Multiple sequence alignment - TraesCS6B01G211100

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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 TraesCS6B01G211100 chr6B 100.000 6979 0 0 1 6979 279043860 279050838 0.000000e+00 12888.0
1 TraesCS6B01G211100 chr6B 94.366 71 3 1 3648 3717 279047437 279047507 2.660000e-19 108.0
2 TraesCS6B01G211100 chr6B 94.366 71 3 1 3578 3648 279047507 279047576 2.660000e-19 108.0
3 TraesCS6B01G211100 chr6D 95.652 2852 86 16 811 3648 156443655 156446482 0.000000e+00 4545.0
4 TraesCS6B01G211100 chr6D 97.466 1539 29 6 3649 5179 156446412 156447948 0.000000e+00 2617.0
5 TraesCS6B01G211100 chr6D 95.596 1635 49 13 5334 6951 156449578 156451206 0.000000e+00 2599.0
6 TraesCS6B01G211100 chr6D 91.379 116 6 4 5165 5278 320709353 320709240 9.370000e-34 156.0
7 TraesCS6B01G211100 chr6D 97.059 68 2 0 684 751 406229637 406229704 1.590000e-21 115.0
8 TraesCS6B01G211100 chr6D 93.846 65 4 0 5272 5336 156447946 156448010 1.600000e-16 99.0
9 TraesCS6B01G211100 chr6A 95.432 2802 109 13 854 3648 209893717 209896506 0.000000e+00 4447.0
10 TraesCS6B01G211100 chr6A 97.403 1540 31 5 3649 5179 209896436 209897975 0.000000e+00 2614.0
11 TraesCS6B01G211100 chr6A 95.451 1275 38 12 5272 6534 209897973 209899239 0.000000e+00 2015.0
12 TraesCS6B01G211100 chr6A 95.322 684 28 4 1 682 575554651 575555332 0.000000e+00 1083.0
13 TraesCS6B01G211100 chr6A 90.346 694 40 19 1 684 480579949 480579273 0.000000e+00 885.0
14 TraesCS6B01G211100 chr6A 94.344 389 10 5 6571 6951 209900912 209901296 2.800000e-163 586.0
15 TraesCS6B01G211100 chr6A 95.385 65 2 1 684 747 575555357 575555421 1.240000e-17 102.0
16 TraesCS6B01G211100 chr6A 92.537 67 4 1 6527 6592 209900205 209900271 2.070000e-15 95.3
17 TraesCS6B01G211100 chr1D 96.930 684 21 0 1 684 376738809 376738126 0.000000e+00 1147.0
18 TraesCS6B01G211100 chr1D 96.345 684 24 1 1 684 381107494 381106812 0.000000e+00 1123.0
19 TraesCS6B01G211100 chr1D 96.875 64 2 0 684 747 381106758 381106695 2.660000e-19 108.0
20 TraesCS6B01G211100 chr2B 95.468 684 31 0 1 684 730846722 730846039 0.000000e+00 1092.0
21 TraesCS6B01G211100 chr2B 88.025 643 50 17 52 684 384334993 384335618 0.000000e+00 736.0
22 TraesCS6B01G211100 chr2B 89.744 156 11 3 6112 6265 190023043 190022891 1.990000e-45 195.0
23 TraesCS6B01G211100 chr2B 81.871 171 29 2 3277 3446 42619506 42619337 7.300000e-30 143.0
24 TraesCS6B01G211100 chr2B 77.470 253 48 5 3277 3528 42759824 42759580 7.300000e-30 143.0
25 TraesCS6B01G211100 chr2B 77.075 253 49 5 3277 3528 42828317 42828073 3.390000e-28 137.0
26 TraesCS6B01G211100 chr2B 75.723 173 24 14 6413 6580 166284581 166284740 3.490000e-08 71.3
27 TraesCS6B01G211100 chr2D 95.322 684 30 2 1 684 387911385 387910704 0.000000e+00 1085.0
28 TraesCS6B01G211100 chr2D 94.883 684 34 1 1 684 636411399 636412081 0.000000e+00 1068.0
29 TraesCS6B01G211100 chr2D 88.125 160 14 2 6108 6265 79056163 79056319 1.200000e-42 185.0
30 TraesCS6B01G211100 chr2D 92.308 117 9 0 5167 5283 442441830 442441946 4.330000e-37 167.0
31 TraesCS6B01G211100 chr2D 95.652 69 2 1 684 751 80736927 80736995 7.400000e-20 110.0
32 TraesCS6B01G211100 chr2D 95.652 69 2 1 684 751 636412135 636412203 7.400000e-20 110.0
33 TraesCS6B01G211100 chr7A 95.029 684 34 0 1 684 688910470 688909787 0.000000e+00 1075.0
34 TraesCS6B01G211100 chr7A 94.118 68 3 1 684 751 688909733 688909667 1.240000e-17 102.0
35 TraesCS6B01G211100 chr7A 83.908 87 10 4 4983 5069 145452839 145452921 5.800000e-11 80.5
36 TraesCS6B01G211100 chr4D 89.870 691 42 19 1 681 127154299 127154971 0.000000e+00 863.0
37 TraesCS6B01G211100 chr4D 84.685 111 13 4 6474 6581 352541366 352541257 2.660000e-19 108.0
38 TraesCS6B01G211100 chr2A 85.975 713 62 20 1 676 688247068 688246357 0.000000e+00 728.0
39 TraesCS6B01G211100 chr2A 91.228 114 9 1 5172 5284 377135620 377135507 3.370000e-33 154.0
40 TraesCS6B01G211100 chr7D 91.929 508 22 10 246 751 610523546 610523056 0.000000e+00 693.0
41 TraesCS6B01G211100 chr7D 88.344 163 12 4 6105 6265 447053661 447053504 9.240000e-44 189.0
42 TraesCS6B01G211100 chr7D 83.721 86 10 4 4984 5069 38012248 38012167 2.090000e-10 78.7
43 TraesCS6B01G211100 chr7B 92.917 240 16 1 456 695 44518136 44517898 1.440000e-91 348.0
44 TraesCS6B01G211100 chr4B 90.385 156 10 2 6112 6265 106227409 106227561 4.270000e-47 200.0
45 TraesCS6B01G211100 chr4B 90.598 117 11 0 5163 5279 262872619 262872503 9.370000e-34 156.0
46 TraesCS6B01G211100 chr3D 89.375 160 13 3 6108 6264 315480420 315480578 1.540000e-46 198.0
