Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_38
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: 389546
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 2
Found at i:453 original size:10 final size:10
Alignment explanation
Indices: 438--483 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
428 AAAAAGGAAT
438 GAGCTAAAAC
1 GAGCTAAAAC
*
448 GAGCTAAATTC
1 GAGCTAAA-AC
*
459 GAGCTCAAAC
1 GAGCTAAAAC
469 GAGCTAAAAC
1 GAGCTAAAAC
479 GAGCT
1 GAGCT
484 CAAGTGAGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 23 0.74
11 8 0.26
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.15
Consensus pattern (10 bp):
GAGCTAAAAC
Found at i:492 original size:20 final size:21
Alignment explanation
Indices: 438--495 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
428 AAAAAGGAAT
* *
438 GAGCTAAAACGAGCTAAATTC
1 GAGCTCAAACGAGCTAAATAC
459 GAGCTCAAACGAGCTAAA-AC
1 GAGCTCAAACGAGCTAAATAC
**
479 GAGCTCAAGTGAGCTAA
1 GAGCTCAAACGAGCTAA
496 TGGGAACTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.16
Consensus pattern (21 bp):
GAGCTCAAACGAGCTAAATAC
Found at i:2630 original size:19 final size:20
Alignment explanation
Indices: 2606--2646 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
2596 AATCTCAATT
2606 TCTTTTCTTTGTTT-TTCTC
1 TCTTTTCTTTGTTTCTTCTC
2625 TCTTTTCTTTGTTTCTTCTC
1 TCTTTTCTTTGTTTCTTCTC
2645 TC
1 TC
2647 AATTTCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.00, C:0.24, G:0.05, T:0.71
Consensus pattern (20 bp):
TCTTTTCTTTGTTTCTTCTC
Found at i:3239 original size:14 final size:14
Alignment explanation
Indices: 3220--3246 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3210 TAAAATAGAC
3220 ACAAAATCCTCACT
1 ACAAAATCCTCACT
3234 ACAAAATCCTCAC
1 ACAAAATCCTCAC
3247 AAGTTCACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.19
Consensus pattern (14 bp):
ACAAAATCCTCACT
Found at i:10166 original size:20 final size:20
Alignment explanation
Indices: 10143--10189 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
10133 GGGTTAAGAT
*
10143 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
10163 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
10183 TGAGCTG
1 TGAGCTG
10190 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:11855 original size:20 final size:20
Alignment explanation
Indices: 11832--11878 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
11822 GGGTTAAGAT
* *
11832 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGATCGAG
* *
11852 TGAGTTGACTTGAGATCGAG
1 TGAGCTGAATTGAGATCGAG
11872 TGAGCTG
1 TGAGCTG
11879 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.11, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGATCGAG
Found at i:13608 original size:47 final size:47
Alignment explanation
Indices: 13546--13649 Score: 133
Period size: 47 Copynumber: 2.2 Consensus size: 47
13536 TTGTCTTTTC
*
13546 TTTCTTTTTCAATTTCTCTT-T-TTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCT-TTCTCTT-CTCACATCCTTT-TTCAATCTCAA
* *
13593 TTTCTTTTTCGATTTCTTTCTCTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTTTCTCTTCTCACATCCTTTTTCAATCTCAA
13640 TTTCTTTTTC
1 TTTCTTTTTC
13650 CATGACACTC
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
46 2 0.04
47 43 0.84
48 6 0.12
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (47 bp):
TTTCTTTTTCAATTTCTTTCTCTTCTCACATCCTTTTTCAATCTCAA
Found at i:14693 original size:21 final size:20
Alignment explanation
Indices: 14664--14726 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
14654 ACTCCAAGAC
*
14664 TTTTCACTTTTTTTTGTTTGT
1 TTTTCACTTTTTTTTCTTT-T
*
14685 TTTTTACTTTTTTTTCTTTT
1 TTTTCACTTTTTTTTCTTTT
14705 TTTGCTCACTTCTTTTTT-TTTT
1 TTT--TCACTT-TTTTTTCTTTT
14727 GAATTTTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.11
21 17 0.47
22 9 0.25
23 6 0.17
ACGTcount: A:0.05, C:0.13, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTTCACTTTTTTTTCTTTT
Found at i:16264 original size:20 final size:20
Alignment explanation
Indices: 16241--16287 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
16231 GGGTTAAGAT
* *
16241 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGATCGAG
* *
16261 TGAGTTGACTTGAGATCGAG
1 TGAGCTGAATTGAGATCGAG
16281 TGAGCTG
1 TGAGCTG
16288 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.11, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGATCGAG
Found at i:22784 original size:28 final size:28
Alignment explanation
Indices: 22727--22906 Score: 285
Period size: 28 Copynumber: 6.5 Consensus size: 28
22717 TAAATTGTAC
*
22727 AGCACTAAGTGTGCGA-ATTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
22754 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
22782 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
22810 AGCACTAAGTGTGCGAG-TTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* *
22837 AGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* *
22865 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
22892 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
22907 GACTTAATAA
Statistics
Matches: 145, Mismatches: 6, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
27 65 0.45
28 80 0.55
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:22792 original size:55 final size:54
Alignment explanation
Indices: 22727--22906 Score: 279
Period size: 55 Copynumber: 3.3 Consensus size: 54
22717 TAAATTGTAC
22727 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAG-TTGACTATGT
*
22782 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
* * * *
22837 AGCACTAAGTGTGCGAGTATGATTATGTAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAAT-TGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
*
22892 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
22907 GACTTAATAA
Statistics
Matches: 117, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
54 1 0.01
55 89 0.76
56 27 0.23
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (54 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
Found at i:22842 original size:83 final size:82
Alignment explanation
Indices: 22727--22906 Score: 297
Period size: 83 Copynumber: 2.2 Consensus size: 82
22717 TAAATTGTAC
*
22727 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTATGACTATGTAGCACTAAGT
*
22792 GTGCGAGTTTGACTATGT
66 GTGCGAG-TTGACTATAT
* *
22810 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGTAGCACTAAGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTATGACTATGTAGCACTAAGT
*
22875 GTGCGAGTTGATTATAT
66 GTGCGAGTTGACTATAT
*
22892 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
22907 GACTTAATAA
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
82 22 0.24
83 69 0.76
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (82 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTATGACTATGTAGCACTAAGT
GTGCGAGTTGACTATAT
Found at i:42122 original size:13 final size:12
Alignment explanation
Indices: 42104--42154 Score: 59
Period size: 11 Copynumber: 4.2 Consensus size: 12
