Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 101 of 311
Found at i:33235885 original size:5 final size:5
Alignment explanation
Indices: 33235875--33235938 Score: 60
Period size: 5 Copynumber: 12.2 Consensus size: 5
33235865 GTAAAGAGAA
*
33235875 AAAAG AAAAG AAAAG AAAAAG AAAAG -CAAG AAGAAG AAAAAG AAAATG
1 AAAAG AAAAG AAAAG -AAAAG AAAAG AAAAG AA-AAG -AAAAG AAAA-G
33235923 AAATA- AAAAG AAAAG A
1 AAA-AG AAAAG AAAAG A
33235939 GAGGCAAGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.08
5 28 0.56
6 15 0.30
7 3 0.06
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:33235905 original size:15 final size:16
Alignment explanation
Indices: 33235874--33235938 Score: 71
Period size: 16 Copynumber: 4.1 Consensus size: 16
33235864 TGTAAAGAGA
33235874 AAAAAGAAAAGAAAAG
1 AAAAAGAAAAGAAAAG
*
33235890 AAAAAGAAAAG-CAAG
1 AAAAAGAAAAGAAAAG
*
33235905 AAGAAGAAAAAGAAAATG
1 AAAAAG-AAAAGAAAA-G
*
33235923 AAATA-AAAAGAAAAG
1 AAAAAGAAAAGAAAAG
33235938 A
1 A
33235939 GAGGCAAGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
15 10 0.24
16 25 0.61
17 2 0.05
18 4 0.10
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAG
Found at i:33235938 original size:21 final size:21
Alignment explanation
Indices: 33235875--33235936 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
33235865 GTAAAGAGAA
33235875 AAAAGAAA-AGAAAAGAAAAAG
1 AAAAGAAAGA-AAAAGAAAAAG
* *
33235896 AAAAGCAAGAAGAAGAAAAAG
1 AAAAGAAAGAAAAAGAAAAAG
*
33235917 AAAATGAAATAAAAAGAAAA
1 AAAA-GAAAGAAAAAGAAAA
33235937 GAGAGGCAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 21 0.62
22 13 0.38
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (21 bp):
AAAAGAAAGAAAAAGAAAAAG
Found at i:33236018 original size:11 final size:12
Alignment explanation
Indices: 33235986--33236016 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
33235976 TTGAGAGAAC
33235986 TTGAAAAAGCCT
1 TTGAAAAAGCCT
33235998 TTGAAAAAGCCT
1 TTGAAAAAGCCT
33236010 TTGAAAA
1 TTGAAAA
33236017 GCAAAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:33236028 original size:6 final size:6
Alignment explanation
Indices: 33236019--33236094 Score: 73
Period size: 6 Copynumber: 12.7 Consensus size: 6
33236009 TTTGAAAAGC
* * *
33236019 AAAATG AAAATG AAAATG AAAATG AAAATG AAAA-G AAATTTG AGAGTG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAA-ATG AAAATG
* * * *
33236067 AAAAAG AAGATG AAAAAG AAATTG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAA
33236095 CAAAAGAATC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
5 4 0.07
6 48 0.87
7 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:33236032 original size:18 final size:17
Alignment explanation
Indices: 33236011--33236056 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 17
33236001 AAAAAGCCTT
33236011 TGAAAAGCAAAATGAAAA
1 TGAAAAG-AAAATGAAAA
33236029 TGAAAATGAAAATGAAAA
1 TGAAAA-GAAAATGAAAA
33236047 TGAAAAGAAA
1 TGAAAAGAAA
33236057 TTTGAGAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.15
18 22 0.81
19 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.17, T:0.13
Consensus pattern (17 bp):
TGAAAAGAAAATGAAAA
Found at i:33238207 original size:30 final size:30
Alignment explanation
Indices: 33238173--33238269 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
33238163 AGCTCACTCC
33238173 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
33238203 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
33238233 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
33238263 TAGCTCA
1 TAGCTCA
33238270 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:33245772 original size:13 final size:13
Alignment explanation
Indices: 33245754--33245778 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33245744 AATAGTTGTG
33245754 TGTTATTTAATTA
1 TGTTATTTAATTA
33245767 TGTTATTTAATT
1 TGTTATTTAATT
33245779 TTGTAGGTTA
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:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:33250736 original size:26 final size:25
Alignment explanation
Indices: 33250628--33250728 Score: 166
Period size: 26 Copynumber: 3.9 Consensus size: 25
33250618 CATGAAATTC
33250628 TTATCATGAACATTTACCTAACCCA
1 TTATCATGAACATTTACCTAACCCA
33250653 TTATCATGAAACATTTACCTAACCCA
1 TTATCATG-AACATTTACCTAACCCA
*
33250679 TTATCATGGAACATTTACCTAACCTA
1 TTATCAT-GAACATTTACCTAACCCA
33250705 TTATCATTGAACATTTACCTAACC
1 TTATCA-TGAACATTTACCTAACC
33250729 TGTTATCAAT
Statistics
Matches: 72, Mismatches: 1, Indels: 5
0.92 0.01 0.06
Matches are distributed among these distances:
25 8 0.11
26 62 0.86
27 2 0.03
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.34
Consensus pattern (25 bp):
TTATCATGAACATTTACCTAACCCA
Found at i:33252923 original size:30 final size:30
Alignment explanation
Indices: 33252889--33252985 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
33252879 TAAACTAAAA
33252889 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
33252919 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
33252949 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
33252978 ATGAGCTA
1 -TGAGCTA
33252986 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:33256788 original size:29 final size:29
Alignment explanation
Indices: 33256722--33256778 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
33256712 GATTCAAAGA
*
33256722 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
33256751 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
33256779 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:33261556 original size:20 final size:20
Alignment explanation
Indices: 33261533--33261586 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
33261523 AGTTTTTCCC
*
33261533 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
33261553 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
33261573 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
33261587 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:33261568 original size:30 final size:30
Alignment explanation
Indices: 33261533--33261606 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
33261523 AGTTTTTCCC
33261533 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
33261563 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
33261593 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
33261607 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:33261596 original size:20 final size:20
Alignment explanation
Indices: 33261533--33261597 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
33261523 AGTTTTTCCC
* * * *
33261533 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
33261553 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
33261572 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
33261593 AGCTC
1 AGCTC
33261598 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:33264365 original size:18 final size:18
Alignment explanation
Indices: 33264339--33264424 Score: 73
Period size: 18 Copynumber: 4.6 Consensus size: 18
33264329 AAATTGAAAG
*
33264339 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
*
33264357 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
33264375 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
33264393 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
33264414 AAAAGAAAAAG
1 AAAAGAAAAAG
33264425 CGAAAAAAGA
Statistics
Matches: 52, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
18 33 0.63
19 5 0.10
20 8 0.15
21 6 0.12
ACGTcount: A:0.72, C:0.03, G:0.19, T:0.06
