Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3042.1
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: 166911
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4015 characters in sequence are not A, C, G, or T
Found at i:3959 original size:29 final size:29
Alignment explanation
Indices: 3925--3996 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
3915 ATATTCATAT
*
3925 GGCCCATTAGGCCCAAATCACCTGTATAG
1 GGCCCATTAGGCCCAAATCACATGTATAG
* *
3954 GGCCCATTAGGCCCAAATCACATTTATAT
1 GGCCCATTAGGCCCAAATCACATGTATAG
*
3983 GGCCCGTT-GGCCCA
1 GGCCCATTAGGCCCA
3997 GTCACATTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 6 0.15
29 33 0.85
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.22
Consensus pattern (29 bp):
GGCCCATTAGGCCCAAATCACATGTATAG
Found at i:5377 original size:16 final size:16
Alignment explanation
Indices: 5358--5390 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5348 AAATAAAGAA
5358 AATTCAGGATTTTGAG
1 AATTCAGGATTTTGAG
5374 AATTCAGGATTTTGAG
1 AATTCAGGATTTTGAG
5390 A
1 A
5391 TTTTTGGATT
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:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (16 bp):
AATTCAGGATTTTGAG
Found at i:5399 original size:16 final size:16
Alignment explanation
Indices: 5364--5414 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
5354 AGAAAATTCA
* **
5364 GGATTTTGAGAATTCA
1 GGATTTTGAGATTTTT
5380 GGATTTTGAGATTTTT
1 GGATTTTGAGATTTTT
5396 GGATTTT-AGGATTTTT
1 GGATTTTGA-GATTTTT
5412 GGA
1 GGA
5415 GCATTACAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 1 0.03
16 30 0.97
ACGTcount: A:0.24, C:0.02, G:0.27, T:0.47
Consensus pattern (16 bp):
GGATTTTGAGATTTTT
Found at i:10184 original size:38 final size:43
Alignment explanation
Indices: 10071--10174 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 43
10061 AATGCCTCTA
* * * *
10071 TCCCAGATAGGGTCTTATACG-AAA-TCAGATACGATGTCGATG
1 TCCCAGACATGGTCTTACACGTAAATTCA-ATTCGATGTCGATG
10113 TCCCAGACATGGTCTTACACGTAAATTTCAATTCGATGTCTG-TG
1 TCCCAGACATGGTCTTACACGTAAA-TTCAATTCGATGTC-GATG
10157 TCCCAGACATGGTCTTAC
1 TCCCAGACATGGTCTTAC
10175 CTGATAATTC
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
42 18 0.33
43 3 0.06
44 29 0.54
45 4 0.07
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGTAAATTCAATTCGATGTCGATG
Found at i:21911 original size:30 final size:30
Alignment explanation
Indices: 21875--21972 Score: 74
Period size: 30 Copynumber: 3.3 Consensus size: 30
21865 AGCTCACTCC
21875 TAGCTCATATTCAGTTCACGAGCTAAACCT
1 TAGCTCATATTCAGTTCACGAGCTAAACCT
** * * * *
21905 TAGCTCAGCTTCAGCTT-AGGAGTTTAATCT
1 TAGCTCATATTCAG-TTCACGAGCTAAACCT
* * * *
21935 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGTTCACGAGCTAAACCT
21965 TAGCTCAT
1 TAGCTCAT
21973 TTTAGTTTAA
Statistics
Matches: 49, Mismatches: 15, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
29 1 0.02
30 46 0.94
31 2 0.04
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (30 bp):
TAGCTCATATTCAGTTCACGAGCTAAACCT
Found at i:28687 original size:93 final size:93
Alignment explanation
Indices: 28579--28750 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
28569 CGCCCATAAG
* *
28579 CGAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28644 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
28672 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28737 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
28751 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:28747 original size:46 final size:46
Alignment explanation
Indices: 28572--28747 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
28562 TGTAACCCGC
* * * *
28572 CCATAAGCGAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
28618 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
28668 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
28711 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
28748 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.56
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:28766 original size:46 final size:46
Alignment explanation
Indices: 28621--28759 Score: 144
Period size: 47 Copynumber: 3.0 Consensus size: 46
28611 TTCGCATCCA
28621 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC
* * * * *
28669 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATC
28714 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
28760 CTAGTGACAT
Statistics
Matches: 75, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
44 8 0.11
45 2 0.03
46 28 0.37
47 30 0.40
48 2 0.03
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
Found at i:40416 original size:25 final size:27
Alignment explanation
Indices: 40369--40422 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
40359 AATTTGTCCC
*
40369 AGCTACTACAAGGTTTATATGTGTCTTA
1 AGCTACTACAA-GATTATATGTGTCTTA
40397 AGCTACTACAA-ATTAT-TGTGTCTTA
1 AGCTACTACAAGATTATATGTGTCTTA
40422 A
1 A
40423 TAGGATTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 10 0.40
26 4 0.16
28 11 0.44
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (27 bp):
AGCTACTACAAGATTATATGTGTCTTA
Found at i:42595 original size:21 final size:21
Alignment explanation
Indices: 42569--42631 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
42559 TTGGTATTTG
42569 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
42590 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
42611 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
42632 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:44663 original size:15 final size:15
