Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008377.1 Corchorus capsularis cultivar CVL-1 contig08398, 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: 27568
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4903 original size:27 final size:27
Alignment explanation
Indices: 4865--4919 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
4855 GGACACCCTC
*
4865 AGACTCAAGAAAGATTTTCAGCCATGT
1 AGACTCAAGAAAGATTTGCAGCCATGT
4892 AGACTCAAGAAAGATTTGCAGCCATGT
1 AGACTCAAGAAAGATTTGCAGCCATGT
4919 A
1 A
4920 TCAACACCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (27 bp):
AGACTCAAGAAAGATTTGCAGCCATGT
Found at i:7686 original size:49 final size:49
Alignment explanation
Indices: 7585--8319 Score: 546
Period size: 49 Copynumber: 15.1 Consensus size: 49
7575 CATTTTAAGA
* * * * * * * *
7585 AAAAGCGAGTAAAACT-AATGCCTTCCATCCGGGAAGGGCGTTTTAGGA
1 AAAAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGG
* * * * *
7633 AAAAGCAAGTAAAAATTAGTGCCTTCCGTCGGGGAAGGGCACTTTGGGG
1 AAAAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGG
*** ** * * * ** * *
7682 AAAAGTGGGTAAAAATAAGCGTCTTCCATCCGGGAAGGGCATTTTTGGA
1 AAAAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGG
* * * * * * *
7731 AAATAGCAAGT-AAGATAAGTGCCTTCTGGCTGGGAAGGGC-ATTTTGGG
1 AAA-AGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGG
* * * * * * * *
7779 AAAAAC-GGTAAAGATTAGTGCCTTCCGTC--CGAAGGGCG-TTTTGGG
1 AAAAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGG
* * ** * * * * * *
7824 AAAAACAGGTAGTAATCAGTGCCTTCCGTCCGGGAGGGGCG-TTTTGGG
1 AAAAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGG
* * *
7872 AAATAGCAAGTAAAGATAAACGGCTTCCGTCTGGGAAGGGCGTTTTGGGG
1 AAA-AGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGG
*
7922 AGATAGCAAG-AAAAAGTAAATGGCTTCCGTCTGGGAAGGGCGCTTT-GGG
1 A-AAAGCAAGTAAAAA-TAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGG
**
7971 AAATAGCAAGCGAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTT-GGG
1 AAA-AGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGG
* *
8020 AAATAGCCAGT-AAAATAAGTGGCTTCCGTCTGGGAAGGGCGCTTTGGGG
1 AAA-AGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGG
* * * *
8069 AAAAGTAAGTAAAGATGAATGGCTTCCGTCTGGGAAGAGCGCTTTGGGG
1 AAAAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGG
* * * *
8118 AAAAGTAAGTAAAGATGAATGGCTTCCGTCTGGGAAGAGCGCTTTGGGG
1 AAAAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGG
* * *
8167 AAAAGTAAGTAAAGATGAATGGCTTCCGTCTGGGAAGGGCGCTTT-GGG
1 AAAAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGG
* * * * *
8215 AAATAGCGAGTAAAAATGAAGTGCCTTCCGTGC-AGGAAGGGCG-TTTAGGGA
1 AAA-AGCAAGTAAAAAT-AAATGGCTTCCGT-CTGGGAAGGGCGCTTT-GGGG
* * * * * * *
8266 AAAAGCAAGTAAAAACAAACGCCTTCCATCCGGGAAGGGCGTTTTGGGA
1 AAAAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGG
8315 AAAAG
1 AAAAG
8320 TAGGTAACGA
Statistics
Matches: 579, Mismatches: 86, Indels: 43
0.82 0.12 0.06
Matches are distributed among these distances:
45 20 0.03
46 21 0.04
47 18 0.03
48 86 0.15
49 345 0.60
50 82 0.14
51 7 0.01
ACGTcount: A:0.31, C:0.15, G:0.33, T:0.22
Consensus pattern (49 bp):
AAAAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGG
Found at i:9014 original size:27 final size:26
Alignment explanation
Indices: 8963--9014 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
8953 TCATTAGGAA
***
8963 AAATTAAAAGCCCAATTGTTTAAAAG
1 AAATTAAAAGCCCAATTAAATAAAAG
8989 AAATTAAAAGCCCAAATTAAATAAAA
1 AAATTAAAAGCCC-AATTAAATAAAA
9015 AGATTTGAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.58, C:0.12, G:0.08, T:0.23
Consensus pattern (26 bp):
AAATTAAAAGCCCAATTAAATAAAAG
Found at i:13718 original size:74 final size:74
Alignment explanation
Indices: 13592--13779 Score: 349
Period size: 74 Copynumber: 2.5 Consensus size: 74
13582 GTCTACATAG
* *
13592 TGTCTCAACGTGCGAAAGGCCCGGCGGGAAACTTCTGTTTGGATACTTACGGGTCCCTAGTGGAG
1 TGTCGCAACGTGCGAAAGGCCCGGCGGGAAACTTCTGTTTGGATACTTACGGGTCCCCAGTGGAG
13657 TCGCCAAGC
66 TCGCCAAGC
*
13666 TGTCGCAACGTGCGAAAGGCCCGGCGGGAAACCTCTGTTTGGATACTTACGGGTCCCCAGTGGAG
1 TGTCGCAACGTGCGAAAGGCCCGGCGGGAAACTTCTGTTTGGATACTTACGGGTCCCCAGTGGAG
13731 TCGCCAAGC
66 TCGCCAAGC
13740 TGTCGCAACGTGCGAAAGGCCCGGCGGGAAACTTCTGTTT
1 TGTCGCAACGTGCGAAAGGCCCGGCGGGAAACTTCTGTTT
13780 AGTTAAGGTT
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 110 1.00
ACGTcount: A:0.20, C:0.27, G:0.32, T:0.21
Consensus pattern (74 bp):
TGTCGCAACGTGCGAAAGGCCCGGCGGGAAACTTCTGTTTGGATACTTACGGGTCCCCAGTGGAG
TCGCCAAGC
Found at i:14349 original size:36 final size:32
Alignment explanation
Indices: 14268--14360 Score: 107
Period size: 36 Copynumber: 2.8 Consensus size: 32
14258 TTTTTTTTTT
*
14268 ATTAAGTTCTTTATTCTACTTAATTACCCTGA
1 ATTAAGTTCTTTATTCTACTTAATTACACTGA
*
14300 ATTAAG-CCTTTTATTGACCTCACTTAATTACACTGA
1 ATTAAGTTC-TTTATT---CT-ACTTAATTACACTGA
*
14336 ATTAAGTTCTTTATTTTACTTAATT
1 ATTAAGTTCTTTATTCTACTTAATT
14361 TCCTTTCCTG
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
31 1 0.02
32 20 0.39
33 1 0.02
35 2 0.04
36 26 0.51
37 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.47
Consensus pattern (32 bp):
ATTAAGTTCTTTATTCTACTTAATTACACTGA
Found at i:14480 original size:107 final size:106
Alignment explanation
Indices: 14364--14603 Score: 326
Period size: 107 Copynumber: 2.3 Consensus size: 106
14354 CTTAATTTCC
* *
14364 TTTCC-TGAAATTAAG-CATGT-GTCTTTTTACTTAATTTCCTTGAAATCAAGCCAGTCTTCCCT
1 TTTCCTTGAAATTAAGCCA-GTCTTC-TTTTACCTAATTTCCTTGAAATCAAGCCAGTCTTCCCT
*
14426 TTACCTAATTTCCTTGAAATTAAGCCAGTCATT-TCTTTACCTAA
64 TTACCTAATTTCCTTGAAACTAAGCCAGTC-TTCT-TTTACCTAA
* * **
14470 TTTCCTTGAAACTAAGCCAGTCTTCTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTT
1 TTTCCTTGAAATTAAGCCAGTCTTCTTTTACCTAATTTCCTTGAAATCAAGCCAGTCTTCCCTTT
* *
14535 ACTTAATTTCCTTGAAACTAAGCTAGTCTTCTTTTACCTAA
66 ACCTAATTTCCTTGAAACTAAGCCAGTCTTCTTTTACCTAA
