Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold149
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1065560
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 107426 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:8192 original size:2 final size:2
Alignment explanation
Indices: 8185--8215 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8175 TTATTCAAAT
8185 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
8216 CACACACAAG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11934 original size:2 final size:2
Alignment explanation
Indices: 11929--11976 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
11919 GGGGGGGGGG
11929 GA GA 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 GA GA
11971 GA GA GA
1 GA GA GA
11977 ATTAAAACAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12376 original size:11 final size:11
Alignment explanation
Indices: 12360--12384 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12350 AACTTTATAC
12360 TATAAATCATA
1 TATAAATCATA
12371 TATAAATCATA
1 TATAAATCATA
12382 TAT
1 TAT
12385 CTTTCCTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (11 bp):
TATAAATCATA
Found at i:14171 original size:4 final size:4
Alignment explanation
Indices: 14156--14209 Score: 74
Period size: 4 Copynumber: 13.8 Consensus size: 4
14146 ATCACATTTT
* * *
14156 GTCC GT-C GTCC GTCC GTCC GTCC GTCT GTCC GTCC GTCT GTCC GTCT
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC
14203 GTCC GTC
1 GTCC GTC
14210 TGTAAACTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 3 0.07
4 40 0.93
ACGTcount: A:0.00, C:0.43, G:0.26, T:0.31
Consensus pattern (4 bp):
GTCC
Found at i:15859 original size:164 final size:164
Alignment explanation
Indices: 15420--16022 Score: 875
Period size: 168 Copynumber: 3.6 Consensus size: 164
15410 AGCTCATCTG
* * *
15420 AGGGTGGGGCCACAATTGGGGG-TCGAAGTTTAACAAATGAATATAAAGAGTAAATCTTTAAAAA
1 AGGGTGGGGCCACAA-TGGGGGATCGAAGTTTAACATAGGAATATATAGAG-AAATCTTTAAAAA
* * *
15484 TCTTCTCCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCATCAGGTAATG
64 TCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTG
* * *
15549 TAGATACAAATTTGTGAAAATCATGATCCCCGGAGGT
129 TAGATTCAAAGTTGTGAAAATCATGACCCCCGG-GGT
** * * *
15586 AGGGTGGGGCCACAATGAAGGATCGAAATTTTACATAGGAATATATATAGAATAAATCTTTAAAA
1 AGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGG-A-ATATATAG-AGAAATCTTTAAAA
* * * * *
15651 ATCTTCTTCTCAGAAACTAAACGGCCAGGAAAGCTGACACTTGTGTGGAAGGATCCTCAGGTAGT
63 ATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGT
15716 GTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGT
128 GTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGT
*
15753 ACGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGAAATCTTTAAAAATC
1 AGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGAAATCTTTAAAAATC
15818 TTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTA
66 TTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTA
*
15883 GATTCATAGTTGTGAAAATCATGACCCCCGGGGGT
131 GATTCAAAGTTGTGAAAATCATGACCCCC-GGGGT
* * * * *
15918 AGGGTGGGGCCACAATGGGGGGTCGATGTTTTACATAGGAATATACAGAGAAATCTTTAAAAATT
1 AGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGAAATCTTTAAAAATC
* *
15983 TTCCTCTCAGAAACTAATCAGCCAGGAAAAGCTAAAACTT
66 TTCTTCTCAGAAACTAATCAGCCAGG-AAAGCTGAAACTT
16023 ATGNAGATTT
Statistics
Matches: 392, Mismatches: 39, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
164 104 0.27
165 101 0.26
166 41 0.10
167 38 0.10
168 107 0.27
169 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (164 bp):
AGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGAAATCTTTAAAAATC
TTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTA
GATTCAAAGTTGTGAAAATCATGACCCCCGGGGT
Found at i:16007 original size:165 final size:165
Alignment explanation
Indices: 15420--16022 Score: 861
Period size: 164 Copynumber: 3.6 Consensus size: 165
15410 AGCTCATCTG
* * *
15420 AGGGTGGGGCCACAATTGGGGG-TCGAAGTTTAACAAATGAATATAAAGAGTAAATCTTTAAAAA
1 AGGGTGGGGCCACAA-TGGGGGATCGAAGTTTAACATAGGAATATATAGAG-AAATCTTTAAAAA
* *
15484 TCTT-CTCCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCATCAGGTAAT
64 TCTTCCT-CTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGT
* * * *
15548 GTAGATACAAATTTGTGAAAATCATGATCCCCGGAGGT
128 GTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGT
** * * *
15586 AGGGTGGGGCCACAATGAAGGATCGAAATTTTACATAGGAATATATATAGAATAAATCTTTAAAA
1 AGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGG-A-ATATATAG-AGAAATCTTTAAAA
* * * * * *
15651 ATCTTCTTCTCAGAAACTAAACGGCCAGGAAAGCTGACACTTGTGTGGAAGGATCCTCAGGTAGT
63 ATCTTCCTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGT
15716 GTAGATTCAAAGTTGTGAAAATCATGACCCCC-GGGGT
128 GTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGT
*
15753 ACGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGAAATCTTTAAAAATC
1 AGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGAAATCTTTAAAAATC
*
15818 TTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTA
66 TTCCTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTA
*
15883 GATTCATAGTTGTGAAAATCATGACCCCCGGGGGT
131 GATTCAAAGTTGTGAAAATCATGACCCCCGGGGGT
* * * * *
15918 AGGGTGGGGCCACAATGGGGGGTCGATGTTTTACATAGGAATATACAGAGAAATCTTTAAAAATT
1 AGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGAAATCTTTAAAAATC
*
15983 TTCCTCTCAGAAACTAATCAGCCAGGAAAAGCTAAAACTT
66 TTCCTCTCAGAAACTAATCAGCCAGG-AAAGCTGAAACTT
16023 ATGNAGATTT
Statistics
Matches: 390, Mismatches: 40, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
164 104 0.27
165 101 0.26
166 41 0.11
167 39 0.10
168 103 0.26
169 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (165 bp):
AGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGAAATCTTTAAAAATC
TTCCTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTA
GATTCAAAGTTGTGAAAATCATGACCCCCGGGGGT
Found at i:17048 original size:13 final size:13
Alignment explanation
Indices: 17030--17058 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
17020 CTGCTCTACA
17030 ATGAGAAGAAAAG
1 ATGAGAAGAAAAG
17043 ATGAGAAGAAAAG
1 ATGAGAAGAAAAG
17056 ATG
1 ATG
17059 TTAATTAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.31, T:0.10
Consensus pattern (13 bp):
ATGAGAAGAAAAG
Found at i:19412 original size:132 final size:132
Alignment explanation
Indices: 19175--19415 Score: 392
Period size: 132 Copynumber: 1.8 Consensus size: 132
19165 GTCTGTCTGC
* *
19175 AAATTCGTATCCGGTCCATATCTTTCTTATGGAGAAACATTGAAAGTTCTTACTTCACACAAAGA
1 AAATTCGTATCAGGTCCATATCTTTCTTATGGAGAAACATTGAAAGTTCTTACGTCACACAAAGA
* ** *
19240 TTGCTTATGACCTGAGAGTGTGTCATGACCTTGACTCAAGGTCAAGGTCGATGGCAGAAAAAGTG
66 TTGCTTAAGACCAAAGAGTGTGTCATGACCTTGACCCAAGGTCAAGGTCGATGGCAGAAAAAGTG
19305 CA
131 CA
* * *
19307 AAATTCGTGTCAGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACGTCACACAAATA
1 AAATTCGTATCAGGTCCATATCTTTCTTATGGAGAAACATTGAAAGTTCTTACGTCACACAAAGA
*
19372 TTGCTTAAGACCAAAGGGTGTGTCATGACCTTGACCCAAGGTCA
66 TTGCTTAAGACCAAAGAGTGTGTCATGACCTTGACCCAAGGTCA
19416 TTTGGGCAAG
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
132 99 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (132 bp):
AAATTCGTATCAGGTCCATATCTTTCTTATGGAGAAACATTGAAAGTTCTTACGTCACACAAAGA
TTGCTTAAGACCAAAGAGTGTGTCATGACCTTGACCCAAGGTCAAGGTCGATGGCAGAAAAAGTG
CA
Found at i:19540 original size:145 final size:146
Alignment explanation
Indices: 19276--19560 Score: 364
Period size: 145 Copynumber: 2.0 Consensus size: 146
19266 GACCTTGACT
* * * *
19276 CAAGGTCAAGGTCGATGGCAGAAAAAGTGCAAAATTCGTGTCAGGTCCATATCTTTCTTATGGAG
1 CAAGGTCAAGGTCGATGGCAGAAAAAGTGCAAAAGTCGTATCAGGTCCATATATTTCTTATGGAC
* *
19341 AAACATTGGAAGTTCTTACGTCACACAAATATTGCTTAAGACCAAAGGGTGTGTCATGACCTTGA
66 AAACATTGGAAGTTCTTAAGTCACACAAAGATTGCTTAAGACCAAAGGGTGTGTCATGACCTTGA
19406 CCCAAGGTCATTTGGG
131 CCCAAGGTCATTTGGG
* * *
19422 CAAGGTCAAGGTC-ACTGGCAGAAAAA-TGCAAAAGTCAG-ATCCGGTCTATTTATTTCTTATGG
1 CAAGGTCAAGGTCGA-TGGCAGAAAAAGTGCAAAAGTC-GTATCAGGTCCATATATTTCTTATGG
* * * * **
19484 ACAAATATTGGAAGTTCTTAATTCATATAAAGATTGCTTATA-ACTTGAA-GGTGTGTCATGACC
64 ACAAACATTGGAAGTTCTTAAGTCACACAAAGATTGCTTA-AGAC-CAAAGGGTGTGTCATGACC
19547 TTGACCCAAGGTCA
127 TTGACCCAAGGTCA
19561 ATTAAGGAAG
Statistics
Matches: 120, Mismatches: 15, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
145 92 0.77
146 28 0.23
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (146 bp):
CAAGGTCAAGGTCGATGGCAGAAAAAGTGCAAAAGTCGTATCAGGTCCATATATTTCTTATGGAC
AAACATTGGAAGTTCTTAAGTCACACAAAGATTGCTTAAGACCAAAGGGTGTGTCATGACCTTGA
CCCAAGGTCATTTGGG
Found at i:19869 original size:18 final size:18
Alignment explanation
Indices: 19846--19882 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
19836 GTTTGATTCG
19846 AGTCATGTTTGTTAACAT
1 AGTCATGTTTGTTAACAT
19864 AGTCATGTTTGTTAACAT
1 AGTCATGTTTGTTAACAT
19882 A
1 A
19883 AGGATGCAAA
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:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (18 bp):
AGTCATGTTTGTTAACAT
Found at i:24560 original size:6 final size:6
Alignment explanation
Indices: 24511--24559 Score: 64
Period size: 6 Copynumber: 7.8 Consensus size: 6
24501 TTATCTGAAT
24511 TTTTTG TTTGTCTG TTTTTTG TTTTTG TTTTTG TTTTTG TTTTT- TTTTT
1 TTTTTG TTT-T-TG -TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
24560 TAACAAAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
5 5 0.12
6 26 0.65
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:31309 original size:4 final size:4
Alignment explanation
Indices: 31293--31341 Score: 71
Period size: 4 Copynumber: 12.2 Consensus size: 4
31283 CTTTCCTCTG
* * *
31293 CGTC CGTC AGTC CGTC CGTC CGTC TGTC CGTC CGTC CGTC CGTC TGTC
1 CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC
31341 C
1 C
31342 CACTTCAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.02, C:0.45, G:0.24, T:0.29
Consensus pattern (4 bp):
CGTC
Found at i:40271 original size:28 final size:28