47 TraesCS6B01G211100 chr3D 86.857 175 17 4 6094 6265 441388648 441388819 2.570000e-44 191.0
48 TraesCS6B01G211100 chr3D 88.235 102 11 1 6450 6551 604669363 604669263 3.420000e-23 121.0
49 TraesCS6B01G211100 chr3B 89.375 160 14 2 6108 6264 404830477 404830318 1.540000e-46 198.0
50 TraesCS6B01G211100 chr3B 88.235 102 11 1 6450 6551 812340311 812340211 3.420000e-23 121.0
51 TraesCS6B01G211100 chr3A 88.957 163 12 4 6105 6265 582283209 582283367 5.520000e-46 196.0
52 TraesCS6B01G211100 chr3A 96.939 98 3 0 5177 5274 287684685 287684782 1.560000e-36 165.0
53 TraesCS6B01G211100 chr3A 88.235 102 11 1 6450 6551 734786211 734786111 3.420000e-23 121.0
54 TraesCS6B01G211100 chr3A 83.908 87 10 4 4983 5069 714570387 714570305 5.800000e-11 80.5
55 TraesCS6B01G211100 chr1B 75.391 447 61 22 3994 4415 684586611 684586189 3.350000e-38 171.0
56 TraesCS6B01G211100 chr5D 95.238 105 5 0 5175 5279 180472059 180472163 4.330000e-37 167.0
57 TraesCS6B01G211100 chr5D 95.455 66 2 1 687 751 221145221 221145286 3.440000e-18 104.0
58 TraesCS6B01G211100 chr5B 96.939 98 3 0 5177 5274 625959559 625959462 1.560000e-36 165.0
59 TraesCS6B01G211100 chr5B 91.228 114 8 2 5161 5274 428959013 428958902 3.370000e-33 154.0
60 TraesCS6B01G211100 chr5B 84.906 159 15 5 598 751 663985080 663984926 1.210000e-32 152.0
61 TraesCS6B01G211100 chr5B 84.146 82 9 4 4988 5069 576798571 576798648 7.510000e-10 76.8
62 TraesCS6B01G211100 chr1A 92.593 108 8 0 5167 5274 590991967 590991860 9.370000e-34 156.0
63 TraesCS6B01G211100 chr4A 83.140 172 23 5 6414 6581 580297855 580297686 1.210000e-32 152.0
64 TraesCS6B01G211100 chr4A 87.654 81 7 2 6474 6552 112852022 112852101 2.680000e-14 91.6
65 TraesCS6B01G211100 chr4A 85.057 87 9 3 4983 5069 331467509 331467591 1.250000e-12 86.1
66 TraesCS6B01G211100 chr4A 87.143 70 8 1 4983 5051 38715198 38715267 2.090000e-10 78.7
67 TraesCS6B01G211100 chrUn 76.491 285 54 7 3249 3528 364972353 364972629 7.300000e-30 143.0
68 TraesCS6B01G211100 chr5A 85.057 87 9 3 4983 5069 398259142 398259060 1.250000e-12 86.1


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 TraesCS6B01G211100 chr6B 279043860 279050838 6978 False 4368.00 12888 96.2440 1 6979 3 chr6B.!!$F1 6978
1 TraesCS6B01G211100 chr6D 156443655 156451206 7551 False 2465.00 4545 95.6400 811 6951 4 chr6D.!!$F2 6140
2 TraesCS6B01G211100 chr6A 209893717 209901296 7579 False 1951.46 4447 95.0334 854 6951 5 chr6A.!!$F1 6097
3 TraesCS6B01G211100 chr6A 480579273 480579949 676 True 885.00 885 90.3460 1 684 1 chr6A.!!$R1 683
4 TraesCS6B01G211100 chr6A 575554651 575555421 770 False 592.50 1083 95.3535 1 747 2 chr6A.!!$F2 746
5 TraesCS6B01G211100 chr1D 376738126 376738809 683 True 1147.00 1147 96.9300 1 684 1 chr1D.!!$R1 683
6 TraesCS6B01G211100 chr1D 381106695 381107494 799 True 615.50 1123 96.6100 1 747 2 chr1D.!!$R2 746
7 TraesCS6B01G211100 chr2B 730846039 730846722 683 True 1092.00 1092 95.4680 1 684 1 chr2B.!!$R5 683
8 TraesCS6B01G211100 chr2B 384334993 384335618 625 False 736.00 736 88.0250 52 684 1 chr2B.!!$F2 632
9 TraesCS6B01G211100 chr2D 387910704 387911385 681 True 1085.00 1085 95.3220 1 684 1 chr2D.!!$R1 683
10 TraesCS6B01G211100 chr2D 636411399 636412203 804 False 589.00 1068 95.2675 1 751 2 chr2D.!!$F4 750
11 TraesCS6B01G211100 chr7A 688909667 688910470 803 True 588.50 1075 94.5735 1 751 2 chr7A.!!$R1 750
12 TraesCS6B01G211100 chr4D 127154299 127154971 672 False 863.00 863 89.8700 1 681 1 chr4D.!!$F1 680
13 TraesCS6B01G211100 chr2A 688246357 688247068 711 True 728.00 728 85.9750 1 676 1 chr2A.!!$R2 675

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
658 746 0.600255 CTGCGACAAAGACCGGAACT 60.600 55.000 9.46 3.91 0.0 3.01 F
1524 1680 1.143684 ACTCATTCAGCACACCAGGTT 59.856 47.619 0.00 0.00 0.0 3.50 F
2016 2172 1.785353 TTAAGTGGCGGGGCTCCTTT 61.785 55.000 0.00 0.00 0.0 3.11 F
3235 3396 1.881973 TGCAAACCTGTTCAGCTCATC 59.118 47.619 8.30 0.00 0.0 2.92 F
3783 3945 0.035820 TCGAGCGCCCAGGTAAATTT 60.036 50.000 2.29 0.00 0.0 1.82 F
5193 5362 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1993 2149 1.002502 AGCCCCGCCACTTAACTTC 60.003 57.895 0.00 0.00 0.00 3.01 R
2743 2903 0.930310 CTTCCATGACATACGGTGCG 59.070 55.000 0.00 0.00 0.00 5.34 R
3533 3694 0.969149 ACCATCACTTCTCGCTGACA 59.031 50.000 0.00 0.00 0.00 3.58 R
4071 4233 1.271597 ACTCACCTGCCAATGGAACTC 60.272 52.381 2.05 0.00 0.00 3.01 R
5264 5433 0.543749 AGTTGCATGCTACTCCCTCC 59.456 55.000 26.06 2.49 0.00 4.30 R
