Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015185.1 Kokia drynarioides strain JFW-HI SEQ_130229, whole genome shotgun sequence
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: 201118
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 256 characters in sequence are not A, C, G, or T
Found at i:858 original size:71 final size:71
Alignment explanation
Indices: 741--878 Score: 267
Period size: 71 Copynumber: 1.9 Consensus size: 71
731 ACGTAAATCT
741 AGATAATAATGCCGTATTCAAGTTGACAATTTCTTGGGGGTATTAGCATCACATGTAAATTGAAT
1 AGATAATAATGCCGTATTCAAGTTGACAATTTCTTGGGGGTATTAGCATCACATGTAAATTGAAT
806 TGCAGA
66 TGCAGA
*
812 AGATAATAATGCCGTATTCAAGTTGACAATTTCTTGGGGGTTTTAGCATCACATGTAAATTGAAT
1 AGATAATAATGCCGTATTCAAGTTGACAATTTCTTGGGGGTATTAGCATCACATGTAAATTGAAT
877 TG
66 TG
879 AATTGCAGAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (71 bp):
AGATAATAATGCCGTATTCAAGTTGACAATTTCTTGGGGGTATTAGCATCACATGTAAATTGAAT
TGCAGA
Found at i:1245 original size:27 final size:27
Alignment explanation
Indices: 1215--1270 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
1205 TCAGTTTATA
*
1215 TTTTTAAAAATTAATTTTATTCTTTTT
1 TTTTTAAAAATTAATTTTATTATTTTT
* * *
1242 TTTTTTATAATTGATTTTATTATTTTT
1 TTTTTAAAAATTAATTTTATTATTTTT
1269 TT
1 TT
1271 CAGTAAAAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTTTAAAAATTAATTTTATTATTTTT
Found at i:1340 original size:21 final size:20
Alignment explanation
Indices: 1282--1351 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 20
1272 AGTAAAAGGG
*
1282 AAAACATGGGGTTTTATAGAGA
1 AAAACAT-GGTTTTTATAG-GA
* *
1304 ACTAACTTGGTTTTTATAGGA
1 A-AAACATGGTTTTTATAGGA
*
1325 AAAACATGGATTTTTACAGGGA
1 AAAACATGG-TTTTTATA-GGA
1347 AAAAC
1 AAAAC
1352 CATTTTATCC
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 6 0.15
21 10 0.26
22 19 0.49
23 4 0.10
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (20 bp):
AAAACATGGTTTTTATAGGA
Found at i:1857 original size:3 final size:3
Alignment explanation
Indices: 1849--1879 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1839 AAAATGTGCC
1849 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1880 TAAAACTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3314 original size:3 final size:3
Alignment explanation
Indices: 3308--3335 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3298 ATAAACTCTC
3308 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
3336 ATTGAGTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:7705 original size:21 final size:21
Alignment explanation
Indices: 7667--7706 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
7657 GAGGAAGAGA
*
7667 AAAAAAAACTTTAAAAAGGCG
1 AAAAAAAACTTGAAAAAGGCG
7688 AAAAAAAA-TTGAAGAAAGG
1 AAAAAAAACTTGAA-AAAGG
7707 AAAAGGTCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.65, C:0.05, G:0.17, T:0.12
Consensus pattern (21 bp):
AAAAAAAACTTGAAAAAGGCG
Found at i:11039 original size:9 final size:9
Alignment explanation
Indices: 11017--11087 Score: 67
Period size: 9 Copynumber: 7.8 Consensus size: 9
11007 ATGTCACATA
11017 ATAAATAATT
1 ATAAA-AATT
11027 -TAAAAATT
1 ATAAAAATT
11035 ATAAAAATT
1 ATAAAAATT
11044 -T-AAAATT
1 ATAAAAATT
*
11051 AAAAAAATAT
1 ATAAAAAT-T
11061 ATAAATAATT
1 ATAAA-AATT
11071 CATAAAAATT
1 -ATAAAAATT
*
11081 TTAAAAA
1 ATAAAAA
11088 ATAGTATGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
7 6 0.12
8 5 0.10
9 23 0.44
10 10 0.19
11 8 0.15
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:12661 original size:59 final size:58
Alignment explanation
Indices: 12598--12920 Score: 289
Period size: 59 Copynumber: 5.5 Consensus size: 58
12588 TGGACATCCG
* *
12598 GGGGT-AAAATGGTAATTTTAGGAAGTTTCAGAGTCAAAAATGGAATTTTTAGAAGTATC
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTCAGAGTCAAAAATGGGATTTTTAGAAGT-TC
* * * **
12657 GGGGTTAAAAATGGAA-TTTTGGAAATTCCA-AGGTCGAAAATGGGATTTTGGGAAGTTC
1 GGGG-TAAAAATGGAATTTTTGGAAGTTTCAGA-GTCAAAAATGGGATTTTTAGAAGTTC
* * *
12715 GGGGCT-AAAACGGGATTTTTGGAAGTTTC-GAGATCAAAAATGGGATTTTTAGAAGTTTG
1 GGGG-TAAAAATGGAATTTTTGGAAGTTTCAGAG-TCAAAAATGGGATTTTTAGAAG-TTC
* * ** * * * *
12774 GGGGTAAAAATAGAATTTTTGGAGGTTTTGGGGACAAAATTGGGATTTTTAGAAGTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTCAGAGTCAAAAATGGGATTTTTAGAAGTTC
* ** *
12832 GAGGGT-AAAATCGAGATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTAGAAGTTC
1 G-GGGTAAAAATGGA-ATTTTTGGAAGTTTCAGAGTCAAAAATGGGATTTTTAGAAGTTC
* * *
12891 GAGGGTGAAAACGGGATTTTTGGAAGTTTC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTC
12921 GAGGCCCTTA
Statistics
Matches: 218, Mismatches: 34, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
57 8 0.04
58 50 0.23
59 143 0.66
60 10 0.05
61 7 0.03
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (58 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTCAGAGTCAAAAATGGGATTTTTAGAAGTTC
Found at i:12806 original size:30 final size:30
Alignment explanation
Indices: 12569--12919 Score: 145
Period size: 30 Copynumber: 11.9 Consensus size: 30
12559 TGGAAAATTC
* **
12569 GGGGTAAAAATGGATTTTTTGGACA--TCCG
1 GGGGTAAAAATGGAATTTTTGGA-AGTTTTG
* *
12598 GGGGT-AAAATGGTAATTTTAGGAAG-TTTC
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTTG
* * * * *
12627 AGAGTCAAAAATGGAATTTTTAGAAGTATCG
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTTG
* * **
12658 GGGTTAAAAATGGAA-TTTTGGAA-ATTCC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTTG
** * * * *
12686 AAGGTCGAAAATGGGATTTTGGGAAG-TTCG
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTTG
* * * *
12716 GGGCT-AAAACGGGATTTTTGGAAG-TTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTTG
* * * *
12744 GAGATCAAAAATGGGATTTTTAGAAG-TTTG
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTTG
* *
12774 GGGGTAAAAATAGAATTTTTGGAGGTTTTG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTTG
** * * *
12804 GGGACAAAATTGGGATTTTTAGAAG-TTTG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTTG
* *
12833 AGGGT-AAAATCGAGATTTTTGGAAGTTTT-
1 GGGGTAAAAATGGA-ATTTTTGGAAGTTTTG
* * *
12862 GGGGTCAAAAATGGGATTTTTAGAAG-TTCG
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTTG
* * * *
12892 AGGGTGAAAACGGGATTTTTGGAAGTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTT
12920 CGAGGCCCTT
Statistics
Matches: 238, Mismatches: 67, Indels: 33
0.70 0.20 0.10
Matches are distributed among these distances:
28 39 0.16
29 87 0.37
30 96 0.40
31 16 0.07
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.32
Consensus pattern (30 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTTG
Found at i:12924 original size:30 final size:30
Alignment explanation
Indices: 12556--12924 Score: 220
Period size: 29 Copynumber: 12.6 Consensus size: 30
12546 GAAACGGTAA
**
12556 TTTTGGAAAATTCG-GGGTAAAAAT-GGATT
1 TTTTGGAAGTTTCGAGGGTAAAAATGGGA-T
* * *
12585 TTTTGGACA--TCCGGGGGT-AAAATGGTAAT
1 TTTTGGA-AGTTTCGAGGGTAAAAATGG-GAT
* * *
12614 TTTAGGAAGTTTC-AGAGTCAAAAATGGAAT
1 TTTTGGAAGTTTCGAGGGT-AAAAATGGGAT
* * *
12644 TTTTAGAAGTATCG-GGGTTAAAAAT-GGAA
1 TTTTGGAAGTTTCGAGGG-TAAAAATGGGAT
* * * *
12673 TTTTGGAA-ATTCCAAGGTCGAAAATGGGAT
1 TTTTGGAAGTTTCGAGGGT-AAAAATGGGAT
* *
12703 TTTGGGAAG-TTCG-GGGCT-AAAACGGGAT
1 TTTTGGAAGTTTCGAGGG-TAAAAATGGGAT
*
12731 TTTTGGAAGTTTCGA-GATCAAAAATGGGAT
1 TTTTGGAAGTTTCGAGGGT-AAAAATGGGAT
* * * *
12761 TTTTAGAAGTTT-GGGGGTAAAAATAGAAT
1 TTTTGGAAGTTTCGAGGGTAAAAATGGGAT
* *
12790 TTTTGGAGGTTTTG-GGG-ACAAAATTGGGAT
1 TTTTGGAAGTTTCGAGGGTA-AAAA-TGGGAT
* *
12820 TTTTAGAAGTTT-GAGGGT-AAAATCGAGAT
1 TTTTGGAAGTTTCGAGGGTAAAAAT-GGGAT
*
12849 TTTTGGAAGTTTTG-GGGTCAAAAATGGGAT
