Multiple sequence alignment - TraesCS7D01G526000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G526000 chr7D 100.000 6380 0 0 1 6380 621488364 621481985 0.000000e+00 11782.0
1 TraesCS7D01G526000 chr7D 93.204 103 7 0 684 786 368886914 368887016 1.110000e-32 152.0
2 TraesCS7D01G526000 chr7D 86.957 115 13 2 6002 6115 483282718 483282831 1.870000e-25 128.0
3 TraesCS7D01G526000 chr7D 86.170 94 6 2 3080 3173 548805135 548805221 1.890000e-15 95.3
4 TraesCS7D01G526000 chr7B 94.430 3806 135 26 1987 5734 718467936 718471722 0.000000e+00 5782.0
5 TraesCS7D01G526000 chr7B 96.741 1258 32 3 768 2022 718466684 718467935 0.000000e+00 2087.0
6 TraesCS7D01G526000 chr7B 89.520 687 45 9 17 689 718466010 718466683 0.000000e+00 845.0
7 TraesCS7D01G526000 chr7B 93.156 263 12 2 5859 6115 718471737 718471999 1.300000e-101 381.0
8 TraesCS7D01G526000 chr7A 91.017 2026 110 27 1990 3991 717040161 717038184 0.000000e+00 2667.0
9 TraesCS7D01G526000 chr7A 95.288 1252 52 3 772 2022 717041410 717040165 0.000000e+00 1978.0
10 TraesCS7D01G526000 chr7A 92.632 1398 58 23 4332 5710 717037826 717036455 0.000000e+00 1969.0
11 TraesCS7D01G526000 chr7A 92.000 350 22 3 5768 6115 717036455 717036110 2.670000e-133 486.0
12 TraesCS7D01G526000 chr7A 89.412 340 27 4 4017 4348 717038185 717037847 2.750000e-113 420.0
13 TraesCS7D01G526000 chr7A 85.116 430 36 11 1 420 717042227 717041816 1.280000e-111 414.0
14 TraesCS7D01G526000 chr7A 89.011 273 22 4 415 687 717041676 717041412 1.330000e-86 331.0
15 TraesCS7D01G526000 chr4D 95.918 98 4 0 676 773 191234896 191234799 6.620000e-35 159.0
16 TraesCS7D01G526000 chr6D 96.842 95 2 1 687 781 443958604 443958511 2.380000e-34 158.0
17 TraesCS7D01G526000 chr6D 86.957 115 13 2 6002 6115 164765800 164765913 1.870000e-25 128.0
18 TraesCS7D01G526000 chr4A 94.949 99 5 0 687 785 544888202 544888300 8.560000e-34 156.0
19 TraesCS7D01G526000 chr4A 93.269 104 7 0 679 782 698479951 698479848 3.080000e-33 154.0
20 TraesCS7D01G526000 chr2D 93.396 106 5 1 679 782 631239697 631239802 8.560000e-34 156.0
21 TraesCS7D01G526000 chr2D 91.667 60 5 0 3076 3135 27601158 27601217 4.100000e-12 84.2
22 TraesCS7D01G526000 chr5A 97.753 89 2 0 683 771 455446984 455447072 3.080000e-33 154.0
23 TraesCS7D01G526000 chr5A 84.444 135 19 2 5982 6115 547211307 547211440 1.440000e-26 132.0
24 TraesCS7D01G526000 chr1B 96.667 90 3 0 686 775 555953798 555953887 3.980000e-32 150.0
25 TraesCS7D01G526000 chr3D 91.667 108 7 2 671 778 535817324 535817429 1.430000e-31 148.0
26 TraesCS7D01G526000 chr1D 86.567 134 18 0 5982 6115 149057866 149057999 1.430000e-31 148.0
27 TraesCS7D01G526000 chr1D 83.704 135 20 2 5982 6115 48792933 48792800 6.720000e-25 126.0
28 TraesCS7D01G526000 chr3B 86.923 130 15 2 5982 6110 70690757 70690885 1.850000e-30 145.0
29 TraesCS7D01G526000 chr3B 87.500 120 13 2 5992 6110 674484607 674484489 3.100000e-28 137.0
30 TraesCS7D01G526000 chr2A 85.567 97 12 2 3078 3173 14959774 14959869 4.070000e-17 100.0
31 TraesCS7D01G526000 chr4B 94.828 58 3 0 3078 3135 604049703 604049646 2.450000e-14 91.6
32 TraesCS7D01G526000 chr4B 94.737 57 2 1 3080 3135 465733240 465733296 3.170000e-13 87.9
33 TraesCS7D01G526000 chr1A 98.039 51 1 0 3085 3135 236718398 236718448 8.810000e-14 89.8
34 TraesCS7D01G526000 chr5D 96.226 53 2 0 3082 3134 60476969 60477021 3.170000e-13 87.9
35 TraesCS7D01G526000 chr6A 97.222 36 1 0 3136 3171 20255177 20255142 1.920000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G526000 chr7D 621481985 621488364 6379 True 11782.000000 11782 100.000000 1 6380 1 chr7D.!!$R1 6379
1 TraesCS7D01G526000 chr7B 718466010 718471999 5989 False 2273.750000 5782 93.461750 17 6115 4 chr7B.!!$F1 6098
2 TraesCS7D01G526000 chr7A 717036110 717042227 6117 True 1180.714286 2667 90.639429 1 6115 7 chr7A.!!$R1 6114

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
267 283 0.388649 GTAGTATGCCGCCTCCATCG 60.389 60.000 0.00 0.00 0.00 3.84 F
1660 1832 1.971167 GGGTTGGTCGCATGCTCAA 60.971 57.895 17.13 14.04 0.00 3.02 F
1975 2147 1.239296 TGCAAGCAGCTGGTAGCAAG 61.239 55.000 20.51 8.21 45.56 4.01 F
2507 2720 1.398692 GGCTGAACCTTTGTCACCAA 58.601 50.000 0.00 0.00 34.51 3.67 F
3745 3986 0.620556 CATTACCAGTGGAGTGCCCT 59.379 55.000 18.40 0.00 35.38 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 2001 0.399949 TGGATAAGGTCTGCCCCGAT 60.400 55.000 0.00 0.00 34.57 4.18 R
2791 3004 0.108424 GCTGATCAGAAGCTCGTGGT 60.108 55.000 27.04 0.00 37.69 4.16 R
3203 3418 1.033746 AGCATCGAACAGGCCCATTG 61.034 55.000 0.00 0.00 0.00 2.82 R
4253 4499 4.645588 CCAAACAACCCACAACCTTTAGTA 59.354 41.667 0.00 0.00 0.00 1.82 R
5667 5985 0.179037 ATCACCATCCGGATGTGCTG 60.179 55.000 36.09 27.53 37.11 4.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 57 6.154021 GGCCGTTAACCCTAGAATCATAGATA 59.846 42.308 0.00 0.00 0.00 1.98
83 89 2.362120 GGCTGCCCACTCTTGCAT 60.362 61.111 7.66 0.00 36.79 3.96
104 110 7.522542 TGCATAATTGAGGCTTTTAGGGTATA 58.477 34.615 0.00 0.00 35.30 1.47
224 240 4.529769 TGATTAACAAATGCCATGGAACCA 59.470 37.500 18.40 4.12 0.00 3.67
249 265 5.432060 AGTTAAGGATAATACCCTGCTTGGT 59.568 40.000 3.23 3.23 42.62 3.67
257 273 0.546598 ACCCTGCTTGGTAGTATGCC 59.453 55.000 0.00 0.00 43.46 4.40
267 283 0.388649 GTAGTATGCCGCCTCCATCG 60.389 60.000 0.00 0.00 0.00 3.84
342 359 2.263895 ATGCTTGGTAGTAGGGGTCA 57.736 50.000 0.00 0.00 0.00 4.02