42094 ATAGTAGTTT
42104 CTCGAAAAAAATA
1 CTCGAAAAAAA-A
42117 CTCGAAAAAAAAA
1 CTCG-AAAAAAAA
*
42130 GTC-AAAAAAAA
1 CTCGAAAAAAAA
*
42141 TTCGAAAAAAAA
1 CTCGAAAAAAAA
42153 CT
1 CT
42155 AGTTTCCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
11 10 0.30
12 9 0.27
13 7 0.21
14 7 0.21
ACGTcount: A:0.65, C:0.14, G:0.08, T:0.14
Consensus pattern (12 bp):
CTCGAAAAAAAA
Found at i:42208 original size:13 final size:13
Alignment explanation
Indices: 42190--42228 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
42180 GGATATCAAG
*
42190 TTGTGAAAAAAAT
1 TTGTGAAAAAAAA
42203 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
42216 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
42229 GAGAGCTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:44285 original size:10 final size:10
Alignment explanation
Indices: 44231--44287 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
44221 ATAAAATAAA
*
44231 TGAGCTGAAT
1 TGAGCTCAAT
*
44241 TGTAGCTAAAT
1 TG-AGCTCAAT
*
44252 TGAGCTCGAT
1 TGAGCTCAAT
* *
44262 TGAGCTGAAA
1 TGAGCTCAAT
*
44272 TGAGGTCAAT
1 TGAGCTCAAT
44282 TGAGCT
1 TGAGCT
44288 GGTCGGAGTT
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
10 27 0.75
11 9 0.25
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (10 bp):
TGAGCTCAAT
Found at i:44288 original size:20 final size:20
Alignment explanation
Indices: 44228--44288 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
44218 CCAATAAAAT
*
44228 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
44248 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
*
44269 AAATGAGGTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
44289 GTCGGAGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:46749 original size:23 final size:22
Alignment explanation
Indices: 46697--46749 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
46687 TCCACGTCTT
*
46697 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
46719 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
46742 TTTCTTTT
1 TTTCTTTT
46750 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:47853 original size:10 final size:10
Alignment explanation
Indices: 47829--47877 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
47819 AGCTCGTTTC
*
47829 CAGCTCACTT
1 CAGCTCAATT
* *
47839 GAGCTCAAGT
1 CAGCTCAATT
47849 CAGCTC-ATT
1 CAGCTCAATT
47858 CGAGCTCAATT
1 C-AGCTCAATT
47869 CAGCTCAAT
1 CAGCTCAAT
47878 CTTAACCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 25 0.78
11 4 0.12
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:47854 original size:20 final size:20
Alignment explanation
Indices: 47829--47875 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
47819 AGCTCGTTTC
47829 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCTCAAGT
*
47849 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAAGT
47869 CAGCTCA
1 CAGCTCA
47876 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAAGT
Found at i:51626 original size:18 final size:17
Alignment explanation
Indices: 51605--51649 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
51595 GAGTGACGAG
51605 AGAAAAAGAAATCGAAAA
1 AGAAAAA-AAATCGAAAA
*
51623 AGAAACAAAAATTGAAAA
1 AGAAA-AAAAATCGAAAA
51641 AGAGAAAAA
1 AGA-AAAAA
51650 GATTGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (17 bp):
AGAAAAAAAATCGAAAA
Found at i:51654 original size:18 final size:18
Alignment explanation
Indices: 51603--51654 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
51593 AAGAGTGACG
*
51603 AGAGAAAAAGAAATCGAAAA
1 AGAGAAAAAG--ATTGAAAA
*
51623 AGA-AACAAAAATTGAAAA
1 AGAGAA-AAAGATTGAAAA
51641 AGAGAAAAAGATTG
1 AGAGAAAAAGATTG
51655 GAGAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 17 0.63
19 4 0.15
20 6 0.22
ACGTcount: A:0.67, C:0.04, G:0.19, T:0.10
Consensus pattern (18 bp):
AGAGAAAAAGATTGAAAA
Found at i:54728 original size:31 final size:31
Alignment explanation
Indices: 54633--54730 Score: 112
Period size: 31 Copynumber: 3.1 Consensus size: 31
54623 TCAAGGTGGG
54633 ATTGAATTTAAACCAAGCTCAAACGAGCTGA
1 ATTGAATTTAAACCAAGCTCAAACGAGCTGA
* *
54664 ATT-AATTTAGCTAA--AGAGCTAATAATGAGCTGA
1 ATTGAATTTA---AACCA-AGCTCA-AACGAGCTGA
54697 ATTGAATTTAAACCAAGCTCAAACGAGCTGA
1 ATTGAATTTAAACCAAGCTCAAACGAGCTGA
54728 ATT
1 ATT
54731 AAGCTCATCT
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
30 6 0.11
31 18 0.33
32 10 0.18
33 15 0.27
34 6 0.11
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (31 bp):
ATTGAATTTAAACCAAGCTCAAACGAGCTGA
Found at i:57729 original size:12 final size:11
Alignment explanation
Indices: 57697--57728 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
57687 TCAAAAAAAA
57697 AATTTTTTTTG
1 AATTTTTTTTG
57708 AATTTTTTTTG
1 AATTTTTTTTG
57719 AATTTTTTTT
1 AATTTTTTTT
57729 TCAAATTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:63991 original size:48 final size:48
Alignment explanation
Indices: 63936--64041 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
63926 TTGTCTTTTC
*
63936 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
63984 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
64032 TTTCTTTTTC
1 TTTCTTTTTC
64042 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:64084 original size:18 final size:18
Alignment explanation
Indices: 64017--64084 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
64007 TTTTCACATC
* *
64017 CTTTTTCAATCTCAATTT
1 CTTTTTCAATCTCACTCT
* **
64035 CTTTTTCCATGACACTCGTTT
1 CTTTTTCAATCTCACTC---T
64056 CTTTCTTCAATCTCACTCT
1 CTTT-TTCAATCTCACTCT
64075 CTTTTTCAAT
1 CTTTTTCAAT
64085 TTCTTGTTCC
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
18 18 0.47
19 5 0.13
21 5 0.13
22 10 0.26
ACGTcount: A:0.18, C:0.28, G:0.03, T:0.51
Consensus pattern (18 bp):
CTTTTTCAATCTCACTCT
Found at i:69171 original size:30 final size:30
Alignment explanation
Indices: 69137--69233 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
69127 TAAACTAAAA
69137 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
69167 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
69197 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
69227 TGAGCTA
1 TGAGCTA
69234 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:71407 original size:31 final size:31
Alignment explanation
Indices: 71340--71397 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
71330 GTTTCTTTTG
71340 TTTC-AATTTCTTTTTCATCTTCTTTTTCAC
1 TTTCAAATTTCTTTTTCATCTTCTTTTTCAC
* *
71370 TCTCAAATTTCTTTTTCATTTTCTTTTT
1 TTTCAAATTTCTTTTTCATCTTCTTTTT
71398 GCTTTTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.66
Consensus pattern (31 bp):
TTTCAAATTTCTTTTTCATCTTCTTTTTCAC
Found at i:71415 original size:12 final size:12
Alignment explanation
Indices: 71400--71430 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
71390 TTCTTTTTGC
71400 TTTTCAAAGGCT
1 TTTTCAAAGGCT
71412 TTTTCAAAGGCT
1 TTTTCAAAGGCT
71424 TTTTCAA
1 TTTTCAA
71431 GTTCTGATAC
