Multiple sequence alignment - TraesCS1A01G294700

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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 TraesCS1A01G294700 chr1A 100.000 3613 0 0 1 3613 489602347 489598735 0.000000e+00 6673.0
1 TraesCS1A01G294700 chr1A 99.145 117 1 0 3317 3433 489598918 489598802 1.020000e-50 211.0
2 TraesCS1A01G294700 chr1A 99.145 117 1 0 3430 3546 489599031 489598915 1.020000e-50 211.0
3 TraesCS1A01G294700 chr1A 96.970 66 2 0 728 793 489601554 489601489 1.060000e-20 111.0
4 TraesCS1A01G294700 chr1A 96.970 66 2 0 794 859 489601620 489601555 1.060000e-20 111.0
5 TraesCS1A01G294700 chr1D 95.330 1349 50 7 2094 3433 395558615 395557271 0.000000e+00 2130.0
6 TraesCS1A01G294700 chr1D 97.244 1125 31 0 971 2095 395559771 395558647 0.000000e+00 1906.0
7 TraesCS1A01G294700 chr1D 87.102 597 51 10 221 793 395565418 395564824 0.000000e+00 652.0
8 TraesCS1A01G294700 chr1D 92.935 184 11 1 3430 3611 395557387 395557204 2.140000e-67 267.0
9 TraesCS1A01G294700 chr1B 95.866 1161 26 7 957 2095 526349096 526347936 0.000000e+00 1858.0
10 TraesCS1A01G294700 chr1B 93.990 1248 40 6 2197 3433 526347584 526346361 0.000000e+00 1857.0
11 TraesCS1A01G294700 chr1B 88.642 810 60 14 12 793 526352267 526351462 0.000000e+00 957.0
12 TraesCS1A01G294700 chr1B 91.304 184 14 1 3430 3611 526346477 526346294 2.150000e-62 250.0
13 TraesCS1A01G294700 chr1B 95.238 105 5 0 2094 2198 526347904 526347800 2.230000e-37 167.0
14 TraesCS1A01G294700 chr7D 86.071 1400 108 43 1126 2484 573898034 573899387 0.000000e+00 1424.0
15 TraesCS1A01G294700 chr7D 100.000 34 0 0 1978 2011 573905557 573905590 3.010000e-06 63.9
16 TraesCS1A01G294700 chr7D 91.111 45 4 0 1731 1775 268330215 268330259 1.080000e-05 62.1
17 TraesCS1A01G294700 chr7B 83.514 1656 141 63 883 2484 632684402 632685979 0.000000e+00 1424.0
18 TraesCS1A01G294700 chr7B 83.333 156 18 5 1791 1939 19975506 19975352 1.750000e-28 137.0
19 TraesCS1A01G294700 chr7B 82.667 150 13 8 2170 2310 19955768 19955623 1.760000e-23 121.0
20 TraesCS1A01G294700 chr7B 78.488 172 16 10 2100 2254 19959619 19959452 3.840000e-15 93.5
21 TraesCS1A01G294700 chr7B 95.455 44 2 0 67 110 632684288 632684331 1.800000e-08 71.3
22 TraesCS1A01G294700 chr7B 100.000 34 0 0 1978 2011 632688538 632688571 3.010000e-06 63.9
23 TraesCS1A01G294700 chr3B 83.333 936 96 34 1124 2021 733574000 733574913 0.000000e+00 809.0
24 TraesCS1A01G294700 chr3B 82.870 899 121 21 1152 2024 733628624 733629515 0.000000e+00 776.0
25 TraesCS1A01G294700 chr3B 76.398 322 51 19 2104 2407 733601782 733602096 2.250000e-32 150.0
26 TraesCS1A01G294700 chr3D 82.580 907 114 22 1152 2024 552782381 552783277 0.000000e+00 760.0
27 TraesCS1A01G294700 chr3D 82.046 518 76 15 1126 1634 552755132 552755641 3.330000e-115 425.0
28 TraesCS1A01G294700 chr3D 77.778 306 44 14 2098 2384 552771168 552771468 2.230000e-37 167.0
29 TraesCS1A01G294700 chr3D 91.525 59 5 0 2840 2898 37502966 37503024 8.310000e-12 82.4
30 TraesCS1A01G294700 chr3A 81.655 894 113 25 1151 2024 689111918 689112780 0.000000e+00 695.0
31 TraesCS1A01G294700 chr3A 81.467 518 83 12 1128 1635 689007193 689007707 2.600000e-111 412.0
32 TraesCS1A01G294700 chr3A 79.085 306 39 15 2098 2384 689074199 689074498 1.710000e-43 187.0
33 TraesCS1A01G294700 chr2D 77.401 708 106 16 1204 1869 489009828 489009133 4.410000e-99 372.0
34 TraesCS1A01G294700 chr2D 76.344 372 57 18 2874 3238 488993450 488993103 1.720000e-38 171.0
35 TraesCS1A01G294700 chr4D 89.447 199 17 2 2706 2901 131266750 131266947 7.750000e-62 248.0
36 TraesCS1A01G294700 chr4D 93.243 74 5 0 3320 3393 131267262 131267335 3.810000e-20 110.0
37 TraesCS1A01G294700 chr4D 91.892 74 6 0 3433 3506 131267262 131267335 1.770000e-18 104.0
38 TraesCS1A01G294700 chr4A 88.325 197 18 3 2706 2898 706852548 706852353 7.800000e-57 231.0
39 TraesCS1A01G294700 chr5D 86.364 198 22 4 2706 2898 333382212 333382015 1.020000e-50 211.0
40 TraesCS1A01G294700 chr5D 92.105 76 6 0 3320 3395 333381730 333381655 1.370000e-19 108.0
41 TraesCS1A01G294700 chr5D 90.789 76 7 0 3433 3508 333381730 333381655 6.380000e-18 102.0
42 TraesCS1A01G294700 chr2B 90.291 103 10 0 1791 1893 759301363 759301261 6.290000e-28 135.0
43 TraesCS1A01G294700 chr2A 90.291 103 10 0 1791 1893 751197303 751197201 6.290000e-28 135.0
44 TraesCS1A01G294700 chr2A 80.132 151 14 10 2100 2236 619560304 619560452 8.260000e-17 99.0
45 TraesCS1A01G294700 chr6B 96.078 51 1 1 2976 3026 252551544 252551495 8.310000e-12 82.4


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 TraesCS1A01G294700 chr1A 489598735 489602347 3612 True 1463.400000 6673 98.446000 1 3613 5 chr1A.!!$R1 3612