*
14576 TTTCCTTGAAATTAAGTCAGTCTTCTTT
1 TTTCCTTGAAATTAAGCCAGTCTTCTTT
14604 CAGTCTTCTT
Statistics
Matches: 119, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
106 42 0.35
107 73 0.61
108 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.09, T:0.43
Consensus pattern (106 bp):
TTTCCTTGAAATTAAGCCAGTCTTCTTTTACCTAATTTCCTTGAAATCAAGCCAGTCTTCCCTTT
ACCTAATTTCCTTGAAACTAAGCCAGTCTTCTTTTACCTAA
Found at i:14507 original size:35 final size:35
Alignment explanation
Indices: 14364--14603 Score: 308
Period size: 36 Copynumber: 6.8 Consensus size: 35
14354 CTTAATTTCC
* *
14364 TTTCC-TGAAATTAAG-CATGT-GTCTTTTTACTTAA
1 TTTCCTTGAAATTAAGCCA-GTCTTC-TTTTACCTAA
* *
14398 TTTCCTTGAAATCAAGCCAGTCTTCCCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCTT-CTTTTACCTAA
14434 TTTCCTTGAAATTAAGCCAGTCATT-TCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTC-TTCT-TTTACCTAA
*
14470 TTTCCTTGAAACTAAGCCAGTCTTCTTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCTTCTTTTACCTAA
* *
14505 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTTCT-TTTACCTAA
* *
14541 TTTCCTTGAAACTAAGCTAGTCTTCTTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCTTCTTTTACCTAA
*
14576 TTTCCTTGAAATTAAGTCAGTCTTCTTT
1 TTTCCTTGAAATTAAGCCAGTCTTCTTT
14604 CAGTCTTCTT
Statistics
Matches: 181, Mismatches: 17, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
34 5 0.03
35 79 0.44
36 94 0.52
37 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.09, T:0.43
Consensus pattern (35 bp):
TTTCCTTGAAATTAAGCCAGTCTTCTTTTACCTAA
Found at i:14597 original size:71 final size:71
Alignment explanation
Indices: 14364--14599 Score: 354
Period size: 71 Copynumber: 3.3 Consensus size: 71
14354 CTTAATTTCC
* * *
14364 TTTCC-TGAAATTAAG-CATGTGTCTT-TTTACTTAATTTCCTTGAAA-TCAAGCCAGTCTTCCC
1 TTTCCTTGAAATTAAGCCA-GTCTTTTCTTTACTTAATTTCCTTGAAACT-AAGCCAGTCTT-CT
14425 TTTACCTAA
63 TTTACCTAA
* *
14434 TTTCCTTGAAATTAAGCCAGTCATTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCTTCTTTT
1 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACTTAATTTCCTTGAAACTAAGCCAGTCTTCTTTT
14499 ACCTAA
66 ACCTAA
*
14505 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACTTAATTTCCTTGAAACTAAGCTAGTCTTCTTTT
1 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACTTAATTTCCTTGAAACTAAGCCAGTCTTCTTTT
14570 ACCTAA
66 ACCTAA
*
14576 TTTCCTTGAAATTAAGTCAGTCTT
1 TTTCCTTGAAATTAAGCCAGTCTT
14600 CTTTCAGTCT
Statistics
Matches: 153, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
70 5 0.03
71 115 0.75
72 32 0.21
73 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.43
Consensus pattern (71 bp):
TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACTTAATTTCCTTGAAACTAAGCCAGTCTTCTTTT
ACCTAA
Found at i:14606 original size:11 final size:11
Alignment explanation
Indices: 14592--14726 Score: 137
Period size: 11 Copynumber: 11.7 Consensus size: 11
14582 TGAAATTAAG
14592 TCAGTCTTCTT
1 TCAGTCTTCTT
14603 TCAGTCTTCTT
1 TCAGTCTTCTT
* *
14614 TTAGT-TTTTT
1 TCAGTCTTCTT
14624 TCAGTCTTCTCTT
1 TCAGTC-T-TCTT
*
14637 TCAGTCTTGTT
1 TCAGTCTTCTT
*
14648 TCAGTCTTTTT
1 TCAGTCTTCTT
*
14659 TCAGTCCTCTT
1 TCAGTCTTCTT
*
14670 TCAGTCTTTTTTTTT
1 TCAGTC----TTCTT
14685 TCAGTCTTCTT
1 TCAGTCTTCTT
14696 TCAGTCTTCTTT
1 TCAGTCTTC-TT
*
14708 TCAGTCTTATT
1 TCAGTCTTCTT
14719 TCAGTCTT
1 TCAGTCTT
14727 TTGCCTAATT
Statistics
Matches: 104, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
10 8 0.08
11 66 0.63
12 12 0.12
13 9 0.09
15 9 0.09
ACGTcount: A:0.10, C:0.22, G:0.10, T:0.59
Consensus pattern (11 bp):
TCAGTCTTCTT
Found at i:14642 original size:34 final size:33
Alignment explanation
Indices: 14592--14726 Score: 151
Period size: 34 Copynumber: 4.2 Consensus size: 33
14582 TGAAATTAAG
14592 TCAGTCTTCTTTCAGTCTTCTTTTAGT-TTTTT
1 TCAGTCTTCTTTCAGTCTTCTTTTAGTCTTTTT
* *
14624 TCAGTCTTCTCTTTCAGTCTTGTTTCAGTCTTTTT
1 TCAGTC-T-TCTTTCAGTCTTCTTTTAGTCTTTTT
*
14659 TCAGTCCTCTTTCAG---TC-TTT--T-TTTTT
1 TCAGTCTTCTTTCAGTCTTCTTTTAGTCTTTTT
*
14685 TCAGTCTTCTTTCAGTCTTCTTTTCAGTCTTATT
1 TCAGTCTTCTTTCAGTCTTCTTTT-AGTCTTTTT
14719 TCAGTCTT
1 TCAGTCTT
14727 TTGCCTAATT
Statistics
Matches: 85, Mismatches: 7, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
26 19 0.22
27 1 0.01
29 4 0.05
30 4 0.05
32 6 0.07
33 10 0.12
34 30 0.35
35 11 0.13
ACGTcount: A:0.10, C:0.22, G:0.10, T:0.59
Consensus pattern (33 bp):
TCAGTCTTCTTTCAGTCTTCTTTTAGTCTTTTT
Found at i:14708 original size:23 final size:23
Alignment explanation
Indices: 14592--14726 Score: 168
Period size: 23 Copynumber: 5.8 Consensus size: 23
14582 TGAAATTAAG
14592 TCAGTCTTCTTTCAGTCTTCTTT
1 TCAGTCTTCTTTCAGTCTTCTTT
*
14615 T-AGT-TTTTTTCAGTCTTCTCTT
1 TCAGTCTTCTTTCAGTCTTCT-TT
*
14637 TCAGTCTTGTTTCAGTCTT-TTT
1 TCAGTCTTCTTTCAGTCTTCTTT
* *
14659 TCAGTCCTCTTTCAGTCTTTTTTTTT
1 TCAGTCTTCTTTCAGTC---TTCTTT
14685 TCAGTCTTCTTTCAGTCTTCTTT
1 TCAGTCTTCTTTCAGTCTTCTTT
*
14708 TCAGTCTTATTTCAGTCTT
1 TCAGTCTTCTTTCAGTCTT
14727 TTGCCTAATT
Statistics
Matches: 98, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
21 14 0.14
22 23 0.23
23 28 0.29
24 12 0.12
25 2 0.02
26 19 0.19
ACGTcount: A:0.10, C:0.22, G:0.10, T:0.59
Consensus pattern (23 bp):
TCAGTCTTCTTTCAGTCTTCTTT
Found at i:14882 original size:35 final size:35
Alignment explanation
Indices: 14783--14967 Score: 300
Period size: 36 Copynumber: 5.2 Consensus size: 35
14773 TCATCTTTGG
* *
14783 ATTAAATCTTTGCTGACTTTACTTAATTCTTGTGAA
1 ATTAAGTCTTTGCT-AATTTACTTAATTCTTGTGAA
14819 ATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAA
1 ATTAAGTCTTTGCTAA-TTTACTTAATTCTTGTGAA
14855 ATTAAGTCTTTGCTAATTTACTTAATTCTTGTGAA
1 ATTAAGTCTTTGCTAATTTACTTAATTCTTGTGAA
*
14890 ATTAAGTCTGTGCTAATTTACTTAATTCTTGTGAA
1 ATTAAGTCTTTGCTAATTTACTTAATTCTTGTGAA
14925 ATTAAGTCTTTG-TCAATTTTACTTAATTCTTGTGAA
1 ATTAAGTCTTTGCT-AA-TTTACTTAATTCTTGTGAA
14961 ATTAAGT
1 ATTAAGT