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:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:73162 original size:14 final size:15
Alignment explanation
Indices: 73137--73166 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
73127 AAATTGGCAC
73137 AAGTATAAGAAAGAA
1 AAGTATAAGAAAGAA
73152 AAGTA-AAGAAAGAA
1 AAGTATAAGAAAGAA
73166 A
1 A
73167 TCGAAAACAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (15 bp):
AAGTATAAGAAAGAA
Found at i:78414 original size:30 final size:30
Alignment explanation
Indices: 78329--78425 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
78319 TAAACTAAAA
*
78329 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
78359 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
78389 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
78418 ATGAGCTA
1 -TGAGCTA
78426 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:78790 original size:30 final size:30
Alignment explanation
Indices: 78756--78852 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
78746 TAAACTAAAA
*
78756 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
* * * * * *
78786 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCATGAGCTAAAGT
* *
78816 TGAGCTAAGGTTTAGCTCATGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCATGAGCT-AAAGT
78846 TGAGCTA
1 TGAGCTA
78853 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:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
Found at i:82069 original size:11 final size:10
Alignment explanation
Indices: 82044--82104 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
82034 AACCAATAAA
82044 TAAA-TGAGC
1 TAAATTGAGC
*
82053 TGAATTGTAGC
1 TAAATTG-AGC
82064 TAAATTGAGC
1 TAAATTGAGC
**
82074 TCGATTGAGC
1 TAAATTGAGC
82084 TGAAA-TGAGC
1 T-AAATTGAGC
*
82094 TCAATTGAGC
1 TAAATTGAGC
82104 T
1 T
82105 GGTCAGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:82105 original size:20 final size:20
Alignment explanation
Indices: 82045--82105 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
82035 ACCAATAAAT
*
82045 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
82065 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
82086 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
82106 GTCAGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:82523 original size:30 final size:30
Alignment explanation
Indices: 82452--82534 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
82442 CTTTTGTTTC
*
82452 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCACTCTCA
* *
82483 AATTT-ATTTTCGTTCTCTTTTTCAGTCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCACTCTCA
* *
82512 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
82535 GCTTTTCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
29 4 0.09
30 32 0.74
31 7 0.16
ACGTcount: A:0.13, C:0.20, G:0.02, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCACTCTCA
Found at i:82534 original size:18 final size:18
Alignment explanation
Indices: 82488--82540 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
82478 TCTCAAATTT
* *
82488 ATTTTCGTTCTCTTTTTC
1 ATTTTCATTTTCTTTTTC
* *
82506 AGTCTCATTTTCTTTTTC
1 ATTTTCATTTTCTTTTTC
*
82524 ATTTTCTTTTTGCTTTT
1 ATTTTCATTTT-CTTTT
82541 CAAAGGCTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.08, C:0.19, G:0.06, T:0.68
Consensus pattern (18 bp):
ATTTTCATTTTCTTTTTC
Found at i:82541 original size:12 final size:12
Alignment explanation
Indices: 82510--82534 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
82500 TTTTTCAGTC
82510 TCATTTTCTTTT
1 TCATTTTCTTTT
82522 TCATTTTCTTTT
1 TCATTTTCTTTT
82534 T
1 T
82535 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:84106 original size:30 final size:30
Alignment explanation
Indices: 84020--84117 Score: 88
Period size: 30 Copynumber: 3.3 Consensus size: 30
84010 TTAAACTAAA
* *
84020 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGGTTTAGCTCGTGAGCTGAAG
* * * * * ***
84050 TTGAGCTGAGGCTAAACTCCCAAGCTGAAG
1 ATGAGCTAAGGTTTAGCTCGTGAGCTGAAG
* *
84080 GTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGGTTTAGCTCGTGAGCTGAAG
84110 ATGAGCTA
1 ATGAGCTA
84118 GGAGTGAGCT
Statistics
Matches: 48, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (30 bp):
ATGAGCTAAGGTTTAGCTCGTGAGCTGAAG
Found at i:84343 original size:5 final size:5
Alignment explanation
Indices: 84333--84387 Score: 51
Period size: 5 Copynumber: 10.6 Consensus size: 5
84323 CTCTTGCCTC
*
84333 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
84380 TCTTT TCT
1 TCTTT TCT
84388 CTATTTTCTC
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
4 4 0.10
5 27 0.64
6 6 0.14
7 5 0.12
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (5 bp):
TCTTT
Found at i:84836 original size:30 final size:31
Alignment explanation
Indices: 84802--84898 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
84792 AGCTCACTCC
*
84802 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
84832 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
84862 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
84892 TAGCTCA
1 TAGCTCA
84899 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:87222 original size:30 final size:30
Alignment explanation
Indices: 87158--87224 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
87148 TAAACTAAAA
*
87158 TGAGCTAAGCTTTAGCTCATGAGCTAATGT
1 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
* * *
87188 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCATGAGCT-AAAGT
87218 TGAGCTA
1 TGAGCTA
87225 GGAGTGAGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 29 0.91
31 3 0.09
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.31
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
Found at i:90944 original size:12 final size:12
Alignment explanation
Indices: 90929--90959 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
90919 TTCTTTTTGC
90929 TTTTCAAAGGCT
1 TTTTCAAAGGCT
90941 TTTTCAAAGGCT
1 TTTTCAAAGGCT
90953 TTTTCAA
1 TTTTCAA
90960 GTTCTCTCAA
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:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:91028 original size:16 final size:15
Alignment explanation
Indices: 91005--91050 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
90995 GCCTTTTGCC
91005 TTTCTTTTCTTTTTA
1 TTTCTTTTCTTTTTA
*
91020 TTTCATTTTCTTTTTCTT
1 TTTC-TTTTC-TTTT-TA
91038 TTTCTTTTCTTTT
1 TTTCTTTTCTTTT
91051 CTTTGTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 4 0.15
16 9 0.33
17 9 0.33
18 5 0.19
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTCTTTTCTTTTTA
Found at i:91029 original size:6 final size:5
Alignment explanation
Indices: 91005--91054 Score: 57
Period size: 5 Copynumber: 9.4 Consensus size: 5
90995 GCCTTTTGCC
91005 TTTCT TTTCT TTT-T ATTTCAT TTTCTT TTTCTT TTTCT TTTCT TTTCT
1 TTTCT TTTCT TTTCT -TTTC-T TTTC-T TTTC-T TTTCT TTTCT TTTCT
91053 TT
1 TT
91055 GTTTTCTCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
4 1 0.02
5 24 0.59
6 15 0.37
7 1 0.02