454 615 9.567776 TGGAAAAATTGTCTATGAACTCTAACA 57.432 29.630 0.00 0.00 0.00 2.41
502 663 3.752747 TCCTGTGTGTTCTATGCATGTTG 59.247 43.478 10.16 0.00 0.00 3.33
574 743 2.760092 GGGCATTAACTCCATGCTTTCA 59.240 45.455 4.97 0.00 45.49 2.69
681 850 6.866770 TCTGTATGAGCTGTTAGTGTTGTTAC 59.133 38.462 0.00 0.00 0.00 2.50
689 858 7.442656 AGCTGTTAGTGTTGTTACTTCATACT 58.557 34.615 0.00 0.00 32.19 2.12
690 859 7.599245 AGCTGTTAGTGTTGTTACTTCATACTC 59.401 37.037 0.00 0.00 32.19 2.59
691 860 7.148623 GCTGTTAGTGTTGTTACTTCATACTCC 60.149 40.741 0.00 0.00 32.19 3.85
692 861 7.156673 TGTTAGTGTTGTTACTTCATACTCCC 58.843 38.462 0.00 0.00 32.19 4.30
693 862 7.015877 TGTTAGTGTTGTTACTTCATACTCCCT 59.984 37.037 0.00 0.00 32.19 4.20
694 863 6.038997 AGTGTTGTTACTTCATACTCCCTC 57.961 41.667 0.00 0.00 0.00 4.30
695 864 5.780793 AGTGTTGTTACTTCATACTCCCTCT 59.219 40.000 0.00 0.00 0.00 3.69
696 865 5.869888 GTGTTGTTACTTCATACTCCCTCTG 59.130 44.000 0.00 0.00 0.00 3.35
697 866 5.542635 TGTTGTTACTTCATACTCCCTCTGT 59.457 40.000 0.00 0.00 0.00 3.41
698 867 6.722590 TGTTGTTACTTCATACTCCCTCTGTA 59.277 38.462 0.00 0.00 0.00 2.74
699 868 7.233962 TGTTGTTACTTCATACTCCCTCTGTAA 59.766 37.037 0.00 0.00 0.00 2.41
700 869 7.786046 TGTTACTTCATACTCCCTCTGTAAA 57.214 36.000 0.00 0.00 0.00 2.01
701 870 7.609056 TGTTACTTCATACTCCCTCTGTAAAC 58.391 38.462 0.00 0.00 0.00 2.01
702 871 7.453752 TGTTACTTCATACTCCCTCTGTAAACT 59.546 37.037 0.00 0.00 0.00 2.66
703 872 8.964772 GTTACTTCATACTCCCTCTGTAAACTA 58.035 37.037 0.00 0.00 0.00 2.24
704 873 9.537852 TTACTTCATACTCCCTCTGTAAACTAA 57.462 33.333 0.00 0.00 0.00 2.24
705 874 8.611051 ACTTCATACTCCCTCTGTAAACTAAT 57.389 34.615 0.00 0.00 0.00 1.73
706 875 9.710818 ACTTCATACTCCCTCTGTAAACTAATA 57.289 33.333 0.00 0.00 0.00 0.98
713 882 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
714 883 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
715 884 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
716 885 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
717 886 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
734 903 9.570488 AAGAGCGTTTAGATTACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
735 904 8.954350 AGAGCGTTTAGATTACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
736 905 9.733219 GAGCGTTTAGATTACTAAAGTAGTGAT 57.267 33.333 0.00 0.00 45.42 3.06
737 906 9.733219 AGCGTTTAGATTACTAAAGTAGTGATC 57.267 33.333 10.62 10.62 46.38 2.92
765 934 9.490379 AAATGCTCTTATATTAGTTTACGGAGG 57.510 33.333 0.00 0.00 0.00 4.30
766 935 6.989659 TGCTCTTATATTAGTTTACGGAGGG 58.010 40.000 0.00 0.00 0.00 4.30
770 939 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
1019 1191 3.338249 TCATGAAGCCTGAAGTTACTGC 58.662 45.455 0.00 0.00 0.00 4.40
1043 1215 6.089954 GCTCATTTGCCAAAATCAGAAAGTAC 59.910 38.462 0.00 0.00 33.59 2.73
1052 1224 8.088365 GCCAAAATCAGAAAGTACTAAACCAAT 58.912 33.333 0.00 0.00 0.00 3.16
1607 1779 3.741344 CCGATGAAGGTAATTAAGGCTCG 59.259 47.826 0.00 0.00 0.00 5.03
1639 1811 4.053295 CAATTCAAAGCCAGTGGTTTCTG 58.947 43.478 12.10 11.95 40.06 3.02
1660 1832 1.971167 GGGTTGGTCGCATGCTCAA 60.971 57.895 17.13 14.04 0.00 3.02
1735 1907 4.637534 CACCTGATACCTTCATTCACTTGG 59.362 45.833 0.00 0.00 32.72 3.61
1753 1925 8.472007 TCACTTGGTTATTTGGTATTTTGTCT 57.528 30.769 0.00 0.00 0.00 3.41
1755 1927 9.541143 CACTTGGTTATTTGGTATTTTGTCTTT 57.459 29.630 0.00 0.00 0.00 2.52
1829 2001 4.640789 AATTAAGTTTTGTGTGCGTGGA 57.359 36.364 0.00 0.00 0.00 4.02
1908 2080 6.206829 GCCACAAACTTTTCAGGACTATACTT 59.793 38.462 0.00 0.00 0.00 2.24
1911 2083 9.665264 CACAAACTTTTCAGGACTATACTTTTC 57.335 33.333 0.00 0.00 0.00 2.29
1919 2091 7.718334 TCAGGACTATACTTTTCTGTCATGA 57.282 36.000 0.00 0.00 43.11 3.07
1975 2147 1.239296 TGCAAGCAGCTGGTAGCAAG 61.239 55.000 20.51 8.21 45.56 4.01
1988 2160 2.238898 GGTAGCAAGGAGGGCTCTTTAA 59.761 50.000 0.00 0.00 42.62 1.52
2016 2224 2.028561 ATCCCATGCACCAAGGTTTT 57.971 45.000 0.00 0.00 0.00 2.43
2022 2230 2.663826 TGCACCAAGGTTTTGACAAC 57.336 45.000 0.00 0.00 36.36 3.32
2038 2251 2.801111 GACAACGAGTTCCCTTCTGTTC 59.199 50.000 0.00 0.00 0.00 3.18
2507 2720 1.398692 GGCTGAACCTTTGTCACCAA 58.601 50.000 0.00 0.00 34.51 3.67
2791 3004 7.954666 AAGGCAGCAAGAAGGTAATAATTAA 57.045 32.000 0.00 0.00 0.00 1.40
2875 3088 7.152645 TCTGTGAGTTTGGTCAAGTATCTTAC 58.847 38.462 0.00 0.00 0.00 2.34
2888 3101 4.437239 AGTATCTTACATGTGCACTGAGC 58.563 43.478 19.41 0.00 45.96 4.26
2889 3102 3.623906 ATCTTACATGTGCACTGAGCT 57.376 42.857 19.41 0.00 45.94 4.09
3185 3400 7.168905 GGGAACAGAGGGTTTATAAGATATGG 58.831 42.308 0.00 0.00 40.63 2.74
3297 3536 9.466497 AAGTGAGGCTTGATATTTTATCTTGAA 57.534 29.630 0.00 0.00 35.80 2.69
3530 3769 6.384305 ACTGGCTAGGAACTGATAGTTATTGT 59.616 38.462 0.85 0.00 38.80 2.71
3539 3778 5.962433 ACTGATAGTTATTGTGTGCTACGT 58.038 37.500 0.00 0.00 0.00 3.57
3541 3780 7.713750 ACTGATAGTTATTGTGTGCTACGTAT 58.286 34.615 0.00 0.00 0.00 3.06
3745 3986 0.620556 CATTACCAGTGGAGTGCCCT 59.379 55.000 18.40 0.00 35.38 5.19
3870 4114 4.769345 TGAGGCATATGTACACATTGGA 57.231 40.909 0.00 0.00 37.76 3.53
3922 4166 3.055385 TCAGGGACCATTGCTGTACTTAC 60.055 47.826 0.00 0.00 0.00 2.34
4172 4416 6.569179 TTCAAAGGGTAGCTGTTATTTGTC 57.431 37.500 0.00 0.00 0.00 3.18
4180 4424 6.992715 GGGTAGCTGTTATTTGTCTGATATGT 59.007 38.462 0.00 0.00 0.00 2.29
4253 4499 3.631227 GCGTCTGGTATGTAAGTCTAGGT 59.369 47.826 0.00 0.00 0.00 3.08