1 TTTTGGAAGTTTCGAGGGT-AAAAATGGGAT
* * *
12879 TTTTAGAAG-TTCGAGGGTGAAAACGGGAT
1 TTTTGGAAGTTTCGAGGGTAAAAATGGGAT
12908 TTTTGGAAGTTTCGAGG
1 TTTTGGAAGTTTCGAGG
12925 CCCTTAGGGT
Statistics
Matches: 264, Mismatches: 45, Indels: 61
0.71 0.12 0.16
Matches are distributed among these distances:
28 32 0.12
29 116 0.44
30 103 0.39
31 13 0.05
ACGTcount: A:0.31, C:0.06, G:0.30, T:0.33
Consensus pattern (30 bp):
TTTTGGAAGTTTCGAGGGTAAAAATGGGAT
Found at i:14682 original size:17 final size:17
Alignment explanation
Indices: 14662--14716 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
14652 ACCTGGACAT
*
14662 TAAAATTAAATTTATAA
1 TAAATTTAAATTTATAA
*
14679 TAAATTTAAATTTCA-AC
1 TAAATTTAAATTT-ATAA
14696 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
14713 TAAA
1 TAAA
14717 CTCAATTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 1 0.03
17 31 0.94
18 1 0.03
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:15904 original size:2 final size:2
Alignment explanation
Indices: 15897--15932 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
15887 TTATGGAGAA
15897 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15933 GATTATGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16378 original size:15 final size:15
Alignment explanation
Indices: 16335--16383 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
16325 AACTTTTTCG
*
16335 AATCGAATCTAGTGA
1 AATCGAATCAAGTGA
*
16350 AAT-GAAATTCAAGTCA
1 AATCG-AA-TCAAGTGA
16366 AATCGAATCAAGTGA
1 AATCGAATCAAGTGA
16381 AAT
1 AAT
16384 TGTTTGAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 1 0.04
15 15 0.54
16 11 0.39
17 1 0.04
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.24
Consensus pattern (15 bp):
AATCGAATCAAGTGA
Found at i:16660 original size:17 final size:18
Alignment explanation
Indices: 16623--16660 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
16613 TTAGAATTTT
*
16623 TTTTAAAAAATTATAACA
1 TTTTAAAAAATTATAAAA
*
16641 TTTTAATAAA-TATAAAA
1 TTTTAAAAAATTATAAAA
16658 TTT
1 TTT
16661 GGAATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTTAAAAAATTATAAAA
Found at i:17131 original size:2 final size:2
Alignment explanation
Indices: 17124--17150 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17114 CATTATACAC
17124 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
17151 TTGTTTGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21378 original size:22 final size:21
Alignment explanation
Indices: 21353--21396 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
21343 TTTTTAATTT
*
21353 TTTTAATATTTATATTATTTTA
1 TTTTAATATTTA-ATAATTTTA
21375 TTTTAATATTTAATAATTTTA
1 TTTTAATATTTAATAATTTTA
21396 T
1 T
21397 ATATTTAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTAATATTTAATAATTTTA
Found at i:21383 original size:16 final size:16
Alignment explanation
Indices: 21344--21402 Score: 52
Period size: 16 Copynumber: 3.7 Consensus size: 16
21334 TTCATATTAT
21344 TTTTAAT-TTTTTTAA
1 TTTTAATATTTTTTAA
21359 TATTT-ATATTATTTT-A
1 T-TTTAATATT-TTTTAA
**
21375 TTTTAATATTTAATAA
1 TTTTAATATTTTTTAA
21391 TTTTATATATTT
1 TTTTA-ATATTT
21403 AGTATAGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
15 8 0.22
16 18 0.50
17 10 0.28
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTAATATTTTTTAA
Found at i:24342 original size:18 final size:18
Alignment explanation
Indices: 24307--24370 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 18
24297 TAAAATAACA
24307 TATATTTATATAAATTTT
1 TATATTTATATAAATTTT
24325 TATATGTTAT-T-AA-TTT
1 TATAT-TTATATAAATTTT
*
24341 T-TA-TTACATAAATTTT
1 TATATTTATATAAATTTT
24357 ATCATATTTATATA
1 -T-ATATTTATATA
24371 TGTATATCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
13 3 0.08
14 1 0.03
15 4 0.11
16 7 0.19
17 3 0.08
18 6 0.17
19 6 0.17
20 6 0.17
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (18 bp):
TATATTTATATAAATTTT
Found at i:25714 original size:21 final size:21
Alignment explanation
Indices: 25690--25763 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 21
25680 CCAAGATATG
25690 CTCTCTAAAATCAACAACAAT
1 CTCTCTAAAATCAACAACAAT
** *
25711 CTCTAAAGCACAATCAATCCAAGATAT
1 CTCTCTA--A-AATCAA--CAACA-AT
25738 GCTCTCTAAAATCAACAACAAT
1 -CTCTCTAAAATCAACAACAAT
25760 CTCT
1 CTCT
25764 AAAGCACAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
21 9 0.22
22 2 0.05
23 5 0.12
24 6 0.15
25 6 0.15
26 5 0.12
27 2 0.05
28 5 0.12
ACGTcount: A:0.43, C:0.28, G:0.04, T:0.24
Consensus pattern (21 bp):
CTCTCTAAAATCAACAACAAT
Found at i:25723 original size:49 final size:49
Alignment explanation
Indices: 25666--25811 Score: 247
Period size: 49 Copynumber: 3.0 Consensus size: 49
25656 AATAATAATC
25666 AAAGCACAATCAATCCAAGATATGCTCTCTAAAATCAACAACAATCTCT
1 AAAGCACAATCAATCCAAGATATGCTCTCTAAAATCAACAACAATCTCT
25715 AAAGCACAATCAATCCAAGATATGCTCTCTAAAATCAACAACAATCTCT
1 AAAGCACAATCAATCCAAGATATGCTCTCTAAAATCAACAACAATCTCT
* * * **
25764 AAAGCACAATCAATCTAAGATATGATCTCCAAAATCAGTAACAATCTC
1 AAAGCACAATCAATCCAAGATATGCTCTCTAAAATCAACAACAATCTC
25812 AATCAAATGT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 92 1.00
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.23
Consensus pattern (49 bp):
AAAGCACAATCAATCCAAGATATGCTCTCTAAAATCAACAACAATCTCT
Found at i:25727 original size:24 final size:24
Alignment explanation
Indices: 25698--25776 Score: 74
Period size: 24 Copynumber: 3.2 Consensus size: 24
25688 TGCTCTCTAA
25698 AATCAACAACAATCTCTAAAGCAC
1 AATCAACAACAATCTCTAAAGCAC
* **
25722 AATCAATCCAAGATATGCTCTCTA--A-
1 AATCAA--CAACA-AT-CTCTAAAGCAC
25747 AATCAACAACAATCTCTAAAGCAC
1 AATCAACAACAATCTCTAAAGCAC
25771 AATCAA
1 AATCAA
25777 TCTAAGATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
21 5 0.12
22 2 0.05
23 5 0.12
24 12 0.29
25 6 0.14
26 5 0.12
27 2 0.05
28 5 0.12
ACGTcount: A:0.48, C:0.27, G:0.05, T:0.20
Consensus pattern (24 bp):
AATCAACAACAATCTCTAAAGCAC
Found at i:27483 original size:21 final size:21
Alignment explanation
Indices: 27457--27497 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
27447 TCCCTGACCC
27457 GTGTTGCCGTCGTCAGAGCCT
1 GTGTTGCCGTCGTCAGAGCCT
27478 GTGTTGCCGTCGTCAGAGCC
1 GTGTTGCCGTCGTCAGAGCC
27498 CGCGTCGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.29, G:0.34, T:0.27
Consensus pattern (21 bp):
GTGTTGCCGTCGTCAGAGCCT
Found at i:28498 original size:29 final size:30
Alignment explanation
Indices: 28457--28888 Score: 311
Period size: 29 Copynumber: 14.7 Consensus size: 30
28447 GAAGGTCCCT
* *
28457 AAACTGTCTAAAAATTACCATTTAACCCTCA
1 AAACT-TCCAAAAATTACCATTTGACCCTCA
* *
28488 AAA-TTCCAAAAA-TCCCATTTTTGACCC-CG
1 AAACTTCCAAAAATTACCA--TTTGACCCTCA
28517 AAACTTCCAAAAATTACCATTT-ACCCT--
1 AAACTTCCAAAAATTACCATTTGACCCTCA
* *
28544 GAACTTCCAAAAA-TCCCATTTTGACCC-CA
1 AAACTTCCAAAAATTACCA-TTTGACCCTCA
* * *
28573 AAACTTCCGAAAATTACCATTTTACCC-CC
1 AAACTTCCAAAAATTACCATTTGACCCTCA
28602 AAACTTCCAAAAA-T-CTCATTTTTGA-CCTCA
1 AAACTTCCAAAAATTAC-CA--TTTGACCCTCA
* *
28632 AAACTTCCAAAAATTACCATTTTACCCT-T
1 AAACTTCCAAAAATTACCATTTGACCCTCA
* * *
28661 AAACTT-CAAAAAATCCCATTTTTAACCCT-A
1 AAACTTCCAAAAATTACCA--TTTGACCCTCA
*
28691 AAACTTCCAAAAATTACCATTTTACCCT-A
1 AAACTTCCAAAAATTACCATTTGACCCTCA
*
28720 AAACTTCCAAAAA-TCCCATTTTTGA-CCTCA
1 AAACTTCCAAAAATTACCA--TTTGACCCTCA
* * *
28750 AAACTTCCAAAAATTACCCTTTTACCC-CT
1 AAACTTCCAAAAATTACCATTTGACCCTCA
* *
28779 AAACTTCTAAAAA-TCCCAATTTTGACCC-CA
1 AAACTTCCAAAAATTACC-A-TTTGACCCTCA
* *
28809 AAACTTCC-AAAATTACCATTTTACCC-CC
1 AAACTTCCAAAAATTACCATTTGACCCTCA
* * *
28837 GAACTCCCAAAAA-TCCCATTTTTGACCCT-A