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:33264367 original size:6 final size:6
Alignment explanation
Indices: 33264335--33264424 Score: 65
Period size: 6 Copynumber: 14.7 Consensus size: 6
33264325 AAAGAAATTG
* * ** **
33264335 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATCGAA AAAGTG
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* * *
33264382 AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA AAAGAA AAAG
33264425 CGAAAAAAGA
Statistics
Matches: 63, Mismatches: 18, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
5 3 0.05
6 49 0.78
7 7 0.11
8 4 0.06
ACGTcount: A:0.72, C:0.03, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:33264406 original size:14 final size:13
Alignment explanation
Indices: 33264385--33264422 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
33264375 AAAAGTGAGA
33264385 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
33264397 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
33264412 GAAAAAGAAAA
1 GAAAAAGAAAA
33264423 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:33264476 original size:33 final size:33
Alignment explanation
Indices: 33264439--33264501 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
33264429 AAAAGAAATT
33264439 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
33264472 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
33264502 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:33266301 original size:20 final size:20
Alignment explanation
Indices: 33266278--33266331 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
33266268 AGTTTTTCCC
*
33266278 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
33266298 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
33266318 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
33266332 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:33266313 original size:30 final size:30
Alignment explanation
Indices: 33266278--33266351 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
33266268 AGTTTTTCCC
33266278 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
33266308 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
33266338 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
33266352 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:33266341 original size:20 final size:20
Alignment explanation
Indices: 33266278--33266342 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
33266268 AGTTTTTCCC
* * * *
33266278 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
33266298 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
33266317 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
33266338 AGCTC
1 AGCTC
33266343 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:33268783 original size:31 final size:29
Alignment explanation
Indices: 33268727--33268784 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
33268717 TTTCTTCCAC
* *
33268727 ACTTTCTTTTTGCTCACTCTCTTTTTCAA
1 ACTTTCTTTTTGCACACACTCTTTTTCAA
33268756 ACTTTACTTTCTTGCACACACTCTTTTTC
1 ACTTT-CTTT-TTGCACACACTCTTTTTC
33268785 TTTTTCGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.20
30 4 0.16
31 16 0.64
ACGTcount: A:0.16, C:0.29, G:0.03, T:0.52
Consensus pattern (29 bp):
ACTTTCTTTTTGCACACACTCTTTTTCAA
Found at i:33272307 original size:39 final size:39
Alignment explanation
Indices: 33272251--33272405 Score: 265
Period size: 39 Copynumber: 4.0 Consensus size: 39
33272241 TTCAGTGATG
*
33272251 TATATCCGGACTGAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
33272290 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
*
33272329 TATATCGGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
* * *
33272368 TATATCTGGACTTAAGGTCCGCAGGCTACGTGCTGGAA
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAA
33272406 ATATGTTCGG
Statistics
Matches: 111, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 111 1.00
ACGTcount: A:0.21, C:0.20, G:0.32, T:0.27
Consensus pattern (39 bp):
TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
Found at i:33272433 original size:78 final size:78
Alignment explanation
Indices: 33272267--33272425 Score: 232
Period size: 78 Copynumber: 2.1 Consensus size: 78
33272257 CGGACTGAGG
* * *
33272267 GTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTAT
1 GTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATAT
**
33272332 ATCGGGACTTAGG
66 ATCGGGACTTAAA
*
33272345 GTCCGCAGGCTATGTGCTGGAATTATATCTGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATAT
1 GTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATAT
*
33272410 GTTCGGG-C-TAAA
66 -ATCGGGACTTAAA
33272422 GTCC
1 GTCC
33272426 CGTAGGCTTC
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
77 6 0.08
78 62 0.85
79 5 0.07
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (78 bp):
GTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATAT
ATCGGGACTTAAA
Found at i:33272442 original size:78 final size:78
Alignment explanation
Indices: 33272267--33272449 Score: 219
Period size: 78 Copynumber: 2.3 Consensus size: 78
33272257 CGGACTGAGG
* * * *
33272267 GTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTAT
1 GTCCGCAGGCTATGAGCTGGAATTATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATAT
**
33272332 ATCGGGACTTAGG
66 ATCGGGACTTAAA
* *
33272345 GTCCGCAGGCTATGTGCTGGAATTATATCTGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATAT
1 GTCCGCAGGCTATGAGCTGGAATTATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATAT
*
33272410 GTTCGGG-C-TAAA
66 -ATCGGGACTTAAA
* *
33272422 GTCCCGTAGGCT-TCGAGCTGGTATTATA
1 GT-CCGCAGGCTAT-GAGCTGGAATTATA
33272450 CCGAGTTTAA
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
77 5 0.05
78 82 0.89
79 5 0.05
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (78 bp):
GTCCGCAGGCTATGAGCTGGAATTATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATAT
ATCGGGACTTAAA
Found at i:33280604 original size:23 final size:22
Alignment explanation
Indices: 33280570--33280612 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
33280560 CGTCTTTTTC
33280570 TTTTCTTTCTTT-TTCTAACTCA
1 TTTTCTTTCTTTCTTC-AACTCA
33280592 TTTTCTCTTCTTTCTTCAACT
1 TTTTCT-TTCTTTCTTCAACT
33280613 TCTTTGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 10 0.53
24 3 0.16
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTCTTTCTTTCTTCAACTCA
Found at i:33282475 original size:13 final size:13
Alignment explanation
Indices: 33282454--33282490 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
33282444 AGAGAATAAG
33282454 GAAAG-GAAAAAT
1 GAAAGTGAAAAAT
*
33282466 GAAATTGAAAAA-
1 GAAAGTGAAAAAT
33282478 GAAAGTGAAAAAT
1 GAAAGTGAAAAAT
33282491 AAAAAGAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.14
Consensus pattern (13 bp):
GAAAGTGAAAAAT
Found at i:33284573 original size:20 final size:21
Alignment explanation
Indices: 33284550--33284597 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
33284540 AGCTCTGTCT
33284550 AGCTCAACTT-AGCTCATTTG
1 AGCTCAACTTCAGCTCATTTG
** *
33284570 AGCTC-GTTTCAGCTCGTTTG
1 AGCTCAACTTCAGCTCATTTG
33284590 AGCTCAAC
1 AGCTCAAC
33284598 CGAACTTACT
Statistics
Matches: 21, Mismatches: 5, Indels: 3
0.72 0.17 0.10
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (21 bp):
AGCTCAACTTCAGCTCATTTG
Found at i:33291408 original size:30 final size:30
Alignment explanation
Indices: 33291313--33291409 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
33291303 AGCTCACTCC
*
33291313 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * * *
33291343 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * *
33291373 CAGCTCAACTTTAGCTCACAAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
33291403 TAGCTCA
1 TAGCTCA
33291410 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 46 0.92
31 4 0.08
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:33293096 original size:11 final size:12
Alignment explanation
Indices: 33293080--33293132 Score: 56
Period size: 11 Copynumber: 4.6 Consensus size: 12
33293070 TATACAAGTA
33293080 AAAAAAATTC-G
1 AAAAAAATTCAG
*
33293091 AAAAAAATTCAA
1 AAAAAAATTCAG
*
33293103 AAAAAAATT-TG
1 AAAAAAATTCAG
* *
33293114 AAAAAAAATCTG
1 AAAAAAATTCAG
33293126 AAAAAAA
1 AAAAAAA
33293133 GTGTTTAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
11 18 0.50
12 18 0.50
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.17
Consensus pattern (12 bp):
AAAAAAATTCAG
Found at i:33293096 original size:12 final size:12
Alignment explanation
Indices: 33293079--33293132 Score: 67
Period size: 12 Copynumber: 4.6 Consensus size: 12
33293069 TTATACAAGT
33293079 AAAAAAAATTCG
1 AAAAAAAATTCG
*
33293091 -AAAAAAATTCA
1 AAAAAAAATTCG
*
33293102 AAAAAAAATTTG
1 AAAAAAAATTCG
33293114 AAAAAAAA-TCTG
1 AAAAAAAATTC-G
33293126 AAAAAAA
1 AAAAAAA
33293133 GTGTTTAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 11 0.31
12 25 0.69
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.17
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:33293129 original size:23 final size:23
Alignment explanation
Indices: 33293079--33293132 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
33293069 TTATACAAGT
*
33293079 AAAAAAAATTCGAAAAAAATTCA
1 AAAAAAAATTCGAAAAAAAATCA
* *
33293102 AAAAAAAATTTGAAAAAAAATCT
1 AAAAAAAATTCGAAAAAAAATCA
*
33293125 GAAAAAAA
1 AAAAAAAA
33293133 GTGTTTAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.17
Consensus pattern (23 bp):
AAAAAAAATTCGAAAAAAAATCA
Found at i:33294051 original size:9 final size:10
Alignment explanation
Indices: 33294044--33294102 Score: 59
Period size: 11 Copynumber: 5.7 Consensus size: 10
33294034 AAGAGAAAAC
33294044 AAAGAAAAGA
1 AAAGAAAAGA
33294054 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
33294066 AAAGAAGA-A
1 AAAGAAAAGA
33294075 AAAGAAAATGA
1 AAAGAAAA-GA
33294086 AATA-AAAAGA
1 AA-AGAAAAGA
33294096 AAAGAAA
1 AAAGAAA
33294103 GGCAAGAGGC
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
9 9 0.22
10 11 0.27
11 15 0.37
12 6 0.15
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:33294067 original size:21 final size:20
Alignment explanation
Indices: 33294033--33294102 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
33294023 ACATTATTGT
33294033 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
33294054 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
33294075 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
33294096 AAAGAAA
1 AAAGAAA
33294103 GGCAAGAGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
20 8 0.19
21 29 0.69
22 5 0.12
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:33294068 original size:6 final size:5
Alignment explanation
Indices: 33294044--33294102 Score: 59
Period size: 5 Copynumber: 11.4 Consensus size: 5
33294034 AAGAGAAAAC
*
33294044 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
33294091 AAAGA AAAGA AA
1 AAAGA AAAGA AA
33294103 GGCAAGAGGC
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
4 4 0.09
5 27 0.59
6 14 0.30
7 1 0.02
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:33294102 original size:15 final size:15
Alignment explanation
Indices: 33294044--33294103 Score: 77
Period size: 16 Copynumber: 3.9 Consensus size: 15
33294034 AAGAGAAAAC
33294044 AAAGAAAAGAAAAGAA
1 AAAGAAAAG-AAAGAA
33294060 AAAGCAAAAG-AAGAA
1 AAAG-AAAAGAAAGAA
*
33294075 AAAGAAAATGAAATAA
1 AAAGAAAA-GAAAGAA
33294091 AAAGAAAAGAAAG
1 AAAGAAAAGAAAG
33294104 GCAAGAGGCA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
14 4 0.10
15 14 0.36
16 16 0.41
17 5 0.13
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (15 bp):
AAAGAAAAGAAAGAA
Found at i:33294180 original size:11 final size:12
Alignment explanation
Indices: 33294148--33294178 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
33294138 TTGAGAGAAC
33294148 TTGAAAAAGCCT
1 TTGAAAAAGCCT
33294160 TTGAAAAAGCCT
1 TTGAAAAAGCCT
33294172 TTGAAAA
1 TTGAAAA
33294179 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:33294215 original size:30 final size:31
Alignment explanation
Indices: 33294181--33294262 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
33294171 TTTGAAAAGC
* *
33294181 AAAAAGAAAAAGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAGAAGAAAAAGAAATATGAGAGTG
* *
33294211 AAAAAG-AGAACAAAAAGAAATTTGAGAGTG
1 AAAAAGAAGAAGAAAAAGAAATATGAGAGTG
*
33294241 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAGAAGAAAAAGAAAT
33294263 TGAAACAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 12 0.27
30 19 0.43
31 13 0.30
ACGTcount: A:0.67, C:0.01, G:0.21, T:0.11
Consensus pattern (31 bp):
AAAAAGAAGAAGAAAAAGAAATATGAGAGTG
Found at i:33296451 original size:30 final size:30
Alignment explanation
Indices: 33296356--33296452 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
33296346 AGCTCACTCC
*
33296356 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * * *
33296386 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * *
33296416 CAGCTCAACTTTAGCTCACAAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
33296446 TAGCTCA
1 TAGCTCA
33296453 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 46 0.92
31 4 0.08
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:33309930 original size:23 final size:22
Alignment explanation
Indices: 33309879--33309930 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
33309869 CCTCGTCTTT
*
33309879 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
33309901 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
33309924 TTCTTTT
1 TTCTTTT
33309931 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:33312844 original size:14 final size:14
Alignment explanation
Indices: 33312825--33312873 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
33312815 CAATCTATTG
33312825 AAAGAGAAAAAGAA
1 AAAGAGAAAAAGAA
*
33312839 AAAGAGAAAAATAA
1 AAAGAGAAAAAGAA
33312853 AAAGA-ATGAAAAGAA
1 AAAGAGA--AAAAGAA
33312868 AAAGAG
1 AAAGAG
33312874 TGGAAAAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 1 0.03
14 18 0.60
15 11 0.37
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (14 bp):
AAAGAGAAAAAGAA
Found at i:33322659 original size:14 final size:14
Alignment explanation
Indices: 33322642--33322681 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
33322632 CGAATGGAAT
*
33322642 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
33322656 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
33322670 GATATGAACAAA
1 GGTAGGAACAAA
33322682 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:33326157 original size:21 final size:22
Alignment explanation
Indices: 33326118--33326161 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
33326108 ATGCTTACTC
33326118 CTTCAAGCTCAAATCAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
* *
33326140 CTTCAA-CTCAACTTAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
33326161 C
1 C
33326162 GAGCTCGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.34, C:0.34, G:0.07, T:0.25
Consensus pattern (22 bp):
CTTCAAGCTCAAATCAGCTCAA
Found at i:33333384 original size:19 final size:18
Alignment explanation
Indices: 33333360--33333396 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
33333350 CATAAATCAC