4302 4548 1.669999 CCGACTTACCCCTGTACCGG 61.670 65.000 0.00 0.00 32.26 5.28
4762 5057 3.085533 ACACCATTGCCGTTAAATGCTA 58.914 40.909 0.00 0.00 34.35 3.49
4897 5193 1.190643 AGAAGAGGGAGCGAGAAAGG 58.809 55.000 0.00 0.00 0.00 3.11
5002 5300 3.254657 CGTGGCTATTCAACCTTTTTCCA 59.745 43.478 0.00 0.00 0.00 3.53
5278 5576 4.489771 CACCCTCCGTGGATGCCC 62.490 72.222 0.00 0.00 38.96 5.36
5301 5599 0.249911 GCATATCACCACCCTCCGTC 60.250 60.000 0.00 0.00 0.00 4.79
5343 5641 2.912956 ACCCGCTGTGGATATGGATATT 59.087 45.455 9.25 0.00 42.00 1.28
5565 5879 8.661352 ATGTTCTGTAAAACAATTGGAAAAGG 57.339 30.769 10.83 0.00 42.10 3.11
5569 5883 8.299990 TCTGTAAAACAATTGGAAAAGGAGAA 57.700 30.769 10.83 0.00 0.00 2.87
5667 5985 1.444119 TTTTGCCTGCAGTCGTGACC 61.444 55.000 13.81 0.00 0.00 4.02
5694 6030 0.392863 CCGGATGGTGATGCACAGAA 60.393 55.000 0.00 0.00 35.86 3.02
5709 6045 0.806102 CAGAATGGCCGACAGGTACG 60.806 60.000 0.00 0.00 40.50 3.67
5734 6070 3.066481 CAGGGTAACTACGCTAGGACTTC 59.934 52.174 6.17 0.00 46.10 3.01
5735 6071 3.019564 GGGTAACTACGCTAGGACTTCA 58.980 50.000 0.00 0.00 36.36 3.02
5736 6072 3.181492 GGGTAACTACGCTAGGACTTCAC 60.181 52.174 0.00 0.00 36.36 3.18
5737 6073 3.693578 GGTAACTACGCTAGGACTTCACT 59.306 47.826 0.00 0.00 0.00 3.41
5738 6074 4.201901 GGTAACTACGCTAGGACTTCACTC 60.202 50.000 0.00 0.00 0.00 3.51
5739 6075 3.069079 ACTACGCTAGGACTTCACTCA 57.931 47.619 0.00 0.00 0.00 3.41
5740 6076 3.622630 ACTACGCTAGGACTTCACTCAT 58.377 45.455 0.00 0.00 0.00 2.90
5741 6077 4.778579 ACTACGCTAGGACTTCACTCATA 58.221 43.478 0.00 0.00 0.00 2.15
5742 6078 4.575645 ACTACGCTAGGACTTCACTCATAC 59.424 45.833 0.00 0.00 0.00 2.39
5743 6079 3.353557 ACGCTAGGACTTCACTCATACA 58.646 45.455 0.00 0.00 0.00 2.29
5744 6080 3.954904 ACGCTAGGACTTCACTCATACAT 59.045 43.478 0.00 0.00 0.00 2.29
5745 6081 4.202060 ACGCTAGGACTTCACTCATACATG 60.202 45.833 0.00 0.00 0.00 3.21
5746 6082 4.202060 CGCTAGGACTTCACTCATACATGT 60.202 45.833 2.69 2.69 0.00 3.21
5747 6083 5.046529 GCTAGGACTTCACTCATACATGTG 58.953 45.833 9.11 0.00 35.68 3.21
5748 6084 5.163509 GCTAGGACTTCACTCATACATGTGA 60.164 44.000 9.11 0.00 40.86 3.58
5749 6085 5.946942 AGGACTTCACTCATACATGTGAT 57.053 39.130 9.11 0.00 41.93 3.06
5750 6086 5.668471 AGGACTTCACTCATACATGTGATG 58.332 41.667 9.11 8.56 41.93 3.07
5751 6087 4.813161 GGACTTCACTCATACATGTGATGG 59.187 45.833 9.11 5.68 41.93 3.51
5752 6088 4.194640 ACTTCACTCATACATGTGATGGC 58.805 43.478 9.11 0.00 41.93 4.40
5753 6089 4.080695 ACTTCACTCATACATGTGATGGCT 60.081 41.667 9.11 0.00 41.93 4.75
5754 6090 3.800531 TCACTCATACATGTGATGGCTG 58.199 45.455 9.11 7.43 38.15 4.85
5755 6091 3.198417 TCACTCATACATGTGATGGCTGT 59.802 43.478 9.11 6.27 38.15 4.40
5756 6092 3.558829 CACTCATACATGTGATGGCTGTC 59.441 47.826 9.11 0.00 36.38 3.51
5757 6093 3.198417 ACTCATACATGTGATGGCTGTCA 59.802 43.478 9.11 0.00 33.60 3.58
5758 6094 3.800531 TCATACATGTGATGGCTGTCAG 58.199 45.455 9.11 0.00 33.60 3.51
5759 6095 3.451902 TCATACATGTGATGGCTGTCAGA 59.548 43.478 9.11 0.00 33.60 3.27
5760 6096 4.102054 TCATACATGTGATGGCTGTCAGAT 59.898 41.667 9.11 0.00 32.88 2.90
5761 6097 2.915349 ACATGTGATGGCTGTCAGATC 58.085 47.619 3.32 0.00 30.51 2.75
5762 6098 2.237893 ACATGTGATGGCTGTCAGATCA 59.762 45.455 3.32 1.98 30.51 2.92
5763 6099 3.275999 CATGTGATGGCTGTCAGATCAA 58.724 45.455 3.32 0.00 30.51 2.57
5764 6100 2.703416 TGTGATGGCTGTCAGATCAAC 58.297 47.619 3.32 0.88 0.00 3.18
5765 6101 2.303890 TGTGATGGCTGTCAGATCAACT 59.696 45.455 3.32 0.00 0.00 3.16
5766 6102 3.244665 TGTGATGGCTGTCAGATCAACTT 60.245 43.478 3.32 0.00 0.00 2.66
5792 6128 0.679505 TCTGAAACTGACACTCGGGG 59.320 55.000 0.00 0.00 0.00 5.73
5793 6129 0.320771 CTGAAACTGACACTCGGGGG 60.321 60.000 0.00 0.00 0.00 5.40
5804 6140 1.815421 CTCGGGGGAGTTTCATGCG 60.815 63.158 0.00 0.00 0.00 4.73
5808 6144 1.305930 GGGGGAGTTTCATGCGTGAC 61.306 60.000 8.48 0.00 33.11 3.67
5819 6155 1.738908 CATGCGTGACCATGAACATGA 59.261 47.619 15.21 0.00 44.12 3.07
5837 6173 1.271543 TGAAAGATGCTGGGTGTCCTG 60.272 52.381 0.00 0.00 35.38 3.86
5849 6187 1.301716 TGTCCTGCCGCTTCAAGTC 60.302 57.895 0.00 0.00 0.00 3.01
5856 6194 0.668535 GCCGCTTCAAGTCCAAAACT 59.331 50.000 0.00 0.00 41.10 2.66
5860 6198 3.813166 CCGCTTCAAGTCCAAAACTTCTA 59.187 43.478 0.00 0.00 45.28 2.10
5990 6334 3.955145 TGGTACATGAAGGGTGCAG 57.045 52.632 0.00 0.00 0.00 4.41
6000 6344 2.600470 GGGTGCAGTTGGTTCCCC 60.600 66.667 0.00 0.00 32.66 4.81
6094 6438 5.417266 TGCGTAATTCAAAGGAATGGAATGA 59.583 36.000 0.00 0.00 42.87 2.57
6135 6479 8.948631 TGGTTAAATTTTGTAAGTTTGATGCA 57.051 26.923 0.00 0.00 0.00 3.96
6136 6480 8.821894 TGGTTAAATTTTGTAAGTTTGATGCAC 58.178 29.630 0.00 0.00 0.00 4.57
6137 6481 8.279800 GGTTAAATTTTGTAAGTTTGATGCACC 58.720 33.333 0.00 0.00 0.00 5.01
6138 6482 8.821894 GTTAAATTTTGTAAGTTTGATGCACCA 58.178 29.630 0.00 0.00 0.00 4.17
6139 6483 6.843069 AATTTTGTAAGTTTGATGCACCAC 57.157 33.333 0.00 0.00 0.00 4.16
6140 6484 4.314740 TTTGTAAGTTTGATGCACCACC 57.685 40.909 0.00 0.00 0.00 4.61
6141 6485 3.222173 TGTAAGTTTGATGCACCACCT 57.778 42.857 0.00 0.00 0.00 4.00
6142 6486 3.561143 TGTAAGTTTGATGCACCACCTT 58.439 40.909 0.00 0.00 0.00 3.50
6143 6487 4.720046 TGTAAGTTTGATGCACCACCTTA 58.280 39.130 0.00 0.00 0.00 2.69
6144 6488 5.133941 TGTAAGTTTGATGCACCACCTTAA 58.866 37.500 1.76 0.00 0.00 1.85
6145 6489 4.853924 AAGTTTGATGCACCACCTTAAG 57.146 40.909 0.00 0.00 0.00 1.85