1 AAACTTCCAAAAATTACCA--TTTGACCCTCA
*
28867 AAACCTCCAAAAATTACCATTT
1 AAACTTCCAAAAATTACCATTT
28889 TTACCCCCAG
Statistics
Matches: 320, Mismatches: 48, Indels: 68
0.73 0.11 0.16
Matches are distributed among these distances:
26 4 0.01
27 16 0.05
28 50 0.16
29 111 0.35
30 111 0.35
31 27 0.08
32 1 0.00
ACGTcount: A:0.38, C:0.30, G:0.03, T:0.29
Consensus pattern (30 bp):
AAACTTCCAAAAATTACCATTTGACCCTCA
Found at i:28526 original size:30 final size:28
Alignment explanation
Indices: 28474--28895 Score: 366
Period size: 30 Copynumber: 14.4 Consensus size: 28
28464 CTAAAAATTA
*
28474 CCATTTAACCCTCAAAA-TTCCAAAAATC
1 CCATTTTACCC-CAAAACTTCCAAAAATC
* *
28502 CCATTTTTGACCCCGAAACTTCCAAAAATTA
1 CCA-TTTT-ACCCCAAAACTTCCAAAAA-TC
**
28533 CCA-TTTA-CCCTGAACTTCCAAAAATC
1 CCATTTTACCCCAAAACTTCCAAAAATC
* *
28559 CCATTTTGACCCCAAAACTTCCGAAAATTA
1 CCATTTT-ACCCCAAAACTTCC-AAAAATC
*
28589 CCATTTTACCCCCAAACTTCCAAAAATC
1 CCATTTTACCCCAAAACTTCCAAAAATC
* * *
28617 TCATTTTTGACCTCAAAACTTCCAAAAATTA
1 CCA-TTTT-ACCCCAAAACTTCCAAAAA-TC
** *
28648 CCATTTTACCCTTAAACTTCAAAAAATC
1 CCATTTTACCCCAAAACTTCCAAAAATC
* *
28676 CCATTTTTAACCCTAAAACTTCCAAAAATTA
1 CCA-TTTT-ACCCCAAAACTTCCAAAAA-TC
*
28707 CCATTTTACCCTAAAACTTCCAAAAATC
1 CCATTTTACCCCAAAACTTCCAAAAATC
*
28735 CCATTTTTGACCTCAAAACTTCCAAAAATTAC
1 CCA-TTTT-ACCCCAAAACTTCCAAAAA-T-C
* *
28767 CC-TTTTACCCCTAAACTTCTAAAAATC
1 CCATTTTACCCCAAAACTTCCAAAAATC
* *
28794 CCAATTTTGACCCCAAAACTTCCAAAATTA
1 CC-ATTTT-ACCCCAAAACTTCCAAAAATC
** *
28824 CCATTTTACCCCCGAACTCCCAAAAATC
1 CCATTTTACCCCAAAACTTCCAAAAATC
* * *
28852 CCATTTTTGACCCTAAAACCTCCAAAAATTA
1 CCA-TTTT-ACCCCAAAACTTCCAAAAA-TC
28883 CCATTTTTACCCC
1 CCA-TTTTACCCC
28896 CAGATGTCCG
Statistics
Matches: 322, Mismatches: 48, Indels: 46
0.77 0.12 0.11
Matches are distributed among these distances:
26 4 0.01
27 21 0.07
28 40 0.12
29 108 0.34
30 125 0.39
31 21 0.07
32 3 0.01
ACGTcount: A:0.37, C:0.32, G:0.02, T:0.29
Consensus pattern (28 bp):
CCATTTTACCCCAAAACTTCCAAAAATC
Found at i:28645 original size:59 final size:59
Alignment explanation
Indices: 28457--28897 Score: 602
Period size: 59 Copynumber: 7.5 Consensus size: 59
28447 GAAGGTCCCT
* * * * *
28457 AAACTGTCTAAAAATTACCATTTAACCCTCAAAATTCCAAAAATCCCATTTTTGACCCCG
1 AAACT-TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
**
28517 AAACTTCCAAAAATTACCA-TTTA-CCCTGAACTTCCAAAAATCCCA-TTTTGACCCCA
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * *
28573 AAACTTCCGAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCTCA
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
** * * *
28632 AAACTTCCAAAAATTACCATTTTACCCTTAAACTTCAAAAAATCCCATTTTTAACCCTA
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
** *
28691 AAACTTCCAAAAATTACCATTTTACCCTAAAACTTCCAAAAATCCCATTTTTGACCTCA
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * * *
28750 AAACTTCCAAAAATTACCCTTTTACCCCTAAACTTCTAAAAATCCCAATTTTGACCCCA
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * *
28809 AAACTTCC-AAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTGACCCTA
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
*
28867 AAACCTCCAAAAATTACCATTTTTACCCCCA
1 AAACTTCCAAAAATTACCA-TTTTACCCCCA
28898 GATGTCCGAA
Statistics
Matches: 336, Mismatches: 40, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
56 28 0.08
57 22 0.07
58 72 0.21
59 199 0.59
60 15 0.04
ACGTcount: A:0.38, C:0.31, G:0.02, T:0.29
Consensus pattern (59 bp):
AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:29903 original size:12 final size:12
Alignment explanation
Indices: 29886--29915 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
29876 GGTTTCGACA
29886 CAAAATAAAATT
1 CAAAATAAAATT
*
29898 CAAAATAAATTT
1 CAAAATAAAATT
29910 CAAAAT
1 CAAAAT
29916 TTCAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (12 bp):
CAAAATAAAATT
Found at i:29935 original size:20 final size:20
Alignment explanation
Indices: 29891--29936 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
29881 CGACACAAAA
*
29891 TAAAATTCAAAATAAATTTC
1 TAAATTTCAAAATAAATTTC
* * *
29911 AAAATTTCAAAATAATTTTT
1 TAAATTTCAAAATAAATTTC
29931 TAAATT
1 TAAATT
29937 AAAAAATTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAATTTCAAAATAAATTTC
Found at i:29999 original size:19 final size:19
Alignment explanation
Indices: 29964--30000 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29954 ATCAAAATTT
* *
29964 ATATTTAAAAAATTTAAAA
1 ATATATAAAAAAGTTAAAA
29983 ATATATAAAAAAGTTAAA
1 ATATATAAAAAAGTTAAA
30001 TTTTTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
ATATATAAAAAAGTTAAAA
Found at i:30019 original size:18 final size:19
Alignment explanation
Indices: 29967--30019 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 19
29957 AAAATTTATA
* * *
29967 TTTAAAAAATTTAAAAATA
1 TTTAAAAAAGTTAAAATTT
*
29986 TATAAAAAAGTT-AAATTT
1 TTTAAAAAAGTTAAAATTT
30004 TTTAAAAAA-TTAAAAT
1 TTTAAAAAAGTTAAAAT
30020 AATAATTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 2 0.07
18 16 0.57
19 10 0.36
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TTTAAAAAAGTTAAAATTT
Found at i:31729 original size:32 final size:31
Alignment explanation
Indices: 31693--31776 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 31
31683 AAATTGAACT
* *
31693 CCTTAAAAACTGAAAAAAAAAAATTTCGGGTC
1 CCTTAAAAACT-AAAAAAAAAAATTTCGAGCC
* *
31725 CCTTAAAAGCTAAAAAAAATAAATTTTGAGCC
1 CCTTAAAAACTAAAAAAAA-AAATTTCGAGCC
* *
31757 CCTTACAAATTAAAAAAAAA
1 CCTTAAAAACTAAAAAAAAA
31777 TTCTGAACCC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
31 9 0.20
32 35 0.80
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (31 bp):
CCTTAAAAACTAAAAAAAAAAATTTCGAGCC
Found at i:35553 original size:49 final size:49
Alignment explanation
Indices: 35481--35577 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 49
35471 NNNNNNNNNN
* *
35481 AAAGCACAATCAATCCAAGATATGCTCTCTAAAATCAACAACAATCTCT
1 AAAGCACAATCAATCCAAGATATGATCTCCAAAATCAACAACAATCTCT
* **
35530 AAAGCACAATCAATCTAAGATATGATCTCCAAAATCAGTAACAATCTC
1 AAAGCACAATCAATCCAAGATATGATCTCCAAAATCAACAACAATCTC
35578 AATCAAATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.23
Consensus pattern (49 bp):
AAAGCACAATCAATCCAAGATATGATCTCCAAAATCAACAACAATCTCT
Found at i:37249 original size:21 final size:21
Alignment explanation
Indices: 37223--37263 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
37213 TCCCTGACCC
37223 GTGTTGCCGTCGTCAGAGCCT
1 GTGTTGCCGTCGTCAGAGCCT
37244 GTGTTGCCGTCGTCAGAGCC
1 GTGTTGCCGTCGTCAGAGCC
37264 CGCGTCGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.29, G:0.34, T:0.27
Consensus pattern (21 bp):
GTGTTGCCGTCGTCAGAGCCT
Found at i:38264 original size:29 final size:30
Alignment explanation
Indices: 38223--38654 Score: 311
Period size: 29 Copynumber: 14.7 Consensus size: 30
38213 GAAGGTCCCT
* *
38223 AAACTGTCTAAAAATTACCATTTAACCCTCA
1 AAACT-TCCAAAAATTACCATTTGACCCTCA
* *
38254 AAA-TTCCAAAAA-TCCCATTTTTGACCC-CG
1 AAACTTCCAAAAATTACCA--TTTGACCCTCA
38283 AAACTTCCAAAAATTACCATTT-ACCCT--
1 AAACTTCCAAAAATTACCATTTGACCCTCA
* *
38310 GAACTTCCAAAAA-TCCCATTTTGACCC-CA
1 AAACTTCCAAAAATTACCA-TTTGACCCTCA
* * *
38339 AAACTTCCGAAAATTACCATTTTACCC-CC
1 AAACTTCCAAAAATTACCATTTGACCCTCA
38368 AAACTTCCAAAAA-T-CTCATTTTTGA-CCTCA
1 AAACTTCCAAAAATTAC-CA--TTTGACCCTCA
* *
38398 AAACTTCCAAAAATTACCATTTTACCCT-T
1 AAACTTCCAAAAATTACCATTTGACCCTCA
* * *
38427 AAACTT-CAAAAAATCCCATTTTTAACCCT-A
1 AAACTTCCAAAAATTACCA--TTTGACCCTCA
*
38457 AAACTTCCAAAAATTACCATTTTACCCT-A
1 AAACTTCCAAAAATTACCATTTGACCCTCA
*
38486 AAACTTCCAAAAA-TCCCATTTTTGA-CCTCA
1 AAACTTCCAAAAATTACCA--TTTGACCCTCA
