTTTTTAGAGAAGCGCCGCTAATGCTCCGGT
1 CTTTAGCGGCGTTTTTTGAGAAGCGCCGCTAATGCTCCGGT
*
43087488 CTTTAGCGGTGTTTTTTGAGAAGCGCCGCTAATGCTCCGAG-
1 CTTTAGCGGCGTTTTTTGAGAAGCGCCGCTAATGCTCCG-GT
* * *
43087529 CTTTAGCGGCGTTTTTGGAGAAGCGCAGCTAATGCT-CAGT
1 CTTTAGCGGCGTTTTTTGAGAAGCGCCGCTAATGCTCCGGT
* *
43087569 GCTTTAGCGGAG-TTTTTGAAAAAGCGCCGC
1 -CTTTAGCGGCGTTTTTTG-AGAAGCGCCGC
43087599 AAAAACAGTT
Statistics
Matches: 97, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
39 1 0.01
40 6 0.06
41 89 0.92
42 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.30
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTTGAGAAGCGCCGCTAATGCTCCGGT
Found at i:43087584 original size:82 final size:82
Alignment explanation
Indices: 43087446--43087598 Score: 229
Period size: 82 Copynumber: 1.9 Consensus size: 82
43087436 ACCTTTCAGG
* * * *
43087446 GCTTTAGCGGCGTTTTTAGAGAAGCGCCGCTAATGCTCCGGTCTTTAGCGGTGTTTTTTG-AGAA
1 GCTTTAGCGGCGTTTTTAGAGAAGCGCAGCTAATGCTCAGGTCTTTAGCGGAG-TTTTTGAAAAA
43087510 GCGCCGCTAATGCTCCGA
65 GCGCCGCTAATGCTCCGA
*
43087528 GCTTTAGCGGCGTTTTTGGAGAAGCGCAGCTAATGCTCA-GTGCTTTAGCGGAGTTTTTGAAAAA
1 GCTTTAGCGGCGTTTTTAGAGAAGCGCAGCTAATGCTCAGGT-CTTTAGCGGAGTTTTTGAAAAA
43087592 GCGCCGC
65 GCGCCGC
43087599 AAAAACAGTT
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
81 8 0.12
82 56 0.88
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (82 bp):
GCTTTAGCGGCGTTTTTAGAGAAGCGCAGCTAATGCTCAGGTCTTTAGCGGAGTTTTTGAAAAAG
CGCCGCTAATGCTCCGA
Found at i:43088054 original size:119 final size:119
Alignment explanation
Indices: 43087913--43088150 Score: 467
Period size: 119 Copynumber: 2.0 Consensus size: 119
43087903 NNNNNNNNNN
*
43087913 TAATTAATTATCATTATAGTTTAGGGTTTAATATATATGGTTTAGGGTATATGGTTAATTTAGAA
1 TAATTAATTATCATTATAGTTTAGGGTTTAATATATATGGTTTAGGGTATATGATTAATTTAGAA
43087978 TTTAAGGCCGGTTTAGGAGTTACAATTTTAAGGTTTATATATTATGGATTTGGG
66 TTTAAGGCCGGTTTAGGAGTTACAATTTTAAGGTTTATATATTATGGATTTGGG
43088032 TAATTAATTATCATTATAGTTTAGGGTTTAATATATATGGTTTAGGGTATATGATTAATTTAGAA
1 TAATTAATTATCATTATAGTTTAGGGTTTAATATATATGGTTTAGGGTATATGATTAATTTAGAA
43088097 TTTAAGGCCGGTTTAGGAGTTACAATTTTAAGGTTTATATATTATGGATTTGGG
66 TTTAAGGCCGGTTTAGGAGTTACAATTTTAAGGTTTATATATTATGGATTTGGG
43088151 GATTATGAAT
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
119 118 1.00
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.45
Consensus pattern (119 bp):
TAATTAATTATCATTATAGTTTAGGGTTTAATATATATGGTTTAGGGTATATGATTAATTTAGAA
TTTAAGGCCGGTTTAGGAGTTACAATTTTAAGGTTTATATATTATGGATTTGGG
Found at i:43088202 original size:14 final size:13
Alignment explanation
Indices: 43088188--43088230 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
43088178 AGGTTGTGGT
*
43088188 TTAGGGATTAGGG
1 TTAGAGATTAGGG
*
43088201 TTAGAGATTAAGAG
1 TTAGAGATT-AGGG
43088215 TTAGAGATTTAGGG
1 TTAGAGA-TTAGGG
43088229 TT
1 TT
43088231 TATGAATTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 8 0.32
14 15 0.60
15 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.35, T:0.35
Consensus pattern (13 bp):
TTAGAGATTAGGG
Found at i:43088416 original size:14 final size:14
Alignment explanation
Indices: 43088397--43088425 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
43088387 GGGTTAGTAG
43088397 TTGTGGTTAGGGGT
1 TTGTGGTTAGGGGT
43088411 TTGTGGTTAGGGGT
1 TTGTGGTTAGGGGT
43088425 T
1 T
43088426 AGGGCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.00, G:0.48, T:0.45
Consensus pattern (14 bp):
TTGTGGTTAGGGGT
Found at i:43089860 original size:16 final size:17