6467 8218 1.767759 AGGAAAATTGCCATCCTCGG 58.232 50.000 0.00 0.00 39.36 4.63 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
63 65 3.188048 GCAACTCTTGTGAAGTCCATCAG 59.812 47.826 0.00 0.00 0.00 2.90
173 175 3.526534 GGTGTTTTGCAAGCAAGGTTTA 58.473 40.909 7.60 0.00 37.24 2.01
183 185 4.217550 GCAAGCAAGGTTTACCATAGTTCA 59.782 41.667 1.13 0.00 38.89 3.18
191 193 4.263594 GGTTTACCATAGTTCAGGGTCCAA 60.264 45.833 0.00 0.00 41.49 3.53
205 207 2.235891 GGTCCAACTCGTTTTTGGGAT 58.764 47.619 11.00 0.00 43.38 3.85
410 413 0.982852 TCATGGTCAGCTCCGGGATT 60.983 55.000 0.00 0.00 0.00 3.01
429 432 6.246919 GGGATTATCTAGTAGAGCACCAGTA 58.753 44.000 5.98 0.00 0.00 2.74
639 727 1.616865 GACAGTTTTAAGGGTTGGGGC 59.383 52.381 0.00 0.00 0.00 5.80
652 740 3.056328 GGGGCTGCGACAAAGACC 61.056 66.667 0.00 0.00 42.77 3.85
653 741 3.423154 GGGCTGCGACAAAGACCG 61.423 66.667 0.00 0.00 31.66 4.79
658 746 0.600255 CTGCGACAAAGACCGGAACT 60.600 55.000 9.46 3.91 0.00 3.01
733 877 6.650427 ATTCTCAACCCTTAAACTGGTTTC 57.350 37.500 1.77 0.00 42.09 2.78
735 879 5.511363 TCTCAACCCTTAAACTGGTTTCAA 58.489 37.500 1.77 0.00 42.09 2.69
751 895 5.073965 TGGTTTCAAGGTTTGAGGGTACTAT 59.926 40.000 0.00 0.00 41.38 2.12
752 896 6.008331 GGTTTCAAGGTTTGAGGGTACTATT 58.992 40.000 0.00 0.00 41.38 1.73
753 897 6.492429 GGTTTCAAGGTTTGAGGGTACTATTT 59.508 38.462 0.00 0.00 41.38 1.40
754 898 7.014905 GGTTTCAAGGTTTGAGGGTACTATTTT 59.985 37.037 0.00 0.00 41.38 1.82
755 899 8.418662 GTTTCAAGGTTTGAGGGTACTATTTTT 58.581 33.333 0.00 0.00 41.38 1.94
779 923 6.947644 TTTTTGAGGTAAGTTCAAGGGTAC 57.052 37.500 0.00 0.00 36.07 3.34
780 924 5.899631 TTTGAGGTAAGTTCAAGGGTACT 57.100 39.130 0.00 0.00 36.07 2.73
781 925 4.884668 TGAGGTAAGTTCAAGGGTACTG 57.115 45.455 0.00 0.00 0.00 2.74
782 926 3.007614 TGAGGTAAGTTCAAGGGTACTGC 59.992 47.826 0.00 0.00 0.00 4.40
783 927 3.248888 AGGTAAGTTCAAGGGTACTGCT 58.751 45.455 0.00 0.00 0.00 4.24
784 928 4.422984 AGGTAAGTTCAAGGGTACTGCTA 58.577 43.478 0.00 0.00 0.00 3.49
785 929 4.466726 AGGTAAGTTCAAGGGTACTGCTAG 59.533 45.833 0.00 0.00 0.00 3.42
786 930 4.222366 GGTAAGTTCAAGGGTACTGCTAGT 59.778 45.833 0.00 0.00 0.00 2.57
787 931 3.963428 AGTTCAAGGGTACTGCTAGTG 57.037 47.619 0.00 0.00 0.00 2.74
788 932 3.507411 AGTTCAAGGGTACTGCTAGTGA 58.493 45.455 0.00 0.00 0.00 3.41
789 933 4.097418 AGTTCAAGGGTACTGCTAGTGAT 58.903 43.478 0.00 0.00 0.00 3.06
790 934 4.081420 AGTTCAAGGGTACTGCTAGTGATG 60.081 45.833 0.00 0.00 0.00 3.07
791 935 2.168521 TCAAGGGTACTGCTAGTGATGC 59.831 50.000 0.00 0.00 0.00 3.91
792 936 2.166907 AGGGTACTGCTAGTGATGCT 57.833 50.000 0.00 0.00 0.00 3.79
793 937 2.035632 AGGGTACTGCTAGTGATGCTC 58.964 52.381 0.00 0.00 0.00 4.26
794 938 2.035632 GGGTACTGCTAGTGATGCTCT 58.964 52.381 0.00 0.00 0.00 4.09
795 939 3.117474 AGGGTACTGCTAGTGATGCTCTA 60.117 47.826 0.00 0.00 0.00 2.43
796 940 3.637229 GGGTACTGCTAGTGATGCTCTAA 59.363 47.826 0.00 0.00 0.00 2.10
797 941 4.099573 GGGTACTGCTAGTGATGCTCTAAA 59.900 45.833 0.00 0.00 0.00 1.85
798 942 5.285651 GGTACTGCTAGTGATGCTCTAAAG 58.714 45.833 0.00 0.00 0.00 1.85
799 943 5.163499 GGTACTGCTAGTGATGCTCTAAAGT 60.163 44.000 0.00 0.00 0.00 2.66
800 944 4.753233 ACTGCTAGTGATGCTCTAAAGTG 58.247 43.478 0.00 0.00 0.00 3.16
801 945 4.464244 ACTGCTAGTGATGCTCTAAAGTGA 59.536 41.667 0.00 0.00 0.00 3.41
802 946 5.003692 TGCTAGTGATGCTCTAAAGTGAG 57.996 43.478 0.00 0.00 37.16 3.51
1007 1151 3.515286 GGCGAGGACGATGGACGA 61.515 66.667 0.00 0.00 45.77 4.20
1121 1272 2.298446 CTCTCTCTCTTTCTGTGGTGCA 59.702 50.000 0.00 0.00 0.00 4.57
1170 1321 1.699656 CCTCTTTGCCGCTGACATCG 61.700 60.000 0.00 0.00 0.00 3.84
1270 1421 4.623932 TTACTGAGAAGTTGAGCCACAT 57.376 40.909 0.00 0.00 0.00 3.21
1337 1488 9.953825 GAAAATCGATATAGCTTTGGTATAACG 57.046 33.333 15.29 15.29 42.06 3.18
1342 1493 8.245491 TCGATATAGCTTTGGTATAACGCATTA 58.755 33.333 16.09 3.25 41.21 1.90
1358 1511 9.878599 ATAACGCATTAATACTAAATGTTGAGC 57.121 29.630 0.00 0.00 36.82 4.26
1395 1551 8.729805 AGATACTCAGGAAAGATGACAATTTC 57.270 34.615 7.61 7.61 35.19 2.17
1408 1564 7.173722 AGATGACAATTTCAACCTTCTCAGAT 58.826 34.615 0.00 0.00 37.92 2.90
1410 1566 6.537355 TGACAATTTCAACCTTCTCAGATCT 58.463 36.000 0.00 0.00 0.00 2.75
1421 1577 8.474025 CAACCTTCTCAGATCTCTATACTTTGT 58.526 37.037 0.00 0.00 0.00 2.83
1482 1638 1.335496 GCGTTTGCTAAGGACCAACAA 59.665 47.619 4.77 0.00 38.39 2.83
1524 1680 1.143684 ACTCATTCAGCACACCAGGTT 59.856 47.619 0.00 0.00 0.00 3.50
1548 1704 6.500684 TGGATCTTGTGAAATTAGAACTGC 57.499 37.500 0.00 0.00 0.00 4.40