*
33333360 TTTTTTTCGATTTTTTTTA
1 TTTTTTT-GAATTTTTTTA
33333379 TTTTTTTGAATTTTTTTA
1 TTTTTTTGAATTTTTTTA
33333397 ACTTGTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.14, C:0.03, G:0.05, T:0.78
Consensus pattern (18 bp):
TTTTTTTGAATTTTTTTA
Found at i:33333764 original size:14 final size:14
Alignment explanation
Indices: 33333747--33333786 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
33333737 CGAATGGAAT
*
33333747 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
33333761 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
33333775 GATATGAACAAA
1 GGTAGGAACAAA
33333787 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:33335340 original size:19 final size:19
Alignment explanation
Indices: 33335316--33335355 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
33335306 AGCTCCCATG
33335316 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
33335335 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
33335354 TA
1 TA
33335356 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:33336523 original size:15 final size:15
Alignment explanation
Indices: 33336503--33336550 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
33336493 TCAAAGATGG
33336503 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
33336518 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
33336532 GTTTATGGATATAAA
1 GTTTATGGATATGAA
33336547 GTTT
1 GTTT
33336551 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:33336537 original size:14 final size:14
Alignment explanation
Indices: 33336497--33336540 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
33336487 AAGGATTCAA
33336497 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
33336511 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
33336526 AGATGGGTTTATGG
1 AGATGGGTTTATGG
33336540 A
1 A
33336541 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:33336566 original size:29 final size:29
Alignment explanation
Indices: 33336497--33336556 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
33336487 AAGGATTCAA
*
33336497 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
33336526 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
33336555 AG
1 AG
33336557 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:33340015 original size:17 final size:19
Alignment explanation
Indices: 33339993--33340037 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
33339983 TTTATCTCAA
33339993 TTTCTTTTTCCAC-TT-TT
1 TTTCTTTTTCCACATTCTT
*
33340010 TTTCTTGTT-CACATTCTT
1 TTTCTTTTTCCACATTCTT
*
33340028 TCTCTTTTTC
1 TTTCTTTTTC
33340038 GCTTCTCTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
16 3 0.14
17 10 0.45
18 9 0.41
ACGTcount: A:0.07, C:0.24, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTCTTTTTCCACATTCTT
Found at i:33341376 original size:15 final size:15
Alignment explanation
Indices: 33341356--33341403 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
33341346 TCAAAGATGG
33341356 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
33341371 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
33341385 GTTTATGGATATAAA
1 GTTTATGGATATGAA
33341400 GTTT
1 GTTT
33341404 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:33341390 original size:14 final size:14
Alignment explanation
Indices: 33341350--33341393 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
33341340 AAGGATTCAA
33341350 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
33341364 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
33341379 AGATGGGTTTATGG
1 AGATGGGTTTATGG
33341393 A
1 A
33341394 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:33341419 original size:29 final size:29
Alignment explanation
Indices: 33341350--33341409 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
33341340 AAGGATTCAA
*
33341350 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
33341379 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
33341408 AG
1 AG
33341410 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:33342424 original size:14 final size:14
Alignment explanation
Indices: 33342382--33342426 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
33342372 TTAAAGAAGC
33342382 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
33342396 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
33342409 AACTCATTTAATTA
1 AACTCATTAAATTA
33342423 AACT
1 AACT
33342427 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:33343033 original size:14 final size:14
Alignment explanation
Indices: 33343011--33343058 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
33343001 ACCTAAACTG
* *
33343011 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
33343025 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
33343039 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
33343053 ACCATT
1 ACCATT
33343059 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:33345744 original size:20 final size:20
Alignment explanation
Indices: 33345721--33345767 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33345711 GGGTTAAGAT
*
33345721 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
33345741 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
33345761 TGAGCTG
1 TGAGCTG
33345768 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:33346953 original size:48 final size:48
Alignment explanation
Indices: 33346901--33347006 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
33346891 ATTGTCTTTC
*
33346901 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
33346949 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
33346997 TTTCTTTTTC
1 TTTCTTTTTC
33347007 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:33349633 original size:20 final size:20
Alignment explanation
Indices: 33349610--33349656 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33349600 GGGTTAAGAT
*
33349610 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
33349630 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
33349650 TGAGCTG
1 TGAGCTG
33349657 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:33352239 original size:15 final size:16
Alignment explanation
Indices: 33352200--33352240 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
33352190 AACAACACTC
33352200 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
33352216 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
33352230 CTTTCTTTTTC
1 CTTTCTTTTTC
33352241 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:33353459 original size:12 final size:13
Alignment explanation
Indices: 33353439--33353476 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
33353429 AATTGAATAC
**
33353439 AATTTTTTTTTTG
1 AATTTTTTTTTCA
33353452 AATTTTTTTTTCA
1 AATTTTTTTTTCA
33353465 AATTTTTTTTTC
1 AATTTTTTTTTC
33353477 CTTTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (13 bp):
AATTTTTTTTTCA
Found at i:33355589 original size:30 final size:31
Alignment explanation
Indices: 33355555--33355651 Score: 110
Period size: 30 Copynumber: 3.2 Consensus size: 31
33355545 AGCTCACTCC
*
33355555 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
33355585 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
*
33355615 TAGCTCAACTTT-AGCTCACGAGCTAAAACT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
33355645 TAGCTCA
1 TAGCTCA
33355652 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
30 49 0.92
31 4 0.08
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:33356046 original size:22 final size:22
Alignment explanation
