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 85 of 202
Found at i:25206671 original size:28 final size:27
Alignment explanation
Indices: 25206629--25206685 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 27
25206619 AAATTTTCAA
*
25206629 AAAAAAATTTGATCTATTTTTGTAATATTT
1 AAAAAAA-TTGATCT-TTTTT-TAAAATTT
25206659 AAAAAAA-TGATCTTTTTTTAAAATTT
1 AAAAAAATTGATCTTTTTTTAAAATTT
25206685 A
1 A
25206686 GTCCAAGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 8 0.31
27 5 0.19
28 6 0.23
30 7 0.27
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (27 bp):
AAAAAAATTGATCTTTTTTTAAAATTT
Found at i:25208286 original size:41 final size:37
Alignment explanation
Indices: 25208212--25208283 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
25208202 GAACAAAAAA
* *
25208212 AAAAAAAGAGTGGTAAAGGTTATCTAAGTAAGAAACT
1 AAAAAAAGAGTGGGAAAGGTTATATAAGTAAGAAACT
25208249 AAAAAAAGAGTGGGAAAGGTTATATAAGTAAGAAA
1 AAAAAAAGAGTGGGAAAGGTTATATAAGTAAGAAA
25208284 GAACATGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.54, C:0.03, G:0.24, T:0.19
Consensus pattern (37 bp):
AAAAAAAGAGTGGGAAAGGTTATATAAGTAAGAAACT
Found at i:25235750 original size:33 final size:33
Alignment explanation
Indices: 25235708--25235770 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
25235698 TTTATATTTA
25235708 AAATAATTAAAGA-ATTATTAAAATTATAAATAT
1 AAATAATTAAA-ATATTATTAAAATTATAAATAT
* *
25235741 AAATTATTAAAATATTTTTAAAATTATAAA
1 AAATAATTAAAATATTATTAAAATTATAAA
25235771 AAAAATTGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 1 0.04
33 26 0.96
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (33 bp):
AAATAATTAAAATATTATTAAAATTATAAATAT
Found at i:25235806 original size:22 final size:22
Alignment explanation
Indices: 25235760--25235806 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
25235750 AAATATTTTT
*
25235760 AAAATTATAAAAAAAATTGCAA
1 AAAATTATAAAAAAAATAGCAA
*
25235782 AAAATTATAAAAGAAACTAGCAA
1 AAAATTATAAAA-AAAATAGCAA
25235805 AA
1 AA
25235807 TAAAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.19
Consensus pattern (22 bp):
AAAATTATAAAAAAAATAGCAA
Found at i:25235852 original size:27 final size:27
Alignment explanation
Indices: 25235803--25235859 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
25235793 AGAAACTAGC
*
25235803 AAAATAAAAAATTATATAGATTAAGAA
1 AAAATAAAAAATTATAAAGATTAAGAA
* * *
25235830 AAAATAAAAAATTGTAAATATTATGAA
1 AAAATAAAAAATTATAAAGATTAAGAA
25235857 AAA
1 AAA
25235860 TGTTTAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (27 bp):
AAAATAAAAAATTATAAAGATTAAGAA
Found at i:25235921 original size:27 final size:25
Alignment explanation
Indices: 25235864--25235949 Score: 64
Period size: 27 Copynumber: 3.3 Consensus size: 25
25235854 GAAAAATGTT
* * **
25235864 TAAAATATAGAAAATTATTAAAACTA
1 TAAAAAATAGAAAAGTACAAAAAC-A
* *
25235890 TTAAAAAATGGAAAAGTGCAAAAAATCA
1 -TAAAAAATAGAAAAGTAC-AAAAA-CA
* *
25235918 TAAAATATAGAAAATTACAAAAACA
1 TAAAAAATAGAAAAGTACAAAAACA
25235943 TAAAAAA
1 TAAAAAA
25235950 AATGTTCACA
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
25 8 0.17
26 5 0.11
27 27 0.59
28 5 0.11
29 1 0.02
ACGTcount: A:0.65, C:0.06, G:0.07, T:0.22
Consensus pattern (25 bp):
TAAAAAATAGAAAAGTACAAAAACA
Found at i:25244307 original size:14 final size:15
Alignment explanation
Indices: 25244250--25244338 Score: 51
Period size: 15 Copynumber: 5.7 Consensus size: 15
25244240 ATTGGGTTTA
25244250 TTTTATTTAATTTTGAAT
1 TTTTATTT-A-TTT-AAT
*
25244268 TTTGTTTTTATTT-AT
1 TTT-TATTTATTTAAT
*
25244283 TGTTTACTATTATTTGAT
1 T-TTTA-T-TTATTTAAT
25244301 TTTTATTTATTTAAT
1 TTTTATTTATTTAAT
* *
25244316 TTTGAATTA--T-AT
1 TTTTATTTATTTAAT
25244328 TTTTATTTATT
1 TTTTATTTATT
25244339 GCTTACTATT
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
12 9 0.16
13 1 0.02
15 19 0.33
16 4 0.07
17 13 0.23
18 7 0.12
19 4 0.07
ACGTcount: A:0.24, C:0.01, G:0.06, T:0.70
Consensus pattern (15 bp):
TTTTATTTATTTAAT
Found at i:25244329 original size:27 final size:26
Alignment explanation
Indices: 25244246--25244338 Score: 82
Period size: 27 Copynumber: 3.4 Consensus size: 26
25244236 ATCAATTGGG
*
25244246 TTTATTTTATTTAATTTTGAATTTTGTT
1 TTTA-TTTATTTAATTTTGAA-TTTATT
* *
25244274 TTTATTTATTGTTTACTATT--ATTTGATT
1 TTTATTTA---TTTAATTTTGAATTT-ATT
25244302 TTTATTTATTTAATTTTGAATTATATT
1 TTTATTTATTTAATTTTGAATT-TATT
25244329 TTTATTTATT
1 TTTATTTATT
25244339 GCTTACTATT
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
25 7 0.13
27 23 0.43
28 16 0.30
30 7 0.13
ACGTcount: A:0.24, C:0.01, G:0.05, T:0.70
Consensus pattern (26 bp):
TTTATTTATTTAATTTTGAATTTATT
Found at i:25244331 original size:55 final size:55
Alignment explanation
Indices: 25244246--25244372 Score: 200
Period size: 55 Copynumber: 2.3 Consensus size: 55
25244236 ATCAATTGGG
* * *
25244246 TTTATTTTATTTAATTTTGAATTTTGTTTTTATTTATTGTTTACTATTATTTGATT
1 TTTA-TTTATTTAATTTTGAATTATATTTTTATTTATTGCTTACTATTATTTGATT
*
25244302 TTTATTTATTTAATTTTGAATTATATTTTTATTTATTGCTTACTATTCTTTGATT
1 TTTATTTATTTAATTTTGAATTATATTTTTATTTATTGCTTACTATTATTTGATT
*
25244357 TTTATATATTTAATTT
1 TTTATTTATTTAATTT
25244373 CGTATTACTT
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
55 62 0.94
56 4 0.06
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.68
Consensus pattern (55 bp):
TTTATTTATTTAATTTTGAATTATATTTTTATTTATTGCTTACTATTATTTGATT
Found at i:25244358 original size:28 final size:27
Alignment explanation
Indices: 25244268--25244366 Score: 89
Period size: 28 Copynumber: 3.6 Consensus size: 27
25244258 AATTTTGAAT
25244268 TTTG-TTTTTATTTATTGTTTACTATTA
1 TTTGATTTTTATTTATTG-TTACTATTA
* *
25244295 TTTGATTTTTATTTA-T-TTAATTTTGAA
1 TTTGATTTTTATTTATTGTTACTATT--A
*
25244322 TTAT-ATTTTTATTTATTGCTTACTATTC
1 TT-TGATTTTTATTTATTG-TTACTATTA
*
25244350 TTTGATTTTTATATATT
1 TTTGATTTTTATTTATT
25244367 TAATTTCGTA
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
25 6 0.10
27 20 0.34
28 26 0.45
30 6 0.10
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.68
Consensus pattern (27 bp):
TTTGATTTTTATTTATTGTTACTATTA
Found at i:25253026 original size:33 final size:33
Alignment explanation
Indices: 25252954--25253029 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 33
25252944 ATGTTTATAT
* * *
25252954 GTAAGATCATAGCTGGGCTATGGCATTTTAATA
1 GTAAGACCATAACTGGGCTATGGCACTTTAATA
** *
25252987 AAAAGACCATAACTGGGTTATGGCACTTTAA-A
1 GTAAGACCATAACTGGGCTATGGCACTTTAATA
25253019 CGTAAGACCAT
1 -GTAAGACCAT
25253030 GGTTAGACCA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
32 1 0.03
33 33 0.97
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.28
Consensus pattern (33 bp):
GTAAGACCATAACTGGGCTATGGCACTTTAATA
Found at i:25260444 original size:33 final size:33
Alignment explanation
Indices: 25260403--25260559 Score: 95
Period size: 33 Copynumber: 4.7 Consensus size: 33
25260393 GTTTATATGT
25260403 AAGACCATAGCTGGGCTATGGCATTTTAATGAA
1 AAGACCATAGCTGGGCTATGGCATTTTAATGAA
* * * * * *
25260436 AAGACCATAACTGAGTTATGGCACTTTGAACG-T
1 AAGACCATAGCTGGGCTATGGCA-TTTTAATGAA
* * * * *
25260469 AAGACCATGGTTCGACCATGGCAATATTT-AT-AA
1 AAGACCATAGCTGGGCTATGGC-AT-TTTAATGAA
* * * *
25260502 GTAAGACCATAGCTAGGCTATGGCATTCTGATGAT
1 --AAGACCATAGCTGGGCTATGGCATTTTAATGAA
* *
25260537 AAGACCATAACTGGGTTATGGCA
1 AAGACCATAGCTGGGCTATGGCA
25260560 CTACGAATGT
Statistics
Matches: 89, Mismatches: 27, Indels: 16
0.67 0.20 0.12
Matches are distributed among these distances:
33 58 0.65
34 13 0.15
35 18 0.20
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (33 bp):
AAGACCATAGCTGGGCTATGGCATTTTAATGAA
Found at i:25260542 original size:101 final size:101
Alignment explanation
Indices: 25260367--25260594 Score: 321
Period size: 101 Copynumber: 2.3 Consensus size: 101
25260357 AATTGACGGA
* * * * *
25260367 TAAGACCATGGTTGGACCATGGAAATGTTTATATGTAAGACCATAGCTGGGCTATGGCATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATATTTATAAGTAAGACCATAGCTAGGCTATGGCATTCTAA
**
25260432 TGAAAAGACCATAACTGAGTTATGGCACTTTGAACG
66 TGAAAAGACCATAACTGAGTTATGGCACTACGAACG
* *
25260468 TAAGACCATGGTTCGACCATGGCAATATTTATAAGTAAGACCATAGCTAGGCTATGGCATTCTGA
1 TAAGACCATGGTTGGACCATGGCAATATTTATAAGTAAGACCATAGCTAGGCTATGGCATTCTAA
* * *
25260533 TGATAAGACCATAACTGGGTTATGGCACTACGAATG
66 TGAAAAGACCATAACTGAGTTATGGCACTACGAACG
* * *
25260569 TAAGACCTTGGCTGGGCCATGGCAAT
1 TAAGACCATGGTTGGACCATGGCAAT
25260595 GCATGTGTAA
Statistics
Matches: 111, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
101 111 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATATTTATAAGTAAGACCATAGCTAGGCTATGGCATTCTAA
TGAAAAGACCATAACTGAGTTATGGCACTACGAACG
Found at i:25260573 original size:33 final size:32
Alignment explanation
Indices: 25260502--25260575 Score: 78
Period size: 33 Copynumber: 2.2 Consensus size: 32
25260492 ATATTTATAA
* *
25260502 GTAAGACCATAGCTAGGCTATGGCATTCTGAT
1 GTAAGACCATAACTAGGCTATGGCATACTGAT
* *
25260534 GATAAGACCATAACTGGGTTATGGCACTAC-GAAT
1 G-TAAGACCATAACTAGGCTATGGCA-TACTG-AT
25260568 GTAAGACC
1 GTAAGACC
25260576 TTGGCTGGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 1 0.03
33 29 0.83
34 5 0.14
