Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold336
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: 503701
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.32
Warning! 20849 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:293368 original size:159 final size:158
Alignment explanation
Indices: 293003--293366 Score: 493
Period size: 159 Copynumber: 2.3 Consensus size: 158
292993 TTTGTTCGGT
* * * * *
293003 TTTTATTACTTTTAAAAAATATATTATTTTCGT-GTCTATTTATTTTATTTTATTTTAGTACATA
1 TTTTATTACTTTCAAAAAATATAATATTTTC-TATTTTATTTATTTTATATTATTTTAGTACATA
293067 ATGTTTGAAATGTATTATTTTAGTGTGTTTTTATATAAATTTAGTAAAAAAAACCCTTATTTTGG
65 ATGTTTGAAATGTATTATTTTAGTGTGTTTTTATATAAATTTAGT-AAAAAAACCCTTATTTTGG
** *
293132 CCTTTTATTCGTATTTTTCTTATTTTCGGA
129 CAATTTATTCGTATTTTTCTTATTTTCAGA
293162 TTTTATTACTTTCAAAAAATATAATATTTTCGTATTTTA-TTATTTTATATTATTTTAGTACATA
1 TTTTATTACTTTCAAAAAATATAATATTTTC-TATTTTATTTATTTTATATTATTTTAGTACATA
* *
293226 ATGTTTGAAATGTATTATTTTTGTGTGTTTTTTATATAAATTTAGT-GAAAAACCCTTATTTTGG
65 ATGTTTGAAATGTATTATTTTAGTGTG-TTTTTATATAAATTTAGTAAAAAAACCCTTATTTTGG
* *
293290 CAATTTGTTCGTATTTTTCTCTTTTTTTCAGA
129 CAATTTATTCGTA-TTTT-TCTTATTTTCAGA
** * *
293322 TTTTATTACTTTCAGTAAATTTACTATTTT-TATTTTTATTTATTT
1 TTTTATTACTTTCAAAAAATATAATATTTTCTA-TTTTATTTATTT
293367 ATTTTCGTAT
Statistics
Matches: 183, Mismatches: 16, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
158 29 0.16
159 90 0.49
160 64 0.35
ACGTcount: A:0.28, C:0.07, G:0.09, T:0.56
Consensus pattern (158 bp):
TTTTATTACTTTCAAAAAATATAATATTTTCTATTTTATTTATTTTATATTATTTTAGTACATAA
TGTTTGAAATGTATTATTTTAGTGTGTTTTTATATAAATTTAGTAAAAAAACCCTTATTTTGGCA
ATTTATTCGTATTTTTCTTATTTTCAGA
Found at i:293516 original size:27 final size:27
Alignment explanation
Indices: 293469--293537 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
293459 AACAAAGTGG
* *
293469 GGTGCCGCCTATGGCCGTGGCACCTTT
1 GGTGCCGCCTATGGCCCTGGCACCATT
*
293496 GGTGCCGCCTCT-GCCACTGGCACCATT
1 GGTGCCGCCTATGGCC-CTGGCACCATT
293523 GGTGCCGCCTATGGC
1 GGTGCCGCCTATGGC
293538 AGTCCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 3 0.08
27 31 0.86
28 2 0.06
ACGTcount: A:0.09, C:0.36, G:0.32, T:0.23
Consensus pattern (27 bp):
GGTGCCGCCTATGGCCCTGGCACCATT
Found at i:303821 original size:42 final size:42
Alignment explanation
Indices: 303773--304019 Score: 251
Period size: 42 Copynumber: 5.9 Consensus size: 42
303763 GCGTTTTTGT
*
303773 AAAAAAACGCTGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
* * **
303815 AAAAAAATGCTGCTAAAGAACATGTTCTTTAATGGCGCTTAG
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
* *
303857 TAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
* * * **
303899 AGAAAAACGCCGCTAAATAACATGTTCTTTAGCGGCGTTTTT
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
**** * * * * **
303941 TCTTAAGCGCAGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
* ** * *
303983 TACTAAGCGCCGCTAAAGAATATGTTCTTTAGCGGCG
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG
304020 TTTTTGTTTA
Statistics
Matches: 176, Mismatches: 29, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 176 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
Found at i:304452 original size:16 final size:17
Alignment explanation
Indices: 304420--304452 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
304410 ACTATAATTA
304420 TAATAAATATATAAAAT
1 TAATAAATATATAAAAT
*
304437 TAATAATTAT-TAAAAT
1 TAATAAATATATAAAAT
304453 CTATAAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATAAATATATAAAAT
Found at i:307705 original size:88 final size:87
Alignment explanation
Indices: 307568--307807 Score: 264
Period size: 88 Copynumber: 2.7 Consensus size: 87
307558 GCTCCGCAAC
* * * * * * * *
307568 GACCCAAAGTGAAACACGTATCTACCAGGCCTAAGCCCGCACGAGATGTCAGTACTAGGAATAGA
1 GACCCAGAGTGAGACACGTGTCCAGCAGGCCTAAGCCCGCACGAAATGTCAGTACTAGGAACAAA
* * * *
307633 AAGGACCACGTGCTCCGCAGGT
66 AAGAACCACGTCCACCACAGGT
* * *
307655 GACCCAGAGTGAGACATGTGTCCAGCCGGCCTGAAGCCCGCACGAAATGTCAGCACTAGGAACAA
1 GACCCAGAGTGAGACACGTGTCCAGCAGGCCT-AAGCCCGCACGAAATGTCAGTACTAGGAACAA
*
307720 AAAGAACCGCGTCCACCACAGGT
65 AAAGAACCACGTCCACCACAGGT