Alignment explanation
Indices: 43089833--43089870 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
43089823 TAGGTTTTTA
43089833 TTTCTATTTGGGGTTCT
1 TTTCTATTTGGGGTTCT
43089850 TTTCT-TTTGGGGTTCT
1 TTTCTATTTGGGGTTCT
43089866 TTTCT
1 TTTCT
43089871 GGGTTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.03, C:0.13, G:0.21, T:0.63
Consensus pattern (17 bp):
TTTCTATTTGGGGTTCT
Found at i:43090743 original size:2 final size:2
Alignment explanation
Indices: 43090736--43090763 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43090726 TCTTGAACTA
43090736 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43090764 CCTTGCAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43094592 original size:44 final size:42
Alignment explanation
Indices: 43094514--43094678 Score: 138
Period size: 43 Copynumber: 3.9 Consensus size: 42
43094504 TTTTTACGAG
* * *
43094514 AAGCGTCGCTAAAGGT-TTGTTCTATAGCGGCGTTTATGATAAA
1 AAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTATG-T-AA
* *
43094557 AAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTAT-GTAA
* * ** * * *
43094600 AAGCGCCGCTAAAGATCGTATTCTATA-AGGCGTTTGTGTGA
1 AAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTATGTAA
* * *
43094641 AAGCGCTGCTAAAGGTCAT-GACTTTTAGCGGCGTTTAT
1 AAGCGCCGCTAAAGGTCATGGTC-TATAGCGGCGTTTAT
43094679 TTCTAAAAAC
Statistics
Matches: 98, Mismatches: 20, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
40 1 0.01
41 21 0.21
42 17 0.17
43 40 0.41
44 18 0.18
45 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.29
Consensus pattern (42 bp):
AAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTATGTAA
Found at i:43095812 original size:16 final size:17
Alignment explanation
Indices: 43095782--43095814 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
43095772 TATTTAGGCT
*
43095782 ATTTAAATTTTATAAAA
1 ATTTAAATTTAATAAAA
43095799 ATTTAAA-TTAATAAAA
1 ATTTAAATTTAATAAAA
43095815 GTAAAATCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAATAAAA
Found at i:43117980 original size:25 final size:25
Alignment explanation
Indices: 43117933--43117980 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
43117923 ACATTGTCAT
*** *
43117933 CTAAAATATAACATTTTATAAATGA
1 CTAAAATATAACATGAGACAAATGA
43117958 CTAAAATATAACATGAGACAAAT
1 CTAAAATATAACATGAGACAAAT
43117981 AAAAATAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.29
Consensus pattern (25 bp):
CTAAAATATAACATGAGACAAATGA
Found at i:43127441 original size:6 final size:6
Alignment explanation
Indices: 43127432--43127465 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
43127422 ATGATTGAGA
43127432 TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG TTTT
1 TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG TTTT
43127466 CGATTGAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (6 bp):
TTTTGG
Found at i:43130157 original size:15 final size:14
Alignment explanation
Indices: 43130135--43130169 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
43130125 ATTATTTCAA
43130135 AAAATTAAAAAAAT
1 AAAATTAAAAAAAT
*
43130149 AATAATTAAAAATAT
1 AA-AATTAAAAAAAT
43130164 AAAATT
1 AAAATT
43130170 TGACCATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATTAAAAAAAT
Found at i:43132663 original size:47 final size:50
Alignment explanation
Indices: 43132565--43132673 Score: 134
Period size: 47 Copynumber: 2.2 Consensus size: 50
43132555 CATGACAATA
* *
43132565 TGTGATATGTGATTTCCGTATAAGACCATAGTTGGGCTATGGCATC-A-G