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.24
Consensus pattern (32 bp):
GTAAGACCATAACTAGGCTATGGCATACTGAT
Found at i:25260936 original size:215 final size:216
Alignment explanation
Indices: 25260564--25261001 Score: 770
Period size: 215 Copynumber: 2.0 Consensus size: 216
25260554 ATGGCACTAC
* * *
25260564 GAATGTAAGACCTTGGCTGGGCCATGGCAATGCATGTGTAAGACCATAGTTGGACTATGGCACAA
1 GAATGTAAGACCATGGCTGGGCCATGACAATGCATGTGTAAGACCATAGTTGGACTATCGCACAA
* *
25260629 AAAAAATGATGTACTCATACCCGTAAGTCGTTCATCGATTCAGTAAGAATTGGTAAAAGACCTAT
66 AAAAAACGATGTACTCATACCCGTAAGTCGTTCATCAATTCAGTAAGAATTGGTAAAAGACCTAT
*
25260694 GTGAATGAATTGAAAGATATATTGATTATTAATGATATTGATCTAAAGGAAGTCTGTTCATTGAC
131 GTGAATGAATTAAAAGATATATTGATTATTAATGATATTGATCTAAAGGAAGTCTGTTCATTGAC
25260759 TTATGTTGTATTTGACAAGGA
196 TTATGTTGTATTTGACAAGGA
* *
25260780 GAATGTAAGACCATGGCTGGGTCATGACAATGC-TGTGTAAGACCATAGTTGGACTATCGCCCAA
1 GAATGTAAGACCATGGCTGGGCCATGACAATGCATGTGTAAGACCATAGTTGGACTATCGCACAA
*
25260844 AAAAAACGATGTACTCATACCCGTAAGTCGTTCCTCAATTCAGTAAGAATTGGTAAAAGACCTAT
66 AAAAAACGATGTACTCATACCCGTAAGTCGTTCATCAATTCAGTAAGAATTGGTAAAAGACCTAT
*
25260909 GTGAATGAATTAAAAGATATATTGATTATTAATGATATTGATCTAAAGGAAGTTTGTTCATTGAC
131 GTGAATGAATTAAAAGATATATTGATTATTAATGATATTGATCTAAAGGAAGTCTGTTCATTGAC
*
25260974 TTATGTTGTATTTGACAGGGA
196 TTATGTTGTATTTGACAAGGA
25260995 GAATGTA
1 GAATGTA
25261002 TGATTTATTT
Statistics
Matches: 211, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
215 181 0.86
216 30 0.14
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (216 bp):
GAATGTAAGACCATGGCTGGGCCATGACAATGCATGTGTAAGACCATAGTTGGACTATCGCACAA
AAAAAACGATGTACTCATACCCGTAAGTCGTTCATCAATTCAGTAAGAATTGGTAAAAGACCTAT
GTGAATGAATTAAAAGATATATTGATTATTAATGATATTGATCTAAAGGAAGTCTGTTCATTGAC
TTATGTTGTATTTGACAAGGA
Found at i:25264243 original size:41 final size:41
Alignment explanation
Indices: 25264186--25264286 Score: 184
Period size: 41 Copynumber: 2.5 Consensus size: 41
25264176 TTTAACATAT
*
25264186 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
25264227 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
25264268 TCACCGGCACTTAGCCTGC
1 TCACCGGCACTTAGCCTGC
25264287 CAGACTTAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.27
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:25264409 original size:41 final size:41
Alignment explanation
Indices: 25264268--25264412 Score: 175
Period size: 41 Copynumber: 3.5 Consensus size: 41
25264258 CTGATTCAGA
* * * * **
25264268 TCACCGGCACTT-AGCCTGCCAGACTTAAAGTCCGAATTGTT
1 TCACCGGCA-TTAAGCCTGCTAGACATAAAGTCTGAAATAAT
*
25264309 TCACCGGCCTTAAGCCTGCTAGACATAAAGTCTGAAATAAT
1 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
*
25264350 TCACCGGCATTTAGCCTGCTAGACATAAAGTCTGAAATAAT
1 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
* * *
25264391 TCATCGGTATTAACCCTGCTAG
1 TCACCGGCATTAAGCCTGCTAG
25264413 GCATCGAGCC
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 2 0.02
41 88 0.98
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (41 bp):
TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
Found at i:25264426 original size:41 final size:41
Alignment explanation
Indices: 25264308--25264426 Score: 139
Period size: 41 Copynumber: 2.9 Consensus size: 41
25264298 TCCGAATTGT
* * *
25264308 TTCACCGGCCTTAAGCCTGCTAGACATAAAGTCTGAAATAA
1 TTCACCGGCATTAACCCTGCTAGACATAAAGCCTGAAATAA
* * *
25264349 TTCACCGGCATTTAGCCTGCTAGACATAAAGTCTGAAATAA
1 TTCACCGGCATTAACCCTGCTAGACATAAAGCCTGAAATAA
* * * **
25264390 TTCATCGGTATTAACCCTGCTAGGCATCGAGCCTGAA
1 TTCACCGGCATTAACCCTGCTAGACATAAAGCCTGAA
25264427 TACCACGGAT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (41 bp):
TTCACCGGCATTAACCCTGCTAGACATAAAGCCTGAAATAA
Found at i:25273584 original size:30 final size:31
Alignment explanation
Indices: 25273549--25273621 Score: 76
Period size: 32 Copynumber: 2.4 Consensus size: 31
25273539 TTGATACATC
*
25273549 AACTTTAATTTGGTAC-AATTATACACATGA
1 AACTTTAATTTGGTACAAAATATACACATGA
* * * * *
25273579 AACTTTGATTGTGGTTCAAAATGTATATATGA
1 AACTTTAATT-TGGTACAAAATATACACATGA
25273611 AACTTTAATTT
1 AACTTTAATTT
25273622 TTATTTAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
30 9 0.26
31 6 0.18
32 19 0.56
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (31 bp):
AACTTTAATTTGGTACAAAATATACACATGA
Found at i:25274432 original size:38 final size:38
Alignment explanation
Indices: 25274390--25274469 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
25274380 ATTTGGTTTT
* * *
25274390 AATACAAAATTGAATATTGA-AACTAAATTTAAGTATCA
1 AATACAAAATTAAACATT-ATAACTAAATTTAAGTATAA
* *
25274428 AATACTAAATTAAACATTATAATTAAATTTAAGTATAA
1 AATACAAAATTAAACATTATAACTAAATTTAAGTATAA
25274466 AATA
1 AATA
25274470 ATATATTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
37 1 0.03
38 35 0.97
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34
Consensus pattern (38 bp):
AATACAAAATTAAACATTATAACTAAATTTAAGTATAA
Found at i:25286603 original size:12 final size:12
Alignment explanation
Indices: 25286586--25286610 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25286576 CGTCGTAGTT
25286586 ATCATCATAATC
1 ATCATCATAATC
25286598 ATCATCATAATC
1 ATCATCATAATC
25286610 A
1 A
25286611 AGTCCATAGT
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:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (12 bp):
ATCATCATAATC
Found at i:25289915 original size:25 final size:25
Alignment explanation
Indices: 25289885--25289950 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
25289875 GCTCTCTCTC
25289885 GAGCCATATAATGGGAAACTCATGT-
1 GAGCCATATAATGGGAAACTCAT-TA
* * *
25289910 GAGCCATGTAACGGGAAGCTCATTA
1 GAGCCATATAATGGGAAACTCATTA
*
25289935 GAGCCATA-ATTGGGAA
1 GAGCCATATAATGGGAA
25289951 GTTAATCGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
24 7 0.21
25 27 0.79
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (25 bp):
GAGCCATATAATGGGAAACTCATTA
Found at i:25289998 original size:25 final size:25
Alignment explanation
Indices: 25289958--25290071 Score: 81
Period size: 25 Copynumber: 4.5 Consensus size: 25
25289948 GAAGTTAATC
*
25289958 GAGCCA-T-ATCAGGAAGCTC-AGGA
1 GAGCCATTAATCAAGAAGCTCTA-GA
*
25289981 GAGCCATTAATCAAGAAGCTCATAAAA
1 GAGCCATTAATCAAGAAGCTC-T-AGA
* ***
25290008 GAGCCTTTAATTGGGAAGCTCTAGA
1 GAGCCATTAATCAAGAAGCTCTAGA
* *
25290033 GAGCCATTAATCGAGAAGCTCATGAAA
1 GAGCCATTAATCAAGAAGCTC-T-AGA
*
25290060 GAGCCTTTAATC
1 GAGCCATTAATC
25290072 GGGAAGTTTC
Statistics
Matches: 72, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
23 6 0.08
24 1 0.01
25 31 0.43
26 2 0.03
27 31 0.43
28 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (25 bp):
GAGCCATTAATCAAGAAGCTCTAGA
Found at i:25290018 original size:27 final size:26
Alignment explanation
Indices: 25289980--25290077 Score: 108
Period size: 27 Copynumber: 3.7 Consensus size: 26
25289970 GAAGCTCAGG
*
25289980 AGAGCCATTAATCAAGAAGCTCATAAA
1 AGAGCCATTAATCGAGAAGCTCAT-AA
* * * *
25290007 AGAGCCTTTAATTGGGAAGCTC-TAG
1 AGAGCCATTAATCGAGAAGCTCATAA
25290032 AGAGCCATTAATCGAGAAGCTCATGAA
1 AGAGCCATTAATCGAGAAGCTCAT-AA
* *
25290059 AGAGCCTTTAATCGGGAAG
1 AGAGCCATTAATCGAGAAG
25290078 TTTCGGAGAG
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
25 20 0.34
26 2 0.03
27 36 0.62
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (26 bp):
AGAGCCATTAATCGAGAAGCTCATAA
Found at i:25290026 original size:52 final size:52
Alignment explanation
Indices: 25289969--25290091 Score: 178
Period size: 52 Copynumber: 2.4 Consensus size: 52
25289959 AGCCATATCA
*
25289969 GGAAGCTCAGGAGAGCCATTAATCAAGAAGCTCATAAAAGAGCCTTTAATTG
1 GGAAGCTCAGGAGAGCCATTAATCAAGAAGCTCATAAAAGAGCCTTTAATCG
* *
25290021 GGAAGCTCTA-GAGAGCCATTAATCGAGAAGCTCATGAAAGAGCCTTTAATCG
1 GGAAGCTC-AGGAGAGCCATTAATCAAGAAGCTCATAAAAGAGCCTTTAATCG
*
25290073 GGAAGTTTC-GGAGAGCCAT
1 GGAAG-CTCAGGAGAGCCAT
25290092 ATATCTGGAT
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
52 61 0.95
53 3 0.05
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (52 bp):
GGAAGCTCAGGAGAGCCATTAATCAAGAAGCTCATAAAAGAGCCTTTAATCG
Found at i:25290191 original size:24 final size:25
Alignment explanation
Indices: 25290164--25290210 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
25290154 GGATGCTTCG
*
25290164 AAGAGCTAT-TAACGGGAAGCTCGC
1 AAGAACTATATAACGGGAAGCTCGC
25290188 AAGAACTATATAACGGGAAGCTC
1 AAGAACTATATAACGGGAAGCTC
25290211 ATGAGAGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (25 bp):
AAGAACTATATAACGGGAAGCTCGC
Found at i:25293331 original size:13 final size:13
Alignment explanation
Indices: 25293288--25293364 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
25293278 TTTAGTATTG
* *
25293288 CTTTTGAGAAGGA
1 CTTTTGAAAAGTA
25293301 C-TTTGAAAAAGTGA
1 CTTTTG-AAAAGT-A
*
25293315 -TTTTGAGAAGTA
1 CTTTTGAAAAGTA
25293327 CTTTTGAAAAGTGA
1 CTTTTGAAAAGT-A
*
25293341 -TTTTGAGAAGTA
1 CTTTTGAAAAGTA
25293353 CTTTTGAAAAGT
1 CTTTTGAAAAGT
25293365 TTAGTTTAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
12 6 0.12
13 40 0.77
14 6 0.12
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.36