Alignment explanation
Indices: 40215--40325 Score: 161
Period size: 28 Copynumber: 4.0 Consensus size: 28
40205 CAACCTCATG
40215 TTCAGTTGGTTATTTATATAAGTGGTTT
1 TTCAGTTGGTTATTTATATAAGTGGTTT
40243 TTCAGTT-GTTATTTATATAAGTGGTTT
1 TTCAGTTGGTTATTTATATAAGTGGTTT
* *
40270 TTCAGTTGGTTATTTACATTAGTGGTTT
1 TTCAGTTGGTTATTTATATAAGTGGTTT
* * * *
40298 TTCAGTTCGTAATTTATTTCAGTGGTTT
1 TTCAGTTGGTTATTTATATAAGTGGTTT
40326 CTTATGCAAC
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
27 27 0.36
28 48 0.64
ACGTcount: A:0.20, C:0.06, G:0.20, T:0.54
Consensus pattern (28 bp):
TTCAGTTGGTTATTTATATAAGTGGTTT
Found at i:40281 original size:55 final size:56
Alignment explanation
Indices: 40215--40325 Score: 170
Period size: 55 Copynumber: 2.0 Consensus size: 56
40205 CAACCTCATG
* *
40215 TTCAGTTGGTTATTTATATAAGTGGTTTTTCAGTT-GTTATTTATATAAGTGGTTT
1 TTCAGTTGGTTATTTACATAAGTGGTTTTTCAGTTCGTAATTTATATAAGTGGTTT
* * *
40270 TTCAGTTGGTTATTTACATTAGTGGTTTTTCAGTTCGTAATTTATTTCAGTGGTTT
1 TTCAGTTGGTTATTTACATAAGTGGTTTTTCAGTTCGTAATTTATATAAGTGGTTT
40326 CTTATGCAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
55 33 0.66
56 17 0.34
ACGTcount: A:0.20, C:0.06, G:0.20, T:0.54
Consensus pattern (56 bp):
TTCAGTTGGTTATTTACATAAGTGGTTTTTCAGTTCGTAATTTATATAAGTGGTTT
Found at i:40522 original size:2 final size:2
Alignment explanation
Indices: 40515--40551 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
40505 TTCTCATACA
40515 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
40552 GGTATACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:46770 original size:2 final size:2
Alignment explanation
Indices: 46763--46802 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
46753 TTATACGTAT
46763 GA 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 GA
46803 CCTTCGGATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:48723 original size:44 final size:45
Alignment explanation
Indices: 48639--48738 Score: 168
Period size: 44 Copynumber: 2.3 Consensus size: 45
48629 TCCTTTCCGA
48639 TATATTTCA-TTTTATCAAATAAAATATACAACATGACTATGTTG
1 TATATTTCATTTTTATCAAATAAAATATACAACATGACTATGTTG
*
48683 TATATTTCATTTTTATCATATAAAATATACAACATG-CTATGTTG
1 TATATTTCATTTTTATCAAATAAAATATACAACATGACTATGTTG
*
48727 TATATTTTATTT
1 TATATTTCATTT
48739 GATAAAATGA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
44 28 0.53
45 25 0.47
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (45 bp):
TATATTTCATTTTTATCAAATAAAATATACAACATGACTATGTTG
Found at i:49384 original size:22 final size:22
Alignment explanation
Indices: 49345--49393 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
49335 TCACCCTAGC
49345 AAATTA-TTATATCATTTTTAA
1 AAATTATTTATATCATTTTTAA
49366 AAATTATTTATA-CATTTTTAA
1 AAATTATTTATATCATTTTTAA
49387 AAATTAT
1 AAATTAT
49394 AACATCTGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATTATTTATATCATTTTTAA
Found at i:50072 original size:17 final size:17
Alignment explanation
Indices: 50040--50073 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
50030 TTACATTGGT
*
50040 AGTAAGTAAGTAATTTA
1 AGTAAGTAAATAATTTA
*
50057 AGTAAGTAAATGATTTA
1 AGTAAGTAAATAATTTA
50074 TTTAAGTGGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (17 bp):
AGTAAGTAAATAATTTA
Found at i:56836 original size:10 final size:10
Alignment explanation
Indices: 56812--56842 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
56802 ACACGGTTAC
56812 ATTTAAATAAT
1 ATTTAAAT-AT
56823 ATTTAAATAT
1 ATTTAAATAT
56833 ATTTAAATAT
1 ATTTAAATAT
56843 TAAAAATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.60
11 8 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
ATTTAAATAT
Found at i:70555 original size:2 final size:2
Alignment explanation
Indices: 70548--70598 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
70538 AACAACCAAT
* *
70548 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
70590 TC TC TC TC T
1 TC TC TC TC T
70599 TCCAAGGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:70831 original size:16 final size:16
Alignment explanation
Indices: 70806--70836 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
70796 ACCAAAGGTT
70806 GTTCGACTGTCCGTCC
1 GTTCGACTGTCCGTCC
*
70822 GTTCGTCTGTCCGTC
1 GTTCGACTGTCCGTC
70837 TGAAAACTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.35, G:0.26, T:0.35
Consensus pattern (16 bp):
GTTCGACTGTCCGTCC
Found at i:73277 original size:18 final size:18
Alignment explanation
Indices: 73254--73302 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 18
73244 CATGATCAAC
73254 TTTTGTTTTGTTTTTGTT
1 TTTTGTTTTGTTTTTGTT
*
73272 TTTTGTGTTG--TTT-TT
1 TTTTGTTTTGTTTTTGTT
*
73287 TTTTATTTTGTTTTTG
1 TTTTGTTTTGTTTTTG
73303 GAGGGTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
15 10 0.40
16 3 0.12
17 3 0.12
18 9 0.36
ACGTcount: A:0.02, C:0.00, G:0.16, T:0.82
Consensus pattern (18 bp):
TTTTGTTTTGTTTTTGTT
Found at i:80180 original size:72 final size:72
Alignment explanation
Indices: 80012--80196 Score: 225
Period size: 72 Copynumber: 2.6 Consensus size: 72
80002 GATAAATACG
* * * *
80012 TTGT-TTGGTTAAATTATATTCCTCGAGTTTTCATTGTCGTTATGATTGTTTTAGTGCGAAAAAA
1 TTGTATTGGTTAAATAATATTTCTCGAGTTTTCATTGTCGTTA-GATTGTTTAAGTGAGAAAAAA
80076 AAAATTGT
65 AAAATTGT
* *
80084 TTCATATTGGTTGAATAATATTTCTCGAGTTTTCATTGTC-TTA-ATTGTTTAAGTGAGAGAGAA
1 TT-GTATTGGTTAAATAATATTTCTCGAGTTTTCATTGTCGTTAGATTGTTTAAGTGAGA-A-AA
80147 AAAAATATT-T
63 AAAAA-ATTGT
* *
80157 TTGTATTGGTTAAATAATGTTTCTCGAGATTTCATTGTCG
1 TTGTATTGGTTAAATAATATTTCTCGAGTTTTCATTGTCG
80197 CATGAGTAAG
Statistics
Matches: 97, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
71 13 0.13
72 36 0.37
73 14 0.14
74 34 0.35
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (72 bp):
TTGTATTGGTTAAATAATATTTCTCGAGTTTTCATTGTCGTTAGATTGTTTAAGTGAGAAAAAAA
AAATTGT
Found at i:86384 original size:21 final size:21
Alignment explanation
Indices: 86358--86405 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
86348 TTTTTATTGA
*
86358 ATATGTCGATATGCAAAATAG
1 ATATGTCGACATGCAAAATAG
* *
86379 ATATGTTGACATGCAATATAG
1 ATATGTCGACATGCAAAATAG
*
86400 TTATGT
1 ATATGT
86406 AAACATGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (21 bp):
ATATGTCGACATGCAAAATAG
Found at i:86411 original size:21 final size:21
Alignment explanation
Indices: 86368--86412 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
86358 ATATGTCGAT
**
86368 ATGCAAAATAGATATGTTGAC
1 ATGCAAAATAGATATGTAAAC
* *
86389 ATGCAATATAGTTATGTAAAC
1 ATGCAAAATAGATATGTAAAC
86410 ATG
1 ATG
86413 TAACAATACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (21 bp):
ATGCAAAATAGATATGTAAAC
Found at i:89245 original size:1 final size:1
Alignment explanation
Indices: 89239--89275 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
89229 GGTTTGAAAG
89239 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
89276 GGATTTACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:89262 original size:67 final size:66
Alignment explanation
Indices: 89146--89274 Score: 168
Period size: 67 Copynumber: 1.9 Consensus size: 66
89136 TAGCATTTTC
89146 TTTCATGTTTCAGAATGCTATGAAAGTTTGTTGTTGTTGTTGTTGTTTTTTTTTTTTTTTTTGGT
1 TTTCATGTTTCAGAATGCTATGAAAGTTTGTTGTTGTTGTTGTTGTTTTTTTTTTTTTTTTTGGT
89211 T
66 T
* * * * * * * * *
89212 TTTCTATGTTTTAGAATGGTTTGAAAGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTC-ATGTTTCAGAATGCTATGAAAGTTTGTTGTTGTTGTTGTTGTTTTTTTTTTTTTTTTT
89275 TGGATTTACT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
66 4 0.08
67 49 0.92
ACGTcount: A:0.12, C:0.03, G:0.15, T:0.71
Consensus pattern (66 bp):
TTTCATGTTTCAGAATGCTATGAAAGTTTGTTGTTGTTGTTGTTGTTTTTTTTTTTTTTTTTGGT
T
Found at i:90093 original size:2 final size:2
Alignment explanation
Indices: 90086--90137 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
90076 TGTATAATAT
90086 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
90128 TC TC TC TC TC
1 TC TC TC TC TC
90138 ATACACACAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:90348 original size:10 final size:10
Alignment explanation
Indices: 90333--90357 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
90323 GTTGTTGCAA
90333 CCCACCCTCC
1 CCCACCCTCC
90343 CCCACCCTCC
1 CCCACCCTCC
90353 CCCAC
1 CCCAC
90358 ACCACAATAT
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:0.12, C:0.80, G:0.00, T:0.08
Consensus pattern (10 bp):
CCCACCCTCC
Found at i:92472 original size:18 final size:18
Alignment explanation
Indices: 92445--92485 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
92435 AAGACTGTTG
* *
92445 ACATACAACATCCAATGA
1 ACATAAAACATCCAATAA
*
92463 ACATAAAACATTCAATAA
1 ACATAAAACATCCAATAA
92481 ACATA
1 ACATA
92486 TACAAGAGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.56, C:0.22, G:0.02, T:0.20
Consensus pattern (18 bp):
ACATAAAACATCCAATAA
Found at i:92582 original size:14 final size:14
Alignment explanation
Indices: 92545--92571 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
92535 CAATTAAATA
92545 GTATATATGTATAT
1 GTATATATGTATAT
92559 GTATATATGTATA
1 GTATATATGTATA
92572 ATTATGTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (14 bp):
GTATATATGTATAT
Found at i:92735 original size:1 final size:1
Alignment explanation
Indices: 92729--92758 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
92719 AACCGTCGAA
*
92729 CCCCCCCCCCCCCCCCCCCCCCCGCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
92759 GAAAATTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.97, G:0.03, T:0.00
Consensus pattern (1 bp):
C
Found at i:100267 original size:3 final size:3
Alignment explanation
Indices: 100259--100294 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
100249 TTCATAGTTG
* *
100259 TGA TGA TGA TGA AGA TGA TGA TGA CGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
100295 GGACCGGCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.36, C:0.03, G:0.33, T:0.28