6146 6490 2.558359 AGTTTGATGCACCACCTTAAGC 59.442 45.455 0.00 0.00 0.00 3.09
6147 6491 2.284754 TTGATGCACCACCTTAAGCA 57.715 45.000 0.00 0.00 41.73 3.91
6148 6492 2.284754 TGATGCACCACCTTAAGCAA 57.715 45.000 0.00 0.00 40.76 3.91
6149 6493 2.806434 TGATGCACCACCTTAAGCAAT 58.194 42.857 0.00 0.00 40.76 3.56
6150 6494 3.961849 TGATGCACCACCTTAAGCAATA 58.038 40.909 0.00 0.00 40.76 1.90
6151 6495 4.339748 TGATGCACCACCTTAAGCAATAA 58.660 39.130 0.00 0.00 40.76 1.40
6152 6496 4.769488 TGATGCACCACCTTAAGCAATAAA 59.231 37.500 0.00 0.00 40.76 1.40
6153 6497 4.782019 TGCACCACCTTAAGCAATAAAG 57.218 40.909 0.00 0.00 33.48 1.85
6154 6498 4.402829 TGCACCACCTTAAGCAATAAAGA 58.597 39.130 0.00 0.00 33.48 2.52
6155 6499 4.217550 TGCACCACCTTAAGCAATAAAGAC 59.782 41.667 0.00 0.00 33.48 3.01
6156 6500 4.380550 GCACCACCTTAAGCAATAAAGACC 60.381 45.833 0.00 0.00 0.00 3.85
6157 6501 5.010282 CACCACCTTAAGCAATAAAGACCT 58.990 41.667 0.00 0.00 0.00 3.85
6158 6502 5.123979 CACCACCTTAAGCAATAAAGACCTC 59.876 44.000 0.00 0.00 0.00 3.85
6159 6503 4.640647 CCACCTTAAGCAATAAAGACCTCC 59.359 45.833 0.00 0.00 0.00 4.30
6160 6504 5.501156 CACCTTAAGCAATAAAGACCTCCT 58.499 41.667 0.00 0.00 0.00 3.69
6161 6505 5.946377 CACCTTAAGCAATAAAGACCTCCTT 59.054 40.000 0.00 0.00 36.47 3.36
6162 6506 6.434340 CACCTTAAGCAATAAAGACCTCCTTT 59.566 38.462 0.00 0.00 46.21 3.11
6163 6507 6.659668 ACCTTAAGCAATAAAGACCTCCTTTC 59.340 38.462 0.00 0.00 43.61 2.62
6164 6508 6.095580 CCTTAAGCAATAAAGACCTCCTTTCC 59.904 42.308 0.00 0.00 43.61 3.13
6165 6509 3.969553 AGCAATAAAGACCTCCTTTCCC 58.030 45.455 0.00 0.00 43.61 3.97
6166 6510 3.024547 GCAATAAAGACCTCCTTTCCCC 58.975 50.000 0.00 0.00 43.61 4.81
6167 6511 3.632333 CAATAAAGACCTCCTTTCCCCC 58.368 50.000 0.00 0.00 43.61 5.40
6168 6512 1.282382 TAAAGACCTCCTTTCCCCCG 58.718 55.000 0.00 0.00 43.61 5.73
6169 6513 2.138453 AAAGACCTCCTTTCCCCCGC 62.138 60.000 0.00 0.00 40.97 6.13
6170 6514 3.327404 GACCTCCTTTCCCCCGCA 61.327 66.667 0.00 0.00 0.00 5.69
6171 6515 2.856988 ACCTCCTTTCCCCCGCAA 60.857 61.111 0.00 0.00 0.00 4.85
6172 6516 2.420466 GACCTCCTTTCCCCCGCAAA 62.420 60.000 0.00 0.00 0.00 3.68
6173 6517 1.228737 CCTCCTTTCCCCCGCAAAA 60.229 57.895 0.00 0.00 0.00 2.44
6174 6518 0.830023 CCTCCTTTCCCCCGCAAAAA 60.830 55.000 0.00 0.00 0.00 1.94
6175 6519 1.266178 CTCCTTTCCCCCGCAAAAAT 58.734 50.000 0.00 0.00 0.00 1.82
6176 6520 1.623311 CTCCTTTCCCCCGCAAAAATT 59.377 47.619 0.00 0.00 0.00 1.82
6177 6521 1.346068 TCCTTTCCCCCGCAAAAATTG 59.654 47.619 0.00 0.00 0.00 2.32
6178 6522 1.346068 CCTTTCCCCCGCAAAAATTGA 59.654 47.619 0.00 0.00 0.00 2.57
6179 6523 2.027285 CCTTTCCCCCGCAAAAATTGAT 60.027 45.455 0.00 0.00 0.00 2.57
6180 6524 3.196685 CCTTTCCCCCGCAAAAATTGATA 59.803 43.478 0.00 0.00 0.00 2.15
6181 6525 4.432712 CTTTCCCCCGCAAAAATTGATAG 58.567 43.478 0.00 0.00 0.00 2.08
6182 6526 1.754226 TCCCCCGCAAAAATTGATAGC 59.246 47.619 0.00 0.00 0.00 2.97
6183 6527 1.202521 CCCCCGCAAAAATTGATAGCC 60.203 52.381 0.00 0.00 0.00 3.93
6184 6528 1.480137 CCCCGCAAAAATTGATAGCCA 59.520 47.619 0.00 0.00 0.00 4.75
6185 6529 2.093764 CCCCGCAAAAATTGATAGCCAA 60.094 45.455 0.00 0.00 39.41 4.52
6186 6530 3.189285 CCCGCAAAAATTGATAGCCAAG 58.811 45.455 0.00 0.00 38.31 3.61
6187 6531 2.604462 CCGCAAAAATTGATAGCCAAGC 59.396 45.455 0.00 0.00 38.31 4.01
6188 6532 3.252400 CGCAAAAATTGATAGCCAAGCA 58.748 40.909 0.00 0.00 38.31 3.91
6189 6533 3.061161 CGCAAAAATTGATAGCCAAGCAC 59.939 43.478 0.00 0.00 38.31 4.40
6190 6534 3.995705 GCAAAAATTGATAGCCAAGCACA 59.004 39.130 0.00 0.00 38.31 4.57
6191 6535 4.632688 GCAAAAATTGATAGCCAAGCACAT 59.367 37.500 0.00 0.00 38.31 3.21
6192 6536 5.811613 GCAAAAATTGATAGCCAAGCACATA 59.188 36.000 0.00 0.00 38.31 2.29
6193 6537 6.313411 GCAAAAATTGATAGCCAAGCACATAA 59.687 34.615 0.00 0.00 38.31 1.90
6194 6538 7.011669 GCAAAAATTGATAGCCAAGCACATAAT 59.988 33.333 0.00 0.00 38.31 1.28
6195 6539 8.332464 CAAAAATTGATAGCCAAGCACATAATG 58.668 33.333 0.00 0.00 38.31 1.90
6196 6540 5.717078 ATTGATAGCCAAGCACATAATGG 57.283 39.130 0.00 0.00 38.31 3.16
6207 6551 4.330250 AGCACATAATGGCTTATAGCTGG 58.670 43.478 0.00 0.00 41.99 4.85
6208 6552 4.042062 AGCACATAATGGCTTATAGCTGGA 59.958 41.667 0.00 0.00 41.99 3.86
6209 6553 4.154918 GCACATAATGGCTTATAGCTGGAC 59.845 45.833 0.00 0.00 41.99 4.02
6210 6554 5.308014 CACATAATGGCTTATAGCTGGACA 58.692 41.667 0.00 0.00 41.99 4.02
6211 6555 5.180117 CACATAATGGCTTATAGCTGGACAC 59.820 44.000 0.00 0.00 41.99 3.67
6212 6556 3.931907 AATGGCTTATAGCTGGACACA 57.068 42.857 0.00 0.00 41.99 3.72
6213 6557 2.691409 TGGCTTATAGCTGGACACAC 57.309 50.000 0.00 0.00 41.99 3.82
6214 6558 1.905894 TGGCTTATAGCTGGACACACA 59.094 47.619 0.00 0.00 41.99 3.72
6215 6559 2.505407 TGGCTTATAGCTGGACACACAT 59.495 45.455 0.00 0.00 41.99 3.21
6216 6560 2.874701 GGCTTATAGCTGGACACACATG 59.125 50.000 0.00 0.00 41.99 3.21
6217 6561 2.874701 GCTTATAGCTGGACACACATGG 59.125 50.000 0.00 0.00 38.45 3.66
6218 6562 3.470709 CTTATAGCTGGACACACATGGG 58.529 50.000 0.00 0.00 0.00 4.00
6219 6563 1.289160 ATAGCTGGACACACATGGGT 58.711 50.000 0.00 0.00 0.00 4.51
6220 6564 1.064003 TAGCTGGACACACATGGGTT 58.936 50.000 0.00 0.00 0.00 4.11
6221 6565 0.250901 AGCTGGACACACATGGGTTC 60.251 55.000 0.00 0.00 0.00 3.62
6222 6566 0.250901 GCTGGACACACATGGGTTCT 60.251 55.000 0.00 0.00 0.00 3.01
6223 6567 1.003118 GCTGGACACACATGGGTTCTA 59.997 52.381 0.00 0.00 0.00 2.10