Consensus pattern (13 bp):
CTTTTGAAAAGTA
Found at i:25293363 original size:26 final size:26
Alignment explanation
Indices: 25293289--25293364 Score: 127
Period size: 26 Copynumber: 2.9 Consensus size: 26
25293279 TTAGTATTGC
*
25293289 TTTTGAGAAGGAC-TTTGAAAAAGTGA
1 TTTTGAGAAGTACTTTTG-AAAAGTGA
25293315 TTTTGAGAAGTACTTTTGAAAAGTGA
1 TTTTGAGAAGTACTTTTGAAAAGTGA
25293341 TTTTGAGAAGTACTTTTGAAAAGT
1 TTTTGAGAAGTACTTTTGAAAAGT
25293365 TTAGTTTAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
26 44 0.92
27 4 0.08
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.37
Consensus pattern (26 bp):
TTTTGAGAAGTACTTTTGAAAAGTGA
Found at i:25305496 original size:27 final size:27
Alignment explanation
Indices: 25305469--25305530 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
25305459 CTTATAAATT
*
25305469 ATAATATA-TATTTATTATTAAAATATTA
1 ATAATA-AGTATTT-TTAATAAAATATTA
25305497 ATAGA-AAGTATTTTTAATAAAATATTA
1 ATA-ATAAGTATTTTTAATAAAATATTA
25305524 ATAATAA
1 ATAATAA
25305531 AAAGTATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 1 0.03
27 19 0.63
28 9 0.30
29 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (27 bp):
ATAATAAGTATTTTTAATAAAATATTA
Found at i:25305515 original size:16 final size:15
Alignment explanation
Indices: 25305492--25305544 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
25305482 ATTATTAAAA
25305492 TATTAATAGAAAGTAT
1 TATTAATA-AAAGTAT
*
25305508 TTTTAATAAAA-TAT
1 TATTAATAAAAGTAT
*
25305522 TAATAATAAAAAGTAT
1 TATTAAT-AAAAGTAT
*
25305538 AATTAAT
1 TATTAAT
25305545 GTTAAAACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 8 0.27
15 7 0.23
16 15 0.50
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (15 bp):
TATTAATAAAAGTAT
Found at i:25305587 original size:16 final size:18
Alignment explanation
Indices: 25305554--25305594 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
25305544 TGTTAAAACT
25305554 TATTATTAAAATAAAATTG
1 TATTATTAAAAT-AAATTG
25305573 TATTATT-AAAT-AATTG
1 TATTATTAAAATAAATTG
*
25305589 AATTAT
1 TATTAT
25305595 AGTAATAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 10 0.48
18 4 0.19
19 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (18 bp):
TATTATTAAAATAAATTG
Found at i:25306027 original size:2 final size:2
Alignment explanation
Indices: 25306020--25306050 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25306010 CATTACCCAT
25306020 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25306051 CTTTTGCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25309779 original size:7 final size:7
Alignment explanation
Indices: 25309767--25309803 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
25309757 ATCAACCAAA
25309767 TCAAGAT
1 TCAAGAT
25309774 TCAAGAT
1 TCAAGAT
25309781 TCAAGAT
1 TCAAGAT
25309788 TCAAGAT
1 TCAAGAT
25309795 TCAAGAT
1 TCAAGAT
25309802 TC
1 TC
25309804 CATTAGTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (7 bp):
TCAAGAT
Found at i:25325305 original size:18 final size:18
Alignment explanation
Indices: 25325287--25325320 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25325277 AATAAAATGA
25325287 AAAATTT-TTATAAATTG
1 AAAATTTATTATAAATTG
*
25325304 AAAATTTATTCTAAATT
1 AAAATTTATTATAAATT
25325321 TGGTTGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
AAAATTTATTATAAATTG
Found at i:25328891 original size:29 final size:27
Alignment explanation
Indices: 25328833--25328948 Score: 92
Period size: 28 Copynumber: 4.1 Consensus size: 27
25328823 AATTTTTGTA
* * *
25328833 AAAGTGAA-CCTTTGTGGATATCTTTGTT
1 AAAG-GAAGCCTTTGT-GCTATCTCTATT
25328861 AAAGGAAGCCTTTGTGTCTAATCTCTATT
1 AAAGGAAGCCTTTGTG-CT-ATCTCTATT
* * *
25328890 AAATGAAGCTTTTGTGGTGATCTCTATT
1 AAAGGAAGCCTTTGTGCT-ATCTCTATT
*
25328918 AAAGGAATCCCTTATG-GCTATCTCTATT
1 AAAGGAA-GCCTT-TGTGCTATCTCTATT
25328946 AAA
1 AAA
25328949 AAAGATTCCA
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
27 4 0.06
28 40 0.56
29 26 0.36
30 2 0.03
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (27 bp):
AAAGGAAGCCTTTGTGCTATCTCTATT
Found at i:25328968 original size:30 final size:30
Alignment explanation
Indices: 25328932--25329035 Score: 104
Period size: 30 Copynumber: 3.5 Consensus size: 30
25328922 GAATCCCTTA
25328932 TGGCTATCTCTATTAAAAAAGATTCCATTG
1 TGGCTATCTCTATTAAAAAAGATTCCATTG
* * * * *
25328962 TGGCTATCTCTGTTACAAAGGA-TGCATTTA
1 TGGCTATCTCTATTAAAAAAGATTCCA-TTG
* * *
25328992 TGACTATCTCTATT-AAAAAGATACCTTTG
1 TGGCTATCTCTATTAAAAAAGATTCCATTG
*
25329021 TGGCTATCTCAATTA
1 TGGCTATCTCTATTA
25329036 CATGAATGCC
Statistics
Matches: 56, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
29 22 0.39
30 34 0.61
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (30 bp):
TGGCTATCTCTATTAAAAAAGATTCCATTG
Found at i:25332547 original size:14 final size:14
Alignment explanation
Indices: 25332528--25332567 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
25332518 TTGATTGGCA
25332528 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
25332542 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
25332556 GGAAAATGTTTT
1 GTAAAATGTTTT
25332568 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:25332580 original size:34 final size:35
Alignment explanation
Indices: 25332536--25332602 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
25332526 CAGTAAAATG
* *
25332536 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
25332570 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
25332603 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:25332589 original size:20 final size:20
Alignment explanation
Indices: 25332551--25332590 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
25332541 CGTAAAATGA
**
25332551 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
25332571 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
25332591 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:25337602 original size:24 final size:24
Alignment explanation
Indices: 25337570--25337623 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
25337560 TATGCGAATC
25337570 CAGAAACAGACACAAAAACAAAAA
1 CAGAAACAGACACAAAAACAAAAA
* *
25337594 CAGAAACAGACCCAGAAACAAAAA
1 CAGAAACAGACACAAAAACAAAAA
*
25337618 TAGAAA
1 CAGAAA
25337624 ATAAAATCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.67, C:0.20, G:0.11, T:0.02
Consensus pattern (24 bp):
CAGAAACAGACACAAAAACAAAAA
Found at i:25344212 original size:17 final size:17
Alignment explanation
Indices: 25344182--25344214 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
25344172 TGACCCTGTC
25344182 TCACTAAAATTAAAATA
1 TCACTAAAATTAAAATA
25344199 TCAC-AAAATATAAAAT
1 TCACTAAAAT-TAAAAT
25344215 TCTTTTGCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (17 bp):
TCACTAAAATTAAAATA
Found at i:25345135 original size:50 final size:50
Alignment explanation
Indices: 25345073--25345201 Score: 150
Period size: 50 Copynumber: 2.6 Consensus size: 50
25345063 CAATGTCATA
* * ** * * * *
25345073 TCCCAGATATGGTCTTACATGGGAGTTTTCATATCGGTGCCTATGCCATG
1 TCCCAGACATGGTCTTACGTGGGACCTCTAATATCGGTGCCAACGCCATG
* * *
25345123 TCCCAGACATGGTCTTACGGGGGACCTCTAATCTTGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACGTGGGACCTCTAATATCGGTGCCAACGCCATG
*
25345173 TCCCAGACATTGTCTTACGTGGGACCTCT
1 TCCCAGACATGGTCTTACGTGGGACCTCT
25345202 CATAACCTCA
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.29
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACGTGGGACCTCTAATATCGGTGCCAACGCCATG
Found at i:25349768 original size:22 final size:23
Alignment explanation
Indices: 25349695--25349790 Score: 124
Period size: 23 Copynumber: 4.2 Consensus size: 23
25349685 TTTAAGAGGA
25349695 TGTGTTTGGAGGGTATATTTGGT
1 TGTGTTTGGAGGGTATATTTGGT
* *
25349718 TGTGTTGGGAGGATATATTTGGT
1 TGTGTTTGGAGGGTATATTTGGT
* *
25349741 TGTGTTTGGAGGGTA-AATTGTT
1 TGTGTTTGGAGGGTATATTTGGT
*
25349763 TGTGTTTGGAGGCTATGA-TTGGT
1 TGTGTTTGGAGGGTAT-ATTTGGT
25349786 TGTGT
1 TGTGT
25349791 GGGTGATAGC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
22 19 0.30
23 43 0.68
24 1 0.02
ACGTcount: A:0.15, C:0.01, G:0.39, T:0.46
Consensus pattern (23 bp):
TGTGTTTGGAGGGTATATTTGGT
Found at i:25349785 original size:45 final size:46
Alignment explanation
Indices: 25349695--25349790 Score: 133
Period size: 45 Copynumber: 2.1 Consensus size: 46
25349685 TTTAAGAGGA
*
25349695 TGTGTTTGGAGGGTATATTTGGTTGTGTTGGGAGGATATATTTGGT
1 TGTGTTTGGAGGGTATAATTGGTTGTGTTGGGAGGATATATTTGGT
* * *
25349741 TGTGTTTGGAGGGTA-AATTGTTTGTGTTTGGAGGCTATGA-TTGGT
1 TGTGTTTGGAGGGTATAATTGGTTGTGTTGGGAGGATAT-ATTTGGT
25349786 TGTGT
1 TGTGT
25349791 GGGTGATAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
45 29 0.64
46 16 0.36
ACGTcount: A:0.15, C:0.01, G:0.39, T:0.46
Consensus pattern (46 bp):
TGTGTTTGGAGGGTATAATTGGTTGTGTTGGGAGGATATATTTGGT
Found at i:25350572 original size:135 final size:135
Alignment explanation
Indices: 25350330--25350601 Score: 508
Period size: 135 Copynumber: 2.0 Consensus size: 135
25350320 ACTAGCTTAT
25350330 ACATGCCATTGATTTCCAAAATAAAGTTTCTTTATATACCGAGATCTTGAGGTTGATAGTGTGAT