Consensus pattern (3 bp):
TGA
Found at i:100277 original size:12 final size:12
Alignment explanation
Indices: 100260--100294 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
100250 TCATAGTTGT
100260 GATGATGATGAA
1 GATGATGATGAA
*
100272 GATGATGATGAC
1 GATGATGATGAA
100284 GATGATGATGA
1 GATGATGATGA
100295 GGACCGGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.37, C:0.03, G:0.34, T:0.26
Consensus pattern (12 bp):
GATGATGATGAA
Found at i:106978 original size:15 final size:15
Alignment explanation
Indices: 106958--107002 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
106948 GCTGAAAAAA
106958 CATTACATTTTGCGT
1 CATTACATTTTGCGT
*
106973 CATTACATTTTGTGGT
1 CATTACATTTTG-CGT
*
106989 -ATTACATTTCGCGT
1 CATTACATTTTGCGT
107003 TGCTACAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 2 0.08
15 22 0.85
16 2 0.08
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.47
Consensus pattern (15 bp):
CATTACATTTTGCGT
Found at i:113141 original size:4 final size:4
Alignment explanation
Indices: 113132--113196 Score: 130
Period size: 4 Copynumber: 16.2 Consensus size: 4
113122 GGTTTAAAGG
113132 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
113180 TATC TATC TATC TATC T
1 TATC TATC TATC TATC T
113197 TTTTTGTTTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 61 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:113557 original size:4 final size:4
Alignment explanation
Indices: 113548--113617 Score: 95
Period size: 4 Copynumber: 17.5 Consensus size: 4
113538 CAGTTTAGGT
*
113548 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAAA
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
* * * *
113596 GAAA GAAA GAAA GAGA AAGA GA
1 GAGA GAGA GAGA GAGA GAGA GA
113618 TGGCCCGTGT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 62 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (4 bp):
GAGA
Found at i:113559 original size:6 final size:6
Alignment explanation
Indices: 113548--113617 Score: 95
Period size: 6 Copynumber: 11.7 Consensus size: 6
113538 CAGTTTAGGT
*
113548 GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAAA
1 GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA
* * * *
113596 GAAAGA AAGAAA GAGAAA GAGA
1 GAGAGA GAGAGA GAGAGA GAGA
113618 TGGCCCGTGT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (6 bp):
GAGAGA
Found at i:128312 original size:55 final size:55
Alignment explanation
Indices: 128228--128471 Score: 364
Period size: 55 Copynumber: 4.4 Consensus size: 55
128218 TGTTGGTGTT
* * *
128228 GGGGGTGGACAGTGACC-GCGAGGTGATGTGACTTACCGTTTTCGAGTCCGTTGTC
1 GGGGGTGGACAGTGACCTTC-AGGTAATGTGACTTACCGTTTTAGAGTCCGTTGTC
* * *
128283 GGGGGTGGACATTGACCATCAGGTGATGTGACTTACCGTTTTAGAGTCCGTTGTC
1 GGGGGTGGACAGTGACCTTCAGGTAATGTGACTTACCGTTTTAGAGTCCGTTGTC
*
128338 GGGGGTGGACAGTGACCTTGAGGTAATGTGACTTACCGTTTTAGAGTCCGTTGTC
1 GGGGGTGGACAGTGACCTTCAGGTAATGTGACTTACCGTTTTAGAGTCCGTTGTC
* * *
128393 GGGGGTGGACAGTGACCTTGAGGTAATGTTACTTACCGTTTTCGAGTCCGTTGTC
1 GGGGGTGGACAGTGACCTTCAGGTAATGTGACTTACCGTTTTAGAGTCCGTTGTC
* *
128448 GGGAGTGGACAGTGACCTTGAGGT
1 GGGGGTGGACAGTGACCTTCAGGT
128472 GTGGGAGTCG
Statistics
Matches: 178, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
55 177 0.99
56 1 0.01
ACGTcount: A:0.17, C:0.18, G:0.36, T:0.30
Consensus pattern (55 bp):
GGGGGTGGACAGTGACCTTCAGGTAATGTGACTTACCGTTTTAGAGTCCGTTGTC
Found at i:130601 original size:26 final size:26
Alignment explanation
Indices: 130570--130620 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
130560 ACCAATCTCT
130570 CTCCATAATAATTTACTATTGAATCC
1 CTCCATAATAATTTACTATTGAATCC
130596 CTCCATAATAATTTACTATTGAATC
1 CTCCATAATAATTTACTATTGAATC
130621 AATGACTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (26 bp):
CTCCATAATAATTTACTATTGAATCC
Found at i:131989 original size:2 final size:2
Alignment explanation
Indices: 131982--132021 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
131972 CAGAAAGGTT
131982 GA 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 GA
132022 ATTTCTGCAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:133938 original size:2 final size:2
Alignment explanation
Indices: 133933--133976 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
133923 ACATTTATAT
* *
133933 TC TC TC TC TC -C TC TC TC TC TC TC TC TC TC TT TC TT TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
133974 TC T
1 TC T
133977 TTTACACATG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:134239 original size:169 final size:171
Alignment explanation
Indices: 134046--134362 Score: 469
Period size: 169 Copynumber: 1.8 Consensus size: 171
134036 TCATATATAT
* * * *
134046 ACTCAAATCTCTGAACTTGTTTAATTAATGCATTTACTATATATATATTTATACATGAATAGATT
1 ACTCAAATCTCTGAACTTGTTTAATAAATGCATTTACTACAAATATATTAATACATGAATAGATT
*
134111 CTCAC-ATAATAAT-AT-TATGTAGTAATACTATGTAAATTAACAAAGAACAATTTTTTTCCATT
66 CTCACAATAATAATAATATATGCAGTAATACTATGTAAATTAACAAAGAACAATTTTTTTCCATT
134173 CAACACATTCNTATATATATATGTATATATATATATATACAC
131 CAACACATTC-TATATATATATGTATATATATATATATACAC
* *
134215 ACTCAATTCTTTGAACTTGTTTAATAAATGCATTTACTACAAATATATTAATACATGAATAGATT
1 ACTCAAATCTCTGAACTTGTTTAATAAATGCATTTACTACAAATATATTAATACATGAATAGATT
134280 CTCACATAATAATAATAAATCAACAATATGCAGTAATACTATGTAAATTAACAAAGAACAATTTT
66 CTCAC--AATAATAAT-AAT-----ATATGCAGTAATACTATGTAAATTAACAAAGAACAATTTT
134345 TTTCCATTCAACACATTC
123 TTTCCATTCAACACATTC
134363 CAAAACTAGA
Statistics
Matches: 130, Mismatches: 7, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
169 64 0.49
172 8 0.06
174 2 0.02
180 56 0.43
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (171 bp):
ACTCAAATCTCTGAACTTGTTTAATAAATGCATTTACTACAAATATATTAATACATGAATAGATT
CTCACAATAATAATAATATATGCAGTAATACTATGTAAATTAACAAAGAACAATTTTTTTCCATT
CAACACATTCTATATATATATGTATATATATATATATACAC
Found at i:139459 original size:26 final size:25
Alignment explanation
Indices: 139426--139477 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 25
139416 CTTCGGACCC
139426 CCCCTGGAAAAAATTTCTGGATCCG
1 CCCCTGGAAAAAATTTCTGGATCCG
139451 NCCCCTGGAAAAAATTTCTGGATCCG
1 -CCCCTGGAAAAAATTTCTGGATCCG
139477 C
1 C
139478 GCATGATACC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.23
Consensus pattern (25 bp):
CCCCTGGAAAAAATTTCTGGATCCG
Found at i:144685 original size:2 final size:2
Alignment explanation
Indices: 144680--144725 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
144670 TACCCCCCCC
144680 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
144722 CT CT
1 CT CT
144726 GGTGCCCTCG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:145741 original size:180 final size:179
Alignment explanation
Indices: 145433--145786 Score: 690
Period size: 180 Copynumber: 2.0 Consensus size: 179
145423 AAAAATTCAA
145433 AATATACTCATGTTTTTTTTTTTATAATTTATACCTTGATTTTTTTTCTTGCGTACCTAAAATCG
1 AATATACTCATGTTTTTTTTTTTATAATTTATACCTTGATTTTTTTTCTTGCGTACCTAAAATCG
145498 GCCTTACATTTGTTCACATAACCTTCATAGTATGAAATATATGCATAAATATTGATCTCAGAAAA
66 GCCTTACATTTGTTCACATAACCTTCATAGTATGAAATATATGCATAAATATTGATCTCAGAAAA
145563 AAATCTTTAATCAAATGATTTTGCATAGGCGTCGGAACCGGGGGGTGGG
131 AAATCTTTAATCAAATGATTTTGCATAGGCGTCGGAACCGGGGGGTGGG
*
145612 NAATATCCTCATGTTTTTTTTTTTATAATTTATACCTTGATTTTTTTTCTTGCGTACCTAAAATC
1 -AATATACTCATGTTTTTTTTTTTATAATTTATACCTTGATTTTTTTTCTTGCGTACCTAAAATC
145677 GGCCTTACATTTGTTCACATAACCTTCATAGTATGAAATATATGCATAAATATTGATCTCAGAAA
65 GGCCTTACATTTGTTCACATAACCTTCATAGTATGAAATATATGCATAAATATTGATCTCAGAAA
145742 AAAATCTTTAATCAAATGATTTTGCATAGGCGTCGGAACCGGGGG
130 AAAATCTTTAATCAAATGATTTTGCATAGGCGTCGGAACCGGGGG
145787 NNNNNNNNNN
Statistics
Matches: 173, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 173 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (179 bp):
AATATACTCATGTTTTTTTTTTTATAATTTATACCTTGATTTTTTTTCTTGCGTACCTAAAATCG
GCCTTACATTTGTTCACATAACCTTCATAGTATGAAATATATGCATAAATATTGATCTCAGAAAA
AAATCTTTAATCAAATGATTTTGCATAGGCGTCGGAACCGGGGGGTGGG
Found at i:150576 original size:4 final size:4
Alignment explanation
Indices: 150569--150646 Score: 74
Period size: 4 Copynumber: 20.0 Consensus size: 4
150559 TTCTCTCTCC
* *
150569 GTCT GTCT GTCT GGCT CTCT -T-T GTCT GTCT GTCT GGGTCT GTCT GTCT
1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT --GTCT GTCT GTCT
* *
150617 GTC- -TCT GTCT GTCT CTCT GTCA GTCT GTCT
1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT
150647 CTCTCTCTCT
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
2 3 0.05
3 2 0.03
4 52 0.85
6 4 0.07
ACGTcount: A:0.01, C:0.27, G:0.24, T:0.47
Consensus pattern (4 bp):
GTCT
Found at i:150587 original size:22 final size:22
Alignment explanation
Indices: 150561--150679 Score: 98
Period size: 22 Copynumber: 5.4 Consensus size: 22
150551 CTCTCTCTTT
*
150561 CTCTCTCCGTCTGTCTGTCTGG
1 CTCTCTCTGTCTGTCTGTCTGG
*
150583 CTCTCTTTGTCTGTCTGTCTGG
1 CTCTCTCTGTCTGTCTGTCTGG
* *
150605 GTCTGTCTGTCTGTCTCTGTCT-G
1 CTCTCTCTGTCTG--TCTGTCTGG
* **
150628 -TCTCTCTGTCAGTCTGTCTCT
1 CTCTCTCTGTCTGTCTGTCTGG
* * * **
150649 CTCTCTCTCTCTCTCTCTCTCT
1 CTCTCTCTGTCTGTCTGTCTGG
150671 CTCTCTCTG
1 CTCTCTCTG
150680 ATTGACACAC
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
20 7 0.09
22 65 0.81
23 1 0.01
24 7 0.09
ACGTcount: A:0.01, C:0.35, G:0.17, T:0.47
Consensus pattern (22 bp):
CTCTCTCTGTCTGTCTGTCTGG
Found at i:150611 original size:18 final size:18
Alignment explanation
Indices: 150564--150637 Score: 76
Period size: 18 Copynumber: 4.1 Consensus size: 18
150554 TCTCTTTCTC
*
150564 TCTCCGTCTGTCTGTCTG
1 TCTCGGTCTGTCTGTCTG
* ** *
150582 GCTCTCTTTGTCTGTCTG
1 TCTCGGTCTGTCTGTCTG
*
150600 TCTGGGTCTGTCTGTCTG
1 TCTCGGTCTGTCTGTCTG
* *
150618 TCTCTGTCTGTCTCTCTG
1 TCTCGGTCTGTCTGTCTG
150636 TC
1 TC
150638 AGTCTGTCTC
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.00, C:0.30, G:0.23, T:0.47
Consensus pattern (18 bp):
TCTCGGTCTGTCTGTCTG
Found at i:150647 original size:14 final size:14
Alignment explanation