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:91037 original size:22 final size:22
Alignment explanation
Indices: 91005--91054 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
90995 GCCTTTTGCC
91005 TTTC-TTTTCTTTTT-ATTTCAT
1 TTTCTTTTTCTTTTTCATTTC-T
*
91026 TTTCTTTTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTTTTCATTTCT
91048 TTTCTTT
1 TTTCTTT
91055 GTTTTCTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 4 0.15
22 18 0.69
23 4 0.15
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTCTTTTTCTTTTTCATTTCT
Found at i:94464 original size:30 final size:30
Alignment explanation
Indices: 94430--94527 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
94420 AGCTCACTCC
94430 TAGCTCATATTCAGCTTACGAGCTAAACCT
1 TAGCTCATATTCAGCTTACGAGCTAAACCT
** * * * * *
94460 TAGCTCAGCTTCTGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTTACGAGCTAAACCT
* * * *
94490 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTTACGAGCTAAACCT
94520 TAGCTCAT
1 TAGCTCAT
94528 TTTAGTTTAA
Statistics
Matches: 49, Mismatches: 17, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.32
Consensus pattern (30 bp):
TAGCTCATATTCAGCTTACGAGCTAAACCT
Found at i:98239 original size:23 final size:22
Alignment explanation
Indices: 98188--98239 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
98178 CCTCGTCTTT
*
98188 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
98210 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
98233 TTCTTTT
1 TTCTTTT
98240 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:101048 original size:22 final size:22
Alignment explanation
Indices: 101020--101064 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
101010 GTTATACAAG
101020 TCAAAAAGAAAATTCAAAAAAAT
1 TCAAAAA-AAAATTCAAAAAAAT
*
101043 TCAAAAAAAAATTCGAAAAAAT
1 TCAAAAAAAAATTCAAAAAAAT
101065 AAATTCTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.69, C:0.09, G:0.04, T:0.18
Consensus pattern (22 bp):
TCAAAAAAAAATTCAAAAAAAT
Found at i:101052 original size:14 final size:14
Alignment explanation
Indices: 101035--101080 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
101025 AAGAAAATTC
101035 AAAAAAATTC--AA
1 AAAAAAATTCGAAA
101047 AAAAAAATTCGAAA
1 AAAAAAATTCGAAA
*
101061 AAATAAATTCTGAAA
1 AAAAAAATTC-GAAA
101076 AAAAA
1 AAAAA
101081 GTGTTTAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.34
14 11 0.38
15 8 0.28
ACGTcount: A:0.72, C:0.07, G:0.04, T:0.17
Consensus pattern (14 bp):
AAAAAAATTCGAAA
Found at i:102011 original size:21 final size:21
Alignment explanation
Indices: 101985--102034 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
101975 ACATTCTTGT
101985 AAAGAAAAAACAAAGAAAAG-A
1 AAAGAAAAAACAAA-AAAAGAA
* *
102006 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAACAAAAAAAGAA
102027 AAAGAAAA
1 AAAGAAAA
102035 TGAAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (21 bp):
AAAGAAAAAACAAAAAAAGAA
Found at i:102020 original size:6 final size:5
Alignment explanation
Indices: 101985--102052 Score: 59
Period size: 5 Copynumber: 13.0 Consensus size: 5
101975 ACATTCTTGT
* *
101985 AAAGA AAAAA CAAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA
1 AAAGA AAAGA -AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA
102032 AAATGA AATA-A AAAGA AAAGA
1 AAA-GA AA-AGA AAAGA AAAGA
102053 GAGGCAAGAG
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
4 4 0.08
5 29 0.56
6 18 0.35
7 1 0.02
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:102025 original size:15 final size:14
Alignment explanation
Indices: 101996--102052 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
101986 AAGAAAAAAC
101996 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
102012 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
102027 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
102043 AAAGAAAAGA
1 AAAGAAAAGA
102053 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:102153 original size:24 final size:24
Alignment explanation
Indices: 102126--102188 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
102116 AAAACAAAAA
*
102126 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAAAGAGATT
* * *
102150 GAAAAAGAGAATGAAAAAGAGTTT
1 GAAAAAGAAAAAGAAAAAGAGATT
* *
102174 GAGAGAGAAAAAGAA
1 GAAAAAGAAAAAGAA
102189 TGTGAACAAG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.63, C:0.00, G:0.25, T:0.11
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAAAGAGATT
Found at i:102155 original size:13 final size:12
Alignment explanation
Indices: 102126--102170 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
102116 AAAACAAAAA
* *
102126 GAAAAAGAAAAA
1 GAAAAAGAGAAT
* *
102138 GAAAATGAGATT
1 GAAAAAGAGAAT
102150 GAAAAAGAGAAT
1 GAAAAAGAGAAT
102162 GAAAAAGAG
1 GAAAAAGAG
102171 TTTGAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (12 bp):
GAAAAAGAGAAT
Found at i:102217 original size:18 final size:19
Alignment explanation
Indices: 102181--102219 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
102171 TTTGAGAGAG
* *
102181 AAAAAGAATGTGAACAAGA
1 AAAAAAAATGTGAAAAAGA
102200 AAAAAAAATG-GAAAAAGA
1 AAAAAAAATGTGAAAAAGA
102218 AA
1 AA
102220 TTGAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.08
Consensus pattern (19 bp):
AAAAAAAATGTGAAAAAGA
Found at i:104010 original size:30 final size:30
Alignment explanation
Indices: 103976--104072 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
103966 AGCTCACTCC
103976 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * ** * *
104006 TAGCTCAACTTCTGCTTAGGAATTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
104036 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
104066 TAGCTCA
1 TAGCTCA
104073 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
29 1 0.02
30 48 0.98
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:109773 original size:30 final size:30
Alignment explanation
Indices: 109690--109774 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
109680 GCTCATATTC
* *
109690 AGCTCATGAGCTAAACCTTAGCTCAGCTTT
1 AGCTCACGAGCTAAACCTTAGCTCAACTTT
* * * * * *
109720 AGCTTAGGAGTTTAATCTCAGCTCAACTTT
1 AGCTCACGAGCTAAACCTTAGCTCAACTTT
*
109750 AGCTCACGAGCTAAAGCTTAGCTCA
1 AGCTCACGAGCTAAACCTTAGCTCA
109775 TTTTAGTTTA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (30 bp):
AGCTCACGAGCTAAACCTTAGCTCAACTTT
Found at i:111893 original size:19 final size:19
Alignment explanation
Indices: 111869--111908 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
111859 AGCTCCCATG
111869 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
111888 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
111907 TA
1 TA
111909 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:113402 original size:30 final size:31
Alignment explanation
Indices: 113368--113452 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 31
113358 TAAACTAAAA
* *
113368 TGAGCTAAGCTTTAGCTCGTGAGCTA-AAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAGAAGC
* * * * *