Indices: 33356016--33356059 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
33356006 TTTGGTATTT
33356016 GGGAATTGGAACGAAATGGTAA
1 GGGAATTGGAACGAAATGGTAA
* *
33356038 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGAACGAAATGGTAA
33356060 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.36, T:0.23
Consensus pattern (22 bp):
GGGAATTGGAACGAAATGGTAA
Found at i:33358092 original size:17 final size:17
Alignment explanation
Indices: 33358067--33358120 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
33358057 TCTCTTTTCA
*
33358067 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
33358084 TTCTTTTTTTTTCATTT
1 TTCTTTTTTTTTGAATT
* *
33358101 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
33358118 TTC
1 TTC
33358121 GCTCTTTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:33360672 original size:22 final size:22
Alignment explanation
Indices: 33360642--33360685 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33360632 TTTGGTATTT
33360642 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
33360664 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
33360686 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:33366067 original size:9 final size:10
Alignment explanation
Indices: 33366060--33366116 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
33366050 AAGAGAAAAT
33366060 AAAGAAAAGA
1 AAAGAAAAGA
33366070 AAAGAAAAAGA
1 AAAG-AAAAGA
*
33366081 AAA-AGAAGAA
1 AAAGAAAAG-A
33366091 AAAGAAAATGA
1 AAAGAAAA-GA
33366102 AATA-AAAAGA
1 AA-AGAAAAGA
33366112 AAAGA
1 AAAGA
33366117 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 5 0.13
10 13 0.33
11 19 0.49
12 2 0.05
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:33366070 original size:5 final size:5
Alignment explanation
Indices: 33366060--33366116 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
33366050 AAGAGAAAAT
*
33366060 AAAGA AAAGA AAAGAA AAAGA AAA-A GAAGAA AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAGA AAAGA AAAG-A AAAGA AAA-GA AA-AGA
33366107 AAAGA AAAGA
1 AAAGA AAAGA
33366117 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 26 0.59
6 13 0.30
7 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:33366193 original size:12 final size:12
Alignment explanation
Indices: 33366185--33366209 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33366175 TTTGAAAAGC
33366185 AAAAAGAAAATG
1 AAAAAGAAAATG
33366197 AAAAAGAAAATG
1 AAAAAGAAAATG
33366209 A
1 A
33366210 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:33366206 original size:18 final size:18
Alignment explanation
Indices: 33366179--33366234 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
33366169 AAAGCCTTTG
33366179 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
33366198 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
33366216 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
33366233 AA
1 AA
33366235 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:33366219 original size:30 final size:31
Alignment explanation
Indices: 33366185--33366259 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
33366175 TTTGAAAAGC
*
33366185 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
33366215 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
33366245 AAAAAGAAATTGAAA
1 AAAAAGAAAATGAAA
33366260 CAAAAGAATC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 8 0.22
30 26 0.72
31 2 0.06
ACGTcount: A:0.64, C:0.01, G:0.21, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:33367192 original size:13 final size:13
Alignment explanation
Indices: 33367174--33367198 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33367164 AATAGTTGTG
33367174 TGTTATTTAATTA
1 TGTTATTTAATTA
33367187 TGTTATTTAATT
1 TGTTATTTAATT
33367199 TTGTAGGTTA
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:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:33370101 original size:30 final size:31
Alignment explanation
Indices: 33370067--33370163 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 31
33370057 AGCTCACTCC
33370067 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAACTCACGAGCTAAACCT
* * * * * *
33370097 TAGCTCAAC-TTCACCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAACTCACGAGCTAAACCT
* * *
33370127 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAACTCACGAGCTAAACCT
33370157 TAGCTCA
1 TAGCTCA
33370164 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
30 46 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAACTCACGAGCTAAACCT
Found at i:33372233 original size:13 final size:13
Alignment explanation
Indices: 33372217--33372262 Score: 85
Period size: 13 Copynumber: 3.6 Consensus size: 13
33372207 AGGAAATTTG
33372217 AAAAAAAAATTCA
1 AAAAAAAAATTCA
33372230 AAAAAAAAATTC-
1 AAAAAAAAATTCA
33372242 AAAAAAAAATTCA
1 AAAAAAAAATTCA
33372255 AAAAAAAA
1 AAAAAAAA
33372263 TTTTGAAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.38
13 20 0.62
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAAAAAATTCA
Found at i:33372234 original size:12 final size:12
Alignment explanation
Indices: 33372217--33372264 Score: 87
Period size: 12 Copynumber: 3.9 Consensus size: 12
33372207 AGGAAATTTG
33372217 AAAAAAAAATTC
1 AAAAAAAAATTC
33372229 AAAAAAAAAATTC
1 -AAAAAAAAATTC
33372242 AAAAAAAAATTC
1 AAAAAAAAATTC
33372254 AAAAAAAAATT
1 AAAAAAAAATT
33372265 TTGAAGTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 23 0.66
13 12 0.34
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:33373248 original size:18 final size:18
Alignment explanation
Indices: 33373192--33373251 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
33373182 AGTACGAGCG
33373192 AGAAAAAGAAATCGAAAGAAA
1 AGAAAAAGAAAT--AAA-AAA
* **
33373213 AGAAAAAGAGATTGAAAA
1 AGAAAAAGAAATAAAAAA
33373231 AGAAAAAGAAATAAAAAA
1 AGAAAAAGAAATAAAAAA
33373249 AGA
1 AGA
33373252 GTGAGGTCGA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 21 0.64
19 1 0.03
21 11 0.33
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATAAAAAA
Found at i:33375460 original size:33 final size:34
Alignment explanation
Indices: 33375423--33375488 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
33375413 ATTAAAGTGT
*
33375423 TGTTCTACATGC-ATGGAACGGCAATT-AATGAGA
1 TGTTCCACATGCAATGG-ACGGCAATTAAATGAGA
*
33375456 TGTTCCACATGCAATGGACGGCATTTAAATGAG
1 TGTTCCACATGCAATGGACGGCAATTAAATGAG
33375489 GGAGAGTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 19 0.66
34 10 0.34
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (34 bp):
TGTTCCACATGCAATGGACGGCAATTAAATGAGA
Found at i:33376642 original size:30 final size:31
Alignment explanation
Indices: 33376608--33376704 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
33376598 AGCTCACTCC
*
33376608 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
33376638 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
33376668 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
33376698 TAGCTCA
1 TAGCTCA
33376705 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:33379056 original size:20 final size:19
Alignment explanation
Indices: 33379033--33379097 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
33379023 AAGCTCAAAC
33379033 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
33379053 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
33379073 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
33379093 GAGCT
1 GAGCT
33379098 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:33380911 original size:33 final size:33
Alignment explanation