1 TraesCS1A01G294700 chr1D 395557204 395559771 2567 True 1434.333333 2130 95.169667 971 3611 3 chr1D.!!$R2 2640
2 TraesCS1A01G294700 chr1D 395564824 395565418 594 True 652.000000 652 87.102000 221 793 1 chr1D.!!$R1 572
3 TraesCS1A01G294700 chr1B 526346294 526352267 5973 True 1017.800000 1858 93.008000 12 3611 5 chr1B.!!$R1 3599
4 TraesCS1A01G294700 chr7D 573898034 573899387 1353 False 1424.000000 1424 86.071000 1126 2484 1 chr7D.!!$F2 1358
5 TraesCS1A01G294700 chr7B 632684288 632688571 4283 False 519.733333 1424 92.989667 67 2484 3 chr7B.!!$F1 2417
6 TraesCS1A01G294700 chr3B 733574000 733574913 913 False 809.000000 809 83.333000 1124 2021 1 chr3B.!!$F1 897
7 TraesCS1A01G294700 chr3B 733628624 733629515 891 False 776.000000 776 82.870000 1152 2024 1 chr3B.!!$F3 872
8 TraesCS1A01G294700 chr3D 552782381 552783277 896 False 760.000000 760 82.580000 1152 2024 1 chr3D.!!$F4 872
9 TraesCS1A01G294700 chr3D 552755132 552755641 509 False 425.000000 425 82.046000 1126 1634 1 chr3D.!!$F2 508
10 TraesCS1A01G294700 chr3A 689111918 689112780 862 False 695.000000 695 81.655000 1151 2024 1 chr3A.!!$F3 873
11 TraesCS1A01G294700 chr3A 689007193 689007707 514 False 412.000000 412 81.467000 1128 1635 1 chr3A.!!$F1 507
12 TraesCS1A01G294700 chr2D 489009133 489009828 695 True 372.000000 372 77.401000 1204 1869 1 chr2D.!!$R2 665

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
405 415 0.107066 TCAATGCGTGGATGGATGCT 60.107 50.0 0.0 0.0 0.0 3.79 F
581 608 0.741915 TTTTTCCCACACGGTCTTGC 59.258 50.0 0.0 0.0 0.0 4.01 F
2081 4552 0.114954 TTTTGAAGCCATGCCCCTCT 59.885 50.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1355 3705 1.764854 GGGATCCAGGCCGAGGTAA 60.765 63.158 15.23 0.0 0.00 2.85 R
2261 5020 2.478134 CTCCTGCGATTTGATTCGATCC 59.522 50.000 0.00 0.0 41.62 3.36 R
3029 7177 2.694628 AGCAACTGAGGATGCAAACAAA 59.305 40.909 13.64 0.0 42.55 2.83 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
36 37 2.776312 TCGAAGACAGTGACAGTGAC 57.224 50.000 17.24 10.78 0.00 3.67
41 42 2.509569 AGACAGTGACAGTGACGATCT 58.490 47.619 17.24 6.32 0.00 2.75
54 55 5.752472 CAGTGACGATCTAGATGAGCAATTT 59.248 40.000 10.74 0.00 0.00 1.82
130 131 1.115467 AGATCGTGCCGAGAAGGATT 58.885 50.000 3.76 0.00 45.00 3.01
145 146 7.658982 CCGAGAAGGATTGATTAATTCATGAGA 59.341 37.037 0.00 0.00 45.00 3.27
156 157 9.730705 TGATTAATTCATGAGAAAGTGAAGACT 57.269 29.630 0.00 0.00 37.72 3.24
166 167 6.916387 TGAGAAAGTGAAGACTAAGTTGTACG 59.084 38.462 0.00 0.00 0.00 3.67
181 182 2.388735 TGTACGAGGAAGATGAGCCAT 58.611 47.619 0.00 0.00 0.00 4.40
239 243 6.760770 GGGAACATGAAATTCAACTTCAAACA 59.239 34.615 0.00 0.00 36.43 2.83
288 296 3.380637 AGATTTCAAGCATGGCATGAGTC 59.619 43.478 30.69 14.81 37.56 3.36
301 311 2.096496 GCATGAGTCGGAACAATTGAGG 59.904 50.000 13.59 0.00 0.00 3.86
318 328 2.241941 TGAGGAGATTTGGCAAGCCATA 59.758 45.455 15.49 10.82 46.64 2.74
327 337 7.224522 GATTTGGCAAGCCATATCTAAGAAT 57.775 36.000 26.86 16.51 45.14 2.40
349 359 5.871396 TGAGGTACAAAAGAGAGTGAAGT 57.129 39.130 0.00 0.00 0.00 3.01
366 376 6.288426 GTGAAGTTCACCAAGACTAGAAAC 57.712 41.667 23.03 0.00 41.37 2.78
389 399 4.579869 GAGAATGTCTACTTTGGGCTCAA 58.420 43.478 0.00 0.00 0.00 3.02
392 402 2.436417 TGTCTACTTTGGGCTCAATGC 58.564 47.619 11.92 0.00 41.94 3.56
402 412 0.820891 GGCTCAATGCGTGGATGGAT 60.821 55.000 0.00 0.00 44.05 3.41
405 415 0.107066 TCAATGCGTGGATGGATGCT 60.107 50.000 0.00 0.00 0.00 3.79
410 420 1.825341 CGTGGATGGATGCTCCTGA 59.175 57.895 4.21 0.00 37.46 3.86
527 537 5.396485 AGAGATGACTGCTCCTTATCTCAT 58.604 41.667 13.17 0.00 43.77 2.90
538 548 9.118300 CTGCTCCTTATCTCATAAAGAAATGTT 57.882 33.333 0.00 0.00 37.61 2.71
539 549 9.113838 TGCTCCTTATCTCATAAAGAAATGTTC 57.886 33.333 0.00 0.00 37.61 3.18
581 608 0.741915 TTTTTCCCACACGGTCTTGC 59.258 50.000 0.00 0.00 0.00 4.01
607 635 3.252554 TGGGTTGTTTTTGCTAGGGAT 57.747 42.857 0.00 0.00 0.00 3.85
615 643 5.141182 TGTTTTTGCTAGGGATGTAAACCA 58.859 37.500 0.00 0.00 0.00 3.67
616 644 5.242838 TGTTTTTGCTAGGGATGTAAACCAG 59.757 40.000 0.00 0.00 0.00 4.00
628 657 7.064229 GGGATGTAAACCAGGTCCATTTAATA 58.936 38.462 0.00 0.00 0.00 0.98
631 660 7.690952 TGTAAACCAGGTCCATTTAATACAC 57.309 36.000 0.00 0.00 0.00 2.90
632 661 7.463431 TGTAAACCAGGTCCATTTAATACACT 58.537 34.615 0.00 0.00 0.00 3.55
681 710 6.984740 TTTTCCGAAGAAAATGAACAATCG 57.015 33.333 0.00 0.00 44.99 3.34
690 719 4.871993 AAATGAACAATCGAGCTAGCTG 57.128 40.909 24.99 14.56 0.00 4.24
713 742 3.326747 AGCTAACTAAACAGGACTTGCG 58.673 45.455 0.00 0.00 0.00 4.85
737 766 3.520569 GCACCGTTCATTTGCCATTTAT 58.479 40.909 0.00 0.00 0.00 1.40
745 774 6.514376 CGTTCATTTGCCATTTATACCCCTAC 60.514 42.308 0.00 0.00 0.00 3.18