113398 TGAGCTGAGATTAAACTCCTAAG-TAGAAGC
1 TGAGCTAAGATTTAGCTCGTGAGCTAGAAGC
*
113428 TGAGCTAAGGTTTAGCTCGTGAGCT
1 TGAGCTAAGATTTAGCTCGTGAGCT
113453 GAATATGAGC
Statistics
Matches: 40, Mismatches: 13, Indels: 3
0.71 0.23 0.05
Matches are distributed among these distances:
29 2 0.05
30 37 0.93
31 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.28
Consensus pattern (31 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAGAAGC
Found at i:113462 original size:30 final size:30
Alignment explanation
Indices: 113367--113464 Score: 74
Period size: 30 Copynumber: 3.3 Consensus size: 30
113357 TTAAACTAAA
* *
113367 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAA-T
* * * * * *
113398 -TGAGCTGAGATTAAACTCCTAAG-TAGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCT-GAAT
* *
113427 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAT
113457 ATGAGCTA
1 ATGAGCTA
113465 GGAGTGAGCT
Statistics
Matches: 48, Mismatches: 16, Indels: 7
0.68 0.23 0.10
Matches are distributed among these distances:
29 1 0.02
30 46 0.96
31 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAT
Found at i:115216 original size:29 final size:29
Alignment explanation
Indices: 115174--115235 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
115164 GAATCCTTTT
115174 ACATAGATTCCACCATTATTTACGTTAAA
1 ACATAGATTCCACCATTATTTACGTTAAA
115203 ACATAGATTCCACCATTATTTACGTTAAA
1 ACATAGATTCCACCATTATTTACGTTAAA
115232 ACAT
1 ACAT
115236 CCTTTTGAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.34
Consensus pattern (29 bp):
ACATAGATTCCACCATTATTTACGTTAAA
Found at i:118755 original size:12 final size:12
Alignment explanation
Indices: 118740--118798 Score: 57
Period size: 12 Copynumber: 4.7 Consensus size: 12
118730 AAAAAATCAA
118740 AAAAAAAAATTG
1 AAAAAAAAATTG
118752 AAAAAAAATTTGATTG
1 AAAAAAAA----ATTG
118768 AAAAAAAAATT-
1 AAAAAAAAATTG
* *
118779 CAAAAAAAAGTG
1 AAAAAAAAATTG
118791 AAAAAAAA
1 AAAAAAAA
118799 TCGAGCAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
11 9 0.23
12 18 0.46
16 12 0.31
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:119907 original size:18 final size:18
Alignment explanation
Indices: 119881--119949 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
119871 AAATTGAAAG
*
119881 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
119899 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
* *
119917 AAAAGAAAAAGAAATCAA
1 AAAAGAAAAAGAAAACGA
**
119935 AAAAGTGAAAGAAAA
1 AAAAGAAAAAGAAAA
119950 AGAAGATGAG
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.74, C:0.06, G:0.14, T:0.06
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:119909 original size:6 final size:6
Alignment explanation
Indices: 119877--119953 Score: 59
Period size: 6 Copynumber: 13.0 Consensus size: 6
119867 AAAGAAATTG
* * ** *
119877 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* **
119924 AAAGAA ATCA-AA AAAGTG AAAGAA AAAGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA
119954 GATGAGTGTG
Statistics
Matches: 53, Mismatches: 16, Indels: 5
0.72 0.22 0.07
Matches are distributed among these distances:
5 4 0.08
6 48 0.91
7 1 0.02
ACGTcount: A:0.74, C:0.05, G:0.16, T:0.05
Consensus pattern (6 bp):
AAAGAA
Found at i:125087 original size:16 final size:16
Alignment explanation
Indices: 125049--125079 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
125039 GTAGGGGATT
125049 ATACATGAATGGTTGA
1 ATACATGAATGGTTGA
125065 ATACATGAATGGTTG
1 ATACATGAATGGTTG
125080 GATTCATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.32
Consensus pattern (16 bp):
ATACATGAATGGTTGA
Found at i:129713 original size:16 final size:16
Alignment explanation
Indices: 129675--129705 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
129665 GTAGGGGATT
129675 ATACATGAATGGTTGA
1 ATACATGAATGGTTGA
129691 ATACATGAATGGTTG
1 ATACATGAATGGTTG
129706 GATTCATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.32
Consensus pattern (16 bp):
ATACATGAATGGTTGA
Found at i:132165 original size:12 final size:12
Alignment explanation
Indices: 132150--132192 Score: 70
Period size: 12 Copynumber: 3.6 Consensus size: 12
132140 AAAAAACCGA
132150 AAAAAAATTTCG
1 AAAAAAATTTCG
132162 AAAAAAATTTCG
1 AAAAAAATTTCG
132174 AAAAAAATATTC-
1 AAAAAAAT-TTCG
132186 AAAAAAA
1 AAAAAAA
132193 AGTGATTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 27 0.90
13 3 0.10
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (12 bp):
AAAAAAATTTCG
Found at i:135695 original size:13 final size:13
Alignment explanation
Indices: 135677--135705 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
135667 CGACTAACCT
135677 ACATAATTAAATA
1 ACATAATTAAATA
135690 ACATAATTAAATA
1 ACATAATTAAATA
135703 ACA
1 ACA
135706 CACAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:135964 original size:10 final size:10
Alignment explanation
Indices: 135931--135979 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
135921 AAAAAGGAAT
*
135931 GAGCTGAAAC
1 GAGCTCAAAC
135941 GAGCT-AAATTC
1 GAGCTCAAA--C
135952 GAGCTCAAAC
1 GAGCTCAAAC
*
135962 GAGCTAAAAC
1 GAGCTCAAAC
135972 GAGCTCAA
1 GAGCTCAA
135980 GTGAGCTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 3 0.09
10 22 0.65
11 6 0.18
12 3 0.09
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:135986 original size:20 final size:21
Alignment explanation
Indices: 135931--135979 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
135921 AAAAAGGAAT
* *
135931 GAGCTGAAACGAGCTAAATTC
1 GAGCTCAAACGAGCTAAATAC
135952 GAGCTCAAACGAGCTAAA-AC
1 GAGCTCAAACGAGCTAAATAC
135972 GAGCTCAA
1 GAGCTCAA
135980 GTGAGCTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (21 bp):
GAGCTCAAACGAGCTAAATAC
Found at i:137668 original size:20 final size:20
Alignment explanation
Indices: 137645--137698 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
137635 AGTTTTTCCC
*
137645 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
137665 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
137685 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
137699 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:137680 original size:30 final size:30
Alignment explanation
Indices: 137645--137718 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
137635 AGTTTTTCCC
137645 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
137675 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
137705 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
137719 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:137708 original size:20 final size:20
Alignment explanation
Indices: 137645--137709 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
137635 AGTTTTTCCC
* * * *
137645 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
137665 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
137684 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
137705 AGCTC
1 AGCTC
137710 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:139344 original size:16 final size:15