Indices: 33380873--33380935 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
33380863 GATTACTCAC
33380873 TTCAC-TCATTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTTCATTTCTTTTCA-AG-CTCTCTTTCTTT
*
33380906 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTTCATTTCTTTTCAAGCTCTCTTTC
33380936 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 14 0.52
34 12 0.44
35 1 0.04
ACGTcount: A:0.14, C:0.27, G:0.05, T:0.54
Consensus pattern (33 bp):
TTCACTTCATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:33380962 original size:21 final size:21
Alignment explanation
Indices: 33380933--33380988 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
33380923 CAAGCTCTCT
*
33380933 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
33380954 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
33380975 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
33380989 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:33380981 original size:14 final size:14
Alignment explanation
Indices: 33380932--33380988 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
33380922 TCAAGCTCTC
33380932 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
33380945 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
33380959 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
33380973 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
33380987 TT
1 TT
33380989 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:33381076 original size:6 final size:6
Alignment explanation
Indices: 33380950--33381063 Score: 79
Period size: 6 Copynumber: 18.7 Consensus size: 6
33380940 TCTTTTTTCG
* * * **
33380950 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * ** *
33381001 -TGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CTTTTT CGTTTT
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
33381049 CTTTTT -GTTTT CTTT
1 CTTTTT CTTTTT CTTT
33381064 CAATTTCTTT
Statistics
Matches: 80, Mismatches: 23, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
5 5 0.06
6 62 0.77
7 10 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.73
Consensus pattern (6 bp):
CTTTTT
Found at i:33381078 original size:12 final size:12
Alignment explanation
Indices: 33381010--33381085 Score: 59
Period size: 12 Copynumber: 6.6 Consensus size: 12
33381000 TTGATTTCTT
*
33381010 TTTCTTTTGCAA
1 TTTCTTTTTCAA
**
33381022 TTTCTTTTTCTT
1 TTTCTTTTTCAA
**
33381034 TTTCTTTTTCGT
1 TTTCTTTTTCAA
*
33381046 TTTCTTTTT--G
1 TTTCTTTTTCAA
*
33381056 TTT-TCTTTCAA
1 TTTCTTTTTCAA
33381067 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
33381079 TCTCTTT
1 TTTCTTT
33381086 CTCCTTTTCT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
9 4 0.08
10 3 0.06
11 3 0.06
12 42 0.81
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:33382158 original size:157 final size:157
Alignment explanation
Indices: 33381872--33382185 Score: 628
Period size: 157 Copynumber: 2.0 Consensus size: 157
33381862 TCATCTCACA
33381872 AATTCGTAATTCGTCTCGATAGACTTAATTTGCTGCTTGAGGGTCGGTTTCAAACTGGGTTACAA
1 AATTCGTAATTCGTCTCGATAGACTTAATTTGCTGCTTGAGGGTCGGTTTCAAACTGGGTTACAA
33381937 GGGATAATGTCGGTGTAGGGTAGGCTAAACAAAATAAAATCAAGGCTAAGTGTGGCGTTGGGATG
66 GGGATAATGTCGGTGTAGGGTAGGCTAAACAAAATAAAATCAAGGCTAAGTGTGGCGTTGGGATG
33382002 GGTAAATAATGGTAGGAAGGGAAACTT
131 GGTAAATAATGGTAGGAAGGGAAACTT
33382029 AATTCGTAATTCGTCTCGATAGACTTAATTTGCTGCTTGAGGGTCGGTTTCAAACTGGGTTACAA
1 AATTCGTAATTCGTCTCGATAGACTTAATTTGCTGCTTGAGGGTCGGTTTCAAACTGGGTTACAA
33382094 GGGATAATGTCGGTGTAGGGTAGGCTAAACAAAATAAAATCAAGGCTAAGTGTGGCGTTGGGATG
66 GGGATAATGTCGGTGTAGGGTAGGCTAAACAAAATAAAATCAAGGCTAAGTGTGGCGTTGGGATG
33382159 GGTAAATAATGGTAGGAAGGGAAACTT
131 GGTAAATAATGGTAGGAAGGGAAACTT
33382186 GATGATCGGA
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 157 1.00
ACGTcount: A:0.31, C:0.11, G:0.30, T:0.28
Consensus pattern (157 bp):
AATTCGTAATTCGTCTCGATAGACTTAATTTGCTGCTTGAGGGTCGGTTTCAAACTGGGTTACAA
GGGATAATGTCGGTGTAGGGTAGGCTAAACAAAATAAAATCAAGGCTAAGTGTGGCGTTGGGATG
GGTAAATAATGGTAGGAAGGGAAACTT
Found at i:33382293 original size:11 final size:11
Alignment explanation
Indices: 33382268--33382310 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
33382258 TTTGCTCACC
*
33382268 TTTTTTTTCACT
1 TTTTTTTTGA-T
33382280 TTTTTTTTGAT
1 TTTTTTTTGAT
33382291 TTTTTTTTG-T
1 TTTTTTTTGAT
33382301 TTGTTTTTTG
1 TT-TTTTTTG
33382311 TTACTCCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 3 0.10
11 17 0.59
12 9 0.31
ACGTcount: A:0.05, C:0.05, G:0.09, T:0.81
Consensus pattern (11 bp):
TTTTTTTTGAT
Found at i:33390441 original size:24 final size:22
Alignment explanation
Indices: 33390388--33390444 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 22
33390378 CTTGTAAGAG
*
33390388 AAAACAGAAGAAAGAAAAGAAA
1 AAAAAAGAAGAAAGAAAAGAAA
33390410 AAGCAAAAGAAGAAAAGAAAATGAAA
1 AA--AAAAGAAG-AAAGAAAA-GAAA
*
33390436 TAAAAAGAA
1 AAAAAAGAA
33390445 ATGAGAGGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 2 0.07
24 14 0.48
25 8 0.28
26 5 0.17
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.04
Consensus pattern (22 bp):
AAAAAAGAAGAAAGAAAAGAAA
Found at i:33390544 original size:28 final size:28
Alignment explanation
Indices: 33390513--33390587 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 28
33390503 TTTGAAAAGC
*
33390513 AAAAGAAAAAGAAAAAGAATGAGATTGA
1 AAAAGAAAAAGAAAAAGAATGAGAGTGA
* * **
33390541 AAAAGAGAACGAACAAA-TTTGAGAGTGA
1 AAAAGAAAAAGAA-AAAGAATGAGAGTGA
* *
33390569 AAAAGAAGATGAAAAAGAA
1 AAAAGAAAAAGAAAAAGAA
33390588 ATTGAAACAA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
27 3 0.09
28 29 0.83
29 3 0.09
ACGTcount: A:0.64, C:0.03, G:0.23, T:0.11
Consensus pattern (28 bp):
AAAAGAAAAAGAAAAAGAATGAGAGTGA
Found at i:33392802 original size:14 final size:14
Alignment explanation
Indices: 33392783--33392816 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
33392773 ATACTTCGAA
33392783 TTTTTTTTTGAATT
1 TTTTTTTTTGAATT
33392797 TTTTTTTTTGAATT
1 TTTTTTTTTGAATT
33392811 TTTTTT
1 TTTTTT
33392817 CAAATTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (14 bp):
TTTTTTTTTGAATT
Found at i:33398143 original size:19 final size:19
Alignment explanation
Indices: 33398119--33398158 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
33398109 AGCTCCCATG
33398119 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
33398138 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
33398157 TA
1 TA
33398159 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:33401734 original size:30 final size:30
Alignment explanation
Indices: 33401649--33401745 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
33401639 TAAACTAAAA
* *
33401649 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
33401679 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
33401709 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
33401738 ATGAGCTA
1 -TGAGCTA
33401746 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:33403891 original size:29 final size:29
Alignment explanation
Indices: 33403842--33403911 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
33403832 TTCTTTTGTT
*
33403842 TCAATTTCTTTTCATCTTC-TTTTCACTC
1 TCAATTTCTTTTCATCTTCTTTTTCAATC
*
33403870 TCAAATTTCTTTTCGT-TCTCTTTTTCAATC
1 TC-AATTTCTTTTCATCT-TCTTTTTCAATC
*
33403900 TCATTTTCTTTT
1 TCAATTTCTTTT
33403912 TGCTTTTCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 3 0.08
29 23 0.64
30 10 0.28
ACGTcount: A:0.14, C:0.24, G:0.01, T:0.60
Consensus pattern (29 bp):
TCAATTTCTTTTCATCTTCTTTTTCAATC
Found at i:33403991 original size:5 final size:5