1581 1737 8.021396 GTGATAAAACTAGTTCATGTTTGACCC 58.979 37.037 8.95 0.00 36.63 4.46
1632 1788 2.932614 CACACATCTAGCAGCCAGTAAC 59.067 50.000 0.00 0.00 0.00 2.50
1688 1844 2.076100 TGCTGCCGAACAACTTGATAG 58.924 47.619 0.00 0.00 0.00 2.08
1719 1875 9.489084 TCATGTAAGCGCTATGAATTTAAGTAT 57.511 29.630 16.96 0.00 0.00 2.12
1747 1903 7.117454 CGCTATCAAATACAACTTTTCTACCG 58.883 38.462 0.00 0.00 0.00 4.02
1789 1945 9.465199 TGTGATTTATCATGGAAATCTCTTTCA 57.535 29.630 23.20 15.57 41.75 2.69
1931 2087 2.217393 CGAGCATTCATAGCGACTTCAC 59.783 50.000 0.00 0.00 37.01 3.18
1976 2132 2.234661 TGAGGACCTCACTAACAGCATG 59.765 50.000 20.74 0.00 37.64 4.06
2016 2172 1.785353 TTAAGTGGCGGGGCTCCTTT 61.785 55.000 0.00 0.00 0.00 3.11
2046 2202 4.916983 TCAGCTACAAGTTGTGCAATTT 57.083 36.364 18.90 2.17 30.52 1.82
2047 2203 6.384258 TTCAGCTACAAGTTGTGCAATTTA 57.616 33.333 18.90 0.00 30.52 1.40
2048 2204 6.384258 TCAGCTACAAGTTGTGCAATTTAA 57.616 33.333 18.90 0.00 30.52 1.52
2116 2272 3.887741 TGCACAATTGATGTCGAAACTG 58.112 40.909 13.59 0.00 41.46 3.16
2361 2517 5.927030 TCAATTTCACATCGAAGCTGTTAC 58.073 37.500 0.00 0.00 34.32 2.50
2410 2566 5.008613 GCACACTCATTTTGGTGTCTTCTTA 59.991 40.000 0.00 0.00 43.65 2.10
2413 2569 7.805071 CACACTCATTTTGGTGTCTTCTTATTC 59.195 37.037 0.00 0.00 43.65 1.75
2500 2656 9.965824 CAATTTAAGCAAAGTTTTCCTCTTCTA 57.034 29.630 0.00 0.00 0.00 2.10
2562 2718 2.234143 TCGCTCCTCTAGTCATGATGG 58.766 52.381 0.00 0.00 0.00 3.51
2633 2793 4.350368 TGGTCACTATCTCAACTGCAAA 57.650 40.909 0.00 0.00 0.00 3.68
2634 2794 4.065088 TGGTCACTATCTCAACTGCAAAC 58.935 43.478 0.00 0.00 0.00 2.93
2635 2795 4.065088 GGTCACTATCTCAACTGCAAACA 58.935 43.478 0.00 0.00 0.00 2.83
2636 2796 4.515191 GGTCACTATCTCAACTGCAAACAA 59.485 41.667 0.00 0.00 0.00 2.83
2793 2953 1.974236 AGAGCAAACCTGTCACTAGCT 59.026 47.619 0.00 0.00 0.00 3.32
2897 3057 6.666546 TGCCAGTTACTACCATACTAGTTCTT 59.333 38.462 0.00 0.00 0.00 2.52
3183 3344 6.873605 CCTTATACAGTGAGTGAATGTGTTCA 59.126 38.462 0.00 0.00 41.89 3.18
3235 3396 1.881973 TGCAAACCTGTTCAGCTCATC 59.118 47.619 8.30 0.00 0.00 2.92
3533 3694 6.485648 GTCAGCGGATTATTTGTAAACCCTAT 59.514 38.462 0.00 0.00 0.00 2.57
3684 3846 7.881775 AAAAGATGAACTGTTACAACTTCCT 57.118 32.000 12.25 5.00 30.94 3.36
3685 3847 7.881775 AAAGATGAACTGTTACAACTTCCTT 57.118 32.000 12.25 0.00 30.94 3.36
3686 3848 7.497925 AAGATGAACTGTTACAACTTCCTTC 57.502 36.000 0.00 0.00 0.00 3.46
3687 3849 6.591935 AGATGAACTGTTACAACTTCCTTCA 58.408 36.000 0.00 0.00 0.00 3.02
3688 3850 7.054124 AGATGAACTGTTACAACTTCCTTCAA 58.946 34.615 0.00 0.00 0.00 2.69
3689 3851 7.721399 AGATGAACTGTTACAACTTCCTTCAAT 59.279 33.333 0.00 0.00 0.00 2.57
3690 3852 7.639113 TGAACTGTTACAACTTCCTTCAATT 57.361 32.000 0.00 0.00 0.00 2.32
3691 3853 8.740123 TGAACTGTTACAACTTCCTTCAATTA 57.260 30.769 0.00 0.00 0.00 1.40
3692 3854 9.349713 TGAACTGTTACAACTTCCTTCAATTAT 57.650 29.630 0.00 0.00 0.00 1.28
3783 3945 0.035820 TCGAGCGCCCAGGTAAATTT 60.036 50.000 2.29 0.00 0.00 1.82
3925 4087 4.380973 GCTTTTGGTTTCTTCCTATGGCTC 60.381 45.833 0.00 0.00 0.00 4.70
4224 4389 8.474025 TGTGTAAGTGATTTCTCATTTTGGTTT 58.526 29.630 0.00 0.00 33.78 3.27
4422 4587 3.713764 AGGCACCTGCTCTTAGTAATGAT 59.286 43.478 0.00 0.00 41.70 2.45
4500 4665 2.123428 GCGCCCATTCATCTTGGCT 61.123 57.895 0.00 0.00 41.80 4.75
4509 4674 4.319046 CCATTCATCTTGGCTAAATCGACG 60.319 45.833 0.00 0.00 0.00 5.12
4526 4691 5.327616 TCGACGGATATTTTGGTCAACTA 57.672 39.130 0.00 0.00 0.00 2.24
4714 4879 0.539051 ACAGTGGATCTACAGCTGCC 59.461 55.000 15.27 7.03 0.00 4.85
4827 4993 6.870439 GTGCTATGTGCTGATAGTTGATATGA 59.130 38.462 4.97 0.00 43.37 2.15
5177 5346 4.218417 AGGCGCTAAAAATTCTTGTGATGT 59.782 37.500 7.64 0.00 0.00 3.06
5178 5347 5.414454 AGGCGCTAAAAATTCTTGTGATGTA 59.586 36.000 7.64 0.00 0.00 2.29
5179 5348 5.511729 GGCGCTAAAAATTCTTGTGATGTAC 59.488 40.000 7.64 0.00 0.00 2.90
5180 5349 6.314784 GCGCTAAAAATTCTTGTGATGTACT 58.685 36.000 0.00 0.00 0.00 2.73
5181 5350 6.466097 GCGCTAAAAATTCTTGTGATGTACTC 59.534 38.462 0.00 0.00 0.00 2.59
5182 5351 6.961554 CGCTAAAAATTCTTGTGATGTACTCC 59.038 38.462 0.00 0.00 0.00 3.85
5183 5352 7.251281 GCTAAAAATTCTTGTGATGTACTCCC 58.749 38.462 0.00 0.00 0.00 4.30
5184 5353 7.121315 GCTAAAAATTCTTGTGATGTACTCCCT 59.879 37.037 0.00 0.00 0.00 4.20
5185 5354 7.454260 AAAAATTCTTGTGATGTACTCCCTC 57.546 36.000 0.00 0.00 0.00 4.30
5186 5355 4.762289 ATTCTTGTGATGTACTCCCTCC 57.238 45.455 0.00 0.00 0.00 4.30
5187 5356 2.100197 TCTTGTGATGTACTCCCTCCG 58.900 52.381 0.00 0.00 0.00 4.63