751 780 8.896722 TTTGCCATTTATACCCCTACTTTTTA 57.103 30.769 0.00 0.00 0.00 1.52
754 783 8.062536 TGCCATTTATACCCCTACTTTTTACAT 58.937 33.333 0.00 0.00 0.00 2.29
755 784 8.573885 GCCATTTATACCCCTACTTTTTACATC 58.426 37.037 0.00 0.00 0.00 3.06
756 785 9.635404 CCATTTATACCCCTACTTTTTACATCA 57.365 33.333 0.00 0.00 0.00 3.07
761 790 8.980481 ATACCCCTACTTTTTACATCAAGATG 57.020 34.615 8.45 8.45 44.15 2.90
796 825 6.868339 ACAATATTTGTTTCTACAAGGCTTGC 59.132 34.615 26.45 10.00 44.56 4.01
797 826 3.726291 TTTGTTTCTACAAGGCTTGCC 57.274 42.857 26.45 2.97 44.56 4.52
798 827 2.356665 TGTTTCTACAAGGCTTGCCA 57.643 45.000 26.45 13.88 0.00 4.92
799 828 2.875296 TGTTTCTACAAGGCTTGCCAT 58.125 42.857 26.45 10.48 0.00 4.40
800 829 3.230134 TGTTTCTACAAGGCTTGCCATT 58.770 40.909 26.45 10.11 0.00 3.16
801 830 3.640967 TGTTTCTACAAGGCTTGCCATTT 59.359 39.130 26.45 9.73 0.00 2.32
802 831 4.830046 TGTTTCTACAAGGCTTGCCATTTA 59.170 37.500 26.45 10.37 0.00 1.40
803 832 5.480073 TGTTTCTACAAGGCTTGCCATTTAT 59.520 36.000 26.45 8.26 0.00 1.40
804 833 6.661377 TGTTTCTACAAGGCTTGCCATTTATA 59.339 34.615 26.45 8.98 0.00 0.98
805 834 6.693315 TTCTACAAGGCTTGCCATTTATAC 57.307 37.500 26.45 0.00 0.00 1.47
806 835 5.130350 TCTACAAGGCTTGCCATTTATACC 58.870 41.667 26.45 0.00 0.00 2.73
807 836 3.031013 ACAAGGCTTGCCATTTATACCC 58.969 45.455 26.45 0.00 0.00 3.69
808 837 2.365293 CAAGGCTTGCCATTTATACCCC 59.635 50.000 15.25 0.00 0.00 4.95
809 838 1.859574 AGGCTTGCCATTTATACCCCT 59.140 47.619 14.54 0.00 0.00 4.79
810 839 3.060611 AGGCTTGCCATTTATACCCCTA 58.939 45.455 14.54 0.00 0.00 3.53
811 840 3.154710 GGCTTGCCATTTATACCCCTAC 58.845 50.000 6.79 0.00 0.00 3.18
812 841 3.181433 GGCTTGCCATTTATACCCCTACT 60.181 47.826 6.79 0.00 0.00 2.57
813 842 4.470602 GCTTGCCATTTATACCCCTACTT 58.529 43.478 0.00 0.00 0.00 2.24
814 843 4.893524 GCTTGCCATTTATACCCCTACTTT 59.106 41.667 0.00 0.00 0.00 2.66
815 844 5.362717 GCTTGCCATTTATACCCCTACTTTT 59.637 40.000 0.00 0.00 0.00 2.27
816 845 6.127168 GCTTGCCATTTATACCCCTACTTTTT 60.127 38.462 0.00 0.00 0.00 1.94
817 846 6.783708 TGCCATTTATACCCCTACTTTTTG 57.216 37.500 0.00 0.00 0.00 2.44
818 847 5.128008 TGCCATTTATACCCCTACTTTTTGC 59.872 40.000 0.00 0.00 0.00 3.68
819 848 5.128008 GCCATTTATACCCCTACTTTTTGCA 59.872 40.000 0.00 0.00 0.00 4.08
820 849 6.183360 GCCATTTATACCCCTACTTTTTGCAT 60.183 38.462 0.00 0.00 0.00 3.96
832 861 5.266733 ACTTTTTGCATCAAGATGTGTGT 57.733 34.783 11.35 1.26 40.80 3.72
860 889 5.540911 ACAATATTTGTTTCCACAAGGCAG 58.459 37.500 0.00 0.00 43.92 4.85
867 897 1.896220 TTCCACAAGGCAGTGCTAAG 58.104 50.000 16.11 7.35 38.18 2.18
870 900 2.158682 TCCACAAGGCAGTGCTAAGAAA 60.159 45.455 16.11 0.00 38.18 2.52
872 902 3.550842 CCACAAGGCAGTGCTAAGAAAAC 60.551 47.826 16.11 0.00 38.18 2.43
967 3267 5.230306 CGAAAATCAACTTACTAGAGCGAGG 59.770 44.000 0.00 0.00 0.00 4.63
980 3280 1.446966 GCGAGGAGGTCTGTCTTGC 60.447 63.158 0.00 0.00 0.00 4.01
1119 3450 4.135153 CTCACCTCCGGCCTCACG 62.135 72.222 0.00 0.00 0.00 4.35
1260 3595 2.686835 GCCTCCTGGAGCTCCACT 60.687 66.667 32.00 0.00 42.01 4.00
1355 3705 2.683867 CTCGGACGTCTTCAAGGTCTAT 59.316 50.000 16.46 0.00 41.51 1.98
1443 3796 1.810030 GTCTCCGCCGTCAACATCC 60.810 63.158 0.00 0.00 0.00 3.51
1766 4193 0.679002 ACAAGGCGCTCGACTACCTA 60.679 55.000 7.64 0.00 30.17 3.08
2076 4547 1.137675 GATCCCTTTTGAAGCCATGCC 59.862 52.381 0.00 0.00 0.00 4.40
2081 4552 0.114954 TTTTGAAGCCATGCCCCTCT 59.885 50.000 0.00 0.00 0.00 3.69
2254 5013 7.607607 AGTGTAATGTTGAACTGCATCTTATCA 59.392 33.333 0.00 0.00 0.00 2.15
2261 5020 5.128205 TGAACTGCATCTTATCAATGGGAG 58.872 41.667 0.00 0.00 0.00 4.30
2271 5030 5.543790 TCTTATCAATGGGAGGATCGAATCA 59.456 40.000 0.00 0.00 34.37 2.57
2292 5051 5.984725 TCAAATCGCAGGAGGTATCTTAAA 58.015 37.500 0.00 0.00 0.00 1.52
2293 5052 6.411376 TCAAATCGCAGGAGGTATCTTAAAA 58.589 36.000 0.00 0.00 0.00 1.52
2337 5096 4.649088 AGTACAATGTCGTAGCTGCATA 57.351 40.909 1.02 0.00 0.00 3.14
2389 5148 2.231235 GACAAAATGGTGATTTCGGGCT 59.769 45.455 0.00 0.00 30.02 5.19
2479 5252 3.765894 TAATGGCGTGCATCCCCCG 62.766 63.158 5.63 0.00 0.00 5.73
2499 5272 3.296628 CGTTTGGGAATCGTGTTTTCTG 58.703 45.455 0.00 0.00 0.00 3.02
2500 5273 3.002862 CGTTTGGGAATCGTGTTTTCTGA 59.997 43.478 0.00 0.00 0.00 3.27
2671 5486 2.109425 AGAATGAGGTAAACACCCGC 57.891 50.000 0.00 0.00 0.00 6.13
2678 5493 1.064979 AGGTAAACACCCGCCCTATTG 60.065 52.381 0.00 0.00 0.00 1.90
2760 6900 2.793790 GTCGCTCTGTTCATCTATGCTG 59.206 50.000 0.00 0.00 0.00 4.41
2768 6908 7.175347 TCTGTTCATCTATGCTGTCTAGTTT 57.825 36.000 0.00 0.00 0.00 2.66
2853 7001 1.507140 TCGGGAGAACCATGCCTATT 58.493 50.000 0.00 0.00 40.22 1.73
3234 7389 2.673775 TGATGACCCTTTTCCAGCAA 57.326 45.000 0.00 0.00 0.00 3.91