Alignment explanation
Indices: 44638--44684 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
44628 AGAAAAGAAT
44638 AAAGAAAATGAAAATG
1 AAAG-AAATGAAAATG
*
44654 AAAGAAATGAAAAAG
1 AAAGAAATGAAAATG
*
44669 AAA-AATGTGAAAATG
1 AAAGAA-ATGAAAATG
44684 A
1 A
44685 GATTTCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 2 0.07
15 21 0.78
16 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.19, T:0.13
Consensus pattern (15 bp):
AAAGAAATGAAAATG
Found at i:44673 original size:28 final size:29
Alignment explanation
Indices: 44628--44684 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
44618 ATTTTGAGCG
44628 AGAAAAGAATAAAGAAAA-TGAAAATGAA
1 AGAAAAGAATAAAGAAAAGTGAAAATGAA
*
44656 AGAAATGAA-AAAGAAAAATGTGAAAATGA
1 AGAAAAGAATAAAG-AAAA-GTGAAAATGA
44685 GATTTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 4 0.16
28 12 0.48
30 9 0.36
ACGTcount: A:0.68, C:0.00, G:0.19, T:0.12
Consensus pattern (29 bp):
AGAAAAGAATAAAGAAAAGTGAAAATGAA
Found at i:44731 original size:12 final size:12
Alignment explanation
Indices: 44714--44789 Score: 50
Period size: 12 Copynumber: 6.3 Consensus size: 12
44704 AGTGAAAAGC
44714 AAAAAGAGATTG
1 AAAAAGAGATTG
*
44726 AAAAAGAAATTG
1 AAAAAGAGATTG
*
44738 --AAAGAGA-AG
1 AAAAAGAGATTG
*
44747 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
44762 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
44774 AAAGAGAGCTTG
1 AAAAAGAGATTG
44786 AAAA
1 AAAA
44790 GAAATCGAGT
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
9 1 0.02
10 6 0.12
11 4 0.08
12 25 0.52
13 5 0.10
15 7 0.15
ACGTcount: A:0.62, C:0.01, G:0.25, T:0.12
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:44755 original size:15 final size:15
Alignment explanation
Indices: 44737--44770 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
44727 AAAAGAAATT
44737 GAAAGAGAAGAAAAA
1 GAAAGAGAAGAAAAA
**
44752 GAAAGAGTGGAAAAA
1 GAAAGAGAAGAAAAA
44767 GAAA
1 GAAA
44771 TTGAAAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (15 bp):
GAAAGAGAAGAAAAA
Found at i:46837 original size:150 final size:150
Alignment explanation
Indices: 46566--46866 Score: 584
Period size: 150 Copynumber: 2.0 Consensus size: 150
46556 TGTCTAATTT
* *
46566 AATTTATGTTTAATTAGTGTGTCTAAATTATATTAATGTTTGTTCAGTTGAATTTTATGTGATTT
1 AATTTATGTTTAATTAGTGTGTCTAAATTATATTAATGTTTGTTCAGCTAAATTTTATGTGATTT
46631 AATTTTGGTTCATGTGTTTTTGTAGGTGAGTTGAATTTGGAGAGTAATTAAACAAGGTTCATGCA
66 AATTTTGGTTCATGTGTTTTTGTAGGTGAGTTGAATTTGGAGAGTAATTAAACAAGGTTCATGCA
46696 TGATAGGTTCAATGTATGGG
131 TGATAGGTTCAATGTATGGG
46716 AATTTATGTTTAATTAGTGTGTCTAAATTATATTAATGTTTGTTCAGCTAAATTTTATGTGATTT
1 AATTTATGTTTAATTAGTGTGTCTAAATTATATTAATGTTTGTTCAGCTAAATTTTATGTGATTT
46781 AATTTTGGTTCATGTGTTTTTGTAGGTGAGTTGAATTTGGAGAGTAATTAAACAAGGTTCATGCA
66 AATTTTGGTTCATGTGTTTTTGTAGGTGAGTTGAATTTGGAGAGTAATTAAACAAGGTTCATGCA
46846 TGATAGGTTCAATGTATGGG
131 TGATAGGTTCAATGTATGGG
46866 A
1 A
46867 CGGTGCATGT
Statistics
Matches: 149, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 149 1.00
ACGTcount: A:0.28, C:0.05, G:0.22, T:0.45
Consensus pattern (150 bp):
AATTTATGTTTAATTAGTGTGTCTAAATTATATTAATGTTTGTTCAGCTAAATTTTATGTGATTT
AATTTTGGTTCATGTGTTTTTGTAGGTGAGTTGAATTTGGAGAGTAATTAAACAAGGTTCATGCA
TGATAGGTTCAATGTATGGG
Found at i:48304 original size:30 final size:30
Alignment explanation
Indices: 48270--48367 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
48260 AGCTCACTCC
48270 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
48300 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
48330 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
48360 TAGCTCAT
1 TAGCTCAT
48368 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:48679 original size:19 final size:19
Alignment explanation
Indices: 48655--48691 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
48645 AGGTGCATGT
48655 ATGACCAGATTCAAGGTGC
1 ATGACCAGATTCAAGGTGC
48674 ATGACCAGATTCAAGGTG
1 ATGACCAGATTCAAGGTG
48692 TTTAGAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (19 bp):
ATGACCAGATTCAAGGTGC
Found at i:50166 original size:30 final size:30
Alignment explanation
Indices: 50095--50177 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
50085 CTTTTGTTTC
* *
50095 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
50126 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
50155 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
50178 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:50177 original size:18 final size:18
Alignment explanation
Indices: 50128--50183 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
50118 CACTCTCAAA
* *
50128 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
50145 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
50163 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
50182 TT
1 TT
50184 CAAAGGCTTT
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:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:50184 original size:12 final size:12
Alignment explanation
Indices: 50153--50177 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50143 TTTTTCAATC
50153 TCATTTTCTTTT
1 TCATTTTCTTTT
50165 TCATTTTCTTTT
1 TCATTTTCTTTT
50177 T
1 T
50178 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:51230 original size:12 final size:12
Alignment explanation
Indices: 51193--51237 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
51183 TTTTCATTTT
51193 TTTTCTTTTCGAAA
1 TTTT-TTTTCG-AA
*
51207 ATTTTTTT-GAA