* * *
38516 AAACTTCCAAAAATTACCCTTTTACCC-CT
1 AAACTTCCAAAAATTACCATTTGACCCTCA
* *
38545 AAACTTCTAAAAA-TCCCAATTTTGACCC-CA
1 AAACTTCCAAAAATTACC-A-TTTGACCCTCA
* *
38575 AAACTTCC-AAAATTACCATTTTACCC-CC
1 AAACTTCCAAAAATTACCATTTGACCCTCA
* * *
38603 GAACTCCCAAAAA-TCCCATTTTTGACCCT-A
1 AAACTTCCAAAAATTACCA--TTTGACCCTCA
*
38633 AAACCTCCAAAAATTACCATTT
1 AAACTTCCAAAAATTACCATTT
38655 TTACCCCCAG
Statistics
Matches: 320, Mismatches: 48, Indels: 68
0.73 0.11 0.16
Matches are distributed among these distances:
26 4 0.01
27 16 0.05
28 50 0.16
29 111 0.35
30 111 0.35
31 27 0.08
32 1 0.00
ACGTcount: A:0.38, C:0.30, G:0.03, T:0.29
Consensus pattern (30 bp):
AAACTTCCAAAAATTACCATTTGACCCTCA
Found at i:38292 original size:30 final size:28
Alignment explanation
Indices: 38240--38661 Score: 366
Period size: 30 Copynumber: 14.4 Consensus size: 28
38230 CTAAAAATTA
*
38240 CCATTTAACCCTCAAAA-TTCCAAAAATC
1 CCATTTTACCC-CAAAACTTCCAAAAATC
* *
38268 CCATTTTTGACCCCGAAACTTCCAAAAATTA
1 CCA-TTTT-ACCCCAAAACTTCCAAAAA-TC
**
38299 CCA-TTTA-CCCTGAACTTCCAAAAATC
1 CCATTTTACCCCAAAACTTCCAAAAATC
* *
38325 CCATTTTGACCCCAAAACTTCCGAAAATTA
1 CCATTTT-ACCCCAAAACTTCC-AAAAATC
*
38355 CCATTTTACCCCCAAACTTCCAAAAATC
1 CCATTTTACCCCAAAACTTCCAAAAATC
* * *
38383 TCATTTTTGACCTCAAAACTTCCAAAAATTA
1 CCA-TTTT-ACCCCAAAACTTCCAAAAA-TC
** *
38414 CCATTTTACCCTTAAACTTCAAAAAATC
1 CCATTTTACCCCAAAACTTCCAAAAATC
* *
38442 CCATTTTTAACCCTAAAACTTCCAAAAATTA
1 CCA-TTTT-ACCCCAAAACTTCCAAAAA-TC
*
38473 CCATTTTACCCTAAAACTTCCAAAAATC
1 CCATTTTACCCCAAAACTTCCAAAAATC
*
38501 CCATTTTTGACCTCAAAACTTCCAAAAATTAC
1 CCA-TTTT-ACCCCAAAACTTCCAAAAA-T-C
* *
38533 CC-TTTTACCCCTAAACTTCTAAAAATC
1 CCATTTTACCCCAAAACTTCCAAAAATC
* *
38560 CCAATTTTGACCCCAAAACTTCCAAAATTA
1 CC-ATTTT-ACCCCAAAACTTCCAAAAATC
** *
38590 CCATTTTACCCCCGAACTCCCAAAAATC
1 CCATTTTACCCCAAAACTTCCAAAAATC
* * *
38618 CCATTTTTGACCCTAAAACCTCCAAAAATTA
1 CCA-TTTT-ACCCCAAAACTTCCAAAAA-TC
38649 CCATTTTTACCCC
1 CCA-TTTTACCCC
38662 CAGATGTCCG
Statistics
Matches: 322, Mismatches: 48, Indels: 46
0.77 0.12 0.11
Matches are distributed among these distances:
26 4 0.01
27 21 0.07
28 40 0.12
29 108 0.34
30 125 0.39
31 21 0.07
32 3 0.01
ACGTcount: A:0.37, C:0.32, G:0.02, T:0.29
Consensus pattern (28 bp):
CCATTTTACCCCAAAACTTCCAAAAATC
Found at i:38411 original size:59 final size:59
Alignment explanation
Indices: 38223--38663 Score: 602
Period size: 59 Copynumber: 7.5 Consensus size: 59
38213 GAAGGTCCCT
* * * * *
38223 AAACTGTCTAAAAATTACCATTTAACCCTCAAAATTCCAAAAATCCCATTTTTGACCCCG
1 AAACT-TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
**
38283 AAACTTCCAAAAATTACCA-TTTA-CCCTGAACTTCCAAAAATCCCA-TTTTGACCCCA
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * *
38339 AAACTTCCGAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCTCA
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
** * * *
38398 AAACTTCCAAAAATTACCATTTTACCCTTAAACTTCAAAAAATCCCATTTTTAACCCTA
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
** *
38457 AAACTTCCAAAAATTACCATTTTACCCTAAAACTTCCAAAAATCCCATTTTTGACCTCA
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * * *
38516 AAACTTCCAAAAATTACCCTTTTACCCCTAAACTTCTAAAAATCCCAATTTTGACCCCA
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * *
38575 AAACTTCC-AAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTGACCCTA
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
*
38633 AAACCTCCAAAAATTACCATTTTTACCCCCA
1 AAACTTCCAAAAATTACCA-TTTTACCCCCA
38664 GATGTCCGAA
Statistics
Matches: 336, Mismatches: 40, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
56 28 0.08
57 22 0.07
58 72 0.21
59 199 0.59
60 15 0.04
ACGTcount: A:0.38, C:0.31, G:0.02, T:0.29
Consensus pattern (59 bp):
AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:39669 original size:12 final size:12
Alignment explanation
Indices: 39652--39681 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
39642 GGTTTCGACA
39652 CAAAATAAAATT
1 CAAAATAAAATT
*
39664 CAAAATAAATTT
1 CAAAATAAAATT
39676 CAAAAT
1 CAAAAT
39682 TTCAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (12 bp):
CAAAATAAAATT
Found at i:39701 original size:20 final size:20
Alignment explanation
Indices: 39657--39702 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
39647 CGACACAAAA
*
39657 TAAAATTCAAAATAAATTTC
1 TAAATTTCAAAATAAATTTC
* * *
39677 AAAATTTCAAAATAATTTTT
1 TAAATTTCAAAATAAATTTC
39697 TAAATT
1 TAAATT
39703 AAAAAATTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAATTTCAAAATAAATTTC
Found at i:39765 original size:19 final size:19
Alignment explanation
Indices: 39730--39766 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39720 ATCAAAATTT
* *
39730 ATATTTAAAAAATTTAAAA
1 ATATATAAAAAAGTTAAAA
39749 ATATATAAAAAAGTTAAA
1 ATATATAAAAAAGTTAAA
39767 TTTTTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
ATATATAAAAAAGTTAAAA
Found at i:39785 original size:18 final size:19
Alignment explanation
Indices: 39733--39785 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 19
39723 AAAATTTATA
* * *
39733 TTTAAAAAATTTAAAAATA
1 TTTAAAAAAGTTAAAATTT
*
39752 TATAAAAAAGTT-AAATTT
1 TTTAAAAAAGTTAAAATTT
39770 TTTAAAAAA-TTAAAAT
1 TTTAAAAAAGTTAAAAT
39786 AATAATTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 2 0.07
18 16 0.57
19 10 0.36
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TTTAAAAAAGTTAAAATTT
Found at i:41495 original size:32 final size:31
Alignment explanation
Indices: 41459--41542 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 31
41449 AAATTGAACT
* *
41459 CCTTAAAAACTGAAAAAAAAAAATTTCGGGTC
1 CCTTAAAAACT-AAAAAAAAAAATTTCGAGCC
* *
41491 CCTTAAAAGCTAAAAAAAATAAATTTTGAGCC
1 CCTTAAAAACTAAAAAAAA-AAATTTCGAGCC
* *
41523 CCTTACAAATTAAAAAAAAA
1 CCTTAAAAACTAAAAAAAAA
41543 TTCTGAACCC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
31 9 0.20
32 35 0.80
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (31 bp):
CCTTAAAAACTAAAAAAAAAAATTTCGAGCC
Found at i:53074 original size:18 final size:18
Alignment explanation
Indices: 53053--53095 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
53043 AGAAGGCTGA
*
53053 GCTGCTGCTGCAGCTGGT
1 GCTGCTGCTGCAGCTGGC
* **
53071 GCTGCAGCTGGTGCTGGC
1 GCTGCTGCTGCAGCTGGC
53089 GCTGCTG
1 GCTGCTG
53096 GTGAAGCAGC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.28, G:0.42, T:0.26
Consensus pattern (18 bp):
GCTGCTGCTGCAGCTGGC
Found at i:53092 original size:12 final size:12
Alignment explanation
Indices: 53048--53086 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
53038 GCCACAGAAG
*
53048 GCTG-AGCTGCT
1 GCTGCAGCTGGT
53059 GCTGCAGCTGGT
1 GCTGCAGCTGGT
53071 GCTGCAGCTGGT
1 GCTGCAGCTGGT
53083 GCTG
1 GCTG
53087 GCGCTGCTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 4 0.15
12 22 0.85
ACGTcount: A:0.08, C:0.26, G:0.41, T:0.26
Consensus pattern (12 bp):
GCTGCAGCTGGT
Found at i:53136 original size:6 final size:6
Alignment explanation
Indices: 53125--53149 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
53115 ACCGGCTGAG
53125 GGTGCA GGTGCA GGTGCA GGTGCA G
1 GGTGCA GGTGCA GGTGCA GGTGCA G
53150 CAACTTTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.52, T:0.16
Consensus pattern (6 bp):
GGTGCA
Found at i:62028 original size:28 final size:27
Alignment explanation
Indices: 61985--62043 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
61975 AATAAAAGGC
*
61985 TAATTTTAATCCAATTGTAATTCAATTT
1 TAATTTTAATCCAATTAT-ATTCAATTT
** *
62013 TAATTTTAATTTAATTATATTCATTTT
1 TAATTTTAATCCAATTATATTCAATTT
62040 TAAT
1 TAAT