3313 7468 1.656652 GGTCTCTGTACATGCGCAAT 58.343 50.000 17.11 8.76 0.00 3.56
3432 7588 8.618702 TTTAATCATGTTTTGTGATGCCATTT 57.381 26.923 0.00 0.00 36.49 2.32
3433 7589 9.716531 TTTAATCATGTTTTGTGATGCCATTTA 57.283 25.926 0.00 0.00 36.49 1.40
3434 7590 7.599630 AATCATGTTTTGTGATGCCATTTAC 57.400 32.000 0.00 0.00 36.49 2.01
3435 7591 6.094193 TCATGTTTTGTGATGCCATTTACA 57.906 33.333 0.00 0.00 0.00 2.41
3436 7592 5.925397 TCATGTTTTGTGATGCCATTTACAC 59.075 36.000 0.00 0.00 0.00 2.90
3437 7593 5.528043 TGTTTTGTGATGCCATTTACACT 57.472 34.783 0.00 0.00 34.81 3.55
3438 7594 5.911752 TGTTTTGTGATGCCATTTACACTT 58.088 33.333 0.00 0.00 34.81 3.16
3439 7595 7.043961 TGTTTTGTGATGCCATTTACACTTA 57.956 32.000 0.00 0.00 34.81 2.24
3440 7596 7.665690 TGTTTTGTGATGCCATTTACACTTAT 58.334 30.769 0.00 0.00 34.81 1.73
3441 7597 7.812191 TGTTTTGTGATGCCATTTACACTTATC 59.188 33.333 0.00 0.00 34.81 1.75
3442 7598 7.701539 TTTGTGATGCCATTTACACTTATCT 57.298 32.000 0.00 0.00 34.81 1.98
3443 7599 7.701539 TTGTGATGCCATTTACACTTATCTT 57.298 32.000 0.00 0.00 34.81 2.40
3444 7600 8.800370 TTGTGATGCCATTTACACTTATCTTA 57.200 30.769 0.00 0.00 34.81 2.10
3445 7601 8.437360 TGTGATGCCATTTACACTTATCTTAG 57.563 34.615 0.00 0.00 34.81 2.18
3446 7602 7.012327 TGTGATGCCATTTACACTTATCTTAGC 59.988 37.037 0.00 0.00 34.81 3.09
3447 7603 7.227512 GTGATGCCATTTACACTTATCTTAGCT 59.772 37.037 0.00 0.00 0.00 3.32
3448 7604 7.775093 TGATGCCATTTACACTTATCTTAGCTT 59.225 33.333 0.00 0.00 0.00 3.74
3449 7605 7.553881 TGCCATTTACACTTATCTTAGCTTC 57.446 36.000 0.00 0.00 0.00 3.86
3450 7606 7.109501 TGCCATTTACACTTATCTTAGCTTCA 58.890 34.615 0.00 0.00 0.00 3.02
3451 7607 7.775093 TGCCATTTACACTTATCTTAGCTTCAT 59.225 33.333 0.00 0.00 0.00 2.57
3452 7608 8.286097 GCCATTTACACTTATCTTAGCTTCATC 58.714 37.037 0.00 0.00 0.00 2.92
3453 7609 9.553064 CCATTTACACTTATCTTAGCTTCATCT 57.447 33.333 0.00 0.00 0.00 2.90
3464 7620 7.849804 TCTTAGCTTCATCTTATTTGTGGAC 57.150 36.000 0.00 0.00 0.00 4.02
3465 7621 6.535150 TCTTAGCTTCATCTTATTTGTGGACG 59.465 38.462 0.00 0.00 0.00 4.79
3466 7622 4.832248 AGCTTCATCTTATTTGTGGACGA 58.168 39.130 0.00 0.00 0.00 4.20
3467 7623 5.431765 AGCTTCATCTTATTTGTGGACGAT 58.568 37.500 0.00 0.00 0.00 3.73
3468 7624 5.882557 AGCTTCATCTTATTTGTGGACGATT 59.117 36.000 0.00 0.00 0.00 3.34
3469 7625 6.037610 AGCTTCATCTTATTTGTGGACGATTC 59.962 38.462 0.00 0.00 0.00 2.52
3470 7626 6.183360 GCTTCATCTTATTTGTGGACGATTCA 60.183 38.462 0.00 0.00 0.00 2.57
3471 7627 7.626240 GCTTCATCTTATTTGTGGACGATTCAA 60.626 37.037 0.00 0.00 0.00 2.69
3472 7628 7.864108 TCATCTTATTTGTGGACGATTCAAT 57.136 32.000 0.00 0.00 0.00 2.57
3473 7629 7.919690 TCATCTTATTTGTGGACGATTCAATC 58.080 34.615 0.00 0.00 0.00 2.67
3474 7630 7.552330 TCATCTTATTTGTGGACGATTCAATCA 59.448 33.333 0.00 0.00 0.00 2.57
3475 7631 7.680442 TCTTATTTGTGGACGATTCAATCAA 57.320 32.000 0.00 0.00 0.00 2.57
3476 7632 8.105097 TCTTATTTGTGGACGATTCAATCAAA 57.895 30.769 0.00 0.00 0.00 2.69
3477 7633 8.739039 TCTTATTTGTGGACGATTCAATCAAAT 58.261 29.630 0.00 0.00 37.62 2.32
3478 7634 9.357652 CTTATTTGTGGACGATTCAATCAAATT 57.642 29.630 0.00 0.00 36.15 1.82
3479 7635 7.585286 ATTTGTGGACGATTCAATCAAATTG 57.415 32.000 0.00 0.00 41.57 2.32
3480 7636 5.956068 TGTGGACGATTCAATCAAATTGA 57.044 34.783 0.00 0.00 46.77 2.57
3495 7651 9.388346 CAATCAAATTGAACATGACAAAATTGG 57.612 29.630 21.87 12.74 42.83 3.16
3496 7652 7.493743 TCAAATTGAACATGACAAAATTGGG 57.506 32.000 21.87 11.69 33.34 4.12
3497 7653 7.278135 TCAAATTGAACATGACAAAATTGGGA 58.722 30.769 21.87 12.89 33.34 4.37
3498 7654 7.937942 TCAAATTGAACATGACAAAATTGGGAT 59.062 29.630 21.87 5.52 33.34 3.85
3499 7655 8.569641 CAAATTGAACATGACAAAATTGGGATT 58.430 29.630 0.00 0.00 31.19 3.01
3500 7656 8.694581 AATTGAACATGACAAAATTGGGATTT 57.305 26.923 0.00 0.00 37.06 2.17
3501 7657 7.727331 TTGAACATGACAAAATTGGGATTTC 57.273 32.000 0.00 0.00 34.44 2.17
3502 7658 6.824553 TGAACATGACAAAATTGGGATTTCA 58.175 32.000 0.00 0.00 34.44 2.69
3503 7659 7.278135 TGAACATGACAAAATTGGGATTTCAA 58.722 30.769 0.00 0.00 34.44 2.69
3504 7660 7.772292 TGAACATGACAAAATTGGGATTTCAAA 59.228 29.630 0.00 0.00 34.44 2.69
3505 7661 7.495135 ACATGACAAAATTGGGATTTCAAAC 57.505 32.000 0.00 0.00 34.44 2.93
3506 7662 6.202570 ACATGACAAAATTGGGATTTCAAACG 59.797 34.615 0.00 0.00 34.44 3.60
3507 7663 5.665459 TGACAAAATTGGGATTTCAAACGT 58.335 33.333 0.00 0.00 34.44 3.99
3508 7664 5.521735 TGACAAAATTGGGATTTCAAACGTG 59.478 36.000 0.00 0.00 34.44 4.49
3509 7665 4.272261 ACAAAATTGGGATTTCAAACGTGC 59.728 37.500 0.00 0.00 34.44 5.34
3510 7666 4.335400 AAATTGGGATTTCAAACGTGCT 57.665 36.364 0.00 0.00 29.53 4.40
3511 7667 5.461032 AAATTGGGATTTCAAACGTGCTA 57.539 34.783 0.00 0.00 29.53 3.49