1 TTTTTTTTCGAA
51218 TTTTTTTTCGAA
1 TTTTTTTTCGAA
51230 TTTTTTTT
1 TTTTTTTT
51238 ACTTGTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 9 0.32
12 12 0.43
13 4 0.14
14 3 0.11
ACGTcount: A:0.18, C:0.07, G:0.07, T:0.69
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:51254 original size:42 final size:39
Alignment explanation
Indices: 51179--51257 Score: 95
Period size: 42 Copynumber: 1.9 Consensus size: 39
51169 CATTAAACAC
* *
51179 TTTTTTTTCATTTTTTTTCTTTTCGAAAATTTTTTTGAA
1 TTTTTTTTCATTTTTTTTCTTGTAGAAAATTTTTTTGAA
* *
51218 TTTTTTTTCGAATTTTTTTTACTTGTATAAATTTTTTTTG
1 TTTTTTTTC--ATTTTTTTT-CTTGTAGAAAATTTTTTTG
51258 TACTATATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 9 0.27
41 9 0.27
42 15 0.45
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (39 bp):
TTTTTTTTCATTTTTTTTCTTGTAGAAAATTTTTTTGAA
Found at i:53047 original size:30 final size:30
Alignment explanation
Indices: 53013--53109 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
53003 TAAACTAAAA
53013 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
53043 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
53073 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
53103 TGAGCTA
1 TGAGCTA
53110 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:53872 original size:16 final size:16
Alignment explanation
Indices: 53851--53885 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
53841 TTTTTTTGAA
53851 TTTTTTTTC-GAATTT
1 TTTTTTTTCTGAATTT
53866 TTTTTTTTCTGAATTT
1 TTTTTTTTCTGAATTT
53882 TTTT
1 TTTT
53886 ATACTTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTTTTTTCTGAATTT
Found at i:53885 original size:13 final size:12
Alignment explanation
Indices: 53825--53871 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
53815 TGCACAAATC
53825 ATTTTTTTTTGAA
1 ATTTTTTTTTG-A
*
53838 ACTTTTTTTTGA
1 ATTTTTTTTTGA
*
53850 ATTTTTTTTCGA
1 ATTTTTTTTTGA
53862 ATTTTTTTTT
1 ATTTTTTTTT
53872 TTCTGAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 20 0.67
13 10 0.33
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.72
Consensus pattern (12 bp):
ATTTTTTTTTGA
Found at i:59100 original size:43 final size:43
Alignment explanation
Indices: 59052--59136 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
59042 TGTATGTCCT
59052 CCAAACATTGAACCGGTCCATGAATGTATCCTCCCGTTCAATG
1 CCAAACATTGAACCGGTCCATGAATGTATCCTCCCGTTCAATG
*
59095 CCAAACATTGAACCGGTCCATGCATGTATCCTCCCGTTCAAT
1 CCAAACATTGAACCGGTCCATGAATGTATCCTCCCGTTCAAT
59137 TAACTTTCCC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.26
Consensus pattern (43 bp):
CCAAACATTGAACCGGTCCATGAATGTATCCTCCCGTTCAATG
Found at i:59517 original size:20 final size:20
Alignment explanation
Indices: 59470--59517 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
59460 AGTAAGCTCG
59470 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
59490 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
59510 GTTGAGCT
1 GTTGAGCT
59518 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:62077 original size:11 final size:12
Alignment explanation
Indices: 62049--62075 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
62039 GAGAACTTGC
62049 AAAAGCCTTTGA
1 AAAAGCCTTTGA
62061 AAAAGCCTTTGA
1 AAAAGCCTTTGA
62073 AAA
1 AAA
62076 GCAAAATGAA
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:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (12 bp):
AAAAGCCTTTGA
Found at i:62114 original size:30 final size:28
Alignment explanation
Indices: 62079--62152 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 28
62069 TTGAAAAGCA
*
62079 AAATGAAAATGAAAATGAGATTGAAAAAG
1 AAATGAAAA-GAAAATGAGAGTGAAAAAG
**
62108 AGAATGAAAAGCAATTTGAGAGTGAAAAAG
1 A-AATGAAAAG-AAAATGAGAGTGAAAAAG
62138 AAGATGAAAAAGAAA
1 AA-ATG-AAAAGAAA
62153 TTGAAACAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
29 3 0.08
30 29 0.78
31 5 0.14
ACGTcount: A:0.61, C:0.01, G:0.23, T:0.15
Consensus pattern (28 bp):
AAATGAAAAGAAAATGAGAGTGAAAAAG
Found at i:62134 original size:42 final size:42
Alignment explanation
Indices: 62069--62158 Score: 103
Period size: 42 Copynumber: 2.1 Consensus size: 42
62059 GAAAAAGCCT
*
62069 TTGAAAAGCAAAATGAAAATGAAAATG-AGATTGAAAAAGAGAA
1 TTGAAAAGCAAAATGAAAATGAAAAAGAAGA-TGAAAAAGA-AA
** * *
62112 -TGAAAAGCAATTTGAGAGTGAAAAAGAAGATGAAAAAGAAA
1 TTGAAAAGCAAAATGAAAATGAAAAAGAAGATGAAAAAGAAA
62153 TTGAAA
1 TTGAAA
62159 CAAAAGAAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
41 2 0.05
42 35 0.88
43 3 0.08
ACGTcount: A:0.59, C:0.02, G:0.22, T:0.17
Consensus pattern (42 bp):
TTGAAAAGCAAAATGAAAATGAAAAAGAAGATGAAAAAGAAA
Found at i:65635 original size:47 final size:47
Alignment explanation
Indices: 65566--65683 Score: 218
Period size: 47 Copynumber: 2.5 Consensus size: 47
65556 CGCCCATAAG
65566 TGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 TGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
*
65613 TGAACTTGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 TGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
*
65660 CGAACTCGGACTCAACTCAACGAG
1 TGAACTCGGACTCAACTCAACGAG
65684 TTTGGACAGT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 68 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (47 bp):
TGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:65754 original size:46 final size:48
Alignment explanation
Indices: 65564--65754 Score: 170
Period size: 47 Copynumber: 4.1 Consensus size: 48
65554 CCCGCCCATA
*
65564 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAG-TACATCTCT