Alignment explanation
Indices: 139336--139388 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
139326 AAAAAATTCG
**
139336 AAAAAAAAATTGATTG
1 AAAAAAAAATTGA-AA
*
139352 AAAAAAAAATTCAAA
1 AAAAAAAAATTGAAA
* *
139367 AAATAAAAAGTGAAA
1 AAAAAAAAATTGAAA
139382 AAAAAAA
1 AAAAAAA
139389 TCGAGCAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 18 0.60
16 12 0.40
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (15 bp):
AAAAAAAAATTGAAA
Found at i:139367 original size:12 final size:12
Alignment explanation
Indices: 139313--139369 Score: 53
Period size: 12 Copynumber: 4.4 Consensus size: 12
139303 TTGGAGTAAC
139313 AAAAAAAA-TCA
1 AAAAAAAATTCA
139324 AAAAAAAATTCGAA
1 AAAAAAAATTC--A
*
139338 AAAAAAATTGATTGA
1 AAAAAAA---ATTCA
139353 AAAAAAAATTCA
1 AAAAAAAATTCA
139365 AAAAA
1 AAAAA
139370 TAAAAAGTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
11 8 0.21
12 11 0.29
14 8 0.21
15 8 0.21
17 3 0.08
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:139399 original size:17 final size:17
Alignment explanation
Indices: 139379--139420 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
139369 ATAAAAAGTG
139379 AAAAAAAAA-ATCGAGCA
1 AAAAAAAAAGAT-GAGCA
*
139396 AAAAAAAAAGGTGAGCA
1 AAAAAAAAAGATGAGCA
139413 AAAAAAAA
1 AAAAAAAA
139421 TCAAGTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.74, C:0.07, G:0.14, T:0.05
Consensus pattern (17 bp):
AAAAAAAAAGATGAGCA
Found at i:140373 original size:15 final size:16
Alignment explanation
Indices: 140353--140384 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
140343 AGAAAATGAA
140353 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
140368 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
140384 A
1 A
140385 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:140499 original size:17 final size:18
Alignment explanation
Indices: 140467--140500 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
140457 AAAAGAGAGT
*
140467 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
140485 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
140501 GGAGTGTTGT
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:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:141789 original size:20 final size:20
Alignment explanation
Indices: 141766--141819 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
141756 AGTTTTTCCC
*
141766 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
141786 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
141806 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
141820 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:141801 original size:30 final size:30
Alignment explanation
Indices: 141766--141839 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
141756 AGTTTTTCCC
141766 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
141796 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
141826 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
141840 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:141829 original size:20 final size:20
Alignment explanation
Indices: 141766--141830 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
141756 AGTTTTTCCC
* * * *
141766 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
141786 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
141805 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
141826 AGCTC
1 AGCTC
141831 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:149489 original size:18 final size:18
Alignment explanation
Indices: 149468--149502 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
149458 TTTTTCTTTT
149468 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
149486 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
149503 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:149499 original size:6 final size:6
Alignment explanation
Indices: 149490--149594 Score: 52
Period size: 6 Copynumber: 17.2 Consensus size: 6
149480 TCAATCTCAA
* * * ** **
149490 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTAT TTTGAT
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCT-T TTTCTT
* ** * *
149542 TT-CTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
149588 TTTCTT T
1 TTTCTT T
149595 CAATTTCTTT
Statistics
Matches: 69, Mismatches: 25, Indels: 10
0.66 0.24 0.10
Matches are distributed among these distances:
5 7 0.10
6 49 0.71
7 10 0.14
8 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:149607 original size:6 final size:6
Alignment explanation
Indices: 149541--149594 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
149531 ACTATTTTGA
* ** * *
149541 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
149588 TTTCTT T
1 TTTCTT T
149595 CAATTTCTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:150698 original size:30 final size:30
Alignment explanation
Indices: 150664--150760 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
150654 AGCTCACTCC
150664 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * * *
150694 TAGCTCAACTTCAACTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
150724 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
150754 TAGCTCA
1 TAGCTCA
150761 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
29 1 0.02
30 48 0.98
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:152359 original size:11 final size:12
Alignment explanation
Indices: 152354--152386 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
152344 CAAAATCAAA
152354 AAAAAAAGAAGTC
1 AAAAAAA-AAGTC
152367 AAAAAAAAA-TC
1 AAAAAAAAAGTC
152378 AAAAAAAAA
1 AAAAAAAAA
152387 ATTTGAGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 2 0.10
13 7 0.35
ACGTcount: A:0.82, C:0.06, G:0.06, T:0.06
Consensus pattern (12 bp):
AAAAAAAAAGTC
Found at i:152485 original size:13 final size:13
Alignment explanation
Indices: 152467--152505 Score: 57
Period size: 11 Copynumber: 3.2 Consensus size: 13
152457 AAAGGAGAAG
152467 AAATTCAGAAAAA
1 AAATTCAGAAAAA
152480 AAATTCA-AAAAA
1 AAATTCAGAAAAA
152492 AAA-TC-GAAAAA
1 AAATTCAGAAAAA
152503 AAA
1 AAA
152506 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.40
12 8 0.32
13 7 0.28
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (13 bp):
AAATTCAGAAAAA
Found at i:152489 original size:11 final size:12
Alignment explanation
Indices: 152474--152531 Score: 52
Period size: 11 Copynumber: 5.2 Consensus size: 12
152464 AAGAAATTCA
*
152474 GAAAAAAAATTC
1 GAAAAAAAAATC
152486 -AAAAAAAAATC
1 GAAAAAAAAATC
*
152497 G-AAAAAAAA-G
1 GAAAAAAAAATC
*
152507 GAAAAAAAAGT-
1 GAAAAAAAAATC
*
152518 GACAAAAAAATC
1 GAAAAAAAAATC
152530 GA
1 GA
152532 GTTAAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
10 1 0.03
11 34 0.92
12 2 0.05
ACGTcount: A:0.72, C:0.07, G:0.12, T:0.09
Consensus pattern (12 bp):
GAAAAAAAAATC
Found at i:152492 original size:12 final size:12
Alignment explanation