* * ** * *
307743 GATCCAGAGTGAGACACGTGTCCAGCAAGCCTAAAGCCTACACGAATTGTCAGTACTAAGAACAA
1 GACCCAGAGTGAGACACGTGTCCAGCAGGCCT-AAGCCCGCACGAAATGTCAGTACTAGGAACAA
307808 CGAAGTCAAG
Statistics
Matches: 126, Mismatches: 26, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
87 25 0.20
88 101 0.80
ACGTcount: A:0.33, C:0.28, G:0.25, T:0.14
Consensus pattern (87 bp):
GACCCAGAGTGAGACACGTGTCCAGCAGGCCTAAGCCCGCACGAAATGTCAGTACTAGGAACAAA
AAGAACCACGTCCACCACAGGT
Found at i:310603 original size:23 final size:23
Alignment explanation
Indices: 310568--310618 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
310558 ACCTATTTTT
* *
310568 TTACTGTAATAATTTTCGGGGTA
1 TTACAGTAATAATTTTCGGGATA
*
310591 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAATAATTTTCGGGATA
310614 TTACA
1 TTACA
310619 CCCCATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (23 bp):
TTACAGTAATAATTTTCGGGATA
Found at i:310995 original size:19 final size:19
Alignment explanation
Indices: 310958--310995 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
310948 AAAAATTACA
*
310958 TTTTTTACATTTAATATAT
1 TTTTTTACATTTAAAATAT
310977 TTTTTTA-ATTTCAAAATAT
1 TTTTTTACATTT-AAAATAT
310996 ATAGTGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTTACATTTAAAATAT
Found at i:312203 original size:56 final size:55
Alignment explanation
Indices: 312126--312230 Score: 138
Period size: 56 Copynumber: 1.9 Consensus size: 55
312116 TATTATTGAA
* * * * *
312126 TATGTTATATTACCTTGTTTGGTTCATTTACTTAGAATGTAAGGTATTGTCCAAG
1 TATGTTACATTACCTTATTTGGTTCATTTACTTAAAATATAAAGTATTGTCCAAG
* *
312181 TATGTTTACATTACTTTATTTGGTTCATTTAGTTAAAATATAAAGTATTG
1 TATG-TTACATTACCTTATTTGGTTCATTTACTTAAAATATAAAGTATTG
312231 CTATTTGACA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
55 4 0.10
56 38 0.90
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.48
Consensus pattern (55 bp):
TATGTTACATTACCTTATTTGGTTCATTTACTTAAAATATAAAGTATTGTCCAAG
Found at i:328748 original size:3 final size:3
Alignment explanation
Indices: 328735--328778 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
328725 GGAACTCTTG
*
328735 AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
328779 CCTTATAGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:329298 original size:51 final size:51
Alignment explanation
Indices: 329222--329324 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
329212 ATTTGAATAA
329222 TTTGTAAGAATTTCCAGATGAATTAGATCTATCAACCTGGTCGTCTAACTT
1 TTTGTAAGAATTTCCAGATGAATTAGATCTATCAACCTGGTCGTCTAACTT
329273 TTTGTAAGAATTTCCAGATGAATTAGATCTATCAACCTGGTCGTCTAACTT
1 TTTGTAAGAATTTCCAGATGAATTAGATCTATCAACCTGGTCGTCTAACTT
329324 T
1 T
329325 CACGCAAGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (51 bp):
TTTGTAAGAATTTCCAGATGAATTAGATCTATCAACCTGGTCGTCTAACTT
Found at i:333312 original size:3 final size:3
Alignment explanation
Indices: 333304--333330 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
333294 ATTCGCCCAA
333304 CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC
333331 ATCTTCATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CTC
Found at i:338412 original size:26 final size:24
Alignment explanation
Indices: 338377--338425 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
338367 ATTTTATTGG
338377 ATTTTAAATTTATGTTTATATTTTAT
1 ATTTTAAATTTA-GTTTAT-TTTTAT
*
338403 ATTTTCAATTTAGTTTATTTTTA
1 ATTTTAAATTTAGTTTATTTTTA
338426 GTAAGAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
25 6 0.27
26 11 0.50
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (24 bp):
ATTTTAAATTTAGTTTATTTTTAT
Found at i:356089 original size:2 final size:2
Alignment explanation
Indices: 356082--356112 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
356072 TGGTATGAAT
356082 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
356113 AATAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:358072 original size:10 final size:10
Alignment explanation
Indices: 358059--358083 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
358049 GCTCAACTAA
358059 GCAACCTTCT
1 GCAACCTTCT
358069 GCAACCTTCT
1 GCAACCTTCT
358079 GCAAC
1 GCAAC