1 ACATGCCATTGATTTCCAAAATAAAGTTTCTTTATATACCGAGATCTTGAGGTTGATAGTGTGAT
* * *
25350395 ACGTCTCTGACTGAATCCGACCTTCGAGCTCTTAACACTACAAAACAGGGGAAAAAGAAACAGGG
66 ACATCTCTGACCGAATCCGACCTACGAGCTCTTAACACTACAAAACAGGGGAAAAAGAAACAGGG
25350460 TAAGC
131 TAAGC
25350465 ACATGCCATTGATTTCCAAAATAAAGTTTCTTTATATACCGAGATCTTGAGGTTGATAGTGTGAT
1 ACATGCCATTGATTTCCAAAATAAAGTTTCTTTATATACCGAGATCTTGAGGTTGATAGTGTGAT
*
25350530 ACATCTCTGACCGAATCCGACCTACTAGCTCTTAACACTACAAAACAGGGGAAAAAGAAACAGGG
66 ACATCTCTGACCGAATCCGACCTACGAGCTCTTAACACTACAAAACAGGGGAAAAAGAAACAGGG
25350595 TAAGC
131 TAAGC
25350600 AC
1 AC
25350602 TTTGTGCTTT
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
135 133 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (135 bp):
ACATGCCATTGATTTCCAAAATAAAGTTTCTTTATATACCGAGATCTTGAGGTTGATAGTGTGAT
ACATCTCTGACCGAATCCGACCTACGAGCTCTTAACACTACAAAACAGGGGAAAAAGAAACAGGG
TAAGC
Found at i:25354953 original size:17 final size:17
Alignment explanation
Indices: 25354906--25354953 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
25354896 CCTATTCCTA
**
25354906 AAAAATAAAAATTGTCC
1 AAAAATAAAAATAATCC
* **
25354923 AAAATTAATTATAATCC
1 AAAAATAAAAATAATCC
25354940 AAAAATAAAAATAA
1 AAAAATAAAAATAA
25354954 AAAGTTTGGG
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (17 bp):
AAAAATAAAAATAATCC
Found at i:25363047 original size:29 final size:29
Alignment explanation
Indices: 25363005--25363062 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
25362995 GAAGTAAGTA
25363005 ATAGTGTGTCTATTCCGTGGTATTTTGGT
1 ATAGTGTGTCTATTCCGTGGTATTTTGGT
*
25363034 ATAGTGTGTCTATTCTGTGGTATTTTGGT
1 ATAGTGTGTCTATTCCGTGGTATTTTGGT
25363063 GATGAAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.14, C:0.09, G:0.28, T:0.50
Consensus pattern (29 bp):
ATAGTGTGTCTATTCCGTGGTATTTTGGT
Found at i:25366615 original size:31 final size:29
Alignment explanation
Indices: 25366571--25366628 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
25366561 ATTTATCTAC
25366571 AAGATAAACATTAA-ATTAAACTTAATATT
1 AAGATAAACATTAATATTAAA-TTAATATT
*
25366600 AAGATAATCACATTAATGTTAAATTAATA
1 AAGATAA--ACATTAATATTAAATTAATA
25366629 AAATCCTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 7 0.28
31 13 0.52
32 5 0.20
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.34
Consensus pattern (29 bp):
AAGATAAACATTAATATTAAATTAATATT
Found at i:25366652 original size:12 final size:12
Alignment explanation
Indices: 25366635--25366665 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
25366625 AATAAAATCC
25366635 TATTAAAATAAA
1 TATTAAAATAAA
*
25366647 TATTAAACTAAA
1 TATTAAAATAAA
25366659 TATTAAA
1 TATTAAA
25366666 TCTATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (12 bp):
TATTAAAATAAA
Found at i:25379622 original size:21 final size:21
Alignment explanation
Indices: 25379580--25379623 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
25379570 TTGATTCTAC
*
25379580 TTAGGTACATTTAGTAGAATT
1 TTAGGTACATTTACTAGAATT
*
25379601 TTAGG-ACATTTCACTAGTATT
1 TTAGGTACATTT-ACTAGAATT
25379622 TT
1 TT
25379624 TATCATTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (21 bp):
TTAGGTACATTTACTAGAATT
Found at i:25380807 original size:36 final size:36
Alignment explanation
Indices: 25380747--25380846 Score: 148
Period size: 36 Copynumber: 2.7 Consensus size: 36
25380737 AGAAAAAGAT
25380747 TAAATTGTAGAACAAATTGT-AAATTTAGTAATAGGGAC
1 TAAATTGT-GAA-AAATT-TAAAATTTAGTAATAGGGAC
*
25380785 TAAATTGTGAAAAATTTAAAATTGAGTAATAGGGAC
1 TAAATTGTGAAAAATTTAAAATTTAGTAATAGGGAC
*
25380821 TAAATTGTGAAAATTTTAAAATTTAG
1 TAAATTGTGAAAAATTTAAAATTTAG
25380847 GGGTTTACTT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
35 1 0.02
36 46 0.79
37 3 0.05
38 8 0.14
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (36 bp):
TAAATTGTGAAAAATTTAAAATTTAGTAATAGGGAC
Found at i:25390440 original size:12 final size:12
Alignment explanation
Indices: 25390423--25390456 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
25390413 TTCAGCTTTA
*
25390423 GGTTTGGGTTTG
1 GGTTTGGGTCTG
25390435 GGTTTGGGTCTG
1 GGTTTGGGTCTG
*
25390447 GGTCTGGGTC
1 GGTTTGGGTC
25390457 AATCAATGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.09, G:0.50, T:0.41
Consensus pattern (12 bp):
GGTTTGGGTCTG
Found at i:25391796 original size:5 final size:5
Alignment explanation
Indices: 25391786--25391823 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
25391776 ACTGATATCT
* *
25391786 ATATA ATATA ATATA ATATA GTATA GTATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATA
25391824 GGCTGGGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:25394798 original size:18 final size:19
Alignment explanation
Indices: 25394772--25394810 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
25394762 CTCATATCCG
*
25394772 ATAATTCCTGAT-AAATGA
1 ATAAGTCCTGATAAAATGA
25394790 ATAAGTCCTGATAAAATGA
1 ATAAGTCCTGATAAAATGA
25394809 AT
1 AT
25394811 GAAACTCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (19 bp):
ATAAGTCCTGATAAAATGA
Found at i:25406140 original size:49 final size:49
Alignment explanation
Indices: 25406079--25406201 Score: 151
Period size: 50 Copynumber: 2.5 Consensus size: 49
25406069 CAAAGCCCTG
* *
25406079 TCCCAGACATGGTCTTACATGGGATGTT-TCTTGTAC-TACCAATGCCATA
1 TCCCAGACATGGTCTTACATGGGA-GTTCTCATCT-CGTACCAATGCCATA
* * *
25406128 TCCCAGATATGGTCTTACATGGGAGTTCTCATCTCGGTGCCAATGCCATG
1 TCCCAGACATGGTCTTACATGGGAGTTCTCATCTC-GTACCAATGCCATA
*
25406178 TCCTAGACATGGTCTTACATGGGA
1 TCCCAGACATGGTCTTACATGGGA
25406202 CCTCTTTACC
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
48 4 0.06
49 27 0.42
50 33 0.52
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (49 bp):
TCCCAGACATGGTCTTACATGGGAGTTCTCATCTCGTACCAATGCCATA
Found at i:25406191 original size:50 final size:49
Alignment explanation
Indices: 25406066--25406201 Score: 159
Period size: 49 Copynumber: 2.8 Consensus size: 49
25406056 GATAATAACA
* * * *
25406066 TGCCAAAGCCCTGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATCTAC
* * *
25406115 TACCAATGCCATATCCCAGATATGGTCTTACATGGGA-GTTCTCATCT-C
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCATCTAC
*
25406163 GGTGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA
1 --TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
25406202 CCTCTTTACC
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
48 4 0.05
49 36 0.49
50 33 0.45
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATCTAC
Found at i:25406581 original size:30 final size:30
Alignment explanation
Indices: 25406545--25406601 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
25406535 CTCGACTCTT
25406545 AACTTTTACAAAATTACGATTTTGCCCTTA
1 AACTTTTACAAAATTACGATTTTGCCCTTA
* *
25406575 AACTTTTACATAATTACGCTTTTGCCC
1 AACTTTTACAAAATTACGATTTTGCCC
25406602 CAAAGTTCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (30 bp):
AACTTTTACAAAATTACGATTTTGCCCTTA
Found at i:25407780 original size:23 final size:23
Alignment explanation
Indices: 25407754--25407801 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
25407744 AATCAGCTTC
25407754 TTTAATAC-ACCTATTAGGACACA
1 TTTAA-ACGACCTATTAGGACACA
*
25407777 TTTAAACGACTTATTAGGACACA
1 TTTAAACGACCTATTAGGACACA
25407800 TT
1 TT
25407802 AATCATACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (23 bp):
TTTAAACGACCTATTAGGACACA
Found at i:25415765 original size:25 final size:25
Alignment explanation
Indices: 25415737--25415795 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
25415727 CGATTCTCAA
* *
25415737 CTCGTATGAGC-TTATTGATTTATAG
1 CTCGTATGAGCATT-TCGATTCATAG
25415762 CTCGTGA-GAGCATTTCGATTCATAG
1 CTCGT-ATGAGCATTTCGATTCATAG
25415787 CTCGTATGA
1 CTCGTATGA
25415796 ACATACATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 1 0.03
25 25 0.86
26 3 0.10
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (25 bp):
CTCGTATGAGCATTTCGATTCATAG
Found at i:25428711 original size:17 final size:17
Alignment explanation
Indices: 25428689--25428725 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
25428679 TAGATAGAGG
25428689 TTTTGGTCGACCTAGTT
1 TTTTGGTCGACCTAGTT
25428706 TTTTGGTCGACCTAGTT
1 TTTTGGTCGACCTAGTT
25428723 TTT
1 TTT
25428726 CACCTTGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.16, G:0.22, T:0.51
Consensus pattern (17 bp):
TTTTGGTCGACCTAGTT
Found at i:25432574 original size:25 final size:25
Alignment explanation
Indices: 25432509--25432586 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 25
25432499 GTCATTAGGG
*
25432509 TTATCTATTCTCAGCTCTTATGAGC
1 TTATCAATTCTCAGCTCTTATGAGC
* *
25432534 TTACCAATT-TGTAGCTCTTGA-GAGC
1 TTATCAATTCT-CAGCTCTT-ATGAGC
* **
25432559 TTATCGATTCTCAGCTCGGATGAGC
1 TTATCAATTCTCAGCTCTTATGAGC
25432584 TTA
1 TTA
25432587 CTGATTTACA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
24 2 0.05
25 37 0.90
26 2 0.05
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (25 bp):
TTATCAATTCTCAGCTCTTATGAGC
Found at i:25437592 original size:10 final size:11
Alignment explanation
Indices: 25437543--25437601 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 11
25437533 AGATAAATAT
25437543 TATTTTATTAA