Indices: 152467--152505 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
152457 AAAGGAGAAG
152467 AAATTCAGAAAAA
1 AAATTCA-AAAAA
152480 AAATTCAAAAAA
1 AAATTCAAAAAA
152492 AAA-TCGAAAAAA
1 AAATTC-AAAAAA
152504 AA
1 AA
152506 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 2 0.08
12 16 0.64
13 7 0.28
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:153493 original size:37 final size:37
Alignment explanation
Indices: 153442--153512 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
153432 CATTCTTGTA
153442 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
153479 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
153513 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:153512 original size:6 final size:6
Alignment explanation
Indices: 153452--153501 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
153442 AAGAGAAAAC
*
153452 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
153501 A
1 A
153502 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:155792 original size:30 final size:30
Alignment explanation
Indices: 155758--155854 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
155748 AGCTCACTCC
155758 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
155788 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
155818 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
155848 TAGCTCA
1 TAGCTCA
155855 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:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:157528 original size:17 final size:17
Alignment explanation
Indices: 157480--157530 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
157470 CTCGCAAGAC
157480 TTTTCACTT-TTTTTTT
1 TTTTCACTTCTTTTTTT
* **
157496 CTTTTAAC-TCGATTTTT
1 -TTTTCACTTCTTTTTTT
157513 TTTTCACTTCTTTTTTT
1 TTTTCACTTCTTTTTTT
157530 T
1 T
157531 AATTTTTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.10, C:0.16, G:0.02, T:0.73
Consensus pattern (17 bp):
TTTTCACTTCTTTTTTT
Found at i:160295 original size:22 final size:23
Alignment explanation
Indices: 160270--160329 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
160260 TGGACTGAAT
160270 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
160292 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
160314 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
160330 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:160297 original size:4 final size:4
Alignment explanation
Indices: 160279--160312 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
160269 TATAAAAATT
160279 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
160313 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:161718 original size:23 final size:22
Alignment explanation
Indices: 161667--161718 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
161657 CCTCGTCTTT
*
161667 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
161689 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
161712 TTCTTTT
1 TTCTTTT
161719 TCAAATTTCT
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:164120 original size:22 final size:23
Alignment explanation
Indices: 164095--164154 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
164085 TGGACTGAAT
164095 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
164117 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
164139 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
164155 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:164122 original size:4 final size:4
Alignment explanation
Indices: 164104--164137 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
164094 TATAAAAATT
164104 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
164138 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:167923 original size:20 final size:20
Alignment explanation
Indices: 167898--167972 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
167888 TGTGGTTCAA
*
167898 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
167918 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
167938 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
167958 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
167973 TTTAACTCGT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:169787 original size:14 final size:13
Alignment explanation
Indices: 169770--169814 Score: 74
Period size: 12 Copynumber: 3.5 Consensus size: 13
169760 AAAAAAAAGG
169770 AAAAAAAATTCGAA
1 AAAAAAAATTC-AA
169784 AAAAAAAATTC-A
1 AAAAAAAATTCAA
169796 AAAAAAAATTCAA
1 AAAAAAAATTCAA
169809 AAAAAA
1 AAAAAA
169815 TTTGTATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.40
13 7 0.23
14 11 0.37
ACGTcount: A:0.78, C:0.07, G:0.02, T:0.13
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:171364 original size:16 final size:15
Alignment explanation
Indices: 171345--171374 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
171335 AGTATCAATT
171345 TTTGATTGGTGATGAC
1 TTTGATTGG-GATGAC
171361 TTTGATTGGGATGA
1 TTTGATTGGGATGA
171375 TGGATTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
TTTGATTGGGATGAC
Found at i:171487 original size:45 final size:45
Alignment explanation
Indices: 171437--171526 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
171427 GAAGCAAGAT
171437 TAAAACAACACAAACAAAATTTGGGATTGTGTGATGAAAAGTTGA
1 TAAAACAACACAAACAAAATTTGGGATTGTGTGATGAAAAGTTGA
171482 TAAAACAACACAAACAAAATTTGGGATTGTGTGATGAAAAGTTGA
1 TAAAACAACACAAACAAAATTTGGGATTGTGTGATGAAAAGTTGA
171527 CATCTAATCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.47, C:0.09, G:0.20, T:0.24
Consensus pattern (45 bp):
TAAAACAACACAAACAAAATTTGGGATTGTGTGATGAAAAGTTGA
Found at i:172331 original size:20 final size:20
Alignment explanation
Indices: 172306--172360 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
172296 TGTGGTTCAA
*
172306 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
172326 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
172346 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
172361 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:175039 original size:12 final size:11
Alignment explanation
Indices: 175022--175061 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
175012 ATACAAGTTT
175022 AAAAAAAATCCG
1 AAAAAAAAT-CG
175034 AAAAAAAATCG
1 AAAAAAAATCG
175045 AAAAAAAA--G
1 AAAAAAAATCG
175054 AAAAAAAA
1 AAAAAAAA
175062 GTGATTTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.32
11 10 0.36
12 9 0.32
ACGTcount: A:0.80, C:0.07, G:0.07, T:0.05
Consensus pattern (11 bp):
AAAAAAAATCG
Found at i:194440 original size:13 final size:13
Alignment explanation
Indices: 194422--194446 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
194412 TGCTGGTTTA
194422 CACGACTGTGTCG
1 CACGACTGTGTCG
194435 CACGACTGTGTC
1 CACGACTGTGTC
194447 TAGCTTCGTT
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:0.16, C:0.32, G:0.28, T:0.24
Consensus pattern (13 bp):
CACGACTGTGTCG
Found at i:197747 original size:30 final size:30