* *
65613 --TGAACTTGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAG-TACATCTCT
* * * *
65660 --CGAACTCGGACTCAACTCAACGAGTTTGGA----CAGTCGCATC-CAT
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAGT-ACATCTC-T
* * *
65703 AAGTGAACTCGGACTCAACTCAACGAGTTTGGATGCCCA-AACATC-CT
1 -AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAGTACATCTCT
65750 AGTGA
1 AGTGA
65755 CATGTCACTT
Statistics
Matches: 123, Mismatches: 10, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 7 0.06
46 34 0.28
47 73 0.59
48 5 0.04
50 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (48 bp):
AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAGTACATCTCT
Found at i:69604 original size:169 final size:169
Alignment explanation
Indices: 69325--69664 Score: 626
Period size: 169 Copynumber: 2.0 Consensus size: 169
69315 ATTTTAAATT
69325 ATGTTAGACAACTTGTGCTACTCGGTTTTAAGTGAAAACGAGTAAAAGGGCTTAATAGGTAAAAA
1 ATGTTAGACAACTTGTGCTACTCGGTTTTAAGTGAAAACGAGTAAAAGGGCTTAATAGGTAAAAA
*
69390 TACCTAATAGTCATAAATGCATGTTAGAGTGTGAATTTGATGCTATCATAGAAGGGAAAAATGAT
66 TACCGAATAGTCATAAATGCATGTTAGAGTGTGAATTTGATGCTATCATAGAAGGGAAAAATGAT
69455 CAACATGTCATAAAACATAAGAATAAGGGCTGAAATTAA
131 CAACATGTCATAAAACATAAGAATAAGGGCTGAAATTAA
*
69494 ATGTTAGACAACTTGTGCTACTCGGTTTTAAGTGAAAACGAGTAAAAGGGCTTAATCGGTAAAAA
1 ATGTTAGACAACTTGTGCTACTCGGTTTTAAGTGAAAACGAGTAAAAGGGCTTAATAGGTAAAAA
* * *
69559 TACCGAATATTCATAAGTGCATGTTAGAGTGTGAATTTGATGCTATCTTAGAAGGGAAAAATGAT
66 TACCGAATAGTCATAAATGCATGTTAGAGTGTGAATTTGATGCTATCATAGAAGGGAAAAATGAT
*
69624 CAGCATGTCATAAAACATAAGAATAAGGGCTGAAATTAA
131 CAACATGTCATAAAACATAAGAATAAGGGCTGAAATTAA
69663 AT
1 AT
69665 TCCCGAGCCT
Statistics
Matches: 165, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
169 165 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (169 bp):
ATGTTAGACAACTTGTGCTACTCGGTTTTAAGTGAAAACGAGTAAAAGGGCTTAATAGGTAAAAA
TACCGAATAGTCATAAATGCATGTTAGAGTGTGAATTTGATGCTATCATAGAAGGGAAAAATGAT
CAACATGTCATAAAACATAAGAATAAGGGCTGAAATTAA
Found at i:70468 original size:49 final size:49
Alignment explanation
Indices: 70396--70582 Score: 252
Period size: 49 Copynumber: 3.8 Consensus size: 49
70386 TGAGGTCACG
*
70396 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * * * *
70445 TGTGTAGTACTAAGTGCAGGCTACTA--TGCTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTG-TACCAGATAA-T-TGGTCGCA
*
70495 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* *
70544 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
70583 GCTTCGGCTA
Statistics
Matches: 119, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
47 2 0.02
48 8 0.07
49 68 0.57
50 32 0.27
51 7 0.06
52 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:70562 original size:99 final size:101
Alignment explanation
Indices: 70382--70577 Score: 351
Period size: 99 Copynumber: 2.0 Consensus size: 101
70372 CAAATGAACT
*
70382 ACTGTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATG
1 ACTGTGA-GTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATG
70447 TGTAGTACTAAGTGCAGGCTACTATGC-TACCCGAAA
65 TGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAA
*
70483 ACTGTGA-TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCATGT
1 ACTGTGAGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGT
70547 GTAGTACTAAGTGCAGGCTACTATGCGTACC
66 GTAGTACTAAGTGCAGGCTACTATGCGTACC
70578 AGATAGCTTC
Statistics
Matches: 92, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
99 81 0.88
100 4 0.04
101 7 0.08
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (101 bp):
ACTGTGAGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGT
GTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAA
Found at i:74747 original size:43 final size:43
Alignment explanation
Indices: 74683--74769 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
74673 TGAAAGAGCG
74683 GTTGACCAAAGCACCAATGTTAGTGCAACCCGAGTCGGGGAAA
1 GTTGACCAAAGCACCAATGTTAGTGCAACCCGAGTCGGGGAAA
*
74726 GTTGACCAAAGCACCAGTGTTAGTGCAACCCGAGTCGGGGAAA
1 GTTGACCAAAGCACCAATGTTAGTGCAACCCGAGTCGGGGAAA
74769 G
1 G
74770 AATTTGTGAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.31, C:0.23, G:0.30, T:0.16
Consensus pattern (43 bp):
GTTGACCAAAGCACCAATGTTAGTGCAACCCGAGTCGGGGAAA
Found at i:75600 original size:30 final size:30
Alignment explanation
Indices: 75564--75661 Score: 74
Period size: 30 Copynumber: 3.3 Consensus size: 30
75554 AGCTCACTCC
75564 TAGCTCATATTCAGTTCACGAGCTAAACCT
1 TAGCTCATATTCAGTTCACGAGCTAAACCT
** * * * *
75594 TAGCTCAGCTTCAGCTT-AGGAGTTTAATCT
1 TAGCTCATATTCAG-TTCACGAGCTAAACCT
* * * *
75624 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGTTCACGAGCTAAACCT
75654 TAGCTCAT
1 TAGCTCAT
75662 TTTAGTTTAA
Statistics
Matches: 49, Mismatches: 15, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
29 1 0.02
30 46 0.94
31 2 0.04
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (30 bp):
TAGCTCATATTCAGTTCACGAGCTAAACCT
Found at i:82560 original size:46 final size:46
Alignment explanation
Indices: 82493--82667 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
82483 TGTAACCCGC
*
82493 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* *
82539 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * * *
82589 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGGAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
82632 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG
82668 ATGCTCAACC
Statistics
Matches: 109, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 2 0.02
44 2 0.02
45 2 0.02