62044 AATAAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (27 bp):
TAATTTTAATCCAATTATATTCAATTT
Found at i:63257 original size:24 final size:24
Alignment explanation
Indices: 63230--63327 Score: 135
Period size: 24 Copynumber: 4.1 Consensus size: 24
63220 TAATTCTCAG
*
63230 GCAAATGTTGCAGCCAGA-AGGCCA
1 GCAAGTGTTGCAGCCA-ATAGGCCA
*
63254 GCAAGTGTCGCAGCCAATAGGCCA
1 GCAAGTGTTGCAGCCAATAGGCCA
* * *
63278 GCAATTGTTGCGGCCAATAGGTCA
1 GCAAGTGTTGCAGCCAATAGGCCA
63302 GCAAGTGTTGCAGCCAATAGGCCA
1 GCAAGTGTTGCAGCCAATAGGCCA
63326 GC
1 GC
63328 GCCAGCAAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 1 0.02
24 63 0.98
ACGTcount: A:0.29, C:0.26, G:0.30, T:0.16
Consensus pattern (24 bp):
GCAAGTGTTGCAGCCAATAGGCCA
Found at i:69903 original size:241 final size:241
Alignment explanation
Indices: 69396--69913 Score: 682
Period size: 241 Copynumber: 2.1 Consensus size: 241
69386 TTGGAAAGTT
* * * ** *
69396 GATCCTTAATTGAGAGTCAGATTAATGTCGACTTTATTGAATTAAGAGTTTAATTTTCCTTTCAT
1 GATCCTTAATTGAGAGTCAAATTAATATCGACTTTACTGAATTAAGAGTCCAACTTTCCTTTCAT
* *
69461 TTGCATGCGATGATGAAAAAAAAATGAAAATTAAACTCATAATCCAGCAAAATTGACATTATAAG
66 TTGCATGCAATGATG--AAAAAAATGAAAATTAAACTCATAATCCAGCAAAATTGACATTATAAA
* * * * *
69526 GCTACGAGCATTGGAAAGCATGTATATTTGTTAAAAATAGATAAATGGCTACTAATTAATAGATT
129 GCTACGAGCATTGAAAAACATGTATATTTGTTAAAAATAAATAAATGGCTACTAATTAATAAATC
** **
69591 GATCACGGTCAATTTAAATCAATCTAGTTTGTTTATCTAATAAATATT
194 GATCACGACCAATTTAAATCAATCTAGTTTGTTTATCTAATAAATACG
* * *
69639 GATCCTTAATTGAGAGCCAAATTAATATCGACTTTGCTGAATTATGAGTCCAACTTTCCTTTCAT
1 GATCCTTAATTGAGAGTCAAATTAATATCGACTTTACTGAATTAAGAGTCCAACTTTCCTTTCAT
* * *
69704 TTGCATGCAATGATG-AAGAAATGAAAATTAGACTCATAATCCAGCAAAATTGATATTATAAAGC
66 TTGCATGCAATGATGAAAAAAATGAAAATTAAACTCATAATCCAGCAAAATTGACATTATAAAGC
* * *
69768 TACGAGCATTGAAAAACAACT-TATATTTGTTGAAACTAAATAAATAGG-TATTAATTAATAAAT
131 TACGAGCATTGAAAAAC-A-TGTATATTTGTTAAAAATAAATAAAT-GGCTACTAATTAATAAAT
* ** * *
69831 CGATCATGACCGGTTTCAATCGATCTAGTTTGTTTATCTAATAAATACG
193 CGATCACGACCAATTTAAATCAATCTAGTTTGTTTATCTAATAAATACG
*
69880 GATCCTTAATTGAAAGTCAAATTAATATCGACTT
1 GATCCTTAATTGAGAGTCAAATTAATATCGACTT
69914 CTCTAAATTA
Statistics
Matches: 239, Mismatches: 33, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
240 60 0.25
241 106 0.44
242 3 0.01
243 70 0.29
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (241 bp):
GATCCTTAATTGAGAGTCAAATTAATATCGACTTTACTGAATTAAGAGTCCAACTTTCCTTTCAT
TTGCATGCAATGATGAAAAAAATGAAAATTAAACTCATAATCCAGCAAAATTGACATTATAAAGC
TACGAGCATTGAAAAACATGTATATTTGTTAAAAATAAATAAATGGCTACTAATTAATAAATCGA
TCACGACCAATTTAAATCAATCTAGTTTGTTTATCTAATAAATACG
Found at i:70532 original size:22 final size:22
Alignment explanation
Indices: 70481--70535 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
70471 AAAATGATTT
* *
70481 TTCCTTGTAAAAACCCAAAATT
1 TTCCTTATAAAAACCCAAAATA
*
70503 TTCC-TATAAAAA-TCAAAATAA
1 TTCCTTATAAAAACCCAAAAT-A
70524 TTCCTTATAAAA
1 TTCCTTATAAAA
70536 CACTATAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 6 0.21
21 11 0.39
22 11 0.39
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (22 bp):
TTCCTTATAAAAACCCAAAATA
Found at i:71637 original size:30 final size:32
Alignment explanation
Indices: 71601--71673 Score: 91
Period size: 30 Copynumber: 2.4 Consensus size: 32
71591 ATTCTTTTTT
* *
71601 AACTTTTAAAG-GT-AAAATTTTTTTTTTACC
1 AACTTTTAAAGAATCAAAATTTTTTTTCTACC
*
71631 AACTTTTAAAGAATCTAAATTTTTTTTCTACC
1 AACTTTTAAAGAATCAAAATTTTTTTTCTACC
71663 -AC-TTTAAAGAA
1 AACTTTTAAAGAA
71674 CCTTAAACAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 20 0.53
31 3 0.08
32 15 0.39
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.45
Consensus pattern (32 bp):
AACTTTTAAAGAATCAAAATTTTTTTTCTACC
Found at i:71656 original size:32 final size:30
Alignment explanation
Indices: 71615--71673 Score: 91
Period size: 32 Copynumber: 1.9 Consensus size: 30
71605 TTTAAAGGTA
*
71615 AAATTTTTTTTTTACCAACTTTTAAAGAATCT
1 AAATTTTTTTTCTACC-AC-TTTAAAGAATCT
71647 AAATTTTTTTTCTACCACTTTAAAGAA
1 AAATTTTTTTTCTACCACTTTAAAGAA
71674 CCTTAAACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 9 0.35
31 2 0.08
32 15 0.58
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (30 bp):
AAATTTTTTTTCTACCACTTTAAAGAATCT
Found at i:76895 original size:188 final size:188
Alignment explanation
Indices: 76585--77196 Score: 796
Period size: 188 Copynumber: 3.2 Consensus size: 188
76575 GATTGATCAT
* * *
76585 TTGCAATCCATTGTTAATAGCCTTATAATGTTGACTTTGTTGGATTATGAGCCTAGTTTGTTTTT
1 TTGCTATCCATTGCTAATAGCCTTATAATGTTGACTTTGCTGGATTATGAG-CTA----GTTTTT
* *
76650 ATCTTTTCATCAACTAATGGTTGCATGTC-AATGAAAGGAAAACTAGACTCATAATTCAGCGAAG
61 ATCTTTTCATCAACTAATGATTGCATG-CAAATGAAAGGAAAACTAGACTCATAATTCAGCAAAG
* * * **
76714 TTGACATTAAATTGGCTCTCAATTAAGGATCAACATGTGTTGATTGTTTGTTGGCAAGTACAAG
125 TCGACATTAATTTGGCTCTCAATTAAGGATCAACATGTGTTGATTGATCATTGGCAAGTACAAG
*
76778 TTGCTATCCATTGCTAATAGCCTTGTAATGTTGACTTTGCTGGATTATGAGTCTAGTTTTTATC-
1 TTGCTATCCATTGCTAATAGCCTTATAATGTTGACTTTGCTGGATTATGAG-CTAGTTTTTATCT
* *
76842 TTTCATCAACTAATGATTGCATGCAAATGAAAGGAAAACTAGACTCGTAATTCAACAAAGTCGAC
65 TTTCATCAACTAATGATTGCATGCAAATGAAAGGAAAACTAGACTCATAATTCAGCAAAGTCGAC
* *
76907 ATTATTTTGGCTCTCAATTTAGGATCAACATGTGTTGATTGATCATTGGCAAGTACAAG
130 ATTAATTTGGCTCTCAATTAAGGATCAACATGTGTTGATTGATCATTGGCAAGTACAAG
** * * * * *
76966 TTGAGATCCGTTTCTAATAGCCCTATAATGTTGACTTTGCTAGATTATGAGCTTAATTTTTATCT
1 TTGCTATCCATTGCTAATAGCCTTATAATGTTGACTTTGCTGGATTATGAGC-TAGTTTTTATC-
* * * *
77031 TTTTCATCGACTAATGATTGCATGCAAATGAAAGGAAAACTAGACTCACAATTCAGTAAAATCGA
64 TTTTCATCAACTAATGATTGCATGCAAATGAAAGGAAAACTAGACTCATAATTCAGCAAAGTCGA
* * * * *
77096 CATTAATTTGGCTCCCAATTAAGGATTAACATTTGCTAATTGATCATTGGCAAGTACAAG
129 CATTAATTTGGCTCTCAATTAAGGATCAACATGTGTTGATTGATCATTGGCAAGTACAAG
* * ** * *
77156 TTGCTATCGATTGTTAATAGTGTTATAATGTCGATTTTGCT
1 TTGCTATCCATTGCTAATAGCCTTATAATGTTGACTTTGCT
77197 AAATTGTGAA
Statistics
Matches: 367, Mismatches: 48, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
187 2 0.01
188 165 0.45
189 9 0.02
190 141 0.38
193 50 0.14
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (188 bp):
TTGCTATCCATTGCTAATAGCCTTATAATGTTGACTTTGCTGGATTATGAGCTAGTTTTTATCTT
TTCATCAACTAATGATTGCATGCAAATGAAAGGAAAACTAGACTCATAATTCAGCAAAGTCGACA
TTAATTTGGCTCTCAATTAAGGATCAACATGTGTTGATTGATCATTGGCAAGTACAAG
Found at i:82915 original size:17 final size:17
Alignment explanation
Indices: 82893--82929 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
82883 GAAGCGGGCT
*
82893 TGGACCTTAAAGAATTG
1 TGGACCCTAAAGAATTG
82910 TGGACCCTAAAGAATTG
1 TGGACCCTAAAGAATTG
82927 TGG
1 TGG
82930 TGCCACCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (17 bp):
TGGACCCTAAAGAATTG
Found at i:83229 original size:17 final size:18
Alignment explanation
Indices: 83209--83252 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
83199 TTAAATTTAT
*
83209 TTTAAAATTAATTT-AAG
1 TTTAAAATTAATTTCAAA
*
83226 TTTAAAATTATTTTCAAA
1 TTTAAAATTAATTTCAAA
83244 TTTAAAATT
1 TTTAAAATT
83253 TAAAATAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
TTTAAAATTAATTTCAAA
Found at i:93128 original size:48 final size:48
Alignment explanation
Indices: 93074--93170 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
93064 AAACAAACCC
*
93074 TATAAAAATAGTCACTTTCACCATAAACTAATATTGCTTATGGATGAA
1 TATAAAAATAGTCACTTTCACCATAAACAAATATTGCTTATGGATGAA
* *
93122 TATAAAAATAGTCACTTTCACCATGAACAAATATTGTTTATGGATGAA
1 TATAAAAATAGTCACTTTCACCATAAACAAATATTGCTTATGGATGAA
93170 T
1 T
93171 CGGTATAACG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.34