Indices: 150592--150676 Score: 75
Period size: 14 Copynumber: 6.2 Consensus size: 14
150582 GCTCTCTTTG
**
150592 TCTGTCTGTCTGGG
1 TCTGTCTGTCTGTC
150606 TCTGTCTGTCTGTC
1 TCTGTCTGTCTGTC
150620 TCTGTCTGTC--TC
1 TCTGTCTGTCTGTC
*
150632 TCTGTCAGTCTGTC
1 TCTGTCTGTCTGTC
* * *
150646 TCTCTCTCTCTCTC
1 TCTGTCTGTCTGTC
* * *
150660 TCTCTCTCTCTCTC
1 TCTGTCTGTCTGTC
150674 TCT
1 TCT
150677 CTGATTGACA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
12 11 0.18
14 51 0.82
ACGTcount: A:0.01, C:0.35, G:0.15, T:0.48
Consensus pattern (14 bp):
TCTGTCTGTCTGTC
Found at i:150649 original size:2 final size:2
Alignment explanation
Indices: 150644--150678 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
150634 TGTCAGTCTG
150644 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
150679 GATTGACACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:152159 original size:27 final size:27
Alignment explanation
Indices: 152129--152214 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 27
152119 ATATTGAGCT
152129 TATCGACCAACATCACGATGTCGATAA
1 TATCGACCAACATCACGATGTCGATAA
* * * * * ***
152156 TATCG-CGATAAAGCACGATATTGAGCT
1 TATCGACCA-ACATCACGATGTCGATAA
152183 TATCGACCAACATCACGATGTCGATAA
1 TATCGACCAACATCACGATGTCGATAA
152210 TATCG
1 TATCG
152215 CGATAAAGCA
Statistics
Matches: 41, Mismatches: 16, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
26 2 0.05
27 37 0.90
28 2 0.05
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.24
Consensus pattern (27 bp):
TATCGACCAACATCACGATGTCGATAA
Found at i:152197 original size:54 final size:54
Alignment explanation
Indices: 152115--152224 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
152105 ACAGAATTAA
152115 CACGATATTGAGCTTATCGACCAACATCACGATGTCGATAATATCGCGATAAAG
1 CACGATATTGAGCTTATCGACCAACATCACGATGTCGATAATATCGCGATAAAG
152169 CACGATATTGAGCTTATCGACCAACATCACGATGTCGATAATATCGCGATAAAG
1 CACGATATTGAGCTTATCGACCAACATCACGATGTCGATAATATCGCGATAAAG
152223 CA
1 CA
152225 TCGTGCATTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (54 bp):
CACGATATTGAGCTTATCGACCAACATCACGATGTCGATAATATCGCGATAAAG
Found at i:161556 original size:44 final size:44
Alignment explanation
Indices: 161506--162042 Score: 300
Period size: 44 Copynumber: 12.2 Consensus size: 44
161496 TTATTACCTT
* *
161506 CTAGAATAGGATGATCCATATAGACGTTAGGGTGATAATAAATC
1 CTAGAATAGGATCATCCATATAGACGTTAGGTTGATAATAAATC
** * *
161550 CTAGAATAGGATCATTTATATAGAAGTTAGGTTG-CAATAAATC
1 CTAGAATAGGATCATCCATATAGACGTTAGGTTGATAATAAATC
* * *
161593 CTAGAATAGGATCA-GC-GATAGACATAGTAGGTTGATAATAAATC
1 CTAGAATAGGATCATCCATATAGACGT--TAGGTTGATAATAAATC
* * * *
161637 CTAGAATAGAATCATCGATAAAGACAGTT-GGTTGACT-ATGAATC
1 CTAGAATAGGATCATCCATATAGAC-GTTAGGTTGA-TAATAAATC
* * * * * *
161681 CTAGAATAGGATCATCGATAAAATACGGTAGATTGACAATAAATC
1 CTAGAATAGGATCATCCAT-ATAGACGTTAGGTTGATAATAAATC
* * * * * * * *
161726 CTAAAATAGGATAATCTATAGAAACGTTAGTTTAACAATAAATC
1 CTAGAATAGGATCATCCATATAGACGTTAGGTTGATAATAAATC
* * ** * * ** **
161770 CCAGAAAAGGATCATAGATAAAGTCAG-TAGGTTGGCAACGAATC
1 CTAGAATAGGATCATCCATATAGAC-GTTAGGTTGATAATAAATC
* * * * * * * * *
161814 CTAGAATAGGATCATCAATAGACACGGTATGTTTACAAAAAAGC
1 CTAGAATAGGATCATCCATATAGACGTTAGGTTGATAATAAATC
** * ** *
161858 CTAGAATATTA-CAATCGATCGAGACGTTAGGTTGACAATAAATC
1 CTAGAATAGGATC-ATCCATATAGACGTTAGGTTGATAATAAATC
* * * * *
161902 CTAGAATAGGATCAGCGATAGACACAG-TAGGTTGACAATAAATC
1 CTAGAATAGGATCATCCATATAGAC-GTTAGGTTGATAATAAATC
* * * *
161946 CTAGAATAGGATCATCGATAAAGACAG-TAGGTTGACAATGAATC
1 CTAGAATAGGATCATCCATATAGAC-GTTAGGTTGATAATAAATC
* * * * * * * *
161990 CCAAAATAGGATCATCGATAGACACGGTAGGTTGACAAAAAATC
1 CTAGAATAGGATCATCCATATAGACGTTAGGTTGATAATAAATC
*
162034 GTAGAATAG
1 CTAGAATAG
162043 CTAGGTTCAC
Statistics
Matches: 389, Mismatches: 88, Indels: 32
0.76 0.17 0.06
Matches are distributed among these distances:
41 6 0.02
43 32 0.08
44 308 0.79
45 37 0.10
46 5 0.01
47 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.25
Consensus pattern (44 bp):
CTAGAATAGGATCATCCATATAGACGTTAGGTTGATAATAAATC
Found at i:161835 original size:88 final size:87
Alignment explanation
Indices: 161506--162042 Score: 435
Period size: 88 Copynumber: 6.1 Consensus size: 87
161496 TTATTACCTT
* * * * * * **
161506 CTAGAATAGGATGATCCATATAGAC-GTTAGGGTGATAATAAATCCTAGAATAGGATCATTTATA
1 CTAGAATAGGATCATCGATAAAGTCAG-TAGGTTGACAATAAATCCTAGAATAGGATCATCGATA
* *
161570 TAGAA-GTTAGGTTGCAATAAATC
65 GA-AACGTTAGGTTACAATAAATC
* * *
161593 CTAGAATAGGATCAGCGATAGACA-T-AGTAGGTTGATAATAAATCCTAGAATAGAATCATCGAT
1 CTAGAATAGGATCATCGATA-A-AGTCAGTAGGTTGACAATAAATCCTAGAATAGGATCATCGAT
* *
161656 A-AAGACAGTT-GGTTGACTATGAATC
64 AGAA-AC-GTTAGGTT-ACAATAAATC
* * * * * *
161681 CTAGAATAGGATCATCGATAAAATACGGTAGATTGACAATAAATCCTAAAATAGGATAATCTATA
1 CTAGAATAGGATCATCGATAAAGT-CAGTAGGTTGACAATAAATCCTAGAATAGGATCATCGATA
*
161746 GAAACGTTAGTTTAACAATAAATC
65 GAAACGTTAGGTT-ACAATAAATC
* * * * ** *
161770 CCAGAAAAGGATCATAGATAAAGTCAGTAGGTTGGCAACGAATCCTAGAATAGGATCATCAATAG
1 CTAGAATAGGATCATCGATAAAGTCAGTAGGTTGACAATAAATCCTAGAATAGGATCATCGATAG
* * * * *
161835 ACACGGTATGTTTACAAAAAAGC
66 AAACGTTA-GGTTACAATAAATC
** ** * *
161858 CTAGAATATTA-CAATCGATCGAGAC-GTTAGGTTGACAATAAATCCTAGAATAGGATCAGCGAT
1 CTAGAATAGGATC-ATCGATAAAGTCAG-TAGGTTGACAATAAATCCTAGAATAGGATCATCGAT
*
161921 AGACACAG-TAGGTTGACAATAAATC
64 AGAAAC-GTTAGGTT-ACAATAAATC
* * * *
161946 CTAGAATAGGATCATCGATAAAGACAGTAGGTTGACAATGAATCCCAAAATAGGATCATCGATAG
1 CTAGAATAGGATCATCGATAAAGTCAGTAGGTTGACAATAAATCCTAGAATAGGATCATCGATAG
* * *
162011 ACACGGTAGGTTGACAAAAAATC
66 AAACGTTAGGTT-ACAATAAATC
*
162034 GTAGAATAG
1 CTAGAATAG
162043 CTAGGTTCAC
Statistics
Matches: 364, Mismatches: 66, Indels: 39
0.78 0.14 0.08
Matches are distributed among these distances:
85 1 0.00
86 3 0.01
87 62 0.17
88 223 0.61
89 73 0.20
90 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.25
Consensus pattern (87 bp):
CTAGAATAGGATCATCGATAAAGTCAGTAGGTTGACAATAAATCCTAGAATAGGATCATCGATAG
AAACGTTAGGTTACAATAAATC
Found at i:161930 original size:132 final size:133
Alignment explanation
Indices: 161620--162042 Score: 433
Period size: 132 Copynumber: 3.2 Consensus size: 133
161610 ATAGACATAG
* * * *
161620 TAGGTTGATAATAAATCCTAGAATAGAATCATCGATAAAGACAGTTGGTTGACTATGAATCCTAG
1 TAGGTTGACAATAAATCCTAGAATAGGATCATCGATAAAGACAGTAGGTTGACAATGAATCCTAG
* * * * * *
161685 AATAGGATCATCGATAAAATACGGTAGATTGACAATAAATCCTAAAATAGGATAATCTATAGAAA
66 AATAGGATCATCAATAAAACACGGTAGATTGACAAAAAAGCCTAAAATAGGACAATCGATAGAAA
161750 CGT
131 CGT
* * * * * * * *
161753 TAGTTTAACAATAAATCCCAGAAAAGGATCATAGATAAAGTCAGTAGGTTGGCAACGAATCCTAG
1 TAGGTTGACAATAAATCCTAGAATAGGATCATCGATAAAGACAGTAGGTTGACAATGAATCCTAG
* * * ** * *
161818 AATAGGATCATCAAT-AGACACGGTATG-TTTACAAAAAAGCCTAGAATATTACAATCGATCGAG
66 AATAGGATCATCAATAAAACACGGTA-GATTGACAAAAAAGCCTAAAATAGGACAATCGATAGAA
161881 ACGT
130 ACGT
* * * *
161885 TAGGTTGACAATAAATCCTAGAATAGGATCAGCGATAGACACAGTAGGTTGACAATAAATCCTAG
1 TAGGTTGACAATAAATCCTAGAATAGGATCATCGATAAAGACAGTAGGTTGACAATGAATCCTAG
* * ** * *
161950 AATAGGATCATCGATAAAGACA--GTAGGTTGACAATGAATCCCAAAATAGGATC-ATCGATAGA
66 AATAGGATCATCAATAAA-ACACGGTAGATTGACAAAAAAGCCTAAAATAGGA-CAATCGATAGA
* *
162012 CACGG
129 AACGT
* *
162017 TAGGTTGACAAAAAATCGTAGAATAG
1 TAGGTTGACAATAAATCCTAGAATAG
162043 CTAGGTTCAC
Statistics
Matches: 233, Mismatches: 52, Indels: 11
0.79 0.18 0.04
Matches are distributed among these distances:
131 1 0.00
132 159 0.68
133 70 0.30
134 3 0.01
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (133 bp):
TAGGTTGACAATAAATCCTAGAATAGGATCATCGATAAAGACAGTAGGTTGACAATGAATCCTAG
AATAGGATCATCAATAAAACACGGTAGATTGACAAAAAAGCCTAAAATAGGACAATCGATAGAAA
CGT
Found at i:161959 original size:176 final size:178
Alignment explanation
Indices: 161506--162042 Score: 563
Period size: 176 Copynumber: 3.1 Consensus size: 178
161496 TTATTACCTT
* * * * * *
161506 CTAGAATAGGATGATCCAT-ATAGACGTTAGGGTGATAATAAATCCTAGAATAGGATCATTTATA
1 CTAGAATAGGATCATCGATAAAAGACGTTAGGTTGACAATAAATCCTAGAATAGGATCATCTATA
* * * *
161570 TAGA-AGTTAGGTTG-CAATAAATCCTAGAATAGGATCAGCGATAGACA-T-AGTAGGTTGATAA
66 GAAACAGTTAGGTTGACAATAAATCCTAGAATAGGATCATCGATA-A-AGTCAGTAGGTTGACAA
* * * * * * **
161631 TAAATCCTAGAATAGAATCATCGATAAAGACAGT-TGGTTGACTATGAATC
129 TGAATCCTAGAATAGGATCATCGATAGACACGGTAT-GTTGACAAAAAATC
* * * * *
161681 CTAGAATAGGATCATCGATAAAATACGGTAGATTGACAATAAATCCTAAAATAGGATAATCTATA
1 CTAGAATAGGATCATCGATAAAAGACGTTAGGTTGACAATAAATCCTAGAATAGGATCATCTATA
* * * * * * *
161746 GAAAC-GTTAGTTTAACAATAAATCCCAGAAAAGGATCATAGATAAAGTCAGTAGGTTGGCAACG
66 GAAACAGTTAGGTTGACAATAAATCCTAGAATAGGATCATCGATAAAGTCAGTAGGTTGACAATG
* * *
161810 AATCCTAGAATAGGATCATCAATAGACACGGTATGTTTACAAAAAAGC
131 AATCCTAGAATAGGATCATCGATAGACACGGTATGTTGACAAAAAATC
** ** * *
161858 CTAGAATATTA-CAATCGAT-CGAGACGTTAGGTTGACAATAAATCCTAGAATAGGATCAGCGAT
1 CTAGAATAGGATC-ATCGATAAAAGACGTTAGGTTGACAATAAATCCTAGAATAGGATCATCTAT
* *
161921 AGACACAG-TAGGTTGACAATAAATCCTAGAATAGGATCATCGATAAAGACAGTAGGTTGACAAT
65 AGAAACAGTTAGGTTGACAATAAATCCTAGAATAGGATCATCGATAAAGTCAGTAGGTTGACAAT
* * *
161985 GAATCCCAAAATAGGATCATCGATAGACACGGTAGGTTGACAAAAAATC
130 GAATCCTAGAATAGGATCATCGATAGACACGGTATGTTGACAAAAAATC
*
162034 GTAGAATAG
1 CTAGAATAG
162043 CTAGGTTCAC
Statistics
Matches: 293, Mismatches: 61, Indels: 15
0.79 0.17 0.04
Matches are distributed among these distances:
175 18 0.06
176 186 0.63
177 88 0.30
178 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.25
Consensus pattern (178 bp):
CTAGAATAGGATCATCGATAAAAGACGTTAGGTTGACAATAAATCCTAGAATAGGATCATCTATA
GAAACAGTTAGGTTGACAATAAATCCTAGAATAGGATCATCGATAAAGTCAGTAGGTTGACAATG
AATCCTAGAATAGGATCATCGATAGACACGGTATGTTGACAAAAAATC
Found at i:164749 original size:18 final size:18
Alignment explanation
Indices: 164728--164765 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
164718 GTCTCTGTAT
164728 GTTGTATTGTGTGTTACA
1 GTTGTATTGTGTGTTACA
164746 GTTGTATTGTGTGTTACA
1 GTTGTATTGTGTGTTACA
164764 GT
1 GT