14968 TTGTGTTTAT
Statistics
Matches: 142, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
34 1 0.01
35 67 0.47
36 74 0.52
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.48
Consensus pattern (35 bp):
ATTAAGTCTTTGCTAATTTACTTAATTCTTGTGAA
Found at i:14884 original size:20 final size:20
Alignment explanation
Indices: 14820--14919 Score: 53
Period size: 20 Copynumber: 5.5 Consensus size: 20
14810 TCTTGTGAAA
14820 TTAAGTCTTTGCTAATTTTAC
1 TTAAGTCTTTGCTAA-TTTAC
*
14841 TTAATTC-TTG-TGAA---A-
1 TTAAGTCTTTGCT-AATTTAC
14856 TTAAGTCTTTGCTAATTTAC
1 TTAAGTCTTTGCTAATTTAC
*
14876 TTAATTC-TTG-TGAA---A-
1 TTAAGTCTTTGCT-AATTTAC
*
14891 TTAAGTCTGTGCTAATTTAC
1 TTAAGTCTTTGCTAATTTAC
*
14911 TTAATTCTT
1 TTAAGTCTT
14920 GTGAAATTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 29
0.62 0.07 0.31
Matches are distributed among these distances:
15 12 0.21
16 11 0.19
17 2 0.03
18 1 0.02
19 8 0.14
20 18 0.31
21 6 0.10
ACGTcount: A:0.27, C:0.12, G:0.11, T:0.50
Consensus pattern (20 bp):
TTAAGTCTTTGCTAATTTAC
Found at i:14892 original size:71 final size:71
Alignment explanation
Indices: 14783--14972 Score: 303
Period size: 71 Copynumber: 2.7 Consensus size: 71
14773 TCATCTTTGG
* * * *
14783 ATTAAATCTTTGCTGACTTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTTTACTTAATTC
1 ATTAAGTCTTTGCTCAATTTACTTAATTCTTGTGAAATTAAGTCTGTGCTAA-TTTACTTAATTC
14848 TTGTGAA
65 TTGTGAA
14855 ATTAAGTCTTTGCT-AATTTACTTAATTCTTGTGAAATTAAGTCTGTGCTAATTTACTTAATTCT
1 ATTAAGTCTTTGCTCAATTTACTTAATTCTTGTGAAATTAAGTCTGTGCTAATTTACTTAATTCT
14919 TGTGAA
66 TGTGAA
*
14925 ATTAAGTCTTTG-TCAATTTTACTTAATTCTTGTGAAATTAAGTTTGTG
1 ATTAAGTCTTTGCTCAA-TTTACTTAATTCTTGTGAAATTAAGTCTGTG
14973 TTTATCCTTA
Statistics
Matches: 112, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
69 1 0.01
70 33 0.29
71 65 0.58
72 13 0.12
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (71 bp):
ATTAAGTCTTTGCTCAATTTACTTAATTCTTGTGAAATTAAGTCTGTGCTAATTTACTTAATTCT
TGTGAA
Found at i:17064 original size:34 final size:34
Alignment explanation
Indices: 17026--17579 Score: 478
Period size: 34 Copynumber: 15.8 Consensus size: 34
17016 AGTCAAATTA
17026 CTTAATTTCAAGGAAATTAAGTAAAATAGACTGG
1 CTTAATTTCAAGGAAATTAAGTAAAATAGACTGG
17060 CTTAATTTCAAGGAAATTAAGTAAAATAGACTGG
1 CTTAATTTCAAGGAAATTAAGTAAAATAGACTGG
*
17094 TTTAATTTCAAGGAAATTAAGTAAAATAGACTGG
1 CTTAATTTCAAGGAAATTAAGTAAAATAGACTGG
* *
17128 CTTAATTTCAAGGATATTAAGT-AAATAAACTGG
1 CTTAATTTCAAGGAAATTAAGTAAAATAGACTGG
*
17161 CTTAATTTCAAGGAAATTAGGT-AAATAGACTGG
1 CTTAATTTCAAGGAAATTAAGTAAAATAGACTGG
* * *
17194 CTTAATTTCAAGGAAATTAGGTAAGATAGACTAG
1 CTTAATTTCAAGGAAATTAAGTAAAATAGACTGG
* *
17228 CTTAATTTCAAAGAAATTACGTAAAATAGACTGG
1 CTTAATTTCAAGGAAATTAAGTAAAATAGACTGG
*
17262 CTTAATTTCAAGGATATTAAGTAAAA-AGAACTGG
1 CTTAATTTCAAGGAAATTAAGTAAAATAG-ACTGG
* * *
17296 CTTAATTTCAAGAAAAGAAATTAGGTAAAGGAAAGATTGG
1 CTTAATTTCAAG----GAAATTAAGTAAA--ATAGACTGG
17336 CTTAATTTCAAGGAAATTAAGTAAAGA-AGACTGG
1 CTTAATTTCAAGGAAATTAAGTAAA-ATAGACTGG
* * * * * *
17370 CTCAGTTTTAGGAAAGGAAATTAAGTAAGGATAAGCACAGA
1 CTTA-ATTT---CAAGGAAATTAAGTAA-AAT-AG-ACTGG
* ** *
17411 CTTAATTTCACA-GAAATTAAGTAAAGTGAGCAAAGA
1 CTTAATTTCA-AGGAAATTAAGTAAAAT-AG-ACTGG
* ** *
17447 CTTAATTTCACAAG-AATTAAGTAAAATTAGTAAAGA
1 CTTAATTTCA-AGGAAATTAAGTAAAA-TAG-ACTGG
* * * *
17483 CTTAATTTCACAAG-AATTAAGTAAATTAGCACAGA
1 CTTAATTTCA-AGGAAATTAAGTAAAATAG-ACTGG
* * ** *
17518 CTTAATTTCACAAG-AATTAAGTAAATTAGCAAAGA
1 CTTAATTTCA-AGGAAATTAAGTAAAATAG-ACTGG
*
17553 CTTAATTTCACAAG-AATTAAGTAAAAT
1 CTTAATTTCA-AGGAAATTAAGTAAAAT
17580 TGGCAAAGAC
Statistics
Matches: 459, Mismatches: 41, Indels: 39
0.85 0.08 0.07
Matches are distributed among these distances:
33 64 0.14
34 175 0.38
35 72 0.16
36 75 0.16
37 15 0.03
38 28 0.06
40 22 0.05
41 8 0.02
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29
Consensus pattern (34 bp):
CTTAATTTCAAGGAAATTAAGTAAAATAGACTGG
Found at i:17304 original size:168 final size:172
Alignment explanation
Indices: 17026--17435 Score: 499
Period size: 168 Copynumber: 2.3 Consensus size: 172
17016 AGTCAAATTA
* *
17026 CTTAATTTCAAGGAAATTAAGTAAAATAGACTGGCTTAATTTCAAGGAAATTAAGTAAAATAGAC
1 CTTAATTTCAAGGAAATTAAGTAAAATAGACTAGCTTAATTTCAAAGAAATTAAGTAAAATAGAC
* * *
17091 TGGTTTAATTTCAAGGAAATTAAGTAAAATAGACTGGCTTAATTTCAAG-GATATTAAGTAAA-T
66 TGGCTTAATTTCAAGGAAATTAAGTAAAATAGACTGGCTTAATTTCAAGAGAAATTAAGTAAAGA
* *
17154 AA-ACTGGCTTAATTTCAAGGAAATTAGGTAAA-TAGACTGG
131 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAGACTGG
* * *
17194 CTTAATTTCAAGGAAATTAGGTAAGATAGACTAGCTTAATTTCAAAGAAATTACGTAAAATAGAC
1 CTTAATTTCAAGGAAATTAAGTAAAATAGACTAGCTTAATTTCAAAGAAATTAAGTAAAATAGAC
* *
17259 TGGCTTAATTTCAAGGATATTAAGTAAAA-AGAACTGGCTTAATTTCAAGAAAAGAAATTAGGTA
66 TGGCTTAATTTCAAGGAAATTAAGTAAAATAG-ACTGGCTTAATTTCAAG---AGAAATTAAGTA
*
17323 AAGGAAAGATTGGCTTAATTTCAAGGAAATTAAGTAAAGAAGACTGG
127 AA-GAAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAGACTGG
* * * * *
17370 CTCAGTTTTAGGAAAGGAAATTAAGTAAGGATAAGCAC-AGACTTAATTTCACAGAAATTAAGTA
1 CTTA-ATTT---CAAGGAAATTAAGTAA-AAT-AG-ACTAG-CTTAATTTCAAAGAAATTAAGTA
17434 AA
58 AA
17436 GTGAGCAAAG
Statistics
Matches: 206, Mismatches: 19, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
167 2 0.01
168 104 0.50
172 11 0.05
174 2 0.01
175 28 0.14
176 10 0.05
177 3 0.01
180 14 0.07
181 3 0.01
182 4 0.02
183 25 0.12
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.29
Consensus pattern (172 bp):
CTTAATTTCAAGGAAATTAAGTAAAATAGACTAGCTTAATTTCAAAGAAATTAAGTAAAATAGAC
TGGCTTAATTTCAAGGAAATTAAGTAAAATAGACTGGCTTAATTTCAAGAGAAATTAAGTAAAGA
AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAGACTGG
Found at i:17455 original size:36 final size:35
Alignment explanation
Indices: 17388--17773 Score: 549
Period size: 36 Copynumber: 10.8 Consensus size: 35
17378 TAGGAAAGGA
* *