3512 7668 3.907894 TTGGGATTTCAAACGTGCTAC 57.092 42.857 0.00 0.00 0.00 3.58
3513 7669 3.134574 TGGGATTTCAAACGTGCTACT 57.865 42.857 0.00 0.00 0.00 2.57
3514 7670 2.811431 TGGGATTTCAAACGTGCTACTG 59.189 45.455 0.00 0.00 0.00 2.74
3515 7671 2.812011 GGGATTTCAAACGTGCTACTGT 59.188 45.455 0.00 0.00 0.00 3.55
3516 7672 3.120304 GGGATTTCAAACGTGCTACTGTC 60.120 47.826 0.00 0.00 0.00 3.51
3517 7673 3.746492 GGATTTCAAACGTGCTACTGTCT 59.254 43.478 0.00 0.00 0.00 3.41
3518 7674 4.377431 GGATTTCAAACGTGCTACTGTCTG 60.377 45.833 0.00 0.00 0.00 3.51
3519 7675 2.882927 TCAAACGTGCTACTGTCTGT 57.117 45.000 0.00 0.00 0.00 3.41
3520 7676 3.173668 TCAAACGTGCTACTGTCTGTT 57.826 42.857 0.00 0.00 0.00 3.16
3521 7677 3.527533 TCAAACGTGCTACTGTCTGTTT 58.472 40.909 0.00 0.00 0.00 2.83
3522 7678 3.936453 TCAAACGTGCTACTGTCTGTTTT 59.064 39.130 0.00 0.00 0.00 2.43
3523 7679 5.110598 TCAAACGTGCTACTGTCTGTTTTA 58.889 37.500 0.00 0.00 0.00 1.52
3524 7680 5.581479 TCAAACGTGCTACTGTCTGTTTTAA 59.419 36.000 0.00 0.00 0.00 1.52
3525 7681 6.259167 TCAAACGTGCTACTGTCTGTTTTAAT 59.741 34.615 0.00 0.00 0.00 1.40
3526 7682 5.840940 ACGTGCTACTGTCTGTTTTAATC 57.159 39.130 0.00 0.00 0.00 1.75
3527 7683 5.294356 ACGTGCTACTGTCTGTTTTAATCA 58.706 37.500 0.00 0.00 0.00 2.57
3528 7684 5.932303 ACGTGCTACTGTCTGTTTTAATCAT 59.068 36.000 0.00 0.00 0.00 2.45
3529 7685 6.128553 ACGTGCTACTGTCTGTTTTAATCATG 60.129 38.462 0.00 0.00 0.00 3.07
3530 7686 6.128553 CGTGCTACTGTCTGTTTTAATCATGT 60.129 38.462 0.00 0.00 0.00 3.21
3531 7687 7.571244 CGTGCTACTGTCTGTTTTAATCATGTT 60.571 37.037 0.00 0.00 0.00 2.71
3532 7688 8.076178 GTGCTACTGTCTGTTTTAATCATGTTT 58.924 33.333 0.00 0.00 0.00 2.83
3533 7689 8.629158 TGCTACTGTCTGTTTTAATCATGTTTT 58.371 29.630 0.00 0.00 0.00 2.43
3534 7690 8.905702 GCTACTGTCTGTTTTAATCATGTTTTG 58.094 33.333 0.00 0.00 0.00 2.44
3535 7691 9.950680 CTACTGTCTGTTTTAATCATGTTTTGT 57.049 29.630 0.00 0.00 0.00 2.83
3536 7692 8.633075 ACTGTCTGTTTTAATCATGTTTTGTG 57.367 30.769 0.00 0.00 0.00 3.33
3537 7693 8.465999 ACTGTCTGTTTTAATCATGTTTTGTGA 58.534 29.630 0.00 0.00 0.00 3.58
3538 7694 9.467258 CTGTCTGTTTTAATCATGTTTTGTGAT 57.533 29.630 0.00 0.00 37.91 3.06
3539 7695 9.247126 TGTCTGTTTTAATCATGTTTTGTGATG 57.753 29.630 0.00 0.00 36.49 3.07
3540 7696 8.216453 GTCTGTTTTAATCATGTTTTGTGATGC 58.784 33.333 0.00 0.00 36.49 3.91
3541 7697 7.384660 TCTGTTTTAATCATGTTTTGTGATGCC 59.615 33.333 0.00 0.00 36.49 4.40
3542 7698 6.988580 TGTTTTAATCATGTTTTGTGATGCCA 59.011 30.769 0.00 0.00 36.49 4.92
3596 7752 7.217200 TCTATACTAATGAAGTGCATTCCCAC 58.783 38.462 0.00 0.00 43.64 4.61
3605 7761 0.313672 TGCATTCCCACTTTGCGAAC 59.686 50.000 0.00 0.00 39.23 3.95
3611 7767 1.278637 CCACTTTGCGAACCGTGTC 59.721 57.895 5.59 0.00 0.00 3.67
3612 7768 1.157870 CCACTTTGCGAACCGTGTCT 61.158 55.000 5.59 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.211584 GTCTTCGACCTCTTCTTTTGTTCC 59.788 45.833 0.00 0.00 0.00 3.62
3 4 4.766375 TGTCTTCGACCTCTTCTTTTGTT 58.234 39.130 0.00 0.00 0.00 2.83
4 5 4.141914 ACTGTCTTCGACCTCTTCTTTTGT 60.142 41.667 0.00 0.00 0.00 2.83
5 6 4.210120 CACTGTCTTCGACCTCTTCTTTTG 59.790 45.833 0.00 0.00 0.00 2.44
6 7 4.099573 TCACTGTCTTCGACCTCTTCTTTT 59.900 41.667 0.00 0.00 0.00 2.27
7 8 3.637229 TCACTGTCTTCGACCTCTTCTTT 59.363 43.478 0.00 0.00 0.00 2.52
8 9 3.004944 GTCACTGTCTTCGACCTCTTCTT 59.995 47.826 0.00 0.00 0.00 2.52
9 10 2.554893 GTCACTGTCTTCGACCTCTTCT 59.445 50.000 0.00 0.00 0.00 2.85
10 11 2.293677 TGTCACTGTCTTCGACCTCTTC 59.706 50.000 0.00 0.00 0.00 2.87
17 18 1.002792 CGTCACTGTCACTGTCTTCGA 60.003 52.381 0.00 0.00 0.00 3.71
36 37 9.288124 CTATCACTAAATTGCTCATCTAGATCG 57.712 37.037 1.03 0.00 0.00 3.69
41 42 8.918116 AGTCACTATCACTAAATTGCTCATCTA 58.082 33.333 0.00 0.00 0.00 1.98
116 117 5.296780 TGAATTAATCAATCCTTCTCGGCAC 59.703 40.000 0.00 0.00 34.30 5.01
130 131 9.730705 AGTCTTCACTTTCTCATGAATTAATCA 57.269 29.630 0.00 0.00 43.67 2.57
145 146 6.040166 TCCTCGTACAACTTAGTCTTCACTTT 59.960 38.462 0.00 0.00 33.62 2.66
156 157 4.142227 GGCTCATCTTCCTCGTACAACTTA 60.142 45.833 0.00 0.00 0.00 2.24
213 217 5.467035 TGAAGTTGAATTTCATGTTCCCC 57.533 39.130 14.22 0.00 30.03 4.81
239 243 9.420118 TCTCCATGCCTACAACATTAATAAATT 57.580 29.630 0.00 0.00 0.00 1.82
246 250 5.692115 TCTTCTCCATGCCTACAACATTA 57.308 39.130 0.00 0.00 0.00 1.90
257 261 4.360563 CATGCTTGAAATCTTCTCCATGC 58.639 43.478 0.00 0.00 0.00 4.06
288 296 3.428045 GCCAAATCTCCTCAATTGTTCCG 60.428 47.826 5.13 0.00 0.00 4.30
301 311 6.000219 TCTTAGATATGGCTTGCCAAATCTC 59.000 40.000 18.76 11.96 0.00 2.75
318 328 9.041354 ACTCTCTTTTGTACCTCATTCTTAGAT 57.959 33.333 0.00 0.00 0.00 1.98
322 332 7.067496 TCACTCTCTTTTGTACCTCATTCTT 57.933 36.000 0.00 0.00 0.00 2.52
325 335 6.831976 ACTTCACTCTCTTTTGTACCTCATT 58.168 36.000 0.00 0.00 0.00 2.57