Alignment explanation
Indices: 33403981--33404037 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
33403971 CTCTTGCCTC
*
33403981 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
33404028 TCTTT TCTTT
1 TCTTT TCTTT
33404038 ATTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:33404021 original size:15 final size:14
Alignment explanation
Indices: 33403981--33404037 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
33403971 CTCTTGCCTC
*
33403981 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
33403996 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
33404011 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
33404028 TCTTTTCTTT
1 TCTTTTCTTT
33404038 ATTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:33404047 original size:21 final size:20
Alignment explanation
Indices: 33403979--33404048 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
33403969 GCCTCTTGCC
33403979 TCTCTTTTCTTTTTATTTCATTT
1 TCTCTTTTC-TTTT-TTT-ATTT
**
33404002 TCT-TTTTCTTCTTTTGCTTT
1 TCTCTTTTCTT-TTTTTATTT
33404022 T-TCTTTTCTTTTCTTTATTT
1 TCTCTTTTCTTTT-TTTATTT
33404042 TCTCTTT
1 TCTCTTT
33404049 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
19 3 0.08
20 17 0.44
21 9 0.23
22 7 0.18
23 3 0.08
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTATTT
Found at i:33406376 original size:50 final size:49
Alignment explanation
Indices: 33406252--33406427 Score: 203
Period size: 50 Copynumber: 3.5 Consensus size: 49
33406242 TGAGGTCGCA
* * * *
33406252 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGT-GATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CC--AGACTGTAGGTCACG
* **
33406303 TGTGTAGTACTAAGTGCAAGCTACTACGTGTATTAGA-TGGTGAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACT-GT-AGGTCACG
* * *
33406353 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTAGGTCACG
33406402 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
33406428 TGCATACCAG
Statistics
Matches: 108, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
47 1 0.01
48 4 0.04
49 31 0.29
50 42 0.39
51 30 0.28
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTAGGTCACG
Found at i:33410203 original size:20 final size:20
Alignment explanation
Indices: 33410180--33410233 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
33410170 AGTTTTTCCC
*
33410180 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
33410200 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
33410220 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
33410234 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:33410215 original size:30 final size:30
Alignment explanation
Indices: 33410180--33410253 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
33410170 AGTTTTTCCC
33410180 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
33410210 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
33410240 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
33410254 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:33410243 original size:20 final size:20
Alignment explanation
Indices: 33410180--33410244 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
33410170 AGTTTTTCCC
* * * *
33410180 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
33410200 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
33410219 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
33410240 AGCTC
1 AGCTC
33410245 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:33411769 original size:13 final size:12
Alignment explanation
Indices: 33411751--33411783 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
33411741 GTTCGTAACG
*
33411751 AAAAAAAAAGTC
1 AAAAAAAAAATC
33411763 AAAAAAAAAATC
1 AAAAAAAAAATC
33411775 AAAAAAAAA
1 AAAAAAAAA
33411784 TTTGAGTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.85, C:0.06, G:0.03, T:0.06
Consensus pattern (12 bp):
AAAAAAAAAATC
Found at i:33411876 original size:12 final size:12
Alignment explanation
Indices: 33411859--33411897 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
33411849 AAAAAAAGAG
33411859 AAAAATTCAAAA
1 AAAAATTCAAAA
33411871 AAAAATTC--AA
1 AAAAATTCAAAA
*
33411881 AAAAATTGAAAA
1 AAAAATTCAAAA
33411893 AAAAA
1 AAAAA
33411898 AAAAAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 9 0.38
12 15 0.62
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (12 bp):
AAAAATTCAAAA
Found at i:33411904 original size:22 final size:22
Alignment explanation
Indices: 33411849--33411919 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
33411839 TATTGGATTT
* * *
33411849 AAAAAAAGAGAAAAATTCAAAA
1 AAAAAAAAAAAAAAATTGAAAA
***
33411871 AAAAATTCAAAAAAATTGAAAA
1 AAAAAAAAAAAAAAATTGAAAA
* * *
33411893 AAAAAAAAAAAAGAAGTGACAA
1 AAAAAAAAAAAAAAATTGAAAA
33411915 AAAAA
1 AAAAA
33411920 TCGAGTTAAA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.77, C:0.04, G:0.08, T:0.10
Consensus pattern (22 bp):
AAAAAAAAAAAAAAATTGAAAA
Found at i:33412957 original size:6 final size:6
Alignment explanation
Indices: 33412948--33413047 Score: 74
Period size: 6 Copynumber: 16.2 Consensus size: 6
33412938 GAAAGAGATT
* ** * **
33412948 GAAAAA GAAAAC GAAAAA GAAAAA GAAATT GCAAAA GAAAAA GAAATC
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
** * * *
33412996 GAAAAA GTGAGA GAAAAA GAAAAT GAAGAAAA GAAAATT GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA-A GAAAAA GAAAAA
33413047 G
1 G
33413048 CGAAAAAAGA
Statistics
Matches: 69, Mismatches: 22, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
6 58 0.84
7 7 0.10
8 4 0.06
ACGTcount: A:0.70, C:0.03, G:0.20, T:0.07
Consensus pattern (6 bp):
GAAAAA
Found at i:33412963 original size:12 final size:12
Alignment explanation
Indices: 33412948--33413059 Score: 66
Period size: 12 Copynumber: 8.8 Consensus size: 12
33412938 GAAAGAGATT
33412948 GAAAAAGAAAAC
1 GAAAAAGAAAAC
*
33412960 GAAAAAGAAAAA
1 GAAAAAGAAAAC
**
33412972 GAAATTGCAAAA-
1 GAAAAAG-AAAAC
*
33412984 GAAAAAGAAATC
1 GAAAAAGAAAAC
* *
33412996 GAAAAAGTGAGA-
1 GAAAAAG-AAAAC
*
33413008 GAAAAAGAAAAT
1 GAAAAAGAAAAC
*
33413020 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAA-C
33413035 GAAAAAGAAAAAGC
1 GAAAAAG-AAAA-C
33413049 GAAAAAAGAAA
1 G-AAAAAGAAA
33413060 TTGAAAGAGA
Statistics
Matches: 78, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
11 5 0.06
12 36 0.46
13 11 0.14
14 18 0.23
15 8 0.10
ACGTcount: A:0.71, C:0.04, G:0.20, T:0.06
Consensus pattern (12 bp):
GAAAAAGAAAAC
Found at i:33412969 original size:18 final size:18
Alignment explanation
Indices: 33412948--33413047 Score: 83
Period size: 18 Copynumber: 5.4 Consensus size: 18
33412938 GAAAGAGATT
33412948 GAAAAAGAAAACGAAAAA
1 GAAAAAGAAAACGAAAAA
** *
33412966 GAAAAAGAAATTGCAAAA
1 GAAAAAGAAAACGAAAAA
*
33412984 GAAAAAGAAATCGAAAAA
1 GAAAAAGAAAACGAAAAA
** * * *
33413002 GTGAGAGAAAAAGAAAAT
1 GAAAAAGAAAACGAAAAA
*
33413020 GAAGAAAAGAAAATTGAAAAA
1 G-A-AAAAGAAAA-CGAAAAA
33413041 GAAAAAG
1 GAAAAAG
33413048 CGAAAAAAGA
Statistics
Matches: 63, Mismatches: 16, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
18 44 0.70
19 5 0.08
20 8 0.13
21 6 0.10
ACGTcount: A:0.70, C:0.03, G:0.20, T:0.07
Consensus pattern (18 bp):
GAAAAAGAAAACGAAAAA
Found at i:33413029 original size:14 final size:13
Alignment explanation
Indices: 33413008--33413045 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
33412998 AAAAGTGAGA
33413008 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
33413020 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
33413035 GAAAAAGAAAA