17388 AATTAAGTAAGGATAAGCACAGACTTAATTTCAC-AG
1 AATTAAGTAA--ATTAGCAAAGACTTAATTTCACAAG
*
17424 AAATTAAGTAAAGTGAGCAAAGACTTAATTTCACAAG
1 -AATTAAGTAAA-TTAGCAAAGACTTAATTTCACAAG
*
17461 AATTAAGTAAAATTAGTAAAGACTTAATTTCACAAG
1 AATTAAGT-AAATTAGCAAAGACTTAATTTCACAAG
*
17497 AATTAAGTAAATTAGCACAGACTTAATTTCACAAG
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
17532 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
* * *
17567 AATTAAGTAAAATTGGCAAAGACTTAACTTCACATG
1 AATTAAGT-AAATTAGCAAAGACTTAATTTCACAAG
17603 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGT-AAATTAGCAAAGACTTAATTTCACAAG
17639 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
* * * *
17674 AATTAAGTAAAATTGGTAAAGACTTAACTTCACATG
1 AATTAAGT-AAATTAGCAAAGACTTAATTTCACAAG
17710 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGT-AAATTAGCAAAGACTTAATTTCACAAG
* *
17746 AATTAAGTAAAGTCAGCAAAGATTTAAT
1 AATTAAGTAAA-TTAGCAAAGACTTAAT
17774 CCAAAGATGA
Statistics
Matches: 320, Mismatches: 23, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
35 106 0.33
36 199 0.62
37 15 0.05
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (35 bp):
AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
Found at i:17540 original size:107 final size:107
Alignment explanation
Indices: 17388--17794 Score: 624
Period size: 107 Copynumber: 3.8 Consensus size: 107
17378 TAGGAAAGGA
* * * *
17388 AATTAAGTAAGGATAAGCACAGACTTAATTTCAC-AGAAATTAAGTAAAGTGAGCAAAGACTTAA
1 AATTAAGTAA-AATTAGCAAAGACTTAATTTCACAAG-AATTAAGTAAA-TTAGCAAAGACTTAA
* * *
17452 TTTCACAAGAATTAAGTAAAATTAGTAAAGACTTAATTTCACAAG
63 TTTCACAAGAATTAAGTAAAATTGGTAAAGACTTAACTTCACATG
*
17497 AATTAAGT-AAATTAGCACAGACTTAATTTCACAAGAATTAAGTAAATTAGCAAAGACTTAATTT
1 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCAAAGACTTAATTT
*
17561 CACAAGAATTAAGTAAAATTGGCAAAGACTTAACTTCACATG
66 CACAAGAATTAAGTAAAATTGGTAAAGACTTAACTTCACATG
17603 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCAAAGACTTAATTT
1 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCAAAGACTTAATTT
17668 CACAAGAATTAAGTAAAATTGGTAAAGACTTAACTTCACATG
66 CACAAGAATTAAGTAAAATTGGTAAAGACTTAACTTCACATG
* *
17710 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAGTCAGCAAAGATTTAA-T
1 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAA-TTAGCAAAGACTTAATT
*
17774 CCA-AAGATGATTAAGTAAAAT
65 TCACAAGA--ATTAAGTAAAAT
17795 CAGACAAAGG
Statistics
Matches: 281, Mismatches: 12, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
106 67 0.24
107 178 0.63
108 28 0.10
109 8 0.03
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (107 bp):
AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCAAAGACTTAATTT
CACAAGAATTAAGTAAAATTGGTAAAGACTTAACTTCACATG
Found at i:17586 original size:142 final size:142
Alignment explanation
Indices: 17388--17773 Score: 578
Period size: 142 Copynumber: 2.7 Consensus size: 142
17378 TAGGAAAGGA
* * *
17388 AATTAAGTAAGGATAAGCACAGACTTAATTTCAC-AGAAATTAAGT-AAAGTGAGCAAAGACTTA
1 AATTAAGTAA--ATTAGCAAAGACTTAATTTCACAAG-AATTAAGTAAAATTG-GCAAAGACTTA
* *
17451 ATTTCACAAGAATTAAGTAAAATTAGTAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCACA
62 ATTTCACAAGAATTAAGTAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCAAA
17516 GACTTAATTTCACAAG
127 GACTTAATTTCACAAG
*
17532 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAATTGGCAAAGACTTAACTT
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAATTGGCAAAGACTTAATTT
*
17597 CACATGAATTAAGTAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCAAAGACT
66 CACAAGAATTAAGTAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCAAAGACT
17662 TAATTTCACAAG
131 TAATTTCACAAG
* * * * *
17674 AATTAAGTAAAATTGGTAAAGACTTAACTTCACATGAATTAAGTAAAATTAGCAAAGACTTAATT
1 AATTAAGT-AAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAATTGGCAAAGACTTAATT
* * *
17739 TCACAAGAATTAAGTAAAGTCAGCAAAGATTTAAT
65 TCACAAGAATTAAGTAAAATTAGCAAAGACTTAAT
17774 CCAAAGATGA
Statistics
Matches: 222, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
142 124 0.56
143 88 0.40
144 10 0.05
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (142 bp):
AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAATTGGCAAAGACTTAATTT
CACAAGAATTAAGTAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCAAAGACT
TAATTTCACAAG
Found at i:17853 original size:11 final size:11
Alignment explanation
Indices: 17830--18121 Score: 365
Period size: 11 Copynumber: 25.7 Consensus size: 11
17820 AATTAGACAA
17830 AAGACTGAAAG
1 AAGACTGAAAG
* *
17841 AACACTAAAAG
1 AAGACTGAAAG
17852 AAGACTGAAAAG
1 AAGACTG-AAAG
*
17864 AAGACTGAAAA
1 AAGACTGAAAG
17875 AAGACTGAAAG
1 AAGACTGAAAG
17886 AAGACTGAAAG
1 AAGACTGAAAG
17897 AAGACTGAAAG
1 AAGACTGAAAG
17908 AAGACTGAAAAG
1 AAGACTG-AAAG
17920 AAGACTGAAAG
1 AAGACTGAAAG
17931 AAGACTGAAA-
1 AAGACTGAAAG
*
17941 ATAGACTGAAAC
1 A-AGACTGAAAG
17953 AAGACTGAAAGAG
1 AAGACTG-AA-AG
*
17966 AAGACTGAAAC
1 AAGACTGAAAG
17977 AAGACTGAAAG
1 AAGACTGAAAG
17988 AAGACTGAAAAG
1 AAGACTG-AAAG
18000 AAGACTGAAAAG
1 AAGACTG-AAAG
18012 AAGACTGAAAG
1 AAGACTGAAAG
18023 AAGACTGAAAG
1 AAGACTGAAAG
18034 AAGACTGAAAG
1 AAGACTGAAAG
18045 AAGACTGAAA-
1 AAGACTGAAAG
*
18055 ATAGACTAAAAGAG
1 A-AGACT-GAA-AG
*
18069 AAGACTGAAAC
1 AAGACTGAAAG
*
18080 AAGACTAAAAGAG
1 AAGACT-GAA-AG
*
18093 AAGACT-AAAA
1 AAGACTGAAAG
*
18103 AAGATTGAAAG
1 AAGACTGAAAG
18114 AAGACTGA
1 AAGACTGA
18122 CTTAATTTCA
Statistics
Matches: 249, Mismatches: 18, Indels: 28
0.84 0.06 0.09
Matches are distributed among these distances:
10 8 0.03
11 163 0.65
12 56 0.22
13 21 0.08
14 1 0.00
ACGTcount: A:0.57, C:0.10, G:0.23, T:0.10
Consensus pattern (11 bp):
AAGACTGAAAG
Found at i:17869 original size:34 final size:34
Alignment explanation
Indices: 17830--18119 Score: 351
Period size: 34 Copynumber: 8.5 Consensus size: 34
17820 AATTAGACAA
*
17830 AAGACTGAAAGAACACTAAAAGAAGACTGAAAAG
1 AAGACTGAAAGAAGACTAAAAGAAGACTGAAAAG