327 337 5.871396 ACTTCACTCTCTTTTGTACCTCA 57.129 39.130 0.00 0.00 0.00 3.86
349 359 5.524971 TTCTCGTTTCTAGTCTTGGTGAA 57.475 39.130 0.00 0.00 0.00 3.18
366 376 3.190874 GAGCCCAAAGTAGACATTCTCG 58.809 50.000 0.00 0.00 0.00 4.04
389 399 4.469883 GAGCATCCATCCACGCAT 57.530 55.556 0.00 0.00 0.00 4.73
460 470 3.913548 TGTGTGTTCACCAACATATGC 57.086 42.857 1.58 0.00 44.47 3.14
527 537 5.937540 TCATCTTCAGCCGAACATTTCTTTA 59.062 36.000 0.00 0.00 0.00 1.85
538 548 1.207811 TGCAAGATCATCTTCAGCCGA 59.792 47.619 0.00 0.00 33.78 5.54
539 549 1.329906 GTGCAAGATCATCTTCAGCCG 59.670 52.381 0.00 0.00 33.78 5.52
574 601 4.778143 ACCCATCCGCGCAAGACC 62.778 66.667 8.75 0.00 43.02 3.85
576 603 2.745884 CAACCCATCCGCGCAAGA 60.746 61.111 8.75 3.34 43.02 3.02
580 607 1.006688 AAAAACAACCCATCCGCGC 60.007 52.632 0.00 0.00 0.00 6.86
581 608 1.281566 GCAAAAACAACCCATCCGCG 61.282 55.000 0.00 0.00 0.00 6.46
607 635 7.463431 AGTGTATTAAATGGACCTGGTTTACA 58.537 34.615 0.00 1.26 0.00 2.41
615 643 8.102484 AGACCATAAGTGTATTAAATGGACCT 57.898 34.615 6.65 1.27 39.60 3.85
616 644 9.841295 TTAGACCATAAGTGTATTAAATGGACC 57.159 33.333 6.65 0.00 39.60 4.46
628 657 7.450074 TGATTGAACTGTTAGACCATAAGTGT 58.550 34.615 0.00 0.00 0.00 3.55
631 660 8.553459 ACTTGATTGAACTGTTAGACCATAAG 57.447 34.615 0.00 0.00 0.00 1.73
632 661 8.918202 AACTTGATTGAACTGTTAGACCATAA 57.082 30.769 0.00 0.00 0.00 1.90
690 719 4.143094 CGCAAGTCCTGTTTAGTTAGCTTC 60.143 45.833 0.00 0.00 0.00 3.86
713 742 2.261361 GCAAATGAACGGTGCCCC 59.739 61.111 0.00 0.00 31.94 5.80
721 750 5.869649 AGGGGTATAAATGGCAAATGAAC 57.130 39.130 0.00 0.00 0.00 3.18
737 766 7.827236 CACATCTTGATGTAAAAAGTAGGGGTA 59.173 37.037 14.86 0.00 32.74 3.69
771 800 6.868339 GCAAGCCTTGTAGAAACAAATATTGT 59.132 34.615 6.28 0.00 44.79 2.71
772 801 6.311200 GGCAAGCCTTGTAGAAACAAATATTG 59.689 38.462 6.28 0.00 44.79 1.90
773 802 6.014669 TGGCAAGCCTTGTAGAAACAAATATT 60.015 34.615 12.96 0.00 44.79 1.28
774 803 5.480073 TGGCAAGCCTTGTAGAAACAAATAT 59.520 36.000 12.96 0.00 44.79 1.28
775 804 4.830046 TGGCAAGCCTTGTAGAAACAAATA 59.170 37.500 12.96 0.00 44.79 1.40
776 805 3.640967 TGGCAAGCCTTGTAGAAACAAAT 59.359 39.130 12.96 0.00 44.79 2.32
777 806 3.027412 TGGCAAGCCTTGTAGAAACAAA 58.973 40.909 12.96 0.00 44.79 2.83
778 807 2.660572 TGGCAAGCCTTGTAGAAACAA 58.339 42.857 12.96 0.00 43.32 2.83
779 808 2.356665 TGGCAAGCCTTGTAGAAACA 57.643 45.000 12.96 0.00 36.94 2.83
780 809 3.942130 AATGGCAAGCCTTGTAGAAAC 57.058 42.857 12.96 0.00 36.94 2.78
781 810 6.096282 GGTATAAATGGCAAGCCTTGTAGAAA 59.904 38.462 12.96 0.00 36.94 2.52
782 811 5.592688 GGTATAAATGGCAAGCCTTGTAGAA 59.407 40.000 12.96 0.00 36.94 2.10
783 812 5.130350 GGTATAAATGGCAAGCCTTGTAGA 58.870 41.667 12.96 0.02 36.94 2.59
784 813 4.278419 GGGTATAAATGGCAAGCCTTGTAG 59.722 45.833 12.96 0.00 36.94 2.74
785 814 4.211920 GGGTATAAATGGCAAGCCTTGTA 58.788 43.478 12.96 6.00 36.94 2.41
786 815 3.031013 GGGTATAAATGGCAAGCCTTGT 58.969 45.455 12.96 3.71 36.94 3.16
787 816 2.365293 GGGGTATAAATGGCAAGCCTTG 59.635 50.000 12.96 0.00 36.94 3.61
788 817 2.247372 AGGGGTATAAATGGCAAGCCTT 59.753 45.455 12.96 2.83 36.94 4.35
789 818 1.859574 AGGGGTATAAATGGCAAGCCT 59.140 47.619 12.96 0.00 36.94 4.58
790 819 2.381752 AGGGGTATAAATGGCAAGCC 57.618 50.000 3.61 3.61 0.00 4.35
791 820 4.100279 AGTAGGGGTATAAATGGCAAGC 57.900 45.455 0.00 0.00 0.00 4.01
792 821 7.264947 CAAAAAGTAGGGGTATAAATGGCAAG 58.735 38.462 0.00 0.00 0.00 4.01
793 822 6.351456 GCAAAAAGTAGGGGTATAAATGGCAA 60.351 38.462 0.00 0.00 0.00 4.52
794 823 5.128008 GCAAAAAGTAGGGGTATAAATGGCA 59.872 40.000 0.00 0.00 0.00 4.92
795 824 5.128008 TGCAAAAAGTAGGGGTATAAATGGC 59.872 40.000 0.00 0.00 0.00 4.40
796 825 6.783708 TGCAAAAAGTAGGGGTATAAATGG 57.216 37.500 0.00 0.00 0.00 3.16
797 826 8.006298 TGATGCAAAAAGTAGGGGTATAAATG 57.994 34.615 0.00 0.00 0.00 2.32
798 827 8.602472 TTGATGCAAAAAGTAGGGGTATAAAT 57.398 30.769 0.00 0.00 0.00 1.40
799 828 7.891183 TCTTGATGCAAAAAGTAGGGGTATAAA 59.109 33.333 10.53 0.00 0.00 1.40
800 829 7.406916 TCTTGATGCAAAAAGTAGGGGTATAA 58.593 34.615 10.53 0.00 0.00 0.98
801 830 6.964464 TCTTGATGCAAAAAGTAGGGGTATA 58.036 36.000 10.53 0.00 0.00 1.47
802 831 5.826643 TCTTGATGCAAAAAGTAGGGGTAT 58.173 37.500 10.53 0.00 0.00 2.73
803 832 5.249780 TCTTGATGCAAAAAGTAGGGGTA 57.750 39.130 10.53 0.00 0.00 3.69
804 833 4.112634 TCTTGATGCAAAAAGTAGGGGT 57.887 40.909 10.53 0.00 0.00 4.95
805 834 4.463891 ACATCTTGATGCAAAAAGTAGGGG 59.536 41.667 10.20 2.41 0.00 4.79
806 835 5.047802 ACACATCTTGATGCAAAAAGTAGGG 60.048 40.000 10.20 8.45 0.00 3.53
807 836 5.860182 CACACATCTTGATGCAAAAAGTAGG 59.140 40.000 10.20 5.54 0.00 3.18
808 837 6.441274 ACACACATCTTGATGCAAAAAGTAG 58.559 36.000 10.20 7.67 0.00 2.57