164766 ACGGCAGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.05, G:0.29, T:0.50
Consensus pattern (18 bp):
GTTGTATTGTGTGTTACA
Found at i:166344 original size:381 final size:379
Alignment explanation
Indices: 165642--166408 Score: 1419
Period size: 381 Copynumber: 2.0 Consensus size: 379
165632 AGTCTGCTCC
* *
165642 TAAATCAAGCATTCCCTTACTTCTATATGAACGTGTTTGATGAAATATGGAATGGATAATTAAAA
1 TAAATCAAGCATTCACTTACTTCTATATGAACGTGTTTGATGAAATATGGAATAGATAATTAAAA
*
165707 TAGTAAATTTTTACTCCCATATTTGCAATTGCAACTTCTCGGACATTTACGGCAGAGCTCGGAAA
66 TAGTAAATTTTTACTCCCATATTTGCAATTGCAACTTCTCGGACATTTACGACAGAGCTCGGAAA
165772 AAATTCCGAGCTCTGCCGGAAAGACACGAGAAGTCCCGATTGTGATCTTTTGGTCAATTTGACAA
131 AAATTCCGAGCTCTGCCGGAAAGACACGAGAAGTCCCGATTGTGATCTTTTGGTCAATTTGACAA
165837 CAAACAATCGATTTCAAAAAGTCCCGCCATGCAGTGCTGTCTTACTTCCTCTGTCTGATTACCGA
196 CAAACAATCGATTTCAAAAAGTCCCGCCATGCAGTGCTGTCTTACTTCCTCTGTCTGATTACCGA
*
165902 GAAGTTTCCAATACGATTTATTTCATATCCGAGAAATTTTTGAATAAATTACTTGTTATTTAAGC
261 GAAGTTTCCAATACAATTTATTTCATATCCGAGAAATTTTTGAATAAATTACTTGTTATTTAAGC
*
165967 TATTTAAAAATGAATTAAAACAGATATATGAATGTGTGAAAGTAAAGTGTAGAA
326 TATTTAAAAATAAATTAAAACAGATATATGAATGTGTGAAAGTAAAGTGTAGAA
166021 NTAAATCAAGCATTCACTTACTTCTATATGAACGTGTTTGATGAAATATGGAATAGATAATTAAA
1 -TAAATCAAGCATTCACTTACTTCTATATGAACGTGTTTGATGAAATATGGAATAGATAATTAAA
* * *
166086 ATTGTAAATTTTTACTCCCATATTTGCAATTGCAACTTTTCGGGCATTTACGACAGAGCTCGGAA
65 ATAGTAAATTTTTACTCCCATATTTGCAATTGCAACTTCTCGGACATTTACGACAGAGCTCGG-A
166151 AAAAATTCCGAGCTCTGCCGGAAAGACACGAGAAGTCCCGATTGTGATCTTTTGGTCAATTTGAC
129 AAAAATTCCGAGCTCTGCCGGAAAGACACGAGAAGTCCCGATTGTGATCTTTTGGTCAATTTGAC
*
166216 AAGAAACAATCGATTTCAAAAAGTCCCGCCATGCAGTGCTGTCTTACTTCCTCTGTCTGATTACC
194 AACAAACAATCGATTTCAAAAAGTCCCGCCATGCAGTGCTGTCTTACTTCCTCTGTCTGATTACC
*
166281 GAGAAGTTTCCAATACAATTTATTTCATTTCCGAGAAATTTTTGAATAAATTACTTGTTATTTAA
259 GAGAAGTTTCCAATACAATTTATTTCATATCCGAGAAATTTTTGAATAAATTACTTGTTATTTAA
166346 GCTATTTAAAAATAAATTAAAACAGATATATGAATGTGTGAAAGTAAAGTGTAGAA
324 GCTATTTAAAAATAAATTAAAACAGATATATGAATGTGTGAAAGTAAAGTGTAGAA
166402 -AAATCAA
1 TAAATCAA
166409 TGTTATTTTC
Statistics
Matches: 376, Mismatches: 10, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
379 7 0.02
380 121 0.32
381 248 0.66
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (379 bp):
TAAATCAAGCATTCACTTACTTCTATATGAACGTGTTTGATGAAATATGGAATAGATAATTAAAA
TAGTAAATTTTTACTCCCATATTTGCAATTGCAACTTCTCGGACATTTACGACAGAGCTCGGAAA
AAATTCCGAGCTCTGCCGGAAAGACACGAGAAGTCCCGATTGTGATCTTTTGGTCAATTTGACAA
CAAACAATCGATTTCAAAAAGTCCCGCCATGCAGTGCTGTCTTACTTCCTCTGTCTGATTACCGA
GAAGTTTCCAATACAATTTATTTCATATCCGAGAAATTTTTGAATAAATTACTTGTTATTTAAGC
TATTTAAAAATAAATTAAAACAGATATATGAATGTGTGAAAGTAAAGTGTAGAA
Found at i:179092 original size:2 final size:2
Alignment explanation
Indices: 179085--179120 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
179075 AATTATGTAT
179085 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
179121 ATGAACATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:181806 original size:16 final size:15
Alignment explanation
Indices: 181781--181811 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
181771 GGATGATTTA
181781 TTTTTTATAATAATT
1 TTTTTTATAATAATT
181796 TTTTTTGATAATAATT
1 TTTTTT-ATAATAATT
181812 CAAAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (15 bp):
TTTTTTATAATAATT
Found at i:183980 original size:15 final size:16
Alignment explanation
Indices: 183962--183999 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
183952 CACTCGATGG
183962 CTCGAACTTC-GATCT
1 CTCGAACTTCTGATCT
*
183977 CTCGAAGTTCTTGATCT
1 CTCGAACTTC-TGATCT
183994 CTCGAA
1 CTCGAA
184000 GTGAACTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
17 11 0.55
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (16 bp):
CTCGAACTTCTGATCT
Found at i:185958 original size:4 final size:4
Alignment explanation
Indices: 185949--186090 Score: 230
Period size: 4 Copynumber: 35.0 Consensus size: 4
185939 AATGTTTATA
*
185949 AGAT AGAT AGAT GGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
* * *
185997 AGAT AGAT ACAGAC AGAC AGAC AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT --AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
186047 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
186091 TGATTGATTG
Statistics
Matches: 132, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
4 129 0.98
6 3 0.02
ACGTcount: A:0.49, C:0.03, G:0.25, T:0.23
Consensus pattern (4 bp):
AGAT
Found at i:198124 original size:42 final size:42
Alignment explanation
Indices: 198076--198159 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
198066 ACAATACGTA
*
198076 TATTACGGGGCGCCCGCTCCCGTACAGGACTAA-TACTGGGCC
1 TATTACGGGGCGCCCGCTCCCGTACAGAACTAACTA-TGGGCC
* *
198118 TATTACGGGGCGCTCTCTCCCGTACAGAACTAACTATGGGCC
1 TATTACGGGGCGCCCGCTCCCGTACAGAACTAACTATGGGCC
198160 AACCGTGAGC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 36 0.95
43 2 0.05
ACGTcount: A:0.20, C:0.32, G:0.26, T:0.21
Consensus pattern (42 bp):
TATTACGGGGCGCCCGCTCCCGTACAGAACTAACTATGGGCC
Found at i:216600 original size:7 final size:7
Alignment explanation
Indices: 216585--216651 Score: 80
Period size: 7 Copynumber: 9.6 Consensus size: 7
216575 TTTAGATATT
216585 GAATCTC
1 GAATCTC
*
216592 GAATTTC
1 GAATCTC
216599 GAATCTC
1 GAATCTC
216606 GAATCTC
1 GAATCTC
* *
216613 GTATTTC
1 GAATCTC
216620 GAATCTC
1 GAATCTC
* *
216627 GTATTTC
1 GAATCTC
216634 GAATCTC
1 GAATCTC
*
216641 GAATCTT
1 GAATCTC
216648 GAAT
1 GAAT
216652 GATCCTTCTC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (7 bp):
GAATCTC
Found at i:216610 original size:21 final size:21
Alignment explanation
Indices: 216585--216651 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
216575 TTTAGATATT
216585 GAATCTCGAATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
*
216606 GAATCTCGTATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
* * * *
216627 GTATTTCGAATCTCGAATCTT
1 GAATCTCGAATTTCGAATCTC
216648 GAAT
1 GAAT
216652 GATCCTTCTC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (21 bp):
GAATCTCGAATTTCGAATCTC
Found at i:217424 original size:12 final size:12
Alignment explanation
Indices: 217407--217440 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
217397 TATGTCCTTC
217407 GTCCGTCTGTCT
1 GTCCGTCTGTCT
*
217419 GTCCGTCTGCCT
1 GTCCGTCTGTCT
217431 GTCCGTCTGT
1 GTCCGTCTGT
217441 AAACTTTTCA
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:0.35, G:0.26, T:0.38
Consensus pattern (12 bp):
GTCCGTCTGTCT
Found at i:218828 original size:44 final size:44
Alignment explanation
Indices: 218779--218868 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
218769 TTTAAAGCAG
218779 TTTAAAACATGAATAAATATATCATCCTTATTCTTAAGAACATA
1 TTTAAAACATGAATAAATATATCATCCTTATTCTTAAGAACATA
* * *
218823 TTTAAAACATGGATAAATGTATTATCCTTATTCTTAAGAACATA
1 TTTAAAACATGAATAAATATATCATCCTTATTCTTAAGAACATA
218867 TT
1 TT
218869 ACAGCGAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (44 bp):
TTTAAAACATGAATAAATATATCATCCTTATTCTTAAGAACATA
Found at i:219740 original size:182 final size:180
Alignment explanation
Indices: 219473--219851 Score: 555
Period size: 182 Copynumber: 2.1 Consensus size: 180
219463 AATATTGCAT
* * * * * * *
219473 ATATTGCATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTT
1 ATATTGCATATAGGGGACCCCCATTGAACGGAAAACTCATCCTACAGTTCTCAAGATAGGAACTT
*
219538 ATTCTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATATT-CTAGGATTTTGATTTCCAA
66 ATTCTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGAATTTTGATTTCCAA
* * *
219602 TATTTA-TGGAAAAAATACCAGCTTTTGAACTTTAGTTAGTCATTTTTGGCAAA
131 TAATTATTGAAAAAAATACCAGCTTTTGAAC-TTAGTCA-T--TTTTTGGCAAA
*
219655 ATATTGCATATAGGGGACCCCCATTGAACGGAAAACTCATCCTACAGTTCTCAAGATAGGATCTT
1 ATATTGCATATAGGGGACCCCCATTGAACGGAAAACTCATCCTACAGTTCTCAAGATAGGAACTT
* * *
219720 GTTCTTTTGCAGATCAATTGTACATATATCAGAGGTGTGGATATTGCTAGAATTTTGATTTCCGA
66 ATTCTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGAATTTTGATTTCCAA
219785 TAATTATTGAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAA
131 TAATTATTGAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAA
219835 ATATTGAGCATATAGGG
1 ATATT--GCATATAGGG
219852 TACTCCATTT
Statistics
Matches: 178, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
180 16 0.09
182 111 0.62
183 28 0.16
184 23 0.13
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (180 bp):
ATATTGCATATAGGGGACCCCCATTGAACGGAAAACTCATCCTACAGTTCTCAAGATAGGAACTT
ATTCTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGAATTTTGATTTCCAA
TAATTATTGAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAA
Found at i:225746 original size:17 final size:17
Alignment explanation
Indices: 225721--225754 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
225711 TCTAAGAAAA
225721 AATTGTTCAAAGTGCGT
1 AATTGTTCAAAGTGCGT
*
225738 AATTTTTCAAAGTGCGT
1 AATTGTTCAAAGTGCGT
225755 TGTAACAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (17 bp):
AATTGTTCAAAGTGCGT
Found at i:225990 original size:16 final size:16
Alignment explanation
Indices: 225969--226007 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
225959 TGTTGTCGGC
* *
225969 TTGACAGGTTAACTGG
1 TTGACAGGTCAACGGG
*
225985 TTGACAGGTCGACGGG
1 TTGACAGGTCAACGGG
226001 TTGACAG
1 TTGACAG
226008 ACTGACAGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.23, C:0.15, G:0.36, T:0.26
Consensus pattern (16 bp):
TTGACAGGTCAACGGG
Found at i:226032 original size:24 final size:24
Alignment explanation
Indices: 225986--226032 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
225976 GTTAACTGGT
***
225986 TGACAGGTCGACGGGTTGACAGAC
1 TGACAGGTCGACAAATTGACAGAC
*
226010 TGACAGGTCGACAAATTGCCAGA
1 TGACAGGTCGACAAATTGACAGA
226033 TGGTTGGCAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.21, G:0.32, T:0.17
Consensus pattern (24 bp):
TGACAGGTCGACAAATTGACAGAC
Found at i:234377 original size:12 final size:12