5188 5357 1.825474 CTTGTGATGTACTCCCTCCGT 59.175 52.381 0.00 0.00 0.00 4.69
5189 5358 1.471119 TGTGATGTACTCCCTCCGTC 58.529 55.000 0.00 0.00 0.00 4.79
5190 5359 0.745468 GTGATGTACTCCCTCCGTCC 59.255 60.000 0.00 0.00 0.00 4.79
5191 5360 0.396695 TGATGTACTCCCTCCGTCCC 60.397 60.000 0.00 0.00 0.00 4.46
5192 5361 0.396695 GATGTACTCCCTCCGTCCCA 60.397 60.000 0.00 0.00 0.00 4.37
5193 5362 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
5194 5363 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
5195 5364 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
5196 5365 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
5197 5366 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
5198 5367 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
5199 5368 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
5200 5369 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
5201 5370 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
5202 5371 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
5203 5372 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
5204 5373 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
5205 5374 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
5206 5375 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
5207 5376 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
5208 5377 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
5209 5378 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
5210 5379 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
5211 5380 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
5212 5381 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
5213 5382 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
5214 5383 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
5215 5384 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
5216 5385 8.621286 CCAAAATAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
5222 5391 8.788325 AAGTGACTCAACTTTGTACTAACTTT 57.212 30.769 0.00 0.00 37.05 2.66
5223 5392 9.880157 AAGTGACTCAACTTTGTACTAACTTTA 57.120 29.630 0.00 0.00 37.05 1.85
5224 5393 9.530633 AGTGACTCAACTTTGTACTAACTTTAG 57.469 33.333 0.00 0.00 36.82 1.85
5225 5394 9.310716 GTGACTCAACTTTGTACTAACTTTAGT 57.689 33.333 6.85 6.85 45.39 2.24
5250 5419 9.909644 GTAGAATCTTAGTACAAACTTGAGTCA 57.090 33.333 0.00 0.00 35.97 3.41
5251 5420 8.819643 AGAATCTTAGTACAAACTTGAGTCAC 57.180 34.615 0.00 0.00 35.97 3.67
5252 5421 8.643324 AGAATCTTAGTACAAACTTGAGTCACT 58.357 33.333 0.00 0.00 35.97 3.41
5253 5422 9.262358 GAATCTTAGTACAAACTTGAGTCACTT 57.738 33.333 0.00 0.00 37.15 3.16
5260 5429 8.621286 AGTACAAACTTGAGTCACTTATTTTGG 58.379 33.333 9.57 0.00 29.00 3.28
5261 5430 6.805713 ACAAACTTGAGTCACTTATTTTGGG 58.194 36.000 9.57 0.00 0.00 4.12
5262 5431 6.605594 ACAAACTTGAGTCACTTATTTTGGGA 59.394 34.615 9.57 0.00 0.00 4.37
5263 5432 6.635030 AACTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 0.00 4.46
5264 5433 4.755123 ACTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
5265 5434 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
5266 5435 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
5267 5436 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
5268 5437 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
5269 5438 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
5270 5439 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
5271 5440 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
5855 7594 7.425606 GTGTGTTTTCTCCAATTGTTGTATCT 58.574 34.615 4.43 0.00 0.00 1.98
5899 7638 7.730364 TTTGTTTTAGAAAGGCTGAGAGTAG 57.270 36.000 0.00 0.00 0.00 2.57
5910 7649 6.619329 AGGCTGAGAGTAGAAAAATTCTCT 57.381 37.500 0.00 0.00 41.14 3.10
6020 7759 3.698289 AGAGGAAGATGTACCGAGAACA 58.302 45.455 0.00 0.00 0.00 3.18
6099 7838 1.372087 CTTGCCATTGTCTCGGAGCC 61.372 60.000 0.00 0.00 0.00 4.70
6121 7860 4.656112 CCACTGAAATATGTACTCCCTCCT 59.344 45.833 0.00 0.00 0.00 3.69
6326 8073 8.121305 TGGACTGCATGTTTTTATTTATCAGT 57.879 30.769 0.00 0.00 35.29 3.41
6406 8155 6.855836 TGATGGAATGCTAAAAATCTGACAC 58.144 36.000 0.00 0.00 0.00 3.67
6407 8156 6.433716 TGATGGAATGCTAAAAATCTGACACA 59.566 34.615 0.00 0.00 0.00 3.72
6485 8236 0.746659 CCCGAGGATGGCAATTTTCC 59.253 55.000 0.00 0.00 0.00 3.13
6554 9282 5.464389 GGATTTGCCATGCTTGCTAAAATAG 59.536 40.000 0.00 0.00 36.34 1.73
6567 9296 7.421530 TTGCTAAAATAGTTATCATCCTCGC 57.578 36.000 0.00 0.00 0.00 5.03
6570 9299 6.531948 GCTAAAATAGTTATCATCCTCGCGAT 59.468 38.462 10.36 0.00 0.00 4.58