358084 ATCCTCCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.40, G:0.12, T:0.24
Consensus pattern (10 bp):
GCAACCTTCT
Found at i:365126 original size:19 final size:19
Alignment explanation
Indices: 365102--365155 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
365092 AATCATATCT
365102 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
365121 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
365140 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
365156 CTTGAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:366446 original size:5 final size:5
Alignment explanation
Indices: 366441--366474 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
366431 TAAATAAAAT
*
366441 TTAAT TTAAC TTAAC TTAAC TTAAC TTAAC TTAA
1 TTAAC TTAAC TTAAC TTAAC TTAAC TTAAC TTAA
366475 AATTTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (5 bp):
TTAAC
Found at i:366544 original size:17 final size:17
Alignment explanation
Indices: 366522--366571 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
366512 TAAAATAAAA
366522 TTTTAAATAGTTTTAAC
1 TTTTAAATAGTTTTAAC
**
366539 TTTTAAA-ATGTTTTAGT
1 TTTTAAATA-GTTTTAAC
366556 TTTTAACATA-TTTTAA
1 TTTTAA-ATAGTTTTAA
366572 AAAAATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 1 0.04
17 24 0.89
18 1 0.04
19 1 0.04
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTTAAATAGTTTTAAC
Found at i:372192 original size:26 final size:26
Alignment explanation
Indices: 372163--372225 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
372153 CCAGCTACCA
* * *
372163 CAACTCACTAGACCCATTGGCGACCC
1 CAACTCGCTAGACCCACTGACGACCC
* * *
372189 CAACTTGCTAGGCTCACTGACGACCC
1 CAACTCGCTAGACCCACTGACGACCC
372215 CAACTCGCTAG
1 CAACTCGCTAG
372226 GCTCACTGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.25, C:0.40, G:0.17, T:0.17
Consensus pattern (26 bp):
CAACTCGCTAGACCCACTGACGACCC
Found at i:372248 original size:26 final size:26
Alignment explanation
Indices: 372183--372233 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
372173 GACCCATTGG
*
372183 CGACCCCAACTTGCTAGGCTCACTGA
1 CGACCCCAACTCGCTAGGCTCACTGA
372209 CGACCCCAACTCGCTAGGCTCACTG
1 CGACCCCAACTCGCTAGGCTCACTG
372234 GTGACCCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.22, C:0.41, G:0.20, T:0.18
Consensus pattern (26 bp):
CGACCCCAACTCGCTAGGCTCACTGA
Found at i:373211 original size:19 final size:19
Alignment explanation
Indices: 373187--373225 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
373177 CAGTTAAGGG
*
373187 TAATTAGCGATTTAATTGA
1 TAATTAGCGATGTAATTGA
*
373206 TAATTAGGGATGTAATTGA
1 TAATTAGCGATGTAATTGA
373225 T
1 T
373226 CATAGGCCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.41
Consensus pattern (19 bp):
TAATTAGCGATGTAATTGA
Found at i:377723 original size:18 final size:18
Alignment explanation
Indices: 377700--377775 Score: 68
Period size: 17 Copynumber: 4.4 Consensus size: 18
377690 AGATTTATGG
*
377700 GCCCACATACCCGTGTGA
1 GCCCACATGCCCGTGTGA
* *
377718 GCCCACACGCCTGTGTGA
1 GCCCACATGCCCGTGTGA
*
377736 -CCCATATGCCCGTGTG-
1 GCCCACATGCCCGTGTGA
* * *
377752 GCCTACACGCCTGTGTG-
1 GCCCACATGCCCGTGTGA
377769 GCCCACA
1 GCCCACA
377776 CACCCAGATT
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
17 31 0.67
18 15 0.33
ACGTcount: A:0.17, C:0.39, G:0.25, T:0.18
Consensus pattern (18 bp):
GCCCACATGCCCGTGTGA
Found at i:377750 original size:17 final size:18
Alignment explanation
Indices: 377709--377776 Score: 70
Period size: 17 Copynumber: 3.9 Consensus size: 18
377699 GGCCCACATA
377709 CCCGTGTGAGCCCACACG
1 CCCGTGTGAGCCCACACG
* * *
377727 CCTGTGTGA-CCCATATG
1 CCCGTGTGAGCCCACACG
*
377744 CCCGTGTG-GCCTACACG
1 CCCGTGTGAGCCCACACG
*
377761 CCTGTGTG-GCCCACAC
1 CCCGTGTGAGCCCACAC
377777 ACCCAGATTG
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
17 32 0.80
18 8 0.20
ACGTcount: A:0.15, C:0.40, G:0.26, T:0.19
Consensus pattern (18 bp):
CCCGTGTGAGCCCACACG
Found at i:379625 original size:41 final size:41
Alignment explanation
Indices: 379553--379638 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 41
379543 CATGTTAACG
* * * * *
379553 CATATCGATGCCACTGTCCGAGATAGGGTCTTATACG-AAT