1 TATTTTATTAA
25437554 TATTTTGACTTGAA
1 TATTTT-A-TT-AA
*
25437568 -A-TTTATTTA
1 TATTTTATTAA
25437577 TATTTTATTAA
1 TATTTTATTAA
25437588 T-TTTTAGTTAA
1 TATTTTA-TTAA
25437599 TAT
1 TAT
25437602 ATAAGGAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
9 1 0.03
10 8 0.21
11 20 0.51
12 5 0.13
13 3 0.08
14 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:25437933 original size:21 final size:21
Alignment explanation
Indices: 25437904--25437957 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
25437894 AGAGGTTTAT
*
25437904 TAAGTTCAAGTGGTAAGACCC
1 TAAGGTCAAGTGGTAAGACCC
*
25437925 TAAGGTCAAATGGTAAGACCC
1 TAAGGTCAAGTGGTAAGACCC
25437946 TAAGGTCAAGTG
1 TAAGGTCAAGTG
25437958 TTTTAGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (21 bp):
TAAGGTCAAGTGGTAAGACCC
Found at i:25442394 original size:19 final size:19
Alignment explanation
Indices: 25442355--25442409 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
25442345 TATAAAAATT
* *
25442355 TACAAGAAAATATTGATAAA
1 TACAAGAATATA-TGAAAAA
25442375 TA-AAGAATATAGTGAAAAA
1 TACAAGAATATA-TGAAAAA
25442394 TACAAGAATATATGAA
1 TACAAGAATATATGAA
25442410 TATATTAGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 20 0.65
20 11 0.35
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.24
Consensus pattern (19 bp):
TACAAGAATATATGAAAAA
Found at i:25442934 original size:22 final size:22
Alignment explanation
Indices: 25442886--25443006 Score: 107
Period size: 22 Copynumber: 5.5 Consensus size: 22
25442876 AAATTTAGCA
* * *
25442886 TGCTTACTGTCTTGCGCTTTTG
1 TGCTTACTGTTTTGCACTTTGG
* * *
25442908 CGCTTACTGTTTCGCACTTTGT
1 TGCTTACTGTTTTGCACTTTGG
* *
25442930 TGCTTACCGTTTTGCACTTCGG
1 TGCTTACTGTTTTGCACTTTGG
* *
25442952 TACCTACTGTTTTGCACTTTGG
1 TGCTTACTGTTTTGCACTTTGG
* * * *
25442974 TGCTTAGTGATTTGGACTTCGG
1 TGCTTACTGTTTTGCACTTTGG
*
25442996 TGCCTACTGTT
1 TGCTTACTGTT
25443007 CTTATCTCTG
Statistics
Matches: 75, Mismatches: 24, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 75 1.00
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.45
Consensus pattern (22 bp):
TGCTTACTGTTTTGCACTTTGG
Found at i:25442960 original size:44 final size:44
Alignment explanation
Indices: 25442912--25443006 Score: 127
Period size: 44 Copynumber: 2.2 Consensus size: 44
25442902 CTTTTGCGCT
* *
25442912 TACTGTTTCGCACTTTGTTGCTTACCGTTTTGCACTTCGGTACC
1 TACTGTTTCGCACTTTGGTGCTTACCGATTTGCACTTCGGTACC
* ** * *
25442956 TACTGTTTTGCACTTTGGTGCTTAGTGATTTGGACTTCGGTGCC
1 TACTGTTTCGCACTTTGGTGCTTACCGATTTGCACTTCGGTACC
25443000 TACTGTT
1 TACTGTT
25443007 CTTATCTCTG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (44 bp):
TACTGTTTCGCACTTTGGTGCTTACCGATTTGCACTTCGGTACC
Found at i:25445863 original size:24 final size:24
Alignment explanation
Indices: 25445836--25445890 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
25445826 AAGAAATAAC
25445836 AAATATTTTATGCTAATAAATGA-T
1 AAATATTTTATGCTAATAAAT-ACT
*
25445860 AAATATATTATGCTAATAAATACT
1 AAATATTTTATGCTAATAAATACT
25445884 AAATATT
1 AAATATT
25445891 CTAGAAACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.40
Consensus pattern (24 bp):
AAATATTTTATGCTAATAAATACT
Found at i:25460660 original size:14 final size:15
Alignment explanation
Indices: 25460641--25460670 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
25460631 CCTTCTTTTC
25460641 TTCTTTCTTTC-TTT
1 TTCTTTCTTTCATTT
25460655 TTCTTTCTTTCATTT
1 TTCTTTCTTTCATTT
25460670 T
1 T
25460671 GCATGTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (15 bp):
TTCTTTCTTTCATTT
Found at i:25462401 original size:13 final size:13
Alignment explanation
Indices: 25462385--25462414 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
25462375 TATAAGAAGG
25462385 AAATAAAATAAAT
1 AAATAAAATAAAT
*
25462398 AAATAAAATGAAT
1 AAATAAAATAAAT
25462411 AAAT
1 AAAT
25462415 CACAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:25463508 original size:5 final size:6
Alignment explanation
Indices: 25463490--25463515 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
25463480 AAAGGTAACG
25463490 AATAAA AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AA
25463516 ACAAAGTCGG
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:25464325 original size:50 final size:49
Alignment explanation
Indices: 25464271--25465205 Score: 317
Period size: 50 Copynumber: 18.7 Consensus size: 49
25464261 GTGATGTCGA
* * * * *
25464271 GGAAGCACGGTTCGCCATTGTGGCTTCAATCTGTTCCACTACACTGTCTG
1 GGAAGCAAGATTCGCCGTTGTGGCTT-AATCTGTTCCACTGCACTGTCAG
* * * * * *
25464321 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCT-TTCTAACTGCAATATCAG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTC-CACTGCACTGTCAG
*
25464371 GGAAGCAAGATTCGCCGTTGTGGCGTTAATCTGTTCCACTGCACTGTTTA-
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTG-TCAG
* * * * * * ** * *
25464421 AGAAGTAAGATTTGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTCAG
* * * ** * * *
25464471 GGAAGCAAGGTTCGCCATCGTGGCTTTAATCTACTCTACTGTA-TCGCCAG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACT-GTCAG
* * * ** * *
25464521 AGG-AGTAAGATTCGCTGTTGTGGCTTCAATCTTTTTAACTGCAATGTCGG
1 -GGAAGCAAGATTCGCCGTTGTGGCTT-AATCTGTTCCACTGCACTGTCAG
* * * * * * *
25464571 GGAAGCAAGATTCACCGATGTGGCTTTAATCTATTCCACTGTACCGCCTGG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTC-AG
* * * * * * * ** * * *
25464622 GGAA-TAAGATTTGCCATTATAGCTTTAGTCTTTTTAACTGCAATGCCGG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTCAG
* * * * *
25464671 GGAAGCGAGATTCACTGATGTGGCTTTAATCTGCTCCACTGCA-TCG-CAAG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACT-GTC-AG
* * * * * ** * *
25464721 AGAAGTAAGATTCGCTGCTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTCAG
* * * * * *
25464771 GGAAGCAATATTCACCGATGTGGCCTTAATCTGCTCCACGGCA-TCGCCAG
1 GGAAGCAAGATTCGCCGTTGTGG-CTTAATCTGTTCCACTGCACT-GTCAG
* * * * * ** * *
25464821 GGCAGTAGGATTCGTCGCTGTGGCTTTAATCT-TTTTA-TGCAATGTCGG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTCAG
* * * * * * *
25464869 GGAAGCAAGATTCACCGATGTAGCTTTAATCTGATCCACTGCACCGCCTG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTCAG
* * * * * * ** * * * **
25464919 GGGAGTAAGATTCGCTGTTATAGCTTTAATCTTTTTAAATGAAATGTTGG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTCAG
* * * * *
25464969 GGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGTACCG-CTTG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTC-AG
* * * ** * * ** * * *
25465019 AGAAGTAAAATTCGTTGTTGTAGCTTTAATCTTTTTAACTGTAATGTCGG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTCAG
* * * * * *
25465069 GGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCATTGCATTGCCAG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTCAG
* * * * ** *
25465119 AGAAGTAAGACTCGCCGTTGTGGCTTCAATCTTTTTAACTGCAATGTCAG
1 GGAAGCAAGATTCGCCGTTGTGGCTT-AATCTGTTCCACTGCACTGTCAG
*
25465169 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTGTTCC
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCC
25465206 GTTGCATTAT
Statistics
Matches: 627, Mismatches: 231, Indels: 54
0.69 0.25 0.06
Matches are distributed among these distances:
48 31 0.05
49 26 0.04
50 546 0.87
51 24 0.04
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (49 bp):
GGAAGCAAGATTCGCCGTTGTGGCTTAATCTGTTCCACTGCACTGTCAG
Found at i:25465213 original size:100 final size:100
Alignment explanation
Indices: 25464244--25465201 Score: 1034
Period size: 100 Copynumber: 9.6 Consensus size: 100
25464234 TAACTCGTAA
* ** * * * * * *
25464244 CTTTAATCTGTTTAACTGTGATGTCGAGGAAGCACGGTTCGCC-ATTGTGGCTTCAATCTGTTCC
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGA-TGTGGCTTTAATCTGCTCC
* * * *
25464308 ACTACA-CTGTCTGGGAAGTAAGATTCGCTGTTGTAG
65 ACTGCATC-GCCAGAGAAGTAAGATTCGCTGTTGTAG
* * * * * * *
25464344 CTTTAATCTTTCTAACTGCAATATCAGGGAAGCAAGATTCGCCGTTGTGGCGTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
** *
25464409 CTGCA-CTGTTTA-AGAAGTAAGATTTGCTGTTGTAG
66 CTGCATC-G-CCAGAGAAGTAAGATTCGCTGTTGTAG
* * * *
25464444 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGGTTCGCC-ATCGTGGCTTTAATCTACTCT
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGAT-GTGGCTTTAATCTGCTCC
* * *
25464508 ACTGTATCGCCAGAGGAGTAAGATTCGCTGTTGTGG
65 ACTGCATCGCCAGAGAAGTAAGATTCGCTGTTGTAG
* **
25464544 CTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTATTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
* * * * * ** *
25464609 CTGTACCGCCTGGGGAA-TAAGATTTGCCATTATAG
66 CTGCATCGCC-AGAGAAGTAAGATTCGCTGTTGTAG
* * * *
25464644 CTTTAGTCTTTTTAACTGCAATGCCGGGGAAGCGAGATTCACTGATGTGGCTTTAATCTGCTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
* * *
25464709 CTGCATCGCAAGAGAAGTAAGATTCGCTGCTGTGG
66 CTGCATCGCCAGAGAAGTAAGATTCGCTGTTGTAG
* *
25464744 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAATATTCACCGATGTGGCCTTAATCTGCTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
* * * * * *
25464809 CGGCATCGCCAGGGCAGTAGGATTCG-TCGCTGTGG
66 CTGCATCGCCAGAGAAGTAAGATTCGCT-GTTGTAG
* *
25464844 CTTTAATCTTTTT-A-TGCAATGTCGGGGAAGCAAGATTCACCGATGTAGCTTTAATCTGATCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