Alignment explanation
Indices: 234360--234412 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
234350 CTCGTTTGCA
234360 ATTTCTTCTTTG
1 ATTTCTTCTTTG
* *
234372 ATTTCTGCTTTA
1 ATTTCTTCTTTG
*
234384 ATTTCCTCTTTG
1 ATTTCTTCTTTG
*
234396 ATTTCTTCTTTT
1 ATTTCTTCTTTG
234408 ATTTC
1 ATTTC
234413 AGTTTTTATC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.11, C:0.19, G:0.06, T:0.64
Consensus pattern (12 bp):
ATTTCTTCTTTG
Found at i:234387 original size:24 final size:24
Alignment explanation
Indices: 234359--234412 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
234349 ACTCGTTTGC
*
234359 AATTTCTTCTTTGATTTCTGCTTT
1 AATTTCCTCTTTGATTTCTGCTTT
*
234383 AATTTCCTCTTTGATTTCTTCTTT
1 AATTTCCTCTTTGATTTCTGCTTT
*
234407 TATTTC
1 AATTTC
234413 AGTTTTTATC
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:0.13, C:0.19, G:0.06, T:0.63
Consensus pattern (24 bp):
AATTTCCTCTTTGATTTCTGCTTT
Found at i:243441 original size:22 final size:21
Alignment explanation
Indices: 243416--243464 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
243406 ATTTGGGTCC
243416 ACTCGGTGTTAACTATGGGTTT
1 ACTCGG-GTTAACTATGGGTTT
* *
243438 ACTCTGGGTTTACTTTGGGTTT
1 ACTC-GGGTTAACTATGGGTTT
243460 ACTCG
1 ACTCG
243465 AGAATTGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 21 0.88
23 2 0.08
ACGTcount: A:0.14, C:0.16, G:0.27, T:0.43
Consensus pattern (21 bp):
ACTCGGGTTAACTATGGGTTT
Found at i:243447 original size:11 final size:11
Alignment explanation
Indices: 243431--243463 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
243421 GTGTTAACTA
243431 TGGGTTTACTC
1 TGGGTTTACTC
*
243442 TGGGTTTACTT
1 TGGGTTTACTC
243453 TGGGTTTACTC
1 TGGGTTTACTC
243464 GAGAATTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.15, G:0.27, T:0.48
Consensus pattern (11 bp):
TGGGTTTACTC
Found at i:243634 original size:11 final size:11
Alignment explanation
Indices: 243616--243655 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
243606 CTGTGTCCAA
243616 TCTGGGTTTAC
1 TCTGGGTTTAC
243627 T-TGTGGTTTAC
1 TCTG-GGTTTAC
243638 TCTGGGTTTAC
1 TCTGGGTTTAC
243649 TCTGGGT
1 TCTGGGT
243656 CCACTCTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 2 0.07
11 23 0.85
12 2 0.07
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.47
Consensus pattern (11 bp):
TCTGGGTTTAC
Found at i:243661 original size:22 final size:22
Alignment explanation
Indices: 243604--243662 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
243594 GAGGTTTACT
* *
243604 CTCTGTGTCCAATCTGGGTTTA
1 CTCTGGGTCCACTCTGGGTTTA
**
243626 CT-TGTGGTTTACTCTGGGTTTA
1 CTCTG-GGTCCACTCTGGGTTTA
243648 CTCTGGGTCCACTCT
1 CTCTGGGTCCACTCT
243663 AGTAAACCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
21 2 0.07
22 25 0.86
23 2 0.07
ACGTcount: A:0.10, C:0.24, G:0.24, T:0.42
Consensus pattern (22 bp):
CTCTGGGTCCACTCTGGGTTTA
Found at i:243690 original size:13 final size:13
Alignment explanation
Indices: 243663--243697 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
243653 GGTCCACTCT
243663 AGTAAACCC--AA
1 AGTAAACCCAGAA
243674 AGTAAACCCAGAA
1 AGTAAACCCAGAA
243687 AGTAAACCCAG
1 AGTAAACCCAG
243698 GGTTTATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 9 0.41
13 13 0.59
ACGTcount: A:0.51, C:0.26, G:0.14, T:0.09
Consensus pattern (13 bp):
AGTAAACCCAGAA
Found at i:246821 original size:2 final size:2
Alignment explanation
Indices: 246814--246863 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
246804 TGTATTCAAC
246814 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
246856 AG AG AG AG
1 AG AG AG AG
246864 CGTAAAATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:246938 original size:14 final size:15
Alignment explanation
Indices: 246919--246947 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
246909 ATGGTTGGAC
246919 AGTGCATTC-TTTTT
1 AGTGCATTCATTTTT
246933 AGTGCATTCATTTTT
1 AGTGCATTCATTTTT
246948 GCTTTTTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.55
Consensus pattern (15 bp):
AGTGCATTCATTTTT
Found at i:258180 original size:168 final size:167
Alignment explanation
Indices: 257949--258735 Score: 986
Period size: 168 Copynumber: 4.7 Consensus size: 167
257939 CTTCATGTCC
* * * * ** *
257949 TGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAAAGGAG-ATTGTGGATATCATAA
1 TGAACCCCTGACCCAGGGGTCATAAATTTCACAATTTA-GTAGAGG-GCCTCATGGACATCATAA
* * * ** ** * * * * *
258013 CCATGTATTCAGTTTTTTGCCCACATCTGTGGGAGTAGAGAAGAAGATTTTTTAAGATTTAA-AT
64 TCATGCATTTAGTTTTTAACAAATATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATA-
258077 CATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCA
128 CATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCA
* * ** *
258117 TGAACACCTAACAAAGGGGTCATAAATTTCACAATTTTAGTAGAGAGCCTCATGGACATCATAAT
1 TGAACCCCTGACCCAGGGGTCATAAATTTCACAA-TTTAGTAGAGGGCCTCATGGACATCATAAT
258182 CATGCATTTAGTTTTTAACAAATATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
65 CATGCATTTAGTTTTTAACAAATATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
* * *
258247 TTTTTACTATTTGGCCATATCGGCCCCACCCTAGAGCC
130 TTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCA
* * * * *
258285 TGAACCCCTGACCGAGGGGTCATGAATTTCACAATTTAGGATGAGGGCTTCATGGACATCATTAT
1 TGAACCCCTGACCCAGGGGTCATAAATTTCACAATTTAGTA-GAGGGCCTCATGGACATCATAAT
* * *
258350 CATGCATTTAGGTTTTAACAAATATATATGATAGTAGAAAAGAAGATTTTCTAAGATTTAATACA
65 CATGCATTTAGTTTTTAACAAATATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
* *
258415 TTTTTACTATATGGCCATATTGGTCCCACCCTAGAGCC
130 TTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCA
* * * *
258453 TGAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCTTCATGGACATCATAAT
1 TGAACCCCTGACCCAGGGGTCATAAATTTCACAATTTA-GTAGAGGGCCTCATGGACATCATAAT
258518 CATGCATTTAGTTTTTAACAAATATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
65 CATGCATTTAGTTTTTAACAAATATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
* *
258583 TTTTTACTATATGGCCATATTTGCCGCACCCTAGAGCCA
130 TTTTTACTATATGGCCATATTGGCCCCACCCTAGAG-CA
* * *
258622 -GAACCCCTGACCCAGGGGCCATAAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATAAC
1 TGAACCCCTGACCCAGGGGTCATAAATTTCACAA-TTTAGTAGAGGGCCTCATGGACATCATAAT
* * ** ** * * *
258686 CATGAATTCAGTTTTTTCCTCATATGTGTGGAAGTAGAGAAGAAGATTTT
65 CATGCATTTAGTTTTTAACAAATATATATGGTAGTAGAGAAGAAGATTTT
258736 TGAAAATTTG
Statistics
Matches: 543, Mismatches: 69, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
167 7 0.01
168 525 0.97
169 11 0.02
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (167 bp):
TGAACCCCTGACCCAGGGGTCATAAATTTCACAATTTAGTAGAGGGCCTCATGGACATCATAATC
ATGCATTTAGTTTTTAACAAATATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACAT
TTTTACTATATGGCCATATTGGCCCCACCCTAGAGCA
Found at i:258317 original size:336 final size:334
Alignment explanation
Indices: 257947--258736 Score: 1095
Period size: 336 Copynumber: 2.3 Consensus size: 334
257937 CCCTTCATGT
* * * *
257947 CCTGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAAAGGAGATTGTGGATATCATA
1 CCTGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAGAGG-GCTTATGGACATCATA
* * * *
258012 ACCATGTATTCAGTTTTTTGCCCACATCTGTGGGAGTAGAGAAGAAGATTTTTTAAGATTTAA-A
65 ACCATGAATTCAGTTTTTT-CCCATATATGTGGAAGTAGAGAAGAAGATTTTTTAAGATTTAATA
258076 TCATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCATGAA-CACCTAACAAAGGGGTCAT
129 -CATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCATGAATC-CCTAACAAAGGGGTCAT
*
258140 AAATTTCACAATTTTA-GTAGAGAGCCTCATGGACATCATAATCATGCATTTAGTTTTTAACAAA
192 AAATTTCACAA-TTTAGGAAGAGAGCCTCATGGACATCATAATCATGCATTTAGTTTTTAACAAA
*
258204 TATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATCG
256 TATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATCG
258269 GCCCCACCCTAGAG
321 GCCCCACCCTAGAG
* *
258283 CCTGAACCCCTGACCGAGGGGTCATGAATTTCACAATTTAGG-ATGAGGGCTTCATGGACATCAT
1 CCTGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTA-GAGGGCTT-ATGGACATCAT
* * * * ** ** * * *
258347 TATCATGCATTTAGGTTTTAACAAATATATAT-GATAGTAGAAAAGAAGATTTTCTAAGATTTAA
64 AACCATGAATTCA-GTTTTTTCCCATATATGTGGA-AGTAGAGAAGAAGATTTTTTAAGATTTAA
* * * **
258411 TACATTTTTACTATATGGCCATATTGGTCCCACCCTAGAGCCTGAATCCCTGACCCAGGGGTCAT
127 TACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCATGAATCCCTAACAAAGGGGTCAT
* * *
258476 GAATTTCACAATTTAGGAAGAGGGCTTCATGGACATCATAATCATGCATTTAGTTTTTAACAAAT
192 AAATTTCACAATTTAGGAAGAGAGCCTCATGGACATCATAATCATGCATTTAGTTTTTAACAAAT
**
258541 ATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTTG
257 ATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATCGG
*
258606 CCGCACCCTAGAG
322 CCCCACCCTAGAG
* * * *
258619 CCAGAACCCCTGACCCAGGGGCCATAAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATA
1 CCTGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAGAGGG-CTTATGGACATCATA
*
258684 ACCATGAATTCAGTTTTTTCCTCATATGTGTGGAAGTAGAGAAGAAGATTTTT
65 ACCATGAATTCAGTTTTTTCC-CATATATGTGGAAGTAGAGAAGAAGATTTTT
258737 GAAAATTTGG
Statistics
Matches: 392, Mismatches: 51, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
335 15 0.04
336 365 0.93
337 12 0.03
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (334 bp):
CCTGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAGAGGGCTTATGGACATCATAA
CCATGAATTCAGTTTTTTCCCATATATGTGGAAGTAGAGAAGAAGATTTTTTAAGATTTAATACA
TTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCATGAATCCCTAACAAAGGGGTCATAAAT
TTCACAATTTAGGAAGAGAGCCTCATGGACATCATAATCATGCATTTAGTTTTTAACAAATATAT
ATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATCGGCCCC
ACCCTAGAG
Found at i:267452 original size:20 final size:20
Alignment explanation
Indices: 267427--267464 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
267417 CATATATAAT
267427 CTACTAGTTATCAACAATCC
1 CTACTAGTTATCAACAATCC
*
267447 CTACTAGTTTTCAACAAT
1 CTACTAGTTATCAACAAT
267465 GTCCAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.34