1 CATATCGATGCCAATGTCCCAGACAGAGTCTTACACGAAAT
*
379593 CATATACGATGCCAATGTCCCAGACATAGTCTTACACGAAAT
1 CATAT-CGATGCCAATGTCCCAGACAGAGTCTTACACGAAAT
379635 CATA
1 CATA
379639 CCTCCGAAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 5 0.13
41 26 0.68
42 7 0.18
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (41 bp):
CATATCGATGCCAATGTCCCAGACAGAGTCTTACACGAAAT
Found at i:379814 original size:31 final size:31
Alignment explanation
Indices: 379778--379912 Score: 157
Period size: 31 Copynumber: 4.4 Consensus size: 31
379768 ATATACATAT
*
379778 TCATATACGAATCAAATTCGACAATGTATAA
1 TCATATACGAATCAAATTCGGCAATGTATAA
** * *
379809 TCATATAAAAATC-AATTTGGCAATGTAGAA
1 TCATATACGAATCAAATTCGGCAATGTATAA
* * *
379839 CCATATATGAATCAAGTTCGGCAATGTATAA
1 TCATATACGAATCAAATTCGGCAATGTATAA
*
379870 TCATATGC-AAGTCAAATTCGGCAATGTATAA
1 TCATATACGAA-TCAAATTCGGCAATGTATAA
*
379901 CCATATACGAAT
1 TCATATACGAAT
379913 TAATTTGGCT
Statistics
Matches: 84, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
30 26 0.31
31 56 0.67
32 2 0.02
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (31 bp):
TCATATACGAATCAAATTCGGCAATGTATAA
Found at i:379851 original size:61 final size:62
Alignment explanation
Indices: 379779--379912 Score: 189
Period size: 61 Copynumber: 2.2 Consensus size: 62
379769 TATACATATT
*
379779 CATATACGAATCAAATTCGACAATGTATAATCATATAAAAATC-AATTTGGCAATGTAGAAC
1 CATATACGAATCAAATTCGACAATGTATAATCATATAAAAATCAAATTCGGCAATGTAGAAC
* * * ** * *
379840 CATATATGAATCAAGTTCGGCAATGTATAATCATATGCAAGTCAAATTCGGCAATGTATAAC
1 CATATACGAATCAAATTCGACAATGTATAATCATATAAAAATCAAATTCGGCAATGTAGAAC
379902 CATATACGAAT
1 CATATACGAAT
379913 TAATTTGGCT
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
61 37 0.59
62 26 0.41
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (62 bp):
CATATACGAATCAAATTCGACAATGTATAATCATATAAAAATCAAATTCGGCAATGTAGAAC
Found at i:379961 original size:92 final size:92
Alignment explanation
Indices: 379755--379961 Score: 206
Period size: 92 Copynumber: 2.2 Consensus size: 92
379745 CCAATGGTCA
* *
379755 AATCAATTT-AACAATATACATATTCATATACGAATCAAATTCGACAATGTATAATCATATAAAA
1 AATCAATTTCAACAATAT--ATAATCATATACGAATCAAATTCGACAATGTATAACCATATAAAA
*
379819 ATCAATTTGGCAATGTAGAACCATATATG
64 ATCAATTTGGCAATGTAGAACCATATATC
* ** * * * **
379848 AATCAAGTTCGGCAATGTATAATCATATGC-AAGTCAAATTCGGCAATGTATAACCATATACGAA
1 AATCAATTTCAACAATATATAATCATATACGAA-TCAAATTCGACAATGTATAACCATATAAAAA
* * * *
379912 TTAATTTGGCTACT-TATATCCATATA-C
65 TCAATTTGGC-AATGTAGAACCATATATC
379939 AATTCAATTTCAACAATATATAA
1 AA-TCAATTTCAACAATATATAA
379962 CCATGTACAA
Statistics
Matches: 91, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
91 4 0.04
92 72 0.79
93 10 0.11
94 5 0.05
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (92 bp):
AATCAATTTCAACAATATATAATCATATACGAATCAAATTCGACAATGTATAACCATATAAAAAT
CAATTTGGCAATGTAGAACCATATATC
Found at i:379992 original size:31 final size:30
Alignment explanation
Indices: 379890--379992 Score: 84
Period size: 31 Copynumber: 3.4 Consensus size: 30
379880 GTCAAATTCG
* *
379890 GCAATGTATAACCATATACGAATTAATTT-G
1 GCAAAGTATAACCATATAC-AATTAATTTCA
* ** *
379920 GCTACTTATATCCATATACAATTCAATTTCA
1 GCAAAGTATAACCATATACAATT-AATTTCA
* *
379951 ACAATA-TATAACCATGTACAAATTAATTTCA
1 GCAA-AGTATAACCATATAC-AATTAATTTCA
379982 GCAAAGTATAA
1 GCAAAGTATAA
379993 TTGTAATACC
Statistics
Matches: 57, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
29 4 0.07
30 21 0.37
31 28 0.49
32 4 0.07
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.33
Consensus pattern (30 bp):
GCAAAGTATAACCATATACAATTAATTTCA
Found at i:388103 original size:50 final size:50
Alignment explanation
Indices: 387948--388109 Score: 145
Period size: 50 Copynumber: 3.2 Consensus size: 50
387938 AGCCGTTGTA
* * * *
387948 GCTTTAATATT-TTTAATTGCAATGTCGGGGAAGCAAGATTCACTAATGTG
1 GCTTTAATCTTGTTT-ACTGCAATGTCGGGGAAGTAAGATTCACTGATGTG
** * * *
387998 GCTTTAATC-TGCTCCACTGC-ATCGCCTGGGG-AGATAAGATT-AGCTGTTGTA
1 GCTTTAATCTTG-TTTACTGCAAT-GTC-GGGGAAG-TAAGATTCA-CTGATGTG
*
388049 GCTTTAATCTTGTTTACTGCAATGTCGGGGAAGTAAGATTCACCGATGTG
1 GCTTTAATCTTGTTTACTGCAATGTCGGGGAAGTAAGATTCACTGATGTG