809 838 6.389830 ACACACATCTTGATGCAAAAAGTA 57.610 33.333 10.20 0.90 0.00 2.24
810 839 5.266733 ACACACATCTTGATGCAAAAAGT 57.733 34.783 10.20 0.00 0.00 2.66
811 840 7.878477 ATTACACACATCTTGATGCAAAAAG 57.122 32.000 10.20 0.00 0.00 2.27
812 841 9.190858 GTTATTACACACATCTTGATGCAAAAA 57.809 29.630 10.20 0.00 0.00 1.94
813 842 8.355913 TGTTATTACACACATCTTGATGCAAAA 58.644 29.630 10.20 0.00 0.00 2.44
814 843 7.880105 TGTTATTACACACATCTTGATGCAAA 58.120 30.769 10.20 0.00 0.00 3.68
815 844 7.446001 TGTTATTACACACATCTTGATGCAA 57.554 32.000 10.20 0.00 0.00 4.08
816 845 7.446001 TTGTTATTACACACATCTTGATGCA 57.554 32.000 10.20 0.00 32.98 3.96
860 889 7.415653 CCAAGGAGGAATATGTTTTCTTAGCAC 60.416 40.741 0.00 0.00 41.22 4.40
919 953 9.667107 TCGAAATCTCAAAATACTAGTCCATTT 57.333 29.630 0.00 0.00 0.00 2.32
967 3267 0.394565 ACCACAGCAAGACAGACCTC 59.605 55.000 0.00 0.00 0.00 3.85
980 3280 3.082579 GCTCCCTCCGCTACCACAG 62.083 68.421 0.00 0.00 0.00 3.66
1068 3399 2.907042 GGAGAGGAGAGAAAGGTTGGAA 59.093 50.000 0.00 0.00 0.00 3.53
1355 3705 1.764854 GGGATCCAGGCCGAGGTAA 60.765 63.158 15.23 0.00 0.00 2.85
1957 4405 2.967599 TCGGACTGTCAGATTGATGG 57.032 50.000 6.91 0.00 0.00 3.51
2076 4547 6.426328 GTCTGCATAAATGAGTGATAAGAGGG 59.574 42.308 0.00 0.00 0.00 4.30
2081 4552 7.066163 CCACAAGTCTGCATAAATGAGTGATAA 59.934 37.037 0.00 0.00 0.00 1.75
2254 5013 4.067896 CGATTTGATTCGATCCTCCCATT 58.932 43.478 0.00 0.00 41.62 3.16
2261 5020 2.478134 CTCCTGCGATTTGATTCGATCC 59.522 50.000 0.00 0.00 41.62 3.36
2292 5051 5.482908 AGTACGACAGATGAAGCTGATTTT 58.517 37.500 1.98 0.00 39.20 1.82
2293 5052 5.078411 AGTACGACAGATGAAGCTGATTT 57.922 39.130 1.98 0.00 39.20 2.17
2337 5096 9.899661 AATTCAATTTGATCATCCATGAACAAT 57.100 25.926 11.69 0.00 45.05 2.71
2389 5148 8.309656 TGGCATCACAAAACATGATTATAACAA 58.690 29.630 0.00 0.00 34.49 2.83
2432 5195 6.090483 TCTTGCTATCCATGCTAAGTCTAC 57.910 41.667 0.00 0.00 0.00 2.59
2444 5217 5.555017 GCCATTAAGAGATCTTGCTATCCA 58.445 41.667 5.34 0.00 37.40 3.41
2479 5252 4.561735 TCAGAAAACACGATTCCCAAAC 57.438 40.909 0.00 0.00 0.00 2.93
2499 5272 3.853831 TCATCACAAACACCATGCATC 57.146 42.857 0.00 0.00 0.00 3.91
2500 5273 3.131577 GGATCATCACAAACACCATGCAT 59.868 43.478 0.00 0.00 0.00 3.96
2671 5486 6.321181 ACATAATAACACAAGGCACAATAGGG 59.679 38.462 0.00 0.00 0.00 3.53
2678 5493 4.217550 ACCACACATAATAACACAAGGCAC 59.782 41.667 0.00 0.00 0.00 5.01
2793 6933 2.684881 CAGCAGAATAAACTGGCCGAAT 59.315 45.455 0.00 0.00 38.22 3.34
2848 6996 9.588096 ACCCCTAATGAAGCTAATTAAAATAGG 57.412 33.333 0.00 0.00 0.00 2.57
2853 7001 9.930158 ACATTACCCCTAATGAAGCTAATTAAA 57.070 29.630 7.33 0.00 41.31 1.52
3029 7177 2.694628 AGCAACTGAGGATGCAAACAAA 59.305 40.909 13.64 0.00 42.55 2.83
3115 7270 6.714356 TGGATCAGTTATCACAATTCACAACA 59.286 34.615 0.00 0.00 36.20 3.33
3281 7436 6.172630 TGTACAGAGACCGTAAGTGTACATA 58.827 40.000 9.06 0.00 44.58 2.29
3438 7594 9.547753 GTCCACAAATAAGATGAAGCTAAGATA 57.452 33.333 0.00 0.00 0.00 1.98
3439 7595 7.225538 CGTCCACAAATAAGATGAAGCTAAGAT 59.774 37.037 0.00 0.00 0.00 2.40
3440 7596 6.535150 CGTCCACAAATAAGATGAAGCTAAGA 59.465 38.462 0.00 0.00 0.00 2.10
3441 7597 6.535150 TCGTCCACAAATAAGATGAAGCTAAG 59.465 38.462 0.00 0.00 0.00 2.18
3442 7598 6.403049 TCGTCCACAAATAAGATGAAGCTAA 58.597 36.000 0.00 0.00 0.00 3.09
3443 7599 5.972935 TCGTCCACAAATAAGATGAAGCTA 58.027 37.500 0.00 0.00 0.00 3.32
3444 7600 4.832248 TCGTCCACAAATAAGATGAAGCT 58.168 39.130 0.00 0.00 0.00 3.74
3445 7601 5.741388 ATCGTCCACAAATAAGATGAAGC 57.259 39.130 0.00 0.00 0.00 3.86
3446 7602 7.307493 TGAATCGTCCACAAATAAGATGAAG 57.693 36.000 0.00 0.00 0.00 3.02
3447 7603 7.680442 TTGAATCGTCCACAAATAAGATGAA 57.320 32.000 0.00 0.00 0.00 2.57
3448 7604 7.552330 TGATTGAATCGTCCACAAATAAGATGA 59.448 33.333 0.18 0.00 0.00 2.92
3449 7605 7.696755 TGATTGAATCGTCCACAAATAAGATG 58.303 34.615 0.18 0.00 0.00 2.90
3450 7606 7.864108 TGATTGAATCGTCCACAAATAAGAT 57.136 32.000 0.18 0.00 0.00 2.40
3451 7607 7.680442 TTGATTGAATCGTCCACAAATAAGA 57.320 32.000 0.18 0.00 0.00 2.10
3452 7608 8.915871 ATTTGATTGAATCGTCCACAAATAAG 57.084 30.769 0.00 0.00 35.64 1.73
3453 7609 9.138062 CAATTTGATTGAATCGTCCACAAATAA 57.862 29.630 0.00 0.00 42.83 1.40
3454 7610 8.518702 TCAATTTGATTGAATCGTCCACAAATA 58.481 29.630 0.00 0.00 45.57 1.40
3455 7611 7.377398 TCAATTTGATTGAATCGTCCACAAAT 58.623 30.769 0.18 0.00 45.57 2.32
3456 7612 6.743110 TCAATTTGATTGAATCGTCCACAAA 58.257 32.000 0.18 0.00 45.57 2.83
3457 7613 6.324561 TCAATTTGATTGAATCGTCCACAA 57.675 33.333 0.18 0.00 45.57 3.33
3458 7614 5.956068 TCAATTTGATTGAATCGTCCACA 57.044 34.783 0.18 0.00 45.57 4.17
3469 7625 9.388346 CCAATTTTGTCATGTTCAATTTGATTG 57.612 29.630 18.53 16.60 41.57 2.67