* *
17864 AAGACTGAAAAAAGACTGAAAGAAGACTG-AAAG
1 AAGACTGAAAGAAGACTAAAAGAAGACTGAAAAG
17897 AAGACTGAAAGAAGACTGAAAAGAAGACTG-AAAG
1 AAGACTGAAAGAAGACT-AAAAGAAGACTGAAAAG
* *
17931 AAGACTGAAA-ATAGACTGAAACAAGACTGAAAGAG
1 AAGACTGAAAGA-AGACTAAAAGAAGACTGAAA-AG
* *
17966 AAGACTGAAACAAGACTGAAAGAAGACTGAAAAG
1 AAGACTGAAAGAAGACTAAAAGAAGACTGAAAAG
*
18000 AAGACTGAAAAGAAGACTGAAAGAAGACTG-AAAG
1 AAGACTG-AAAGAAGACTAAAAGAAGACTGAAAAG
* *
18034 AAGACTGAAAGAAGACTGAAAA-TAGACTAAAAGAG
1 AAGACTGAAAGAAGACT-AAAAGAAGACTGAAA-AG
*
18069 AAGACTGAAACAAGACTAAAAGAGAAGACT-AAAA-
1 AAGACTGAAAGAAGACT-AAA-AGAAGACTGAAAAG
*
18103 AAGATTGAAAGAAGACT
1 AAGACTGAAAGAAGACT
18120 GACTTAATTT
Statistics
Matches: 228, Mismatches: 17, Indels: 22
0.85 0.06 0.08
Matches are distributed among these distances:
33 46 0.20
34 98 0.43
35 74 0.32
36 5 0.02
37 5 0.02
ACGTcount: A:0.57, C:0.10, G:0.23, T:0.10
Consensus pattern (34 bp):
AAGACTGAAAGAAGACTAAAAGAAGACTGAAAAG
Found at i:17985 original size:46 final size:45
Alignment explanation
Indices: 17830--18121 Score: 396
Period size: 45 Copynumber: 6.4 Consensus size: 45
17820 AATTAGACAA
* *
17830 AAGACTGAAAGAACACTAAAAGAAGACTGAAAAGAAGACTGAAAA-
1 AAGACTGAAAGAAGACTGAAAGAAGACTG-AAAGAAGACTGAAAAG
17875 AAGACTGAAAGAAGACTGAAAGAAGACTGAAAGAAGACTGAAAAG
1 AAGACTGAAAGAAGACTGAAAGAAGACTGAAAGAAGACTGAAAAG
*
17920 AAGACTGAAAGAAGACTGAAA-ATAGACTGAAACAAGACTGAAAGAG
1 AAGACTGAAAGAAGACTGAAAGA-AGACTGAAAGAAGACTGAAA-AG
*
17966 AAGACTGAAACAAGACTGAAAGAAGACTGAAAAGAAGACTGAAAAG
1 AAGACTGAAAGAAGACTGAAAGAAGACTG-AAAGAAGACTGAAAAG
18012 AAGACTGAAAGAAGACTGAAAGAAGACTGAAAGAAGACTGAAAA-
1 AAGACTGAAAGAAGACTGAAAGAAGACTGAAAGAAGACTGAAAAG
* * * *
18056 TAGACTAAAAGAGAAGACTGAAACAAGACTAAAAGAGAAGACT-AAAA-
1 AAGACT-GAA-AGAAGACTGAAAGAAGACT-GAA-AGAAGACTGAAAAG
*
18103 AAGATTGAAAGAAGACTGA
1 AAGACTGAAAGAAGACTGA
18122 CTTAATTTCA
Statistics
Matches: 225, Mismatches: 13, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
44 21 0.09
45 94 0.42
46 78 0.35
47 24 0.11
48 8 0.04
ACGTcount: A:0.57, C:0.10, G:0.23, T:0.10
Consensus pattern (45 bp):
AAGACTGAAAGAAGACTGAAAGAAGACTGAAAGAAGACTGAAAAG
Found at i:18037 original size:103 final size:101
Alignment explanation
Indices: 17828--18121 Score: 295
Period size: 103 Copynumber: 2.9 Consensus size: 101
17818 GAAATTAGAC
* * * *
17828 AAAAGACTG-AA-AGAACACTAAAAGAAGACTGAAAAGAAGACTGAAAAAAGACTGAAAGAAGAC
1 AAAAGACTGAAAGAGAAGACTGAAACAAGACTG-AAAGAAGACTGAAAGAAGACTGAAAGAAGAC
*
17891 TG-AAAGAAGACTGAAAGAAGACTGAAAAGAAGACTGA
65 TGAAAAGAAGACTGAAAGAAGACTGAAAA-TAGACTGA
* *
17928 AAGAAGACTGAAA-A-TAGACTGAAACAAGACTGAAAGAGAAGACTGAAACAAGACTGAAAGAAG
1 AA-AAGACTGAAAGAGAAGACTGAAACAAGACTG-AA-AGAAGACTGAAAGAAGACTGAAAGAAG
17991 ACTGAAAAGAAGACTGAAAAGAAGACTGAAAGA-AGACTGA
63 ACTGAAAAGAAGACTG-AAAGAAGACTGAAA-ATAGACTGA
* * *
18031 AAGAAGACTG-AA-AGAAGACTGAAA-ATAGACTAAAAGAGAAGACTGAAACAAGACTAAAAGAG
1 AA-AAGACTGAAAGAGAAGACTGAAACA-AGACT-GAA-AGAAGACTGAAAGAAGACT-GAA-AG
*
18093 AAGACT-AAAA-AAGATTGAAAGAAGACTGA
60 AAGACTGAAAAGAAGACTGAAAGAAGACTGA
18122 CTTAATTTCA
Statistics
Matches: 174, Mismatches: 9, Indels: 20
0.86 0.04 0.10
Matches are distributed among these distances:
100 2 0.01
101 24 0.14
102 49 0.28
103 70 0.40
104 20 0.11
105 9 0.05
ACGTcount: A:0.57, C:0.10, G:0.23, T:0.10
Consensus pattern (101 bp):
AAAAGACTGAAAGAGAAGACTGAAACAAGACTGAAAGAAGACTGAAAGAAGACTGAAAGAAGACT
GAAAAGAAGACTGAAAGAAGACTGAAAATAGACTGA
Found at i:18196 original size:36 final size:36
Alignment explanation
Indices: 18114--18384 Score: 345
Period size: 36 Copynumber: 7.7 Consensus size: 36
18104 AGATTGAAAG
* * *
18114 AAGACTGACTTAATTTCAAGGAAATTAGGTAAA-AG
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
*
18149 AAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* * *
18185 AAGACTGGCTTAATTTCAAGCAAATTAGGTAAAG-G
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* *
18220 AAGACTGGCTTAGTTTCAAGGAAACTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* * *
18256 AATACTGGCTTAGTTTCAAGGAAACTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* * *
18292 ATGACTGGCTTAATTTCAACGAAATTAAGTAAAGGA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
*
18328 AAGACTGGCTTAATTTCAAGGAAATTAA-TTAA-AA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* *
18362 AACACAGGCTTAATTTC-AGGAAA
1 AAGACTGGCTTAATTTCAAGGAAA
18385 GGAAATTAAA
Statistics
Matches: 208, Mismatches: 26, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
33 6 0.03
34 16 0.08
35 63 0.30
36 123 0.59
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (36 bp):
AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
Found at i:18197 original size:71 final size:71
Alignment explanation
Indices: 18114--18384 Score: 359
Period size: 71 Copynumber: 3.8 Consensus size: 71
18104 AGATTGAAAG
* * *
18114 AAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAATTAAGT
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAAGAAGACTGGCTTAATTTCAAGGAAATTAAGT
18179 AAAGAA
66 AAAGAA
* * * * *
18185 AAGACTGGCTTAATTTCAAGCAAATTAGGTAAAGGAAGACTGGCTTAGTTTCAAGGAAACTAAGT
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAAGAAGACTGGCTTAATTTCAAGGAAATTAAGT
18250 AAAGAA
66 AAAGAA
* * * *
18256 AATACTGGCTTAGTTTCAAGGAAACTAAGT-AAAGAAATGACTGGCTTAATTTCAACGAAATTAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAAG-AA-GACTGGCTTAATTTCAAGGAAATTAA
*
18320 GTAAAGGA
64 GTAAAGAA
* * *
18328 AAGACTGGCTTAATTTCAAGGAAATTAATTAAAA-AACACAGGCTTAATTTC-AGGAAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAAGAAGACTGGCTTAATTTCAAGGAAA
18385 GGAAATTAAA
Statistics
Matches: 176, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
69 5 0.03
70 16 0.09
71 96 0.55
72 56 0.32
73 3 0.02
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (71 bp):
AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAAGAAGACTGGCTTAATTTCAAGGAAATTAAGT
AAAGAA