388099 GCTTTAATCTT
1 GCTTTAATCTT
388110 CTCCGCTACT
Statistics
Matches: 87, Mismatches: 15, Indels: 20
0.71 0.12 0.16
Matches are distributed among these distances:
49 3 0.03
50 44 0.51
51 36 0.41
52 4 0.05
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (50 bp):
GCTTTAATCTTGTTTACTGCAATGTCGGGGAAGTAAGATTCACTGATGTG
Found at i:389536 original size:13 final size:13
Alignment explanation
Indices: 389503--389570 Score: 75
Period size: 13 Copynumber: 5.0 Consensus size: 13
389493 TTAGCCTCTC
389503 CATTTTTACTTTTT
1 CATTTTT-CTTTTT
389517 CATTTTTTCATTTTT
1 CA-TTTTTC-TTTTT
389532 C-TTTTTCATTTTT
1 CATTTTTC-TTTTT
* *
389545 CATCTCTCTTTTT
1 CATTTTTCTTTTT
389558 CATTTTTCTTTTT
1 CATTTTTCTTTTT
389571 TTTTTGAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
13 29 0.62
14 7 0.15
15 11 0.23
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (13 bp):
CATTTTTCTTTTT
Found at i:389543 original size:20 final size:20
Alignment explanation
Indices: 389503--389575 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
389493 TTAGCCTCTC
389503 CATTTTTACTTTTTCATTTTTT
1 CATTTTT-CTTTTTCA-TTTTT
389525 CATTTTTCTTTTTCATTTTT
1 CATTTTTCTTTTTCATTTTT
* *
389545 CATCTCTCTTTTTCATTTTT
1 CATTTTTCTTTTTCATTTTT
389565 C-TTTTT-TTTTT
1 CATTTTTCTTTTT
389576 GAATTGGTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
18 5 0.11
19 3 0.06
20 24 0.51
21 8 0.17
22 7 0.15
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (20 bp):
CATTTTTCTTTTTCATTTTT
Found at i:389571 original size:7 final size:7
Alignment explanation
Indices: 389503--389570 Score: 72
Period size: 7 Copynumber: 10.0 Consensus size: 7
389493 TTAGCCTCTC
389503 CATTTTT
1 CATTTTT
389510 -ACTTTTT
1 CA-TTTTT
389517 CATTTTTT
1 CA-TTTTT
389525 CATTTTT
1 CATTTTT
389532 C-TTTTT
1 CATTTTT
389538 CATTTTT
1 CATTTTT
* *
389545 CATCTCT
1 CATTTTT
389552 C-TTTTT
1 CATTTTT
389558 CATTTTT
1 CATTTTT
389565 C-TTTTT
1 CATTTTT
389571 TTTTTGAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
6 16 0.31
7 28 0.54
8 8 0.15
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (7 bp):
CATTTTT
Found at i:390324 original size:22 final size:23
Alignment explanation
Indices: 390269--390328 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
390259 GAAGTCTTCT
*
390269 TTTTTCATTTTTGATTTGGATGAC
1 TTTTT-ATTTTTGATTTGGATCAC
390293 TTTTTA-TTTTGACTTT-GATCA-
1 TTTTTATTTTTGA-TTTGGATCAC
390314 TTTTTATTTTT-ATTT
1 TTTTTATTTTTGATTT
390329 TTTTTGTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 3 0.09
21 7 0.21
22 14 0.42
23 4 0.12
24 5 0.15
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.67
Consensus pattern (23 bp):
TTTTTATTTTTGATTTGGATCAC
Found at i:414169 original size:18 final size:18
Alignment explanation
Indices: 414136--414171 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
414126 TAATTAAACA
*
414136 TATAAAAAATTATAAAAT
1 TATAAAAAAATATAAAAT
*
414154 TATAAAAAAATCTAAAAT
1 TATAAAAAAATATAAAAT
414172 CTGAAACTTT
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:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
TATAAAAAAATATAAAAT
Found at i:415728 original size:21 final size:21
Alignment explanation
Indices: 415702--415743 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
415692 ATTTTCCCTT
415702 TCTCCTTTCTCTTCTAAGCAA
1 TCTCCTTTCTCTTCTAAGCAA
415723 TCTCCTTTCTCTTCTAAGCAA
1 TCTCCTTTCTCTTCTAAGCAA
415744 ATTTTCTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.05, T:0.43
Consensus pattern (21 bp):
TCTCCTTTCTCTTCTAAGCAA
Found at i:415980 original size:15 final size:15
Alignment explanation
Indices: 415960--415990 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
415950 TCCAAATTGT
*
415960 TTGTTGAAGCTTCCA
1 TTGTTGAAGATTCCA
415975 TTGTTGAAGATTCCA
1 TTGTTGAAGATTCCA
415990 T
1 T
415991 AAAACATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (15 bp):
TTGTTGAAGATTCCA
Found at i:416302 original size:15 final size:13
Alignment explanation
Indices: 416276--416301 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
416266 TCAGGTTAGG
416276 AGTGAGAGATATA
1 AGTGAGAGATATA
416289 AGTGAGAGATATA
1 AGTGAGAGATATA
416302 TGAATAATGG