6582 9311 6.220201 TCATCCTCGCGATAACATAATTTGA 58.780 36.000 10.36 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 65 2.286826 GGCACCCCATTTTTCTCCC 58.713 57.895 0.00 0.00 0.00 4.30
173 175 2.572104 GAGTTGGACCCTGAACTATGGT 59.428 50.000 0.00 0.00 32.47 3.55
213 216 4.597004 ACATTTCATGATGCTCTCCAAGT 58.403 39.130 0.00 0.00 0.00 3.16
222 225 6.097356 AGAATCACACAACATTTCATGATGC 58.903 36.000 0.00 0.00 36.63 3.91
410 413 5.163184 ACTGCTACTGGTGCTCTACTAGATA 60.163 44.000 0.00 0.00 40.06 1.98
639 727 0.600255 AGTTCCGGTCTTTGTCGCAG 60.600 55.000 0.00 0.00 0.00 5.18
652 740 1.235724 GGTTGGGTTTGAGAGTTCCG 58.764 55.000 0.00 0.00 0.00 4.30
653 741 1.145119 AGGGTTGGGTTTGAGAGTTCC 59.855 52.381 0.00 0.00 0.00 3.62
658 746 4.566070 CCGTTATAAGGGTTGGGTTTGAGA 60.566 45.833 14.83 0.00 0.00 3.27
756 900 6.544564 CAGTACCCTTGAACTTACCTCAAAAA 59.455 38.462 0.00 0.00 32.57 1.94
757 901 6.059484 CAGTACCCTTGAACTTACCTCAAAA 58.941 40.000 0.00 0.00 32.57 2.44
758 902 5.617252 CAGTACCCTTGAACTTACCTCAAA 58.383 41.667 0.00 0.00 32.57 2.69
759 903 4.504340 GCAGTACCCTTGAACTTACCTCAA 60.504 45.833 0.00 0.00 0.00 3.02
760 904 3.007614 GCAGTACCCTTGAACTTACCTCA 59.992 47.826 0.00 0.00 0.00 3.86
761 905 3.261137 AGCAGTACCCTTGAACTTACCTC 59.739 47.826 0.00 0.00 0.00 3.85
762 906 3.248888 AGCAGTACCCTTGAACTTACCT 58.751 45.455 0.00 0.00 0.00 3.08
763 907 3.697619 AGCAGTACCCTTGAACTTACC 57.302 47.619 0.00 0.00 0.00 2.85
764 908 5.047519 TCACTAGCAGTACCCTTGAACTTAC 60.048 44.000 0.00 0.00 0.00 2.34
765 909 5.081728 TCACTAGCAGTACCCTTGAACTTA 58.918 41.667 0.00 0.00 0.00 2.24
766 910 3.901844 TCACTAGCAGTACCCTTGAACTT 59.098 43.478 0.00 0.00 0.00 2.66
767 911 3.507411 TCACTAGCAGTACCCTTGAACT 58.493 45.455 0.00 0.00 0.00 3.01
768 912 3.955650 TCACTAGCAGTACCCTTGAAC 57.044 47.619 0.00 0.00 0.00 3.18
769 913 3.369471 GCATCACTAGCAGTACCCTTGAA 60.369 47.826 0.00 0.00 0.00 2.69
770 914 2.168521 GCATCACTAGCAGTACCCTTGA 59.831 50.000 0.00 0.00 0.00 3.02
771 915 2.169352 AGCATCACTAGCAGTACCCTTG 59.831 50.000 0.00 0.00 0.00 3.61
772 916 2.432510 GAGCATCACTAGCAGTACCCTT 59.567 50.000 0.00 0.00 33.17 3.95
773 917 2.035632 GAGCATCACTAGCAGTACCCT 58.964 52.381 0.00 0.00 33.17 4.34
774 918 2.035632 AGAGCATCACTAGCAGTACCC 58.964 52.381 0.00 0.00 37.82 3.69
775 919 4.920640 TTAGAGCATCACTAGCAGTACC 57.079 45.455 0.00 0.00 37.82 3.34
776 920 5.746245 CACTTTAGAGCATCACTAGCAGTAC 59.254 44.000 0.00 0.00 37.82 2.73
777 921 5.652452 TCACTTTAGAGCATCACTAGCAGTA 59.348 40.000 0.00 0.00 37.82 2.74
778 922 4.464244 TCACTTTAGAGCATCACTAGCAGT 59.536 41.667 0.00 0.00 37.82 4.40
779 923 5.003692 TCACTTTAGAGCATCACTAGCAG 57.996 43.478 0.00 0.00 37.82 4.24
780 924 5.003692 CTCACTTTAGAGCATCACTAGCA 57.996 43.478 0.00 0.00 37.82 3.49
802 946 3.764885 ATTTTTGGAGTGAGCGTATGC 57.235 42.857 0.00 0.00 43.24 3.14
803 947 5.123186 TGGTAATTTTTGGAGTGAGCGTATG 59.877 40.000 0.00 0.00 0.00 2.39
804 948 5.250200 TGGTAATTTTTGGAGTGAGCGTAT 58.750 37.500 0.00 0.00 0.00 3.06
805 949 4.643463 TGGTAATTTTTGGAGTGAGCGTA 58.357 39.130 0.00 0.00 0.00 4.42
806 950 3.482436 TGGTAATTTTTGGAGTGAGCGT 58.518 40.909 0.00 0.00 0.00 5.07
807 951 4.155826 TCATGGTAATTTTTGGAGTGAGCG 59.844 41.667 0.00 0.00 0.00 5.03
808 952 5.183904 ACTCATGGTAATTTTTGGAGTGAGC 59.816 40.000 0.00 0.00 35.25 4.26
809 953 6.824305 ACTCATGGTAATTTTTGGAGTGAG 57.176 37.500 0.00 0.00 37.25 3.51
810 954 7.595819 AAACTCATGGTAATTTTTGGAGTGA 57.404 32.000 0.00 0.00 34.64 3.41
811 955 9.357652 CATAAACTCATGGTAATTTTTGGAGTG 57.642 33.333 0.00 0.00 34.64 3.51
812 956 8.034804 GCATAAACTCATGGTAATTTTTGGAGT 58.965 33.333 0.00 0.00 35.80 3.85
1121 1272 1.362717 CGCCCGAGTCCGAATACAT 59.637 57.895 0.00 0.00 38.22 2.29
1170 1321 1.456705 ATCGCTCCCCTCTCCACTC 60.457 63.158 0.00 0.00 0.00 3.51
1335 1486 7.315247 TGCTCAACATTTAGTATTAATGCGT 57.685 32.000 0.00 0.00 36.65 5.24
1370 1526 8.324306 TGAAATTGTCATCTTTCCTGAGTATCT 58.676 33.333 6.14 0.00 31.30 1.98
1379 1535 6.986250 AGAAGGTTGAAATTGTCATCTTTCC 58.014 36.000 6.28 0.00 40.43 3.13
1384 1540 6.808008 TCTGAGAAGGTTGAAATTGTCATC 57.192 37.500 0.00 0.00 35.70 2.92
1395 1551 8.474025 ACAAAGTATAGAGATCTGAGAAGGTTG 58.526 37.037 0.00 0.00 0.00 3.77
1426 1582 6.127026 GCCTAAGGAGAAGAAAAGGAGTCATA 60.127 42.308 0.00 0.00 0.00 2.15
1428 1584 4.020128 GCCTAAGGAGAAGAAAAGGAGTCA 60.020 45.833 0.00 0.00 0.00 3.41
1429 1585 4.509616 GCCTAAGGAGAAGAAAAGGAGTC 58.490 47.826 0.00 0.00 0.00 3.36
1444 1600 1.751927 CTGCAGCAAGGGCCTAAGG 60.752 63.158 6.41 0.00 42.56 2.69