Consensus pattern (20 bp):
CTACTAGTTATCAACAATCC
Found at i:268374 original size:2 final size:2
Alignment explanation
Indices: 268369--268401 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
268359 AAAAGTAGGA
268369 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
268402 TATATTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:270133 original size:2 final size:2
Alignment explanation
Indices: 270128--270154 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
270118 AATATATATA
270128 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
270155 ATTTATTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:273587 original size:2 final size:2
Alignment explanation
Indices: 273580--273617 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
273570 CTGAAATAAA
273580 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
273618 ATATGCTTTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:277749 original size:14 final size:14
Alignment explanation
Indices: 277732--277759 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
277722 GCACTATATA
277732 AATGTTATAATAAT
1 AATGTTATAATAAT
277746 AATGTTATAATAAT
1 AATGTTATAATAAT
277760 CTATTAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
AATGTTATAATAAT
Found at i:283602 original size:2 final size:2
Alignment explanation
Indices: 283595--283631 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
283585 ATATCCAGAG
283595 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
283632 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:283649 original size:2 final size:2
Alignment explanation
Indices: 283644--283674 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
283634 ATATATATAT
283644 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
283675 AGTCATATCC
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:289444 original size:13 final size:14
Alignment explanation
Indices: 289426--289461 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
289416 GCCACGAAAT
289426 GGAGGGGGG-GGGG
1 GGAGGGGGGTGGGG
289439 GGAGGGGGGTGGGG
1 GGAGGGGGGTGGGG
289453 GG-GGGGGGT
1 GGAGGGGGGT
289462 AAATTGGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.06, C:0.00, G:0.89, T:0.06
Consensus pattern (14 bp):
GGAGGGGGGTGGGG
Found at i:290453 original size:14 final size:14
Alignment explanation
Indices: 290436--290470 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
290426 CTGCTCAGAT
*
290436 TGTTTACCACTGTG
1 TGTTCACCACTGTG
290450 TGTTCACCACTGTG
1 TGTTCACCACTGTG
290464 TGTTCAC
1 TGTTCAC
290471 ATTGTTTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (14 bp):
TGTTCACCACTGTG
Found at i:298218 original size:13 final size:13
Alignment explanation
Indices: 298200--298224 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
298190 ATTAAAGTCC
298200 AGTCATTGATGAG
1 AGTCATTGATGAG
298213 AGTCATTGATGA
1 AGTCATTGATGA
298225 CTCCCCCTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (13 bp):
AGTCATTGATGAG
Found at i:298533 original size:2 final size:2
Alignment explanation
Indices: 298526--298568 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
298516 CTTTTTAAAA
298526 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
298568 T
1 T
298569 NNNNNNNNNN
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:298595 original size:2 final size:2
Alignment explanation
Indices: 298588--298653 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
298578 NNNNNNNNNN
298588 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
298630 CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT
298654 TCCTAAACTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:302501 original size:190 final size:189
Alignment explanation
Indices: 302168--302549 Score: 746
Period size: 190 Copynumber: 2.0 Consensus size: 189
302158 AAATAATCGC
*
302168 GATCGCGGTGAATAAGTCCTTCGGTGTTTATTATGAGCCGGTCATTATGTCGTTGTCCTCCCTCT
1 GATCGCGGTCAATAAGTCCTTCGGTGTTTATTATGAGCCGGTCATTATGTCGTTGTCCTCCCTCT
302233 GTTGTCGCCTATTTAAGACAATTTACACAAAACACAGTCTTTTGTATAAAGTTCTAATCCGACAT
66 GTTGTCGCCTATTTAAGACAATTTACACAAAACACAGTCTTTTGTATAAAGTTCTAATCCGACAT
302298 AATTATCCCTGATATATAAAAACACCGGCAGTATCAATACAAATTAAGCCTCGTTCTGA
131 AATTATCCCTGATATATAAAAACACCGGCAGTATCAATACAAATTAAGCCTCGTTCTGA
302357 GATNCGCGGTCAATAAGTCCTTCGGTGTTTATTATGAGCCGGTCATTATGTCGTTGTCCTCCCTC
1 GAT-CGCGGTCAATAAGTCCTTCGGTGTTTATTATGAGCCGGTCATTATGTCGTTGTCCTCCCTC
302422 TGTTGTCGCCTATTTAAGACAATTTACACAAAACACAGTCTTTTGTATAAAGTTCTAATCCGACA
65 TGTTGTCGCCTATTTAAGACAATTTACACAAAACACAGTCTTTTGTATAAAGTTCTAATCCGACA
302487 TAATTATCCCTGATATATAAAAACACCGGCAGTATCAATACAAATTAAGCCTCGTTCTGA
130 TAATTATCCCTGATATATAAAAACACCGGCAGTATCAATACAAATTAAGCCTCGTTCTGA
302547 GAT
1 GAT
302550 TGCACCTTTC
Statistics
Matches: 191, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
189 3 0.02
190 188 0.98
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (189 bp):
GATCGCGGTCAATAAGTCCTTCGGTGTTTATTATGAGCCGGTCATTATGTCGTTGTCCTCCCTCT
GTTGTCGCCTATTTAAGACAATTTACACAAAACACAGTCTTTTGTATAAAGTTCTAATCCGACAT
AATTATCCCTGATATATAAAAACACCGGCAGTATCAATACAAATTAAGCCTCGTTCTGA
Found at i:303909 original size:16 final size:16
Alignment explanation
Indices: 303882--303927 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
303872 ATACTGCGAT
303882 GAAAACAAAAATGTGAA
1 GAAAA-AAAAATGTGAA
303899 GAAAAAAAAATGTGAA
1 GAAAAAAAAATGTGAA
303915 -AAATAAGAAAATG
1 GAAA-AA-AAAATG
303928 AAATACTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 3 0.11
16 13 0.48
17 11 0.41
ACGTcount: A:0.67, C:0.02, G:0.17, T:0.13
Consensus pattern (16 bp):
GAAAAAAAAATGTGAA
Found at i:311294 original size:4 final size:4
Alignment explanation
Indices: 311285--311330 Score: 83
Period size: 4 Copynumber: 11.5 Consensus size: 4
311275 GTTACCCTGT
*
311285 TCCG TCCG TCCG TCCG TCCG TCTG TCCG TCCG TCCG TCCG TCCG TC
1 TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCCG TC
311331 TGTCACGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.00, C:0.48, G:0.24, T:0.28
Consensus pattern (4 bp):
TCCG
Found at i:311976 original size:162 final size:161
Alignment explanation
Indices: 311808--312250 Score: 545
Period size: 163 Copynumber: 2.7 Consensus size: 161
311798 GTTTTTTTGC
* * * * ** * *
311808 AAAAAAAAATATGGTTCCCAGAACTCCTCTTACAACTTT-TGGAGTAGCTACGTCATCTCTTGGG
1 AAAAAAAAACATAGATCCAAGAACTCCTCTTATGA-TTTATGGA-TAGC-ACATCATATCTTGGG
* * *
311872 ATATAATTGGGGCTGTCCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATTTCATCCAGGGAG
63 ATATGATAGGGACTGTCCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATTTCATCCAGGGAG
*
311937 TCAAATAGTAGCAGAAAATTGACGTTTATCACTA
128 TCAAAAAGTAGCAGAAAATTGACGTTTATCACTA
* *
311971 AAAAAACAAACATTGATCCAAGAGCTCCTCTTATGATTTAATGGATAG-ACAATCATATCTTGGG
1 AAAAAA-AAACATAGATCCAAGAACTCCTCTTATGATTT-ATGGATAGCAC-ATCATATCTTGGG
* * *
312035 ATATGATAGGGACTGTTCTATAGATGTGCAGTAAGGTTTTCAAAATTTAAATTTCATCCAGGGAG
63 ATATGATAGGGACTGTCCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATTTCATCCAGGGAG
312100 TCAAAAAGTAGCAGAAAATTGACGTTTATCACT-
128 TCAAAAAGTAGCAGAAAATTGACGTTTATCACTA
** * *
312133 TCAAAAAAACATAGATCCTAGAACTCCTTTTATGATTTAATGGATAGACACATCATATCTTGGGA
1 AAAAAAAAACATAGATCCAAGAACTCCTCTTATGATTT-ATGGATAG-CACATCATATCTTGGGA
* * *
312198 TATGATAGGAACTGTTCC-ATAGATGTGCATTACGGTTTTGAAAAA-TTAAATTT
64 TATGATAGGGACTG-TCCTATAGATGTGCAATAAGGTTTT-AAAAATTTAAATTT
312251 AACCCTGAGG
Statistics
Matches: 245, Mismatches: 27, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
161 37 0.15
162 60 0.24
163 119 0.49
164 25 0.10
165 4 0.02
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (161 bp):
AAAAAAAAACATAGATCCAAGAACTCCTCTTATGATTTATGGATAGCACATCATATCTTGGGATA
TGATAGGGACTGTCCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATTTCATCCAGGGAGTCA
AAAAGTAGCAGAAAATTGACGTTTATCACTA
Found at i:312063 original size:163 final size:162
Alignment explanation
Indices: 311860--312250 Score: 579
Period size: 163 Copynumber: 2.4 Consensus size: 162
311850 AGTAGCTACG
* * * * *
311860 TCATCTCTTGGGATATAATTGGGGCTGTCCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATT
1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATT
* *
311925 TCATCCAGGGAGTCAAATAGTAGCAGAAAATTGACGTTTATCACTAAAAAAACAAACATTGATCC
66 TCATCCAGGGAGTCAAAAAGTAGCAGAAAATTGACGTTTATCACT-AAAAAA-AAACATAGATCC
*
311990 AAGAGCTCCTCTTATGATTTAATGGATAGACA-A
129 AAGAACTCCTCTTATGATTTAATGGATAGACACA
* *
312023 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAGTAAGGTTTTCAAAATTTAAATT
1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATT
** *
312088 TCATCCAGGGAGTCAAAAAGTAGCAGAAAATTGACGTTTATCACTTCAAAAAAACATAGATCCTA
66 TCATCCAGGGAGTCAAAAAGTAGCAGAAAATTGACGTTTATCACTAAAAAAAAACATAGATCCAA
*
312153 GAACTCCTTTTATGATTTAATGGATAGACACA
131 GAACTCCTCTTATGATTTAATGGATAGACACA
* * * *
312185 TCATATCTTGGGATATGATAGGAACTGTTCCATAGATGTGCATTACGGTTTTGAAAAA-TTAAAT
1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTT-AAAAATTTAAAT
312249 TT
65 TT
312251 AACCCTGAGG
Statistics
Matches: 207, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
161 40 0.19
162 61 0.29
163 106 0.51
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (162 bp):
TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATT
TCATCCAGGGAGTCAAAAAGTAGCAGAAAATTGACGTTTATCACTAAAAAAAAACATAGATCCAA
GAACTCCTCTTATGATTTAATGGATAGACACA
Found at i:312446 original size:135 final size:135
Alignment explanation
Indices: 312298--312596 Score: 392
Period size: 134 Copynumber: 2.2 Consensus size: 135
312288 GATGCCCTTT
* *
312298 AAGGATCAAGAATATATATGGTTAAGGGGTGGGGATCTCAACCGTTTTCG-AGATATT-CGTGCA
1 AAGGAACAAGAATATATATGGTTAAGGGGTGGGGATCTCAACCGTTTT-GAAGATATTAAG-GCA
* * * * *
312361 CTTCCTGTTCAAGGGGGGTCATGACCACCCCCGGGGCCCATGACCTACATACCGTTTGATGCCCC
64 CTTCCTGTTCAA-GGGGGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTTGATGCCCC
312426 TTGACA-C
128 TTGACATC
* *
312433 AAGGAACAAGAATATATATGGTTTAA-GGGTGGGGATCTCAACTGTTTTGAAGATATTAAGGGAC