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:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (13 bp):
AGTGAGAGATATA
Found at i:418664 original size:14 final size:14
Alignment explanation
Indices: 418641--418677 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
418631 AAACACCAAA
418641 AAAT-ATTTT-CAG
1 AAATCATTTTCCAG
418653 TAAATCATTTTCCAG
1 -AAATCATTTTCCAG
418668 AAATCATTTT
1 AAATCATTTT
418678 ACGGGAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.18
14 15 0.68
15 3 0.14
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:424075 original size:18 final size:18
Alignment explanation
Indices: 424034--424075 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
424024 ATAGCAGTGT
424034 AAAGAACAAAAGGAAAAA
1 AAAGAACAAAAGGAAAAA
* *
424052 AGAGAAGAAAA-GAAAAGA
1 AAAGAACAAAAGGAAAA-A
424070 AAAGAA
1 AAAGAA
424076 TATATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAGAACAAAAGGAAAAA
Found at i:426590 original size:1 final size:1
Alignment explanation
Indices: 426584--426608 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
426574 GAAGAAGGCC
426584 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
426609 GAATGTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:426782 original size:289 final size:290
Alignment explanation
Indices: 426271--426851 Score: 1121
Period size: 289 Copynumber: 2.0 Consensus size: 290
426261 AGTTATCCGA
*
426271 AAAGAATTAAAAAAGAAGAAGGCCAAAATAACAAAAAAAAAAAAAAAAAAAATGTTAAGCATTAA
1 AAAGAATT-AAAAAGAAGAAGGCCAAAATAAAAAAAAAAAAAAAAAAAAAAATGTTAAGCATTAA
426336 CTTAATGAGTGTGCCTTTACTTAGCTTTTGAAATTAAGTTATTTTATTAAACTGACGAATCTATA
65 CTTAATGAGTGTGCCTTTACTTAGCTTTTGAAATTAAGTTATTTTATTAAACTGACGAATCTATA
426401 AAAGATAACAATTTTATATTTAATTAATTAAATCATGAAAAACAAAAACAAAAGAGAAGTTTGTC
130 AAAGATAACAATTTTATATTTAATTAATTAAATCATGAAAAACAAAAACAAAAGAGAAGTTTGTC
426466 ATTTACTTATGAATTACTTTAGGTCAAACGGTTTATGAGAACCTTTAAAACGACAAGCCGGTTTG
195 ATTTACTTATGAATTACTTTAGGTCAAACGGTTTATGAGAACCTTTAAAACGACAAGCCGGTTTG
426531 ATCATGTCAAGAGCCAACTTTTTATCCGTCT
260 ATCATGTCAAGAGCCAACTTTTTATCCGTCT
426562 AAAGAATT-AAAAGAAGAAGGCCAAAA-AAAAAAAAAAAAAAAAAAAAAGAATGTTAAGCATTAA
1 AAAGAATTAAAAAGAAGAAGGCCAAAATAAAAAAAAAAAAAAAAAAAAA-AATGTTAAGCATTAA
426625 CTTAATGAGTGTGCCTTTACTTAGCTTTTGAAATTAAGTTATTTTATTAAACTGACGAATCTATA
65 CTTAATGAGTGTGCCTTTACTTAGCTTTTGAAATTAAGTTATTTTATTAAACTGACGAATCTATA
426690 AAAGATAACAATTTTATATTTAATTAATTAAATCATGAAAAACAAAAACAAAAGAGAAGTTTGTC
130 AAAGATAACAATTTTATATTTAATTAATTAAATCATGAAAAACAAAAACAAAAGAGAAGTTTGTC
426755 ATTTACTTATGAATTACTTTAGGTCAAACGGTTTATGAGAACCTTTAAAACGACAAGCCGGTTTG
195 ATTTACTTATGAATTACTTTAGGTCAAACGGTTTATGAGAACCTTTAAAACGACAAGCCGGTTTG
426820 ATCATGTCAAGAGCCAACTTTTTATCCGTCT
260 ATCATGTCAAGAGCCAACTTTTTATCCGTCT
426851 A
1 A
426852 TTAAGGTTGC
Statistics
Matches: 288, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
288 20 0.07
289 260 0.90
291 8 0.03
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (290 bp):
AAAGAATTAAAAAGAAGAAGGCCAAAATAAAAAAAAAAAAAAAAAAAAAAATGTTAAGCATTAAC
TTAATGAGTGTGCCTTTACTTAGCTTTTGAAATTAAGTTATTTTATTAAACTGACGAATCTATAA
AAGATAACAATTTTATATTTAATTAATTAAATCATGAAAAACAAAAACAAAAGAGAAGTTTGTCA
TTTACTTATGAATTACTTTAGGTCAAACGGTTTATGAGAACCTTTAAAACGACAAGCCGGTTTGA
TCATGTCAAGAGCCAACTTTTTATCCGTCT
Found at i:433019 original size:2 final size:2
Alignment explanation
Indices: 433012--433049 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
433002 CTATTTGTAT
433012 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
433050 ATCTTACATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:443520 original size:21 final size:22
Alignment explanation
Indices: 443467--443528 Score: 56
Period size: 26 Copynumber: 2.7 Consensus size: 22
443457 ATGTTTTAAT
443467 AATTATTCACTTTTTTTTACAAAA
1 AATTATTCAC-TTTTTTTA-AAAA
*
443491 ATGATTATTCACTTTTTTT-AAAG
1 A--ATTATTCACTTTTTTTAAAAA
*
443514 AATTATT-ACTCTTTT
1 AATTATTCACTTTTTT
443529 AATAAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
20 7 0.21
21 6 0.18
23 4 0.12
24 1 0.03
25 7 0.21
26 9 0.26
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.53
Consensus pattern (22 bp):
AATTATTCACTTTTTTTAAAAA