1524 1680 6.071952 GGCAGTTCTAATTTCACAAGATCCAA 60.072 38.462 0.00 0.00 0.00 3.53
1548 1704 4.925054 TGAACTAGTTTTATCACGGTTCGG 59.075 41.667 10.02 0.00 37.22 4.30
1632 1788 1.651987 CCACAGGCATGTACCTAACG 58.348 55.000 2.51 0.00 38.26 3.18
1719 1875 7.681939 AGAAAAGTTGTATTTGATAGCGGAA 57.318 32.000 0.00 0.00 0.00 4.30
1737 1893 6.870769 TGGAAATAGACCTACGGTAGAAAAG 58.129 40.000 16.59 2.44 35.25 2.27
1887 2043 5.619981 CGGATCATTTCCAAACACTTCTTCC 60.620 44.000 0.00 0.00 45.78 3.46
1920 2076 3.934457 TTGATCACAGTGAAGTCGCTA 57.066 42.857 7.50 0.00 34.49 4.26
1931 2087 4.491676 CAGGGCAAAGAAATTGATCACAG 58.508 43.478 0.00 0.00 41.85 3.66
1993 2149 1.002502 AGCCCCGCCACTTAACTTC 60.003 57.895 0.00 0.00 0.00 3.01
2016 2172 6.321717 CACAACTTGTAGCTGAAACTTGAAA 58.678 36.000 0.00 0.00 0.00 2.69
2046 2202 8.777413 GTGCAAATCACTATCAGAGCATTATTA 58.223 33.333 0.00 0.00 42.38 0.98
2047 2203 7.646314 GTGCAAATCACTATCAGAGCATTATT 58.354 34.615 0.00 0.00 42.38 1.40
2048 2204 7.199541 GTGCAAATCACTATCAGAGCATTAT 57.800 36.000 0.00 0.00 42.38 1.28
2083 2239 7.383687 ACATCAATTGTGCATCAGAATTTCTT 58.616 30.769 5.13 0.00 35.62 2.52
2116 2272 6.034683 GTGAATGATGCTTGCTGAAATTCTTC 59.965 38.462 0.00 0.00 0.00 2.87
2361 2517 7.869429 GCAATCCCTCATAAAATCATTACAAGG 59.131 37.037 0.00 0.00 0.00 3.61
2410 2566 4.261031 GCACGTAAACAAACAGGAGTGAAT 60.261 41.667 0.00 0.00 0.00 2.57
2413 2569 2.612212 AGCACGTAAACAAACAGGAGTG 59.388 45.455 0.00 0.00 0.00 3.51
2500 2656 6.174049 GGGAGCTTCTTGAAAGTACTTGTAT 58.826 40.000 9.34 0.00 0.00 2.29
2580 2736 9.625747 AAACCAAACCAAACAATAATTCAAGAT 57.374 25.926 0.00 0.00 0.00 2.40
2743 2903 0.930310 CTTCCATGACATACGGTGCG 59.070 55.000 0.00 0.00 0.00 5.34
2793 2953 1.421268 ACTGATCAACCTGCAGGAACA 59.579 47.619 39.19 24.94 38.94 3.18
2850 3010 5.384336 CATGGTCCCATGTAATTGGATACA 58.616 41.667 16.60 0.00 46.46 2.29
2897 3057 1.078918 CCCGCAATCTCTGTGCTGA 60.079 57.895 0.00 0.00 39.95 4.26
3235 3396 6.422223 GGTAATCAGTTAATCACATTCGCAG 58.578 40.000 0.00 0.00 0.00 5.18
3392 3553 7.559590 ACTATTATTGATTGACAGGCTCAAC 57.440 36.000 0.00 0.00 41.87 3.18
3533 3694 0.969149 ACCATCACTTCTCGCTGACA 59.031 50.000 0.00 0.00 0.00 3.58
3659 3821 8.293699 AGGAAGTTGTAACAGTTCATCTTTTT 57.706 30.769 0.00 0.00 0.00 1.94
3660 3822 7.881775 AGGAAGTTGTAACAGTTCATCTTTT 57.118 32.000 0.00 0.00 0.00 2.27
3661 3823 7.556275 TGAAGGAAGTTGTAACAGTTCATCTTT 59.444 33.333 0.00 0.00 0.00 2.52
3662 3824 7.054124 TGAAGGAAGTTGTAACAGTTCATCTT 58.946 34.615 0.00 0.00 0.00 2.40
3663 3825 6.591935 TGAAGGAAGTTGTAACAGTTCATCT 58.408 36.000 0.00 0.00 0.00 2.90
3664 3826 6.861065 TGAAGGAAGTTGTAACAGTTCATC 57.139 37.500 0.00 0.00 0.00 2.92
3665 3827 7.823745 ATTGAAGGAAGTTGTAACAGTTCAT 57.176 32.000 0.00 0.00 0.00 2.57
3666 3828 7.639113 AATTGAAGGAAGTTGTAACAGTTCA 57.361 32.000 0.00 0.00 0.00 3.18
3783 3945 4.286813 AGGGAGATCCAGGACTAATCAA 57.713 45.455 0.47 0.00 38.24 2.57
3925 4087 4.324402 GCATTTATCACAAGAAAACTGCCG 59.676 41.667 0.00 0.00 0.00 5.69
4071 4233 1.271597 ACTCACCTGCCAATGGAACTC 60.272 52.381 2.05 0.00 0.00 3.01
4224 4389 3.072211 GCTGCAGCAGATTGATAGCATA 58.928 45.455 33.36 0.00 41.59 3.14
4422 4587 6.757010 GTCGATTATTGAAAAGGAGAGTGCTA 59.243 38.462 0.00 0.00 0.00 3.49
4500 4665 6.819649 AGTTGACCAAAATATCCGTCGATTTA 59.180 34.615 0.00 0.00 0.00 1.40
5177 5346 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
5178 5347 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
5179 5348 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
5180 5349 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
5181 5350 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
5182 5351 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
5183 5352 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
5184 5353 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
5185 5354 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
5186 5355 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
5187 5356 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
5188 5357 6.605594 ACAAAGTTGAGTCACTTATTTTGGGA 59.394 34.615 12.94 0.00 35.87 4.37
5189 5358 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
5190 5359 8.621286 AGTACAAAGTTGAGTCACTTATTTTGG 58.379 33.333 12.94 0.78 35.87 3.28
5196 5365 9.880157 AAAGTTAGTACAAAGTTGAGTCACTTA 57.120 29.630 0.00 0.00 35.87 2.24
5197 5366 8.788325 AAAGTTAGTACAAAGTTGAGTCACTT 57.212 30.769 0.00 0.00 38.74 3.16
5198 5367 9.530633 CTAAAGTTAGTACAAAGTTGAGTCACT 57.469 33.333 0.00 0.00 0.00 3.41