Consensus pattern (48 bp):
TATAAAAATAGTCACTTTCACCATAAACAAATATTGCTTATGGATGAA
Found at i:103511 original size:6 final size:6
Alignment explanation
Indices: 103495--103530 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
103485 CCTACCAATA
103495 CCACCG CCCACCG CCACCG CCACCG CCACCG CCACC
1 CCACCG -CCACCG CCACCG CCACCG CCACCG CCACC
103531 AATGGTTCCG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.17, C:0.69, G:0.14, T:0.00
Consensus pattern (6 bp):
CCACCG
Found at i:111307 original size:12 final size:12
Alignment explanation
Indices: 111290--111327 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
111280 ATCGGCATCA
111290 TCTTCATCGTCG
1 TCTTCATCGTCG
*
111302 TCTTCATCGTCA
1 TCTTCATCGTCG
*
111314 TCTTCCTCGTCG
1 TCTTCATCGTCG
111326 TC
1 TC
111328 ATCTTCAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.08, C:0.37, G:0.13, T:0.42
Consensus pattern (12 bp):
TCTTCATCGTCG
Found at i:111553 original size:6 final size:6
Alignment explanation
Indices: 111531--111569 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
111521 TGAGAGTAAG
* *
111531 AAGCAA TAAGCAG AAGCAA AAGCAA ACGCAA AAGCAA AA
1 AAGCAA -AAGCAA AAGCAA AAGCAA AAGCAA AAGCAA AA
111570 CCCTAAAACC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.62, C:0.18, G:0.18, T:0.03
Consensus pattern (6 bp):
AAGCAA
Found at i:116019 original size:23 final size:23
Alignment explanation
Indices: 115976--116027 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
115966 ATCTAAATTT
*
115976 TAAAATTTTAAAAATAAAAAATAA
1 TAAAATTTTAAAAATAAAAAGT-A
*
116000 TAAAATTTATGAAAAT-AAAAGTA
1 TAAAATTT-TAAAAATAAAAAGTA
116023 TAAAA
1 TAAAA
116028 AAGTACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 13 0.52
25 6 0.24
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (23 bp):
TAAAATTTTAAAAATAAAAAGTA
Found at i:117853 original size:55 final size:55
Alignment explanation
Indices: 117750--117853 Score: 120
Period size: 55 Copynumber: 1.9 Consensus size: 55
117740 TTTAAATTAT
* * * * * *
117750 TTTTTTTATTATATTATATTTTATATAGTTTATCATAGTGATTTAATTACAATGA
1 TTTTTATATTATATTATATTTTATATAGTTTATCACAATAACTCAATTACAATGA
* *
117805 TTTTTATATTGTATTATATTTTATAT-GATTTTTCACAATAACTCAATTA
1 TTTTTATATTATATTATATTTTATATAG-TTTATCACAATAACTCAATTA
117854 TTTAAAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
54 1 0.03
55 39 0.98
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (55 bp):
TTTTTATATTATATTATATTTTATATAGTTTATCACAATAACTCAATTACAATGA
Found at i:122206 original size:18 final size:17
Alignment explanation
Indices: 122177--122258 Score: 78
Period size: 17 Copynumber: 4.7 Consensus size: 17
122167 AATTTTAAAG
* *
122177 TTTAAGTTTAAAAATTA
1 TTTAAATTTAAAAATAA
*
122194 TTTCAAATTT-AAACTAAA
1 TTT-AAATTTAAAAAT-AA
*
122212 TTGAAATTTAAAACA-AA
1 TTTAAATTTAAAA-ATAA
122229 TTTAAATTTAAAAATGAA
1 TTTAAATTTAAAAAT-AA
122247 TTTAAATTTAAA
1 TTTAAATTTAAA
122259 TTTAAAGTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
16 1 0.02
17 27 0.51
18 25 0.47
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (17 bp):
TTTAAATTTAAAAATAA
Found at i:122235 original size:6 final size:6
Alignment explanation
Indices: 122156--122279 Score: 78
Period size: 6 Copynumber: 21.0 Consensus size: 6
122146 TTGTAAATGG
* * * *
122156 AATTTG AATTTA ATTTTA AAGTTTA AGTTTAA AAATT- -ATTTCA AATTTA
1 AATTTA AATTTA AATTTA AA-TTTA AATTT-A AATTTA AATTT-A AATTTA
* * ** ** *
122205 AA-CTA AATTGA AATTTA AA-ACA AATTTA AATTTA AAAATG AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
122251 AATTTA AATTTA AA-GTA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA
122280 GAAATAAATC
Statistics
Matches: 87, Mismatches: 23, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
4 3 0.03
5 11 0.13
6 60 0.69
7 13 0.15
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:122253 original size:41 final size:41
Alignment explanation
Indices: 122203--122293 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
122193 ATTTCAAATT
122203 TAAA-CTAAATTGAAATTTAAAACAAATTTAAATTTAAAAA
1 TAAATCTAAATTGAAATTTAAAACAAATTTAAATTTAAAAA
* * * ** *
122243 TGAATTTAAATTTAAATTTAAAGTAAATTTAAATTTAGAAA
1 TAAATCTAAATTGAAATTTAAAACAAATTTAAATTTAAAAA
122284 TAAATCTAAA
1 TAAATCTAAA
122294 ATAATTTAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 3 0.07
41 39 0.93
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.36
Consensus pattern (41 bp):
TAAATCTAAATTGAAATTTAAAACAAATTTAAATTTAAAAA
Found at i:122465 original size:24 final size:24
Alignment explanation
Indices: 122421--122466 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
122411 AAACACCTCA
* *
122421 TAATTTATTATATTATCTTAATTT
1 TAATTTATTATAATATATTAATTT
122445 TAATTTCATTA-AATATATTAAT
1 TAATTT-ATTATAATATATTAAT
122467 AATAAATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (24 bp):
TAATTTATTATAATATATTAATTT
Found at i:124639 original size:166 final size:165
Alignment explanation
Indices: 124365--124712 Score: 473
Period size: 166 Copynumber: 2.1 Consensus size: 165
124355 TGCGTGTCCG
** * * * *
124365 TCTTGGTGAGTATGGTTCGATGTGGTTGCATACTAGTATTAAAGCTTAAGCTTTTACCTATGGTA
1 TCTTGGTGAGTATGGTTAAATGTAGTCGCACACTAGTATTAAAGCTTAAGCTTTTACCTATGATA
* * ** *
124430 ACATTGCTATTACTAGTAAGTGGAGTATTATTATTGTTTTTGATTACTAGTTTAAATATGGCTTC
66 ACATTACTATTACTAGTAAGTGGAGTATTATTATTGTTTTTGATTACTAGCTTAAATACCG-ATC
*
124495 TTGATTTATTTTTCATA-TGCTTGCATTGTATGTTAA
130 TTGATTTATGTTTCA-AGTGCTTGCATTGTATGTTAA
* *
124531 TCTTGGTGAGTATGGTTAAATGTAGTCGCACACTTGTATTAAAGCTTAAGCTTTTACCTATGATG
1 TCTTGGTGAGTATGGTTAAATGTAGTCGCACACTAGTATTAAAGCTTAAGCTTTTACCTATGATA
* * *
124596 ACATTATTATTACTAGTAAGTGGAGTCTTATTATTGTTTTTGATTGCTAGCTTAAATACCGATCT
66 ACATTACTATTACTAGTAAGTGGAGTATTATTATTGTTTTTGATTACTAGCTTAAATACCGATCT
* * *
124661 TGATTTATGTTTCAAGTGCTTGCTTTGTGTGTTCA
131 TGATTTATGTTTCAAGTGCTTGCATTGTATGTTAA
* *
124696 TGTAGGTGAGTATGGTT
1 TCTTGGTGAGTATGGTT
124713 TGCAGTATCC
Statistics
Matches: 159, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
164 1 0.01
165 47 0.30
166 111 0.70
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (165 bp):
TCTTGGTGAGTATGGTTAAATGTAGTCGCACACTAGTATTAAAGCTTAAGCTTTTACCTATGATA
ACATTACTATTACTAGTAAGTGGAGTATTATTATTGTTTTTGATTACTAGCTTAAATACCGATCT
TGATTTATGTTTCAAGTGCTTGCATTGTATGTTAA
Found at i:130029 original size:20 final size:22
Alignment explanation
Indices: 129990--130029 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
129980 ATATTAATCC
129990 TTAATAAGATTTATTTATTTTA
1 TTAATAAGATTTATTTATTTTA
130012 TTAA-AAGATTTA-TTATTT
1 TTAATAAGATTTATTTATTT
130030 ATAACCCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 8 0.44
22 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TTAATAAGATTTATTTATTTTA
Found at i:131943 original size:88 final size:88
Alignment explanation
Indices: 131794--131971 Score: 356
Period size: 88 Copynumber: 2.0 Consensus size: 88
131784 ACTTTAGTGG
131794 ACATGGAGTTGTGAAGCTCATTGACCCCAACCAGCCTTCCAAGAAGGGTGAAGCAATTGTGCCTT
1 ACATGGAGTTGTGAAGCTCATTGACCCCAACCAGCCTTCCAAGAAGGGTGAAGCAATTGTGCCTT
131859 ATGATCTCAATCTCATTTTTGGT
66 ATGATCTCAATCTCATTTTTGGT
131882 ACATGGAGTTGTGAAGCTCATTGACCCCAACCAGCCTTCCAAGAAGGGTGAAGCAATTGTGCCTT
1 ACATGGAGTTGTGAAGCTCATTGACCCCAACCAGCCTTCCAAGAAGGGTGAAGCAATTGTGCCTT
131947 ATGATCTCAATCTCATTTTTGGT
66 ATGATCTCAATCTCATTTTTGGT
131970 AC
1 AC
131972 GTAATCAACT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 90 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.29
Consensus pattern (88 bp):
ACATGGAGTTGTGAAGCTCATTGACCCCAACCAGCCTTCCAAGAAGGGTGAAGCAATTGTGCCTT
ATGATCTCAATCTCATTTTTGGT