1 TGTGATATGTGACTTCCGTATAAGAACATAGTTGGGCTATGGCATCGATG
* * * * *
43132613 TGTGATATGTG-CTTCCGTGTAAGAACATGGTTGGGCTATGGCTTTGGTG
1 TGTGATATGTGACTTCCGTATAAGAACATAGTTGGGCTATGGCATCGATG
43132662 TGTGATATGTGA
1 TGTGATATGTGA
43132674 TTATATGCAA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
47 28 0.55
48 11 0.22
49 12 0.24
ACGTcount: A:0.21, C:0.12, G:0.31, T:0.36
Consensus pattern (50 bp):
TGTGATATGTGACTTCCGTATAAGAACATAGTTGGGCTATGGCATCGATG
Found at i:43133262 original size:25 final size:25
Alignment explanation
Indices: 43133210--43133271 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
43133200 ACCTTAGCGC
* * *
43133210 GCTCTCTTATTATTAGCACATCAGT
1 GCTCTCTGATTATTAACACATCAAT
* *
43133235 GCTCTCTGATTATTAACACGTTAAT
1 GCTCTCTGATTATTAACACATCAAT
*
43133260 GCTCTCCGATTA
1 GCTCTCTGATTA
43133272 GCAAATCTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (25 bp):
GCTCTCTGATTATTAACACATCAAT
Found at i:43136468 original size:28 final size:28
Alignment explanation
Indices: 43136437--43136500 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
43136427 TAAAAAATAA
**
43136437 CAAAATATTATAACTTTTTTTTATTTAC
1 CAAAATATTATAAAATTTTTTTATTTAC
43136465 CAAAATATTATAAAATTTTTTTATTTAC
1 CAAAATATTATAAAATTTTTTTATTTAC
43136493 CAAAATAT
1 CAAAATAT
43136501 AAATAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (28 bp):
CAAAATATTATAAAATTTTTTTATTTAC
Found at i:43136506 original size:29 final size:28
Alignment explanation
Indices: 43136437--43136508 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
43136427 TAAAAAATAA
* **
43136437 CAAAATATTATAACTTTTTTTTATTTAC
1 CAAAATATAATAAAATTTTTTTATTTAC
*
43136465 CAAAATATTATAAAATTTTTTTATTTAC
1 CAAAATATAATAAAATTTTTTTATTTAC
43136493 CAAAATATAAATAAAA
1 CAAAATAT-AATAAAA
43136509 AATAAAAAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 34 0.85
29 6 0.15
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (28 bp):
CAAAATATAATAAAATTTTTTTATTTAC
Found at i:43136954 original size:19 final size:19
Alignment explanation
Indices: 43136930--43136995 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
43136920 ATTAAAATAG
43136930 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
* *
43136949 TTTAATGTAATAA-ACTAT
1 TTTAATTTAATAACTCTAT
* *
43136967 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
43136986 TTTAATTTAA
1 TTTAATTTAA
43136996 AAAAATTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:43137675 original size:12 final size:12
Alignment explanation
Indices: 43137658--43137682 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43137648 TAACATGGTA
43137658 AATTTGCATGTC
1 AATTTGCATGTC
43137670 AATTTGCATGTC
1 AATTTGCATGTC
43137682 A
1 A
43137683 GGTCCTTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
AATTTGCATGTC
Found at i:43137804 original size:27 final size:27
Alignment explanation
Indices: 43137720--43137805 Score: 118
Period size: 27 Copynumber: 3.2 Consensus size: 27
43137710 TTTTAGTCCT
* *
43137720 TTGGCACCATTGGTGCCGCCAGTCACA
1 TTGGCACCATTGGTGCCGCCAATCTCA
*
43137747 TTGGCACCATTGGTGCCGCCAATCTCT
1 TTGGCACCATTGGTGCCGCCAATCTCA
* * *
43137774 TTGGCACCTTTGGTGCCGCCAATGTGA
1 TTGGCACCATTGGTGCCGCCAATCTCA
43137801 TTGGC
1 TTGGC
43137806 CTCATCAGGC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.15, C:0.30, G:0.27, T:0.28
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATCTCA
Found at i:43145524 original size:25 final size:24
Alignment explanation
Indices: 43145484--43145552 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 24