* * * * *
25464907 CTGCACCGCCTGGGGAGTAAGATTCGCTGTTATAG
66 CTGCATCGCCAGAGAAGTAAGATTCGCTGTTGTAG
* * * *
25464942 CTTTAATCTTTTTAAATGAAATGTTGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
* * ** * *
25465007 CTGTACCGCTTGAGAAGTAAAATTCGTTGTTGTAG
66 CTGCATCGCCAGAGAAGTAAGATTCGCTGTTGTAG
*
25465042 CTTTAATCTTTTTAACTGTAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
* * * * *
25465107 TTGCATTGCCAGAGAAGTAAGACTCGCCGTTGTGG
66 CTGCATCGCCAGAGAAGTAAGATTCGCTGTTGTAG
* * * * *
25465142 CTTCAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCGCTGTTGTGGCTTTAATCTG
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTG
25465202 TTCCGTTGCA
Statistics
Matches: 727, Mismatches: 119, Indels: 24
0.84 0.14 0.03
Matches are distributed among these distances:
98 83 0.11
99 10 0.01
100 627 0.86
101 7 0.01
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (100 bp):
CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
CTGCATCGCCAGAGAAGTAAGATTCGCTGTTGTAG
Found at i:25465285 original size:46 final size:46
Alignment explanation
Indices: 25465218--25465325 Score: 180
Period size: 46 Copynumber: 2.3 Consensus size: 46
25465208 TGCATTATCT
* *
25465218 GGGAGATAAGGTCTGAAATTCTTTGGTCTATTCCACTGTAATCTCA
1 GGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCA
*
25465264 GGGAGAGAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCA
1 GGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCA
*
25465310 GGGAGATAAGACCTGA
1 GGGAGATAAGATCTGA
25465326 TGCGATCTAC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 57 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (46 bp):
GGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCA
Found at i:25466743 original size:15 final size:15
Alignment explanation
Indices: 25466723--25466757 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
25466713 TTAGCCTCTC
*
25466723 CATTTTTAC-TTTTT
1 CATTTTTTCATTTTT
25466737 CATTTTTTCATTTTT
1 CATTTTTTCATTTTT
25466752 CATTTT
1 CATTTT
25466758 CATCTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (15 bp):
CATTTTTTCATTTTT
Found at i:25472298 original size:30 final size:31
Alignment explanation
Indices: 25472264--25472324 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
25472254 AAAAGATAAA
25472264 AAAGAT-AAAAAACCTAAGGGCTTCGTTCCC
1 AAAGATAAAAAAACCTAAGGGCTTCGTTCCC
25472294 AAAGATAAAAAAACCTAAGGGCTTCGTTCCC
1 AAAGATAAAAAAACCTAAGGGCTTCGTTCCC
25472325 TTCCCAAGCG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (31 bp):
AAAGATAAAAAAACCTAAGGGCTTCGTTCCC
Found at i:25474685 original size:29 final size:29
Alignment explanation
Indices: 25474635--25474690 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
25474625 ATACTATAAT
*
25474635 AAATCTAAAATATATGATAATTTATAAACA
1 AAATCTAAAATATATGA-AAATTATAAACA
*
25474665 AAATTTAAAA-ATATGAAAATTATAAA
1 AAATCTAAAATATATGAAAATTATAAA
25474691 GGGACGACCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.38
29 6 0.25
30 9 0.38
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (29 bp):
AAATCTAAAATATATGAAAATTATAAACA
Found at i:25475203 original size:14 final size:14
Alignment explanation
Indices: 25475184--25475218 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
25475174 CAGAGTCTAG
25475184 GTTGGTGTTGCTGT
1 GTTGGTGTTGCTGT
*
25475198 GTTGGTTTTGCTGT
1 GTTGGTGTTGCTGT
25475212 GTTGGTG
1 GTTGGTG
25475219 CAACAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.06, G:0.43, T:0.51
Consensus pattern (14 bp):
GTTGGTGTTGCTGT
Found at i:25478592 original size:21 final size:21
Alignment explanation
Indices: 25478566--25478606 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
25478556 TTAAGAGATA
*
25478566 TTACTTGAATAGTTGTATCTC
1 TTACTTGAATAGTTATATCTC
*
25478587 TTACTTTAATAGTTATATCT
1 TTACTTGAATAGTTATATCT
25478607 ATGTAAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (21 bp):
TTACTTGAATAGTTATATCTC
Found at i:25481560 original size:6 final size:6
Alignment explanation
Indices: 25481548--25481622 Score: 62
Period size: 6 Copynumber: 12.7 Consensus size: 6
25481538 AAGAAGAAGA
* * * * * *
25481548 AAAAAT AACAAT AAAAAT AAAAGT AAAAAG AAAAAC AAAAAC AAAAAC
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* * *
25481596 AAAAAC AAAAAC AAAAA- CAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
25481623 CTAGGTAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
5 4 0.07
6 56 0.93
ACGTcount: A:0.81, C:0.09, G:0.03, T:0.07
Consensus pattern (6 bp):
AAAAAT
Found at i:25481587 original size:12 final size:12
Alignment explanation
Indices: 25481572--25481617 Score: 83
Period size: 12 Copynumber: 3.8 Consensus size: 12
25481562 AAATAAAAGT
*
25481572 AAAAAGAAAAAC
1 AAAAACAAAAAC
25481584 AAAAACAAAAAC
1 AAAAACAAAAAC
25481596 AAAAACAAAAAC
1 AAAAACAAAAAC
25481608 AAAAACAAAA
1 AAAAACAAAA
25481618 TAAAACTAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.85, C:0.13, G:0.02, T:0.00
Consensus pattern (12 bp):
AAAAACAAAAAC
Found at i:25481593 original size:18 final size:18
Alignment explanation
Indices: 25481572--25481617 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
25481562 AAATAAAAGT
*
25481572 AAAAAGAAAAACAAAAAC
1 AAAAACAAAAACAAAAAC
25481590 AAAAACAAAAACAAAAAC
1 AAAAACAAAAACAAAAAC
25481608 AAAAACAAAA
1 AAAAACAAAA
25481618 TAAAACTAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.85, C:0.13, G:0.02, T:0.00
Consensus pattern (18 bp):
AAAAACAAAAACAAAAAC
Found at i:25494274 original size:9 final size:9
Alignment explanation
Indices: 25494262--25494289 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
25494252 GATTAATTCG
25494262 ATTATAGTT
1 ATTATAGTT
25494271 ATTATAGTT
1 ATTATAGTT
25494280 ATTATAGTT
1 ATTATAGTT
25494289 A
1 A
25494290 GTTAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.54
Consensus pattern (9 bp):
ATTATAGTT
Found at i:25494314 original size:35 final size:35
Alignment explanation
Indices: 25494274--25494345 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
25494264 TATAGTTATT
*
25494274 ATAGTTATTATAGTTAGTTAATTAAAGTTCCATAA
1 ATAGTTATTATAGTTAGTTAATTAAAGTACCATAA
25494309 ATAGTTATTATAGTTAGTTAATTAAAGTACCATAA
1 ATAGTTATTATAGTTAGTTAATTAAAGTACCATAA
25494344 AT
1 AT
25494346 TAATTCAGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.42
Consensus pattern (35 bp):
ATAGTTATTATAGTTAGTTAATTAAAGTACCATAA
Found at i:25494718 original size:13 final size:13
Alignment explanation
Indices: 25494700--25494725 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25494690 TAAGTTGGAA
25494700 AAATACAAAAGTG
1 AAATACAAAAGTG
25494713 AAATACAAAAGTG
1 AAATACAAAAGTG
25494726 GGAGTTTGAT
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:0.62, C:0.08, G:0.15, T:0.15
Consensus pattern (13 bp):
AAATACAAAAGTG
Found at i:25495286 original size:21 final size:21
Alignment explanation
Indices: 25495260--25495361 Score: 195
Period size: 21 Copynumber: 4.9 Consensus size: 21
25495250 AAAAAACAAG
25495260 ATCGTCAAGGAGTCCATCGTC
1 ATCGTCAAGGAGTCCATCGTC
25495281 ATCGTCAAGGAGTCCATCGTC
1 ATCGTCAAGGAGTCCATCGTC
25495302 ATCGTCAAGGAGTCCATCGTC
1 ATCGTCAAGGAGTCCATCGTC
25495323 ATCGTCAAGGAGTCCATCGTC
1 ATCGTCAAGGAGTCCATCGTC
*
25495344 ATCGTCAAGGAGTTCATC
1 ATCGTCAAGGAGTCCATC
25495362 TTCCTATGAG
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
21 80 1.00
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (21 bp):
ATCGTCAAGGAGTCCATCGTC
Found at i:25499591 original size:13 final size:13
Alignment explanation
Indices: 25499573--25499610 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
25499563 AGTTCTTTAT
25499573 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
25499586 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
25499599 TGCTTTTGAGAA
1 TGCTTTTGAGAA
25499611 ATTTGAGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.29, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:25499821 original size:24 final size:23
Alignment explanation
Indices: 25499788--25499847 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
25499778 TATTTTAATA
25499788 TATAAT-ATTAATTTTAAATATT
1 TATAATAATTAATTTTAAATATT
* * *
25499810 TCTAAGTAATTAATATTAATTATT
1 TATAA-TAATTAATTTTAAATATT
*
25499834 TATAATATTTAATT
1 TATAATAATTAATT
25499848 AGAATATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 4 0.13
23 8 0.27
24 18 0.60
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TATAATAATTAATTTTAAATATT
Found at i:25500241 original size:12 final size:12
Alignment explanation
Indices: 25500224--25500249 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
25500214 ATTGTTTGAT
25500224 TCACCATCATCA
1 TCACCATCATCA
25500236 TCACCATCATCA
1 TCACCATCATCA
25500248 TC
1 TC
25500250 GTCGTCGTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.42, G:0.00, T:0.27
Consensus pattern (12 bp):
TCACCATCATCA
Found at i:25501839 original size:72 final size:72
Alignment explanation
Indices: 25501677--25501813 Score: 238
Period size: 72 Copynumber: 1.9 Consensus size: 72
25501667 CTAATTTAGT
*
25501677 ATAAATAAGTAGAACATAAATTCAATATCCAAAGACCAAACATAAACAACTATTAATAAAACTAG