Found at i:138601 original size:23 final size:22
Alignment explanation
Indices: 138552--138722 Score: 146
Period size: 23 Copynumber: 7.4 Consensus size: 22
138542 NNNNNNNNNN
* *
138552 CAGAGAGCACATAAGTGCTGGGCAA
1 CAGAGAGCACACAAGTGCT---AAA
138577 CAGAGAGCACACATAGTGCTAAA
1 CAGAGAGCACACA-AGTGCTAAA
* * *
138600 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACAC-AAGTGCTAAA
*
138623 CAGAGAGCACAC-AGTGCTAAT
1 CAGAGAGCACACAAGTGCTAAA
*
138644 CAGAGAGCAAACACAGTGCTAATAA
1 CAGAGAGCACACA-AGTGCT-A-AA
* *
138669 CAGAGAGCACGAGACGTGCTAAA
1 CAGAGAGCAC-ACAAGTGCTAAA
* *
138692 CAGAGAGCAGACACAGTGCTAAT
1 CAGAGAGCACACA-AGTGCTAAA
138715 CAGAGAGC
1 CAGAGAGC
138723 GCGCTAGTTC
Statistics
Matches: 122, Mismatches: 16, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
21 19 0.16
22 2 0.02
23 63 0.52
24 3 0.02
25 27 0.22
26 8 0.07
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (22 bp):
CAGAGAGCACACAAGTGCTAAA
Found at i:138699 original size:48 final size:44
Alignment explanation
Indices: 138577--138722 Score: 175
Period size: 46 Copynumber: 3.2 Consensus size: 44
138567 TGCTGGGCAA
* * * *
138577 CAGAGAGCACACATAGTGCTAAACAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACAC--AGTGCTAAACAGAGAGCAAACACAGTGCTAAT
*
138623 CAGAGAGCACACAGTGCTAATCAGAGAGCAAACACAGTGCTAAT
1 CAGAGAGCACACAGTGCTAAACAGAGAGCAAACACAGTGCTAAT
* *
138667 AACAGAGAGCACGAGACGTGCTAAACAGAGAGCAGACACAGTGCTAAT
1 --CAGAGAGCAC-ACA-GTGCTAAACAGAGAGCAAACACAGTGCTAAT
138715 CAGAGAGC
1 CAGAGAGC
138723 GCGCTAGTTC
Statistics
Matches: 88, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
44 27 0.31
46 30 0.34
47 2 0.02
48 29 0.33
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.12
Consensus pattern (44 bp):
CAGAGAGCACACAGTGCTAAACAGAGAGCAAACACAGTGCTAAT
Found at i:147058 original size:29 final size:29
Alignment explanation
Indices: 147026--147401 Score: 325
Period size: 29 Copynumber: 12.8 Consensus size: 29
147016 ATCCAAGGGC
* *
147026 AAAATGGTAATTTTTGAAAGTTTTGGAGTAA
1 AAAATGG-AATTTTTGGAAGTTTTGGGGT-A
* * *
147057 AAAATGGAAATTTTAG-AGGTTTGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTA
* * * *
147085 AAAATAGAATTTTTGGAAGTTTCGAGGTCG
1 AAAATGGAATTTTTGGAAGTTTTGGGGT-A
*
147115 AAAATGGAATTTTTGGAAG-TTCGAGGTGTA
1 AAAATGGAATTTTTGGAAGTTTTG-GG-GTA
*
147145 AAAATGGAATTTTTGGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGT-A
* *
147175 AAAATGGAA-TTTTAGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTTG-GGGTA
* * * *
147203 AAAATTGATTTTTTGGAAGTTTCGGGGTT
1 AAAATGGAATTTTTGGAAGTTTTGGGGTA
* *
147232 AAAATAGG-ATTTTTGAAAGTTTAGGGGTA
1 AAAAT-GGAATTTTTGGAAGTTTTGGGGTA
*
147261 AAAATGGAATTTTTGGAAGTTTCT-AGGTCA
1 AAAATGGAATTTTTGGAAGTTT-TGGGGT-A
* **
147291 AAAATGGGATTTTTGGAAGTTCAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTA
*
147320 AAAATGGAATTTTTGGAAGTTTTGAGGTTA
1 AAAATGGAATTTTTGGAAGTTTTG-GGGTA
* * *
147350 AAAATGGGATTTTTGGAAG-CTTGAGGGCA
1 AAAATGGAATTTTTGGAAGTTTTG-GGGTA
* *
147379 AAAATGTAATTTTCGGATAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
147402 AGGGACCTTT
Statistics
Matches: 280, Mismatches: 48, Indels: 34
0.77 0.13 0.09
Matches are distributed among these distances:
28 26 0.09
29 133 0.47
30 109 0.39
31 12 0.04
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTA
Found at i:147089 original size:59 final size:58
Alignment explanation
Indices: 147026--147401 Score: 336
Period size: 59 Copynumber: 6.4 Consensus size: 58
147016 ATCCAAGGGC
* * * *
147026 AAAATGGTAATTTTTGAAAGTTTTGGAGTAAAAAATGGAAATTTTAGAGGTTTG-GGGTA
1 AAAATGG-AATTTTTGGAAGTTTTGGAGTCAAAAATGG-AATTTTGGAAGTTTGAGGGTA
* * * *
147085 AAAATAGAATTTTTGGAAG-TTTCGAGGTCGAAAATGGAATTTTTGGAAGTTCGAGGTGTA
1 AAAATGGAATTTTTGGAAGTTTTGGA-GTCAAAAATGGAA-TTTTGGAAGTTTGAGG-GTA
* *
147145 AAAATGGAATTTTTGGAAGTTTTAGG-GTCAAAAATGGAATTTTAGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTT-GGAGTCAAAAATGGAATTTTGGAAGTTTGAGGGTA
* * * * * * *
147203 AAAATTGATTTTTTGGAAGTTTCGGGGT-TAAAATAGGATTTTTGAAAGTTT-AGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGGAGTCAAAAAT-GGAATTTTGGAAGTTTGA-GGGTA
* * *
147261 AAAATGGAATTTTTGGAAGTTTCTAG-GTCAAAAATGGGATTTTTGGAAG-TTCAGGGGTA
1 AAAATGGAATTTTTGGAAGTTT-TGGAGTCAAAAAT-GGAATTTTGGAAGTTTGA-GGGTA
* * * *
147320 AAAATGGAATTTTTGGAAGTTTT-GAGGTTAAAAATGGGATTTTTGGAAGCTTGAGGGCA
1 AAAATGGAATTTTTGGAAGTTTTGGA-GTCAAAAAT-GGAATTTTGGAAGTTTGAGGGTA
* *
147379 AAAATGTAATTTTCGGATAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
147402 AGGGACCTTT
Statistics
Matches: 269, Mismatches: 32, Indels: 31
0.81 0.10 0.09
Matches are distributed among these distances:
57 16 0.06
58 97 0.36
59 111 0.41
60 41 0.15
61 3 0.01
62 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTTTGGAGTCAAAAATGGAATTTTGGAAGTTTGAGGGTA
Found at i:148416 original size:3 final size:3
Alignment explanation
Indices: 148408--148477 Score: 61
Period size: 3 Copynumber: 23.0 Consensus size: 3
148398 GTTTTATTTT
* * * * *
148408 TTA TTA TTA TTA ATA TTAA TTA ATA TTA TAA TTA TTA -CA ATA TTTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
148454 TTA TTA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
148478 GTGTCATTTA
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
2 1 0.02
3 47 0.89
4 5 0.09
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:149215 original size:17 final size:17
Alignment explanation
Indices: 149190--149269 Score: 88
Period size: 17 Copynumber: 4.6 Consensus size: 17
149180 TAAATAGATT
*
149190 TAAACTTTAAATTTATAA
1 TAAA-TTTAAATTTAAAA
* *
149208 TAAATTTAAATTTGAAG
1 TAAATTTAAATTTAAAA
* *
149225 TAAATCTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
149242 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
149259 TAATTTTAAAT
1 TAAATTTAAAT
149270 CCTGCTGGGC
Statistics
Matches: 50, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
17 46 0.92
18 4 0.08
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:157005 original size:5 final size:5
Alignment explanation
Indices: 156995--157031 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
156985 AAAAGTAAGC
156995 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
157032 GAGAGGAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:161050 original size:6 final size:6
Alignment explanation
Indices: 161039--161063 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
161029 TACTTATCCT
161039 ATATAA ATATAA ATATAA ATATAA A
1 ATATAA ATATAA ATATAA ATATAA A
161064 AATTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:163457 original size:16 final size:16
Alignment explanation
Indices: 163425--163478 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 16
163415 TTCGAGTCAT
163425 TTTTTAGTTTGAAAAATA
1 TTTTT-GTTT-AAAAATA
*
163443 TTTTTTTTTAAAAATA
1 TTTTTGTTTAAAAATA
* *
163459 -ATTTGTTTAGAAATA
1 TTTTTGTTTAAAAATA
163474 TTTTT
1 TTTTT
163479 ATCTCAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 12 0.40
16 10 0.33
17 3 0.10
18 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (16 bp):
TTTTTGTTTAAAAATA
Found at i:168007 original size:14 final size:13
Alignment explanation
Indices: 167975--168007 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
167965 TTAAAAAATT
167975 TTAAAAATTTAAA
1 TTAAAAATTTAAA
167988 -TAAAAATATTAAA
1 TTAAAAAT-TTAAA
168001 TTAAAAA
1 TTAAAAA
168008 AAAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.39
13 5 0.28
14 6 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TTAAAAATTTAAA
Found at i:168448 original size:5 final size:5
Alignment explanation
Indices: 168438--168463 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