1 GAAAAAGAAAA
33413046 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:33413059 original size:21 final size:21
Alignment explanation
Indices: 33413009--33413059 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
33412999 AAAGTGAGAG
*
33413009 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
33413030 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
33413051 AAAAAGAAA
1 AAAAAGAAA
33413060 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:33413099 original size:33 final size:33
Alignment explanation
Indices: 33413062--33413124 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
33413052 AAAAGAAATT
33413062 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
33413095 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
33413125 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:33414920 original size:20 final size:20
Alignment explanation
Indices: 33414897--33414950 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
33414887 AGTTTTTCCC
*
33414897 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
33414917 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
33414937 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
33414951 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:33414932 original size:30 final size:30
Alignment explanation
Indices: 33414897--33414970 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
33414887 AGTTTTTCCC
33414897 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
33414927 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
33414957 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
33414971 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:33414960 original size:20 final size:20
Alignment explanation
Indices: 33414897--33414961 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
33414887 AGTTTTTCCC
* * * *
33414897 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
33414917 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
33414936 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
33414957 AGCTC
1 AGCTC
33414962 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:33416958 original size:30 final size:30
Alignment explanation
Indices: 33416922--33417022 Score: 87
Period size: 30 Copynumber: 3.4 Consensus size: 30
33416912 AGCTCACTCC
*
33416922 TAGCTCATTTTCAACTCACGAGCTAAACCT
1 TAGCTCATTTTCAGCTCACGAGCTAAACCT
** * * * * *
33416952 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCATTTTCAGCTCACGAGCTAAACCT
* * *
33416982 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTC-ATTTTCAGCTCACGAGCTAAACCT
33417012 TAGCTCATTTT
1 TAGCTCATTTT
33417023 AGTTTAAACT
Statistics
Matches: 51, Mismatches: 19, Indels: 3
0.70 0.26 0.04
Matches are distributed among these distances:
29 4 0.08
30 44 0.86
31 3 0.06
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.32
Consensus pattern (30 bp):
TAGCTCATTTTCAGCTCACGAGCTAAACCT
Found at i:33420821 original size:15 final size:16
Alignment explanation
Indices: 33420782--33420822 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
33420772 AACAACACTC
33420782 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
33420798 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
33420812 CTTTCTTTTTC
1 CTTTCTTTTTC
33420823 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:33421017 original size:17 final size:15
Alignment explanation
Indices: 33420980--33421018 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
33420970 TATCTCCCAC
33420980 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
33420996 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
33421013 TCATTT
1 TCATTT
33421019 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:33424420 original size:17 final size:18
Alignment explanation
Indices: 33424398--33424431 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33424388 TTTTTCTTTT
33424398 TCAATTT-TTTCTCAATC
1 TCAATTTCTTTCTCAATC
*
33424415 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTCTCAAT
33424432 TTTCTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.56
Consensus pattern (18 bp):
TCAATTTCTTTCTCAATC
Found at i:33424449 original size:27 final size:28
Alignment explanation
Indices: 33424389--33424455 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
33424379 TTCAACATCT
33424389 TTTTCTTTTTCAATTTTTTCTCAATCTCA
1 TTTTCTTTTTCAATTTTTTCTC-ATCTCA
* *
33424418 ATTTCTTTTTCAATTTTCTTTTC-T-TCA
1 TTTTCTTTTTCAATTTT-TTCTCATCTCA
33424445 TTTTCTTTTTC
1 TTTTCTTTTTC
33424456 TCTCACTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.38
28 1 0.03
29 16 0.47
30 4 0.12
ACGTcount: A:0.13, C:0.19, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTTCTTTTTCAATTTTTTCTCATCTCA
Found at i:33424518 original size:11 final size:12
Alignment explanation
Indices: 33424488--33424523 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
33424478 TCTTTTGCAA
*
33424488 TTTCTTTTTCTT
1 TTTCGTTTTCTT
33424500 TTTCGTTTTCTT
1 TTTCGTTTTCTT
33424512 TTT-GTTTTCTT
1 TTTCGTTTTCTT
33424523 T
1 T
33424524 CAATTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTCGTTTTCTT
Found at i:33425596 original size:13 final size:13
Alignment explanation
Indices: 33425563--33425610 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
33425553 TTTTAACTCG
*
33425563 ATTTTTTTTGTCA
1 ATTTTTTTTTTCA
*
33425576 CTTCTTTTTTTT-A
1 ATT-TTTTTTTTCA
*
33425589 ATTTTTTTTTTCG
1 ATTTTTTTTTTCA
33425602 ATTTTTTTT
1 ATTTTTTTT
33425611 ATTTTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 8 0.28
13 14 0.48
14 7 0.24
ACGTcount: A:0.10, C:0.08, G:0.04, T:0.77
Consensus pattern (13 bp):
ATTTTTTTTTTCA
Found at i:33428170 original size:31 final size:32
Alignment explanation
Indices: 33428122--33428199 Score: 126
Period size: 32 Copynumber: 2.5 Consensus size: 32
33428112 TTTCAATCAC
33428122 TCTTTTTTTTTTCAATTTCG-ATTTTTCTTCT
1 TCTTTTTTTTTTCAATTTCGAATTTTTCTTCT
33428153 TCTTCTTTTTTTT-AATTTCGAATTTTTCTTCT
1 TCTT-TTTTTTTTCAATTTCGAATTTTTCTTCT
33428185 TC-TTTTTTTTTCAAT
1 TCTTTTTTTTTTCAAT
33428200 ACTAAATACA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
30 8 0.18
31 15 0.34
32 21 0.48
ACGTcount: A:0.12, C:0.15, G:0.03, T:0.71
Consensus pattern (32 bp):
TCTTTTTTTTTTCAATTTCGAATTTTTCTTCT
Found at i:33428256 original size:14 final size:14
Alignment explanation
Indices: 33428237--33428281 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
33428227 GAATACAAAC
33428237 TTTTTTT-GAATTT
1 TTTTTTTCGAATTT
33428250 TTTTTTTCGAA-TT
1 TTTTTTTCGAATTT
33428263 TTTTTTTC-AAGTTT
1 TTTTTTTCGAA-TTT
33428277 TTTTT
1 TTTTT
33428282 ATTTATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.07
13 17 0.59
14 10 0.34
ACGTcount: A:0.13, C:0.04, G:0.07, T:0.76
Consensus pattern (14 bp):
TTTTTTTCGAATTT
Found at i:33431243 original size:16 final size:16
Alignment explanation
Indices: 33431224--33431256 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
33431214 ATGGCCGGCC
33431224 ATAAAAATGGTGTGCT
1 ATAAAAATGGTGTGCT
33431240 ATAAAAATGGTGTGCT
1 ATAAAAATGGTGTGCT
33431256 A
1 A
33431257 CTGATTGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.30
Consensus pattern (16 bp):
ATAAAAATGGTGTGCT
Found at i:33434396 original size:29 final size:29
Alignment explanation
Indices: 33434330--33434386 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
33434320 GATTCAAAGA
*
33434330 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
33434359 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
33434387 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Done.