Found at i:18285 original size:107 final size:106
Alignment explanation
Indices: 18113--18384 Score: 379
Period size: 107 Copynumber: 2.6 Consensus size: 106
18103 AAGATTGAAA
* * * * *
18113 GAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAATTAAG
1 GAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAAAAACACTGGCTTAGTTTCAAGGAAACTAAG
*
18178 TAAAGAAAAGACTGGCTTAATTTCAA-GCAAATTAGGTAAAG
66 TAAAGAAAAGACTGGCTTAATTTCAACG-AAATTAAGTAAAG
* * *
18219 GAAGACTGGCTTAGTTTCAAGGAAACTAAGTAAAGAAAATACTGGCTTAGTTTCAAGGAAACTAA
1 GAAGACTGGCTTAATTTCAAGGAAATTAAGTAAA-AAAACACTGGCTTAGTTTCAAGGAAACTAA
*
18284 GTAAAGAAATGACTGGCTTAATTTCAACGAAATTAAGTAAAG
65 GTAAAGAAAAGACTGGCTTAATTTCAACGAAATTAAGTAAAG
* * *
18326 GAAAGACTGGCTTAATTTCAAGGAAATTAA-TTAAAAAACACAGGCTTAATTTC-AGGAAA
1 G-AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAAAAACACTGGCTTAGTTTCAAGGAAA
18385 GGAAATTAAA
Statistics
Matches: 148, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
105 6 0.04
106 46 0.31
107 69 0.47
108 27 0.18
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (106 bp):
GAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAAAAACACTGGCTTAGTTTCAAGGAAACTAAG
TAAAGAAAAGACTGGCTTAATTTCAACGAAATTAAGTAAAG
Found at i:18477 original size:32 final size:35
Alignment explanation
Indices: 18396--18514 Score: 138
Period size: 36 Copynumber: 3.4 Consensus size: 35
18386 GAAATTAAAA
18396 AATAAAGAACTTAATTCAGGGTAATTAAGTGAGGTC
1 AATAAAGAACTTAATTCAGGGTAATTAAGTGAGG-C
*
18432 AATAAA-AGGCTTAATTCAGGGTAATTAAGT-A-G-
1 AATAAAGA-ACTTAATTCAGGGTAATTAAGTGAGGC
* *
18464 AATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTC
1 AATAAAGAACTTAATTCAGGGTAATTAAGTG-AGGC
* *
18500 GATAAACAACTTAAT
1 AATAAAGAACTTAAT
18515 CTAAAAAGAG
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
32 26 0.37
33 1 0.01
34 2 0.03
35 2 0.03
36 40 0.56
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.28
Consensus pattern (35 bp):
AATAAAGAACTTAATTCAGGGTAATTAAGTGAGGC
Found at i:22747 original size:49 final size:49
Alignment explanation
Indices: 22652--22776 Score: 144
Period size: 49 Copynumber: 2.6 Consensus size: 49
22642 TGACTGAAGA
* *
22652 AAATTAAGAGAAGTAAATCTTAAGTCAGCAAAATTAGGGAAAATAAAAG
1 AAATTAAGAGAAGTAAATCTTAATTCAGCAAAATAAGGGAAAATAAAAG
* ** * * *
22701 AAATTAAGAGAAGTAAATCTTAATTTAGTGAACTGAAGGG-ACATAAAGG
1 AAATTAAGAGAAGTAAATCTTAATTCAGCAAAAT-AAGGGAAAATAAAAG
* *
22750 AAATTAAGAGATGTGAATCTTAATTCA
1 AAATTAAGAGAAGTAAATCTTAATTCA
22777 TAGAAATTAA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 60 0.94
50 4 0.06
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (49 bp):
AAATTAAGAGAAGTAAATCTTAATTCAGCAAAATAAGGGAAAATAAAAG
Found at i:22942 original size:16 final size:16
Alignment explanation
Indices: 22921--22951 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22911 AAGAAAAGGC
22921 AGGCTTAATTTCAAGA
1 AGGCTTAATTTCAAGA
*
22937 AGGCTTAGTTTCAAG
1 AGGCTTAATTTCAAG
22952 GAAACTAGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (16 bp):
AGGCTTAATTTCAAGA
Found at i:22963 original size:52 final size:54
Alignment explanation
Indices: 22885--22989 Score: 169
Period size: 52 Copynumber: 2.0 Consensus size: 54
22875 ATCATAGCAC
*
22885 AGGCTTAGTTTGAAGGAAACAAGGTAAAGAAAAG-G-CAGGCTTAATTTCAAGA
1 AGGCTTAGTTTCAAGGAAACAAGGTAAAGAAAAGAGACAGGCTTAATTTCAAGA
* *
22937 AGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGAGACTGGCTTAATTTCAAG
1 AGGCTTAGTTTCAAGGAAACAAGGTAAAGAAAAGAGACAGGCTTAATTTCAAG
22990 TAAAGAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 32 0.67
53 1 0.02
54 15 0.31
ACGTcount: A:0.41, C:0.10, G:0.26, T:0.23
Consensus pattern (54 bp):
AGGCTTAGTTTCAAGGAAACAAGGTAAAGAAAAGAGACAGGCTTAATTTCAAGA
Found at i:22989 original size:38 final size:35
Alignment explanation
Indices: 22938--23048 Score: 116
Period size: 39 Copynumber: 3.0 Consensus size: 35
22928 ATTTCAAGAA
* *
22938 GGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGAGACT
1 GGCTTAATTTCAAGGAAATTAGGTAAAG--AA-AGACT
*
22976 GGCTTAATTTCAAGTAAAGAAATTAGGTAAAGAAAGATT
1 GGCTTAATTTCAAG----GAAATTAGGTAAAGAAAGACT
*
23015 GGCTTAATTTCAAGGAAATTAAGTAAA-AAAGACT
1 GGCTTAATTTCAAGGAAATTAGGTAAAGAAAGACT
23049 AGCTCAGTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
34 6 0.09
35 12 0.19
38 13 0.20
39 18 0.28
40 2 0.03
42 13 0.20
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.25
Consensus pattern (35 bp):
GGCTTAATTTCAAGGAAATTAGGTAAAGAAAGACT
Found at i:23218 original size:106 final size:107
Alignment explanation
Indices: 23092--23294 Score: 383
Period size: 106 Copynumber: 1.9 Consensus size: 107
23082 TAAGCACATA
23092 CTTAATTTCACAAGAATTAAGTAAAATTGACAAAGACTTAATTTCACAAGAATTAAGT-AAATTA
1 CTTAATTTCACAAGAATTAAGTAAAATTGACAAAGACTTAATTTCACAAGAATTAAGTAAAATTA
23156 GCACAA-ACTTAATTTCACAAGAATTAAGTAAATTAACAAAGG
66 GCA-AAGACTTAATTTCACAAGAATTAAGTAAATTAACAAAGG
23198 CTTAATTTCACAAGAATTAAGTAAAATTGACAAAGACTTAATTTCACAAGAATTAAGTAAAATTA
1 CTTAATTTCACAAGAATTAAGTAAAATTGACAAAGACTTAATTTCACAAGAATTAAGTAAAATTA
23263 GCAAAGACTTAATTTCACAAGAATTAAGTAAA
66 GCAAAGACTTAATTTCACAAGAATTAAGTAAA
23295 GTCAGCAAAG
Statistics
Matches: 95, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
106 60 0.63
107 35 0.37
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (107 bp):
CTTAATTTCACAAGAATTAAGTAAAATTGACAAAGACTTAATTTCACAAGAATTAAGTAAAATTA
GCAAAGACTTAATTTCACAAGAATTAAGTAAATTAACAAAGG
Found at i:23302 original size:36 final size:36
Alignment explanation
Indices: 23091--23311 Score: 335
Period size: 36 Copynumber: 6.2 Consensus size: 36
23081 ATAAGCACAT
23091 ACTTAATTTCACAAGAATTAAGTAAAATT-GACAAAG
1 ACTTAATTTCACAAGAATTAAGTAAAATTAG-CAAAG
23127 ACTTAATTTCACAAGAATTAAGT-AAATTAGCACAA-
1 ACTTAATTTCACAAGAATTAAGTAAAATTAGCA-AAG
*
23162 ACTTAATTTCACAAGAATTAAGT-AAATTAACAAAG
1 ACTTAATTTCACAAGAATTAAGTAAAATTAGCAAAG
*
23197 GCTTAATTTCACAAGAATTAAGTAAAATT-GACAAAG