43145474 CCCATACGAG
* * *
43145484 CATATAATTGGGAAGCTCTTTTGATC
1 CATATAA-AGGGAAGCTCTGTT-AGC
43145510 CATATAAAGGGAAGCTCATGTTAGC
1 CATATAAAGGGAAGCTC-TGTTAGC
* *
43145535 CATGTAACGGGAAGCTCT
1 CATATAAAGGGAAGCTCT
43145553 AGAGAGCCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 1 0.03
25 26 0.70
26 10 0.27
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (24 bp):
CATATAAAGGGAAGCTCTGTTAGC
Found at i:43145583 original size:24 final size:25
Alignment explanation
Indices: 43145509--43145648 Score: 69
Period size: 24 Copynumber: 5.7 Consensus size: 25
43145499 CTCTTTTGAT
* * * **
43145509 CCATATAAAGGGAAGCTCATGTTAG
1 CCATGTAACGGGAAGCTCAAGAGAG
*
43145534 CCATGTAACGGGAAGCTCTAGAGAG
1 CCATGTAACGGGAAGCTCAAGAGAG
* * *
43145559 CCAT-TAACGGGAGGTTCAAGCGAG
1 CCATGTAACGGGAAGCTCAAGAGAG
* * *
43145583 CCA-ATATCGAGAAGCTCCGAA-A-AG
1 CCATGTAACGGGAAGCT-C-AAGAGAG
*
43145607 CCAT-TAACGGGAAACTCATA-AGAG
1 CCATGTAACGGGAAGCTCA-AGAGAG
*
43145631 CCAT-TGATCGGGAAGCTC
1 CCATGT-AACGGGAAGCTC
43145649 TGAAGACCCA
Statistics
Matches: 88, Mismatches: 20, Indels: 14
0.72 0.16 0.11
Matches are distributed among these distances:
22 1 0.01
23 3 0.03
24 48 0.55
25 34 0.39
26 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.18
Consensus pattern (25 bp):
CCATGTAACGGGAAGCTCAAGAGAG
Found at i:43145654 original size:25 final size:24
Alignment explanation
Indices: 43145626--43145697 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
43145616 GGAAACTCAT
* * *
43145626 AAGAGCCATTGATCGGGAAGCTCTG
1 AAGAGCCAAT-ATCGAGAAGCTCCG
*
43145651 AAGACCCAAATATCGAGAAGCTCCG
1 AAGAGCC-AATATCGAGAAGCTCCG
*
43145676 AAGAG-CAATAAACGAGAAGCTC
1 AAGAGCCAAT-ATCGAGAAGCTC
43145698 AAAAGAAAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
23 3 0.08
24 12 0.31
25 22 0.56
26 2 0.05
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.14
Consensus pattern (24 bp):
AAGAGCCAATATCGAGAAGCTCCG
Found at i:43145676 original size:74 final size:75
Alignment explanation
Indices: 43145585--43145724 Score: 192
Period size: 74 Copynumber: 1.9 Consensus size: 75
43145575 CAAGCGAGCC
* * * * * *
43145585 AATATCGAGAAGCTCCGAAAAGCCATTAACGGGAAACTCATAAG-AGCCATTGATCGGGAAGCTC
1 AATATCGAGAAGCTCCGAAAAGCAATAAACGAGAAACTCAAAAGAAGCCATTAATCAGGAAGCTC
43145649 TGAAGACCCA
66 TGAAGACCCA
* *
43145659 AATATCGAGAAGCTCCGAAGAGCAATAAACGAGAAGCTCAAAAGAAAGCCATTAATCAGGAAGCT
1 AATATCGAGAAGCTCCGAAAAGCAATAAACGAGAAACTCAAAAG-AAGCCATTAATCAGGAAGCT
43145724 C
65 C
43145725 GCAAGAATCA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
74 38 0.68
76 18 0.32
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.15
Consensus pattern (75 bp):
AATATCGAGAAGCTCCGAAAAGCAATAAACGAGAAACTCAAAAGAAGCCATTAATCAGGAAGCTC
TGAAGACCCA
Found at i:43154017 original size:25 final size:25
Alignment explanation
Indices: 43153981--43154077 Score: 88
Period size: 25 Copynumber: 3.9 Consensus size: 25
43153971 GCTCTCTCTC
*
43153981 GAGCCATATAACAGGAAGCTCATAT
1 GAGCCATATAACAGGAAGCTCATAA
* * * **
43154006 GAGCCATGTAACGGGAAGCTTATCC
1 GAGCCATATAACAGGAAGCTCATAA
* ** *
43154031 GGGCTGTATAACGGGAAGCTCATAA
1 GAGCCATATAACAGGAAGCTCATAA
*
43154056 GAGCCATA-ATCAGGAAGCTCAT
1 GAGCCATATAACAGGAAGCTCAT
43154078 GCTAGCCAAT
Statistics
Matches: 55, Mismatches: 17, Indels: 1
0.75 0.23 0.01
Matches are distributed among these distances:
24 12 0.22
25 43 0.78
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.20
Consensus pattern (25 bp):
GAGCCATATAACAGGAAGCTCATAA
Done.