Alignment explanation
Indices: 197713--197809 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
197703 GAAACTAAAA
197713 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
197743 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
197773 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
197803 TGAGCTA
1 TGAGCTA
197810 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:199940 original size:12 final size:12
Alignment explanation
Indices: 199901--199954 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
199891 ATTTCTTTTA
199901 TTTCAATTTCTT
1 TTTCAATTTCTT
* *
199913 TCTCTTAATCTCTT
1 T-T-TCAATTTCTT
199927 TTTCAATTTC-T
1 TTTCAATTTCTT
*
199938 TTTCAACTTCTT
1 TTTCAATTTCTT
199950 TTTCA
1 TTTCA
199955 CTCTCAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
11 10 0.29
12 13 0.38
13 2 0.06
14 9 0.26
ACGTcount: A:0.17, C:0.22, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTCAATTTCTT
Found at i:199965 original size:30 final size:29
Alignment explanation
Indices: 199929--199999 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
199919 AATCTCTTTT
*
199929 TCAATTTCTTTTCAACT-TCTTTTTCACTC
1 TCAATTTCTTTTC-ACTCTCTTTTTCAATC
*
199958 TCAAATTTCTTTTCATTCTCTTTTTCAATC
1 TC-AATTTCTTTTCACTCTCTTTTTCAATC
*
199988 TCATTTTCTTTT
1 TCAATTTCTTTT
200000 TGCTTTTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 13 0.35
30 24 0.65
ACGTcount: A:0.17, C:0.24, G:0.00, T:0.59
Consensus pattern (29 bp):
TCAATTTCTTTTCACTCTCTTTTTCAATC
Found at i:200017 original size:11 final size:12
Alignment explanation
Indices: 200001--200029 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
199991 TTTTCTTTTT
200001 GCTTTT-CAAAG
1 GCTTTTGCAAAG
200012 GCTTTTGCAAAG
1 GCTTTTGCAAAG
200024 GCTTTT
1 GCTTTT
200030 TTAAGTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (12 bp):
GCTTTTGCAAAG
Found at i:200103 original size:6 final size:5
Alignment explanation
Indices: 200081--200128 Score: 53
Period size: 5 Copynumber: 9.0 Consensus size: 5
200071 CTTTTGCCTC
200081 TCTTT TCTTT T-TATT TCGTTT TCTTCT TCTTTT TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTT-T TC-TTT TCTTT TCTTT TCTTT
200129 GTTTTCTCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
4 1 0.03
5 24 0.63
6 10 0.26
7 3 0.08
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:200111 original size:22 final size:21
Alignment explanation
Indices: 200081--200128 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
200071 CTTTTGCCTC
200081 TCTTTTCTTTTT-ATTTCGTTT
1 TCTTTTCTTTTTCATTTC-TTT
*
200102 TCTTCTTCTTTTTCTTTTCTTT
1 TCTT-TTCTTTTTCATTTCTTT
200124 TCTTT
1 TCTTT
200129 GTTTTCTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.21
22 15 0.62
23 4 0.17
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (21 bp):
TCTTTTCTTTTTCATTTCTTT
Found at i:204198 original size:23 final size:22
Alignment explanation
Indices: 204146--204198 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
204136 TCCACGTCTT
*
204146 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
204168 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
204191 TTTCTTTT
1 TTTCTTTT
204199 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:208178 original size:23 final size:22
Alignment explanation
Indices: 208126--208178 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
208116 TCCACGTCTT
*
208126 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
208148 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
208171 TTTCTTTT
1 TTTCTTTT
208179 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:223816 original size:22 final size:22
Alignment explanation
Indices: 223765--223830 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
223755 GGTATTTGGG
* *
223765 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
223786 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
223808 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
223831 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:225190 original size:20 final size:20
Alignment explanation
Indices: 225167--225220 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
225157 AGTTTTACCC
*
225167 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
225187 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
225207 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
225221 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:225202 original size:30 final size:30
Alignment explanation
Indices: 225167--225240 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
225157 AGTTTTACCC
225167 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
225197 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
225227 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
225241 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:225230 original size:20 final size:20
Alignment explanation
Indices: 225167--225231 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
225157 AGTTTTACCC
* * * *
225167 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
225187 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
225206 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
225227 AGCTC
1 AGCTC
225232 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:226881 original size:22 final size:22
Alignment explanation
Indices: 226856--226914 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 22
226846 AAATTCGAAA
226856 AAAAAAGAAGTGAGCAAAAAAG-A-
1 AAAAAA-AAGTGA--AAAAAAGAAG
226879 AAAAAAAAGT-AAAAAAAGAAG
1 AAAAAAAAGTGAAAAAAAGAAG
226900 AAAAAAAAGTGAAAA
1 AAAAAAAAGTGAAAA
226915 GTCTTGCGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
19 7 0.21
20 1 0.03
21 11 0.33
22 8 0.24
23 6 0.18
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.05
Consensus pattern (22 bp):
AAAAAAAAGTGAAAAAAAGAAG
Found at i:231007 original size:10 final size:10
Alignment explanation
Indices: 230994--231031 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
230984 TTGTAGCTAA
230994 ATTGAGCTCG
1 ATTGAGCTCG
231004 ATTGAGCT-G
1 ATTGAGCTCG
231013 ACTTGAGCTCG
1 A-TTGAGCTCG
*
231024 AGTGAGCT
1 ATTGAGCT
231032 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:231011 original size:20 final size:20
Alignment explanation
Indices: 230971--231031 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
230961 ACCAATAAAA
230971 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
230991 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
231011 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
231031 T
1 T
231032 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:231032 original size:20 final size:20
Alignment explanation
Indices: 230995--231032 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
230985 TGTAGCTAAA
*
230995 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
231015 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
231033 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Done.