46 62 0.57
47 28 0.26
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:82613 original size:93 final size:93
Alignment explanation
Indices: 82500--82671 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
82490 CGCCCATAAG
* *
82500 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
82565 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
82593 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGGATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
82658 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
82672 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:87735 original size:39 final size:39
Alignment explanation
Indices: 87681--87762 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
87671 AGTAGTCTGG
*
87681 GATTTAGGACCCACATTTTGCTTCCTATAATTCCCATAN
1 GATTTAGGACCCACATTTTGCTTCCTATAATTCCCATAT
*
87720 GATTTAGGACCCACATTTTGCTTCTTATAATTCCCATAT
1 GATTTAGGACCCACATTTTGCTTCCTATAATTCCCATAT
87759 GATT
1 GATT
87763 GCCCAGTTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.39
Consensus pattern (39 bp):
GATTTAGGACCCACATTTTGCTTCCTATAATTCCCATAT
Found at i:88118 original size:24 final size:23
Alignment explanation
Indices: 88090--88134 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
88080 ATATTACCTT
*
88090 GCTTCAGCTCAATAAATTCTTTAC
1 GCTTCAGATCAATAAA-TCTTTAC
*
88114 GCTTCTGATCAATAAATCTTT
1 GCTTCAGATCAATAAATCTTT
88135 CACTAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (23 bp):
GCTTCAGATCAATAAATCTTTAC
Found at i:94356 original size:86 final size:85
Alignment explanation
Indices: 94250--94410 Score: 222
Period size: 86 Copynumber: 1.9 Consensus size: 85
94240 AGGATTTTGT
* *
94250 TATCTGTTTTCGTGTAAGACCAC-GTCTGGGA-CGTTGGCATCGACT-TTT-ATTTTACATGTAA
1 TATCTGATTTCGTGTAAGACC-CTGTCTGGGATAG-TGGCATCGA-TGTTTGA--TTACATGTAA
*
94311 GACCATGTCTGGGACATCGGTATCG
61 GACCAGGTCTGGGACATCGGTATCG
94336 TATCTGATTTCGTGTAAGACCCTGTCTGGGATAGTGGCATCGATGTTTGATTACATGTAAGACCA
1 TATCTGATTTCGTGTAAGACCCTGTCTGGGATAGTGGCATCGATGTTTGATTACATGTAAGACCA
94401 GGTCTGGGAC
66 GGTCTGGGAC
94411 GTTGGCATTG
Statistics
Matches: 68, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
85 26 0.38
86 40 0.59
87 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (85 bp):
TATCTGATTTCGTGTAAGACCCTGTCTGGGATAGTGGCATCGATGTTTGATTACATGTAAGACCA
GGTCTGGGACATCGGTATCG
Found at i:94398 original size:43 final size:42
Alignment explanation
Indices: 94301--94410 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 42
94291 GACTTTTATT
*
94301 TTACATGTAAGACCATGTCTGGGACATCGGTATCGTATCTGA
1 TTACATGTAAGACCATGTCTGGGACATCGGCATCGTATCTGA
* * * * * *
94343 TTTCGTGTAAGACCCTGTCTGGGATAGT-GGCATCGATGTTTGA
1 TTACATGTAAGACCATGTCTGGGACA-TCGGCATCG-TATCTGA
*
94386 TTACATGTAAGACCAGGTCTGGGAC
1 TTACATGTAAGACCATGTCTGGGAC
94411 GTTGGCATTG
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
42 28 0.52
43 26 0.48
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (42 bp):
TTACATGTAAGACCATGTCTGGGACATCGGCATCGTATCTGA
Found at i:94417 original size:43 final size:42
Alignment explanation
Indices: 94262--94418 Score: 149
Period size: 43 Copynumber: 3.7 Consensus size: 42
94252 TCTGTTTTCG
*
94262 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTTT-ATTTTACA
1 TGTAAGACCATGTCTGGGACGTTGGCATCGA-TTTTGA--TTACA
* * * * * *
94306 TGTAAGACCATGTCTGGGACATCGGTATCG-TATCTGATTTCG
1 TGTAAGACCATGTCTGGGACGTTGGCATCGAT-TTTGATTACA
* *
94348 TGTAAGACCCTGTCTGGGATAG-TGGCATCGATGTTTGATTACA
1 TGTAAGACCATGTCTGGGA-CGTTGGCATCGAT-TTTGATTACA
*
94391 TGTAAGACCAGGTCTGGGACGTTGGCAT
1 TGTAAGACCATGTCTGGGACGTTGGCAT
94419 TGTATATGTT
Statistics
Matches: 89, Mismatches: 19, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
42 29 0.33
43 33 0.37
44 27 0.30
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.32
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACGTTGGCATCGATTTTGATTACA
Found at i:98336 original size:13 final size:13
Alignment explanation
Indices: 98318--98344 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
98308 AAGATAGGGT
98318 AGATAATACAAAC
1 AGATAATACAAAC
98331 AGATAATACAAAC
1 AGATAATACAAAC
98344 A
1 A
98345 TCGAGCCACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.15, G:0.07, T:0.15
Consensus pattern (13 bp):
AGATAATACAAAC
Found at i:102213 original size:12 final size:12
Alignment explanation
Indices: 102196--102227 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
102186 ATCACTAACC
102196 CAATACCCAAAT
1 CAATACCCAAAT
102208 CAATACCCAAAT
1 CAATACCCAAAT
*
102220 TAATACCC
1 CAATACCC
102228 TAGCCCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (12 bp):
CAATACCCAAAT
Found at i:103576 original size:25 final size:25
Alignment explanation
Indices: 103544--103625 Score: 98
Period size: 25 Copynumber: 3.3 Consensus size: 25
103534 TAAAATTCTC
103544 TTTATGTAAATTTATATTTAAAATA
1 TTTATGTAAATTTATATTTAAAATA
* *
103569 TTTATGT-AATATT-TA-TTCACATA
1 TTTATGTAAAT-TTATATTTAAAATA
*
103592 CATTATGTAAATTTATATTTAAAATA
1 -TTTATGTAAATTTATATTTAAAATA
103618 TTTATGTA
1 TTTATGTA
103626 GTATTCATTC
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
23 6 0.13
24 13 0.28
25 21 0.46
26 6 0.13
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (25 bp):
TTTATGTAAATTTATATTTAAAATA
Found at i:103598 original size:49 final size:49
Alignment explanation
Indices: 103545--103644 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
103535 AAAATTCTCT
*
103545 TTATGTAAATTTATATTTAAAATATTTATGTAATATTTATTCACATACA
1 TTATGTAAATTTATATTTAAAATATTTATGTAATATTCATTCACATACA
* *