6224 6568 2.552155 GCTGGACACACATGGGTTCTAA 60.552 50.000 0.00 0.00 0.00 2.10
6225 6569 3.750371 CTGGACACACATGGGTTCTAAA 58.250 45.455 0.00 0.00 0.00 1.85
6226 6570 4.335416 CTGGACACACATGGGTTCTAAAT 58.665 43.478 0.00 0.00 0.00 1.40
6227 6571 4.078537 TGGACACACATGGGTTCTAAATG 58.921 43.478 0.00 0.00 0.00 2.32
6228 6572 4.202514 TGGACACACATGGGTTCTAAATGA 60.203 41.667 0.00 0.00 0.00 2.57
6229 6573 4.396166 GGACACACATGGGTTCTAAATGAG 59.604 45.833 0.00 0.00 0.00 2.90
6230 6574 3.758554 ACACACATGGGTTCTAAATGAGC 59.241 43.478 0.00 0.00 0.00 4.26
6231 6575 4.012374 CACACATGGGTTCTAAATGAGCT 58.988 43.478 0.00 0.00 0.00 4.09
6232 6576 4.012374 ACACATGGGTTCTAAATGAGCTG 58.988 43.478 0.00 0.00 0.00 4.24
6233 6577 3.019564 ACATGGGTTCTAAATGAGCTGC 58.980 45.455 0.00 0.00 0.00 5.25
6234 6578 2.877097 TGGGTTCTAAATGAGCTGCA 57.123 45.000 1.02 0.00 0.00 4.41
6235 6579 2.436417 TGGGTTCTAAATGAGCTGCAC 58.564 47.619 1.02 0.00 0.00 4.57
6236 6580 2.040278 TGGGTTCTAAATGAGCTGCACT 59.960 45.455 1.02 0.00 0.00 4.40
6237 6581 2.421424 GGGTTCTAAATGAGCTGCACTG 59.579 50.000 1.02 0.00 0.00 3.66
6238 6582 2.421424 GGTTCTAAATGAGCTGCACTGG 59.579 50.000 1.02 0.00 0.00 4.00
6239 6583 3.338249 GTTCTAAATGAGCTGCACTGGA 58.662 45.455 1.02 0.00 0.00 3.86
6240 6584 2.977914 TCTAAATGAGCTGCACTGGAC 58.022 47.619 1.02 0.00 0.00 4.02
6241 6585 2.302733 TCTAAATGAGCTGCACTGGACA 59.697 45.455 1.02 0.00 0.00 4.02
6242 6586 2.211250 AAATGAGCTGCACTGGACAT 57.789 45.000 1.02 0.00 0.00 3.06
6243 6587 1.460504 AATGAGCTGCACTGGACATG 58.539 50.000 1.02 0.00 0.00 3.21
6244 6588 0.327259 ATGAGCTGCACTGGACATGT 59.673 50.000 0.00 0.00 0.00 3.21
6245 6589 0.109153 TGAGCTGCACTGGACATGTT 59.891 50.000 0.00 0.00 0.00 2.71
6246 6590 0.801251 GAGCTGCACTGGACATGTTC 59.199 55.000 0.00 0.00 0.00 3.18
6247 6591 0.607489 AGCTGCACTGGACATGTTCC 60.607 55.000 0.46 4.58 46.13 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.308046 GGCCTATTGGAGATGAGATTCCC 60.308 52.174 0.00 0.00 34.57 3.97
51 57 1.027357 CAGCCCAATTAGCGCAAGAT 58.973 50.000 11.47 0.00 43.02 2.40
71 77 2.360165 GCCTCAATTATGCAAGAGTGGG 59.640 50.000 0.00 0.00 0.00 4.61
79 85 4.609301 ACCCTAAAAGCCTCAATTATGCA 58.391 39.130 0.00 0.00 0.00 3.96
83 89 7.947890 CCCAATATACCCTAAAAGCCTCAATTA 59.052 37.037 0.00 0.00 0.00 1.40
199 215 5.351189 GGTTCCATGGCATTTGTTAATCAAC 59.649 40.000 6.96 1.06 35.61 3.18
212 228 2.109128 TCCTTAACTTGGTTCCATGGCA 59.891 45.455 6.96 0.00 0.00 4.92
213 229 2.802719 TCCTTAACTTGGTTCCATGGC 58.197 47.619 6.96 0.00 0.00 4.40
224 240 6.069029 ACCAAGCAGGGTATTATCCTTAACTT 60.069 38.462 0.00 0.00 43.89 2.66
249 265 0.826256 ACGATGGAGGCGGCATACTA 60.826 55.000 13.08 0.09 0.00 1.82
257 273 2.509336 GTCACCACGATGGAGGCG 60.509 66.667 10.46 0.00 40.96 5.52
267 283 3.782046 ACTACTGCGATTATGTCACCAC 58.218 45.455 0.00 0.00 0.00 4.16
342 359 0.250381 TGGGAAACGGTGTGCGTTAT 60.250 50.000 0.00 0.00 0.00 1.89
472 633 5.817296 GCATAGAACACACAGGACAATCATA 59.183 40.000 0.00 0.00 0.00 2.15
502 663 3.821033 AGAAGGGTGAACACAGTAAATGC 59.179 43.478 7.25 0.00 0.00 3.56
574 743 4.341806 TGAATCTGGAACAAAATGTGTGCT 59.658 37.500 0.00 0.00 40.60 4.40
689 858 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
690 859 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
691 860 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
708 877 9.570488 CACTACTTTAGTAATCTAAACGCTCTT 57.430 33.333 0.00 0.00 40.05 2.85
709 878 8.954350 TCACTACTTTAGTAATCTAAACGCTCT 58.046 33.333 0.00 0.00 40.05 4.09
710 879 9.733219 ATCACTACTTTAGTAATCTAAACGCTC 57.267 33.333 0.00 0.00 40.05 5.03
711 880 9.733219 GATCACTACTTTAGTAATCTAAACGCT 57.267 33.333 0.00 0.00 40.05 5.07
712 881 9.733219 AGATCACTACTTTAGTAATCTAAACGC 57.267 33.333 0.00 0.00 40.05 4.84
739 908 9.490379 CCTCCGTAAACTAATATAAGAGCATTT 57.510 33.333 0.00 0.00 0.00 2.32
740 909 8.095169 CCCTCCGTAAACTAATATAAGAGCATT 58.905 37.037 0.00 0.00 0.00 3.56
741 910 7.453752 TCCCTCCGTAAACTAATATAAGAGCAT 59.546 37.037 0.00 0.00 0.00 3.79
742 911 6.779049 TCCCTCCGTAAACTAATATAAGAGCA 59.221 38.462 0.00 0.00 0.00 4.26
743 912 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
744 913 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
745 914 9.512588 CTACTCCCTCCGTAAACTAATATAAGA 57.487 37.037 0.00 0.00 0.00 2.10
746 915 9.512588 TCTACTCCCTCCGTAAACTAATATAAG 57.487 37.037 0.00 0.00 0.00 1.73
749 918 8.953223 AATCTACTCCCTCCGTAAACTAATAT 57.047 34.615 0.00 0.00 0.00 1.28
750 919 8.773033 AAATCTACTCCCTCCGTAAACTAATA 57.227 34.615 0.00 0.00 0.00 0.98
751 920 7.672122 AAATCTACTCCCTCCGTAAACTAAT 57.328 36.000 0.00 0.00 0.00 1.73
752 921 7.486407 AAAATCTACTCCCTCCGTAAACTAA 57.514 36.000 0.00 0.00 0.00 2.24
753 922 8.773033 ATAAAATCTACTCCCTCCGTAAACTA 57.227 34.615 0.00 0.00 0.00 2.24
754 923 7.672122 ATAAAATCTACTCCCTCCGTAAACT 57.328 36.000 0.00 0.00 0.00 2.66
755 924 8.728337 AAATAAAATCTACTCCCTCCGTAAAC 57.272 34.615 0.00 0.00 0.00 2.01
759 928 8.935741 AGATAAAATAAAATCTACTCCCTCCGT 58.064 33.333 0.00 0.00 30.65 4.69
760 929 9.209175 CAGATAAAATAAAATCTACTCCCTCCG 57.791 37.037 0.00 0.00 31.25 4.63
1019 1191 7.373493 AGTACTTTCTGATTTTGGCAAATGAG 58.627 34.615 14.29 9.84 35.52 2.90
1043 1215 4.722194 CGTGGTCATTGTGATTGGTTTAG 58.278 43.478 0.00 0.00 0.00 1.85
1052 1224 1.514678 GGCTTGCGTGGTCATTGTGA 61.515 55.000 0.00 0.00 0.00 3.58