Found at i:446141 original size:73 final size:74
Alignment explanation
Indices: 446039--446186 Score: 289
Period size: 73 Copynumber: 2.0 Consensus size: 74
446029 TATTAATATA
446039 TAATTTGTAATAAAAAAATAATAAATTATAATTTTATGGAAATTGAAACTAAAAAAATATTAAAG
1 TAATTTGTAATAAAAAAATAATAAATTATAATTTTATGGAAATTGAAACTAAAAAAATATTAAAG
446104 AAACTGTAC
66 AAACTGTAC
446113 TAATTTGTAA-AAAAAAATAATAAATTATAATTTTATGGAAATTGAAACTAAAAAAATATTAAAG
1 TAATTTGTAATAAAAAAATAATAAATTATAATTTTATGGAAATTGAAACTAAAAAAATATTAAAG
446177 AAACTGTAC
66 AAACTGTAC
446186 T
1 T
446187 TCTTTAAAAA
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 64 0.86
74 10 0.14
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.32
Consensus pattern (74 bp):
TAATTTGTAATAAAAAAATAATAAATTATAATTTTATGGAAATTGAAACTAAAAAAATATTAAAG
AAACTGTAC
Found at i:446895 original size:17 final size:17
Alignment explanation
Indices: 446873--446918 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
446863 ATGTATATAT
*
446873 AGAGAGAGATAGAGGGA
1 AGAGAGAGAGAGAGGGA
446890 AGAGAGAGAGAGAGGG-
1 AGAGAGAGAGAGAGGGA
* *
446906 GGAGGGAGAGAGA
1 AGAGAGAGAGAGA
446919 TGGTGGGCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.43, C:0.00, G:0.54, T:0.02
Consensus pattern (17 bp):
AGAGAGAGAGAGAGGGA
Found at i:450156 original size:19 final size:19
Alignment explanation
Indices: 450132--450183 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
450122 AATCTTCAAG
450132 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
450151 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
450170 GATATGCAATCTTA
1 GATATGCAATCTTA
450184 CAAGATATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:450176 original size:38 final size:40
Alignment explanation
Indices: 450132--450208 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
450122 AATCTTCAAG
450132 GATATGCAATCTT-AGATATGA-TATGTAATCTTAGATAT
1 GATATGCAATCTTAAGATATGATTATGTAATCTTAGATAT
*
450170 GATATGCAATCTTACAAGATATGATTTTGTAATCTTAGA
1 GATATGCAATCTT--AAGATATGATTATGTAATCTTAGA
450209 GATTTAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 13 0.38
41 8 0.24
42 13 0.38
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (40 bp):
GATATGCAATCTTAAGATATGATTATGTAATCTTAGATAT
Found at i:450648 original size:17 final size:17
Alignment explanation
Indices: 450617--450660 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
450607 CATAACTTTT
*
450617 ATATACA-TATATATAC
1 ATATACATTTTATATAC
*
450633 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
450650 ATATACATTTT
1 ATATACATTTT
450661 TTATTTCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:450730 original size:20 final size:21
Alignment explanation
Indices: 450707--450760 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
450697 TTATATTTTT
450707 TTTTATATTTTTA-ATGCATA
1 TTTTATATTTTTATATGCATA
* *
450727 TTTTATA-ATTTATATGTATA
1 TTTTATATTTTTATATGCATA
450747 TATTTATATATTTT
1 T-TTTATAT-TTTT
450761 TCTTTATTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 4 0.15
20 14 0.52
21 6 0.22
23 3 0.11
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (21 bp):
TTTTATATTTTTATATGCATA
Found at i:450741 original size:14 final size:13
Alignment explanation
Indices: 450696--450760 Score: 51
Period size: 14 Copynumber: 4.8 Consensus size: 13
450686 TATATACACT
*
450696 TTTATATTTTT-T
1 TTTATATTTTTAA
450708 TTTATATTTTTAA
1 TTTATATTTTTAA
**
450721 TGCATATTTTATAA
1 TTTATATTTT-TAA
* *
450735 TTTATATGTATATA
1 TTTATATTTTTA-A
450749 TTTATATATTTT
1 TTTATAT-TTTT
450761 TCTTTATTGT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
12 11 0.28
13 10 0.25
14 17 0.43
15 2 0.05
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (13 bp):
TTTATATTTTTAA
Found at i:482170 original size:41 final size:41
Alignment explanation
Indices: 482108--482191 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
482098 GTCGCAAAGT
*
482108 CTACACTGACATTATAAGTTGGGGAATGTTAGTATAACACC
1 CTACACTGACATTATAAGTTGGGAAATGTTAGTATAACACC
*
482149 CTACACTGACATTATATGTTGGGAAATGTTAGTATAACACC
1 CTACACTGACATTATAAGTTGGGAAATGTTAGTATAACACC
482190 CT
1 CT
482192 TAACCCCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (41 bp):