103594 TTATGTAAATTTATATTTAAAATATTTATGTAGTATTCATTCTCATACA
1 TTATGTAAATTTATATTTAAAATATTTATGTAATATTCATTCACATACA
103643 TT
1 TT
103645 GATATTTATA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (49 bp):
TTATGTAAATTTATATTTAAAATATTTATGTAATATTCATTCACATACA
Found at i:104319 original size:19 final size:18
Alignment explanation
Indices: 104290--104330 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 18
104280 GATATTGTTA
104290 ATTTCAAATAAATGTTTT
1 ATTTCAAATAAATGTTTT
104308 ATTTCTAAATAAATGTTTT
1 ATTTC-AAATAAATGTTTT
104327 ATTT
1 ATTT
104331 GATTCAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (18 bp):
ATTTCAAATAAATGTTTT
Found at i:107353 original size:29 final size:29
Alignment explanation
Indices: 107290--107397 Score: 103
Period size: 29 Copynumber: 3.8 Consensus size: 29
107280 TTCACATACC
* * *
107290 TATATCTGGCCTATTAAGCCC-AATCATA
1 TATATATGGCCTATTAGGCCCAAATCACA
* *
107318 TTTATATGGCCTATTAGGCCCAAATCACC
1 TATATATGGCCTATTAGGCCCAAATCACA
* *
107347 TATATATGGTCC-ATTAGGCCTAAATCGCA
1 TATATATGG-CCTATTAGGCCCAAATCACA
* **
107376 TTTATATGGCCCGTTAGGCCCA
1 TATATATGGCCTATTAGGCCCA
107398 GTCACATTCA
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
28 20 0.31
29 43 0.66
30 2 0.03
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (29 bp):
TATATATGGCCTATTAGGCCCAAATCACA
Found at i:107649 original size:16 final size:16
Alignment explanation
Indices: 107628--107678 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
107618 AACTTTAGGC
107628 TTTCGGCATTTCAGCT
1 TTTCGGCATTTCAGCT
107644 TTTCGGCATTTCAG-T
1 TTTCGGCATTTCAGCT
*
107659 ATTTCGGCATTTCGGCT
1 -TTTCGGCATTTCAGCT
107676 TTT
1 TTT
107679 GTCAATTCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 1 0.03
16 30 0.94
17 1 0.03
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.47
Consensus pattern (16 bp):
TTTCGGCATTTCAGCT
Found at i:107672 original size:8 final size:8
Alignment explanation
Indices: 107628--107674 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
107618 AACTTTAGGC
107628 TTTCGGCA
1 TTTCGGCA
* *
107636 TTTCAGCT
1 TTTCGGCA
107644 TTTCGGCA
1 TTTCGGCA
* *
107652 TTTCAGTA
1 TTTCGGCA
107660 TTTCGGCA
1 TTTCGGCA
107668 TTTCGGC
1 TTTCGGC
107675 TTTTGTCAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (8 bp):
TTTCGGCA
Found at i:111843 original size:28 final size:28
Alignment explanation
Indices: 111800--111942 Score: 171
Period size: 28 Copynumber: 5.0 Consensus size: 28
111790 TACCTGTATC
** *
111800 TGGCCCATTAACCCCAATCATATTTATA
1 TGGCCCATTAGGCCCAATCACATTTATA
111828 TGGCCCATTAGGCCCAAATCAC-TTGTATA
1 TGGCCCATTAGGCCC-AATCACATT-TATA
*
111857 TGGCCCATTAGGTCCAAATCACATTTATA
1 TGGCCCATTAGG-CCCAATCACATTTATA
* *
111886 TGGCCCGTTAGGCCCAGTCACATTTATA
1 TGGCCCATTAGGCCCAATCACATTTATA
* * *
111914 TGGCCCGTTAGGCCCAGTCACATTCATA
1 TGGCCCATTAGGCCCAATCACATTTATA
111942 T
1 T
111943 TCATGCTCAC
Statistics
Matches: 103, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
28 57 0.55
29 42 0.41
30 4 0.04
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAATCACATTTATA
Found at i:111888 original size:58 final size:56
Alignment explanation
Indices: 111800--111942 Score: 162
Period size: 57 Copynumber: 2.5 Consensus size: 56
111790 TACCTGTATC
** * *
111800 TGGCCCATTAACCCCAATCATATTTATATGGCCCATTAGGCCCAAATCAC-TTGTATA
1 TGGCCCATTAGGCCAAATCACATTTATATGGCCCATTAGGCCC-AATCACATT-TATA
* *
111857 TGGCCCATTAGGTCCAAATCACATTTATATGGCCCGTTAGGCCCAGTCACATTTATA
1 TGGCCCATTAGG-CCAAATCACATTTATATGGCCCATTAGGCCCAATCACATTTATA
* * * *
111914 TGGCCCGTTAGGCCCAGTCACATTCATAT
1 TGGCCCATTAGGCCAAATCACATTTATAT
111943 TCATGCTCAC
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
56 14 0.19
57 30 0.41
58 30 0.41
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (56 bp):
TGGCCCATTAGGCCAAATCACATTTATATGGCCCATTAGGCCCAATCACATTTATA
Found at i:113043 original size:40 final size:40
Alignment explanation
Indices: 112999--113225 Score: 328
Period size: 40 Copynumber: 5.7 Consensus size: 40
112989 CCAACCTAAT
* * ** *
112999 TGCCTTCGGGATTTAGCCCGGATGTAACAACCAGCACAAA
1 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
* * *
113039 TGCCTTCGGGACTTAACCCGGAAATAGCGACCAGGACGAA
1 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
* **
113079 TGCCTTCGGGGCTTAACCTAGAAATAACAACCAGCACGAA
1 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
*
113119 TGCCTTCGGGACTTAACCCGGAAATAACAACTAGCACGAA
1 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
*
113159 TGCCTTCGGGACTTAACCCGGAAATAGCAACCAGCACGAA
1 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
*
113199 TGCCTTCGGGACTTAACCCGGATATAA
1 TGCCTTCGGGACTTAACCCGGAAATAA
113226 TCCTCAATTG
Statistics
Matches: 165, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 165 1.00
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.18
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
Found at i:119667 original size:15 final size:15
Alignment explanation
Indices: 119649--119682 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
119639 GCAAAGGTTG
119649 AAAA-GCTGAAAAGCC
1 AAAAGGCTGAAAAG-C
119664 AAAAGGCTGAAAAGC
1 AAAAGGCTGAAAAGC
119679 AAAA
1 AAAA
119683 AAAGTGGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.59, C:0.15, G:0.21, T:0.06
Consensus pattern (15 bp):
AAAAGGCTGAAAAGC
Found at i:119683 original size:16 final size:15
Alignment explanation
Indices: 119649--119683 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
119639 GCAAAGGTTG
119649 AAAAGCTGAAAAGCCA
1 AAAAGCTGAAAAG-CA
*
119665 AAAGGCTGAAAAGCA