1409 1581 0.592637 TGCAAACTCATCGGTGCTTG 59.407 50.000 0.00 0.00 37.87 4.01
1607 1779 2.397549 GCTTTGAATTGACAGCCACAC 58.602 47.619 0.00 0.00 0.00 3.82
1639 1811 3.134127 GCATGCGACCAACCCTCC 61.134 66.667 0.00 0.00 0.00 4.30
1645 1817 1.885233 TGAATTTGAGCATGCGACCAA 59.115 42.857 13.01 14.66 0.00 3.67
1660 1832 7.088905 GTCAATGTCTTCTTTGCAGATGAATT 58.911 34.615 0.00 0.00 35.52 2.17
1760 1932 7.362662 AGCAGTACATTAAAATCATATTGCCG 58.637 34.615 0.00 0.00 0.00 5.69
1798 1970 8.325282 GCACACAAAACTTAATTTTTACCTGTC 58.675 33.333 3.50 0.00 38.50 3.51
1829 2001 0.399949 TGGATAAGGTCTGCCCCGAT 60.400 55.000 0.00 0.00 34.57 4.18
1935 2107 6.480763 TGCAAAGGTGTCTCTGGATTATTAA 58.519 36.000 0.00 0.00 0.00 1.40
1936 2108 6.061022 TGCAAAGGTGTCTCTGGATTATTA 57.939 37.500 0.00 0.00 0.00 0.98
1937 2109 4.922206 TGCAAAGGTGTCTCTGGATTATT 58.078 39.130 0.00 0.00 0.00 1.40
1938 2110 4.574674 TGCAAAGGTGTCTCTGGATTAT 57.425 40.909 0.00 0.00 0.00 1.28
1939 2111 4.326826 CTTGCAAAGGTGTCTCTGGATTA 58.673 43.478 0.00 0.00 41.27 1.75
1955 2127 0.822944 TTGCTACCAGCTGCTTGCAA 60.823 50.000 21.77 21.77 45.94 4.08
1975 2147 6.657117 GGATAGAATGATTTAAAGAGCCCTCC 59.343 42.308 0.00 0.00 0.00 4.30
1988 2160 4.458256 TGGTGCATGGGATAGAATGATT 57.542 40.909 0.00 0.00 0.00 2.57
2016 2224 1.760613 ACAGAAGGGAACTCGTTGTCA 59.239 47.619 0.00 0.00 42.68 3.58
2022 2230 2.263077 CATCGAACAGAAGGGAACTCG 58.737 52.381 0.00 0.00 42.68 4.18
2791 3004 0.108424 GCTGATCAGAAGCTCGTGGT 60.108 55.000 27.04 0.00 37.69 4.16
2875 3088 1.205179 AGAGAGAGCTCAGTGCACATG 59.795 52.381 21.04 14.18 43.81 3.21
2888 3101 3.311322 GTCCACATGACTACGAGAGAGAG 59.689 52.174 0.00 0.00 41.03 3.20
2889 3102 3.271729 GTCCACATGACTACGAGAGAGA 58.728 50.000 0.00 0.00 41.03 3.10
2980 3193 6.856426 AGTTTAGCTTATTTTCTGCGTGAAAC 59.144 34.615 0.00 0.00 43.55 2.78
3203 3418 1.033746 AGCATCGAACAGGCCCATTG 61.034 55.000 0.00 0.00 0.00 2.82
3530 3769 6.814644 GGCATATAAACCATATACGTAGCACA 59.185 38.462 0.08 0.00 0.00 4.57
3539 3778 8.896658 ACAGGGTTAAGGCATATAAACCATATA 58.103 33.333 12.43 0.00 41.66 0.86
3541 3780 7.156694 ACAGGGTTAAGGCATATAAACCATA 57.843 36.000 12.43 0.00 41.66 2.74
3870 4114 5.191727 TCATGTGGTATTCATGACCCTTT 57.808 39.130 0.00 0.00 44.14 3.11
3922 4166 8.394121 GCCAACTTACTTCAGATAAGATCAAAG 58.606 37.037 0.00 0.00 34.36 2.77
4007 4251 4.667262 CTGATGCGTATCTATCAGCTACC 58.333 47.826 14.76 0.00 42.48 3.18
4156 4400 8.438676 AACATATCAGACAAATAACAGCTACC 57.561 34.615 0.00 0.00 0.00 3.18
4172 4416 7.935755 ACCAACTCATCCATCTTAACATATCAG 59.064 37.037 0.00 0.00 0.00 2.90
4180 4424 5.945784 CCAAGAACCAACTCATCCATCTTAA 59.054 40.000 0.00 0.00 0.00 1.85
4253 4499 4.645588 CCAAACAACCCACAACCTTTAGTA 59.354 41.667 0.00 0.00 0.00 1.82
4302 4548 5.878627 TGGAAGGAGTATAGAGTACTAGGC 58.121 45.833 0.00 0.00 31.78 3.93
4609 4896 7.508636 CCATCATCCATACTGCTATATACTCCT 59.491 40.741 0.00 0.00 0.00 3.69
5002 5300 4.074970 ACGGTCTTCTTCATCTGCAAAAT 58.925 39.130 0.00 0.00 0.00 1.82
5278 5576 1.475751 GGAGGGTGGTGATATGCTGTG 60.476 57.143 0.00 0.00 0.00 3.66
5301 5599 4.024893 GGTGGTAATATGCTGTTGACATCG 60.025 45.833 0.00 0.00 0.00 3.84
5343 5641 1.000486 CTCTCCTTCCTCCCCGTCA 60.000 63.158 0.00 0.00 0.00 4.35
5384 5682 9.528018 GTATGAGAAACAAATCACAAGGAAAAA 57.472 29.630 0.00 0.00 0.00 1.94
5389 5687 6.241207 ACGTATGAGAAACAAATCACAAGG 57.759 37.500 0.00 0.00 0.00 3.61
5390 5688 9.265938 CAATACGTATGAGAAACAAATCACAAG 57.734 33.333 9.24 0.00 0.00 3.16
5391 5689 8.779303 ACAATACGTATGAGAAACAAATCACAA 58.221 29.630 9.24 0.00 0.00 3.33
5393 5691 8.227791 ACACAATACGTATGAGAAACAAATCAC 58.772 33.333 9.24 0.00 0.00 3.06
5394 5692 8.317891 ACACAATACGTATGAGAAACAAATCA 57.682 30.769 9.24 0.00 0.00 2.57
5395 5693 9.685005 GTACACAATACGTATGAGAAACAAATC 57.315 33.333 9.24 0.00 0.00 2.17
5396 5694 8.662141 GGTACACAATACGTATGAGAAACAAAT 58.338 33.333 9.24 0.00 0.00 2.32
5576 5890 5.715070 ACACAAGCACTTCACTACTATCTC 58.285 41.667 0.00 0.00 0.00 2.75
5609 5927 2.443260 TACACCACCATCGCAAGCGT 62.443 55.000 14.57 0.00 40.74 5.07
5667 5985 0.179037 ATCACCATCCGGATGTGCTG 60.179 55.000 36.09 27.53 37.11 4.41
5677 6013 1.679680 CCATTCTGTGCATCACCATCC 59.320 52.381 0.00 0.00 32.73 3.51
5709 6045 0.388294 CTAGCGTAGTTACCCTGGCC 59.612 60.000 0.00 0.00 0.00 5.36
5734 6070 3.538591 ACAGCCATCACATGTATGAGTG 58.461 45.455 0.00 6.66 37.10 3.51
5735 6071 3.198417 TGACAGCCATCACATGTATGAGT 59.802 43.478 0.00 3.57 30.46 3.41
5736 6072 3.800531 TGACAGCCATCACATGTATGAG 58.199 45.455 0.00 0.00 30.46 2.90
5737 6073 3.451902 TCTGACAGCCATCACATGTATGA 59.548 43.478 0.00 0.00 0.00 2.15
5738 6074 3.800531 TCTGACAGCCATCACATGTATG 58.199 45.455 0.00 3.32 0.00 2.39
5739 6075 4.102054 TGATCTGACAGCCATCACATGTAT 59.898 41.667 0.00 0.00 0.00 2.29
5740 6076 3.451902 TGATCTGACAGCCATCACATGTA 59.548 43.478 0.00 0.00 0.00 2.29
5741 6077 2.237893 TGATCTGACAGCCATCACATGT 59.762 45.455 0.00 0.00 0.00 3.21
5742 6078 2.914059 TGATCTGACAGCCATCACATG 58.086 47.619 0.00 0.00 0.00 3.21
5743 6079 3.054582 AGTTGATCTGACAGCCATCACAT 60.055 43.478 6.38 0.00 0.00 3.21
5744 6080 2.303890 AGTTGATCTGACAGCCATCACA 59.696 45.455 6.38 0.00 0.00 3.58
5745 6081 2.983229 AGTTGATCTGACAGCCATCAC 58.017 47.619 6.38 3.69 0.00 3.06
5746 6082 3.244665 ACAAGTTGATCTGACAGCCATCA 60.245 43.478 10.54 0.00 0.00 3.07
5747 6083 3.126514 CACAAGTTGATCTGACAGCCATC 59.873 47.826 10.54 0.00 0.00 3.51