CTACACTGACATTATAAGTTGGGAAATGTTAGTATAACACC
Found at i:483746 original size:19 final size:20
Alignment explanation
Indices: 483714--483777 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 20
483704 ATCTTTGAAT
**
483714 TCATTTCAAAATTT-ACATC
1 TCATTTCATCATTTCACATC
* *
483733 TCATTTCATCATTTCATATT
1 TCATTTCATCATTTCACATC
*
483753 TCATTTC-TCATTTCATAT-
1 TCATTTCATCATTTCACATC
483771 TCATTTC
1 TCATTTC
483778 TCAACTTTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
18 7 0.17
19 23 0.57
20 10 0.25
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.52
Consensus pattern (20 bp):
TCATTTCATCATTTCACATC
Found at i:486039 original size:13 final size:13
Alignment explanation
Indices: 486021--486047 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
486011 CTATCATTTT
486021 AAATTGTATGATA
1 AAATTGTATGATA
486034 AAATTGTATGATA
1 AAATTGTATGATA
486047 A
1 A
486048 TAATACTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (13 bp):
AAATTGTATGATA
Found at i:490349 original size:72 final size:73
Alignment explanation
Indices: 490229--490379 Score: 268
Period size: 72 Copynumber: 2.1 Consensus size: 73
490219 CGACAAAGGC
*
490229 ATTGGCGGAGAGGTAATGTCTGATTAAAGAACGCATGCAAAAAGAACCATTAAAACTTCTTTT-A
1 ATTGGCGGAGAGGTAATGTCTGATTAAAGAACGCATGCAAAAAAAACCATTAAAACTTCTTTTAA
* *
490293 TTGGCTCT
66 CTAGCTCT
490301 ATTGGCGGAGAGGTAATGTCTGATTAAAGAACGCATGCAAAAAAAACCATTAAAACTTCTTTTAA
1 ATTGGCGGAGAGGTAATGTCTGATTAAAGAACGCATGCAAAAAAAACCATTAAAACTTCTTTTAA
490366 CTAGCTCT
66 CTAGCTCT
490374 ATTGGC
1 ATTGGC
490380 TTATCCATGT
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
72 62 0.83
73 13 0.17
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (73 bp):
ATTGGCGGAGAGGTAATGTCTGATTAAAGAACGCATGCAAAAAAAACCATTAAAACTTCTTTTAA
CTAGCTCT
Found at i:492247 original size:24 final size:25
Alignment explanation
Indices: 492220--492276 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
492210 GAAGGATGAT
*
492220 AAGGCTGAGACAAA-A-AAGGAAGTG
1 AAGGCTGAGA-AAAGAGAAGGAAGCG
492244 AAGGCTGA-AAAAGAGAAGGAAGCG
1 AAGGCTGAGAAAAGAGAAGGAAGCG
492268 AAGGCTGAG
1 AAGGCTGAG
492277 TGAAAATGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 3 0.10
23 2 0.07
24 24 0.83
ACGTcount: A:0.47, C:0.09, G:0.37, T:0.07
Consensus pattern (25 bp):
AAGGCTGAGAAAAGAGAAGGAAGCG
Found at i:497170 original size:16 final size:17
Alignment explanation
Indices: 497152--497187 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
497142 AAAGTAAAGT
497152 AAAGAGCAGAAAAAATA
1 AAAGAGCAGAAAAAATA
*
497169 AAAGAGTAGAAAAAA-A
1 AAAGAGCAGAAAAAATA
497185 AAA
1 AAA
497188 CACCTTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.06
Consensus pattern (17 bp):
AAAGAGCAGAAAAAATA
Found at i:501495 original size:23 final size:23
Alignment explanation
Indices: 501466--501518 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
501456 TTAGGAACGT
* * *
501466 CAAAGTGCTAAATATGGGAGTAC
1 CAAAGTGCTAAACATAGGAGCAC
*
501489 CAGAGTGCTAAACATAGGAGCAC
1 CAAAGTGCTAAACATAGGAGCAC
501512 CAAAGTG
1 CAAAGTG
501519 TTCAATACAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (23 bp):
CAAAGTGCTAAACATAGGAGCAC
Found at i:501936 original size:48 final size:48
Alignment explanation
Indices: 501877--501972 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
501867 AATTTAAAGA
501877 ATATCTATAATTTCAATTACAACAATCACAAGATATTATTCACTAAAT
1 ATATCTATAATTTCAATTACAACAATCACAAGATATTATTCACTAAAT
*
501925 ATATCTGTAATTTCAATTACAACAATCACAAGATATTATTCACTAAAT
1 ATATCTATAATTTCAATTACAACAATCACAAGATATTATTCACTAAAT
501973 CCTTAGTCCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (48 bp):
ATATCTATAATTTCAATTACAACAATCACAAGATATTATTCACTAAAT
Found at i:502897 original size:5 final size:5
Alignment explanation
Indices: 502879--502928 Score: 68
Period size: 5 Copynumber: 10.2 Consensus size: 5
502869 TTCCTTTATT
*
502879 TAAT- TAAT- TAATA TAATA TAATA TAATA TAATA TAATA CTAAAA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA -TAATA TAATA
502928 T
1 T
502929 TATTTATAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
4 8 0.19
5 30 0.71
6 4 0.10
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Done.