1 AAAAGCTGAAAAGCA
119680 AAAA
1 AAAA
119684 AAGTGGGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.60, C:0.14, G:0.20, T:0.06
Consensus pattern (15 bp):
AAAAGCTGAAAAGCA
Found at i:119859 original size:84 final size:84
Alignment explanation
Indices: 119718--119879 Score: 279
Period size: 84 Copynumber: 1.9 Consensus size: 84
119708 GTGTGTCGGC
* * *
119718 GCCCGTGTGGCAGGCCGTGTGACAAAACATGGTTGTGTGGTCTACGAGATGGCCATGAGAGTCTT
1 GCCCGCGTGGCAGGCCGTGTGACAAAACATGGCTGTGTGGTCGACGAGATGGCCATGAGAGTCTT
119783 CATGGGCCGAAACGATTAT
66 CATGGGCCGAAACGATTAT
*
119802 GCCCGCGTGGCAGGCCGTGTGACAAAACATGGCTGTGTGGTCGACGAGATGGCCATGAGCGTCTT
1 GCCCGCGTGGCAGGCCGTGTGACAAAACATGGCTGTGTGGTCGACGAGATGGCCATGAGAGTCTT
*
119867 CATGGGCTGAAAC
66 CATGGGCCGAAAC
119880 AATACTGTGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.35, T:0.22
Consensus pattern (84 bp):
GCCCGCGTGGCAGGCCGTGTGACAAAACATGGCTGTGTGGTCGACGAGATGGCCATGAGAGTCTT
CATGGGCCGAAACGATTAT
Found at i:135729 original size:44 final size:44
Alignment explanation
Indices: 135666--136198 Score: 690
Period size: 44 Copynumber: 12.1 Consensus size: 44
135656 CGAATCCCAT
* * *
135666 AGATTTAGCGTCTCTGTATTGTCAGAGGGCAGATCGAAGATAGC
1 AGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGC
* * *
135710 AGATTTGGCGTCTCTGTATTGGCGGAGAACAGATCGAAGATAAC
1 AGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGC
* *
135754 AGATTTGGCGTCTCTATATTGGCAGGGAGCAGATCGAAGATAGC
1 AGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGC
* * * *
135798 AGATTTGGCGTCTCTGTATTGTCAGAGGGTAGATCGAAGATAGT
1 AGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGC
* * * * *
135842 AGATTTGGCGTCTCTATATTGGCGGAGAGTAGATTGAAGATAAC
1 AGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGC
* * * *
135886 AGATTTGGCGTCCCTATATTGGGAGGGAGCAGATCGAAGATAGC
1 AGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGC
* * *
135930 AGATTTGGCGTCTCTGTATTGTCAGAGGGCAGATCGAAGATAGA
1 AGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGC
* * *
135974 AGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCAAAGATAAC
1 AGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGC
*
136018 AGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCAAAGATAGC
1 AGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGC
** * * *
136062 AGATTTGGCACCTCTATATTGGCGGAGAGCAGATCAAAGATAGC
1 AGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGC
* *
136106 AGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGAT-GAC
1 AGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG-C
* * * * *
136150 AGATTTGGCATCTCTATATTGGCAGAGAGCAGATAGAAAATAAC
1 AGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGC
136194 AGATT
1 AGATT
136199 GGTGTTCCTG
Statistics
Matches: 427, Mismatches: 60, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
43 1 0.00
44 426 1.00
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (44 bp):
AGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGC
Found at i:135903 original size:132 final size:132
Alignment explanation
Indices: 135666--136198 Score: 796
Period size: 132 Copynumber: 4.0 Consensus size: 132
135656 CGAATCCCAT
*
135666 AGATTTAGCGTCTCTGTATTGTCAGAGGGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTG
1 AGATTTGGCGTCTCTGTATTGTCAGAGGGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTG
* *
135731 GCGGAGAACAGATCGAAGATAACAGATTTGGCGTCTCTATATTGGCAGGGAGCAGATCGAAGATA
66 GCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTATATTGGCAGAGAGCAGATCGAAGATA
135796 GC
131 GC
* * *
135798 AGATTTGGCGTCTCTGTATTGTCAGAGGGTAGATCGAAGATAGTAGATTTGGCGTCTCTATATTG
1 AGATTTGGCGTCTCTGTATTGTCAGAGGGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTG
* * * * *
135863 GCGGAGAGTAGATTGAAGATAACAGATTTGGCGTCCCTATATTGGGAGGGAGCAGATCGAAGATA
66 GCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTATATTGGCAGAGAGCAGATCGAAGATA
135928 GC
131 GC
*
135930 AGATTTGGCGTCTCTGTATTGTCAGAGGGCAGATCGAAGATAGAAGATTTGGCGTCTCTGTATTG
1 AGATTTGGCGTCTCTGTATTGTCAGAGGGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTG
* * *
135995 GCGGAGAGCAGATCAAAGATAACAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCAAAGATA
66 GCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTATATTGGCAGAGAGCAGATCGAAGATA
136060 GC
131 GC
** * * * * * *
136062 AGATTTGGCACCTCTATATTGGCGGAGAGCAGATCAAAGATAGCAGATTTGGCATCTCTGTATTG
1 AGATTTGGCGTCTCTGTATTGTCAGAGGGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTG
* * * * * *
136127 ACAGAGAGCAGATCGAAGATGACAGATTTGGCATCTCTATATTGGCAGAGAGCAGATAGAAAATA
66 GCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTATATTGGCAGAGAGCAGATCGAAGATA
*
136192 AC
131 GC
136194 AGATT
1 AGATT
136199 GGTGTTCCTG
Statistics
Matches: 362, Mismatches: 39, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
132 362 1.00
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (132 bp):
AGATTTGGCGTCTCTGTATTGTCAGAGGGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTG
GCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTATATTGGCAGAGAGCAGATCGAAGATA
GC
Found at i:148619 original size:48 final size:47
Alignment explanation
Indices: 148563--148887 Score: 407
Period size: 48 Copynumber: 6.8 Consensus size: 47
148553 CCTATGGTAT
* *
148563 TGTGATCCCATGTAAGACCAAGTTAGGGAAATGGCATTGGCATCGATA
1 TGTGATCCCATGTAAGACCATGTT-GGGACATGGCATTGGCATCGATA
* * * *
148611 TATGATCCCATGTAAGACCATATTTGAGACATGGCATTGGCATTGATA
1 TGTGATCCCATGTAAGACCAT-GTTGGGACATGGCATTGGCATCGATA
* * *
148659 TGTGATCCCATGTAAAACCATGTCTGGGATATGGCATTAGCATCGATA
1 TGTGATCCCATGTAAGACCATGT-TGGGACATGGCATTGGCATCGATA