5748 6084 3.079578 CACAAGTTGATCTGACAGCCAT 58.920 45.455 10.54 0.00 0.00 4.40
5749 6085 2.158769 ACACAAGTTGATCTGACAGCCA 60.159 45.455 10.54 0.00 0.00 4.75
5750 6086 2.498167 ACACAAGTTGATCTGACAGCC 58.502 47.619 10.54 0.00 0.00 4.85
5751 6087 5.641209 AGATTACACAAGTTGATCTGACAGC 59.359 40.000 10.54 0.00 31.95 4.40
5752 6088 6.870439 TCAGATTACACAAGTTGATCTGACAG 59.130 38.462 22.01 0.00 43.54 3.51
5753 6089 6.758254 TCAGATTACACAAGTTGATCTGACA 58.242 36.000 22.01 9.04 43.54 3.58
5754 6090 7.658179 TTCAGATTACACAAGTTGATCTGAC 57.342 36.000 24.13 8.35 45.53 3.51
5755 6091 7.933577 AGTTTCAGATTACACAAGTTGATCTGA 59.066 33.333 22.01 22.01 44.94 3.27
5756 6092 8.013947 CAGTTTCAGATTACACAAGTTGATCTG 58.986 37.037 19.22 19.22 42.48 2.90
5757 6093 7.933577 TCAGTTTCAGATTACACAAGTTGATCT 59.066 33.333 10.54 4.44 32.78 2.75
5758 6094 8.012241 GTCAGTTTCAGATTACACAAGTTGATC 58.988 37.037 10.54 1.96 0.00 2.92
5759 6095 7.498900 TGTCAGTTTCAGATTACACAAGTTGAT 59.501 33.333 10.54 0.00 0.00 2.57
5760 6096 6.821160 TGTCAGTTTCAGATTACACAAGTTGA 59.179 34.615 10.54 0.00 0.00 3.18
5761 6097 6.907212 GTGTCAGTTTCAGATTACACAAGTTG 59.093 38.462 0.00 0.00 37.69 3.16
5762 6098 6.823689 AGTGTCAGTTTCAGATTACACAAGTT 59.176 34.615 0.00 0.00 39.66 2.66
5763 6099 6.349300 AGTGTCAGTTTCAGATTACACAAGT 58.651 36.000 0.00 0.00 39.66 3.16
5764 6100 6.346120 CGAGTGTCAGTTTCAGATTACACAAG 60.346 42.308 0.00 0.00 39.66 3.16
5765 6101 5.462068 CGAGTGTCAGTTTCAGATTACACAA 59.538 40.000 0.00 0.00 39.66 3.33
5766 6102 4.982295 CGAGTGTCAGTTTCAGATTACACA 59.018 41.667 0.00 0.00 39.66 3.72
5792 6128 1.131126 CATGGTCACGCATGAAACTCC 59.869 52.381 0.00 0.00 36.31 3.85
5793 6129 2.076100 TCATGGTCACGCATGAAACTC 58.924 47.619 0.00 0.00 36.31 3.01
5804 6140 4.157289 AGCATCTTTCATGTTCATGGTCAC 59.843 41.667 12.02 0.00 0.00 3.67
5808 6144 3.181479 CCCAGCATCTTTCATGTTCATGG 60.181 47.826 12.02 0.00 0.00 3.66
5819 6155 0.610232 GCAGGACACCCAGCATCTTT 60.610 55.000 0.00 0.00 43.64 2.52
5837 6173 0.668535 AGTTTTGGACTTGAAGCGGC 59.331 50.000 0.00 0.00 33.92 6.53
5849 6187 3.573967 ACCATTGCACCTAGAAGTTTTGG 59.426 43.478 0.00 0.00 0.00 3.28
5856 6194 3.411446 CAAGTGACCATTGCACCTAGAA 58.589 45.455 0.00 0.00 36.95 2.10
5860 6198 1.181098 GCCAAGTGACCATTGCACCT 61.181 55.000 0.00 0.00 36.95 4.00
6000 6344 4.000325 TGACATTCCATTACACTCCGTTG 59.000 43.478 0.00 0.00 0.00 4.10
6115 6459 6.259829 GGTGGTGCATCAAACTTACAAAATTT 59.740 34.615 0.00 0.00 0.00 1.82
6116 6460 5.757808 GGTGGTGCATCAAACTTACAAAATT 59.242 36.000 0.00 0.00 0.00 1.82
6117 6461 5.070313 AGGTGGTGCATCAAACTTACAAAAT 59.930 36.000 0.00 0.00 0.00 1.82
6118 6462 4.404073 AGGTGGTGCATCAAACTTACAAAA 59.596 37.500 0.00 0.00 0.00 2.44
6119 6463 3.957497 AGGTGGTGCATCAAACTTACAAA 59.043 39.130 0.00 0.00 0.00 2.83
6120 6464 3.561143 AGGTGGTGCATCAAACTTACAA 58.439 40.909 0.00 0.00 0.00 2.41
6121 6465 3.222173 AGGTGGTGCATCAAACTTACA 57.778 42.857 0.00 0.00 0.00 2.41
6122 6466 5.699097 TTAAGGTGGTGCATCAAACTTAC 57.301 39.130 19.46 0.37 0.00 2.34
6123 6467 4.217550 GCTTAAGGTGGTGCATCAAACTTA 59.782 41.667 17.04 17.04 0.00 2.24
6124 6468 3.005791 GCTTAAGGTGGTGCATCAAACTT 59.994 43.478 18.68 18.68 0.00 2.66
6125 6469 2.558359 GCTTAAGGTGGTGCATCAAACT 59.442 45.455 0.00 0.00 0.00 2.66
6126 6470 2.295909 TGCTTAAGGTGGTGCATCAAAC 59.704 45.455 0.00 0.00 0.00 2.93
6127 6471 2.591923 TGCTTAAGGTGGTGCATCAAA 58.408 42.857 0.00 0.00 0.00 2.69
6128 6472 2.284754 TGCTTAAGGTGGTGCATCAA 57.715 45.000 0.00 0.00 0.00 2.57
6129 6473 2.284754 TTGCTTAAGGTGGTGCATCA 57.715 45.000 0.00 0.00 35.27 3.07
6130 6474 4.981806 TTATTGCTTAAGGTGGTGCATC 57.018 40.909 4.29 0.00 35.27 3.91
6131 6475 5.016173 TCTTTATTGCTTAAGGTGGTGCAT 58.984 37.500 4.29 0.00 35.27 3.96
6132 6476 4.217550 GTCTTTATTGCTTAAGGTGGTGCA 59.782 41.667 4.29 0.00 0.00 4.57
6133 6477 4.380550 GGTCTTTATTGCTTAAGGTGGTGC 60.381 45.833 4.29 0.00 0.00 5.01
6134 6478 5.010282 AGGTCTTTATTGCTTAAGGTGGTG 58.990 41.667 4.29 0.00 0.00 4.17
6135 6479 5.254115 GAGGTCTTTATTGCTTAAGGTGGT 58.746 41.667 4.29 0.00 0.00 4.16
6136 6480 4.640647 GGAGGTCTTTATTGCTTAAGGTGG 59.359 45.833 4.29 0.00 0.00 4.61
6137 6481 5.501156 AGGAGGTCTTTATTGCTTAAGGTG 58.499 41.667 4.29 0.00 0.00 4.00
6138 6482 5.780958 AGGAGGTCTTTATTGCTTAAGGT 57.219 39.130 4.29 0.00 0.00 3.50
6139 6483 6.095580 GGAAAGGAGGTCTTTATTGCTTAAGG 59.904 42.308 4.29 0.00 45.00 2.69
6140 6484 6.095580 GGGAAAGGAGGTCTTTATTGCTTAAG 59.904 42.308 0.00 0.00 45.00 1.85
6141 6485 5.949952 GGGAAAGGAGGTCTTTATTGCTTAA 59.050 40.000 0.00 0.00 45.00 1.85
6142 6486 5.506708 GGGAAAGGAGGTCTTTATTGCTTA 58.493 41.667 0.00 0.00 45.00 3.09
6143 6487 4.344978 GGGAAAGGAGGTCTTTATTGCTT 58.655 43.478 0.00 0.00 45.00 3.91
6144 6488 3.309193 GGGGAAAGGAGGTCTTTATTGCT 60.309 47.826 0.00 0.00 45.00 3.91
6145 6489 3.024547 GGGGAAAGGAGGTCTTTATTGC 58.975 50.000 0.00 0.00 45.00 3.56
6146 6490 3.632333 GGGGGAAAGGAGGTCTTTATTG 58.368 50.000 0.00 0.00 45.00 1.90
6147 6491 2.241430 CGGGGGAAAGGAGGTCTTTATT 59.759 50.000 0.00 0.00 45.00 1.40
6148 6492 1.844497 CGGGGGAAAGGAGGTCTTTAT 59.156 52.381 0.00 0.00 45.00 1.40
6149 6493 1.282382 CGGGGGAAAGGAGGTCTTTA 58.718 55.000 0.00 0.00 45.00 1.85
6151 6495 2.603652 GCGGGGGAAAGGAGGTCTT 61.604 63.158 0.00 0.00 37.28 3.01
6152 6496 3.009714 GCGGGGGAAAGGAGGTCT 61.010 66.667 0.00 0.00 0.00 3.85
6153 6497 2.420466 TTTGCGGGGGAAAGGAGGTC 62.420 60.000 0.00 0.00 0.00 3.85