1 ACTTAATTTCACAAGAATTAAGTAAAATTAG-CAAAG
23233 ACTTAATTTCACAAGAATTAAGTAAAATTAGCAAAG
1 ACTTAATTTCACAAGAATTAAGTAAAATTAGCAAAG
* *
23269 ACTTAATTTCACAAGAATTAAGTAAAGTCAGCAAAG
1 ACTTAATTTCACAAGAATTAAGTAAAATTAGCAAAG
*
23305 ATTTAAT
1 ACTTAAT
23312 CCAAAGATGA
Statistics
Matches: 172, Mismatches: 7, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
34 2 0.01
35 60 0.35
36 109 0.63
37 1 0.01
ACGTcount: A:0.49, C:0.12, G:0.11, T:0.29
Consensus pattern (36 bp):
ACTTAATTTCACAAGAATTAAGTAAAATTAGCAAAG
Found at i:23325 original size:36 final size:36
Alignment explanation
Indices: 23091--23353 Score: 261
Period size: 36 Copynumber: 7.3 Consensus size: 36
23081 ATAAGCACAT
* *
23091 ACTTAATTTCACAAGAATTAAGTAAAAT-TGACAAAG
1 ACTTAATTCCACAAGAATTAAGTAAAATCAG-CAAAG
* *
23127 ACTTAATTTCACAAGAATTAAGT-AAATTAGCACAA-
1 ACTTAATTCCACAAGAATTAAGTAAAATCAGCA-AAG
* * *
23162 ACTTAATTTCACAAGAATTAAGT-AAATTAACAAAG
1 ACTTAATTCCACAAGAATTAAGTAAAATCAGCAAAG
* * *
23197 GCTTAATTTCACAAGAATTAAGTAAAAT-TGACAAAG
1 ACTTAATTCCACAAGAATTAAGTAAAATCAG-CAAAG
* *
23233 ACTTAATTTCACAAGAATTAAGTAAAATTAGCAAAG
1 ACTTAATTCCACAAGAATTAAGTAAAATCAGCAAAG
* *
23269 ACTTAATTTCACAAGAATTAAGTAAAGTCAGCAAAG
1 ACTTAATTCCACAAGAATTAAGTAAAATCAGCAAAG
* *
23305 ATTTAA-TCCA-AAGATGATTAAGTAAGATCAGACAAAGG
1 ACTTAATTCCACAAGA--ATTAAGTAAAATCAG-CAAA-G
*
23343 GCTTAATTCCA
1 ACTTAATTCCA
23354 AGGAAATTAG
Statistics
Matches: 201, Mismatches: 15, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
34 6 0.03
35 62 0.31
36 119 0.59
37 5 0.02
38 5 0.02
39 4 0.02
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (36 bp):
ACTTAATTCCACAAGAATTAAGTAAAATCAGCAAAG
Found at i:23392 original size:11 final size:11
Alignment explanation
Indices: 23368--23496 Score: 107
Period size: 11 Copynumber: 10.7 Consensus size: 11
23358 AATTAGGCAA
23368 AAGACTGAAAAG
1 AAGACTG-AAAG
23380 AAGACTGAAAG
1 AAGACTGAAAG
*
23391 AAGACTGAAAAAAAA
1 AAGACTG----AAAG
23406 AAGACTGAAAG
1 AAGACTGAAAG
23417 AAGACTGAAAGAG
1 AAGACTG-AA-AG
*
23430 AAGACTGAAAC
1 AAGACTGAAAG
23441 AAGACTGAAAGAG
1 AAGACTG-AA-AG
*
23454 AAGACTGAAAAAA
1 AAGACTG--AAAG
*
23467 AAAACTGAAAG
1 AAGACTGAAAG
23478 -AGTACTGAAAG
1 AAG-ACTGAAAG
23489 AAGACTGA
1 AAGACTGA
23497 CTTAGTTTCA
Statistics
Matches: 98, Mismatches: 8, Indels: 23
0.76 0.06 0.18
Matches are distributed among these distances:
10 1 0.01
11 45 0.46
12 15 0.15
13 24 0.24
14 3 0.03
15 10 0.10
ACGTcount: A:0.58, C:0.09, G:0.23, T:0.09
Consensus pattern (11 bp):
AAGACTGAAAG
Found at i:23424 original size:37 final size:40
Alignment explanation
Indices: 23366--23463 Score: 129
Period size: 37 Copynumber: 2.6 Consensus size: 40
23356 GAAATTAGGC
23366 AAAAGACTGAAAAGAAGACTG-AA-AGAAGACTGAAAAAA
1 AAAAGACTGAAAAGAAGACTGAAAGAGAAGACTGAAAAAA
23404 AAAAGACTG-AAAGAAGACTGAAAGAGAAGACTG----AA
1 AAAAGACTGAAAAGAAGACTGAAAGAGAAGACTGAAAAAA
*
23439 ACAAGACTGAAAGAGAAGACTGAAA
1 AAAAGACTGAAA-AGAAGACTGAAA
23464 AAAAAAACTG
Statistics
Matches: 55, Mismatches: 1, Indels: 9
0.85 0.02 0.14
Matches are distributed among these distances:
35 10 0.18
36 2 0.04
37 23 0.42
38 11 0.20
39 9 0.16
ACGTcount: A:0.59, C:0.09, G:0.23, T:0.08
Consensus pattern (40 bp):
AAAAGACTGAAAAGAAGACTGAAAGAGAAGACTGAAAAAA
Found at i:23438 original size:24 final size:24
Alignment explanation
Indices: 23368--23496 Score: 147
Period size: 24 Copynumber: 5.3 Consensus size: 24
23358 AATTAGGCAA
23368 AAGACTGAAA-AGAAGACTGAAAG
1 AAGACTGAAAGAGAAGACTGAAAG
* *
23391 AAGACTGAAAAAAAAAAGACTGAAAG
1 AAGACTG--AAAGAGAAGACTGAAAG
*
23417 AAGACTGAAAGAGAAGACTGAAAC
1 AAGACTGAAAGAGAAGACTGAAAG
*
23441 AAGACTGAAAGAGAAGACTGAAAAAA
1 AAGACTGAAAGAGAAGACTG--AAAG
* *
23467 AAAACTGAAAGAG--TACTGAAAG
1 AAGACTGAAAGAGAAGACTGAAAG
23489 AAGACTGA
1 AAGACTGA
23497 CTTAGTTTCA
Statistics
Matches: 92, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
22 10 0.11
23 7 0.08
24 38 0.41
25 3 0.03
26 34 0.37
ACGTcount: A:0.58, C:0.09, G:0.23, T:0.09
Consensus pattern (24 bp):
AAGACTGAAAGAGAAGACTGAAAG
Found at i:23571 original size:36 final size:36
Alignment explanation
Indices: 23489--23724 Score: 257
Period size: 36 Copynumber: 6.7 Consensus size: 36
23479 GTACTGAAAG
* * *
23489 AAGACTGACTTAGTTTCAAGGAAATTACGTAAA-AG
1 AAGACTGGCTTAGTTTCAAGGAAATTAGGTAAAGAA
*
23524 AAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAATTAGGTAAAGAA
* * * *
23560 AAGACTAGCTTAATTTCAAGGAATTTAGGTAAA-AG
1 AAGACTGGCTTAGTTTCAAGGAAATTAGGTAAAGAA
* *
23595 AAGATTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAATTAGGTAAAGAA
* * * *
23631 ATGATTGGCTTAATTTCAAGGAAATTAGGTAAAGGA
1 AAGACTGGCTTAGTTTCAAGGAAATTAGGTAAAGAA
*
23667 AAGACTGGCTT-GATTTCAAGGAAATTAAGTAAA-AA
1 AAGACTGGCTTAG-TTTCAAGGAAATTAGGTAAAGAA
* * * *
23702 GACACAGGCTTAATTTC-AGGAAA
1 AAGACTGGCTTAGTTTCAAGGAAA
23725 GGAAATTAAG
Statistics
Matches: 170, Mismatches: 27, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
34 6 0.04
35 73 0.43
36 91 0.54
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.26
Consensus pattern (36 bp):
AAGACTGGCTTAGTTTCAAGGAAATTAGGTAAAGAA
Found at i:23577 original size:71 final size:71
Alignment explanation
Indices: 23489--23724 Score: 293
Period size: 71 Copynumber: 3.3 Consensus size: 71
23479 GTACTGAAAG
* *
23489 AAGACT-GACTTAGTTTCAAGGAAATTACGTAAAAGAAGACTGGCTTAGTTTCAAGGAAATTAAG
1 AAGACTAG-CTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAATTAAG
23553 TAAAGAA
65 TAAAGAA
* * * *
23560 AAGACTAGCTTAATTTCAAGGAATTTAGGTAAAAGAAGATTGGCTTAGTTTCAAGGAAACTAGGT
1 AAGACTAGCTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAATTAAGT
23625 AAAGAA
66 AAAGAA
* * * *
23631 ATGATTGGCTTAATTTCAAGGAAATTAGGTAAAGGAAAGACTGGCTT-GATTTCAAGGAAATTAA
1 AAGACTAGCTTAATTTCAAGGAAATTAGGTAAAAG-AAGACTGGCTTAG-TTTCAAGGAAATTAA
23695 GTAAA-AA
64 GTAAAGAA
* *
23702 GACAC-AGGCTTAATTTC-AGGAAA
1 AAGACTA-GCTTAATTTCAAGGAAA
23725 GGAAATTAAG