5199 5368 9.310716 ACTAAAGTTAGTACAAAGTTGAGTCAC 57.689 33.333 1.81 0.00 41.92 3.67
5224 5393 9.909644 TGACTCAAGTTTGTACTAAGATTCTAC 57.090 33.333 0.00 0.00 33.17 2.59
5225 5394 9.909644 GTGACTCAAGTTTGTACTAAGATTCTA 57.090 33.333 0.00 0.00 33.17 2.10
5226 5395 8.643324 AGTGACTCAAGTTTGTACTAAGATTCT 58.357 33.333 0.00 0.00 33.17 2.40
5227 5396 8.819643 AGTGACTCAAGTTTGTACTAAGATTC 57.180 34.615 0.00 0.00 33.17 2.52
5234 5403 8.621286 CCAAAATAAGTGACTCAAGTTTGTACT 58.379 33.333 15.07 0.00 35.68 2.73
5235 5404 7.860872 CCCAAAATAAGTGACTCAAGTTTGTAC 59.139 37.037 15.07 0.00 0.00 2.90
5236 5405 7.776030 TCCCAAAATAAGTGACTCAAGTTTGTA 59.224 33.333 15.07 5.29 0.00 2.41
5237 5406 6.605594 TCCCAAAATAAGTGACTCAAGTTTGT 59.394 34.615 15.07 0.00 0.00 2.83
5238 5407 6.918022 GTCCCAAAATAAGTGACTCAAGTTTG 59.082 38.462 11.50 11.50 0.00 2.93
5239 5408 6.238648 CGTCCCAAAATAAGTGACTCAAGTTT 60.239 38.462 0.00 0.00 0.00 2.66
5240 5409 5.238650 CGTCCCAAAATAAGTGACTCAAGTT 59.761 40.000 0.00 0.00 0.00 2.66
5241 5410 4.755123 CGTCCCAAAATAAGTGACTCAAGT 59.245 41.667 0.00 0.00 0.00 3.16
5242 5411 4.154195 CCGTCCCAAAATAAGTGACTCAAG 59.846 45.833 0.00 0.00 0.00 3.02
5243 5412 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
5244 5413 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
5245 5414 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
5246 5415 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
5247 5416 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
5248 5417 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
5249 5418 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
5250 5419 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
5251 5420 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
5252 5421 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
5253 5422 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
5254 5423 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
5255 5424 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
5256 5425 1.262640 GCTACTCCCTCCGTCCCAAA 61.263 60.000 0.00 0.00 0.00 3.28
5257 5426 1.684734 GCTACTCCCTCCGTCCCAA 60.685 63.158 0.00 0.00 0.00 4.12
5258 5427 2.043248 GCTACTCCCTCCGTCCCA 60.043 66.667 0.00 0.00 0.00 4.37
5259 5428 1.457831 ATGCTACTCCCTCCGTCCC 60.458 63.158 0.00 0.00 0.00 4.46
5260 5429 1.742768 CATGCTACTCCCTCCGTCC 59.257 63.158 0.00 0.00 0.00 4.79
5261 5430 1.068250 GCATGCTACTCCCTCCGTC 59.932 63.158 11.37 0.00 0.00 4.79
5262 5431 1.264749 TTGCATGCTACTCCCTCCGT 61.265 55.000 20.33 0.00 0.00 4.69
5263 5432 0.811616 GTTGCATGCTACTCCCTCCG 60.812 60.000 22.60 0.00 0.00 4.63
5264 5433 0.543749 AGTTGCATGCTACTCCCTCC 59.456 55.000 26.06 2.49 0.00 4.30
5265 5434 1.208052 TCAGTTGCATGCTACTCCCTC 59.792 52.381 28.33 4.56 30.18 4.30
5266 5435 1.065854 GTCAGTTGCATGCTACTCCCT 60.066 52.381 28.33 8.71 30.18 4.20
5267 5436 1.339055 TGTCAGTTGCATGCTACTCCC 60.339 52.381 28.33 21.37 30.18 4.30
5268 5437 2.099141 TGTCAGTTGCATGCTACTCC 57.901 50.000 28.33 21.67 30.18 3.85
5269 5438 4.631377 TGTAATGTCAGTTGCATGCTACTC 59.369 41.667 28.33 19.60 30.18 2.59
5270 5439 4.578871 TGTAATGTCAGTTGCATGCTACT 58.421 39.130 26.06 26.06 32.63 2.57
5271 5440 4.944962 TGTAATGTCAGTTGCATGCTAC 57.055 40.909 22.44 22.44 0.00 3.58
5418 7157 8.172741 ACAAGGGATGGATGTTATAAGCATAAT 58.827 33.333 0.00 0.00 0.00 1.28
5549 7288 4.217550 TCCAAAAGCAACTGGTAGCATAAC 59.782 41.667 0.00 0.00 34.11 1.89
5744 7483 3.131223 TCTGATAGCTCCAAGTAGCACAC 59.869 47.826 0.00 0.00 45.30 3.82
5910 7649 5.552766 TCCCATCCTGGAATGATATCAATGA 59.447 40.000 9.99 1.13 40.96 2.57
6099 7838 5.878406 AGGAGGGAGTACATATTTCAGTG 57.122 43.478 0.00 0.00 0.00 3.66
6347 8094 2.614057 CAGAAAAGAGTGCAAGTTCCGT 59.386 45.455 0.00 0.00 0.00 4.69
6467 8218 1.767759 AGGAAAATTGCCATCCTCGG 58.232 50.000 0.00 0.00 39.36 4.63
6485 8236 7.148356 TGTCAGAAATTGTCATGCTAGCTAAAG 60.148 37.037 17.23 3.19 0.00 1.85
6582 9311 9.330063 TCGAATATCAGATTTCTTTTAGCATGT 57.670 29.630 0.00 0.00 0.00 3.21
6602 9993 3.133183 TGGATTCCACCACGAATCGAATA 59.867 43.478 10.55 0.00 46.09 1.75
6801 10192 7.426169 GTGCTTTGCTATTTTCAAAACACAAAG 59.574 33.333 20.01 20.01 43.96 2.77
6802 10193 7.118971 AGTGCTTTGCTATTTTCAAAACACAAA 59.881 29.630 18.17 9.89 45.53 2.83
6803 10194 6.593382 AGTGCTTTGCTATTTTCAAAACACAA 59.407 30.769 18.17 4.18 45.53 3.33
6873 10271 6.933521 ACAAGATACTTTAGCATATGAGCTGG 59.066 38.462 6.97 0.00 46.11 4.85


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

AutoCloner maintained by Alex Coulton.