1 ATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTAATAAAACTAG
25501742 ATTACAC
66 ATTACAC
* * *
25501749 ATAAATAAGTAGAACATAAATTCAATGTCCAAAAACCAAACATAAATAACTATTGATAAAACTAG
1 ATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTAATAAAACTAG
25501814 TTTAGCATTG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.55, C:0.15, G:0.07, T:0.23
Consensus pattern (72 bp):
ATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTAATAAAACTAG
ATTACAC
Found at i:25503739 original size:44 final size:45
Alignment explanation
Indices: 25503689--25503779 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
25503679 CAAGAAAACA
25503689 TTTCTGCTAAATT-AAAAAAAAACAATAAGAAGGTAATATTTTTT
1 TTTCTGCTAAATTAAAAAAAAAACAATAAGAAGGTAATATTTTTT
25503733 TTTCTGCTAAATTAAAAAAAAAACAATAAGAAGGTAATATTTTTT
1 TTTCTGCTAAATTAAAAAAAAAACAATAAGAAGGTAATATTTTTT
25503778 TT
1 TT
25503780 CTTTTTTTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 13 0.28
45 33 0.72
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (45 bp):
TTTCTGCTAAATTAAAAAAAAAACAATAAGAAGGTAATATTTTTT
Found at i:25508161 original size:16 final size:17
Alignment explanation
Indices: 25508140--25508186 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
25508130 AGTTTAATTC
25508140 ATTTCTTTATTTTT-TT
1 ATTTCTTTATTTTTGTT
25508156 ATTTCTTTATTTTTGTT
1 ATTTCTTTATTTTTGTT
* *
25508173 ATTTATTAATTTTT
1 ATTTCTTTATTTTT
25508187 ATTCCTCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (17 bp):
ATTTCTTTATTTTTGTT
Found at i:25512565 original size:138 final size:137
Alignment explanation
Indices: 25512310--25512566 Score: 302
Period size: 138 Copynumber: 1.9 Consensus size: 137
25512300 GGTCTGCTCA
* *
25512310 CACAAGCTGACGGTCAAAATGTAGCTACACGATGTCGCTCACACAAGCTGACAAGTATCCGCAAC
1 CACAAGCTGACAGTCAAAATGTAGCTACACAATGTCGCTCACACAAGCTGACAAGTATCCGCAAC
** * * * **
25512375 AAATGTTGGAACTCAGCCATCGGTAGGACATTCAAGACCAGCACCCTCAACATGGTAACCTGGGT
66 AAATGCCGGAACTAAGCCATCGGTAGAACATTCAAGACCAGAACCCAAAACATGGTAACCTGGGT
25512440 CTACTAT
131 CTACTAT
** * * **
25512447 CACAAGCTGACAGTCGGAATGTAAGCTACACAATG-CTGCTTACACAAGTTGATGAGTATCCGCA
1 CACAAGCTGACAGTCAAAATGT-AGCTACACAATGTC-GCTCACACAAGCTGACAAGTATCCGCA
* * * *
25512511 ACAAATGCC-GAGCCTAAGGCATCGGTAGAACATTCAGGACCGGAACCCAAAACATG
64 ACAAATGCCGGA-ACTAAGCCATCGGTAGAACATTCAAGACCAGAACCCAAAACATG
25512567 AAAACCCTAA
Statistics
Matches: 98, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
137 22 0.22
138 76 0.78
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.19
Consensus pattern (137 bp):
CACAAGCTGACAGTCAAAATGTAGCTACACAATGTCGCTCACACAAGCTGACAAGTATCCGCAAC
AAATGCCGGAACTAAGCCATCGGTAGAACATTCAAGACCAGAACCCAAAACATGGTAACCTGGGT
CTACTAT
Found at i:25518869 original size:5 final size:5
Alignment explanation
Indices: 25518859--25518894 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
25518849 TTTAACTAAC
25518859 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA
25518895 GTACCAATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:25520339 original size:11 final size:11
Alignment explanation
Indices: 25520325--25520362 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
25520315 AAAATAAATC
25520325 AAAATTATTAT
1 AAAATTATTAT
25520336 AAAATTATTAT
1 AAAATTATTAT
*
25520347 AAAATTAAT-T
1 AAAATTATTAT
25520357 AAAATT
1 AAAATT
25520363 CTATGTGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 7 0.27
11 19 0.73
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AAAATTATTAT
Found at i:25527772 original size:50 final size:50
Alignment explanation
Indices: 25527661--25527907 Score: 192
Period size: 50 Copynumber: 4.8 Consensus size: 50
25527651 ATTTGGGTAA
* * *
25527661 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCA-C--CGAG---ATG
** * *
25527717 AGAGGTTTCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAGATG
* *** ** * *
25527767 GGAGGTCCCCCATAAGACCATATCACGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAGATG
** * * *
25527817 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTGCAGG
1 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAG-ATG
* ** * *
25527866 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCA
25527908 TGTTATTATC
Statistics
Matches: 154, Mismatches: 36, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
48 1 0.01
49 38 0.25
50 73 0.47
53 3 0.02
55 1 0.01
56 38 0.25
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAGATG
Found at i:25532304 original size:18 final size:18
Alignment explanation
Indices: 25532281--25532317 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
25532271 TTGAGTGTTT
25532281 TTTGACAACTCAATCCTA
1 TTTGACAACTCAATCCTA
25532299 TTTGACAACTCAATCCTA
1 TTTGACAACTCAATCCTA
25532317 T
1 T
25532318 CTTCTTATTT
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:0.32, C:0.27, G:0.05, T:0.35
Consensus pattern (18 bp):
TTTGACAACTCAATCCTA
Found at i:25534927 original size:52 final size:52
Alignment explanation
Indices: 25534844--25534944 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
25534834 GTGTTTTAGC
*
25534844 ACACTTAAACTCAGGTCTTTTTACATCGACAACAATGCCCATGTCAATCAAT
1 ACACTTAAACTCAGGTCTTTTTACATCGACAACAATACCCATGTCAATCAAT
* * * *
25534896 ACACTTGAACTTAGGTTTTTTTACATTGACAACAATACCCATGTCAATC
1 ACACTTAAACTCAGGTCTTTTTACATCGACAACAATACCCATGTCAATC
25534945 GAGCTAAAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.32
Consensus pattern (52 bp):
ACACTTAAACTCAGGTCTTTTTACATCGACAACAATACCCATGTCAATCAAT
Found at i:25535691 original size:18 final size:18
Alignment explanation
Indices: 25535650--25535692 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
25535640 TCATTGCAAT
25535650 ATATATAAAAATAATTTA
1 ATATATAAAAATAATTTA
* *
25535668 AAATATAAAAAT-TTATTA
1 ATATATAAAAATAAT-TTA
25535686 ATATATA
1 ATATATA
25535693 TTAATATATG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATATAAAAATAATTTA
Found at i:25535823 original size:20 final size:20
Alignment explanation
Indices: 25535798--25535837 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
25535788 AATATTTTCC
*
25535798 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
25535818 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
25535838 TTATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:25535852 original size:34 final size:35
Alignment explanation
Indices: 25535786--25535852 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
25535776 CAAACACAAG
*
25535786 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
25535821 AAAACATTTTCCAG-AAATTATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
25535853 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:25539496 original size:16 final size:16
Alignment explanation
Indices: 25539477--25539509 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
25539467 CTTGCAATTC
25539477 GACAGGCTCACACTTT
1 GACAGGCTCACACTTT
*
25539493 GACAGGCTCGCACTTT
1 GACAGGCTCACACTTT
25539509 G
1 G
25539510 CTTACTATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.24
Consensus pattern (16 bp):
GACAGGCTCACACTTT
Found at i:25539696 original size:25 final size:25
Alignment explanation
Indices: 25539668--25539754 Score: 86
Period size: 25 Copynumber: 3.4 Consensus size: 25
25539658 CTGAGCTCAT
* *
25539668 AGCTCGCACTTCTCGCTAAGCTTGC
1 AGCTTGCACATCTCGCTAAGCTTGC
*
25539693 AGCTTTG-ACATCTTGCTAAGCTTGC
1 AGC-TTGCACATCTCGCTAAGCTTGC
* * *
25539718 AGCTTGCACATTTTTGCTGAGCTTGC
1 AGCTTGCACA-TCTCGCTAAGCTTGC
*
25539744 TGCTTGCACAT
1 AGCTTGCACAT
25539755 TGGAAAGCTC
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
24 3 0.06
25 26 0.49
26 24 0.45
ACGTcount: A:0.17, C:0.28, G:0.21, T:0.34
Consensus pattern (25 bp):
AGCTTGCACATCTCGCTAAGCTTGC
Found at i:25539741 original size:26 final size:26
Alignment explanation
Indices: 25539668--25539755 Score: 101
Period size: 26 Copynumber: 3.5 Consensus size: 26
25539658 CTGAGCTCAT
* *
25539668 AGCTCGCAC-TTCTCGCTAAGCTTGC
1 AGCTTGCACATTCTTGCTAAGCTTGC
25539693 AGCTTTG-ACA-TCTTGCTAAGCTTGC
1 AGC-TTGCACATTCTTGCTAAGCTTGC
* *
25539718 AGCTTGCACATTTTTGCTGAGCTTGC
1 AGCTTGCACATTCTTGCTAAGCTTGC
*
25539744 TGCTTGCACATT
1 AGCTTGCACATT
25539756 GGAAAGCTCA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
24 3 0.06
25 25 0.46
26 26 0.48
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.35
Consensus pattern (26 bp):
AGCTTGCACATTCTTGCTAAGCTTGC
Found at i:25539908 original size:65 final size:65
Alignment explanation
Indices: 25539838--25539959 Score: 217
Period size: 65 Copynumber: 1.9 Consensus size: 65
25539828 GAGCTGATGC
*
25539838 TGTCTTTTCTACAAGTAGTCCTTAATGACATGCTTGTGTTTTGACAGCTTCTTTCTTGCTGTTGT
1 TGTCTTTTCTACAAGCAGTCCTTAATGACATGCTTGTGTTTTGACAGCTTCTTTCTTGCTGTTGT
**
25539903 TGTCTTTTCTACAAGCAGTCCTTAATGACATGCTTGTGTTTTGACATTTTCTTTCTT
1 TGTCTTTTCTACAAGCAGTCCTTAATGACATGCTTGTGTTTTGACAGCTTCTTTCTT
25539960 TTTAACAAGC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (65 bp):
TGTCTTTTCTACAAGCAGTCCTTAATGACATGCTTGTGTTTTGACAGCTTCTTTCTTGCTGTTGT
Found at i:25540679 original size:4 final size:4
Alignment explanation