6154 6498 2.014033 TTTTGCGGGGGAAAGGAGGT 62.014 55.000 0.00 0.00 0.00 3.85
6155 6499 0.830023 TTTTTGCGGGGGAAAGGAGG 60.830 55.000 0.00 0.00 0.00 4.30
6156 6500 1.266178 ATTTTTGCGGGGGAAAGGAG 58.734 50.000 0.00 0.00 0.00 3.69
6157 6501 1.346068 CAATTTTTGCGGGGGAAAGGA 59.654 47.619 0.00 0.00 0.00 3.36
6158 6502 1.346068 TCAATTTTTGCGGGGGAAAGG 59.654 47.619 0.00 0.00 0.00 3.11
6159 6503 2.829741 TCAATTTTTGCGGGGGAAAG 57.170 45.000 0.00 0.00 0.00 2.62
6160 6504 3.368948 GCTATCAATTTTTGCGGGGGAAA 60.369 43.478 0.00 0.00 0.00 3.13
6161 6505 2.167487 GCTATCAATTTTTGCGGGGGAA 59.833 45.455 0.00 0.00 0.00 3.97
6162 6506 1.754226 GCTATCAATTTTTGCGGGGGA 59.246 47.619 0.00 0.00 0.00 4.81
6163 6507 1.202521 GGCTATCAATTTTTGCGGGGG 60.203 52.381 0.00 0.00 0.00 5.40
6164 6508 1.480137 TGGCTATCAATTTTTGCGGGG 59.520 47.619 0.00 0.00 0.00 5.73
6165 6509 2.957491 TGGCTATCAATTTTTGCGGG 57.043 45.000 0.00 0.00 0.00 6.13
6166 6510 2.604462 GCTTGGCTATCAATTTTTGCGG 59.396 45.455 0.00 0.00 34.45 5.69
6167 6511 3.061161 GTGCTTGGCTATCAATTTTTGCG 59.939 43.478 0.00 0.00 34.45 4.85
6168 6512 3.995705 TGTGCTTGGCTATCAATTTTTGC 59.004 39.130 0.00 0.00 34.45 3.68
6169 6513 7.830940 TTATGTGCTTGGCTATCAATTTTTG 57.169 32.000 0.00 0.00 34.45 2.44
6170 6514 7.496591 CCATTATGTGCTTGGCTATCAATTTTT 59.503 33.333 0.00 0.00 34.45 1.94
6171 6515 6.987992 CCATTATGTGCTTGGCTATCAATTTT 59.012 34.615 0.00 0.00 34.45 1.82
6172 6516 6.518493 CCATTATGTGCTTGGCTATCAATTT 58.482 36.000 0.00 0.00 34.45 1.82
6173 6517 6.092955 CCATTATGTGCTTGGCTATCAATT 57.907 37.500 0.00 0.00 34.45 2.32
6174 6518 5.717078 CCATTATGTGCTTGGCTATCAAT 57.283 39.130 0.00 0.00 34.45 2.57
6182 6526 4.763793 AGCTATAAGCCATTATGTGCTTGG 59.236 41.667 22.12 15.56 46.66 3.61
6183 6527 5.335426 CCAGCTATAAGCCATTATGTGCTTG 60.335 44.000 22.12 12.22 46.66 4.01
6185 6529 4.042062 TCCAGCTATAAGCCATTATGTGCT 59.958 41.667 3.04 3.04 43.77 4.40
6186 6530 4.154918 GTCCAGCTATAAGCCATTATGTGC 59.845 45.833 0.00 0.00 43.77 4.57
6187 6531 5.180117 GTGTCCAGCTATAAGCCATTATGTG 59.820 44.000 0.00 0.00 43.77 3.21
6188 6532 5.163205 TGTGTCCAGCTATAAGCCATTATGT 60.163 40.000 0.00 0.00 43.77 2.29
6189 6533 5.180117 GTGTGTCCAGCTATAAGCCATTATG 59.820 44.000 0.00 0.00 43.77 1.90
6190 6534 5.163205 TGTGTGTCCAGCTATAAGCCATTAT 60.163 40.000 0.00 0.00 43.77 1.28
6191 6535 4.163268 TGTGTGTCCAGCTATAAGCCATTA 59.837 41.667 0.00 0.00 43.77 1.90
6192 6536 3.054434 TGTGTGTCCAGCTATAAGCCATT 60.054 43.478 0.00 0.00 43.77 3.16
6193 6537 2.505407 TGTGTGTCCAGCTATAAGCCAT 59.495 45.455 0.00 0.00 43.77 4.40
6194 6538 1.905894 TGTGTGTCCAGCTATAAGCCA 59.094 47.619 0.00 0.00 43.77 4.75
6195 6539 2.691409 TGTGTGTCCAGCTATAAGCC 57.309 50.000 0.00 0.00 43.77 4.35
6196 6540 2.874701 CCATGTGTGTCCAGCTATAAGC 59.125 50.000 0.00 0.00 42.84 3.09
6197 6541 3.118261 ACCCATGTGTGTCCAGCTATAAG 60.118 47.826 0.00 0.00 0.00 1.73
6198 6542 2.843730 ACCCATGTGTGTCCAGCTATAA 59.156 45.455 0.00 0.00 0.00 0.98
6199 6543 2.477245 ACCCATGTGTGTCCAGCTATA 58.523 47.619 0.00 0.00 0.00 1.31
6200 6544 1.289160 ACCCATGTGTGTCCAGCTAT 58.711 50.000 0.00 0.00 0.00 2.97
6201 6545 1.003118 GAACCCATGTGTGTCCAGCTA 59.997 52.381 0.00 0.00 0.00 3.32
6202 6546 0.250901 GAACCCATGTGTGTCCAGCT 60.251 55.000 0.00 0.00 0.00 4.24
6203 6547 0.250901 AGAACCCATGTGTGTCCAGC 60.251 55.000 0.00 0.00 0.00 4.85
6204 6548 3.417069 TTAGAACCCATGTGTGTCCAG 57.583 47.619 0.00 0.00 0.00 3.86
6205 6549 3.866703 TTTAGAACCCATGTGTGTCCA 57.133 42.857 0.00 0.00 0.00 4.02
6206 6550 4.331968 TCATTTAGAACCCATGTGTGTCC 58.668 43.478 0.00 0.00 0.00 4.02
6207 6551 4.142600 GCTCATTTAGAACCCATGTGTGTC 60.143 45.833 0.00 0.00 0.00 3.67
6208 6552 3.758554 GCTCATTTAGAACCCATGTGTGT 59.241 43.478 0.00 0.00 0.00 3.72
6209 6553 4.012374 AGCTCATTTAGAACCCATGTGTG 58.988 43.478 0.00 0.00 0.00 3.82
6210 6554 4.012374 CAGCTCATTTAGAACCCATGTGT 58.988 43.478 0.00 0.00 0.00 3.72
6211 6555 3.181493 GCAGCTCATTTAGAACCCATGTG 60.181 47.826 0.00 0.00 0.00 3.21
6212 6556 3.019564 GCAGCTCATTTAGAACCCATGT 58.980 45.455 0.00 0.00 0.00 3.21
6213 6557 3.018856 TGCAGCTCATTTAGAACCCATG 58.981 45.455 0.00 0.00 0.00 3.66
6214 6558 3.019564 GTGCAGCTCATTTAGAACCCAT 58.980 45.455 0.00 0.00 0.00 4.00
6215 6559 2.040278 AGTGCAGCTCATTTAGAACCCA 59.960 45.455 0.00 0.00 0.00 4.51
6216 6560 2.421424 CAGTGCAGCTCATTTAGAACCC 59.579 50.000 0.00 0.00 0.00 4.11
6217 6561 2.421424 CCAGTGCAGCTCATTTAGAACC 59.579 50.000 0.00 0.00 0.00 3.62
6218 6562 3.126000 GTCCAGTGCAGCTCATTTAGAAC 59.874 47.826 0.00 0.00 0.00 3.01
6219 6563 3.244526 TGTCCAGTGCAGCTCATTTAGAA 60.245 43.478 0.00 0.00 0.00 2.10
6220 6564 2.302733 TGTCCAGTGCAGCTCATTTAGA 59.697 45.455 0.00 0.00 0.00 2.10
6221 6565 2.703416 TGTCCAGTGCAGCTCATTTAG 58.297 47.619 0.00 0.00 0.00 1.85
6222 6566 2.857186 TGTCCAGTGCAGCTCATTTA 57.143 45.000 0.00 0.00 0.00 1.40
6223 6567 1.816835 CATGTCCAGTGCAGCTCATTT 59.183 47.619 0.00 0.00 0.00 2.32
6224 6568 1.271762 ACATGTCCAGTGCAGCTCATT 60.272 47.619 0.00 0.00 0.00 2.57
6225 6569 0.327259 ACATGTCCAGTGCAGCTCAT 59.673 50.000 0.00 0.00 0.00 2.90
6226 6570 0.109153 AACATGTCCAGTGCAGCTCA 59.891 50.000 0.00 0.00 0.00 4.26
6227 6571 0.801251 GAACATGTCCAGTGCAGCTC 59.199 55.000 0.00 0.00 0.00 4.09
6228 6572 0.607489 GGAACATGTCCAGTGCAGCT 60.607 55.000 0.00 0.00 46.97 4.24
6229 6573 1.878775 GGAACATGTCCAGTGCAGC 59.121 57.895 0.00 0.00 46.97 5.25


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.