1 AAGGAACAAGAATATATATGG-TTAAGGGGTGGGGATCTCAACCGTTTTGAAGATATTAAGGCAC
* **
312497 TTGCTGTTTGAGGGGGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTTGATGCCCCTT
65 TTCCTGTTCAAGGGGGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTTGATGCCCCTT
312562 GACATC
130 GACATC
* * *
312568 -AGAAACATGAATATATATGGTTTAGGGGT
1 AAGGAACAAGAATATATATGGTTAAGGGGT
312597 CATGATTATA
Statistics
Matches: 144, Mismatches: 15, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
133 3 0.02
134 76 0.53
135 60 0.42
136 5 0.03
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.26
Consensus pattern (135 bp):
AAGGAACAAGAATATATATGGTTAAGGGGTGGGGATCTCAACCGTTTTGAAGATATTAAGGCACT
TCCTGTTCAAGGGGGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTTGATGCCCCTTG
ACATC
Found at i:317421 original size:1 final size:1
Alignment explanation
Indices: 317415--317440 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
317405 AATTTGGAAA
317415 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
317441 CCATTTGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:321917 original size:18 final size:18
Alignment explanation
Indices: 321896--321934 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
321886 ATTAGAGTAC
321896 TACAGAATATTTACATTG
1 TACAGAATATTTACATTG
321914 TACAGAATATTTACATTG
1 TACAGAATATTTACATTG
321932 TAC
1 TAC
321935 TAATCGCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (18 bp):
TACAGAATATTTACATTG
Found at i:323182 original size:20 final size:22
Alignment explanation
Indices: 323143--323183 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
323133 CTTATAAGAC
*
323143 ATTGTATGATTTTTGTTTTCTA
1 ATTGTATGATTTTCGTTTTCTA
323165 ATTGTAT-A-TTTCGTTTTCT
1 ATTGTATGATTTTCGTTTTCT
323184 CAGATCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 1 0.06
22 7 0.39
ACGTcount: A:0.17, C:0.07, G:0.12, T:0.63
Consensus pattern (22 bp):
ATTGTATGATTTTCGTTTTCTA
Found at i:338526 original size:12 final size:12
Alignment explanation
Indices: 338509--338535 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
338499 TATTGTTCCA
338509 AAAAAAAAAAAT
1 AAAAAAAAAAAT
338521 AAAAAAAAAAAT
1 AAAAAAAAAAAT
338533 AAA
1 AAA
338536 TAATTTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (12 bp):
AAAAAAAAAAAT
Found at i:338529 original size:16 final size:16
Alignment explanation
Indices: 338508--338538 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
338498 GTATTGTTCC
338508 AAAAAAAAAAAATAAA
1 AAAAAAAAAAAATAAA
*
338524 AAAAAAAATAAATAA
1 AAAAAAAAAAAATAA
338539 TTTTAGTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (16 bp):
AAAAAAAAAAAATAAA
Found at i:341958 original size:21 final size:20
Alignment explanation
Indices: 341932--341977 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
341922 GTCGTTGTCT
*
341932 TTGTCTTTGCTGTTGTTATCG
1 TTGTCTTT-CTGTTGTTATCA
341953 TTGTC--TCTGTTGTTATCA
1 TTGTCTTTCTGTTGTTATCA
341971 TTGTCTT
1 TTGTCTT
341978 AATGTTGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 16 0.73
19 1 0.05
21 5 0.23
ACGTcount: A:0.07, C:0.15, G:0.20, T:0.59
Consensus pattern (20 bp):
TTGTCTTTCTGTTGTTATCA
Found at i:341962 original size:18 final size:18
Alignment explanation
Indices: 341941--341976 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
341931 TTTGTCTTTG
*
341941 CTGTTGTTATCGTTGTCT
1 CTGTTGTTATCATTGTCT
341959 CTGTTGTTATCATTGTCT
1 CTGTTGTTATCATTGTCT
341977 TAATGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.17, G:0.19, T:0.56
Consensus pattern (18 bp):
CTGTTGTTATCATTGTCT
Found at i:342099 original size:83 final size:82
Alignment explanation
Indices: 341913--342169 Score: 281
Period size: 83 Copynumber: 3.1 Consensus size: 82
341903 CCTTGTTGAT
* * * * * *
341913 GTTGTTGTTGTCGTTGTCTTTGTCTTTGCTGTTGTTATCGTTGTCTCTGTTGTTATCATTG-TC-
1 GTTGTTGTTGTCGTTGTCTTTGTCTGTACTGTTGTTATAGTTGTCTCTGATGTTGTTATTGTTCT
*
341976 TTAATGTTGATATTCTA
66 TTAATGTTGTTATTCTA
* * *
341993 GTTGTTTTTGTCGTTGTCATTGTCTGT-CT-TATGGTTATAGTTGTCTTTGATGTTGTTATTGTT
1 GTTGTTGTTGTCGTTGTCTTTGTCTGTACTGT-T-GTTATAGTTGTCTCTGATGTTGTTATTGTT
*
342056 CTATTAATGATGTTATTCTA
64 CT-TTAATGTTGTTATTCTA
* * * * * *
342076 GGTGTTGTTGTCGTGGTCTTTGTCTGTACTGTTGTTAAAGCTGTCTCTGATGTTGTTACTGTTGT
1 GTTGTTGTTGTCGTTGTCTTTGTCTGTACTGTTGTTATAGTTGTCTCTGATGTTGTTATTGTTCT
342141 CTTAATGTTGTTA-TCGTA
66 -TTAATGTTGTTATTC-TA
342159 GTTGTTGTTGT
1 GTTGTTGTTGT
342170 TGTAACATCA
Statistics
Matches: 147, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 3 0.02
80 47 0.32
81 2 0.01
82 2 0.01
83 88 0.60
84 3 0.02
85 1 0.01
ACGTcount: A:0.12, C:0.11, G:0.23, T:0.54
Consensus pattern (82 bp):
GTTGTTGTTGTCGTTGTCTTTGTCTGTACTGTTGTTATAGTTGTCTCTGATGTTGTTATTGTTCT
TTAATGTTGTTATTCTA
Found at i:346258 original size:2 final size:2
Alignment explanation
Indices: 346251--346277 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
346241 AAAGAAAGAT
346251 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
346278 TTGAAAGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:348249 original size:18 final size:19
Alignment explanation
Indices: 348213--348250 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
348203 ATTCGTTGAC
*
348213 AAAAAAAAAAGAAATTAAT
1 AAAAAAAAAAGAAAGTAAT
*
348232 AAAAATAAAAG-AAGTAAT
1 AAAAAAAAAAGAAAGTAAT
348250 A
1 A
348251 TTCTTCGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (19 bp):
AAAAAAAAAAGAAAGTAAT
Found at i:351310 original size:83 final size:83
Alignment explanation
Indices: 351169--351338 Score: 304
Period size: 83 Copynumber: 2.0 Consensus size: 83
351159 TCTGTACAGT
* *
351169 AGATGTACAATAGGTTTACAGTAGTGTAGAGTGATTGCACAGTAGATATCAGATGATGTCAGTCA
1 AGATGTACAATAGGTTTACAGTAGTGTAGAGTGATTGCACAGTAAATATCAGACGATGTCAGTCA
351234 ATTCTCGGGAATATCAGC
66 ATTCTCGGGAATATCAGC
351252 AGATGTACAATAGGTTTACAGTAGTGTAGAGTGATTGCACAGTAAATATCAGACGATGTCAGTCA
1 AGATGTACAATAGGTTTACAGTAGTGTAGAGTGATTGCACAGTAAATATCAGACGATGTCAGTCA
* *
351317 ATTTTCGGGAATATCAGT
66 ATTCTCGGGAATATCAGC
351335 AGAT
1 AGAT
351339 TTTGAATTAA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (83 bp):
AGATGTACAATAGGTTTACAGTAGTGTAGAGTGATTGCACAGTAAATATCAGACGATGTCAGTCA
ATTCTCGGGAATATCAGC
Found at i:352097 original size:4 final size:4
Alignment explanation
Indices: 352090--352131 Score: 57
Period size: 4 Copynumber: 10.2 Consensus size: 4
352080 TAGAAAAAAA
* *
352090 AAAC AAAC AAAGC AAAC AAAC AAAC AAGC AAAC AATC AAAC A
1 AAAC AAAC AAA-C AAAC AAAC AAAC AAAC AAAC AAAC AAAC A
352132 TTTTCAACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 29 0.88
5 4 0.12
ACGTcount: A:0.69, C:0.24, G:0.05, T:0.02
Consensus pattern (4 bp):
AAAC
Found at i:352120 original size:16 final size:16
Alignment explanation
Indices: 352090--352131 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
352080 TAGAAAAAAA
352090 AAACAAACAAAGCAAAC
1 AAACAAAC-AAGCAAAC
352107 AAACAAACAAGCAAAC
1 AAACAAACAAGCAAAC
*
352123 AATCAAACA
1 AAACAAACA
352132 TTTTCAACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.69, C:0.24, G:0.05, T:0.02
Consensus pattern (16 bp):
AAACAAACAAGCAAAC
Found at i:359064 original size:1 final size:1
Alignment explanation
Indices: 359058--359093 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
359048 AATACTGTGT
359058 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
359094 CGAGAAGACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:366418 original size:154 final size:153
Alignment explanation
Indices: 366201--366508 Score: 607
Period size: 154 Copynumber: 2.0 Consensus size: 153
366191 TTGCAAAAGA
366201 TCATGAACCGTGTATAATGCACCTGATATTTACCTTTTTACGAAGTATGATTAAAGGTCACTGTG
1 TCATGAACCGTGTATAATGCACCTGATATTTACCTTTTTACGAAGTATGATTAAAGGTCACTGTG
366266 ACGCCTAATGTAGATACCAGCGATGAATAAAAATACCATTCATAAACTTTGATTCATGATCTTCT
66 ACGCCTAATGTAGATACCAGCGATGAATAAAAATACCATTCATAAACTTTGATTCATGATCTTCT
366331 CCATCCAGTCTATGCATTAACAC
131 CCATCCAGTCTATGCATTAACAC
366354 TNCATGAACCGTGTATAATGCACCTGATATTTACCTTTTTACGAAGTATGATTAAAGGTCACTGT
1 T-CATGAACCGTGTATAATGCACCTGATATTTACCTTTTTACGAAGTATGATTAAAGGTCACTGT
366419 GACGCCTAATGTAGATACCAGCGATGAATAAAAATACCATTCATAAACTTTGATTCATGATCTTC
65 GACGCCTAATGTAGATACCAGCGATGAATAAAAATACCATTCATAAACTTTGATTCATGATCTTC
366484 TCCATCCAGTCTATGCATTAACAC
130 TCCATCCAGTCTATGCATTAACAC
366508 T
1 T
366509 TTGAGAACAA
Statistics
Matches: 154, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
153 1 0.01
154 153 0.99
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (153 bp):
TCATGAACCGTGTATAATGCACCTGATATTTACCTTTTTACGAAGTATGATTAAAGGTCACTGTG
ACGCCTAATGTAGATACCAGCGATGAATAAAAATACCATTCATAAACTTTGATTCATGATCTTCT
CCATCCAGTCTATGCATTAACAC
Found at i:367044 original size:10 final size:10
Alignment explanation
Indices: 367026--367059 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
367016 GTTCAAATCT
367026 CATAGCATAC
1 CATAGCATAC
* *
367036 CATACCATAG
1 CATAGCATAC
367046 CATAGCATAC
1 CATAGCATAC
367056 CATA
1 CATA
367060 TAGTTAAACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.41, C:0.29, G:0.09, T:0.21
Consensus pattern (10 bp):
CATAGCATAC
Found at i:367046 original size:15 final size:15
Alignment explanation
Indices: 367026--367059 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
367016 GTTCAAATCT
367026 CATAGCATACCATAC
1 CATAGCATACCATAC
*
367041 CATAGCATAGCATAC
1 CATAGCATACCATAC
367056 CATA
1 CATA
367060 TAGTTAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.29, G:0.09, T:0.21
Consensus pattern (15 bp):
CATAGCATACCATAC
Found at i:387433 original size:10 final size:10
Alignment explanation
Indices: 387415--387448 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
387405 GTTCAAATCT
387415 CATAGCATAC
1 CATAGCATAC
* *
387425 CATACCATAG
1 CATAGCATAC
387435 CATAGCATAC
1 CATAGCATAC
387445 CATA
1 CATA
387449 TAATTAAACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.41, C:0.29, G:0.09, T:0.21
Consensus pattern (10 bp):
CATAGCATAC
Done.