Statistics
Matches: 142, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
70 6 0.04
71 107 0.75
72 29 0.20
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.26
Consensus pattern (71 bp):
AAGACTAGCTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAATTAAGT
AAAGAA
Found at i:23712 original size:107 final size:105
Alignment explanation
Indices: 23497--23724 Score: 282
Period size: 107 Copynumber: 2.2 Consensus size: 105
23487 AGAAGACTGA
* *
23497 CTTAGTTTCAAGGAAATTACGTAAAAGAAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAGAAAA
1 CTTAGTTTCAAGGAAACTACGTAAAAGAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAAA
* * *
23562 GACTAGCTTAATTTCAAGGAATTTAGGTAAAAGAAGATTGG
66 GACTAGCTTAATTTCAAGGAAATTAAGTAAAAGAACA-TGG
* * * *
23603 CTTAGTTTCAAGGAAACTAGGT-AAAGAAATGATTGGCTTAATTTCAAGGAAATTAGGTAAAGGA
1 CTTAGTTTCAAGGAAACTACGTAAAAG-AA-GACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* *
23667 AAGACTGGCTTGATTTCAAGGAAATTAAGTAAAAAGACACA-GG
64 AAGACTAGCTTAATTTCAAGGAAATTAAGT-AAAAGA-ACATGG
*
23710 CTTAATTTC-AGGAAA
1 CTTAGTTTCAAGGAAA
23725 GGAAATTAAG
Statistics
Matches: 106, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
105 4 0.04
106 28 0.26
107 66 0.62
108 6 0.06
109 2 0.02
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (105 bp):
CTTAGTTTCAAGGAAACTACGTAAAAGAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAAA
GACTAGCTTAATTTCAAGGAAATTAAGTAAAAGAACATGG
Found at i:23778 original size:36 final size:34
Alignment explanation
Indices: 23738--23856 Score: 129
Period size: 36 Copynumber: 3.4 Consensus size: 34
23728 AATTAAGTAA
23738 AATAAAGAACTTAATTCAGTGTAATTAAGTGAGGTC
1 AATAAAGAACTTAATTCAG-GTAATTAAGTGA-GTC
**
23774 AATAAA-AGGTTTAATTCAGGGTAATTAAGT-AG--
1 AATAAAGA-ACTTAATTCA-GGTAATTAAGTGAGTC
*
23806 AATAAAGAACTTAATTCAAGGTAATTAAGTGAAATC
1 AATAAAGAACTTAATTC-AGGTAATTAAGTG-AGTC
23842 AATAAAGAACTTAAT
1 AATAAAGAACTTAAT
23857 CAAAAAAAGA
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
32 24 0.34
33 2 0.03
34 2 0.03
35 2 0.03
36 39 0.56
37 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.29
Consensus pattern (34 bp):
AATAAAGAACTTAATTCAGGTAATTAAGTGAGTC
Found at i:23856 original size:68 final size:68
Alignment explanation
Indices: 23728--23856 Score: 181
Period size: 68 Copynumber: 1.9 Consensus size: 68
23718 CAGGAAAGGA
** **
23728 AATTAAGTAAAATAAAGAACTTAATTCAGTGTAATTAAGTGAGGTCAATAAAAGGTTTAATTCAG
1 AATTAAGTAAAATAAAGAACTTAATTCAGTGTAATTAAGTGAAATCAATAAAAGACTTAATTCAG
23793 GGT
66 GGT
*
23796 AATTAAGTAGAATAAAGAACTTAATTCAAG-GTAATTAAGTGAAATCAAT-AAAGAACTTAAT
1 AATTAAGTAAAATAAAGAACTTAATTC-AGTGTAATTAAGTGAAATCAATAAAAG-ACTTAAT
23857 CAAAAAAAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
67 4 0.07
68 48 0.89
69 2 0.04
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.29
Consensus pattern (68 bp):
AATTAAGTAAAATAAAGAACTTAATTCAGTGTAATTAAGTGAAATCAATAAAAGACTTAATTCAG
GGT
Found at i:25928 original size:230 final size:230
Alignment explanation
Indices: 25504--25967 Score: 693
Period size: 230 Copynumber: 2.0 Consensus size: 230
25494 ATTAAGCCTT
* * *
25504 CTTTTGTCCTCATTGTCCGATGGAAAGTGTTTAGATGCCTCGTCCATGTACACACCTCATTTCAT
1 CTTTTGTCCCCATTGTCCGATGGAAAGTGTTTAGATGCCTCATCCATGTACAAACCTCATTTCAT
* *
25569 TCAAGGATAGCATCATTACTCATGTTATAACTTGTCATAACATTCATCTGCATCATTTGCATAAA
66 TCAAGGATAG-------ACTCATGTTATAACTTGCCATAACATTCATCTGCATCAATT-CATAAA
25634 GGCAAGAACCCTGATTATTCACAGAATTGTAAATGGTCACGACTTTTAGCTTGTGGAAGTTCCTA
123 GGCAAGAACCCTGATTATTCACAGAATTGTAAATGGTCACGACTTTTAGCTTGTGGAAGTTCCTA
25699 CCAAATTGTGGAGGGACTCCACACCTTTAAAAATCTTAACTAC
188 CCAAATTGTGGAGGGACTCCACACCTTTAAAAATCTTAACTAC
*
25742 CTTTTGTCCCCATTTGTCCGGTGGCAAA-TGTTTAGATGCCTCATCCATGTACAAACCTCATTTC
1 CTTTTGTCCCCA-TTGTCCGATGG-AAAGTGTTTAGATGCCTCATCCATGTACAAACCTCATTTC
* *
25806 ATTCAAGGATAG-CTCATGTTATAATTTGCCGTAACATTCAT-TCGCATCAATT-ATAAATGGCA
64 ATTCAAGGATAGACTCATGTTATAACTTGCCATAACATTCATCT-GCATCAATTCATAAA-GGCA
* *
25868 AGAACCCTGATTATTCACAGAATTGTAAATGGTCACGGCTTTTGGCTTGTGGAAGTTCCTACCAA
127 AGAACCCTGATTATTCACAGAATTGTAAATGGTCACGACTTTTAGCTTGTGGAAGTTCCTACCAA
*
25933 ATTGTGGAGGGACTCCACACCTTTAAAGATCTTAA
192 ATTGTGGAGGGACTCCACACCTTTAAAAATCTTAA
25968 ATAACTTGGT
Statistics
Matches: 211, Mismatches: 11, Indels: 16
0.89 0.05 0.07
Matches are distributed among these distances:
229 5 0.02
230 102 0.48
231 34 0.16
238 11 0.05
239 56 0.27
240 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (230 bp):
CTTTTGTCCCCATTGTCCGATGGAAAGTGTTTAGATGCCTCATCCATGTACAAACCTCATTTCAT
TCAAGGATAGACTCATGTTATAACTTGCCATAACATTCATCTGCATCAATTCATAAAGGCAAGAA
CCCTGATTATTCACAGAATTGTAAATGGTCACGACTTTTAGCTTGTGGAAGTTCCTACCAAATTG
TGGAGGGACTCCACACCTTTAAAAATCTTAACTAC
Found at i:26484 original size:21 final size:21
Alignment explanation
Indices: 26460--26522 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
26450 ATGCATACAT
26460 TATATATTAGGCAATCATTTG
1 TATATATTAGGCAATCATTTG
26481 TATATA-T---C-ATACA--T-
1 TATATATTAGGCAAT-CATTTG
26495 TATATATTAGGCAATCATTTG
1 TATATATTAGGCAATCATTTG
26516 TATATAT
1 TATATAT
26523 CATGCAACCA
Statistics
Matches: 33, Mismatches: 0, Indels: 18
0.65 0.00 0.35
Matches are distributed among these distances:
14 6 0.18
15 2 0.06
16 2 0.06
17 3 0.09
18 3 0.09
19 2 0.06
20 2 0.06
21 13 0.39
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (21 bp):
TATATATTAGGCAATCATTTG
Found at i:26499 original size:35 final size:35
Alignment explanation
Indices: 26453--26525 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
26443 TACGCTCATG
26453 CATACATTATATATTAGGCAATCATTTGTATATAT
1 CATACATTATATATTAGGCAATCATTTGTATATAT
26488 CATACATTATATATTAGGCAATCATTTGTATATAT
1 CATACATTATATATTAGGCAATCATTTGTATATAT
26523 CAT
1 CAT
26526 GCAACCATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.42
Consensus pattern (35 bp):
CATACATTATATATTAGGCAATCATTTGTATATAT
Done.