Indices: 25540672--25540708 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
25540662 CCTACATATA
25540672 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
25540709 GCGTGTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:25542796 original size:34 final size:34
Alignment explanation
Indices: 25542749--25542823 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
25542739 TCGTTTTTAA
* * *
25542749 TAGGGTTAGGGTTTTGTTTATTGAAATTAGGATT
1 TAGGGTTAAGGTTTTATTTATTGAAAGTAGGATT
* *
25542783 TAGGGTTAAGGTTTTATTTATTTAAAGTAGGGTT
1 TAGGGTTAAGGTTTTATTTATTGAAAGTAGGATT
25542817 TAGGGTT
1 TAGGGTT
25542824 TTTTTAGATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (34 bp):
TAGGGTTAAGGTTTTATTTATTGAAAGTAGGATT
Found at i:25546013 original size:25 final size:25
Alignment explanation
Indices: 25545917--25546042 Score: 64
Period size: 25 Copynumber: 5.1 Consensus size: 25
25545907 CATTAGGGAT
25545917 TACCGATT-ACAGCTCGT-ATGAGCA
1 TACCGATTCACAGCTCGTGA-GAGCA
* * * ***
25545941 TACTGATT-GCAGCTCGTGAAATTT
1 TACCGATTCACAGCTCGTGAGAGCA
* * * * *
25545965 TACAGATTCTCAACTCAT-ATGAGCT
1 TACCGATTCACAGCTCGTGA-GAGCA
*
25545990 TACCGATTTACAGCTCGTGAGAGCA
1 TACCGATTCACAGCTCGTGAGAGCA
* *
25546015 TATCGATTCATAGCTCGT-ATGAGCA
1 TACCGATTCACAGCTCGTGA-GAGCA
25546040 TAC
1 TAC
25546043 ATGTACAGGC
Statistics
Matches: 74, Mismatches: 23, Indels: 9
0.70 0.22 0.08
Matches are distributed among these distances:
24 25 0.34
25 48 0.65
26 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (25 bp):
TACCGATTCACAGCTCGTGAGAGCA
Found at i:25549364 original size:12 final size:12
Alignment explanation
Indices: 25549347--25549371 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25549337 TATTTTTTGA
25549347 TATAACTGAGTT
1 TATAACTGAGTT
25549359 TATAACTGAGTT
1 TATAACTGAGTT
25549371 T
1 T
25549372 TTTTTAAGCT
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TATAACTGAGTT
Found at i:25551052 original size:76 final size:78
Alignment explanation
Indices: 25550898--25551073 Score: 221
Period size: 76 Copynumber: 2.3 Consensus size: 78
25550888 ATATTATATA
* * * * *
25550898 AATTGAATTAAAGTTATGAATTTTATATATTTATATGTGAGGTTCGAATATATATGTATATACAT
1 AATTGAATTAAAGGTATGAATTTTACATATGTATATGTGAGATTCGAATATAGATGTATATACAT
* * *
25550963 GTATAAGTTCTTG
66 ATACAAGTACTTG
* * *
25550976 AATTAAATTAAAGGTATGAATTTTACATATGTATGTGTGTGATTC-AA-ATAGATGTATATACAT
1 AATTGAATTAAAGGTATGAATTTTACATATGTATATGTGAGATTCGAATATAGATGTATATACAT
25551039 ATACAAGTACTTG
66 ATACAAGTACTTG
* *
25551052 AGTTGAATTAAAAGTATGAATT
1 AATTGAATTAAAGGTATGAATT
25551074 GTAAATACTT
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
76 44 0.52
77 2 0.02
78 38 0.45
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.41
Consensus pattern (78 bp):
AATTGAATTAAAGGTATGAATTTTACATATGTATATGTGAGATTCGAATATAGATGTATATACAT
ATACAAGTACTTG
Found at i:25552330 original size:24 final size:24
Alignment explanation
Indices: 25552276--25552331 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
25552266 TTATAAAGTA
*
25552276 TATAAAAAAAATATATTTGCATTT
1 TATAAAAAAAATATATTTGCATTG
*
25552300 TAAAAAAAAAAT-TATGTT-CATATG
1 TATAAAAAAAATATAT-TTGCAT-TG
25552324 TATAAAAA
1 TATAAAAA
25552332 TTAGTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (24 bp):
TATAAAAAAAATATATTTGCATTG
Found at i:25552405 original size:23 final size:24
Alignment explanation
Indices: 25552373--25552431 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
25552363 TATGTATACT
*
25552373 AAAATAAAT-ATATACATATAGATA
1 AAAATAAATAAT-TACATATAAATA
25552397 AAAAT-AATAATTACATATAAAT-
1 AAAATAAATAATTACATATAAATA
25552419 -AAATAAATAATTA
1 AAAATAAATAATTA
25552432 TATTATACTG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 4 0.12
22 8 0.25
23 13 0.41
24 7 0.22
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (24 bp):
AAAATAAATAATTACATATAAATA
Found at i:25552948 original size:21 final size:21
Alignment explanation
Indices: 25552918--25552966 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
25552908 TTTATTCCTC
25552918 CTCC-TTTTTTTATTGATTCT
1 CTCCTTTTTTTTATTGATTCT
25552938 CTCCTTTTTTTTATTGATTCT
1 CTCCTTTTTTTTATTGATTCT
25552959 CTCCTTTT
1 CTCCTTTT
25552967 CTACAATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.08, C:0.22, G:0.04, T:0.65
Consensus pattern (21 bp):
CTCCTTTTTTTTATTGATTCT
Found at i:25553123 original size:21 final size:21
Alignment explanation
Indices: 25553097--25553172 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
25553087 AATCATATCT
*
25553097 TCTAAGATTGTATATATCATA
1 TCTAAGATTGCATATATCATA
25553118 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
*
25553139 CCTAAGATTGCATATA--ATA
1 TCTAAGATTGCATATATCATA
*
25553158 TCTAAGATTGTATAT
1 TCTAAGATTGCATAT
25553173 CCTCGAAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.31
21 35 0.69
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:25553132 original size:19 final size:19
Alignment explanation
Indices: 25553110--25553173 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
25553100 AAGATTGTAT
25553110 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
*
25553129 ATATATCATACCTAAGATTGC
1 --ATATCATATCTAAGATTGC
* *
25553150 ATATAATATCTAAGATTGT
1 ATATCATATCTAAGATTGC
25553169 ATATC
1 ATATC
25553174 CTCGAAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 20 0.53
21 18 0.47
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:25553529 original size:66 final size:66
Alignment explanation
Indices: 25553444--25553675 Score: 308
Period size: 66 Copynumber: 3.5 Consensus size: 66
25553434 ATTTATATCT
* * * * * *
25553444 TATTTGATAAGTATTTATATGCATTCAGTTATATACCTTTGAAGTGTATATGCTTTCAATTATAA
1 TATTTGATAGGTATATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAA
25553509 G
66 G
25553510 TATTTGATAGGTATATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAA
1 TATTTGATAGGTATATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAA
25553575 G
66 G
* * *
25553576 TATTTGATAGG--TATATATGCATTCGGTTGTATACATTTGATGTGTATATGCATTCGGTTATAA
1 TATTTGATAGGTATATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAA
25553639 G
66 G
* * * * *
25553640 TAGTTGAT-GAGTAGATACATACATTTGGTTATATAC
1 TATTTGATAG-GTATATATATGCATTCGGTTATATAC
25553676 ATTCGATGGG
Statistics
Matches: 148, Mismatches: 15, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
63 1 0.01
64 58 0.39
66 89 0.60
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.44
Consensus pattern (66 bp):
TATTTGATAGGTATATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAA
G
Found at i:25553647 original size:31 final size:30
Alignment explanation
Indices: 25553459--25553648 Score: 141
Period size: 31 Copynumber: 5.9 Consensus size: 30
25553449 GATAAGTATT
* *
25553459 TATATGCATTCAGTTAT-ATACCTTTGAAGTG
1 TATATGCATTCGGTTATAATA--TTTGATGTG
* ** *
25553490 TATATGCTTTCAATTATAAGTATTTGATAGGTATA
1 TATATGCATTCGGTTATAA-TATTTGAT--G--TG
25553525 TATATGCATTCGGTTAT-ATACCTTTGATGTG
1 TATATGCATTCGGTTATAATA--TTTGATGTG
* *
25553556 TATATGCATTCGATTATAAGTATTTGATAGGTA
1 TATATGCATTCGGTTATAA-TATTTGAT--GTG
* *
25553589 TATATGCATTCGGTTGTATACATTTGATGTG
1 TATATGCATTCGGTTATA-ATATTTGATGTG
*
25553620 TATATGCATTCGGTTATAAGTAGTTGATG
1 TATATGCATTCGGTTATAA-TATTTGATG
25553649 AGTAGATACA
Statistics
Matches: 128, Mismatches: 17, Indels: 28
0.74 0.10 0.16
Matches are distributed among these distances:
30 1 0.01
31 69 0.54
32 2 0.02
33 33 0.26
34 2 0.02
35 21 0.16
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (30 bp):
TATATGCATTCGGTTATAATATTTGATGTG
Found at i:25559078 original size:18 final size:19
Alignment explanation
Indices: 25559041--25559079 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
25559031 ATTACAAAAT
*
25559041 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTATAA
*
25559060 AATTCAGAAT-ATTTATAA
1 AATTCAAAATAATTTATAA
25559078 AA
1 AA
25559080 AATTAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (19 bp):
AATTCAAAATAATTTATAA
Found at i:25561956 original size:4 final size:4
Alignment explanation
Indices: 25561947--25561987 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
25561937 ACCAAATCTT
25561947 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
25561988 CACCAAGCAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:25563216 original size:11 final size:11
Alignment explanation
Indices: 25563193--25563228 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
25563183 AACTAATCCT
25563193 CTCTCATATTTC
1 CTCTCA-ATTTC
25563205 CTCTCAATTTC
1 CTCTCAATTTC
25563216 CTCTCAATTTC
1 CTCTCAATTTC
25563227 CT
1 CT
25563229 TCCAAAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 18 0.75
12 6 0.25
ACGTcount: A:0.17, C:0.36, G:0.00, T:0.47
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:25564431 original size:7 final size:7
Alignment explanation
Indices: 25564419--25564444 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
25564409 TAGTCGATTG
25564419 GTATTTA
1 GTATTTA
25564426 GTATTTA
1 GTATTTA
25564433 GTATTTA
1 GTATTTA
25564440 GTATT
1 GTATT
25564445 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Done.