3470 7626 8.569641 CCCAATTTTGTCATGTTCAATTTGATT 58.430 29.630 18.53 10.87 0.00 2.57
3471 7627 7.937942 TCCCAATTTTGTCATGTTCAATTTGAT 59.062 29.630 18.53 0.00 0.00 2.57
3472 7628 7.278135 TCCCAATTTTGTCATGTTCAATTTGA 58.722 30.769 18.53 0.00 0.00 2.69
3473 7629 7.493743 TCCCAATTTTGTCATGTTCAATTTG 57.506 32.000 0.00 7.35 0.00 2.32
3474 7630 8.694581 AATCCCAATTTTGTCATGTTCAATTT 57.305 26.923 0.00 0.00 0.00 1.82
3475 7631 8.694581 AAATCCCAATTTTGTCATGTTCAATT 57.305 26.923 0.00 0.00 30.79 2.32
3476 7632 7.937942 TGAAATCCCAATTTTGTCATGTTCAAT 59.062 29.630 0.00 0.00 35.21 2.57
3477 7633 7.278135 TGAAATCCCAATTTTGTCATGTTCAA 58.722 30.769 0.00 0.00 35.21 2.69
3478 7634 6.824553 TGAAATCCCAATTTTGTCATGTTCA 58.175 32.000 0.00 0.00 35.21 3.18
3479 7635 7.727331 TTGAAATCCCAATTTTGTCATGTTC 57.273 32.000 0.00 0.00 35.21 3.18
3480 7636 7.254727 CGTTTGAAATCCCAATTTTGTCATGTT 60.255 33.333 0.00 0.00 35.21 2.71
3481 7637 6.202570 CGTTTGAAATCCCAATTTTGTCATGT 59.797 34.615 0.00 0.00 35.21 3.21
3482 7638 6.202570 ACGTTTGAAATCCCAATTTTGTCATG 59.797 34.615 0.00 0.00 35.21 3.07
3483 7639 6.202570 CACGTTTGAAATCCCAATTTTGTCAT 59.797 34.615 0.00 0.00 35.21 3.06
3484 7640 5.521735 CACGTTTGAAATCCCAATTTTGTCA 59.478 36.000 0.00 0.00 35.21 3.58
3485 7641 5.558083 GCACGTTTGAAATCCCAATTTTGTC 60.558 40.000 0.00 0.00 35.21 3.18
3486 7642 4.272261 GCACGTTTGAAATCCCAATTTTGT 59.728 37.500 0.00 0.00 35.21 2.83
3487 7643 4.511082 AGCACGTTTGAAATCCCAATTTTG 59.489 37.500 0.00 0.00 35.21 2.44
3488 7644 4.702831 AGCACGTTTGAAATCCCAATTTT 58.297 34.783 0.00 0.00 35.21 1.82
3489 7645 4.335400 AGCACGTTTGAAATCCCAATTT 57.665 36.364 0.00 0.00 37.80 1.82
3490 7646 4.522789 AGTAGCACGTTTGAAATCCCAATT 59.477 37.500 0.00 0.00 0.00 2.32
3491 7647 4.079253 AGTAGCACGTTTGAAATCCCAAT 58.921 39.130 0.00 0.00 0.00 3.16
3492 7648 3.252215 CAGTAGCACGTTTGAAATCCCAA 59.748 43.478 0.00 0.00 0.00 4.12
3493 7649 2.811431 CAGTAGCACGTTTGAAATCCCA 59.189 45.455 0.00 0.00 0.00 4.37
3494 7650 2.812011 ACAGTAGCACGTTTGAAATCCC 59.188 45.455 0.00 0.00 0.00 3.85
3495 7651 3.746492 AGACAGTAGCACGTTTGAAATCC 59.254 43.478 0.00 0.00 0.00 3.01
3496 7652 4.211374 ACAGACAGTAGCACGTTTGAAATC 59.789 41.667 0.00 0.00 0.00 2.17
3497 7653 4.127171 ACAGACAGTAGCACGTTTGAAAT 58.873 39.130 0.00 0.00 0.00 2.17
3498 7654 3.527533 ACAGACAGTAGCACGTTTGAAA 58.472 40.909 0.00 0.00 0.00 2.69
3499 7655 3.173668 ACAGACAGTAGCACGTTTGAA 57.826 42.857 0.00 0.00 0.00 2.69
3500 7656 2.882927 ACAGACAGTAGCACGTTTGA 57.117 45.000 0.00 0.00 0.00 2.69
3501 7657 3.944422 AAACAGACAGTAGCACGTTTG 57.056 42.857 0.00 0.00 0.00 2.93
3502 7658 6.259167 TGATTAAAACAGACAGTAGCACGTTT 59.741 34.615 0.00 0.00 0.00 3.60
3503 7659 5.756347 TGATTAAAACAGACAGTAGCACGTT 59.244 36.000 0.00 0.00 0.00 3.99
3504 7660 5.294356 TGATTAAAACAGACAGTAGCACGT 58.706 37.500 0.00 0.00 0.00 4.49
3505 7661 5.839262 TGATTAAAACAGACAGTAGCACG 57.161 39.130 0.00 0.00 0.00 5.34
3506 7662 7.133891 ACATGATTAAAACAGACAGTAGCAC 57.866 36.000 0.00 0.00 0.00 4.40
3507 7663 7.744087 AACATGATTAAAACAGACAGTAGCA 57.256 32.000 0.00 0.00 0.00 3.49
3508 7664 8.905702 CAAAACATGATTAAAACAGACAGTAGC 58.094 33.333 0.00 0.00 0.00 3.58
3509 7665 9.950680 ACAAAACATGATTAAAACAGACAGTAG 57.049 29.630 0.00 0.00 0.00 2.57
3510 7666 9.729023 CACAAAACATGATTAAAACAGACAGTA 57.271 29.630 0.00 0.00 0.00 2.74
3511 7667 8.465999 TCACAAAACATGATTAAAACAGACAGT 58.534 29.630 0.00 0.00 0.00 3.55
3512 7668 8.854979 TCACAAAACATGATTAAAACAGACAG 57.145 30.769 0.00 0.00 0.00 3.51
3513 7669 9.247126 CATCACAAAACATGATTAAAACAGACA 57.753 29.630 0.00 0.00 34.49 3.41
3514 7670 8.216453 GCATCACAAAACATGATTAAAACAGAC 58.784 33.333 0.00 0.00 34.49 3.51
3515 7671 7.384660 GGCATCACAAAACATGATTAAAACAGA 59.615 33.333 0.00 0.00 34.49 3.41
3516 7672 7.171167 TGGCATCACAAAACATGATTAAAACAG 59.829 33.333 0.00 0.00 34.49 3.16
3517 7673 6.988580 TGGCATCACAAAACATGATTAAAACA 59.011 30.769 0.00 0.00 34.49 2.83
3518 7674 7.418840 TGGCATCACAAAACATGATTAAAAC 57.581 32.000 0.00 0.00 34.49 2.43
3519 7675 8.618702 AATGGCATCACAAAACATGATTAAAA 57.381 26.923 0.00 0.00 34.49 1.52
3520 7676 8.618702 AAATGGCATCACAAAACATGATTAAA 57.381 26.923 0.00 0.00 34.49 1.52
3521 7677 8.618702 AAAATGGCATCACAAAACATGATTAA 57.381 26.923 0.00 0.00 34.49 1.40
3522 7678 8.618702 AAAAATGGCATCACAAAACATGATTA 57.381 26.923 0.00 0.00 34.49 1.75
3523 7679 7.513371 AAAAATGGCATCACAAAACATGATT 57.487 28.000 0.00 0.00 34.49 2.57
3563 7719 9.123902 TGCACTTCATTAGTATAGATTGCAATT 57.876 29.630 14.33 6.39 34.56 2.32
3566 7722 8.681486 AATGCACTTCATTAGTATAGATTGCA 57.319 30.769 0.00 0.00 43.24 4.08


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

AutoCloner maintained by Alex Coulton.