* *
148707 TGTGATCCCATGTAAGACCATGTCTGGGACATAGCATTGGCATCGATC
1 TGTGATCCCATGTAAGACCATGT-TGGGACATGGCATTGGCATCGATA
148755 TGTGATCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATCGATA
1 TGTGATCCCATGTAAGACCATG-TTGGGACATGGCATTGGCATCGATA
* * * * *
148803 TGTGATCCTATGTAAGACCATATCTGGGATATGGCGTTAGCATCGATA
1 TGTGATCCCATGTAAGACCATGT-TGGGACATGGCATTGGCATCGATA
** * *
148851 TGTGATTTCGTGTAAGACCATGTCAGGGACATGGCAT
1 TGTGATCCCATGTAAGACCATGT-TGGGACATGGCAT
148888 CGATATGAGA
Statistics
Matches: 240, Mismatches: 33, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
47 2 0.01
48 235 0.98
49 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (47 bp):
TGTGATCCCATGTAAGACCATGTTGGGACATGGCATTGGCATCGATA
Found at i:148761 original size:144 final size:144
Alignment explanation
Indices: 148563--148887 Score: 490
Period size: 144 Copynumber: 2.3 Consensus size: 144
148553 CCTATGGTAT
* *
148563 TGTGATCCCATGTAAGACCAAGT-TAGGGAAATGGCATTGGCATCGATATATGATCCCATGTAAG
1 TGTGATCCCATGTAAGACCATGTCT-GGGACATGGCATTGGCATCGATATATGATCCCATGTAAG
* *
148627 ACCATATTTGAGACATGGCATTGGCATTGATATGTGATCCCATGTAAAACCATGTCTGGGATATG
65 ACCATATTTGAGACATGGCATTGGCATCGATATGTGATCCCATGTAAAACCATATCTGGGATATG
148692 GCATTAGCATCGATA
130 GCATTAGCATCGATA
* * *
148707 TGTGATCCCATGTAAGACCATGTCTGGGACATAGCATTGGCATCGATCTGTGATCCCATGTAAGA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATATGATCCCATGTAAGA
* * * *
148772 CCATGTTTGGGACATGGCATTGGCATCGATATGTGATCCTATGTAAGACCATATCTGGGATATGG
66 CCATATTTGAGACATGGCATTGGCATCGATATGTGATCCCATGTAAAACCATATCTGGGATATGG
*
148837 CGTTAGCATCGATA
131 CATTAGCATCGATA
** * *
148851 TGTGATTTCGTGTAAGACCATGTCAGGGACATGGCAT
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCAT
148888 CGATATGAGA
Statistics
Matches: 163, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
144 162 0.99
145 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (144 bp):
TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATATGATCCCATGTAAGA
CCATATTTGAGACATGGCATTGGCATCGATATGTGATCCCATGTAAAACCATATCTGGGATATGG
CATTAGCATCGATA
Found at i:151435 original size:28 final size:28
Alignment explanation
Indices: 151357--151438 Score: 74
Period size: 33 Copynumber: 2.8 Consensus size: 28
151347 TAAATAGTGC
* *
151357 ATGCAGTAATAGTCTGGGCCTGAGCCCT
1 ATGCAGTAACAGTATGGGCCTGAGCCCT
* * *
151385 ATTCAGTATCAGTACAGTTTGGGCCTTAGCCCT
1 ATGCAG--T-A--ACAGTATGGGCCTGAGCCCT
151418 ATGCAGTAACAGTATGGGCCT
1 ATGCAGTAACAGTATGGGCCT
151439 ACGCCCAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
28 17 0.40
30 2 0.05
31 2 0.05
33 22 0.51
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (28 bp):
ATGCAGTAACAGTATGGGCCTGAGCCCT
Found at i:151857 original size:27 final size:27
Alignment explanation
Indices: 151827--151882 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
151817 GGAACATAAA
151827 GGCATAATC-GTCATTTTACCATACAGG
1 GGCATAA-CGGTCATTTTACCATACAGG
* *
151854 GGCATTACGGTCATTTTACCCTACAGG
1 GGCATAACGGTCATTTTACCATACAGG
151881 GG
1 GG
151883 TTTCAGCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (27 bp):
GGCATAACGGTCATTTTACCATACAGG
Found at i:152941 original size:47 final size:47
Alignment explanation
Indices: 152872--152965 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
152862 CAAGAGAAAG
152872 AACATACGAGTACCTATCGACTCGTCAGAACTCTTGCGAGACCAAAA
1 AACATACGAGTACCTATCGACTCGTCAGAACTCTTGCGAGACCAAAA
*
152919 AACATACGAGTCCCTATCGACTCGTCAGAACTCTTGCGAGACCAAAA
1 AACATACGAGTACCTATCGACTCGTCAGAACTCTTGCGAGACCAAAA
152966 CCACAACACC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (47 bp):
AACATACGAGTACCTATCGACTCGTCAGAACTCTTGCGAGACCAAAA
Found at i:153199 original size:12 final size:12
Alignment explanation
Indices: 153184--153210 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
153174 AATTATGGAG
153184 AAGAGAAAAGAA
1 AAGAGAAAAGAA
153196 AAGAGAAAAGAA
1 AAGAGAAAAGAA
153208 AAG
1 AAG
153211 CTTCGGAGAA
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:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AAGAGAAAAGAA
Found at i:157433 original size:40 final size:40
Alignment explanation
Indices: 157374--157591 Score: 307
Period size: 40 Copynumber: 5.5 Consensus size: 40
157364 CGGATGATAA
* *
157374 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* *
157414 CCGAGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
157454 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
157494 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
157534 CCGGGCTAAGTCCCGAAGGCATTTGAGTGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
157574 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
157592 TACTCTGTTT
Statistics
Matches: 161, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
39 17 0.11
40 143 0.89
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:165582 original size:40 final size:40
Alignment explanation
Indices: 165527--165704 Score: 254
Period size: 40 Copynumber: 4.5 Consensus size: 40
165517 CGGATGATAA
* *
165527 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
165567 CCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
165607 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* **
165647 CCGGGCTAAGTCCCAAAGGCATTTGAACGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
165687 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
165705 TACTCGGTTT
Statistics
Matches: 127, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
39 16 0.13
40 110 0.87
41 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Done.