168428 CTCAATTATG
168438 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
168464 CGTCATTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:174051 original size:2 final size:2
Alignment explanation
Indices: 174044--174087 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
174034 TTATTTTTAA
174044 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
174086 AT
1 AT
174088 CTAAATATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:175133 original size:12 final size:14
Alignment explanation
Indices: 175103--175169 Score: 75
Period size: 15 Copynumber: 4.7 Consensus size: 14
175093 AAGGGTTGTG
*
175103 GTGGTGGTGG-T-G
1 GTGGTGGTGGATCA
175115 GTGGTGGTGGATCA
1 GTGGTGGTGGATCA
175129 TGTGGTGGTGGATCA
1 -GTGGTGGTGGATCA
175144 TGTGGTGGTGGATCA
1 -GTGGTGGTGGATCA
*
175159 TGTGGTTGTGG
1 -GTGGTGGTGG
175170 GAGGTCCGGC
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
12 10 0.20
13 1 0.02
15 39 0.78
ACGTcount: A:0.09, C:0.04, G:0.52, T:0.34
Consensus pattern (14 bp):
GTGGTGGTGGATCA
Found at i:175133 original size:15 final size:15
Alignment explanation
Indices: 175115--175169 Score: 101
Period size: 15 Copynumber: 3.7 Consensus size: 15
175105 GGTGGTGGTG
175115 GTGGTGGTGGATCAT
1 GTGGTGGTGGATCAT
175130 GTGGTGGTGGATCAT
1 GTGGTGGTGGATCAT
175145 GTGGTGGTGGATCAT
1 GTGGTGGTGGATCAT
*
175160 GTGGTTGTGG
1 GTGGTGGTGG
175170 GAGGTCCGGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.11, C:0.05, G:0.49, T:0.35
Consensus pattern (15 bp):
GTGGTGGTGGATCAT
Found at i:175139 original size:3 final size:3
Alignment explanation
Indices: 175100--175124 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
175090 TGCAAGGGTT
175100 GTG GTG GTG GTG GTG GTG GTG GTG G
1 GTG GTG GTG GTG GTG GTG GTG GTG G
175125 ATCATGTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (3 bp):
GTG
Found at i:176494 original size:17 final size:17
Alignment explanation
Indices: 176448--176495 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 17
176438 TTGAGTTCGG
176448 ATTAAAATT--TTAAAA
1 ATTAAAATTAATTAAAA
*
176463 TTTAAAA--AATATAAAA
1 ATTAAAATTAAT-TAAAA
176479 ATTAAAATTAATTAAAA
1 ATTAAAATTAATTAAAA
176496 TAAAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
15 7 0.27
16 11 0.42
17 5 0.19
18 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTAAAATTAATTAAAA
Found at i:177900 original size:18 final size:18
Alignment explanation
Indices: 177873--178097 Score: 225
Period size: 18 Copynumber: 12.5 Consensus size: 18
177863 GCCTGCGAAG
* *
177873 CCTAAGGAACCTGAAAAA
1 CCTAAAGAACCCGAAAAA
* * *
177891 CCCAAAGAACCCGAGAAG
1 CCTAAAGAACCCGAAAAA
* *
177909 CCTAAAGTACCAGAAAAA
1 CCTAAAGAACCCGAAAAA
*
177927 CCAAAAGAACCCGAAAAA
1 CCTAAAGAACCCGAAAAA
* *
177945 CCCAAAGAACCCGAGAAA
1 CCTAAAGAACCCGAAAAA
* *
177963 CCTAAACAACCCGAAAAG
1 CCTAAAGAACCCGAAAAA
*
177981 CCTAAGGAACCCGAAAAA
1 CCTAAAGAACCCGAAAAA
* *
177999 CCCAAAGAACCCGAGAAA
1 CCTAAAGAACCCGAAAAA
*
178017 CCTAAACAACCCGAAAAA
1 CCTAAAGAACCCGAAAAA
* * *
178035 CCCAAAGAACCCGAGAAG
1 CCTAAAGAACCCGAAAAA
* *
178053 CCTAAACAACCCGAAAAG
1 CCTAAAGAACCCGAAAAA
* * *
178071 CCTAAGGAACCTGAGAAA
1 CCTAAAGAACCCGAAAAA
*
178089 CCAAAAGAA
1 CCTAAAGAA
178098 GCACCAGCTC
Statistics
Matches: 165, Mismatches: 42, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 165 1.00
ACGTcount: A:0.51, C:0.29, G:0.15, T:0.04
Consensus pattern (18 bp):
CCTAAAGAACCCGAAAAA
Found at i:177961 original size:54 final size:54
Alignment explanation
Indices: 177879--178097 Score: 269
Period size: 54 Copynumber: 4.1 Consensus size: 54
177869 GAAGCCTAAG
* * ** *
177879 GAACCTGAAAAACCCAAAGAACCCGAGAAGCCTAAAGTACCAGAAAAACCAAAA
1 GAACCCGAAAAACCCAAAGAACCCGAGAAACCTAAACAACCCGAAAAACCAAAA
* * *
177933 GAACCCGAAAAACCCAAAGAACCCGAGAAACCTAAACAACCCGAAAAGCCTAAG
1 GAACCCGAAAAACCCAAAGAACCCGAGAAACCTAAACAACCCGAAAAACCAAAA
*
177987 GAACCCGAAAAACCCAAAGAACCCGAGAAACCTAAACAACCCGAAAAACCCAAA
1 GAACCCGAAAAACCCAAAGAACCCGAGAAACCTAAACAACCCGAAAAACCAAAA
* * * * ** * *
178041 GAACCCGAGAAGCCTAAACAACCCGA-AAAGCCTAAGGAACCTGAGAAACCAAAA
1 GAACCCGAAAAACCCAAAGAACCCGAGAAA-CCTAAACAACCCGAAAAACCAAAA
178095 GAA
1 GAA
178098 GCACCAGCTC
Statistics
Matches: 144, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
53 3 0.02
54 141 0.98
ACGTcount: A:0.52, C:0.29, G:0.15, T:0.04
Consensus pattern (54 bp):
GAACCCGAAAAACCCAAAGAACCCGAGAAACCTAAACAACCCGAAAAACCAAAA
Found at i:187157 original size:30 final size:30
Alignment explanation
Indices: 187116--187184 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
187106 TTAAATTAGT
* *
187116 AATAGTAAAATTGTATTTTAACTCC-TTAAA
1 AATAATAAAATTGTAATTTAA-TCCTTTAAA
*
187146 AATAATAAAATTTTAATTTAATCCTTTAAA
1 AATAATAAAATTGTAATTTAATCCTTTAAA
*
187176 AATTATAAA
1 AATAATAAA
187185 GGTATCAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 3 0.09
30 31 0.91
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (30 bp):
AATAATAAAATTGTAATTTAATCCTTTAAA
Found at i:188198 original size:31 final size:29
Alignment explanation
Indices: 188134--188257 Score: 105
Period size: 31 Copynumber: 4.2 Consensus size: 29
188124 TACTATTAAA
* *
188134 AAAGATTAGGTACCAAATTAGGAAAGTGT
1 AAAGTTTAGGTACCAAATTAGGAAAATGT
* *
188163 AAAGTTTAGGTACTAGATTAGGAAAAAATGT
1 AAAGTTTAGGTACCAAATTAGG--AAAATGT
188194 AAAGTTT-GAGTACCAAATT-GGACCAAA---
1 AAAGTTTAG-GTACCAAATTAGGA--AAATGT
188221 AAAGTTTAGGTACCAAATTAAGGAAAAGTGT
1 AAAGTTTAGGTACCAAATT-AGGAAAA-TGT
*
188252 CAAGTT
1 AAAGTT
188258 CAAGTAGCAA
Statistics
Matches: 76, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
27 20 0.26
28 2 0.03
29 22 0.29
30 6 0.08
31 26 0.34
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.26
Consensus pattern (29 bp):
AAAGTTTAGGTACCAAATTAGGAAAATGT
Found at i:193731 original size:31 final size:29
Alignment explanation
Indices: 193693--193762 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
193683 ATACTAAAAC
* *
193693 TATACATGAACTATGGTTTAATGTGCAATTG
1 TATACATGAACTATGATTT--TGTGCAATTA
* *
193724 TATACATGAATTTTGATTTTGTGCAATTA
1 TATACATGAACTATGATTTTGTGCAATTA
193753 TATACATGAA
1 TATACATGAA
193763 ATTTTGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (29 bp):
TATACATGAACTATGATTTTGTGCAATTA
Found at i:193756 original size:29 final size:30
Alignment explanation
Indices: 193714--193772 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
193704 TATGGTTTAA
*
193714 TGTGCAATTGTATACATG-AATTTTGATTT
1 TGTGCAATTATATACATGAAATTTTGATTT
193743 TGTGCAATTATATACATGAAATTTTGATTT
1 TGTGCAATTATATACATGAAATTTTGATTT
193773 GATCCAATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (30 bp):
TGTGCAATTATATACATGAAATTTTGATTT
Found at i:193781 original size:30 final size:29
Alignment explanation
Indices: 193718--193781 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
193708 GTTTAATGTG
* *
193718 CAATTGTATACATGAATTTTGATTTTGTG
1 CAATTATATACATGAATTTTGATTTTGTC
193747 CAATTATATACATGAAATTTTGA-TTTGATC
1 CAATTATATACATG-AATTTTGATTTTG-TC
193777 CAATT
1 CAATT
193782 CTTGTAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 17 0.55
30 14 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (29 bp):
CAATTATATACATGAATTTTGATTTTGTC
Found at i:198200 original size:15 final size:15
Alignment explanation
Indices: 198180--198209 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
198170 ATTAAAACTT
*
198180 CTTAATTTTAGTTTC
1 CTTAATTGTAGTTTC
198195 CTTAATTGTAGTTTC
1 CTTAATTGTAGTTTC
198210 TTGTTCTACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.13, G:0.10, T:0.57
Consensus pattern (15 bp):
CTTAATTGTAGTTTC
Done.